Patent Application
20160003786
1. Field of Invention
This present application encompasses proteins and peptide fragments of those proteins produced by proteolytic digestion that are useful for diagnosing or monitoring for the presence of cancer in an individual.
2. Description of the Related Art
Screening mammograms typically have a sensitivity of 75% and specificity of around 98% resulting in a false positive rate of roughly 5% per mammogram
(Brown, Houn, Sickles, & Kessler, 1995; Kolb, Lichy, & Newhouse, 2002; Luftner & Possinger, 2002). Follow up imaging to evaluate false positives costs the US over 4 B with an additional 1.6 B for biopsies alone. In 2010 of the 1.6 M biopsies performed as little as 16% (only 261,000) were found to have cancer (Grady, 2012). The answer to increasing the diagnostic parameters of imaging can be found in the pre and post image diagnostics which focuses on genetic and proteomic information, more specifically, biomarkers (Armstrong, Handorf, Chen, & Bristol Demeter, 2013; Li, Zhang, Rosenzweig, Wang, & Chan, 2002).
Tissue and serum are commonly the most logical place for beginning biomarker research, however the large dynamic range of both mediums makes discovery quite difficult (Schiess, Wollscheid, & Aebersold, 2009). The answers may lie in less complex biological fluids, such as saliva and tears. The use of tears as diagnostic medium is not a novel application as the tear proteome has been extensively investigated previously (Böhm et al., 2012; 2011; Lebrecht, Boehm, Schmidt, Koelbl, & Grus, 2009a; Lebrecht et al., 2009b; Wu & Zhang, 2007). In this application a quantitative assay for the detection of a panel of tear-based biomarkers in response to cancer by triple quadrupole LC mass spectrometry is proposed. From this quantitative information, the framework for a Certified Laboratory Improvement Amendments (CLIA) protocol will be defined.
Methods of determining whether a subject has cancer are provided herein. The methods include obtaining a sample from the subject and performing steps for or detecting the level of at least one of the markers provided in Table 2A or Table 2B in the sample. The subject is likely to have cancer if the levels of the markers of Table 2A are increased or if the markers in Table 2B are decreased as compared to the levels in a control sample lacking cancer. The sample is optionally lacrimal secretions, such as an ocular wash, saliva or other bodily fluid.
Kits for performing the methods described herein are also provided. The kits may comprise an eye wash solution and collection materials such as tubes. The tube for collection may comprise a protease inhibitor or other protein stabilizing agent.
Provided herein are proteins and trypsin produced polypeptides (as defined in Table 2A and 2B in the Examples and the actual trypsin sequences and full length amino acid sequences of the proteins identified as being up regulated and down regulated in cancer samples are provided in Appendix I and Appendix II, respectively) which are shown in the Examples to increase or decrease in biological samples in response to the presence of breast cancer as compared to controls. These proteins and peptides are biomarkers and will be used to determine the disease state of a patient or other subject.
Subjects include humans, domesticated animals such as cats, dogs, cows, pigs or other animals susceptible to cancer. A “patient” indicates a subject who is diagnosed with a disease or with cancer or being tested for having cancer. Thus subject and cancer may be used interchangeably herein. The subjects may be suspected of having cancer, in particular breast cancer. The subjects may have an increased risk of developing breast cancer. For example, the subject may be at increased risk of cancer or suspected of having cancer because of a positive mammography result, by detection of a lump in the breast, testing positive for a gene known to increase the risk of cancer such as BRCA, or already have had a resection, biopsy or other procedure to remove the cancer. The subject may be undergoing or have previously undergone treatment for cancer and the methods and kits herein are used to monitor progression of treatment or alternatively to monitor for recurrence or spread of the cancer. The cancer may be detected as early as stage I or II cancer, but later stages will also be detected.
Also provided herein are methods and kits to collect ocular wash samples for use to determine the expression levels of the identified proteins or polypeptides in lacrimal secretions. In addition, the use of tubes for collection containing protease inhibitor or protein stabilizing agents is covered. The kits further contain buffers or reagents for the elution of breast cancer biomarkers from the eye. The design of devices to collect the applied saline solution from the corner of the exposed ocular surface as well as the packaging of this device together with saline and a pre-prepared sample collection tube are also disclosed.
