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Xavier V, Martinelli S, Corbyn R, Pennie R, Rakovic K, Powley IR, Officer-Jones L, Ruscica V, Galloway A, Carlin LM, Cowling VH, Le Quesne J, Martinou JC, MacVicar T. Mitochondrial double-stranded RNA homeostasis depends on cell-cycle progression. Life Sci Alliance 2024; 7:e202402764. [PMID: 39209534 PMCID: PMC11361371 DOI: 10.26508/lsa.202402764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 08/19/2024] [Accepted: 08/21/2024] [Indexed: 09/04/2024] Open
Abstract
Mitochondrial gene expression is a compartmentalised process essential for metabolic function. The replication and transcription of mitochondrial DNA (mtDNA) take place at nucleoids, whereas the subsequent processing and maturation of mitochondrial RNA (mtRNA) and mitoribosome assembly are localised to mitochondrial RNA granules. The bidirectional transcription of circular mtDNA can lead to the hybridisation of polycistronic transcripts and the formation of immunogenic mitochondrial double-stranded RNA (mt-dsRNA). However, the mechanisms that regulate mt-dsRNA localisation and homeostasis are largely unknown. With super-resolution microscopy, we show that mt-dsRNA overlaps with the RNA core and associated proteins of mitochondrial RNA granules but not nucleoids. Mt-dsRNA foci accumulate upon the stimulation of cell proliferation and their abundance depends on mitochondrial ribonucleotide supply by the nucleoside diphosphate kinase, NME6. Consequently, mt-dsRNA foci are profuse in cultured cancer cells and malignant cells of human tumour biopsies. Our results establish a new link between cell proliferation and mitochondrial nucleic acid homeostasis.
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Affiliation(s)
- Vanessa Xavier
- The CRUK Scotland Institute, Glasgow, UK
- Department of Molecular and Cellular Biology, University of Geneva, Genève, Switzerland
| | - Silvia Martinelli
- The CRUK Scotland Institute, Glasgow, UK
- https://ror.org/00vtgdb53 School of Cancer Sciences, University of Glasgow, Glasgow, UK
| | | | - Rachel Pennie
- The CRUK Scotland Institute, Glasgow, UK
- https://ror.org/00vtgdb53 School of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Kai Rakovic
- The CRUK Scotland Institute, Glasgow, UK
- https://ror.org/00vtgdb53 School of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Ian R Powley
- The CRUK Scotland Institute, Glasgow, UK
- https://ror.org/00vtgdb53 School of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Leah Officer-Jones
- The CRUK Scotland Institute, Glasgow, UK
- https://ror.org/00vtgdb53 School of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Vincenzo Ruscica
- https://ror.org/00vtgdb53 MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | | | - Leo M Carlin
- The CRUK Scotland Institute, Glasgow, UK
- https://ror.org/00vtgdb53 School of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Victoria H Cowling
- The CRUK Scotland Institute, Glasgow, UK
- https://ror.org/00vtgdb53 School of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - John Le Quesne
- The CRUK Scotland Institute, Glasgow, UK
- https://ror.org/00vtgdb53 School of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Jean-Claude Martinou
- Department of Molecular and Cellular Biology, University of Geneva, Genève, Switzerland
| | - Thomas MacVicar
- The CRUK Scotland Institute, Glasgow, UK
- https://ror.org/00vtgdb53 School of Cancer Sciences, University of Glasgow, Glasgow, UK
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2
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Park MD, Berichel JL, Hamon P, Wilk CM, Belabed M, Yatim N, Saffon A, Boumelha J, Falcomatà C, Tepper A, Hegde S, Mattiuz R, Soong BY, LaMarche NM, Rentzeperis F, Troncoso L, Halasz L, Hennequin C, Chin T, Chen EP, Reid AM, Su M, Cahn AR, Koekkoek LL, Venturini N, Wood-isenberg S, D’souza D, Chen R, Dawson T, Nie K, Chen Z, Kim-Schulze S, Casanova-Acebes M, Swirski FK, Downward J, Vabret N, Brown BD, Marron TU, Merad M. Hematopoietic aging promotes cancer by fueling IL-1⍺-driven emergency myelopoiesis. Science 2024; 386:eadn0327. [PMID: 39236155 PMCID: PMC7616710 DOI: 10.1126/science.adn0327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Revised: 06/18/2024] [Accepted: 08/22/2024] [Indexed: 09/07/2024]
Abstract
Age is a major risk factor for cancer, but how aging impacts tumor control remains unclear. In this study, we establish that aging of the immune system, regardless of the age of the stroma and tumor, drives lung cancer progression. Hematopoietic aging enhances emergency myelopoiesis, resulting in the local accumulation of myeloid progenitor-like cells in lung tumors. These cells are a major source of interleukin (IL)-1⍺, which drives the enhanced myeloid response. The age-associated decline of DNA methyltransferase 3A enhances IL-1⍺ production, and disrupting IL-1 receptor 1 signaling early during tumor development normalized myelopoiesis and slowed the growth of lung, colonic, and pancreatic tumors. In human tumors, we identified an enrichment for IL-1⍺-expressing monocyte-derived macrophages linked to age, poorer survival, and recurrence, unraveling how aging promotes cancer and offering actionable therapeutic strategies.
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Affiliation(s)
- Matthew D. Park
- Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai; New York, NY10029, USA
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai; New York, NY10029, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai; New York, NY10029, USA
| | - Jessica Le Berichel
- Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai; New York, NY10029, USA
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai; New York, NY10029, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai; New York, NY10029, USA
| | - Pauline Hamon
- Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai; New York, NY10029, USA
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai; New York, NY10029, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai; New York, NY10029, USA
| | - C. Matthias Wilk
- Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai; New York, NY10029, USA
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai; New York, NY10029, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai; New York, NY10029, USA
| | - Meriem Belabed
- Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai; New York, NY10029, USA
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai; New York, NY10029, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai; New York, NY10029, USA
| | - Nader Yatim
- Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai; New York, NY10029, USA
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai; New York, NY10029, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai; New York, NY10029, USA
| | - Alexis Saffon
- Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai; New York, NY10029, USA
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai; New York, NY10029, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai; New York, NY10029, USA
- INSERM U932, Immunity and Cancer, Institut Curie, Paris-Cité University; Paris, France
| | - Jesse Boumelha
- Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai; New York, NY10029, USA
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai; New York, NY10029, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai; New York, NY10029, USA
| | - Chiara Falcomatà
- Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai; New York, NY10029, USA
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai; New York, NY10029, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai; New York, NY10029, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai; New York, NY10029, USA
| | - Alexander Tepper
- Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai; New York, NY10029, USA
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai; New York, NY10029, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai; New York, NY10029, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai; New York, NY10029, USA
| | - Samarth Hegde
- Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai; New York, NY10029, USA
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai; New York, NY10029, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai; New York, NY10029, USA
| | - Raphaël Mattiuz
- Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai; New York, NY10029, USA
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai; New York, NY10029, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai; New York, NY10029, USA
| | - Brian Y. Soong
- Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai; New York, NY10029, USA
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai; New York, NY10029, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai; New York, NY10029, USA
| | - Nelson M. LaMarche
- Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai; New York, NY10029, USA
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai; New York, NY10029, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai; New York, NY10029, USA
| | - Frederika Rentzeperis
- Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai; New York, NY10029, USA
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai; New York, NY10029, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai; New York, NY10029, USA
| | - Leanna Troncoso
- Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai; New York, NY10029, USA
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai; New York, NY10029, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai; New York, NY10029, USA
| | - Laszlo Halasz
- Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai; New York, NY10029, USA
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai; New York, NY10029, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai; New York, NY10029, USA
| | - Clotilde Hennequin
- Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai; New York, NY10029, USA
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai; New York, NY10029, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai; New York, NY10029, USA
| | - Theodore Chin
- Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai; New York, NY10029, USA
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai; New York, NY10029, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai; New York, NY10029, USA
| | - Earnest P. Chen
- Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai; New York, NY10029, USA
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai; New York, NY10029, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai; New York, NY10029, USA
| | - Amanda M. Reid
- Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai; New York, NY10029, USA
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai; New York, NY10029, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai; New York, NY10029, USA
| | - Matthew Su
- Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai; New York, NY10029, USA
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai; New York, NY10029, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai; New York, NY10029, USA
| | - Ashley Reid Cahn
- Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai; New York, NY10029, USA
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai; New York, NY10029, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai; New York, NY10029, USA
| | - Laura L. Koekkoek
- Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai; New York, NY10029, USA
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai; New York, NY10029, USA
- Brain and Body Research Center, Icahn School of Medicine at Mount Sinai; New York, NY10029, USA
| | - Nicholas Venturini
- Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai; New York, NY10029, USA
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai; New York, NY10029, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai; New York, NY10029, USA
| | - Shira Wood-isenberg
- Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai; New York, NY10029, USA
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai; New York, NY10029, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai; New York, NY10029, USA
| | - Darwin D’souza
- Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai; New York, NY10029, USA
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai; New York, NY10029, USA
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai; New York, NY10029, USA
| | - Rachel Chen
- Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai; New York, NY10029, USA
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai; New York, NY10029, USA
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai; New York, NY10029, USA
| | - Travis Dawson
- Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai; New York, NY10029, USA
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai; New York, NY10029, USA
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai; New York, NY10029, USA
| | - Kai Nie
- Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai; New York, NY10029, USA
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai; New York, NY10029, USA
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai; New York, NY10029, USA
| | - Zhihong Chen
- Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai; New York, NY10029, USA
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai; New York, NY10029, USA
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai; New York, NY10029, USA
| | - Seunghee Kim-Schulze
- Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai; New York, NY10029, USA
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai; New York, NY10029, USA
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai; New York, NY10029, USA
| | - Maria Casanova-Acebes
- Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai; New York, NY10029, USA
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai; New York, NY10029, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai; New York, NY10029, USA
| | - Filip K. Swirski
- Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai; New York, NY10029, USA
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai; New York, NY10029, USA
- Brain and Body Research Center, Icahn School of Medicine at Mount Sinai; New York, NY10029, USA
- Cardiovascular Research Institute, Icahn School of Medicine at Mount Sinai; New York, NY10029, USA
| | - Julian Downward
- Oncogene Biology Laboratory, Francis Crick Institute; London, UK
- Lung Cancer Group, Division of Molecular Pathology, Institute of Cancer Research; London, UK
| | - Nicolas Vabret
- Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai; New York, NY10029, USA
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai; New York, NY10029, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai; New York, NY10029, USA
| | - Brian D. Brown
- Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai; New York, NY10029, USA
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai; New York, NY10029, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai; New York, NY10029, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai; New York, NY10029, USA
| | - Thomas U. Marron
- Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai; New York, NY10029, USA
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai; New York, NY10029, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai; New York, NY10029, USA
- Division of Hematology/Oncology, Icahn School of Medicine at Mount Sinai; New York, NY10029, USA
- Center for Thoracic Oncology, Icahn School of Medicine at Mount Sinai; New York, NY10029, USA
| | - Miriam Merad
- Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai; New York, NY10029, USA
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai; New York, NY10029, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai; New York, NY10029, USA
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai; New York, NY10029, USA
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3
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Phan J, Chen B, Zhao Z, Allies G, Iannaccone A, Paul A, Cansiz F, Spina A, Leven AS, Gellhaus A, Schadendorf D, Kimmig R, Mettlen M, Tasdogan A, Morrison SJ. Retrotransposons are co-opted to activate hematopoietic stem cells and erythropoiesis. Science 2024:eado6836. [PMID: 39446896 DOI: 10.1126/science.ado6836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 06/21/2024] [Accepted: 08/30/2024] [Indexed: 10/26/2024]
Abstract
Hematopoietic stem cells (HSCs) and erythropoiesis are activated during pregnancy and after bleeding by the derepression of retrotransposons, including endogenous retroviruses and LINE elements. Retrotransposon transcription activates the innate immune sensors cyclic GMP-AMP synthase (cGAS) and stimulator of interferon (IFN) genes (STING), which induce IFN and IFN-regulated genes in HSCs, increasing HSC division and erythropoiesis. Inhibition of reverse transcriptase or deficiency for cGAS or STING had little or no effect on hematopoiesis in non-pregnant mice but depleted HSCs and erythroid progenitors in pregnant mice, reducing red blood cell counts. Retrotransposons and IFN regulated genes were also induced in mouse HSCs after serial bleeding and in human HSCs during pregnancy. Reverse transcriptase inhibitor use was associated with anemia in pregnant, but not non-pregnant, people suggesting conservation of these mechanisms from mice to humans.
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Affiliation(s)
- Julia Phan
- Children's Research Institute and the Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Brandon Chen
- Children's Research Institute and the Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Zhiyu Zhao
- Children's Research Institute and the Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Gabriele Allies
- Department of Dermatology, University Hospital Essen & German Cancer Consortium; Essen, & National Center for Tumor Diseases (NCT-West), Campus Essen & Research Alliance Ruhr, Research Center One Health, University Duisburg-Essen, Campus Essen, Essen, Germany
| | - Antonella Iannaccone
- Department of Gynecology and Obstetrics, University Hospital Essen, 45147 Essen, Germany
| | - Animesh Paul
- Children's Research Institute and the Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Feyza Cansiz
- Department of Dermatology, University Hospital Essen & German Cancer Consortium; Essen, & National Center for Tumor Diseases (NCT-West), Campus Essen & Research Alliance Ruhr, Research Center One Health, University Duisburg-Essen, Campus Essen, Essen, Germany
| | - Alberto Spina
- Department of Gynecology and Obstetrics, University Hospital Essen, 45147 Essen, Germany
| | - Anna-Sophia Leven
- Department of Dermatology, University Hospital Essen & German Cancer Consortium; Essen, & National Center for Tumor Diseases (NCT-West), Campus Essen & Research Alliance Ruhr, Research Center One Health, University Duisburg-Essen, Campus Essen, Essen, Germany
| | - Alexandra Gellhaus
- Department of Gynecology and Obstetrics, University Hospital Essen, 45147 Essen, Germany
| | - Dirk Schadendorf
- Department of Dermatology, University Hospital Essen & German Cancer Consortium; Essen, & National Center for Tumor Diseases (NCT-West), Campus Essen & Research Alliance Ruhr, Research Center One Health, University Duisburg-Essen, Campus Essen, Essen, Germany
| | - Rainer Kimmig
- Department of Gynecology and Obstetrics, University Hospital Essen, 45147 Essen, Germany
| | - Marcel Mettlen
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75235, USA
| | - Alpaslan Tasdogan
- Department of Dermatology, University Hospital Essen & German Cancer Consortium; Essen, & National Center for Tumor Diseases (NCT-West), Campus Essen & Research Alliance Ruhr, Research Center One Health, University Duisburg-Essen, Campus Essen, Essen, Germany
| | - Sean J Morrison
- Children's Research Institute and the Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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4
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Espinet E, Natoli G. Leveraging the tug-of-war with genomic retroelements to enhance immunotherapy of pancreatic cancer. Gut 2024:gutjnl-2024-333702. [PMID: 39438125 DOI: 10.1136/gutjnl-2024-333702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2024] [Accepted: 10/08/2024] [Indexed: 10/25/2024]
Affiliation(s)
- Elisa Espinet
- Pathology and Experimental Therapy, University of Barcelona, L'Hospitalet de Llobregat, Spain
- Oncobell, IDIBELL, Barcelona, Spain
| | - Gioacchino Natoli
- Department of Experimental Oncology, European Institute of Oncology, Milano, Italy
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5
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Wang FQ, Dang X, Su H, Lei Y, She CH, Zhang C, Chen X, Yang X, Yang J, Feng H, Yang W. Association of hyperactivated transposon expression with exacerbated immune activation in systemic lupus erythematosus. Mob DNA 2024; 15:23. [PMID: 39427224 PMCID: PMC11490001 DOI: 10.1186/s13100-024-00335-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Accepted: 10/14/2024] [Indexed: 10/21/2024] Open
Abstract
BACKGROUND Systemic Lupus Erythematosus (SLE) is a complex autoimmune disorder, and transposable elements (TEs) have been hypothesized to play a significant role in its development. However, limited research has explored this connection. Our study aimed to examine the relationship between TE expression and SLE pathogenesis. METHODS We analyzed whole blood RNA-seq datasets from 198 SLE patients and 84 healthy controls. The REdiscoverTE pipeline was employed to quantify TE and other gene expressions, identifying differentially expressed TEs. A TE score was calculated to measure overall TE expression for each sample. Gene ontology and gene set enrichment analyses were conducted to explore the functional implications of TE upregulation. Independent datasets were utilized to replicate the results and investigate cell type-specific TE expression. RESULTS Our analysis identified two distinct patient groups: one with high TE expression and another with TE expression comparable to controls. Patients with high TE expression exhibited upregulation of pathways involving nucleic acid sensors, and TE expression was strongly correlated with interferon (IFN) signatures. Furthermore, these patients displayed deregulated cell composition, including increased neutrophils and decreased regulatory T cells. Neutrophils were suggested as the primary source of TE expression, contributing to IFN production. CONCLUSIONS Our findings suggest that TE expression may serve as a crucial mediator in maintaining the activation of interferon pathways, acting as an endogenous source of nucleic acid stimulators in SLE patients.
