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Chen M, Zhu H, Li J, Luo D, Zhang J, Liu W, Wang J. Research progress on the relationship between AURKA and tumorigenesis: the neglected nuclear function of AURKA. Ann Med 2024; 56:2282184. [PMID: 38738386 PMCID: PMC11095293 DOI: 10.1080/07853890.2023.2282184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Accepted: 10/31/2023] [Indexed: 05/14/2024] Open
Abstract
AURKA is a threonine or serine kinase that needs to be activated by TPX2, Bora and other factors. AURKA is located on chromosome 20 and is amplified or overexpressed in many human cancers, such as breast cancer. AURKA regulates some basic cellular processes, and this regulation is realized via the phosphorylation of downstream substrates. AURKA can function in either the cytoplasm or the nucleus. It can promote the transcription and expression of oncogenes together with other transcription factors in the nucleus, including FoxM1, C-Myc, and NF-κB. In addition, it also sustains carcinogenic signaling, such as N-Myc and Wnt signaling. This article will focus on the role of AURKA in the nucleus and its carcinogenic characteristics that are independent of its kinase activity to provide a theoretical explanation for mechanisms of resistance to kinase inhibitors and a reference for future research on targeted inhibitors.
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Affiliation(s)
- Menghua Chen
- Department of Radiation Oncology, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Huijun Zhu
- Department of Radiation Oncology, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Jian Li
- Department of Radiation Oncology, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Danjing Luo
- Department of Radiation Oncology, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Jiaming Zhang
- Department of Radiation Oncology, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Wenqi Liu
- Department of Radiation Oncology, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Jue Wang
- Department of Radiation Oncology, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
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2
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Zhu Y, Li J, Li S, Yang Z, Qiao Z, Gu X, He Z, Wu D, Ma X, Yao S, Yang C, Yang M, Cao L, Zhang J, Wang W, Rong P. ZMAT2 condensates regulate the alternative splicing of TRIM28 to reduce cellular ROS accumulation, thereby promoting the proliferation of HCC cells. Cell Commun Signal 2024; 22:407. [PMID: 39164737 PMCID: PMC11337747 DOI: 10.1186/s12964-024-01790-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Accepted: 08/12/2024] [Indexed: 08/22/2024] Open
Abstract
Dysregulation of splicing factor expression plays a crucial role in the progression of hepatocellular carcinoma (HCC). Our research found that the expression level of splicing factor ZMAT2 was increased in HCC, promoting the proliferation of HCC cells. RNAseq data indicated that the absence of ZMAT2 induced skipping exon of mRNA, while RIPseq data further revealed the mRNA binding motifs of ZMAT2. A comprehensive analysis of RNAseq and RIPseq data indicateed that ZMAT2 played a crucial role in the maturation process of TRIM28 mRNA. Knocking down of ZMAT2 led to the deletion of 25 bases in exon 11 of TRIM28, ultimately resulting in nonsense-mediated decay (NMD). Our data revealed that ZMAT2 could regulate TRIM28 to reduce the accumulation of ROS in HCC cells, thereby promoting their proliferation. Our research also discovered that ZMAT2 was capable of undergoing phase separation, resulting in the formation of liquid droplet condensates within HCC cells. Additionally, it was found that ZMAT2 was able to form protein-nucleic acid condensates with TRIM28 mRNA. In summary, this study is the first to reveal that ZMAT2 and TRIM28 mRNA form protein-nucleic acid condensates, thereby regulating the splicing of TRIM28 mRNA. The increased expression of ZMAT2 in HCC leads to upregulated TRIM28 expression and reduced ROS accumulation, ultimately accelerating the proliferation of HCC cells.
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Affiliation(s)
- Yaning Zhu
- Department of Radiology, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Jiong Li
- Department of Radiology, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
- Postdoctoral Station of Medical Aspects of Specific Environments, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Sang Li
- Engineering and Technology Research Center for Xenotransplantation of Human Province, Changsha, China
| | - Zhe Yang
- College of Life Science, Liaoning University, Shenyang, China
- Shenyang Key Laboratory of Chronic Disease Occurrence and Nutrition Intervention, College of Life Sciences, Liaoning University, Shenyang, China
| | - Zhengkang Qiao
- College of Life Science, Liaoning University, Shenyang, China
| | - Xingshi Gu
- Department of Radiology, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Zhenhu He
- Department of Radiology, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Di Wu
- Department of Radiology, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Xiaoqian Ma
- Department of Radiology, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Shanhu Yao
- Department of Radiology, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Cejun Yang
- Department of Radiology, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Min Yang
- Department of Radiology, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Lu Cao
- Department of Radiology, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Juan Zhang
- Department of Radiology, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Wei Wang
- Department of Radiology, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Pengfei Rong
- Department of Radiology, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China.
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3
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Yang M, Liu J, Kim P, Zhou X. Study of prognostic splicing factors in cancer using machine learning approaches. Hum Mol Genet 2024; 33:1131-1141. [PMID: 38538560 PMCID: PMC11190612 DOI: 10.1093/hmg/ddae047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Revised: 02/11/2024] [Accepted: 03/07/2024] [Indexed: 04/12/2024] Open
Abstract
Splicing factors (SFs) are the major RNA-binding proteins (RBPs) and key molecules that regulate the splicing of mRNA molecules through binding to mRNAs. The expression of splicing factors is frequently deregulated in different cancer types, causing the generation of oncogenic proteins involved in cancer hallmarks. In this study, we investigated the genes that encode RNA-binding proteins and identified potential splicing factors that contribute to the aberrant splicing applying a random forest classification model. The result suggested 56 splicing factors were related to the prognosis of 13 cancers, two SF complexes in liver hepatocellular carcinoma, and one SF complex in esophageal carcinoma. Further systematic bioinformatics studies on these cancer prognostic splicing factors and their related alternative splicing events revealed the potential regulations in a cancer-specific manner. Our analysis found high ILF2-ILF3 expression correlates with poor prognosis in LIHC through alternative splicing. These findings emphasize the importance of SFs as potential indicators for prognosis or targets for therapeutic interventions. Their roles in cancer exhibit complexity and are contingent upon the specific context in which they operate. This recognition further underscores the need for a comprehensive understanding and exploration of the role of SFs in different types of cancer, paving the way for their potential utilization in prognostic assessments and the development of targeted therapies.
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Affiliation(s)
- Mengyuan Yang
- School of Life Sciences, Zhengzhou University, No. 100, Kexue Avenue, Zhengzhou, Henan 450001, China
| | - Jiajia Liu
- Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, 7000 Fannin St Suite 600, Houston, Texas 77030, United States
| | - Pora Kim
- Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, 7000 Fannin St Suite 600, Houston, Texas 77030, United States
| | - Xiaobo Zhou
- Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, 7000 Fannin St Suite 600, Houston, Texas 77030, United States
- McGovern Medical School, The University of Texas Health Science Center at Houston, 6431 Fannin St, Houston, Texas 77030, United States
- School of Dentistry, The University of Texas Health Science Center at Houston, 7500 Cambridge St, Houston, Texas 77054, United States
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4
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Mao S, Wu D, Cheng X, Wu J. Circ_0007432 promotes non-small cell lung cancer progression and macrophage M2 polarization through SRSF1/KLF12 axis. iScience 2024; 27:109861. [PMID: 38799570 PMCID: PMC11126953 DOI: 10.1016/j.isci.2024.109861] [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: 11/08/2023] [Revised: 03/05/2024] [Accepted: 04/27/2024] [Indexed: 05/29/2024] Open
Abstract
Circular RNAs (circRNAs) plays critical roles in non-small cell lung cancer (NSCLC) development. Herein, we illustrated the effects of circ_0007432 on malignant features of NSCLC. We found that circ_0007432 played a promoting role in NSCLC progression, lying in accelerating cell viability, migration and invasion of NSCLC cells, promoting M2 macrophage polarization, suppressing cell apoptosis of NSCLC cells, and enhancing tumor growth in vivo. Mechanistically, the interactions among circ_0007432, SRSF1, KLF12, and IL-8 were validated by RNA-binding protein immunoprecipitation (RIP), electrophoretic mobility shift assay (EMSA), RNA pull-down, dual luciferase reporter assay and chromatin immunoprecipitation (ChIP) assays. Circ_0007432 upregulated KLF12 by recruiting SRSF1. KLF12 facilitated IL-8 expression and release by binding to IL-8 promoter. Furthermore, the role of circ_0007432/SRSF1/KLF12/IL-8 axis in malignant phenotypes of tumor cells or macrophage polarization was investigated using rescue experiments. In conclusion, circ_0007432 bound with SRSF1 to stabilize KLF12 and then promote IL-8 release, thus promoting malignant behaviors of NSCLC cells and M2 macrophage polarization.
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Affiliation(s)
- Shanshan Mao
- Radiotherapy Department, The First Affiliated Hospital of Hainan Medical University, Haikou 570102, Hainan Province, P.R. China
- Department of Medical Oncology, Haikou People’s Hospital, Haikou 570208, Hainan Province, P.R. China
| | - Dongyu Wu
- Radiotherapy Department, The First Affiliated Hospital of Hainan Medical University, Haikou 570102, Hainan Province, P.R. China
| | - Xiaozhen Cheng
- Department of Medical Oncology, Haikou People’s Hospital, Haikou 570208, Hainan Province, P.R. China
| | - Jinsheng Wu
- Radiotherapy Department, The First Affiliated Hospital of Hainan Medical University, Haikou 570102, Hainan Province, P.R. China
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5
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Roesmann F, Müller L, Klaassen K, Heß S, Widera M. Interferon-Regulated Expression of Cellular Splicing Factors Modulates Multiple Levels of HIV-1 Gene Expression and Replication. Viruses 2024; 16:938. [PMID: 38932230 PMCID: PMC11209495 DOI: 10.3390/v16060938] [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: 04/30/2024] [Revised: 05/31/2024] [Accepted: 06/03/2024] [Indexed: 06/28/2024] Open
Abstract
Type I interferons (IFN-Is) are pivotal in innate immunity against human immunodeficiency virus I (HIV-1) by eliciting the expression of IFN-stimulated genes (ISGs), which encompass potent host restriction factors. While ISGs restrict the viral replication within the host cell by targeting various stages of the viral life cycle, the lesser-known IFN-repressed genes (IRepGs), including RNA-binding proteins (RBPs), affect the viral replication by altering the expression of the host dependency factors that are essential for efficient HIV-1 gene expression. Both the host restriction and dependency factors determine the viral replication efficiency; however, the understanding of the IRepGs implicated in HIV-1 infection remains greatly limited at present. This review provides a comprehensive overview of the current understanding regarding the impact of the RNA-binding protein families, specifically the two families of splicing-associated proteins SRSF and hnRNP, on HIV-1 gene expression and viral replication. Since the recent findings show specifically that SRSF1 and hnRNP A0 are regulated by IFN-I in various cell lines and primary cells, including intestinal lamina propria mononuclear cells (LPMCs) and peripheral blood mononuclear cells (PBMCs), we particularly discuss their role in the context of the innate immunity affecting HIV-1 replication.
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Affiliation(s)
- Fabian Roesmann
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt, Paul-Ehrlich-Str. 40, 60596 Frankfurt am Main, Germany
| | - Lisa Müller
- Institute of Virology, Medical Faculty, University Hospital Düsseldorf, Heinrich-Heine-University Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Katleen Klaassen
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt, Paul-Ehrlich-Str. 40, 60596 Frankfurt am Main, Germany
| | - Stefanie Heß
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt, Paul-Ehrlich-Str. 40, 60596 Frankfurt am Main, Germany
| | - Marek Widera
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt, Paul-Ehrlich-Str. 40, 60596 Frankfurt am Main, Germany
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Rodríguez-Piña AL, Castaño de la Serna E, Jiménez-Bremont JF. The serine-arginine (SR) protein UmRrm75 from Ustilago maydis is a functional ortholog of yeast ScHrb1. Int Microbiol 2024; 27:819-830. [PMID: 37776379 DOI: 10.1007/s10123-023-00432-3] [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: 02/07/2023] [Revised: 08/09/2023] [Accepted: 09/16/2023] [Indexed: 10/02/2023]
Abstract
The Basidiomycete fungus Ustilago maydis is a biotrophic pathogen of maize. The U. maydis UmRrm75 gene encodes an RNA-binding protein (RBP). In a previous study, we reported that ΔUmRrm75 null mutant strains accumulate H2O2, exhibit slow growth, and have decreased virulence in maize. Herein, we describe UmRrm75 as an ortholog of the ScHrb1, a serine-arginine (SR) protein identified in the yeast Saccharomyces cerevisiae, which plays a role in nuclear quality control, specifically in mRNA splicing and export processes. The yeast ScHrb1 mutant (ΔScHrb1) exhibits an increased sensitivity to elevated levels of boron. We noticed that the ΔScHrb1 displayed sensitivity to H2O2, which is consistent with previous findings in the ΔUmRrm75 mutant. We reversed the sensitivity phenotypes of boron and H2O2 by introducing the UmRrm75 gene into the ΔScHrb1 mutant. Furthermore, we generated complementary strains of U. maydis by expressing UmRrm75-GFP under its native promoter in the ∆UmRrm75 mutants. The UmRrm75-GFP/∆UmRrm75 complementary strains successfully recovered their growth capability under stressors, H2O2 and boron, resembling the parental strains FB2 and AB33. The subcellular localization experiments conducted in U. maydis revealed that the UmRrm75 protein is localized within the nucleus of both yeast and hyphae. The nuclear localization of the UmRrm75 protein remains unaltered even under conditions of heat or oxidative stress. This suggests that UmRrm75 might perform its RBP activity in the nucleus, as previously reported for ScHrb1. Our data contribute to understanding the role of the nuclear RBP UmRrm75 from the corn smut fungus U. maydis.
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Affiliation(s)
- Alma Laura Rodríguez-Piña
- Laboratorio de Biotecnología Molecular Plantas, División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica A.C., San Luis Potosi, San Luis Potosi, Mexico
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán A.C., Merida, Yucatan, Mexico
| | - Enrique Castaño de la Serna
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán A.C., Merida, Yucatan, Mexico
| | - Juan Francisco Jiménez-Bremont
- Laboratorio de Biotecnología Molecular Plantas, División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica A.C., San Luis Potosi, San Luis Potosi, Mexico.
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7
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Segovia D, Adams DW, Hoffman N, Safaric Tepes P, Wee TL, Cifani P, Joshua-Tor L, Krainer AR. SRSF1 interactome determined by proximity labeling reveals direct interaction with spliceosomal RNA helicase DDX23. Proc Natl Acad Sci U S A 2024; 121:e2322974121. [PMID: 38743621 PMCID: PMC11126954 DOI: 10.1073/pnas.2322974121] [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: 01/03/2024] [Accepted: 04/15/2024] [Indexed: 05/16/2024] Open
Abstract
SRSF1 is the founding member of the SR protein family. It is required-interchangeably with other SR proteins-for pre-mRNA splicing in vitro, and it regulates various alternative splicing events. Dysregulation of SRSF1 expression contributes to cancer and other pathologies. Here, we characterized SRSF1's interactome using proximity labeling and mass spectrometry. This approach yielded 190 proteins enriched in the SRSF1 samples, independently of the N- or C-terminal location of the biotin-labeling domain. The detected proteins reflect established functions of SRSF1 in pre-mRNA splicing and reveal additional connections to spliceosome proteins, in addition to other recently identified functions. We validated a robust interaction with the spliceosomal RNA helicase DDX23/PRP28 using bimolecular fluorescence complementation and in vitro binding assays. The interaction is mediated by the N-terminal RS-like domain of DDX23 and both RRM1 and the RS domain of SRSF1. During pre-mRNA splicing, DDX23's ATPase activity is essential for the pre-B to B spliceosome complex transition and for release of U1 snRNP from the 5' splice site. We show that the RS-like region of DDX23's N-terminal domain is important for spliceosome incorporation, while larger deletions in this domain alter subnuclear localization. We discuss how the identified interaction of DDX23 with SRSF1 and other SR proteins may be involved in the regulation of these processes.
