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Yang J, Xu J, Wang W, Zhang B, Yu X, Shi S. Epigenetic regulation in the tumor microenvironment: molecular mechanisms and therapeutic targets. Signal Transduct Target Ther 2023; 8:210. [PMID: 37217462 DOI: 10.1038/s41392-023-01480-x] [Citation(s) in RCA: 55] [Impact Index Per Article: 55.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 04/17/2023] [Accepted: 04/28/2023] [Indexed: 05/24/2023] Open
Abstract
Over decades, researchers have focused on the epigenetic control of DNA-templated processes. Histone modification, DNA methylation, chromatin remodeling, RNA modification, and noncoding RNAs modulate many biological processes that are crucial to the development of cancers. Dysregulation of the epigenome drives aberrant transcriptional programs. A growing body of evidence suggests that the mechanisms of epigenetic modification are dysregulated in human cancers and might be excellent targets for tumor treatment. Epigenetics has also been shown to influence tumor immunogenicity and immune cells involved in antitumor responses. Thus, the development and application of epigenetic therapy and cancer immunotherapy and their combinations may have important implications for cancer treatment. Here, we present an up-to-date and thorough description of how epigenetic modifications in tumor cells influence immune cell responses in the tumor microenvironment (TME) and how epigenetics influence immune cells internally to modify the TME. Additionally, we highlight the therapeutic potential of targeting epigenetic regulators for cancer immunotherapy. Harnessing the complex interplay between epigenetics and cancer immunology to develop therapeutics that combine thereof is challenging but could yield significant benefits. The purpose of this review is to assist researchers in understanding how epigenetics impact immune responses in the TME, so that better cancer immunotherapies can be developed.
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Affiliation(s)
- Jing Yang
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Shanghai Pancreatic Cancer Institute, Shanghai, China
- Pancreatic Cancer Institute, Fudan University, Shanghai, China
| | - Jin Xu
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Shanghai Pancreatic Cancer Institute, Shanghai, China
- Pancreatic Cancer Institute, Fudan University, Shanghai, China
| | - Wei Wang
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Shanghai Pancreatic Cancer Institute, Shanghai, China
- Pancreatic Cancer Institute, Fudan University, Shanghai, China
| | - Bo Zhang
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Shanghai Pancreatic Cancer Institute, Shanghai, China
- Pancreatic Cancer Institute, Fudan University, Shanghai, China
| | - Xianjun Yu
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
- Shanghai Pancreatic Cancer Institute, Shanghai, China.
- Pancreatic Cancer Institute, Fudan University, Shanghai, China.
| | - Si Shi
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
- Shanghai Pancreatic Cancer Institute, Shanghai, China.
- Pancreatic Cancer Institute, Fudan University, Shanghai, China.
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52
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Chen R, Li F, Guo X, Bi Y, Li C, Pan S, Coin LJM, Song J. ATTIC is an integrated approach for predicting A-to-I RNA editing sites in three species. Brief Bioinform 2023; 24:bbad170. [PMID: 37150785 PMCID: PMC10565902 DOI: 10.1093/bib/bbad170] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 04/12/2023] [Accepted: 04/14/2023] [Indexed: 05/09/2023] Open
Abstract
A-to-I editing is the most prevalent RNA editing event, which refers to the change of adenosine (A) bases to inosine (I) bases in double-stranded RNAs. Several studies have revealed that A-to-I editing can regulate cellular processes and is associated with various human diseases. Therefore, accurate identification of A-to-I editing sites is crucial for understanding RNA-level (i.e. transcriptional) modifications and their potential roles in molecular functions. To date, various computational approaches for A-to-I editing site identification have been developed; however, their performance is still unsatisfactory and needs further improvement. In this study, we developed a novel stacked-ensemble learning model, ATTIC (A-To-I ediTing predICtor), to accurately identify A-to-I editing sites across three species, including Homo sapiens, Mus musculus and Drosophila melanogaster. We first comprehensively evaluated 37 RNA sequence-derived features combined with 14 popular machine learning algorithms. Then, we selected the optimal base models to build a series of stacked ensemble models. The final ATTIC framework was developed based on the optimal models improved by the feature selection strategy for specific species. Extensive cross-validation and independent tests illustrate that ATTIC outperforms state-of-the-art tools for predicting A-to-I editing sites. We also developed a web server for ATTIC, which is publicly available at http://web.unimelb-bioinfortools.cloud.edu.au/ATTIC/. We anticipate that ATTIC can be utilized as a useful tool to accelerate the identification of A-to-I RNA editing events and help characterize their roles in post-transcriptional regulation.
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Affiliation(s)
- Ruyi Chen
- College of Information Engineering, Northwest A&F University, Shaanxi 712100, China
- The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, VIC 3000, Australia
| | - Fuyi Li
- College of Information Engineering, Northwest A&F University, Shaanxi 712100, China
- The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, VIC 3000, Australia
| | - Xudong Guo
- College of Information Engineering, Northwest A&F University, Shaanxi 712100, China
| | - Yue Bi
- Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, VIC 3800, Australia
| | - Chen Li
- Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, VIC 3800, Australia
| | - Shirui Pan
- School of Information and Communication Technology, Griffith University, QLD 4222, Australia
| | - Lachlan J M Coin
- The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, VIC 3000, Australia
| | - Jiangning Song
- Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, VIC 3800, Australia
- Monash Data Futures Institute, Monash University, VIC 3800, Australia
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53
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Han J, Wu M, Liu Z. Dysregulation in IFN-γ signaling and response: the barricade to tumor immunotherapy. Front Immunol 2023; 14:1190333. [PMID: 37275859 PMCID: PMC10233742 DOI: 10.3389/fimmu.2023.1190333] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 04/14/2023] [Indexed: 06/07/2023] Open
Abstract
Interferon-gamma (IFN-γ) has been identified as a crucial factor in determining the responsiveness to immunotherapy. Produced primarily by natural killer (NK) and T cells, IFN-γ promotes activation, maturation, proliferation, cytokine expression, and effector function in immune cells, while simultaneously inducing antigen presentation, growth arrest, and apoptosis in tumor cells. However, tumor cells can hijack the IFN-γ signaling pathway to mount IFN-γ resistance: rather than increasing antigenicity and succumbing to death, tumor cells acquire stemness characteristics and express immunosuppressive molecules to defend against antitumor immunity. In this review, we summarize the potential mechanisms of IFN-γ resistance occurring at two critical stages: disrupted signal transduction along the IFNG/IFNGR/JAK/STAT pathway, or preferential expression of specific interferon-stimulated genes (ISGs). Elucidating the molecular mechanisms through which tumor cells develop IFN-γ resistance help identify promising therapeutic targets to improve immunotherapy, with broad application value in conjugation with targeted, antibody or cellular therapies.
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Affiliation(s)
- Jiashu Han
- Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Department of General Surgery, Peking Union Medical College Hospital (CAMS), Beijing, China
| | - Mengwei Wu
- Department of General Surgery, Peking Union Medical College Hospital (CAMS), Beijing, China
| | - Ziwen Liu
- Department of General Surgery, Peking Union Medical College Hospital (CAMS), Beijing, China
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54
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Liang Z, Chalk AM, Taylor S, Goradia A, Heraud‐Farlow JE, Walkley CR. The phenotype of the most common human ADAR1p150 Zα mutation P193A in mice is partially penetrant. EMBO Rep 2023; 24:e55835. [PMID: 36975179 PMCID: PMC10157378 DOI: 10.15252/embr.202255835] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 02/13/2023] [Accepted: 02/28/2023] [Indexed: 03/29/2023] Open
Abstract
ADAR1 -mediated A-to-I RNA editing is a self-/non-self-discrimination mechanism for cellular double-stranded RNAs. ADAR mutations are one cause of Aicardi-Goutières Syndrome, an inherited paediatric encephalopathy, classed as a "Type I interferonopathy." The most common ADAR1 mutation is a proline 193 alanine (p.P193A) mutation, mapping to the ADAR1p150 isoform-specific Zα domain. Here, we report the development of an independent murine P195A knock-in mouse, homologous to human P193A. The Adar1P195A/P195A mice are largely normal and the mutation is well tolerated. When the P195A mutation is compounded with an Adar1 null allele (Adar1P195A/- ), approximately half the animals are runted with a shortened lifespan while the remaining Adar1P195A/- animals are normal, contrasting with previous reports. The phenotype of the Adar1P195A/- animals is both associated with the parental genotype and partly non-genetic/environmental. Complementation with an editing-deficient ADAR1 (Adar1P195A/E861A ), or the loss of MDA5, rescues phenotypes in the Adar1P195A/- mice.
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Affiliation(s)
- Zhen Liang
- St Vincent's Institute of Medical ResearchFitzroyVic.Australia
- Department of Medicine, Eastern Hill Precinct, Melbourne Medical SchoolUniversity of MelbourneFitzroyVic.Australia
| | - Alistair M Chalk
- St Vincent's Institute of Medical ResearchFitzroyVic.Australia
- Department of Medicine, Eastern Hill Precinct, Melbourne Medical SchoolUniversity of MelbourneFitzroyVic.Australia
| | - Scott Taylor
- St Vincent's Institute of Medical ResearchFitzroyVic.Australia
| | - Ankita Goradia
- St Vincent's Institute of Medical ResearchFitzroyVic.Australia
| | - Jacki E Heraud‐Farlow
- St Vincent's Institute of Medical ResearchFitzroyVic.Australia
- Department of Medicine, Eastern Hill Precinct, Melbourne Medical SchoolUniversity of MelbourneFitzroyVic.Australia
| | - Carl R Walkley
- St Vincent's Institute of Medical ResearchFitzroyVic.Australia
- Department of Medicine, Eastern Hill Precinct, Melbourne Medical SchoolUniversity of MelbourneFitzroyVic.Australia
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55
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Yin M, Dong J, Sun C, Liu X, Liu Z, Liu L, Kuang Z, Zhang N, Xiao D, Zhou X, Deng H. Raddeanin A Enhances Mitochondrial DNA-cGAS/STING Axis-Mediated Antitumor Immunity by Targeting Transactive Responsive DNA-Binding Protein 43. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2206737. [PMID: 36876644 PMCID: PMC10161045 DOI: 10.1002/advs.202206737] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 01/29/2023] [Indexed: 05/06/2023]
Abstract
Immune checkpoint therapies (ICT) have achieved unprecedented efficacy in multiple cancer treatments, but are still limited by low clinical response rates. Identification of immunogenic cell death (ICD)-inducing drugs that can induce tumor cell immunogenicity and reprogram the tumor microenvironment is an attractive approach to enhance antitumor immunity. In the present study, Raddeanin A (RA), an oleanane class triterpenoid saponin isolated from Anemone raddeana Regel, is uncovered as a potent ICD inducer through an ICD reporter assay combined with a T cell activation assay. RA significantly increases high-mobility group box 1 release in tumor cells and promotes dendritic cell (DC) maturation and CD8+ T cell activation for tumor control. Mechanistically, RA directly binds to transactive responsive DNA-binding protein 43 (TDP-43) and induces TDP-43 localization to mitochondria and mtDNA leakage, leading to cyclic GMP-AMP synthase/stimulator of interferon gene-dependent upregulation of nuclear factor κB and type I interferon signaling, thereby potentiating the DC-mediated antigen cross-presentation and T cell activation. Moreover, combining RA with anti-programmed death 1 antibody effectively enhances the efficacy of ICT in animals. These findings highlight the importance of TDP-43 in ICD drug-induced antitumor immunity and reveal a potential chemo-immunotherapeutic role of RA in enhancing the efficacy of cancer immunotherapy.
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Affiliation(s)
- Mingxiao Yin
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, P. R. China
| | - Jingwen Dong
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, P. R. China
| | - Cuicui Sun
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, P. R. China
| | - Xiaojia Liu
- Beijing Institute of Clinical Pharmacy, Beijing Friendship Hospital, Capital Medical University, Beijing, 100050, P. R. China
| | - Zhirui Liu
- National Engineering Research Center for the Emergency Drug, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, P. R. China
| | - Lu Liu
- Qingdao Women and Children's Hospital, Qingdao University, Qingdao, 266034, P. R. China
| | - Zean Kuang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, P. R. China
| | - Na Zhang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, P. R. China
| | - Dian Xiao
- National Engineering Research Center for the Emergency Drug, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, P. R. China
| | - Xinbo Zhou
- National Engineering Research Center for the Emergency Drug, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, P. R. China
| | - Hongbin Deng
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, P. R. China
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56
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Zhou X, Mitra R, Hou F, Zhou S, Wang L, Jiang W. Genomic Landscape and Potential Regulation of RNA Editing in Drug Resistance. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2207357. [PMID: 36912579 PMCID: PMC10190536 DOI: 10.1002/advs.202207357] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 01/31/2023] [Indexed: 05/18/2023]
Abstract
Adenosine-to-inosine RNA editing critically affects the response of cancer therapies. However, comprehensive identification of drug resistance-related RNA editing events and systematic understanding of how RNA editing mediates anticancer drug resistance remain unclear. Here, 7157 differential editing sites (DESs) are identified from 98 127 informative RNA editing sites in tumor tissues, many of which are validated in cancer cell lines. Diverse editing patterns of DESs are discovered in resistant samples, which could not be fully explained by adenosine deaminase acting on RNA enzymes. Some RNA-binding proteins are identified that potentially regulate these editing events. Notably, the DESs are significantly enriched in 3'-untranslated regions (3'-UTRs). The impact of DESs in 3'-UTR on the microRNA (miRNA) regulations is explored, and some triplets (DES, miRNA, and gene) that may contribute to drug resistance are identified. In addition, it is determined that the functions of genes enriched with DESs are associated with drug resistance, such as apoptosis, drug metabolism, and DNA synthesis involved in DNA repair. An online resource (http://www.jianglab.cn/REDR/) to support convenient retrieval of DESs is also built. The findings reveal the landscape and potential regulatory mechanism of RNA editing in drug resistance, providing new therapeutic targets for reversing drug resistance.
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Affiliation(s)
- Xu Zhou
- Department of Biomedical EngineeringNanjing University of Aeronautics and AstronauticsNanjing211106P. R. China
| | - Ramkrishna Mitra
- Department of PharmacologyPhysiology, and Cancer BiologySidney Kimmel Cancer CenterThomas Jefferson UniversityPhiladelphiaPennsylvania19107USA
| | - Fei Hou
- Department of Biomedical EngineeringNanjing University of Aeronautics and AstronauticsNanjing211106P. R. China
| | - Shunheng Zhou
- Department of Biomedical EngineeringNanjing University of Aeronautics and AstronauticsNanjing211106P. R. China
| | - Lihong Wang
- Department of PathophysiologySchool of MedicineSoutheast UniversityNanjing210009P. R. China
| | - Wei Jiang
- Department of Biomedical EngineeringNanjing University of Aeronautics and AstronauticsNanjing211106P. R. China
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57
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Abstract
Our defenses against infection rely on the ability of the immune system to distinguish invading pathogens from self. This task is exceptionally challenging, if not seemingly impossible, in the case of retroviruses that have integrated almost seamlessly into the host. This review examines the limits of innate and adaptive immune responses elicited by endogenous retroviruses and other retroelements, the targets of immune recognition, and the consequences for host health and disease. Contrary to theoretical expectation, endogenous retroelements retain substantial immunogenicity, which manifests most profoundly when their epigenetic repression is compromised, contributing to autoinflammatory and autoimmune disease and age-related inflammation. Nevertheless, recent evidence suggests that regulated immune reactivity to endogenous retroelements is integral to immune system development and function, underpinning cancer immunosurveillance, resistance to infection, and responses to the microbiota. Elucidation of the interaction points with endogenous retroelements will therefore deepen our understanding of immune system function and contribution to disease.
