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Leighow SM, Reynolds JA, Sokirniy I, Yao S, Yang Z, Inam H, Wodarz D, Archetti M, Pritchard JR. Programming tumor evolution with selection gene drives to proactively combat drug resistance. Nat Biotechnol 2024:10.1038/s41587-024-02271-7. [PMID: 38965430 DOI: 10.1038/s41587-024-02271-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 05/06/2024] [Indexed: 07/06/2024]
Abstract
Most targeted anticancer therapies fail due to drug resistance evolution. Here we show that tumor evolution can be reproducibly redirected to engineer therapeutic opportunity, regardless of the exact ensemble of pre-existing genetic heterogeneity. We develop a selection gene drive system that is stably introduced into cancer cells and is composed of two genes, or switches, that couple an inducible fitness advantage with a shared fitness cost. Using stochastic models of evolutionary dynamics, we identify the design criteria for selection gene drives. We then build prototypes that harness the selective pressure of multiple approved tyrosine kinase inhibitors and employ therapeutic mechanisms as diverse as prodrug catalysis and immune activity induction. We show that selection gene drives can eradicate diverse forms of genetic resistance in vitro. Finally, we demonstrate that model-informed switch engagement effectively targets pre-existing resistance in mouse models of solid tumors. These results establish selection gene drives as a powerful framework for evolution-guided anticancer therapy.
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Affiliation(s)
- Scott M Leighow
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, PA, USA
- Huck Institute For The Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Joshua A Reynolds
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, PA, USA
| | - Ivan Sokirniy
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, PA, USA
- Huck Institute For The Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Shun Yao
- Huck Institute For The Life Sciences, The Pennsylvania State University, University Park, PA, USA
- Department of Biology, The Pennsylvania State University, University Park, PA, USA
| | - Zeyu Yang
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, PA, USA
| | - Haider Inam
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, PA, USA
| | - Dominik Wodarz
- Department of Biology, University of California San Diego, San Diego, CA, USA
| | - Marco Archetti
- Huck Institute For The Life Sciences, The Pennsylvania State University, University Park, PA, USA
- Department of Biology, The Pennsylvania State University, University Park, PA, USA
| | - Justin R Pritchard
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, PA, USA.
- Huck Institute For The Life Sciences, The Pennsylvania State University, University Park, PA, USA.
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2
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Patterson SC, Pomeroy AE, Palmer AC. Ultrasensitive Response Explains the Benefit of Combination Chemotherapy Despite Drug Antagonism. Mol Cancer Ther 2024; 23:995-1009. [PMID: 38530117 PMCID: PMC11219261 DOI: 10.1158/1535-7163.mct-23-0642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 01/30/2024] [Accepted: 03/19/2024] [Indexed: 03/27/2024]
Abstract
Most aggressive lymphomas are treated with combination chemotherapy, commonly as multiple cycles of concurrent drug administration. Concurrent administration is in theory optimal when combination therapies have synergistic (more than additive) drug interactions. We investigated pharmacodynamic interactions in the standard 4-drug "CHOP" regimen in peripheral T-cell lymphoma (PTCL) cell lines and found that CHOP consistently exhibits antagonism and not synergy. We tested whether staggered treatment schedules could improve tumor cell kill by avoiding antagonism, using in vitro models of concurrent or staggered treatments. Surprisingly, we observed that tumor cell kill is maximized by concurrent drug administration despite antagonistic drug-drug interactions. We propose that an ultrasensitive dose response, as described in radiology by the linear-quadratic (LQ) model, can reconcile these seemingly contradictory experimental observations. The LQ model describes the relationship between cell survival and dose, and in radiology has identified scenarios favoring hypofractionated radiotherapy-the administration of fewer large doses rather than multiple smaller doses. Specifically, hypofractionated treatment can be favored when cells require an accumulation of DNA damage, rather than a "single hit," to die. By adapting the LQ model to combination chemotherapy and accounting for tumor heterogeneity, we find that tumor cell kill is maximized by concurrent administration of multiple drugs, even when chemotherapies have antagonistic interactions. Thus, our study identifies a new mechanism by which combination chemotherapy can be clinically beneficial that is not contingent on positive drug-drug interactions.
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Affiliation(s)
- Sarah C. Patterson
- Department of Pharmacology, Computational Medicine Program, UNC Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Amy E. Pomeroy
- Department of Pharmacology, Computational Medicine Program, UNC Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Adam C. Palmer
- Department of Pharmacology, Computational Medicine Program, UNC Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
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3
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Wang M, Scott JG, Vladimirsky A. Threshold-awareness in adaptive cancer therapy. PLoS Comput Biol 2024; 20:e1012165. [PMID: 38875286 PMCID: PMC11210878 DOI: 10.1371/journal.pcbi.1012165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 06/27/2024] [Accepted: 05/09/2024] [Indexed: 06/16/2024] Open
Abstract
Although adaptive cancer therapy shows promise in integrating evolutionary dynamics into treatment scheduling, the stochastic nature of cancer evolution has seldom been taken into account. Various sources of random perturbations can impact the evolution of heterogeneous tumors, making performance metrics of any treatment policy random as well. In this paper, we propose an efficient method for selecting optimal adaptive treatment policies under randomly evolving tumor dynamics. The goal is to improve the cumulative "cost" of treatment, a combination of the total amount of drugs used and the total treatment time. As this cost also becomes random in any stochastic setting, we maximize the probability of reaching the treatment goals (tumor stabilization or eradication) without exceeding a pre-specified cost threshold (or a "budget"). We use a novel Stochastic Optimal Control formulation and Dynamic Programming to find such "threshold-aware" optimal treatment policies. Our approach enables an efficient algorithm to compute these policies for a range of threshold values simultaneously. Compared to treatment plans shown to be optimal in a deterministic setting, the new "threshold-aware" policies significantly improve the chances of the therapy succeeding under the budget, which is correlated with a lower general drug usage. We illustrate this method using two specific examples, but our approach is far more general and provides a new tool for optimizing adaptive therapies based on a broad range of stochastic cancer models.
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Affiliation(s)
- MingYi Wang
- Center for Applied Mathematics, Cornell University, Ithaca, New York, United States of America
| | - Jacob G. Scott
- Department of Translational Hematology and Oncology Research, Cleveland Clinic, Cleveland, Ohio, United States of America
| | - Alexander Vladimirsky
- Department of Mathematics and Center for Applied Mathematics, Cornell University, Ithaca, New York, United States of America
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4
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Maltas J, Tadele DS, Durmaz A, McFarland CD, Hinczewski M, Scott JG. Frequency-dependent ecological interactions increase the prevalence, and shape the distribution, of pre-existing drug resistance. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.03.16.533001. [PMID: 36993678 PMCID: PMC10055114 DOI: 10.1101/2023.03.16.533001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
The evolution of resistance remains one of the primary challenges for modern medicine from infectious diseases to cancers. Many of these resistance-conferring mutations often carry a substantial fitness cost in the absence of treatment. As a result, we would expect these mutants to undergo purifying selection and be rapidly driven to extinction. Nevertheless, pre-existing resistance is frequently observed from drug-resistant malaria to targeted cancer therapies in non-small cell lung cancer (NSCLC) and melanoma. Solutions to this apparent paradox have taken several forms from spatial rescue to simple mutation supply arguments. Recently, in an evolved resistant NSCLC cell line, we found that frequency-dependent ecological interactions between ancestor and resistant mutant ameliorate the cost of resistance in the absence of treatment. Here, we hypothesize that frequency-dependent ecological interactions in general play a major role in the prevalence of pre-existing resistance. We combine numerical simulations with robust analytical approximations to provide a rigorous mathematical framework for studying the effects of frequency-dependent ecological interactions on the evolutionary dynamics of pre-existing resistance. First, we find that ecological interactions significantly expand the parameter regime under which we expect to observe pre-existing resistance. Next, even when positive ecological interactions between mutants and ancestors are rare, these resistant clones provide the primary mode of evolved resistance because even weak positive interaction leads to significantly longer extinction times. We then find that even in the case where mutation supply alone is sufficient to predict pre-existing resistance, frequency-dependent ecological forces still contribute a strong evolutionary pressure that selects for increasingly positive ecological effects (negative frequency-dependent selection). Finally, we genetically engineer several of the most common clinically observed resistance mechanisms to targeted therapies in NSCLC, a treatment notorious for pre-existing resistance. We find that each engineered mutant displays a positive ecological interaction with their ancestor. As a whole, these results suggest that frequency-dependent ecological effects can play a crucial role in shaping the evolutionary dynamics of pre-existing resistance.
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Affiliation(s)
- Jeff Maltas
- Cleveland Clinic, Translational Hematology Oncology Research, Cleveland, OH
- Case Western Reserve University, School of Medicine, Cleveland, OH
| | - Dagim Shiferaw Tadele
- Cleveland Clinic, Translational Hematology Oncology Research, Cleveland, OH
- Oslo University Hospital, Ullevål, Department of Medical Genetics, Oslo, Norway
| | - Arda Durmaz
- Cleveland Clinic, Translational Hematology Oncology Research, Cleveland, OH
| | - Christopher D. McFarland
- Case Western Reserve University, School of Medicine, Cleveland, OH
- Case Comprehensive Cancer Center, Cleveland, OH
| | | | - Jacob G. Scott
- Cleveland Clinic, Translational Hematology Oncology Research, Cleveland, OH
- Case Western Reserve University, School of Medicine, Cleveland, OH
- Case Western Reserve University, Department of Physics, Cleveland, OH
- Case Comprehensive Cancer Center, Cleveland, OH
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5
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Crozier D, Gray JM, Maltas JA, Bonomo RA, Burke ZDC, Card KJ, Scott JG. The evolution of diverse antimicrobial responses in vancomycin-intermediate Staphylococcus aureus and its therapeutic implications. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.30.569373. [PMID: 38077036 PMCID: PMC10705500 DOI: 10.1101/2023.11.30.569373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/24/2023]
Abstract
Staphylococcus aureus causes endocarditis, osteomyelitis, and bacteremia. Clinicians often prescribe vancomycin as an empiric therapy to account for methicillin-resistant S. aureus (MRSA) and narrow treatment based on culture susceptibility results. However, these results reflect a single time point before empiric treatment and represent a limited subset of the total bacterial population within the patient. Thus, while they may indicate that the infection is susceptible to a particular drug, this recommendation may no longer be accurate during therapy. Here, we addressed how antibiotic susceptibility changes over time by accounting for evolution. We evolved 18 methicillin-susceptible S. aureus (MSSA) populations under increasing vancomycin concentrations until they reached intermediate resistance levels. Sequencing revealed parallel mutations that affect cell membrane stress response and cell-wall biosynthesis. The populations exhibited repeated cross-resistance to daptomycin and varied responses to meropenem, gentamicin, and nafcillin. We accounted for this variability by deriving likelihood estimates that express a population's probability of exhibiting a drug response following vancomycin treatment. Our results suggest antistaphylococcal penicillins are preferable first-line treatments for MSSA infections but also highlight the inherent uncertainty that evolution poses to effective therapies. Infections may take varied evolutionary paths; therefore, considering evolution as a probabilistic process should inform our therapeutic choices.
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6
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Baygin RC, Yilmaz KC, Acar A. Characterization of dabrafenib-induced drug insensitivity via cellular barcoding and collateral sensitivity to second-line therapeutics. Sci Rep 2024; 14:286. [PMID: 38167959 PMCID: PMC10762103 DOI: 10.1038/s41598-023-50443-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Accepted: 12/20/2023] [Indexed: 01/05/2024] Open
Abstract
Drug insensitivity is arguably one of the biggest challenges in cancer therapeutics. Although effective therapeutic solutions in cancer are limited due to the emergence of drug insensitivity, exploiting evolutionary understanding in this context can provide potential second-line therapeutics sensitizing the drug insensitive populations. Targeted therapeutic agent dabrafenib is used to treat CRC patients with BRAF V600E genotype and insensitivity to dabrafenib is often observed. Understanding underlying clonal architecture of dabrafenib-induced drug insensitivity and identification of potential second-line therapeutics that could sensitize dabrafenib insensitive populations remain to be elucidated. For this purpose, we utilized cellular barcoding technology to decipher dabrafenib-induced clonal evolution in BRAF V600E mutant HT-29 cells. This approach revealed the detection of both pre-existing and de novo barcodes with increased frequencies as a result of dabrafenib insensitivity. Furthermore, our longitudinal monitoring of drug insensitivity based on barcode detection from floating DNA within used medium enabled to identify temporal dynamics of pre-existing and de novo barcodes in relation to dabrafenib insensitivity in HT-29 cells. Moreover, whole-exome sequencing analysis exhibited possible somatic CNVs and SNVs contributing to dabrafenib insensitivity in HT-29 cells. Last, collateral drug sensitivity testing demonstrated oxaliplatin and capecitabine, alone or in combination, as successful second-like therapeutics in inducing collateral sensitivity in dabrafenib-insensitive HT-29 cells. Overall, our findings demonstrate clonal dynamics of dabrafenib-insensitivity in HT-29 cells. In addition, oxaliplatin and capecitabine, alone or in combination, were successful second-line therapeutics in inducing collateral sensitivity in dabrafenib-insensitive HT-29 cells.
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Affiliation(s)
- Rana Can Baygin
- Department of Biological Sciences, Middle East Technical University, Universiteler Mah. Dumlupınar Bulvarı 1, Çankaya, 06800, Ankara, Turkey
| | - Kubra Celikbas Yilmaz
- Department of Biological Sciences, Middle East Technical University, Universiteler Mah. Dumlupınar Bulvarı 1, Çankaya, 06800, Ankara, Turkey
| | - Ahmet Acar
- Department of Biological Sciences, Middle East Technical University, Universiteler Mah. Dumlupınar Bulvarı 1, Çankaya, 06800, Ankara, Turkey.
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7
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Maltas J, Killarney ST, Singleton KR, Strobl MAR, Washart R, Wood KC, Wood KB. Drug dependence in cancer is exploitable by optimally constructed treatment holidays. Nat Ecol Evol 2024; 8:147-162. [PMID: 38012363 PMCID: PMC10918730 DOI: 10.1038/s41559-023-02255-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 10/19/2023] [Indexed: 11/29/2023]
Abstract
Cancers with acquired resistance to targeted therapy can become simultaneously dependent on the presence of the targeted therapy drug for survival, suggesting that intermittent therapy may slow resistance. However, relatively little is known about which tumours are likely to become dependent and how to schedule intermittent therapy optimally. Here we characterized drug dependence across a panel of over 75 MAPK-inhibitor-resistant BRAFV600E mutant melanoma models at the population and single-clone levels. Melanocytic differentiated models exhibited a much greater tendency to give rise to drug-dependent progeny than their dedifferentiated counterparts. Mechanistically, acquired loss of microphthalmia-associated transcription factor in differentiated melanoma models drives ERK-JunB-p21 signalling to enforce drug dependence. We identified the optimal scheduling of 'drug holidays' using simple mathematical models that we validated across short and long timescales. Without detailed knowledge of tumour characteristics, we found that a simple adaptive therapy protocol can produce near-optimal outcomes using only measurements of total population size. Finally, a spatial agent-based model showed that optimal schedules derived from exponentially growing cells in culture remain nearly optimal in the context of tumour cell turnover and limited environmental carrying capacity. These findings may guide the implementation of improved evolution-inspired treatment strategies for drug-dependent cancers.
