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Khunger A, Rytlewski JA, Fields P, Yusko EC, Tarhini AA. The impact of CTLA-4 blockade and interferon-α on clonality of T-cell repertoire in the tumor microenvironment and peripheral blood of metastatic melanoma patients. Oncoimmunology 2019; 8:e1652538. [PMID: 31646098 DOI: 10.1080/2162402x.2019.1652538] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [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: 03/28/2019] [Revised: 07/24/2019] [Accepted: 07/31/2019] [Indexed: 02/06/2023] Open
Abstract
Patients with metastatic melanoma were treated with tremelimumab and interferon-α (IFN) in a previously reported clinical trial [NCT00610857]. Responses were assessed by RECIST criteria as complete (CR) or partial (PR), stable disease (SD) or progressive disease (PD). In this study, T-cell receptor (TCR) beta-chain repertoire was immunosequenced in peripheral blood mononuclear cells (PBMC) specimens (N = 33) and tumor samples (N = 18) utilizing the immunoSEQ® Assay to determine repertoire clonality and T cell fractions at pre-treatment (tumor and PBMC), one month (PBMC) and 3 months (PBMC) time points and evaluate its association with clinical outcomes. In the pretreatment tumor microenvironment (TME), T cell clonality was significantly (p = .035) different and greater in patients who achieved disease control (CR, PR, SD) versus those with non-disease control (PD) as best response to treatment. Further, there was significantly (p = .001) increased TCR fraction in tissue of responders (CR, PR) versus non-responders (PD, SD). In examining T cell clonality in the circulation (PBMC), no significant associations were found in the pretreatment samples. However, early on-treatment (4 weeks) there was a significant decrease in T cell clonality that was associated with improved overall survival (p = .01) and progression-free survival (p = .04). In addition, analysis of temporal changes in tumor-infiltrating lymphocytes (TIL) and peripheral TCR repertoire revealed that responders had significantly higher clonal expansion of TIL in the circulation at 4 weeks than non-responders (p = .036). Our study provided interesting mechanistic data related to CTLA-4 Blockade and IFN and potential biomarkers of immunotherapeutic benefit.
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Affiliation(s)
- Arjun Khunger
- Department of Hematology and Oncology, Cleveland Clinic, Cleveland, OH, USA
| | | | | | | | - Ahmad A Tarhini
- Department of Cutaneous Oncology, Moffitt Comprehensive Cancer Center, Tampa, Florida, USA
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Fischer GM, Jalali A, Kircher DA, Lee WC, McQuade JL, Haydu LE, Joon AY, Reuben A, de Macedo MP, Carapeto FCL, Yang C, Srivastava A, Ambati CR, Sreekumar A, Hudgens CW, Knighton B, Deng W, Ferguson SD, Tawbi HA, Glitza IC, Gershenwald JE, Vashisht Gopal YN, Hwu P, Huse JT, Wargo JA, Futreal PA, Putluri N, Lazar AJ, DeBerardinis RJ, Marszalek JR, Zhang J, Holmen SL, Tetzlaff MT, Davies MA. Molecular Profiling Reveals Unique Immune and Metabolic Features of Melanoma Brain Metastases. Cancer Discov 2019; 9:628-645. [PMID: 30787016 PMCID: PMC6497554 DOI: 10.1158/2159-8290.cd-18-1489] [Citation(s) in RCA: 192] [Impact Index Per Article: 38.4] [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: 12/20/2018] [Revised: 02/08/2019] [Accepted: 02/12/2019] [Indexed: 12/24/2022]
Abstract
There is a critical need to improve our understanding of the pathogenesis of melanoma brain metastases (MBM). Thus, we performed RNA sequencing on 88 resected MBMs and 42 patient-matched extracranial metastases; tumors with sufficient tissue also underwent whole-exome sequencing, T-cell receptor sequencing, and IHC. MBMs demonstrated heterogeneity of immune infiltrates that correlated with prior radiation and post-craniotomy survival. Comparison with patient-matched extracranial metastases identified significant immunosuppression and enrichment of oxidative phosphorylation (OXPHOS) in MBMs. Gene-expression analysis of intracranial and subcutaneous xenografts, and a spontaneous MBM model, confirmed increased OXPHOS gene expression in MBMs, which was also detected by direct metabolite profiling and [U-13C]-glucose tracing in vivo. IACS-010759, an OXPHOS inhibitor currently in early-phase clinical trials, improved survival of mice bearing MAPK inhibitor-resistant intracranial melanoma xenografts and inhibited MBM formation in the spontaneous MBM model. The results provide new insights into the pathogenesis and therapeutic resistance of MBMs. SIGNIFICANCE: Improving our understanding of the pathogenesis of MBMs will facilitate the rational development and prioritization of new therapeutic strategies. This study reports the most comprehensive molecular profiling of patient-matched MBMs and extracranial metastases to date. The data provide new insights into MBM biology and therapeutic resistance.See related commentary by Egelston and Margolin, p. 581.This article is highlighted in the In This Issue feature, p. 565.
