LYSINE ACETYLATION SITES

FIELD OF THE INVENTION

The invention relates generally to novel lysine acetylation sites, methods and compositions for detecting, quantitating and modulating same.

BACKGROUND OF THE INVENTION

The activation of proteins by post-translational modification is an important cellular mechanism for regulating most aspects of biological organization and control, including growth, development, homeostasis, and cellular communication. Protein acetylation, for example, plays a critical role in the etiology of many pathological conditions and diseases, including to mention but a few: cancer, developmental disorders, autoimmune diseases, and diabetes. Yet, in spite of the importance of protein modification, it is not yet well understood at the molecular level, due to the extraordinary complexity of signaling pathways, and the slow development of technology necessary to unravel it.

Protein acetylation plays a complex and critical role in the regulation of biological processes and may prove to be important to diagnostic or therapeutic targets for molecular medicine. Protein acetylation on lysine residues is a dynamic, reversible and highly regulated chemical modification. Historically, histones were perceived as the most important substrate of acetylation, if not the sole substrate. It was proposed 40 years ago that structural modification of histones by acetylation plays an important role in chromatin remodeling and gene expression. Two groups of enzymes, histone deacetylases (HDACs) and histone acetyltransferases (HATs), are responsible for deacetylating and acetylating the histones.

Recent studies have revealed that HDACs are involved in a much broader assay of biological processes. For example, HDAC6 has been implicated in the regulation of microtubules, growth factor-induced chemotaxis and misfolded protein stress response. See Cohen et al., Science, vol 245:42 (2004). Consistant with these non-histone functions, HDAC6 is mainly located to the cytoplasm.

A growing list of acetylated proteins is currently available. It shows that both cytoplasmic and nuclear proteins can undergo reversible acetylation, and protein acetylation can have the following effects on its function: 1) Protein stability. Both acetylation and ubiquitylation often occur on the same lysine, competition between these two modifications affects the protein stability. It has been shown that HDACs can decrease the half-life of some proteins by exposing the lysine for ubiquitylation. 2) Protein-protein interactions. It has been shown that acetylation induces STAT3 dimerization and subsequently nuclear translocation. In the case of nuclear DNA-damage-response protein Ku70, the deacetylated form of Ku70 sequesters BAX, the pro-apoptotic protein, in the cytoplasm and protects cells from apoptosis. In response to apoptotic stimuli, Ku70 becomes acetylated and subsequently releases Bax from its sequestration, leading to translocation of BAX to the mitochondria and activation of apoptotic cascade. 3) Protein translocation. As described for STAT3 and BAX, reversible acetylation affects the subcellular localization. In the case of STAT3, its nuclear localization signal contains lysine residues that favor nuclear retension when acetylated. 4) DNA binding. It have been shown that acetylation of p53 regulates its stability, its DNA binding and its transcriptional activity. Similarly, the DNA binding affinity of NF-kB and its transcriptional activation are also regulated by HATs and HDACs. See Minucci et al., Nature Cancer Reviews, 6: 38-51 (2005).

HATs and HDACs have been linked to pathogenesis of cancer. Specific HATs (p300 and CBP) are targets of viral oncoproteins (adenoviral E1A, human papilloma virus E6 and SV40 T antigen). See Eckner, R. et al., Cold Spring Harb. Symp. Quant. Biol., 59: 85-95 (1994). Structural alterations in HATs, including translocation, amplifications, deletions and point mutations have been found in various human cancers. See Iyer, N G. et al., Oncogene, 23: 4225-4231 (2004). For HDACs, increased expression of HDAC1 has been detected in gastric cancers, oesophageal squamous cell carcinoma, and prostate cancer. See Halkidou, K. et al., Prostate 59: 177-189 (2004). Increased expression of HDAC2 has been detected in colon cancer and has been shown to interact functionally with Wnt pathway. Knockdown of HDAC2 by siRNA in colon cancer cells resulted in cell death. See Zhu, P. et al., Cancer Cell, 5: 455-463 (2004). Increased expression of HDAC6 has been linked to better survival in breast cancer, See Zhang, Z. et al., Clin. Cancer Res., 10: 6962-6968 (2004), while reduced expression of HDAC5 and 10 have been associated with poor prognosis in lung cancer patients. See Osada, H. et al., Cancer, 112: 26-32 (2004).

HDAC inhibitors (HDACi) are promising new targeted anti-cancer agents, and first-generation HDACi in several clinical trials show significant activity against a spectrum of both hematologic and solid tumors at doses that are well tolerated by the patients. See Drummond, D C. et al., Annu. Rev. Pharmacol. Toxicol., 45: 495-528 (2005). However, the relationship between the toxicity of HDACi and their pharmacokinetic properties is still largely unknown, which makes it difficult to optimize HDACi treatment. More importantly the key targets for HDACi action are unknown. This makes it difficult to select patients who are most likely to respond to HDACi. Proposed surrogate markers, like measuring the level of acetylated histone from blood cells before and after treatment, should be serve as indicators of effectiveness, but these need to be validated clinically yet and do not always correlated with pharmacokinetic profile. Therefore, to identify the entire spectrum of acetylated proteins deserves a much more systematic experimental strategy which would optimally involve a dynamic map of the acetylated proteins and their functions.

Despite the identification of a few key molecules involved in protein acetylation signaling pathways, the vast majority of signaling protein changes underlying these pathways remains unknown. There is, therefore, relatively scarce information about acetylation-driven signaling pathways and acetylation sites relevant to the pathogenisis of cancer and other human diseases. This has hampered a complete and accurate understanding of how protein activation within signaling pathways may be driving different human diseases, including cancer.

Presently, diagnosis of carcinoma and other types of cancer is made by tissue biopsy and detection of different cell surface markers. However, misdiagnosis can occur since some carcinoma cases can be negative for certain markers and because these markers may not indicate which genes or protein kinases may be deregulated. Although the genetic translocations and/or mutations characteristic of a particular form of carcinoma can be sometimes detected, it is clear that other downstream effectors of constitutively active kinases having potential diagnostic, predictive, or therapeutic value, remain to be elucidated.

Accordingly, identification of downstream signaling molecules and acetylation sites involved in different types of diseases including for example, cancer and development of new reagents to detect and quantify these sites and proteins may lead to improved diagnostic/prognostic markers, as well as novel drug targets, for the detection and treatment of many diseases.

SUMMARY OF THE INVENTION

The present invention provides in one aspect novel lysine acetylation sites (Table 1) identified in signal transduction proteins and pathways relevant to protein acetylation signaling. The novel sites occur in proteins such as: adaptor/scaffold proteins, adhesion or extracellular matrix proteins, apoptosis proteins, calcium-binding proteins, cell cycle regulation proteins, chaperone proteins, chormatin or DNA binding/repair/replication proteins, cytoskeletal proteins, enzyme proteins, endoplasmic reticulum proteins or golgi proteins, g proteins or regulator proteins, inhibitor proteins, mitochondrial proteins, motor or contractile proteins, proteases, phosphatases, receptor/channel/transporter/cell surface proteins, kinases RNA binding proteins, transcriptional regulators, translational regulators and sectreted proteins.

In another aspect, the invention provides peptides comprising the novel acetylation sites of the invention, and proteins and peptides that are mutated to eliminate the novel acetylation sites.

In another aspect, the invention provides modulators that modulate lysine acetylation at a novel acetylation site of the invention, including small molecules, peptides comprising a novel acetylation site, and binding molecules that specifically bind at a novel acetylation site, including but not limited to antibodies or antigen-binding fragments thereof.

In another aspect, the invention provides compositions for detecting, quantitating or modulating a novel acetylation site of the invention, including peptides comprising a novel acetylation site and antibodies or antigen-binding fragments thereof that specifically bind at a novel acetylation site. In certain embodiments, the compositions for detecting, quantitating or modulating a novel acetylation site of the invention are Heavy-Isotype Labeled Peptides (AQUA peptides) comprising a novel acetylation site.

In another aspect, the invention discloses acetylation site specific antibodies or antigen-binding fragments thereof. In one embodiment, the antibodies specifically bind to an amino acid sequence comprising a acetylation site identified in Table 1 when the lysine identified in Column D is acetylated, and do not significantly bind when the lysine is not acetylated. In another embodiment, the antibodies specifically bind to an amino acid sequence comprising an acetylation site when the lysine is not acetylated, and do not significantly bind when the lysine is acetylated.

In another aspect, the invention provides a method for making acetylation site-specific antibodies.

In another aspect, the invention provides compositions comprising a peptide, protein, or antibody of the invention, including pharmaceutical compositions.

In a further aspect, the invention provides methods of treating or preventing cancer in a subject, wherein the cancer is associated with the acetylation state of a novel acetylation site in Table 1, whether acetylated or deacetylated. In certain embodiments, the methods comprise administering to a subject a therapeutically effective amount of a peptide comprising a novel acetylation site of the invention. In certain embodiments, the methods comprise administering to a subject a therapeutically effective amount of an antibody or antigen-binding fragment thereof that specifically binds at a novel acetylation site of the invention.

In a further aspect, the invention provides methods for detecting and quantitating acetylation at a novel lysine acetylation site of the invention.

In another aspect, the invention provides a method for identifying an agent that modulates lysine acetylation at a novel acetylation site of the invention, comprising: contacting a peptide or protein comprising a novel acetylation site of the invention with a candidate agent, and determining the acetylation state or level at the novel acetylation site. A change in the acetylation state or level at the specified lysine in the presence of the test agent, as compared to a control, indicates that the candidate agent potentially modulates lysine acetylation at a novel acetylation site of the invention.

In another aspect, the invention discloses immunoassays for binding, purifying, quantifying and otherwise generally detecting the acetylation of a protein or peptide at a novel acetylation site of the invention.

Also provided are pharmaceutical compositions and kits comprising one or more antibodies or peptides of the invention and methods of using them.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 is a diagram depicting the immuno-affinity isolation and mass-spectrometric characterization methodology (IAP) used in the Examples to identify the novel acetylation sites disclosed herein.

FIG. 2 is a table (corresponding to Table 1) summarizing the 322 novel acetylation sites of the invention: Column A=the parent proteins from which the acetylation sites are derived; Column B=the SwissProt accession number for the human homologue of the identified parent proteins; Column C=the protein type/classification; Column D=the lysine residues at which acetylation occurs (each number refers to the amino acid residue position of the lysine in the parent human protein, according to the published sequence retrieved by the SwissProt accession number); Column E=flanking sequences of the phosphorylatable lysine residues; sequences (SEQ ID NOs) were identified using Trypsin digestion of the parent proteins; in each sequence, the lysine (see corresponding rows in Column D) appears in lowercase; Column F=the type of disease in which each of the acetylation site was discovered; Column G=the cell type(s)/Tissue/Patient Sample in which each of the acetylation site was discovered; and Column H=the SEQ ID NOs of the trypsin-digested peptides identified in Column E.

FIG. 3 is an exemplary mass spectrograph depicting the detection of the acetylation of lysine 60 in RAN, as further described in Example 1 (red and blue indicate ions detected in MS/MS spectrum); K* indicates the acetylated lysine (corresponds to lowercase “k” in Column E of Table 1; SEQ ID NO: 195).

FIG. 4 is an exemplary mass spectrograph depicting the detection of the acetylation of lysine 143 in DLD, as further described in Example 1 (red and blue indicate ions detected in MS/MS spectrum); K* indicates the acetylated lysine (corresponds to lowercase “k” in Column E of Table 1; SEQ ID NO: 203).

FIG. 5 is an exemplary mass spectrograph depicting the detection of the acetylation of lysine 334 in BAT1, as further described in Example 1 (red and blue indicate ions detected in MS/MS spectrum); K* indicates the acetylated lysine (corresponds to lowercase “k” in Column E of Table 1; SEQ ID NO: 253).

FIG. 6 is an exemplary mass spectrograph depicting the detection of the acetylation of 392 in eEF1A-1, as further described in Example 1 (red and blue indicate ions detected in MS/MS spectrum); K* indicates the acetylated lysine (corresponds to lowercase “k” in Column E of Table 1; SEQ ID NO: 339).

FIG. 7 is an exemplary mass spectrograph depicting the detection of the acetylation of lysine 64 acetylation site in YB-1, as further described in Example 1 (red and blue indicate ions detected in MS/MS spectrum); K* indicates the acetylated lysine (corresponds to lowercase “k” in Column E of Table 1; SEQ ID NO: 334).

DETAILED DESCRIPTION OF THE INVENTION

The inventors have discovered and disclosed herein novel lysine acetylation sites in signaling proteins extracted from cancer cells, including carcinoma cells. The newly discovered acetylation sites significantly extend our knowledge of kinase substrates and of the proteins in which the novel sites occur. The disclosure herein of the novel acetylation sites and reagents including peptides and antibodies specific for the sites add important new tools for the elucidation of signaling pathways that are associate with a host of biological processes including cell division, growth, differentiation, developmental changes and disease. Their discovery in cancer cells (including carcinoma cells) provides and focuses further elucidation of the disease process. And, the novel sites provide additional diagnostic and therapeutic targets.

1. Novel Acetylation Sites in Cancer Cell Lines Including Carcinoma

In one aspect, the invention provides 332 novel lysine acetylation sites in signaling proteins from cellular extracts from a variety of human cancer-derived cell lines and tissue samples (such as HCT8, sw480, etc., as further described below in Examples), identified using the techniques described in “Immunoaffinity Isolation of Modified Peptides From Complex Mixtures,” U.S. Patent Publication No. 20030044848, Rush et al., using Table 1 summarizes the identified novel acetylation sites.

These acetylation sites thus occur in proteins found in cancer. The sequences of the human homologues are publicly available in SwissProt database and their Accession numbers listed in Column B of Table 1. The novel sites occur in proteins such as: adaptor/scaffold proteins, adhesion or extracellular matrix proteins, apoptosis proteins, calcium-binding proteins, cell cycle regulation proteins, chaperone proteins, chormatin or DNA binding/repair/replication proteins, cytoskeletal proteins, enzyme proteins, endoplasmic reticulum proteins or golgi proteins, g proteins or regulator proteins, inhibitor proteins, mitochondrial proteins, motor or contractile proteins, proteases, phosphatases, receptor/channel/transporter/cell surface proteins, kinases RNA binding proteins, transcriptional regulators, translational regulators and sectreted proteins. (see Column C of Table 1).

The novel acetylation sites of the invention were identified according to the methods described by Rush et al., U.S. Patent Publication No. 20030044848, which are herein incorporated by reference in its entirety. Briefly, acetylation sites were isolated and characterized by immunoaffinity isolation and mass-spectrometric characterization (IAP) (FIG. 1), using the following human carcinoma-derived cell lines and/or tissue samples: H23, H3255, H520, HCC78, HCC827, HCT116, HCT15, HCT8, HEP-G2, HeLa, Jurkat (pervanadate/calyculin), MV4; 11, MV4; 11 (SAHA), NB-4, NCI-H716, Nomo-1, OCI/AML2, OCI/AML3, RC-K8, RC-K8 (SAHA), SEM, SEM (SAHA), SIL-ALL, SNU-C2B, SW48, SW620, sw48, sw480. In addition to the newly discovered acetylation sites (all having an acetylatable lysine), many known acetylation sites were also identified.

The immunoaffinity/mass spectrometric technique described in Rush et al, i.e., the “IAP” method, is described in detail in the Examples and briefly summarized below.

The IAP method generally comprises the following steps: (a) a proteinaceous preparation (e.g., a digested cell extract) comprising acetylpeptides from two or more different proteins is obtained from an organism; (b) the preparation is contacted with at least one immobilized general acetylated-lysine-specific antibody; (c) at least one acetylpeptide specifically bound by the immobilized antibody in step (b) is isolated; and (d) the modified peptide isolated in step (c) is characterized by mass spectrometry (MS) and/or tandem mass spectrometry (MS-MS). Subsequently, (e) a search program (e.g., Sequest) may be utilized to substantially match the spectra obtained for the isolated, modified peptide during the characterization of step (d) with the spectra for a known peptide sequence. A quantification step, e.g., using SILAC or AQUA, may also be used to quantify isolated peptides in order to compare peptide levels in a sample to a baseline.

In the IAP method as disclosed herein, a general acetylated lysine-specific monoclonal antibody (commercially available from Cell Signaling Technology, Inc., Beverly, Mass., Cat #9681) may be used in the immunoaffinity step to isolate the widest possible number of acetyl-lysine containing peptides from the cell extracts.

As described in more detail in the Examples, lysates may be prepared from various cancer cell lines or tissue samples and digested with trypsin after treatment with DTT and iodoacetamide to alkylate cysteine residues. Before the immunoaffinity step, peptides may be pre-fractionated (e.g., by reversed-phase solid phase extraction using Sep-Pak C₁₈columns) to separate peptides from other cellular components. The solid phase extraction cartridges may then be eluted (e.g., with acetonitrile). Each lyophilized peptide fraction can be redissolved and treated with acetyl-lysine specific antibody (e.g., CST Catalogue #8691) immobilized on protein Agarose. Immunoaffinity-purified peptides can be eluted and a portion of this fraction may be concentrated (e.g., with Stage or Zip tips) and analyzed by LC-MS/MS (e.g., using a ThermoFinnigan LCQ Deca XP Plus ion trap mass spectrometer or LTQ). MS/MS spectra can be evaluated using, e.g., the program Sequest with the NCBI human protein database.

The novel acetylation sites identified are summarized in Table 1/FIG. 2. Column A lists the parent (signaling) protein in which the acetylation site occurs. Column D identifies the lysine residue at which acetylation occurs (each number refers to the amino acid residue position of the lysine in the parent human protein, according to the published sequence retrieved by the SwissProt accession number). Column E shows flanking sequences of the identified lysine residues (which are the sequences of trypsin-digested peptides). FIG. 2 also shows the particular type of cancer (see Column G) and cell line(s) (see Column F) in which a particular acetylation site was discovered.

TABLE 1

Novel Acetylation Sites in Cancer, Including Carcinoma.

A

D

Protein
B
C
Phospho-
E
H

1
Name
Accession No.
Protein Type
Residue
Acetylation Site Sequence
SEQ ID NO

2
GSTP1
NP_000843.1
Enzyme, misc.
K191
LkAFLASPEYVNLPINGNGKQ
SEQ ID NO: 149

3
14-3-3 beta
NP_003395.1
Adaptor/scaffold
K117
YLIPNATQPESkVFYLK
SEQ ID NO: 1

4
14-3-3 eta
NP_003396.1
Adaptor/scaffold
K120
NCNDFQYESkVFYLK
SEQ ID NO: 2

5
14-3-3
NP_036611.2
Adaptor/scaffold
K120
NCSETQYESkVFYLK
SEQ ID NO: 3

gamma

6
14-3-3
NP_006133.1
Adaptor/scaffold
K32
GAVEkGEELSCEER
SEQ ID NO: 4

sigma

7
14-3-3 zeta
NP_003397.1
Adaptor/scaffold
K115
FLIPNASQAESkVFYLK
SEQ ID NO: 5

8
COPS5
NP_006828.2
Adaptor/scaffold
K326
DkLFNQINIS
SEQ ID NO: 6

9
CSDE1
NP_009089.4
Adaptor/scaffold
K403
FLGTVEkEATFSNPK
SEQ ID NO: 7

10
G3BP-1
NP_005745.1
Adaptor/scaffold
K376
INSGGkLPNFGFVVFDDSEPVQK
SEQ ID NO: 8

11
COL5A3
NP_056534.2
Adhesion or
K254
KGKGKGRkK
SEQ ID NO: 10

extracellular

matrix protein

12
DCN
NP_001911.1
Adhesion or
K138
LERLYLSkNQLKELPEKMPK
SEQ ID NO: 11

extracellular

matrix protein

13
DCN
NP_001911.1
Adhesion or
K147
LERLYLSKNQLKELPEkMPK
SEQ ID NO: 12

extracellular

matrix protein

14
DSG1
NP_001933.1
Adhesion or
K450
NKVTkEQYNMLGGK
SEQ ID NO: 13

extracellular

matrix protein

15
laminin
NP_002286.2
Adhesion or
K89
AVLkFAAATGATPIAGR
SEQ ID NO: 14

receptor 1

extracellular

matrix protein

16
SPOCK1
NP_004589.1
Adhesion or
K118
HLLPRQkKGNVAQK
SEQ ID NO: 15

extracellular

matrix protein

17
vinculin
NP_003364.1
Adhesion or
K1002
ILSTVkATMLGR
SEQ ID NO: 16

extracellular

matrix protein

18
zyxin
NP_003452.1
Adhesion or
K265
GPPASSPAPAPkFSPVTPK
SEQ ID NO: 17

extracellular

matrix protein

19
zyxin
NP_003452.1
Adhesion or
K272
FSPVTPkFTPVASK
SEQ ID NO: 18

extracellular

matrix protein

20
zyxin
NP_003452.1
Adhesion or
K528
VVALDkNFHMK
SEQ ID NO: 19

extracellular

matrix protein

21
DBC-1
NP_066997.3
Apoptosis
K287
IQVSSEkEAAPDAGAEPITADSDPAYSSK
SEQ ID NO: 20

22
GRP94
NP_003290.1
Apoptosis
K613
EAVEkEFEPLLNWMK
SEQ ID NO: 21

23
p400
NP_056224.2
Apoptosis
K346
TAVPPGLSSLPLTSVGNTGMKk
SEQ ID NO: 22

24
p400
NP_056224.2
Apoptosis
K1516
HQPASASSTAASPAHPAkLR
SEQ ID NO: 23

25
AIM1
NP_001615.1
Calcium-binding
K747
VFDPkVFTFGLGK
SEQ ID NO: 24

protein

26
ANXA1
NP_000691.1
Calcium-binding
K281
CATSKPAFFAEk
SEQ ID NO: 25

protein

27
ANXA2
NP_004030.1
Calcium-binding
K227
SVPHLQkVFDR
SEQ ID NO: 26

protein

28
ANXA2
NP_004030.1
Calcium-binding
K157
TDLEkDIISDTSGDFRK
SEQ ID NO: 27

protein

29
Calmodulin
NP_005175.2
Calcium-binding
K116
HVMTNLGEkLTDEEVDEMIR
SEQ ID NO: 28

protein

30
S100A2
NP_005969.1
Calcium-binding
K26
YSCQEGDkFK
SEQ ID NO: 29

protein

31
CENPF
NP_057427.3
Cell cycle
K1577
LEEKMESQGIMkNK
SEQ ID NO: 30

regulation

32
KI-67
NP_002408.3
Cell cycle
K1938
LDLLGNLPGSkR
SEQ ID NO: 31

regulation

33
NOL1
AAA36398.1
Cell cycle
K105
GISAGAVQTAGkK
SEQ ID NO: 32

regulation

34
NuMA-1
NP_006176.2
Cell cycle
K1766
LPPkVESLESLYFTPIPAR
SEQ ID NO: 33

regulation

35
NuMA-1
NP_006176.2
Cell cycle
K379
CLEEkNEILQGK
SEQ ID NO: 34

regulation

36
securin
NP_004210.1
Cell cycle
K48
FGkTFDAPPALPK
SEQ ID NO: 35

regulation

37
septin 9
NP_006631.1
Cell cycle
K44
ATVASSTQkFQDLGVK
SEQ ID NO: 36

regulation

38
SMC2L1
NP_006435.2
Cell cycle
K1158
EGMFNNANVLFkTK
SEQ ID NO: 37

regulation

39
CCT5
NP_036205.1
Chaperone
K232
GVIVDkDFSHPQMPK
SEQ ID NO: 38

40
CCT7
NP_006420.1
Chaperone
K366
YNFFTGCPkAK
SEQ ID NO: 39

41
CCT7
NP_006420.1
Chaperone
K172
LISQQkAFFAK
SEQ ID NO: 40

42
CCT-zeta
NP_001753.1
Chaperone
K365
FTFIEkCNNPR
SEQ ID NO: 41

43
GRP58
NP_005304.3
Chaperone
K104
VDCTANTNTCNKYGVSGYPTLkIFR
SEQ ID NO: 42

44
HSC70
NP_006588.1
Chaperone
K108
VQVEYkGETKSFYPEEVSSMVLTK
SEQ ID NO: 43

45
HSC70
NP_006588.1
Chaperone
K3
SkGPAVGIDLGTTY
SEQ ID NO: 44

46
HSC70
NP_006588.1
Chaperone
K112
VQVEYKGETkSFYPEEVSSMVLTK
SEQ ID NO: 45

47
HSP60
NP_002147.2
Chaperone
K72
TVIIEQSWGSPkVTK
SEQ ID NO: 46

48
HSP70
NP_005337.1
Chaperone
K3
AkAAAIGIDLGTTY
SEQ ID NO: 47

49
HSP75
NP_057376.1
Chaperone
K424
LIkFFIDQSK
SEQ ID NO: 48

50
HSP90A
NP_005339.2
Chaperone
K224
HSQFIGYPITLFVEk
SEQ ID NO: 49

51
HSP90B
NP_031381.2
Chaperone
K219
HSQFIGYPITLYLEk
SEQ ID NO: 50

52
HSP90B
NP_031381.2
Chaperone
K306
NPDDITQEEYGEFYk
SEQ ID NO: 51

53
HSPA5
NP_005338.1
Chaperone
K376
IQQLVkEFFNGKEPSR
SEQ ID NO: 52

54
HSPA5
NP_005338.1
Chaperone
K547
MVNDAEkFAEEDK
SEQ ID NO: 53

55
HSPA5
NP_005338.1
Chaperone
K601
AVEEkIEWLESHQDADIEDFK
SEQ ID NO: 54

56
HSPA5
NP_005338.1
Chaperone
K585
LGGkLSSEDKETMEK
SEQ ID NO: 56

57
HSPA9B
NP_004125.3
Chaperone
K567
NAEkYAEEDR
SEQ ID NO: 57

58
HSPA9B
NP_004125.3
Chaperone
K288
HIVkEFK
SEQ ID NO: 58

59
PDIA4
NP_004902.1
Chaperone
K256
RFDVSGYPTLkIFR
SEQ ID NO: 59

60
PDIA4
NP_004902.1
Chaperone
K533
VVVGkTFDSIVMDPK
SEQ ID NO: 60

61
PPIB
NP_000933.1
Chaperone
K98
VIkDFMIQGGDFTR
SEQ ID NO: 61

62
PPIB
NP_000933.1
Chaperone
K145
HYGPGWVSMANAGkDTNGSQFFITTVK
SEQ ID NO: 62

63
PPIB
NP_000933.1
Chaperone
K165
TAWLDGkHVVFGK
SEQ ID NO: 63

64
APRIN
NP_055847.1
Chromatin, DNA-
K1103
FFTQPDkNFSNTK
SEQ ID NO: 64

binding, DNA

repair or DNA

replication protein

65
BAZ1A
NP_038476.2
Chromatin, DNA-
K973
SSNAYDPSQMCAEkQLELR
SEQ ID NO: 65

binding, DNA

repair or DNA

replication protein

66
HMG-2
NP_002120.1
Chromatin, DNA-
K157
YEkDIAAYR
SEQ ID NO: 66

binding, DNA

repair or DNA

replication protein

67
HMGB1
NP_002119.1
Chromatin, DNA-
K157
YEkDIAAYR
SEQ ID NO: 67

binding, DNA

repair or DNA

replication protein

68
HMGB3
NP_005333.2
Chromatin, DNA-
K12
GkMSAYAFFVQTCR
SEQ ID NO: 68

binding, DNA

repair or DNA

replication protein

69
HMGN2
NP_005508.1
Chromatin, DNA-
K54
GEKVPkGKKGK
SEQ ID NO: 69

binding, DNA

repair or DNA

replication protein

70
HMGN2
NP_005508.1
Chromatin, DNA-
K56
GEKVPKGkKGK
SEQ ID NO: 70

binding, DNA

repair or DNA

replication protein

71
HMGN2
NP_005508.1
Chromatin, DNA-
K59
GEKVPKGKKGk
SEQ ID NO: 71

binding, DNA

repair or DNA

replication protein

72
PMS2
NP_000526.1
Chromatin, DNA-
K210
VSCTNQLGQGkR
SEQ ID NO: 72

binding, DNA

repair or DNA

replication protein

73
RPA1
NP_002936.1
Chromatin, DNA-
K502
CEkCDTEFPNFK
SEQ ID NO: 73

binding, DNA

repair or DNA

replication protein

74
RPA1
NP_002936.1
Chromatin, DNA-
K267
IANkQFTAVK
SEQ ID NO: 74

binding, DNA

repair or DNA

replication protein

75
XRCC1
NP_006288.1
Chromatin, DNA-
K256
kTPSKPPAQLSPSVPK
SEQ ID NO: 75

binding, DNA

repair or DNA

replication protein

76
XRCC1
NP_006288.1
Chromatin, DNA-
K260
KTPSkPPAQLSPSVPK
SEQ ID NO: 76

binding, DNA

repair or DNA

replication protein

77
XRCC1
NP_006288.1
Chromatin, DNA-
K271
KTPSKPPAQLSPSVPk
SEQ ID NO: 77

binding, DNA

repair or DNA

replication protein

78
ZNF261
NP_005087.1
Chromatin, DNA-
K439
LCSDSCFSkFR
SEQ ID NO: 78

binding, DNA

repair or DNA

replication protein

79
actin,
NP_001091.1
Cytoskeletal
K328
EITALAPSTMkIK
SEQ ID NO: 79

alpha 1

protein

80
actin, beta
NP_001092.1
Cytoskeletal
K326
EITALAPSTMkIK
SEQ ID NO: 80

protein

81
actin,
NP_001605.1
Cytoskeletal
K326
EITALAPSTMkIK
SEQ ID NO: 81

gamma 1

protein

82
Arp3
NP_005712.1
Cytoskeletal
K244
EFNkYDTDGSK
SEQ ID NO: 82

protein

83
CAPZA1
NP_006126.1
Cytoskeletal
K97
ISFkFDHLR
SEQ ID NO: 83

protein

84
K18
NP_000215.1
Cytoskeletal
K81
GGMGSGGLATGIAGGLAGMGGIQNEkETM
SEQ ID NO: 84

protein

QSLNDR

85
CLIM1
NP_066272.1
Cytoskeletal
K22
LVGGkDFEQPLAISR
SEQ ID NO: 85

protein

86
cortactin
NP_005222.2
Cytoskeletal
K87
ASHGYGGkFGVEQDR
SEQ ID NO: 86

protein

87
DNCLI1
NP_057225.1
Cytoskeletal
K429
SVSSNVASVSPIPAGSKk
SEQ ID NO: 87

protein

88
DST
NP_056363.2
Cytoskeletal
K4563
KLEEkRAELNK
SEQ ID NO: 88

protein

89
FLNA
NP_001447.1
Cytoskeletal
K1071
VkAFGPGLQGGSAGSPAR
SEQ ID NO: 89

protein

90
FLNB
NP_001448.2
Cytoskeletal
K681
APLkIFAQDGEGQR
SEQ ID NO: 90

protein

91
FLNB
NP_001448.2
Cytoskeletal
K677
DAGkAPLKIFAQDGEGQR
SEQ ID NO: 91

protein

92
K16
NP_005548.2
Cytoskeletal
K162
QRPSEIkDYSPYFKTIEDLR
SEQ ID NO: 92

protein

93
K16
NP_005548.2
Cytoskeletal
K169
QRPSEIKDYSPYFkTIEDLR
SEQ ID NO: 93

protein

94
Lasp-1
NP_006139.1
Cytoskeletal
K23
VNCLDkFWHK
SEQ ID NO: 94

protein

95
MAP1B
NP_005900.1
Cytoskeletal
K693
EEVKKEVKKEIKKEEkK
SEQ ID NO: 95

protein

96
MAP1B
NP_005900.1
Cytoskeletal
K685
EEVKKEVkKEIKKEEKK
SEQ ID NO: 96

protein

97
MAP1B
NP_005900.1
Cytoskeletal
K686
EEVKKEVKkEIKKEEKK
SEQ ID NO: 97

protein

98
MAP1B
NP_005900.1
Cytoskeletal
K694
EEVKKEVKKEIKKEEKk
SEQ ID NO: 98

protein

99
PARVA
NP_060692.1
Cytoskeletal
K32
KKDDSFLGkLGGTLAR
SEQ ID NO: 99

protein

100
PARVB
NP_037459.2
Cytoskeletal
K24
MKKDESFLGkLGGTLARK
SEQ ID NO: 100

protein

101
PARVB
NP_037459.2
Cytoskeletal
K16
MkKDESFLGKLGGTLARK
SEQ ID NO: 101

protein

102
SLP-2
NP_038470.1
Cytoskeletal
K145
LSLDkVFR
SEQ ID NO: 102

protein

103
SPTB1
NP_000338.3
Cytoskeletal
K1258
kNNEKAQEASVLLR
SEQ ID NO: 103

protein

104
SPTB1
NP_000338.3
Cytoskeletal
K1262
KNNEkAQEASVLLR
SEQ ID NO: 104

protein

105
TES
NP_056456.1
Cytoskeletal
K101
NVMILTNPVAAkK
SEQ ID NO: 105

protein

106
TMSB4X
NP_066932.1
Cytoskeletal
K4
SDkPDMAEIEKF
SEQ ID NO: 106

protein

107
TMSB4X
NP_066932.1
Cytoskeletal
K39
ETIEQEkQAGES
SEQ ID NO: 107

protein

108
TPM1
NP_000357.3
Cytoskeletal
K118
LATALQKLEEAEkAADESER
SEQ ID NO: 108

protein

109
TPM2
NP_003280.2
Cytoskeletal
K118
LATALQKLEEAEkAADESER
SEQ ID NO: 109

protein

110
TPM3
NP_689476.1
Cytoskeletal
K77
LATALQKLEEAEkAADESER
SEQ ID NO: 110

protein

111
TPM4
NP_003281.1
Cytoskeletal
K82
LATALQKLEEAEkAADESER
SEQ ID NO: 111

protein

112
tubulin,
NP_006073.2
Cytoskeletal
K280
IHFPLATYAPVISAEk
SEQ ID NO: 112

alpha,

protein

ubiquitous

113
tubulin,
NP_005991.1
Cytoskeletal
K280
IHFPLATYAPVISAEk
SEQ ID NO: 113

alpha-1

protein

114
tubutin,
NP_005992.1
Cytoskeletal
K280
IHFPLATYAPVISAEk
SEQ ID NO: 114

alpha-2

protein

115
tubulin,
NP_116093.1
Cytoskeletal
K280
IHFPLATYAPVISAEk
SEQ ID NO: 115

alpha-6

protein

116
tubulin,
NP_821133.1
Cytoskeletal
K216
TLkLTTPTYGDLNHLVSATMSGVTTCLR
SEQ ID NO: 116