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Affiliation(s)
- Danilo Segovia
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY11724
- Graduate Program in Molecular and Cellular Biology, Stony Brook University, Stony Brook, NY11794
| | - Dexter W. Adams
- HHMI, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY11724
- W. M. Keck Structural Biology Laboratory, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY11724
- Graduate Program in Genetics, Stony Brook University, Stony Brook, NY11794
| | | | | | - Tse-Luen Wee
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY11724
| | - Paolo Cifani
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY11724
| | - Leemor Joshua-Tor
- HHMI, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY11724
- W. M. Keck Structural Biology Laboratory, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY11724
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8
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Sarka K, Katzman S, Zahler AM. A role for SNU66 in maintaining 5' splice site identity during spliceosome assembly. RNA (NEW YORK, N.Y.) 2024; 30:695-709. [PMID: 38443114 PMCID: PMC11098459 DOI: 10.1261/rna.079971.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 02/21/2024] [Indexed: 03/07/2024]
Abstract
In spliceosome assembly, the 5' splice site is initially recognized by U1 snRNA. U1 leaves the spliceosome during the assembly process, therefore other factors contribute to the maintenance of 5' splice site identity as it is loaded into the catalytic site. Recent structural data suggest that human tri-snRNP 27K (SNRP27) M141 and SNU66 H734 interact to stabilize the U4/U6 quasi-pseudo knot at the base of the U6 snRNA ACAGAGA box in pre-B complex. Previously, we found that mutations in Caenorhabditis elegans at SNRP-27 M141 promote changes in alternative 5'ss usage. We tested whether the potential interaction between SNRP-27 M141 and SNU-66 H765 (the C. elegans equivalent position to human SNU66 H734) contributes to maintaining 5' splice site identity during spliceosome assembly. We find that SNU-66 H765 mutants promote alternative 5' splice site usage. Many of the alternative 5' splicing events affected by SNU-66(H765G) overlap with those affected SNRP-27(M141T). Double mutants of snrp-27(M141T) and snu-66(H765G) are homozygous lethal. We hypothesize that mutations at either SNRP-27 M141 or SNU-66 H765 allow the spliceosome to load alternative 5' splice sites into the active site. Tests with mutant U1 snRNA and swapped 5' splice sites indicate that the ability of SNRP-27 M141 and SNU-66 H765 mutants to affect a particular 5' splice alternative splicing event is dependent on both the presence of a weaker consensus 5'ss nearby and potentially nearby splicing factor binding sites. Our findings confirm a new role for the C terminus of SNU-66 in maintenance of 5' splice site identity during spliceosome assembly.
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Affiliation(s)
- Kenna Sarka
- Center for Molecular Biology of RNA and Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California 95064, USA
| | - Sol Katzman
- UCSC Genomics Institute, University of California Santa Cruz, Santa Cruz, California 95064, USA
| | - Alan M Zahler
- Center for Molecular Biology of RNA and Department of Molecular, Cellular and Developmental Biology, University of California Santa Cruz, Santa Cruz, California 95064, USA
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9
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Graham SV. HPV and RNA Binding Proteins: What We Know and What Remains to Be Discovered. Viruses 2024; 16:783. [PMID: 38793664 PMCID: PMC11126060 DOI: 10.3390/v16050783] [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: 04/04/2024] [Revised: 05/08/2024] [Accepted: 05/12/2024] [Indexed: 05/26/2024] Open
Abstract
Papillomavirus gene regulation is largely post-transcriptional due to overlapping open reading frames and the use of alternative polyadenylation and alternative splicing to produce the full suite of viral mRNAs. These processes are controlled by a wide range of cellular RNA binding proteins (RPBs), including constitutive splicing factors and cleavage and polyadenylation machinery, but also factors that regulate these processes, for example, SR and hnRNP proteins. Like cellular RNAs, papillomavirus RNAs have been shown to bind many such proteins. The life cycle of papillomaviruses is intimately linked to differentiation of the epithelial tissues the virus infects. For example, viral late mRNAs and proteins are expressed only in the most differentiated epithelial layers to avoid recognition by the host immune response. Papillomavirus genome replication is linked to the DNA damage response and viral chromatin conformation, processes which also link to RNA processing. Challenges with respect to elucidating how RBPs regulate the viral life cycle include consideration of the orchestrated spatial aspect of viral gene expression in an infected epithelium and the epigenetic nature of the viral episomal genome. This review discusses RBPs that control viral gene expression, and how the connectivity of various nuclear processes might contribute to viral mRNA production.
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Affiliation(s)
- Sheila V Graham
- MRC-University of Glasgow Centre for Virus Research, School of Infection and Immunity, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow G61 1QH, UK
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10
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Forman TE, Sajek MP, Larson ED, Mukherjee N, Fantauzzo KA. PDGFRα signaling regulates Srsf3 transcript binding to affect PI3K signaling and endosomal trafficking. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.03.587975. [PMID: 38617350 PMCID: PMC11014628 DOI: 10.1101/2024.04.03.587975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Signaling through the platelet-derived growth factor receptor alpha (PDGFRa) plays a critical role in craniofacial development, as mutations in PDGFRA are associated with cleft lip/palate in humans and Pdgfra mutant mouse models display varying degrees of facial clefting. Phosphatidylinositol 3-kinase (PI3K)/Akt is the primary effector of PDGFRα signaling during skeletal development in the mouse. We previously demonstrated that Akt phosphorylates the RNA-binding protein serine/arginine-rich splicing factor 3 (Srsf3) downstream of PI3K-mediated PDGFRa signaling in mouse embryonic palatal mesenchyme (MEPM) cells, leading to its nuclear translocation. We further showed that ablation of Srsf3 in the murine neural crest lineage results in severe midline facial clefting, due to defects in proliferation and survival of cranial neural crest cells, and widespread alternative RNA splicing (AS) changes. Here, we sought to determine the molecular mechanisms by which Srsf3 activity is regulated downstream of PDGFRa signaling to control AS of transcripts necessary for craniofacial development. We demonstrated via enhanced UV-crosslinking and immunoprecipitation (eCLIP) of MEPM cells that PDGF-AA stimulation leads to preferential binding of Srsf3 to exons and loss of binding to canonical Srsf3 CA-rich motifs. Through the analysis of complementary RNA-seq data, we showed that Srsf3 activity results in the preferential inclusion of exons with increased GC content and lower intron to exon length ratio. Moreover, we found that the subset of transcripts that are bound by Srsf3 and undergo AS upon PDGFRα signaling commonly encode regulators of PI3K signaling and early endosomal trafficking. Functional validation studies further confirmed that Srsf3 activity downstream of PDGFRα signaling leads to retention of the receptor in early endosomes and increases in downstream PI3K-mediated Akt signaling. Taken together, our findings reveal that growth factor-mediated phosphorylation of an RNA-binding protein underlies gene expression regulation necessary for mammalian craniofacial development.
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Affiliation(s)
- Thomas E. Forman
- Department of Craniofacial Biology, School of Dental Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Medical Scientist Training Program, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Marcin P. Sajek
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
| | - Eric D. Larson
- Department of Otolaryngology – Head and Neck Surgery, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Basic and Translational Sciences, Penn Dental Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Neelanjan Mukherjee
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Katherine A. Fantauzzo
- Department of Craniofacial Biology, School of Dental Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
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11
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Liu D, Yu H, Xue N, Bao H, Gao Q, Tian Y. Alternative splicing patterns of hnrnp genes in gill tissues of rainbow trout (Oncorhynchus mykiss) during salinity changes. Comp Biochem Physiol B Biochem Mol Biol 2024; 271:110948. [PMID: 38281704 DOI: 10.1016/j.cbpb.2024.110948] [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: 11/06/2023] [Revised: 01/25/2024] [Accepted: 01/25/2024] [Indexed: 01/30/2024]
Abstract
Alternative splicing (AS) plays an important role in various physiological processes in eukaryotes, such as the stress response. However, patterns of AS events remain largely unexplored during salinity acclimation in fishes. In this study, we conducted AS analysis using RNA-seq datasets to explore splicing patterns in the gill tissues of rainbow trout exposed to altered salinity environments, ranging from 0 ‰ (T0) to 30 ‰ (T30). The results revealed 1441, 351, 483, 1051 and 1049 differentially alternatively spliced (DAS) events in 5 pairwise comparisons, including T6 vs. T0, T12 vs. T0, T18 vs. T0, T24 vs. T0, and T30 vs. T0, respectively. These DAS events were derived from 1290, 328, 444, 963 and 948 genes. Enrichment analysis indicated that these DAS genes were related to RNA splicing and processing. Among these, 14 DAS genes were identified as members of the large heterogeneous nuclear RNP (hnRNP) gene family. Alternative 3' splice site (A3SS), exon skipping (SE) and intron retention (RI) events resulted in the fragmentation or even loss of the functional RNA recognition motif (RRM) domains in hnrnpa0, hnrnp1a, hnrnp1b and hnrnpc genes. The incomplete RRM domains would hinder the interactions between hnRNP genes and pre-mRNAs. It would in turn influence the splicing patterns and mRNA stability of downstream target genes in response to salinity changes. The study provides insights into salinity acclimation in gill tissues of rainbow trout and serves as a significant reference on the osmoregulation mechanisms at post-transcription regulation levels in fish.
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Affiliation(s)
- Dazhi Liu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, Shandong Province, China
| | - Han Yu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, Shandong Province, China
| | - Na Xue
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, Shandong Province, China
| | - Hancheng Bao
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, Shandong Province, China
| | - Qinfeng Gao
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, Shandong Province, China.
| | - Yuan Tian
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, Shandong Province, China.
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12
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Fan C, Lyu M, Zeng B, He Q, Wang X, Lu MZ, Liu B, Liu J, Esteban E, Pasha A, Provart NJ, Wang H, Zhang J. Profiling of the gene expression and alternative splicing landscapes of Eucalyptus grandis. PLANT, CELL & ENVIRONMENT 2024; 47:1363-1378. [PMID: 38221855 DOI: 10.1111/pce.14814] [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: 10/21/2023] [Revised: 12/05/2023] [Accepted: 01/01/2024] [Indexed: 01/16/2024]
Abstract
Eucalyptus is a widely planted hardwood tree species due to its fast growth, superior wood properties and adaptability. However, the post-transcriptional regulatory mechanisms controlling tissue development and stress responses in Eucalyptus remain poorly understood. In this study, we performed a comprehensive analysis of the gene expression profile and the alternative splicing (AS) landscape of E. grandis using strand-specific RNA-Seq, which encompassed 201 libraries including different organs, developmental stages, and environmental stresses. We identified 10 416 genes (33.49%) that underwent AS, and numerous differentially expressed and/or differential AS genes involved in critical biological processes, such as primary-to-secondary growth transition of stems, adventitious root formation, aging and responses to phosphorus- or boron-deficiency. Co-expression analysis of AS events and gene expression patterns highlighted the potential upstream regulatory role of AS events in multiple processes. Additionally, we highlighted the lignin biosynthetic pathway to showcase the potential regulatory functions of AS events in the KNAT3 and IRL3 genes within this pathway. Our high-quality expression atlas and AS landscape serve as valuable resources for unravelling the genetic control of woody plant development, long-term adaptation, and understanding transcriptional diversity in Eucalyptus. Researchers can conveniently access these resources through the interactive ePlant browser (https://bar.utoronto.ca/eplant_eucalyptus).
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Affiliation(s)
- Chunjie Fan
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of State Forestry and Grassland Administration on Tropical Forestry, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, China
- State Key Laboratory of Subtropical Silviculture, College of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, Zhejiang, China
| | - Mingjie Lyu
- National Key Facility for Crop Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
- Institute of Crop Germplasm and Biotechnology, Tianjin Academy of Agricultural Sciences, Tianjin, China
| | - Bingshan Zeng
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of State Forestry and Grassland Administration on Tropical Forestry, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, China
| | - Qiang He
- National Key Facility for Crop Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaoping Wang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of State Forestry and Grassland Administration on Tropical Forestry, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, China
| | - Meng-Zhu Lu
- State Key Laboratory of Subtropical Silviculture, College of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, Zhejiang, China
| | - Bobin Liu
- Jiansu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, School of Wetlands, Yancheng Teachers University, Yancheng, China
| | - Jun Liu
- National Key Facility for Crop Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Eddi Esteban
- Department of Cell and Systems Biology, Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario, Canada
| | - Asher Pasha
- Department of Cell and Systems Biology, Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario, Canada
| | - Nicholas J Provart
- Department of Cell and Systems Biology, Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario, Canada
| | - Huan Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jin Zhang
- State Key Laboratory of Subtropical Silviculture, College of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, Zhejiang, China
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13
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Osterhoudt K, Bagno O, Katzman S, Zahler AM. Spliceosomal helicases DDX41/SACY-1 and PRP22/MOG-5 both contribute to proofreading against proximal 3' splice site usage. RNA (NEW YORK, N.Y.) 2024; 30:404-417. [PMID: 38282418 PMCID: PMC10946429 DOI: 10.1261/rna.079888.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 01/12/2024] [Indexed: 01/30/2024]
Abstract
RNA helicases drive necessary rearrangements and ensure fidelity during the pre-mRNA splicing cycle. DEAD-box helicase DDX41 has been linked to human disease and has recently been shown to interact with DEAH-box helicase PRP22 in the spliceosomal C* complex, yet its function in splicing remains unknown. Depletion of DDX41 homolog SACY-1 from somatic cells has been previously shown to lead to changes in alternative 3' splice site (3'ss) usage. Here, we show by transcriptomic analysis of published and novel data sets that SACY-1 perturbation causes a previously unreported pattern in alternative 3' splicing in introns with pairs of 3' splice sites ≤18 nt away from each other. We find that both SACY-1 depletion and the allele sacy-1(G533R) lead to a striking unidirectional increase in the usage of the proximal (upstream) 3'ss. We previously discovered a similar alternative splicing pattern between germline tissue and somatic tissue, in which there is a unidirectional increase in proximal 3'ss usage in the germline for ∼200 events; many of the somatic SACY-1 alternative 3' splicing events overlap with these developmentally regulated events. We generated targeted mutant alleles of the Caenorhabditis elegans homolog of PRP22, mog-5, in the region of MOG-5 that is predicted to interact with SACY-1 based on the human C* structure. These viable alleles, and a mimic of the myelodysplastic syndrome-associated allele DDX41(R525H), all promote the usage of proximal alternative adjacent 3' splice sites. We show that PRP22/MOG-5 and DDX41/SACY-1 have overlapping roles in proofreading the 3'ss.
