1
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Frangieh CJ, Melms JC, Thakore PI, Geiger-Schuller KR, Ho P, Luoma AM, Cleary B, Jerby-Arnon L, Malu S, Cuoco MS, Zhao M, Ager CR, Rogava M, Hovey L, Rotem A, Bernatchez C, Wucherpfennig KW, Johnson BE, Rozenblatt-Rosen O, Schadendorf D, Regev A, Izar B. Multimodal pooled Perturb-CITE-seq screens in patient models define mechanisms of cancer immune evasion. Nat Genet 2021; 53:332-341. [PMID: 33649592 PMCID: PMC8376399 DOI: 10.1038/s41588-021-00779-1] [Citation(s) in RCA: 90] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 01/04/2021] [Indexed: 01/05/2023]
Abstract
Resistance to immune checkpoint inhibitors (ICIs) is a key challenge in cancer therapy. To elucidate underlying mechanisms, we developed Perturb-CITE-sequencing (Perturb-CITE-seq), enabling pooled clustered regularly interspaced short palindromic repeat (CRISPR)-Cas9 perturbations with single-cell transcriptome and protein readouts. In patient-derived melanoma cells and autologous tumor-infiltrating lymphocyte (TIL) co-cultures, we profiled transcriptomes and 20 proteins in ~218,000 cells under ~750 perturbations associated with cancer cell-intrinsic ICI resistance (ICR). We recover known mechanisms of resistance, including defects in the interferon-γ (IFN-γ)-JAK/STAT and antigen-presentation pathways in RNA, protein and perturbation space, and new ones, including loss/downregulation of CD58. Loss of CD58 conferred immune evasion in multiple co-culture models and was downregulated in tumors of melanoma patients with ICR. CD58 protein expression was not induced by IFN-γ signaling, and CD58 loss conferred immune evasion without compromising major histocompatibility complex (MHC) expression, suggesting that it acts orthogonally to known mechanisms of ICR. This work provides a framework for the deciphering of complex mechanisms by large-scale perturbation screens with multimodal, single-cell readouts, and discovers potentially clinically relevant mechanisms of immune evasion.
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Affiliation(s)
- Chris J Frangieh
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Johannes C Melms
- Columbia Center for Translational Immunology, New York, NY, USA
- Department of Medicine, Division of Hematology and Oncology, Columbia University Medical Center, New York, NY, USA
| | - Pratiksha I Thakore
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kathryn R Geiger-Schuller
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Genentech, South San Francisco, CA, USA
| | - Patricia Ho
- Columbia Center for Translational Immunology, New York, NY, USA
- Department of Medicine, Division of Hematology and Oncology, Columbia University Medical Center, New York, NY, USA
| | - Adrienne M Luoma
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Brian Cleary
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Livnat Jerby-Arnon
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Shruti Malu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Immunitas Therapeutics, Waltham, MA, USA
| | - Michael S Cuoco
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Maryann Zhao
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Casey R Ager
- Columbia Center for Translational Immunology, New York, NY, USA
| | - Meri Rogava
- Columbia Center for Translational Immunology, New York, NY, USA
- Department of Medicine, Division of Hematology and Oncology, Columbia University Medical Center, New York, NY, USA
| | - Lila Hovey
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Asaf Rotem
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Cancer Genomics, Dana-Farber Cancer Institute, Boston, MA, USA
- AstraZeneca, Waltham, MA, USA
| | - Chantale Bernatchez
- Department of Melanoma Medical Oncology, MD Anderson Cancer Center, Houston, TX, USA
| | - Kai W Wucherpfennig
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Bruce E Johnson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Cancer Genomics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Orit Rozenblatt-Rosen
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Genentech, South San Francisco, CA, USA
| | - Dirk Schadendorf
- Department of Dermatology, University Hospital Essen and German Cancer Consortium, Partner Site, Essen, Germany
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
- Genentech, South San Francisco, CA, USA.
| | - Benjamin Izar
- Columbia Center for Translational Immunology, New York, NY, USA.
- Department of Medicine, Division of Hematology and Oncology, Columbia University Medical Center, New York, NY, USA.
- Program for Mathematical Genomics, Columbia University, New York, NY, USA.
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2
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Punt S, Malu S, McKenzie JA, Manrique SZ, Doorduijn EM, Mbofung RM, Williams L, Silverman DA, Ashkin EL, Dominguez AL, Wang Z, Chen JQ, Maiti SN, Tieu TN, Liu C, Xu C, Forget MA, Haymaker C, Khalili JS, Satani N, Muller F, Cooper LJN, Overwijk WW, Amaria RN, Bernatchez C, Heffernan TP, Peng W, Roszik J, Hwu P. Aurora kinase inhibition sensitizes melanoma cells to T-cell-mediated cytotoxicity. Cancer Immunol Immunother 2020; 70:1101-1113. [PMID: 33123754 PMCID: PMC7979613 DOI: 10.1007/s00262-020-02748-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 10/13/2020] [Indexed: 12/13/2022]
Abstract
Although immunotherapy has achieved impressive durable clinical responses, many cancers respond only temporarily or not at all to immunotherapy. To find novel, targetable mechanisms of resistance to immunotherapy, patient-derived melanoma cell lines were transduced with 576 open reading frames, or exposed to arrayed libraries of 850 bioactive compounds, prior to co-culture with autologous tumor-infiltrating lymphocytes (TILs). The synergy between the targets and TILs to induce apoptosis, and the mechanisms of inhibiting resistance to TILs were interrogated. Gene expression analyses were performed on tumor samples from patients undergoing immunotherapy for metastatic melanoma. Finally, the effect of inhibiting the top targets on the efficacy of immunotherapy was investigated in multiple preclinical models. Aurora kinase was identified as a mediator of melanoma cell resistance to T-cell-mediated cytotoxicity in both complementary screens. Aurora kinase inhibitors were validated to synergize with T-cell-mediated cytotoxicity in vitro. The Aurora kinase inhibition-mediated sensitivity to T-cell cytotoxicity was shown to be partially driven by p21-mediated induction of cellular senescence. The expression levels of Aurora kinase and related proteins were inversely correlated with immune infiltration, response to immunotherapy and survival in melanoma patients. Aurora kinase inhibition showed variable responses in combination with immunotherapy in vivo, suggesting its activity is modified by other factors in the tumor microenvironment. These data suggest that Aurora kinase inhibition enhances T-cell cytotoxicity in vitro and can potentiate antitumor immunity in vivo in some but not all settings. Further studies are required to determine the mechanism of primary resistance to this therapeutic intervention.
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Affiliation(s)
- Simone Punt
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX, 77030, USA
| | - Shruti Malu
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX, 77030, USA.,Immunitas Therapeutics, Cambridge, MA, USA
| | - Jodi A McKenzie
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX, 77030, USA.,Eisai Inc., Woodcliff Lake, NJ, USA
| | - Soraya Zorro Manrique
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX, 77030, USA
| | - Elien M Doorduijn
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX, 77030, USA
| | - Rina M Mbofung
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX, 77030, USA.,Merck Research Laboratories, Palo Alto, CA, USA
| | - Leila Williams
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX, 77030, USA.,KSQ Therapeutics Inc., Cambridge, MA, USA
| | - Deborah A Silverman
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX, 77030, USA
| | - Emily L Ashkin
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX, 77030, USA
| | - Ana Lucía Dominguez
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX, 77030, USA
| | - Zhe Wang
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX, 77030, USA.,Nature Cell Biology, Springer Nature, Shanghai City, China
| | - Jie Qing Chen
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX, 77030, USA.,EMD Serono, Rockland, MA, USA
| | - Sourindra N Maiti
- Department of Pediatrics, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX, 77030, USA
| | - Trang N Tieu
- Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX, 77030, USA.,C4 Therapeutics, Watertown, MA, USA
| | - Chengwen Liu
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX, 77030, USA
| | - Chunyu Xu
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX, 77030, USA.,University of Houston, Houston, TX, USA
| | - Marie-Andrée Forget
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX, 77030, USA
| | - Cara Haymaker
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX, 77030, USA
| | - Jahan S Khalili
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX, 77030, USA.,SystImmune Inc., Redmond, WA, USA
| | - Nikunj Satani
- Department of Cancer Systems Imaging, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX, 77030, USA
| | - Florian Muller
- Department of Cancer Systems Imaging, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX, 77030, USA
| | - Laurence J N Cooper
- Department of Pediatrics, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX, 77030, USA.,ZIOPHARM Oncology Inc., Boston, MA, USA
| | - Willem W Overwijk
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX, 77030, USA.,Nektar Therapeutics, San Francisco, CA, USA
| | - Rodabe N Amaria
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX, 77030, USA
| | - Chantale Bernatchez
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX, 77030, USA
| | - Timothy P Heffernan
- Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX, 77030, USA
| | - Weiyi Peng
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX, 77030, USA.,University of Houston, Houston, TX, USA
| | - Jason Roszik
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX, 77030, USA
| | - Patrick Hwu
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX, 77030, USA. .,Sarcoma Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX, 77030, USA. .,Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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3
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Tan B, Malu S, Roth KD. Development of ion pairing LC-MS/MS method for itaconate and cis-aconitate in cell extract and cell media. J Chromatogr B Analyt Technol Biomed Life Sci 2020; 1146:122120. [PMID: 32361631 DOI: 10.1016/j.jchromb.2020.122120] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [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: 11/23/2019] [Revised: 04/04/2020] [Accepted: 04/13/2020] [Indexed: 01/23/2023]
Abstract
Accumulation of Immune Responsive Gene 1(IRG1) in macrophage induced by lipopolysaccharide (LPS) and interferon gamma (IFN-γ) leads to production of itaconate by decarboxylation of cis-aconitate. The biology associated with IRG1 and itaconate is not fully understood. A rapid and sensitive method for measurement of itaconate will benefit the study of IRG1 biology. Multiple HPLC and derivatization methods were tested. An ion pairing LC-MS/MS method using tributylamine/formic acid as ion pairing agents and a HypercarbTM guard column we proposed demonstrated better peak shape and better sensitivity for itaconate. The current protocol allows baseline separation of itaconate, citraconate, and cis-aconitate without derivatization and direct analysis of analytes in 80% methanol/water solution to avoid the dry-down step. It provides the limit of quantitation (LOQ) of 30 pg itaconate on column with a 4.5-minute run time. This method is validated for measurement of itaconate and cis-aconitate in RAW264.7 cell extract and cell media in a 96-well plate format. We applied this method to successfully measure the increase of itaconate and the decrease of cis-aconitate in RAW cell extract and cell media after LPS/IFN-γ treatment.
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Affiliation(s)
- Bo Tan
- Quantitative Biology, Lilly Research Laboratories, Lilly Corporate Center, Indianapolis, IN 46285, United States.
| | - Shruti Malu
- Cancer Research, Lilly Research Laboratories, Lilly Corporate Center, Indianapolis, IN 46285, United States
| | - Kenneth D Roth
- Quantitative Biology, Lilly Research Laboratories, Lilly Corporate Center, Indianapolis, IN 46285, United States
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4
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McKenzie JA, Mbofung RM, Malu S, Zhang M, Ashkin E, Devi S, Williams L, Tieu T, Peng W, Pradeep S, Xu C, Zorro Manrique S, Liu C, Huang L, Chen Y, Forget MA, Haymaker C, Bernatchez C, Satani N, Muller F, Roszik J, Kalra A, Heffernan T, Sood A, Hu J, Amaria R, Davis RE, Hwu P. The Effect of Topoisomerase I Inhibitors on the Efficacy of T-Cell-Based Cancer Immunotherapy. J Natl Cancer Inst 2019; 110:777-786. [PMID: 29267866 PMCID: PMC6037061 DOI: 10.1093/jnci/djx257] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 11/08/2017] [Indexed: 12/17/2022] Open
Abstract
Background Immunotherapy has increasingly become a staple in cancer treatment. However, substantial limitations in the durability of response highlight the need for more rational therapeutic combinations. The aim of this study is to investigate how to make tumor cells more sensitive to T-cell-based cancer immunotherapy. Methods Two pairs of melanoma patient-derived tumor cell lines and their autologous tumor-infiltrating lymphocytes were utilized in a high-throughput screen of 850 compounds to identify bioactive agents that could be used in combinatorial strategies to improve T-cell-mediated killing of tumor cells. RNAi, overexpression, and gene expression analyses were utilized to identify the mechanism underlying the effect of Topoisomerase I (Top1) inhibitors on T-cell-mediated killing. Using a syngeneic mouse model (n = 5 per group), the antitumor efficacy of the combination of a clinically relevant Top1 inhibitor, liposomal irinotecan (MM-398), with immune checkpoint inhibitors was also assessed. All statistical tests were two-sided. Results We found that Top1 inhibitors increased the sensitivity of patient-derived melanoma cell lines (n = 7) to T-cell-mediated cytotoxicity (P < .001, Dunnett’s test). This enhancement is mediated by TP53INP1, whose overexpression increased the susceptibility of melanoma cell lines to T-cell cytotoxicity (2549 cell line: P = .009, unpaired t test), whereas its knockdown impeded T-cell killing of Top1 inhibitor–treated melanoma cells (2549 cell line: P < .001, unpaired t test). In vivo, greater tumor control was achieved with MM-398 in combination with α-PD-L1 or α-PD1 (P < .001, Tukey’s test). Prolonged survival was also observed in tumor-bearing mice treated with MM-398 in combination with α-PD-L1 (P = .002, log-rank test) or α-PD1 (P = .008, log-rank test). Conclusions We demonstrated that Top1 inhibitors can improve the antitumor efficacy of cancer immunotherapy, thus providing the basis for developing novel strategies using Top1 inhibitors to augment the efficacy of immunotherapy.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Sunila Pradeep
- Department of Gynecologic Oncology and Reproductive Medicine
| | - Chunyu Xu
- Department of Melanoma Medical Oncology
| | | | | | - Lu Huang
- Department of Melanoma Medical Oncology
| | - Yuan Chen
- Department of Melanoma Medical Oncology
| | | | | | | | | | | | | | - Ashish Kalra
- The University of Texas MD Anderson Cancer Center, Houston, TX; Merrimack Pharmaceuticals, Cambridge, MA
| | | | - Anil Sood
- Department of Gynecologic Oncology and Reproductive Medicine.,Center for RNA Interference and Non-coding RNA
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5
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Jerby L, Shah P, Cuoco MS, Rodman C, Su MJ, Melms JM, Leeson R, Kanodia A, Mei S, Lin JR, Wang S, Rabasha B, Liu D, Zhang G, Margolais C, Ashenberg O, Ott PA, Buchbinder EI, Haq R, Hodi S, Boland GM, Sullivan RJ, Frederick D, Miao B, Moll T, Flaherty K, Herlyn M, Jenkins RS, Thummalapalli R, Kowalczyk MS, Canadas I, Schilling B, Cartwright AN, Luoma AM, Malu S, Hwu P, Bernatchez C, Forget MA, Barbie DA, Shalek AK, Tirosh I, Sorger PK, Wucherpfennig KW, Allen EMV, Schadendorf D, Johnson BE, Rotem A, Rosenblatt-Rozen O, Garraway LA, Yoon CH, Izar B, Regev A. Abstract A082: Single-cell RNA-sequencing of metastatic melanoma identifies a cancer cell-intrinsic program associated with immune checkpoint inhibitor resistance. Cancer Immunol Res 2019. [DOI: 10.1158/2326-6074.cricimteatiaacr18-a082] [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
Immune checkpoint inhibitors (ICI) produce durable responses in some melanoma patients, but many patients derive no clinical benefit. The molecular underpinnings of ICI resistance involve intricate cell-cell interactions that are yet elusive. To systematically map the interactions between malignant and immune cells in the tumor ecosystem, we applied single-cell RNA sequencing to 31 human melanoma tumors, profiling thousands of malignant, immune, and stromal cells. We identified a transcriptional program in malignanT-cells that is strongly associated with T-cell exclusion and immunotherapy resistance. Using highly multiplexed in situ imaging we first demonstrated that this program characterizes malignanT-cells in “cold” niches. Next, we showed that the program predicts clinical responses to ICI according to multiple independent validation cohorts, including a new cohort that we obtained from 112 melanoma patients treated with anti-PD-1 therapy. We then identified CDK4/6 as master regulators of this resistance program, and found that CDK4/6 inhibitors repress the program and shift melanoma cells into a senescence-associated secretory phenotype. Lastly, we showed that CDK4/6-inhibition leads to a substantial reduction in melanoma tumor outgrowth in a B16 mouse model when given in combination with immunotherapy. Taken together, our study provides a high-resolution landscape of ICI-resistant cell states, identifies clinically predictive signatures, and forms a basis for the development of novel therapeutic strategies that could overcome immunotherapy resistance.