beta-1

protein

117
tubulin,
NP_006079.1
Cytoskeletal
K216
TLkLTTPTYGDLNHLVSATMSGVTTCLR
SEQ ID NO: 117

beta-2

protein

118
tubulin,
NP_006078.2
Cytoskeletal
K216
TLkLTTPTYGDLNHLVSATMSGVTTCLR
SEQ ID NO: 118

beta-4

protein

119
WDR1
NP_059830.1
Cytoskeletal
K180
LATGSDDNCAAFFEGPPFkFK
SEQ ID NO: 119

protein

120
WDR1
NP_059830.1
Cytoskeletat
K182
LATGSDDNCAAFFEGPPFKFk
SEQ ID NO: 120

protein

121
DNAJB11
NP_057390.1
Endoplasmic
K47
KAYRkLALQLHPDR
SEQ ID NO: 121

reticulum or golgi

122
DNAJB11
NP_057390.1
Endoplasmic
K43
kAYRKLALQLHPDR
SEQ ID NO: 122

reticulum or golgi

123
ACADVL
NP_000009.1
Enzyme, misc.
K276
TPVTDPATGAVkEK
SEQ ID NO: 123

124
ACADVL
NP_000009.1
Enzyme, misc.
K71
AESkSFAVGMFK
SEQ ID NO: 124

125
ACAT1
NP_000010.1
Enzyme, misc.
K124
QAVLGAGLPISTPCTTINkVCASGMK
SEQ ID NO: 125

126
aldolase A
NP_000025.1
Enzyme, misc.
K294
CPLLkPWALTFSYGR
SEQ ID NO: 126

127
ALP
NP_078938.1
Enzyme, misc.
K426
SLSLkLIQQLR
SEQ ID NO: 127

128
BDH
NP_004042.1
Enzyme, misc.
K283
IAkMETYCSSGSTDTSPVIDAVTHALTA
SEQ ID NO: 128

TTPYTR

129
C8orf36
NP_775956.1
Enzyme, misc.
K125
NSDADFQNNEkFVQFK
SEQ ID NO: 129

130
DDX42
NP_031398.2
Enzyme, misc.
K25
GFGFGGFAISAGkK
SEQ ID NO: 130

131
DDX46
NP_055644.2
Enzyme, misc.
K776
SSGFSGkGFK
SEQ ID NO: 131

132
DHRS2
NP_005785.1
Enzyme, misc.
K147
ILSVNVkSPALLLSQLLPYMENR
SEQ ID NO: 132

133
DHRS6
NP_064524.3
Enzyme, misc.
K151
CVYSTTkAAVIGLTK
SEQ ID NO: 133

134
DNMT1
NP_001370.1
Enzyme, misc.
K1115
GkGKGKPK
SEQ ID NO: 134

135
DNMT1
NP_001370.1
Enzyme, misc.
K1119
GKGKGkPK
SEQ ID NO: 135

136
dUTPase
NP_001939.1
Enzyme, misc.
K91
SGLAAkHFIDVGAGVIDEDYR
SEQ ID NO: 136

137
ENO1
NP_001419.1
Enzyme, misc.
K406
LAkYNQLLR
SEQ ID NO: 137

138
esterase D
NP_001975.1
Enzyme, misc.
K10
QISSNkCFGGLQK
SEQ ID NO: 138

139
FARSLA
NP_004452.1
Enzyme, misc.
K349
KPFTPVkYFSIDR
SEQ ID NO: 139

140
FASN
NP_004095.4
Enzyme, misc.
K1444
GILADEDSSRPVWLkAINCATSGVVG
SEQ ID NO: 140

LVNCLR

141
FASN
NP_004095.4
Enzyme, misc.
K1878
LMSAISkTFCPAHK
SEQ ID NO: 141

142
GALNT7
NP_059119.1
Enzyme, misc.
K270
LWNGLVkVFR
SEQ ID NO: 142

143
GCLC
NP_001489.1
Enzyme, misc.
K412
FkPPPPNSDIGWR
SEQ ID NO: 143

144
GLUD1
NP_005262.1
Enzyme, misc.
K545
TAAYVNAIEkVFK
SEQ ID NO: 144

145
GLUL
NP_002056.2
Enzyme, misc.
K372
TCLLNETGDEPFQYkN
SEQ ID NO: 145

146
GNPAT
NP_055051.1
Enzyme, misc.
K128
FCAFTLSkVFK
SEQ ID NO: 146

147
GSS
NP_000169.1
Enzyme, misc.
K186
ILSNNPSkGLALGIAK
SEQ ID NO: 147

148
GSTA1
NP_000838.3
Enzyme, misc.
K87
YNLYGKDIkER
SEQ ID NO: 148

149
HADHB
NP_000174.1
Enzyme, misc.
K201
LSLISkFR
SEQ ID NO: 150

150
HIBCH
NP_055177.2
Enzyme, misc.
K92
GAGGkAFCAGGDIR
SEQ ID NO: 151

151
HMGCS1
NP_002121.3
Enzyme, misc.
K409
VTQDATPGSALDKITASLCDLk
SEQ ID NO: 152

152
HSD17B4
NP_000405.1
Enzyme, misc.
K707
LDPQkAFFSGR
SEQ ID NO: 153

153
IDH3A
NP_005521.1
Enzyme, misc.
K200
SNVTAVHkANIMRMSDGLFLQK
SEQ ID NO: 154

154
IDH3A
NP_005521.1
Enzyme, misc.
K214
SNVTAVHKANIMRMSDGLFLQk
SEQ ID NO: 155

155
Ku80
NP_066964.1
Enzyme, misc.
K338
SEGkCFSVLGFCK
SEQ ID NO: 156

156
LDH-A
NP_005557.1
Enzyme, misc.
K118
NVNIFkFIIPNVVK
SEQ ID NO: 157

157
LDH-B
NP_002291.1
Enzyme, misc.
K82
IVADkDYSVTANSK
SEQ ID NO: 158

158
LDH-B
NP_002291.1
Enzyme, misc.
K318
LKDDEVAQLkK
SEQ ID NO: 159

159
MDH2
NP_005909.2
Enzyme, misc.
K301
KGIEkNLGIGK
SEQ ID NO: 160

160
MDH2
NP_005909.2
Enzyme, misc.
K297
kGIEKNLGIGK
SEQ ID NO: 161

161
MDH2
NP_005909.2
Enzyme, misc.
K165
HGVYNPNkIFGVTTLDIVR
SEQ ID NO: 162

162
ME2
NP_002387.1
Enzyme, misc.
K94
NEkLFYR
SEQ ID NO: 163

163
METTL1
NP_005362.1
Enzyme, misc.
K250
NGGkNFPAIFR
SEQ ID NO: 164

164
MPO
NP_000241.1
Enzyme, misc.
K103
SGSASPMELLSYFkQPVAATR
SEQ ID NO: 165

165
MYST4
NP_036462.2
Enzyme, misc.
K1038
QSPAkVQSKNK
SEQ ID NO: 166

166
MYST4
NP_036462.2
Enzyme, misc.
K1042
QSPAKVQSkNK
SEQ ID NO: 167

167
NDUFA4
NP_002480.1
Enzyme, misc.
K55
NNPEPWNkLGPNDQYK
SEQ ID NO: 168

168
NKEF-A
NP_002565.1
Enzyme, misc.
K168
LVQAFQFTDk
SEQ ID NO: 169

169
OAS1
NP_001027581.1
Enzyme, misc.
K42
MQINHAIDIICGFLkER
SEQ ID NO: 170

170
PDIA1
NP_000909.2
Enzyme, misc.
K375
VLVGkNFEDVAFDEK
SEQ ID NO: 171

171
PDIA1
NP_000909.2
Enzyme, misc.
K444
VHSFPTLkFFPASADR
SEQ ID NO: 172

172
PDIA1
NP_000909.2
Enzyme, misc.
K103
GYPTIkFFR
SEQ ID NO: 173

173
PGAM-1
NP_002620.1
Enzyme, misc.
K113
HGEAQVkIWR
SEQ ID NO: 174

174
PIGG
NP_060203.2
Enzyme, misc.
K742
PDSkDISKGIIEAR
SEQ ID NO: 176

175
PIGG
NP_060203.2
Enzyme, misc.
K746
PDSKDISkGIIEAR
SEQ ID NO: 177

176
PKM2
NP_002645.3
Enzyme, misc.
K151
ITLDNAYMEk
SEQ ID NO: 178

177
PKM2
NP_002645.3
Enzyme, misc.
K498
VNFAMNVGkAR
SEQ ID NO: 179

178
PLCB1
NP_056007.1
Enzyme, misc.
K1074
KMDkKRQEK
SEQ ID NO: 180

179
PPIA
NP_066953.1
Enzyme, misc.
K44
ALSTGEkGFGYK
SEQ ID NO: 181

180
PPIA
NP_066953.1
Enzyme, misc.
K125
TEWLDGkHVVFGK
SEQ ID NO: 182

181
PRDX3
NP_006784.1
Enzyme, misc.
K91
DLSLDDFkGK
SEQ ID NO: 183

182
RPN2
NP_002942.2
Enzyme, misc.
K460
NVYkFELDTSER
SEQ ID NO: 184

183
SETDB2
NP_114121.1
Enzyme, misc.
K373
VVQHGPQVRLQVFkTEQK
SEQ ID NO: 185

184
TALDO1
NP_006746.1
Enzyme, misc.
K337
MFNAENGk
SEQ ID NO: 186

185
TKT
NP_001055.1
Enzyme, misc.
K456
SVPTSTVFYPSDGVATEkAVELAANTK
SEQ ID NO: 187

186
TOP1
NP_003277.1
Enzyme, misc.
K712
LEVQATDREENkQIALGTSK
SEQ ID NO: 188

187
TPI1
NP_000356.1
Enzyme, misc.
K238
ELASQPDVDGFLVGGASLkPEFVDIINAK
SEQ ID NO: 189

188
UBE2J1
NP_057105.2
Enzyme, misc.
K17
YNLKSPAVKRLMkEAAELK
SEQ ID NO: 192

189
UBE2J1
NP_057105.2
Enzyme, misc.
K8
YNLkSPAVKRLMKEAAELK
SEQ ID NO: 193

190
Ran
NP_006316.1
G protein or
K159
SNYNFEkPFLWLAR
SEQ ID NO: 194

regulator

191
Ran
NP_006316.1
G protein or
K60
GPIkFNVWDTAGQEK
SEQ ID NO: 195

regulator

192
TD-60
NP_061185.1
G protein or
K377
LVkLFDFPGR
SEQ ID NO: 196

regulator

193
A2M
NP_000005.2
Inhibitor protein
K811
GEAFTLkATVLNYLPK
SEQ ID NO: 197

194
ICEBERG
NP_067546.1
Inhibitor protein
K53
DENDTVMDkARVLIDLVTGKGPKSCCK
SEQ ID NO: 198

195
ICEBERG
NP_067546.1
inhibitor protein
K64
DENDTVMDKARVLIDLVTGkGPKSCCK
SEQ ID NO: 199

196
ICEBERG
NP_067546.1
Inhibitor protein
K67
DENDTVMDKARVLIDLVTGKGPkSCCK
SEQ ID NO: 200

197
TK
NP_003249.1
Kinase (non-
K220
kLFAPQQILQCSPAN
SEQ ID NO: 201

protein)

198
ACO2
NP_001089.1
Mitochondrial
K520
FNPETDYLTGTDGkK
SEQ ID NO: 202

protein

199
DLD
NP_000099.2
Mitochondrial
K143
ALTGGIAHLFkQNK
SEQ ID NO: 203

protein

200
HMGCL
NP_000182.2
Mitochondrial
K48
DGLQNEkNIVSTPVK
SEQ ID NO: 204

protein

201
MFN2
NP_055689.1
Mitochondrial
K36
HFVTAkKK
SEQ ID NO: 205

protein

202
MRPS23
NP_057154.2
Mitochondrial
K102
FVEkYTELQK
SEQ ID NO: 206

protein

203
MYH10
NP_005955.1
Motor or
K1345
QLEEEkNSLQEQQEEEEEAR
SEQ ID NO: 208

contractile protein

204
MYH9
NP_002464.1
Motor or
K1828
IAQLEEQLDNETkER
SEQ ID NO: 209

contractile protein

205
MYO9B
NP_004136.2
Motor or
K980
MVLERRHFLQMk
SEQ ID NO: 210

contractile protein

206
AF-4
NP_005926.1
Phosphatase
K809
SkLAKK
SEQ ID NO: 211

207
AF-4;
NP_036234.2
Phosphatase
K1158
SkLAKK
SEQ ID NO: 212

DRPLA;

PTPRK;

RERE

208
DRPLA
NP_001931.2
Phosphatase
K791
SkLAKK
SEQ ID NO: 213

209
MTMR9
NP_056273.2
Phosphatase
K219
EDEkLINATLRAGK
SEQ ID NO: 214

210
MTMR9
NP_056273.2
Phosphatase
K229
EDEKLINATLRAGk
SEQ ID NO: 215

211
Pnk1
NP_009185.2
Phosphatase
K183
SGkVFPTGPSDWR
SEQ ID NO: 216

212
PPME1
NP_057231.1
Phosphatase
K30
LPSRPPLPGSGGSQSGAkMR
SEQ ID NO: 217

213
PTPRK
NP_002835.2
Phosphatase
K779
SkLAKK
SEQ ID NO: 218

214
ADAMTS12
NP_112217.2
Protease
K1014
GTISNGkNPPTLK
SEQ ID NO: 219

215
CAPNS1
NP_001740.1
Protease
K9
LkGGGGGGGGGGGL
SEQ ID NO: 220

216
CAPNS1
NP_001740.1
Protease
K179
WQAIYkQFDTDR
SEQ ID NO: 221

217
PSMA2
NP_002778.1
Protease
K171
NYVNGkTFLEK
SEQ ID NO: 222

218
PSMC6
NP_002797.2
Protease
K15
ALQDYRKkLLEHKEIDGR
SEQ ID NO: 223

219
PSMC6
NP_002797.2
Protease
K20
ALQDYRKKLLEHkEIDGR
SEQ ID NO: 224

220
PSME2
NP_002809.2
Protease
K108
CGFLPGNEKVLSLLALVkPEVWTLK
SEQ ID NO: 225

221
PSME2
NP_002809.2
Protease
K99
CGFLPGNEkVLSLLALVKPEVWTLK
SEQ ID NO: 226

222
TBP7
NP_006494.1
Protease
K397
YIVLAkDFEK
SEQ ID NO: 227

223
IBTK
NP_056340.2
Protein kinase,
K984
TKAKkK
SEQ ID NO: 228

regulatory subunit

224
BRD2
NP_005095.1
Protein kinase,
K10
MLQNVTPHNkLPGEGNAGLLGLGPEAAAP
SEQ ID NO: 229

Ser/Thr (non-

GKR

receptor)

225
BRD2
NP_005095.1
Protein kinase,
K31
LPGEGNAGLLGLGPEAAAPGkR
SEQ ID NO: 230

Ser/Thr (non-

receptor)

226
BRDT
NP_001717.2
Protein kinase,
K483
MCEQMRLKEk
SEQ ID NO: 231

Ser/Thr (non-

receptor)

227
Cdc2
NP_001777.1
Protein kinase,
K34
TTGQVVAMKk
SEQ ID NO: 232

Ser/Thr (non-

receptor)

228
CHED
NP_003709.2
Protein kinase,
K704
CVDkFDIIGIIGEGTYGQVYK
SEQ ID NO: 233

Ser/Thr (non-

receptor)

229
CRK7
NP_057591.1
Protein kinase,
K726
CVDkFDIIGIIGEGTYGQVYK
SEQ ID NO: 235

Ser/Thr (non-

receptor)

230
OSR1
NP_005100.1
Protein kinase,
K46
EKVAIkRINLEK
SEQ ID NO: 236

Ser/Thr (non-

receptor)

231
OSR1
NP_005100.1
Protein kinase,
K42
EkVAIKRINLEK
SEQ ID NO: 237

Ser/Thr (non-

receptor)

232
p90RSK
NP_002944.2
Protein kinase,
K75
VLGQGSFGkVFLVR
SEQ ID NO: 238

Ser/Thr (non-

receptor)

233
PRP4
NP_003904.3
Protein kinase,
K656
AAGIGkDFK
SEQ ID NO: 239

Ser/Thr (non-

receptor)

234
RSK2
NP_004577.1
Protein kinase,
K81
VLGQGSFGkVFLVK
SEQ ID NO: 240

Ser/Thr (non-

receptor)

235
RSK4
NP_055311.1
Protein kinase,
K86
VLGQGSFGkVFLVR
SEQ ID NO: 241

Ser/Thr (non-

receptor)

236
SMG1
NP_055907.3
Protein kinase,
K173
QLkEFIQQPENK
SEQ ID NO: 242

Ser/Thr (non-

receptor)

237
C1QBP
NP_001203.1
Receptor,
K91
AFVDFLSDEIkEER
SEQ ID NO: 243

channel,

transporter or cell

surface protein

238
CLIC1
NP_001279.2
Receptor,
K131
NSNPALNDNLEk
SEQ ID NO: 244

channel,

transporter or cell

surface protein

239
HBEGF
NP_001936.1
Receptor,
K95
RkKKGKGLGKKR
SEQ ID NO: 245

channel,

transporter or cell

surface protein

240
KPNB3
NP_002262.3
Receptor,
K45
kQAEETYENIPGQSK
SEQ ID NO: 246

channel,

transporter or cell

surface protein

241
TOMM70A
NP_055635.3
Receptor,
K441
LRPESALAQAQkCFALYR
SEQ ID NO: 247

channel,

transporter or cell

surface protein

242
VDAC-1
NP_003365.1
Receptor,
K20
DVFTkGYGFGLIK
SEQ ID NO: 248

channel,

transporter or cell

surface protein

243
VDAC2
NP_003366.2
Receptor,
K31
DIFNkGFGFGLVK
SEQ ID NO: 249

channel,

transporter or cell

surface protein

244
VDAC-3
NP_005653.3
Receptor,
K63
YkVCNYGLTFTQK
SEQ ID NO: 250

channel,

transporter or cell

surface protein

245
ARPP-19
NP_006619.1
RNA binding
K42
ARYPHLGQkPGGSDFLR
SEQ ID NO: 251

protein

246
ARPP-19
NP_006619.1
RNA binding
K58
GQkYFDSGDYNMAK
SEQ ID NO: 252

protein

247
BAT1
NP_004631.1
RNA binding
K334
YQQFkDFQR
SEQ ID NO: 253

protein

248
CPSF1
NP_037423.2
RNA binding
K809
LVFLVkNFPVGQR
SEQ ID NO: 254

protein

249
DDX3
NP_001347.3
RNA binding
K130
WCDkSDEDDWSKPLPPSER
SEQ ID NO: 255

protein

250
DDX39
NP_005795.2
RNA binding
K333
YQQFkDFQR
SEQ ID NO: 256

protein

251
DDX5
NP_004387.1
RNA binding
K32
AGPLSGkK
SEQ ID NO: 257

protein

252
DDX5
NP_004387.1
RNA binding
K33
AGPLSGKkFGNPGEK
SEQ ID NO: 258

protein

253
DHX38
NP_054722.2
RNA binding
K489
KEEEPDkAVTEDGKVDYRTEQK
SEQ ID NO: 259

protein

254
ENSA
NP_004427.1
RNA binding
K63
GQkYFDSGDYNMAK
SEQ ID NO: 260

protein

255
hnRNP R
NP_005817.1
RNA binding
K103
SAFLCGVMkTYR
SEQ ID NO: 261

protein

256
hnRNP-
NP_004491.1
RNA binding
K39
SDVEAIFSkYGK
SEQ ID NO: 262

C1/C2

protein

257
hnRNP-
NP_004491.1
RNA binding
K50
IVGCSVHkGFAFVQYVNER
SEQ ID NO: 263

C1/C2

protein

258
hnRNP-L
NP_001524.2
RNA binding
K59
YYGGGSEGGRAPkR
SEQ ID NO: 264

protein

259
HNRPCL1
NP_001013653.1
RNA binding
K39
SDVEAIFSkYGK
SEQ ID NO: 265

protein

260
CFIM25
NP_008937.1
RNA binding
K23
GVTQFGNkYIQQTK
SEQ ID NO: 266

protein

261
NCL
NP_005372.2
RNA binding
K370
ALELTGLkVFGNEIK
SEQ ID NO: 267

protein

262
NCL
NP_005372.2
RNA binding
K449
TEADAEKTFEEk
SEQ ID NO: 268

protein

263
NCL
NP_005372.2
RNA binding
K467
SISLYYTGEk
SEQ ID NO: 269

protein

264
NCL
NP_005372.2
RNA binding
K109
TVTPAKAVTTPGkK
SEQ ID NO: 270

protein

265
NCL
NP_005372.2
RNA binding
K102
TVTPAkAVTTPGKK
SEQ ID NO: 271

protein

266
NSAP1
NP_006363.3
RNA binding
K100
SAFLCGVMkTYR
SEQ ID NO: 272

protein

267
PABP 1
NP_002559.2
RNA binding
K104
SGVGNIFIkNLDK
SEQ ID NO: 273

protein

268
PABPC5
NP_543022.1
RNA binding
K111
SGVGNIFIkNLDK
SEQ ID NO: 274

protein

269
PARN
NP_002573.1
RNA binding
K566
NNSFTAPSTVGkR
SEQ ID NO: 275

protein

270
PNPT1
NP_149100.1
RNA binding
K275
RTPQkLFTPSPEIVK
SEQ ID NO: 276

protein

271
RNU3IP2
NP_004695.1
RNA binding
K25
GKPASGAGAGAGAGkR
SEQ ID NO: 277

protein

272
Sam68
NP_006550.1
RNA binding
K165
VLIPVkQYPK
SEQ ID NO: 278

protein

273
snRNP A′
NP_003081.2
RNA binding
K179
SkTFNPGAGLPTDK
SEQ ID NO: 279

protein

274
snRNP B1
NP_003082.1
RNA binding
K32
IFIGTFkAFDK
SEQ ID NO: 280

protein

275
SNRPN
NP_003088.1
RNA binding
K32
IFIGTFkAFDK
SEQ ID NO: 281

protein

276
SRP9
NP_003124.1
RNA binding
K52
VTDDLVCLVYkTDQAQDVK
SEQ ID NO: 282

protein

277
AFP
NP_001125.1
Secreted protein
K161
ETFMNkFIYEIAR
SEQ ID NO: 284

278
CCL21
NP_002980.1
Secreted protein
K120
TGKKGKGSk
SEQ ID NO: 285

279
CCL21
NP_002980.1
Secreted protein
K117
TGKKGkGSK
SEQ ID NO: 286

280
CCL21
NP_002980.1
Secreted protein
K115
TGKkGKGSK
SEQ ID NO: 287

281
CCL21
NP_002980.1
Secreted protein
K114
TGkKGKGSK
SEQ ID NO: 288

282
G6PI
NP_000166.2
Secreted protein
K12
DPQFQkLQQWYR
SEQ ID NO: 289

283
G6PI
NP_000166.2
Secreted protein
K466
LLPHkVFEGNRPTNSIVFTK
SEQ ID NO: 290

284
LTF
NP_002334.2
Secreted protein
K565
CLAENAGDVAFVkDVTVLQNTDGNNNEAW
SEQ ID NO: 291

AK

285
SEMA3E
NP_036563.1
Secreted protein
K748
LKMSPSkWKYANPQEK
SEQ ID NO: 292

286
SEMA3E
NP_036563.1
Secreted protein
K750
LKMSPSKWkYANPQEK
SEQ ID NO: 293

287
SEMA3E
NP_036563.1
Secreted protein
K757
LKMSPSKWKYANPQEk
SEQ ID NO: 294

288
SFRP1
NP_003003.3
Secreted protein
K224
EVKKENGDKkIVPKKKKPLKLGPIK
SEQ ID NO: 295

289
SFRP1
NP_003003.3
Secreted protein
K223
EVKKENGDkKIVPKKKKPLKLGPIK
SEQ ID NO: 296

290
SFRP1
NP_003003.3
Secreted protein
K231
EVKKENGDKKIVPKKKkPLKLGPIK
SEQ ID NO: 297

291
SFRP1
NP_003003.3
Secreted protein
K239
EVKKENGDKKIVPKKKKPLKLGPIk
SEQ ID NO: 298

292
transterrin
NP_001054.1
Secreted protein
K546
CLVEkGDVAFVK
SEQ ID NO: 299

293
AATF
NP_036270.1
Transcriptional
K383
LGkGFGAFER
SEQ ID NO: 300

regulator

294
AP-4
NP_003214.1
Transcriptional
K85
LSkAAILQQTAEYIFSLEQEK
SEQ ID NO: 301

regulator

295
ATF-4
NP_001666.2
Transcriptional
K343
DLIEEVRkARGKKR
SEQ ID NO: 302

regulator

296
ATF-4
NP_001666.2
Transcriptional
K348
DLIEEVRKARGKkR
SEQ ID NO: 303

regulator

297
CBX8
NP_065700.1
Transcriptional
K240
KLDDTPSGAGkFPAGHSVIQLAR
SEQ ID NO: 304

regulator

298
GLI1
NP_005260.1
Transcriptional
K365
PYVCkLPGCTKRYTDPSSLR
SEQ ID NO: 305

regulator

299
GLI1
NP_005260.1
Transcriptional
K371
PYVCKLPGCTkRYTDPSSLR
SEQ ID NO: 306

regulator

300
GRF-1
NP_004482.3
Transcriptional
K193
TKkPIVVVLTK
SEQ ID NO: 307

regulator

301
HBXAP
NP_057662.3
Transcriptional
K1050
GkDISTITGHR
SEQ ID NO: 308

regulator

302
ING3
NP_061944.2
Transcriptional
K181
FKSEALLSTLTSDASkENTLGCR
SEQ ID NO: 309

regulator

303
ING3
NP_061944.2
Transcriptional
K264
NNDFQLGkEFSMAR
SEQ ID NO: 310

regulator

304
MAML1
NP_055572.1
Transcriptional
K138
NLDSATSPQNGDQQNGYGDLFPGHkK
SEQ ID NO: 311

regulator

305
MBD1
NP_002375.1
Transcriptional
K366
RPSSARRHHLGPTLk
SEQ ID NO: 312

regulator

306
MED12
NP_005111.2
Transcriptional
K1798
SQPATkTEDYGMGPGR
SEQ ID NO: 313

regulator

307
MLL2
NP_003473.1
Transcriptional
K2880
VEPAPAANSLGLGLkPGQSMMGSR
SEQ ID NO: 314

regulator

308
MTF1
NP_005946.1
Transcriptional
K227
LHTGkTFNCESEGCSK
SEQ ID NO: 315

regulator

309
NCOA2
NP_006531.1
Transcriptional
K780
TDPASNTkLIAMK
SEQ ID NO: 316

regulator

310
NF-GMB
NP_003642.2
Transcriptional
K96
VLGTVkWFNVR
SEQ ID NO: 317

regulator

311
NUFIP1
NP_036477.1
Transcriptional
K260
KKLkLEKEKR
SEQ ID NO: 318

regulator

312
PA2G4
NP_006182.1
Transcriptional
K298
MGVVECAkHELLQPFNVLYEKEGEFV
SEQ ID NO: 319

regulator

AQFK

313
Per1
NP_002607.1
Transcriptional
K1096
SSQSSHTSkYFGSIDSSEAEAGAAR
SEQ ID NO: 320

regulator

314
POLR2A
NP_000928.1
Transcriptional
K710
AkQDVIEVIEK
SEQ ID NO: 321

regulator

315
Sin3A
NP_056292.1
Transcriptional
K875
LLFSNTAAQkLR
SEQ ID NO: 322

regulator

316
SMARCA2
NP_003061.3
Transcriptional
K1547
DDkGRDKGKGKKR
SEQ ID NO: 323

regulator

317
SMARCA2
NP_003061.3
Transcriptional
K1551
DDKGRDkGKGKKR
SEQ ID NO: 324

regulator

318
SP100
NP_003104.2
Transcriptional
K306
EKPFSNSkVECQAQAR
SEQ ID NO: 325

regulator

319
SSB
NP_003133.1
Transcriptional
K360
VQFQGkK
SEQ ID NO: 326

regulator

320
SUPT6H
NP_003161.2
Transcriptional
K402
VWQWDEkWTQLR
SEQ ID NO: 327

regulator

321
TAF140
AAH62352.1
Transcriptional
K685
KKDREKGKkDK
SEQ ID NO: 328

regulator

322
TAF140
AAH62352.1
Transcriptional
K678
KkDREKGKKDK
SEQ ID NO: 329

regulator

323
TAF140
AAH62352.1
Transcriptional
K682
KKDREkGKKDK
SEQ ID NO: 330

regulator

324
TCF20
NP_005641.1
Transcriptional
K1267
SFISPIPSkR
SEQ ID NO: 331

regulator

325
TEF
NP_003207.1
Transcriptional
K40
GLSGSFPLVLkK
SEQ ID NO: 332

regulator

326
UBF
NP_055048.1
Transcriptional
K61
VAFkDFSGDMCK
SEQ ID NO: 333

regulator

327
YB-1
NP_004550.2
Transcriptional
K64
VLGTVkWFNVR
SEQ ID NO: 334

regulator

328
YY1
NP_003394.1
Transcriptional
K174
VKkGGGKKSGKK
SEQ ID NO: 335

regulator

329
ZNF318
NP_055160.1
Transcriptional
K1095
ESPTSSSFGkFSWK
SEQ ID NO: 336

(C-term)

regulator

330
BOLL
NP_149019.1
Translational
K102
kLNIGPAIRK
SEQ ID NO: 337

regulator

331
BOLL
NP_149019.1
Translational
K111
KLNIGPAIRk
SEQ ID NO: 338

regulator

332
eEF1A-1
NP_001393.1
Translational
K392
KLEDGPkFLK
SEQ ID NO: 339

regulator

333
eEF1A-1
NP_001393.1
Translational
K212
IGYNPDTVAFVPISGWNGDNMLEPSANMP
SEQ ID NO: 340

regulator

WFkGWK

One of skill in the art will appreciate that, in many instances the utility of the instant invention is best understood in conjunction with an appreciation of the many biological roles and significance of the various target signaling proteins/polypeptides of the invention. The foregoing is illustrated in the following paragraphs summarizing the knowledge in the art relevant to a few non-limiting representative peptides containing selected acetylation sites according to the invention.

