1
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Biswas J, Boussi L, Stein E, Abdel-Wahab O. Aberrant pre-mRNA processing in cancer. J Exp Med 2024; 221:e20230891. [PMID: 39316554 PMCID: PMC11448470 DOI: 10.1084/jem.20230891] [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: 06/14/2024] [Revised: 07/29/2024] [Accepted: 08/26/2024] [Indexed: 09/26/2024] Open
Abstract
Dysregulation of the flow of information from genomic DNA to RNA to protein occurs within all cancer types. In this review, we described the current state of understanding of how RNA processing is dysregulated in cancer with a focus on mutations in the RNA splicing factor machinery that are highly prevalent in hematologic malignancies. We discuss the downstream effects of these mutations highlighting both individual genes as well as common pathways that they perturb. We highlight examples of how alterations in RNA processing have been harnessed for therapeutic intent as well as to promote the selective toxicity of cancer cells.
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Affiliation(s)
- Jeetayu Biswas
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Leora Boussi
- Department of Medicine, Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Eytan Stein
- Department of Medicine, Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Omar Abdel-Wahab
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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2
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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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3
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Kina E, Larouche JD, Thibault P, Perreault C. The cryptic immunopeptidome in health and disease. Trends Genet 2024:S0168-9525(24)00210-5. [PMID: 39389870 DOI: 10.1016/j.tig.2024.09.003] [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: 05/23/2024] [Revised: 08/01/2024] [Accepted: 09/17/2024] [Indexed: 10/12/2024]
Abstract
Peptides presented by MHC proteins regulate all aspects of T cell biology. These MHC-associated peptides (MAPs) form what is known as the immunopeptidome and their comprehensive analysis has catalyzed the burgeoning field of immunopeptidomics. Advances in mass spectrometry (MS) and next-generation sequencing have facilitated significant breakthroughs in this area, some of which are highlighted in this article on the cryptic immunopeptidome. Here, 'cryptic' refers to peptides and proteins encoded by noncanonical open reading frames (ORFs). Cryptic MAPs derive mainly from short unstable proteins found in normal, infected, and neoplastic cells. Cryptic MAPs show minimal overlap with cryptic proteins found in whole-cell extracts. In many cancer types, most cancer-specific MAPs are cryptic.
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Affiliation(s)
- Eralda Kina
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Québec, Canada
| | - Jean-David Larouche
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Québec, Canada
| | - Pierre Thibault
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Québec, Canada
| | - Claude Perreault
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Québec, Canada.
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4
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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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5
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Borowicz P, King CG, Dustin ML, Wherry EJ, Koretzky GA, Spurkland A. The future of immunology: a Lofoten perspective. Immunol Cell Biol 2024; 102:760-765. [PMID: 38994681 DOI: 10.1111/imcb.12805] [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: 07/13/2024]
Abstract
This Future Challenges article summarizes views on future directions in immunological research presented at round-table discussions at the 4th Immunology workshop in the Lofoten Islands in Norway, held in August 2023, and subsequent responses to surveys sent to meeting participants. It also summarizes some of the conversations around the responsibility of scientists to communicate with the non-science community, and the approaches that we may use to meet this obligation.
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Affiliation(s)
- Pawel Borowicz
- Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Carolyn G King
- Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Michael L Dustin
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
| | - E John Wherry
- Institute of Immunology and Immune Health, University of Pennsylvania, Philadelphia, PA, USA
| | - Gary A Koretzky
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Department of Immunology and Microbiology, Cornell University, Ithaca, NY, USA
| | - Anne Spurkland
- Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
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6
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Kjer-Hansen P, Phan TG, Weatheritt RJ. Protein isoform-centric therapeutics: expanding targets and increasing specificity. Nat Rev Drug Discov 2024; 23:759-779. [PMID: 39232238 DOI: 10.1038/s41573-024-01025-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/31/2024] [Indexed: 09/06/2024]
Abstract
Most protein-coding genes produce multiple protein isoforms; however, these isoforms are commonly neglected in drug discovery. The expression of protein isoforms can be specific to a disease, tissue and/or developmental stage, and this specific expression can be harnessed to achieve greater drug specificity than pan-targeting of all gene products and to enable improved treatments for diseases caused by aberrant protein isoform production. In recent years, several protein isoform-centric therapeutics have been developed. Here, we collate these studies and clinical trials to highlight three distinct but overlapping modes of action for protein isoform-centric drugs: isoform switching, isoform introduction or depletion, and modulation of isoform activity. In addition, we discuss how protein isoforms can be used clinically as targets for cell type-specific drug delivery and immunotherapy, diagnostic biomarkers and sources of cancer neoantigens. Collectively, we emphasize the value of a focus on isoforms as a route to discovering drugs with greater specificity and fewer adverse effects. This approach could enable the targeting of proteins for which pan-inhibition of all isoforms is toxic and poorly tolerated.
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Affiliation(s)
- Peter Kjer-Hansen
- EMBL Australia, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia.
- St. Vincent's Healthcare Clinical Campus, School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Darlinghurst, New South Wales, Australia.
| | - Tri Giang Phan
- St. Vincent's Healthcare Clinical Campus, School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Darlinghurst, New South Wales, Australia
- Precision Immunology Program, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Robert J Weatheritt
- EMBL Australia, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia.
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia.
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7
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Nesta A, Veiga DFT, Banchereau J, Anczukow O, Beck CR. Alternative splicing of transposable elements in human breast cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.26.615242. [PMID: 39386569 PMCID: PMC11463404 DOI: 10.1101/2024.09.26.615242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/12/2024]
Abstract
Transposable elements (TEs) drive genome evolution and can affect gene expression through diverse mechanisms. In breast cancer, disrupted regulation of TE sequences may facilitate tumor-specific transcriptomic alterations. We examine 142,514 full-length isoforms derived from long-read RNA sequencing (LR-seq) of 30 breast samples to investigate the effects of TEs on the breast cancer transcriptome. Approximately half of these isoforms contain TE sequences, and these contribute to half of the novel annotated splice junctions. We quantify splicing of these LR-seq derived isoforms in 1,135 breast tumors from The Cancer Genome Atlas (TCGA) and 1,329 healthy tissue samples from the Genotype-Tissue Expression (GTEx), and find 300 TE-overlapping tumor-specific splicing events. Some splicing events are enriched in specific breast cancer subtypes - for example, a TE-driven transcription start site upstream of ERBB2 in HER2+ tumors, and several TE-mediated splicing events are associated with patient survival and poor prognosis. The full-length sequences we capture with LR-seq reveal thousands of isoforms with signatures of RNA editing, including a novel isoform belonging to RHOA ; a gene previously implicated in tumor progression. We utilize our full-length isoforms to discover polymorphic TE insertions that alter splicing and validate one of these events in breast cancer cell lines. Together, our results demonstrate the widespread effects of dysregulated TEs on breast cancer transcriptomes and highlight the advantages of long-read isoform sequencing for understanding TE biology. TE-derived isoforms may alter the expression of genes important in cancer and can potentially be used as novel, disease-specific therapeutic targets or biomarkers. One Sentence Summary Transposable elements generate alternative isoforms and alter post-transcriptional regulation in human breast cancer.
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8
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Zhao Y, Qin C, Lin C, Li Z, Zhao B, Li T, Zhang X, Wang W. Pancreatic ductal adenocarcinoma cells reshape the immune microenvironment: Molecular mechanisms and therapeutic targets. Biochim Biophys Acta Rev Cancer 2024; 1879:189183. [PMID: 39303859 DOI: 10.1016/j.bbcan.2024.189183] [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: 06/09/2024] [Revised: 08/23/2024] [Accepted: 09/13/2024] [Indexed: 09/22/2024]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a digestive system malignancy characterized by challenging early detection, limited treatment alternatives, and generally poor prognosis. Although there have been significant advancements in immunotherapy for hematological malignancies and various solid tumors in recent decades, with impressive outcomes in recent preclinical and clinical trials, the effectiveness of these therapies in treating PDAC continues to be modest. The unique immunological microenvironment of PDAC, especially the abnormal distribution, complex composition, and variable activation states of tumor-infiltrating immune cells, greatly restricts the effectiveness of immunotherapy. Undoubtedly, integrating data from both preclinical models and human studies helps accelerate the identification of reliable molecules and pathways responsive to targeted biological therapies and immunotherapies, thereby continuously optimizing therapeutic combinations. In this review, we delve deeply into how PDAC cells regulate the immune microenvironment through complex signaling networks, affecting the quantity and functional status of immune cells to promote immune escape and tumor progression. Furthermore, we explore the multi-modal immunotherapeutic strategies currently under development, emphasizing the transformation of the immunosuppressive environment into an anti-tumor milieu by targeting specific molecular and cellular pathways, providing insights for the development of novel treatment strategies.
