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Amaria R, Knisely A, Vining D, Kopetz S, Overman MJ, Javle M, Antonoff MB, Tzeng CWD, Wolff RA, Pant S, Lito K, Rangel K, Fellman B, Yuan Y, Lu KH, Sakellariou-Thompson D, Haymaker CL, Forget MA, Hwu P, Bernatchez C, Jazaeri AA. Efficacy and safety of autologous tumor-infiltrating lymphocytes in recurrent or refractory ovarian cancer, colorectal cancer, and pancreatic ductal adenocarcinoma. J Immunother Cancer 2024; 12:e006822. [PMID: 38309721 PMCID: PMC10840042 DOI: 10.1136/jitc-2023-006822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/09/2024] [Indexed: 02/05/2024] Open
Abstract
BACKGROUND Tumor-infiltrating lymphocyte (TIL) therapy has shown efficacy in metastatic melanoma, non-small cell lung cancer, and other solid tumors. Our preclinical work demonstrated more robust CD8 predominant TIL production when agonistic anti-4-1BB and CD3 antibodies were used in early ex vivo TIL culture. METHODS Patients with treatment-refractory metastatic colorectal (CRC), pancreatic (PDAC) and ovarian (OVCA) cancers were eligible. Lymphodepleting chemotherapy was followed by infusion of ex vivo expanded TIL, manufactured at MD Anderson Cancer Center with IL-2 and agonistic stimulation of CD3 and 4-1BB (urelumab). Patients received up to six doses of high-dose IL-2 after TIL infusion. Primary endpoint was evaluation of objective response rate at 12 weeks using Response Evaluation Criteria in Solid Tumors version 1.1 with secondary endpoints including disease control rate (DCR), duration of response, progression-free survival (PFS), overall survival (OS), and safety. RESULTS 17 patients underwent TIL harvest and 16 were treated on protocol (NCT03610490), including 8 CRC, 5 PDAC, and 3 OVCA patients. Median age was 57.5 (range 33-70) and 50% were females. Median number of lines of prior therapy was 2 (range 1-8). No responses were observed at 12 weeks. Ten subjects achieved at least one stable disease (SD) assessment for a DCR of 62.5% (95% CI 35.4% to 84.8%). Best response included prolonged SD in a patient with PDAC lasting 17 months. Median PFS and OS across cohorts were 2.53 months (95% CI 1.54 to 4.11) and 18.86 months (95% CI 4.86 to NR), respectively. Grade 3 or higher toxicities attributable to therapy were seen in 14 subjects (87.5%; 95% CI 61.7% to 98.4%). Infusion product analysis showed the presence of effector memory cells with high expression of CD39 irrespective of tumor type and low expression of checkpoint markers. CONCLUSIONS TIL manufactured with assistance of 4-1BB and CD3 agonism is feasible and treatment is associated with no new safety signals. While no responses were observed, a significant portion of patients achieved SD suggesting early/partial immunological effect. Further research is required to identify factors associated with resistance and functionally enhance T cells for a more effective therapy.
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Affiliation(s)
- Rodabe Amaria
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Anne Knisely
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - David Vining
- Department of Diagnostic Radiology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Scott Kopetz
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Michael J Overman
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Milind Javle
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Mara B Antonoff
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Ching-Wei D Tzeng
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Robert A Wolff
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Shubham Pant
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Kathryn Lito
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Kelly Rangel
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Bryan Fellman
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Ying Yuan
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Karen H Lu
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | | | - Cara L Haymaker
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Marie-Andrée Forget
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | | | - Chantale Bernatchez
- SVP Discovery & Platforms, Therapeutics Discovery, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Amir A Jazaeri
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
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2
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Ho P, Melms JC, Rogava M, Frangieh CJ, Poźniak J, Shah SB, Walsh Z, Kyrysyuk O, Amin AD, Caprio L, Fullerton BT, Soni RK, Ager CR, Biermann J, Wang Y, Khosravi-Maharlooei M, Zanetti G, Mu M, Fatima H, Moore EK, Vasan N, Bakhoum SF, Reiner SL, Bernatchez C, Sykes M, Mace EM, Wucherpfennig KW, Schadendorf D, Bechter O, Shah P, Schwartz GK, Marine JC, Izar B. The CD58-CD2 axis is co-regulated with PD-L1 via CMTM6 and shapes anti-tumor immunity. Cancer Cell 2023; 41:1207-1221.e12. [PMID: 37327789 PMCID: PMC10524902 DOI: 10.1016/j.ccell.2023.05.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 04/10/2023] [Accepted: 05/22/2023] [Indexed: 06/18/2023]
Abstract
The cell-autonomous balance of immune-inhibitory and -stimulatory signals is a critical process in cancer immune evasion. Using patient-derived co-cultures, humanized mouse models, and single-cell RNA-sequencing of patient melanomas biopsied before and on immune checkpoint blockade, we find that intact cancer cell-intrinsic expression of CD58 and ligation to CD2 is required for anti-tumor immunity and is predictive of treatment response. Defects in this axis promote immune evasion through diminished T cell activation, impaired intratumoral T cell infiltration and proliferation, and concurrently increased PD-L1 protein stabilization. Through CRISPR-Cas9 and proteomics screens, we identify and validate CMTM6 as critical for CD58 stability and upregulation of PD-L1 upon CD58 loss. Competition between CD58 and PD-L1 for CMTM6 binding determines their rate of endosomal recycling over lysosomal degradation. Overall, we describe an underappreciated yet critical axis of cancer immunity and provide a molecular basis for how cancer cells balance immune inhibitory and stimulatory cues.
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Affiliation(s)
- Patricia Ho
- Department of Medicine, Division of Hematology and Oncology, Columbia University, New York, NY 10032, USA; Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY 10032, USA
| | - Johannes C Melms
- Department of Medicine, Division of Hematology and Oncology, Columbia University, New York, NY 10032, USA; Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY 10032, USA
| | - Meri Rogava
- Department of Medicine, Division of Hematology and Oncology, Columbia University, New York, NY 10032, USA; Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY 10032, USA
| | - Chris J Frangieh
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Klarman Cell Observatory, the Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Joanna Poźniak
- Laboratory for Molecular Cancer Biology, Center for Cancer Biology, VIB, 3000 Leuven, Belgium; Department of Oncology, KU Leuven, 3000 Leuven, Belgium
| | - Shivem B Shah
- Department of Medicine, Division of Hematology and Oncology, Columbia University, New York, NY 10032, USA; Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY 10032, USA
| | - Zachary Walsh
- Department of Medicine, Division of Hematology and Oncology, Columbia University, New York, NY 10032, USA; Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY 10032, USA
| | - Oleksandr Kyrysyuk
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Amit Dipak Amin
- Department of Medicine, Division of Hematology and Oncology, Columbia University, New York, NY 10032, USA; Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY 10032, USA
| | - Lindsay Caprio
- Department of Medicine, Division of Hematology and Oncology, Columbia University, New York, NY 10032, USA; Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY 10032, USA
| | - Benjamin T Fullerton
- Department of Medicine, Division of Hematology and Oncology, Columbia University, New York, NY 10032, USA
| | - Rajesh Kumar Soni
- Proteomics and Macromolecular Crystallography Shared Resource, Columbia University, New York, NY 10032, USA
| | - Casey R Ager
- Department of Medicine, Division of Hematology and Oncology, Columbia University, New York, NY 10032, USA; Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY 10032, USA
| | - Jana Biermann
- Department of Medicine, Division of Hematology and Oncology, Columbia University, New York, NY 10032, USA; Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY 10032, USA; Program for Mathematical Genomics, Department of Systems Biology, Columbia University, New York, NY 10032, USA
| | - Yiping Wang
- Department of Medicine, Division of Hematology and Oncology, Columbia University, New York, NY 10032, USA; Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY 10032, USA; Program for Mathematical Genomics, Department of Systems Biology, Columbia University, New York, NY 10032, USA
| | - Mohsen Khosravi-Maharlooei
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY 10032, USA; Department of Immunology, Mayo Clinic, Scottsdale, AZ 85259, USA
| | - Giorgia Zanetti
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY 10032, USA
| | - Michael Mu
- Department of Medicine, Division of Hematology and Oncology, Columbia University, New York, NY 10032, USA; Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY 10032, USA
| | - Hijab Fatima
- Department of Pediatrics, Columbia University, New York, NY 10032, USA
| | - Emily K Moore
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY 10032, USA; Department of Medicine, Division of Rheumatology, Columbia University, New York, NY 10032, USA
| | - Neil Vasan
- Department of Medicine, Division of Hematology and Oncology, Columbia University, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY 10032, USA
| | - Samuel F Bakhoum
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Steven L Reiner
- Department of Pediatrics, Columbia University, New York, NY 10032, USA; Department of Microbiology and Immunology, Columbia University, New York, NY 10032, USA
| | - Chantale Bernatchez
- Department of Medical Oncology, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Megan Sykes
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY 10032, USA; Department of Microbiology and Immunology, Columbia University, New York, NY 10032, USA; Department of Surgery, Columbia University, New York, NY 10032, USA
| | - Emily M Mace
- Department of Pediatrics, Columbia University, New York, NY 10032, USA
| | - Kai W Wucherpfennig
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Dirk Schadendorf
- Department of Dermatology, University Hospital Essen and German Cancer Consortium, Partner Site, 45147 Essen, Germany
| | | | - Parin Shah
- Department of Medicine, Division of Hematology and Oncology, Columbia University, New York, NY 10032, USA
| | - Gary K Schwartz
- Department of Medicine, Division of Hematology and Oncology, Columbia University, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY 10032, USA
| | - Jean-Christophe Marine
- Laboratory for Molecular Cancer Biology, Center for Cancer Biology, VIB, 3000 Leuven, Belgium; Department of Oncology, KU Leuven, 3000 Leuven, Belgium
| | - Benjamin Izar
- Department of Medicine, Division of Hematology and Oncology, Columbia University, New York, NY 10032, USA; Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY 10032, USA; Program for Mathematical Genomics, Department of Systems Biology, Columbia University, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY 10032, USA.
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3
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Hahn AW, Menk AV, Rivadeneira DB, Augustin RC, Xu M, Li J, Wu X, Mishra AK, Gide TN, Quek C, Zang Y, Spencer CN, Menzies AM, Daniel CR, Hudgens CW, Nowicki T, Haydu LE, Khan MAW, Gopalakrishnan V, Burton EM, Malke J, Simon JM, Bernatchez C, Putluri N, Woodman SE, Vashisht Gopal YN, Guerrieri R, Fischer GM, Wang J, Wani KM, Thompson JF, Lee JE, Hwu P, Ajami N, Gershenwald JE, Long GV, Scolyer RA, Tetzlaff MT, Lazar AJ, Schadendorf D, Wargo JA, Kirkwood JM, DeBerardinis RJ, Liang H, Futreal A, Zhang J, Wilmott JS, Peng W, Davies MA, Delgoffe GM, Najjar YG, McQuade JL. Obesity Is Associated with Altered Tumor Metabolism in Metastatic Melanoma. Clin Cancer Res 2023; 29:154-164. [PMID: 36166093 DOI: 10.1158/1078-0432.ccr-22-2661] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 09/14/2022] [Accepted: 09/22/2022] [Indexed: 02/06/2023]
Abstract
PURPOSE Overweight/obese (OW/OB) patients with metastatic melanoma unexpectedly have improved outcomes with immune checkpoint inhibitors (ICI) and BRAF-targeted therapies. The mechanism(s) underlying this association remain unclear, thus we assessed the integrated molecular, metabolic, and immune profile of tumors, as well as gut microbiome features, for associations with patient body mass index (BMI). EXPERIMENTAL DESIGN Associations between BMI [normal (NL < 25) or OW/OB (BMI ≥ 25)] and tumor or microbiome characteristics were examined in specimens from 782 patients with metastatic melanoma across 7 cohorts. DNA associations were evaluated in The Cancer Genome Atlas cohort. RNA sequencing from 4 cohorts (n = 357) was batch corrected and gene set enrichment analysis (GSEA) by BMI category was performed. Metabolic profiling was conducted in a subset of patients (x = 36) by LC/MS, and in flow-sorted melanoma tumor cells (x = 37) and patient-derived melanoma cell lines (x = 17) using the Seahorse XF assay. Gut microbiome features were examined in an independent cohort (n = 371). RESULTS DNA mutations and copy number variations were not associated with BMI. GSEA demonstrated that tumors from OW/OB patients were metabolically quiescent, with downregulation of oxidative phosphorylation and multiple other metabolic pathways. Direct metabolite analysis and functional metabolic profiling confirmed decreased central carbon metabolism in OW/OB metastatic melanoma tumors and patient-derived cell lines. The overall structure, diversity, and taxonomy of the fecal microbiome did not differ by BMI. CONCLUSIONS These findings suggest that the host metabolic phenotype influences melanoma metabolism and provide insight into the improved outcomes observed in OW/OB patients with metastatic melanoma treated with ICIs and targeted therapies. See related commentary by Smalley, p. 5.
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Affiliation(s)
- Andrew W Hahn
- Division of Cancer Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Ashley V Menk
- Department of Immunology, University of Pittsburgh, Pittsburgh, Pennsylvania
| | | | - Ryan C Augustin
- Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Mingchu Xu
- Department of Genomic Medicine, Division of Cancer Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jun Li
- Department of Bioinformatics and Computational Biology, Division of Basic Sciences, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Xiaogang Wu
- Department of Genomic Medicine, Division of Cancer Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Aditya K Mishra
- Department of Genomic Medicine, Division of Cancer Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Tuba N Gide
- Melanoma Institute of Australia, The University of Sydney, Sydney, New South Wales, Australia
| | - Camelia Quek
- Melanoma Institute of Australia, The University of Sydney, Sydney, New South Wales, Australia
| | - Yan Zang
- Department of Immunology, University of Pittsburgh, Pittsburgh, Pennsylvania
| | | | - Alexander M Menzies
- Melanoma Institute of Australia, The University of Sydney, Sydney, New South Wales, Australia
| | - Carrie R Daniel
- Department of Epidemiology, Division of Cancer Prevention and Population Sciences, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Courtney W Hudgens
- Department of Translational Molecular Pathology, Division of Pathology and Laboratory Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Theodore Nowicki
- Division of Pediatric Hematology-Oncology, Department of Pediatrics, University of California Los Angeles, Los Angeles, California.,Jonsson Comprehensive Cancer Center, University of California Los Angeles, Los Angeles, California.,Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, University of California Los Angeles, Los Angeles, California
| | - Lauren E Haydu
- Department of Surgical Oncology, Division of Surgery, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - M A Wadud Khan
- Department of Surgical Oncology, Division of Surgery, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Vancheswaran Gopalakrishnan
- Department of Surgical Oncology, Division of Surgery, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Elizabeth M Burton
- Department of Genomic Medicine, Division of Cancer Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jared Malke
- Department of Surgical Oncology, Division of Surgery, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Julie M Simon
- Department of Surgical Oncology, Division of Surgery, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Chantale Bernatchez
- Department of Biologics Development, Division of Therapeutics Discovery, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Nagireddy Putluri
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas
| | - Scott E Woodman
- Department of Genomic Medicine, Division of Cancer Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Y N Vashisht Gopal
- Department of Melanoma Medical Oncology, Division of Cancer Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Renato Guerrieri
- Department of Melanoma Medical Oncology, Division of Cancer Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Grant M Fischer
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts
| | - Jian Wang
- Department of Biostatistics, Division of Biosciences, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Khalida M Wani
- Department of Translational Molecular Pathology, Division of Pathology and Laboratory Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - John F Thompson
- Melanoma Institute of Australia, The University of Sydney, Sydney, New South Wales, Australia
| | - Jeffrey E Lee
- Department of Surgical Oncology, Division of Surgery, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Patrick Hwu
- Department of Cutaneous Oncology, Moffitt Cancer Center, Tampa Bay, Florida
| | - Nadim Ajami
- Department of Genomic Medicine, Division of Cancer Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jeffrey E Gershenwald
- Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, University of California Los Angeles, Los Angeles, California
| | - Georgina V Long
- Melanoma Institute of Australia, The University of Sydney, Sydney, New South Wales, Australia.,Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia.,Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia
| | - Richard A Scolyer
- Melanoma Institute of Australia, The University of Sydney, Sydney, New South Wales, Australia.,Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia.,Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia.,Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital and NSW Health Pathology, Sydney, New South Wales, Australia
| | - Michael T Tetzlaff
- Division of Dermatopathology, Department of Pathology, University of California San Francisco, San Francisco, California
| | - Alexander J Lazar
- Department of Genomic Medicine, Division of Cancer Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas.,Department of Translational Molecular Pathology, Division of Pathology and Laboratory Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Dirk Schadendorf
- Department of Dermatology, Venereology, and Allergology, University Hospital Essen and German Cancer Consortium, Partner site Essen, Germany
| | - Jennifer A Wargo
- Department of Genomic Medicine, Division of Cancer Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas.,Department of Surgical Oncology, Division of Surgery, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - John M Kirkwood
- Division of Hematology/Oncology, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Ralph J DeBerardinis
- Children's Medical Research Institute and Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Han Liang
- Department of Bioinformatics and Computational Biology, Division of Basic Sciences, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Andrew Futreal
- Department of Genomic Medicine, Division of Cancer Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jianhua Zhang
- Department of Genomic Medicine, Division of Cancer Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - James S Wilmott
- Melanoma Institute of Australia, The University of Sydney, Sydney, New South Wales, Australia
| | - Weiyi Peng
- Department of Biology and Biochemistry, University of Houston, Houston, Texas
| | - Michael A Davies
- Department of Melanoma Medical Oncology, Division of Cancer Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Greg M Delgoffe
- Department of Immunology, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Yana G Najjar
- Division of Hematology/Oncology, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Jennifer L McQuade
- Department of Melanoma Medical Oncology, Division of Cancer Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas
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4
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Hou J, Liang S, Xu C, Wei Y, Wang Y, Tan Y, Sahni N, McGrail D, Bernatchez C, Davies M, Li Y, Chen R, Yi S, Chen Y, Yee C, Chen K, Peng W. Single-cell CRISPR immune screens reveal immunological roles of tumor intrinsic factors. NAR Cancer 2022; 4:zcac038. [PMID: 36518525 PMCID: PMC9732527 DOI: 10.1093/narcan/zcac038] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 10/15/2022] [Accepted: 11/16/2022] [Indexed: 12/14/2022] Open
Abstract
Genetic screens are widely exploited to develop novel therapeutic approaches for cancer treatment. With recent advances in single-cell technology, single-cell CRISPR screen (scCRISPR) platforms provide opportunities for target validation and mechanistic studies in a high-throughput manner. Here, we aim to establish scCRISPR platforms which are suitable for immune-related screens involving multiple cell types. We integrated two scCRISPR platforms, namely Perturb-seq and CROP-seq, with both in vitro and in vivo immune screens. By leveraging previously generated resources, we optimized experimental conditions and data analysis pipelines to achieve better consistency between results from high-throughput and individual validations. Furthermore, we evaluated the performance of scCRISPR immune screens in determining underlying mechanisms of tumor intrinsic immune regulation. Our results showed that scCRISPR platforms can simultaneously characterize gene expression profiles and perturbation effects present in individual cells in different immune screen conditions. Results from scCRISPR immune screens also predict transcriptional phenotype associated with clinical responses to cancer immunotherapy. More importantly, scCRISPR screen platforms reveal the interactive relationship between targeting tumor intrinsic factors and T cell-mediated antitumor immune response which cannot be easily assessed by bulk RNA-seq. Collectively, scCRISPR immune screens provide scalable and reliable platforms to elucidate molecular determinants of tumor immune resistance.
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Affiliation(s)
- Jiakai Hou
- Department of Biology and Biochemistry, University of Houston, Houston, TX, USA
| | - Shaoheng Liang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Computer Science, Rice University, Houston, TX, USA
| | - Chunyu Xu
- Department of Biology and Biochemistry, University of Houston, Houston, TX, USA
| | - Yanjun Wei
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yunfei Wang
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yukun Tan
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Nidhi Sahni
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Daniel J McGrail
- Center for Immunotherapy and Precision Immuno-Oncology, Cleveland Clinic, Cleveland, OH, USA
| | - Chantale Bernatchez
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Michael Davies
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yumei Li
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Rui Chen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - S Stephen Yi
- Department of Oncology, Livestrong Cancer Institutes, and Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX, USA
- Interdisciplinary Life Sciences Graduate Programs (ILSGP) and Oden Institute for Computational Engineering and Sciences (ICES), The University of Texas at Austin, Austin, TX, USA
| | - Yiwen Chen
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Cassian Yee
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ken Chen
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Weiyi Peng
- Department of Biology and Biochemistry, University of Houston, Houston, TX, USA
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5
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Babiker H, Borazanci E, Subbiah V, Agarwala S, Algazi A, Schachter J, Lotem M, Maurice-Dror C, Hendler D, Rahimian S, Minderman H, Haymaker C, Mahadevan D, Bernatchez C, Murthy R, Hultsch R, Kaplan N, Woodhead G, Hennemeyer C, Chunduru S, Anderson PM, Diab A, Puzanov I. Tilsotolimod Exploits the TLR9 Pathway to Promote Antigen Presentation and Type 1 IFN Signaling in Solid Tumors: A Multicenter International Phase I/II Trial (ILLUMINATE-101). Clin Cancer Res 2022; 28:5079-5087. [PMID: 35917516 DOI: 10.1158/1078-0432.ccr-21-4486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 02/28/2022] [Accepted: 07/27/2022] [Indexed: 01/24/2023]
Abstract
PURPOSE Tilsotolimod is an investigational synthetic Toll-like receptor 9 (TLR9) agonist that has demonstrated antitumor activity in preclinical models. The ILLUMINATE-101 phase I study explored the safety, dose, efficacy, and immune effects of intratumoral (it) tilsotolimod monotherapy in multiple solid tumors. PATIENTS AND METHODS Patients with a diagnosis of refractory cancer not amenable to curative therapies received tilsotolimod in doses escalating from 8 to 32 mg into a single lesion at weeks 1, 2, 3, 5, 8, and 11. Additional patients with advanced malignant melanoma were enrolled into an expansion cohort at the 8 mg dose. Objectives included characterizing the safety, establishing the dose, efficacy, and immunologic assessment. Blood samples and tumor biopsies of injected and noninjected lesions were obtained at baseline and 24 hours after treatment for immune analyses. RESULTS Thirty-eight and 16 patients were enrolled into the dose escalation and melanoma expansion cohorts, respectively. Deep visceral injections were conducted in 91% of patients. No dose-limiting toxicities (DLT) or grade 4 treatment-related adverse events were observed. Biopsies 24 hours after treatment demonstrated an increased IFN pathway signature and dendritic cell maturation. Immunologic profiling revealed upregulation of IFN-signaling genes and modulation of genes for checkpoint proteins. In the dose escalation cohort, 12 (34%) of 35 evaluable patients achieved a best overall response rate (ORR) of stable disease (SD), whereas 3 (19%) of 16 evaluable patients in the melanoma cohort achieved stable disease. CONCLUSIONS Overall, tilsotolimod monotherapy was generally well tolerated and induced rapid, robust alterations in the tumor microenvironment. See related commentary by Punekar and Weber, p. 5007.
