EPITHELIAL OVARIAN CANCER DIFFERENTIATION MARKER

Abstract
An object of the present invention is to develop and provide an epithelial ovarian cancer diagnosis marker with which epithelial ovarian cancer can be detected inexpensively, conveniently, and low invasively with high accuracy, and a method for determining the presence or absence of epithelial ovarian cancer using the marker. The present invention provides a glycoprotein having a glycan-linked asparagine residue at a particular site of the glycoprotein secreted from an epithelial ovarian cancer cell, or a fragment thereof having the glycan as an epithelial ovarian cancer diagnosis marker. The present invention also provides a method for determining the presence or absence of epithelial ovarian cancer using the glycoprotein.
Description
TECHNICAL FIELD

The present invention relates to a glycoprotein for an epithelial ovarian cancer diagnosis marker or a fragment thereof having the glycan, and a method for determining the presence or absence of epithelial ovarian cancer using the marker.


BACKGROUND ART

Ovarian cancer is a cancer having the second-highest incidence after breast cancer among gynecological cancers. The early detection of ovarian cancer is difficult because of almost no subjective symptom at an early stage in the course of the disease. In many cases, its symptoms have already progressed when found. Hence, the ovarian cancer results in poor prognosis and the highest mortality rate among gynecological cancers.


Ovarian cancer is known to include surface epithelial-stromal tumor (epithelial ovarian cancer), which is developed from the surface epithelial cells of the ovary, germ cell tumor, which is developed from germ cells, and the like, depending on the area affected. Of them, epithelial ovarian cancer accounts for approximately 90% of all ovarian cancer cases and is often found, particularly, in middle-aged and elderly persons over forties. Thus, the early detection of epithelial ovarian cancer, if possible, can decrease the mortality rate of ovarian cancer.


Unlike uterine cancer, neither can epithelial ovarian cancer be examined endoscopically nor its cells can be collected directly ab extra. Hence, laparotomy is required even for direct examination or cytological diagnosis. In addition, early detection by palpation is also difficult. The cancer is often undetected until its symptoms have progressed and the ovary has become enlarged. Although echography, MRI, CT, etc., is relatively effective for early detection, the examination itself is extensive work and entails high cost. Another problem of the examination is that the accuracy of benign or malignant diagnosis is not always high.


Against this background, tumor markers have received attention in recent years. The tumor markers refer to substances produced by cancer cells or substances produced by cells in response to cancer cells. The amounts of the tumor markers contained in body fluids such as serum reflect the amount, histological type, or grade (prognosis) of tumor. The tumor markers can therefore serve as an index for, for example, determining the presence or absence of cancer. The tumor markers have the advantages that for example, they permit examination using body fluids, leading to low invasiveness, and also enable such examination to be conducted conveniently with relatively low cost.


Various cancer-associated antigens such as CAl25, CA602, CA130, CA72-4, CA546, CA19-9, and STN have been known so far as tumor markers for epithelial ovarian cancer (Non Patent Literatures 1 to 6). All of these tumor markers, however, are based on the difference in expression level, i.e., increase or decrease in protein expression level, in serum between normal individuals and epithelial ovarian cancer patients. Such proteins are usually expressed in no small amount even in normal cells and are therefore low specific for epithelial ovarian cancer. Hence, these proteins produce high false-positive and false-negative rates and as such, are far from high accuracy as tumor markers. In addition, these tumor markers are used mainly for the diagnosis of prognosis of epithelial ovarian cancer. A tumor marker that contributes to the early detection of primary cancer still remains to be obtained.


CITATION LIST
Non Patent Literature



  • Non Patent Literature 1: Bast R.C. Jr. et al., 1983, N. Engl. J. Med., 309: 883-887

  • Non Patent Literature 2: Suzuki M. et al., 1990, Nippon Gan Chiryo Gakkai Shi, 25: 1454-1460

  • Non Patent Literature 3: Inaba N. et al., 1989, Nippon Gan Chiryo Gakkai Shi, 24: 2426-2435

  • Non Patent Literature 4: Ohuchi N. et al., 1988, Gan To Kagaku Ryoho, 15, 2767-2772

  • Non Patent Literature 5: Nozawa S. et al., 1996, Nippon Rinsho, 54: 1665-1673

  • Non Patent Literature 6: Charpin C. et al., 1982, Int. J. Gynecol. Pathol., 1: 231-245



SUMMARY OF INVENTION
Technical Problem

An object of the present invention is to develop and provide an epithelial ovarian cancer diagnosis biomarker with which epithelial ovarian cancer can be detected inexpensively, conveniently, and low invasively with high accuracy from a body fluid, a cell, or a peritoneal lavage fluid, and a method for determining the presence or absence of epithelial ovarian cancer using the marker.


Solution to Problem

The composition, structures, and glycosylation sites of glycans that are linked to proteins secreted from cells are known to be controlled by the balanced expression of glycan-related genes and vary according to cell differentiation. The composition and structures of the glycans also vary according to the degree of cancer progression. Thus, glycoproteins found in particular cancer cells can be used as disease condition index markers including tumor markers. In recent years, such glycan-related tumor markers based on (glyco)proteomics have been searched for actively.


In order to attain the object, the present inventors have searched for epithelial ovarian cancer diagnosis markers using a lectin microarray method and glycoproteomics. As a result, the present inventors have successfully identified novel glycoprotein or glycopeptide groups having epithelial ovarian cancer-specific structures. The present inventors have also revealed that the presence or absence of epithelial ovarian cancer can be determined using these glycoprotein or glycopeptide groups. The present inventors have further found that the histological type of epithelial ovarian cancer can be determined by analogy using some members in these glycoprotein or glycopeptide groups. The present invention is based on these findings and provides the followings:


(1) A glycoprotein for an epithelial ovarian cancer diagnosis marker having at least one glycan-linked asparagine residue at a glycosylation site shown in Table 1 in the amino acid sequence of a protein shown in Table 1:














TABLE 1










Epithelial





Glycosylation
ovarian cancer

SEQ














Protein #
Protein name
gi (ID)
site
AAL(+)
WFA(+)
Peptide sequence
NO.


