Citation Format: Livnat Jerby, Parin Shah, Michael S. Cuoco, Christopher Rodman, Mei-Ju Su, Johannes M. Melms, Rachel Leeson, Abhay Kanodia, Shaolin Mei, Jia-Ren Lin, Shu Wang, Bokang Rabasha, David Liu, Gao Zhang, Claire Margolais, Orr Ashenberg, Patrick A. Ott, Elizabeth I. Buchbinder, Riz Haq, Stephen Hodi, Genevieve M. Boland, Ryan J. Sullivan, Dennie Frederick, Benchun Miao, Tabea Moll, Keith Flaherty, Meenhard Herlyn, Russell S. Jenkins, Rohit Thummalapalli, Monika S. Kowalczyk, Israel Canadas, Bastian Schilling, Adam N.R Cartwright, Adrienne M. Luoma, Shruti Malu, Patrick Hwu, Chantale Bernatchez, Marie-Andree Forget, David A. Barbie, Alex K. Shalek, Itay Tirosh, Peter K. Sorger, Kai W. Wucherpfennig, Eliezer M. Van Allen, Dirk Schadendorf, Bruce E. Johnson, Asaf Rotem, Orit Rosenblatt-Rozen, Levi A. Garraway, Charles H. Yoon, Benjamin Izar, Aviv Regev. Single-cell RNA-sequencing of metastatic melanoma identifies a cancer cell-intrinsic program associated with immune checkpoint inhibitor resistance [abstract]. In: Proceedings of the Fourth CRI-CIMT-EATI-AACR International Cancer Immunotherapy Conference: Translating Science into Survival; Sept 30-Oct 3, 2018; New York, NY. Philadelphia (PA): AACR; Cancer Immunol Res 2019;7(2 Suppl):Abstract nr A082.
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Affiliation(s)
- Livnat Jerby
- Broad Institute of MIT and Harvard, Cambridge, MA; Dana-Farber Cancer Institute, Boston, MA; Harvard Medical School, Boston, MA; The Wistar Institute, Philadelphia, PA; Massachusetts General Hospital Cancer Center, Boston, MA; The University of Texas MD Anderson Cancer Center, Houston, TX; University Duisburg-Essen and the German Cancer Consortium (DKTK) , Essen, Germany; Brigham and Women’s Hospital, Boston, MA
| | - Parin Shah
- Broad Institute of MIT and Harvard, Cambridge, MA; Dana-Farber Cancer Institute, Boston, MA; Harvard Medical School, Boston, MA; The Wistar Institute, Philadelphia, PA; Massachusetts General Hospital Cancer Center, Boston, MA; The University of Texas MD Anderson Cancer Center, Houston, TX; University Duisburg-Essen and the German Cancer Consortium (DKTK) , Essen, Germany; Brigham and Women’s Hospital, Boston, MA
| | - Michael S. Cuoco
- Broad Institute of MIT and Harvard, Cambridge, MA; Dana-Farber Cancer Institute, Boston, MA; Harvard Medical School, Boston, MA; The Wistar Institute, Philadelphia, PA; Massachusetts General Hospital Cancer Center, Boston, MA; The University of Texas MD Anderson Cancer Center, Houston, TX; University Duisburg-Essen and the German Cancer Consortium (DKTK) , Essen, Germany; Brigham and Women’s Hospital, Boston, MA
| | - Christopher Rodman
- Broad Institute of MIT and Harvard, Cambridge, MA; Dana-Farber Cancer Institute, Boston, MA; Harvard Medical School, Boston, MA; The Wistar Institute, Philadelphia, PA; Massachusetts General Hospital Cancer Center, Boston, MA; The University of Texas MD Anderson Cancer Center, Houston, TX; University Duisburg-Essen and the German Cancer Consortium (DKTK) , Essen, Germany; Brigham and Women’s Hospital, Boston, MA
| | - Mei-Ju Su
- Broad Institute of MIT and Harvard, Cambridge, MA; Dana-Farber Cancer Institute, Boston, MA; Harvard Medical School, Boston, MA; The Wistar Institute, Philadelphia, PA; Massachusetts General Hospital Cancer Center, Boston, MA; The University of Texas MD Anderson Cancer Center, Houston, TX; University Duisburg-Essen and the German Cancer Consortium (DKTK) , Essen, Germany; Brigham and Women’s Hospital, Boston, MA
| | - Johannes M. Melms
- Broad Institute of MIT and Harvard, Cambridge, MA; Dana-Farber Cancer Institute, Boston, MA; Harvard Medical School, Boston, MA; The Wistar Institute, Philadelphia, PA; Massachusetts General Hospital Cancer Center, Boston, MA; The University of Texas MD Anderson Cancer Center, Houston, TX; University Duisburg-Essen and the German Cancer Consortium (DKTK) , Essen, Germany; Brigham and Women’s Hospital, Boston, MA
| | - Rachel Leeson
- Broad Institute of MIT and Harvard, Cambridge, MA; Dana-Farber Cancer Institute, Boston, MA; Harvard Medical School, Boston, MA; The Wistar Institute, Philadelphia, PA; Massachusetts General Hospital Cancer Center, Boston, MA; The University of Texas MD Anderson Cancer Center, Houston, TX; University Duisburg-Essen and the German Cancer Consortium (DKTK) , Essen, Germany; Brigham and Women’s Hospital, Boston, MA
| | - Abhay Kanodia
- Broad Institute of MIT and Harvard, Cambridge, MA; Dana-Farber Cancer Institute, Boston, MA; Harvard Medical School, Boston, MA; The Wistar Institute, Philadelphia, PA; Massachusetts General Hospital Cancer Center, Boston, MA; The University of Texas MD Anderson Cancer Center, Houston, TX; University Duisburg-Essen and the German Cancer Consortium (DKTK) , Essen, Germany; Brigham and Women’s Hospital, Boston, MA
| | - Shaolin Mei
- Broad Institute of MIT and Harvard, Cambridge, MA; Dana-Farber Cancer Institute, Boston, MA; Harvard Medical School, Boston, MA; The Wistar Institute, Philadelphia, PA; Massachusetts General Hospital Cancer Center, Boston, MA; The University of Texas MD Anderson Cancer Center, Houston, TX; University Duisburg-Essen and the German Cancer Consortium (DKTK) , Essen, Germany; Brigham and Women’s Hospital, Boston, MA
| | - Jia-Ren Lin
- Broad Institute of MIT and Harvard, Cambridge, MA; Dana-Farber Cancer Institute, Boston, MA; Harvard Medical School, Boston, MA; The Wistar Institute, Philadelphia, PA; Massachusetts General Hospital Cancer Center, Boston, MA; The University of Texas MD Anderson Cancer Center, Houston, TX; University Duisburg-Essen and the German Cancer Consortium (DKTK) , Essen, Germany; Brigham and Women’s Hospital, Boston, MA
| | - Shu Wang
- Broad Institute of MIT and Harvard, Cambridge, MA; Dana-Farber Cancer Institute, Boston, MA; Harvard Medical School, Boston, MA; The Wistar Institute, Philadelphia, PA; Massachusetts General Hospital Cancer Center, Boston, MA; The University of Texas MD Anderson Cancer Center, Houston, TX; University Duisburg-Essen and the German Cancer Consortium (DKTK) , Essen, Germany; Brigham and Women’s Hospital, Boston, MA
| | - Bokang Rabasha
- Broad Institute of MIT and Harvard, Cambridge, MA; Dana-Farber Cancer Institute, Boston, MA; Harvard Medical School, Boston, MA; The Wistar Institute, Philadelphia, PA; Massachusetts General Hospital Cancer Center, Boston, MA; The University of Texas MD Anderson Cancer Center, Houston, TX; University Duisburg-Essen and the German Cancer Consortium (DKTK) , Essen, Germany; Brigham and Women’s Hospital, Boston, MA
| | - David Liu
- Broad Institute of MIT and Harvard, Cambridge, MA; Dana-Farber Cancer Institute, Boston, MA; Harvard Medical School, Boston, MA; The Wistar Institute, Philadelphia, PA; Massachusetts General Hospital Cancer Center, Boston, MA; The University of Texas MD Anderson Cancer Center, Houston, TX; University Duisburg-Essen and the German Cancer Consortium (DKTK) , Essen, Germany; Brigham and Women’s Hospital, Boston, MA
| | - Gao Zhang
- Broad Institute of MIT and Harvard, Cambridge, MA; Dana-Farber Cancer Institute, Boston, MA; Harvard Medical School, Boston, MA; The Wistar Institute, Philadelphia, PA; Massachusetts General Hospital Cancer Center, Boston, MA; The University of Texas MD Anderson Cancer Center, Houston, TX; University Duisburg-Essen and the German Cancer Consortium (DKTK) , Essen, Germany; Brigham and Women’s Hospital, Boston, MA
| | - Claire Margolais
- Broad Institute of MIT and Harvard, Cambridge, MA; Dana-Farber Cancer Institute, Boston, MA; Harvard Medical School, Boston, MA; The Wistar Institute, Philadelphia, PA; Massachusetts General Hospital Cancer Center, Boston, MA; The University of Texas MD Anderson Cancer Center, Houston, TX; University Duisburg-Essen and the German Cancer Consortium (DKTK) , Essen, Germany; Brigham and Women’s Hospital, Boston, MA
| | - Orr Ashenberg
- Broad Institute of MIT and Harvard, Cambridge, MA; Dana-Farber Cancer Institute, Boston, MA; Harvard Medical School, Boston, MA; The Wistar Institute, Philadelphia, PA; Massachusetts General Hospital Cancer Center, Boston, MA; The University of Texas MD Anderson Cancer Center, Houston, TX; University Duisburg-Essen and the German Cancer Consortium (DKTK) , Essen, Germany; Brigham and Women’s Hospital, Boston, MA
| | - Patrick A. Ott
- Broad Institute of MIT and Harvard, Cambridge, MA; Dana-Farber Cancer Institute, Boston, MA; Harvard Medical School, Boston, MA; The Wistar Institute, Philadelphia, PA; Massachusetts General Hospital Cancer Center, Boston, MA; The University of Texas MD Anderson Cancer Center, Houston, TX; University Duisburg-Essen and the German Cancer Consortium (DKTK) , Essen, Germany; Brigham and Women’s Hospital, Boston, MA
| | - Elizabeth I. Buchbinder
- Broad Institute of MIT and Harvard, Cambridge, MA; Dana-Farber Cancer Institute, Boston, MA; Harvard Medical School, Boston, MA; The Wistar Institute, Philadelphia, PA; Massachusetts General Hospital Cancer Center, Boston, MA; The University of Texas MD Anderson Cancer Center, Houston, TX; University Duisburg-Essen and the German Cancer Consortium (DKTK) , Essen, Germany; Brigham and Women’s Hospital, Boston, MA
| | - Riz Haq
- Broad Institute of MIT and Harvard, Cambridge, MA; Dana-Farber Cancer Institute, Boston, MA; Harvard Medical School, Boston, MA; The Wistar Institute, Philadelphia, PA; Massachusetts General Hospital Cancer Center, Boston, MA; The University of Texas MD Anderson Cancer Center, Houston, TX; University Duisburg-Essen and the German Cancer Consortium (DKTK) , Essen, Germany; Brigham and Women’s Hospital, Boston, MA
| | - Stephen Hodi
- Broad Institute of MIT and Harvard, Cambridge, MA; Dana-Farber Cancer Institute, Boston, MA; Harvard Medical School, Boston, MA; The Wistar Institute, Philadelphia, PA; Massachusetts General Hospital Cancer Center, Boston, MA; The University of Texas MD Anderson Cancer Center, Houston, TX; University Duisburg-Essen and the German Cancer Consortium (DKTK) , Essen, Germany; Brigham and Women’s Hospital, Boston, MA
| | - Genevieve M. Boland
- Broad Institute of MIT and Harvard, Cambridge, MA; Dana-Farber Cancer Institute, Boston, MA; Harvard Medical School, Boston, MA; The Wistar Institute, Philadelphia, PA; Massachusetts General Hospital Cancer Center, Boston, MA; The University of Texas MD Anderson Cancer Center, Houston, TX; University Duisburg-Essen and the German Cancer Consortium (DKTK) , Essen, Germany; Brigham and Women’s Hospital, Boston, MA
| | - Ryan J. Sullivan
- Broad Institute of MIT and Harvard, Cambridge, MA; Dana-Farber Cancer Institute, Boston, MA; Harvard Medical School, Boston, MA; The Wistar Institute, Philadelphia, PA; Massachusetts General Hospital Cancer Center, Boston, MA; The University of Texas MD Anderson Cancer Center, Houston, TX; University Duisburg-Essen and the German Cancer Consortium (DKTK) , Essen, Germany; Brigham and Women’s Hospital, Boston, MA
| | - Dennie Frederick
- Broad Institute of MIT and Harvard, Cambridge, MA; Dana-Farber Cancer Institute, Boston, MA; Harvard Medical School, Boston, MA; The Wistar Institute, Philadelphia, PA; Massachusetts General Hospital Cancer Center, Boston, MA; The University of Texas MD Anderson Cancer Center, Houston, TX; University Duisburg-Essen and the German Cancer Consortium (DKTK) , Essen, Germany; Brigham and Women’s Hospital, Boston, MA
| | - Benchun Miao
- Broad Institute of MIT and Harvard, Cambridge, MA; Dana-Farber Cancer Institute, Boston, MA; Harvard Medical School, Boston, MA; The Wistar Institute, Philadelphia, PA; Massachusetts General Hospital Cancer Center, Boston, MA; The University of Texas MD Anderson Cancer Center, Houston, TX; University Duisburg-Essen and the German Cancer Consortium (DKTK) , Essen, Germany; Brigham and Women’s Hospital, Boston, MA
| | - Tabea Moll
- Broad Institute of MIT and Harvard, Cambridge, MA; Dana-Farber Cancer Institute, Boston, MA; Harvard Medical School, Boston, MA; The Wistar Institute, Philadelphia, PA; Massachusetts General Hospital Cancer Center, Boston, MA; The University of Texas MD Anderson Cancer Center, Houston, TX; University Duisburg-Essen and the German Cancer Consortium (DKTK) , Essen, Germany; Brigham and Women’s Hospital, Boston, MA
| | - Keith Flaherty
- Broad Institute of MIT and Harvard, Cambridge, MA; Dana-Farber Cancer Institute, Boston, MA; Harvard Medical School, Boston, MA; The Wistar Institute, Philadelphia, PA; Massachusetts General Hospital Cancer Center, Boston, MA; The University of Texas MD Anderson Cancer Center, Houston, TX; University Duisburg-Essen and the German Cancer Consortium (DKTK) , Essen, Germany; Brigham and Women’s Hospital, Boston, MA
| | - Meenhard Herlyn
- Broad Institute of MIT and Harvard, Cambridge, MA; Dana-Farber Cancer Institute, Boston, MA; Harvard Medical School, Boston, MA; The Wistar Institute, Philadelphia, PA; Massachusetts General Hospital Cancer Center, Boston, MA; The University of Texas MD Anderson Cancer Center, Houston, TX; University Duisburg-Essen and the German Cancer Consortium (DKTK) , Essen, Germany; Brigham and Women’s Hospital, Boston, MA