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Affiliation(s)
- George Kassiotis
- Retroviral Immunology Laboratory, The Francis Crick Institute, London, United Kingdom;
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, United Kingdom
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58
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Tiedt R, King FJ, Stamm C, Niederst MJ, Delach S, Zumstein-Mecker S, Meltzer J, Mulford IJ, Labrot E, Engstler BS, Baltschukat S, Kerr G, Golji J, Wyss D, Schnell C, Ainscow E, Engelman JA, Sellers WR, Barretina J, Caponigro G, Porta DG. Integrated CRISPR screening and drug profiling identifies combination opportunities for EGFR, ALK, and BRAF/MEK inhibitors. Cell Rep 2023; 42:112297. [PMID: 36961816 DOI: 10.1016/j.celrep.2023.112297] [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: 05/06/2021] [Revised: 01/11/2022] [Accepted: 03/03/2023] [Indexed: 03/25/2023] Open
Abstract
Anti-tumor efficacy of targeted therapies is variable across patients and cancer types. Even in patients with initial deep response, tumors are typically not eradicated and eventually relapse. To address these challenges, we present a systematic screen for targets that limit the anti-tumor efficacy of EGFR and ALK inhibitors in non-small cell lung cancer and BRAF/MEK inhibitors in colorectal cancer. Our approach includes genome-wide CRISPR screens with or without drugs targeting the oncogenic driver ("anchor therapy"), and large-scale pairwise combination screens of anchor therapies with 351 other drugs. Interestingly, targeting of a small number of genes, including MCL1, BCL2L1, and YAP1, sensitizes multiple cell lines to the respective anchor therapy. Data from drug combination screens with EGF816 and ceritinib indicate that dasatinib and agents disrupting microtubules act synergistically across many cell lines. Finally, we show that a higher-order-combination screen with 26 selected drugs in two resistant EGFR-mutant lung cancer cell lines identified active triplet combinations.
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Affiliation(s)
- Ralph Tiedt
- Novartis Institutes for BioMedical Research, Oncology Disease Area, Basel, Switzerland
| | - Frederick J King
- Novartis Institutes for BioMedical Research, Genomics Institute of the Novartis Research Foundation, La Jolla, CA, USA
| | - Christelle Stamm
- Novartis Institutes for BioMedical Research, Oncology Disease Area, Basel, Switzerland
| | - Matthew J Niederst
- Novartis Institutes for BioMedical Research, Oncology Disease Area, Cambridge, MA, USA.
| | - Scott Delach
- Novartis Institutes for BioMedical Research, Oncology Disease Area, Cambridge, MA, USA
| | | | - Jodi Meltzer
- Novartis Institutes for BioMedical Research, Oncology Disease Area, Cambridge, MA, USA
| | - Iain J Mulford
- Novartis Institutes for BioMedical Research, Oncology Disease Area, Cambridge, MA, USA
| | - Emma Labrot
- Novartis Institutes for BioMedical Research, Oncology Disease Area, Cambridge, MA, USA
| | | | - Sabrina Baltschukat
- Novartis Institutes for BioMedical Research, Oncology Disease Area, Basel, Switzerland
| | - Grainne Kerr
- Novartis Institutes for BioMedical Research, Oncology Disease Area, Basel, Switzerland
| | - Javad Golji
- Novartis Institutes for BioMedical Research, Oncology Disease Area, Cambridge, MA, USA
| | - Daniel Wyss
- Novartis Institutes for BioMedical Research, Oncology Disease Area, Basel, Switzerland
| | - Christian Schnell
- Novartis Institutes for BioMedical Research, Oncology Disease Area, Basel, Switzerland
| | - Edward Ainscow
- Novartis Institutes for BioMedical Research, Genomics Institute of the Novartis Research Foundation, La Jolla, CA, USA
| | - Jeffrey A Engelman
- Novartis Institutes for BioMedical Research, Oncology Disease Area, Cambridge, MA, USA
| | - William R Sellers
- Novartis Institutes for BioMedical Research, Oncology Disease Area, Cambridge, MA, USA
| | - Jordi Barretina
- Novartis Institutes for BioMedical Research, Oncology Disease Area, Cambridge, MA, USA
| | - Giordano Caponigro
- Novartis Institutes for BioMedical Research, Oncology Disease Area, Cambridge, MA, USA
| | - Diana Graus Porta
- Novartis Institutes for BioMedical Research, Oncology Disease Area, Basel, Switzerland
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59
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Sharifnia T, Wawer MJ, Goodale A, Lee Y, Kazachkova M, Dempster JM, Muller S, Levy J, Freed DM, Sommer J, Kalfon J, Vazquez F, Hahn WC, Root DE, Clemons PA, Schreiber SL. Mapping the landscape of genetic dependencies in chordoma. Nat Commun 2023; 14:1933. [PMID: 37024492 PMCID: PMC10079670 DOI: 10.1038/s41467-023-37593-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 03/21/2023] [Indexed: 04/08/2023] Open
Abstract
Identifying the spectrum of genes required for cancer cell survival can reveal essential cancer circuitry and therapeutic targets, but such a map remains incomplete for many cancer types. We apply genome-scale CRISPR-Cas9 loss-of-function screens to map the landscape of selectively essential genes in chordoma, a bone cancer with few validated targets. This approach confirms a known chordoma dependency, TBXT (T; brachyury), and identifies a range of additional dependencies, including PTPN11, ADAR, PRKRA, LUC7L2, SRRM2, SLC2A1, SLC7A5, FANCM, and THAP1. CDK6, SOX9, and EGFR, genes previously implicated in chordoma biology, are also recovered. We find genomic and transcriptomic features that predict specific dependencies, including interferon-stimulated gene expression, which correlates with ADAR dependence and is elevated in chordoma. Validating the therapeutic relevance of dependencies, small-molecule inhibitors of SHP2, encoded by PTPN11, have potent preclinical efficacy against chordoma. Our results generate an emerging map of chordoma dependencies to enable biological and therapeutic hypotheses.
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Affiliation(s)
- Tanaz Sharifnia
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA.
| | - Mathias J Wawer
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
- Kojin Therapeutics, Boston, MA, 02210, USA
| | - Amy Goodale
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - Yenarae Lee
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - Mariya Kazachkova
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
- University of California San Diego, La Jolla, CA, 92093, USA
| | | | - Sandrine Muller
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - Joan Levy
- Chordoma Foundation, Durham, NC, 27702, USA
- Melanoma Research Alliance, Washington, D.C., 20005, USA
| | | | | | - Jérémie Kalfon
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | | | - William C Hahn
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
- Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - David E Root
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - Paul A Clemons
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - Stuart L Schreiber
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA.
- Harvard University, Cambridge, MA, 02138, USA.
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60
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Gong L, Huang D, Shi Y, Liang Z, Bu H. Regulated cell death in cancer: from pathogenesis to treatment. Chin Med J (Engl) 2023; 136:653-665. [PMID: 35950752 PMCID: PMC10129203 DOI: 10.1097/cm9.0000000000002239] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Indexed: 12/24/2022] Open
Abstract
ABSTRACT Regulated cell death (RCD), including apoptosis, pyroptosis, necroptosis, and ferroptosis, is regulated by a series of evolutionarily conserved pathways, and is required for development and tissue homeostasis. Based on previous genetic and biochemical explorations of cell death subroutines, the characteristics of each are generally considered distinctive. However, recent in-depth studies noted the presence of crosstalk between the different forms of RCD; hence, the concept of PANoptosis appeared. Cancer, a complex genetic disease, is characterized by stepwise deregulation of cell apoptosis and proliferation, with significant morbidity and mortality globally. At present, studies on the different RCD pathways, as well as the intricate relationships between different cell death subroutines, mainly focus on infectious diseases, and their roles in cancer remain unclear. As cancers are characterized by dysregulated cell death and inflammatory responses, most current treatment strategies aim to selectively induce cell death via different RCD pathways in cancer cells. In this review, we describe five types of RCD pathways in detail with respect to tumorigenesis and cancer progression. The potential value of some of these key effector molecules in tumor diagnosis and therapeutic response has also been raised. We then review and highlight recent progress in cancer treatment based on PANoptosis and ferroptosis induced by small-molecule compounds, immune checkpoint inhibitors, and nanoparticles. Together, these findings may provide meaningful evidence to fill in the gaps between cancer pathogenesis and RCD pathways to develop better cancer therapeutic strategies.
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Affiliation(s)
- Linjing Gong
- Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
- Institute of Clinical Pathology, Key Laboratory of Transplant Engineering and Immunology, NHC, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Dong Huang
- Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
- Institute of Clinical Pathology, Key Laboratory of Transplant Engineering and Immunology, NHC, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Yujun Shi
- Institute of Clinical Pathology, Key Laboratory of Transplant Engineering and Immunology, NHC, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Zong’an Liang
- Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Hong Bu
- Institute of Clinical Pathology, Key Laboratory of Transplant Engineering and Immunology, NHC, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
- Department of Pathology, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
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61
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Ran XB, Ding LW, Sun QY, Yang H, Said JW, Zhentang L, Madan V, Dakle P, Xiao JF, Loh X, Li Y, Xu L, Xiang XQ, Wang LZ, Goh BC, Lin DC, Chng WJ, Tan SY, Jha S, Koeffler HP. Targeting RNA Exonuclease XRN1 Potentiates Efficacy of Cancer Immunotherapy. Cancer Res 2023; 83:922-938. [PMID: 36638333 DOI: 10.1158/0008-5472.can-21-3052] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 06/29/2022] [Accepted: 01/11/2023] [Indexed: 01/15/2023]
Abstract
Despite the remarkable clinical responses achieved with immune checkpoint blockade therapy, the response rate is relatively low and only a subset of patients can benefit from the treatment. Aberrant RNA accumulation can mediate IFN signaling and stimulate an immune response, suggesting that targeting RNA decay machinery might sensitize tumor cells to immunotherapy. With this in mind, we identified an RNA exoribonuclease, XRN1, as a potential therapeutic target to suppress RNA decay and stimulate antitumor immunity. Silencing of XRN1 suppressed tumor growth in syngeneic immunocompetent mice and potentiated immunotherapy efficacy, while silencing of XRN1 alone did not affect tumor growth in immunodeficient mice. Mechanistically, XRN1 depletion activated IFN signaling and the viral defense pathway; both pathways play determinant roles in regulating immune evasion. Aberrant RNA-sensing signaling proteins (RIG-I/MAVS) mediated the expression of IFN genes, as depletion of each of them blunted the elevation of antiviral/IFN signaling in XRN1-silenced cells. Analysis of pan-cancer CRISPR-screening data indicated that IFN signaling triggered by XRN1 silencing is a common phenomenon, suggesting that the effect of XRN1 silencing may be extended to multiple types of cancers. Overall, XRN1 depletion triggers aberrant RNA-mediated IFN signaling, highlighting the importance of the aberrant RNA-sensing pathway in regulating immune responses. These findings provide the molecular rationale for developing XRN1 inhibitors and exploring their potential clinical application in combination with cancer immunotherapy. SIGNIFICANCE Targeting XRN1 activates an intracellular innate immune response mediated by RNA-sensing signaling and potentiates cancer immunotherapy efficacy, suggesting inhibition of RNA decay machinery as a novel strategy for cancer treatment.
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Affiliation(s)
- Xue-Bin Ran
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Ling-Wen Ding
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Qiao-Yang Sun
- Department of Hematology, Singapore General Hospital, Singapore, Singapore
| | - Henry Yang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Jonathan W Said
- Santa Monica-University of California, Los Angeles Medical Center, California, Los Angeles
| | - Lao Zhentang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- Department of Hematology, Singapore General Hospital, Singapore, Singapore
| | - Vikas Madan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Pushkar Dakle
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Jin-Fen Xiao
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- Division of Hematology/Oncology, Cedars-Sinai Medical Center, UCLA School of Medicine, California, Los Angeles
| | - Xinyi Loh
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Ying Li
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Liang Xu
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- College of life Science, Zhejiang University, Hangzhou, China
| | - Xiao-Qiang Xiang
- Department of Clinical Pharmacy and Pharmacy Administration, School of Pharmacy, Fudan University, Shanghai, China
| | - Ling-Zhi Wang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Boon Cher Goh
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - De-Chen Lin
- Division of Hematology/Oncology, Cedars-Sinai Medical Center, UCLA School of Medicine, California, Los Angeles
| | - Wee Joo Chng
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Soo-Yong Tan
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Sudhakar Jha
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- NUS Center for Cancer Research, Yong Loo Lin School of Medicine, National University, Singapore, Singapore
- Department of Physiological Sciences, College of Veterinary Medicine, Oklahoma State University, Stillwater, Oklahoma
| | - H Phillip Koeffler
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- Division of Hematology/Oncology, Cedars-Sinai Medical Center, UCLA School of Medicine, California, Los Angeles
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62
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Nakahama T, Kawahara Y. The RNA-editing enzyme ADAR1: a regulatory hub that tunes multiple dsRNA-sensing pathways. Int Immunol 2023; 35:123-133. [PMID: 36469491 DOI: 10.1093/intimm/dxac056] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 11/29/2022] [Indexed: 12/12/2022] Open
Abstract
Adenosine deaminase acting on RNA 1 (ADAR1) is an RNA-editing enzyme that catalyzes adenosine-to-inosine conversions in double-stranded RNAs (dsRNAs). In mammals, ADAR1 is composed of two isoforms: a nuclear short p110 isoform and a cytoplasmic long p150 isoform. Whereas both isoforms contain right-handed dsRNA-binding and deaminase domains, ADAR1 p150 harbors a Zα domain that binds to left-handed dsRNAs, termed Z-RNAs. Myeloma differentiation-associated gene 5 (MDA5) sensing of endogenous dsRNAs as non-self leads to the induction of type I interferon (IFN)-stimulated genes, but recent studies revealed that ADAR1 p150-mediated RNA editing, but not ADAR1 p110, prevents this MDA5-mediated sensing. ADAR1 p150-specific RNA-editing sites are present and at least a Zα domain-Z-RNA interaction is required for this specificity. Mutations in the ADAR1 gene cause Aicardi-Goutières syndrome (AGS), an infant encephalopathy with type I IFN overproduction. Insertion of a point mutation in the Zα domain of the Adar1 gene induces AGS-like encephalopathy in mice, which is rescued by concurrent deletion of MDA5. This finding indicates that impaired ADAR1 p150-mediated RNA-editing is a mechanism underlying AGS caused by an ADAR1 mutation. ADAR1 p150 also prevents ZBP1 sensing of endogenous Z-RNA, which leads to programmed cell death, via the Zα domain and its RNA-editing activity. Furthermore, ADAR1 prevents protein kinase R (PKR) sensing of endogenous right-handed dsRNAs, which leads to translational shutdown and growth arrest. Thus, ADAR1 acts as a regulatory hub that blocks sensing of endogenous dsRNAs as non-self by multiple sensor proteins, both in RNA editing-dependent and -independent manners, and is a potential therapeutic target for diseases, especially cancer.
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Affiliation(s)
- Taisuke Nakahama
- Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan.,Integrated Frontier Research for Medical Science Division and RNA Frontier Science Division, Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Suita, Osaka 565-0871, Japan.,Division of Microbiology and Immunology, Center for Infectious Disease Education and Research (CiDER), Osaka University, Suita, Osaka 565-0871, Japan
| | - Yukio Kawahara
- Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan.,Integrated Frontier Research for Medical Science Division and RNA Frontier Science Division, Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Suita, Osaka 565-0871, Japan.,Division of Microbiology and Immunology, Center for Infectious Disease Education and Research (CiDER), Osaka University, Suita, Osaka 565-0871, Japan
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63
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Zhan D, Zheng N, Zhao B, Cheng F, Tang Q, Liu X, Wang J, Wang Y, Liua H, Li X, Su J, Zhong X, Bu Q, Cheng Y, Wang Y, Qin J. Expanding individualized therapeutic options via genoproteomics. Cancer Lett 2023; 560:216123. [PMID: 36907503 DOI: 10.1016/j.canlet.2023.216123] [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: 01/04/2023] [Revised: 03/08/2023] [Accepted: 03/09/2023] [Indexed: 03/13/2023]
Abstract
Clinical next-generation sequencing (NGS)2 tests have enabled treatment recommendations for cancer patients with driver gene mutations. Targeted therapy options for patients without driver gene mutations are currently unavailable. Herein, we performed NGS and proteomics tests on 169 formalin-fixed paraffin-embedded (FFPE)3 samples of non-small cell lung cancers (NSCLC, 65),4 colorectal cancers (CRC, 61),5 thyroid carcinomas (THCA, 14),6 gastric cancers (GC, 2),7 gastrointestinal stromal tumors (GIST, 11),8 and malignant melanomas (MM, 6).9 Of the 169 samples, NGS detected 14 actionable mutated genes in 73 samples, providing treatment options for 43% of the patients. Proteomics identified 61 actionable clinical drug targets approved by the FDA or undergoing clinical trials in 122 samples, providing treatment options for 72% of the patients. In vivo experiments demonstrated that the Mitogen-Activated Protein Kinase (MEK)10 inhibitor induced the overexpression of MEK1 (Map2k1) to block lung tumor growth in mice. Therefore, protein overexpression is a potentially feasible indicator for guiding targeted therapies. Collectively, our analysis suggests that combining NGS and proteomics (genoproteomics) could expand the targeted treatment options to 85% of cancer patients.
