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Shirguppe S, Gapinske M, Swami D, Gosstola N, Acharya P, Miskalis A, Joulani D, Szkwarek MG, Bhattacharjee A, Elias G, Stilger M, Winter J, Woods WS, Anand D, Lim CKW, Gaj T, Perez-Pinera P. In vivo CRISPR base editing for treatment of Huntington's disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.05.602282. [PMID: 39005280 PMCID: PMC11245100 DOI: 10.1101/2024.07.05.602282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Huntington's disease (HD) is an inherited and ultimately fatal neurodegenerative disorder caused by an expanded polyglutamine-encoding CAG repeat within exon 1 of the huntingtin (HTT) gene, which produces a mutant protein that destroys striatal and cortical neurons. Importantly, a critical event in the pathogenesis of HD is the proteolytic cleavage of the mutant HTT protein by caspase-6, which generates fragments of the N-terminal domain of the protein that form highly toxic aggregates. Given the role that proteolysis of the mutant HTT protein plays in HD, strategies for preventing this process hold potential for treating the disorder. By screening 141 CRISPR base editor variants targeting splice elements in the HTT gene, we identified platforms capable of producing HTT protein isoforms resistant to caspase-6-mediated proteolysis via editing of the splice acceptor sequence for exon 13. When delivered to the striatum of a rodent HD model, these base editors induced efficient exon skipping and decreased the formation of the N-terminal fragments, which in turn reduced HTT protein aggregation and attenuated striatal and cortical atrophy. Collectively, these results illustrate the potential for CRISPR base editing to decrease the toxicity of the mutant HTT protein for HD.
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Morales-Romero B, Muñoz-Pujol G, Artuch R, García-Cazorla A, O'Callaghan M, Sykut-Cegielska J, Campistol J, Moreno-Lozano PJ, Oud MM, Wevers RA, Lefeber DJ, Esteve-Codina A, Yepez VA, Gagneur J, Wortmann SB, Prokisch H, Ribes A, García-Villoria J, Tort F. Genome and RNA sequencing were essential to reveal cryptic intronic variants associated to defective ATP6AP1 mRNA processing. Mol Genet Metab 2024; 142:108511. [PMID: 38878498 DOI: 10.1016/j.ymgme.2024.108511] [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: 02/23/2024] [Revised: 05/28/2024] [Accepted: 05/29/2024] [Indexed: 07/05/2024]
Abstract
The diagnosis of Mendelian disorders has notably advanced with integration of whole exome and genome sequencing (WES and WGS) in clinical practice. However, challenges in variant interpretation and uncovered variants by WES still leave a substantial percentage of patients undiagnosed. In this context, integrating RNA sequencing (RNA-seq) improves diagnostic workflows, particularly for WES inconclusive cases. Additionally, functional studies are often necessary to elucidate the impact of prioritized variants on gene expression and protein function. Our study focused on three unrelated male patients (P1-P3) with ATP6AP1-CDG (congenital disorder of glycosylation), presenting with intellectual disability and varying degrees of hepatopathy, glycosylation defects, and an initially inconclusive diagnosis through WES. Subsequent RNA-seq was pivotal in identifying the underlying genetic causes in P1 and P2, detecting ATP6AP1 underexpression and aberrant splicing. Molecular studies in fibroblasts confirmed these findings and identified the rare intronic variants c.289-233C > T and c.289-289G > A in P1 and P2, respectively. Trio-WGS also revealed the variant c.289-289G > A in P3, which was a de novo change in both patients. Functional assays expressing the mutant alleles in HAP1 cells demonstrated the pathogenic impact of these variants by reproducing the splicing alterations observed in patients. Our study underscores the role of RNA-seq and WGS in enhancing diagnostic rates for genetic diseases such as CDG, providing new insights into ATP6AP1-CDG molecular bases by identifying the first two deep intronic variants in this X-linked gene. Additionally, our study highlights the need to integrate RNA-seq and WGS, followed by functional validation, in routine diagnostics for a comprehensive evaluation of patients with an unidentified molecular etiology.
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Affiliation(s)
- Blai Morales-Romero
- Section of Inborn Errors of Metabolism-IBC, Biochemistry and Molecular Genetics Department, Hospital Clínic de Barcelona, IDIBAPS, CIBERER, ISCIII, Barcelona, Spain.
| | - Gerard Muñoz-Pujol
- Section of Inborn Errors of Metabolism-IBC, Biochemistry and Molecular Genetics Department, Hospital Clínic de Barcelona, IDIBAPS, CIBERER, ISCIII, Barcelona, Spain.
| | - Rafael Artuch
- Clinical Biochemistry Department, Institut de Recerca Sant Joan de Déu, Hospital Sant Joan de Déu, CIBERER, Esplugues de Llobregat, Barcelona, Spain.
| | - Angels García-Cazorla
- Neurology Department, Hospital Sant Joan de Déu, Institut de Recerca Hospital Sant Joan de Déu, CIBERER and MetabERN, Esplugues de Llobregat, Barcelona, Spain.
| | - Mar O'Callaghan
- Neurology Department, Hospital Sant Joan de Déu, Institut de Recerca Hospital Sant Joan de Déu, CIBERER and MetabERN, Esplugues de Llobregat, Barcelona, Spain.
| | - Jolanta Sykut-Cegielska
- Department of Inborn Errors of Metabolism and Pediatrics, Institute of Mother and Child, Warsaw, Poland
| | - Jaume Campistol
- Neurology Department, Hospital Sant Joan de Déu, Institut de Recerca Hospital Sant Joan de Déu, CIBERER and MetabERN, Esplugues de Llobregat, Barcelona, Spain.
| | - Pedro Juan Moreno-Lozano
- Inherited Metabolic Diseases and Muscle Disorders' Research Group, Department of Internal Medicine, Hospital Clinic de Barcelona, IDIBAPS, Faculty of Medicine and Health Sciences, University of Barcelona, Barcelona, Spain.
| | - Machteld M Oud
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands.
| | - Ron A Wevers
- Department of Human Genetics, Translational Metabolic Laboratory (TML), Radboud University Medical Center, Nijmegen, the Netherlands; United for Metabolic Diseases, The Netherlands.
| | - Dirk J Lefeber
- Department of Human Genetics, Translational Metabolic Laboratory (TML), Radboud University Medical Center, Nijmegen, the Netherlands; Department of Neurology, Donders Institute for Brain, Cognition, and Behavior, Radboud University Medical Center, Nijmegen, the Netherlands.
| | - Anna Esteve-Codina
- Centro Nacional de Análisis Genómico (CNAG), Parc Científic de Barcelona, Barcelona, Spain.
| | - Vicente A Yepez
- Institute of Human Genetics, School of Medicine, Technical University of Munich, 81675 Munich, Germany; TUM School of Computation, Information and Technology, Technical University of Munich, 85748 Garching, Germany.
| | - Julien Gagneur
- Institute of Human Genetics, School of Medicine, Technical University of Munich, 81675 Munich, Germany; TUM School of Computation, Information and Technology, Technical University of Munich, 85748 Garching, Germany.
| | - Saskia B Wortmann
- University Children's Hospital Salzburg, Paracelsus Medical University, Salzburg, Austria; Amalia Children's Hospital, Department of Pediatrics, Radboudumc, Nijmegen, the Netherlands.
| | - Holger Prokisch
- Institute of Human Genetics, School of Medicine, Technical University of Munich, 81675 Munich, Germany; Institute of Neurogenomics, Helmholtz Zentrum München, 85764 Neuherberg, Germany.
| | - Antonia Ribes
- Section of Inborn Errors of Metabolism-IBC, Biochemistry and Molecular Genetics Department, Hospital Clínic de Barcelona, IDIBAPS, CIBERER, ISCIII, Barcelona, Spain.
| | - Judit García-Villoria
- Section of Inborn Errors of Metabolism-IBC, Biochemistry and Molecular Genetics Department, Hospital Clínic de Barcelona, IDIBAPS, CIBERER, ISCIII, Barcelona, Spain.
| | - Frederic Tort
- Section of Inborn Errors of Metabolism-IBC, Biochemistry and Molecular Genetics Department, Hospital Clínic de Barcelona, IDIBAPS, CIBERER, ISCIII, Barcelona, Spain.
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3
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Himmelreich N, Ramón-Maiques S, Navarrete R, Castejon-Fernandez N, Garbade SF, Martinez A, Desviat LR, Pérez B, Blau N. Significance of utilizing in silico structural analysis and phenotypic data to characterize phenylalanine hydroxylase variants: A PAH landscape. Mol Genet Metab 2024; 142:108514. [PMID: 38905920 DOI: 10.1016/j.ymgme.2024.108514] [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: 04/27/2024] [Revised: 06/10/2024] [Accepted: 06/12/2024] [Indexed: 06/23/2024]
Abstract
Phenylketonuria (PKU) is a genetic disorder caused by variations in the phenylalanine hydroxylase (PAH) gene. Among the 3369 reported PAH variants, 33.7% are missense alterations. Unfortunately, 30% of these missense variants are classified as variants of unknown significance (VUS), posing challenges for genetic risk assessment. In our study, we focused on analyzing 836 missense PAH variants following the American College of Medical Genetics and Genomics/Association for Molecular Pathology (ACMG/AMP) guidelines specified by ClinGen PAH Variant Curation Expert Panel (VCEP) criteria. We utilized and compared variant annotator tools like Franklin and Varsome, conducted 3D structural analysis of PAH, and examined active and regulatory site hotspots. In addition, we assessed potential splicing effect of apparent missense variants. By evaluating phenotype data from 22962 PKU patients, our aim was to reassess the pathogenicity of missense variants. Our comprehensive approach successfully reclassified 309 VUSs out of 836 missense variants as likely pathogenic or pathogenic (37%), upgraded 370 likely pathogenic variants to pathogenic, and reclassified one previously considered likely benign variant as likely pathogenic. Phenotypic information was available for 636 missense variants, with 441 undergoing 3D structural analysis and active site hotspot identification for 180 variants. After our analysis, only 6% of missense variants were classified as VUSs, and three of them (c.23A>C/p.Asn8Thr, c.59_60delinsCC/p.Gln20Pro, and c.278A >T/p.Asn93Ile) may be influenced by abnormal splicing. Moreover, a pathogenic variant (c.168G>T/p.Glu56Asp) was identified to have a risk exceeding 98% for modifications of the consensus splice site, with high scores indicating a donor loss of 0.94. The integration of ACMG/AMP guidelines with in silico structural analysis and phenotypic data significantly reduced the number of missense VUSs, providing a strong basis for genetic counseling and emphasizing the importance of metabolic phenotype information in variant curation. This study also sheds light on the current landscape of PAH variants.
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Affiliation(s)
- Nastassja Himmelreich
- Dietmar-Hopp Metabolic Center and Centre for Pediatrics and Adolescent Medicine, University Children's Hospital, Heidelberg, Germany
| | - Santiago Ramón-Maiques
- Instituto de Biomedicina de Valencia (IBV), CSIC, Valencia, Spain; Group 739, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER)-Instituto de Salud Carlos III, Valencia, Spain
| | - Rosa Navarrete
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular, CIBERER, IdiPAZ, Universidad Autónoma de Madrid, Madrid, Spain
| | - Natalia Castejon-Fernandez
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular, CIBERER, IdiPAZ, Universidad Autónoma de Madrid, Madrid, Spain
| | - Sven F Garbade
- Dietmar-Hopp Metabolic Center and Centre for Pediatrics and Adolescent Medicine, University Children's Hospital, Heidelberg, Germany
| | - Aurora Martinez
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Lourdes R Desviat
- Centro de Biología Molecular Severo Ochoa UAM-CSIC, CIBERER, IdiPAZ, Universidad Autónoma de Madrid, Madrid, Spain
| | - Belén Pérez
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular, CIBERER, IdiPAZ, Universidad Autónoma de Madrid, Madrid, Spain.
| | - Nenad Blau
- Divisions of Metabolism, University Children's Hospital, Zürich, Switzerland.
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Sundaresan Y, Rivera A, Obolensky A, Gopalakrishnan P, Ohayon Hadad H, Shemesh A, Khateb S, Ross M, Ofri R, Durst S, Newman H, Leibu R, Soudry S, Zur D, Ben-Yosef T, Banin E, Sharon D. Genetic and Clinical Analyses of the KIZ-c.226C>T Variant Resulting in a Dual Mutational Mechanism. Genes (Basel) 2024; 15:804. [PMID: 38927740 PMCID: PMC11202946 DOI: 10.3390/genes15060804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2024] [Revised: 06/11/2024] [Accepted: 06/17/2024] [Indexed: 06/28/2024] Open
Abstract
Retinitis pigmentosa (RP) is a heterogeneous inherited retinal disorder. Mutations in KIZ cause autosomal recessive (AR) RP. We aimed to characterize the genotype, expression pattern, and phenotype in a large cohort of KIZ cases. Sanger and whole exome sequencing were used to identify the KIZ variants. Medical records were reviewed and analyzed. Thirty-one patients with biallelic KIZ mutations were identified: 28 homozygous for c.226C>T (p.R76*), 2 compound heterozygous for p.R76* and c.3G>A (p.M1?), and one homozygous for c.247C>T (p.R83*). c.226C>T is a founder mutation among patients of Jewish descent. The clinical parameters were less severe in KIZ compared to DHDDS and FAM161A cases. RT-PCR analysis in fibroblast cells revealed the presence of four different transcripts in both WT and mutant samples with a lower percentage of the WT transcript in patients. Sequence analysis identified an exonic sequence enhancer (ESE) that includes the c.226 position which is affected by the mutation. KIZ mutations are an uncommon cause of IRD worldwide but are not rare among Ashkenazi Jews. Our data indicate that p.R76* affect an ESE which in turn results in the pronounced skipping of exon 3. Therefore, RNA-based therapies might show low efficacy since the mutant transcripts are spliced.
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Affiliation(s)
- Yogapriya Sundaresan
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel; (Y.S.); (A.R.); (P.G.); (E.B.)
| | - Antonio Rivera
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel; (Y.S.); (A.R.); (P.G.); (E.B.)
| | - Alexey Obolensky
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel; (Y.S.); (A.R.); (P.G.); (E.B.)
| | - Prakadeeswari Gopalakrishnan
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel; (Y.S.); (A.R.); (P.G.); (E.B.)
| | - Hanit Ohayon Hadad
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel; (Y.S.); (A.R.); (P.G.); (E.B.)
| | - Aya Shemesh
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel; (Y.S.); (A.R.); (P.G.); (E.B.)
| | - Samer Khateb
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel; (Y.S.); (A.R.); (P.G.); (E.B.)
| | - Maya Ross
- Koret School of Veterinary Medicine, The Hebrew University of Jerusalem, Rehovot 76100, Israel
| | - Ron Ofri
- Koret School of Veterinary Medicine, The Hebrew University of Jerusalem, Rehovot 76100, Israel
| | - Sharon Durst
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel; (Y.S.); (A.R.); (P.G.); (E.B.)
| | - Hadas Newman
- Ophthalmology Division, Tel Aviv Sourasky Medical Center, Affiliated to Faculty of Medical & Health Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Rina Leibu
- Department of Ophthalmology, Rambam Health Care Center, Haifa 31096, Israel
| | - Shiri Soudry
- Department of Ophthalmology, Rabin Medical Center, Petah Tikva 49100, Israel
| | - Dinah Zur
- Ophthalmology Division, Tel Aviv Sourasky Medical Center, Affiliated to Faculty of Medical & Health Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Tamar Ben-Yosef
- The Ruth & Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa 31096, Israel
| | - Eyal Banin
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel; (Y.S.); (A.R.); (P.G.); (E.B.)
| | - Dror Sharon
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel; (Y.S.); (A.R.); (P.G.); (E.B.)
