# Patent

## Title
TLE3 as a marker for chemotherapy

## Abstract

Methods of using TLE3 as a marker for predicting the likelihood that a patient's cancer will respond to chemotherapy. Methods of using TLE3 as a marker for selecting a chemotherapy for a cancer.

## Background
CROSS REFERENCE TO RELATED APPLICATION
This application claims priority to U.S. Provisional Patent Application Ser. No. 60/991,487, filed Nov. 30, 2007, the entirety of which is hereby incorporated herein by reference.


BACKGROUND OF THE INVENTION
A major challenge of cancer treatment is the selection of chemotherapies that maximize efficacy and minimize toxicity for a given patient. Assays for cell surface markers, e.g., using immunohistochemistry (IHC), have provided means for dividing certain cancers into subclasses. For example, one factor considered in prognosis and treatment decisions for breast cancer is the presence or absence of the estrogen receptor (ER). ER-positive breast cancers typically respond much more readily to hormonal therapies such as tamoxifen, which acts as an anti-estrogen in breast tissue, than ER-negative cancers. Though useful, these analyses only in part predict the clinical behavior of breast cancers. There is phenotypic diversity present in cancers that current diagnostic tools fail to detect. As a consequence, there is still much controversy over how to stratify patients amongst potential treatments in order to optimize outcome (e.g., for breast cancer see “NIH Consensus Development Conference Statement: Adjuvant Therapy for Breast Cancer, Nov. 1-3, 2000”, J. Nat. Cancer Inst. Monographs, 30:5-15, 2001 and Di Leo et al., Int. J. Clin. Oncol. 7:245-253, 2002). In particular, there is currently no tool for predicting a patient's likely response to treatment with paclitaxel, a chemotherapeutic with particularly adverse side-effects. There clearly exists a need for improved methods and reagents for classifying cancers and thereby selecting therapeutic regimens that maximize efficacy and minimize toxicity for a given patient.
SUMMARY OF THE INVENTION
We have identified a correlation between the expression of TLE3 (transducin-like enhancer of split 3, Entrez Gene ID 7090) and a cancer's response to chemotherapy. This correlation has been demonstrated using TLE3 antibodies and samples from breast cancer cohorts which include both treated and untreated patients with known outcome. The inventors have also observed that binding of TLE3 antibodies in samples from treated ovarian cancer patients correlates with improved prognosis. In one aspect, the present invention therefore provides methods of using TLE3 as a marker for predicting the likelihood that a patient's cancer will respond to chemotherapy. In another aspect, the present invention provides methods of using TLE3 as a marker for deciding whether to administer chemotherapy to a cancer patient. In yet another aspect, the present invention provides methods of using TLE3 as a marker for selecting a chemotherapy for a cancer patient.
Expression of TLE3 can be detected using any known method. Thus, while the inventive methods have been exemplified by detecting TLE3 polypeptides using antibodies, in certain embodiments TLE3 polynucleotides may be detected using one or more primers as is well known in the art.
In general, TLE3 can be used in conjunction with other markers or clinical factors (e.g., stage, tumor size, node characteristics, age, etc.) to further improve the predictive power of the inventive methods.
BRIEF DESCRIPTION OF THE APPENDIX
This patent application refers to material comprising a table and data presented as Appendix A. Specifically, Appendix A is a table that lists a variety of markers that could be used in a panel in conjunction with the TLE3 marker in an inventive method. The table includes the antibody ID, parent gene name, Entrez Gene ID, known aliases for the parent gene, peptides that may be used in preparing antibodies and exemplary antibody titers for staining. Using the parent gene name, Entrez Gene ID and/or known aliases for the parent gene, a skilled person can readily obtain the nucleotide (and corresponding amino acid) sequences for each and every one of the parent genes that are listed in Appendix A from a public database (e.g., GenBank, Swiss-Prot or any future derivative of these). The nucleotide and corresponding amino acid sequences for each and every one of the parent genes that are listed in Appendix A are hereby incorporated by reference from these public databases. Antibodies with IDs that begin with S5 or S6 may be obtained from commercial sources as indicated.



BRIEF DESCRIPTION OF THE DRAWING
FIG. 1 compares IHC images of TLE3-negative (S0643−) and TLE3-positive (S0643+) samples from breast cancer patients.
FIG. 2 shows Kaplan-Meier recurrence curves that were generated using all patients in the Huntsville Hospital (HH) breast cancer cohort after classification based on staining with an antibody raised against the TLE3 marker. Recurrence data from TLE3-positive and TLE3-negative patients were used to generate the top and bottom curves, respectively. As shown in the Figure, antibody binding to the TLE3 marker correlates with improved prognosis across this breast cancer cohort (HR=0.573, p<0.004).
FIG. 3 shows Kaplan-Meier recurrence curves that were generated using all patients in the Roswell Park Cancer Institute (RP) breast cancer cohort after classification based on staining with an antibody raised against the TLE3 marker. The selected patients in the RP cohort were all triple negative for the ER (estrogen receptor, Entrez GeneID 2099), PR (progesterone receptor, Entrez GeneID 5241) and HER-2 markers (v-erb-b2 erythroblastic leukemia viral oncogene homolog 2, Entrez GeneID 2064). Recurrence data from TLE3-positive and TLE3-negative patients were used to generate the top and bottom curves, respectively. As shown in the Figure, antibody binding to the TLE3 marker correlates with improved prognosis across this breast cancer cohort (HR=0.24, p<0.011).
FIG. 4 shows Kaplan-Meier recurrence curves that were generated using patients in the HH breast cancer cohort of FIG. 1 that did not receive chemotherapy. Recurrence data from TLE3-positive and TLE3-negative patients in this subset were used to generate the top and bottom curves, respectively. As shown in the Figure, antibody binding to the TLE3 marker loses its correlation with prognosis in breast cancer patients that did not receive chemotherapy (HR=0.788, p=0.49).
FIG. 5 shows Kaplan-Meier recurrence curves that were generated using patients in the HH breast cancer cohort of FIG. 1 that did receive chemotherapy. Recurrence data from TLE3-positive and TLE3-negative patients in this subset were used to generate the top and bottom curves, respectively. As shown in the Figure, the correlation between antibody binding to the TLE3 marker and prognosis was restored in patients that did receive chemotherapy (HR=0.539, p<0.013).
FIG. 6 shows Kaplan-Meier recurrence curves that were generated using patients in the RP breast cancer cohort of FIG. 2 that did receive chemotherapy. Recurrence data from TLE3-positive and TLE3-negative patients in this subset were used to generate the top and bottom curves, respectively. As shown in the Figure, antibody binding to the TLE3 marker correlates with improved prognosis across this subset of breast cancer patients (HR=0.194, p=0.010). These results parallel those obtained in FIG. 5 with the HH cohort.
FIG. 7 shows Kaplan-Meier recurrence curves that were generated using patients in the HH breast cancer cohort of FIG. 5 that received CMF (cyclophosphamide, methotrexate and 5-fluorouracil) chemotherapy. Recurrence data from TLE3-positive and TLE3-negative patients in this subset were used to generate the top and bottom curves, respectively. As shown in the Figure, antibody binding to the TLE3 marker correlates with improved prognosis across this subset of treated patients (HR=0.398, p<0.019).
FIG. 8 shows Kaplan-Meier recurrence curves that were generated using patients in the HH breast cancer cohort of FIG. 5 that received CA (cyclophosphamide and adriamycin) or CAF (cyclophosphamide, adriamycin and 5-fluorouracil) chemotherapy (with or without a taxane). Recurrence data from TLE3-positive and TLE3-negative patients in this subset were used to generate the top and bottom curves, respectively. As shown in the Figure, the correlation between antibody binding to the TLE3 marker and prognosis loses significance in this subset of treated patients (HR=0.666, p=0.22).
FIG. 9 shows Kaplan-Meier recurrence curves that were generated using patients in the HH breast cancer cohort of FIG. 8 that received CA or CAF chemotherapy only (i.e., without a taxane). Recurrence data from TLE3-positive and TLE3-negative patients in this subset were used to generate the top and bottom curves, respectively. As shown in the Figure, there is no correlation between antibody binding to the TLE3 marker and prognosis in this subset of treated patients (HR=1.03, p=0.95).
FIG. 10 shows Kaplan-Meier recurrence curves that were generated using patients in the HH breast cancer cohort of FIG. 8 that received CA or CAF in combination with a taxane. Recurrence data from TLE3-positive and TLE3-negative patients in this subset were used to generate the top and bottom curves, respectively. As shown in the Figure, the correlation between antibody binding to the TLE3 marker and prognosis was restored in this subset of treated patients (HR=0.114, p=0.038).
FIG. 11 shows Kaplan-Meier recurrence curves that were generated using patients in the RP breast cancer cohort of FIG. 6 that received CA chemotherapy only (i.e., without a taxane). Recurrence data from TLE3-positive and TLE3-negative patients in this subset were used to generate the top and bottom curves, respectively. As shown in the Figure, there is no correlation between antibody binding to the TLE3 marker and prognosis in this subset of treated patients (HR=0.759, p=0.81).
FIG. 12 shows Kaplan-Meier recurrence curves that were generated using patients in the RP breast cancer cohort of FIG. 6 that received CA in combination with a taxane. Recurrence data from TLE3-positive and TLE3-negative patients in this subset were used to generate the top and bottom curves, respectively. As shown in the Figure, antibody binding to the TLE3 marker correlates with improved prognosis across this subset of treated patients (HR=0.142, p=0.011).
FIG. 13 shows Kaplan-Meier recurrence curves that were generated using patients in the RP breast cancer cohort of FIG. 6 that received a taxane or CMF. Some of the patients receiving a taxane also received CA. Recurrence data from TLE3-positive and TLE3-negative patients in this subset were used to generate the top and bottom curves, respectively. As shown in the Figure, antibody binding to the TLE3 marker correlates with improved prognosis across this subset of treated patients (HR=0.137, p=0.011).
FIG. 14 shows Kaplan-Meier recurrence curves that were generated using patients in the RP breast cancer cohort of FIG. 6 that received neoadjuvant chemotherapy. Recurrence data from TLE3-positive and TLE3-negative patients in this subset were used to generate the top and bottom curves, respectively. The sample size was small (N=12); however, as shown in the Figure, antibody binding to the TLE3 marker showed significant correlation with improved prognosis across this subset of treated patients when measured using the Fisher Exact Test (p=0.005).
FIGS. 15-17 show Kaplan-Meier recurrence curves that were generated using patients in the RP breast cancer cohort of FIG. 6 that received chemotherapy. Recurrence data from TLE3-positive and TLE3-negative patients with stage II+ (FIG. 15), stage IIb+ (FIG. 16) and stage III+ (FIG. 17) cancers were used to generate the top and bottom curves, respectively. In each case, antibody binding to the TLE3 marker correlated with improved prognosis across these subsets of treated patients. The sample size was small in the subset of FIG. 17 (N=19); however significance was obtained when measured using the Fisher Exact Test (p=0.020).
FIG. 18 shows Kaplan-Meier recurrence curves that were generated using patients in the University of Alabama at Birmingham (UAB) ovarian cancer cohort. All patients received paclitaxel. Most patients also received platinum chemotherapy (carboplatin or cisplatin). Recurrence data from TLE3-positive and TLE3-negative patients in this subset were used to generate the top and bottom curves, respectively. As shown in the Figure, antibody binding to the TLE3 marker correlated with prognosis in these treated patients (HR=0.64, p<0.049).