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Affiliation(s)
- Kenneth Osterhoudt
- Department of Molecular Cell and Developmental Biology, Center for Molecular Biology of RNA, University of California, Santa Cruz, California 95064, USA
| | - Orazio Bagno
- Department of Molecular Cell and Developmental Biology, Center for Molecular Biology of RNA, University of California, Santa Cruz, California 95064, USA
| | - Sol Katzman
- UCSC Genomics Institute, University of California, Santa Cruz, Santa Cruz, California 95064, USA
| | - Alan M Zahler
- Department of Molecular Cell and Developmental Biology, Center for Molecular Biology of RNA, University of California, Santa Cruz, California 95064, USA
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An W, Yang Q, Xi Y, Pan H, Huang H, Chen Q, Wang Y, Hua D, Shi C, Wang Q, Sun C, Luo W, Li X, Yu S, Zhou X. Identification of SRSF10 as a promising prognostic biomarker with functional significance among SRSFs for glioma. Life Sci 2024; 338:122392. [PMID: 38160788 DOI: 10.1016/j.lfs.2023.122392] [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: 11/02/2023] [Revised: 12/18/2023] [Accepted: 12/25/2023] [Indexed: 01/03/2024]
Abstract
AIMS The serine/arginine-rich splicing factor (SRSF) protein family members are essential mediators of the alternative splicing (AS) regulatory network, which is tightly implicated in cancer progression. However, the expression, clinical correlation, immune infiltration, and prognostic value of SRSFs in gliomas remain unclear. MATERIALS AND METHODS Glioma samples were extracted from The Cancer Genome Atlas (TCGA) and Chinese Glioma Genome Atlas (CGGA) datasets. Several databases, such as HPA, DAVID, UALCAN were used to comprehensively explore the roles of SRSFs. In addition, experimental validation of SRSF10 was also conducted. KEY FINDINGS Here, we found the expression alterations of the SRSF family in glioma samples using data from the TCGA and CGGA_325 datasets. Among the 12 genes, most were found to be closely associated with glioma clinical features, which linked to poor prognosis in glioma patients. Interestingly, survival analysis identified only SRSF10 as a potential independent risk prognostic biomarker for glioma patients. Immune analysis indicated that glioma patients with high SRSF10 expression may respond well to immunotherapies targeting immune checkpoint (ICP) genes. Finally, knocking down SRSF10 reduced glioma cell viability, induced G1 cell cycle arrest, and induced the exclusion of bcl-2-associated transcription factor 1 (BCLAF1) exon 5a. SIGNIFICANCE Overall, this study uncovers the oncogenic roles of most SRSF family members in glioma, with the exception of SRSF5, while highlighting SRSF10 as a potential novel independent prognostic biomarker for glioma.
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Affiliation(s)
- Wenzhe An
- Department of Neuropathology, Tianjin Key Laboratory of Injuries, Variations and Regeneration of the Nervous System, Key Laboratory of Post-trauma Neuro-repair and Regeneration in Central Nervous System of Education Ministry, Tianjin Neurological Institute, Tianjin Medical University General Hospital, Tianjin, PR China
| | - Qingqing Yang
- Department of Neuropathology, Tianjin Key Laboratory of Injuries, Variations and Regeneration of the Nervous System, Key Laboratory of Post-trauma Neuro-repair and Regeneration in Central Nervous System of Education Ministry, Tianjin Neurological Institute, Tianjin Medical University General Hospital, Tianjin, PR China
| | - Yunlan Xi
- Department of Neuropathology, Tianjin Key Laboratory of Injuries, Variations and Regeneration of the Nervous System, Key Laboratory of Post-trauma Neuro-repair and Regeneration in Central Nervous System of Education Ministry, Tianjin Neurological Institute, Tianjin Medical University General Hospital, Tianjin, PR China
| | - Hongli Pan
- Tianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenvironment, Tianjin Lung Cancer Institute, Department of Lung Cancer Surgery, Tianjin Medical University General Hospital, Tianjin, PR China
| | - Hua Huang
- Tianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenvironment, Tianjin Lung Cancer Institute, Department of Lung Cancer Surgery, Tianjin Medical University General Hospital, Tianjin, PR China
| | - Qiang Chen
- Tianjin Key Laboratory of Cancer Prevention and Therapy, Department of Thoracic Oncology, Tianjin Lung Cancer Center, Tianjin's Clinical Research Center for Cancer, National Clinical Research Center for Cancer, Tianjin Cancer Institute & Hospital, Tianjin Medical University, Tianjin, PR China; Department of Respiratory and Critical Medicine, Tianjin Chest Hospital, Tianjin, PR China
| | - Yixuan Wang
- Tianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenvironment, Tianjin Lung Cancer Institute, Department of Lung Cancer Surgery, Tianjin Medical University General Hospital, Tianjin, PR China
| | - Dan Hua
- Department of Neuropathology, Tianjin Key Laboratory of Injuries, Variations and Regeneration of the Nervous System, Key Laboratory of Post-trauma Neuro-repair and Regeneration in Central Nervous System of Education Ministry, Tianjin Neurological Institute, Tianjin Medical University General Hospital, Tianjin, PR China
| | - Cuijuan Shi
- Department of Neuropathology, Tianjin Key Laboratory of Injuries, Variations and Regeneration of the Nervous System, Key Laboratory of Post-trauma Neuro-repair and Regeneration in Central Nervous System of Education Ministry, Tianjin Neurological Institute, Tianjin Medical University General Hospital, Tianjin, PR China
| | - Qian Wang
- Department of Neuropathology, Tianjin Key Laboratory of Injuries, Variations and Regeneration of the Nervous System, Key Laboratory of Post-trauma Neuro-repair and Regeneration in Central Nervous System of Education Ministry, Tianjin Neurological Institute, Tianjin Medical University General Hospital, Tianjin, PR China
| | - Cuiyun Sun
- Department of Neuropathology, Tianjin Key Laboratory of Injuries, Variations and Regeneration of the Nervous System, Key Laboratory of Post-trauma Neuro-repair and Regeneration in Central Nervous System of Education Ministry, Tianjin Neurological Institute, Tianjin Medical University General Hospital, Tianjin, PR China
| | - Wenjun Luo
- Department of Neuropathology, Tianjin Key Laboratory of Injuries, Variations and Regeneration of the Nervous System, Key Laboratory of Post-trauma Neuro-repair and Regeneration in Central Nervous System of Education Ministry, Tianjin Neurological Institute, Tianjin Medical University General Hospital, Tianjin, PR China
| | - Xuebing Li
- Tianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenvironment, Tianjin Lung Cancer Institute, Department of Lung Cancer Surgery, Tianjin Medical University General Hospital, Tianjin, PR China.
| | - Shizhu Yu
- Department of Neuropathology, Tianjin Key Laboratory of Injuries, Variations and Regeneration of the Nervous System, Key Laboratory of Post-trauma Neuro-repair and Regeneration in Central Nervous System of Education Ministry, Tianjin Neurological Institute, Tianjin Medical University General Hospital, Tianjin, PR China.
| | - Xuexia Zhou
- Department of Neuropathology, Tianjin Key Laboratory of Injuries, Variations and Regeneration of the Nervous System, Key Laboratory of Post-trauma Neuro-repair and Regeneration in Central Nervous System of Education Ministry, Tianjin Neurological Institute, Tianjin Medical University General Hospital, Tianjin, PR China.
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15
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Shen W, Yuan L, Cheng F, Wu Z, Li X. SRSF7 is a promising prognostic biomarker in hepatocellular carcinoma and is associated with immune infiltration. Genes Genomics 2024; 46:49-64. [PMID: 37985547 DOI: 10.1007/s13258-023-01463-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 09/30/2023] [Indexed: 11/22/2023]
Abstract
BACKGROUND Previous studies indicate that the splicing process, regulated by the cellular machinery of tumors (spliceosome), undergoes alterations, leading to oncogenic splicing events associated with the progression of tumors towards aggressiveness. However, the role of serine/arginine-rich splicing factor 7 (SRSF7) in hepatocellular carcinoma (HCC) and the tumor microenvironment (TME) remains unclear. METHODS This study was aimed to explore the role and clinical significance of SRSF7 in HCC. By conducting functional analysis and gene set enrichment analysis, it was discovered that SRSF7 contributes to multiple pathways associated with immune response and tumor advancement. Further experiments verified that silencing of SRSF7 obviously inhibits progression of HCC. RESULTS Aberrant expression of SRSF7, which were referred as an independent prognostic risk factor, effectively predicts the prognosis of patients with HCC. Functional and gene enrichment analyses revealed that SRSF7 is linked with multiple immune and tumor progression-related pathways, including the B cell receptor signaling pathway, positive regulation of leukocyte and immunoglobulin receptor binding cell activation, nuclear division, membrane invagination, cell cycle, as well as mTOR signaling pathway. Furthermore, increased SRSF7 expression was associated with tumor-infiltrating inflammatory cells (CD4+, monocytes/macrophages, CD8 + and endothelial). Additionally, multiple immune checkpoint genes were markedly positively related to SRSF7. The efficiency of SRSF7 in predicting immunomodulator and chemokine responses were also assessed in microenvironment. Moreover, in vitro analyses demonstrated that knockdown of SRSF7 suppressed the malignant evolution of HCC possibly by deactivating the PI3K/AKT/mTOR signaling. CONCLUSION The role of SRSF7 in the tumor microenvironment has been successfully assessed. It may be a valid bio-index for predicting the HCC prognosis, thereby guiding individualized immunotherapy for cancer.
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Affiliation(s)
- Wei Shen
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi, People's Republic of China.
| | - Lebin Yuan
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi, People's Republic of China
| | - Fei Cheng
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi, People's Republic of China
| | - Zhao Wu
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi, People's Republic of China
| | - Xiaodong Li
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi, People's Republic of China
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16
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Russo M, Piccolo V, Polizzese D, Prosperini E, Borriero C, Polletti S, Bedin F, Marenda M, Michieletto D, Mandana GM, Rodighiero S, Cuomo A, Natoli G. Restrictor synergizes with Symplekin and PNUTS to terminate extragenic transcription. Genes Dev 2023; 37:1017-1040. [PMID: 38092518 PMCID: PMC10760643 DOI: 10.1101/gad.351057.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 11/29/2023] [Indexed: 12/28/2023]
Abstract
Transcription termination pathways mitigate the detrimental consequences of unscheduled promiscuous initiation occurring at hundreds of thousands of genomic cis-regulatory elements. The Restrictor complex, composed of the Pol II-interacting protein WDR82 and the RNA-binding protein ZC3H4, suppresses processive transcription at thousands of extragenic sites in mammalian genomes. Restrictor-driven termination does not involve nascent RNA cleavage, and its interplay with other termination machineries is unclear. Here we show that efficient termination at Restrictor-controlled extragenic transcription units involves the recruitment of the protein phosphatase 1 (PP1) regulatory subunit PNUTS, a negative regulator of the SPT5 elongation factor, and Symplekin, a protein associated with RNA cleavage complexes but also involved in cleavage-independent and phosphatase-dependent termination of noncoding RNAs in yeast. PNUTS and Symplekin act synergistically with, but independently from, Restrictor to dampen processive extragenic transcription. Moreover, the presence of limiting nuclear levels of Symplekin imposes a competition for its recruitment among multiple transcription termination machineries, resulting in mutual regulatory interactions. Hence, by synergizing with Restrictor, Symplekin and PNUTS enable efficient termination of processive, long-range extragenic transcription.
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Affiliation(s)
- Marta Russo
- Department of Experimental Oncology, European Institute of Oncology (IEO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan I-20139, Italy
| | - Viviana Piccolo
- Department of Experimental Oncology, European Institute of Oncology (IEO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan I-20139, Italy
| | - Danilo Polizzese
- Department of Experimental Oncology, European Institute of Oncology (IEO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan I-20139, Italy
| | - Elena Prosperini
- Department of Experimental Oncology, European Institute of Oncology (IEO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan I-20139, Italy
| | - Carolina Borriero
- Department of Experimental Oncology, European Institute of Oncology (IEO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan I-20139, Italy
| | - Sara Polletti
- Department of Experimental Oncology, European Institute of Oncology (IEO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan I-20139, Italy
| | - Fabio Bedin
- Department of Experimental Oncology, European Institute of Oncology (IEO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan I-20139, Italy
| | - Mattia Marenda
- Department of Experimental Oncology, European Institute of Oncology (IEO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan I-20139, Italy
| | - Davide Michieletto
- School of Physics and Astronomy, University of Edinburgh, Edinburgh EH9 3FD, United Kingdom
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Gaurav Madappa Mandana
- Department of Experimental Oncology, European Institute of Oncology (IEO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan I-20139, Italy
| | - Simona Rodighiero
- Department of Experimental Oncology, European Institute of Oncology (IEO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan I-20139, Italy
| | - Alessandro Cuomo
- Department of Experimental Oncology, European Institute of Oncology (IEO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan I-20139, Italy
| | - Gioacchino Natoli
- Department of Experimental Oncology, European Institute of Oncology (IEO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan I-20139, Italy;
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17
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Polvèche H, Valat J, Fontrodona N, Lapendry A, Clerc V, Janczarski S, Mortreux F, Auboeuf D, Bourgeois CF. SplicingLore: a web resource for studying the regulation of cassette exons by human splicing factors. Database (Oxford) 2023; 2023:baad091. [PMID: 38128543 PMCID: PMC10735282 DOI: 10.1093/database/baad091] [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: 07/09/2023] [Revised: 11/06/2023] [Accepted: 12/06/2023] [Indexed: 12/23/2023]
Abstract
One challenge faced by scientists from the alternative RNA splicing field is to decode the cooperative or antagonistic effects of splicing factors (SFs) to understand and eventually predict splicing outcomes on a genome-wide scale. In this manuscript, we introduce SplicingLore, an open-access database and web resource that help to fill this gap in a straightforward manner. The database contains a collection of RNA-sequencing-derived lists of alternative exons regulated by a total of 75 different SFs. All datasets were processed in a standardized manner, ensuring valid comparisons and correlation analyses. The user can easily retrieve a factor-specific set of differentially included exons from the database or provide a list of exons and search which SF(s) control(s) their inclusion. Our simple workflow is fast and easy to run, and it ensures a reliable calculation of correlation scores between the tested datasets. As a proof of concept, we predicted and experimentally validated a novel functional cooperation between the RNA helicases DDX17 and DDX5 and the heterogeneous nuclear ribonucleoprotein C (HNRNPC) protein. SplicingLore is available at https://splicinglore.ens-lyon.fr/. Database URL: https://splicinglore.ens-lyon.fr/.
