1
|
van Gemert F, Drakaki A, Lozano IM, de Groot D, Uiterkamp M, Proost N, Lieftink C, van de Ven M, Beijersbergen R, Jacobs H, te Riele H. ADARp150 counteracts whole genome duplication. Nucleic Acids Res 2024; 52:10370-10384. [PMID: 39189458 PMCID: PMC11417406 DOI: 10.1093/nar/gkae700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 07/10/2024] [Accepted: 08/07/2024] [Indexed: 08/28/2024] Open
Abstract
Impaired control of the G1/S checkpoint allows initiation of DNA replication under non-permissive conditions. Unscheduled S-phase entry is associated with DNA replication stress, demanding for other checkpoints or cellular pathways to maintain proliferation. Here, we uncovered a requirement for ADARp150 to sustain proliferation of G1/S-checkpoint-defective cells under growth-restricting conditions. Besides its well-established mRNA editing function in inversely oriented short interspersed nuclear elements (SINEs), we found ADARp150 to exert a critical function in mitosis. ADARp150 depletion resulted in tetraploidization, impeding cell proliferation in mitogen-deprived conditions. Mechanistically we show that ADAR1 depletion induced aberrant expression of Cyclin B3, which was causative for mitotic failure and whole-genome duplication. Finally, we find that also in vivo ADAR1-depletion-provoked tetraploidization hampers tumor outgrowth.
Collapse
Affiliation(s)
- Frank van Gemert
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Alexandra Drakaki
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Isabel Morales Lozano
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Daniël de Groot
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Maud Schoot Uiterkamp
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Natalie Proost
- Mouse Clinic for Cancer and Aging Research, Preclinical Intervention Unit, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Cor Lieftink
- Division of Molecular Carcinogenesis, NKI Robotics and Screening Center, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Marieke van de Ven
- Mouse Clinic for Cancer and Aging Research, Preclinical Intervention Unit, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Roderick L Beijersbergen
- Division of Molecular Carcinogenesis, NKI Robotics and Screening Center, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Heinz Jacobs
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Hein te Riele
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| |
Collapse
|
2
|
Young AA, Bohlin HE, Pierce JR, Cottrell KA. Suppression of double-stranded RNA sensing in cancer: molecular mechanisms and therapeutic potential. Biochem Soc Trans 2024:BST20230727. [PMID: 39221819 DOI: 10.1042/bst20230727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2024] [Revised: 08/15/2024] [Accepted: 08/20/2024] [Indexed: 09/04/2024]
Abstract
Immunotherapy has emerged as a therapeutic option for many cancers. For some tumors, immune checkpoint inhibitors show great efficacy in promoting anti-tumor immunity. However, not all tumors respond to immunotherapies. These tumors often exhibit reduced inflammation and are resistant to checkpoint inhibitors. Therapies that turn these 'cold' tumors 'hot' could improve the efficacy and applicability of checkpoint inhibitors, and in some cases may be sufficient on their own to promote anti-tumor immunity. One strategy to accomplish this goal is to activate innate immunity pathways within the tumor. Here we describe how this can be accomplished by activating double-stranded RNA (dsRNA) sensors. These sensors evolved to detect and respond to dsRNAs arising from viral infection but can also be activated by endogenous dsRNAs. A set of proteins, referred to as suppressors of dsRNA sensing, are responsible for preventing sensing 'self' dsRNA and activating innate immunity pathways. The mechanism of action of these suppressors falls into three categories: (1) Suppressors that affect mature RNAs through editing, degradation, restructuring, or binding. (2) Suppressors that affect RNA processing. (3) Suppressors that affect RNA expression. In this review we highlight suppressors that function through each mechanism, provide examples of the effects of disrupting those suppressors in cancer cell lines and tumors, and discuss the therapeutic potential of targeting these proteins and pathways.
Collapse
Affiliation(s)
- Addison A Young
- Department of Biochemistry, Purdue University, West Lafayette, IN, U.S.A
| | - Holly E Bohlin
- Department of Biochemistry, Purdue University, West Lafayette, IN, U.S.A
| | - Jackson R Pierce
- Department of Biochemistry, Purdue University, West Lafayette, IN, U.S.A
| | - Kyle A Cottrell
- Department of Biochemistry, Purdue University, West Lafayette, IN, U.S.A
| |
Collapse
|
3
|
Sinigaglia K, Cherian A, Du Q, Lacovich V, Vukić D, Melicherová J, Linhartova P, Zerad L, Stejskal S, Malik R, Prochazka J, Bondurand N, Sedláček R, O'Connell MA, Keegan LP. An ADAR1 dsRBD3-PKR kinase domain interaction on dsRNA inhibits PKR activation. Cell Rep 2024; 43:114618. [PMID: 39146181 DOI: 10.1016/j.celrep.2024.114618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 05/30/2024] [Accepted: 07/25/2024] [Indexed: 08/17/2024] Open
Abstract
Adar null mutant mouse embryos die with aberrant double-stranded RNA (dsRNA)-driven interferon induction, and Adar Mavs double mutants, in which interferon induction is prevented, die soon after birth. Protein kinase R (Pkr) is aberrantly activated in Adar Mavs mouse pup intestines before death, intestinal crypt cells die, and intestinal villi are lost. Adar Mavs Eifak2 (Pkr) triple mutant mice rescue all defects and have long-term survival. Adenosine deaminase acting on RNA 1 (ADAR1) and PKR co-immunoprecipitate from cells, suggesting PKR inhibition by direct interaction. AlphaFold studies on an inhibitory PKR dsRNA binding domain (dsRBD)-kinase domain interaction before dsRNA binding and on an inhibitory ADAR1 dsRBD3-PKR kinase domain interaction on dsRNA provide a testable model of the inhibition. Wild-type or editing-inactive human ADAR1 expressed in A549 cells inhibits activation of endogenous PKR. ADAR1 dsRNA binding is required for, but is not sufficient for, PKR inhibition. Mutating the ADAR1 dsRBD3-PKR contact prevents co-immunoprecipitation, ADAR1 inhibition of PKR activity, and co-localization of ADAR1 and PKR in cells.
Collapse
Affiliation(s)
- Ketty Sinigaglia
- Central European Institute for Technology at Masaryk University (CEITEC MU), Building E35, Kamenice 735/5, 625 00 Brno, Czechia; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czechia
| | - Anna Cherian
- Central European Institute for Technology at Masaryk University (CEITEC MU), Building E35, Kamenice 735/5, 625 00 Brno, Czechia; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czechia
| | - Qiupei Du
- Central European Institute for Technology at Masaryk University (CEITEC MU), Building E35, Kamenice 735/5, 625 00 Brno, Czechia; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czechia
| | - Valentina Lacovich
- Central European Institute for Technology at Masaryk University (CEITEC MU), Building E35, Kamenice 735/5, 625 00 Brno, Czechia
| | - Dragana Vukić
- Central European Institute for Technology at Masaryk University (CEITEC MU), Building E35, Kamenice 735/5, 625 00 Brno, Czechia; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czechia
| | - Janka Melicherová
- Central European Institute for Technology at Masaryk University (CEITEC MU), Building E35, Kamenice 735/5, 625 00 Brno, Czechia; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czechia
| | - Pavla Linhartova
- Central European Institute for Technology at Masaryk University (CEITEC MU), Building E35, Kamenice 735/5, 625 00 Brno, Czechia
| | - Lisa Zerad
- Laboratory of Embryology and Genetics of Human Malformation, Imagine Institute, INSERM UMR 1163, Université de Paris Cité, 75015 Paris, France
| | - Stanislav Stejskal
- Central European Institute for Technology at Masaryk University (CEITEC MU), Building E35, Kamenice 735/5, 625 00 Brno, Czechia
| | - Radek Malik
- Laboratory of Epigenetic Regulation, Institute of Molecular Genetics of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague, Czechia
| | - Jan Prochazka
- Institute of Molecular Genetics of the Czech Academy of Sciences, Prumyslova 595, 252 50 Vestec, Czechia
| | - Nadège Bondurand
- Laboratory of Embryology and Genetics of Human Malformation, Imagine Institute, INSERM UMR 1163, Université de Paris Cité, 75015 Paris, France
| | - Radislav Sedláček
- Institute of Molecular Genetics of the Czech Academy of Sciences, Prumyslova 595, 252 50 Vestec, Czechia
| | - Mary A O'Connell
- Central European Institute for Technology at Masaryk University (CEITEC MU), Building E35, Kamenice 735/5, 625 00 Brno, Czechia.
| | - Liam P Keegan
- Central European Institute for Technology at Masaryk University (CEITEC MU), Building E35, Kamenice 735/5, 625 00 Brno, Czechia.
| |
Collapse
|
4
|
Mao JX, Li JJ, Lu XY, Zhong HX, Zhao YY, Zhu LY, Fu H, Ding GS, Teng F, Chen M, Guo WY. Dichotomous roles of ADAR1 in liver hepatocellular carcinoma and kidney renal cell carcinoma: Unraveling the complex tumor microenvironment and prognostic significance. Int Immunopharmacol 2024; 136:112340. [PMID: 38820962 DOI: 10.1016/j.intimp.2024.112340] [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: 03/13/2024] [Revised: 05/14/2024] [Accepted: 05/22/2024] [Indexed: 06/02/2024]
Abstract
BACKGROUND Adenosine deaminase acting on RNA 1 (ADAR1) is an RNA-editing enzyme that significantly impacts cancer progression and various biological processes. The expression of ADAR1 mRNA has been examined in multiple cancer types using The Cancer Genome Atlas (TCGA) dataset, revealing distinct patterns in kidney chromophobe (KICH), kidney renal clear cell carcinoma (KIRC), kidney renal papillary cell carcinoma (KIRP), and liver hepatocellular carcinoma (LIHC) compared to normal controls. However, the reasons for these differential expressions remain unclear. METHODS In this study, we performed RT-PCR and western blotting (WB) to validate ADAR1 expression patterns in clinical tissue samples. Survival analysis and immune microenvironment analysis (including immune score and stromal score) were conducted using TCGA data to determine the specific cell types associated with ADAR1, as well as the key genes in those cell types. The relationship between ADAR1 and specific cell types' key genes was verified by immunohistochemistry (IHC), using clinical liver and kidney cancer samples. RESULTS Our validation analysis revealed that ADAR1 expression was downregulated in KICH, KIRC, and KIRP, while upregulated in LIHC compared to normal tissues. Notably, a significant correlation was found between ADAR1 mRNA expression and patient prognosis, particularly in KIRC, KIRP, and LIHC. Interestingly, we observed a positive correlation between ADAR1 expression and stromal scores in KIRC, whereas a negative correlation was observed in LIHC. Cell type analysis highlighted distinct relationships between ADAR1 expression and the two stromal cell types, blood endothelial cells (BECs) and lymphatic endothelial cells (LECs), and further determined the signature gene claudin-5 (CLDN5), in KIRC and LIHC. Moreover, ADAR1 was inversely related with CLDN5 in KIRC (n = 26) and LIHC (n = 30) samples, verified via IHC. CONCLUSIONS ADAR1 plays contrasting roles in LIHC and KIRC, associated with the enrichment of BECs and LECs within tumors. This study sheds light on the significant roles of stromal cells within the complex tumor microenvironment (TME) and provides new insights for future research in tumor immunotherapy and precision medicine.
Collapse
MESH Headings
- Adenosine Deaminase/genetics
- Adenosine Deaminase/metabolism
- Humans
- Tumor Microenvironment
- Liver Neoplasms/genetics
- Liver Neoplasms/pathology
- Liver Neoplasms/metabolism
- Carcinoma, Hepatocellular/genetics
- Carcinoma, Hepatocellular/metabolism
- Carcinoma, Hepatocellular/pathology
- Carcinoma, Hepatocellular/mortality
- Kidney Neoplasms/genetics
- Kidney Neoplasms/pathology
- Kidney Neoplasms/metabolism
- Kidney Neoplasms/mortality
- Carcinoma, Renal Cell/genetics
- Carcinoma, Renal Cell/metabolism
- Carcinoma, Renal Cell/pathology
- RNA-Binding Proteins/metabolism
- RNA-Binding Proteins/genetics
- Prognosis
- Gene Expression Regulation, Neoplastic
- Female
- Male
- Biomarkers, Tumor/metabolism
- Biomarkers, Tumor/genetics
- Middle Aged
Collapse
Affiliation(s)
- Jia-Xi Mao
- Department of Liver Surgery and Organ Transplantation, Changzheng Hospital, Naval Medical University, Shanghai 200003, China
| | - Jing-Jing Li
- Department of Liver Surgery and Organ Transplantation, Changzheng Hospital, Naval Medical University, Shanghai 200003, China
| | - Xin-Yi Lu
- Department of Liver Surgery and Organ Transplantation, Changzheng Hospital, Naval Medical University, Shanghai 200003, China
| | - Han-Xiang Zhong
- Department of Liver Surgery and Organ Transplantation, Changzheng Hospital, Naval Medical University, Shanghai 200003, China
| | - Yuan-Yu Zhao
- Department of Liver Surgery and Organ Transplantation, Changzheng Hospital, Naval Medical University, Shanghai 200003, China
| | - Li-Ye Zhu
- Department of Immunology and Medical Immunology State Key Laboratory, Naval Medical University, Shanghai 200433, China
| | - Hong Fu
- Department of Liver Surgery and Organ Transplantation, Changzheng Hospital, Naval Medical University, Shanghai 200003, China
| | - Guo-Shan Ding
- Department of Liver Surgery and Organ Transplantation, Changzheng Hospital, Naval Medical University, Shanghai 200003, China
| | - Fei Teng
- Department of Liver Surgery and Organ Transplantation, Changzheng Hospital, Naval Medical University, Shanghai 200003, China.
| | - Ming Chen
- Department of Urology, Changzheng Hospital, Naval Medical University, Shanghai 200003, China.
| | - Wen-Yuan Guo
- Department of Liver Surgery and Organ Transplantation, Changzheng Hospital, Naval Medical University, Shanghai 200003, China.
| |
Collapse
|
5
|
Gan WL, Ren X, Ng VHE, Ng L, Song Y, Tano V, Han J, An O, Xie J, Ng BYL, Tay DJT, Tang SJ, Shen H, Khare S, Chong KHC, Young DY, Wu B, DasGupta R, Chen L. Hepatocyte-macrophage crosstalk via the PGRN-EGFR axis modulates ADAR1-mediated immunity in the liver. Cell Rep 2024; 43:114400. [PMID: 38935501 DOI: 10.1016/j.celrep.2024.114400] [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: 10/05/2023] [Revised: 04/23/2024] [Accepted: 06/11/2024] [Indexed: 06/29/2024] Open
Abstract
ADAR1-mediated RNA editing establishes immune tolerance to endogenous double-stranded RNA (dsRNA) by preventing its sensing, primarily by MDA5. Although deleting Ifih1 (encoding MDA5) rescues embryonic lethality in ADAR1-deficient mice, they still experience early postnatal death, and removing other MDA5 signaling proteins does not yield the same rescue. Here, we show that ablation of MDA5 in a liver-specific Adar knockout (KO) murine model fails to rescue hepatic abnormalities caused by ADAR1 loss. Ifih1;Adar double KO (dKO) hepatocytes accumulate endogenous dsRNAs, leading to aberrant transition to a highly inflammatory state and recruitment of macrophages into dKO livers. Mechanistically, progranulin (PGRN) appears to mediate ADAR1 deficiency-induced liver pathology, promoting interferon signaling and attracting epidermal growth factor receptor (EGFR)+ macrophages into dKO liver, exacerbating hepatic inflammation. Notably, the PGRN-EGFR crosstalk communication and consequent immune responses are significantly repressed in ADAR1high tumors, revealing that pre-neoplastic or neoplastic cells can exploit ADAR1-dependent immune tolerance to facilitate immune evasion.
