Addressing genetic tumor heterogeneity through computationally predictive combination therapy

Cancer Discovery

Volumn 4, Issue 2, 2014, Pages 166-174

  Zhao, Boyang ^a   Pritchard, Justin R ^a,b,c   Lauffenburger, Douglas A ^a,b   Hemann, Michael T ^a,b  

^a David H Koch Institute for Integrative Cancer Research   (United States)

^b MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

^c ARIAD PHARMACEUTICALS INC   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CHLORAMBUCIL; IRINOTECAN; SHORT HAIRPIN RNA; VINCRISTINE; VORINOSTAT;

ALGORITHM; ANIMAL CELL; ANIMAL EXPERIMENT; ANIMAL MODEL; ARTICLE; CANCER SURVIVAL; CELL HETEROGENEITY; CONTROLLED STUDY; FEMALE; FLOW CYTOMETRY; FLUORESCENCE IMAGING; GENE EXPRESSION; GENETIC HETEROGENEITY; HIGH THROUGHPUT SEQUENCING; LOSS OF FUNCTION MUTATION; LYMPHOMA; MATHEMATICAL MODEL; MOUSE; NONHUMAN; POLYPHARMACY; PREDICTION; PRINCIPAL COMPONENT ANALYSIS; RNA INTERFERENCE;

ALGORITHMS; ANIMALS; ANTINEOPLASTIC COMBINED CHEMOTHERAPY PROTOCOLS; COMPUTER SIMULATION; DISEASE MODELS, ANIMAL; FEMALE; GENETIC HETEROGENEITY; HUMANS; LYMPHOMA; MICE; MODELS, BIOLOGICAL; NEOPLASMS; PHARMACOGENETICS; PROGNOSIS; REPRODUCIBILITY OF RESULTS; RNA INTERFERENCE; TREATMENT OUTCOME; XENOGRAFT MODEL ANTITUMOR ASSAYS;

EID: 84896727479     PISSN: 21598274     EISSN: 21598290     Source Type: Journal    
DOI: 10.1158/2159-8290.CD-13-0465     Document Type: Article

References (40)

