High-throughput mutational analysis of the human cancer genome

Pharmacogenomics

Volumn 7, Issue 4, 2006, Pages 597-612

  Ma, Patrick C ^a   Zhang, Xiaodong ^a   Wang, Zhenghe J ^a  

^a CASE WESTERN RESERVE UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

Genome; Kinases; Mutation; Neoplasms; Phosphatases

Indexed keywords

2 MORPHOLINO 8 PHENYLCHROMONE; ANTINEOPLASTIC AGENT; APC PROTEIN; BETA CATENIN; CETUXIMAB; DASATINIB; EPIDERMAL GROWTH FACTOR RECEPTOR; EPIDERMAL GROWTH FACTOR RECEPTOR 2; ERLOTINIB; GEFITINIB; IMATINIB; LAPATINIB; MONOCLONAL ANTIBODY 5D5; PHA 665752; PHOSPHATASE; PHOSPHATIDYLINOSITOL 3 KINASE; PROTEIN BAX; PROTEIN KINASE; PROTEIN NOXA; PROTEIN SERINE KINASE; PROTEIN TYROSINE KINASE; PROTEIN TYROSINE PHOSPHATASE; SCATTER FACTOR RECEPTOR; SU 11274; TRASTUZUMAB; UNCLASSIFIED DRUG;

BRAIN CANCER; BREAST CANCER; CANCER GENETICS; CARCINOGENESIS; CHROMOSOMAL INSTABILITY; CHRONIC MYELOID LEUKEMIA; CHRONIC MYELOMONOCYTIC LEUKEMIA; COLON CANCER; COLORECTAL CANCER; DNA SEQUENCE; DRUG TARGETING; ENDOMETRIUM CANCER; GENE MUTATION; GENETIC DISORDER; GENETIC SCREENING; GERM CELL TUMOR; GLIOBLASTOMA; HIGH THROUGHPUT SCREENING; HUMAN; HUMAN GENOME; HYPEREOSINOPHILIC SYNDROME; LIVER CANCER; LUNG CANCER; MELANOMA; MESOTHELIOMA; MULTIGENE FAMILY; MUTATIONAL ANALYSIS; MYELOFIBROSIS; MYELOID METAPLASIA; MYELOPROLIFERATIVE DISORDER; OVARY CANCER; POLYCYTHEMIA VERA; PROTEIN FAMILY; REVIEW; SIGNAL TRANSDUCTION; STOMACH CANCER; SYSTEMIC MASTOCYTOSIS; THROMBOCYTHEMIA;

1-PHOSPHATIDYLINOSITOL 3-KINASE; BREAST NEOPLASMS; CHROMOSOMAL INSTABILITY; COLORECTAL NEOPLASMS; DNA MUTATIONAL ANALYSIS; FEMALE; GENES, ERBB-2; GENOME, HUMAN; GLIOBLASTOMA; HUMANS; LUNG NEOPLASMS; MALE; MUTATION; MYELOPROLIFERATIVE DISORDERS; NEOPLASMS; ONCOGENES; PHARMACOGENETICS; PROTEIN-TYROSINE KINASES; PROTEIN-TYROSINE-PHOSPHATASE; RECEPTOR, EPIDERMAL GROWTH FACTOR; TESTICULAR NEOPLASMS;

EID: 33745170363     PISSN: 14622416     EISSN: 17448042     Source Type: Journal    
DOI: 10.2217/14622416.7.4.597     Document Type: Review

References (98)