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Affiliation(s)
- Jeff Maltas
- Department of Biophysics, University of Michigan, Ann Arbor, MI, USA
| | - Shane T Killarney
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC, USA
| | | | - Maximilian A R Strobl
- Department of Translational Hematology and Oncology Research, Cleveland Clinic, Cleveland, OH, USA
| | - Rachel Washart
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC, USA
| | - Kris C Wood
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC, USA.
| | - Kevin B Wood
- Department of Biophysics, University of Michigan, Ann Arbor, MI, USA.
- Department of Physics, University of Michigan, Ann Arbor, MI, USA.
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8
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Pu Y, Li L, Peng H, Liu L, Heymann D, Robert C, Vallette F, Shen S. Drug-tolerant persister cells in cancer: the cutting edges and future directions. Nat Rev Clin Oncol 2023; 20:799-813. [PMID: 37749382 DOI: 10.1038/s41571-023-00815-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/25/2023] [Indexed: 09/27/2023]
Abstract
Drug-tolerant persister (DTP) cell populations were originally discovered in antibiotic-resistant bacterial biofilms. Similar populations with comparable features have since been identified among cancer cells and have been linked with treatment resistance that lacks an underlying genomic alteration. Research over the past decade has improved our understanding of the biological roles of DTP cells in cancer, although clinical knowledge of the role of these cells in treatment resistance remains limited. Nonetheless, targeting this population is anticipated to provide new treatment opportunities. In this Perspective, we aim to provide a clear definition of the DTP phenotype, discuss the underlying characteristics of these cells, their biomarkers and vulnerabilities, and encourage further research on DTP cells that might improve our understanding and enable the development of more effective anticancer therapies.
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Affiliation(s)
- Yi Pu
- Department of Thoracic Surgery and Institute of Thoracic Oncology, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
- Department of Burn Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Lu Li
- Lung Cancer Centre, West China Hospital, Sichuan University, Chengdu, China
| | - Haoning Peng
- Department of Thoracic Surgery and Institute of Thoracic Oncology, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Lunxu Liu
- Department of Thoracic Surgery and Institute of Thoracic Oncology, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Dominique Heymann
- Nantes Université, CNRS, UMR6286, US2B, Nantes, France
- Institut de Cancérologie de l'Ouest, Saint-Herblain, France
| | - Caroline Robert
- INSERM U981, Gustave Roussy Cancer Campus, Villejuif, France
- Université Paris-Saclay, Le Kremlin-Bicêtre, France
| | - François Vallette
- Institut de Cancérologie de l'Ouest, Saint-Herblain, France.
- Nantes Université, INSERM, U1307, CRCI2NA, Nantes, France.
| | - Shensi Shen
- Department of Thoracic Surgery and Institute of Thoracic Oncology, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China.
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9
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Szebényi K, Füredi A, Bajtai E, Sama SN, Csiszar A, Gombos B, Szabó P, Grusch M, Szakács G. Effective targeting of breast cancer by the inhibition of P-glycoprotein mediated removal of toxic lipid peroxidation byproducts from drug tolerant persister cells. Drug Resist Updat 2023; 71:101007. [PMID: 37741091 DOI: 10.1016/j.drup.2023.101007] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 09/11/2023] [Accepted: 09/13/2023] [Indexed: 09/25/2023]
Abstract
Therapy resistance has long been considered to occur through the selection of pre-existing clones equipped to survive and quickly regrow, or through the acquisition of mutations during chemotherapy. Here we show that following in vitro treatment by chemotherapy, epithelial breast cancer cells adopt a transient drug tolerant phenotype characterized by cell cycle arrest, epithelial-to-mesenchymal transition (EMT) and the reversible upregulation of the multidrug resistance (MDR) efflux transporter P-glycoprotein (P-gp). The drug tolerant persister (DTP) state is reversible, as cells eventually resume proliferation, giving rise to a cell population resembling the initial, drug-naïve cell lines. However, recovery after doxorubicin treatment is almost completely eliminated when DTP cells are cultured in the presence of the P-gp inhibitor Tariquidar. Mechanistically, P-gp contributes to the survival of DTP cells by removing reactive oxygen species-induced lipid peroxidation products resulting from doxorubicin exposure. In vivo, prolonged administration of Tariquidar during doxorubicin treatment holidays resulted in a significant increase of the overall survival of Brca1-/-;p53-/- mammary tumor bearing mice. These results indicate that prolonged administration of a P-gp inhibitor during drug holidays would likely benefit patients without the risk of aggravated side effects related to the concomitantly administered toxic chemotherapy. Effective targeting of DTPs through the inhibition of P-glycoprotein may result in a paradigm shift, changing the focus from countering drug resistance mechanisms to preventing or delaying therapy resistance.
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Affiliation(s)
- Kornélia Szebényi
- Center for Cancer Research, Medical University of Vienna, Vienna, Austria; Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary.
| | - András Füredi
- Center for Cancer Research, Medical University of Vienna, Vienna, Austria; Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary; Institute of Technical Physics and Materials Science, Centre of Energy Research, Budapest, Hungary
| | - Eszter Bajtai
- Center for Cancer Research, Medical University of Vienna, Vienna, Austria; Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary; Doctoral School of Pathological Sciences, Semmelweis University, Budapest, Hungary
| | - Sai Nagender Sama
- Center for Cancer Research, Medical University of Vienna, Vienna, Austria
| | - Agnes Csiszar
- Center for Cancer Research, Medical University of Vienna, Vienna, Austria
| | - Balázs Gombos
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary; Doctoral School of Molecular Medicine, Semmelweis University, Budapest, Hungary
| | - Pál Szabó
- Centre for Structural Study, Research Centre for Natural Sciences, Budapest, Hungary
| | - Michael Grusch
- Center for Cancer Research, Medical University of Vienna, Vienna, Austria
| | - Gergely Szakács
- Center for Cancer Research, Medical University of Vienna, Vienna, Austria; Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary.
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10
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Liu C, Leighow SM, McIlroy K, Lu M, Dennis KA, Abello K, Brown DJ, Moore CJ, Shah A, Inam H, Rivera VM, Pritchard JR. Excessive concentrations of kinase inhibitors in translational studies impede effective drug repurposing. Cell Rep Med 2023; 4:101227. [PMID: 37852183 PMCID: PMC10591048 DOI: 10.1016/j.xcrm.2023.101227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 06/20/2023] [Accepted: 09/13/2023] [Indexed: 10/20/2023]
Abstract
Drug repositioning seeks to leverage existing clinical knowledge to identify alternative clinical settings for approved drugs. However, repositioning efforts fail to demonstrate improved success rates in late-stage clinical trials. Focusing on 11 approved kinase inhibitors that have been evaluated in 139 repositioning hypotheses, we use data mining to characterize the state of clinical repurposing. Then, using a simple experimental correction with human serum proteins in in vitro pharmacodynamic assays, we develop a measurement of a drug's effective exposure. We show that this metric is remarkably predictive of clinical activity for a panel of five kinase inhibitors across 23 drug variant targets in leukemia. We then validate our model's performance in six other kinase inhibitors for two types of solid tumors: non-small cell lung cancer (NSCLC) and gastrointestinal stromal tumors (GISTs). Our approach presents a straightforward strategy to use existing clinical information and experimental systems to decrease the clinical failure rate in drug repurposing studies.
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Affiliation(s)
- Chuan Liu
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, PA 16802, USA; Department of Oncology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, China
| | - Scott M Leighow
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, PA 16802, USA.
| | - Kyle McIlroy
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Mengrou Lu
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Kady A Dennis
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Kerry Abello
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Donovan J Brown
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Connor J Moore
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Anushka Shah
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Haider Inam
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | | | - Justin R Pritchard
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, PA 16802, USA; The Huck Institute for the Life Sciences, Center for Resistance Evolution, The Pennsylvania State University, University Park, PA 16802, USA.
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11
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Danisik N, Yilmaz KC, Acar A. Identification of collateral sensitivity and evolutionary landscape of chemotherapy-induced drug resistance using cellular barcoding technology. Front Pharmacol 2023; 14:1178489. [PMID: 37497108 PMCID: PMC10366361 DOI: 10.3389/fphar.2023.1178489] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 06/27/2023] [Indexed: 07/28/2023] Open
Abstract
Background: One of the most significant challenges impeding cancer treatment effectiveness is drug resistance. Combining evolutionary understanding with drug resistance can pave the way for the identification of second-line drug options that can overcome drug resistance. Although capecitabine and irinotecan are commonly used therapeutic agents in the treatment of CRC patients, resistance to these agents is common. The underlying clonal dynamics of resistance to these agents using high-resolution barcode technology and identification of effective second-line drugs in this context remain unclear. Methods and materials: Caco-2 and HT-29 cell lines were barcoded, and then capecitabine and irinotecan resistant derivatives of these cell lines were established. The frequencies of barcodes from resistant cell lines and harvested medium, longitudinally, were determined. Collateral drug sensitivity testing was carried out on resistant Caco-2 and HT-29 cell lines using single agents or drug combinations. The SyngeryFinder tool was used to analyse drug combination testing. Results: In Caco-2 and HT-29 cell lines, barcode frequency measurements revealed clonal dynamics of capecitabine and irinotecan formed by both pre-existing and de novo barcodes, indicating the presence of polyclonal drug resistance. The temporal dynamics of clonal evolution in Caco-2 and HT-29 cell lines were demonstrated by longitudinal analysis of pre-existing and de novo barcodes from harvested medium. In Caco-2 and HT-29 cell lines, collateral drug sensitivity revealed a number of drugs that were effective alone and in combination. Conclusion: The use of barcoding technology reveals the clonal dynamics of chemotherapy-induced drug resistance not only from harvested cell populations, but also from longitudinal sampling throughout the course of clonal evolution. Second-line drugs that sensitize drug-resistant CRC cell lines are identified through collateral drug testing.
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12
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Ingles Garces AH, Porta N, Graham TA, Banerji U. Clinical trial designs for evaluating and exploiting cancer evolution. Cancer Treat Rev 2023; 118:102583. [PMID: 37331179 DOI: 10.1016/j.ctrv.2023.102583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 05/21/2023] [Accepted: 05/23/2023] [Indexed: 06/20/2023]
Abstract
The evolution of drug-resistant cell subpopulations causes cancer treatment failure. Current preclinical evidence shows that it is possible to model herding of clonal evolution and collateral sensitivity where an initial treatment could favourably influence the response to a subsequent one. Novel therapy strategies exploiting this understanding are being considered, and clinical trial designs for steering cancer evolution are needed. Furthermore, preclinical evidence suggests that different subsets of drug-sensitive and resistant clones could compete between themselves for nutrients/blood supply, and clones that populate a tumour do so at the expense of other clones. Treatment paradigms based on this clinical application of exploiting cell-cell competition include intermittent dosing regimens or cycling different treatments before progression. This will require clinical trial designs different from the conventional practice of evaluating responses to individual therapy regimens. Next-generation sequencing to assess clonal dynamics longitudinally will improve current radiological assessment of clinical response/resistance and be incorporated into trials exploiting evolution. Furthermore, if understood, clonal evolution can be used to therapeutic advantage, improving patient outcomes based on a new generation of clinical trials.
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Affiliation(s)
- Alvaro H Ingles Garces
- Drug Development Unit, The Institute of Cancer Research and The Royal Marsden NHS Foundation Trust, UK
| | - Nuria Porta
- Clinical Trials and Statistical Unit, The Institute of Cancer Research, UK
| | - Trevor A Graham
- Centre for Evolution and Cancer, The Institute of Cancer Research, UK
| | - Udai Banerji
- Drug Development Unit, The Institute of Cancer Research and The Royal Marsden NHS Foundation Trust, UK.
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13
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Wong TL, Loh JJ, Lu S, Yan HHN, Siu HC, Xi R, Chan D, Kam MJF, Zhou L, Tong M, Copland JA, Chen L, Yun JP, Leung SY, Ma S. ADAR1-mediated RNA editing of SCD1 drives drug resistance and self-renewal in gastric cancer. Nat Commun 2023; 14:2861. [PMID: 37208334 PMCID: PMC10199093 DOI: 10.1038/s41467-023-38581-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 05/05/2023] [Indexed: 05/21/2023] Open
Abstract
Targetable drivers governing 5-fluorouracil and cisplatin (5FU + CDDP) resistance remain elusive due to the paucity of physiologically and therapeutically relevant models. Here, we establish 5FU + CDDP resistant intestinal subtype GC patient-derived organoid lines. JAK/STAT signaling and its downstream, adenosine deaminases acting on RNA 1 (ADAR1), are shown to be concomitantly upregulated in the resistant lines. ADAR1 confers chemoresistance and self-renewal in an RNA editing-dependent manner. WES coupled with RNA-seq identify enrichment of hyper-edited lipid metabolism genes in the resistant lines. Mechanistically, ADAR1-mediated A-to-I editing on 3'UTR of stearoyl-CoA desaturase (SCD1) increases binding of KH domain-containing, RNA-binding, signal transduction-associated 1 (KHDRBS1), thereby augmenting SCD1 mRNA stability. Consequently, SCD1 facilitates lipid droplet formation to alleviate chemotherapy-induced ER stress and enhances self-renewal through increasing β-catenin expression. Pharmacological inhibition of SCD1 abrogates chemoresistance and tumor-initiating cell frequency. Clinically, high proteomic level of ADAR1 and SCD1, or high SCD1 editing/ADAR1 mRNA signature score predicts a worse prognosis. Together, we unveil a potential target to circumvent chemoresistance.
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Affiliation(s)
- Tin-Lok Wong
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- The University of Hong Kong - Shenzhen Hospital, Shenzhen, Guangdong, China
| | - Jia-Jian Loh
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Shixun Lu
- Department of Pathology, Sun Yat-Sen University Cancer Centre, Guangzhou, Guangdong, China
| | - Helen H N Yan
- Department of Pathology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Queen Mary Hospital, Hong Kong, China
| | - Hoi Cheong Siu
- Department of Pathology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Queen Mary Hospital, Hong Kong, China
| | - Ren Xi
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Dessy Chan
- Department of Pathology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Queen Mary Hospital, Hong Kong, China
| | - Max J F Kam
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Lei Zhou
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- The University of Hong Kong - Shenzhen Hospital, Shenzhen, Guangdong, China
| | - Man Tong
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- The University of Hong Kong - Shenzhen Hospital, Shenzhen, Guangdong, China
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - John A Copland
- Department of Cancer Biology, Mayo Clinic Florida, Jacksonville, FL, USA
| | - Leilei Chen
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Jing-Ping Yun
- Department of Pathology, Sun Yat-Sen University Cancer Centre, Guangzhou, Guangdong, China
| | - Suet Yi Leung
- Department of Pathology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Queen Mary Hospital, Hong Kong, China
- The Jockey Club Centre for Clinical Innovation and Discovery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Stephanie Ma
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China.
