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Pan F, Zhang R, Liu X, Shi X, Xin Q, Qiao D, Li C, Zhang Y, Chen M, Guo W, Luan S, Shao L. Three exonic variants in the PHEX gene cause aberrant splicing in a minigene assay. Front Genet 2024; 15:1353674. [PMID: 38841723 PMCID: PMC11150636 DOI: 10.3389/fgene.2024.1353674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 04/24/2024] [Indexed: 06/07/2024] Open
Abstract
Background: X-linked hypophosphatemia (XLH, OMIM 307800) is a rare phosphorus metabolism disorder caused by PHEX gene variants. Many variants simply classified as missense or nonsense variants were only analyzed at the DNA level. However, growing evidence indicates that some of these variants may alter pre-mRNA splicing, causing diseases. Therefore, this study aimed to use bioinformatics tools and a minigene assay to ascertain the effects of PHEX variations on pre-mRNA splicing. Methods: We analyzed 174 variants in the PHEX gene described as missense or nonsense variants. Finally, we selected eight candidate variants using bioinformatics tools to evaluate their effects on pre-mRNA splicing using a minigene assay system. The complementary DNA (cDNA) sequence for the PHEX gene (RefSeq NM_000444.6) serves as the basis for DNA variant numbering. Results: Of the eight candidate variants, three were found to cause abnormal splicing. Variants c.617T>G p.(Leu206Trp) and c.621T>A p.(Tyr207*) in exon 5 altered the splicing of pre-mRNA, owing to the activation of a cryptic splice site in exon 5, which produced an aberrant transcript lacking a part of exon 5, whereas variant c.1700G>C p.(Arg567Pro) in exon 16 led to the activation of a cryptic splice site in intron 16, resulting in a partial inclusion of intron 16. Conclusion: Our study employed a minigene system, which has a great degree of flexibility to assess abnormal splicing patterns under the circumstances of patient mRNA samples that are not available, to explore the impact of the exonic variants on pre-mRNA splicing. Based on the aforementioned experimental findings, we demonstrated the importance of analyzing exonic variants at the mRNA level.
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Affiliation(s)
- Fengjiao Pan
- Department of Nephrology, The Affiliated Qingdao Municipal Hospital of Qingdao University, Qingdao, China
| | - Ruixiao Zhang
- Department of Emergency, The Affiliated Qingdao Municipal Hospital of Qingdao University, Qingdao, China
| | - Xuyan Liu
- Department of Nephrology, The Affiliated Qingdao Municipal Hospital of Qingdao University, Qingdao, China
| | - Xiaomeng Shi
- Department of Nephrology, The Affiliated Qingdao Municipal Hospital of Qingdao University, Qingdao, China
| | - Qing Xin
- Department of Nephrology, The Affiliated Qingdao Municipal Hospital of Qingdao University, Qingdao, China
- Department of Nephrology, The Key Laboratory for the Prevention and Treatment of Chronic Kidney Disease of Chongqing, Chongqing Clinical Research Center of Kidney and Urology Diseases, Xinqiao Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Dan Qiao
- Department of Nephrology, Dalian Medical University, Dalian, China
| | - Changying Li
- Department of Nephrology, The Affiliated Qingdao Municipal Hospital of Qingdao University, Qingdao, China
| | - Yan Zhang
- Department of Nephrology, Weifang Medical University, Weifang, China
| | - Mengke Chen
- Department of Nephrology, Liaocheng Third People’s Hospital, Liaocheng, China
| | - Wencong Guo
- Department of Nephrology, The Affiliated Qingdao Municipal Hospital of Qingdao University, Qingdao, China
- Institute of Nephrology, Zhong Da Hospital, Southeast University School of Medicine, Nanjing, China
| | - Shufang Luan
- Department of Medical Insurance Administration, The Affiliated Qingdao Municipal Hospital of Qingdao University, Qingdao, China
| | - Leping Shao
- Department of Nephrology, The Affiliated Qingdao Municipal Hospital of Qingdao University, Qingdao, China
- Department of Nephrology, The First Affiliated Hospital of Xiamen University, Xiamen, China
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2
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Ma HL, Bizet M, Soares Da Costa C, Murisier F, de Bony EJ, Wang MK, Yoshimi A, Lin KT, Riching KM, Wang X, Beckman JI, Arya S, Droin N, Calonne E, Hassabi B, Zhang QY, Li A, Putmans P, Malbec L, Hubert C, Lan J, Mies F, Yang Y, Solary E, Daniels DL, Gupta YK, Deplus R, Abdel-Wahab O, Yang YG, Fuks F. SRSF2 plays an unexpected role as reader of m 5C on mRNA, linking epitranscriptomics to cancer. Mol Cell 2023; 83:4239-4254.e10. [PMID: 38065062 PMCID: PMC11090011 DOI: 10.1016/j.molcel.2023.11.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 09/06/2023] [Accepted: 11/03/2023] [Indexed: 12/18/2023]
Abstract