The methods disclosed herein encompass the use of these breast cancer biomarkers, singly or in multiples, in a CLIA based protocol utilizing a triple quadrupole LC-MS platform, which will be carried out at a centralized laboratory testing facility. The ocular wash samples collected from individuals may be shipped to the testing facility in this embodiment. The identified proteins and their subsequent proteolytic fragments are used for quantitative analysis of diagnostic peptides produced in the triple quad. A threshold value or a relative or actual value in terms of polypeptide concentration directly relating to the polypeptides listed in Tables 2A and 2B can be defined or samples can be compared directly to non-cancerous controls. The quantitative information in report form could be provided to physicians to help in making decisions regarding the pathway of patient care. Physicians may base treatment decisions on these results and the final step may include administration of an appropriate anti-cancer therapeutic to the subject.
In an alternative embodiment, the polypeptides of Tables 2A and 2B may be detected by implementing binding agents (i.e. antibodies, peptoids, coated surfaces) and reagents that accommodate a binding interaction specific to these proteins to produce a reaction which can be quantitated based on production of a detectable signal such as florescence, color change, or UV absorbance. Implementing these components in a cartridge with a partnering reading instrument that could be used at point of care is also provided. Binding agents for these proteins and polypeptides may also be used for detection in a lateral flow device. Thus methods of detecting the level of protein expression in the samples using a binding partner such as an antibody may be used to detect the markers provided herein in an immunoassay.
The immunoassay typically includes contacting a test sample with an antibody that specifically binds to or otherwise recognizes a biomarker, and detecting the presence of a complex of the antibody bound to the biomarker in the sample. The immunoassay procedure may be selected from a wide variety of immunoassay procedures known to the art involving recognition of antibody/antigen complexes, including enzyme-linked immunosorbent assays (ELISA), radioimmunoassay (RIA), and Western blots, and use of multiplex assays, including use of antibody arrays, wherein several desired antibodies are placed on a support, such as a glass bead or plate, and reacted or otherwise contacted with the test sample. Such assays are well-known to the skilled artisan.
The detection of the biomarkers described herein in a sample may be performed in a variety of ways. In one embodiment, the method provides the reverse-transcription of complementary DNAs from mRNAs obtained from the sample. Fluorescent dye-labeled complementary RNAs may be transcribed from complementary DNAs which are then hybridized to the arrays of oligonucleotide probes. The fluorescent color generated by hybridization is read by machine, such as an Agilent Scanner and data are obtained and processed using software, such as Agilent Feature Extraction Software (9.1). Such array based methods include microarray analysis to develop a gene expression profile. As used herein, the term “gene expression profile” refers to the expression levels of mRNAs or proteins of a panel of genes in the subject. As used herein, the term “panel of diagnostic genes” refers to a panel of genes whose expression level can be relied on to diagnose or predict the status of the disease. Included in this panel of genes are those listed in Tables 2A and 2B, as well as any combination thereof, as provided herein. In other embodiments, complementary DNAs are reverse-transcribed from mRNAs obtained from the sample, amplified and simultaneously quantified by real-time PCR, thereby enabling both detection and quantification (as absolute number of copies or relative amount when normalized to DNA input or additional normalizing genes) of a specific gene product in the complementary DNA sample as well as the original mRNA sample.
The methods of this invention include detecting at least one biomarker. However, any number of biomarkers may be detected. It is preferred that at least two biomarkers are detected in the analysis. However, it is realized that three, four, or more, including all, of the biomarkers described herein may be utilized in the analysis. Thus, not only can one or more markers be detected, one to 40, preferably two to 40, two to 30, two to 20 biomarkers, two to 10 biomarkers, or some other combination, may be detected and analyzed as described herein. In addition, other biomarkers not herein described may be combined with any of the presently disclosed biomarkers to aid in the diagnosis of cancer. Moreover, any combination of the above biomarkers may be detected in accordance with the present invention.
The markers of Table 2A may be increased at least 2 fold, 4 fold, 5 fold, 8 fold, 10 fold or more relative to the level of the marker in the control sample. The markers of Table 2B are decreased at least 1.5 fold, 2 fold, 3 fold, 4 fold or more relative to the level of the marker in the control sample. The control sample may be a sample from a subject that does not have cancer, a pooled sample from subjects that do not have cancer or may be a control or baseline expression level known to be the average expression level of subjects without cancer.