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Affiliation(s)
- Frank Qingyun Wang
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China
| | - Xiao Dang
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China
| | - Huidong Su
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China
| | - Yao Lei
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China
| | - Chun Hing She
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China
| | - Caicai Zhang
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China
| | - Xinxin Chen
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China
| | - Xingtian Yang
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China
| | - Jing Yang
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China
| | - Hong Feng
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China
| | - Wanling Yang
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China.
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6
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Wu B, Zhang B, Li B, Wu H, Jiang M. Cold and hot tumors: from molecular mechanisms to targeted therapy. Signal Transduct Target Ther 2024; 9:274. [PMID: 39420203 PMCID: PMC11491057 DOI: 10.1038/s41392-024-01979-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 08/20/2024] [Accepted: 09/12/2024] [Indexed: 10/19/2024] Open
Abstract
Immunotherapy has made significant strides in cancer treatment, particularly through immune checkpoint blockade (ICB), which has shown notable clinical benefits across various tumor types. Despite the transformative impact of ICB treatment in cancer therapy, only a minority of patients exhibit a positive response to it. In patients with solid tumors, those who respond well to ICB treatment typically demonstrate an active immune profile referred to as the "hot" (immune-inflamed) phenotype. On the other hand, non-responsive patients may exhibit a distinct "cold" (immune-desert) phenotype, differing from the features of "hot" tumors. Additionally, there is a more nuanced "excluded" immune phenotype, positioned between the "cold" and "hot" categories, known as the immune "excluded" type. Effective differentiation between "cold" and "hot" tumors, and understanding tumor intrinsic factors, immune characteristics, TME, and external factors are critical for predicting tumor response and treatment results. It is widely accepted that ICB therapy exerts a more profound effect on "hot" tumors, with limited efficacy against "cold" or "altered" tumors, necessitating combinations with other therapeutic modalities to enhance immune cell infiltration into tumor tissue and convert "cold" or "altered" tumors into "hot" ones. Therefore, aligning with the traits of "cold" and "hot" tumors, this review systematically delineates the respective immune characteristics, influencing factors, and extensively discusses varied treatment approaches and drug targets based on "cold" and "hot" tumors to assess clinical efficacy.
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Affiliation(s)
- Bo Wu
- Department of Neurology, The Fourth Affiliated Hospital, China Medical University, Shenyang, China
| | - Bo Zhang
- Department of Youth League Committee, The Fourth Affiliated Hospital, China Medical University, Shenyang, China
| | - Bowen Li
- Department of Pancreatic and Gastrointestinal Surgery, Ningbo No. 2 Hospital, Ningbo, China
| | - Haoqi Wu
- Department of Gynaecology and Obstetrics, The Second Hospital of Dalian Medical University, Dalian, China
| | - Meixi Jiang
- Department of Neurology, The Fourth Affiliated Hospital, China Medical University, Shenyang, China.
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7
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Laisné M, Lupien M, Vallot C. Epigenomic heterogeneity as a source of tumour evolution. Nat Rev Cancer 2024:10.1038/s41568-024-00757-9. [PMID: 39414948 DOI: 10.1038/s41568-024-00757-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/16/2024] [Indexed: 10/18/2024]
Abstract
In the past decade, remarkable progress in cancer medicine has been achieved by the development of treatments that target DNA sequence variants. However, a purely genetic approach to treatment selection is hampered by the fact that diverse cell states can emerge from the same genotype. In multicellular organisms, cell-state heterogeneity is driven by epigenetic processes that regulate DNA-based functions such as transcription; disruption of these processes is a hallmark of cancer that enables the emergence of defective cell states. Advances in single-cell technologies have unlocked our ability to quantify the epigenomic heterogeneity of tumours and understand its mechanisms, thereby transforming our appreciation of how epigenomic changes drive cancer evolution. This Review explores the idea that epigenomic heterogeneity and plasticity act as a reservoir of cell states and therefore as a source of tumour evolution. Best practices to quantify epigenomic heterogeneity and explore its various causes and consequences are discussed, including epigenomic reprogramming, stochastic changes and lasting memory. The design of new therapeutic approaches to restrict epigenomic heterogeneity, with the long-term objective of limiting cancer development and progression, is also addressed.
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Affiliation(s)
- Marthe Laisné
- CNRS UMR3244, Institut Curie, PSL University, Paris, France
- Translational Research Department, Institut Curie, PSL University, Paris, France
| | - Mathieu Lupien
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontorio, Canada.
- Department of Medical Biophysics, University of Toronto, Toronto, Ontorio, Canada.
- Ontario Institute for Cancer Research, Toronto, Ontorio, Canada.
| | - Céline Vallot
- CNRS UMR3244, Institut Curie, PSL University, Paris, France.
- Translational Research Department, Institut Curie, PSL University, Paris, France.
- Single Cell Initiative, Institut Curie, PSL University, Paris, France.
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8
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Shah S, Yu S, Zhang C, Ali I, Wang X, Qian Y, Xiao T. Retrotransposon SINEs in age-related diseases: Mechanisms and therapeutic implications. Ageing Res Rev 2024; 101:102539. [PMID: 39395576 DOI: 10.1016/j.arr.2024.102539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2024] [Revised: 09/27/2024] [Accepted: 10/03/2024] [Indexed: 10/14/2024]
Abstract
Retrotransposons are self-replicating genomic elements that move from one genomic location to another using a "copy-and-paste" method involving RNA intermediaries. One family of retrotransposon that has garnered considerable attention for its association with age-related diseases and anti-aging interventions is the short interspersed nuclear elements (SINEs). This review summarizes current knowledge on the roles of SINEs in aging processes and therapies. To underscore the significant research on the involvement of SINEs in aging-related diseases, we commence by outlining compelling evidence on the classification and mechanism, highlighting implications in age-related phenomena. The intricate relationship between SINEs and diseases such as neurodegenerative disorders, heart failure, high blood pressure, atherosclerosis, type 2 diabetes mellitus, osteoporosis, visual system dysfunctions, and cancer is explored, emphasizing their roles in various age-related diseases. Recent investigations into the anti-aging potential of SINE-targeted treatments are examined, with particular attention to how SINE antisense RNA mitigate age-related alterations at the cellular and molecular levels, offering insights into potential therapeutic targets for age-related pathologies. This review aims to compile the most recent advances on the multifaceted roles of SINE retrotransposons in age-related diseases and anti-aging interventions, providing valuable insights into underlying mechanisms and therapeutic avenues for promoting healthy aging.
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Affiliation(s)
- Suleman Shah
- Thoracic Surgery Department of the First Affiliated Hospital, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Cell Biology and Genetics, Shenzhen University Medical School, Shenzhen University, Shenzhen 518055, China; Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, National-Regional Key Technology Engineering Laboratory for Medical Ultrasound, School of Biomedical Engineering, Shenzhen University Medical school, Shenzhen 518055, China
| | - Siyi Yu
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, Wuhan 430079, China
| | - Chen Zhang
- Department of Thoracic Surgery, The People's Hospital of Guangxi Zhuang Autonomous Region, Guangxi Academy of Medical Sciences, Nanning 530021, China
| | - Ilyas Ali
- Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, National-Regional Key Technology Engineering Laboratory for Medical Ultrasound, School of Biomedical Engineering, Shenzhen University Medical school, Shenzhen 518055, China
| | - Xiufang Wang
- Department of Genetics, Hebei Medical University, Hebei Key Lab of Laboratory Animal, Shijiazhuang 050017, China
| | - Youhui Qian
- Thoracic Surgery Department of the First Affiliated Hospital, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Cell Biology and Genetics, Shenzhen University Medical School, Shenzhen University, Shenzhen 518055, China.
| | - Tian Xiao
- Thoracic Surgery Department of the First Affiliated Hospital, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Cell Biology and Genetics, Shenzhen University Medical School, Shenzhen University, Shenzhen 518055, China.
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9
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Chour M, Porteu F, Depil S, Alcazer V. Endogenous retroelements in hematological malignancies: From epigenetic dysregulation to therapeutic targeting. Am J Hematol 2024. [PMID: 39387681 DOI: 10.1002/ajh.27501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2024] [Revised: 09/30/2024] [Accepted: 10/02/2024] [Indexed: 10/15/2024]
Abstract
Endogenous retroelements (EREs), which comprise half of the human genome, play a pivotal role in genome dynamics. Some EREs retained the ability to encode proteins, although most degenerated or served as a source for novel genes and regulatory elements during evolution. Despite ERE repression mechanisms developed to maintain genome stability, widespread pervasive ERE activation is observed in cancer including hematological malignancies. Challenging the perception of noncoding DNA as "junk," EREs are underestimated contributors to cancer driver mechanisms as well as antitumoral immunity by providing innate immune ligands and tumor antigens. This review highlights recent progress in understanding ERE co-option events in cancer and focuses on the controversial debate surrounding their causal role in shaping malignant phenotype. We provide insights into the rapidly evolving landscape of ERE research in hematological malignancies and their clinical implications in these cancers.
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Affiliation(s)
- Mohamed Chour
- Département de Biologie, Master Biosciences-Santé, École Normale Supérieure de Lyon, Lyon, France
- Centre International de Recherche en Infectiologie, INSERM U1111 CNRS UMR530, Lyon, France
| | - Françoise Porteu
- Institut Gustave Roussy, INSERM U1287 Université Paris Saclay, Villejuif, France
| | - Stéphane Depil
- Centre de Recherche en Cancérologie de Lyon, UMR INSERM U1052 CNRS 5286 Université Claude Bernard Lyon 1 Centre Léon Bérard, Lyon, France
- ErVimmune, Lyon, France
- Centre Léon Bérard, Lyon, France
- Université Claude Bernard Lyon 1, Lyon, France
| | - Vincent Alcazer
- Centre International de Recherche en Infectiologie, INSERM U1111 CNRS UMR530, Lyon, France
- Université Claude Bernard Lyon 1, Lyon, France
- Service d'hématologie Clinique, Centre Hospitalier Lyon Sud, Hospices Civils de Lyon, Pierre-Bénite, France
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10
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Galassi C, Chan TA, Vitale I, Galluzzi L. The hallmarks of cancer immune evasion. Cancer Cell 2024:S1535-6108(24)00358-1. [PMID: 39393356 DOI: 10.1016/j.ccell.2024.09.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/03/2024] [Revised: 08/27/2024] [Accepted: 09/16/2024] [Indexed: 10/13/2024]
Abstract
According to the widely accepted "three Es" model, the host immune system eliminates malignant cell precursors and contains microscopic neoplasms in a dynamic equilibrium, preventing cancer outgrowth until neoplastic cells acquire genetic or epigenetic alterations that enable immune escape. This immunoevasive phenotype originates from various mechanisms that can be classified under a novel "three Cs" conceptual framework: (1) camouflage, which hides cancer cells from immune recognition, (2) coercion, which directly or indirectly interferes with immune effector cells, and (3) cytoprotection, which shields malignant cells from immune cytotoxicity. Blocking the ability of neoplastic cells to evade the host immune system is crucial for increasing the efficacy of modern immunotherapy and conventional therapeutic strategies that ultimately activate anticancer immunosurveillance. Here, we review key hallmarks of cancer immune evasion under the "three Cs" framework and discuss promising strategies targeting such immunoevasive mechanisms.
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Affiliation(s)
- Claudia Galassi
- Department of Radiation Oncology, Weill Cornell Medicine, New York, NY, USA
| | - Timothy A Chan
- Department of Radiation Oncology, Taussig Cancer Center, Cleveland Clinic, Cleveland, OH, USA; Center for Immunotherapy and Precision Immuno-Oncology, Cleveland Clinic, Cleveland, OH, USA; National Center for Regenerative Medicine, Cleveland, OH, USA; Case Comprehensive Cancer Center, Cleveland, OH, USA
| | - Ilio Vitale
- Italian Institute for Genomic Medicine, c/o IRCSS Candiolo, Torino, Italy; Candiolo Cancer Institute, FPO - IRCCS, Candiolo, Italy.
| | - Lorenzo Galluzzi
- Department of Radiation Oncology, Weill Cornell Medicine, New York, NY, USA; Sandra and Edward Meyer Cancer Center, New York, NY, USA; Caryl and Israel Englander Institute for Precision Medicine, New York, NY, USA; Cancer Signaling and Microenvironment Program, Fox Chase Cancer Center, Philadelphia, PA, USA.
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11
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Wang L, Zhu Y, Zhang N, Xian Y, Tang Y, Ye J, Reza F, He G, Wen X, Jiang X. The multiple roles of interferon regulatory factor family in health and disease. Signal Transduct Target Ther 2024; 9:282. [PMID: 39384770 PMCID: PMC11486635 DOI: 10.1038/s41392-024-01980-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Revised: 08/12/2024] [Accepted: 09/10/2024] [Indexed: 10/11/2024] Open
Abstract
Interferon Regulatory Factors (IRFs), a family of transcription factors, profoundly influence the immune system, impacting both physiological and pathological processes. This review explores the diverse functions of nine mammalian IRF members, each featuring conserved domains essential for interactions with other transcription factors and cofactors. These interactions allow IRFs to modulate a broad spectrum of physiological processes, encompassing host defense, immune response, and cell development. Conversely, their pivotal role in immune regulation implicates them in the pathophysiology of various diseases, such as infectious diseases, autoimmune disorders, metabolic diseases, and cancers. In this context, IRFs display a dichotomous nature, functioning as both tumor suppressors and promoters, contingent upon the specific disease milieu. Post-translational modifications of IRFs, including phosphorylation and ubiquitination, play a crucial role in modulating their function, stability, and activation. As prospective biomarkers and therapeutic targets, IRFs present promising opportunities for disease intervention. Further research is needed to elucidate the precise mechanisms governing IRF regulation, potentially pioneering innovative therapeutic strategies, particularly in cancer treatment, where the equilibrium of IRF activities is of paramount importance.
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Affiliation(s)
- Lian Wang
- Department of Dermatology & Venerology, West China Hospital, Sichuan University, Chengdu, 610041, China
- Laboratory of Dermatology, Clinical Institute of Inflammation and Immunology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Yanghui Zhu
- Department of Dermatology & Venerology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Nan Zhang
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Yali Xian
- Department of Dermatology & Venerology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Yu Tang
- Department of Dermatology & Venerology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Jing Ye
- Department of Dermatology & Venerology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Fekrazad Reza
- Radiation Sciences Research Center, Laser Research Center in Medical Sciences, AJA University of Medical Sciences, Tehran, Iran
- International Network for Photo Medicine and Photo Dynamic Therapy (INPMPDT), Universal Scientific Education and Research Network (USERN), Tehran, Iran
| | - Gu He
- Department of Dermatology & Venerology, West China Hospital, Sichuan University, Chengdu, 610041, China
- Laboratory of Dermatology, Clinical Institute of Inflammation and Immunology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Xiang Wen
- Department of Dermatology & Venerology, West China Hospital, Sichuan University, Chengdu, 610041, China.
| | - Xian Jiang
- Department of Dermatology & Venerology, West China Hospital, Sichuan University, Chengdu, 610041, China.
- Laboratory of Dermatology, Clinical Institute of Inflammation and Immunology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China.
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12
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Grundy EE, Shaw LC, Wang L, Lee AV, Argueta JC, Powell DJ, Ostrowski M, Jones RB, Cruz CRY, Gordish-Dressman H, Chappell NP, Bollard CM, Chiappinelli KB. A T cell receptor specific for an HLA-A*03:01-restricted epitope in the endogenous retrovirus ERV-K-Env exhibits limited recognition of its cognate epitope. Mob DNA 2024; 15:19. [PMID: 39385229 PMCID: PMC11462856 DOI: 10.1186/s13100-024-00333-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Accepted: 10/04/2024] [Indexed: 10/12/2024] Open
Abstract
Transposable elements (TEs) are often expressed at higher levels in tumor cells than normal cells, implicating these genomic regions as an untapped pool of tumor-associated antigens. In ovarian cancer (OC), protein from the TE ERV-K is frequently expressed by tumor cells. Here we determined whether the targeting of previously identified epitope in the envelope gene (env) of ERV-K resulted in target antigen specificity against cancer cells. We found that transducing healthy donor T cells with an ERV-K-Env-specific T cell receptor construct resulted in antigen specificity only when co-cultured with HLA-A*03:01 B lymphoblastoid cells. Furthermore, in vitro priming of several healthy donors with this epitope of ERV-K-Env did not result in target antigen specificity. These data suggest that the T cell receptor is a poor candidate for targeting this specific ERV-K-Env epitope and has limited potential as a T cell therapy for OC.