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Affiliation(s)
- Dongdong Zhan
- KingMed-Pineal Joint Innovation Laboratory of Clinical Proteomics, Guangzhou KingMed Center for Clinical Laboratory Co., Ltd., Guangzhou, 510009, China; Beijing Pineal Diagnostics Co., Ltd., Beijing, 102206, China
| | - Nairen Zheng
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China
| | - Beibei Zhao
- KingMed-Pineal Joint Innovation Laboratory of Clinical Proteomics, Guangzhou KingMed Center for Clinical Laboratory Co., Ltd., Guangzhou, 510009, China; KingMed College of Laboratory Medical of Guangzhou Medical University, Guangzhou, 510005, China
| | - Fang Cheng
- KingMed-Pineal Joint Innovation Laboratory of Clinical Proteomics, Guangzhou KingMed Center for Clinical Laboratory Co., Ltd., Guangzhou, 510009, China; Beijing Pineal Diagnostics Co., Ltd., Beijing, 102206, China
| | - Qi Tang
- KingMed-Pineal Joint Innovation Laboratory of Clinical Proteomics, Guangzhou KingMed Center for Clinical Laboratory Co., Ltd., Guangzhou, 510009, China; KingMed College of Laboratory Medical of Guangzhou Medical University, Guangzhou, 510005, China
| | - Xiangqian Liu
- KingMed-Pineal Joint Innovation Laboratory of Clinical Proteomics, Guangzhou KingMed Center for Clinical Laboratory Co., Ltd., Guangzhou, 510009, China; KingMed College of Laboratory Medical of Guangzhou Medical University, Guangzhou, 510005, China
| | - Juanfei Wang
- KingMed-Pineal Joint Innovation Laboratory of Clinical Proteomics, Guangzhou KingMed Center for Clinical Laboratory Co., Ltd., Guangzhou, 510009, China; KingMed College of Laboratory Medical of Guangzhou Medical University, Guangzhou, 510005, China
| | - Yushen Wang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China
| | - Haibo Liua
- KingMed-Pineal Joint Innovation Laboratory of Clinical Proteomics, Guangzhou KingMed Center for Clinical Laboratory Co., Ltd., Guangzhou, 510009, China; Beijing Pineal Diagnostics Co., Ltd., Beijing, 102206, China
| | - Xinliang Li
- KingMed-Pineal Joint Innovation Laboratory of Clinical Proteomics, Guangzhou KingMed Center for Clinical Laboratory Co., Ltd., Guangzhou, 510009, China; Beijing Pineal Diagnostics Co., Ltd., Beijing, 102206, China
| | - Juming Su
- KingMed-Pineal Joint Innovation Laboratory of Clinical Proteomics, Guangzhou KingMed Center for Clinical Laboratory Co., Ltd., Guangzhou, 510009, China; KingMed College of Laboratory Medical of Guangzhou Medical University, Guangzhou, 510005, China
| | - Xuejun Zhong
- KingMed-Pineal Joint Innovation Laboratory of Clinical Proteomics, Guangzhou KingMed Center for Clinical Laboratory Co., Ltd., Guangzhou, 510009, China; KingMed College of Laboratory Medical of Guangzhou Medical University, Guangzhou, 510005, China
| | - Qing Bu
- Department of Medical Oncology, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, China
| | - Yating Cheng
- KingMed-Pineal Joint Innovation Laboratory of Clinical Proteomics, Guangzhou KingMed Center for Clinical Laboratory Co., Ltd., Guangzhou, 510009, China; KingMed College of Laboratory Medical of Guangzhou Medical University, Guangzhou, 510005, China.
| | - Yi Wang
- KingMed-Pineal Joint Innovation Laboratory of Clinical Proteomics, Guangzhou KingMed Center for Clinical Laboratory Co., Ltd., Guangzhou, 510009, China; State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China.
| | - Jun Qin
- KingMed-Pineal Joint Innovation Laboratory of Clinical Proteomics, Guangzhou KingMed Center for Clinical Laboratory Co., Ltd., Guangzhou, 510009, China; State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China; State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institute of Biomedical Sciences, Fudan University, Shanghai, 200433, China.
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64
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Chan TW, Dodson JP, Arbet J, Boutros PC, Xiao X. Single-Cell Analysis in Lung Adenocarcinoma Implicates RNA Editing in Cancer Innate Immunity and Patient Prognosis. Cancer Res 2023; 83:374-385. [PMID: 36449563 PMCID: PMC9898195 DOI: 10.1158/0008-5472.can-22-1062] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 10/08/2022] [Accepted: 11/23/2022] [Indexed: 12/05/2022]
Abstract
RNA editing modifies single nucleotides of RNAs, regulating primary protein structure and protein abundance. In recent years, the diversity of proteins and complexity of gene regulation associated with RNA editing dysregulation has been increasingly appreciated in oncology. Large-scale shifts in editing have been observed in bulk tumors across various cancer types. However, RNA editing in single cells and individual cell types within tumors has not been explored. By profiling editing in single cells from lung adenocarcinoma biopsies, we found that the increased editing trend of bulk lung tumors was unique to cancer cells. Elevated editing levels were observed in cancer cells resistant to targeted therapy, and editing sites associated with drug response were enriched. Consistent with the regulation of antiviral pathways by RNA editing, higher editing levels in cancer cells were associated with reduced antitumor innate immune response, especially levels of natural killer cell infiltration. In addition, the level of RNA editing in cancer cells was positively associated with somatic point mutation burden. This observation motivated the definition of a new metric, RNA editing load, reflecting the amount of RNA mutations created by RNA editing. Importantly, in lung cancer, RNA editing load was a stronger predictor of patient survival than DNA mutations. This study provides the first single cell dissection of editing in cancer and highlights the significance of RNA editing load in cancer prognosis. SIGNIFICANCE RNA editing analysis in single lung adenocarcinoma cells uncovers RNA mutations that correlate with tumor mutation burden and cancer innate immunity and reveals the amount of RNA mutations that strongly predicts patient survival. See related commentary by Luo and Liang, p. 351.
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Affiliation(s)
- Tracey W. Chan
- Bioinformatics interdepartmental program, University of California, Los Angeles, CA, USA
| | - Jack P. Dodson
- Bioinformatics interdepartmental program, University of California, Los Angeles, CA, USA,Jonsson Comprehensive Cancer Center, University of California, Los Angeles, California, CA, USA,Department of Integrative Biology and Physiology, University of California, Los Angeles, California, CA, USA
| | - Jaron Arbet
- Department of Urology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA.,Department of Human Genetics, University of California, Los Angeles, CA, USA.,Jonsson Comprehensive Cancer Center, University of California, Los Angeles, California, CA, USA
| | - Paul C. Boutros
- Bioinformatics interdepartmental program, University of California, Los Angeles, CA, USA,Department of Urology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA.,Department of Human Genetics, University of California, Los Angeles, CA, USA.,Jonsson Comprehensive Cancer Center, University of California, Los Angeles, California, CA, USA,Molecular Biology Institute, University of California, Los Angeles, California, CA, USA,Institute for Quantitative and Computational Sciences, University of California, Los Angeles, California, CA, USA,Institute for Precision Health, University of California, Los Angeles, California, CA
| | - Xinshu Xiao
- Bioinformatics interdepartmental program, University of California, Los Angeles, CA, USA,Jonsson Comprehensive Cancer Center, University of California, Los Angeles, California, CA, USA,Molecular Biology Institute, University of California, Los Angeles, California, CA, USA,Department of Integrative Biology and Physiology, University of California, Los Angeles, California, CA, USA,Correspondence: Xinshu Xiao, ; 310-206-6522, 611 Charles E. Young Drive South, Terasaki Life Sciences Building, 2000E, UCLA, Los Angeles, CA, 90095
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65
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Zhao Y, Simon M, Seluanov A, Gorbunova V. DNA damage and repair in age-related inflammation. Nat Rev Immunol 2023; 23:75-89. [PMID: 35831609 PMCID: PMC10106081 DOI: 10.1038/s41577-022-00751-y] [Citation(s) in RCA: 96] [Impact Index Per Article: 96.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/07/2022] [Indexed: 02/07/2023]
Abstract
Genomic instability is an important driver of ageing. The accumulation of DNA damage is believed to contribute to ageing by inducing cell death, senescence and tissue dysfunction. However, emerging evidence shows that inflammation is another major consequence of DNA damage. Inflammation is a hallmark of ageing and the driver of multiple age-related diseases. Here, we review the evidence linking DNA damage, inflammation and ageing, highlighting how premature ageing syndromes are associated with inflammation. We discuss the mechanisms by which DNA damage induces inflammation, such as through activation of the cGAS-STING axis and NF-κB activation by ATM. The triggers for activation of these signalling cascades are the age-related accumulation of DNA damage, activation of transposons, cellular senescence and the accumulation of persistent R-loops. We also discuss how epigenetic changes triggered by DNA damage can lead to inflammation and ageing via redistribution of heterochromatin factors. Finally, we discuss potential interventions against age-related inflammation.
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Affiliation(s)
- Yang Zhao
- Department of Biology, University of Rochester, Rochester, NY, USA.,Department of Physiology, Zhejiang University School of Medicine, Hangzhou, China.,Department of Hepatobiliary and Pancreatic Surgery of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Matthew Simon
- Department of Biology, University of Rochester, Rochester, NY, USA
| | - Andrei Seluanov
- Department of Biology, University of Rochester, Rochester, NY, USA. .,Department of Medicine, University of Rochester, Rochester, NY, USA.
| | - Vera Gorbunova
- Department of Biology, University of Rochester, Rochester, NY, USA. .,Department of Medicine, University of Rochester, Rochester, NY, USA.
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66
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Hu SB, Heraud-Farlow J, Sun T, Liang Z, Goradia A, Taylor S, Walkley CR, Li JB. ADAR1p150 Prevents MDA5 and PKR Activation via Distinct Mechanisms to Avert Fatal Autoinflammation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.25.525475. [PMID: 36747811 PMCID: PMC9900771 DOI: 10.1101/2023.01.25.525475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Effective immunity requires the innate immune system to distinguish foreign (non-self) nucleic acids from cellular (self) nucleic acids. Cellular double-stranded RNAs (dsRNAs) are edited by the RNA editing enzyme ADAR1 to prevent their dsRNA structure pattern being recognized as viral dsRNA by cytoplasmic dsRNA sensors including MDA5, PKR and ZBP1. A loss of ADAR1-mediated RNA editing of cellular dsRNA activates MDA5. However, additional RNA editing-independent functions of ADAR1 have been proposed, but a specific mechanism has not been delineated. We now demonstrate that the loss of ADAR1-mediated RNA editing specifically activates MDA5, while loss of the cytoplasmic ADAR1p150 isoform or its dsRNA binding activity enabled PKR activation. Deleting both MDA5 and PKR resulted in complete rescue of the embryonic lethality of Adar1p150 -/- mice to adulthood, contrasting with the limited or no rescue by removing MDA5, PKR or ZBP1 alone, demonstrating that this is a species conserved function of ADAR1p150. Our findings demonstrate that MDA5 and PKR are the primary in vivo effectors of fatal autoinflammation following the loss of ADAR1p150.
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67
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Hoellerbauer P, Biery MC, Arora S, Rao Y, Girard EJ, Mitchell K, Dighe P, Kufeld M, Kuppers DA, Herman JA, Holland EC, Soroceanu L, Vitanza NA, Olson JM, Pritchard JR, Paddison PJ. Functional genomic analysis of adult and pediatric brain tumor isolates. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.05.522885. [PMID: 36711964 PMCID: PMC9881972 DOI: 10.1101/2023.01.05.522885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Background Adult and pediatric tumors display stark differences in their mutation spectra and chromosome alterations. Here, we attempted to identify common and unique gene dependencies and their associated biomarkers among adult and pediatric tumor isolates using functional genetic lethal screens and computational modeling. Methods We performed CRISRP-Cas9 lethality screens in two adult glioblastoma (GBM) tumor isolates and five pediatric brain tumor isolates representing atypical teratoid rhabdoid tumors (ATRT), diffuse intrinsic pontine glioma, GBM, and medulloblastoma. We then integrated the screen results with machine learning-based gene-dependency models generated from data from >900 cancer cell lines. Results We found that >50% of candidate dependencies of 280 identified were shared between adult GBM tumors and individual pediatric tumor isolates. 68% of screen hits were found as nodes in our network models, along with shared and tumor-specific predictors of gene dependencies. We investigated network predictors associated with ADAR, EFR3A, FGFR1 (pediatric-specific), and SMARCC2 (ATRT-specific) gene dependency among our tumor isolates. Conclusions The results suggest that, despite harboring disparate genomic signatures, adult and pediatric tumor isolates share a preponderance of genetic dependences. Further, combining data from primary brain tumor lethality screens with large cancer cell line datasets produced valuable insights into biomarkers of gene dependency, even for rare cancers. Importance of the Study Our results demonstrate that large cancer cell lines data sets can be computationally mined to identify known and novel gene dependency relationships in adult and pediatric human brain tumor isolates. Gene dependency networks and lethality screen results represent a key resource for neuro-oncology and cancer research communities. We also highlight some of the challenges and limitations of this approach.
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Affiliation(s)
- Pia Hoellerbauer
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA USA
| | - Matt C Biery
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA USA
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Sonali Arora
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA USA
| | - Yiyun Rao
- Huck Institute for the Life Sciences, Pennsylvania State University, State College, PA, USA
| | - Emily J Girard
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA USA
| | - Kelly Mitchell
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA USA
| | - Pratiksha Dighe
- California Pacific Medical Center Research Institute, San Francisco, CA 94107, USA
| | - Megan Kufeld
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA USA
| | - Daniel A Kuppers
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA USA
| | - Jacob A Herman
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA USA
| | - Eric C Holland
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA USA
| | - Liliana Soroceanu
- California Pacific Medical Center Research Institute, San Francisco, CA 94107, USA
| | - Nicholas A Vitanza
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - James M Olson
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA USA
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Justin R Pritchard
- Huck Institute for the Life Sciences, Pennsylvania State University, State College, PA, USA
| | - Patrick J Paddison
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA USA
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68
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Gan WL, Ng L, Ng BYL, Chen L. Recent Advances in Adenosine-to-Inosine RNA Editing in Cancer. Cancer Treat Res 2023; 190:143-179. [PMID: 38113001 DOI: 10.1007/978-3-031-45654-1_5] [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] [Indexed: 12/21/2023]
Abstract
RNA epigenetics, or epitranscriptome, is a growing group of RNA modifications historically classified into two categories: RNA editing and RNA modification. RNA editing is usually understood as post-transcriptional RNA processing (except capping, splicing and polyadenylation) that changes the RNA nucleotide sequence encoded by the genome. This processing can be achieved through the insertion or deletion of nucleotides or deamination of nucleobases, generating either standard nucleotides such as uridine (U) or the rare nucleotide inosine (I). Adenosine-to-inosine (A-to-I) RNA editing is the most prevalent type of RNA modification in mammals and is catalyzed by adenosine deaminase acting on the RNA (ADAR) family of enzymes that recognize double-stranded RNAs (dsRNAs). Inosine mimics guanosine (G) in base pairing with cytidine (C), thereby A-to-I RNA editing alters dsRNA secondary structure. Inosine is also recognized as guanosine by the splicing and translation machineries, resulting in mRNA alternative splicing and protein recoding. Therefore, A-to-I RNA editing is an important mechanism that causes and regulates "RNA mutations" in both normal physiology and diseases including cancer. In this chapter, we reviewed current paradigms and developments in the field of A-to-I RNA editing in the context of cancer.