1
collagen, type VI, alpha 1
gi|87196339

212


RNFTAADWGQSR
1


2
biglycan
gi|4502403

270


MIENGSLSFLPTLR
2






311


LLQVVYLHSNNITK
3


3
angiopoietin 2
gi|4557315

240


KIVTATVNNSVLQK
4


4
biotinidase
gi|4557373

349


NPVGLIGAENATGETDPSHSK
5


5
follistatin-like 1
gi|5901956

144


RIIQWLEAEIIPDGWFSKGSNYSEILDK
6


6
L1 cell adhesion molecule 1
gi|4557707
(isoform 1)
671


WYSLGKVPGNQTSTTLK
7






777


VQWRPQGTRGPWQEQIVSDPFLVVSNTSTFVPYEIK
8






979


THNLTDLSPHLR
9




gi|13435353
(isoform 2)
671


WYSLGKVPGNQTSTTLK
7






777


VQWRPQGTRGPWQEQIVSDPFLVVSNTSTFVPYEIK
8


7
pregnancy specific beta-1-glycoprotein
gi|21361296

175


SENYTYIWWLNGQSLPVSPR
10



5


210


ILILPSVTRNETGPYECEIR
11


8
pregnancy specific beta-1-glycoprotein
gi|21314635

303


ILILPSVTRNETGPYQCEIQDR
12



9


9
ribonuclease T2
gi|5231228

106


AYWPDVIHSFPNRS
13






212


QDQQLQNCTEPGEQPSPK
14


10
tissue factor pathway inhibitor 2
gi|5730091

116


YFFNLSSMTCEK
15






170


KIPSFCYSPKDEGLCSANVTR
16


11
tubulointerstitial nephritis antigen-
gi|11545918

78


GRADDCALPYLGAICYCDLFCNRT
17



like 1


12
cysteine-rich secretory protein 3
gi|5174675

239


DSCKASCNCSNSIY
18


13
histidine-rich glycoprotein
gi|4504489

125


VIDFNCTTSSVSSALANTK
19


14
laminin, gamma 1
gi|145309326

1161, 1175


AKVAAANVSVTQPESTGDPNNMTLLAEEAR
20






1205


TANDTSTEAYNLLLR
21






1241


KYEQAKNISQDLEK
22






1380


VNDNKTAAEEALRK
23


15
complement component 4 binding
gi|4502503

506, 528


LSVDKDQYVEPENVTIQCDSGYGVVGPQSITCSGNRT
24



protein,



alpha chain


16
inter-alpha (globulin) inhibitor H4
gi|31542984

517


LPTQNITFQTESSVAEQEAEFQSPK
25


17
cathepsin L2
gi|23110960

221


YRPENSVANDTGFTVVAPGKEK
26






292


NLDHGVLVVGYGFEGANSNNSKYWLVK
27


18
collagen, type XII, alpha 1
gi|93141047
(long isoform)
2528


MLEAYNLTEKNFASVQGVSLESGSFPSYSAYR
28






2679


DIKEAGNITTDGYEILGK
29




gi|93141049
(short isoform)
1364


MLEAYNLTEKNFASVQGVSLESGSFPSYSAYR
28






1515


DIKEAGNITTDGYEILGK
29


19
kallikrein-related peptidase 5
gi|117306172

173


DVRPINVSSHCPSAGTK
30




gi|117306176

208


VLQCLNISVLSQKR
31




gi|6912644


20
laminin alpha 3 subunit
gi|38045910
(isoform 1)
2265


EVIDTNLTTLR
32






2728


ERFNISTPAFR
33






3097


EGSLPGNSTISIR
34




gi|38045908
(isoform 2)
553


QLEEIKRNASGDELVR
35






656


EVIDTNLTTLR
32






975


TFNLNTTEVEPCR
36






1119


ERFNISTPAFR
33






1488


EGSLPGNSTISIR
34


21
netrin 4
gi|93204871

56


KLWADTTCGQNATELYCFYSENTDLTCRQPK
37






163


YFATNCSATFGLEDDVVKK
38


22
plasminogen activator inhibitor type
gi|24307907

118


NKDIVTVANAVFVKNASEIEVPFVTR
39



1,



member 2


23
platelet derived growth factor D
gi|13376808
(isoform 1)
276



NYSVNIREELK

40




gi|15451921
(isoform 2)
270



NYSVNIREELK

40


24
protease, serine, 23
gi|6005882

93


QYLSYETLYANGSR
41






207


GANDSTSAMPEQMKFQWIR
42


25
semaphorin 5A
gi|147904700

147


SLSNLTEIHDQISGMAR
43






591


TRSCDSPAPQCGGWQCEGPGMEIANCSR
44


26
thrombospondin repeat containing 1
gi|38016904
(isoform 1)
773


CGHLPRPNITQSCQLR
45






1001


EVQCLSTNQTLSTR
46




gi|56788359
(isoform 2)
773


CGHLPRPNITQSCQLR
45


27
complement component 1,
gi|4502495

174


NCGVNCSGDVFTALIGEIASPNYPKPYPENSR
47



s subcomponent
gi|41393602

406


YTCEEPYYYMENGGGGEYHCAGNGSWVNEVLGPELPK
48


28
lysyl oxidase-like 2
gi|4505011

288


LGPQVSLDPMKNVTCENGLPAVVSCVPGQVFSPDGPSR
49






293


LGPQVSLDPMKNVTCENGLPAVVSCVPGQVFSPDGPSR






644


HYHSMEVFTHYDLLNLNGTK
50


29
cathepsin D
gi|4503143

263


YYKGSLSYLNVTR
51


30
fibrillin 1
gi|24430141

448


VLPVNVTDYCQLVR
52






1703, 1713


NYYADNQTCDGELLFNMTKK
53


31
peptidylprolyl isomerase B
gi|4758950

148


HYGPGWVSMANAGKDTNGSQFFITTVK
54


32
attractin
gi|21450861
(isoform 1)
264


ISNSSDTVECECSENWK
55






914, 923


AATCINPLNGSVCERPANHSAK
56






1073, 1082


CINQSICEKCENLTTGK
57






1082


CENLTTGKHCETCISGFYGDPTNGGK
58






1250, 1259


NHPNITFFVYVSNFTWPIK
59




gi|21450863
(isoform 2)
914, 923


AATCINPLNGSVCERPANHSAK
56






1073, 1082


CINQSICEKCENLTTGK
57






1082


CENLTTGKHCETCISGFYGDPTNGGK
58


33
growth differentiation factor 15
gi|4758936

70


LRANQSWEDSNTDLVPAPAVR
60


34
heparan sulfate proteoglycan 2
gi|126012571

3780


SLTQGSLIVGDLAPVNGTSQGK
61






4068


SQGLNLHTLLYLGGVEPSVPLSPATNMSAHFR
62


35
ceruloplasmin
gi|4557485

138


NLASRPYTFHSHGITYYKEHEGAIYPDNTTDFQR
63






358


AGLQAFFQVQECNKSSSK
64






397


ENLTAPGSDSAVFFEQGTTR
65






762


ELHHLQEQNVSNAFLDKGEFYIGSK
66


36
serine (or cysteine) proteinase
gi|50363217

70


QLAHQSNSTNIFFSPVSIATAFAMLSLGTK
67



inhibitor,
gi|50363219

107


ADTHDEILEGLNFNLTEIPEAQIHEGFQELLR
68



clade A (alpha-1 antiproteinase,
gi|50363221

271


YLGNATAIFFLPDEGK
69



antitrypsin), member 1


37
quiescin Q6 sulfhydryl oxidase 1
gi|13325075
(isoform a)
130


AFTKNGSGAVFPVAGADVQTLR
70




gi|51873067
(isoform b)
130


AFTKNGSGAVFPVAGADVQTLR
70


38
golgi phosphoprotein 2
gi|29550838

109


LYQDEKAVLVNNITTGER
71




gi|29550850

144


LQQDVLQFQKNQTNLER
72


39
galectin 3 binding protein
gi|5031863

69


ALGFENATQALGR
73






125


DAGVVCTNETR
74






398


YKGLNLTEDTYKPR
75






551


AAIPSALDTNSSK
76






580


TVIRPFYLTNSSGVD
77


40
tissue inhibitor of metalloproteinase
gi|4507509

53


AKFVGTPEVNQTTLYQR
78



1


101


SHNRSEEFLIAGK
79


41
agrin
gi|54873613

135


NELMLNSSLMR
80






250


DPCSNVTCSFGSTCAR
81


42
serpin peptidase inhibitor, clade G
gi|73858568

238


DTFVNASR
82



(C1 inhibitor),
gi|73858570

253


VLSNNSDANLELINTWVAK
83



member 1


352


VGQLQLSHNLSLVILVPQNLK
84


43
complement factor H
gi|62739186
(isoform a)
802


IPCSQPPQIEHGTINSSR
85






802, 822


WDPEVNCSMAQIQLCPPPPQIPNSHNMTTTLNYR
86






882


WQSIPLCVEKIPCSQPPQIEHGTINSSR
87






911


ISEENETTCYMGK
88






1029


MDGASNVTCINSR
89






1095


YQCRSPYEMFGDEEVMCLNGNWTEPPQCK
90


44
kininogen 1
gi|4504893

48


YNSQNQSNNQFVLYR
91






169


HGIQYFNNNTQHSSLFMLNEVKR
92






205


ITYSIVQTNCSK
93






294


LNAENNATFYFK
94


45
vitronectin
gi|88853069

86


NNATVHEQVGGPSLTSDLQAQSK
95


46
apolipoprotein D
gi|4502163

65


CIQANYSLMENGK
96






98


ADGTVNQIEGEATPVNLTEPAKLEVK
97


47
alpha-2-macroglobulin
gi|66932947

55, 70


GCVLLSYLNETVTVSASLESVRGNRS
98






410, 413


GNEANYYSNATTDEHGLVQFSINTTNVMGTSLTVRVNYK
99






1424


TEVSSNHVLIYLDKVSNQTLSLFFTVLQDVPVR
100


48
complement component 4B
gi|50345296

1328


GLNVTLSSTGR
101


49
lumican
gi|4505047

88


NNQIDHIDEKAFENVTDLQWLILDHNLLENSK
102






127


KLHINHNNLTESVGPLPK
103






160


LGSFEGLVNLTFIHLQHNR
104






252


LSHNELADSGIPGNSFNVSSLVELDLSYNK
105


50
phospholipid transfer protein
gi|5453914
(isoform a)
64


GKEGHFYYNISEVK
106






143


MKVSNVSCQASVSR
107






398


IYSNHSALESLALIPLQAPLK
108




gi|33356541
(isoform b)
64


GKEGHFYYNISEVK
106






346


IYSNHSALESLALIPLQAPLKTMLQIGVMPMLNER
109


51
prostaglandin H2 D-isomerase
gi|32171249

51


WFSAGLASNSSWLR
110






78


SVVAPATDGGLNLTSTFLR
111


52
clusterin
gi|42716297
(isoform 1)
138


EDALNETRESETKLK
112






155


LKELPGVCNETMMALWEECKPCLK
113






406


MLNTSSLLEQLNEQFNWVSR
114






406, 426


MLNTSSLLEQLNEQFNWVSRLANLTQGEDQYYLR
115






426


LANLTQGEDQYYLR
116




gi|42740907
(isoform 2)
103


LKELPGVCNETMMALWEECKPCLK
113






354


MLNTSSLLEQLNEQFNWVSR
114






354, 374


MLNTSSLLEQLNEQFNWVSRLANLTQGEDQYYLR
115






374


LANLTQGEDQYYLR
116


53
complement factor B
gi|67782358

122


SPYYNVSDEISFHCYDGYTLR
117


54
alpha-2-HS-glycoprotein
gi|4502005

156


KVCQDCPLLAPLNDTR
118






176


AALAAFNAQNNGSNFQLEEISR
119


55
polymeric immunoglobulin receptor
gi|31377806

83, 90


ANLTNFPENGTFVVNIAQLSQDDSGRYK
120






186


QIGLYPVLVIDSSGYVNPNYTGR
121






421


LSLLEEPGNGTFTVILNQLTSR
122






469


IIEGEPNLKVPGNVTAVLGETLK
123


56
hemopexin
gi|11321561

187


SWPAVGNCSSALR
124






240, 246


GHGHRNGTGHGNSTHHGPEYMR
125






453


ALPQPQNVTSLLGCTH
126


57
orosomucoid 1
gi|9257232

56


WFYIASAFRNEEYNKS
127






72


SVQEIQATFFYFTPNKTEDTIFLR
128






93


QDQCIYNTTYLNVQR
129






93, 98


EYQTRQDQCIYNTTYLNVQRENGTISR
130






 93, 103


QDQCIYNTTYLNVQRENGTISR
131


58
orosomucoid 2
gi|4505529

56


WFYIASAFRNEEYNKS
127






72


SVQEIQATFFYFTPNKTEDTIFLR
128






93


QNQCFYNSSYLNVQR
132






 93, 103


QNQCFYNSSYLNVQRENGTVSR
133


59
serpin peptidase inhibitor,
gi|50659080

106


FNLTETSEAEIHQSFQHLLR
134



clade A, member 3


127


TLNQSSDELQLSMGNAMFVK
135






186


LINDYVKNGTR
136






271


YTGASALFILPDQDKMEEVEAMLLPETLK
137


60
transferrin
gi|4557871

430


CGLVPVLAENYNK
138






432


CGLVPVLAENYNKSDNCEDTPEAGYFAVAVVK
139






630


QQQHLFGSNVTDCSGNFCLFRSETK
140


61
alpha-2-glycoprotein 1, zinc
gi|4502337

109, 112


DIVEYYNDSNGSHVLQGR
141






112


DIVEYYNDSNGSHVLQGR






128


FGCEIENNRSSGAFWK
142


62
laminin alpha 5
gi|21264602

95


LVGGPVAGGDPNQTIR
143






921


LNLTSPDLFWLVFR
144






1330


VWQGHANASFCPHGYGCR
145






2196


GINASSMAWAR
146






2209


LHRLNASIADLQSQLR
147






2707


GVHNASLALSASIGR
148


63
lunatic fringe
gi|93140999
(isoform a)
167


HTGNVVITNCSAAHSR
149




gi|93141005
(isoform b)
167


HTGNVVITNCSAAHSR
149


64
met proto-oncogene
gi|42741655

399


CLQHFYGPNHEHCFNRT
150






607


VLLGNESCTLTLSESTMNTLK
151






785


MVINVHEAGRNFTVACQHR
152


65
prion protein
gi|122056623

197


QHTVTTTTKGENFTETDVK
153




gi|122056625




gi|122056628




gi|34335270




gi|4506113


66
insulin-like growth factor binding
gi|62243248
(isoform a)
116


GLCVNASAVSR
154



protein 3
gi|62243068
(isoform b)
116


GLCVNASAVSR
154






136


LRAYLLPAPPAPGNASESEEDRSAGSVESPSVSSTHR
155






199


YKVDYESQSTDTQNFSSESKR
156


67
lipocalin 2
gi|38455402

85


MYATIYELKEDKSYNVTSVLFR
157


68
coagulation factor XII
gi|145275213

249


TTLSGAPCQPWASEATYRNVTAEQAR
158


69
decorin
gi|19743846
(isoform a)
262


LGLSFNSISAVDNGSLANTPHLR
159




gi|4503271




gi|19743848
(isoform b)
153


LGLSFNSISAVDNGSLANTPHLR
159




gi|19743850
(isoform c)
115


LGLSFNSISAVDNGSLANTPHLR
159


70
amyloid beta A4 protein
gi|4502167
(isoform a)
571


EQNYSDDVLANMISEPR
160




gi|41406055
(isoform b)
552


EQNYSDDVLANMISEPR
160




gi|41406057
(isoform c)
496


EQNYSDDVLANMISEPR
160


71
chorionic gonadotropin
gi|4502789
(beta 3 subunit)
33


CRPINATLAVEK
161




gi|132566537
(beta polypeptide 1)
31


CRPINATLAVEK
161




gi|132566538
(beta polypeptide 2)
31


CRPINATLAVEK
161




gi|15451748
(beta polypeptide 5)
33


CRPINATLAVEK
161




gi|15451750
(beta polypeptide 7)
33


CRPINATLAVEK
161




gi|15426252
(beta polypeptide 8)
33


CRPINATLAVEK
161


72
colony stimulating factor 1
gi|27262661
(isoform a)
154


NVFNETKNLLDKDWNIFSK
162




gi|27262667




gi|27262663
(isoform b)
154


NVFNETKNLLDKDWNIFSK
162




gi|27262665
(isoform c)
154


NVFNETKNLLDKDWNIFSK
162


73
cystatin M
gi|4503113

137


LRCDFEVLVVPWQNSSQLLK
163


74
endothelin converting enzyme 1
gi|4503443

166


HLLENSTASVSEAERK
164


75
FK506 binding protein 10, 65 kDa
gi|21361895

70


YHYNGTFEDGKK
165


76
fucosidase, alpha-L-1, tissue
gi|119360348

268


WGQNCSCHHGGYYNCEDK
166


77
heparan sulfate 6-0-sulfotransferase 1
gi|148747866

320


FIRPFMQYNSTR
167


78
insulin-like growth factor binding
gi|4504619

171


GTCEQGPSIVTPPKDIWNVTGAQVYLSCEVIGIPTPVLIWNK
168



protein 7


79
lectin, mannose-binding 2
gi|5803023

183


VFPYISVMVNNGSLSYDHSKDGR
169


80
leukemia inhibitory factor
gi|4504991

85, 95


LCGPNVTDFPPFHANGTEK
170



(cholinergic differentiation factor)