Several terms are used throughout this disclosure and should be defined as commonly used in the art, or as specifically provided herein. As provided herein, mass spectrometry or MS refers to an analytical technique generating electrical or magnetic fields to determine mass-to-charge ratio of peptides and chemical compounds in order to identify or determine peptide sequence and chemical structures. LC-MS/MS spectrometry refers to an analytical technique combining the separation capabilities of high performance liquid chromatography (HPLC) with the mass analysis of mass spectrometry. Triple quadrupole mass spectrometry refers to a tandem mass spectrometer with three ionizing chambers (Q1, Q2, &Q3). This technique allows for target detection of molecules of interest. Ion pairs refers to a parent peptide detected in Q1 in it's doubly or triply charged form and a resulting y or b ion as generated by Q2 and detected in Q3 of a triple quadrupole mass spectrometry instrument. SIS internal peptide refers to a synthesized isotopically-labeled peptide with the same sequence as the peptide to be monitored in Q1 and used as an internal standard for reference to quantify the peptide of interest. The −y ion refers to an ion generated from the c-terminal of a peptide fragment. The −b ion refers to an ion generated from the n-terminal of a peptide fragment. Quantitative Ion refers to the selected highest intensity y or b ion used to determine the quantity of it's parent protein in a biological sample. Qualitative Ion refers to ion/ions chosen to ensure the integrity of the Qualitative ion to selected protein of interest and labeled peptide to selected standards.
CLIA refers to Clinical Laboratory Improvements Amendments which are federal regulatory standards that apply to all clinical laboratory testing preformed on humans in the united states, except clinical trials and basic research. (CLIA related Federal Register and Code of Federal Regulation Announcements). CLIA approved laboratory refers to a clinical lab which preforms laboratory testing on human specimens for diagnosis, prevention, or treatment of disease or impairment and is approved and monitored by an FDA approved regulatory organization. CLIA waived test refers to a clinical laboratory test meeting specific criteria for risk, error and complexity as defined by the Food and Drug Association (FDA).
Point-of-care device refers to an instrument or cartridge available at the location of patient and physician care containing binding agents to a biomarker, or series of biomarkers of interest, and can generate information on the presence, absence, and in some cases concentrations of detected biomarkers. Analyte refers to any measurable biomarker which can be protein, peptide, macromolecule, metabolite, small molecule, or autoantibody. Biological fluid as used herein refers to tears, whole blood, serum, urine, and saliva. Biomarker refers to any substance (e.g. protein, peptide, metabolite, polynucleotide sequence) whose concentration level changes in the body (e.g. increased or decreased) as a result of a disease or condition. Marker and biomarker may be used interchangeably herein.
Lateral flow test refers to a device used to measure the presence of an analyte in a biological fluid using porous paper of sintered polymer. ELISA refers to Enzyme-linked immunosorbent assay which utilizes antibodies to detect the presence and concentration of an analyte of interest. Diagnostic Panel refers to a group of molecules (e.g. proteins or peptides) whose combined concentrations are used to diagnose a disease state. (e.g. cancer). A breast cancer marker refers to a molecule (e.g. protein, peptide, metabolite, polynucleotide sequence) whose concentration level in the body changes (e.g. is increased or decreased) as a result of breast cancer.
In addition to being useful to diagnose cancer and in particular breast cancer in a subject, the kits and methods provided herein may be used to monitor treatment or recurrence of cancer in an individual previously diagnosed with cancer. Thus if the levels of the markers in Table 2A begin to rise or the levels of the markers in Table 2B begin to decrease over time in the same subject after treatment, further chemotherapeutics targeting the cancer may be administered. The methods and kits may also be used to monitor the effectiveness of a chemotherapeutic treatment. In this alternative, the levels of the biomarkers in Table 2A would decrease over time if the treatment regime is effective and either would not change or may increase over time if the treatment regime is not effective in a single subject. The levels of the biomarkers in Table 2B would increase over time during treatment with a therapeutic that is effective and would either not change or decrease over time if the treatment regime is not effective in a single subject.
