US 20070105105A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2007/0105105 A1 Clelland et al. (43) Pub. Date: May 10, 2007 (54) SURROGATE CELL GENE EXPRESSION Related U.S. Application Data SIGNATURES FOR EVALUATING THE PHYSICAL STATE OF A SUBJECT (60) Provisional application No. 60/473,089, filed on May 23, 2003. (75) Inventors: Catherine Clelland, New York, NY (US); F. Carter Bancroft, Huntington, Publication Classification NY (US); James Clelland, New York, NY (US) (51) Int. Cl. CI2O I/68 (2006.01) Correspondence Address: CI2P 19/34 (2006.01) DARBY & DARBY P.C. (52) U.S. Cl. ............................................... 435/6; 435/91.2 P. O. BOX 5257 NEW YORK, NY 10150-5257 (US) (57) ABSTRACT (73) Assignees: Mount Sinai School of Medicine of New York University, New York, NY (US); The present invention relates to non-invasive and minimally Research Foundation for Mental invasive techniques for evaluating the physical State of a Hygiene, Menands, NY (US) Subject, including diagnosing a disease, disorder, or physical state of the Subject, determining the prognosis of the Subject, (21) Appl. No.: 10/558,277 determining a Subject's Susceptibility for a disease, disorder, (22) PCT Filed: May 24, 2004 or physical state and determining, developing and monitor ing treatment for the same. The invention also relates to (86). PCT No.: PCT/USO4f16365 identifying genetic alterations contributing to, or Suscepti bility for, development of a disease, disorder, or physical S 371(c)(1), state, and for diagnosis, prognosis and treatment of the (2), (4) Date: Dec. 15, 2006 disease, disorder, or physical state. Patent Application Publication May 10, 2007 Sheet 1 of 6 US 2007/0105105 A1 Figure 1 Patent Application Publication May 10, 2007 Sheet 3 of 6 US 2007/0105105 A1 |Effff-3) Figure 3 Patent Application Publication May 10, 2007 Sheet 4 of 6 US 2007/0105105 A1 4A Patent Application Publication May 10, 2007 Sheet 5 of 6 US 2007/0105105 A1 " Figure 5 Patent Application Publication May 10, 2007 Sheet 6 of 6 US 2007/0105105 A1 tractoratar rungsteres segree eggs Figure 6 US 2007/01 05105 A1 May 10, 2007 SURROGATE CELL GENE EXPRESSION Schizophrenia or not too well understood such as in Alzhe SIGNATURES FOR EVALUATING THE PHYSICAL imer's disease, still depend mainly on behavioral evaluation STATE OF A SUBJECT of patients, and no clinically proven, blood-based, tests are available to date. Individual circulating biomarkers, how 0001. This application claims priority from U.S. Provi ever, are beginning to be discovered. In Alzheimer's disease, sional Patent Application No. 60/473,089, filed May 23, for instance, a serum elevation of the iron transporter p97 2003, which is herein incorporated by reference in its (Kim DK, et al. Neuropsychopharmacology 2001; 25(1):84 entirety. 90) or an increase in antibody-mediated brain to plasma 0002 The research leading to this invention was sup amyloid-beta efflux (DeMattos R B, et al., Science 2002, ported, in part, by Grant No. 1 RO3 MH62428-01 awarded 295:2264-2267) have been described. Furthermore, Ilani et by the National Institutes of Mental Health. Accordingly, the al. have shown an increased level of D3 dopamine receptor United States government may have certain rights to this mRNA in circulating blood lymphocytes in individuals with invention. schizophrenia (Ilani et al. Proc Natl Acad Sci USA 2001; FIELD OF THE INVENTION 98(2):625-8). 0008 For cancer, diagnostic tests based on single circu 0003. The present invention relates to non-invasive and lating biomarkers possess a number of limitations, including minimally invasive techniques for evaluating the physical lack of specificity and sensitivity in the diagnosis and, also state of a Subject, including diagnosing a disease, disorder, a lack of prognostic information. This ultimately yields high or physical state of the Subject, determining the prognosis of numbers of false positive diagnoses, and consequently the Subject, determining a Subject's Susceptibility for a unnecessarily large numbers of Surgical biopsies. Alterna disease, disorder, or physical state and determining, devel tively, in a significant number of patients malignancies oping and monitoring treatment for the same. The invention evade detection due to the inherent rate of false negative test also relates to identifying genetic alterations contributing to, results. or Susceptibility for, development of a disease, disorder, or physical state, and for diagnosis, prognosis and treatment of 0009. There is growing evidence that individuals with a the disease, disorder, or physical state. malignant disease such as breast cancer or prostate cancer, exhibit immune responses that can be detected at the level of BACKGROUND OF THE INVENTION altered gene expression in leukocytes circulating in periph 0004 Although cancer mortality rates have decreased eral blood. Quantitation of the mRNA transcripts in leuko over the past decade, through pre-symptomatic screening cytes of a number of individual genes has demonstrated programs and major improvements in cancer treatment, associations between