- The University of Hong Kong - Shenzhen Hospital, Shenzhen, Guangdong, China.
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14
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Waller NJE, Cheung CY, Cook GM, McNeil MB. The evolution of antibiotic resistance is associated with collateral drug phenotypes in Mycobacterium tuberculosis. Nat Commun 2023; 14:1517. [PMID: 36934122 PMCID: PMC10024696 DOI: 10.1038/s41467-023-37184-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 03/06/2023] [Indexed: 03/20/2023] Open
Abstract
The increasing incidence of drug resistance in Mycobacterium tuberculosis has diminished the efficacy of almost all available antibiotics, complicating efforts to combat the spread of this global health burden. Alongside the development of new drugs, optimised drug combinations are needed to improve treatment success and prevent the further spread of antibiotic resistance. Typically, antibiotic resistance leads to reduced sensitivity, yet in some cases the evolution of drug resistance can lead to enhanced sensitivity to unrelated drugs. This phenomenon of collateral sensitivity is largely unexplored in M. tuberculosis but has the potential to identify alternative therapeutic strategies to combat drug-resistant strains that are unresponsive to current treatments. Here, by using drug susceptibility profiling, genomics and evolutionary studies we provide evidence for the existence of collateral drug sensitivities in an isogenic collection M. tuberculosis drug-resistant strains. Furthermore, in proof-of-concept studies, we demonstrate how collateral drug phenotypes can be exploited to select against and prevent the emergence of drug-resistant strains. This study highlights that the evolution of drug resistance in M. tuberculosis leads to collateral drug responses that can be exploited to design improved drug regimens.
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Affiliation(s)
- Natalie J E Waller
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland, New Zealand
| | - Chen-Yi Cheung
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Gregory M Cook
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland, New Zealand
| | - Matthew B McNeil
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand.
- Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland, New Zealand.
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15
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Bassil CF, Anderson GR, Mayro B, Askin KN, Winter PS, Gruber S, Hall TM, Hoj JP, Cerda-Smith C, Hutchinson HM, Killarney ST, Singleton KR, Qin L, Jubien-Girard K, Favreau C, Martin AR, Robert G, Benhida R, Auberger P, Pendergast AM, Lonard DM, Puissant A, Wood KC. MCB-613 exploits a collateral sensitivity in drug resistant EGFR-mutant non-small cell lung cancer through covalent inhibition of KEAP1. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.17.524094. [PMID: 36711936 PMCID: PMC9882253 DOI: 10.1101/2023.01.17.524094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Targeted therapies have revolutionized cancer chemotherapy. Unfortunately, most patients develop multifocal resistance to these drugs within a matter of months. Here, we used a high-throughput phenotypic small molecule screen to identify MCB-613 as a compound that selectively targets EGFR-mutant, EGFR inhibitor-resistant non-small cell lung cancer (NSCLC) cells harboring diverse resistance mechanisms. Subsequent proteomic and functional genomic screens involving MCB-613 identified its target in this context to be KEAP1, revealing that this gene is selectively essential in the setting of EGFR inhibitor resistance. In-depth molecular characterization demonstrated that (1) MCB-613 binds KEAP1 covalently; (2) a single molecule of MCB-613 is capable of bridging two KEAP1 monomers together; and, (3) this modification interferes with the degradation of canonical KEAP1 substrates such as NRF2. Surprisingly, NRF2 knockout sensitizes cells to MCB-613, suggesting that the drug functions through modulation of an alternative KEAP1 substrate. Together, these findings advance MCB-613 as a new tool for exploiting the selective essentiality of KEAP1 in drug-resistant, EGFR-mutant NSCLC cells.
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Affiliation(s)
| | - Gray R Anderson
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC, USA
| | - Benjamin Mayro
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC, USA
| | - Kayleigh N Askin
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC, USA
| | - Peter S Winter
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC, USA
| | - Samuel Gruber
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC, USA
| | - Tierney M Hall
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC, USA
| | - Jacob P Hoj
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC, USA
| | | | - Haley M Hutchinson
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC, USA
| | - Shane T Killarney
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC, USA
| | | | - Li Qin
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Kévin Jubien-Girard
- Université Côte d'Azur, CNRS, Institut de Chimie de Nice UMR 7272 - 06108 Nice, France
| | | | - Anthony R Martin
- Université Côte d'Azur, CNRS, Institut de Chimie de Nice UMR 7272 - 06108 Nice, France
- IBMM, Université de Montpellier, ENSCM, CNRS, Montpellier, France
| | | | - Rachid Benhida
- Université Côte d'Azur, CNRS, Institut de Chimie de Nice UMR 7272 - 06108 Nice, France
- Chemical & Biochemical Sciences Green-Process Engineering (CBS) Mohammed VI Polytechnic University, Lot 660, Hay Moulay Rachid, Benguerir, Morocco
| | | | | | - David M Lonard
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Alexandre Puissant
- Université de Paris, Génomes, Biologie Cellulaire et Thérapeutique U944, INSERM, CNRS, Paris, France
| | - Kris C Wood
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC, USA
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16
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Wild SA, Cannell IG, Nicholls A, Kania K, Bressan D, Hannon GJ, Sawicka K. Clonal transcriptomics identifies mechanisms of chemoresistance and empowers rational design of combination therapies. eLife 2022; 11:e80981. [PMID: 36525288 PMCID: PMC9757829 DOI: 10.7554/elife.80981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 11/10/2022] [Indexed: 12/23/2022] Open
Abstract
Tumour heterogeneity is thought to be a major barrier to successful cancer treatment due to the presence of drug resistant clonal lineages. However, identifying the characteristics of such lineages that underpin resistance to therapy has remained challenging. Here, we utilise clonal transcriptomics with WILD-seq; Wholistic Interrogation of Lineage Dynamics by sequencing, in mouse models of triple-negative breast cancer (TNBC) to understand response and resistance to therapy, including BET bromodomain inhibition and taxane-based chemotherapy. These analyses revealed oxidative stress protection by NRF2 as a major mechanism of taxane resistance and led to the discovery that our tumour models are collaterally sensitive to asparagine deprivation therapy using the clinical stage drug L-asparaginase after frontline treatment with docetaxel. In summary, clonal transcriptomics with WILD-seq identifies mechanisms of resistance to chemotherapy that are also operative in patients and pin points asparagine bioavailability as a druggable vulnerability of taxane-resistant lineages.
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Affiliation(s)
- Sophia A Wild
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson WayCambridgeUnited Kingdom
| | - Ian G Cannell
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson WayCambridgeUnited Kingdom
| | - Ashley Nicholls
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson WayCambridgeUnited Kingdom
| | - Katarzyna Kania
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson WayCambridgeUnited Kingdom
| | - Dario Bressan
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson WayCambridgeUnited Kingdom
| | - Gregory J Hannon
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson WayCambridgeUnited Kingdom
| | - Kirsty Sawicka
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson WayCambridgeUnited Kingdom
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17
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Creixell M, Kim H, Mohammadi F, Peyton SR, Meyer AS. Systems approaches to uncovering the contribution of environment-mediated drug resistance. CURRENT OPINION IN SOLID STATE & MATERIALS SCIENCE 2022; 26:101005. [PMID: 36321161 PMCID: PMC9620953 DOI: 10.1016/j.cossms.2022.101005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Cancer drug response is heavily influenced by the extracellular matrix (ECM) environment. Despite a clear appreciation that the ECM influences cancer drug response and progression, a unified view of how, where, and when environment-mediated drug resistance contributes to cancer progression has not coalesced. Here, we survey some specific ways in which the ECM contributes to cancer resistance with a focus on how materials development can coincide with systems biology approaches to better understand and perturb this contribution. We argue that part of the reason that environment-mediated resistance remains a perplexing problem is our lack of a wholistic view of the entire range of environments and their impacts on cell behavior. We cover a series of recent experimental and computational tools that will aid exploration of ECM reactions space, and how they might be synergistically integrated.
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Affiliation(s)
- Marc Creixell
- Department of Bioengineering, University of California Los Angeles
| | - Hyuna Kim
- Molecular and Cellular Biology Graduate Program, University of Massachusetts Amherst
| | - Farnaz Mohammadi
- Department of Bioengineering, University of California Los Angeles
| | - Shelly R Peyton
- Molecular and Cellular Biology Graduate Program, University of Massachusetts Amherst
- Department of Chemical Engineering, University of Massachusetts Amherst
| | - Aaron S Meyer
- Department of Bioengineering, University of California Los Angeles
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18
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Loria R, Vici P, Di Lisa FS, Soddu S, Maugeri-Saccà M, Bon G. Cross-Resistance Among Sequential Cancer Therapeutics: An Emerging Issue. Front Oncol 2022; 12:877380. [PMID: 35814399 PMCID: PMC9259985 DOI: 10.3389/fonc.2022.877380] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 05/04/2022] [Indexed: 11/13/2022] Open
Abstract
Over the past two decades, cancer treatment has benefited from having a significant increase in the number of targeted drugs approved by the United States Food and Drug Administration. With the introduction of targeted therapy, a great shift towards a new era has taken place that is characterized by reduced cytotoxicity and improved clinical outcomes compared to traditional chemotherapeutic drugs. At present, targeted therapies and other systemic anti-cancer therapies available (immunotherapy, cytotoxic, endocrine therapies and others) are used alone or in combination in different settings (neoadjuvant, adjuvant, and metastatic). As a result, it is not uncommon for patients affected by an advanced malignancy to receive subsequent anti-cancer therapies. In this challenging complexity of cancer treatment, the clinical pathways of real-life patients are often not as direct as predicted by standard guidelines and clinical trials, and cross-resistance among sequential anti-cancer therapies represents an emerging issue. In this review, we summarize the main cross-resistance events described in the diverse tumor types and provide insight into the molecular mechanisms involved in this process. We also discuss the current challenges and provide perspectives for the research and development of strategies to overcome cross-resistance and proceed towards a personalized approach.
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Affiliation(s)
- Rossella Loria
- Cellular Network and Molecular Therapeutic Target Unit, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Patrizia Vici
- Unit of Phase IV Trials, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Francesca Sofia Di Lisa
- Unit of Phase IV Trials, IRCCS Regina Elena National Cancer Institute, Rome, Italy
- Medical Oncology A, Department of Radiological, Oncological, and Anatomo-Pathological Sciences, Umberto I University Hospital, University Sapienza, Rome, Italy
| | - Silvia Soddu
- Cellular Network and Molecular Therapeutic Target Unit, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Marcello Maugeri-Saccà
- Division of Medical Oncology 2, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Giulia Bon
- Cellular Network and Molecular Therapeutic Target Unit, IRCCS Regina Elena National Cancer Institute, Rome, Italy
- *Correspondence: Giulia Bon,
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19
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Gutierrez C, Vilas CK, Wu CJ, Al'Khafaji AM. Functionalized Lineage Tracing Can Enable the Development of Homogenization-Based Therapeutic Strategies in Cancer. Front Immunol 2022; 13:859032. [PMID: 35603167 PMCID: PMC9120583 DOI: 10.3389/fimmu.2022.859032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 03/22/2022] [Indexed: 11/13/2022] Open
Abstract
The therapeutic landscape across many cancers has dramatically improved since the introduction of potent targeted agents and immunotherapy. Nonetheless, success of these approaches is too often challenged by the emergence of therapeutic resistance, fueled by intratumoral heterogeneity and the immense evolutionary capacity inherent to cancers. To date, therapeutic strategies have attempted to outpace the evolutionary tempo of cancer but frequently fail, resulting in lack of tumor response and/or relapse. This realization motivates the development of novel therapeutic approaches which constrain evolutionary capacity by reducing the degree of intratumoral heterogeneity prior to treatment. Systematic development of such approaches first requires the ability to comprehensively characterize heterogeneous populations over the course of a perturbation, such as cancer treatment. Within this context, recent advances in functionalized lineage tracing approaches now afford the opportunity to efficiently measure multimodal features of clones within a tumor at single cell resolution, enabling the linkage of these features to clonal fitness over the course of tumor progression and treatment. Collectively, these measurements provide insights into the dynamic and heterogeneous nature of tumors and can thus guide the design of homogenization strategies which aim to funnel heterogeneous cancer cells into known, targetable phenotypic states. We anticipate the development of homogenization therapeutic strategies to better allow for cancer eradication and improved clinical outcomes.
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Affiliation(s)
- Catherine Gutierrez
- Department of Medicine, Harvard Medical School, Boston, MA, United States
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, United States
| | - Caroline K Vilas
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, United States
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, TX, United States
| | - Catherine J Wu
- Department of Medicine, Harvard Medical School, Boston, MA, United States
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, United States
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, United States
- Broad Institute of MIT and Harvard, Cambridge, MA, United States
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20
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Dalin S, Grauman-Boss B, Lauffenburger DA, Hemann MT. Collateral responses to classical cytotoxic chemotherapies are heterogeneous and sensitivities are sparse. Sci Rep 2022; 12:5453. [PMID: 35361803 PMCID: PMC8971507 DOI: 10.1038/s41598-022-09319-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 03/14/2022] [Indexed: 11/09/2022] Open
Abstract
Chemotherapy resistance is a major obstacle to curing cancer patients. Combination drug regimens have shown promise as a method to overcome resistance; however, to date only some cancers have been cured with this method. Collateral sensitivity-the phenomenon whereby resistance to one drug is co-occurrent with sensitivity to a second drug-has been gaining traction as a promising new concept to guide rational design of combination regimens. Here we evolved over 100 subclones of the Eµ-Myc; p19ARF-/- cell line to be resistant to one of four classical chemotherapy agents: doxorubicin, vincristine, paclitaxel, and cisplatin. We then surveyed collateral responses to acquisition of resistance to these agents. Although numerous collateral sensitivities have been documented for antibiotics and targeted cancer therapies, we observed only one collateral sensitivity: half of cell lines that acquired resistance to paclitaxel also acquired a collateral sensitivity to verapamil. However, we found that the mechanism of this collateral sensitivity was unrelated to the mechanism of paclitaxel resistance. Interestingly, we observed heterogeneity in the phenotypic response to acquisition of resistance to most of the drugs we tested, most notably for paclitaxel, suggesting the existence of multiple different states of resistance. Surprisingly, this phenotypic heterogeneity in paclitaxel resistant cell lines was unrelated to transcriptomic heterogeneity among those cell lines. These features of phenotypic and transcriptomic heterogeneity must be taken into account in future studies of treated tumor subclones and in design of chemotherapy combinations.