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Affiliation(s)
| | - Jessica Valat
- Laboratoire de Biologie et Modelisation de la Cellule, Ecole Normale Superieure de Lyon, CNRS, UMR 5239, Inserm, U1293, Universite Claude Bernard Lyon 1, 46 allee d’Italie, Lyon F-69364, France
- Equipe Labellisee Ligue Contre le Cancer, 4 allee d'Italie, Lyon 69007, France
| | - Nicolas Fontrodona
- Laboratoire de Biologie et Modelisation de la Cellule, Ecole Normale Superieure de Lyon, CNRS, UMR 5239, Inserm, U1293, Universite Claude Bernard Lyon 1, 46 allee d’Italie, Lyon F-69364, France
- Equipe Labellisee Ligue Contre le Cancer, 4 allee d'Italie, Lyon 69007, France
| | - Audrey Lapendry
- Laboratoire de Biologie et Modelisation de la Cellule, Ecole Normale Superieure de Lyon, CNRS, UMR 5239, Inserm, U1293, Universite Claude Bernard Lyon 1, 46 allee d’Italie, Lyon F-69364, France
- Equipe Labellisee Ligue Contre le Cancer, 4 allee d'Italie, Lyon 69007, France
| | - Valentine Clerc
- Laboratoire de Biologie et Modelisation de la Cellule, Ecole Normale Superieure de Lyon, CNRS, UMR 5239, Inserm, U1293, Universite Claude Bernard Lyon 1, 46 allee d’Italie, Lyon F-69364, France
- Equipe Labellisee Ligue Contre le Cancer, 4 allee d'Italie, Lyon 69007, France
| | - Stéphane Janczarski
- Laboratoire de Biologie et Modelisation de la Cellule, Ecole Normale Superieure de Lyon, CNRS, UMR 5239, Inserm, U1293, Universite Claude Bernard Lyon 1, 46 allee d’Italie, Lyon F-69364, France
| | - Franck Mortreux
- Laboratoire de Biologie et Modelisation de la Cellule, Ecole Normale Superieure de Lyon, CNRS, UMR 5239, Inserm, U1293, Universite Claude Bernard Lyon 1, 46 allee d’Italie, Lyon F-69364, France
- Equipe Labellisee Ligue Contre le Cancer, 4 allee d'Italie, Lyon 69007, France
| | - Didier Auboeuf
- Laboratoire de Biologie et Modelisation de la Cellule, Ecole Normale Superieure de Lyon, CNRS, UMR 5239, Inserm, U1293, Universite Claude Bernard Lyon 1, 46 allee d’Italie, Lyon F-69364, France
- Equipe Labellisee Ligue Contre le Cancer, 4 allee d'Italie, Lyon 69007, France
| | - Cyril F Bourgeois
- Laboratoire de Biologie et Modelisation de la Cellule, Ecole Normale Superieure de Lyon, CNRS, UMR 5239, Inserm, U1293, Universite Claude Bernard Lyon 1, 46 allee d’Italie, Lyon F-69364, France
- Equipe Labellisee Ligue Contre le Cancer, 4 allee d'Italie, Lyon 69007, France
- CECS/AFM, I-STEM, 28 rue Henri Desbrueres, Corbeil-Essonnes F-91100, France
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18
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Li WJ, Huang Y, Lin YA, Zhang BD, Li MY, Zou YQ, Hu GS, He YH, Yang JJ, Xie BL, Huang HH, Deng X, Liu W. Targeting PRMT1-mediated SRSF1 methylation to suppress oncogenic exon inclusion events and breast tumorigenesis. Cell Rep 2023; 42:113385. [PMID: 37938975 DOI: 10.1016/j.celrep.2023.113385] [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: 01/14/2023] [Revised: 08/10/2023] [Accepted: 10/23/2023] [Indexed: 11/10/2023] Open
Abstract
PRMT1 plays a vital role in breast tumorigenesis; however, the underlying molecular mechanisms remain incompletely understood. Herein, we show that PRMT1 plays a critical role in RNA alternative splicing, with a preference for exon inclusion. PRMT1 methylome profiling identifies that PRMT1 methylates the splicing factor SRSF1, which is critical for SRSF1 phosphorylation, SRSF1 binding with RNA, and exon inclusion. In breast tumors, PRMT1 overexpression is associated with increased SRSF1 arginine methylation and aberrant exon inclusion, which are critical for breast cancer cell growth. In addition, we identify a selective PRMT1 inhibitor, iPRMT1, which potently inhibits PRMT1-mediated SRSF1 methylation, exon inclusion, and breast cancer cell growth. Combination treatment with iPRMT1 and inhibitors targeting SRSF1 phosphorylation exhibits an additive effect of suppressing breast cancer cell growth. In conclusion, our study dissects a mechanism underlying PRMT1-mediated RNA alternative splicing. Thus, PRMT1 has great potential as a therapeutic target in breast cancer treatment.
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Affiliation(s)
- Wen-Juan Li
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian, China; Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian, China; Xiang An Biomedicine Laboratory, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China
| | - Ying Huang
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian, China; Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian, China; Xiang An Biomedicine Laboratory, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China
| | - Yi-An Lin
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian, China; Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian, China; Xiang An Biomedicine Laboratory, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China
| | - Bao-Ding Zhang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian, China
| | - Mei-Yan Li
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian, China; Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian, China; Xiang An Biomedicine Laboratory, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China
| | - Yi-Qin Zou
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian, China; Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian, China; Xiang An Biomedicine Laboratory, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China
| | - Guo-Sheng Hu
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian, China; Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian, China; Xiang An Biomedicine Laboratory, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China
| | - Yao-Hui He
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian, China; Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian, China; Xiang An Biomedicine Laboratory, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China
| | - Jing-Jing Yang
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian, China; Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian, China; Xiang An Biomedicine Laboratory, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China
| | - Bing-Lan Xie
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian, China; Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian, China
| | - Hai-Hua Huang
- Department of Pathology, The Second Affiliated Hospital, Shantou University Medical College, Shantou, Guangdong, China
| | - Xianming Deng
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian, China.
| | - Wen Liu
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian, China; Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian, China; Xiang An Biomedicine Laboratory, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China.
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19
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Du Y, Cao L, Wang S, Guo L, Tan L, Liu H, Feng Y, Wu W. Differences in alternative splicing and their potential underlying factors between animals and plants. J Adv Res 2023:S2090-1232(23)00354-5. [PMID: 37981087 DOI: 10.1016/j.jare.2023.11.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Revised: 08/16/2023] [Accepted: 11/14/2023] [Indexed: 11/21/2023] Open
Abstract
BACKGROUND Alternative splicing (AS), a posttranscriptional process, contributes to the complexity of transcripts from a limited number of genes in a genome, and AS is considered a great source of genetic and phenotypic diversity in eukaryotes. In animals, AS is tightly regulated during the processes of cell growth and differentiation, and its dysregulation is involved in many diseases, including cancers. Likewise, in plants, AS occurs in all stages of plant growth and development, and it seems to play important roles in the rapid reprogramming of genes in response to environmental stressors. To date, the prevalence and functional roles of AS have been extensively reviewed in animals and plants. However, AS differences between animals and plants, especially their underlying molecular mechanisms and impact factors, are anecdotal and rarely reviewed. AIM OF REVIEW This review aims to broaden our understanding of AS roles in a variety of biological processes and provide insights into the underlying mechanisms and impact factors likely leading to AS differences between animals and plants. KEY SCIENTIFIC CONCEPTS OF REVIEW We briefly summarize the roles of AS regulation in physiological and biochemical activities in animals and plants. Then, we underline the differences in the process of AS between plants and animals and especially analyze the potential impact factors, such as gene exon/intron architecture, 5'/3' untranslated regions (UTRs), spliceosome components, chromatin dynamics and transcription speeds, splicing factors [serine/arginine-rich (SR) proteins and heterogeneous nuclear ribonucleoproteins (hnRNPs)], noncoding RNAs, and environmental stimuli, which might lead to the differences. Moreover, we compare the nonsense-mediated mRNA decay (NMD)-mediated turnover of the transcripts with a premature termination codon (PTC) in animals and plants. Finally, we summarize the current AS knowledge published in animals versus plants and discuss the potential development of disease therapies and superior crops in the future.
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Affiliation(s)
- Yunfei Du
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, 311300, Hangzhou, China
| | - Lu Cao
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, 311300, Hangzhou, China
| | - Shuo Wang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, 311300, Hangzhou, China
| | - Liangyu Guo
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, 311300, Hangzhou, China
| | - Lingling Tan
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, 311300, Hangzhou, China
| | - Hua Liu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, 311300, Hangzhou, China
| | - Ying Feng
- Key Laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health (SINH), Chinese Academy of Sciences (CAS), Shanghai 200032, China.
| | - Wenwu Wu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, 311300, Hangzhou, China.
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20
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Moursy A, Cléry A, Gerhardy S, Betz KM, Rao S, Mazur J, Campagne S, Beusch I, Duszczyk MM, Robinson MD, Panse VG, Allain FHT. RNA recognition by Npl3p reveals U2 snRNA-binding compatible with a chaperone role during splicing. Nat Commun 2023; 14:7166. [PMID: 37935663 PMCID: PMC10630445 DOI: 10.1038/s41467-023-42962-4] [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: 08/31/2022] [Accepted: 10/27/2023] [Indexed: 11/09/2023] Open
Abstract
The conserved SR-like protein Npl3 promotes splicing of diverse pre-mRNAs. However, the RNA sequence(s) recognized by the RNA Recognition Motifs (RRM1 & RRM2) of Npl3 during the splicing reaction remain elusive. Here, we developed a split-iCRAC approach in yeast to uncover the consensus sequence bound to each RRM. High-resolution NMR structures show that RRM2 recognizes a 5´-GNGG-3´ motif leading to an unusual mille-feuille topology. These structures also reveal how RRM1 preferentially interacts with a CC-dinucleotide upstream of this motif, and how the inter-RRM linker and the region C-terminal to RRM2 contribute to cooperative RNA-binding. Structure-guided functional studies show that Npl3 genetically interacts with U2 snRNP specific factors and we provide evidence that Npl3 melts U2 snRNA stem-loop I, a prerequisite for U2/U6 duplex formation within the catalytic center of the Bact spliceosomal complex. Thus, our findings suggest an unanticipated RNA chaperoning role for Npl3 during spliceosome active site formation.
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Affiliation(s)
- Ahmed Moursy
- Department of Biology, Institute of Biochemistry, ETH Zurich, Switzerland
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Antoine Cléry
- Department of Biology, Institute of Biochemistry, ETH Zurich, Switzerland.
| | - Stefan Gerhardy
- Department of Biology, Institute of Biochemistry, ETH Zurich, Switzerland
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
- Sardona Therapeutics, San Francisco, CA, USA
| | - Katharina M Betz
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Sanjana Rao
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Jarosław Mazur
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Sébastien Campagne
- Department of Biology, Institute of Biochemistry, ETH Zurich, Switzerland
- ARNA laboratory, INSERM U1212, University of Bordeaux, Bordeaux, France
| | - Irene Beusch
- Department of Biology, Institute of Biochemistry, ETH Zurich, Switzerland
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
| | | | - Mark D Robinson
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Vikram Govind Panse
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland.
- Faculty of Science, University of Zurich, Zurich, Switzerland.
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21
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Zhu Z, Huo F, Zhang J, Shan H, Pei D. Crosstalk between m6A modification and alternative splicing during cancer progression. Clin Transl Med 2023; 13:e1460. [PMID: 37850412 PMCID: PMC10583157 DOI: 10.1002/ctm2.1460] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 10/06/2023] [Accepted: 10/11/2023] [Indexed: 10/19/2023] Open
Abstract
Background N6-methyladenosine (m6A), the most prevalent internal mRNA modification in eukaryotes, is added by m6A methyltransferases, removed by m6A demethylases and recognised by m6A-binding proteins. This modification significantly influences carious facets of RNA metabolism and plays a pivotal role in cellular and physiological processes. Main body Pre-mRNA alternative splicing, a process that generates multiple splice isoforms from multi-exon genes, contributes significantly to the protein diversity in mammals. Moreover, the presence of crosstalk between m6A modification and alternative splicing, with m6A modifications on pre-mRNAs exerting regulatory control, has been established. The m6A modification modulates alternative splicing patterns by recruiting specific RNA-binding proteins (RBPs) that regulate alternative splicing or by directly influencing the interaction between RBPs and their target RNAs. Conversely, alternative splicing can impact the deposition or recognition of m6A modification on mRNAs. The integration of m6A modifications has expanded the scope of therapeutic strategies for cancer treatment, while alternative splicing offers novel insights into the mechanistic role of m6A methylation in cancer initiation and progression. Conclusion This review aims to highlight the biological functions of alternative splicing of m6A modification machinery and its implications in tumourigenesis. Furthermore, we discuss the clinical relevance of understanding m6A-dependent alternative splicing in tumour therapies.
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Affiliation(s)
- Zhi‐Man Zhu
- Department of PathologyXuzhou Medical UniversityXuzhouJiangsuChina
| | - Fu‐Chun Huo
- Department of PathologyXuzhou Medical UniversityXuzhouJiangsuChina
| | - Jian Zhang
- Department of Respiratory MedicineSecond Affiliated Hospital of Xuzhou Medical UniversityXuzhouJiangsuChina
| | - Hong‐Jian Shan
- Department of OrthopedicsThe Affiliated Jiangning Hospital with Nanjing Medical UniversityNanjingJiangsuChina
| | - Dong‐Sheng Pei
- Department of PathologyXuzhou Medical UniversityXuzhouJiangsuChina
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22
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Ormazábal A, Carletti MS, Saldaño TE, Gonzalez Buitron M, Marchetti J, Palopoli N, Bateman A. Expanding the repertoire of human tandem repeat RNA-binding proteins. PLoS One 2023; 18:e0290890. [PMID: 37729217 PMCID: PMC10511089 DOI: 10.1371/journal.pone.0290890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 08/15/2023] [Indexed: 09/22/2023] Open
Abstract
Protein regions consisting of arrays of tandem repeats are known to bind other molecular partners, including nucleic acid molecules. Although the interactions between repeat proteins and DNA are already widely explored, studies characterising tandem repeat RNA-binding proteins are lacking. We performed a large-scale analysis of human proteins devoted to expanding the knowledge about tandem repeat proteins experimentally reported as RNA-binding molecules. This work is timely because of the release of a full set of accurate structural models for the human proteome amenable to repeat detection using structural methods. The main goal of our analysis was to build a comprehensive set of human RNA-binding proteins that contain repeats at the sequence or structure level. Our results showed that the combination of sequence and structural methods finds significantly more tandem repeat proteins than either method alone. We identified 219 tandem repeat proteins that bind RNA molecules and characterised the overlap between repeat regions and RNA-binding regions as a first step towards assessing their functional relationship. We observed differences in the characteristics of repeat regions predicted by sequence-based or structure-based methods in terms of their sequence composition, their functions and their protein domains.
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Affiliation(s)
- Agustín Ormazábal
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, United Kingdom
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Bernal, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas, Godoy Cruz, Buenos Aires, Argentina
| | - Matías Sebastián Carletti
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Bernal, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas, Godoy Cruz, Buenos Aires, Argentina
| | - Tadeo Enrique Saldaño
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Bernal, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas, Godoy Cruz, Buenos Aires, Argentina
- Departamento de Ciencias Básicas, Facultad de Agronomía, Universidad Nacional del Centro de la Provincia de Buenos Aires, Azul, Buenos Aires, Argentina
| | - Martín Gonzalez Buitron
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Bernal, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas, Godoy Cruz, Buenos Aires, Argentina
| | - Julia Marchetti
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Bernal, Buenos Aires, Argentina
| | - Nicolas Palopoli
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Bernal, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas, Godoy Cruz, Buenos Aires, Argentina
| | - Alex Bateman
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, United Kingdom
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23
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Rodriguez Gallo MC, Uhrig RG. Phosphorylation mediated regulation of RNA splicing in plants. FRONTIERS IN PLANT SCIENCE 2023; 14:1249057. [PMID: 37780493 PMCID: PMC10539000 DOI: 10.3389/fpls.2023.1249057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 08/22/2023] [Indexed: 10/03/2023]
Abstract
For the past two decades, the study of alternative splicing (AS) and its involvement in plant development and stress response has grown in popularity. Only recently however, has the focus shifted to the study of how AS regulation (or lack-thereof) affects downstream mRNA and protein landscapes and how these AS regulatory events impact plant development and stress tolerance. In humans, protein phosphorylation represents one of the predominant mechanisms by which AS is regulated and thus the protein kinases governing these phosphorylation events are of interest for further study. Large-scale phosphoproteomic studies in plants have consistently found that RNA splicing-related proteins are extensively phosphorylated, however, the signaling pathways involved in AS regulation have not been resolved. In this mini-review, we summarize our current knowledge of the three major splicing-related protein kinase families in plants that are suggested to mediate AS phospho-regulation and draw comparisons to their metazoan orthologs. We also summarize and contextualize the phosphorylation events identified as occurring on splicing-related protein families to illustrate the high degree to which splicing-related proteins are modified, placing a new focus on elucidating the impacts of AS at the protein and PTM-level.