81
notch 2
gi|24041035

46


DGYEPCVNEGMCVTYHNGTGYCK
171


82
osteoprotegerin
gi|148743793

289


HIGHANLTFEQLR
172


83
poliovirus receptor
gi|19923372

120


VEDEGNYTCLFVTFPQGSR
173


84
pregnancy specific beta-1-glycoprotein
gi|21361392

259, 268


ENKDVLNFTCEPKSENYTYIWWLNGQSLPVSPR
174



1


268


SENYTYIWWLNGQSLPVSPR
10


85
pregnancy specific beta-1-glycoprotein
gi|109240546

268


SENYTYIWWLNGQSLPVSPR
10



3


303


ILILPSVTRNETGPYQCEIQDR
12


86
pregnancy specific beta-1-glycoprotein
gi|42560235

299, 303


ILILPNVTRNETGPYQCEIR
175



4


87
pregnancy specific beta-1-glycoprotein
gi|4506177

268


SENYTYIWWLNGQSLPVSPR
10



7


88
pregnancy specific beta-1-glycoprotein
gi|51510887

259, 268


ENKDVLNFTCEPKSENYTYIWWLNGQSLPVSPR
174



8


268


SENYTYIWWLNGQSLPVSPR
10


89
solute carrier family 39 (zinc
gi|55741750

191, 198


LHHHLDHNNTHHFHNDSITPSER
176



transporter),



member 10


90
twisted gastrulation
gi|10190664

52


CLIQELCQCRPGEGNCSCCK
177


91
TYR03 protein tyrosine kinase
gi|27597078

240


LSSSNASVAWMPGADGR
178


92
glutaminyl-peptide cyclotransferase
gi|6912618

296


YFQNYSYGGVIQDDHIPFLRR
179


93
alpha 1,4-galactosyltransferase
gi|8392830

121


GLPGGNASLPR
180


94
glucocerebrosidase
gi|54607043

309


DLGPTLANSTHHNVR
181




gi|54607045




gi|54607047




gi|54607049




gi|54607051


95
lysosomal-associated membrane protein
gi|4504957

257


VASVININPNTTHSTGSCR
182



2
gi|7669503


96
quiescin Q6-like 1
gi|145580631

266


LGVSSVPSCYLIYPNGSHGLINVVKPLR
183


97
transmembrane emp24 protein
gi|33457308

117


FTFTSHTPGDHQICLHSNSTR
184



transport domain containing 4


98
neuropilin 1
gi|66912184
(isoform a)
522


FKIGYSNNGSDWK
185




gi|66912178
(isoform b)
522


FKIGYSNNGSDWK
185




gi|66864913
(isoform c)
522


FKIGYSNNGSDWK
185


99
versican
gi|21361116

1442


RGQFESVAPSQNFSDSSESDTHPFVIAK
186


100
coagulation factor II
gi|4503635

416


WVLTAAHCLLYPPWDKNFTENDLLVR
187


101
fibronectin 1
gi|47132557
(isoform 1)
542


RHEEGHMLNCTCFGQGR
188




gi|47132551
(isoform 2)
542


RHEEGHMLNCTCFGQGR
188




gi|16933542
(isoform 3)
542


RHEEGHMLNCTCFGQGR
188




gi|47132555
(isoform 4)
542


RHEEGHMLNCTCFGQGR
188




gi|47132553
(isoform 5)
542


RHEEGHMLNCTCFGQGR
188




gi|47132549
(isoform 6)
542


RHEEGHMLNCTCFGQGR
188




gi|47132547
(isoform 7)
542


RHEEGHMLNCTCFGQGR
188


102
folate receptor 1
gi|4758400

161


GWNWTSGFNK
189




gi|9257205




gi|9257207




gi|9257213




gi|9257215




gi|9257217


103
immunoglobulin superfamily, member 1
gi|45505167

1223


GIGNYSCSYR
190


104
lactotransferrin
gi|54607120

156


TAGWNVPIGTLRPFLNWTGPPEPIEAAVAR
191


105
plasma carboxypeptidase B2
gi|126273569
(isoform a)
 85, 108


AHLNVSGIPCSVLLADVEDLIQQQISNDTVSPR
192




gi|126273559
(isoform b)
 85, 108


AHLNVSGIPCSVLLADVEDLIQQQISNDTVSPR
192


106
plasma kallikrein B1
gi|78191798

396


IVGGTNSSWGEWPWQVSLQVK
193


107
secreted frizzled-related protein 4
gi|4506895

38


HMPWNITR
194


108
CD163 antigen
gi|44662834
(isoform a)
140


HSNCTHQQDAGVTCSDGSNLEMR
195




gi|44889963
(isoform b)
140


HSNCTHQQDAGVTCSDGSNLEMR
195


109
complement component 3
gi|115298678

85


TVLTPATNHMGNVTFTIPANR
196


110
mucin 16
gi|83367077

12586



NTSVGLLYSGCR

197






13193


KFNITESVLQGLLKPLFK
198






14417, 14423



NGTQLQNFTLDR

199


111
acid alpha-glucosidase
gi|119393891

470


GVFITNETGQPLIGK
200




gi|119393893




gi|119393895


112
activating transcription factor 6
gi|56786157

584


DHLLLPATTHNKTTRPK
201


113
bone morphogenetic protein 1
gi|4502421
(isoform 1)
599


LNGSITSPGWPK
202




gi|5902808
(isoform 2)
599


LNGSITSPGWPK
202




gi|5453579
(isoform 3)
599


LNGSITSPGWPK
202


114
cAMP responsive element binding
gi|20631977

610


DHLLLPAISHNKTSRPK
203



protein-like 1


115
carboxylesterase 1
gi|68508967
(isoform a)
80



NATSYPPMCTQDPK

204




gi|68508965
(isoform b)
79



NATSYPPMCTQDPK

204




gi|68508957
(isoform c)
79



NATSYPPMCTQDPK

204


116
carboxypeptidase D
gi|22202611

522


RFANEYPNITR
205






978


HIWSLEISNKPNVSEPEEPKIR
206






1070


GKDLDTDFTNNASQPETK
207


117
carboxypeptidase E
gi|4503009

139


ELLIFLAQYLCNEYQKGNETIVNLIHSTR
208


118
cathepsin F
gi|6042196

195


NFVITYNRT
209


119
cathepsin L1
gi|22202619

221


YSVANDTGFVDIPKQEK
210




gi|4503155


120
CD276 antigen
gi|67188443
(isoform a)
 91, 104


QLVHSFAEGQDQGSAYANRTALFPDLLAQGNASLR
211






215


VVLGANGTYSCLVR
212






309, 332


DQGSAYANRTALFPDLLAQGNASLR
213




gi|13376852
(isoform b)
 91, 104


QLVHSFAEGQDQGSAYANRTALFPDLLAQGNASLR
211






215


VVLGANGTYSCLVR
212


121
chitobiase, di-N-acetyl-
gi|4758092

299


QINSSISGNLWDK
214


122
chromosome 3 open reading frame 9
gi|23308761

373


FLSYNVTR
215




gi|31982953


123
coagulation factor III
gi|4503641

169



NNTFLSLR

216


124
epidermal growth factor receptor
gi|29725609
(isoform a)
603


TCPAGVMGENNTLVWK
217




gi|41327732
(isoform b)
603


TCPAGVMGENNTLVWK
217




gi|41327736
(isoform d)
603


TCPAGVMGENNTLVWK
217


125
GalNAc transferase 10
gi|38195091
(isoform a)
146


YLETLPNTSIIIPFHNEGWSSLLR
218


126
heparan sulfate 6-0-sulfotransferase 3
gi|45580707

380


FISPFTQFNITR
219


127
heparan sulfate D-glucosaminyl
gi|4826764

242, 249


LSPQINASNFYFNKT
220



3-0-sulfotransferase 1


128
granulin
gi|4504151

236


YGCCPMPNATCCSDHLHCCPQDTVCDLIQSK
221


129
integrin alpha 3
gi|4504747
(isoform a)
969


TSIPTINMENKT
222




gi|6006011
(isoform b)
969


TSIPTINMENKT
222


130
integrin alpha-V
gi|4504763

74


MFLLVGAPKANTTQPGIVEGGQVLK
223






704


LSCAFKTENQTR
224


131
laminin, beta 2
gi|119703755

1308


LALNLTLR
225






1348


RANTSALAVPSPVSNSASAR
226


132
laminin subunit beta 3
gi|62868215

604


LRNATASLWSGPGLEDR
227




gi|62868217


133
low density lipoprotein-related
gi|126012562

1511


ANKWTGHNVTVVQR
228



protein 1


134
mannosidase, alpha, class 2A, member 1
gi|51477714

1125


LLNKFIVESLTPSSLSLMHSPPGTQNISEINLSPMEISTFR
229


135
mannosidase, alpha, class 2B, member 2
gi|50659093

748


RPYVSYVNNSIAR
230


136
mannosidase, beta A, lysosomal
gi|84798622

77


WVSLDNWTYSK
231


137
multiple EGF-like-domains 8
gi|145701025

1204


ALLTNVSSVALGSR
232






2147, 2162


TGYTMDNMTGLCRPVCAQGCVNGSCVEPDHCR
233


138
oxidized low density lipoprotein
gi|4505501

183


LLKINSTADLDFIQQAISYSSFPFWMGLSR
234



(lectin-like) receptor 1


139
peptidylprolyl isomerase A
gi|10863927

108


HTGPGILSMANAGPNTNGSQFFICTAK
235


140
plexin A1
gi|49355818

54


LSGNLTLLR
236


141
prominin 2
gi|21389623

725


ILRNVSECFLAR
237


142
protein tyrosine phosphatase,
gi|148728162
(isoform 1)
413


IHVAGETDSSNLNVSEPR
238



receptor type, J
gi|148728160
(isoform 2)
413


IHVAGETDSSNLNVSEPR
238


143
procollagen-lysine,
gi|33636742
(isoform a)
717


FLRYNCSIESPR
239



2-oxoglutarate 5-dioxygenase 2
gi|62739166
(isoform b)
696


FLRYNCSIESPR
239


144
protein tyrosine phosphatase, receptor
gi|18860902

416


RIAVDWESLGYNITR
240



type, K


462


APQHVVNHLPPYTNVSLK
241


145
proton-coupled folate transporter
gi|31543204

58


FSADLGYNGTR
242


146
semaphorin 3F
gi|31377802

126


LIQPWNRT
243


147
sialyltransferase 4A
gi|27765096

323


TGVHDADFESNVTATLASINK
244




gi|4506951


148
solute carrier family 44, member 2
gi|31377727

200


KNITDLVEGAK
245


149
tetraspan NET-6
gi|7657373

137


SVNPNDTCLASCVK
246


150
transmembrane 4 superfamily member 15
gi|6912530

189



NTTEVVNTMCGYK

247


151
transmembrane protein 132A
gi|30089935
(isoform a)
280


HNFTASLLTLR
248




gi|30089937
(isoform b)
280


HNFTASLLTLR
248


152
tumor necrosis factor receptor
gi|7657039

278


VLSSIQEGTVPDNTSSAR
249



superfamily,



member 21


153
complement component 7
gi|45580688

754



NYTLTGRDSCTLPASAEK

250


154
WAP four-disulfide core domain 2
gi|56699495

44


TGVCPELQADQNCTQECVSDSECADNLK
251


155
CD82 antigen
gi|4504813
(isoform 1)
129


DYNSSREDSLQDAWDYVQAQVK
252




gi|67782354
(isoform 2)
104


DYNSSREDSLQDAWDYVQAQVK
252


156
FAT tumor suppressor 1
gi|66346693

998


QVYNLTVR
253


157
membrane-bound transcription factor
gi|4506775

148


YAESDPTVPCNETR
254



site-1 protease


939


LSWAKPQPLNETAPSNLWK
255


158
poliovirus receptor-related 1
gi|42560237
(isoform 1)
286


ADANPPATEYHWTTLNGSLPK
256



(herpesvirus entry mediator C; nectin)
gi|42560231
(isoform 2)
286


ADANPPATEYHWTTLNGSLPK
256




gi|42560233
(isoform 3)
286


ADANPPATEYHWTTLNGSLPK
256


159
solute carrier family 3
gi|61744475
(isoform a)
396


DIENLKDASSFLAEWQNITK
257



(activators of dibasic and neutral


455


SLVTQYLNATGNRWCSWSLSQAR
258



amino acid transport),
gi|61744477
(isoform b)
366


DIENLKDASSFLAEWQNITK
257



member 2


425


SLVTQYLNATGNRWCSWSLSQAR
258




gi|65506891
(isoform c)
365


DIENLKDASSFLAEWQNITK
257






424


SLVTQYLNATGNRWCSWSLSQAR
258




gi|61744479
(isoform d)
334


DIENLKDASSFLAEWQNITK
257






393


SLVTQYLNATGNRWCSWSLSQAR
258




gi|61744481
(isoform e)
303


DIENLKDASSFLAEWQNITK
257






362


SLVTQYLNATGNRWCSWSLSQAR
258




gi|61744483
(isoform f)
264


DIENLKDASSFLAEWQNITK
257






323


SLVTQYLNATGNRWCSWSLSQAR
258


160
activated leukocyte cell adhesion
gi|68163411

167


KLGDCISEDSYPDGNITWYR
259



molecule


265


NAIKEGDNITLK
260






361



NATVVWMKDNIR

261






480


IIISPEENVTLTCTAENQLER
262


161
F11 receptor
gi|21464111

185


AFSNSSYVLNPTTGELVFDPLSASDTGEYSCEAR
263




gi|8393638


162
basigin
gi|38372919
(isoform 1)
160


ILLTCSLNDSATEVTGHR
264






268


ITDSEDKALMNGSESR
265




gi|38372925
(isoform 2)
44


ILLTCSLNDSATEVTGHR
264






152


ITDSEDKALMNGSESR
265




gi|38372921
(isoform 3)
59


ITDSEDKALMNGSESR
265




gi|38372923
(isoform 4)
88


ITDSEDKALMNGSESR
265


163
CD63 antigen
gi|4502679
(isoform A)
130


QQMENYPKNNHTASILDR
266






150


CCGAANYTDWEKIPSMSK
267




gi|91199546
(isoform B)
130


QQMENYPKNNHTASILDR
266






150


CCGAANYTDWEKIPSMSK
267


164
integrin beta 1
gi|19743813
(isoform 1A)
212


LRNPCTSEQNCTSPFSYK
268




gi|19743823




gi|19743815
(isoform 1B)
212


LRNPCTSEQNCTSPFSYK
268




gi|19743817
(isoform 1C-1)
212


LRNPCTSEQNCTSPFSYK
268




gi|19743821
(isoform 1C-2)
212


LRNPCTSEQNCTSPFSYK
268




gi|19743819
(isoform 1D)
212


LRNPCTSEQNCTSPFSYK
268


165
Na+/K+ -ATPase beta 1 subunit
gi|4502277
(isoform a)
158


FKLEWLGNCSGLNDETYGYK
269






193


VLGFKPKPPKNESLETYPVMK
270




gi|49574489
(isoform b)
158


FKLEWLGNCSGLNDETYGYK
269






193


VLGFKPKPPKNESLETYPVMK
270


166
scavenger receptor class B, member 2
gi|5031631

105


ANIQFGDNGTTISAVSNK
271


167
tumor-associated calcium signal
gi|4505057

168


HRPTAGAFNHSDLDAELRR
272



transducer 2


168
carcinoembryonic antigen-related
gi|98986445

204


TLTLFNVTR
273



cell adhesion molecule 5


169
cathepsin H
gi|23110955
(isoform a)
101


HKYLWSEPQNCSATK
274




gi|23110957
(isoform b)
89


HKYLWSEPQNCSATK
274


170
extracellular matrix protein 1
gi|4758236
(isoform 1)
444


HIPGLIHNMTAR
275




gi|12707572
(isoform 2)
319


HIPGLIHNMTAR
275


171
complement factor I
gi|119392081

103


FLNNGTCTAEGK
276






177


FKLSDLSINSTECLHVHCR
277






464


SIPACVPWSPYLFQPNDTCIVSGWGR
278


172
multimerin 2
gi|13376091

845


FNTTYINIGSSYFPEHGYFR
279


173
plexin domain containing 2
gi|40255005

160


VNLSFDFPFYGHFLR
280


174
selectin L
gi|4506875

60


FCRDNYTDLVAIQNK
281






104


IGGIWTWVGTNKS
282


175
basal cell adhesion molecule
gi|31543106
(isoform 1)
377, 383


VAYLDPLELSEGKVLSLPLNSSAVVNCSVHGLPTPALR
283




gi|61742797
(isoform 2)
377, 383


VAYLDPLELSEGKVLSLPLNSSAVVNCSVHGLPTPALR
283


176
AXL receptor tyrosine kinase
gi|21536466
(isoform 1)
198


SLHVPGLNKTSSFSCEAHNAK
284




gi|21536468
(isoform 2)
198


SLHVPGLNKTSSFSCEAHNAK
284


177
carbohydrate (chondroitin 4)
gi|8922112

209


EHVHNASAHLTFNK
285



sulfotransferase 12


280


LYANHTSLPASAR
286


178
carboxypeptidase A4
gi|61743916

260


SRNPGSSCIGADPNRNWNASFAGK
287


179
carcinoembryonic antigen-related cell
gi|40255013

224


RNDAGSYECEIQNPASANRSDPVTLNVLYGPDGPTISPSK
288



adhesion molecule 6 (non-specific



cross reacting antigen)


