A function-blocking CD47 antibody suppresses stem cell and EGF signaling in triple-negative breast cancer

Oncotarget

Volumn 7, Issue 9, 2016, Pages 10133-10152

  Kaur, Sukhbir ^a   Elkahloun, Abdel G ^b   Singh, Satya P ^c   Chen, Qing Rong ^a   Meerzaman, Daoud M ^a   Song, Timothy ^a   Manu, Nidhi ^a   Wu, Weiwei ^b   Mannan, Poonam ^a   Garfield, Susan H ^a   Roberts, David D ^a  

^a NATIONAL CANCER INSTITUTE   (United States)

^b NATIONAL HUMAN GENOME RESEARCH INSTITUTE   (United States)

^c NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES   (United States)

Author keywords

Cancer stem cells; CD47; Epidermal growth factor receptor; Therapeutic antibodies; Triple negative breast cancer

Indexed keywords

ANTIBODY; B6H12 ANTIBODY; CD47 ANTIBODY; CELL ANTIBODY; EPIDERMAL GROWTH FACTOR; EPIDERMAL GROWTH FACTOR RECEPTOR; KRUPPEL LIKE FACTOR 4; MESSENGER RNA; MICRORNA; UNCLASSIFIED DRUG; BLOCKING ANTIBODY; CD47 ANTIGEN; CD47 PROTEIN, HUMAN; DIFFERENTIATION ANTIGEN; IMMUNOGLOBULIN RECEPTOR; MIRN7 MICRORNA, HUMAN; SIRPA PROTEIN, HUMAN; THROMBOSPONDIN 1; THROMBOSPONDIN-1, HUMAN;

ANTIGEN EXPRESSION; ARTICLE; BREAST EPITHELIUM CELL; CANCER CELL; CANCER INHIBITION; CANCER STEM CELL; CELL DIFFERENTIATION; CELL DIVISION; CELL PROLIFERATION; CELL RENEWAL; CONTROLLED STUDY; DRUG TARGETING; GENE EXPRESSION; HUMAN; HUMAN CELL; IN VIVO STUDY; MACROPHAGE; MCF 7 CELL LINE; PHAGOCYTOSIS; PROTEIN PHOSPHORYLATION; SIGNAL TRANSDUCTION; STEM CELL; TRIPLE NEGATIVE BREAST CANCER; TUMOR XENOGRAFT; CELL LINE; CONFOCAL MICROSCOPY; DRUG EFFECTS; FEMALE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETICS; IMMUNOLOGY; MCF-7 CELL LINE; METABOLISM; PATHOLOGY; PHOSPHORYLATION; PROCEDURES; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; TUMOR CELL LINE; WESTERN BLOTTING;

ANTIBODIES, BLOCKING; ANTIGENS, CD47; ANTIGENS, DIFFERENTIATION; BLOTTING, WESTERN; CELL LINE; CELL LINE, TUMOR; CELL PROLIFERATION; EPIDERMAL GROWTH FACTOR; FEMALE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, NEOPLASTIC; HUMANS; MCF-7 CELLS; MICRORNAS; MICROSCOPY, CONFOCAL; NEOPLASTIC STEM CELLS; PHOSPHORYLATION; RECEPTOR, EPIDERMAL GROWTH FACTOR; RECEPTORS, IMMUNOLOGIC; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; SIGNAL TRANSDUCTION; THROMBOSPONDIN 1; TRIPLE NEGATIVE BREAST NEOPLASMS;

EID: 84961590540     PISSN: None     EISSN: 19492553     Source Type: Journal    
DOI: 10.18632/oncotarget.7100     Document Type: Article

References (74)