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Affiliation(s)
| | | | - Vivek Subbiah
- The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Sanjiv Agarwala
- Saint Luke's University Health Network, Easton, Pennsylvania
| | - Alain Algazi
- University of California, San Francisco, California
| | | | - Michael Lotem
- Hadassah Hebrew University Medical Center, Jerusalem, Israel
| | | | | | | | - Hans Minderman
- Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Cara Haymaker
- The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | | | - Ravi Murthy
- The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Rolf Hultsch
- HonorHealth Research Institute, Scottsdale, Arizona
| | - Nadia Kaplan
- Hadassah Hebrew University Medical Center, Jerusalem, Israel
| | | | | | | | | | - Adi Diab
- The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Igor Puzanov
- Roswell Park Comprehensive Cancer Center, Buffalo, New York
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6
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Somaiah N, Conley AP, Parra ER, Lin H, Amini B, Solis Soto L, Salazar R, Barreto C, Chen H, Gite S, Haymaker C, Nassif EF, Bernatchez C, Mitra A, Livingston JA, Ravi V, Araujo DM, Benjamin R, Patel S, Zarzour MA, Sabir S, Lazar AJ, Wang WL, Daw NC, Zhou X, Roland CL, Cooper ZA, Rodriguez-Canales J, Futreal A, Soria JC, Wistuba II, Hwu P. Durvalumab plus tremelimumab in advanced or metastatic soft tissue and bone sarcomas: a single-centre phase 2 trial. Lancet Oncol 2022; 23:1156-1166. [PMID: 35934010 DOI: 10.1016/s1470-2045(22)00392-8] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 06/28/2022] [Accepted: 07/01/2022] [Indexed: 02/03/2023]
Abstract
BACKGROUND Few standard treatment options are available for patients with metastatic sarcomas. We did this trial to evaluate the efficacy, safety, and changes in the tumour microenvironment for durvalumab, an anti-PD-L1 drug, and tremelimumab, an anti-CTLA-4 drug, across multiple sarcoma subtypes. METHODS In this single-centre phase 2 trial, done at The University of Texas MD Anderson Cancer Center (Houston, TX USA), patients aged 18 years or older with advanced or metastatic sarcoma with an Eastern Cooperative Oncology Group performance status of 0 or 1 who had received at least one previous line of systemic therapy were enrolled in disease subtype-specific groups (liposarcoma, leiomyosarcoma, angiosarcoma, undifferentiated pleomorphic sarcoma, synovial sarcoma, osteosarcoma, alveolar soft-part sarcoma, chordoma, and other sarcomas). Patients received 1500 mg intravenous durvalumab and 75 mg intravenous tremelimumab for four cycles, followed by durvalumab alone every 4 weeks for up to 12 months. The primary endpoint was progression-free survival at 12 weeks in the intention-to-treat population (all patients who received at least one dose of treatment). Safety was also analysed in the intention-to-treat population. This trial is registered with ClinicalTrials.gov, NCT02815995, and is completed. FINDINGS Between Aug 17, 2016, and April 9, 2018, 62 patients were enrolled, of whom 57 (92%) received treatment and were included in the intention-to-treat population. With a median follow-up of 37·2 months (IQR 1·8-10·1), progression-free survival at 12 weeks was 49% (95% CI 36-61). 21 grade 3-4 treatment-related adverse events were reported, the most common of which were increased lipase (four [7%] of 57 patients), colitis (three [5%] patients), and pneumonitis (three [5%] patients). Nine (16%) patients had a treatment related serious adverse event. One patient had grade 5 pneumonitis and colitis. INTERPRETATION The combination of durvalumab and tremelimumab is an active treatment regimen for advanced or metastatic sarcoma and merits evaluation in specific subsets in future trials. FUNDING AstraZeneca.
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Affiliation(s)
- Neeta Somaiah
- Department of Sarcoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Anthony P Conley
- Department of Sarcoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Edwin Roger Parra
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Heather Lin
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Behrang Amini
- Department of Musculoskeletal Imaging, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Luisa Solis Soto
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ruth Salazar
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Carmelia Barreto
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Honglei Chen
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Swati Gite
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Cara Haymaker
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Elise F Nassif
- Department of Surgical Oncology, Division of Surgery, 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
| | - Akash Mitra
- Department of Genomic Medicine, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - John Andrew Livingston
- Department of Sarcoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Vinod Ravi
- Department of Sarcoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Dejka M Araujo
- Department of Sarcoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Robert Benjamin
- Department of Sarcoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Shreyaskumar Patel
- Department of Sarcoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Maria A Zarzour
- Department of Sarcoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sharjeel Sabir
- Department of General Interventional Radiology, Scripps Mercy Hospital, San Diego, CA, USA
| | - Alexander J Lazar
- Department of Pathology, Division of Pathology-Lab Medicine Division, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Wei-Lien Wang
- Department of Pathology, Division of Pathology-Lab Medicine Division, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Najat C Daw
- Department of Pediatrics, Division of Pediatrics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Xiao Zhou
- Department of Sarcoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Christina L Roland
- Department of Surgical Oncology, Division of Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Zachary A Cooper
- Oncology Research & Development, AstraZeneca, Gaithersburg, MD, USA
| | | | - Andrew Futreal
- Department of Genomic Medicine, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jean-Charles Soria
- General Director, Gustave Roussy, Paris-Saclay University, Villejuif, France
| | - Ignacio I Wistuba
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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7
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Schalck A, Sakellariou-Thompson D, Forget MA, Sei E, Hughes TG, Reuben A, Bai S, Hu M, Kumar T, Hurd MW, Katz MHG, Tzeng CWD, Pant S, Javle M, Fogelman DR, Maitra A, Haymaker CL, Kim MP, Navin NE, Bernatchez C. Single cell sequencing reveals trajectory of tumor-infiltrating lymphocyte states in pancreatic cancer. Cancer Discov 2022; 12:2330-2349. [PMID: 35849783 PMCID: PMC9547957 DOI: 10.1158/2159-8290.cd-21-1248] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 05/09/2022] [Accepted: 07/14/2022] [Indexed: 11/16/2022]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) has few effective treatments. Immunotherapy, an attractive alternative strategy, remains challenging with the lack of knowledge on the tumor-infiltrating lymphocyte (TIL) landscape in PDAC. To generate a reference of T-cell subpopulations, we profiled 80,000 T cells from 57 PDAC, 22 uninvolved/normal samples, and cultured TIL using single-cell transcriptomic and T-cell receptor analysis. These data revealed 20 cell states and heterogeneous distributions of TIL populations. The CD8+ TIL contained a putative transitional GZMK+ population based on TCR clonotype sharing, and cell-state trajectory analysis showed similarity to a GZMB+PRF1+ cytotoxic and a CXCL13+ dysfunctional population. Statistical analysis suggested that certain TIL states, such as dysfunctional and inhibitory populations, often occurred together. Finally, analysis of cultured TIL revealed that high-frequency clones from effector populations were preferentially expanded. These data provide a framework for understanding the PDAC TIL landscape for future TIL use in immunotherapy for PDAC.
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Affiliation(s)
- Aislyn Schalck
- The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | | | - Marie-Andree Forget
- The University of Texas MD Anderson Cancer Center, Houston, Texas, United States
| | - Emi Sei
- The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Tara G Hughes
- The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Alexandre Reuben
- The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Shanshan Bai
- UT M. D. Anderson Cancer Center, Houston, United States
| | - Min Hu
- The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Tapsi Kumar
- The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Mark W Hurd
- The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Matthew H G Katz
- The University of Texas MD Anderson Cancer Center, Houston, Texas, United States
| | - Ching-Wei D Tzeng
- The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Shubham Pant
- The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Milind Javle
- The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | | | - Anirban Maitra
- The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Cara L Haymaker
- The University of Texas MD Anderson Cancer Center, Houston, Texas, United States
| | - Michael P Kim
- The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | | | - Chantale Bernatchez
- The University of Texas MD Anderson Cancer Center, Houston, Texas, United States
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8
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Andrews MC, Oba J, Wu CJ, Zhu H, Karpinets T, Creasy CA, Forget MA, Yu X, Song X, Mao X, Robertson AG, Romano G, Li P, Burton EM, Lu Y, Sloane RS, Wani KM, Rai K, Lazar AJ, Haydu LE, Bustos MA, Shen J, Chen Y, Morgan MB, Wargo JA, Kwong LN, Haymaker CL, Grimm EA, Hwu P, Hoon DSB, Zhang J, Gershenwald JE, Davies MA, Futreal PA, Bernatchez C, Woodman SE. Multi-modal molecular programs regulate melanoma cell state. Nat Commun 2022; 13:4000. [PMID: 35810190 PMCID: PMC9271073 DOI: 10.1038/s41467-022-31510-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [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: 03/09/2021] [Accepted: 06/20/2022] [Indexed: 12/12/2022] Open
Abstract
Melanoma cells display distinct intrinsic phenotypic states. Here, we seek to characterize the molecular regulation of these states using multi-omic analyses of whole exome, transcriptome, microRNA, long non-coding RNA and DNA methylation data together with reverse-phase protein array data on a panel of 68 highly annotated early passage melanoma cell lines. We demonstrate that clearly defined cancer cell intrinsic transcriptomic programs are maintained in melanoma cells ex vivo and remain highly conserved within melanoma tumors, are associated with distinct immune features within tumors, and differentially correlate with checkpoint inhibitor and adoptive T cell therapy efficacy. Through integrative analyses we demonstrate highly complex multi-omic regulation of melanoma cell intrinsic programs that provide key insights into the molecular maintenance of phenotypic states. These findings have implications for cancer biology and the identification of new therapeutic strategies. Further, these deeply characterized cell lines will serve as an invaluable resource for future research in the field.
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Affiliation(s)
- Miles C. Andrews
- grid.1002.30000 0004 1936 7857Department of Medicine, Monash University, Melbourne, VIC Australia ,grid.240145.60000 0001 2291 4776Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Junna Oba
- grid.240145.60000 0001 2291 4776Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX USA ,grid.26091.3c0000 0004 1936 9959Department of Extended Intelligence for Medicine, The Ishii-Ishibashi Laboratory, Keio University School of Medicine, Tokyo, Japan
| | - Chang-Jiun Wu
- grid.240145.60000 0001 2291 4776Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Haifeng Zhu
- grid.240145.60000 0001 2291 4776Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Tatiana Karpinets
- grid.240145.60000 0001 2291 4776Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Caitlin A. Creasy
- grid.240145.60000 0001 2291 4776Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Marie-Andrée Forget
- grid.240145.60000 0001 2291 4776Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Xiaoxing Yu
- grid.26091.3c0000 0004 1936 9959Department of Extended Intelligence for Medicine, The Ishii-Ishibashi Laboratory, Keio University School of Medicine, Tokyo, Japan
| | - Xingzhi Song
- grid.240145.60000 0001 2291 4776Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Xizeng Mao
- grid.240145.60000 0001 2291 4776Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - A. Gordon Robertson
- grid.434706.20000 0004 0410 5424Canada’s Michael Smith Genome Sciences Center, BC Cancer, Vancouver, BC Canada ,Dxige Research Inc., Courtenay, BC Canada
| | - Gabriele Romano
- grid.240145.60000 0001 2291 4776Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Peng Li
- grid.240145.60000 0001 2291 4776Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Elizabeth M. Burton
- grid.240145.60000 0001 2291 4776Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Yiling Lu
- grid.240145.60000 0001 2291 4776Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Robert Szczepaniak Sloane
- grid.240145.60000 0001 2291 4776Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Khalida M. Wani
- grid.240145.60000 0001 2291 4776Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Kunal Rai
- grid.240145.60000 0001 2291 4776Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Alexander J. Lazar
- grid.240145.60000 0001 2291 4776Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX USA ,grid.240145.60000 0001 2291 4776Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX USA ,grid.240145.60000 0001 2291 4776Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Lauren E. Haydu
- grid.240145.60000 0001 2291 4776Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Matias A. Bustos
- grid.416507.10000 0004 0450 0360Departments of Translational Molecular Medicine and Genomic Sequencing Center, St John’s Cancer Institute, Providence Saint John’s Health Center, Santa Monica, CA USA
| | - Jianjun Shen
- grid.240145.60000 0001 2291 4776Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX USA
| | - Yueping Chen
- grid.240145.60000 0001 2291 4776Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX USA
| | - Margaret B. Morgan
- grid.240145.60000 0001 2291 4776Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Jennifer A. Wargo
- grid.240145.60000 0001 2291 4776Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX USA ,grid.240145.60000 0001 2291 4776Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Lawrence N. Kwong
- grid.240145.60000 0001 2291 4776Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Cara L. Haymaker
- grid.240145.60000 0001 2291 4776Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Elizabeth A. Grimm
- grid.240145.60000 0001 2291 4776Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Patrick Hwu
- grid.240145.60000 0001 2291 4776Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX USA ,grid.468198.a0000 0000 9891 5233H Lee Moffitt Cancer Center, Tampa, FL USA
| | - Dave S. B. Hoon
- grid.416507.10000 0004 0450 0360Departments of Translational Molecular Medicine and Genomic Sequencing Center, St John’s Cancer Institute, Providence Saint John’s Health Center, Santa Monica, CA USA
| | - Jianhua Zhang
- grid.240145.60000 0001 2291 4776Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Jeffrey E. Gershenwald
- grid.240145.60000 0001 2291 4776Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Michael A. Davies
- grid.240145.60000 0001 2291 4776Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - P. Andrew Futreal
- grid.240145.60000 0001 2291 4776Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Chantale Bernatchez
- grid.240145.60000 0001 2291 4776Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX USA ,grid.240145.60000 0001 2291 4776Department of Biologics Development, Division of Therapeutics Discovery, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Scott E. Woodman
- grid.240145.60000 0001 2291 4776Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX USA ,grid.240145.60000 0001 2291 4776Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX USA
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9
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Schmidt ST, Akhave N, Knightly RE, Reuben A, Vokes N, Zhang J, Li J, Fujimoto J, Byers LA, Sanchez-Espiridion B, Diao L, Wang J, Federico L, Forget MA, McGrail DJ, Weissferdt A, Lin SY, Lee Y, Suzuki E, Kovacs JJ, Behrens C, Wistuba II, Futreal A, Vaporciyan A, Sepesi B, Heymach JV, Bernatchez C, Haymaker C, Cascone T, Zhang J, Bristow CA, Heffernan TP, Negrao MV, Gibbons DL. Shared Nearest Neighbors Approach and Interactive Browser for Network Analysis of a Comprehensive Non-Small-Cell Lung Cancer Data Set. JCO Clin Cancer Inform 2022; 6:e2200040. [PMID: 35944232 PMCID: PMC9470146 DOI: 10.1200/cci.22.00040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 05/25/2022] [Accepted: 06/30/2022] [Indexed: 11/20/2022] Open
Abstract
PURPOSE Advances in biological measurement technologies are enabling large-scale studies of patient cohorts across multiple omics platforms. Holistic analysis of these data can generate actionable insights for translational research and necessitate new approaches for data integration and mining. METHODS We present a novel approach for integrating data across platforms on the basis of the shared nearest neighbors algorithm and use it to create a network of multiplatform data from the immunogenomic profiling of non-small-cell lung cancer project. RESULTS Benchmarking demonstrates that the shared nearest neighbors-based network approach outperforms a traditional gene-gene network in capturing established interactions while providing new ones on the basis of the interplay between measurements from different platforms. When used to examine patient characteristics of interest, our approach provided signatures associated with and new leads related to recurrence and TP53 oncogenotype. CONCLUSION The network developed offers an unprecedented, holistic view into immunogenomic profiling of non-small-cell lung cancer, which can be explored through the accompanying interactive browser that we built.
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Affiliation(s)
- Stephanie T. Schmidt
- TRACTION Platform, Division of Therapeutics Discovery, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Neal Akhave
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Ryan E. Knightly
- TRACTION Platform, Division of Therapeutics Discovery, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Alexandre Reuben
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Natalie Vokes
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Jianhua Zhang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Jun Li
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Junya Fujimoto
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Lauren A. Byers
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Lixia Diao
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Jing Wang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Lorenzo Federico
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Marie-Andree Forget
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Daniel J. McGrail
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Annikka Weissferdt
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Shiaw-Yih Lin
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Younghee Lee
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Erika Suzuki
- TRACTION Platform, Division of Therapeutics Discovery, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Jeffrey J. Kovacs
- TRACTION Platform, Division of Therapeutics Discovery, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Carmen Behrens
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Ignacio I. Wistuba
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Andrew Futreal
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Ara Vaporciyan
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Boris Sepesi
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - John V. Heymach
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Chantale Bernatchez
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Cara Haymaker
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Tina Cascone
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Jianjun Zhang
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Christopher A. Bristow
- TRACTION Platform, Division of Therapeutics Discovery, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Timothy P. Heffernan
- TRACTION Platform, Division of Therapeutics Discovery, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Marcelo V. Negrao
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Don L. Gibbons
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
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10
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Fix SM, Forget MA, Sakellariou-Thompson D, Wang Y, Griffiths TM, Lee M, Haymaker CL, Dominguez AL, Basar R, Reyes C, Kumar S, Meyer LA, Hwu P, Bernatchez C, Jazaeri AA. CRISPR-mediated TGFBR2 knockout renders human ovarian cancer tumor-infiltrating lymphocytes resistant to TGF-β signaling. J Immunother Cancer 2022; 10:jitc-2021-003750. [PMID: 35882447 PMCID: PMC9330322 DOI: 10.1136/jitc-2021-003750] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [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] [Accepted: 06/09/2022] [Indexed: 11/30/2022] Open
Abstract
Background The correlation between elevated T-cell infiltration and improved survival of ovarian cancer (OvCa) patients suggests that endogenous tumor-infiltrating lymphocytes (TIL) possess some degree of antitumor activity that can be harnessed for OvCa immunotherapy. We previously optimized a protocol for ex vivo OvCa TIL expansion for adoptive cell therapy, which is now being tested in a clinical trial at our institution (NCT03610490). Building on this success, we embarked on genetic modification of OvCa TIL to overcome key immunosuppressive factors present in the tumor microenvironment. Here, we present the preclinical optimization of CRISPR/Cas9-mediated knockout of the TGF-β receptor 2 (TGFBR2) in patient-derived OvCa TIL. Methods OvCa TILs were generated from four patients’ tumor samples obtained at surgical resection and subjected to CRISPR/Cas9-mediated knockout of TGFBR2 before undergoing a rapid expansion protocol. TGFBR2-directed gRNAs were comprehensively evaluated for their TGFBR2 knockout efficiency and off-target activity. Furthermore, the impact of TGFBR2 knockout on TIL expansion, function, and downstream signaling was assayed. Results TGFBR2 knockout efficiencies ranging from 59±6% to 100%±0% were achieved using 5 gRNAs tested in four independent OvCa TIL samples. TGFBR2 knockout TIL were resistant to immunosuppressive TGF-β signaling as evidenced by a lack of SMAD phosphorylation, a lack of global transcriptional changes in response to TGF-β stimulation, equally strong secretion of proinflammatory cytokines in the presence and absence of TGF-β, and improved cytotoxicity in the presence of TGF-β. CRISPR-modification itself did not alter the ex vivo expansion efficiency, immunophenotype, nor the TCR clonal diversity of OvCa TIL. Importantly for clinical translation, comprehensive analysis of CRISPR off-target effects revealed no evidence of off-target activity for our top two TGFBR2-targeting gRNAs. Conclusions CRISPR/Cas9-mediated gene knockout is feasible and efficient in patient-derived OvCa TIL using clinically-scalable methods. We achieved efficient and specific TGFBR2 knockout, yielding an expanded OvCa TIL product that was resistant to the immunosuppressive effects of TGF-β. This study lays the groundwork for clinical translation of CRISPR-modified TIL, providing opportunities for engineering more potent TIL therapies not only for OvCa treatment, but for the treatment of other solid cancers as well.
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Affiliation(s)
- Samantha M Fix
- Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Marie-Andrée Forget
- Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | | | - Yunfei Wang
- Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Tamara M Griffiths
- Biologics Development, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Minjung Lee
- Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Cara L Haymaker
- Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Ana Lucía Dominguez
- Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Rafet Basar
- Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Christopher Reyes
- Cell Biology R&D, Thermo Fisher Scientific, Carlsbad, California, USA
| | - Sanjay Kumar
- Cell Biology R&D, Thermo Fisher Scientific, Carlsbad, California, USA
| | - Larissa A Meyer
- Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Patrick Hwu
- Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Chantale Bernatchez
- Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Amir A Jazaeri
- Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
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11
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Shin DH, Jiang H, Kim D, Nguyen TT, Sohoni S, Fan X, Yi Y, Van Wieren AC, Al-Atrash G, Bernatchez C, Alemany R, Alonso M, Lang F, Gomez-Manzano C, Ozpolat B, Fueyo J. Abstract 3559: Redirection of anti-virus immunity towards anti-tumor immunity using nanoparticle-induced immune tolerance for oncolytic adenovirus therapy. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-3559] [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
Recent clinical observations that some coronavirus infections induced complete remissions in lymphoma patients emphasized again the potential of cancer virotherapy. Infection of cancer cells with oncolytic viruses reshapes the tumor microenvironment by activating anti-viral and anti-tumor immunity. A phase 1 clinical trial using oncolytic adenovirus Delta-24-RGD (DNX-2401) to treat recurrent malignant gliomas demonstrated activation of CD8+ T-cells and significant clinical benefits for a subset of patients. However, both anti-virus and anti-tumor immune responses are contingent on the activation of respective clones of CD8+ T-cells, which compete for clonal expansion. Thus, overexpansion of T-cells against viral antigens reduces the frequency of subdominant clones against tumor antigens. We hypothesized that inducing immune tolerance for viral antigens will decrease anti-viral immunity and in turn derepress anti-tumor immunity, resulting in enhanced efficacy of cancer virotherapy. In this work, we used nanoparticles encapsulating adenoviral antigens E1A, E1B and hexon that distributed to liver resident macrophages (P<0.0001) and induced peripheral immune tolerance. Functional experiments to restimulate immune cells with viral or tumor antigens showed that injection of nanoparticles induced virus-specific immune tolerance and redirected the focus of the immune response towards tumor peptides as measured by interferon-gamma secretion (P<0.0001). Co-culture experiments also showed increased activation of immune cells against fixed tumor cells after nanoparticle treatment (P<0.0001). Reduction of virus-specific T-cells and concurrent expansion of tumor-specific T-cell clones were further confirmed with E1A or OVA tetramers (P<0.05). Flow cytometry analysis suggested increased anti-tumor responses were due to differences in T-cell clones and not due to other immune populations including natural killer cells or myeloid-derived suppressor cells (P=0.3). Importantly, virotherapy in combination with nanoparticle-induced immune tolerance towards viral antigens in tumor-bearing mice increased the overall survival and doubled the percentage of long-term survivors compared to virus treatment alone. Our data should propel the development of a future clinical trial aiming to maximize the potential of anti-tumor immunity during cancer virotherapies.
Citation Format: Dong Ho Shin, Hong Jiang, Debora Kim, Teresa T. Nguyen, Sagar Sohoni, Xuejun Fan, Yanhua Yi, Arie C. Van Wieren, Gheath Al-Atrash, Chantale Bernatchez, Ramon Alemany, Marta Alonso, Frederick Lang, Candelaria Gomez-Manzano, Bulent Ozpolat, Juan Fueyo. Redirection of anti-virus immunity towards anti-tumor immunity using nanoparticle-induced immune tolerance for oncolytic adenovirus therapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3559.
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Affiliation(s)
| | | | | | | | | | | | - Yanhua Yi
- 1MD Anderson Cancer Center, Houston, TX
| | | | | | | | - Ramon Alemany
- 3IDIBELL – Institut Catala d’Oncologia, Barcelona, Spain
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12
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Bentebibel SE, Johnson D, Amariae R, McGrail D, Lecagoonporn S, Haymaker C, Duose D, Wani K, Safa H, Glitza IC, Patel SP, Wong MK, Tawbi H, Burks J, Yang X, Hwu P, Yee C, Davies MA, Murthy R, Bernatchez C, Ekmekcioglu S, Diab A, Lizée G. Abstract CT039: Intratumoral CD40 agonist sotigalimab with pembrolizumab induces broad innate and adaptive immune activation in local and distant tumors in metastatic melanoma. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-ct039] [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
The use of immune-checkpoint inhibitors (CPI) has become an important modality in the treatment of metastatic melanoma (MM). However, most patients (pts) do not experience durable responses and new treatment options are needed to improve clinical outcomes. Our pre-clinical studies have demonstrated that intratumoral CD40 activation synergizes with anti-PD-1 based therapy and induces systemic and distant anti-tumor effects. In this ongoing phase I/II study, we assessed intratumoral sotigalimab (APX005M), a CD40 agonist antibody, in combination with systemic pembrolizumab in CPI treatment naïve, unresectable stage III or IV MM. A total of 40 participants will be enrolled. As of December 15, 2021, 30 pts were enrolled. Pts received sotigalimab every 3 weeks for a total of 4 doses. The dose escalation portion of the trial has been completed, with 14 pts enrolled in 5 dosing cohorts of sotigalimab at 0.1, 0.5, 1, 3 and 10 mg. The primary objectives include safety and tolerability, determination of the recommended phase 2 dose (RP2D), and assessment of the overall response rate (ORR) by RECIST v1.1. Biomarker analyses of blood and tumor samples were performed to measure immune activation using immunophenotyping including imaging mass cytometry, TCR sequencing, and a cross-cohort comparison of gene expression data (sotigalimab plus pembrolizumab versus anti-PD1 monotherapy). The combination therapy has been well-tolerated, and there were no study discontinuations or death due to treatment-related adverse events (TRAEs). Most common TRAEs were injection-site reactions; six pts experienced grade-3 immune-related adverse events. Efficacy analysis of 30 pts with post-baseline disease evaluations demonstrated an ORR of 50% (5 CR and 10 PR) in distant lesions and a disease control rate of 67%. The ORR at the RP2D of 10 mg is 55% (12/22). Responses were observed in PD-L1 negative pts and those with elevated LDH. Comprehensive transcriptome and immune cell profiling of peripheral blood mononuclear cells and tumor biopsies obtained from local lesions at baseline and 24 hours post sotigalimab injection demonstrate that sotigalimab effectively engaged CD40 pathway. In comparison to anti-PD1 monotherapy, the combination therapy significantly increased expression of genes associated with antigen presentation and effector T cells in local lesions accompanied by an increase in T cell activation genes at distant lesions. Additionally, T cell repertoire analysis demonstrated a significant increase in T cell clonality with expansion of new clones shared between local and distant tumors. Importantly, these immunologic changes were correlated with clinical response. Collectively, this combination therapy is well tolerated and has a notable clinical response rate, accompanied by broad innate and adaptive immune activation at both local and distant lesions.
