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Liu X, Jin W, Bao D, He T, Wang W, Li Z, Yang X, Tong Y, Shu M, Wang Y, Yuan J, Yang Y. DIPAN: Detecting personalized intronic polyadenylation derived neoantigens from RNA sequencing data. Comput Struct Biotechnol J 2024; 23:2057-2066. [PMID: 38783901 PMCID: PMC11112131 DOI: 10.1016/j.csbj.2024.05.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 05/05/2024] [Accepted: 05/06/2024] [Indexed: 05/25/2024] Open
Abstract
Intronic polyadenylation (IPA) refers to a particular type of alternative polyadenylation where a gene makes use of a polyadenylation site located within its introns. Aberrant IPA events have been observed in various types of cancer. IPA can produce noncoding transcripts or truncated protein-coding transcripts with altered coding sequences in the resulting protein product. Therefore, IPA events hold the potential to act as a reservoir of tumor neoantigens. Here, we developed a computational method termed DIPAN, which incorporates IPA detection, protein fragmentation, and MHC binding prediction to predict IPA-derived neoantigens. Utilizing RNA-seq from breast cancer cell lines and ovarian cancer clinical samples, we demonstrated the significant contribution of IPA events to the neoantigen repertoire. Through mass spectrometry immunopeptidome analysis, we further illustrated the processing and presentation of IPA-derived neoantigens on the surface of cancer cells. While most IPA-derived neoantigens are sample-specific, shared neoantigens were identified in both cancer cell lines and clinical samples. Furthermore, we demonstrated an association between IPA-derived neoantigen burden and overall survival in cancer patients.
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Affiliation(s)
- Xiaochuan Liu
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Inflammatory Biology, Tianjin Geriatrics Institute, Tianjin Medical University General Hospital, The Second Hospital of Tianjin Medical University, Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Wen Jin
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Inflammatory Biology, Tianjin Geriatrics Institute, Tianjin Medical University General Hospital, The Second Hospital of Tianjin Medical University, Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
- Department of Pharmacology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Dengyi Bao
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Inflammatory Biology, Tianjin Geriatrics Institute, Tianjin Medical University General Hospital, The Second Hospital of Tianjin Medical University, Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Tongxin He
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Inflammatory Biology, Tianjin Geriatrics Institute, Tianjin Medical University General Hospital, The Second Hospital of Tianjin Medical University, Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Wenhui Wang
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Inflammatory Biology, Tianjin Geriatrics Institute, Tianjin Medical University General Hospital, The Second Hospital of Tianjin Medical University, Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
- Department of Pharmacology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Zekun Li
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Inflammatory Biology, Tianjin Geriatrics Institute, Tianjin Medical University General Hospital, The Second Hospital of Tianjin Medical University, Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Xiaoxiao Yang
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Inflammatory Biology, Tianjin Geriatrics Institute, Tianjin Medical University General Hospital, The Second Hospital of Tianjin Medical University, Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
- Department of Pharmacology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Yang Tong
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Inflammatory Biology, Tianjin Geriatrics Institute, Tianjin Medical University General Hospital, The Second Hospital of Tianjin Medical University, Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Meng Shu
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Inflammatory Biology, Tianjin Geriatrics Institute, Tianjin Medical University General Hospital, The Second Hospital of Tianjin Medical University, Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Yuting Wang
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Inflammatory Biology, Tianjin Geriatrics Institute, Tianjin Medical University General Hospital, The Second Hospital of Tianjin Medical University, Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Jiapei Yuan
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Yang Yang
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Inflammatory Biology, Tianjin Geriatrics Institute, Tianjin Medical University General Hospital, The Second Hospital of Tianjin Medical University, Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
- Department of Pharmacology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
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Yang P, Zhang W, Zeng L, Tao X, Ding K, Wang Z. A novel splice variant in intron 10 of PEX6 is associated with Zellweger Syndrome in a Chinese neonate. Gene 2024; 928:148767. [PMID: 39013483 DOI: 10.1016/j.gene.2024.148767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 04/20/2024] [Accepted: 07/12/2024] [Indexed: 07/18/2024]
Abstract
BACKGROUND Zellweger Syndrome (ZS), or cerebrohepatorenal syndrome, is a rare disorder due to PEX gene mutations affecting peroxisome function. While PEX6 coding mutations are known to cause ZS, the impact of noncoding mutations is less clear. METHODS A Chinese neonate and his family were subjected to whole exome sequencing (WES) and bioinformatics to assess variant pathogenicity. A minigene assay was also performed for detailed splicing variant analysis. RESULTS WES identified compound heterozygous PEX6 variants: c.315G>A (p. Trp105Ter) and c.2095-3 T>G. Minigene assays indicated that the latter variant led to abnormal mRNA splicing and the loss of exon 11 in PEX6 expression, potentially causing nonsense-mediated mRNA decay (NMD) or truncated protein structure. CONCLUSION The study suggests that PEX6: c.2095-3 T>G might be a genetic contributor to the patient's condition, broadening the known mutation spectrum of PEX6. These insights lay groundwork for potential gene therapy for such variants.
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Affiliation(s)
- Pin Yang
- School of Medicine, Department of Medicine, Wuhan University of Science and Technology, Wuhan 430081, China; Division of Neonatology, Wuhan Children's Hospital (Wuhan Maternal and Child Healthcare Hospital), Tongji Medical College, Huazhong University of Science & Technology, Wuhan 430010, China
| | - Weihong Zhang
- Department of Rehabilitation Medicine, Wuhan Children's Hospital (Wuhan Maternal and Child Healthcare Hospital), Tongji Medical College, Huazhong University of Science & Technology, Wuhan 430010, China
| | - Lingkong Zeng
- Division of Neonatology, Wuhan Children's Hospital (Wuhan Maternal and Child Healthcare Hospital), Tongji Medical College, Huazhong University of Science & Technology, Wuhan 430010, China.
| | - Xuwei Tao
- Division of Neonatology, Wuhan Children's Hospital (Wuhan Maternal and Child Healthcare Hospital), Tongji Medical College, Huazhong University of Science & Technology, Wuhan 430010, China
| | - Kaiwei Ding
- Division of Neonatology, Wuhan Children's Hospital (Wuhan Maternal and Child Healthcare Hospital), Tongji Medical College, Huazhong University of Science & Technology, Wuhan 430010, China
| | - Zuo Wang
- Division of Neonatology, Wuhan Children's Hospital (Wuhan Maternal and Child Healthcare Hospital), Tongji Medical College, Huazhong University of Science & Technology, Wuhan 430010, China
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Cunningham ASG, Gorospe M. Striving for clarity in language about gene expression. Nucleic Acids Res 2024:gkae764. [PMID: 39271127 DOI: 10.1093/nar/gkae764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2024] [Revised: 08/15/2024] [Accepted: 08/21/2024] [Indexed: 09/15/2024] Open
Abstract
What do we mean when we say 'gene expression'? In the decades following Crick's 1958 central dogma of molecular biology, whereby genetic information flows from DNA (genes) to RNA (transcripts) to protein (products), we have learned a great deal about DNA, RNA, proteins, and the ensuing phenotypic changes. With the advent of high-throughput technologies (1990s), molecular biologists and computer scientists forged critical collaborations to understand the vast amount of data being generated, rapidly escalating gene expression research to the 'omics' level: entire sets of genes (genomes), transcribed RNAs (transcriptomes), and synthesized proteins (proteomes). However, some concessions came to be made for molecular biologists and computer scientists to understand each other-one of the most prevalent being the increasingly widespread use of 'gene' to mean 'RNAs originating from a DNA segment'. This loosening of terminology, we will argue, creates ambiguity and confusion. We propose guidelines to increase precision and clarity when communicating about gene expression, most notably to reserve 'gene' for the DNA template and 'transcript' for the RNA transcribed from that gene. Striving to use perspicuous terminology will promote rigorous gene expression science and accelerate discovery in this highly promising area of biology.
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Affiliation(s)
- Ana S G Cunningham
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Myriam Gorospe
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
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Xie S, Bao D, Xiao Y, Li H, Guo M, Dai B, Liu S, Huang J, Li M, Ding L, Meng Q, Lv CL, Distler JHW, Luo H, Zhu H. Alternative splicing and intron retention: Their profiles and roles in cutaneous fibrosis of systemic sclerosis. J Autoimmun 2024; 149:103306. [PMID: 39265192 DOI: 10.1016/j.jaut.2024.103306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 07/21/2024] [Accepted: 08/23/2024] [Indexed: 09/14/2024]
Abstract
BACKGROUND Alternative splicing (AS) and intron retention (IR) implicated in multiple pathophysiological processes, have rarely been reported in systemic sclerosis (SSc). METHODS We integrated bulk RNA-seq and 4D label-free mass spectrometry to perform a multi-omics analysis of AS and IR in SSc skin tissue and fibroblasts. RMATS and iREAD were used to identify AS and IR, which were validated by real-time PCR. Spearman correlation and the LASSO method were employed to assess correlations among clinical features, introns, splicing factors (regulators of AS) and proteins. FINDINGS AS profiles showed distinct alterations in SSc skin tissue, with the most pronounced changes occurring in IR. AS and IR were associated with total modified Rodnan skin score (mRSS) and local skin score. Upon TGF-β stimulation, fibroblasts exhibited significant alterations in IR profiles, affecting genes related to fibroblast proliferation and collagen fibril organization. A comprehensive integrated analysis of introns, exons, and proteome profiles revealed that IR exerted a negative impact on protein expression, with certain changes being under intronic control. RT-PCR confirmed the presence of intron and exon-derived sequences of CTTN, OGA, MED16 and PHYKPL. Additionally, notable changes were observed in the regulatory network of splicing factors in SSc skin tissues. These factors are also involved in fibrosis pathways and correlated with clinical features. CONCLUSION Totally, abnormal AS, IR profiles and splicing factors were identified in SSc, altered IRs and splicing factors participated in fibrosis-related pathways. IR exerted a negative impact on protein expression in TGF-β-stimulated fibroblasts. Clarification of the IR mechanisms will provide new insights into the pathophysiology of SSc.
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Affiliation(s)
- Shasha Xie
- Department of Rheumatology and Immunology, Xiangya Hospital, Central South University, Changsha, Hunan, China; Provincial Clinical Research Center for Rheumatic and Immunologic Diseases, Xiangya Hospital, Changsha, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Ding Bao
- Department of Rheumatology and Immunology, Xiangya Hospital, Central South University, Changsha, Hunan, China; Provincial Clinical Research Center for Rheumatic and Immunologic Diseases, Xiangya Hospital, Changsha, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yizhi Xiao
- Department of Rheumatology and Immunology, Xiangya Hospital, Central South University, Changsha, Hunan, China; Provincial Clinical Research Center for Rheumatic and Immunologic Diseases, Xiangya Hospital, Changsha, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Hongdong Li
- Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha, Hunan, China
| | - Muyao Guo
- Department of Rheumatology and Immunology, Xiangya Hospital, Central South University, Changsha, Hunan, China; Provincial Clinical Research Center for Rheumatic and Immunologic Diseases, Xiangya Hospital, Changsha, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Bingying Dai
- Department of Rheumatology and Immunology, Xiangya Hospital, Central South University, Changsha, Hunan, China; Provincial Clinical Research Center for Rheumatic and Immunologic Diseases, Xiangya Hospital, Changsha, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Sijia Liu
- Department of Rheumatology and Immunology, Xiangya Hospital, Central South University, Changsha, Hunan, China; Provincial Clinical Research Center for Rheumatic and Immunologic Diseases, Xiangya Hospital, Changsha, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Jing Huang
- Department of Rheumatology and Immunology, Xiangya Hospital, Central South University, Changsha, Hunan, China; Provincial Clinical Research Center for Rheumatic and Immunologic Diseases, Xiangya Hospital, Changsha, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Muyuan Li
- Department of Rheumatology and Immunology, Xiangya Hospital, Central South University, Changsha, Hunan, China; Provincial Clinical Research Center for Rheumatic and Immunologic Diseases, Xiangya Hospital, Changsha, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Liqing Ding
- Department of Rheumatology and Immunology, Xiangya Hospital, Central South University, Changsha, Hunan, China; Provincial Clinical Research Center for Rheumatic and Immunologic Diseases, Xiangya Hospital, Changsha, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Qiming Meng
- Department of Rheumatology and Immunology, Xiangya Hospital, Central South University, Changsha, Hunan, China; Provincial Clinical Research Center for Rheumatic and Immunologic Diseases, Xiangya Hospital, Changsha, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Chun-Liu Lv
- Department of Breast Tumor Plastic Surgery, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, 283 Tongzipo Road, Changsha, Hunan, 410013, China
| | - Jörg H W Distler
- Department of Rheumatology, University Hospital Düsseldorf, Medical Faculty of Heinrich Heine University, 40225, Düsseldorf, Germany; Hiller Research Center, University Hospital Düsseldorf, Medical Faculty of Heinrich Heine University, 40225, Düsseldorf, Germany
| | - Hui Luo
- Department of Rheumatology and Immunology, Xiangya Hospital, Central South University, Changsha, Hunan, China; Provincial Clinical Research Center for Rheumatic and Immunologic Diseases, Xiangya Hospital, Changsha, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China.
| | - Honglin Zhu
- Department of Rheumatology and Immunology, Xiangya Hospital, Central South University, Changsha, Hunan, China; Provincial Clinical Research Center for Rheumatic and Immunologic Diseases, Xiangya Hospital, Changsha, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China.
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5
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Blázquez-Encinas R, Alors-Pérez E, Moreno-Montilla MT, García-Vioque V, Sánchez-Frías ME, Mafficini A, López-Cánovas JL, Bousquet C, Gahete MD, Lawlor RT, Luque RM, Scarpa A, Arjona-Sánchez Á, Pedraza-Arevalo S, Ibáñez-Costa A, Castaño JP. The Exon Junction Complex component EIF4A3 plays a splicing-linked oncogenic role in pancreatic ductal adenocarcinoma. Cancer Gene Ther 2024:10.1038/s41417-024-00814-3. [PMID: 39232176 DOI: 10.1038/s41417-024-00814-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 07/18/2024] [Accepted: 07/22/2024] [Indexed: 09/06/2024]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal cancers, underscoring the urgent need for in-depth biological research. The phenomenon of alternative RNA splicing dysregulation is a common hallmark in cancer, including PDAC, presenting new avenues for understanding and developing diagnostic and therapeutic tools. Our research focuses on EIF4A3, a core component of the Exon Junction Complex intimately linked to RNA splicing, and its role in PDAC. EIF4A3 is overexpressed in PDAC tissue and associated to clinical parameters of malignancy and poorer patient survival. Mechanistically, exploration of PDAC RNA-seq data unveiled the link of EIF4A3 to diverse malignancy processes, consistent with its association to key molecular pathways. EIF4A3 targeting in vitro decreased essential functional tumor features such as proliferation, migration, colony formation and sphere formation, while its in vivo targeting reduced tumor growth. EIF4A3 silencing in PDAC cell lines severely altered its transcriptional and spliceosomic landscapes, as shown by RNA-seq analyses, suggesting a role for EIF4A3 in maintaining RNA homeostasis. Our results indicate that EIF4A3 dysregulation in PDAC has a pleiotropic regulatory role on RNA biology, influencing key cellular functions. This paves the way to explore its potential as novel biomarker and actionable target candidate for this lethal cancer.