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Affiliation(s)
- Yutong Zhao
- Department of General Surgery, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100023, PR China; Key Laboratory of Research in Pancreatic Tumor, Chinese Academy of Medical Sciences, Beijing 100023, PR China; National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College Hospital, Beijing 100023, PR China
| | - Cheng Qin
- Department of General Surgery, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100023, PR China; Key Laboratory of Research in Pancreatic Tumor, Chinese Academy of Medical Sciences, Beijing 100023, PR China; National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College Hospital, Beijing 100023, PR China
| | - Chen Lin
- Department of General Surgery, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100023, PR China; Key Laboratory of Research in Pancreatic Tumor, Chinese Academy of Medical Sciences, Beijing 100023, PR China; National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College Hospital, Beijing 100023, PR China
| | - Zeru Li
- Department of General Surgery, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100023, PR China; Key Laboratory of Research in Pancreatic Tumor, Chinese Academy of Medical Sciences, Beijing 100023, PR China; National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College Hospital, Beijing 100023, PR China
| | - Bangbo Zhao
- Department of General Surgery, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100023, PR China; Key Laboratory of Research in Pancreatic Tumor, Chinese Academy of Medical Sciences, Beijing 100023, PR China; National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College Hospital, Beijing 100023, PR China
| | - Tianyu Li
- Department of General Surgery, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100023, PR China; Key Laboratory of Research in Pancreatic Tumor, Chinese Academy of Medical Sciences, Beijing 100023, PR China; National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College Hospital, Beijing 100023, PR China
| | - Xiangyu Zhang
- Department of General Surgery, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100023, PR China; Key Laboratory of Research in Pancreatic Tumor, Chinese Academy of Medical Sciences, Beijing 100023, PR China; National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College Hospital, Beijing 100023, PR China
| | - Weibin Wang
- Department of General Surgery, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100023, PR China; Key Laboratory of Research in Pancreatic Tumor, Chinese Academy of Medical Sciences, Beijing 100023, PR China; National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College Hospital, Beijing 100023, PR China.
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9
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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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10
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Hu Z, Guo X, Li Z, Meng Z, Huang S. The neoantigens derived from transposable elements - A hidden treasure for cancer immunotherapy. Biochim Biophys Acta Rev Cancer 2024; 1879:189126. [PMID: 38849060 DOI: 10.1016/j.bbcan.2024.189126] [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: 01/16/2024] [Revised: 05/26/2024] [Accepted: 06/02/2024] [Indexed: 06/09/2024]
Abstract
Neoantigen-based therapy is a promising approach that selectively activates the immune system of the host to recognize and eradicate cancer cells. Preliminary clinical trials have validated the feasibility, safety, and immunogenicity of personalized neoantigen-directed vaccines, enhancing their effectiveness and broad applicability in immunotherapy. While many ongoing oncological trials concentrate on neoantigens derived from mutations, these targets do not consistently provoke an immune response in all patients harboring the mutations. Additionally, tumors like ovarian cancer, which have a low tumor mutational burden (TMB), may be less amenable to mutation-based neoantigen therapies. Recent advancements in next-generation sequencing and bioinformatics have uncovered a rich source of neoantigens from non-canonical RNAs associated with transposable elements (TEs). Considering the substantial presence of TEs in the human genome and the proven immunogenicity of TE-derived neoantigens in various tumor types, this review investigates the latest findings on TE-derived neoantigens, examining their clinical implications, challenges, and unique advantages in enhancing tumor immunotherapy.
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Affiliation(s)
- Zhixiang Hu
- Department of Integrative Oncology, Fudan University Shanghai Cancer Center, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xinyi Guo
- Department of Integrative Oncology, Fudan University Shanghai Cancer Center, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Ziteng Li
- Department of Integrative Oncology, Fudan University Shanghai Cancer Center, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Zhiqiang Meng
- Department of Integrative Oncology, Fudan University Shanghai Cancer Center, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
| | - Shenglin Huang
- Department of Integrative Oncology, Fudan University Shanghai Cancer Center, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
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11
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Dharani S, Cho H, Fernandez JP, Juillerat A, Valton J, Duchateau P, Poirot L, Das S. TALEN-edited allogeneic inducible dual CAR T cells enable effective targeting of solid tumors while mitigating off-tumor toxicity. Mol Ther 2024:S1525-0016(24)00540-9. [PMID: 39169622 DOI: 10.1016/j.ymthe.2024.08.018] [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: 11/04/2023] [Revised: 04/29/2024] [Accepted: 08/16/2024] [Indexed: 08/23/2024] Open
Abstract
Adoptive cell therapy using chimeric antigen receptor (CAR) T cells has proven to be lifesaving for many cancer patients. However, its therapeutic efficacy has been limited in solid tumors. One key factor for this is cancer-associated fibroblasts (CAFs) that modulate the tumor microenvironment (TME) to inhibit T cell infiltration and induce "T cell dysfunction." Additionally, the sparsity of tumor-specific antigens (TSA) and expression of CAR-directed tumor-associated antigens (TAA) on normal tissues often results in "on-target off-tumor" cytotoxicity, raising safety concerns. Using TALEN-mediated gene editing, we present here an innovative CAR T cell engineering strategy to overcome these challenges. Our allogeneic "Smart CAR T cells" are designed to express a constitutive CAR, targeting FAP+ CAFs in solid tumors. Additionally, a second CAR targeting a TAA such as mesothelin is specifically integrated at a TCR signaling-inducible locus like PDCD1. FAPCAR-mediated CAF targeting induces expression of the mesothelin CAR, establishing an IF/THEN-gated circuit sensitive to dual antigen sensing. Using this approach, we observe enhanced anti-tumor cytotoxicity, while limiting "on-target off-tumor" toxicity. Our study thus demonstrates TALEN-mediated gene editing capabilities for design of allogeneic IF/THEN-gated dual CAR T cells that efficiently target immunotherapy-recalcitrant solid tumors while mitigating potential safety risks, encouraging clinical development of this strategy.
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Affiliation(s)
| | - Hana Cho
- Cellectis Inc, New York, NY 10016, USA
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12
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Mustelin T, Andrade F. Autoimmunity: the neoantigen hypothesis. Front Immunol 2024; 15:1432985. [PMID: 38994353 PMCID: PMC11236689 DOI: 10.3389/fimmu.2024.1432985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Accepted: 06/17/2024] [Indexed: 07/13/2024] Open
Affiliation(s)
- Tomas Mustelin
- Division of Rheumatology, Department of Medicine, University of Washington, Seattle, WA, United States
| | - Felipe Andrade
- Division of Rheumatology, The Johns Hopkins University School of Medicine, Baltimore, MD, United States
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13
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Grundy EE, Shaw LC, Wang L, Powell DJ, Ostrowski M, Jones RB, Cruz CRY, Gordish-Dressman H, Bollard CM, Chiappinelli KB. Limited Immunogenicity of an HLA-A*03:01-restricted Epitope of Erv-k-env in Non-hiv-1 Settings: Implications for Adoptive Cell Therapy in Cancer. RESEARCH SQUARE 2024:rs.3.rs-4432372. [PMID: 38854052 PMCID: PMC11160923 DOI: 10.21203/rs.3.rs-4432372/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Repetitive elements (REs) 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 RE ERV-K is frequently expressed by tumor cells. Here we determined whether the targeting of a previously identified immunogenic epitope in the envelope gene (env) of ERV-K resulted in target antigen specificity in non-HIV-1 settings. 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, these transduced T cells were not specific for HLA-A*03:01 + OC cells nor for the cognate peptide in HLA-matched systems from multiple healthy donors. These data suggest that the ERV-K-Env epitope recognized by this T cell receptor is of low immunogenicity and has limited potential as a T cell target for OC.
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Affiliation(s)
| | | | | | | | | | - R Brad Jones
- Weill Cornell Graduate School of Medical Medical Sciences
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14
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Yang K, Lu R, Mei J, Cao K, Zeng T, Hua Y, Huang X, Li W, Yin Y. The war between the immune system and the tumor - using immune biomarkers as tracers. Biomark Res 2024; 12:51. [PMID: 38816871 PMCID: PMC11137916 DOI: 10.1186/s40364-024-00599-5] [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: 12/06/2023] [Accepted: 05/10/2024] [Indexed: 06/01/2024] Open
Abstract
Nowadays, immunotherapy is one of the most promising anti-tumor therapeutic strategy. Specifically, immune-related targets can be used to predict the efficacy and side effects of immunotherapy and monitor the tumor immune response. In the past few decades, increasing numbers of novel immune biomarkers have been found to participate in certain links of the tumor immunity to contribute to the formation of immunosuppression and have entered clinical trials. Here, we systematically reviewed the oncogenesis and progression of cancer in the view of anti-tumor immunity, particularly in terms of tumor antigen expression (related to tumor immunogenicity) and tumor innate immunity to complement the cancer-immune cycle. From the perspective of integrated management of chronic cancer, we also appraised emerging factors affecting tumor immunity (including metabolic, microbial, and exercise-related markers). We finally summarized the clinical studies and applications based on immune biomarkers. Overall, immune biomarkers participate in promoting the development of more precise and individualized immunotherapy by predicting, monitoring, and regulating tumor immune response. Therefore, targeting immune biomarkers may lead to the development of innovative clinical applications.