Citation Format: Salah-Eddine Bentebibel, Daniel Johnson, Rodabe Amariae, Daniel McGrail, Srisuda Lecagoonporn, Cara Haymaker, Dzifa Duose, Khalida Wani, Houssein Safa, Isabella Claudia Glitza, Sapna Pradyuman Patel, Michael K. Wong, Hussein Tawbi, Jared Burks, Xiaodong Yang, Patrick Hwu, Cassian Yee, Michael A. Davies, Ravi Murthy, Chantale Bernatchez, Suhendan Ekmekcioglu, Adi Diab, Gregory Lizée. Intratumoral CD40 agonist sotigalimab with pembrolizumab induces broad innate and adaptive immune activation in local and distant tumors in metastatic melanoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr CT039.
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Affiliation(s)
| | - Daniel Johnson
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Rodabe Amariae
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Daniel McGrail
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Cara Haymaker
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Dzifa Duose
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Khalida Wani
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Houssein Safa
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | | | - Michael K. Wong
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Hussein Tawbi
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Jared Burks
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Patrick Hwu
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Cassian Yee
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Ravi Murthy
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | | | - Adi Diab
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Gregory Lizée
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
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13
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Schalck A, Sakellariou-Thompson D, Forget MA, Sei E, Hughes T, Bai S, Hu M, Kumar T, Hurd M, Katz M, Tzeng CW, Pant S, Javle M, Maitra A, Haymaker C, Kim M, Navin N, Bernatchez C. Abstract 2847: Simultaneous TCR and transcriptomic sequencing of single Tcells defines biological subtypes in pancreatic cancer for adoptive Tcell therapy. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-2847] [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
Pancreatic ductal adenocarcinoma (PDAC) is a highly fatal tumor-type with very few effective treatment strategies. Attempts to improve outcomes using immune checkpoint blockade therapy have also failed, likely because the overall Tcell infiltration in this tumor-type is low. Despite this, the presence of CD3+CD8+ tumor-infiltrating lymphocytes (TIL) in PDAC is associated with improved survival outcomes, suggesting that other immune-based strategies could be more successful. Here, we examine ex vivo tumor-infiltrating Tcell expansion for adoptive Tcell therapy (ACT) as a potential strategy for treating PDAC. The focus of this study is to understand the transcriptional states of Tcells in the pancreas and PDACs and how they change with ex vivo expansion and re-infusion into patients as treatment strategy. We have performed both single cell transcriptome and TCR sequencing (scRNA-TCRseq) on 54,579 Tcells from 8 human PDAC samples and the ex vivo grown TIL from a subset of 6 patients and found 13 purported substates. Through TCR tracking of the Tcell clonotypes, we find that the expansion protocol is able to expand Tcells found in many different Tcell states in the primary tumor. Furthermore, we compared our thirteen tumor-infiltrating substates with 41,935 Tcells from two other independent single cell studies across 71 samples, and confirmed our substates to be present across all datasets.
Citation Format: Aislyn Schalck, Donastas Sakellariou-Thompson, Marie-Andrée Forget, Emi Sei, Tara Hughes, Shanshan Bai, Min Hu, Tapsi Kumar, Mark Hurd, Matthew Katz, Chine-Wei Tzeng, Shubham Pant, Milind Javle, Anirban Maitra, Cara Haymaker, Michael Kim, Nicholas Navin, Chantale Bernatchez. Simultaneous TCR and transcriptomic sequencing of single Tcells defines biological subtypes in pancreatic cancer for adoptive Tcell therapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2847.
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Affiliation(s)
| | | | | | - Emi Sei
- 1UT MD Anderson Cancer Center, Houston, TX
| | | | | | - Min Hu
- 1UT MD Anderson Cancer Center, Houston, TX
| | | | - Mark Hurd
- 1UT MD Anderson Cancer Center, Houston, TX
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14
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Le X, Wang R, Vokes N, Elamin Y, Kalhor N, McGrail D, Xi Y, III ST, Hong L, Du R, Blumenschein G, Gay C, Negrao M, Altan M, Tran H, Hu L, Wang J, Heeke S, Nilsson M, Robichaux J, Dang M, Han G, Byers L, Tsao A, Sepesi B, Bernatchez C, Zhang J, Wang L, Heymach J. Abstract 3260: Enhanced lineage plasticity in RTK-independent TKI-resistant EGFR-mutant NSCLC. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-3260] [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
Background: Resistance to targeted tyrosine kinase inhibitors (TKI) inevitably develops in metastatic EGFR-mutant non-small cell lung cancer (NSCLC). Resistance mechanisms are diverse, and mechanisms beyond receptor tyrosine kinase (RTK) pathway mutations are poorly understood. We hypothesized that the use of osimertinib as first-line therapy is increasing the prevalence of RTK-independent resistance mechanisms, and that RTK-independent resistant tumors undergo enhanced tumor cell lineage plasticity as an escape mechanism to EGFR TKI therapy.
Methods: We identified patients who developed osimertinib resistance (OR) after first line (1L, n=54) and second line (2L, n=42) treatments and determined the resistance mechanisms based on clinical sequencing and histopathology. We also performed single-cell RNA-seq of 24 samples from 13 patients with EGFRm NSCLC at TKI treatment-naïve (TN, n=2), residual disease (RD, n=4), and progression disease (PD, n=7) stages.
Results: Compared to 2L OR tumors, 1L OR tumors had increased RTK-independent mechanisms of resistance (76% vs. 46%, p=0.002), including 8% with small cell transformation (n=4), 2% with squamous transformation (n=1) and 66% with unknown mechanisms (n=34). To understand inter- and intra-tumor heterogeneity, we analyzed transcriptomic profiles of 76,266 single cells. Lung developmental lineages were assigned to 10,250 EpCAM+ cells, including 4,735 cells classified as malignant cells by inferCNV and RTK signaling analysis. In the two EGFRm TN tumors, the malignant cells demonstrated bronchoalveolar lineage and moderate EGFR expression. In the TKI resistant cases (PD, n=7), both RTK-dependent and RTK-independent resistance were observed. The RTK-dependent tumors (EGFR T790M n=1; ERBB2 amplification n=1) demonstrated preserved bronchoalveolar lineage identity. In the RTK-independent resistant tumors (n=5), one had complete lineage switch from epithelial to small cell neuroendocrine and very low expression level of EGFR. The remaining 4 PD tumors displayed varying expression of epithelial-to-mesenchymal transformation (EMT) features. One tumor had sarcomatoid histology and a high proportion of cells having positive VIM expression (84%) and 92% of cells having complete loss of NAPSA expression; 3 tumors had partial EMT demonstrated by heterogeneous proportion of cells having VIM expression (18-56%) and loss of NAPSA (26-67%). Interestingly, some of the cells with EMT and partial-EMT had moderate levels of EGFR expression, similar to the levels in the TN tumors.
Conclusion: With osimertinib use at 1L, the incidence of RTK-independent resistance has increased to become the dominant mechanism, whereas RTK-dependent resistance has decreased. Increased lineage plasticity (small cell neuroendocrine, squamous and EMT) potentially serves as an RTK-independent TKI-resistance mechanism in EGFRm NSCLC.
Citation Format: Xiuning Le, Ruiping Wang, Natalie Vokes, Yasir Elamin, Neda Kalhor, Daniel McGrail, Yuanxin Xi, Santiago Treviño III, Lingzhi Hong, Robyn Du, George Blumenschein, Carl Gay, Marcelo Negrao, Mehmet Altan, Hai Tran, Limei Hu, Jing Wang, Simon Heeke, Monique Nilsson, Jacqulyne Robichaux, Minghao Dang, Guangchun Han, Lauren Byers, Anne Tsao, Boris Sepesi, Chantale Bernatchez, Jianjun Zhang, Linghua Wang, John Heymach. Enhanced lineage plasticity in RTK-independent TKI-resistant EGFR-mutant NSCLC [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3260.
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Affiliation(s)
- Xiuning Le
- 1UT MD Anderson Cancer Center, Houston, TX
| | | | | | | | | | | | - Yuanxin Xi
- 1UT MD Anderson Cancer Center, Houston, TX
| | | | | | - Robyn Du
- 1UT MD Anderson Cancer Center, Houston, TX
| | | | - Carl Gay
- 1UT MD Anderson Cancer Center, Houston, TX
| | | | | | - Hai Tran
- 1UT MD Anderson Cancer Center, Houston, TX
| | - Limei Hu
- 1UT MD Anderson Cancer Center, Houston, TX
| | - Jing Wang
- 1UT MD Anderson Cancer Center, Houston, TX
| | | | | | | | | | | | | | - Anne Tsao
- 1UT MD Anderson Cancer Center, Houston, TX
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15
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Amaria RN, Vining DJ, Kopetz S, Overman MJ, Javle MM, Antonoff M, Tzeng CWD, Wolff RA, Pant S, Lito K, Rangel KM, Wilson L, Fellman BM, Haymaker CL, Yuan Y, Forget MA, Hwu P, Bernatchez C, Jazaeri AA. Efficacy and safety of autologous expanded tumor infiltrating lymphocytes (TILs) in multiple solid tumors. J Clin Oncol 2022. [DOI: 10.1200/jco.2022.40.16_suppl.2536] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
2536 Background: TIL therapy has been used extensively in metastatic melanoma patients for many years, now with ongoing efforts to commercialize treatment. The efficacy of TIL outside of melanoma is largely unknown thus we designed and implemented a trial using TIL manufactured at a single academic center for treatment refractory metastatic colorectal (CRC), pancreas (PDAC) and ovarian (OVA) cancers. Methods: Patients with CRC, PDAC and OVA refractory to standard therapies with ECOG PS 0-1 and normal organ function were eligible for TIL harvest. Ex vivo TIL expansion and manufacturing was conducted at the MD Anderson TIL lab under conditions that included IL2 and 41BB stimulation (using urelumab). All patients received a lymphodepletion regimen consisting of cyclophosphamide 60mg/kg days -7 and -6 and fludarabine 25mg/m2 days -5 through day -1, followed by infusion of pooled ex-vivo expanded TIL. Patients received up to 6 doses of high dose IL-2 (600,000 IU/kg) after TIL infusion. The primary endpoint was evaluation of the objective response rate (ORR) using RECIST 1.1 criteria with secondary endpoints including disease control rate, duration of response, PFS, OS and safety. Results: A total of 17 patients underwent TIL harvest and 16 were treated on protocol; including 8 CRC, 5 PDAC and 3 OVA. Median age was 57.5 (range 33-70) and 50% were females. Median number of lines of prior therapy was 2 (range 1-8). Median number of TIL infused was 76 X 109 (range 20.3 x 109-150 x 109). Median doses of cyclophosphamide and fludarabine administered were 2 (range, 2-2) and 3 (range, 1-5), respectively. Median doses of IL-2 administered was 6 (range, 1-6). There were no responders. Best response included prolonged SD in a patient with PDAC lasting until 18 months. Grade 3 or higher toxicities attributable to therapy was seen in 14 subjects (87.5%; 95% CI: 61.7 – 98.4) with the majority of toxicities representing expected pancytopenia from lymphodepletion. Infusion product analysis showed the presence of effector memory cells with high expression of CD39 irrespective of tumor type. Early on-treatment biopsy of PDAC patient with prolonged SD showed presence of proliferating (KI67+) CD4+ and CD8+ TIL. Conclusions: Generation of TIL at a single academic center for CRC, PDAC and OVA is feasible and treatment is associated with no new safety signals. For these tumor types, further research is required to identify host factors associated with resistance to TIL therapy and optimize manufacturing processes to create more effective TIL cell therapy. Clinical trial information: NCT03610490.
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Affiliation(s)
| | - David J. Vining
- Department of Diagnostic Radiology, The University of Texas M.D. Anderson Cancer Center, Houston, TX
| | - Scott Kopetz
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | | | - Mara Antonoff
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Robert A. Wolff
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Shubham Pant
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | | | | | - Bryan M. Fellman
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Ying Yuan
- Department of Biostatistics, 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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16
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Creasy CA, Meng YJ, Forget MA, Karpinets T, Tomczak K, Stewart C, Torres-Cabala CA, Pilon-Thomas S, Sarnaik AA, Mulé JJ, Garraway L, Bustos M, Zhang J, Patel SP, Diab A, Glitza IC, Yee C, Tawbi H, Wong MK, McQuade J, Hoon DSB, Davies MA, Hwu P, Amaria RN, Haymaker C, Beroukhim R, Bernatchez C. Genomic Correlates of Outcome in Tumor-Infiltrating Lymphocyte Therapy for Metastatic Melanoma. Clin Cancer Res 2022; 28:1911-1924. [PMID: 35190823 DOI: 10.1158/1078-0432.ccr-21-1060] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 07/01/2021] [Accepted: 02/16/2022] [Indexed: 11/16/2022]
Abstract
PURPOSE Adoptive cell therapy (ACT) of tumor-infiltrating lymphocytes (TIL) historically yields a 40%-50% response rate in metastatic melanoma. However, the determinants of outcome are largely unknown. EXPERIMENTAL DESIGN We investigated tumor-based genomic correlates of overall survival (OS), progression-free survival (PFS), and response to therapy by interrogating tumor samples initially collected to generate TIL infusion products. RESULTS Whole-exome sequencing (WES) data from 64 samples indicated a positive correlation between neoantigen load and OS, but not PFS or response to therapy. RNA sequencing analysis of 34 samples showed that expression of PDE1C, RTKN2, and NGFR was enriched in responders who had improved PFS and OS. In contrast, the expression of ELFN1 was enriched in patients with unfavorable response, poor PFS and OS, whereas enhanced methylation of ELFN1 was observed in patients with favorable outcomes. Expression of ELFN1, NGFR, and PDE1C was mainly found in cancer-associated fibroblasts and endothelial cells in tumor tissues across different cancer types in publicly available single-cell RNA sequencing datasets, suggesting a role for elements of the tumor microenvironment in defining the outcome of TIL therapy. CONCLUSIONS Our findings suggest that transcriptional features of melanomas correlate with outcomes after TIL therapy and may provide candidates to guide patient selection.
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Affiliation(s)
- Caitlin A Creasy
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center (MDACC), Houston, Texas
| | - Yuzhong Jeff Meng
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Marie-Andrée Forget
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center (MDACC), Houston, Texas
| | - Tatiana Karpinets
- Department of Genomic Medicine, The University of Texas MDACC, Houston, Texas
| | - Katarzyna Tomczak
- Department of Translational Molecular Pathology, The University of Texas MDACC, Houston, Texas
| | - Chip Stewart
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | | | - Shari Pilon-Thomas
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida.,Department of Cutaneous Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Amod A Sarnaik
- Department of Cutaneous Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - James J Mulé
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Levi Garraway
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Matias Bustos
- Department of Translational Molecular Medicine, Saint John's Cancer Institute, Saint John's Health Center, Santa Monica, California
| | - Jianhua Zhang
- Department of Genomic Medicine, The University of Texas MDACC, Houston, Texas
| | - Sapna P Patel
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center (MDACC), Houston, Texas
| | - Adi Diab
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center (MDACC), Houston, Texas
| | - Isabella C Glitza
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center (MDACC), Houston, Texas
| | - Cassian Yee
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center (MDACC), Houston, Texas
| | - Hussein Tawbi
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center (MDACC), Houston, Texas
| | - Michael K Wong
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center (MDACC), Houston, Texas
| | - Jennifer McQuade
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center (MDACC), Houston, Texas
| | - Dave S B Hoon
- Department of Translational Molecular Medicine, Saint John's Cancer Institute, Saint John's Health Center, Santa Monica, California
| | - Michael A Davies
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center (MDACC), Houston, Texas
| | - Patrick Hwu
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center (MDACC), Houston, Texas
| | - Rodabe N Amaria
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center (MDACC), Houston, Texas
| | - Cara Haymaker
- Department of Translational Molecular Pathology, The University of Texas MDACC, Houston, Texas
| | - Rameen Beroukhim
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Chantale Bernatchez
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center (MDACC), Houston, Texas.,Department of Translational Molecular Pathology, The University of Texas MDACC, Houston, Texas
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17
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Shah P, Forget MA, Frank ML, Jiang P, Sakellariou-Thompson D, Federico L, Khairullah R, Neutzler CA, Wistuba I, Chow CWB, Long Y, Fujimoto J, Lin SY, Maitra A, Negrao MV, Mitchell KG, Weissferdt A, Vaporciyan AA, Cascone T, Roth JA, Zhang J, Sepesi B, Gibbons DL, Heymach JV, Haymaker CL, McGrail DJ, Reuben A, Bernatchez C. Combined IL-2, agonistic CD3 and 4-1BB stimulation preserve clonotype hierarchy in propagated non-small cell lung cancer tumor-infiltrating lymphocytes. J Immunother Cancer 2022; 10:jitc-2021-003082. [PMID: 35110355 PMCID: PMC8811607 DOI: 10.1136/jitc-2021-003082] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [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] [Accepted: 12/20/2021] [Indexed: 12/15/2022] Open
Abstract
Background Adoptive cell transfer (ACT) of tumor-infiltrating lymphocytes (TIL) yielded clinical benefit in patients with checkpoint blockade immunotherapy-refractory non-small cell lung cancer (NSCLC) prompting a renewed interest in TIL-ACT. This preclinical study explores the feasibility of producing a NSCLC TIL product with sufficient numbers and enhanced attributes using an improved culture method. Methods TIL from resected NSCLC tumors were initially cultured using (1) the traditional method using interleukin (IL)-2 alone in 24-well plates (TIL 1.0) or (2) IL-2 in combination with agonistic antibodies against CD3 and 4-1BB (Urelumab) in a G-Rex flask (TIL 3.0). TIL subsequently underwent a rapid expansion protocol (REP) with anti-CD3. Before and after the REP, expanded TIL were phenotyped and the complementarity-determining region 3 β variable region of the T-cell receptor (TCR) was sequenced to assess the T-cell repertoire. Results TIL 3.0 robustly expanded NSCLC TIL while enriching for CD8+ TIL in a shorter manufacturing time when compared with the traditional TIL 1.0 method, achieving a higher success rate and producing 5.3-fold more TIL per successful expansion. The higher proliferative capacity and CD8 content of TIL 3.0 was also observed after the REP. Both steps of expansion did not terminally differentiate/exhaust the TIL but a lesser differentiated population was observed after the first step. TIL initially expanded with the 3.0 method exhibited higher breadth of clonotypes than TIL 1.0 corresponding to a higher repertoire homology with the original tumor, including a higher proportion of the top 10 most prevalent clones from the tumor. TIL 3.0 also retained a higher proportion of putative tumor-specific TCR when compared with TIL 1.0. Numerical expansion of TIL in a REP was found to perturb the clonal hierarchy and lessen the proportion of putative tumor-specific TIL from the TIL 3.0 process. Conclusions We report the feasibility of robustly expanding a T-cell repertoire recapitulating the clonal hierarchy of the T cells in the NSCLC tumor, including a large number of putative tumor-specific TIL clones, using the TIL 3.0 methodology. If scaled up and employed as a sole expansion platform, the robustness and speed of TIL 3.0 may facilitate the testing of TIL-ACT approaches in NSCLC.
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Affiliation(s)
- Parin Shah
- Melanoma Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Marie-Andrée Forget
- Melanoma Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA.,Biologics Development, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Meredith L Frank
- Thoracic/Head and Neck Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Peixin Jiang
- Thoracic/Head and Neck Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | | | - Lorenzo Federico
- Melanoma Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Roohussaba Khairullah
- Thoracic/Head and Neck Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | | | - Ignacio Wistuba
- Thoracic/Head and Neck Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA.,Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Chi-Wan B Chow
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Yan Long
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Junya Fujimoto
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Shiaw-Yih Lin
- Department of Systems Biology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Anirban Maitra
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Marcelo V Negrao
- Thoracic/Head and Neck Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Kyle Gregory Mitchell
- Thoracic and Cardiovascular Surgery, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Annikka Weissferdt
- Department of Pathology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Ara A Vaporciyan
- Thoracic and Cardiovascular Surgery, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Tina Cascone
- Thoracic/Head and Neck Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Jack A Roth
- Thoracic and Cardiovascular Surgery, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Jianjun Zhang
- Thoracic/Head and Neck Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Boris Sepesi
- Thoracic and Cardiovascular Surgery, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Don L Gibbons
- Thoracic/Head and Neck Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - John V Heymach
- Thoracic/Head and Neck Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Cara L Haymaker
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Daniel J McGrail
- Department of Systems Biology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Alexandre Reuben
- Thoracic/Head and Neck Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Chantale Bernatchez
- Melanoma Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA .,Biologics Development, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
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18
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Deboever N, McGrail DJ, Lee Y, Tran HT, Mitchell KG, Antonoff MB, Hofstetter WL, Mehran RJ, Rice DC, Roth JA, Swisher SG, Vaporciyan AA, Walsh GL, Bernatchez C, Vailati Negrao M, Zhang J, Wistuba II, Heymach JV, Cascone T, Gibbons DL, Haymaker CL, Sepesi B. Surgical approach does not influence changes in circulating immune cell populations following lung cancer resection. Lung Cancer 2022; 164:69-75. [PMID: 35038676 DOI: 10.1016/j.lungcan.2022.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 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] [Received: 11/04/2021] [Revised: 12/27/2021] [Accepted: 01/02/2022] [Indexed: 10/19/2022]
Abstract
INTRODUCTION The multimodal management of operable non-small cell lung cancer (NSCLC) continues to evolve rapidly. The immune milieu allowing for immunotherapeutic benefit can be affected by multiple parameters including clinicopathologic and genetic. Surgery induced physiological changes has received attention for modulating and affecting post-operative oncotaxis and immunosuppression. Here, we sought to investigate how surgical stress influences phenotype of peripheral blood mononuclear cells (PBMCs) in patients with NSCLC who underwent lobectomy. METHODS Blood was prospectively collected from patients with Stage IA-IIIA NSCLC undergoing lung resection between 2016 and 2018. Samples were obtained pre-operatively, 24 h and 4 weeks after surgery. PBMCs were isolated and subject to high-dimensional flow cytometry, analyzing a total of 115 cell populations with a focus on myeloid cells, T cell activation, and T cell trafficking. We further evaluated how surgical approach influenced post-operative PBMC changes, whether the operation was conducted in an open fashion with thoracotomy, or with minimally invasive Video Assisted Thoracoscopic Surgery (VATS). RESULTS A total of 76 patients met the inclusion criteria (Open n = 55, VATS n = 21). Surgical resection coincided with a decrease in T lymphocyte populations, including total CD3+ T cells, CD8+ T cells, and T effector memory cells, as well as an increase in monocytic myeloid-derived suppressor cells (mMDSC). Post-operative changes in PBMC populations were resolved after 4 weeks. Surgical-induced changes in immune populations were equivalent in patients undergoing open thoracotomy and VATS. DISCUSSION Surgical stress resulted in transient reduction in T cells and T effector memory cells, and increase of mMDSC following resection in NSCLC patients. The immune profile modulation was similar regardless of surgical approach. These findings suggest that surgical approach does not seem to affect mononuclear cell lines obtained from peripheral blood. Thus, the decision regarding surgical approach should be patient centered, rather than based on post-operative treatment response optimization.