DEFINITIONS
Binds—When an interaction partner “binds” a marker they are linked by direct non-covalent interactions.
Cancer markers—“Cancer markers” or “markers” are molecular entities that are detectable in cancer samples. Generally, markers may be polypeptides (e.g., TLE3 protein) or polynucleotides (e.g., TLE3 mRNA) that are indicative of the expression of a gene (e.g., TLE3 gene) and present within the cancer sample, e.g., within the cytoplasm or membranes of cancerous cells and/or secreted from such cells.
Cancer sample—As used herein, the term “cancer sample” or “sample” is taken broadly to include cell or tissue samples removed from a cancer patient (e.g., from a tumor, from the bloodstream, etc.), cells derived from a tumor that may be located elsewhere in the body (e.g., cells in the bloodstream or at a site of metastasis), or any material derived from such a sample. Derived material may include, for example, nucleic acids or proteins extracted from the sample, cell progeny, etc. In one embodiment, a cancer sample may be a tumor sample.
Correlation—“Correlation” refers to the degree to which one variable can be predicted from another variable, e.g., the degree to which a cancer's response to therapy can be predicted from the expression of a marker in a cancer sample. A variety of statistical methods may be used to measure correlation between two variables, e.g., without limitation the student t-test, the Fisher exact test, the Pearson correlation coefficient, the Spearman correlation coefficient, the Chi squared test, etc. Results are traditionally given as a measured correlation coefficient with a p-value that provides a measure of the likelihood that the correlation arose by chance. A correlation with a p-value that is less than 0.05 is generally considered to be statistically significant. Preferred correlations have p-values that are less than 0.01, especially less than 0.001.
Hybridized—When a primer and a marker are physically “hybridized” with one another as described herein, they are non-covalently linked by base pair interactions.
Interaction partner—An “interaction partner” is an entity that binds a polypeptide marker. For example and without limitation, an interaction partner may be an antibody or a fragment thereof that binds a marker. In general, an interaction partner is said to “bind specifically” with a marker if it binds at a detectable level with the marker and does not bind detectably with unrelated molecular entities (e.g., other markers) under similar conditions. Specific association between a marker and an interaction partner will typically be dependent upon the presence of a particular structural feature of the target marker such as an antigenic determinant or epitope recognized by the interaction partner. In general, it is to be understood that specificity need not be absolute. For example, it is well known in the art that antibodies frequently cross-react with other epitopes in addition to the target epitope. Such cross-reactivity may be acceptable depending upon the application for which the interaction partner is to be used. Thus the degree of specificity of an interaction partner will depend on the context in which it is being used. In general, an interaction partner exhibits specificity for a particular marker if it favors binding with that partner above binding with other potential partners, e.g., other markers. One of ordinary skill in the art will be able to select interaction partners having a sufficient degree of specificity to perform appropriately in any given application (e.g., for detection of a target marker, for therapeutic purposes, etc.). It is also to be understood that specificity may be evaluated in the context of additional factors such as the affinity of the interaction partner for the target marker versus the affinity of the interaction partner for other potential partners, e.g., other markers. If an interaction partner exhibits a high affinity for a target marker and low affinity for non-target molecules, the interaction partner will likely be an acceptable reagent for diagnostic purposes even if it lacks specificity.
Primer—A “primer” is an oligonucleotide entity that physically hybridizes with a polynucleotide marker. In general, a primer is said to “hybridize specifically” with a marker if it hybridizes at a detectable level with the marker and does not hybridize detectably with unrelated molecular entities (e.g., other markers) under similar conditions. Specific hybridization between a marker and a primer will typically be dependent upon the presence of a particular nucleotide sequence of the target marker which is complementary to the nucleotide sequence of the primer. In general, it is to be understood that specificity need not be absolute. The degree of specificity of a primer will depend on the context in which it is being used. In general, a primer exhibits specificity for a particular marker if it favors hybridization with that partner above hybridization with other potential partners, e.g., other markers. One of ordinary skill in the art will be able to select primers having a sufficient degree of specificity to perform appropriately in any given application. It is also to be understood that specificity may be evaluated in the context of additional factors such as the affinity of the primer for the target marker versus the affinity of the primer for other potential partners, e.g., other markers. If a primer exhibits a high affinity for a target marker and low affinity for non-target molecules, the primer will likely be an acceptable reagent for diagnostic purposes even if it lacks specificity.
Response—The “response” of a cancer to therapy may represent any detectable change, for example at the molecular, cellular, organellar, or organismal level. For instance, tumor size, patient life expectancy, recurrence, or the length of time the patient survives, etc., are all responses. Responses can be measured in any of a variety of ways, including for example non-invasive measuring of tumor size (e.g., CT scan, image-enhanced visualization, etc.), invasive measuring of tumor size (e.g., residual tumor resection, etc.), surrogate marker measurement (e.g., serum PSA, etc.), clinical course variance (e.g., measurement of patient quality of life, time to relapse, survival time, etc.). Small molecule—A “small molecule” is a non-polymeric molecule. A small molecule can be synthesized in a laboratory (e.g., by combinatorial synthesis) or found in nature (e.g., a natural product). A small molecule is typically characterized in that it contains several carbon-carbon bonds and has a molecular weight of less than about 1500 Da, although this characterization is not intended to be limiting for the purposes of the present invention.
DETAILED DESCRIPTION OF CERTAIN PREFERRED EMBODIMENTS OF THE INVENTION
As noted above, we have identified a correlation between the expression of TLE3 (transducin-like enhancer of split 3, Entrez Gene ID 7090) in a cancer sample and a cancer's response to chemotherapy. As described in the Examples, this correlation has been demonstrated using TLE3 antibodies and samples from two breast cancer cohorts which include both treated and untreated patients with known outcome. We have also shown that this predictive model is consistent when applied to samples from a cohort of treated ovarian cancer patients. We have also demonstrated the utility of TLE3 for predicting response to specific types of chemotherapies including treatments which involve the administration of cell cycle specific chemotherapeutics, e.g., methotrexate and taxanes. Since these chemotherapeutics have known utility across different cancer types, these results suggest that the inventive methods will also be useful in predicting their efficacy across different cancer types.
Predicting Response to Chemotherapy and Selecting Chemotherapy
In one aspect, the present invention provides methods of using TLE3 as a marker for predicting the likelihood that a patient's cancer will respond to chemotherapy. In general, these methods involve providing a cancer sample from a cancer patient, determining whether TLE3 is expressed in the cancer sample, and predicting the likelihood that the patient's cancer will respond to chemotherapy based upon a result of the step of determining. In one embodiment, the step of predicting comprises predicting that the patient's cancer is likely to respond to chemotherapy based upon the presence of TLE3 expression in the cancer sample. In one embodiment, the step of predicting comprises predicting that the patient's cancer is unlikely to respond to chemotherapy based upon the absence of TLE3 expression in the cancer sample.
In certain embodiments, a negative control sample is provided and the step of determining comprises detecting a level of TLE3 expression in the cancer sample and the negative control sample and comparing the level of expression of TLE3 in the cancer sample and the negative control sample. In general, the negative control sample can be any sample that does not reproducibly express TLE3. In one embodiment, the negative control sample can be a sample that does not reproducibly bind TLE3 antibodies. In one embodiment, the negative control sample can be a sample that does not reproducibly produce a detectable level of TLE3 mRNA. In one embodiment, the negative control sample can be from a patient with a TLE3-negative cancer. In one embodiment, the negative control sample can be from a patient without cancer. In certain embodiments the negative control sample may originate from the same tissue type as the cancer in question (e.g., breast tissue when considering breast cancer). In other embodiments, the negative control sample may originate from a different tissue type or even a different organism, or a cell line.
Additionally or alternatively, in certain embodiments, a positive control sample is provided and the step of determining comprises detecting a level of TLE3 expression in the cancer sample and the positive control sample and comparing the level of expression of TLE3 in the cancer sample and the positive control sample. In general, the positive control sample can be any sample that reproducibly expresses TLE3. In one embodiment, the negative control sample can be a sample that reproducibly bind TLE3 antibodies. In one embodiment, the negative control sample can be a sample that reproducibly produces a detectable level of TLE3 mRNA. In one embodiment, the positive control sample can be from a patient with a TLE3-positive cancer. In certain embodiments the positive control sample may originate from the same tissue type as the cancer in question (e.g., breast tissue when considering breast cancer). In other embodiments, the positive control sample may originate from a different tissue type or even a different organism, or cell line.
Expression of TLE3 can be determined using any known method.
In one embodiment, TLE3 polypeptides may be detected using an interaction partner that binds a TLE3 polypeptide (e.g., TLE3 protein or an antigenic fragment thereof). For example, as described below one may use a TLE3 antibody as an interaction partner and detect TLE3 expression by contacting the cancer sample with the TLE3 antibody. In such embodiments, the inventive methods may involve providing a cancer sample from a cancer patient, contacting the cancer sample with an antibody directed to TLE3, and predicting the likelihood that the patient's cancer will respond to chemotherapy based upon binding of the antibody to the cancer sample. In one embodiment, the step of predicting may comprise predicting that the patient's cancer is likely to respond to chemotherapy based upon binding of the antibody to the cancer sample. In another embodiment, the step of predicting may comprise predicting that the patient's cancer is unlikely to respond to chemotherapy based upon lack of binding of the antibody to the cancer sample.
In another embodiment, TLE3 polynucleotides may be detected using one or more primers that hybridize with a TLE3 polynucleotide (e.g., a TLE3 mRNA, cDNA or RNA). In such embodiments, the inventive methods may involve providing a cancer sample from a cancer patient, contacting the cancer sample with one or more primers that hybridize with TLE3, and predicting the likelihood that the patient's cancer will respond to chemotherapy based upon hybridization of the one or more primers to the cancer sample. In one embodiment, the step of predicting may comprise predicting that the patient's cancer is likely to respond to chemotherapy based upon hybridization of the one or more primers to the cancer sample. In another embodiment, the step of predicting may comprise predicting that the patient's cancer is unlikely to respond to chemotherapy based upon lack of hybridization of the one or more primers to the cancer sample.
In another aspect, the present invention provides methods for deciding whether to administer chemotherapy to the cancer patient based upon the likelihood that the patient's cancer will respond to chemotherapy. In one embodiment, the step of deciding comprises deciding to administer chemotherapy to the cancer patient based upon the presence of TLE3 expression in the cancer sample. In one embodiment, the step of deciding comprises deciding not to administer chemotherapy to the cancer patient based upon the absence of TLE3 expression in the cancer sample.
In yet another aspect, the present invention provides methods for selecting a chemotherapy for a cancer patient. In general, these methods comprise providing a cancer sample from a cancer patient, determining whether TLE3 is expressed in the cancer sample, and selecting a chemotherapy for the cancer patient based upon the results of the step of determining. In one embodiment, the step of selecting comprises selecting a chemotherapy based upon the presence of TLE3 expression in the cancer sample.
As described in the Examples, we have demonstrated that TLE3 expression correlates with response to chemotherapy with methotrexate (see FIG. 7) and taxanes (see FIGS. 10, 12 and 13). Methotrexate and taxanes are thought to be cell cycle specific chemotherapeutics (e.g., see Goodman & Gilman's The Pharmacological Basis of Therapeutics, IX. Chemotherapy of Neoplastic Diseases Chapter 51. Antineoplastic Agents, 11th Edition, Laurence L. Brunton, editor-in-chief, John S. Lazo and Keith L. Parker, Associate Editors). Cell cycle specific chemotherapeutics exhibit their mechanism of action within a specific phase of the cell cycle in contrast to non-cell cycle specific chemotherapeutics that work equally with all phases including the resting phase (G0). Other plant alkaloids besides the taxanes have also been classified in the literature as cell cycle specific chemotherapeutics as have other antimetabolites besides methotrexate. In contrast, many alkylating agents such as cisplatin and cyclophosamide have been classified as non-cell cycle specific chemotherapeutics. Our results suggest that the predictive power of TLE3 may extend to other cell cycle specific chemotherapeutics besides methotrexate and taxanes.
In some embodiments, the inventive methods may therefore be used to select, or decide whether to administer, a cell cycle specific chemotherapeutic. In one embodiment, the inventive methods may be used to select, or decide whether to administer, an antimetabolite. In one embodiment, the inventive methods may be used to select, or decide whether to administer, a plant alkaloid. In one embodiment, the inventive methods may be used to select, or decide whether to administer, methotrexate. In another embodiment, the inventive methods may be used to select, or decide whether to administer, a taxane. In one embodiment the taxane is paclitaxel. In one embodiment the taxane is docetaxel.
In each case it will be appreciated that these chemotherapeutics may be administered alone or in combination with other chemotherapeutics as is known in the art and discussed below. It will also be appreciated that the present invention encompasses methods in which the selected chemotherapeutic is a methotrexate or taxane derivative, i.e., a compound with a structure which is derived from methotrexate or a taxane. Derivatives will typically share most of the structure of the parent compound but may include different substituents, heteroatoms, ring fusions, levels of saturation, isomerism, stereoisomerism, etc. at one or more positions within the parent compound. Without limitation, the following U.S. patents describe the preparation of exemplary methotrexate derivatives that could be employed according to an inventive method: U.S. Pat. Nos. 6,559,149 and 4,374,987. Without limitation, the following U.S. patents describe the preparation of exemplary taxane derivatives that could be employed according to an inventive method: U.S. Pat. Nos. 7,074,945; 7,063,977; 6,906,101; 6,649,778; 6,596,880; 6,552,205; 6,531,611; 6,482,963; 6,482,850; 6,462,208; 6,455,575; 6,441,026; 6,433,180; 6,392,063; 6,369,244; 6,339,164; 6,291,690; 6,268,381; 6,239,167; 6,218,553; 6,214,863; 6,201,140; 6,191,290; 6,187,916; 6,162,920; 6,147,234; 6,136,808; 6,114,550; 6,107,332; 6,051,600; 6,025,385; 6,011,056; 5,955,489; 5,939,567; 5,912,263; 5,908,835; 5,869,680; 5,861,515; 5,821,263; 5,763,477; 5,750,561; 5,728,687; 5,726,346; 5,726,318; 5,721,268; 5,719,177; 5,714,513; 5,714,512; 5,703,117; 5,698,582; 5,686,623; 5,677,462; 5,646,176; 5,637,723; 5,621,121; 5,616,739; 5,606,083; 5,580,899; 5,476,954; 5,403,858; 5,380,916; 5,254,703; and 5,250,722. The entire contents of each of the aforementioned patents and any other reference which is cited herein is hereby incorporated by reference.
Methotrexate acts by inhibiting the metabolism of folic acid and has been approved for the treatment of bladder cancer, breast cancer, gastric cancer, choriocarcinoma, head and neck cancer, leptomeningeal cancer, leukemia (acute meningeal, acute lymphoblastic, acute lymphocytic), lymphoma (Burkitt's, childhood, non-Hodgkin's), mycosis fungoides, primary unknown cancer and lymphatic sarcoma (Methotrexate in BC Cancer Agency Cancer Drug Manual, 2007). Methotrexate has also been shown to be useful for treating esophageal cancer, lung cancer and testicular cancer (Methotrexate in UpToDate, 2007). In certain embodiments, the inventive methods comprise a step of selecting, or deciding whether to administer, methotrexate in combination with one or more additional chemotherapeutics. For example, methotrexate is commonly administered to cancer patients as a combination called CMF which also includes cyclophosphamide and 5-fluorouracil.
Taxanes are diterpenes produced by the plants of the genus Taxus. Taxanes can be obtained from natural sources or produced synthetically. Taxanes include paclitaxel (TAXOLTM) and docetaxel (TAXOTERETM). Taxanes work by interfering with normal microtubule growth during cell division. In certain embodiments, the inventive methods comprise a step of selecting, or deciding whether to administer, a taxane (e.g., paclitaxel or docetaxel) in combination with one or more additional chemotherapeutics. For example, taxanes are commonly administered to cancer patients in combination with cyclophosphamide and adriamycin (doxorubicin) and optionally 5-fluorouracil (i.e., with CA or CAF).
Paclitaxel has been approved for the treatment of breast cancer, Kaposi's sarcoma, lung cancer and ovarian cancer (Paclitaxel in BC Cancer Agency Cancer Drug Manual, 2007 and Mekhail and Markman, Expert Opin. Pharmacother. 3:755-66, 2002). Paclitaxel has also been shown to be useful in treating cervical cancer (pp. 1124-34 in AHFS 2005 Drug Information. Bethesda, Md.: American Society of Health-System Pharmacists, 2005), endometrial cancer (Paclitaxel in BC Cancer Agency Cancer Drug Manual, 2007), bladder cancer (Paclitaxel in UpToDate, 2007), head and neck cancer (Paclitaxel in UpToDate, 2007), leukemia (Paclitaxel in UpToDate, 2007) and malignant melanoma (Paclitaxel in UpToDate, 2007). Side effects of paclitaxel include hypersensitivity reactions such as flushing of the face, skin rash, or shortness of breath. Patients often receive medication to prevent hypersensitivity reactions before they take paclitaxel. Paclitaxel can also cause temporary damage to the bone marrow. Bone marrow damage can cause a person to be more susceptible to infection, anemia, and bruise or bleed easily. Other side effects may include joint or muscle pain in the arms or legs; diarrhea; nausea and vomiting; numbness, burning, or tingling in the hands or feet; and loss of hair.
Docetaxel has been approved for the treatment of breast cancer (Aapro, Seminars in Oncology 25(5 Suppl 12):7-11, 1998; Nabholtz et al., Journal of Clinical Oncology 17(5):1413-24, 1999; Sjostrom et al., European Journal of Cancer 35(8):1194-201, 1999; and Burstein et al., Journal of Clinical Oncology 18(6):1212-9, 2000), non-small cell lung cancer (Fossella et al., Journal of Clinical Oncology 18(12):2354-62, 2000 and Hainsworth et al., Cancer 89(2):328-33, 2000) and ovarian cancer (Kaye et al., European Journal of Cancer 33(13):2167-70, 1997). Docetaxel has also been shown to be useful in treating esothelioma (Vorobiof et al., Proc Am Soc Clin Oncol 19:578a, 2000), prostate cancer (Picus et al., Seminars in Oncology 26(5 Suppl 17):14-8, 1999 and Petrylak et al., Journal of Clinical Oncology 17(3):958-67, 1999), urothelial transitional cell cancer (Dimopoulos et al., Annals of Oncology 10(11): 1385-8, 1999 and Pectasides et al., European Journal of Cancer 36(1):74-9, 2000), head and neck cancer (Docetaxel in USP DI, 2000 and Couteau et al., British Journal of Cancer 81(3):457-62, 1999) and small cell lung cancer (Smyth et al., European Journal of Cancer 30A(8):1058-60, 1994).
Our observation that improved response to chemotherapy is observed for both breast and ovarian cancer patients that are TLE3-positive suggests that the inventive methods may be useful across different cancer types. Our observation that TLE3 expression is associated with improved response to treatment with methotrexate and taxanes further suggest that the inventive methods may be applicable across cancers that respond to these chemotherapeutics. As discussed above, this includes without limitation breast cancer, ovarian cancer, lung cancer, bladder cancer, gastric cancer, head and neck cancer, and leukemia.
In one embodiment, the inventive methods may be used with a cancer patient that has breast cancer. In one embodiment, the inventive methods may be used with a cancer patient that has ovarian cancer. In one embodiment, the inventive methods may be used with a cancer patient that has lung cancer. In one embodiment, the inventive methods may be used with a cancer patient that has bladder cancer. In one embodiment, the inventive methods may be used with a cancer patient that has gastric cancer. In one embodiment, the inventive methods may be used with a cancer patient that has head and neck cancer. In one embodiment, the inventive methods may be used with a cancer patient that has leukemia.
As demonstrated in the Examples, in one embodiment, the correlation between TLE3 expression and response to chemotherapy was observed with breast cancer patients that are triple negative for the ER (estrogen receptor, Entrez GeneID 2099), PR (progesterone receptor, Entrez GeneID 5241) and HER-2 markers (v-erb-b2 erythroblastic leukemia viral oncogene homolog 2, Entrez GeneID 2064). In certain embodiments, the inventive methods may therefore be used with breast cancer patients that belong to this class.
As demonstrated in the Examples, the correlation between TLE3 expression and response to chemotherapy was found to also exist when treatment was administered in a neoadjuvant setting. Thus, in certain embodiments, the inventive methods may be used with patients receiving chemotherapy in a neoadjuvant setting. In other embodiments, the chemotherapy may be administered in an adjuvant setting.
As demonstrated in the Examples, the correlation between TLE3 expression and response to chemotherapy was also found to be independent of stage. Thus, in certain embodiments, the inventive methods may be used with patients with a stage II+ (i.e., stage II or greater) cancer. In certain embodiments, the inventive methods may be used with patients with a stage IIb+ or a stage III+ cancer.
Detecting TLE3 Expression
As mentioned above, expression of TLE3 can be determined using any known method. In one embodiment, TLE3 expression may be determined by detecting TLE3 polypeptide markers using interaction partners (e.g., antibodies). In another embodiment, TLE3 expression may be determined by detecting TLE3 polynucleotide markers using primers.
Detecting TLE3 Polypeptide Markers TLE3 polypeptide markers may be detected using any interaction partner that binds a TLE3 polypeptide marker (which could be a TLE3 protein or an antigenic fragment thereof). Thus, any entity that binds detectably to the TLE3 marker may be utilized as an interaction partner in accordance with the present invention, so long as it binds the marker with an appropriate combination of affinity and specificity.
Particularly preferred interaction partners are antibodies, or fragments (e.g., F(ab) fragments, F(ab′)2 fragments, Fv fragments, or sFv fragments, etc.; see, for example, Inbar et al., Proc. Nat. Acad. Sci. USA 69:2659, 1972; Hochman et al., Biochem. 15:2706, 1976; and Ehrlich et al., Biochem. 19:4091, 1980; Huston et al., Proc. Nat. Acad. Sci. USA 85:5879, 1998; U.S. Pat. Nos. 5,091,513 and 5,132,405 to Huston et al.; and U.S. Pat. No. 4,946,778 to Ladner et al., each of which is incorporated herein by reference). In certain embodiments, interaction partners may be selected from libraries of mutant antibodies (or fragments thereof). For example, collections of antibodies that each include different point mutations may be screened for their association with a marker of interest. Yet further, chimeric antibodies may be used as interaction partners, e.g., “humanized” or “veneered” antibodies as described in greater detail below.
When antibodies are used as interaction partners, these may be prepared by any of a variety of techniques known to those of ordinary skill in the art (e.g., see Harlow and Lane, Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory, 1988, see also the Examples). For example, antibodies can be produced by cell culture techniques, including the generation of monoclonal antibodies, or via transfection of antibody genes into suitable bacterial or mammalian cell hosts, in order to allow for the production of recombinant antibodies. In one technique, an “immunogen” comprising an antigenic portion of a marker of interest (or the marker itself) is initially injected into any of a wide variety of mammals (e.g., mice, rats, rabbits, sheep or goats). In this step, a marker (or an antigenic portion thereof) may serve as the immunogen without modification. Alternatively, particularly for relatively short markers, a superior immune response may be elicited if the marker is joined to a carrier protein, such as bovine serum albumin or keyhole limpet hemocyanin (KLH). The immunogen is injected into the animal host, preferably according to a predetermined schedule incorporating one or more booster immunizations and the animals are bled periodically. Polyclonal antibodies specific for the marker may then be purified from such antisera by, for example, affinity chromatography using the marker (or an antigenic portion thereof) coupled to a suitable solid support. An exemplary method is described in the Examples.
If desired for diagnostic or therapeutic purposes, monoclonal antibodies specific for TLE3 may be prepared, for example, using the technique of Kohler and Milstein, Eur. J. Immunol. 6:511, 1976 and improvements thereto. Briefly, these methods involve the preparation of immortal cell lines capable of producing antibodies having the desired specificity (i.e., reactivity with the marker of interest). Such cell lines may be produced, for example, from spleen cells obtained from an animal immunized as described above. The spleen cells are then immortalized by, for example, fusion with a myeloma cell fusion partner, preferably one that is syngeneic with the immunized animal. A variety of fusion techniques may be employed. For example, the spleen cells and myeloma cells may be combined with a nonionic detergent for a few minutes and then plated at low density on a selective medium that supports the growth of hybrid cells, but not myeloma cells. A preferred selection technique uses HAT (hypoxanthine, aminopterin, thymidine) selection. After a sufficient time, usually about 1 to 2 weeks, colonies of hybrids are observed. Single colonies are selected and their culture supernatants tested for binding activity against the marker. Hybridomas having high reactivity and specificity are preferred.
Monoclonal antibodies may be isolated from the supernatants of growing hybridoma colonies. In addition, various techniques may be employed to enhance the yield, such as injection of the hybridoma cell line into the peritoneal cavity of a suitable vertebrate host, such as a mouse. Monoclonal antibodies may then be harvested from the ascites fluid or the blood. Contaminants may be removed from the antibodies by conventional techniques, such as chromatography, gel filtration, precipitation and extraction. TLE3 may be used in the purification process in, for example, an affinity chromatography step.
It is to be understood that the present invention is not limited to using antibodies or antibody fragments as interaction partners. In particular, the present invention also encompasses the use of synthetic interaction partners that mimic the functions of antibodies. Several approaches to designing and/or identifying antibody mimics have been proposed and demonstrated (e.g., see the reviews by Hsieh-Wilson et al., Acc. Chem. Res. 29:164, 2000 and Peczuh and Hamilton, Chem. Rev. 100:2479, 2000). For example, small molecules that bind protein surfaces in a fashion similar to that of natural proteins have been identified by screening synthetic libraries of small molecules or natural product isolates (e.g., see Gallop et al., J. Med. Chem. 37:1233, 1994; Gordon et al., J. Med. Chem. 37:1385, 1994; DeWitt et al., Proc. Natl. Acad. Sci. U.S.A. 90:6909, 1993; Bunin et al., Proc. Natl. Acad. Sci. U.S.A. 91:4708, 1994; Virgilio and Ellman, J. Am. Chem. Soc. 116:11580, 1994; Wang et al., J. Med. Chem. 38:2995, 1995; and Kick and Ellman, J. Med. Chem. 38:1427, 1995). Similarly, combinatorial approaches have been successfully applied to screen libraries of peptides and proteins for their ability to bind arange of proteins (e.g., see Cull et al., Proc. Natl. Acad. Sci. U.S.A. 89:1865, 1992; Mattheakis et al., Proc. Natl. Acad. Sci. U.S.A. 91:9022, 1994; Scott and Smith, Science 249:386, 1990; Devlin et al., Science 249:404, 1990; Corey et al., Gene 128:129, 1993; Bray et al., Tetrahedron Lett. 31:5811, 1990; Fodor et al., Science 251:767, 1991; Houghten et al., Nature 354:84, 1991; Lam et al., Nature 354:82, 1991; Blake and Litzi-Davis, Bioconjugate Chem. 3:510, 1992; Needels et al., Proc. Natl. Acad. Sci. U.S.A. 90:10700, 1993; and Ohlmeyer et al., Proc. Natl. Acad. Sci. U.S.A. 90:10922, 1993). Similar approaches have also been used to study carbohydrate-protein interactions (e.g., see Oldenburg et al., Proc. Natl. Acad. Sci. U.S.A. 89:5393, 1992) and polynucleotide-protein interactions (e.g., see Ellington and Szostak, Nature 346:818, 1990 and Tuerk and Gold, Science 249:505, 1990). These approaches have also been extended to study interactions between proteins and unnatural biopolymers such as oligocarbamates, oligoureas, oligosulfones, etc. (e.g., see Zuckermann et al., J. Am. Chem. Soc. 114:10646, 1992; Simon et al., Proc. Natl. Acad. Sci. U.S.A. 89:9367, 1992; Zuckermann et al., J. Med. Chem. 37:2678, 1994; Burgess et al., Angew. Chem., Int. Ed. Engl. 34:907, 1995; and Cho et al., Science 261:1303, 1993). Yet further, alternative protein scaffolds that are loosely based around the basic fold of antibody molecules have been suggested and may be used in the preparation of inventive interaction partners (e.g., see Ku and Schultz Proc. Natl. Acad. Sci. U.S.A. 92:6552, 1995). Antibody mimics comprising a scaffold of a small molecule such as 3-aminomethylbenzoic acid and a substituent consisting of a single peptide loop have also been constructed. The peptide loop performs the binding function in these mimics (e.g., see Smythe et al., J. Am. Chem. Soc. 116:2725, 1994). A synthetic antibody mimic comprising multiple peptide loops built around a calixarene unit has also been described (e.g., see U.S. Pat. No. 5,770,380 to Hamilton et al.).
Any available strategy or system may be utilized to detect association between an interaction partner and the TLE3 marker. In certain embodiments, association can be detected by adding a detectable label to the interaction partner. In other embodiments, association can be detected by using a labeled secondary interaction partner that binds specifically with the primary interaction partner, e.g., as is well known in the art of antigen/antibody detection. The detectable label may be directly detectable or indirectly detectable, e.g., through combined action with one or more additional members of a signal producing system. Examples of directly detectable labels include radioactive, paramagnetic, fluorescent, light scattering, absorptive and calorimetric labels. Examples of indirectly detectable include chemiluminescent labels, e.g., enzymes that are capable of converting a substrate to a chromogenic product such as alkaline phosphatase, horseradish peroxidase and the like.
Once a labeled interaction partner has bound the TLE3 marker, the complex may be visualized or detected in a variety of ways, with the particular manner of detection being chosen based on the particular detectable label, where representative detection means include, e.g., scintillation counting, autoradiography, measurement of paramagnetism, fluorescence measurement, light absorption measurement, measurement of light scattering and the like.
In general, association between an interaction partner and the TLE3 marker may be assayed by contacting the interaction partner with a cancer sample that includes the marker. Depending upon the nature of the sample, appropriate methods include, but are not limited to, immunohistochemistry (IHC), radioimmunoassay, ELISA, immunoblotting and fluorescence activates cell sorting (FACS). In the case where the protein is to be detected in a tissue sample, e.g., a biopsy sample, IHC is a particularly appropriate detection method. Techniques for obtaining tissue and cell samples and performing IHC and FACS are well known in the art.
Where large numbers of samples are to be handled (e.g., when simultaneously analyzing several samples from the same patient or samples from different patients), it may be desirable to utilize arrayed and/or automated formats. In certain embodiments, tissue arrays as described in the Examples may be used. Tissue arrays may be constructed according to a variety of techniques. According to one procedure, a commercially-available mechanical device (e.g., the manual tissue arrayer MTA1 from Beecher Instruments of Sun Prairie, Wis.) is used to remove an 0.6-micron-diameter, full thickness “core” from a paraffin block (the donor block) prepared from each patient, and to insert the core into a separate paraffin block (the recipient block) in a designated location on a grid. In preferred embodiments, cores from as many as about 400 patients (or multiple cores from the same patient) can be inserted into a single recipient block; preferably, core-to-core spacing is approximately 1 mm. The resulting tissue array may be processed into thin sections for staining with interaction partners according to standard methods applicable to paraffin embedded material.
Whatever the format, and whatever the detection strategy, identification of a discriminating titer can simplify binding studies to assess the desirability of using an interaction partner. In such studies, the interaction partner is contacted with a plurality of different samples that preferably have at least one common trait (e.g., tissue of origin), and often have multiple common traits (e.g., tissue of origin, stage, microscopic characteristics, etc.). In some cases, it will be desirable to select a group of samples with at least one common trait and at least one different trait, so that a titer is determined that distinguishes the different trait. In other cases, it will be desirable to select a group of samples with no detectable different traits, so that a titer is determined that distinguishes among previously indistinguishable samples. Those of ordinary skill in the art will understand, however, that the present invention often will allow both of these goals to be accomplished even in studies of sample collections with varying degrees of similarity and difference.
As discussed above and in the Examples, the inventors have applied these techniques to samples from breast and ovarian cancer patients. The invention also encompasses the recognition that markers that are secreted from the cells in which they are produced may be present in serum, enabling their detection through a blood test rather than requiring a biopsy specimen. An interaction partner that binds to such markers represents a particularly preferred embodiment of the invention.
In general, the results of such an assay can be presented in any of a variety of formats. The results can be presented in a qualitative fashion. For example, the test report may indicate only whether or not the TLE3 marker was detected, perhaps also with an indication of the limits of detection. Additionally the test report may indicate the subcellular location of binding, e.g., nuclear versus cytoplasmic and/or the relative levels of binding in these different subcellular locations. The results may be presented in a semi-quantitative fashion. For example, various ranges may be defined and the ranges may be assigned a score (e.g., 0 to 5) that provides a certain degree of quantitative information. Such a score may reflect various factors, e.g., the number of cells in which the marker is detected, the intensity of the signal (which may indicate the level of expression of the marker), etc. The results may be presented in a quantitative fashion, e.g., as a percentage of cells in which the marker is detected, as a concentration, etc. As will be appreciated by one of ordinary skill in the art, the type of output provided by a test will vary depending upon the technical limitations of the test and the biological significance associated with detection of the marker. For example, in certain circumstances a purely qualitative output (e.g., whether or not the marker is detected at a certain detection level) provides significant information. In other cases a more quantitative output (e.g., a ratio of the level of expression of the marker in two samples) is necessary.
Detecting TLE3 Polynucleotide Markers
Although in many cases detection of polypeptide markers using interaction partners such as antibodies may represent the most convenient means of determining whether TLE3 is expressed in a particular sample, the inventive methods also encompass the use of primers for the detection of polynucleotide markers. A variety of methods for detecting the presence of a particular polynucleotide marker are known in the art and may be used in the inventive methods. In general, these methods rely on hybridization between one or more primers and the polynucleotide marker.
Any available strategy or system may be utilized to detect hybridization between primers and the TLE3 polynucleotides (which could be a TLE3 mRNA, a cDNA produced by RT-PCR from mRNA, RNA produced from such cDNA, etc.). In certain embodiments, hybridization can be detected by simply adding a detectable label to the primer. In other embodiments, hybridization can be detected by using a labeled secondary primer that hybridizes specifically with the primary primer (e.g., a region of the primary primer that does not hybridize with the TLE3 marker). In yet other embodiments it may be advantageous to amplify the TLE3 marker within the cancer sample by PCR using a set of primers designed to amplify a region of the TLE3 gene. The resulting product can then be detected, e.g., using a labeled secondary primer that hybridizes with the amplified product. Those skilled in the art will appreciate variations on these embodiments.
Considerations for primer design are well known in the art and are described, for example, in Newton, et al. (eds.) PCR: Essential data Series, John Wiley & Sons; PCR Primer: A Laboratory Manual, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., 1995; White, et al. (eds.) PCR Protocols: Current methods and Applications, Methods in Molecular Biology, The Humana Press, Totowa, N.J., 1993. In addition, a variety of computer programs known in the art may be used to select appropriate primers.
In general, a detectable label may be directly detectable or indirectly detectable, e.g., through combined action with one or more additional members of a signal producing system. Examples of directly detectable labels include radioactive, paramagnetic, fluorescent, light scattering, absorptive and calorimetric labels. Examples of indirectly detectable include chemiluminescent labels, e.g., enzymes that are capable of converting a substrate to a chromogenic product such as alkaline phosphatase, horseradish peroxidase and the like.
Once a labeled primer has hybridized with the TLE3 marker, the complex may be visualized or detected in a variety of ways, with the particular manner of detection being chosen based on the particular detectable label, where representative detection means include, e.g., scintillation counting, autoradiography, measurement of paramagnetism, fluorescence measurement, light absorption measurement, measurement of light scattering and the like.
In general, hybridization between a primer and the TLE3 marker may be assayed by contacting the primer with a cancer sample that includes the marker. Depending upon the nature of the cancer sample, appropriate methods include, but are not limited to, microarray analysis, in situ hybridization, Northern blot, and various nucleic acid amplification techniques such as PCR, RT-PCR, quantitative PCR, the ligase chain reaction, etc.
Identification of Novel Therapies
The predictive power of TLE3 is useful according to the present invention not only to classify cancers with respect to their likely responsiveness to known therapies, but also to identify potential new therapies or therapeutic agents that could be useful in the treatment of cancer.
Indeed, TLE3 represents an attractive candidate for identification of new therapeutic agents (e.g., via screens to detect compounds or entities that bind or hybridize to the marker, preferably with at least a specified affinity and/or specificity, and/or via screens to detect compounds or entities that modulate (i.e., increase or decrease) expression, localization, modification, or activity of the marker. Thus, in one embodiment the present invention provides methods comprising steps of contacting a test compound with a cell expressing the TLE3 marker (e.g., individual engineered cells or in the context of a tissue, etc.); and determining whether the test compound modulates the expression, localization, modification, or activity of the TLE3 marker. In many instances, interaction partners or primers (e.g., antisense or RNAi primers) themselves may prove to be useful therapeutics.
Thus the present invention provides interaction partners and primers that are themselves useful therapeutic agents. For example, binding by an antibody raised against TLE3 to cancerous cells might inhibit growth of those cells. Alternatively or additionally, interaction partners defined or prepared according to the present invention could be used to deliver a therapeutic agent to a cancer cell. In particular, interaction partners (e.g., an antibody raised against TLE3) may be coupled to one or more therapeutic agents. Suitable agents in this regard include radionuclides and drugs. Preferred radionuclides include 90Y, 123I, 125I, 131I, 186Re, 188Re, 211 At and 212Bi. Preferred drugs include chlorambucil, ifosphamide, meclorethamine, cyclophosphamide, carboplatin, cisplatin, procarbazine, decarbazine, carmustine, cytarabine, hydroxyurea, mercaptopurine, methotrexate, paclitaxel, docetaxel, thioguanine, 5-fluorouracil, actinomycin D, bleomycin, daunorubicin, doxorubicin, etoposide, vinblastine, vincristine, L-asparginase, adrenocorticosteroids, canciclovir triphosphate, adenine arabinonucleoside triphosphate, 5-aziridinyl-4-hydroxylamino-2-nitrobenzamide, acrolein, phosphoramide mustard, 6-methylpurine, etoposide, benzoic acid mustard, cyanide and nitrogen mustard.
According to such embodiments, the therapeutic agent may be coupled with an interaction partner by direct or indirect covalent or non-covalent interactions. A direct interaction between a therapeutic agent and an interaction partner is possible when each possesses a substituent capable of reacting with the other. For example, a nucleophilic group, such as an amino or sulfhydryl group, on one may be capable of reacting with a carbonyl-containing group, such as an anhydride or an acid halide, or with an alkyl group containing a good leaving group (e.g., a halide) on the other. Indirect interactions might involve a linker group that is itself non-covalently bound to both the therapeutic agent and the interaction partner. A linker group can function as a spacer to distance an interaction partner from an agent in order to avoid interference with association capabilities. A linker group can also serve to increase the chemical reactivity of a substituent on an agent or an interaction partner and thus increase the coupling efficiency. An increase in chemical reactivity may also facilitate the use of agents, or functional groups on agents, which otherwise would not be possible.
It will be evident to those skilled in the art that a variety of bifunctional or polyfunctional reagents, both homo- and hetero-functional (such as those described in the catalog of the Pierce Chemical Co., Rockford, Ill.), may be employed as the linker group. Coupling may be effected, for example, through amino groups, carboxyl groups, sulfydryl groups or oxidized carbohydrate residues. There are numerous references describing such methodology, e.g., U.S. Pat. No. 4,671,958, to Rodwell et al. It will further be appreciated that a therapeutic agent and an interaction partner may be coupled via non-covalent interactions, e.g., ligand/receptor type interactions. Any ligand/receptor pair with a sufficient stability and specificity to operate in the context of the invention may be employed to couple a therapeutic agent and an interaction partner. To give but an example, a therapeutic agent may be covalently linked with biotin and an interaction partner with avidin. The strong non-covalent binding of biotin to avidin would then allow for coupling of the therapeutic agent and the interaction partner. Typical ligand/receptor pairs include protein/co-factor and enzyme/substrate pairs. Besides the commonly used biotin/avidin pair, these include without limitation, biotin/streptavidin, digoxigenin/anti-digoxigenin, FK506/FK506-binding protein (FKBP), rapamycin/FKBP, cyclophilin/cyclosporin and glutathione/glutathione transferase pairs. Other suitable ligand/receptor pairs would be recognized by those skilled in the art, e.g., monoclonal antibodies paired with a epitope tag such as, without limitation, glutathione-S-transferase (GST), c-myc, FLAG® and maltose binding protein (MBP) and further those described in Kessler pp. 105-152 of Advances in Mutagenesis” Ed. by Kessler, Springer-Verlag, 1990; “Affinity Chromatography: Methods and Protocols (Methods in Molecular Biology)” Ed. by Pascal Baillon, Humana Press, 2000; and “Immobilized Affinity Ligand Techniques” by Hermanson et al., Academic Press, 1992.
Where a therapeutic agent is more potent when free from the interaction partner, it may be desirable to use a linker group which is cleavable during or upon internalization into a cell. A number of different cleavable linker groups have been described. The mechanisms for the intracellular release of an agent from these linker groups include cleavage by reduction of a disulfide bond (e.g., U.S. Pat. No. 4,489,710 to Spitler), by irradiation of a photolabile bond (e.g., U.S. Pat. No. 4,625,014 to Senter et al.), by hydrolysis of derivatized amino acid side chains (e.g., U.S. Pat. No. 4,638,045 to Kohn et al.), by serum complement-mediated hydrolysis (e.g., U.S. Pat. No. 4,671,958 to Rodwell et al.) and by acid-catalyzed hydrolysis (e.g., U.S. Pat. No. 4,569,789 to Blattler et al.).
In certain embodiments, it may be desirable to couple more than one therapeutic agent to an interaction partner. In one embodiment, multiple molecules of an agent are coupled to one interaction partner molecule. In another embodiment, more than one type of therapeutic agent may be coupled to one interaction partner molecule. Regardless of the particular embodiment, preparations with more than one agent may be prepared in a variety of ways. For example, more than one agent may be coupled directly to an interaction partner molecule, or linkers that provide multiple sites for attachment can be used.
Alternatively, a carrier can be used. A carrier may bear the agents in a variety of ways, including covalent bonding either directly or via a linker group. Suitable carriers include proteins such as albumins (e.g., U.S. Pat. No. 4,507,234 to Kato et al.), peptides, and polysaccharides such as aminodextran (e.g., U.S. Pat. No. 4,699,784 to Shih et al.). A carrier may also bear an agent by non-covalent bonding or by encapsulation, such as within a liposome vesicle (e.g., U.S. Pat. No. 4,429,008 to Martin et al. and U.S. Pat. No. 4,873,088 to Mayhew et al.). Carriers specific for radionuclide agents include radiohalogenated small molecules and chelating compounds. For example, U.S. Pat. No. 4,735,792 to Srivastava discloses representative radiohalogenated small molecules and their synthesis. A radionuclide chelate may be formed from chelating compounds that include those containing nitrogen and sulfur atoms as the donor atoms for binding the metal, or metal oxide, radionuclide. For example, U.S. Pat. No. 4,673,562 to Davison et al. discloses representative chelating compounds and their synthesis.
When interaction partners are themselves therapeutics, it will be understood that, in many cases, any interaction partner that binds the same marker may be so used.
In one preferred embodiment of the invention, the therapeutic agents (whether interaction partners or otherwise) are antibodies, e.g., an antibody against the TLE3 marker. As is well known in the art, when using an antibody or fragment thereof for therapeutic purposes it may prove advantageous to use a “humanized” or “veneered” version of an antibody of interest to reduce any potential immunogenic reaction. In general, “humanized” or “veneered” antibody molecules and fragments thereof minimize unwanted immunological responses toward antihuman antibody molecules which can limit the duration and effectiveness of therapeutic applications of those moieties in human recipients.
A number of “humanized” antibody molecules comprising an antigen binding portion derived from a non-human immunoglobulin have been described in the art, including chimeric antibodies having rodent variable regions and their associated complementarity-determining regions (CDRs) fused to human constant domains (e.g., see Winter et al., Nature 349:293, 1991; Lobuglio et al., Proc. Nat. Acad. Sci. USA 86:4220, 1989; Shaw et al., J. Immunol. 138:4534, 1987; and Brown et al., Cancer Res. 47:3577, 1987), rodent CDRs grafted into a human supporting framework region (FR) prior to fusion with an appropriate human antibody constant domain (e.g., see Riechmann et al., Nature 332:323, 1988; Verhoeyen et al., Science 239:1534, 1988; and Jones et al. Nature 321:522, 1986) and rodent CDRs supported by recombinantly veneered rodent FRs (e.g., see European Patent Publication No. 519,596, published Dec. 23, 1992). It is to be understood that the invention also encompasses “fully human” antibodies produced using the XenoMouseTM technology (AbGenix Corp., Fremont, Calif.) according to the techniques described in U.S. Pat. No. 6,075,181.
Yet further, so-called “veneered” antibodies may be used that include “veneered FRs”. The process of veneering involves selectively replacing FR residues from, e.g., a murine heavy or light chain variable region, with human FR residues in order to provide a xenogeneic molecule comprising an antigen binding portion which retains substantially all of the native FR protein folding structure. Veneering techniques are based on the understanding that the antigen binding characteristics of an antigen binding portion are determined primarily by the structure and relative disposition of the heavy and light chain CDR sets within the antigen-association surface (e.g., see Davies et al., Ann. Rev. Biochem. 59:439, 1990). Thus, antigen association specificity can be preserved in a humanized antibody only wherein the CDR structures, their interaction with each other and their interaction with the rest of the variable region domains are carefully maintained. By using veneering techniques, exterior (e.g., solvent-accessible) FR residues which are readily encountered by the immune system are selectively replaced with human residues to provide a hybrid molecule that comprises either a weakly immunogenic, or substantially non-immunogenic veneered surface.
Preferably, interaction partners suitable for use as therapeutics (or therapeutic agent carriers) exhibit high specificity for the target marker (e.g., TLE3) and low background binding to other markers. In certain embodiments, monoclonal antibodies are preferred for therapeutic purposes.
Pharmaceutical Compositions
As mentioned above, the present invention provides new therapies and methods for identifying these. In certain embodiments, an interaction partner or primer may be a useful therapeutic agent. Alternatively or additionally, interaction partners defined or prepared according to the present invention bind to markers (e.g., TLE3) that serve as targets for therapeutic agents. Also, inventive interaction partners may be used to deliver a therapeutic agent to a cancer cell. For example, interaction partners provided in accordance with the present invention may be coupled to one or more therapeutic agents.
The invention includes pharmaceutical compositions comprising these inventive therapeutic agents. In general, a pharmaceutical composition will include a therapeutic agent in addition to one or more inactive agents such as a sterile, biocompatible carrier including, but not limited to, sterile water, saline, buffered saline, or dextrose solution. The pharmaceutical compositions may be administered either alone or in combination with other therapeutic agents including other chemotherapeutic agents, hormones, vaccines and/or radiation therapy. By “in combination with”, here and elsewhere in the specification, it is not intended to imply that the agents must be administered at the same time or formulated for delivery together, although these methods of delivery are within the scope of the invention. In general, each agent will be administered at a dose and on a time schedule determined for that agent. Additionally, the invention encompasses the delivery of the inventive pharmaceutical compositions in combination with agents that may improve their bioavailability, reduce or modify their metabolism, inhibit their excretion, or modify their distribution within the body. Although the pharmaceutical compositions of the present invention can be used for treatment of any subject (e.g., any animal) in need thereof, they are most preferably used in the treatment of humans.
The pharmaceutical compositions of this invention can be administered to humans and other animals by a variety of routes including oral, intravenous, intramuscular, intra-arterial, subcutaneous, intraventricular, transdermal, rectal, intravaginal, intraperitoneal, topical (as by powders, ointments, or drops), bucal, or as an oral or nasal spray or aerosol. In general the most appropriate route of administration will depend upon a variety of factors including the nature of the agent (e.g., its stability in the environment of the gastrointestinal tract), the condition of the patient (e.g., whether the patient is able to tolerate oral administration), etc. At present the intravenous route is most commonly used to deliver therapeutic antibodies. However, the invention encompasses the delivery of the inventive pharmaceutical composition by any appropriate route taking into consideration likely advances in the sciences of drug delivery.
General considerations in the formulation and manufacture of pharmaceutical agents may be found, for example, in Remington's Pharmaceutical Sciences, 19th ed., Mack Publishing Co., Easton, Pa., 1995.
EXEMPLIFICATION
Example 1
Raising Antibodies
This example describes a method that was employed to generate the TLE3 antibodies used in these Examples. Similar methods may be used to generate an antibody that binds to any marker of interest (e.g., to proteins that are or are derived from other markers listed in Appendix A). In some cases, antibodies may be obtained from commercial sources (e.g., Chemicon, Dako, Oncogene Research Products, NeoMarkers, etc.) or other publicly available sources (e.g., Imperial Cancer Research Technology, etc.).
Materials and Solutions


