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Cotton JL, Estrada Diez J, Sagar V, Chen J, Piquet M, Alford J, Song Y, Li X, Riester M, DiMare MT, Schumacher K, Boulay G, Sprouffske K, Fan L, Burks T, Mansur L, Wagner J, Bhang HEC, Iartchouk O, Reece-Hoyes J, Morris EJ, Hammerman PS, Ruddy DA, Korn JM, Engelman JA, Niederst MJ. Expressed Barcoding Enables High-Resolution Tracking of the Evolution of Drug Tolerance. Cancer Res 2023; 83:3611-3623. [PMID: 37603596 DOI: 10.1158/0008-5472.can-23-0144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 05/11/2023] [Accepted: 08/15/2023] [Indexed: 08/23/2023]
Abstract
For a majority of patients with non-small cell lung cancer with EGFR mutations, treatment with EGFR inhibitors (EGFRi) induces a clinical response. Despite this initial reduction in tumor size, residual disease persists that leads to disease relapse. Elucidating the preexisting biological differences between sensitive cells and surviving drug-tolerant persister cells and deciphering how drug-tolerant cells evolve in response to treatment could help identify strategies to improve the efficacy of EGFRi. In this study, we tracked the origins and clonal evolution of drug-tolerant cells at a high resolution by using an expressed barcoding system coupled with single-cell RNA sequencing. This platform enabled longitudinal profiling of gene expression and drug sensitivity in response to EGFRi across a large number of clones. Drug-tolerant cells had higher expression of key survival pathways such as YAP and EMT at baseline and could also differentially adapt their gene expression following EGFRi treatment compared with sensitive cells. In addition, drug combinations targeting common downstream components (MAPK) or orthogonal factors (chemotherapy) showed greater efficacy than EGFRi alone, which is attributable to broader targeting of the heterogeneous EGFRi-tolerance mechanisms present in tumors. Overall, this approach facilitates thorough examination of clonal evolution in response to therapy that could inform the development of improved diagnostic approaches and treatment strategies for targeting drug-tolerant cells. SIGNIFICANCE The evolution and heterogeneity of EGFR inhibitor tolerance are identified in a large number of clones at enhanced cellular and temporal resolution using an expressed barcode technology coupled with single-cell RNA sequencing.
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Affiliation(s)
- Jennifer L Cotton
- Oncology Disease Area, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Javier Estrada Diez
- Oncology Disease Area, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Vivek Sagar
- Oncology Disease Area, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Julie Chen
- Oncology Disease Area, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Michelle Piquet
- Oncology Disease Area, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - John Alford
- Chemical Biology & Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Youngchul Song
- Oncology Disease Area, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Xiaoyan Li
- Oncology Disease Area, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Markus Riester
- Oncology Disease Area, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Matthew T DiMare
- Oncology Disease Area, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Katja Schumacher
- Oncology Disease Area, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Gaylor Boulay
- Oncology Disease Area, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Kathleen Sprouffske
- Oncology Disease Area, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Lin Fan
- Chemical Biology & Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Tyler Burks
- Chemical Biology & Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Leandra Mansur
- Chemical Biology & Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Joel Wagner
- Oncology Disease Area, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Hyo-Eun C Bhang
- Oncology Disease Area, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Oleg Iartchouk
- Chemical Biology & Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - John Reece-Hoyes
- Chemical Biology & Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Erick J Morris
- Oncology Disease Area, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Peter S Hammerman
- Oncology Disease Area, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - David A Ruddy
- Oncology Disease Area, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Joshua M Korn
- Oncology Disease Area, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Jeffrey A Engelman
- Oncology Disease Area, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Matthew J Niederst
- Oncology Disease Area, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
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Bhang HEC, DiMare MT, Kodack DP, Tan L, Kerr G, Radhakrishna VK, Golji J, Ruddy DA, Yuan T, Niederst MJ, Korn JM, Porta DG, Hammerman PS, Engelman JA, Abrams T, Williams J. Abstract 394: In vivo shRNA screens under treatment pressure by BRAF and MEK inhibitors to identify novel combination treatment strategies for BRAF-mutant colorectal cancer. Cancer Res 2019. [DOI: 10.1158/1538-7445.am2019-394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Approximately 10% of patients with colorectal cancer (CRC) harbor the BRAF V600E driver mutation. Unlike melanoma, the response rate of BRAF-mutant CRC to the combination of BRAF and MEK inhibitors is limited. In order to target the MAPK signaling pathway more effectively by blocking EGFR-mediated re-activation of the pathway, triple combination trials of BRAF, MEK and EGFR inhibitors are on-going, but the response is underwhelming.