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Affiliation(s)
- Ricardo Blázquez-Encinas
- Maimonides Institute for Biomedical Research of Cordoba (IMIBIC), Córdoba, Spain
- Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Córdoba, Spain
- Reina Sofia University Hospital, Córdoba, Spain
| | - Emilia Alors-Pérez
- Maimonides Institute for Biomedical Research of Cordoba (IMIBIC), Córdoba, Spain
- Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Córdoba, Spain
- Reina Sofia University Hospital, Córdoba, Spain
| | - María Trinidad Moreno-Montilla
- Maimonides Institute for Biomedical Research of Cordoba (IMIBIC), Córdoba, Spain
- Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Córdoba, Spain
- Reina Sofia University Hospital, Córdoba, Spain
| | - Víctor García-Vioque
- Maimonides Institute for Biomedical Research of Cordoba (IMIBIC), Córdoba, Spain
- Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Córdoba, Spain
- Reina Sofia University Hospital, Córdoba, Spain
| | - Marina Esther Sánchez-Frías
- Maimonides Institute for Biomedical Research of Cordoba (IMIBIC), Córdoba, Spain
- Reina Sofia University Hospital, Córdoba, Spain
- Pathology Service, Reina Sofía University Hospital, Córdoba, Spain
| | - Andrea Mafficini
- Department of Engineering for Innovation Medicine, Section of Innovation Biomedicine, University and Hospital Trust of Verona, Verona, Italy
- ARC-Net Research Centre, University and Hospital Trust of Verona, Verona, Italy
| | - Juan L López-Cánovas
- Maimonides Institute for Biomedical Research of Cordoba (IMIBIC), Córdoba, Spain
- Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Córdoba, Spain
- Reina Sofia University Hospital, Córdoba, Spain
| | - Corinne Bousquet
- INSERM UMR-1037, Cancer Research Center of Toulouse (CRCT), Team 'Labellisée Ligue Contre le Cancer', University of Toulouse, Toulouse, France
| | - Manuel D Gahete
- Maimonides Institute for Biomedical Research of Cordoba (IMIBIC), Córdoba, Spain
- Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Córdoba, Spain
- Reina Sofia University Hospital, Córdoba, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Córdoba, Spain
| | - Rita T Lawlor
- Department of Engineering for Innovation Medicine, Section of Innovation Biomedicine, University and Hospital Trust of Verona, Verona, Italy
- ARC-Net Research Centre, University and Hospital Trust of Verona, Verona, Italy
| | - Raúl M Luque
- Maimonides Institute for Biomedical Research of Cordoba (IMIBIC), Córdoba, Spain
- Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Córdoba, Spain
- Reina Sofia University Hospital, Córdoba, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Córdoba, Spain
| | - Aldo Scarpa
- ARC-Net Research Centre, University and Hospital Trust of Verona, Verona, Italy
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Verona, Italy
| | - Álvaro Arjona-Sánchez
- Maimonides Institute for Biomedical Research of Cordoba (IMIBIC), Córdoba, Spain
- Reina Sofia University Hospital, Córdoba, Spain
- Surgery Service, Reina Sofia University Hospital, Córdoba, Spain
| | - Sergio Pedraza-Arevalo
- Maimonides Institute for Biomedical Research of Cordoba (IMIBIC), Córdoba, Spain
- Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Córdoba, Spain
- Reina Sofia University Hospital, Córdoba, Spain
| | - Alejandro Ibáñez-Costa
- Maimonides Institute for Biomedical Research of Cordoba (IMIBIC), Córdoba, Spain.
- Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Córdoba, Spain.
- Reina Sofia University Hospital, Córdoba, Spain.
| | - Justo P Castaño
- Maimonides Institute for Biomedical Research of Cordoba (IMIBIC), Córdoba, Spain.
- Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Córdoba, Spain.
- Reina Sofia University Hospital, Córdoba, Spain.
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Córdoba, Spain.
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Conn VM, Chinnaiyan AM, Conn SJ. Circular RNA in cancer. Nat Rev Cancer 2024; 24:597-613. [PMID: 39075222 DOI: 10.1038/s41568-024-00721-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/13/2024] [Indexed: 07/31/2024]
Abstract
Over the past decade, circular RNA (circRNA) research has evolved into a bona fide research field shedding light on the functional consequence of this unique family of RNA molecules in cancer. Although the method of formation and the abundance of circRNAs can differ from their cognate linear mRNA, the spectrum of interacting partners and their resultant cellular functions in oncogenesis are analogous. However, with 10 times more diversity in circRNA variants compared with linear RNA variants, combined with their hyperstability in the cell, circRNAs are equipped to influence every stage of oncogenesis. This is an opportune time to address the breadth of circRNA in cancer focused on their spatiotemporal expression, mutations in biogenesis factors and contemporary functions through each stage of cancer. In this Review, we highlight examples of functional circRNAs in specific cancers, which satisfy critical criteria, including their physical co-association with the target and circRNA abundance at stoichiometrically valid quantities. These considerations are essential to develop strategies for the therapeutic exploitation of circRNAs as biomarkers and targeted anticancer agents.
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Affiliation(s)
- Vanessa M Conn
- Flinders Health and Medical Research Institute, College of Medicine and Public Health, Flinders University, South Australia, Australia
| | - Arul M Chinnaiyan
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Urology, University of Michigan, Ann Arbor, MI, USA
| | - Simon J Conn
- Flinders Health and Medical Research Institute, College of Medicine and Public Health, Flinders University, South Australia, Australia.
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7
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Martinek V, Martin J, Belair C, Payea M, Malla S, Alexiou P, Maragkakis M. Deep learning and direct sequencing of labeled RNA captures transcriptome dynamics. NAR Genom Bioinform 2024; 6:lqae116. [PMID: 39211330 PMCID: PMC11358824 DOI: 10.1093/nargab/lqae116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 07/29/2024] [Accepted: 08/19/2024] [Indexed: 09/04/2024] Open
Abstract
In eukaryotes, genes produce a variety of distinct RNA isoforms, each with potentially unique protein products, coding potential or regulatory signals such as poly(A) tail and nucleotide modifications. Assessing the kinetics of RNA isoform metabolism, such as transcription and decay rates, is essential for unraveling gene regulation. However, it is currently impeded by lack of methods that can differentiate between individual isoforms. Here, we introduce RNAkinet, a deep convolutional and recurrent neural network, to detect nascent RNA molecules following metabolic labeling with the nucleoside analog 5-ethynyl uridine and long-read, direct RNA sequencing with nanopores. RNAkinet processes electrical signals from nanopore sequencing directly and distinguishes nascent from pre-existing RNA molecules. Our results show that RNAkinet prediction performance generalizes in various cell types and organisms and can be used to quantify RNA isoform half-lives. RNAkinet is expected to enable the identification of the kinetic parameters of RNA isoforms and to facilitate studies of RNA metabolism and the regulatory elements that influence it.
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Affiliation(s)
- Vlastimil Martinek
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
- Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
| | - Jessica Martin
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
- Center for Alzheimer's and Related Dementias, National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Cedric Belair
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Matthew J Payea
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Sulochan Malla
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Panagiotis Alexiou
- Centre for Molecular Medicine & Biobanking, University of Malta, MSD 2080 Msida, Malta
| | - Manolis Maragkakis
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
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8
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Shen J, Shentu J, Zhong C, Huang Q, Duan S. RNA splicing factor RBFOX2 is a key factor in the progression of cancer and cardiomyopathy. Clin Transl Med 2024; 14:e1788. [PMID: 39243148 PMCID: PMC11380049 DOI: 10.1002/ctm2.1788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 07/15/2024] [Accepted: 07/19/2024] [Indexed: 09/09/2024] Open
Abstract
BACKGROUND Alternative splicing of pre-mRNA is a fundamental regulatory process in multicellular eukaryotes, significantly contributing to the diversification of the human proteome. RNA-binding fox-1 homologue 2 (RBFOX2), a member of the evolutionarily conserved RBFOX family, has emerged as a critical splicing regulator, playing a pivotal role in the alternative splicing of pre-mRNA. This review provides a comprehensive analysis of RBFOX2, elucidating its splicing activity through direct and indirect binding mechanisms. RBFOX2 exerts substantial influence over the alternative splicing of numerous transcripts, thereby shaping essential cellular processes such as differentiation and development. MAIN BODY OF THE ABSTRACT Dysregulation of RBFOX2-mediated alternative splicing has been closely linked to a spectrum of cardiovascular diseases and malignant tumours, underscoring its potential as a therapeutic target. Despite significant progress, current research faces notable challenges. The complete structural characterisation of RBFOX2 remains elusive, limiting in-depth exploration beyond its RNA-recognition motif. Furthermore, the scarcity of studies focusing on RBFOX2-targeting drugs poses a hindrance to translating research findings into clinical applications. CONCLUSION This review critically assesses the existing body of knowledge on RBFOX2, highlighting research gaps and limitations. By delineating these areas, this analysis not only serves as a foundational reference for future studies but also provides strategic insights for bridging these gaps. Addressing these challenges will be instrumental in unlocking the full therapeutic potential of RBFOX2, paving the way for innovative and effective treatments in various diseases.
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Affiliation(s)
- Jinze Shen
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, China
| | - Jianqiao Shentu
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, China
| | - Chenming Zhong
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, China
| | - Qiankai Huang
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, China
| | - Shiwei Duan
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, China
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9
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Cui H, Shi Q, Macarios CM, Schimmel P. Metabolic regulation of mRNA splicing. Trends Cell Biol 2024; 34:756-770. [PMID: 38431493 DOI: 10.1016/j.tcb.2024.02.002] [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: 11/07/2023] [Revised: 01/30/2024] [Accepted: 02/01/2024] [Indexed: 03/05/2024]
Abstract
Alternative mRNA splicing enables the diversification of the proteome from a static genome and confers plasticity and adaptiveness on cells. Although this is often explored in development, where hard-wired programs drive the differentiation and specialization, alternative mRNA splicing also offers a way for cells to react to sudden changes in outside stimuli such as small-molecule metabolites. Fluctuations in metabolite levels and availability in particular convey crucial information to which cells react and adapt. We summarize and highlight findings surrounding the metabolic regulation of mRNA splicing. We discuss the principles underlying the biochemistry and biophysical properties of mRNA splicing, and propose how these could intersect with metabolite levels. Further, we present examples in which metabolites directly influence RNA-binding proteins and splicing factors. We also discuss the interplay between alternative mRNA splicing and metabolite-responsive signaling pathways. We hope to inspire future research to obtain a holistic picture of alternative mRNA splicing in response to metabolic cues.
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Affiliation(s)
- Haissi Cui
- Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada.
| | - Qingyu Shi
- Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada
| | | | - Paul Schimmel
- Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA 92037, USA.
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10
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Zhu LS, Lai C, Zhou CW, Chen HY, Liu ZQ, Guo Z, Man H, Du HY, Lu Y, Hu F, Chen Z, Shu K, Zhu LQ, Liu D. Postsynaptic lncRNA Sera/Pkm2 pathway orchestrates the transition from social competition to rank by remodeling the neural ensemble in mPFC. Cell Discov 2024; 10:87. [PMID: 39160208 PMCID: PMC11333582 DOI: 10.1038/s41421-024-00706-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 07/01/2024] [Indexed: 08/21/2024] Open
Abstract
Individuals' continuous success in competitive interactions with conspecifics strongly affects their social hierarchy. Medial prefrontal cortex (mPFC) is the key brain region mediating both social competition and hierarchy. However, the molecular regulatory mechanisms underlying the neural ensemble in the mPFC remains unclear. Here, we demonstrate that in excitatory neurons of prelimbic cortex (PL), lncRNA Sera remodels the utilization of Pkm Exon9 and Exon10, resulting in a decrease in the Pkm1/2 ratio in highly competitive mice. By employing a tet-on/off system, we disrupt or rebuild the normal Pkm1/2 ratio by controlling the expression of Pkm2 in PL excitatory neurons. We find that long-term Pkm2 modulation induces timely competition alteration and hysteretic rank change, through phosphorylating the Ser845 site of GluA1. Together, this study uncovers a crucial role of lncRNA Sera/Pkm2 pathway in the transition of social competition to rank by remodeling neural ensemble in mPFC.
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Affiliation(s)
- Ling-Shuang Zhu
- Department of Pathophysiology, Key Lab of Neurological Disorder of Education Ministry, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Chuan Lai
- Department of Pathophysiology, Key Lab of Neurological Disorder of Education Ministry, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Chao-Wen Zhou
- Department of Pathophysiology, Key Lab of Neurological Disorder of Education Ministry, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Hui-Yang Chen
- Department of Pathophysiology, Key Lab of Neurological Disorder of Education Ministry, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Zhi-Qiang Liu
- Department of Pathophysiology, Key Lab of Neurological Disorder of Education Ministry, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Ziyuan Guo
- Center for Stem Cell and Organoid Medicine (CuSTOM), Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Hengye Man
- Department of Biology, Boston University, Boston, MA, USA
| | - Hui-Yun Du
- Department of Pathophysiology, Key Lab of Neurological Disorder of Education Ministry, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Youming Lu
- Department of Pathophysiology, Key Lab of Neurological Disorder of Education Ministry, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Feng Hu
- Department of Neurosurgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Zhiye Chen
- Department of Neurosurgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Kai Shu
- Department of Neurosurgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.
| | - Ling-Qiang Zhu
- Department of Pathophysiology, Key Lab of Neurological Disorder of Education Ministry, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.
| | - Dan Liu
- Department of Pathophysiology, Key Lab of Neurological Disorder of Education Ministry, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.
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11
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Santucci K, Cheng Y, Xu SM, Janitz M. Enhancing novel isoform discovery: leveraging nanopore long-read sequencing and machine learning approaches. Brief Funct Genomics 2024:elae031. [PMID: 39158328 DOI: 10.1093/bfgp/elae031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Revised: 07/29/2024] [Accepted: 07/31/2024] [Indexed: 08/20/2024] Open
Abstract
Long-read sequencing technologies can capture entire RNA transcripts in a single sequencing read, reducing the ambiguity in constructing and quantifying transcript models in comparison to more common and earlier methods, such as short-read sequencing. Recent improvements in the accuracy of long-read sequencing technologies have expanded the scope for novel splice isoform detection and have also enabled a far more accurate reconstruction of complex splicing patterns and transcriptomes. Additionally, the incorporation and advancements of machine learning and deep learning algorithms in bioinformatic software have significantly improved the reliability of long-read sequencing transcriptomic studies. However, there is a lack of consensus on what bioinformatic tools and pipelines produce the most precise and consistent results. Thus, this review aims to discuss and compare the performance of available methods for novel isoform discovery with long-read sequencing technologies, with 25 tools being presented. Furthermore, this review intends to demonstrate the need for developing standard analytical pipelines, tools, and transcript model conventions for novel isoform discovery and transcriptomic studies.
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Affiliation(s)
- Kristina Santucci
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Yuning Cheng
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Si-Mei Xu
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Michael Janitz
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
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12
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Yustis JC, Devoucoux M, Côté J. The Functional Relationship Between RNA Splicing and the Chromatin Landscape. J Mol Biol 2024; 436:168614. [PMID: 38762032 DOI: 10.1016/j.jmb.2024.168614] [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: 03/04/2024] [Revised: 04/27/2024] [Accepted: 05/13/2024] [Indexed: 05/20/2024]
Abstract
Chromatin is a highly regulated and dynamic structure that has been shown to play an essential role in transcriptional and co-transcriptional regulation. In the context of RNA splicing, early evidence suggested a loose connection between the chromatin landscape and splicing. More recently, it has been shown that splicing occurs in a co-transcriptional manner, meaning that the splicing process occurs in the context of chromatin. Experimental and computational evidence have also shown that chromatin dynamics can influence the splicing process and vice versa. However, much of this evidence provides mainly correlative relationships between chromatin and splicing with just a few concrete examples providing defined molecular mechanisms by which these two processes are functionally related. Nevertheless, it is clear that chromatin and RNA splicing are tightly interconnected to one another. In this review, we highlight the current state of knowledge of the relationship between chromatin and splicing.
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Affiliation(s)
- Juan-Carlos Yustis
- St-Patrick Research Group in Basic Oncology, Laval University Cancer Research Center, Oncology Division of the CHU de Québec-Université Laval Research Center, Quebec City, Quebec G1R 3S3, Canada
| | - Maëva Devoucoux
- St-Patrick Research Group in Basic Oncology, Laval University Cancer Research Center, Oncology Division of the CHU de Québec-Université Laval Research Center, Quebec City, Quebec G1R 3S3, Canada
| | - Jacques Côté
- St-Patrick Research Group in Basic Oncology, Laval University Cancer Research Center, Oncology Division of the CHU de Québec-Université Laval Research Center, Quebec City, Quebec G1R 3S3, Canada.
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13
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Jin B, Han Y, Xu F, Wang J, Zhao Y, Liu H, Wang F, Wang Z, Lu W, Wang M, Cui L, Zhao Y, Hao J, Chai G. Translatome analysis in acute ischemic stroke: Astrocytes and microglia exhibit differences in poststroke alternative splicing of expressed transcripts. FASEB J 2024; 38:e23855. [PMID: 39096134 DOI: 10.1096/fj.202400341r] [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: 02/13/2024] [Revised: 06/28/2024] [Accepted: 07/21/2024] [Indexed: 08/04/2024]
Abstract
Astrocytes and microglia undergo dynamic and complex morphological and functional changes following ischemic stroke, which are instrumental in both inflammatory responses and neural repair. While gene expression alterations poststroke have been extensively studied, investigations into posttranscriptional regulatory mechanisms, specifically alternative splicing (AS), remain limited. Utilizing previously reported Ribo-Tag-seq data, this study analyzed AS alterations in poststroke astrocytes and microglia from young adult male and female mice. Our findings reveal that in astrocytes, compared to the sham group, 109 differential alternative splicing (DAS) events were observed at 4 h poststroke, which increased to 320 at day 3. In microglia, these numbers were 316 and 266, respectively. Interestingly, the disparity between DAS genes and differentially expressed genes is substantial, with fewer than 10 genes shared at both poststroke time points in astrocytes and microglia. Gene ontology enrichment analysis revealed the involvement of these DAS genes in diverse functions, encompassing immune response (Adam8, Ccr1), metabolism (Acsl6, Pcyt2, Myo5a), and developmental cell growth (App), among others. Selective DAS events were further validated by semiquantitative RT-PCR. Overall, this study comprehensively describes the AS alterations in astrocytes and microglia during the hyperacute and acute phases of ischemic stroke and underscores the significance of certain hub DAS events in neuroinflammatory processes.