A common mRNA modification is 5-methylcytosine (m5C), whose role in gene-transcript processing and cancer remains unclear. Here, we identify serine/arginine-rich splicing factor 2 (SRSF2) as a reader of m5C and impaired SRSF2 m5C binding as a potential contributor to leukemogenesis. Structurally, we identify residues involved in m5C recognition and the impact of the prevalent leukemia-associated mutation SRSF2P95H. We show that SRSF2 binding and m5C colocalize within transcripts. Furthermore, knocking down the m5C writer NSUN2 decreases mRNA m5C, reduces SRSF2 binding, and alters RNA splicing. We also show that the SRSF2P95H mutation impairs the ability of the protein to read m5C-marked mRNA, notably reducing its binding to key leukemia-related transcripts in leukemic cells. In leukemia patients, low NSUN2 expression leads to mRNA m5C hypomethylation and, combined with SRSF2P95H, predicts poor outcomes. Altogether, we highlight an unrecognized mechanistic link between epitranscriptomics and a key oncogenesis driver.
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Affiliation(s)
- Hai-Li Ma
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université libre de Bruxelles (ULB), Institut Jules Bordet, Brussels 1070, Belgium
| | - Martin Bizet
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université libre de Bruxelles (ULB), Institut Jules Bordet, Brussels 1070, Belgium
| | - Christelle Soares Da Costa
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université libre de Bruxelles (ULB), Institut Jules Bordet, Brussels 1070, Belgium
| | - Frédéric Murisier
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université libre de Bruxelles (ULB), Institut Jules Bordet, Brussels 1070, Belgium
| | - Eric James de Bony
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université libre de Bruxelles (ULB), Institut Jules Bordet, Brussels 1070, Belgium
| | - Meng-Ke Wang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics and Chinese Academy of Sciences, China National Center for Bioinformation, Beijing 100101, China
| | - Akihide Yoshimi
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Kuan-Ting Lin
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | | | - Xing Wang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics and Chinese Academy of Sciences, China National Center for Bioinformation, Beijing 100101, China
| | - John I Beckman
- Greehey Children's Cancer Research Institute, Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Shailee Arya
- Greehey Children's Cancer Research Institute, Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Nathalie Droin
- Université Paris-Saclay, INSERM U1287, and Department of Hematology, Gustave Roussy Cancer Center, Villejuif 94800, France
| | - Emilie Calonne
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université libre de Bruxelles (ULB), Institut Jules Bordet, Brussels 1070, Belgium
| | - Bouchra Hassabi
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université libre de Bruxelles (ULB), Institut Jules Bordet, Brussels 1070, Belgium
| | - Qing-Yang Zhang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics and Chinese Academy of Sciences, China National Center for Bioinformation, Beijing 100101, China
| | - Ang Li
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics and Chinese Academy of Sciences, China National Center for Bioinformation, Beijing 100101, China
| | - Pascale Putmans
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université libre de Bruxelles (ULB), Institut Jules Bordet, Brussels 1070, Belgium
| | - Lionel Malbec
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université libre de Bruxelles (ULB), Institut Jules Bordet, Brussels 1070, Belgium
| | - Céline Hubert
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université libre de Bruxelles (ULB), Institut Jules Bordet, Brussels 1070, Belgium
| | - Jie Lan
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université libre de Bruxelles (ULB), Institut Jules Bordet, Brussels 1070, Belgium
| | - Frédérique Mies
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université libre de Bruxelles (ULB), Institut Jules Bordet, Brussels 1070, Belgium
| | - Ying Yang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics and Chinese Academy of Sciences, China National Center for Bioinformation, Beijing 100101, China
| | - Eric Solary
- Université Paris-Saclay, INSERM U1287, and Department of Hematology, Gustave Roussy Cancer Center, Villejuif 94800, France
| | | | - Yogesh K Gupta
- Greehey Children's Cancer Research Institute, Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Rachel Deplus
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université libre de Bruxelles (ULB), Institut Jules Bordet, Brussels 1070, Belgium
| | - Omar Abdel-Wahab
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Yun-Gui Yang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics and Chinese Academy of Sciences, China National Center for Bioinformation, Beijing 100101, China.
| | - François Fuks
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université libre de Bruxelles (ULB), Institut Jules Bordet, Brussels 1070, Belgium.