GSTP1, phosphorylated at K191, is among the proteins listed in this patent. This protein has potential diagnostic and/or therapeutic implications based on the following findings. Polymorphism in the GSTP1 gene correlates with adenocarcinoma tumors associated with esophageal neoplasms (Cancer Res 59: 586-9 (1999)). Decreased expression of GSTP1 protein correlates with carcinoma tumors associated with prostatic neoplasms (PNAS 91: 11733-7 (1994)). Decreased expression of GSTP1 in bronchi correlates with bronchogenic carcinoma (Cancer Res 60: 1609-18. (2000)). Missense mutation in the GSTP1 gene correlates with bladder neoplasms (Carcinogenesis 18: 641-4 (1997)). Increased expression of GSTP1 protein correlates with increased occurrence of disease progression associated with B-cell lymphoma (Leukemia 17: 972-7 (2003)). Polymorphism in the GSTP1 gene correlates with Barrett esophagus associated with esophageal neoplasms (Cancer Res 59: 586-9 (1999)). Missense mutation in the GSTP1 gene correlates with increased occurrence of more severe form of skin neoplasms (Pharmacogenetics 10: 545-56 (2000)). Increased expression of GSTP1 protein correlates with non-small-cell lung carcinoma associated with lung neoplasms (Cancer 73: 1377-82. (1994)). Polymorphism in the GSTP1 gene correlates with increased occurrence of familial form of prostatic neoplasms (Anticancer Res 23: 2897-902 (2003)). Increased expression of GSTP1 protein correlates with decreased cell proliferation associated with non-small-cell lung carcinoma (Cancer 70: 764-9. (1992)). Increased expression of GSTP1 protein correlates with decreased response to drug associated with hepatocellular carcinoma (Mol Carcinog 29: 170-8 (2000)). Increased expression of GSTP1 mRNA correlates with decreased response to drug associated with ovarian neoplasms (Anticancer Res 14: 193-200 (1994)). Increased expression of GSTP1 protein correlates with drug-induced form of lung neoplasms (Br J Cancer 64: 700-4. (1991)). Increased expression of GSTP1 protein may correlate with decreased response to drug associated with non-small-cell lung carcinoma (Cancer 73: 1377-82. (1994)). Increased expression of GSTP1 protein may correlate with increased occurrence of drug-resistant form of bone neoplasms (Cancer 79: 2336-44. (1997)). Increased expression of GSTP1 protein may correlate with osteosarcoma tumors associated with bone neoplasms (Cancer 79: 2336-44. (1997)). Increased expression of GSTP1 protein correlates with decreased response to drug associated with ovarian neoplasms (Cancer 79: 521-7. (1997)). Polymorphism in the GSTP1 gene correlates with decreased occurrence of genetic predisposition to disease associated with prostatic neoplasms (Int J Cancer 95: 152-5 (2001)). Hypermethylation of the GSTP1 promoter correlates with non-small-cell lung carcinoma associated with lung neoplasms (Cancer Res 61: 249-55. (2001)). Polymorphism in the GSTP1 gene correlates with increased response to chemical stimulus associated with asthma (Pharmacogenetics 11: 437-45. (2001)). Decreased expression of GSTP1 in epithelium/epithelial cells correlates with bronchogenic carcinoma (Cancer Res 60: 1609-18. (2000)). Increased expression of GSTP1 mRNA correlates with recurrence associated with acute myelocytic leukemia (Leukemia 10: 426-33. (1996)). Polymorphism in the GSTP1 gene may cause abnormal response to oxidative stress associated with breast neoplasms (Cancer Lett 151: 87-95. (2000)). Amplification of the GSTP1 gene correlates with drug-resistant form of squamous cell carcinoma (Cancer Res 63: 8097-102 (2003)). Hypermethylation of the GSTP1 promoter correlates with carcinoma tumors associated with breast neoplasms (Cancer Res 58: 4515-8. (1998)). Increased expression of GSTP1 protein correlates with decreased occurrence of death associated with ovarian neoplasms (Br J Cancer 68: 235-9 (1993)). Hypermethylation of the GSTP1 promoter may correlate with precancerous conditions associated with non-small-cell lung carcinoma (Cancer Res 61: 249-55. (2001)). Hypermethylation of the GSTP1 promoter correlates with carcinoma tumors associated with prostatic neoplasms (Proc Natl Acad Sci USA 91: 11733-7 (1994)). Hypermethylation of the GSTP1 promoter correlates with increased aflatoxin B1 metabolic process associated with liver neoplasms (Cancer Lett 221: 135-43 (2005)). Polymorphism in the GSTP1 gene correlates with acute lymphocytic leukemia (L1) (Pharmacogenetics 12: 655-8 (2002)). Decreased expression of GSTP1 protein correlates with carcinoma tumors associated with prostatic neoplasms (Proc Natl Acad Sci USA 91: 11733-7 (1994)). Polymorphism in the GSTP1 gene correlates with increased occurrence of genetic predisposition to disease associated with prostatic neoplasms (Anticancer Res 23: 2897-902 (2003)). Increased expression of GSTP1 protein correlates with decreased severity of pathologic neovascularization associated with lung neoplasms (Carcinogenesis 16: 2129-33. (1995)). Decreased expression of GSTP1 protein may cause increased response to drug associated with hepatocellular carcinoma (J Biol Chem 277: 38954-64-(2002)). Polymorphism in the GSTP1 gene may cause increased occurrence of early onset form of prostatic neoplasms (Pharmacogenetics 11: 325-30 (2001)). Hypermethylation of the GSTP1 gene correlates with prostatic intraepithelial neoplasia associated with prostatic neoplasms (Int J Cancer 106: 382-7 (2003)). Polymorphism in the GSTP1 gene correlates with disease susceptibility associated with breast neoplasms (Int J Cancer 91: 334-9. (2001)). Missense mutation in the GSTP1 gene correlates with decreased occurrence of death associated with multiple myeloma (Blood 102: 2345-50 (2003)). Hypermethylation of the GSTP1 gene correlates with prostatic neoplasms (Cancer Lett 205: 181-8 (2004)). Lack of expression of GSTP1 protein correlates with drug-sensitive form of non-small-cell lung carcinoma (Cancer 78: 416-21. (1996)). Decreased glutathione transferase activity of GSTP1 may cause decreased response to toxin associated with lung neoplasms (Pharmacogenetics 11: 757-64. (2001)). Hypermethylation of the GSTP1 promoter correlates with early stage or low grade form of prostatic neoplasms (J Natl Cancer Inst 93: 1747-52 (2001)). Lack of expression of GSTP1 protein correlates with drug-sensitive form of lung neoplasms (Cancer 78: 416-21. (1996)). Polymorphism in the GSTP1 gene correlates with squamous cell carcinoma tumors associated with esophageal neoplasms (Int J Cancer 79: 517-20 (1998)). Increased expression of GSTP1 protein correlates with lung neoplasms (Carcinogenesis 16: 707-11. (1995)). Increased expression of GSTP1 protein correlates with decreased cell proliferation associated with lung neoplasms (Cancer 70: 764-9. (1992)). Hypermethylation of the GSTP1 promoter correlates with carcinoma tumors associated with prostatic neoplasms (Proc Natl Acad Sci USA 91: 11733-7 (1994)). Polymorphism in the GSTP1 gene may cause decreased response to toxin associated with lung neoplasms (Pharmacogenetics 11: 757-64. (2001)). Polymorphism in the GSTP1 gene correlates with disease susceptibility associated with small cell carcinoma (Carcinogenesis 23: 1475-81. (2002)). Hypermethylation of the GSTP1 promoter correlates with carcinoma tumors associated with prostatic neoplasms (PNAS 91: 11733-7 (1994)). Polymorphism in the GSTP1 gene correlates with decreased incidence of recurrence associated with acute lymphocytic leukemia (L1) (Blood 95: 1222-8. (2000)). Increased expression of GSTP1 protein may correlate with decreased response to drug associated with lung neoplasms (Cancer 73: 1377-82. (1994)). Hypermethylation of the GSTP1 promoter correlates with non-familial form of breast neoplasms (Hum Mol Genet. 10: 3001-3007. (2001)). Increased expression of GSTP1 mRNA correlates with esophageal neoplasms (Cancer 67: 2560-4 (1991)). Increased expression of GSTP1 protein correlates with increased occurrence of death associated with B-cell lymphoma (Leukemia 17: 972-7 (2003)). Hypermethylation of the GSTP1 promoter correlates with increased aflatoxin B1 metabolic process associated with hepatocellular carcinoma (Cancer Lett 221: 135-43 (2005)). Increased expression of GSTP1 mRNA may prevent increased occurrence of Barrett esophagus associated with esophageal neoplasms (Mol Carcinog 24: 128-36 (1999)). Polymorphism in the GSTP1 gene may cause increased response to UV associated with squamous cell carcinoma (Kidney Int 58: 2186-93 (2000)). Decreased glutathione transferase activity of GSTP1 correlates with decreased occurrence of death associated with breast neoplasms (Cancer Res 60: 5621-4. (2000)). Polymorphism in the GSTP1 gene correlates with Hodgkin's disease (Hum Mol Genet. 10: 1265-73. (2001)). Increased expression of GSTP1 protein may correlate with increased occurrence of local neoplasm recurrence associated with breast neoplasms (J Natl Cancer Inst 89: 639-45. (1997)). Increased expression of GSTP1 protein correlates with drug-resistant form of non-small-cell lung carcinoma (Br J Cancer 64: 700-4. (1991)). Polymorphism in the GSTP1 gene correlates with squamous cell carcinoma tumors associated with esophageal neoplasms (Int J Cancer 89: 458-64 (2000)). Increased expression of GSTP1 protein correlates with decreased response to drug associated with liver neoplasms (Mol Carcinog 29: 170-8 (2000)). Hypermethylation of the GSTP1 gene correlates with prostatic neoplasms (Cancer Res 64: 1975-86 (2004)). Single nucleotide polymorphism in the GSTP1 gene correlates with decreased occurrence of death associated with multiple myeloma (Blood 102: 2345-50 (2003)). Increased expression of GSTP1 mRNA may correlate with drug-resistant form of neuroblastoma (Int J Cancer 47: 732-7 (1991)). Hypermethylation of the GSTP1 promoter may correlate with precancerous conditions associated with lung neoplasms (Cancer Res 61: 249-55. (2001)). Hypermethylation of the GSTP1 promoter correlates with adenocarcinoma tumors associated with prostatic neoplasms (J Natl Cancer Inst 93: 1747-52 (2001)). Increased expression of GSTP1 protein correlates with decreased severity of pathologic neovascularization associated with non-small-cell lung carcinoma (Carcinogenesis 16: 2129-33. (1995)). Decreased expression of GSTP1 mRNA correlates with chronic lymphocytic leukemia (Leukemia 9: 1742-7 (1995)). Hypomethylation of the GSTP1 promoter may prevent prostatic neoplasms (Cancer Res 61: 8611-6. (2001)). Decreased glutathione transferase activity of GSTP1 may correlate with disease susceptibility associated with lung neoplasms (Cancer Lett 173: 155-62. (2001)). Hypermethylation of the GSTP1 promoter correlates with increased response to toxin associated with liver neoplasms (Cancer Lett 221: 135-43 (2005)). Polymorphism in the GSTP1 gene correlates with increased occurrence of central nervous system neoplasms associated with acute lymphocytic leukemia (Pharmacogenetics 10: 715-26 (2000)). Decreased expression of GSTP1 protein may cause increased response to drug associated with hepatocellular carcinoma (JBC 277: 38954-64 (2002)). Increased expression of GSTP1 protein correlates with drug-resistant form of lung neoplasms (Br J Cancer 64: 700-4. (1991)). Hypermethylation of the GSTP1 promoter correlates with carcinoma tumors associated with prostatic neoplasms (Cancer Res 60: 5941-5 (2000)). Polymorphism in the GSTP1 gene correlates with decreased occurrence of lymphatic metastasis associated with breast neoplasms (Pharmacogenetics 8: 441-7. (1998)). Increased expression of GSTP1 protein correlates with drug-induced form of non-small-cell lung carcinoma (Br J Cancer 64: 700-4. (1991)). Hypermethylation of the GSTP1 promoter correlates with bladder neoplasms (Cancer Res 61: 8659-63. (2001)). Decreased expression of GSTP1 protein correlates with carcinoma associated with cervix neoplasms (Anticancer Res 17: 4305-9 (1997)). Polymorphism in the GSTP1 gene correlates with increased occurrence of small cell carcinoma associated with lung neoplasms (Carcinogenesis 23: 1475-81. (2002)). Increased expression of GSTP1 protein correlates with non-small-cell lung carcinoma (Cancer 73: 1377-82. (1994)). Decreased glutathione transferase activity of GSTP1 may cause decreased response to toxin associated with squamous cell carcinoma (Pharmacogenetics 11: 757-64. (2001)). Polymorphism in the GSTP1 gene correlates with disease susceptibility associated with lung neoplasms (Carcinogenesis 23: 1475-81. (2002)). Decreased glutathione transferase activity of GSTP1 may cause Barrett esophagus associated with esophageal neoplasms (Cancer Res 59: 586-9 (1999)). Polymorphism in the GSTP1 gene correlates with non-Hodgkin's lymphoma (Hum Mol Genet. 10: 1265-73. (2001)). Hypermethylation of the GSTP1 promoter correlates with increased response to toxin associated with hepatocellular carcinoma (Cancer Lett 221: 135-43 (2005)). Polymorphism in the GSTP1 gene correlates with disease susceptibility associated with lung neoplasms (Cancer Res 62: 2819-23. (2002)). Decreased expression of GSTP1 protein correlates with carcinoma tumors associated with prostatic neoplasms (Proc Natl Acad Sci USA 91: 11733-7 (1994)). Decreased glutathione transferase activity of GSTP1 may cause adenocarcinoma tumors associated with esophageal neoplasms (Cancer Res 59: 586-9 (1999)). Hypermethylation of the GSTP1 promoter correlates with adenocarcinoma tumors associated with prostatic neoplasms (J Natl Cancer Inst 95: 1634-7 (2003)). Polymorphism in the GSTP1 gene correlates with squamous cell carcinoma tumors associated with skin neoplasms (Kidney Int 58: 2186-93 (2000)). Hypermethylation of the GSTP1 promoter correlates with hepatocellular carcinoma associated with liver neoplasms (Cancer Lett 221: 135-43 (2005)). Polymorphism in the GSTP1 gene may cause decreased response to toxin associated with squamous cell carcinoma (Pharmacogenetics 11: 757-64. (2001)). Hypermethylation of the GSTP1 promoter correlates with non-small-cell lung carcinoma associated with non-small-cell lung carcinoma (Cancer Res 61: 249-55. (2001)). Increased expression of GSTP1 protein correlates with decreased response to drug associated with ovarian neoplasms (Br J Cancer 68: 235-9 (1993)). Hypermethylation of the GSTP1 promoter may correlate with hormone-dependent neoplasms associated with breast neoplasms (Gene 210: 1-7 (1998)). Polymorphism in the GSTP1 gene correlates with decreased occurrence of death associated with breast neoplasms (Cancer Res 60: 5621-4. (2000)). Decreased glutathione transferase activity of GSTP1 may correlate with increased response to drug associated with breast neoplasms (Cancer Res 60: 5621-4. (2000)). (PhosphoSite®, Cell Signaling Technology (Danvers, Mass.), Human PSD™, Biobase Corporation, (Beverly, Mass.)).

TOP1, phosphorylated at K712, is among the proteins listed in this patent. This protein has potential diagnostic and/or therapeutic implications based on the following findings. Induced inhibition of the DNA topoisomerase type I activity of TOP1 may prevent carcinoma tumors associated with colonic neoplasms (Cancer Res 61: 2961-7. (2001)). Induced inhibition of the DNA topoisomerase type I activity of TOP1 may cause increased apoptosis associated with colonic neoplasms (Oncol Res 8: 317-23. (1996)). Induced inhibition of the DNA topoisomerase type I activity of TOP1 may cause increased apoptosis associated with lung neoplasms (Anticancer Res 22: 4029-37. (2002)). Decreased expression of TOP1 protein may correlate with decreased response to drug associated with breast neoplasms (Biochem Pharmacol 60: 831-7. (2000)). Induced inhibition of the DNA topoisomerase type I activity of TOP1 may correlate with increased apoptosis associated with prostatic neoplasms (Cancer Res 64: 9144-51 (2004)). Induced inhibition of the DNA topoisomerase type I activity of TOP1 may prevent disease progression associated with lung neoplasms (J Natl Cancer Inst 83: 1164-8. (1991)). Induced inhibition of the DNA topoisomerase type I activity of TOP1 may prevent increased severity of advanced stage or high grade form of non-small-cell lung carcinoma (J Natl Cancer Inst 83: 1164-8. (1991)). Induced inhibition of the DNA topoisomerase type I activity of TOP1 may prevent increased cell proliferation associated with colonic neoplasms (Cancer Res 61: 2961-7. (2001)). Induced stimulation of the DNA topoisomerase type I activity of TOP1 may cause increased cell death associated with non-small-cell lung carcinoma (J Biol Chem 276: 8029-36. (2001)). Mutation in the TOP1 gene may cause decreased response to drug associated with leukemia (Cancer Res 55: 1339-46 (1995)). Increased DNA topoisomerase type I activity of TOP1 correlates with increased response to drug associated with colonic neoplasms (Int J Cancer 70: 335-40. (1997)). Increased expression of TOP1 mRNA correlates with increased occurrence of recurrence associated with breast neoplasms (Cancer 98: 18-23. (2003)). Induced stimulation of the DNA topoisomerase type I activity of TOP1 may cause increased cell death associated with non-small-cell lung carcinoma (JBC 276: 8029-36. (2001)). Missense mutation in the TOP1 gene may cause decreased response to drug associated with leukemia (Nucleic Acids Res 19: 69-75 (1991)). Decreased expression of TOP1 mRNA may correlate with increased response to drug associated with breast neoplasms (Cancer Res 58: 1876-85 (1998)). Missense mutation in the TOP1 gene correlates with drug-resistant form of leukemia (Nucleic Acids Res 19: 69-75 (1991)). Translocation of the TOP1 gene correlates with acute lymphocytic leukemia (Blood 94: 3258-61. (1999)). Induced inhibition of the DNA topoisomerase type I activity of TOP1 may prevent disease progression associated with non-small-cell lung carcinoma (J Natl Cancer Inst 83: 1164-8. (1991)). Increased presence of TOP1 autoimmune antibody correlates with systemic scleroderma (J Immunol 164: 6138-46. (2000)). (PhosphoSite®, Cell Signaling Technology (Danvers, Mass.), Human PSD™, Biobase Corporation, (Beverly, Mass.)).

ENO1, phosphorylated at K406, is among the proteins listed in this patent. This protein has potential diagnostic and/or therapeutic implications based on the following findings. Increased expression of ENO1 protein correlates with glioblastoma associated with brain neoplasms (J Neurochem 66: 2484-90. (1996)). Increased expression of ENO1 protein may prevent increased activation of MAPK activity associated with prostatic neoplasms (J Biol Chem 280: 14325-30 (2005)). Increased expression of ENO1 protein correlates with meningioma associated with brain neoplasms (J Neurochem 66: 2484-90. (1996)). Increased expression of ENO1 protein may prevent increased positive regulation of protein biosynthetic process associated with prostatic neoplasms (JBC 280: 14325-30 (2005)). Decreased phosphopyruvate hydratase activity of ENO1 correlates with meningioma associated with brain neoplasms (J Neurochem 66: 2484-90. (1996)). Increased expression of ENO1 protein may cause decreased viral genome replication associated with HIV infections (J Cell Biochem 64: 565-72.(1997)). Increased expression of ENO1 protein may prevent increased activation of MAPK activity associated with prostatic neoplasms (JBC 280: 14325-30 (2005)). Decreased phosphopyruvate hydratase activity of ENO1 correlates with astrocytoma (J Neurochem 66: 2484-90. (1996)). Increased expression of ENO1 protein may prevent increased positive regulation of protein biosynthetic process associated with prostatic neoplasms (J Biol Chem 280: 14325-30 (2005)). Decreased phosphopyruvate hydratase activity of ENO1 correlates with glioblastoma (J Neurochem 66: 2484-90. (1996)). Increased presence of ENO1 autoimmune antibody correlates with Behcet Syndrome (Cancer 101: 2106-15 (2004)). Increased expression of ENO1 protein may prevent invasive form of breast neoplasms (Cancer Res 55: 3747-51. (1995)). Autoimmune antibody to ENO1 correlates with connective tissue diseases (Eur J Immunol 30: 3575-3584. (2000)). Increased expression of ENO1 protein correlates with astrocytoma (J Neurochem 66: 2484-90. (1996)). Increased presence of ENO1 autoimmune antibody correlates with drug-sensitive form of autoimmune thyroiditis (FEBS Lett 528: 197-202. (2002)). Increased expression of ENO1 in cerebrospinal fluid correlates with early onset form of lymphocytic leukemia (Leukemia 1: 820-1 (1987)). Increased expression of ENO1 protein may prevent increased activation of NF-kappaB transcription factor associated with prostatic neoplasms (J Biol Chem 280: 14325-30 (2005)). Increased presence of ENO1 autoimmune antibody correlates with systemic lupus erythematosus (Biochem Biophys Res Commun 298: 169-77. (2002)). Increased expression of ENO1 protein may prevent increased activation of NF-kappaB transcription factor associated with prostatic neoplasms (JBC 280: 14325-30 (2005)). Increased expression of ENO1 mRNA may correlate with mouth neoplasms (Oncogene 18: 827-31 (1999)). Increased expression of ENO1 protein correlates with glioblastoma (J Neurochem 66: 2484-90. (1996)). Decreased phosphopyruvate hydratase activity of ENO1 correlates with astrocytoma associated with brain neoplasms (J Neurochem 66: 2484-90. (1996)). Increased expression of ENO1 protein correlates with adenocarcinoma associated with pancreatic neoplasms (Cancer Res 64: 9018-26 (2004)). Increased expression of ENO1 protein correlates with meningioma (J Neurochem 66: 2484-90. (1996)). Decreased phosphopyruvate hydratase activity of ENO1 correlates with glioblastoma associated with brain neoplasms (J Neurochem 66: 2484-90. (1996)). Decreased phosphopyruvate hydratase activity of ENO1 correlates with meningioma (J Neurochem 66: 2484-90. (1996)). Increased expression of ENO1 protein correlates with astrocytoma associated with brain neoplasms (J Neurochem 66: 2484-90. (1996)). Increased presence of ENO1 autoimmune antibody correlates with chronic brain damage associated with autoimmune thyroiditis (FEBS Lett 528: 197-202. (2002)). Increased expression of ENO1 protein may prevent increased cell proliferation associated with prostatic neoplasms (J Biol Chem 280: 14325-30 (2005)). Increased expression of ENO1 protein may prevent increased cell proliferation associated with prostatic neoplasms (JBC 280: 14325-30 (2005)). Autoimmune antibody to ENO1 may correlate with discoid lupus erythematosus (Immunology 92: 362-8. (1997)). Autoimmune antibody to ENO1 correlates with inflammation associated with pituitary diseases (J Clin Endocrinol Metab 87: 752-7 (2002)). (PhosphoSite®, Cell Signaling Technology (Danvers, Mass.), Human PSD™, Biobase Corporation, (Beverly, Mass.)).

PKM2, phosphorylated at K498, is among the proteins listed in this patent. This protein has potential diagnostic and/or therapeutic implications based on the following findings. PKM2, one of the isoforms of pyruvate kinase, a rate-limiting enzyme in glycolysis, is one of the key enzymes that controls metabolic activity in the cell. It controls the conversion of glucose into pyruvate and ATP. Pyruvate is a building block for biosynthetic pathways in the cell, while ATP is the principal source of energy for all metabolic activities of the cell. PKM2 is a key regulator of the supply of available energy for the cell.

PKM2 interacts with thyroid hormone, and thus may mediate cellular metabolic effects induced by thyroid hormones. Binds Opa protein, a bacterial outer membrane protein involved in gonococcal adherence to and invasion of human cells, suggesting a role of this protein in bacterial pathogensis.

In several tumor types, cells have been found to be unresponsive to apoptosis stimuli. In many instances, this phenomenon may be attributed to the cells ability to adapt to hypoxia by modulating the glycolytic rate. Recent studies have shown that pyruvate kinase (PK), a rate-limiting enzyme in glycolysis, is converted to a less active dimer form of PKM2 isoenzyme during oncogenesis (see e.g., Cancer Res. 2007 Feb. 15; 67(4):1602-8).

As discussed, PKM2 is thus known to be over-expressed and/or deregulated in many cancer types also correlating with increased glutamine catabolic process associated with neoplasms (Anticancer Res 23: 1149-54 (2003)). The increased expression of plasma PKM2 protein show a relationship with abnormal metabolic process associated with gastrointestinal neoplasms (Anticancer Res 20: 5151-4 (2000); (Anticancer Res 20: 4965-8 (2000); Anticancer Res 23: 851-3. (2003); Anticancer Res 17: 3153-6. (1997); Anticancer Res 23: 855-7 (2003)). Similarly, the increased expression of PKM2 in plasma correlates with lung neoplasia: small cell carcinoma (Anticancer Res 23: 899-906); squamous cell carcinoma tumors associated with lung neoplasms (Anticancer Res 23: 899-906 (2003); advanced stage or high grade form of lung neoplasms (Cancer Lett 193: 91-8 (2003)); non-small-cell lung carcinoma (Cancer Lett 193: 91-8 (2003); advanced stage or high grade form of lung neoplasms (Anticancer Res 22: 311-8 (2002). Increased expression of PKM2 protein correlates with lung neoplasms (Anticancer Res 22: 311-8. (2002)). Increased expressed of PKM2 has also been reported in breast neoplasia. Increased expression of PKM2 in plasma correlates with advanced stage or high grade form of breast neoplasms (Anticancer Res 23: 991-7. (2003); with malignant form of breast neoplasms (Cancer Lett 187: 223-8 (2002); with advanced stage or high grade form of breast neoplasms (Anticancer Res 20: 5077-82 (2000). The increased phosphorylation of PKM2 has also been correlated with advanced stage or high grade form of breast neoplasms (Anticancer Res 23: 991-7 (2003)). The increased expression of PKM2 in serum correlates with malignant form of renal cell carcinoma and with recurrence associated with renal cell carcinoma (Anticancer Res 19: 2583-90 (1999)). Viral exploitation of the pyruvate kinase activity of PKM2 may cause increased transformation of host cell by virus associated with papillomavirus infections (Proc Natl Acad Sci USA 96: 1291-6 (1999)).

Post-translational modifications such as the acetylation of PKM2 according to the invention therefore regulate the activity of PKM2 in normal cells, cancer cells, diabetic cells, hypoxic cells, ischemic tissue, and in many metabolic disorders that involve metabolic pathways. According to an embodiment, the invention provides molecular probes capable of discerning the acetylation state of certain sites of PKM2 useful to elucidate the cell biology of PKM2, the role of acetylation (e.g., K498) of PKM2 in the molecular mechanisms involved in oncogenesis. One of skill in the art will appreciate that such a probe constitutes a diagnostic or prognostic marker for tumor and/or other disease states, and for monitoring patients' responses to various modalities of therapy.

ACADVL, phosphorylated at K276, is among the proteins listed in this patent. This protein has potential diagnostic and/or therapeutic implications based on the following findings. Decreased expression of ACADVL in fibroblasts correlates with abnormal fatty acid beta-oxidation associated with inborn errors lipid metabolism (J Clin Invest 95: 2465-73 (1995)). Nonsense mutation in the ACADVL gene correlates with hypoglycemia associated with inborn errors lipid metabolism (Biochem Biophys Res Commun 264: 483-7. (1999)). Mutation in the ACADVL gene may cause cardiac sudden death associated with inborn errors lipid metabolism (PNAS 92: 10496-500 (1995)). Missense mutation in the ACADVL gene may cause decreased fatty acid beta-oxidation associated with myocardial diseases (Proc Natl Acad Sci USA 92: 10496-500 (1995)). Missense mutation in the ACADVL gene may cause decreased fatty acid beta-oxidation associated with myocardial diseases (PNAS 92: 10496-500 (1995)). Missense mutation in the ACADVL gene may cause myocardial diseases associated with inborn errors lipid metabolism (PNAS 92: 10496-500 (1995)). Mutation in the ACADVL gene may cause cardiac sudden death associated with inborn errors lipid metabolism (Proc Natl Acad Sci USA 92: 10496-500 (1995)). Splice site mutation in the ACADVL gene may cause myocardial diseases associated with inborn errors lipid metabolism (Proc Natl Acad Sci USA 92: 10496-500 (1995)). Missense mutation in the ACADVL gene may cause myocardial diseases associated with inborn errors lipid metabolism (Proc Natl Acad Sci USA 92: 10496-500 (1995)). MRNA instability of ACADVL may correlate with hypoglycemia associated with inborn errors lipid metabolism (Biochem Biophys Res Commun 264: 483-7. (1999)). Missense mutation in the ACADVL gene may cause decreased fatty acid beta-oxidation associated with myocardial diseases (Proc Natl Acad Sci USA 92: 10496-500 (1995)). Missense mutation in the ACADVL gene correlates with hypoglycemia associated with inborn errors lipid metabolism (Biochem Biophys Res Commun 264: 483-7. (1999)). Splice site mutation in the ACADVL gene may cause decreased fatty acid beta-oxidation associated with myocardial diseases (Proc Natl Acad Sci USA 92: 10496-500 (1995)). Decreased expression of ACADVL in fibroblasts correlates with myocardial diseases associated with inborn errors lipid metabolism (J Clin Invest 95: 2465-73 (1995)). Splice site mutation in the ACADVL gene may cause myocardial diseases associated with inborn errors lipid metabolism (Proc Natl Acad Sci USA 92: 10496-500 (1995)). Mutation in the ACADVL gene may cause decreased fatty acid beta-oxidation associated with cardiac sudden death (Proc Natl Acad Sci USA 92: 10496-500 (1995)). Mutation in the ACADVL gene may cause decreased fatty acid beta-oxidation associated with cardiac sudden death (PNAS 92: 10496-500 (1995)). Decreased expression of ACADVL in fibroblasts correlates with hypertrophic cardiomyopathy associated with inborn errors lipid metabolism (J Clin Invest 95: 2465-73 (1995)). Abnormal mRNA splicing of ACADVL causes decreased fatty acid beta-oxidation associated with inborn errors lipid metabolism (Am J Hum Genet. 57: 273-83 (1995)). Splice site mutation in the ACADVL gene may cause myocardial diseases associated with inborn errors lipid metabolism (PNAS 92: 10496-500 (1995)). Splice site mutation in the ACADVL gene may cause decreased fatty acid beta-oxidation associated with myocardial diseases (Proc Natl Acad Sci USA 92: 10496-500 (1995)). Mutation in the ACADVL gene may cause cardiac sudden death associated with inborn errors lipid metabolism (Proc Natl Acad Sci USA 92: 10496-500 (1995)). Mutation in the ACADVL gene may cause decreased fatty acid beta-oxidation associated with cardiac sudden death (Proc Natl Acad Sci USA 92: 10496-500 (1995)). Splice site mutation in the ACADVL gene may cause decreased fatty acid beta-oxidation associated with myocardial diseases (PNAS 92: 10496-500 (1995)). Missense mutation in the ACADVL gene may cause myocardial diseases associated with inborn errors lipid metabolism (Proc Natl Acad Sci USA 92: 10496-500 (1995)). (PhosphoSite®g, Cell Signaling Technology (Danvers, Mass.), Human PSD™, Biobase Corporation, (Beverly, Mass.)).

ACADVL, phosphorylated at K71, is among the proteins listed in this patent. This protein has potential diagnostic and/or therapeutic implications based on the following findings. Decreased expression of ACADVL in fibroblasts correlates with abnormal fatty acid beta-oxidation associated with inborn errors lipid metabolism (J Clin Invest 95: 2465-73 (1995)). Nonsense mutation in the ACADVL gene correlates with hypoglycemia associated with inborn errors lipid metabolism (Biochem Biophys Res Commun 264: 483-7. (1999)). Mutation in the ACADVL gene may cause cardiac sudden death associated with inborn errors lipid metabolism (PNAS 92: 10496-500 (1995)). Missense mutation in the ACADVL gene may cause decreased fatty acid beta-oxidation associated with myocardial diseases (Proc Natl Acad Sci USA 92: 10496-500 (1995)). Missense mutation in the ACADVL gene may cause decreased fatty acid beta-oxidation associated with myocardial diseases (PNAS 92: 10496-500 (1995)). Missense mutation in the ACADVL gene may cause myocardial diseases associated with inborn errors lipid metabolism (PNAS 92: 10496-500 (1995)). Mutation in the ACADVL gene may cause cardiac sudden death associated with inborn errors lipid metabolism (Proc Natl Acad Sci USA 92: 10496-500 (1995)). Splice site mutation in the ACADVL gene may cause myocardial diseases associated with inborn errors lipid metabolism (Proc Natl Acad Sci USA 92: 10496-500 (1995)). Missense mutation in the ACADVL gene may cause myocardial diseases associated with inborn errors lipid metabolism (Proc Natl Acad Sci USA 92: 10496-500 (1995)). MRNA instability of ACADVL may correlate with hypoglycemia associated with inborn errors lipid metabolism (Biochem Biophys Res Commun 264: 483-7. (1999)). Missense mutation in the ACADVL gene may cause decreased fatty acid beta-oxidation associated with myocardial diseases (Proc Natl Acad Sci USA 92: 10496-500 (1995)). Missense mutation in the ACADVL gene correlates with hypoglycemia associated with inborn errors lipid metabolism (Biochem Biophys Res Commun 264: 483-7. (1999)). Splice site mutation in the ACADVL gene may cause decreased fatty acid beta-oxidation associated with myocardial diseases (Proc Natl Acad Sci USA 92: 10496-500 (1995)). Decreased expression of ACADVL in fibroblasts correlates with myocardial diseases associated with inborn errors lipid metabolism (J Clin Invest 95: 2465-73 (1995)). Splice site mutation in the ACADVL gene may cause myocardial diseases associated with inborn errors lipid metabolism (Proc Natl Acad Sci USA 92: 10496-500 (1995)). Mutation in the ACADVL gene may cause decreased fatty acid beta-oxidation associated with cardiac sudden death (Proc Natl Acad Sci USA 92: 10496-500 (1995)). Mutation in the ACADVL gene may cause decreased fatty acid beta-oxidation associated with cardiac sudden death (PNAS 92: 10496-500 (1995)). Decreased expression of ACADVL in fibroblasts correlates with hypertrophic cardiomyopathy associated with inborn errors lipid metabolism (J Clin Invest 95: 2465-73 (1995)). Abnormal mRNA splicing of ACADVL causes decreased fatty acid beta-oxidation associated with inborn errors lipid metabolism (Am J Hum Genet. 57: 273-83 (1995)). Splice site mutation in the ACADVL gene may cause myocardial diseases associated with inborn errors lipid metabolism (PNAS 92: 10496-500 (1995)). Splice site mutation in the ACADVL gene may cause decreased fatty acid beta-oxidation associated with myocardial diseases (Proc Natl Acad Sci USA 92: 10496-500 (1995)). Mutation in the ACADVL gene may cause cardiac sudden death associated with inborn errors lipid metabolism (Proc Natl Acad Sci USA 92: 10496-500 (1995)). Mutation in the ACADVL gene may cause decreased fatty acid beta-oxidation associated with cardiac sudden death (Proc Natl Acad Sci USA 92: 10496-500 (1995)). Splice site mutation in the ACADVL gene may cause decreased fatty acid beta-oxidation associated with myocardial diseases (PNAS 92: 10496-500 (1995)). Missense mutation in the ACADVL gene may cause myocardial diseases associated with inborn errors lipid metabolism (Proc Natl Acad Sci USA 92: 10496-5

ACAT1, phosphorylated at K124, is among the proteins listed in this patent. This protein has potential diagnostic and/or therapeutic implications based on the following findings. Polymorphism in the ACAT1 gene correlates with decreased fatty acid metabolic process associated with inborn errors of amino acid metabolism (Hum Genet. 90: 208-10. (1992)). (PhosphoSite®, Cell Signaling Technology (Danvers, Mass.), Human PSD™, Biobase Corporation, (Beverly, Mass.)).

aldolase A, phosphorylated at K294, is among the proteins listed in this patent. This protein has potential diagnostic and/or therapeutic implications based on the following findings. Increased expression of ALDOA protein correlates with lung neoplasms (Cancer 67: 2153-8. (1991)). Increased expression of ALDOA mRNA may correlate with increased response to hypoxia associated with anoxia (JBC 269: 23757-63. (1994)). Loss of function mutation in the ALDOA gene causes hemolytic anemia (Proc Natl Acad Sci USA 84: 8623-7 (1987)). Nonsense mutation in the ALDOA gene correlates with rhabdomyolysis associated with congenital hemolytic anemia (Blood 103: 2401-3 (2004)). Decreased stability of ALDOA causes familial form of hemolytic anemia (Proc Natl Acad Sci USA 84: 8623-7 (1987)). Decreased stability of ALDOA causes familial form of hemolytic anemia (PNAS 84: 8623-7 (1987)). Decreased stability of ALDOA causes familial form of hemolytic anemia (Proc Natl Acad Sci USA 84: 8623-7 (1987)). Missense mutation in the ALDOA gene correlates with rhabdomyolysis associated with congenital hemolytic anemia (Blood 103: 2401-3 (2004)). Increased expression of ALDOA mRNA may correlate with increased response to hypoxia associated with anoxia (J Biol Chem 269: 23757-63. (1994)). Loss of function mutation in the ALDOA gene causes hemolytic anemia (PNAS 84: 8623-7 (1987)). Loss of function mutation in the ALDOA gene causes hemolytic anemia (Proc Natl Acad Sci USA 84: 8623-7 (1987)). Autoimmune antibody to ALDOA correlates with lung neoplasms (Cancer Res 58: 1034-41 (1998)). Increased expression of ALDOA mRNA may correlate with increased response to hypoxia associated with anoxia (J Biol Chem 271: 32529-37 (1996)). Decreased fructose-bisphosphate aldolase activity of ALDOA correlates with congenital hemolytic anemia (Biochem J 380: 51-6 (2004)). Increased expression of ALDOA protein may correlate with increased anaerobic glycolysis associated with pancreatic neoplasms (Cancer Res 61: 6548-54. (2001)). Increased expression of ALDOA mRNA may correlate with increased response to hypoxia associated with anoxia (JBC 271: 32529-37 (1996)). (PhosphoSite®, Cell Signaling Technology (Danvers, Mass.), Human PSD™, Biobase Corporation, (Beverly, Mass.)).