| | - Russell S. Jenkins
- Broad Institute of MIT and Harvard, Cambridge, MA; Dana-Farber Cancer Institute, Boston, MA; Harvard Medical School, Boston, MA; The Wistar Institute, Philadelphia, PA; Massachusetts General Hospital Cancer Center, Boston, MA; The University of Texas MD Anderson Cancer Center, Houston, TX; University Duisburg-Essen and the German Cancer Consortium (DKTK) , Essen, Germany; Brigham and Women’s Hospital, Boston, MA
| | - Rohit Thummalapalli
- Broad Institute of MIT and Harvard, Cambridge, MA; Dana-Farber Cancer Institute, Boston, MA; Harvard Medical School, Boston, MA; The Wistar Institute, Philadelphia, PA; Massachusetts General Hospital Cancer Center, Boston, MA; The University of Texas MD Anderson Cancer Center, Houston, TX; University Duisburg-Essen and the German Cancer Consortium (DKTK) , Essen, Germany; Brigham and Women’s Hospital, Boston, MA
| | - Monika S. Kowalczyk
- Broad Institute of MIT and Harvard, Cambridge, MA; Dana-Farber Cancer Institute, Boston, MA; Harvard Medical School, Boston, MA; The Wistar Institute, Philadelphia, PA; Massachusetts General Hospital Cancer Center, Boston, MA; The University of Texas MD Anderson Cancer Center, Houston, TX; University Duisburg-Essen and the German Cancer Consortium (DKTK) , Essen, Germany; Brigham and Women’s Hospital, Boston, MA
| | - Israel Canadas
- Broad Institute of MIT and Harvard, Cambridge, MA; Dana-Farber Cancer Institute, Boston, MA; Harvard Medical School, Boston, MA; The Wistar Institute, Philadelphia, PA; Massachusetts General Hospital Cancer Center, Boston, MA; The University of Texas MD Anderson Cancer Center, Houston, TX; University Duisburg-Essen and the German Cancer Consortium (DKTK) , Essen, Germany; Brigham and Women’s Hospital, Boston, MA
| | - Bastian Schilling
- Broad Institute of MIT and Harvard, Cambridge, MA; Dana-Farber Cancer Institute, Boston, MA; Harvard Medical School, Boston, MA; The Wistar Institute, Philadelphia, PA; Massachusetts General Hospital Cancer Center, Boston, MA; The University of Texas MD Anderson Cancer Center, Houston, TX; University Duisburg-Essen and the German Cancer Consortium (DKTK) , Essen, Germany; Brigham and Women’s Hospital, Boston, MA
| | - Adam N.R Cartwright
- Broad Institute of MIT and Harvard, Cambridge, MA; Dana-Farber Cancer Institute, Boston, MA; Harvard Medical School, Boston, MA; The Wistar Institute, Philadelphia, PA; Massachusetts General Hospital Cancer Center, Boston, MA; The University of Texas MD Anderson Cancer Center, Houston, TX; University Duisburg-Essen and the German Cancer Consortium (DKTK) , Essen, Germany; Brigham and Women’s Hospital, Boston, MA
| | - Adrienne M. Luoma
- Broad Institute of MIT and Harvard, Cambridge, MA; Dana-Farber Cancer Institute, Boston, MA; Harvard Medical School, Boston, MA; The Wistar Institute, Philadelphia, PA; Massachusetts General Hospital Cancer Center, Boston, MA; The University of Texas MD Anderson Cancer Center, Houston, TX; University Duisburg-Essen and the German Cancer Consortium (DKTK) , Essen, Germany; Brigham and Women’s Hospital, Boston, MA
| | - Shruti Malu
- Broad Institute of MIT and Harvard, Cambridge, MA; Dana-Farber Cancer Institute, Boston, MA; Harvard Medical School, Boston, MA; The Wistar Institute, Philadelphia, PA; Massachusetts General Hospital Cancer Center, Boston, MA; The University of Texas MD Anderson Cancer Center, Houston, TX; University Duisburg-Essen and the German Cancer Consortium (DKTK) , Essen, Germany; Brigham and Women’s Hospital, Boston, MA
| | - Patrick Hwu
- Broad Institute of MIT and Harvard, Cambridge, MA; Dana-Farber Cancer Institute, Boston, MA; Harvard Medical School, Boston, MA; The Wistar Institute, Philadelphia, PA; Massachusetts General Hospital Cancer Center, Boston, MA; The University of Texas MD Anderson Cancer Center, Houston, TX; University Duisburg-Essen and the German Cancer Consortium (DKTK) , Essen, Germany; Brigham and Women’s Hospital, Boston, MA
| | - Chantale Bernatchez
- Broad Institute of MIT and Harvard, Cambridge, MA; Dana-Farber Cancer Institute, Boston, MA; Harvard Medical School, Boston, MA; The Wistar Institute, Philadelphia, PA; Massachusetts General Hospital Cancer Center, Boston, MA; The University of Texas MD Anderson Cancer Center, Houston, TX; University Duisburg-Essen and the German Cancer Consortium (DKTK) , Essen, Germany; Brigham and Women’s Hospital, Boston, MA
| | - Marie-Andree Forget
- Broad Institute of MIT and Harvard, Cambridge, MA; Dana-Farber Cancer Institute, Boston, MA; Harvard Medical School, Boston, MA; The Wistar Institute, Philadelphia, PA; Massachusetts General Hospital Cancer Center, Boston, MA; The University of Texas MD Anderson Cancer Center, Houston, TX; University Duisburg-Essen and the German Cancer Consortium (DKTK) , Essen, Germany; Brigham and Women’s Hospital, Boston, MA
| | - David A. Barbie
- Broad Institute of MIT and Harvard, Cambridge, MA; Dana-Farber Cancer Institute, Boston, MA; Harvard Medical School, Boston, MA; The Wistar Institute, Philadelphia, PA; Massachusetts General Hospital Cancer Center, Boston, MA; The University of Texas MD Anderson Cancer Center, Houston, TX; University Duisburg-Essen and the German Cancer Consortium (DKTK) , Essen, Germany; Brigham and Women’s Hospital, Boston, MA
| | - Alex K. Shalek
- Broad Institute of MIT and Harvard, Cambridge, MA; Dana-Farber Cancer Institute, Boston, MA; Harvard Medical School, Boston, MA; The Wistar Institute, Philadelphia, PA; Massachusetts General Hospital Cancer Center, Boston, MA; The University of Texas MD Anderson Cancer Center, Houston, TX; University Duisburg-Essen and the German Cancer Consortium (DKTK) , Essen, Germany; Brigham and Women’s Hospital, Boston, MA
| | - Itay Tirosh
- Broad Institute of MIT and Harvard, Cambridge, MA; Dana-Farber Cancer Institute, Boston, MA; Harvard Medical School, Boston, MA; The Wistar Institute, Philadelphia, PA; Massachusetts General Hospital Cancer Center, Boston, MA; The University of Texas MD Anderson Cancer Center, Houston, TX; University Duisburg-Essen and the German Cancer Consortium (DKTK) , Essen, Germany; Brigham and Women’s Hospital, Boston, MA
| | - Peter K. Sorger
- Broad Institute of MIT and Harvard, Cambridge, MA; Dana-Farber Cancer Institute, Boston, MA; Harvard Medical School, Boston, MA; The Wistar Institute, Philadelphia, PA; Massachusetts General Hospital Cancer Center, Boston, MA; The University of Texas MD Anderson Cancer Center, Houston, TX; University Duisburg-Essen and the German Cancer Consortium (DKTK) , Essen, Germany; Brigham and Women’s Hospital, Boston, MA
| | - Kai W. Wucherpfennig
- Broad Institute of MIT and Harvard, Cambridge, MA; Dana-Farber Cancer Institute, Boston, MA; Harvard Medical School, Boston, MA; The Wistar Institute, Philadelphia, PA; Massachusetts General Hospital Cancer Center, Boston, MA; The University of Texas MD Anderson Cancer Center, Houston, TX; University Duisburg-Essen and the German Cancer Consortium (DKTK) , Essen, Germany; Brigham and Women’s Hospital, Boston, MA
| | - Eliezer M. Van Allen
- Broad Institute of MIT and Harvard, Cambridge, MA; Dana-Farber Cancer Institute, Boston, MA; Harvard Medical School, Boston, MA; The Wistar Institute, Philadelphia, PA; Massachusetts General Hospital Cancer Center, Boston, MA; The University of Texas MD Anderson Cancer Center, Houston, TX; University Duisburg-Essen and the German Cancer Consortium (DKTK) , Essen, Germany; Brigham and Women’s Hospital, Boston, MA
| | - Dirk Schadendorf
- Broad Institute of MIT and Harvard, Cambridge, MA; Dana-Farber Cancer Institute, Boston, MA; Harvard Medical School, Boston, MA; The Wistar Institute, Philadelphia, PA; Massachusetts General Hospital Cancer Center, Boston, MA; The University of Texas MD Anderson Cancer Center, Houston, TX; University Duisburg-Essen and the German Cancer Consortium (DKTK) , Essen, Germany; Brigham and Women’s Hospital, Boston, MA
| | - Bruce E. Johnson
- Broad Institute of MIT and Harvard, Cambridge, MA; Dana-Farber Cancer Institute, Boston, MA; Harvard Medical School, Boston, MA; The Wistar Institute, Philadelphia, PA; Massachusetts General Hospital Cancer Center, Boston, MA; The University of Texas MD Anderson Cancer Center, Houston, TX; University Duisburg-Essen and the German Cancer Consortium (DKTK) , Essen, Germany; Brigham and Women’s Hospital, Boston, MA
| | - Asaf Rotem
- Broad Institute of MIT and Harvard, Cambridge, MA; Dana-Farber Cancer Institute, Boston, MA; Harvard Medical School, Boston, MA; The Wistar Institute, Philadelphia, PA; Massachusetts General Hospital Cancer Center, Boston, MA; The University of Texas MD Anderson Cancer Center, Houston, TX; University Duisburg-Essen and the German Cancer Consortium (DKTK) , Essen, Germany; Brigham and Women’s Hospital, Boston, MA
| | - Orit Rosenblatt-Rozen
- Broad Institute of MIT and Harvard, Cambridge, MA; Dana-Farber Cancer Institute, Boston, MA; Harvard Medical School, Boston, MA; The Wistar Institute, Philadelphia, PA; Massachusetts General Hospital Cancer Center, Boston, MA; The University of Texas MD Anderson Cancer Center, Houston, TX; University Duisburg-Essen and the German Cancer Consortium (DKTK) , Essen, Germany; Brigham and Women’s Hospital, Boston, MA
| | - Levi A. Garraway
- Broad Institute of MIT and Harvard, Cambridge, MA; Dana-Farber Cancer Institute, Boston, MA; Harvard Medical School, Boston, MA; The Wistar Institute, Philadelphia, PA; Massachusetts General Hospital Cancer Center, Boston, MA; The University of Texas MD Anderson Cancer Center, Houston, TX; University Duisburg-Essen and the German Cancer Consortium (DKTK) , Essen, Germany; Brigham and Women’s Hospital, Boston, MA
| | - Charles H. Yoon
- Broad Institute of MIT and Harvard, Cambridge, MA; Dana-Farber Cancer Institute, Boston, MA; Harvard Medical School, Boston, MA; The Wistar Institute, Philadelphia, PA; Massachusetts General Hospital Cancer Center, Boston, MA; The University of Texas MD Anderson Cancer Center, Houston, TX; University Duisburg-Essen and the German Cancer Consortium (DKTK) , Essen, Germany; Brigham and Women’s Hospital, Boston, MA
| | - Benjamin Izar
- Broad Institute of MIT and Harvard, Cambridge, MA; Dana-Farber Cancer Institute, Boston, MA; Harvard Medical School, Boston, MA; The Wistar Institute, Philadelphia, PA; Massachusetts General Hospital Cancer Center, Boston, MA; The University of Texas MD Anderson Cancer Center, Houston, TX; University Duisburg-Essen and the German Cancer Consortium (DKTK) , Essen, Germany; Brigham and Women’s Hospital, Boston, MA
| | - Aviv Regev
- Broad Institute of MIT and Harvard, Cambridge, MA; Dana-Farber Cancer Institute, Boston, MA; Harvard Medical School, Boston, MA; The Wistar Institute, Philadelphia, PA; Massachusetts General Hospital Cancer Center, Boston, MA; The University of Texas MD Anderson Cancer Center, Houston, TX; University Duisburg-Essen and the German Cancer Consortium (DKTK) , Essen, Germany; Brigham and Women’s Hospital, Boston, MA
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6
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Jerby-Arnon L, Shah P, Cuoco MS, Rodman C, Su MJ, Melms JC, Leeson R, Kanodia A, Mei S, Lin JR, Wang S, Rabasha B, Liu D, Zhang G, Margolais C, Ashenberg O, Ott PA, Buchbinder EI, Haq R, Hodi FS, Boland GM, Sullivan RJ, Frederick DT, Miao B, Moll T, Flaherty KT, Herlyn M, Jenkins RW, Thummalapalli R, Kowalczyk MS, Cañadas I, Schilling B, Cartwright ANR, Luoma AM, Malu S, Hwu P, Bernatchez C, Forget MA, Barbie DA, Shalek AK, Tirosh I, Sorger PK, Wucherpfennig K, Van Allen EM, Schadendorf D, Johnson BE, Rotem A, Rozenblatt-Rosen O, Garraway LA, Yoon CH, Izar B, Regev A. A Cancer Cell Program Promotes T Cell Exclusion and Resistance to Checkpoint Blockade. Cell 2018; 175:984-997.e24. [PMID: 30388455 PMCID: PMC6410377 DOI: 10.1016/j.cell.2018.09.006] [Citation(s) in RCA: 720] [Impact Index Per Article: 120.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 06/18/2018] [Accepted: 09/05/2018] [Indexed: 12/12/2022]
Abstract
Immune checkpoint inhibitors (ICIs) produce durable responses in some melanoma patients, but many patients derive no clinical benefit, and the molecular underpinnings of such resistance remain elusive. Here, we leveraged single-cell RNA sequencing (scRNA-seq) from 33 melanoma tumors and computational analyses to interrogate malignant cell states that promote immune evasion. We identified a resistance program expressed by malignant cells that is associated with T cell exclusion and immune evasion. The program is expressed prior to immunotherapy, characterizes cold niches in situ, and predicts clinical responses to anti-PD-1 therapy in an independent cohort of 112 melanoma patients. CDK4/6-inhibition represses this program in individual malignant cells, induces senescence, and reduces melanoma tumor outgrowth in mouse models in vivo when given in combination with immunotherapy. Our study provides a high-resolution landscape of ICI-resistant cell states, identifies clinically predictive signatures, and suggests new therapeutic strategies to overcome immunotherapy resistance.
