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Keshari S, Shavkunov AS, Miao Q, Saha A, Williams CD, Highsmith AM, Pineda JE, Alspach E, Hu KH, Pauken KE, Chen K, Gubin MM. Neoantigen Cancer Vaccines and Different Immune Checkpoint Therapies Each Utilize Both Converging and Distinct Mechanisms that in Combination Enable Synergistic Therapeutic Efficacy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.20.570816. [PMID: 38187708 PMCID: PMC10769249 DOI: 10.1101/2023.12.20.570816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
The goal of therapeutic cancer vaccines and immune checkpoint therapy (ICT) is to eliminate cancer by expanding and/or sustaining T cells with anti-tumor capabilities. However, whether cancer vaccines and ICT enhance anti-tumor immunity by distinct or overlapping mechanisms remains unclear. Here, we compared effective therapeutic tumor-specific mutant neoantigen (NeoAg) cancer vaccines with anti-CTLA-4 and/or anti-PD-1 ICT in preclinical models. Both NeoAg vaccines and ICT induce expansion of intratumoral NeoAg-specific CD8 T cells, though the degree of expansion and acquisition of effector activity was much more substantial following NeoAg vaccination. Further, we found that NeoAg vaccines are particularly adept at inducing proliferating and stem-like NeoAg-specific CD8 T cells. Single cell T cell receptor (TCR) sequencing revealed that TCR clonotype expansion and diversity of NeoAg-specific CD8 T cells relates to their phenotype and functional state associated with specific immunotherapies employed. Effective NeoAg vaccines and ICT required both CD8 and CD4 T cells. While NeoAg vaccines and anti-PD-1 affected the CD4 T cell compartment, it was to less of an extent than observed with anti-CTLA-4, which notably induced ICOS+Bhlhe40+ Th1-like CD4 T cells and, when combined with anti-PD-1, a small subset of Th2-like CD4 T cells. Although effective NeoAg vaccines or ICT expanded intratumoral M1-like iNOS+ macrophages, NeoAg vaccines expanded rather than suppressed (as observed with ICT) M2-like CX3CR1+CD206+ macrophages, associated with the vaccine adjuvant. Further, combining NeoAg vaccination with ICT induced superior efficacy compared to either therapy in isolation, highlighting the utility of combining these modalities to eliminate cancer.
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Affiliation(s)
- Sunita Keshari
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Alexander S. Shavkunov
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Qi Miao
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Akata Saha
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Charmelle D. Williams
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Anna M. Highsmith
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Josué E. Pineda
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Elise Alspach
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, St. Louis, MO, USA
| | - Kenneth H. Hu
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- The Parker Institute for Cancer Immunotherapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- The James P. Allison Institute, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kristen E. Pauken
- 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
| | - Matthew M. Gubin
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- The Parker Institute for Cancer Immunotherapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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2
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Hibler W, Merlino G, Yu Y. CAR NK Cell Therapy for the Treatment of Metastatic Melanoma: Potential & Prospects. Cells 2023; 12:2750. [PMID: 38067178 PMCID: PMC10706172 DOI: 10.3390/cells12232750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 11/22/2023] [Accepted: 11/26/2023] [Indexed: 12/18/2023] Open
Abstract
Melanoma is among the most lethal forms of cancer, accounting for 80% of deaths despite comprising just 5% of skin cancer cases. Treatment options remain limited due to the genetic and epigenetic mechanisms associated with melanoma heterogeneity that underlie the rapid development of secondary drug resistance. For this reason, the development of novel treatments remains paramount to the improvement of patient outcomes. Although the advent of chimeric antigen receptor-expressing T (CAR-T) cell immunotherapies has led to many clinical successes for hematological malignancies, these treatments are limited in their utility by their immune-induced side effects and a high risk of systemic toxicities. CAR natural killer (CAR-NK) cell immunotherapies are a particularly promising alternative to CAR-T cell immunotherapies, as they offer a more favorable safety profile and have the capacity for fine-tuned cytotoxic activity. In this review, the discussion of the prospects and potential of CAR-NK cell immunotherapies touches upon the clinical contexts of melanoma, the immunobiology of NK cells, the immunosuppressive barriers preventing endogenous immune cells from eliminating tumors, and the structure and design of chimeric antigen receptors, then finishes with a series of proposed design innovations that could improve the efficacy CAR-NK cell immunotherapies in future studies.
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Affiliation(s)
| | | | - Yanlin Yu
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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3
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Gerard C, Shum B, Nathan P, Turajlic S. Immuno-oncology approaches in uveal melanoma: tebentafusp and beyond. IMMUNO-ONCOLOGY TECHNOLOGY 2023; 19:100386. [PMID: 37483658 PMCID: PMC10362360 DOI: 10.1016/j.iotech.2023.100386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/25/2023]
Abstract
Uveal melanoma (UM) is the most common ocular malignancy in adults, associated with the poorest prognosis, with metastatic disease occurring in up to 50% of patients. In contrast to metastatic cutaneous melanoma, the use of immune checkpoint inhibitors is associated with poor outcomes in metastatic uveal melanoma (mUM). Tebentafusp, a bispecific molecule, has recently become the first treatment in decades to improve overall survival for mUM. This review summarises the existing and emerging immuno-oncology approaches for the treatment of mUM, and biomarkers of response and resistance to the same. Finally, we propose future research directions that could maximise treatment benefit to a wider pool of patients with UM.
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Affiliation(s)
- C. Gerard
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, UK
- Precision Oncology Center, Oncology Department, Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - B. Shum
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, UK
- Skin and Renal Unit, The Royal Marsden NHS Foundation Trust, London
| | - P. Nathan
- Mount Vernon Cancer Centre, East and North Herts NHS Trust, Northwood, UK
| | - S. Turajlic
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, UK
- Skin and Renal Unit, The Royal Marsden NHS Foundation Trust, London
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4
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Berner F, Flatz L. Autoimmunity in immune checkpoint inhibitor-induced immune-related adverse events: A focus on autoimmune skin toxicity and pneumonitis. Immunol Rev 2023; 318:37-50. [PMID: 37548043 DOI: 10.1111/imr.13258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 06/29/2023] [Indexed: 08/08/2023]
Abstract
Immune checkpoint inhibitors (ICIs) have revolutionized cancer therapy. However, their use is frequently associated with immune-related adverse events (irAEs) potentially affecting any organ. The mechanisms mediating such irAEs remain poorly understood and biomarkers to predict the development of irAEs are lacking. Growing evidence shows the importance of self-antigens in mediating irAEs during ICI therapy, in particular the well-described melanocyte differentiation antigens in melanoma patients. This review will focus on two novel classes of self-antigens involved in mediating autoimmune skin toxicity and pneumonitis in non-small cell lung cancer patients treated with immunotherapy. T cells specific for these self-antigens are thought to not only mediate irAEs but are thought to simultaneously mediate anti-tumor responses and are therefore associated with both autoimmune toxicity and response to ICI therapy. We further discuss emerging cellular and proteomic immune signatures of irAEs that may serve as biomarkers to help predict which patients are at higher risk of developing these irAEs. The determination of new tumor antigens involved in ICI therapy and the identification of related biomarkers brings us a step forward in the mechanistic understanding of ICIs and will help to monitor patients at higher risk of developing irAEs. Lastly, we discuss the current challenges in collecting research samples for the study of ICI-related mechanisms and in distinguishing between immune signatures of response and those of irAEs.