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Affiliation(s)
- Erin E Grundy
- Department of Microbiology, Immunology and Tropical Medicine, The George Washington University, Washington, DC, USA
- The George Washington University Cancer Center, Washington, DC, USA
- The Integrated Biomedical Sciences at the George Washington University, Washington, DC, USA
| | - Lauren C Shaw
- Department of Pathology and Laboratory Medicine, Center for Cellular Immunotherapies, Perelman School of Medicine, Ovarian Cancer Research Center, The University of Pennsylvania, Philadelphia, PA, USA
| | - Loretta Wang
- Department of Microbiology, Immunology and Tropical Medicine, The George Washington University, Washington, DC, USA
- The George Washington University Cancer Center, Washington, DC, USA
| | - Abigail V Lee
- Department of Microbiology, Immunology and Tropical Medicine, The George Washington University, Washington, DC, USA
- The George Washington University Cancer Center, Washington, DC, USA
- The Integrated Biomedical Sciences at the George Washington University, Washington, DC, USA
| | - James Castro Argueta
- The George Washington School of Medicine and Health Sciences, The George Washington University, Washington, DC, USA
| | - Daniel J Powell
- Department of Pathology and Laboratory Medicine, Center for Cellular Immunotherapies, Perelman School of Medicine, Ovarian Cancer Research Center, The University of Pennsylvania, Philadelphia, PA, USA
| | - Mario Ostrowski
- Department of Medicine, University of Toronto, Toronto, Canada
| | - R Brad Jones
- Weill Cornell Medicine Graduate School of Medical Sciences, New York, NY, USA
| | - C Russell Y Cruz
- The George Washington University Cancer Center, Washington, DC, USA
- The Integrated Biomedical Sciences at the George Washington University, Washington, DC, USA
- Center for Cancer and Immunology, , Children's National Hospital, Washington, DC, United States
| | - Heather Gordish-Dressman
- The George Washington School of Medicine and Health Sciences, The George Washington University, Washington, DC, USA
- The Center for Translational Research, Children's National Hospital, Washington, DC, USA
| | | | - Catherine M Bollard
- The George Washington University Cancer Center, Washington, DC, USA
- The Integrated Biomedical Sciences at the George Washington University, Washington, DC, USA
- Center for Cancer and Immunology, , Children's National Hospital, Washington, DC, United States
| | - Katherine B Chiappinelli
- Department of Microbiology, Immunology and Tropical Medicine, The George Washington University, Washington, DC, USA.
- The George Washington University Cancer Center, Washington, DC, USA.
- The Integrated Biomedical Sciences at the George Washington University, Washington, DC, USA.
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13
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Duval KL, Artis AR, Goll MG. The emerging H3K9me3 chromatin landscape during zebrafish embryogenesis. Genetics 2024; 228:iyae138. [PMID: 39166515 PMCID: PMC11457944 DOI: 10.1093/genetics/iyae138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2024] [Revised: 08/07/2024] [Accepted: 08/07/2024] [Indexed: 08/23/2024] Open
Abstract
The structural organization of eukaryotic genomes is contingent upon the fractionation of DNA into transcriptionally permissive euchromatin and repressive heterochromatin. However, we have a limited understanding of how these distinct states are first established during animal embryogenesis. Histone 3 lysine 9 trimethylation (H3K9me3) is critical to heterochromatin formation, and bulk establishment of this mark is thought to help drive large-scale remodeling of an initially naive chromatin state during animal embryogenesis. However, a detailed understanding of this process is lacking. Here, we leverage CUT&RUN to define the emerging H3K9me3 landscape of the zebrafish embryo with high sensitivity and temporal resolution. Despite the prevalence of DNA transposons in the zebrafish genome, we found that LTR transposons are preferentially targeted for embryonic H3K9me3 deposition, with different families exhibiting distinct establishment timelines. High signal-to-noise ratios afforded by CUT&RUN revealed new, emerging sites of low-amplitude H3K9me3 that initiated before the major wave of zygotic genome activation (ZGA). Early sites of establishment predominated at specific subsets of transposons and were particularly enriched for transposon sequences with maternal piRNAs and pericentromeric localization. Notably, the number of H3K9me3 enriched sites increased linearly across blastula development, while quantitative comparison revealed a >10-fold genome-wide increase in H3K9me3 signal at established sites over just 30 min at the onset of major ZGA. Continued maturation of the H3K9me3 landscape was observed beyond the initial wave of bulk establishment.
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Affiliation(s)
- Katherine L Duval
- Department of Genetics, University of Georgia, Athens, GA, 30602, USA
| | - Ashley R Artis
- Department of Genetics, University of Georgia, Athens, GA, 30602, USA
| | - Mary G Goll
- Department of Genetics, University of Georgia, Athens, GA, 30602, USA
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14
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Zhou Y, Zhang Y, Li M, Ming T, Zhang C, Huang C, Li J, Li F, Li H, Zhao E, Shu F, Liu L, Pan X, Gao Y, Tian L, Song L, Huang H, Liao W. Oncogenic KRAS drives immunosuppression of colorectal cancer by impairing DDX60-mediated dsRNA accumulation and viral mimicry. Sci Immunol 2024; 9:eado8758. [PMID: 39365875 DOI: 10.1126/sciimmunol.ado8758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2024] [Accepted: 09/11/2024] [Indexed: 10/06/2024]
Abstract
The interferon (IFN) response is vital for the effectiveness of immune checkpoint inhibition (ICI) therapy. Our previous research showed that KRAS (Kirsten rat sarcoma viral) mutation impairs the IFN response in colorectal cancer (CRC), with an unclear mechanism. Here, we demonstrate that KRAS accelerates double-stranded RNA (dsRNA) degradation, impairing dsRNA sensing and IFN response by down-regulating DExD/H-box helicase 6 (DDX60). DDX60 was identified as a KRAS target here and could bind to dsRNAs to protect against RNA-induced silencing complex (RISC)-mediated degradation. Overexpressing DDX60 induced dsRNA accumulation, reactivated IFN signaling, and increased CRC sensitivity to ICI therapy. Mechanistically, KRAS engaged the AKT (also known as protein kinase B)-GSK3β (glycogen synthase kinase-3 beta) pathway to suppress STAT3 phosphorylation, thereby inhibiting STAT3-driven DDX60 transcription. Our findings reveal a role for KRAS in dsRNA homeostasis, suggesting potential strategies to convert "cold" tumors to "hot" and to overcome ICI resistance in CRC with KRAS mutations.
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Affiliation(s)
- Yi Zhou
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou 510060, P. R. China
| | - Yaxin Zhang
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou 510060, P. R. China
| | - Mingzhou Li
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou 510060, P. R. China
| | - Tian Ming
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou 510060, P. R. China
| | - Chao Zhang
- Department of Pathology, Sun Yat-sen University Cancer Center, Guangzhou 510060, P. R. China
| | - Chengmei Huang
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou 510060, P. R. China
| | - Jiexi Li
- Department of Cancer Biology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Fengtian Li
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou 510060, P. R. China
| | - Huali Li
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou 510060, P. R. China
| | - Enen Zhao
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou 510060, P. R. China
| | - Feng Shu
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou 510060, P. R. China
| | - Lingtao Liu
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou 510060, P. R. China
| | - Xingyan Pan
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou 510060, P. R. China
| | - Yijun Gao
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou 510060, P. R. China
| | - Lin Tian
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou 510060, P. R. China
| | - Libing Song
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou 510060, P. R. China
| | - Huilin Huang
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou 510060, P. R. China
| | - Wenting Liao
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou 510060, P. R. China
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15
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Esteller M, Dawson MA, Kadoch C, Rassool FV, Jones PA, Baylin SB. The Epigenetic Hallmarks of Cancer. Cancer Discov 2024; 14:1783-1809. [PMID: 39363741 DOI: 10.1158/2159-8290.cd-24-0296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 05/08/2024] [Accepted: 06/24/2024] [Indexed: 10/05/2024]
Abstract
Cancer is a complex disease in which several molecular and cellular pathways converge to foster the tumoral phenotype. Notably, in the latest iteration of the cancer hallmarks, "nonmutational epigenetic reprogramming" was newly added. However, epigenetics, much like genetics, is a broad scientific area that deserves further attention due to its multiple roles in cancer initiation, progression, and adaptive nature. Herein, we present a detailed examination of the epigenetic hallmarks affected in human cancer, elucidating the pathways and genes involved, and dissecting the disrupted landscapes for DNA methylation, histone modifications, and chromatin architecture that define the disease. Significance: Cancer is a disease characterized by constant evolution, spanning from its initial premalignant stages to the advanced invasive and disseminated stages. It is a pathology that is able to adapt and survive amidst hostile cellular microenvironments and diverse treatments implemented by medical professionals. The more fixed setup of the genetic structure cannot fully provide transformed cells with the tools to survive but the rapid and plastic nature of epigenetic changes is ready for the task. This review summarizes the epigenetic hallmarks that define the ecological success of cancer cells in our bodies.
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Affiliation(s)
- Manel Esteller
- Cancer Epigenetics Group, Josep Carreras Leukaemia Research Institute (IJC), Barcelona, Spain
- Centro de Investigacion Biomedica en Red Cancer (CIBERONC), Madrid, Spain
- Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
- Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona (UB), Barcelona, Spain
| | - Mark A Dawson
- Peter MacCallum Cancer Centre, Melbourne, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Australia
- Centre for Cancer Research, University of Melbourne, Melbourne, Australia
| | - Cigall Kadoch
- Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Howard Hughes Medical Institute, Chevy Chase, Maryland
| | - Feyruz V Rassool
- Marlene and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, Maryland
- Department of Radiation Oncology, University of Maryland School of Medicine, Baltimore, Maryland
| | - Peter A Jones
- Department of Epigenetics, Van Andel Institute, Grand Rapids, Michigan
| | - Stephen B Baylin
- Department of Epigenetics, Van Andel Institute, Grand Rapids, Michigan
- Department of Oncology, The Johns Hopkins School of Medicine, The Sidney Kimmel Comprehensive Cancer Center, Baltimore, Maryland
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16
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He MY, Tong KI, Liu T, Whittaker Hawkins R, Shelton V, Zeng Y, Bakhtiari M, Xiao Y, Zheng G, Sakhdari A, Yang L, Xu W, Brooks DG, Laister RC, He HH, Kridel R. GNAS knockout potentiates HDAC3 inhibition through viral mimicry-related interferon responses in lymphoma. Leukemia 2024; 38:2210-2224. [PMID: 39117798 PMCID: PMC11436380 DOI: 10.1038/s41375-024-02325-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 06/18/2024] [Accepted: 06/20/2024] [Indexed: 08/10/2024]
Abstract
Despite selective HDAC3 inhibition showing promise in a subset of lymphomas with CREBBP mutations, wild-type tumors generally exhibit resistance. Here, using unbiased genome-wide CRISPR screening, we identify GNAS knockout (KO) as a sensitizer of resistant lymphoma cells to HDAC3 inhibition. Mechanistically, GNAS KO-induced sensitization is independent of the canonical G-protein activities but unexpectedly mediated by viral mimicry-related interferon (IFN) responses, characterized by TBK1 and IRF3 activation, double-stranded RNA formation, and transposable element (TE) expression. GNAS KO additionally synergizes with HDAC3 inhibition to enhance CD8+ T cell-induced cytotoxicity. Moreover, we observe in human lymphoma patients that low GNAS expression is associated with high baseline TE expression and upregulated IFN signaling and shares common disrupted biological activities with GNAS KO in histone modification, mRNA processing, and transcriptional regulation. Collectively, our findings establish an unprecedented link between HDAC3 inhibition and viral mimicry in lymphoma. We suggest low GNAS expression as a potential biomarker that reflects viral mimicry priming for enhanced response to HDAC3 inhibition in the clinical treatment of lymphoma, especially the CREBBP wild-type cases.
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Affiliation(s)
- Michael Y He
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Kit I Tong
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Ting Liu
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Ryder Whittaker Hawkins
- Department of Immunology, University of Toronto, Toronto, ON, Canada
- Cell Biology Program, Hospital for Sick Children, Toronto, ON, Canada
| | - Victoria Shelton
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Yong Zeng
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Mehran Bakhtiari
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Yufeng Xiao
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL, USA
| | - Guangrong Zheng
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL, USA
| | - Ali Sakhdari
- Laboratory Medicine and Pathobiology, University Health Network, Toronto, ON, Canada
| | - Lin Yang
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Wenxi Xu
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - David G Brooks
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Immunology, University of Toronto, Toronto, ON, Canada
| | - Rob C Laister
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Housheng Hansen He
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Robert Kridel
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.
- Institute of Medical Science, University of Toronto, Toronto, ON, Canada.
- Department of Medicine, University of Toronto, Toronto, ON, Canada.
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17
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You E, Danaher P, Lu C, Sun S, Zou L, Phillips IE, Rojas AS, Ho NI, Song Y, Raabe MJ, Xu KH, Richieri PM, Li H, Aston N, Porter RL, Patel BK, Nieman LT, Schurman N, Hudson BM, North K, Church SE, Deshpande V, Liss AS, Kim TK, Cui Y, Kim Y, Greenbaum BD, Aryee MJ, Ting DT. Disruption of cellular plasticity by repeat RNAs in human pancreatic cancer. Cell 2024:S0092-8674(24)01072-9. [PMID: 39383862 DOI: 10.1016/j.cell.2024.09.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 07/02/2024] [Accepted: 09/13/2024] [Indexed: 10/11/2024]
Abstract
Aberrant expression of repeat RNAs in pancreatic ductal adenocarcinoma (PDAC) mimics viral-like responses with implications on tumor cell state and the response of the surrounding microenvironment. To better understand the relationship of repeat RNAs in human PDAC, we performed spatial molecular imaging at single-cell resolution in 46 primary tumors, revealing correlations of high repeat RNA expression with alterations in epithelial state in PDAC cells and myofibroblast phenotype in cancer-associated fibroblasts (CAFs). This loss of cellular identity is observed with dosing of extracellular vesicles (EVs) and individual repeat RNAs of PDAC and CAF cell culture models pointing to cell-cell intercommunication of these viral-like elements. Differences in PDAC and CAF responses are driven by distinct innate immune signaling through interferon regulatory factor 3 (IRF3). The cell-context-specific viral-like responses to repeat RNAs provide a mechanism for modulation of cellular plasticity in diverse cell types in the PDAC microenvironment.
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Affiliation(s)
- Eunae You
- Mass General Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | | | - Chenyue Lu
- Mass General Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA; Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Siyu Sun
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Luli Zou
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Ildiko E Phillips
- Mass General Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Alexandra S Rojas
- Mass General Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Natalie I Ho
- Mass General Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Yuhui Song
- Mass General Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Michael J Raabe
- Mass General Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Katherine H Xu
- Mass General Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Peter M Richieri
- Mass General Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Hao Li
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Natalie Aston
- Mass General Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Rebecca L Porter
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Bidish K Patel
- Mass General Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Linda T Nieman
- Mass General Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | | | | | | | | | - Vikram Deshpande
- Mass General Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA; Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Andrew S Liss
- Department of Surgery, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Tae K Kim
- NanoString Technologies, Seattle, WA 98109, USA
| | - Yi Cui
- NanoString Technologies, Seattle, WA 98109, USA
| | - Youngmi Kim
- NanoString Technologies, Seattle, WA 98109, USA
| | - Benjamin D Greenbaum
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Physiology, Biophysics & Systems Biology, Weill Cornell Medicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Martin J Aryee
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.
| | - David T Ting
- Mass General Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA; Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.
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18
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Yeh CY, Aguirre K, Laveroni O, Kim S, Wang A, Liang B, Zhang X, Han LM, Valbuena R, Bassik MC, Kim YM, Plevritis SK, Snyder MP, Howitt BE, Jerby L. Mapping spatial organization and genetic cell-state regulators to target immune evasion in ovarian cancer. Nat Immunol 2024; 25:1943-1958. [PMID: 39179931 PMCID: PMC11436371 DOI: 10.1038/s41590-024-01943-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 07/25/2024] [Indexed: 08/26/2024]
Abstract
The drivers of immune evasion are not entirely clear, limiting the success of cancer immunotherapies. Here we applied single-cell spatial and perturbational transcriptomics to delineate immune evasion in high-grade serous tubo-ovarian cancer. To this end, we first mapped the spatial organization of high-grade serous tubo-ovarian cancer by profiling more than 2.5 million cells in situ in 130 tumors from 94 patients. This revealed a malignant cell state that reflects tumor genetics and is predictive of T cell and natural killer cell infiltration levels and response to immune checkpoint blockade. We then performed Perturb-seq screens and identified genetic perturbations-including knockout of PTPN1 and ACTR8-that trigger this malignant cell state. Finally, we show that these perturbations, as well as a PTPN1/PTPN2 inhibitor, sensitize ovarian cancer cells to T cell and natural killer cell cytotoxicity, as predicted. This study thus identifies ways to study and target immune evasion by linking genetic variation, cell-state regulators and spatial biology.