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Affiliation(s)
| | - Parin Shah
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | | | - Mei-Ju Su
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Center for Cancer Precision Medicine of Dana-Farber Cancer Institute, Boston, MA, USA
| | - Johannes C Melms
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Rachel Leeson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Center for Cancer Precision Medicine of Dana-Farber Cancer Institute, Boston, MA, USA
| | - Abhay Kanodia
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Center for Cancer Precision Medicine of Dana-Farber Cancer Institute, Boston, MA, USA
| | - Shaolin Mei
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Laboratory for Systems Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Jia-Ren Lin
- Laboratory for Systems Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Shu Wang
- Laboratory for Systems Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Bokang Rabasha
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - David Liu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Gao Zhang
- Molecular & Cellular Oncogenesis Program and Melanoma Research Center, The Wistar Institute, Philadelphia, PA, USA
| | - Claire Margolais
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Orr Ashenberg
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Patrick A Ott
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Rizwan Haq
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - F Stephen Hodi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Ryan J Sullivan
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | | | - Benchun Miao
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Tabea Moll
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | | | - Meenhard Herlyn
- Molecular & Cellular Oncogenesis Program and Melanoma Research Center, The Wistar Institute, Philadelphia, PA, USA
| | - Russell W Jenkins
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Rohit Thummalapalli
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Monika S Kowalczyk
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Celsius Therapeutics, Cambridge, MA, USA
| | - Israel Cañadas
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Bastian Schilling
- Department of Dermatology, University Hospital Essen, West German Cancer Center, University Duisburg-Essen and the German Cancer Consortium, Essen, Germany; Department of Dermatology, Venereology and Allergology, University Hospital Würzburg, Würzburg, Germany
| | - Adam N R Cartwright
- Center for Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Adrienne M Luoma
- Center for Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Shruti Malu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Patrick Hwu
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Chantale Bernatchez
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Marie-Andrée Forget
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - David A Barbie
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Alex K Shalek
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Itay Tirosh
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Peter K Sorger
- Laboratory for Systems Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Kai Wucherpfennig
- Center for Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Eliezer M Van Allen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Dirk Schadendorf
- Department of Dermatology, University Hospital Essen, West German Cancer Center, University Duisburg-Essen and the German Cancer Consortium, Essen, Germany
| | - Bruce E Johnson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Center for Cancer Precision Medicine of Dana-Farber Cancer Institute, Boston, MA, USA
| | - Asaf Rotem
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Center for Cancer Precision Medicine of Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Levi A Garraway
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Center for Cancer Precision Medicine of Dana-Farber Cancer Institute, Boston, MA, USA; Ludwig Center for Cancer Research at Harvard, Boston, MA, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Charles H Yoon
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Brigham and Women's Hospital, Department of Surgical Oncology, Boston, MA, USA
| | - Benjamin Izar
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Center for Cancer Precision Medicine of Dana-Farber Cancer Institute, Boston, MA, USA; Laboratory for Systems Pharmacology, Harvard Medical School, Boston, MA, USA; Center for Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA; Ludwig Center for Cancer Research at Harvard, Boston, MA, USA.
| | - Aviv Regev
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA; Ludwig Center for Cancer Research at MIT, Boston, MA, USA; Massachusetts Institute of Technology, Department of Biology, Cambridge, MA, USA
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7
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Huang L, Malu S, McKenzie JA, Andrews MC, Talukder AH, Tieu T, Karpinets T, Haymaker C, Forget MA, Williams LJ, Wang Z, Mbofung RM, Wang ZQ, Davis RE, Lo RS, Wargo JA, Davies MA, Bernatchez C, Heffernan T, Amaria RN, Korkut A, Peng W, Roszik J, Lizée G, Woodman SE, Hwu P. The RNA-binding Protein MEX3B Mediates Resistance to Cancer Immunotherapy by Downregulating HLA-A Expression. Clin Cancer Res 2018; 24:3366-3376. [PMID: 29496759 PMCID: PMC9872773 DOI: 10.1158/1078-0432.ccr-17-2483] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 11/30/2017] [Accepted: 02/21/2018] [Indexed: 01/27/2023]
Abstract
Purpose: Cancer immunotherapy has shown promising clinical outcomes in many patients. However, some patients still fail to respond, and new strategies are needed to overcome resistance. The purpose of this study was to identify novel genes and understand the mechanisms that confer resistance to cancer immunotherapy.Experimental Design: To identify genes mediating resistance to T-cell killing, we performed an open reading frame (ORF) screen of a kinome library to study whether overexpression of a gene in patient-derived melanoma cells could inhibit their susceptibility to killing by autologous tumor-infiltrating lymphocytes (TIL).Results: The RNA-binding protein MEX3B was identified as a top candidate that decreased the susceptibility of melanoma cells to killing by TILs. Further analyses of anti-PD-1-treated melanoma patient tumor samples suggested that higher MEX3B expression is associated with resistance to PD-1 blockade. In addition, significantly decreased levels of IFNγ were secreted from TILs incubated with MEX3B-overexpressing tumor cells. Interestingly, this phenotype was rescued upon overexpression of exogenous HLA-A2. Consistent with this, we observed decreased HLA-A expression in MEX3B-overexpressing tumor cells. Finally, luciferase reporter assays and RNA-binding protein immunoprecipitation assays suggest that this is due to MEX3B binding to the 3' untranslated region (UTR) of HLA-A to destabilize the mRNA.Conclusions: MEX3B mediates resistance to cancer immunotherapy by binding to the 3' UTR of HLA-A to destabilize the HLA-A mRNA and thus downregulate HLA-A expression on the surface of tumor cells, thereby making the tumor cells unable to be recognized and killed by T cells. Clin Cancer Res; 24(14); 3366-76. ©2018 AACRSee related commentary by Kalbasi and Ribas, p. 3239.
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Affiliation(s)
- Lu Huang
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Shruti Malu
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jodi A. McKenzie
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Miles C. Andrews
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Amjad H. Talukder
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Trang Tieu
- Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Tatiana Karpinets
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Cara Haymaker
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Marie-Andrée Forget
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Leila J. Williams
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Zhe Wang
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Rina M. Mbofung
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Zhi-Qiang Wang
- Department of Lymphoma/Myeloma, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Richard Eric Davis
- Department of Lymphoma/Myeloma, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Roger S. Lo
- Department of Medicine, The University of California, Los Angeles, Los Angeles, California
| | - Jennifer A. Wargo
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Michael A. Davies
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Chantale Bernatchez
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Timothy Heffernan
- Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Rodabe N. Amaria
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Anil Korkut
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Weiyi Peng
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jason Roszik
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Gregory Lizée
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Scott E. Woodman
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Patrick Hwu
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
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8
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Peng W, Cascone T, McKenzie J, Mbofung R, Punt S, Wang Z, Xu C, Williams L, Wang Z, Bristow C, Carugo A, Peoples M, Li L, Karpinets T, Huang L, Malu S, Creasy C, Leahey S, Chen J, Bernatchez C, Gopal V, Heffernan T, Hu J, Wang J, Amaria R, Wistuba I, Woodman S, Roszik J, Davis E, Davies M, Heymach J, Hwu P. The metabolic basis of resistance to Adoptive T Cell Therapy (ACT) in patients with solid tumors. The Journal of Immunology 2018. [DOI: 10.4049/jimmunol.200.supp.177.1] [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] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Abstract
Adoptive T cell therapy (ACT) has produced impressive responses in a subset of patients with advanced malignancies. However, majority of patients still failed to respond. Thus, there is an urgent need to understand the resistant mechanisms in non-responders and develop more effective ACT strategies. Here, we employed two independent and unbiased approaches to identify novel molecular determinants of immune resistance. We generated gene expression profiles on an immune resistant melanoma cell line to identify alternative immunosuppressive mechanisms. In addition, we utilized a new high-throughput shRNA screening platform developed by our group to functionally interrogate immune resistance in patient-derived melanoma cells. Results from both analyses implicated tumor-associated glycolysis as a critical pathway that enables tumor cells to evade T cell-mediated antitumor activity. By using samples from melanoma and non-small cell lung cancer patients, we showed that increased expression of glycolysis-related genes is associated with poor T cell infiltration of tumors. Moreover, we found that increasing tumor glycolysis impaired T cell killing of melanoma cells, while inhibiting glycolysis restored T cell-mediated apoptosis of tumor cells. More importantly, from two non-overlapping ACT-treated patient cohorts, we discovered that tumor glycolytic activity in patients who experienced disease progression following ACT was significantly higher compared to those patients who were responsive to therapy. Taken together, our results demonstrate that tumor glycolytic metabolism is associated with the efficacy of ACT and identify glycolysis as a candidate target for combinatorial therapeutic intervention.
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9
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Cascone T, McKenzie JA, Mbofung RM, Punt S, Wang Z, Xu C, Williams LJ, Wang Z, Bristow CA, Carugo A, Peoples MD, Li L, Karpinets T, Huang L, Malu S, Creasy C, Leahey SE, Chen J, Chen Y, Pelicano H, Bernatchez C, Gopal YNV, Heffernan TP, Hu J, Wang J, Amaria RN, Garraway LA, Huang P, Yang P, Wistuba II, Woodman SE, Roszik J, Davis RE, Davies MA, Heymach JV, Hwu P, Peng W. Increased Tumor Glycolysis Characterizes Immune Resistance to Adoptive T Cell Therapy. Cell Metab 2018; 27:977-987.e4. [PMID: 29628419 PMCID: PMC5932208 DOI: 10.1016/j.cmet.2018.02.024] [Citation(s) in RCA: 353] [Impact Index Per Article: 58.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/22/2017] [Revised: 01/10/2018] [Accepted: 02/27/2018] [Indexed: 12/18/2022]
Abstract
Adoptive T cell therapy (ACT) produces durable responses in some cancer patients; however, most tumors are refractory to ACT and the molecular mechanisms underlying resistance are unclear. Using two independent approaches, we identified tumor glycolysis as a pathway associated with immune resistance in melanoma. Glycolysis-related genes were upregulated in melanoma and lung cancer patient samples poorly infiltrated by T cells. Overexpression of glycolysis-related molecules impaired T cell killing of tumor cells, whereas inhibition of glycolysis enhanced T cell-mediated antitumor immunity in vitro and in vivo. Moreover, glycolysis-related gene expression was higher in melanoma tissues from ACT-refractory patients, and tumor cells derived from these patients exhibited higher glycolytic activity. We identified reduced levels of IRF1 and CXCL10 immunostimulatory molecules in highly glycolytic melanoma cells. Our findings demonstrate that tumor glycolysis is associated with the efficacy of ACT and identify the glycolysis pathway as a candidate target for combinatorial therapeutic intervention.
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Affiliation(s)
- Tina Cascone
- Department of Thoracic/Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jodi A McKenzie
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Rina M Mbofung
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Simone Punt
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Zhe Wang
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Chunyu Xu
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Leila J Williams
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Zhiqiang Wang
- Department of Lymphoma/Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Christopher A Bristow
- Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Alessandro Carugo
- Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Michael D Peoples
- Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Lerong Li
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Tatiana Karpinets
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Lu Huang
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Shruti Malu
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Caitlin Creasy
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Sara E Leahey
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jiong Chen
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yuan Chen
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Helen Pelicano
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Chantale Bernatchez
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Y N Vashisht Gopal
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Timothy P Heffernan
- Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jianhua Hu
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jing Wang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Rodabe N Amaria
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Levi A Garraway
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Peng Huang
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Peiying Yang
- Department of Palliative, Rehabilitation and Integrative Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ignacio I Wistuba
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Scott E Woodman
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jason Roszik
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - R Eric Davis
- Department of Lymphoma/Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Michael A Davies
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - John V Heymach
- Department of Thoracic/Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Patrick Hwu
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
| | - Weiyi Peng
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
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10
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Mbofung RM, McKenzie JA, Malu S, Zhang M, Peng W, Liu C, Kuiatse I, Tieu T, Williams L, Devi S, Ashkin E, Xu C, Huang L, Zhang M, Talukder AH, Tripathi SC, Khong H, Satani N, Muller FL, Roszik J, Heffernan T, Allison JP, Lizee G, Hanash SM, Proia D, Amaria R, Davis RE, Hwu P. HSP90 inhibition enhances cancer immunotherapy by upregulating interferon response genes. Nat Commun 2017; 8:451. [PMID: 28878208 PMCID: PMC5587668 DOI: 10.1038/s41467-017-00449-z] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 06/29/2017] [Indexed: 01/05/2023] Open
Abstract
T-cell-based immunotherapies are promising treatments for cancer patients. Although durable responses can be achieved in some patients, many patients fail to respond to these therapies, underscoring the need for improvement with combination therapies. From a screen of 850 bioactive compounds, we identify HSP90 inhibitors as candidates for combination with immunotherapy. We show that inhibition of HSP90 with ganetespib enhances T-cell-mediated killing of patient-derived human melanoma cells by their autologous T cells in vitro and potentiates responses to anti-CTLA4 and anti-PD1 therapy in vivo. Mechanistic studies reveal that HSP90 inhibition results in upregulation of interferon response genes, which are essential for the enhanced killing of ganetespib treated melanoma cells by T cells. Taken together, these findings provide evidence that HSP90 inhibition can potentiate T-cell-mediated anti-tumor immune responses, and rationale to explore the combination of immunotherapy and HSP90 inhibitors. Many patients fail to respond to T cell based immunotherapies. Here, the authors, through a high-throughput screening, identify HSP90 inhibitors as a class of preferred drugs for treatment combination with immunotherapy.