Treating cancer includes, but is not limited to, reducing the number of cancer cells or the size of a tumor or mass in the subject, reducing progression of a cancer to a more aggressive form, reducing proliferation of cancer cells or reducing the speed of tumor growth, killing of cancer cells, reducing metastasis of cancer cells or reducing the likelihood of recurrence of a cancer in a subject. Treating a subject as used herein refers to any type of treatment that imparts a benefit to a subject afflicted with a disease or at risk of developing the disease, including improvement in the condition of the subject (e.g., in one or more symptoms), delay in the progression of the disease, delay the onset of symptoms or slow the progression of symptoms, etc.
The present disclosure is not limited to the specific details of construction, arrangement of components, or method steps set forth herein. The compositions and methods disclosed herein are capable of being made, practiced, used, carried out and/or formed in various ways that will be apparent to one of skill in the art in light of the disclosure that follows. The phraseology and terminology used herein is for the purpose of description only and should not be regarded as limiting to the scope of the claims. Ordinal indicators, such as first, second, and third, as used in the description and the claims to refer to various structures or method steps, are not meant to be construed to indicate any specific structures or steps, or any particular order or configuration to such structures or steps. All methods described herein can be performed in any suitable order unless otherwise indicated herein or otherwise clearly contradicted by context. The use of any and all examples, or exemplary language (e.g., “such as”) provided herein, is intended merely to facilitate the disclosure and does not imply any limitation on the scope of the disclosure unless otherwise claimed. No language in the specification, and no structures shown in the drawings, should be construed as indicating that any non-claimed element is essential to the practice of the disclosed subject matter. The use herein of the terms “including.” “comprising,” or “having,” and variations thereof, is meant to encompass the elements listed thereafter and equivalents thereof, as well as additional elements. Embodiments recited as “including,” “comprising,” or “having” certain elements are also contemplated as “consisting essentially of” and “consisting of” those certain elements.
Recitation of ranges of values herein are merely intended to serve as a shorthand method of referring individually to each separate value falling within the range, unless otherwise indicated herein, and each separate value is incorporated into the specification as if it were individually recited herein. For example, if a concentration range is stated as 1% to 50, it is intended that values such as 2% to 40%, 10% to 30%, or 1% to 3%, etc., are expressly enumerated in this specification. These are only examples of what is specifically intended, and all possible combinations of numerical values between and including the lowest value and the highest value enumerated are to be considered to be expressly stated in this disclosure. Use of the word “about” to describe a particular recited amount or range of amounts is meant to indicate that values very near to the recited amount are included in that amount, such as values that could or naturally would be accounted for due to manufacturing tolerances, instrument and human error in forming measurements, and the like. All percentages referring to amounts are by weight unless indicated otherwise.
No admission is made that any reference, including any non-patent or patent document cited in this specification, constitutes prior art. In particular, it will be understood that, unless otherwise stated, reference to any document herein does not constitute an admission that any of these documents forms part of the common general knowledge in the art in the United States or in any other country. Any discussion of the references states what their authors assert, and the applicant reserves the right to challenge the accuracy and pertinence of any of the documents cited herein. All references cited herein are fully incorporated by reference, unless explicitly indicated otherwise. The present disclosure shall control in the event there are any disparities between any definitions and/or description found in the cited references.
The following examples are meant only to be illustrative and are not meant as limitations on the scope of the invention or of the appended claims.
This study was carried out under institutional review board approval and participants were recruited at two clinics based in Arkansas, The Breast Center and Highlands Oncology Group, as well as two clinics based in Washington, PeaceHealth Southwest and PeaceHealth Longview Surgery Center. Inclusion/exclusion criteria used by the clinic for patient selection is given in Table 1.
Ocular wash samples were obtained by rinsing the exposed surface of the eye with Optics Laboratory single use Eye-Cept Rewetting drops. The single use dropper, selected to eliminate contamination, was used to apply approximately five drops of rewetting saline to the outside corner of the eye. After application the solution naturally flowed across the surface of the eye and pooled in the inner corner/duct next to the nose. The solution was then collected by suction using a one mL tuberculine syringe, with no needle attached, and transferred to a pre-labeled 0.5 mL tube with an o-ring screw top cap. The optimal total volume from each collection is approximately 100 μL, however actual volumes can vary. Samples were stored between −20° C. and −80° C. (depending on freezer unit available) within two hours of collection.