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Affiliation(s)
- Fiamma Berner
- Institute of Immunobiology, Kantonsspital St. Gallen, St. Gallen, Switzerland
| | - Lukas Flatz
- Institute of Immunobiology, Kantonsspital St. Gallen, St. Gallen, Switzerland
- Department of Dermatology, University Hospital Tübingen, University of Tübingen, Tübingen, Germany
- Department of Dermatology, Kantonsspital St. Gallen, St. Gallen, Switzerland
- Department of Dermatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
- Department of Oncology and Hematology, Kantonsspital St. Gallen, St. Gallen, Switzerland
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5
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Li J, Xiao Z, Wang D, Jia L, Nie S, Zeng X, Hu W. The screening, identification, design and clinical application of tumor-specific neoantigens for TCR-T cells. Mol Cancer 2023; 22:141. [PMID: 37649123 PMCID: PMC10466891 DOI: 10.1186/s12943-023-01844-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 08/16/2023] [Indexed: 09/01/2023] Open
Abstract
Recent advances in neoantigen research have accelerated the development of tumor immunotherapies, including adoptive cell therapies (ACTs), cancer vaccines and antibody-based therapies, particularly for solid tumors. With the development of next-generation sequencing and bioinformatics technology, the rapid identification and prediction of tumor-specific antigens (TSAs) has become possible. Compared with tumor-associated antigens (TAAs), highly immunogenic TSAs provide new targets for personalized tumor immunotherapy and can be used as prospective indicators for predicting tumor patient survival, prognosis, and immune checkpoint blockade response. Here, the identification and characterization of neoantigens and the clinical application of neoantigen-based TCR-T immunotherapy strategies are summarized, and the current status, inherent challenges, and clinical translational potential of these strategies are discussed.
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Affiliation(s)
- Jiangping Li
- Division of Thoracic Tumor Multimodality Treatment, Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, People's Republic of China.
| | - Zhiwen Xiao
- Department of Otolaryngology Head and Neck Surgery, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, People's Republic of China
| | - Donghui Wang
- Department of Radiation Oncology, The Third Affiliated Hospital Sun Yat-Sen University, Guangzhou, 510630, People's Republic of China
| | - Lei Jia
- International Health Medicine Innovation Center, Shenzhen University, Shenzhen, 518060, People's Republic of China
| | - Shihong Nie
- Department of Radiation Oncology, West China Hospital, Sichuan University, Cancer Center, Chengdu, 610041, People's Republic of China
| | - Xingda Zeng
- Department of Parasitology of Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Wei Hu
- Division of Vascular Surgery, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, 610072, People's Republic of China
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6
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Cuevas MVR, Hardy MP, Larouche JD, Apavaloaei A, Kina E, Vincent K, Gendron P, Laverdure JP, Durette C, Thibault P, Lemieux S, Perreault C, Ehx G. BamQuery: a proteogenomic tool to explore the immunopeptidome and prioritize actionable tumor antigens. Genome Biol 2023; 24:188. [PMID: 37582761 PMCID: PMC10426134 DOI: 10.1186/s13059-023-03029-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 07/31/2023] [Indexed: 08/17/2023] Open
Abstract
MHC-I-associated peptides deriving from non-coding genomic regions and mutations can generate tumor-specific antigens, including neoantigens. Quantifying tumor-specific antigens' RNA expression in malignant and benign tissues is critical for discriminating actionable targets. We present BamQuery, a tool attributing an exhaustive RNA expression to MHC-I-associated peptides of any origin from bulk and single-cell RNA-sequencing data. We show that many cryptic and mutated tumor-specific antigens can derive from multiple discrete genomic regions, abundantly expressed in normal tissues. BamQuery can also be used to predict MHC-I-associated peptides immunogenicity and identify actionable tumor-specific antigens de novo.
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Affiliation(s)
- Maria Virginia Ruiz Cuevas
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC, H3C 3J7, Canada
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montreal, QC, H3C 3J7, Canada
| | - Marie-Pierre Hardy
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC, H3C 3J7, Canada
| | - Jean-David Larouche
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC, H3C 3J7, Canada
- Department of Medicine, Université de Montréal, Montreal, QC, H3C 3J7, Canada
| | - Anca Apavaloaei
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC, H3C 3J7, Canada
- Department of Medicine, Université de Montréal, Montreal, QC, H3C 3J7, Canada
| | - Eralda Kina
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC, H3C 3J7, Canada
- Department of Medicine, Université de Montréal, Montreal, QC, H3C 3J7, Canada
| | - Krystel Vincent
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC, H3C 3J7, Canada
| | - Patrick Gendron
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC, H3C 3J7, Canada
| | - Jean-Philippe Laverdure
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC, H3C 3J7, Canada
| | - Chantal Durette
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC, H3C 3J7, Canada
| | - Pierre Thibault
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC, H3C 3J7, Canada
- Department of Chemistry, Université de Montréal, Montreal, QC, H3C 3J7, Canada
| | - Sébastien Lemieux
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC, H3C 3J7, Canada
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montreal, QC, H3C 3J7, Canada
| | - Claude Perreault
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC, H3C 3J7, Canada
- Department of Medicine, Université de Montréal, Montreal, QC, H3C 3J7, Canada
| | - Grégory Ehx
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC, H3C 3J7, Canada.
- Laboratory of Hematology, GIGA-I3, University of Liege, CHU of Liege, Liege, Belgium.
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7
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Berner F, Bomze D, Lichtensteiger C, Walter V, Niederer R, Hasan Ali O, Wyss N, Bauer J, Freudenmann LK, Marcu A, Wolfschmitt EM, Haen S, Gross T, Abdou MT, Diem S, Knöpfli S, Sinnberg T, Hofmeister K, Cheng HW, Toma M, Klümper N, Purde MT, Pop OT, Jochum AK, Pascolo S, Joerger M, Früh M, Jochum W, Rammensee HG, Läubli H, Hölzel M, Neefjes J, Walz J, Flatz L. Autoreactive napsin A-specific T cells are enriched in lung tumors and inflammatory lung lesions during immune checkpoint blockade. Sci Immunol 2022; 7:eabn9644. [PMID: 36054337 DOI: 10.1126/sciimmunol.abn9644] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Cancer treatment with immune checkpoint blockade (ICB) often induces immune-related adverse events (irAEs). We hypothesized that proteins coexpressed in tumors and normal cells could be antigenic targets in irAEs and herein described DITAS (discovery of tumor-associated self-antigens) for their identification. DITAS computed transcriptional similarity between lung tumors and healthy lung tissue based on single-sample gene set enrichment analysis. This identified 10 lung tissue-specific genes highly expressed in the lung tumors. Computational analysis was combined with functional T cell assays and single-cell RNA sequencing of the antigen-specific T cells to validate the lung tumor self-antigens. In patients with non-small cell lung cancer (NSCLC) treated with ICB, napsin A was a self-antigen that elicited strong CD8+ T cell responses, with ICB responders harboring higher frequencies of these CD8+ T cells compared with nonresponders. Human leukocyte antigen (HLA) class I ligands derived from napsin A were present in human lung tumors and in nontumor lung tissues, and napsin A tetramers confirmed the presence of napsin A-specific CD8+ T cells in blood and tumors of patients with NSCLC. Napsin A-specific T cell clonotypes were enriched in lung tumors and ICB-induced inflammatory lung lesions and could kill immortalized HLA-matched NSCLC cells ex vivo. Single-cell RNA sequencing revealed that these T cell clonotypes expressed proinflammatory cytokines and cytotoxic markers. Thus, DITAS successfully identified self-antigens, including napsin A, that likely mediate effective antitumor T cell responses in NSCLC and may simultaneously underpin lung irAEs.