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Grants
- P30 CA124435 NCI NIH HHS
- U01 HG012069 NHGRI NIH HHS
- L.J. holds a Career Award at the Scientific Interface from the Burroughs Wellcome Fund (BWF) and a Liz Tilberis Early Career Award from the Ovarian Cancer Research Alliance (OCRA). This study was supported by the BWF (1019508.01; L.J.), National Human Genome Research Institute (NHGRI, U01HG012069; L.J.), OCRA (889076; L.J), Under One Umbrella, Stanford Women’s Cancer Center, Stanford Cancer Institute, a National Cancer Institute (NCI)-designated Comprehensive Cancer Center (251217; B.E.H., L.J.), as well as funds from the Departments of Genetics (L.J.) at Stanford University and from the Chan Zuckerberg Biohub (L.J.).
- This study was partially supported by the Stanford Women’s Cancer Center (251217; B.E.H., L.J.), and an NCI Center Support Grant (P30CA124435; B.E.H.), as well as funds from the Departments of Pathology (B.E.H.).
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Affiliation(s)
- Christine Yiwen Yeh
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Karmen Aguirre
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Cancer Biology Program, Stanford University, Stanford, CA, USA
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Olivia Laveroni
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Subin Kim
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Aihui Wang
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Brooke Liang
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Xiaoming Zhang
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Lucy M Han
- Department of Pathology, California Pacific Medical Center, San Francisco, CA, USA
| | - Raeline Valbuena
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Michael C Bassik
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Young-Min Kim
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Sylvia K Plevritis
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, USA
- Department of Radiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Michael P Snyder
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Brooke E Howitt
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.
| | - Livnat Jerby
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
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19
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Hossain SM, Ly K, Sung YJ, Braithwaite A, Li K. Immune Checkpoint Inhibitor Therapy for Metastatic Melanoma: What Should We Focus on to Improve the Clinical Outcomes? Int J Mol Sci 2024; 25:10120. [PMID: 39337605 PMCID: PMC11432671 DOI: 10.3390/ijms251810120] [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: 06/05/2024] [Revised: 09/16/2024] [Accepted: 09/17/2024] [Indexed: 09/30/2024] Open
Abstract
Immune checkpoint inhibitors (ICIs) have transformed cancer treatment by enhancing anti-tumour immune responses, demonstrating significant efficacy in various malignancies, including melanoma. However, over 50% of patients experience limited or no response to ICI therapy. Resistance to ICIs is influenced by a complex interplay of tumour intrinsic and extrinsic factors. This review summarizes current ICIs for melanoma and the factors involved in resistance to the treatment. We also discuss emerging evidence that the microbiota can impact ICI treatment outcomes by modulating tumour biology and anti-tumour immune function. Furthermore, microbiota profiles may offer a non-invasive method for predicting ICI response. Therefore, future research into microbiota manipulation could provide cost-effective strategies to enhance ICI efficacy and improve outcomes for melanoma patients.
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Affiliation(s)
- Sultana Mehbuba Hossain
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin 9016, New Zealand
| | - Kevin Ly
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin 9016, New Zealand
| | - Yih Jian Sung
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin 9016, New Zealand
| | - Antony Braithwaite
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin 9016, New Zealand
| | - Kunyu Li
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin 9016, New Zealand
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20
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Li S, Liang X, Shao Q, Wang G, Huang Y, Wen P, Jiang D, Zeng X. Research hotspots and trends of epigenetic therapy in oncology: a bibliometric analysis from 2004 to 2023. Front Pharmacol 2024; 15:1465954. [PMID: 39329125 PMCID: PMC11424529 DOI: 10.3389/fphar.2024.1465954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2024] [Accepted: 08/30/2024] [Indexed: 09/28/2024] Open
Abstract
Background Epigenetics denotes heritable alterations in gene expression patterns independent of changes in DNA sequence. Epigenetic therapy seeks to reprogram malignant cells to a normal phenotype and has been extensively investigated in oncology. This study conducts a bibliometric analysis of epigenetic therapy in cancer, providing a comprehensive overview of current research, identifying trends, and highlighting key areas of investigation. Methods Publications concerning epigenetic inhibitors in cancer spanning 2004 to 2023 were retrieved from the Web of Science Core Collection (WoSCC). Co-occurrence analysis using VOSviewer assessed current status and focal points. Evolutionary trends and bursts in the knowledge domain were analyzed using CiteSpace. Bibliometrix facilitated topic evolution and revealed trends in keywords. National, institutional, and author affiliations and collaborations were also examined. Results A total of 2,153 articles and reviews on epigenetic therapy in oncology were identified, demonstrating a consistent upward trend over time. The United States (745 papers), University of Texas MD Anderson Cancer Center (57 papers), and Stephen B. Baylin (27 papers) emerged as the most productive country, institution, and author, respectively. Keyword co-occurrence analysis identified five primary clusters: tumor, DNA methylation, epigenetic therapy, expression, and immunotherapy. In the past 5 years, newly emerging themes with increased centrality and density include "drug resistance," "immunotherapy," and "combination therapy." The most cited publication reviewed current understanding of potential causes of epigenetic diseases and proposed future therapeutic strategies. Conclusion In the past two decades, the importance of epigenetic therapy in cancer research has become increasingly prominent. The United States occupies a key position in this field, while China, despite having published a large number of related papers, still has relatively limited influence. Current research focuses on the "combination therapy" of epigenetic drugs. Future studies should further explore the sequencing and scheduling of combination therapies, optimize trial designs and dosing regimens to improve clinical efficacy.
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Affiliation(s)
- Sisi Li
- Department of Breast Cancer Center, Chongqing University Cancer Hospital, Chongqing, China
- Chongqing Key Laboratory for Intelligent Oncology in Breast Cancer (iCQBC), Chongqing University Cancer Hospital, Chongqing, China
| | - Xinrui Liang
- Department of Breast Cancer Center, Chongqing University Cancer Hospital, Chongqing, China
| | - Qing Shao
- Department of Breast Cancer Center, Chongqing University Cancer Hospital, Chongqing, China
- Chongqing Key Laboratory for Intelligent Oncology in Breast Cancer (iCQBC), Chongqing University Cancer Hospital, Chongqing, China
| | - Guanwen Wang
- Department of Breast Cancer Center, Chongqing University Cancer Hospital, Chongqing, China
- Chongqing Key Laboratory for Intelligent Oncology in Breast Cancer (iCQBC), Chongqing University Cancer Hospital, Chongqing, China
| | - Yuxin Huang
- School of Medicine, Chongqing University, Chongqing, China
| | - Ping Wen
- School of Medicine, Chongqing University, Chongqing, China
| | - Dongping Jiang
- School of Medicine, Chongqing University, Chongqing, China
| | - Xiaohua Zeng
- Department of Breast Cancer Center, Chongqing University Cancer Hospital, Chongqing, China
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21
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Mombach DM, Mercuri RLV, da Fontoura Gomes TMF, Galante PAF, Loreto ELS. Transposable elements alter gene expression and may impact response to cisplatin therapy in ovarian cancer. Carcinogenesis 2024; 45:685-695. [PMID: 38722203 DOI: 10.1093/carcin/bgae029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 03/25/2024] [Accepted: 05/08/2024] [Indexed: 09/12/2024] Open
Abstract
Cisplatin is widely employed for cancer treatment; therefore, understanding resistance to this drug is critical for therapeutic practice. While studies have delved into differential gene expression in the context of cisplatin resistance, findings remain somewhat scant. We performed a comprehensive investigation of transposable elements (TEs) expression and their impact in host genes in two cisplatin-treated ovarian cancer cell lines. RNA-seq, ATAC-seq, and in-depth bioinformatics analysis were used to compare cisplatin-sensitive and -resistant ovarian cancer cell lines. Our results reveal that cisplatin therapy alters not only the expression of protein-coding genes, but also key TEs, including LINE1, Alu, and endogenous retroviruses, in both cisplatin-sensitive and -resistant cell lines. By co-expressing with downstream genes or by creating chimeric transcripts with host genes at their insertion sites, these TEs seem to control the expression of protein-coding genes, including tumor-related genes. Our model uncovers TEs influencing the expression of cancer genes and cancer pathways. Collectively, our findings indicate that TE alterations associated with cisplatin treatment occur in critical cancer genes and cellular pathways synergically. This research highlights the importance of considering the entire spectrum of transcribed elements in the genome, especially TE expression, for a complete understanding of complex models like cancer response to treatment.
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Affiliation(s)
- Daniela Moreira Mombach
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Rafael Luiz Vieira Mercuri
- Hospital Sírio-Libanês, São Paulo, São Paulo, Brazil
- Interunidades em Bioinformática, Universidade de São Paulo, São Paulo, Brazil
| | | | | | - Elgion Lucio Silva Loreto
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Santa Maria, Santa Maria, Rio Grande do Sul, Brazil
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22
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Pospiech M, Beckford J, Kumar AMS, Tamizharasan M, Brito J, Liang G, Mangul S, Alachkar H. The DNA methylation landscape across the TCR loci in patients with acute myeloid leukemia. Int Immunopharmacol 2024; 138:112376. [PMID: 38917523 DOI: 10.1016/j.intimp.2024.112376] [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: 02/06/2024] [Revised: 05/09/2024] [Accepted: 05/28/2024] [Indexed: 06/27/2024]
Abstract
The capacity of T cells to initiate anti-leukemia immune responses is determined by the ability of their receptors (TCRs) to recognize leukemia neoantigens. Epigenetic mechanisms including DNA methylation contribute to shaping the TCR repertoire composition and diversity. The DNA hypomethylating agents (HMAs) have been widely used in the treatment of acute myeloid leukemia (AML) and myelodysplastic syndrome (MDS). Whether DNA HMAs directly influence TCR gene loci methylation patterns remains unknown. By analyzing public datasets, we compared methylation patterns across TCR loci in AML patients and healthy controls. We also explored how HMAs influence TCR loci DNA methylation in patients with AML. While methylation patterns are largely conserved across the TCR loci, certain V genes exhibit high interindividual variability. Although overall methylation levels within the TCR loci did not show significant differences, specific sites, including 32 TRAV and 12 TRBV sites exhibited distinct methylation patterns when comparing T cells from healthy donors to those from patients with AML. In leukemic cells, decitabine treatment demethylates sites across the TRAV and TRBV genes. While not as significant, a similar pattern of demethylation is observed in T cells. Pretreatment AML samples exhibit higher methylation beta values in differentially methylated positions (DMPs) compared with non-DMPs. Methylation levels of certain TRAV and TRBV genes in leukemic cells are associated with patients' risk status. The presence of disease specific TCR loci methylated signatures that are associated with clinical outcome presents an opportunity for therapeutic intervention. HMAs can modulate the TCR loci methylation patterns, yet whether they could reprogram the TCR repertoire composition remains to be explored.
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MESH Headings
- Humans
- DNA Methylation
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/drug therapy
- Leukemia, Myeloid, Acute/immunology
- Decitabine/pharmacology
- Decitabine/therapeutic use
- Receptors, Antigen, T-Cell/genetics
- T-Lymphocytes/immunology
- Epigenesis, Genetic
- Antimetabolites, Antineoplastic/therapeutic use
- Antimetabolites, Antineoplastic/pharmacology
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Affiliation(s)
- Mateusz Pospiech
- Department of Clinical Pharmacy, USC Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA, the United States of America
| | - John Beckford
- Department of Clinical Pharmacy, USC Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA, the United States of America
| | - Advaith Maya Sanjeev Kumar
- Department of Clinical Pharmacy, USC Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA, the United States of America; Department of Computer Science, University of Southern California, Los Angeles, CA, the United States of America
| | - Mukund Tamizharasan
- Department of Clinical Pharmacy, USC Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA, the United States of America; Department of Computer Science, University of Southern California, Los Angeles, CA, the United States of America
| | - Jaqueline Brito
- Department of Clinical Pharmacy, USC Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA, the United States of America
| | - Gangning Liang
- Department of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA, the United States of America
| | - Serghei Mangul
- Department of Clinical Pharmacy, USC Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA, the United States of America
| | - Houda Alachkar
- Department of Clinical Pharmacy, USC Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA, the United States of America.
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23
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Dang T, Guan X, Cui L, Ruan Y, Chen Z, Zou H, Lan Y, Liu C, Zhang Y. Epigenetics and immunotherapy in colorectal cancer: progress and promise. Clin Epigenetics 2024; 16:123. [PMID: 39252116 PMCID: PMC11385519 DOI: 10.1186/s13148-024-01740-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 09/02/2024] [Indexed: 09/11/2024] Open
Abstract
Colorectal cancer (CRC) is a common malignant tumor with the third and second highest incidence and mortality rates among various malignant tumors. Despite significant advancements in the present therapy for CRC, the majority of CRC cases feature proficient mismatch repair/microsatellite stability and have no response to immunotherapy. Therefore, the search for new treatment options holds immense importance in the diagnosis and treatment of CRC. In recent years, clinical research on immunotherapy combined with epigenetic therapy has gradually increased, which may bring hope for these patients. This review explores the role of epigenetic regulation in exerting antitumor effects through its action on immune cell function and highlights the potential of certain epigenetic genes that can be used as markers of immunotherapy to predict therapeutic efficacy. We also discuss the application of epigenetic drug sensitization immunotherapy to develop new treatment options combining epigenetic therapy and immunotherapy.
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Affiliation(s)
- Tianjiao Dang
- Department of Gastrointestinal Medical Oncology, Harbin Medical University Cancer Hospital, 150 Haping Road, Harbin, 150001, Heilongjiang, People's Republic of China
- Key Laboratory of Tumor Immunology in Heilongjiang, Harbin, China
- Clinical Research Center for Colorectal Cancer in Heilongjiang, Harbin, China
| | - Xin Guan
- Department of Gastrointestinal Medical Oncology, Harbin Medical University Cancer Hospital, 150 Haping Road, Harbin, 150001, Heilongjiang, People's Republic of China
- Key Laboratory of Tumor Immunology in Heilongjiang, Harbin, China
- Clinical Research Center for Colorectal Cancer in Heilongjiang, Harbin, China
| | - Luying Cui
- Department of Gastrointestinal Medical Oncology, Harbin Medical University Cancer Hospital, 150 Haping Road, Harbin, 150001, Heilongjiang, People's Republic of China
- Key Laboratory of Tumor Immunology in Heilongjiang, Harbin, China
- Clinical Research Center for Colorectal Cancer in Heilongjiang, Harbin, China
| | - Yuli Ruan
- Department of Gastrointestinal Medical Oncology, Harbin Medical University Cancer Hospital, 150 Haping Road, Harbin, 150001, Heilongjiang, People's Republic of China
- Key Laboratory of Tumor Immunology in Heilongjiang, Harbin, China
- Clinical Research Center for Colorectal Cancer in Heilongjiang, Harbin, China
| | - Zhuo Chen
- Department of Gastrointestinal Medical Oncology, Harbin Medical University Cancer Hospital, 150 Haping Road, Harbin, 150001, Heilongjiang, People's Republic of China
| | - Haoyi Zou
- Department of Gastrointestinal Medical Oncology, Harbin Medical University Cancer Hospital, 150 Haping Road, Harbin, 150001, Heilongjiang, People's Republic of China
- Key Laboratory of Tumor Immunology in Heilongjiang, Harbin, China
- Clinical Research Center for Colorectal Cancer in Heilongjiang, Harbin, China
| | - Ya Lan
- Department of Gastrointestinal Medical Oncology, Harbin Medical University Cancer Hospital, 150 Haping Road, Harbin, 150001, Heilongjiang, People's Republic of China
| | - Chao Liu
- Department of Gastrointestinal Medical Oncology, Harbin Medical University Cancer Hospital, 150 Haping Road, Harbin, 150001, Heilongjiang, People's Republic of China.
- Key Laboratory of Tumor Immunology in Heilongjiang, Harbin, China.
- Clinical Research Center for Colorectal Cancer in Heilongjiang, Harbin, China.
| | - Yanqiao Zhang
- Department of Gastrointestinal Medical Oncology, Harbin Medical University Cancer Hospital, 150 Haping Road, Harbin, 150001, Heilongjiang, People's Republic of China.
- Key Laboratory of Tumor Immunology in Heilongjiang, Harbin, China.
- Clinical Research Center for Colorectal Cancer in Heilongjiang, Harbin, China.