Collapse
Affiliation(s)
- Wei Liang Gan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Xi Ren
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Vanessa Hui En Ng
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Larry Ng
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Yangyang Song
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Vincent Tano
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Jian Han
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Omer An
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Jinghe Xie
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore; School of Biomedical Sciences and Engineering, Guangzhou International Campus, South China University of Technology, Guangzhou, P.R. China
| | - Bryan Y L Ng
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Daryl Jin Tai Tay
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Sze Jing Tang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Haoqing Shen
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Shruti Khare
- Genome Institute of Singapore, Agency for Science Technology and Research, 60 Biopolis Street, Genome, #02-01, Singapore, Singapore
| | - Kelvin Han Chung Chong
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore; NTU Institute of Structural Biology, Nanyang Technological University, Singapore, Singapore
| | - Dan Yock Young
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore; Division of Gastroenterology and Hepatology, National University Health System, Singapore, Singapore
| | - Bin Wu
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore; NTU Institute of Structural Biology, Nanyang Technological University, Singapore, Singapore
| | - Ramanuj DasGupta
- Genome Institute of Singapore, Agency for Science Technology and Research, 60 Biopolis Street, Genome, #02-01, Singapore, Singapore
| | - Leilei Chen
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore; NUS Center for Cancer Research, Yong Loo Lin School of Medicine, National University Singapore, Singapore, Singapore; Department of Anatomy, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
| |
Collapse
|
6
|
Rehwinkel J, Mehdipour P. ADAR1: from basic mechanisms to inhibitors. Trends Cell Biol 2024:S0962-8924(24)00120-X. [PMID: 39030076 DOI: 10.1016/j.tcb.2024.06.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 06/17/2024] [Accepted: 06/20/2024] [Indexed: 07/21/2024]
Abstract
Adenosine deaminase acting on RNA 1 (ADAR1) converts adenosine to inosine in double-stranded RNA (dsRNA) molecules, a process known as A-to-I editing. ADAR1 deficiency in humans and mice results in profound inflammatory diseases characterised by the spontaneous induction of innate immunity. In cells lacking ADAR1, unedited RNAs activate RNA sensors. These include melanoma differentiation-associated gene 5 (MDA5) that induces the expression of cytokines, particularly type I interferons (IFNs), protein kinase R (PKR), oligoadenylate synthase (OAS), and Z-DNA/RNA binding protein 1 (ZBP1). Immunogenic RNAs 'defused' by ADAR1 may include transcripts from repetitive elements and other long duplex RNAs. Here, we review these recent fundamental discoveries and discuss implications for human diseases. Some tumours depend on ADAR1 to escape immune surveillance, opening the possibility of unleashing anticancer therapies with ADAR1 inhibitors.
Collapse
Affiliation(s)
- Jan Rehwinkel
- Medical Research Council Translational Immune Discovery Unit, Medical Research Council Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK.
| | - Parinaz Mehdipour
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Headington, Oxford OX3 7DQ, UK.
| |
Collapse
|
7
|
Bernal YA, Durán E, Solar I, Sagredo EA, Armisén R. ADAR-Mediated A>I(G) RNA Editing in the Genotoxic Drug Response of Breast Cancer. Int J Mol Sci 2024; 25:7424. [PMID: 39000531 PMCID: PMC11242177 DOI: 10.3390/ijms25137424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2024] [Revised: 06/13/2024] [Accepted: 06/24/2024] [Indexed: 07/16/2024] Open
Abstract
Epitranscriptomics is a field that delves into post-transcriptional changes. Among these modifications, the conversion of adenosine to inosine, traduced as guanosine (A>I(G)), is one of the known RNA-editing mechanisms, catalyzed by ADARs. This type of RNA editing is the most common type of editing in mammals and contributes to biological diversity. Disruption in the A>I(G) RNA-editing balance has been linked to diseases, including several types of cancer. Drug resistance in patients with cancer represents a significant public health concern, contributing to increased mortality rates resulting from therapy non-responsiveness and disease progression, representing the greatest challenge for researchers in this field. The A>I(G) RNA editing is involved in several mechanisms over the immunotherapy and genotoxic drug response and drug resistance. This review investigates the relationship between ADAR1 and specific A>I(G) RNA-edited sites, focusing particularly on breast cancer, and the impact of these sites on DNA damage repair and the immune response over anti-cancer therapy. We address the underlying mechanisms, bioinformatics, and in vitro strategies for the identification and validation of A>I(G) RNA-edited sites. We gathered databases related to A>I(G) RNA editing and cancer and discussed the potential clinical and research implications of understanding A>I(G) RNA-editing patterns. Understanding the intricate role of ADAR1-mediated A>I(G) RNA editing in breast cancer holds significant promise for the development of personalized treatment approaches tailored to individual patients' A>I(G) RNA-editing profiles.
Collapse
Affiliation(s)
- Yanara A Bernal
- Centro de Genética y Genómica, Instituto de Ciencias e Innovación en Medicina (ICIM), Facultad de Medicina Clínica Alemana Universidad del Desarrollo, Santiago 7610658, Chile
| | - Eduardo Durán
- Subdepartamento de Genómica y Genética Molecular, Sección Genética Humana, Instituto de Salud Pública de Chile, Avenida Marathon 1000, Ñuñoa, Santiago 7780050, Chile
| | - Isidora Solar
- Centro de Genética y Genómica, Instituto de Ciencias e Innovación en Medicina (ICIM), Facultad de Medicina Clínica Alemana Universidad del Desarrollo, Santiago 7610658, Chile
| | - Eduardo A Sagredo
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 77 Stockholm, Sweden
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE-171 77 Stockholm, Sweden
| | - Ricardo Armisén
- Centro de Genética y Genómica, Instituto de Ciencias e Innovación en Medicina (ICIM), Facultad de Medicina Clínica Alemana Universidad del Desarrollo, Santiago 7610658, Chile
| |
Collapse
|
8
|
Hu SB, Li JB. RNA editing and immune control: from mechanism to therapy. Curr Opin Genet Dev 2024; 86:102195. [PMID: 38643591 PMCID: PMC11162905 DOI: 10.1016/j.gde.2024.102195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 04/02/2024] [Accepted: 04/02/2024] [Indexed: 04/23/2024]
Abstract
Adenosine-to-inosine RNA editing, catalyzed by the enzymes ADAR1 and ADAR2, stands as a pervasive RNA modification. A primary function of ADAR1-mediated RNA editing lies in labeling endogenous double-stranded RNAs (dsRNAs) as 'self', thereby averting their potential to activate innate immune responses. Recent findings have highlighted additional roles of ADAR1, independent of RNA editing, that are crucial for immune control. Here, we focus on recent progress in understanding ADAR1's RNA editing-dependent and -independent roles in immune control. We describe how ADAR1 regulates various dsRNA innate immune receptors through distinct mechanisms. Furthermore, we discuss the implications of ADAR1 and RNA editing in diseases, including autoimmune diseases and cancers.
Collapse
Affiliation(s)
- Shi-Bin Hu
- Department of Genetics, Stanford University, Stanford, CA 94305, USA.
| | - Jin Billy Li
- Department of Genetics, Stanford University, Stanford, CA 94305, USA.
| |
Collapse
|
9
|
Huang E, Frydman C, Xiao X. Navigating the landscape of epitranscriptomics and host immunity. Genome Res 2024; 34:515-529. [PMID: 38702197 PMCID: PMC11146601 DOI: 10.1101/gr.278412.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/06/2024]
Abstract
RNA modifications, also termed epitranscriptomic marks, encompass chemical alterations to individual nucleotides, including processes such as methylation and editing. These marks contribute to a wide range of biological processes, many of which are related to host immune system defense. The functions of immune-related RNA modifications can be categorized into three main groups: regulation of immunogenic RNAs, control of genes involved in innate immune response, and facilitation of adaptive immunity. Here, we provide an overview of recent research findings that elucidate the contributions of RNA modifications to each of these processes. We also discuss relevant methods for genome-wide identification of RNA modifications and their immunogenic substrates. Finally, we highlight recent advances in cancer immunotherapies that aim to reduce cancer cell viability by targeting the enzymes responsible for RNA modifications. Our presentation of these dynamic research avenues sets the stage for future investigations in this field.
Collapse
Affiliation(s)
- Elaine Huang
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, California 90095, USA
| | - Clara Frydman
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, California 90095, USA
| | - Xinshu Xiao
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, California 90095, USA;
- Department of Integrative Biology and Physiology, University of California, Los Angeles, California 90095, USA
- Molecular Biology Interdepartmental Program, University of California, Los Angeles, California 90095, USA
- Molecular Biology Institute, University of California, Los Angeles, California 90095, USA
| |
Collapse
|
10
|
Cottrell KA, Ryu S, Donelick H, Mai H, Pierce JR, Bass BL, Weber JD. Activation of PKR by a short-hairpin RNA. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.08.592371. [PMID: 38766230 PMCID: PMC11100704 DOI: 10.1101/2024.05.08.592371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Recognition of viral infection often relies on the detection of double-stranded RNA (dsRNA), a process that is conserved in many different organisms. In mammals, proteins such as MDA5, RIG-I, OAS, and PKR detect viral dsRNA, but struggle to differentiate between viral and endogenous dsRNA. This study investigates an shRNA targeting DDX54's potential to activate PKR, a key player in the immune response to dsRNA. Knockdown of DDX54 by a specific shRNA induced robust PKR activation in human cells, even when DDX54 is overexpressed, suggesting an off-target mechanism. Activation of PKR by the shRNA was enhanced by knockdown of ADAR1, a dsRNA binding protein that suppresses PKR activation, indicating a dsRNA-mediated mechanism. In vitro assays confirmed direct PKR activation by the shRNA. These findings emphasize the need for rigorous controls and alternative methods to validate gene function and minimize unintended immune pathway activation.
Collapse
Affiliation(s)
- Kyle A. Cottrell
- Department of Medicine, Division of Molecular Oncology, Washington University School of Medicine, Saint Louis, Missouri, USA
- ICCE Institute, Washington University School of Medicine, Saint Louis, Missouri, USA
- Department of Biochemistry, Purdue University, West Lafayette, IN, USA
| | - Sua Ryu
- Department of Medicine, Division of Molecular Oncology, Washington University School of Medicine, Saint Louis, Missouri, USA
- ICCE Institute, Washington University School of Medicine, Saint Louis, Missouri, USA
| | - Helen Donelick
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
| | - Hung Mai
- Department of Medicine, Division of Molecular Oncology, Washington University School of Medicine, Saint Louis, Missouri, USA
- ICCE Institute, Washington University School of Medicine, Saint Louis, Missouri, USA
| | - Jackson R. Pierce
- Department of Biochemistry, Purdue University, West Lafayette, IN, USA
| | - Brenda L. Bass
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
| | - Jason D. Weber
- Department of Medicine, Division of Molecular Oncology, Washington University School of Medicine, Saint Louis, Missouri, USA
- Department of Cell Biology and Physiology, Washington University School of Medicine, Saint Louis, Missouri, USA
- Department of Biology, Siteman Cancer Center, Washington University School of Medicine, Saint Louis, Missouri, USA
- ICCE Institute, Washington University School of Medicine, Saint Louis, Missouri, USA
| |
Collapse
|
11
|
Li Z, Liu S, Gao Z, Ji L, Jiao J, Zheng N, Li X, Wang G, Qin J, Wang Y. Dynamic Proteomic Changes in Tumor and Immune Organs Reveal Systemic Immune Response to Tumor Development. Mol Cell Proteomics 2024; 23:100756. [PMID: 38554776 PMCID: PMC11060955 DOI: 10.1016/j.mcpro.2024.100756] [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: 09/05/2023] [Revised: 03/20/2024] [Accepted: 03/27/2024] [Indexed: 04/02/2024] Open
Abstract
In orthotopic mouse tumor models, tumor progression is a complex process, involving interactions among tumor cells, host cell-derived stromal cells, and immune cells. Much attention has been focused on the tumor and its tumor microenvironment, while the host's macroenvironment including immune organs in response to tumorigenesis is poorly understood. Here, we report a temporal proteomic analysis on a subcutaneous tumor and three immune organs (LN, MLN, and spleen) collected on Days 0, 3, 7, 10, 14, and 21 after inoculation of mouse forestomach cancer cells in a syngeneic mouse model. Bioinformatics analysis identified key biological processes during distinct tumor development phases, including an initial acute immune response, the attack by the host immune system, followed by the adaptive immune activation, and the build-up of extracellular matrix. Proteomic changes in LN and spleen largely recapitulated the dynamics of the immune response in the tumor, consistent with an acute defense response on D3, adaptive immune response on D10, and immune evasion by D21. In contrast, the immune response in MLN showed a gradual and sustained activation, suggesting a delayed response from a distal immune organ. Combined analyses of tumors and host immune organs allowed the identification of potential therapeutic targets. A proof-of-concept experiment demonstrated that significant growth reduction can be achieved by dual inhibition of MEK and DDR2. Together, our temporal proteomic dataset of tumors and immune organs provides a useful resource for understanding the interaction between tumors and the immune system and has the potential for identifying new therapeutic targets for cancer treatment.