1. Stingl J, Eaves CJ, Zandieh I and Emerman JT. Characterization of bipotent mammary epithelial progenitor cells in normal adult human breast tissue. Breast Cancer Res Treat. 2001; 67:93-109.
2. Petersen OW and Polyak K. Stem cells in the human breast. Cold Spring Harb Perspect Biol. 2010; 2:a003160.
3. Rosen PP, Groshen S, Saigo PE, Kinne DW and Hellman S. Pathological prognostic factors in stage I (T1N0M0) and stage II (T1N1M0) breast carcinoma: a study of 644 patients with median follow-up of 18 years. J Clin Oncol. 1989; 7:1239-1251.
4. Singh SK, Hawkins C, Clarke ID, Squire JA, Bayani J, Hide T, Henkelman RM, Cusimano MD and Dirks PB. Identification of human brain tumour initiating cells. Nature. 2004; 432:396-401.
5. Wright MH, Calcagno AM, Salcido CD, Carlson MD, Ambudkar SV and Varticovski L. Brca1 breast tumors contain distinct CD44+/CD24-and CD133+ cells with cancer stem cell characteristics. Breast Cancer Res. 2008; 10:R10.
6. Sheridan C, Kishimoto H, Fuchs RK, Mehrotra S, Bhat-Nakshatri P, Turner CH, Goulet R, Jr., Badve S and Nakshatri H. CD44+/CD24-breast cancer cells exhibit enhanced invasive properties: an early step necessary for metastasis. Breast Cancer Res. 2006; 8:R59.
7. Sorlie T. Molecular portraits of breast cancer: tumour subtypes as distinct disease entities. Eur J Cancer. 2004; 40:2667-2675.
8. Al-Ejeh F, Shi W, Miranda M, Simpson PT, Vargas AC, Song S, Wiegmans AP, Swarbrick A, Welm AL, Brown MP, Chenevix-Trench G, Lakhani SR and Khanna KK. Treatment of triple-negative breast cancer using anti-EGFR-directed radioimmunotherapy combined with radiosensitizing chemotherapy and PARP inhibitor. J Nucl Med. 2013; 54:913-921.
9. Zhao XW, van Beek EM, Schornagel K, Van der Maaden H, Van Houdt M, Otten MA, Finetti P, Van Egmond M, Matozaki T, Kraal G, Birnbaum D, van Elsas A, Kuijpers TW, Bertucci F and van den Berg TK. CD47-signal regulatory protein-alpha (SIRPalpha) interactions form a barrier for antibody-mediated tumor cell destruction. Proc Natl Acad Sci U S A. 2011; 108:18342-18347.
10. Willingham SB, Volkmer JP, Gentles AJ, Sahoo D, Dalerba P, Mitra SS, Wang J, Contreras-Trujillo H, Martin R, Cohen JD, Lovelace P, Scheeren FA, Chao MP, Weiskopf K, Tang C, Volkmer AK, et al. The CD47-signal regulatory protein alpha (SIRPa) interaction is a therapeutic target for human solid tumors. Proc Natl Acad Sci U S A. 2012; 109:6662-6667.
11. Jaiswal S, Chao MP, Majeti R and Weissman IL. Macrophages as mediators of tumor immunosurveillance. Trends Immunol. 2010; 31:212-219.
12. Soto-Pantoja DR, Terabe M, Ghosh A, Ridnour LA, DeGraff WG, Wink DA, Berzofsky JA and Roberts DD. CD47 in the tumor microenvironment limits cooperation between antitumor T-cell immunity and radiotherapy. Cancer Res. 2014; 74:6771-6783.
13. Soto-Pantoja DR, Miller TW, Frazier WA and Roberts DD. Inhibitory signaling through signal regulatory protein-alpha is not sufficient to explain the antitumor activities of CD47 antibodies. Proc Natl Acad Sci U S A. 2012; 109:E2842; author reply E2844-2845.
14. Okuda H, Xing F, Pandey PR, Sharma S, Watabe M, Pai SK, Mo YY, Iiizumi-Gairani M, Hirota S, Liu Y, Wu K, Pochampally R and Watabe K. miR-7 suppresses brain metastasis of breast cancer stem-like cells by modulating KLF4. Cancer Res. 2013; 73:1434-1444.
