Supplementary Table 1: Genes on the Array and Their Known Link to Cancer

Supplementary Table 1: Genes on the array and their known link to cancer.

REFERENCES CITED

1.Sethi, S., Benninger, M.S., Lu, M., Havard, S. & Worsham, M.J. Noninvasive molecular detection of head and neck squamous cell carcinoma: an exploratory analysis. Diagn Mol Pathol18, 81-7 (2009).

2.Dasari, V.K. et al. Expression analysis of Y chromosome genes in human prostate cancer. J Urol165, 1335-41 (2001).

3.Tsuei, D.J., Chang, M.H., Chen, P.J., Hsu, T.Y. & Ni, Y.H. Characterization of integration patterns and flanking cellular sequences of hepatitis B virus in childhood hepatocellular carcinomas. J Med Virol68, 513-21 (2002).

4.Tsuei, D.J. et al. RBMY, a male germ cell-specific RNA-binding protein, activated in human liver cancers and transforms rodent fibroblasts. Oncogene23, 5815-22 (2004).

5.Tabernero, M.D. et al. Patient gender is associated with distinct patterns of chromosomal abnormalities and sex chromosome linked gene-expression profiles in meningiomas. Oncologist12, 1225-36 (2007).

6.Bianco, B., Lipay, M., Guedes, A., Oliveira, K. & Verreschi, I.T. SRY gene increases the risk of developing gonadoblastoma and/or nontumoral gonadal lesions in Turner syndrome. Int J Gynecol Pathol28, 197-202 (2009).

7.Deng, S. et al. Over-expression of genes and proteins of ubiquitin specific peptidases (USPs) and proteasome subunits (PSs) in breast cancer tissue observed by the methods of RFDD-PCR and proteomics. Breast Cancer Res Treat104, 21-30 (2007).

8.Nava, V.E., Hobson, J.P., Murthy, S., Milstien, S. & Spiegel, S. Sphingosine kinase type 1 promotes estrogen-dependent tumorigenesis of breast cancer MCF-7 cells. Exp Cell Res281, 115-27 (2002).

9.Sarkar, S. et al. Sphingosine kinase 1 is required for migration, proliferation and survival of MCF-7 human breast cancer cells. FEBS Lett579, 5313-7 (2005).

10.Sukocheva, O., Wang, L., Verrier, E., Vadas, M.A. & Xia, P. Restoring endocrine response in breast cancer cells by inhibition of the sphingosine kinase-1 signaling pathway. Endocrinology150, 4484-92 (2009).

11.Ruckhaberle, E. et al. Microarray analysis of altered sphingolipid metabolism reveals prognostic significance of sphingosine kinase 1 in breast cancer. Breast Cancer Res Treat112, 41-52 (2008).

12.Imamura, T., Miyauchi-Senda, N., Tanaka, S. & Shiota, K. Identification of genetic and epigenetic similarities of SPHK1/Sphk1 in mammals. J Vet Med Sci66, 1387-93 (2004).

13.Dessen P., L.M.S. in Atlas of Genetics and Cytogenetics in Oncology and Haematology (2002).

14.Dessen P., L.M.S. in Atlas of Genetics and Cytogenetics in Oncology and Haematology (2002).

15.Kohno, T. et al. Aberrant expression of BAFF receptor, a member of the tumor necrosis factor receptor family, in malignant cells of nonhematopoietic origins. Genes Cells13, 1061-73 (2008).

16.Paterson, J.C. et al. The differential expression of LCK and BAFF-receptor and their role in apoptosis in human lymphomas. Haematologica91, 772-80 (2006).

17.Rodig, S.J., Shahsafaei, A., Li, B., Mackay, C.R. & Dorfman, D.M. BAFF-R, the major B cell-activating factor receptor, is expressed on most mature B cells and B-cell lymphoproliferative disorders. Hum Pathol36, 1113-9 (2005).

18.Novak, A.J. et al. Expression of BCMA, TACI, and BAFF-R in multiple myeloma: a mechanism for growth and survival. Blood103, 689-94 (2004).

19.Chen, Y. & Hughes-Fulford, M. Human prostate cancer cells lack feedback regulation of low-density lipoprotein receptor and its regulator, SREBP2. Int J Cancer91, 41-5 (2001).

20.Ettinger, S.L. et al. Dysregulation of sterol response element-binding proteins and downstream effectors in prostate cancer during progression to androgen independence. Cancer Res64, 2212-21 (2004).