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Affiliation(s)
- Rina M Mbofung
- Department of Melanoma Medical Oncology Unit 904, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX, 77030, USA
| | - Jodi A McKenzie
- Department of Melanoma Medical Oncology Unit 904, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX, 77030, USA
| | - Shruti Malu
- Department of Melanoma Medical Oncology Unit 904, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX, 77030, USA
| | - Min Zhang
- Department of Lymphoma/Myeloma Unit 903, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX, 77030, USA
| | - Weiyi Peng
- Department of Melanoma Medical Oncology Unit 904, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX, 77030, USA
| | - Chengwen Liu
- Department of Melanoma Medical Oncology Unit 904, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX, 77030, USA
| | - Isere Kuiatse
- Department of Lymphoma/Myeloma Unit 903, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX, 77030, USA
| | - Trang Tieu
- Institute for Applied Cancer Sciences Unit 1956, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX, 77030, USA
| | - Leila Williams
- Department of Melanoma Medical Oncology Unit 904, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX, 77030, USA
| | - Seram Devi
- Department of Melanoma Medical Oncology Unit 904, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX, 77030, USA
| | - Emily Ashkin
- Department of Melanoma Medical Oncology Unit 904, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX, 77030, USA
| | - Chunyu Xu
- Department of Melanoma Medical Oncology Unit 904, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX, 77030, USA
| | - Lu Huang
- Department of Melanoma Medical Oncology Unit 904, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX, 77030, USA
| | - Minying Zhang
- Department of Melanoma Medical Oncology Unit 904, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX, 77030, USA
| | - Amjad H Talukder
- Department of Melanoma Medical Oncology Unit 904, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX, 77030, USA
| | - Satyendra C Tripathi
- Department of Clinical Cancer Prevention Unit 1013, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX, 77030, USA
| | - Hiep Khong
- Department of Melanoma Medical Oncology Unit 904, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX, 77030, USA
| | - Nikunj Satani
- Cancer Imaging Systems Unit 1907, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX, 77030, USA
| | - Florian L Muller
- Cancer Imaging Systems Unit 1907, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX, 77030, USA
| | - Jason Roszik
- Department of Melanoma Medical Oncology Unit 904, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX, 77030, USA
| | - Timothy Heffernan
- Institute for Applied Cancer Sciences Unit 1956, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX, 77030, USA
| | - James P Allison
- Department of Immunology Unit 901, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX, 77030, USA
| | - Gregory Lizee
- Department of Melanoma Medical Oncology Unit 904, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX, 77030, USA
| | - Sam M Hanash
- Department of Clinical Cancer Prevention Unit 1013, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX, 77030, USA
| | - David Proia
- Synta Pharmaceuticals Inc., 45 Hartwell Avenue, Lexington, MA, 02421, USA
| | - Rodabe Amaria
- Department of Melanoma Medical Oncology Unit 904, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX, 77030, USA
| | - R Eric Davis
- Department of Lymphoma/Myeloma Unit 903, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX, 77030, USA
| | - Patrick Hwu
- Department of Melanoma Medical Oncology Unit 904, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX, 77030, USA.
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11
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de Graaff MA, Malu S, Guardiola I, Kruisselbrink AB, de Jong Y, Corver WE, Gelderblom H, Hwu P, Nielsen TO, Lazar AJ, Somaiah N, Bovée JVMG. High-Throughput Screening of Myxoid Liposarcoma Cell Lines: Survivin Is Essential for Tumor Growth. Transl Oncol 2017; 10:546-554. [PMID: 28654818 PMCID: PMC5487254 DOI: 10.1016/j.tranon.2017.05.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Revised: 05/17/2017] [Accepted: 05/22/2017] [Indexed: 02/07/2023] Open
Abstract
Myxoid liposarcoma (MLS) is a soft tissue sarcoma characterized by a recurrent t(12;16) translocation. Although tumors are initially radio- and chemosensitive, the management of inoperable or metastatic MLS can be challenging. Therefore, our aim was to identify novel targets for systemic therapy. We performed an in vitro high-throughput drug screen using three MLS cell lines (402091, 1765092, DL-221), which were treated with 273 different drugs at four different concentrations. Cell lines and tissue microarrays were used for validation. As expected, all cell lines revealed a strong growth inhibition to conventional chemotherapeutic agents, such as anthracyclines and taxanes. A good response was observed to compounds interfering with Src and the mTOR pathway, which are known to be affected in these tumors. Moreover, BIRC5 was important for MLS survival because a strong inhibitory effect was seen at low concentration using the survivin inhibitor YM155, and siRNA for BIRC5 decreased cell viability. Immunohistochemistry revealed abundant expression of survivin restricted to the nucleus in all 32 tested primary tumor specimens. Inhibition of survivin in 402-91 and 1765-92 by YM155 increased the percentage S-phase but did not induce apoptosis, which warrants further investigation before application in the treatment of metastatic MLS. Thus, using a 273-compound drug screen, we confirmed previously identified targets (mTOR, Src) in MLS and demonstrate survivin as essential for MLS survival.
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Affiliation(s)
- Marieke A de Graaff
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands
| | - Shruti Malu
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Irma Guardiola
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | - Yvonne de Jong
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands
| | - Willem E Corver
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands
| | - H Gelderblom
- Department of Medical Oncology, Leiden University Medical Center, Leiden, the Netherlands
| | - Patrick Hwu
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Torsten O Nielsen
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Alexander J Lazar
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Neeta Somaiah
- Department of Sarcoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Judith V M G Bovée
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands.
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12
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McKenzie JA, Mbofung RM, Malu S, Amaria RN, Ashkin EL, Devi SN, Peng W, Williams LJ, Davis RE, Roszik J, Tieu TN, Heffernan T, Hwu P. Abstract B110: Topoisomerase I inhibitors enhance efficacy of immunotherapy through a p53 regulatory pathway. Cancer Immunol Res 2016. [DOI: 10.1158/2326-6066.imm2016-b110] [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
Cancer immunotherapy has transformed the treatment landscape for a number of cancer patients, with some achieving durable and long lasting clinical benefit. Cancer immunotherapy engages and intensifies the host immune response to attack and kill tumor cells. However, as evidenced by the heterogeneous response to immunotherapy, tumor cells have evolved a host of known and unknown mechanisms to evade, inhibit or supersede the immune response. Consequently, scientists and clinicians are unable to accurately predict which patients will respond, or how well they will respond to cancer immunotherapy.To address this shortfall, we have asked the question of how we can modulate tumor cells in order to make them more amenable to immunotherapy, thereby increasing its efficacy. We approached this question by conducting a high throughput drug screen of 850 compounds, to identify bioactive drugs that can increase T cell mediated killing of tumor cells. The goal here is to develop rational combination treatment strategies involving T cell based cancer immunotherapy that will increase the breadth and depth of the clinical response to cancer immunotherapy. One of three top hits from the screen was Topoisomerase I (Top1) inhibitors including irinotecan, topotecan, and camptothecin. We then utilized multiple patient-derived cell lines in an in vitro cytotoxicity assay to validate that treatment of melanoma tumor cells with a Top1 inhibitor, before incubation with their autologous tumor infiltrating lymphocytes (TILs) results in a synergistic increase in T cell mediated killing of tumor cells.These findings were further corroborated in a pre-clinical mouse model, where we found that tumor-bearing mice treated with a combination of a clinically relevant Top1 inhibitor nal-IRI (nano-liposomal irinotecan) and an anti-PD-L1 antibody, showed enhanced tumor regression compared to mice treated with either single agent (mean tumor volume: combo vs nal-IRI vs α-PDL1 = 40.04 ± 5.66 vs 136.30 ± 28.96 vs 373.04 ± 23.96 mm3 respectively, on day 21 after tumor inoculation, p < 0.0001). Significantly longer survival was also achieved in tumor-bearing mice treated with the combination in comparison to cohorts treated with either single agent. To investigate the molecular changes being mediated by Top1 inhibitors in the tumor cells, we conducted gene expression analysis on Top1 inhibitor-treated tumor cells. One striking gene expression change in Top1 inhibitor-treated tumor cells was an upregulation of a number of genes known to be functionally important for p53 signaling including TP53INP1 (Teap). We then focused on the functional relevance of Teap to the increased T cell mediated killing of Top1 inhibitor-treated melanoma cells. Overexpression of Teap in melanoma cells resulted in increased T cell mediated killing, recapitulating the phenotype observed in Top1 inhibitor-treated melanoma cells. Complementary to this, silencing of Teap via shRNA in melanoma cells, inhibited T cell mediated killing of Top1 inhibitor-treated cells, indicating that the enhancement of T cell mediated killing observed in Top1 inhibitor-treated cells is dependent on the p53 regulatory gene Teap. These results support our goal of developing combinations involving T cell based cancer immunotherapy to improve therapeutic efficacy in cancer patients. We have demonstrated that Top1 inhibitors can be effectively combined with T cell based cancer immunotherapy. The results are also indicative of a role for p53 signaling in regulating response to T cell based immunotherapy. By understanding the molecular mechanisms in the tumor that can dictate response or resistance to immunotherapy, we can develop a more comprehensive picture of the cancer immunity response cycle and develop more effective strategies to combat not only melanoma, but also other tumor types where immunotherapy is not yet applicable.
Citation Format: Jodi A. McKenzie, Rina M. Mbofung, Shruti Malu, Rodabe N. Amaria, Emily L. Ashkin, Seram N. Devi, Weiyi Peng, Leila J. Williams, Richard E. Davis, Jason Roszik, Trang N. Tieu, Timothy Heffernan, Patrick Hwu. Topoisomerase I inhibitors enhance efficacy of immunotherapy through a p53 regulatory pathway [abstract]. In: Proceedings of the Second CRI-CIMT-EATI-AACR International Cancer Immunotherapy Conference: Translating Science into Survival; 2016 Sept 25-28; New York, NY. Philadelphia (PA): AACR; Cancer Immunol Res 2016;4(11 Suppl):Abstract nr B110.
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Affiliation(s)
| | | | | | | | | | - Seram N. Devi
- 1University of Texas MD Anderson Cancer Center, Houston, TX
| | - Weiyi Peng
- 1University of Texas MD Anderson Cancer Center, Houston, TX
| | | | | | - Jason Roszik
- 1University of Texas MD Anderson Cancer Center, Houston, TX
| | - Trang N. Tieu
- 1University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Patrick Hwu
- 1University of Texas MD Anderson Cancer Center, Houston, TX
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Williams L, Malu S, McKenzie J, Mbofung R, Roszik J, Hwu P. Abstract B118: Using a high throughput T-cell cytotoxicity assay to develop combination strategies for immunotherapy. Cancer Immunol Res 2016. [DOI: 10.1158/2326-6066.imm2016-b118] [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
T-cells play a critical role in cancer immunosurveillance and control. As such, there has been a recent emergence of T cell based immunotherapies with durable clinical outcomes. These include the immune checkpoint inhibitors Ipilimumab (anti-CTLA-4) and Nivolumab (anti-PD-1), and adoptive cell therapy, which have conferred clinical response rates of up to 50%. Despite these encouraging outcomes, there is still a large cohort of patients for which these treatments are currently not applicable. They are either inherently resistant to or acquire resistance to immunotherapy. As such, understanding mechanisms of resistance to immune response and ascertaining efficacious therapy combinations is important in overcoming immune-resistance and developing novel treatment regimens.
To address this need we performed preliminary screening of about 850 different bioactive compounds (Selleckem) to find candidate drugs that could modulate the sensitivity of tumor cells to T- cell mediated killing, using an established protocol for an in vitro T-cell mediated cytotoxicity screen. We hypothesized that either tumor cells treated with different compounds will increase or decrease their sensitivity to T cell mediated killing, and compounds that increase T cell killing can be used in combination with immunotherapy. Using patient-derived melanoma tumor cells and their autologous tumor infiltrating T cells (TILs), we assessed the increase or decrease of T cell killing of tumor cells following treatment with the test compounds via intracellular detection of active caspase-3 by flow cytometry in a 96-well format. This initial screen identified Heat shock protein 90 (Hsp90), Aurora Kinase and Topoisomerase I inhibitors as enhancers of T cell mediated killing, and studies to understand their mechanisms of action are currently underway.
However, as this screening process is very time-intensive, we have increased the efficiency and feasibility of this screen by miniaturizing the workflow. This work highlights the development and initial findings of the screening method that is performed in 384-well plates. This format allows for a larger library of compounds, with a greater drug concentration range, and for more autologous tumor and T-cell pairs to be screened within a shorter time. The miniaturized assay also utilises robotics to streamline and increase output. Additionally, by understanding the signaling pathways and molecular factors that regulate tumor response to T cell mediated killing, we can translate these findings applicable to other cancer. This project aims to discover novel compounds that work synergistically with T-cell mediated tumor cell cytotoxicity, understand their mechanism of action and how the inhibited pathways contribute to resistance to immunotherapy and as a result better inform combination strategies with immunotherapy for clinical use.
Citation Format: Leila Williams, Shruti Malu, Jodi McKenzie, Rina Mbofung, Jason Roszik, Patrick Hwu. Using a high throughput T-cell cytotoxicity assay to develop combination strategies for immunotherapy [abstract]. In: Proceedings of the Second CRI-CIMT-EATI-AACR International Cancer Immunotherapy Conference: Translating Science into Survival; 2016 Sept 25-28; New York, NY. Philadelphia (PA): AACR; Cancer Immunol Res 2016;4(11 Suppl):Abstract nr B118.