1. Davies H, Bignell GR, Cox C et al.: Mutations of the BRAF gene in human cancer. Nature 417 (6892), 949-954 (2002).
2. Vogelstein B, Kinzler KW. Cancer genes and the pathways they control. Nature Med. 10(8), 799-799 (2004).
3. Kinzler KW, Vogelstein B: Lessons from hereditary colorectal cancer. Cell 87(2), 159-170 (1996).
4. Sparks AB, Morin PJ, Vogelstein B, Kinzler KW: Mutational analysis of the APC/β-catenin/Tcf pathway in colorectal cancer. Cancer Res. 58(6), 1130-1134 (1998).
5. Powell SM, Zilz N, Beazer-Barclay Y et al.: APC mutations occur early during colorectal tumorigenesis. Nature 359 (6392), 235-237 (1992).
6. Miyoshi Y, Ando, H, Nagase H et al.: Germ-line mutations of the APC gene in 53 familial adenomatous polyposis patients. Proc. Natl Acad. Sci. USA 89 (10), 452-4456 (1992).
7. Jen J, Powell SM, Papadopoulos N et al.: Molecular determinants of dysplasia in colorectal lesions. Cancer Res. 54 (21), 5523-5526 (1994).
8. Rajagopalan H, Bardelli A, Lengauer C, Kinzler KW, Vogelstein B, Velculescu VE: Tumorigenesis: RAF/RAS oncogenes and mismatch-repair status. Nature 418 (6901), 934 (2002).
9. Vogelstein B, Fearon ER, Hamilton SR et al.: Genetic alterations during colorectal-tumor development. N. Engl. J. Med. 319(9), 525-532 (1988).
10. Thiagalingam S, Lengauer C, Leach FS et al.: Evaluation of candidate tumour suppressor genes on chromosome 18 in colorectal cancers. Nature Genet. 13(3), 343-346 (1996).
11. Fearon ER, Vogelstein B: A genetic model for colorectal tumorigenesis. Cell 61(5), 759-767 (1990).
12. Baker SJ, Fearon ER, Nigro JM et al.: Chromosome 17 deletions and p53 gene mutations in colorectal carcinomas. Science 244(4901), 217-221 (1989).
13. Baker SJ, Markowitz S, Fearon ER, Willson JK, Vogelstein B: Suppression of human colorectal carcinoma cell growth by wild-type p53. Science 249(4971), 912-915 (1990).
14. el-Deiry WS, Tokino T, Velculescu VE et al.: WAF1, a potential mediator of p53 tumor suppression. Cell 75(4), 817-825 (1993).
15. Hermeking H, Lengauer C, Polyak K et al.: 14-3-3 sigma is a p53-regutated inhibitor of G2/M progression. Mol. Cell 1(1), 3-11 (1997).
16. Oda E, Ohki R, Murasawa H et al.: Noxa, a BH3-only member of the Bcl-2 family and candidate mediator of p53-induced apoptosis. Science 288(5468); 1053-1058 (2000).
17. Yu J, Zhang L, Hwang PM, Kinzler KW, Vogelstein B: PUMA induces the rapid apoptosis of colorectal cancer cells. Mol. Cell 7(3), 673-682 (2001).
18. Blume-Jensen P, Hunter T: Oncogenic kinase signaling. Nature 411(6835), 355-365 (2001).
19. Manning G, Whyte DB, Martinez R, Hunter T, Sudarsanam S: The protein kinase complement of the human genome. Science 298(5600), 1912-1934 (2002).
20. Bardelli A, Parsons DW, Silliman N et al.: Mutational analysis of the tyrosine kinome in colorectal cancers. Science 300(5621), 949(2003).
21. Davies H, Hunter C, Smith R et al.: Somatic mutations of the protein kinase gene family in human lung cancer. Cancer Res. 65(17), 7591-7595 (2005).
22. Stephens P, Edkins S, Davies H et al.: A screen of the complete protein kinase gene family identifies diverse patterns of somatic mutations in human breast cancer. Nature Genet. 37(6), 590-592 (2005).
23. Vivanco I, Sawyers CL: The phosphatidylinositol 3-Kinase AKT pathway in human cancer. Natre Rev. Cancer 2(7), 489-501 (2002).