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5
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van der Smagt JJ, Lampri AP, de Lange I, Alders M, Houben ML, Koudijs MJ, van Jaarsveld RH. Identification of a pathogenic deep intronic variant in ATRX ends a diagnostic odyssey. Eur J Med Genet 2024; 69:104949. [PMID: 38797245 DOI: 10.1016/j.ejmg.2024.104949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 05/16/2024] [Accepted: 05/23/2024] [Indexed: 05/29/2024]
Abstract
Variation in the non-coding genome is being increasingly recognized to be involved in monogenic disease etiology. However, the interpretation of non-coding variation is complicated by a lack of understanding of how non-coding genetic elements function. Additional lines of evidence are therefore needed to recognize non-coding variants as pathogenic. We here present a case where a collective body of evidence resulted in the identification and conclusive classification of a pathogenic deep intronic variant in ATRX. This report demonstrates the utility of a multi-platform approach in aiding the identification of pathogenic variants outside coding regions. Furthermore, it marks the first reported instance of a deep intronic pathogenic variant in ATRX.
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Affiliation(s)
| | - Angeliki P Lampri
- Department of Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Iris de Lange
- Department of Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Mariëlle Alders
- Amsterdam UMC, Department of Human Genetics, Genome Diagnostics Laboratory, Amsterdam Reproduction & Development, University of Amsterdam, Amsterdam, the Netherlands
| | - Michiel L Houben
- Department of Pediatrics, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Marco J Koudijs
- Department of Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
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Trundle J, Lu-Nguyen N, Malerba A, Popplewell L. Targeted Antisense Oligonucleotide-Mediated Skipping of Murine Postn Exon 17 Partially Addresses Fibrosis in D2. mdx Mice. Int J Mol Sci 2024; 25:6113. [PMID: 38892298 PMCID: PMC11172600 DOI: 10.3390/ijms25116113] [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: 04/26/2024] [Revised: 05/28/2024] [Accepted: 05/30/2024] [Indexed: 06/21/2024] Open
Abstract
Periostin, a multifunctional 90 kDa protein, plays a pivotal role in the pathogenesis of fibrosis across various tissues, including skeletal muscle. It operates within the transforming growth factor beta 1 (Tgf-β1) signalling pathway and is upregulated in fibrotic tissue. Alternative splicing of Periostin's C-terminal region leads to six protein-coding isoforms. This study aimed to elucidate the contribution of the isoforms containing the amino acids encoded by exon 17 (e17+ Periostin) to skeletal muscle fibrosis and investigate the therapeutic potential of manipulating exon 17 splicing. We identified distinct structural differences between e17+ Periostin isoforms, affecting their interaction with key fibrotic proteins, including Tgf-β1 and integrin alpha V. In vitro mouse fibroblast experimentation confirmed the TGF-β1-induced upregulation of e17+ Periostin mRNA, mitigated by an antisense approach that induces the skipping of exon 17 of the Postn gene. Subsequent in vivo studies in the D2.mdx mouse model of Duchenne muscular dystrophy (DMD) demonstrated that our antisense treatment effectively reduced e17+ Periostin mRNA expression, which coincided with reduced full-length Periostin protein expression and collagen accumulation. The grip strength of the treated mice was rescued to the wild-type level. These results suggest a pivotal role of e17+ Periostin isoforms in the fibrotic pathology of skeletal muscle and highlight the potential of targeted exon skipping strategies as a promising therapeutic approach for mitigating fibrosis-associated complications.
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MESH Headings
- Animals
- Cell Adhesion Molecules/genetics
- Cell Adhesion Molecules/metabolism
- Mice
- Fibrosis
- Exons
- Mice, Inbred mdx
- Oligonucleotides, Antisense/pharmacology
- Oligonucleotides, Antisense/genetics
- Alternative Splicing
- Muscular Dystrophy, Duchenne/genetics
- Muscular Dystrophy, Duchenne/therapy
- Muscular Dystrophy, Duchenne/metabolism
- Muscular Dystrophy, Duchenne/pathology
- Muscle, Skeletal/metabolism
- Muscle, Skeletal/pathology
- Transforming Growth Factor beta1/metabolism
- Transforming Growth Factor beta1/genetics
- Fibroblasts/metabolism
- Disease Models, Animal
- Protein Isoforms/genetics
- Protein Isoforms/metabolism
- Male
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Affiliation(s)
- Jessica Trundle
- Department of Biological Sciences, School of Life Sciences and Environment, Royal Holloway University of London, Surrey TW20 0EX, UK; (J.T.); (N.L.-N.)
- Developmental Biology and Cancer Research and Teaching Department, University College London Great Ormond Street Institute of Child Health, London WC1N 1EH, UK
| | - Ngoc Lu-Nguyen
- Department of Biological Sciences, School of Life Sciences and Environment, Royal Holloway University of London, Surrey TW20 0EX, UK; (J.T.); (N.L.-N.)
| | - Alberto Malerba
- Department of Biological Sciences, School of Life Sciences and Environment, Royal Holloway University of London, Surrey TW20 0EX, UK; (J.T.); (N.L.-N.)
| | - Linda Popplewell
- Department of Biological Sciences, School of Life Sciences and Environment, Royal Holloway University of London, Surrey TW20 0EX, UK; (J.T.); (N.L.-N.)
- National Horizons Centre, Teesside University, Darlington DL1 1HG, UK
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7
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Peng Q, Cui Y, Wu J, Wu L, Liu J, Han Y, Lu G. A c.726C>G (p.Tyr242Ter) nonsense mutation-associated with splicing alteration (NASA) of WDR45 gene underlies β-propeller protein-associated neurodegeneration (BPAN). Heliyon 2024; 10:e30438. [PMID: 38765101 PMCID: PMC11098806 DOI: 10.1016/j.heliyon.2024.e30438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Revised: 04/24/2024] [Accepted: 04/25/2024] [Indexed: 05/21/2024] Open
Abstract
Neurodegeneration with brain iron accumulation (NBIA) is a clinically and genetically heterogeneous disease characterized by increased iron deposition in the basal ganglia and progressive degeneration of the nervous system in adulthood. However, in early childhood, there were no characteristic features to perform early diagnosis. In our study, a female child exhibited global developmental delay, intellectual disability, and febrile seizure without other distinct clinical phenotypes. Through whole exome sequencing (WES), a de novo nonsense mutation (c.726C > G, p. Tyr242Ter) of WDR45 gene was identified in this child. She was finally diagnosed as β-propeller protein-associated neurodegeneration (BPAN), one of the recently identified subtypes of NBIA. This mutation could act as a premature stop codon (PSC) which rendered the mutated transcripts to be degraded by nonsense-mediated mRNA decay (NMD), leading to decreased levels of PSC-containing mRNAs. Additionally, through mini-gene splicing assays, this mutation could result in an unprecedented novel transcript with the exon 9 of WDR45 excluded by nonsense-associated splicing alteration (NASA). Transcriptome sequencing (RNA-seq) on total RNAs from PBMCs of the trio revealed three types of alternative splicing events in the patient. Further research implied that downregulation of iron transport genes (TFRC, TFR2, SCARA5) might be the underlying mechanism for the iron accumulation in patients with deficient WDR45. This is the first report about NASA happening in WDR45. It implies that nonsense mutations approximal to splicing sites could affect the disease pathogenesis through more than one molecular mechanism and should be taken into consideration when conducting genetic counseling.
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Affiliation(s)
- Qiongling Peng
- Department of Child Healthcare, Shenzhen Bao'an Women's and Children's Hospital, 56 Yulyu Road, Bao'an District, Shenzhen, 518000, China
| | - Ying Cui
- Department of Blood Transfusion, The First Affiliated Hospital of Xi'an Jiaotong University, No. 277 West Yanta Road, Xi'an, 710061, China
| | - Jin Wu
- Laboratory of Translational Medicine Research, Department of Pathology, Affiliated Deyang People's Hospital of Sichuan Traditional Medical University, No. 103 First Section of Taishanbei Road, Jingyang District, Deyang, 618000, China
- Deyang Key Laboratory of Tumor Molecular Research, No. 103 First Section of Taishanbei Road, Jingyang District, Deyang, 618000, China
| | - Lianying Wu
- Laboratory of Translational Medicine Research, Department of Pathology, Affiliated Deyang People's Hospital of Sichuan Traditional Medical University, No. 103 First Section of Taishanbei Road, Jingyang District, Deyang, 618000, China
- Deyang Key Laboratory of Tumor Molecular Research, No. 103 First Section of Taishanbei Road, Jingyang District, Deyang, 618000, China
| | - Jiajia Liu
- Department of Child Healthcare, Shenzhen Bao'an Women's and Children's Hospital, 56 Yulyu Road, Bao'an District, Shenzhen, 518000, China
| | - Yangyun Han
- Sichuan Clinical Medical Research Center for Neurological Diseases, No. 103 First Section of Taishanbei Road, Jingyang District, Deyang, 618000, China
| | - Guanting Lu
- Laboratory of Translational Medicine Research, Department of Pathology, Affiliated Deyang People's Hospital of Sichuan Traditional Medical University, No. 103 First Section of Taishanbei Road, Jingyang District, Deyang, 618000, China
- Deyang Key Laboratory of Tumor Molecular Research, No. 103 First Section of Taishanbei Road, Jingyang District, Deyang, 618000, China
- Sichuan Clinical Medical Research Center for Neurological Diseases, No. 103 First Section of Taishanbei Road, Jingyang District, Deyang, 618000, China
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8
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Santos-Rebouças CB, Ferreira CDS, Nogueira JDS, Brustolini OJ, de Almeida LGP, Gerber AL, Guimarães APDC, Piergiorge RM, Struchiner CJ, Porto LC, de Vasconcelos ATR. Immune response stability to the SARS-CoV-2 mRNA vaccine booster is influenced by differential splicing of HLA genes. Sci Rep 2024; 14:8982. [PMID: 38637586 PMCID: PMC11026523 DOI: 10.1038/s41598-024-59259-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 04/08/2024] [Indexed: 04/20/2024] Open
Abstract
Many molecular mechanisms that lead to the host antibody response to COVID-19 vaccines remain largely unknown. In this study, we used serum antibody detection combined with whole blood RNA-based transcriptome analysis to investigate variability in vaccine response in healthy recipients of a booster (third) dose schedule of the mRNA BNT162b2 vaccine against COVID-19. The cohort was divided into two groups: (1) low-stable individuals, with antibody concentration anti-SARS-CoV IgG S1 below 0.4 percentile at 180 days after boosting vaccination; and (2) high-stable individuals, with antibody values greater than 0.6 percentile of the range in the same period (median 9525 [185-80,000] AU/mL). Differential gene expression, expressed single nucleotide variants and insertions/deletions, differential splicing events, and allelic imbalance were explored to broaden our understanding of the immune response sustenance. Our analysis revealed a differential expression of genes with immunological functions in individuals with low antibody titers, compared to those with higher antibody titers, underscoring the fundamental importance of the innate immune response for boosting immunity. Our findings also provide new insights into the determinants of the immune response variability to the SARS-CoV-2 mRNA vaccine booster, highlighting the significance of differential splicing regulatory mechanisms, mainly concerning HLA alleles, in delineating vaccine immunogenicity.
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Affiliation(s)
- Cíntia Barros Santos-Rebouças
- Department of Genetics, Institute of Biology Roberto Alcantara Gomes, Rio de Janeiro State University, Rio de Janeiro, Brazil
| | - Cristina Dos Santos Ferreira
- Bioinformatics Laboratory-LABINFO, National Laboratory of Scientific Computation LNCC/MCTIC, Getúlio Vargas, Av., 333, Quitandinha, Petrópolis, Rio de Janeiro, 25651‑075, Brazil
| | - Jeane de Souza Nogueira
- Histocompatibility and Cryopreservation Laboratory, Rio de Janeiro State University, Rio de Janeiro, Brazil
| | - Otávio José Brustolini
- Bioinformatics Laboratory-LABINFO, National Laboratory of Scientific Computation LNCC/MCTIC, Getúlio Vargas, Av., 333, Quitandinha, Petrópolis, Rio de Janeiro, 25651‑075, Brazil
| | - Luiz Gonzaga Paula de Almeida
- Bioinformatics Laboratory-LABINFO, National Laboratory of Scientific Computation LNCC/MCTIC, Getúlio Vargas, Av., 333, Quitandinha, Petrópolis, Rio de Janeiro, 25651‑075, Brazil
| | - Alexandra Lehmkuhl Gerber
- Bioinformatics Laboratory-LABINFO, National Laboratory of Scientific Computation LNCC/MCTIC, Getúlio Vargas, Av., 333, Quitandinha, Petrópolis, Rio de Janeiro, 25651‑075, Brazil
| | - Ana Paula de Campos Guimarães
- Bioinformatics Laboratory-LABINFO, National Laboratory of Scientific Computation LNCC/MCTIC, Getúlio Vargas, Av., 333, Quitandinha, Petrópolis, Rio de Janeiro, 25651‑075, Brazil
| | - Rafael Mina Piergiorge
- Department of Genetics, Institute of Biology Roberto Alcantara Gomes, Rio de Janeiro State University, Rio de Janeiro, Brazil
| | - Cláudio José Struchiner
- School of Applied Mathematics, Getúlio Vargas Foundation, Rio de Janeiro, Brazil
- Social Medicine Institute Hesio Cordeiro, Rio de Janeiro State University, Rio de Janeiro, Brazil
| | - Luís Cristóvão Porto
- Histocompatibility and Cryopreservation Laboratory, Rio de Janeiro State University, Rio de Janeiro, Brazil
| | - Ana Tereza Ribeiro de Vasconcelos
- Bioinformatics Laboratory-LABINFO, National Laboratory of Scientific Computation LNCC/MCTIC, Getúlio Vargas, Av., 333, Quitandinha, Petrópolis, Rio de Janeiro, 25651‑075, Brazil.
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Miskalis A, Shirguppe S, Winter J, Elias G, Swami D, Nambiar A, Stilger M, Woods WS, Gosstola N, Gapinske M, Zeballos A, Moore H, Maslov S, Gaj T, Perez-Pinera P. SPLICER: A Highly Efficient Base Editing Toolbox That Enables In Vivo Therapeutic Exon Skipping. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.01.587650. [PMID: 38883727 PMCID: PMC11178003 DOI: 10.1101/2024.04.01.587650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2024]
Abstract
Exon skipping technologies enable exclusion of targeted exons from mature mRNA transcripts, which has broad applications in molecular biology, medicine, and biotechnology. Existing exon skipping techniques include antisense oligonucleotides, targetable nucleases, and base editors, which, while effective for specific applications at some target exons, remain hindered by shortcomings, including transient effects for oligonucleotides, genotoxicity for nucleases and inconsistent exon skipping for base editors. To overcome these limitations, we created SPLICER, a toolbox of next-generation base editors consisting of near-PAMless Cas9 nickase variants fused to adenosine or cytosine deaminases for the simultaneous editing of splice acceptor (SA) and splice donor (SD) sequences. Synchronized SA and SD editing with SPLICER improves exon skipping, reduces aberrant outcomes, including cryptic splicing and intron retention, and enables skipping of exons refractory to single splice-site editing. To demonstrate the therapeutic potential of SPLICER, we targeted APP exon 17, which encodes the amino acid residues that are cleaved to form the Aβ plaques in Alzheimer's disease. SPLICER reduced the formation of Aβ42 peptides in vitro and enabled efficient exon skipping in a mouse model of Alzheimer's disease. Overall, SPLICER is a widely applicable and efficient toolbox for exon skipping with broad therapeutic applications.
