Table of Contents > Abs + Ref
   |    |  Full-text      |  

Yonsei Med J. 2009 Aug;50(4):464-473.
Published online 2009 August 19.  doi: 10.3349/ymj.2009.50.4.464.
© Copyright: Yonsei University College of Medicine 2009
Divide and Conquer: Progress in the Molecular Stratification of Cancer
Patrick Tan
Duke-NUS Graduate Medical School, Genome Institute of Singapore, Singapore; Cancer Science Institute of Singapore, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.

Corresponding author: Dr. Patrick Tan, Duke-NUS Graduate Medical School, 8 College Road, Singapore 138672. Tel: 65-6-436-8345, Fax: 65-6-226-5694, Email: gmstanp@duke-nus.edu.sg
Received June 29, 2009.

This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0) which permits unrestricted noncommercial use, distribution, and reproduction in any medium, provided the original work is properly cited.


Abstract

Cancer remains an outstanding cause of global morbidity and mortality, despite intensive research and unprecedented insights into the basic mechanisms of cancer development. A plethora of clinical and experimental evidence suggests that cancers from individual patients are likely to be molecularly heterogeneous in their use of distinct oncogenic pathways and biological programs. Efforts to significantly impact cancer patient outcomes will almost certainly require the development of robust strategies to subdivide such heterogeneous panels of cancers into biologically and clinically homogenous subgroups, for the purposes of personalizing treatment protocols and identifying optimal drug targets. In this review, I describe recent progress in the development of both targeted and genome-wide approaches for the molecular stratification of cancers, drawing examples from both the haematopoietic and solid tumor malignancies.

Keywords: Molecular stratification, cancer genomics, targeted therapies.

References
1. Parkin DM,Bray F,Ferlay J,Pisani P. Global cancer statistics, 2002. CA Cancer J Clin 2005;55:74–108.
2. National Center for Health Statistics. Health, United States, 2006 With Chartbook on Trends in the Health of Americans. 2006.
3. Parkin DM. International variation. Oncogene 2004;23:6329–6340.
4. Singapore Cancer Registry. Interim Report - Trends In Cancer Incidence In Singapore (2002-2006). 2008.
5. National Cancer Information Center. 2002 Annual report of the Korea central cancer registry. 2003.
6. Pagano JS,Blaser M,Buendia MA,Damania B,Khalili K,Raab-Traub N,et al. Infectious agents and cancer: criteria for a causal relation. Semin Cancer Biol 2004;14:453–471.
7. Parkin DM,Moss SM. Lung cancer screening: improved survival but no reduction in deaths--the role of "overdiagnosis". Cancer 2000;89(11) Suppl:2369–2376.
8. Wanebo HJ,Kennedy BJ,Chmiel J,Steele G Jr,Winchester D,Osteen R. Cancer of the stomach. A patient care study by the American College of Surgeons. Ann Surg 1993;218:583–592.
9. Ajani JA. Evolving chemotherapy for advanced gastric cancer. Oncologist 2005;10 Suppl 3:49–58.
10. Cunningham D,Starling N,Rao S,Iveson T,Nicolson M,Coxon F,et al. Capecitabine and oxaliplatin for advanced esophagogastric cancer. N Engl J Med 2008;358:36–46.
11. Van Cutsem E,Moiseyenko VM,Tjulandin S,Majlis A,Constenla M,Boni C,et al. Phase III study of docetaxel and cisplatin plus fluorouracil compared with cisplatin and fluorouracil as first-line therapy for advanced gastric cancer: a report of the V325 Study Group. J Clin Oncol 2006;24:4991–4997.
12. Press MF,Lenz HJ. EGFR, HER2 and VEGF pathways: validated targets for cancer treatment. Drugs 2007;67:2045–2075.
13. Wagner AD,Moehler M. Development of targeted therapies in advanced gastric cancer: promising exploratory steps in a new era. Curr Opin Oncol 2009;21:381–385.