BAT1, phosphorylated at K334, is among the proteins listed in this patent. This protein has potential diagnostic and/or therapeutic implications based on the following findings. BAT1 map position correlates with cystinuria (Kidney Int 59: 1821-33. (2001)). BAT1 map position correlates with disease susceptibility associated with rheumatoid arthritis (Genomics 71: 263-70. (2001)). (PhosphoSite®, Cell Signaling Technology (Danvers, Mass.), Human PSD™, Biobase Corporation, (Beverly, Mass.)).

CCL21, phosphorylated at K117, is among the proteins listed in this patent. This protein has potential diagnostic and/or therapeutic implications based on the following findings. Increased expression of CCL21 in endothelium/endothelial cells may cause increased cellular extravasation associated with ulcerative colitis (J Immunol 170: 4638-48. (2003)). Increased expression of CCL21 in endothelium/endothelial cells may cause increased cellular extravasation associated with autoimmune diseases (J Immunol 170: 4638-48. (2003)). Increased expression of CCL21 protein may prevent herpes simplex (J Virol 77: 12742-52. (2003)). Increased expression of CCL21 in endothelium/endothelial cells correlates with lichen planus associated with autoimmune diseases (Blood 101: 801-6. (2003)). Increased expression of CCL21 in endothelium/endothelial cells may cause increased cellular extravasation associated with rheumatoid arthritis (J Immunol 170: 4638-48. (2003)). Increased expression of CCL21 in endothelium/endothelial cells correlates with atopic dermatitis (Blood 101: 801-6. (2003)). Increased expression of CCL21 in lymph node may cause malignant form of breast neoplasms (Nature 410: 50-6. (2001)). Increased expression of CCL21 in endothelium/endothelial cells may cause increased lymphocyte chemotaxis associated with ulcerative colitis (J Immunol 170: 4638-48. (2003)). Increased expression of CCL21 protein correlates with lymphatic diseases associated with chronic lymphocytic leukemia (Blood 99: 2977-84. (2002)). Increased expression of CCL21 in endothelium/endothelial cells may cause abnormal T-lymphocytes migration associated with autoimmune diseases (J Immunol 170: 4638-48. (2003)). Increased expression of CCL21 in endothelium/endothelial cells correlates with graft-vs-host disease associated with autoimmune diseases (Blood 101: 801-6. (2003)). Increased expression of CCL21 in endothelium/endothelial cells correlates with lichen planus (Blood 101: 801-6. (2003)). Increased expression of CCL21 in endothelium/endothelial cells may cause abnormal T-lymphocytes migration associated with rheumatoid arthritis (J Immunol 170: 4638-48. (2003)). Increased expression of CCL21 protein correlates with increased leukocyte chemotaxis associated with rheumatoid arthritis (J Immunol 168: 5333-41. (2002)). Increased expression of CCL21 in endothelium/endothelial cells correlates with atopic dermatitis associated with autoimmune diseases (Blood 101: 801-6. (2003)). Increased expression of CCL21 in endothelium/endothelial cells correlates with graft-vs-host disease (Blood 101: 801-6. (2003)). Increased expression of CCL21 protein may cause increased chemotaxis associated with chronic lymphocytic leukemia (Blood 99: 2977-84. (2002)). Increased expression of CCL21 protein correlates with autoimmune thyroiditis (J Immunol 170: 6320-8. (2003)). Increased expression of CCL21 in lymph node may cause increased chemotaxis associated with breast neoplasms (Nature 410: 50-6. (2001)). Increased expression of CCL21 in endothelium/endothelial cells may cause increased lymphocyte chemotaxis associated with autoimmune diseases (J Immunol 170: 4638-48. (2003)). Increased expression of CCL21 in endothelium/endothelial cells may cause increased lymphocyte chemotaxis associated with rheumatoid arthritis (J Immunol 170: 4638-48. (2003)). Increased expression of CCL21 in endothelium/endothelial cells may cause abnormal T-lymphocytes migration associated with ulcerative colitis (J Immunol 170: 4638-48. (2003)). (PhosphoSite®, Cell Signaling Technology (Danvers, Mass.), Human PSD™, Biobase Corporation, (Beverly, Mass.)).

Cdc2, phosphorylated at K34, is among the proteins listed in this patent. This protein has potential diagnostic and/or therapeutic implications based on the following findings. Decreased phosphorylation of CDC2 correlates with increased response to drug associated with ovarian neoplasms (Int J Cancer 92: 738-47 (2001)). Increased expression of CDC2 protein correlates with carcinoma associated with colorectal neoplasms (Cancer 85: 546-53. (1999)). Induced inhibition of the cyclin-dependent protein kinase activity of CDC2 may prevent increased cell proliferation associated with melanoma (J Biol Chem 276: 6797-806. (2001)). Decreased expression of CDC2 mRNA correlates with increased response to drug associated with skin neoplasms (Cancer Res 59: 399-404 (1999)). Induced stimulation of the cyclin-dependent protein kinase activity of CDC2 may cause increased apoptosis associated with breast neoplasms (Cell Growth Differ 9: 23-9. (1998)). Induced inhibition of the cyclin-dependent protein kinase activity of CDC2 may cause increased cell cycle arrest associated with lung neoplasms (Int J Cancer 55: 616-22. (1993)). Induced inhibition of the cyclin-dependent protein kinase activity of CDC2 may cause increased cell cycle arrest associated with small cell carcinoma (Anticancer Res 16: 3387-95. (1996)). Induced inhibition of the cyclin-dependent protein kinase activity of CDC2 may cause increased cell cycle arrest associated with breast neoplasms (J Cell Biochem 79: 594-600. (2000)). Increased tyrosine phosphorylation of CDC2 may cause increased cell cycle arrest associated with lung neoplasms (Int J Cancer 55: 616-22. (1993)). Increased expression of CDC2 protein correlates with colonic neoplasms (Anticancer Res 19: 741-8. (1999)). Deletion mutation in the CDC2 gene correlates with breast neoplasms (Cancer Res 58: 1095-8 (1998)). Increased tyrosine phosphorylation of CDC2 may prevent increased cell proliferation associated with myeloid leukemia (Biochemistry Usa 34: 1058-63. (1995)). Induced stimulation of the cyclin-dependent protein kinase activity of CDC2 may correlate with increased response to drug associated with leukemia (Cancer Res 63: 1822-33. (2003)). Induced stimulation of the cyclin-dependent protein kinase activity of CDC2 may cause increased cell cycle arrest associated with colonic neoplasms (Anticancer Res 21: 873-8. (2001)). Increased expression of CDC2 protein correlates with carcinoma tumors associated with colonic neoplasms (Int J Cancer 53: 36-41. (1993)). Increased expression of CDC2 mRNA correlates with breast neoplasms (PNAS 90: 1112-6 (1993)). Decreased phosphorylation of CDC2 may cause increased cell cycle arrest associated with breast neoplasms (Biochem Pharmacol 46: 1831-40. (1993)). Increased expression of CDC2 protein correlates with increased incidence of lymphatic metastasis associated with breast neoplasms (Anticancer Res 19: 163-9. (1999)). Increased expression of CDC2 mRNA correlates with second primary neoplasms associated with myeloid leukemia (Proc Natl Acad Sci USA 99: 14925-30. (2002)). Induced stimulation of the cyclin-dependent protein kinase activity of CDC2 may correlate with increased apoptosis associated with colonic neoplasms (Exp Cell Res 234: 388-97. (1997)). Increased expression of CDC2 protein correlates with colorectal neoplasms (Br J Cancer 71: 1231-6. (1995)). Increased tyrosine phosphorylation of CDC2 may cause increased cell cycle arrest associated with breast neoplasms (J Cell Biochem 79: 594-600. (2000)). Increased tyrosine phosphorylation of CDC2 may correlate with increased response to drug associated with multiple myeloma (Cancer Res 60: 3065-71 (2000)). Induced inhibition of the protein kinase activity of CDC2 may correlate with increased response to drug associated with squamous cell carcinoma (Cancer Res 62: 1401-9 (2002)). Increased expression of CDC2 mRNA correlates with second primary neoplasms associated with myeloid leukemia (PNAS 99: 14925-30. (2002)). Decreased expression of CDC2 protein may correlate with drug-sensitive form of prostatic neoplasms (Cancer Res 63: 52-9 (2003)). Increased expression of CDC2 mRNA correlates with second primary neoplasms associated with myeloid leukemia (Proc Natl Acad Sci USA 99: 14925-30. (2002)). Induced inhibition of the cyclin-dependent protein kinase activity of CDC2 may cause increased cell cycle arrest associated with non-small-cell lung carcinoma (Anticancer Res 16: 3387-95. (1996)). Increased expression of CDC2 protein correlates with increased cell cycle arrest associated with breast neoplasms (Anticancer Res 19: 163-9. (1999)). Decreased expression of CDC2 protein may cause increased cell cycle arrest associated with colonic neoplasms (Mol Carcinog 28: 102-10. (2000)). Induced stimulation of CDC2 protein may correlate with increased response to drug associated with multiple myeloma (Blood 100: 3333-43 (2002)). Induced inhibition of the cyclin-dependent protein kinase activity of CDC2 may prevent increased cell proliferation associated with leukemia (Leukemia 16: 299-305 (2002)). Increased phosphorylation of CDC2 may correlate with increased response to drug associated with pancreatic neoplasms (Oncogene 23: 71-81 (2004)). Increased expression of CDC2 mRNA correlates with breast neoplasms (Proc Natl Acad Sci USA 90: 1112-6 (1993)). Abnormal expression of CDC2 mRNA may correlate with increased cell cycle arrest associated with non-small-cell lung carcinoma (Anticancer Res 20: 693-702. (2000)). Induced inhibition of the protein kinase activity of CDC2 may correlate with increased apoptosis associated with glioma (Oncogene 23: 446-56 (2004)). Decreased expression of CDC2 mRNA may correlate with drug-sensitive form of prostatic neoplasms (Cancer Res 63: 52-9 (2003)). Increased expression of CDC2 protein correlates with increased apoptosis associated with breast neoplasms (Anticancer Res 19: 163-9. (1999)). Increased phosphorylation of CDC2 may correlate with acute promyelocytic leukemia (J Cell Physiol 196: 276-83. (2003)). Induced inhibition of the cyclin-dependent protein kinase activity of CDC2 may cause increased cell cycle arrest associated with colonic neoplasms (Mol Carcinog 28: 102-10. (2000)). Increased tyrosine phosphorylation of CDC2 may prevent increased cell proliferation associated with myeloid leukemia (Biochemistry 34: 1058-63. (1995)). Induced inhibition of the cyclin-dependent protein kinase activity of CDC2 may prevent increased cell proliferation associated with melanoma (JBC 276: 6797-806. (2001)). Increased expression of CDC2 protein correlates with non-Hodgkin's lymphoma (Leukemia 9: 1382-8 (1995)). Decreased expression of CDC2 protein may correlate with increased response to organic substance associated with pancreatic neoplasms (Carcinogenesis 25: 1701-9 (2004)). Decreased expression of CDC2 protein may cause increased cell cycle arrest associated with breast neoplasms (Anticancer Res 21: 413-20. (2001)). Induced inhibition of the cyclin-dependent protein kinase activity of CDC2 may prevent increased cell proliferation associated with skin neoplasms (Biochem Pharmacol 61: 1205-15 (2001)). Increased expression of CDC2 mRNA correlates with breast neoplasms (Proc Natl Acad Sci USA 90: 1112-6 (1993)). (PhosphoSite®, Cell Signaling Technology (Danvers, Mass.), Human PSD™, Biobase Corporation, (Beverly, Mass.)).

CPSF1, phosphorylated at K809, is among the proteins listed in this patent. CPSF1, Cleavage and polyadenylation specific factor 1 (160 kDa), binds to pre-mRNA, poly(A) polymerase, and CSTF3, promotes mRNA polyadenylation and possibly mRNA cleavage. (PhosphoSiteREGISTERED, Cell Signaling Technology (Danvers, Mass.), Human PSDTRADEMARK, Biobase Corporation, (Beverly, Mass.)).

DDX39, phosphorylated at K333, is among the proteins listed in this patent. DDX39, DEAD (Asp-Glu-Ala-Asp) box polypeptide 39, a putative ATP-dependent RNA helicase which may be involved in nuclear export of mRNA and mRNA splicing. (PhosphoSite®, Cell Signaling Technology (Danvers, Mass.), Human PSD™, Biobase Corporation, (Beverly, Mass.)).

DLD, phosphorylated at K143, is among the proteins listed in this patent. This protein has potential diagnostic and/or therapeutic implications based on the following findings. Mutation in the DLD gene correlates with acidosis (Biochim Biophys Acta 1362: 160-8. (1997)). (PhosphoSite®, Cell Signaling Technology (Danvers, Mass.), Human PSD™, Biobase Corporation, (Beverly, Mass.)).

dUTPase, phosphorylated at K91, is among the proteins listed in this patent. This protein has potential diagnostic and/or therapeutic implications based on the following findings. Increased expression of DUT protein correlates with drug-resistant form of colorectal neoplasms (Cancer Res 60: 3493-503 (2000)). Increased expression of DUT protein may correlate with increased cell proliferation associated with colorectal neoplasms (Int J Cancer 84: 614-7. (1999)). (PhosphoSite®, Cell Signaling Technology (Danvers, Mass.), Human PSD™, Biobase Corporation, (Beverly, Mass.)).

eEF1A-1, CC chemokine phosphorylated at K392, is among the proteins listed in this patent. eEF1A-1, receptor 5, a G protein-coupled receptor that binds chemokines and is a coreceptor for HIV-1 glycoprotein 120, may modulate immune and inflammatory responses, inhibition may be therapeutic for HIV infections and multiple sclerosis. This protein has potential diagnostic and/or therapeutic implications based on the following findings. Induced inhibition of the coreceptor activity of CCR5 may prevent HIV infections (J Virol 74: 9328-32. (2000)). Polymorphism in the CCR5 gene correlates with increased incidence of death associated with breast neoplasms (J Exp Med 198: 1381-9. (2003)). Deletion mutation in the CCR5 gene correlates with late onset form of HIV infections (Mol Med 6: 28-36 (2000)). Increased expression of CCR5 in T-lymphocytes correlates with more severe form of HIV infections (J Infect Dis 181: 927-32 (2000)). Induced inhibition of the viral receptor activity of CCR5 may prevent abnormal initiation of viral infection associated with HIV infections (Cell 86: 367-77 (1996)). Induced inhibition of the coreceptor activity of CCR5 may prevent HIV infections (J Virol 73: 3443-8. (1999)). Polymorphism in the CCR5 promoter correlates with increased occurrence of acquired immunodeficiency syndrome associated with HIV infections (Science 282: 1907-11 (1998)). Deletion mutation in the CCR5 gene correlates with decreased occurrence of disease susceptibility associated with asthma (Lancet 354: 1264-5 (1999)). Increased expression of CCR5 in leukocytes correlates with pulmonary tuberculosis associated with AIDS-related opportunistic infections (J Infect Dis 183: 1801-4. (2001)). Decreased expression of CCR5 in T-lymphocytes correlates with abnormal T-lymphocytes migration associated with chronic hepatitis C (J Infect Dis 185: 1803-7. (2002)). Increased expression of CCR5 mRNA correlates with inflammation (J Clin Invest 101: 746-54. (1998)). Decreased expression of CCR5 in leukocytes correlates with type I diabetes mellitus (Diabetes 51: 2474-80. (2002)). Monoclonal antibody to CCR5 may prevent abnormal initiation of viral infection associated with HIV infections (PNAS 97: 3388-93 (2000)). Increased expression of CCR5 in T-lymphocytes correlates with schistosomiasis mansoni (Infect Immun 71: 6668-71. (2003)). Polymorphism in the CCR5 gene correlates with increased occurrence of disease susceptibility associated with diabetic nephropathies (Diabetes 54: 3331-5 (2005)). Increased expression of CCR5 in T-lymphocytes correlates with advanced stage or high grade form of HIV infections (J Immunol 163: 4597-603 (1999)). Viral exploitation of the coreceptor activity of CCR5 may cause HIV infections (J Virol 79: 1686-700 (2005)). Increased viral receptor activity of CCR5 correlates with advanced stage or high grade form of acquired immunodeficiency syndrome (J Virol 73: 9741-55. (1999)). Increased expression of CCR5 in dendritic cells correlates with optic neuritis associated with multiple sclerosis (Clin Exp Immunol 127: 519-26. (2002)). Abnormal expression of CCR5 protein correlates with Graves' disease (Clin Exp Immunol 127: 479-85. (2002)). Monoclonal antibody to CCR5 may prevent abnormal initiation of viral infection associated with HIV infections (Proc Natl Acad Sci USA 97: 3388-93 (2000)). Increased expression of CCR5 in T-lymphocytes correlates with inflammation associated with chronic hepatitis C (J Infect Dis 190: 989-97 (2004)). Increased expression of CCR5 in monocytes correlates with schistosomiasis mansoni (Infect Immun 71: 6668-71. (2003)). Polymorphism in the CCR5 gene correlates with diabetic angiopathies associated with type I diabetes mellitus (Cytokine 26: 114-21 (2004)). Decreased plasma membrane localization of CCR5 may prevent HIV infections (PNAS 94: 11567-72 (1997)). Viral exploitation of the coreceptor activity of CCR5 may cause defective initiation of viral infection associated with HIV infections (J Virol 71: 7478-87. (1997)). Increased expression of CCR5 in T-lymphocytes correlates with more severe form of HIV infections (Blood 96: 2649-54 (2000)). Increased expression of CCR5 protein correlates with kidney diseases (Kidney Int 56: 52-64 (1999)). Single nucleotide polymorphism in the CCR5 promoter correlates with diabetic nephropathies (Diabetes 51: 238-42. (2002)). Polymorphism in the CCR5 promoter correlates with increased occurrence of disease progression associated with acquired immunodeficiency syndrome (Science 282: 1907-11 (1998)). Polymorphism in the CCR5 gene correlates with decreased occurrence of AIDS-related lymphoma associated with acquired immunodeficiency syndrome (Blood 93: 1838-42. (1999)). Induced inhibition of the viral receptor activity of CCR5 may prevent abnormal initiation of viral infection associated with HIV infections (Nature 382: 722-5 (1996)). Polymorphism in the CCR5 promoter correlates with more severe form of HIV infections (J Infect Dis 183: 814-8. (2001)). Increased expression of CCR5 in B-lymphocytes correlates with inflammation associated with chronic hepatitis C (J Infect Dis 190: 989-97 (2004)). Induced inhibition of the coreceptor activity of CCR5 may prevent HIV infections (PNAS 98: 12718-23. (2001)). Decreased plasma membrane localization of CCR5 may prevent HIV infections (Proc Natl Acad Sci USA 94: 11567-72 (1997)). Decreased expression of CCR5 in T-lymphocytes may prevent HIV infections (PNAS 100: 183-8. (2003)). Absence of plasma membrane localization of CCR5 causes decreased initiation of viral infection associated with HIV infections (Cell 86: 367-77 (1996)). Abnormal expression of CCR5 in T-lymphocytes correlates with rheumatoid arthritis (Clin Exp Immunol 132: 371-8. (2003)). Viral exploitation of the chemokine receptor activity of CCR5 may cause increased initiation of viral infection associated with acquired immunodeficiency syndrome (Proc Natl Acad Sci USA 96: 7496-501 (1999)). Increased expression of CCR5 in T-lymphocytes correlates with rheumatoid arthritis (J Immunol 174: 1693-700 (2005)). Viral exploitation of the coreceptor activity of CCR5 causes increased initiation of viral infection associated with HIV infections (Cell 85: 1135-48 (1996)). Deletion mutation in the CCR5 gene correlates with abnormal immune response associated with HIV infections (Mol Med 6: 28-36 (2000)). Single nucleotide polymorphism in the CCR5 promoter correlates with increased incidence of diabetic nephropathies associated with type II diabetes mellitus (Diabetes 51: 238-42. (2002)). Deletion mutation in the CCR5 gene correlates with decreased occurrence of non-Hodgkin's lymphoma associated with acquired immunodeficiency syndrome (Blood 93: 1838-42. (1999)). Antibody to CCR5 may prevent increased initiation of viral infection associated with HIV infections (Proc Natl Acad Sci USA 97: 805-10 (2000)). Increased expression of CCR5 in T-lymphocytes may correlate with pulmonary tuberculosis associated with HIV infections (J Infect Dis 183: 1801-4. (2001)). Viral exploitation of the coreceptor activity of CCR5 correlates with acute form of HIV infections (Blood 98: 3169-71. (2001)). Increased expression of CCR5 in lymphocytes correlates with chronic hepatitis C (J Immunol 163: 6236-43 (1999)). Increased expression of CCR5 in fibroblasts correlates with rheumatoid arthritis (J Immunol 167: 5381-5. (2001)). Increased expression of CCR5 in T-lymphocytes may correlate with AIDS-related opportunistic infections associated with HIV infections (J Infect Dis 183: 1801-4. (2001)). Mutation in the CCR5 gene correlates with decreased occurrence of acquired immunodeficiency syndrome associated with HIV infections (Science 277: 959-65 (1997)). Decreased expression of CCR5 in T-lymphocytes may prevent HIV infections (Proc Natl Acad Sci USA 100: 183-8. (2003)). Increased expression of CCR5 protein correlates with inflammation associated with periodontitis (Cytokine 20: 70-7. (2002)). Polymorphism in the CCR5 promoter correlates with more severe form of HIV infections (J Infect Dis 184: 89-92. (2001)). Loss of function mutation in the CCR5 gene causes decreased initiation of viral infection associated with HIV infections (Mol Med 3: 23-36. (1997)). Decreased chemokine receptor activity of CCR5 correlates with decreased occurrence of recurrence associated with multiple sclerosis (J Neuroimmunol 102: 98-106. (2000)). Decreased expression of CCR5 in T-lymphocytes correlates with Crohn disease (Clin Exp Immunol 132: 332-8. (2003)). Viral exploitation of the chemokine receptor activity of CCR5 may cause increased initiation of viral infection associated with acquired immunodeficiency syndrome (PNAS 96: 7496-501 (1999)). Viral exploitation of the CCR5 protein causes increased entry of virus into host cell associated with HIV infections (J Neuroimmunol 110: 230-9 (2000)). Deletion mutation in the CCR5 gene correlates with decreased occurrence of AIDS-related lymphoma associated with acquired immunodeficiency syndrome (Blood 93: 1838-42. (1999)). Increased expression of CCR5 in lymphocytes correlates with increased T-helper 1 type immune response associated with Behcet Syndrome (Clin Exp Immunol 139: 371-8 (2005)). Increased presence of CCR5 antibody may prevent HIV infections (Clin Exp Immunol 129: 493-501. (2002)). Antibody to CCR5 may prevent increased initiation of viral infection associated with HIV infections (PNAS 97: 805-10 (2000)). Antibody to CCR5 may prevent increased initiation of viral infection associated with HIV infections (Proc Natl Acad Sci USA 97: 805-10 (2000)). Viral exploitation of the coreceptor activity of CCR5 correlates with AIDS dementia complex (Virology 279: 509-26. (2001)). Viral exploitation of the coreceptor activity of CCR5 causes increased initiation of viral infection associated with HIV infections (J Exp Med 185: 621-8. (1997)). Induced inhibition of the chemokine receptor activity of CCR5 may prevent recurrence associated with multiple sclerosis (J Neuroimmunol 102: 98-106. (2000)). Increased expression of CCR5 in lymphocytes correlates with autoimmune diseases associated with thyroid diseases (J Clin Endocrinol Metab 86: 5008-16. (2001)). Viral exploitation of the chemokine receptor activity of CCR5 may cause increased initiation of viral infection associated with acquired immunodeficiency syndrome (Proc Natl Acad Sci USA 96: 7496-501 (1999)). Loss of function mutation in the CCR5 gene correlates with decreased severity of disease progression associated with HIV infections (Mol Med 3: 23-36. (1997)). Polymorphism in the CCR5 promoter correlates with more severe form of HIV infections (J Virol 73: 10264-71. (1999)). Absence of the viral receptor activity of CCR5 causes decreased initiation of viral infection associated with HIV infections (Nature 382: 722-5 (1996)). Increased expression of CCR5 in leukocytes correlates with AIDS-related opportunistic infections associated with HIV infections (J Infect Dis 183: 1801-4. (2001)). Deletion mutation in the CCR5 gene correlates with decreased occurrence of recurrence associated with multiple sclerosis (J Neuroimmunol 102: 98-106. (2000)). Induced inhibition of the coreceptor activity of CCR5 may prevent HIV infections (Proc Natl Acad Sci USA 98: 12718-23. (2001)). Absence of plasma membrane localization of CCR5 causes decreased initiation of viral infection associated with HIV infections (Nature 382: 722-5 (1996)). Deletion mutation in the CCR5 gene may prevent disease progression associated with acquired immunodeficiency syndrome (Science 273: 1856-62 (1996)). Increased expression of CCR5 in T-lymphocytes may correlate with pulmonary tuberculosis associated with AIDS-related opportunistic infections (J Infect Dis 183: 1801-4. (2001)). Deletion mutation in the CCR5 gene causes decreased initiation of viral infection associated with HIV infections (Nature 382: 722-5 (1996)). Viral exploitation of the chemokine receptor activity of CCR5 may cause increased induction by virus of cell-cell fusion in host associated with HIV infections (J Virol 71: 8405-15. (1997)). Polymorphism in the CCR5 gene correlates with decreased (delayed) early viral mRNA transcription associated with HIV seropositivity (J Virol 76: 662-72. (2002)). Absence of the viral receptor activity of CCR5 causes decreased initiation of viral infection associated with HIV infections (Cell 86: 367-77 (1996)). Increased expression of CCR5 in leukocytes correlates with pulmonary tuberculosis associated with HIV infections (J Infect Dis 183: 1801-4. (2001)). Deletion mutation in the CCR5 gene may prevent HIV infections (Science 273: 1856-62 (1996)). Increased expression of CCR5 in monocytes correlates with more severe form of HIV infections (J Exp Med 187: 439-44. (1998)). Increased expression of CCR5 in B-lymphocytes correlates with relapsing-remitting multiple sclerosis (J Neuroimmunol 122: 125-31. (2002)). Increased expression of CCR5 mRNA correlates with periapical granuloma (Cytokine 16: 62-6. (2001)). Deletion mutation in the CCR5 gene causes decreased initiation of viral infection associated with HIV infections (Cell 86: 367-77 (1996)). Increased expression of CCR5 in T-lymphocytes may cause increased T-helper 1 type immune response associated with relapsing-remitting multiple sclerosis (J Neuroimmunol 114: 207-12. (2001)). Abnormal expression of CCR5 in NK cells may correlate with increased severity of leukemia associated with lymphoproliferative disorders (Leukemia 19: 1169-74 (2005)). Increased expression of CCR5 in B-lymphocytes correlates with Hodgkin's disease (Blood 97: 1543-8. (2001)). Viral exploitation of the CCR5 protein may cause increased induction by virus of cell-cell fusion in host associated with HIV infections (Blood 103: 1211-7 (2004)). Monoclonal antibody to CCR5 may prevent abnormal initiation of viral infection associated with HIV infections (Proc Natl Acad Sci USA 97: 3388-93 (2000)). Induced inhibition of the coreceptor activity of CCR5 may prevent HIV infections (Proc Natl Acad Sci USA 98: 12718-23. (2001)). Polymorphism in the CCR5 promoter correlates with decreased occurrence of acquired immunodeficiency syndrome associated with HIV infections (Lancet 352: 866-70. (1998)). Polymorphism in the CCR5 gene correlates with increased initiation of viral infection associated with HIV infections (J Infect Dis 183: 1574-85. (2001)). Increased expression of CCR5 in T-lymphocytes correlates with Hodgkin's disease (Blood 97: 1543-8. (2001)). Decreased expression of CCR5 protein correlates with chronic myeloid leukemia (J Immunol 162: 6191-9 (1999)). Decreased plasma membrane localization of CCR5 may prevent HIV infections (Proc Natl Acad Sci USA 94: 11567-72 (1997)). Decreased expression of CCR5 in T-lymphocytes may prevent HIV infections (Proc Natl Acad Sci USA 100: 183-8. (2003)). Viral exploitation of the chemokine receptor activity of CCR5 may cause increased induction by virus of cell-cell fusion in host associated with acquired immunodeficiency syndrome (J Virol 71: 8405-15. (1997)). Increased expression of CCR5 in NK cells correlates with inflammation associated with chronic hepatitis C (J Infect Dis 190: 989-97 (2004)). (PhosphoSite®, Cell Signaling Technology (Danvers, Mass.), Human PSD™, Biobase Corporation, (Beverly, Mass.)).

endosulfine alpha, phosphorylated at K63, is among the proteins listed in this patent. endosulfine alpha, Endosulfine alpha, an inhibitor of ATP-sensitive potassium channels in pancreatic beta cells, may act to promote insulin (INS) release, expression is reduced in the brains of Alzheimer's disease patients. (PhosphoSite®, Cell Signaling Technology (Danvers, Mass.), Human PSD™, Biobase Corporation, (Beverly, Mass.)).

esterase D, phosphorylated at K10, is among the proteins listed in this patent. This protein has potential diagnostic and/or therapeutic implications based on the following findings. ESD map position may correlate with hepatolenticular degeneration (Hum Genet. 87: 465-8. (1991)). (PhosphoSite®, Cell Signaling Technology (Danvers, Mass.), Human PSD™, Biobase Corporation, (Beverly, Mass.)).

FASN, phosphorylated at K1878, is among the proteins listed in this patent. This protein has potential diagnostic and/or therapeutic implications based on the following findings. Induced inhibition of the fatty-acid synthase activity of FASN may prevent increased cell proliferation associated with breast neoplasms (PNAS 91: 6379-83. (1994)). Induced inhibition of the fatty-acid synthase activity of FASN may prevent increased fatty acid biosynthetic process associated with ovarian neoplasms (Cancer Res 56: 1189-93. (1996)). Increased expression of FASN protein correlates with increased occurrence of more severe form of breast neoplasms (Cancer 77: 474-82. (1996)). Increased expression of FASN in serum correlates with breast neoplasms (Cancer Lett 167: 99-104. (2001)). Increased expression of FASN protein correlates with increased occurrence of invasive form of prostatic neoplasms (Int J Cancer 98: 19-22. (2002)). Induced inhibition of FASN protein may cause increased apoptosis associated with breast neoplasms (Cancer Res 56: 2745-7. (1996)). Induced inhibition of FASN protein may prevent increased cell proliferation associated with breast neoplasms (Cancer Res 60: 213-8. (2000)). Induced inhibition of the fatty-acid synthase activity of FASN may prevent increased cell proliferation associated with breast neoplasms (Proc Natl Acad Sci USA 91: 6379-83. (1994)). Increased expression of FASN mRNA may correlate with breast neoplasms (Cancer Lett 149: 43-51. (2000)). Induced inhibition of the fatty-acid synthase activity of FASN may prevent increased cell proliferation associated with breast neoplasms (Proc Natl Acad Sci USA 91: 6379-83. (1994)). (PhosphoSite®, Cell Signaling Technology (Danvers, Mass.), Human PSD™, Biobase Corporation, (Beverly, Mass.)).

G6PI, phosphorylated at K466, is among the proteins listed in this patent. This protein has potential diagnostic and/or therapeutic implications based on the following findings. Increased expression of GPI protein may cause increased anti-apoptosis associated with neoplasms (Cancer Res 63: 242-9. (2003)). Alternative form of GPI mRNA may cause increased severity of inflammation associated with rheumatoid arthritis (Biochem Biophys Res Commun 323: 518-22 (2004)). Increased cleavage of GPI may correlate with neoplasms (Cancer Res 58: 2667-74. (1998)). Increased expression of GPI protein may cause neoplastic cell transformation associated with neoplasms (Cancer Res 63: 242-9. (2003)). Decreased glucose-6-phosphate isomerase activity of GPI may cause chronic form of hemolytic anemia (Blood 88: 2306-10. (1996)). Nonsense mutation in the GPI gene causes chronic form of hemolytic anemia (Blood 88: 2306-10. (1996)). Increased secretion of GPI may correlate with neoplasms (Cancer Res 58: 2667-74. (1998)). Deletion mutation in the GPI gene causes chronic form of hemolytic anemia (Blood 88: 2306-10. (1996)). Missense mutation in the GPI gene causes chronic form of hemolytic anemia (Blood 88: 2306-10. (1996)). Increased expression of GPI mRNA may cause increased cell migration associated with pancreatic neoplasms (Br J Cancer 86: 1914-9. (2002)). Missense mutation in the GPI gene correlates with decreased erythrocytes function associated with hemolytic anemia (Blood 88: 2321-5. (1996)). (PhosphoSite®, Cell Signaling Technology (Danvers, Mass.), Human PSD™, Biobase Corporation, (Beverly, Mass.)).

GCLC, phosphorylated at K412, is among the proteins listed in this patent. This protein has potential diagnostic and/or therapeutic implications based on the following findings. Increased expression of GCLC mRNA may correlate with drug-resistant form of acute promyelocytic leukemia (J Biol Chem 271: 14981-8. (1996)). Increased expression of GCLC mRNA may correlate with drug-resistant form of acute promyelocytic leukemia (JBC 271: 14981-8. (1996)). Increased expression of GCLC mRNA may correlate with decreased response to drug associated with mesothelioma (Int J Cancer 75: 757-61. (1998)). Missense mutation in the GCLC gene correlates with decreased glutathione biosynthetic process associated with hemolytic anemia (Blood 94: 2890-4. (1999)). Increased expression of GCLC protein correlates with increased cell differentiation associated with non-small-cell lung carcinoma (Cancer 92: 2911-9. (2001)). Decreased expression of GCLC protein correlates with increased apoptosis associated with non-small-cell lung carcinoma (Cancer 92: 2911-9. (2001)). Missense mutation in the GCLC gene causes hemolytic anemia (Blood 95: 2193-6. (2000)). Increased expression of GCLC mRNA correlates with colorectal neoplasms (Cancer Res 56: 3642-4 (1996)). Increased expression of GCLC protein correlates with squamous cell carcinoma associated with non-small-cell lung carcinoma (Cancer 92: 2911-9. (2001)). Increased expression of GCLC protein correlates with carcinoma associated with colorectal neoplasms (Int J Cancer 97: 21-7. (2002)). (PhosphoSite®, Cell Signaling Technology (Danvers, Mass.), Human PSD™, Biobase Corporation, (Beverly, Mass.)).