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24
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Hojjatipour T, Ajeli M, Maali A, Azad M. Epigenetic-modifying agents: The potential game changers in the treatment of hematologic malignancies. Crit Rev Oncol Hematol 2024; 204:104498. [PMID: 39244179 DOI: 10.1016/j.critrevonc.2024.104498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2024] [Revised: 08/27/2024] [Accepted: 08/30/2024] [Indexed: 09/09/2024] Open
Abstract
Hematologic malignancies are lethal diseases arising from accumulated leukemic cells with substantial genetic or epigenetic defects in their natural development. Epigenetic modifications, including DNA methylation and histone modifications, are critical in hematologic malignancy formation, propagation, and treatment response. Both mutations and aberrant recruitment of epigenetic modifiers are reported in different hematologic malignancies, which regarding the reversible nature of epigenetic regulations, make them a potential target for cancer treatment. Here, we have first outlined a comprehensive overview of current knowledge related to epigenetic regulation's impact on the development and prognosis of hematologic malignancies. Furthermore, we have presented an updated overview regarding the current status of epigenetic-based drugs in hematologic malignancies treatment. And finally, discuss current challenges and ongoing clinical trials based on the manipulation of epigenetic modifies in hematologic malignancies.
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Affiliation(s)
- Tahereh Hojjatipour
- Cancer Immunology Group, School of Medicine, University of Nottingham Biodiscovery Institute, Nottingham, United Kingdom
| | - Mina Ajeli
- Department of Medical Laboratory Sciences, Guilan University of Medical Sciences, Guilan, Iran
| | - Amirhosein Maali
- Department of Immunology, Pasteur Institute of Iran, Tehran, Iran; Department of Medical Biotechnology, Faculty of Allied Medicine, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Mehdi Azad
- Department of Medical Laboratory Sciences, School of Paramedicine, Qazvin University of Medical Sciences, Qazvin, Iran.
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25
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Galassi C, Esteller M, Vitale I, Galluzzi L. Epigenetic control of immunoevasion in cancer stem cells. Trends Cancer 2024:S2405-8033(24)00171-7. [PMID: 39244477 DOI: 10.1016/j.trecan.2024.08.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Revised: 07/24/2024] [Accepted: 08/12/2024] [Indexed: 09/09/2024]
Abstract
Cancer stem cells (CSCs) are a poorly differentiated population of malignant cells that (at least in some neoplasms) is responsible for tumor progression, resistance to therapy, and disease relapse. According to a widely accepted model, all stages of cancer progression involve the ability of neoplastic cells to evade recognition or elimination by the host immune system. In line with this notion, CSCs are not only able to cope with environmental and therapy-elicited stress better than their more differentiated counterparts but also appear to better evade tumor-targeting immune responses. We summarize epigenetic modifications of DNA and histones through which CSCs evade immune recognition or elimination, and propose that such alterations constitute promising therapeutic targets to increase the sensitivity of some malignancies to immunotherapy.
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Affiliation(s)
- Claudia Galassi
- Department of Radiation Oncology, Weill Cornell Medical College, New York, NY, USA
| | - Manel Esteller
- Cancer Epigenetics Group, Josep Carreras Leukaemia Research Institute (IJC), Barcelona, Spain; Centro de Investigacion Biomedica en Red Cancer (CIBERONC), Madrid, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain; Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona (UB), Barcelona, Catalonia, Spain
| | - Ilio Vitale
- Italian Institute for Genomic Medicine, Istituto di Ricovero e Cura a Carattere Scientifico (IRCSS) Candiolo, Torino, Italy; Candiolo Cancer Institute, FPO - IRCCS, Candiolo, Italy.
| | - Lorenzo Galluzzi
- Department of Radiation Oncology, Weill Cornell Medical College, New York, NY, USA; Sandra and Edward Meyer Cancer Center, New York, NY, USA; Caryl and Israel Englander Institute for Precision Medicine, New York, NY, USA.
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26
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Young AA, Bohlin HE, Pierce JR, Cottrell KA. Suppression of double-stranded RNA sensing in cancer: molecular mechanisms and therapeutic potential. Biochem Soc Trans 2024:BST20230727. [PMID: 39221819 DOI: 10.1042/bst20230727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2024] [Revised: 08/15/2024] [Accepted: 08/20/2024] [Indexed: 09/04/2024]
Abstract
Immunotherapy has emerged as a therapeutic option for many cancers. For some tumors, immune checkpoint inhibitors show great efficacy in promoting anti-tumor immunity. However, not all tumors respond to immunotherapies. These tumors often exhibit reduced inflammation and are resistant to checkpoint inhibitors. Therapies that turn these 'cold' tumors 'hot' could improve the efficacy and applicability of checkpoint inhibitors, and in some cases may be sufficient on their own to promote anti-tumor immunity. One strategy to accomplish this goal is to activate innate immunity pathways within the tumor. Here we describe how this can be accomplished by activating double-stranded RNA (dsRNA) sensors. These sensors evolved to detect and respond to dsRNAs arising from viral infection but can also be activated by endogenous dsRNAs. A set of proteins, referred to as suppressors of dsRNA sensing, are responsible for preventing sensing 'self' dsRNA and activating innate immunity pathways. The mechanism of action of these suppressors falls into three categories: (1) Suppressors that affect mature RNAs through editing, degradation, restructuring, or binding. (2) Suppressors that affect RNA processing. (3) Suppressors that affect RNA expression. In this review we highlight suppressors that function through each mechanism, provide examples of the effects of disrupting those suppressors in cancer cell lines and tumors, and discuss the therapeutic potential of targeting these proteins and pathways.
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Affiliation(s)
- Addison A Young
- Department of Biochemistry, Purdue University, West Lafayette, IN, U.S.A
| | - Holly E Bohlin
- Department of Biochemistry, Purdue University, West Lafayette, IN, U.S.A
| | - Jackson R Pierce
- Department of Biochemistry, Purdue University, West Lafayette, IN, U.S.A
| | - Kyle A Cottrell
- Department of Biochemistry, Purdue University, West Lafayette, IN, U.S.A
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27
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Su P, Liu Y, Chen T, Xue Y, Zeng Y, Zhu G, Chen S, Teng M, Ci X, Guo M, He MY, Hao J, Chu V, Xu W, Wang S, Mehdipour P, Xu X, Marhon SA, Soares F, Pham NA, Wu BX, Her PH, Feng S, Alshamlan N, Khalil M, Krishnan R, Yu F, Chen C, Burrows F, Hakem R, Lupien M, Harding S, Lok BH, O'Brien C, Berlin A, De Carvalho DD, Brooks DG, Schramek D, Tsao MS, He HH. In vivo CRISPR screens identify a dual function of MEN1 in regulating tumor-microenvironment interactions. Nat Genet 2024; 56:1890-1902. [PMID: 39227744 PMCID: PMC11387198 DOI: 10.1038/s41588-024-01874-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 07/18/2024] [Indexed: 09/05/2024]
Abstract
Functional genomic screens in two-dimensional cell culture models are limited in identifying therapeutic targets that influence the tumor microenvironment. By comparing targeted CRISPR-Cas9 screens in a two-dimensional culture with xenografts derived from the same cell line, we identified MEN1 as the top hit that confers differential dropout effects in vitro and in vivo. MEN1 knockout in multiple solid cancer types does not impact cell proliferation in vitro but significantly promotes or inhibits tumor growth in immunodeficient or immunocompetent mice, respectively. Mechanistically, MEN1 knockout redistributes MLL1 chromatin occupancy, increasing H3K4me3 at repetitive genomic regions, activating double-stranded RNA expression and increasing neutrophil and CD8+ T cell infiltration in immunodeficient and immunocompetent mice, respectively. Pharmacological inhibition of the menin-MLL interaction reduces tumor growth in a CD8+ T cell-dependent manner. These findings reveal tumor microenvironment-dependent oncogenic and tumor-suppressive functions of MEN1 and provide a rationale for targeting MEN1 in solid cancers.
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Affiliation(s)
- Peiran Su
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Yin Liu
- Department of Laboratory Medicine, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Tianyi Chen
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Yibo Xue
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Yong Zeng
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Guanghui Zhu
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- West China School of Public Health and West China Fourth Hospital, and State Key Laboratory of Biotherapy, Sichuan University, Chengdu, China
| | - Sujun Chen
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- West China School of Public Health and West China Fourth Hospital, and State Key Laboratory of Biotherapy, Sichuan University, Chengdu, China
| | - Mona Teng
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Xinpei Ci
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Mengdi Guo
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Immunology, University of Toronto, Toronto, Ontario, Canada
| | - Michael Y He
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Jun Hao
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Vivian Chu
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Wenxi Xu
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Shiyan Wang
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Parinaz Mehdipour
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Xin Xu
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Sajid A Marhon
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Fraser Soares
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Nhu-An Pham
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Bell Xi Wu
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Peter Hyunwuk Her
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Shengrui Feng
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Najd Alshamlan
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Maryam Khalil
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Rehna Krishnan
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Fangyou Yu
- Department of Laboratory Medicine, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Chang Chen
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | | | - Razqallah Hakem
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Mathieu Lupien
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Shane Harding
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Benjamin H Lok
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Catherine O'Brien
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Alejandro Berlin
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Daniel D De Carvalho
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - David G Brooks
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Immunology, University of Toronto, Toronto, Ontario, Canada
| | - Daniel Schramek
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Ming-Sound Tsao
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada.
| | - Housheng Hansen He
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.
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28
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Jang HJ, Shah NM, Maeng JH, Liang Y, Basri NL, Ge J, Qu X, Mahlokozera T, Tzeng SC, Williams RB, Moore MJ, Annamalai D, Chen JY, Lee HJ, DeSouza PA, Li D, Xing X, Kim AH, Wang T. Epigenetic therapy potentiates transposable element transcription to create tumor-enriched antigens in glioblastoma cells. Nat Genet 2024; 56:1903-1913. [PMID: 39223316 DOI: 10.1038/s41588-024-01880-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 07/23/2024] [Indexed: 09/04/2024]
Abstract
Inhibiting epigenetic modulators can transcriptionally reactivate transposable elements (TEs). These TE transcripts often generate unique peptides that can serve as immunogenic antigens for immunotherapy. Here, we ask whether TEs activated by epigenetic therapy could appreciably increase the antigen repertoire in glioblastoma, an aggressive brain cancer with low mutation and neoantigen burden. We treated patient-derived primary glioblastoma stem cell lines, an astrocyte cell line and primary fibroblast cell lines with epigenetic drugs, and identified treatment-induced, TE-derived transcripts that are preferentially expressed in cancer cells. We verified that these transcripts could produce human leukocyte antigen class I-presented antigens using liquid chromatography with tandem mass spectrometry pulldown experiments. Importantly, many TEs were also transcribed, even in proliferating nontumor cell lines, after epigenetic therapy, which suggests that targeted strategies like CRISPR-mediated activation could minimize potential side effects of activating unwanted genomic regions. The results highlight both the need for caution and the promise of future translational efforts in harnessing treatment-induced TE-derived antigens for targeted immunotherapy.
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Affiliation(s)
- H Josh Jang
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
| | - Nakul M Shah
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Ju Heon Maeng
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Yonghao Liang
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Noah L Basri
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Jiaxin Ge
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Xuan Qu
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Tatenda Mahlokozera
- Department of Neurological Surgery, Washington University School of Medicine, St Louis, MO, USA
| | | | | | - Michael J Moore
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Devi Annamalai
- Department of Neurological Surgery, Washington University School of Medicine, St Louis, MO, USA
| | - Justin Y Chen
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Hyung Joo Lee
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Patrick A DeSouza
- Department of Neurological Surgery, Washington University School of Medicine, St Louis, MO, USA
| | - Daofeng Li
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Xiaoyun Xing
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Albert H Kim
- Department of Neurological Surgery, Washington University School of Medicine, St Louis, MO, USA.
- The Brain Tumor Center, Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA.
| | - Ting Wang
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA.
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA.
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA.
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29
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Kwok DW, Okada H, Costello JF. Activating the dark genome to illuminate cancer vaccine targets. Nat Genet 2024; 56:1770-1771. [PMID: 39223317 PMCID: PMC11456370 DOI: 10.1038/s41588-024-01850-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Epigenetic therapy awakens myriad transposable elements to generate new antigens that could prime tumor cells for immunotherapy. A new study of glioblastoma discovers indiscriminate awakening in normal cells also and then presents a more selective strategy for potential therapeutic targeting.
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Affiliation(s)
- Darwin W Kwok
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Hideho Okada
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA.
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA.
| | - Joseph F Costello
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA.
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30
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Flynn A, Waszak SM, Weischenfeldt J. Somatic CpG hypermutation is associated with mismatch repair deficiency in cancer. Mol Syst Biol 2024; 20:1006-1024. [PMID: 39026103 PMCID: PMC11369196 DOI: 10.1038/s44320-024-00054-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 06/17/2024] [Accepted: 06/28/2024] [Indexed: 07/20/2024] Open
Abstract
Somatic hypermutation in cancer has gained momentum with the increased use of tumour mutation burden as a biomarker for immune checkpoint inhibitors. Spontaneous deamination of 5-methylcytosine to thymine at CpG dinucleotides is one of the most ubiquitous endogenous mutational processes in normal and cancer cells. Here, we performed a systematic investigation of somatic CpG hypermutation at a pan-cancer level. We studied 30,191 cancer patients and 103 cancer types and developed an algorithm to identify somatic CpG hypermutation. Across cancer types, we observed the highest prevalence in paediatric leukaemia (3.5%), paediatric high-grade glioma (1.7%), and colorectal cancer (1%). We discovered germline variants and somatic mutations in the mismatch repair complex MutSα (MSH2-MSH6) as genetic drivers of somatic CpG hypermutation in cancer, which frequently converged on CpG sites and TP53 driver mutations. We further observe an association between somatic CpG hypermutation and response to immune checkpoint inhibitors. Overall, our study identified novel cancer types that display somatic CpG hypermutation, strong association with MutSα-deficiency, and potential utility in cancer immunotherapy.
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Affiliation(s)
- Aidan Flynn
- Biotech Research & Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
- The Finsen Laboratory, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
- Department of Clinical Pathology and Centre for Cancer Research, University of Melbourne, Parkville, VIC, Australia
| | - Sebastian M Waszak
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
- Centre for Molecular Medicine Norway, Nordic EMBL Partnership, University of Oslo and Oslo University Hospital, Oslo, Norway.
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA.
| | - Joachim Weischenfeldt
- Biotech Research & Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark.
- The Finsen Laboratory, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark.
- The DCCC Brain Tumor Center, Danish Comprehensive Cancer Center, Copenhagen, Denmark.
- Department of Urology, Charité University Hospital, Berlin, Germany.
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31
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Wang ZY, Ge LP, Ouyang Y, Jin X, Jiang YZ. Targeting transposable elements in cancer: developments and opportunities. Biochim Biophys Acta Rev Cancer 2024; 1879:189143. [PMID: 38936517 DOI: 10.1016/j.bbcan.2024.189143] [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: 12/07/2023] [Revised: 05/23/2024] [Accepted: 06/19/2024] [Indexed: 06/29/2024]
Abstract
Transposable elements (TEs), comprising nearly 50% of the human genome, have transitioned from being perceived as "genomic junk" to key players in cancer progression. Contemporary research links TE regulatory disruptions with cancer development, underscoring their therapeutic potential. Advances in long-read sequencing, computational analytics, single-cell sequencing, proteomics, and CRISPR-Cas9 technologies have enriched our understanding of TEs' clinical implications, notably their impact on genome architecture, gene regulation, and evolutionary processes. In cancer, TEs, including long interspersed element-1 (LINE-1), Alus, and long terminal repeat (LTR) elements, demonstrate altered patterns, influencing both tumorigenic and tumor-suppressive mechanisms. TE-derived nucleic acids and tumor antigens play critical roles in tumor immunity, bridging innate and adaptive responses. Given their central role in oncology, TE-targeted therapies, particularly through reverse transcriptase inhibitors and epigenetic modulators, represent a novel avenue in cancer treatment. Combining these TE-focused strategies with existing chemotherapy or immunotherapy regimens could enhance efficacy and offer a new dimension in cancer treatment. This review delves into recent TE detection advancements, explores their multifaceted roles in tumorigenesis and immune regulation, discusses emerging diagnostic and therapeutic approaches centered on TEs, and anticipates future directions in cancer research.
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Affiliation(s)
- Zi-Yu Wang
- Department of Breast Surgery, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Li-Ping Ge
- Department of Breast Surgery, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Yang Ouyang
- Department of Breast Surgery, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Xi Jin
- Department of Breast Surgery, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Yi-Zhou Jiang
- Department of Breast Surgery, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China.