15. Idowu MO, Kmieciak M, Dumur C, Burton RS, Grimes MM, Powers CN and Manjili MH. CD44(+)/CD24(-/low) cancer stem/progenitor cells are more abundant in triplenegative invasive breast carcinoma phenotype and are associated with poor outcome. Hum Pathol. 2012; 43:364-373.
16. Jaiswal S, Jamieson CH, Pang WW, Park CY, Chao MP, Majeti R, Traver D, van Rooijen N and Weissman IL. CD47 is upregulated on circulating hematopoietic stem cells and leukemia cells to avoid phagocytosis. Cell. 2009; 138:271-285.
17. Lee TK, Cheung VC, Lu P, Lau EY, Ma S, Tang KH, Tong M, Lo J and Ng IO. Blockade of CD47-mediated cathepsin S/protease-activated receptor 2 signaling provides a therapeutic target for hepatocellular carcinoma. Hepatology. 2014; 60:179-191.
18. Yoshida K, Tsujimoto H, Matsumura K, Kinoshita M, Takahata R, Matsumoto Y, Hiraki S, Ono S, Seki S, Yamamoto J and Hase K. CD47 is an adverse prognostic factor and a therapeutic target in gastric cancer. Cancer Med. 2015; 4:1322-1333.
19. Zhang H, Lu H, Xiang L, Bullen JW, Zhang C, Samanta D, Gilkes DM, He J and Semenza GL. HIF-1 regulates CD47 expression in breast cancer cells to promote evasion of phagocytosis and maintenance of cancer stem cells. Proc Natl Acad Sci U S A. 2015; 112:E6215-6223.
20. Kaur S, Soto-Pantoja DR, Stein EV, Liu C, Elkahloun AG, Pendrak ML, Nicolae A, Singh SP, Nie Z, Levens D, Isenberg JS and Roberts DD. Thrombospondin-1 signaling through CD47 inhibits self-renewal by regulating c-Myc and other stem cell transcription factors. Sci Rep. 2013; 3:1673.
21. Liu W, Jeganathan G, Amiri S, Morgan KM, Ryan BM and Pine SR. Asymmetric segregation of template DNA strands in basal-like human breast cancer cell lines. Mol Cancer. 2013; 12:139.
22. Ghiabi P, Jiang J, Pasquier J, Maleki M, Abu-Kaoud N, Rafii S and Rafii A. Endothelial cells provide a notchdependent pro-tumoral niche for enhancing breast cancer survival, stemness and pro-metastatic properties. PLoS One. 2014; 9:e112424.
23. Pine SR, Ryan BM, Varticovski L, Robles AI and Harris CC. Microenvironmental modulation of asymmetric cell division in human lung cancer cells. Proc Natl Acad Sci U S A. 2010; 107:2195-2200.
24. Yu F, Li J, Chen H, Fu J, Ray S, Huang S, Zheng H and Ai W. Kruppel-like factor 4 (KLF4) is required for maintenance of breast cancer stem cells and for cell migration and invasion. Oncogene. 2011; 30:2161-2172.
25. Shin KH, Kim RH, Kim RH, Kang MK and Park NH. hnRNP G elicits tumor-suppressive activity in part by upregulating the expression of Txnip. Biochem Biophys Res Commun. 2008; 372:880-885.
26. Min C, Yu Z, Kirsch KH, Zhao Y, Vora SR, Trackman PC, Spicer DB, Rosenberg L, Palmer JR and Sonenshein GE. A loss-of-function polymorphism in the propeptide domain of the LOX gene and breast cancer. Cancer Res. 2009; 69:6685-6693.
27. Lin CS, Aebersold RH and Leavitt J. Correction of the N-terminal sequences of the human plastin isoforms by using anchored polymerase chain reaction: identification of a potential calcium-binding domain. Mol Cell Biol. 1990; 10:1818-1821.
28. Lin CS, Park T, Chen ZP and Leavitt J. Human plastin genes. Comparative gene structure, chromosome location, and differential expression in normal and neoplastic cells. J Biol Chem. 1993; 268:2781-2792.
29. Pedersen IS, Dervan PA, Broderick D, Harrison M, Miller N, Delany E, O'Shea D, Costello P, McGoldrick A, Keating G, Tobin B, Gorey T and McCann A. Frequent loss of imprinting of PEG1/MEST in invasive breast cancer. Cancer Res. 1999; 59:5449-5451.