21.Brickner, A.G. et al. The PANE1 gene encodes a novel human minor histocompatibility antigen that is selectively expressed in B-lymphoid cells and B-CLL. Blood107, 3779-86 (2006).

22.Katoh, M. Characterization of human ARHGAP10 gene in silico. Int J Oncol25, 1201-6 (2004).

23.Katoh, Y. & Katoh, M. Identification and characterization of ARHGAP27 gene in silico. Int J Mol Med14, 943-7 (2004).

24.Dessen P., L.M.S. in Atlas of Genetics and Cytogenetics in Oncology and Haematology (2002).

25.Abiko, Y. et al. Immunohistochemical localization of amelogenin in human odontogenic tumors, using a polyclonal antibody against bovine amelogenin. Med Electron Microsc34, 185-9 (2001).

26.Gibson, C.W. et al. Transgenic mice that express normal and mutated amelogenins. J Dent Res86, 331-5 (2007).

27.Vey, N. et al. Identification of new classes among acute myelogenous leukaemias with normal karyotype using gene expression profiling. Oncogene23, 9381-91 (2004).

28.Manohar, C.F., Salwen, H.R., Furtado, M.R. & Cohn, S.L. Up-regulation of HOXC6, HOXD1, and HOXD8 homeobox gene expression in human neuroblastoma cells following chemical induction of differentiation. Tumour Biol17, 34-47 (1996).

29.Jacinto, F.V., Ballestar, E., Ropero, S. & Esteller, M. Discovery of epigenetically silenced genes by methylated DNA immunoprecipitation in colon cancer cells. Cancer Res67, 11481-6 (2007).

30.Rauch, T., Li, H., Wu, X. & Pfeifer, G.P. MIRA-assisted microarray analysis, a new technology for the determination of DNA methylation patterns, identifies frequent methylation of homeodomain-containing genes in lung cancer cells. Cancer Res66, 7939-47 (2006).

31.Makiyama, K. et al. Aberrant expression of HOX genes in human invasive breast carcinoma. Oncol Rep13, 673-9 (2005).

32.Furuta, J. et al. Silencing of Peroxiredoxin 2 and aberrant methylation of 33 CpG islands in putative promoter regions in human malignant melanomas. Cancer Res66, 6080-6 (2006).

33.Tan, Y. et al. Transcriptional inhibiton of Hoxd4 expression by miRNA-10a in human breast cancer cells. BMC Mol Biol10, 12 (2009).

34.Cantile, M. et al. HOX D13 expression across 79 tumor tissue types. Int J Cancer125, 1532-41 (2009).

35.Miyamoto, K. et al. Identification of 20 genes aberrantly methylated in human breast cancers. Int J Cancer116, 407-14 (2005).

36.Kron, K. et al. Discovery of novel hypermethylated genes in prostate cancer using genomic CpG island microarrays. PLoS One4, e4830 (2009).

37.Fassan, M. et al. MicroRNA expression profiling of male breast cancer. Breast Cancer Res11, R58 (2009).

38.Carrio, M., Arderiu, G., Myers, C. & Boudreau, N.J. Homeobox D10 induces phenotypic reversion of breast tumor cells in a three-dimensional culture model. Cancer Res65, 7177-85 (2005).

39.Hoene, V. et al. GATA factors in human neuroblastoma: distinctive expression patterns in clinical subtypes. Br J Cancer101, 1481-9 (2009).

40.Yang, Z. et al. Increased c-Jun expression and reduced GATA2 expression promote aberrant monocytic differentiation induced by activating PTPN11 mutants. Mol Cell Biol29, 4376-93 (2009).

41.Zhang, S.J., Shi, J.Y. & Li, J.Y. GATA-2 L359 V mutation is exclusively associated with CML progression but not other hematological malignancies and GATA-2 P250A is a novel single nucleotide polymorphism. Leuk Res33, 1141-3 (2009).

42.Ben-Porath, I. et al. An embryonic stem cell-like gene expression signature in poorly differentiated aggressive human tumors. Nat Genet40, 499-507 (2008).

43.Suomela, S. et al. HCR, a candidate gene for psoriasis, is expressed differently in psoriasis and other hyperproliferative skin disorders and is downregulated by interferon-gamma in keratinocytes. J Invest Dermatol121, 1360-4 (2003).

44.Harada, T. et al. Genome-wide DNA copy number analysis in pancreatic cancer using high-density single nucleotide polymorphism arrays. Oncogene27, 1951-60 (2008).