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32
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Gualandi N, Minisini M, Bertozzo A, Brancolini C. Dissecting transposable elements and endogenous retroviruses upregulation by HDAC inhibitors in leiomyosarcoma cells: Implications for the interferon response. Genomics 2024; 116:110909. [PMID: 39103003 DOI: 10.1016/j.ygeno.2024.110909] [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: 04/04/2024] [Revised: 07/22/2024] [Accepted: 07/31/2024] [Indexed: 08/07/2024]
Abstract
Transposable elements (TEs) are of interest as immunomodulators for cancer therapies. TEs can fold into dsRNAs that trigger the interferon response. Here, we investigated the effect of different HDAC inhibitors (HDACIs) on the expression of TEs in leiomyosarcoma cells. Our data show that endogenous retroviruses (ERVs), especially ERV1 elements, are upregulated after treatment with HDAC1/2/3-specific inhibitors. Surprisingly, the interferon response was not activated. We observed an increase in A-to-I editing of upregulated ERV1. This could have an impact on the stability of dsRNAs and the activation of the interferon response. We also found that H3K27ac levels are increased in the LTR12 subfamilies, which could be regulatory elements controlling the expression of proapoptotic genes such as TNFRSF10B. In summary, we provide a detailed characterization of TEs modulation in response to HDACIs and suggest the use of HDACIs in combination with ADAR inhibitors to induce cell death and support immunotherapy in cancer.
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Affiliation(s)
- Nicolò Gualandi
- Department of Medicine, Università degli Studi di Udine, P.le Kolbe 4, 33100 Udine, Italy
| | - Martina Minisini
- Department of Medicine, Università degli Studi di Udine, P.le Kolbe 4, 33100 Udine, Italy
| | - Alessio Bertozzo
- Department of Medicine, Università degli Studi di Udine, P.le Kolbe 4, 33100 Udine, Italy
| | - Claudio Brancolini
- Department of Medicine, Università degli Studi di Udine, P.le Kolbe 4, 33100 Udine, Italy.
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33
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Flanagan L, Coughlan A, Cosgrove N, Roe A, Wang Y, Gilmore S, Drozdz I, Comerford C, Ryan J, Minihane E, Parvin S, O'Dwyer M, Quinn J, Murphy P, Furney S, Glavey S, Chonghaile TN, Foundation LR, Ireland SF, Research BC. Steroid-free combination of 5-azacytidine and venetoclax for the treatment of multiple myeloma. Haematologica 2024; 109:2930-2943. [PMID: 38511268 PMCID: PMC11367189 DOI: 10.3324/haematol.2023.283771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Indexed: 03/22/2024] Open
Abstract
Multiple myeloma (MM) is an incurable plasma cell malignancy that, despite an unprecedented increase in overall survival, lacks truly risk-adapted or targeted treatments. A proportion of patients with MM depend on BCL-2 for survival, and, recently, the BCL-2 antagonist venetoclax has shown clinical efficacy and safety in t(11;14) and BCL-2 overexpressing MM. However, only a small proportion of MM patients rely on BCL-2 (approx. 20%), and there is a need to broaden the patient population outside of t(11;14) that can be treated with venetoclax. Therefore, we took an unbiased screening approach and screened epigenetic modifiers to enhance venetoclax sensitivity in 2 non-BCL-2 dependent MM cell lines. The demethylase inhibitor 5-azacytidine was one of the lead hits from the screen, and the enhanced cell killing of the combination was confirmed in additional MM cell lines. Using dynamic BH3 profiling and immunoprecipitations, we identified the potential mechanism of synergy is due to increased NOXA expression, through the integrated stress response. Knockdown of PMAIP1 or PKR partially rescues cell death of the venetoclax and 5-azacytidine combination treatment. The addition of a steroid to the combination treatment did not enhance the cell death, and, interestingly, we found enhanced death of the immune cells with steroid addition, suggesting that a steroid-sparing regimen may be more beneficial in MM. Lastly, we show for the first time in primary MM patient samples that 5-azacytidine enhances the response to venetoclax ex vivo across diverse anti-apoptotic dependencies (BCL-2 or MCL-1) and diverse cytogenetic backgrounds. Overall, our data identify 5-azacytidine and venetoclax as an effective treatment combination, which could be a tolerable steroid-sparing regimen, particularly for elderly MM patients.
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Affiliation(s)
- Lyndsey Flanagan
- Physiology and Medical Physics, Royal College of Surgeons in Ireland, 123 St. Stephen's Green, Dublin 2
| | - Aisling Coughlan
- Physiology and Medical Physics, Royal College of Surgeons in Ireland, 123 St. Stephen's Green, Dublin 2
| | - Nicola Cosgrove
- Physiology and Medical Physics, Royal College of Surgeons in Ireland, 123 St. Stephen's Green, Dublin 2
| | - Andrew Roe
- Physiology and Medical Physics, Royal College of Surgeons in Ireland, 123 St. Stephen's Green, Dublin 2
| | - Yu Wang
- Physiology and Medical Physics, Royal College of Surgeons in Ireland, 123 St. Stephen's Green, Dublin 2
| | - Stephanie Gilmore
- Physiology and Medical Physics, Royal College of Surgeons in Ireland, 123 St. Stephen's Green, Dublin 2
| | - Izabela Drozdz
- Department of Pathology, Royal College of Surgeons in Ireland
| | - Claire Comerford
- Department of Pathology, Royal College of Surgeons in Ireland; Department of Haematology, Beaumont Hospital, Dublin
| | - Jeremy Ryan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Emma Minihane
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Salma Parvin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Michael O'Dwyer
- Department of Medicine/Haematology, University of Galway, Galway
| | - John Quinn
- Department of Pathology, Royal College of Surgeons in Ireland; Department of Haematology, Beaumont Hospital, Dublin
| | - Philip Murphy
- Department of Pathology, Royal College of Surgeons in Ireland; Department of Haematology, Beaumont Hospital, Dublin
| | - Simon Furney
- Physiology and Medical Physics, Royal College of Surgeons in Ireland, 123 St. Stephen's Green, Dublin 2
| | - Siobhan Glavey
- Department of Pathology, Royal College of Surgeons in Ireland; Department of Haematology, Beaumont Hospital, Dublin
| | - Tríona Ní Chonghaile
- Physiology and Medical Physics, Royal College of Surgeons in Ireland, 123 St. Stephen's Green, Dublin 2.
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Miglietta G, Russo M, Capranico G, Marinello J. Stimulation of cGAS-STING pathway as a challenge in the treatment of small cell lung cancer: a feasible strategy? Br J Cancer 2024:10.1038/s41416-024-02821-5. [PMID: 39215193 DOI: 10.1038/s41416-024-02821-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 08/03/2024] [Accepted: 08/06/2024] [Indexed: 09/04/2024] Open
Abstract
Lung cancer has a significant incidence among the population and, unfortunately, has an unfavourable prognosis in most cases. The World Health Organization (WHO) classifies lung tumours into two subtypes based on their phenotype: the Non-Small Cell Lung Cancer (NSCLC) and the Small Cell Lung Cancer (SCLC). SCLC treatment, despite advances in chemotherapy and radiotherapy, is often unsuccessful for cancer recurrence highlighting the need to develop novel therapeutic strategies. In this review, we describe the genetic landscape and tumour microenvironment that characterize the pathological processes of SCLC and how they are responsible for tumour immune evasion. The immunosuppressive mechanisms engaged in SCLC are critical factors to understand the failure of immunotherapy in SCLC and, conversely, suggest that new signalling pathways, such as cGAS/STING, should be investigated as possible targets to stimulate an innate immune response in this subtype of lung cancer. The full comprehension of the innate immunity of cancer cells is thus crucial to open new challenges for successful immunotherapy in treating SCLC and improving patient outcomes.
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Affiliation(s)
- Giulia Miglietta
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum-University of Bologna, Bologna, Italy
| | - Marco Russo
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum-University of Bologna, Bologna, Italy
| | - Giovanni Capranico
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum-University of Bologna, Bologna, Italy.
| | - Jessica Marinello
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum-University of Bologna, Bologna, Italy.
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Trovato M, Bunina D, Yildiz U, Fernandez-Novel Marx N, Uckelmann M, Levina V, Perez Y, Janeva A, Garcia BA, Davidovich C, Zaugg JB, Noh KM. Histone H3.3 lysine 9 and 27 control repressive chromatin at cryptic enhancers and bivalent promoters. Nat Commun 2024; 15:7557. [PMID: 39214979 PMCID: PMC11364623 DOI: 10.1038/s41467-024-51785-w] [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: 04/26/2023] [Accepted: 08/15/2024] [Indexed: 09/04/2024] Open
Abstract
Histone modifications are associated with distinct transcriptional states, but it is unclear whether they instruct gene expression. To investigate this, we mutate histone H3.3 K9 and K27 residues in mouse embryonic stem cells (mESCs). Here, we find that H3.3K9 is essential for controlling specific distal intergenic regions and for proper H3K27me3 deposition at promoters. The H3.3K9A mutation resulted in decreased H3K9me3 at regions encompassing endogenous retroviruses and induced a gain of H3K27ac and nascent transcription. These changes in the chromatin environment unleash cryptic enhancers, resulting in the activation of distinctive transcriptional programs and culminating in protein expression normally restricted to specialized immune cell types. The H3.3K27A mutant disrupts the deposition and spreading of the repressive H3K27me3 mark, particularly impacting bivalent genes with higher basal levels of H3.3 at promoters. Therefore, H3.3K9 and K27 crucially orchestrate repressive chromatin states at cis-regulatory elements and bivalent promoters, respectively, and instruct proper transcription in mESCs.
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Affiliation(s)
- Matteo Trovato
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
- Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany
| | - Daria Bunina
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
- European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Heidelberg, Germany
| | - Umut Yildiz
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
- Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany
| | | | - Michael Uckelmann
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, and EMBL-Australia, Clayton, VIC, Australia
| | - Vita Levina
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, and EMBL-Australia, Clayton, VIC, Australia
| | - Yekaterina Perez
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
| | - Ana Janeva
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Benjamin A Garcia
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
| | - Chen Davidovich
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, and EMBL-Australia, Clayton, VIC, Australia
| | - Judith B Zaugg
- European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Heidelberg, Germany
| | - Kyung-Min Noh
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany.
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36
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Truong P, Shen S, Joshi S, Islam MI, Zhong L, Raftery MJ, Afrasiabi A, Alinejad-Rokny H, Nguyen M, Zou X, Bhuyan GS, Sarowar CH, Ghodousi ES, Stonehouse O, Mohamed S, Toscan CE, Connerty P, Kakadia PM, Bohlander SK, Michie KA, Larsson J, Lock RB, Walkley CR, Thoms JAI, Jolly CJ, Pimanda JE. TOPORS E3 ligase mediates resistance to hypomethylating agent cytotoxicity in acute myeloid leukemia cells. Nat Commun 2024; 15:7360. [PMID: 39198401 PMCID: PMC11358519 DOI: 10.1038/s41467-024-51646-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Accepted: 08/14/2024] [Indexed: 09/01/2024] Open
Abstract
Hypomethylating agents (HMAs) are frontline therapies for Myelodysplastic Neoplasms (MDS) and Acute Myeloid Leukemia (AML). However, acquired resistance and treatment failure are commonplace. To address this, we perform a genome-wide CRISPR-Cas9 screen in a human MDS-derived cell line, MDS-L, and identify TOPORS as a loss-of-function target that synergizes with HMAs, reducing leukemic burden and improving survival in xenograft models. We demonstrate that depletion of TOPORS mediates sensitivity to HMAs by predisposing leukemic blasts to an impaired DNA damage response (DDR) accompanied by an accumulation of SUMOylated DNMT1 in HMA-treated TOPORS-depleted cells. The combination of HMAs with targeting of TOPORS does not impair healthy hematopoiesis. While inhibitors of TOPORS are unavailable, we show that inhibition of protein SUMOylation with TAK-981 partially phenocopies HMA-sensitivity and DDR impairment. Overall, our data suggest that the combination of HMAs with inhibition of SUMOylation or TOPORS is a rational treatment option for High-Risk MDS (HR-MDS) or AML.
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MESH Headings
- Humans
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/drug therapy
- Leukemia, Myeloid, Acute/pathology
- Leukemia, Myeloid, Acute/metabolism
- Animals
- Drug Resistance, Neoplasm/genetics
- Drug Resistance, Neoplasm/drug effects
- Cell Line, Tumor
- Mice
- Myelodysplastic Syndromes/drug therapy
- Myelodysplastic Syndromes/genetics
- Myelodysplastic Syndromes/pathology
- Myelodysplastic Syndromes/metabolism
- CRISPR-Cas Systems
- Sumoylation/drug effects
- Ubiquitin-Protein Ligases/metabolism
- Ubiquitin-Protein Ligases/genetics
- DNA Damage/drug effects
- DNA Methylation/drug effects
- Xenograft Model Antitumor Assays
- DNA (Cytosine-5-)-Methyltransferase 1/metabolism
- DNA (Cytosine-5-)-Methyltransferase 1/genetics
- DNA (Cytosine-5-)-Methyltransferase 1/antagonists & inhibitors
- Female
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Affiliation(s)
- Peter Truong
- School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Sydney, NSW, Australia
| | - Sylvie Shen
- School of Biomedical Sciences, UNSW Sydney, Sydney, NSW, Australia
| | - Swapna Joshi
- School of Biomedical Sciences, UNSW Sydney, Sydney, NSW, Australia
| | | | - Ling Zhong
- Bioanalytical Mass Spectrometry Facility, Mark Wainwright Analytical Centre, UNSW Sydney, Sydney, NSW, Australia
| | - Mark J Raftery
- Bioanalytical Mass Spectrometry Facility, Mark Wainwright Analytical Centre, UNSW Sydney, Sydney, NSW, Australia
| | - Ali Afrasiabi
- UNSW BioMedical Machine Learning Lab (BML), The Graduate School of Biomedical Engineering, UNSW Sydney, Sydney, NSW, Australia
| | - Hamid Alinejad-Rokny
- UNSW BioMedical Machine Learning Lab (BML), The Graduate School of Biomedical Engineering, UNSW Sydney, Sydney, NSW, Australia
- Tyree Institute of Health Engineering (IHealthE), UNSW Sydney, Sydney, NSW, Australia
| | - Mary Nguyen
- School of Biomedical Sciences, UNSW Sydney, Sydney, NSW, Australia
| | - Xiaoheng Zou
- School of Biomedical Sciences, UNSW Sydney, Sydney, NSW, Australia
| | | | | | - Elaheh S Ghodousi
- School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Sydney, NSW, Australia
| | | | - Sara Mohamed
- School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Sydney, NSW, Australia
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia
- UNSW Centre for Childhood Cancer Research, UNSW Sydney, Sydney, NSW, Australia
| | - Cara E Toscan
- School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Sydney, NSW, Australia
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia
- UNSW Centre for Childhood Cancer Research, UNSW Sydney, Sydney, NSW, Australia
| | - Patrick Connerty
- School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Sydney, NSW, Australia
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia
- UNSW Centre for Childhood Cancer Research, UNSW Sydney, Sydney, NSW, Australia
| | - Purvi M Kakadia
- Leukaemia and Blood Cancer Research Unit, Department of Molecular Medicine and Pathology, University of Auckland, Auckland, New Zealand
| | - Stefan K Bohlander
- Leukaemia and Blood Cancer Research Unit, Department of Molecular Medicine and Pathology, University of Auckland, Auckland, New Zealand
| | - Katharine A Michie
- Structural Biology Facility, Mark Wainwright Analytical Centre, UNSW Sydney, Sydney, NSW, Australia
| | - Jonas Larsson
- Division of Molecular Medicine and Gene Therapy, Lund Stem Cell Centre, Lund University, Lund, Sweden
| | - Richard B Lock
- School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Sydney, NSW, Australia
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia
- UNSW Centre for Childhood Cancer Research, UNSW Sydney, Sydney, NSW, Australia
| | - Carl R Walkley
- St Vincent's Institute of Medical Research, University of Melbourne, Melbourne, VIC, Australia
- Department of Medicine, University of Melbourne, Melbourne, VIC, Australia
| | - Julie A I Thoms
- School of Biomedical Sciences, UNSW Sydney, Sydney, NSW, Australia
| | | | - John E Pimanda
- School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Sydney, NSW, Australia.
- School of Biomedical Sciences, UNSW Sydney, Sydney, NSW, Australia.
- Haematology Department, Prince of Wales Hospital, Sydney, NSW, Australia.