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Affiliation(s)
- Simona Dalin
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.,Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Beatrice Grauman-Boss
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.,Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Douglas A Lauffenburger
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA. .,Department of Biological Engineering, Massachusetts Institute of Technology, Room: 16-343, Cambridge, MA, 02139, USA.
| | - Michael T Hemann
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA. .,Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
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21
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Ali M, Lu M, Ang HX, Soderquist RS, Eyler CE, Hutchinson HM, Glass C, Bassil CF, Lopez OM, Kerr DL, Falcon CJ, Yu HA, Hata AN, Blakely CM, McCoach CE, Bivona TG, Wood KC. Small-molecule targeted therapies induce dependence on DNA double-strand break repair in residual tumor cells. Sci Transl Med 2022; 14:eabc7480. [PMID: 35353542 PMCID: PMC9516479 DOI: 10.1126/scitranslmed.abc7480] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Residual cancer cells that survive drug treatments with targeted therapies act as a reservoir from which eventual resistant disease emerges. Although there is great interest in therapeutically targeting residual cells, efforts are hampered by our limited knowledge of the vulnerabilities existing in this cell state. Here, we report that diverse oncogene-targeted therapies, including inhibitors of epidermal growth factor receptor (EGFR), anaplastic lymphoma kinase (ALK), KRAS, and BRAF, induce DNA double-strand breaks and, consequently, ataxia-telangiectasia mutated (ATM)-dependent DNA repair in oncogene-matched residual tumor cells. This DNA damage response, observed in cell lines, mouse xenograft models, and human patients, is driven by a pathway involving the activation of caspases 3 and 7 and the downstream caspase-activated deoxyribonuclease (CAD). CAD is, in turn, activated through caspase-mediated degradation of its endogenous inhibitor, ICAD. In models of EGFR mutant non-small cell lung cancer (NSCLC), tumor cells that survive treatment with small-molecule EGFR-targeted therapies are thus synthetically dependent on ATM, and combined treatment with an ATM kinase inhibitor eradicates these cells in vivo. This led to more penetrant and durable responses in EGFR mutant NSCLC mouse xenograft models, including those derived from both established cell lines and patient tumors. Last, we found that rare patients with EGFR mutant NSCLC harboring co-occurring, loss-of-function mutations in ATM exhibit extended progression-free survival on first generation EGFR inhibitor therapy relative to patients with EGFR mutant NSCLC lacking deleterious ATM mutations. Together, these findings establish a rationale for the mechanism-based integration of ATM inhibitors alongside existing targeted therapies.
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Affiliation(s)
- Moiez Ali
- Department of Pharmacology and Cancer Biology and Duke Cancer Institute, Duke University, Durham, NC 27710, USA
| | - Min Lu
- Department of Pharmacology and Cancer Biology and Duke Cancer Institute, Duke University, Durham, NC 27710, USA
| | - Hazel Xiaohui Ang
- Department of Pharmacology and Cancer Biology and Duke Cancer Institute, Duke University, Durham, NC 27710, USA
| | - Ryan S. Soderquist
- Department of Pharmacology and Cancer Biology and Duke Cancer Institute, Duke University, Durham, NC 27710, USA
| | - Christine E. Eyler
- Department of Pharmacology and Cancer Biology and Duke Cancer Institute, Duke University, Durham, NC 27710, USA
| | - Haley M. Hutchinson
- Department of Pharmacology and Cancer Biology and Duke Cancer Institute, Duke University, Durham, NC 27710, USA
| | - Carolyn Glass
- Department of Pathology, Duke University, Durham, NC 27710, USA
| | - Christopher F. Bassil
- Department of Pharmacology and Cancer Biology and Duke Cancer Institute, Duke University, Durham, NC 27710, USA
| | - Omar M. Lopez
- Department of Pharmacology and Cancer Biology and Duke Cancer Institute, Duke University, Durham, NC 27710, USA
| | - D. Lucas Kerr
- Department of Medicine and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Christina J. Falcon
- Thoracic Oncology Service, Division of Solid Tumor Oncology, Department of Medicine, Memorial Sloan Kettering Cancer Center, Weill Cornell Medical College, New York, NY 10065, USA
| | - Helena A. Yu
- Thoracic Oncology Service, Division of Solid Tumor Oncology, Department of Medicine, Memorial Sloan Kettering Cancer Center, Weill Cornell Medical College, New York, NY 10065, USA
| | - Aaron N. Hata
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, MA 02129, USA
| | - Collin M. Blakely
- Department of Medicine and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Caroline E. McCoach
- Department of Medicine and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Trever G. Bivona
- Department of Medicine and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Kris C. Wood
- Department of Pharmacology and Cancer Biology and Duke Cancer Institute, Duke University, Durham, NC 27710, USA
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22
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Weiss F, Lauffenburger D, Friedl P. Towards targeting of shared mechanisms of cancer metastasis and therapy resistance. Nat Rev Cancer 2022; 22:157-173. [PMID: 35013601 PMCID: PMC10399972 DOI: 10.1038/s41568-021-00427-0] [Citation(s) in RCA: 119] [Impact Index Per Article: 59.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/22/2021] [Indexed: 02/07/2023]
Abstract
Resistance to therapeutic treatment and metastatic progression jointly determine a fatal outcome of cancer. Cancer metastasis and therapeutic resistance are traditionally studied as separate fields using non-overlapping strategies. However, emerging evidence, including from in vivo imaging and in vitro organotypic culture, now suggests that both programmes cooperate and reinforce each other in the invasion niche and persist upon metastatic evasion. As a consequence, cancer cell subpopulations exhibiting metastatic invasion undergo multistep reprogramming that - beyond migration signalling - supports repair programmes, anti-apoptosis processes, metabolic adaptation, stemness and survival. Shared metastasis and therapy resistance signalling are mediated by multiple mechanisms, such as engagement of integrins and other context receptors, cell-cell communication, stress responses and metabolic reprogramming, which cooperate with effects elicited by autocrine and paracrine chemokine and growth factor cues present in the activated tumour microenvironment. These signals empower metastatic cells to cope with therapeutic assault and survive. Identifying nodes shared in metastasis and therapy resistance signalling networks should offer new opportunities to improve anticancer therapy beyond current strategies, to eliminate both nodular lesions and cells in metastatic transit.
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Affiliation(s)
- Felix Weiss
- Department of Cell Biology, RIMLS, Radboud University Medical Center, Nijmegen, Netherlands
| | - Douglas Lauffenburger
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Peter Friedl
- Department of Cell Biology, RIMLS, Radboud University Medical Center, Nijmegen, Netherlands.
- David H. Koch Center for Applied Research of Genitourinary Cancers, Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- Cancer Genomics Center, Utrecht, Netherlands.
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23
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Venugopal K, Feng Y, Nowialis P, Xu H, Shabashvili DE, Berntsen CM, Kaur P, Krajcik KI, Taragjini C, Zaroogian Z, Casellas Román HL, Posada LM, Gunaratne C, Li J, Dupéré-Richer D, Bennett RL, Pondugula S, Riva A, Cogle CR, Opavsky R, Law BK, Bhaduri-McIntosh S, Kubicek S, Staber PB, Licht JD, Bird JE, Guryanova OA. DNMT3A Harboring Leukemia-Associated Mutations Directs Sensitivity to DNA Damage at Replication Forks. Clin Cancer Res 2021; 28:756-769. [PMID: 34716195 DOI: 10.1158/1078-0432.ccr-21-2863] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 10/10/2021] [Accepted: 10/27/2021] [Indexed: 11/16/2022]
Abstract
PURPOSE In acute myeloid leukemia (AML), recurrent DNA methyltransferase 3A (DNMT3A) mutations are associated with chemoresistance and poor prognosis, especially in advanced-age patients. Gene-expression studies in DNMT3A-mutated cells identified signatures implicated in deregulated DNA damage response and replication fork integrity, suggesting sensitivity to replication stress. Here, we tested whether pharmacologically induced replication fork stalling, such as with cytarabine, creates a therapeutic vulnerability in cells with DNMT3A(R882) mutations. EXPERIMENTAL DESIGN Leukemia cell lines, genetic mouse models, and isogenic cells with and without DNMT3A(mut) were used to evaluate sensitivity to nucleoside analogues such as cytarabine in vitro and in vivo, followed by analysis of DNA damage and signaling, replication restart, and cell-cycle progression on treatment and after drug removal. Transcriptome profiling identified pathways deregulated by DNMT3A(mut) expression. RESULTS We found increased sensitivity to pharmacologically induced replication stress in cells expressing DNMT3A(R882)-mutant, with persistent intra-S-phase checkpoint activation, impaired PARP1 recruitment, and elevated DNA damage, which was incompletely resolved after drug removal and carried through mitosis. Pulse-chase double-labeling experiments with EdU and BrdU after cytarabine washout demonstrated a higher rate of fork collapse in DNMT3A(mut)-expressing cells. RNA-seq studies supported deregulated cell-cycle progression and p53 activation, along with splicing, ribosome biogenesis, and metabolism. CONCLUSIONS Together, our studies show that DNMT3A mutations underlie a defect in recovery from replication fork arrest with subsequent accumulation of unresolved DNA damage, which may have therapeutic tractability. These results demonstrate that, in addition to its role in epigenetic control, DNMT3A contributes to preserving genome integrity during replication stress.
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Affiliation(s)
- Kartika Venugopal
- Department of Pharmacology and Therapeutics, University of Florida College of Medicine, Gainesville, Florida
| | - Yang Feng
- Department of Pharmacology and Therapeutics, University of Florida College of Medicine, Gainesville, Florida
| | - Pawel Nowialis
- Department of Anatomy and Cell Biology, University of Florida College of Medicine, Gainesville, Florida
| | - Huanzhou Xu
- Department of Pediatrics, Division of Infectious Diseases, University of Florida College of Medicine, Gainesville, Florida
| | - Daniil E Shabashvili
- Department of Pharmacology and Therapeutics, University of Florida College of Medicine, Gainesville, Florida
| | - Cassandra M Berntsen
- Department of Pharmacology and Therapeutics, University of Florida College of Medicine, Gainesville, Florida
| | - Prabhjot Kaur
- Department of Pharmacology and Therapeutics, University of Florida College of Medicine, Gainesville, Florida
| | - Kathryn I Krajcik
- Department of Pharmacology and Therapeutics, University of Florida College of Medicine, Gainesville, Florida
| | - Christina Taragjini
- Department of Pharmacology and Therapeutics, University of Florida College of Medicine, Gainesville, Florida
| | - Zachary Zaroogian
- Department of Pharmacology and Therapeutics, University of Florida College of Medicine, Gainesville, Florida
| | - Heidi L Casellas Román
- Department of Pharmacology and Therapeutics, University of Florida College of Medicine, Gainesville, Florida
| | - Luisa M Posada
- Department of Pharmacology and Therapeutics, University of Florida College of Medicine, Gainesville, Florida
| | - Chamara Gunaratne
- Department of Pharmacology and Therapeutics, University of Florida College of Medicine, Gainesville, Florida
| | - Jianping Li
- Department of Medicine, Division of Hematology/ Oncology, University of Florida College of Medicine, Gainesville, Florida
| | - Daphné Dupéré-Richer
- Department of Medicine, Division of Hematology/ Oncology, University of Florida College of Medicine, Gainesville, Florida
| | - Richard L Bennett
- Department of Medicine, Division of Hematology/ Oncology, University of Florida College of Medicine, Gainesville, Florida.,University of Florida Health Cancer Center, Gainesville, Florida
| | - Santhi Pondugula
- Department of Pharmacology and Therapeutics, University of Florida College of Medicine, Gainesville, Florida
| | - Alberto Riva
- University of Florida Health Cancer Center, Gainesville, Florida.,Bioinformatics Core, Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, Florida
| | - Christopher R Cogle
- Department of Medicine, Division of Hematology/ Oncology, University of Florida College of Medicine, Gainesville, Florida.,University of Florida Health Cancer Center, Gainesville, Florida
| | - Rene Opavsky
- Department of Anatomy and Cell Biology, University of Florida College of Medicine, Gainesville, Florida.,University of Florida Health Cancer Center, Gainesville, Florida
| | - Brian K Law
- Department of Pharmacology and Therapeutics, University of Florida College of Medicine, Gainesville, Florida.,University of Florida Health Cancer Center, Gainesville, Florida
| | - Sumita Bhaduri-McIntosh
- Department of Pediatrics, Division of Infectious Diseases, University of Florida College of Medicine, Gainesville, Florida.,University of Florida Health Cancer Center, Gainesville, Florida.,Department of Molecular Genetics and Microbiology, University of Florida College of Medicine, Gainesville, Florida
| | - Stefan Kubicek
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Philipp B Staber
- Division of Hematology and Hemostaseology, Department of Medicine 1, Comprehensive Cancer Center Vienna, Medical University of Vienna, Vienna, Austria
| | - Jonathan D Licht
- Department of Medicine, Division of Hematology/ Oncology, University of Florida College of Medicine, Gainesville, Florida.,University of Florida Health Cancer Center, Gainesville, Florida
| | - Jonathan E Bird
- Department of Pharmacology and Therapeutics, University of Florida College of Medicine, Gainesville, Florida
| | - Olga A Guryanova
- Department of Pharmacology and Therapeutics, University of Florida College of Medicine, Gainesville, Florida. .,University of Florida Health Cancer Center, Gainesville, Florida
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24
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Beckley AM, Wright ES. Identification of antibiotic pairs that evade concurrent resistance via a retrospective analysis of antimicrobial susceptibility test results. LANCET MICROBE 2021; 2:e545-e554. [PMID: 34632433 PMCID: PMC8496867 DOI: 10.1016/s2666-5247(21)00118-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Background Some antibiotic pairs display a property known as collateral sensitivity in which the evolution of resistance to one antibiotic increases sensitivity to the other. Alternating between collaterally sensitive antibiotics has been proposed as a sustainable solution to the problem of antibiotic resistance. We aimed to identify antibiotic pairs that could be considered for treatment strategies based on alternating antibiotics. Methods We did a retrospective analysis of 448 563 antimicrobial susceptibility test results acquired over a 4-year period (Jan 1, 2015, to Dec 31, 2018) from 23 hospitals in the University of Pittsburgh Medical Center (Pittsburgh, PA, USA) hospital system. We used a score based on mutual information to identify pairs of antibiotics displaying disjoint resistance, wherein resistance to one antibiotic is commonly associated with susceptibility to the other and vice versa. We applied this approach to the six most frequently isolated bacterial pathogens (Escherichia coli, Staphylococcus aureus, Klebsiella pneumoniae, Enterococcus faecalis, Pseudomonas aeruginosa, and Proteus mirabilis) and subpopulations of each created by conditioning on resistance to individual antibiotics. To identify higher-order antibiotic interactions, we predicted rates of multidrug resistance for triplets of antibiotics using Markov random fields and compared these to the observed rates. Findings We identified 69 antibiotic pairs displaying varying degrees of disjoint resistance for subpopulations of the six bacterial species. However, disjoint resistance was rarely conserved at the species level, with only 6 (0·7%) of 875 antibiotic pairs showing evidence of disjoint resistance. Instead, more than half of antibiotic pairs (465 [53·1%] of 875) exhibited signatures of concurrent resistance, whereby resistance to one antibiotic is associated with resistance to another. We found concurrent resistance to extend to more than two antibiotics, with observed rates of resistance to three antibiotics being higher than predicted from pairwise information alone. Interpretation The high frequency of concurrent resistance shows that bacteria have means of counteracting multiple antibiotics at a time. The almost complete absence of disjoint resistance at the species level implies that treatment strategies based on alternating between antibiotics might require subspecies level pathogen identification and be limited to a few antibiotic pairings. Funding US National Institutes of Health.