24. Bader AG, Kang S, Zhao L, Vogt PK: Oncogenic PI3K deregulates transcription and translation. Nature Rev. Cancer 5(12), 921-929 (2005).
25. Li J, Yen C, Liaw D et al.: PTEN a putative protein tyrosine phosphatase gene mutated in human brain, breast, and prostate cancer. Science 275(5308), 1943-1947 (1997).
26. Parsons R: Human cancer, PTEN and the PI-3 kinase pathway. Semin. Cell Dev. Biol. 15(2), 171-176 (2004).
27. Samuels Y, Wang Z, Bardelli A et al.: High frequency of mutations of the PIK3CA gene in human cancers. Science 304(5670), 554 (2004).
28. Samuels Y, Diaz LA Jr, Schmidt-Kittler O et al.: Mutant PIK3CA promotes cell growth and invasion of human cancer cells. Cancer Cell 7(6), 561-573 (2005).
29. Parsons DW, Wang TL, Samuels Y et al.: Colorectal cancer: mutations in a signaling pathway. Nature 436(7052), 792 (2005).
30. Neel BG, Gu H, Pao L: The 'Shp'ing news: SH2 domain-containing tyrosine phosphatases in cell signaling. Trends Biochem. Sci. 28(6), 284-293 (2003).
31. Wang Z, Shen D, Parsons DW et al.: Mutational analysis of the tyrosine phosphatome in colorectal cancers. Science 304(5674), 1164-1166 (2004).
32. Neel BG, Tonks NR: Protein tyrosine phosphatases in signal transduction. Curr. Opin. Cell Biol. 9(2), 193-204 (1997).
33. Erdmann KS: The protein tyrosine phosphatase PTP-Basophil/Basophil-like. Interacting proteins and molecular functions. Eur. J. Biochem. 270(24), 4789-4798 (2003).
34. Collier LS, Carlson CM, Ravimohan S, Dupuy AJ, Largaespada DA: Cancer gene discovery in solid tumours using transposon-based somatic mutagenesis in the mouse. Nature 436 (7048), 272-276 (2005).
35. Aricescu AR, Hon WC, Stebold C, Lu W, van der Merwe PA, Jones EY. Molecular analysis of receptor protein tyrosine phosphatase μ-mediated cell adhesion. Embo. J. 25(4), 701-712 (2006).
36. Wang Z, Cummins JM, Shen D et al.: Three classes of genes mutated in colorectal cancers with chromosomal instability. Cancer Res. 64(9), 2998-3001 (2004).
37. Lengauer C, Wang Z: From spindle checkpoint to cancer. Nature Genet. 36(11), 1144-1145 (2004).
38. Cahill DP, Lengauer C, Yu J et al.: Mutations of mitotic checkpoint genes in human cancers. Nature 392(6673), 300-303 (1998).
39. Hanks S, Coleman K, Reid S et al.: Constitutional aneuploidy and cancer predisposition caused by biallelic mutations in BUB1B. Nature Genet. 36(11), 1159-1161 (2004).
40. Jemal A, Murray T, Ward E et al.: Cancer statistics, 2005. CA Cancer J. Clin. 55(1), 10-30 (2005).
41. Choong NW, Ma PC, Salgia R: Therapeutic targeting of receptor tyrosine kinases in lung cancer. Expert Opin. Ther. Targets 9(3), 533-559 (2005).
42. Ma PC, Jagadeeswaran R, Jagadeesh S et al.: Functional expression and mutations of c-Met and its therapeutic inhibition with SU11274 and small interfering RNA in non-small cell lung cancer. Cancer Res. 65(4), 1479-1488 (2005).
43. Ma PC, Kijima T, Maulik G et al.: c-MET mutational analysis in small cell lung cancer: novel juxtemembrane domain mutations regulating cytoskeletal functions. Cancer Res. 63(19), 6272-6281 (2003).
44. Jagadeeswaran R, Ma PC, Seiwert TY et al.: Functional analysis of c-Met/ hepatocyte growth factor pathway in malignant pleural mesothelioma. Cancer Res. 66(1), 352-361 (2006).