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Affiliation(s)
| | - R. Glen Uhrig
- University of Alberta, Department of Biological Sciences, Edmonton, AB, Canada
- University of Alberta, Department of Biochemistry, Edmonton, AB, Canada
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24
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Lei WL, Li YY, Du Z, Su R, Meng TG, Ning Y, Hou G, Schatten H, Wang ZB, Han Z, Sun F, Qian WP, Liu C, Sun QY. SRSF1-mediated alternative splicing is required for spermatogenesis. Int J Biol Sci 2023; 19:4883-4897. [PMID: 37781512 PMCID: PMC10539708 DOI: 10.7150/ijbs.83474] [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: 02/12/2023] [Accepted: 08/25/2023] [Indexed: 10/03/2023] Open
Abstract
Alternative splicing (AS) plays significant roles in a multitude of fundamental biological activities. AS is prevalent in the testis, but the regulations of AS in spermatogenesis is only little explored. Here, we report that Serine/arginine-rich splicing factor 1 (SRSF1) plays critical roles in alternative splicing and male reproduction. Male germ cell-specific deletion of Srsf1 led to complete infertility by affecting spermatogenesis. Mechanistically, by combining RNA-seq data with LACE-seq data, we showed that SRSF1 affected the AS of Stra8 in a direct manner and Dazl, Dmc1, Mre11a, Syce2 and Rif1 in an indirect manner. Our findings demonstrate that SRSF1 has crucial functions in spermatogenesis and male fertility by regulating alternative splicing.
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Affiliation(s)
- Wen-Long Lei
- Guangdong and Shenzhen Key Laboratory of Reproductive Medicine and Genetics, The Center of Reproductive Medicine, Peking University Shenzhen Hospital, Shenzhen 518000, China
- Department of Urology & Andrology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310016, China
| | - Yuan-Yuan Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zongchang Du
- School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ruibao Su
- Guangzhou Key Laboratory of Metabolic Diseases and Reproductive Health, Guangdong-Hongkong Metabolism & Reproduction Joint Laboratory, Reproductive Medicine Center, Guangdong Second Provincial General Hospital, Guangzhou, 510317, China
| | - Tie-Gang Meng
- Guangzhou Key Laboratory of Metabolic Diseases and Reproductive Health, Guangdong-Hongkong Metabolism & Reproduction Joint Laboratory, Reproductive Medicine Center, Guangdong Second Provincial General Hospital, Guangzhou, 510317, China
| | - Yan Ning
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Guanmei Hou
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Heide Schatten
- Department of Veterinary Pathobiology, University of Missouri, Columbia, MO 65211, USA
| | - Zhen-Bo Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China
| | - Zhiming Han
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China
| | - Fei Sun
- Department of Urology & Andrology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310016, China
| | - Wei-Ping Qian
- Guangdong and Shenzhen Key Laboratory of Reproductive Medicine and Genetics, The Center of Reproductive Medicine, Peking University Shenzhen Hospital, Shenzhen 518000, China
| | - Chenli Liu
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Qing-Yuan Sun
- Guangzhou Key Laboratory of Metabolic Diseases and Reproductive Health, Guangdong-Hongkong Metabolism & Reproduction Joint Laboratory, Reproductive Medicine Center, Guangdong Second Provincial General Hospital, Guangzhou, 510317, China
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25
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Shenasa H, Bentley DL. Pre-mRNA splicing and its cotranscriptional connections. Trends Genet 2023; 39:672-685. [PMID: 37236814 PMCID: PMC10524715 DOI: 10.1016/j.tig.2023.04.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 04/23/2023] [Accepted: 04/26/2023] [Indexed: 05/28/2023]
Abstract
Transcription of eukaryotic genes by RNA polymerase II (Pol II) yields RNA precursors containing introns that must be spliced out and the flanking exons ligated together. Splicing is catalyzed by a dynamic ribonucleoprotein complex called the spliceosome. Recent evidence has shown that a large fraction of splicing occurs cotranscriptionally as the RNA chain is extruded from Pol II at speeds of up to 5 kb/minute. Splicing is more efficient when it is tethered to the transcription elongation complex, and this linkage permits functional coupling of splicing with transcription. We discuss recent progress that has uncovered a network of connections that link splicing to transcript elongation and other cotranscriptional RNA processing events.
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Affiliation(s)
- Hossein Shenasa
- Department of Biochemistry and Molecular Genetics, RNA Bioscience Initiative, University of Colorado School of Medicine, PO Box 6511, Aurora, CO 80045, USA
| | - David L Bentley
- Department of Biochemistry and Molecular Genetics, RNA Bioscience Initiative, University of Colorado School of Medicine, PO Box 6511, Aurora, CO 80045, USA.
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26
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Cun Y, An S, Zheng H, Lan J, Chen W, Luo W, Yao C, Li X, Huang X, Sun X, Wu Z, Hu Y, Li Z, Zhang S, Wu G, Yang M, Tang M, Yu R, Liao X, Gao G, Zhao W, Wang J, Li J. Specific Regulation of m 6A by SRSF7 Promotes the Progression of Glioblastoma. GENOMICS, PROTEOMICS & BIOINFORMATICS 2023; 21:707-728. [PMID: 34954129 PMCID: PMC10787126 DOI: 10.1016/j.gpb.2021.11.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 11/06/2021] [Accepted: 12/14/2021] [Indexed: 02/07/2023]
Abstract
Serine/arginine-rich splicing factor 7 (SRSF7), a known splicing factor, has been revealed to play oncogenic roles in multiple cancers. However, the mechanisms underlying its oncogenic roles have not been well addressed. Here, based on N6-methyladenosine (m6A) co-methylation network analysis across diverse cell lines, we find that the gene expression of SRSF7 is positively correlated with glioblastoma (GBM) cell-specific m6A methylation. We then indicate that SRSF7 is a novel m6A regulator, which specifically facilitates the m6A methylation near its binding sites on the mRNAs involved in cell proliferation and migration, through recruiting the methyltransferase complex. Moreover, SRSF7 promotes the proliferation and migration of GBM cells largely dependent on the presence of the m6A methyltransferase. The two m6A sites on the mRNA for PDZ-binding kinase (PBK) are regulated by SRSF7 and partially mediate the effects of SRSF7 in GBM cells through recognition by insulin-like growth factor 2 mRNA-binding protein 2 (IGF2BP2). Together, our discovery reveals a novel role of SRSF7 in regulating m6A and validates the presence and functional importance of temporal- and spatial-specific regulation of m6A mediated by RNA-binding proteins (RBPs).
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Affiliation(s)
- Yixian Cun
- Department of Rehabilitation Medicine, Key Laboratory of Liver Disease of Guangdong Province, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China; Department of Biochemistry, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Sanqi An
- Department of Medical Informatics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University, Guangzhou 510080, China; Biosafety Level-3 Laboratory, Life Sciences Institute, Guangxi Medical University, Nanning 530020, China
| | - Haiqing Zheng
- Department of Rehabilitation Medicine, Key Laboratory of Liver Disease of Guangdong Province, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
| | - Jing Lan
- Department of Obstetrics and Gynecology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
| | - Wenfang Chen
- Department of Medical Informatics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University, Guangzhou 510080, China
| | - Wanjun Luo
- Department of Obstetrics and Gynecology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
| | - Chengguo Yao
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University, Guangzhou 510080, China
| | - Xincheng Li
- Department of Rehabilitation Medicine, Key Laboratory of Liver Disease of Guangdong Province, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China; Department of Biochemistry, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Xiang Huang
- Department of Medical Informatics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University, Guangzhou 510080, China
| | - Xiang Sun
- Department of Medical Informatics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University, Guangzhou 510080, China
| | - Zehong Wu
- Department of Medical Informatics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University, Guangzhou 510080, China
| | - Yameng Hu
- Department of Rehabilitation Medicine, Key Laboratory of Liver Disease of Guangdong Province, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China; Department of Biochemistry, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Ziwen Li
- Department of Rehabilitation Medicine, Key Laboratory of Liver Disease of Guangdong Province, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China; Department of Biochemistry, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Shuxia Zhang
- Department of Rehabilitation Medicine, Key Laboratory of Liver Disease of Guangdong Province, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China; Department of Biochemistry, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Geyan Wu
- State Key Laboratory of Oncology in South China, Cancer Center, Sun Yat-sen University, Guangzhou 510080, China
| | - Meisongzhu Yang
- Department of Rehabilitation Medicine, Key Laboratory of Liver Disease of Guangdong Province, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China; Department of Biochemistry, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Miaoling Tang
- State Key Laboratory of Oncology in South China, Cancer Center, Sun Yat-sen University, Guangzhou 510080, China
| | - Ruyuan Yu
- Department of Rehabilitation Medicine, Key Laboratory of Liver Disease of Guangdong Province, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China; Department of Biochemistry, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Xinyi Liao
- Department of Rehabilitation Medicine, Key Laboratory of Liver Disease of Guangdong Province, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China; Department of Biochemistry, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Guicheng Gao
- Department of Medical Informatics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University, Guangzhou 510080, China
| | - Wei Zhao
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University, Guangzhou 510080, China
| | - Jinkai Wang
- Department of Medical Informatics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University, Guangzhou 510080, China; RNA Biomedical Institute, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510080, China.
| | - Jun Li
- Department of Rehabilitation Medicine, Key Laboratory of Liver Disease of Guangdong Province, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China; Department of Biochemistry, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China.
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Yao Z, Liu N, Lin H, Zhou Y. The Role of miR-1183: A Potential Suppressor in Hepatocellular Carcinoma via Regulating Splicing Factor SRSF1. J Hepatocell Carcinoma 2023; 10:1169-1180. [PMID: 37497429 PMCID: PMC10368139 DOI: 10.2147/jhc.s408542] [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: 02/14/2023] [Accepted: 07/07/2023] [Indexed: 07/28/2023] Open
Abstract
Purpose Hepatocellular carcinoma (HCC) is a severe global health problem, causing many deaths of patients all over the world. Serine and arginine-rich splicing factor 1 (SRSF1) functions as an important oncogenic role in tumorigenesis and progression in HCC. Therefore, therapies targeting SRSF1 may provide promising therapeutic approaches. MiRNAs are virtually involved at the post-transcriptional level and bind to 3' untranslated region (3'-UTR) of their target messenger RNA (mRNA) to suppress expression. Methods Quantitative reverse transcription-polymerase chain reaction (qRT-PCR) was used to detect the expression of SRSF1 and miR-1183 in HCC cell lines. CCK8 assay, colony formation assay and wound healing assay were used to detect the function of miR-1183 in HCC cell lines in vitro. Luciferase reporter assay and Western blot were applied to detect the regulation of particular molecules. Xenograft tumor assay was used to detect the function of miR-1183 in HCC cell lines in vivo. Immunohistochemistry (IHC) was used to detect the expression of SRSF1 in HCC tissues and Xenograft tumors. Results In this study, we identified that miR-1183 was downregulated in HCC cell lines. Functional assays indicated that miR-1183-upregulation cells show weakened proliferation ability and migration ability in vitro and inhibit subcutaneous tumor formation in vivo. With respect to the underlying mechanism, we found that miR-1183 function as a tumor suppressor by specifically binding to SRSF1. Conclusion This study is the first to demonstrate that miR-1183 function as an important tumor-suppressing role by binding to the 3'-UTR of SRSF1 mRNA and suppressing its protein level in HCC cells in vitro and in vivo. Further, miR-1183 may be a potential target in the prognosis and treatment of HCC.
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Affiliation(s)
- Zhilu Yao
- Department of Gastroenterology, Jingan District Zhabei Central Hospital, Shanghai, 200072, People’s Republic of China
- Clinical Medical College of Shanghai Tenth People’s Hospital, Nanjing Medical University, Nanjing, Jiangsu, 211166, People’s Republic of China
| | - Ning Liu
- Department of Gastroenterology, Changzhou Maternal and Child Health Hospital, Changzhou, 213004, People’s Republic of China
| | - Hui Lin
- Department of Gastroenterology, Jingan District Zhabei Central Hospital, Shanghai, 200072, People’s Republic of China
| | - Yingqun Zhou
- Clinical Medical College of Shanghai Tenth People’s Hospital, Nanjing Medical University, Nanjing, Jiangsu, 211166, People’s Republic of China
- Department of Gastroenterology, Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai, 200072, People’s Republic of China
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Laloum T, Carvalho SD, Martín G, Richardson DN, Cruz TMD, Carvalho RF, Stecca KL, Kinney AJ, Zeidler M, Barbosa ICR, Duque P. The SCL30a SR protein regulates ABA-dependent seed traits and germination under stress. PLANT, CELL & ENVIRONMENT 2023; 46:2112-2127. [PMID: 37098235 DOI: 10.1111/pce.14593] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 04/03/2023] [Accepted: 04/10/2023] [Indexed: 05/23/2023]
Abstract
SR proteins are conserved RNA-binding proteins best known as splicing regulators that have also been implicated in other steps of gene expression. Despite mounting evidence for a role in plant development and stress responses, the molecular pathways underlying SR protein regulation of these processes remain poorly understood. Here we show that the plant-specific SCL30a SR protein negatively regulates ABA signaling to control seed traits and stress responses during germination in Arabidopsis. Transcriptome-wide analyses revealed that loss of SCL30a function barely affects splicing, but largely induces ABA-responsive gene expression and genes repressed during germination. Accordingly, scl30a mutant seeds display delayed germination and hypersensitivity to ABA and high salinity, while transgenic plants overexpressing SCL30a exhibit reduced ABA and salt stress sensitivity. An ABA biosynthesis inhibitor rescues the enhanced mutant seed stress sensitivity, and epistatic analyses confirm that this hypersensitivity requires a functional ABA pathway. Finally, seed ABA levels are unchanged by altered SCL30a expression, indicating that the gene promotes seed germination under stress by reducing sensitivity to the phytohormone. Our results reveal a new player in ABA-mediated control of early development and stress response.
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Affiliation(s)
- Tom Laloum
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | | | | | | | | | | | - Kevin L Stecca
- Crop Genetics Research and Development, DuPont Experimental Station, Wilmington, Delaware, USA
| | - Anthony J Kinney
- Crop Genetics Research and Development, DuPont Experimental Station, Wilmington, Delaware, USA
| | - Mathias Zeidler
- Institute of Plant Physiology, Justus-Liebig-University Gießen, Gießen, Germany
| | | | - Paula Duque
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
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29
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Wilton J, de Mendonça FL, Pereira-Castro I, Tellier M, Nojima T, Costa AM, Freitas J, Murphy S, Oliveira MJ, Proudfoot NJ, Moreira A. Pro-inflammatory polarization and colorectal cancer modulate alternative and intronic polyadenylation in primary human macrophages. Front Immunol 2023; 14:1182525. [PMID: 37359548 PMCID: PMC10286830 DOI: 10.3389/fimmu.2023.1182525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 05/09/2023] [Indexed: 06/28/2023] Open
Abstract
Introduction Macrophages are essential cells of the immune system that alter their inflammatory profile depending on their microenvironment. Alternative polyadenylation in the 3'UTR (3'UTR-APA) and intronic polyadenylation (IPA) are mechanisms that modulate gene expression, particularly in cancer and activated immune cells. Yet, how polarization and colorectal cancer (CRC) cells affect 3'UTR-APA and IPA in primary human macrophages was unclear. Methods In this study, we isolated primary human monocytes from healthy donors, differentiated and polarized them into a pro-inflammatory state and performed indirect co-cultures with CRC cells. ChrRNA-Seq and 3'RNA-Seq was performed to quantify gene expression and characterize new 3'UTR-APA and IPA mRNA isoforms. Results Our results show that polarization of human macrophages from naïve to a pro-inflammatory state causes a marked increase of proximal polyA site selection in the 3'UTR and IPA events in genes relevant to macrophage functions. Additionally, we found a negative correlation between differential gene expression and IPA during pro-inflammatory polarization of primary human macrophages. As macrophages are abundant immune cells in the CRC microenvironment that either promote or abrogate cancer progression, we investigated how indirect exposure to CRC cells affects macrophage gene expression and 3'UTR-APA and IPA events. Co-culture with CRC cells alters the inflammatory phenotype of macrophages, increases the expression of pro-tumoral genes and induces 3'UTR-APA alterations. Notably, some of these gene expression differences were also found in tumor-associated macrophages of CRC patients, indicating that they are physiologically relevant. Upon macrophage pro-inflammatory polarization, SRSF12 is the pre-mRNA processing gene that is most upregulated. After SRSF12 knockdown in M1 macrophages there is a global downregulation of gene expression, in particular in genes involved in gene expression regulation and in immune responses. Discussion Our results reveal new 3'UTR-APA and IPA mRNA isoforms produced during pro-inflammatory polarization of primary human macrophages and CRC co-culture that may be used in the future as diagnostic or therapeutic tools. Furthermore, our results highlight a function for SRSF12 in pro-inflammatory macrophages, key cells in the tumor response.
