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Birkeälv S, Harland M, Matsuyama LSAS, Rashid M, Mehta I, Laye JP, Haase K, Mell T, Iyer V, Robles‐Espinoza CD, McDermott U, van Loo P, Kuijjer ML, Possik PA, Maria Engler SS, Bishop DT, Newton‐Bishop J, Adams DJ. Mutually exclusive genetic interactions and gene essentiality shape the genomic landscape of primary melanoma. J Pathol 2023; 259:56-68. [PMID: 36219477 PMCID: PMC10098817 DOI: 10.1002/path.6019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 09/02/2022] [Accepted: 09/28/2022] [Indexed: 11/09/2022]
Abstract
Melanoma is a heterogenous malignancy with an unpredictable clinical course. Most patients who present in the clinic are diagnosed with primary melanoma, yet large-scale sequencing efforts have focused primarily on metastatic disease. In this study we sequence-profiled 524 American Joint Committee on Cancer Stage I-III primary tumours. Our analysis of these data reveals recurrent driver mutations, mutually exclusive genetic interactions, where two genes were never or rarely co-mutated, and an absence of co-occurring genetic events. Further, we intersected copy number calls from our primary melanoma data with whole-genome CRISPR screening data to identify the transcription factor interferon regulatory factor 4 (IRF4) as a melanoma-associated dependency. © 2022 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Sofia Birkeälv
- Wellcome Sanger InstituteWellcome Trust Genome CampusCambridgeUK
| | - Mark Harland
- Division of Haematology and ImmunologyUniversity of Leeds School of MedicineLeedsUK
| | - Larissa Satiko Alcantara Sekimoto Matsuyama
- Wellcome Sanger InstituteWellcome Trust Genome CampusCambridgeUK
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical SciencesUniversity of Sao PauloSao PauloBrazil
| | - Mamun Rashid
- Wellcome Sanger InstituteWellcome Trust Genome CampusCambridgeUK
| | - Ishan Mehta
- Wellcome Sanger InstituteWellcome Trust Genome CampusCambridgeUK
| | - Jonathan P Laye
- Division of Haematology and ImmunologyUniversity of Leeds School of MedicineLeedsUK
| | | | - Tracey Mell
- Division of Haematology and ImmunologyUniversity of Leeds School of MedicineLeedsUK
| | - Vivek Iyer
- Wellcome Sanger InstituteWellcome Trust Genome CampusCambridgeUK
| | - Carla Daniela Robles‐Espinoza
- Wellcome Sanger InstituteWellcome Trust Genome CampusCambridgeUK
- Laboratorio Internacional de Investigación sobre el Genoma HumanoUniversidad Nacional Autónoma de México, Campus JuriquillaSantiago de QuerétaroMexico
| | - Ultan McDermott
- Wellcome Sanger InstituteWellcome Trust Genome CampusCambridgeUK
| | | | - Marieke L Kuijjer
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, Faculty of MedicineUniversity of OsloOsloNorway
- Department of Pathology and Leiden Center for Computational OncologyLeiden University Medical CenterLeidenthe Netherlands
| | - Patricia A Possik
- Division of Experimental and Translational ResearchBrazilian National Cancer InstituteRio de JaneiroBrazil
| | - Silvya Stuchi Maria Engler
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical SciencesUniversity of Sao PauloSao PauloBrazil
| | - D Timothy Bishop
- Division of Haematology and ImmunologyUniversity of Leeds School of MedicineLeedsUK
| | - Julia Newton‐Bishop
- Division of Haematology and ImmunologyUniversity of Leeds School of MedicineLeedsUK
| | - David J Adams
- Wellcome Sanger InstituteWellcome Trust Genome CampusCambridgeUK
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2
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Yang Q, Xie H, Li X, Feng Y, Xie S, Qu J, Xie A, Zhu Y, Zhou L, Yang J, Hu X, Wei H, Qiu H, Qin W, Huang J. Interferon Regulatory Factor 4 Regulates the Development of Polymorphonuclear Myeloid-Derived Suppressor Cells Through the Transcription of c-Myc in Cancer. Front Immunol 2021; 12:627072. [PMID: 33708218 PMCID: PMC7940347 DOI: 10.3389/fimmu.2021.627072] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Accepted: 01/11/2021] [Indexed: 01/13/2023] Open
Abstract