    
    
        Anisole (Cat. No. A4405, Sigma, St. Louis, Mo.)
        2,2′-azino-di-(3-ethyl-benzthiazoline-sulfonic acid) (ABTS) (Cat. No. A6499, Molecular Probes, Eugene, Oreg.)
        Activated maleimide Keyhole Limpet Hemocyanin (Cat. No. 77106, Pierce, Rockford, Ill.)
        Keyhole Limpet Hemocyanin (Cat. No. 77600, Pierce, Rockford, Ill.)
        Phosphoric Acid (H3PO4) (Cat. No. P6560, Sigma)
        Glacial Acetic Acid (Cat No. BP1185-500, Fisher)
        EDC (EDAC) (Cat No. 341006, Calbiochem)
        25% Glutaraldehyde (Cat No. G-5882, Sigma)
        Glycine (Cat No. G-8898, Sigma)
        Biotin (Cat. No. B2643, Sigma)
        Boric acid (Cat. No. B0252, Sigma)
        Sepharose 4B (Cat. No. 17-0120-01, LKB/Pharmacia, Uppsala, Sweden)
        Bovine Serum Albumin (LP) (Cat. No. 100 350, Boehringer Mannheim, Indianapolis, Ind.)
        Cyanogen bromide (Cat. No. C6388, Sigma)
        Dialysis tubing Spectra/Por Membrane MWCO: 6-8,000 (Cat. No. 132 665, Spectrum Industries, Laguna Hills, Calif.)
        Dimethyl formamide (DMF) (Cat. No. 22705-6, Aldrich, Milwaukee, Wis.)
        DIC (Cat. No. BP 592-500, Fisher)
        Ethanedithiol (Cat. No. 39, 802-0, Aldrich)
        Ether (Cat. No. TX 1275-3, EM Sciences)
        Ethylenediaminetetraacetatic acid (EDTA) (Cat. No. BP 120-1, Fisher, Springfield, N.J.)
        1-ethyl-3-(3′dimethylaminopropyl)-carbodiimide, HCL (EDC) (Cat. no. 341-006, Calbiochem, San Diego, Calif.)
        Freund's Adjuvant, complete (Cat. No. M-0638-50B, Lee Laboratories, Grayson, Ga.)
        Freund's Adjuvant, incomplete (Cat. No. M-0639-50B, Lee Laboratories)
        Fritted chromatography columns (Column part No. 12131011; Frit Part No. 12131029, Varian Sample Preparation Products, Harbor City, Calif.)
        Gelatin from Bovine Skin (Cat. No. G9382, Sigma)
        Goat anti-rabbit IgG, biotinylated (Cat. No. A 0418, Sigma)
        HOBt (Cat. No. 01-62-0008, Calbiochem)
        Horseradish peroxidase (HRP) (Cat. No. 814 393, Boehringer Mannheim)
        HRP-Streptavidin (Cat. No. S 5512, Sigma)
        Hydrochloric Acid (Cat. No. 71445-500, Fisher)
        Hydrogen Peroxide 30% w/w (Cat. No. H1009, Sigma)
        Methanol (Cat. No. A412-20, Fisher)
        Microtiter plates, 96 well (Cat. No. 2595, Corning-Costar, Pleasanton, Calif.)
        N-□-Fmoc protected amino acids from Calbiochem. See '97-'98 Catalog pp. 1-45.
        N-□-Fmoc protected amino acids attached to Wang Resin from Calbiochem. See '97-'98 Catalog pp. 161-164.
        NMP (Cat. No. CAS 872-50-4, Burdick and Jackson, Muskegon, Mich.)
        Peptide (Synthesized by Research Genetics. Details given below)
        Piperidine (Cat. No. 80640, Fluka, available through Sigma)
        Sodium Bicarbonate (Cat. No. BP328-1, Fisher)
        Sodium Borate (Cat. No. B9876, Sigma)
        Sodium Carbonate (Cat. No. BP357-1, Fisher)
        Sodium Chloride (Cat. No. BP 358-10, Fisher)
        Sodium Hydroxide (Cat. No. SS 255-1, Fisher)
        Streptavidin (Cat. No. 1 520, Boehringer Mannheim)
        Thioanisole (Cat. No. T-2765, Sigma)
        Trifluoroacetic acid (Cat. No. TX 1275-3, EM Sciences)
        Tween-20 (Cat. No. BP 337-500, Fisher)
        Wetbox (Rectangular Servin' SaverTM Part No. 3862, Rubbermaid, Wooster, Ohio)
        BBS—Borate Buffered Saline with EDTA dissolved in distilled water (pH 8.2 to 8.4 with HCl or NaOH), 25 mM Sodium borate (Borax), 100 mM Boric Acid, 75 mM NaCl and 5 mM EDTA.
        0.1 N HCl in saline as follows: concentrated HCl (8.3 ml/0.917 liter distilled water) and 0.154 M NaCl
        Glycine (pH 2.0 and pH 3.0) dissolved in distilled water and adjusted to the desired pH, 0.1 M glycine and 0.154 M NaCl.
        5× Borate 1× Sodium Chloride dissolved in distilled water, 0.11 M NaCl, 60 mM Sodium Borate and 250 mM Boric Acid.
        Substrate Buffer in distilled water adjusted to pH 4.0 with sodium hydroxide, 50 to 100 mM Citric Acid.
        AA solution: HOBt is dissolved in NMP (8.8 grams HOBt to 1 liter NMP). Fmoc-N-a-amino at a concentration at 0.53 M.
        DIC solution: 1 part DIC to 3 parts NMP.
        Deprotecting solution: 1 part Piperidine to 3 parts DMF.
        Reagent R: 2 parts anisole, 3 parts ethanedithiol, 5 parts thioanisole and 90 parts trifluoroacetic acid.

Equipment

        MRX Plate Reader (Dynatech, Chantilly, Va.)
        Hamilton Eclipse (Hamilton Instruments, Reno, Nev.)
        Beckman TJ-6 Centrifuge (Model No. TJ-6, Beckman Instruments, Fullerton, Calif.)
        Chart Recorder (Recorder 1 Part No. 18-1001-40, Pharmacia LKB Biotechnology)
        UV Monitor (Uvicord SII Part No. 18-1004-50, Pharmacia LKB Biotechnology)
        Amicon Stirred Cell Concentrator (Model 8400, Amicon, Beverly, Mass.)
        30 kD MW cut-off filter (Cat. No. YM-30 Membranes Cat. No. 13742, Amicon)
        Multi-channel Automated Pipettor (Cat. No. 4880, Corning Costar, Cambridge, Mass.)
        pH Meter Corning 240 (Corning Science Products, Corning Glassworks, Corning, N.Y.)
        ACT396 peptide synthesizer (Advanced ChemTech, Louisville, Ky.)
        Vacuum dryer (Box from Labconco, Kansas City, Mo. and Pump from Alcatel, Laurel, Md.).
    
    


Lyophilizer (Unitop 600sl in tandem with Freezemobile 12, both from Virtis, Gardiner, N.Y.)
Peptide Selection
Peptide or peptides against which antibodies would be raised were selected from within the protein sequence of interest using a program that uses the Hopp/Woods method (described in Hopp and Woods, Mol. Immunol. 20:483, 1983 and Hopp and Woods, Proc. Nat. Acad. Sci. U.S.A. 78:3824, 1981). The program uses a scanning window that identifies peptide sequences of 15-20 amino acids containing several putative antigenic epitopes as predicted by low solvent accessibility. This is in contrast to most implementations of the Hopp/Woods method, which identify single short ( ̃6 amino acids) presumptive antigenic epitopes. Occasionally the predicted solvent accessibility was further assessed by PHD prediction of loop structures (described in Rost and Sander, Proteins 20:216, 1994). Preferred peptide sequences display minimal similarity with additional known human proteins. Similarity was determined by performing BLASTP alignments, using a wordsize of 2 (described in Altschul et al., J. Mol. Biol. 215:403, 1990). All alignments given an EXPECT value less than 1000 were examined and alignments with similarities of greater than 60% or more than four residues in an exact contiguous non-gapped alignment forced those peptides to be rejected. When it was desired to target regions of proteins exposed outside the cell membrane, extracellular regions of the protein of interest were determined from the literature or as defined by predicted transmembrane domains using a hidden Markov model (described in Krogh et al., J. Mol. Biol. 305:567, 2001). When the peptide sequence was in an extracellular domain, peptides were rejected if they contained N-linked glycosylation sites. As shown in Appendix A, for the preparation of TLE3 antibodies a single peptide was used having the amino acid sequence KNHHELDHRERESSAN (SEQ ID NO. 383). Appendix A provides one to three peptide sequences that can be used in preparing antibodies against other markers.
Peptide Synthesis
The sequence of the desired peptide was provided to the peptide synthesizer. The C-terminal residue was determined and the appropriate Wang Resin was attached to the reaction vessel. The peptide or peptides were synthesized C-terminus to N-terminus by adding one amino acid at a time using a synthesis cycle. Which amino acid is added was controlled by the peptide synthesizer, which looks to the sequence of the peptide that was entered into its database. The synthesis steps were performed as follows:
Step 1—Resin Swelling: Added 2 ml DMF, incubated 30 minutes, drained DMF.
Step 2—Synthesis cycle (repeated over the length of the peptide)

    
    
        2a—Deprotection: 1 ml deprotecting solution was added to the reaction vessel and incubated for 20 minutes.
        2b—Wash Cycle
        2c—Coupling: 750 ml of amino acid solution (changed as the sequence listed in the peptide synthesizer dictated) and 250 ml of DIC solution were added to the reaction vessel. The reaction vessel was incubated for thirty minutes and washed once. The coupling step was repeated once.
        2d—Wash Cycle
    
    


Step 3—Final Deprotection: Steps 2a and 2b were performed one last time.
Resins were deswelled in methanol (rinsed twice in 5 ml methanol, incubated 5 minutes in 5 ml methanol, rinsed in 5 ml methanol) and then vacuum dried.
Peptide was removed from the resin by incubating 2 hours in reagent R and then precipitated into ether. Peptide was washed in ether and then vacuum dried. Peptide was resolubilized in diH2O, frozen and lyophilized overnight.
Conjugation of Peptide with Keyhole Limpet Hemocyanin
Peptide (6 mg) was conjugated with Keyhole Limpet Hemocyanin (KLH). If the selected peptide includes at least one cysteine, three aliquots (2 mg) can be dissolved in PBS (2 ml) and coupled to KLH via glutaraldehyde, EDC or maleimide activated KLH (2 mg) in 2 ml of PBS for a total volume of 4 ml. When the peptide lacks cysteine (as in the TLE3 peptide), two aliquots (3 mg) can be coupled via glutaraldehyde and EDC methods.
Maleimide coupling can be accomplished by mixing 2 mg of peptide with 2 mg of maleimide-activated KLH dissolved in PBS (4 ml) and incubating 4 hr.
EDC coupling can be accomplished by mixing 2 mg of peptide, 2 mg unmodified KLH, and 20 mg of EDC in 4 ml PBS (lowered to pH 5 by the addition of phosphoric acid), and incubating for 4 hours. The reaction is then stopped by the slow addition of 1.33 ml acetic acid (pH 4.2). When using EDC to couple 3 mg of peptide, the amounts listed above are increased by a factor of 1.5.
Glutaraldehyde coupling occurs when 2 mg of peptide are mixed with 2 mg of KLH in 0.9 ml of PBS. 0.9 ml of 0.2% glutaraldehyde in PBS is added and mixed for one hour. 0.46 ml of 1 M glycine in PBS is added and mixed for one hour. When using glutaraldehyde to couple 3 mg of peptide, the above amounts are increased by a factor of 1.5.
The conjugated aliquots were subsequently repooled, mixed for two hours, dialyzed in 1 liter PBS and lyophilized.
Immunization of Rabbits
Two New Zealand White Rabbits were injected with 250 μg (total) KLH conjugated peptide in an equal volume of complete Freund's adjuvant and saline in a total volume of 1 ml. 100 μg KLH conjugated peptide in an equal volume of incomplete Freund's Adjuvant and saline were then injected into three to four subcutaneous dorsal sites for a total volume of 1 ml two, six, eight and twelve weeks after the first immunization. The immunization schedule was as follows:
