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Affiliation(s)
- Fiamma Berner
- Institute of Immunobiology, Kantonsspital St. Gallen, St. Gallen, Switzerland
| | - David Bomze
- Institute of Immunobiology, Kantonsspital St. Gallen, St. Gallen, Switzerland.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | | | - Vincent Walter
- Department of Dermatology, University Hospital Tübingen, University of Tübingen, Tübingen, Germany
| | - Rebekka Niederer
- Institute of Immunobiology, Kantonsspital St. Gallen, St. Gallen, Switzerland.,Department of Dermatology, Kantonsspital St. Gallen, St. Gallen, Switzerland
| | - Omar Hasan Ali
- Institute of Immunobiology, Kantonsspital St. Gallen, St. Gallen, Switzerland.,Department of Medical Genetics, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada.,Department of Dermatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Nina Wyss
- Institute of Immunobiology, Kantonsspital St. Gallen, St. Gallen, Switzerland.,Department of Dermatology, Kantonsspital St. Gallen, St. Gallen, Switzerland
| | - Jens Bauer
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany.,Interfaculty Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany.,Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
| | - Lena Katharina Freudenmann
- Interfaculty Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany.,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Partner Site Tübingen, Tübingen, Germany
| | - Ana Marcu
- Interfaculty Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
| | - Eva-Maria Wolfschmitt
- Interfaculty Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
| | - Sebastian Haen
- Interfaculty Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
| | - Thorben Gross
- Interfaculty Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
| | - Marie-Therese Abdou
- Institute of Immunobiology, Kantonsspital St. Gallen, St. Gallen, Switzerland
| | - Stefan Diem
- Department of Oncology and Hematology, Kantonsspital St. Gallen, St. Gallen, Switzerland
| | - Stella Knöpfli
- Institute of Immunobiology, Kantonsspital St. Gallen, St. Gallen, Switzerland
| | - Tobias Sinnberg
- Department of Dermatology, University Hospital Tübingen, University of Tübingen, Tübingen, Germany.,Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
| | - Kathrin Hofmeister
- Department of Dermatology, University Hospital Tübingen, University of Tübingen, Tübingen, Germany
| | - Hung-Wei Cheng
- Institute of Immunobiology, Kantonsspital St. Gallen, St. Gallen, Switzerland
| | - Marieta Toma
- Institute of Pathology, University Hospital Bonn (UKB), University of Bonn, Bonn, Germany
| | - Niklas Klümper
- Department of Urology, University Hospital Bonn (UKB), University of Bonn, Bonn, Germany.,Institute of Experimental Oncology, University Hospital Bonn (UKB), University of Bonn, Bonn, Germany
| | - Mette-Triin Purde
- Institute of Immunobiology, Kantonsspital St. Gallen, St. Gallen, Switzerland
| | - Oltin Tiberiu Pop
- Institute of Immunobiology, Kantonsspital St. Gallen, St. Gallen, Switzerland
| | - Ann-Kristin Jochum
- Institute of Immunobiology, Kantonsspital St. Gallen, St. Gallen, Switzerland.,Institute of Pathology, Kantonsspital St. Gallen, St. Gallen, Switzerland
| | - Steve Pascolo
- Department of Dermatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Markus Joerger
- Department of Oncology and Hematology, Kantonsspital St. Gallen, St. Gallen, Switzerland
| | - Martin Früh
- Department of Oncology and Hematology, Kantonsspital St. Gallen, St. Gallen, Switzerland.,Department of Oncology, University of Bern, Bern, Switzerland
| | - Wolfram Jochum
- Institute of Pathology, Kantonsspital St. Gallen, St. Gallen, Switzerland
| | - Hans-Georg Rammensee
- Interfaculty Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany.,Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany.,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Partner Site Tübingen, Tübingen, Germany
| | - Heinz Läubli
- Division of Oncology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Michael Hölzel
- Institute of Experimental Oncology, University Hospital Bonn (UKB), University of Bonn, Bonn, Germany
| | - Jacques Neefjes
- Department of Cell and Chemical Biology, Oncode Institute, Leiden University Medical Center, Netherlands
| | - Juliane Walz
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany.,Interfaculty Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany.,Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany.,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Partner Site Tübingen, Tübingen, Germany.,Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology and Robert Bosch Center for Tumor Diseases (RBCT), Stuttgart, Germany
| | - Lukas Flatz
- Institute of Immunobiology, Kantonsspital St. Gallen, St. Gallen, Switzerland.,Department of Dermatology, University Hospital Tübingen, University of Tübingen, Tübingen, Germany.,Department of Dermatology, Kantonsspital St. Gallen, St. Gallen, Switzerland.,Department of Dermatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.,Department of Oncology and Hematology, Kantonsspital St. Gallen, St. Gallen, Switzerland
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8
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Sander CA, Rush EA, Shi J, Arantes LMRB, Tesi RJ, Ross MA, Calderon MJ, Watkins SC, Kirkwood JM, Ferris RL, Butterfield LH, Vujanovic L. Co-expression of TNF receptors 1 and 2 on melanomas facilitates soluble TNF-induced resistance to MAPK pathway inhibitors. J Transl Med 2022; 20:331. [PMID: 35879777 PMCID: PMC9310383 DOI: 10.1186/s12967-022-03538-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 07/15/2022] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND The effectiveness of MAPK pathway inhibitors (MAPKi) used to treat patients with BRAF-mutant melanoma is limited by a range of resistance mechanisms, including soluble TNF (solTNF)-mediated NF-kB signaling. solTNF preferentially signals through type-1 TNF receptor (TNFR1), however, it can also bind to TNFR2, a receptor that is primarily expressed on leukocytes. Here, we investigate the TNFR2 expression pattern on human BRAFV600E+ melanomas and its role in solTNF-driven resistance reprogramming to MAPKi. METHODS Flow cytometry was used to test TNFR1, TNFR2 and CD271 expression on, as well as NF-kB phosphorylation in human BRAF-mutant melanoma. The ability of melanoma cell lines to acquire MAPKi resistance in response to recombinant or macrophage-derived TNF was evaluated using the MTT cytotoxicity assay. Gene editing was implemented to knock out or knock in TNF receptors in melanoma cell lines. Knockout and knock-in cell line variants were employed to assess the intrinsic roles of these receptors in TNF-induced resistance to MAPKi. Multicolor immunofluorescence microscopy was utilized to test TNFR2 expression by melanoma in patients receiving MAPKi therapy. RESULTS TNFR1 and TNFR2 are co-expressed at various levels on 4/7 BRAFV600E+ melanoma cell lines evaluated in this study. In vitro treatments with solTNF induce MAPKi resistance solely in TNFR2-expressing BRAFV600E+ melanoma cell lines. TNFR1 and TNFR2 knockout and knock-in studies indicate that solTNF-mediated MAPKi resistance in BRAFV600E+ melanomas is predicated on TNFR1 and TNFR2 co-expression, where TNFR1 is the central mediator of NF-kB signaling, while TNFR2 plays an auxiliary role. solTNF-mediated effects are transient and can be abrogated with biologics. Evaluation of patient specimens indicates that TNFR2 is expressed on 50% of primary BRAFV600E+ melanoma cells and that MAPKi therapy may lead to the enrichment of TNFR2-expressing tumor cells. CONCLUSIONS Our data suggest that TNFR2 is essential to solTNF-induced MAPKi resistance and a possible biomarker to identify melanoma patients that can benefit from solTNF-targeting therapies.