Collapse
Affiliation(s)
- Zhike Li
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Shuwen Liu
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Zhouyong Gao
- Department of Thoracic Surgery, Baodi Clinical College, Tianjin Medical University, Tianjin, China; Department of Child Health Care, Kunshan Maternity and Child Health Care Institute, Kunshan, China
| | - Linlin Ji
- Department of Thoracic Surgery, Baodi Clinical College, Tianjin Medical University, Tianjin, China; Department of Thoracic Surgery, Weifang People's Hospital, Weifang, China
| | - Jiaqi Jiao
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Nairen Zheng
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Xianju Li
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Guangshun Wang
- Department of Thoracic Surgery, Baodi Clinical College, Tianjin Medical University, Tianjin, China
| | - Jun Qin
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Yi Wang
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China.
| |
Collapse
|
12
|
Jarmoskaite I, Li JB. Multifaceted roles of RNA editing enzyme ADAR1 in innate immunity. RNA (NEW YORK, N.Y.) 2024; 30:500-511. [PMID: 38531645 PMCID: PMC11019752 DOI: 10.1261/rna.079953.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 02/09/2024] [Indexed: 03/28/2024]
Abstract
Innate immunity must be tightly regulated to enable sensitive pathogen detection while averting autoimmunity triggered by pathogen-like host molecules. A hallmark of viral infection, double-stranded RNAs (dsRNAs) are also abundantly encoded in mammalian genomes, necessitating surveillance mechanisms to distinguish "self" from "nonself." ADAR1, an RNA editing enzyme, has emerged as an essential safeguard against dsRNA-induced autoimmunity. By converting adenosines to inosines (A-to-I) in long dsRNAs, ADAR1 covalently marks endogenous dsRNAs, thereby blocking the activation of the cytoplasmic dsRNA sensor MDA5. Moreover, beyond its editing function, ADAR1 binding to dsRNA impedes the activation of innate immune sensors PKR and ZBP1. Recent landmark studies underscore the utility of silencing ADAR1 for cancer immunotherapy, by exploiting the ADAR1-dependence developed by certain tumors to unleash an antitumor immune response. In this perspective, we summarize the genetic and mechanistic evidence for ADAR1's multipronged role in suppressing dsRNA-mediated autoimmunity and explore the evolving roles of ADAR1 as an immuno-oncology target.
Collapse
Affiliation(s)
- Inga Jarmoskaite
- Department of Genetics, Stanford University, Stanford, California 94305, USA
- AIRNA Corporation, Cambridge, Massachusetts 02142, USA
| | - Jin Billy Li
- Department of Genetics, Stanford University, Stanford, California 94305, USA
| |
Collapse
|
13
|
Cottrell KA, Ryu S, Pierce JR, Soto Torres L, Bohlin HE, Schab AM, Weber JD. Induction of Viral Mimicry Upon Loss of DHX9 and ADAR1 in Breast Cancer Cells. CANCER RESEARCH COMMUNICATIONS 2024; 4:986-1003. [PMID: 38530197 PMCID: PMC10993856 DOI: 10.1158/2767-9764.crc-23-0488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 01/24/2024] [Accepted: 03/19/2024] [Indexed: 03/27/2024]
Abstract
Detection of viral double-stranded RNA (dsRNA) is an important component of innate immunity. However, many endogenous RNAs containing double-stranded regions can be misrecognized and activate innate immunity. The IFN-inducible ADAR1-p150 suppresses dsRNA sensing, an essential function for adenosine deaminase acting on RNA 1 (ADAR1) in many cancers, including breast. Although ADAR1-p150 has been well established in this role, the functions of the constitutively expressed ADAR1-p110 isoform are less understood. We used proximity labeling to identify putative ADAR1-p110-interacting proteins in breast cancer cell lines. Of the proteins identified, the RNA helicase DHX9 was of particular interest. Knockdown of DHX9 in ADAR1-dependent cell lines caused cell death and activation of the dsRNA sensor PKR. In ADAR1-independent cell lines, combined knockdown of DHX9 and ADAR1, but neither alone, caused activation of multiple dsRNA sensing pathways leading to a viral mimicry phenotype. Together, these results reveal an important role for DHX9 in suppressing dsRNA sensing by multiple pathways. SIGNIFICANCE These findings implicate DHX9 as a suppressor of dsRNA sensing. In some cell lines, loss of DHX9 alone is sufficient to cause activation of dsRNA sensing pathways, while in other cell lines DHX9 functions redundantly with ADAR1 to suppress pathway activation.
Collapse
Affiliation(s)
- Kyle A. Cottrell
- Department of Medicine, Division of Molecular Oncology, Washington University School of Medicine, St. Louis, Missouri
- ICCE Institute, Washington University School of Medicine, St. Louis, Missouri
- Department of Biochemistry, Purdue University, West Lafayette, Indiana
| | - Sua Ryu
- Department of Medicine, Division of Molecular Oncology, Washington University School of Medicine, St. Louis, Missouri
- ICCE Institute, Washington University School of Medicine, St. Louis, Missouri
| | - Jackson R. Pierce
- Department of Biochemistry, Purdue University, West Lafayette, Indiana
| | - Luisangely Soto Torres
- Department of Medicine, Division of Molecular Oncology, Washington University School of Medicine, St. Louis, Missouri
- ICCE Institute, Washington University School of Medicine, St. Louis, Missouri
| | - Holly E. Bohlin
- Department of Biochemistry, Purdue University, West Lafayette, Indiana
| | - Angela M. Schab
- Department of Medicine, Division of Molecular Oncology, Washington University School of Medicine, St. Louis, Missouri
- ICCE Institute, Washington University School of Medicine, St. Louis, Missouri
| | - Jason D. Weber
- Department of Medicine, Division of Molecular Oncology, Washington University School of Medicine, St. Louis, Missouri
- ICCE Institute, Washington University School of Medicine, St. Louis, Missouri
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, Missouri
- Department of Biology, Siteman Cancer Center, St. Louis, Missouri
| |
Collapse
|
14
|
Pan Y, Kang X. Limited dsRNA editing impedes leukemia stem cells. Trends Cancer 2024; 10:280-282. [PMID: 38458943 PMCID: PMC11047023 DOI: 10.1016/j.trecan.2024.02.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 02/26/2024] [Indexed: 03/10/2024]
Abstract
Understanding the mechanisms underlying the generation and maintenance of leukemia stem cells (LSCs) is crucial for the development of effective therapies against T cell acute lymphoblastic leukemia (T-ALL). In a recent study, Rivera et al. discovered that elevated adenosine deaminase acting on RNA (ADAR)-1-mediated RNA editing is a distinguishing feature of T-ALL relapse, and that ADAR1 suppresses apoptosis triggered by the double-stranded (ds)RNA-sensing pathway.
Collapse
Affiliation(s)
- Yi Pan
- Division of Hematology and Oncology, Center for Precision Medicine, Department of Medicine, University of Missouri School of Medicine, Columbia, MO 65212, USA
| | - XunLei Kang
- Division of Hematology and Oncology, Center for Precision Medicine, Department of Medicine, University of Missouri School of Medicine, Columbia, MO 65212, USA; Ellis Fischel Cancer Center at MU Health Care, University of Missouri, Columbia, MO 65212, USA.
| |
Collapse
|
15
|
Zou T, Zhou M, Gupta A, Zhuang P, Fishbein AR, Wei HY, Capcha-Rodriguez D, Zhang Z, Cherniack AD, Meyerson M. XRN1 deletion induces PKR-dependent cell lethality in interferon-activated cancer cells. Cell Rep 2024; 43:113600. [PMID: 38261514 PMCID: PMC10989277 DOI: 10.1016/j.celrep.2023.113600] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 10/12/2023] [Accepted: 12/05/2023] [Indexed: 01/25/2024] Open
Abstract
Emerging data suggest that induction of viral mimicry responses through activation of double-stranded RNA (dsRNA) sensors in cancer cells is a promising therapeutic strategy. One approach to induce viral mimicry is to target molecular regulators of dsRNA sensing pathways. Here, we show that the exoribonuclease XRN1 is a negative regulator of the dsRNA sensor protein kinase R (PKR) in cancer cells with high interferon-stimulated gene expression. XRN1 deletion causes PKR pathway activation and consequent cancer cell lethality. Disruption of interferon signaling with the JAK1/2 inhibitor ruxolitinib can decrease cellular PKR levels and rescue sensitivity to XRN1 deletion. Conversely, interferon-β stimulation can increase PKR levels and induce sensitivity to XRN1 inactivation. Lastly, XRN1 deletion causes accumulation of endogenous complementary sense/anti-sense RNAs, which may represent candidate PKR ligands. Our data demonstrate how XRN1 regulates PKR and how this interaction creates a vulnerability in cancer cells with an activated interferon cell state.
Collapse
Affiliation(s)
- Tao Zou
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Meng Zhou
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Akansha Gupta
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Patrick Zhuang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Alyssa R Fishbein
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Hope Y Wei
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Diego Capcha-Rodriguez
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Zhouwei Zhang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Andrew D Cherniack
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Matthew Meyerson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
| |
Collapse
|
16
|
Rivera M, Zhang H, Pham J, Isquith J, Zhou QJ, Balaian L, Sasik R, Enlund S, Mark A, Ma W, Holm F, Fisch KM, Kuo DJ, Jamieson C, Jiang Q. Malignant A-to-I RNA editing by ADAR1 drives T cell acute lymphoblastic leukemia relapse via attenuating dsRNA sensing. Cell Rep 2024; 43:113704. [PMID: 38265938 PMCID: PMC10962356 DOI: 10.1016/j.celrep.2024.113704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 10/24/2023] [Accepted: 01/09/2024] [Indexed: 01/26/2024] Open
Abstract
Leukemia-initiating cells (LICs) are regarded as the origin of leukemia relapse and therapeutic resistance. Identifying direct stemness determinants that fuel LIC self-renewal is critical for developing targeted approaches. Here, we show that the RNA-editing enzyme ADAR1 is a crucial stemness factor that promotes LIC self-renewal by attenuating aberrant double-stranded RNA (dsRNA) sensing. Elevated adenosine-to-inosine editing is a common attribute of relapsed T cell acute lymphoblastic leukemia (T-ALL) regardless of molecular subtype. Consequently, knockdown of ADAR1 severely inhibits LIC self-renewal capacity and prolongs survival in T-ALL patient-derived xenograft models. Mechanistically, ADAR1 directs hyper-editing of immunogenic dsRNA to avoid detection by the innate immune sensor melanoma differentiation-associated protein 5 (MDA5). Moreover, we uncover that the cell-intrinsic level of MDA5 dictates the dependency on the ADAR1-MDA5 axis in T-ALL. Collectively, our results show that ADAR1 functions as a self-renewal factor that limits the sensing of endogenous dsRNA. Thus, targeting ADAR1 presents an effective therapeutic strategy for eliminating T-ALL LICs.