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Affiliation(s)
- Bingxue Jin
- Department of Neurology, National Center for Neurological Disorders, Xuanwu Hospital Capital Medical University, Beijing, China
- Beijing Municipal Geriatric Medical Research Center, Beijing, China
| | - Yilai Han
- Department of Neurology, National Center for Neurological Disorders, Xuanwu Hospital Capital Medical University, Beijing, China
- Beijing Municipal Geriatric Medical Research Center, Beijing, China
| | - Fang Xu
- Department of Neurology, National Center for Neurological Disorders, Xuanwu Hospital Capital Medical University, Beijing, China
- Beijing Municipal Geriatric Medical Research Center, Beijing, China
| | - Junjie Wang
- Department of Neurology, National Center for Neurological Disorders, Xuanwu Hospital Capital Medical University, Beijing, China
- Beijing Municipal Geriatric Medical Research Center, Beijing, China
| | - Yunzhi Zhao
- Department of Neurology, National Center for Neurological Disorders, Xuanwu Hospital Capital Medical University, Beijing, China
- Beijing Municipal Geriatric Medical Research Center, Beijing, China
| | - Haijie Liu
- Department of Neurology, National Center for Neurological Disorders, Xuanwu Hospital Capital Medical University, Beijing, China
- Beijing Municipal Geriatric Medical Research Center, Beijing, China
| | - Fei Wang
- Department of Neurology, National Center for Neurological Disorders, Xuanwu Hospital Capital Medical University, Beijing, China
- Beijing Municipal Geriatric Medical Research Center, Beijing, China
| | - Ze Wang
- Department of Neurology, National Center for Neurological Disorders, Xuanwu Hospital Capital Medical University, Beijing, China
- Beijing Municipal Geriatric Medical Research Center, Beijing, China
| | - Wanting Lu
- Department of Neurology, National Center for Neurological Disorders, Xuanwu Hospital Capital Medical University, Beijing, China
- Beijing Municipal Geriatric Medical Research Center, Beijing, China
| | - Mingyang Wang
- Department of Neurology, National Center for Neurological Disorders, Xuanwu Hospital Capital Medical University, Beijing, China
- Beijing Municipal Geriatric Medical Research Center, Beijing, China
| | - Lili Cui
- Department of Neurology, National Center for Neurological Disorders, Xuanwu Hospital Capital Medical University, Beijing, China
- Beijing Municipal Geriatric Medical Research Center, Beijing, China
| | - Yinan Zhao
- Department of Neurology, National Center for Neurological Disorders, Xuanwu Hospital Capital Medical University, Beijing, China
- Beijing Municipal Geriatric Medical Research Center, Beijing, China
| | - Junwei Hao
- Department of Neurology, National Center for Neurological Disorders, Xuanwu Hospital Capital Medical University, Beijing, China
- Beijing Municipal Geriatric Medical Research Center, Beijing, China
- Key Laboratory for Neurodegenerative Diseases of Ministry of Education, Beijing, China
| | - Guoliang Chai
- Department of Neurology, National Center for Neurological Disorders, Xuanwu Hospital Capital Medical University, Beijing, China
- Beijing Municipal Geriatric Medical Research Center, Beijing, China
- Key Laboratory for Neurodegenerative Diseases of Ministry of Education, Beijing, China
- Chinese Institutes for Medical Research, Beijing, China
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14
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Patyal P, Ameer FS, Verma A, Zhang X, Azhar G, Shrivastava J, Sharma S, Zhang R, Wei JY. The Role of Sirtuin-1 Isoforms in Regulating Mitochondrial Function. Curr Issues Mol Biol 2024; 46:8835-8851. [PMID: 39194739 DOI: 10.3390/cimb46080522] [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: 07/22/2024] [Revised: 08/05/2024] [Accepted: 08/10/2024] [Indexed: 08/29/2024] Open
Abstract
The sirtuin-1 (SIRT1) gene contains multiple exons that usually undergo alternative splicing. The exclusion of one or more exons causes domain loss in the alternatively spliced isoforms and may change their functions. However, it is not completely established to what extent the loss of a non-catalytic domain could affect its regulatory function. Using muscle cells and SIRT1-knockout cells, we examined the function of the constitutively spliced isoform (SIRT1-v1) versus the alternatively spliced isoforms SIRT1-v2 and SIRT1-v3 that had lost part of the N-terminal region. Our data indicate that partial loss of the N-terminal domains in SIRT1-v2 and SIRT1-v3 attenuated their function. The full-length SIRT1-v1 significantly increased the oxidative phosphorylation and ATP production rate. Furthermore, SIRT1-v1 specifically upregulated the mitochondrial respiratory complex I without affecting the activity of complexes II, III, and IV. Additionally, domain loss affected the regulation of site-specific lysine acetylation in the histone H4 protein, the gene expression of respiratory complex I subunits, and the metabolic balance of oxidative phosphorylation versus glycolysis. Since alternatively spliced isoforms tend to increase with advancing age, the impact of SIRT1 isoforms on mitochondrial respiratory complexes warrants further investigation.
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Affiliation(s)
- Pankaj Patyal
- Donald W. Reynolds Department of Geriatrics and Institute on Aging, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Fathima S Ameer
- Donald W. Reynolds Department of Geriatrics and Institute on Aging, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Ambika Verma
- Donald W. Reynolds Department of Geriatrics and Institute on Aging, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Xiaomin Zhang
- Donald W. Reynolds Department of Geriatrics and Institute on Aging, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Gohar Azhar
- Donald W. Reynolds Department of Geriatrics and Institute on Aging, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Jyotsna Shrivastava
- Donald W. Reynolds Department of Geriatrics and Institute on Aging, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Shakshi Sharma
- Donald W. Reynolds Department of Geriatrics and Institute on Aging, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Rachel Zhang
- Donald W. Reynolds Department of Geriatrics and Institute on Aging, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Jeanne Y Wei
- Donald W. Reynolds Department of Geriatrics and Institute on Aging, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
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15
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do Nascimento RRNR, Quaio CRDC, Chung CH, de Moraes Vasconcelos D, Sztajnbok FR, Rosa Neto NS, Perazzio SF. Principles of clinical genetics for rheumatologists: clinical indications and interpretation of broad-based genetic testing. Adv Rheumatol 2024; 64:59. [PMID: 39143637 DOI: 10.1186/s42358-024-00400-z] [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: 01/29/2024] [Accepted: 08/05/2024] [Indexed: 08/16/2024] Open
Abstract
Advances in DNA sequencing technologies, especially next-generation sequencing (NGS), which is the basis for whole-exome sequencing (WES) and whole-genome sequencing (WGS), have profoundly transformed immune-mediated rheumatic disease diagnosis. Recently, substantial cost reductions have facilitated access to these diagnostic tools, expanded the capacity of molecular diagnostics and enabled the pursuit of precision medicine in rheumatology. Understanding the fundamental principles of genetics and diversity in genetic variant classification is a crucial milestone in rheumatology. However, despite the growing availability of DNA sequencing platforms, a significant number of autoinflammatory diseases (AIDs), neuromuscular disorders, hereditary collagen diseases, and monogenic bone diseases remain unsolved, and variants of uncertain significance (VUS) pose a formidable challenge to addressing these unmet needs in the coming decades. This article aims to provide an overview of the clinical indications and interpretation of comprehensive genetic testing in the medical field, addressing the related complexities and implications.
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Affiliation(s)
| | | | | | | | | | | | - Sandro Félix Perazzio
- Disciplina de Reumatologia, Universidade Federal de Sao Paulo, Escola Paulista de Medicina, Rua Otonis, 863, Sao Paulo, SP, 04025-002, Brazil.
- Fleury Medicina e Saude, Sao Paulo, Brazil.
- Universidade de Sao Paulo Faculdade de Medicina (USP FM), Sao Paulo, Brazil.
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16
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Ren H, Wu Z, Tan J, Tao H, Zou W, Cao Z, Wen B, Cai Z, Du J, Deng Z. Co-delivery Nano System of MS-275 and V-9302 Induces Pyroptosis and Enhances Anti-Tumor Immunity Against Uveal Melanoma. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2404375. [PMID: 38889339 PMCID: PMC11336933 DOI: 10.1002/advs.202404375] [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: 04/24/2024] [Revised: 06/10/2024] [Indexed: 06/20/2024]
Abstract
In the treatment of uveal melanoma (UVM), histone deacetylase inhibitors (HDACi) have emerged as a promising epigenetic therapy. However, their clinical efficacy is hindered by the suboptimal pharmacokinetics and the strong self-rescue of tumor cells. To overcome these limitations, reactive oxygen species (ROS)-responsive nanoparticles (NPs) are designed that encapsulate HDACi MS-275 and the glutamine metabolism inhibitor V-9302. Upon reaching the tumor microenvironment, these NPs can disintegrate, thereby releasing MS-275 to increase the level of ROS and V-9302 to reduce the production of glutathione (GSH) related to self-rescue. These synergistic effects lead to a lethal ROS storm and induce cell pyroptosis. When combined with programmed cell death protein 1 monoclonal antibodies (α-PD-1), these NPs facilitate immune cell infiltration, improving anti-tumor immunity, converting "immune-cold" tumors into "immune-hot" tumors, and enhancing immune memory in mice. The findings present a nano-delivery strategy for the co-delivery of epigenetic therapeutics and metabolic inhibitors, which induces pyroptosis in tumors cells and improves the effectiveness of chemotherapy and immunotherapy.
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Affiliation(s)
- Hong Ren
- Department of OphthalmologyThe Third Xiangya HospitalCentral South UniversityChangshaHunan410013China
| | - Zhenkai Wu
- Department of OphthalmologyChangde HospitalXiangya School of MedicineCentral South UniversityChangdeHunan415000China
- Department of OphthalmologyThe first people's hospital of Changde cityChangdeHunan415000China
| | - Jia Tan
- Eye Center of Xiangya HospitalCentral South UniversityChangshaHunan410008China
- Hunan Key Laboratory of Ophthalmology and National Clinical Research Center for Geriatric DisordersXiangya HospitalCentral South UniversityChangshaHunan410008China
| | - Hui Tao
- Department of OphthalmologyThe Third Xiangya HospitalCentral South UniversityChangshaHunan410013China
| | - Wangyuan Zou
- Department of AnesthesiologyXiangya HospitalCentral South UniversityChangshaHunan410008China
| | - Zheng Cao
- Department of Chemical and Biomolecular EngineeringUniversity of CaliforniaLos AngelesCA90066USA
| | - Binyu Wen
- Department of OphthalmologyThe Third Xiangya HospitalCentral South UniversityChangshaHunan410013China
| | - Ziyi Cai
- Department of OphthalmologyThe Third Xiangya HospitalCentral South UniversityChangshaHunan410013China
| | - Jiaqi Du
- Department of OphthalmologyThe Third Xiangya HospitalCentral South UniversityChangshaHunan410013China
| | - Zhihong Deng
- Department of OphthalmologyThe Third Xiangya HospitalCentral South UniversityChangshaHunan410013China
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17
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Fernandes M, Mario de Andrade E, Reis da Silva SG, Romagnoli VDS, Ortega JM, Antônio de Oliveira Mendes T. Geneapp: A web application for visualizing alternative splicing for biomedicine. Comput Biol Med 2024; 178:108789. [PMID: 38936077 DOI: 10.1016/j.compbiomed.2024.108789] [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: 10/02/2023] [Revised: 06/17/2024] [Accepted: 06/18/2024] [Indexed: 06/29/2024]
Abstract
Alternative Splicing (AS) is an essential mechanism for eukaryotes. However, the consequences of deleting a single exon can be dramatic for the organism and can lead to cancer in humans. Additionally, alternative 5' and 3' splice sites, which define the boundaries of exons, also play key roles to human disorders. Therefore, Investigating AS events is crucial for understanding the molecular basis of human diseases and developing therapeutic strategies. Workflow for AS event analysis can be sampling followed by data analysis with bioinformatics to identify the different AS events in the control and case samples, data visualization for curation, and selection of relevant targets for experimental validation. The raw output of the analysis software does not favor the inspection of events by bioinformaticians requiring custom scripts for data visualization. In this work, we propose the Geneapp application with three modules: GeneappScript, GeneappServer, and GeneappExplorer. GeneappScript is a wrapper that assists in identifying AS in samples compared in two different approaches, while GeneappServer integrates data from AS analysis already performed by the user. In GeneappExplorer, the user visualizes the previous dataset by exploring AS events in genes with functional annotation. This targeted screens that Geneapp allows to perform helps in the identification of targets for experimental validation to confirm the hypotheses under study. The Geneapp is freely available for non-commercial use at https://geneapp.net to advance research on AS for bioinformatics.
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Affiliation(s)
- Miquéias Fernandes
- Postgraduation Program in Bioinformatics, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil; Department of Biochemistry and Molecular Biology, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil; Institute of Applied Biotechnology to Agriculture (BIOAGRO), Universidade Federal de Viçosa, Minas Gerais, Brazil.
| | - Edson Mario de Andrade
- Postgraduation Program in Bioinformatics, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil; Department of Biochemistry and Molecular Biology, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil; Institute of Applied Biotechnology to Agriculture (BIOAGRO), Universidade Federal de Viçosa, Minas Gerais, Brazil
| | - Saymon Gazolla Reis da Silva
- Department of Biochemistry and Molecular Biology, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil; Institute of Applied Biotechnology to Agriculture (BIOAGRO), Universidade Federal de Viçosa, Minas Gerais, Brazil
| | - Vinícius Dos Santos Romagnoli
- Department of Biochemistry and Molecular Biology, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil; Institute of Applied Biotechnology to Agriculture (BIOAGRO), Universidade Federal de Viçosa, Minas Gerais, Brazil
| | - José Miguel Ortega
- Postgraduation Program in Bioinformatics, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Tiago Antônio de Oliveira Mendes
- Postgraduation Program in Bioinformatics, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil; Department of Biochemistry and Molecular Biology, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil; Institute of Applied Biotechnology to Agriculture (BIOAGRO), Universidade Federal de Viçosa, Minas Gerais, Brazil.
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Ferrucci L, Tanaka T, Polidori MC. Can geroscience be translated into healthcare? Z Gerontol Geriatr 2024; 57:349-354. [PMID: 38981884 PMCID: PMC11315797 DOI: 10.1007/s00391-024-02326-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Accepted: 06/07/2024] [Indexed: 07/11/2024]
Abstract
As an introduction to this special issue on geroscience, the present work focuses on the complexity of disentangling biomolecular mechanisms of aging from biopsychosocial causes of accelerated aging. Due to this complexity, the biomolecular aging hallmarks of frailty and multimorbidity as predominant aging phenotypes in geriatrics reflect single aspects of the aging process. A possible approach to facilitate the integration of geroscience into healthcare might be to consider aging as the dynamic ratio between damage accumulation at the molecular and cellular level and resilience as strategies that prevent or repair such damage. There is a large body of evidence to show that geroscience has the potential to change healthcare; however, reaching a consensus and translating the best tool to measure aging needs more research on 1) the sensitivity of biomarkers to interventions and 2) the relationship between changes in biomarkers and changes in health trajectories.
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Affiliation(s)
- Luigi Ferrucci
- Translational Gerontology Branch, Intramural Research Program, National Institute on Aging, National Institutes of Health, 251 Bayview Boulevard, 21224, Baltimore, MD, USA.
| | - Toshiko Tanaka
- Translational Gerontology Branch, Intramural Research Program, National Institute on Aging, National Institutes of Health, 251 Bayview Boulevard, 21224, Baltimore, MD, USA
| | - M Cristina Polidori
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, Ageing Clinical Research, Cologne, Germany
- Cluster of Excellence-Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, Cologne, Germany
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19
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Vallés‐Martí A, de Goeij‐de Haas RR, Henneman AA, Piersma SR, Pham TV, Knol JC, Verheij J, Dijk F, Halfwerk H, Giovannetti E, Jiménez CR, Bijlsma MF. Kinase activities in pancreatic ductal adenocarcinoma with prognostic and therapeutic avenues. Mol Oncol 2024; 18:2020-2041. [PMID: 38650175 PMCID: PMC11306541 DOI: 10.1002/1878-0261.13625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 12/12/2023] [Accepted: 02/21/2024] [Indexed: 04/25/2024] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a devastating disease with a limited number of known driver mutations but considerable cancer cell heterogeneity. Phosphoproteomics provides a direct read-out of aberrant signaling and the resultant clinically relevant phenotype. Mass spectrometry (MS)-based proteomics and phosphoproteomics were applied to 42 PDAC tumors. Data encompassed over 19 936 phosphoserine or phosphothreonine (pS/T; in 5412 phosphoproteins) and 1208 phosphotyrosine (pY; in 501 phosphoproteins) sites and a total of 3756 proteins. Proteome data identified three distinct subtypes with tumor intrinsic and stromal features. Subsequently, three phospho-subtypes were apparent: two tumor intrinsic (Phos1/2) and one stromal (Phos3), resembling known PDAC molecular subtypes. Kinase activity was analyzed by the Integrative iNferred Kinase Activity (INKA) scoring. Phospho-subtypes displayed differential phosphorylation signals and kinase activity, such as FGR and GSK3 activation in Phos1, SRC kinase family and EPHA2 in Phos2, and EGFR, INSR, MET, ABL1, HIPK1, JAK, and PRKCD in Phos3. Kinase activity analysis of an external PDAC cohort supported our findings and underscored the importance of PI3K/AKT and ERK pathways, among others. Interestingly, unfavorable patient prognosis correlated with higher RTK, PAK2, STK10, and CDK7 activity and high proliferation, whereas long survival was associated with MYLK and PTK6 activity, which was previously unknown. Subtype-associated activity profiles can guide therapeutic combination approaches in tumor and stroma-enriched tissues, and emphasize the critical role of parallel signaling pathways. In addition, kinase activity profiling identifies potential disease markers with prognostic significance.