Samples collected at participating clinics were retrieved by Ascendant personnel on a weekly basis and transferred on dry ice to Ascendant's laboratory facility. In the case of the Washington based clinics, samples were shipped to Ascendant on dry ice on a monthly basis.
Data collected from the participants included: sex, race, age, previous cancer history, family history of breast cancer, stage of current cancer (I, II, III, IV) tumor size, breast cancer subtype (Ductal Carcinoma In Situ, Invasive Ductal Carcinoma, Invasive Lobular Carcinoma, Lobular Carcinoma In Situ, and Unknown) and tumor grade. A spreadsheet was created to track data and stratify samples based on selected criteria.
Control samples were collected, using the procedure detailed above, from volunteers between the ages of 18-100 who reported they were cancer and mass free as per the inclusion criteria outlined in the IRB approved collection protocol. Exclusion criteria are the same as for the breast cancer patients. All control participants were recruited from the general population; consent and sample collected was performed by Ascendant Diagnostics personnel. Data collected from control participants included: sex, age, race, previous history of breast cancer, family history of breast cancer, and current medications.
All samples in the tear bank were stored at −80° C. and freeze thaw cycles were limited to three times, as protein degradation was observed after three freeze thaw cycles. In some cases samples were aliquoted to minimize freeze thaw cycles further.
Eight pooled samples (four breast cancer pools and four control pools) each with a total volume of 300 μL were assembled from banked tear samples for the purpose of label free quantitation using in-gel digestion. All breast cancer ocular wash samples used were taken from individuals with stage I &II breast cancer and were collected prior to treatment. Controls were age matched for accuracy of comparison.
To ensure sample integrity, MALDI-TOF data was collected on aliquots from each of the individual samples, which were included in the pooled samples. Prior to MALDI testing, tear samples were purified using ZipTipe18. This procedure serves to remove any contaminates which may be present in the sample and to concentrate the proteins in order to increase ease of detection. A 15 μL aliquot was removed from the freezer and thawed at room temperature for 10 minutes (˜22° C.). The protocol for ZipTipe18 was adapted from the user manual supplied by Millipore and a variable pipette with a total volume capacity of 10 μL was used for all sample preparations. The ZipTipe18 was equilibrated in a wetting solution of acetonitrile (ACN) 0.1% TFA for 10 cycles (1 cycle involves aspirating 10 μL of solution into the tip and dispensing). Following equilibration, the tip was washed with ddH2O (0.1% TFA) for 10 cycles. The sample was then loaded for 10 cycles, followed by a wash with ddH2O (0.1% TFA) for 10 cycles. The load procedure, followed by the wash procedure was carried out a total of five times to ensure maximum protein binding. Bound proteins were eluted in 5 μL of ACN (0.1% TFA) for 20 cycles into a clean tube. The ACN (0.1% TFA) was removed using an eppendorf vacufuge plus for 10 minutes at 45° C. Samples were then reconstituted in 5 μL ddH2O (0.1% TFA) and spotted onto a ground steel MALDI target. Each sample was spotted a total of three times at 1 μL each time, allowing complete drying of the spot before more material was added. After the final spotting was completely dry, 1 μL of a saturated solution of 40 mgs of Sinapinic Acid matrix prepared in 1 mL of 50:50 solution of ACN/ddH2O (0.1% TFA) was spotted onto each sample and all samples were allowed to dry completely on the bench top prior to data collection. One microliter of protein standard was added to several locations on the MALDI target as well. The protein standard was spotted only once and followed by addition of the sinapinic acid matrix used for the OW samples.
Data was collected on a Bruker Reflex III MALDI-IOF mass spectrometer in its linear positive mode, as linear mode increases the sensitivity. Acquisition of all spectra was performed both manually and automatically (user unbiased acquisition) using Bruker Daltonics flex Control software. For each spot, MALDI-TOF mass spectra were acquired at least three times, with a total of 200 laser shots accumulated for each run. Shot accumulation was programmed using a fuzzy logic operator to only consider spectra with S/N better than 20 in between m/z 2000-45,000. Sample integrity was evaluated by visual inspection of the generated MALDI-TOF spectrum. High mass peak splitting together with increased quantity of low mass peaks suggest protein degredation has occurred and the sample was not used further.