Collapse
Affiliation(s)
- Maria Rivera
- Division of Regenerative Medicine, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Moores Cancer Center, La Jolla, CA 92037, USA
| | - Haoran Zhang
- Division of Regenerative Medicine, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Moores Cancer Center, La Jolla, CA 92037, USA
| | - Jessica Pham
- Division of Regenerative Medicine, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jane Isquith
- Division of Regenerative Medicine, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Qingchen Jenny Zhou
- Division of Regenerative Medicine, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Moores Cancer Center, La Jolla, CA 92037, USA
| | - Larisa Balaian
- Division of Regenerative Medicine, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Roman Sasik
- Center for Computational Biology & Bioinformatics (CCBB), University of California, San Diego, La Jolla, CA 92093-0681, USA
| | - Sabina Enlund
- Department of Women's and Children's Health, Division of Pediatric Oncology and Pediatric Surgery, Karolinska Institutet, Solna, Sweden
| | - Adam Mark
- Center for Computational Biology & Bioinformatics (CCBB), University of California, San Diego, La Jolla, CA 92093-0681, USA
| | - Wenxue Ma
- Division of Regenerative Medicine, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Frida Holm
- Department of Women's and Children's Health, Division of Pediatric Oncology and Pediatric Surgery, Karolinska Institutet, Solna, Sweden
| | - Kathleen M Fisch
- Center for Computational Biology & Bioinformatics (CCBB), University of California, San Diego, La Jolla, CA 92093-0681, USA; Department of Obstetrics, Gynecology & Reproductive Sciences, University of California, San Diego, La Jolla, CA 92037, USA
| | - Dennis John Kuo
- Moores Cancer Center, La Jolla, CA 92037, USA; Division of Pediatric Hematology-Oncology, Rady Children's Hospital San Diego, University of California, San Diego, San Diego, CA 92123, USA
| | - Catriona Jamieson
- Division of Regenerative Medicine, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Moores Cancer Center, La Jolla, CA 92037, USA
| | - Qingfei Jiang
- Division of Regenerative Medicine, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Moores Cancer Center, La Jolla, CA 92037, USA.
| |
Collapse
|
17
|
Hosseini A, Lindholm HT, Chen R, Mehdipour P, Marhon SA, Ishak CA, Moore PC, Classon M, Di Gioacchino A, Greenbaum B, De Carvalho DD. Retroelement decay by the exonuclease XRN1 is a viral mimicry dependency in cancer. Cell Rep 2024; 43:113684. [PMID: 38261511 DOI: 10.1016/j.celrep.2024.113684] [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: 07/06/2023] [Revised: 10/31/2023] [Accepted: 01/03/2024] [Indexed: 01/25/2024] Open
Abstract
Viral mimicry describes the immune response induced by endogenous stimuli such as double-stranded RNA (dsRNA) from endogenous retroelements. Activation of viral mimicry has the potential to kill cancer cells or augment anti-tumor immune responses. Here, we systematically identify mechanisms of viral mimicry adaptation associated with cancer cell dependencies. Among the top hits is the RNA decay protein XRN1 as an essential gene for the survival of a subset of cancer cell lines. XRN1 dependency is mediated by mitochondrial antiviral signaling protein and protein kinase R activation and is associated with higher levels of cytosolic dsRNA, higher levels of a subset of Alus capable of forming dsRNA, and higher interferon-stimulated gene expression, indicating that cells die due to induction of viral mimicry. Furthermore, dsRNA-inducing drugs such as 5-aza-2'-deoxycytidine and palbociclib can generate a synthetic dependency on XRN1 in cells initially resistant to XRN1 knockout. These results indicate that XRN1 is a promising target for future cancer therapeutics.
Collapse
Affiliation(s)
- Amir Hosseini
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7DQ, UK
| | - Håvard T Lindholm
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Pathology, Oslo University Hospital-Rikshospitalet, 0372 Oslo, Norway
| | - Raymond Chen
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Parinaz Mehdipour
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7DQ, UK
| | - Sajid A Marhon
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Charles A Ishak
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Paul C Moore
- Pfizer Centers for Therapeutic Innovation, South San Francisco, CA 94080, USA
| | - Marie Classon
- Pfizer Centers for Therapeutic Innovation, South San Francisco, CA 94080, USA
| | - Andrea Di Gioacchino
- Laboratoire de Physique de l'Ecole Normale Supérieure, PSL & CNRS UMR8063, Sorbonne Université, Université de Paris, Paris, France
| | - Benjamin Greenbaum
- Physiology, Biophysics & Systems Biology, Weill Cornell Medicine, Weill Cornell Medical College, New York, NY 10065, USA; Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Daniel D De Carvalho
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada.
| |
Collapse
|
18
|
Karki A, Campbell KB, Mozumder S, Fisher AJ, Beal PA. Impact of Disease-Associated Mutations on the Deaminase Activity of ADAR1. Biochemistry 2024; 63:282-293. [PMID: 38190734 PMCID: PMC10872254 DOI: 10.1021/acs.biochem.3c00405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2024]
Abstract
The innate immune system relies on molecular sensors to detect distinctive molecular patterns, including viral double-stranded RNA (dsRNA), which triggers responses resulting in apoptosis and immune infiltration. Adenosine Deaminases Acting on RNA (ADARs) catalyze the deamination of adenosine (A) to inosine (I), serving as a mechanism to distinguish self from non-self RNA and prevent aberrant immune activation. Loss-of-function mutations in the ADAR1 gene are one cause of Aicardi Goutières Syndrome (AGS), a severe autoimmune disorder in children. Although seven out of the eight AGS-associated mutations in ADAR1 occur within the catalytic domain of the ADAR1 protein, their specific effects on the catalysis of adenosine deamination remain poorly understood. In this study, we carried out a biochemical investigation of four AGS-causing mutations (G1007R, R892H, K999N, and Y1112F) in ADAR1 p110 and truncated variants. These studies included adenosine deamination rate measurements with two different RNA substrates derived from human transcripts known to be edited by ADAR1 p110 (glioma-associated oncogene homologue 1 (hGli1), 5-hydroxytryptamine receptor 2C (5-HT2cR)). Our results indicate that AGS-associated mutations at two amino acid positions directly involved in stabilizing the base-flipped conformation of the ADAR-RNA complex (G1007R and R892H) had the most detrimental impact on catalysis. The K999N mutation, positioned near the RNA binding interface, altered catalysis contextually. Finally, the Y1112F mutation had small effects in each of the assays described here. These findings shed light on the differential effects of disease-associated mutations on adenosine deamination by ADAR1, thereby advancing our structural and functional understanding of ADAR1-mediated RNA editing.
Collapse
Affiliation(s)
- Agya Karki
- Department of Chemistry, University of California, Davis, CA, USA 95616
| | | | - Sukanya Mozumder
- Department of Chemistry, University of California, Davis, CA, USA 95616
- Department of Molecular and Cellular Biology, University of California, Davis, CA, USA 95616
| | - Andrew J. Fisher
- Department of Chemistry, University of California, Davis, CA, USA 95616
- Department of Molecular and Cellular Biology, University of California, Davis, CA, USA 95616
| | - Peter A. Beal
- Department of Chemistry, University of California, Davis, CA, USA 95616
| |
Collapse
|
19
|
Qian CJ, He YS, Guo T, Tao J, Wei ZY, Zhang JL, Bao C, Chen JH. ADAR-mediated RNA editing regulates PVR immune checkpoint in colorectal cancer. Biochem Biophys Res Commun 2024; 695:149373. [PMID: 38176170 DOI: 10.1016/j.bbrc.2023.149373] [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: 11/20/2023] [Revised: 12/05/2023] [Accepted: 12/06/2023] [Indexed: 01/06/2024]
Abstract
Recent studies have revealed that tumor immunotherapy resistance is influenced by ADAR-mediated RNA editing, but its targets remain unelucidated. Our current study identified the poliovirus receptor (PVR) oncogene, which encodes an immune checkpoint in colorectal cancer (CRC), as a potential target for RNA editing. We performed transcriptome sequencing analysis and experimental validation in two Chinese CRC cohorts. PVR and ADAR expressions significantly increased in CRC tumors and showed positive correlations in both cohorts, coupled with upregulated PVR RNA editing in CRC tumors. Manipulation of ADAR expression by over-expression or knockdown substantially changed PVR expression and RNA editing in HTC116 CRC cells. Luciferase reporter and actinomycin D assays further revealed that RNA editing in PVR 3'-UTR could upregulate PVR RNA expression, probably by increasing the RNA stability. By increasing PVR expression, ADAR-mediate RNA editing might contribute to tumor- and immune-related gene functions and pathways in CRC. Moreover, a signature combining PVR RNA editing and expression showed promising predictive performance in CRC diagnosis in both Chinese CRC cohorts. Our findings thus highlight the importance of ADAR-mediated RNA editing in PVR up-regulation in CRC tumors and provide new insight into the application of PVR RNA editing as a novel diagnostic biomarker for CRC.
Collapse
Affiliation(s)
- Cheng-Jia Qian
- Department of General Surgery, Affiliated Hospital of Jiangnan University, Wuxi, China; Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, 1800 Lihu Avenue, Wuxi, China
| | - Yu-Shan He
- Department of General Surgery, Affiliated Hospital of Jiangnan University, Wuxi, China; Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, 1800 Lihu Avenue, Wuxi, China; Joint Primate Research Center for Chronic Diseases, Jiangnan University and Institute of Zoology, Guangdong Academy of Science, Guangzhou, China; Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, China
| | - Tao Guo
- Department of General Surgery, Affiliated Hospital of Jiangnan University, Wuxi, China; Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, 1800 Lihu Avenue, Wuxi, China; Joint Primate Research Center for Chronic Diseases, Jiangnan University and Institute of Zoology, Guangdong Academy of Science, Guangzhou, China; Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, China
| | - Ji Tao
- Department of General Surgery, Affiliated Hospital of Jiangnan University, Wuxi, China; Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, 1800 Lihu Avenue, Wuxi, China; Joint Primate Research Center for Chronic Diseases, Jiangnan University and Institute of Zoology, Guangdong Academy of Science, Guangzhou, China; Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, China
| | - Zhi-Yuan Wei
- Department of General Surgery, Affiliated Hospital of Jiangnan University, Wuxi, China; Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, 1800 Lihu Avenue, Wuxi, China; Joint Primate Research Center for Chronic Diseases, Jiangnan University and Institute of Zoology, Guangdong Academy of Science, Guangzhou, China; Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, China
| | - Jia-Li Zhang
- Department of General Surgery, Affiliated Hospital of Jiangnan University, Wuxi, China; Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, 1800 Lihu Avenue, Wuxi, China; Joint Primate Research Center for Chronic Diseases, Jiangnan University and Institute of Zoology, Guangdong Academy of Science, Guangzhou, China; Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, China
| | - Chuanqing Bao
- Department of Gastrointestinal Surgery, Affiliated Hospital of Jiangnan University, No. 1000 Hefeng Road, Wuxi, China.
| | - Jian-Huan Chen
- Department of General Surgery, Affiliated Hospital of Jiangnan University, Wuxi, China; Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, 1800 Lihu Avenue, Wuxi, China; Joint Primate Research Center for Chronic Diseases, Jiangnan University and Institute of Zoology, Guangdong Academy of Science, Guangzhou, China; Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, China.
| |
Collapse
|
20
|
Mueller F, Witteveldt J, Macias S. Antiviral Defence Mechanisms during Early Mammalian Development. Viruses 2024; 16:173. [PMID: 38399949 PMCID: PMC10891733 DOI: 10.3390/v16020173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 01/11/2024] [Accepted: 01/20/2024] [Indexed: 02/25/2024] Open
Abstract
The type-I interferon (IFN) response constitutes the major innate immune pathway against viruses in mammals. Despite its critical importance for antiviral defence, this pathway is inactive during early embryonic development. There seems to be an incompatibility between the IFN response and pluripotency, the ability of embryonic cells to develop into any cell type of an adult organism. Instead, pluripotent cells employ alternative ways to defend against viruses that are typically associated with safeguard mechanisms against transposable elements. The absence of an inducible IFN response in pluripotent cells and the constitutive activation of the alternative antiviral pathways have led to the hypothesis that embryonic cells are highly resistant to viruses. However, some findings challenge this interpretation. We have performed a meta-analysis that suggests that the susceptibility of pluripotent cells to viruses is directly correlated with the presence of receptors or co-receptors for viral adhesion and entry. These results challenge the current view of pluripotent cells as intrinsically resistant to infections and raise the fundamental question of why these cells have sacrificed the major antiviral defence pathway if this renders them susceptible to viruses.
Collapse
Affiliation(s)
- Felix Mueller
- Institute of Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, King’s Buildings, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK; (F.M.); (J.W.)
- Centre for Virus Research, MRC-University of Glasgow, Garscube Campus, 464 Bearsden Road, Glasgow G61 1QH, UK
| | - Jeroen Witteveldt
- Institute of Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, King’s Buildings, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK; (F.M.); (J.W.)
| | - Sara Macias
- Institute of Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, King’s Buildings, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK; (F.M.); (J.W.)
| |
Collapse
|
21
|
Jiao Y, Xu Y, Liu C, Miao R, Liu C, Wang Y, Liu J. The role of ADAR1 through and beyond its editing activity in cancer. Cell Commun Signal 2024; 22:42. [PMID: 38233935 PMCID: PMC10795376 DOI: 10.1186/s12964-023-01465-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 12/27/2023] [Indexed: 01/19/2024] Open
Abstract
Adenosine-to-inosine (A-to-I) editing of RNA, catalyzed by adenosine deaminase acting on RNA (ADAR) enzymes, is a prevalent RNA modification in mammals. It has been shown that A-to-I editing plays a critical role in multiple diseases, such as cardiovascular disease, neurological disorder, and particularly cancer. ADARs are the family of enzymes, including ADAR1, ADAR2, and ADAR3, that catalyze the occurrence of A-to-I editing. Notably, A-to-I editing is mainly catalyzed by ADAR1. Given the significance of A-to-I editing in disease development, it is important to unravel the complex roles of ADAR1 in cancer for the development of novel therapeutic interventions.In this review, we briefly describe the progress of research on A-to-I editing and ADARs in cancer, mainly focusing on the role of ADAR1 in cancer from both editing-dependent and independent perspectives. In addition, we also summarized the factors affecting the expression and editing activity of ADAR1 in cancer.