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Affiliation(s)
- Kai Yang
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, P. R. China
| | - Rongrong Lu
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, P. R. China
| | - Jie Mei
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, P. R. China
| | - Kai Cao
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, P. R. China
| | - Tianyu Zeng
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, P. R. China
| | - Yijia Hua
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, P. R. China
- Gusu School, Nanjing Medical University, Nanjing, China
| | - Xiang Huang
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, P. R. China.
| | - Wei Li
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, P. R. China.
| | - Yongmei Yin
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, P. R. China.
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15
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Lang F, Sorn P, Suchan M, Henrich A, Albrecht C, Köhl N, Beicht A, Riesgo-Ferreiro P, Holtsträter C, Schrörs B, Weber D, Löwer M, Sahin U, Ibn-Salem J. Prediction of tumor-specific splicing from somatic mutations as a source of neoantigen candidates. BIOINFORMATICS ADVANCES 2024; 4:vbae080. [PMID: 38863673 PMCID: PMC11165244 DOI: 10.1093/bioadv/vbae080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 03/26/2024] [Accepted: 05/28/2024] [Indexed: 06/13/2024]
Abstract
Motivation Neoantigens are promising targets for cancer immunotherapies and might arise from alternative splicing. However, detecting tumor-specific splicing is challenging because many non-canonical splice junctions identified in tumors also appear in healthy tissues. To increase tumor-specificity, we focused on splicing caused by somatic mutations as a source for neoantigen candidates in individual patients. Results We developed the tool splice2neo with multiple functionalities to integrate predicted splice effects from somatic mutations with splice junctions detected in tumor RNA-seq and to annotate the resulting transcript and peptide sequences. Additionally, we provide the tool EasyQuant for targeted RNA-seq read mapping to candidate splice junctions. Using a stringent detection rule, we predicted 1.7 splice junctions per patient as splice targets with a false discovery rate below 5% in a melanoma cohort. We confirmed tumor-specificity using independent, healthy tissue samples. Furthermore, using tumor-derived RNA, we confirmed individual exon-skipping events experimentally. Most target splice junctions encoded neoepitope candidates with predicted major histocompatibility complex (MHC)-I or MHC-II binding. Compared to neoepitope candidates from non-synonymous point mutations, the splicing-derived MHC-I neoepitope candidates had lower self-similarity to corresponding wild-type peptides. In conclusion, we demonstrate that identifying mutation-derived, tumor-specific splice junctions can lead to additional neoantigen candidates to expand the target repertoire for cancer immunotherapies. Availability and implementation The R package splice2neo and the python package EasyQuant are available at https://github.com/TRON-Bioinformatics/splice2neo and https://github.com/TRON-Bioinformatics/easyquant, respectively.
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Affiliation(s)
- Franziska Lang
- TRON—Translational Oncology at the University Medical Center of Johannes Gutenberg University Mainz gGmbH, Mainz 55131, Germany
- Faculty of Biology, Johannes Gutenberg University Mainz, Mainz 55128, Germany
| | - Patrick Sorn
- TRON—Translational Oncology at the University Medical Center of Johannes Gutenberg University Mainz gGmbH, Mainz 55131, Germany
| | - Martin Suchan
- TRON—Translational Oncology at the University Medical Center of Johannes Gutenberg University Mainz gGmbH, Mainz 55131, Germany
| | - Alina Henrich
- TRON—Translational Oncology at the University Medical Center of Johannes Gutenberg University Mainz gGmbH, Mainz 55131, Germany
| | - Christian Albrecht
- TRON—Translational Oncology at the University Medical Center of Johannes Gutenberg University Mainz gGmbH, Mainz 55131, Germany
| | - Nina Köhl
- TRON—Translational Oncology at the University Medical Center of Johannes Gutenberg University Mainz gGmbH, Mainz 55131, Germany
| | - Aline Beicht
- TRON—Translational Oncology at the University Medical Center of Johannes Gutenberg University Mainz gGmbH, Mainz 55131, Germany
| | - Pablo Riesgo-Ferreiro
- TRON—Translational Oncology at the University Medical Center of Johannes Gutenberg University Mainz gGmbH, Mainz 55131, Germany
| | - Christoph Holtsträter
- TRON—Translational Oncology at the University Medical Center of Johannes Gutenberg University Mainz gGmbH, Mainz 55131, Germany
| | - Barbara Schrörs
- TRON—Translational Oncology at the University Medical Center of Johannes Gutenberg University Mainz gGmbH, Mainz 55131, Germany
| | - David Weber
- TRON—Translational Oncology at the University Medical Center of Johannes Gutenberg University Mainz gGmbH, Mainz 55131, Germany
| | - Martin Löwer
- TRON—Translational Oncology at the University Medical Center of Johannes Gutenberg University Mainz gGmbH, Mainz 55131, Germany
| | - Ugur Sahin
- TRON—Translational Oncology at the University Medical Center of Johannes Gutenberg University Mainz gGmbH, Mainz 55131, Germany
- BioNTech SE, Mainz 55131, Germany
- Institute of Immunology, University Medical Center of the Johannes-Gutenberg University, Mainz 55131, Germany
| | - Jonas Ibn-Salem
- TRON—Translational Oncology at the University Medical Center of Johannes Gutenberg University Mainz gGmbH, Mainz 55131, Germany
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16
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Larouche JD, Laumont CM, Trofimov A, Vincent K, Hesnard L, Brochu S, Côté C, Humeau JF, Bonneil É, Lanoix J, Durette C, Gendron P, Laverdure JP, Richie ER, Lemieux S, Thibault P, Perreault C. Transposable elements regulate thymus development and function. eLife 2024; 12:RP91037. [PMID: 38635416 PMCID: PMC11026094 DOI: 10.7554/elife.91037] [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: 04/20/2024] Open
Abstract
Transposable elements (TEs) are repetitive sequences representing ~45% of the human and mouse genomes and are highly expressed by medullary thymic epithelial cells (mTECs). In this study, we investigated the role of TEs on T-cell development in the thymus. We performed multiomic analyses of TEs in human and mouse thymic cells to elucidate their role in T-cell development. We report that TE expression in the human thymus is high and shows extensive age- and cell lineage-related variations. TE expression correlates with multiple transcription factors in all cell types of the human thymus. Two cell types express particularly broad TE repertoires: mTECs and plasmacytoid dendritic cells (pDCs). In mTECs, transcriptomic data suggest that TEs interact with transcription factors essential for mTEC development and function (e.g., PAX1 and REL), and immunopeptidomic data showed that TEs generate MHC-I-associated peptides implicated in thymocyte education. Notably, AIRE, FEZF2, and CHD4 regulate small yet non-redundant sets of TEs in murine mTECs. Human thymic pDCs homogenously express large numbers of TEs that likely form dsRNA, which can activate innate immune receptors, potentially explaining why thymic pDCs constitutively secrete IFN ɑ/β. This study highlights the diversity of interactions between TEs and the adaptive immune system. TEs are genetic parasites, and the two thymic cell types most affected by TEs (mTEcs and pDCs) are essential to establishing central T-cell tolerance. Therefore, we propose that orchestrating TE expression in thymic cells is critical to prevent autoimmunity in vertebrates.