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Affiliation(s)
- Joana Wilton
- Graduate Program in Areas of Basic and Applied Biology (GABBA) PhD Program, ICBAS-Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
- Gene Regulation - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IBMC-Instituto de Biologia Molecular e Celular Universidade do Porto, Porto, Portugal
| | - Filipa Lopes de Mendonça
- Gene Regulation - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IBMC-Instituto de Biologia Molecular e Celular Universidade do Porto, Porto, Portugal
| | - Isabel Pereira-Castro
- Gene Regulation - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IBMC-Instituto de Biologia Molecular e Celular Universidade do Porto, Porto, Portugal
| | - Michael Tellier
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Takayuki Nojima
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Angela M. Costa
- Tumour and Microenvironment Interactions Group – Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- INEB-Instituto Nacional de Engenharia Biomédica Universidade do Porto, Porto, Portugal
| | - Jaime Freitas
- Gene Regulation - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Shona Murphy
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Maria Jose Oliveira
- Tumour and Microenvironment Interactions Group – Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- INEB-Instituto Nacional de Engenharia Biomédica Universidade do Porto, Porto, Portugal
- Faculdade de Medicina, Universidade do Porto, Porto, Portugal
- ICBAS- Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
| | | | - Alexandra Moreira
- Gene Regulation - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IBMC-Instituto de Biologia Molecular e Celular Universidade do Porto, Porto, Portugal
- ICBAS- Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
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Schäfer M, Schneider M, Müller T, Franz N, Braspenning-Wesch I, Stephan S, Schmidt G, Krijgsveld J, Helm D, Rösl F, Hasche D. Spatial tissue proteomics reveals distinct landscapes of heterogeneity in cutaneous papillomavirus-induced keratinocyte carcinomas. J Med Virol 2023; 95:e28850. [PMID: 37322807 DOI: 10.1002/jmv.28850] [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: 03/20/2023] [Revised: 05/24/2023] [Accepted: 05/26/2023] [Indexed: 06/17/2023]
Abstract
Infection with certain cutaneous human papillomaviruses (HPV), in conjunction with chronic ultraviolet (UV) exposure, are the major cofactors of non-melanoma skin cancer (NMSC), the most frequent cancer type worldwide. Cutaneous squamous cell carcinomas (SCCs) as well as tumors in general represent three-dimensional entities determined by both temporal and spatial constraints. Whole tissue proteomics is a straightforward approach to understand tumorigenesis in better detail, but studies focusing on different progression states toward a dedifferentiated SCC phenotype on a spatial level are rare. Here, we applied an innovative proteomic workflow on formalin-fixed, paraffin-embedded (FFPE) epithelial tumors derived from the preclinical animal model Mastomys coucha. This rodent is naturally infected with its genuine cutaneous papillomavirus and closely mimics skin carcinogenesis in the context of cutaneous HPV infections in humans. We deciphered cellular networks by comparing diverse epithelial tissues with respect to their differentiation level and infection status. Our study reveals novel regulatory proteins and pathways associated with virus-induced tumor initiation and progression of SCCs. This approach provides the basis to better comprehend the multistep process of skin carcinogenesis.
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Affiliation(s)
- Miriam Schäfer
- Division of Viral Transformation Mechanisms, Research Program "Infection, Inflammation and Cancer", German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Martin Schneider
- Proteomics Core Facility, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Torsten Müller
- Division Proteomics of Stem Cells and Cancer, Research Program "Functional and Structural Genomics", German Cancer Research Center (DKFZ), Heidelberg, Germany
- Heidelberg University, Medical Faculty, Heidelberg, Germany
| | - Natascha Franz
- Division of Viral Transformation Mechanisms, Research Program "Infection, Inflammation and Cancer", German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ilona Braspenning-Wesch
- Division of Viral Transformation Mechanisms, Research Program "Infection, Inflammation and Cancer", German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Sonja Stephan
- Division of Viral Transformation Mechanisms, Research Program "Infection, Inflammation and Cancer", German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Gabriele Schmidt
- Core Facility Unit Light Microscopy, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jeroen Krijgsveld
- Division Proteomics of Stem Cells and Cancer, Research Program "Functional and Structural Genomics", German Cancer Research Center (DKFZ), Heidelberg, Germany
- Heidelberg University, Medical Faculty, Heidelberg, Germany
| | - Dominic Helm
- Proteomics Core Facility, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Frank Rösl
- Division of Viral Transformation Mechanisms, Research Program "Infection, Inflammation and Cancer", German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Daniel Hasche
- Division of Viral Transformation Mechanisms, Research Program "Infection, Inflammation and Cancer", German Cancer Research Center (DKFZ), Heidelberg, Germany
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Razi K, Muneer S. Grafting enhances drought tolerance by regulating and mobilizing proteome, transcriptome and molecular physiology in okra genotypes. FRONTIERS IN PLANT SCIENCE 2023; 14:1178935. [PMID: 37251756 PMCID: PMC10214962 DOI: 10.3389/fpls.2023.1178935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 04/06/2023] [Indexed: 05/31/2023]
Abstract
Drought stress poses a serious concern to the growth, development, and quality of the okra crop due to factors including decreased yield, inadequate development of dietary fibre, increased mite infestation, and decreased seed viability. Grafting is one of the strategies that have been developed to increase the drought stress tolerance of crops. We conducted proteomics, transcriptomics and integrated it with molecular physiology to assess the response of sensitive okra genotypes; NS7772 (G1), Green gold (G2) and OH3312 (G3) (scion) grafted to NS7774 (rootstock). In our studies we observed that sensitive okra genotypes grafted to tolerant genotypes mitigated the deleterious effects of drought stress through an increase in physiochemical parameters, and lowered reactive oxygen species. A comparative proteomic analysis showed a stress responsive proteins related to Photosynthesis, energy and metabolism, defence response, protein and nucleic acid biosynthesis. A proteomic investigation demonstrated that scions grafted onto okra rootstocks increased more photosynthesis-related proteins during drought stress, indicating an increase in photosynthetic activity when plants were subjected to drought stress. Furthermore, transcriptome of RD2, PP2C, HAT22, WRKY and DREB increased significantly, specifically for grafted NS7772 genotype. Furthermore, our study also indicated that grafting improved the yield components such as number of pods and seeds per plant, maximum fruit diameter, and maximum plant height in all genotypes which directly contributed towards their high resistance towards drought stress.
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Affiliation(s)
- Kaukab Razi
- Horticulture and Molecular Physiology Lab, Department of Horticulture and Food Science, School of Agricultural Innovations and Advanced Learning, Vellore Institute of Technology, Tamil Nadu, Vellore, India
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Sowbiya Muneer
- Horticulture and Molecular Physiology Lab, Department of Horticulture and Food Science, School of Agricultural Innovations and Advanced Learning, Vellore Institute of Technology, Tamil Nadu, Vellore, India
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Kumar K, Sinha SK, Maity U, Kirti PB, Kumar KRR. Insights into established and emerging roles of SR protein family in plants and animals. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1763. [PMID: 36131558 DOI: 10.1002/wrna.1763] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 08/11/2022] [Accepted: 08/22/2022] [Indexed: 05/13/2023]
Abstract
Splicing of pre-mRNA is an essential part of eukaryotic gene expression. Serine-/arginine-rich (SR) proteins are highly conserved RNA-binding proteins present in all metazoans and plants. SR proteins are involved in constitutive and alternative splicing, thereby regulating the transcriptome and proteome diversity in the organism. In addition to their role in splicing, SR proteins are also involved in mRNA export, nonsense-mediated mRNA decay, mRNA stability, and translation. Due to their pivotal roles in mRNA metabolism, SR proteins play essential roles in normal growth and development. Hence, any misregulation of this set of proteins causes developmental defects in both plants and animals. SR proteins from the animal kingdom are extensively studied for their canonical and noncanonical functions. Compared with the animal kingdom, plant genomes harbor more SR protein-encoding genes and greater diversity of SR proteins, which are probably evolved for plant-specific functions. Evidence from both plants and animals confirms the essential role of SR proteins as regulators of gene expression influencing cellular processes, developmental stages, and disease conditions. This article is categorized under: RNA Processing > Splicing Mechanisms RNA Processing > Splicing Regulation/Alternative Splicing.
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Affiliation(s)
- Kundan Kumar
- Department of Biotechnology, Indira Gandhi National Tribal University (IGNTU), Amarkantak, India
| | - Shubham Kumar Sinha
- Department of Biotechnology, Indira Gandhi National Tribal University (IGNTU), Amarkantak, India
| | - Upasana Maity
- Department of Biotechnology, Indira Gandhi National Tribal University (IGNTU), Amarkantak, India
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Xue J, Ma T, Zhang X. TRA2: The dominant power of alternative splicing in tumors. Heliyon 2023; 9:e15516. [PMID: 37151663 PMCID: PMC10161706 DOI: 10.1016/j.heliyon.2023.e15516] [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: 01/06/2023] [Revised: 03/30/2023] [Accepted: 04/12/2023] [Indexed: 05/09/2023] Open
Abstract
The dysregulation of alternative splicing (AS) is frequently found in cancer and considered as key markers for cancer progression and therapy. Transformer 2 (TRA2), a nuclear RNA binding protein, consists of transformer 2 alpha homolog (TRA2A) and transformer 2 beta homolog (TRA2B), and plays a role in the regulation of pre-mRNA splicing. Growing evidence has been provided that TRA2A and TRA2B are dysregulated in several types of tumors, and participate in the regulation of proliferation, migration, invasion, and chemotherapy resistance in cancer cells through alteration of AS of cancer-related genes. In this review, we highlight the role of TRA2 in tumorigenesis and metastasis, and discuss potential molecular mechanisms how TRA2 influences tumorigenesis and metastasis via controlling AS of pre-mRNA. We propose that TRA2Ais a novel biomarker and therapeutic target for cancer progression and therapy.
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Affiliation(s)
- Jiancheng Xue
- Medical Research Center, Shengjing Hospital of China Medical University, Shenyang, China
- Key Laboratory of Research and Application of Animal Model for Environmental and Metabolic Diseases, Shenyang, China
| | - Tie Ma
- Department of Pathology, Shengjing Hospital of China Medical University, Shenyang, China
- Corresponding author.
| | - Xiaowen Zhang
- Medical Research Center, Shengjing Hospital of China Medical University, Shenyang, China
- Key Laboratory of Research and Application of Animal Model for Environmental and Metabolic Diseases, Shenyang, China
- Corresponding author. Medical Research Center, Shengjing Hospital of China Medical University, #36 Sanhao Street, Heping District, Shenyang, 110004, China.
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Boumpas P, Merabet S, Carnesecchi J. Integrating transcription and splicing into cell fate: Transcription factors on the block. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1752. [PMID: 35899407 DOI: 10.1002/wrna.1752] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 06/22/2022] [Accepted: 07/01/2022] [Indexed: 11/10/2022]
Abstract
Transcription factors (TFs) are present in all life forms and conserved across great evolutionary distances in eukaryotes. From yeast to complex multicellular organisms, they are pivotal players of cell fate decision by orchestrating gene expression at diverse molecular layers. Notably, TFs fine-tune gene expression by coordinating RNA fate at both the expression and splicing levels. They regulate alternative splicing, an essential mechanism for cell plasticity, allowing the production of many mRNA and protein isoforms in precise cell and tissue contexts. Despite this apparent role in splicing, how TFs integrate transcription and splicing to ultimately orchestrate diverse cell functions and cell fate decisions remains puzzling. We depict substantial studies in various model organisms underlining the key role of TFs in alternative splicing for promoting tissue-specific functions and cell fate. Furthermore, we emphasize recent advances describing the molecular link between the transcriptional and splicing activities of TFs. As TFs can bind both DNA and/or RNA to regulate transcription and splicing, we further discuss their flexibility and compatibility for DNA and RNA substrates. Finally, we propose several models integrating transcription and splicing activities of TFs in the coordination and diversification of cell and tissue identities. This article is categorized under: RNA Processing > Splicing Regulation/Alternative Splicing RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications RNA Processing > Splicing Mechanisms.
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Affiliation(s)
- Panagiotis Boumpas
- Institut de Génomique Fonctionnelle de Lyon, UMR5242, Ecole Normale Supérieure de Lyon, Centre National de la Recherche Scientifique, Université Claude Bernard-Lyon 1, Lyon, France
| | - Samir Merabet
- Institut de Génomique Fonctionnelle de Lyon, UMR5242, Ecole Normale Supérieure de Lyon, Centre National de la Recherche Scientifique, Université Claude Bernard-Lyon 1, Lyon, France
| | - Julie Carnesecchi
- Institut de Génomique Fonctionnelle de Lyon, UMR5242, Ecole Normale Supérieure de Lyon, Centre National de la Recherche Scientifique, Université Claude Bernard-Lyon 1, Lyon, France
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Abstract
Dysregulated RNA splicing is a molecular feature that characterizes almost all tumour types. Cancer-associated splicing alterations arise from both recurrent mutations and altered expression of trans-acting factors governing splicing catalysis and regulation. Cancer-associated splicing dysregulation can promote tumorigenesis via diverse mechanisms, contributing to increased cell proliferation, decreased apoptosis, enhanced migration and metastatic potential, resistance to chemotherapy and evasion of immune surveillance. Recent studies have identified specific cancer-associated isoforms that play critical roles in cancer cell transformation and growth and demonstrated the therapeutic benefits of correcting or otherwise antagonizing such cancer-associated mRNA isoforms. Clinical-grade small molecules that modulate or inhibit RNA splicing have similarly been developed as promising anticancer therapeutics. Here, we review splicing alterations characteristic of cancer cell transcriptomes, dysregulated splicing's contributions to tumour initiation and progression, and existing and emerging approaches for targeting splicing for cancer therapy. Finally, we discuss the outstanding questions and challenges that must be addressed to translate these findings into the clinic.
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Affiliation(s)
- Robert K Bradley
- Computational Biology Program, Public Health Sciences Division and Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.
| | - Olga Anczuków
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.
- Department of Genetics and Genome Sciences, UConn Health, Farmington, CT, USA.