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3
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Rayani K, Davies B, Cheung M, Comber D, Roberts JD, Tadros R, Green MS, Healey JS, Simpson CS, Sanatani S, Steinberg C, MacIntyre C, Angaran P, Duff H, Hamilton R, Arbour L, Leather R, Seifer C, Fournier A, Atallah J, Kimber S, Makanjee B, Alqarawi W, Cadrin-Tourigny J, Joza J, Gardner M, Talajic M, Bagnall RD, Krahn AD, Laksman ZWM. Identification and in-silico characterization of splice-site variants from a large cardiogenetic national registry. Eur J Hum Genet 2023; 31:512-520. [PMID: 36138163 PMCID: PMC10172209 DOI: 10.1038/s41431-022-01193-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Revised: 08/23/2022] [Accepted: 09/08/2022] [Indexed: 11/08/2022] Open
Abstract
Splice-site variants in cardiac genes may predispose carriers to potentially lethal arrhythmias. To investigate, we screened 1315 probands and first-degree relatives enrolled in the Canadian Hearts in Rhythm Organization (HiRO) registry. 10% (134/1315) of patients in the HiRO registry carry variants within 10 base-pairs of the intron-exon boundary with 78% (104/134) otherwise genotype negative. These 134 probands were carriers of 57 unique variants. For each variant, American College of Medical Genetics and Genomics (ACMG) classification was revisited based on consensus between nine in silico tools. Due in part to the in silico algorithms, seven variants were reclassified from the original report, with the majority (6/7) downgraded. Our analyses predicted 53% (30/57) of variants to be likely/pathogenic. For the 57 variants, an average of 9 tools were able to score variants within splice sites, while 6.5 tools responded for variants outside these sites. With likely/pathogenic classification considered a positive outcome, the ACMG classification was used to calculate sensitivity/specificity of each tool. Among these, Combined Annotation Dependent Depletion (CADD) had good sensitivity (93%) and the highest response rate (131/134, 98%), dbscSNV was also sensitive (97%), and SpliceAI was the most specific (64%) tool. Splice variants remain an important consideration in gene elusive inherited arrhythmia syndromes. Screening for intronic variants, even when restricted to the ±10 positions as performed here may improve genetic testing yield. We compare 9 freely available in silico tools and provide recommendations regarding their predictive capabilities. Moreover, we highlight several novel cardiomyopathy-associated variants which merit further study.
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Affiliation(s)
- Kaveh Rayani
- Center for Cardiovascular Innovation, Division of Cardiology, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Brianna Davies
- Center for Cardiovascular Innovation, Division of Cardiology, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Matthew Cheung
- Center for Cardiovascular Innovation, Division of Cardiology, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Drake Comber
- Center for Cardiovascular Innovation, Division of Cardiology, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Jason D Roberts
- Section of Cardiac Electrophysiology, Division of Cardiology, Department of Medicine, Western University, London, ON, Canada
| | - Rafik Tadros
- Cardiovascular Genetics Center, Montreal Heart Institute, Montreal, QC, Canada
- Department of Medicine, Universite de Montreal, Montreal, QC, Canada
| | - Martin S Green
- Heart Institute, University of Ottawa, Ottawa, ON, Canada
| | | | | | | | - Christian Steinberg
- Institut Universitaire de Cardiologie et Pneumologie de Quebec, Laval University, Quebec City, QC, Canada
| | - Ciorsti MacIntyre
- Division of Cardiology, QEII Health Sciences Center, Halifax, NS, Canada
| | - Paul Angaran
- St Michael's Hospital, University of Toronto, Toronto, ON, Canada
| | - Henry Duff
- Libin Cardiovascular Institute, University of Calgary, Calgary, AB, Canada
| | - Robert Hamilton
- Division of Cardiology, The Hospital for Sick Children (SickKids), Toronto, ON, Canada
| | - Laura Arbour
- Division of Medical Genetics, Island Health, Victoria, BC, Canada