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Mbofung RM, McKenzie JA, Malu S, Liu C, Peng W, Kuiatse I, Williams L, Devi S, Wang Z, Tieu T, Heffernan T, Davis RE, Amaria R, Hwu P. Abstract B105: HSP90 inhibitor, ganetespib, enhances responses to cancer immunotherapy through increased expression of interferon response genes. Cancer Immunol Res 2016. [DOI: 10.1158/2326-6066.imm2016-b105] [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
Recently, T cell based immunotherapies have moved to the forefront of cancer immunotherapy with the success of Adoptive T cell therapy (ACT) and Immune checkpoint blockade. ACT, where patients are treated with tumor infiltrating T cells (TILs), conferred a clinical response rate of ∼50%. Treatment with anti-CTLA4 therapy, Ipilimumab, conferred response rates of 10-20%, greatly improving the overall survival of patients with advanced melanoma. Despite the encouraging outcomes, there are relatively low response rates coupled with the delay of weeks to months before tumor shrinkage can be appreciated. Thus, understanding mechanisms of resistance to immune therapies, to improve response rates, shorten time to treatment effect and developing predictive biomarkers of response are vital to the care of melanoma patients. In order to identify possible resistance mechanisms to immunotherapy, a high-throughput in vitro screen with 850 different bio-active compounds (Selleckchem), was designed to search for agents that could either increase or decrease the resistance of melanoma tumor cells to T cell mediated killing. Paired patient derived human melanoma tumor samples and TILs were used to assess which compounds when used to treat the melanoma cell lines can enhance the cytotoxic activity of the TILs against the paired melanoma sample, using a flow cytometry based assay in which active caspase 3 was used as a read out of apoptosis. We identified heat shock protein 90 (HSP90) inhibitors amongst the top compounds that improved T cell mediated cytotoxicity of treated tumor cells. We show that treatment with the HSP90 inhibitor ganetespib (Synta) greatly improves T cell mediated cytotoxicity of human cancer cells lines in vitro. Furthermore, in vivo murine studies using the MC38/gp100 tumor model show that ganestespib in combination with anti-CTLA4, resulted in superior antitumor effect and survival compared to either treatment alone (Average tumor volume at day 21 of treatment: Vehicle 294.3mm3, α-CTLA4 193 mm3, Ganetespib 237.5 mm3 and Ganetespib + α-CTLA4 105.8 mm3, P < 0.0001). Microarray analysis of human cell lines treated with ganetespib in vitro revealed an increase in interferon response genes including IFIT1, IFIT2, IFIT3. We confirmed these findings with quantitative real time PCR and western blot analyses and found IFIT1, IFIT2 and IFIT3 to be consistently upregulated across multiple melanoma cell lines following treatment with ganetespib. We next sought to verify the importance of the IFIT genes in the synergy observed between ganetespib treatment and T cell killing. First, we overexpressed IFIT1, IFIT2 and IFIT3 in human melanoma cell lines to recapitulate the improved sensitivity of the human melanoma cell lines to T cell killing following treatment with ganetespib. We then co-cultured these cells with their autologous T cells and found that overexpressing IFIT1, IFIT2 and IFIT3 mimicked the effects of ganetespib by increasing the sensitivity to T cell killing over the GFP control. On the other hand, silencing IFIT1, IFIT2 and IFIT3 simultaneously, abrogated the synergy between ganetespib and T cell killing. We are further elucidating the role of these genes in lowering the apoptotic threshold of cancer cells and contributing to the synergy of ganetespib and immunotherapy. This will enable the emergence of a new combination therapy of HSP90 inhibitors and anti-CTLA4 for the treatment of melanoma patients that will increase the percentage of patients responding to immunotherapy and achieving long term responses.
Citation Format: Rina M. Mbofung, Jodi A. McKenzie, Shruti Malu, Chengwen Liu, Weiyi Peng, Isere Kuiatse, Leila Williams, Seram Devi, Zhe Wang, Trang Tieu, Tim Heffernan, Richard E. Davis, Rodabe Amaria, Patrick Hwu. HSP90 inhibitor, ganetespib, enhances responses to cancer immunotherapy through increased expression of interferon response genes [abstract]. In: Proceedings of the Second CRI-CIMT-EATI-AACR International Cancer Immunotherapy Conference: Translating Science into Survival; 2016 Sept 25-28; New York, NY. Philadelphia (PA): AACR; Cancer Immunol Res 2016;4(11 Suppl):Abstract nr B105.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Zhe Wang
- 1MD Anderson Cancer Center, Houston, TX
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Peng W, Chen JQ, Liu C, Malu S, Creasy C, Tetzlaff M, Xu C, McKenzie J, Zhang C, Liang X, Williams L, Deng W, Chen G, Mbofung R, Lazar A, Torres-Cabala C, Cooper Z, Chen PL, Tieu T, Spranger S, Yu X, Bernatchez C, Forget MA, Haymaker C, Amaria R, McQuade J, Glitza I, Cascone T, Li H, Kwong L, Heffernan T, Hu J, Bassett R, Bosenberg M, Woodman S, Overwijk W, Lizée G, Roszik J, Gajewski T, Wargo J, Gershenwald J, Radvanyi L, Davies M, Hwu P. Abstract 4363: Loss of PTEN promotes resistance to T cell-mediated immunotherapy. Immunology 2016. [DOI: 10.1158/1538-7445.am2016-4363] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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Williams L, Malu S, McKenzie J, Mbofung R, Forget MA, Bernatchez C, Hwu P. Abstract 4010: Identification of novel targeted and immunotherapy combinations by a high throughput assay of T cell-mediated cytotoxicity. Cancer Res 2016. [DOI: 10.1158/1538-7445.am2016-4010] [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
Melanoma is the major cause of skin cancer-related deaths. However, the recent emergence of immune checkpoint inhibitors such as Ipilimumab (anti-CTLA-4) and Nivolumab (anti-PD-1), and adoptive cell therapy, using tumor infiltrating lymphocytes (TILs), has improved clinical outcomes and produced response rates of approximately 50%. Despite the progress made in melanoma immunotherapy, there is a large cohort of patients for which these treatments are currently not applicable. They are either inherently resistant to or acquire resistance to immunotherapy. As such, understanding mechanisms of resistance to immune response and ascertaining efficacious therapy combinations is important in overcoming immunoresistance and developing novel treatment regimens.
As proof of principle, preliminary work using a unique protocol for an in vitro T-cell mediated cytotoxicity screen was established. In this assay, intracellular staining of active caspase-3 in tumor cells, a marker of apoptosis, is measured by flow cytometry in a 96-well format. Using patient-derived tumor and TIL pairs, a screen of 850 compounds was performed to find candidate drugs that could modulate the sensitivity of tumor cells to T- cell mediated killing. Initial screens identified classes of compounds that inhibit Heat shock protein 90 (Hsp90), Aurora Kinase and Topoisomerase I, and studies to understand their mechanisms of action are currently underway.
However, as this screening process is very time-intensive, we are currently increasing the efficiency and feasibility of this screen by miniaturizing this workflow. This work presents the development of a screening method that is performed in a 384-well format, with a greater drug concentration range, and utilizing robotics to streamline and increase output. With this, we can specifically identify novel targeted and immunotherapy combinations that may be used in the clinic to treat melanoma. Additionally, by understanding the signaling pathways and molecular factors that regulate tumor response to T cell mediated killing, we can translate these findings into making immune-based cancer therapies applicable to other tumor types. This project aims to discover novel compounds that work synergistically with T-cell mediated tumor cell cytotoxicity, understand their mechanism of action and how they contribute to resistance and as a result identify innovative immune-based therapies that can be translated into clinical use.
Citation Format: Leila Williams, Shruti Malu, Jodi McKenzie, Rina Mbofung, Marie-Andree Forget, Chantale Bernatchez, Patrick Hwu. Identification of novel targeted and immunotherapy combinations by a high throughput assay of T cell-mediated cytotoxicity. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 4010.
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Wang Z, Malu S, Peng W, McKenzie J, Mbofung R, Williams L, Seth S, Heffernan T, Hwu P. Abstract 1441: Systems-level interrogation of resistance mechanisms to immunotherapy through pooled shRNA screens. Cancer Res 2016. [DOI: 10.1158/1538-7445.am2016-1441] [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
Despite the impressive clinical efficacy of immunotherapy in some patients, many still do not respond or progress following an initial response. The molecular mechanisms underlying the tumor resistance in those non-responders remain largely undefined. To address this issue, we set out to perform high-throughput unbiased pooled shRNA screens to identify critical genes that confer immune resistance. Patient-derived melanoma cells were transduced with barcoded pooled lentiviral shRNA libraries that targeted the human kinome, followed by exposure to cytotoxicity mediated by autologous tumor infiltrating lymphocytes. Tumor cells were then subject to genomic deep sequencing and integrated analysis to identify depleted barcodes and corresponding genes. One identified candidate of particular interest is Aurora Kinase A (AURKA), a cell cycle regulator that has previously been shown to contribute to tumorigenesis and correlate with poor prognosis for cancer patients. Importantly, our independent screening with a bioactive compound library also implicated Aurora Kinase as an immune resistance candidate against T cell immunotherapy. Further studies showed that suppression of Aurora kinase activity with a pan inhibitor - AMG900, exhibited a synergistic cytotoxic effect with tumor infiltrating lymphocyte-mediated killing on autologous tumor cells from patients. Furthermore, our Nanostring analysis of tumor biopsies from patients that received adoptive T cell therapy revealed significantly increased expression of AURKA in tumors from non-responding patient when compared with responder counterparts. These results have substantiated the validity of our pooled shRNA screening platform. Further investigations are ongoing to elucidate the underpinnings of Aurora kinase-mediated tumor resistance to immunotherapy and to functionally and physiologically validate other putative targets we have identified.
Citation Format: Zhe Wang, Shruti Malu, Weiyi Peng, Jodi McKenzie, Rina Mbofung, Leila Williams, Sahil Seth, Tim Heffernan, Patrick Hwu. Systems-level interrogation of resistance mechanisms to immunotherapy through pooled shRNA screens. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1441.
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Affiliation(s)
- Zhe Wang
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Shruti Malu
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Weiyi Peng
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Jodi McKenzie
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Rina Mbofung
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Leila Williams
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Sahil Seth
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Tim Heffernan
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Patrick Hwu
- The University of Texas MD Anderson Cancer Center, Houston, TX
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Mbofung RM, McKenzie JA, Malu S, Liu C, Williams L, Peng W, Wang Z, Tripathi S, Tieu T, Zhao S, Devi S, Kuiatse I, Ashkin E, Bailey L, Roszik J, Hanash S, Heffernan T, Davis RE, Amaria RN, Hwu P. Abstract 4360: Inhibition of HSP90 enhances T cell-mediated antitumor immune responses through expression of interferon-alpha response Genes. Cancer Res 2016. [DOI: 10.1158/1538-7445.am2016-4360] [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
Recently, T cell based immunotherapies have moved to the forefront of cancer immunotherapy with the success of Adoptive T cell therapy (ACT) and Immune checkpoint blockade. ACT, where patients are treated with tumor infiltrating T cells (TILs), conferred a clinical response rate of ∼50%. Treatment with anti-CTLA4 therapy, Ipilimumab, conferred response rates of 10-20%, greatly improving the overall survival of patients with advanced melanoma. Despite the encouraging outcomes, there are relatively low response rates coupled with the delay of weeks to months before tumor shrinkage can be appreciated. Thus, understanding mechanisms of resistance to immune therapies, to improve response rates, shorten time to treatment effect and developing predictive biomarkers of response are vital to the care of melanoma patients. In order to identify possible resistance mechanisms to immunotherapy, a high-throughput in vitro screen with 850 different bio-active compounds (Selleckchem), was designed to search for agents that could either increase or decrease the resistance of melanoma tumor cells to T cell mediated killing. Paired tumor samples and TILs from melanoma patients were used to assess which compounds when used to treat the melanoma cell lines can enhance the cytotoxic activity of the TILs against the paired melanoma sample, using a flow cytometry based assay in which active caspase 3 was used as a read out of apoptosis. We identified heat shock protein 90 (HSP90) inhibitors amongst compounds that improved T cell mediated cytotoxicity. We show that treatment with the HSP90 inhibitor ganetespib (Synta) greatly improves T cell mediated cytotoxicity of both human and murine cancer cells lines in vitro. Furthermore, in vivo murine studies using the MC38/gp100 tumor model show that ganestespib in combination with anti-CTLA4, resulted in superior antitumor effect and survival compared to either treatment alone (Average tumor volume at day 21 of treatment: Vehicle 294.3mm3, α-CTLA4 193 mm3, Ganetespib 237.5 mm3 and Ganetespib + α-CTLA4 105.8 mm3, P < 0.0001). Microarray analysis of human cell lines treated with ganetespib in vitro revealed an increase in interferon alpha (IFN-α) response genes including IFIT1, IFIT2, IFIT3 and IFIH1. Silencing IFIT2 abrogated the synergy observed with ganetespib treatment and T cell mediated killing, suggesting that the IFN-α response pathway plays an important role in this combination therapy. We are further elucidating the role of these genes in the synergy observed. This will enable the emergence of a new combination therapy of HSP90 inhibitors and anti-CTLA4 for the treatment of melanoma patients that will increase the percentage of patients responding to immunotherapy and achieving long term responses.
Citation Format: Rina M. Mbofung, Jodi A. McKenzie, Shruti Malu, Chengwen Liu, Leila Williams, Weiyi Peng, Zhe Wang, Satyendra Tripathi, Trang Tieu, Shuping Zhao, Seram Devi, Isere Kuiatse, Emily Ashkin, Leah Bailey, Jason Roszik, Samir Hanash, Timothy Heffernan, Richard E. Davis, Rodabe N. Amaria, Patrick Hwu. Inhibition of HSP90 enhances T cell-mediated antitumor immune responses through expression of interferon-alpha response Genes. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 4360.
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Affiliation(s)
| | | | | | | | | | | | - Zhe Wang
- 1MD Anderson Cancer Center, Houston, TX
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McKenzie JA, Mbofung RM, Malu S, Amaria RN, Davis RE, Zhang L, Tieu TN, Heffernan TP, Hwu P. Abstract 4002: Enhancing the antitumor efficacy of immunotherapy by using the topoisomerase I inhibitor MM398. Cancer Res 2016. [DOI: 10.1158/1538-7445.am2016-4002] [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
Melanoma is a highly aggressive form of skin cancer, whose rates of morbidity and mortality are increasing. The development of immunotherapies like anti-PDL1 and anti-CTLA4 antibodies has resulted in fundamental advances in the treatment of some cancers. However, long lasting responses are only observed in a subset of immunotherapy-treated patients. This shortfall highlights the need for a better understanding of the molecular mechanisms that govern tumor response to immunotherapy.
To address this need, autologous patient-derived tumor cell lines and tumor infiltrating lymphocytes (TILs) were utilized in an in vitro high throughput screen, to identify compounds that increase the sensitivity of melanoma cells to T cell mediated cytotoxicity. The screen consisted of an 850 compound library. One group of compounds that was most able to enhance T cell killing of melanoma cells was topoisomerase I (Top1) inhibitors such as topotecan and irinotecan.