Day 0
Pre-immune bleed, primary immunization



Day 15
1st boost



Day 27
1st bleed



Day 44
2nd boost



Day 57
2nd bleed and 3rd boost



Day 69
3rd bleed



Day 84
4th boost



Day 98
4th bleed










Collection of Rabbit Serum

The rabbits were bled (30 to 50 ml) from the auricular artery. The blood was allowed to clot at room temperature for 15 minutes and the serum was separated from the clot using an IEC DPR-6000 centrifuge at 5000 g. Cell-free serum was decanted gently into a clean test tube and stored at −20° C. for affinity purification.
Determination of Antibody Titer
All solutions with the exception of wash solution were added by the Hamilton Eclipse, a liquid handling dispenser. The antibody titer was determined in the rabbits using an ELISA assay with peptide on the solid phase. Flexible high binding ELISA plates were passively coated with peptide diluted in BBS (100 μl, 1 μg/well) and the plate was incubated at 4° C. in a wetbox overnight (air-tight container with moistened cotton balls). The plates were emptied and then washed three times with BBS containing 0.1% Tween-20 (BBS-TW) by repeated filling and emptying using a semi-automated plate washer. The plates were blocked by completely filling each well with BBS-TW containing 1% BSA and 0.1% gelatin (BBS-TW-BG) and incubating for 2 hours at room temperature. The plates were emptied and sera of both pre- and post-immune serum were added to wells. The first well contained sera at 1:50 in BBS. The sera were then serially titrated eleven more times across the plate at a ratio of 1:1 for a final (twelfth) dilution of 1:204,800. The plates were incubated overnight at 4° C. The plates were emptied and washed three times as described.
Biotinylated goat anti-rabbit IgG (100 μl) was added to each microtiter plate test well and incubated for four hours at room temperature. The plates were emptied and washed three times. Horseradish peroxidase-conjugated Streptavidin (100 μl diluted 1:10,000 in BBS-TW-BG) was added to each well and incubated for two hours at room temperature. The plates were emptied and washed three times. The ABTS was prepared fresh from stock by combining 10 ml of citrate buffer (0.1 M at pH 4.0), 0.2 ml of the stock solution (15 mg/ml in water) and 10 μl of 30% hydrogen peroxide. The ABTS solution (100 μl) was added to each well and incubated at room temperature. The plates were read at 414 nm, 20 minutes following the addition of substrate.
Preparation of Peptide Affinity Purification Column:
The affinity column was prepared by conjugating 5 mg of peptide to 10 ml of cyanogen bromide-activated Sepharose 4B and 5 mg of peptide to hydrazine-Sepharose 4B. Briefly, 100 μl of DMF was added to peptide (5 mg) and the mixture was vortexed until the contents were completely wetted. Water was then added (900 μl) and the contents were vortexed until the peptide dissolved. Half of the dissolved peptide (500 μl) was added to separate tubes containing 10 ml of cyanogen-bromide activated Sepharose 4B in 0.1 ml of borate buffered saline at pH 8.4 (BBS) and 10 ml of hydrazine-Sepharose 4B in 0.1 M carbonate buffer adjusted to pH 4.5 using excess EDC in citrate buffer pH 6.0. The conjugation reactions were allowed to proceed overnight at room temperature. The conjugated Sepharose was pooled and loaded onto fritted columns, washed with 10 ml of BBS, blocked with 10 ml of 1 M glycine and washed with 10 ml 0.1 M glycine adjusted to pH 2.5 with HCl and re-neutralized in BBS. The column was washed with enough volume for the optical density at 280 nm to reach baseline.
Affinity Purification of Antibodies
The peptide affinity column was attached to a UV monitor and chart recorder. The titered rabbit antiserum was thawed and pooled. The serum was diluted with one volume of BBS and allowed to flow through the columns at 10 ml per minute. The non-peptide immunoglobulins and other proteins were washed from the column with excess BBS until the optical density at 280 nm reached baseline. The columns were disconnected and the affinity purified column was eluted using a stepwise pH gradient from pH 7.0 to 1.0. The elution was monitored at 280 nm and fractions containing antibody (pH 3.0 to 1.0) were collected directly into excess 0.5 M BBS. Excess buffer (0.5 M BBS) in the collection tubes served to neutralize the antibodies collected in the acidic fractions of the pH gradient.
The entire procedure was repeated with “depleted” serum to ensure maximal recovery of antibodies. The eluted material was concentrated using a stirred cell apparatus and a membrane with a molecular weight cutoff of 30 kD. The concentration of the final preparation was determined using an optical density reading at 280 nm. The concentration was determined using the following formula: mg/ml=OD280/1.4.
It will be appreciated that in certain embodiments, additional steps may be used to purify antibodies of the invention. In particular, it may prove advantageous to repurify antibodies, e.g., against one of the peptides that was used in generating the antibodies. It is to be understood that the present invention encompasses antibodies that have been prepared with such additional purification or repurification steps. It will also be appreciated that the purification process may affect the binding between samples and the inventive antibodies.
Example 2
Preparing and Staining Tissue Arrays
This example describes a method that was employed to prepare the tissue arrays that were used in the Examples. This example also describes how the antibody staining was performed.
Tissue arrays were prepared by inserting full-thickness cores from a large number of paraffin blocks (donor blocks) that contain fragments of tissue derived from many different patients and/or different tissues or fragments of tissues from a single patient, into a virgin paraffin block (recipient block) in a grid pattern at designated locations in a grid. A standard slide of the paraffin embedded tissue (donor block) was then made which contained a thin section of the specimen amenable to H & E staining. A trained pathologist, or the equivalent versed in evaluating tumor and normal tissue, designated the region of interest for sampling on the tissue array (e.g., a tumor area as opposed to stroma). A commercially available tissue arrayer from Beecher Instruments was then used to remove a core from the donor block which was then inserted into the recipient block at a designated location. The process was repeated until all donor blocks had been inserted into the recipient block. The recipient block was then thin-sectioned to yield 50-300 slides containing cores from all cases inserted into the block.
The selected antibodies were then used to perform immunohistochemical staining using the DAKO Envision+, Peroxidase IHC kit (DAKO Corp., Carpenteria, Calif.) with DAB substrate according to the manufacturer's instructions. FIG. 1 shows exemplary IHC staining images of samples that are TLE3-negative (S0643−) and TLE3-positive (S0643+).
Example 3
TLE3 Expression Correlates with Response to Chemotherapy in Cancer Patients
Tumor samples from two different breast cancer cohorts—Huntsville Hospital (HH) and Roswell Park Cancer Institute (RP)—were stained with the TLE3 antibody of Example 1. Treatment and recurrence data were available for all patients in both cohorts. FIG. 2 shows Kaplan-Meier recurrence curves that were generated using all patients in the HH cohort after classification based on staining with the TLE3 antibody. Recurrence data from TLE3-positive and TLE3-negative patients were used to generate the top and bottom curves, respectively. As shown in the Figure, antibody binding to the TLE3 marker correlates with improved prognosis across this breast cancer cohort (HR=0.573, p=0.004). FIG. 3 shows Kaplan-Meier recurrence curves that were generated in a similar fashion using all patients in the RP cohort. As with the HH cohort, antibody binding to the TLE3 marker was found to correlate with improved prognosis (HR=0.239, p=0.011).
In order to determine whether TLE3 expression is correlated with response to chemotherapy, separate Kaplan-Meier recurrence curves were generated using HH cohort patients that did or did not receive chemotherapy (FIGS. 4 and 5, respectively). As shown in FIG. 4, antibody binding to the TLE3 marker lost its correlation with prognosis in patients that did not receive chemotherapy (HR=0.788, p=0.490). However, as shown in FIG. 5, the correlation was restored in patients that did receive chemotherapy (HR=0.539, p=0.013). These results demonstrate that TLE3 expression is correlated with improved response to chemotherapy (i.e., TLE3-positive cancers are more likely to respond to chemotherapy than TLE-3 negative cancers). Kaplan-Meier recurrence curves that were generated using patients in the RP breast cancer cohort that received chemotherapy are consistent with this prediction model (see FIG. 6, HR=0.194, p=0.010). Kaplan-Meier recurrence curves that were generated using patients in the UAB ovarian cancer cohort that received chemotherapy are also consistent with this prediction model (see FIG. 18, HR=0.64, p=0.049).
Example 4
Specific Chemotherapeutic Correlations
Since different patients in the HH and RP cohorts received different types of chemotherapy we were also able to determine whether TLE3 expression correlates with response to specific types of chemotherapy.
FIG. 7 shows Kaplan-Meier recurrence curves that were generated using patients in the HH breast cancer cohort of FIG. 5 that received CMF (cyclophosphamide, methotrexate and 5-fluorouracil) chemotherapy. Recurrence data from TLE3-positive and TLE3-negative patients in this subset were used to generate the top and bottom curves, respectively. As shown in FIG. 7, antibody binding to the TLE3 marker correlates with improved prognosis across this subset of treated patients (HR=0.398, p=0.019). Based on the results below which demonstrated a loss of correlation for patients in the HH cohort that were treated with CA (cyclophosphamide and adriamycin, HR=1.000) or CAF (cyclophosphamide, adriamycin and 5-fluorouracil, HR=1.000) we were able to establish that the predictive correlation in FIG. 7 is between TLE3 binding and treatment with methotrexate (see also FIG. 9 which combines the CA and CAF treated subsets, HR=1.030).
FIG. 8 shows Kaplan-Meier recurrence curves that were generated using patients in the HH breast cancer cohort of FIG. 5 that received CA or CAF chemotherapy (with or without a taxane). As shown in the Figure, the correlation between antibody binding to the TLE3 marker and prognosis loses significance in this subset of treated patients (HR=0.666, p=0.22). When the curves were generated using patients that received CA or CAF chemotherapy only (i.e., without a taxane) the significance was further reduced (see FIG. 9, HR=1.030, p=0.95). However, the correlation was restored in patients that received CA or CAF in combination with a taxane (see FIG. 10, HR=0.114, p=0.038). These results demonstrate a correlation between TLE3 binding and treatment with a taxane.
FIG. 11 shows Kaplan-Meier recurrence curves that were generated using patients in the RP breast cancer cohort of FIG. 6 that received CA chemotherapy only (i.e., without a taxane). Recurrence data from TLE3-positive and TLE3-negative patients in this subset were used to generate the top and bottom curves, respectively. As shown in the Figure, there is no correlation between antibody binding to the TLE3 marker and prognosis in this subset of treated patients (HR=0.759, p=0.81). The correlation was restored when the curves were generated using patients that received CA chemotherapy in combination with a taxane (see FIG. 12, HR=0.153, p=0.018). These results support the results of FIGS. 8 and 9 that were obtained using samples from the HH cohort.
FIG. 13 shows Kaplan-Meier recurrence curves that were generated using patients in the RP breast cancer cohort of FIG. 6 that received a taxane or CMF. Some of the patients receiving a taxane also received CA. Recurrence data from TLE3-positive and TLE3-negative patients in this subset were used to generate the top and bottom curves, respectively. As shown in the Figure, antibody binding to the TLE3 marker correlates with improved prognosis across this subset of treated patients (HR=0.137, p=0.011).
FIG. 14 shows Kaplan-Meier recurrence curves that were generated using patients in the RP breast cancer cohort of FIG. 6 that received neoadjuvant chemotherapy. Recurrence data from TLE3-positive and TLE3-negative patients in this subset were used to generate the top and bottom curves, respectively. The sample size was small (N=12); however, as shown in the Figure, antibody binding to the TLE3 marker showed significant correlation with improved prognosis across this subset of treated patients when measured using the Fisher Exact Test (p=0.005). In addition, of the 12 patients receiving neoadjuvant chemotherapy, two received CA (both showed recurrence) while ten received CA with a taxane (seven showed recurrence, three did not). Notably, the three patients that did not show any recurrence were the only patients with TLE3-positive samples. These results are significant since they show that the correlation between TLE3 binding and response to chemotherapy applies irrespective of whether treatment is administered in an adjuvant or neoadjuvant setting.
FIGS. 15-17 show Kaplan-Meier recurrence curves that were generated using patients in the RP breast cancer cohort of FIG. 6 that received chemotherapy. Recurrence data from TLE3-positive and TLE3-negative patients with stage II+ (FIG. 15), stage IIb+ (FIG. 16) and stage III+ (FIG. 17) cancers were used to generate the top and bottom curves, respectively. In each case, antibody binding to the TLE3 marker correlated with improved prognosis across these subsets of treated patients. The sample size was small in the subset of FIG. 17 (N=19); however significance was obtained when measured using the Fisher Exact Test (p=0.020). These results are of clinical importance since they demonstrate that the predictive power of the TLE3 marker is independent of stage and remains significant even in patients with the worst prognosis (e.g., stage III+ patients).
Example 5
Bivariate Analysis
In order to confirm that the predictive power of TLE3 is independent of other clinical factors (e.g., age, tumor size, nodes status, necrosis, etc.) we performed bivariate statistical analysis using results from the RP breast cohort. The results are summarized in Table 1 below. As shown in the Table, prediction using TLE3 remained significant in all bivariate analyses demonstrating its independence of other clinical factors.







TABLE 1







Bivariate Analysis













Factor
Factor

HR for
p for




1
2
N
TLE3
TLE3
HR
p





TLE3
—
81
0.239
0.0110
—
—


TLE3
Age
81
0.223
0.0082
0.967
0.1200


TLE3
Tumor Size
78
0.219
0.0077
1.292
0.0002


TLE3
Nodes Met Ca1
79
0.252
0.0150
1.066
0.0086


TLE3
Necrosis
72
0.232
0.0100
1.903
0.2600


TLE3
Vasc. Lymph Inv.2
74
0.205
0.0071
0.412
0.0790


TLE3
Stage
80
0.284
0.0280
2.063
0.0130


TLE3
Contains Tax3
70
0.168
0.0061
2.749
0.0980





1Nodes found with metastatic cancer.


2Vascular lymphatic invasion.


3Taxane containing regimens.






Other Embodiments
Other embodiments of the invention will be apparent to those skilled in the art from a consideration of the specification or practice of the invention disclosed herein. It is intended that the specification and examples be considered as exemplary only, with the true scope of the invention being indicated by the following claims.















APPENDIX A









PEPTIDE 1
PEPTIDE 2
PEPTIDE 3






ENTREZ

(SEQ ID
(SEQ ID
(SEQ ID




AGI ID
GENE NAME
GENE ID
ALIASES
NO.)
NO.)
NO.)
TITER























S0011
vav 3 oncogene
10451
VAV3; VAV3 ONCOGENE;
TEESINDEDIY
EKRTNGLRR
DYISKSKEDV
1:90-






ONCOGENE VAV3; vav 3
KGLPDLIDE
TPKQVD
KLK
1:300





oncogene
(1)
(2)
(3)


 


S0017
WAP four-
10406
WFDC2; WAP5; dJ461P17.6;
EKTGVCPELQ
PNDKEGSCP
RDQCQVDTQ
1:25-



disulfide

major epididymis-specific
ADQNCTQE
QVNIN (5)
CPGQMK (6)
1:500



core domain 2

protein E4; epididymal
(4)





secretory protein E4; WAP





four-disulfide core domain





2; WAP domain containing





protein HE4-V4;





epididymis-specific, whey-





acidic protein type, four-





disulfide core; WAP four-





disulfide


 


S0018
secretoglobin,
4250
UGB2; MGB1; SCGB2A2;
SKTINPQVSKT
DDNATTNAID
NQTDETLSNV
1:300-



family 2A,

mammaglobin 1; secreto-
EYKELLQE
ELKEC (8)
EVFMQ (9)
1:1000



member 2

globin, family 2A,
(7)





member 2


 


S0020
PPAR binding
5469
RB18A; TRIP2; PPARGBP;
SSDDGIRPLPE
DGKSKDKPP
NKTKKKKSSR
1:100



protein

PBP; CRSP1; PPARBP;
YSTEKHKK
KRKKADTE
LPPEK (12)





CRSP200; DRIP230; PPAR-
(10)
(11)





BINDING PROTEIN; PPARG





binding protein; PPAR





binding protein; CRSP,





200 KD SUBUNIT;





PEROXISOME PROLIFERATOR-





ACTIVATED RECEPTOR-





BINDING PROTEIN; THYROID





HORMONE RECEPTOR





INTERACTOR 2; RECOGN


 


S0021
hypothetical
222256
FLJ23834; hypothetical
KNKEPLTKKG
KLTCTDLDSS
EVDYENPSNL
1:200-



protein

protein FLJ23834
ETKTAERD
PRSFRYS
AAGNKYT
1:2500



FLJ23834


(13)
(14)
(15)


 


S0022
cytochrome
199974
CYP4Z1; cytochrome P450
KTLQVFNPLR
QHFAIIECKV
RKFLAPDHSR
1:50-



P450 4Z1

4Z1; cytochrome P450,
FSRENSEKIH
AVALT (17)
PPQPVRQ
1:500





family 4, subfamily Z,
(16)

(18)





polypeptide 1


 


S0024
RAS-like,
85004
RERG; RAS-like, estrogen-
MAKSAEVKLAI
VLPLKNILDEI
YELCREVRR
1:900-



estrogen-

regulated, growth-
FGRAGVGK
KKPKN (20)
RRMVQGKT
1:2700



regulated

inhibitor
(19)

(21)



growth-



inhibitor


 


S0032
fatty acid
2170
MDGI; O-FABP: FABP3;
TKPTTIIEKNG
KNTEISFKLG
HLQKWDGQE
1:225



binding

FABP11; H-FABP; FATTY
DILTLKTH
VEFDE (23)
TTLVRE (24)



protein 3,

ACID-BINDING PROTEIN,
(22)



muscle and

SKELETAL MUSCLE; Fatty



heart

acid-binding protein 3,



(mammary-

muscle; fatty acid



derived

binding protein 11; FATTY



growth

ACID-BINDING PROTEIN,



inhibitor)

MUSCLE AND HEART; fatty





acid binding protein 3,





muscle and heart





(mammary-de


 


S0036
gamma-
2568
GABRP; GAMMA-AMINOBUTYRIC
DGNDVEFTWL
LQQMAAKDR
KRKISFASIEI
1:250-



aminobutyric

ACID RECEPTOR; PI; GABA-A
RGNDSVRGLE
GTTKEVEEV
SSDNVDYSD
1:500



acid (GABA)

RECEPTOR, PI POLYPEPTIDE;
H (25)
S (26)
(27)



A receptor,

gamma-aminobutyric acid



pi

(GABA) A receptor, pi


 


S0037
annexin AB
244
ANX8; ANXA8; annexin VIII;
QRQQIAKSFK
REIMKAYEED
EEYEKIANKSI
1:30-1:40





annexin A8
AQFGKDLTE
YGSSLEEDIQ
EDSIKSE






(28)
(29)
(30)


 


S0039
CDNA FLJ25076
134111
similar to 3110006E14Rik
EGGSLVPAAR
RKAGKSKKS
KTHEKYGWV
1:50-



fis, clone

protein; CDNA FLJ25076
QQHCTQVRS
FSRKEAE
TPPVSDG
1:30000



CBL06117

fis, done CBL06117
RR (31)
(32)
(33)


 


S0040
ATP-binding
5243
P-gp; PGY1; CLCS; ABCB1;
MDLEGDRNG
NLEDLMSNIT
RGSQAQDRK
1:200-



cassette,

ABC20; CD243; GP170;
GAKKKN (34)
NRSDINDTG
LSTKEA (36)
1:400



sub-family B

MDR1; doxorubicin resis-

(35)



(MDR/TAP),

tance; colchicin



member 1

sensitivity; P-GLYCOPRO-





TEIN 1; multidrug resis-





tance 1; P glycoprotein





1; ATP-binding cassette





sub-family B member 1;





ATP-BINDING CASSETTE,





SUBFAMILY B, MEMBER 1;





ATP-bin


 


S0041
ATP-binding
5244
MDR3; PGY3; PFIC-3;
MDLEAAKNGT
NFSFPVNFSL
KNSQMCQKS
1:60-



cassette, sub-

ABCB4; ABC21; MDR2/3;
AWRPTSAE
SLLNPGK
LDVETDG
1:300



family B

P-GLYCOPROTEIN 3;
(37)
(38)
(39)



(MDR/TAP),

MULTIDRUG RESISTANCE 3;



member 4

P-glycoprotein-3/multiple





drug resistance-3; P





glycoprotein 3/multiple





drug resistance 3; ATP-





binding cassette, sub-





family B (MDR/TAP),





member 4; ATP-binding





cassette, sub


 


S0042
ATP-binding
4363
ABCC1; MRP1; GS-X; ABC29;
MALRGFCSAD
KNWKKECAK
DSIERRPVKD
1:40-



cassette,

multidrug resistance
GSD (40)
TRKQPVK
GGGTNS (42)
1:500



sub-family C

protein; MULTIDRUG RESIS-

(41)



(CFTR/MRP),

TANCE-ASSOCIATED PROTEIN



member 1

1; multiple drug





resistance-associated





protein; multiple drug





resistance protein 1;





ATP-BINDING CASSETTE,





SUBFAMILY C, MEMBER 1;





ATP-binding cassette,





sub-fami


 


S0043
ATP-binding
1244
MRP2; cMRP; CMOAT; ABCC2;
MLEKFCNSTF
SILCGTQFQ
ENNESSNNP
1:50-



cassette,

ABC30; DJS; MULTIDRUG
WNSSFLDSPE
TLIRT (44)
SSIAS (45)
1:333



sub-family C

RESISTANCE-ASSOCIATED
(43)



(CFTR/MRP),

PROTEIN 2; canalicular



member 2

multispecific organic





anion transporter; MULTI-





SPECIFIC ORGANIC ANION





TRANSPORTER, CANALICULAR;





ATP-BINDING CASSETTE,





SUBFAMILY C, MEMBER 2;





ATP-binding cassette,


 


S0044
ATP-binding
10257
MOAT-B; MRP4; MOATB;
QEVKPNPLQD
DEISQRNRQ
VQDFTAFWD
1:20-



cassette,

ABCC4; EST170205; MULTI-
ANICSR (46)
LPSDGKK
KASETPTLQ
1:100



sub-family C

DRUG RESISTANCE-

(47)
(48)



(CFTR/MRP),

ASSOCIATED PROTEIN 4;



member 4

MULTISPECIFIC ORGANIC





ANION TRANSPORTER B;





ATP-binding cassette,





sub-family C, member 4;





ATP-BINDING CASSETTE,





SUBFAMILY C, MEMBER 4;





ATP-binding cassette,





sub-family C (CFT


 


S0045
ATP-binding
8714
MOAT-D; ABC31; MLP2;
MDALCGSGEL
RKQEKQTAR
DPQSVERKTI
1:2000



cassette,

ABCC3; EST90757; cMOAT2;
GSKFWDSN
HKASAA (50)
SPG (51)



sub-family C

MULTIDRUG RESISTANCE-
(49)



(CFTR/MRP),

ASSOCIATED PROTEIN 3;



member 3

canicular multispecific





organic anion





transporter; CANALICULAR





MULTISPECIFIC ORGANIC





ANION TRANSPORTER 2; ATP-





BINDING CASSETTE, SUB-





FAMILY C. MEMBER 3; ATP-





binding cas


 


S0046
ATP-binding
10057
MOAT-C; ABCC5; MRP5;
MKDIDIGKEYI
RDREDSKFR
SKHESSDVN
1:100-



cassette,

EST277145; ABC33; SMRP;
IPSPGYRS
RTRPLECQD
CRRLER (54)
1:4500



sub-family C

pABC11; MOATC; MULTIDRUG
(52)
(53)



(CFTR/MRP),

RESISTANCE-ASSOCIATED



member 5

PROTEIN 5; canalicular





multispecific organic





anion transporter C;





ATP-binding cassette,





sub-family C, member 5;





ATP-BINDING CASSETTE,





SUBFAMILY C, MEMBER 5;





ATP-bi


 


S0047
ATP-binding
368
MRP6; ARA; EST349056;
MAAPAEPCAG
DRGVVDSSS
HTLVAENAM
1:50



cassette,

ABCC6; MOATE; PXE; MLP1;
QGVWNQTEP
SGSAAGKD
NAEK (57)



sub-family C

ABC34; ANTHRACYCLINE;
E (55)
(56)



(CFTR/MRP),

RESISTANCE-ASSOCIATED



member 6

PROTEIN; MULTIDRUG





RESISTANCE-ASSOCIATED





PROTEIN 6; ATP-binding





cassette, sub-family C,





member 6; ATP-BINDING





CASSETTE, SUBFAMILY C,





MEMBER 6; ATP-binding





cassette,


 


S0048
ATP-binding
8647
BSEP; ABCB11; PFIC-2;
MSDSVILRSIK
TNSSLNQNM
QEVLSKIQHG
1:600



cassette

SPGP; PGY4; PFIC2; ABC16;
KFGEEND
TNGTR (59)
HTIIS (60)



sub-family B

SISTER OF P-GLYCOPROTEIN
(58)



(MDR/TAP),

bile salt export pump;



member 11

progressive familial





intrahepatic cholestasis





2; ABC member 16, MDR/TAP





subfamily; ATP-BINDING





CASSETTE, SUBFAMILY B,





MEMBER 11; ATP-binding





cassette, sub-fam


 


S0049
ATP-binding
23456
MTABC2; EST20237; MABC2;
GADDPSSVTA
NAVASPEFP
KPNGIYRKLM
1:10-1:25



cassette,

M-ABC2; ABCB10; MITO-
EEIQR (61)
PRFNT (62)
NKQSFISA



sub-family B

CHONDRIAL ABC PROTEIN 2;


(63)



(MDR/TAP),

ATP-BINDING CASSETTE,



member 10

SUBFAMILY B, MEMBER 10;





ATP-binding cassette,





sub-family B, member 10;





ATP-binding cassette,





sub-family B (MDR/TAP),





member 10


 


S0050
transporter 1,
6890
RING4; ABC17; D6S114E;
MASSRCPAPR
QGGSGNPVR
EFVGDGIYNN
1:80



ATP-binding

ABCB2; TAP1; APT1;
GCR (64)
R (65)
TMGHVHS



cassette,

PEPTIDE TRANSPORTER PSF1;


(66)



sub-family B

TRANSPORTER, ABC, MHC, 1;



(MDR/TAP)

ABC transporter, MHC 1;





antigen peptide





transporter 1; peptide





supply factor 1; ABC





TRANSPORTER, MHC, 1; ATP-





BINDING CASSETTE,





SUBFAMILY B, MEMBER 2;





TRANSPORTER


 


S0052
ATP-binding
6833
SUR1; MRP8; PHHI; ABC36;
MPLAFCGSEN
DHLGKENDV
EIREEQCAPH
1:25-



cassette,

ABCC8; HRINS; sulfonylurea
HSAAYR
FQPKTQFLG
EPTPQG
1:150



sub-family C

receptor (hyperinsuli-
(67)
(68)
(69)