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10
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Zhang J, Wang Y, Zhao Y, Liu F. A new atypical splice mutation in PKD2 leading to autosomal dominant polycystic kidney disease in a Chinese family. Singapore Med J 2024; 65:229-234. [PMID: 34749493 PMCID: PMC11132625 DOI: 10.11622/smedj.2021162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2018] [Accepted: 07/25/2021] [Indexed: 02/05/2023]
Abstract
INTRODUCTION Autosomal dominant polycystic kidney disease (ADPKD) is a very common hereditary renal disorder. Mutations in PKD1 and PKD2 , identified as disease-causing genes, account for 85% and 15% of the ADPKD cases, respectively. METHODS In this study, the mutation analysis of polycystic kidney disease (PKD) genes was performed in a Chinese family with suspected ADPKD using targeted clinical exome sequencing (CES). The candidate pathogenic variants were further tested by using Sanger sequencing and validated for co-segregation. In addition, reverse transcription-polymerase chain reaction (RT-PCR) was performed to test for abnormal splicing and assess its potential pathogenicity. RESULTS A novel atypical splicing mutation that belongs to unclassified variants (UCVs), IVS6+5G>C, was identified in three family members by CES and was shown to co-segregate only with the affected individuals. The RT-PCR revealed the abnormal splicing of exon 6, which thus caused truncating mutation. These findings suggested that the atypical splice site alteration, IVS6+5G>C, in the PKD2 gene was the potential pathogenic mutation leading to ADPKD in this Chinese family. CONCLUSION The data available in this study provided strong evidence that IVS6+5G>C is the potential pathogenic mutation for ADPKD. In addition, our findings emphasised the significance of functional analysis of UCVs and genotype-phenotype correlation in ADPKD.
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Affiliation(s)
- Junlin Zhang
- Division of Nephrology, West China Hospital of Sichuan University, Chengdu, Sichuan, China
| | - Yiting Wang
- Division of Nephrology, West China Hospital of Sichuan University, Chengdu, Sichuan, China
| | - Yingwang Zhao
- Joy Orient Translational Medicine Research Center Co Ltd, Beijing, China
| | - Fang Liu
- Division of Nephrology, West China Hospital of Sichuan University, Chengdu, Sichuan, China
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11
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Suárez-Herrera N, Li CHZ, Leijsten N, Karjosukarso DW, Corradi Z, Bukkems F, Duijkers L, Cremers FPM, Hoyng CB, Garanto A, Collin RWJ. Preclinical Development of Antisense Oligonucleotides to Rescue Aberrant Splicing Caused by an Ultrarare ABCA4 Variant in a Child with Early-Onset Stargardt Disease. Cells 2024; 13:601. [PMID: 38607040 PMCID: PMC11011354 DOI: 10.3390/cells13070601] [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: 12/21/2023] [Revised: 03/19/2024] [Accepted: 03/27/2024] [Indexed: 04/13/2024] Open
Abstract
Precision medicine is rapidly gaining recognition in the field of (ultra)rare conditions, where only a few individuals in the world are affected. Clinical trial design for a small number of patients is extremely challenging, and for this reason, the development of N-of-1 strategies is explored to accelerate customized therapy design for rare cases. A strong candidate for this approach is Stargardt disease (STGD1), an autosomal recessive macular degeneration characterized by high genetic and phenotypic heterogeneity. STGD1 is caused by pathogenic variants in ABCA4, and amongst them, several deep-intronic variants alter the pre-mRNA splicing process, generally resulting in the insertion of pseudoexons (PEs) into the final transcript. In this study, we describe a 10-year-old girl harboring the unique deep-intronic ABCA4 variant c.6817-713A>G. Clinically, she presents with typical early-onset STGD1 with a high disease symmetry between her two eyes. Molecularly, we designed antisense oligonucleotides (AONs) to block the produced PE insertion. Splicing rescue was assessed in three different in vitro models: HEK293T cells, fibroblasts, and photoreceptor precursor cells, the last two being derived from the patient. Overall, our research is intended to serve as the basis for a personalized N-of-1 AON-based treatment to stop early vision loss in this patient.
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Affiliation(s)
- Nuria Suárez-Herrera
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; (N.S.-H.); (N.L.); (D.W.K.); (Z.C.); (F.B.); (L.D.); (F.P.M.C.); (A.G.)
| | - Catherina H. Z. Li
- Department of Ophthalmology, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; (C.H.Z.L.); (C.B.H.)
| | - Nico Leijsten
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; (N.S.-H.); (N.L.); (D.W.K.); (Z.C.); (F.B.); (L.D.); (F.P.M.C.); (A.G.)
| | - Dyah W. Karjosukarso
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; (N.S.-H.); (N.L.); (D.W.K.); (Z.C.); (F.B.); (L.D.); (F.P.M.C.); (A.G.)
| | - Zelia Corradi
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; (N.S.-H.); (N.L.); (D.W.K.); (Z.C.); (F.B.); (L.D.); (F.P.M.C.); (A.G.)
| | - Femke Bukkems
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; (N.S.-H.); (N.L.); (D.W.K.); (Z.C.); (F.B.); (L.D.); (F.P.M.C.); (A.G.)
| | - Lonneke Duijkers
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; (N.S.-H.); (N.L.); (D.W.K.); (Z.C.); (F.B.); (L.D.); (F.P.M.C.); (A.G.)
| | - Frans P. M. Cremers
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; (N.S.-H.); (N.L.); (D.W.K.); (Z.C.); (F.B.); (L.D.); (F.P.M.C.); (A.G.)
| | - Carel B. Hoyng
- Department of Ophthalmology, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; (C.H.Z.L.); (C.B.H.)
- Dutch Center for RNA Therapeutics, 2311 EZ Leiden, The Netherlands
| | - Alejandro Garanto
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; (N.S.-H.); (N.L.); (D.W.K.); (Z.C.); (F.B.); (L.D.); (F.P.M.C.); (A.G.)
- Dutch Center for RNA Therapeutics, 2311 EZ Leiden, The Netherlands
- Department of Pediatrics, Amalia Children’s Hospital, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Rob W. J. Collin
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; (N.S.-H.); (N.L.); (D.W.K.); (Z.C.); (F.B.); (L.D.); (F.P.M.C.); (A.G.)
- Dutch Center for RNA Therapeutics, 2311 EZ Leiden, The Netherlands
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12
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Chen K, Zhou Y, Ding M, Wang Y, Ren Z, Yang Y. Self-supervised learning on millions of primary RNA sequences from 72 vertebrates improves sequence-based RNA splicing prediction. Brief Bioinform 2024; 25:bbae163. [PMID: 38605640 PMCID: PMC11009468 DOI: 10.1093/bib/bbae163] [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: 01/04/2024] [Revised: 02/22/2024] [Accepted: 03/19/2024] [Indexed: 04/13/2024] Open
Abstract
Language models pretrained by self-supervised learning (SSL) have been widely utilized to study protein sequences, while few models were developed for genomic sequences and were limited to single species. Due to the lack of genomes from different species, these models cannot effectively leverage evolutionary information. In this study, we have developed SpliceBERT, a language model pretrained on primary ribonucleic acids (RNA) sequences from 72 vertebrates by masked language modeling, and applied it to sequence-based modeling of RNA splicing. Pretraining SpliceBERT on diverse species enables effective identification of evolutionarily conserved elements. Meanwhile, the learned hidden states and attention weights can characterize the biological properties of splice sites. As a result, SpliceBERT was shown effective on several downstream tasks: zero-shot prediction of variant effects on splicing, prediction of branchpoints in humans, and cross-species prediction of splice sites. Our study highlighted the importance of pretraining genomic language models on a diverse range of species and suggested that SSL is a promising approach to enhance our understanding of the regulatory logic underlying genomic sequences.
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Affiliation(s)
- Ken Chen
- School of Computer Science and Engineering, Sun Yat-sen University, Guangzhou, China
| | - Yue Zhou
- Peng Cheng Laboratory, Shenzhen, China
| | - Maolin Ding
- School of Computer Science and Engineering, Sun Yat-sen University, Guangzhou, China
| | - Yu Wang
- Peng Cheng Laboratory, Shenzhen, China
| | | | - Yuedong Yang
- School of Computer Science and Engineering, Sun Yat-sen University, Guangzhou, China
- Key Laboratory of Machine Intelligence and Advanced Computing (Sun Yat-sen University), Ministry of Education, China
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13
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Rajcsanyi LS, Zheng Y, Herpertz-Dahlmann B, Seitz J, de Zwaan M, Herzog W, Ehrlich S, Zipfel S, Giel K, Egberts K, Burghardt R, Föcker M, Antel J, Fischer-Posovszky P, Hebebrand J, Hinney A. Unexpected identification of obesity-associated mutations in LEP and MC4R genes in patients with anorexia nervosa. Sci Rep 2024; 14:7067. [PMID: 38528040 PMCID: PMC10963783 DOI: 10.1038/s41598-024-57517-w] [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: 01/10/2024] [Accepted: 03/19/2024] [Indexed: 03/27/2024] Open
Abstract
Mutations leading to a reduced or loss of function in genes of the leptin-melanocortin system confer a risk for monogenic forms of obesity. Yet, gain of function variants in the melanocortin-4-receptor (MC4R) gene predispose to a lower BMI. In individuals with reduced body weight, we thus expected mutations leading to an enhanced function in the respective genes, like leptin (LEP) and MC4R. Therefore, we have Sanger sequenced the coding regions of LEP and MC4R in 462 female patients with anorexia nervosa (AN), and 445 healthy-lean controls. In total, we have observed four and eight variants in LEP and MC4R, respectively. Previous studies showed different functional in vitro effects for the detected frameshift and non-synonymous variants: (1) LEP: reduced/loss of function (p.Val94Met), (2) MC4R: gain of function (p.Val103Ile, p.Ile251Leu), reduced or loss of function (p.Thr112Met, p.Ser127Leu, p.Leu211fsX) and without functional in vitro data (p.Val50Leut). In LEP, the variant p.Val94Met was detected in one patient with AN. For MC4R variants, one patient with AN carried the frameshift variant p.Leu211fsX. One patient with AN was heterozygous for two variants at the MC4R (p.Val103Ile and p.Ser127Leu). All other functionally relevant variants were detected in similar frequencies in patients with AN and lean individuals.
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Affiliation(s)
- Luisa Sophie Rajcsanyi
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, University Hospital Essen, University of Duisburg-Essen, Virchowstraße 174, 45147, Essen, Germany.
- Center for Translational Neuro- and Behavioural Sciences, University Hospital Essen, Essen, Germany.
- Section for Molecular Genetics of Mental Disorders, University Hospital Essen, Essen, Germany.
- Institute of Sex- and Gender-Sensitive Medicine, University Hospital Essen, Essen, Germany.
| | - Yiran Zheng
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, University Hospital Essen, University of Duisburg-Essen, Virchowstraße 174, 45147, Essen, Germany
- Center for Translational Neuro- and Behavioural Sciences, University Hospital Essen, Essen, Germany
| | - Beate Herpertz-Dahlmann
- Department of Child and Adolescent Psychiatry and Psychotherapy, University Hospital of the RWTH Aachen, Aachen, Germany
| | - Jochen Seitz
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, University Hospital Essen, University of Duisburg-Essen, Virchowstraße 174, 45147, Essen, Germany
- Department of Child and Adolescent Psychiatry and Psychotherapy, University Hospital of the RWTH Aachen, Aachen, Germany
| | - Martina de Zwaan
- Department of Psychosomatic Medicine and Psychotherapy, Hannover Medical School, Hannover, Germany
| | - Wolfgang Herzog
- Department of Internal Medicine II, General Internal and Psychosomatic Medicine, University of Heidelberg, Heidelberg, Germany
| | - Stefan Ehrlich
- Eating Disorders Research and Treatment Center, Department of Child and Adolescent Psychiatry, Faculty of Medicine, TU Dresden, Dresden, Germany
- Translational Developmental Neuroscience Section, Division of Psychological and Social Medicine and Developmental Neurosciences, Faculty of Medicine, TU Dresden, Dresden, Germany
| | - Stephan Zipfel
- Department of Psychosomatic Medicine and Psychotherapy, Medical University Hospital Tübingen, Tübingen, Germany
- Center of Excellence in Eating Disorders KOMET, Tübingen, Germany
| | - Katrin Giel
- Department of Psychosomatic Medicine and Psychotherapy, Medical University Hospital Tübingen, Tübingen, Germany
- Center of Excellence in Eating Disorders KOMET, Tübingen, Germany
| | - Karin Egberts
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, University Hospital Würzburg, Würzburg, Germany
| | - Roland Burghardt
- Oberberg Clinic for Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, Fasanenkiez, Berlin, Germany
| | - Manuel Föcker
- Department of Child and Adolescent Psychiatry, University Hospital Münster, Munster, Germany
- LWL-University Hospital Hamm for Child and Adolescent Psychiatry, Ruhr-University Bochum, Hamm, Germany
| | - Jochen Antel
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, University Hospital Essen, University of Duisburg-Essen, Virchowstraße 174, 45147, Essen, Germany
- Center for Translational Neuro- and Behavioural Sciences, University Hospital Essen, Essen, Germany
| | | | - Johannes Hebebrand
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, University Hospital Essen, University of Duisburg-Essen, Virchowstraße 174, 45147, Essen, Germany
- Center for Translational Neuro- and Behavioural Sciences, University Hospital Essen, Essen, Germany
| | - Anke Hinney
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, University Hospital Essen, University of Duisburg-Essen, Virchowstraße 174, 45147, Essen, Germany
- Center for Translational Neuro- and Behavioural Sciences, University Hospital Essen, Essen, Germany
- Section for Molecular Genetics of Mental Disorders, University Hospital Essen, Essen, Germany
- Institute of Sex- and Gender-Sensitive Medicine, University Hospital Essen, Essen, Germany
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14
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Yamada M, Maeta K, Suzuki H, Kurosawa R, Takenouchi T, Awaya T, Ajiro M, Takeuchi A, Nishio H, Hagiwara M, Miya F, Matsuo M, Kosaki K. Successful skipping of abnormal pseudoexon by antisense oligonucleotides in vitro for a patient with beta-propeller protein-associated neurodegeneration. Sci Rep 2024; 14:6506. [PMID: 38499569 PMCID: PMC10948761 DOI: 10.1038/s41598-024-56704-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Accepted: 03/09/2024] [Indexed: 03/20/2024] Open
Abstract
Pathogenic variants in WDR45 on chromosome Xp11 cause neurodegenerative disorder beta-propeller protein-associated neurodegeneration (BPAN). Currently, there is no effective therapy for BPAN. Here we report a 17-year-old female patient with BPAN and show that antisense oligonucleotide (ASO) was effective in vitro. The patient had developmental delay and later showed extrapyramidal signs since the age of 15 years. MRI findings showed iron deposition in the globus pallidus and substantia nigra on T2 MRI. Whole genome sequencing and RNA sequencing revealed generation of pseudoexon due to inclusion of intronic sequences triggered by an intronic variant that is remote from the exon-intron junction: WDR45 (OMIM #300526) chrX(GRCh37):g.48935143G > C, (NM_007075.4:c.235 + 159C > G). We recapitulated the exonization of intron sequences by a mini-gene assay and further sought antisense oligonucleotide that induce pseudoexon skipping using our recently developed, a dual fluorescent splicing reporter system that encodes two fluorescent proteins, mCherry, a transfection marker designed to facilitate evaluation of exon skipping and split eGFP, a splicing reaction marker. The results showed that the 24-base ASO was the strongest inducer of pseudoexon skipping. Our data presented here have provided supportive evidence for in vivo preclinical studies.