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Affiliation(s)
- Wei Liang Gan
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Singapore, 117599, Singapore
| | - Larry Ng
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Singapore, 117599, Singapore
| | - Bryan Y L Ng
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Singapore, 117599, Singapore
| | - Leilei Chen
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Singapore, 117599, Singapore.
- Department of Anatomy, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117594, Singapore.
- NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University Singapore, Singapore, Singapore.
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69
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Pinto SM, Subbannayya Y, Kim H, Hagen L, Górna MW, Nieminen AI, Bjørås M, Espevik T, Kainov D, Kandasamy RK. Multi-OMICs landscape of SARS-CoV-2-induced host responses in human lung epithelial cells. iScience 2022; 26:105895. [PMID: 36590899 PMCID: PMC9794516 DOI: 10.1016/j.isci.2022.105895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 12/03/2022] [Accepted: 12/22/2022] [Indexed: 12/29/2022] Open
Abstract
COVID-19 pandemic continues to remain a global health concern owing to the emergence of newer variants. Several multi-Omics studies have produced extensive evidence on host-pathogen interactions and potential therapeutic targets. Nonetheless, an increased understanding of host signaling networks regulated by post-translational modifications and their ensuing effect on the cellular dynamics is critical to expanding the current knowledge on SARS-CoV-2 infections. Through an unbiased transcriptomics, proteomics, acetylomics, phosphoproteomics, and exometabolome analysis of a lung-derived human cell line, we show that SARS-CoV-2 Norway/Trondheim-S15 strain induces time-dependent alterations in the induction of type I IFN response, activation of DNA damage response, dysregulated Hippo signaling, among others. We identified interplay of phosphorylation and acetylation dynamics on host proteins and its effect on the altered release of metabolites, especially organic acids and ketone bodies. Together, our findings serve as a resource of potential targets that can aid in designing novel host-directed therapeutic strategies.
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Affiliation(s)
- Sneha M. Pinto
- Centre of Molecular Inflammation Research (CEMIR), and Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology, 7491 Trondheim, Norway,Corresponding author
| | - Yashwanth Subbannayya
- Centre of Molecular Inflammation Research (CEMIR), and Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Hera Kim
- Centre of Molecular Inflammation Research (CEMIR), and Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Lars Hagen
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway,Proteomics and Modomics Experimental Core, PROMEC, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway
| | - Maria W. Górna
- Structural Biology Group, Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Warsaw, Poland
| | - Anni I. Nieminen
- Institute for Molecular Medicine Finland, University of Helsinki, 00014Helsinki, Finland
| | - Magnar Bjørås
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway
| | - Terje Espevik
- Centre of Molecular Inflammation Research (CEMIR), and Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Denis Kainov
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway
| | - Richard K. Kandasamy
- Centre of Molecular Inflammation Research (CEMIR), and Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology, 7491 Trondheim, Norway,Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway,Department of Laboratory Medicine and Pathology, Centre for Individualized Medicine, Mayo Clinic, Rochester, MN, USA,Corresponding author
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70
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Karmon M, Kopel E, Barzilai A, Geva P, Eisenberg E, Levanon EY, Greenberger S. Altered RNA Editing in Atopic Dermatitis Highlights the Role of Double-Stranded RNA for Immune Surveillance. J Invest Dermatol 2022; 143:933-943.e8. [PMID: 36502941 DOI: 10.1016/j.jid.2022.11.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 10/03/2022] [Accepted: 11/10/2022] [Indexed: 12/13/2022]
Abstract
Atopic dermatitis (AD) is associated with dysregulated type 1 IFN‒mediated responses, in parallel with the dominant type 2 inflammation. However, the pathophysiology of this dysregulation is largely unknown. Adenosine-to-inosine RNA editing plays a critical role in immune regulation by preventing double-stranded RNA recognition by MDA5 and IFN activation. We studied global adenosine-to-inosine editing in AD to elucidate the role played by altered editing in the pathophysiology of this disease. Analysis of three RNA-sequencing datasets of AD skin samples revealed reduced levels of adenosine-to-inosine RNA editing in AD. This reduction was seen globally throughout Alu repeats as well as in coding genes and in specific pre-mRNA loci expected to create long double-stranded RNA, the main substrate of MDA5 leading to type I IFN activation. Consistently, IFN signature genes were upregulated. In contrast, global editing was not altered in systemic lupus erythematosus and systemic sclerosis, despite IFN activation. Our results indicate that altered editing leading to impairment of the innate immune response may be involved in the pathogenesis of AD. Possibly, it may be relevant for additional autoimmune and inflammatory diseases.
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Affiliation(s)
- Miriam Karmon
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Eli Kopel
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Aviv Barzilai
- Department of Dermatology, Sheba Medical Center, Tel Hashomer, Israel; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Polina Geva
- Department of Dermatology, Sheba Medical Center, Tel Hashomer, Israel
| | - Eli Eisenberg
- Raymond & Beverly Sackler School of Physics & Astronomy, Raymond & Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Erez Y Levanon
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Shoshana Greenberger
- Department of Dermatology, Sheba Medical Center, Tel Hashomer, Israel; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.
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71
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Kwart D, He J, Srivatsan S, Lett C, Golubov J, Oswald EM, Poon P, Ye X, Waite J, Zaretsky AG, Haxhinasto S, Au-Yeung E, Gupta NT, Chiu J, Adler C, Cherravuru S, Malahias E, Negron N, Lanza K, Coppola A, Ni M, Song H, Wei Y, Atwal GS, Macdonald L, Oristian NS, Poueymirou W, Jankovic V, Fury M, Lowy I, Murphy AJ, Sleeman MA, Wang B, Skokos D. Cancer cell-derived type I interferons instruct tumor monocyte polarization. Cell Rep 2022; 41:111769. [PMID: 36476866 DOI: 10.1016/j.celrep.2022.111769] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 06/29/2022] [Accepted: 11/11/2022] [Indexed: 12/12/2022] Open
Abstract
Monocytes are highly plastic immune cells that modulate antitumor immunity. Therefore, identifying factors that regulate tumor monocyte functions is critical for developing effective immunotherapies. Here, we determine that endogenous cancer cell-derived type I interferons (IFNs) control monocyte functional polarization. Guided by single-cell transcriptomic profiling of human and mouse tumors, we devise a strategy to distinguish and separate immunostimulatory from immunosuppressive tumor monocytes by surface CD88 and Sca-1 expression. Leveraging this approach, we show that cGAS-STING-regulated cancer cell-derived IFNs polarize immunostimulatory monocytes associated with anti-PD-1 immunotherapy response in mice. We also demonstrate that immunosuppressive monocytes convert into immunostimulatory monocytes upon cancer cell-intrinsic cGAS-STING activation. Consistently, we find that human cancer cells can produce type I IFNs that polarize monocytes, and our immunostimulatory monocyte gene signature is enriched in patient tumors that respond to anti-PD-1 immunotherapy. Our work exposes a role for cancer cell-derived IFNs in licensing monocyte functions that influence immunotherapy outcomes.
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Affiliation(s)
- Dylan Kwart
- Regeneron Pharmaceuticals, Tarrytown, NY 10591, USA
| | - Jing He
- Regeneron Pharmaceuticals, Tarrytown, NY 10591, USA
| | | | | | | | | | - Patrick Poon
- Regeneron Pharmaceuticals, Tarrytown, NY 10591, USA
| | - Xuan Ye
- Regeneron Pharmaceuticals, Tarrytown, NY 10591, USA
| | | | | | | | | | | | - Joyce Chiu
- Regeneron Pharmaceuticals, Tarrytown, NY 10591, USA
| | | | | | | | | | | | | | - Min Ni
- Regeneron Pharmaceuticals, Tarrytown, NY 10591, USA
| | - Hang Song
- Regeneron Pharmaceuticals, Tarrytown, NY 10591, USA
| | - Yi Wei
- Regeneron Pharmaceuticals, Tarrytown, NY 10591, USA
| | | | | | | | | | | | - Matthew Fury
- Regeneron Pharmaceuticals, Tarrytown, NY 10591, USA
| | - Israel Lowy
- Regeneron Pharmaceuticals, Tarrytown, NY 10591, USA
| | | | | | - Bei Wang
- Regeneron Pharmaceuticals, Tarrytown, NY 10591, USA.
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72
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Janku F, Han SW, Doi T, Amatu A, Ajani JA, Kuboki Y, Cortez A, Cellitti SE, Mahling PC, Subramanian K, Schoenfeld HA, Choi SM, Iaconis LA, Lee LH, Pelletier MR, Dranoff G, Askoxylakis V, Siena S. Preclinical Characterization and Phase I Study of an Anti-HER2-TLR7 Immune-Stimulator Antibody Conjugate in Patients with HER2+ Malignancies. Cancer Immunol Res 2022; 10:1441-1461. [PMID: 36129967 DOI: 10.1158/2326-6066.cir-21-0722] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 04/29/2022] [Accepted: 09/16/2022] [Indexed: 01/10/2023]
Abstract
Immune-stimulator antibody conjugates (ISAC) combining tumor-targeting monoclonal antibodies with immunostimulatory agents allow targeted delivery of immune activators into tumors. NJH395 is a novel, first-in-class ISAC comprising a Toll-like receptor 7 (TLR7) agonist conjugated to an anti-HER2 antibody via a noncleavable linker payload. Preclinical characterization showed ISAC-mediated activation of myeloid cells in the presence of antigen-expressing cancer cells, with antigen targeting and TLR7 agonism contributing to antitumor activity. Safety, efficacy, immunogenicity, pharmacokinetics, and pharmacodynamics were investigated in a phase I, multicenter, open-label study in patients with HER2+ non-breast advanced malignancies (NCT03696771). Data from 18 patients enrolled in single ascending dose escalation demonstrated delivery of the TLR7-agonist payload in HER2+ tumor cells and induction of type I IFN responses, which correlated with immune modulation in the tumor microenvironment. Cytokine release syndrome was a common, but manageable, drug-related adverse event. Antidrug antibodies and neuroinflammation at high doses represented significant clinical challenges. Data provide proof-of-mechanism and critical insights for novel immunotherapies.
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Affiliation(s)
- Filip Janku
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Sae-Won Han
- Department of Internal Medicine, Seoul National University Hospital and Seoul National University Cancer Research Institute, Seoul, Republic of Korea
| | | | - Alessio Amatu
- Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | - Jaffer A Ajani
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | - Alex Cortez
- Novartis Institutes for BioMedical Research, San Diego, California
| | - Susan E Cellitti
- Novartis Institutes for BioMedical Research, San Diego, California
| | | | | | | | - Sarah M Choi
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Lori A Iaconis
- Novartis Institutes for BioMedical Research, San Diego, California
| | - Lang Ho Lee
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Marc R Pelletier
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Glenn Dranoff
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | | | - Salvatore Siena
- Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, Milan, Italy
- Department of Oncology and Hemato-Oncology, Università degli Studi di Milano, Milan, Italy
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73
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IFITM proteins: Understanding their diverse roles in viral infection, cancer, and immunity. J Biol Chem 2022; 299:102741. [PMID: 36435199 PMCID: PMC9800550 DOI: 10.1016/j.jbc.2022.102741] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 09/27/2022] [Accepted: 11/15/2022] [Indexed: 11/24/2022] Open
Abstract
Interferon-induced transmembrane proteins (IFITMs) are broad spectrum antiviral factors that inhibit the entry of a wide range of clinically important pathogens including influenza A virus, HIV-1, and Dengue virus. IFITMs are thought to act primarily by antagonizing virus-cell membrane fusion in this regard. However, recent work on these proteins has uncovered novel post-entry viral restriction mechanisms. IFITMs are also increasingly thought to have a role regulating immune responses, including innate antiviral and inflammatory responses as well as adaptive T-cell and B-cell responses. Further, IFITMs may have pathological activities in cancer, wherein IFITM expression can be a marker of therapeutically resistant and aggressive disease courses. In this review, we summarize the respective literatures concerning these apparently diverse functions with a view to identifying common themes and potentially yielding a more unified understanding of IFITM biology.
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74
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Liu J, Ji Q, Cheng F, Chen D, Geng T, Huang Y, Zhang J, He Y, Song T. The lncRNAs involved in regulating the RIG-I signaling pathway. Front Cell Infect Microbiol 2022; 12:1041682. [PMID: 36439216 PMCID: PMC9682092 DOI: 10.3389/fcimb.2022.1041682] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 10/21/2022] [Indexed: 09/23/2023] Open
Abstract
Understanding the targets and interactions of long non-coding RNAs (lncRNAs) related to the retinoic acid-inducible gene-I (RIG-I) signaling pathway is essential for developing interventions, which would enable directing the host inflammatory response regulation toward protective immunity. In the RIG-I signaling pathway, lncRNAs are involved in the important processes of ubiquitination, phosphorylation, and glycolysis, thus promoting the transport of the interferon regulatory factors 3 and 7 (IRF3 and IRF7) and the nuclear factor kappa B (NF-κB) into the nucleus, and activating recruitment of type I interferons (IFN-I) and inflammatory factors to the antiviral action site. In addition, the RIG-I signaling pathway has recently been reported to contain the targets of coronavirus disease-19 (COVID-19)-related lncRNAs. The molecules in the RIG-I signaling pathway are directly regulated by the lncRNA-microRNAs (miRNAs)-messenger RNA (mRNA) axis. Therefore, targeting this axis has become a novel strategy for the diagnosis and treatment of cancer. In this paper, the studies on the regulation of the RIG-I signaling pathway by lncRNAs during viral infections and cancer are comprehensively analyzed. The aim is to provide a solid foundation of information for conducting further detailed studies on lncRNAs and RIG-I in the future and also contribute to clinical drug development.
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Affiliation(s)
- Jing Liu
- Department of Immunology, Zunyi Medical University, Zunyi, China
| | - Qinglu Ji
- School of Pharmacy, Zunyi Medical University, Zunyi, China
| | - Feng Cheng
- Department of Immunology, Zunyi Medical University, Zunyi, China
| | - Dengwang Chen
- Department of Immunology, Zunyi Medical University, Zunyi, China
| | - Tingting Geng
- Department of Immunology, Zunyi Medical University, Zunyi, China
| | - Yueyue Huang
- Department of Immunology, Zunyi Medical University, Zunyi, China
| | - Jidong Zhang
- Department of Immunology, Zunyi Medical University, Zunyi, China
- Collaborative Innovation Center of Tissue Damage Repair and Regeneration Medicine, Zunyi Medical University, Zunyi, China
- Special Key Laboratory of Gene Detection and Therapy of Guizhou Province, Zunyi Medical University, Zunyi, China
| | - Yuqi He
- School of Pharmacy, Zunyi Medical University, Zunyi, China
| | - Tao Song
- Department of Immunology, Zunyi Medical University, Zunyi, China
- Collaborative Innovation Center of Tissue Damage Repair and Regeneration Medicine, Zunyi Medical University, Zunyi, China
- Special Key Laboratory of Gene Detection and Therapy of Guizhou Province, Zunyi Medical University, Zunyi, China
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75
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Chen W, Li Y, Ruan GX, Huang H, Zhang R, Wang J, Ouyang Y, Li Y, Xu S, Ou X. Adenosine deaminase acting on RNA-1 is essential for early B lymphopoiesis. Cell Rep 2022; 41:111687. [DOI: 10.1016/j.celrep.2022.111687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 09/07/2022] [Accepted: 10/27/2022] [Indexed: 11/23/2022] Open
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76
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Song W, Song SJ, Kuang J, Yang H, Yu T, Yang F, Wan T, Xu Y, Wei ST, Li MX, Xiong Y, Zhou Y, Qiu WX. Activating Innate Immunity by a STING Signal Amplifier for Local and Systemic Immunotherapy. ACS NANO 2022; 16:15977-15993. [PMID: 36190834 DOI: 10.1021/acsnano.2c03509] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The number of patients who benefit from acquired immunotherapy is limited. Stimulator of interferon genes (STING) signal activation is a significant component to enhance innate immunity, which has been used to realize broad-spectrum immunotherapy. Here, M@P@HA nanoparticles, as a STING signal amplifier, are constructed to enhance innate immunotherapy. Briefly, when M@P@HA was targeted into tumor cells, the nanoparticles decomposed with Mn2+ and activated the release of protoporphyrin (PpIX). Under light irradiation, the generated reactive oxygen species disrupt the cellular redox homeostasis to lead cytoplasm leakage of damaged mitochondrial double-stranded (ds) DNA, which is the initiator of the STING signal. Simultaneously, Mn2+ as the immunoregulator could significantly increase the activity of related protein of a STING signal, such as cyclic GMP-AMP synthase (cGAS) and STING, to further amplify the STING signal of tumor cells. Subsequently, the STING signal of tumor-associated macrophages (TAM) is also activated by capturing dsDNA and Mn2+ that escaped from tumor cells, so as to enhance innate immunity. It is found that, by amplifying the STING signal of tumor tissue, M@P@HA could not only activate innate immunity but also cascade to activate CD8+ T cell infiltration even in a tumor with low immunogenicity.