(CFTR/MRP),

nemia); SULFONYLUREA



member 8

RECEPTOR, BETA-CELL HIGH-





AFFINITY; ATP-binding





cassette, sub-family C,





member 8; ATP-BINDING





CASSETTE, SUBFAMILY C,





MEMBER 8; ATP-binding





cassette, sub-family C


 


S0053
ATP-binding
10060
ABCC9; ABC37; sulfony-
MSLSFCGNNI
QRVNETQNG
DEIGDDSWR
1:25-1:50



cassette,

lurea receptor 2A; ATP-
SS (70)
TNNTTGISE
TGESSLPFE



sub-family C

BINDING CASSETTE,

(71)
(72)



(CFTR/MRP),

SUBFAMILY C, MEMBER 9;



member 9

ATP-binding cassette, sub-





family C (CFTR/MRP),





member 9; ATP-binding





cassette, sub-famly C,





member 9 isoform SUR2B;





ATP-binding cassette, sub-





family C, member 9 isoform


 


S0055
integral mem-
9445
E25B; ABRI; E3-16; FBD;
MVKVTFNSAL
QTIEENIKIFE
HDKETYKLQ
1:450-



brane protein

BRI2; BRICD2B; ITM2B; BRI
AQKEAKKDEP
EEEVE (74)
RRETIKGIQK
1:500



2B

GENE; BRICHOS domain con-
K (73)

RE (75)





taining 2B; integral





membrane protein 2B


 


S0057
ankyrin 3,
288
ankyrin-G; ANK3; ankyrin-
MAHAASQLKK
HKKETESDQ
EGFKVKTKKE
1:750



node of

3, node of Ranvier;
NRDLEINAEE
DDEIEKTDRR
IRHVEKKSHS



Ranvier

ankyrin 3 isoform 1;
(76)
Q (77)
(78)



(ankyrin G)

ankyrin 3 isoform 2;





ankyrin 3, node of Ranvier





(ankyrin G)


 


S0058
hypothetical
80004
FLJ21918; hypothetical
ERALAAAQRC
TAGMKDLLS
DPPRTVLQAP
1:20



protein

protein FLJ21918
HKKVMKER
VFQAYQ (80)
KEWVCL (81)



FLJ21918


(79)


 


S0059
tripartite
23650
ATDC; TRIM29; tripartite
MEAADASRSN
ELHLKPHLEG
EGEGLGQSL
1:50-



motif-

motif-containing 29;
GSSPEARDAR
AAFRDHQ
GNFKDDLLN
1:3000



containing 29

ataxia-telangiectasia
(82)
(83)
(84)





group D-assocaited





protein; tripartite motif





protein TRIM29 isoform





alpha; tripartite motif





protein TRIM29 isoform





beta


 


S0059P2
tripartite
23650
ATDC; TRIM29; tripartite
ELHLKPHLEG
N/A
N/A
1:30-1:90



motif-

motif-containing 29;
AAFRDHQ



containing 29

ataxia-telangiectasia
(85)





group D-associated





protein; tripartite motif





protein TRIM29 isoform





alpha; tripartite motif





protein TRIM29 isoform





beta


 


S0063
iroquois
79191
IRX3; iroquois homeobox
GSEERGAGR
KIWSLAETAT
KKLLKTAFQP
1:200-



homeobox

protein 3
GSSGGREE
SPDNPRRS
VPRRPQNHL
1:1200



protein 3


(86)
(87)
D (88)


 


S0068
RAS-like,
85004
RERG; RAS-like, estrogen-
RRSSTTHVKQ
N/A
N/A
1:500-



estrogen-

regulated, growth-
AINKMLTKIS


1:40000



regulated,

inhibitor
S (89)



growth-



inhibitor


 


S0070
G protein-
26996
GPCR150; GPR160; putative
MRRKNTCQNF
NETILYYFPFS
KVQIPAYIEM
1:10-



coupled

G protein-coupled
MEYFCISLAF
SHSSYTVRS
NIPLVILCQ
1:100



receptor 160

receptor; G protein-
(90)
KK (91)
(92)





coupled receptor 160


 


S0072
S100 calcium
6279
CP-10; L1Ag; CALPROTECTIN;
MLTELEKALN
RDDKKLLET
KMGVAAHKK
1:6500-



binding

60B8AG; S100A8; MIF; CAGA;
SIIDVYTHK
ECPQYIRKKG
SHEESHKE
1:10000



protein A8

NIF; MRP8; MA387; 
(93)
AD (94)
(95)



(calgranulin

CFAG; CGLA S100A8/



A)

S100A9 COMPLEX; cystic





fibrosis antigen; S100





calcium-binding protein





A8; S100 calcium binding





protien A8 (calgranlin A)


 


S0073
forkhead box
3169
HNF3A; MGC33105; TCF3A;
PESRKDPSGA
HGLAPHESQ
EQQHKLDFK
1:100-



A1

FOXA1; forkhead box A1;
SNPSADS
LHLKGD (97)
AYEQALQYS
1:2700





HEPATOCYTE NUCLEAR FACTOR
(96)

(98)





3-ALPHA; hepatocyte





nuclear factor 3, alpha


 


S0073P2
forkhead box
3169
HNF3A; MGC33105; TCF3A;
HGLAPHESQL
N/A
N/A
1:50-



A1

FOXA1; forkhead box A1;
HLKGD


1:450





HEPATOCYTE NUCLEAR FACTOR
(99)





3-ALPHA; hepatocyte





nuclear factor 3, alpha


 


S0074
trefoil factor
7033
TFF3; trefoil factor 3,
EEYVGLSANQ
RVDCGYPHV
VPWCFKPLQ
1:2500-



3 (intestinal)

(intestinal); trefoil
CAVPAKDRVD
TPKECN
EAECTF
1:30000





factor 3, HITF, human
(100)
(101)
(102)





intestinal trefoil factor


 


S0074P3
trefoil factor
7033
TFF3; trefoil factor 3,
VPWCFKPLQE
N/A
N/A
1:400-



3 (intestinal)

(intestinal); trefoil
AECTF (103)


1:810





factor 3, HITF, human





intestinal trefoil factor


 


S0076x1
keratin 17
3872
PC2; PCHC1; KRT17; K17;
KKEPVTTRQV
QDGKVISSR
SSSIKGSSGL
1:200





CYTOKERATIN 17; keratin 17
RTIVEE
EQVHQTTR
GGGSS (106)






(104)
(105)


 


S0078
kynureninase
8942
3.71.3; XANTHURENICACI-
DEEDKLRHFR
KPREGEETL
EERGCQLTIT
1:180-



(L-kynurenine

DURIA; KYNU; HYDROXYKYNUR-
ECFIPKIQD
RIEDILEVIEK
FSVPNKDVF
1:200



hydrolase)

ENINURIA; KYNURENINASE
(107)
E (108)
QE (109)





DEFICIENCY; XANTHURENIC





ACIDURIA; kynureninase





(L-kynurenine hydrolase)


 


S0079
solute
25800
SLC39A6; LIV-1 protein,
DHNHAASGKN
EEPAMEMKR
QRYSREELK
1:200-



carrier

estrogen relulated; solute
KRKALCPDHD
GPLFSHLSS
DAGVATL
1:800



family 39

carrier family 39 (zinc
(110)
QNI (111)
(112)



(zinc

transporter), member 6;



transporter),

solute carrier family 39



member 6

(metal ion transporter),





member 6


 


S0081
N-acetyl-
9
AAC1; 2.3.1.5; NAT1;
MDIEAYLERIG
QMWQPLELI
FNISLQRKLV
1:10-



transferase 1

arylamine N-acetyltrans-
YKKSRNKLDL
SGKDQPQVP
PKHGDRFFTI
1:240



(arylamine N-

ferase-1; ACETYL-CoA:
E (113)
CVFR (114)
(115)



acetyltrans-

ARYLAMINE N-ACETYLTRANS-



ferase)

FERASE; ARYLAMINE N-





ACETYLTRANSFERASE 1;





N-acetyltransgerase 1





(arylamine N-acetyltrans-





ferase); arylamide





acetylase 1 (N-acetyl-





transferase 1)


 


S0086
X-box binding
7494
XBP2; TREB5; XBP1; X-box-
RQRLTHLSPE
EKTHGLVVE
QPPFLCQWG
1:180-



protein 1

binding protein-1; X BOX-
EKALRRKLKN
NQELRQRLG
RHQPSWKPL
1:400





BINDING PROTEIN 1; X BOX-
R (116)
MD (117)
MN (118)





BINDING PROTEIN 2; X-box





binding protein 1


 


S0088
claudin 10
9071
CPETRL3; OSP-L; CLDN10;
NKITTEFFDPL
FSISDNNKTP
EDFKTTNPSK
1:333-





claudin 10; claudin 10
FVEQK (119)
RYTYNGAT
QFDKNAYV
1:1000





isoform a; claudin 10

(120)
(121)





isoform b


 


S0090
sparc/
9806
KIAA0275; testican-2;
EGDAKGLKEG
EWCFCFWR
EEEGEAGEA
1:100-



osteonectin,

SPOCK2; TESTICAN 2; SPARC/
ETPGNFMEDE
EKPPCLAELE
DDGGYIW
1:800



cwcv and

OSTEONECTIN, CWCV, AND
(122)
R (123)
(124)



kazal-like

KAZAL-LIKE DOMAINS



domains pro-

PROTEOGLYCAN 2; sparc/



teoglycan

osteonectin, cwcv and



(testican) 2

kazal-like domains





proteoglycan (testican) 2


 


S0091
lipocalin 2
3934
UTEROCALIN; NGAL; LCN2;
DKDPQKMYAT
KKCDYWIRT
ENFIRFSKYL
1:100



(oncogene

NEUTROPHIL GELATINASE-
IYE (125)
FVPGCQ
GLPEN (127)



24p3)

ASSOCIATED LIPOCALIN;

(126)





ONOGENIC LIPOCALIN 24P3;





lipocalin 2 (oncogene





24p3)


 


S0092
paired box
7849
PAX8; paired box gene 8;
DDSDQDSCRL
RQHYPEAYA
NTPLGRNLST
1:30-



gene 8

paired box gene 8 isoform
SIDSQ (128)
SPSHTK
HQTYPVVAD
1:100





PAX8C; paired box gene 8

(129)
(130)





isoform PAX8D; paired box





gene 8 isoform PAX8E;





paired box gene 8 isoform





PAX8A; paired box gene 8





isoform PAX8B; PAIRED





DOMAIN GENE 8 PAX8/





PPARG FUSION GENE


 


S0093
mesothelin
10232
CAK1; SMR; MSLN;
RLVSCPGPLD
KMSPEDIRK
SPEELSSVPP
1:500





mesothelin; MEGAKARYOCYTE-
QDQQE (131)
WNVTSLETL
SSIWAVRPQ





POTENTIATING FACTOR;

K (132)
D (133)





SOLUBLE MPF/MESOTHELIN-





RELATED PROTEIN;





mesothelin isoform 2





precursor; mesothelin





isoform 1 precursor,





megakaryocyte potentiating





factor precursor; ANTIGEN





RECOGNIZED BY MONOCLONAL





ANTIBODY


 


S0094
kallikrein 6
5653
Bssp; PRSS18; KLK6; Klk7;
EEQNKLVHGG
ELIQPLPLER
GKTADGDFP
1:150-



(neurosin,

SP59; PRSS9; MGC9355;
PCDKTSH
DCSANT
DTIQC (136)
1:300



zyme)

protease M; kallikrein 6
(134)
(135)





preproprotein; protease,





serine, 18; protease,





serine, 9; kallikrein 6





(neurosin, zyme)


 


S0095
Rap guanine
10411
bcm910; MGC21410;
REQWPERRR
KVNSAGDAI
QQLKVIDNQR
1:250-



nucleotide

93301705Rik; EPAC;
CHRLENGCGN
GLQPDAR
ELSRLSRELE
1:1000



exchange

RAPGEF3; cAMP-GEFI; RAP
A (137)
(139)
(140)



factor (GEF) 3

guanine-nucleotide-





exchange factor 3;





EXCHANGE PROTEIN ACTIVATED





BY cAMP; RAP guanine-





nucleotide-exchange factor





(GEF) 3; cAMP-REGULATED





GUANINE NUCLEOTIDE





EXCHANGE FACTOR I; RAP





GUANINE NUCLE


 


S0096
ATPase, H+
525
Vma2; VPP3; ATP6V1B1;
REHMQAVTRN
KKSKAVLDY
DEFYSREGR
1:100-



transporting,

RTA1B; 3.63.14; VATB;
YITHPR
HDDN (142)
LQDLAPDTAL
1:800



lysosomal 56/

ATP6B1; V-ATPase B1
(141)

(143)



58 kDa, V1

subunit; H+-ATPase



subunit B,

beta 1 subunit; H(+)-



isoform 1

transporting two-sector



(Renal tubular

ATPase, 58 kD subunit;



acidosis with

vacuolar proton pump,



deafness)

subunit 3; endomembrane





proton pump 58 kDa





subunit; ATPase, H+





transporting, lysos


 


S0097
frizzled
8325
FZ-8; hFZ8; FZD8; frizzled
KQQDGPTKTH
ELRVLSKANA
RRGGEGGEE
1:100-



homolog 8

8; frizzled homolog 8
KLEKLMIR
IVPGLSGGE
NPSAAKGHL
1:500



(Drosophila)

(Drosophila; FRIZZLED,
(144)
(145)
MG (146)





DROSOPHILA, HOMOLOG OF, 8


 


S0099
histone 1,
255626
HIST1H2BA; histone 1, H2ba
MPEVSSKGAT
GFKKAVVKT
KEGKKRKRT
1:333-



H2ba


ISKK (147)
QK (148)
RKE (149)
1:500


 


S0110
hypothetical
84259
MGC2714; hypothetical
RYAFDFARDK
SVFYQYLEQ
EDGAWPVLL
1:500-



protein

protein MGC2714
DQRSLDID
SKYRVMNKD
DEFVEWQKV
1:2500



MGC2714


(150)
Q (151)
RQTS (152)


 


S0117
reproduction 8
7993
D8S2298E; REP8; repro-
SFKSPQVYLK
RKKQQEAQG
EDIGITVDTVL
1:200-





duction 8; Reproduction/
EEEEKNEKR
EKASRYIE
ILEEKEQTN
1:375





chromoshome 8
(153)
(154)
(155)


 


S0119
slit homolog 1
6585
SLIT3; MEGF4; SLIL 1;
KAFRGATDLK
DFRCEEGQE
DGTSFAEEVE
1:900



(Drosophila)

Slit-1; SLIT1; slit
NLRLDKNQ
EGGCLPRPQ
KPTKCGCAL





homolog 1 (Drosophila);
(156)
(157)
CA (158)





SLIT, DROSOPHILA, HOMOLOG





OF 1; MULTIPLE EPIDERMAL





GROWTH FACTOR-LIKE DOMAINS





4


 


S0122
leucyl-tRNA
23395
6.1.1.4; MGC26121;
QRIKEQASKIS
HAKTKEKLEV
KSPQPQLLSN
1:150



synthetase 2

KIAA0028; LEURS; LARS2;
EADKSKPKF
TWEKMSKSK
KEKAEARK



mitochondrial

leucine trnslase; leucine-
(159)
HN (160)
(161)





tRNA ligase; LEUCYL-tRNA





SYNTHETASE, MITOCHONDRIAL;





leucyl-tRNA synthetase 2,





mitochondrial; leucyl-tRNA





synthetase 2,





mitochondrial precursor


 


S0123
homeo box D4
3233
HOX4B; HOXD4; HHO.C13;
MLFEQGQQAL
KDQKAKGILH
HSSQGRLPE
1:100-





HOX-5.1; HOMEOBOX D4;
ELPECT
SPASQSPER
APKLTHL
1:500





HOMEOBOX 4B; HOMEOBOX X;
(162)
S (163)
(164)





homeo box D4; homeobox





protein Hox-D4; Hox-4.2,





mouse, homolog of homeo





box X


 


S0124
sphingosine-1
8879
KIAA1252; SPL; SGPL1;
KRGARRGGW
KIVRVPLTKM
QFLKDIRESV
1:990-



phosphate

sphingosine-1-phosphate
KRKMPSTDL
MEVDR
TQIMKNPKA
1:1500



lyase 1

lyase 1
(165)
(166)
(167)


 


S0126
HBxAg trans-
55789
XTP1; HBxAg transactivated
SKQGVVILDD
VQTFSRCILC
LKKPFQPFQR
1:450-



activated

protein 1
KSKELPHW
SKDEVDLDEL
TRSFRM
1:1600



protein 1


(168)
(169)
(170)


 


S0132
SRY (sex
6662
SRA1; CMD1; SOX9; SRY-BOX
MNLLDPFMKM
NTFPKGEPD
KNGQAEAEE
1:100-



determining

9; transcription factor
TDEQEKGLS
LKKESEEDK
ATEQTHISPN
1:500



region Y)-box

SOX9; SRY-RELATED HMG-BOX
(171)
(172)
(173)



9 (campomelic

GENE 9; SEX REVERSAL,



dysplasia,

AUTOSOMAL, 1; SRY (sex-



autosomal sex-

determining region Y)-box



reversal)

9 protein; SRY (sex-





determining region Y)-box





9 (campomelic dysplasia,





autosomal sex-reversal);





SRY(


 


S0137
cadherin, EGF
1952
Flamingo1; CELSR2; EGFL2;
QASSLRLEPG
ELKGFAERL
RSGKSQPSYI
1:1800-



LAG seven-pass

KIAA0279; MEGF3; CDHF 10;
RANDGWH
QRNESGLDS
PFLLREE
1:5000



G-type

EGF-like-domain, multiple
(174)
GR (175)
(176)



receptor 2

2; epidermal growth



(flamingo

factor-like 2; multiple



homolog,

epidermal growth factor-



Drosophila)

like domains 3; cadherin





EGF LAG seven-pass G-type





receptor 2; cadherin, EGF





LAG seven-pass G-type





receptor 2


 


S0139
gamma-
8836
3.4.19.9; GGH; gamma-
RRSDYAKVAKI
KNFTMNEKL
EFFVNEARKN
1:12500-



glutamyl

glutamyl hydrolase
FYNLSIQSFDD
KKFFNVLTTN
NHHFKSESE
1:30000



hydrolase

precursor; gamma-glutamyl
(177)
(178)
E (179)



conjugase,

hydrolase (conjugase,



folypolygamma-

folypolygammaglutamyl



glutamyl

hydrolase)



hydrolase)


 


S0140
bullous
667
BP240; FLJ13425; FLJ32235;
KNTQAAEALV
QENQPENSK
KQMEKDLAF
1:250-



pemphigoid

FLJ21489; FLJ30627; CATX-
KLYETKLCE
TLATQLNQ
QKQVARKQL
1:20000



antigen 1,

15; KIAA0728; BPAG1;
(180)
(181)
K (182)



230/240 kDa

dystonin; hemidesmosomal





plaque protein; bullous





pemphigoid antigen 1, 230/





240 kDa; bullous





pemphigoid antigen 1





(230/240 kD); bullous





pemphigoid antigen 1





isoform 1eA precursor;





bullo


 


S0143
fatty acid
2194
2.3.1.85; OA-519; FASN;
EFVEQLRKEG
DRHPQALEA
REVRQLTLRK
1:5000-



synthase

MGC14367; MGC15706; fatty
VFAKEVR
AQAELQQHD
LQELSSKADE
1:30000





acid synthase
(183)
(184)
(185)


 


S0143P3
fatty acid
2194
2.3.1.85; OA-519; FASN;
REVRQLTRK
N/A
N/A
1:200-



synthase

MGC14367; MGC15706; fatty
LQELSSKADE


1:630





acid synthase
(186)


 


S0144
matrix
4323
MMP-X1; 3.4.24-; MMP14;
AYIREGHEKQ
DEASLEPGY
RGSFMGSDE
1:500-



metallopro-

MTMMP1; MT1-MMP; membrane-
ADIMFFAE
PKHIKELGR
VFTYFYK
1:20000



teinase 14

type-1 matrix metallopro-
(187)
(188)
(189)



(membrane-

teinase 14 preproprotein;



inserted)

MATRIX METALLOPROTEINASE





14, MEMBRANE-TYPE; matrix





metalloproteinase 14





(membrane-inserted);





membrane-type matrix





metalloprotein


 


S0147
cystatin A
1475
STF1; CSTA; STFA; cystatin
MIPGGLSEAK
NETYGKLEA
DLVLTGYQVD
1:100-



(stefin A)

AS; cystatin A (stefin A)
PATPEIQEIV
VQYKTQ
KNKDDELTGF
1:50000






(190)
(191)
(192)


 


S0149
transient
55503
TRPV6; ECAC2: CAT1; CATL;
RQEHCMSEHF
QGHKWGES
RACGKRVSE
1:400-



receptor

CALCIUM TRANSPORTER 1;
KNRPACLGAR
PSQGTQAGA
GDRNGSGGG
1:20000



potential

CALCIUM TRANSPORTER-LIKE
(193)
GK (194)
KWG (195)



cation

PROTEIN; EPITHELIAL



channel, sub-

CALCIUM CHANNEL 2;



family V,

transient receptor



member 6

potential cation channel,





subfamily V, member 6


 


S0156
fatty acid
2173
B-FABP; FABP7; FABPB; MRG;
MVEAFCATWK
QVGNVTKPT
KVVIRTLSTFK
1:100-



binding

mammary-derived growth
LTNSQN
VIISQE
NTE (198)
1:20000



protein 7,

inhibitor-related; FATTY
(196)
(197)



brain

ACID-BINDING PROTEIN 7;





FATTY ACID-BINDING





PROTEIN, BRAIN; fatty acid





binding protein 7, brain


 


S0158
cadherin 3,
1001
CDHP; HJMD; PCAD; CDH3;
RAVFREAEVT
QEPALFSTD
QKYEAHVPE
1:150-



type 1, P-

placental cadherin;
LEAGGAEQE
NDDFTVRN
NAVGHE
1:2000



cadherin

CADHERIN, PLACENTAL;
(199)
(200)
(201)



(placental)

cadherin 3, P-cadherin





(placental); calcium-





dependent adhesion





protein, placental;





cadhedrin 3, type 1





preproprotein; cadherin 3,





type 1, P-cadherin





(placental)


 


S0165
chemokine (C-
2919
MGSA-a; NAP-3; CXCL1;
KKIIEKMLNSD
N/A
N/A
1:100-



X-C motif)

SCYB1; GROa; GRO1,
KSN (202)


1:500



ligand 1

FORMERLY; GRO PROTEIN,



(melanoma

ALPHA; GRO 1 ONCOGENE,



growth

FORMERLY; MELANOMA GROWTH



stimulaing

STIMULATORY ACTIVITY,



activity,

ALPHA; GRO 1 oncogene



alpha)

(melanoma growth-





stimulating activity);





CHEMOKINE, CXC MOTIF,





LIGAND 1; GRO1 oncogene





(melanoma grow


 


S0171
baculoviral
null
BIRC5; baculoviral IAP
GKPGNQNSK
QAEAPLVPLS
NCFLTERKAQ
1:22500-



IAP repeat-

repeat-containing 5
NEPPKKRERE
RQNK (204)
PDE (205)
1:30000



containing 5

(survivin)
R (203)



(survivin)


 


S0193
procollagen-
5352
PLOD2; LYSYL HYDROXYLASE
EFDTVDLSAV
NKEVYHEKDI
KQVDLENVW
1:20000



lysine, 2-

2; LYSINE HYDROXYLASE 2;
DVHPN (206)
KVFFDKAK
LDFIRE



oxoglutarate

PROCOLLAGEN-LYSINE, 2-

(207)
(208)



5-dioxygenase

OXOGLUTARATE 5-DIOXY-



(lysine

GENASE 2; procollagen-



hydroxylase) 2

lysine, 2-oxoglutarate





5-dixoygenase (lysine





hydroxylase) 2;





procollagen-lysine,





2-oxoglutarate 5-dioxy-





genase (lysine hydroxy-





lase) 2 isoform


 


S0202
PTK7 protein
5754
PTK7; CCK4; protein-
LKKPQDSQLE
KAKRLQKQP
KDRPSFSEIA
1:500-



tyrosine

tyrosine kinase PTK7;
EGKPGYLD
EGEEPEME
SALGDSTVDS
1:800



kinase 7

colon carcinoma kinase-4;
(209)
(210)
KP (211)





PTK7 protein tyrosine





kinase 7; PTK7 protein





tyrosine kinase 7 isoform





e precursor; PTK7 protein





tyrosine kinase 7 isoform





a precursor; PTK7 protein





tryosine kinase 7 isoform





d precursor;


 


S0211
cytochrome
1549
CYPIIA; P450-IIA4;
KRGIEERIQEE
DRVIGKNRQ
NPQHFLDDK
1:500-



P450, family

1.14.14.1; CPA7; CYP2A7;
SGFLIE
PKFEDRTK
GQFKKSD
1:2500



2, subfamily

CPAD; CYTOCHROME P450,
(212)
(213)
(214)