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Affiliation(s)
- Nathaniel Deboever
- Department of Thoracic and Cardiovascular Surgery, University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Daniel J McGrail
- Department of Bioinformatics and Computational Biology, University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Younghee Lee
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Hai T Tran
- Department of Thoracic/Head and Neck Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Kyle G Mitchell
- Department of Thoracic and Cardiovascular Surgery, University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Mara B Antonoff
- Department of Thoracic and Cardiovascular Surgery, University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Wayne L Hofstetter
- Department of Thoracic and Cardiovascular Surgery, University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Reza J Mehran
- Department of Thoracic and Cardiovascular Surgery, University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - David C Rice
- Department of Thoracic and Cardiovascular Surgery, University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Jack A Roth
- Department of Thoracic and Cardiovascular Surgery, University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Stephen G Swisher
- Department of Thoracic and Cardiovascular Surgery, University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Ara A Vaporciyan
- Department of Thoracic and Cardiovascular Surgery, University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Garrett L Walsh
- Department of Thoracic and Cardiovascular Surgery, University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Chantale Bernatchez
- Department of Melanoma Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Marcelo Vailati Negrao
- Department of Thoracic/Head and Neck Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Jianjun Zhang
- Department of Thoracic/Head and Neck Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Ignacio I Wistuba
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - John V Heymach
- Department of Thoracic/Head and Neck Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Tina Cascone
- Department of Thoracic/Head and Neck Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Don L Gibbons
- Department of Thoracic/Head and Neck Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, United States; Department of Molecular and Cellular Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Cara L Haymaker
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Boris Sepesi
- Department of Thoracic and Cardiovascular Surgery, University of Texas MD Anderson Cancer Center, Houston, TX, United States
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19
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Fulbright OJ, Forget MA, Haymaker C, Bernatchez C. Isolation and Maintenance of Tumor-Infiltrating Lymphocytes for Translational and Clinical Applications: Established Methods and New Developments. Methods Mol Biol 2022; 2435:43-71. [PMID: 34993939 DOI: 10.1007/978-1-0716-2014-4_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Adoptive cell transfer (ACT) of in vitro expanded tumor-infiltrating lymphocytes (TIL) for the treatment of patients with advanced stages of metastatic melanoma remains one of the most beneficial therapies eliciting long-lasting responses. Methods and protocols used to expand TIL have evolved over time, utilizing different culture devices and other tools, to streamline and maximize the end product in both numbers and quality. Summarized in this chapter are the latest protocols used in the TIL program at MDACC.
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Affiliation(s)
- Orenthial J Fulbright
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center (MDACC), Houston, TX, USA
| | - Marie-Andrée Forget
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center (MDACC), Houston, TX, USA
| | - Cara Haymaker
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center (MDACC), Houston, TX, USA
| | - Chantale Bernatchez
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center (MDACC), Houston, TX, USA.
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20
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Federico L, McGrail DJ, Bentebibel SE, Haymaker C, Ravelli A, Forget MA, Karpinets T, Jiang P, Reuben A, Negrao MV, Li J, Khairullah R, Zhang J, Weissferdt A, Vaporciyan AA, Antonoff MB, Walsh G, Lin SY, Futreal A, Wistuba I, Roth J, Byers LA, Gaudreau PO, Uraoka N, Cruz AF, Dejima H, Lazcano RN, Solis LM, Parra ER, Lee JJ, Swisher S, Cascone T, Heymach JV, Zhang J, Sepesi B, Gibbons DL, Bernatchez C. Distinct tumor-infiltrating lymphocyte landscapes are associated with clinical outcomes in localized non-small-cell lung cancer. Ann Oncol 2022; 33:42-56. [PMID: 34653632 PMCID: PMC10019222 DOI: 10.1016/j.annonc.2021.09.021] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 09/11/2021] [Accepted: 09/30/2021] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Despite the importance of tumor-infiltrating T lymphocytes (TILs) in cancer biology, the relationship between TIL phenotypes and their prognostic relevance for localized non-small-cell lung cancer (NSCLC) has not been well established. PATIENTS AND METHODS Fresh tumor and normal adjacent tissue was prospectively collected from 150 patients with localized NSCLC. Tissue was comprehensively characterized by high-dimensional flow cytometry of TILs integrated with immunogenomic data from multiplex immunofluorescence, T-cell receptor sequencing, exome sequencing, RNA sequencing, targeted proteomics, and clinicopathologic features. RESULTS While neither the magnitude of TIL infiltration nor specific TIL subsets were significantly prognostic alone, the integration of high-dimensional flow cytometry data identified two major immunotypes (IM1 and IM2) that were predictive of recurrence-free survival independent of clinical characteristics. IM2 was associated with poor prognosis and characterized by the presence of proliferating TILs expressing cluster of differentiation 103, programmed cell death protein 1, T-cell immunoglobulin and mucin-domain containing protein 3, and inducible T-cell costimulator. Conversely, IM1 was associated with good prognosis and differentiated by an abundance of CD8+ T cells expressing cytolytic enzymes, CD4+ T cells lacking the expression of inhibitory receptors, and increased levels of B-cell infiltrates and tertiary lymphoid structures. While increased B-cell infiltration was associated with good prognosis, the best prognosis was observed in patients with tumors exhibiting high levels of both B cells and T cells. These findings were validated in patient tumors from The Cancer Genome Atlas. CONCLUSIONS Our study suggests that although the number of infiltrating T cells is not associated with patient survival, the nature of the infiltrating T cells, resolved in distinct TIL immunotypes, is prognostically relevant in NSCLC and may inform therapeutic approaches to clinical care.
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Affiliation(s)
- L Federico
- Therapeutics Discovery Division, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - D J McGrail
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - S-E Bentebibel
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - C Haymaker
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - A Ravelli
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - M-A Forget
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - T Karpinets
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - P Jiang
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - A Reuben
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - M V Negrao
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - J Li
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - R Khairullah
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - J Zhang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - A Weissferdt
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - A A Vaporciyan
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - M B Antonoff
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - G Walsh
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - S-Y Lin
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - A Futreal
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - I Wistuba
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - J Roth
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - L A Byers
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - P-O Gaudreau
- Department of Oncology, Queens' University and the Canadian Cancer Trials Group, Kingston, Canada
| | - N Uraoka
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - A F Cruz
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - H Dejima
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - R N Lazcano
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - L M Solis
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - E R Parra
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - J J Lee
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - S Swisher
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - T Cascone
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - J V Heymach
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - J Zhang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, USA; Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, USA.
| | - B Sepesi
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, USA.
| | - D L Gibbons
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, USA; Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, USA.
| | - C Bernatchez
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, USA.
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21
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Schmidt ST, Akhave N, Reuben A, Cascone T, Zhang J, Li J, Fujimoto J, Byers LA, Sanchez-Espiridion B, Diao L, Wang J, Federico L, Forget MA, McGrail DJ, Weissferdt A, Lin SY, Lee Y, Vokes N, Behrens C, Wistuba II, Futreal A, Vaporciyan A, Sepesi B, Heymach JV, Bernatchez C, Haymaker C, Zhang J, Bristow CA, Heffernan TP, Negrao MV, Gibbons DL. Abstract P009: A shared nearest neighbors approach for integrated, multi-platform networks and its application to the exploration of multiomics data from early-stage non-small cell lung cancers. Mol Cancer Ther 2021. [DOI: 10.1158/1535-7163.targ-21-p009] [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
Background: The ImmunogenomiC prOfiling of Non-small cell lung cancer (NSCLC) Project (ICON) represents an ambitious undertaking to comprehensively characterize immuno-genomic diversity in NSCLC across diverse platforms. The depth and breadth of this cohort presented a unique opportunity to develop a specialized method for multi-platform data integration and exploration, which can be broadly applied to forthcoming large-scale patient profiling studies. Such a holistic approach can unlock insights for therapeutic targets, biomarkers, and treatment plans by providing a more complete view of phenomena driving disease pathogenesis and evolution. Purpose: We developed a novel shared nearest neighbors (SNN) approach to create an integrated network of ICON’s multi-platform data and identified collections of closely related measurements within the resulting network tied to noteworthy patient characteristics, including recurrence and oncogenotype. Methods: The ICON dataset is derived from tumor and normal lung tissue samples collected from 150 patients at time of resection as well as blood samples collected then and at intervals during the year following. Tissue samples underwent RNA-sequencing (RNA-seq), whole exome sequencing, T-cell receptor sequencing, multiplex immunofluorescence for immune cells, and reverse phase protein array profiling; flow cytometry for immune cells was performed on tissue and blood samples. From these data, the ICON data network was built using an integrative approach based on the SNN algorithm in which genes were linked on the basis of their shared top correlates in orthogonal datasets. Results: The ICON data network currently includes over 20,000 genes linked by over 500,000 connections derived from correlations between RNA-seq and orthogonal platforms. We captured established associations between cancer-related genes and examined these along with new ones in the network. To do so, we used the InfoMap algorithm to extract more interpretable sub-networks, termed modules, from the ICON data network. Single sample gene set enrichment scores for each module were used in multivariate analysis to highlight modules linked to clinical characteristics of interest. As an example, we found modules significantly tied to disease recurrence. The most notable of these was strongly associated with metabolic pathways, and other modules associated with platelets and ion channels were also identified. The metabolic pathway module is being explored as a prognostic biomarker, underscoring the opportunites enabled by mining the network. Conclusions: Through the framework developed, we identified modules in the ICON data network significantly associated with important patient characteristics like recurrence and oncogenotype. We are validating the gene sets identified as potential biomarkers and are developing an interactive application to facilitate further mining of the network. Taken together, our SNN network-building approach enables the integration and exploration of patient data from diverse platforms.
Citation Format: Stephanie T. Schmidt, Neal Akhave, Alexandre Reuben, Tina Cascone, Jianhua Zhang, Jun Li, Junya Fujimoto, Lauren A. Byers, Beatriz Sanchez-Espiridion, Lixia Diao, Jing Wang, Lorenzo Federico, Marie-Andree Forget, Daniel J McGrail, Annikka Weissferdt, Shiaw-Yih Lin, Younghee Lee, Natalie Vokes, Carmen Behrens, Ignacio I. Wistuba, Andrew Futreal, Ara Vaporciyan, Boris Sepesi, John V. Heymach, Chantale Bernatchez, Cara Haymaker, Jianjun Zhang, Christopher A. Bristow, Timothy P. Heffernan, Marcelo V. Negrao, Don L. Gibbons. A shared nearest neighbors approach for integrated, multi-platform networks and its application to the exploration of multiomics data from early-stage non-small cell lung cancers [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2021 Oct 7-10. Philadelphia (PA): AACR; Mol Cancer Ther 2021;20(12 Suppl):Abstract nr P009.
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Affiliation(s)
| | - Neal Akhave
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Tina Cascone
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Jianhua Zhang
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Jun Li
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Junya Fujimoto
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Lauren A. Byers
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Lixia Diao
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Jing Wang
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | | | | | | | - Shiaw-Yih Lin
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Younghee Lee
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Natalie Vokes
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Carmen Behrens
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Andrew Futreal
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Ara Vaporciyan
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Boris Sepesi
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - John V. Heymach
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Cara Haymaker
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Jianjun Zhang
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | | | | | - Don L. Gibbons
- The University of Texas MD Anderson Cancer Center, Houston, TX
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22
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Frank M, Shah P, Forget MA, Federico L, Jiang P, Khairullah R, Wistuba I, Chow CW, Long Y, Fujimoto J, Lin SY, Maitra A, Negrao M, Mitchell K, Weissferdt A, Vaporciyan A, Cascone T, Roth J, Zhang J, Sepesi B, Gibbons D, Heymach J, Haymaker C, McGrail D, Bernatchez C, Reuben A. 174 Combined IL-2, agonistic CD3 and 4–1BB stimulation preserve clonotype hierarchy in propagated non-small cell lung cancer tumor-infiltrating lymphocytes. J Immunother Cancer 2021. [DOI: 10.1136/jitc-2021-sitc2021.174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
BackgroundWhile immune checkpoint blockade is regarded as standard of care for treatment of non-small cell lung cancer (NSCLC), up to 50% of patients with metastatic NSCLC do not achieve an optimal response.1–3 Previous work by our group and others in adoptive cell therapy (ACT) of metastatic melanoma (MM) has shown that infusion of a CD8+-rich TIL product significantly improved clinical outcomes, yet traditional IL-2 expansion methods have resulted in a predominantly CD4+ NSCLC TIL expansion product.7–12 This preclinical study explores the feasibility of producing a tumor-specific, CD8+-enriched NSCLC TIL product for ACT with an improved culture method.MethodsTIL from resected NSCLC tumors were cultured using 1) the traditional method using IL-2 alone in 24-well plates (TIL 1.0) or 2) IL-2 in combination with agonistic antibodies against CD3 and 4-1BB (Urelumab) in a G-Rex flask (TIL 3.0). Expanded TIL were phenotyped using flow cytometry for CD4 and CD8 subset assessment and the CDR3-beta variable region of the T-cell receptor (TCR) involved in antigen binding was sequenced to assess the T-cell repertoire.ResultsIn a shorter manufacturing time (median of 14 days vs 27.5 days), TIL 3.0 expanded on average 5.3-times more NSCLC TIL (95% CI= 4.3–6.2, p<0.0001) and achieved a higher expansion success rate than the traditional TIL 1.0 method (100% vs 62.5%, respectively, p<0.0001). Additionally, TIL 3.0 greatly enriched for CD3+CD8+ TIL (81.8% vs 36.9%, p=0.001) and expanded a larger breadth of clonotypes (p=0.039) which shared greater homology with the total clonotypes found in the repertoire of the resected tumor (p=0.0007), and contained a greater fraction of the clones found at high frequency in the tumor (p<0.00001). TIL 3.0 also retained a higher proportion of putative tumor-specific TCR when compared to TIL 1.0 (p=0.0039), defined based on exclusion of known viral-specific TCR and other TCR found in the paired uninvolved lung tissue.ConclusionsThis study reports the feasibility of using the TIL 3.0 methodology to robustly expand a CD8+ T-cell repertoire which maintains the respective clonal hierarchy in NSCLC tumors and enriches for putative tumor-specific TIL clones. The robustness and speed of the new process may facilitate testing and implementing effective TIL ACT in NSCLC.ReferencesGaron EB, Rizvi NA, Hui R, Leighl N, Balmanoukian AS, Eder JP, et al. Pembrolizumab for the treatment of non-small-cell lung cancer. N Engl J Med 2015;372(21):2018–28.Borghaei H, Paz-Ares L, Horn L, Spigel DR, Steins M, Ready NE, et al. Nivolumab versus Docetaxel in Advanced Nonsquamous Non-Small-Cell Lung Cancer. N Engl J Med 2015;373(17):1627–39.Gettinger S, Horn L, Jackman D, Spigel D, Antonia S, Hellmann M, et al. Five-Year Follow-Up of Nivolumab in Previously Treated Advanced Non-Small-Cell Lung Cancer: Results from the CA209–003 Study. J Clin Oncol 2018;36(17):1675–84.Melioli G, Ratto G, Guastella M, Meta M, Biassoni R, Semino C, et al. Isolation and in vitro expansion of lymphocytes infiltrating non-small cell lung carcinoma: functional and molecular characterisation for their use in adoptive immunotherapy. Eur J Cancer 1994;30A(1):97–102.McGranahan N, Furness AJ, Rosenthal R, Ramskov S, Lyngaa R, Saini SK, et al. Clonal neoantigens elicit T cell immunoreactivity and sensitivity to immune checkpoint blockade. Science 2016;351(6280):1463–9.Rosenberg SA, Yang JC, Sherry RM, Kammula US, Hughes MS, Phan GQ, et al. Durable complete responses in heavily pretreated patients with metastatic melanoma using T-cell transfer immunotherapy. Clin Cancer Res 2011;17(13):4550–7.Besser MJ, Shapira-Frommer R, Treves AJ, Zippel D, Itzhaki O, Hershkovitz L, et al. Clinical responses in a phase II study using adoptive transfer of short-term cultured tumor infiltration lymphocytes in metastatic melanoma patients. Clin Cancer Res 2010;16(9):2646–55.Pilon-Thomas S, Kuhn L, Ellwanger S, Janssen W, Royster E, Marzban S, et al. Efficacy of adoptive cell transfer of tumor-infiltrating lymphocytes after lymphopenia induction for metastatic melanoma. J Immunother 2012;35(8):615–20.Radvanyi LG, Bernatchez C, Zhang M, Fox PS, Miller P, Chacon J, et al. Specific Lymphocyte Subsets Predict Response to Adoptive Cell Therapy Using Expanded Autologous Tumor-Infiltrating Lymphocytes in Metastatic Melanoma Patients. Clinical Cancer Research 2012;18(24):6758–70.Forget MA, Haymaker C, Hess KR, Meng YJ, Creasy C, Karpinets T, et al. Prospective Analysis of Adoptive TIL Therapy in Patients with Metastatic Melanoma: Response, Impact of Anti-CTLA4, and Biomarkers to Predict Clinical Outcome. Clin Cancer Res 2018;24(18):4416–28.Ben-Avi R, Farhi R, Ben-Nun A, Gorodner M, Greenberg E, Markel G, et al. Establishment of adoptive cell therapy with tumor infiltrating lymphocytes for non-small cell lung cancer patients. Cancer Immunol Immunother 2018;67(8):1221–30.Ma Y, Ou J, Lin T, Chen L, Wang J, Qiao D, et al. Phenotypic analysis of tumor-infiltrating lymphocytes from non-small cell lung cancer and their potential application for adoptive cell therapy. Immunopharmacol Immunotoxicol 2020;42(4):319–29Ethics ApprovalThis study was performed on NSCLC tumor tissue resected from 16 patients enrolled, following informed consent, in the ImmunogenomiC prOfiling of early-stage NSCLC (ICON) project. This study was approved by the University of Texas MD Anderson Cancer Center‘s Institutional Review Board (protocol number PA15-1112_MODCR001).
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Lee JJ, Bernard V, Semaan A, Monberg ME, Huang J, Stephens BM, Lin D, Rajapakshe KI, Weston BR, Bhutani MS, Haymaker CL, Bernatchez C, Taniguchi CM, Maitra A, Guerrero PA. Elucidation of Tumor-Stromal Heterogeneity and the Ligand-Receptor Interactome by Single-Cell Transcriptomics in Real-world Pancreatic Cancer Biopsies. Clin Cancer Res 2021; 27:5912-5921. [PMID: 34426439 PMCID: PMC8563410 DOI: 10.1158/1078-0432.ccr-20-3925] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Revised: 06/22/2021] [Accepted: 08/18/2021] [Indexed: 01/01/2023]
Abstract
PURPOSE Precision medicine approaches in pancreatic ductal adenocarcinoma (PDAC) are imperative for improving disease outcomes. With molecular subtypes of PDAC gaining relevance in the context of therapeutic stratification, the ability to characterize heterogeneity of cancer-specific gene expression patterns is of great interest. In addition, understanding patterns of immune evasion within PDAC is of importance as novel immunotherapeutic strategies are developed. EXPERIMENTAL DESIGN Single-cell RNA sequencing (scRNA-seq) is readily applicable to limited biopsies from human primary and metastatic PDAC and identifies most cancers as being an admixture of previously described epithelial transcriptomic subtypes. RESULTS Integrative analyses of our data provide an in-depth characterization of the heterogeneity within the tumor microenvironment, including cancer-associated fibroblast subclasses, and predicts for a multitude of ligand-receptor interactions, revealing potential targets for immunotherapy approaches. CONCLUSIONS Our analysis demonstrates that the use of de novo biopsies from patients with PDAC paired with scRNA-seq may facilitate therapeutic prediction from limited biopsy samples.