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Affiliation(s)
- Wen Song
- Institute of Biology and Medicine, College of Life Science and Health, Wuhan University of Science and Technology, Wuhan 430081, Hubei, China
| | - Shu-Jun Song
- Institute of Biology and Medicine, College of Life Science and Health, Wuhan University of Science and Technology, Wuhan 430081, Hubei, China
| | - Jing Kuang
- Institute of Pathology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Hang Yang
- Institute of Biology and Medicine, College of Life Science and Health, Wuhan University of Science and Technology, Wuhan 430081, Hubei, China
| | - Tao Yu
- Department of Orthopedic Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Ruijin second Road, Shanghai 200025, China
| | - Fan Yang
- Institute of Biology and Medicine, College of Life Science and Health, Wuhan University of Science and Technology, Wuhan 430081, Hubei, China
| | - Tao Wan
- Institute of Biology and Medicine, College of Life Science and Health, Wuhan University of Science and Technology, Wuhan 430081, Hubei, China
| | - Yi Xu
- Institute of Biology and Medicine, College of Life Science and Health, Wuhan University of Science and Technology, Wuhan 430081, Hubei, China
| | - Si-Tian Wei
- Institute of Biology and Medicine, College of Life Science and Health, Wuhan University of Science and Technology, Wuhan 430081, Hubei, China
| | - Mu-Xuan Li
- Institute of Biology and Medicine, College of Life Science and Health, Wuhan University of Science and Technology, Wuhan 430081, Hubei, China
| | - Yuan Xiong
- Department of Orthopaedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Ying Zhou
- Institute of Biology and Medicine, College of Life Science and Health, Wuhan University of Science and Technology, Wuhan 430081, Hubei, China
| | - Wen-Xiu Qiu
- Institute of Biology and Medicine, College of Life Science and Health, Wuhan University of Science and Technology, Wuhan 430081, Hubei, China
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77
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Li Y, Goldberg EM, Chen X, Xu X, McGuire JT, Leuzzi G, Karagiannis D, Tate T, Farhangdoost N, Horth C, Dai E, Li Z, Zhang Z, Izar B, Que J, Ciccia A, Majewski J, Yoon AJ, Ailles L, Mendelsohn CL, Lu C. Histone methylation antagonism drives tumor immune evasion in squamous cell carcinomas. Mol Cell 2022; 82:3901-3918.e7. [PMID: 36206767 PMCID: PMC9588679 DOI: 10.1016/j.molcel.2022.09.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 07/27/2022] [Accepted: 09/07/2022] [Indexed: 11/06/2022]
Abstract
How cancer-associated chromatin abnormalities shape tumor-immune interaction remains incompletely understood. Recent studies have linked DNA hypomethylation and de-repression of retrotransposons to anti-tumor immunity through the induction of interferon response. Here, we report that inactivation of the histone H3K36 methyltransferase NSD1, which is frequently found in squamous cell carcinomas (SCCs) and induces DNA hypomethylation, unexpectedly results in diminished tumor immune infiltration. In syngeneic and genetically engineered mouse models of head and neck SCCs, NSD1-deficient tumors exhibit immune exclusion and reduced interferon response despite high retrotransposon expression. Mechanistically, NSD1 loss results in silencing of innate immunity genes, including the type III interferon receptor IFNLR1, through depletion of H3K36 di-methylation (H3K36me2) and gain of H3K27 tri-methylation (H3K27me3). Inhibition of EZH2 restores immune infiltration and impairs the growth of Nsd1-mutant tumors. Thus, our work uncovers a druggable chromatin cross talk that regulates the viral mimicry response and enables immune evasion of DNA hypomethylated tumors.
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Affiliation(s)
- Yinglu Li
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Elizabeth M Goldberg
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Xiao Chen
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Xinjing Xu
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - John T McGuire
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Giuseppe Leuzzi
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Dimitris Karagiannis
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Tiffany Tate
- Department of Urology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Nargess Farhangdoost
- Department of Human Genetics, McGill University, Montreal, QC H3A 1B1, Canada; McGill University Genome Centre, Montreal, QC H3A 0G1, Canada
| | - Cynthia Horth
- Department of Human Genetics, McGill University, Montreal, QC H3A 1B1, Canada; McGill University Genome Centre, Montreal, QC H3A 0G1, Canada
| | - Esther Dai
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Zhiming Li
- Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Zhiguo Zhang
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA; Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Benjamin Izar
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Medicine, Division of Hematology and Oncology, Columbia University Irving Medical Center, New York, NY 10032, USA; Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Jianwen Que
- Division of Digestive and Liver Diseases, Department of Medicine, Columbia Center for Human Development, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Alberto Ciccia
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Jacek Majewski
- Department of Human Genetics, McGill University, Montreal, QC H3A 1B1, Canada; McGill University Genome Centre, Montreal, QC H3A 0G1, Canada
| | - Angela J Yoon
- Division of Oral and Maxillofacial Pathology, Columbia University College of Dental Medicine and Department of Pathology & Cell Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Laurie Ailles
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Cathy Lee Mendelsohn
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Urology, Columbia University Irving Medical Center, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Chao Lu
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA.
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78
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Li S, Mirlekar B, Johnson BM, Brickey WJ, Wrobel JA, Yang N, Song D, Entwistle S, Tan X, Deng M, Cui Y, Li W, Vincent BG, Gale M, Pylayeva-Gupta Y, Ting JPY. STING-induced regulatory B cells compromise NK function in cancer immunity. Nature 2022; 610:373-380. [PMID: 36198789 PMCID: PMC9875944 DOI: 10.1038/s41586-022-05254-3] [Citation(s) in RCA: 106] [Impact Index Per Article: 53.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 08/19/2022] [Indexed: 02/08/2023]
Abstract
An immunosuppressive tumour microenvironment is a major obstacle in the control of pancreatic and other solid cancers1-3. Agonists of the stimulator of interferon genes (STING) protein trigger inflammatory innate immune responses to potentially overcome tumour immunosuppression4. Although these agonists hold promise as potential cancer therapies5, tumour resistance to STING monotherapy has emerged in clinical trials and the mechanism(s) is unclear5-7. Here we show that the administration of five distinct STING agonists, including cGAMP, results in an expansion of human and mouse interleukin (IL)-35+ regulatory B cells in pancreatic cancer. Mechanistically, cGAMP drives expression of IL-35 by B cells in an IRF3-dependent but type I interferon-independent manner. In several preclinical cancer models, the loss of STING signalling in B cells increases tumour control. Furthermore, anti-IL-35 blockade or genetic ablation of IL-35 in B cells also reduces tumour growth. Unexpectedly, the STING-IL-35 axis in B cells reduces proliferation of natural killer (NK) cells and attenuates the NK-driven anti-tumour response. These findings reveal an intrinsic barrier to systemic STING agonist monotherapy and provide a combinatorial strategy to overcome immunosuppression in tumours.
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Affiliation(s)
- Sirui Li
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Microbiology-Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Bhalchandra Mirlekar
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Brandon M Johnson
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Microbiology-Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - W June Brickey
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Microbiology-Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - John A Wrobel
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Microbiology-Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Na Yang
- Functional Epigenomics Unit (HNN-2G5), National Institute on Aging, Bethesda, MD, USA
| | - Dingka Song
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Microbiology-Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Sarah Entwistle
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Xianming Tan
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Meng Deng
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Division of Craniofacial and Surgical Care, School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ya Cui
- Division of Computational Biomedicine, Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Wei Li
- Division of Computational Biomedicine, Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Benjamin G Vincent
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Michael Gale
- Department of Immunology, Center for Innate Immunity and Immune Disease, University of Washington, Seattle, WA, USA
| | - Yuliya Pylayeva-Gupta
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Jenny P-Y Ting
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Department of Microbiology-Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Division of Craniofacial and Surgical Care, School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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79
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Wang X, Ye F, Xiong M, Xiu B, Chi W, Zhang Q, Xue J, Chen M, Zhang L, Wu J, Chi Y. Cross-talk of four types of RNA modification proteins with adenosine reveals the landscape of multivariate prognostic patterns in breast cancer. Front Genet 2022; 13:943378. [PMID: 36118888 PMCID: PMC9479131 DOI: 10.3389/fgene.2022.943378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 08/10/2022] [Indexed: 11/13/2022] Open
Abstract
Background: Breast cancer (BC) is the most common malignant tumour, and its heterogeneity is one of its major characteristics. N6-methyladenosine (m6A), N1-methyladenosine (m1A), alternative polyadenylation (APA), and adenosine-to-inosine (A-to-I) RNA editing constitute the four most common adenosine-associated RNA modifications and represent the most typical and critical forms of epigenetic regulation contributing to the immunoinflammatory response, tumorigenesis and tumour heterogeneity. However, the cross-talk and potential combined profiles of these RNA-modified proteins (RMPs) in multivariate prognostic patterns of BC remain unknown.Methods: A total of 48 published RMPs were analysed and found to display significant expression alterations and genomic mutation rates between tumour and normal tissues in the TCGA-BRCA cohort. Data from 4188 BC patients with clinical outcomes were downloaded from the Gene Expression Omnibus (GEO), the Cancer Genome Atlas (TCGA), and the Molecular Taxonomy of Breast Cancer International Consortium (METABRIC), normalized and merged into one cohort. The prognostic value and interconnections of these RMPs were also studied. The four prognosis-related genes (PRGs) with the greatest prognostic value were then selected to construct diverse RMP-associated prognostic models through univariate Cox (uniCox) regression analysis, differential expression analysis, Least absolute shrinkage and selection operator (LASSO) regression and multivariate Cox (multiCox) regression. Alterations in biological functional pathways, genomic mutations, immune infiltrations, RNAss scores and drug sensitivities among different models, as well as their prognostic value, were then explored.Results: Utilizing a large number of samples and a comprehensive set of genes contributing to adenosine-associated RNA modification, our study revealed the joint potential bio-functions and underlying features of these diverse RMPs and provided effective models (PRG clusters, gene clusters and the risk model) for predicting the clinical outcomes of BC. The individuals with higher risk scores showed poor prognoses, cell cycle function enrichment, upregulation of stemness scores, higher tumour mutation burdens (TMBs), immune activation and specific drug resistance. This work highlights the significance of comprehensively examining post-transcriptional RNA modification genes.Conclusion: Here, we designed and verified an advanced forecasting model to reveal the underlying links between BC and RMPs and precisely predict the clinical outcomes of multivariate prognostic patterns for individuals.
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Affiliation(s)
- Xuliren Wang
- Department of Breast Surgery, Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Fangdie Ye
- Department of Urology, Huashan Hospital, Fudan University, Shanghai, China
| | - Min Xiong
- Department of Breast Surgery, Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Bingqiu Xiu
- Department of Breast Surgery, Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Weiru Chi
- Department of Breast Surgery, Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Qi Zhang
- Department of Breast Surgery, Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Jingyan Xue
- Department of Breast Surgery, Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Ming Chen
- Department of Breast Surgery, Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Liyi Zhang
- Department of Breast Surgery, Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Jiong Wu
- Department of Breast Surgery, Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Shanghai, China
- Collaborative Innovation Center for Cancer Medicine, Shanghai, China
- *Correspondence: Jiong Wu, ; Yayun Chi,
| | - Yayun Chi
- Department of Breast Surgery, Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Shanghai, China
- *Correspondence: Jiong Wu, ; Yayun Chi,
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80
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Tian X, Xu F, Zhu Q, Feng Z, Dai W, Zhou Y, You QD, Xu X. Medicinal chemistry perspective on cGAS-STING signaling pathway with small molecule inhibitors. Eur J Med Chem 2022; 244:114791. [DOI: 10.1016/j.ejmech.2022.114791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 09/18/2022] [Accepted: 09/20/2022] [Indexed: 11/04/2022]
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81
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Jin R, Cao X, Lu M, Gao Q, Ma T. The intersection molecule MDA5 in Cancer and COVID-19. Front Immunol 2022; 13:963051. [PMID: 36119095 PMCID: PMC9471860 DOI: 10.3389/fimmu.2022.963051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 08/09/2022] [Indexed: 11/13/2022] Open
Abstract
The connections between pattern recognition receptors (PRRs) and pathogen-associated molecular patterns (PAMPs) constitutes the crucial signaling pathways in the innate immune system. Cytoplasmic nucleic acid sensor melanoma differentiation-associated gene 5 (MDA5) serves as an important pattern recognition receptor in the innate immune system by recognizing viral RNA. MDA5 also plays a role in identifying the cytoplasmic RNA from damaged, dead cancer cells or autoimmune diseases. MDA5’s recognition of RNA triggers innate immune responses, induces interferon (IFN) response and a series of subsequent signaling pathways to produce immunomodulatory factors and inflammatory cytokines. Here we review the latest progress of MDA5 functions in triggering anti-tumor immunity by sensing cytoplasmic dsRNA, and recognizing SARS-CoV-2 virus infection for antiviral response, in which the virus utilizes multiple ways to evade the host defense mechanism.
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Affiliation(s)
- Renjing Jin
- Cancer Research Center, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Xiaoqing Cao
- Department of Thoracic Surgery, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Mingjun Lu
- Cancer Research Center, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Qing Gao
- Cancer Research Center, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Teng Ma
- Cancer Research Center, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
- *Correspondence: Teng Ma,
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82
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Luo Z, Liang X, He T, Qin X, Li X, Li Y, Li L, Loh XJ, Gong C, Liu X. Lanthanide-Nucleotide Coordination Nanoparticles for STING Activation. J Am Chem Soc 2022; 144:16366-16377. [PMID: 36037283 DOI: 10.1021/jacs.2c03266] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Activation of the stimulator of interferon genes (STING) is essential for blocking viral infections and eliciting antitumor immune responses. Local injection of synthetic STING agonists, such as 2'3'-cGAMP [cGAMP = cyclic 5'-guanosine monophosphate (cGMP)-adenosine monophosphate (AMP)], is a promising approach to enhance antiviral functions and cancer immunotherapy. However, the application of such agonists has been hindered by complicated synthetic procedures, high doses, and unsatisfactory systemic immune responses. Herein, we report the design and synthesis of a series of 2'3'-cGAMP surrogates in nanoparticle formulations formed by reactions of AMP, GMP, and coordinating lanthanides. These nanoparticles can stimulate the type-I interferon (IFN) response in both mouse macrophages and human monocytes. We further demonstrate that the use of europium-based nanoparticles as STING-targeted adjuvants significantly promotes the maturation of mouse bone-marrow-derived dendritic cells and major histocompatibility complex class I antigen presentation. Dynamic molecular docking analysis revealed that these nanoparticles bind with high affinity to mouse STING and human STING. Compared with soluble ovalbumin (OVA), subcutaneously immunized europium-based nanovaccines exhibit significantly increased production of primary and secondary anti-OVA antibodies (∼180-fold) in serum, as well as IL-5 (∼28-fold), IFN-γ (∼27-fold), and IFN-α/β (∼4-fold) in splenocytes ex vivo. Compared with the 2'3'-cGAMP/OVA formulation, subcutaneous administration of nanovaccines significantly inhibits B16F10-OVA tumor growth and prolongs the survival of tumor-bearing mice in both therapeutic and protective models. Given the rich supramolecular chemistry with lanthanides, this work will enable a readily accessible platform for potent humoral and cellular immunity while opening new avenues for cost-effective, highly efficient therapeutic delivery of STING agonists.