Collapse
Affiliation(s)
- Yue Jiao
- School of Basic Medicine Sciences, Weifang Medical University, Weifang, 261053, China
| | - Yuqin Xu
- School of Basic Medicine Sciences, Weifang Medical University, Weifang, 261053, China
| | - Chengbin Liu
- School of Basic Medicine Sciences, Weifang Medical University, Weifang, 261053, China
| | - Rui Miao
- School of Basic Medicine Sciences, Weifang Medical University, Weifang, 261053, China
| | - Chunyan Liu
- School of Basic Medicine Sciences, Weifang Medical University, Weifang, 261053, China
| | - Yilong Wang
- School of Basic Medicine Sciences, Weifang Medical University, Weifang, 261053, China
| | - Jiao Liu
- School of Basic Medicine Sciences, Weifang Medical University, Weifang, 261053, China.
| |
Collapse
|
22
|
Milham LT, Morris GP, Konen LM, Rentsch P, Avgan N, Vissel B. Quantification of AMPA receptor subunits and RNA editing-related proteins in the J20 mouse model of Alzheimer's disease by capillary western blotting. Front Mol Neurosci 2024; 16:1338065. [PMID: 38299128 PMCID: PMC10828003 DOI: 10.3389/fnmol.2023.1338065] [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: 11/14/2023] [Accepted: 12/29/2023] [Indexed: 02/02/2024] Open
Abstract
Introduction Accurate modelling of molecular changes in Alzheimer's disease (AD) dementia is crucial for understanding the mechanisms driving neuronal pathology and for developing treatments. Synaptic dysfunction has long been implicated as a mechanism underpinning memory dysfunction in AD and may result in part from changes in adenosine deaminase acting on RNA (ADAR) mediated RNA editing of the GluA2 subunit of AMPA receptors and changes in AMPA receptor function at the post synaptic cleft. However, few studies have investigated changes in proteins which influence RNA editing and notably, AD studies that focus on studying changes in protein expression, rather than changes in mRNA, often use traditional western blotting. Methods Here, we demonstrate the value of automated capillary western blotting to investigate the protein expression of AMPA receptor subunits (GluA1-4), the ADAR RNA editing proteins (ADAR1-3), and proteins known to regulate RNA editing (PIN1, WWP2, FXR1P, and CREB1), in the J20 AD mouse model. We describe extensive optimisation and validation of the automated capillary western blotting method, demonstrating the use of total protein to normalise protein load, in addition to characterising the optimal protein/antibody concentrations to ensure accurate protein quantification. Following this, we assessed changes in proteins of interest in the hippocampus of 44-week-old J20 AD mice. Results We observed an increase in the expression of ADAR1 p110 and GluA3 and a decrease in ADAR2 in the hippocampus of 44-week-old J20 mice. These changes signify a shift in the balance of proteins that play a critical role at the synapse. Regression analysis revealed unique J20-specific correlations between changes in AMPA receptor subunits, ADAR enzymes, and proteins that regulate ADAR stability in J20 mice, highlighting potential mechanisms mediating RNA-editing changes found in AD. Discussion Our findings in J20 mice generally reflect changes seen in the human AD brain. This study underlines the importance of novel techniques, like automated capillary western blotting, to assess protein expression in AD. It also provides further evidence to support the hypothesis that a dysregulation in RNA editing-related proteins may play a role in the initiation and/or progression of AD.
Collapse
Affiliation(s)
- Luke T. Milham
- Centre for Neuroscience and Regenerative Medicine, St Vincent’s Centre for Applied Medical Research, St Vincent’s Hospital, Sydney, NSW, Australia
- St Vincent’s Clinical School, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
| | - Gary P. Morris
- Centre for Neuroscience and Regenerative Medicine, St Vincent’s Centre for Applied Medical Research, St Vincent’s Hospital, Sydney, NSW, Australia
- Tasmanian School of Medicine, College of Health and Medicine, University of Tasmania, Hobart, TAS, Australia
| | - Lyndsey M. Konen
- Centre for Neuroscience and Regenerative Medicine, St Vincent’s Centre for Applied Medical Research, St Vincent’s Hospital, Sydney, NSW, Australia
| | - Peggy Rentsch
- Centre for Neuroscience and Regenerative Medicine, St Vincent’s Centre for Applied Medical Research, St Vincent’s Hospital, Sydney, NSW, Australia
- St Vincent’s Clinical School, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
| | - Nesli Avgan
- Centre for Neuroscience and Regenerative Medicine, St Vincent’s Centre for Applied Medical Research, St Vincent’s Hospital, Sydney, NSW, Australia
| | - Bryce Vissel
- Centre for Neuroscience and Regenerative Medicine, St Vincent’s Centre for Applied Medical Research, St Vincent’s Hospital, Sydney, NSW, Australia
- St Vincent’s Clinical School, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
| |
Collapse
|
23
|
Cottrell KA, Andrews RJ, Bass BL. The competitive landscape of the dsRNA world. Mol Cell 2024; 84:107-119. [PMID: 38118451 PMCID: PMC10843539 DOI: 10.1016/j.molcel.2023.11.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 11/20/2023] [Accepted: 11/22/2023] [Indexed: 12/22/2023]
Abstract
The ability to sense and respond to infection is essential for life. Viral infection produces double-stranded RNAs (dsRNAs) that are sensed by proteins that recognize the structure of dsRNA. This structure-based recognition of viral dsRNA allows dsRNA sensors to recognize infection by many viruses, but it comes at a cost-the dsRNA sensors cannot always distinguish between "self" and "nonself" dsRNAs. "Self" RNAs often contain dsRNA regions, and not surprisingly, mechanisms have evolved to prevent aberrant activation of dsRNA sensors by "self" RNA. Here, we review current knowledge about the life of endogenous dsRNAs in mammals-the biosynthesis and processing of dsRNAs, the proteins they encounter, and their ultimate degradation. We highlight mechanisms that evolved to prevent aberrant dsRNA sensor activation and the importance of competition in the regulation of dsRNA sensors and other dsRNA-binding proteins.
Collapse
Affiliation(s)
- Kyle A Cottrell
- Department of Biochemistry, Purdue University, West Lafayette, IN, USA.
| | - Ryan J Andrews
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
| | - Brenda L Bass
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA.
| |
Collapse
|
24
|
Weng S, Yang X, Yu N, Wang PC, Xiong S, Ruan H. Harnessing ADAR-Mediated Site-Specific RNA Editing in Immune-Related Disease: Prediction and Therapeutic Implications. Int J Mol Sci 2023; 25:351. [PMID: 38203521 PMCID: PMC10779106 DOI: 10.3390/ijms25010351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/15/2023] [Accepted: 12/23/2023] [Indexed: 01/12/2024] Open
Abstract
ADAR (Adenosine Deaminases Acting on RNA) proteins are a group of enzymes that play a vital role in RNA editing by converting adenosine to inosine in RNAs. This process is a frequent post-transcriptional event observed in metazoan transcripts. Recent studies indicate widespread dysregulation of ADAR-mediated RNA editing across many immune-related diseases, such as human cancer. We comprehensively review ADARs' function as pattern recognizers and their capability to contribute to mediating immune-related pathways. We also highlight the potential role of site-specific RNA editing in maintaining homeostasis and its relationship to various diseases, such as human cancers. More importantly, we summarize the latest cutting-edge computational approaches and data resources for predicting and analyzing RNA editing sites. Lastly, we cover the recent advancement in site-directed ADAR editing tool development. This review presents an up-to-date overview of ADAR-mediated RNA editing, how site-specific RNA editing could potentially impact disease pathology, and how they could be harnessed for therapeutic applications.
Collapse
Affiliation(s)
- Shenghui Weng
- Jiangsu Key Laboratory of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou 215123, China; (S.W.); (P.-C.W.)
| | - Xinyi Yang
- Jiangsu Key Laboratory of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou 215123, China; (S.W.); (P.-C.W.)
| | - Nannan Yu
- Jiangsu Key Laboratory of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou 215123, China; (S.W.); (P.-C.W.)
| | - Peng-Cheng Wang
- Jiangsu Key Laboratory of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou 215123, China; (S.W.); (P.-C.W.)
| | - Sidong Xiong
- Jiangsu Key Laboratory of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou 215123, China; (S.W.); (P.-C.W.)
| | - Hang Ruan
- Jiangsu Key Laboratory of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou 215123, China; (S.W.); (P.-C.W.)
- MOE Key Laboratory of Geriatric Diseases and Immunology, Suzhou Medical College of Soochow University, Suzhou 215123, China
| |
Collapse
|
25
|
Ramsoomair CK, Ceccarelli M, Heiss JD, Shah AH. The epitranscriptome of high-grade gliomas: a promising therapeutic target with implications from the tumor microenvironment to endogenous retroviruses. J Transl Med 2023; 21:893. [PMID: 38071304 PMCID: PMC10709919 DOI: 10.1186/s12967-023-04725-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 11/13/2023] [Indexed: 12/18/2023] Open
Abstract
Glioblastoma (GBM) comprises 45.6% of all primary malignant brain cancers and is one of the most common and aggressive intracranial tumors in adults. Intratumoral heterogeneity with a wide range of proteomic, genetic, and epigenetic dysregulation contributes to treatment resistance and poor prognosis, thus demanding novel therapeutic approaches. To date, numerous clinical trials have been developed to target the proteome and epigenome of high-grade gliomas with promising results. However, studying RNA modifications, or RNA epitranscriptomics, is a new frontier within neuro-oncology. RNA epitranscriptomics was discovered in the 1970s, but in the last decade, the extent of modification of mRNA and various non-coding RNAs has emerged and been implicated in transposable element activation and many other oncogenic processes within the tumor microenvironment. This review provides background information and discusses the therapeutic potential of agents modulating epitranscriptomics in high-grade gliomas. A particular emphasis will be placed on how combination therapies that include immune agents targeting hERV-mediated viral mimicry could improve the treatment of GBM.
Collapse
Affiliation(s)
- Christian K Ramsoomair
- Section of Virology and Immunotherapy, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, 1095 NW 14Th Terrace, Miami, FL, 33136, USA.
- Medical Scientist Training Program, University of Miami Miller School of Medicine, 1095 NW 14Th Terrace, Miami, FL, 33136, USA.
| | - Michele Ceccarelli
- Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, 1550 N.W. 10Th Avenue, Miami, FL, 33136, USA
| | - John D Heiss
- Surgical Neurology Branch, Disorders and Stroke, National Institute of Neurological, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Ashish H Shah
- Section of Virology and Immunotherapy, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, 1095 NW 14Th Terrace, Miami, FL, 33136, USA.
| |
Collapse
|
26
|
Frezza V, Chellini L, Del Verme A, Paronetto MP. RNA Editing in Cancer Progression. Cancers (Basel) 2023; 15:5277. [PMID: 37958449 PMCID: PMC10648226 DOI: 10.3390/cancers15215277] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 10/31/2023] [Accepted: 10/31/2023] [Indexed: 11/15/2023] Open
Abstract
Coding and noncoding RNA molecules play their roles in ensuring cell function and tissue homeostasis in an ordered and systematic fashion. RNA chemical modifications can occur both at bases and ribose sugar, and, similarly to DNA and histone modifications, can be written, erased, and recognized by the corresponding enzymes, thus modulating RNA activities and fine-tuning gene expression programs. RNA editing is one of the most prevalent and abundant forms of post-transcriptional RNA modification in normal physiological processes. By altering the sequences of mRNAs, it makes them different from the corresponding genomic template. Hence, edited mRNAs can produce protein isoforms that are functionally different from the corresponding genome-encoded variants. Abnormalities in regulatory enzymes and changes in RNA-modification patterns are closely associated with the occurrence and development of various human diseases, including cancer. To date, the roles played by RNA modifications in cancer are gathering increasing interest. In this review, we focus on the role of RNA editing in cancer transformation and provide a new perspective on its impact on tumorigenesis, by regulating cell proliferation, differentiation, invasion, migration, stemness, metabolism, and drug resistance.
Collapse
Affiliation(s)
- Valentina Frezza
- Laboratory of Molecular and Cellular Neurobiology, Fondazione Santa Lucia, CERC, Via del Fosso di Fiorano, 64, 00143 Rome, Italy; (V.F.); (L.C.); (A.D.V.)
| | - Lidia Chellini
- Laboratory of Molecular and Cellular Neurobiology, Fondazione Santa Lucia, CERC, Via del Fosso di Fiorano, 64, 00143 Rome, Italy; (V.F.); (L.C.); (A.D.V.)
| | - Arianna Del Verme
- Laboratory of Molecular and Cellular Neurobiology, Fondazione Santa Lucia, CERC, Via del Fosso di Fiorano, 64, 00143 Rome, Italy; (V.F.); (L.C.); (A.D.V.)
| | - Maria Paola Paronetto
- Laboratory of Molecular and Cellular Neurobiology, Fondazione Santa Lucia, CERC, Via del Fosso di Fiorano, 64, 00143 Rome, Italy; (V.F.); (L.C.); (A.D.V.)
- Department of Movement, Human and Health Sciences, University of Rome “Foro Italico”, Piazza Lauro de Bosis, 15, 00135 Rome, Italy
| |
Collapse
|
27
|
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. Mol Cell 2023; 83:3869-3884.e7. [PMID: 37797622 DOI: 10.1016/j.molcel.2023.09.018] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 07/14/2023] [Accepted: 09/12/2023] [Indexed: 10/07/2023]
Abstract
Effective immunity requires the innate immune system to distinguish foreign nucleic acids from cellular ones. Cellular double-stranded RNAs (dsRNAs) are edited by the RNA-editing enzyme ADAR1 to evade being recognized as viral dsRNA by cytoplasmic dsRNA sensors, including MDA5 and PKR. The loss of ADAR1-mediated RNA editing of cellular dsRNA activates MDA5. 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, whereas 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 or PKR alone. Our findings demonstrate that MDA5 and PKR are the primary in vivo effectors of fatal autoinflammation following the loss of ADAR1p150.
Collapse
Affiliation(s)
- Shi-Bin Hu
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Jacki Heraud-Farlow
- St. Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia; Department of Medicine, Eastern Hill Precinct, Melbourne Medical School, University of Melbourne, Fitzroy, VIC 3065, Australia
| | - Tao Sun
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Zhen Liang
- St. Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia; Department of Medicine, Eastern Hill Precinct, Melbourne Medical School, University of Melbourne, Fitzroy, VIC 3065, Australia
| | - Ankita Goradia
- St. Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia
| | - Scott Taylor
- St. Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia
| | - Carl R Walkley
- St. Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia; Department of Medicine, Eastern Hill Precinct, Melbourne Medical School, University of Melbourne, Fitzroy, VIC 3065, Australia.
| | - Jin Billy Li
- Department of Genetics, Stanford University, Stanford, CA 94305, USA.
| |
Collapse
|
28
|
Dorrity TJ, Chung H. A tale of two pathways: Two distinct mechanisms of ADAR1 prevent fatal autoinflammation. Mol Cell 2023; 83:3760-3762. [PMID: 37922869 PMCID: PMC11056273 DOI: 10.1016/j.molcel.2023.10.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 10/11/2023] [Accepted: 10/11/2023] [Indexed: 11/07/2023]
Abstract
In this issue, Hu and Heraud-Farlow et al.1 demonstrate that ADAR1 dsRNA editing and dsRNA binding activities are critical to repress MDA5 and PKR, respectively, and that PKR and MDA5 act in concert to induce fatality in ADAR1 KO mice.