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Affiliation(s)
- Andrea Vallés‐Martí
- Department of Medical Oncology, Amsterdam University Medical CenterVU UniversityAmsterdamThe Netherlands
- OncoProteomics LaboratoryCancer Center AmsterdamThe Netherlands
- Cancer BiologyCancer Center AmsterdamThe Netherlands
- Pharmacology LaboratoryCancer Center AmsterdamThe Netherlands
| | - Richard R. de Goeij‐de Haas
- Department of Medical Oncology, Amsterdam University Medical CenterVU UniversityAmsterdamThe Netherlands
- OncoProteomics LaboratoryCancer Center AmsterdamThe Netherlands
| | - Alex A. Henneman
- Department of Medical Oncology, Amsterdam University Medical CenterVU UniversityAmsterdamThe Netherlands
- OncoProteomics LaboratoryCancer Center AmsterdamThe Netherlands
| | - Sander R. Piersma
- Department of Medical Oncology, Amsterdam University Medical CenterVU UniversityAmsterdamThe Netherlands
- OncoProteomics LaboratoryCancer Center AmsterdamThe Netherlands
| | - Thang V. Pham
- Department of Medical Oncology, Amsterdam University Medical CenterVU UniversityAmsterdamThe Netherlands
- OncoProteomics LaboratoryCancer Center AmsterdamThe Netherlands
| | - Jaco C. Knol
- Department of Medical Oncology, Amsterdam University Medical CenterVU UniversityAmsterdamThe Netherlands
- OncoProteomics LaboratoryCancer Center AmsterdamThe Netherlands
| | - Joanne Verheij
- Department of PathologyAmsterdam University Medical CenterThe Netherlands
| | - Frederike Dijk
- Department of PathologyAmsterdam University Medical CenterThe Netherlands
| | - Hans Halfwerk
- Department of PathologyAmsterdam University Medical CenterThe Netherlands
| | - Elisa Giovannetti
- Department of Medical Oncology, Amsterdam University Medical CenterVU UniversityAmsterdamThe Netherlands
- Pharmacology LaboratoryCancer Center AmsterdamThe Netherlands
- Cancer Pharmacology Lab, AIRC Start‐Up UnitFondazione Pisana per la ScienzaSan Giuliano TermeItaly
| | - Connie R. Jiménez
- Department of Medical Oncology, Amsterdam University Medical CenterVU UniversityAmsterdamThe Netherlands
- OncoProteomics LaboratoryCancer Center AmsterdamThe Netherlands
| | - Maarten F. Bijlsma
- Cancer BiologyCancer Center AmsterdamThe Netherlands
- Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Amsterdam University Medical CenterUniversity of AmsterdamThe Netherlands
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20
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Best AJ, Braunschweig U, Wu M, Farhangmehr S, Pasculescu A, Lim JJ, Comsa LC, Jen M, Wang J, Datti A, Wrana JL, Cordes SP, Al-Awar R, Han H, Blencowe BJ. High-throughput sensitive screening of small molecule modulators of microexon alternative splicing using dual Nano and Firefly luciferase reporters. Nat Commun 2024; 15:6328. [PMID: 39068192 PMCID: PMC11283458 DOI: 10.1038/s41467-024-50399-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Accepted: 07/03/2024] [Indexed: 07/30/2024] Open
Abstract
Disruption of alternative splicing frequently causes or contributes to human diseases and disorders. Consequently, there is a need for efficient and sensitive reporter assays capable of screening chemical libraries for compounds with efficacy in modulating important splicing events. Here, we describe a screening workflow employing dual Nano and Firefly luciferase alternative splicing reporters that affords efficient, sensitive, and linear detection of small molecule responses. Applying this system to a screen of ~95,000 small molecules identified compounds that stimulate or repress the splicing of neuronal microexons, a class of alternative exons often disrupted in autism and activated in neuroendocrine cancers. One of these compounds rescues the splicing of several analyzed microexons in the cerebral cortex of an autism mouse model haploinsufficient for Srrm4, a major activator of brain microexons. We thus describe a broadly applicable high-throughput screening system for identifying candidate splicing therapeutics, and a resource of small molecule modulators of microexons with potential for further development in correcting aberrant splicing patterns linked to human disorders and disease.
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Affiliation(s)
- Andrew J Best
- Donnelly Centre, University of Toronto, Toronto, ON, Canada.
| | | | - Mingkun Wu
- Donnelly Centre, University of Toronto, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Shaghayegh Farhangmehr
- Donnelly Centre, University of Toronto, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Adrian Pasculescu
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
| | - Justin J Lim
- Donnelly Centre, University of Toronto, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Lim Caden Comsa
- Donnelly Centre, University of Toronto, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Mark Jen
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
| | - Jenny Wang
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
| | - Alessandro Datti
- Department of Agricultural, Food, and Environmental Sciences, University of Perugia, Perugia, Italy
| | - Jeffrey L Wrana
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
| | - Sabine P Cordes
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
| | - Rima Al-Awar
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, Canada
| | - Hong Han
- Donnelly Centre, University of Toronto, Toronto, ON, Canada
| | - Benjamin J Blencowe
- Donnelly Centre, University of Toronto, Toronto, ON, Canada.
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
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21
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Chen X, Wei H, Yue A, Zhang H, Zheng Y, Sun W, Zhou Y, Wang Y. KPNA2 promotes the progression of gastric cancer by regulating the alternative splicing of related genes. Sci Rep 2024; 14:17140. [PMID: 39060340 PMCID: PMC11282077 DOI: 10.1038/s41598-024-66678-7] [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: 01/09/2024] [Accepted: 07/03/2024] [Indexed: 07/28/2024] Open
Abstract
RNA-binding proteins (RBPs) play critical roles in genome regulation. In this study, we explored the latent function of KPNA2, which is an essential member of the RBP family, in the regulation of alternative splicing (AS) in gastric cancer (GC). We analyzed the role of KPNA2 in regulating differential expression and AS via RNA sequencing (RNA-seq) and improved RNA immunoprecipitation sequencing (iRIP-seq). Clinical specimens were used to analyze the associations between KPNA2 expression and clinicopathological characteristics. CCK8 assays, transwell assays and wound healing assays were performed to explore the effect of KPNA2/WDR62 on GC cell progression. KPNA2 was shown to be highly expressed in GC cells and tissues and associated with lymph node metastases. KPNA2 promoted the proliferation, migration and invasion of GC cells and primarily regulated exon skipping, alternative 3's splice sites (A3SSs), alternative 5' splice sites (A5SSs), and cassette exons. We further revealed that KPNA2 participated in biological processes related to cell proliferation, and the immune response in GC via the regulation of transcription. In addition, KPNA2 preferentially bound to intron regions. Notably, KPNA2 regulated the A3SS AS mode of WDR62, and upregulation of WDR62 reversed the KPNA2 downregulation-induced inhibition of GC cell proliferation, migration and invasion. Finally, we discovered that the AS of immune-related molecules could be regulated by KPNA2. Overall, our results demonstrated for the first time that KPNA2 functions as an oncogenic splicing factor in GC that regulated the AS and differential expression of GC-related genes, and KPNA2 may be a potential target for GC treatment.
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Affiliation(s)
- Xia Chen
- The First Clinical Medical College, Lanzhou University, Lanzhou, 730000, China
- Department of Gastroenterology, Key Laboratory for Gastrointestinal Diseases of Gansu Province, The First Hospital of Lanzhou University, Lanzhou, 730000, Gansu Province, China
- Gansu Province Clinical Research Center for Digestive Diseases, The First Hospital of Lanzhou University, Lanzhou, 730000, China
| | - Hui Wei
- The First Clinical Medical College, Lanzhou University, Lanzhou, 730000, China
- Department of Gastroenterology, Key Laboratory for Gastrointestinal Diseases of Gansu Province, The First Hospital of Lanzhou University, Lanzhou, 730000, Gansu Province, China
- Gansu Province Clinical Research Center for Digestive Diseases, The First Hospital of Lanzhou University, Lanzhou, 730000, China
| | - Ailin Yue
- The First Clinical Medical College, Lanzhou University, Lanzhou, 730000, China
- Department of Gastroenterology, Key Laboratory for Gastrointestinal Diseases of Gansu Province, The First Hospital of Lanzhou University, Lanzhou, 730000, Gansu Province, China
- Gansu Province Clinical Research Center for Digestive Diseases, The First Hospital of Lanzhou University, Lanzhou, 730000, China
| | - Huiyun Zhang
- The First Clinical Medical College, Lanzhou University, Lanzhou, 730000, China
- Department of Gastroenterology, Key Laboratory for Gastrointestinal Diseases of Gansu Province, The First Hospital of Lanzhou University, Lanzhou, 730000, Gansu Province, China
- Gansu Province Clinical Research Center for Digestive Diseases, The First Hospital of Lanzhou University, Lanzhou, 730000, China
| | - Ya Zheng
- Department of Gastroenterology, Key Laboratory for Gastrointestinal Diseases of Gansu Province, The First Hospital of Lanzhou University, Lanzhou, 730000, Gansu Province, China
- Gansu Province Clinical Research Center for Digestive Diseases, The First Hospital of Lanzhou University, Lanzhou, 730000, China
| | - Weiming Sun
- Department of Endocrinology, The First Hospital of Lanzhou University, Lanzhou, 730000, China
| | - Yongning Zhou
- Department of Gastroenterology, Key Laboratory for Gastrointestinal Diseases of Gansu Province, The First Hospital of Lanzhou University, Lanzhou, 730000, Gansu Province, China.
- Gansu Province Clinical Research Center for Digestive Diseases, The First Hospital of Lanzhou University, Lanzhou, 730000, China.
| | - Yuping Wang
- Department of Gastroenterology, Key Laboratory for Gastrointestinal Diseases of Gansu Province, The First Hospital of Lanzhou University, Lanzhou, 730000, Gansu Province, China.
- Gansu Province Clinical Research Center for Digestive Diseases, The First Hospital of Lanzhou University, Lanzhou, 730000, China.
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22
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Bao N, Wang Z, Fu J, Dong H, Jin Y. RNA structure in alternative splicing regulation: from mechanism to therapy. Acta Biochim Biophys Sin (Shanghai) 2024. [PMID: 39034824 DOI: 10.3724/abbs.2024119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/23/2024] Open
Abstract
Alternative splicing is a highly intricate process that plays a crucial role in post-transcriptional regulation and significantly expands the functional proteome of a limited number of coding genes in eukaryotes. Its regulation is multifactorial, with RNA structure exerting a significant impact. Aberrant RNA conformations lead to dysregulation of splicing patterns, which directly affects the manifestation of disease symptoms. In this review, the molecular mechanisms of RNA secondary structure-mediated splicing regulation are summarized, with a focus on the complex interplay between aberrant RNA conformations and disease phenotypes resulted from splicing defects. This study also explores additional factors that reshape structural conformations, enriching our understanding of the mechanistic network underlying structure-mediated splicing regulation. In addition, an emphasis has been placed on the clinical role of targeting aberrant splicing corrections in human diseases. The principal mechanisms of action behind this phenomenon are described, followed by a discussion of prospective development strategies and pertinent challenges.
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23
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Xiao Y, Gao L, Zhao X, Zhao W, Mai L, Ma C, Han Y, Li X. Novel prognostic alternative splicing events in colorectal Cancer: Impact on immune infiltration and therapy response. Int Immunopharmacol 2024; 139:112603. [PMID: 39043103 DOI: 10.1016/j.intimp.2024.112603] [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: 01/15/2024] [Revised: 06/06/2024] [Accepted: 06/29/2024] [Indexed: 07/25/2024]
Abstract
OBJECTIVE This study aims to comprehensively analyze alternative splicing (AS) features in colorectal cancer (CRC) using integrative multi-omics and to elucidate their relationship with the CRC immune microenvironment. METHODS Transcriptomic data, clinical information, and Percent Spliced In (PSI) values of AS events for CRC patients were obtained from The Cancer Genome Atlas (TCGA) and TCGA SpliceSeq databases. Differentially expressed AS events were identified. Univariate Cox analysis was used to pinpoint prognosis-related AS events. A prognostic risk model was developed and validated using multivariate Cox analysis, patient survival analysis, and the area under the receiver operating characteristic (ROC) curve (AUC). Gene Set Enrichment Analysis (GSEA), immune infiltration, immunotherapy, chemotherapy sensitivity analyses, and regulatory relationships between AS events and splicing factors (SFs) were conducted. Single-cell sequencing was used to study the distribution of key factors. siRNA and overexpression vectors were utilized to silence/overexpress BCAS1 in CRC cells and evaluate their effects on cell growth, migration, and invasion. Furthermore, the interaction between BCAS1 and ANO7 pre-mRNA was investigated using RIP-PCR. RESULTS 82 prognosis-related AS events were identified in CRC patients. A 15-AS prognostic model was constructed, which correlated with immune cell infiltration and showed differences in immunotherapy and chemotherapy sensitivity. BCAS1 was identified as a potential regulator of the ANO7|58341|AT splicing event in CRC. Single-cell sequencing analysis revealed the distribution of BCAS1 and ANO7 in cancer stem cells. In vitro experiments demonstrated that overexpression of BCAS1 and silencing of ANO7 inhibit the proliferation, migration, and invasion of CRC cells. Moreover, BCAS1 suppresses the progression of CRC by modulating ANO7 alternative splicing. CONCLUSION This study provides new insights into the role of alternative splicing in colorectal cancer, particularly the potential regulatory action of BCAS1 on the ANO7|58341|AT splicing event. It also identifies the impact of alternative splicing on the tumor microenvironment and potential implications for immunotherapy, highlighting its relevance for the in-depth study and treatment of CRC.
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Affiliation(s)
- Yizhi Xiao
- Department of Gastroenterology, Fifth Affiliated Hospital of Sun Yat-sen University, No. 52, Meihua East Road, Xiangzhou District, Zhuhai 519000, Guangdong Province, China
| | - Liangqing Gao
- Department of Gastroenterology, Fifth Affiliated Hospital of Sun Yat-sen University, No. 52, Meihua East Road, Xiangzhou District, Zhuhai 519000, Guangdong Province, China
| | - Xiaojuan Zhao
- Department of Gastroenterology, Fifth Affiliated Hospital of Sun Yat-sen University, No. 52, Meihua East Road, Xiangzhou District, Zhuhai 519000, Guangdong Province, China
| | - Wang Zhao
- Department of Gastroenterology, Fifth Affiliated Hospital of Sun Yat-sen University, No. 52, Meihua East Road, Xiangzhou District, Zhuhai 519000, Guangdong Province, China
| | - Lei Mai
- Department of Gastroenterology, Fifth Affiliated Hospital of Sun Yat-sen University, No. 52, Meihua East Road, Xiangzhou District, Zhuhai 519000, Guangdong Province, China
| | - Chengmin Ma
- Department of Gastroenterology, Fifth Affiliated Hospital of Sun Yat-sen University, No. 52, Meihua East Road, Xiangzhou District, Zhuhai 519000, Guangdong Province, China
| | - Yanzhi Han
- Department of Gastroenterology, Fifth Affiliated Hospital of Sun Yat-sen University, No. 52, Meihua East Road, Xiangzhou District, Zhuhai 519000, Guangdong Province, China.
| | - Xiaofeng Li
- Department of Gastroenterology, Fifth Affiliated Hospital of Sun Yat-sen University, No. 52, Meihua East Road, Xiangzhou District, Zhuhai 519000, Guangdong Province, China.