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Bhowmick S, Ahmed M, Filippov A, Loaiza LC, Shah FU, Johansson P. Ambient temperature liquid salt electrolytes. Chem Commun (Camb) 2023; 59:2620-2623. [PMID: 36757288 DOI: 10.1039/d3cc00318c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Alkali metal salts usually have high melting points due to strong electrostatic interactions and solvents are needed to create ambient temperature liquid electrolytes. Here, we report on six phosphate-anion-based alkali metal salts, Li/Na/K, all of which are liquids at room temperature, with glass transition temperatures ranging from -61 to -29 °C, and are thermally stable up to at least 225 °C. While the focus herein is on various physico-chemical properties, these salts also exhibit high anodic stabilities, up to 6 V vs. M/M+ (M = Li/Na/K), and deliver some battery performance - at elevated temperatures as there are severe viscosity limitations at room-temperature. While the battery performance arguably is sub-par, solvent-free electrolytes based on alkali metal salts such as these should pave the way for conceptually different Li/Na/K-batteries, either by refined anion design or by using several salts to create eutectic mixtures.
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Affiliation(s)
- Sourav Bhowmick
- Chemistry of Interfaces, Luleå University of Technology, SE-971 87 Luleå, Sweden.
| | - Mukhtiar Ahmed
- Chemistry of Interfaces, Luleå University of Technology, SE-971 87 Luleå, Sweden.
| | - Andrei Filippov
- Chemistry of Interfaces, Luleå University of Technology, SE-971 87 Luleå, Sweden.
| | - Laura C Loaiza
- Department of Physics, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden.
| | - Faiz Ullah Shah
- Chemistry of Interfaces, Luleå University of Technology, SE-971 87 Luleå, Sweden.
| | - Patrik Johansson
- Department of Physics, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden. .,ALISTORE-European Research Institute, CNRS FR 3104, Hub de l'Energie, 80039 Amiens, France
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Novel roles of RNA-binding proteins in drug resistance of breast cancer: from molecular biology to targeting therapeutics. Cell Death Discov 2023; 9:52. [PMID: 36759501 PMCID: PMC9911762 DOI: 10.1038/s41420-023-01352-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 01/25/2023] [Accepted: 01/30/2023] [Indexed: 02/11/2023] Open
Abstract
Therapy resistance remains a huge challenge for current breast cancer treatments. Exploring molecular mechanisms of therapy resistance might provide therapeutic targets for patients with advanced breast cancer and improve their prognosis. RNA-binding proteins (RBPs) play an important role in regulating therapy resistance. Here we summarize the functions of RBPs, highlight their tremendously important roles in regulating therapy sensitivity and resistance and we also reveal current therapeutic approaches reversing abnormal functions of RBPs in breast cancer.
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Arif W, Mathur B, Saikali MF, Chembazhi UV, Toohill K, Song YJ, Hao Q, Karimi S, Blue SM, Yee BA, Van Nostrand EL, Bangru S, Guzman G, Yeo GW, Prasanth KV, Anakk S, Cummins CL, Kalsotra A. Splicing factor SRSF1 deficiency in the liver triggers NASH-like pathology and cell death. Nat Commun 2023; 14:551. [PMID: 36759613 PMCID: PMC9911759 DOI: 10.1038/s41467-023-35932-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 01/09/2023] [Indexed: 02/11/2023] Open
Abstract
Regulation of RNA processing contributes profoundly to tissue development and physiology. Here, we report that serine-arginine-rich splicing factor 1 (SRSF1) is essential for hepatocyte function and survival. Although SRSF1 is mainly known for its many roles in mRNA metabolism, it is also crucial for maintaining genome stability. We show that acute liver damage in the setting of targeted SRSF1 deletion in mice is associated with the excessive formation of deleterious RNA-DNA hybrids (R-loops), which induce DNA damage. Combining hepatocyte-specific transcriptome, proteome, and RNA binding analyses, we demonstrate that widespread genotoxic stress following SRSF1 depletion results in global inhibition of mRNA transcription and protein synthesis, leading to impaired metabolism and trafficking of lipids. Lipid accumulation in SRSF1-deficient hepatocytes is followed by necroptotic cell death, inflammation, and fibrosis, resulting in NASH-like liver pathology. Importantly, SRSF1-depleted human liver cancer cells recapitulate this pathogenesis, illustrating a conserved and fundamental role for SRSF1 in preserving genome integrity and tissue homeostasis. Thus, our study uncovers how the accumulation of detrimental R-loops impedes hepatocellular gene expression, triggering metabolic derangements and liver damage.
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Affiliation(s)
- Waqar Arif
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL, USA
- College of Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Bhoomika Mathur
- Department of Molecular and Integrative Physiology, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Michael F Saikali
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, Canada
| | - Ullas V Chembazhi
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Katelyn Toohill
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - You Jin Song
- Department of Cell and Developmental Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Qinyu Hao
- Department of Cell and Developmental Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Saman Karimi
- Department of Pathology, College of Medicine, Cancer Center, University of Illinois Hospital and Health Science Chicago, Chicago, IL, USA
| | - Steven M Blue
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California at San Diego, La Jolla, CA, USA
| | - Brian A Yee
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California at San Diego, La Jolla, CA, USA
| | - Eric L Van Nostrand
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California at San Diego, La Jolla, CA, USA
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Sushant Bangru
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Cancer Center @ Illinois, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Grace Guzman
- Department of Pathology, College of Medicine, Cancer Center, University of Illinois Hospital and Health Science Chicago, Chicago, IL, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California at San Diego, La Jolla, CA, USA
| | - Kannanganattu V Prasanth
- Department of Cell and Developmental Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Cancer Center @ Illinois, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Sayeepriyadarshini Anakk
- Department of Molecular and Integrative Physiology, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Cancer Center @ Illinois, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Carolyn L Cummins
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, Canada
| | - Auinash Kalsotra
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL, USA.
- Cancer Center @ Illinois, University of Illinois Urbana-Champaign, Urbana, IL, USA.
- Carl R. Woese Institute of Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA.
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Qiu J, Ma L, Wang T, Chen J, Wang D, Guo Y, Li Y, Ma X, Chen G, Luo Y, Cheng X, Xu L. Bioinformatic analysis of single-cell RNA sequencing dataset dissects cellular heterogeneity of triple-negative breast cancer in transcriptional profile, splicing event and crosstalk network. CLINICAL & TRANSLATIONAL ONCOLOGY : OFFICIAL PUBLICATION OF THE FEDERATION OF SPANISH ONCOLOGY SOCIETIES AND OF THE NATIONAL CANCER INSTITUTE OF MEXICO 2023; 25:1856-1868. [PMID: 36692641 DOI: 10.1007/s12094-023-03083-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Accepted: 01/09/2023] [Indexed: 01/25/2023]
Abstract
BACKGROUND Triple-negative breast cancer (TNBC) is a subtype of breast cancer with high tumoral heterogeneity, while the detailed regulatory network is not well known. METHODS Via single-cell RNA-sequencing (scRNA-seq) data analysis, we comprehensively investigated the transcriptional profile of different subtypes of TNBC epithelial cells with gene regulatory network (GRN) and alternative splicing (AS) event analysis, as well as the crosstalk between epithelial and non-epithelial cells. RESULTS Of note, we found that luminal progenitor subtype exhibited the most complex GRN and splicing events. Besides, hnRNPs negatively regulates AS events in luminal progenitor subtype. In addition, we explored the cellular crosstalk among endothelial cells, stromal cells and immune cells in TNBC and discovered that NOTCH4 was a key receptor and prognostic marker in endothelial cells, which provide potential biomarker and target for TNBC intervention. CONCLUSIONS In summary, our study elaborates on the cellular heterogeneity of TNBC, revealing that NOTCH4 in endothelial cells was critical for TNBC intervention. This in-depth understanding of epithelial cell and non-epithelial cell network would provide theoretical basis for the development of new drugs targeting this sophisticated network in TNBC.
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Affiliation(s)
- Jin Qiu
- Department of Oncology, Shanghai Chest Hospital, Shanghai Jiaotong University, Shanghai, 200030, China
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Lu Ma
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Tingting Wang
- Department of Anaesthesia, Changning Maternity and Infant Health Hospital, East China Normal University, Shanghai, 200050, China
| | - Juntong Chen
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Dongmei Wang
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Yuhan Guo
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Yin Li
- Department of Oncology, Shanghai Chest Hospital, Shanghai Jiaotong University, Shanghai, 200030, China
| | - Xinran Ma
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China
- Department of Anaesthesia, Changning Maternity and Infant Health Hospital, East China Normal University, Shanghai, 200050, China
- Chongqing Key Laboratory of Precision Optics, Chongqing Institute of East China Normal University, Chongqing, 401120, China
| | - Geng Chen
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Ying Luo
- Prenatal Diagnosis Center, Department of Clinical Laboratory, Changning Maternity and Infant Health Hospital, East China Normal University, Shanghai, 200050, China.
| | - Xinghua Cheng
- Department of Oncology, Shanghai Chest Hospital, Shanghai Jiaotong University, Shanghai, 200030, China.
| | - Lingyan Xu
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China.
- Department of Anaesthesia, Changning Maternity and Infant Health Hospital, East China Normal University, Shanghai, 200050, China.
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Wagner AR, Weindel CG, West KO, Scott HM, Watson RO, Patrick KL. SRSF6 balances mitochondrial-driven innate immune outcomes through alternative splicing of BAX. eLife 2022; 11:e82244. [PMID: 36409059 PMCID: PMC9718523 DOI: 10.7554/elife.82244] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 11/20/2022] [Indexed: 11/23/2022] Open
Abstract
To mount a protective response to infection while preventing hyperinflammation, gene expression in innate immune cells must be tightly regulated. Despite the importance of pre-mRNA splicing in shaping the proteome, its role in balancing immune outcomes remains understudied. Transcriptomic analysis of murine macrophage cell lines identified Serine/Arginine Rich Splicing factor 6 (SRSF6) as a gatekeeper of mitochondrial homeostasis. SRSF6-dependent orchestration of mitochondrial health is directed in large part by alternative splicing of the pro-apoptosis pore-forming protein BAX. Loss of SRSF6 promotes accumulation of BAX-κ, a variant that sensitizes macrophages to undergo cell death and triggers upregulation of interferon stimulated genes through cGAS sensing of cytosolic mitochondrial DNA. Upon pathogen sensing, macrophages regulate SRSF6 expression to control the liberation of immunogenic mtDNA and adjust the threshold for entry into programmed cell death. This work defines BAX alternative splicing by SRSF6 as a critical node not only in mitochondrial homeostasis but also in the macrophage's response to pathogens.
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Affiliation(s)
- Allison R Wagner
- Department of Microbial Pathogenesis and Immunology, Texas A&M Health, School of MedicineBryanUnited States
| | - Chi G Weindel
- Department of Microbial Pathogenesis and Immunology, Texas A&M Health, School of MedicineBryanUnited States
| | - Kelsi O West
- Department of Microbial Pathogenesis and Immunology, Texas A&M Health, School of MedicineBryanUnited States
| | - Haley M Scott
- Department of Microbial Pathogenesis and Immunology, Texas A&M Health, School of MedicineBryanUnited States
| | - Robert O Watson
- Department of Microbial Pathogenesis and Immunology, Texas A&M Health, School of MedicineBryanUnited States
| | - Kristin L Patrick
- Department of Microbial Pathogenesis and Immunology, Texas A&M Health, School of MedicineBryanUnited States
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Urbanski L, Brugiolo M, Park S, Angarola BL, Leclair NK, Yurieva M, Palmer P, Sahu SK, Anczuków O. MYC regulates a pan-cancer network of co-expressed oncogenic splicing factors. Cell Rep 2022; 41:111704. [DOI: 10.1016/j.celrep.2022.111704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 05/16/2022] [Accepted: 11/01/2022] [Indexed: 11/23/2022] Open
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Sequences and proteins that influence mRNA processing in Trypanosoma brucei: Evolutionary conservation of SR-domain and PTB protein functions. PLoS Negl Trop Dis 2022; 16:e0010876. [PMID: 36288402 PMCID: PMC9639853 DOI: 10.1371/journal.pntd.0010876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 11/07/2022] [Accepted: 10/07/2022] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND Spliced leader trans splicing is the addition of a short, capped sequence to the 5' end of mRNAs. It is widespread in eukaryotic evolution, but factors that influence trans splicing acceptor site choice have been little investigated. In Kinetoplastids, all protein-coding mRNAs are 5' trans spliced. A polypyrimidine tract is usually found upstream of the AG splice acceptor, but there is no branch point consensus; moreover, splicing dictates polyadenylation of the preceding mRNA, which is a validated drug target. METHODOLOGY AND PRINCIPAL FINDINGS We here describe a trans splicing reporter system that can be used for studies and screens concerning the roles of sequences and proteins in processing site choice and efficiency. Splicing was poor with poly(U) tracts less than 9 nt long, and was influenced by an intergenic region secondary structure. A screen for signals resulted in selection of sequences that were on average 45% U and 35% C. Tethering of either the splicing factor SF1, or the cleavage and polyadenylation factor CPSF3 within the intron stimulated processing in the correct positions, while tethering of two possible homologues of Opisthokont PTB inhibited processing. In contrast, tethering of SR-domain proteins RBSR1, RBSR2, or TSR1 or its interaction partner TSR1IP, promoted use of alternative signals upstream of the tethering sites. RBSR1 interacts predominantly with proteins implicated in splicing, whereas the interactome of RBSR2 is more diverse. CONCLUSIONS Our selectable constructs are suitable for screens of both sequences, and proteins that affect mRNA processing in T. brucei. Our results suggest that the functions of PTB and SR-domain proteins in splice site definition may already have been present in the last eukaryotic common ancestor.
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Bishola Tshitenge T, Clayton C. The Trypanosoma brucei RNA-binding protein DRBD18 ensures correct mRNA trans splicing and polyadenylation patterns. RNA (NEW YORK, N.Y.) 2022; 28:1239-1262. [PMID: 35793904 PMCID: PMC9380746 DOI: 10.1261/rna.079258.122] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 06/23/2022] [Indexed: 06/15/2023]
Abstract
The parasite Trypanosoma brucei grows as bloodstream forms in mammals, and as procyclic forms in tsetse flies. Transcription is polycistronic, all mRNAs are trans spliced, and polyadenylation sites are defined by downstream splicing signals. Expression regulation therefore depends heavily on post-transcriptional mechanisms. The RNA-binding protein DRBD18 was previously implicated in the export of some mRNAs from the nucleus in procyclic forms. It copurifies the outer ring of the nuclear pore, mRNA export factors and exon-junction-complex proteins. We show that for more than 200 mRNAs, DRBD18 depletion caused preferential accumulation of versions with shortened 3'-untranslated regions, arising from use of polyadenylation sites that were either undetectable or rarely seen in nondepleted cells. The shortened mRNAs were often, but not always, more abundant in depleted cells than the corresponding longer versions in normal cells. Their appearance was linked to the appearance of trans-spliced, polyadenylated RNAs containing only downstream 3'-untranslated region-derived sequences. Experiments with one mRNA suggested that nuclear retention alone, through depletion of MEX67, did not affect mRNA length, suggesting a specific effect of DRBD18 on processing. DRBD18-bound mRNAs were enriched in polypyrimidine tract motifs, and DRBD18 was found in both the nucleus and the cytoplasm. We therefore suggest that in the nucleus, DRBD18 might bind to polypyrimidine tracts in 3'-UTRs of mRNA precursors. Such binding might both prevent recognition of mRNA-internal polypyrimidine tracts by splicing factors, and promote export of the processed bound mRNAs to the cytosol.