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Affiliation(s)
- Mamiko Yamada
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan
| | - Kazuhiro Maeta
- KNC Department of Nucleic Acid Drug Discovery, Faculty of Rehabilitation, Kobe Gakuin University, Kobe, Japan
| | - Hisato Suzuki
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan
| | - Ryo Kurosawa
- Department of Anatomy and Developmental Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Toshiki Takenouchi
- Department of Pediatrics, Keio University School of Medicine, Tokyo, Japan
| | - Tomonari Awaya
- Department of Anatomy and Developmental Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Center for Anatomical Studies, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Masahiko Ajiro
- Division of Cancer RNA Research, National Cancer Center Research Institute, Tokyo, Japan
- Department of Drug Discovery Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Atsuko Takeuchi
- Faculty of Health Sciences, Kobe Tokiwa University, Kobe, Japan
| | - Hisahide Nishio
- Faculty of Rehabilitation, Kobe Gakuin University, Kobe, Japan
| | - Masatoshi Hagiwara
- Department of Anatomy and Developmental Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Fuyuki Miya
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan.
| | - Masafumi Matsuo
- Faculty of Health Sciences, Kobe Tokiwa University, Kobe, Japan.
| | - Kenjiro Kosaki
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan
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15
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Spangsberg Petersen US, Dembic M, Martínez-Pizarro A, Richard E, Holm LL, Havelund JF, Doktor TK, Larsen MR, Færgeman NJ, Desviat LR, Andresen BS. Regulating PCCA gene expression by modulation of pseudoexon splicing patterns to rescue enzyme activity in propionic acidemia. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102101. [PMID: 38204914 PMCID: PMC10776996 DOI: 10.1016/j.omtn.2023.102101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 12/08/2023] [Indexed: 01/12/2024]
Abstract
Pseudoexons are nonfunctional intronic sequences that can be activated by deep-intronic sequence variation. Activation increases pseudoexon inclusion in mRNA and interferes with normal gene expression. The PCCA c.1285-1416A>G variation activates a pseudoexon and causes the severe metabolic disorder propionic acidemia by deficiency of the propionyl-CoA carboxylase enzyme encoded by PCCA and PCCB. We characterized this pathogenic pseudoexon activation event in detail and identified hnRNP A1 to be important for normal repression. The PCCA c.1285-1416A>G variation disrupts an hnRNP A1-binding splicing silencer and simultaneously creates a splicing enhancer. We demonstrate that blocking this region of regulation with splice-switching antisense oligonucleotides restores normal splicing and rescues enzyme activity in patient fibroblasts and in a cellular model created by CRISPR gene editing. Interestingly, the PCCA pseudoexon offers an unexploited potential to upregulate gene expression because healthy tissues show relatively high inclusion levels. By blocking inclusion of the nonactivated wild-type pseudoexon, we can increase both PCCA and PCCB protein levels, which increases the activity of the heterododecameric enzyme. Surprisingly, we can increase enzyme activity from residual levels in not only patient fibroblasts harboring PCCA missense variants but also those harboring PCCB missense variants. This is a potential treatment strategy for propionic acidemia.
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Affiliation(s)
- Ulrika Simone Spangsberg Petersen
- Department of Biochemistry and Molecular Biology and the Villum Center for Bioanalytical Sciences, University of Southern Denmark, 5230 Odense M, Denmark
| | - Maja Dembic
- Department of Biochemistry and Molecular Biology and the Villum Center for Bioanalytical Sciences, University of Southern Denmark, 5230 Odense M, Denmark
- Department of Clinical Genetics, Odense University Hospital, 5000 Odense C, Denmark
- Department of Mathematics and Computer Science, University of Southern Denmark, 5230 Odense M, Denmark
| | - Ainhoa Martínez-Pizarro
- Centro de Biología Molecular Severo Ochoa, UAM-CSIC, CEDEM, CIBERER, IdiPaz, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Eva Richard
- Centro de Biología Molecular Severo Ochoa, UAM-CSIC, CEDEM, CIBERER, IdiPaz, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Lise Lolle Holm
- Department of Biochemistry and Molecular Biology and the Villum Center for Bioanalytical Sciences, University of Southern Denmark, 5230 Odense M, Denmark
| | - Jesper Foged Havelund
- Department of Biochemistry and Molecular Biology and the Villum Center for Bioanalytical Sciences, University of Southern Denmark, 5230 Odense M, Denmark
| | - Thomas Koed Doktor
- Department of Biochemistry and Molecular Biology and the Villum Center for Bioanalytical Sciences, University of Southern Denmark, 5230 Odense M, Denmark
| | - Martin Røssel Larsen
- Department of Biochemistry and Molecular Biology and the Villum Center for Bioanalytical Sciences, University of Southern Denmark, 5230 Odense M, Denmark
| | - Nils J. Færgeman
- Department of Biochemistry and Molecular Biology and the Villum Center for Bioanalytical Sciences, University of Southern Denmark, 5230 Odense M, Denmark
| | - Lourdes Ruiz Desviat
- Centro de Biología Molecular Severo Ochoa, UAM-CSIC, CEDEM, CIBERER, IdiPaz, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Brage Storstein Andresen
- Department of Biochemistry and Molecular Biology and the Villum Center for Bioanalytical Sciences, University of Southern Denmark, 5230 Odense M, Denmark
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16
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Khanal S, de Cruz M, Strickland B, Mansfield K, Lai E, Flynt A. A tailed mirtron promotes longevity in Drosophila. Nucleic Acids Res 2024; 52:1080-1089. [PMID: 38048325 PMCID: PMC10853799 DOI: 10.1093/nar/gkad1158] [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: 04/03/2023] [Revised: 11/09/2023] [Accepted: 11/17/2023] [Indexed: 12/06/2023] Open
Abstract
Thousands of atypical microRNAs (miRNAs) have been described in the genomes of animals; however, it is unclear if many of these non-canonical miRNAs can measurably influence phenotypes. Mirtrons are the largest class of non-canonical miRNAs that are produced from hairpins excised by splicing, which after debranching become substrates for Dicer and load into RISC. Most mirtrons require additional processing after splicing to remove 'tail' residues interposed between one of the host intron splice sites and base of the hairpin precursor structure. Despite most mirtrons requiring tail removal no function has been elucidated for a tailed species, indeed for all mirtrons identified function has only been assigned to a single species. Here we study miR-1017, a mirtron with a 3' tail, which is well expressed and conserved in Drosophila species. We found that miR-1017 can extend lifespan when ectopically expressed in the neurons, which seems partly due to this miRNA targeting its host transcript, acetylcholine receptor Dα2. Unexpectedly we found that not only did miR-1017 function in trans but also in cis by affecting splicing of Dα2. This suggests a mechanism for mirtron evolution where initial roles of structural elements in splicing lead to secondary acquisition of trans-regulatory function.
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Affiliation(s)
- Sweta Khanal
- Cellular and Molecular Biology, School of Biological, Environmental, and Earth Sciences University of Southern Mississippi, USA
| | - Matthew de Cruz
- Cellular and Molecular Biology, School of Biological, Environmental, and Earth Sciences University of Southern Mississippi, USA
| | - Britton Strickland
- Cellular and Molecular Biology, School of Biological, Environmental, and Earth Sciences University of Southern Mississippi, USA
| | - Kody Mansfield
- Cellular and Molecular Biology, School of Biological, Environmental, and Earth Sciences University of Southern Mississippi, USA
| | - Eric C Lai
- Department of Developmental Biology, Sloan Kettering Institute, USA
| | - Alex Flynt
- Cellular and Molecular Biology, School of Biological, Environmental, and Earth Sciences University of Southern Mississippi, USA
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17
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Schwartz S, Wu C, Kajitani N. RNA elements that control human papillomavirus mRNA splicing-targets for therapy? J Med Virol 2024; 96:e29473. [PMID: 38362929 DOI: 10.1002/jmv.29473] [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: 12/22/2023] [Revised: 01/31/2024] [Accepted: 02/05/2024] [Indexed: 02/17/2024]
Abstract
Human papillomaviruses (HPVs) cause more than 4.5% of all cancer in the world and more than half of these cases are attributed to human papillomavirus type 16 (HPV16). Prophylactic vaccines are available but antiviral drugs are not. Novel targets for therapy are urgently needed. Alternative RNA splicing is extensively used by HPVs to express all their genes and HPV16 is no exception. This process must function to perfection since mis-splicing could perturb the HPV gene expression program by altering mRNA levels or by generating dysfunctional mRNAs. Cis-acting RNA elements on the viral mRNAs and their cognate cellular trans-acting factors control papillomavirus RNA splicing. The precise but delicate nature of the splicing process renders splicing sensitive to interference. As such, papillomavirus RNA splicing is a potential target for therapy. Here we summarize our current understanding of cis-acting HPV16 RNA elements that control HPV16 mRNA splicing via cellular proteins and discuss how they may be exploited as targets for therapy to papillomavirus infections and cancer.
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Affiliation(s)
- Stefan Schwartz
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Chengjun Wu
- School of Health and Life Sciences, University of Health and Rehabilitation Sciences, Qingdao, China
| | - Naoko Kajitani
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
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18
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Blinova VG, Gladilina YA, Abramova AA, Eliseeva DD, Vtorushina VV, Shishparenok AN, Zhdanov DD. Modulation of Suppressive Activity and Proliferation of Human Regulatory T Cells by Splice-Switching Oligonucleotides Targeting FoxP3 Pre-mRNA. Cells 2023; 13:77. [PMID: 38201281 PMCID: PMC10777989 DOI: 10.3390/cells13010077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 12/05/2023] [Accepted: 12/21/2023] [Indexed: 01/12/2024] Open
Abstract
The maturation, development, and function of regulatory T cells (Tregs) are under the control of the crucial transcription factor Forkhead Box Protein 3 (FoxP3). Through alternative splicing, the human FoxP3 gene produces four different splice variants: a full-length variant (FL) and truncated variants with deletions of each of exons 2 (∆2 variant) or 7 (∆7 variant) or a deletion of both exons (∆2∆7 variant). Their involvement in the biology of Tregs as well as their association with autoimmune diseases remains to be clarified. The aim of this work was to induce a single FoxP3 splice variant in human Tregs by splice switching oligonucleotides and to monitor their phenotype and proliferative and suppressive activity. We demonstrated that Tregs from peripheral blood from patients with multiple sclerosis preferentially expressed truncated splice variants, while the FL variant was the major variant in healthy donors. Tregs with induced expression of truncated FoxP3 splice variants demonstrated lower suppressive activity than those expressing FL variants. Reduced suppression was associated with the decreased expression of Treg-associated suppressive surface molecules and the production of cytokines. The deletion of exons 2 and/or 7 also reduced the cell proliferation rate. The results of this study show an association between FoxP3 splice variants and Treg function and proliferation. The modulation of Treg suppressive activity by the induction of the FoxP3 FL variant can become a promising strategy for regenerative immunotherapy.
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Affiliation(s)
- Varvara G. Blinova
- Laboratory of Medical Biotechnology, Institute of Biomedical Chemistry, Pogodinskaya st. 10/8, 119121 Moscow, Russia; (V.G.B.); (Y.A.G.); (A.A.A.); (A.N.S.)
| | - Yulia A. Gladilina
- Laboratory of Medical Biotechnology, Institute of Biomedical Chemistry, Pogodinskaya st. 10/8, 119121 Moscow, Russia; (V.G.B.); (Y.A.G.); (A.A.A.); (A.N.S.)
| | - Anna A. Abramova
- Laboratory of Medical Biotechnology, Institute of Biomedical Chemistry, Pogodinskaya st. 10/8, 119121 Moscow, Russia; (V.G.B.); (Y.A.G.); (A.A.A.); (A.N.S.)
- Research Center of Neurology, Volokolamskoe Shosse, 80, 125367 Moscow, Russia;
| | - Daria D. Eliseeva
- Research Center of Neurology, Volokolamskoe Shosse, 80, 125367 Moscow, Russia;
| | - Valentina V. Vtorushina
- National Medical Research Center for Obstetrics, Gynecology and Perinatology Named after Academician V.I. Kulakov of Ministry of Healthcare of the Russian Federation, Laboratory of Clinical Immunology, Academician Oparin st. 4, 117997 Moscow, Russia;
| | - Anastasia N. Shishparenok
- Laboratory of Medical Biotechnology, Institute of Biomedical Chemistry, Pogodinskaya st. 10/8, 119121 Moscow, Russia; (V.G.B.); (Y.A.G.); (A.A.A.); (A.N.S.)
| | - Dmitry D. Zhdanov
- Laboratory of Medical Biotechnology, Institute of Biomedical Chemistry, Pogodinskaya st. 10/8, 119121 Moscow, Russia; (V.G.B.); (Y.A.G.); (A.A.A.); (A.N.S.)
- Department of Biochemistry, People’s Friendship University of Russia Named after Patrice Lumumba (RUDN University), Miklukho-Maklaya st. 6, 117198 Moscow, Russia
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19
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Stanbury K, Stavinohova R, Pettitt L, Dixon C, Schofield EC, Mclaughlin B, Pettinen I, Lohi H, Ricketts SL, Oliver JA, Mellersh CS. Multiocular defect in the Old English Sheepdog: A canine form of Stickler syndrome type II associated with a missense variant in the collagen-type gene COL11A1. PLoS One 2023; 18:e0295851. [PMID: 38153936 PMCID: PMC10754463 DOI: 10.1371/journal.pone.0295851] [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: 07/04/2023] [Accepted: 11/30/2023] [Indexed: 12/30/2023] Open
Abstract
Multiocular defect has been described in different canine breeds, including the Old English Sheepdog. Affected dogs typically present with multiple and various ocular abnormalities. We carried out whole genome sequencing on an Old English Sheepdog that had been diagnosed with hereditary cataracts at the age of five and then referred to a board-certified veterinary ophthalmologist due to owner-reported visual deterioration. An ophthalmic assessment revealed that there was bilateral vitreal degeneration, macrophthalmos, and spherophakia in addition to cataracts. Follow-up consultations revealed cataract progression, retinal detachment, uveitis and secondary glaucoma. Whole genome sequence filtered variants private to the case, shared with another Old English Sheepdog genome and predicted to be deleterious were genotyped in an initial cohort of six Old English Sheepdogs (three affected by multiocular defect and three control dogs without evidence of inherited eye disease). Only one of the twenty-two variants segregated correctly with multiocular defect. The variant is a single nucleotide substitution, located in the collagen-type gene COL11A1, c.1775T>C, that causes an amino acid change, p.Phe1592Ser. Genotyping of an additional 14 Old English Sheepdogs affected by multiocular defect revealed a dominant mode of inheritance with four cases heterozygous for the variant. Further genotyping of hereditary cataract-affected Old English Sheepdogs revealed segregation of the variant in eight out of nine dogs. In humans, variants in the COL11A1 gene are associated with Stickler syndrome type II, also dominantly inherited.
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Affiliation(s)
- Katherine Stanbury
- Kennel Club Genetics Centre, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | | | - Louise Pettitt
- Kennel Club Genetics Centre, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | | | - Ellen C. Schofield
- Kennel Club Genetics Centre, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Bryan Mclaughlin
- Kennel Club Genetics Centre, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Inka Pettinen
- Department of Veterinary Biosciences, Department of Medical and Clinical Genetics, University of Helsinki and Folkhälsan Research Center, Helsinki, Finland
| | - Hannes Lohi
- Department of Veterinary Biosciences, Department of Medical and Clinical Genetics, University of Helsinki and Folkhälsan Research Center, Helsinki, Finland
| | - Sally L. Ricketts
- Kennel Club Genetics Centre, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | | | - Cathryn S. Mellersh
- Kennel Club Genetics Centre, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
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20
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Stepankiw N, Yang AWH, Hughes TR. The human genome contains over a million autonomous exons. Genome Res 2023; 33:gr.277792.123. [PMID: 37945377 PMCID: PMC10760453 DOI: 10.1101/gr.277792.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Accepted: 10/27/2023] [Indexed: 11/12/2023]
Abstract
Mammalian mRNA and lncRNA exons are often small compared to introns. The exon definition model predicts that exons splice autonomously, dependent on proximal exon sequence features, explaining their delineation within large introns. This model has not been examined on a genome-wide scale, however, leaving open the question of how often mRNA and lncRNA exons are autonomous. It is also unknown how frequently such exons can arise by chance. Here, we directly assayed large fragments (500-1000 bp) of the human genome by exon trapping, which detects exons spliced into a heterologous transgene, here designed with a large intron context. We define the trapped exons as "autonomous." We obtained ∼1.25 million trapped exons, including most known mRNA and well-annotated lncRNA internal exons, demonstrating that human exons are predominantly autonomous. mRNA exons are trapped with the highest efficiency. Nearly a million of the trapped exons are unannotated, most located in intergenic regions and antisense to mRNA, with depletion from the forward strand of introns. These exons are not conserved, suggesting they are nonfunctional and arose from random mutations. They are nonetheless highly enriched with known splicing promoting sequence features that delineate known exons. Novel autonomous exons are more numerous than annotated lncRNA exons, and computational models also indicate they will occur with similar frequency in any randomly generated sequence. These results show that most human coding exons splice autonomously, and provide an explanation for the existence of many unconserved lncRNAs, as well as a new annotation and inclusion levels of spliceable loci in the human genome.