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24
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Wu Y, Yang M, Wu SB, Luo PQ, Zhang C, Ruan CS, Cui W, Zhao QR, Chen LX, Meng JJ, Song Q, Zhang WJ, Pei QQ, Li F, Zeng T, Du HX, Xu LX, Zhang W, Zhang XX, Luo XH. Zinc finger BED-type containing 3 promotes hepatic steatosis by interacting with polypyrimidine tract-binding protein 1. Diabetologia 2024:10.1007/s00125-024-06224-2. [PMID: 39037604 DOI: 10.1007/s00125-024-06224-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 04/03/2024] [Indexed: 07/23/2024]
Abstract
AIMS/HYPOTHESIS The relationship between metabolic dysfunction-associated steatotic liver disease (MASLD) and type 2 diabetes mellitus, insulin resistance and the metabolic syndrome is well established. While zinc finger BED-type containing 3 (ZBED3) has been linked to type 2 diabetes mellitus and the metabolic syndrome, its role in MASLD remains unclear. In this study, we aimed to investigate the function of ZBED3 in the context of MASLD. METHODS Expression levels of ZBED3 were assessed in individuals with MASLD, as well as in cellular and animal models of MASLD. In vitro and in vivo analyses were conducted using a cellular model of MASLD induced by NEFA and an animal model of MASLD induced by a high-fat diet (HFD), respectively, to investigate the role of ZBED3 in MASLD. ZBED3 expression was increased by lentiviral infection or tail-vein injection of adeno-associated virus. RNA-seq and bioinformatics analysis were employed to examine the pathways through which ZBED3 modulates lipid accumulation. Findings from these next-generation transcriptome sequencing studies indicated that ZBED3 controls SREBP1c (also known as SREBF1; a gene involved in fatty acid de novo synthesis); thus, co-immunoprecipitation and LC-MS/MS were utilised to investigate the molecular mechanisms by which ZBED3 regulates the sterol regulatory element binding protein 1c (SREBP1c). RESULTS In this study, we found that ZBED3 was significantly upregulated in the liver of individuals with MASLD and in MASLD animal models. ZBED3 overexpression promoted NEFA-induced triglyceride accumulation in hepatocytes in vitro. Furthermore, the hepatocyte-specific overexpression of Zbed3 promoted hepatic steatosis. Conversely, the hepatocyte-specific knockout of Zbed3 resulted in resistance of HFD-induced hepatic steatosis. Mechanistically, ZBED3 interacts directly with polypyrimidine tract-binding protein 1 (PTBP1) and affects its binding to the SREBP1c mRNA precursor to regulate SREBP1c mRNA stability and alternative splicing. CONCLUSIONS/INTERPRETATION This study indicates that ZBED3 promotes hepatic steatosis and serves as a critical regulator of the progression of MASLD. DATA AVAILABILITY RNA-seq data have been deposited in the NCBI Gene Expression Omnibus ( www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE231875 ). MS proteomics data have been deposited to the ProteomeXchange Consortium via the iProX partner repository ( https://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD041743 ).
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Affiliation(s)
- Yao Wu
- Department of Laboratory Medicine, Chongqing University Three Gorges Hospital, Chongqing, China
- The Center of Clinical Research of Endocrinology and Metabolic Diseases in Chongqing, Chongqing University Three Gorges Hospital, Chongqing, China
| | - Min Yang
- Department of Laboratory Medicine, Chongqing University Three Gorges Hospital, Chongqing, China
- The Center of Clinical Research of Endocrinology and Metabolic Diseases in Chongqing, Chongqing University Three Gorges Hospital, Chongqing, China
| | - Shao-Bo Wu
- The Center of Clinical Research of Endocrinology and Metabolic Diseases in Chongqing, Chongqing University Three Gorges Hospital, Chongqing, China
| | - Pei-Qi Luo
- The Center of Clinical Research of Endocrinology and Metabolic Diseases in Chongqing, Chongqing University Three Gorges Hospital, Chongqing, China
| | - Cheng Zhang
- The Center of Clinical Research of Endocrinology and Metabolic Diseases in Chongqing, Chongqing University Three Gorges Hospital, Chongqing, China
| | - Chang-Shun Ruan
- The Center of Clinical Research of Endocrinology and Metabolic Diseases in Chongqing, Chongqing University Three Gorges Hospital, Chongqing, China
| | - Wei Cui
- Central Laboratory Department, Chongqing University Three Gorges Hospital, Chongqing, China
| | - Qiu-Rong Zhao
- Central Laboratory Department, Chongqing University Three Gorges Hospital, Chongqing, China
| | - Lin-Xin Chen
- Central Laboratory Department, Chongqing University Three Gorges Hospital, Chongqing, China
| | - Juan-Juan Meng
- Central Laboratory Department, Chongqing University Three Gorges Hospital, Chongqing, China
| | - Qiang Song
- Central Laboratory Department, Chongqing University Three Gorges Hospital, Chongqing, China
| | - Wen-Jin Zhang
- The Center of Clinical Research of Endocrinology and Metabolic Diseases in Chongqing, Chongqing University Three Gorges Hospital, Chongqing, China
| | - Qin-Qin Pei
- Central Laboratory Department, Chongqing University Three Gorges Hospital, Chongqing, China
| | - Fang Li
- Department of Laboratory Medicine, Chongqing University Three Gorges Hospital, Chongqing, China
- The Center of Clinical Research of Endocrinology and Metabolic Diseases in Chongqing, Chongqing University Three Gorges Hospital, Chongqing, China
| | - Ting Zeng
- Department of Laboratory Medicine, Chongqing University Three Gorges Hospital, Chongqing, China
| | - Hong-Xin Du
- Department of Laboratory Medicine, Chongqing University Three Gorges Hospital, Chongqing, China
| | - Li-Xin Xu
- Chongqing Municipality Clinical Research Center for Geriatric Diseases, Chongqing University Three Gorges Hospital, Chongqing, China
| | - Weizhen Zhang
- Department of Physiology and Pathophysiology, Peking University Health Science Center, Beijing, China
- Department of Surgery, University of Michigan Medical Center, Ann Arbor, MI, USA
| | - Xian-Xiang Zhang
- The Center of Clinical Research of Endocrinology and Metabolic Diseases in Chongqing, Chongqing University Three Gorges Hospital, Chongqing, China.
| | - Xiao-He Luo
- Department of Laboratory Medicine, Chongqing University Three Gorges Hospital, Chongqing, China.
- The Center of Clinical Research of Endocrinology and Metabolic Diseases in Chongqing, Chongqing University Three Gorges Hospital, Chongqing, China.
- Central Laboratory Department, Chongqing University Three Gorges Hospital, Chongqing, China.
- Chongqing Municipality Clinical Research Center for Geriatric Diseases, Chongqing University Three Gorges Hospital, Chongqing, China.
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25
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Gál L, Schamberger A, Wachtl G, Orbán TI. The Effect of Alternative Splicing Sites on Mirtron Formation and Arm Selection of Precursor microRNAs. Int J Mol Sci 2024; 25:7643. [PMID: 39062888 PMCID: PMC11277307 DOI: 10.3390/ijms25147643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Revised: 06/25/2024] [Accepted: 07/08/2024] [Indexed: 07/28/2024] Open
Abstract
Mirtrons represent a subclass of microRNAs (miRNAs) that rely on the splicing machinery for their maturation. However, the molecular details of this Drosha-independent processing are still not fully understood; as an example, the Microprocessor complex cannot process the mirtronic pre-miRNA from the transcript even if splice site mutations are present. To investigate the influence of alternative splicing sites on mirtron formation, we generated Enhanced Green Fluorescent Protein (EGFP) reporters containing artificial introns to compare the processing of canonical miRNAs and mirtrons. Although mutations of both splice sites generated a complex pattern of alternative transcripts, mirtron formation was always severely affected as opposed to the normal processing of the canonical hsa-mir-33b miRNA. However, we also detected that while its formation was also hindered, the mirtron-derived hsa-mir-877-3p miRNA was less affected by certain mutations than the hsa-mir-877-5p species. By knocking down Drosha, we showed that this phenomenon is not dependent on Microprocessor activity but rather points toward the potential stability difference between the miRNAs from the different arms. Our results indicate that when the major splice sites are mutated, mirtron formation cannot be rescued by nearby alternative splice sites, and stability differences between 5p and 3p species should also be considered for functional studies of mirtrons.
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Affiliation(s)
- Luca Gál
- Gene Regulation Research Group, Institute of Molecular Life Sciences, HUN-REN Research Centre for Natural Sciences, 1117 Budapest, Hungary
- Doctoral School of Biology, Institute of Biology, ELTE Eötvös Loránd University, 1117 Budapest, Hungary
| | - Anita Schamberger
- Gene Regulation Research Group, Institute of Molecular Life Sciences, HUN-REN Research Centre for Natural Sciences, 1117 Budapest, Hungary
- Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences, 2100 Gödöllő, Hungary
| | - Gerda Wachtl
- Gene Regulation Research Group, Institute of Molecular Life Sciences, HUN-REN Research Centre for Natural Sciences, 1117 Budapest, Hungary
| | - Tamás I. Orbán
- Gene Regulation Research Group, Institute of Molecular Life Sciences, HUN-REN Research Centre for Natural Sciences, 1117 Budapest, Hungary
- Doctoral School of Biology, Institute of Biology, ELTE Eötvös Loránd University, 1117 Budapest, Hungary
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26
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Li JD, Taipale M, Blencowe BJ. Efficient, specific, and combinatorial control of endogenous exon splicing with dCasRx-RBM25. Mol Cell 2024; 84:2573-2589.e5. [PMID: 38917795 DOI: 10.1016/j.molcel.2024.05.028] [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: 09/15/2023] [Revised: 04/24/2024] [Accepted: 05/30/2024] [Indexed: 06/27/2024]
Abstract
Efficient targeted control of splicing is a major goal of functional genomics and therapeutic applications. Guide (g)RNA-directed, deactivated (d)Cas CRISPR enzymes fused to splicing effectors represent a promising strategy due to the flexibility of these systems. However, efficient, specific, and generalizable activation of endogenous exons using this approach has not been previously reported. By screening over 300 dCasRx-splicing factor fusion proteins tethered to splicing reporters, we identify dCasRx-RBM25 as a potent activator of exons. Moreover, dCasRx-RBM25 efficiently activates the splicing of ∼90% of targeted endogenous alternative exons and displays high on-target specificity. Using gRNA arrays for combinatorial targeting, we demonstrate that dCasRx-RBM25 enables multiplexed activation and repression of exons. Using this feature, the targeting of neural-regulated exons in Ptpb1 and Puf60 in embryonic stem cells reveals combinatorial effects on downstream alternative splicing events controlled by these factors. Collectively, our results enable versatile, combinatorial exon-resolution functional assays and splicing-directed therapeutic applications.
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Affiliation(s)
- Jack Daiyang Li
- Donnelly Centre, University of Toronto, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Mikko Taipale
- Donnelly Centre, University of Toronto, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
| | - Benjamin J Blencowe
- Donnelly Centre, University of Toronto, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
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27
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Xiao MS, Damodaran AP, Kumari B, Dickson E, Xing K, On TA, Parab N, King HE, Perez AR, Guiblet WM, Duncan G, Che A, Chari R, Andresson T, Vidigal JA, Weatheritt RJ, Aregger M, Gonatopoulos-Pournatzis T. Genome-scale exon perturbation screens uncover exons critical for cell fitness. Mol Cell 2024; 84:2553-2572.e19. [PMID: 38917794 PMCID: PMC11246229 DOI: 10.1016/j.molcel.2024.05.024] [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: 10/01/2023] [Revised: 04/04/2024] [Accepted: 05/24/2024] [Indexed: 06/27/2024]
Abstract
CRISPR-Cas technology has transformed functional genomics, yet understanding of how individual exons differentially shape cellular phenotypes remains limited. Here, we optimized and conducted massively parallel exon deletion and splice-site mutation screens in human cell lines to identify exons that regulate cellular fitness. Fitness-promoting exons are prevalent in essential and highly expressed genes and commonly overlap with protein domains and interaction interfaces. Conversely, fitness-suppressing exons are enriched in nonessential genes, exhibiting lower inclusion levels, and overlap with intrinsically disordered regions and disease-associated mutations. In-depth mechanistic investigation of the screen-hit TAF5 alternative exon-8 revealed that its inclusion is required for assembly of the TFIID general transcription initiation complex, thereby regulating global gene expression output. Collectively, our orthogonal exon perturbation screens established a comprehensive repository of phenotypically important exons and uncovered regulatory mechanisms governing cellular fitness and gene expression.
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Affiliation(s)
- Mei-Sheng Xiao
- RNA Biology Laboratory, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Frederick, MD 21702, USA
| | - Arun Prasath Damodaran
- RNA Biology Laboratory, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Frederick, MD 21702, USA.
| | - Bandana Kumari
- RNA Biology Laboratory, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Frederick, MD 21702, USA
| | - Ethan Dickson
- RNA Biology Laboratory, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Frederick, MD 21702, USA
| | - Kun Xing
- RNA Biology Laboratory, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Frederick, MD 21702, USA
| | - Tyler A On
- Molecular Targets Program, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Frederick, MD 21702, USA
| | - Nikhil Parab
- RNA Biology Laboratory, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Frederick, MD 21702, USA
| | - Helen E King
- EMBL Australia and Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
| | - Alexendar R Perez
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD 20892, USA; Department of Anesthesia and Perioperative Care, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Wilfried M Guiblet
- RNA Biology Laboratory, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Frederick, MD 21702, USA
| | - Gerard Duncan
- Protein Characterization Laboratory, Frederick National Laboratory for Cancer Research (FNLCR), Frederick, MD 21701, USA
| | - Anney Che
- Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research (FNLCR), Frederick, MD 21701, USA
| | - Raj Chari
- Genome Modification Core, Frederick National Laboratory for Cancer Research (FNLCR), Frederick, MD 21702, USA
| | - Thorkell Andresson
- Protein Characterization Laboratory, Frederick National Laboratory for Cancer Research (FNLCR), Frederick, MD 21701, USA
| | - Joana A Vidigal
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Robert J Weatheritt
- EMBL Australia and Garvan Institute of Medical Research, Sydney, NSW 2010, Australia; School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2010, Australia
| | - Michael Aregger
- Molecular Targets Program, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Frederick, MD 21702, USA.
| | - Thomas Gonatopoulos-Pournatzis
- RNA Biology Laboratory, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Frederick, MD 21702, USA.
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28
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Huang P, Wen F, Tuerhong N, Yang Y, Li Q. Neoantigens in cancer immunotherapy: focusing on alternative splicing. Front Immunol 2024; 15:1437774. [PMID: 39055714 PMCID: PMC11269099 DOI: 10.3389/fimmu.2024.1437774] [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: 05/24/2024] [Accepted: 07/01/2024] [Indexed: 07/27/2024] Open
Abstract
Alternative splicing (AS) functions as a crucial program in transcriptional modulation, leading to proteomic diversity and functional alterations of proteins. These splicing actions induce various neoantigens that hold prognostic significance and contribute to various aspects of cancer progression, including immune responses against cancer. The advent of immunotherapy has remarkably revolutionized tumor therapy. In this regard, AS-derived neoantigens are potent targets for cancer vaccines and chimeric antigen receptor (CAR) T cell therapies. In this review, we outline that AS-derived neoantigens serve as promising immunotherapeutic targets and guide immunotherapy strategies. This evidence contributes to a deeper comprehension of the complexity of proteomic diversity and provides novel perspectives and techniques for precision medicine in immunotherapy. Moreover, we underscore the obstacles that are awaited to be addressed for this novel approach to become clinically applicable.
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Affiliation(s)
- Peng Huang
- Division of Abdominal Tumor Multimodality Treatment, Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
- Department of Medical Oncology, Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Feng Wen
- Division of Abdominal Tumor Multimodality Treatment, Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
- Department of Radiation Oncology, Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Nuerye Tuerhong
- Division of Abdominal Tumor Multimodality Treatment, Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
- Department of Medical Oncology, Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yang Yang
- Division of Abdominal Tumor Multimodality Treatment, Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
- Department of Medical Oncology, Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Qiu Li
- Division of Abdominal Tumor Multimodality Treatment, Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
- Department of Medical Oncology, Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
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Jiang J, Wu H, Ji Y, Han K, Tang JM, Hu S, Lei W. Development and disease-specific regulation of RNA splicing in cardiovascular system. Front Cell Dev Biol 2024; 12:1423553. [PMID: 39045460 PMCID: PMC11263117 DOI: 10.3389/fcell.2024.1423553] [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: 04/26/2024] [Accepted: 06/17/2024] [Indexed: 07/25/2024] Open
Abstract
Alternative splicing is a complex gene regulatory process that distinguishes itself from canonical splicing by rearranging the introns and exons of an immature pre-mRNA transcript. This process plays a vital role in enhancing transcriptomic and proteomic diversity from the genome. Alternative splicing has emerged as a pivotal mechanism governing complex biological processes during both heart development and the development of cardiovascular diseases. Multiple alternative splicing factors are involved in a synergistic or antagonistic manner in the regulation of important genes in relevant physiological processes. Notably, circular RNAs have only recently garnered attention for their tissue-specific expression patterns and regulatory functions. This resurgence of interest has prompted a reevaluation of the topic. Here, we provide an overview of our current understanding of alternative splicing mechanisms and the regulatory roles of alternative splicing factors in cardiovascular development and pathological process of different cardiovascular diseases, including cardiomyopathy, myocardial infarction, heart failure and atherosclerosis.