A, poly-

SUBFAMILY IIA, POLY-



peptide 7

PEPTIDE 7; cytochrome





P450, subfamily IIA





(phenobarbital-inducible),





polypeptide 7; cytochrome





P450, family 2, subfamily





A, polypeptide 7; cyto-





chrome P450, family 2, su


 


S0218
solute carrier
222962
SLC29A4; solute carrier
RHCILGEWLPI
KQRELAGNT
RNAHGSCLH
1:20-1:50



family 29

family 29 (nucleoside
LIMAVFN
MTVSYMS
ASTANGSILA



(nucleoside

transporters), member 4
(215)
(216)
GL (217)



transporters),




member 4


 


S0221
solute carrier
9153
HCNT2; SLC28A2; HsT17153;
ELMEKEVEPE
KARSFCKTH
KNKRLSGME
1:500-



family 28

SPNT1; CONCENTRATIVE
GSKRTD
ARLFNK
EWIEGEK
1:1200



(sodium-

NUCLEOSIDE TRANSPORTER 2;
(218)
(219)
(220)



coupled

SODIUM-DEPENDENT PURINE



nucleoside

NUCLESIDE TRANSPORTER 1;



transporter),

solute carrier family 28



member 2

(sodium-coupled nucleoside





transporter), member 2


 


S0223
angiopoietin-
51129
HFARP; FIAF; ANGPTL4;
EGSTDLPLAP
KVAQQQRHL
DHKHLDHEV
1:30-



like 4

PGAR; angiopoietin-like 4;
ESRVDPE
EKQHLR
AKPARRKRLP
1:10000





FASTING-INDUCED ADIPOSE
(221)
(222)
E (223)





FACTOR; PPARG ANGIO-





POIETIN-RELATED PROTEIN;





HEPATIC FIBRINOGEN/





ANGIOPOIETIN-RELATED





PROTEIN


 


S0235
carcino-
1048
CEACAM5; CD66e; carcino-
KLTIESTPFNV
KSDLVNEEA
KPVEDKDAVA
1:500-



embryonic

embryonic antigen-related
AEGKEC
TGQFRVYPE
FTCEPEAQ
1:4500



antigen-

cell adhesion molecule 5
(224)
LPK (225)
(226)



related cell



adhesion



molecule 5


 


S0237
podocalyxin-
5420
podocalyxin-like; Gp200;
DEKLISLICRA
KDKWDELKE
DSWIVPLDNL
1:1000-



like

PCLP; PODXL; PODOCALYXIN-
VKATFNPAQDK
AGVSDMKLG
TKDDLDEEED
1:2000





LIKE PROTEIN;
(227)
D (228)
THL (229)





podocalyxin-like





precursor


 


S0238
xenotropic
9213
X3; XPR1; X RECEPTOR;
EAVVTNELED
RRYRDTKRA
KARDTKVLIE
1:100-



and polytropic

SYG1, YEAST. HOMOLOG OF;
GDRQKAMKRL
FPHLVNAGK
DTDDEANT
1:500



retrovirus

xenotropic and polytropic
R (230)
(231)
(232)



receptor

retrovirus receptor


 


S0241
glycyl-tRNA
2617
GlyRS; GARS; CMT2D;
RKRVLEAKEL
RHGVSHKVD
EARYPLFEG
1:500-



synthetase

6.1.1.14; SMAD1; GLYCYL-
ALQPKDDIVD
DSSGSIGRR
QETGKKETIE
1:7500





tRNA SYNTHETASE; glycine,
(233)
YAR (234)
E (235)





tRNA ligase; Charcot-





Marie-Tooth nuuropathy,





neuronal type, D


 


S0244
dashshund
1602
DACH1; FLJ0138; dachshund
DLAGHDMGH
EKQVQLEKT
EADRSGGRT
1:100-



homolog 1

homolog (Drosophila);
ESKRMHIEKD
ELKMDFLRE
DAETIQDGR
1:3000



(Drosophila)

DACHSHUND, DROSOPHILA,
E (236)
RE (237)
(238)





HOMOLOG OF; dachshund





homolog 1 (Drosophila);





dachshund homolog 1





isoform a; dachshund





homolog 1 isoform b;





dachshund homolog 1





isoform c


 


S0251
transcription
29841
TFCP2L2; LBP-32; MGR; GRHL
EALYPQRRSY
DYYKVPRER
DKYDVPHDI
1:5400



factor CP2-

1; mammailan grainyhead;
TSEDEAWK
RSSTAKPEV
GKIFKKCKK



like 2

LBP protein 32; transcrip-
(239)
E (240)
(241)





tion factor CP2-like 2;





leader-binding protein 32





isoform 2; leader-binding





protein 32 isoform 1


 


S0253
lysosomal
55353
LAPTM4B; lysosomal
DPDQYNFSSS
EYIRQLPPNF
DTTVLLPPYD
1:500-



associated

associated protein trans-
ELGGDFEFMD
PYRDD
DATVNGAAK
1:2000



protein

membrane 4 beta
D (242)
(243)
E (244)



transmembrane



4 beta


 


S0255
cyclin E2
9134
CYCE2; CCNE2; cyclin E2;
RREEVTKKHQ
KESRYVHDK
DFFDRFMLT
1:1000-





G1/S-specific cyclin E2;
YEIR (245)
HFEVLHSDLE
QKDINK
1:2000





cyclin E2 isoform 2;

(246)
(247)





cyclin E2 isoform 3;





cyclin E2 isoform 1


 


S0260
nicastrin
23385
KIAA0253; nicastrin;
ESKHFTRDLM
ETDRLPRCV
ESRWKDIRA
1:2400-





NCSTN; APH2; ANTERIOR
EKLKGRTSR
RSTARLAR
RIFLIASKELE
1:5400





PHARYNX DEFECTIVE 2,
(248)
(249)
(250)





C. ELEGANS,





HOMOLOG OF


 


S0265
FXYD domain
5349
MAT-8; MAT8; PLML; FXYD3;
KVTLGLLVFLA
SEWRSSGE
KCKCKFGQK
1:400-



containing

phospholemman-like
GFPVLDANDL
QAGR (252)
SGHHPGE
1:1200



ion transport

protien; MAMMARY TUMOR,
ED (251)

(253)



regulator 3

8 KD; FXYD domain-





containing ion transport





regulator 3; FXYD domain





containing ion transport





regulator 3; FXYD





domain containing ion





transport regulator 3





isoform 2 precursor;





FXYD domai


 


S0267
immunoglobulin
3321
EWI-3; V8; IGSF3; immuno-
KVAKESDSVF
EREKTVTGE
KRAEDTAGQ
1:200-



superfamily,

globin superfamily, member
VLKIYHLRQED
FIDKESKRPK
TALTVMRPD
1:250



member 3

3; immunoglobulin
(254)
(255)
(256)





superfamily, member 3


 


S0270
signal trans-
10254
STAM2B; STAM2;
KVARKVRALY
ETEVAAVDKL
EIKKSEPEPV
1:1000-



ducing

DKFZp564C047; Hbp; STAM2A;
DFEAVEDNE
NVIDDDVE
YIDEDKMDR
1:9000



adaptor

SIGNAL-TRANSDUCING ADAPTOR
(257)
(258)
(259)



molecule (SH3

MOLECULE 2; signal trans-



domain and

ducing adaptor molecule 2;



ITAM motif) 2

STAM-like protein





containing SH3 and ITAM





domains 2; signal trans-





ducing adaptor molecule





(SH3 domain and ITAM





motif) 2


 


S0273
dickkopf
22943
DKK1; DKK-1; SK; dickkopf-
DEECGTDEYC
RGEIEETITE
N/A
1:400-



homolog 1

1 like; dickkopf (Xenopus
ASPTRGGD
SFGNDHSTL

1:500



(Xenopus

laevia) homolog 1;
(260)
D (261)



laevis)

dickkopf homolog 1





(Xenopus laevis);





DICKKOPF, XENOPUS,





HOMOLOG OF, 1


 


S0280
solute carrier
65010
SLC26A6; solute carrier
MDLRRRDYH
DTDIYRDVAE
EFYSDALKQR
1:1800-



family 26,

family 26, member 6
MERPLLNQEH
YSEAKE
CGVDVDFLIS
1:2400



member 6


LEE (262)
(263)
QKKK (264)


 


S0286
WNT inhibitory
11197
WIF1; WIF-1; WNT
DAHQARVLIG
ERRICECPD
KRYEASLIHA
1:90



factor 1

inhibitory factor 1;
FEEDLIIVSE
GFHGPHCEK
LRPAGAQLR





Wnt inhibitory factor-1
(265)
(266)
(267)





precursor


 


S0288
preferentially
23532
MAPE; PRAME; OPA-INTER-
KRKVDGLSTE
KEGACDELF
DIKMILKMVQ
1:1200



expressed

ACTING PROTEIN 4; Opa-
AEQPFIPVE
SYLIEKVKRK
LDSIEDLE



antigen in

interacting protein OIP4;
(268)
K (269)
(270)



melanoma

preferentially expressed





antigen in melanoma;





melanoma antigen





preferentially expressed





in tumors


 


S0295
prostaglandin
9536
PGES; TP53I12; MGST1L1;
RLRKKAFANP
RSDPDVERC
RVAHTVAYLG
1:100-



E synthase

PP1294; PP102; PTGES;
EDALR
LRAHRND
KLRAPIR
1:2400





MGC10317; PIG12; MGST1-L1;
(271)
(272)
(273)





MGST-IV; MGST1-like 1;





p53-INDUCED GENE 12;





prostaglandin E synthase;





p53-induced apoptosis





protein 12; prostaglandin





E synthase isoform 2;





prostaglandin E synthase





isoform 1; micros


 


S0296
solute carrier
8140
SLC7A5; MPE16; D16S469E;
KRRALAAPAA
EAREKMLAA
MIWLRHRKP
1:300-



family 7

CD98; LAT1; 4F2 light
EEKEEAR
KSADGSAPA
ELERPIK
1:5000



(cationic

chain; Membrane protein
(274)
GE (275)
(276)



amino acid

E16; L-TYPE AMINO ACID



transporter,

TRANSPORTER 1; Solute



y+system),

carrier family 7, member



member 5

5; solute carrier family





7 (cationic amino acid





transporter, y+system),





member 5


 


S0296P1
solute carrier
8140
SLC7A5; MPE16; D16S469E;
KRRALAAPAA
N/A
N/A
1:225-



family 7

CD98; LAT1; 4F2 light
EEKEEAR


1:3150



(cationic

chain; Membrane protein
(277)



amino acid

E16; L-TYPE AMINO ACID



transporter,

TRANSPORTER 1; Solute



y+system),

carrier family 7, member



member 5

5; solute carrier family





7 (cationic amino acid





transporter, y+system),





member 5


 


S0297
v-maf
7975
FLJ32205; NFE2U; MAFK;
KPNKALKVKK
KRVTQKEEL
RLELDALRSK
1:333-



musculoapon-

NFE2, 18 KD SUBUNIT;
EAGE (278)
ERQRVELQQ
YE (280)
1:800



eurotic

nuclear factor erythroid-

EVEK (279)



fibrosarcoma

2, ubiquitous (p18);



oncogene

NUCLEAR FACTOR ERYTHROID



homolog K

2, UBIQUITOUS SUBUNIT;



(avian)

v-maf musculoapoeurotic





fibrosarcoma oncogene





homolog K (avian); v-maf





avian musculoaponeurotic





fibrosarcoma oncogen


 


S0301
signal pep-
57758
SCUBE2; signal peptide,
KMHTDGRSCL
KKGFKLLTDE
KRTEKRLRKA
1:3500-



tide, CUB

CUB domain, EGF-like 2
EREDTVLEVT
KSCQDVDE
IRTLRKAVHR
1:5400



domain, EGF-


E (281)
(282)
E (283)



like 2


 


S0303
gamma-amino-
2564
GABRE; GABA-A RECEPTOR,
RVEGPQTESK
EETKSTETET
KWENFKLEIN
1:300-



butyric acid

EPSILON POLYPEPTIDE;
NEASSRD
GSRVGKLPE
EKNSWKLFQ
1:500



(GABA) A

GAMMA-AMINOBUTYRIC ACID
(284)
(285)
FD (286)



receptor,

RECEPTOR, EPSILON; gamma-



epsilon

aminobutyric acid (GABA) A





receptor, epsilon; gamma-





aminobutyric acid (GABA) A





receptor, epsilon isoform





2; gamma-aminobutyric acid





(GABA) A receptor, epsilon





is


 


S0305
S100 calcium
6281
CAL1L; GP11; p10; 42C;
DKGYLTKEDL
KDPLAVDKIM
N/A
1:8332-



binding

S100A10; ANX2LG; CLP11;
RVLMEKE
KDLDQCRDG

1:24996



protein A10

Ca[1]; CALPACTIN I,
(287)
K (288)



(annexin II

p11 SUBUNIT; ANNEXIN II,



ligand,

LIGHT CHAIN; CALPACTIN I,



calpactin I,

LIGHT CHAIN; S100 calcium-



light poly-

binding protein A10



peptide (p11))

(annexin II ligand,





calpactin I, light





polypeptide (p11); S100





calcium binding protein





A10


 


S0311
v-myb
4605
MYBL2; MGC15600; MYB-
MSRRTRCEDL
EEDLKEVLRS
RRSPIKKVRK
1:750-



myeloblastosis

RELATED GENE BMYB; MYB-
DELHYQDTDS
EAGIELIIEDD
SLALDIVDED
1:5000



viral onco-

related protein B; v-myb
D (289)
IR (290)
(291)



gene homolog

myeloblastosis viral



(avian)-like

oncogene homolog (avian)-



2

like 2; V-MYB AVIAN





MYELOBLASTOSIS VIRAL





ONCOGENE HOMOLOG-LIKE 2


 


S0312
nucleoside
4860
NP; 2.42.1; nucleoside
EDYKNTAEWL
DERFGDRFP
KVIMDYESLE
1:100-



phosphorylase

phosphorylase; PURINE-
LSHTKHR
AMSDAYDRT
KANHEE
1:3600





NUCLEOSIDE:ORTHOPHOSPHATE
(292)
MRQR (293)
(294)





RIBOSYLTRANSFERASE; purine





nucleoside phosphorylase;





PNP NUCLEOSIDE





PHOSPHORYLASE DEFIENCY;





ATAXIA WITH DEFICIENT





CELLULAR IMMUNITY


 


S0314
chaperonin
22948
KIAA0098; CCt5; chaperonin
DQDRKSRLM
KGVIVDKDFS
RMILKIDDIRK
1:6000-



containing

containing TCP1, subunit 5
GLEALKSHIMA
HPQMPKKVE
PGESEE
1:30000



TCP1, subunit

(epsilon)
AK (295)
D (296)
(297)



5 (epsilon)


 


S0315
non-
4830
GAAD; NME1; NDPKA; 2.74.6;
RLQPEFKPKQ
KFMQASEDL
DSVESAEKEI
1:9000-



metastatic

NM23-H1; AWD NM23H1B;
LEGTMANCER
LKEHYVDLKD
GLWFHPEEL
1:18000



cells 1,

GZMA-ACTIVATED DNase;
(298)
R (299)
VD (300)



protein

NUCLEOSIDE DIPHOSPHATE



(NM23A)

KINASE-A; AWD, DROSOPHILA,



epressed in

HOMOLOG OF; METASTASIS





INHIBITION FACTOR NM23;





nucleoside-diphosphate





kinase 1 isoform b;





NONMETASTATIC PROTEIN 23,





HOMOLOG 1; nucleo


 


S0316
squalene
6713
SQLE; 1.14.99.7; squalene
KSPPESENKE
RDGRKVTVIE
DHLKEPFLEA
1:1000-



epoxidase

epoxidase; squalene
QLEAPPPP
RDLKEPDR
TDNSHLR
1:10000





monooxygenase
(301)
(302)
(303)


 


S0319
pregnancy-
29948
OKL38; pregnancy-induced
DLEVKDWMQ
EYHKVHQMM
RHQLLCFKED
1:900



induced

growth inhibitor;
KKRRGLRNSR
REQSILSPSP
CQAVFQDLE



growth

PREGNANCY-INDUCED GROWTH
(304)
YEGYR (305)
GVEK (306)



inhibitor

INHIBITOR OKL38


 


S0326
mal, T-cell
114569
MAL2; mal, T-cell dif-
GPDILRTYSGA
CSLGLALRR
N/A
1:120-



differentia-

ferentiation protein 2
FVCLE (307)
WRP (308)

1:1200



tion protein 2


 


S0330
aldo-keto
1645
1.1.1.213; 2-ALPHA-HSD;
RYLTLDIFAGP
N/A
N/A
1:2500-



reductase

1.3.1.20; 20-ALPHA-HSD;
PNYPFSDEY


1:75000



family 1,

MGC8954; H-37 HAKRC; MBAB;
(309)



member C1/2

C9; DDH1; AKR1C1; trans-



(dihydrodiol

1,2-dihydrobenzene-1,2-



dehydrogenase

diol dehydrogenase;



1; 20-alpha

chlordecone reductase



(3-alpha)-

homolog; aldo-keto



hydroxysteroid

reductase C; 20 alpha-



dehydrohenase)

hydroxysteroid dehydro-





genase; hepatic





dihydrodiol


 


S0330-x1
aldo-keto
1645
1.1.1.213; 2-ALPHA-HSD;
RYLTLDIFAGP
N/A
N/A
1:600



reductase

1.3.1.20; 20-ALPHA-HSD;
PNYPFSDEY



family 1,

MGC8954; H-37 HAKRC; MBAB;
(310)



member C1/2

C9; DDH1; AKR1C1; trans-



(dihydrodiol

1,2-dihydrobenzene-1,2-



dehydrogenase

diol dehydrogenase;



1; 20-alpha

chlordecone reductase



(3-alpha)-

homolog; aldo-keto



hydroxysteroid

reductase C; 20 alpha-



dehydrohenase)

hydroxysteroid dehydro-





genase; hepatic





dihydrodiol


 


S0331
aldo-keto
8644
HA1753; 1.1.1.188; DD3;
HYFNSDSFAS
N/A
N/A
1:300-



reductase

hluPGFS; HSD17B5; 1.31.20;
HPNYPYSDEY


1:999



family 1,

1.1.1.213; AKR1C3;
(311)



member C3

KIAA0119; HAKRB; HAKRe;



(3-alpha

trans-1,2-dihydrobenzene-



hydroxysteroid

1,2-diol dehydrogenase;



dehydrogenase,

chlordecone reductase



type II)

homolog; dihydrodiol,





dehydrogenase 3;





prostaglandin F synthase;





ALDO-KETO REDUCTASE B; 3-


 


S0331-x1
aldo-keto
8644
HA1753; 1.1.1.188; DD3;
HYFNSDSFAS
N/A
N/A
1:150-



reductase

hluPGFS; HSD17B5; 1.31.20;
HPNYPYSDEY


1:300



family 1,

1.1.1.213; AKR1C3;
(312)



member C3

KIAA0119; HAKRB; HAKRe;



(3-alpha

trans-1,2-dihydrobenzene-



hydroxysteroid

1,2-diol dehydrogenase;



dehydrogenase,

chlordecone reductase



type II)

homolog; dihydrodiol,





dehydrogenase 3;





prostaglandin F synthase;





ALDO-KETO REDUCTASE B; 3-


 


S0332
aldo-keto
1645
1.1.1.213; 2-ALPHA-HSD;
RYVVMDFLMD
N/A
N/A
1:300-



reductase

1.3.1.20; 20-ALPHA-HSD;
HPDYPFSDEY


1:400



family 1,

MGC8954; H-37; HAKRC;
(313)



member C4

MBAB; C9; DDH1; AKR1C1;



(dihydrodiol

trans-1,2-dihydrobenzene-



dehydrogenase

1,2-diol dehydrogenase;



1; 20-alpha

chlordecone reductase



(3-alpha)-

homolog; aldo-keto



hydroxysteroid

reductase C; 20 alpha-



dehydrogenase)

hydrocysteroid dehydro-





genase; hepatic





dihydrodiol


 


S0332-x1
aldo-keto
1645
1.1.1.213; 2-ALPHA-HSD;
RYVVMDFLMD
N/A
N/A
1:75-



reductase

1.3.1.20; 20-ALPHA-HSD;
HPDYPFSDEY


1:150



family 1,

MGC8954; H-37; HAKRC;
(314)



member C4

MBAB; C9; DDH1; AKR1C1;



(dihydrodiol

trans-1,2-dihydrobenzene-



dehydrogenase

1,2-diol dehydrogenase;



1; 20-alpha

chlordecone reductase



(3-alpha)-

homolog; aldo-keto



hydroxysteroid

reductase C; 20 alpha-



dehydrogenase)

hydrocysteroid dehydro-





genase; hepatic





dihydrodiol


 


S0336
chromosome 20
140809
C20orf139; chromosome 20
DPAKVQSLVD
RETIPAKLVQ
N/A
1:600-



open reading

open reading frame 139
TIREDPD
STLSDLR

1:2400



frame 139


(315)
(316)


 


S0342
solute carrier
154091
SLC2A12; solute carrier
SDTTEELTVIK
N/A
N/A
1:400-



family 2

family 2 (facilitated
SSLKDE


1:1250



(facilitated

glucose transporter),
(317)



glucose trans-

member 12



porter),



member 12


 


S0343
solute carrier
154091
SLC2A12; solute carrier
HSRSSLMPLR
N/A
N/A
1:50-



family 2

family 2 (facilitated
NDVDKR


1:125



(facilitated

glucose transporter),
(318)



glucose trans-

member 12



porter),



member 12


 


S0357
HTPAP protein
84513
HTPAP; HTPAP protein
YRNPYVEAEY
N/A
N/A
1:100-






FPTKPMFVIA


1:300






(319)


 


S0364
KIAA0746
23231
KIAA0746; KIAA0746
KKFPRFRNRE
N/A
N/A
1:200-



protein

protein
LEATRRQRMD


1:300






(320)


 


S0367
peroxisomal
122970
PTE2B; peroxisomal acyl-
SGNTAINYKH
N/A
N/A
1:200-



acyl-CoA

CoA thioesterase 2B
SSIP (321)


1:600



thioesterase



2B


 


S0374
chloride
53405
CLIC5; chloride intra-
DANTCGEDKG
N/A
N/A
1:5000-



intracellular

cellular channel 5
SRRKFLDGDE


1:9000



channel 5


(322)


 


S0380
keratinocyte
200634
KRTCAP3; keratinocyte
QLEEMTELES
N/A
N/A
1:200-



associated

associated protein 3
PKCKRQENEQ


1:9000



protein 3


(323)


 


S0384
FERM, RhoGEF
10160
p63RHoGEF; CDEP; FARP1;
QADGAASAPT
N/A
N/A
1:100



(ARHGEF) and

chondrocyte-derived ezrin-
EEEEEVVKDR



pleckstrin

like protein; FERM,
(324)



domain

RhoGEF, and pleckstrin



protein 1

domain protein 1; FERM,



(chondrocyte-

ARHGEF, AND PLECKSTRIN



derived)

DOMAIN-CONTAINING PROTEIN





1; FERM, RhoGEF (ARHGEF)





and pleckstrin domain





protein 1 (chondrocyte-





derived)


 


S0388
trichorhino-
7227
GC79; TRPS1; TRPS1 GENE;
SGDSLETKED
N/A
N/A
1:600



phalangeal

trichorhinophalangeal
QKMSPKATEE



syndrome I

syndrome I; zinc finger
(325)





transcription factor TRPS1


 


S0396
cytochrome
1576
1.114.14.1; HLP; CYPA3;
RKSVKRMKES
N/A
N/A
1:15



P450, family

CYP3A4; P450C3; NF-25;
RLEDTQKHRV



3, subfamily

CP33; CP34; P450-III,
(326)



A, polypeptide

STEROID-INDUCIBLE;



4

nifedipine oxidase;





glucocorticoid-inducible





P450, CYTOCHROME





P450PCN1; P450, FAMILY





III; P450-III, steroid





inducible; cytochrome





P450, subfamily





IIIA, polypeptide 4;


 


S0398
FAT tumor
2195
CDHF7; FAT; cadherin ME5;
KIRLPEREKPD
N/A
N/A
1:45-



suppressor

FAT tumor suppressor
RERNARREP


1:200



homolog 1

precursor; cadherin-
(327)



(Drosophila)

related tumor suppressor





homolog precursor;





cadherin family member 7





precursor; homolog of





Drosophila Fat protein





precursor; FAT tumor





suppressor homolog 1





(Drosophila); FAT





TUMOR SUPPRESS


 