30. Foley J, Nickerson NK, Nam S, Allen KT, Gilmore JL, Nephew KP and Riese DJ, 2nd. EGFR signaling in breast cancer: bad to the bone. Semin Cell Dev Biol. 2010; 21:951-960.
31. Wang Y, Klijn JG, Zhang Y, Sieuwerts AM, Look MP, Yang F, Talantov D, Timmermans M, Meijer-van Gelder ME, Yu J, Jatkoe T, Berns EM, Atkins D and Foekens JA. Gene-expression profiles to predict distant metastasis of lymph-node-negative primary breast cancer. Lancet. 2005; 365:671-679.
32. Bos PD, Zhang XH, Nadal C, Shu W, Gomis RR, Nguyen DX, Minn AJ, van de Vijver MJ, Gerald WL, Foekens JA and Massague J. Genes that mediate breast cancer metastasis to the brain. Nature. 2009; 459:1005-1009.
33. Dontu G, El-Ashry D and Wicha MS. Breast cancer, stem/progenitor cells and the estrogen receptor. Trends Endocrinol Metab. 2004; 15:193-197.
34. Zhu X, Zhou X, Lewis MT, Xia L and Wong S. Cancer stem cell, niche and EGFR decide tumor development and treatment response: A bio-computational simulation study. J Theor Biol. 2011; 269:138-149.
35. Webster RJ, Giles KM, Price KJ, Zhang PM, Mattick JS and Leedman PJ. Regulation of epidermal growth factor receptor signaling in human cancer cells by microRNA-7. J Biol Chem. 2009; 284:5731-5741.
36. Kaur S, Martin-Manso G, Pendrak ML, Garfield SH, Isenberg JS and Roberts DD. Thrombospondin-1 inhibits VEGF receptor-2 signaling by disrupting its association with CD47. J Biol Chem. 2010; 285:38923-38932.
37. Cancer Genome Atlas N. Comprehensive molecular portraits of human breast tumours. Nature. 2012; 490:61-70.
38. Gao J, Aksoy BA, Dogrusoz U, Dresdner G, Gross B, Sumer SO, Sun Y, Jacobsen A, Sinha R, Larsson E, Cerami E, Sander C and Schultz N. Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal. Sci Signal. 2013; 6:pl1.
39. Cerami E, Gao J, Dogrusoz U, Gross BE, Sumer SO, Aksoy BA, Jacobsen A, Byrne CJ, Heuer ML, Larsson E, Antipin Y, Reva B, Goldberg AP, Sander C and Schultz N. The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data. Cancer Discov. 2012; 2:401-404.
40. Carpenter BL, Chen M, Knifley T, Davis KA, Harrison SM, Stewart RL and O'Connor KL. Integrin alpha6beta4 Promotes Autocrine Epidermal Growth Factor Receptor (EGFR) Signaling to Stimulate Migration and Invasion toward Hepatocyte Growth Factor (HGF). J Biol Chem. 2015; 290:27228-27238.
41. Peng C, Zeng W, Su J, Kuang Y, He Y, Zhao S, Zhang J, Ma W, Bode AM, Dong Z and Chen X. Cyclin-dependent kinase 2 (CDK2) is a key mediator for EGF-induced cell transformation mediated through the ELK4/c-Fos signaling pathway. Oncogene. 2015.
42. Kedashiro S, Pastuhov SI, Nishioka T, Watanabe T, Kaibuchi K, Matsumoto K and Hanafusa H. LRRK1-phosphorylated CLIP-170 regulates EGFR trafficking by recruiting p150Glued to microtubule plus ends. J Cell Sci. 2015; 128:385-396.
43. Siu MK, Abou-Kheir W, Yin JJ, Chang YS, Barrett B, Suau F, Casey O, Chen WY, Fang L, Hynes P, Hsieh YY, Liu YN, Huang J and Kelly K. Loss of EGFR signaling regulated miR-203 promotes prostate cancer bone metastasis and tyrosine kinase inhibitors resistance. Oncotarget. 2014; 5:3770-3784. doi: 10.18632/oncotarget.1994.
44. Ghosh P, Beas AO, Bornheimer SJ, Garcia-Marcos M, Forry EP, Johannson C, Ear J, Jung BH, Cabrera B, Carethers JM and Farquhar MG. A Gαi-GIV molecular complex binds epidermal growth factor receptor and determines whether cells migrate or proliferate. Mol Biol Cell. 2010; 21:2338-2354.