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Affiliation(s)
- Jinxiu Jiang
- Department of Cardiovascular Surgery of the First Affiliated Hospital and Institute for Cardiovascular Science, State Key Laboratory of Radiation Medicine and Protection, Suzhou Medical College, Soochow University, Suzhou, China
| | - Hongchun Wu
- Department of Cardiovascular Surgery of the First Affiliated Hospital and Institute for Cardiovascular Science, State Key Laboratory of Radiation Medicine and Protection, Suzhou Medical College, Soochow University, Suzhou, China
| | - Yabo Ji
- Department of Cardiovascular Surgery of the First Affiliated Hospital and Institute for Cardiovascular Science, State Key Laboratory of Radiation Medicine and Protection, Suzhou Medical College, Soochow University, Suzhou, China
| | - Kunjun Han
- Department of Cardiovascular Surgery of the First Affiliated Hospital and Institute for Cardiovascular Science, State Key Laboratory of Radiation Medicine and Protection, Suzhou Medical College, Soochow University, Suzhou, China
| | - Jun-Ming Tang
- Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Shiyan, China
| | - Shijun Hu
- Department of Cardiovascular Surgery of the First Affiliated Hospital and Institute for Cardiovascular Science, State Key Laboratory of Radiation Medicine and Protection, Suzhou Medical College, Soochow University, Suzhou, China
| | - Wei Lei
- Department of Cardiovascular Surgery of the First Affiliated Hospital and Institute for Cardiovascular Science, State Key Laboratory of Radiation Medicine and Protection, Suzhou Medical College, Soochow University, Suzhou, China
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30
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Bangru S, Chen J, Baker N, Das D, Chembazhi UV, Derham JM, Chorghade S, Arif W, Alencastro F, Duncan AW, Carstens RP, Kalsotra A. ESRP2-microRNA-122 axis directs the postnatal onset of liver polyploidization and maturation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.06.602336. [PMID: 39026848 PMCID: PMC11257421 DOI: 10.1101/2024.07.06.602336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Hepatocyte polyploidy and maturity are critical to acquiring specialized liver functions. Multiple intra- and extracellular factors influence ploidy, but how they cooperate temporally to steer liver polyploidization and maturation or how post-transcriptional mechanisms integrate into these paradigms is unknown. Here, we identified an important regulatory hierarchy in which postnatal activation of Epithelial-Splicing-Regulatory-Protein-2 (ESRP2) stimulates biogenesis of liver-specific microRNA (miR-122), thereby facilitating polyploidization, maturation, and functional competence of hepatocytes. By determining transcriptome-wide protein-RNA interactions in vivo and integrating them with single-cell and bulk hepatocyte RNA-seq datasets, we delineate an ESRP2-driven RNA processing program that drives sequential replacement of fetal-to-adult transcript isoforms. Specifically, ESRP2 binds the primary miR-122 host gene transcript to promote its processing/biogenesis. Combining constitutive and inducible ESRP2 gain- and loss-of-function mice models with miR-122 rescue experiments, we demonstrate that timed activation of ESRP2 augments miR-122-driven program of cytokinesis failure, ensuring proper onset and extent of hepatocyte polyploidization.
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31
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Liang W, Xu F, Li L, Peng C, Sun H, Qiu J, Sun J. Epigenetic control of skeletal muscle atrophy. Cell Mol Biol Lett 2024; 29:99. [PMID: 38978023 PMCID: PMC11229277 DOI: 10.1186/s11658-024-00618-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Accepted: 06/26/2024] [Indexed: 07/10/2024] Open
Abstract
Skeletal muscular atrophy is a complex disease involving a large number of gene expression regulatory networks and various biological processes. Despite extensive research on this topic, its underlying mechanisms remain elusive, and effective therapeutic approaches are yet to be established. Recent studies have shown that epigenetics play an important role in regulating skeletal muscle atrophy, influencing the expression of numerous genes associated with this condition through the addition or removal of certain chemical modifications at the molecular level. This review article comprehensively summarizes the different types of modifications to DNA, histones, RNA, and their known regulators. We also discuss how epigenetic modifications change during the process of skeletal muscle atrophy, the molecular mechanisms by which epigenetic regulatory proteins control skeletal muscle atrophy, and assess their translational potential. The role of epigenetics on muscle stem cells is also highlighted. In addition, we propose that alternative splicing interacts with epigenetic mechanisms to regulate skeletal muscle mass, offering a novel perspective that enhances our understanding of epigenetic inheritance's role and the regulatory network governing skeletal muscle atrophy. Collectively, advancements in the understanding of epigenetic mechanisms provide invaluable insights into the study of skeletal muscle atrophy. Moreover, this knowledge paves the way for identifying new avenues for the development of more effective therapeutic strategies and pharmaceutical interventions.
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Affiliation(s)
- Wenpeng Liang
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-Innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, Nantong, 26001, China
- Department of Prenatal Screening and Diagnosis Center, Affiliated Maternity and Child Health Care Hospital of Nantong University, Nantong, 226001, China
| | - Feng Xu
- Department of Endocrinology, Affiliated Hospital 2 of Nantong University and First People's Hospital of Nantong City, Nantong, 226001, China
| | - Li Li
- Nantong Center for Disease Control and Prevention, Medical School of Nantong University, Nantong, 226001, China
| | - Chunlei Peng
- Department of Medical Oncology, Tumor Hospital Affiliated to Nantong University, Nantong, 226000, China
| | - Hualin Sun
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-Innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, Nantong, 26001, China
| | - Jiaying Qiu
- Department of Prenatal Screening and Diagnosis Center, Affiliated Maternity and Child Health Care Hospital of Nantong University, Nantong, 226001, China.
| | - Junjie Sun
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-Innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, Nantong, 26001, China.
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32
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Zhang N, Gao S, Peng H, Wu J, Li H, Gibson C, Wu S, Zhu J, Zheng Q. Chemical Proteomic Profiling of Protein Dopaminylation in Colorectal Cancer Cells. J Proteome Res 2024; 23:2651-2660. [PMID: 38838187 DOI: 10.1021/acs.jproteome.4c00379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2024]
Abstract
Histone dopaminylation is a newly identified epigenetic mark that plays a role in the regulation of gene transcription, where an isopeptide bond is formed between the fifth amino acid of H3 (i.e., glutamine) and dopamine. Recently, we developed a chemical probe to specifically label and enrich histone dopaminylation via bioorthogonal chemistry. Given this powerful tool, we found that histone H3 glutamine 5 dopaminylation (H3Q5dop) was highly enriched in colorectal tumors, which could be attributed to the high expression level of its regulator, transglutaminase 2 (TGM2), in colon cancer cells. Due to the enzyme promiscuity of TGM2, nonhistone proteins have also been identified as dopaminylation targets; however, the dopaminylated proteome in cancer cells still remains elusive. Here, we utilized our chemical probe to enrich dopaminylated proteins from colorectal cancer cells in a bioorthogonal manner and performed the chemical proteomics analysis. Therefore, 425 dopaminylated proteins were identified, many of which are involved in nucleic acid metabolism and transcription pathways. More importantly, a number of dopaminylation sites were identified and attributed to the successful application of our chemical probe. Overall, these findings shed light on the significant association between cellular protein dopaminylation and cancer development, further suggesting that targeting these pathways may become a promising anticancer strategy.
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Affiliation(s)
- Nan Zhang
- Department of Radiation Oncology, College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
- Center for Cancer Metabolism, James Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, United States
| | - Shuaixin Gao
- Human Nutrition Program, Department of Human Sciences, College of Education and Human Ecology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Haidong Peng
- Department of Radiation Oncology, College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
- Center for Cancer Metabolism, James Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, United States
| | - Jinghua Wu
- Department of Radiation Oncology, College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
- Center for Cancer Metabolism, James Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, United States
| | - Huapeng Li
- Department of Radiation Oncology, College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
- Center for Cancer Metabolism, James Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, United States
- Molecular, Cellular, and Developmental Biology Graduate Program, The Ohio State University, Columbus, Ohio 43210, United States
| | - Connor Gibson
- Department of Radiation Oncology, College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
- Center for Cancer Metabolism, James Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, United States
| | - Sophia Wu
- Department of Radiation Oncology, College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
- Center for Cancer Metabolism, James Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, United States
- Columbus Academy, Gahanna, Ohio 43230, United States
| | - Jiangjiang Zhu
- Center for Cancer Metabolism, James Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, United States
- Human Nutrition Program, Department of Human Sciences, College of Education and Human Ecology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Qingfei Zheng
- Department of Radiation Oncology, College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
- Center for Cancer Metabolism, James Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, United States
- Molecular, Cellular, and Developmental Biology Graduate Program, The Ohio State University, Columbus, Ohio 43210, United States
- Department of Biological Chemistry and Pharmacology, College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
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33
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Wan CY, Davis J, Chauhan M, Gleeson J, Prawer YJ, De Paoli-Iseppi R, Wells C, Choi J, Clark M. IsoVis - a webserver for visualization and annotation of alternative RNA isoforms. Nucleic Acids Res 2024; 52:W341-W347. [PMID: 38709877 PMCID: PMC11223830 DOI: 10.1093/nar/gkae343] [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: 01/30/2024] [Revised: 03/28/2024] [Accepted: 04/18/2024] [Indexed: 05/08/2024] Open
Abstract
Genes commonly express multiple RNA products (RNA isoforms), which differ in exonic content and can have different functions. Making sense of the plethora of known and novel RNA isoforms being identified by transcriptomic approaches requires a user-friendly way to visualize gene isoforms and how they differ in exonic content, expression levels and potential functions. Here we introduce IsoVis, a freely available webserver that accepts user-supplied transcriptomic data and visualizes the expressed isoforms in a clear, intuitive manner. IsoVis contains numerous features, including the ability to visualize all RNA isoforms of a gene and their expression levels; the annotation of known isoforms from external databases; mapping of protein domains and features to exons, allowing changes to protein sequence and function between isoforms to be established; and extensive species compatibility. Datasets visualised on IsoVis remain private to the user, allowing analysis of sensitive data. IsoVis visualisations can be downloaded to create publication-ready figures. The IsoVis webserver enables researchers to perform isoform analyses without requiring programming skills, is free to use, and available at https://isomix.org/isovis/.
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Affiliation(s)
- Ching Yin Wan
- Department of Anatomy and Physiology, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Jack Davis
- Department of Anatomy and Physiology, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Manveer Chauhan
- Department of Anatomy and Physiology, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Josie Gleeson
- Department of Anatomy and Physiology, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Yair D J Prawer
- Department of Anatomy and Physiology, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Ricardo De Paoli-Iseppi
- Department of Anatomy and Physiology, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Christine A Wells
- Department of Anatomy and Physiology, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Jarny Choi
- Department of Anatomy and Physiology, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Michael B Clark
- Department of Anatomy and Physiology, The University of Melbourne, Parkville, Victoria, 3010, Australia
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34
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Xiao D, Zhang M, Qu Y, Su X. Functions of methyltransferase-like 3 in breast cancer: pathogenesis, drug resistance, and therapeutic target. Breast Cancer Res 2024; 26:110. [PMID: 38961497 PMCID: PMC11223289 DOI: 10.1186/s13058-024-01869-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Accepted: 07/01/2024] [Indexed: 07/05/2024] Open
Abstract
Breast cancer (BC) is a highly prevalent malignancy worldwide, with complex pathogenesis and treatment challenges. Research reveals that methyltransferase-like 3 (METTL3) is widely involved in the pathogenesis of several tumors through methylation of its target RNAs, and its role and mechanisms in BC are also extensively studied. In this review, we aim to provide a comprehensive interpretation of available studies and elucidate the relationship between METTL3 and BC. This review suggests that high levels of METTL3 are associated with the pathogenesis, poor prognosis, and drug resistance of BC, suggesting METTL3 as a potential diagnostic or prognostic biomarker and therapeutic target. Collectively, this review provides a comprehensive understanding of how METTL3 functions through RNA methylation, which provides a valuable reference for future fundamental studies and clinical applications.
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Affiliation(s)
- Dongqiong Xiao
- Department of Pediatrics/Key Laboratory of Birth Defects and Related Diseases of Women and Children (Ministry of Education), West China Second University Hospital, Sichuan University, Chengdu, 610041, China
- NHC Key Laboratory of Chronobiology (Sichuan University), Chengdu, 610041, China
| | - Mingfu Zhang
- Department of Pediatrics/Key Laboratory of Birth Defects and Related Diseases of Women and Children (Ministry of Education), West China Second University Hospital, Sichuan University, Chengdu, 610041, China
- NHC Key Laboratory of Chronobiology (Sichuan University), Chengdu, 610041, China
| | - Yi Qu
- Department of Pediatrics/Key Laboratory of Birth Defects and Related Diseases of Women and Children (Ministry of Education), West China Second University Hospital, Sichuan University, Chengdu, 610041, China
- NHC Key Laboratory of Chronobiology (Sichuan University), Chengdu, 610041, China
| | - Xiaojuan Su
- Department of Pediatrics/Key Laboratory of Birth Defects and Related Diseases of Women and Children (Ministry of Education), West China Second University Hospital, Sichuan University, Chengdu, 610041, China.
- NHC Key Laboratory of Chronobiology (Sichuan University), Chengdu, 610041, China.
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35
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Villagra UMM, da Cunha BR, Polachini GM, Henrique T, Stefanini ACB, de Castro TB, da Silva CHTP, Feitosa OA, Fukuyama EE, López RVM, Dias-Neto E, Nunes FD, Severino P, Tajara EH. Expression of Truncated Products at the 5'-Terminal Region of RIPK2 and Evolutive Aspects that Support Their Biological Importance. Genome Biol Evol 2024; 16:evae106. [PMID: 38752399 PMCID: PMC11221433 DOI: 10.1093/gbe/evae106] [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] [Accepted: 05/10/2024] [Indexed: 07/04/2024] Open
Abstract
Alternative splicing is the process of generating different mRNAs from the same primary transcript, which contributes to increase the transcriptome and proteome diversity. Abnormal splicing has been associated with the development of several diseases including cancer. Given that mutations and abnormal levels of the RIPK2 transcript and RIP-2 protein are frequent in tumors, and that RIP-2 modulates immune and inflammatory responses, we investigated alternative splicing events that result in partial deletions of the kinase domain at the N-terminus of RIP-2. We also investigated the structure and expression of the RIPK2 truncated variants and isoforms in different environments. In addition, we searched data throughout Supraprimates evolution that could support the biological importance of RIPK2 alternatively spliced products. We observed that human variants and isoforms were differentially regulated following temperature stress, and that the truncated transcript was more expressed than the long transcript in tumor samples. The inverse was found for the longer protein isoform. The truncated variant was also detected in chimpanzee, gorilla, hare, pika, mouse, rat, and tree shrew. The fact that the same variant has been preserved in mammals with divergence times up to 70 million years raises the hypothesis that it may have a functional significance.