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Jarosz AS, Halo JV. Transcription of Endogenous Retroviruses: Broad and Precise Mechanisms of Control. Viruses 2024; 16:1312. [PMID: 39205286 PMCID: PMC11359688 DOI: 10.3390/v16081312] [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: 06/24/2024] [Revised: 08/07/2024] [Accepted: 08/16/2024] [Indexed: 09/04/2024] Open
Abstract
Endogenous retroviruses (ERVs) are the remnants of retroviral germline infections and are highly abundant in the genomes of vertebrates. At one time considered to be nothing more than inert 'junk' within genomes, ERVs have been tolerated within host genomes over vast timescales, and their study continues to reveal complex co-evolutionary histories within their respective host species. For example, multiple instances have been characterized of ERVs having been 'borrowed' for normal physiology, from single copies to ones involved in various regulatory networks such as innate immunity and during early development. Within the cell, the accessibility of ERVs is normally tightly controlled by epigenetic mechanisms such as DNA methylation or histone modifications. However, these silencing mechanisms of ERVs are reversible, and epigenetic alterations to the chromatin landscape can thus lead to their aberrant expression, as is observed in abnormal cellular environments such as in tumors. In this review, we focus on ERV transcriptional control and draw parallels and distinctions concerning the loss of regulation in disease, as well as their precise regulation in early development.
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Affiliation(s)
- Abigail S. Jarosz
- Science and Mathematics Division, Lorrain County Community College, Lorrain, OH 44035, USA;
| | - Julia V. Halo
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH 43403, USA
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Cutts Z, Patterson S, Maliskova L, Taylor KE, Ye CJ, Dall'Era M, Yazdany J, Criswell LA, Fragiadakis GK, Langelier C, Capra JA, Sirota M, Lanata CM. Cell-Specific Transposable Element and Gene Expression Analysis Across Systemic Lupus Erythematosus Phenotypes. ACR Open Rheumatol 2024. [PMID: 39143499 DOI: 10.1002/acr2.11713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 03/06/2024] [Accepted: 06/04/2024] [Indexed: 08/16/2024] Open
Abstract
OBJECTIVE There is an established yet unexplained link between interferon (IFN) and systemic lupus erythematosus (SLE). The expression of sequences derived from transposable elements (TEs) may contribute to SLE phenotypes, specifically production of type I IFNs and generation of autoantibodies. METHODS We profiled cell-sorted RNA-sequencing data (CD4+ T cells, CD14+ monocytes, CD19+ B cells, and natural killer cells) from peripheral blood mononuclear cells of 120 patients with SLE and quantified TE expression identifying 27,135 TEs. We tested for differential TE expression across 10 SLE phenotypes, including autoantibody production and disease activity. RESULTS We found 731 differentially expressed (DE) TEs across all SLE phenotypes that were mostly cell specific and phenotype specific. DE TEs were enriched for specific families and open reading frames of viral genes encoded in TE sequences. Increased expression of DE TEs was associated with genes involved in antiviral activity, such as LY6E, ISG15, and TRIM22, and pathways such as IFN signaling. CONCLUSION These findings suggest that expression of TEs contributes to activation of SLE-related mechanisms in a cell-specific manner, which can impact disease diagnostics and therapeutics.
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Affiliation(s)
- Zachary Cutts
- University of California, San Francisco, San Francisco
| | | | | | | | | | | | | | | | | | | | - John A Capra
- University of California, San Francisco, San Francisco
| | - Marina Sirota
- University of California, San Francisco, San Francisco
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39
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Yang Z, Chu B, Tu Y, Li L, Chen D, Huang S, Huang W, Fan W, Li Q, Zhang C, Yuan Z, Huang J, Leung ELH, Jiang Y. Dual inhibitors of DNMT and HDAC remodels the immune microenvironment of colorectal cancer and enhances the efficacy of anti-PD-L1 therapy. Pharmacol Res 2024; 206:107271. [PMID: 38906202 DOI: 10.1016/j.phrs.2024.107271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 06/10/2024] [Accepted: 06/16/2024] [Indexed: 06/23/2024]
Abstract
Colorectal cancer is the second most prevalent and deadly cancer worldwide. The emergence of immune checkpoint therapy has provided a revolutionary strategy for the treatment of solid tumors. However, less than 5 % of colorectal cancer patients respond to immune checkpoint therapy. Thus, it is of great scientific significance to develop "potentiators" for immune checkpoint therapy. In this study, we found that knocking down different DNMT and HDAC isoforms could increase the expression of IFNs in colorectal cancer cells, which can enhance the effectiveness of immune checkpoint therapy. Therefore, the combined inhibition of DNMT and HDAC cloud synergistically enhance the effect of immunotherapy. We found that dual DNMT and HDAC inhibitors C02S could inhibit tumor growth in immunocompetent mice but not in immunocompromised nude mice, which indicates that C02S exerts its antitumor effects through the immune system. Mechanistically, C02S could increase the expression of ERVs, which generated the intracellular levels of dsRNA in tumor cells, and then promotes the expression of IFNs through the RIG-I/MDA5-MAVS signaling pathway. Moreover, C02S increased the immune infiltration of DCs and T cells in microenvironment, and enhanced the efficacy of anti-PD-L1 therapy in MC38 and CT26 mice model. These results confirmed that C02S can activate IFNs through the RIG-I/MDA5-MAVS signaling pathway, remodel the tumor immune microenvironment and enhance the efficacy of immune checkpoint therapy, which provides new evidence and solutions for the development of "potentiator" for colorectal cancer immunotherapy.
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Affiliation(s)
- Zhanbo Yang
- Guangdong Provincial Key Laboratory of Chinese Medicine Ingredients and Gut Microbiomics, School of Pharmacy, Shenzhen University Medical School, Shenzhen University, Shenzhen 518055, China
| | - Bizhu Chu
- Guangdong Provincial Key Laboratory of Chinese Medicine Ingredients and Gut Microbiomics, School of Pharmacy, Shenzhen University Medical School, Shenzhen University, Shenzhen 518055, China.
| | - Yao Tu
- Guangdong Provincial Key Laboratory of Chinese Medicine Ingredients and Gut Microbiomics, School of Pharmacy, Shenzhen University Medical School, Shenzhen University, Shenzhen 518055, China
| | - Lulu Li
- State Key Laboratory of Chemical Oncogenomics, Tsinghua Shenzhen International Graduate School, Shenzhen 518055, China
| | - Dawei Chen
- Shenzhen Kivita Innovative Drug Discovery Institute, Shenzhen 518057, China
| | - Shouhui Huang
- Guangdong Provincial Key Laboratory of Chinese Medicine Ingredients and Gut Microbiomics, School of Pharmacy, Shenzhen University Medical School, Shenzhen University, Shenzhen 518055, China
| | - Wenjun Huang
- Guangdong Provincial Key Laboratory of Chinese Medicine Ingredients and Gut Microbiomics, School of Pharmacy, Shenzhen University Medical School, Shenzhen University, Shenzhen 518055, China
| | - Weiwen Fan
- Guangdong Provincial Key Laboratory of Chinese Medicine Ingredients and Gut Microbiomics, School of Pharmacy, Shenzhen University Medical School, Shenzhen University, Shenzhen 518055, China
| | - Qinyuan Li
- State Key Laboratory of Chemical Oncogenomics, Tsinghua Shenzhen International Graduate School, Shenzhen 518055, China
| | - Cunlong Zhang
- Shenzhen Kivita Innovative Drug Discovery Institute, Shenzhen 518057, China
| | - Zigao Yuan
- State Key Laboratory of Chemical Oncogenomics, Tsinghua Shenzhen International Graduate School, Shenzhen 518055, China
| | - Jumin Huang
- MOE Frontiers Science Center for Precision Oncology, University of Macau, 999078, Macao Special Administrative Region of China; Cancer Center, Faculty of Health Sciences, University of Macau, 999078, Macao Special Administrative Region of China
| | - Elaine Lai-Han Leung
- MOE Frontiers Science Center for Precision Oncology, University of Macau, 999078, Macao Special Administrative Region of China; Cancer Center, Faculty of Health Sciences, University of Macau, 999078, Macao Special Administrative Region of China.
| | - Yuyang Jiang
- Guangdong Provincial Key Laboratory of Chinese Medicine Ingredients and Gut Microbiomics, School of Pharmacy, Shenzhen University Medical School, Shenzhen University, Shenzhen 518055, China; State Key Laboratory of Chemical Oncogenomics, Tsinghua Shenzhen International Graduate School, Shenzhen 518055, China.
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40
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Chan FF, Yuen VWH, Shen J, Chin DWC, Law CT, Wong BPY, Chan CYK, Cheu JWS, Ng IOL, Wong CCL, Wong CM. Inhibition of CAF-1 histone chaperone complex triggers cytosolic DNA and dsRNA sensing pathways and induces intrinsic immunity of hepatocellular carcinoma. Hepatology 2024; 80:295-311. [PMID: 38051950 DOI: 10.1097/hep.0000000000000709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 11/07/2023] [Indexed: 12/07/2023]
Abstract
BACKGROUND AND AIMS Chromatin assembly factor 1 (CAF-1) is a replication-dependent epigenetic regulator that controls cell cycle progression and chromatin dynamics. In this study, we aim to investigate the immunomodulatory role and therapeutic potential of the CAF-1 complex in HCC. APPROACH AND RESULTS CAF-1 complex knockout cell lines were established using the CRISPR/Cas9 system. The effects of CAF-1 in HCC were studied in HCC cell lines, nude mice, and immunocompetent mice. RNA-sequencing, ChIP-Seq, and assay for transposase accessible chromatin with high-throughput sequencing (ATAC-Seq) were used to explore the changes in the epigenome and transcriptome. CAF-1 complex was significantly upregulated in human and mouse HCCs and was associated with poor prognosis in patients with HCC. Knockout of CAF-1 remarkably suppressed HCC growth in both in vitro and in vivo models. Mechanistically, depletion of CAF-1 induced replicative stress and chromatin instability, which eventually led to cytoplasmic DNA leakage as micronuclei. Also, chromatin immunoprecipitation sequencing analyses revealed a massive H3.3 histone variant replacement upon CAF-1 knockout. Enrichment of euchromatic H3.3 increased chromatin accessibility and activated the expression of endogenous retrovirus elements, a phenomenon known as viral mimicry. However, cytosolic micronuclei and endogenous retroviruses are recognized as ectopic elements by the stimulator of interferon genes and dsRNA viral sensing pathways, respectively. As a result, the knockout of CAF-1 activated inflammatory response and antitumor immune surveillance and thereby significantly enhanced the anticancer effect of immune checkpoint inhibitors in HCC. CONCLUSIONS Our findings suggest that CAF-1 is essential for HCC development; targeting CAF-1 may awaken the anticancer immune response and may work cooperatively with immune checkpoint inhibitor treatment in cancer therapy.
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Affiliation(s)
- For-Fan Chan
- State Key Laboratory of Liver Research, Department of Pathology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Vincent Wai-Hin Yuen
- State Key Laboratory of Liver Research, Department of Pathology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- Centre for Oncology and Immunology, Hong Kong Science Park, Hong Kong SAR, China
| | - Jialing Shen
- State Key Laboratory of Liver Research, Department of Pathology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Don Wai-Ching Chin
- State Key Laboratory of Liver Research, Department of Pathology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Cheuk-Ting Law
- State Key Laboratory of Liver Research, Department of Pathology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Bowie Po-Yee Wong
- State Key Laboratory of Liver Research, Department of Pathology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- Centre for Oncology and Immunology, Hong Kong Science Park, Hong Kong SAR, China
| | - Cerise Yuen-Ki Chan
- State Key Laboratory of Liver Research, Department of Pathology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- Centre for Oncology and Immunology, Hong Kong Science Park, Hong Kong SAR, China
| | - Jacinth Wing-Sum Cheu
- State Key Laboratory of Liver Research, Department of Pathology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- Centre for Oncology and Immunology, Hong Kong Science Park, Hong Kong SAR, China
| | - Irene Oi-Lin Ng
- State Key Laboratory of Liver Research, Department of Pathology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Carmen Chak-Lui Wong
- State Key Laboratory of Liver Research, Department of Pathology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- Centre for Oncology and Immunology, Hong Kong Science Park, Hong Kong SAR, China
| | - Chun-Ming Wong
- State Key Laboratory of Liver Research, Department of Pathology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
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Yi JM. Epigenetic regulation of HERVs: Implications for cancer immunotherapy. Genes Genomics 2024:10.1007/s13258-024-01546-2. [PMID: 39088189 DOI: 10.1007/s13258-024-01546-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Accepted: 07/07/2024] [Indexed: 08/02/2024]
Abstract
BACKGROUND Human endogenous retroviruses (HERVs), integrated into the human genome during primate evolution, constitute approximately 8% of the human genome. Although most HERVs are non-protein-coding owing to mutations, insertions, deletions, and truncations, recent research has revealed their diverse roles in biological processes, including disease pathogenesis. OBJECTIVE Although many HERVs remain inactive, they have been implicated in various diseases, particularly cancer, prompting an increased interest in harnessing HERVs for therapeutic purposes. This review explores the recent advancements in our understanding of the biological roles of HERVs, emphasizing their clinical relevance in cancer treatment. METHODS Here, we discuss how the detection of transposable elements (TEs), including HERVs, by the immune system triggers innate immune responses in human cancers. CONCLUSION Additionally, we outline recent progress in elucidating the implications of HERV activation in cancer and how targeting HERVs holds promise for anti-cancer treatments by modulating epigenetic plasticity and disrupting cancer initiation and progression.
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Affiliation(s)
- Joo Mi Yi
- Department of Microbiology and Immunology, College of Medicine, Inje University, Busan, 47392, South Korea.
- Department of Medical & Molecular Genetics, Indiana University School of Medicine, Bloomington, IN, 47405, USA.
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Gong N, Alameh MG, El-Mayta R, Xue L, Weissman D, Mitchell MJ. Enhancing in situ cancer vaccines using delivery technologies. Nat Rev Drug Discov 2024; 23:607-625. [PMID: 38951662 DOI: 10.1038/s41573-024-00974-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/17/2024] [Indexed: 07/03/2024]
Abstract
In situ cancer vaccination refers to any approach that exploits tumour antigens available at a tumour site to induce tumour-specific adaptive immune responses. These approaches hold great promise for the treatment of many solid tumours, with numerous candidate drugs under preclinical or clinical evaluation and several products already approved. However, there are challenges in the development of effective in situ cancer vaccines. For example, inadequate release of tumour antigens from tumour cells limits antigen uptake by immune cells; insufficient antigen processing by antigen-presenting cells restricts the generation of antigen-specific T cell responses; and the suppressive immune microenvironment of the tumour leads to exhaustion and death of effector cells. Rationally designed delivery technologies such as lipid nanoparticles, hydrogels, scaffolds and polymeric nanoparticles are uniquely suited to overcome these challenges through the targeted delivery of therapeutics to tumour cells, immune cells or the extracellular matrix. Here, we discuss delivery technologies that have the potential to reduce various clinical barriers for in situ cancer vaccines. We also provide our perspective on this emerging field that lies at the interface of cancer vaccine biology and delivery technologies.
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Affiliation(s)
- Ningqiang Gong
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
- School of Basic Medical Sciences, Division of Life Sciences and Medicine, Center for BioAnalytical Chemistry, Hefei National Research Center for Physical Science at the Microscale, University of Science and Technology of China, Hefei, China
| | - Mohamad-Gabriel Alameh
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn institute for RNA innovation, University of Pennsylvania, Philadelphia, PA, USA
- Department of Bioengineering, George Mason University, Fairfax, VA, USA
| | - Rakan El-Mayta
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Lulu Xue
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
| | - Drew Weissman
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Penn institute for RNA innovation, University of Pennsylvania, Philadelphia, PA, USA.
| | - Michael J Mitchell
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA.
- Penn institute for RNA innovation, University of Pennsylvania, Philadelphia, PA, USA.
- Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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43
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Pan D, Wang Q, Shen A, Qi Z, Zheng C, Hu B. When DNA damage responses meet tumor immunity: From mechanism to therapeutic opportunity. Int J Cancer 2024; 155:384-399. [PMID: 38655783 DOI: 10.1002/ijc.34954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 03/12/2024] [Accepted: 03/26/2024] [Indexed: 04/26/2024]
Abstract
DNA damage is a prevalent phenomenon in the context of cancer progression. Evidence suggests that DNA damage responses (DDR) are pivotal in overcoming tumor immune evasion. Alternatively, traditional radiotherapy and chemotherapy operate by inducing DNA damage, consequently stimulating the immune system to target tumors. The intricate interplay between signaling pathways involved in DDR and immune activation underscores the significance of considering both factors in developing improved immunotherapies. By delving deeper into the mechanisms underlying immune activation brought on by DNA damage, it becomes possible to identify novel treatment approaches that boost the anticancer immune response while minimizing undesirable side effects. This review explores the mechanisms behind DNA damage-induced antitumor immune responses, the importance of DNA damage in antitumor immunity, and potential therapeutic approaches for cancer immunotherapy targeting DDR. Additionally, we discuss the challenges of combination therapy and strategies for integrating DNA damage-targeting therapies with current cancer immunotherapy. In summary, this review highlights the critical role of DNA damage in tumor immunology, underscoring the potential of DDR inhibitors as promising therapeutic modalities for cancer treatment.
