Understanding the Genetic Mechanisms of Cancer Drug Resistance Using Genomic Approaches.

A major obstacle in precision cancer medicine is the inevitable resistance to targeted therapies. Tremendous effort and progress has been made over the past few years to understand the biochemical and genetic mechanisms underlying drug resistance, with the goal to eventually overcome such daunting challenges. Diverse mechanisms, such as secondary mutations, oncogene bypass, and epigenetic alterations, can all lead to drug resistance, and the number of known involved genes is growing rapidly, thus providing many possibilities to overcome resistance. The finding of these mechanisms and genes invariably requires the application of genomic and functional genomic approaches to tumors or cancer models. In this review, we briefly highlight the major drug-resistance mechanisms known today, and then focus primarily on the technological approaches leading to the advancement of this field.

[1]  J. Mesirov,et al.  Systematic investigation of genetic vulnerabilities across cancer cell lines reveals lineage-specific dependencies in ovarian cancer , 2011, Proceedings of the National Academy of Sciences.

[2]  Douglas A Lauffenburger,et al.  Addressing genetic tumor heterogeneity through computationally predictive combination therapy. , 2013, Cancer discovery.

[3]  Alan Mackay,et al.  Functional viability profiles of breast cancer. , 2011, Cancer discovery.

[4]  Ji Luo,et al.  A SUMOylation-Dependent Transcriptional Subprogram Is Required for Myc-Driven Tumorigenesis , 2012, Science.

[5]  Donald P. McDonnell,et al.  Systematic identification of signaling pathways with potential to confer anticancer drug resistance , 2014, Science Signaling.

[6]  Zemin Zhang,et al.  Activation of the BMP-BMPR pathway conferred resistance to EGFR-TKIs in lung squamous cell carcinoma patients with EGFR mutations , 2015, Proceedings of the National Academy of Sciences.

[7]  K. Kinzler,et al.  Cancer Genome Landscapes , 2013, Science.

[8]  R. Bernards,et al.  Reduced NF1 expression confers resistance to EGFR inhibition in lung cancer. , 2014, Cancer discovery.

[9]  W. Hahn,et al.  RSK3/4 mediate resistance to PI3K pathway inhibitors in breast cancer. , 2013, The Journal of clinical investigation.

[10]  R. Soldi,et al.  A phase I/II study of decitabine in combination with panitumumab in patients with wild-type (wt) KRAS metastatic colorectal cancer , 2013, Investigational New Drugs.

[11]  William C. Hahn,et al.  Towards systematic functional characterization of cancer genomes , 2011, Nature Reviews Genetics.

[12]  Mark J. Ratain,et al.  Tumour heterogeneity in the clinic , 2013, Nature.

[13]  Bo Zhang,et al.  A formal model for analyzing drug combination effects and its application in TNF-α-induced NFκB pathway , 2010, BMC Systems Biology.

[14]  Ho-June Lee,et al.  Drug resistance via feedback activation of Stat3 in oncogene-addicted cancer cells. , 2014, Cancer cell.

[15]  Philippe Dessen,et al.  Characterization of a Large Panel of Patient-Derived Tumor Xenografts Representing the Clinical Heterogeneity of Human Colorectal Cancer , 2012, Clinical Cancer Research.

[16]  Yun Zheng,et al.  Integrated analysis of DNA methylation and mRNA expression profiling reveals candidate genes associated with cisplatin resistance in non-small cell lung cancer , 2014, Epigenetics.

[17]  Aik Choon Tan,et al.  Patient-derived tumour xenografts as models for oncology drug development , 2012, Nature Reviews Clinical Oncology.

[18]  R. Bernards,et al.  Reversible and adaptive resistance to BRAF(V600E) inhibition in melanoma , 2014, Nature.

[19]  M. Gore,et al.  A randomised, phase II trial of the DNA-hypomethylating agent 5-aza-2′-deoxycytidine (decitabine) in combination with carboplatin vs carboplatin alone in patients with recurrent, partially platinum-sensitive ovarian cancer , 2014, British Journal of Cancer.