180
cell adhesion molecule 4
gi|21686977

67


QTLFFNGTR
289


181
EGF-like-domain, multiple 3
gi|110347457

961, 972


SACNCTAGAACDAVNGSCLCPAGR
290


182
fibroblast growth factor receptor 1
gi|105990522
(isoform 1)
264


SPHRPILQAGLPANKT
291






296


HIEVNGSKIGPDNLPYVQILK
292




gi|13186251
(isoform 2)
262


SPHRPILQAGLPANKT
291






294


HIEVNGSKIGPDNLPYVQILK
292




gi|13186234
(isoform 3)
175


SPHRPILQAGLPANKT
291






207


HIEVNGSKIGPDNLPYVQILK
292




gi|13186236
(isoform 4)
173


SPHRPILQAGLPANKT
291






205


HIEVNGSKIGPDNLPYVQILK
292




gi|13186238
(isoform 5)
175


SPHRPILQAGLPANKT
291






207


HIEVNGSKIGPDNLPYVQILK
292




gi|13186241
(isoform 6)
173


SPHRPILQAGLPANKT
291






205


HIEVNGSKIGPDNLPYVQILK
292




gi|13186249
(isoform 9)
264


SPHRPILQAGLPANKT
291






296


HIEVNGSKIGPDNLPYVQILK
292


183
fibulin 1
gi|34734068
(isoform A)
535, 539


NCQDIDECVTGIHNCSINETCFNIQGGFR
293




gi|34734064
(isoform B)
535, 539


NCQDIDECVTGIHNCSINETCFNIQGGFR
293




gi|34734062
(isoform C)
535, 539


NCQDIDECVTGIHNCSINETCFNIQGGFR
293




gi|34734066
(isoform D)
535, 539


NCQDIDECVTGIHNCSINETCFNIQGGFR
293


184
G protein-coupled receptor 126
gi|74048357
(alpha 1)
324


ILSNLSCNVK
294






593, 600, 605


EANEVANQILNLTADGQNLTSANITNIVEQVKR
295




gi|74048422
(alpha 2)
324


ILSNLSCNVK
294






565, 572, 577


EANEVANQILNLTADGQNLTSANITNIVEQVKR
295




gi|50355941
(beta 1)
324


ILSNLSCNVK
294






593, 600, 605


EANEVANQILNLTADGQNLTSANITNIVEQVKR
295




gi|74048403
(beta 2)
324


ILSNLSCNVK
294






565, 572, 577


EANEVANQILNLTADGQNLTSANITNIVEQVKR
295


185
inducible T-cell co-stimulator ligand
gi|27477039

102


LFNVTPQDEQK
296


186
platelet-derived growth factor C
gi|9994187

55


IITVSTNGSIHSPR
297


187
plexin B1
gi|40254442

1253


YTLDPNITSAGPTK
298


188
prosaposin
gi|11386147
(isoform a)
80


SLPCDICKDVVTAAGDMLKDNATEEEILVYLEK
299






101


TCDWLPKPNMSASCK
300






426



NSTKQEILAALEK

301




gi|110224476
(isoform b)
80


SLPCDICKDVVTAAGDMLKDNATEEEILVYLEK
299






101


TCDWLPKPNMSASCK
300






429



NSTKQEILAALEK

301




gi|110224479
(isoform c)
80


SLPCDICKDVVTAAGDMLKDNATEEEILVYLEK
299






101


TCDWLPKPNMSASCK
300






428



NSTKQEILAALEK

301


189
semaphorin 7A
gi|4504237

105


VYLFDFPEGKNASVR
302






157


HPSCWNLVNGTVVPLGEMR
303


190
UDP-Gal:betaGlcNAc
gi|4502349

385


RPPARPGPLSTANHTALRGSH
304



beta 1,4-galactosyltransferase 3


191
UDP-GlcNAc:betaGal
gi|5802984

204


VAQPGINYALGTNVSYPNNLLR
305



beta-1,3-N-



acetylglucosaminyltransferase 1


300


NELVQLYQVGEVRPFYYGLCTPCQAPTNYSR
306


192
UDP-GlcNAc:betaGal
gi|9845238

173


ESWGQESNAGNQTVVR
307



beta-1,3-N-



acetylglucosaminyltransferase 2


193
intercellular adhesion molecule 1
gi|4557878

267


LNPTVTYGNDSFSAK
308


194
haptoglobin-related protein
gi|45580723

126


MVSHHNLTTGATLINEQWLLTTAK
309






149, 153


NLFLNHSENATAKDIAPTLTLYVGKK
310


195
lysosomal-associated membrane protein
gi|112380628

62


SGPKNMTFDLPSDATVVLNR
311



1


62, 76


SGPKNMTFDLPSDATVVLNRS
312






121, 130


YSVQLMSFVYNLSDTHLFPNASSK
313


196
fibrinogen, gamma chain
gi|70906437
(A precursor)
78


VDKDLQSLEDILHQVENKT
314




gi|70906439
(B precursor)
78


VDKDLQSLEDILHQVENKT
314


197
leucine-rich alpha-2-glycoprotein 1
gi|16418467

186


KLPPGLLANFTLLR
315


198
ADAM metallopeptidase with
gi|21265034
(isoform 1)
667


YGEEYGNLTRPDITFTYFQPKPR
316



thrombospondin type 1 motif, 13
gi|73695936
(isoform 2)
667


YGEEYGNLTRPDITFTYFQPKPR
316




gi|21265043
(isoform 3)
636


YGEEYGNLTRPDITFTYFQPKPR
316


199
butyrylcholinesterase
gi|4557351

85


WSDIWNATK
317


200
complement component 1,
gi|7705753

146


RNPPMGGNVVIFDTVITNQEEPYQNHSGR
318



q subcomponent, A chain


201
polydom
gi|148886654

2876


VCLANGSWSGATPDCVPVR
319






2992


CLSNGSWSGSSPSCLPCR
320


202
protease inhibitor 16
gi|70780384

403, 409


SLPNFPNTSATANATGGR
321


203
alpha 1B-glycoprotein
gi|21071030

179


EGDHEFLEVPEAQEDVEATFPVHQPGNYSCSYR
322


204
apolipoprotein H
gi|4557327

162


VYKPSAGNNSLYR
323






183, 193


DTAVFECLPQHAMFGNDTITCTTHGNWTKLPECR
324






253


LGNWSAMPSCK
325


205
complement component 4A
gi|67190748

226


FSDGLESNSSTQFEVKK
326






1328


GLNVTLSSTGR
101


206
mesothelin
gi|53988378
(isoform 1)
488


LAFQNMNGSEYFVK
327




gi|53988380
(isoform 2)
496


LAFQNMNGSEYFVK
327


207
multimerin 1
gi|45269141

114, 120


LQNLTLPTNASIK
328






136


FNPGAESVVLSNSTLK
329


208
serine (or cysteine) proteinase
gi|4502261

128


LGACNDTLQQLMEVFKFDTISEK
330



inhibitor,


224


AAINKWVSNKTEGR
331



clade C (antithrombin), member 1


209
fibrinogen, beta chain
gi|70906435

394


GTAGNALMDGASQLMGENRT
332


210
major histocompatibility complex,
gi|52630342

110


GYYNQSEDGSHTLQR
333



class I, C


211
oxygen regulated protein
gi|5453832

830


LSALDNLLNHSSMFLK
334






862, 869


VINETWAWKNATLAEQAK
335






922, 931


DKNGTRAEPPLNASASDQGEK
336


212
cathepsin B
gi|22538431

38



NTTWQAGHNFYNVDMSYLKR

337




gi|22538433




gi|22538435




gi|22538437




gi|4503139


213
alpha-galactosidase A
gi|4504009

215


SIVYSCEWPLYMWPFQKPNYTEIR
338


214
ADAM metallopeptidase domain 9
gi|4501915
(isoform 1)
125


GYVEGVHNSSIALSDCFGLR
339






144, 154


GLLHLENASYGIEPLQNSSHFEHIIYR
340




gi|54292121
(isoform 2)
125


GYVEGVHNSSIALSDCFGLR
339






144, 154


GLLHLENASYGIEPLQNSSHFEHIIYR
340


215
calcium activated nucleotidase 1
gi|20270339

88


LGQAPANWYNDTYPLSPPQRTPAGIR
341


216
serine protease inhibitor, Kunitz
gi|10863909

94


KCATVTENATGDLATSR
342



type, 2


217
tripeptidyl-peptidase I
gi|5729770

443


FLSSSPHLPPSSYFNASGR
343


218
angiopoietin-like 4 protein
gi|21536398
(isoform a)
177


LPEMAQPVDPAHNVSR
344


219
olfactomedin-like 3
gi|9910270

177


IYVLDGTQNDTAFVFPR
345


220
olfactomedin-like 2A
gi|116014339

184


HYENHSAIMLGIKK
346


221
aspartate beta-hydroxylase
gi|14589866
(isoform a)
452


LVQLFPNDTSLK
347


222
galactosidase, beta 1-like
gi|40255043

486


LSFGSNSSDFK
348


223
neuronal cell adhesion molecule
gi|81158224
(isoform B)
842


VNVVNSTLAEVHWDPVPLK
349


224
semaphorin 3C
gi|5454048

585



NNTTFLECAPK

350


225
adlican
gi|139948432

2415


SDSGNYTCLVR
351


226
amiloride binding protein 1
gi|73486661

538


LENITNPWSPR
352


227
astacin-like metalloendopeptidase (M12
gi|66392154

266


WNLSASDITR
353



family)


228
carbonic anhydrase XI
gi|9951923

108


HVSFLPAPRPVVNVSGGPLLYSHR
354


229
follistatin-like 3 glycoprotein
gi|5031701

73


AECCASGNIDTAWSNLTHPGNK
355


230
glycosylphosphatidylinositol specific
gi|29171717
(isoform 1)
568, 591


LNVEAANWTVRGEEDFSWFGYSLHGVTVDNRT
356



phospholipase D1


231
H factor (complement)-like 3
gi|5031695

126


LQNNENNISCVER
357


232
inhibin beta B subunit
gi|9257225

93


GRPNITHAVPK
358


233
latent transforming growth factor
gi|18497288

349


LNSTHCQDINECAMPGVCR
359



beta binding protein 3


234
legumain
gi|56682962

263, 272


SHTNTSHVMQYGNKTISTMK
360


235
serine (or cysteine) proteinase
gi|21361302

108


SQILEGLGFNLTELSESDVHR
361



inhibitor,



clade A (alpha-1 antiproteinase,



antitrypsin), member 4


236
spondin 1, extracellular matrix
gi|110347423

214


LTFYGNWSEK
362



protein


237
ABI gene family, member 3 (NESH)
gi|33667044

44


VHINTTSDSILLK
363



binding protein


238
asporin (LRR class 1)
gi|41350214

282


LGLGNNKITDIENGSLANIPR
364


239
carboxypeptidase X, member 1
gi|9994201

318


QVQEQCPNITR
365


240
chordin-like 1
gi|34147715

291


AFGIVECVLCTCNVTK
366


241
immunoglobulin J chain
gi|21489959

71


IIVPLNNRENISDPTSPLR
367


242
desmoglein 2
gi|116534898

462


YVQNGTYTVK
368


243
slit-like 2
gi|88702793

117


LHEITNETFR
369


244
paraoxonase 1
gi|19923106

324


VTQVYAENGTVLQGSTVASVYK
370


245
cathepsin C
gi|4503141
(isoform a)
276


ILTNNSQTPILSPQEVVSCSQYAQGCEGGFPYLIAGK
371


246
ceroid-lipofuscinosis, neuronal 5
gi|5729772

304


NIETNYTR
372


247
claudin domain containing 1 protein
gi|11096340
(isoform a)
42


SPVQENSSDLNK
373


248
fibroblast growth factor receptor-like
gi|51988910

293


RVEYGAEGRHNSTIDVGGQK
374



1


249
oncostatin M receptor
gi|4557040

176


NIQNNVSCYLEGK
375


250
semaphorin 3A
gi|5174673

590


IIYGVENSSTFLECSPK
376


251
superoxide dismutase 3, extracellular
gi|118582275

107


AKLDAFFALEGFPTEPNSSSR
377


252
tissue inhibitor of metalloproteinase
gi|4507513

207


GWAPPDKSIINATDP
378



3


253
laminin alpha 2 subunit
gi|28559088
(isoform a)
2657


YMQNLTVEQPIEVK
379


254
serine (or cysteine) proteinase
gi|21361195

262


VVGVPYQGNATALFILPSEGK
380



inhibitor,



clade A (alpha-1 antiproteinase,



antitrypsin), member 5


255
periostin, osteoblast specific factor
gi|5453834

599


IFLKEVNDTLLVNELKSK
381


256
peroxidasin homolog
gi|109150416

1368


QGEHLSNSTSAFSTR
382


257
pregnancy specific beta-1-glycoprotein
gi|4506175
(isoform a)
302


ILILPSVTRNETGPYQCEIR
383



6


258
glycoprotein hormones, alpha
gi|4502787

76


TMLVQKNVTSESTCCVAK
384



polypeptide


259
PTK7 protein tyrosine kinase 7
gi|15826840
(isoform a)
175


DGTPLSDGQSNHTVSSK
385


260
protein tyrosine phosphatase,
gi|104487006
(isoform 1)
733


726/KVEAEALNATAIR/738
386



receptor type, sigma


261
unc5C
gi|16933525

236


LSDTANYTCVAK
387


262
latent transforming growth factor
gi|110347437
(isoform c)
62



NATSVDSGAPGGAAPGGPGFR

388



beta binding protein 4









(2) The glycoprotein for an epithelial ovarian cancer diagnosis marker according to (1), wherein the glycan is a fucosylated glycan and/or a glycan comprising terminal N-acetylgal acto samine.


(3) The glycoprotein for an epithelial ovarian cancer diagnosis marker according to (1) or (2), wherein the glycan binds to AAL lectin and/or WFA lectin.


(4) The glycoprotein for an epithelial ovarian cancer diagnosis marker according to any of (1) to (3), wherein the epithelial ovarian cancer is at least one of clear cell carcinoma, mucinous carcinoma, serous carcinoma, and endometrioid carcinoma.


(5) The glycoprotein for an epithelial ovarian cancer diagnosis marker according to (4), wherein the protein is collagen type VI alpha 1, and the epithelial ovarian cancer is clear cell carcinoma or serous carcinoma.


(6) A fragment of a glycoprotein for an epithelial ovarian cancer diagnosis marker according to any of (1) to (5), comprising at least one glycan-linked asparagine residue at the glycosylation site shown in Table 1.