GLUD1, phosphorylated at K545, is among the proteins listed in this patent. This protein has potential diagnostic and/or therapeutic implications based on the following findings. Altered allosteric regulation of the glutamate dehydrogenase activity of GLUD1 causes hyperammonemia associated with hyperinsulinism (Diabetes 49: 667-73. (2000)). Missense mutation in the GLUD1 gene causes hyperammonemia (Diabetes 49: 667-73. (2000)). Missense mutation in the GLUD1 gene causes hypoglycemia (J Clin Endocrinol Metab 86: 1782-7. (2001)). Missense mutation in the GLUD1 gene causes hyperammonemia associated with hyperinsulinism (Diabetes 49: 667-73. (2000)). Increased glutamate dehydrogenase activity of GLUD1 causes hyperammonemia associated with hyperinsulinism (Hum Genet. 104: 476-9. (1999)). Missense mutation in the GLUD1 gene causes less severe form of hyperinsulinism (Hum Genet. 108: 66-71. (2001)). Missense mutation in the GLUD1 gene causes hyperammonemia associated with hyperinsulinism (Hum Genet. 104: 476-9. (1999)). Missense mutation in the GLUD1 gene causes autosomal dominant form of hyperinsulinism (J Clin Endocrinol Metab 86: 1782-7. (2001)). Increased glutamate dehydrogenase activity of GLUD1 causes hyperammonemia (Hum Genet. 104: 476-9. (1999)). Altered allosteric regulation of the glutamate dehydrogenase activity of GLUD1 causes hyperammonemia (Hum Genet. 108: 66-71. (2001)). Missense mutation in the GLUD1 gene causes more severe form of hyperinsulinism (Hum Genet. 104: 476-9. (1999)). Missense mutation in the GLUD1 gene causes hyperammonemia (J Clin Endocrinol Metab 86: 1782-7. (2001)). Missense mutation in the GLUD1 gene causes hyperammonemia (Hum Genet. 108: 66-71. (2001)). Altered allosteric regulation of the glutamate dehydrogenase activity of GLUD1 causes hyperammonemia associated with hyperinsulinism (J Clin Endocrinol Metab 86: 1782-7. (2001)). Missense mutation in the GLUD1 gene causes hyperammonemia associated with hyperinsulinism (J Clin Endocrinol Metab 86: 1782-7. (2001)). Altered allosteric regulation of the glutamate dehydrogenase activity of GLUD1 causes hyperammonemia associated with hyperinsulinism (Hum Genet. 108: 66-71. (2001)). Missense mutation in the GLUD1 gene causes hypoglycemia associated with hyperinsulinism (J Clin Endocrinol Metab 86: 1782-7. (2001)). Missense mutation in the GLUD1 gene causes hyperammonemia associated with hyperinsulinism (Hum Genet. 108: 66-71. (2001)). Missense mutation in the GLUD1 gene causes hyperammonemia (Hum Genet. 104: 476-9. (1999)). Missense mutation in the GLUD1 gene causes familial form of hyperinsulinism (Hum Genet. 108: 66-71. (2001)). Altered allosteric regulation of the glutamate dehydrogenase activity of GLUD1 causes hyperammonemia (Diabetes 49: 667-73. (2000)). (PhosphoSite®, Cell Signaling Technology (Danvers, Mass.), Human PSD™, Biobase Corporation, (Beverly, Mass.)).

GSS, phosphorylated at K186, is among the proteins listed in this patent. This protein has potential diagnostic and/or therapeutic implications based on the following findings. Decreased glutathione synthase activity of GSS causes inborn errors of amino acid metabolism (Hum Mol Genet. 6: 1147-52. (1997)). Missense mutation in the GSS gene causes increased severity of acidosis associated with congenital nonspherocytic hemolytic anemia (Hum Mol Genet. 6: 1147-52. (1997)). Missense mutation in the GSS gene causes more severe form of acidosis (Hum Mol Genet. 6: 1147-52. (1997)). Decreased glutathione synthase activity of GSS causes nervous system diseases associated with congenital nonspherocytic hemolytic anemia (Hum Mol Genet. 6: 1147-52. (1997)). Missense mutation in the GSS gene causes inborn errors of amino acid metabolism (Hum Mol Genet. 6: 1147-52. (1997)). Decreased glutathione synthase activity of GSS causes increased severity of acidosis associated with congenital nonspherocytic hemolytic anemia (Hum Mol Genet. 6: 1147-52. (1997)). Missense mutation in the GSS gene causes nervous system diseases associated with congenital nonspherocytic hemolytic anemia (Hum Mol Genet. 6: 1147-52. (1997)). Decreased glutathione synthase activity of GSS causes more severe form of acidosis (Hum Mol Genet. 6: 1147-52. (1997)). (PhosphoSite®, Cell Signaling Technology (Danvers, Mass.), Human PSD™, Biobase Corporation, (Beverly, Mass.)).

HADHB, phosphorylated at K201, is among the proteins listed in this patent. This protein has potential diagnostic and/or therapeutic implications based on the following findings. Decreased expression of HADHB protein may cause sudden infant death associated with inborn errors lipid metabolism (Hum Mol Genet. 6: 1215-24 (1997)). Decreased expression of HADHB protein may cause abnormal fatty acid beta-oxidation associated with myocardial diseases (Hum Mol Genet. 6: 1215-24 (1997)). Insertion mutation in the HADHB gene may cause abnormal fatty acid beta-oxidation associated with myocardial diseases (Hum Mol Genet. 6: 1215-24 (1997)). Decreased expression of HADHB protein may cause myocardial diseases associated with inborn errors lipid metabolism (Hum Mol Genet. 6: 1215-24 (1997)). Decreased expression of HADHB protein may cause abnormal fatty acid beta-oxidation associated with sudden infant death (Hum Mol Genet. 6: 1215-24 (1997)). Insertion mutation in the HADHB gene may cause abnormal fatty acid beta-oxidation associated with sudden infant death (Hum Mol Genet. 6: 1215-24 (1997)). Decreased expression of HADHB protein may cause hypoglycemia associated with inborn errors lipid metabolism (Hum Mol Genet. 6: 1215-24 (1997)). Insertion mutation in the HADHB gene may cause hypoglycemia associated with inborn errors lipid metabolism (Hum Mol Genet. 6: 1215-24 (1997)). Point mutation in the HADHB gene may cause sudden infant death associated with inborn errors lipid metabolism (Hum Mol Genet. 6: 1215-24 (1997)). Decreased expression of HADHB protein may cause abnormal fatty acid beta-oxidation associated with hypoglycemia (Hum Mol Genet. 6: 1215-24 (1997)). Point mutation in the HADHB gene causes inborn errors lipid metabolism (Am J Hum Genet. 58: 979-88. (1996)). Point mutation in the HADHB gene may cause hypoglycemia associated with inborn errors lipid metabolism (Hum Mol Genet. 6: 1215-24 (1997)). Point mutation in the HADHB gene may cause myocardial diseases associated with inborn errors lipid metabolism (Hum Mol Genet. 6: 1215-24 (1997)). Decreased acetyl-CoA C-acyltransferase activity of HADHB may cause sudden infant death associated with inborn errors lipid metabolism (Hum Mol Genet. 6: 1215-24 (1997)). Insertion mutation in the HADHB gene may cause sudden infant death associated with inborn errors lipid metabolism (Hum Mol Genet. 6: 1215-24 (1997)). Decreased acetyl-CoA C-acyltransferase activity of HADHB may cause hypoglycemia associated with inborn errors lipid metabolism (Hum Mol Genet. 6: 1215-24 (1997)). Decreased acetyl-CoA C-acyltransferase activity of HADHB may cause myocardial diseases associated with inborn errors lipid metabolism (Hum Mol Genet. 6: 1215-24 (1997)). Decreased acetyl-CoA C-acyltransferase activity of HADHB may cause abnormal fatty acid beta-oxidation associated with myocardial diseases (Hum Mol Genet. 6: 1215-24 (1997)). Point mutation in the HADHB gene may cause abnormal fatty acid beta-oxidation associated with myocardial diseases (Hum Mol Genet. 6: 1215-24 (1997)). Decreased expression of HADHB protein may cause abnormal fatty acid beta-oxidation associated with inborn errors lipid metabolism (Hum Mol Genet. 6: 1215-24 (1997)). Deletion mutation in the HADHB gene causes inborn errors lipid metabolism (Am J Hum Genet. 58: 979-88. (1996)). Insertion mutation in the HADHB gene may cause myocardial diseases associated with inborn errors lipid metabolism (Hum Mol Genet. 6: 1215-24 (1997)). Insertion mutation in the HADHB gene may cause abnormal fatty acid beta-oxidation associated with hypoglycemia (Hum Mol Genet. 6: 1215-24 (1997)). Decreased acetyl-CoA C-acyltransferase activity of HADHB may cause abnormal fatty acid beta-oxidation associated with hypoglycemia (Hum Mol Genet. 6: 1215-24 (1997)). Decreased acetyl-CoA C-acyltransferase activity of HADHB may cause abnormal fatty acid beta-oxidation associated with sudden infant death (Hum Mol Genet. 6: 1215-24 (1997)). Point mutation in the HADHB gene may cause abnormal fatty acid beta-oxidation associated with sudden infant death (Hum Mol Genet. 6: 1215-24 (1997)). Point mutation in the HADHB gene may cause abnormal fatty acid beta-oxidation associated with hypoglycemia (Hum Mol Genet. 6: 1215-24 (1997)). Point mutation in the HADHB gene may cause abnormal fatty acid beta-oxidation associated with inborn errors lipid metabolism (Hum Mol Genet. 6: 1215-24 (1997)). Decreased acetyl-CoA C-acyltransferase activity of HADHB may cause abnormal fatty acid beta-oxidation associated with inborn errors lipid metabolism (Hum Mol Genet. 6: 1215-24 (1997)). Insertion mutation in the HADHB gene may cause abnormal fatty acid beta-oxidation associated with inborn errors lipid metabolism (Hum Mol Genet. 6: 1215-24 (1997)). (PhosphoSite®, Cell Signaling Technology (Danvers, Mass.), Human PSD™, Biobase Corporation, (Beverly, Mass.)).

HMGCL, phosphorylated at K48, is among the proteins listed in this patent. This protein has potential diagnostic and/or therapeutic implications based on the following findings. Frameshift mutation in the HMGCL gene causes inborn errors of metabolism (Am J Hum Genet. 62: 295-300. (1998)). Deletion mutation in the HMGCL gene causes liver diseases associated with inborn errors of metabolism (Hum Genet. 107: 320-6. (2000)). Abnormal mRNA splicing of HMGCL correlates with inborn errors metal metabolism (J Lipid Res 37: 2420-32. (1996)). Deletion mutation in the HMGCL gene causes seizures associated with inborn errors of metabolism (Hum Genet. 107: 320-6. (2000)). Deletion mutation in the HMGCL gene causes acidosis associated with inborn errors of metabolism (Hum Genet. 107: 320-6. (2000)). Splice site mutation in the HMGCL gene causes inborn errors of metabolism (J Lipid Res 38: 2303-13. (1997)). Mutation in the HMGCL gene causes hyperammonemia associated with inborn errors of metabolism (Hum Genet. 107: 320-6. (2000)). Point mutation in the HMGCL gene causes inborn errors of metabolism (Am J Hum Genet. 62: 295-300. (1998)). Deletion mutation in the HMGCL gene causes hypoglycemia associated with inborn errors of metabolism (Hum Genet. 107: 320-6. (2000)). Mutation in the HMGCL gene causes coma associated with inborn errors of metabolism (Am J Hum Genet. 62: 295-300. (1998)). Decreased hydroxymethylglutaryl-CoA lyase activity of HMGCL causes hypoglycemia associated with inborn errors of metabolism (Am J Hum Genet. 62: 295-300. (1998)). Decreased hydroxymethylglutaryl-CoA lyase activity of HMGCL causes inborn errors of metabolism (J Biol Chem 271: 24604-9. (1996)). Decreased hydroxymethylglutaryl-CoA lyase activity of HMGCL causes coma associated with inborn errors of metabolism (Am J Hum Genet. 62: 295-300. (1998)). Decreased hydroxymethylglutaryl-CoA lyase activity of HMGCL causes inborn errors of metabolism (JBC 271: 24604-9. (1996)). Missense mutation in the HMGCL gene causes inborn errors of metabolism (Am J Hum Genet. 62: 295-300. (1998)). Mutation in the HMGCL gene causes defective liver function associated with inborn errors of metabolism (Hum Genet. 107: 320-6. (2000)). Mutation in the HMGCL gene causes hypoglycemia associated with inborn errors of metabolism (Am J Hum Genet. 62: 295-300. (1998)). (PhosphoSite®, Cell Signaling Technology (Danvers, Mass.), Human PSD™, Biobase Corporation, (Beverly, Mass.)).

HMGCS1, phosphorylated at K409, is among the proteins listed in this patent. HMGCS1, 3-Hydroxy-3-methylglutaryl-Coenzyme A (HMG-CoA) synthase, cytosolic enzyme that catalyzes an early reaction in cholesterol biosynthesis, inhibited by the beta-lactone L-659,699. (PhosphoSite®, Cell Signaling Technology (Danvers, Mass.), Human PSD™, Biobase Corporation, (Beverly, Mass.)).

HSC70, phosphorylated at K112, is among the proteins listed in this patent. This protein has potential diagnostic and/or therapeutic implications based on the following findings. Deletion mutation in the HSPA8 gene correlates with carcinoma tumors associated with breast neoplasms (Cancer Res 59: 4219-21. (1999)). Increased expression of HSPA8 mRNA correlates with colorectal neoplasms associated with adenocarcinoma (FEBS Lett 463: 77-82. (1999)). Antibody to HSPA8 correlates with mixed connective tissue disease (Clin Exp Immunol 100: 486-8 (1995)). Increased expression of HSPA8 mRNA correlates with colorectal neoplasms (FEBS Lett 463: 77-82. (1999)). Increased expression of HSPA8 protein may prevent decreased cell death associated with stress (Mol Cell Biol 20: 7146-59 (2000)). Increased expression of HSPA8 protein may prevent decreased cell death associated with stress (Mol. Cell. Biol. 20: 7146-59 (2000)). Increased expression of HSPA8 protein may prevent decreased cell death associated with stress (MCB 20: 7146-59 (2000)). Deletion mutation in the HSPA8 gene correlates with non-familial form of breast neoplasms (Cancer Res 59: 4219-21. (1999)). Increased expression of HSPA8 protein may prevent decreased cell death associated with stress (Mol Cell Biol. 20: 7146-59 (2000)). Increased expression of HSPA8 protein may prevent decreased cell death associated with stress (Mol. Cell. Biol 20: 7146-59 (2000)). Abnormal expression of HSPA8 in brain correlates with Alzheimer disease (Biochem Biophys Res Commun 280: 249-58. (2001)). (PhosphoSite®, Cell Signaling Technology (Danvers, Mass.), Human PSD™, Biobase Corporation, (Beverly, Mass.)).

HSPA5, phosphorylated at K585, is among the proteins listed in this patent. This protein has potential diagnostic and/or therapeutic implications based on the following findings. Increased expression of HSPA5 mRNA may correlate with drug-sensitive form of colonic neoplasms (Biochem Biophys Res Commun 257: 361-8 (1999)). Increased expression of HSPA5 in endothelium/endothelial cells may correlate with stress (Biochem J 332: 213-21 (1998)). Increased expression of HSPA5 in fibroblasts may correlate with increased response to unfolded protein associated with osteogenesis imperfecta (J Biol Chem 270: 8642-9. (1995)). Increased expression of HSPA5 in fibroblasts may correlate with increased response to unfolded protein associated with osteogenesis imperfecta (JBC 270: 8642-9. (1995)). Increased expression of HSPA5 mRNA correlates with adenocarcinoma (Cancer Res 61: 8322-30. (2001)). Increased expression of HSPA5 protein may correlate with increased response to hypoxia associated with stomach neoplasms (Cancer Res 61: 8322-30. (2001)). Increased expression of HSPA5 mRNA correlates with stomach neoplasms (Cancer Res 61: 8322-30. (2001)). Increased expression of HSPA5 protein may correlate with increased response to hypoxia associated with adenocarcinoma (Cancer Res 61: 8322-30. (2001)). (PhosphoSite®, Cell Signaling Technology (Danvers, Mass.), Human PSD™, Biobase Corporation, (Beverly, Mass.)).

KPNB3, phosphorylated at K45, is among the proteins listed in this patent. KPNB3, Karyopherin beta 3, a subunit of the nuclear localization signal receptor complex, plays a role in nuclear import of ribosomal proteins, inhibited by interaction with hepatitis C virus nonstructural protein 5A. (PhosphoSite®, Cell Signaling Technology (Danvers, Mass.), Human PSD™, Biobase Corporation, (Beverly, Mass.)).

Ku80, phosphorylated at K338, is among the proteins listed in this patent. This protein has potential diagnostic and/or therapeutic implications based on the following findings. Decreased expression of XRCC5 protein correlates with abnormal response to radiation associated with cervix neoplasms (Br J Cancer 83: 1702-6. (2000)). Decreased expression of XRCC5 protein may correlate with decreased cell proliferation associated with colonic neoplasms (Cell Signal 12: 745-750. (2000)). Abnormal expression of XRCC5 protein correlates with drug-sensitive form of myeloid leukemia (Anticancer Res 22: 1787-93. (2002)). Increased expression of XRCC5 protein correlates with less severe form of breast neoplasms (Oncogene 20: 739-47. (2001)). Alternative form of XRCC5 protein correlates with drug-sensitive form of chronic lymphocytic leukemia (Oncogene 15: 2343-8. (1997)). Decreased expression of XRCC5 protein correlates with adenoma tumors associated with colonic neoplasms (Cancer Res 61: 8381-4. (2001)). Increased protein binding of XRCC5 may correlate with Werner syndrome (J Biol Chem 279: 13659-67 (2004)). Increased expression of XRCC5 protein may cause increased cell proliferation associated with stomach neoplasms (JBC 277: 46093-100. (2002)). Increased presence of XRCC5 antibody may prevent abnormal double-strand break repair via nonhomologous end joining associated with myeloid leukemia (Cancer Res 62: 2791-7. (2002)). Polymorphism in the XRCC5 gene may correlate with genetic predisposition to disease associated with breast neoplasms (Cancer Res 63: 2440-6. (2003)). Increased expression of XRCC5 protein may cause increased cell proliferation associated with stomach neoplasms (J Biol Chem 277: 46093-100. (2002)). Alternative form of XRCC5 protein causes decreased double-strand break repair associated with multiple myeloma (J Immunol 165: 6347-55. (2000)). Induced inhibition of XRCC5 protein may prevent drug-resistant form of breast neoplasms (J Pharmacol Exp Ther 303: 753-9. (2002)). Increased protein binding of XRCC5 may correlate with Werner syndrome (JBC 276: 9896-902. (2001)). Increased protein binding of XRCC5 may correlate with Werner syndrome (JBC 279: 13659-67 (2004)). Decreased expression of XRCC5 protein correlates with malignant form of melanoma (Anticancer Res 22: 193-6. (2002)). Decreased expression of XRCC5 protein correlates with carcinoma tumors associated with colonic neoplasms (Cancer Res 61: 8381-4. (2001)). Increased protein binding of XRCC5 may correlate with Werner syndrome (J Biol Chem 276: 9896-902. (2001)). (PhosphoSite®, Cell Signaling Technology (Danvers, Mass.), Human PSD™, Biobase Corporation, (Beverly, Mass.)).

MDH2, phosphorylated at K165, is among the proteins listed in this patent. MDH2, Mitochondrial malate dehydrogenase, part of the malate-aspartate shuttle, putatively catalyzes the oxidation of malate to oxaloacetate; increased mitochondrial malate dehydrogenase activity correlates with vitiligo. (PhosphoSite®, Cell Signaling Technology (Danvers, Mass.), Human PSD™, Biobase Corporation, (Beverly, Mass.)).

NCL, phosphorylated at K467, is among the proteins listed in this patent. This protein has potential diagnostic and/or therapeutic implications based on the following findings. Induced inhibition of NCL protein may prevent respirovirus infections (J Virol 78: 8146-58 (2004)). Autoimmune antibody to NCL correlates with systemic lupus erythematosus (Mol Biol Rep 16: 263-6. (1992)). Decreased cytoplasm localization of NCL may correlate with increased apoptosis associated with myeloid leukemia (J Biol Chem 278: 8572-9. (2003)). Decreased cytoplasm localization of NCL may correlate with increased apoptosis associated with myeloid leukemia (JBC 278: 8572-9. (2003)). Increased cytoplasm localization of NCL correlates with increased entry of virus into host cell associated with HIV infections (Exp Cell Res 276: 155-73. (2002)). Decreased nucleus localization of NCL may correlate with increased apoptosis associated with myeloid leukemia (JBC 278: 8572-9. (2003)). Mislocalization of NCL protein correlates with increased response to drug associated with breast neoplasms (Int J Cancer 106: 486-95 (2003)). Decreased nucleus localization of NCL may correlate with increased apoptosis associated with myeloid leukemia (J Biol Chem 278: 8572-9. (2003)). (PhosphoSite®, Cell Signaling Technology (Danvers, Mass.), Human PSD™, Biobase Corporation, (Beverly, Mass.)).

NuMA-1, phosphorylated at K379, is among the proteins listed in this patent. This protein has potential diagnostic and/or therapeutic implications based on the following findings. Increased expression of NUMA1 mutant protein correlates with acute promyelocytic leukemia (Nat Genet. 17: 109-13 (1997)). Abnormal expression of NUMA1 mRNA correlates with aneuploidy associated with myeloid leukemia (Oncogene 23: 2379-84 (2004)). Single nucleotide polymorphism in the NUMA1 gene correlates with increased occurrence of disease susceptibility associated with breast neoplasms (PNAS 102: 2004-9 (2005)). Translocation of the NUMA1 gene correlates with acute promyelocytic leukemia (Nat Genet. 17: 109-13 (1997)). Abnormal expression of NUMA1 mRNA correlates with chromosome aberrations associated with myeloid leukemia (Oncogene 23: 2379-84 (2004)). Single nucleotide polymorphism in the NUMA1 gene correlates with increased occurrence of disease susceptibility associated with breast neoplasms (Proc Natl Acad Sci USA 102: 2004-9 (2005)). Single nucleotide polymorphism in the NUMA1 gene correlates with increased occurrence of disease susceptibility associated with breast neoplasms (Proc Natl Acad Sci USA 102: 2004-9 (2005)). Increased expression of NUMA1 protein correlates with colorectal neoplasms (Anticancer Res 19: 2415-20. (1999)). (PhosphoSite®, Cell Signaling Technology (Danvers, Mass.), Human PSD™, Biobase Corporation, (Beverly, Mass.)).

OSR1, phosphorylated at K46, is among the proteins listed in this patent. OSR1, Oxidative-stress responsive 1, a serine-threonine kinase that binds and threonine phosphorylates p21 activated kinase 1 (PAK1) and is activated by osmotic stress. (PhosphoSite®, Cell Signaling Technology (Danvers, Mass.), Human PSD™, Biobase Corporation, (Beverly, Mass.)).

PABP 1, phosphorylated at K104, is among the proteins listed in this patent. This protein has potential diagnostic and/or therapeutic implications based on the following findings. Increased proteolysis of PABPC1 may cause increased suppression by virus of host termination of protein biosynthetic process associated with coxsackievirus infections (J Virol 73: 709-17. (1999)). Viral exploitation of the PABPC1 protein may cause increased suppression by virus of host termination of protein biosynthetic process associated with coxsackievirus infections (J Virol 73: 709-17. (1999)). Increased proteolysis of PABPC1 may cause increased suppression by virus of host termination of protein biosynthetic process associated with poliomyelitis (J Virol 73: 718-27. (1999)). Viral exploitation of the PABPC1 protein may cause increased suppression by virus of host termination of protein biosynthetic process associated with poliomyelitis (J Virol 73: 718-27. (1999)). (PhosphoSite®, Cell Signaling Technology (Danvers, Mass.), Human PSD™, Biobase Corporation, (Beverly, Mass.)).

PDIA1, phosphorylated at K103, 375 and 444 is among the proteins listed in this patent. PDIA1, Prolyl 4-hydroxylase beta subunit, a subunit of prolyl 4-hydroxylase, which catalyzes hydroxylation of prolyl residues in preprocollagen, as a monomer functions as a protein disulfide isomerase, mediates protein folding and protein solubility. (PhosphoSite®, Cell Signaling Technology (Danvers, Mass.), Human PSD™, Biobase Corporation, (Beverly, Mass.)).

PDIA4, phosphorylated at K256 and K533, is among the proteins listed in this patent. PDIA4, Protein disulfide isomerase family A member 4, binds to and plays a role in the oxidative refolding of SERPINA1, acts in unfolded protein response, may act in protein processing, binds to beta-amyloid protein in sporadic inclusion body myositis. (PhosphoSite®, Cell Signaling Technology (Danvers, Mass.), Human PSD™, Biobase Corporation, (Beverly, Mass.)).

Pnk1, phosphorylated at K183, is among the proteins listed in this patent. Pnk1, Polynucleotide kinase 3′-phosphatase, has 5′-DNA kinase and 3′-phosphatase activities, and functions in the repair of DNA strand breaks due to oxidative damage. (PhosphoSite®, Cell Signaling Technology (Danvers, Mass.), Human PSD™, Biobase Corporation, (Beverly, Mass.)).

POLR2A, phosphorylated at K710, is among the proteins listed in this patent. This protein has potential diagnostic and/or therapeutic implications based on the following findings. Increased presence of POLR2A autoimmune antibody correlates with systemic scleroderma (J Immunol 167: 7126-33. (2001)). Increased expression of POLR2A in fibroblasts correlates with systemic scleroderma (J Immunol 167: 7126-33. (2001)). (PhosphoSite®, Cell Signaling Technology (Danvers, Mass.), Human PSD™, Biobase Corporation, (Beverly, Mass.)).

PPIA, phosphorylated at K125 and K144, is among the proteins listed in this patent. This protein has potential diagnostic and/or therapeutic implications based on the following findings. Increased expression of PPIA protein may cause increased viral infectious cycle associated with HIV infections (J Virol 72: 6430-6. (1998)). Increased protein binding of PPIA may cause increased viral genome replication associated with acquired immunodeficiency syndrome (J Virol 70: 3551-60 (1996)). Increased protein binding of PPIA correlates with HIV infections (Nature 372: 363-5. (1994)). Increased expression of PPIA in synovial fluid correlates with rheumatoid arthritis (J Exp Med 185: 975-80. (1997)). Increased cyclosporin A binding of PPIA may prevent increased viral assembly, maturation, egress, and release associated with HIV infections (J Gen Virol 78: 825-35 (1997)). Abnormal protein binding of PPIA may cause increased virion attachment to host cell surface receptor associated with acquired immunodeficiency syndrome (EMBO 18: 6771-85. (1999)). Abnormal protein binding of PPIA may cause increased virion attachment to host cell surface receptor associated with HIV infections (EMBO J 18: 6771-85. (1999)). Abnormal protein binding of PPIA may cause increased virion attachment to host cell surface receptor associated with HIV infections (EMBO 18: 6771-85. (1999)). Increased expression of PPIA protein may cause increased viral infectious cycle associated with HIV infections (EMBO J: 20: 1300-9. (2001)). Increased expression of PPIA protein correlates with non-small-cell lung carcinoma associated with lung neoplasms (Cancer Res 63: 1652-6. (2003)). Abnormal protein binding of PPIA may cause increased virion attachment to host cell surface receptor associated with acquired immunodeficiency syndrome (EMBO J 18: 6771-85. (1999)). Increased expression of PPIA protein may cause increased viral infectious cycle associated with HIV infections (EMBO J 20: 1300-9. (2001)). Abnormal protein binding of PPIA may cause increased virion attachment to host cell surface receptor associated with HIV infections (EMBO J. 18: 6771-85. (1999)). Increased expression of PPIA protein may cause increased viral infectious cycle associated with HIV infections (EMBO 20: 1300-9. (2001)). Abnormal protein binding of PPIA may cause increased virion attachment to host cell surface receptor associated with acquired immunodeficiency syndrome (EMBO J. 18: 6771-85. (1999)). (PhosphoSite®, Cell Signaling Technology (Danvers, Mass.), Human PSD™, Biobase Corporation, (Beverly, Mass.)).

PPIB, phosphorylated at K98, is among the proteins listed in this patent. PPIB, Peptidylprolyl isomerase B (cyclophilin B), binds to and is inhibited by the immunosuppressive drug cyclosporin A, functions in chemotaxis and T cell activation, may play a role in protein folding and host-derived replication of Hepatitis C virus. (PhosphoSite®, Cell Signaling Technology (Danvers, Mass.), Human PSD™, Biobase Corporation, (Beverly, Mass.)).

PRDX3, phosphorylated at K91, is among the proteins listed in this patent. This protein has potential diagnostic and/or therapeutic implications based on the following findings. Increased expression of PRDX3 protein correlates with breast neoplasms (Anticancer Res 21: 2085-90. (2001)). Increased expression of PRDX3 protein may cause abnormal cell redox homeostasis associated with hepatocellular carcinoma (Anticancer Res 22: 3331-5. (2002)). Increased expression of PRDX3 protein may cause increased cell proliferation associated with breast neoplasms (Anticancer Res 21: 2085-90. (2001)). Increased expression of PRDX3 protein correlates with hepatocellular carcinoma (Anticancer Res 22: 3331-5. (2002)). (PhosphoSite®, Cell Signaling Technology (Danvers, Mass.), Human PSD™, Biobase Corporation, (Beverly, Mass.)).

Ran, phosphorylated at K159 and K60, is among the proteins listed in this patent. Ran, Ras-related nuclear protein, a GTPase that acts in nucleocytoplasmic transport, binding to the polyglutamine tract in the androgen receptor may contribute to Kennedy disease, increased mRNA expression correlates with prostatic intraepithelial neoplasia. (PhosphoSite®, Cell Signaling Technology (Danvers, Mass.), Human PSD™, Biobase Corporation, (Beverly, Mass.)).

PSMA2, phosphorylated at K171, is among the proteins listed in this patent. This protein has potential diagnostic and/or therapeutic implications based on the following findings. Increased expression of PSMA2 in skeletal muscle may correlate with sepsis (J Clin Invest 99: 163-8. (1997)). (PhosphoSite®, Cell Signaling Technology (Danvers, Mass.), Human PSD™, Biobase Corporation, (Beverly, Mass.)).

RPN2, phosphorylated at K460, is among the proteins listed in this patent. This protein has potential diagnostic and/or therapeutic implications based on the following findings. Increased expression of RPN2 mRNA correlates with colorectal neoplasms (FEBS Lett 463: 77-82. (1999)). (PhosphoSite®, Cell Signaling Technology (Danvers, Mass.), Human PSD™, Biobase Corporation, (Beverly, Mass.)).

RSK2, phosphorylated at K81, is among the proteins listed in this patent. This protein has potential diagnostic and/or therapeutic implications based on the following findings. Splice site mutation in the RPS6KA3 gene causes multiple abnormalities associated with Coffin-Lowry syndrome (Am J Hum Genet. 63: 1631-40. (1998)). Nonsense mutation in the RPS6KA3 gene causes multiple abnormalities associated with Coffin-Lowry syndrome (Am J Hum Genet. 63: 1631-40. (1998)). Frameshift mutation in the RPS6KA3 gene causes multiple abnormalities associated with Coffin-Lowry syndrome (Am J Hum Genet. 63: 1631-40. (1998)). Missense mutation in the RPS6KA3 gene causes multiple abnormalities associated with Coffin-Lowry syndrome (Am J Hum Genet. 63: 1631-40. (1998)). Induced inhibition of the protein serine/threonine kinase activity of RPS6KA3 may prevent increased cell proliferation associated with prostatic neoplasms (Cancer Res 65: 3108-16 (2005)). Increased expression of RPS6KA3 protein correlates with prostatic neoplasms (Cancer Res 65: 3108-16 (2005)). (PhosphoSite®, Cell Signaling Technology (Danvers, Mass.), Human PSD™, Biobase Corporation, (Beverly, Mass.)).

Sam68, phosphorylated at K165, is among the proteins listed in this patent. This protein has potential diagnostic and/or therapeutic implications based on the following findings. Increased expression of KHDRBS1 protein may prevent increased cell proliferation associated with breast neoplasms (JBC 280: 38639-47 (2005)). Increased tyrosine phosphorylation of KHDRBS1 may correlate with increased cell proliferation associated with breast neoplasms (J Biol Chem 280: 38639-47 (2005)). Increased cytoplasm localization of KHDRBS1 may correlate with increased viral infectious cycle associated with poliomyelitis (Proc Natl Acad Sci USA 93: 2296-301. (1996)). Increased tyrosine phosphorylation of KHDRBS1 may correlate with increased protein amino acid phosphorylation associated with breast neoplasms (J Biol Chem 280: 38639-47 (2005)). Increased enzyme binding of KHDRBS1 may correlate with increased viral infectious cycle associated with poliomyelitis (Proc Natl Acad Sci USA 93: 2296-301. (1996)). Increased expression of KHDRBS1 protein may prevent increased cell proliferation associated with breast neoplasms (J Biol Chem 280: 38639-47 (2005)). Increased tyrosine phosphorylation of KHDRBS1 may correlate with increased cell proliferation associated with breast neoplasms (JBC 280: 38639-47 (2005)). Increased enzyme binding of KHDRBS1 may correlate with increased viral infectious cycle associated with poliomyelitis (PNAS 93: 2296-301. (1996)). Increased cytoplasm localization of KHDRBS1 may correlate with increased viral infectious cycle associated with poliomyelitis (Proc Natl Acad Sci USA 93: 2296-301. (1996)). Increased cytoplasm localization of KHDRBS1 may correlate with increased viral infectious cycle associated with poliomyelitis (PNAS 93: 2296-301. (1996)). Increased protein binding of KHDRBS1 may correlate with enterovirus infections (J Virol 73: 3587-94. (1999)). Increased enzyme binding of KHDRBS1 may correlate with increased viral infectious cycle associated with poliomyelitis (Proc Natl Acad Sci USA 93: 2296-301. (1996)). Increased tyrosine phosphorylation of KHDRBS1 may correlate with increased protein amino acid phosphorylation associated with breast neoplasms (JBC 280: 38639-47 (2005)). (PhosphoSite®, Cell Signaling Technology (Danvers, Mass.), Human PSD™, Biobase Corporation, (Beverly, Mass.)).