| | | | - Colette Seifer
- Section of Cardiology, Department of Internal Medicine, University of Manitoba, Winnipeg, MB, Canada
| | - Anne Fournier
- Division of Pediatric Cardiology, CHU Sainte-Justine, Universite de Montreal, Montreal, QC, Canada
| | - Joseph Atallah
- Division of Pediatric Cardiology, University of Alberta Stollery Children's Hospital, Edmonton, AB, Canada
| | - Shane Kimber
- Division of Cardiology, Department of Medicine, University of Alberta, Edmonton, AB, Canada
| | - Bhavanesh Makanjee
- Heart Health Institute, Scarborough Health Network, Scarborough, ON, Canada
| | - Wael Alqarawi
- Heart Institute, University of Ottawa, Ottawa, ON, Canada
| | - Julia Cadrin-Tourigny
- Cardiovascular Genetics Center, Montreal Heart Institute, Montreal, QC, Canada
- Department of Medicine, Universite de Montreal, Montreal, QC, Canada
| | - Jacqueline Joza
- Division of Cardiology, McGill University Health Centre, Montreal, QC, Canada
| | - Martin Gardner
- Division of Cardiology, QEII Health Sciences Center, Halifax, NS, Canada
| | - Mario Talajic
- Cardiovascular Genetics Center, Montreal Heart Institute, Montreal, QC, Canada
- Department of Medicine, Universite de Montreal, Montreal, QC, Canada
| | - Richard D Bagnall
- Agnes Ginges Centre for Molecular Cardiology at Centenary Institute, The University of Sydney, Sydney, NSW, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Andrew D Krahn
- Center for Cardiovascular Innovation, Division of Cardiology, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Zachary W M Laksman
- Center for Cardiovascular Innovation, Division of Cardiology, Department of Medicine, University of British Columbia, Vancouver, BC, Canada.
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4
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Liu L, Lv Z, Wang M, Zhang D, Liu D, Zhu F. HBV Enhances Sorafenib Resistance in Hepatocellular Carcinoma by Reducing Ferroptosis via SRSF2-Mediated Abnormal PCLAF Splicing. Int J Mol Sci 2023; 24:ijms24043263. [PMID: 36834680 PMCID: PMC9967099 DOI: 10.3390/ijms24043263] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 02/02/2023] [Accepted: 02/03/2023] [Indexed: 02/11/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the most lethal human cancers. Hepatitis B virus (HBV) infection accounts for nearly 50% of HCC cases. Recent studies indicate that HBV infection induces resistance to sorafenib, the first-line systemic treatment for advanced HCC for more than a decade, from 2007 to 2020. Our previous research shows that variant 1 (tv1) of proliferating cell nuclear antigen clamp-associated factor (PCLAF), overexpressed in HCC, protects against doxorubicin-induced apoptosis. However, there are no reports on the relevance of PCLAF in sorafenib resistance in HBV-related HCC. In this article, we found that PCLAF levels were higher in HBV-related HCC than in non-virus-related HCC using bioinformatics analysis. Immunohistochemistry (IHC) staining of clinical samples and the splicing reporter minigene assay using HCC cells revealed that PCLAF tv1 was elevated by HBV. Furthermore, HBV promoted the splicing of PCLAF tv1 by downregulating serine/arginine-rich splicing factor 2 (SRSF2), which hindered the inclusion of PCLAF exon 3 through a putative cis-element (116-123), "GATTCCTG". The CCK-8 assay showed that HBV decreased cell susceptibility to sorafenib through SRSF2/PCLAF tv1. HBV reduced ferroptosis by decreasing intracellular Fe2+ levels and activating GPX4 expression via the SRSF2/PCLAF tv1 axis, according to a mechanism study. Suppressed ferroptosis, on the other hand, contributed to HBV-mediated sorafenib resistance through SRSF2/PCLAF tv1. These data suggested that HBV regulated PCLAF abnormal alternative splicing by suppressing SRSF2. HBV caused sorafenib resistance by reducing ferroptosis via the SRSF2/PCLAF tv1 axis. As a result, the SRSF2/PCLAF tv1 axis may be a prospective molecular therapeutic target in HBV-related HCC, as well as a predictor of sorafenib resistance. The inhibition of the SRSF2/PCLAF tv1 axis may be crucial in the emergence of systemic chemotherapy resistance in HBV-associated HCC.