14. Romond EH,Perez EA,Bryant J,Suman VJ,Geyer CE Jr,Davidson NE,et al. Trastuzumab plus adjuvant chemotherapy for operable HER2-positive breast cancer. N Engl J Med 2005;353:1673–1684.
15. Sequist LV,Martins RG,Spigel D,Grunberg SM,Spira A,Jänne PA,et al. First-line gefitinib in patients with advanced non-small-cell lung cancer harboring somatic EGFR mutations. J Clin Oncol 2008;26:2442–2449.
16. Fukuoka M,Yano S,Giaccone G,Tamura T,Nakagawa K,Douillard JY,et al. Multi-institutional randomized phase II trial of gefitinib for previously treated patients with advanced non-small-cell lung cancer (The IDEAL 1 Trial) [corrected]. J Clin Oncol 2003;21:2237–2246.
17. Kris MG,Natale RB,Herbst RS,Lynch TJ Jr,Prager D,Belani CP,et al. Efficacy of gefitinib, an inhibitor of the epidermal growth factor receptor tyrosine kinase, in symptomatic patients with non-small cell lung cancer: a randomized trial. JAMA 2003;290:2149–2158.
18. Lauren P. The two histological main types of gastric carcinoma: diffuse and so-called intestinal-type carcinoma. An attempt at a histo-clinical classification. Acta Pathol Microbiol Scand 1965;64:31–49.
19. Wood LD,Parsons DW,Jones S,Lin J,Sjöblom T,Leary RJ,et al. The genomic landscapes of human breast and colorectal cancers. Science 2007;318:1108–1113.
20. Weir BA,Woo MS,Getz G,Perner S,Ding L,Beroukhim R,et al. Characterizing the cancer genome in lung adenocarcinoma. Nature 2007;450:893–898.
21. Ding L,Getz G,Wheeler DA,Mardis ER,McLellan MD,Cibulskis K,et al. Somatic mutations affect key pathways in lung adenocarcinoma. Nature 2008;455:1069–1075.
22. Parsons DW,Jones S,Zhang X,Lin JC,Leary RJ,Angenendt P,et al. An integrated genomic analysis of human glioblastoma multiforme. Science 2008;321:1807–1812.
23. Cancer Genome Atlas Research Network. Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature 2008;455:1061–1068.
24. Cunningham D,Allum WH,Stenning SP,Thompson JN,Van de Velde CJ,Nicolson M,et al. Perioperative chemotherapy versus surgery alone for resectable gastroesophageal cancer. N Engl J Med 2006;355:11–20.
25. Strauss GM,Herndon JE 2nd,Maddaus MA,Johnstone DW,Johnson EA,Harpole DH,et al. Adjuvant paclitaxel plus carboplatin compared with observation in stage IB non-small-cell lung cancer: CALGB 9633 with the Cancer and Leukemia Group B, Radiation Therapy Oncology Group, and North Central Cancer Treatment Group Study Groups. J Clin Oncol 2008;26:5043–5051.
26. Grann VR,Troxel AB,Zojwalla NJ,Jacobson JS,Hershman D,Neugut AI. Hormone receptor status and survival in a population-based cohort of patients with breast carcinoma. Cancer 2005;103:2241–2251.
27. Early Breast Cancer Trialists' Collaborative Group (EBCTCG). Effects of chemotherapy and hormonal therapy for early breast cancer on recurrence and 15-year survival: an overview of the randomised trials. Lancet 2005;365:1687–1717.
28. Lynch TJ,Bell DW,Sordella R,Gurubhagavatula S,Okimoto RA,Brannigan BW,et al. Activating mutations in the epidermal growth factor receptor underlying responsiveness of non-small-cell lung cancer to gefitinib. N Engl J Med 2004;350:2129–2139.
29. Paez JG,Jänne PA,Lee JC,Tracy S,Greulich H,Gabriel S,et al. EGFR mutations in lung cancer: correlation with clinical response to gefitinib therapy. Science 2004;304:1497–1500.