To find alternative combination strategies that could deepen therapeutic responses driven by a BRAFi and MEKi combination, we performed pooled shRNA screens under the treatment pressure of the dual combination of the BRAF inhibitor dabrafenib and MEK inhibitor trametinib. In some of the BRAF-mutant CRC models, we observed marked discrepancies in the therapeutic responses between in vitro and in vivo conditions. Therefore, shRNA screens were conducted in cancer cell lines grown both in vitro (i.e. 2D and 3D culture conditions) and in vivo in xenograft tumor models. The aim of the study was to identify novel targets to combine with BRAFi/MEKi, and to compare the results of the screens preformed in vitro and in vivo.
The biggest technical challenge for an in vivo pooled screening approach is achieving adequate library representation after the bottleneck of cell implantation and engraftment in mice. Our in vivo screen had an additional bottleneck due to the dabrafenib/trametinib combination treatment. Therefore, by performing a pilot screen with the BRAF-mutant cell line model HT29 we aimed to address two questions: 1) whether the in vivo screen under treatment pressure would be technically feasible and 2) if novel combination partners to dabrafenib/trametinib would be identified to potentially improve efficacy beyond that observed with the triple combination with EGFR inhibitors.
We were able to achieve comparable intra-group variability and repeatability between in vitro and in vivo conditions, whereby gene level analysis revealed several differential hits between the two conditions, which were both sensitizers and activators to the dabrafenib/trametinib combination treatment. We identified targets specific for the in vivo condition that had not been identified in vitro and vice versa. Thus, in vivo screening may identify powerful hits that would not be realized by in vitro investigations. With success of this pilot effort, the screen is currently being expanded into additional BRAF-mutant CRC models.
Citation Format: Hyo-eun C. Bhang, Matthew T. DiMare, David P. Kodack, Lujian Tan, Grainne Kerr, Viveksagar Krishnamurthy Radhakrishna, Javad Golji, David A. Ruddy, Tina Yuan, Matthew J. Niederst, Joshua M. Korn, Diana Graus Porta, Peter S. Hammerman, Jeffrey A. Engelman, Tinya Abrams, Juliet Williams. In vivo shRNA screens under treatment pressure by BRAF and MEK inhibitors to identify novel combination treatment strategies for BRAF-mutant colorectal cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 394.
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Affiliation(s)
| | | | | | - Lujian Tan
- 1Novartis Insts. for BioMedical Research, Cambridge, MA
| | - Grainne Kerr
- 2Novartis Insts. for BioMedical Research, Basel, Switzerland
| | | | - Javad Golji
- 1Novartis Insts. for BioMedical Research, Cambridge, MA
| | | | - Tina Yuan
- 1Novartis Insts. for BioMedical Research, Cambridge, MA
| | | | | | | | | | | | - Tinya Abrams
- 1Novartis Insts. for BioMedical Research, Cambridge, MA
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Baltschukat S, Engstler BS, Huang A, Hao HX, Tam A, Wang HQ, Liang J, DiMare MT, Bhang HEC, Wang Y, Furet P, Sellers WR, Hofmann F, Schoepfer J, Tiedt R. Capmatinib (INC280) Is Active Against Models of Non–Small Cell Lung Cancer and Other Cancer Types with Defined Mechanisms of MET Activation. Clin Cancer Res 2019; 25:3164-3175. [DOI: 10.1158/1078-0432.ccr-18-2814] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 12/12/2018] [Accepted: 01/18/2019] [Indexed: 11/16/2022]
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Rago F, DiMare MT, Elliott G, Ruddy DA, Sovath S, Kerr G, Bhang HEC, Jagani Z. Degron mediated BRM/SMARCA2 depletion uncovers novel combination partners for treatment of BRG1/SMARCA4-mutant cancers. Biochem Biophys Res Commun 2018; 508:109-116. [PMID: 30527810 DOI: 10.1016/j.bbrc.2018.09.009] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 08/23/2018] [Accepted: 09/02/2018] [Indexed: 12/11/2022]
Abstract
Recent studies have highlighted that cancer cells with a loss of the SWI/SNF complex catalytic subunit BRG1 are dependent on the remaining ATPase, BRM, making it an attractive target for cancer therapy. However, an understanding of the extent of target inhibition required to arrest cell growth, necessary to develop an appropriate therapeutic strategy, remains unknown. Here, we utilize tunable depletion of endogenous BRM using the SMASh degron, and interestingly observe that BRG1-mutant lung cancer cells require near complete depletion of BRM to robustly inhibit growth both in vitro and in vivo. Therefore, to identify pathways that synergize with partial BRM depletion and afford a deeper response, we performed a genome-wide CRISPR screen and discovered a combinatorial effect between BRM depletion and the knockout of various genes of the oxidative phosphorylation pathway and the anti-apoptotic gene MCL1. Together these studies provide an important framework to elucidate the requirements of BRM inhibition in the BRG1-mutant state with implications on the feasibility of targeting BRM alone, as well as reveal novel insights into pathways that can be exploited in combination toward deeper anti-tumor responses.