45. Kong-Beltran M, Seshagiri S, Zha J et al.: Somatic mutations lead to an oncogenic deletion of MET in lung cancer. Cancer Res. 66(1), 283-289 (2006).
46. Shigematsu H, Gazdar AF: Somatic mutations of epidermal growth factor receptor signaling pathway in lung cancers. Int. J. Cancer 118(2), 57-62 (2006).
47. Lynch TJ, Bell DW, Sordella R et al.: Activating mutations in the epidermal growth factor receptor underlying responsiveness of non-small cell lung cancer to gefitinib. N. Engl. J. Med. 350(21), 2129-2139 (2004).
48. Paez JG, Jenne PA, Lee JC et al.: EGFR mutations in lung cancer: correlation with clinical response to gefitinib therapy. Science 304(5676), 1497-1500 (2004).
49. Marchetti A, Martella C, Felicioni L et al: EGFR mutattons in non-small cell lung cancer: analysis of a large series of cases and development of a rapid and sensitive method for diagnostic screening with potential implications on pharmacologic treatment J. Clin. Oncol. 23(4),857-865 (2005).
50. Toyooka S, Tokumo M, Shigematsu H et al.: Mutational and epigenetic evidence for independent pathways for lung adenocarcinomas arising in smokers and never smokers. Cancer Res. 66(3), 1371-1375 (2006).
51. Pao W, Miller V, Zakowski M et al.: EGF receptor gene mutations are common in lung cancers from 'never smokers' and are associated with sensitivity of tumors to gefitinib and erlotinib. Proc. Natl Acad. Sci. USA 101(36), 13306-13311 (2004).
52. Choong NW, Dietrich S, Seiwert TY et al.: Gefitinib response of erlotinib-refractory lung cancer involving meninges-role of EGFR mutation. Nature Clin. Pract. Oncol. 3(1), 50-57 (2006).
53. Kobayashi S, Boggon TJ, Dayaram T et al.: EGFR mutation and resistance of non-small cell lung cancer to gefitinib. N. Engl. J. Med. 352(8), 786-792 (2005).
54. Pao W, Miller VA, Politi KA et al.: Acquired resistance of lung adenocarcinomas to gefitinib or erlotinib is associated with a second mutation in the EGFR kinase domain. PLoS Med. 2(3), e73 (2005).
55. Stephens P, Hunter C, Bignell G et al.: Lung cancer: intragenic ERBB2 kinase mutations in tumours. Nature 431(7008), 525-526 (2004).
56. Shigematsu H, Takahashi T, Nomura M et al.: Somatic mutations of the HER2 kinase domain in lung adenocarcinomas. Cancer Res. 65(5), 1642-1646 (2005).
57. Sasaki H, Shimizu S, Endo K et al.: EGFR and erbB2 mutation status in Japanese lung cancer patients. Int. J. Cancer 118(1), 180-184 (2006).
58. Maulik G, Shrikhande A, Kijima T, Ma PC, Morrison PT, Salgia R: Role of the hepatocyte growth factor receptor, c-Met, in oncogenesis and potential for therapeutic inhibition. Cytokine Growth Factor Rev. 13(1), 41-59 (2002).
59. Schmidt L, Duh FM, Chen F et al.: Germline and somatic mutations in the tyrosine kinase domain of the MET proto-oncogene in papillary renal carcinomas. Nature Genet. 16(1), 68-73 (1997).
60. Zaffaroni D, Spinola M, Gahran A et al.: Met proto-oncogene juxtamembrane rare variations in mouse and humans: differetial effects of Arg and Cys alleles on mouse lung tumorigenesis. Oncogene 24(6), 1084-1090 (2005).
61. Gherardi E, Youles ME, Miguel RN et al.: Functional map and domain structure of MET, the product of the c-met protooncogene and receptor for hepatocyte growth factor/scatter factor. Proc. Natl Acad. Sci. USA 100(21), 12039-12044 (2003).