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Affiliation(s)
- Nicholas Stepankiw
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada M5S 3E1
| | - Ally W H Yang
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada M5S 3E1
| | - Timothy R Hughes
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada M5S 3E1;
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada M5S 1A8
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21
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Weber AI, Parthasarathy S, Borisova E, Epifanova E, Preußner M, Rusanova A, Ambrozkiewicz MC, Bessa P, Newman A, Müller L, Schaal H, Heyd F, Tarabykin V. Srsf1 and Elavl1 act antagonistically on neuronal fate choice in the developing neocortex by controlling TrkC receptor isoform expression. Nucleic Acids Res 2023; 51:10218-10237. [PMID: 37697438 PMCID: PMC10602877 DOI: 10.1093/nar/gkad703] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 07/24/2023] [Accepted: 08/15/2023] [Indexed: 09/13/2023] Open
Abstract
The seat of higher-order cognitive abilities in mammals, the neocortex, is a complex structure, organized in several layers. The different subtypes of principal neurons are distributed in precise ratios and at specific positions in these layers and are generated by the same neural progenitor cells (NPCs), steered by a spatially and temporally specified combination of molecular cues that are incompletely understood. Recently, we discovered that an alternatively spliced isoform of the TrkC receptor lacking the kinase domain, TrkC-T1, is a determinant of the corticofugal projection neuron (CFuPN) fate. Here, we show that the finely tuned balance between TrkC-T1 and the better known, kinase domain-containing isoform, TrkC-TK+, is cell type-specific in the developing cortex and established through the antagonistic actions of two RNA-binding proteins, Srsf1 and Elavl1. Moreover, our data show that Srsf1 promotes the CFuPN fate and Elavl1 promotes the callosal projection neuron (CPN) fate in vivo via regulating the distinct ratios of TrkC-T1 to TrkC-TK+. Taken together, we connect spatio-temporal expression of Srsf1 and Elavl1 in the developing neocortex with the regulation of TrkC alternative splicing and transcript stability and neuronal fate choice, thus adding to the mechanistic and functional understanding of alternative splicing in vivo.
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Affiliation(s)
- A Ioana Weber
- Charité Universitätsmedizin Berlin, Institute of Cell Biology and Neurobiology, Charitéplatz 1, 10117 Berlin, Germany
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, Takustr. 6, 14195, Berlin, Germany
| | - Srinivas Parthasarathy
- Charité Universitätsmedizin Berlin, Institute of Cell Biology and Neurobiology, Charitéplatz 1, 10117 Berlin, Germany
| | - Ekaterina Borisova
- Charité Universitätsmedizin Berlin, Institute of Cell Biology and Neurobiology, Charitéplatz 1, 10117 Berlin, Germany
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, 634009, Tomsk, Russia
| | - Ekaterina Epifanova
- Charité Universitätsmedizin Berlin, Institute of Cell Biology and Neurobiology, Charitéplatz 1, 10117 Berlin, Germany
| | - Marco Preußner
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, Takustr. 6, 14195, Berlin, Germany
| | - Alexandra Rusanova
- Charité Universitätsmedizin Berlin, Institute of Cell Biology and Neurobiology, Charitéplatz 1, 10117 Berlin, Germany
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, 634009, Tomsk, Russia
| | - Mateusz C Ambrozkiewicz
- Charité Universitätsmedizin Berlin, Institute of Cell Biology and Neurobiology, Charitéplatz 1, 10117 Berlin, Germany
| | - Paraskevi Bessa
- Charité Universitätsmedizin Berlin, Institute of Cell Biology and Neurobiology, Charitéplatz 1, 10117 Berlin, Germany
| | - Andrew G Newman
- Charité Universitätsmedizin Berlin, Institute of Cell Biology and Neurobiology, Charitéplatz 1, 10117 Berlin, Germany
| | - Lisa Müller
- Heinrich Heine Universität Düsseldorf, Institute of Virology, Medical Faculty, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Heiner Schaal
- Heinrich Heine Universität Düsseldorf, Institute of Virology, Medical Faculty, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Florian Heyd
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, Takustr. 6, 14195, Berlin, Germany
| | - Victor Tarabykin
- Charité Universitätsmedizin Berlin, Institute of Cell Biology and Neurobiology, Charitéplatz 1, 10117 Berlin, Germany
- Institute of Neuroscience, Lobachevsky State University of Nizhny Novgorod, 603950, Nizhny Novgorod Oblast, Russia
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22
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Farshadyeganeh P, Nazim M, Zhang R, Ohkawara B, Nakajima K, Rahman MA, Nasrin F, Ito M, Takeda JI, Ohe K, Miyasaka Y, Ohno T, Masuda A, Ohno K. Splicing regulation of GFPT1 muscle-specific isoform and its roles in glucose metabolisms and neuromuscular junction. iScience 2023; 26:107746. [PMID: 37744035 PMCID: PMC10514471 DOI: 10.1016/j.isci.2023.107746] [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: 05/10/2023] [Revised: 07/29/2023] [Accepted: 08/24/2023] [Indexed: 09/26/2023] Open
Abstract
Glutamine:fructose-6-phosphate transaminase 1 (GFPT1) is the rate-limiting enzyme of the hexosamine biosynthetic pathway (HBP). A 54-bp exon 9 of GFPT1 is specifically included in skeletal and cardiac muscles to generate a long isoform of GFPT1 (GFPT1-L). We showed that SRSF1 and Rbfox1/2 cooperatively enhance, and hnRNP H/F suppresses, the inclusion of human GFPT1 exon 9 by modulating recruitment of U1 snRNP. Knockout (KO) of GFPT1-L in skeletal muscle markedly increased the amounts of GFPT1 and UDP-HexNAc, which subsequently suppressed the glycolytic pathway. Aged KO mice showed impaired insulin-mediated glucose uptake, as well as muscle weakness and fatigue likely due to abnormal formation and maintenance of the neuromuscular junction. Taken together, GFPT1-L is likely to be acquired in evolution in mammalian striated muscles to attenuate the HBP for efficient glycolytic energy production, insulin-mediated glucose uptake, and the formation and maintenance of the neuromuscular junction.
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Affiliation(s)
- Paniz Farshadyeganeh
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
| | - Mohammad Nazim
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Ruchen Zhang
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
| | - Bisei Ohkawara
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
| | - Kazuki Nakajima
- Institute for Glyco-core Research (iGCORE), Gifu University, Gifu 501-1193, Japan
| | - Mohammad Alinoor Rahman
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
- Department of Biochemistry and Molecular Biology, Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences (UAMS), Little Rock, AR 72205, USA
| | - Farhana Nasrin
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
- Department of Biochemistry and Molecular Biology, Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences (UAMS), Little Rock, AR 72205, USA
| | - Mikako Ito
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
| | - Jun-ichi Takeda
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
| | - Kenji Ohe
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
- Faculty of Pharmaceutical Sciences, Fukuoka University, Fukuoka 814-0180, Japan
| | - Yuki Miyasaka
- Division of Experimental Animals, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
| | - Tamio Ohno
- Division of Experimental Animals, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
| | - Akio Masuda
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
| | - Kinji Ohno
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
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23
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Seidizadeh O, Cairo A, Baronciani L, Valenti L, Peyvandi F. Population-based prevalence and mutational landscape of von Willebrand disease using large-scale genetic databases. NPJ Genom Med 2023; 8:31. [PMID: 37845247 PMCID: PMC10579253 DOI: 10.1038/s41525-023-00375-8] [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: 03/13/2023] [Accepted: 09/29/2023] [Indexed: 10/18/2023] Open
Abstract
Von Willebrand disease (VWD) is a common bleeding disorder caused by mutations in the von Willebrand factor gene (VWF). The true global prevalence of VWD has not been accurately established. We estimated the worldwide and within-population prevalence of inherited VWD by analyzing exome and genome data of 141,456 individuals gathered by the genome Aggregation Database (gnomAD). We also extended our data deepening by mining the main databases containing VWF variants i.e., the Leiden Open Variation Database (LOVD) and the Human Gene Mutation Database (HGMD) with the goal to explore the global mutational spectrum of VWD. A total of 4,313 VWF variants were identified in the gnomAD population, of which 505 were predicted to be pathogenic or already reported to be associated with VWD. Among the 282,912 alleles analyzed, 31,785 were affected by the aforementioned variants. The global prevalence of dominant VWD in 1000 individuals was established to be 74 for type 1, 3 for 2A, 3 for 2B and 6 for 2M. The global prevalences for recessive VWD forms (type 2N and type 3) were 0.31 and 0.7 in 1000 individuals, respectively. This comprehensive analysis provided a global mutational landscape of VWF by means of 927 already reported variants in the HGMD and LOVD datasets and 287 novel pathogenic variants identified in the gnomAD. Our results reveal that there is a considerably higher than expected prevalence of putative disease alleles and variants associated with VWD and suggest that a large number of VWD patients are undiagnosed.
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Affiliation(s)
- Omid Seidizadeh
- Fondazione IRCCS Ca'Granda Ospedale Maggiore Policlinico, Angelo Bianchi Bonomi Hemophilia and Thrombosis Center, Milan, Italy
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy
| | - Andrea Cairo
- Fondazione IRCCS Ca'Granda Ospedale Maggiore Policlinico, Angelo Bianchi Bonomi Hemophilia and Thrombosis Center, Milan, Italy
| | - Luciano Baronciani
- Fondazione IRCCS Ca'Granda Ospedale Maggiore Policlinico, Angelo Bianchi Bonomi Hemophilia and Thrombosis Center, Milan, Italy
| | - Luca Valenti
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy
- Fondazione IRCCS Ca'Granda Ospedale Maggiore Policlinico, Precision Medicine Lab, Biological Resource Center, Department of Transfusion Medicine, Milan, Italy
| | - Flora Peyvandi
- Fondazione IRCCS Ca'Granda Ospedale Maggiore Policlinico, Angelo Bianchi Bonomi Hemophilia and Thrombosis Center, Milan, Italy.
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy.
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24
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Shemirani R, Le M, Nakano Y. Mutations Causing X-Linked Amelogenesis Imperfecta Alter miRNA Formation from Amelogenin Exon4. J Dent Res 2023; 102:1210-1219. [PMID: 37563801 PMCID: PMC10548775 DOI: 10.1177/00220345231180572] [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] [Indexed: 08/12/2023] Open
Abstract
Amelogenin plays a crucial role in tooth enamel formation, and mutations on X-chromosomal amelogenin cause X-linked amelogenesis imperfecta (AI). Amelogenin pre-messenger RNA (mRNA) is highly alternatively spliced, and during alternative splicing, exon4 is mostly skipped, leading to the formation of a microRNA (miR-exon4) that has been suggested to function in enamel and bone formation. While delivering the functional variation of amelogenin proteins, alternative splicing of exon4 is the decisive first step to producing miR-exon4. However, the factors that regulate the splicing of exon4 are not well understood. This study aimed to investigate the association between known mutations in exon4 and exon5 of X chromosome amelogenin that causes X-linked AI, the splicing of exon4, and miR-exon4 formation. Our results showed mutations in exon4 and exon5 of the amelogenin gene, including c.120T>C, c.152C>T, c.155C>G, and c.155delC, significantly affected the splicing of exon4 and subsequent miR-exon4 production. Using an amelogenin minigene transfected in HEK-293 cells, we observed increased inclusion of exon4 in amelogenin mRNA and reduced miR-exon4 production with these mutations. In silico analysis predicted that Ser/Arg-rich RNA splicing factor (SRSF) 2 and SRSF5 were the regulatory factors for exon4 and exon5 splicing, respectively. Electrophoretic mobility shift assay confirmed that SRSF2 binds to exon4 and SRSF5 binds to exon5, and mutations in each exon can alter SRSF binding. Transfection of the amelogenin minigene to LS8 ameloblastic cells suppressed expression of the known miR-exon4 direct targets, Nfia and Prkch, related to multiple pathways. Given the mutations on the minigene, the expression of Prkch has been significantly upregulated with c.155C>G and c.155delC mutations. Together, we confirmed that exon4 splicing is critical for miR-exon4 production, and mutations causing X-linked AI in exon4 and exon5 significantly affect exon4 splicing and following miR-exon4 production. The change in miR-exon4 would be an additional etiology of enamel defects seen in some X-linked AI.
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Affiliation(s)
- R. Shemirani
- Department of Orofacial Sciences, School of Dentistry, University of California, San Francisco, CA, USA
- Oral and Craniofacial Science, Graduate Division, University of California, San Francisco, CA, USA
| | - M.H. Le
- Oral and Craniofacial Science, Graduate Division, University of California, San Francisco, CA, USA
- Department of Preventive and Restorative Dental Sciences, University of California, San Francisco, CA, USA
- College of Dental Medicine, California Northstate University, Elk Grove, CA, USA
| | - Y. Nakano
- Department of Orofacial Sciences, School of Dentistry, University of California, San Francisco, CA, USA
- Center for Children’s Oral Health Research, School of Dentistry, University of California, San Francisco, CA, USA
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25
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Ramzan M, Duman D, Hendricks LCP, Guo S, Mutlu A, Kalcioglu MT, Seyhan S, Carranza C, Bonyadi M, Mahdieh N, Yildirim-Baylan M, Figueroa-Ildefonso E, Alper O, Atik T, Ayral A, Bozan N, Balta B, Rivas C, Manzoli GN, Huesca-Hernandez F, Kuchay RAH, Durgut M, Bademci G, Tekin M. Genome sequencing identifies coding and non-coding variants for non-syndromic hearing loss. J Hum Genet 2023; 68:657-669. [PMID: 37217689 DOI: 10.1038/s10038-023-01159-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 04/27/2023] [Accepted: 05/05/2023] [Indexed: 05/24/2023]
Abstract
Hearing loss (HL) is a common heterogeneous trait that involves variants in more than 200 genes. In this study, we utilized exome (ES) and genome sequencing (GS) to effectively identify the genetic cause of presumably non-syndromic HL in 322 families from South and West Asia and Latin America. Biallelic GJB2 variants were identified in 58 probands at the time of enrollment these probands were excluded. In addition, upon review of phenotypic findings, 38/322 probands were excluded based on syndromic findings at the time of ascertainment and no further evaluation was performed on those samples. We performed ES as a primary diagnostic tool on one or two affected individuals from 212/226 families. Via ES we detected a total of 78 variants in 30 genes and showed their co-segregation with HL in 71 affected families. Most of the variants were frameshift or missense and affected individuals were either homozygous or compound heterozygous in their respective families. We employed GS as a primary test on a subset of 14 families and a secondary tool on 22 families which were unsolved by ES. Although the cumulative detection rate of causal variants by ES and GS is 40% (89/226), GS alone has led to a molecular diagnosis in 7 of 14 families as the primary tool and 5 of 22 families as the secondary test. GS successfully identified variants present in deep intronic or complex regions not detectable by ES.