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Affiliation(s)
- Andrew M Beckley
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Erik S Wright
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, PA, USA; Pittsburgh Center for Evolutionary Biology and Medicine, Pittsburgh, PA, USA
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25
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Vendramin R, Litchfield K, Swanton C. Cancer evolution: Darwin and beyond. EMBO J 2021; 40:e108389. [PMID: 34459009 PMCID: PMC8441388 DOI: 10.15252/embj.2021108389] [Citation(s) in RCA: 109] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 06/04/2021] [Accepted: 06/25/2021] [Indexed: 12/16/2022] Open
Abstract
Clinical and laboratory studies over recent decades have established branched evolution as a feature of cancer. However, while grounded in somatic selection, several lines of evidence suggest a Darwinian model alone is insufficient to fully explain cancer evolution. First, the role of macroevolutionary events in tumour initiation and progression contradicts Darwin's central thesis of gradualism. Whole-genome doubling, chromosomal chromoplexy and chromothripsis represent examples of single catastrophic events which can drive tumour evolution. Second, neutral evolution can play a role in some tumours, indicating that selection is not always driving evolution. Third, increasing appreciation of the role of the ageing soma has led to recent generalised theories of age-dependent carcinogenesis. Here, we review these concepts and others, which collectively argue for a model of cancer evolution which extends beyond Darwin. We also highlight clinical opportunities which can be grasped through targeting cancer vulnerabilities arising from non-Darwinian patterns of evolution.
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Affiliation(s)
- Roberto Vendramin
- Cancer Research UK Lung Cancer Centre of ExcellenceUniversity College London Cancer InstituteLondonUK
| | - Kevin Litchfield
- Cancer Research UK Lung Cancer Centre of ExcellenceUniversity College London Cancer InstituteLondonUK
| | - Charles Swanton
- Cancer Research UK Lung Cancer Centre of ExcellenceUniversity College London Cancer InstituteLondonUK
- Cancer Evolution and Genome Instability LaboratoryThe Francis Crick InstituteLondonUK
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26
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Joshi SK, Nechiporuk T, Bottomly D, Piehowski PD, Reisz JA, Pittsenbarger J, Kaempf A, Gosline SJC, Wang YT, Hansen JR, Gritsenko MA, Hutchinson C, Weitz KK, Moon J, Cendali F, Fillmore TL, Tsai CF, Schepmoes AA, Shi T, Arshad OA, McDermott JE, Babur O, Watanabe-Smith K, Demir E, D'Alessandro A, Liu T, Tognon CE, Tyner JW, McWeeney SK, Rodland KD, Druker BJ, Traer E. The AML microenvironment catalyzes a stepwise evolution to gilteritinib resistance. Cancer Cell 2021; 39:999-1014.e8. [PMID: 34171263 PMCID: PMC8686208 DOI: 10.1016/j.ccell.2021.06.003] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 03/22/2021] [Accepted: 06/03/2021] [Indexed: 12/18/2022]
Abstract
Our study details the stepwise evolution of gilteritinib resistance in FLT3-mutated acute myeloid leukemia (AML). Early resistance is mediated by the bone marrow microenvironment, which protects residual leukemia cells. Over time, leukemia cells evolve intrinsic mechanisms of resistance, or late resistance. We mechanistically define both early and late resistance by integrating whole-exome sequencing, CRISPR-Cas9, metabolomics, proteomics, and pharmacologic approaches. Early resistant cells undergo metabolic reprogramming, grow more slowly, and are dependent upon Aurora kinase B (AURKB). Late resistant cells are characterized by expansion of pre-existing NRAS mutant subclones and continued metabolic reprogramming. Our model closely mirrors the timing and mutations of AML patients treated with gilteritinib. Pharmacological inhibition of AURKB resensitizes both early resistant cell cultures and primary leukemia cells from gilteritinib-treated AML patients. These findings support a combinatorial strategy to target early resistant AML cells with AURKB inhibitors and gilteritinib before the expansion of pre-existing resistance mutations occurs.
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MESH Headings
- Aniline Compounds/pharmacology
- Aurora Kinase B/genetics
- Aurora Kinase B/metabolism
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Drug Resistance, Neoplasm
- Exome
- Gene Expression Regulation, Neoplastic/drug effects
- Humans
- Leukemia, Myeloid, Acute/drug therapy
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/pathology
- Metabolome
- Protein Kinase Inhibitors/pharmacology
- Proteome
- Pyrazines/pharmacology
- Tumor Cells, Cultured
- Tumor Microenvironment
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Affiliation(s)
- Sunil K Joshi
- Knight Cancer Institute, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA; Department of Physiology & Pharmacology, School of Medicine, Oregon Health & Science University, Portland, OR, USA; Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Tamilla Nechiporuk
- Knight Cancer Institute, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA; Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Daniel Bottomly
- Knight Cancer Institute, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA; Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR, USA
| | - Paul D Piehowski
- Environmental and Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA; Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Julie A Reisz
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Janét Pittsenbarger
- Knight Cancer Institute, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA; Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Andy Kaempf
- Knight Cancer Institute, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA; Biostatistics Shared Resource, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Sara J C Gosline
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Yi-Ting Wang
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Joshua R Hansen
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Marina A Gritsenko
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Chelsea Hutchinson
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Karl K Weitz
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Jamie Moon
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Francesca Cendali
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Thomas L Fillmore
- Environmental and Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA; Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Chia-Feng Tsai
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Athena A Schepmoes
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Tujin Shi
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Osama A Arshad
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Jason E McDermott
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Ozgun Babur
- Department of Computer Science, University of Massachusetts, Boston, MA, USA
| | - Kevin Watanabe-Smith
- Knight Cancer Institute, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA; Computational Biology Program, Oregon Health & Science University, Portland, OR, USA
| | - Emek Demir
- Knight Cancer Institute, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA; Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR, USA; Computational Biology Program, Oregon Health & Science University, Portland, OR, USA
| | - Angelo D'Alessandro
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Tao Liu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Cristina E Tognon
- Knight Cancer Institute, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA; Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Jeffrey W Tyner
- Knight Cancer Institute, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA; Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA; Department of Cell, Development, & Cancer Biology, Oregon Health & Science University, Portland, OR, USA
| | - Shannon K McWeeney
- Knight Cancer Institute, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA; Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR, USA
| | - Karin D Rodland
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA; Department of Cell, Development, & Cancer Biology, Oregon Health & Science University, Portland, OR, USA
| | - Brian J Druker
- Knight Cancer Institute, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA; Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA; Department of Cell, Development, & Cancer Biology, Oregon Health & Science University, Portland, OR, USA
| | - Elie Traer
- Knight Cancer Institute, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA; Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA; Department of Cell, Development, & Cancer Biology, Oregon Health & Science University, Portland, OR, USA.
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27
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Hayford CE, Tyson DR, Robbins CJ, Frick PL, Quaranta V, Harris LA. An in vitro model of tumor heterogeneity resolves genetic, epigenetic, and stochastic sources of cell state variability. PLoS Biol 2021; 19:e3000797. [PMID: 34061819 PMCID: PMC8195356 DOI: 10.1371/journal.pbio.3000797] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 06/11/2021] [Accepted: 03/16/2021] [Indexed: 12/30/2022] Open
Abstract
Tumor heterogeneity is a primary cause of treatment failure and acquired resistance in cancer patients. Even in cancers driven by a single mutated oncogene, variability in response to targeted therapies is well known. The existence of additional genomic alterations among tumor cells can only partially explain this variability. As such, nongenetic factors are increasingly seen as critical contributors to tumor relapse and acquired resistance in cancer. Here, we show that both genetic and nongenetic factors contribute to targeted drug response variability in an experimental model of tumor heterogeneity. We observe significant variability to epidermal growth factor receptor (EGFR) inhibition among and within multiple versions and clonal sublines of PC9, a commonly used EGFR mutant nonsmall cell lung cancer (NSCLC) cell line. We resolve genetic, epigenetic, and stochastic components of this variability using a theoretical framework in which distinct genetic states give rise to multiple epigenetic "basins of attraction," across which cells can transition driven by stochastic noise. Using mutational impact analysis, single-cell differential gene expression, and correlations among Gene Ontology (GO) terms to connect genomics to transcriptomics, we establish a baseline for genetic differences driving drug response variability among PC9 cell line versions. Applying the same approach to clonal sublines, we conclude that drug response variability in all but one of the sublines is due to epigenetic differences; in the other, it is due to genetic alterations. Finally, using a clonal drug response assay together with stochastic simulations, we attribute subclonal drug response variability within sublines to stochastic cell fate decisions and confirm that one subline likely contains genetic resistance mutations that emerged in the absence of drug treatment.
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Affiliation(s)
- Corey E. Hayford
- Chemical and Physical Biology Graduate Program, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Darren R. Tyson
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - C. Jack Robbins
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Peter L. Frick
- Chemical and Physical Biology Graduate Program, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Vito Quaranta
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
- Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Leonard A. Harris
- Department of Biomedical Engineering, University of Arkansas, Fayetteville, Arkansas, United States of America
- Interdisciplinary Graduate Program in Cell and Molecular Biology, University of Arkansas, Fayetteville, Arkansas, United States of America
- Cancer Biology Program, Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
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28
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Pacini L, Jenks AD, Lima NC, Huang PH. Targeting the Fibroblast Growth Factor Receptor (FGFR) Family in Lung Cancer. Cells 2021; 10:1154. [PMID: 34068816 PMCID: PMC8151052 DOI: 10.3390/cells10051154] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 05/05/2021] [Accepted: 05/07/2021] [Indexed: 12/12/2022] Open
Abstract
Lung cancer is the most common cause of cancer-related deaths globally. Genetic alterations, such as amplifications, mutations and translocations in the fibroblast growth factor receptor (FGFR) family have been found in non-small cell lung cancer (NSCLC) where they have a role in cancer initiation and progression. FGFR aberrations have also been identified as key compensatory bypass mechanisms of resistance to targeted therapy against mutant epidermal growth factor receptor (EGFR) and mutant Kirsten rat sarcoma 2 viral oncogene homolog (KRAS) in lung cancer. Targeting FGFR is, therefore, of clinical relevance for this cancer type, and several selective and nonselective FGFR inhibitors have been developed in recent years. Despite promising preclinical data, clinical trials have largely shown low efficacy of these agents in lung cancer patients with FGFR alterations. Preclinical studies have highlighted the emergence of multiple intrinsic and acquired resistance mechanisms to FGFR tyrosine kinase inhibitors, which include on-target FGFR gatekeeper mutations and activation of bypass signalling pathways and alternative receptor tyrosine kinases. Here, we review the landscape of FGFR aberrations in lung cancer and the array of targeted therapies under clinical evaluation. We also discuss the current understanding of the mechanisms of resistance to FGFR-targeting compounds and therapeutic strategies to circumvent resistance. Finally, we highlight our perspectives on the development of new biomarkers for stratification and prediction of FGFR inhibitor response to enable personalisation of treatment in patients with lung cancer.
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Affiliation(s)
| | | | | | - Paul H. Huang
- Division of Molecular Pathology, The Institute of Cancer Research, London SM2 5NG, UK; (L.P.); (A.D.J.); (N.C.L.)
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29
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Aldonza MBD, Reyes RDD, Kim YS, Ku J, Barsallo AM, Hong JY, Lee SK, Ryu HS, Park Y, Cho JY, Kim Y. Chemotherapy confers a conserved secondary tolerance to EGFR inhibition via AXL-mediated signaling bypass. Sci Rep 2021; 11:8016. [PMID: 33850249 PMCID: PMC8044124 DOI: 10.1038/s41598-021-87599-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 03/31/2021] [Indexed: 02/01/2023] Open
Abstract
Drug resistance remains the major culprit of therapy failure in disseminated cancers. Simultaneous resistance to multiple, chemically different drugs feeds this failure resulting in cancer relapse. Here, we investigate co-resistance signatures shared between antimitotic drugs (AMDs) and inhibitors of receptor tyrosine kinases (RTKs) to probe mechanisms of secondary resistance. We map co-resistance ranks in multiple drug pairs and identified a more widespread occurrence of co-resistance to the EGFR-tyrosine kinase inhibitor (TKI) gefitinib in hundreds of cancer cell lines resistant to at least 11 AMDs. By surveying different parameters of genomic alterations, we find that the two RTKs EGFR and AXL displayed similar alteration and expression signatures. Using acquired paclitaxel and epothilone B resistance as first-line AMD failure models, we show that a stable collateral resistance to gefitinib can be relayed by entering a dynamic, drug-tolerant persister state where AXL acts as bypass signal. Delayed AXL degradation rendered this persistence to become stably resistant. We probed this degradation process using a new EGFR-TKI candidate YD and demonstrated that AXL bypass-driven collateral resistance can be suppressed pharmacologically. The findings emphasize that AXL bypass track is employed by chemoresistant cancer cells upon EGFR inhibition to enter a persister state and evolve resistance to EGFR-TKIs.
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Affiliation(s)
- Mark Borris D Aldonza
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Korea
- Department of Biological Sciences, KAIST, Daejeon, 34141, Korea
- KI for Health Science and Technology (KIHST), KAIST, Daejeon, 34141, Korea
- Department of Biochemistry, College of Veterinary Medicine, Seoul National University, Seoul, 151-742, Korea
- BK21 PLUS Program for Creative Veterinary Science Research and Research Institute for Veterinary Science, Seoul National University, Seoul, 151-742, Korea
| | | | - Young Seo Kim
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Korea
- Tomocube Inc, Daejeon, 34051, Korea
| | - Jayoung Ku
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Korea
- KI for Health Science and Technology (KIHST), KAIST, Daejeon, 34141, Korea
| | - Ana Melisa Barsallo
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Korea
- Department of Biological Sciences, KAIST, Daejeon, 34141, Korea
| | - Ji-Young Hong
- College of Pharmacy, Natural Products Research Institute, Seoul National University, Seoul, 08826, Korea
| | - Sang Kook Lee
- College of Pharmacy, Natural Products Research Institute, Seoul National University, Seoul, 08826, Korea
| | - Han Suk Ryu
- Department of Pathology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, 03080, Korea
| | - YongKeun Park
- KI for Health Science and Technology (KIHST), KAIST, Daejeon, 34141, Korea
- Tomocube Inc, Daejeon, 34051, Korea
- Department of Physics, KAIST, Daejeon, 34141, Korea
| | - Je-Yoel Cho
- Department of Biochemistry, College of Veterinary Medicine, Seoul National University, Seoul, 151-742, Korea.