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Affiliation(s)
- Cindy A. Sander
- grid.21925.3d0000 0004 1936 9000UPMC Hillman Cancer Center, University of Pittsburgh, L2.19 Hillman Cancer Center, 5117 Centre Avenue, Pittsburgh, PA USA ,grid.21925.3d0000 0004 1936 9000Department of Medicine, University of Pittsburgh, Pittsburgh, PA USA
| | - Elizabeth A. Rush
- grid.21925.3d0000 0004 1936 9000UPMC Hillman Cancer Center, University of Pittsburgh, L2.19 Hillman Cancer Center, 5117 Centre Avenue, Pittsburgh, PA USA ,grid.21925.3d0000 0004 1936 9000Department of Medicine, University of Pittsburgh, Pittsburgh, PA USA
| | - Jian Shi
- grid.21925.3d0000 0004 1936 9000UPMC Hillman Cancer Center, University of Pittsburgh, L2.19 Hillman Cancer Center, 5117 Centre Avenue, Pittsburgh, PA USA ,grid.21925.3d0000 0004 1936 9000Department of Medicine, University of Pittsburgh, Pittsburgh, PA USA
| | - Lidia M. R. B. Arantes
- grid.21925.3d0000 0004 1936 9000UPMC Hillman Cancer Center, University of Pittsburgh, L2.19 Hillman Cancer Center, 5117 Centre Avenue, Pittsburgh, PA USA ,grid.21925.3d0000 0004 1936 9000Department of Otolaryngology, University of Pittsburgh, Pittsburgh, PA USA ,grid.427783.d0000 0004 0615 7498Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, SP Brazil
| | | | - Mark A. Ross
- grid.21925.3d0000 0004 1936 9000Department of Cell Biology, University of Pittsburgh, Pittsburgh, PA USA
| | - Michael J. Calderon
- grid.21925.3d0000 0004 1936 9000Department of Cell Biology, University of Pittsburgh, Pittsburgh, PA USA
| | - Simon C. Watkins
- grid.21925.3d0000 0004 1936 9000Department of Cell Biology, University of Pittsburgh, Pittsburgh, PA USA
| | - John M. Kirkwood
- grid.21925.3d0000 0004 1936 9000UPMC Hillman Cancer Center, University of Pittsburgh, L2.19 Hillman Cancer Center, 5117 Centre Avenue, Pittsburgh, PA USA ,grid.21925.3d0000 0004 1936 9000Department of Medicine, University of Pittsburgh, Pittsburgh, PA USA
| | - Robert L. Ferris
- grid.21925.3d0000 0004 1936 9000UPMC Hillman Cancer Center, University of Pittsburgh, L2.19 Hillman Cancer Center, 5117 Centre Avenue, Pittsburgh, PA USA ,grid.21925.3d0000 0004 1936 9000Department of Otolaryngology, University of Pittsburgh, Pittsburgh, PA USA ,grid.21925.3d0000 0004 1936 9000Department of Immunology, University of Pittsburgh, Pittsburgh, PA USA
| | - Lisa H. Butterfield
- grid.21925.3d0000 0004 1936 9000UPMC Hillman Cancer Center, University of Pittsburgh, L2.19 Hillman Cancer Center, 5117 Centre Avenue, Pittsburgh, PA USA ,grid.21925.3d0000 0004 1936 9000Department of Medicine, University of Pittsburgh, Pittsburgh, PA USA ,grid.21925.3d0000 0004 1936 9000Department of Immunology, University of Pittsburgh, Pittsburgh, PA USA ,grid.21925.3d0000 0004 1936 9000School of Medicine Department of Surgery, University of Pittsburgh, Pittsburgh, PA USA ,grid.489192.f0000 0004 7782 4884Parker Institute for Cancer Immunotherapy, San Francisco, CA USA
| | - Lazar Vujanovic
- grid.21925.3d0000 0004 1936 9000UPMC Hillman Cancer Center, University of Pittsburgh, L2.19 Hillman Cancer Center, 5117 Centre Avenue, Pittsburgh, PA USA ,grid.21925.3d0000 0004 1936 9000Department of Medicine, University of Pittsburgh, Pittsburgh, PA USA ,grid.21925.3d0000 0004 1936 9000Department of Otolaryngology, University of Pittsburgh, Pittsburgh, PA USA
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9
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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] [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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10
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Recent Advances and Challenges in Uveal Melanoma Immunotherapy. Cancers (Basel) 2022; 14:cancers14133094. [PMID: 35804863 PMCID: PMC9264803 DOI: 10.3390/cancers14133094] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 06/19/2022] [Accepted: 06/21/2022] [Indexed: 12/13/2022] Open
Abstract
Simple Summary Uveal melanoma is the most common primary intraocular malignancy in adults. Although it can be controlled locally, half of the patients still develop metastases. To date, there have been no standard therapeutic strategies for the prevention or treatment of metastases. Existing therapies, such as chemotherapy and targeted therapies, induce only minimal responses. This review focuses on newly published research on immunotherapy. We highlight expanding treatments and their clinical outcomes, as well as propose promising new treatments and feasible checkpoints. Based on these findings, we provide innovative insights into feasible strategies for the treatment of patients with uveal melanoma. Abstract Uveal melanoma (UM) is the most common primary intraocular malignancy in adults. Compared to cutaneous melanoma (CM), which mainly harbors BRAF or NRAS mutations, UM predominantly harbors GNAQ or GNA11 mutations. Although primary UM can be controlled locally, approximately 50% of patients still develop metastases. To date, there have been no standard therapeutic strategies for the prevention or treatment of metastases. Unfortunately, chemotherapy and targeted therapies only induce minimal responses in patients with metastatic UM, with a median survival time of only 4–5 months after metastasis detection. Immunotherapy agents, such as immune checkpoint inhibitors, have achieved pioneering outcomes in CM but have shown limited effects in UM. Researchers have explored several feasible checkpoints to identify options for future therapies. Cancer vaccines have shown little in the way of therapeutic benefit in patients with UM, and there are few ongoing trials providing favorable evidence, but adoptive cell transfer-related therapies seem promising and deserve further investigation. More recently, the immune-mobilizing monoclonal T-cell receptor against the cancer molecule tebentafusp showed impressive antitumor effects. Meanwhile, oncolytic viruses and small molecule inhibitors have also gained ground. This review highlights recent progress in burgeoning treatments and provides innovative insights on feasible strategies for the treatment of UM.
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11
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Chai S, Smith CC, Kochar TK, Hunsucker SA, Beck W, Olsen KS, Vensko S, Glish GL, Armistead PM, Prins JF, Vincent BG. NeoSplice: a bioinformatics method for prediction of splice variant neoantigens. BIOINFORMATICS ADVANCES 2022; 2:vbac032. [PMID: 35669345 PMCID: PMC9154024 DOI: 10.1093/bioadv/vbac032] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 04/14/2022] [Accepted: 05/04/2022] [Indexed: 01/27/2023]
Abstract
Motivation Splice variant neoantigens are a potential source of tumor-specific antigen (TSA) that are shared between patients in a variety of cancers, including acute myeloid leukemia. Current tools for genomic prediction of splice variant neoantigens demonstrate promise. However, many tools have not been well validated with simulated and/or wet lab approaches, with no studies published that have presented a targeted immunopeptidome mass spectrometry approach designed specifically for identification of predicted splice variant neoantigens. Results In this study, we describe NeoSplice, a novel computational method for splice variant neoantigen prediction based on (i) prediction of tumor-specific k-mers from RNA-seq data, (ii) alignment of differentially expressed k-mers to the splice graph and (iii) inference of the variant transcript with MHC binding prediction. NeoSplice demonstrates high sensitivity and precision (>80% on average across all splice variant classes) through in silico simulated RNA-seq data. Through mass spectrometry analysis of the immunopeptidome of the K562.A2 cell line compared against a synthetic peptide reference of predicted splice variant neoantigens, we validated 4 of 37 predicted antigens corresponding to 3 of 17 unique splice junctions. Lastly, we provide a comparison of NeoSplice against other splice variant prediction tools described in the literature. NeoSplice provides a well-validated platform for prediction of TSA vaccine targets for future cancer antigen vaccine studies to evaluate the clinical efficacy of splice variant neoantigens. Availability and implementation https://github.com/Benjamin-Vincent-Lab/NeoSplice. Supplementary information Supplementary data are available at Bioinformatics Advances online.
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Affiliation(s)
- Shengjie Chai
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27514, USA,Curriculum in Bioinformatics and Computational Biology, UNC School of Medicine, Chapel Hill, NC, 27599, USA
| | - Christof C Smith
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27514, USA,Department of Microbiology and Immunology, UNC School of Medicine, Chapel Hill, NC, 27599, USA
| | - Tavleen K Kochar
- Department of Chemistry, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Sally A Hunsucker
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27514, USA
| | - Wolfgang Beck
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27514, USA,Department of Microbiology and Immunology, UNC School of Medicine, Chapel Hill, NC, 27599, USA
| | - Kelly S Olsen
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27514, USA,Department of Microbiology and Immunology, UNC School of Medicine, Chapel Hill, NC, 27599, USA
| | - Steven Vensko
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27514, USA
| | - Gary L Glish
- Department of Chemistry, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Paul M Armistead
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27514, USA,Division of Hematology, Department of Medicine, UNC School of Medicine, Chapel Hill, NC, 27599, USA
| | - Jan F Prins
- Curriculum in Bioinformatics and Computational Biology, UNC School of Medicine, Chapel Hill, NC, 27599, USA,Department of Computer Science, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Benjamin G Vincent
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27514, USA,Curriculum in Bioinformatics and Computational Biology, UNC School of Medicine, Chapel Hill, NC, 27599, USA,Department of Microbiology and Immunology, UNC School of Medicine, Chapel Hill, NC, 27599, USA,Division of Hematology, Department of Medicine, UNC School of Medicine, Chapel Hill, NC, 27599, USA,Computational Medicine Program, UNC School of Medicine, Chapel Hill, NC, 27599, USA,To whom correspondence should be addressed.