62. Stamos J, Lazarus RA, Yao X, Kirchhofer D, Wiesmann C: Crystal structure of the HGF β-chain in complex with the Sema domain of the Met receptor. Embo. J. 23(12), 2325-2335 (2004).
63. Gherardi E, Love CA, Esnouf RM, Jones EY: The sema domain. Curr. Opin. Struct. Biol. 14(6), 669-678 (2004).
64. Ma PC, Maulik G. Christensen J, Salgia R: c-Met: structure, functions and potential for therapeutic inhibition. Cancer Metastasis Rev. 22(4), 309-325 (2003).
65. Dietrich S, Uppalapati R, Seiwert TY, Ma PC: Role of c-MET in upper aerodigestive malignancies - from biology to novel therapies. J. Environ. Pathol. Toxicol. Oncol. 24(3), 149-162 (2005).
66. Ma PC, Schaefer E, Christensen JG, Salgia R: A selective small molecule c-MET Inhibitor, PHA665752, cooperates with rapamycin. Clin. Cancer Res. 11(6), 2312-2319 (2005).
67. Burgess T, Coxon A, Meyer S. et al.: Fully human monoclonal antibodies to hepatocyte growth factor with therapeutic potential against hepatocyte growth factor/c-Met-dependent human tumors. Cancer Res. 66(3), 1721-1729 (2006).
68. Jiao Y, Zhao P. Zhu J et al.: Construction of human naive Fab library and characterization of anti-met Fab fragment generated from the library. Mol. Biotechnol. 31(1), 41-54 (2005).
69. Slamon DJ, Clark GM, Wong SG, Levin WJ, Ullrich A, McGuire WL: Human breast cancer: correlation of relapse and survival with amplification of the HER-2/neu oncogene. Science 235(4785), 177-182 (1987).
70. Bachman KE, Argani P, Samuels Y et al.: The PIK3CA gene is mutated with high frequency in human breast cancers. Cancer Biol. Ther. 3(8), 772-775 (2004).
71. Campbell IG, Russell SE, Choong DY et al.: Mutation of the PIK3CA gem in ovarian and breast cancer. Cancer Res. 64(21), 7678-7681 (2004).
72. Broderick DK, Di C, Parrett TJ et al. Mutations of PIK3CA in anaplastic oligodendrogliomas, high-grade astrocytomas, and medulloblastomas. Cancer Res. 64(15), 5048-5050 (2004).
73. Lee JW, Soong YH, Kim SY et al.: PIK3CA gene is frequently mutated in breast carcinomas and hepatocellular carcinomas. Oncogene 24(8), 1477-1480 (2005).
74. Levine DA, Bogomolniy F, Yee CJ et al.: Frequent mutation of the PIK3CA gene in ovarian and breast cancers. Clin. Cancer Res. 11(8), 2875-2878 (2005).
75. Li VS, Wong CW, Chan TL et al.: Mutations of PIK3CA in gastric adenocarcinoma. BMC Cancer 5, 29 (2005).
76. Saal LH, Holm K, Maurer M et al.: PIK3CA mutations correlate with hormone receptors, node metastasis, and ERBB2, and are mutually exclusive with PTEN loss in human breast carcinoma. Cancer Res. 65(7), 2554-2559 (2005).
77. Oda K, Stokoe D, Taketani Y, McCormick F: High frequency of coexistent mutations of PIK3CA and PTEN genes in endometrial carcinoma. Cancer Res. 65(23). 10669-10673(2005).
78. Wong AJ, Bigner SH, Bigner DD, Kinzler KW, Hamilton SR, Vogelstein B: Increased expression of the epidermal growth factor receptor gene in malignant gliomas is invariably associated with gene amplification. Proc. Natl Acad. Sci. USA 84(19), 6899-6903 (1987).
79. Sugawa N, Ekstrand AJ, James CD, Collins VP: Identical splicing of aberrant epidermal growth factor receptor transcripts from amplified rearranged genes in human glioblastomas. Proc. Natl Acad. Sci. USA 87(21), 8602-8606 (1990).
80. Mellinghoff IK, Wang MY, Vivanco I et al.: Molecular determinants of the response of glioblastomas to EGFR kinase inhibitors. N. Engl. J. Med. 353(19), 2012-2024 (2005).