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Affiliation(s)
- Ulises M M Villagra
- Faculty of Exact Sciences, Biotechnology and Molecular Biology Institute (IBBM), National University of La Plata-CCT, CONICET, La Plata, Argentina
| | - Bianca R da Cunha
- Department of Molecular Biology, School of Medicine of São José do Rio Preto/FAMERP, São José do Rio Preto, SP, Brazil
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo/USP, São Paulo, SP, Brazil
| | - Giovana M Polachini
- Department of Molecular Biology, School of Medicine of São José do Rio Preto/FAMERP, São José do Rio Preto, SP, Brazil
| | - Tiago Henrique
- Department of Molecular Biology, School of Medicine of São José do Rio Preto/FAMERP, São José do Rio Preto, SP, Brazil
| | - Ana Carolina Buzzo Stefanini
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo/USP, São Paulo, SP, Brazil
| | - Tialfi Bergamin de Castro
- Department of Molecular Biology, School of Medicine of São José do Rio Preto/FAMERP, São José do Rio Preto, SP, Brazil
- Microbial Pathogenesis Department, University of Maryland Baltimore, School of Dentistry, Baltimore, MD, USA
| | - Carlos H T P da Silva
- Computational Laboratory of Pharmaceutical Chemistry, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo/USP, Ribeirão Preto, SP, Brazil
| | - Olavo A Feitosa
- Computational Laboratory of Pharmaceutical Chemistry, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo/USP, Ribeirão Preto, SP, Brazil
| | - Erica E Fukuyama
- Head and Neck Surgery Department, Arnaldo Vieira de Carvalho Cancer Institute, São Paulo, SP, Brazil
| | - Rossana V M López
- Comprehensive Center for Precision Oncology, Center for Translational Research in Oncology, State of São Paulo Cancer Institute—ICESP, Clinics Hospital, Sao Paulo University Medical School, São Paulo, SP, Brazil
| | - Emmanuel Dias-Neto
- Laboratory of Medical Genomics, A.C. Camargo Cancer Center, São Paulo, SP, Brazil
| | - Fabio D Nunes
- Department of Stomatology, School of Dentistry, University of São Paulo/USP, São Paulo, SP, Brazil
| | - Patricia Severino
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo/USP, São Paulo, SP, Brazil
- Albert Einstein Research and Education Institute, Hospital Israelita Albert Einstein, São Paulo, SP, Brazil
| | - Eloiza H Tajara
- Department of Molecular Biology, School of Medicine of São José do Rio Preto/FAMERP, São José do Rio Preto, SP, Brazil
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo/USP, São Paulo, SP, Brazil
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Ulicevic J, Shao Z, Jasnovidova O, Bressin A, Gajos M, Ng AH, Annaldasula S, Meierhofer D, Church GM, Busskamp V, Mayer A. Uncovering the dynamics and consequences of RNA isoform changes during neuronal differentiation. Mol Syst Biol 2024; 20:767-798. [PMID: 38755290 PMCID: PMC11219738 DOI: 10.1038/s44320-024-00039-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 04/16/2024] [Accepted: 04/18/2024] [Indexed: 05/18/2024] Open
Abstract
Static gene expression programs have been extensively characterized in stem cells and mature human cells. However, the dynamics of RNA isoform changes upon cell-state-transitions during cell differentiation, the determinants and functional consequences have largely remained unclear. Here, we established an improved model for human neurogenesis in vitro that is amenable for systems-wide analyses of gene expression. Our multi-omics analysis reveals that the pronounced alterations in cell morphology correlate strongly with widespread changes in RNA isoform expression. Our approach identifies thousands of new RNA isoforms that are expressed at distinct differentiation stages. RNA isoforms mainly arise from exon skipping and the alternative usage of transcription start and polyadenylation sites during human neurogenesis. The transcript isoform changes can remodel the identity and functions of protein isoforms. Finally, our study identifies a set of RNA binding proteins as a potential determinant of differentiation stage-specific global isoform changes. This work supports the view of regulated isoform changes that underlie state-transitions during neurogenesis.
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Affiliation(s)
- Jelena Ulicevic
- Otto-Warburg-Laboratory, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Zhihao Shao
- Otto-Warburg-Laboratory, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Department of Mathematics and Computer Science, Freie Universität Berlin, Berlin, Germany
| | - Olga Jasnovidova
- Otto-Warburg-Laboratory, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Annkatrin Bressin
- Otto-Warburg-Laboratory, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Martyna Gajos
- Otto-Warburg-Laboratory, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Department of Mathematics and Computer Science, Freie Universität Berlin, Berlin, Germany
| | - Alex Hm Ng
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, USA
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, USA
| | - Siddharth Annaldasula
- Otto-Warburg-Laboratory, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - David Meierhofer
- Mass Spectrometry Facility, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - George M Church
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, USA
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, USA
| | - Volker Busskamp
- Department of Ophthalmology, University Hospital Bonn, Medical Faculty, Bonn, Germany
| | - Andreas Mayer
- Otto-Warburg-Laboratory, Max Planck Institute for Molecular Genetics, Berlin, Germany.
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37
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Shine M, Gordon J, Schärfen L, Zigackova D, Herzel L, Neugebauer KM. Co-transcriptional gene regulation in eukaryotes and prokaryotes. Nat Rev Mol Cell Biol 2024; 25:534-554. [PMID: 38509203 PMCID: PMC11199108 DOI: 10.1038/s41580-024-00706-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/19/2024] [Indexed: 03/22/2024]
Abstract
Many steps of RNA processing occur during transcription by RNA polymerases. Co-transcriptional activities are deemed commonplace in prokaryotes, in which the lack of membrane barriers allows mixing of all gene expression steps, from transcription to translation. In the past decade, an extraordinary level of coordination between transcription and RNA processing has emerged in eukaryotes. In this Review, we discuss recent developments in our understanding of co-transcriptional gene regulation in both eukaryotes and prokaryotes, comparing methodologies and mechanisms, and highlight striking parallels in how RNA polymerases interact with the machineries that act on nascent RNA. The development of RNA sequencing and imaging techniques that detect transient transcription and RNA processing intermediates has facilitated discoveries of transcription coordination with splicing, 3'-end cleavage and dynamic RNA folding and revealed physical contacts between processing machineries and RNA polymerases. Such studies indicate that intron retention in a given nascent transcript can prevent 3'-end cleavage and cause transcriptional readthrough, which is a hallmark of eukaryotic cellular stress responses. We also discuss how coordination between nascent RNA biogenesis and transcription drives fundamental aspects of gene expression in both prokaryotes and eukaryotes.
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Affiliation(s)
- Morgan Shine
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Jackson Gordon
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Leonard Schärfen
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Dagmar Zigackova
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Lydia Herzel
- Department of Biology, Chemistry, and Pharmacy, Freie Universität Berlin, Berlin, Germany.
| | - Karla M Neugebauer
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.
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38
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Gao M, Ooms JF, Leurs R, Vischer HF. Histamine H 3 Receptor Isoforms: Insights from Alternative Splicing to Functional Complexity. Biomolecules 2024; 14:761. [PMID: 39062475 PMCID: PMC11274711 DOI: 10.3390/biom14070761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Revised: 06/20/2024] [Accepted: 06/24/2024] [Indexed: 07/28/2024] Open
Abstract
Alternative splicing significantly enhances the diversity of the G protein-coupled receptor (GPCR) family, including the histamine H3 receptor (H3R). This post-transcriptional modification generates multiple H3R isoforms with potentially distinct pharmacological and physiological profiles. H3R is primarily involved in the presynaptic inhibition of neurotransmitter release in the central nervous system. Despite the approval of pitolisant for narcolepsy (Wakix®) and daytime sleepiness in adults with obstructive sleep apnea (Ozawade®) and ongoing clinical trials for other H3R antagonists/inverse agonists, the functional significance of the numerous H3R isoforms remains largely enigmatic. Recent publicly available RNA sequencing data have confirmed the expression of multiple H3R isoforms in the brain, with some isoforms exhibiting unique tissue-specific distribution patterns hinting at isoform-specific functions and interactions within neural circuits. In this review, we discuss the complexity of H3R isoforms with a focus on their potential roles in central nervous system (CNS) function. Comparative analysis across species highlights evolutionary conservation and divergence in H3R splicing, suggesting species-specific regulatory mechanisms. Understanding the functionality of H3R isoforms is crucial for the development of targeted therapeutics. This knowledge will inform the design of more precise pharmacological interventions, potentially enhancing therapeutic efficacy and reducing adverse effects in the treatment of neurological and psychiatric disorders.
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Affiliation(s)
| | | | | | - Henry F. Vischer
- Amsterdam Institute of Molecular and Life Sciences, Division of Medicinal Chemistry, Faculty of Science, Vrije Universiteit Amsterdam, 1081 HZ Amsterdam, The Netherlands; (M.G.); (J.F.O.); (R.L.)
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Wu X, Lu M, Yun D, Gao S, Sun F. Long-read single-cell sequencing reveals the transcriptional landscape of spermatogenesis in obstructive azoospermia and Sertoli cell-only patients. QJM 2024; 117:422-435. [PMID: 38192002 DOI: 10.1093/qjmed/hcae009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 12/16/2023] [Indexed: 01/10/2024] Open
Abstract
BACKGROUND High-throughput single-cell RNA sequencing (scRNA-seq) is widely used in spermatogenesis. However, it only reveals short reads in germ and somatic cells, limiting the discovery of novel transcripts and genes. AIM This study shows the long-read transcriptional landscape of spermatogenesis in obstructive azoospermia (OA) and Sertoli cell-only patients. DESIGN Single cells were isolated from testicular biopsies of OA and non-obstructive azoospermia (NOA) patients. Cell culture was identified by comparing PacBio long-read single-cell sequencing (OA n = 3, NOA n = 3) with short-read scRNA-seq (OA n = 6, NOA n = 6). Ten germ cell types and eight somatic cell types were classified based on known markers. METHODS PacBio long-read single-cell sequencing, short-read scRNA-seq, polymerase chain reaction. RESULTS A total of 130 426 long-read transcripts (100 517 novel transcripts and 29 909 known transcripts) and 49 508 long-read transcripts (26 002 novel transcripts and 23 506 known transcripts) have been detected in OA and NOA patients, respectively. Moreover, 36 373 and 1642 new genes are identified in OA and NOA patients, respectively. Importantly, specific expressions of long-read transcripts were detected in germ and stomatic cells during normal spermatogenesis. CONCLUSION We have identified total full-length transcripts in OA and NOA, and new genes were found. Furthermore, specific expressed full-length transcripts were detected, and the genomic structure of transcripts was mapped in different cell types. These findings may provide valuable information on human spermatogenesis and the treatment of male infertility.
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Affiliation(s)
- X Wu
- Department of Urology and Andrology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - M Lu
- Department of Urology and Andrology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - D Yun
- Institute of Reproductive Medicine, Medical School of Nantong University, Nantong, Jiangsu, China
| | - S Gao
- Institute of Reproductive Medicine, Medical School of Nantong University, Nantong, Jiangsu, China
| | - F Sun
- Department of Urology and Andrology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
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40
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Zhuravskaya A, Yap K, Hamid F, Makeyev EV. Alternative splicing coupled to nonsense-mediated decay coordinates downregulation of non-neuronal genes in developing mouse neurons. Genome Biol 2024; 25:162. [PMID: 38902825 PMCID: PMC11188260 DOI: 10.1186/s13059-024-03305-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Accepted: 06/07/2024] [Indexed: 06/22/2024] Open
Abstract
BACKGROUND The functional coupling between alternative pre-mRNA splicing (AS) and the mRNA quality control mechanism called nonsense-mediated decay (NMD) can modulate transcript abundance. Previous studies have identified several examples of such a regulation in developing neurons. However, the systems-level effects of AS-NMD in this context are poorly understood. RESULTS We developed an R package, factR2, which offers a comprehensive suite of AS-NMD analysis functions. Using this tool, we conducted a longitudinal analysis of gene expression in pluripotent stem cells undergoing induced neuronal differentiation. Our analysis uncovers hundreds of AS-NMD events with significant potential to regulate gene expression. Notably, this regulation is significantly overrepresented in specific functional groups of developmentally downregulated genes. Particularly strong association with gene downregulation is detected for alternative cassette exons stimulating NMD upon their inclusion into mature mRNA. By combining bioinformatic analyses with CRISPR/Cas9 genome editing and other experimental approaches we show that NMD-stimulating cassette exons regulated by the RNA-binding protein PTBP1 dampen the expression of their genes in developing neurons. We also provided evidence that the inclusion of NMD-stimulating cassette exons into mature mRNAs is temporally coordinated with NMD-independent gene repression mechanisms. CONCLUSIONS Our study provides an accessible workflow for the discovery and prioritization of AS-NMD targets. It further argues that the AS-NMD pathway plays a widespread role in developing neurons by facilitating the downregulation of functionally related non-neuronal genes.
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Affiliation(s)
- Anna Zhuravskaya
- Centre for Developmental Neurobiology, King's College London, London, SE1 1UL, UK
| | - Karen Yap
- Centre for Developmental Neurobiology, King's College London, London, SE1 1UL, UK
| | - Fursham Hamid
- Centre for Developmental Neurobiology, King's College London, London, SE1 1UL, UK.
| | - Eugene V Makeyev
- Centre for Developmental Neurobiology, King's College London, London, SE1 1UL, UK.
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Bedi K, Magnuson B, Narayanan IV, McShane A, Ashaka M, Paulsen MT, Wilson TE, Ljungman M. Isoform and pathway-specific regulation of post-transcriptional RNA processing in human cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.12.598705. [PMID: 38915566 PMCID: PMC11195214 DOI: 10.1101/2024.06.12.598705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Steady-state levels of RNA transcripts are controlled by their rates of synthesis and degradation. Here we used nascent RNA Bru-seq and BruChase-seq to profile RNA dynamics across 16 human cell lines as part of ENCODE4 Deeply Profiled Cell Lines collection. We show that RNA turnover dynamics differ widely between transcripts of different genes and between different classes of RNA. Gene set enrichment analysis (GSEA) revealed that transcripts encoding proteins belonging to the same pathway often show similar turnover dynamics. Furthermore, transcript isoforms show distinct dynamics suggesting that RNA turnover is important in regulating mRNA isoform choice. Finally, splicing across newly made transcripts appears to be cooperative with either all or none type splicing. These data sets generated as part of ENCODE4 illustrate the intricate and coordinated regulation of RNA dynamics in controlling gene expression to allow for the precise coordination of cellular functions.
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Affiliation(s)
- Karan Bedi
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
- Rogel Cancer Center and Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Brian Magnuson
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Pathology and Department of Human Genetics, University of Michigan Medical School, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Ariel McShane
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI 48109, USA
- Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Mario Ashaka
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Michelle T Paulsen
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Thomas E Wilson
- Rogel Cancer Center and Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Pathology and Department of Human Genetics, University of Michigan Medical School, University of Michigan, Ann Arbor, MI 48109, USA
| | - Mats Ljungman
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI 48109, USA
- Rogel Cancer Center and Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
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42
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Cao Y, Qiu G, Dong Y, Zhao W, Wang Y. Exploring the role of m 6 A writer RBM15 in cancer: a systematic review. Front Oncol 2024; 14:1375942. [PMID: 38915367 PMCID: PMC11194397 DOI: 10.3389/fonc.2024.1375942] [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: 01/24/2024] [Accepted: 05/17/2024] [Indexed: 06/26/2024] Open
Abstract
In the contemporary epoch, cancer stands as the predominant cause of premature global mortality, necessitating a focused exploration of molecular markers and advanced therapeutic strategies. N6-methyladenosine (m6A), the most prevalent mRNA modification, undergoes dynamic regulation by enzymes referred to as methyltransferases (writers), demethylases (erasers), and effective proteins (readers). Despite lacking methylation activity, RNA-binding motif protein 15 (RBM15), a member of the m6A writer family, assumes a crucial role in recruiting the methyltransferase complex (MTC) and binding to mRNA. Although the impact of m6A modifications on cancer has garnered widespread attention, RBM15 has been relatively overlooked. This review briefly outlines the structure and operational mechanism, and delineates the unique role of RBM15 in various cancers, shedding light on its molecular basis and providing a groundwork for potential tumor-targeted therapies.
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Affiliation(s)
- Yuan Cao
- Fourth Department of Orthopedic Surgery, Central Hospital Affiliated to Shenyang Medical College, Shenyang, Liaoning, China
| | - Guanzhen Qiu
- Fourth Department of Orthopedic Surgery, Central Hospital Affiliated to Shenyang Medical College, Shenyang, Liaoning, China
- Shenyang 242 Hospital, Shenyang, Liaoning, China
| | - Yu Dong
- Fourth Department of Orthopedic Surgery, Central Hospital Affiliated to Shenyang Medical College, Shenyang, Liaoning, China
| | - Wei Zhao
- Fourth Department of Orthopedic Surgery, Central Hospital Affiliated to Shenyang Medical College, Shenyang, Liaoning, China
| | - Yong Wang
- Fourth Department of Orthopedic Surgery, Central Hospital Affiliated to Shenyang Medical College, Shenyang, Liaoning, China
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Shelton WJ, Zandpazandi S, Nix JS, Gokden M, Bauer M, Ryan KR, Wardell CP, Vaske OM, Rodriguez A. Long-read sequencing for brain tumors. Front Oncol 2024; 14:1395985. [PMID: 38915364 PMCID: PMC11194609 DOI: 10.3389/fonc.2024.1395985] [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: 03/05/2024] [Accepted: 05/27/2024] [Indexed: 06/26/2024] Open
Abstract
Brain tumors and genomics have a long-standing history given that glioblastoma was the first cancer studied by the cancer genome atlas. The numerous and continuous advances through the decades in sequencing technologies have aided in the advanced molecular characterization of brain tumors for diagnosis, prognosis, and treatment. Since the implementation of molecular biomarkers by the WHO CNS in 2016, the genomics of brain tumors has been integrated into diagnostic criteria. Long-read sequencing, also known as third generation sequencing, is an emerging technique that allows for the sequencing of longer DNA segments leading to improved detection of structural variants and epigenetics. These capabilities are opening a way for better characterization of brain tumors. Here, we present a comprehensive summary of the state of the art of third-generation sequencing in the application for brain tumor diagnosis, prognosis, and treatment. We discuss the advantages and potential new implementations of long-read sequencing into clinical paradigms for neuro-oncology patients.