[20]  Adam A. Margolin,et al.  The Cancer Cell Line Encyclopedia enables predictive modeling of anticancer drug sensitivity , 2012, Nature.

[21]  T. Golub,et al.  Tumour micro-environment elicits innate resistance to RAF inhibitors through HGF secretion , 2012, Nature.

[22]  S. Ramaswamy,et al.  Systematic identification of genomic markers of drug sensitivity in cancer cells , 2012, Nature.

[23]  Marc Hafner,et al.  Profiles of Basal and Stimulated Receptor Signaling Networks Predict Drug Response in Breast Cancer Lines , 2013, Science Signaling.

[24]  Laura Tolosi,et al.  Predicting drug susceptibility of non-small cell lung cancers based on genetic lesions. , 2009, The Journal of clinical investigation.

[25]  E. Lander,et al.  Lessons from the Cancer Genome , 2013, Cell.

[26]  M. Spector,et al.  Organoid Models of Human and Mouse Ductal Pancreatic Cancer , 2015, Cell.

[27]  Dennis C. Friedrich,et al.  MAP kinase pathway alterations in BRAF-mutant melanoma patients with acquired resistance to combined RAF/MEK inhibition. , 2014, Cancer discovery.

[28]  Nikhil Wagle,et al.  Dissecting therapeutic resistance to RAF inhibition in melanoma by tumor genomic profiling. , 2011, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[29]  Marc Vidal,et al.  COT/MAP3K8 drives resistance to RAF inhibition through MAP kinase pathway reactivation , 2010, Nature.

[30]  Thomas M Green,et al.  A public genome-scale lentiviral expression library of human ORFs , 2011, Nature Methods.

[31]  A. Ashworth,et al.  Parallel high-throughput RNA interference screens identify PINK1 as a potential therapeutic target for the treatment of DNA mismatch repair-deficient cancers. , 2011, Cancer research.

[32]  W. Hahn,et al.  PRKACA Mediates Resistance to HER2-Targeted Therapy in Breast Cancer Cells and Restores Anti-Apoptotic Signaling , 2014, Oncogene.

[33]  H. Woo,et al.  Integrative Analysis of Proteomic Signatures, Mutations, and Drug Responsiveness in the NCI 60 Cancer Cell Line Set , 2010, Molecular Cancer Therapeutics.

[34]  Travis J Cohoon,et al.  Synthetic lethal interaction of combined BCL-XL and MEK inhibition promotes tumor regressions in KRAS mutant cancer models. , 2013, Cancer cell.

[35]  Li Ding,et al.  Endocrine-therapy-resistant ESR1 variants revealed by genomic characterization of breast-cancer-derived xenografts. , 2013, Cell reports.

[36]  Benjamin Haibe-Kains,et al.  Inconsistency in large pharmacogenomic studies , 2013, Nature.

[37]  P. Meltzer,et al.  NCI-60 Whole Exome Sequencing and Pharmacological CellMiner Analyses , 2014, PloS one.

[38]  P. Meltzer,et al.  The exomes of the NCI-60 panel: a genomic resource for cancer biology and systems pharmacology. , 2013, Cancer research.

[39]  A. Ashworth,et al.  Identification of novel determinants of resistance to lapatinib in ERBB2-amplified cancers , 2014, Oncogene.

[40]  Chris Albanese,et al.  ROCK inhibitor and feeder cells induce the conditional reprogramming of epithelial cells. , 2012, The American journal of pathology.

[41]  J. Weinstein,et al.  mRNA and microRNA Expression Profiles of the NCI-60 Integrated with Drug Activities , 2010, Molecular Cancer Therapeutics.

[42]  H. Clevers,et al.  Single Lgr5 stem cells build crypt–villus structures in vitro without a mesenchymal niche , 2009, Nature.

[43]  Chris Sander,et al.  Drug Synergy Screen and Network Modeling in Dedifferentiated Liposarcoma Identifies CDK4 and IGF1R as Synergistic Drug Targets , 2013, Science Signaling.