Total protein content of each pool was determined using a bicinchoninic acid protein assay kit with a 1:20 (v/v) ratio of standard and unknown to working reagent and an incubation time of 30 min at 37° C. To ensure reliable total protein content calculation, a series of dilutions were made for each sample (i.e. 1:2, 1:4, 1:6) and all dilutions were plated in triplicate. A standard curve using diluted albumin (2 mg/ml, 1.5 mg/ml, 1 m/ml, 0.75 mg/ml, 0.5 mg/ml, 0.25 mg/ml 0.125 mg/ml 0.025 mg/ml and 0 mg/ml) was generated and blank subtraction was applied to all standards and unknowns. The protein concentration for each unknown was calculated using a four-parameter fit of the standard curve. Concentrations were multiplied by the dilution factor and averaged to give an accurate total protein content calculation. Assays were only considered valid if the coefficient of variation (% CV) was 15% or below.
Using the total protein content determined by BCA, 25 μg of protein from each pool was loaded onto a NuPAGE Bis-Tris 4-12% gradient separation gel and run using methods standard for an individual skilled in the art as shown in
Twenty μL from each trypsin digestion reaction was loaded onto a nanoAcquity UPLC (Waters) and eluted using a gradient from 3-99% 0.1% formic acid, 75% acetonitrile over 30 minutes. A LTQ Orbitrap Velos (Thermo Scientific) was used for detection of the peptides produced by proteolytic cleavage. Raw data files from the LC-MS/MS analysis were uploaded into the MASCOT database for protein identification using the UniProtKB database, 2 ppm peptide mass tolerance, and 0.5 Da fragment mass tolerance. The output from MASCOT was then uploaded into the software packages Scaffold and MaxQuant for analysis.
Greater than 700 protein hits were identified using this method. In order to isolate potential biomarker candidates, peak intensities for each group (cancer and control) were averaged for each protein and fold change was determined with respect to cancer. In addition a student's T-test was applied to each protein providing a p-value. All proteins with a fold change of greater than 1.5 and a p-value <0.05 were, considered as possible biomarker candidates. P-values and fold changes were assessed on a case by case basis and some proteins with higher p-values were included in the candidate biomarkers list. The list was then narrowed based on biological relevance to breast cancer, other cancer subtypes, and cancer processes. The complete list of candidate biomarkers is given in Tables 2A and 2B and shown in graphic form in
To further confirm protein identity, the peptide sequences produced by trypsin digestion were mapped back to the original protein sequence. Trypsin products unique to particular proteins were noted, as these sequences have the potential to be used as diagnostic peptides as well as isotopically labeled standards in the final CLIA triple quadrupole mass spectrometry assay. The sequences of the trypsin products and the full-length proteins markers identified in Tables 2A and 2B are provided in Appendix I and Appendix II, respectively.
Institutional review board approval was obtained for the collection of tears using Schirmer strips. For collection, the rounded tip of the Schirmer strip was folded over at the 0 mm line forming a lip. The folded portion was placed in the lower eyelid of the participant and they were asked to close their eye and keep it in the closed position for a period of 5 minutes. After five minutes the strip was removed and placed in a sterile 1.5 mL pre-labeled snap top tube and placed at −20° C. or −80° C. depending on availability. Collection criteria stated that if the 35 mm mark was reached prior to the five minute time, the strip could be removed.
Data collected from participants included the following, age, sex, race, currently taking birth control or on hormone replacement therapy, ophthamological infections, current or recent chemotherapy treatments, family history of cancer, genetic testing (BRAC1/2) if available, cancer stage, cancer type, hormone receptor status, size of mass, tumor grad, previous history of cancer. A spreadsheet was constructed to house this information and allow for sample stratification based on desired characteristics. Sample total protein content was also entered into the database.