30. Ogunbiyi OA,Goodfellow PJ,Herfarth K,Gagliardi G,Swanson PE,Birnbaum EH,et al. Confirmation that chromosome 18q allelic loss in colon cancer is a prognostic indicator. J Clin Oncol 1998;16:427–433.
31. Schleicher C,Poremba C,Wolters H,Schäfer KL,Senninger N,Colombo-Benkmann M. Gain of chromosome 8q: a potential prognostic marker in resectable adenocarcinoma of the pancreas?. Ann Surg Oncol 2007;14:1327–1335.
32. Gusterson BA,Gelber RD,Goldhirsch A,Price KN,Säve-Söderborgh J,Anbazhagan R,et al. Prognostic importance of c-erbB-2 expression in breast cancer. International (Ludwig) Breast Cancer Study Group. J Clin Oncol 1992;10:1049–1056.
33. Borg A,Tandon AK,Sigurdsson H,Clark GM,Ferno M,Fuqua SA,et al. HER-2/neu amplification predicts poor survival in node-positive breast cancer. Cancer Res 1990;50:4332–4337.
34. Smith I,Procter M,Gelber RD,Guillaume S,Feyereislova A,Dowsett M,et al. 2-year follow-up of trastuzumab after adjuvant chemotherapy in HER2-positive breast cancer: a randomised controlled trial. Lancet 2007;369:29–36.
35. Perou CM,Sorlie T,Eisen MB,van de Rijn M,Jeffrey SS,Rees CA,et al. Molecular portraits of human breast tumours. Nature 2000;406:747–752.
36. Bertucci F,Finetti P,Cervera N,Charafe-Jauffret E,Buttarelli M,Jacquemier J,et al. How different are luminal A and basal breast cancers?. Int J Cancer 2009;124:1338–1348.
37. Sorlie T,Tibshirani R,Parker J,Hastie T,Marron JS,Nobel A,et al. Repeated observation of breast tumor subtypes in independent gene expression data sets. Proc Natl Acad Sci U S A 2003;100:8418–8423.
38. Yu K,Lee CH,Tan PH,Tan P. Conservation of breast cancer molecular subtypes and transcriptional patterns of tumor progression across distinct ethnic populations. Clin Cancer Res 2004;10:5508–5517.
39. Tan BK,Tan LK,Yu K,Tan PH,Lee M,Sii LH,et al. Clinical validation of a customized multiple signature microarray for breast cancer. Clin Cancer Res 2008;14:461–469.
40. Bild AH,Yao G,Chang JT,Wang Q,Potti A,Chasse D,et al. Oncogenic pathway signatures in human cancers as a guide to targeted therapies. Nature 2006;439:353–357.
41. Chang JT,Carvalho C,Mori S,Bild AH,Gatza ML,Wang Q,et al. A genomic strategy to elucidate modules of oncogenic pathway signaling networks. Mol Cell 2009;34:104–114.
42. Ley TJ,Mardis ER,Ding L,Fulton B,McLellan MD,Chen K,et al. DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome. Nature 2008;456:66–72.
43. Hampton OA,Den Hollander P,Miller CA,Delgado DA,Li J,Coarfa C,et al. A sequence-level map of chromosomal breakpoints in the MCF-7 breast cancer cell line yields insights into the evolution of a cancer genome. Genome Res 2009;19:167–177.
44. Early Breast Cancer Trialists' Collaborative Group. Polychemotherapy for early breast cancer: an overview of the randomised trials. Lancet 1998;352:930–942.
45. Early Breast Cancer Trialists' Collaborative Group. Tamoxifen for early breast cancer: an overview of the randomised trials. Early Breast Cancer Trialists' Collaborative Group. Lancet 1998;351:1451–1467.
46. van't Veer LJ,Dai H,van de Vijver MJ,He YD,Hart AA,Mao M,et al. Gene expression profiling predicts clinical outcome of breast cancer. Nature 2002;415:530–536.
47. Buyse M,Loi S,van't Veer L,Viale G,Delorenzi M,Glas AM,et al. Validation and clinical utility of a 70-gene prognostic signature for women with node-negative breast cancer. J Natl Cancer Inst 2006;98:1183–1192.