S0401
granulin
2896
ACROGRANIN; PROEPITHELIN;
RGTKCLRREA
N/A
N/A
1:600-





PROGRANULIN; PEPI; PCDGF;
PRWDAPLRDP


1:3000





granulin; GRN; EPITHELIN
(328)





PRECURSOR


 


S0404
N-myc down-
10397
HMSNL; TARG1; CMT4D; RTP;
GTRSRSHTSE
N/A
N/A
1:100-



stream

PROXY1; NDRG1; GC4; NMSL;
GTRSRSHTSE


1:900



regulated

TDD5; RIT42; NDR1;
(329)



gene 1

differentiation-related





gene 1 protein; nickel-





specific induction protein





Cap43; protein regulated





by oxygen 1; NMYC DOWN-





STREAM-REGULATED GENE 1;





reducing agents and





tunicamycin-respon


 


S0411
fatty acid
2171
PAFABP; EFABP; E-FABP;
EETTADGRKT
N/A
N/A
1:1800



binding

FABP5; PA-FABP; FATTY
QTVCNFTD



protein 5

ACID-BINDING PROTEIN;
(330)



(psoriasis-

EPIDERMAL; FATTY ACID-



associated)

BINDING PROTEIN 5; FATTY





ACID-BINDING PROTEIN,





PSORIASIS-ASSOCIATED;





fatty acid binding protein





5 (psoriasis-associated)


 


S0413
cyclin-
1028
WBS; p57(KIP2); BWCR;
AKRKRSAPEK
N/A
N/A
1:2700



dependent

CDKN1C; BWS; Beckwith-
SSGDVP



kinase

Wiedemann syndrome;
(331)



inhibitor 1C

cyclin-dependent kinase



(p57, Kip2)

inhibitor 1C (p57, Kip2)


 


S0414
alpha-
23600
AMACR; 5.1.99.4; ALPHA-
RVDRPGSRYD
N/A
N/A
1:100



methylacyl-CoA

METHYLACYL-CoA RACEMASE;
VSRLGRGKRS



racemase

AMACR DEFICIENCY; AMACR
(332)





ALPHA-METHYLACYL-CoA





RACEMASE DEFICIENCY;





alpha-methylacyl-CoA





racemase isoform 1;





alpha-methylacyl-CoA





racemase isoform 2


 


S0415
gamma-
2562
MGC9051; GABRB3; GABA-A
ETVDKLLKGY
N/A
N/A
1:600-



aminobutyric

RECEPTOR, BETA-3 POLY-
DIRLRPD


1:1800



acid (GABA)

PEPTIDE; GAMMA-AMINO-
(333)



A receptor,

BUTYRIC ACID RECEPTOR,



beta 3

BETA-3; gamma-aminobutyric





acid (GABA) A receptor,





beta 3; gamma-aminoburyric





acid (GABA) A receptor,





beta 3 isoform 2





precursor; gamma-amino-





butyric acid (GABA) A





rece


 


S0417
HSV-1
22879
HDRG1; KIAA0872; HSV-1
APGGAEDLED
N/A
N/A
1:9000



stimulation-

stimulation-related 1;
TQFPSEEARE



related gene 1

HSV-1 stimulation-
(334)





related gene 1


 


S0425
tumor necrosis
27242
TNFRSF21; DR6; BM-018;
RKSSRTLKKG
N/A
N/A
1:9000



factor

TNFR-related death
PRQDPSAIVE



receptor

receptor 6; tumor necrosis
(335)



superfamily,

factor receptor super-



member 21

family, member 21; tumor





necrosis factor receptor





superfamily, member 21





precursor


 


S0429
jumonji domain
221037
JMJD1C; TRIP8; jumonji
GSESGDSDES
N/A
N/A
1:1200



containing 1C

domain containing 1C;
ESKSEQRTKR





THYROID HORMONE RECEPTOR
(336)





INTERACTOR 8


 


S0432
chromosome 9
null
C9orf140; chromosome 9
EADSGDARRL
N/A
N/A
1:90-



open reading

open reading frame 140
PRARGERRRH


1:300



frame 140


(337)


 


S0440
cell division
994
3.1.3.48; CDC25B; cell
RLERPQDRDT
N/A
N/A
1:350-



cycle 25B

division cycle 25B; cell
PVQNKRRRS


1:3600





division cycle 25B isoform
(338)





4; cell division cycle 25B





isoform 5; cell division





cycle 25B isoform 1; cell





division cycle 25B isoform





2; cell division cycle 25B





isoform 3


 


S0445
laminin, beta
3912
LAMB1; LAMININ, BETA-1;
DRVEDVMME
N/A
N/A
1:600-



1

CUTIS LAXA-MARFANOID
RESQFKEKQE


1:1800





SYNDROME; laminin, beta 1;
(339)





laminin, beta 1 precursor;





LAMB1 NEONATAL CUTIS LAXA





WITH MARFANOID PHENOTYPE


 


S0447
papillary
5546
TPRC; MGC17178; MGC4723;
DEAFKRLQGK
N/A
N/A
1:4000-



renal cell

PRCC; proline-rich PRCC;
RNRGREE


1:6000



carcinoma

RCCP1 PRCC/TFE3 FUSION
(340)



(trans-

GENE; papillary renal cell



location-

carcinoma (translocation-



associataed)

associatied); RENAL CELL





CARCINOMA, PAPILLARY, 1





GENE; papillary renal cell





carcinoma translocation-





associated gene product


 


S0455
tumor necrosis
8743
APO2L; TL2; Apo-2L;
RFQEEIKENTK
N/A
N/A
1:900



factor

TNFSF10; Apo-2 ligand;
NDKQ (341)



(ligand)

APO2 LIGAND; TNF-RELATED



superfamily,

APOPTOSIS-INDUCING LIGAND;



member 10

TNF-related apoptosis





inducing ligand TRAIL;





tumor necrosis factor





(ligand) superfamily,





member 10; TUMOR NECROSIS





FACTOR LIGAND SUPERFAMILY,





MEMBER 10


 


S0459
titin
7273
connectin; TMD; titin;
KRDKEGVRW
N/A
N/A
1:2700-





CMD1G; CMPD4; TTN;
TKCNKKTLTD


1:8100





FLJ32040; CMH9, included;
(342)





titin isoform N2-A; titin





isoform N2-B; titin





isoform novex-1; titin





isoform novex-2; titin





isoform novex-3; cardio-





myopathy, dilated 1G





(autosomal dominant); TTN





CARDIOMYOPATHY, FAMILIAL


 


S0469
DNA fragmenta-
1676
DFF45; DFF1; DFFA; ICAD;
KEGSLLSKQE
N/A
N/A
1:600



tion factor,

DFF-45; INHIBITOR OF
ESKAAFGEE



45 kDa, alpha

CASPASE-ACTIVATED DNase;
(343)



polypeptide

DNA FRAGMENTATION FACTOR,





45 KD, ALPHA SUBUNIT; DNA





fragmentation factor, 45





kDa, alpha polypeptide;





DNA fragmentation factor,





45 kD, alpha subunit; DNA





fragmentation factor, 45





kD, alp


 


S0494
caspase 2,
835
ICH-1L/1S; CASP2; ICH1;
ESDAGKEKLP
N/A
N/A
1:2000



apoptosis-

CASP-2; ICH-1 protease;
KMRLPTRSD



related

caspase 2 isoform 3;
(334)



cysteine pro-

caspase 2 isoform 4; NEDD2



tease (neural

apoptosis regulatory gene;



precursor cell

caspase 2 isoform 2



expressed,

precursor; caspase 2



developmental-

isoform 1 preproprotein;



ly down-

NEURAL PRECURSOR CELL



regulated 2)

EXPRESSED, DEVELOPMENTALLY





DOWNREGULATED 2;


 


S0501
G1 to S phase
2935
GSPT1; eRF3a; ETF3A; GST1,
ERDKGKTVEV
N/A
N/A
1:15000



transition 1

YEAST, HOMOLOG OF; PEPTIDE
GRAYFETEK





CHAIN RELEASE FACTOR 3A;
(345)





G1- TO S-PHASE TRANSITION





1; G1 to S phase





transition 1


 


S0502
GCN5 general
2648
hGCN5; GCN5L2; GCN5
EKFRVEKDKL
N/A
N/A
1:9000



control of

(general control of
VPEKR



amino-acid

amino-acid synthesis,
(346)



synthesis 5-

yeast, homolog)-like 2;



like 2

GCN5 general control of



(yeast)

amino-acid synthesis 5-





like 2 (yeast); General





control of amino acid





synthesis, yeast, homolog-





like 2


 


S0503
geminin, DNA
51053
GMNN; geminin, DNA
EVAEKRRKAL
N/A
N/A
1:333



replication

replication inhibitor
YEALKENEK



inhibitor


(347)


 


S0507
ADP-ribo-
64225
ARL6IP2; ADP-ribosylation
ENYEDDDLVN
N/A
N/A
1:8000-



sylation

factor-like 6 interacting
SDEVMKKP


1:9000



factor-like

protein 2
(348)



6 interacting



protein 2


 


S0511
DNA replica-
51659
Pfs2; DNA replication
PKADEIRTLVK
N/A
N/A
1:2000



tion complex

complex GINS protein PSF2
DMWDTR



GINS protein


(349)



PSF2


 


S0524
ankyrin repeat
55608
ANKRD10; ankyrin repeat
RKRCLEDSED
N/A
N/A
1:4500



domain 10

domain 10
FGVKKARTE






(350)


 


S0527
potassium
null
KCTD2; potassium channel
EPKSFLCRLC
N/A
N/A
1:900-



channel tetra-

tetramerisation domain
CQEDPELDS


1:1500



merisation

containing 2
(351)



domain con-



taining 2


 


S0528
rabconnecin-3
23312
RC3; KIAA0856;
EEYDRESKSS
N/A
N/A
1:350-





rabconnectin-3
DDVDYRGS


1:1200






(352)


 


S0538
acidic
81611
ANP32E; acidic (leucine-
CVNGEIEGLN
N/A
N/A
1:1200



(leucine-rich)

rich) nuclear phospho-
DTFKELEF



nuclear

protein 32 family,
(353)



phosphoprotein

member E



32 family



member E


 


S0544
chromosome 9
84904
C9orf100; chromosome 9
EQRARWERK
N/A
N/A
1:40-



open reading

open reading frame 100
RACTARE


1:240



frame 100


(354)


 


S0545
Hpall tiny
27037
D22S1733E; HTF9C; Hpall
ERKQLECEQV
N/A
N/A
1:900-



fragments

tiny fragments locus 9C;
LQKLAKE


1:5400



locus 9C

Hpall tiny fragments locus
(355)





9C isoform2; Hpall tiny





fragments locus 9C





isoform 1


 


S0546
cell division
157313
CDCA2; cell division cycle
RNSETKVRRS
N/A
N/A
1:1200



cycle

associated 2
TRLQKDLEN



associaed 2


(356)


 


S0553
mitotic
129401
MP44; NUP35; LOC129401;
SDYQVISDRQ
N/A
N/A
1:3000-



phosphoprotein

NUCLEOPORIN
TPKKDE


1:5400



44

35 KD; mitotic
(357)





phosphoprotein 44


 


S0557
SMC4
10051
SMC4L; CAPC; hCAP-C;
DIEGKLPQTE
N/A
N/A
1:200



structural

chromosome-associated
QELKE



maintenance of

polypeptide C; SMC4
(358)



chromosomes 4-

(structural maintenance



like 1 (yeast)

of chromosomes 4, yeast)-





like 1; SMC4 structural





maintenance of chromosomes





4-like 1 (yeast);





structural maintenance of





chromosomes (SMC) family





member, chromosome-ass


 


S0564
phosphatidyl-
9791
KIAA0024; PSSA; PTDSS1;
DDVNYKMHFR
N/A
N/A
1:100-



serine 

phosphatidylserine
MINEQQVED


1:8000



synthase 1

synthase 1
(359)


 


S0565
polo-like
5347
2.7.1-; PLK1; STPK13;
ENPLPERPRE
N/A
N/A
1:10-



kinase 1

polo-like kinase
KEEPVVR


1:100



(Drosophilia)

(Drosophila); polo
(360)





(Drosophila)-like





kinase; SERINE/THREONINE





PROTEIN KINASE 13; polo-





like kinase 1





(Drosophila)


 


S0567
Pirin
8544
Pirin; PIR
REQSEGVGAR
N/A
N/A
1:240






VRRSIGRPE






(361)


 


S0578
ATP-binding
21
ABCA3; ABC3; LBM180;
PRAVAGKEEE
N/A
N/A
1:1500



cassette,

ABC-C; EST111653; ABC
DSDPEKALR



sub-family A

transporter 3; ATP-
(362)



(ABC1),

binding cassette 3; ATP-



member 3

BINDING CASSETTE TRANS-





PORTER 3; ATP-BINDING





CASSETTE, SUBFAMILY A,





MEMBER 3; ATP-binding





cassette, sub-family A





member 3; ATP-binding





cassette, sub-family A





(ABC1), memb


 


S0579
ATP-binding
10347
ABCX; ABCA7; ABCA-SSN;
EKADTDMEGS
N/A
N/A
1:300-



cassette, sub-

autoantigen SS-N; macro-
VDTRQEK


1:400



family A

phage ABC transporter;
(363)



(ABC1),

SJOGREN SYNDROME ANTIGEN



member 7

SS-N; ATP-BINDING





CASSETTE, SUBFAMILY A,





MEMBER 7; ATP-binding





cassette, sub-family A





(ABC1), member 7; ATP-





binding cassette, sub-





family A, member 7 isoform





a; A


 


S0581
ATP-binding
22
ABCB7; Atm1p; ASAT; ABC7;
RVQNHDNPK
N/A
N/A
1:4000-



cassette,

EST140535; ABC TRANSPORTER
WEAKKENISK


1:10000



sub-family B

7; ATP-binding cassette 7;
(364)



(MDR/TAP),

ATP-BINDING CASSETTE



member 7

TRANSPORTER 7; Anemia,





sideroblastic, with spino-





cerebellar ataxia; ATP-





BINDING CASSETTE,





SUBFAMILY B, MEMBER 7;





ATP-binding cassette,





sub-family B, member


 


S0585
ATP-binding
94160
MRP9; ABCC12; MULTIDRUG
RSPPAKGATG
N/A
N/A
1:500



cassette,

RESISTANCE-ASSOCIATED 9;
PEEQSDSLK



sub-family C

ATP-BINDING CASSETTE,
(365)



(CFTR/MRP),

SUBFAMILY C, MEMBER 12;



member 12

ATP-binding cassette, sub-





family C (CFTR/MRP),





member 12


 


S0586
ATP-binding
9429
ABC15; MXR1; ABCP;
REEDFKATEII
N/A
N/A
1:333-



cassette,

EST157481; MRX; ABCG2;
EPSKQDKP


1:400



sub-family G

BCRP1; BMDP; MITOXANTRONE-
(366)



(WHITE),

RESISTANCE PROTEIN;



member 2

mitoxantrone resistance





protein; placenta specific





MDR protein; ATP-BINDING





CASSETTE TRANSPORTER,





PLACENTA-SPECIFIC; breast





cancer resistance protein;





ATP-BINDING CASS


 


S0593
solute carrier
28234
OATP1B3; SLC21A8; OATP8;
DKTCMKWST
N/A
N/A
1:500-



organic anion

SLCO1B3; ORGANIC ANION
NSCGAQ


1:2400



transporter

TRANSPORTER 8; solute
(367)



family,

carrier organic anion



member 1B3

transporter family, member





1B3; SOLUTE CARRIER FAMILY





21, MEMBER 8 (ORGANIC





ANION TRANSPORTER); solute





carrier family 21 (organic





anion transporter), member





8


 


S0597
solute carrier
9356
ROAT1; MGC45260; HOAT1;
DANLSKNGGL
N/A
N/A
1:3000



family 22

PAHT; SLC22A6; PAH
EVWL (368)



(organic anion

TRANSPORTER; para-amino-



transporter),

hippurate transporter;



member 6

renal organic anion





transporter 1; solute





carrier family 22 member





6 isoform b; solute





carrier family 22 member





6 isoform c; solute





carrier family 22 member





6 isoform


 


S0604
solute carrier
7355
UGT2; UGTL; UGAT; SLC35A2;
EPFLPKLLTK
N/A
N/A
1:2400



family 35

UGT1; UDP-galactose
(369)



(UDP-

translocator, UDP-



galactose

GALACTOSE TRANSPORTER,



transporter),

ISOFORM 2; UGALT UDP-



member A2

GALACTOSE TRANSPORTER,





ISOFORM 1; solute carrier





family 35 (UDP-galactose





transporter), member A2;





solute carrier family 35





(UDP-galactose transpo


 


S0607
cell division
994
3.1.3.48; CDC25B; cell
RKSEAGSGAA
N/A
N/A
1:1800



cycle 25B

division cycle 25B; cell
SSSGEDKEN





division cycle 25B isoform
(370)





4; cell division cycle 25B





isoform 5; cell division





cycle 25B isoform 1; cell





division cycle 25B isoform





2; cell division cycle 25B





isoform 3


 


S0609
stearoyl-CoA
6319
SCD; acyl-CoA desaturase;
DDIYDPTYKDK
N/A
N/A
1:2000-



desaturase

stearoly-CoA desaturase
EGPSPKVE


1:5000



(delta-9-

(delta-9-desaturase);
(371)



desaturase)

fatty acid desaturase


 


S0611
mitogen-
6300
SAPK3; p38gamma; SAPK-3;
QSDEAKNNMK
N/A
N/A
1:100



activated

p38-GAMMA; PRKM12; MAPK12;
GLPELEKKD



protein

ERK3; ERK6; EXTRACELLULAR
(372)



kinase 12

SIGNAL-REGULATED KINASE 6;





mitogen-activated protein





kinase 3; stress-activated





protein kinase 3; mitogen-





activated protein kinase





12


 


S0612
nuclear factor
4791
LYT-10; LYT10; NFKB2;
SRPQGLTEAE
N/A
N/A
1:4500



of kappa

ONCOGENE LYT 10;
QRELEQEAK



light poly-

TRANSCRIPTION FACTOR
(373)



peptide gene

NFKB2; NFKB, p52/p100



enhancer in

SUBUNIT; LYMPHOCYTE



B-cells 2

TRANSLOCATION CHROMOSOME



(p49/p100)

10; NUCLEAR FACTOR





KAPPA-B, SUBUNIT 2;





Nuclear factor of kappa





light chain gene enhancer





in B-cells 2; nuclear





factor of kappa I


 


S0613
tumor necrosis
958
Bp50; TNFRSF5; MGC9013;
RVQQKGTSET
N/A
N/A
1:250-



factor

CDW40; CD40 antigen; CD40L
DTIC (374)


1:270



receptor

receptor, B CELL-



superfamily,

ASSOCIATED MOLECULE CD40;



member 5

CD40 type II isoform; B





cell surface antigen CD40;





nerve growth factor





receptor-related B-





lymphocyte activation





molecule; tumor necrosis





factor receptor superfam


 


S0614
Epstein-Barr
10148
EBI3; IL27, EBI3 SUBUNIT;
VRLSPLAERQ
N/A
N/A
1:1200-



virus induced

EPSTEIN-BARR VIRUS-INDUCED
LQVQWE


1:3000



gene 3

GENE 3; INTERLEUKIN 27,
(375)





EBI3 SUBUNIT; Epstein-Barr





virus induced gene 3;





Epstein-Barr virus induced





gene 3 precursor


 


S0616
zinc finger
58495
ZNF339; zinc finger
RRSLGVSVRS
N/A
N/A
1:2500



protein 339

protein 339
WDELPDEKR






(376)


 


S0617
DAB2
153090
DAB2IP; DAB2 interacting
DEGLGPDPPH
N/A
N/A
1:600



interacting

protein
RDRLRSK



protein


(377)


 


S0618
protein
8500
MGC26800; LIP1; PPFIA1;
SGKRSSDGSL
N/A
N/A
1:150



tyrosine

LIP.1; LAR-interacting
SHEEDLAK



phosphatase,

protein 1; PTPRF
(378)



receptor type,

interacting protein alpha



f polypeptide

1 isoform a; PTPRF



(PTPRF),

interacting protein alpha



interacting

1 isoform b; protein



protein

tyrosine phosphatase,



(liprin),

receptor type, f poly-



alpha 1

peptide (PTPRF), inter-





acting protein (liprin),





alpha 1


 


S0631
RGM domain
56963
RGMA; REPULSIVE GUIDANCE
SQERSDSPEI
N/A
N/A
1:600



family, member

MOLECULE; RGM domain
CHYEKSFHK



A

family, member A
(379)


 


S0633
hypothetical
144347
LOC144347; hypothetical
KVNPEPTHEIR
N/A
N/A
1:100-



protein

protein LOC144347
CNSEVK


1:200



LOC144347


(380)


 


S0639
tetratrico-
57217
TTC7; tetratricopeptide
RELREVLRTV
N/A
N/A
1:2000-



peptide

repeat domain 7
ETKATQN


1:3000



repeat


(381)



domain 7


 


S0640
protein C
5624
PROC; 3.4.21.69; PROC
RDTEDQEDQV
N/A
N/A
1:1000-



(inactivator

DEFIENCY PROTEIN C;
DPRLIDGK


1:1800



of coagula-

THROMBOPHILIA,
(382)



tion factors

HEREDITARY, DUE TO PC



Va and VIIIa)

DEFINCIENCY; PROTEIN C





DEFINCIENCY, CONGENITAL





THROMBOTIC DISEASE DUE





TO; protein C (inactivator





of coagulation factors Va





and VIIIa)


 


S0643
transducin-
7090
HsT18976; KIAA1547; ESG3;
KNHHELDHRE
N/A
N/A
1:200-



like enhancer

TLE3; transducin-like
RESSAN


1:1440



of split 3

enhancer protein 3;
(383)



(E(sp1)

enhancer of split groucho



homolog,

3; transducin-like en-



Drosophila)

hancer of split 3 (E(sp1)





homolog, Drosophila)


 


S0645
frizzled
8324
FzE3; FZD7; frizzled 7;
SDGRGRPAFP
N/A
N/A
1:900



homolog 7

frizzled homolog 7
FSCPRQ



(Drosophila)

(Drosophila); Frizzled,
(384)





drosophila, homolog





of, 7


 


S0646
solute carrier
6520
MDU1; 4T2HC; SLC3A2;
GSKEDFDSLL
N/A
N/A
1:3600-



family 3

NACAE; 4F2HC; 4F2 HEAVY
QSAKK


1:5400



(activators of

CHAIN; CD98 HEAVY CHAIN;
(385)



dibasic and

CD98 MONOCLONAL ANTIBODY



neutral amino

44D7; ANTIGEN DEFINED BY



acid trans-

MONOCLONAL ANTIBODY 4F2,



port), member

HEAVY CHAIN; antigen



2

identified by monoclonal





antibodies 4F2, TRA1.10,





TROP4, and T43; SOLUTE





CARRIER FAMILY 3


 


S0648
KIAA0738 gene
9747
KIAA0738; KIAA0738 gene
EYRNQTNLPT
N/A
N/A
1:200



product

product
ENVDK






(386)


 


S0651
phospholipase
22925
PLA2IR; PLA2-R; PLA2R1;
QKEEKTWHEA
N/A
N/A
1:3600



A2 receptor

PLA2G1R; PHOSPHOLIPASE
LRSCQADN



1, 180 kDa

A2 RECEPTOR, 180 KD;
(387)





phospholipase A2





receptor 1, 180 kDa


 


S0654
KIAA0182
23199
KIAA0182; KIAA0182 protein
EKAEEGPRKR
N/A
N/A
1:400



protein


EPAPLDK






(388)


 


S0659
thymidine
7084
TK2; THYMIDINE KINASE,
EQNRDRILTPE
N/A
N/A
1:300



kinase 2,

MITOCHONDRIAL; thymidine
NRK (389)



mitochondrial

kinase 2, mitochondrial


 


S0663
chromosome 14
64430
C14orf135; chromosome 14
RDWYIGLVSD
N/A
N/A
1:900



open reading

open reading frame 135
EKWK



frame 135


(390)


 


S0665
KIAA1007
23019
KIAA1007; KIAA1007
DSYLKTRSPV
N/A
N/A
1:1500-



protein

protein; adrenal gland
TFLSDLR


1:3000





protein AD-005; KIAA1007
(391)





protein isoform a;





KIAA1007 protein isoform b


 


S0670
DKFZ566O1646
25936
DC8; DKFZP566O1646 protein
KCRGETVAKEI
N/A
N/A
1:900



protein


SEAMKS






(392)


 


S0672
B-cell CLL/
605
BCL7A; B-cell CLL/
QRGSQIGREPI
N/A
N/A
1:800



lymphoma 7A

lymphoma-7; B-cell CLL/
GLSGD





lymphoma 7A
(393)


 