- BK21 PLUS Program for Creative Veterinary Science Research and Research Institute for Veterinary Science, Seoul National University, Seoul, 151-742, Korea.
| | - Yoosik Kim
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Korea.
- KI for Health Science and Technology (KIHST), KAIST, Daejeon, 34141, Korea.
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30
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Litchfield K, Reading JL, Puttick C, Thakkar K, Abbosh C, Bentham R, Watkins TBK, Rosenthal R, Biswas D, Rowan A, Lim E, Al Bakir M, Turati V, Guerra-Assunção JA, Conde L, Furness AJS, Saini SK, Hadrup SR, Herrero J, Lee SH, Van Loo P, Enver T, Larkin J, Hellmann MD, Turajlic S, Quezada SA, McGranahan N, Swanton C. Meta-analysis of tumor- and T cell-intrinsic mechanisms of sensitization to checkpoint inhibition. Cell 2021; 184:596-614.e14. [PMID: 33508232 PMCID: PMC7933824 DOI: 10.1016/j.cell.2021.01.002] [Citation(s) in RCA: 456] [Impact Index Per Article: 152.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 06/26/2020] [Accepted: 01/04/2021] [Indexed: 12/22/2022]
Abstract
Checkpoint inhibitors (CPIs) augment adaptive immunity. Systematic pan-tumor analyses may reveal the relative importance of tumor-cell-intrinsic and microenvironmental features underpinning CPI sensitization. Here, we collated whole-exome and transcriptomic data for >1,000 CPI-treated patients across seven tumor types, utilizing standardized bioinformatics workflows and clinical outcome criteria to validate multivariable predictors of CPI sensitization. Clonal tumor mutation burden (TMB) was the strongest predictor of CPI response, followed by total TMB and CXCL9 expression. Subclonal TMB, somatic copy alteration burden, and histocompatibility leukocyte antigen (HLA) evolutionary divergence failed to attain pan-cancer significance. Dinucleotide variants were identified as a source of immunogenic epitopes associated with radical amino acid substitutions and enhanced peptide hydrophobicity/immunogenicity. Copy-number analysis revealed two additional determinants of CPI outcome supported by prior functional evidence: 9q34 (TRAF2) loss associated with response and CCND1 amplification associated with resistance. Finally, single-cell RNA sequencing (RNA-seq) of clonal neoantigen-reactive CD8 tumor-infiltrating lymphocytes (TILs), combined with bulk RNA-seq analysis of CPI-responding tumors, identified CCR5 and CXCL13 as T-cell-intrinsic markers of CPI sensitivity.
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Affiliation(s)
- Kevin Litchfield
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6BT, UK
| | - James L Reading
- Cancer Immunology Unit, Research Department of Hematology, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6BT, UK; Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6BT, UK
| | - Clare Puttick
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Krupa Thakkar
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6BT, UK
| | - Chris Abbosh
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6BT, UK
| | - Robert Bentham
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6BT, UK
| | - Thomas B K Watkins
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Rachel Rosenthal
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Dhruva Biswas
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Andrew Rowan
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Emilia Lim
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Maise Al Bakir
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Virginia Turati
- Stem Cell Group, Cancer Institute, University College London, London WC1E 6DD, UK
| | - José Afonso Guerra-Assunção
- Bill Lyons Informatics Centre, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6BT, UK
| | - Lucia Conde
- Bill Lyons Informatics Centre, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6BT, UK
| | - Andrew J S Furness
- Renal and Skin Units, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Sunil Kumar Saini
- Department of Health Technology, Technical University of Denmark, Copenhagen, Denmark
| | - Sine R Hadrup
- Department of Health Technology, Technical University of Denmark, Copenhagen, Denmark
| | - Javier Herrero
- Bill Lyons Informatics Centre, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6BT, UK
| | - Se-Hoon Lee
- Department of Health Sciences and Technology, Samsung Advanced Institute of Health Sciences and Technology, Sungkyunkwan University, Seoul, South Korea; Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Peter Van Loo
- Cancer Genomics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Tariq Enver
- Stem Cell Group, Cancer Institute, University College London, London WC1E 6DD, UK
| | - James Larkin
- Renal and Skin Units, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Matthew D Hellmann
- Thoracic Oncology Service, Division of Solid Tumor Oncology, Department of Medicine, Memorial Sloan Kettering Cancer Center, Weill Cornell Medical College, and Parker Center for Cancer Immunotherapy, 885 2nd Avenue, New York, NY 10017, USA
| | - Samra Turajlic
- Renal and Skin Units, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK; Cancer Dynamics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Sergio A Quezada
- Cancer Immunology Unit, Research Department of Hematology, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6BT, UK; Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6BT, UK.
| | - Nicholas McGranahan
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6BT, UK.
| | - Charles Swanton
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6BT, UK.
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31
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Fuertes T, Ramiro AR, de Yebenes VG. miRNA-Based Therapies in B Cell Non-Hodgkin Lymphoma. Trends Immunol 2020; 41:932-947. [PMID: 32888820 DOI: 10.1016/j.it.2020.08.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 08/06/2020] [Accepted: 08/06/2020] [Indexed: 12/17/2022]
Abstract
Non-Hodgkin lymphoma (NHL) is a diverse class of hematological cancers, many of which arise from germinal center (GC)-experienced B cells. Thus GCs, the sites of antibody affinity maturation triggered during immune responses, also provide an environment that facilitates B cell oncogenic transformation. miRNAs provide attractive and mechanistically different strategies to treat these malignancies based on their potential for simultaneous modulation of multiple targets. Here, we discuss the scientific rationale for miRNA-based therapeutics in B cell neoplasias and review recent advances that may help establish a basis for novel candidate miRNA-based therapies for B cell-NHL (B-NHL).
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Affiliation(s)
- Teresa Fuertes
- Centro Nacional de Investigaciones Cardiovasculares, Madrid, Spain
| | | | - Virginia G de Yebenes
- Universidad Complutense de Madrid School of Medicine, Department of Immunology, Ophthalmology and ENT, 12 de Octubre Health Research Institute (imas12), Madrid, Spain.
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32
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Melnikov SV, Stevens DL, Fu X, Kwok HS, Zhang JT, Shen Y, Sabina J, Lee K, Lee H, Söll D. Exploiting evolutionary trade-offs for posttreatment management of drug-resistant populations. Proc Natl Acad Sci U S A 2020; 117:17924-17931. [PMID: 32661175 PMCID: PMC7395499 DOI: 10.1073/pnas.2003132117] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Antibiotic resistance frequently evolves through fitness trade-offs in which the genetic alterations that confer resistance to a drug can also cause growth defects in resistant cells. Here, through experimental evolution in a microfluidics-based turbidostat, we demonstrate that antibiotic-resistant cells can be efficiently inhibited by amplifying the fitness costs associated with drug-resistance evolution. Using tavaborole-resistant Escherichia coli as a model, we show that genetic mutations in leucyl-tRNA synthetase (that underlie tavaborole resistance) make resistant cells intolerant to norvaline, a chemical analog of leucine that is mistakenly used by tavaborole-resistant cells for protein synthesis. We then show that tavaborole-sensitive cells quickly outcompete tavaborole-resistant cells in the presence of norvaline due to the amplified cost of the molecular defect of tavaborole resistance. This finding illustrates that understanding molecular mechanisms of drug resistance allows us to effectively amplify even small evolutionary vulnerabilities of resistant cells to potentially enhance or enable adaptive therapies by accelerating posttreatment competition between resistant and susceptible cells.
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Affiliation(s)
- Sergey V Melnikov
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520;
| | - David L Stevens
- Department of Chemistry, Yale University, New Haven, CT 06520
| | - Xian Fu
- Guangdong Provincial Key Laboratory of Genome Read and Write, 518120 Shenzhen, China
- BGI-Shenzhen, 518083 Shenzhen, China
- China National Genebank, BGI-Shenzhen, 518120 Shenzhen, China
| | - Hui Si Kwok
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520
| | - Jin-Tao Zhang
- BGI-Shenzhen, 518083 Shenzhen, China
- China National Genebank, BGI-Shenzhen, 518120 Shenzhen, China
| | - Yue Shen
- Guangdong Provincial Key Laboratory of Genome Read and Write, 518120 Shenzhen, China
- BGI-Shenzhen, 518083 Shenzhen, China
- China National Genebank, BGI-Shenzhen, 518120 Shenzhen, China
| | | | | | | | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520;
- Department of Chemistry, Yale University, New Haven, CT 06520
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33
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Characterizing the ecological and evolutionary dynamics of cancer. Nat Genet 2020; 52:759-767. [DOI: 10.1038/s41588-020-0668-4] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 06/22/2020] [Indexed: 12/14/2022]
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34
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Pisa R, Kapoor TM. Chemical strategies to overcome resistance against targeted anticancer therapeutics. Nat Chem Biol 2020; 16:817-825. [PMID: 32694636 DOI: 10.1038/s41589-020-0596-8] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 06/17/2020] [Indexed: 12/12/2022]
Abstract
Emergence of resistance is a major factor limiting the efficacy of molecularly targeted anticancer drugs. Understanding the specific mutations, or other genetic or cellular changes, that confer drug resistance can help in the development of therapeutic strategies with improved efficacies. Here, we outline recent progress in understanding chemotype-specific mechanisms of resistance and present chemical strategies, such as designing drugs with distinct binding modes or using proteolysis targeting chimeras, to overcome resistance. We also discuss how targeting multiple binding sites with bifunctional inhibitors or identifying collateral sensitivity profiles can be exploited to limit the emergence of resistance. Finally, we highlight how incorporating analyses of resistance early in drug development can help with the design and evaluation of therapeutics that can have long-term benefits for patients.
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Affiliation(s)
- Rudolf Pisa
- Laboratory of Chemistry and Cell Biology, The Rockefeller University, New York, NY, USA.,Tri-Institutional PhD Program in Chemical Biology, The Rockefeller University, New York, NY, USA.,Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Tarun M Kapoor
- Laboratory of Chemistry and Cell Biology, The Rockefeller University, New York, NY, USA.
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35
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Identifying States of Collateral Sensitivity during the Evolution of Therapeutic Resistance in Ewing's Sarcoma. iScience 2020; 23:101293. [PMID: 32623338 PMCID: PMC7334607 DOI: 10.1016/j.isci.2020.101293] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 05/06/2020] [Accepted: 06/15/2020] [Indexed: 12/19/2022] Open
Abstract
Advances in the treatment of Ewing's sarcoma (EWS) are desperately needed, particularly in the case of metastatic disease. A deeper understanding of collateral sensitivity, where the evolution of therapeutic resistance to one drug aligns with sensitivity to another drug, may improve our ability to effectively target this disease. For the first time in a solid tumor, we produced a temporal collateral sensitivity map that demonstrates the evolution of collateral sensitivity and resistance in EWS. We found that the evolution of collateral resistance was predictable with some drugs but had significant variation in response to other drugs. Using this map of temporal collateral sensitivity in EWS, we can see that the path toward collateral sensitivity is not always repeatable, nor is there always a clear trajectory toward resistance or sensitivity. Identifying transcriptomic changes that accompany these states of transient collateral sensitivity could improve treatment planning for patients with EWS. Ewing's sarcoma cell lines were evolved to become resistant to standard chemotherapy A temporal collateral sensitivity map shows response to alternative drugs over time Collateral drug response is repeatable in some instances and stochastic in others Differential gene expression elucidates potential biomarkers of drug response
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36
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Grolmusz VK, Chen J, Emond R, Cosgrove PA, Pflieger L, Nath A, Moos PJ, Bild AH. Exploiting collateral sensitivity controls growth of mixed culture of sensitive and resistant cells and decreases selection for resistant cells in a cell line model. Cancer Cell Int 2020; 20:253. [PMID: 32565737 PMCID: PMC7301982 DOI: 10.1186/s12935-020-01337-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 06/09/2020] [Indexed: 12/14/2022] Open
Abstract
Background CDK4/6 inhibitors such as ribociclib are becoming widely used targeted therapies in hormone-receptor-positive (HR+) human epidermal growth factor receptor 2-negative (HER2-) breast cancer. However, cancers can advance due to drug resistance, a problem in which tumor heterogeneity and evolution are key features. Methods Ribociclib-resistant HR+/HER2- CAMA-1 breast cancer cells were generated through long-term ribociclib treatment. Characterization of sensitive and resistant cells were performed using RNA sequencing and whole exome sequencing. Lentiviral labeling with different fluorescent proteins enabled us to track the proliferation of sensitive and resistant cells under different treatments in a heterogeneous, 3D spheroid coculture system using imaging microscopy and flow cytometry. Results Transcriptional profiling of sensitive and resistant cells revealed the downregulation of the G2/M checkpoint in the resistant cells. Exploiting this acquired vulnerability; resistant cells exhibited collateral sensitivity for the Wee-1 inhibitor, adavosertib (AZD1775). The combination of ribociclib and adavosertib achieved additional antiproliferative effect exclusively in the cocultures compared to monocultures, while decreasing the selection for resistant cells. Conclusions Our results suggest that optimal antiproliferative effects in heterogeneous cancers can be achieved via an integrative therapeutic approach targeting sensitive and resistant cancer cell populations within a tumor, respectively.