(7) A method for determining the presence or absence of epithelial ovarian cancer, comprising the steps of: detecting at least one glycoprotein for an epithelial ovarian cancer diagnosis marker according to any of (1) to (5) and/or at least one fragment of the glycoprotein for an epithelial ovarian cancer diagnosis marker according to (6) from a sample collected from a test subject; and determining that the test subject is cotracted with epithelial ovarian cancer when the glycoprotein for an epithelial ovarian cancer diagnosis marker and/or the fragment of the glycoprotein have been detected.


(8) The method according to (7), wherein the detection step comprises a glycoprotein enrichment step and a protein detection step.


(9) The method according to (7) or (8), wherein the glycoprotein for an epithelial ovarian cancer diagnosis marker and/or the fragment of the glycoprotein are detected using at least one glycan probe binding to the glycan.


(10) The method according to (9), wherein the glycan probe is a lectin, an antibody, or a phage antibody.


(11) The method according to (10), wherein the lectin is AAL or WFA.


(12) The method according to any of (7) to (11), wherein the sample is a body fluid, a cell, or a peritoneal lavage fluid.


(13) The method according to any of (7) to (12), wherein the epithelial ovarian cancer is at least one of clear cell carcinoma, mucinous carcinoma, serous carcinoma, and endometrioid carcinoma.


Advantageous Effects of Invention

The epithelial ovarian cancer diagnosis marker and the method for determining the presence or absence of epithelial ovarian cancer according to the present invention enable the presence or absence of epithelial ovarian cancer to be determined conveniently, relatively inexpensively, and low invasively with high accuracy using a body fluid, a cell, or a peritoneal lavage fluid.





BRIEF DESCRIPTION OF DRAWINGS


FIG. 1 shows results of selecting probe lectins. RMUG-S, RMG-I, RMG-II, RMG-V, and RTSG are cultured cells derived from epithelial ovarian cancer. Colo205 and Colo201 are cultured cells derived from colon cancer. KATO III is cultured cells derived from stomach cancer. FIG. 1A shows the results about WFA lectin selected as a probe lectin. FIG. 1B shows the results about AAL lectin also selected as a probe lectin.



FIG. 2 is a Western blot image showing the presence of collagen type VI alpha 1 (COL6α1) glycoprotein in peritoneal lavage fluids collected from clear cell adenocarcinoma patients, endometrioid adenocarcinoma patients, serous adenocarcinoma patients, and stomach cancer patients (two patients each). Each peritoneal lavage fluid was subjected to AAL lectin column chromatography to enrich and separate glycoproteins binding to AAL lectin, followed by the detection of COL6α1 with an anti-COL6α1 antibody.



FIG. 3 is a Western blot image showing the presence of LOXL2 (lysyl oxidase-like 2) glycoprotein in peritoneal lavage fluids collected from clear cell adenocarcinoma patients, endometrioid adenocarcinoma patients, serous adenocarcinoma patients, and stomach cancer patients (two patients each). Each peritoneal lavage fluid was subjected to WFA lectin column chromatography to enrich and separate glycoproteins binding to WFA lectin, followed by the detection of LOXL2 with an anti-LOXL2 antibody.



FIG. 4 is a Western blot image showing the presence of ceruloplasmin (CP) glycoprotein in peritoneal lavage fluids collected from clear cell adenocarcinoma patients, endometrioid adenocarcinoma patients, serous adenocarcinoma patients, and a stomach cancer patient (two patients each except for one stomach cancer patient). Each peritoneal lavage fluid was subjected to WFA lectin column chromatography to enrich and separate glycoproteins binding to WFA lectin, followed by the detection of CP with an anti-CP antibody.



FIG. 5 is a Western blot image showing the presence of SERPING1 glycoprotein in peritoneal lavage fluids collected from clear cell adenocarcinoma patients, endometrioid adenocarcinoma patients, serous adenocarcinoma patients, and stomach cancer patients (two patients each). Each peritoneal lavage fluid was subjected to WFA lectin column chromatography to enrich and separate glycoproteins binding to WFA lectin, followed by the detection of SERPING1 with an anti-SERPING1 antibody.



FIG. 6 is a Western blot image showing the presence of F12 (blood coagulation factor XII) glycoprotein in peritoneal lavage fluids collected from clear cell adenocarcinoma patients, endometrioid adenocarcinoma patients, serous adenocarcinoma patients, and stomach cancer patients (two patients each). Each peritoneal lavage fluid was subjected to WFA lectin column chromatography to enrich and separate glycoproteins binding to WFA lectin, followed by the detection of F12 with an anti-F12 antibody.





DESCRIPTION OF EMBODIMENTS

1. Glycoprotein for Epithelial Ovarian Cancer Diagnosis Marker and Fragment thereof having Glycan


The first embodiment of the present invention provides a glycoprotein for an epithelial ovarian cancer diagnosis marker described in Table 1 and a fragment of the glycoprotein.


1-1. Glycoprotein for Epithelial Ovarian Cancer Diagnosis Marker

The “glycoprotein for an epithelial ovarian cancer diagnosis marker” of this embodiment is a glycoprotein represented by any of Protein #1 to #262 in Table 1, wherein, in its amino acid sequence, a glycan specific for epithelial ovarian cancer is linked to an asparagine residue at least at a position (counted from the initiating amino acid residue (initiating methionine) as the first position) represented by “Glycosylation site” in Table 1. For example, the glycoprotein of Protein #1 in Table 1 corresponds to collagen type VI alpha 1 protein (hereinafter, referred to as “COL6α1”) having a glycan-linked asparagine residue at least at position 212 on its amino acid sequence. In the case where a plurality of glycosylation sites per protein are described in Table 1, the glycan may be linked to at least one of these sites. In the case where two asparagine residues are described as to, for example, biglycan of Protein #2 having (positions 270 and 311) or complement component 4 (C4) binding protein alpha chain of Protein #15 (positions 506 and 528), each protein in which the glycan is linked to at least one of the asparagine residues suffices as the glycoprotein for an epithelial ovarian cancer diagnosis marker of the present invention. Hereinafter, in the present specification, such a glycosylated protein is referred to as a “glycoprotein”, and a base protein moiety excluding a glycan is referred to as a “core protein”.


In the table, “gi(ID)” represents the ID number of the core protein in each glycoprotein of this embodiment. A plurality of gi(ID) numbers registered for one core protein are all described in the table. Also, a plurality of possible isoforms of one core protein are indicated by isoform numbers together with their gi(ID) numbers in the table. In the case where the position of a glycosylation site counted from the initiating amino acid residue differs among the isoforms due to mRNA splicing or the like, the corresponding glycosylation site of each isoform is described in the table.


The glycan linked to the asparagine residue in the glycoprotein of this embodiment is not particularly limited as long as the glycan is specific for epithelial ovarian cancer. In this context, the “glycan specific for epithelial ovarian cancer” include, for example, a fucosylated glycan and/or a glycan comprising terminal N-acetylgalactosamine (hereinafter, referred to as “GalNAc”). These glycans can be identified using a lectin, an antibody, or a phage antibody that specifically recognizes and binds to each glycan. Examples of the lectin against the fucosylated glycan include Aleuria aurantia-derived AAL lectin and Lens culinaris-derived LCA lectin, which each specifically bind to thereto. Examples of the lectin against the terminal GalNAc include Wisteria floribunda-derived WFA lectin, which specifically binds thereto.


In Table 1, each glycoprotein for an epithelial ovarian cancer diagnosis marker confirmed to bind to AAL lectin or WFA lectin is indicated in circle (∘), while an unconfirmed one is indicated in dash (−).


The histological types of “epithelial ovarian cancer” are known to consist principally of clear cell carcinoma, mucinous carcinoma, endometrioid carcinoma, and serous carcinoma. At least one of these histological types can be diagnosed using the glycoprotein for an epithelial ovarian cancer diagnosis marker of this embodiment. For example, lysyl oxidase-like 2 (LOXL2) glycoprotein represented by Protein #28, ceruloplasmin (CP) glycoprotein represented by Protein #35, blood coagulation factor XII (F12) glycoprotein represented by Protein #68, and serpin peptidase inhibitor clade G(Cl inhibitor) member 1 (SERPING1) glycoprotein represented by Protein #42 in Table 1 each permit the diagnosis of all of the histological types, i.e., clear cell carcinoma, mucinous carcinoma, endometrioid carcinoma, and serous carcinoma (see Example 2 described below). In other words, these glycoproteins can serve as epithelial ovarian cancer diagnosis markers useful for determining whether or not a test subject has epithelial ovarian cancer, irrespective of the histological types. On the other hand, collagen type VI alpha 1 (COL6α1) glycoprotein represented by Protein #1 in Table 1 permits the diagnosis of clear cell carcinoma and serous carcinoma (see Example 2 described below). The clear cell carcinoma is a histological type that occurs with increased frequency in Japan compared with Western countries and results in poorer prognosis than that of the serous carcinoma, and is also known to be complicated by endometriosis with high frequency, as with the endometrioid carcinoma (Yoshikawa H. et al., 2000, Gynecol. Obstet., 1: 11-17). Thus, the COL6α1 glycoprotein can serve as a marker capable of determining whether or not the histological type of epithelial ovarian cancer complicated by endometriosis is clear cell carcinoma. Since the clear cell carcinoma has a high rate of reoccurrence and exhibits chemotherapy resistance, this histological type requires strict follow-up even for cases where their lesions have been detected early and thereby excised. Hence, a marker, such as the COL6α1 glycoprotein, which is capable of identifying the clear cell carcinoma can serve as a very useful epithelial ovarian cancer diagnosis marker.


1-2. Fragment of Glycoprotein for Epithelial Ovarian Cancer Diagnosis Marker

The “fragment of the glycoprotein for an epithelial ovarian cancer diagnosis marker” of this embodiment refers to an oligopeptide or polypeptide fragment consisting of a portion of the glycoprotein for an epithelial ovarian cancer diagnosis marker. This fragment comprises, in its amino acid sequence, at least one asparagine residue at the glycosylation site shown in Table 1, wherein the glycan specific for epithelial ovarian cancer described in the paragraph “1-1. Glycoprotein for epithelial ovarian cancer diagnosis marker” is linked to this asparagine residue.


The amino acid length of the fragment of the glycoprotein for an epithelial ovarian cancer diagnosis marker is not particularly limited and is preferably 5 to 100 amino acids, 8 to 80 amino acids, or 8 to 50 amino acids.


Hereinafter, the glycoprotein for an epithelial ovarian cancer diagnosis marker and the fragment of the glycoprotein for a marker are also collectively referred to as an “epithelial ovarian cancer diagnosis marker”.


Specific examples of the fragment of the glycoprotein for an epithelial ovarian cancer diagnosis marker include glycopeptides consisting of amino acid sequences represented by SEQ ID NOs: 1 to 388, wherein the glycan specific for epithelial ovarian cancer is linked to an asparagine residue corresponding to the glycosylation site shown in Table 1. The glycopeptides listed are fragments of glycoproteins for epithelial ovarian cancer diagnosis markers that were obtained by an IGOT method (described later) in identifying the glycoprotein for an epithelial ovarian cancer diagnosis marker of this embodiment. All of these fragments can be used to determine the presence or absence of epithelial ovarian cancer. In each amino acid sequence shown in Table 1, the underlined asparagine residue (N) represents a glycan-linked asparagine residue. In the case where a plurality of underlined asparagine residues exist in the amino acid sequence shown in Table 1, each glycopeptide in which the glycan is linked to at least one of the asparagine residues suffices as the fragment of the glycoprotein for an epithelial ovarian cancer diagnosis marker of the present embodiment.


2. Method for Determining Presence or Absence of Epithelial Ovarian Cancer

The second embodiment of the present invention provides a method for determining the presence or absence of epithelial ovarian cancer.


The method of this embodiment comprises a detection step and a confirmation step. Hereinafter, each step will be described specifically.


2-1. Detection Step

The “detection step” is the step of detecting at least one glycoprotein for an epithelial ovarian cancer diagnosis marker and/or at least one fragment of the glycoprotein, i.e., the epithelial ovarian cancer diagnosis marker(s), according to Embodiment 1 from a sample collected from a test subject. This step further comprises, if necessary, a glycoprotein enrichment step and a protein detection step.


In the present specification, the “test subject” refers to a person to be subjected to examination, i.e., a human donor of a sample described later. The test subject may be any patient having a certain disease or any normal individual. The test subject is preferably a person possibly having epithelial ovarian cancer or an epithelial ovarian cancer patient.


The “sample” refers to a part that is obtained from the test subject and subjected to the determination method of this embodiment. For example, a body fluid, a cell (including cell extracts), or a peritoneal lavage fluid applies to the sample.


The “body fluid” refers to a biological sample in a liquid state collected directly from the test subject. Examples thereof include blood (including serum, plasma, and interstitial fluid), lymph, ascitic fluid, pleural effusion, sputum, spinal fluid, lacrimal fluid, nasal discharge, saliva, urine, vaginal fluid, and seminal fluid. The sample is preferably a body fluid such as blood, lymph, or ascitic fluid, or a peritoneal lavage fluid obtained using saline. The body fluid or the peritoneal lavage fluid collected from the test subject may be used, if necessary, after pretreatment such as dilution or concentration or the addition of an anticoagulant such as heparin thereto, or may be used directly without such pretreatment. Alternatively, the cell may be disrupted by a method known in the art to obtain its extracts. For the method for preparing cell extracts, see methods described in, for example, McMamee M. G. 1989, Biotechniques, 7: 466-475 or Johnson B.H. et al., 1994, Biotechnology (N Y), 12: 1357-1360. The body fluid or the peritoneal lavage fluid may be collected on the basis of a method known in the art. For example, blood or lymph can be collected according to a blood collection method known in the art. Specifically, peripheral blood can be collected from the vein or the like of a peripheral site by injection. Alternatively, the ascitic fluid or the peritoneal lavage fluid can be collected by transabdominal ultrasound-guided aspiration steering around the intestinal tract, or collected by aspiration using a syringe or the like from the Douglas' pouch after intraperitoneal injection of approximately 100 mL of saline during laparotomy. As for the cell, cells to be subjected to examination can be surgically collected from an appropriate organ or tissue.