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Affiliation(s)
- Dong Pan
- Department of Radiation Medicine, School of Public Health, Wenzhou Medical University, Wenzhou, Zhejiang, China
- Department of Dermatology, Duke University Medical Center, Durham, North Carolina, USA
| | - Qi Wang
- Department of Radiation Medicine, School of Public Health, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Aihua Shen
- Department of Radiation Medicine, School of Public Health, Wenzhou Medical University, Wenzhou, Zhejiang, China
- Zhejiang Engineering Research Center for Innovation and Application of Intelligent Radiotherapy Technology, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
- Zhejiang Provincial Key Laboratory of Watershed Sciences and Health, Wenzhou Medical University, Wenzhou, Zhejiang, China
- Wenzhou Key Laboratory of Basic Science and Translational Research of Radiation Oncology, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Zhihao Qi
- Department of Radiation Medicine, School of Public Health, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Chunfu Zheng
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Burong Hu
- Department of Radiation Medicine, School of Public Health, Wenzhou Medical University, Wenzhou, Zhejiang, China
- Zhejiang Engineering Research Center for Innovation and Application of Intelligent Radiotherapy Technology, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
- Zhejiang Provincial Key Laboratory of Watershed Sciences and Health, Wenzhou Medical University, Wenzhou, Zhejiang, China
- Wenzhou Key Laboratory of Basic Science and Translational Research of Radiation Oncology, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
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44
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Yu VZ, So SS, Lung BCC, Hou GZ, Wong CWY, Chow LKY, Chung MKY, Wong IYH, Wong CLY, Chan DKK, Chan FSY, Law BTT, Xu K, Tan ZZ, Lam KO, Lo AWI, Lam AKY, Kwong DLW, Ko JMY, Dai W, Law S, Lung ML. ΔNp63-restricted viral mimicry response impedes cancer cell viability and remodels tumor microenvironment in esophageal squamous cell carcinoma. Cancer Lett 2024; 595:216999. [PMID: 38823762 DOI: 10.1016/j.canlet.2024.216999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Revised: 05/10/2024] [Accepted: 05/27/2024] [Indexed: 06/03/2024]
Abstract
Tumor protein p63 isoform ΔNp63 plays roles in the squamous epithelium and squamous cell carcinomas (SCCs), including esophageal SCC (ESCC). By integrating data from cell lines and our latest patient-derived organoid cultures, derived xenograft models, and clinical sample transcriptomic analyses, we identified a novel and robust oncogenic role of ΔNp63 in ESCC. We showed that ΔNp63 maintains the repression of cancer cell endogenous retrotransposon expression and cellular double-stranded RNA sensing. These subsequently lead to a restricted cancer cell viral mimicry response and suppressed induction of tumor-suppressive type I interferon (IFN-I) signaling through the regulations of Signal transducer and activator of transcription 1, Interferon regulatory factor 1, and cGAS-STING pathway. The cancer cell ΔNp63/IFN-I signaling axis affects both the cancer cell and tumor-infiltrating immune cell (TIIC) compartments. In cancer cells, depletion of ΔNp63 resulted in reduced cell viability. ΔNp63 expression is negatively associated with the anticancer responses to viral mimicry booster treatments targeting cancer cells. In the tumor microenvironment, cancer cell TP63 expression negatively correlates with multiple TIIC signatures in ESCC clinical samples. ΔNp63 depletion leads to increased cancer cell antigen presentation molecule expression and enhanced recruitment and reprogramming of tumor-infiltrating myeloid cells. Similar IFN-I signaling and TIIC signature association with ΔNp63 were also observed in lung SCC. These results support the potential application of ΔNp63 as a therapeutic target and a biomarker to guide candidate anticancer treatments exploring viral mimicry responses.
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Affiliation(s)
- Valen Zhuoyou Yu
- Department of Clinical Oncology, Centre of Cancer Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - Shan Shan So
- Department of Clinical Oncology, Centre of Cancer Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - Bryan Chee-Chad Lung
- Department of Clinical Oncology, Centre of Cancer Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - George Zhaozheng Hou
- Department of Clinical Oncology, Centre of Cancer Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - Carissa Wing-Yan Wong
- Department of Clinical Oncology, Centre of Cancer Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - Larry Ka-Yue Chow
- Department of Clinical Oncology, Centre of Cancer Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - Michael King-Yung Chung
- Department of Clinical Oncology, Centre of Cancer Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - Ian Yu-Hong Wong
- Department of Surgery, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - Claudia Lai-Yin Wong
- Department of Surgery, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - Desmond Kwan-Kit Chan
- Department of Surgery, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - Fion Siu-Yin Chan
- Department of Surgery, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - Betty Tsz-Ting Law
- Department of Surgery, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - Kaiyan Xu
- Department of Clinical Oncology, Centre of Cancer Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - Zack Zhen Tan
- Department of Clinical Oncology, Centre of Cancer Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - Ka-On Lam
- Department of Clinical Oncology, Centre of Cancer Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - Anthony Wing-Ip Lo
- Division of Anatomical Pathology, Queen Mary Hospital, Pokfulam, Hong Kong
| | - Alfred King-Yin Lam
- Divsion of Cancer Molecular Pathology, School of Medicine and Dentistry and Menzies Health Institute Queensland, Griffith University, Gold Coast, Australia
| | - Dora Lai-Wan Kwong
- Department of Clinical Oncology, Centre of Cancer Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - Josephine Mun-Yee Ko
- Department of Clinical Oncology, Centre of Cancer Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - Wei Dai
- Department of Clinical Oncology, Centre of Cancer Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - Simon Law
- Department of Surgery, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - Maria Li Lung
- Department of Clinical Oncology, Centre of Cancer Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong.
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45
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Honer MA, Ferman BI, Gray ZH, Bondarenko EA, Whetstine JR. Epigenetic modulators provide a path to understanding disease and therapeutic opportunity. Genes Dev 2024; 38:473-503. [PMID: 38914477 PMCID: PMC11293403 DOI: 10.1101/gad.351444.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
The discovery of epigenetic modulators (writers, erasers, readers, and remodelers) has shed light on previously underappreciated biological mechanisms that promote diseases. With these insights, novel biomarkers and innovative combination therapies can be used to address challenging and difficult to treat disease states. This review highlights key mechanisms that epigenetic writers, erasers, readers, and remodelers control, as well as their connection with disease states and recent advances in associated epigenetic therapies.
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Affiliation(s)
- Madison A Honer
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
- Nuclear Dynamics and Cancer Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
- Biomedical Sciences Program, Lewis Katz School of Medicine, Temple University, Philadelphia, Pennsylvania 19140, USA
| | - Benjamin I Ferman
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
- Nuclear Dynamics and Cancer Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
- Biomedical Sciences Program, Lewis Katz School of Medicine, Temple University, Philadelphia, Pennsylvania 19140, USA
| | - Zach H Gray
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
- Nuclear Dynamics and Cancer Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
- Biomedical Sciences Program, Lewis Katz School of Medicine, Temple University, Philadelphia, Pennsylvania 19140, USA
| | - Elena A Bondarenko
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
- Nuclear Dynamics and Cancer Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
| | - Johnathan R Whetstine
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA;
- Nuclear Dynamics and Cancer Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
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46
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Cristalli C, Scotlandi K. Targeting DNA Methylation Machinery in Pediatric Solid Tumors. Cells 2024; 13:1209. [PMID: 39056791 PMCID: PMC11275080 DOI: 10.3390/cells13141209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Revised: 07/08/2024] [Accepted: 07/16/2024] [Indexed: 07/28/2024] Open
Abstract
DNA methylation is a key epigenetic regulatory mechanism that plays a critical role in a variety of cellular processes, including the regulation of cell fate during development, maintenance of cell identity, and genome stability. DNA methylation is tightly regulated by enzymatic reactions and its deregulation plays an important role in the development of cancer. Specific DNA methylation alterations have been found in pediatric solid tumors, providing new insights into the development of these tumors. In addition, DNA methylation profiles have greatly contributed to tune the diagnosis of pediatric solid tumors and to define subgroups of patients with different risks of progression, leading to the reduction in unwanted toxicity and the improvement of treatment efficacy. This review highlights the dysregulated DNA methylome in pediatric solid tumors and how this information provides promising targets for epigenetic therapies, particularly inhibitors of DNMT enzymes (DNMTis). Opportunities and limitations are considered, including the ability of DNMTis to induce viral mimicry and immune signaling by tumors. Besides intrinsic action against cancer cells, DNMTis have the potential to sensitize immune-cold tumors to immunotherapies and may represent a remarkable option to improve the treatment of challenging pediatric solid tumors.
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Affiliation(s)
- Camilla Cristalli
- Laboratory of Experimental Oncology, IRCCS Istituto Ortopedico Rizzoli, Via di Barbiano, 1/10, 40136 Bologna, Italy
| | - Katia Scotlandi
- Laboratory of Experimental Oncology, IRCCS Istituto Ortopedico Rizzoli, Via di Barbiano, 1/10, 40136 Bologna, Italy
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47
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Rehwinkel J, Mehdipour P. ADAR1: from basic mechanisms to inhibitors. Trends Cell Biol 2024:S0962-8924(24)00120-X. [PMID: 39030076 DOI: 10.1016/j.tcb.2024.06.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 06/17/2024] [Accepted: 06/20/2024] [Indexed: 07/21/2024]
Abstract
Adenosine deaminase acting on RNA 1 (ADAR1) converts adenosine to inosine in double-stranded RNA (dsRNA) molecules, a process known as A-to-I editing. ADAR1 deficiency in humans and mice results in profound inflammatory diseases characterised by the spontaneous induction of innate immunity. In cells lacking ADAR1, unedited RNAs activate RNA sensors. These include melanoma differentiation-associated gene 5 (MDA5) that induces the expression of cytokines, particularly type I interferons (IFNs), protein kinase R (PKR), oligoadenylate synthase (OAS), and Z-DNA/RNA binding protein 1 (ZBP1). Immunogenic RNAs 'defused' by ADAR1 may include transcripts from repetitive elements and other long duplex RNAs. Here, we review these recent fundamental discoveries and discuss implications for human diseases. Some tumours depend on ADAR1 to escape immune surveillance, opening the possibility of unleashing anticancer therapies with ADAR1 inhibitors.
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Affiliation(s)
- Jan Rehwinkel
- Medical Research Council Translational Immune Discovery Unit, Medical Research Council Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK.
| | - Parinaz Mehdipour
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Headington, Oxford OX3 7DQ, UK.
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48
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Pitarresi JR, Fitzgerald KA. Unmasking immune suppression. Science 2024; 385:140-142. [PMID: 38991086 DOI: 10.1126/science.adq5196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/13/2024]
Abstract
Inhibition of a mutated metabolic enzyme puts the sting back in antitumor immunity.
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Affiliation(s)
- Jason R Pitarresi
- Division of Hematology-Oncology, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Katherine A Fitzgerald
- Division of Innate Immunity, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA
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49
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Sarre LA, Kim IV, Ovchinnikov V, Olivetta M, Suga H, Dudin O, Sebé-Pedrós A, de Mendoza A. DNA methylation enables recurrent endogenization of giant viruses in an animal relative. SCIENCE ADVANCES 2024; 10:eado6406. [PMID: 38996012 PMCID: PMC11244446 DOI: 10.1126/sciadv.ado6406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Accepted: 06/07/2024] [Indexed: 07/14/2024]
Abstract
5-Methylcytosine (5mC) is a widespread silencing mechanism that controls genomic parasites. In eukaryotes, 5mC has gained complex roles in gene regulation beyond parasite control, yet 5mC has also been lost in many lineages. The causes for 5mC retention and its genomic consequences are still poorly understood. Here, we show that the protist closely related to animals Amoebidium appalachense features both transposon and gene body methylation, a pattern reminiscent of invertebrates and plants. Unexpectedly, hypermethylated genomic regions in Amoebidium derive from viral insertions, including hundreds of endogenized giant viruses, contributing 14% of the proteome. Using a combination of inhibitors and genomic assays, we demonstrate that 5mC silences these giant virus insertions. Moreover, alternative Amoebidium isolates show polymorphic giant virus insertions, highlighting a dynamic process of infection, endogenization, and purging. Our results indicate that 5mC is critical for the controlled coexistence of newly acquired viral DNA into eukaryotic genomes, making Amoebidium a unique model to understand the hybrid origins of eukaryotic DNA.
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Affiliation(s)
- Luke A. Sarre
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Iana V. Kim
- CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Vladimir Ovchinnikov
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Marine Olivetta
- Swiss Institute for Experimental Cancer Research, School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
| | - Hiroshi Suga
- Faculty of Life and Environmental Sciences, Prefectural University of Hiroshima, Shobara, Japan
| | - Omaya Dudin
- Swiss Institute for Experimental Cancer Research, School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
| | - Arnau Sebé-Pedrós
- CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- ICREA, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Alex de Mendoza
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
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50
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Wu MJ, Kondo H, Kammula AV, Shi L, Xiao Y, Dhiab S, Xu Q, Slater CJ, Avila OI, Merritt J, Kato H, Kattel P, Sussman J, Gritti I, Eccleston J, Sun Y, Cho HM, Olander K, Katsuda T, Shi DD, Savani MR, Smith BC, Cleary JM, Mostoslavsky R, Vijay V, Kitagawa Y, Wakimoto H, Jenkins RW, Yates KB, Paik J, Tassinari A, Saatcioglu DH, Tron AE, Haas W, Cahill D, McBrayer SK, Manguso RT, Bardeesy N. Mutant IDH1 inhibition induces dsDNA sensing to activate tumor immunity. Science 2024; 385:eadl6173. [PMID: 38991060 DOI: 10.1126/science.adl6173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 05/09/2024] [Indexed: 07/13/2024]
Abstract
Isocitrate dehydrogenase 1 (IDH1) is the most commonly mutated metabolic gene across human cancers. Mutant IDH1 (mIDH1) generates the oncometabolite (R)-2-hydroxyglutarate, disrupting enzymes involved in epigenetics and other processes. A hallmark of IDH1-mutant solid tumors is T cell exclusion, whereas mIDH1 inhibition in preclinical models restores antitumor immunity. Here, we define a cell-autonomous mechanism of mIDH1-driven immune evasion. IDH1-mutant solid tumors show selective hypermethylation and silencing of the cytoplasmic double-stranded DNA (dsDNA) sensor CGAS, compromising innate immune signaling. mIDH1 inhibition restores DNA demethylation, derepressing CGAS and transposable element (TE) subclasses. dsDNA produced by TE-reverse transcriptase (TE-RT) activates cGAS, triggering viral mimicry and stimulating antitumor immunity. In summary, we demonstrate that mIDH1 epigenetically suppresses innate immunity and link endogenous RT activity to the mechanism of action of a US Food and Drug Administration-approved oncology drug.
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Affiliation(s)
- Meng-Ju Wu
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston MA, USA
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Hiroshi Kondo
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston MA, USA
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Ashwin V Kammula
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Lei Shi
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston MA, USA
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Yi Xiao
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Sofiene Dhiab
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston MA, USA
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Qin Xu
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston MA, USA
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Chloe J Slater
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston MA, USA
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Universite Paris-Saclay, Institut Gustave Roussy, INSERM U1015, Villejuif, France
- Servier Pharmaceuticals LLC, Boston, MA, USA
| | - Omar I Avila
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Joshua Merritt
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston MA, USA
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Hiroyuki Kato
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston MA, USA
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Prabhat Kattel
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston MA, USA
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Jonathan Sussman
- Abramson Family Cancer Research Institute and Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Graduate Group in Genomics and Computational Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Ilaria Gritti
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston MA, USA
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Jason Eccleston
- Abramson Family Cancer Research Institute and Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Yi Sun
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston MA, USA
| | - Hyo Min Cho
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston MA, USA
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Kira Olander
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Takeshi Katsuda
- Abramson Family Cancer Research Institute and Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Diana D Shi
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Radiation Oncology, Dana-Farber/Brigham and Women's Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Milan R Savani
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Medical Scientist Training Program, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Bailey C Smith
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | | | - Raul Mostoslavsky
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston MA, USA
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Vindhya Vijay
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston MA, USA
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Yosuke Kitagawa
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Hiroaki Wakimoto
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Russell W Jenkins
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
- Laboratory of Systems Pharmacology, Harvard Program in Therapeutic Sciences, Harvard Medical School, Boston, MA, USA
| | - Kathleen B Yates
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Jihye Paik
- Department of Pathology and Laboratory Medicine, Sandra and Edward Meyer Cancer Center, Weill Medical College of Cornell University, New York, NY, USA
| | | | | | | | - Wilhelm Haas
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Daniel Cahill
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Samuel K McBrayer
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Robert T Manguso
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Nabeel Bardeesy
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston MA, USA
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
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