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Affiliation(s)
- Memoona Ramzan
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Duygu Duman
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
- Division of Genetics, Department of Pediatrics, Ankara University School of Medicine, Ankara, Turkey
| | - LeShon Chere Peart Hendricks
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Shengru Guo
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Ahmet Mutlu
- Department of Otorhinolaryngology, Istanbul Medeniyet University Faculty of Medicine, Istanbul, Turkey
- Goztepe Prof. Dr. Suleyman Yalcin City Hospital, Istanbul, Turkey
| | - Mahmut Tayyar Kalcioglu
- Department of Otorhinolaryngology, Istanbul Medeniyet University Faculty of Medicine, Istanbul, Turkey
- Goztepe Prof. Dr. Suleyman Yalcin City Hospital, Istanbul, Turkey
| | - Serhat Seyhan
- Department of Medical Genetics, Faculty of Medicine, Uskudar University, Istanbul, Turkey
| | - Claudia Carranza
- Institute for Research on Genetic and Metabolic Diseases, INVEGEM, Guatemala City, Guatemala
| | - Murtaza Bonyadi
- Faculty of Natural Sciences, Center of Excellence for Biodiversity, University of Tabriz, Tabriz, Iran
| | - Nejat Mahdieh
- Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran
| | | | - Erick Figueroa-Ildefonso
- Neurogenetics Research Center, Instituto Nacional de Ciencias Neurológicas, Lima, Peru
- Universidad Peruana Cayetano Heredia, Lima, 15102, Peru
| | - Ozgul Alper
- Department of Medical Biology and Genetics, Faculty of Medicine, Akdeniz University, Antalya, Turkey
| | - Tahir Atik
- Division of Pediatric Genetics, Department of Pediatrics, School of Medicine, Ege University, Izmir, Turkey
| | - Abdurrahman Ayral
- Department of Otolaryngology, Faculty of Medicine, Yuzuncu Yıl University, Van, Turkey
| | - Nazim Bozan
- Department of Otolaryngology, Faculty of Medicine, Yuzuncu Yıl University, Van, Turkey
| | - Burhan Balta
- Department of Medical Genetics, Kayseri Training and Research Hospital, Kayseri, Turkey
| | | | - Gabrielle N Manzoli
- Gonçalo Moniz Research Center (CPqGM), Oswaldo Cruz Foundation (FIOCRUZ), Salvador, Bahia, Brazil
| | - Fabiola Huesca-Hernandez
- Genetics and Genomic Medicine Service. National Institute of Rehabilitation, Mexico City, Mexico
| | - Raja A H Kuchay
- Department of Biotechnology, Baba Ghulam Shah Badshah University, Rajouri, J&K, India
| | - Merve Durgut
- Kocaeli University Otorhinolaryngology Department- Audiology Unit, İzmit, Turkey
| | - Guney Bademci
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Mustafa Tekin
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA.
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA.
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Votsi C, Koutsou P, Ververis A, Georghiou A, Nicolaou P, Tanteles G, Christodoulou K. Spinal muscular atrophy type I associated with a novel SMN1 splicing variant that disrupts the expression of the functional transcript. Front Neurol 2023; 14:1241195. [PMID: 37799281 PMCID: PMC10548546 DOI: 10.3389/fneur.2023.1241195] [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: 06/16/2023] [Accepted: 08/31/2023] [Indexed: 10/07/2023] Open
Abstract
Introduction Spinal muscular atrophy (SMA) is an autosomal recessive neuromuscular disorder caused by pathogenic variants in the SMN1 gene. The majority of SMA patients harbor a homozygous deletion of SMN1 exon 7 (95%). Heterozygosity for a conventional variant and a deletion is rare (5%) and not easily detected, due to the highly homologous SMN2 gene interference. SMN2 mainly produces a truncated non-functional protein (SMN-d7) instead of the full-length functional (SMN-FL). We hereby report a novel SMN1 splicing variant in an infant with severe SMA. Methods MLPA was used for SMN1/2 exon dosage determination. Sanger sequencing approaches and long-range PCR were employed to search for an SMN1 variant. Conventional and improved Real-time PCR assays were developed for the qualitative and quantitative SMN1/2 RNA analysis. Results The novel SMN1 splice-site variant c.835-8_835-5delinsG, was identified in compound heterozygosity with SMN1 exons 7/8 deletion. RNA studies revealed complete absence of SMN1 exon 7, thus confirming a disruptive effect of the variant on SMN1 splicing. No expression of the functional SMN1-FL transcript, remarkable expression of the SMN1-d7 and increased levels of the SMN2-FL/SMN2-d7 transcripts were observed. Discussion We verified the occurrence of a non-deletion SMN1 variant and supported its pathogenicity, thus expanding the SMN1 variants spectrum. We discuss the updated SMA genetic findings in the Cypriot population, highlighting an increased percentage of intragenic variants compared to other populations.
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Affiliation(s)
- Christina Votsi
- Neurogenetics Department, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Pantelitsa Koutsou
- Neurogenetics Department, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Antonis Ververis
- Neurogenetics Department, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Anthi Georghiou
- Neurogenetics Department, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Paschalis Nicolaou
- Neurogenetics Department, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - George Tanteles
- Clinical Genetics Department, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Kyproula Christodoulou
- Neurogenetics Department, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
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Lui A, Patel RS, Krause-Hauch M, Sparks RP, Patel NA. Regulation of Human Sortilin Alternative Splicing by Glucagon-like Peptide-1 (GLP1) in Adipocytes. Int J Mol Sci 2023; 24:14324. [PMID: 37762628 PMCID: PMC10531797 DOI: 10.3390/ijms241814324] [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: 09/01/2023] [Revised: 09/13/2023] [Accepted: 09/15/2023] [Indexed: 09/29/2023] Open
Abstract
Type 2 diabetes mellitus is a chronic metabolic disease with no cure. Adipose tissue is a major site of systemic insulin resistance. Sortilin is a central component of the glucose transporter -Glut4 storage vesicles (GSV) which translocate to the plasma membrane to uptake glucose from circulation. Here, using human adipocytes we demonstrate the presence of the alternatively spliced, truncated sortilin variant (Sort_T) whose expression is significantly increased in diabetic adipose tissue. Artificial-intelligence-based modeling, molecular dynamics, intrinsically disordered region analysis, and co-immunoprecipitation demonstrated association of Sort_T with Glut4 and decreased glucose uptake in adipocytes. The results show that glucagon-like peptide-1 (GLP1) hormone decreases Sort_T. We deciphered the molecular mechanism underlying GLP1 regulation of alternative splicing of human sortilin. Using splicing minigenes and RNA-immunoprecipitation assays, the results show that GLP1 regulates Sort_T alternative splicing via the splice factor, TRA2B. We demonstrate that targeted antisense oligonucleotide morpholinos reduces Sort_T levels and improves glucose uptake in diabetic adipocytes. Thus, we demonstrate that GLP1 regulates alternative splicing of sortilin in human diabetic adipocytes.
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Affiliation(s)
- Ashley Lui
- Department of Molecular Medicine, University of South Florida, Tampa, FL 33612, USA; (A.L.); (M.K.-H.)
| | - Rekha S. Patel
- Research Service, James A. Haley Veterans Hospital, Tampa, FL 33612, USA; (R.S.P.); (R.P.S.)
| | - Meredith Krause-Hauch
- Department of Molecular Medicine, University of South Florida, Tampa, FL 33612, USA; (A.L.); (M.K.-H.)
| | - Robert P. Sparks
- Research Service, James A. Haley Veterans Hospital, Tampa, FL 33612, USA; (R.S.P.); (R.P.S.)
- Department of Medicine, Division of Gastroenterology, UMass Chan Medical School, Worcester, MA 01655, USA
| | - Niketa A. Patel
- Department of Molecular Medicine, University of South Florida, Tampa, FL 33612, USA; (A.L.); (M.K.-H.)
- Research Service, James A. Haley Veterans Hospital, Tampa, FL 33612, USA; (R.S.P.); (R.P.S.)
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Bhat GR, Jamwal RS, Sethi I, Bhat A, Shah R, Verma S, Sharma M, Sadida HQ, Al-Marzooqi SK, Masoodi T, Mirza S, Haris M, Macha MA, Akil ASA, Bhat AA, Kumar R. Associations between telomere attrition, genetic variants in telomere maintenance genes, and non-small cell lung cancer risk in the Jammu and Kashmir population of North India. BMC Cancer 2023; 23:874. [PMID: 37718447 PMCID: PMC10506276 DOI: 10.1186/s12885-023-11387-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 09/07/2023] [Indexed: 09/19/2023] Open
Abstract
BACKGROUND Telomeres are repetitive DNA sequences located at the ends of chromosomes, playing a vital role in maintaining chromosomal integrity and stability. Dysregulation of telomeres has been implicated in the development of various cancers, including non-small cell lung cancer (NSCLC), which is the most common type of lung cancer. Genetic variations within telomere maintenance genes may influence the risk of developing NSCLC. The present study aimed to evaluate the genetic associations of select variants within telomere maintenance genes in a population from Jammu and Kashmir, North India, and to investigate the relationship between telomere length and NSCLC risk. METHODS We employed the cost-effective and high-throughput MassARRAY MALDI-TOF platform to assess the genetic associations of select variants within telomere maintenance genes in a population from Jammu and Kashmir, North India. Additionally, we used TaqMan genotyping to validate our results. Furthermore, we investigated telomere length variation and its relation to NSCLC risk in the same population using dual-labeled fluorescence-based qPCR. RESULTS Our findings revealed significant associations of TERT rs10069690 and POT1 rs10228682 with NSCLC risk (adjusted p-values = 0.019 and 0.002, respectively), while TERF2 rs251796 and rs2975843 showed no significant associations. The TaqMan genotyping validation further substantiated the associations of TERT rs10069690 and rs2242652 with NSCLC risk (adjusted p-values = 0.02 and 0.003, respectively). Our results also demonstrated significantly shorter telomere lengths in NSCLC patients compared to controls (p = 0.0004). CONCLUSION This study highlights the crucial interplay between genetic variation in telomere maintenance genes, telomere attrition, and NSCLC risk in the Jammu and Kashmir population of North India. Our findings suggest that TERT and POT1 gene variants, along with telomere length, may serve as potential biomarkers and therapeutic targets for NSCLC in this population. Further research is warranted to elucidate the underlying mechanisms and to explore the potential clinical applications of these findings.
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Affiliation(s)
- Gh Rasool Bhat
- School of Biotechnology, Shri Mata Vaishno Devi University, Katra, Jammu and Kashmir, 182320, India
| | - Rajeshwer Singh Jamwal
- School of Biotechnology, Shri Mata Vaishno Devi University, Katra, Jammu and Kashmir, 182320, India
| | - Itty Sethi
- Institute of Human Genetics, University of Jammu, Jammu and Kashmir, 180001, India
| | - Amrita Bhat
- Institute of Human Genetics, University of Jammu, Jammu and Kashmir, 180001, India
| | - Ruchi Shah
- School of Biotechnology, Shri Mata Vaishno Devi University, Katra, Jammu and Kashmir, 182320, India
| | - Sonali Verma
- School of Biotechnology, Shri Mata Vaishno Devi University, Katra, Jammu and Kashmir, 182320, India
| | - Minerva Sharma
- School of Biotechnology, Shri Mata Vaishno Devi University, Katra, Jammu and Kashmir, 182320, India
| | - Hana Q Sadida
- Department of Human Genetics-Precision Medicine in Diabetes, Obesity & Cancer Program, Sidra Medicine, 26999, Doha, Qatar
| | - Sara K Al-Marzooqi
- Department of Human Genetics-Precision Medicine in Diabetes, Obesity & Cancer Program, Sidra Medicine, 26999, Doha, Qatar
| | - Tariq Masoodi
- Laboratory of Cancer Immunology and Genetics, Sidra Medicine, 26999, Doha, Qatar
| | - Sameer Mirza
- Department of Chemistry, College of Sciences, United Arab , Emirates University, 15551, Al-Ain, United Arab Emirates
| | - Mohammad Haris
- Center for Advanced Metabolic Imaging in Precision Medicine, Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA
| | - Muzafar A Macha
- Watson-Crick Centre for Molecular Medicine, Islamic University of Science and Technology, 192122, Jammu and Kashmir, India
| | - Ammira S Alshabeeb Akil
- Department of Human Genetics-Precision Medicine in Diabetes, Obesity & Cancer Program, Sidra Medicine, 26999, Doha, Qatar
| | - Ajaz A Bhat
- Department of Human Genetics-Precision Medicine in Diabetes, Obesity & Cancer Program, Sidra Medicine, 26999, Doha, Qatar.
| | - Rakesh Kumar
- School of Biotechnology, Shri Mata Vaishno Devi University, Katra, Jammu and Kashmir, 182320, India.
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Wang Y, Ding Y, Liu S, Wang C, Zhang E, Chen C, Zhu M, Zhang J, Zhu C, Ji M, Dai J, Jin G, Hu Z, Shen H, Ma H. Integrative splicing-quantitative-trait-locus analysis reveals risk loci for non-small-cell lung cancer. Am J Hum Genet 2023; 110:1574-1589. [PMID: 37562399 PMCID: PMC10502736 DOI: 10.1016/j.ajhg.2023.07.008] [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: 03/14/2023] [Revised: 07/13/2023] [Accepted: 07/14/2023] [Indexed: 08/12/2023] Open
Abstract
Splicing quantitative trait loci (sQTLs) have been demonstrated to contribute to disease etiology by affecting alternative splicing. However, the role of sQTLs in the development of non-small-cell lung cancer (NSCLC) remains unknown. Thus, we performed a genome-wide sQTL study to identify genetic variants that affect alternative splicing in lung tissues from 116 individuals of Chinese ancestry, which resulted in the identification of 1,385 sQTL-harboring genes (sGenes) containing 378,210 significant variant-intron pairs. A comprehensive characterization of these sQTLs showed that they were enriched in actively transcribed regions, genetic regulatory elements, and splicing-factor-binding sites. Moreover, sQTLs were largely distinct from expression quantitative trait loci (eQTLs) and showed significant enrichment in potential risk loci of NSCLC. We also integrated sQTLs into NSCLC GWAS datasets (13,327 affected individuals and 13,328 control individuals) by using splice-transcriptome-wide association study (spTWAS) and identified alternative splicing events in 19 genes that were significantly associated with NSCLC risk. By using functional annotation and experiments, we confirmed an sQTL variant, rs35861926, that reduced the risk of lung adenocarcinoma (rs35861926-T, OR = 0.88, 95% confidence interval [CI]: 0.82-0.93, p = 1.87 × 10-5) by promoting FARP1 exon 20 skipping to downregulate the expression level of the long transcript FARP1-011. Transcript FARP1-011 promoted the migration and proliferation of lung adenocarcinoma cells. Overall, our study provided informative lung sQTL resources and insights into the molecular mechanisms linking sQTL variants to NSCLC risk.
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Affiliation(s)
- Yuzhuo Wang
- Department of Medical Informatics, School of Biomedical Engineering and Informatics, Nanjing Medical University, Nanjing, Jiangsu 211166, China; Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Yue Ding
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China; Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Su Liu
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China; Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Cheng Wang
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China; Department of Bioinformatics, School of Biomedical Engineering and Informatics, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Erbao Zhang
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China; Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Congcong Chen
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China; Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Meng Zhu
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China; Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Jing Zhang
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China; Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Chen Zhu
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China; Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, Jiangsu 211166, China; Department of Cancer Prevention, The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, Zhejiang 310022, China
| | - Mengmeng Ji
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China; Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Juncheng Dai
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China; Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Guangfu Jin
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China; Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Zhibin Hu
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China; Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Hongbing Shen
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China; Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, Jiangsu 211166, China; Research Units of Cohort Study on Cardiovascular Diseases and Cancers, Chinese Academy of Medical Sciences, Beijing 100730, China.
| | - Hongxia Ma
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China; Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, Jiangsu 211166, China.