[44]  R. Bernards,et al.  MED12 Controls the Response to Multiple Cancer Drugs through Regulation of TGF-β Receptor Signaling , 2012, Cell.

[45]  Nikhil Wagle,et al.  Clinical Acquired Resistance to RAF Inhibitor Combinations in BRAF-Mutant Colorectal Cancer through MAPK Pathway Alterations. , 2015, Cancer discovery.

[46]  Robert Brown,et al.  Candidate DNA methylation drivers of acquired cisplatin resistance in ovarian cancer identified by methylome and expression profiling , 2012, Oncogene.

[47]  S. Digumarthy,et al.  Genotypic and Histological Evolution of Lung Cancers Acquiring Resistance to EGFR Inhibitors , 2011, Science Translational Medicine.

[48]  M. Schuler,et al.  Phase I study of panobinostat and imatinib in patients with treatment-refractory metastatic gastrointestinal stromal tumors , 2014, British Journal of Cancer.

[49]  T. Phang,et al.  Wnt/Ca2+/NFAT signaling maintains survival of Ph+ leukemia cells upon inhibition of Bcr-Abl. , 2010, Cancer cell.

[50]  C. Scott,et al.  Prioritizing therapeutic targets using patient-derived xenograft models. , 2015, Biochimica et biophysica acta.

[51]  Sridhar Ramaswamy,et al.  Patient-derived models of acquired resistance can identify effective drug combinations for cancer , 2014, Science.

[52]  Julian Downward,et al.  The GATA2 Transcriptional Network Is Requisite for RAS Oncogene-Driven Non-Small Cell Lung Cancer , 2012, Cell.

[53]  A. McKenna,et al.  The genetic landscape of clinical resistance to RAF inhibition in metastatic melanoma. , 2014, Cancer discovery.

[54]  J. Engelman,et al.  Bypass Mechanisms of Resistance to Receptor Tyrosine Kinase Inhibition in Lung Cancer , 2013, Science Signaling.

[55]  A. Sood,et al.  Methylation and histone deacetylase inhibition in combination with platinum treatment in patients with advanced malignancies , 2013, Investigational New Drugs.

[56]  A. Ashworth,et al.  Genome-wide functional screen identifies a compendium of genes affecting sensitivity to tamoxifen , 2011, Proceedings of the National Academy of Sciences.

[57]  J. Weinstein,et al.  High Resolution Copy Number Variation Data in the NCI-60 Cancer Cell Lines from Whole Genome Microarrays Accessible through CellMiner , 2014, PloS one.

[58]  J. Keats,et al.  RNAi screen of the druggable genome identifies modulators of proteasome inhibitor sensitivity in myeloma including CDK5. , 2009, Blood.

[59]  Yiling Lu,et al.  Identification of optimal drug combinations targeting cellular networks: integrating phospho-proteomics and computational network analysis. , 2010, Cancer research.

[60]  A. Ashworth,et al.  Parallel RNA interference screens identify EGFR activation as an escape mechanism in FGFR3-mutant cancer. , 2013, Cancer discovery.

[61]  S. Gabriel,et al.  A functional landscape of resistance to ALK inhibition in lung cancer. , 2015, Cancer cell.

[62]  A. Iafrate,et al.  Identification of genotype-correlated sensitivity to selective kinase inhibitors by using high-throughput tumor cell line profiling , 2007, Proceedings of the National Academy of Sciences.

[63]  Joel Greshock,et al.  Molecular target class is predictive of in vitro response profile. , 2010, Cancer research.

[64]  Hans Clevers,et al.  Organoid Cultures Derived from Patients with Advanced Prostate Cancer , 2014, Cell.

[65]  Erik Sahai,et al.  Intravital Imaging Reveals How BRAF Inhibition Generates Drug-Tolerant Microenvironments with High Integrin β1/FAK Signaling , 2015, Cancer cell.

[66]  Joshy George,et al.  Whole–genome characterization of chemoresistant ovarian cancer , 2015, Nature.