The accumulation of myeloid-derived suppressor cells (MDSCs) is one of the major obstacles to achieve an appropriate anti-tumor immune response and successful tumor immunotherapy. MDSCs in tumor-bearing hosts are primarily polymorphonuclear (PMN-MDSCs). However, the mechanisms regulating the development of MDSCs remain poorly understood. In this report, we showed that interferon regulatory factor 4 (IRF4) plays a key role in the development of PMN-MDSCs, but not monocytic MDSCs. IRF4 deficiency caused a significant elevation of PMN-MDSCs and enhanced the suppressive activity of PMN-MDSCs, increasing tumor growth and metastasis in mice. Mechanistic studies showed that c-Myc was up-regulated by the IRF4 protein. Over-expression of c-Myc almost abrogated the effects of IRF4 deletion on PMN-MDSCs development. Importantly, the IRF4 expression level was negatively correlated with the PMN-MDSCs frequency and tumor development but positively correlated with c-Myc expression in clinical cancer patients. In summary, this study demonstrated that IRF4 represents a novel regulator of PMN-MDSCs development in cancer, which may have predictive value for tumor progression.
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Affiliation(s)
- Quan Yang
- The State Key Laboratory of Respiratory Disease, The First Affliated Hospital, Guangzhou Medical University, Guangzhou, China.,Sino-French Hoffmann Institute, Guangzhou Medical University, Guangzhou, China
| | - Hongyan Xie
- The State Key Laboratory of Respiratory Disease, The First Affliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Xing Li
- Department of Medical Oncology and Guangdong Key Laboratory of Liver Disease Research, The Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Yuanfa Feng
- The State Key Laboratory of Respiratory Disease, The First Affliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Shihao Xie
- The State Key Laboratory of Respiratory Disease, The First Affliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Jiale Qu
- The State Key Laboratory of Respiratory Disease, The First Affliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Anqi Xie
- The State Key Laboratory of Respiratory Disease, The First Affliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Yiqiang Zhu
- The State Key Laboratory of Respiratory Disease, The First Affliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Lu Zhou
- The State Key Laboratory of Respiratory Disease, The First Affliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Jinxue Yang
- The State Key Laboratory of Respiratory Disease, The First Affliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Xiaohao Hu
- The State Key Laboratory of Respiratory Disease, The First Affliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Haixia Wei
- The State Key Laboratory of Respiratory Disease, The First Affliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Huaina Qiu
- The State Key Laboratory of Respiratory Disease, The First Affliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Wenjuan Qin
- Department of Radiation Oncology, Zhongshan Hospital Affiliated, Xiamen University, Xiamen, China
| | - Jun Huang
- The State Key Laboratory of Respiratory Disease, The First Affliated Hospital, Guangzhou Medical University, Guangzhou, China.,Sino-French Hoffmann Institute, Guangzhou Medical University, Guangzhou, China
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Buchele V, Konein P, Vogler T, Kunert T, Enderle K, Khan H, Büttner-Herold M, Lehmann CHK, Amon L, Wirtz S, Dudziak D, Neurath MF, Neufert C, Hildner K. Th17 Cell-Mediated Colitis Is Positively Regulated by Interferon Regulatory Factor 4 in a T Cell- Extrinsic Manner. Front Immunol 2021; 11:590893. [PMID: 33584655 PMCID: PMC7879684 DOI: 10.3389/fimmu.2020.590893] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 12/08/2020] [Indexed: 01/14/2023] Open
Abstract
Inflammatory bowel diseases (IBDs) are characterized by chronic, inflammatory gastrointestinal lesions and often require life-long treatment with immunosuppressants and repetitive surgical interventions. Despite progress in respect to the characterization of molecular mechanisms e.g. exerted by TNF-alpha, currently clinically approved therapeutics fail to provide long-term disease control for most patients. The transcription factor interferon regulatory factor 4 (IRF4) has been shown to play important developmental as well as functional roles within multiple immune cells. In the context of colitis, a T cell-intrinsic role of IRF4 in driving immune-mediated gut pathology is established. Here, we conversely addressed