Collapse
Affiliation(s)
- Tyler J Dorrity
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Hachung Chung
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA.
| |
Collapse
|
29
|
Cottrell KA, Ryu S, Torres LS, Schab AM, Weber JD. Induction of viral mimicry upon loss of DHX9 and ADAR1 in breast cancer cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.27.530307. [PMID: 36909617 PMCID: PMC10002699 DOI: 10.1101/2023.02.27.530307] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
Detection of viral double-stranded RNA (dsRNA) is an important component of innate immunity. However, many endogenous RNAs containing double-stranded regions can be misrecognized and activate innate immunity. The interferon inducible ADAR1-p150 suppresses dsRNA sensing, an essential function for ADAR1 in many cancers, including breast. Although ADAR1-p150 has been well established in this role, the functions of the constitutively expressed ADAR1-p110 isoform are less understood. We used proximity labeling to identify putative ADAR1-p110 interacting proteins in breast cancer cell lines. Of the proteins identified, the RNA helicase DHX9 was of particular interest. Knockdown of DHX9 in ADAR1-dependent cell lines caused cell death and activation of the dsRNA sensor PKR. In ADAR1-independent cell lines, combined knockdown of DHX9 and ADAR1, but neither alone, caused activation of multiple dsRNA sensing pathways leading to a viral mimicry phenotype. Together, these results reveal an important role for DHX9 in suppressing dsRNA sensing by multiple pathways.
Collapse
Affiliation(s)
- Kyle A. Cottrell
- Department of Medicine, Division of Molecular Oncology, Washington University School of Medicine, Saint Louis, Missouri, USA
- ICCE Institute, Washington University School of Medicine, Saint Louis, Missouri, USA
- Department of Biochemistry, Purdue University, West Lafayette, IN, USA
| | - Sua Ryu
- Department of Medicine, Division of Molecular Oncology, Washington University School of Medicine, Saint Louis, Missouri, USA
- ICCE Institute, Washington University School of Medicine, Saint Louis, Missouri, USA
| | - Luisangely Soto Torres
- Department of Medicine, Division of Molecular Oncology, Washington University School of Medicine, Saint Louis, Missouri, USA
- ICCE Institute, Washington University School of Medicine, Saint Louis, Missouri, USA
| | - Angela M. Schab
- Department of Medicine, Division of Molecular Oncology, Washington University School of Medicine, Saint Louis, Missouri, USA
- ICCE Institute, Washington University School of Medicine, Saint Louis, Missouri, USA
| | - Jason D. Weber
- Department of Medicine, Division of Molecular Oncology, Washington University School of Medicine, Saint Louis, Missouri, USA
- Department of Cell Biology and Physiology, Washington University School of Medicine, Saint Louis, Missouri, USA
- Department of Biology, Siteman Cancer Center, Washington University School of Medicine, Saint Louis, Missouri, USA
- ICCE Institute, Washington University School of Medicine, Saint Louis, Missouri, USA
| |
Collapse
|
30
|
Datta R, Adamska JZ, Bhate A, Li JB. A-to-I RNA editing by ADAR and its therapeutic applications: From viral infections to cancer immunotherapy. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 15:e1817. [PMID: 37718249 PMCID: PMC10947335 DOI: 10.1002/wrna.1817] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Revised: 08/29/2023] [Accepted: 08/29/2023] [Indexed: 09/19/2023]
Abstract
ADAR deaminases catalyze adenosine-to-inosine (A-to-I) editing on double-stranded RNA (dsRNA) substrates that regulate an umbrella of biological processes. One of the two catalytically active ADAR enzymes, ADAR1, plays a major role in innate immune responses by suppression of RNA sensing pathways which are orchestrated through the ADAR1-dsRNA-MDA5 axis. Unedited immunogenic dsRNA substrates are potent ligands for the cellular sensor MDA5. Upon activation, MDA5 leads to the induction of interferons and expression of hundreds of interferon-stimulated genes with potent antiviral activity. In this way, ADAR1 acts as a gatekeeper of the RNA sensing pathway by striking a fine balance between innate antiviral responses and prevention of autoimmunity. Reduced editing of immunogenic dsRNA by ADAR1 is strongly linked to the development of common autoimmune and inflammatory diseases. In viral infections, ADAR1 exhibits both antiviral and proviral effects. This is modulated by both editing-dependent and editing-independent functions, such as PKR antagonism. Several A-to-I RNA editing events have been identified in viruses, including in the insidious viral pathogen, SARS-CoV-2 which regulates viral fitness and infectivity, and could play a role in shaping viral evolution. Furthermore, ADAR1 is an attractive target for immuno-oncology therapy. Overexpression of ADAR1 and increased dsRNA editing have been observed in several human cancers. Silencing ADAR1, especially in cancers that are refractory to immune checkpoint inhibitors, is a promising therapeutic strategy for cancer immunotherapy in conjunction with epigenetic therapy. The mechanistic understanding of dsRNA editing by ADAR1 and dsRNA sensing by MDA5 and PKR holds great potential for therapeutic applications. This article is categorized under: RNA Processing > RNA Editing and Modification RNA in Disease and Development > RNA in Disease.
Collapse
Affiliation(s)
- Rohini Datta
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Julia Z Adamska
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Amruta Bhate
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Jin Billy Li
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| |
Collapse
|
31
|
Zhong Y, Zhong X, Qiao L, Wu H, Liu C, Zhang T. Zα domain proteins mediate the immune response. Front Immunol 2023; 14:1241694. [PMID: 37771585 PMCID: PMC10523160 DOI: 10.3389/fimmu.2023.1241694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Accepted: 08/23/2023] [Indexed: 09/30/2023] Open
Abstract
The Zα domain has a compact α/β architecture containing a three-helix bundle flanked on one side by a twisted antiparallel β sheet. This domain displays a specific affinity for double-stranded nucleic acids that adopt a left-handed helical conformation. Currently, only three Zα-domain proteins have been identified in eukaryotes, specifically ADAR1, ZBP1, and PKZ. ADAR1 is a double-stranded RNA (dsRNA) binding protein that catalyzes the conversion of adenosine residues to inosine, resulting in changes in RNA structure, function, and expression. In addition to its editing function, ADAR1 has been shown to play a role in antiviral defense, gene regulation, and cellular differentiation. Dysregulation of ADAR1 expression and activity has been associated with various disease states, including cancer, autoimmune disorders, and neurological disorders. As a sensing molecule, ZBP1 exhibits the ability to recognize nucleic acids with a left-handed conformation. ZBP1 harbors a RIP homotypic interaction motif (RHIM), composed of a highly charged surface region and a leucine-rich hydrophobic core, enabling the formation of homotypic interactions between proteins with similar structure. Upon activation, ZBP1 initiates a downstream signaling cascade leading to programmed cell death, a process mediated by RIPK3 via the RHIM motif. PKZ was identified in fish, and contains two Zα domains at the N-terminus. PKZ is essential for normal growth and development and may contribute to the regulation of immune system function in fish. Interestingly, some pathogenic microorganisms also encode Zα domain proteins, such as, Vaccinia virus and Cyprinid Herpesvirus. Zα domain proteins derived from pathogenic microorganisms have been demonstrated to be pivotal contributors in impeding the host immune response and promoting virus replication and spread. This review focuses on the mammalian Zα domain proteins: ADAR1 and ZBP1, and thoroughly elucidates their functions in the immune response.
Collapse
Affiliation(s)
- Yuhan Zhong
- Laboratory of Liver Transplantation, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Xiao Zhong
- Laboratory of Liver Transplantation, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
- Institute of Life Sciences, Chongqing Medical University, Chongqing, China
| | - Liangjun Qiao
- Institute of Life Sciences, Chongqing Medical University, Chongqing, China
| | - Hong Wu
- Laboratory of Liver Transplantation, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Chang Liu
- Division of Liver, Department of General Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Ting Zhang
- Laboratory of Liver Transplantation, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| |
Collapse
|
32
|
Liang Z, Goradia A, Walkley CR, Heraud-Farlow JE. Generation of a new Adar1p150 -/- mouse demonstrates isoform-specific roles in embryonic development and adult homeostasis. RNA (NEW YORK, N.Y.) 2023; 29:1325-1338. [PMID: 37290963 PMCID: PMC10573302 DOI: 10.1261/rna.079509.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 05/09/2023] [Indexed: 06/10/2023]
Abstract
The RNA editing enzyme adenosine deaminase acting on RNA 1 (ADAR1) is an essential regulator of the innate immune response to both cellular and viral double-stranded RNA (dsRNA). Adenosine-to-inosine (A-to-I) editing by ADAR1 modifies the sequence and structure of endogenous dsRNA and masks it from the cytoplasmic dsRNA sensor melanoma differentiation-associated protein 5 (MDA5), preventing innate immune activation. Loss-of-function mutations in ADAR are associated with rare autoinflammatory disorders including Aicardi-Goutières syndrome (AGS), defined by a constitutive systemic up-regulation of type I interferon (IFN). The murine Adar gene encodes two protein isoforms with distinct functions: ADAR1p110 is constitutively expressed and localizes to the nucleus, whereas ADAR1p150 is primarily cytoplasmic and is inducible by IFN. Recent studies have demonstrated the critical requirement for ADAR1p150 to suppress innate immune activation by self dsRNAs. However, detailed in vivo characterization of the role of ADAR1p150 during development and in adult mice is lacking. We identified a new ADAR1p150-specific knockout mouse mutant based on a single nucleotide deletion that resulted in the loss of the ADAR1p150 protein without affecting ADAR1p110 expression. The Adar1p150 -/- died embryonically at E11.5-E12.5 accompanied by cell death in the fetal liver and an activated IFN response. Somatic loss of ADAR1p150 in adults was lethal and caused rapid hematopoietic failure, demonstrating an ongoing requirement for ADAR1p150 in vivo. The generation and characterization of this mouse model demonstrates the essential role of ADAR1p150 in vivo and provides a new tool for dissecting the functional differences between ADAR1 isoforms and their physiological contributions.
Collapse
Affiliation(s)
- Zhen Liang
- St. Vincent's Institute of Medical Research, Fitzroy, Victoria 3065, Australia
- Department of Medicine, Eastern Hill Precinct, Melbourne Medical School, University of Melbourne, Fitzroy, Victoria 3065, Australia
| | - Ankita Goradia
- St. Vincent's Institute of Medical Research, Fitzroy, Victoria 3065, Australia
| | - Carl R Walkley
- St. Vincent's Institute of Medical Research, Fitzroy, Victoria 3065, Australia
- Department of Medicine, Eastern Hill Precinct, Melbourne Medical School, University of Melbourne, Fitzroy, Victoria 3065, Australia
| | - Jacki E Heraud-Farlow
- St. Vincent's Institute of Medical Research, Fitzroy, Victoria 3065, Australia
- Department of Medicine, Eastern Hill Precinct, Melbourne Medical School, University of Melbourne, Fitzroy, Victoria 3065, Australia
| |
Collapse
|
33
|
Cai M, Liu X, Luo A, Yang X, Yan Y, Liu S, Wang X, Luo Z, Wu X, Huang K, Yang L, Jiang H, Xu L, Liu X. ADAR1 polymorphisms contribute to increased susceptibility in pediatric acute lymphoblastic leukemia. Ann Hematol 2023; 102:2483-2492. [PMID: 37217676 DOI: 10.1007/s00277-023-05285-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 05/18/2023] [Indexed: 05/24/2023]
Abstract
Adenosine deaminase acting on RNA1 (ADAR1), catalyzing post-transcriptional adenosine-to-inosine RNA editing, promotes cancer progression and therapeutic resistance. However, very little is known about the association of ADAR1 variants with acute lymphoblastic leukemia (ALL). Here we first explored the potential association of three polymorphisms (rs9616, rs2229857, and rs1127313) of ADAR1 with susceptibility in Chinese children ALL, then functionally characterized ADAR1 in ALL. Our results demonstrated that rs9616 T and rs2229857 T were associated with increased expression of ADAR1 mRNA and higher risk to ALL. Of note, a stronger risk effect of rs2229857 T genotypes was found among relapse children. Furthermore, ADAR1 knockdown specifically inhibited proliferation and promoted apoptosis in ALL cells. These findings give insights into a mechanism by which the risk variant at rs9616 and rs2229857 modulate ADAR1 expression and confers a predisposition and relapse risk to ALL, and representing a potential novel biomarker for pediatric ALL.