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Chen X, Liu X, Li QH, Lu BF, Xie BM, Ji YM, Zhao Y. A patient-derived organoid-based study identified an ASO targeting SNORD14E for endometrial cancer through reducing aberrant FOXM1 Expression and β-catenin nuclear accumulation. J Exp Clin Cancer Res 2023; 42:230. [PMID: 37667311 PMCID: PMC10478245 DOI: 10.1186/s13046-023-02801-2] [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: 03/13/2023] [Accepted: 08/16/2023] [Indexed: 09/06/2023] Open
Abstract
BACKGROUND Most of the endometrial cancer (EC) patients are diagnosis in early stage with a good prognosis while the patients with locally advanced recurrent or metastatic result in a poor prognosis. Adjuvant therapy could benefit the prognosis of patients with high-risk factors. Unfortunately, the molecular classification of great prognostic value has not yet reached an agreement and need to be further refined. The present study aims to identify new targets that have prognostic value in EC based on the method of EC patient-derived organ-like organs (PDOs), and further investigate their efficacy and mechanism. METHODS The Cancer Genome Atlas (TCGA) database was used to determine SNORD14E expression. The effects of SNORD14E were investigated using CCK8, Transwell, wound-healing assays, and a xenograft model experiment; apoptosis was measured by flow cytometry. Antisense oligonucleotide (ASO) targeting SNORD14E was designed and patient-derived organoids (PDO) models in EC patients was established. A xenograft mouse and PDO model were employed to evaluate the effects of ASO targeting SNORD14E. RNA-seq, Nm-seq, and RNA immunoprecipitation (RIP) experiments were employed to confirm the alternative splicing (AS) and modification induced by SNORD14E. A minigene reporter gene assay was conducted to confirm AS and splicing factors on a variable exon. Actinomycin-d (Act-D) and Reverse Transcription at Low deoxy-ribonucleoside triphosphate concentrations followed by PCR (RTL-P) were utilized to confirm the effects of 2'-O methylation modification on FOXM1. RESULTS We found that SNORD14E was overexpressed in EC tissues and patients with high expressed SNORD14E were distributed in the TCGA biomolecular classification subgroups without difference. Further, SNORD14E could reduce disease-free survival (DFS) and recurrence free survival (RFS) of EC patients. SNORD14E promoted proliferation, migration, and invasion and inhibited the apoptosis of EC cells in vitro. ASOs targeting SNORD14E inhibited cell proliferation, migration, invasion while promoted cell apoptosis. ASOs targeting SNORD14E inhibited tumor growth in the xenograft mouse model. TCGA-UCEC database showed that the proportion of patients with high expression of SNORD14E in middle-high risk and high-risk patients recommended by EMSO-ESGO-ESTRO guidelines for adjuvant therapy is more than 50%. Next, we enrolled 8 cases of high-risk and high-risk EC patients according to EMSO-ESGO-ESTRO guidelines and successfully constructed EC-PDOs. ASOs targeting SNORD14E inhibited the EC-PDO growth. Mechanistically, SNORD14E could recognize the mRNA of FOXM1 and recruit SRSF1 to promote the shearing of the variable exon VIIa of FOXM1, resulting in the overexpression of the FOXM1 malignant subtypes FOXM1b and FOXM1c. In addition, SNORD14E modified FOXM1 mRNA with 2`-O-methylation, which prolonged the half-life of FOXM1 mRNA. The nucleus accumulation of β-catenin caused by aberrant FOXM1 expression led to EC progression. CONCLUSIONS ASO targeting SNORD14E can be an effective treatment for EC.
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Affiliation(s)
- Xi Chen
- Department of Obstetrics and Gynecology, Department of Gynecologic Oncology Research Office, Guangzhou Key Laboratory of Targeted Therapy for Gynecologic Oncology, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, No.63 Duobao Road, Liwan District, Guangzhou, 510150, Guangdong Province, PR China
| | - Xin Liu
- Department of Obstetrics and Gynecology, Department of Gynecologic Oncology Research Office, Guangzhou Key Laboratory of Targeted Therapy for Gynecologic Oncology, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, No.63 Duobao Road, Liwan District, Guangzhou, 510150, Guangdong Province, PR China
| | - Qian-Hui Li
- Department of Obstetrics and Gynecology, Department of Gynecologic Oncology Research Office, Guangzhou Key Laboratory of Targeted Therapy for Gynecologic Oncology, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, No.63 Duobao Road, Liwan District, Guangzhou, 510150, Guangdong Province, PR China
| | - Bing-Feng Lu
- Department of Obstetrics and Gynecology, Department of Gynecologic Oncology Research Office, Guangzhou Key Laboratory of Targeted Therapy for Gynecologic Oncology, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, No.63 Duobao Road, Liwan District, Guangzhou, 510150, Guangdong Province, PR China
| | - Bu-Min Xie
- Department of Obstetrics and Gynecology, Department of Gynecologic Oncology Research Office, Guangzhou Key Laboratory of Targeted Therapy for Gynecologic Oncology, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, No.63 Duobao Road, Liwan District, Guangzhou, 510150, Guangdong Province, PR China
| | - Yu-Meng Ji
- Department of Obstetrics and Gynecology, Department of Gynecologic Oncology Research Office, Guangzhou Key Laboratory of Targeted Therapy for Gynecologic Oncology, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, No.63 Duobao Road, Liwan District, Guangzhou, 510150, Guangdong Province, PR China
| | - Yang Zhao
- Department of Obstetrics and Gynecology, Department of Gynecologic Oncology Research Office, Guangzhou Key Laboratory of Targeted Therapy for Gynecologic Oncology, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, No.63 Duobao Road, Liwan District, Guangzhou, 510150, Guangdong Province, PR China.
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McElroy A, Gray‐Edwards H, Coghill LM, Lyons LA. Precision medicine using whole genome sequencing in a cat identifies a novel COL5A1 variant for classical Ehlers-Danlos syndrome. J Vet Intern Med 2023; 37:1716-1724. [PMID: 37594181 PMCID: PMC10473008 DOI: 10.1111/jvim.16805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 06/28/2023] [Indexed: 08/19/2023] Open
Abstract
BACKGROUND Ehlers-Danlos syndromes (EDS) are a heterogeneous group of heritable connective tissue disorders occurring in both human and veterinary patients. The genetics of these disorders are poorly described in small animal patients. HYPOTHESIS/OBJECTIVES Define the clinical manifestations and genetic cause of a suspected form of EDS in a cat. ANIMALS A 14-week-old male domestic medium hair cat was presented with skin hyperextensibility and fragility. The classic tragic facial expression was observed as well as chronic pruritus and mild hyperesthesia. METHODS Blood samples and a skin biopsy sample were collected from the affected cat. Clinical examinations, histology, electron microscopy and whole genome sequencing were conducted to characterize the clinical presentation and identify possible pathogenic DNA variants to support a diagnosis. Criteria defining variant pathogenicity were examined including human disease variant databases. RESULTS Histology showed sparse, disorganized collagen and an increase in cutaneous mast cells. Electron microscopy identified ultrastructural defects commonly seen in collagen type V alpha 1 chain (COL5A1) variants including flower-like collagen fibrils in cross-section. Whole genome sequencing and comparison with 413 cats in the 99 Lives Cat Genome Sequencing Consortium database identified a novel splice acceptor site variant at exon 4 in COL5A1 (c.501-2A>C). CONCLUSIONS AND CLINICAL IMPORTANCE Our report broadens the current understanding of EDS in veterinary patients and supports the use of precision medicine techniques in clinical veterinary practice. The classification of variants for pathogenicity should be considered in companion animals.
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Affiliation(s)
- Abigail McElroy
- Horae Gene Therapy CenterUniversity of Massachusetts Chan Medical SchoolWorcesterMassachusettsUSA
| | - Heather Gray‐Edwards
- Horae Gene Therapy CenterUniversity of Massachusetts Chan Medical SchoolWorcesterMassachusettsUSA
- Department of RadiologyUniversity of Massachusetts Chan Medical SchoolWorcesterMassachusettsUSA
| | - Lyndon M. Coghill
- Department of Veterinary Pathobiology, College of Veterinary MedicineUniversity of MissouriColumbiaMissouriUSA
| | - Leslie A. Lyons
- Department of Veterinary Medicine & Surgery, College of Veterinary MedicineUniversity of MissouriColumbiaMissouriUSA
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Jin B, Zhu J, Pan T, Yang Y, Liang L, Zhou Y, Zhang T, Teng Y, Wang Z, Wang X, Tian Q, Guo B, Li H, Chen T. MEN1 is a regulator of alternative splicing and prevents R-loop-induced genome instability through suppression of RNA polymerase II elongation. Nucleic Acids Res 2023; 51:7951-7971. [PMID: 37395406 PMCID: PMC10450199 DOI: 10.1093/nar/gkad548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 06/02/2023] [Accepted: 06/15/2023] [Indexed: 07/04/2023] Open
Abstract
The fidelity of alternative splicing (AS) patterns is essential for growth development and cell fate determination. However, the scope of the molecular switches that regulate AS remains largely unexplored. Here we show that MEN1 is a previously unknown splicing regulatory factor. MEN1 deletion resulted in reprogramming of AS patterns in mouse lung tissue and human lung cancer cells, suggesting that MEN1 has a general function in regulating alternative precursor mRNA splicing. MEN1 altered exon skipping and the abundance of mRNA splicing isoforms of certain genes with suboptimal splice sites. Chromatin immunoprecipitation and chromosome walking assays revealed that MEN1 favored the accumulation of RNA polymerase II (Pol II) in regions encoding variant exons. Our data suggest that MEN1 regulates AS by slowing the Pol II elongation rate and that defects in these processes trigger R-loop formation, DNA damage accumulation and genome instability. Furthermore, we identified 28 MEN1-regulated exon-skipping events in lung cancer cells that were closely correlated with survival in patients with lung adenocarcinoma, and MEN1 deficiency sensitized lung cancer cells to splicing inhibitors. Collectively, these findings led to the identification of a novel biological role for menin in maintaining AS homeostasis and link this role to the regulation of cancer cell behavior.
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Affiliation(s)
- Bangming Jin
- Department of Physiology, School of Basic Medical Sciences, Guizhou Medical University, 550025 Guiyang, China
- Department of Surgery, Affiliated Hospital of Guizhou Medical University, 550025 Guiyang, China
- Transformation Engineering Research Center of Chronic Disease Diagnosis and Treatment, Guizhou Medical University, Guiyang, China
- Guizhou Provincial Key Laboratory of Pathogenesis and Drug Research on Common Chronic Diseases, Guizhou Medical University, 550025 Guiyang, China
| | - Jiamei Zhu
- Department of Physiology, School of Basic Medical Sciences, Guizhou Medical University, 550025 Guiyang, China
- Transformation Engineering Research Center of Chronic Disease Diagnosis and Treatment, Guizhou Medical University, Guiyang, China
- Guizhou Provincial Key Laboratory of Pathogenesis and Drug Research on Common Chronic Diseases, Guizhou Medical University, 550025 Guiyang, China
| | - Ting Pan
- Department of Physiology, School of Basic Medical Sciences, Guizhou Medical University, 550025 Guiyang, China
- Transformation Engineering Research Center of Chronic Disease Diagnosis and Treatment, Guizhou Medical University, Guiyang, China
- Guizhou Provincial Key Laboratory of Pathogenesis and Drug Research on Common Chronic Diseases, Guizhou Medical University, 550025 Guiyang, China
| | - Yunqiao Yang
- Department of Physiology, School of Basic Medical Sciences, Guizhou Medical University, 550025 Guiyang, China
- Department of Surgery, Affiliated Hospital of Guizhou Medical University, 550025 Guiyang, China
- Transformation Engineering Research Center of Chronic Disease Diagnosis and Treatment, Guizhou Medical University, Guiyang, China
- Guizhou Provincial Key Laboratory of Pathogenesis and Drug Research on Common Chronic Diseases, Guizhou Medical University, 550025 Guiyang, China
| | - Li Liang
- Department of Physiology, School of Basic Medical Sciences, Guizhou Medical University, 550025 Guiyang, China
- Transformation Engineering Research Center of Chronic Disease Diagnosis and Treatment, Guizhou Medical University, Guiyang, China
- Guizhou Provincial Key Laboratory of Pathogenesis and Drug Research on Common Chronic Diseases, Guizhou Medical University, 550025 Guiyang, China
| | - Yuxia Zhou
- Department of Physiology, School of Basic Medical Sciences, Guizhou Medical University, 550025 Guiyang, China
- Transformation Engineering Research Center of Chronic Disease Diagnosis and Treatment, Guizhou Medical University, Guiyang, China
- Guizhou Provincial Key Laboratory of Pathogenesis and Drug Research on Common Chronic Diseases, Guizhou Medical University, 550025 Guiyang, China
| | - Tuo Zhang
- Department of Physiology, School of Basic Medical Sciences, Guizhou Medical University, 550025 Guiyang, China
- Transformation Engineering Research Center of Chronic Disease Diagnosis and Treatment, Guizhou Medical University, Guiyang, China
- Guizhou Provincial Key Laboratory of Pathogenesis and Drug Research on Common Chronic Diseases, Guizhou Medical University, 550025 Guiyang, China
| | - Yin Teng
- Department of Surgery, Affiliated Hospital of Guizhou Medical University, 550025 Guiyang, China
- Guizhou Institute of Precision Medicine, Affiliated Hospital of Guizhou Medical University, 550025 Guiyang, China
| | - Ziming Wang
- Department of Physiology, School of Basic Medical Sciences, Guizhou Medical University, 550025 Guiyang, China
- Transformation Engineering Research Center of Chronic Disease Diagnosis and Treatment, Guizhou Medical University, Guiyang, China
- Guizhou Provincial Key Laboratory of Pathogenesis and Drug Research on Common Chronic Diseases, Guizhou Medical University, 550025 Guiyang, China
| | - Xuyan Wang
- Department of Physiology, School of Basic Medical Sciences, Guizhou Medical University, 550025 Guiyang, China
- Transformation Engineering Research Center of Chronic Disease Diagnosis and Treatment, Guizhou Medical University, Guiyang, China
- Guizhou Provincial Key Laboratory of Pathogenesis and Drug Research on Common Chronic Diseases, Guizhou Medical University, 550025 Guiyang, China
| | - Qianting Tian
- Transformation Engineering Research Center of Chronic Disease Diagnosis and Treatment, Guizhou Medical University, Guiyang, China
- Guizhou Institute of Precision Medicine, Affiliated Hospital of Guizhou Medical University, 550025 Guiyang, China
| | - Bing Guo
- Department of Physiology, School of Basic Medical Sciences, Guizhou Medical University, 550025 Guiyang, China
- Transformation Engineering Research Center of Chronic Disease Diagnosis and Treatment, Guizhou Medical University, Guiyang, China
- Guizhou Provincial Key Laboratory of Pathogenesis and Drug Research on Common Chronic Diseases, Guizhou Medical University, 550025 Guiyang, China
| | - Haiyang Li
- Department of Surgery, Affiliated Hospital of Guizhou Medical University, 550025 Guiyang, China
- Guizhou Institute of Precision Medicine, Affiliated Hospital of Guizhou Medical University, 550025 Guiyang, China
| | - Tengxiang Chen
- Department of Physiology, School of Basic Medical Sciences, Guizhou Medical University, 550025 Guiyang, China
- Department of Surgery, Affiliated Hospital of Guizhou Medical University, 550025 Guiyang, China
- Transformation Engineering Research Center of Chronic Disease Diagnosis and Treatment, Guizhou Medical University, Guiyang, China
- Guizhou Provincial Key Laboratory of Pathogenesis and Drug Research on Common Chronic Diseases, Guizhou Medical University, 550025 Guiyang, China
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Ferreira CS, Francisco Junior RDS, Gerber AL, Guimarães APDC, de Carvalho FAA, Dos Reis BCS, Pinto-Mariz F, de Souza MS, de Vasconcelos ZFM, Goudouris ES, Vasconcelos ATR. Genetic screening in a Brazilian cohort with inborn errors of immunity. BMC Genom Data 2023; 24:47. [PMID: 37592284 PMCID: PMC10433585 DOI: 10.1186/s12863-023-01148-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 08/07/2023] [Indexed: 08/19/2023] Open
Abstract
BACKGROUND Inherited genetic defects in immune system-related genes can result in Inborn Errors of Immunity (IEI), also known as Primary Immunodeficiencies (PID). Diagnosis of IEI disorders is challenging due to overlapping clinical manifestations. Accurate identification of disease-causing germline variants is crucial for appropriate treatment, prognosis, and genetic counseling. However, genetic sequencing is challenging in low-income countries like Brazil. This study aimed to perform genetic screening on patients treated within Brazil's public Unified Health System to identify candidate genetic variants associated with the patient's phenotype. METHODS Thirteen singleton unrelated patients from three hospitals in Rio de Janeiro were enrolled in this study. Genomic DNA was extracted from the peripheral blood lymphocytes of each patient, and whole exome sequencing (WES) analyses were conducted using Illumina NextSeq. Germline genetic variants in IEI-related genes were prioritized using a computational framework considering their molecular consequence in coding regions; minor allele frequency ≤ 0.01; pathogenicity classification based on American College of Medical Genetics and Genomics and the Association for Molecular Pathology (ACMG/AMP) guidelines gathered from the VarSome clinical database; and IEI-related phenotype using the Franklin tool. The genes classification into IEI categories follows internationally recognized guidelines informed by the International Union of Immunological Societies Expert Committee. Additional methods for confirmation of the variant included Sanger sequencing, phasing analysis, and splice site prediction. RESULTS A total of 16 disease-causing variants in nine genes, encompassing six different IEI categories, were identified. X-Linked Agammaglobulinemia, caused by BTK variations, emerged as the most prevalent IEI disorder in the cohort. However, pathogenic and likely pathogenic variants were also reported in other known IEI-related genes, namely CD40LG, CARD11, WAS, CYBB, C6, and LRBA. Interestingly, two patients with suspected IEI exhibited pathogenic variants in non-IEI-related genes, ABCA12 and SLC25A13, potentially explaining their phenotypes. CONCLUSIONS Genetic screening through WES enabled the detection of potentially harmful variants associated with IEI disorders. These findings contribute to a better understanding of patients' clinical manifestations by elucidating the genetic basis underlying their phenotypes.