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Affiliation(s)
- Jaewon J Lee
- Sheikh Ahmed Center for Pancreatic Cancer Research, 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
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Vincent Bernard
- Sheikh Ahmed Center for Pancreatic Cancer Research, 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
| | - Alexander Semaan
- Sheikh Ahmed Center for Pancreatic Cancer Research, 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
| | - Maria E Monberg
- Sheikh Ahmed Center for Pancreatic Cancer Research, 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
| | - Jonathan Huang
- Sheikh Ahmed Center for Pancreatic Cancer Research, 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
| | - Bret M Stephens
- Sheikh Ahmed Center for Pancreatic Cancer Research, 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
| | - Daniel Lin
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Kimal I Rajapakshe
- Sheikh Ahmed Center for Pancreatic Cancer Research, 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
| | - Brian R Weston
- Department of Gastroenterology, Hepatology, and Nutrition, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Manoop S Bhutani
- Department of Gastroenterology, Hepatology, and Nutrition, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Cara L Haymaker
- Department of Translational Molecular Pathology, 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
| | - Cullen M Taniguchi
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Anirban Maitra
- Sheikh Ahmed Center for Pancreatic Cancer Research, 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
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Paola A Guerrero
- Sheikh Ahmed Center for Pancreatic Cancer Research, 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
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Paniagua MA, Haymaker C, Adolacion JR, An X, Creasy C, Fathi M, Rezvan A, Geiger T, Harel M, Robinson J, Amritkar A, Woodman S, Hwu P, Bernatchez C, Varadarajan N. 187 Multi-omic single-cell profiling demonstrates that competition for fatty acids and fatty acid oxidation enables tumor-infiltrating lymphocyte function and survival. J Immunother Cancer 2021. [DOI: 10.1136/jitc-2021-sitc2021.187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
BackgroundAdoptive transfer of ex vivo expanded tumor-infiltrating lymphocytes (TIL) have shown durable responses in metastatic melanoma, yet these responses are unpredictable. Bioenergetics dictates the function and fate of adoptively transferred human T cells within the tumor microenvironment but the nature of metabolic competition leading to T-cell function and dysfunction are incompletely understood.MethodsWe integrated the profiling of TIL co-cultured with their autologous primary tumor cells with the aid of a suite of high-throughput single-cell functional assays, transcriptional, and proteomic assays. We validated the results of the model using flow cytometry and confocal microscopy. Association of functional features with clinical outcome was assessed.ResultsTimelapse Imaging Microscopy In Nanowell Grids (TIMING) demonstrated that while TIL frequencies in killing autologous tumor cells are equivalent across the donors, R-TIL had a significantly higher survival rate than NR-TILs. Tumor cells from NR patients had higher motility and showed increased elongation compared to R-tumors. RNA-sequencing (RNA-seq) and proteomics showed that NR-tumors were enriched in pathways associated with utilization of fatty acids (FAs) and adipogenesis, as well as cancer cell metastasis, cellular motility, adhesion, and migration. Candidate genes associated with ameboidal migration (MYH9, MYH2; WNT5B and SERPINE1) and FA utilization (CD36 and PPARG) were enriched in the NR-tumors. Flow cytometry and confocal microscopy confirmed that NR-tumors showed increased CD36 expression and FA uptake compared to R-tumors. To simulate metabolic competition, we co-cultured the TIL with autologous tumors and sorted TIL for RNAseq. The R-TIL were enriched in pathways related to mitochondrial and carbohydrate metabolism; fatty acid oxidation (FAO), and long-chain FAs with a direct enrichment in fatty acyl CoA biosynthesis and both peroxisomal and mitochondrial FAO. Since patient-derived TILs were limiting for metabolomics type assays, we utilized genome-scale metabolic models to infer relevant metabolic pathways by comparison to the human metabolic Atlas (HMR2). At the level of individual metabolites, the significantly enriched metabolites within R TILs were dominated by peroxisome and mitochondria derived fatty acyl-CoA: e.g. palmitoyl-CoA, linoleoyl-CoA, and oleoyl-CoA. We utilized flow cytometry and confocal microscopy to perform pulse-chase assays with FAs for validation. R-TILs showed an increased accumulation of FA into the mitochondria confirming a direct role for TIL FAO.ConclusionsEfficient competition for FAs is a key attribute of T-cell efficacy in ACT. R-TILs are able to utilize FAs via FAO when in competition with autologous tumor cells whereas NR tumors effectively uptake and store FAs preventing T-cell function.AcknowledgementsThis abstract was supported by the NIH (R01CA174385); CPRIT (RP180466); MRA Established Investigator Award to NV (509800), Welch Foundation (E1774); NSF (1705464); CDMRP (CA160591); Owens Foundation (NV). We would like to acknowledge the MDACC Flow Cytometry and Cellular Imaging Core facility for the FACS sorting (NCI P30CA16672), UH Seq-n-edit core for RNA-seq, Intel for the loan of computing cluster, and the UH Center for Advanced Computing and Data Systems (CACDS) for high-performance computing facilities.Trial Registration protocol (2004–0069)Ethics ApprovalApproved by the Institutional Review Board (IRB) of the MD Anderson Cancer Center (Houston, TX) and an FDA- approved Investigational New Drug (IND) application (NCT00338377)
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Schmidt S, Lee Y, Leung C, Federico L, Lin H, Weissferdt A, Pataer A, Dejima H, Francisco-Cruz A, Rojas F, Solis L, Parra E, Pradhan M, Guo H, William W, Reuben A, Kadara H, Wistuba I, Zhang J, Swisher S, Vaporciyan A, Negrao M, Bristow C, Heffernan T, Bernatchez C, Lee J, Heymach J, Sepesi B, Gibbons D, Haymaker C, Cascone T. 962 Integrative immunomics highlight the immunomodulatory impact of neoadjuvant chemotherapy and immune-based treatments in resected non-small-cell lung cancer. J Immunother Cancer 2021. [DOI: 10.1136/jitc-2021-sitc2021.962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
BackgroundHow neoadjuvant chemo-immunotherapy modulates tumor immune composition and response is not completely understood. We interrogate immunomodulation of neoadjuvant platinum-based chemotherapy (C), nivolumab (N), and N-plus-C (NC) and their connections to therapeutic efficacy in resected non-small cell lung cancer (NSCLC) by integrating immunomic data from the ImmunogenomiC PrOfiling of NSCLC (ICON) study and NEOSTAR trial cohorts.MethodsIn NEOSTAR (NCT03158129), patients with stage I-IIIA (single N2) resectable NSCLC (AJCC7th) received N (3 mg/kg IV, D1,15,29); patients with stage IB(≥4cm)-IIIA (single N2) resectable NSCLC received NC (N 360 mg IV plus C, D1,22,43 for 3 cycles, every 3 weeks) before surgery; major pathologic response (MPR) was the primary endpoint. In ICON, patients with stage IB(≥4cm)-IIIA resectable NSCLC received C before surgery. Surgically resected tumor samples underwent immune profiling via flow cytometry (n=16,13,9 for C,N,NC), immunohistochemistry (IHC;n=0,18,14), and multiplexed immunofluorescence (mIF;n=28,16,10). Treatment-associated immunomodulation and associations with therapeutic efficacy were analyzed using: 1) a shared nearest neighbors-based network we developed linking measurements across datasets; 2) MetaCyto, a specialized cytometry analysis method for identifying cell subsets by clustering.ResultsWe holistically explored the immunomic data by integration across cohorts. Through hierarchical regression of the integrated data, we determined the overall effect of a given treatment controlling for the presence or absence of the other treatment.We examined C’s effects across all cohorts controlling for N. Across all patients, regardless of MPR, C is associated with immunosuppression, increasing PD1+ T cell (CD45+CD3+) populations: regulatory (CD4+CD25+FOXP3+), helper (CD4+), and effector (CD8+) (effect size(ES):1.48,1.61,1.26;q<0.05). C also decreases proliferative (Ki67+) populations: helper and effector T cells as well as NK (CD45+CD3-CD56+) cells (ES:-1.27,-1.43;-1.36;q<0.05). In patients without MPR (i.e., non-responding patients), immunosuppression appears heightened by increased Ki67+ regulatory T cells (ES:1.86;q<0.05).Conversely, we examined N’s effects across all cohorts controlling for C. Across all patients, regardless of MPR, N is associated with immune activation, increasing ICOS+ T cell populations: regulatory, helper, and effector (ES:1.29,1.29,1.47;q<0.05). Comparing N and NC reveals that adding C may drive exhaustion by increasing TIM3+ regulatory, helper and effector T cells (ES:1.16,1.17,1.23;q<0.05), an effect more pronounced in non-responding patients (ES:1.31,1.33,1.35;q<0.05).ConclusionsWe report the first integrated examination of the immunomodulatory effect of neoadjuvant C and N. C is associated with immunosuppression while N with immune activation; together, N appears to lessen C’s suppressive effects. Incorporation of transcriptomics into this integrated network of flow cytometry, mIF, and IHC immune profiling data is ongoing to augment translational insights for neoadjuvant chemo/immunotherapies.
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Fix S, Forget MA, Sakellariou-Thompson D, Wang Y, Dominguez AL, Basar R, Reyes C, Kumar S, Meyer L, Hwu P, Bernatchez C, Jazaeri A. 172 Overcoming immunosuppressive TGF-β signaling in human ovarian cancer-derived tumor infiltrating lymphocytes via non-viral CRISPR engineering. J Immunother Cancer 2021. [DOI: 10.1136/jitc-2021-sitc2021.172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
BackgroundOur ongoing clinical trial for the treatment of melanoma with TGF-β-resistant tumor-infiltrating lymphocytes (TIL) [TGF-β dominant negative receptor 2 (TGFβDNR2) transduced-TIL] has yielded long-term responses in checkpoint refractory patients (NCT01955460). Building on this success, we sought to extend the impact of TGF-β–resistant TIL therapy to additional cancers while optimizing a non-viral alternative to transduction with a TGFβDNR2. Ovarian cancer (OvCa), which is characterized by an abundance of TGF-β, a dysfunctional immune infiltrate, and a paucity of novel treatment options, is an ideal candidate for TGF-β–resistant TIL therapy. Here, we present an optimized and clinically-scalable method for CRISPR/Cas9-mediated deletion of the TGF-β receptor (TGFBR2) in OvCa TIL.MethodsOvCa TIL were generated from tumor fragments1 and subjected to CRISPR-mediated knockout of TGFBR2 before going through a rapid expansion protocol. Resistance of TGFBR2-knockout TIL to TGF-β signaling was evaluated via quantification of downstream SMAD-2/-3 phosphorylation, global transcriptional changes upon TGF-β exposure, and cytokine release following TCR stimulation in the presence of TGF-β. The impact of CRISPR modification on TIL expansion and TCR clonal diversity was evaluated. Finally, the risk of off-target CRISPR activity throughout the genome was evaluated using Target Enriched GUIDE-seq (TEG-seq)2 followed by next generation sequencing (NGS) validation of putative off-target sites.ResultsUsing five TGFBR2-directed guide RNAs (gRNAs), we achieved gene disruption efficiencies ranging from 48%–90%, which correlated inversely with the degree of SMAD phosphorylation after TGF-β exposure (r=-0.9440, p=0.0158, n=4 donors) (figure 1A-C). TGF-β exposure induced a strong transcriptional response in wild-type TIL but had little to no effect on TGFBR2-knockout TIL (figure 2). TGFBR2-knockout TIL functioned well in the presence of exogenous TGF-β as evidenced by equally strong secretion of pro-inflammatory cytokines in the presence and absence of TGF-β (figure 3). CRISPR-modification did not hamper the ex vivo expansion efficiency nor the TCR clonal diversity of expanded OvCa TIL (figure 4). Using TEG-seq, we identified ≤5 low-probability off-target sites for gRNA-#3 and gRNA-#4, each of which were attributed to background sequencing artifacts upon further validation by NGS of specific amplicons (figure 5).Abstract 172 Figure 1(A) Genomic-level TGFBR2 knockout efficiency using 5 different gRNAs as evidenced by NGS of specific amplicons (n=1 TIL donor). (B) SMAD-2 and SMAD-3 phosphorylation in TGFBR2 knockout TIL vs. control TIL after 30 min exposure to TGF-β1. The left panel shows representative histograms of phospho-SMAD staining, and the right panel shows quantification of cells positive for phospho-SMAD-2/-3 after TGF-β exposure (n=4 TIL donors). The statistical significance of each experimental condition compared to the non-transfected control is shown. (C) Inverse correlation of TGFBR2 knockout efficiency and TGF-β-mediated SMAD phosphorylation.Abstract 172 Figure 2Top 100 differentially expressed genes in non-transfected (WT) TIL exposed to TGF-β. TGFBR2 knockout (KO) TIL display minimal gene expression changes upon TGF-β exposure (n=3 technical replicates).Abstract 172 Figure 3TIL were collected after 14 days of expansion and re-stimulated with 300 ng/mL plate-bound anti-CD3 in the presence of 3000 IU/mL IL2 and 10 ng/mL human TGF-β1 or vehicle. Cell culture supernatant was collected after 72 hrs of stimulation and assayed for the presence of 10 proinflammatory cytokines (IFN-γ, IL-1β, IL-2, IL-4, IL-6, IL-8, IL-10, IL-12p70, IL-13, and TNF-α). For TIL with intact TGFBR2 (non-transfected and Cas9 mock transfected TIL), the production of many pro-inflammatory cytokines decreased significantly in the presence of TGF-β. Conversely, TGFBR2 knockout TIL (generated using gRNA #3 or gRNA #4) retain cytokine secretion in the presence of TGF-β. IL-12p70 was below the limit of detection in this assay and is therefore not presented.Abstract 172 Figure 4(A) Control and CRISPR-modified OvCa TIL expand with equal efficiency during a 14-day rapid expansion protocol. Fold expansions ranging from 1000× - 3000× were observed across 4 independent patient samples. (B) The TCR clonal diversity of TIL after 14-day expansion was assessed by TCRB sequencing. Productive Simpson Clonality was equivalent in CRISPR-modified TIL compared to control TIL samples.Abstract 172 Figure 5TEG-seq revealed 3 putative off-target sites for gRNA #3 and 5 putative off-target sites for gRNA #4. The aligned sequences show similarities and differences between the gRNA sequence and the reference genome site. Dots represent exact matches in the reference genome compared to the gRNA sequence. Dashes represent missing bases, lower-case letters represent extra bases, and upper-case letters represent a base mismatch. Validation by NGS of specific amplicons confirmed the presence of TEG-seq Tag integration and large indels at the on-target cleavage sites for gRNA #3 and #4, indicating successful Cas9 editing and Tag integration in our experiment. NGS validation revealed that all putative low probability off-target sites were background artifacts as evidenced by the lack of Tag identification and lack of large indels.ConclusionsCRISPR/Cas9-mediated knockout of TGFBR2 is feasible and efficient in patient-derived OvCa TIL using clinically-scalable methods that yield little to no evidence of off-target activity. This study lays the groundwork for clinical translation of CRISPR-modified, TGF-β-resistant TIL for OvCa treatment, which will not only provide a novel immunotherapy for OvCa patients but also a platform for engineering more potent TIL therapies in general.ReferencesSakellariou-Thompson D, Forget MA, Hinchcliff E, Celestino J, Hwu P, Jazaeri AA, et al. Potential clinical application of tumor-infiltrating lymphocyte therapy for ovarian epithelial cancer prior or post-resistance to chemotherapy. Cancer Immunology, Immunotherapy: CII 2019;68(11):1747–57.Tang PZ, Ding B, Peng L, Mozhayskiy V, Potter J, Chesnut JD. TEG-seq: an ion torrent-adapted NGS workflow for in cellulo mapping of CRISPR specificity. Bio Techniques 2018;65(5):259–67.Ethics ApprovalAll procedures performed were in accordance with the 1975 Helsinki declaration. Ethical approval and tissue from surgical resections used to expand TIL were both obtained under protocols (PA16-0912 and LAB02-188) approved by the Institutional Review Board of The University of Texas MD Anderson Cancer Center. Written informed consent was obtained from all individual participants included in the study for their specimens and data to be used in research and for publication.
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Sloane RAS, White MG, Witt RG, Banerjee A, Davies MA, Han G, Burton E, Ajami N, Simon JM, Bernatchez C, Haydu LE, Tawbi HA, Gershenwald JE, Keung E, Ross M, McQuade J, Amaria RN, Wani K, Lazar AJ, Woodman SE, Wang L, Andrews MC, Wargo JA. Identification of MicroRNA-mRNA Networks in Melanoma and Their Association with PD-1 Checkpoint Blockade Outcomes. Cancers (Basel) 2021; 13:5301. [PMID: 34771465 PMCID: PMC8582574 DOI: 10.3390/cancers13215301] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 10/14/2021] [Accepted: 10/18/2021] [Indexed: 01/04/2023] Open
Abstract
Metastatic melanoma is a deadly malignancy with poor outcomes historically. Immuno-oncology (IO) agents, targeting immune checkpoint molecules such as cytotoxic T-lymphocyte associated protein-4 (CTLA-4) and programmed cell death-1 (PD-1), have revolutionized melanoma treatment and outcomes, achieving significant response rates and remarkable long-term survival. Despite these vast improvements, roughly half of melanoma patients do not achieve long-term clinical benefit from IO therapies and there is an urgent need to understand and mitigate mechanisms of resistance. MicroRNAs are key post-transcriptional regulators of gene expression that regulate many aspects of cancer biology, including immune evasion. We used network analysis to define two core microRNA-mRNA networks in melanoma tissues and cell lines corresponding to 'MITF-low' and 'Keratin' transcriptomic subsets of melanoma. We then evaluated expression of these core microRNAs in pre-PD-1-inhibitor-treated melanoma patients and observed that higher expression of miR-100-5p and miR-125b-5p were associated with significantly improved overall survival. These findings suggest that miR-100-5p and 125b-5p are potential markers of response to PD-1 inhibitors, and further evaluation of these microRNA-mRNA interactions may yield further insight into melanoma resistance to PD-1 inhibitors.
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Affiliation(s)
- Robert A. Szczepaniak Sloane
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (R.A.S.S.); (M.G.W.); (R.G.W.); (A.B.); (E.B.); (J.M.S.); (L.E.H.); (J.E.G.); (E.K.); (M.R.); (M.C.A.)
| | - Michael G. White
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (R.A.S.S.); (M.G.W.); (R.G.W.); (A.B.); (E.B.); (J.M.S.); (L.E.H.); (J.E.G.); (E.K.); (M.R.); (M.C.A.)
| | - Russell G. Witt
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (R.A.S.S.); (M.G.W.); (R.G.W.); (A.B.); (E.B.); (J.M.S.); (L.E.H.); (J.E.G.); (E.K.); (M.R.); (M.C.A.)
| | - Anik Banerjee
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (R.A.S.S.); (M.G.W.); (R.G.W.); (A.B.); (E.B.); (J.M.S.); (L.E.H.); (J.E.G.); (E.K.); (M.R.); (M.C.A.)
| | - Michael A. Davies
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (M.A.D.); (H.A.T.); (J.M.); (R.N.A.); (S.E.W.)
| | - Guangchun Han
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (G.H.); (N.A.); (K.W.); (A.J.L.); (L.W.)
| | - Elizabeth Burton
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (R.A.S.S.); (M.G.W.); (R.G.W.); (A.B.); (E.B.); (J.M.S.); (L.E.H.); (J.E.G.); (E.K.); (M.R.); (M.C.A.)
| | - Nadim Ajami
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (G.H.); (N.A.); (K.W.); (A.J.L.); (L.W.)
| | - Julie M. Simon
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (R.A.S.S.); (M.G.W.); (R.G.W.); (A.B.); (E.B.); (J.M.S.); (L.E.H.); (J.E.G.); (E.K.); (M.R.); (M.C.A.)
| | - Chantale Bernatchez
- Department of Biologics Development, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA;
| | - Lauren E. Haydu
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (R.A.S.S.); (M.G.W.); (R.G.W.); (A.B.); (E.B.); (J.M.S.); (L.E.H.); (J.E.G.); (E.K.); (M.R.); (M.C.A.)
| | - Hussein A. Tawbi
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (M.A.D.); (H.A.T.); (J.M.); (R.N.A.); (S.E.W.)
| | - Jeffrey E. Gershenwald
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (R.A.S.S.); (M.G.W.); (R.G.W.); (A.B.); (E.B.); (J.M.S.); (L.E.H.); (J.E.G.); (E.K.); (M.R.); (M.C.A.)
| | - Emily Keung
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (R.A.S.S.); (M.G.W.); (R.G.W.); (A.B.); (E.B.); (J.M.S.); (L.E.H.); (J.E.G.); (E.K.); (M.R.); (M.C.A.)
| | - Merrick Ross
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (R.A.S.S.); (M.G.W.); (R.G.W.); (A.B.); (E.B.); (J.M.S.); (L.E.H.); (J.E.G.); (E.K.); (M.R.); (M.C.A.)
| | - Jennifer McQuade
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (M.A.D.); (H.A.T.); (J.M.); (R.N.A.); (S.E.W.)
| | - Rodabe N. Amaria
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (M.A.D.); (H.A.T.); (J.M.); (R.N.A.); (S.E.W.)
| | - Khalida Wani
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (G.H.); (N.A.); (K.W.); (A.J.L.); (L.W.)
| | - Alexander J. Lazar
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (G.H.); (N.A.); (K.W.); (A.J.L.); (L.W.)
| | - Scott E. Woodman
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (M.A.D.); (H.A.T.); (J.M.); (R.N.A.); (S.E.W.)
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (G.H.); (N.A.); (K.W.); (A.J.L.); (L.W.)
| | - Linghua Wang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (G.H.); (N.A.); (K.W.); (A.J.L.); (L.W.)
| | - Miles C. Andrews
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (R.A.S.S.); (M.G.W.); (R.G.W.); (A.B.); (E.B.); (J.M.S.); (L.E.H.); (J.E.G.); (E.K.); (M.R.); (M.C.A.)
- Department of Medicine, Central Clinical School, Monash University, Melbourne, VIC 3004, Australia
| | - Jennifer A. Wargo
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (R.A.S.S.); (M.G.W.); (R.G.W.); (A.B.); (E.B.); (J.M.S.); (L.E.H.); (J.E.G.); (E.K.); (M.R.); (M.C.A.)
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (G.H.); (N.A.); (K.W.); (A.J.L.); (L.W.)
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Lu T, Zhang Z, Zhu J, Wang Y, Jiang P, Xiao X, Bernatchez C, Heymach JV, Gibbons DL, Wang J, Xu L, Reuben A, Wang T. Deep learning-based prediction of the T cell receptor-antigen binding specificity. NAT MACH INTELL 2021; 3:864-875. [PMID: 36003885 PMCID: PMC9396750 DOI: 10.1038/s42256-021-00383-2] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [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: 02/05/2023]
Abstract
Neoantigens play a key role in the recognition of tumor cells by T cells. However, only a small proportion of neoantigens truly elicit T cell responses, and fewer clues exist as to which neoantigens are recognized by which T cell receptors (TCRs). We built a transfer learning-based model, named pMHC-TCR binding prediction network (pMTnet), to predict TCR-binding specificities of neoantigens, and T cell antigens in general, presented by class I major histocompatibility complexes (pMHCs). pMTnet was comprehensively validated by a series of analyses, and showed advance over previous work by a large margin. By applying pMTnet in human tumor genomics data, we discovered that neoantigens were generally more immunogenic than self-antigens, but HERV-E, a special type of self-antigen that is re-activated in kidney cancer, is more immunogenic than neoantigens. We further discovered that patients with more clonally expanded T cells exhibiting better affinity against truncal, rather than subclonal, neoantigens, had more favorable prognosis and treatment response to immunotherapy, in melanoma and lung cancer but not in kidney cancer. Predicting TCR-neoantigen/antigen pairs is one of the most daunting challenges in modern immunology. However, we achieved an accurate prediction of the pairing only using the TCR sequence (CDR3β), antigen sequence, and class I MHC allele, and our work revealed unique insights into the interactions of TCRs and pMHCs in human tumors using pMTnet as a discovery tool.
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Affiliation(s)
- Tianshi Lu
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA, 75390
| | - Ze Zhang
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA, 75390
| | - James Zhu
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA, 75390
| | - Yunguan Wang
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA, 75390
| | - Peixin Jiang
- Department of Thoracic/Head & Neck Medical Oncology, MD Anderson Cancer Center, Houston, TX USA, 77030
| | - Xue Xiao
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA, 75390
| | - Chantale Bernatchez
- Department of Melanoma Medical Oncology, MD Anderson Cancer Center, Houston, TX USA, 77030
| | - John V. Heymach
- Department of Thoracic/Head & Neck Medical Oncology, MD Anderson Cancer Center, Houston, TX USA, 77030
| | - Don L. Gibbons
- Department of Thoracic/Head & Neck Medical Oncology, MD Anderson Cancer Center, Houston, TX USA, 77030
| | - Jun Wang
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016
| | - Lin Xu
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA, 75390
| | - Alexandre Reuben
- Department of Thoracic/Head & Neck Medical Oncology, MD Anderson Cancer Center, Houston, TX USA, 77030.,Corresponding authors: (1) Tao Wang, Ph.D., Quantitative Biomedical Research Center, Department of Population and Data Sciences, UT Southwestern Medical Center, Dallas, TX, 75390, USA; (lead contact). (2) Alexandre Reuben, Ph.D., Department of Thoracic/Head & Neck Medical Oncology, MD Anderson Cancer Center, Houston, TX, 77030, USA;
| | - Tao Wang
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA, 75390.,Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, USA, 75390.,Corresponding authors: (1) Tao Wang, Ph.D., Quantitative Biomedical Research Center, Department of Population and Data Sciences, UT Southwestern Medical Center, Dallas, TX, 75390, USA; (lead contact). (2) Alexandre Reuben, Ph.D., Department of Thoracic/Head & Neck Medical Oncology, MD Anderson Cancer Center, Houston, TX, 77030, USA;
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29
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Chen HX, Song M, Maecker HT, Gnjatic S, Patton D, Lee JJ, Adam SJ, Moravec R, Liu XS, Cerami E, Lindsay J, Tang M, Hodi FS, Wu CJ, Wistuba II, Al-Atrash G, Bernatchez C, Bendall SC, Hewitt SM, Sharon E, Streicher H, Enos RA, Bowman MD, Tatard-Leitman VM, Sanchez-Espiridion B, Ranasinghe S, Pichavant M, Del Valle DM, Yu J, Janssens S, Peterson-Klaus J, Rowe C, Bongers G, Jenq RR, Chang CC, Abrams JS, Mooney M, Doroshow JH, Harris LN, Thurin M. Network for Biomarker Immunoprofiling for Cancer Immunotherapy: Cancer Immune Monitoring and Analysis Centers and Cancer Immunologic Data Commons (CIMAC-CIDC). Clin Cancer Res 2021; 27:5038-5048. [PMID: 33419780 PMCID: PMC8491462 DOI: 10.1158/1078-0432.ccr-20-3241] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [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: 08/17/2020] [Revised: 11/09/2020] [Accepted: 12/23/2020] [Indexed: 11/16/2022]
Abstract
PURPOSE Immunoprofiling to identify biomarkers and integration with clinical trial outcomes are critical to improving immunotherapy approaches for patients with cancer. However, the translational potential of individual studies is often limited by small sample size of trials and the complexity of immuno-oncology biomarkers. Variability in assay performance further limits comparison and interpretation of data across studies and laboratories. EXPERIMENTAL DESIGN To enable a systematic approach to biomarker identification and correlation with clinical outcome across trials, the Cancer Immune Monitoring and Analysis Centers and Cancer Immunologic Data Commons (CIMAC-CIDC) Network was established through support of the Cancer MoonshotSM Initiative of the National Cancer Institute (NCI) and the Partnership for Accelerating Cancer Therapies (PACT) with industry partners via the Foundation for the NIH. RESULTS The CIMAC-CIDC Network is composed of four academic centers with multidisciplinary expertise in cancer immunotherapy that perform validated and harmonized assays for immunoprofiling and conduct correlative analyses. A data coordinating center (CIDC) provides the computational expertise and informatics platforms for the storage, integration, and analysis of biomarker and clinical data. CONCLUSIONS This overview highlights strategies for assay harmonization to enable cross-trial and cross-site data analysis and describes key elements for establishing a network to enhance immuno-oncology biomarker development. These include an operational infrastructure, validation and harmonization of core immunoprofiling assays, platforms for data ingestion and integration, and access to specimens from clinical trials. Published in the same volume are reports of harmonization for core analyses: whole-exome sequencing, RNA sequencing, cytometry by time of flight, and IHC/immunofluorescence.