the impact of IRF4 inactivation in non-T cells on T cell driven colitis in vivo. Employing the CD4+CD25- naïve T cell transfer model, we found that T cells fail to elicit colitis in IRF4-deficient compared to IRF4-proficient Rag1-/- mice. Reduced colitis activity in the absence of IRF4 was accompanied by hampered T cell expansion both within the mesenteric lymph node (MLN) and colonic lamina propria (cLP). Furthermore, the influx of various myeloids, presumably inflammation-promoting cells was abrogated overall leading to a less disrupted intestinal barrier. Mechanistically, gene profiling experiments revealed a Th17 response dominated molecular expression signature in colon tissues of IRF4-proficient, colitic Rag1-/- but not in colitis-protected Rag1-/-Irf4-/- mice. Colitis mitigation in Rag1-/-Irf4-/- T cell recipients resulted in reduced frequencies and absolute numbers of IL-17a-producing T cell subsets in MLN and cLP possibly due to a regulation of conventional dendritic cell subset 2 (cDC2) known to impact Th17 differentiation. Together, extending the T cell-intrinsic role for IRF4 in the context of Th17 cell driven colitis, the provided data demonstrate a Th17-inducing and thereby colitis-promoting role of IRF4 through a T cell-extrinsic mechanism highlighting IRF4 as a putative molecular master switch among transcriptional regulators driving immune-mediated intestinal inflammation through both T cell-intrinsic and T cell-extrinsic mechanisms. Future studies need to further dissect IRF4 controlled pathways within distinct IRF4-expressing myeloid cell types, especially cDC2s, to elucidate the precise mechanisms accounting for hampered Th17 formation and, according to our data, the predominant mechanism of colitis protection in Rag1-/-Irf4-/- T cell receiving mice.
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Affiliation(s)
- Vera Buchele
- Department of Medicine 1, University Hospital Erlangen, University of Erlangen-Nuremberg, Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), University Hospital Erlangen, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Patrick Konein
- Department of Medicine 1, University Hospital Erlangen, University of Erlangen-Nuremberg, Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), University Hospital Erlangen, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Tina Vogler
- Department of Medicine 1, University Hospital Erlangen, University of Erlangen-Nuremberg, Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), University Hospital Erlangen, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Timo Kunert
- Department of Medicine 1, University Hospital Erlangen, University of Erlangen-Nuremberg, Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), University Hospital Erlangen, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Karin Enderle
- Department of Medicine 1, University Hospital Erlangen, University of Erlangen-Nuremberg, Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), University Hospital Erlangen, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Hanif Khan
- Department of Medicine 1, University Hospital Erlangen, University of Erlangen-Nuremberg, Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), University Hospital Erlangen, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Maike Büttner-Herold
- Institute of Pathology, Department of Nephropathology, University Hospital Erlangen, Erlangen, Germany
| | - Christian H. K. Lehmann
- Deutsches Zentrum Immuntherapie (DZI), University Hospital Erlangen, University of Erlangen-Nuremberg, Erlangen, Germany
- Laboratory of Dendritic Cell Biology, Department of Dermatology, University Hospital Erlangen, Friedrich-Alexander University of Erlangen-Nuremberg, Erlangen, Germany
| | - Lukas Amon
- Deutsches Zentrum Immuntherapie (DZI), University Hospital Erlangen, University of Erlangen-Nuremberg, Erlangen, Germany
- Laboratory of Dendritic Cell Biology, Department of Dermatology, University Hospital Erlangen, Friedrich-Alexander University of Erlangen-Nuremberg, Erlangen, Germany
| | - Stefan Wirtz
- Department of Medicine 1, University Hospital Erlangen, University of Erlangen-Nuremberg, Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), University Hospital Erlangen, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Diana Dudziak