Collapse
Affiliation(s)
- Mansi Cai
- Department of Hematology/Oncology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, 9 Jinsui Road, Zhujiang Newtown, Tianhe District, Guangzhou, 510623, Guangdong, China
- Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, 510623, China
| | - Xiaoping Liu
- Department of Hematology/Oncology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, 9 Jinsui Road, Zhujiang Newtown, Tianhe District, Guangzhou, 510623, Guangdong, China
- Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, 510623, China
| | - Ailing Luo
- Department of Hematology/Oncology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, 9 Jinsui Road, Zhujiang Newtown, Tianhe District, Guangzhou, 510623, Guangdong, China
- Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, 510623, China
| | - Xu Yang
- Department of Hematology/Oncology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, 9 Jinsui Road, Zhujiang Newtown, Tianhe District, Guangzhou, 510623, Guangdong, China
- Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, 510623, China
| | - Yaping Yan
- Department of Hematology/Oncology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, 9 Jinsui Road, Zhujiang Newtown, Tianhe District, Guangzhou, 510623, Guangdong, China
- Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, 510623, China
| | - Shanshan Liu
- Department of Hematology/Oncology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, 9 Jinsui Road, Zhujiang Newtown, Tianhe District, Guangzhou, 510623, Guangdong, China
- Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, 510623, China
| | - Xueliang Wang
- Department of Hematology/Oncology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, 9 Jinsui Road, Zhujiang Newtown, Tianhe District, Guangzhou, 510623, Guangdong, China
| | - Ziyan Luo
- Department of Hematology/Oncology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, 9 Jinsui Road, Zhujiang Newtown, Tianhe District, Guangzhou, 510623, Guangdong, China
| | - Xuedong Wu
- Department of Pediatrics, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Ke Huang
- Department of Pediatrics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Lihua Yang
- Pediatric Hematology Department, Pediatric Center of Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Hua Jiang
- Department of Hematology/Oncology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, 9 Jinsui Road, Zhujiang Newtown, Tianhe District, Guangzhou, 510623, Guangdong, China
| | - Ling Xu
- Department of Hematology/Oncology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, 9 Jinsui Road, Zhujiang Newtown, Tianhe District, Guangzhou, 510623, Guangdong, China.
| | - Xiaodan Liu
- Department of Hematology/Oncology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, 9 Jinsui Road, Zhujiang Newtown, Tianhe District, Guangzhou, 510623, Guangdong, China.
- Division of Birth Cohort Study, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, 9 Jinsui Road, Zhujiang Newtown, Tianhe District, Guangzhou, 510623, Guangdong, China.
| |
Collapse
|
34
|
Zou T, Zhou M, Gupta A, Zhuang P, Fishbein AR, Wei HY, Zhang Z, Cherniack AD, Meyerson M. XRN1 deletion induces PKR-dependent cell lethality in interferon-activated cancer cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.01.551488. [PMID: 37577567 PMCID: PMC10418227 DOI: 10.1101/2023.08.01.551488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Emerging data suggest that induction of viral mimicry responses through activation of double-stranded RNA (dsRNA) sensors in cancer cells is a promising therapeutic strategy. One approach to induce viral mimicry is to target molecular regulators of dsRNA sensing pathways. Here, we show that the exoribonuclease XRN1 is a negative regulator of the dsRNA sensor protein kinase R (PKR) in cancer cells with high interferon-stimulated gene (ISG) expression. XRN1 deletion causes PKR activation and consequent cancer cell lethality. Disruption of interferon signaling with the JAK1/2 inhibitor ruxolitinib can decrease cellular PKR levels and rescue sensitivity to XRN1 deletion. Conversely, interferon-β stimulation can increase PKR levels and induce sensitivity to XRN1 inactivation. Lastly, XRN1 deletion causes accumulation of endogenous complementary sense/anti-sense RNAs, which may represent candidate PKR ligands. Our data demonstrate how XRN1 regulates PKR and nominate XRN1 as a potential therapeutic target in cancer cells with an activated interferon cell state.
Collapse
Affiliation(s)
- Tao Zou
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - Meng Zhou
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - Akansha Gupta
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - Patrick Zhuang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - Alyssa R. Fishbein
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - Hope Y. Wei
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - Zhouwei Zhang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - Andrew D. Cherniack
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - Matthew Meyerson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
- Center for Cancer Genomics, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| |
Collapse
|
35
|
Hoblos R, Kefalakes H. Immunology of hepatitis D virus infection: General concepts and present evidence. Liver Int 2023; 43 Suppl 1:47-59. [PMID: 36074070 DOI: 10.1111/liv.15424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 08/27/2022] [Accepted: 09/05/2022] [Indexed: 02/13/2023]
Abstract
Infection with the hepatitis D virus induces the most severe form of chronic viral hepatitis, affecting over 12 million people worldwide. Chronic HDV infection leads to rapid development of liver cirrhosis and hepatocellular carcinoma in ~70% of patients within 15 years of infection. Recent evidence suggests that an interplay of different components of the immune system are contributing to viral control and may even be implicated in liver disease pathogenesis. This review will describe general concepts of antiviral immune response and elicit the present evidence concerning the interplay of the hepatitis D virus with the immune system.
Collapse
Affiliation(s)
- Reem Hoblos
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover, Germany
| | - Helenie Kefalakes
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover, Germany
| |
Collapse
|
36
|
Pomaville MM, He C. Advances in targeting RNA modifications for anticancer therapy. Trends Cancer 2023; 9:528-542. [PMID: 37147166 PMCID: PMC10330282 DOI: 10.1016/j.trecan.2023.04.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/03/2023] [Accepted: 04/06/2023] [Indexed: 05/07/2023]
Abstract
Numerous strategies are employed by cancer cells to control gene expression and facilitate tumorigenesis. In the study of epitranscriptomics, a diverse set of modifications to RNA represent a new player of gene regulation in disease and in development. N6-methyladenosine (m6A) is the most common modification on mammalian messenger RNA and tends to be aberrantly placed in cancer. Recognized by a series of reader proteins that dictate the fate of the RNA, m6A-modified RNA could promote tumorigenesis by driving protumor gene expression signatures and altering the immunologic response to tumors. Preclinical evidence suggests m6A writer, reader, and eraser proteins are attractive therapeutic targets. First-in-human studies are currently testing small molecule inhibition against the methyltransferase-like 3 (METTL3)/methyltransferase-like 14 (METTL14) methyltransferase complex. Additional modifications to RNA are adopted by cancers to drive tumor development and are under investigation.
Collapse
Affiliation(s)
- Monica M Pomaville
- Department of Pediatrics, University of Chicago Comer Children's Hospital, Chicago, IL, USA; Howard Hughes Medical Institute, University of Chicago, Chicago, IL, USA; Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA.
| | - Chuan He
- Howard Hughes Medical Institute, University of Chicago, Chicago, IL, USA; Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA
| |
Collapse
|
37
|
Xing Y, Nakahama T, Wu Y, Inoue M, Kim JI, Todo H, Shibuya T, Kato Y, Kawahara Y. RNA editing of AZIN1 coding sites is catalyzed by ADAR1 p150 after splicing. J Biol Chem 2023; 299:104840. [PMID: 37209819 PMCID: PMC10404624 DOI: 10.1016/j.jbc.2023.104840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 05/09/2023] [Accepted: 05/12/2023] [Indexed: 05/22/2023] Open
Abstract
Adenosine-to-inosine RNA editing is catalyzed by nuclear adenosine deaminase acting on RNA 1 (ADAR1) p110 and ADAR2, and cytoplasmic ADAR1 p150 in mammals, all of which recognize dsRNAs as targets. RNA editing occurs in some coding regions, which alters protein functions by exchanging amino acid sequences, and is therefore physiologically significant. In general, such coding sites are edited by ADAR1 p110 and ADAR2 before splicing, given that the corresponding exon forms a dsRNA structure with an adjacent intron. We previously found that RNA editing at two coding sites of antizyme inhibitor 1 (AZIN1) is sustained in Adar1 p110/Aadr2 double KO mice. However, the molecular mechanisms underlying RNA editing of AZIN1 remain unknown. Here, we showed that Azin1 editing levels were increased upon type I interferon treatment, which activated Adar1 p150 transcription, in mouse Raw 264.7 cells. Azin1 RNA editing was observed in mature mRNA but not precursor mRNA. Furthermore, we revealed that the two coding sites were editable only by ADAR1 p150 in both mouse Raw 264.7 and human embryonic kidney 293T cells. This unique editing was achieved by forming a dsRNA structure with a downstream exon after splicing, and the intervening intron suppressed RNA editing. Therefore, deletion of a nuclear export signal from ADAR1 p150, shifting its localization to the nucleus, decreased Azin1 editing levels. Finally, we demonstrated that Azin1 RNA editing was completely absent in Adar1 p150 KO mice. Thus, these findings indicate that RNA editing of AZIN1 coding sites is exceptionally catalyzed by ADAR1 p150 after splicing.
Collapse
Affiliation(s)
- Yanfang Xing
- Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Taisuke Nakahama
- Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, Suita, Osaka, 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, Japan; Center for Infectious Disease Education and Research (CiDER), Osaka University, Suita, Osaka, Japan.
| | - Yuke Wu
- Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan; Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan
| | - Maal Inoue
- Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Jung In Kim
- Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Hiroyuki Todo
- Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Toshiharu Shibuya
- Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Yuki Kato
- Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, Suita, Osaka, 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, Japan
| | - Yukio Kawahara
- Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, Suita, Osaka, 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, Japan; Center for Infectious Disease Education and Research (CiDER), Osaka University, Suita, Osaka, Japan; Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan; Genome Editing Research and Development Center, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan.
| |
Collapse
|
38
|
Yuan J, Xu L, Bao HJ, Wang JL, Zhao Y, Chen S. Biological roles of A-to-I editing: implications in innate immunity, cell death, and cancer immunotherapy. J Exp Clin Cancer Res 2023; 42:149. [PMID: 37328893 DOI: 10.1186/s13046-023-02727-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 06/02/2023] [Indexed: 06/18/2023] Open
Abstract
Adenosine-to-inosine (A-to-I) editing, a key RNA modification widely found in eukaryotes, is catalyzed by adenosine deaminases acting on RNA (ADARs). Such RNA editing destabilizes endogenous dsRNAs, which are subsequently recognized by the sensors of innate immune and other proteins as autologous dsRNAs. This prevents the activation of innate immunity and type I interferon-mediated responses, thereby reducing the downstream cell death induced by the activation of the innate immune sensing system. ADARs-mediated editing can also occur in mRNAs and non-coding RNAs (ncRNAs) in different species. In mRNAs, A-to-I editing may lead to missense mutations and the selective splicing of coding regions. Meanwhile, in ncRNAs, A-to-I editing may affect targeting and disrupt ncRNAs maturation, leading to anomalous cell proliferation, invasion, and responses to immunotherapy. This review highlights the biological functions of A-to-I editing, its role in regulating innate immunity and cell death, and its potential molecular significance in tumorigenesis and cancer targeted therapy and immunotherapy.
Collapse
Affiliation(s)
- Jing Yuan
- Department of Obstetrics and Gynecology, Department of Gynecologic Oncology Research Office, Guangzhou Key Laboratory of Targeted Therapy for Gynecologic Oncology, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, No.63 Duobao Road, Liwan District, Guangzhou City, Guangdong Province, 510150, P. R. China
| | - Li Xu
- Department of Laboratory Medicine, The First Hospital of China Medical University, Shenyang, 110001, China
| | - Hai-Juan Bao
- Department of Obstetrics and Gynecology, Department of Gynecologic Oncology Research Office, Guangzhou Key Laboratory of Targeted Therapy for Gynecologic Oncology, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, No.63 Duobao Road, Liwan District, Guangzhou City, Guangdong Province, 510150, P. R. China
| | - Jie-Lin Wang
- Department of Obstetrics and Gynecology, Department of Gynecologic Oncology Research Office, Guangzhou Key Laboratory of Targeted Therapy for Gynecologic Oncology, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, No.63 Duobao Road, Liwan District, Guangzhou City, Guangdong Province, 510150, P. R. China
| | - Yang Zhao
- Department of Obstetrics and Gynecology, Department of Gynecologic Oncology Research Office, Guangzhou Key Laboratory of Targeted Therapy for Gynecologic Oncology, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, No.63 Duobao Road, Liwan District, Guangzhou City, Guangdong Province, 510150, P. R. China.
| | - Shuo Chen
- Department of Obstetrics and Gynecology, Department of Gynecologic Oncology Research Office, Guangzhou Key Laboratory of Targeted Therapy for Gynecologic Oncology, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, No.63 Duobao Road, Liwan District, Guangzhou City, Guangdong Province, 510150, P. R. China.
| |
Collapse
|
39
|
Pecori R, Ren W, Pirmoradian M, Wang X, Liu D, Berglund M, Li W, Tasakis RN, Di Giorgio S, Ye X, Li X, Arnold A, Wüst S, Schneider M, Selvasaravanan KD, Fuell Y, Stafforst T, Amini RM, Sonnevi K, Enblad G, Sander B, Wahlin BE, Wu K, Zhang H, Helm D, Binder M, Papavasiliou FN, Pan-Hammarström Q. ADAR1-mediated RNA editing promotes B cell lymphomagenesis. iScience 2023; 26:106864. [PMID: 37255666 PMCID: PMC10225930 DOI: 10.1016/j.isci.2023.106864] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 02/27/2023] [Accepted: 05/08/2023] [Indexed: 06/01/2023] Open
Abstract
Diffuse large B cell lymphoma (DLBCL) is one of the most common types of aggressive lymphoid malignancies. Here, we explore the contribution of RNA editing to DLBCL pathogenesis. We observed that DNA mutations and RNA editing events are often mutually exclusive, suggesting that tumors can modulate pathway outcomes by altering sequences at either the genomic or the transcriptomic level. RNA editing targets transcripts within known disease-driving pathways such as apoptosis, p53 and NF-κB signaling, as well as the RIG-I-like pathway. In this context, we show that ADAR1-mediated editing within MAVS transcript positively correlates with MAVS protein expression levels, associating with increased interferon/NF-κB signaling and T cell exhaustion. Finally, using targeted RNA base editing tools to restore editing within MAVS 3'UTR in ADAR1-deficient cells, we demonstrate that editing is likely to be causal to an increase in downstream signaling in the absence of activation by canonical nucleic acid receptor sensing.