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Affiliation(s)
- Zichao Luo
- Department of Chemistry, National University of Singapore, Singapore 117543, Singapore
| | - Xiuqi Liang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, P. R. China
| | - Tao He
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, P. R. China
| | - Xian Qin
- Department of Chemistry, National University of Singapore, Singapore 117543, Singapore
| | - Xinchao Li
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, P. R. China
| | - Yueshan Li
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, P. R. China
| | - Lu Li
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, P. R. China
| | - Xian Jun Loh
- Agency for Science, Technology and Research, Institute of Materials Research and Engineering, Singapore 138634, Singapore
| | - Changyang Gong
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, P. R. China
| | - Xiaogang Liu
- Department of Chemistry, National University of Singapore, Singapore 117543, Singapore.,Agency for Science, Technology and Research, Institute of Materials Research and Engineering, Singapore 138634, Singapore.,The N.1 Institute for Health, National University of Singapore, Singapore 117456, Singapore
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83
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Molony RD, Funk T, Trabucco G, Corcoran E, Ruddy D, Varadarajan M, Elliot G, Piquet M, Lam J, Meyer MJ, Wang HQ, Kurtulus S, Lu H. CRISPR screening identifies T cell-intrinsic regulators of CD3-bispecific antibody responses. Front Immunol 2022; 13:909979. [PMID: 35990699 PMCID: PMC9388929 DOI: 10.3389/fimmu.2022.909979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 07/11/2022] [Indexed: 11/13/2022] Open
Abstract
CD3-engaging bispecific antibodies (BsAbs) enable the formation of an immune synapse between T cells and tumor cells, resulting in robust target cell killing not dependent on a preexisting tumor specific T cell receptor. While recent studies have shed light on tumor cell-specific factors that modulate BsAb sensitivity, the T cell-intrinsic determinants of BsAb efficacy and response durability are poorly understood. To better clarify the genes that shape BsAb-induced T cell responses, we conducted targeted analyses and a large-scale unbiased in vitro CRISPR/Cas9-based screen to identify negative regulators of BsAb-induced T cell proliferation. These analyses revealed that CD8+ T cells are dependent on CD4+ T cell-derived signaling factors in order to achieve sustained killing in vitro. Moreover, the mammalian target of rapamycin (mTOR) pathway and several other candidate genes were identified as intrinsic regulators of BsAb-induced T cell proliferation and/or activation, highlighting promising approaches to enhancing the utility of these potent therapeutics.
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84
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Vella V, De Francesco EM, Bonavita E, Lappano R, Belfiore A. IFN-I signaling in cancer: the connection with dysregulated Insulin/IGF axis. Trends Endocrinol Metab 2022; 33:569-586. [PMID: 35691786 DOI: 10.1016/j.tem.2022.04.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 04/15/2022] [Accepted: 04/26/2022] [Indexed: 01/12/2023]
Abstract
Type I interferons (IFN-Is) are prototypical inflammatory cytokines produced in response to stress. IFN-Is have a critical role in antitumor immunity by driving the activation of leukocytes and favoring the elimination of malignant cells. However, IFN-I signaling in cancer, specifically in the tumor microenvironment (TME), can have opposing roles. Sustained IFN-I stimulation can promote immune exhaustion or enable tumor cell-intrinsic malignant features. Herein, we discuss the potential impact of the insulin/insulin-like growth factor system (I/IGFs) and of metabolic disorders in aberrant IFN-I signaling in cancer. We consider the possibility that targeting I/IGFs, especially in patients with cancer affected by metabolic disorders, contributes to an effective strategy to inhibit deleterious IFN-I signaling, thereby restoring sensitivity to various cancer therapies, including immunotherapy.
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Affiliation(s)
- Veronica Vella
- Endocrinology Unit, Department of Clinical and Experimental Medicine, University of Catania, Garibaldi-Nesima Hospital, 95122 Catania, Italy
| | - Ernestina Marianna De Francesco
- Endocrinology Unit, Department of Clinical and Experimental Medicine, University of Catania, Garibaldi-Nesima Hospital, 95122 Catania, Italy
| | - Eduardo Bonavita
- IRCCS Humanitas Research Hospital, Fondazione Humanitas per la Ricerca, Laboratory of Cellular and Molecular Oncoimmunology, 20089 Rozzano, Italy; Cancer Research UK Manchester Institute, The University of Manchester, Alderley Park SK10 4TG, UK
| | - Rosamaria Lappano
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036 Rende, Italy
| | - Antonino Belfiore
- Endocrinology Unit, Department of Clinical and Experimental Medicine, University of Catania, Garibaldi-Nesima Hospital, 95122 Catania, Italy.
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85
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Kwon J, Choi H, Han C. A Dual Role of DDX3X in dsRNA-Derived Innate Immune Signaling. Front Mol Biosci 2022; 9:912727. [PMID: 35874614 PMCID: PMC9299366 DOI: 10.3389/fmolb.2022.912727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 06/09/2022] [Indexed: 11/18/2022] Open
Abstract
DEAD-Box Helicase 3 X-Linked (DDX3X) is essential for RNA metabolism and participates in various cellular processes involving RNA. DDX3X has been implicated in cancer growth and metastasis. DDX3X is involved in antiviral responses for viral RNAs and contributes to pro- or anti-microbial responses. A better understanding of how human cells regulate innate immune response against the viral “non-self” double-stranded RNAs (dsRNAs) and endogenous viral-like “self” dsRNAs is critical to understanding innate immune sensing, anti-microbial immunity, inflammation, immune cell homeostasis, and developing novel therapeutics for infectious, immune-mediated diseases, and cancer. DDX3X has known for activating the viral dsRNA-sensing pathway and innate immunity. However, accumulating research reveals a more complex role of DDX3X in regulating dsRNA-mediated signaling in cells. Here, we discuss the role of DDX3X in viral dsRNA- or endogenous dsRNA-mediated immune signaling pathways.
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Affiliation(s)
- Juntae Kwon
- Department of Oncology, Georgetown University School of Medicine, Washington, DC, United States
| | - Hyeongjwa Choi
- Department of Biomedical Science and Technology, Konkuk University, Seoul, South Korea
| | - Cecil Han
- Department of Oncology, Georgetown University School of Medicine, Washington, DC, United States.,Lombardi Comprehensive Cancer Center, Washington, DC, United States
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86
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Reggiardo RE, Maroli SV, Halasz H, Ozen M, Hrabeta-Robinson E, Behera A, Peddu V, Carrillo D, LaMontagne E, Whitehead L, Kim E, Malik S, Fernandes J, Marinov G, Collisson E, Brooks A, Demirci U, Kim DH. Mutant KRAS regulates transposable element RNA and innate immunity via KRAB zinc-finger genes. Cell Rep 2022; 40:111104. [PMID: 35858545 PMCID: PMC9374308 DOI: 10.1016/j.celrep.2022.111104] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Revised: 04/04/2022] [Accepted: 06/27/2022] [Indexed: 12/22/2022] Open
Abstract
RAS genes are the most frequently mutated oncogenes in cancer, yet the effects of oncogenic RAS signaling on the noncoding transcriptome remain unclear. We analyzed the transcriptomes of human airway and bronchial epithelial cells transformed with mutant KRAS to define the landscape of KRAS-regulated noncoding RNAs. We find that oncogenic KRAS signaling upregulates noncoding transcripts throughout the genome, many of which arise from transposable elements (TEs). These TE RNAs exhibit differential expression, are preferentially released in extracellular vesicles, and are regulated by KRAB zinc-finger (KZNF) genes, which are broadly downregulated in mutant KRAS cells and lung adenocarcinomas in vivo. Moreover, mutant KRAS induces an intrinsic IFN-stimulated gene (ISG) signature that is often seen across many different cancers. Our results indicate that mutant KRAS remodels the repetitive noncoding transcriptome, demonstrating the broad scope of intracellular and extracellular RNAs regulated by this oncogenic signaling pathway. Many human cancers are driven by mutant KRAS, but its effects on noncoding RNA are unclear. Reggiardo et al. show that mutant KRAS regulates this RNA landscape by silencing KRAB zinc-finger genes that normally repress transposable element noncoding RNAs, which are preferentially released from mutant KRAS cells in extracellular vesicles.
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Affiliation(s)
- Roman E Reggiardo
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Sreelakshmi Velandi Maroli
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Haley Halasz
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Mehmet Ozen
- Canary Center at Stanford for Cancer Early Detection, Department of Radiology, Stanford University School of Medicine, Palo Alto, CA 94305, USA
| | - Eva Hrabeta-Robinson
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Amit Behera
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Vikas Peddu
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - David Carrillo
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Erin LaMontagne
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Lila Whitehead
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Eejung Kim
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Shivani Malik
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Jason Fernandes
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Georgi Marinov
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Eric Collisson
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Angela Brooks
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA; Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95064, USA; Center for Molecular Biology of RNA, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Utkan Demirci
- Canary Center at Stanford for Cancer Early Detection, Department of Radiology, Stanford University School of Medicine, Palo Alto, CA 94305, USA
| | - Daniel H Kim
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA; Canary Center at Stanford for Cancer Early Detection, Department of Radiology, Stanford University School of Medicine, Palo Alto, CA 94305, USA; Institute for the Biology of Stem Cells, University of California, Santa Cruz, Santa Cruz, CA 95064, USA; Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95064, USA; Center for Molecular Biology of RNA, University of California, Santa Cruz, Santa Cruz, CA 95064, USA.
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87
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Nguyen TA, Heng JWJ, Kaewsapsak P, Kok EPL, Stanojević D, Liu H, Cardilla A, Praditya A, Yi Z, Lin M, Aw JGA, Ho YY, Peh KLE, Wang Y, Zhong Q, Heraud-Farlow J, Xue S, Reversade B, Walkley C, Ho YS, Šikić M, Wan Y, Tan MH. Direct identification of A-to-I editing sites with nanopore native RNA sequencing. Nat Methods 2022; 19:833-844. [PMID: 35697834 DOI: 10.1038/s41592-022-01513-3] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 05/02/2022] [Indexed: 12/26/2022]
Abstract
Inosine is a prevalent RNA modification in animals and is formed when an adenosine is deaminated by the ADAR family of enzymes. Traditionally, inosines are identified indirectly as variants from Illumina RNA-sequencing data because they are interpreted as guanosines by cellular machineries. However, this indirect method performs poorly in protein-coding regions where exons are typically short, in non-model organisms with sparsely annotated single-nucleotide polymorphisms, or in disease contexts where unknown DNA mutations are pervasive. Here, we show that Oxford Nanopore direct RNA sequencing can be used to identify inosine-containing sites in native transcriptomes with high accuracy. We trained convolutional neural network models to distinguish inosine from adenosine and guanosine, and to estimate the modification rate at each editing site. Furthermore, we demonstrated their utility on the transcriptomes of human, mouse and Xenopus. Our approach expands the toolkit for studying adenosine-to-inosine editing and can be further extended to investigate other RNA modifications.
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Affiliation(s)
- Tram Anh Nguyen
- School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore, Singapore.,Genome Institute of Singapore, Agency for Science Technology and Research, Singapore, Singapore
| | - Jia Wei Joel Heng
- School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore, Singapore.,Genome Institute of Singapore, Agency for Science Technology and Research, Singapore, Singapore
| | - Pornchai Kaewsapsak
- Genome Institute of Singapore, Agency for Science Technology and Research, Singapore, Singapore.,Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Eng Piew Louis Kok
- Genome Institute of Singapore, Agency for Science Technology and Research, Singapore, Singapore
| | - Dominik Stanojević
- Genome Institute of Singapore, Agency for Science Technology and Research, Singapore, Singapore.,University of Zagreb, Faculty of Electrical Engineering and Computing, Zagreb, Croatia
| | - Hao Liu
- School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore, Singapore.,Genome Institute of Singapore, Agency for Science Technology and Research, Singapore, Singapore
| | - Angelysia Cardilla
- School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore, Singapore.,Genome Institute of Singapore, Agency for Science Technology and Research, Singapore, Singapore
| | - Albert Praditya
- School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore, Singapore.,Genome Institute of Singapore, Agency for Science Technology and Research, Singapore, Singapore
| | - Zirong Yi
- School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore, Singapore.,Genome Institute of Singapore, Agency for Science Technology and Research, Singapore, Singapore
| | - Mingwan Lin
- Genome Institute of Singapore, Agency for Science Technology and Research, Singapore, Singapore.,National Junior College, Singapore, Singapore
| | - Jong Ghut Ashley Aw
- Genome Institute of Singapore, Agency for Science Technology and Research, Singapore, Singapore.,School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Yin Ying Ho
- Bioprocessing Technology Institute, Agency for Science Technology and Research, Singapore, Singapore
| | - Kai Lay Esther Peh
- Bioprocessing Technology Institute, Agency for Science Technology and Research, Singapore, Singapore
| | - Yuanming Wang
- School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore, Singapore.,Genome Institute of Singapore, Agency for Science Technology and Research, Singapore, Singapore
| | - Qixing Zhong
- Genome Institute of Singapore, Agency for Science Technology and Research, Singapore, Singapore
| | - Jacki Heraud-Farlow
- St. Vincent's Institute of Medical Research and Department of Medicine, University of Melbourne, Fitzroy, Victoria, Australia
| | - Shifeng Xue
- Institute of Molecular and Cell Biology, Agency for Science Technology and Research, Singapore, Singapore.,Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Bruno Reversade
- Genome Institute of Singapore, Agency for Science Technology and Research, Singapore, Singapore.,Institute of Molecular and Cell Biology, Agency for Science Technology and Research, Singapore, Singapore.,Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Department of Medical Genetics, School of Medicine (KUSoM), Koç University, Istanbul, Turkey
| | - Carl Walkley
- St. Vincent's Institute of Medical Research and Department of Medicine, University of Melbourne, Fitzroy, Victoria, Australia
| | - Ying Swan Ho
- Bioprocessing Technology Institute, Agency for Science Technology and Research, Singapore, Singapore
| | - Mile Šikić
- Genome Institute of Singapore, Agency for Science Technology and Research, Singapore, Singapore.,University of Zagreb, Faculty of Electrical Engineering and Computing, Zagreb, Croatia
| | - Yue Wan
- Genome Institute of Singapore, Agency for Science Technology and Research, Singapore, Singapore.,School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.,Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Meng How Tan
- School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore, Singapore. .,Genome Institute of Singapore, Agency for Science Technology and Research, Singapore, Singapore. .,HP-NTU Digital Manufacturing Corporate Lab, Nanyang Technological University, Singapore, Singapore.