SMG1, phosphorylated at K173, is among the proteins listed in this patent. SMG1, PI-3-kinase-related kinase SMG-1, a serine kinase that phosphorylates proteins involved in DNA stress response pathways, activity is important for genomic maintenance and integrity. (PhosphoSite®, Cell Signaling Technology (Danvers, Mass.), Human PSD™, Biobase Corporation, (Beverly, Mass.)).

snRNP B1, phosphorylated at K32, is among the proteins listed in this patent. This protein has potential diagnostic and/or therapeutic implications based on the following findings. Increased expression of SNRPB mRNA may correlate with melanoma (Proc Natl Acad Sci USA 97: 12684-9 (2000)). Increased presence of SNRPB autoimmune antibody correlates with systemic lupus erythematosus (Clin Exp Immunol 92: 263-7. (1993)). Increased expression of SNRPB protein may prevent more severe form of Prader-Willi syndrome (Nucleic Acids Res 27: 4577-84 (1999)). Increased presence of SNRPB autoimmune antibody correlates with systemic lupus erythematosus (Biochem Biophys Res Commun 285: 1206-12. (2001)). Increased expression of SNRPB mRNA may correlate with melanoma (PNAS 97: 12684-9 (2000)). Increased expression of SNRPB mRNA may correlate with melanoma (Proc Natl Acad Sci USA 97: 12684-9 (2000)). Alternative form of SNRPB protein correlates with systemic lupus erythematosus (Biochem Biophys Res Commun 285: 1206-12. (2001)). (PhosphoSite®, Cell Signaling Technology (Danvers, Mass.), Human PSD™, Biobase Corporation, (Beverly, Mass.)).

SNRPN, phosphorylated at K32, is among the proteins listed in this patent. This protein has potential diagnostic and/or therapeutic implications based on the following findings. Deletion mutation in the SNRPN promoter causes Prader-Willi syndrome (Am J Hum Genet. 64: 397-413 (1999)). Autoimmune antibody to SNRPN correlates with systemic lupus erythematosus (Clin Exp Immunol 98: 419-26. (1994)). Mutation in the SNRPN gene causes Prader-Willi syndrome (Am J Hum Genet. 64: 70-6 (1999)). Lack of expression of SNRPN mRNA may cause Prader-Willi syndrome (Hum Mol Genet. 10: 201-10. (2001)). SNRPN map position correlates with Prader-Willi syndrome (Genome Res 7: 642-8. (1997)). Deletion mutation in the SNRPN locus causes Angelman syndrome (Am J Hum Genet. 68: 1290-4. (2001)). Loss of imprinting of the SNRPN gene may cause Prader-Willi syndrome (Hum Mol Genet. 2: 2001-5 (1993)). Deletion mutation in the SNRPN gene causes Angelman syndrome (Nat Genet. 26: 440-3 (2000)). Lack of expression of SNRPN mRNA may cause Prader-Willi syndrome (Nat Genet. 6: 163-7 (1994)). Lack of expression of SNRPN mRNA correlates with Prader-Willi syndrome (Nat Genet. 6: 163-7 (1994)). Imprinting of the SNRPN gene correlates with Rett syndrome (Hum Genet. 110: 545-52. (2002)). Deletion mutation in the SNRPN enhancer causes Angelman syndrome (Am J Hum Genet. 64: 385-96 (1999)). Translocation of the SNRPN locus correlates with Prader-Willi syndrome (Hum Mol Genet. 10: 201-10. (2001)). Deletion mutation in the SNRPN enhancer causes Prader-Willi syndrome (Am J Hum Genet. 64: 385-96 (1999)). Deletion mutation in the SNRPN gene causes Prader-Willi syndrome (Nat Genet. 26: 440-3 (2000)). Loss of imprinting of the SNRPN gene correlates with early onset form of germinoma (Cancer Res 61: 7268-76. (2001)). Hypomethylation of the SNRPN gene correlates with early onset form of germinoma (Cancer Res 61: 7268-76. (2001)). (PhosphoSite®, Cell Signaling Technology (Danvers, Mass.), Human PSD™, Biobase Corporation, (Beverly, Mass.)).

TPI1, phosphorylated at K238, is among the proteins listed in this patent. This protein has potential diagnostic and/or therapeutic implications based on the following findings. Increased expression of TPI1 protein may prevent nervous system diseases associated with congenital nonspherocytic hemolytic anemia (Blood 94: 3193-8. (1999)). Missense mutation in the TPI1 gene correlates with nervous system diseases associated with congenital nonspherocytic hemolytic anemia (Proc Natl Acad Sci USA 97: 1026-31. (2000)). Missense mutation in the TPI1 protein may cause inborn errors of amino acid metabolism (PNAS 97: 1026-31. (2000)). Missense mutation in the TPI1 protein may cause inborn errors of amino acid metabolism (Proc Natl Acad Sci USA 97: 1026-31. (2000)). Nonsense mutation in the TPI1 protein may cause inborn errors of amino acid metabolism (Proc Natl Acad Sci USA 97: 1026-31. (2000)). Nonsense mutation in the TPI1 gene correlates with nervous system diseases associated with congenital nonspherocytic hemolytic anemia (Proc Natl Acad Sci USA 97: 1026-31. (2000)). Nonsense mutation in the TPI1 protein may cause inborn errors of amino acid metabolism (PNAS 97: 1026-31. (2000)). Missense mutation in the TPI1 gene may correlate with abnormal T cell activation associated with melanoma (J Exp Med 189: 757-66. (1999)). Missense mutation in the TPI1 gene correlates with nervous system diseases associated with congenital nonspherocytic hemolytic anemia (Proc Natl Acad Sci USA 97: 1026-31. (2000)). Missense mutation in the TPI1 gene correlates with nervous system diseases associated with congenital nonspherocytic hemolytic anemia (PNAS 97: 1026-31. (2000)). Missense mutation in the TPI1 protein may cause inborn errors of amino acid metabolism (Proc Natl Acad Sci USA 97: 1026-31. (2000)). Nonsense mutation in the TPI1 gene correlates with nervous system diseases associated with congenital nonspherocytic hemolytic anemia (PNAS 97: 1026-31. (2000)). Nonsense mutation in the TPI1 protein may cause inborn errors of amino acid metabolism (Proc Natl Acad Sci USA 97: 1026-31. (2000)). Lack of expression of TPI1 protein may cause abnormal protein modification associated with inborn errors of metabolism (Biochim Biophys Acta 1639: 121-32 (2003)). Nonsense mutation in the TPI1 gene correlates with nervous system diseases associated with congenital nonspherocytic hemolytic anemia (Proc Natl Acad Sci USA 97: 1026-31. (2000)). Increased presence of TPI1 autoimmune antibody correlates with central nervous system lupus vasculitis (Biochem Biophys Res Commun 321: 949-53 (2004)). (PhosphoSite®, Cell Signaling Technology (Danvers, Mass.), Human PSD™, Biobase Corporation, (Beverly, Mass.)).

VDAC-3, phosphorylated at K63, is among the proteins listed in this patent. VDAC-3, Voltage-dependent anion channel 3, may function as a voltage-gated pore of the outer mitochondrial membrane that binds hexokinase and glycerol kinase and transports adenine nucleotides; mouse Vdac3 is downregulated in the mdx muscular dystrophy mouse. (PhosphoSite®, Cell Signaling Technology (Danvers, Mass.), Human PSD™, Biobase Corporation, (Beverly, Mass.)).

The invention also provides peptides comprising a novel acetylation site of the invention. In one particular embodiment, the peptides comprise any one of the an amino acid sequences as set forth in column E of Table 1 and FIG. 2, which are trypsin-digested peptide fragments of the parent proteins. Alternatively, a parent signaling protein listed in Table 1 may be digested with another protease, and the sequence of a peptide fragment comprising a acetylation site can be obtained in a similar way. Suitable proteases include, but are not limited to, serine proteases (e.g. hepsin), metallo proteases (e.g. PUMP1), chymotrypsin, cathepsin, pepsin, thermolysin, carboxypeptidases, etc.

The invention also provides proteins and peptides that are mutated to eliminate a novel acetylation site of the invention. Such proteins and peptides are particular useful as research tools to understand complex signaling transduction pathways of cancer cells, for example, to identify new upstream acetylase(s) or deacetylase(s) or other proteins that regulates the activity of a signaling protein; to identify downstream effector molecules that interact with a signaling protein, etc.

Various methods that are well known in the art can be used to eliminate a acetylation site. For example, the acetylatable lysine may be mutated into a non-acetylatable residue, such as glutamine. An “acetylatable” amino acid refers to an amino acid that is capable of being modified by addition of a and acetyl group (any includes both acetylated form and unacetylated form). Alternatively, the lysine may be deleted. Residues other than the lysine may also be modified (e.g., delete or mutated) if such modification inhibits the acetylation of the lysine residue. For example, residues flanking the lysine may be deleted or mutated, so that an acetylase can not recognize/acetylate the mutated protein or the peptide. Standard mutagenesis and molecular cloning techniques can be used to create amino acid substitutions or deletions.

2. Modulators of the Acetylation Sites

In another aspect, the invention provides a modulator that modulates lysine acetylation at a novel acetylation site of the invention, including small molecules, peptides comprising a novel acetylation site, and binding molecules that specifically bind at a novel acetylation site, including but not limited to antibodies or antigen-binding fragments thereof.

Modulators of an acetylation site include any molecules that directly or indirectly counteract, reduce, antagonize or inhibit lysine acetylation of the site. The modulators may compete or block the binding of the acetylation site to its upstream acetylase(s) or deacetylase(s), or to its downstream signaling transduction molecule(s).

The modulators may directly interact with an acetylation site. The modulator may also be a molecule that does not directly interact with an acetylation site. For example, the modulators can be dominant negative mutants, i.e., proteins and peptides that are mutated to eliminate the acetylation site. Such mutated proteins or peptides could retain the binding ability to a downstream signaling molecule but lose the ability to trigger downstream signaling transduction of the wild type parent signaling protein.

The modulators include small molecules that modulate the lysine acetylation at a novel acetylation site of the invention. Chemical agents, referred to in the art as “small molecule” compounds are typically organic, non-peptide molecules, having a molecular weight less than 10,000, less than 5,000, less than 1,000, or less than 500 daltons. This class of modulators includes chemically synthesized molecules, for instance, compounds from combinatorial chemical libraries. Synthetic compounds may be rationally designed or identified based on known or inferred properties of an acetylation site of the invention or may be identified by screening compound libraries. Alternative appropriate modulators of this class are natural products, particularly secondary metabolites from organisms such as plants or fungi, which can also be identified by screening compound libraries. Methods for generating and obtaining compounds are well known in the art (Schreiber S L, Science 151: 1964-1969 (2000); Radmann J. and Gunther J., Science 151: 1947-1948 (2000)).

The modulators also include peptidomimetics, small protein-like chains designed to mimic peptides. Peptidomimetics may be analogues of a peptide comprising a acetylation site of the invention. Peptidomimetics may also be analogues of a modified peptide that are mutated to eliminate an acetylation site of the invention. Peptidomimetics (both peptide and non-peptidyl analogues) may have improved properties (e.g., decreased proteolysis, increased retention or increased bioavailability). Peptidomimetics generally have improved oral availability, which makes them especially suited to treatment of disorders in a human or animal.

In certain embodiments, the modulators are peptides comprising a novel acetylation site of the invention. In certain embodiments, the modulators are antibodies or antigen-binding fragments thereof that specifically bind at a novel acetylation site of the invention.

3. Heavy-Isotope Labeled Peptides (AQUA Peptides).

In another aspect, the invention provides peptides comprising a novel acetylation site of the invention. In a particular embodiment, the invention provides Heavy-Isotype Labeled Peptides (AQUA peptides) comprising a novel acetylation site. Such peptides are useful to generate acetylation site-specific antibodies for a novel acetylation site. Such peptides are also useful as potential diagnostic tools for screening different types of cancer including carcinoma, or as potential therapeutic agents for treating cancer including carcinoma.

The peptides may be of any length, typically six to fifteen amino acids. The novel lysine acetylation site can occur at any position in the peptide; if the peptide will be used as an immunogen, it preferably is from seven to twenty amino acids in length. In some embodiments, the peptide is labeled with a detectable marker.

“Heavy-isotope labeled peptide” (used interchangeably with AQUA peptide) refers to a peptide comprising at least one heavy-isotope label, as described in WO/03016861, “Absolute Quantification of Proteins and Modified Forms Thereof by Multistage Mass Spectrometry” (Gygi et al.) (the teachings of which are hereby incorporated herein by reference, in their entirety). The amino acid sequence of an AQUA peptide is identical to the sequence of a proteolytic fragment of the parent protein in which the novel acetylation site occurs. AQUA peptides of the invention are highly useful for detecting, quantitating or modulating an acetylation site of the invention (both in acetylated and unacetylated forms) in a biological sample.

A peptide of the invention, including an AQUA peptides comprises any novel acetylation site. Preferably, the peptide or AQUA peptide comprises a novel acetylation site of a protein in Table 1 that is an enzyme protein, cytoskeletal protein, transcriptional regulator, RNA binding protein, chaperone protein, chormatin or DNA binding/repair/replication protein, protease, receptor/channel/transporter/cell surface protein or mitochondrial protein.

Particularly preferred peptides and AQUA peptides are these comprising a novel lysine acetylation site (shown as a lower case “k” in a sequence listed in Table 1) selected from the group consisting of SEQ ID NOs: 125 (ACAT1); 137 (ENO1); 143 (GCLC); 162 (MDH2); 169 (NKEF-A); 173 (PDIA1); 188 (TOP1); 189 (TPI1); 79 (alpha 1); 81 (gamma 1); 117 (beta-2); 119 (WDR1); 312 (MBD1); 317 (NF-GMB); 319 (PA2G4); 323 (SMARCA2); 324 (SMARCA2); 334 (TB-1); 253 (BAT1); 273 (PABP1); 43 (HSC70); 45 (HSC70); 51 (HSP90B); 52 (HSPA5); 53 (HSPA5); 56 (HSPA5); 61 (PPIB); 62 (PPIB); 63 (PPIB); 73 (RPA1); 22 (p400); 223 (PSMC6); 224 (PSMC6); 227 (TPB7); 246 (KPNB3); 203 (DLD); 194 (Ran); 195 (Ran); 339 (eEF1A-1); and 340 (eEF1A-1).

In some embodiments, the peptide or AQUA peptide comprises the amino acid sequence shown in any one of the above listed SEQ ID NOs. In some embodiments, the peptide or AQUA peptide consists of the amino acid sequence in said SEQ ID NOs. In some embodiments, the peptide or AQUA peptide comprises a fragment of the amino acid sequence in said SEQ ID NOs., wherein the fragment is six to twenty amino acid long and includes the acetylatable lysine. In some embodiments, the peptide or AQUA peptide consists of a fragment of the amino acid sequence in said SEQ ID NOs., wherein the fragment is six to twenty amino acid long and includes the acetylatable lysine.

In certain embodiments, the peptide or AQUA peptide comprises any one of the SEQ ID NOs listed in column H, which are trypsin-digested peptide fragments of the parent proteins.

It is understood that parent protein listed in Table 1 may be digested with any suitable protease (e.g., serine proteases (e.g. trypsin, hepsin), metallo proteases (e.g. PUMP1), chymotrypsin, cathepsin, pepsin, thermolysin, carboxypeptidases, etc), and the resulting peptide sequence comprising a acetylated site of the invention may differ from that of trypsin-digested fragments (as set forth in Column E), depending the cleavage site of a particular enzyme. An AQUA peptide for a particular a parent protein sequence should be chosen based on the amino acid sequence of the parent protein and the particular protease for digestion; that is, the AQUA peptide should match the amino acid sequence of a proteolytic fragment of the parent protein in which the novel acetylation site occurs.

An AQUA peptide is preferably at least about 6 amino acids long. The preferred ranged is about 7 to 15 amino acids.

The AQUA method detects and quantifies a target protein in a sample by introducing a known quantity of at least one heavy-isotope labeled peptide standard (which has a unique signature detectable by LC-SRM chromatography) into a digested biological sample. By comparing to the peptide standard, one may readily determines the quantity of a peptide having the same sequence and protein modification(s) in the biological sample. Briefly, the AQUA methodology has two stages: (1) peptide internal standard selection and validation; method development; and (2) implementation using validated peptide internal standards to detect and quantify a target protein in a sample. The method is a powerful technique for detecting and quantifying a given peptide/protein within a complex biological mixture, such as a cell lysate, and may be used, e.g., to quantify change in protein acetylation as a result of drug treatment, or to quantify a protein in different biological states.

Generally, to develop a suitable internal standard, a particular peptide (or modified peptide) within a target protein sequence is chosen based on its amino acid sequence and a particular protease for digestion. The peptide is then generated by solid-phase peptide synthesis such that one residue is replaced with that same residue containing stable isotopes (¹³C, ¹⁵N). The result is a peptide that is chemically identical to its native counterpart formed by proteolysis, but is easily distinguishable by MS via a mass shift. A newly synthesized AQUA internal standard peptide is then evaluated by LC-MS/MS. This process provides qualitative information about peptide retention by reverse-phase chromatography, ionization efficiency, and fragmentation via collision-induced dissociation. Informative and abundant fragment ions for sets of native and internal standard peptides are chosen and then specifically monitored in rapid succession as a function of chromatographic retention to form a selected reaction monitoring (LC-SRM) method based on the unique profile of the peptide standard.

The second stage of the AQUA strategy is its implementation to measure the amount of a protein or the modified form of the protein from complex mixtures. Whole cell lysates are typically fractionated by SDS-PAGE gel electrophoresis, and regions of the gel consistent with protein migration are excised. This process is followed by in-gel proteolysis in the presence of the AQUA peptides and LC-SRM analysis. (See Gerber et al. supra.) AQUA peptides are spiked in to the complex peptide mixture obtained by digestion of the whole cell lysate with a proteolytic enzyme and subjected to immunoaffinity purification as described above. The retention time and fragmentation pattern of the native peptide formed by digestion (e.g., trypsinization) is identical to that of the AQUA internal standard peptide determined previously; thus, LC-MS/MS analysis using an SRM experiment results in the highly specific and sensitive measurement of both internal standard and analyte directly from extremely complex peptide mixtures. Because an absolute amount of the AQUA peptide is added (e.g. 250 fmol), the ratio of the areas under the curve can be used to determine the precise expression levels of a protein or acetylated form of a protein in the original cell lysate. In addition, the internal standard is present during in-gel digestion as native peptides are formed, such that peptide extraction efficiency from gel pieces, absolute losses during sample handling (including vacuum centrifugation), and variability during introduction into the LC-MS system do not affect the determined ratio of native and AQUA peptide abundances.

An AQUA peptide standard may be developed for a known acetylation site previously identified by the IAP-LC-MS/MS method within a target protein. One AQUA peptide incorporating the acetylated form of the site, and a second AQUA peptide incorporating the unacetylated form of site may be developed. In this way, the two standards may be used to detect and quantify both the acetylated and unacetylated forms of the site in a biological sample.

Peptide internal standards may also be generated by examining the primary amino acid sequence of a protein and determining the boundaries of peptides produced by protease cleavage. Alternatively, a protein may actually be digested with a protease and a particular peptide fragment produced can then sequenced. Suitable proteases include, but are not limited to, serine proteases (e.g. trypsin, hepsin), metallo proteases (e.g. PUMP1), chymotrypsin, cathepsin, pepsin, thermolysin, carboxypeptidases, etc.

A peptide sequence within a target protein is selected according to one or more criteria to optimize the use of the peptide as an internal standard. Preferably, the size of the peptide is selected to minimize the chances that the peptide sequence will be repeated elsewhere in other non-target proteins. Thus, a peptide is preferably at least about 6 amino acids. The size of the peptide is also optimized to maximize ionization frequency. Thus, peptides longer than about 20 amino acids are not preferred. The preferred ranged is about 7 to 15 amino acids. A peptide sequence is also selected that is not likely to be chemically reactive during mass spectrometry, thus sequences comprising cysteine, tryptophan, or methionine are avoided.

A peptide sequence that is outside a acetylation site may be selected as internal standard to determine the quantity of all forms of the target protein. Alternatively, a peptide encompassing an acetylated site may be selected as internal standard to detect and quantify only the acetylated form of the target protein. Peptide standards for both acetylated form and unacetylated form can be used together, to determine the extent of acetylation in a particular sample.

The peptide is labeled using one or more labeled amino acids (i.e. the label is an actual part of the peptide) or less preferably, labels may be attached after synthesis according to standard methods. Preferably, the label is a mass-altering label selected based on the following considerations: The mass should be unique to shift fragment masses produced by MS analysis to regions of the spectrum with low background; the ion mass signature component is the portion of the labeling moiety that preferably exhibits a unique ion mass signature in MS analysis; the sum of the masses of the constituent atoms of the label is preferably uniquely different than the fragments of all the possible amino acids. As a result, the labeled amino acids and peptides are readily distinguished from unlabeled ones by the ion/mass pattern in the resulting mass spectrum. Preferably, the ion mass signature component imparts a mass to a protein fragment that does not match the residue mass for any of the 20 natural amino acids.

The label should be robust under the fragmentation conditions of MS and not undergo unfavorable fragmentation. Labeling chemistry should be efficient under a range of conditions, particularly denaturing conditions, and the labeled tag preferably remains soluble in the MS buffer system of choice. The label preferably does not suppress the ionization efficiency of the protein and is not chemically reactive. The label may contain a mixture of two or more isotopically distinct species to generate a unique mass spectrometric pattern at each labeled fragment position. Stable isotopes, such as ¹³C, ¹⁵N, ¹⁷O, ¹⁸O, or ³⁴S, are among preferred labels. Pairs of peptide internal standards that incorporate a different isotope label may also be prepared. Preferred amino acid residues into which a heavy isotope label may be incorporated include leucine, proline, valine, and phenylalanine.

Peptide internal standards are characterized according to their mass-to-charge (m/z) ratio, and preferably, also according to their retention time on a chromatographic column (e.g. an HPLC column). Internal standards that co-elute with unlabeled peptides of identical sequence are selected as optimal internal standards. The internal standard is then analyzed by fragmenting the peptide by any suitable means, for example by collision-induced dissociation (CID) using, e.g., argon or helium as a collision gas. The fragments are then analyzed, for example by multi-stage mass spectrometry (MSⁿ) to obtain a fragment ion spectrum, to obtain a peptide fragmentation signature. Preferably, peptide fragments have significant differences in m/z ratios to enable peaks corresponding to each fragment to be well separated, and a signature that is unique for the target peptide is obtained. If a suitable fragment signature is not obtained at the first stage, additional stages of MS are performed until a unique signature is obtained.

Fragment ions in the MS/MS and MS³spectra are typically highly specific for the peptide of interest, and, in conjunction with LC methods, allow a highly selective means of detecting and quantifying a target peptide/protein in a complex protein mixture, such as a cell lysate, containing many thousands or tens of thousands of proteins. Any biological sample potentially containing a target protein/peptide of interest may be assayed. Crude or partially purified cell extracts are preferably used. Generally, the sample has at least 0.01 mg of protein, typically a concentration of 0.1-10 mg/mL, and may be adjusted to a desired buffer concentration and pH.

A known amount of a labeled peptide internal standard, preferably about 10 femtomoles, corresponding to a target protein to be detected/quantified is then added to a biological sample, such as a cell lysate. The spiked sample is then digested with one or more protease(s) for a suitable time period to allow digestion. A separation is then performed (e.g., by HPLC, reverse-phase HPLC, capillary electrophoresis, ion exchange chromatography, etc.) to isolate the labeled internal standard and its corresponding target peptide from other peptides in the sample. Microcapillary LC is a preferred method.

Each isolated peptide is then examined by monitoring of a selected reaction in the MS. This involves using the prior knowledge gained by the characterization of the peptide internal standard and then requiring the MS to continuously monitor a specific ion in the MS/MS or MSⁿspectrum for both the peptide of interest and the internal standard. After elution, the area under the curve (AUC) for both peptide standard and target peptide peaks are calculated. The ratio of the two areas provides the absolute quantification that can be normalized for the number of cells used in the analysis and the protein's molecular weight, to provide the precise number of copies of the protein per cell. Further details of the AQUA methodology are described in Gygi et al., and Gerber et al. supra.

Accordingly, AQUA internal peptide standards (heavy-isotope labeled peptides) may be produced, as described above, for any of the 332 novel acetylation sites of the invention (see Table 1/FIG. 2). For example, peptide standards for a given acetylation site (e.g., an AQUA peptide having the sequence zyxin (SEQ ID NO: 19), wherein “k” corresponds to acetylatable lysine 528 of zyxin) may be produced for both the acetylated and unacetylated forms of the sequence. Such standards may be used to detect and quantify both acetylated form and unacetylated form of the parent signaling protein (e.g., zyxin) in a biological sample.

Heavy-isotope labeled equivalents of a acetylation site of the invention, both in acetylated and unacetylated form, can be readily synthesized and their unique MS and LC-SRM signature determined, so that the peptides are validated as AQUA peptides and ready for use in quantification.

The novel acetylation sites of the invention are particularly well suited for development of corresponding AQUA peptides, since the IAP method by which they were identified (see Part A above and Example 1) inherently confirmed that such peptides are in fact produced by enzymatic digestion (e.g., trypsinization) and are in fact suitably fractionated/ionized in MS/MS. Thus, heavy-isotope labeled equivalents of these peptides (both in acetylated and unacetylated form) can be readily synthesized and their unique MS and LC-SRM signature determined, so that the peptides are validated as AQUA peptides and ready for use in quantification experiments.

Accordingly, the invention provides heavy-isotope labeled peptides (AQUA peptides) that may be used for detecting, quantitating, or modulating any of the acetylation sites of the invention (Table 1). For example, an AQUA peptide having the sequence GAVEkGEELSCEER (SEQ ID NO: 4), wherein k (Lys 32) may be either acetyl-lysine or lysine, and wherein V=labeled valine (e.g., ¹⁴C)) is provided for the quantification of acetylated (or unacetylated) form of 14-3-3 sigma (an adaptor/scaffold protein) in a biological sample.

Example 4 is provided to further illustrate the construction and use, by standard methods described above, of exemplary AQUA peptides provided by the invention. For example, AQUA peptides corresponding to both the acetylated and unacetylated forms of SEQ ID NO: 4 (a trypsin-digested fragment of 14-3-3 sigma, with a lysine 32 acetylation site) may be used to quantify the amount of acetylated 14-3-3 sigma in a biological sample, e.g., a tumor cell sample or a sample before or after treatment with a therapeutic agent.

Peptides and AQUA peptides provided by the invention will be highly useful in the further study of signal transduction anomalies underlying cancer, including carcinomas. Peptides and AQUA peptides of the invention may also be used for identifying diagnostic/bio-markers of carcinomas, identifying new potential drug targets, and/or monitoring the effects of test therapeutic agents on signaling proteins and pathways.

4. Acetylation Site-Specific Antibodies

In another aspect, the invention discloses acetylation site-specific binding molecules that specifically bind at a novel lysine acetylation site of the invention, and that distinguish between the acetylated and unacetylated forms. In one embodiment, the binding molecule is an antibody or an antigen-binding fragment thereof. The antibody may specifically bind to an amino acid sequence comprising a acetylation site identified in Table 1.

In some embodiments, the antibody or antigen-binding fragment thereof specifically binds the acetylated site. In other embodiments, the antibody or antigen-binding fragment thereof specially binds the unacetylated site. An antibody or antigen-binding fragment thereof specially binds an amino acid sequence comprising a novel lysine acetylation site in Table 1 when it does not significantly bind any other site in the parent protein and does not significantly bind a protein other than the parent protein. An antibody of the invention is sometimes referred to herein as an “acetyl-lysine specific” antibody.

An antibody or antigen-binding fragment thereof specially binds an antigen when the dissociation constant is ≦1 mM, preferably ≦100 nM, and more preferably ≦10 nM.

In some embodiments, the antibody or antigen-binding fragment of the invention binds an amino acid sequence that comprises a novel acetylation site of a protein in Table 1 that is a an enzyme protein, cytoskeletal protein, transcriptional regulator, RNA binding protein, chaperone protein, chormatin or DNA binding/repair/replication protein, protease, receptor/channel/transporter/cell surface protein or mitochondrial protein.

In particularly preferred embodiments, an antibody or antigen-binding fragment thereof of the invention specially binds an amino acid sequence comprising a novel lysine acetylation site shown as a lower case “k” in a sequence listed in Table 1 selected from the group consisting of SEQ ID NOS: 125 (ACAT1); 137 (ENO1); 143 (GCLC); 162 (MDH2); 169 (NKEF-A); 173 (PDIA1); 188 (TOP1); 189 (TPI1); 79 (alpha 1); 81 (gamma 1); 117 (beta-2); 119 (WDR1); 312 (MBD1); 317 (NF-GMB); 319 (PA2G4); 323 (SMARCA2); 324 (SMARCA2); 334 (TB-1); 253 (BAT1); 273 (PABP1); 43 (HSC70); 45 (HSC70); 51 (HSP90B); 52 (HSPA5); 53 (HSPA5); 56 (HSPA5); 61 (PPIB); 62 (PPIB); 63 (PPIB); 73 (RPA1); 22 (p400); 223 (PSMC6); 224 (PSMC6); 227 (TPB7); 246 (KPNB3); 203 (DLD); 194 (Ran); 195 (Ran); 339 (eEF1A-1); and 340 (eEF1A-1).

In some embodiments, an antibody or antigen-binding fragment thereof of the invention specifically binds an amino acid sequence comprising any one of the above listed SEQ ID NOs. In some embodiments, an antibody or antigen-binding fragment thereof of the invention especially binds an amino acid sequence comprises a fragment of one of said SEQ ID NOs., wherein the fragment is four to twenty amino acid long and includes the acetylatable lysine.

In certain embodiments, an antibody or antigen-binding fragment thereof of the invention specially binds an amino acid sequence that comprises a peptide produced by proteolysis of the parent protein with a protease wherein said peptide comprises a novel lysine acetylation site of the invention. In some embodiments, the peptides are produced from trypsin digestion of the parent protein. The parent protein comprising the novel lysine acetylation site can be from any species, preferably from a mammal including but not limited to non-human primates, rabbits, mice, rats, goats, cows, sheep, and guinea pigs. In some embodiments, the parent protein is a human protein and the antibody binds an epitope comprising the novel lysine acetylation site shown by a lower case “k” in Column E of Table 1. Such peptides include any one of the SEQ ID NOs.

An antibody of the invention can be an intact, four immunoglobulin chain antibody comprising two heavy chains and two light chains. The heavy chain of the antibody can be of any isotype including IgM, IgG, IgE, IgG, IgA or IgD or sub-isotype including IgG1, IgG2, IgG3, IgG4, IgE2, IgE2, etc. The light chain can be a kappa light chain or a lambda light chain.

Also within the invention are antibody molecules with fewer than 4 chains, including single chain antibodies, Camelid antibodies and the like and components of the antibody, including a heavy chain or a light chain. The term “antibody” (or “antibodies”) refers to all types of immunoglobulins. The term “an antigen-binding fragment of an antibody” refers to any portion of an antibody that retains specific binding of the intact antibody. An exemplary antigen-binding fragment of an antibody is the heavy chain and/or light chain CDR, or the heavy and/or light chain variable region. The term “does not bind,” when appeared in context of an antibody's binding to one acetyl-form (e.g., acetylated form) of a sequence, means that the antibody does not substantially react with the other acetyl-form (e.g., non-acetylated form) of the same sequence. One of skill in the art will appreciate that the expression may be applicable in those instances when (1) an acetyl-specific antibody either does not apparently bind to the non-phospho form of the antigen as ascertained in commonly used experimental detection systems (Western blotting, IHC, Immunofluorescence, etc.); (2) where there is some reactivity with the surrounding amino acid sequence, but that the acetylated residue is an immunodominant feature of the reaction. In cases such as these, there is an apparent difference in affinities for the two sequences. Dilutional analyses of such antibodies indicates that the antibodies apparent affinity for the acetylated form is at least 10-100 fold higher than for the non-acetylated form; or where (3) the acetyl-specific antibody reacts no more than an appropriate control antibody would react under identical experimental conditions. A control antibody preparation might be, for instance, purified immunoglobulin from a pre-immune animal of the same species, an isotype- and species-matched monoclonal antibody. Tests using control antibodies to demonstrate specificity are recognized by one of skill in the art as appropriate and definitive.

In some embodiments an immunoglobulin chain may comprise in order from 5′ to 3′, a variable region and a constant region. The variable region may comprise three complementarity determining regions (CDRs), with interspersed framework (FR) regions for a structure FR1, CDR1, FR2, CDR2, FR3, CDR3 and FR4. Also within the invention are heavy or light chain variable regions, framework regions and CDRs. An antibody of the invention may comprise a heavy chain constant region that comprises some or all of a CH1 region, hinge, CH2 and CH3 region.

An antibody of the invention may have an binding affinity (K_D) of 1×10⁻⁷M or less. In other embodiments, the antibody binds with a K_Dof 1×10⁻⁸M, 1×10⁻⁹M, 1×10⁻¹⁰M, 1×10⁻¹¹M, 1×10⁻¹²M or less. In certain embodiments, the K_Dis 1 pM to 500 pM, between 500 pM to 1 μM, between 1 μM to 100 nM, or between 100 mM to 10 nM.

Antibodies of the invention can be derived from any species of animal, preferably a mammal. Non-limiting exemplary natural antibodies include antibodies derived from human, chicken, goats, and rodents (e.g., rats, mice, hamsters and rabbits), including transgenic rodents genetically engineered to produce human antibodies (see, e.g., Lonberg et al., WO93/12227; U.S. Pat. No. 5,545,806; and Kucherlapati, et al., WO91/10741; U.S. Pat. No. 6,150,584, which are herein incorporated by reference in their entirety). Natural antibodies are the antibodies produced by a host animal. “Genetically altered antibodies” refer to antibodies wherein the amino acid sequence has been varied from that of a native antibody. Because of the relevance of recombinant DNA techniques to this application, one need not be confined to the sequences of amino acids found in natural antibodies; antibodies can be redesigned to obtain desired characteristics. The possible variations are many and range from the changing of just one or a few amino acids to the complete redesign of, for example, the variable or constant region. Changes in the constant region will, in general, be made in order to improve or alter characteristics, such as complement fixation, interaction with membranes and other effector functions. Changes in the variable region will be made in order to improve the antigen binding characteristics.

The antibodies of the invention include antibodies of any isotype including IgM, IgG, IgD, IgA and IgE, and any sub-isotype, including IgG1, IgG2a, IgG2b, IgG3 and IgG4, IgE1, IgE2 etc. The light chains of the antibodies can either be kappa light chains or lambda light chains.

Antibodies disclosed in the invention may be polyclonal or monoclonal. As used herein, the term “epitope” refers to the smallest portion of a protein capable of selectively binding to the antigen binding site of an antibody. It is well accepted by those skilled in the art that the minimal size of a protein epitope capable of selectively binding to the antigen binding site of an antibody is about five or six to seven amino acids.