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Affiliation(s)
- Helen X Chen
- Cancer Therapy Evaluation Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute (NCI), Bethesda, Maryland.
| | - Minkyung Song
- Cancer Therapy Evaluation Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute (NCI), Bethesda, Maryland
| | - Holden T Maecker
- The Human Immune Monitoring Center (HIMC), Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, California
| | - Sacha Gnjatic
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - David Patton
- Center for Biomedical Informatics and Information Technology, NCI, Bethesda, Maryland
| | - J Jack Lee
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Stacey J Adam
- Foundation for the National Institutes of Health, North Bethesda, Maryland
| | - Radim Moravec
- Cancer Diagnosis Program, Division of Cancer Treatment and Diagnosis, NCI, Bethesda, Maryland
- Kelly Services, Rockville, Maryland
| | - Xiaole Shirley Liu
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Ethan Cerami
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - James Lindsay
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Ming Tang
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - F Stephen Hodi
- Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Catherine J Wu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts
- Harvard Medical School, Boston, Massachusetts
- Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
| | - Ignacio I Wistuba
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Gheath Al-Atrash
- Department of Stem Cell Transplantation and Cellular Therapy, 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
| | - Sean C Bendall
- Department of Pathology, School of Medicine, Stanford University, Stanford, California
| | - Stephen M Hewitt
- Laboratory of Pathology, Center for Cancer Research, NCI, Bethesda, Maryland
| | - Elad Sharon
- Cancer Therapy Evaluation Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute (NCI), Bethesda, Maryland
| | - Howard Streicher
- Cancer Therapy Evaluation Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute (NCI), Bethesda, Maryland
| | | | | | | | - Beatriz Sanchez-Espiridion
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Srinika Ranasinghe
- Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Mina Pichavant
- The Human Immune Monitoring Center (HIMC), Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, California
| | - Diane M Del Valle
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Joyce Yu
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | | | | | - Cathy Rowe
- Center for Biomedical Informatics and Information Technology, NCI, Bethesda, Maryland
- Essex Management, Rockville, Maryland
| | - Gerold Bongers
- Microbiome Translational Center, Precision Immunology Institute, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Robert R Jenq
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Chia-Chi Chang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jeffrey S Abrams
- Cancer Therapy Evaluation Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute (NCI), Bethesda, Maryland
| | - Margaret Mooney
- Cancer Therapy Evaluation Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute (NCI), Bethesda, Maryland
| | - James H Doroshow
- Division of Cancer Treatment and Diagnosis, NCI, Bethesda, Maryland
| | - Lyndsay N Harris
- Cancer Diagnosis Program, Division of Cancer Treatment and Diagnosis, NCI, Bethesda, Maryland
| | - Magdalena Thurin
- Cancer Diagnosis Program, Division of Cancer Treatment and Diagnosis, NCI, Bethesda, Maryland.
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30
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Sahaf B, Pichavant M, Lee BH, Duault C, Thrash EM, Davila M, Fernandez N, Millerchip K, Bentebibel SE, Haymaker C, Sigal N, Del Valle DM, Ranasinghe S, Fayle S, Sanchez-Espiridion B, Zhang J, Bernatchez C, Wu CJ, Wistuba II, Kim-Schulze S, Gnjatic S, Bendall SC, Song M, Thurin M, Lee JJ, Maecker HT, Rahman A. Immune Profiling Mass Cytometry Assay Harmonization: Multicenter Experience from CIMAC-CIDC. Clin Cancer Res 2021; 27:5062-5071. [PMID: 34266889 PMCID: PMC8448982 DOI: 10.1158/1078-0432.ccr-21-2052] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 06/04/2021] [Revised: 07/10/2021] [Accepted: 07/12/2021] [Indexed: 11/16/2022]
Abstract
PURPOSE The Cancer Immune Monitoring and Analysis Centers - Cancer Immunologic Data Commons (CIMAC-CIDC) Network is supported by the NCI to identify biomarkers of response to cancer immunotherapies across clinical trials using state-of-the-art assays. A primary platform for CIMAC-CIDC studies is cytometry by time of flight (CyTOF), performed at all CIMAC laboratories. To ensure the ability to generate comparable CyTOF data across labs, a multistep cross-site harmonization effort was undertaken. EXPERIMENTAL DESIGN We first harmonized standard operating procedures (SOPs) across the CIMAC sites. Because of a new acquisition protocol comparing original narrow- or new wide-bore injector introduced by the vendor (Fluidigm), we also tested this protocol across sites before finalizing the harmonized SOP. We then performed cross-site assay harmonization experiments using five shared cryopreserved and one lyophilized internal control peripheral blood mononuclear cell (PBMC) with a shared lyophilized antibody cocktail consisting of 14 isotype-tagged antibodies previously validated, plus additional liquid antibodies. These reagents and samples were distributed to the CIMAC sites and the data were centrally analyzed by manual gating and automated methods (Astrolabe). RESULTS Average coefficients of variation (CV) across sites for each cell population were reported and compared with a previous multisite CyTOF study. We reached an intersite CV of under 20% for most cell subsets, very similar to a previously published study. CONCLUSIONS These results establish the ability to reproduce CyTOF data across sites in multicenter clinical trials, and also highlight the importance of quality control procedures, such as the use of spike-in control samples, for tracking variability in this assay.
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Affiliation(s)
- Bita Sahaf
- Stanford Cancer Institute, Stanford Medicine, Stanford University, California.
| | - Mina Pichavant
- Stanford Institute for Immunity, Transplantation and Infection, Stanford Medicine, Stanford university, California
| | - Brian H Lee
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Caroline Duault
- Stanford Institute for Immunity, Transplantation and Infection, Stanford Medicine, Stanford university, California
| | - Emily M Thrash
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Melanie Davila
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Nicolas Fernandez
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Karen Millerchip
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Salah-Eddine Bentebibel
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Cara Haymaker
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Natalia Sigal
- Stanford Institute for Immunity, Transplantation and Infection, Stanford Medicine, Stanford university, California
| | - Diane M Del Valle
- Human Immune Monitoring Center, Tisch Cancer Institute and the Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Srinika Ranasinghe
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Sarah Fayle
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Beatriz Sanchez-Espiridion
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jiexin Zhang
- Department of Bioinformatics & Computational Biology, 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
| | - Catherine J Wu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Harvard Medical School, Harvard University, Boston, Massachusetts
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Ignacio I Wistuba
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Seunghee Kim-Schulze
- Human Immune Monitoring Center, Tisch Cancer Institute and the Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Sacha Gnjatic
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Sean C Bendall
- Department of Pathology, Stanford Medicine, Stanford University, Stanford, California
| | - Minkyung Song
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, Maryland
| | - Magdalena Thurin
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, Maryland
| | - J Jack Lee
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Holden T Maecker
- Stanford Institute for Immunity, Transplantation and Infection, Stanford Medicine, Stanford university, California
| | - Adeeb Rahman
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, New York
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
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31
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Mitchell KG, Diao L, Karpinets T, Negrao MV, Tran HT, Parra ER, Corsini EM, Reuben A, Federico L, Bernatchez C, Dejima H, Francisco-Cruz A, Wang J, Antonoff MB, Vaporciyan AA, Swisher SG, Cascone T, Wistuba II, Heymach JV, Gibbons DL, Zhang J, Haymaker CL, Sepesi B. Neutrophil expansion defines an immunoinhibitory peripheral and intratumoral inflammatory milieu in resected non-small cell lung cancer: a descriptive analysis of a prospectively immunoprofiled cohort. J Immunother Cancer 2021; 8:jitc-2019-000405. [PMID: 32350118 PMCID: PMC7213906 DOI: 10.1136/jitc-2019-000405] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [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] [Accepted: 03/30/2020] [Indexed: 01/03/2023] Open
Abstract
Background The biological underpinnings of the prognostic and predictive significance of a relative neutrophilia in patients with non-small lung cancer (NSCLC) are undefined. We sought to comprehensively examine the relationships between circulating and intratumoral neutrophil populations and features of the immune contexture in patients undergoing NSCLC resection. Methods Preoperative soluble cytokine and angiogenic factors; tumor multiplex immunofluorescence; RNA, whole exome, and T-cell receptor sequencing; and flow cytometry were analyzed for relationships with populations of circulating (from complete blood counts) and intratumoral neutrophils (transcriptional signatures) in a prospectively enrolled resected NSCLC cohort (n=66). In a historical cohort (n=1524), preoperative circulating neutrophil and lymphocyte counts were analyzed for associations with overall survival (OS). Results Circulating neutrophil populations were positively correlated with increased tumor burden, and surgical tumor resection was followed by a subsequent reduction in peripheral neutrophil counts. Expansion of the circulating neutrophil compartment was associated with increased levels of pro-granulopoietic (IL-1β, IL-17A, TNFα, IL-6) and TH2-associated (IL-5, IL-13) cytokines. Tumors with high intratumoral neutrophil burden were marked by a blunted T-cell response characterized by reduced expression of cytotoxic T-cell genes (CD8A, CD8B, GZMA, GZMB), decreased CD3+CD8+ cell infiltration, and diminished expression of IFNγ-related genes. The associations between increased intratumoral neutrophil burden and reduced CD3+CD8+ infiltration persisted after adjustment for tumor size, histology, mutational burden, and PD-L1 expression. In 1524 patients, elevated preoperative circulating neutrophil count was independently associated with worse OS (main effect HR 1.82, 95% CI 1.24 to 2.68, p=0.002). Conclusions Our findings demonstrate that neutrophil expansion reflects protumorigenic and immunosuppressive processes that manifest as worse OS in patients undergoing NSCLC resection. These results justify further investigation of therapeutic strategies targeting neutrophil-associated immune evasion.
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Affiliation(s)
- Kyle G Mitchell
- Thoracic and Cardiovascular Surgery, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Lixia Diao
- Bioinformatics and Computational Biology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Tatiana Karpinets
- Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Marcelo V Negrao
- Thoracic/Head and Neck Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Hai T Tran
- Thoracic/Head and Neck Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Edwin R Parra
- Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Erin M Corsini
- Thoracic and Cardiovascular Surgery, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Alexandre Reuben
- Thoracic/Head and Neck Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Lorenzo Federico
- Melanoma Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Chantale Bernatchez
- Melanoma Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Hitoshi Dejima
- Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Alejandro Francisco-Cruz
- Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Jing Wang
- Bioinformatics and Computational Biology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Mara B Antonoff
- Thoracic and Cardiovascular Surgery, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Ara A Vaporciyan
- Thoracic and Cardiovascular Surgery, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Stephen G Swisher
- Thoracic and Cardiovascular Surgery, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Tina Cascone
- Thoracic/Head and Neck Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Ignacio I Wistuba
- Thoracic/Head and Neck Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA.,Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - John V Heymach
- Thoracic/Head and Neck Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Don L Gibbons
- Thoracic/Head and Neck Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA.,Molecular and Cellular Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Jianjun Zhang
- Thoracic/Head and Neck Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Cara L Haymaker
- Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Boris Sepesi
- Thoracic and Cardiovascular Surgery, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
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Haymaker C, Johnson DH, Murthy R, Bentebibel SE, Uemura MI, Hudgens CW, Safa H, James M, Andtbacka RHI, Johnson DB, Shaheen M, Davies MA, Rahimian S, Chunduru SK, Milton DR, Tetzlaff MT, Overwijk WW, Hwu P, Gabrail N, Agrawal S, Doolittle G, Puzanov I, Markowitz J, Bernatchez C, Diab A. Tilsotolimod with Ipilimumab Drives Tumor Responses in Anti-PD-1 Refractory Melanoma. Cancer Discov 2021; 11:1996-2013. [PMID: 33707233 PMCID: PMC8544022 DOI: 10.1158/2159-8290.cd-20-1546] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [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: 10/26/2020] [Revised: 02/08/2021] [Accepted: 03/09/2021] [Indexed: 11/16/2022]
Abstract
Many patients with advanced melanoma are resistant to immune checkpoint inhibition. In the ILLUMINATE-204 phase I/II trial, we assessed intratumoral tilsotolimod, an investigational Toll-like receptor 9 agonist, with systemic ipilimumab in patients with anti-PD-1- resistant advanced melanoma. In all patients, 48.4% experienced grade 3/4 treatment-emergent adverse events. The overall response rate at the recommended phase II dose of 8 mg was 22.4%, and an additional 49% of patients had stable disease. Responses in noninjected lesions and in patients expected to be resistant to ipilimumab monotherapy were observed. Rapid induction of a local IFNα gene signature, dendritic cell maturation and enhanced markers of antigen presentation, and T-cell clonal expansion correlated with clinical response. A phase III clinical trial with this combination (NCT03445533) is ongoing. SIGNIFICANCE: Despite recent developments in advanced melanoma therapies, most patients do not experience durable responses. Intratumoral tilsotolimod injection elicits a rapid, local type 1 IFN response and, in combination with ipilimumab, activates T cells to promote clinical activity, including in distant lesions and patients not expected to respond to ipilimumab alone.This article is highlighted in the In This Issue feature, p. 1861.
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Affiliation(s)
- Cara Haymaker
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Daniel H Johnson
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Ravi Murthy
- Department of Interventional Radiology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Salah-Eddine Bentebibel
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Marc I Uemura
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Courtney W Hudgens
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Houssein Safa
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Marihella James
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Robert H I Andtbacka
- Surgical Oncology Department of Surgery, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
| | - Douglas B Johnson
- Division of Oncology, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Montaser Shaheen
- Department of Medicine and Cancer Center, University of Arizona, Tucson, Arizona
| | - Michael A Davies
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | | | - Denái R Milton
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Michael T Tetzlaff
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Department of Pathology, 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
| | - Patrick Hwu
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Nashat Gabrail
- Department of Oncology, Gabrail Cancer Center, Canton, Ohio
| | - Sudhir Agrawal
- Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Gary Doolittle
- Department of Oncology, University of Kansas Medical Center, Kansas City, Kansas
| | - Igor Puzanov
- Department of Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Joseph Markowitz
- Department of Cutaneous Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Chantale Bernatchez
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas.
| | - Adi Diab
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas.
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Terranova CJ, Tang M, Maitituoheti M, Raman AT, Ghosh AK, Schulz J, Amin SB, Orouji E, Tomczak K, Sarkar S, Oba J, Creasy C, Wu CJ, Khan S, Lazcano R, Wani K, Singh A, Barrodia P, Zhao D, Chen K, Haydu LE, Wang WL, Lazar AJ, Woodman SE, Bernatchez C, Rai K. Reprogramming of bivalent chromatin states in NRAS mutant melanoma suggests PRC2 inhibition as a therapeutic strategy. Cell Rep 2021; 36:109410. [PMID: 34289358 PMCID: PMC8369408 DOI: 10.1016/j.celrep.2021.109410] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 05/13/2021] [Accepted: 06/25/2021] [Indexed: 12/27/2022] Open
Abstract
The dynamic evolution of chromatin state patterns during metastasis, their relationship with bona fide genetic drivers, and their therapeutic vulnerabilities are not completely understood. Combinatorial chromatin state profiling of 46 melanoma samples reveals an association of NRAS mutants with bivalent histone H3 lysine 27 trimethylation (H3K27me3) and Polycomb repressive complex 2. Reprogramming of bivalent domains during metastasis occurs on master transcription factors of a mesenchymal phenotype, including ZEB1, TWIST1, and CDH1. Resolution of bivalency using pharmacological inhibition of EZH2 decreases invasive capacity of melanoma cells and markedly reduces tumor burden in vivo, specifically in NRAS mutants. Coincident with bivalent reprogramming, the increased expression of pro-metastatic and melanocyte-specific cell-identity genes is associated with exceptionally wide H3K4me3 domains, suggesting a role for this epigenetic element. Overall, we demonstrate that reprogramming of bivalent and broad domains represents key epigenetic alterations in metastatic melanoma and that EZH2 plus MEK inhibition may provide a promising therapeutic strategy for NRAS mutant melanoma patients.
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Affiliation(s)
- Christopher J Terranova
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Ming Tang
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA; FAS informatics, Department of Molecular Biology, Harvard, Cambridge, MA 02138, USA
| | - Mayinuer Maitituoheti
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Ayush T Raman
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA; Epigenomics Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Graduate Program in Quantitative Sciences, Baylor College of Medicine, Houston, TX 77030, USA
| | - Archit K Ghosh
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Jonathan Schulz
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Samir B Amin
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA; The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Elias Orouji
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA; Epigenetics Initiative, Princess Margaret Genomics Centre, Toronto, ON M5G 2C1, Canada
| | - Katarzyna Tomczak
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Sharmistha Sarkar
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Junna Oba
- Department of Melanoma Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Caitlin Creasy
- Department of Melanoma Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Chang-Jiun Wu
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Samia Khan
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Rossana Lazcano
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Khalida Wani
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Anand Singh
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Praveen Barrodia
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Dongyu Zhao
- Houston Methodist Academic Institute, Methodist Hospital Research Institute, Houston, TX 77030, USA
| | - Kaifu Chen
- Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Lauren E Haydu
- Surgical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Wei-Lien Wang
- Department of Pathology, University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Alexander J Lazar
- Department of Pathology, University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Scott E Woodman
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA; Department of Melanoma Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA; Department of Systems Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Chantale Bernatchez
- Department of Melanoma Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Kunal Rai
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA.
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Li F, Deng L, Jackson KR, Talukder AH, Katailiha AS, Bradley SD, Zou Q, Chen C, Huo C, Chiu Y, Stair M, Feng W, Bagaev A, Kotlov N, Svekolkin V, Ataullakhanov R, Miheecheva N, Frenkel F, Wang Y, Zhang M, Hawke D, Han L, Zhou S, Zhang Y, Wang Z, Decker WK, Sonnemann HM, Roszik J, Forget MA, Davies MA, Bernatchez C, Yee C, Bassett R, Hwu P, Du X, Lizee G. Neoantigen vaccination induces clinical and immunologic responses in non-small cell lung cancer patients harboring EGFR mutations. J Immunother Cancer 2021; 9:jitc-2021-002531. [PMID: 34244308 PMCID: PMC8268925 DOI: 10.1136/jitc-2021-002531] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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] [Accepted: 06/07/2021] [Indexed: 12/22/2022] Open
Abstract
Background Neoantigen (NeoAg) peptides displayed at the tumor cell surface by human leukocyte antigen molecules show exquisite tumor specificity and can elicit T cell mediated tumor rejection. However, few NeoAgs are predicted to be shared between patients, and none to date have demonstrated therapeutic value in the context of vaccination. Methods We report here a phase I trial of personalized NeoAg peptide vaccination (PPV) of 24 stage III/IV non-small cell lung cancer (NSCLC) patients who had previously progressed following multiple conventional therapies, including surgery, radiation, chemotherapy, and tyrosine kinase inhibitors (TKIs). Primary endpoints of the trial evaluated feasibility, tolerability, and safety of the personalized vaccination approach, and secondary trial endpoints assessed tumor-specific immune reactivity and clinical responses. Of the 16 patients with epidermal growth factor receptor (EGFR) mutations, nine continued TKI therapy concurrent with PPV and seven patients received PPV alone. Results Out of 29 patients enrolled in the trial, 24 were immunized with personalized NeoAg peptides. Aside from transient rash, fatigue and/or fever observed in three patients, no other treatment-related adverse events were observed. Median progression-free survival and overall survival of the 24 vaccinated patients were 6.0 and 8.9 months, respectively. Within 3–4 months following initiation of PPV, seven RECIST-based objective clinical responses including one complete response were observed. Notably, all seven clinical responders had EGFR-mutated tumors, including four patients that had continued TKI therapy concurrently with PPV. Immune monitoring showed that five of the seven responding patients demonstrated vaccine-induced T cell responses against EGFR NeoAg peptides. Furthermore, two highly shared EGFR mutations (L858R and T790M) were shown to be immunogenic in four of the responding patients, all of whom demonstrated increases in peripheral blood neoantigen-specific CD8+ T cell frequencies during the course of PPV. Conclusions These results show that personalized NeoAg vaccination is feasible and safe for advanced-stage NSCLC patients. The clinical and immune responses observed following PPV suggest that EGFR mutations constitute shared, immunogenic neoantigens with promising immunotherapeutic potential for large subsets of NSCLC patients. Furthermore, PPV with concurrent EGFR inhibitor therapy was well tolerated and may have contributed to the induction of PPV-induced T cell responses.
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Affiliation(s)
- Fenge Li
- Department of Melanoma, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Ligang Deng
- Tianjin HengJia Biotechnology Development Co Ltd, Tianjin, China
| | - Kyle R Jackson
- Department of Melanoma, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Amjad H Talukder
- Department of Melanoma, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Arjun S Katailiha
- Department of Melanoma, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Sherille D Bradley
- Department of Melanoma, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Qingwei Zou
- Tianjin HengJia Biotechnology Development Co Ltd, Tianjin, China
| | - Caixia Chen
- Tianjin HengJia Biotechnology Development Co Ltd, Tianjin, China
| | - Chong Huo
- Tianjin HengJia Biotechnology Development Co Ltd, Tianjin, China
| | - Yulun Chiu
- Department of Melanoma, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Matthew Stair
- Mary Bird Perkins Cancer Center, Baton Rouge, Louisiana, USA
| | - Weihong Feng
- Department of Oncology, Tianjin Beichen Hospital, Tianjin, China
| | | | | | | | | | | | | | - Yaling Wang
- Tianjin HengJia Biotechnology Development Co Ltd, Tianjin, China
| | - Minying Zhang
- Department of Melanoma, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - David Hawke
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Ling Han
- Department of Oncology, Tianjin Beichen Hospital, Tianjin, China
| | - Shuo Zhou
- Provincial Clinical College, Fujian Medical University, Fujian, China
| | - Yan Zhang
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China
| | - Zhenglu Wang
- Biological Sample Resource Sharing Center, Tianjin First Central Hospital, Tianjin, China
| | - William K Decker
- Department of Immunology, Baylor College of Medicine, Houston, Texas, USA
| | - Heather M Sonnemann
- Department of Melanoma, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Jason Roszik
- Department of Melanoma, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Marie-Andree Forget
- Department of Melanoma, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Michael A Davies
- Department of Melanoma, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Chantale Bernatchez
- Department of Melanoma, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Cassian Yee
- Department of Melanoma, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA.,Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Roland Bassett
- Department of Immunology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas, USA
| | - Patrick Hwu
- Department of Melanoma, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Xueming Du
- Department of Oncology, Tianjin Beichen Hospital, Tianjin, China
| | - Gregory Lizee
- Department of Melanoma, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA .,Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
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Lee Y, McGrail D, Tran H, Vasquez ME, Ramos C, Reuben A, Vaporciyan AA, Weissferdt A, Bernatchez C, Cascone T, Wistuba II, Zhang J, Heymach J, Negrao MV, Gibbons DL, Sepesi B, Haymaker CL. Abstract 1670: Circulating biomarkers are associated with recurrence following complete resection of non-small cell lung cancer. Cancer Res 2021. [DOI: 10.1158/1538-7445.am2021-1670] [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
Background: We have previously demonstrated that the presence of a proinflammatory peripheral cytokine milieu correlates with high levels of circulating neutrophils at the time of surgery and reduced overall survival and recurrence-free survival. In this study, we hypothesized that functional immune features or states in circulation may indicate early tumor recurrence when assessed longitudinally. We also investigated whether potential deficiencies in peripheral immune functionality at the time of lung cancer resection could identify correlates with subsequent outcome.
Methods: We performed flow cytometry and luminex profiling of blood samples collected from patients with stage I-IIIA resected NSCLC (n=150) and enrolled on the Immunogenomic profiling of NSCLC (ICON) prospective protocol. Patient characteristics include 75 adenocarcinomas, 30 squamous and 12 mixed or other histologies. Only patients who underwent primary cancer resection without neoadjuvant therapy were included. At a median follow up of 18.2 months, 37 patients had disease recurrence. Blood was collected at the time of primary lung cancer resection, at 4 weeks, and 4 months thereafter with PBMCs utilized for flow cytometry and plasma for cytokine assessment. Changes in cytokines were assessed by normalizing to baseline levels.