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Affiliation(s)
- Jean-David Larouche
- Institute for Research in Immunology and Cancer, Université de MontréalMontrealCanada
- Department of Medicine, Université de MontréalMontréalCanada
| | - Céline M Laumont
- Deeley Research Centre, BC CancerVictoriaCanada
- Department of Medical Genetics, University of British ColumbiaVancouverCanada
| | - Assya Trofimov
- Institute for Research in Immunology and Cancer, Université de MontréalMontrealCanada
- Department of Computer Science and Operations Research, Université de MontréalMontréalCanada
- Fred Hutchinson Cancer CenterSeattleUnited States
- Department of Physics, University of WashingtonSeattleUnited States
| | - Krystel Vincent
- Institute for Research in Immunology and Cancer, Université de MontréalMontrealCanada
| | - Leslie Hesnard
- Institute for Research in Immunology and Cancer, Université de MontréalMontrealCanada
| | - Sylvie Brochu
- Institute for Research in Immunology and Cancer, Université de MontréalMontrealCanada
| | - Caroline Côté
- Institute for Research in Immunology and Cancer, Université de MontréalMontrealCanada
| | - Juliette F Humeau
- Institute for Research in Immunology and Cancer, Université de MontréalMontrealCanada
| | - Éric Bonneil
- Institute for Research in Immunology and Cancer, Université de MontréalMontrealCanada
| | - Joel Lanoix
- Institute for Research in Immunology and Cancer, Université de MontréalMontrealCanada
| | - Chantal Durette
- Institute for Research in Immunology and Cancer, Université de MontréalMontrealCanada
| | - Patrick Gendron
- Institute for Research in Immunology and Cancer, Université de MontréalMontrealCanada
| | | | - Ellen R Richie
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas M.D. Anderson Cancer CenterHoustonUnited States
| | - Sébastien Lemieux
- Institute for Research in Immunology and Cancer, Université de MontréalMontrealCanada
- Department of Biochemistry and Molecular Medicine, Université de MontréalMontrealCanada
| | - Pierre Thibault
- Institute for Research in Immunology and Cancer, Université de MontréalMontrealCanada
- Department of Chemistry, Université de MontréalMontréalCanada
| | - Claude Perreault
- Institute for Research in Immunology and Cancer, Université de MontréalMontrealCanada
- Department of Medicine, Université de MontréalMontréalCanada
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17
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Yu J, Qiu P, Ai J, Liu B, Han GZ, Zhu F, Zhang W, Cui J. Endogenous retrovirus activation: potential for immunology and clinical applications. Natl Sci Rev 2024; 11:nwae034. [PMID: 38495812 PMCID: PMC10941811 DOI: 10.1093/nsr/nwae034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 01/23/2024] [Accepted: 01/23/2024] [Indexed: 03/19/2024] Open
Affiliation(s)
- Jundan Yu
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, China
- CAS Key Laboratory of Molecular Virology & Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, China
- University of Chinese Academy of Sciences, China
| | - Peishan Qiu
- CAS Key Laboratory of Molecular Virology & Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, China
- University of Chinese Academy of Sciences, China
| | - Jingwen Ai
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, China
- Shanghai Huashen Institute of Microbes and Infections, China
| | - Bo Liu
- CAS Key Laboratory of Molecular Virology & Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, China
- University of Chinese Academy of Sciences, China
| | - Guan-Zhu Han
- College of Life Sciences, Nanjing Normal University, China
| | - Fan Zhu
- State Key Laboratory of Virology and Department of Medical Microbiology, School of Basic Medical Sciences, Wuhan University, China
| | - Wenhong Zhang
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, China
- Shanghai Huashen Institute of Microbes and Infections, China
- The Institute of Infection and Health Research, Fudan University, China
- Key Laboratory of Medical Molecular Virology (MOE/MOH), Shanghai Medical College, Fudan University, China
| | - Jie Cui
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, China
- CAS Key Laboratory of Molecular Virology & Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, China
- University of Chinese Academy of Sciences, China
- Shanghai Huashen Institute of Microbes and Infections, China
- The Institute of Infection and Health Research, Fudan University, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, China
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18
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Chen W, Geng D, Chen J, Han X, Xie Q, Guo G, Chen X, Zhang W, Tang S, Zhong X. Roles and mechanisms of aberrant alternative splicing in melanoma - implications for targeted therapy and immunotherapy resistance. Cancer Cell Int 2024; 24:101. [PMID: 38462618 PMCID: PMC10926661 DOI: 10.1186/s12935-024-03280-x] [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: 10/29/2023] [Accepted: 02/22/2024] [Indexed: 03/12/2024] Open
Abstract
BACKGROUND Despite advances in therapeutic strategies, resistance to immunotherapy and the off-target effects of targeted therapy have significantly weakened the benefits for patients with melanoma. MAIN BODY Alternative splicing plays a crucial role in transcriptional reprogramming during melanoma development. In particular, aberrant alternative splicing is involved in the efficacy of immunotherapy, targeted therapy, and melanoma metastasis. Abnormal expression of splicing factors and variants may serve as biomarkers or therapeutic targets for the diagnosis and prognosis of melanoma. Therefore, comprehensively integrating their roles and related mechanisms is essential. This review provides the first detailed summary of the splicing process in melanoma and the changes occurring in this pathway. CONCLUSION The focus of this review is to provide strategies for developing novel diagnostic biomarkers and summarize their potential to alter resistance to targeted therapies and immunotherapy.
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Affiliation(s)
- Wanxian Chen
- Department of Plastic and Burns Surgery, The Second Affiliated Hospital of Shantou University Medical College, Shantou, 515000, P. R. China
- Plastic Surgery Research Institute, Ear Deformities Treatment Center and Cleft Lip and Palate Treatment Center, Shantou University Medical College, Shantou, China
| | - Deyi Geng
- Department of Plastic and Burns Surgery, The Second Affiliated Hospital of Shantou University Medical College, Shantou, 515000, P. R. China
- Plastic Surgery Research Institute, Ear Deformities Treatment Center and Cleft Lip and Palate Treatment Center, Shantou University Medical College, Shantou, China
| | - Jiasheng Chen
- Department of Plastic and Burns Surgery, The Second Affiliated Hospital of Shantou University Medical College, Shantou, 515000, P. R. China
- Plastic Surgery Research Institute, Ear Deformities Treatment Center and Cleft Lip and Palate Treatment Center, Shantou University Medical College, Shantou, China
| | - Xiaosha Han
- Department of Plastic and Burns Surgery, The Second Affiliated Hospital of Shantou University Medical College, Shantou, 515000, P. R. China
- Plastic Surgery Research Institute, Ear Deformities Treatment Center and Cleft Lip and Palate Treatment Center, Shantou University Medical College, Shantou, China
| | - Qihu Xie
- Department of Plastic and Burns Surgery, The Second Affiliated Hospital of Shantou University Medical College, Shantou, 515000, P. R. China
- Plastic Surgery Research Institute, Ear Deformities Treatment Center and Cleft Lip and Palate Treatment Center, Shantou University Medical College, Shantou, China
| | - Genghong Guo
- Department of Plastic and Burns Surgery, The Second Affiliated Hospital of Shantou University Medical College, Shantou, 515000, P. R. China
- Plastic Surgery Research Institute, Ear Deformities Treatment Center and Cleft Lip and Palate Treatment Center, Shantou University Medical College, Shantou, China
| | - Xuefen Chen
- Department of Plastic and Burns Surgery, The Second Affiliated Hospital of Shantou University Medical College, Shantou, 515000, P. R. China
- Plastic Surgery Research Institute, Ear Deformities Treatment Center and Cleft Lip and Palate Treatment Center, Shantou University Medical College, Shantou, China
| | - Wancong Zhang
- Department of Plastic and Burns Surgery, The Second Affiliated Hospital of Shantou University Medical College, Shantou, 515000, P. R. China
- Plastic Surgery Research Institute, Ear Deformities Treatment Center and Cleft Lip and Palate Treatment Center, Shantou University Medical College, Shantou, China
| | - Shijie Tang
- Department of Plastic and Burns Surgery, The Second Affiliated Hospital of Shantou University Medical College, Shantou, 515000, P. R. China
- Plastic Surgery Research Institute, Ear Deformities Treatment Center and Cleft Lip and Palate Treatment Center, Shantou University Medical College, Shantou, China
| | - Xiaoping Zhong
- Department of Plastic and Burns Surgery, The Second Affiliated Hospital of Shantou University Medical College, Shantou, 515000, P. R. China.
- Plastic Surgery Research Institute, Ear Deformities Treatment Center and Cleft Lip and Palate Treatment Center, Shantou University Medical College, Shantou, China.
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19
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Dopkins N, Nixon DF. Activation of human endogenous retroviruses and its physiological consequences. Nat Rev Mol Cell Biol 2024; 25:212-222. [PMID: 37872387 DOI: 10.1038/s41580-023-00674-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/27/2023] [Indexed: 10/25/2023]
Abstract
Human endogenous retroviruses (HERVs) are abundant sequences that persist within the human genome as remnants of ancient retroviral infections. These sequences became fixed and accumulate mutations or deletions over time. HERVs have affected human evolution and physiology by providing a unique repertoire of coding and non-coding sequences to the genome. In healthy individuals, HERVs participate in immune responses, formation of syncytiotrophoblasts and cell-fate specification. In this Review, we discuss how endogenized retroviral motifs and regulatory sequences have been co-opted into human physiology and how they are tightly regulated. Infections and mutations can derail this regulation, leading to differential HERV expression, which may contribute to pathologies including neurodegeneration, pathological inflammation and oncogenesis. Emerging evidence demonstrates that HERVs are crucial to human health and represent an understudied facet of many diseases, and we therefore argue that investigating their fundamental properties could improve existing therapies and help develop novel therapeutic strategies.
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Affiliation(s)
- Nicholas Dopkins
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA.
| | - Douglas F Nixon
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA.