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12
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Liu Y, Chi W, Tao L, Wang G, Deepak RK, Sheng L, Chen T, Feng Y, Cao X, Cheng L, Zhao X, Liu X, Deng H, Fan H, Jiang P, Chen L. Ablation of H+/glucose Exporter SLC45A2 Enhances Melanosomal Glycolysis to Inhibit Melanin Biosynthesis and Promote Melanoma Metastasis. J Invest Dermatol 2022; 142:2744-2755.e9. [DOI: 10.1016/j.jid.2022.04.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 03/11/2022] [Accepted: 04/11/2022] [Indexed: 01/13/2023]
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13
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Strobel SB, Machiraju D, Hassel JC. TCR-Directed Therapy in the Treatment of Metastatic Uveal Melanoma. Cancers (Basel) 2022; 14:1215. [PMID: 35267523 PMCID: PMC8909175 DOI: 10.3390/cancers14051215] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 02/21/2022] [Accepted: 02/24/2022] [Indexed: 12/11/2022] Open
Abstract
Metastatic uveal melanoma (mUM) is one of the most rapidly progressing tumors, with a bad prognosis and no standard-of-care treatment. Immune checkpoint inhibitors have revolutionized cancer therapy and improved overall survival in patients with metastatic cutaneous melanoma (mCM). However, this approach has been largely unimpressive, with no significant impact on the survival of mUM patients. Technical advances in immunotherapies have led to the development of novel T cell receptor (TCR)-based approaches to fight cancer. For the first time in over 50 years, compelling evidence demonstrates the power of TCR-based approaches for survival in mUM patients. Hence, this review summarizes novel TCR-based immunotherapeutic strategies currently in clinical studies for mUM treatment. We also discuss the potential combinational treatments to these strategies to maximize the clinical benefits.
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Affiliation(s)
| | | | - Jessica C. Hassel
- Department of Dermatology, National Center for Tumor Diseases, University Hospital Heidelberg, Code, 69120 Heidelberg, Germany; (S.B.S.); (D.M.)
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14
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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: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [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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15
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Pan K, Chiu Y, Huang E, Chen M, Wang J, Lai I, Singh S, Shaw R, MacCoss M, Yee C. Immunogenic SARS-CoV2 Epitopes Defined by Mass Spectrometry. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021. [PMID: 34312620 DOI: 10.1101/2021.07.20.453160] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
SARS-CoV-2 infections elicit both humoral and cellular immune responses. For the prevention and treatment of COVID19, the disease caused by SARS-CoV-2, T cell responses are important in mediating recovery and immune-protection. The identification of immunogenic epitopes that can elicit a meaningful T cell response can be elusive. Traditionally, this has been achieved using sophisticated in silico methods to predict putative epitopes; however, our previous studies find that 'immunodominant' SARS-CoV-2 peptides defined by such in silico methods often fail to elicit T cell responses recognizing SARS-CoV-2. We postulated that immunogenic epitopes for SARS-CoV-2 are best defined by directly analyzing peptides eluted from the peptide-MHC complex and then validating immunogenicity empirically by determining if such peptides can elicit T cells recognizing SARS-CoV-2 antigen-expressing cells. Using a tandem mass spectrometry approach, we identified epitopes of SARS-CoV-2 derived not only from structural but also non-structural genes in regions highly conserved among SARS-CoV-2 strains including recently recognized variants. We report here, for the first time, several novel SARS-CoV-2 epitopes from membrane glycol-protein (MGP) and non-structure protein-13 (NSP13) defined by mass-spectrometric analysis of MHC-eluted peptides, provide empiric evidence for their immunogenicity to induce T cell response. Significance Statement Current state of the art uses putative epitope peptides based on in silico prediction algorithms to evaluate the T cell response among COVID-19 patients. However, none of these peptides have been tested for immunogenicity, i.e. the ability to elicit a T cell response capable of recognizing endogenously presented peptide. In this study, we used MHC immune-precipitation, acid elution and tandem mass spectrometry to define the SARS-CoV-2 immunopeptidome for membrane glycol-protein and the non-structural protein. Furthermore, taking advantage of a highly robust endogenous T cell (ETC) workflow, we verify the immunogenicity of these MS-defined peptides by in vitro generation of MGP and NSP13 peptide-specific T cells and confirm T cell recognition of MGP or NSP13 endogenously expressing cell lines.
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16
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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: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [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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17
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Chen W, Huang F, Huang J, Li Y, Peng J, Zhuang Y, Huang X, Lu L, Zhu Z, Zhang S. SLC45A4 promotes glycolysis and prevents AMPK/ULK1-induced autophagy in TP53 mutant pancreatic ductal adenocarcinoma. J Gene Med 2021; 23:e3364. [PMID: 34010493 PMCID: PMC8459293 DOI: 10.1002/jgm.3364] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Accepted: 05/15/2021] [Indexed: 12/21/2022] Open
Abstract
Background Somatic mutations of the TP53 gene occur frequently in pancreatic ductal adenocarcinoma (PDA). Solute carrier family 45 member A4 (SLC45A4) is a H+‐dependent sugar cotransporter. The role of SLC45A4 in PDA, especially in TP53 mutant PDA, remains poorly understood. Methods We explored the TCGA datasets to identify oncogenes in TP53 mutant PDA. MTS [3‐(4,5‐dimethylthiazol‐2‐yl)‐5‐(3‐carboxymethoxyphenyl)‐2‐(4‐sulfophenyl)‐2H‐tetrazolium], colony formation and 5‐ethynyl‐2′‐deoxyuridine (Edu) assays were performed to investigate the function of SLC45A4 in vitro. Glucose consumption, lactate production and ATP production were detected to evaluate glucose utilization. Extracellular acidification rate and oxygen consumption rate assays were used to evaluate glycolysis and oxidative phosphorylation. The subcutaneous xenotransplantation models were conducted to explore the function of SLC45A4 in vivo. RNA‐sequencing and gene set enrichment analysis were employed to explore the biological alteration caused by SLC45A4 knockdown. Western blotting was performed to evaluate the activation of glycolysis, as well as the AMPK pathway and autophagy. Results SLC45A4 was overexpressed in PDA for which the expression was significantly higher in TP53 mutant PDA than that in wild‐type PDA tissues. Moreover, high level of SLC45A4 expression was tightly associated with poor clinical outcomes in PDA patients. Silencing SLC45A4 inhibited proliferation in TP53 mutant PDA cells. Knockdown of SLC45A4 reduced glucose uptake and ATP production, which led to activation of autophagy via AMPK/ULK1 pathway. Deleting SLC45A4 in TP53 mutant HPAF‐II cells inhibited the growth of xenografts in nude mice. Conclusions The present study found that SLC45A4 prevents autophagy via AMPK/ULK1 axis in TP53 mutant PDA, which may be a promising biomarker and therapeutic target in TP53 mutant PDA.