Results: Larger tumors as well as advanced clinical and pathological stages were associated with higher frequencies of proliferating Ki67+CD4+ and Ki67+CD8+ T cells in circulation at time of resection, suggesting an activated circulating immune response. We identified novel strong correlations in the plasma between soluble BTLA and Tim3 (r= 0.87, p=1.74e-140), PD1 and CD80 (r=0.72, p=6.41e-74) and moderate correlations between soluble PD1 and PDL1 (r=0.39, p=8.41e-18). Efforts are ongoing to determine the association of specific circulating immune states with the presence of these soluble receptors. CD8+Tim3+ T cells (FC=5.2%, p=0.028) and CTLA4+NK cells (FC=47.7%, p=0.002) as well as CTLA4+Tregs (FC=25.2%, p=0.05) were found to be increased in circulation at pre-recurrence time points (either 4 weeks or 4 months) relative to resection. This suggests the emergence of a suppressive cell type as well as induction of specific checkpoint receptors on effector cells that correlate with tumor recurrence. Finally, we identified a cytokine signature associated with recurrence by testing three sets within the ICON cohort with a training set AUC = 0.76 and the test set AUC=0.72, which was validated in a third set of patients yielding an AUC = 0.76.
Conclusions: We identified circulating immune features associated with initial tumor size and overall stage as well as unique associations among soluble proteins. Increased presence of potentially inhibited or suppressed CD8+ T cells and NK cells as well as Tregs are suggestive of mechanisms of immune suppression relative to tumor recurrence.
Citation Format: Younghee Lee, Daniel McGrail, Hai Tran, Mayra E. Vasquez, Carlos Ramos, Alexandre Reuben, Ara A. Vaporciyan, Annikka Weissferdt, Chantale Bernatchez, Tina Cascone, Ignacio I. Wistuba, Jianjun Zhang, John Heymach, Marcelo V. Negrao, Don L. Gibbons, Boris Sepesi, Cara L. Haymaker. Circulating biomarkers are associated with recurrence following complete resection of non-small cell lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1670.
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Affiliation(s)
- Younghee Lee
- University of Texas MD Anderson Cancer Center, Houston, TX
| | - Daniel McGrail
- University of Texas MD Anderson Cancer Center, Houston, TX
| | - Hai Tran
- University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Carlos Ramos
- University of Texas MD Anderson Cancer Center, Houston, TX
| | | | | | | | | | - Tina Cascone
- University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Jianjun Zhang
- University of Texas MD Anderson Cancer Center, Houston, TX
| | - John Heymach
- University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Don L. Gibbons
- University of Texas MD Anderson Cancer Center, Houston, TX
| | - Boris Sepesi
- University of Texas MD Anderson Cancer Center, Houston, TX
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Mitra A, Somaiah N, Conley AP, Amini B, Lin H, Sanchez BE, Garcia-Prieto C, Mathew G, Bernatchez C, Ravi V, Araujo D, Zarzour MA, Livingston JA, Roland CL, Daw N, Baguley J, Wang WL, Beird H, Tate T, Haymaker C, Little LD, Gumbs C, Song X, Keung EZ, Zhang S, Gite S, Zhang J, Solis L, Tawbi H, Wang L, Patel S, Benjamin RS, Lazar AJ, Wistuba II, Futreal A. Abstract 518: Immunogenomic correlates of response to combination immune checkpoint blockade in advanced sarcoma. Cancer Res 2021. [DOI: 10.1158/1538-7445.am2021-518] [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
Sarcomas encompass a rare but highly diverse set of tumor malignancies, contributing disproportionately to years of life lost. Immune checkpoint blockade (ICB) has been successful across various tumor types; however, their efficacy and predictability in sarcomas remain unknown. We conducted a translational study using pre- and on-treatment tumor biopsies collected prospectively on a Phase II clinical trial (NCT02815995) evaluating the role of combination anti-PD-L1 and anti-CTLA-4 in 57 patients, enrolled across multiple histologies of metastatic sarcoma. We obtained tumor biopsies at baseline and after 6 weeks of treatment and performed whole-exome, T-cell repertoire (TCR) and RNA-sequencing, along with multiplexed-immunofluorescence (mIF).We deconvoluted substantial variability present in the tumor microenvironment (TME) within sarcomas and found instances of relatively inflamed tumors which failed to respond to ICB. However, amongst those potential molecular correlates of response analyzed, elevated levels of B-cells both at the transcriptome and through validation staining (p = 0.047 and p = 0.022) were most significantly correlated with response. In order to gain more insight into the phenotype and function of B-cells in contributing to response, we inferred BCR-templates and found higher levels of both IGH and IGL diversity (p = 0.0276 and p = 0. 0889 respectively) in responders to ICB. Additionally, we detected increased levels of hyperexpanded IGH clones at the on-treatment time point in patients that responded to therapy (p = 0.048). This B-cell enrichment was validated and found to be predictive of response (p = 0.043) in an independent sarcoma anti-PD-1 treated cohort with matched molecular data. Responsive tumors were also associated with higher levels of TCR richness indicating a strong association of diversity in the TCR of responders (p = 0.047). This work demonstrates the potential for multi-lineage immune cell enrichment and frames the potential molecular features of the TME that may influence response in ICB treated sarcomas.
Citation Format: Akash Mitra, Neeta Somaiah, Anthony P. Conley, Behrang Amini, Heather Lin, Beatriz E. Sanchez, Celia Garcia-Prieto, Grace Mathew, Chantale Bernatchez, Vinod Ravi, Dejka Araujo, Maria A. Zarzour, John A. Livingston, Christina L. Roland, Najat Daw, Joshua Baguley, Wei-Lien Wang, Hannah Beird, Taylor Tate, Cara Haymaker, Latasha D. Little, Curtis Gumbs, Xingshi Song, Emily Z. Keung, Shaojun Zhang, Swati Gite, Jianhua Zhang, Luisa Solis, Hussein Tawbi, Linghua Wang, Shreyaskumar Patel, Robert S. Benjamin, Alexander J. Lazar, Ignacio I. Wistuba, Andrew Futreal. Immunogenomic correlates of response to combination immune checkpoint blockade in advanced sarcoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 518.
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Affiliation(s)
- Akash Mitra
- University of Texas MD Anderson Cancer Center, Houston, TX
| | - Neeta Somaiah
- University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Behrang Amini
- University of Texas MD Anderson Cancer Center, Houston, TX
| | - Heather Lin
- University of Texas MD Anderson Cancer Center, Houston, TX
| | | | | | - Grace Mathew
- University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Vinod Ravi
- University of Texas MD Anderson Cancer Center, Houston, TX
| | - Dejka Araujo
- University of Texas MD Anderson Cancer Center, Houston, TX
| | | | | | | | - Najat Daw
- University of Texas MD Anderson Cancer Center, Houston, TX
| | - Joshua Baguley
- University of Texas MD Anderson Cancer Center, Houston, TX
| | - Wei-Lien Wang
- University of Texas MD Anderson Cancer Center, Houston, TX
| | - Hannah Beird
- University of Texas MD Anderson Cancer Center, Houston, TX
| | - Taylor Tate
- University of Texas MD Anderson Cancer Center, Houston, TX
| | - Cara Haymaker
- University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Curtis Gumbs
- University of Texas MD Anderson Cancer Center, Houston, TX
| | - Xingshi Song
- University of Texas MD Anderson Cancer Center, Houston, TX
| | - Emily Z. Keung
- University of Texas MD Anderson Cancer Center, Houston, TX
| | - Shaojun Zhang
- University of Texas MD Anderson Cancer Center, Houston, TX
| | - Swati Gite
- University of Texas MD Anderson Cancer Center, Houston, TX
| | - Jianhua Zhang
- University of Texas MD Anderson Cancer Center, Houston, TX
| | - Luisa Solis
- University of Texas MD Anderson Cancer Center, Houston, TX
| | - Hussein Tawbi
- University of Texas MD Anderson Cancer Center, Houston, TX
| | - Linghua Wang
- University of Texas MD Anderson Cancer Center, Houston, TX
| | | | | | | | | | - Andrew Futreal
- University of Texas MD Anderson Cancer Center, Houston, TX
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Naing A, Meric-Bernstam F, Stephen B, Karp DD, Hajjar J, Rodon Ahnert J, Piha-Paul SA, Colen RR, Jimenez C, Raghav KP, Ferrarotto R, Tu SM, Campbell M, Wang L, Sabir SH, Tapia C, Bernatchez C, Frumovitz M, Tannir N, Ravi V, Khan S, Painter JM, Abonofal A, Gong J, Alshawa A, McQuinn LM, Xu M, Ahmed S, Subbiah V, Hong DS, Pant S, Yap TA, Tsimberidou AM, Dumbrava EEI, Janku F, Fu S, Simon RM, Hess KR, Varadhachary GR, Habra MA. Phase 2 study of pembrolizumab in patients with advanced rare cancers. J Immunother Cancer 2021; 8:jitc-2019-000347. [PMID: 32188704 PMCID: PMC7078933 DOI: 10.1136/jitc-2019-000347] [Citation(s) in RCA: 74] [Impact Index Per Article: 24.7] [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] [Accepted: 02/20/2020] [Indexed: 02/07/2023] Open
Abstract
Background Patients with advanced rare cancers have poor prognosis and few treatment options. As immunotherapy is effective across multiple cancer types, we aimed to assess pembrolizumab (programmed cell death 1 (PD-1) inhibitor) in patients with advanced rare cancers. Methods In this open-label, phase 2 trial, patients with advanced rare cancers whose tumors had progressed on standard therapies, if available, within the previous 6 months were enrolled in nine tumor-specific cohorts and a 10th cohort for other rare histologies. Pembrolizumab 200 mg was administered intravenously every 21 days. The primary endpoint was non-progression rate (NPR) at 27 weeks; secondary endpoints were safety and tolerability, objective response rate (ORR), and clinical benefit rate (CBR). Results A total of 127 patients treated between August 15, 2016 and July 27, 2018 were included in this analysis. At the time of data cut-off, the NPR at 27 weeks was 28% (95% CI, 19% to 37%). A confirmed objective response (OR) was seen in 15 of 110 (14%) evaluable patients (complete response in one and partial response in 14). CBR, defined as the percentage of patients with an OR or stable disease ≥4 months, was 38% (n=42). Treatment was ongoing in 11 of 15 patients with OR at last follow-up. In the cohort with squamous cell carcinoma (SCC) of the skin, the NPR at 27 weeks was 36%, ORR 31%, and CBR 38%. In patients with adrenocortical carcinoma (ACC), NPR at 27 weeks was 31%, ORR 15%, and CBR 54%. In the patients with carcinoma of unknown primary (CUP), NPR at 27 weeks was 33%, ORR 23%, and CBR 54%. In the paraganglioma–pheochromocytoma cohort, NPR at 27 weeks was 43%, ORR 0%, and CBR 75%. Treatment-related adverse events (TRAEs) occurred in 66 of 127 (52%) patients, and 12 (9%) had grade ≥3 TRAEs. The most common TRAEs were fatigue (n=25) and rash (n=17). There were six deaths, all of which were unrelated to the study drug. Conclusions The favorable toxicity profile and antitumor activity seen in patients with SCC of skin, ACC, CUP, and paraganglioma–pheochromocytoma supports further evaluation of pembrolizumab in this patient population. Trial registration number NCT02721732
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Affiliation(s)
- Aung Naing
- Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Funda Meric-Bernstam
- Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Bettzy Stephen
- Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Daniel D Karp
- Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Joud Hajjar
- Section of Immunology, Allergy and Rheumatology, Texas Children's Hospital, Baylor College of Medicine, Houston, Texas, USA
| | - Jordi Rodon Ahnert
- Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Sarina A Piha-Paul
- Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Rivka R Colen
- Cancer Systems Imaging, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Camilo Jimenez
- Endocrine Neoplasia and Hormonal Disorders, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Kanwal P Raghav
- Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Renata Ferrarotto
- Thoracic/Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Shi-Ming Tu
- Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Matthew Campbell
- Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Linghua Wang
- Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Sarjeel H Sabir
- Interventional Radiology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Coya Tapia
- Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Chantale Bernatchez
- Melanoma Medical Oncology-Research, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Michael Frumovitz
- Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Nizar Tannir
- Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Vinod Ravi
- Sarcoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Saria Khan
- Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Jeane M Painter
- Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Abulrahman Abonofal
- Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Jing Gong
- Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Anas Alshawa
- Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Lacey M McQuinn
- Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Mingxuan Xu
- Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Sara Ahmed
- Cancer Systems Imaging, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Vivek Subbiah
- Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - David S Hong
- Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Shubham Pant
- Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Timothy A Yap
- Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Apostolia M Tsimberidou
- Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | | | - Filip Janku
- Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Siqing Fu
- Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | | | - Kenneth R Hess
- Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Gauri R Varadhachary
- Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Mouhammed Amir Habra
- Endocrine Neoplasia and Hormonal Disorders, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
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Paczesny S, Pasquini MC, Pavletic SZ, Agarwal A, Spellman S, Kean L, Bernatchez C, Gust J, Staedtke V, Perales MA. Blueprint for the discovery of biomarkers of toxicity and efficacy for CAR T cells and T-cell engagers. Blood Adv 2021; 5:2519-2522. [PMID: 34100901 PMCID: PMC8238483 DOI: 10.1182/bloodadvances.2021004604] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 04/10/2021] [Indexed: 01/16/2023] Open
Affiliation(s)
- Sophie Paczesny
- Department of Microbiology and Immunology, Medical University of South Carolina, Charleston, SC
| | - Marcelo C Pasquini
- Center for International Blood and Marrow Transplant Research, Medical College of Wisconsin, Milwaukee, WI
| | - Steven Z Pavletic
- National Cancer Institute, National Institutes of Health, Bethesda, MD
| | | | - Stephen Spellman
- Center for International Blood and Marrow Transplant Research, National Marrow Donor Program, Minneapolis, MN
| | - Leslie Kean
- Boston Children's Hospital, Dana-Farber Cancer Institute, Boston, MA
| | | | | | - Verena Staedtke
- Johns Hopkins Comprehensive Neurofibromatosis Center, Johns Hopkins University, Baltimore, MD; and
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Corsini EM, Mitchell KG, Zhou N, Bernatchez C, Forget MA, Haymaker CL, Hofstetter WL, Mehran RJ, Rajaram R, Rice DC, Roth JA, Sepesi B, Swisher SG, Vaporciyan AA, Walsh GL, Amaria RN, Jazaeri AA, Antonoff MB. Pulmonary resection for tissue harvest in adoptive tumor-infiltrating lymphocyte therapy: Safety and feasibility. J Surg Oncol 2021; 124:699-703. [PMID: 34057733 DOI: 10.1002/jso.26548] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 08/29/2020] [Revised: 04/03/2021] [Accepted: 05/12/2021] [Indexed: 11/11/2022]
Abstract
BACKGROUND AND OBJECTIVES Adoptive T-cell therapies (ACTs) using expansion of tumor-infiltrating lymphocyte (TIL) populations are of great interest for advanced malignancies, with promising response rates in trial settings. However, postoperative outcomes following pulmonary TIL harvest have not been widely documented, and surgeons may be hesitant to operate in the setting of widespread disease. METHODS Patients who underwent pulmonary TIL harvest were identified, and postoperative outcomes were studied, including pulmonary, cardiovascular, infectious, and wound complications. RESULTS 83 patients met inclusion criteria. Pulmonary TIL harvest was undertaken primarily via a thoracoscopy with a median operative blood loss and duration of 30 ml and 65 min, respectively. The median length of stay was 2 days. Postoperative events were rare, occurring in only five (6%) patients, including two discharged with a chest tube, one discharged with oxygen, one episode of urinary retention, and one blood transfusion. No reoperations occurred. The median time from TIL harvest to ACT infusion was 37 days. CONCLUSIONS Pulmonary TIL harvest is safe and feasible, without major postoperative events in our cohort. All patients were able to receive intended ACT infusion without delays. Therefore, thoracic surgeons should actively participate in ongoing ACT trials and aggressively seek to enroll patients on these protocols.
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Affiliation(s)
- Erin M Corsini
- Department of Thoracic and Cardiovascular Surgery, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Kyle G Mitchell
- Department of Thoracic and Cardiovascular Surgery, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Nicolas Zhou
- Department of Thoracic and Cardiovascular Surgery, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Chantale Bernatchez
- Department of Melanoma Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Marie-Andrée Forget
- Department of Melanoma Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Cara L Haymaker
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Wayne L Hofstetter
- Department of Thoracic and Cardiovascular Surgery, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Reza J Mehran
- Department of Thoracic and Cardiovascular Surgery, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Ravi Rajaram
- Department of Thoracic and Cardiovascular Surgery, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - David C Rice
- Department of Thoracic and Cardiovascular Surgery, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Jack A Roth
- Department of Thoracic and Cardiovascular Surgery, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Boris Sepesi
- Department of Thoracic and Cardiovascular Surgery, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Stephen G Swisher
- Department of Thoracic and Cardiovascular Surgery, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Ara A Vaporciyan
- Department of Thoracic and Cardiovascular Surgery, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Garrett L Walsh
- Department of Thoracic and Cardiovascular Surgery, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Rodabe N Amaria
- Department of Melanoma Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Amir A Jazaeri
- Department of Gynecologic Oncology and Reproductive Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Mara B Antonoff
- Department of Thoracic and Cardiovascular Surgery, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
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40
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Saberian C, Amaria RN, Najjar AM, Radvanyi LG, Haymaker CL, Forget MA, Bassett RL, Faria SC, Glitza IC, Alvarez E, Parshottam S, Prieto V, Lizée G, Wong MK, McQuade JL, Diab A, Yee C, Tawbi HA, Patel S, Shpall EJ, Davies MA, Hwu P, Bernatchez C. Randomized phase II trial of lymphodepletion plus adoptive cell transfer of tumor-infiltrating lymphocytes, with or without dendritic cell vaccination, in patients with metastatic melanoma. J Immunother Cancer 2021; 9:jitc-2021-002449. [PMID: 34021033 PMCID: PMC8144048 DOI: 10.1136/jitc-2021-002449] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [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] [Accepted: 03/26/2021] [Indexed: 11/04/2022] Open
Abstract
BACKGROUND The adoptive transfer of tumor-infiltrating lymphocytes (TIL) has demonstrated robust efficacy in metastatic melanoma patients. Tumor antigen-loaded dendritic cells (DCs) are believed to optimally activate antigen-specific T lymphocytes. We hypothesized that the combined transfer of TIL, containing a melanoma antigen recognized by T cells 1 (MART-1) specific population, with MART-1-pulsed DC will result in enhanced proliferation and prolonged survival of transferred MART-1 specific T cells in vivo ultimately leading to improved clinical responses. DESIGN We tested the combination of TIL and DC in a phase II clinical trial of patients with advanced stage IV melanoma. HLA-A0201 patients whose early TIL cultures demonstrated reactivity to MART-1 peptide were randomly assigned to receive TIL alone or TIL +DC pulsed with MART-1 peptide. The primary endpoint was to evaluate the persistence of MART-1 TIL in the two arms. Secondary endpoints were to evaluate clinical response and survival. RESULTS Ten patients were given TIL alone while eight patients received TIL+DC vaccine. Infused MART-1 reactive CD8+ TIL were tracked in the blood over time by flow cytometry and results show good persistence in both arms, with no difference in the persistence of MART-1 between the two arms. The objective response rate was 30% (3/10) in the TIL arm and 50% (4/8) in the TIL+DC arm. All treatments were well tolerated. CONCLUSIONS The combination of TIL +DC showed no difference in the persistence of MART-1 TIL compared with TIL therapy alone. Although more patients showed a clinical response to TIL+DC therapy, this study was not powered to resolve differences between groups. TRIAL REGISTRATION NUMBER NCT00338377.
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Affiliation(s)
- Chantal Saberian
- Melanoma Medical Onoclogy, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Rodabe N Amaria
- Melanoma Medical Onoclogy, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Amer M Najjar
- Department of Pediatrics - Research, Division of Pediatrics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Laszlo G Radvanyi
- Melanoma Medical Onoclogy, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA.,Ontario Institute for Cancer Research, Ontario, Ontario, Canada
| | - Cara L Haymaker
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA, Houston, TX, USA
| | - Marie-Andrée Forget
- Melanoma Medical Onoclogy, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Roland L Bassett
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Silvana C Faria
- Department of Radiology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Isabella C Glitza
- Melanoma Medical Onoclogy, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Enrique Alvarez
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Sapna Parshottam
- Department of Biologics Development, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Victor Prieto
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Gregory Lizée
- Melanoma Medical Onoclogy, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Michael K Wong
- Melanoma Medical Onoclogy, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Jennifer L McQuade
- Melanoma Medical Onoclogy, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Adi Diab
- Melanoma Medical Onoclogy, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Cassian Yee
- Melanoma Medical Onoclogy, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Hussein A Tawbi
- Melanoma Medical Onoclogy, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Sapna Patel
- Melanoma Medical Onoclogy, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Elizabeth J Shpall
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Michael A Davies
- Melanoma Medical Onoclogy, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Patrick Hwu
- Melanoma Medical Onoclogy, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Chantale Bernatchez
- Melanoma Medical Onoclogy, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA .,Department of Biologics Development, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
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41
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Kanikarla Marie P, Haymaker C, Parra ER, Kim YU, Lazcano R, Gite S, Lorenzini D, Wistuba II, Tidwell RSS, Song X, Foo WC, Maru DM, Chun YS, Futreal A, Kee B, Menter D, Solis L, Tzeng CW, Parseghian C, Raghav K, Morris V, Chang CC, Jenq R, Tam A, Bernatchez C, Kopetz S, Vauthey JN, Overman MJ. Pilot Clinical Trial of Perioperative Durvalumab and Tremelimumab in the Treatment of Resectable Colorectal Cancer Liver Metastases. Clin Cancer Res 2021; 27:3039-3049. [PMID: 33811152 DOI: 10.1158/1078-0432.ccr-21-0163] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 03/11/2021] [Accepted: 03/30/2021] [Indexed: 12/13/2022]
Abstract
PURPOSE Despite the prognostic importance of immune infiltrate in colorectal cancer, immunotherapy has demonstrated limited clinical activity in refractory metastatic proficient mismatch-repair (pMMR) colorectal cancer. This study explores combining anti-CTLA-4 and an anti-PD-L1 therapy in the preoperative management of resectable colorectal cancer liver metastases with the intent to improve immune responses in this disease setting. PATIENTS AND METHODS Patients with resectable colorectal cancer liver-only metastases received one dose of tremelimumab and durvalumab preoperatively followed by single-agent durvalumab postoperatively. Primary objectives were to determine feasibility and safety. RESULTS A total of 24 patients were enrolled between November 2016 and November 2019. Twenty-three patients received treatment [21 pMMR and 2 deficient mismatch-repair (dMMR)] and subsequently 17 (74%; 95% CI: 53%-88%) underwent surgical resection. Grade 3/4 treatment-related immune toxicity and postoperative grade 3/4 toxicity were seen in 5/23 (22%; 95% CI: 10%-44%) and 2/17 (12%; 95% CI: 2%-38%) patients. The median relapse-free survival (RFS) was 9.7 (95% CI: 8.1-17.8) months, and overall survival was 24.5 (95% CI: 16.5-28.4) months. Four patients demonstrated complete pathologic response, two dMMR patients and two POLE mutation patients. Pre- and post-tumor tissue analysis by flow cytometry, immunofluorescence, and RNA sequencing revealed similar levels of T-cell infiltration, but did demonstrate evidence of CD8+ and CD4+ activation posttreatment. An increase in B-cell transcriptome signature and B-cell density was present in posttreatment samples from patients with prolonged RFS. CONCLUSIONS This study demonstrates the safety of neoadjuvant combination tremelimumab and durvalumab prior to colorectal cancer liver resection. Evidence for T- and B-cell activation following this therapy was seen in pMMR metastatic colorectal cancer.
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Affiliation(s)
- Preeti Kanikarla Marie
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Cara Haymaker
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Edwin Roger Parra
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Young Uk Kim
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Rossana Lazcano
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Swati Gite
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Daniele Lorenzini
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Ignacio I Wistuba
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Rebecca S Slack Tidwell
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Xiaofei Song
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Wai Chin Foo
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Dipen M Maru
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Yun Shin Chun
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Andy Futreal
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Bryan Kee
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - David Menter
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Luisa Solis
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Ching-Wei Tzeng
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Christine Parseghian
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Kanwal Raghav
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Van Morris
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Chia-Chi Chang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Robert Jenq
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Alda Tam
- Department of Interventional Radiology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Chantale Bernatchez
- Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Scott Kopetz
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jean-Nicolas Vauthey
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Michael J Overman
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas.