Collapse
Affiliation(s)
- Riccardo Pecori
- Division of Immune Diversity (D150), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Helmholtz Institute for Translational Oncology (HI-TRON), Mainz, Germany
| | - 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
| | - Mohammad Pirmoradian
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - 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
| | - Dongbing Liu
- BGI-Shenzhen, Shenzhen, China
- Guangdong Provincial Key Laboratory of Human Disease Genomics, Shenzhen Key Laboratory of Genomics, Shenzhen, China
| | - Mattias Berglund
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - 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
| | - Rafail Nikolaos Tasakis
- Division of Immune Diversity (D150), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Graduate Program in Biosciences, University of Heidelberg, Heidelberg, Germany
| | - Salvatore Di Giorgio
- Division of Immune Diversity (D150), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Xiaofei Ye
- 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
| | - Xiaobo Li
- BGI-Shenzhen, Shenzhen, China
- Guangdong Provincial Key Laboratory of Human Disease Genomics, Shenzhen Key Laboratory of Genomics, Shenzhen, China
| | - Annette Arnold
- Division of Immune Diversity (D150), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Sandra Wüst
- Research Group "Dynamics of Early Viral Infection and the Innate Antiviral Response", Division Virus-Associated Carcinogenesis (F170), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Martin Schneider
- Proteomics Core Facility (W120), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Yvonne Fuell
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
| | - Thorsten Stafforst
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
| | - Rose-Marie Amini
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Kristina Sonnevi
- Hematology Unit, Department of Medicine, Huddinge, Karolinska Institutet and Medical Unit Hematology, Karolinska University Hospital, Solna, StockholmSweden
| | - Gunilla Enblad
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Birgitta Sander
- Department of Laboratory Medicine, Karolinska University Hospital, Huddinge, Stockholm, Sweden
| | - Björn Engelbrekt Wahlin
- Hematology Unit, Department of Medicine, Huddinge, Karolinska Institutet and Medical Unit Hematology, Karolinska University Hospital, Solna, StockholmSweden
| | - Kui Wu
- BGI-Shenzhen, Shenzhen, China
- Guangdong Provincial Key Laboratory of Human Disease Genomics, Shenzhen Key Laboratory of Genomics, Shenzhen, 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
| | - Dominic Helm
- Proteomics Core Facility (W120), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Marco Binder
- Research Group "Dynamics of Early Viral Infection and the Innate Antiviral Response", Division Virus-Associated Carcinogenesis (F170), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - F. Nina Papavasiliou
- Division of Immune Diversity (D150), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Graduate Program in Biosciences, University of Heidelberg, Heidelberg, Germany
| | - 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
| |
Collapse
|
40
|
Rivera M, Zhang H, Pham J, Isquith J, Zhou QJ, Sasik R, Mark A, Ma W, Holm F, Fisch KM, Kuo DJ, Jamieson C, Jiang Q. Malignant A-to-I RNA editing by ADAR1 drives T-cell acute lymphoblastic leukemia relapse via attenuating dsRNA sensing. RESEARCH SQUARE 2023:rs.3.rs-2444524. [PMID: 37398458 PMCID: PMC10312963 DOI: 10.21203/rs.3.rs-2444524/v2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Leukemia initiating cells (LICs) are regarded as the origin of leukemia relapse and therapeutic resistance. Identifying direct stemness determinants that fuel LIC self-renewal is critical for developing targeted approaches to eliminate LICs and prevent relapse. Here, we show that the RNA editing enzyme ADAR1 is a crucial stemness factor that promotes LIC self-renewal by attenuating aberrant double-stranded RNA (dsRNA) sensing. Elevated adenosine-to-inosine (A-to-I) editing is a common attribute of relapsed T-ALL regardless of molecular subtypes. Consequently, knockdown of ADAR1 severely inhibits LIC self-renewal capacity and prolongs survival in T-ALL PDX models. Mechanistically, ADAR1 directs hyper-editing of immunogenic dsRNA and retains unedited nuclear dsRNA to avoid detection by the innate immune sensor MDA5. Moreover, we uncovered that the cell intrinsic level of MDA5 dictates the dependency on ADAR1-MDA5 axis in T-ALL. Collectively, our results show that ADAR1 functions as a self-renewal factor that limits the sensing of endogenous dsRNA. Thus, targeting ADAR1 presents a safe and effective therapeutic strategy for eliminating T-ALL LICs.
Collapse
Affiliation(s)
- Maria Rivera
- Division of Regenerative Medicine, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
- Moores Cancer Center, La Jolla, CA 92037, USA
| | - Haoran Zhang
- Division of Regenerative Medicine, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
- Moores Cancer Center, La Jolla, CA 92037, USA
| | - Jessica Pham
- Division of Regenerative Medicine, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Jane Isquith
- Division of Regenerative Medicine, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Qingchen Jenny Zhou
- Division of Regenerative Medicine, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
- Moores Cancer Center, La Jolla, CA 92037, USA
| | - Roman Sasik
- Center for Computational Biology & Bioinformatics (CCBB), University of California, San Diego, La Jolla, 92093-0681
| | - Adam Mark
- Center for Computational Biology & Bioinformatics (CCBB), University of California, San Diego, La Jolla, 92093-0681
| | - Wenxue Ma
- Division of Regenerative Medicine, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Frida Holm
- Department of Women’s and Children’s Health, Division of Pediatric Oncology and Surgery, Karolinska Institutet, Sweden
| | - Kathleen M Fisch
- Center for Computational Biology & Bioinformatics (CCBB), University of California, San Diego, La Jolla, 92093-0681
- Department of Obstetrics, Gynecology & Reproductive Sciences, University of California, San Diego, La Jolla, CA
| | - Dennis John Kuo
- Moores Cancer Center, La Jolla, CA 92037, USA
- Division of Pediatric Hematology-Oncology, Rady Children’s Hospital San Diego, University of California, San Diego, CA
| | - Catriona Jamieson
- Division of Regenerative Medicine, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
- Moores Cancer Center, La Jolla, CA 92037, USA
| | - Qingfei Jiang
- Division of Regenerative Medicine, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
- Moores Cancer Center, La Jolla, CA 92037, USA
| |
Collapse
|
41
|
Booth BJ, Nourreddine S, Katrekar D, Savva Y, Bose D, Long TJ, Huss DJ, Mali P. RNA editing: Expanding the potential of RNA therapeutics. Mol Ther 2023; 31:1533-1549. [PMID: 36620962 PMCID: PMC9824937 DOI: 10.1016/j.ymthe.2023.01.005] [Citation(s) in RCA: 31] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 12/06/2022] [Accepted: 01/04/2023] [Indexed: 01/09/2023] Open
Abstract
RNA therapeutics have had a tremendous impact on medicine, recently exemplified by the rapid development and deployment of mRNA vaccines to combat the COVID-19 pandemic. In addition, RNA-targeting drugs have been developed for diseases with significant unmet medical needs through selective mRNA knockdown or modulation of pre-mRNA splicing. Recently, RNA editing, particularly antisense RNA-guided adenosine deaminase acting on RNA (ADAR)-based programmable A-to-I editing, has emerged as a powerful tool to manipulate RNA to enable correction of disease-causing mutations and modulate gene expression and protein function. Beyond correcting pathogenic mutations, the technology is particularly well suited for therapeutic applications that require a transient pharmacodynamic effect, such as the treatment of acute pain, obesity, viral infection, and inflammation, where it would be undesirable to introduce permanent alterations to the genome. Furthermore, transient modulation of protein function, such as altering the active sites of enzymes or the interface of protein-protein interactions, opens the door to therapeutic avenues ranging from regenerative medicine to oncology. These emerging RNA-editing-based toolsets are poised to broadly impact biotechnology and therapeutic applications. Here, we review the emerging field of therapeutic RNA editing, highlight recent laboratory advancements, and discuss the key challenges on the path to clinical development.
Collapse
Affiliation(s)
| | - Sami Nourreddine
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | | | | | | | | | | | - Prashant Mali
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA.
| |
Collapse
|
42
|
Mendez Ruiz S, Chalk AM, Goradia A, Heraud-Farlow J, Walkley C. Over-expression of ADAR1 in mice does not initiate or accelerate cancer formation in vivo. NAR Cancer 2023; 5:zcad023. [PMID: 37275274 PMCID: PMC10233902 DOI: 10.1093/narcan/zcad023] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 04/27/2023] [Accepted: 05/16/2023] [Indexed: 06/07/2023] Open
Abstract
Adenosine to inosine editing (A-to-I) in regions of double stranded RNA (dsRNA) is mediated by adenosine deaminase acting on RNA 1 (ADAR1) or ADAR2. ADAR1 and A-to-I editing levels are increased in many human cancers. Inhibition of ADAR1 has emerged as a high priority oncology target, however, whether ADAR1 overexpression enables cancer initiation or progression has not been directly tested. We established a series of in vivo models to allow overexpression of full-length ADAR1, or its individual isoforms, to test if increased ADAR1 expression was oncogenic. Widespread over-expression of ADAR1 or the p110 or p150 isoforms individually as sole lesions was well tolerated and did not result in cancer initiation. Therefore, ADAR1 overexpression alone is not sufficient to initiate cancer. We demonstrate that endogenous ADAR1 and A-to-I editing increased upon immortalization in murine cells, consistent with the observations from human cancers. We tested if ADAR1 over-expression could co-operate with cancer initiated by loss of tumour suppressors using a model of osteosarcoma. We did not see a disease potentiating or modifying effect of overexpressing ADAR1 or its isoforms in the models assessed. We conclude that increased ADAR1 expression and A-to-I editing in cancers is most likely a consequence of tumor formation.
Collapse
Affiliation(s)
- Shannon Mendez Ruiz
- St Vincent's Institute of Medical Research, Fitzroy, Victoria 3065, Australia
- Department of Medicine, Eastern Hill Precinct, Melbourne Medical School, University of Melbourne, Fitzroy, Victoria 3065, Australia
| | - Alistair M Chalk
- St Vincent's Institute of Medical Research, Fitzroy, Victoria 3065, Australia
- Department of Medicine, Eastern Hill Precinct, Melbourne Medical School, University of Melbourne, Fitzroy, Victoria 3065, Australia
| | - Ankita Goradia
- St Vincent's Institute of Medical Research, Fitzroy, Victoria 3065, Australia
| | | | - Carl R Walkley
- To whom correspondence should be addressed. Tel: +61 3 9231 2480;
| |
Collapse
|
43
|
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: 53] [Impact Index Per Article: 53.0] [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.
Collapse
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.
| |
Collapse
|
44
|
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.
Collapse
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
| |
Collapse
|
45
|
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: 4] [Impact Index Per Article: 4.0] [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.
Collapse
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.
| |
Collapse
|
46
|
Paget M, Cadena C, Ahmad S, Wang HT, Jordan TX, Kim E, Koo B, Lyons SM, Ivanov P, tenOever B, Mu X, Hur S. Stress granules are shock absorbers that prevent excessive innate immune responses to dsRNA. Mol Cell 2023; 83:1180-1196.e8. [PMID: 37028415 PMCID: PMC10170497 DOI: 10.1016/j.molcel.2023.03.010] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 09/08/2022] [Accepted: 03/08/2023] [Indexed: 04/09/2023]
Abstract
Proper defense against microbial infection depends on the controlled activation of the immune system. This is particularly important for the RIG-I-like receptors (RLRs), which recognize viral dsRNA and initiate antiviral innate immune responses with the potential of triggering systemic inflammation and immunopathology. Here, we show that stress granules (SGs), molecular condensates that form in response to various stresses including viral dsRNA, play key roles in the controlled activation of RLR signaling. Without the SG nucleators G3BP1/2 and UBAP2L, dsRNA triggers excessive inflammation and immune-mediated apoptosis. In addition to exogenous dsRNA, host-derived dsRNA generated in response to ADAR1 deficiency is also controlled by SG biology. Intriguingly, SGs can function beyond immune control by suppressing viral replication independently of the RLR pathway. These observations thus highlight the multi-functional nature of SGs as cellular "shock absorbers" that converge on protecting cell homeostasis by dampening both toxic immune response and viral replication.
Collapse
Affiliation(s)
- Max Paget
- Program in Virology, Division of Medical Sciences, Harvard Medical School, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Cristhian Cadena
- Program in Virology, Division of Medical Sciences, Harvard Medical School, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Sadeem Ahmad
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston, MA 02115, USA
| | - Hai-Tao Wang
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Tristan X Jordan
- Department of Microbiology, New York University, Grossman School of Medicine, New York, NY 10016, USA
| | - Ehyun Kim
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Beechui Koo
- Morrisey School of Arts and Science, Boston College, Boston, MA 02467, USA
| | - Shawn M Lyons
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Pavel Ivanov
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Benjamin tenOever
- Department of Microbiology, New York University, Grossman School of Medicine, New York, NY 10016, USA
| | - Xin Mu
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Sun Hur
- Program in Virology, Division of Medical Sciences, Harvard Medical School, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston, MA 02115, USA.
| |
Collapse
|
47
|
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.
Collapse
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
| |
Collapse
|
48
|
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.
Collapse
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
| |
Collapse
|
49
|
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.
Collapse
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.
| |
Collapse
|
50
|
Karki R, Kanneganti TD. ADAR1 and ZBP1 in innate immunity, cell death, and disease. Trends Immunol 2023; 44:201-216. [PMID: 36710220 PMCID: PMC9974732 DOI: 10.1016/j.it.2023.01.001] [Citation(s) in RCA: 33] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 12/28/2022] [Accepted: 01/04/2023] [Indexed: 01/28/2023]
Abstract
ADAR1 and ZBP1 are the only two mammalian proteins that contain Zα domains, which are thought to bind to nucleic acids in the Z-conformation. These two molecules are crucial in regulating diverse biological processes. While ADAR1-mediated RNA editing supports host survival and development, ZBP1-mediated immune responses provide host defense against infection and disease. Recent studies have expanded our understanding of the functions of ADAR1 and ZBP1 beyond their classical roles and established their fundamental regulation of innate immune responses, including NLRP3 inflammasome activation, inflammation, and cell death. Their roles in these processes have physiological impacts across development, infectious and inflammatory diseases, and cancer. In this review, we discuss the functions of ADAR1 and ZBP1 in regulating innate immune responses in development and disease.
Collapse
Affiliation(s)
- Rajendra Karki
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | | |
Collapse
|