81. Rand V, Huang J, Stockwell T et al.: Sequence survey of receptor tyrosine kinases reveals mutations in glioblastomas. Proc. Natl Acad. Sci. USA 102(40), 14344-14349 (2005).
82. Clarke ID, Dirks PB: A human brain tumor-derived PDGFR-α deletion mutant is transforming. Oncogen 22(5),722-733 (2003).
83. Tian Q, Frierson HF Jr, Krystal GW, Moskaluk CA: Activating C-KIT gene mutations in human germ cell tumors. Am J. Pathol. 154(6), 1643-1647 (1999).
84. Kemmer K, Corless CL, Fletcher JA et al.: KIT mutations are common in testicular seminomas. Am. J. Pathol. 164(1), 305-313 (2004).
85. Bignell G, Smith P, Hunter C et al.: Sequence analysis of the protein kinase gene family in human testcular germ-cell tumors of adolescents and adults. Genes Chromosomes Cancer 45(1), 42-46 (2006).
86. Ley TJ, Minx PJ, Walter MJ et al.: A pilot study of high-throughput, sequence-based mutational profiling of primary human acute myeloid leukemia cell genomes. Proc. Natl Acad. Sci. USA 100(24), 14275-14280 (2003).
87. Golub TR, Barker GF, Lovett M, Gilliland DG: Fusion of PDGF receptor β to a novel ETS-like gene, tel, in chronic myelomonocytic leukemia with t(5;12) chromosomal translocation. Cell 77(2). 307-316 (1994).
88. Cools J, DeAngelo DJ, Goft J et al.: A tyrosine kinase created by fusion of the PDGFRA and FIP1L1 genes as a therapeutic target of imatinib in idiopathic hypereosinophilic syndrome. N. Engl. J. Med. 348(13). 1201-1214 (2003).
89. Levine RL, Wadleigh M, Cools J et al.: Activating mutation in the tyrosine kinase JAK2 in polycythemia vera, essential thrombocythemia, and myeloid metaplasia with myelofibrosis. Cancer Cell 7(4), 387-397 (2005).
90. Kralovics R, Passamonti F, Buser AS et al.: A gain-of-function mutation of JAK2 in myeloproliferative disorders. N. Engl. J. Med. 352(17), 1779-1790 (2005).
91. James C, Ugo V, Couedic JL et al: A unique clonal JAK2 mutation leading to constitutive signaling causes polycythaemia vera. Nature 434(7037), 1144-1148 (2005).
92. Thatcher N, Chang A. Parikh P et al.: Gefitinib plus best supportive care in previously treated patients with reftactory advanced non-small cell lung cancer: results from a randomised, placebo-controlled, multicentre study (Iressa Survival Evaluation in Lung Cancer). Lancet 366(9496), 1527-1537 (2005).
93. Buzin CH, Gatti RA, Nguyen VQ et al.: Comprehensive scanning of the ATM gene with DOVAM-S. Hum. Mutat. 21(2), 123-131 (2003).
94. Maitra, A, Cohen Y, Gillespie SE et al.: The Human MitoChip: a high-throughput sequencing microarray for mitochondrial mutation detection. Genome Res. 14(5), 812-819 (2004).
95. Dressman D, Yan H, Traverso G, Kinzler KW, Vogeistein B: Transforming single DNA molecules into fluorescent magnetic particles for detection and enumeration of genetic variations. Proc. Natl Acad. Sci. USA 100(15), 88174822 (2003).
96. Margulies M, Egholm M, Altman WE et al.: Genome sequencing in microfabricated high-density picolitre reactors. Nature 437(7057), 376-380 (2005).
97. Shendure J, Porreca GJ, Reppas NB et al.: Accurate multiplex polony sequencing of an evolved bacterial genome. Science 309(5741), 1728-1732 (2005).
98. Sawyers C: Targeted cancer therapy. Nature 432(7015), 294-297 (2004).