1. Swanton C. Intratumor heterogeneity: evolution through space and time. Cancer Res 2012; 72: 4875-82.
2. Fisher R, Pusztai L, Swanton C. Cancer heterogeneity: implications for targeted therapeutics. Br J Cancer 2013; 108: 479-85.
3. Anderson K, Lutz C, van Delft FW, Bateman CM, Guo Y, Colman SM, et al. Genetic variegation of clonal architecture and propagating cells in leukaemia. Nature 2011; 469: 356-61.
4. Walter MJ, Shen D, Ding L, Shao J, Koboldt DC, Chen K, et al. Clonal architecture of secondary acute myeloid leukemia. N Engl J Med 2012; 366: 1090-8.
5. Gerlinger M, Rowan AJ, Horswell S, Larkin J, Endesfelder D, Gronroos E, et al. Intratumor heterogeneity and branched evolution revealed by multiregion sequencing. N Engl J Med 2012; 366: 883-92.
6. Yachida S, Jones S, Bozic I, Antal T, Leary R, Fu B, et al. Distant metastasis occurs late during the genetic evolution of pancreatic cancer. Nature 2010; 467: 1114-7.
7. Campbell PJ, Yachida S, Mudie LJ, Stephens PJ, Pleasance ED, Stebbings La, et al. The patterns and dynamics of genomic instability in metastatic pancreatic cancer. Nature 2010; 467: 1109-13.
8. Shah SP, Morin RD, Khattra J, Prentice L, Pugh T, Burleigh A, et al. Mutational evolution in a lobular breast tumour profiled at single nucleotide resolution. Nature 2009; 461: 809-13.
9. Ding L, Ellis MJ, Li S, Larson DE, Chen K, Wallis JW, et al. Genome remodelling in a basal-like breast cancer metastasis and xenograft. Nature 2010; 464: 999-1005.
10. Navin N, Kendall J, Troge J, Andrews P, Rodgers L, McIndoo J, et al. Tumour evolution inferred by single-cell sequencing. Nature 2011; 472: 90-4.
11. Wu X, Northcott PA, Dubuc A, Dupuy AJ, Shih DJH, Witt H, et al. Clonal selection drives genetic divergence of metastatic medulloblastoma. Nature 2012; 482: 529-33.
12. Mullighan CG, Phillips LA, Su X, Ma J, Miller CB, Shurtleff SA, et al. Genomic analysis of the clonal origins of relapsed acute lymphoblastic leukemia. Science 2008; 322: 1377-80.
13. Ding L, Ley TJ, Larson DE, Miller CA, Koboldt DC, Welch JS, et al. Clonal evolution in relapsed acute myeloid leukaemia revealed by whole-genome sequencing. Nature 2012; 481: 506-10.
14. Schuh A, Becq J, Humphray S, Alexa A, Burns A, Clifford R, et al. Monitoring chronic lymphocytic leukemia progression by whole genome sequencing reveals heterogeneous clonal evolution patterns. Blood 2012; 120: 4191-6.
15. Keats JJ, Chesi M, Egan JB, Garbitt VM, Palmer SE, Braggio E, et al. Clonal competition with alternating dominance in multiple myeloma. Blood 2012; 120: 1067-76.
16. Landau DA, Carter SL, Stojanov P, McKenna A, Stevenson K, Lawrence MS, et al. Evolution and impact of subclonal mutations in chronic lymphocytic leukemia. Cell 2013; 152: 714-26.
17. Foo J, Michor F. Evolution of resistance to anti-cancer therapy during general dosing schedules. J Theor Biol 2010; 263: 179-88.
18. Panetta JC. A mathematical model of drug resistance: heterogeneous tumors. Math Biosci 1998; 147: 41-61.
19. Beckman RA, Schemmann GS, Yeang C-H. Impact of genetic dynamics and single-cell heterogeneity on development of nonstandard personalized medicine strategies for cancer. Proc Natl Acad Sci U S A 2012; 109: 14586-91.
20. Coldman AJ, Goldie JH. A stochastic model for the origin and treatment of tumors containing drug-resistant cells. Bull Math Biol 1986; 48: 279-92.
21. Chmielecki J, Foo J, Oxnard GR, Hutchinson K, Ohashi K, Somwar R, et al. Optimization of dosing for EGFR-mutant non-small cell lung cancer with evolutionary cancer modeling. Sci Transl Med 2011; 3: 90ra59.
22. Das Thakur M, Salangsang F, Landman AS, Sellers WR, Pryer NK, Levesque MP, et al. Modelling vemurafenib resistance in melanoma reveals a strategy to forestall drug resistance. Nature 2013; 494: 251-5.
23. Pritchard JR, Bruno PM, Gilbert LA, Capron KL, Lauffenburger DA, Hemann MT. Defining principles of combination drug mechanisms of action. Proc Natl Acad Sci U S A 2013; 110: E170-9.
24. Jiang H, Pritchard JR, Williams RT, Lauffenburger DA, Hemann MT. A mammalian functional-genetic approach to characterizing cancer therapeutics. Nat Chem Biol 2011; 7: 92-100.
25. Janes KA, Albeck JG, Gaudet S, Sorger PK, Lauffenburger Da, Yaffe MB. A systems model of signaling identifies a molecular basis set for cytokine-induced apoptosis. Science 2005; 310: 1646-53.
26. Cosgrove BD, Alexopoulos LG, Hang T, Hendriks BS, Sorger PK, Griffith LG, et al. Cytokine-associated drug toxicity in human hepatocytes is associated with signaling network dysregulation. Mol Biosyst 2010; 6: 1195-206.
27. Adams JM, Harris AW, Pinkert CA, Corcoran LM, Alexander WS, Cory S, et al. The c-myc oncogene driven by immunoglobulin enhancers induces lymphoid malignancy in transgenic mice. Nature 1985; 318: 533-8.
28. Schmitt CA, McCurrach ME, de Stanchina E, Wallace-Brodeur RR, Lowe SW. INK4a/ARF mutations accelerate lymphomagenesis and promote chemoresistance by disabling p53. Genes Dev 1999; 13: 2670-7.
29. Nowell PC. The clonal evolution of tumor cell populations. Science 1976; 194: 23-8.
30. Szerlip NJ, Pedraza A, Chakravarty D, Azim M, McGuire J, Fang Y, et al. Intratumoral heterogeneity of receptor tyrosine kinases EGFR and PDGFRA amplification in glioblastoma defines subpopulations with distinct growth factor response. Proc Natl Acad Sci U S A 2012; 109: 3041-6.
31. Snuderl M, Fazlollahi L, Le LP, Nitta M, Zhelyazkova BH, Davidson CJ, et al. Mosaic amplification of multiple receptor tyrosine kinase genes in glioblastoma. Cancer Cell 2011; 20: 810-7.
32. Notta F, Mullighan CG, Wang JCY, Poeppl A, Doulatov S, Phillips LA, et al. Evolution of human BCR-ABL1 lymphoblastic leukaemiainitiating cells. Nature 2011; 469: 362-7.
33. Kreso A, O'Brien CA, van Galen P, Gan OI, Notta F, Brown A MK, et al. Variable clonal repopulation dynamics influence chemotherapy response in colorectal cancer. Science 2013; 339: 543-8.
34. Law LW. Origin of the resistance of leukaemic cells to folic acid antagonists. Nature 1952; 169: 628-9.
35. Law LW. Effects of combinations of antileukemic agents on an acute lymphocytic leukemia of mice. Cancer Res 1952; 12: 871-8.
36. Goldie JH, Coldman AJ. A mathematic model for relating the drug sensitivity of tumors to their spontaneous mutation rate. Cancer Treat Rep 1979; 63: 1727-33.
37. Goldie JH, Coldman AJ. The genetic origin of drug resistance in neoplasms: implications for systemic therapy. Cancer Res 1984; 44: 3643-53.
38. Pinkel D, Hernandez K, Borella L, Holton C, Aur R, Samoy G, et al. Drug dosage and remission duration in childhood lymphocytic leukemia. Cancer 1971; 27: 247-56.
39. Gutiérrez MI, Bhatia K, Cherney B, Capello D, Gaidano G, Magrath I. Intraclonal molecular heterogeneity suggests a hierarchy of pathogenetic events in Burkitt's lymphoma. Ann Oncol 1997; 8: 987-94.
40. Dickins RA, Hemann MT, Zilfou JT, Simpson DR, Ibarra I, Hannon GJ, et al. Probing tumor phenotypes using stable and regulated synthetic microRNA precursors. Nat Genet 2005; 37: 1289-95.