48. van de Vijver MJ,He YD,van't Veer LJ,Dai H,Hart AA,Voskuil DW,et al. A gene-expression signature as a predictor of survival in breast cancer. N Engl J Med 2002;347:1999–2009.
49. Solit DB,Garraway LA,Pratilas CA,Sawai A,Getz G,Basso A,et al. BRAF mutation predicts sensitivity to MEK inhibition. Nature 2006;439:358–362.
50. Klampfer L,Huang J,Shirasawa S,Sasazuki T,Augenlicht L. Histone deacetylase inhibitors induce cell death selectively in cells that harbor activated kRasV12: The role of signal transducers and activators of transcription 1 and p21. Cancer Res 2007;67:8477–8485.
51. Karapetis CS,Khambata-Ford S,Jonker DJ,O'Callaghan CJ,Tu D,Tebbutt NC,et al. K-ras mutations and benefit from cetuximab in advanced colorectal cancer. N Engl J Med 2008;359:1757–1765.
52. Berns K,Horlings HM,Hennessy BT,Madiredjo M,Hijmans EM,Beelen K,et al. A functional genetic approach identifies the PI3K pathway as a major determinant of trastuzumab resistance in breast cancer. Cancer Cell 2007;12:395–402.
53. McGrogan BT,Gilmartin B,Carney DN,McCann A. Taxanes, microtubules and chemoresistant breast cancer. Biochim Biophys Acta 2008;1785:96–132.
54. Ciaparrone M,Quirino M,Schinzari G,Zannoni G,Corsi DC,Vecchio FM,et al. Predictive role of thymidylate synthase, dihydropyrimidine dehydrogenase and thymidine phosphorylase expression in colorectal cancer patients receiving adjuvant 5-fluorouracil. Oncology 2006;70:366–377.
55. Wehling M. Assessing the translatability of drug projects: what needs to be scored to predict success?. Nat Rev Drug Discov. 2009
advanced online publication
56. Trusheim MR,Berndt ER,Douglas FL. Stratified medicine: strategic and economic implications of combining drugs and clinical biomarkers. Nat Rev Drug Discov 2007;6:287–293.
57. Pui CH,Evans WE. Treatment of acute lymphoblastic leukemia. N Engl J Med 2006;354:166–178.
58. Pui CH,Robison LL,Look AT. Acute lymphoblastic leukaemia. Lancet 2008;371:1030–1043.
59. Armstrong SA,Look AT. Molecular genetics of acute lymphoblastic leukemia. J Clin Oncol 2005;23:6306–6315.
60. Rowley JD. Chromosomal translocations: revisited yet again. Blood 2008;112:2183–2189.
61. Yeoh EJ,Ross ME,Shurtleff SA,Williams WK,Patel D,Mahfouz R,et al. Classification, subtype discovery, and prediction of outcome in pediatric acute lymphoblastic leukemia by gene expression profiling. Cancer Cell 2002;1:133–143.
62. Armstrong SA,Staunton JE,Silverman LB,Pieters R,den Boer ML,Minden MD,et al. MLL translocations specify a distinct gene expression profile that distinguishes a unique leukemia. Nat Genet 2002;30:41–47.
63. Woessmann W,Seidemann K,Mann G,Zimmermann M,Burkhardt B,Oschlies I,et al. The impact of the methotrexate administration schedule and dose in the treatment of children and adolescents with B-cell neoplasms: a report of the BFM Group Study NHL-BFM95. Blood 2005;105:948–958.
64. Lee EJ,Petroni GR,Schiffer CA,Freter CE,Johnson JL,Barcos M,et al. Brief-duration high-intensity chemotherapy for patients with small noncleaved-cell lymphoma or FAB L3 acute lymphocytic leukemia: results of cancer and leukemia group B study 9251. J Clin Oncol 2001;19:4014–4022.
65. Landau H,Lamanna N. Clinical manifestations and treatment of newly diagnosed acute lymphoblastic leukemia in adults. Curr Hematol Malig Rep 2006:171–179.