Our results indicate that treatment of melanoma cells with a Top1 inhibitor prior to exposure to autologous T cells produced a synergistic increase in tumor cell death, as measured by intracellular staining of activated caspase 3. We have also recapitulated this finding in an in vivo model, where a better anti-tumor effect was observed in tumor bearing mice treated with an antibody against the co-inhibitory molecule PDL1 in combination with MM398 (nanoliposomal irinotecan), than in cohorts treated with either α-PDL1 or Top1 inhibitor alone. These findings suggest synergism between Top1 inhibitors and immune-based therapies in the treatment of melanoma.
Molecular changes elicited by inhibition of Top1 are now being investigated to identify the factors that mediate the effect of Top1 inhibitors on T cell-mediated killing of melanoma. We have identified a p53-driven gene signature in Top1 inhibitor-treated melanoma cell lines and are investigating the functional relevance of Tumor Protein p53 Inducible Nuclear Protein 1 (TP53INP1) in mediating increased T cell killing of Top1 inhibitor-treated melanoma cells. Our results indicate that TP53INP1 is a critical component of this apoptotic response, as overexpression of TP53INP1 in melanoma cells increased their susceptibility to T cell mediated cytotoxicity. Complementary to this observation, we have also found that knockdown of TP53INP1 by shRNA, impedes the sensitivity of Top1 inhibitor-treated melanoma cells to T cell mediated killing.
Understanding how Top1 inhibitors enhance melanoma killing by immunotherapy will allow for the development of predictive biomarkers, and also augment immune-based therapeutic strategies to ensure durable responses in a larger population of melanoma patients. By using melanoma as a model disease system, we can gain valuable insights into the dynamics of cancer immune response that may be applied to other cancers where effective treatment strategies are also lacking.
Citation Format: Jodi A. McKenzie, Rina M. Mbofung, Shruti Malu, Rodabe N. Amaria, Richard E. Davis, Li Zhang, Trang N. Tieu, Tim P. Heffernan, Patrick Hwu. Enhancing the antitumor efficacy of immunotherapy by using the topoisomerase I inhibitor MM398. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 4002.
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Affiliation(s)
| | - Rina M. Mbofung
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Shruti Malu
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | | | - Li Zhang
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Trang N. Tieu
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Patrick Hwu
- The University of Texas MD Anderson Cancer Center, Houston, TX
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McKenzie JA, Mbofung RM, Malu S, Hwu P. Abstract B152: Increasing the antitumor efficacy of immunotherapy in melanoma by using topoisomerase I inhibitors. Cancer Immunol Res 2016. [DOI: 10.1158/2326-6074.cricimteatiaacr15-b152] [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
Melanoma is a highly aggressive form of skin cancer, whose rates of morbidity and mortality are continuously increasing. The development of immunotherapeutic agents like anti-PDL1 and anti-CTLA4 antibodies has resulted in fundamental advances in the treatment of melanoma. However, long lasting responses are only observed in a small subset of immunotherapy-treated melanoma patients. This shortfall highlights the need for a better understanding of the molecular mechanisms that govern tumor sensitivity or resistance to immunotherapy. To address this need, autologous patient-derived tumor cell lines and tumor infiltrating lymphocytes (TILs) were utilized in an in vitro activated caspase 3-based high-throughput screen, to identify compounds that increase the sensitivity of melanoma cells to T-cell mediated cytotoxicity. The screen consisted of a library of 850 bioactive compounds. One group of compounds that was most able to enhance T-cell killing of melanoma cells was topoisomerase I (Top1) inhibitors including: topotecan, and irinotecan.
Topoisomerases are a family of DNA enzymes, which are involved in unwinding DNA and relieving torsional strain during replication and transcription. Our results indicate that treatment of melanoma tumor cells with a Top1 inhibitor prior to exposure to autologous T cells, produced a synergistic increase in tumor cell death, as measured by intracellular staining of activated caspase 3, and computed using CalcuSyn. We have also recapitulated this finding in an in vivo model, where a better anti-tumor effect was observed in tumor- bearing mice treated with an antibody against the co-inhibitory molecule Programmed Death Ligand 1 (PDL1) in combination with a nanoparticle liposomal formulation of irinotecan, than in cohorts treated with either antibody or drug alone. These findings suggest synergism between Top1 inhibitors and immune-based therapies in the treatment of melanoma.
Genomic and proteomic changes elicited by inhibition of Top1 are now being investigated to identify the molecular factors that mediate the effect of Top1 inhibitors on T cell-mediated killing of melanoma. Our goal is to identify molecular changes mediated by Top1 inhibition in melanoma tumor cells, and/or the tumor microenvironment, that relieves immunosuppression and potentiates the activity of cytotoxic T cell-based immunotherapy.
Understanding how Top1 inhibitors enhance melanoma killing by immunotherapy will allow for the development of predictive biomarkers, and also augment immune-based therapeutic strategies to ensure durable responses in a larger population of melanoma patients. By using melanoma as a model disease system, we can gain valuable insights into the dynamics of cancer immune response that may be applied to other cancers where effective treatment strategies are also lacking.
Citation Format: Jodi A. McKenzie, Rina M. Mbofung, Shruti Malu, Patrick Hwu. Increasing the antitumor efficacy of immunotherapy in melanoma by using topoisomerase I inhibitors. [abstract]. In: Proceedings of the CRI-CIMT-EATI-AACR Inaugural International Cancer Immunotherapy Conference: Translating Science into Survival; September 16-19, 2015; New York, NY. Philadelphia (PA): AACR; Cancer Immunol Res 2016;4(1 Suppl):Abstract nr B152.
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Affiliation(s)
| | - Rina M. Mbofung
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Shruti Malu
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Patrick Hwu
- The University of Texas MD Anderson Cancer Center, Houston, TX
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Peng W, Chen JQ, Liu C, Malu S, Creasy C, Tetzlaff MT, Xu C, McKenzie JA, Zhang C, Liang X, Williams LJ, Deng W, Chen G, Mbofung R, Lazar AJ, Torres-Cabala CA, Cooper ZA, Chen PL, Tieu TN, Spranger S, Yu X, Bernatchez C, Forget MA, Haymaker C, Amaria R, McQuade JL, Glitza IC, Cascone T, Li HS, Kwong LN, Heffernan TP, Hu J, Bassett RL, Bosenberg MW, Woodman SE, Overwijk WW, Lizée G, Roszik J, Gajewski TF, Wargo JA, Gershenwald JE, Radvanyi L, Davies MA, Hwu P. Loss of PTEN Promotes Resistance to T Cell-Mediated Immunotherapy. Cancer Discov 2015. [PMID: 26645196 DOI: 10.1158/2159-8290.cd-15-0283.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
UNLABELLED T cell-mediated immunotherapies are promising cancer treatments. However, most patients still fail to respond to these therapies. The molecular determinants of immune resistance are poorly understood. We show that loss of PTEN in tumor cells in preclinical models of melanoma inhibits T cell-mediated tumor killing and decreases T-cell trafficking into tumors. In patients, PTEN loss correlates with decreased T-cell infiltration at tumor sites, reduced likelihood of successful T-cell expansion from resected tumors, and inferior outcomes with PD-1 inhibitor therapy. PTEN loss in tumor cells increased the expression of immunosuppressive cytokines, resulting in decreased T-cell infiltration in tumors, and inhibited autophagy, which decreased T cell-mediated cell death. Treatment with a selective PI3Kβ inhibitor improved the efficacy of both anti-PD-1 and anti-CTLA-4 antibodies in murine models. Together, these findings demonstrate that PTEN loss promotes immune resistance and support the rationale to explore combinations of immunotherapies and PI3K-AKT pathway inhibitors. SIGNIFICANCE This study adds to the growing evidence that oncogenic pathways in tumors can promote resistance to the antitumor immune response. As PTEN loss and PI3K-AKT pathway activation occur in multiple tumor types, the results support the rationale to further evaluate combinatorial strategies targeting the PI3K-AKT pathway to increase the efficacy of immunotherapy.
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Affiliation(s)
- Weiyi Peng
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jie Qing Chen
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Chengwen Liu
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Shruti Malu
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Caitlin Creasy
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Michael T Tetzlaff
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas. Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Chunyu Xu
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jodi A McKenzie
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Chunlei Zhang
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Xiaoxuan Liang
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Leila J Williams
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Wanleng Deng
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Guo Chen
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Rina Mbofung
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Alexander J Lazar
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Carlos A Torres-Cabala
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Zachary A Cooper
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas. Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Pei-Ling Chen
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Trang N Tieu
- Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Stefani Spranger
- Department of Pathology, University of Chicago, Chicago, Illinois
| | - Xiaoxing Yu
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Chantale Bernatchez
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Marie-Andree Forget
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Cara Haymaker
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Rodabe Amaria
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jennifer L McQuade
- Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Isabella C Glitza
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Tina Cascone
- Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Haiyan S Li
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Lawrence N Kwong
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Timothy P Heffernan
- Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jianhua Hu
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Roland L Bassett
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Marcus W Bosenberg
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut
| | - Scott E Woodman
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Willem W Overwijk
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Gregory Lizée
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jason Roszik
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas. Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | - Jennifer A Wargo
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas. Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jeffrey E Gershenwald
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Laszlo Radvanyi
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Michael A Davies
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas.
| | - Patrick Hwu
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas.
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Peng W, Chen JQ, Liu C, Malu S, Creasy C, Tetzlaff MT, Xu C, McKenzie JA, Zhang C, Liang X, Williams LJ, Deng W, Chen G, Mbofung R, Lazar AJ, Torres-Cabala CA, Cooper ZA, Chen PL, Tieu TN, Spranger S, Yu X, Bernatchez C, Forget MA, Haymaker C, Amaria R, McQuade JL, Glitza IC, Cascone T, Li HS, Kwong LN, Heffernan TP, Hu J, Bassett RL, Bosenberg MW, Woodman SE, Overwijk WW, Lizée G, Roszik J, Gajewski TF, Wargo JA, Gershenwald JE, Radvanyi L, Davies MA, Hwu P. Loss of PTEN Promotes Resistance to T Cell-Mediated Immunotherapy. Cancer Discov 2015. [PMID: 26645196 DOI: 10.1158/2159?8290.cd?15?0283] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
UNLABELLED T cell-mediated immunotherapies are promising cancer treatments. However, most patients still fail to respond to these therapies. The molecular determinants of immune resistance are poorly understood. We show that loss of PTEN in tumor cells in preclinical models of melanoma inhibits T cell-mediated tumor killing and decreases T-cell trafficking into tumors. In patients, PTEN loss correlates with decreased T-cell infiltration at tumor sites, reduced likelihood of successful T-cell expansion from resected tumors, and inferior outcomes with PD-1 inhibitor therapy. PTEN loss in tumor cells increased the expression of immunosuppressive cytokines, resulting in decreased T-cell infiltration in tumors, and inhibited autophagy, which decreased T cell-mediated cell death. Treatment with a selective PI3Kβ inhibitor improved the efficacy of both anti-PD-1 and anti-CTLA-4 antibodies in murine models. Together, these findings demonstrate that PTEN loss promotes immune resistance and support the rationale to explore combinations of immunotherapies and PI3K-AKT pathway inhibitors. SIGNIFICANCE This study adds to the growing evidence that oncogenic pathways in tumors can promote resistance to the antitumor immune response. As PTEN loss and PI3K-AKT pathway activation occur in multiple tumor types, the results support the rationale to further evaluate combinatorial strategies targeting the PI3K-AKT pathway to increase the efficacy of immunotherapy.
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Affiliation(s)
- Weiyi Peng
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jie Qing Chen
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Chengwen Liu
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Shruti Malu
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Caitlin Creasy
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Michael T Tetzlaff
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas. Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Chunyu Xu
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jodi A McKenzie
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Chunlei Zhang
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Xiaoxuan Liang
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Leila J Williams
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Wanleng Deng
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Guo Chen
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Rina Mbofung
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Alexander J Lazar
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Carlos A Torres-Cabala
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Zachary A Cooper
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas. Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Pei-Ling Chen
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Trang N Tieu
- Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Stefani Spranger
- Department of Pathology, University of Chicago, Chicago, Illinois
| | - Xiaoxing Yu
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Chantale Bernatchez
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Marie-Andree Forget
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Cara Haymaker
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Rodabe Amaria
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jennifer L McQuade
- Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Isabella C Glitza
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Tina Cascone
- Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Haiyan S Li
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Lawrence N Kwong
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Timothy P Heffernan
- Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jianhua Hu
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Roland L Bassett
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Marcus W Bosenberg
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut
| | - Scott E Woodman
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Willem W Overwijk
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Gregory Lizée
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jason Roszik
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas. Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | - Jennifer A Wargo
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas. Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jeffrey E Gershenwald
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Laszlo Radvanyi
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Michael A Davies
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas.
| | - Patrick Hwu
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas.
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23
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Peng W, Chen JQ, Liu C, Malu S, Creasy C, Tetzlaff MT, Xu C, McKenzie JA, Zhang C, Liang X, Williams LJ, Deng W, Chen G, Mbofung R, Lazar AJ, Torres-Cabala CA, Cooper ZA, Chen PL, Tieu TN, Spranger S, Yu X, Bernatchez C, Forget MA, Haymaker C, Amaria R, McQuade JL, Glitza IC, Cascone T, Li HS, Kwong LN, Heffernan TP, Hu J, Bassett RL, Bosenberg MW, Woodman SE, Overwijk WW, Lizée G, Roszik J, Gajewski TF, Wargo JA, Gershenwald JE, Radvanyi L, Davies MA, Hwu P. Loss of PTEN Promotes Resistance to T Cell-Mediated Immunotherapy. Cancer Discov 2015; 6:202-16. [PMID: 26645196 DOI: 10.1158/2159-8290.cd-15-0283] [Citation(s) in RCA: 1057] [Impact Index Per Article: 117.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 12/03/2015] [Indexed: 12/15/2022]
Abstract
UNLABELLED T cell-mediated immunotherapies are promising cancer treatments. However, most patients still fail to respond to these therapies. The molecular determinants of immune resistance are poorly understood. We show that loss of PTEN in tumor cells in preclinical models of melanoma inhibits T cell-mediated tumor killing and decreases T-cell trafficking into tumors. In patients, PTEN loss correlates with decreased T-cell infiltration at tumor sites, reduced likelihood of successful T-cell expansion from resected tumors, and inferior outcomes with PD-1 inhibitor therapy. PTEN loss in tumor cells increased the expression of immunosuppressive cytokines, resulting in decreased T-cell infiltration in tumors, and inhibited autophagy, which decreased T cell-mediated cell death. Treatment with a selective PI3Kβ inhibitor improved the efficacy of both anti-PD-1 and anti-CTLA-4 antibodies in murine models. Together, these findings demonstrate that PTEN loss promotes immune resistance and support the rationale to explore combinations of immunotherapies and PI3K-AKT pathway inhibitors. SIGNIFICANCE This study adds to the growing evidence that oncogenic pathways in tumors can promote resistance to the antitumor immune response. As PTEN loss and PI3K-AKT pathway activation occur in multiple tumor types, the results support the rationale to further evaluate combinatorial strategies targeting the PI3K-AKT pathway to increase the efficacy of immunotherapy.
