Compositions, kits, and methods for identification, assessment, prevention, and therapy of cancer

#Cancer represents the phenotypic end-point of multiple genetic lesions that endow cells with a full range of biological properties required for tumorigenesis. Indeed, a hallmark genomic feature of many cancers, including, for example, B cell cancer, lung cancer, breast cancer, ovarian cancer, pancreatic cancer, and colon cancer, is the presence of numerous complex chromosome structural aberrations—including non-reciprocal translocations, amplifications and deletions.

#Karyotype analyses (Johansson, B., et al. (1992) Cancer 69, 1674-81; Bardi, G., et al. (1993) Br J Cancer 67, 1106-12; Griffin, C. A., et al. (1994) Genes Chromosomes Cancer 9, 93-100; Griffin, C. A., et al. (1995) Cancer Res 55, 2394-9; Gorunova, L., et al. (1995) Genes Chromosomes Cancer 14, 259-66; Gorunova, L., et al. (1998) Genes Chromosomes Cancer 23, 81-99), chromosomal CGH and array CGH (Wolf M et al. (2004) Neoplasia 6(3)240; Kimura Y, et al. (2004) Mod. Pathol. 21 May (epub); Finkel, et al. (1998) Nature Genetics 20:211; Solinas-Toldo, S., et al. (1996) Cancer Res 56, 3803-7; Mahlamaki, E. H., et al. (1997) Genes Chromosomes Cancer 20, 383-91; Mahlamaki, E. H., et al. (2002) Genes Chromosomes Cancer 35, 353-8; Fukushige, S., et al. (1997) Genes Chromosomes Cancer 19:161-9; Curtis, L. J., et al. (1998) Genomics 53, 42-55; Ghadimi, B. M., et al. (1999) Am J Pathol 154, 525-36; Armengol, G., et al. (2000) Cancer Genet Cytogenet 116, 133-41), fluorescence in situ hybridization (FISH) analysis (Nilsson M et al. (2004) Int J Cancer 109(3):363-9; Kawasaki K et al. (2003) Int J Mol Med. 12(5):727-31) and loss of heterozygosity (LOH) mapping (Wang Z C et al. (2004) Cancer Res 64(1):64-71; Seymour, A. B., et al. (1994) Cancer Res 54, 2761-4; Hahn, S. A., et al. (1995) Cancer Res 55, 4670-5; Kimura, M., et al. (1996) Genes Chromosomes Cancer 17, 88-93) have identified recurrent regions of copy number change or allelic loss in various cancers.

#Multiple Myeloma (MM) is characterized by clonal proliferation of abnormal plasma cells in the bone marrow, usually with elevated serum and urine monoclonal paraprotein levels and associated end-organ sequelae. MM accounts for more than 10% of all hematological malignancies and is the second most frequent hematological cancer in the US after non-Hodgkin lymphoma. MM is typically preceded by an age-progressive condition termed Monoclonal Gammopathy of Undetermined Significance (MGUS), a condition present in 1% of adults over age of 25 that progresses to malignant MM at a rate of 0.5-3% per year (Kyle, R. A., and Rajkumar, S. V. (2004) N Engl J Med 351, 1860-1873; Mitsiades et al. (2004) Cancer Cell 6, 439-444; Bergsagel et al. (2005) Blood 106, 296-303). MM remains incurable despite high-dose chemotherapy with stem cell support. Novel agents such as thalidomide, the immunoregulator Revlimid, and the proteasome inhibitor bortezomid can achieve responses in patients with relapsed and refractory MM, however, the median survival remains at 6 years with only 10% of the patients surviving at 10 years (Barlogie et al. (2004) Blood 103, 20-32; Richardson et al. (2005) Best Pract Res Clin Haematol 18, 619-634; Rajkumar, S. V., and Kyle, R. A. (2005) Mayo Clin Proc 80, 1371-1382).

#FIGS. 1A-B depict a gNMF classification wherein rank K=2, identifies two subgroups, kA and kB, reminiscent of the MM hyperdiploid/non-hyperdiploid subgroups. (A). The aCGH profiles of 67 clinically annotated primary tumors were subjected to NMF analyses (1000 repetitions). With rank k=2, two distinct subgroups kA and kB were identified (y axis) and the centroids of each group are shown. The x-axis coordinate represents genomic map order (from chr1 to chr22). The colors denote gain (red), euploid (yellow/green) or deleted (blue) chromosome material. (B). Kaplan-Meier event-free-survival (EFS; left) and overall survival (OS; right) curves for 64 MM patients demonstrate no significant difference in survival (p=0.25 and 0.1 respectively) when divided into subgroups kA vs. kB.

#FIGS. 2A-B depict a gNMF classification wherein rank K=4 identifies 4 distinct subgroups (A). The aCGH profiles of 67 clinically annotated primary tumors were subjected to NMF analyses (1000 repetitions). y-axis indicates the 4 subgroups identified by NMF. The x-axis coordinate represents genomic map order (from chr1 top chr22). The colors denote gain (red), euploid (yellow/green) or deleted (blue) chromosome material. (B). Kaplan-Meier event-free-survival (EFS; left) and overall survival (OS; right) curves for 64 MM patients for k1 and k2 subgroups. k1 shows significantly better event-free-survival than k2 (p=0.012) while OS did not reach statistical significance (p=0.12).

#FIGS. 3A-B depict a distribution of genes differentially expressed between k1 and k2 subgroups and residing on chromosomes 1q (A) and 13 (B). Expression probe sets (Affymetrix) are mapped to their respective genomic positions and are shown as vertical hash marks along the bottom of each plot. Black hash marks denote genes found to be differentially expressed between k1 and k2 subgroups by SAM (see methods). Count of significant genes within a moving 10 MB window is shown (y-axis) and asterisks indicate the center of regions of significant clustering (p<0.05 by permutation testing). The significant region spans approximately 143-158 MB for ch1 and 38-50 MB for ch13, though boundaries are approximate based on the moving window width.

#Table 1 shows high-confidence MCRs in Multiple Myeloma: Gains and Amplifications. For each MCR, the number of NCBI known genes is reported. Number of transcripts is based on Build 35 of the National Center for Biotechnology Information. Within the amplified MCR, some of the genes showing both copy number-driven expression and overexpression also in the absence of amplification (see Materials and Methods) are reported (candidate genes). In bold face MCRs validated by QPCR and/or FISH, Black diamonds identify MCRs associated with poor survival (PS-MCRs). MCR recurrence is denoted as percentage of the total dataset. Only the known genes within the boundaries have been included. Known hotspots for proviral integration residing within MCRs and MCR containing microRNAs are indicated. The MCR in 1q was subjected to further fine mapping (FIG. 7).

#Table 2 shows high-confidence MCRs in Multiple Myeloma: Losses and Deletions. For each MCR, the number of NCBI known genes is reported. Number of transcripts is based on Build 35 of the National Center for Biotechnology Information. In bold face MCRs validated by QPCR and/or FISH, Black diamonds identify MCRs associated with poor survival (PS-MCRs). Potential tumor suppressor genes residing within the MCRs are indicated. Known hotspots for proviral integration residing within MCRs and MCR containing microRNAs are indicated. The MCR at 11q11 has recently been shown by Sebat et al. (Sebat et al., 2004) to be a copy number polymorphism (ORF511, chromosome 11q11).

#Table 3 is a list of CD138 purified primary tumor cells subjected to aCGH and expression profiling analysis. Clinical outcome information is provided for the 64 tumor samples on which this information was available.