- Deutsches Zentrum Immuntherapie (DZI), University Hospital Erlangen, University of Erlangen-Nuremberg, Erlangen, Germany
- Laboratory of Dendritic Cell Biology, Department of Dermatology, University Hospital Erlangen, Friedrich-Alexander University of Erlangen-Nuremberg, Erlangen, Germany
| | - Markus F. Neurath
- Department of Medicine 1, University Hospital Erlangen, University of Erlangen-Nuremberg, Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), University Hospital Erlangen, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Clemens Neufert
- Department of Medicine 1, University Hospital Erlangen, University of Erlangen-Nuremberg, Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), University Hospital Erlangen, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Kai Hildner
- Department of Medicine 1, University Hospital Erlangen, University of Erlangen-Nuremberg, Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), University Hospital Erlangen, University of Erlangen-Nuremberg, Erlangen, Germany
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Davis DA, Shrestha P, Aisabor AI, Stream A, Galli V, Pise-Masison CA, Tagawa T, Ziegelbauer JM, Franchini G, Yarchoan R. Pomalidomide increases immune surface marker expression and immune recognition of oncovirus-infected cells. Oncoimmunology 2018; 8:e1546544. [PMID: 30713808 PMCID: PMC6343774 DOI: 10.1080/2162402x.2018.1546544] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 10/17/2018] [Accepted: 11/04/2018] [Indexed: 01/03/2023] Open
Abstract
Most chronic viruses evade T-cell and natural killer (NK) immunity through downregulation of immune surface markers. Previously we showed that Pomalidomide (Pom) increases surface expression of major histocompatibility complex class I (MHC-I) in Kaposi sarcoma-associated herpesvirus-infected latent and lytic cells and restores ICAM-1 and B7-2 in latent cells. We explored the ability of Pom to increase immune surface marker expression in cells infected by other chronic viruses, including human T-cell leukemia virus type-1 (HTLV-1), Epstein-Barr virus (EBV), human papilloma virus (HPV), Merkel cell polyoma virus (MCV), and human immunodeficiency virus type-1 (HIV-1). Pom increased MHC-1, ICAM-1, and B7-2/CD86 in immortalized T-cell lines productively infected with HTLV-1 and also significantly increased their susceptibility to NK cell-mediated cytotoxicity. Pom enhancement of MHC-I and ICAM-1 in primary cells infected with HTLV-1 was abrogated by knockout of HTLV-1 orf-1. Pom increased expression of ICAM-1, B7-2 and MHC class I polypeptide related sequence A (MICA) surface expression in the EBV-infected Daudi cells and increased their T-cell activation and susceptibility to NK cells. Moreover, Pom increased expression of certain of these surface markers on Akata, Raji, and EBV lymphoblastic cell lines. The increased expression of immune surface markers in these virus-infected lines was generally associated with a decrease in IRF4 expression. By contrast, Pom treatment of HPV, MCV and HIV-1 infected cells did not increase these immune surface markers. Pom and related drugs may be clinically beneficial for the treatment of HTLV-1 and EBV-induced tumors by rendering infected cells more susceptible to both innate and adaptive host immune responses.
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Affiliation(s)
- David A Davis
- HIV & AIDS Malignancy Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Prabha Shrestha
- HIV & AIDS Malignancy Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Ashley I Aisabor
- HIV & AIDS Malignancy Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Alexandra Stream
- HIV & AIDS Malignancy Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Veronica Galli
- Vaccine Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Cynthia A Pise-Masison
- Vaccine Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Takanobu Tagawa
- HIV & AIDS Malignancy Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Joseph M Ziegelbauer
- HIV & AIDS Malignancy Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Genoveffa Franchini
- Vaccine Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Robert Yarchoan
- HIV & AIDS Malignancy Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
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