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Affiliation(s)
| | | | | | | | | | - Fan Zhu
- Correspondence: ; Tel.: +86-189-4290-0238
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5
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Jin X, Yan Y, Zhang C, Tai Y, An L, Yu X, Zhang L, Hao S, Cao X, Yin C, Ma X. Identification of novel deep intronic PAH gene variants in patients diagnosed with phenylketonuria. Hum Mutat 2021; 43:56-66. [PMID: 34747549 DOI: 10.1002/humu.24292] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 10/21/2021] [Accepted: 10/28/2021] [Indexed: 12/17/2022]
Abstract
Phenylketonuria (PKU) is caused by phenylalanine hydroxylase (PAH) gene variants. Previously, 94.21% of variants were identified using Sanger sequencing and multiplex ligation-dependent probe amplification. To investigate the remaining variants, we performed whole-genome sequencing for four patients with PKU and unknown genotypes to identify deep intronic or structural variants. We identified three novel heterozygous variants (c.706+368T>C, c.1065+241C>A, and c.1199+502A>T) in a deep PAH gene intron. We detected a c.1199+502A>T variant in 60% (6/10) of PKU patients with genetically undetermined PKU. In silico predictions indicated that the three deep variants may impact splice site selection and result in the inclusion of a pseudo-exon. A c.1199+502A>T PAH minigene and reverse transcription PCR (RT-PCR) on blood RNA from a PKU patient with biallelic variants c.1199+502A>T and c.1199G>A confirmed that the c.1199+502A>T variant may strengthen the predicted branch point and leads to the inclusion of a 25-nt pseudo-exon in the PAH mRNA. Reverse transcription polymerase chain reaction (RT-PCR) on the minigene revealed that c.706+368T>C may create an SRSF2 (SC35) binding site via a 313-nt pseudo-exon, whereas c.1065+241C>A may produce an 81-nt pseudo-exon that strengthens the predicted SRSF1 (SF2/ASF) binding site. These results augment current knowledge of PAH genotypes and show that deep intronic analysis of PAH can genetically diagnose PKU.
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Affiliation(s)
- Xiaohua Jin
- National Research Institute for Family Planning, Beijing, China.,National Human Genetic Resources Center, Beijing, China
| | - Yousheng Yan
- Prenatal Diagnostic Center, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing, China
| | - Chuan Zhang
- National Research Institute for Family Planning, Beijing, China.,National Human Genetic Resources Center, Beijing, China.,Gansu Province Medical Genetics Center, Gansu Provincial Maternity and Child-Care Hospital, Lanzhou, China
| | - Ya Tai
- Department of Obstetrics and Gynecology, Peking University International Hospital, Beijing, China
| | - Lisha An
- National Research Institute for Family Planning, Beijing, China.,National Human Genetic Resources Center, Beijing, China
| | - Xinyou Yu
- Department of Prenatal Diagnosis Center, General Hospital of Ningxia Medical University, Yinchuan, China
| | - Linlin Zhang
- Clinical Lab, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Shengju Hao
- Gansu Province Medical Genetics Center, Gansu Provincial Maternity and Child-Care Hospital, Lanzhou, China
| | - Xiaofang Cao
- National Research Institute for Family Planning, Beijing, China.,National Human Genetic Resources Center, Beijing, China
| | - Chenghong Yin
- Prenatal Diagnostic Center, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing, China
| | - Xu Ma
- National Research Institute for Family Planning, Beijing, China.,National Human Genetic Resources Center, Beijing, China
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Wu W, Syed F, Simpson E, Lee CC, Liu J, Chang G, Dong C, Seitz C, Eizirik DL, Mirmira RG, Liu Y, Evans-Molina C. The Impact of Pro-Inflammatory Cytokines on Alternative Splicing Patterns in Human Islets. Diabetes 2021; 71:db200847. [PMID: 34697029 PMCID: PMC8763875 DOI: 10.2337/db20-0847] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 10/18/2021] [Indexed: 01/05/2023]
Abstract
Alternative splicing (AS) within the β cell has been proposed as one potential pathway that may exacerbate autoimmunity and unveil novel immunogenic epitopes in type 1 diabetes (T1D). We employed a computational strategy to prioritize pathogenic splicing events in human islets treated with IL-1β + IFN-γ as an ex vivo model of T1D and coupled this analysis with a k-mer based approach to predict RNA binding proteins involved in AS. In total, 969 AS events were identified in cytokine-treated islets, with the majority (44.8%) involving a skipped exon. ExonImpact identified 129 events predicted to impact protein structure. AS occurred with high frequency in MHC Class II-related mRNAs, and targeted qPCR validated reduced inclusion of Exon5 in the MHC Class II gene HLA-DMB. Single molecule RNA FISH confirmed increased HLA-DMB splicing in pancreatic sections from human donors with established T1D and autoantibody positivity. Serine and Arginine Rich Splicing Factor 2 was implicated in 37.2% of potentially pathogenic events, including Exon5 exclusion in HLA-DMB. Together, these data suggest that dynamic control of AS plays a role in the β cell response to inflammatory signals during T1D evolution.