45. McNulty DE, Li Z, White CD, Sacks DB and Annan RS. MAPK scaffold IQGAP1 binds the EGF receptor and modulates its activation. J Biol Chem. 2011; 286:15010-15021.
46. Soto-Pantoja DR, Miller TW, Pendrak ML, DeGraff WG, Sullivan C, Ridnour LA, Abu-Asab M, Wink DA, Tsokos M and Roberts DD. CD47 deficiency confers cell and tissue radioprotection by activation of autophagy. Autophagy. 2012; 8:1628-1642.
47. Kim SY, Kang JW, Song X, Kim BK, Yoo YD, Kwon YT and Lee YJ. Role of the IL-6-JAK1-STAT3-Oct-4 pathway in the conversion of non-stem cancer cells into cancer stemlike cells. Cell Signal. 2013; 25:961-969.
48. Kadota M, Sato M, Duncan B, Ooshima A, Yang HH, Diaz-Meyer N, Gere S, Kageyama S, Fukuoka J, Nagata T, Tsukada K, Dunn BK, Wakefield LM and Lee MP. Identification of novel gene amplifications in breast cancer and coexistence of gene amplification with an activating mutation of PIK3CA. Cancer Res. 2009; 69:7357-7365.
49. Kanda T, Raychoudhuri A, Steele R, Sagartz JE, West C and Ray RB. MBP-1 inhibits breast cancer growth and metastasis in immunocompetent mice. Cancer Res. 2009; 69:9354-9359.
50. Contino F, Mazzarella C, Ferro A, Lo Presti M, Roz E, Lupo C, Perconti G, Giallongo A and Feo S. Negative transcriptional control of ERBB2 gene by MBP-1 and HDAC1: diagnostic implications in breast cancer. BMC Cancer. 2013; 13:81.
51. Grond A. [Modern lung examination]. Lebensversicher Med. 1974; 26:142-144.
52. Casimiro MC, Velasco-Velazquez M, Aguirre-Alvarado C and Pestell RG. Overview of cyclins D1 function in cancer and the CDK inhibitor landscape: past and present. Expert Opin Investig Drugs. 2014; 23:295-304.
53. Talvinen K, Karra H, Pitkanen R, Ahonen I, Nykanen M, Lintunen M, Soderstrom M, Kuopio T and Kronqvist P. Low cdc27 and high securin expression predict short survival for breast cancer patients. APMIS. 2013; 121:945-953.
54. Sinha A, Agarwal S, Parashar D, Verma A, Saini S, Jagadish N, Ansari AS, Lohiya NK and Suri A. Down regulation of SPAG9 reduces growth and invasive potential of triple-negative breast cancer cells: possible implications in targeted therapy. J Exp Clin Cancer Res. 2013; 32:69.
55. Tan J, Li Z, Lee PL, Guan P, Aau MY, Lee ST, Feng M, Lim CZ, Lee EY, Wee ZN, Lim YC, Karuturi RK and Yu Q. PDK1 signaling toward PLK1-MYC activation confers oncogenic transformation, tumor-initiating cell activation, and resistance to mTOR-targeted therapy. Cancer Discov. 2013; 3:1156-1171.
56. Casamayor A, Morrice NA and Alessi DR. Phosphorylation of Ser-241 is essential for the activity of 3-phosphoinositidedependent protein kinase-1: identification of five sites of phosphorylation in vivo. Biochem J. 1999; 342 ( Pt 2):287-292.
57. Ow JR, Ma H, Jean A, Goh Z, Lee YH, Chong YM, Soong R, Fu XY, Yang H and Wu Q. Patz1 regulates embryonic stem cell identity. Stem Cells Dev. 2014; 23:1062-1073.
58. Ma H, Ow JR, Tan BC, Goh Z, Feng B, Loh YH, Fedele M, Li H and Wu Q. The dosage of Patz1 modulates reprogramming process. Sci Rep. 2014; 4:7519.
59. Zheng Y, Zou F, Wang J, Yin G, Le V, Fei Z and Liu J. Photodynamic Therapy-mediated Cancer Vaccination Enhances Stem-like Phenotype and Immune Escape, Which Can Be Blocked by Thrombospondin-1 Signaling through CD47 Receptor Protein. J Biol Chem. 2015; 290:8975-8986.