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Affiliation(s)
- Wenying Chen
- Department of Gastroenterology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China.,Department of Oncology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Fengting Huang
- Department of Gastroenterology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Jing Huang
- Department of General Surgery, Peking University Shenzhen Hospital, Shenzhen, China
| | - Yuanhua Li
- Department of Gastroenterology, Tungwah Hospital of Sun Yat-Sen University, Dongguan, China
| | - Juanfei Peng
- Department of Gastroenterology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Yanyan Zhuang
- Department of Gastroenterology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Xianxian Huang
- Center of Digestive Endoscopy, The Eighth Affiliated Hospital, Sun Yat-Sen University, Shenzhen, China
| | - Liting Lu
- Department of Gastroenterology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Zhe Zhu
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA
| | - Shineng Zhang
- Department of Gastroenterology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
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18
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Masaoutis C, Kokkali S, Theocharis S. Immunotherapy in uveal melanoma: novel strategies and opportunities for personalized treatment. Expert Opin Investig Drugs 2021; 30:555-569. [PMID: 33650931 DOI: 10.1080/13543784.2021.1898587] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
INTRODUCTION Uveal melanoma (UM) is the most common intraocular cancer and represents a discrete subtype of melanoma. Metastatic disease, which occurs in half of patients, has a dismal prognosis. Immunotherapy with immune checkpoint inhibitors has produced promising results in cutaneous melanoma but has failed to show analogous efficacy in metastatic UM. This is attributable to UM's distinct genetics and its complex interaction with the immune system. Hence, more efficacious immunotherapeutic approaches are under investigation. AREAS COVERED We discuss those novel immunotherapeutic strategies in clinical and preclinical studies for advanced disease and which are thought to overcome the hurdles set by UM in terms of immune recognition. We also highlight the need to determine predictive markers in relation to these strategies to improve clinical outcomes. We used a simple narrative analysis to summarize the data. The search methodology is located in the Introduction. EXPERT OPINION Novel immunotherapeutic strategies focus on transforming immune excluded tumor microenvironment in metastatic UM to T cell inflamed. Preliminary results of approaches such as vaccines, adoptive cell transfer and other novel molecules are encouraging. Factors such as HLA compatibility and expression level of targeted antigens should be considered to optimize personalized management.
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Affiliation(s)
- Christos Masaoutis
- First Department of Pathology, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Stefania Kokkali
- First Department of Pathology, Medical School, National and Kapodistrian University of Athens, Athens, Greece.,First Medical Oncology Clinic, Saint-Savvas Anticancer Hospital, Athens, Greece
| | - Stamatios Theocharis
- First Department of Pathology, Medical School, National and Kapodistrian University of Athens, Athens, Greece
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19
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Bradley SD, Talukder AH, Lai I, Davis R, Alvarez H, Tiriac H, Zhang M, Chiu Y, Melendez B, Jackson KR, Katailiha A, Sonnemann HM, Li F, Kang Y, Qiao N, Pan BF, Lorenzi PL, Hurd M, Mittendorf EA, Peterson CB, Javle M, Bristow C, Kim M, Tuveson DA, Hawke D, Kopetz S, Wolff RA, Hwu P, Maitra A, Roszik J, Yee C, Lizée G. Vestigial-like 1 is a shared targetable cancer-placenta antigen expressed by pancreatic and basal-like breast cancers. Nat Commun 2020; 11:5332. [PMID: 33087697 PMCID: PMC7577998 DOI: 10.1038/s41467-020-19141-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Accepted: 09/24/2020] [Indexed: 12/13/2022] Open
Abstract
Cytotoxic T lymphocyte (CTL)-based cancer immunotherapies have shown great promise for inducing clinical regressions by targeting tumor-associated antigens (TAA). To expand the TAA landscape of pancreatic ductal adenocarcinoma (PDAC), we performed tandem mass spectrometry analysis of HLA class I-bound peptides from 35 PDAC patient tumors. This identified a shared HLA-A*0101 restricted peptide derived from co-transcriptional activator Vestigial-like 1 (VGLL1) as a putative TAA demonstrating overexpression in multiple tumor types and low or absent expression in essential normal tissues. Here we show that VGLL1-specific CTLs expanded from the blood of a PDAC patient could recognize and kill in an antigen-specific manner a majority of HLA-A*0101 allogeneic tumor cell lines derived not only from PDAC, but also bladder, ovarian, gastric, lung, and basal-like breast cancers. Gene expression profiling reveals VGLL1 as a member of a unique group of cancer-placenta antigens (CPA) that may constitute immunotherapeutic targets for patients with multiple cancer types.
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MESH Headings
- Antigens, Neoplasm/genetics
- Antigens, Neoplasm/immunology
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/immunology
- Breast Neoplasms/genetics
- Breast Neoplasms/immunology
- Carcinoma, Pancreatic Ductal/genetics
- Carcinoma, Pancreatic Ductal/immunology
- Carcinoma, Pancreatic Ductal/therapy
- Cell Line, Tumor
- Cytotoxicity, Immunologic
- DNA-Binding Proteins/genetics
- DNA-Binding Proteins/immunology
- Female
- Gene Expression Profiling
- HLA-A1 Antigen/immunology
- Humans
- Immunotherapy, Adoptive
- Pancreatic Neoplasms/genetics
- Pancreatic Neoplasms/immunology
- Pancreatic Neoplasms/therapy
- Placenta/immunology
- Pregnancy
- Prognosis
- T-Lymphocytes, Cytotoxic/immunology
- Transcription Factors/genetics
- Transcription Factors/immunology
- Pancreatic Neoplasms
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Affiliation(s)
- Sherille D Bradley
- Department of Melanoma Medical Oncology, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Amjad H Talukder
- Department of Melanoma Medical Oncology, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Ivy Lai
- Department of Melanoma Medical Oncology, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Rebecca Davis
- Department of Melanoma Medical Oncology, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Hector Alvarez
- Department of Hematopathology, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Herve Tiriac
- Cold Spring Harbor Laboratory Cancer Center, Cold Spring Harbor, NY, USA
| | - Minying Zhang
- Department of Melanoma Medical Oncology, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Yulun Chiu
- Department of Melanoma Medical Oncology, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Brenda Melendez
- Department of Melanoma Medical Oncology, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Kyle R Jackson
- Department of Melanoma Medical Oncology, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Arjun Katailiha
- Department of Melanoma Medical Oncology, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Heather M Sonnemann
- Department of Melanoma Medical Oncology, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Fenge Li
- Department of Melanoma Medical Oncology, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Yaan Kang
- Department of Surgical Oncology, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Na Qiao
- Department of Breast Surgery Research, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Bih-Fang Pan
- Department of Systems Biology, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Philip L Lorenzi
- Department of Bioinformatics and Computational Biology, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Mark Hurd
- Ahmed Center for Pancreatic Cancer Research, UT MD Anderson Cancer Center, Houston, TX, USA
| | | | | | - Milind Javle
- Department of Gastrointestinal Medical Oncology, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Christopher Bristow
- Center for Co-clinical Trials, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Michael Kim
- Department of Surgical Oncology, UT MD Anderson Cancer Center, Houston, TX, USA
| | - David A Tuveson
- Cold Spring Harbor Laboratory Cancer Center, Cold Spring Harbor, NY, USA
| | - David Hawke
- Department of Systems Biology, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Scott Kopetz
- Department of Gastrointestinal Medical Oncology, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Robert A Wolff
- Department of Gastrointestinal Medical Oncology, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Patrick Hwu
- Department of Melanoma Medical Oncology, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Anirban Maitra
- Department of Pathology, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Jason Roszik
- Department of Melanoma Medical Oncology, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Cassian Yee
- Department of Melanoma Medical Oncology, UT MD Anderson Cancer Center, Houston, TX, USA.
- Department of Immunology, UT MD Anderson Cancer Center, Houston, TX, USA.
| | - Gregory Lizée
- Department of Melanoma Medical Oncology, UT MD Anderson Cancer Center, Houston, TX, USA.
- Department of Immunology, UT MD Anderson Cancer Center, Houston, TX, USA.