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Affiliation(s)
- Vince Kornél Grolmusz
- Department of Medical Oncology and Therapeutics Research, Beckman Research Institute, City of Hope National Medical Center, 1218 S Fifth Ave, Monrovia, CA 91016 USA
| | - Jinfeng Chen
- Department of Medical Oncology and Therapeutics Research, Beckman Research Institute, City of Hope National Medical Center, 1218 S Fifth Ave, Monrovia, CA 91016 USA
| | - Rena Emond
- Department of Medical Oncology and Therapeutics Research, Beckman Research Institute, City of Hope National Medical Center, 1218 S Fifth Ave, Monrovia, CA 91016 USA
| | - Patrick A Cosgrove
- Department of Medical Oncology and Therapeutics Research, Beckman Research Institute, City of Hope National Medical Center, 1218 S Fifth Ave, Monrovia, CA 91016 USA
| | - Lance Pflieger
- Department of Medical Oncology and Therapeutics Research, Beckman Research Institute, City of Hope National Medical Center, 1218 S Fifth Ave, Monrovia, CA 91016 USA
| | - Aritro Nath
- Department of Medical Oncology and Therapeutics Research, Beckman Research Institute, City of Hope National Medical Center, 1218 S Fifth Ave, Monrovia, CA 91016 USA
| | - Philip J Moos
- Department of Pharmacology and Toxicology, University of Utah, 30 S 2000 East, Salt Lake City, UT 84112 USA
| | - Andrea H Bild
- Department of Medical Oncology and Therapeutics Research, Beckman Research Institute, City of Hope National Medical Center, 1218 S Fifth Ave, Monrovia, CA 91016 USA
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37
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Vander Velde R, Yoon N, Marusyk V, Durmaz A, Dhawan A, Miroshnychenko D, Lozano-Peral D, Desai B, Balynska O, Poleszhuk J, Kenian L, Teng M, Abazeed M, Mian O, Tan AC, Haura E, Scott J, Marusyk A. Resistance to targeted therapies as a multifactorial, gradual adaptation to inhibitor specific selective pressures. Nat Commun 2020; 11:2393. [PMID: 32409712 PMCID: PMC7224215 DOI: 10.1038/s41467-020-16212-w] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 04/17/2020] [Indexed: 12/21/2022] Open
Abstract
Despite high initial efficacy, targeted therapies eventually fail in advanced cancers, as tumors develop resistance and relapse. In contrast to the substantial body of research on the molecular mechanisms of resistance, understanding of how resistance evolves remains limited. Using an experimental model of ALK positive NSCLC, we explored the evolution of resistance to different clinical ALK inhibitors. We found that resistance can originate from heterogeneous, weakly resistant subpopulations with variable sensitivity to different ALK inhibitors. Instead of the commonly assumed stochastic single hit (epi) mutational transition, or drug-induced reprogramming, we found evidence for a hybrid scenario involving the gradual, multifactorial adaptation to the inhibitors through acquisition of multiple cooperating genetic and epigenetic adaptive changes. Additionally, we found that during this adaptation tumor cells might present unique, temporally restricted collateral sensitivities, absent in therapy naïve or fully resistant cells, suggesting the potential for new therapeutic interventions, directed against evolving resistance. Acquired resistance to cancer therapies reflects the ability of cancers to adapt to therapy-imposed selective pressures. Here, the authors elucidate the dynamics of developing resistance to ALK inhibitors in an ALK+ lung cancer cell line showing that resistance originates from drug-specific tolerant cancer cells and it develops as a gradual adaptation.
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Affiliation(s)
- Robert Vander Velde
- Department of Cancer Physiology, H Lee Moffitt Cancer Centre and Research Institute, Tampa, FL, USA.,Department of Molecular Medicine, University of South Florida, Tampa, FL, USA
| | - Nara Yoon
- Department of Translational Hematology and Oncology Research, Cleveland Clinic, Cleveland, OH, USA
| | - Viktoriya Marusyk
- Department of Cancer Physiology, H Lee Moffitt Cancer Centre and Research Institute, Tampa, FL, USA
| | - Arda Durmaz
- Department of Translational Hematology and Oncology Research, Cleveland Clinic, Cleveland, OH, USA.,Systems Biology and Bioinformatics, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Andrew Dhawan
- Department of Translational Hematology and Oncology Research, Cleveland Clinic, Cleveland, OH, USA
| | - Daria Miroshnychenko
- Department of Cancer Physiology, H Lee Moffitt Cancer Centre and Research Institute, Tampa, FL, USA
| | - Diego Lozano-Peral
- Department of Cancer Physiology, H Lee Moffitt Cancer Centre and Research Institute, Tampa, FL, USA.,Supercomputer and Bioinnovation Center, University of Málaga, Málaga, Spain
| | - Bina Desai
- Department of Cancer Physiology, H Lee Moffitt Cancer Centre and Research Institute, Tampa, FL, USA.,University of South Florida Cancer Biology PhD Program, Tampa, FL, USA
| | - Olena Balynska
- Department of Cancer Physiology, H Lee Moffitt Cancer Centre and Research Institute, Tampa, FL, USA
| | - Jan Poleszhuk
- Nalecz Institute of Biocybernetics and Biomedical Engineering, Polish Academy of Sciences, Warsaw, Poland
| | - Liu Kenian
- Department of Pathology, H Lee Moffitt Cancer Centre and Research Institute, Tampa, FL, USA
| | - Mingxiang Teng
- Department of Biostatistic and Bioinformatics, H Lee Moffitt Cancer Centre and Research Institute, Tampa, FL, USA
| | - Mohamed Abazeed
- Department of Translational Hematology and Oncology Research, Cleveland Clinic, Cleveland, OH, USA
| | - Omar Mian
- Department of Translational Hematology and Oncology Research, Cleveland Clinic, Cleveland, OH, USA
| | - Aik Choon Tan
- Department of Biostatistic and Bioinformatics, H Lee Moffitt Cancer Centre and Research Institute, Tampa, FL, USA
| | - Eric Haura
- Department of Thoracic Oncology, H Lee Moffitt Cancer Centre and Research Institute, Tampa, FL, USA
| | - Jacob Scott
- Department of Translational Hematology and Oncology Research, Cleveland Clinic, Cleveland, OH, USA. .,Systems Biology and Bioinformatics, Case Western Reserve University School of Medicine, Cleveland, OH, USA.
| | - Andriy Marusyk
- Department of Cancer Physiology, H Lee Moffitt Cancer Centre and Research Institute, Tampa, FL, USA. .,Department of Molecular Medicine, University of South Florida, Tampa, FL, USA.
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38
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Lima NC, Atkinson E, Bunney TD, Katan M, Huang PH. Targeting the Src Pathway Enhances the Efficacy of Selective FGFR Inhibitors in Urothelial Cancers with FGFR3 Alterations. Int J Mol Sci 2020; 21:E3214. [PMID: 32370101 PMCID: PMC7246793 DOI: 10.3390/ijms21093214] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Revised: 04/24/2020] [Accepted: 04/27/2020] [Indexed: 01/08/2023] Open
Abstract
Selective FGFR inhibitors such as infigratinib (BGJ398) and erdafitinib (JNJ-42756493) have been evaluated in clinical trials for cancers with FGFR3 molecular alterations, particularly in urothelial carcinoma patients. However, a substantial proportion of these patients (up to 50%) display intrinsic resistance to these drugs and receive minimal clinical benefit. There is thus an unmet need for alternative therapeutic strategies to overcome primary resistance to selective FGFR inhibitors. In this study, we demonstrate that cells expressing cancer-associated activating FGFR3 mutants and the FGFR3-TACC3 fusion showed primary resistance to infigratinib in long-term colony formation assays in both NIH-3T3 and urothelial carcinoma models. We find that expression of these FGFR3 molecular alterations resulted in elevated constitutive Src activation compared to wildtype FGFR3 and that cells co-opted this pathway as a means to achieve intrinsic resistance to infigratinib. Targeting the Src pathway with low doses of the kinase inhibitor dasatinib synergistically sensitized multiple urothelial carcinoma lines harbouring endogenous FGFR3 alterations to infigratinib. Our data provide preclinical rationale that supports the use of dasatinib in combination with selective FGFR inhibitors as a means to overcome intrinsic drug resistance in the salvage therapy setting in urothelial cancer patients with FGFR3 molecular alterations.
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Affiliation(s)
- Nadia Carvalho Lima
- Division of Molecular Pathology, The Institute of Cancer Research, London SM2 5NG, UK; (N.C.L.); (E.A.)
| | - Eliza Atkinson
- Division of Molecular Pathology, The Institute of Cancer Research, London SM2 5NG, UK; (N.C.L.); (E.A.)
| | - Tom D. Bunney
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, UK; (T.D.B.); (M.K.)
| | - Matilda Katan
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, UK; (T.D.B.); (M.K.)
| | - Paul H. Huang
- Division of Molecular Pathology, The Institute of Cancer Research, London SM2 5NG, UK; (N.C.L.); (E.A.)
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Development of a Model for Chemical Screening Based on Collateral Sensitivity to Target BTK C481S Mutant. Cancers (Basel) 2020; 12:cancers12040901. [PMID: 32272741 PMCID: PMC7226254 DOI: 10.3390/cancers12040901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 03/30/2020] [Accepted: 04/02/2020] [Indexed: 11/18/2022] Open
Abstract
Targeted therapies have improved the outcome of cancer, but their efficacy is intrinsically limited by the emergence of subclones with a mutation in the gene encoding the target protein. A few examples of collateral sensitivity have demonstrated that the conformational changes induced by these mutations can create unexpected sensitivity to other kinase inhibitors, but whether this concept can be generalized is unknown. Here is described the development of a model to screen a library of kinase inhibitors for collateral sensitivity drugs active on the Bruton Tyrosine Kinase (BTK) protein with the ibrutinib resistance mutation C481S. First, we demonstrate that overexpression of the constitutively active mutant of BTK harboring the E41K mutation in Ba/F3 cells creates an oncogenic addiction to BTK. Then, we have exploited this phenotype to perform a screen of a kinase inhibitor library on cells with or without the ibrutinib resistance mutation. The BTK inhibitors showed the expected sensitivity profile, but none of the drugs tested had a specific activity against the C481S mutant of BTK, suggesting that extending the collateral sensitivity paradigm to all kinases targeted by cancer therapy might not be trivial.
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40
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Using antagonistic pleiotropy to design a chemotherapy-induced evolutionary trap to target drug resistance in cancer. Nat Genet 2020; 52:408-417. [PMID: 32203462 PMCID: PMC7398704 DOI: 10.1038/s41588-020-0590-9] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 02/11/2020] [Indexed: 02/05/2023]
Abstract
Local adaptation directs populations towards environment-specific fitness maxima through acquisition of positively selected traits. However, rapid environmental changes can identify hidden fitness trade-offs that turn adaptation into maladaptation, resulting in evolutionary traps. Cancer, a disease that is prone to drug resistance, is in principle susceptible to such traps. We therefore performed pooled CRISPR-Cas9 knockout screens in acute myeloid leukemia (AML) cells treated with various chemotherapies to map the drug-dependent genetic basis of fitness trade-offs, a concept known as antagonistic pleiotropy (AP). We identified a PRC2-NSD2/3-mediated MYC regulatory axis as a drug-induced AP pathway whose ability to confer resistance to bromodomain inhibition and sensitivity to BCL-2 inhibition templates an evolutionary trap. Across diverse AML cell-line and patient-derived xenograft models, we find that acquisition of resistance to bromodomain inhibition through this pathway exposes coincident hypersensitivity to BCL-2 inhibition. Thus, drug-induced AP can be leveraged to design evolutionary traps that selectively target drug resistance in cancer.
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41
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Aldonza MBD, Ku J, Hong JY, Kim D, Yu SJ, Lee MS, Prayogo MC, Tan S, Kim D, Han J, Lee SK, Im SG, Ryu HS, Kim Y. Prior acquired resistance to paclitaxel relays diverse EGFR-targeted therapy persistence mechanisms. SCIENCE ADVANCES 2020; 6:eaav7416. [PMID: 32083171 PMCID: PMC7007258 DOI: 10.1126/sciadv.aav7416] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 11/22/2019] [Indexed: 06/10/2023]
Abstract
Secondary drug resistance stems from dynamic clonal evolution during the development of a prior primary resistance. This collateral type of resistance is often a characteristic of cancer recurrence. Yet, mechanisms that drive this collateral resistance and their drug-specific trajectories are still poorly understood. Using resistance selection and small-scale pharmacological screens, we find that cancer cells with primary acquired resistance to the microtubule-stabilizing drug paclitaxel often develop tolerance to epidermal growth factor receptor-tyrosine kinase inhibitors (EGFR-TKIs), leading to formation of more stable resistant cell populations. We show that paclitaxel-resistant cancer cells follow distinct selection paths under EGFR-TKIs by enriching the stemness program, developing a highly glycolytic adaptive stress response, and rewiring an apoptosis control pathway. Collectively, our work demonstrates the alterations in cellular state stemming from paclitaxel failure that result in collateral resistance to EGFR-TKIs and points to new exploitable vulnerabilities during resistance evolution in the second-line treatment setting.
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Affiliation(s)
- Mark Borris D. Aldonza
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
- Department of Biological Sciences, KAIST, Daejeon 34141, Korea
- KI for Health Science and Technology (KIHST), KAIST, Daejeon 34141, Korea
| | - Jayoung Ku
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
- KI for Health Science and Technology (KIHST), KAIST, Daejeon 34141, Korea
| | - Ji-Young Hong
- College of Pharmacy, Seoul National University, Seoul 08826, Korea
| | - Donghwa Kim
- College of Pharmacy, Seoul National University, Seoul 08826, Korea
| | - Seung Jung Yu
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
| | - Min-Seok Lee
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
| | - Monica Celine Prayogo
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
| | - Stephanie Tan
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
| | - Dayeon Kim
- Biomedical Science and Engineering Interdisciplinary Program, KAIST, Daejeon 34141, Korea
| | - Jinju Han
- Biomedical Science and Engineering Interdisciplinary Program, KAIST, Daejeon 34141, Korea
- Graduate School of Medical Science and Engineering (GSMSE), KAIST, Daejeon 34141, Korea
| | - Sang Kook Lee
- College of Pharmacy, Seoul National University, Seoul 08826, Korea
| | - Sung Gap Im
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
| | - Han Suk Ryu
- Department of Pathology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul 03080, Korea
| | - Yoosik Kim
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
- KI for Health Science and Technology (KIHST), KAIST, Daejeon 34141, Korea
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42
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Goodman JR, Ashrafian H. The Promising Connection Between Data Science and Evolutionary Theory in Oncology. Front Oncol 2020; 9:1527. [PMID: 32039014 PMCID: PMC6984404 DOI: 10.3389/fonc.2019.01527] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 12/18/2019] [Indexed: 12/19/2022] Open
Abstract
Theoretical and empirical work over the past several decades suggests that oncogenesis and disease progression represents an evolutionary story. Despite this knowledge, current anti-resistance strategies to drugs are often managed through treating cancers as independent biological agents divorced from human activity. Yet once drug resistance to cancer treatment is understood as a product of artificial or anthropogenic rather than unconscious selection, oncologists could improve outcomes for their patients by consulting evolutionary studies of oncology prior to clinical trial and treatment plan design. In the setting of multiple cancer types, for example, a machine learning algorithm can predict the genetic changes known to be related to drug resistance. In this way, a unity between technology and theory might have practical clinical implications—and may pave the way for a new paradigm shift in medicine.
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Affiliation(s)
- Jonathan R Goodman
- Leverhulme Centre for Human Evolutionary Studies, University of Cambridge, Cambridge, United Kingdom
| | - Hutan Ashrafian
- Institute of Global Health Innovation, Imperial College London, London, United Kingdom
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43
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Palmer AC, Chidley C, Sorger PK. A curative combination cancer therapy achieves high fractional cell killing through low cross-resistance and drug additivity. eLife 2019; 8:50036. [PMID: 31742555 PMCID: PMC6897534 DOI: 10.7554/elife.50036] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 11/18/2019] [Indexed: 12/12/2022] Open
Abstract
Curative cancer therapies are uncommon and nearly always involve multi-drug combinations developed by experimentation in humans; unfortunately, the mechanistic basis for the success of such combinations has rarely been investigated in detail, obscuring lessons learned. Here, we use isobologram analysis to score pharmacological interaction, and clone tracing and CRISPR screening to measure cross-resistance among the five drugs comprising R-CHOP, a combination therapy that frequently cures Diffuse Large B-Cell Lymphomas. We find that drugs in R-CHOP exhibit very low cross-resistance but not synergistic interaction: together they achieve a greater fractional kill according to the null hypothesis for both the Loewe dose-additivity model and the Bliss effect-independence model. These data provide direct evidence for the 50 year old hypothesis that a curative cancer therapy can be constructed on the basis of independently effective drugs having non-overlapping mechanisms of resistance, without synergistic interaction, which has immediate significance for the design of new drug combinations.