To elute the proteins bound to the Schirmer strip, the strips were first diced and placed in a clean sterile 1.5 mL snap top tube. 200 μL of 1×PBS was added to the diced strip and the sample was incubated at 4° C. with mild shaking overnight. Following elution, the samples were spun briefly to collect the strip fragments at the bottom of the tube, and the supernatant was transferred to a new clean 1.5 mL snap top tube. Total protein content was determined using BCA assay, as described above, and the samples were stored at −80° C. until further use.
Sequences shown to be up regulated in subjects with cancer:
FALDQKMRPS TDTITVMVEN SHGLRVRKKE VYMPSSIFQD
DALEK
(14)
LNMGI TDLQGLRLYV AAAIIESPGG EMEEAELTSW
IPVKVSATVS SPGSVPEVQD IQQNTDGSGQ VSIPIIIPQT
DVQAGACEGK LELSVDGAKQ YRNGESVKLH LETDSLALVA
VNFQKAINEK LGQYASPTAK RCCQDGVTRL PMMRSCEQRA
FPVGDAVSKV LQIEKEGAIH REELVYELNP LDHRGRTLEI
ASLLRLPRGC GEQTMIYLAP TLAASR(25)YLDK TEQWSTLPPE
TK
(2)
DHAVDLIQ KGYMRIQQFR KADGSYAAWL SRDSSTWLTA
(2)
LGSLGAACEQ TQTEGAKADG SWSCWSSWSV CRAGIQERRR
MLCAGTKEGG KDSCEGDSGG PLVCNRTLYG IVSWGDFPCG
(2)
DSCTLPASAE KACGACPLWG KCDAESSKCV CREASECEEE
YK(2)QGGFLGLS NIKFRPGSVV VQLTLAFREG TINVHDVETQ
PAQQKTKQK
LRVVISLQLT AEKRVATPVD WKDGDSVMVL PTIPEEEAKK
PKCLRLCFFP FVENGRSESS GQTHLEGDTV QIICNTGYRL
RQMSKYPSGE RVRYECRSPY EMFGDEEVMC LNGNWTEPPQ
FLLTGDTQGR YRCR(8)SGLSTG WTQLSK(5)LLEL TGPKSLPAPW
PWSEIRNISF NDKKFVIKPI DKK(2)APDFVFY APRLRINKRI
FFQGDREWFW DLATGTMKER SWPAVGNCSS ALRWLGRYYC
DAAFICPGSS RLHIMAGRRL WWLDLK(10)SGAQ ATWTELPWPH
EK
(11)
VDGALCME KSLGPNSCSA NGPGLYLIHG PNLYCYSDVE
NYRHSNPKDR MTSLKCGENL YMSSASSSWS QAIQSWFDEY
HANSEVEVK
(4)
SVVDFIQKHGN FKGFIDLHSY SQLLMYPYGY
PDLGTEGCWD QLSAPR
(2)
TFTL LDPKASLLTM AFLNGALDGV
HMFRQLRFES TMK(6)R(2)DPTAEQ FQEELEK(3)FQQ AIDSREDPVS
EIVMTQSPVT LSVSPGERAT LSCRASQSIS NSYLAWYQQK
VATLR
(23)
ETYGE MADCCAK(61)(62)QEP ER(55)(56)NECFLQHK (18)DDNPNLPR(47)(48)LV
RPEVDVMCTA FHDNEETFLK
(53)
K
(87,88)
YLYEIARR(24)H PYFYAPELLF FAKR(89,90)YK(2)(3)AAFT
ECCQAADK
(1)
AA CLLPK
(39)(38)
LDELR DEGKASSAKQ R(49)LK(12)CASLQKFGERAFKAWAV
RADLAK
(85,86)
YICE NQDSISSK(41)LK (23)ECCEKPLLEK (69,70,71)SHCIAEVEND EMPADLPSLA
ADFVESK
(21)
DVC K(58)(59)NYAEAK(22)DVFLGMFLYEYAR (68)R(33)HPDYSVVLL
LR
(35)
LAK
(78,79)