The body fluid or the peritoneal lavage fluid may be used immediately after the collection, or may be cryopreserved for a given period and then treated, if necessary, by thawing or the like before use. In this embodiment, in the case of using serum or the peritoneal lavage fluid, the epithelial ovarian cancer diagnosis marker can be detected typically using a volume of 10 μL to 100 μL.


The epithelial ovarian cancer diagnosis marker to be detected in this step may be any epithelial ovarian cancer diagnosis marker described in Table 1. One epithelial ovarian cancer diagnosis marker may be detected, or two or more epithelial ovarian cancer diagnosis markers may be detected. Each individual epithelial ovarian cancer diagnosis marker can be sufficiently detected by the detection of at least one glycan-linked asparagine residue at a glycosylation site shown in Table 1 in a glycoprotein for this epithelial ovarian cancer diagnosis marker.


The method for detecting the epithelial ovarian cancer diagnosis marker may be any method without particular limitations as long as the method is known in the art and is capable of detecting the glycoprotein. At least one glycan probe that binds to the glycan in each epithelial ovarian cancer diagnosis marker can be used in the detection.


In the present specification, the “glycan probe” refers to a determinant that specifically recognizes a particular glycan and/or glycoconjugate such as a glycoprotein and binds thereto. Examples thereof include lectins, antibodies, and phage antibodies. When the glycan probe is a lectin, examples of the lectin that may be used in this step include AAL lectin, LCA lectin, and WFA lectin.


Specifically, the detection method that can be used is a method comprising, in combination, for example, a glycoprotein enrichment step of using a glycan probe specifically binding to the glycan in each epithelial ovarian cancer diagnosis marker to selectively enrich glycoproteins having the glycan, and a protein detection step of detecting the epithelial ovarian cancer diagnosis marker using an antibody or the like specific for its core protein. More specifically, the detection method is as follows, for example.


Glycoprotein enrichment step: A glycoprotein group contained in a peritoneal lavage fluid or a body fluid (e.g., serum) obtained from a test subject is separated using a glycan probe, for example, a lectin (hereinafter, in the present specification, referred to as lectin A for the sake of convenience), specifically binding to the glycan in the glycoproteins.


Protein detection step: Subsequently, a moiety other than the glycan specifically binding to lectin A, for example, the core protein, in the epithelial ovarian cancer diagnosis marker to be detected is detected using, an antibody or the like that specifically recognizes the core protein, for example, an anti-core protein antibody (hereinafter, in the present specification, referred to as “antibody B” for the sake of convenience).


As a result, the epithelial ovarian cancer diagnosis marker of interest having the glycan specifically binding to lectin A can be detected. These enrichment and detection steps for the core protein in the glycoprotein may be carried out in any order. For example, a protein enrichment step of enriching core proteins using the antibody B may be followed by the detection of the glycoprotein of interest using a glycan probe (e.g., lectin A) (glycoprotein detection step).


Alternatively, a method using an antibody that is specific for the epithelial ovarian cancer diagnosis marker having the glycan specifically binding to lectin A and recognizes both of its glycan and protein moieties as epitopes can be used for detecting the epithelial ovarian cancer diagnosis marker of interest. This method is convenient because the epithelial ovarian cancer diagnosis marker of interest, i.e., the epithelial ovarian cancer diagnosis marker having the glycan specifically binding to lectin A, contained in a peritoneal lavage fluid or serum obtained from a test subject can be detected by one step.


This method can be achieved by use of a lectin A-immobilized column or array, and means of detecting the epithelial ovarian cancer diagnosis marker, more specifically, for example, lectin-antibody sandwich ELISA, antibody-overlay lectin array method, lectin-overlay-antibody array method, mass spectrometry (including high-performance liquid chromatography-mass spectrometry (LC-MS), high-performance liquid chromatography-tandem mass spectrometry (LC-MS/MS), gas chromatography-mass spectrometry (GC-MS), gas chromatography-tandem mass spectrometry (GC-MS/MS), capillary electrophoresis-mass spectrometry (CE-MS), and ICP-mass spectrometry (ICP-MS)), immunoassay, enzymatic activity assay, capillary electrophoresis, gold colloid method, radioimmunoassay, latex agglutination immunoassay, fluorescent immunoassay, Western blotting, immunohistochemical method, surface plasmon resonance spectroscopy (SPR method), or quartz crystal microbalance (QCM) method, using an antibody against the epithelial ovarian cancer diagnosis marker, preferably a monoclonal or polyclonal antibody specific for the epithelial ovarian cancer diagnosis marker having the glycan specifically binding to lectin A. All of these methods are known in the art and can be carried out according to ordinary methods in the art. As specific examples, the lectin-antibody sandwich ELISA, the antibody-overlay lectin array method, and the lectin-overlay-antibody array method will be described below.


The lectin-antibody sandwich ELISA is based on the same fundamental principles as those of sandwich ELISA using two types of antibodies except that one of the antibodies in the sandwich ELISA is merely replaced by a lectin. Thus, this approach is also applicable to automatization using an existing automatic immunodetection apparatus. The point to be noted is only the reaction between antibodies and lectins to be used for sandwiching antigens. Each antibody has at least two N-linked glycans. When the lectins used recognize glycans on the antibodies, background noise occurs during sandwich detection due to the binding reaction therebetween. A possible method for preventing the generation of this noise signal involves modifying the glycan moieties on the antibodies or using only Fab fragments, which contain no such glycan moieties. For these purposes, approaches known in the art can be used. The method for modifying the glycan moieties is described in, for example, Chen S. et al., 2007, Nat. Methods, 4: 437-44 or Comunale M.A. et al., 2009, J. Proteome Res., 8: 595-602. The method using Fab fragments is described in, for example, Matsumoto H. et al., 2010, Clin. Chem. Lab. Med., 48: 505-512.


The antibody-overlay lectin array method is a method using a lectin microarray. The lectin array refers to a substrate on which plural types of lectins differing in specificity are immobilized in parallel (i.e., in the form of array) as glycan probes. The lectin array can realize concurrent analysis on the types of lectins interacted with analyte glycoconjugates and the degrees of these interactions. The fundamental principles of this lectin microarray technique are described in, for example, Kuno A. et al. 2005, Nat. Methods 2: 851-856. A lectin array in which 45 types of lectins are immobilized on a substrate is commercially available as LecChip from GP BioSciences Ltd. and may therefore be used. In the antibody-overlay lectin array method, a fluorescent group or the like can be introduced indirectly into the sample of the test subject via an antibody, and concurrent multisample analysis can be achieved conveniently and quickly using the lectin array. The specific procedures of this method are described in Kuno A. et al., 2009, Mol. Cell Proteomics 8: 99-108, Jun Hirabayashi et al., 2007, Experimental Medicine, extra number “Study on Cancer Diagnosis at Molecular Level—Challenge to Clinical Application”, Yodosha Co., Ltd., Vol. 25 (17): 164-171, and Atsushi Kuno et al., 2008, Genetic Medicine MOOK No. 11, pp. 34-39, Medical Do, Inc.


For example, glycan moieties in glycoproteins in the sample of the test subject are specifically recognized by lectins on the lectin microarray. Thus, antibodies against the core protein moieties thereof can be overlaid on the glycoproteins to thereby specifically and highly sensitively detect the glycoproteins without labeling the test glycoproteins or highly purifying them.


The lectin overlay-antibody microarray method is a method using, instead of the lectin microarray for the antibody-overlay lectin array method, an antibody array in which antibodies against core proteins are immobilized in parallel (i.e., in the form of array) on a substrate such as a glass substrate. This method is based on the same fundamental principles as those of the antibody-overlay lectin array method except that the relationship between the lectins and the antibodies is merely reversed. The method, however, requires the same number of antibodies as the number of epithelial ovarian cancer diagnosis markers to be examined and also requires determining lectins in advance for detecting the alteration of glycans.


In these various detection methods, a commercially available polyclonal or monoclonal antibody that specifically recognizes the epithelial ovarian cancer diagnosis marker used or its core protein may be used. If such an antibody is not easily obtainable, this antibody can be prepared, for example, by a method given below.


First, the polyclonal antibody against the anti-epithelial ovarian cancer diagnosis marker glycopeptide can be prepared using a method well known in the art. Specifically, an adjuvant is added to the glycoprotein for an epithelial ovarian cancer diagnosis marker or the glycopeptide as an antigen to be detected. The glycopeptide for an epithelial ovarian cancer diagnosis marker containing glycosylation site(s) (asparagine residue(s)) may be synthesized and used as an antigen. Examples of the adjuvant include complete Freund's adjuvant and incomplete Freund's adjuvant. These adjuvants may be used as a mixture. The antigen may be inoculated, together with the adjuvant, to an antibody-producing animal to thereby boost antibody production. Alternatively, this peptide may be covalently bonded to commercially available keyhole limpet hemocyanin (KLH) or the like and inoculated to an antibody-producing animal. In this operation, granulocyte-macrophage colony stimulating factor (GM-CSF) may also be administered to the animal simultaneously therewith to thereby boost antibody production. Examples of the antibody-producing animal that can be used in antigen inoculation include mammals, for example, mice, rats, horses, monkeys, rabbits, goats, and sheep. The immunization can employ any of existing methods and is performed mainly by intravenous injection, hypodermic injection, intraperitoneal injection, or the like. The interval between immunization doses is not particularly limited and is an interval of several days to several weeks, preferably 4 to 21 days.


2 to 3 days after the final immunization date, whole blood is collected from the immunized animal. After serum separation, the polyclonal antibody can be prepared.


Alternatively, for example, the monoclonal antibody against the anti-epithelial ovarian cancer marker glycopeptide can be prepared by the method of Kohler & Milstein (Nature, 256: 495-497 (1975)). For example, antibody-producing cells obtained from the antigen-immunized animal are fused with myeloma cells to prepare hybridomas. From the obtained hybridomas, clones producing the anti-epithelial ovarian cancer diagnosis marker glycopeptide monoclonal antibody can be selected to thereby prepare the monoclonal antibody.


Specifically, 2 to 3 days after the final immunization date in the preparation of the polyclonal antibody, antibody-producing cells are collected. Examples of the antibody-producing cells include spleen cells, lymph node cells, and peripheral blood cells.


A cell line that is derived from any of various animals (e.g., mice, rats, and humans) and is generally obtainable by those skilled in the art is used as the myeloma cells to be fused with the antibody-producing cells. The cell line used is a drug-resistant cell line that cannot survive in a selective medium (e.g., HAT medium) in an unfused state, but can characteristically survive therein only in a fused state. In general, 8-azaguanine-resistant line is used. This cell line is deficient in hypoxanthine-guanine-phosphoribosyl transferase and cannot grow in a hypoxanthine-aminopterin-thymidine (HAT) medium.


The myeloma cells have already been known in the art, and various cell lines can be used preferably, for example, P3 (P3x63Ag8.653) (Kearney J. F. et al., 1979, J. Immunol., 123: 1548-1550), P3x63Ag8U.1 (Yelton D.E. et al., 1978, Curr. Top. Microbiol. Immunol., 81: 1-7), NS-1 (Kohler G. et al., 1976, Eur. J. Immunol., 6: 511-519), MPC-11 (Margulies D. H. et al., 1976, Cell, 8: 405-415), SP2/0 (Shulman M. et al., 1978, Nature, 276: 269-270), FO (de St. Groth S. F. et al., 1980, J. Immunol. Methods, 35: 1-21), 5194 (Trowbridge I.S. 1978, J. Exp. Med., 148: 313-323), and 8210 (Galfre G. et al., 1979, Nature, 277: 131-133).


Next, the myeloma cells and the antibody-producing cells are fused with each other. This cell fusion is performed by the contact between the myeloma cells and the antibody-producing cells at a mixing ratio of 1:1 to 1:10 at 30 to 37° C. for 1 to 15 minutes in the presence of a fusion promoter in a medium for animal cell culture such as MEM, DMEM, or RPMI-1640 medium or in a commercially available medium for cloning or cell fusion. A fusion promoter or a fusion virus, such as polyethylene glycol or polyvinyl alcohol having an average molecular weight of 1,000 to 6,000 or Sendai virus can be used for promoting the cell fusion. Alternatively, the antibody-producing cells and the myeloma cells may be fused with each other using a commercially available cell fusion apparatus based on electrical stimulation (e.g., electroporation).


After the cell fusion, hybridomas of interest are selected from the fused cells. Examples of the method therefor include a method using the selective growth of the cells in a selective medium. Specifically, the cell suspension is diluted with an appropriate medium and then seeded over a microtiter plate. A selective medium (e.g., HAT medium) is added to each well, and the cells are subsequently cultured with the selective medium appropriately replaced by a fresh one. As a result, the cells that have grown can be obtained as hybridomas.


The screening of the hybridoma is performed by, for example, a limiting dilution method or a fluorescence excitation method using a cell sorter. Finally, monoclonal antibody-producing hybridomas are obtained. Examples of the method for obtaining the monoclonal antibody from the obtained hybridomas include ordinary cell culture and ascitic fluid formation methods.


2-2. Confirmation Step

The “confirmation step” is the step of confirming the test subject with epithelial ovarian cancer when the epithelial ovarian cancer diagnosis marker has been detected in the detection step from the sample collected from the test subject.


The detection of the epithelial ovarian cancer diagnosis marker can be confirmed on the basis of whether or not the epithelial ovarian cancer diagnosis marker of interest has been detected as a result of conducting the detection method described in the detection step. When the determinant (e.g., glycan probe) has high specificity for the epithelial ovarian cancer diagnosis marker and exhibits no cross reactivity (i.e., when the determinant is an antibody), accurate diagnosis can be achieved by merely confirming the presence or absence of this detection.