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Kalaora S, Nagler A, Nejman D, Alon M, Barbolin C, Barnea E, Ketelaars SLC, Cheng K, Vervier K, Shental N, Bussi Y, Rotkopf R, Levy R, Benedek G, Trabish S, Dadosh T, Levin-Zaidman S, Geller LT, Wang K, Greenberg P, Yagel G, Peri A, Fuks G, Bhardwaj N, Reuben A, Hermida L, Johnson SB, Galloway-Peña JR, Shropshire WC, Bernatchez C, Haymaker C, Arora R, Roitman L, Eilam R, Weinberger A, Lotan-Pompan M, Lotem M, Admon A, Levin Y, Lawley TD, Adams DJ, Levesque MP, Besser MJ, Schachter J, Golani O, Segal E, Geva-Zatorsky N, Ruppin E, Kvistborg P, Peterson SN, Wargo JA, Straussman R, Samuels Y. Identification of bacteria-derived HLA-bound peptides in melanoma. Nature 2021; 592:138-143. [PMID: 33731925 PMCID: PMC9717498 DOI: 10.1038/s41586-021-03368-8] [Citation(s) in RCA: 159] [Impact Index Per Article: 53.0] [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: 11/04/2019] [Accepted: 02/17/2021] [Indexed: 01/31/2023]
Abstract
A variety of species of bacteria are known to colonize human tumours1-11, proliferate within them and modulate immune function, which ultimately affects the survival of patients with cancer and their responses to treatment12-14. However, it is not known whether antigens derived from intracellular bacteria are presented by the human leukocyte antigen class I and II (HLA-I and HLA-II, respectively) molecules of tumour cells, or whether such antigens elicit a tumour-infiltrating T cell immune response. Here we used 16S rRNA gene sequencing and HLA peptidomics to identify a peptide repertoire derived from intracellular bacteria that was presented on HLA-I and HLA-II molecules in melanoma tumours. Our analysis of 17 melanoma metastases (derived from 9 patients) revealed 248 and 35 unique HLA-I and HLA-II peptides, respectively, that were derived from 41 species of bacteria. We identified recurrent bacterial peptides in tumours from different patients, as well as in different tumours from the same patient. Our study reveals that peptides derived from intracellular bacteria can be presented by tumour cells and elicit immune reactivity, and thus provides insight into a mechanism by which bacteria influence activation of the immune system and responses to therapy.
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Affiliation(s)
- Shelly Kalaora
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Adi Nagler
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Deborah Nejman
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Michal Alon
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Chaya Barbolin
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Eilon Barnea
- Department of Biology, Technion - Israel Institute of Technology, Haifa, Israel
| | - Steven L C Ketelaars
- Division of Molecular Oncology and Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Kuoyuan Cheng
- Cancer Data Science Laboratory (CDSL), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, USA
| | | | - Noam Shental
- Department of Mathematics and Computer Science, Open University of Israel, Raanana, Israel
| | - Yuval Bussi
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
| | - Ron Rotkopf
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Ronen Levy
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Gil Benedek
- Tissue Typing and Immunogenetics Unit, Hadassah Medical Center, Jerusalem, Israel
| | - Sophie Trabish
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Tali Dadosh
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, Israel
| | - Smadar Levin-Zaidman
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, Israel
| | - Leore T Geller
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Kun Wang
- Cancer Data Science Laboratory (CDSL), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Polina Greenberg
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Gal Yagel
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Aviyah Peri
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Garold Fuks
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot, Israel
| | - Neerupma Bhardwaj
- The Ruth and Bruce Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel
| | - Alexandre Reuben
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Leandro Hermida
- Cancer Data Science Laboratory (CDSL), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Sarah B Johnson
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Genomic Medicine, 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
| | - Cara Haymaker
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Reetakshi Arora
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Lior Roitman
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Raya Eilam
- Department of Veterinary Resources, Weizmann Institute of Science, Rehovot, Israel
| | - Adina Weinberger
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
| | - Maya Lotan-Pompan
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
| | - Michal Lotem
- Sharett Institute of Oncology, Hadassah Hebrew University Medical Center, Jerusalem, Israel
| | - Arie Admon
- Department of Biology, Technion - Israel Institute of Technology, Haifa, Israel
| | - Yishai Levin
- The de Botton Institute for Protein Profiling, The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | | | | | - Mitchell P Levesque
- Faculty of Medicine, University of Zurich Hospital, University of Zurich, Zurich, Switzerland
| | - Michal J Besser
- The Ella Lemelbaum Institute for Immuno Oncology and Melanoma, Chaim Sheba Medical Center, Tel Hashomer, Israel
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Jacob Schachter
- The Ella Lemelbaum Institute for Immuno Oncology and Melanoma, Chaim Sheba Medical Center, Tel Hashomer, Israel
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ofra Golani
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Eran Segal
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
| | - Naama Geva-Zatorsky
- The Ruth and Bruce Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel
- MaRS Centre, Canadian Institute for Advanced Research (CIFAR) Azrieli Global Scholar, Toronto, Ontario, Canada
| | - Eytan Ruppin
- Cancer Data Science Laboratory (CDSL), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Pia Kvistborg
- Division of Molecular Oncology and Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Scott N Peterson
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Jennifer A Wargo
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ravid Straussman
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Yardena Samuels
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel.
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Le X, Negrao MV, Reuben A, Federico L, Diao L, McGrail D, Nilsson M, Robichaux J, Munoz IG, Patel S, Elamin Y, Fan YH, Lee WC, Parra E, Solis Soto LM, Chen R, Li J, Karpinets T, Khairullah R, Kadara H, Behrens C, Sepesi B, Wang R, Zhu M, Wang L, Vaporciyan A, Roth J, Swisher S, Haymaker C, Zhang J, Wang J, Wong KK, Byers LA, Bernatchez C, Zhang J, Wistuba II, Gibbons DL, Akbay EA, Heymach JV. Characterization of the Immune Landscape of EGFR-Mutant NSCLC Identifies CD73/Adenosine Pathway as a Potential Therapeutic Target. J Thorac Oncol 2021; 16:583-600. [PMID: 33388477 DOI: 10.1016/j.jtho.2020.12.010] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 11/22/2020] [Accepted: 12/19/2020] [Indexed: 01/13/2023]
Abstract
INTRODUCTION Lung adenocarcinomas harboring EGFR mutations do not respond to immune checkpoint blockade therapy and their EGFR wildtype counterpart. The mechanisms underlying this lack of clinical response have been investigated but remain incompletely understood. METHODS We analyzed three cohorts of resected lung adenocarcinomas (Profiling of Resistance Patterns of Oncogenic Signaling Pathways in Evaluation of Cancer of Thorax, Immune Genomic Profiling of NSCLC, and The Cancer Genome Atlas) and compared tumor immune microenvironment of EGFR-mutant tumors to EGFR wildtype tumors, to identify actionable regulators to target and potentially enhance the treatment response. RESULTS EGFR-mutant NSCLC exhibited low programmed death-ligand 1, low tumor mutational burden, decreased number of cytotoxic T cells, and low T cell receptor clonality, consistent with an immune-inert phenotype, though T cell expansion ex vivo was preserved. In an analysis of 75 immune checkpoint genes, the top up-regulated genes in the EGFR-mutant tumors (NT5E and ADORA1) belonged to the CD73/adenosine pathway. Single-cell analysis revealed that the tumor cell population expressed CD73, both in the treatment-naive and resistant tumors. Using coculture systems with EGFR-mutant NSCLC cells, T regulatory cell proportion was decreased with CD73 knockdown. In an immune-competent mouse model of EGFR-mutant lung cancer, the CD73/adenosine pathway was markedly up-regulated and CD73 blockade significantly inhibited tumor growth. CONCLUSIONS Our work revealed that EGFR-mutant NSCLC has an immune-inert phenotype. We identified the CD73/adenosine pathway as a potential therapeutic target for EGFR-mutant NSCLC.
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Affiliation(s)
- Xiuning Le
- Department of Thoracic/Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Marcelo V Negrao
- Department of Thoracic/Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Alexandre Reuben
- Department of Thoracic/Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Lorenzo Federico
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Lixia Diao
- Department of Bioinformatics and Computational Biology, Division of Basic Sciences, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Daniel McGrail
- Department of System Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Monique Nilsson
- Department of Thoracic/Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jacqulyne Robichaux
- Department of Thoracic/Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Irene Guijarro Munoz
- Department of Thoracic/Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Sonia Patel
- Department of Thoracic/Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Yasir Elamin
- Department of Thoracic/Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - You-Hong Fan
- Department of Thoracic/Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Won-Chul Lee
- Department of Thoracic/Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Edwin Parra
- Department of Translational Molecular Pathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Luisa Maren Solis Soto
- Department of Translational Molecular Pathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Runzhe Chen
- Department of Thoracic/Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jun Li
- Department of Genomic Medicine, 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
| | - Roohussaba Khairullah
- Department of Thoracic/Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Humam Kadara
- Department of Translational Molecular Pathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Carmen Behrens
- Department of Translational Molecular Pathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Boris Sepesi
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Ruiping Wang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Mingrui Zhu
- Department of Pathology, The University of Texas Southwestern Medical Center, Dallas, Texas
| | - Linghua Wang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Ara Vaporciyan
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jack Roth
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Stephen Swisher
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Cara Haymaker
- Department of Translational Molecular Pathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jianhua Zhang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jing Wang
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Kwok-Kin Wong
- Division of Hematology and Medical Oncology, NYU Perlmutter Cancer Center, New York, New York; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Lauren A Byers
- Department of Thoracic/Head & Neck 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; Department of Translational Molecular Pathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jianjun Zhang
- Department of Thoracic/Head & Neck 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
| | - Ignacio I Wistuba
- Department of Translational Molecular Pathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Don L Gibbons
- Department of Thoracic/Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Esra A Akbay
- Department of Pathology, The University of Texas Southwestern Medical Center, Dallas, Texas; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - John V Heymach
- Department of Thoracic/Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas.
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44
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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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Abstract
The elevated expression of PD-1, BTLA, and other co-inhibitory molecules on T cells from cancer patients has become an accepted signature for a state called T-cell “exhaustion” that has emerged almost as dogma in the field. However, here we propose that in some cases this “exhausted” T-cell phenotype may instead be an indicator of T cells that are in a more heightened state of T-cell activation more susceptible to negative regulation rather than being “exhausted.” This alternative interpretation fits in line with the view that CD8+ T-cell activation in cancer results from a continuum of signals regulating their differentiation towards potent effector cells.
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Affiliation(s)
- Cara Haymaker
- Department of Melanoma Medical Oncology; University of Texas; MD Anderson Cancer Center; Houston, TX USA
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46
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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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47
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Gaudreau PO, Negrao MV, Mitchell KG, Reuben A, Corsini EM, Li J, Karpinets TV, Wang Q, Diao L, Wang J, Federico L, Parra-Cuentas ER, Khairullah R, Behrens C, Correa AM, Gomez D, Little L, Gumbs C, Kadara HN, Fujimoto J, McGrail DJ, Vaporciyan AA, Swisher SG, Walsh G, Antonoff MB, Weissferdt A, Tran H, Roarty E, Haymaker C, Bernatchez C, Zhang J, Futreal PA, Wistuba II, Cascone T, Heymach JV, Sepesi B, Zhang J, Gibbons DL. Neoadjuvant Chemotherapy Increases Cytotoxic T Cell, Tissue Resident Memory T Cell, and B Cell Infiltration in Resectable NSCLC. J Thorac Oncol 2020; 16:127-139. [PMID: 33096269 DOI: 10.1016/j.jtho.2020.09.027] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 07/31/2020] [Accepted: 09/18/2020] [Indexed: 12/26/2022]
Abstract
INTRODUCTION The combination of programmed cell death protein-1 or programmed death-ligand 1 immune checkpoint blockade and chemotherapy has revolutionized the treatment of advanced NSCLC, but the mechanisms underlying this synergy remain incompletely understood. In this study, we explored the relationships between neoadjuvant chemotherapy and the immune microenvironment (IME) of resectable NSCLC to identify novel mechanisms by which chemotherapy may enhance the effect of immune checkpoint blockade. METHODS Genomic, transcriptomic, and immune profiling data of 511 patients treated with neoadjuvant chemotherapy followed by surgery (NCT) versus upfront surgery (US) were compared with determined differential characteristics of the IMEs derived from whole-exome sequencing (NCT = 18; US = 73), RNA microarray (NCT = 45; US = 202), flow cytometry (NCT = 17; US = 39), multiplex immunofluorescence (NCT = 10; US = 72), T-cell receptor sequencing (NCT = 16 and US = 63), and circulating cytokines (NCT = 18; US = 73). RESULTS NCT was associated with increased infiltration of cytotoxic CD8+ T cells and CD20+ B cells. Moreover, NCT was associated with increases in CD8+CD103+ and CD4+CD103+PD-1+TIM3- tissue resident memory T cells. Gene expression profiling supported memory function of CD8+ and CD4+ T cells. However, NCT did not affect T-cell receptor clonality, richness, or tumor mutational burden. Finally, NCT was associated with decreased plasma BDNF (TrkB) at baseline and week 4 after surgery. CONCLUSIONS Our study supports that, in the context of resectable NSCLC, neoadjuvant chemotherapy promotes antitumor immunity through T and B cell recruitment in the IME and through a phenotypic change toward cytotoxic and memory CD8+ and CD4+ memory helper T cells.
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Affiliation(s)
- Pierre-Olivier Gaudreau
- Department of Oncology, Queens' University and the Canadian Cancer Trials Group, Kingston, Ontario, Canada
| | - Marcelo V Negrao
- Department of Thoracic and Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Kyle G Mitchell
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Alexandre Reuben
- Department of Thoracic and Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Erin M Corsini
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jun Li
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Tatiana V Karpinets
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Qi Wang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Lixia Diao
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jing Wang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Lorenzo Federico
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Edwin R Parra-Cuentas
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Roohussaba Khairullah
- Department of Thoracic and Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Carmen Behrens
- Department of Thoracic and Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Arlene M Correa
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Daniel Gomez
- Department of Radiation Oncology, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Latasha Little
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Curtis Gumbs
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Humam N Kadara
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Junya Fujimoto
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Daniel J McGrail
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Ara A Vaporciyan
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Stephen G Swisher
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Garrett Walsh
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Mara B Antonoff
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Annikka Weissferdt
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Hai Tran
- Department of Thoracic and Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Emily Roarty
- Department of Thoracic and Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Cara Haymaker
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Chantale Bernatchez
- Biologics Development Department, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jianhua Zhang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - P Andrew Futreal
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Ignacio I Wistuba
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Tina Cascone
- Department of Thoracic and Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - John V Heymach
- Department of Thoracic and Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Boris Sepesi
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jianjun Zhang
- Department of Thoracic and Head & Neck 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.
| | - Don L Gibbons
- Department of Oncology, Queens' University and the Canadian Cancer Trials Group, Kingston, Ontario, Canada; Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
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Dai-Ogata, Creasy CA, Kim SH, Roszik J, Hwu P, Grimm EA, Bernatchez C, Ekmekcioglu S. Abstract PR15: CD74 regulated inflammatory pattern is associated with TIL growth and favorable response to adoptive immunotherapy. Cancer Res 2020. [DOI: 10.1158/1538-7445.mel2019-pr15] [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
We previously reported that in Stage III melanoma patients’ tumors, positive expression of CD74 together with low or absent Macrophage Migration Inhibitory Factor (MIF) associates with favorable prognosis (Ekmekcioglu et al., CCR 2016). As both are known to be regulated by IFN-g, we suggest a differential IFN-g response as well as a novel role for CD74 that may be exploited to improve patient outcome. Our further analyses of The Cancer Genome Atlas (TCGA) datasets confirmed the role of CD74 in prognosis for patient survival, which is likely attributed to regulation of MHC-Class II and antigen presentation in the tumor microenvironment. Immune infiltration of T cells (TIL) into the melanoma microenvironment has been associated with improved survival for some patients, and also has been exploited to grow TIL in vitro for adoptive therapy. However, prognostic significance of immune infiltrating cells in melanoma and other tumors remains a relatively new concept, and markers related to suppressive versus active functional TIL remain unclear. From an ongoing clinical trial using TIL intended for adoptive immunotherapy, we have studied the melanoma patient tumor specimens (FFPE) from 20 patients whose autologous TIL lines grew to sufficient number for possible use clinically. We also examined another 20 sets of melanoma tumor from which the TIL did not grow or did not grow well. We analyzed the differences in the two groups of tumors (40 total FFPE) for CD74 regulated pathway features and inflammatory marker expression. CD74 regulated markers included CD44, MIF, and downstream inflammatory targets including inducible nitric oxide synthase (iNOS), nitrotyrosine (NT) and microsomal prostaglandin E synthase-1 (mPGES1). Our findings confirm our previous report in that tumor CD74 expression significantly associates with favorable OS and PFS (both, p=0.0038) and provides new data that in this set of patients the CD74 also correlates with best irRC of TIL treated patients. New findings include that the NT expression in tumor cells associated with poor TIL growth (p=0.014), as well as lack of clinical response to TIL treatment (p=0.02). We have also found that tumor cell-derived MIF and iNOS expression correlate with unfavorable prognosis for both OS and PFS (p=0.016 and 0.018, respectively). The iNOS and MIF coexpression characteristics and cellular distributions in the tumor are currently under way. In conclusion, we have identified the protein expression of CD74, MIF and of iNOS as providing survival information, and proposed that CD74+/MIF-/iNOS- together be considered to form a “signature” of good prognosis in general melanoma outcomes as well as TIL growth and favorable responses for these patients. Use of this signature for selecting patients for entry into TIL and possibly other immunotherapy trials, as well as research on the differential pathways of IFN-g signaling in melanoma, appear as important areas for future mechanistic research to improve patient outcome.
This abstract is also being presented as Poster B14.
Citation Format: Dai-Ogata, Caitlin A. Creasy, Sun-Hee Kim, Jason Roszik, Patrick Hwu, Elizabeth A. Grimm, Chantale Bernatchez, Suhendan Ekmekcioglu. CD74 regulated inflammatory pattern is associated with TIL growth and favorable response to adoptive immunotherapy [abstract]. In: Proceedings of the AACR Special Conference on Melanoma: From Biology to Target; 2019 Jan 15-18; Houston, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(19 Suppl):Abstract nr PR15.
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Affiliation(s)
- Dai-Ogata
- University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Sun-Hee Kim
- University of Texas MD Anderson Cancer Center, Houston, TX
| | - Jason Roszik
- University of Texas MD Anderson Cancer Center, Houston, TX
| | - Patrick Hwu
- University of Texas MD Anderson Cancer Center, Houston, TX
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Zhu H, Oba J, Yu X, Creasy CA, Forget MA, Carapeto F, Haymaker CL, Wu CJ, Karpinets TV, Wang WL, Tetzlaff MT, Lazar AJ, Mills GB, Moore AR, Chen Y, Zhang J, Gershenwald JE, Wargo JA, Bernatchez C, Hwu P, Futreal PA, Woodman SE. Abstract PR03: Nongenomic BAP1 aberrancy drives highly aggressive cutaneous melanoma phenotype. Cancer Res 2020. [DOI: 10.1158/1538-7445.mel2019-pr03] [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
The purpose of this study was to determine the role of BAP1 levels in cutaneous melanoma (CM). BAP1 is a tumor suppressor in which loss of heterozygosity (LOH) from mutation and copy number alteration is well described in germline and somatic cancers. Although BAP1 genomic alterations in CM are extremely rare (2% of 665 samples from 5 datasets), marked variability in BAP1 expression is observed in CM. We show that low nuclear BAP1 levels portend a significantly worse clinical outcome in stage III CM (n=37, log rank p ≤0.01 for both overall survival and progression-free survival). Gene Set Enrichment Analysis (GSEA) revealed low BAP1 expression to be most highly ranked with an increased epithelial–mesenchymal transition (EMT) gene expression profile in CM tumors (n=379, FDR q = 1.34E-26) and cell lines (n=53, FDR q = 2.86E-116). We identify the expression of ZEB1, a master regulator of EMT, to be significantly associated with low BAP1 expression in CM tumors and cell lines (p= 1.5E-04 and 3.3E-05, respectively). Analysis of the BAP1 promoter indicates three canonical ZEB1 binding sites. Functional experiments show ZEB1 to bind to the BAP1 promoter, and luciferase activity assays indicate that ZEB1 acts as a transcriptional suppressor of BAP1 expression with differential utilization of the promoter binding sites. Targeted reduction of endogenous ZEB1 caused increased BAP1 levels, while targeted reduction of BAP1 did not modulate ZEB1 levels, consistent with ZEB1 having a suppressive effect on BAP1. Phenotypically, targeted reduction of BAP1 in CM cells resulted in a switch from a more differentiated, melanocytic state, to a less differentiated, more migratory and invasive phenotype. Extinguishing melanocyte-specific BAP1 in mice with a BRAF V600E mutant genetic background resulted in the emergence of primary melanoma tumors, with a marked EMT gene expression profile, and resultant metastases. Given the phenotypic changes associated with BAP1 levels in our mouse and human studies, we then tested the effect of modulating BAP1 on BRAF targeted therapy. Exogenous expression of BAP1 sensitized BRAF inhibitor (vemurafenib)-resistant melanoma cells, while the targeted reduction of BAP1 desensitized BRAF inhibitor-sensitive melanoma cells. BRAF mutant/BAP1 loss mice failed to exhibit a marked response to vemurafenib treatment compared to control mice. These data implicate regulation of BAP1 to be a major mechanism that characterizes a highly malignant and treatment-resistant subset of tumors. Our study indicates that nongenomic reduction in BAP1 through ZEB1 transcriptional modulation may be a key factor in aggressive CM.
This abstract is also being presented as Poster A30.
Citation Format: Haifeng Zhu, Junna Oba, Xiaoxing Yu, Caitlin A. Creasy, Marie-Andrée Forget, Fernando Carapeto, Cara L. Haymaker, Chang-Jiun Wu, Tatiana V. Karpinets, Wei-Lien Wang, Michael T. Tetzlaff, Alexander J. Lazar, Gordon B. Mills, Amanda R. Moore, Yu Chen, Jianhua Zhang, Jeffrey E. Gershenwald, Jennifer A. Wargo, Chantale Bernatchez, Patrick Hwu, P. Andrew Futreal, Scott E. Woodman. Nongenomic BAP1 aberrancy drives highly aggressive cutaneous melanoma phenotype [abstract]. In: Proceedings of the AACR Special Conference on Melanoma: From Biology to Target; 2019 Jan 15-18; Houston, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(19 Suppl):Abstract nr PR03.
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Affiliation(s)
- Haifeng Zhu
- 1University of Texas MD Anderson Cancer Center, Houston, TX,
| | - Junna Oba
- 1University of Texas MD Anderson Cancer Center, Houston, TX,
| | - Xiaoxing Yu
- 1University of Texas MD Anderson Cancer Center, Houston, TX,
| | | | | | | | | | - Chang-Jiun Wu
- 1University of Texas MD Anderson Cancer Center, Houston, TX,
| | | | - Wei-Lien Wang
- 1University of Texas MD Anderson Cancer Center, Houston, TX,
| | | | | | - Gordon B. Mills
- 1University of Texas MD Anderson Cancer Center, Houston, TX,
| | | | - Yu Chen
- 2Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jianhua Zhang
- 1University of Texas MD Anderson Cancer Center, Houston, TX,
| | | | | | | | - Patrick Hwu
- 1University of Texas MD Anderson Cancer Center, Houston, TX,
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Haymaker C, Andtbacka R, Johnson D, Shaheen M, Rahimian S, Chunduru S, Gabrail N, Doolittle G, Puzanov I, Markowitz J, Bernatchez C, Diab A. 1083MO Final results from ILLUMINATE-204, a phase I/II trial of intratumoral tilsotolimod in combination with ipilimumab in PD-1 inhibitor refractory advanced melanoma. Ann Oncol 2020. [DOI: 10.1016/j.annonc.2020.08.1207] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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