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88
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Zhang T, Yin C, Fedorov A, Qiao L, Bao H, Beknazarov N, Wang S, Gautam A, Williams RM, Crawford JC, Peri S, Studitsky V, Beg AA, Thomas PG, Walkley C, Xu Y, Poptsova M, Herbert A, Balachandran S. ADAR1 masks the cancer immunotherapeutic promise of ZBP1-driven necroptosis. Nature 2022; 606:594-602. [PMID: 35614224 PMCID: PMC9373927 DOI: 10.1038/s41586-022-04753-7] [Citation(s) in RCA: 160] [Impact Index Per Article: 80.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 04/11/2022] [Indexed: 12/11/2022]
Abstract
Only a small proportion of patients with cancer show lasting responses to immune checkpoint blockade (ICB)-based monotherapies. The RNA-editing enzyme ADAR1 is an emerging determinant of resistance to ICB therapy and prevents ICB responsiveness by repressing immunogenic double-stranded RNAs (dsRNAs), such as those arising from the dysregulated expression of endogenous retroviral elements (EREs)1-4. These dsRNAs trigger an interferon-dependent antitumour response by activating A-form dsRNA (A-RNA)-sensing proteins such as MDA-5 and PKR5. Here we show that ADAR1 also prevents the accrual of endogenous Z-form dsRNA elements (Z-RNAs), which were enriched in the 3' untranslated regions of interferon-stimulated mRNAs. Depletion or mutation of ADAR1 resulted in Z-RNA accumulation and activation of the Z-RNA sensor ZBP1, which culminated in RIPK3-mediated necroptosis. As no clinically viable ADAR1 inhibitors currently exist, we searched for a compound that can override the requirement for ADAR1 inhibition and directly activate ZBP1. We identified a small molecule, the curaxin CBL0137, which potently activates ZBP1 by triggering Z-DNA formation in cells. CBL0137 induced ZBP1-dependent necroptosis in cancer-associated fibroblasts and reversed ICB unresponsiveness in mouse models of melanoma. Collectively, these results demonstrate that ADAR1 represses endogenous Z-RNAs and identifies ZBP1-mediated necroptosis as a new determinant of tumour immunogenicity masked by ADAR1. Therapeutic activation of ZBP1-induced necroptosis provides a readily translatable avenue for rekindling the immune responsiveness of ICB-resistant human cancers.
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Affiliation(s)
- Ting Zhang
- Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Chaoran Yin
- Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Aleksandr Fedorov
- Laboratory of Bioinformatics, Faculty of Computer Science, National Research University Higher School of Economics, Moscow, Russia
| | - Liangjun Qiao
- College of Basic Medicine, Chongqing Medical University, Chongqing, China
| | - Hongliang Bao
- Division of Chemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazaki, Kiyotake, Japan
| | - Nazar Beknazarov
- Laboratory of Bioinformatics, Faculty of Computer Science, National Research University Higher School of Economics, Moscow, Russia
| | - Shiyu Wang
- Division of Chemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazaki, Kiyotake, Japan
| | - Avishekh Gautam
- Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Riley M Williams
- Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia, PA, USA
| | | | - Suraj Peri
- Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Vasily Studitsky
- Cancer Signaling and Epigenetics Program, Fox Chase Cancer Center, Philadelphia, PA, USA
- Biology Faculty, Lomonosov Moscow State University, Moscow, Russia
| | - Amer A Beg
- Department of Immunology and Thoracic Oncology, Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Paul G Thomas
- Department of Immunology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Carl Walkley
- Cancer & RNA Biology, St Vincent's Institute for Medical Research and Department of Medicine, St Vincent's Hospital, University of Melbourne, Fitzroy, Victoria, Australia
| | - Yan Xu
- Division of Chemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazaki, Kiyotake, Japan
| | - Maria Poptsova
- Laboratory of Bioinformatics, Faculty of Computer Science, National Research University Higher School of Economics, Moscow, Russia
| | - Alan Herbert
- Laboratory of Bioinformatics, Faculty of Computer Science, National Research University Higher School of Economics, Moscow, Russia.
- InsideOutBio, Charlestown, MA, USA.
| | - Siddharth Balachandran
- Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia, PA, USA.
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89
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Sakowska J, Arcimowicz Ł, Jankowiak M, Papak I, Markiewicz A, Dziubek K, Kurkowiak M, Kote S, Kaźmierczak-Siedlecka K, Połom K, Marek-Trzonkowska N, Trzonkowski P. Autoimmunity and Cancer-Two Sides of the Same Coin. Front Immunol 2022; 13:793234. [PMID: 35634292 PMCID: PMC9140757 DOI: 10.3389/fimmu.2022.793234] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 04/12/2022] [Indexed: 02/06/2023] Open
Abstract
Autoimmune disease results from the immune response against self-antigens, while cancer develops when the immune system does not respond to malignant cells. Thus, for years, autoimmunity and cancer have been considered as two separate fields of research that do not have a lot in common. However, the discovery of immune checkpoints and the development of anti-cancer drugs targeting PD-1 (programmed cell death receptor 1) and CTLA-4 (cytotoxic T lymphocyte antigen 4) pathways proved that studying autoimmune diseases can be extremely helpful in the development of novel anti-cancer drugs. Therefore, autoimmunity and cancer seem to be just two sides of the same coin. In the current review, we broadly discuss how various regulatory cell populations, effector molecules, genetic predisposition, and environmental factors contribute to the loss of self-tolerance in autoimmunity or tolerance induction to cancer. With the current paper, we also aim to convince the readers that the pathways involved in cancer and autoimmune disease development consist of similar molecular players working in opposite directions. Therefore, a deep understanding of the two sides of immune tolerance is crucial for the proper designing of novel and selective immunotherapies.
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Affiliation(s)
- Justyna Sakowska
- Department of Medical Immunology, Medical University of Gdańsk, Gdańsk, Poland
| | - Łukasz Arcimowicz
- International Centre for Cancer Vaccine Science, University of Gdańsk, Gdańsk, Poland
| | - Martyna Jankowiak
- Department of Medical Immunology, Medical University of Gdańsk, Gdańsk, Poland
| | - Ines Papak
- International Centre for Cancer Vaccine Science, University of Gdańsk, Gdańsk, Poland
| | - Aleksandra Markiewicz
- Laboratory of Translational Oncology, Intercollegiate Faculty of Biotechnology, University of Gdańsk and Medical University of Gdańsk, Gdańsk, Poland
| | - Katarzyna Dziubek
- International Centre for Cancer Vaccine Science, University of Gdańsk, Gdańsk, Poland
| | - Małgorzata Kurkowiak
- International Centre for Cancer Vaccine Science, University of Gdańsk, Gdańsk, Poland
| | - Sachin Kote
- International Centre for Cancer Vaccine Science, University of Gdańsk, Gdańsk, Poland
| | | | - Karol Połom
- Department of Surgical Oncology, Medical University of Gdańsk, Gdańsk, Poland
| | - Natalia Marek-Trzonkowska
- International Centre for Cancer Vaccine Science, University of Gdańsk, Gdańsk, Poland
- Laboratory of Immunoregulation and Cellular Therapies, Department of Family Medicine, Medical University of Gdańsk, Gdańsk, Poland
| | - Piotr Trzonkowski
- Department of Medical Immunology, Medical University of Gdańsk, Gdańsk, Poland
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90
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Ren W, Wang X, Yang M, Wan H, Li X, Ye X, Meng B, Li W, Yu J, Lei M, Xie F, Jiang W, Kimby E, Huang H, Liu D, Li ZM, Wu K, Zhang H, Pan-Hammarström Q. Distinct clinical and genetic features of hepatitis B virus-associated follicular lymphoma in Chinese patients. Blood Adv 2022; 6:2731-2744. [PMID: 35030632 PMCID: PMC9092402 DOI: 10.1182/bloodadvances.2021006410] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 12/19/2021] [Indexed: 12/15/2022] Open
Abstract
Hepatitis B virus (HBV) infection has been associated with an increased risk for B-cell lymphomas. We previously showed that 20% of diffuse large B-cell lymphoma (DLBCL) patients from China, an endemic area of HBV infection, have chronic HBV infection (surface antigen-positive, HBsAg+) and are characterized by distinct clinical and genetic features. Here, we showed that 24% of follicular lymphoma (FL) Chinese patients are HBsAg+. Compared with the HBsAg- FL patients, HBsAg+ patients are younger, have a higher histological grade at diagnosis, and have a higher incidence of disease progression within 24 months. Moreover, by sequencing the genomes of 109 FL tumors, we observed enhanced mutagenesis and distinct genetic profile in HBsAg+ FLs, with a unique set of preferentially mutated genes (TNFAIP3, FAS, HIST1H1C, KLF2, TP53, PIM1, TMSB4X, DUSP2, TAGAP, LYN, and SETD2) but lack of the hallmark of HBsAg- FLs (ie, IGH/BCL2 translocations and CREBBP mutations). Transcriptomic analyses further showed that HBsAg+ FLs displayed gene-expression signatures resembling the activated B-cell-like subtype of diffuse large B-cell lymphoma, involving IRF4-targeted genes and NF-κB/MYD88 signaling pathways. Finally, we identified an increased infiltration of CD8+ memory T cells, CD4+ Th1 cells, and M1 macrophages and higher T-cell exhaustion gene signature in HBsAg+ FL samples. Taken together, we present new genetic/epigenetic evidence that links chronic HBV infection to B-cell lymphomagenesis, and HBV-associated FL is likely to have a distinct cell-of-origin and represent as a separate subtype of FL. Targetable genetic/epigenetic alterations identified in tumors and their associated tumor microenvironment may provide potential novel therapeutic approaches for this subgroup of patients.
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Affiliation(s)
- Weicheng Ren
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
- Department of Lymphoma, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
| | - Xianhuo Wang
- Department of Lymphoma, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
| | - Mingyu Yang
- BGI-Shenzhen, Shenzhen, China
- Guangdong Provincial Key Laboratory of Human Disease Genomics, Shenzhen Key Laboratory of Genomics, Shenzhen, China
| | - Hui Wan
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - Xiaobo Li
- BGI-Shenzhen, Shenzhen, China
- Guangdong Provincial Key Laboratory of Human Disease Genomics, Shenzhen Key Laboratory of Genomics, Shenzhen, China
| | - Xiaofei Ye
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - Bing Meng
- Department of Lymphoma, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
| | - Wei Li
- Department of Lymphoma, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
| | - Jingwei Yu
- Department of Lymphoma, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
| | - Mengyue Lei
- BGI-Shenzhen, Shenzhen, China
- Guangdong Provincial Key Laboratory of Human Disease Genomics, Shenzhen Key Laboratory of Genomics, Shenzhen, China
| | - Fanfan Xie
- BGI-Shenzhen, Shenzhen, China
- Guangdong Provincial Key Laboratory of Human Disease Genomics, Shenzhen Key Laboratory of Genomics, Shenzhen, China
| | - Wenqi Jiang
- Department of Medical Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Eva Kimby
- Unit of Hematology, Department of Medicine at Huddinge, Karolinska Institutet, Stockholm, Sweden; and
| | - Huiqiang Huang
- Department of Medical Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Dongbing Liu
- BGI-Shenzhen, Shenzhen, China
- Guangdong Provincial Key Laboratory of Human Disease Genomics, Shenzhen Key Laboratory of Genomics, Shenzhen, China
| | - Zhi-Ming Li
- Department of Medical Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Kui Wu
- BGI-Shenzhen, Shenzhen, China
- Guangdong Provincial Key Laboratory of Human Disease Genomics, Shenzhen Key Laboratory of Genomics, Shenzhen, China
- Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, China
| | - Huilai Zhang
- Department of Lymphoma, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
| | - Qiang Pan-Hammarström
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
- Department of Lymphoma, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
- BGI-Shenzhen, Shenzhen, China
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91
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Interplay between A-to-I Editing and Splicing of RNA: A Potential Point of Application for Cancer Therapy. Int J Mol Sci 2022; 23:ijms23095240. [PMID: 35563631 PMCID: PMC9105294 DOI: 10.3390/ijms23095240] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 05/05/2022] [Accepted: 05/06/2022] [Indexed: 11/17/2022] Open
Abstract
Adenosine-to-inosine RNA editing is a system of post-transcriptional modification widely distributed in metazoans which is catalyzed by ADAR enzymes and occurs mostly in double-stranded RNA (dsRNA) before splicing. This type of RNA editing changes the genetic code, as inosine generally pairs with cytosine in contrast to adenosine, and this expectably modulates RNA splicing. We review the interconnections between RNA editing and splicing in the context of human cancer. The editing of transcripts may have various effects on splicing, and resultant alternatively spliced isoforms may be either tumor-suppressive or oncogenic. Dysregulated RNA splicing in cancer often causes the release of excess amounts of dsRNA into cytosol, where specific dsRNA sensors provoke antiviral-like responses, including type I interferon signaling. These responses may arrest cell division, causing apoptosis and, externally, stimulate antitumor immunity. Thus, small-molecule spliceosome inhibitors have been shown to facilitate the antiviral-like signaling and are considered to be potential cancer therapies. In turn, a cytoplasmic isoform of ADAR can deaminate dsRNA in cytosol, thereby decreasing its levels and diminishing antitumor innate immunity. We propose that complete or partial inhibition of ADAR may enhance the proapoptotic and cytotoxic effects of splicing inhibitors and that it may be considered a promising addition to cancer therapies targeting RNA splicing.
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92
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Guo Y, Yang C, Liu Y, Li T, Li H, Han J, Jia L, Wang X, Zhang B, Li J, Li L. High Expression of HERV-K (HML-2) Might Stimulate Interferon in COVID-19 Patients. Viruses 2022; 14:996. [PMID: 35632738 PMCID: PMC9143815 DOI: 10.3390/v14050996] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 05/03/2022] [Accepted: 05/06/2022] [Indexed: 12/15/2022] Open
Abstract
Background. Interferon is a marker of host antiviral immunity, which is disordered in COVID-19 patients. ERV can affect the secretion of interferon through the cGAS-STING pathway. In this study, we explored whether IFN-I and HERV-K (HML-2) were activated in COVID-19 patients and whether there was an interaction between them. Methods. We collected blood samples from COVID-19 patients and healthy controls. We first detected the expression of HERV-K (HML-2) gag, env, and pol genes and IFN-I-related genes between patients and healthy people by qPCR, synchronously detected VERO cells infected with SARS-CoV-2. Then, the chromosome distributions of highly expressed HERV-K (HML-2) gag, env, and pol genes were mapped by the next-generation sequencing results, and GO analysis was performed on the related genes. Results. We found that the HERV-K (HML-2) gag, env, and pol genes were highly expressed in COVID-19 patients and VERO cells infected with SARS-CoV-2. The interferon-related genes IFNB1, ISG15, and IFIT1 were also activated in COVID-19 patients, and GO analysis showed that HERV-K (HML-2) can regulate the secretion of interferon. Conclusions. The high expression of HERV-K (HML-2) might activate the increase of interferon in COVID-19 patients, proving that HERV-K does not only play a negative role in the human body.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Lin Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China; (Y.G.); (C.Y.); (Y.L.); (T.L.); (H.L.); (J.H.); (L.J.); (X.W.); (B.Z.); (J.L.)
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93
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Salvetat N, Checa-Robles FJ, Patel V, Cayzac C, Dubuc B, Chimienti F, Abraham JD, Dupré P, Vetter D, Méreuze S, Lang JP, Kupfer DJ, Courtet P, Weissmann D. A game changer for bipolar disorder diagnosis using RNA editing-based biomarkers. Transl Psychiatry 2022; 12:182. [PMID: 35504874 PMCID: PMC9064541 DOI: 10.1038/s41398-022-01938-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 03/30/2022] [Accepted: 04/19/2022] [Indexed: 11/08/2022] Open
Abstract
In clinical practice, differentiating Bipolar Disorder (BD) from unipolar depression is a challenge due to the depressive symptoms, which are the core presentations of both disorders. This misdiagnosis during depressive episodes results in a delay in proper treatment and a poor management of their condition. In a first step, using A-to-I RNA editome analysis, we discovered 646 variants (366 genes) differentially edited between depressed patients and healthy volunteers in a discovery cohort of 57 participants. After using stringent criteria and biological pathway analysis, candidate biomarkers from 8 genes were singled out and tested in a validation cohort of 410 participants. Combining the selected biomarkers with a machine learning approach achieved to discriminate depressed patients (n = 267) versus controls (n = 143) with an AUC of 0.930 (CI 95% [0.879-0.982]), a sensitivity of 84.0% and a specificity of 87.1%. In a second step by selecting among the depressed patients those with unipolar depression (n = 160) or BD (n = 95), we identified a combination of 6 biomarkers which allowed a differential diagnosis of bipolar disorder with an AUC of 0.935 and high specificity (Sp = 84.6%) and sensitivity (Se = 90.9%). The association of RNA editing variants modifications with depression subtypes and the use of artificial intelligence allowed developing a new tool to identify, among depressed patients, those suffering from BD. This test will help to reduce the misdiagnosis delay of bipolar patients, leading to an earlier implementation of a proper treatment.