[67]  Jae Cheol Lee,et al.  Activation of the AXL Kinase Causes Resistance to EGFR-Targeted Therapy in Lung Cancer , 2012, Nature Genetics.

[68]  Rajiv Narayan,et al.  A melanocyte lineage program confers resistance to MAP kinase pathway inhibition , 2013, Nature.

[69]  A. Ashworth,et al.  Identification of CDK10 as an important determinant of resistance to endocrine therapy for breast cancer. , 2008, Cancer cell.

[70]  Steven J. M. Jones,et al.  Mutational Analysis Reveals the Origin and Therapy-Driven Evolution of Recurrent Glioma , 2014, Science.

[71]  Francisco J. Sánchez-Rivera,et al.  Applications of the CRISPR–Cas9 system in cancer biology , 2015, Nature Reviews Cancer.

[72]  A. Letai,et al.  RAS signaling promotes resistance to JAK inhibitors by suppressing BAD-mediated apoptosis , 2014, Science Signaling.

[73]  Martin A Nowak,et al.  Timing and heterogeneity of mutations associated with drug resistance in metastatic cancers , 2014, Proceedings of the National Academy of Sciences.

[74]  Manuel Hidalgo,et al.  Patient-derived xenograft models: an emerging platform for translational cancer research. , 2014, Cancer discovery.

[75]  Ben S. Wittner,et al.  A Chromatin-Mediated Reversible Drug-Tolerant State in Cancer Cell Subpopulations , 2010, Cell.

[76]  R. Bernards,et al.  Unresponsiveness of colon cancer to BRAF(V600E) inhibition through feedback activation of EGFR , 2012, Nature.

[77]  J. Mesirov,et al.  A melanoma cell state distinction influences sensitivity to MAPK pathway inhibitors. , 2014, Cancer discovery.

[78]  Mari Mino-Kenudson,et al.  Acquired resistance to crizotinib from a mutation in CD74-ROS1. , 2013, The New England journal of medicine.

[79]  Jane Fridlyand,et al.  Widespread potential for growth-factor-driven resistance to anticancer kinase inhibitors , 2012, Nature.

[80]  Jan Koster,et al.  NF1 Is a Tumor Suppressor in Neuroblastoma that Determines Retinoic Acid Response and Disease Outcome , 2010, Cell.

[81]  Charles Giardina,et al.  Intestinal organoids as tissue surrogates for toxicological and pharmacological studies. , 2013, Biochemical pharmacology.

[82]  E. Cuppen,et al.  Identification of Multipotent Luminal Progenitor Cells in Human Prostate Organoid Cultures , 2014, Cell.

[83]  P. Jänne,et al.  Allelic dilution obscures detection of a biologically significant resistance mutation in EGFR-amplified lung cancer. , 2006, The Journal of clinical investigation.

[84]  K. Badani,et al.  Single luminal epithelial progenitors can generate prostate organoids in culture , 2014, Nature Cell Biology.

[85]  Hayley E. Francies,et al.  Prospective Derivation of a Living Organoid Biobank of Colorectal Cancer Patients , 2015, Cell.

[86]  T. Golub,et al.  Genetic modifiers of EGFR dependence in non-small cell lung cancer , 2014, Proceedings of the National Academy of Sciences.

[87]  F. Bosch,et al.  Identification of a mutation in the extracellular domain of the Epidermal Growth Factor Receptor conferring cetuximab resistance in colorectal cancer , 2012, Nature Medicine.

[88]  Robert Clarke,et al.  Enhancing reproducibility in cancer drug screening: how do we move forward? , 2014, Cancer research.

[89]  Karen Cichowski,et al.  Drug-Induced Death Signaling Strategy Rapidly Predicts Cancer Response to Chemotherapy , 2015, Cell.

[90]  Michael Peyton,et al.  Synthetic lethal screen identification of chemosensitizer loci in cancer cells , 2007, Nature.

[91]  Thomas D. Wu,et al.  A comprehensive transcriptional portrait of human cancer cell lines , 2014, Nature Biotechnology.