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Affiliation(s)
- Wenting Wu
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
- Center for Diabetes and Metabolic Diseases, Indiana University School of Medicine, Indianapolis, Indiana
| | - Farooq Syed
- Center for Diabetes and Metabolic Diseases, Indiana University School of Medicine, Indianapolis, Indiana
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, USA
- Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Edward Simpson
- Department of BioHealth Informatics, Indiana University School of Informatics and Computing, Indianapolis, IN, USA
| | - Chih-Chun Lee
- Center for Diabetes and Metabolic Diseases, Indiana University School of Medicine, Indianapolis, Indiana
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, USA
- Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Jing Liu
- Department of Physics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, USA
| | - Garrick Chang
- Department of Physics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, USA
| | - Chuanpeng Dong
- Department of BioHealth Informatics, Indiana University School of Informatics and Computing, Indianapolis, IN, USA
| | - Clayton Seitz
- Department of Physics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, USA
| | - Decio L Eizirik
- ULB Center for Diabetes Research, Medical Faculty, Universitê Libre de Bruxelles (ULB), Brussels, Belgium
- Indiana Biosciences Research Institute (IBRI), Indianapolis, Indiana, USA
| | - Raghavendra G Mirmira
- Kovler Diabetes Center and Department of Medicine, The University of Chicago, Chicago, IL, USA
| | - Yunlong Liu
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Carmella Evans-Molina
- Center for Diabetes and Metabolic Diseases, Indiana University School of Medicine, Indianapolis, Indiana
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, USA
- Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA
- Richard L. Roudebush VA Medical Center, Indiana University School of Informatics and Computing, Indianapolis, IN, USA
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7
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Li K, Wang Z. Splicing factor SRSF2-centric gene regulation. Int J Biol Sci 2021; 17:1708-1715. [PMID: 33994855 PMCID: PMC8120470 DOI: 10.7150/ijbs.58888] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 04/04/2021] [Indexed: 01/14/2023] Open
Abstract
Serine/arginine-rich splicing factor 2 (SRSF2) is a splicing factor that is widely expressed in a variety of mammalian cell types. Increasing evidence has confirmed that SRSF2 plays vital roles in a number of biological and pathological processes. Therefore, it is important to understand how its expression is regulated, and how it regulates the expression of its target genes. Recently, we found that SRSF2 expression could be upregulated by herpes simplex virus-1 (HSV-1) infection, and that altered SRSF2 expression, in turn, epigenetically regulates the transcription of HSV-1 genes. Further studies on T cell exhaustion demonstrated that upregulated SRSF2 in exhausted T cells elevated the levels of multiple immune checkpoint molecules by associating with the acyl-transferases, P300 and CBP, and by altering histone modification near the transcription start sites of these genes, thereby influencing signal transducer and activator of transcription 3 binding to these gene promoters. These findings suggest that SRSF2 acts as an important sensor and effector during disease progression. Here, we discuss the molecules that regulate SRSF2 gene expression and their associated mechanisms, and the mechanisms via which SRSF2 regulates the expression of target genes, thus providing novel insights into the central role of SRSF2 in gene regulation.