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Affiliation(s)
| | - Christine Clayton
- Heidelberg University Center for Molecular Biology (ZMBH), D69120 Heidelberg, Germany
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Dahal S, Clayton K, Been T, Fernet-Brochu R, Ocando AV, Balachandran A, Poirier M, Maldonado RK, Shkreta L, Boligan KF, Guvenc F, Rahman F, Branch D, Bell B, Chabot B, Gray-Owen SD, Parent LJ, Cochrane A. Opposing roles of CLK SR kinases in controlling HIV-1 gene expression and latency. Retrovirology 2022; 19:18. [PMID: 35986377 PMCID: PMC9389714 DOI: 10.1186/s12977-022-00605-4] [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: 03/17/2022] [Accepted: 07/29/2022] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The generation of over 69 spliced HIV-1 mRNAs from one primary transcript by alternative RNA splicing emphasizes the central role that RNA processing plays in HIV-1 replication. Control is mediated in part through the action of host SR proteins whose activity is regulated by multiple SR kinases (CLK1-4, SRPKs). METHODS Both shRNA depletion and small molecule inhibitors of host SR kinases were used in T cell lines and primary cells to evaluate the role of these factors in the regulation of HIV-1 gene expression. Effects on virus expression were assessed using western blotting, RT-qPCR, and immunofluorescence. RESULTS The studies demonstrate that SR kinases play distinct roles; depletion of CLK1 enhanced HIV-1 gene expression, reduction of CLK2 or SRPK1 suppressed it, whereas CLK3 depletion had a modest impact. The opposing effects of CLK1 vs. CLK2 depletion were due to action at distinct steps; reduction of CLK1 increased HIV-1 promoter activity while depletion of CLK2 affected steps after transcript initiation. Reduced CLK1 expression also enhanced the response to several latency reversing agents, in part, by increasing the frequency of responding cells, consistent with a role in regulating provirus latency. To determine whether small molecule modulation of SR kinase function could be used to control HIV-1 replication, we screened a GSK library of protein kinase inhibitors (PKIS) and identified several pyrazolo[1,5-b] pyridazine derivatives that suppress HIV-1 gene expression/replication with an EC50 ~ 50 nM. The compounds suppressed HIV-1 protein and viral RNA accumulation with minimal impact on cell viability, inhibiting CLK1 and CLK2 but not CLK3 function, thereby selectively altering the abundance of individual CLK and SR proteins in cells. CONCLUSIONS These findings demonstrate the unique roles played by individual SR kinases in regulating HIV-1 gene expression, validating the targeting of these functions to either enhance latency reversal, essential for "Kick-and-Kill" strategies, or to silence HIV protein expression for "Block-and-Lock" strategies.
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Affiliation(s)
- Subha Dahal
- grid.17063.330000 0001 2157 2938Dept. of Molecular Genetics, University of Toronto, 1 King’s College Circle, Toronto, ON M5S1A8 Canada
| | - Kiera Clayton
- grid.168645.80000 0001 0742 0364Department of Pathology, University of Massachusetts Medical School, Worcester, MA 01605 USA
| | - Terek Been
- grid.17063.330000 0001 2157 2938Dept. of Molecular Genetics, University of Toronto, 1 King’s College Circle, Toronto, ON M5S1A8 Canada
| | - Raphaële Fernet-Brochu
- grid.17063.330000 0001 2157 2938Dept. of Molecular Genetics, University of Toronto, 1 King’s College Circle, Toronto, ON M5S1A8 Canada
| | - Alonso Villasmil Ocando
- grid.461656.60000 0004 0489 3491Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139 USA
| | - Ahalya Balachandran
- grid.17063.330000 0001 2157 2938Dept. of Molecular Genetics, University of Toronto, 1 King’s College Circle, Toronto, ON M5S1A8 Canada
| | - Mikaël Poirier
- grid.86715.3d0000 0000 9064 6198Dept. of Microbiology & Infectious Diseases, Université de Sherbrooke, Sherbrooke, QC Canada
| | - Rebecca Kaddis Maldonado
- grid.240473.60000 0004 0543 9901Department of Medicine, Penn State College of Medicine, Hershey, PA 17033 USA ,grid.240473.60000 0004 0543 9901Microbiology & Immunology, Penn State College of Medicine, Hershey, PA 17033 USA
| | - Lulzim Shkreta
- grid.86715.3d0000 0000 9064 6198Dept. of Microbiology & Infectious Diseases, Université de Sherbrooke, Sherbrooke, QC Canada
| | - Kayluz Frias Boligan
- grid.423370.10000 0001 0285 1288Center for Innovation, Canadian Blood Services, Toronto, ON Canada
| | - Furkan Guvenc
- grid.17063.330000 0001 2157 2938Dept. of Molecular Genetics, University of Toronto, 1 King’s College Circle, Toronto, ON M5S1A8 Canada
| | - Fariha Rahman
- grid.17063.330000 0001 2157 2938Dept. of Molecular Genetics, University of Toronto, 1 King’s College Circle, Toronto, ON M5S1A8 Canada
| | - Donald Branch
- grid.423370.10000 0001 0285 1288Center for Innovation, Canadian Blood Services, Toronto, ON Canada
| | - Brendan Bell
- grid.86715.3d0000 0000 9064 6198Dept. of Microbiology & Infectious Diseases, Université de Sherbrooke, Sherbrooke, QC Canada
| | - Benoit Chabot
- grid.86715.3d0000 0000 9064 6198Dept. of Microbiology & Infectious Diseases, Université de Sherbrooke, Sherbrooke, QC Canada
| | - Scott D. Gray-Owen
- grid.17063.330000 0001 2157 2938Dept. of Molecular Genetics, University of Toronto, 1 King’s College Circle, Toronto, ON M5S1A8 Canada
| | - Leslie J. Parent
- grid.240473.60000 0004 0543 9901Department of Medicine, Penn State College of Medicine, Hershey, PA 17033 USA ,grid.240473.60000 0004 0543 9901Microbiology & Immunology, Penn State College of Medicine, Hershey, PA 17033 USA
| | - Alan Cochrane
- grid.17063.330000 0001 2157 2938Dept. of Molecular Genetics, University of Toronto, 1 King’s College Circle, Toronto, ON M5S1A8 Canada
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A critical update on the strategies towards small molecule inhibitors targeting Serine/arginine-rich (SR) proteins and Serine/arginine-rich proteins related kinases in alternative splicing. Bioorg Med Chem 2022; 70:116921. [PMID: 35863237 DOI: 10.1016/j.bmc.2022.116921] [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: 04/21/2022] [Revised: 07/01/2022] [Accepted: 07/06/2022] [Indexed: 11/02/2022]
Abstract
>90% of genes in the human body undergo alternative splicing (AS) after transcription, which enriches protein species and regulates protein levels. However, there is growing evidence that various genetic isoforms resulting from dysregulated alternative splicing are prevalent in various types of cancers. Dysregulated alternative splicing leads to cancer generation and maintenance of cancer properties such as proliferation differentiation, apoptosis inhibition, invasion metastasis, and angiogenesis. Serine/arginine-rich proteins and SR protein-associated kinases mediate splice site recognition and splice complex assembly during variable splicing. Based on the impact of dysregulated alternative splicing on disease onset and progression, the search for small molecule inhibitors targeting alternative splicing is imminent. In this review, we discuss the structure and specific biological functions of SR proteins and describe the regulation of SR protein function by SR protein related kinases meticulously, which are closely related to the occurrence and development of various types of cancers. On this basis, we summarize the reported small molecule inhibitors targeting SR proteins and SR protein related kinases from the perspective of medicinal chemistry. We mainly categorize small molecule inhibitors from four aspects, including targeting SR proteins, targeting Serine/arginine-rich protein-specific kinases (SRPKs), targeting Cdc2-like kinases (CLKs) and targeting dual-specificity tyrosine-regulated kinases (DYRKs), in terms of structure, inhibition target, specific mechanism of action, biological activity, and applicable diseases. With this review, we are expected to provide a timely summary of recent advances in alternative splicing regulated by kinases and a preliminary introduction to relevant small molecule inhibitors.
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Wu J, Ni X, Yu Z, Wu S, Liu Z. CRNDE inducing cisplatin resistance through SRSF1/TIA1 signaling pathway in ovarian cancer. Pathol Res Pract 2022; 235:153957. [DOI: 10.1016/j.prp.2022.153957] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 05/13/2022] [Accepted: 05/25/2022] [Indexed: 01/04/2023]
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The Rice Serine/Arginine Splicing Factor RS33 Regulates Pre-mRNA Splicing during Abiotic Stress Responses. Cells 2022; 11:cells11111796. [PMID: 35681491 PMCID: PMC9180459 DOI: 10.3390/cells11111796] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 04/27/2022] [Accepted: 05/07/2022] [Indexed: 02/06/2023] Open
Abstract
Abiotic stresses profoundly affect plant growth and development and limit crop productivity. Pre-mRNA splicing is a major form of gene regulation that helps plants cope with various stresses. Serine/arginine (SR)-rich splicing factors play a key role in pre-mRNA splicing to regulate different biological processes under stress conditions. Alternative splicing (AS) of SR transcripts and other transcripts of stress-responsive genes generates multiple splice isoforms that contribute to protein diversity, modulate gene expression, and affect plant stress tolerance. Here, we investigated the function of the plant-specific SR protein RS33 in regulating pre-mRNA splicing and abiotic stress responses in rice. The loss-of-function mutant rs33 showed increased sensitivity to salt and low-temperature stresses. Genome-wide analyses of gene expression and splicing in wild-type and rs33 seedlings subjected to these stresses identified multiple splice isoforms of stress-responsive genes whose AS are regulated by RS33. The number of RS33-regulated genes was much higher under low-temperature stress than under salt stress. Our results suggest that the plant-specific splicing factor RS33 plays a crucial role during plant responses to abiotic stresses.
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Stanley RF, Abdel-Wahab O. Dysregulation and therapeutic targeting of RNA splicing in cancer. NATURE CANCER 2022; 3:536-546. [PMID: 35624337 PMCID: PMC9551392 DOI: 10.1038/s43018-022-00384-z] [Citation(s) in RCA: 58] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 04/22/2022] [Indexed: 05/15/2023]
Abstract
High-throughput sequencing and functional characterization of the cancer transcriptome have uncovered cancer-specific dysregulation of RNA splicing across a variety of cancers. Alterations in the cancer genome and dysregulation of RNA splicing factors lead to missplicing, splicing alteration-dependent gene expression and, in some cases, generation of novel splicing-derived proteins. Here, we review recent advances in our understanding of aberrant splicing in cancer pathogenesis and present strategies to harness cancer-specific aberrant splicing for therapeutic intent.
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Affiliation(s)
- Robert F Stanley
- Human Oncology and Pathogenesis Program and Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Omar Abdel-Wahab
- Human Oncology and Pathogenesis Program and Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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Glushkevich A, Spechenkova N, Fesenko I, Knyazev A, Samarskaya V, Kalinina NO, Taliansky M, Love AJ. Transcriptomic Reprogramming, Alternative Splicing and RNA Methylation in Potato ( Solanum tuberosum L.) Plants in Response to Potato Virus Y Infection. PLANTS (BASEL, SWITZERLAND) 2022; 11:635. [PMID: 35270104 PMCID: PMC8912425 DOI: 10.3390/plants11050635] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 02/09/2022] [Accepted: 02/22/2022] [Indexed: 05/05/2023]
Abstract
Plant-virus interactions are greatly influenced by environmental factors such as temperatures. In virus-infected plants, enhanced temperature is frequently associated with more severe symptoms and higher virus content. However, the mechanisms involved in controlling the temperature regulation of plant-virus interactions are poorly characterised. To elucidate these further, we analysed the responses of potato plants cv Chicago to infection by potato virus Y (PVY) at normal (22 °C) and elevated temperature (28 °C), the latter of which is known to significantly increase plant susceptibility to PVY. Using RNAseq analysis, we showed that single and combined PVY and heat-stress treatments caused dramatic changes in gene expression, affecting the transcription of both protein-coding and non-coding RNAs. Among the newly identified genes responsive to PVY infection, we found genes encoding enzymes involved in the catalysis of polyamine formation and poly ADP-ribosylation. We also identified a range of novel non-coding RNAs which were differentially produced in response to single or combined PVY and heat stress, that consisted of antisense RNAs and RNAs with miRNA binding sites. Finally, to gain more insights into the potential role of alternative splicing and epitranscriptomic RNA methylation during combined stress conditions, direct RNA nanopore sequencing was performed. Our findings offer insights for future studies of functional links between virus infections and transcriptome reprogramming, RNA methylation and alternative splicing.
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Affiliation(s)
- Anna Glushkevich
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia; (A.G.); (N.S.); (I.F.); (A.K.); (V.S.)
| | - Nadezhda Spechenkova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia; (A.G.); (N.S.); (I.F.); (A.K.); (V.S.)
| | - Igor Fesenko
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia; (A.G.); (N.S.); (I.F.); (A.K.); (V.S.)
| | - Andrey Knyazev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia; (A.G.); (N.S.); (I.F.); (A.K.); (V.S.)
| | - Viktoriya Samarskaya
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia; (A.G.); (N.S.); (I.F.); (A.K.); (V.S.)
| | - Natalia O. Kalinina
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia;
| | - Michael Taliansky
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia; (A.G.); (N.S.); (I.F.); (A.K.); (V.S.)
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Andrew J. Love
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
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Habib EB, Mathavarajah S, Dellaire G. Tinker, Tailor, Tumour Suppressor: The Many Functions of PRP4K. Front Genet 2022; 13:839963. [PMID: 35281802 PMCID: PMC8912934 DOI: 10.3389/fgene.2022.839963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 01/28/2022] [Indexed: 11/13/2022] Open
Abstract
Pre-mRNA processing factor 4 kinase (PRP4K, also known as PRPF4B) is an essential kinase first identified in the fission yeast Schizosaccharomyces pombe that is evolutionarily conserved from amoebae to animals. During spliceosomal assembly, PRP4K interacts with and phosphorylates PRPF6 and PRPF31 to facilitate the formation of the spliceosome B complex. However, over the past decade additional evidence has emerged that PRP4K has many diverse cellular roles beyond splicing that contribute to tumour suppression and chemotherapeutic responses in mammals. For example, PRP4K appears to play roles in regulating transcription and the spindle assembly checkpoint (SAC), a key pathway in maintaining chromosomes stability and the response of cancer cells to taxane-based chemotherapy. In addition, PRP4K has been revealed to be a haploinsufficient tumour suppressor that promotes aggressive cancer phenotypes when partially depleted. PRP4K is regulated by both the HER2 and estrogen receptor, and its partial loss increases resistance to the taxanes in multiple malignancies including cervical, breast and ovarian cancer. Moreover, ovarian and triple negative breast cancer patients harboring tumours with low PRP4K expression exhibit worse overall survival. The depletion of PRP4K also enhances both Yap and epidermal growth factor receptor (EGFR) signaling, the latter promoting anoikis resistance in breast and ovarian cancer. Finally, PRP4K is negatively regulated during epithelial-to-mesenchymal transition (EMT), a process that promotes increased cell motility, drug resistance and cancer metastasis. Thus, as we discuss in this review, PRP4K likely plays evolutionarily conserved roles not only in splicing but in a number of cellular pathways that together contribute to tumour suppression.
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Affiliation(s)
- Elias B. Habib
- Dalhousie University, Department of Pathology, Halifax, NS, Canada
| | | | - Graham Dellaire
- Dalhousie University, Department of Pathology, Halifax, NS, Canada
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, Canada
- Beatrice Hunter Cancer Research Institute, Halifax, NS, Canada
- *Correspondence: Graham Dellaire,
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