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20
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Lanciano S, Philippe C, Sarkar A, Pratella D, Domrane C, Doucet AJ, van Essen D, Saccani S, Ferry L, Defossez PA, Cristofari G. Locus-level L1 DNA methylation profiling reveals the epigenetic and transcriptional interplay between L1s and their integration sites. CELL GENOMICS 2024; 4:100498. [PMID: 38309261 PMCID: PMC10879037 DOI: 10.1016/j.xgen.2024.100498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 07/20/2023] [Accepted: 01/09/2024] [Indexed: 02/05/2024]
Abstract
Long interspersed element 1 (L1) retrotransposons are implicated in human disease and evolution. Their global activity is repressed by DNA methylation, but deciphering the regulation of individual copies has been challenging. Here, we combine short- and long-read sequencing to unveil L1 methylation heterogeneity across cell types, families, and individual loci and elucidate key principles involved. We find that the youngest primate L1 families are specifically hypomethylated in pluripotent stem cells and the placenta but not in most tumors. Locally, intronic L1 methylation is intimately associated with gene transcription. Conversely, the L1 methylation state can propagate to the proximal region up to 300 bp. This phenomenon is accompanied by the binding of specific transcription factors, which drive the expression of L1 and chimeric transcripts. Finally, L1 hypomethylation alone is typically insufficient to trigger L1 expression due to redundant silencing pathways. Our results illuminate the epigenetic and transcriptional interplay between retrotransposons and their host genome.
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Affiliation(s)
- Sophie Lanciano
- University Cote d'Azur, INSERM, CNRS, Institute for Research on Cancer and Aging of Nice (IRCAN), Nice, France
| | - Claude Philippe
- University Cote d'Azur, INSERM, CNRS, Institute for Research on Cancer and Aging of Nice (IRCAN), Nice, France
| | - Arpita Sarkar
- University Cote d'Azur, INSERM, CNRS, Institute for Research on Cancer and Aging of Nice (IRCAN), Nice, France
| | - David Pratella
- University Cote d'Azur, INSERM, CNRS, Institute for Research on Cancer and Aging of Nice (IRCAN), Nice, France
| | - Cécilia Domrane
- University Paris Cité, CNRS, Epigenetics and Cell Fate, Paris, France
| | - Aurélien J Doucet
- University Cote d'Azur, INSERM, CNRS, Institute for Research on Cancer and Aging of Nice (IRCAN), Nice, France
| | - Dominic van Essen
- University Cote d'Azur, INSERM, CNRS, Institute for Research on Cancer and Aging of Nice (IRCAN), Nice, France
| | - Simona Saccani
- University Cote d'Azur, INSERM, CNRS, Institute for Research on Cancer and Aging of Nice (IRCAN), Nice, France
| | - Laure Ferry
- University Paris Cité, CNRS, Epigenetics and Cell Fate, Paris, France
| | | | - Gael Cristofari
- University Cote d'Azur, INSERM, CNRS, Institute for Research on Cancer and Aging of Nice (IRCAN), Nice, France.
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21
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Liang Y, Qu X, Shah NM, Wang T. Towards targeting transposable elements for cancer therapy. Nat Rev Cancer 2024; 24:123-140. [PMID: 38228901 DOI: 10.1038/s41568-023-00653-8] [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] [Accepted: 12/04/2023] [Indexed: 01/18/2024]
Abstract
Transposable elements (TEs) represent almost half of the human genome. Historically deemed 'junk DNA', recent technological advancements have stimulated a wave of research into the functional impact of TEs on gene-regulatory networks in evolution and development, as well as in diseases including cancer. The genetic and epigenetic evolution of cancer involves the exploitation of TEs, whereby TEs contribute directly to cancer-specific gene activities. This Review provides a perspective on the role of TEs in cancer as being a 'double-edged sword', both promoting cancer evolution and representing a vulnerability that could be exploited in cancer therapy. We discuss how TEs affect transcriptome regulation and other cellular processes in cancer. We highlight the potential of TEs as therapeutic targets for cancer. We also summarize technical hurdles in the characterization of TEs with genomic assays. Last, we outline open questions and exciting future research avenues.
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Affiliation(s)
- Yonghao Liang
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO, USA
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Xuan Qu
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO, USA
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Nakul M Shah
- Division of Cancer Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ting Wang
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO, USA.
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, Saint Louis, MO, USA.
- McDonnell Genome Institute, Washington University School of Medicine, Saint Louis, MO, USA.
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22
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Moussion C, Delamarre L. Antigen cross-presentation by dendritic cells: A critical axis in cancer immunotherapy. Semin Immunol 2024; 71:101848. [PMID: 38035643 DOI: 10.1016/j.smim.2023.101848] [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: 06/07/2023] [Revised: 10/30/2023] [Accepted: 10/30/2023] [Indexed: 12/02/2023]
Abstract
Dendritic cells (DCs) are professional antigen-presenting cells that play a key role in shaping adaptive immunity. DCs have a unique ability to sample their environment, capture and process exogenous antigens into peptides that are then loaded onto major histocompatibility complex class I molecules for presentation to CD8+ T cells. This process, called cross-presentation, is essential for initiating and regulating CD8+ T cell responses against tumors and intracellular pathogens. In this review, we will discuss the role of DCs in cancer immunity, the molecular mechanisms underlying antigen cross-presentation by DCs, the immunosuppressive factors that limit the efficiency of this process in cancer, and approaches to overcome DC dysfunction and therapeutically promote antitumoral immunity.
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Affiliation(s)
| | - Lélia Delamarre
- Cancer Immunology, Genentech, South San Francisco, CA 94080, USA.
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23
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Rospo G, Chilà R, Matafora V, Basso V, Lamba S, Bartolini A, Bachi A, Di Nicolantonio F, Mondino A, Germano G, Bardelli A. Non-canonical antigens are the largest fraction of peptides presented by MHC class I in mismatch repair deficient murine colorectal cancer. Genome Med 2024; 16:15. [PMID: 38243308 PMCID: PMC10797964 DOI: 10.1186/s13073-023-01275-3] [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: 09/14/2022] [Accepted: 12/12/2023] [Indexed: 01/21/2024] Open
Abstract
BACKGROUND Immunotherapy based on checkpoint inhibitors is highly effective in mismatch repair deficient (MMRd) colorectal cancer (CRC). These tumors carry a high number of mutations, which are predicted to translate into a wide array of neoepitopes; however, a systematic classification of the neoantigen repertoire in MMRd CRC is lacking. Mass spectrometry peptidomics has demonstrated the existence of MHC class I associated peptides (MAPs) originating from non-coding DNA regions. Based on these premises we investigated DNA genomic regions responsible for generating MMRd-induced peptides. METHODS We exploited mouse CRC models in which the MMR gene Mlh1 was genetically inactivated. Isogenic cell lines CT26 Mlh1+/+ and Mlh1-/- were inoculated in immunocompromised and immunocompetent mice. Whole genome and RNA sequencing data were generated from samples obtained before and after injection in murine hosts. First, peptide databases were built from transcriptomes of isogenic cell lines. We then compiled a database of peptides lost after tumor cells injection in immunocompetent mice, likely due to immune editing. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) and matched next-generation sequencing databases were employed to identify the DNA regions from which the immune-targeted MAPs originated. Finally, we adopted in vitro T cell assays to verify whether MAP-specific T cells were part of the in vivo immune response against Mlh1-/- cells. RESULTS Whole genome sequencing analyses revealed an unbalanced distribution of immune edited alterations across the genome in Mlh1-/- cells grown in immunocompetent mice. Specifically, untranslated (UTR) and coding regions exhibited the largest fraction of mutations leading to highly immunogenic peptides. Moreover, the integrated computational and LC-MS/MS analyses revealed that MAPs originate mainly from atypical translational events in both Mlh1+/+ and Mlh1-/- tumor cells. In addition, mutated MAPs-derived from UTRs and out-of-frame translation of coding regions-were highly enriched in Mlh1-/- cells. The MAPs trigger T-cell activation in mice primed with Mlh1-/- cells. CONCLUSIONS Our results suggest that-in comparison to MMR proficient CRC-MMRd tumors generate a significantly higher number of non-canonical mutated peptides able to elicit T cell responses. These results reveal the importance of evaluating the diversity of neoepitope repertoire in MMRd tumors.