66. Larson RA. Management of acute lymphoblastic leukemia in older patients. Semin Hematol 2006;43:126–133.
67. Druker BJ. Imatinib as a paradigm of targeted therapies. Adv Cancer Res 2004;91:1–30.
68. Mullighan CG,Goorha S,Radtke I,Miller CB,Coustan-Smith E,Dalton JD,et al. Genome-wide analysis of genetic alterations in acute lymphoblastic leukaemia. Nature 2007;446:758–764.
69. Mertens F,Johansson B,Höglund M,Mitelman F. Chromosomal imbalance maps of malignant solid tumors: a cytogenetic survey of 3185 neoplasms. Cancer Res 1997;57:2765–2780.
70. Tomlins SA,Rhodes DR,Perner S,Dhanasekaran SM,Mehra R,Sun XW,et al. Recurrent fusion of TMPRSS2 and ETS transcription factor genes in prostate cancer. Science 2005;310:644–648.
71. Soda M,Choi YL,Enomoto M,Takada S,Yamashita Y,Ishikawa S,et al. Identification of the transforming EML4-ALK fusion gene in non-small-cell lung cancer. Nature 2007;448:561–566.
72. Maher CA,Kumar-Sinha C,Cao X,Kalyana-Sundaram S,Han B,Jing X,et al. Transcriptome sequencing to detect gene fusions in cancer. Nature 2009;458:97–101.
73. Jones S,Hruban RH,Kamiyama M,Borges M,Zhang X,Parsons DW,et al. Exomic sequencing identifies PALB2 as a pancreatic cancer susceptibility gene. Science 2009;324:217.
74. Sjöblom T,Jones S,Wood LD,Parsons DW,Lin J,Barber TD,et al. The consensus coding sequences of human breast and colorectal cancers. Science 2006;314:268–274.
75. Jones S,Zhang X,Parsons DW,Lin JC,Leary RJ,Angenendt P,et al. Core signaling pathways in human pancreatic cancers revealed by global genomic analyses. Science 2008;321:1801–1806.
76. Lorusso G,Rüegg C. The tumor microenvironment and its contribution to tumor evolution toward metastasis. Histochem Cell Biol 2008;130:1091–1103.
77. Orimo A,Gupta PB,Sgroi DC,Arenzana-Seisdedos F,Delaunay T,Naeem R,et al. Stromal fibroblasts present in invasive human breast carcinomas promote tumor growth and angiogenesis through elevated SDF-1/CXCL12 secretion. Cell 2005;121:335–348.
78. Atreya I,Neurath MF. Immune cells in colorectal cancer: prognostic relevance and therapeutic strategies. Expert Rev Anticancer Ther 2008;8:561–572.
79. Hoshida Y,Villanueva A,Kobayashi M,Peix J,Chiang DY,Camargo A,et al. Gene expression in fixed tissues and outcome in hepatocellular carcinoma. N Engl J Med 2008;359:1995–2004.
80. Chansky K,Sculier JP,Crowley JJ,Giroux D,Van Meerbeeck J,Goldstraw P. International Staging Committee and Participating Institutions. The International Association for the Study of Lung Cancer Staging Project: prognostic factors and pathologic TNM stage in surgically managed non-small cell lung cancer. J Thorac Oncol 2009;4:792–801.
81. Lim EH,Aggarwal A,Agasthian T,Wong PS,Tan C,Sim E,et al. Feasibility of using low-volume tissue samples for gene expression profiling of advanced non-small cell lung cancers. Clin Cancer Res 2003;9:5980–5987.
82. Lim EH,Zhang SL,Yu K,Nga ME,Ahmed DA,Agasthian T,et al. An alternative approach to determining therapeutic choices in advanced non-small cell lung carcinoma (NSCLC): maximizing the diagnostic procedure and the use of low-volume lung biopsies. J Thorac Oncol 2007;2:387–396.