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Affiliation(s)
- Florencia Rago
- Oncology, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Matthew T DiMare
- Oncology, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - GiNell Elliott
- Oncology, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - David A Ruddy
- Oncology, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Sosathya Sovath
- Oncology, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Grainne Kerr
- Oncology, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Hyo-Eun C Bhang
- Oncology, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Zainab Jagani
- Oncology, Novartis Institutes for Biomedical Research, Cambridge, MA, USA.
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Coppage AL, Heard KR, DiMare MT, Liu Y, Wu W, Lai JH, Bachovchin WW. Human FGF-21 Is a Substrate of Fibroblast Activation Protein. PLoS One 2016; 11:e0151269. [PMID: 26962859 PMCID: PMC4786124 DOI: 10.1371/journal.pone.0151269] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 02/25/2016] [Indexed: 01/10/2023] Open
Abstract
FGF-21 is a key regulator of metabolism and potential drug candidate for the treatment of type II diabetes and other metabolic disorders. However, the half-life of active, circulating, human FGF-21 has recently been shown to be limited in mice and monkeys by a proteolytic cleavage between P171 and S172. Here, we show that fibroblast activation protein is the enzyme responsible for this proteolysis by demonstrating that purified FAP cleaves human FGF-21 at this site in vitro, and that an FAP-specific inhibitor, ARI-3099, blocks the activity in mouse, monkey and human plasma and prolongs the half-life of circulating human FGF-21 in mice. Mouse FGF-21, however, lacks the FAP cleavage site and is not cleaved by FAP. These findings indicate FAP may function in the regulation of metabolism and that FAP inhibitors may prove useful in the treatment of diabetes and metabolic disorders in humans, but pre-clinical proof of concept studies in rodents will be problematic.
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Affiliation(s)
- Andrew L. Coppage
- Department of Developmental, Molecular and Chemical Biology, Tufts University Sackler School of Graduate Biomedical Sciences, Boston, Massachusetts, United States of America
| | - Kathryn R. Heard
- Department of Developmental, Molecular and Chemical Biology, Tufts University Sackler School of Graduate Biomedical Sciences, Boston, Massachusetts, United States of America
- Arisaph Pharmaceuticals Inc., Boston, Massachusetts, United States of America
| | - Matthew T. DiMare
- Department of Developmental, Molecular and Chemical Biology, Tufts University Sackler School of Graduate Biomedical Sciences, Boston, Massachusetts, United States of America
- Arisaph Pharmaceuticals Inc., Boston, Massachusetts, United States of America
| | - Yuxin Liu
- Department of Developmental, Molecular and Chemical Biology, Tufts University Sackler School of Graduate Biomedical Sciences, Boston, Massachusetts, United States of America
- Arisaph Pharmaceuticals Inc., Boston, Massachusetts, United States of America
| | - Wengen Wu
- Department of Developmental, Molecular and Chemical Biology, Tufts University Sackler School of Graduate Biomedical Sciences, Boston, Massachusetts, United States of America
- Arisaph Pharmaceuticals Inc., Boston, Massachusetts, United States of America
| | - Jack H. Lai
- Department of Developmental, Molecular and Chemical Biology, Tufts University Sackler School of Graduate Biomedical Sciences, Boston, Massachusetts, United States of America
- Arisaph Pharmaceuticals Inc., Boston, Massachusetts, United States of America
| | - William W. Bachovchin
- Department of Developmental, Molecular and Chemical Biology, Tufts University Sackler School of Graduate Biomedical Sciences, Boston, Massachusetts, United States of America
- Arisaph Pharmaceuticals Inc., Boston, Massachusetts, United States of America
- * E-mail:
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