S0673
likely ortho-
28987
ART-4; NOB1P; adenocar-
KPPQETEKGH
N/A
N/A
1:50



log of mouse

cinoma antigen recognized
SACEPEN



nin one

by T lymphocytes 4; likely
(394)



binding

ortholog of mouse nin one



protein

binding protein


 


S0676
guanine
2768
RMP; NNX3; GNA12; GUANINE
ERRAGSGARD
N/A
N/A
1:1200-



nucleotide

NUCLEOTIDE-BINDING
AERE


1:2400



binding

PROTEIN, ALPHA-12; guanine
(395)



protein (G

nucleotide binding protein



protein) alpha

(G protein) alpha 12



12


 


S0677
GrpE-like 1,
80273
HMGE; GRPEL1; HUMAN MIRO-
SEQKADPPAT
N/A
N/A
1:500-



mitochondrial

CHONDRIAL GrpE PROTEIN;
EKTLLE


1:1000



(E. coli) 

GrpE-like 1, mitochondrial
(396)





(E. coli); GrpE, E. COLI,





HOMOLOG OF, 1


 


S0684
hypothetical
91607
FLJ34922; hypothetical
EAEWSQGVQ
N/A
N/A
1:8100



protein

protein FLJ34922
GTLRIKKYLT



FLJ34922


(397)


 


S0687
hypothetical
54942
FLJ20457; hypothetical
EESKSITEGLL
N/A
N/A
1:600-



protein

protein FLJ20457
TQKQYE


1:1260



FLJ20457


(398)


 


S0691
solute carrier
23657
CCBR1; SLC7A11; xCT;
QNFKDAFSGR
N/A
N/A
1:1000-



family 7,

cystine/glutamate
DSSITR


1:1575



(cationic

transporter; SYSTEM Xc(−)
(399)



amino acid

TRANSPORTER-RELATED



transporter,

PROTEIN; SOLUTE CARRIER



y+system)

FAMILY 7, MEMBER 11;



member 11

solute carrier family 7,





(cationic amino acid





transporter, y+system)





member 11


 


S0692
glutamate-
2729
GLCLC; GCLC; 6.3.2.2; GCS;
EKIHLDDANES
N/A
N/A
1:100-



cysteine

GAMMA-GLUTAMYLCYSTEINE
DHFEN


1:400



ligase,

SYNTHETASE, CATALYTIC
(400)



catalytic

SUBUNIT; glutamate-



subunit

cysteine ligase, catalytic





subunit


 


S0695
integrin, beta
3691
ITGB4; INTEGRIN, BETA-4;
TEDVDEFRNK
N/A
N/A
1:2700-



4

integrin, beta 4
LQGER


1:4050






(401)


 


S0702
solute carrier
8140
SLC7A5; MPE16; D16S469E;
KGDVSNLDPN
N/A
N/A
1:21160-



family 7

CD98; LAT1; 4F2 light
FSFEGTKLDV


1:178200



(cationic

chain; Membrane protein
(402)



amino acid

E16; L-TYPE AMINO ACID



transporter,

TRANSPORTER 1; Solute



y+system),

carrier family 7, member



member 5

5; solute carrier family





7 (cationic amino acid





transporter, y+system),





member 5


 


S0705
breast cancer
25855
DKFZp564A063; BRMS1;
KARAAVSPQK
N/A
N/A
1:1000-



metastasis

breast cancer metastasis-
RKSDGP


1:2000



suppressor 1

suppressor 1; breast
(403)





cancer metastasis





suppressor 1


 


S0706
KiSS-1
3814
MGC39258; KISS1; KiSS-1
RQIPAPQGAV
N/A
N/A
1:180



metastasis-

metastasis-suppressor;
LVQREKD



suppressor

KISS1 METASTIN; malignant
(404)





melanoma metastasis-





suppressor; KISS1





METASTASIS SUPPRESSOR


 


S0708
cofactor
9439
DKFZp434H0117; CRSP133;
SVKEQVELIIC
N/A
N/A
1:2430



required for

SUR2; DRIP130; CRSP3;
NLKPALK



Sp1 trans-

mediator; transcriptional
(138)



criptional

co-activator CRSP130;



activation,

CRSP; 130 KD SUBUNIT;



subunit 3,

CRSp 130 kD subunit;



130 kDa

133 kDa transcriptional





co-activator; 130 kDa





transcriptional co-





activator; vitamin D3





receptor interacting





protein; c


 












S5002
keratin 14
3861
CK; KRT14; K14; EBS4;
Antibody obtained from
1:50



(epidermolysis

EBS3; cytokeratin 14;
Chemicon



bullosa

CK 14; KERATIN, TYPE I



simplex,

CYTOSKELETAL 14;



Dowling-Meara,

keratin 14 (epider-



Koebner)

molysis bullosa simplex,





Dowling-Meara, Koebner)


 


S5003
keratin 17
3782
PCHC1; PC; PC2; 39.1;
Antibody obtained from Dako
1:10-1:25





KRT17; K17; CYTOKERATIN





17; VERSION 1; CK 17;





KERATIN, TYPE I CYTO-





SKELETAL 17


 


S5004
keratin 18
3875
K18; CYK18; KRT18; CYTO-
Antibody obtained from Dako
1:200-





KERATIN 18; CK 18;

1:400





KERATIN, TYPE I CYTO-





SKELETAL 18


 


S5005
keratin 18
3875
K18; CYK18; KRT18; CYTO-
Antibody obtained from
1:50-





KERATIN 18; CK 18;
Becton Dickinson
1:100





KERATIN, TYPE I CYTO-





SKELETAL 18


 


S5012
tumor-
4072
TROP1; LY74; Ep-CAM;
Antibody obtained from
1:40



associated

GA733-2; EGP40; MK-1;
Oncogene Research Products



calcium signal

CO17-1A; EPCAM; M4S1; KSA;
(Calbiochem)



transducer 1

TACSTD1; EGP; MK-1





antigen; EPITHELIAL





CELLULAR ADHESION





MOLECULE; GASTROINTESTINAL





TUMOR-ASSOCIATED ANTIGEN





2, 35 KD GLYCOPROTEIN;





tumor-associated calcium





signal transducer 1





precurso


 


S5014
estrogen
2100
ER-BETA; ESR-BETA; ESR2;
Antibody obtained from
1:2500



receptor 2

Erb; ESRB; NR3A2; ESTROGEN
Oncogene Research Products



(ER beta)

RECEPTOR, BETA; estrogen
(Calbiochem)





receptor 2 (ER beta)


 


S5038
mucin 1,
4582
PEMT; MUC1; episialin;
Antibody obtained from
1:1



transmembrane

EMA; PUM; H23AG; CD227;
Imperial Cancer Research





PEM; CARCINOMA-ASSOCIATED
Technology (ICRT)





MUCIN; H23 antigen;





TUMOR-ASSOCIATED MUCIN;





DF3 antigen; peanut-





reactive urinary mucin;





mucin 1, transmembrane;





polymorphic epithelial





mucin; MUCIN 1, URINARY;





MUCIN, TUMOR-ASSOCIATE


 


S5044
transferrin
7037
P90; TR; TFRC; TFR; CD71;
Antibody obained from
1:20



receptor (p90,

T9; TRFR; ANTIGEN CD71;
NeoMarkers



CD71)

TRANSFERRIN RECEPTOR





PROTEIN; transferrin





receptor (p90, CD71)


 


S5045
v-erb-b2
2064
HER-2; ERBB2; NGL;
Antibody obtained from
1:600



erythroblastic

P185ERBB2; HER2; C-ERBB-2;
NeoMarkers



leukemia viral

NEU; MLN 19; EC 2.7.1.112;



oncogene

TKR1 HERSTATIN; NEU PROTO-



homolog 2,

ONCOGENE; ONCOGENE ERBB2;



neuro/gliblas-

RECEPTOR PROTEIN-TYROSINE



toma derived

KINASE ERBB-2 PRECURSOR;



oncogene

ONCOGENE NGL, NEUROBLAS-



homolog

TOMA- OR GLIOBLASTOMA-



(avian)

DERIVED; TYROSINE KINASE-





TYPE CELL


 


S5047
major vault
9961
MVP; LRP; VAULT1; LUNG
Antibody obtained from
1:300



protein

LUNG RESISTANCE-RELATED
NeoMarkers





PROTEIN; MAJOR VAULT





PROTEIN, RAT, HOMOLOG OF


 


S5064
tumor protein
8626
LMS; TP73L; KET; SHFM4;
Antibody obtained from Dako
1:50



p73-like

p73H; EEC3; TP63; p51;





TUMOR PROTEIN p63; TUMOR





PROTEIN p73-LIKE; p53-





RELATED PROTEIN p63; tumor





protein 63 kDa with strong





homology to p53


 


S5065
estrogen
2099
ER; NR3A1; ESR1; Era; ESR;
Antibody obtained from Dako
1:20



receptor 1

ER-ALPHA; ESRA; ESTRADIOL





RECEPTOR; ESTROGEN





RECEPTOR, ALPHA; estrogen





receptor 1 (alpha)


 


S5066
v-erb-b2
2064
HER2; ERBB2; NGL;
Antibody obtained from Dako
1:300



erythroblastic

P185ERBB2; HER2; C-ERBB-2;



leukemia viral

NEU; MLN 19; EC 2.7.1.112;



oncogene

TKR1 HERSTATIN; NEU PROTO-



homolog 2,

ONCOGENE; ONCOGENE ERBB2;



neuro/gliblas-

RECEPTOR PROTEIN-TYROSINE



toma derived

KINASE ERBB-2 PRECURSOR;



oncogene

ONCOGENE NGL, NEUROBLAS-



homolog

TOMA- OR GLIOBLASTOMA-



(avian)

DERIVED; TYROSINE KINASE-





TYPE CELL


 


S5067
cathepsin D
1509
CTSD; MGC2311; CPSD; EC
Antibody obtained from Dako
1:20-1:50



(lysosomal

3.4.23.5; cathespin D



aspartyl

preporprotein; Cathepsin



protease)

D precursor; cathespin D





(lysosomal aspartyl





protease);


 


S5069
CA 125
n/a

Antibody obtained from Dako
1:20


 


S5070
CA 15-3
n/a

Antibody obtained from Dako
1:50


 


S5071
CA 19-9
n/a

Antibody obtained from Dako
1:50


 


S5072
v-myc myelo-
4609
c-Myc; MYC; ONCOGENE MYC;
Antibody obtained from Dako
1:50



cytomatosis

Myc proto-oncogene



viral oncogene

protein; PROTOONCOGENE



homolog

HOMOLOGOUS TO MYELOCYTO-



(avain)

MATOSIS VIRUS; v-myc





myelocytomatosis viral





oncogene homolog (avian);





v-myc avian myelocytoma-





tosis viral oncogene





homolog; Avian myelocyto-





matosis viral (v-myc)





onco


 


S5073
cadherin 1,
999
CDH1; Cadherin-1; Arc-1;
Antibody obtained from Dako
1:100-



type 1, E-

ECAD; CDHE; Uvomorulin;

1:150



cadherin

LCAM; Epithelial-cadherin



(epithelial)

precursor; cell-CAM





120/80; CADHERIN,





EPITHELIAL; calcium-





dependent adhesion





protein, epithelial;





cadherin 1, E-cadherin





(epithelial); cadherin 1,





type 1 preproprotein;





cadherin 1,


 


S5074
glutathione S-
2950
GSTP1; DFN7; GSTP1-1;
Antibody obtained from Dako
1:50



transferase pi

GST3; GSTPP; GST class-pi;





glutathione transferase;





EC 2.5.1.18; glutathione





S-transferase; pi; GST,





CLASS PI; deafness,





X-linked 7; GLUTATHIONE S-





TRANSFERASE 3; GLUTATHIONE





S-TRANSFERASE, PI; FAEES3





GLUTATHIONE S-TRANSFERASE





PI PSEUD


 


S5075
tumor protein
7157
p53; TP53; TRP53; PHOSPO-
Antibody obtained from Dako
1:50



p53 (Li-

PROTEIN P53; TRANSFORMA-



Fraumeni

TION-RELATED PROTEIN 53;



syndrome)

TUMOR SUPPRESSOR P53;





CELLULAR TUNOR ANTIGEN





P53; tumor protein p53





(Li-Fraumeni syndrome)


 


S5076
progesterone
5241
NR3C3; PR; PGR;
Antibody obtained from Dako
1:50



receptor

PROGESTERONE RESISTANCE;





PSEUDOCORPUS LUTEUM IN-





SUFFICIENCY PROGESTERONE





RECEPTOR


 


S5077
trefoil
7031

Antibody obtained from Dako
1:50-1:100



factor 1



(breast



cancer,



estrogen-



inducible



sequence



expressed in)


 


S5079
enolase 2,
2026
NSE; ENO2; 2-phospho-D-
Antibody obtained from Dako
1:400



(gamma,

glycerate hydro-lyase;



neuronal)

ENOLASE, GAMMA; neurone-





specific enolase; ENOLASE,





NEURON-SPECIFIC; 2-





phospho-D-glycerate





hydrolyase; EC 4.2.1.11;





Neural enolase; enolase-2,





gamma, neuronal; neuron





specific gamma enolase;





enolase 2, (gamma,


 


S5080
B-cell CLL/
596
BCL2; FOLLICULAR LYMPHOMA;
Antibody obtained from Dako
1:50



lymphoma 2

APOPTOSIS REGULATOR BCL-2;





B-cell CLL/lymphoma 2;





B-cell lymphoma protein 2





alpha; B-cell lymphoma





protein 2 beta; ONCOGENE





B-CELL LEUKEMIA 2





LEUKEMIA, CHRONIC





LYMPHATIC, TYPE 2


 


S5081
retinoblastoma
5925
p105-Rb; PP110; Retino-
Antibody obtained from Dako
1:20



1 (including

blastoma-1; RB; RB1;



osteosarcoma)

RETINOBLASTOMA-ASSOCIATED





PROTEIN; RB OSTEOSARCOMA,





RETINOBLASTOMA-RELATED;





retinoblastoma 1





(including osteosarcoma)


 


S5082
synaptophysin
6855
SYP; Synaptophysin; Major
Antibody obtained from Dako
1:50





synaptic vesicle protein





P38


 


S5083
BCL2-
581
BAX; BCL2-associated X
Antibody obtained from Dako
1:500



associated X

protein; APOPTOSIS



protein

REGULATOR BAX, MEMBRANE





ISOFORM ALPHA


 


S5086
estrogen
2100
ER-BETA; ESR-BETA; ESR2;
Antibody obtained from Abcam
1:200



receptor 2

Erb; ESRB; NR3A2;



(ER beta)

ESTROGEN RECEPTOR, BETA;





estrogen receptor 2





(ER beta)


 


S5087
mucin 1,
4582
PEMT; MUC1; episialin;
Antibody obtained from Zymed
1:200-



transmembrane

EMA; H23AG; CD227; PEM;

1:1600





CARCINOMA-ASSOCIATED





MUCIN; H23 antigen; TUMOR-





ASSOCIATED MUCIN; DF3





antigen; peanut-reactive





urinary mucin; mucin 1,





transmembrane; polymorphic





epithelial mucin; MUCIN 1,





URINARY; MUCIN, TUMOR-





ASSOCIATE


 


S6001
estrogen
2099
ER; NR3A1; ESR1; Era; ESR;
Antibody obtained from U.S. Labs
1:1



receptor 1

ER-ALPHA; ESRA; ESTRADIOL





RECEPTOR; ESTROGEN





RECEPTOR, ALPHA; estrogen





receptor 1 (alpha)


 


S6002
progesterone
5241
NR3C3; PR; PGR;
Antibody obtained from U.S. Labs
1:1



receptor

PROGESTERONE RESISTANCE;





PSEUDOCORPUS LUTEUM





INSUFFICIENCY PROGES-





TERONE RECEPTOR


 


S6003
v-erb-b2
2064
HER2; ERBB2; NGL;
Antibody obtained from U.S. Labs
1:1



erythroblastic

P185ERBB2; HER2; C-ERBB-2;



leukemia viral

NEU; MLN 19; EC 2.7.1.112;



oncogene

TKR1 HERSTATIN; NEU PROTO-



homolog 2,

ONCOGENE; ONCOGENE ERBB2;



neuro/gliblas-

RECEPTOR PROTEIN-TYROSINE



toma derived

KINASE ERBB-2 PRECURSOR;



oncogene

ONCOGENE NGL, NEUROBLAS-



homolog

TOMA- OR GLIOBLASTOMA-



(avian)

DERIVED; TYROSINE KINASE-





TYPE CELL


 


S6004
B-cell CLL/
596
BCL2; FOLLICULAR LYMPHOMA;
Antibody obtained from U.S. Labs
1:1



lymphoma 2

APOPTOSIS REGULATOR BCL-2;





B-cell CLL/lymphoma 2; B-





cell lymphoma protein 2





alpha; B-cell lymphoma





protein 2 beta; ONCOGENE





B-CELL LEUKEMIA 2





LEUKEMIA, CHRONIC





LYMPHATIC, TYPE 2


 


S6005
keratin 5
3852
KRT5; EBS2; Keratin-5; K5;
Antibody obtained from U.S. Labs
1:1



(epidermolysis

CYTOKERATIN 5; CK 5; 58



bullosa

KDA CYTOKERATIN; KERATIN,



simplex,

TYPE II CYTOSKELETAL 5;



Dowling-Meara/

keratin 5 (epidermolysis



Kobner/Weber-

bullosa simplex, Dowling-



Cockayne

Meara/Kobner/Weber-



types)

Cockayne types)


 


S6006
tumor protein
7157
p53; TP53; TRP53; PHOSPHO-
Antibody obtained from U.S. Labs
1:1



p53 (Li-

PROTEIN P53; TRANSFORMA-



Fraumeni

TION-RELATED PROTEIN 53;



syndrome)

TUMOUR SUPPRESSOR P53;





CELLULAR TUMOR ANTIGEN





P53; tumor protein p53





(Li-Fraumeni syndrome)


 


S6007
KI67
n/a

Antibody obtained from U.S. Labs
1:1


 


S6008
epidermal
1956
S7; EGFR; 2.7.1.11; ERBB;
Antibody obtained from U.S. Labs
1:1



growth factor

ONOGENE ERBB; ERBB1



receptor

SPECIES ANTIGEN 7; V-ERB-



(erythro-

B AVIAN ERYTHROBLASTIC



blastic

LEUKEMIA VIRAL ONCOGENE



leukemia viral

HOMOLOG; epidermal growth



(v-erb-b)

factor receptor (avian



oncogene

erythroblastic luekemia



homolog,

viral (v-erb-b) oncogene



avian)

homolog)


 


S6011
enolase 2,
2026
NSE; ENO2; 2-phospho-D-
Antibody obtained from U.S. Labs
1:1



(gamma,

glycerate hydro-lyase;



neuronal)

ENOLASE, GAMMA; neurone-





specific enolase; ENOLASE,





NEURON-SPECIFIC; 2-





phospho-D-glycerate





hydrolyase; EC 4.2.1.11;





Neural enolase; enolase-





2, gamma, neuronal;





neuron specific gamma





enolase; enolase 2,





(gamma,


 


S6012
thyroid trans-
7080
benign chorea; chorea,
Antibody obtained from U.S. Labs
1:1



cription

hereditary benign; NK-2



factor 1

(Drosophila) homolog A





(thyroid nuclear factor);





Thyroid transcription





factor 1 (NK-2,





Drosophila, homolog of,





A); BCH; BHC; TEBP; TTF1;





NKX2A; TTF-1; NKX2.1


 


S6013
v-erb-b2
2064
HER2; ERBB2; NGL;
Antibody obtained from U.S. Labs
1:1



erythroblastic

P185ERBB2; HER2; C-ERBB-2;



leukemia viral

NEU; MLN 19; EC 2.7.1.112;



oncogene

TKR1 HERSTATIN; NEU PROTO-



homolog 2,

ONCOGENE; ONCOGENE ERBB2;



neuro/gliblas-

RECEPTOR PROTEIN-TYROSINE



toma derived

KINASE ERBB-2 PRECURSOR;



oncogene

ONCOGENE NGL, NEUROBLAS-



homolog

TOMA- OR GLIOBLASTOMA-



(avian)

DERIVED; TYROSINE KINASE-





TYPE CELL

## Claims

1. A method for selecting a chemotherapy for a lung or ovarian cancer patient comprising steps of:
providing a cancer sample from a lung or ovarian cancer patient;
detecting the presence of expression of TLE3 in the cancer sample; and
selecting a taxane or taxane derivative for chemotherapy of the cancer patient when the TLE3 expression is present.

2. The method of claim 1, wherein the cancer patient has lung cancer.

3. The method of claim 2, wherein the step of selecting comprises selecting a taxane for chemotherapy.

4. The method of claim 3, wherein the taxane is paclitaxel.

5. The method of claim 3, wherein the taxane is docetaxel.

6. The method of claim 2, wherein the step of detecting comprises steps of:
providing a negative control sample;
detecting a level of TLE3 expression in the negative control sample;
detecting a level of TLE3 expression in the cancer sample; and
comparing the level of TLE3 expression in the cancer sample with the level of TLE3 expression in the negative control sample.

7. The method of claim 2, wherein the step of detecting comprises steps of:
providing a positive control sample;
detecting a level of TLE3 expression in the positive control sample;
detecting a level of TLE3 expression in the cancer sample; and
comparing the level of TLE3 expression in the cancer sample with the level of TLE3 expression in the positive control sample.

8. The method of claim 2, wherein the step of detecting comprises contacting the cancer sample with an interaction partner that binds a TLE3 polypeptide.

9. The method of claim 3, wherein the step of detecting comprises contacting the cancer sample with an interaction partner that binds a TLE3 polypeptide.

10. The method of claim 4, wherein the step of detecting comprises contacting the cancer sample with an interaction partner that binds a TLE3 polypeptide.

11. The method of claim 5, wherein the step of detecting comprises contacting the cancer sample with an interaction partner that binds a TLE3 polypeptide.

12. The method of claim 8, wherein the interaction partner is an antibody.

13. The method of claim 9, wherein the interaction partner is an antibody.

14. The method of claim 10, wherein the interaction partner is an antibody.

15. The method of claim 11, wherein the interaction partner is an antibody.

16. The method of claim 2, wherein the step of detecting comprises contacting the cancer sample with one or more primers that hybridize with a TLE3 polynucleotide.

17. The method of claim 3, wherein the step of detecting comprises contacting the cancer sample with one or more primers that hybridize with a TLE3 polynucleotide.

18. The method of claim 4, wherein the step of detecting comprises contacting the cancer sample with one or more primers that hybridize with a TLE3 polynucleotide.

19. The method of claim 5, wherein the step of detecting comprises contacting the cancer sample with one or more primers that hybridize with a TLE3 polynucleotide.

20. The method of claim 1, wherein the cancer patient has ovarian cancer.

21. The method of claim 20, wherein the step of selecting comprises selecting a taxane for chemotherapy.

22. The method of claim 21, wherein the taxane is paclitaxel.

23. The method of claim 21, wherein the taxane is docetaxel.

24. The method of claim 20, wherein the step of detecting comprises steps of:
providing a negative control sample;
detecting a level of TLE3 expression in the negative control sample;
detecting a level of TLE3 expression in the cancer sample; and
comparing the level of TLE3 expression in the cancer sample with the level of TLE3 expression in the negative control sample.

25. The method of claim 20, wherein the step of detecting comprises steps of:
providing a positive control sample;
detecting a level of TLE3 expression in the positive control sample;
detecting a level of TLE3 expression in the cancer sample; and
comparing the level of TLE3 expression in the cancer sample with the level of TLE3 expression in the positive control sample.

26. The method of claim 20, wherein the step of detecting comprises contacting the cancer sample with an interaction partner that binds a TLE3 polypeptide.

27. The method of claim 21, wherein the step of detecting comprises contacting the cancer sample with an interaction partner that binds a TLE3 polypeptide.

28. The method of claim 22, wherein the step of detecting comprises contacting the cancer sample with an interaction partner that binds a TLE3 polypeptide.

29. The method of claim 23, wherein the step of detecting comprises contacting the cancer sample with an interaction partner that binds a TLE3 polypeptide.

30. The method of claim 26, wherein the interaction partner is an antibody.

31. The method of claim 27, wherein the interaction partner is an antibody.

32. The method of claim 28, wherein the interaction partner is an antibody.

33. The method of claim 29, wherein the interaction partner is an antibody.

34. The method of claim 20, wherein the step of detecting comprises contacting the cancer sample with one or more primers that hybridize with a TLE3 polynucleotide.

35. The method of claim 21, wherein the step of detecting comprises contacting the cancer sample with one or more primers that hybridize with a TLE3 polynucleotide.

36. The method of claim 22, wherein the step of detecting comprises contacting the cancer sample with one or more primers that hybridize with a TLE3 polynucleotide.

37. The method of claim 23, wherein the step of detecting comprises contacting the cancer sample with one or more primers that hybridize with a TLE3 polynucleotide.