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20
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Das I, Chen H, Maddalo G, Tuominen R, Rebecca VW, Herlyn M, Hansson J, Davies MA, Egyházi Brage S. Inhibiting insulin and mTOR signaling by afatinib and crizotinib combination fosters broad cytotoxic effects in cutaneous malignant melanoma. Cell Death Dis 2020; 11:882. [PMID: 33082316 PMCID: PMC7576205 DOI: 10.1038/s41419-020-03097-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 09/18/2020] [Accepted: 09/21/2020] [Indexed: 12/27/2022]
Abstract
Current treatment modalities for disseminated cutaneous malignant melanoma (CMM) improve survival, however disease progression commonly ensues. In a previous study we identified afatinib and crizotinib in combination as a novel potential therapy for CMM independent of BRAF/NRAS mutation status. Herein, we elucidate the underlying mechanisms of the combination treatment effect to find biomarkers and novel targets for development of therapy that may provide clinical benefit by proteomic analysis of CMM cell lines and xenografts using mass spectrometry based analysis and reverse phase protein array. Identified candidates were validated using immunoblotting or immunofluorescence. Our analysis revealed that mTOR/Insulin signaling pathways were significantly decreased by the afatinib and crizotinib combination treatment. Both in vitro and in vivo analyses showed that the combination treatment downregulated pRPS6KB1 and pRPS6, downstream of mTOR signaling, and IRS-1 in the insulin signaling pathway, specifically ablating IRS-1 nuclear signal. Silencing of RPS6 and IRS-1 alone had a similar effect on cell death, which was further induced when IRS-1 and RPS6 were concomitantly silenced in the CMM cell lines. Silencing of IRS-1 and RPS6 resulted in reduced sensitivity towards combination treatment. Additionally, we found that IRS-1 and RPS6KB1 expression levels were increased in advanced stages of CMM clinical samples. We could demonstrate that induced resistance towards combination treatment was reversible by a drug holiday. CD171/L1CAM, mTOR and PI3K-p85 were induced in the combination resistant cells whereas AXL and EPHA2, previously identified mediators of resistance to MAPK inhibitor therapy in CMM were downregulated. We also found that CD171/L1CAM and mTOR were increased at progression in tumor biopsies from two matched cases of patients receiving targeted therapy with BRAFi. Overall, these findings provide insights into the molecular mechanisms behind the afatinib and crizotinib combination treatment effect and leverages a platform for discovering novel biomarkers and therapy regimes for CMM treatment.
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Affiliation(s)
- Ishani Das
- Department of Oncology-Pathology, Karolinska Institutet, 171 64, Stockholm, Sweden
| | - Huiqin Chen
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Gianluca Maddalo
- Science for Life Laboratory, School of Biotechnology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Rainer Tuominen
- Department of Oncology-Pathology, Karolinska Institutet, 171 64, Stockholm, Sweden
| | - Vito W Rebecca
- Molecular and Cellular Oncogenesis, The Wistar Institute, Philadelphia, PA, 19104, USA
| | - Meenhard Herlyn
- Molecular and Cellular Oncogenesis, The Wistar Institute, Philadelphia, PA, 19104, USA
| | - Johan Hansson
- Department of Oncology-Pathology, Karolinska Institutet, 171 64, Stockholm, Sweden
| | - Michael A Davies
- Department of Melanoma Medical Oncology, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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21
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Böhme I, Schönherr R, Eberle J, Bosserhoff AK. Membrane Transporters and Channels in Melanoma. Rev Physiol Biochem Pharmacol 2020; 181:269-374. [PMID: 32737752 DOI: 10.1007/112_2020_17] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Recent research has revealed that ion channels and transporters can be important players in tumor development, progression, and therapy resistance in melanoma. For example, members of the ABC family were shown to support cancer stemness-like features in melanoma cells, while several members of the TRP channel family were reported to act as tumor suppressors.Also, many transporter proteins support tumor cell viability and thus suppress apoptosis induction by anticancer therapy. Due to the high number of ion channels and transporters and the resulting high complexity of the field, progress in understanding is often focused on single molecules and is in total rather slow. In this review, we aim at giving an overview about a broad subset of ion transporters, also illustrating some aspects of the field, which have not been addressed in detail in melanoma. In context with the other chapters in this special issue on "Transportome Malfunctions in the Cancer Spectrum," a comparison between melanoma and these tumors will be possible.
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Affiliation(s)
- Ines Böhme
- Institute of Biochemistry, Emil Fischer Center, Friedrich-Alexander-University of Erlangen-Nürnberg, Erlangen, Germany
| | - Roland Schönherr
- Institute of Biochemistry and Biophysics, Friedrich Schiller University Jena and Jena University Hospital, Jena, Germany
| | - Jürgen Eberle
- Department of Dermatology, Venerology and Allergology, Skin Cancer Center Charité, University Medical Center Charité, Berlin, Germany
| | - Anja Katrin Bosserhoff
- Institute of Biochemistry, Emil Fischer Center, Friedrich-Alexander-University of Erlangen-Nürnberg, Erlangen, Germany. .,Comprehensive Cancer Center (CCC) Erlangen-EMN, Erlangen, Germany.
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22
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Wang J, Hasan F, Frey AC, Li HS, Park J, Pan K, Haymaker C, Bernatchez C, Lee DA, Watowich SS, Yee C. Histone Deacetylase Inhibitors and IL21 Cooperate to Reprogram Human Effector CD8 + T Cells to Memory T Cells. Cancer Immunol Res 2020; 8:794-805. [PMID: 32213626 PMCID: PMC7269845 DOI: 10.1158/2326-6066.cir-19-0619] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 12/27/2019] [Accepted: 03/17/2020] [Indexed: 12/18/2022]
Abstract
Clinical response rates after adoptive cell therapy (ACT) are highly correlated with in vivo persistence of the infused T cells. However, antigen-specific T cells found in tumor sites are often well-differentiated effector cells with limited persistence. Central memory CD8+ T cells, capable of self-renewal, represent desirable ACT products. We report here that exposure to a histone deacetylase inhibitor (HDACi) and IL21 could reprogram differentiated human CD8+ T cells into central memory-like T cells. Dedifferentiation of CD8+ T cells was initiated by increased H3 acetylation and chromatin accessibility at the CD28 promoter region. This led to IL21-mediated pSTAT3 binding to the CD28 region, and subsequent upregulation of surface CD28 and CD62L (markers of central memory T cells). The reprogrammed cells exhibited enhanced proliferation in response to both IL2 and IL15, and a stable memory-associated transcriptional signature (increased Lef1 and Tcf7). Our findings support the application of IL21 and HDACi for the in vitro generation of highly persistent T-cell populations that can augment the efficacy of adoptively transferred T cells.
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Affiliation(s)
- Junmei Wang
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Farah Hasan
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Amanda C Frey
- Molecular and Cellular Biology Program, University of Washington, Seattle, Washington
| | - Haiyan S Li
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jungsun Park
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Ke Pan
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Cara Haymaker
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Chantale Bernatchez
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Dean A Lee
- Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Division of Pediatrics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Stephanie S Watowich
- Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Cassian Yee
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas.
- Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, Texas
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23
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Ott PA, Dotti G, Yee C, Goff SL. An Update on Adoptive T-Cell Therapy and Neoantigen Vaccines. Am Soc Clin Oncol Educ Book 2019; 39:e70-e78. [PMID: 31099621 DOI: 10.1200/edbk_238001] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Adoptive T-cell therapy using tumor-infiltrating lymphocytes (TILs) has demonstrated long-lasting antitumor activity in select patients with advanced melanoma. Cancer vaccines have been used for many decades and have shown some promise but overall relatively modest clinical activity across cancers. Technological advances in genome sequencing capabilities and T-cell engineering have had substantial impact on both adoptive cell therapy and the cancer vaccine field. The ability to identify neoantigens-a class of tumor antigens that is truly tumor specific and encoded by tumor mutations through rapid and relatively inexpensive next-generation sequencing-has already demonstrated the critical importance of these antigens as targets of antitumor-specific T-cell responses in the context of immune checkpoint blockade and other immunotherapies. Therapeutically targeting these antigens with either adoptive T-cell therapy or vaccine approaches has demonstrated early promise in the clinic in patients with advanced solid tumors. Chimeric antigen receptor (CAR) T cells, which are engineered by fusing an antigen-specific, single-chain antibody (scFv) with signaling molecules of the T-cell receptor (TCR)/CD3 complex creating an antibody-like structure on T cells that recognizes antigens independently of major histocompatibility complex (MHC) molecules, have demonstrated remarkable clinical activity in patients with advanced B-cell malignancies, leading to several approvals by the U.S. Food and Drug Administration (FDA).
