Diverse drug-resistance mechanisms can emerge from drug-tolerant cancer persister cells

Cancer therapy has traditionally focused on eliminating fast-growing populations of cells. Yet, an increasing body of evidence suggests that small subpopulations of cancer cells can evade strong selective drug pressure by entering a ‘persister' state of negligible growth. This drug-tolerant state has been hypothesized to be part of an initial strategy towards eventual acquisition of bona fide drug-resistance mechanisms. However, the diversity of drug-resistance mechanisms that can expand from a persister bottleneck is unknown. Here we compare persister-derived, erlotinib-resistant colonies that arose from a single, EGFR-addicted lung cancer cell. We find, using a combination of large-scale drug screening and whole-exome sequencing, that our erlotinib-resistant colonies acquired diverse resistance mechanisms, including the most commonly observed clinical resistance mechanisms. Thus, the drug-tolerant persister state does not limit—and may even provide a latent reservoir of cells for—the emergence of heterogeneous drug-resistance mechanisms.

[1]  F. Parodi,et al.  The histone demethylase KDM5A is a key factor for the resistance to temozolomide in glioblastoma , 2015, Cell cycle.

[2]  John R. Engen,et al.  Novel mutant-selective EGFR kinase inhibitors against EGFR T790M , 2009, Nature.

[3]  S. Ou Second-generation irreversible epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors (TKIs): a better mousetrap? A review of the clinical evidence. , 2012, Critical reviews in oncology/hematology.

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

[5]  G. Getz,et al.  Tumor cells can follow distinct evolutionary paths to become resistant to epidermal growth factor receptor inhibition , 2016, Nature Medicine.

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

[7]  M. Kuwano,et al.  Sensitivity to gefitinib (Iressa, ZD1839) in non-small cell lung cancer cell lines correlates with dependence on the epidermal growth factor (EGF) receptor/extracellular signal-regulated kinase 1/2 and EGF receptor/Akt pathway for proliferation. , 2004, Molecular cancer therapeutics.

[8]  Richard Durbin,et al.  Fast and accurate long-read alignment with Burrows–Wheeler transform , 2010, Bioinform..

[9]  Junfeng Xia,et al.  Next-generation sequencing of paired tyrosine kinase inhibitor-sensitive and -resistant EGFR mutant lung cancer cell lines identifies spectrum of DNA changes associated with drug resistance , 2013, Genome research.

[10]  M. Meyerson,et al.  EGFR mutation and resistance of non-small-cell lung cancer to gefitinib. , 2005, The New England journal of medicine.

[11]  Joon-Oh Park,et al.  MET Amplification Leads to Gefitinib Resistance in Lung Cancer by Activating ERBB3 Signaling , 2007, Science.

[12]  K. Polyak,et al.  Tumor heterogeneity: causes and consequences. , 2010, Biochimica et biophysica acta.

[13]  P. Mischel,et al.  Reversing Melanoma Cross-Resistance to BRAF and MEK Inhibitors by Co-Targeting the AKT/mTOR Pathway , 2011, PloS one.

[14]  Luca Toschi,et al.  Preexistence and clonal selection of MET amplification in EGFR mutant NSCLC. , 2010, Cancer cell.

[15]  Jin Kim,et al.  Robust dose-response curve estimation applied to high content screening data analysis , 2014, Source Code for Biology and Medicine.

[16]  Levi A Garraway,et al.  Reactivation of ERK signaling causes resistance to EGFR kinase inhibitors. , 2012, Cancer discovery.

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

[18]  A. Sivachenko,et al.  Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples , 2013, Nature Biotechnology.

[19]  J. Korn,et al.  Inhibition of Casein Kinase 1 Alpha Prevents Acquired Drug Resistance to Erlotinib in EGFR-Mutant Non-Small Cell Lung Cancer. , 2015, Cancer research.

[20]  Mohammad Fallahi-Sichani,et al.  Metrics other than potency reveal systematic variation in responses to cancer drugs. , 2013, Nature chemical biology.

[21]  N. Socci,et al.  Optimization of Dosing for EGFR-Mutant Non–Small Cell Lung Cancer with Evolutionary Cancer Modeling , 2011, Science Translational Medicine.

[22]  William Pao,et al.  MET amplification occurs with or without T790M mutations in EGFR mutant lung tumors with acquired resistance to gefitinib or erlotinib , 2007, Proceedings of the National Academy of Sciences.

[23]  W. Pao,et al.  Acquired Resistance to the Mutant-Selective EGFR Inhibitor AZD9291 Is Associated with Increased Dependence on RAS Signaling in Preclinical Models. , 2015, Cancer research.

[24]  Frank McCormick,et al.  AKT inactivation causes persistent drug tolerance to EGFR inhibitors. , 2015, Pharmacological research.

[25]  Joshua M. Korn,et al.  Studying clonal dynamics in response to cancer therapy using high-complexity barcoding , 2015, Nature Medicine.

[26]  A. D’Andrea,et al.  DNA Polymerase POLN Participates in Cross-Link Repair and Homologous Recombination , 2009, Molecular and Cellular Biology.

[27]  P. A. Futreal,et al.  Intratumor heterogeneity and branched evolution revealed by multiregion sequencing. , 2012, The New England journal of medicine.

[28]  Clinton C. Dawson,et al.  “Persisters”: Survival at the Cellular Level , 2011, PLoS pathogens.

[29]  W. Pao,et al.  Acquired resistance to TKIs in solid tumours: learning from lung cancer , 2014, Nature Reviews Clinical Oncology.

[30]  Krister Wennerberg,et al.  Quantitative scoring of differential drug sensitivity for individually optimized anticancer therapies , 2014, Scientific Reports.

[31]  John Quackenbush,et al.  Exome sequencing-based copy-number variation and loss of heterozygosity detection: ExomeCNV , 2011, Bioinform..

[32]  Richard Durbin,et al.  Sequence analysis Fast and accurate short read alignment with Burrows – Wheeler transform , 2009 .

[33]  T Hardmeier,et al.  High-throughput tissue microarray analysis of 3p25 (RAF1) and 8p12 (FGFR1) copy number alterations in urinary bladder cancer. , 2001, Cancer research.

[34]  F. Welch,et al.  Causes and Consequences , 2017, Nature.

[35]  M. Ladanyi,et al.  Coexistence of PIK3CA and Other Oncogene Mutations in Lung Adenocarcinoma–Rationale for Comprehensive Mutation Profiling , 2011, Molecular Cancer Therapeutics.

[36]  Steven A. Frank,et al.  Nonheritable Cellular Variability Accelerates the Evolutionary Processes of Cancer , 2012, PLoS biology.

[37]  Lani F. Wu,et al.  GSK-3 modulates cellular responses to a broad spectrum of kinase inhibitors , 2014, Nature chemical biology.

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

[39]  P. Vogt,et al.  Cancer-specific mutations in PIK3CA are oncogenic in vivo , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[40]  M. Glickman,et al.  Converting Cancer Therapies into Cures: Lessons from Infectious Diseases , 2012, Cell.

[41]  T. Bivona,et al.  Mechanisms of Resistance to Epidermal Growth Factor Receptor Inhibitors and Novel Therapeutic Strategies to Overcome Resistance in NSCLC Patients , 2012, Chemotherapy research and practice.

[42]  H. Varmus,et al.  KRAS Mutations and Primary Resistance of Lung Adenocarcinomas to Gefitinib or Erlotinib , 2005, PLoS medicine.

[43]  S. Leibler,et al.  Bacterial Persistence as a Phenotypic Switch , 2004, Science.