On the other hand, when the determinant has relatively low specificity leading to the detection of other glycoproteins, etc. in addition to the epithelial ovarian cancer diagnosis marker to be detected (i.e., when detection background is relatively high), accurate diagnosis cannot be achieved by merely confirming the presence or absence of the detection. In this case, the presence or absence of epithelial ovarian cancer may be determined on the basis of a statistically significant difference in the amount of the target epithelial ovarian cancer diagnosis marker detected in the test subject compared with that in a normal individual. In this context, the “normal individual” is a person who has been shown to have no epithelial ovarian cancer, preferably a healthy person without any disease, more preferably a person similar in biological condition to the test subject, for example, a person having the same or similar sex, age, body weight, constitution (allergy, etc.), anamnesis, birth experience, or the like as that of the test subject.


The results of quantifying the epithelial ovarian cancer diagnosis marker by the detection method described in the detection step can be used as the amount of the epithelial ovarian cancer diagnosis marker detected. In this case, a protein known in the art expected to have no quantitative difference between the samples of the test subject and the normal individual can be used as an internal control to correct the quantification results of the test subject and the normal individual. Thus, the amount of the epithelial ovarian cancer diagnosis marker detected can be obtained more accurately. Examples of the protein for such an internal control include albumin.


The term “statistically significant” means that the statistical processing of the quantitative difference in the epithelial ovarian cancer diagnosis marker to be detected contained in respective samples collected from the test subject and the normal individual shows a significant difference between the samples. Specifically, examples of the significant difference include difference with a significance level smaller than 5%, 1%, or 0.1%. A testing method known in the art capable of determining the presence or absence of significance can be appropriately used as a testing method for the statistical processing without particular limitations. For example, the student's t test or multiple comparison test method can be used (Kanji Suzuki, Toukeigaku No Kiso (Basic of Statistics in English); and Yasushi Nagata, et al., Toukeiteki Tajyuhikakuhou No Kiso (Basic of Statistical Multiple Comparison Method in English)). The term “statistically significant difference” specifically means that the obtained value is higher or lower than a cutoff value defined as a value capable of separating patients from normal individuals such that sensitivity and specificity set by a routine method in multiple-specimen analysis are optimized.


Examples of specific methods for determining the presence or absence of epithelial ovarian cancer by the detection of the epithelial ovarian cancer diagnosis marker include methods given below.


When any one glycoprotein for an epithelial ovarian cancer diagnosis marker described in Table 1 or any one fragment of the glycoprotein, i.e., the epithelial ovarian cancer diagnosis marker, has been detected alone, the test subject as a donor of the sample is confirmed with epithelial ovarian cancer of type diagnosable with the epithelial ovarian cancer diagnosis marker. When no such marker has been detected, the test subject is confirmed not to have at least the epithelial ovarian cancer of type diagnosable with the epithelial ovarian cancer diagnosis marker. Specifically, when the LOXL2 glycoprotein represented by Protein #28 in Table 1, for example, has been detected in the sample, the test subject as a donor of the sample can be confirmed with epithelial ovarian cancer. Alternatively, when the COL6α1 glycoprotein represented by Protein #1 in Table 1 has been detected in the sample, the test subject as a donor of the sample can be confirmed with clear cell carcinoma or serous carcinoma or confirmed to highly possibly have the tumor.


Also, two or more epithelial ovarian cancer diagnosis markers described in Table 1 may be used in the detection. When these markers have been detected, the test subject as a donor of the sample is confirmed with epithelial ovarian cancer of type diagnosable with each of the epithelial ovarian cancer diagnosis markers. When no such markers have been detected, the test subject is confirmed not to have at least the epithelial ovarian cancer of type diagnosable with each of the epithelial ovarian cancer diagnosis markers. Specifically, for example, the LOXL2 glycoprotein represented by Protein #28 and the CP glycoprotein represented by Protein #35 in Table 1 are each used as epithelial ovarian cancer diagnosis markers in detection. When both of them have been detected, the test subject as a donor of the sample can be confirmed with epithelial ovarian cancer or confirmed to very highly possibly have the cancer. On the other hand, when the LOXL2 glycoprotein has been detected but the CP glycoprotein has not been detected, the results of detecting the LOXL2 glycoprotein are false-positive or the results of detecting the CP glycoprotein are false-negative. In this case, redetection, such as an attempt to detect a different epithelial ovarian cancer diagnosis marker can be confirmed to be necessary. Alternatively, the LOXL2 glycoprotein and the COL6α1 glycoprotein represented by Protein #1 are each used as epithelial ovarian cancer diagnosis markers in detection. When both of them have been detected, the test subject as a donor of the sample can be confirmed with epithelial ovarian cancer whose histological type is clear cell carcinoma when complicated by endometriosis. On the other hand, when the LOXL2 glycoprotein has been detected but the COL6α1 glycoprotein has not been detected, the test subject as a donor of the sample can be confirmed with epithelial ovarian cancer whose histological type is neither clear cell carcinoma nor serous carcinoma. Such detection of two or more epithelial ovarian cancer diagnosis markers is preferred as the method for determining the presence or absence of epithelial ovarian cancer according to this embodiment, because this method achieves more highly accurate diagnosis with lower false-positive and false-negative rates than those of the detection of any one epithelial ovarian cancer diagnosis marker alone and also can determine the presence or absence of epithelial ovarian cancer as well as its histological type.


EXAMPLES
Example 1
Selection of Epithelial Ovarian Cancer Diagnosis Marker

1. Selection of Probe Lectin on Lectin Microarray using Culture Supernatant (Method)


(1) Preparation of Culture Supernatants of Epithelial Ovarian Cancer, Stomach Cancer, and Colon Cancer Cell Lines

Five epithelial ovarian cancer cell lines (RMG-I, RMG-II, RTSG, RMG-V, and RMUG-S) were separately cultured using a medium containing 90% Ham F12 and 10% FBS (PS+: penicillin+ & streptomycin), while one stomach cancer cell line (KATO III) and two colon cancer cell lines (Colo201 and Colo205) were separately cultured as non-epithelial ovarian cancer cell lines using a medium containing 90% RPMI-1640 and 10% FBS (PS). In this operation, RMG-I, RMG-V, RMUG-S, RMG-II, and RTSG were each cultured in a dish having a diameter of 14 cm until reaching 80 to 90% confluency. After removal of the FBS-containing medium by suction, the cells of each cell line were washed seven times with 10 mL/dish of a non-supplemented medium (FBS-, PS), then supplemented with 30 mL of the same medium, and cultured for 48 hours. Alternatively, KATO III, Colo201, and Colo205 were each adjusted to 1 x 107 cells per dish having a diameter of 14 cm. The cells of each cell line were washed seven times by suspension through the addition of 10 mL of the non-supplemented medium and removal of the supernatant through centrifugation (1000 rpm, 5 minutes, room temperature), then seeded over a 14-cm dish, and cultured for 48 hours after addition of 30 mL of the non-supplemented medium. The supernatant of each cell line thus cultured was recovered by centrifugation (1000 rpm, 5 minutes, room temperature). The recovered supernatant was centrifuged again (3000 rpm, 5 minutes, room temperature), and the supernatant was recovered and cryopreserved at -80° C. The preserved sample was thawed before use, filtered through a 0.46-pm filter, and then used in subsequent analysis.


(2) Selection of Probe lectin on Lectin Microarray


Each culture supernatant thus prepared was concentrated and desalted using 2-D Clean-Up kit (GE Healthcare Japan Corp.). The obtained precipitates were lysed again in 20 μL of PBS. The protein concentration of each culture supernatant was measured using Micro BCA protein assay kit (Pierce Biotechnology, Inc.). Then, the culture supernatant was diluted with 10-fold with PBS. Proteins were collected in an amount corresponding to 100 ng in total, adjusted to 10 μL with PBSTx (PBS containing 1% Triton X-100), and then reacted at room temperature for 1 hour after addition of 20 ng of a fluorescent labeling reagent (Cy3-SE, GE Healthcare Japan Corp.). After the reaction, 90 μL of a glycine-containing buffer solution was added thereto, and the proteins were further reacted at room temperature for 2 hours to inactivate a redundant labeling reagent. The resulting fluorescently labeled glycoprotein solution was applied to a lectin microarray. The lectin microarray was used in which 3 spots each of 43 different lectins were immobilized. To attain the optimum comparative analysis for acquired binding signals, four dilutions series per sample were prepared and analyzed. Lectin binding reaction was performed at 20° C. for 12 hours. After the reaction, the sample solution on the array was removed, and the array was washed three times with a dedicated buffer solution. Then, signal intensity was measured using a scanner for the lectin microarray (GlycoStation™ Reader 1200, manufactured by GP BioSciences Ltd.). A true value was calculated by the subtraction of a background value, and a mean among 3 spots of each lectin was then calculated. When the largest signal intensity among all of the lectins was defined as a reference, relative values were determined and statistically processed as follows: after conversion of the calculated relative values to common logarithms, two separate groups, i.e., epithelial ovarian cancer and non-epithelial ovarian cancer (stomach cancer and colon cancer) groups, were confirmed by signal pattern analysis using the cluster analysis method and the principal component analysis method. Next, WFA lectin that allowed significant difference to be confirmed between these two groups was extracted by the t study. At the same time, AAL lectin that yielded a high detectable signal in all of the samples subjected to the lectin microarray analysis was extracted. These WFA and AAL lectins were selected as probes for use in subsequent analysis.


(Results)


FIG. 1 shows the binding signal intensities of two types of lectins extracted by the preceding step to glycoproteins derived from each cancer cell line. FIGS. 1 A and 1B show the results about the WFA lectin and the AAL lectin, respectively. As shown in this drawing, the WFA lectin exhibited a high signal for the epithelial ovarian cancer cell lines, but a low signal for the colon cancer cell lines or the stomach cancer cell line as non-epithelial ovarian cancer cell lines. The AAL lectin exhibited a high signal for the epithelial ovarian cancer cell lines and the non-epithelial ovarian cancer cell lines, but a low signal for the stomach cancer cell line (KATO III). The WFA lectin and the AAL lectin had a low signal for RMUG-S, one of the epithelial ovarian cancer cell lines. This is due to the results of this experiment of analyzing the whole glycoproteins in order to select probe lectins and does not indicate behaviors related to the lectin-binding activities of the individual glycoproteins as shown in subsequent Examples. These results demonstrated that the WFA lectin and the AAL lectin can serve as probe lectins binding to the glycans of glycoproteins secreted from epithelial ovarian cancer cell lines.


2. Selection of Glycopeptide Marker by Glycoproteomics (IGOT-LC/MS Method) (Method)
(1) Preparation of Peptide Sample

Sample proteins were prepared from culture supernatants of epithelial ovarian cancer cell lines, and peritoneal lavage fluids. The culture supernatants of epithelial ovarian cancer cell lines were prepared according to the method described in the paragraph 1.(1). The peritoneal lavage fluids used were peritoneal lavage fluids collected from 7 epithelial ovarian cancer patients (56 to 77 years old) (3 clear cell cancer patients, stages IIIC to IV; 1 endometrioid adenocarcinoma patient, stage IV; and 3 serous adenocarcinoma patients, IIIC to IV) during surgery at the Aichi Cancer Center Hospital. Trichloroacetic acid (TCA, 100% saturated aqueous solution) was added at a final concentration of 10% to each of the culture supernatants (1260 to 3300 mL) containing proteins in an amount corresponding to 3.6 to 7.6 mg in total and the peritoneal lavage fluids (0.3 to 300 mL) containing proteins in an amount corresponding to 8.2 to 15.4 mg in total. Each mixture was cooled on ice for 10 to 60 minutes to precipitate proteins. The precipitates were recovered by centrifugation at a high speed at 4° C., then suspended in ice-cold acetone, and washed twice for removal of TCA. A lysis buffer solution (containing 0.5 M tris-HC1 buffer solution (pH 8 to 8.5), 7 M guanidine hydrochloride, and 10 mM EDTA) was added to the obtained precipitates to adjust the protein concentration to 5 to 10 mg/mL, while the proteins were lysed therein to prepare sample proteins. In another method, each culture supernatant or peritoneal lavage fluid was concentrated using an ultrafiltration membrane having a molecular weight cutoff of 10,000 at 4° C. To this concentrate, a lysis buffer solution was added. The protein solution was filtered again to prepare sample proteins.


Subsequently, the sample proteins were subjected to centrifugation at a high speed at 4° C. to remove the residues. Each obtained supernatant was recovered as extracts. Dissolved oxygen was removed by nitrogen gas purging or spraying to the extracts. Then, dithiothreitol (DTT) in the form of a powder or dissolved in a small amount of a lysis buffer solution was added thereto in an amount equal to the protein weight. The mixture was reacted at room temperature for 1 to 2 hours under nitrogen gas purging or in a nitrogen gas atmosphere to reduce the disulfide bond. Subsequently, iodoacetamide for S-alkylation was added thereto in an amount of 2.5 times the protein weight. The mixture was reacted at room temperature for 1 to 2 hours in the dark. The reaction solution was dialyzed at 4° C. against a 50- to 100-fold amount of a buffer solution (10 mM ammonium bicarbonate buffer solution, pH 8.6) as an external solution. The external solution was replaced by a fresh one three to five times to remove the denaturant (guanidine hydrochloride) or an excess of the reagents. Although the partial precipitation of proteins was observed by these procedures, this suspension was subjected directly to protein quantification without recovery of the precipitates. Trypsin (sequencing grade or higher) having a weight of 1/100 to 1/50 of the protein amount was added thereto to digest the proteins overnight (approximately 16 hours) at 37° C. The sufficient progression of the digestion was confirmed by SD S-gel electrophoresis. Then, the reaction was terminated by the addition of phenylmethanesulfonyl fluoride (PMSF) at a final concentration of 5 mM. The obtained protein fragment (peptide) solutions were used as sample peptides.


(2) Collection and Purification of Candidate Glycopeptide

The sample peptides were applied to probe lectin (AAL lectin and/or WFA lectin)-immobilized columns. After washing, glycopeptides were eluted by a method appropriate for the specificity of each lectin, i.e., using a buffer solution containing 5 mM fucose as to the AAL lectin and using a buffer solution containing 10 mM GaINAc as to the WFA lectin. To each obtained glycopeptide solution, an equal volume of ethanol and a 4-fold volume of 1-butanol were added, and the mixture was applied to a Sepharose column equilibrated in advance with water:ethanol:1-butanol (1:1:4 (v/v)). The column was washed with this equilibrating solvent, and glycopeptides were then eluted with 50% ethanol (v/v). Each glycopeptide fraction was transferred in small portions to a microtube containing 2 μL of glycerol and concentrated by repeated removal of water through centrifugation under reduced pressure. The obtained glycerol solutions of purified glycopeptides were used as glycopeptide samples.