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Affiliation(s)
- Kun Li
- Department of Nuclear Medicine, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Jinan 250014, China
| | - Ziqiang Wang
- Department of Nuclear Medicine, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Jinan 250014, China.,Biomedical Sciences College & Shandong Medicinal Biotechnology Centre, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 250062, China
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SRSF9 Regulates Cassette Exon Splicing of Caspase-2 by Interacting with Its Downstream Exon. Cells 2021; 10:cells10030679. [PMID: 33808656 PMCID: PMC8003524 DOI: 10.3390/cells10030679] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 03/01/2021] [Accepted: 03/16/2021] [Indexed: 11/16/2022] Open
Abstract
Alternative splicing (AS) is an important posttranscriptional regulatory process. Damaged or unnecessary cells need to be removed though apoptosis to maintain physiological processes. Caspase-2 pre-mRNA produces pro-apoptotic long mRNA and anti-apoptotic short mRNA isoforms through AS. How AS of Caspase-2 is regulated remains unclear. In the present study, we identified a novel regulatory protein SRSF9 for AS of Caspase-2 cassette exon 9. Knock-down (KD) of SRSF9 increased inclusion of cassette exon and on the other hand, overexpression of SRSF9 decreased inclusion of this exon. Deletion mutagenesis demonstrated that exon 9, parts of intron 9, exon 8 and exon 10 were not required for the role of SRSF9 in Caspase-2 AS. However, deletion and substitution mutation analysis revealed that AGGAG sequence located at exon 10 provided functional target for SRSF9. In addition, RNA-pulldown mediated immunoblotting analysis showed that SRSF9 interacted with this sequence. Gene ontology analysis of RNA-seq from SRSF9 KD cells demonstrates that SRSF9 could regulate AS of a subset of apoptosis related genes. Collectively, our results reveal a basis for regulation of Caspase-2 AS.
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9
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U2AF65-Dependent SF3B1 Function in SMN Alternative Splicing. Cells 2020; 9:cells9122647. [PMID: 33317029 PMCID: PMC7762998 DOI: 10.3390/cells9122647] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Revised: 12/05/2020] [Accepted: 12/07/2020] [Indexed: 11/17/2022] Open
Abstract
Splicing factor 3b subunit 1 (SF3B1) is an essential protein in spliceosomes and mutated frequently in many cancers. While roles of SF3B1 in single intron splicing and roles of its cancer-linked mutant in aberrant splicing have been identified to some extent, regulatory functions of wild-type SF3B1 in alternative splicing (AS) are not well-understood yet. Here, we applied RNA sequencing (RNA-seq) to analyze genome-wide AS in SF3B1 knockdown (KD) cells and to identify a large number of skipped exons (SEs), with a considerable number of alternative 5′ splice-site selection, alternative 3′ splice-site selection, mutually exclusive exons (MXE), and retention of introns (RI). Among altered SEs by SF3B1 KD, survival motor neuron 2 (SMN2) pre-mRNA exon 7 splicing was a regulatory target of SF3B1. RT-PCR analysis of SMN exon 7 splicing in SF3B1 KD or overexpressed HCT116, SH-SY5Y, HEK293T, and spinal muscular atrophy (SMA) patient cells validated the results. A deletion mutation demonstrated that the U2 snRNP auxiliary factor 65 kDa (U2AF65) interaction domain of SF3B1 was required for its function in SMN exon 7 splicing. In addition, mutations to lower the score of the polypyrimidine tract (PPT) of exon 7, resulting in lower affinity for U2AF65, were not able to support SF3B1 function, suggesting the importance of U2AF65 in SF3B1 function. Furthermore, the PPT of exon 7 with higher affinity to U2AF65 than exon 8 showed significantly stronger interactions with SF3B1. Collectively, our results revealed SF3B1 function in SMN alternative splicing.
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Ghigna C, Paronetto MP. Alternative Splicing: Recent Insights into Mechanisms and Functional Roles. Cells 2020; 9:cells9102327. [PMID: 33092102 PMCID: PMC7589716 DOI: 10.3390/cells9102327] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 10/18/2020] [Indexed: 12/13/2022] Open
Affiliation(s)
- Claudia Ghigna
- Istituto di Genetica Molecolare Luigi Luca Cavalli Sforza—Consiglio Nazionale delle Ricerche, via Abbiategrasso 207, 27100 Pavia, Italy
- Correspondence: (C.G.); (M.P.P.)
| | - Maria Paola Paronetto
- Department of Movement, Human and Health Sciences, University of Rome “Foro Italico”, 00135 Rome, Italy
- Correspondence: (C.G.); (M.P.P.)
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