60. Yoshida H, Tomiyama Y, Oritani K, Murayama Y, Ishikawa J, Kato H, Miyagawa Ji J, Honma N, Nishiura T and Matsuzawa Y. Interaction between Src homology 2 domain bearing protein tyrosine phosphatase substrate-1 and CD47 mediates the adhesion of human B lymphocytes to nonactivated endothelial cells. J Immunol. 2002; 168:3213-3220.
61. Tseng D, Volkmer JP, Willingham SB, Contreras-Trujillo H, Fathman JW, Fernhoff NB, Seita J, Inlay MA, Weiskopf K, Miyanishi M and Weissman IL. Anti-CD47 antibodymediated phagocytosis of cancer by macrophages primes an effective antitumor T-cell response. Proc Natl Acad Sci U S A. 2013; 110:11103-11108.
62. Gluz O, Liedtke C, Gottschalk N, Pusztai L, Nitz U and Harbeck N. Triple-negative breast cancer-current status and future directions. Ann Oncol. 2009; 20:1913-1927.
63. Zhang D, LaFortune TA, Krishnamurthy S, Esteva FJ, Cristofanilli M, Liu P, Lucci A, Singh B, Hung MC, Hortobagyi GN and Ueno NT. Epidermal growth factor receptor tyrosine kinase inhibitor reverses mesenchymal to epithelial phenotype and inhibits metastasis in inflammatory breast cancer. Clin Cancer Res. 2009; 15:6639-6648.
64. Friess T, Scheuer W and Hasmann M. Combination treatment with erlotinib and pertuzumab against human tumor xenografts is superior to monotherapy. Clin Cancer Res. 2005; 11:5300-5309.
65. Sohn J, Liu S, Parinyanitikul N, Lee J, Hortobagyi GN, Mills GB, Ueno NT and Gonzalez-Angulo AM. cMET Activation and EGFR-Directed Therapy Resistance in Triple-Negative Breast Cancer. J Cancer. 2014; 5:745-753.
66. Hansen TB, Kjems J and Damgaard CK. Circular RNA and miR-7 in cancer. Cancer Res. 2013; 73:5609-5612.
67. Horsham JL, Kalinowski FC, Epis MR, Ganda C, Brown RA and Leedman PJ. Clinical Potential of microRNA-7 in Cancer. J Clin Med. 2015; 4:1668-1687.
68. Chang YL, Zhou PJ, Wei L, Li W, Ji Z, Fang YX and Gao WQ. MicroRNA-7 inhibits the stemness of prostate cancer stem-like cells and tumorigenesis by repressing KLF4/PI3K/Akt/p21 pathway. Oncotarget. 2015; 6:24017-24031. doi: 10.18632/oncotarget.4447.
69. Shi Y, Luo X, Li P, Tan J, Wang X, Xiang T and Ren G. miR-7-5p suppresses cell proliferation and induces apoptosis of breast cancer cells mainly by targeting REGgamma. Cancer Lett. 2015; 358:27-36.
70. Pettersen RD, Bernard G, Olafsen MK, Pourtein M and Lie SO. CD99 signals caspase-independent T cell death. J Immunol. 2001; 166:4931-4942.
71. Sundararaman B, Avitabile D, Konstandin MH, Cottage CT, Gude N and Sussman MA. Asymmetric chromatid segregation in cardiac progenitor cells is enhanced by Pim-1 kinase. Circ Res. 2012; 110:1169-1173.
72. Kaur S, Singh SP, Elkahloun AG, Wu W, Abu-Asab MS and Roberts DD. CD47-dependent immunomodulatory and angiogenic activities of extracellular vesicles produced by T cells. Matrix Biol. 2014; 37:49-59.
73. Mootha VK, Lindgren CM, Eriksson KF, Subramanian A, Sihag S, Lehar J, Puigserver P, Carlsson E, Ridderstrale M, Laurila E, Houstis N, Daly MJ, Patterson N, Mesirov JP, Golub TR, Tamayo P, et al. PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes. Nat Genet. 2003; 34:267-273.
74. Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, Paulovich A, Pomeroy SL, Golub TR, Lander ES and Mesirov JP. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A. 2005; 102:15545-15550.