Other antibodies specifically contemplated are oligoclonal antibodies. As used herein, the phrase “oligoclonal antibodies” refers to a predetermined mixture of distinct monoclonal antibodies. See, e.g., PCT publication WO 95/20401; U.S. Pat. Nos. 5,789,208 and 6,335,163. In one embodiment, oligoclonal antibodies consisting of a predetermined mixture of antibodies against one or more epitopes are generated in a single cell. In other embodiments, oligoclonal antibodies comprise a plurality of heavy chains capable of pairing with a common light chain to generate antibodies with multiple specificities (e.g., PCT publication WO 04/009618). Oligoclonal antibodies are particularly useful when it is desired to target multiple epitopes on a single target molecule. In view of the assays and epitopes disclosed herein, those skilled in the art can generate or select antibodies or mixtures of antibodies that are applicable for an intended purpose and desired need.

Recombinant antibodies against the acetylation sites identified in the invention are also included in the present application. These recombinant antibodies have the same amino acid sequence as the natural antibodies or have altered amino acid sequences of the natural antibodies in the present application. They can be made in any expression systems including both prokaryotic and eukaryotic expression systems or using phage display methods (see, e.g., Dower et al., WO91/17271 and McCafferty et al., WO92/01047; U.S. Pat. No. 5,969,108, which are herein incorporated by reference in their entirety).

Antibodies can be engineered in numerous ways. They can be made as single-chain antibodies (including small modular immunopharmaceuticals or SMIPs™), Fab and F(ab′)₂fragments, etc. Antibodies can be humanized, chimerized, deimmunized, or fully human. Numerous publications set forth the many types of antibodies and the methods of engineering such antibodies. For example, see U.S. Pat. Nos. 6,355,245; 6,180,370; 5,693,762; 6,407,213; 6,548,640; 5,565,332; 5,225,539; 6,103,889; and 5,260,203.

The genetically altered antibodies should be functionally equivalent to the above-mentioned natural antibodies. In certain embodiments, modified antibodies provide improved stability or/and therapeutic efficacy. Examples of modified antibodies include those with conservative substitutions of amino acid residues, and one or more deletions or additions of amino acids that do not significantly deleteriously alter the antigen binding utility. Substitutions can range from changing or modifying one or more amino acid residues to complete redesign of a region as long as the therapeutic utility is maintained. Antibodies of this application can be modified post-translationally (e.g., phosphorylation, and/or acetylation) or can be modified synthetically (e.g., the attachment of a labeling group).

Antibodies with engineered or variant constant or Fc regions can be useful in modulating effector functions, such as, for example, antigen-dependent cytotoxicity (ADCC) and complement-dependent cytotoxicity (CDC). Such antibodies with engineered or variant constant or Fc regions may be useful in instances where a parent singling protein (Table 1) is expressed in normal tissue; variant antibodies without effector function in these instances may elicit the desired therapeutic response while not damaging normal tissue. Accordingly, certain aspects and methods of the present disclosure relate to antibodies with altered effector functions that comprise one or more amino acid substitutions, insertions, and/or deletions.

In certain embodiments, genetically altered antibodies are chimeric antibodies and humanized antibodies.

The chimeric antibody is an antibody having portions derived from different antibodies. For example, a chimeric antibody may have a variable region and a constant region derived from two different antibodies. The donor antibodies may be from different species. In certain embodiments, the variable region of a chimeric antibody is non-human, e.g., murine, and the constant region is human.

The genetically altered antibodies used in the invention include CDR grafted humanized antibodies. In one embodiment, the humanized antibody comprises heavy and/or light chain CDRs of a non-human donor immunoglobulin and heavy chain and light chain frameworks and constant regions of a human acceptor immunoglobulin. The method of making humanized antibody is disclosed in U.S. Pat. Nos. 5,530,101; 5,585,089; 5,693,761; 5,693,762; and 6,180,370 each of which is incorporated herein by reference in its entirety.

Antigen-binding fragments of the antibodies of the invention, which retain the binding specificity of the intact antibody, are also included in the invention. Examples of these antigen-binding fragments include, but are not limited to, partial or full heavy chains or light chains, variable regions, or CDR regions of any acetylation site-specific antibodies described herein.

In one embodiment of the application, the antibody fragments are truncated chains (truncated at the carboxyl end). In certain embodiments, these truncated chains possess one or more immunoglobulin activities (e.g., complement fixation activity). Examples of truncated chains include, but are not limited to, Fab fragments (consisting of the VL, VH, CL and CH1 domains); Fd fragments (consisting of the VH and CH1 domains); Fv fragments (consisting of VL and VH domains of a single chain of an antibody); dAb fragments (consisting of a VH domain); isolated CDR regions; (Fab′)₂fragments, bivalent fragments (comprising two Fab fragments linked by a disulphide bridge at the hinge region). The truncated chains can be produced by conventional biochemical techniques, such as enzyme cleavage, or recombinant DNA techniques, each of which is known in the art. These polypeptide fragments may be produced by proteolytic cleavage of intact antibodies by methods well known in the art, or by inserting stop codons at the desired locations in the vectors using site-directed mutagenesis, such as after CH1 to produce Fab fragments or after the hinge region to produce (Fab′)₂fragments. Single chain antibodies may be produced by joining VL- and VH-coding regions with a DNA that encodes a peptide linker connecting the VL and VH protein fragments

Papain digestion of antibodies produces two identical antigen-binding fragments, called “Fab” fragments, each with a single antigen-binding site, and a residual “Fc” fragment, whose name reflects its ability to crystallize readily. Pepsin treatment of an antibody yields an F(ab′)₂fragment that has two antigen-combining sites and is still capable of cross-linking antigen.

“Fv” usually refers to the minimum antibody fragment that contains a complete antigen-recognition and -binding site. This region consists of a dimer of one heavy- and one light-chain variable domain in tight, non-covalent association. It is in this configuration that the three CDRs of each variable domain interact to define an antigen-binding site on the surface of the V_H-V_Ldimer. Collectively, the CDRs confer antigen-binding specificity to the antibody. However, even a single variable domain (or half of an Fv comprising three CDRs specific for an antigen) has the ability to recognize and bind antigen, although likely at a lower affinity than the entire binding site.

Thus, in certain embodiments, the antibodies of the application may comprise 1, 2, 3, 4, 5, 6, or more CDRs that recognize the acetylation sites identified in Column E of Table 1.

The Fab fragment also contains the constant domain of the light chain and the first constant domain (CH1) of the heavy chain. Fab′ fragments differ from Fab fragments by the addition of a few residues at the carboxy terminus of the heavy chain CH1 domain including one or more cysteines from the antibody hinge region. Fab′-SH is the designation herein for Fab′ in which the cysteine residue(s) of the constant domains bear a free thiol group. F(ab′)₂antibody fragments originally were produced as pairs of Fab′ fragments that have hinge cysteines between them. Other chemical couplings of antibody fragments are also known.

“Single-chain Fv” or “scFv” antibody fragments comprise the V_Hand V_Ldomains of an antibody, wherein these domains are present in a single polypeptide chain. In certain embodiments, the Fv polypeptide further comprises a polypeptide linker between the V_Hand V_Ldomains that enables the scFv to form the desired structure for antigen binding. For a review of scFv see Pluckthun in The Pharmacology of Monoclonal Antibodies, vol. 113, Rosenburg and Moore, eds. (Springer-Verlag: New York, 1994), pp. 269-315.

SMIPs are a class of single-chain peptides engineered to include a target binding region and effector domain (CH2 and CH3 domains). See, e.g., U.S. Patent Application Publication No. 20050238646. The target binding region may be derived from the variable region or CDRs of an antibody, e.g., a acetylation site-specific antibody of the application. Alternatively, the target binding region is derived from a protein that binds a acetylation site.

Bispecific antibodies may be monoclonal, human or humanized antibodies that have binding specificities for at least two different antigens. In the present case, one of the binding specificities is for the acetylation site, the other one is for any other antigen, such as for example, a cell-surface protein or receptor or receptor subunit. Alternatively, a therapeutic agent may be placed on one arm. The therapeutic agent can be a drug, toxin, enzyme, DNA, radionuclide, etc.

In some embodiments, the antigen-binding-fragment can be a diabody. The term “diabody” refers to small antibody fragments with two antigen-binding sites, which fragments comprise a heavy-chain variable domain (V_H) connected to a light-chain variable domain (V_L) in the same polypeptide chain (V_H-V_L). By using a linker that is too short to allow pairing between the two domains on the same chain, the domains are forced to pair with the complementary domains of another chain and create two antigen-binding sites. Diabodies are described more fully in, for example, EP 404,097; WO 93/11161; and Hollinger et al., Proc. Natl. Acad. Sci. USA, 90: 6444-6448 (1993).

Camelid antibodies refer to a unique type of antibodies that are devoid of light chain, initially discovered from animals of the camelid family. The heavy chains of these so-called heavy-chain antibodies bind their antigen by one single domain, the variable domain of the heavy immunoglobulin chain, referred to as VHH. VHHs show homology with the variable domain of heavy chains of the human VHIII family. The VHHs obtained from an immunized camel, dromedary, or llama have a number of advantages, such as effective production in microorganisms such as Saccharomyces cerevisiae.

In certain embodiments, single chain antibodies, and chimeric, humanized or primatized (CDR-grafted) antibodies, as well as chimeric or CDR-grafted single chain antibodies, comprising portions derived from different species, are also encompassed by the present disclosure as antigen-binding fragments of an antibody. The various portions of these antibodies can be joined together chemically by conventional techniques, or can be prepared as a contiguous protein using genetic engineering techniques. For example, nucleic acids encoding a chimeric or humanized chain can be expressed to produce a contiguous protein. See, e.g., U.S. Pat. Nos. 4,816,567 and 6,331,415; U.S. Pat. No. 4,816,397; European Patent No. 0,120,694; WO 86/01533; European Patent No. 0,194,276 B1; U.S. Pat. No. 5,225,539; and European Patent No. 0,239,400 B1. See also, Newman et al., BioTechnology, 10: 1455-1460 (1992), regarding primatized antibody. See, e.g., Ladner et al., U.S. Pat. No. 4,946,778; and Bird et al., Science, 242: 423-426 (1988)), regarding single chain antibodies.

In addition, functional fragments of antibodies, including fragments of chimeric, humanized, primatized or single chain antibodies, can also be produced. Functional fragments of the subject antibodies retain at least one binding function and/or modulation function of the full-length antibody from which they are derived.

Since the immunoglobulin-related genes contain separate functional regions, each having one or more distinct biological activities, the genes of the antibody fragments may be fused to functional regions from other genes (e.g., enzymes, U.S. Pat. No. 5,004,692, which is incorporated by reference in its entirety) to produce fusion proteins or conjugates having novel properties.

Non-immunoglobulin binding polypeptides are also contemplated. For example, CDRs from an antibody disclosed herein may be inserted into a suitable non-immunoglobulin scaffold to create a non-immunoglobulin binding polypeptide. Suitable candidate scaffold structures may be derived from, for example, members of fibronectin type III and cadherin superfamilies.

Also contemplated are other equivalent non-antibody molecules, such as protein binding domains or aptamers, which bind, in a phospho-specific manner, to an amino acid sequence comprising a novel acetylation site of the invention. See, e.g., Neuberger et al., Nature 312: 604 (1984). Aptamers are oligonucleic acid or peptide molecules that bind a specific target molecule. DNA or RNA aptamers are typically short oligonucleotides, engineered through repeated rounds of selection to bind to a molecular target. Peptide aptamers typically consist of a variable peptide loop attached at both ends to a protein scaffold. This double structural constraint generally increases the binding affinity of the peptide aptamer to levels comparable to an antibody (nanomolar range).

The invention also discloses the use of the acetylation site-specific antibodies with immunotoxins. Conjugates that are immunotoxins including antibodies have been widely described in the art. The toxins may be coupled to the antibodies by conventional coupling techniques or immunotoxins containing protein toxin portions can be produced as fusion proteins. In certain embodiments, antibody conjugates may comprise stable linkers and may release cytotoxic agents inside cells (see U.S. Pat. Nos. 6,867,007 and 6,884,869). The conjugates of the present application can be used in a corresponding way to obtain such immunotoxins. Illustrative of such immunotoxins are those described by Byers et al., Seminars Cell Biol 2:59-70 (1991) and by Fanger et al., Immunol Today 12:51-54 (1991). Exemplary immunotoxins include radiotherapeutic agents, ribosome-inactivating proteins (RIPs), chemotherapeutic agents, toxic peptides, or toxic proteins.

The acetylation site-specific antibodies disclosed in the invention may be used singly or in combination. The antibodies may also be used in an array format for high throughput uses. An antibody microarray is a collection of immobolized antibodies, typically spotted and fixed on a solid surface (such as glass, plastic and silicon chip).

In another aspect, the antibodies of the invention modulate at least one, or all, biological activities of a parent protein identified in Column A of Table 1. The biological activities of a parent protein identified in Column A of Table 1 include: 1) ligand binding activities (for instance, these neutralizing antibodies may be capable of competing with or completely blocking the binding of a parent signaling protein to at least one, or all, of its ligands; 2) signaling transduction activities, such as receptor dimerization, or lysine acetylation; and 3) cellular responses induced by a parent signaling protein, such as oncogenic activities (e.g., cancer cell proliferation mediated by a parent signaling protein), and/or angiogenic activities.

In certain embodiments, the antibodies of the invention may have at least one activity selected from the group consisting of: 1) inhibiting cancer cell growth or proliferation; 2) inhibiting cancer cell survival; 3) inhibiting angiogenesis; 4) inhibiting cancer cell metastasis, adhesion, migration or invasion; 5) inducing apoptosis of cancer cells; 6) incorporating a toxic conjugate; and 7) acting as a diagnostic marker.

In certain embodiments, the acetylation site specific antibodies disclosed in the invention are especially indicated for diagnostic and therapeutic applications as described herein. Accordingly, the antibodies may be used in therapies, including combination therapies, in the diagnosis and prognosis of disease, as well as in the monitoring of disease progression. The invention, thus, further includes compositions comprising one or more embodiments of an antibody or an antigen binding portion of the invention as described herein. The composition may further comprise a pharmaceutically acceptable carrier. The composition may comprise two or more antibodies or antigen-binding portions, each with specificity for a different novel lysine acetylation site of the invention or two or more different antibodies or antigen-binding portions all of which are specific for the same novel lysine acetylation site of the invention. A composition of the invention may comprise one or more antibodies or antigen-binding portions of the invention and one or more additional reagents, diagnostic agents or therapeutic agents.

The present application provides for the polynucleotide molecules encoding the antibodies and antibody fragments and their analogs described herein. Because of the degeneracy of the genetic code, a variety of nucleic acid sequences encode each antibody amino acid sequence. The desired nucleic acid sequences can be produced by de novo solid-phase DNA synthesis or by PCR mutagenesis of an earlier prepared variant of the desired polynucleotide. In one embodiment, the codons that are used comprise those that are typical for human or mouse (see, e.g., Nakamura, Y., Nucleic Acids Res. 28: 292 (2000)).

The invention also provides immortalized cell lines that produce an antibody of the invention. For example, hybridoma clones, constructed as described above, that produce monoclonal antibodies to the targeted signaling protein acetylation sties disclosed herein are also provided. Similarly, the invention includes recombinant cells producing an antibody of the invention, which cells may be constructed by well known techniques; for example the antigen combining site of the monoclonal antibody can be cloned by PCR and single-chain antibodies produced as phage-displayed recombinant antibodies or soluble antibodies in E. coli (see, e.g., ANTIBODY ENGINEERING PROTOCOLS, 1995, Humana Press, Sudhir Paul editor.)

5. Methods of Making Acetylation site-Specific Antibodies

In another aspect, the invention provides a method for making acetylation site-specific antibodies.

Polyclonal antibodies of the invention may be produced according to standard techniques by immunizing a suitable animal (e.g., rabbit, goat, etc.) with an antigen comprising a novel lysine acetylation site of the invention. (i.e. a acetylation site shown in Table 1) in either the acetylated or unacetylated state, depending upon the desired specificity of the antibody, collecting immune serum from the animal, and separating the polyclonal antibodies from the immune serum, in accordance with known procedures and screening and isolating a polyclonal antibody specific for the novel lysine acetylation site of interest as further described below. Methods for immunizing non-human animals such as mice, rats, sheep, goats, pigs, cattle and horses are well known in the art. See, e.g., Harlow and Lane, Antibodies. A Laboratory Manual, New York: Cold Spring Harbor Press, 1990.

The immunogen may be the full length protein or a peptide comprising the novel lysine acetylation site of interest. In some embodiments the immunogen is a peptide of from 7 to 20 amino acids in length, preferably about 8 to 17 amino acids in length. In some embodiments, the peptide antigen desirably will comprise about 3 to 8 amino acids on each side of the phosphorylatable lysine. In yet other embodiments, the peptide antigen desirably will comprise four or more amino acids flanking each side of the phosphorylatable amino acid and encompassing it. Peptide antigens suitable for producing antibodies of the invention may be designed, constructed and employed in accordance with well-known techniques. See, e.g., Antibodies: A Laboratory Manual, Chapter 5, p. 75-76, Harlow & Lane Eds., Cold Spring Harbor Laboratory (1988); Czernik, Methods In Enzymology, 201: 264-283 (1991); Merrifield, J. Am. Chem. Soc. 85: 21-49 (1962)).

Suitable peptide antigens may comprise all or partial sequence of a trypsin-digested fragment as set forth in Column E of Table 1/FIG. 2. Suitable peptide antigens may also comprise all or partial sequence of a peptide fragment produced by another protease digestion.

Preferred immunogens are those that comprise a novel acetylation site of a protein in Table 1 that is a an enzyme protein, cytoskeletal protein, transcriptional regulator, RNA binding protein, chaperone protein, chormatin or DNA binding/repair/replication protein, protease, receptor/channel/transporter/cell surface protein or mitochondrial protein. In some embodiments, the peptide immunogen is an AQUA peptide, for example, any one of the sequences listed in column E of Table one and FIG. 2.

Particularly preferred immunogens are peptides comprising any one of the novel lysine acetylation site shown as a lower case “k” in a sequence listed in Table 1 selected from the group consisting of SEQ ID NOS: 125 (ACAT1); 137 (ENO1); 143 (GCLC); 162 (MDH2); 169 (NKEF-A); 173 (PDIA1); 188 (TOP1); 189 (TPI1); 79 (alpha 1); 81 (gamma 1); 117 (beta-2); 119 (WDR1); 312 (MBD1); 317 (NF-GMB); 319 (PA2G4); 323 (SMARCA2); 324 (SMARCA2); 334 (TB-1); 253 (BAT1); 273 (PABP1); 43 (HSC70); 45 (HSC70); 51 (HSP90B); 52 (HSPA5); 53 (HSPA5); 56 (HSPA5); 61 (PPIB); 62 (PPIB); 63 (PPIB); 73 (RPA1); 22 (p400); 223 (PSMC6); 224 (PSMC6); 227 (TPB7); 246 (KPNB3); 203 (DLD); 194 (Ran); 195 (Ran); 339 (eEF1A-1); and 340 (eEF1A-1).

In some embodiments the immunogen is administered with an adjuvant. Suitable adjuvants will be well known to those of skill in the art. Exemplary adjuvants include complete or incomplete Freund's adjuvant, RIBI (muramyl dipeptides) or ISCOM (immunostimulating complexes).

For example, a peptide antigen comprising the novel receptor lysine kinase acetylation site in SEQ ID NO: 4 shown by the lower case “k” in Table 1 may be used to produce antibodies that specifically bind the novel lysine acetylation site.

When the above-described methods are used for producing polyclonal antibodies, following immunization, the polyclonal antibodies which secreted into the bloodstream can be recovered using known techniques. Purified forms of these antibodies can, of course, be readily prepared by standard purification techniques, such as for example, affinity chromatography with Protein A, anti-immunoglobulin, or the antigen itself. In any case, in order to monitor the success of immunization, the antibody levels with respect to the antigen in serum will be monitored using standard techniques such as ELISA, RIA and the like.

Monoclonal antibodies of the invention may be produced by any of a number of means that are well-known in the art. In some embodiments, antibody-producing B cells are isolated from an animal immunized with a peptide antigen as described above. The B cells may be from the spleen, lymph nodes or peripheral blood. Individual B cells are isolated and screened as described below to identify cells producing an antibody specific for the novel lysine acetylation site of interest. Identified cells are then cultured to produce a monoclonal antibody of the invention.

Alternatively, a monoclonal acetylation site-specific antibody of the invention may be produced using standard hybridoma technology, in a hybridoma cell line according to the well-known technique of Kohler and Milstein. See Nature 265: 495-97 (1975); Kohler and Milstein, Eur. J. Immunol 6: 511 (1976); see also, Current Protocols in Molecular Biology, Ausubel et al. Eds. (1989). Monoclonal antibodies so produced are highly specific, and improve the selectivity and specificity of diagnostic assay methods provided by the invention. For example, a solution containing the appropriate antigen may be injected into a mouse or other species and, after a sufficient time (in keeping with conventional techniques), the animal is sacrificed and spleen cells obtained. The spleen cells are then immortalized by any of a number of standard means. Methods of immortalizing cells include, but are not limited to, transfecting them with oncogenes, infecting them with an oncogenic virus and cultivating them under conditions that select for immortalized cells, subjecting them to carcinogenic or mutating compounds, fusing them with an immortalized cell, e.g., a myeloma cell, and inactivating a tumor suppressor gene. See, e.g., Harlow and Lane, supra. If fusion with myeloma cells is used, the myeloma cells preferably do not secrete immunoglobulin polypeptides (a non-secretory cell line). Typically the antibody producing cell and the immortalized cell (such as but not limited to myeloma cells) with which it is fused are from the same species. Rabbit fusion hybridomas, for example, may be produced as described in U.S. Pat. No. 5,675,063, C. Knight, Issued Oct. 7, 1997. The immortalized antibody producing cells, such as hybridoma cells, are then grown in a suitable selection media, such as hypoxanthine-aminopterin-thymidine (HAT), and the supernatant screened for monoclonal antibodies having the desired specificity, as described below. The secreted antibody may be recovered from tissue culture supernatant by conventional methods such as precipitation, ion exchange or affinity chromatography, or the like.

The invention also encompasses antibody-producing cells and cell lines, such as hybridomas, as described above.

Polyclonal or monoclonal antibodies may also be obtained through in vitro immunization. For example, phage display techniques can be used to provide libraries containing a repertoire of antibodies with varying affinities for a particular antigen. Techniques for the identification of high affinity human antibodies from such libraries are described by Griffiths et al., (1994) EMBO J, 13:3245-3260; Nissim et al., ibid, pp. 692-698 and by Griffiths et al., ibid, 12:725-734, which are incorporated by reference.

The antibodies may be produced recombinantly using methods well known in the art for example, according to the methods disclosed in U.S. Pat. No. 4,349,893 (Reading) or U.S. Pat. No. 4,816,567 (Cabilly et al.) The antibodies may also be chemically constructed by specific antibodies made according to the method disclosed in U.S. Pat. No. 4,676,980 (Segel et al.)

Once a desired acetylation site-specific antibody is identified, polynucleotides encoding the antibody, such as heavy, light chains or both (or single chains in the case of a single chain antibody) or portions thereof such as those encoding the variable region, may be cloned and isolated from antibody-producing cells using means that are well known in the art. For example, the antigen combining site of the monoclonal antibody can be cloned by PCR and single-chain antibodies produced as phage-displayed recombinant antibodies or soluble antibodies in E. coli (see, e.g., Antibody Engineering Protocols, 1995, Humana Press, Sudhir Paul editor.)

Accordingly, in a further aspect, the invention provides such nucleic acids encoding the heavy chain, the light chain, a variable region, a framework region or a CDR of an antibody of the invention. In some embodiments, the nucleic acids are operably linked to expression control sequences. The invention, thus, also provides vectors and expression control sequences useful for the recombinant expression of an antibody or antigen-binding portion thereof of the invention. Those of skill in the art will be able to choose vectors and expression systems that are suitable for the host cell in which the antibody or antigen-binding portion is to be expressed.

Monoclonal antibodies of the invention may be produced recombinantly by expressing the encoding nucleic acids in a suitable host cell under suitable conditions. Accordingly, the invention further provides host cells comprising the nucleic acids and vectors described above.

Monoclonal Fab fragments may also be produced in Escherichia coli by recombinant techniques known to those skilled in the art. See, e.g., W. Huse, Science 246: 1275-81 (1989); Mullinax et al., Proc. Nat'l Acad. Sci. 877: 8095 (1990).

If monoclonal antibodies of a single desired isotype are preferred for a particular application, particular isotypes can be prepared directly, by selecting from the initial fusion, or prepared secondarily, from a parental hybridoma secreting a monoclonal antibody of different isotype by using the sib selection technique to isolate class-switch variants (Steplewski, et al., Proc. Nat'l. Acad. Sci., 82: 8653 (1985); Spira et al., J. Immunol. Methods, 74: 307 (1984)). Alternatively, the isotype of a monoclonal antibody with desirable propertied can be changed using antibody engineering techniques that are well-known in the art.

Acetylation site-specific antibodies of the invention, whether polyclonal or monoclonal, may be screened for epitope and phospho-specificity according to standard techniques. See, e.g., Czernik et al., Methods in Enzymology, 201: 264-283 (1991). For example, the antibodies may be screened against the acetylated and/or unacetylated peptide library by ELISA to ensure specificity for both the desired antigen (i.e. that epitope including an acetylation site of the invention and for reactivity only with the acetylated (or unacetylated) form of the antigen. Peptide competition assays may be carried out to confirm lack of reactivity with other phospho-epitopes on the parent protein. The antibodies may also be tested by Western blotting against cell preparations containing the parent signaling protein, e.g., cell lines over-expressing the parent protein, to confirm reactivity with the desired acetylated epitope/target.

Specificity against the desired acetylated epitope may also be examined by constructing mutants lacking phosphorylatable residues at positions outside the desired epitope that are known to be acetylated, or by mutating the desired phospho-epitope and confirming lack of reactivity. Acetylation site-specific antibodies of the invention may exhibit some limited cross-reactivity to related epitopes in non-target proteins. This is not unexpected as most antibodies exhibit some degree of cross-reactivity, and anti-peptide antibodies will often cross-react with epitopes having high homology to the immunizing peptide. See, e.g., Czernik, supra. Cross-reactivity with non-target proteins is readily characterized by Western blotting alongside markers of known molecular weight. Amino acid sequences of cross-reacting proteins may be examined to identify acetylation sites with flanking sequences that are highly homologous to that of a acetylation site of the invention.

In certain cases, polyclonal antisera may exhibit some undesirable general cross-reactivity to acetyl-lysine itself, which may be removed by further purification of antisera, e.g., over an acetyl-lysine column. Antibodies of the invention specifically bind their target protein (i.e. a protein listed in Column A of Table 1) only when acetylated (or only when not acetylated, as the case may be) at the site disclosed in corresponding Columns D/E, and do not (substantially) bind to the other form (as compared to the form for which the antibody is specific).

Antibodies may be further characterized via immunohistochemical (IHC) staining using normal and diseased tissues to examine acetylation and activation state and level of a acetylation site in diseased tissue. IHC may be carried out according to well-known techniques. See, e.g., Antibodies: A Laboratory Manual, Chapter 10, Harlow & Lane Eds., Cold Spring Harbor Laboratory (1988). Briefly, paraffin-embedded tissue (e.g., tumor tissue) is prepared for immunohistochemical staining by deparaffinizing tissue sections with xylene followed by ethanol; hydrating in water then PBS; unmasking antigen by heating slide in sodium citrate buffer; incubating sections in hydrogen peroxide; blocking in blocking solution; incubating slide in primary antibody and secondary antibody; and finally detecting using ABC avidin/biotin method according to manufacturer's instructions.

Antibodies may be further characterized by flow cytometry carried out according to standard methods. See Chow et al., Cytometry (Communications in Clinical Cytometry) 46: 72-78 (2001). Briefly and by way of example, the following protocol for cytometric analysis may be employed: samples may be centrifuged on Ficoll gradients to remove lysed erythrocytes and cell debris. Adhering cells may be scrapped off plates and washed with PBS. Cells may then be fixed with 2% paraformaldehyde for 10 minutes at 37° C. followed by permeabilization in 90% methanol for 30 minutes on ice. Cells may then be stained with the primary acetylation site-specific antibody of the invention (which detects a parent signaling protein enumerated in Table 1), washed and labeled with a fluorescent-labeled secondary antibody. Additional fluorochrome-conjugated marker antibodies (e.g., CD45, CD34) may also be added at this time to aid in the subsequent identification of specific hematopoietic cell types. The cells would then be analyzed on a flow cytometer (e.g. a Beckman Coulter FC500) according to the specific protocols of the instrument used.

Antibodies of the invention may also be advantageously conjugated to fluorescent dyes (e.g. Alexa488, PE) for use in multi-parametric analyses along with other signal transduction (phospho-CrkL, phospho-Erk 1/2) and/or cell marker (CD34) antibodies.

Acetylation site-specific antibodies of the invention may specifically bind to a signaling protein or polypeptide listed in Table 1 only when acetylated at the specified lysine residue, but are not limited only to binding to the listed signaling proteins of human species, per se. The invention includes antibodies that also bind conserved and highly homologous or identical acetylation sites in respective signaling proteins from other species (e.g., mouse, rat, monkey, yeast), in addition to binding the acetylation site of the human homologue. The term “homologous” refers to two or more sequences or subsequences that have at least about 85%, at least 90%, at least 95%, or higher nucleotide or amino acid residue identity, when compared and aligned for maximum correspondence, as measured using sequence comparison method (e.g., BLAST) and/or by visual inspection. Highly homologous or identical sites conserved in other species can readily be identified by standard sequence comparisons (such as BLAST).

Methods for making bispecific antibodies are within the purview of those skilled in the art. Traditionally, the recombinant production of bispecific antibodies is based on the co-expression of two immunoglobulin heavy-chain/light-chain pairs, where the two heavy chains have different specificities (Milstein and Cuello, Nature, 305:537-539 (1983)). Antibody variable domains with the desired binding specificities (antibody-antigen combining sites) can be fused to immunoglobulin constant domain sequences. In certain embodiments, the fusion is with an immunoglobulin heavy-chain constant domain, including at least part of the hinge, CH2, and CH3 regions. DNAs encoding the immunoglobulin heavy-chain fusions and, if desired, the immunoglobulin light chain, are inserted into separate expression vectors, and are co-transfected into a suitable host organism. For further details of illustrative currently known methods for generating bispecific antibodies see, for example, Suresh et al., Methods in Enzymology, 121:210 (1986); WO 96/27011; Brennan et al., Science 229:81 (1985); Shalaby et al., J. Exp. Med. 175:217-225 (1992); Kostelny et al., J. Immunol. 148(5):1547-1553 (1992); Hollinger et al., Proc. Natl. Acad. Sci. USA 90:6444-6448 (1993); Gruber et al., J. Immunol. 152:5368 (1994); and Tutt et al., J. Immunol. 147:60 (1991). Bispecific antibodies also include cross-linked or heteroconjugate antibodies. Heteroconjugate antibodies may be made using any convenient cross-linking methods. Suitable cross-linking agents are well known in the art, and are disclosed in U.S. Pat. No. 4,676,980, along with a number of cross-linking techniques.

Various techniques for making and isolating bispecific antibody fragments directly from recombinant cell culture have also been described. For example, bispecific antibodies have been produced using leucine zippers. Kostelny et al., J. Immunol., 148(5):1547-1553 (1992). The leucine zipper peptides from the Fos and Jun proteins may be linked to the Fab′ portions of two different antibodies by gene fusion. The antibody homodimers may be reduced at the hinge region to form monomers and then re-oxidized to form the antibody heterodimers. This method can also be utilized for the production of antibody homodimers. A strategy for making bispecific antibody fragments by the use of single-chain Fv (scFv) dimers has also been reported. See Gruber et al., J. Immunol., 152:5368 (1994). Alternatively, the antibodies can be “linear antibodies” as described in Zapata et al. Protein Eng. 8(10):1057-1062 (1995). Briefly, these antibodies comprise a pair of tandem Fd segments (V_H-C_H1-V_H-C_H1) which form a pair of antigen binding regions. Linear antibodies can be bispecific or monospecific.

To produce the chimeric antibodies, the portions derived from two different species (e.g., human constant region and murine variable or binding region) can be joined together chemically by conventional techniques or can be prepared as single contiguous proteins using genetic engineering techniques. The DNA molecules encoding the proteins of both the light chain and heavy chain portions of the chimeric antibody can be expressed as contiguous proteins. The method of making chimeric antibodies is disclosed in U.S. Pat. No. 5,677,427; U.S. Pat. No. 6,120,767; and U.S. Pat. No. 6,329,508, each of which is incorporated by reference in its entirety.

Fully human antibodies may be produced by a variety of techniques. One example is trioma methodology. The basic approach and an exemplary cell fusion partner, SPAZ-4, for use in this approach have been described by Oestberg et al., Hybridoma 2:361-367 (1983); Oestberg, U.S. Pat. No. 4,634,664; and Engleman et al., U.S. Pat. No. 4,634,666 (each of which is incorporated by reference in its entirety).

Human antibodies can also be produced from non-human transgenic animals having transgenes encoding at least a segment of the human immunoglobulin locus. The production and properties of animals having these properties are described in detail by, see, e.g., Lonberg et al., WO93/12227; U.S. Pat. No. 5,545,806; and Kucherlapati, et al., WO91/10741; U.S. Pat. No. 6,150,584, which are herein incorporated by reference in their entirety.

Various recombinant antibody library technologies may also be utilized to produce fully human antibodies. For example, one approach is to screen a DNA library from human B cells according to the general protocol outlined by Huse et al., Science 246:1275-1281 (1989). The protocol described by Huse is rendered more efficient in combination with phage-display technology. See, e.g., Dower et al., WO 91/17271 and McCafferty et al., WO 92/01047; U.S. Pat. No. 5,969,108, (each of which is incorporated by reference in its entirety).

Eukaryotic ribosome can also be used as means to display a library of antibodies and isolate the binding human antibodies by screening against the target antigen, as described in Coia G, et al., J. Immunol. Methods 1: 254 (1-2):191-7 (2001); Hanes J. et al., Nat. Biotechnol. 18(12):1287-92 (2000); Proc. Natl. Acad. Sci. U.S.A. 95(24):14130-5 (1998); Proc. Natl. Acad. Sci. U.S.A. 94(10):4937-42 (1997), each which is incorporated by reference in its entirety.