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Affiliation(s)
- Giuseppe Rospo
- Department of Oncology, Molecular Biotechnology Center, University of Torino, Turin, Italy
- Present address: Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | - Rosaria Chilà
- IFOM ETS - The AIRC Institute of Molecular Oncology, 20139, Milan, Italy
| | - Vittoria Matafora
- IFOM ETS - The AIRC Institute of Molecular Oncology, 20139, Milan, Italy
| | - Veronica Basso
- Lymphocyte Activation Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute Via Olgettina, 58, 20132, Milan, Italy
| | - Simona Lamba
- Department of Oncology, Molecular Biotechnology Center, University of Torino, Turin, Italy
| | - Alice Bartolini
- Candiolo Cancer Institute, FPO-IRCCS, 10060, Candiolo, TO, Italy
| | - Angela Bachi
- IFOM ETS - The AIRC Institute of Molecular Oncology, 20139, Milan, Italy
| | - Federica Di Nicolantonio
- Department of Oncology, Molecular Biotechnology Center, University of Torino, Turin, Italy
- Candiolo Cancer Institute, FPO-IRCCS, 10060, Candiolo, TO, Italy
| | - Anna Mondino
- Lymphocyte Activation Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute Via Olgettina, 58, 20132, Milan, Italy
| | - Giovanni Germano
- Department of Oncology, Molecular Biotechnology Center, University of Torino, Turin, Italy.
- IFOM ETS - The AIRC Institute of Molecular Oncology, 20139, Milan, Italy.
| | - Alberto Bardelli
- Department of Oncology, Molecular Biotechnology Center, University of Torino, Turin, Italy.
- IFOM ETS - The AIRC Institute of Molecular Oncology, 20139, Milan, Italy.
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24
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Li G, Mahajan S, Ma S, Jeffery ED, Zhang X, Bhattacharjee A, Venkatasubramanian M, Weirauch MT, Miraldi ER, Grimes HL, Sheynkman GM, Tilburgs T, Salomonis N. Splicing neoantigen discovery with SNAF reveals shared targets for cancer immunotherapy. Sci Transl Med 2024; 16:eade2886. [PMID: 38232136 DOI: 10.1126/scitranslmed.ade2886] [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: 08/05/2022] [Accepted: 12/13/2023] [Indexed: 01/19/2024]
Abstract
Immunotherapy has emerged as a crucial strategy to combat cancer by "reprogramming" a patient's own immune system. Although immunotherapy is typically reserved for patients with a high mutational burden, neoantigens produced from posttranscriptional regulation may provide an untapped reservoir of common immunogenic targets for new targeted therapies. To comprehensively define tumor-specific and likely immunogenic neoantigens from patient RNA-Seq, we developed Splicing Neo Antigen Finder (SNAF), an easy-to-use and open-source computational workflow to predict splicing-derived immunogenic MHC-bound peptides (T cell antigen) and unannotated transmembrane proteins with altered extracellular epitopes (B cell antigen). This workflow uses a highly accurate deep learning strategy for immunogenicity prediction (DeepImmuno) in conjunction with new algorithms to rank the tumor specificity of neoantigens (BayesTS) and to predict regulators of mis-splicing (RNA-SPRINT). T cell antigens from SNAF were frequently evidenced as HLA-presented peptides from mass spectrometry (MS) and predict response to immunotherapy in melanoma. Splicing neoantigen burden was attributed to coordinated splicing factor dysregulation. Shared splicing neoantigens were found in up to 90% of patients with melanoma, correlated to overall survival in multiple cancer cohorts, induced T cell reactivity, and were characterized by distinct cells of origin and amino acid preferences. In addition to T cell neoantigens, our B cell focused pipeline (SNAF-B) identified a new class of tumor-specific extracellular neoepitopes, which we termed ExNeoEpitopes. ExNeoEpitope full-length mRNA predictions were tumor specific and were validated using long-read isoform sequencing and in vitro transmembrane localization assays. Therefore, our systematic identification of splicing neoantigens revealed potential shared targets for therapy in heterogeneous cancers.
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Affiliation(s)
- Guangyuan Li
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
- Department of Biomedical Informatics, College of Medicine, University of Cincinnati, Cincinnati, OH 45267, USA
| | - Shweta Mahajan
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Siyuan Ma
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Erin D Jeffery
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22903, USA
| | - Xuan Zhang
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Anukana Bhattacharjee
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Meenakshi Venkatasubramanian
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
- Department of Computer Science, University of Cincinnati, Cincinnati, OH 45229, USA
| | - Matthew T Weirauch
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital, Cincinnati, OH 45229, USA
- Division of Human Genetics, Cincinnati Children's Hospital, Cincinnati, OH 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Emily R Miraldi
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - H Leighton Grimes
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Gloria M Sheynkman
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22903, USA
| | - Tamara Tilburgs
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Nathan Salomonis
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
- Department of Biomedical Informatics, College of Medicine, University of Cincinnati, Cincinnati, OH 45267, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
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25
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Gu X, Wang M, Zhang XO. TE-TSS: an integrated data resource of human and mouse transposable element (TE)-derived transcription start site (TSS). Nucleic Acids Res 2024; 52:D322-D333. [PMID: 37956335 PMCID: PMC10767810 DOI: 10.1093/nar/gkad1048] [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: 08/13/2023] [Revised: 10/21/2023] [Accepted: 10/23/2023] [Indexed: 11/15/2023] Open
Abstract
Transposable elements (TEs) are abundant in the genome and serve as crucial regulatory elements. Some TEs function as epigenetically regulated promoters, and these TE-derived transcription start sites (TSSs) play a crucial role in regulating genes associated with specific functions, such as cancer and embryogenesis. However, the lack of an accessible database that systematically gathers TE-derived TSS data is a current research gap. To address this, we established TE-TSS, an integrated data resource of human and mouse TE-derived TSSs (http://xozhanglab.com/TETSS). TE-TSS has compiled 2681 RNA sequencing datasets, spanning various tissues, cell lines and developmental stages. From these, we identified 5768 human TE-derived TSSs and 2797 mouse TE-derived TSSs, with 47% and 38% being experimentally validated, respectively. TE-TSS enables comprehensive exploration of TSS usage in diverse samples, providing insights into tissue-specific gene expression patterns and transcriptional regulatory elements. Furthermore, TE-TSS compares TE-derived TSS regions across 15 mammalian species, enhancing our understanding of their evolutionary and functional aspects. The establishment of TE-TSS facilitates further investigations into the roles of TEs in shaping the transcriptomic landscape and offers valuable resources for comprehending their involvement in diverse biological processes.
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Affiliation(s)
- Xiaobing Gu
- Shanghai Key Laboratory of Maternal and Fetal Medicine, Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Mingdong Wang
- Shanghai Key Laboratory of Maternal and Fetal Medicine, Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Xiao-Ou Zhang
- Shanghai Key Laboratory of Maternal and Fetal Medicine, Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
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26
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Lanciano S, Cristofari G. Cancer Immunotherapy: How to Exploit Transposable Elements? Clin Chem 2024; 70:17-20. [PMID: 37572000 DOI: 10.1093/clinchem/hvad091] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 06/07/2023] [Indexed: 08/14/2023]
Affiliation(s)
- Sophie Lanciano
- University Cote d'Azur, Inserm, CNRS, Institute for Research on Cancer and Aging of Nice (IRCAN), Faculty of Medicine, Nice, France
| | - Gael Cristofari
- University Cote d'Azur, Inserm, CNRS, Institute for Research on Cancer and Aging of Nice (IRCAN), Faculty of Medicine, Nice, France
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27
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Dopkins N, Singh B, Michael S, Zhang P, Marston JL, Fei T, Singh M, Feschotte C, Collins N, Bendall ML, Nixon DF. Ribosomal profiling of human endogenous retroviruses in healthy tissues. BMC Genomics 2024; 25:5. [PMID: 38166631 PMCID: PMC10759522 DOI: 10.1186/s12864-023-09909-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: 06/05/2023] [Accepted: 12/14/2023] [Indexed: 01/05/2024] Open
Abstract
Human endogenous retroviruses (HERVs) are the germline embedded proviral fragments of ancient retroviral infections that make up roughly 8% of the human genome. Our understanding of HERVs in physiology primarily surrounds their non-coding functions, while their protein coding capacity remains virtually uncharacterized. Therefore, we applied the bioinformatic pipeline "hervQuant" to high-resolution ribosomal profiling of healthy tissues to provide a comprehensive overview of translationally active HERVs. We find that HERVs account for 0.1-0.4% of all translation in distinct tissue-specific profiles. Collectively, our study further supports claims that HERVs are actively translated throughout healthy tissues to provide sequences of retroviral origin to the human proteome.