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Affiliation(s)
- Adam C Palmer
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, United States
| | - Christopher Chidley
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, United States
| | - Peter K Sorger
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, United States.,Department of Systems Biology, Harvard Medical School, Boston, United States
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44
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Barbosa C, Römhild R, Rosenstiel P, Schulenburg H. Evolutionary stability of collateral sensitivity to antibiotics in the model pathogen Pseudomonas aeruginosa. eLife 2019; 8:e51481. [PMID: 31658946 PMCID: PMC6881144 DOI: 10.7554/elife.51481] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 10/21/2019] [Indexed: 12/27/2022] Open
Abstract
Evolution is at the core of the impending antibiotic crisis. Sustainable therapy must thus account for the adaptive potential of pathogens. One option is to exploit evolutionary trade-offs, like collateral sensitivity, where evolved resistance to one antibiotic causes hypersensitivity to another one. To date, the evolutionary stability and thus clinical utility of this trade-off is unclear. We performed a critical experimental test on this key requirement, using evolution experiments with Pseudomonas aeruginosa, and identified three main outcomes: (i) bacteria commonly failed to counter hypersensitivity and went extinct; (ii) hypersensitivity sometimes converted into multidrug resistance; and (iii) resistance gains frequently caused re-sensitization to the previous drug, thereby maintaining the trade-off. Drug order affected the evolutionary outcome, most likely due to variation in the effect size of collateral sensitivity, epistasis among adaptive mutations, and fitness costs. Our finding of robust genetic trade-offs and drug-order effects can guide design of evolution-informed antibiotic therapy.
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Affiliation(s)
- Camilo Barbosa
- Department of Evolutionary Ecology and GeneticsUniversity of KielKielGermany
| | - Roderich Römhild
- Department of Evolutionary Ecology and GeneticsUniversity of KielKielGermany
- Max Planck Institute for Evolutionary BiologyPlönGermany
| | | | - Hinrich Schulenburg
- Department of Evolutionary Ecology and GeneticsUniversity of KielKielGermany
- Max Planck Institute for Evolutionary BiologyPlönGermany
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45
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Maltas J, Wood KB. Pervasive and diverse collateral sensitivity profiles inform optimal strategies to limit antibiotic resistance. PLoS Biol 2019; 17:e3000515. [PMID: 31652256 PMCID: PMC6834293 DOI: 10.1371/journal.pbio.3000515] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 11/06/2019] [Accepted: 10/07/2019] [Indexed: 11/19/2022] Open
Abstract
Evolved resistance to one antibiotic may be associated with "collateral" sensitivity to other drugs. Here, we provide an extensive quantitative characterization of collateral effects in Enterococcus faecalis, a gram-positive opportunistic pathogen. By combining parallel experimental evolution with high-throughput dose-response measurements, we measure phenotypic profiles of collateral sensitivity and resistance for a total of 900 mutant-drug combinations. We find that collateral effects are pervasive but difficult to predict because independent populations selected by the same drug can exhibit qualitatively different profiles of collateral sensitivity as well as markedly different fitness costs. Using whole-genome sequencing of evolved populations, we identified mutations in a number of known resistance determinants, including mutations in several genes previously linked with collateral sensitivity in other species. Although phenotypic drug sensitivity profiles show significant diversity, they cluster into statistically similar groups characterized by selecting drugs with similar mechanisms. To exploit the statistical structure in these resistance profiles, we develop a simple mathematical model based on a stochastic control process and use it to design optimal drug policies that assign a unique drug to every possible resistance profile. Stochastic simulations reveal that these optimal drug policies outperform intuitive cycling protocols by maintaining long-term sensitivity at the expense of short-term periods of high resistance. The approach reveals a new conceptual strategy for mitigating resistance by balancing short-term inhibition of pathogen growth with infrequent use of drugs intended to steer pathogen populations to a more vulnerable future state. Experiments in laboratory populations confirm that model-inspired sequences of four drugs reduce growth and slow adaptation relative to naive protocols involving the drugs alone, in pairwise cycles, or in a four-drug uniform cycle.
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Affiliation(s)
- Jeff Maltas
- Department of Biophysics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Kevin B. Wood
- Department of Biophysics, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Physics, University of Michigan, Ann Arbor, Michigan, United States of America
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46
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Goldman A, Khiste S, Freinkman E, Dhawan A, Majumder B, Mondal J, Pinkerton AB, Eton E, Medhi R, Chandrasekar V, Rahman MM, Ichimura T, Gopinath KS, Majumder P, Kohandel M, Sengupta S. Targeting tumor phenotypic plasticity and metabolic remodeling in adaptive cross-drug tolerance. Sci Signal 2019; 12:12/595/eaas8779. [PMID: 31431543 DOI: 10.1126/scisignal.aas8779] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Metastable phenotypic state transitions in cancer cells can lead to the development of transient adaptive resistance or tolerance to chemotherapy. Here, we report that the acquisition of a phenotype marked by increased abundance of CD44 (CD44Hi) by breast cancer cells as a tolerance response to routinely used cytotoxic drugs, such as taxanes, activated a metabolic switch that conferred tolerance against unrelated standard-of-care chemotherapeutic agents, such as anthracyclines. We characterized the sequence of molecular events that connected the induced CD44Hi phenotype to increased activity of both the glycolytic and oxidative pathways and glucose flux through the pentose phosphate pathway (PPP). When given in a specific order, a combination of taxanes, anthracyclines, and inhibitors of glucose-6-phosphate dehydrogenase (G6PD), an enzyme involved in glucose metabolism, improved survival in mouse models of breast cancer. The same sequence of the three-drug combination reduced the viability of patient breast tumor samples in an explant system. Our findings highlight a convergence between phenotypic and metabolic state transitions that confers a survival advantage to cancer cells against clinically used drug combinations. Pharmacologically targeting this convergence could overcome cross-drug tolerance and could emerge as a new paradigm in the treatment of cancer.
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Affiliation(s)
- Aaron Goldman
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA. .,Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA.,Mitra Biotech, Integrative Immuno-Oncology Center, Woburn, MA 01801, USA
| | - Sachin Khiste
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA.,Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Elizaveta Freinkman
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA
| | - Andrew Dhawan
- School of Medicine, Queen's University, Kingston, ON K7L 3N6, Canada
| | - Biswanath Majumder
- Mitra Biotech, Integrative Immuno-Oncology Center, Woburn, MA 01801, USA.,Mitra Biotech, 7, Service Road, Pragathi Nagar, Electronic City, Bengaluru, Karnataka 560100, India
| | - Jayanta Mondal
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA.,Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | | | - Elliot Eton
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Ragini Medhi
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Vineethkrishna Chandrasekar
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - M Mamunur Rahman
- Medical and Biological Laboratories International, Woburn, MA 01801, USA
| | - Takaharu Ichimura
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Kodaganur S Gopinath
- Department of Surgical Oncology, HCG Bangalore Institute of Oncology Specialty Center, Bengaluru, Karnataka 560027, India
| | - Pradip Majumder
- Mitra Biotech, Integrative Immuno-Oncology Center, Woburn, MA 01801, USA
| | - Mohammad Kohandel
- Department of Applied Mathematics, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Shiladitya Sengupta
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA. .,Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA.,Harvard-MIT Division of Health Sciences and Technology, Cambridge, MA 02139, USA.,Dana Farber Cancer Institute, Boston, MA 02115, USA
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47
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Apjok G, Boross G, Nyerges Á, Fekete G, Lázár V, Papp B, Pál C, Csörgő B. Limited Evolutionary Conservation of the Phenotypic Effects of Antibiotic Resistance Mutations. Mol Biol Evol 2019; 36:1601-1611. [PMID: 31058961 PMCID: PMC6657729 DOI: 10.1093/molbev/msz109] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Multidrug-resistant clinical isolates are common in certain pathogens, but rare in others. This pattern may be due to the fact that mutations shaping resistance have species-specific effects. To investigate this issue, we transferred a range of resistance-conferring mutations and a full resistance gene into Escherichia coli and closely related bacteria. We found that resistance mutations in one bacterial species frequently provide no resistance, in fact even yielding drug hypersensitivity in close relatives. In depth analysis of a key gene involved in aminoglycoside resistance (trkH) indicated that preexisting mutations in other genes-intergenic epistasis-underlie such extreme differences in mutational effects between species. Finally, reconstruction of adaptive landscapes under multiple antibiotic stresses revealed that mutations frequently provide multidrug resistance or elevated drug susceptibility (i.e., collateral sensitivity) only with certain combinations of other resistance mutations. We conclude that resistance and collateral sensitivity are contingent upon the genetic makeup of the bacterial population, and such contingency could shape the long-term fate of resistant bacteria. These results underlie the importance of species-specific treatment strategies.
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Affiliation(s)
- Gábor Apjok
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary
| | - Gábor Boross
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary
- Department of Biology, Stanford University, Stanford, CA
| | - Ákos Nyerges
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary
| | - Gergely Fekete
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary
| | - Viktória Lázár
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary
- Technion – Israel Institute of Technology, Faculty of Biology, Haifa, Israel
| | - Balázs Papp
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary
| | - Csaba Pál
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary
| | - Bálint Csörgő
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA
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48
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Abstract
Rebecca S. Shapiro studies antimicrobial resistance and genetic interaction networks. In this mSphere of Influence article, she reflects on how the papers "Bacterial evolution of antibiotic hypersensitivity" by Lázár et al. (V. Lázár, G. Pal Singh, R. Spohn, I. Nagy, et al., Mol Syst Biol 9:700, 2013, https://doi.org/10.1038/msb.2013.57) and "Use of collateral sensitivity networks to design drug cycling protocols that avoid resistance development" by L. Imamovic and M. O. A. Sommer (Sci Transl Med 5:204ra132, 2013, https://doi.org/10.1126/scitranslmed.3006609) impacted her thinking about multigene interaction effects on drug resistance.
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49
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Vlachostergios PJ, Faltas BM. Treatment resistance in urothelial carcinoma: an evolutionary perspective. Nat Rev Clin Oncol 2019; 15:495-509. [PMID: 29720713 DOI: 10.1038/s41571-018-0026-y] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The emergence of treatment-resistant clones is a critical barrier to cure in patients with urothelial carcinoma. Setting the stage for the evolution of resistance, urothelial carcinoma is characterized by extensive mutational heterogeneity, which is detectable even in patients with early stage disease. Chemotherapy and immunotherapy both act as selective pressures that shape the evolutionary trajectory of urothelial carcinoma throughout the course of the disease. A detailed understanding of the dynamics of evolutionary drivers is required for the rational development of curative therapies. Herein, we describe the molecular basis of the clonal evolution of urothelial carcinomas and the use of genomic approaches to predict treatment responses. We discuss various mechanisms of resistance to chemotherapy with a focus on the mutagenic effects of the DNA dC->dU-editing enzymes APOBEC3 family of proteins. We also review the evolutionary mechanisms underlying resistance to immunotherapy, such as the loss of clonal tumour neoantigens. By dissecting treatment resistance through an evolutionary lens, the field will advance towards true precision medicine for urothelial carcinoma.
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Affiliation(s)
- Panagiotis J Vlachostergios
- Department of Medicine, Division of Hematology and Medical Oncology, Weill Cornell Medicine, New York, NY, USA
| | - Bishoy M Faltas
- Department of Medicine, Division of Hematology and Medical Oncology, Weill Cornell Medicine, New York, NY, USA. .,Sandra and Edward Meyer Cancer Center at Weill Cornell Medicine, New York, NY, USA.
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50
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Chapman MP, Risom T, Aswani AJ, Langer EM, Sears RC, Tomlin CJ. Modeling differentiation-state transitions linked to therapeutic escape in triple-negative breast cancer. PLoS Comput Biol 2019; 15:e1006840. [PMID: 30856168 PMCID: PMC6428348 DOI: 10.1371/journal.pcbi.1006840] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 03/21/2019] [Accepted: 02/05/2019] [Indexed: 11/18/2022] Open
Abstract
Drug resistance in breast cancer cell populations has been shown to arise through phenotypic transition of cancer cells to a drug-tolerant state, for example through epithelial-to-mesenchymal transition or transition to a cancer stem cell state. However, many breast tumors are a heterogeneous mixture of cell types with numerous epigenetic states in addition to stem-like and mesenchymal phenotypes, and the dynamic behavior of this heterogeneous mixture in response to drug treatment is not well-understood. Recently, we showed that plasticity between differentiation states, as identified with intracellular markers such as cytokeratins, is linked to resistance to specific targeted therapeutics. Understanding the dynamics of differentiation-state transitions in this context could facilitate the development of more effective treatments for cancers that exhibit phenotypic heterogeneity and plasticity. In this work, we develop computational models of a drug-treated, phenotypically heterogeneous triple-negative breast cancer (TNBC) cell line to elucidate the feasibility of differentiation-state transition as a mechanism for therapeutic escape in this tumor subtype. Specifically, we use modeling to predict the changes in differentiation-state transitions that underlie specific therapy-induced changes in differentiation-state marker expression that we recently observed in the HCC1143 cell line. We report several statistically significant therapy-induced changes in transition rates between basal, luminal, mesenchymal, and non-basal/non-luminal/non-mesenchymal differentiation states in HCC1143 cell populations. Moreover, we validate model predictions on cell division and cell death empirically, and we test our models on an independent data set. Overall, we demonstrate that changes in differentiation-state transition rates induced by targeted therapy can provoke distinct differentiation-state aggregations of drug-resistant cells, which may be fundamental to the design of improved therapeutic regimens for cancers with phenotypic heterogeneity.
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Affiliation(s)
- Margaret P. Chapman
- Department of Electrical Engineering and Computer Sciences, University of California Berkeley, Berkeley, California, United States of America
- * E-mail:
| | - Tyler Risom
- Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, Oregon, United States of America
| | - Anil J. Aswani
- Department of Industrial Engineering and Operations Research, University of California Berkeley, Berkeley, California, United States of America
| | - Ellen M. Langer
- Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, Oregon, United States of America
| | - Rosalie C. Sears
- Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, Oregon, United States of America
- Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon, United States of America
- Center for Spatial Systems Biomedicine, Oregon Health and Science University, Portland, Oregon, United States of America
| | - Claire J. Tomlin
- Department of Electrical Engineering and Computer Sciences, University of California Berkeley, Berkeley, California, United States of America
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