83. Rhodes DR,Barrette TR,Rubin MA,Ghosh D,Chinnaiyan AM. Meta-analysis of microarrays: interstudy validation of gene expression profiles reveals pathway dysregulation in prostate cancer. Cancer Res 2002;62:4427–4433.
84. Aggarwal A,Guo DL,Hoshida Y,Yuen ST,Chu KM,So S,et al. Topological and functional discovery in a gene coexpression metanetwork of gastric cancer. Cancer Res 2006;66:232–241.
85. Sørlie T,Perou CM,Tibshirani R,Aas T,Geisler S,Johnsen H,et al. Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications. Proc Natl Acad Sci U S A 2001;98:10869–10874.
86. Miller LD,Smeds J,George J,Vega VB,Vergara L,Ploner A,et al. An expression signature for p53 status in human breast cancer predicts mutation status, transcriptional effects, and patient survival. Proc Natl Acad Sci U S A 2005;102:13550–13555.
87. Troester MA,Hoadley KA,Sørlie T,Herbert BS,Børresen-Dale AL,Lønning PE,et al. Cell-type-specific responses to chemotherapeutics in breast cancer. Cancer Res 2004;64:4218–4226.
88. Mirzoeva OK,Das D,Heiser LM,Bhattacharya S,Siwak D,Gendelman R,et al. Basal subtype and MAPK/ERK kinase (MEK)-phosphoinositide 3-kinase feedback signaling determine susceptibility of breast cancer cells to MEK inhibition. Cancer Res 2009;69:565–572.
89. Chin K,DeVries S,Fridlyand J,Spellman PT,Roydasgupta R,Kuo WL,et al. Genomic and transcriptional aberrations linked to breast cancer pathophysiologies. Cancer Cell 2006;10:529–541.
90. Tay ST,Leong SH,Yu K,Aggarwal A,Tan SY,Lee CH,et al. A combined comparative genomic hybridization and expression microarray analysis of gastric cancer reveals novel molecular subtypes. Cancer Res 2003;63:3309–3316.
91. Boussioutas A,Li H,Liu J,Waring P,Lade S,Holloway AJ,et al. Distinctive patterns of gene expression in premalignant gastric mucosa and gastric cancer. Cancer Res 2003;63:2569–2577.
92. Tan PK,Downey TJ,Spitznagel EL Jr,Xu P,Fu D,Dimitrov DS,et al. Evaluation of gene expression measurements from commercial microarray platforms. Nucleic Acids Res 2003;31:5676–5684.
93. Fortunel NO,Otu HH,Ng HH,Chen J,Mu X,Chevassut T,et al. Comment on "'Stemness': transcriptional profiling of embryonic and adult stem cells" and "a stem cell molecular signature". Science 2003;302:393.
94. Michiels S,Koscielny S,Hill C. Prediction of cancer outcome with microarrays: a multiple random validation strategy. Lancet 2005;365:488–492.
95. Ioannidis JP. Microarrays and molecular research: noise discovery?. Lancet 2005;365:454–455.
96. Director's Challenge Consortium for the Molecular Classification of Lung Adenocarcinoma. Shedden K,Taylor JM,Enkemann SA,Tsao MS,Yeatman TJ,et al. Gene expression-based survival prediction in lung adenocarcinoma: a multi-site, blinded validation study. Nat Med 2008;14:822–827.
97. Cardoso F,Van't Veer L,Rutgers E,Loi S,Mook S,Piccart-Gebhart MJ. Clinical application of the 70-gene profile: the MINDACT trial. J Clin Oncol 2008;26:729–735.
98. Anguiano A,Potti A. Genomic signatures individualize therapeutic decisions in non-small-cell lung cancer. Expert Rev Mol Diagn 2007;7:837–844.
99. Jänne PA,Engelman JA,Johnson BE. Epidermal growth factor receptor mutations in non-small-cell lung cancer: implications for treatment and tumor biology. J Clin Oncol 2005;23:3227–3234.
100. Tu LC,Foltz G,Lin E,Hood L,Tian Q. Targeting stem cells-clinical implications for cancer therapy. Curr Stem Cell Res Ther 2009;4:147–153.