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Affiliation(s)
- Nicholas Dopkins
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, 10021, USA.
| | - Bhavya Singh
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, 10021, USA
| | - Stephanie Michael
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, 10021, USA
| | - Panpan Zhang
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14850, USA
| | - Jez L Marston
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, 10021, USA
| | - Tongyi Fei
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, 10021, USA
| | - Manvendra Singh
- Clinical Neuroscience, Max Planck Institute for Multidisciplinary Sciences, City Campus, Göttingen, Germany
| | - Cedric Feschotte
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14850, USA
| | - Nicholas Collins
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, New York, NY, 10021, USA
| | - Matthew L Bendall
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, 10021, USA
| | - Douglas F Nixon
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, 10021, USA
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28
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Addala V, Newell F, Pearson JV, Redwood A, Robinson BW, Creaney J, Waddell N. Computational immunogenomic approaches to predict response to cancer immunotherapies. Nat Rev Clin Oncol 2024; 21:28-46. [PMID: 37907723 DOI: 10.1038/s41571-023-00830-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/03/2023] [Indexed: 11/02/2023]
Abstract
Cancer immunogenomics is an emerging field that bridges genomics and immunology. The establishment of large-scale genomic collaborative efforts along with the development of new single-cell transcriptomic techniques and multi-omics approaches have enabled characterization of the mutational and transcriptional profiles of many cancer types and helped to identify clinically actionable alterations as well as predictive and prognostic biomarkers. Researchers have developed computational approaches and machine learning algorithms to accurately obtain clinically useful information from genomic and transcriptomic sequencing data from bulk tissue or single cells and explore tumours and their microenvironment. The rapid growth in sequencing and computational approaches has resulted in the unmet need to understand their true potential and limitations in enabling improvements in the management of patients with cancer who are receiving immunotherapies. In this Review, we describe the computational approaches currently available to analyse bulk tissue and single-cell sequencing data from cancer, stromal and immune cells, as well as how best to select the most appropriate tool to address various clinical questions and, ultimately, improve patient outcomes.
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Affiliation(s)
- Venkateswar Addala
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia.
- Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia.
| | - Felicity Newell
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - John V Pearson
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Alec Redwood
- National Centre for Asbestos Related Diseases, University of Western Australia, Perth, Western Australia, Australia
- Institute of Respiratory Health, Perth, Western Australia, Australia
- School of Biomedical Science, University of Western Australia, Perth, Western Australia, Australia
| | - Bruce W Robinson
- National Centre for Asbestos Related Diseases, University of Western Australia, Perth, Western Australia, Australia
- Institute of Respiratory Health, Perth, Western Australia, Australia
- Department of Respiratory Medicine, Sir Charles Gairdner Hospital, Perth, Western Australia, Australia
- Medical School, University of Western Australia, Perth, Western Australia, Australia
| | - Jenette Creaney
- National Centre for Asbestos Related Diseases, University of Western Australia, Perth, Western Australia, Australia
- Institute of Respiratory Health, Perth, Western Australia, Australia
- School of Biomedical Science, University of Western Australia, Perth, Western Australia, Australia
- Department of Respiratory Medicine, Sir Charles Gairdner Hospital, Perth, Western Australia, Australia
| | - Nicola Waddell
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia.
- Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia.
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29
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Gates TJ, Wangmo D, Zhao X, Subramanian S. Allogeneic tumor cell-derived extracellular vesicles stimulate CD8 T cell response in colorectal cancer. Mol Ther Oncolytics 2023; 31:100727. [PMID: 37822487 PMCID: PMC10562189 DOI: 10.1016/j.omto.2023.100727] [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: 04/15/2023] [Accepted: 09/14/2023] [Indexed: 10/13/2023] Open
Abstract
Most colorectal cancer (CRC) patients present with a microsatellite-stable phenotype, rendering them resistant to immune checkpoint inhibitors (ICIs). Among the contributors to ICI resistance, tumor-derived extracellular vesicles (TEVs) have emerged as critical players. Previously we demonstrated that autologous transfer of TEVs without miR-424 can induce tumor antigen-specific immune responses in CRC models. Therefore, we postulated that allogeneic TEVs, modified to lack miR-424 and derived from an MC38 cells, could induce CD8+ T cell responses while restraining CT26 cell-based tumor. Here, we show that prophylactic administration of MC38 TEVs, without miR-424, showed a significant augmentation in CD8+ T-cells within CT26 tumors. This allogenic TEV effect was evident in CT26 tumors but not B16-F10 melanoma. Furthermore, we demonstrated the capacity of dendritic cells (DCs) to internalize TEVs, a possible mechanism to elicit immune response. Our investigation of autologously administered DCs, which had been exposed to modified TEVs, underscores their potential to dampen tumor growth while elevating CD8+ T cell levels vis-a-vis MC38 wild-type TEVs exposed to DCs. Notably, the modified TEVs were well tolerated and did not increase peripheral blood cytokine levels. Our findings underscore the potential of modified allogeneic TEVs without immune-suppressive factors to elicit robust T cell responses and limit tumor growth.
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Affiliation(s)
- Travis J. Gates
- Department of Pharmacology, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Dechen Wangmo
- Department of Pharmacology, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Xianda Zhao
- Department of Surgery, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Subbaya Subramanian
- Department of Surgery, University of Minnesota Medical School, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota Medical School, Minneapolis, MN, USA
- Center for Immunology, University of Minnesota Medical School, Minneapolis, MN, USA
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30
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Dallmann J, Freitag J, Jung C, Khinvasara K, Merz L, Peters D, Schork M, Beck J. CIMT 2023: report on the 20th Annual Meeting of the Association for Cancer Immunotherapy. IMMUNO-ONCOLOGY TECHNOLOGY 2023; 20:100397. [PMID: 37876518 PMCID: PMC10590812 DOI: 10.1016/j.iotech.2023.100397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/26/2023]
Abstract
The Association for Cancer Immunotherapy (CIMT) celebrated the 20th anniversary of the CIMT Annual Meeting. CIMT2023 was held 3-5 May 2023 in Mainz, Germany. 1051 academic and clinical professionals from over 30 countries attended the meeting and discussed the latest advances in cancer immunology and immunotherapy research. This report summarizes the highlights of CIMT2023.
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Affiliation(s)
- J. Dallmann
- Immunotherapies & Preclinical Research, BioNTech SE, Mainz
| | - J. Freitag
- TRON-Translational Oncology, University Medical Center of the Johannes Gutenberg University Mainz gGmbH, Mainz, Germany
| | - C. Jung
- BioNTech Cell & Gene Therapies GmbH, Mainz
| | - K. Khinvasara
- TRON-Translational Oncology, University Medical Center of the Johannes Gutenberg University Mainz gGmbH, Mainz, Germany
| | - L. Merz
- TRON-Translational Oncology, University Medical Center of the Johannes Gutenberg University Mainz gGmbH, Mainz, Germany
| | - D. Peters
- Immunotherapies & Preclinical Research, BioNTech SE, Mainz
| | - M. Schork
- TRON-Translational Oncology, University Medical Center of the Johannes Gutenberg University Mainz gGmbH, Mainz, Germany
| | - J.D. Beck
- Immunotherapies & Preclinical Research, BioNTech SE, Mainz
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31
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Kwok DW, Stevers NO, Nejo T, Chen LH, Etxeberria I, Jung J, Okada K, Cove MC, Lakshmanachetty S, Gallus M, Barpanda A, Hong C, Chan GKL, Wu SH, Ramos E, Yamamichi A, Liu J, Watchmaker P, Ogino H, Saijo A, Du A, Grishanina N, Woo J, Diaz A, Chang SM, Phillips JJ, Wiita AP, Klebanoff CA, Costello JF, Okada H. Tumor-wide RNA splicing aberrations generate immunogenic public neoantigens. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.19.563178. [PMID: 37904942 PMCID: PMC10614978 DOI: 10.1101/2023.10.19.563178] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/01/2023]
Abstract
T-cell-mediated immunotherapies are limited by the extent to which cancer-specific antigens are homogenously expressed throughout a tumor. We reasoned that recurrent splicing aberrations in cancer represent a potential source of tumor-wide and public neoantigens, and to test this possibility, we developed a novel pipeline for identifying neojunctions expressed uniformly within a tumor across diverse cancer types. Our analyses revealed multiple neojunctions that recur across patients and either exhibited intratumor heterogeneity or, in some cases, were tumor-wide. We identified CD8+ T-cell clones specific for neoantigens derived from tumor-wide and conserved neojunctions in GNAS and RPL22 , respectively. TCR-engineered CD8 + T-cells targeting these mutations conferred neoantigen-specific tumor cell eradication. Furthermore, we revealed that cancer-specific dysregulation in splicing factor expression leads to recurrent neojunction expression. Together, these data reveal that a subset of neojunctions are both intratumorally conserved and public, providing the molecular basis for novel T-cell-based immunotherapies that address intratumoral heterogeneity.