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MESH Headings
- Animals
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/immunology
- Biomarkers, Tumor/metabolism
- Brain Neoplasms/drug therapy
- Brain Neoplasms/immunology
- Brain Neoplasms/metabolism
- Brain Neoplasms/secondary
- Cohort Studies
- Disease Models, Animal
- Female
- Gene Expression Profiling
- Gene Expression Regulation, Neoplastic
- Humans
- Lymphocytes, Tumor-Infiltrating/immunology
- Melanoma/drug therapy
- Melanoma/immunology
- Melanoma/metabolism
- Melanoma/pathology
- Metabolic Flux Analysis
- Metabolome
- Mice
- Mice, Inbred C57BL
- Mice, Nude
- Oxidative Phosphorylation
- Sequence Analysis, RNA/methods
- Tumor Cells, Cultured
- Xenograft Model Antitumor Assays
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Affiliation(s)
- Grant M Fischer
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Department of Melanoma Medical Oncology, 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
| | - Ali Jalali
- Department of Neurosurgery, Baylor College of Medicine, Houston, Texas
| | - David A Kircher
- Department of Oncological Sciences, University of Utah Health Sciences Center, Salt Lake City, Utah
| | - Won-Chul Lee
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jennifer L McQuade
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Lauren E Haydu
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Aron Y Joon
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Alexandre Reuben
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | - Fernando C L Carapeto
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Chendong Yang
- Children's Medical Research Institute, The University of Texas Southwestern Medical Center, Dallas, Texas
| | - Anuj Srivastava
- Department of Computational Sciences, The Jackson Lab for Genomic Medicine, Farmington, Connecticut
| | - Chandrashekar R Ambati
- Department of Molecular and Cell Biology, Baylor College of Medicine, Houston, Texas
- Advanced Technology Core, Alkek Center for Molecular Discovery, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Arun Sreekumar
- Department of Molecular and Cell Biology, Baylor College of Medicine, Houston, Texas
- Advanced Technology Core, Alkek Center for Molecular Discovery, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Courtney W Hudgens
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Barbara Knighton
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Wanleng Deng
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Sherise D Ferguson
- Department of Neurosurgery, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Hussein A Tawbi
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Isabella C Glitza
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jeffrey E Gershenwald
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Y N Vashisht Gopal
- Department of Melanoma Medical Oncology, 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
| | - Patrick Hwu
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jason T Huse
- 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
| | - Jennifer A Wargo
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Department of Surgical Oncology, 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
| | - Nagireddy Putluri
- Department of Molecular and Cell Biology, Baylor College of Medicine, Houston, Texas
- Advanced Technology Core, Alkek Center for Molecular Discovery, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Alexander J Lazar
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Ralph J DeBerardinis
- Children's Medical Research Institute, The University of Texas Southwestern Medical Center, Dallas, Texas
- Howard Hughes Medical Institute, The University of Texas Southwestern Medical Center, Dallas, Texas
| | - Joseph R Marszalek
- Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jianjun Zhang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Sheri L Holmen
- Department of Oncological Sciences, University of Utah Health Sciences Center, Salt Lake City, Utah
- Department of Surgery, University of Utah Health Sciences Center, Salt Lake City, Utah
| | - 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
| | - Michael A Davies
- Department of Melanoma Medical Oncology, 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 Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
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Abstract
Advancements in next-generation sequencing have greatly enhanced the development of biomarker-driven cancer therapies. The affordability and availability of next-generation sequencers have allowed for the commercialization of next-generation sequencing platforms that have found widespread use for clinical-decision making and research purposes. Despite the greater availability of tumor molecular profiling by next-generation sequencing at our doorsteps, the achievement of value-based care, or improving patient outcomes while reducing overall costs or risks, in the era of precision oncology remains a looming challenge. In this review, we highlight available data through a pre-established and conceptualized framework for evaluating value-based medicine to assess the cost (efficiency), clinical benefit (effectiveness), and toxicity (safety) of genomic profiling in cancer care. We also provide perspectives on future directions of next-generation sequencing from targeted panels to whole-exome or whole-genome sequencing and describe potential strategies needed to attain value-based genomics.
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Affiliation(s)
- Jun Gong
- Department of Medical Oncology, City of Hope National Medical Center, Duarte, CA, USA
| | - Kathy Pan
- Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Marwan Fakih
- Department of Medical Oncology, City of Hope National Medical Center, Duarte, CA, USA
| | - Sumanta Pal
- Department of Medical Oncology, City of Hope National Medical Center, Duarte, CA, USA
| | - Ravi Salgia
- Medical Oncology and Experimental Therapeutics, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
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