TYETT LEK(12)CCAAADP HECYAK(80)VFDE FK(40)PLVEEPQN
LIK
(63)(64)
QNCELFE QLGEYK
(32)
FQNA LLVRYTK(52)K(54)VP QVSTPTLVEV SR(57)NLGKVGSK
(15)
CCKHPEAK
(67)R(64)M PCAEDYLSVV LNQLCVLHEK (77)TPVSDRVTK(17)(16)C CTESLVNR(68)RP
CFSALEVDET YVPK
(25)(24)
EFNAETFTF HADICTL
SEKERQIK(51)K(65)Q TALVELVKHK PK(10)(9)ATK(26)EQLK(11)A
VMDDFAAFVEK
(14)
CCK
(4)
ADDK
(28)(27)
ET CFAEEGK
(5)(56)
K
(44)
LV
AASQAALGL
TYPEGTQAIY KCRPGYR(16)SLG NVIMVCRKGE WVALNPLRKC
AMEPDREYHF GQAVRFVCNS GYKIEGDEEM HCSDDGFWSK
NDFTWFKLND TLDYECHDGY ESNTGSTTGS IVCGYNGWSD
LEEHLKNKK(5)E FDHNSNIRYR CRGKEGWIHT VCINGRWDPE
ENYLIQEGEE ITCKDGR
(24)
WQS IPLCVEKIPC SQPPQIEHGT
SSPPQCEGLP CKSPPEISHG VVAHMSDSYQ YGEEVTYKCF
CKRGYRLSSR SHTLR(22)TTCWD GKLEYPTCAK R
SDSKTECTAL
Sequences shown to be down regulated in subjects with cancer:
TPNPCDRKGT QACQDLMGNF FCLCKAGWGG RLCDKDVNEC
EVSAAQLQER LAVLERHLRS PVLTFAGGLP DVPVTSAPVT
GMNEEGWRRA VWEKNMKMIE LHNQEYREGK (1)HSFTMAMNAF
GDMTSEEFRQ VMNGFQNRKP RKGKVFQEPL FYEAPRSVDW
HCGIASAASY PTV
LLEHETMAEV K
(6)
QQASSWVPL LNKNCHAGTQ VFLCSLFAPV
HLCASEFALR MKIKEVKKEN GDKKIVPKKK KPLKLGPIKK
LTAIHKWDKK NKEFKNFMKK MKNHECPTFQ SVFK
SDKPVQDR
(2)
GL VVTDLKAESV VLEHRSYCSA KARDRHFAGD
(5)
YIQTLKDHRP RMVWDSQASE HFFEYKKSRS GRHVVFYPTL
PWSEIRNISF NDKKFVIKPI DKKAPDFVFY APRLRINKRI
EAVEWQQK
(3)
AQ MVQEDLEKTR AELKTAMSTP HVAEPAENEQ
(1)
GACILNMLRE YLSADAFKSG IVQYLQKHSY KNTKNEDLWD
IEFALCRTQN KEKLQWLLDE SFKGDKIKTQ EFPQILTLIG
SPGSYAARQH IMQRIQRLQA DWVLEIDTFL SQTPYGYRSF
LIEGQPNRIM RLRFNHFATE CSWDHLYVYD GDSIYAPLVA
(5)
IMQSSQSMSK LTLTPWVGLR KINVSYWCWE DMSPFTNSLL
SCIKR
(23,24)
DS PIQCIQAIAE NR
(1)
ADAVTLDG GFIYEAGLAP YKLRPVAAE VYGTERQPR
(15,16)
DGAGDVAFI RESTVFE DLSDE AER
(14)
DEYELL CPDNTRKPVDK FK(13)DCHLARVP
(21,22)
DSAIGFSRVP PRIDSGLYL GSGYFTAIQ NLRKSEE EVAAR R(2,3)ARVVWCAV
GEQELRKCNQW SGLSEGSVTC SSASTTEDC IALK(23)GEADA MSLDGGY VYTAG K(6)CGLVPVLA
ENYKSQQSSDP DPNCVDRPVE GYLAVAVVR RSDTSLTWN SVKGKKS CHTAV DRTAGWNIP
R
(7)
CLAENAGDVA FVK
(25,26)DVTVLQN TDGNNNEAW AK(18,19)DLKLADF ALLCLDG KRKPV
This application claims the benefit of provisional patent application No. 61/991,061 filed on 9 May 2014, which is hereby incorporated by reference in its entirety.
| Number | Date | Country | |
|---|---|---|---|
| 61991061 | May 2014 | US |