The yeast system is also suitable for screening mammalian cell-surface or secreted proteins, such as antibodies. Antibody libraries may be displayed on the surface of yeast cells for the purpose of obtaining the human antibodies against a target antigen. This approach is described by Yeung, et al., Biotechnol. Prog. 18(2):212-20 (2002); Boeder, E. T., et al., Nat. Biotechnol. 15(6):553-7 (1997), each of which is herein incorporated by reference in its entirety. Alternatively, human antibody libraries may be expressed intracellularly and screened via the yeast two-hybrid system (WO0200729A2, which is incorporated by reference in its entirety).

Recombinant DNA techniques can be used to produce the recombinant acetylation site-specific antibodies described herein, as well as the chimeric or humanized acetylation site-specific antibodies, or any other genetically-altered antibodies and the fragments or conjugate thereof in any expression systems including both prokaryotic and eukaryotic expression systems, such as bacteria, yeast, insect cells, plant cells, mammalian cells (for example, NS0 cells).

Once produced, the whole antibodies, their dimers, individual light and heavy chains, or other immunoglobulin forms of the present application can be purified according to standard procedures of the art, including ammonium sulfate precipitation, affinity columns, column chromatography, gel electrophoresis and the like (see, generally, Scopes, R., Protein Purification (Springer-Verlag, N.Y., 1982)). Once purified, partially or to homogeneity as desired, the polypeptides may then be used therapeutically (including extracorporeally) or in developing and performing assay procedures, immunofluorescent staining, and the like. (See, generally, Immunological Methods, Vols. I and II (Lefkovits and Pernis, eds., Academic Press, NY, 1979 and 1981).

6. Therapeutic Uses

In a further aspect, the invention provides methods and compositions for therapeutic uses of the peptides or proteins comprising a acetylation site of the invention, and acetylation site-specific antibodies of the invention.

In one embodiment, the invention provides for a method of treating or preventing cancer in a subject, wherein the cancer is associated with the acetylation state of a novel acetylation site in Table 1, whether acetylated or deacetylated, comprising: administering to a subject in need thereof a therapeutically effective amount of a peptide comprising a novel acetylation site (Table 1) and/or an antibody or antigen-binding fragment thereof that specifically bind a novel acetylation site of the invention (Table 1). The antibodies maybe full-length antibodies, genetically engineered antibodies, antibody fragments, and antibody conjugates of the invention.

The term “subject” refers to a vertebrate, such as for example, a mammal, or a human. Although present application are primarily concerned with the treatment of human subjects, the disclosed methods may also be used for the treatment of other mammalian subjects such as dogs and cats for veterinary purposes.

In one aspect, the disclosure provides a method of treating cancer in which a peptide or an antibody that reduces at least one biological activity of a targeted signaling protein is administered to a subject. For example, the peptide or the antibody administered may disrupt or modulate the interaction of the target signaling protein with its ligand. Alternatively, the peptide or the antibody may interfere with, thereby reducing, the down-stream signal transduction of the parent signaling protein. An antibody that specifically binds the novel lysine acetylation site only when the lysine is acetylated, and that does not substantially bind to the same sequence when the lysine is not acetylated, thereby prevents downstream signal transduction triggered by an acetyl-lysine. Alternatively, an antibody that specifically binds the unacetylated target acetylation site reduces the acetylation at that site and thus reduces activation of the protein mediated by acetylation of that site. Similarly, an unacetylated peptide may compete with an endogenous acetylation site for same kinases, thereby preventing or reducing the acetylation of the endogenous target protein. Alternatively, a peptide comprising an acetylated novel lysine site of the invention but lacking the ability to trigger signal transduction may competitively inhibit interaction of the endogenous protein with the same down-stream ligand(s).

The antibodies of the invention may also be used to target cancer cells for effector-mediated cell death. The antibody disclosed herein may be administered as a fusion molecule that includes a acetylation site-targeting portion joined to a cytotoxic moiety to directly kill cancer cells. Alternatively, the antibody may directly kill the cancer cells through complement-mediated or antibody-dependent cellular cytotoxicity.

Accordingly in one embodiment, the antibodies of the present disclosure may be used to deliver a variety of cytotoxic compounds. Any cytotoxic compound can be fused to the present antibodies. The fusion can be achieved chemically or genetically (e.g., via expression as a single, fused molecule). The cytotoxic compound can be a biological, such as a polypeptide, or a small molecule. As those skilled in the art will appreciate, for small molecules, chemical fusion is used, while for biological compounds, either chemical or genetic fusion can be used.

Non-limiting examples of cytotoxic compounds include therapeutic drugs, radiotherapeutic agents, ribosome-inactivating proteins (RIPs), chemotherapeutic agents, toxic peptides, toxic proteins, and mixtures thereof. The cytotoxic drugs can be intracellularly acting cytotoxic drugs, such as short-range radiation emitters, including, for example, short-range, high-energy α-emitters. Enzymatically active toxins and fragments thereof, including ribosome-inactivating proteins, are exemplified by saporin, luffin, momordins, ricin, trichosanthin, gelonin, abrin, etc. Procedures for preparing enzymatically active polypeptides of the immunotoxins are described in WO84/03508 and WO85/03508, which are hereby incorporated by reference. Certain cytotoxic moieties are derived from adriamycin, chlorambucil, daunomycin, methotrexate, neocarzinostatin, and platinum, for example.

Exemplary chemotherapeutic agents that may be attached to an antibody or antigen-binding fragment thereof include taxol, doxorubicin, verapamil, podophyllotoxin, procarbazine, mechlorethamine, cyclophosphamide, camptothecin, ifosfamide, melphalan, chlorambucil, bisulfan, nitrosurea, dactinomycin, daunorubicin, doxorubicin, bleomycin, plicomycin, mitomycin, etoposide (VP 16), tamoxifen, transplatinum, 5-fluorouracil, vincristin, vinblastin, or methotrexate.

Procedures for conjugating the antibodies with the cytotoxic agents have been previously described and are within the purview of one skilled in the art.

Alternatively, the antibody can be coupled to high energy radiation emitters, for example, a radioisotope, such as 1311, a γ-emitter, which, when localized at the tumor site, results in a killing of several cell diameters. See, e.g., S. E. Order, “Analysis, Results, and Future Prospective of the Therapeutic Use of Radiolabeled Antibody in Cancer Therapy”, Monoclonal Antibodies for Cancer Detection and Therapy, Baldwin et al. (eds.), pp. 303-316 (Academic Press 1985), which is hereby incorporated by reference. Other suitable radioisotopes include α-emitters, such as ²¹²Bi, ²¹³Bi, and ²¹¹At, and α-emitters, such as ¹⁸⁶Re and ⁹⁰Y.

Because many of the signaling proteins in which novel lysine acetylation sites of the invention occur also are expressed in normal cells and tissues, it may also be advantageous to administer a acetylation site-specific antibody with a constant region modified to reduce or eliminate ADCC or CDC to limit damage to normal cells. For example, effector function of antibodies may be reduced or eliminated by utilizing an IgG1 constant domain instead of an IgG2/4 fusion domain. Other ways of eliminating effector function can be envisioned such as, e.g., mutation of the sites known to interact with FcR or insertion of a peptide in the hinge region, thereby eliminating critical sites required for FcR interaction. Variant antibodies with reduced or no effector function also include variants as described previously herein.

The peptides and antibodies of the invention may be used in combination with other therapies or with other agents. Other agents include but are not limited to polypeptides, small molecules, chemicals, metals, organometallic compounds, inorganic compounds, nucleic acid molecules, oligonucleotides, aptamers, spiegelmers, antisense nucleic acids, locked nucleic acid (LNA) inhibitors, peptide nucleic acid (PNA) inhibitors, immunomodulatory agents, antigen-binding fragments, prodrugs, and peptidomimetic compounds. In certain embodiments, the antibodies and peptides of the invention may be used in combination with cancer therapies known to one of skill in the art.

In certain aspects, the present disclosure relates to combination treatments comprising a acetylation site-specific antibody described herein and immunomodulatory compounds, vaccines or chemotherapy. Illustrative examples of suitable immunomodulatory agents that may be used in such combination therapies include agents that block negative regulation of T cells or antigen presenting cells (e.g., anti-CTLA4 antibodies, anti-PD-L1 antibodies, anti-PDL-2 antibodies, anti-PD-1 antibodies and the like) or agents that enhance positive co-stimulation of T cells (e.g., anti-CD40 antibodies or anti 4-1 BB antibodies) or agents that increase NK cell number or T-cell activity (e.g., inhibitors such as IMiDs, thalidomide, or thalidomide analogs). Furthermore, immunomodulatory therapy could include cancer vaccines such as dendritic cells loaded with tumor cells, proteins, peptides, RNA, or DNA derived from such cells, patient derived heat-shock proteins (hsp's) or general adjuvants stimulating the immune system at various levels such as CpG, Luivac®, Biostim®, Ribomunyl®, Imudon®, Bronchovaxom® or any other compound or other adjuvant activating receptors of the innate immune system (e.g., toll like receptor agonist, anti-CTLA-4 antibodies, etc.). Also, immunomodulatory therapy could include treatment with cytokines such as IL-2, GM-CSF and IFN-gamma.

Furthermore, combination of antibody therapy with chemotherapeutics could be particularly useful to reduce overall tumor burden, to limit angiogenesis, to enhance tumor accessibility, to enhance susceptibility to ADCC, to result in increased immune function by providing more tumor antigen, or to increase the expression of the T cell attractant LIGHT.

Pharmaceutical compounds that may be used for combinatory anti-tumor therapy include, merely to illustrate: aminoglutethimide, amsacrine, anastrozole, asparaginase, bcg, bicalutamide, bleomycin, buserelin, busulfan, camptothecin, capecitabine, carboplatin, carmustine, chlorambucil, cisplatin, cladribine, clodronate, colchicine, cyclophosphamide, cyproterone, cytarabine, dacarbazine, dactinomycin, daunorubicin, dienestrol, diethylstilbestrol, docetaxel, doxorubicin, epirubicin, estradiol, estramustine, etoposide, exemestane, filgrastim, fludarabine, fludrocortisone, fluorouracil, fluoxymesterone, flutamide, gemcitabine, genistein, goserelin, hydroxyurea, idarubicin, ifosfamide, imatinib, interferon, irinotecan, letrozole, leucovorin, leuprolide, levamisole, lomustine, mechlorethamine, medroxyprogesterone, megestrol, melphalan, mercaptopurine, mesna, methotrexate, mitomycin, mitotane, mitoxantrone, nilutamide, nocodazole, octreotide, oxaliplatin, paclitaxel, pamidronate, pentostatin, plicamycin, porfimer, procarbazine, raltitrexed, rituximab, streptozocin, suramin, tamoxifen, temozolomide, teniposide, testosterone, thioguanine, thiotepa, titanocene dichloride, topotecan, trastuzumab, tretinoin, vinblastine, vincristine, vindesine, and vinorelbine.

These chemotherapeutic anti-tumor compounds may be categorized by their mechanism of action into groups, including, for example, the following classes of agents: anti-metabolites/anti-cancer agents, such as pyrimidine analogs (5-fluorouracil, floxuridine, capecitabine, gemcitabine and cytarabine) and purine analogs, folate inhibitors and related inhibitors (mercaptopurine, thioguanine, pentostatin and 2-chlorodeoxyadenosine (cladribine)); antiproliferative/antimitotic agents including natural products such as vinca alkaloids (vinblastine, vincristine, and vinorelbine), microtubule disruptors such as taxane (paclitaxel, docetaxel), vincristine, vinblastine, nocodazole, epothilones and navelbine, epidipodophyllotoxins (etoposide, teniposide), DNA damaging agents (actinomycin, amsacrine, anthracyclines, bleomycin, busulfan, camptothecin, carboplatin, chlorambucil, cisplatin, cyclophosphamide, cytoxan, dactinomycin, daunorubicin, doxorubicin, epirubicin, hexamethylmelamineoxaliplatin, iphosphamide, melphalan, mechlorethamine, mitomycin, mitoxantrone, nitrosourea, plicamycin, procarbazine, taxol, taxotere, teniposide, triethylenethiophosphoramide and etoposide (VP16)); antibiotics such as dactinomycin (actinomycin D), daunorubicin, doxorubicin (adriamycin), idarubicin, anthracyclines, mitoxantrone, bleomycins, plicamycin (mithramycin) and mitomycin; enzymes (L-asparaginase which systemically metabolizes L-asparagine and deprives cells which do not have the capacity to synthesize their own asparagine); antiplatelet agents; antiproliferative/antimitotic alkylating agents such as nitrogen mustards (mechlorethamine, cyclophosphamide and analogs, melphalan, chlorambucil), ethylenimines and methylmelamines (hexamethylmelamine and thiotepa), alkyl sulfonates-busulfan, nitrosoureas (carmustine (BCNU) and analogs, streptozocin), trazenes-dacarbazinine (DTIC); antiproliferative/antimitotic antimetabolites such as folic acid analogs (methotrexate); platinum coordination complexes (cisplatin, carboplatin), procarbazine, hydroxyurea, mitotane, aminoglutethimide; hormones, hormone analogs (estrogen, tamoxifen, goserelin, bicalutamide, nilutamide) and aromatase inhibitors (letrozole, anastrozole); anticoagulants (heparin, synthetic heparin salts and other inhibitors of thrombin); fibrinolytic agents (such as tissue plasminogen activator, streptokinase and urokinase), aspirin, dipyridamole, ticlopidine, clopidogrel, abciximab; antimigratory agents; antisecretory agents (breveldin); immunosuppressives (cyclosporine, tacrolimus (FK-506), sirolimus (rapamycin), azathioprine, mycophenolate mofetil); immunomodulatory agents (thalidomide and analogs thereof such as lenalidomide (Revlimid, CC-5013) and CC-4047 (Actimid)), cyclophosphamide; anti-angiogenic compounds (TNP-470, genistein) and growth factor inhibitors (vascular endothelial growth factor (VEGF) inhibitors, fibroblast growth factor (FGF) inhibitors); angiotensin receptor blocker; nitric oxide donors; anti-sense oligonucleotides; antibodies (trastuzumab); cell cycle inhibitors and differentiation inducers (tretinoin); mTOR inhibitors, topoisomerase inhibitors (doxorubicin (adriamycin), amsacrine, camptothecin, daunorubicin, dactinomycin, eniposide, epirubicin, etoposide, idarubicin and mitoxantrone, topotecan, irinotecan), corticosteroids (cortisone, dexamethasone, hydrocortisone, methylprednisolone, prednisone, and prenisolone); growth factor signal transduction kinase inhibitors; mitochondrial dysfunction inducers and caspase activators; and chromatin disruptors.

In certain embodiments, pharmaceutical compounds that may be used for combinatory anti-angiogenesis therapy include: (1) inhibitors of release of “angiogenic molecules,” such as bFGF (basic fibroblast growth factor); (2) neutralizers of angiogenic molecules, such as anti-βbFGF antibodies; and (3) inhibitors of endothelial cell response to angiogenic stimuli, including collagenase inhibitor, basement membrane turnover inhibitors, angiostatic steroids, fungal-derived angiogenesis inhibitors, platelet factor 4, thrombospondin, arthritis drugs such as D-penicillamine and gold thiomalate, vitamin D₃analogs, alpha-interferon, and the like. For additional proposed inhibitors of angiogenesis, see Blood et al., Biochim. Biophys. Acta, 1032:89-118 (1990), Moses et al., Science, 248:1408-1410 (1990), Ingber et al., Lab. Invest., 59:44-51 (1988), and U.S. Pat. Nos. 5,092,885, 5,112,946, 5,192,744, 5,202,352, and 6,573,256. In addition, there are a wide variety of compounds that can be used to inhibit angiogenesis, for example, peptides or agents that block the VEGF-mediated angiogenesis pathway, endostatin protein or derivatives, lysine binding fragments of angiostatin, melanin or melanin-promoting compounds, plasminogen fragments (e.g., Kringles 1-3 of plasminogen), troponin subunits, inhibitors of vitronectin α_vβ₃, peptides derived from Saposin B, antibiotics or analogs (e.g., tetracycline or neomycin), dienogest-containing compositions, compounds comprising a MetAP-2 inhibitory core coupled to a peptide, the compound EM-138, chalcone and its analogs, and naaladase inhibitors. See, for example, U.S. Pat. Nos. 6,395,718, 6,462,075, 6,465,431, 6,475,784, 6,482,802, 6,482,810, 6,500,431, 6,500,924, 6,518,298, 6,521,439, 6,525,019, 6,538,103, 6,544,758, 6,544,947, 6,548,477, 6,559,126, and 6,569,845.

7. Diagnostic Uses

In a further aspect, the invention provides methods for detecting and quantitating phosphoyrlation at a novel lysine acetylation site of the invention. For example, peptides, including AQUA peptides of the invention, and antibodies of the invention are useful in diagnostic and prognostic evaluation of cancer, wherein the particular cancer is associated with the acetylation state of a novel acetylation site in Table 1, whether acetylated or deacetylated.

Methods of diagnosis can be performed in vitro using a biological sample (e.g., blood sample, lymph node biopsy or tissue) from a subject, or in vivo. The acetylation state or level at the lysine residue identified in the corresponding row in Column D of Table 1 may be assessed. A change in the acetylation state or level at the acetylation site, as compared to a control, indicates that the subject is suffering from, or susceptible to a for of cancer; for example, carcinoma.

In one embodiment, the acetylation state or level at a novel acetylation site is determined by an AQUA peptide comprising the acetylation site. The AQUA peptide may be acetylated or unacetylated at the specified lysine position.

In another embodiment, the acetylation state or level at a acetylation site is determined by an antibody or antigen-binding fragment thereof, wherein the antibody specifically binds the acetylation site. The antibody may be one that only binds to the acetylation site when the lysine residue is acetylated, but does not bind to the same sequence when the lysine is not acetylated; or vice versa.

In particular embodiments, the antibodies of the present application are attached to labeling moieties, such as a detectable marker. One or more detectable labels can be attached to the antibodies. Exemplary labeling moieties include radiopaque dyes, radiocontrast agents, fluorescent molecules, spin-labeled molecules, enzymes, or other labeling moieties of diagnostic value, particularly in radiologic or magnetic resonance imaging techniques.

A radiolabeled antibody in accordance with this disclosure can be used for in vitro diagnostic tests. The specific activity of an antibody, binding portion thereof, probe, or ligand, depends upon the half-life, the isotopic purity of the radioactive label, and how the label is incorporated into the biological agent. In immunoassay tests, the higher the specific activity, in general, the better the sensitivity. Radioisotopes useful as labels, e.g., for use in diagnostics, include iodine (¹³¹I or ¹²⁵I), indium (¹¹¹In), technetium (⁹⁹Tc), phosphorus (³²P), carbon (¹⁴C), and tritium (³H), or one of the therapeutic isotopes listed above.

Fluorophore and chromophore labeled biological agents can be prepared from standard moieties known in the art. Since antibodies and other proteins absorb light having wavelengths up to about 310 nm, the fluorescent moieties may be selected to have substantial absorption at wavelengths above 310 nm, such as for example, above 400 nm. A variety of suitable fluorescers and chromophores are described by Stryer, Science, 162:526 (1968) and Brand et al., Annual Review of Biochemistry, 41:843-868 (1972), which are hereby incorporated by reference. The antibodies can be labeled with fluorescent chromophore groups by conventional procedures such as those disclosed in U.S. Pat. Nos. 3,940,475, 4,289,747, and 4,376,110, which are hereby incorporated by reference.

The control may be parallel samples providing a basis for comparison, for example, biological samples drawn from a healthy subject, or biological samples drawn from healthy tissues of the same subject. Alternatively, the control may be a pre-determined reference or threshold amount. If the subject is being treated with a therapeutic agent, and the progress of the treatment is monitored by detecting the lysine acetylation state level at an acetylation site of the invention, a control may be derived from biological samples drawn from the subject prior to, or during the course of the treatment.

In certain embodiments, antibody conjugates for diagnostic use in the present application are intended for use in vitro, where the antibody is linked to a secondary binding ligand or to an enzyme (an enzyme tag) that will generate a colored product upon contact with a chromogenic substrate. Examples of suitable enzymes include urease, alkaline phosphatase, (horseradish) hydrogen peroxidase and glucose oxidase. In certain embodiments, secondary binding ligands are biotin and avidin or streptavidin compounds.

Antibodies of the invention may also be optimized for use in a flow cytometry (FC) assay to determine the activation/acetylation status of a target signaling protein in subjects before, during, and after treatment with a therapeutic agent targeted at inhibiting lysine acetylation at the acetylation site disclosed herein. For example, bone marrow cells or peripheral blood cells from patients may be analyzed by flow cytometry for target signaling protein acetylation, as well as for markers identifying various hematopoietic cell types. In this manner, activation status of the malignant cells may be specifically characterized. Flow cytometry may be carried out according to standard methods. See, e.g., Chow et al., Cytometry (Communications in Clinical Cytometry) 46: 72-78 (2001).

Alternatively, antibodies of the invention may be used in immunohistochemical (IHC) staining to detect differences in signal transduction or protein activity using normal and diseased tissues. IHC may be carried out according to well-known techniques. See, e.g., Antibodies: A Laboratory Manual, supra.

Peptides and antibodies of the invention may be also be optimized for use in other clinically-suitable applications, for example bead-based multiplex-type assays, such as IGEN, Luminex™ and/or Bioplex™ assay formats, or otherwise optimized for antibody arrays formats, such as reversed-phase array applications (see, e.g. Paweletz et al., Oncogene 20(16) 1981-89 (2001)). Accordingly, in another embodiment, the invention provides a method for the multiplex detection of the acetylation state or level at two or more acetylation sites of the invention (Table 1) in a biological sample, the method comprising utilizing two or more antibodies or AQUA peptides of the invention. In one preferred embodiment, two to five antibodies or AQUA peptides of the invention are used. In another preferred embodiment, six to ten antibodies or AQUA peptides of the invention are used, while in another preferred embodiment eleven to twenty antibodies or AQUA peptides of the invention are used.

In certain embodiments the diagnostic methods of the application may be used in combination with other cancer diagnostic tests.

The biological sample analyzed may be any sample that is suspected of having abnormal lysine acetylation at a novel acetylation site of the invention, such as a homogenized neoplastic tissue sample.

8. Screening assays

In another aspect, the invention provides a method for identifying an agent that modulates lysine acetylation at a novel acetylation site of the invention, comprising: a) contacting a candidate agent with a peptide or protein comprising a novel acetylation site of the invention; and b) determining the acetylation state or level at the novel acetylation site. A change in the acetylation level of the specified lysine in the presence of the test agent, as compared to a control, indicates that the candidate agent potentially modulates lysine acetylation at a novel acetylation site of the invention.

In particular embodiments, the antibodies of the present application are attached to labeling moieties, such as a detectable marker.

The control may be parallel samples providing a basis for comparison, for example, the acetylation level of the target protein or peptide in absence of the testing agent. Alternatively, the control may be a pre-determined reference or threshold amount.

9. Immunoassays

In another aspect, the present application concerns immunoassays for binding, purifying, quantifying and otherwise generally detecting the acetylation state or level at a novel acetylation site of the invention.

Assays may be homogeneous assays or heterogeneous assays. In a homogeneous assay the immunological reaction usually involves a acetylation site-specific antibody of the invention, a labeled analyte, and the sample of interest. The signal arising from the label is modified, directly or indirectly, upon the binding of the antibody to the labeled analyte. Both the immunological reaction and detection of the extent thereof are carried out in a homogeneous solution. Immunochemical labels that may be used include free radicals, radioisotopes, fluorescent dyes, enzymes, bacteriophages, coenzymes, and so forth.

In a heterogeneous assay approach, the reagents are usually the specimen, a acetylation site-specific antibody of the invention, and suitable means for producing a detectable signal. Similar specimens as described above may be used. The antibody is generally immobilized on a support, such as a bead, plate or slide, and contacted with the specimen suspected of containing the antigen in a liquid phase. The support is then separated from the liquid phase and either the support phase or the liquid phase is examined for a detectable signal using means for producing such signal. The signal is related to the presence of the analyte in the specimen. Means for producing a detectable signal include the use of radioactive labels, fluorescent labels, enzyme labels, and so forth.

Acetylation site-specific antibodies disclosed herein may be conjugated to a solid support suitable for a diagnostic assay (e.g., beads, plates, slides or wells formed from materials such as latex or polystyrene) in accordance with known techniques, such as precipitation.

In certain embodiments, immunoassays are the various types of enzyme linked immunoadsorbent assays (ELISAs) and radioimmunoassays (RIA) known in the art. Immunohistochemical detection using tissue sections is also particularly useful. However, it will be readily appreciated that detection is not limited to such techniques, and Western blotting, dot and slot blotting, FACS analyses, and the like may also be used. The steps of various useful immunoassays have been described in the scientific literature, such as, e.g., Nakamura et al., in Enzyme Immunoassays: Heterogeneous and Homogeneous Systems, Chapter 27 (1987), incorporated herein by reference.

In general, the detection of immunocomplex formation is well known in the art and may be achieved through the application of numerous approaches. These methods are based upon the detection of radioactive, fluorescent, biological or enzymatic tags. Of course, one may find additional advantages through the use of a secondary binding ligand such as a second antibody or a biotin/avidin ligand binding arrangement, as is known in the art.

The antibody used in the detection may itself be conjugated to a detectable label, wherein one would then simply detect this label. The amount of the primary immune complexes in the composition would, thereby, be determined.

Alternatively, the first antibody that becomes bound within the primary immune complexes may be detected by means of a second binding ligand that has binding affinity for the antibody. In these cases, the second binding ligand may be linked to a detectable label. The second binding ligand is itself often an antibody, which may thus be termed a “secondary” antibody. The primary immune complexes are contacted with the labeled, secondary binding ligand, or antibody, under conditions effective and for a period of time sufficient to allow the formation of secondary immune complexes. The secondary immune complexes are washed extensively to remove any non-specifically bound labeled secondary antibodies or ligands, and the remaining label in the secondary immune complex is detected.

An enzyme linked immunoadsorbent assay (ELISA) is a type of binding assay. In one type of ELISA, acetylation site-specific antibodies disclosed herein are immobilized onto a selected surface exhibiting protein affinity, such as a well in a polystyrene microtiter plate. Then, a suspected neoplastic tissue sample is added to the wells. After binding and washing to remove non-specifically bound immune complexes, the bound target signaling protein may be detected.

In another type of ELISA, the neoplastic tissue samples are immobilized onto the well surface and then contacted with the acetylation site-specific antibodies disclosed herein. After binding and washing to remove non-specifically bound immune complexes, the bound acetylation site-specific antibodies are detected.

Irrespective of the format used, ELISAs have certain features in common, such as coating, incubating or binding, washing to remove non-specifically bound species, and detecting the bound immune complexes.

The radioimmunoassay (RIA) is an analytical technique which depends on the competition (affinity) of an antigen for antigen-binding sites on antibody molecules. Standard curves are constructed from data gathered from a series of samples each containing the same known concentration of labeled antigen, and various, but known, concentrations of unlabeled antigen. Antigens are labeled with a radioactive isotope tracer. The mixture is incubated in contact with an antibody. Then the free antigen is separated from the antibody and the antigen bound thereto. Then, by use of a suitable detector, such as a gamma or beta radiation detector, the percent of either the bound or free labeled antigen or both is determined. This procedure is repeated for a number of samples containing various known concentrations of unlabeled antigens and the results are plotted as a standard graph. The percent of bound tracer antigens is plotted as a function of the antigen concentration. Typically, as the total antigen concentration increases the relative amount of the tracer antigen bound to the antibody decreases. After the standard graph is prepared, it is thereafter used to determine the concentration of antigen in samples undergoing analysis.

In an analysis, the sample in which the concentration of antigen is to be determined is mixed with a known amount of tracer antigen. Tracer antigen is the same antigen known to be in the sample but which has been labeled with a suitable radioactive isotope. The sample with tracer is then incubated in contact with the antibody. Then it can be counted in a suitable detector which counts the free antigen remaining in the sample. The antigen bound to the antibody or immunoadsorbent may also be similarly counted. Then, from the standard curve, the concentration of antigen in the original sample is determined.

10. Pharmaceutical Formulations and Methods of Administration

Methods of administration of therapeutic agents, particularly peptide and antibody therapeutics, are well-known to those of skill in the art.

Peptides of the invention can be administered in the same manner as conventional peptide type pharmaceuticals. Preferably, peptides are administered parenterally, for example, intravenously, intramuscularly, intraperitoneally, or subcutaneously. When administered orally, peptides may be proteolytically hydrolyzed. Therefore, oral application may not be usually effective. However, peptides can be administered orally as a formulation wherein peptides are not easily hydrolyzed in a digestive tract, such as liposome-microcapsules. Peptides may be also administered in suppositories, sublingual tablets, or intranasal spray.

If administered parenterally, a preferred pharmaceutical composition is an aqueous solution that, in addition to a peptide of the invention as an active ingredient, may contain for example, buffers such as phosphate, acetate, etc., osmotic pressure-adjusting agents such as sodium chloride, sucrose, and sorbitol, etc., antioxidative or antioxygenic agents, such as ascorbic acid or tocopherol and preservatives, such as antibiotics. The parenterally administered composition also may be a solution readily usable or in a lyophilized form which is dissolved in sterile water before administration.

The pharmaceutical formulations, dosage forms, and uses described below generally apply to antibody-based therapeutic agents, but are also useful and can be modified, where necessary, for making and using therapeutic agents of the disclosure that are not antibodies.

To achieve the desired therapeutic effect, the acetylation site-specific antibodies or antigen-binding fragments thereof can be administered in a variety of unit dosage forms. The dose will vary according to the particular antibody. For example, different antibodies may have different masses and/or affinities, and thus require different dosage levels. Antibodies prepared as Fab or other fragments will also require differing dosages than the equivalent intact immunoglobulins, as they are of considerably smaller mass than intact immunoglobulins, and thus require lower dosages to reach the same molar levels in the patient's blood. The dose will also vary depending on the manner of administration, the particular symptoms of the patient being treated, the overall health, condition, size, and age of the patient, and the judgment of the prescribing physician. Dosage levels of the antibodies for human subjects are generally between about 1 mg per kg and about 100 mg per kg per patient per treatment, such as for example, between about 5 mg per kg and about 50 mg per kg per patient per treatment. In terms of plasma concentrations, the antibody concentrations may be in the range from about 25 μg/mL to about 500 μg/mL. However, greater amounts may be required for extreme cases and smaller amounts may be sufficient for milder cases.

Administration of an antibody will generally be performed by a parenteral route, typically via injection such as intra-articular or intravascular injection (e.g., intravenous infusion) or intramuscular injection. Other routes of administration, e.g., oral (p.o.), may be used if desired and practicable for the particular antibody to be administered. An antibody can also be administered in a variety of unit dosage forms and their dosages will also vary with the size, potency, and in vivo half-life of the particular antibody being administered. Doses of a acetylation site-specific antibody will also vary depending on the manner of administration, the particular symptoms of the patient being treated, the overall health, condition, size, and age of the patient, and the judgment of the prescribing physician.

The frequency of administration may also be adjusted according to various parameters. These include the clinical response, the plasma half-life of the antibody, and the levels of the antibody in a body fluid, such as, blood, plasma, serum, or synovial fluid. To guide adjustment of the frequency of administration, levels of the antibody in the body fluid may be monitored during the course of treatment.

Formulations particularly useful for antibody-based therapeutic agents are also described in U.S. Patent App. Publication Nos. 20030202972, 20040091490 and 20050158316. In certain embodiments, the liquid formulations of the application are substantially free of surfactant and/or inorganic salts. In another specific embodiment, the liquid formulations have a pH ranging from about 5.0 to about 7.0. In yet another specific embodiment, the liquid formulations comprise histidine at a concentration ranging from about 1 mM to about 100 mM. In still another specific embodiment, the liquid formulations comprise histidine at a concentration ranging from 1 mM to 100 mM. It is also contemplated that the liquid formulations may further comprise, one or more excipients such as a saccharide, an amino acid (e.g., arginine, lysine, and methionine) and a polyol. Additional descriptions and methods of preparing and analyzing liquid formulations can be found, for example, in PCT publications WO 03/106644, WO 04/066957, and WO 04/091658.

Wetting agents, emulsifiers and lubricants, such as sodium lauryl sulfate and magnesium stearate, as well as coloring agents, release agents, coating agents, sweetening, flavoring and perfuming agents, preservatives and antioxidants can also be present in the pharmaceutical compositions of the application.

In certain embodiments, formulations of the subject antibodies are pyrogen-free formulations which are substantially free of endotoxins and/or related pyrogenic substances. Endotoxins include toxins that are confined inside microorganisms and are released when the microorganisms are broken down or die. Pyrogenic substances also include fever-inducing, thermostable substances (glycoproteins) from the outer membrane of bacteria and other microorganisms. Both of these substances can cause fever, hypotension and shock if administered to humans. Due to the potential harmful effects, it is advantageous to remove even low amounts of endotoxins from intravenously administered pharmaceutical drug solutions. The Food & Drug Administration (“FDA”) has set an upper limit of 5 endotoxin units (EU) per dose per kilogram body weight in a single one hour period for intravenous drug applications (The United States Pharmacopeial Convention, Pharmacopeial Forum 26 (1):223 (2000)). When therapeutic proteins are administered in amounts of several hundred or thousand milligrams per kilogram body weight, as can be the case with monoclonal antibodies, it is advantageous to remove even trace amounts of endotoxin.

The amount of the formulation which will be therapeutically effective can be determined by standard clinical techniques. In addition, in vitro assays may optionally be used to help identify optimal dosage ranges. The precise dose to be used in the formulation will also depend on the route of administration, and the seriousness of the disease or disorder, and should be decided according to the judgment of the practitioner and each patient's circumstances. Effective doses may be extrapolated from dose-response curves derived from in vitro or animal model test systems. The dosage of the compositions to be administered can be determined by the skilled artisan without undue experimentation in conjunction with standard dose-response studies. Relevant circumstances to be considered in making those determinations include the condition or conditions to be treated, the choice of composition to be administered, the age, weight, and response of the individual patient, and the severity of the patient's symptoms. For example, the actual patient body weight may be used to calculate the dose of the formulations in milliliters (mL) to be administered. There may be no downward adjustment to “ideal” weight. In such a situation, an appropriate dose may be calculated by the following formula:

Dose (mL)=[patient weight (kg)×dose level (mg/kg)/drug concentration (mg/mL)]

For the purpose of treatment of disease, the appropriate dosage of the compounds (for example, antibodies) will depend on the severity and course of disease, the patient's clinical history and response, the toxicity of the antibodies, and the discretion of the attending physician. The initial candidate dosage may be administered to a patient.

LYSINE ACETYLATION SITES

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