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Affiliation(s)
- William J. Shelton
- Department of Neurosurgery, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Sara Zandpazandi
- Department of Neurosurgery, Medical University of South Carolina, Charleston, SC, United States
| | - J Stephen Nix
- Department of Pathology, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Murat Gokden
- Department of Pathology, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Michael Bauer
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Katie Rose Ryan
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Christopher P. Wardell
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Olena Morozova Vaske
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA, United States
| | - Analiz Rodriguez
- Department of Neurosurgery, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, United States
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Tapia AC, Jaromczyk JW, Moore N, Schardl CL. RNA-clique: a method for computing genetic distances from RNA-seq data. BMC Bioinformatics 2024; 25:205. [PMID: 38834962 DOI: 10.1186/s12859-024-05811-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 05/15/2024] [Indexed: 06/06/2024] Open
Abstract
BACKGROUND Although RNA-seq data are traditionally used for quantifying gene expression levels, the same data could be useful in an integrated approach to compute genetic distances as well. Challenges to using mRNA sequences for computing genetic distances include the relatively high conservation of coding sequences and the presence of paralogous and, in some species, homeologous genes. RESULTS We developed a new computational method, RNA-clique, for calculating genetic distances using assembled RNA-seq data and assessed the efficacy of the method using biological and simulated data. The method employs reciprocal BLASTn followed by graph-based filtering to ensure that only orthologous genes are compared. Each vertex in the graph constructed for filtering represents a gene in a specific sample under comparison, and an edge connects a pair of vertices if the genes they represent are best matches for each other in their respective samples. The distance computation is a function of the BLAST alignment statistics and the constructed graph and incorporates only those genes that are present in some complete connected component of this graph. As a biological testbed we used RNA-seq data of tall fescue (Lolium arundinaceum), an allohexaploid plant ( 2 n = 14 Gb ), and bluehead wrasse (Thalassoma bifasciatum), a teleost fish. RNA-clique reliably distinguished individual tall fescue plants by genotype and distinguished bluehead wrasse RNA-seq samples by individual. In tests with simulated RNA-seq data, the ground truth phylogeny was accurately recovered from the computed distances. Moreover, tests of the algorithm parameters indicated that, even with stringent filtering for orthologs, sufficient sequence data were retained for the distance computations. Although comparisons with an alternative method revealed that RNA-clique has relatively high time and memory requirements, the comparisons also showed that RNA-clique's results were at least as reliable as the alternative's for tall fescue data and were much more reliable for the bluehead wrasse data. CONCLUSION Results of this work indicate that RNA-clique works well as a way of deriving genetic distances from RNA-seq data, thus providing a methodological integration of functional and genetic diversity studies.
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Affiliation(s)
- Andrew C Tapia
- Department of Computer Science, University of Kentucky, 329 Rose St, Lexington, KY, 40508, USA.
| | - Jerzy W Jaromczyk
- Department of Computer Science, University of Kentucky, 329 Rose St, Lexington, KY, 40508, USA
| | - Neil Moore
- Department of Computer Science, University of Kentucky, 329 Rose St, Lexington, KY, 40508, USA
| | - Christopher L Schardl
- Department of Plant Pathology, University of Kentucky, 1405 Veterans Dr, Lexington, KY, 40546, USA
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Kubota N, Chen L, Zheng S. Shiba: A unified computational method for robust identification of differential RNA splicing across platforms. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.30.596331. [PMID: 38895326 PMCID: PMC11185541 DOI: 10.1101/2024.05.30.596331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Alternative pre-mRNA splicing (AS) is a fundamental regulatory process that generates transcript diversity and cell type variation. We developed Shiba, a robust method integrating transcript assembly, splicing event identification, read counting, and statistical analysis, to efficiently quantify exon splicing levels across various types of RNA-seq datasets. Compared to existing pipelines, Shiba excels in capturing both annotated and unannotated or cryptic differential splicing events with superior accuracy, sensitivity, and reproducibility. Furthermore, Shiba's unique consideration of junction read imbalance and exon-body read coverage reduces false positives, essential for downstream functional analyses. We have further developed scShiba for single-cell/nucleus (sc/sn) RNA-seq data, enabling the exploration of splicing variations in heterogeneous cell populations. Both simulated and real data demonstrate Shiba's robustness across multiple sample sizes, including n=1 datasets and individual cell clusters from scRNA-seq. Application of Shiba on single replicates of RNA-seq identified new AS-NMD targets, and scShiba on snRNA-seq revealed intricate temporal AS regulation in dopaminergic neurons. Both Shiba and scShiba are provided in Docker/Singularity containers and Snakemake pipeline, enhancing accessibility and reproducibility. The comprehensive capabilities of Shiba and scShiba allow systematic and robust quantification of alternative splicing events, laying a solid foundation for mechanistic exploration of functional complexity in RNA splicing.
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Affiliation(s)
- Naoto Kubota
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, CA 92521, USA
- Center for RNA Biology and Medicine, University of California, Riverside, CA 92521, USA
| | - Liang Chen
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
| | - Sika Zheng
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, CA 92521, USA
- Center for RNA Biology and Medicine, University of California, Riverside, CA 92521, USA
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Zhang YE, Stuelten CH. Alternative splicing in EMT and TGF-β signaling during cancer progression. Semin Cancer Biol 2024; 101:1-11. [PMID: 38614376 PMCID: PMC11180579 DOI: 10.1016/j.semcancer.2024.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 11/20/2023] [Accepted: 04/04/2024] [Indexed: 04/15/2024]
Abstract
Epithelial to mesenchymal transition (EMT) is a physiological process during development where epithelial cells transform to acquire mesenchymal characteristics, which allows them to migrate and colonize secondary tissues. Many cellular signaling pathways and master transcriptional factors exert a myriad of controls to fine tune this vital process to meet various developmental and physiological needs. Adding to the complexity of this network are post-transcriptional and post-translational regulations. Among them, alternative splicing has been shown to play important roles to drive EMT-associated phenotypic changes, including actin cytoskeleton remodeling, cell-cell junction changes, cell motility and invasiveness. In advanced cancers, transforming growth factor-β (TGF-β) is a major inducer of EMT and is associated with tumor cell metastasis, cancer stem cell self-renewal, and drug resistance. This review aims to provide an overview of recent discoveries regarding alternative splicing events and the involvement of splicing factors in the EMT and TGF-β signaling. It will emphasize the importance of various splicing factors involved in EMT and explore their regulatory mechanisms.
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Affiliation(s)
- Ying E Zhang
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA.
| | - Christina H Stuelten
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
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Subramani PG, Fraszczak J, Helness A, Estall JL, Möröy T, Di Noia JM. Conserved role of hnRNPL in alternative splicing of epigenetic modifiers enables B cell activation. EMBO Rep 2024; 25:2662-2697. [PMID: 38744970 PMCID: PMC11169469 DOI: 10.1038/s44319-024-00152-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 04/15/2024] [Accepted: 04/24/2024] [Indexed: 05/16/2024] Open
Abstract
The multifunctional RNA-binding protein hnRNPL is implicated in antibody class switching but its broader function in B cells is unknown. Here, we show that hnRNPL is essential for B cell activation, germinal center formation, and antibody responses. Upon activation, hnRNPL-deficient B cells show proliferation defects and increased apoptosis. Comparative analysis of RNA-seq data from activated B cells and another eight hnRNPL-depleted cell types reveals common effects on MYC and E2F transcriptional programs required for proliferation. Notably, while individual gene expression changes are cell type specific, several alternative splicing events affecting histone modifiers like KDM6A and SIRT1, are conserved across cell types. Moreover, hnRNPL-deficient B cells show global changes in H3K27me3 and H3K9ac. Epigenetic dysregulation after hnRNPL loss could underlie differential gene expression and upregulation of lncRNAs, and explain common and cell type-specific phenotypes, such as dysfunctional mitochondria and ROS overproduction in mouse B cells. Thus, hnRNPL is essential for the resting-to-activated B cell transition by regulating transcriptional programs and metabolism, at least in part through the alternative splicing of several histone modifiers.
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Affiliation(s)
- Poorani Ganesh Subramani
- Institut de Recherches Cliniques de Montréal, 110 avenue des Pins Ouest, Montréal, QC, H2W 1R7, Canada
- Department of Medicine, Division of Experimental Medicine, McGill University, 1001 Boulevard Decarie, Montreal, QC, H4A 3J1, Canada
| | - Jennifer Fraszczak
- Institut de Recherches Cliniques de Montréal, 110 avenue des Pins Ouest, Montréal, QC, H2W 1R7, Canada
| | - Anne Helness
- Institut de Recherches Cliniques de Montréal, 110 avenue des Pins Ouest, Montréal, QC, H2W 1R7, Canada
| | - Jennifer L Estall
- Institut de Recherches Cliniques de Montréal, 110 avenue des Pins Ouest, Montréal, QC, H2W 1R7, Canada
- Department of Medicine, Division of Experimental Medicine, McGill University, 1001 Boulevard Decarie, Montreal, QC, H4A 3J1, Canada
- Molecular Biology Programs, Université de Montréal, C.P. 6128, succ. Centre-ville, Montréal, QC, H3C 3J7, Canada
- Department of Medicine, Université de Montréal, C.P. 6128, succ. Centre-ville, Montréal, QC, H3C 3J7, Canada
| | - Tarik Möröy
- Institut de Recherches Cliniques de Montréal, 110 avenue des Pins Ouest, Montréal, QC, H2W 1R7, Canada
- Department of Medicine, Division of Experimental Medicine, McGill University, 1001 Boulevard Decarie, Montreal, QC, H4A 3J1, Canada
- Molecular Biology Programs, Université de Montréal, C.P. 6128, succ. Centre-ville, Montréal, QC, H3C 3J7, Canada
- Département de microbiologie, infectiologie et immunologie, Université de Montréal, 2900 Boul Edouard-Montpetit, Montréal, QC, H3T 1J4, Canada
| | - Javier M Di Noia
- Institut de Recherches Cliniques de Montréal, 110 avenue des Pins Ouest, Montréal, QC, H2W 1R7, Canada.
- Department of Medicine, Division of Experimental Medicine, McGill University, 1001 Boulevard Decarie, Montreal, QC, H4A 3J1, Canada.
- Molecular Biology Programs, Université de Montréal, C.P. 6128, succ. Centre-ville, Montréal, QC, H3C 3J7, Canada.
- Department of Medicine, Université de Montréal, C.P. 6128, succ. Centre-ville, Montréal, QC, H3C 3J7, Canada.
- Département de microbiologie, infectiologie et immunologie, Université de Montréal, 2900 Boul Edouard-Montpetit, Montréal, QC, H3T 1J4, Canada.
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Hazell Pickering S, Abdelhalim M, Collas P, Briand N. Alternative isoform expression of key thermogenic genes in human beige adipocytes. Front Endocrinol (Lausanne) 2024; 15:1395750. [PMID: 38859907 PMCID: PMC11163967 DOI: 10.3389/fendo.2024.1395750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Accepted: 05/07/2024] [Indexed: 06/12/2024] Open
Abstract
Background The beneficial effect of thermogenic adipocytes in maintaining body weight and protecting against metabolic disorders has raised interest in understanding the regulatory mechanisms defining white and beige adipocyte identity. Although alternative splicing has been shown to propagate adipose browning signals in mice, this has yet to be thoroughly investigated in human adipocytes. Methods We performed parallel white and beige adipogenic differentiation using primary adipose stem cells from 6 unrelated healthy subjects and assessed differential gene and isoform expression in mature adipocytes by RNA sequencing. Results We find 777 exon junctions with robust differential usage between white and beige adipocytes in all 6 subjects, mapping to 562 genes. Importantly, only 10% of these differentially spliced genes are also differentially expressed, indicating that alternative splicing constitutes an additional layer of gene expression regulation during beige adipocyte differentiation. Functional classification of alternative isoforms points to a gain of function for key thermogenic transcription factors such as PPARG and CITED1, and enzymes such as PEMT, or LPIN1. We find that a large majority of the splice variants arise from differential TSS usage, with beige-specific TSSs being enriched for PPARγ and MED1 binding compared to white-specific TSSs. Finally, we validate beige specific isoform expression at the protein level for two thermogenic regulators, PPARγ and PEMT. Discussion These results suggest that differential isoform expression through alternative TSS usage is an important regulatory mechanism for human adipocyte thermogenic specification.
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Affiliation(s)
- Sarah Hazell Pickering
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Mohamed Abdelhalim
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Philippe Collas
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway
- Department of Immunology and Transfusion Medicine, Oslo University Hospital, Oslo, Norway
| | - Nolwenn Briand
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway
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49
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Wolfe Z, Liska D, Norris A. Deep Transcriptomics Reveals Cell-Specific Isoforms of Pan-Neuronal Genes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.16.594572. [PMID: 38826410 PMCID: PMC11142100 DOI: 10.1101/2024.05.16.594572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Profiling gene expression in single neurons using single-cell RNA-Seq is a powerful method for understanding the molecular diversity of the nervous system. Profiling alternative splicing in single neurons using these methods is more challenging, however, due to low capture efficiency and sensitivity. As a result, we know much less about splicing patterns and regulation across neurons than we do about gene expression. Here we leverage unique attributes of the C. elegans nervous system to investigate deep cell-specific transcriptomes complete with biological replicates generated by the CeNGEN consortium, enabling high-confidence assessment of splicing across neuron types even for lowly-expressed genes. Global splicing maps reveal several striking observations, including pan-neuronal genes that harbor cell-specific splice variants, abundant differential intron retention across neuron types, and a single neuron highly enriched for upstream alternative 3' splice sites. We develop an algorithm to identify unique cell-specific expression patterns and use it to discover both cell-specific isoforms and potential regulatory RNA binding proteins that establish these isoforms. Genetic interrogation of these RNA binding proteins in vivo identifies three distinct regulatory factors employed to establish unique splicing patterns in a single neuron. Finally, we develop a user-friendly platform for spatial transcriptomic visualization of these splicing patterns with single-neuron resolution.
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50
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Li S, Huang X, Zheng S, Zhang W, Liu F, Cao Q. High expression of SRSF1 facilitates osteosarcoma progression and unveils its potential mechanisms. BMC Cancer 2024; 24:580. [PMID: 38735973 PMCID: PMC11088775 DOI: 10.1186/s12885-024-12346-y] [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: 08/22/2023] [Accepted: 05/06/2024] [Indexed: 05/14/2024] Open
Abstract
BACKGROUND SRSF1, a member of Serine/Arginine-Rich Splicing Factors (SRSFs), has been observed to significantly influence cancer progression. However, the precise role of SRSF1 in osteosarcoma (OS) remains unclear. This study aims to investigate the functions of SRSF1 and its underlying mechanism in OS. METHODS SRSF1 expression level in OS was evaluated on the TCGA dataset, TAGET-OS database. qRT-PCR and Western blotting were employed to assess SRSF1 expression in human OS cell lines as well as the interfered ectopic expression states. The effect of SRSF1 on cell migration, invasion, proliferation, and apoptosis of OS cells were measured by transwell assay and flow cytometry. RNA sequence and bioinformatic analyses were conducted to elucidate the targeted genes, relevant biological pathways, and alternative splicing (AS) events regulated by SRSF1. RESULTS SRSF1 expression was consistently upregulated in both OS samples and OS cell lines. Diminishing SRSF1 resulted in reduced proliferation, migration, and invasion and increased apoptosis in OS cells while overexpressing SRSF1 led to enhanced growth, migration, invasion, and decreased apoptosis. Mechanistically, Gene Ontology (GO) analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, and Gene Set Enrichment Analysis (GSEA) revealed that the biological functions of SRSF1 were closely associated with the dysregulation of the protein targeting processes, location of the cytosolic ribosome, extracellular matrix (ECM), and proteinaceous extracellular matrix, along with the PI3K-AKT pathway, Wnt pathway, and HIPPO pathway. Transcriptome analysis identified AS events modulated by SRSF1, especially (Skipped Exon) SE events and (Mutually exclusive Exons) MXE events, revealing potential roles of targeted molecules in mRNA surveillance, RNA degradation, and RNA transport during OS development. qRT-PCR confirmed that SRSF1 knockdown resulted in the occurrence of alternative splicing of SRRM2, DMKN, and SCAT1 in OS. CONCLUSIONS Our results highlight the oncogenic role of high SRSF1 expression in promoting OS progression, and further explore the potential mechanisms of action. The significant involvement of SRSF1 in OS development suggests its potential utility as a therapeutic target in OS.
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Affiliation(s)
- Shuqi Li
- Department of Pathology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, China
| | - Xinyi Huang
- Department of Pathology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, China
| | - Shuang Zheng
- Department of Pathology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, China
- Department of Pathology, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, 518107, China
| | - Wenhui Zhang
- Department of Pathology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, China
| | - Fang Liu
- State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Department of Infectious Diseases, Department of Liver Tumor Center, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China.
- Department of Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China.
| | - Qinghua Cao
- Department of Pathology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, China.
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