(3) Glycan Cleavage and Isotope-Coded Glycosylation Site-Specific Tagging (IGOT) Method

A necessary amount of a buffer solution was added to each of the glycopeptide samples, and the mixture was concentrated again by centrifugation under reduced pressure. Then, stable oxygen isotope-18 (18O)-labeled water (H218O) was added thereto to dissolve the concentrate (glycerol concentration: 10% or lower). Peptide-N-glycanase (glycopeptidase F, PNGase) prepared with labeled water was added thereto and reacted overnight at 37° C. This reaction causes the conversion of asparagine at the glycosylation site to aspartic acid, during which the oxygen isotope (18O) in the water is incorporated into the glycopeptide to label the glycopeptide.


(4) LC/MS Shotgun Analysis of Labeled Peptide

The reaction solution containing the glycopeptide labeled by the IGOT method was diluted with 0.1% formic acid and subjected to LC/MS shotgun analysis. A nano-LC system based on a direct nano-flow pump was used for high-separation, high-reproducibility, and high-sensitivity detection. The injected glycopeptide sample was temporarily collected onto a trap column (reverse-phase C18 silica gel carrier) intended for desalting. After washing, glycopeptides were separated by the concentration gradient of acetonitrile using frit-less spray tip nano-columns (inside diameter: 150 μm×50 mL) packed with the same resins. The eluate was ionized via an electrospray interface and introduced directly into a mass spectrometer. The masses of the glycopeptides were analyzed by collision-induced dissociation (CID)-tandem mass spectrometry in a data-dependent mode in which two ions at the maximum were selected.


(5) Search for Candidate Glycopeptide by MS/MS Ion Search Method

Thousands of MS/MS spectra thus obtained were individually smoothed and converted to centroid spectra to prepare peak lists. On the basis of this data, each detected glycopeptide was identified by the MS/MS ion search method using a protein amino acid sequence database. The search engine used was Mascot (Matrix Science Ltd.). The following parameters were used for search conditions: a fragmentation method used: trypsin digestion, the maximum number of missed cleavage: 2, fixed modification: carbamidomethylation of cysteine, variable modifications: deamination of an N-terminal amino group (N-terminal glutamine), oxidation of methionine, 180-incorporating deamidation of asparagine (glycosylation site), error tolerance of MS spectrum: 500 ppm, and error tolerance of MS/MS spectrum: 0.5 Da.


(6) Identification of Glycoprotein for Epithelial Ovarian Cancer Diagnosis Marker

The identification results of the glycopeptides obtained by search under the conditions described above were validated according to criteria (i) to (iv) given below to select glycopeptides that satisfied all of the conditions.


(i) The probability score (coincidence probability: Expectation value) of identification is 0.05 or less.


(ii) The number of fragment ions contributing to identification is 4 or more.


(iii) Error (ppm) is not significantly deviated from systematic error (mass error being 0.5 Da or less).


(iv) Each identified peptide has consensus sequence(s) with the number of Asn modifications (conversion to Asp and incorporation of 18O) equal to or fewer than the number of the consensus sequence(s).


(Results)

The selected glycopeptides are shown in SEQ ID NOs: 1 to 388 as “Peptide sequence” in Table 1. On the basis of the amino acid sequences of these peptides, the whole amino acid sequences of core proteins in the corresponding glycoproteins for epithelial ovarian cancer diagnosis markers were identified from the amino acid sequence database NCBI-Refseq. As a result, 262 glycoproteins for epithelial ovarian cancer diagnosis markers were identified. The names of the core proteins in these glycoproteins for epithelial ovarian cancer diagnosis markers are shown in Table 1.


Example 2
Detection of Epithelial Ovarian Cancer using Epithelial Ovarian Cancer Diagnosis Marker

The detection of epithelial ovarian cancer using the epithelial ovarian cancer diagnosis markers selected and identified in Example 1 was tested.


(Method)

(1) Fractionation of Peritoneal Lavage Fluid using Probe Lectin


The peritoneal lavage fluids used were obtained from ovarian cancer patients having clear cell carcinoma, mucinous carcinoma, serous carcinoma, or endometrioid carcinoma (two patients each), and from two stomach cancer patients with intraperitoneal progression proved by qPCR after recovery of peritoneal lavage fluids using a syringe or the like from the Douglas' pouch after intraperitoneal injection of approximately 100 mL of saline during surgery. The concentration of proteins contained in each peritoneal lavage fluid was measured by the BCA method, and the total amount of proteins was adjusted to equal levels among the samples, which were then subjected to the following AAL lectin or WFA lectin fractionation.


For the AAL fractionation, 2 mL Disposable polystyrene column (Pierce Biotechnology, Inc.) was packed with 0.5 mL of AAL-agarose (Vector Laboratories, Inc.) and washed with TBS (pH 8) in an amount of 10 times the amount of the resin. Then, each peritoneal lavage fluid (total protein amount: 0.25 mg) adjusted to 500 μL with TBS was applied to the column. While the sample was held in the column, the column was left standing at room temperature for overnight reaction. Then, the pass-through sample was recovered, and the column was washed with 10 mL of TBS, followed by elution with 1 mL of 50 mM fucose-TBS (fraction A-1). The column was further left standing at room temperature for 30 minutes for reaction, followed by the recovery of a fraction using 2.4 mL of an eluent (fraction A-2). Then, the column was washed with 4 mL of TBS. Then, the whole amount of the pass-through fraction thus recovered was applied again to the column. While the sample was held in the column, the column was left standing at room temperature for 4-hour reaction. After the reaction, the column was washed with 10 mL of TBS, followed by the recovery of a fraction using 0.6 mL of an eluent (fraction A-3). The column was further left standing at room temperature for 30 minutes for reaction, followed by the recovery of a fraction using 1.4 mL of an eluent (fraction A-4). The fractions A-1 to A-4 were pooled as AAL(+) fractions of the peritoneal lavage fluid.


For the WFA fractionation, 2 mL Disposable polystyrene column (Pierce Biotechnology, Inc.) was packed with 0.3 mL of WFA agarose (Vector Laboratories, Inc.) and washed in the same way as in AAL described above. Then, each peritoneal lavage fluid (total protein amount: 2.5 mg) adjusted to 500 μL with TBS was applied to the column and reacted at room temperature for 30 minutes. After the reaction, the column was washed with 6 mL of TBS, followed by elution with 0.18 mL of 200 mM lactose-TBS (fraction W-1). Next, the column after the elution of the fraction W-1 was left standing at room temperature for 30 minutes, followed by the recovery of a fraction using 0.72 mL of an eluent (fraction W-2). The recovered fractions W-1 and W-2 were pooled as WFA(+) fractions of the peritoneal lavage fluid.


(2) Immunoblotting

Each sample thus pooled was concentrated using Amicon Ultra-154 centrifugal filter units (cutoff: 10 kDa, Millipore Corp.) and then immunoblotted using antibodies specifically binding to the core proteins in the glycoproteins for epithelial ovarian cancer diagnosis markers obtained in Example 1.


The following five glycoproteins for epithelial ovarian cancer diagnosis markers were randomly selected from among the 262 markers obtained in Example 1 as shown in Table 1 on the condition that antibodies specifically recognizing their core proteins were commercially available: collagen type VI alpha 1 protein (COL6α1) of Protein #1, lysyl oxidase-like 2 protein (LOXL2) of Protein #28, ceruloplasmin protein (CP) of Protein #35, SERPING1 protein of Protein #42, and blood coagulation factor XII protein (F12) of Protein #68 in Table 1. The antibodies used were an anti-COL6α1 polyclonal antibody (17023-1-AP; ProteinTech), an anti-LOXL2 polyclonal antibody (GTX105085; GeneTex Inc.), an anti-CP polyclonal antibody (A80-124A; Bethyl Laboratories, Inc.), an anti-SERPING1 monoclonal antibody (3F4-1D9, H00000710-M01; Abnova Corp.), and an anti-F12 antibody (B7C9, GTX21007; GeneTex Inc.). These antibodies were biotinylated using Biotin Labeling Kit-NH2 (Dojindo Laboratories). The biotinylation was performed according to the protocol attached to the kit.


Each AAL(+) fraction or WFA(+) fraction of the peritoneal lavage fluid prepared in the paragraph (1) was developed by SDS-PAGE on a 10% acrylamide gel of XV PANTERA SYSYTEM (Maruko Shokai Co., Ltd.) and then transferred to a PVDF membrane (Bio-Rad Laboratories, Inc.) at 200 mA for 90 minutes. The blocking agent used was PBST (PBS supplemented with 0.1% Tween 20) containing 5% skimmed milk or 5% BSA dissolved therein. The membrane was blocked overnight at 4° C. and then washed three times with PBST for 10 minutes per run. Subsequently, the biotinylated antibodies were added as primary antibodies to the membrane and reacted at room temperature for 1 hour. In this operation, the anti-COL6α1 antibody was added to the AAL(+) fraction-transferred membrane, while the anti-LOXL2 antibody, the anti-CP antibody, the anti-SERPING1 antibody, and the anti-F12 antibody were added to the WFA(+) fraction-transferred membrane. After the reaction, three 10-minute washing runs with PBST were performed again. Then, the membrane was reacted at room temperature for 1 hour with HRP-conjugated streptavidin (1:3000 dilution, GE Healthcare Japan Corp.) as secondary antibodies against the biotinylated antibodies. After three 10-minute washing runs with PBST, the enzymatic reaction of HRP was caused using Western Lightning Chemiluminescence Reagent Plus (PerkinElmer, Inc.). Signals were detected using Amersham Hyperfilm ECL (GE Healthcare Japan Corp.) and subjected to comparative analysis.


(Results)


FIGS. 2 to 6 show the results of detecting each glycoprotein for an epithelial ovarian cancer diagnosis marker in the peritoneal lavage fluids obtained from the cancer patients.


As seen from the results of FIG. 2, COL6α1 was not detected in the patients with stomach cancer which was non-epithelial ovarian cancer. As for the epithelial ovarian cancer patients, this protein was detected in the clear cell adenocarcinoma patients and the serous adenocarcinoma patients, but hardly detected in the endometrioid adenocarcinoma patients. This demonstrated that COL6α1 can serve as a glycoprotein for an epithelial ovarian cancer diagnosis marker capable of selectively identifying clear cell carcinoma or serous carcinoma among epithelial ovarian cancer types. This protein was not detected in endometrioid carcinoma, which is often complicated by endometriosis, as with the clear cell carcinoma, demonstrating that the protein can serve as a marker glycoprotein capable of identifying clear cell carcinoma among types complicated by endometriosis.


As seen from the results of FIGS. 3 to 6, LOXL2, CP, SERPING1, and F12 were all detected in the epithelial ovarian cancer patients having any of the histological types tested, but were not detected in the stomach cancer patients. This demonstrated that the LOXL2, CP, SERPING1, and F12 glycoproteins can each serve as a glycoprotein for an epithelial ovarian cancer diagnosis marker that permits the diagnosis of epithelial ovarian cancer, regardless of its histological type.


Since epithelial ovarian cancer was successfully detected in histological type-specific or -nonspecific manner using any of the 5 markers randomly selected from the glycoproteins for epithelial ovarian cancer diagnosis markers obtained in Example 1 as shown in Table 1, any glycoprotein described in Table 1 was shown to be able to serve as a glycoprotein for an epithelial ovarian cancer diagnosis marker.


All publications, patents, and patent applications cited herein are incorporated herein by reference in their entirety.

Claims
  • 1-13. (canceled)
  • 14. A method for determining the presence or absence of epithelial ovarian cancer in a test subject, comprising the steps of: detecting at least one glycoprotein for an epithelial ovarian cancer diagnosis marker or a fragment thereof in a sample collected from a test subject, anddetermining that the test subject is affected with epithelial ovarian cancer when the glycoprotein and/or the fragment of the glycoprotein have been detected;wherein the glycoprotein and fragment thereof comprise at least one glycan-linked asparagine residue at a glycosylation site,wherein the glycoprotein is selected from the group consisting of ceruloplasmin, lysyl oxidase-like 2, serpin peptidase inhibitor clade G member 1, coagulation factor XII, and collagen type VIα1,wherein the glycan-linked asparagine residue in the amino acid of ceruloplasmin is at positions 138, 358, 397, and 762,wherein the glycan-linked asparagine residue in the amino acid of lysyl oxidase-like 2 is at positions 288, 293, and 644,wherein the glycan-linked asparagine residue in the amino acid of serpin peptidase inhibitor clade G member 1 is at positions 238, 253, and 352,wherein the glycan-linked asparagine residue in the amino acid of coagulation factor XII is at position 249, andwherein the glycan-linked asparagine residue in the amino acid of collagen type VIα1 is at position 212.
  • 15. The method of claim 14, wherein the detecting step comprises a glycoprotein enrichment step and a protein detection step.
  • 16. The method of claim 14, wherein the glycoprotein for an epithelial ovarian cancer diagnosis marker and/or the fragment thereof are detected by binding at least one glycan probe to the glycan.
  • 17. The method of claim 16, wherein the glycan probe is a lectin, an antibody, or a phage antibody.
  • 18. The method of claim 17, wherein the lectin is AAL or WFA.
  • 19. The method of claim 14, wherein the sample is a body fluid, a cell, or a peritoneal lavage fluid.
  • 20. The method of claim 14, wherein the epithelial ovarian cancer is at least one of clear cell carcinoma, mucinous carcinoma, serous carcinoma, and endometrioid carcinoma.
PCT Information
Filing Document Filing Date Country Kind 371c Date
PCT/JP2012/067798 7/12/2012 WO 00 6/8/2015