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Affiliation(s)
- Nicolas Salvetat
- ALCEDIAG/Sys2Diag, CNRS UMR 9005, Parc Euromédecine, Montpellier, France
| | | | - Vipul Patel
- ALCEDIAG/Sys2Diag, CNRS UMR 9005, Parc Euromédecine, Montpellier, France
| | - Christopher Cayzac
- ALCEDIAG/Sys2Diag, CNRS UMR 9005, Parc Euromédecine, Montpellier, France
| | - Benjamin Dubuc
- ALCEDIAG/Sys2Diag, CNRS UMR 9005, Parc Euromédecine, Montpellier, France
| | - Fabrice Chimienti
- ALCEDIAG/Sys2Diag, CNRS UMR 9005, Parc Euromédecine, Montpellier, France
| | | | - Pierrick Dupré
- ALCEDIAG/Sys2Diag, CNRS UMR 9005, Parc Euromédecine, Montpellier, France
| | - Diana Vetter
- ALCEDIAG/Sys2Diag, CNRS UMR 9005, Parc Euromédecine, Montpellier, France
| | - Sandie Méreuze
- ALCEDIAG/Sys2Diag, CNRS UMR 9005, Parc Euromédecine, Montpellier, France
| | - Jean-Philippe Lang
- ALCEDIAG/Sys2Diag, CNRS UMR 9005, Parc Euromédecine, Montpellier, France
- Les Toises. Center for Psychiatry and Psychotherapy, Lausanne, Switzerland
| | - David J Kupfer
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Philippe Courtet
- Department of Psychiatric Emergency & Acute Care, Lapeyronie Hospital, CHU Montpellier, Montpellier, France
| | - Dinah Weissmann
- ALCEDIAG/Sys2Diag, CNRS UMR 9005, Parc Euromédecine, Montpellier, France.
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94
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Chen Z, He L, Zhao L, Zhang G, Wang Z, Zhu P, Liu B. circREEP3 Drives Colorectal Cancer Progression via Activation of FKBP10 Transcription and Restriction of Antitumor Immunity. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2105160. [PMID: 35233964 PMCID: PMC9069384 DOI: 10.1002/advs.202105160] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 02/10/2022] [Indexed: 06/12/2023]
Abstract
Colorectal cancer (CRC) is one of the most common tumors around the world. Circular RNA is widely involved in tumor progression via unclear mechanisms. Here, circREEP3 is found to be upregulated in CRC tissues. circREEP3 upregulation predicts poor patient survival. circREEP3 knockout suppresses CRC tumorigenesis and metastasis, and impairs stem cell-like phenotype. Mechanistically, circREEP3 recruits the chromatin remodeling protein CHD7 to FKBP10 promoter and activates its transcription. Moreover, circREEP3 restricts RIG-1-dependent antitumor immunity. FKBP10 is highly expressed in CRC tissues and associated with poor prognosis. FKBP10 ectopic expression partially rescues the potential of proliferation and metastasis in circREEP3-deficient CRC cells. Thus, the findings support circREEP3-FKBP10 axis drives CRC progression and may be a critical prognostic marker.
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Affiliation(s)
- Zhenzhen Chen
- School of Life SciencesZhengzhou UniversityZhengzhou450001China
| | - Luyun He
- Department of PathophysiologySchool of Basic Medical SciencesZhengzhou UniversityZhengzhou450001China
| | - Liangbo Zhao
- School of Life SciencesZhengzhou UniversityZhengzhou450001China
| | - Guangtan Zhang
- Department of Gastrointestinal SurgeryHenan Provincial People's HospitalPeople's Hospital of Henan UniversityPeople's Hospital of Zhengzhou UniversityZhengzhou450003China
| | - Zhiwei Wang
- School of Life SciencesZhengzhou UniversityZhengzhou450001China
| | - Pingping Zhu
- School of Life SciencesZhengzhou UniversityZhengzhou450001China
| | - Benyu Liu
- Research Center of Basic MedicineAcademy of Medical SciencesZhengzhou UniversityZhengzhou450001China
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95
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Baker AR, Slack FJ. ADAR1 and its implications in cancer development and treatment. Trends Genet 2022; 38:821-830. [PMID: 35459560 PMCID: PMC9283316 DOI: 10.1016/j.tig.2022.03.013] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/14/2022] [Accepted: 03/17/2022] [Indexed: 12/12/2022]
Abstract
The family of adenosine deaminases acting on RNA (ADARs) regulates global gene expression output by catalyzing adenosine-to-inosine (A-to-I) editing of double-stranded RNA (dsRNA) and through interacting with RNA and other proteins. ADARs play important roles in development and disease, including an increasing connection to cancer progression. ADAR1 has demonstrated a largely pro-oncogenic role in a growing list of cancer types, and its function in cancer has been attributed to diverse mechanisms. Here, we review existing literature on ADAR1 biology and function, its roles in human disease including cancer, and summarize known cancer-associated phenotypes and mechanisms. Lastly, we discuss implications and outstanding questions in the field, including strategies for targeting ADAR1 in cancer.
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Affiliation(s)
- Allison R Baker
- Harvard Medical School Initiative for RNA Medicine, Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA
| | - Frank J Slack
- Harvard Medical School Initiative for RNA Medicine, Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA.
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96
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Tassinari V, Cerboni C, Soriani A. Self or Non-Self? It Is also a Matter of RNA Recognition and Editing by ADAR1. BIOLOGY 2022; 11:biology11040568. [PMID: 35453767 PMCID: PMC9024829 DOI: 10.3390/biology11040568] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 04/01/2022] [Accepted: 04/06/2022] [Indexed: 01/19/2023]
Abstract
Simple Summary A fundamental feature of innate immune cells is to detect the presence of non-self, such as potentially harmful nucleic acids, by germline-encoded specialized receptors called pattern recognition receptors (PRRs). ADAR1 is one key enzyme avoiding aberrant type I interferon (IFN-I) production and immune cell activation by the conversion of adenosine to inosine (A-to-I) in double-stranded RNA (dsRNA) structures that arise in self mRNA containing specific repetitive elements. This review intends to give an up-to-date and detailed overview of the ADAR1-mediated ability to modulate the immune response in autoimmune diseases and cancer progression. Abstract A-to-I editing is a post-transcriptional mechanism affecting coding and non-coding dsRNAs, catalyzed by the adenosine deaminases acting on the RNA (ADAR) family of enzymes. A-to-I modifications of endogenous dsRNA (mainly derived from Alu repetitive elements) prevent their recognition by cellular dsRNA sensors, thus avoiding the induction of antiviral signaling and uncontrolled IFN-I production. This process, mediated by ADAR1 activity, ensures the activation of an innate immune response against foreign (non-self) but not self nucleic acids. As a consequence, ADAR1 mutations or its de-regulated activity promote the development of autoimmune diseases and strongly impact cell growth, also leading to cancer. Moreover, the excessive inflammation promoted by Adar1 ablation also impacts T and B cell maturation, as well as the development of dendritic cell subsets, revealing a new role of ADAR1 in the homeostasis of the immune system.
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97
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Chen YG, Hur S. Cellular origins of dsRNA, their recognition and consequences. Nat Rev Mol Cell Biol 2022; 23:286-301. [PMID: 34815573 PMCID: PMC8969093 DOI: 10.1038/s41580-021-00430-1] [Citation(s) in RCA: 143] [Impact Index Per Article: 71.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/12/2021] [Indexed: 01/02/2023]
Abstract
Double-stranded RNA (dsRNA) is associated with most viral infections - it either constitutes the viral genome (in the case of dsRNA viruses) or is generated in host cells during viral replication. Hence, nearly all organisms have the capability of recognizing dsRNA and mounting a response, the primary aim of which is to mitigate the potential infection. In vertebrates, a set of innate immune receptors for dsRNA induce a multitude of cell-intrinsic and cell-extrinsic immune responses upon dsRNA recognition. Notably, recent studies showed that vertebrate cells can accumulate self-derived dsRNAs or dsRNA-like species upon dysregulation of several cellular processes, activating the very same immune pathways as in infected cells. On the one hand, such aberrant immune activation in the absence of infection can lead to pathogenesis of immune disorders, such as Aicardi-Goutières syndrome. On the other hand, the same innate immune reaction can be induced in a controlled setting for a therapeutic benefit, as occurs in immunotherapies. In this Review, we describe mechanisms by which immunostimulatory dsRNAs are generated in mammalian cells, either by viruses or by the host cells, and how cells respond to them, with the focus on recent developments regarding the role of cellular dsRNAs in immune modulation.
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Affiliation(s)
- Y Grace Chen
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA.
| | - Sun Hur
- Harvard Medical School & Boston Children's Hospital, Boston, MA, USA.
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98
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Stok JE, Oosenbrug T, ter Haar LR, Gravekamp D, Bromley CP, Zelenay S, Reis e Sousa C, van der Veen AG. RNA sensing via the RIG-I-like receptor LGP2 is essential for the induction of a type I IFN response in ADAR1 deficiency. EMBO J 2022; 41:e109760. [PMID: 35156720 PMCID: PMC8922249 DOI: 10.15252/embj.2021109760] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 01/07/2022] [Accepted: 01/11/2022] [Indexed: 12/12/2022] Open
Abstract
RNA editing by the adenosine deaminase ADAR1 prevents innate immune responses to endogenous RNAs. In ADAR1-deficient cells, unedited self RNAs form base-paired structures that resemble viral RNAs and inadvertently activate the cytosolic RIG-I-like receptor (RLR) MDA5, leading to an antiviral type I interferon (IFN) response. Mutations in ADAR1 cause Aicardi-Goutières Syndrome (AGS), an autoinflammatory syndrome characterized by chronic type I IFN production. Conversely, ADAR1 loss and the consequent type I IFN production restricts tumor growth and potentiates the activity of some chemotherapeutics. Here, we show that another RIG-I-like receptor, LGP2, also has an essential role in the induction of a type I IFN response in ADAR1-deficient human cells. This requires the canonical function of LGP2 as an RNA sensor and facilitator of MDA5-dependent signaling. Furthermore, we show that the sensitivity of tumor cells to ADAR1 loss requires LGP2 expression. Finally, type I IFN induction in tumor cells depleted of ADAR1 and treated with some chemotherapeutics fully depends on LGP2 expression. These findings highlight a central role for LGP2 in self RNA sensing with important clinical implications.
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Affiliation(s)
- Jorn E Stok
- Department of ImmunologyLeiden University Medical CentreLeidenThe Netherlands
| | - Timo Oosenbrug
- Department of ImmunologyLeiden University Medical CentreLeidenThe Netherlands
| | - Laurens R ter Haar
- Department of ImmunologyLeiden University Medical CentreLeidenThe Netherlands
| | - Dennis Gravekamp
- Department of ImmunologyLeiden University Medical CentreLeidenThe Netherlands
| | - Christian P Bromley
- Cancer Research UK Manchester InstituteThe University of ManchesterAlderley ParkUK
| | - Santiago Zelenay
- Cancer Research UK Manchester InstituteThe University of ManchesterAlderley ParkUK
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99
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Daniel Grass G, Alfonso JCL, Welsh E, Ahmed KA, Teer JK, Pilon-Thomas S, Harrison LB, Cleveland JL, Mulé JJ, Eschrich SA, Enderling H, Torres-Roca JF. The Radiosensitivity Index (RSI) Gene Signature Identifies Distinct Tumor Immune Microenvironment Characteristics Associated with Susceptibility to Radiotherapy. Int J Radiat Oncol Biol Phys 2022; 113:635-647. [PMID: 35289298 DOI: 10.1016/j.ijrobp.2022.03.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 03/02/2022] [Accepted: 03/03/2022] [Indexed: 12/09/2022]
Abstract
PURPOSE Radiotherapy (RT) is a mainstay of cancer care and accumulating evidence suggests the potential for synergism with components of the immune response. However, little data describes the tumor immune contexture in relation to RT-sensitivity. To address this challenge, we employed the radiation sensitivity index (RSI) gene signature to estimate the RT-sensitivity of >10,000 primary tumors and characterized their immune microenvironments in relation to the RSI. MATERIAL AND METHODS We analyzed gene expression profiles of 10,469 primary tumors (31 types) within a prospective tissue collection protocol. The RT-sensitivity of each tumor was estimated by the RSI and respective distributions were characterized. The tumor biology measured by the RSI was evaluated by differentially expressed genes (DEGs) combined with single sample gene set enrichment analysis (ssGSEA). Differences in the expression of immune regulatory molecules were assessed and deconvolution algorithms were used to estimate immune cell infiltrates in relation to the RSI. A subset (n=2,368) of tumors underwent DNA sequencing for mutational frequency characterization. RESULTS We identified a wide range of RSI values within and across various tumor types, with several demonstrating non-unimodal distributions (e.g. colon, renal, lung, prostate, esophagus, pancreas and PAM50 breast subtypes; p <0.05). Across all tumors types, stratifying RSI at a tumor type-specific median, identified 7,148 DEGs, of which 146 were coordinate in direction. Network topology analysis demonstrates RSI measures a coordinated STAT1, IRF1, and CCL4/MIP-1β transcriptional network. Tumors with an estimated high sensitivity to RT demonstrated distinct enrichment of interferon-associated signaling pathways and immune cell infiltrates (e.g. CD8+ T cells, activated natural killer cells, M1-macrophages; q < 0.05), which was in the context of diverse expression patterns of various immunoregulatory molecules. CONCLUSION This analysis describes the immune microenvironments of patient tumors in relation to the RSI gene expression signature.
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Affiliation(s)
- G Daniel Grass
- Departments of Radiation Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa FL, USA
| | - Juan C L Alfonso
- Departments of Braunschweig Integrated Centre of Systems Biology, Helmholtz Centre for Infection Research
| | - Eric Welsh
- Departments of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa FL, USA
| | - Kamran A Ahmed
- Departments of Radiation Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa FL, USA
| | - Jamie K Teer
- Departments of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa FL, USA
| | - Shari Pilon-Thomas
- Departments of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa FL, USA
| | - Louis B Harrison
- Departments of Radiation Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa FL, USA
| | - John L Cleveland
- Departments of Tumor Biology, H. Lee Moffitt Cancer Center and Research Institute, Tampa FL, USA
| | - James J Mulé
- Departments of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa FL, USA
| | - Steven A Eschrich
- Departments of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa FL, USA
| | - Heiko Enderling
- Departments of Radiation Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa FL, USA; Departments of Integrated Mathematical Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa FL, USA.
| | - Javier F Torres-Roca
- Departments of Radiation Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa FL, USA.
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100
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Pasello G, Remon J, Felley-Bosco E. Editorial: Understanding the Interplay Between the Tumor Immune Microenvironment and Genetic Alterations in Thoracic Malignancies. Front Oncol 2022; 12:871544. [PMID: 35359422 PMCID: PMC8960239 DOI: 10.3389/fonc.2022.871544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 02/10/2022] [Indexed: 11/16/2022] Open
Affiliation(s)
- Giulia Pasello
- Department of Surgery, Oncology and Gastroenterology, University of Padua, Padua, Italy
- Medical Oncology 2, Istituto Oncologico Veneto Instituto di Ricerca e Cura a Carattere Scientifico (IOV IRCCS), Padua, Italy
- *Correspondence: Giulia Pasello, ;
| | - Jordi Remon
- Department of Medical Oncology, Centro Integral Oncológico Clara Campal (HM-CIOCC), Hospital HM Nou Delfos, HM Hospitales, Barcelona, Spain
| | - Emanuela Felley-Bosco
- Laboratory of Molecular Oncology, Department of Thoracic Surgery, University Hospital Zurich, Zurich, Switzerland
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