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32
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Xu B, Li X, Zhang S, Lian M, Huang W, Zhang Y, Wang Y, Huang Z. Pan cancer characterization of genes whose expression has been associated with LINE-1 antisense promoter activity. Mob DNA 2023; 14:13. [PMID: 37723560 PMCID: PMC10506190 DOI: 10.1186/s13100-023-00300-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 08/28/2023] [Indexed: 09/20/2023] Open
Abstract
BACKGROUND Long interspersed nuclear element-1 (LINE-1 or L1) comprises 17% of the human genome. As the only autonomous and active retrotransposons, L1 may take part in cancer initiation and progression in some ways. The studies of L1 in cancer mainly focus on the impact of L1 insertion into the new genome locus. The L1 5´ untranslated region (UTR) also contains antisense promoter (ASP) activity, generating L1-gene chimeric transcripts to a neighbor exon. Some of these ASP-associated genes have been reported to be overexpressed in cancer and promote cancer cell growth. However, little is known about overall expression patterns and the roles of L1 ASP-associated genes in human cancers. RESULTS L1 ASP-associated genes were frequently dysregulated in cancer and associated with the cell cycle, the PI3K/AKT pathway, and the GTPase signaling pathway. The expression of L1 ASP-associated genes was correlated with tumor patient prognosis. Hub L1 ASP-associated genes CENPU and MCM2 showed a correlation with immune infiltration, clinical T stage, and cancer stemness in pan-cancer. Knockdown of L1 ASP-associated gene LINC00491 resulted in a significant decrease in tumor growth and migration ability. CONCLUSIONS The expression of L1 ASP-associated genes is significantly dysregulated at the pan-cancer level, which is closely related to the tumor microenvironment, progression, and patient prognosis. Hub genes CENPU and MCM2 are expected to be new tumor diagnostic markers and therapeutic targets.
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Affiliation(s)
- Baohong Xu
- First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, Guangdong, China
| | - Xueer Li
- First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, Guangdong, China
| | - Shaoqi Zhang
- First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, Guangdong, China
| | - Meina Lian
- First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, Guangdong, China
| | - Wenbin Huang
- First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, Guangdong, China
| | - Yin Zhang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China.
| | - Yudong Wang
- First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, Guangdong, China.
| | - Zhiquan Huang
- First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, Guangdong, China.
- Department of Oral and Maxillofacial Surgery, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China.
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Wolf MM, Rathmell WK, de Cubas AA. Immunogenicity in renal cell carcinoma: shifting focus to alternative sources of tumour-specific antigens. Nat Rev Nephrol 2023; 19:440-450. [PMID: 36973495 PMCID: PMC10801831 DOI: 10.1038/s41581-023-00700-5] [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: 02/27/2023] [Indexed: 03/29/2023]
Abstract
Renal cell carcinoma (RCC) comprises a group of malignancies arising from the kidney with unique tumour-specific antigen (TSA) signatures that can trigger cytotoxic immunity. Two classes of TSAs are now considered potential drivers of immunogenicity in RCC: small-scale insertions and deletions (INDELs) that result in coding frameshift mutations, and activation of human endogenous retroviruses. The presence of neoantigen-specific T cells is a hallmark of solid tumours with a high mutagenic burden, which typically have abundant TSAs owing to non-synonymous single nucleotide variations within the genome. However, RCC exhibits high cytotoxic T cell reactivity despite only having an intermediate non-synonymous single nucleotide variation mutational burden. Instead, RCC tumours have a high pan-cancer proportion of INDEL frameshift mutations, and coding frameshift INDELs are associated with high immunogenicity. Moreover, cytotoxic T cells in RCC subtypes seem to recognize tumour-specific endogenous retrovirus epitopes, whose presence is associated with clinical responses to immune checkpoint blockade therapy. Here, we review the distinct molecular landscapes in RCC that promote immunogenic responses, discuss clinical opportunities for discovery of biomarkers that can inform therapeutic immune checkpoint blockade strategies, and identify gaps in knowledge for future investigations.
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Affiliation(s)
- Melissa M Wolf
- Department of Medicine, Program in Cancer Biology, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - W Kimryn Rathmell
- Department of Medicine, Program in Cancer Biology, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA.
| | - Aguirre A de Cubas
- Department of Microbiology and Immunology, Medical University of South Carolina, Charleston, SC, USA.
- Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, USA.
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Singh B, Dopkins N, Fei T, Marston JL, Michael S, Reyes-Gopar H, Curty G, Heymann JJ, Chadburn A, Martin P, Leal FE, Cesarman E, Nixon DF, Bendall ML. Locus specific human endogenous retroviruses reveal new lymphoma subtypes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.08.544208. [PMID: 37333202 PMCID: PMC10274920 DOI: 10.1101/2023.06.08.544208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
The heterogeneity of cancers are driven by diverse mechanisms underlying oncogenesis such as differential 'cell-of-origin' (COO) progenitors, mutagenesis, and viral infections. Classification of B-cell lymphomas have been defined by considering these characteristics. However, the expression and contribution of transposable elements (TEs) to B cell lymphoma oncogenesis or classification have been overlooked. We hypothesized that incorporating TE signatures would increase the resolution of B-cell identity during healthy and malignant conditions. Here, we present the first comprehensive, locus-specific characterization of TE expression in benign germinal center (GC) B-cells, diffuse large B-cell lymphoma (DLBCL), Epstein-Barr virus (EBV)-positive and EBV-negative Burkitt lymphoma (BL), and follicular lymphoma (FL). Our findings demonstrate unique human endogenous retrovirus (HERV) signatures in the GC and lymphoma subtypes whose activity can be used in combination with gene expression to define B-cell lineage in lymphoid malignancies, highlighting the potential of retrotranscriptomic analyses as a tool in lymphoma classification, diagnosis, and the identification of novel treatment groups.
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Affiliation(s)
- Bhavya Singh
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Nicholas Dopkins
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Tongyi Fei
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Jez L. Marston
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Stephanie Michael
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Helena Reyes-Gopar
- Programa de Doctorado en Ciencias Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Departamento de Genómica Computacional, Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - Gislaine Curty
- Brazilian National Cancer Institute (INCA), Rio de Janeiro, Brazil
| | - Jonas J. Heymann
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Amy Chadburn
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Peter Martin
- Division of Hematology and Medical Oncology, Weill Cornell Medicine, New York, NY, USA
| | - Fabio E. Leal
- Brazilian National Cancer Institute (INCA), Rio de Janeiro, Brazil
| | - Ethel Cesarman
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Douglas F. Nixon
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Matthew L. Bendall
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
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Stewart PA, Jaeger AM. Taking the temperature of lung cancer antigens. NATURE CANCER 2023; 4:586-587. [PMID: 37237079 DOI: 10.1038/s43018-023-00552-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Affiliation(s)
- Paul A Stewart
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Alex M Jaeger
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA.
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Gates TJ, Wangmo D, Zhao X, Subramanian S. Allogeneic Tumor Cell-Derived Extracellular Vesicles Stimulate CD8 T Cell Response in Colorectal Cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.17.537250. [PMID: 37131597 PMCID: PMC10153182 DOI: 10.1101/2023.04.17.537250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Colorectal Cancer (CRC) is the second leading cause of cancer-related death in the United States. Most CRC patients present with a microsatellite stable (MSS) phenotype and are highly resistant to immunotherapies. Tumor extracellular vesicles (TEVs), secreted by tumor cells, can contribute to intrinsic resistance to immunotherapy in CRC. We previously showed that autologous TEVs without functional miR-424 induce anti-tumor immune responses. We hypothesized that allogeneic modified CRC-TEVs without miR-424 (mouse homolog miR-322) derived from an MC38 background would effectively stimulate CD8+ T cell response and limit CT26 tumor growth. Here we show that prophylactic administration of MC38 TEVs without functional miR-424 significantly increased CD8+ T cells in CT26 CRC tumors and limited tumor growth, not B16-F10 melanoma tumors. We further show that the depletion of CD4+ and CD8+ T cells abolished the protective effects of MC38 TEVs without functional miR-424. We further show that TEVs can be taken up by DCs in vitro, and subsequent prophylactic administration of autologous DCs exposed to MC38 TEVs without functional miR-424 suppressed tumor growth and increased CD8+ T cells compared to MC38 wild-type TEVs exposed to DCs, in Balb/c mice bearing CT26 tumors. Notably, the modified EVs were well tolerated and did not increase cytokine expression in peripheral blood. These findings suggest that allogeneic-modified CRC-EVs without immune suppressive miR-424 can induce antitumor CD8+ T cell responses and limit tumor growth in vivo.
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Affiliation(s)
- Travis J Gates
- Department of Molecular Pharmacology and Therapeutics, University of Minnesota Medical School, Minneapolis, Minnesota
| | - Dechen Wangmo
- Department of Molecular Pharmacology and Therapeutics, University of Minnesota Medical School, Minneapolis, Minnesota
| | - Xianda Zhao
- Department of Surgery, University of Minnesota Medical School, Minneapolis, Minnesota
| | - Subbaya Subramanian
- Department of Surgery, University of Minnesota Medical School, Minneapolis, Minnesota
- Masonic Cancer Center, University of Minnesota Medical School, Minneapolis, Minnesota
- Center for Immunology, University of Minnesota Medical School, Minneapolis, Minnesota
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