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Affiliation(s)
- Patrick A Ott
- 1 Department of Medical Oncology, Dana-Farber Cancer Institute, and Harvard Medical School, Boston, MA
| | - Gianpietro Dotti
- 2 Department of Microbiology and Immunology, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC
| | - Cassian Yee
- 3 Department of Melanoma Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX
| | - Stephanie L Goff
- 4 Center for Cancer Research, National Cancer Institute, Bethesda, MD
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24
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Wei CY, Zhu MX, Lu NH, Peng R, Yang X, Zhang PF, Wang L, Gu JY. Bioinformatics-based analysis reveals elevated MFSD12 as a key promoter of cell proliferation and a potential therapeutic target in melanoma. Oncogene 2018; 38:1876-1891. [PMID: 30385854 PMCID: PMC6462865 DOI: 10.1038/s41388-018-0531-6] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2018] [Revised: 07/30/2018] [Accepted: 09/10/2018] [Indexed: 12/22/2022]
Abstract
Although recent therapeutic advances based on our understanding of molecular phenomena have prolonged the survival of melanoma patients, the prognosis of melanoma remains dismal and further understanding of the underlying mechanism of melanoma progression is needed. In this study, differential expression analyses revealed that many genes, including AKT1 and CDK2, play important roles in melanoma. Functional analyses of differentially expressed genes (DEGs), obtained from the GEO (Gene Expression Omnibus) database, indicated that high proliferative and metastatic abilities are the main characteristics of melanoma and that the PI3K and MAPK pathways play essential roles in melanoma progression. Among these DEGs, major facilitator superfamily domain-containing 12 (MFSD12) was found to have significantly and specifically upregulated expression in melanoma, and elevated MFSD12 level promoted cell proliferation by promoting cell cycle progression. Mechanistically, MFSD12 upregulation was found to activate PI3K signaling, and a PI3K inhibitor reversed the increase in cell proliferation endowed by MFSD12 upregulation. Clinically, high MFSD12 expression was positively associated with shorter overall survival (OS) and disease-free survival (DFS) in melanoma patients, and MFSD12 was an independent prognostic factor for OS and DFS in melanoma patients. Therapeutically, in vivo assays further confirmed that MFSD12 interference inhibited tumor growth and lung metastasis in melanoma. In conclusion, elevated MFSD12 expression promotes melanoma cell proliferation, and MFSD12 is a valuable prognostic biomarker and promising therapeutic target in melanoma.
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Affiliation(s)
- Chuan-Yuan Wei
- Department of Plastic Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200032, People's Republic of China.,Liver Cancer Institute, Zhongshan Hospital, Fudan University; Key Laboratory of Carcinogenesis and Cancer Invasion (Fudan University), Ministry of Education, Shanghai, 200032, People's Republic of China
| | - Meng-Xuan Zhu
- Liver Cancer Institute, Zhongshan Hospital, Fudan University; Key Laboratory of Carcinogenesis and Cancer Invasion (Fudan University), Ministry of Education, Shanghai, 200032, People's Republic of China
| | - Nan-Hang Lu
- Department of Plastic Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200032, People's Republic of China
| | - Rui Peng
- Liver Cancer Institute, Zhongshan Hospital, Fudan University; Key Laboratory of Carcinogenesis and Cancer Invasion (Fudan University), Ministry of Education, Shanghai, 200032, People's Republic of China
| | - Xuan Yang
- Liver Cancer Institute, Zhongshan Hospital, Fudan University; Key Laboratory of Carcinogenesis and Cancer Invasion (Fudan University), Ministry of Education, Shanghai, 200032, People's Republic of China
| | - Peng-Fei Zhang
- Liver Cancer Institute, Zhongshan Hospital, Fudan University; Key Laboratory of Carcinogenesis and Cancer Invasion (Fudan University), Ministry of Education, Shanghai, 200032, People's Republic of China
| | - Lu Wang
- Department of Plastic Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200032, People's Republic of China
| | - Jian-Ying Gu
- Department of Plastic Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200032, People's Republic of China.
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25
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Gibbs ZA, Whitehurst AW. Emerging Contributions of Cancer/Testis Antigens to Neoplastic Behaviors. Trends Cancer 2018; 4:701-712. [PMID: 30292353 DOI: 10.1016/j.trecan.2018.08.005] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 08/24/2018] [Accepted: 08/27/2018] [Indexed: 02/07/2023]
Abstract
Tumors of nearly every origin activate the expression of genes normally restricted to gametogenic cells. These genes encode proteins termed cancer/testis (CT) antigens, since expression outside of their naturally immune-privileged site can evoke an immune response. Despite extensive efforts to exploit CT antigens as immunotherapeutic targets, investigation of whether these proteins participate in tumorigenic processes has lagged. Here, we discuss emerging evidence that demonstrates that CT antigens can confer a selective advantage to tumor cells by promoting oncogenic processes or permitting evasion of tumor-suppressive mechanisms. These advances indicate the inherent flexibility of tumor cell regulatory networks to engage aberrantly expressed proteins to promote neoplastic behaviors, which could ultimately present novel therapeutic entry points.
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Affiliation(s)
- Zane A Gibbs
- Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX, USA; Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Angelique W Whitehurst
- Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX, USA; Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX, USA.
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26
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César-Razquin A, Girardi E, Yang M, Brehme M, Saez-Rodriguez J, Superti-Furga G. In silico Prioritization of Transporter-Drug Relationships From Drug Sensitivity Screens. Front Pharmacol 2018; 9:1011. [PMID: 30245630 PMCID: PMC6137680 DOI: 10.3389/fphar.2018.01011] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 08/20/2018] [Indexed: 01/28/2023] Open
Abstract
The interplay between drugs and cell metabolism is a key factor in determining both compound potency and toxicity. In particular, how and to what extent transmembrane transporters affect drug uptake and disposition is currently only partially understood. Most transporter proteins belong to two protein families: the ATP-Binding Cassette (ABC) transporter family, whose members are often involved in xenobiotic efflux and drug resistance, and the large and heterogeneous family of solute carriers (SLCs). We recently argued that SLCs are collectively a rather neglected gene group, with most of its members still poorly characterized, and thus likely to include many yet-to-be-discovered associations with drugs. We searched publicly available resources and literature to define the currently known set of drugs transported by ABCs or SLCs, which involved ∼500 drugs and more than 100 transporters. In order to extend this set, we then mined the largest publicly available pharmacogenomics dataset, which involves approximately 1,000 molecularly annotated cancer cell lines and their response to 265 anti-cancer compounds, and used regularized linear regression models (Elastic Net, LASSO) to predict drug responses based on SLC and ABC data (expression levels, SNVs, CNVs). The most predictive models included both known and previously unidentified associations between drugs and transporters. To our knowledge, this represents the first application of regularized linear regression to this set of genes, providing an extensive prioritization of potentially pharmacologically interesting interactions.
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Affiliation(s)
- Adrián César-Razquin
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Enrico Girardi
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Mi Yang
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
- RWTH Aachen University, Faculty of Medicine, Joint Research Centre for Computational Biomedicine (JRC-COMBINE), Aachen, Germany
| | - Marc Brehme
- RWTH Aachen University, Faculty of Medicine, Joint Research Centre for Computational Biomedicine (JRC-COMBINE), Aachen, Germany
- CBmed – Center for Biomarker Research in Medicine GmbH, Graz, Austria
| | - Julio Saez-Rodriguez
- RWTH Aachen University, Faculty of Medicine, Joint Research Centre for Computational Biomedicine (JRC-COMBINE), Aachen, Germany
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, United Kingdom
| | - Giulio Superti-Furga
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
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