45.Gu, Z.D. et al. HOXA13 promotes cancer cell growth and predicts poor survival of patients with esophageal squamous cell carcinoma. Cancer Res69, 4969-73 (2009).

46.Lui, W.O. et al. CREB3L2-PPARgamma fusion mutation identifies a thyroid signaling pathway regulated by intramembrane proteolysis. Cancer Res68, 7156-64 (2008).

47.Thomas, G. et al. Multiple loci identified in a genome-wide association study of prostate cancer. Nat Genet40, 310-5 (2008).

48.Nagaraja, G.M. & Kandpal, R.P. Chromosome 13q12 encoded Rho GTPase activating protein suppresses growth of breast carcinoma cells, and yeast two-hybrid screen shows its interaction with several proteins. Biochem Biophys Res Commun313, 654-65 (2004).

49.Reynolds, P.A. et al. Tumor suppressor p16INK4A regulates polycomb-mediated DNA hypermethylation in human mammary epithelial cells. J Biol Chem281, 24790-802 (2006).

50.Strathdee, G. et al. Inactivation of HOXA genes by hypermethylation in myeloid and lymphoid malignancy is frequent and associated with poor prognosis. Clin Cancer Res13, 5048-55 (2007).

51.Rossi Degl'Innocenti, D. et al. Quantitative expression of the homeobox and integrin genes in human gastric carcinoma. Int J Mol Med20, 621-9 (2007).

52.Ota, T., Gilks, C.B., Longacre, T., Leung, P.C. & Auersperg, N. HOXA7 in epithelial ovarian cancer: interrelationships between differentiation and clinical features. Reprod Sci14, 605-14 (2007).

53.Wu, X. et al. Cooperation between EZH2, NSPc1-mediated histone H2A ubiquitination and Dnmt1 in HOX gene silencing. Nucleic Acids Res36, 3590-9 (2008).

54.Rauch, T. et al. Homeobox gene methylation in lung cancer studied by genome-wide analysis with a microarray-based methylated CpG island recovery assay. Proc Natl Acad Sci U S A104, 5527-32 (2007).

55.Martinez, R. et al. A microarray-based DNA methylation study of glioblastoma multiforme. Epigenetics4, 255-64 (2009).

56.Klausen, C., Leung, P.C. & Auersperg, N. Cell motility and spreading are suppressed by HOXA4 in ovarian cancer cells: possible involvement of beta1 integrin. Mol Cancer Res7, 1425-37 (2009).

57.Mohankumar, K.M. et al. HOXA1-stimulated oncogenicity is mediated by selective upregulation of components of the p44/42 MAP kinase pathway in human mammary carcinoma cells. Oncogene26, 3998-4008 (2007).

58.Tsou, J.A. et al. Identification of a panel of sensitive and specific DNA methylation markers for lung adenocarcinoma. Mol Cancer6, 70 (2007).

59.Henderson, G.S., van Diest, P.J., Burger, H., Russo, J. & Raman, V. Expression pattern of a homeotic gene, HOXA5, in normal breast and in breast tumors. Cell Oncol28, 305-13 (2006).

60.Watson, R.E., Curtin, G.M., Hellmann, G.M., Doolittle, D.J. & Goodman, J.I. Increased DNA methylation in the HoxA5 promoter region correlates with decreased expression of the gene during tumor promotion. Mol Carcinog41, 54-66 (2004).

61.Drabkin, H.A. et al. Quantitative HOX expression in chromosomally defined subsets of acute myelogenous leukemia. Leukemia16, 186-95 (2002).

62.Chu, M.C., Selam, F.B. & Taylor, H.S. HOXA10 regulates p53 expression and matrigel invasion in human breast cancer cells. Cancer Biol Ther3, 568-72 (2004).

63.Antoniou, A.C. et al. Common variants in LSP1, 2q35 and 8q24 and breast cancer risk for BRCA1 and BRCA2 mutation carriers. Hum Mol Genet18, 4442-56 (2009).

64.Meng, L., Lin, T. & Tsai, R.Y. Nucleoplasmic mobilization of nucleostemin stabilizes MDM2 and promotes G2-M progression and cell survival. J Cell Sci121, 4037-46 (2008).

Supplementary Table 2: Primers for MassArray and qRT-PCR.

Supplementary Table 3: Fine mapping of MassArray primers for validation and high-resolution studies.

Supplementary Table 4:

Detailed list of loci differentially methylated between the primary tumors and the lung metastasis.