gene expression levels and the pres Survival rates are still low in patients presenting with a more ence of a tumor in patients with breast and prostate cancer. advanced stage cancer at the time of diagnosis. Thus, 0010. The recent development of microarray technology effective management of any cancer relies heavily on an has permitted simultaneous measurement of the expression early diagnosis, coupled with a need to obtain accurate levels of thousands of genes, and also allowed a comparison information on the classification and stage of the cancer of multiple data sets between multiple experiments. Inves itself, and thus limitations of traditional diagnostic and tigators have begun to employ this technology, based upon prognostic techniques may currently hinder the management sample cDNA probe hybridization to DNA-based microar of cancer. rays, to identify and isolate genes differentially expressed 0005 Current techniques for the screening and risk among many tissues and cell lines. Microarray technology assessment of chronic disease States in general, and cancer will become a global gene expression diagnostic tool (Cole in particular, are frequently based upon the measurement of et al., Nat. Genet. 1999: 21 (1 Suppl):38-1; Howell S B, Mol either individual serum biomarkers, or expression of indi Urol. 1999; 3(3):295-300). Already, breakthrough experi vidual genes in circulating cells, such as disseminated tumor ments have shown that molecular profiles, or gene expres cells. In disease states for which Such non-invasive tests are sion signatures, can be deduced from microarray expression available they usually comprise a prerequisite to more analysis of tumor samples. Researchers have used statistical invasive, Surgical biopsy procedures. algorithms to compare individual expression signatures, and then employed these comparisons to distinguish between 0006 Examples of serum biomarkers used in the clinical forms of myeloid leukemia (Golub et al., Science 1999; diagnosis of cancer include CA 125 (ovarian cancer), CA 286(5439):531-7), and B-cell lymphoma (Alizadeh et al. 15-3 and CA 27-29 (breast cancer), carcinoembryonic anti Nature 2000; 403(6769):503-11). Furthermore, analysis of gen, CEA (ovarian, lung, breast, pancreas, and gastrointes tumor tissue from individual patients has permitted identi tinal tract cancers), prostate specific antigen, PSA (prostate fication of both stages and individual classes of breast cancer cancer), alpha fetoprotein, AFP (primary liver cancer or (Perou et al., Nature 2000: 406(6797):747-52), malignant germ cell cancer), human chorionic gonadotropin, HCG melanoma (Bittner et al., Nature 2000: 406(6795):536-40), (choriocarcinoma, cancers of the testis, ovary, liver, stom and prostate cancer (Dhanasekaran et al., Nature 2001; ach, pancreas, and lung) CA 19-9 (colorectal cancer pan 412(6849):822-6: Luo et al., Mol Carcinog 2002: 33(1):25 creatic, stomach, and bile duct cancer) neuron-specific eno 35). Additionally, utilizing microarray technology vant Veer lase, NSE (neuroblastoma; small cell lung cancer; Wilms et al., have shown that the clinical status and clinical tumor, melanoma; and cancers of the thyroid, kidney, tes outcome of breast cancer can be predicted by gene expres ticle, and pancreas (Source: National Cancer Institute, on the sion analysis of tumor tissue (Nature 2002; 415(6871):530 Worldwide Web at nci.nih.gov) 6). 0007 Diagnosis of psychiatric and neurological diseases 0011 Even at this early stage in the clinical development for which the molecular etiology is largely unknown, Such as of this technology, it is becoming clear that microarray US 2007/01 05105 A1 May 10, 2007 analysis will be able to provide important diagnostic and MLH1 in prostate cancer (Strom et al., Prostate 2001; 1; prognostic information for many tumor types. However, 47(4):269-75). Strom et al., performed RT-PCR analysis of although these investigations of Solid tumors provide leukocyte samples from 70 prostate cancer Subjects (meta detailed information on the pathology and malignant process static patients were excluded from this study), and 97 of the tumor, invasive Surgery or biopsy is always necessary matched controls. Their results implied that although con to obtain the tumor tissue studied, and although investiga siderable variation occurred among patients, the mean tions are underway to determine the feasibility of minimally expression levels for both genes were significantly lower in traumatic biopsy sampling procedures for obtaining tissue the patients than controls. Although the authors conclude for microarray analysis, a current report documents prob that decreased expression of MLH1 is a risk factor for lems such as very low yields of extracted RNA (Assersohn prostate cancer, they also state that the decreased expression et al., Clin Cancer Res. 2002; 8(3):794-801). of both genes may be caused by disease status, a conclusion that is consistent with this hypothesis. The present invention 0012. A link between cancer and altered gene expression provides preliminary data that reproduces these results.