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Affiliation(s)
- Weiyi Peng
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jie Qing Chen
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Chengwen Liu
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Shruti Malu
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Caitlin Creasy
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Michael T Tetzlaff
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas. Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Chunyu Xu
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jodi A McKenzie
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Chunlei Zhang
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Xiaoxuan Liang
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Leila J Williams
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Wanleng Deng
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Guo Chen
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Rina Mbofung
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Alexander J Lazar
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Carlos A Torres-Cabala
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Zachary A Cooper
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas. Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Pei-Ling Chen
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Trang N Tieu
- Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Stefani Spranger
- Department of Pathology, University of Chicago, Chicago, Illinois
| | - Xiaoxing Yu
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Chantale Bernatchez
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Marie-Andree Forget
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Cara Haymaker
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Rodabe Amaria
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jennifer L McQuade
- Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Isabella C Glitza
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Tina Cascone
- Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Haiyan S Li
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Lawrence N Kwong
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Timothy P Heffernan
- Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jianhua Hu
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Roland L Bassett
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Marcus W Bosenberg
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut
| | - Scott E Woodman
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Willem W Overwijk
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Gregory Lizée
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jason Roszik
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas. Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | - Jennifer A Wargo
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas. Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jeffrey E Gershenwald
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Laszlo Radvanyi
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Michael A Davies
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas.
| | - Patrick Hwu
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas.
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24
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Francis DB, Kozlov M, Chavez J, Chu J, Malu S, Hanna M, Cortes P. DNA Ligase IV regulates XRCC4 nuclear localization. DNA Repair (Amst) 2014; 21:36-42. [PMID: 24984242 DOI: 10.1016/j.dnarep.2014.05.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [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: 12/27/2013] [Revised: 05/22/2014] [Accepted: 05/29/2014] [Indexed: 11/17/2022]
Abstract
DNA Ligase IV, along with its interacting partner XRCC4, are essential for repairing DNA double strand breaks by non-homologous end joining (NHEJ). Together, they complete the final ligation step resolving the DNA break. Ligase IV is regulated by XRCC4 and XLF. However, the mechanism(s) by which Ligase IV control the NHEJ reaction and other NHEJ factor(s) remains poorly characterized. Here, we show that a C-terminal region of Ligase IV (aa 620-800), which encompasses a NLS, the BRCT I, and the XRCC4 interacting region (XIR), is essential for nuclear localization of its co-factor XRCC4. In Ligase IV deficient cells, XRCC4 showed deregulated localization remaining in the cytosol even after induction of DNA double strand breaks. DNA Ligase IV was also required for efficient localization of XLF into the nucleus. Additionally, human fibroblasts that harbor hypomorphic mutations within the Ligase IV gene displayed decreased levels of XRCC4 protein, implicating that DNA Ligase IV is also regulating XRCC4 stability. Our results provide evidence for a role of DNA Ligase IV in controlling the cellular localization and protein levels of XRCC4.
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Affiliation(s)
- Dailia B Francis
- Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States; Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States; Graduate School of Biological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States
| | - Mikhail Kozlov
- Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States; Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States
| | - Jose Chavez
- Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States; Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States
| | - Jennifer Chu
- Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States; Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States
| | - Shruti Malu
- Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States; Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States
| | - Mary Hanna
- Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States; Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States
| | - Patricia Cortes
- Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States; Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States; Graduate School of Biological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States.
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25
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Mbofung R, Peng W, Liu C, Xu C, Malu S, Yang Y, Ma W, Wang Z, Overwijk W, Davis E, Lee B, Hwu P. The role of transcription factor Runx2 in tumor infiltrating T cells. J Immunother Cancer 2013. [PMCID: PMC3990955 DOI: 10.1186/2051-1426-1-s1-p23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
- Rina Mbofung
- Graduate School of Biomedical Sciences, University of Texas Health Science Center at Houston, Houston, TX, USA,Melanoma Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Weiyi Peng
- Melanoma Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Chengwen Liu
- Melanoma Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Chunyu Xu
- Melanoma Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Shruti Malu
- Melanoma Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yan Yang
- Graduate School of Biomedical Sciences, University of Texas Health Science Center at Houston, Houston, TX, USA,Melanoma Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Wencai Ma
- Lymphoma and Myeloma, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Zhiqiang Wang
- Lymphoma and Myeloma, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Willem Overwijk
- Melanoma Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Eric Davis
- Lymphoma and Myeloma, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Brendan Lee
- Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Patrick Hwu
- Melanoma Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
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26
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Forget MA, Malu S, Liu H, Toth C, Maiti S, Kale C, Bernatchez C, Huls H, Wang E, Hwu P, Cooper LJ, Radvanyi LG. Genetically modified artificial antigen-presenting cells (aAPC) for expansion of melanoma tumor infiltrating lymphocytes with optimal properties for adoptive cell therapy. J Immunother Cancer 2013. [PMCID: PMC3990965 DOI: 10.1186/2051-1426-1-s1-p8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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27
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Malu S, Mbofung R, Khalili J, Satani N, Forget MA, Haymaker C, Muller F, Bernatchez C, Radvanyi L, Hwu P. Development of novel combinations of targeted and immunotherapies by understanding immune resistance using a high throughput assay of T cell mediated cytotoxicity. J Immunother Cancer 2013. [PMCID: PMC3991170 DOI: 10.1186/2051-1426-1-s1-p164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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28
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Abstract
The pathway of V(D)J recombination was discovered almost three decades ago. Yet it continues to baffle scientists because of its inherent complexity and the multiple layers of regulation that are required to efficiently generate a diverse repertoire of T and B cells. The non-homologous end-joining (NHEJ) DNA repair pathway is an integral part of the V(D)J reaction, and its numerous players perform critical functions in generating this vast diversity, while ensuring genomic stability. In this review, we summarize the efforts of a number of laboratories including ours in providing the mechanisms of V(D)J regulation with a focus on the NHEJ pathway. This involves discovering new players, unraveling unknown roles for known components, and understanding how deregulation of these pathways contributes to generation of primary immunodeficiencies. A long-standing interest of our laboratory has been to elucidate various mechanisms that control RAG activity. Our recent work has focused on understanding the multiple protein-protein interactions and protein-DNA interactions during V(D)J recombination, which allow efficient and regulated generation of the antigen receptors. Exploring how deregulation of this process contributes to immunodeficiencies also continues to be an important area of research for our group.
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Affiliation(s)
- Shruti Malu
- Department of Medicine, Immunology Institute, Mount Sinai School of Medicine, 1425 Madison Avenue, New York, NY 10029, USA
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29
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Malu S, De Ioannes P, Kozlov M, Greene M, Francis D, Hanna M, Pena J, Escalante CR, Kurosawa A, Erdjument-Bromage H, Tempst P, Adachi N, Vezzoni P, Villa A, Aggarwal AK, Cortes P. Artemis C-terminal region facilitates V(D)J recombination through its interactions with DNA Ligase IV and DNA-PKcs. ACTA ACUST UNITED AC 2012; 209:955-63. [PMID: 22529269 PMCID: PMC3348108 DOI: 10.1084/jem.20111437] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Interactions of Artemis with DNA Ligase IV and DNA-PKcs are required for efficient coding joint formation. Artemis is an endonuclease that opens coding hairpin ends during V(D)J recombination and has critical roles in postirradiation cell survival. A direct role for the C-terminal region of Artemis in V(D)J recombination has not been defined, despite the presence of immunodeficiency and lymphoma development in patients with deletions in this region. Here, we report that the Artemis C-terminal region directly interacts with the DNA-binding domain of Ligase IV, a DNA Ligase which plays essential roles in DNA repair and V(D)J recombination. The Artemis–Ligase IV interaction is specific and occurs independently of the presence of DNA and DNA–protein kinase catalytic subunit (DNA-PKcs), another protein known to interact with the Artemis C-terminal region. Point mutations in Artemis that disrupt its interaction with Ligase IV or DNA-PKcs reduce V(D)J recombination, and Artemis mutations that affect interactions with Ligase IV and DNA-PKcs show additive detrimental effects on coding joint formation. Signal joint formation remains unaffected. Our data reveal that the C-terminal region of Artemis influences V(D)J recombination through its interaction with both Ligase IV and DNA-PKcs.
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Affiliation(s)
- Shruti Malu
- Immunology Institute, Mount Sinai School of Medicine, New York, NY 10029, USA
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30
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Mukherjee S, Ahmed A, Malu S, Nandi D. Modulation of cell cycle progression by CTLA4-CD80/CD86 interactions on CD4+ T cells depends on strength of the CD3 signal: critical role for IL-2. J Leukoc Biol 2006; 80:66-74. [PMID: 16624934 DOI: 10.1189/jlb.0505260] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Cytotoxic T-lymphocyte antigen 4 (CTLA4) is a well-studied T cell costimulatory receptor that is known to inhibit T cell activation. In this study, the relationship between strength of the first signal and costimulatory interactions on primary mouse CD4(+) T cells was investigated. CTLA4-CD80/CD86 interactions differentially modulate T cell cycling based on the mode of CD3 signal: Activation with plate-bound (pb) anti-CD3 generates a strong signal compared with a weak signal with soluble (sol) anti-CD3, resulting in approximately sevenfold higher amounts of interleukin (IL)-2 and an increase in cell cycling. Activation of T cells with sol anti-CD3 (weak signal) together with CTLA4-CD80/CD86 blockade lowers IL-2 production and cell cycling, demonstrating an enhancing role for these interactions. Conversely, blockade of CTLA4-CD80/CD86 interactions on T cells activated with pb anti-CD3 (strong signal) increases proliferation, which is consistent with CTLA4 as a negative regulator. Also, coculture of T cells with Chinese hamster ovary cells expressing CD80 or CD86 demonstrates that the strength of the primary signal plays an important role. It is important that modulation of IL-2 amounts leads to distinct alterations in the functional effects of CTLA4-CD80/CD86 interactions. On increasing IL-2 amounts, activation of T cells stimulated with sol anti-CD3 (weak signal) and CTLA4-CD80/CD86 blockade is greater compared with control. Concurrently, neutralization of IL-2 greatly reduces activation of T cells stimulated with pb anti-CD3 (strong signal) and CTLA4-CD80/CD86 blockade compared with control. These results underscore the importance of strength of first signal, CTLA4-CD80/CD86 interactions, and IL-2 amounts in modulating primary CD4(+) T cell responses.
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Affiliation(s)
- Sambuddho Mukherjee
- Department of Biochemistry, Indian Institute of Science, Bangalore, India 560012
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31
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Malu S, Srinivasan S, Kumar Maiti P, Rajagopal D, John B, Nandi D. IFN-gamma bioassay: development of a sensitive method by measuring nitric oxide production by peritoneal exudate cells from C57BL/6 mice. J Immunol Methods 2003; 272:55-65. [PMID: 12505712 DOI: 10.1016/s0022-1759(02)00424-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Interferon-gamma (IFN-gamma) is an important immunomodulatory and pleiotropic cytokine produced, primarily, by activated T lymphocytes and natural killer (NK) cells. We have devised a nitric oxide (NO)-based bioassay for mouse IFN-gamma using resident peritoneal exudate cells (PECs) from C57BL/6 mice. Comparison with three existing bioassays demonstrated that this assay was very sensitive and detected IFN-gamma in the linear range of approximately 0.03-0.25 U/ml. Other cytokines, e.g. interleukin (IL)-2, IL-4, IL-6, IFN-alpha/beta and tumor necrosis factor-alpha (TNF-alpha), either alone or in combination with IFN-gamma, did not greatly modulate NO levels produced by resident peritoneal exudate cells. The presence of exogenous NO(3)(-) and H(2)O(2) did not interfere with the IFN-gamma induced NO production and detection. We also showed that the effect of lipopolysaccharide (LPS), which may be present in samples, could be suppressed by the use of Polymyxin B in the bioassay. The high sensitivity of the bioassay permitted the detection of low amounts of IFN-gamma in 1% mouse serum. In addition, this assay reproducibly detected bioactive IFN-gamma amounts in supernatants of activated T cells. The increase in IFN-gamma production by activated T cells in response to CD28 costimulation was approximately 3-fold by this bioassay and approximately 5-fold by ELISA. In summary, we have devised a simple, sensitive, inexpensive and high throughput method for the reproducible detection of bioactive IFN-gamma.
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Affiliation(s)
- Shruti Malu
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
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Sivasankar B, Raju KR, Anand V, Malu S, Padmanabhan S, Tiwari SC, Das N, Srivastava LM. Levels of plasma soluble complement receptor 1 (sCR1) in normal Indian adult population. Indian J Clin Biochem 1999; 14:237-40. [PMID: 23105224 PMCID: PMC3453580 DOI: 10.1007/bf02867924] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A decrease in the membrane anchored erythrocyte complement receptor 1 (CR1) is reported as an acquired phenomenon in a number of inflammatory and autoimmune diseases with concomitant rise in soluble CR1 (sCR1) levels in plasma. There is a need to establish the normal range of sCR1 in Indian adults to assess the function and disease association of this protein. The plasma sCR1 levels of 50 healthy individuals have been estimated by an indigenously developed sandwich ELISA. sCR1 levels from 26 patients suffering from nephropathies had also been assayed which was much higher than the normal controls. This observation suggests sCR1 as a potential market for the assessment of disease activity in nephropathies.
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Affiliation(s)
- B. Sivasankar
- Department of Biochemistry, All India Institute of Medical Sciences, 110 029 New Delhi, INDIA
| | - K. R. Raju
- Department of Biochemistry, All India Institute of Medical Sciences, 110 029 New Delhi, INDIA
| | - V. Anand
- Department of Biochemistry, All India Institute of Medical Sciences, 110 029 New Delhi, INDIA
| | - S. Malu
- Department of Biochemistry, All India Institute of Medical Sciences, 110 029 New Delhi, INDIA
| | - S. Padmanabhan
- Department of Nephrology, All India Institute of Medical Sciences, 110 029 New Delhi, INDIA
| | - S. C. Tiwari
- Department of Nephrology, All India Institute of Medical Sciences, 110 029 New Delhi, INDIA
| | - Nibhriti Das
- Department of Biochemistry, All India Institute of Medical Sciences, 110 029 New Delhi, INDIA
| | - L. M. Srivastava
- Department of Biochemistry, All India Institute of Medical Sciences, 110 029 New Delhi, INDIA
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