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Affiliation(s)
- Cristina Santos Ferreira
- Bioinformatics Laboratory-LABINFO, National Laboratory of Scientific Computation LNCC/MCTIC, Av. Getúlio Vargas, 333, Quitandinha CEP: 25651-075, Petrópolis, Rio de Janeiro, Brazil
| | - Ronaldo da Silva Francisco Junior
- Bioinformatics Laboratory-LABINFO, National Laboratory of Scientific Computation LNCC/MCTIC, Av. Getúlio Vargas, 333, Quitandinha CEP: 25651-075, Petrópolis, Rio de Janeiro, Brazil
| | - Alexandra Lehmkuhl Gerber
- Bioinformatics Laboratory-LABINFO, National Laboratory of Scientific Computation LNCC/MCTIC, Av. Getúlio Vargas, 333, Quitandinha CEP: 25651-075, Petrópolis, Rio de Janeiro, Brazil
| | - Ana Paula de Campos Guimarães
- Bioinformatics Laboratory-LABINFO, National Laboratory of Scientific Computation LNCC/MCTIC, Av. Getúlio Vargas, 333, Quitandinha CEP: 25651-075, Petrópolis, Rio de Janeiro, Brazil
| | - Flavia Amendola Anisio de Carvalho
- Allergy and Immunology Service of Institute of Women, Children and Adolescents' Health Fernandes Figueira (IFF/FIOCRUZ), Rio de Janeiro, RJ, Brazil
| | - Bárbara Carvalho Santos Dos Reis
- Allergy and Immunology Service of Institute of Women, Children and Adolescents' Health Fernandes Figueira (IFF/FIOCRUZ), Rio de Janeiro, RJ, Brazil
| | - Fernanda Pinto-Mariz
- Allergy and Immunology Service of the Martagão Gesteira Institute for Childcare and Pediatrics (IPPMG) - Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | - Monica Soares de Souza
- Allergy and Immunology Sector of the Pediatric Service of the Federal Hospital of Rio de Janeiro State (HFSE) - Ministry of Health, Rio de Janeiro, RJ, Brazil
| | - Zilton Farias Meira de Vasconcelos
- Laboratory of High Complexity of the Institute of Women, Children and Adolescents' Health Fernandes Figueira (IFF/FIOCRUZ), Rio de Janeiro, RJ, Brazil
| | - Ekaterini Simões Goudouris
- Allergy and Immunology Service of the Martagão Gesteira Institute for Childcare and Pediatrics (IPPMG) - Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | - Ana Tereza Ribeiro Vasconcelos
- Bioinformatics Laboratory-LABINFO, National Laboratory of Scientific Computation LNCC/MCTIC, Av. Getúlio Vargas, 333, Quitandinha CEP: 25651-075, Petrópolis, Rio de Janeiro, Brazil.
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Choquet K, Baxter-Koenigs AR, Dülk SL, Smalec BM, Rouskin S, Churchman LS. Pre-mRNA splicing order is predetermined and maintains splicing fidelity across multi-intronic transcripts. Nat Struct Mol Biol 2023; 30:1064-1076. [PMID: 37443198 PMCID: PMC10653200 DOI: 10.1038/s41594-023-01035-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 06/13/2023] [Indexed: 07/15/2023]
Abstract
Combinatorially, intron excision within a given nascent transcript could proceed down any of thousands of paths, each of which would expose different dynamic landscapes of cis-elements and contribute to alternative splicing. In this study, we found that post-transcriptional multi-intron splicing order in human cells is largely predetermined, with most genes spliced in one or a few predominant orders. Strikingly, these orders were conserved across cell types and stages of motor neuron differentiation. Introns flanking alternatively spliced exons were frequently excised last, after their neighboring introns. Perturbations to the spliceosomal U2 snRNA altered the preferred splicing order of many genes, and these alterations were associated with the retention of other introns in the same transcript. In one gene, early removal of specific introns was sufficient to induce delayed excision of three proximal introns, and this delay was caused by two distinct cis-regulatory mechanisms. Together, our results demonstrate that multi-intron splicing order in human cells is predetermined, is influenced by a component of the spliceosome and ensures splicing fidelity across long pre-mRNAs.
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Affiliation(s)
- Karine Choquet
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | | | - Sarah-Luisa Dülk
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Brendan M Smalec
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Silvi Rouskin
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - L Stirling Churchman
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
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35
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Choi SY, Kim JW, Oh SH, Cheon S, Yee J, Kim SJ, Gwak HS, Chung JE. Prediction of medication-related osteonecrosis of the jaws using machine learning methods from estrogen receptor 1 polymorphisms and clinical information. Front Med (Lausanne) 2023; 10:1140620. [PMID: 37415765 PMCID: PMC10321771 DOI: 10.3389/fmed.2023.1140620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 05/23/2023] [Indexed: 07/08/2023] Open
Abstract
Objective The purpose of this study was to evaluate the effect of estrogen receptor 1 (ESR1) polymorphisms on the development of medication-related osteonecrosis of the jaws (MRONJ) in women with osteoporosis. Methods A total of 125 patients taking bisphosphonates was evaluated the relationship between MRONJ occurrence and single nucleotide polymorphisms (SNPs) of ESR1. Clinical information was collected, including current age, treatment duration, and comorbidity. Univariate and Multivariable regression analyzes were performed to evaluate the independent predictive factors for MRONJ occurrence. Predictive models were constructed using machine learning methods such as Lasso regression, Random forest (RF), and Support vector machine (SVM). The area under the receiver-operating curve (AUROC) was used to evaluate the performance of a binary classifier. Result Two SNPs of ESR1 (rs4870056 and rs78177662) were significantly associated with MRONJ development. Patients with variant allele (A) of rs4870056 showed 2.45 times (95% CI, 1.03-5.87) the odds of MRONJ occurrence compared to those with wild-type homozygote (GG) after adjusting covariates. Additionally, carriers with variant allele (T) of rs78177662 had higher odds than those with wild-type homozygote (CC) (adjusted odds ratio (aOR), 2.64, 95% CI, 1.00-6.94). Among demographic variables, age ≥ 72 years (aOR, 3.98, 95% CI, 1.60-9.87) and bisphosphonate exposure ≥48 months (aOR, 3.16, 95% CI, 1.26-7.93) were also significant risk factors for MRONJ occurrence. AUROC values of machine learning methods ranged between 0.756-0.806 in the study. Conclusion Our study showed that the MRONJ occurrence was associated with ESR1 polymorphisms in osteoporotic women.
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Affiliation(s)
- Seo-Yong Choi
- College of Pharmacy and Institute of Pharmaceutical Science and Technology, Hanyang University, Ansan, Republic of Korea
| | - Jin-Woo Kim
- Department of Oral and Maxillofacial Surgery, School of Medicine, Ewha Womans University, Seoul, Republic of Korea
| | - Sang-Hyeon Oh
- College of Pharmacy and Institute of Pharmaceutical Science and Technology, Hanyang University, Ansan, Republic of Korea
| | - Seunghyun Cheon
- College of Pharmacy and Institute of Pharmaceutical Science and Technology, Hanyang University, Ansan, Republic of Korea
| | - Jeong Yee
- College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul, Republic of Korea
| | - Sun-Jong Kim
- Department of Oral and Maxillofacial Surgery, School of Medicine, Ewha Womans University, Seoul, Republic of Korea
| | - Hye Sun Gwak
- College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul, Republic of Korea
| | - Jee-Eun Chung
- College of Pharmacy and Institute of Pharmaceutical Science and Technology, Hanyang University, Ansan, Republic of Korea
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36
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Whelan L, Dockery A, Stephenson KAJ, Zhu J, Kopčić E, Post IJM, Khan M, Corradi Z, Wynne N, O' Byrne JJ, Duignan E, Silvestri G, Roosing S, Cremers FPM, Keegan DJ, Kenna PF, Farrar GJ. Detailed analysis of an enriched deep intronic ABCA4 variant in Irish Stargardt disease patients. Sci Rep 2023; 13:9380. [PMID: 37296172 PMCID: PMC10256698 DOI: 10.1038/s41598-023-35889-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 05/25/2023] [Indexed: 06/12/2023] Open
Abstract
Over 15% of probands in a large cohort of more than 1500 inherited retinal degeneration patients present with a clinical diagnosis of Stargardt disease (STGD1), a recessive form of macular dystrophy caused by biallelic variants in the ABCA4 gene. Participants were clinically examined and underwent either target capture sequencing of the exons and some pathogenic intronic regions of ABCA4, sequencing of the entire ABCA4 gene or whole genome sequencing. ABCA4 c.4539 + 2028C > T, p.[= ,Arg1514Leufs*36] is a pathogenic deep intronic variant that results in a retina-specific 345-nucleotide pseudoexon inclusion. Through analysis of the Irish STGD1 cohort, 25 individuals across 18 pedigrees harbour ABCA4 c.4539 + 2028C > T and another pathogenic variant. This includes, to the best of our knowledge, the only two homozygous patients identified to date. This provides important evidence of variant pathogenicity for this deep intronic variant, highlighting the value of homozygotes for variant interpretation. 15 other heterozygous incidents of this variant in patients have been reported globally, indicating significant enrichment in the Irish population. We provide detailed genetic and clinical characterization of these patients, illustrating that ABCA4 c.4539 + 2028C > T is a variant of mild to intermediate severity. These results have important implications for unresolved STGD1 patients globally with approximately 10% of the population in some western countries claiming Irish heritage. This study exemplifies that detection and characterization of founder variants is a diagnostic imperative.
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Affiliation(s)
- Laura Whelan
- The School of Genetics and Microbiology, Trinity College Dublin, Dublin 2, Ireland.
| | - Adrian Dockery
- The School of Genetics and Microbiology, Trinity College Dublin, Dublin 2, Ireland
- Next Generation Sequencing Laboratory, Pathology Department, The Mater Misericordiae University Hospital, Dublin 7, Ireland
| | - Kirk A J Stephenson
- Department of Ophthalmology, Royal Victoria Eye and Ear Hospital, Dublin 2, Ireland
- Mater Clinical Ophthalmic Genetics Unit, The Mater Misericordiae University Hospital, Dublin 7, Ireland
| | - Julia Zhu
- Mater Clinical Ophthalmic Genetics Unit, The Mater Misericordiae University Hospital, Dublin 7, Ireland
| | - Ella Kopčić
- The School of Genetics and Microbiology, Trinity College Dublin, Dublin 2, Ireland
| | - Iris J M Post
- The School of Genetics and Microbiology, Trinity College Dublin, Dublin 2, Ireland
| | - Mubeen Khan
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands
- International Max Planck Research School for Language Sciences, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands
| | - Zelia Corradi
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
- Academic Alliance Genetics, Radboud University Medical Center, Nijmegen, and Maastricht University Medical Center+, Maastricht, The Netherlands
| | - Niamh Wynne
- Department of Ophthalmology, Royal Victoria Eye and Ear Hospital, Dublin 2, Ireland
| | - James J O' Byrne
- Mater Clinical Ophthalmic Genetics Unit, The Mater Misericordiae University Hospital, Dublin 7, Ireland
- International Max Planck Research School for Language Sciences, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands
- National Centre for Inherited Metabolic Disorders, The Mater Misericordiae University Hospital, Dublin 7, Ireland
- School of Medicine, Trinity College Dublin, Dublin 2, Ireland
| | - Emma Duignan
- Department of Ophthalmology, Royal Victoria Eye and Ear Hospital, Dublin 2, Ireland
| | - Giuliana Silvestri
- Centre for Experimental Medicine, Queen's University Belfast, Belfast, Northern Ireland, UK
- School of Medicine, University College Dublin, Dublin 4, Ireland
- Department of Ophthalmology, The Royal Victoria Hospital, Belfast, Northern Ireland, UK
| | - Susanne Roosing
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
- Academic Alliance Genetics, Radboud University Medical Center, Nijmegen, and Maastricht University Medical Center+, Maastricht, The Netherlands
| | - Frans P M Cremers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
- Academic Alliance Genetics, Radboud University Medical Center, Nijmegen, and Maastricht University Medical Center+, Maastricht, The Netherlands
| | - David J Keegan
- Mater Clinical Ophthalmic Genetics Unit, The Mater Misericordiae University Hospital, Dublin 7, Ireland
| | - Paul F Kenna
- The School of Genetics and Microbiology, Trinity College Dublin, Dublin 2, Ireland
- Department of Ophthalmology, Royal Victoria Eye and Ear Hospital, Dublin 2, Ireland
| | - G Jane Farrar
- The School of Genetics and Microbiology, Trinity College Dublin, Dublin 2, Ireland
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Sullivan PJ, Gayevskiy V, Davis RL, Wong M, Mayoh C, Mallawaarachchi A, Hort Y, McCabe MJ, Beecroft S, Jackson MR, Arts P, Dubowsky A, Laing N, Dinger ME, Scott HS, Oates E, Pinese M, Cowley MJ. Introme accurately predicts the impact of coding and noncoding variants on gene splicing, with clinical applications. Genome Biol 2023; 24:118. [PMID: 37198692 PMCID: PMC10190034 DOI: 10.1186/s13059-023-02936-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 04/10/2023] [Indexed: 05/19/2023] Open
Abstract
Predicting the impact of coding and noncoding variants on splicing is challenging, particularly in non-canonical splice sites, leading to missed diagnoses in patients. Existing splice prediction tools are complementary but knowing which to use for each splicing context remains difficult. Here, we describe Introme, which uses machine learning to integrate predictions from several splice detection tools, additional splicing rules, and gene architecture features to comprehensively evaluate the likelihood of a variant impacting splicing. Through extensive benchmarking across 21,000 splice-altering variants, Introme outperformed all tools (auPRC: 0.98) for the detection of clinically significant splice variants. Introme is available at https://github.com/CCICB/introme .
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Affiliation(s)
- Patricia J Sullivan
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia
- School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Sydney, NSW, Australia
- University of New South Wales Centre for Childhood Cancer Research, UNSW Sydney, Sydney, NSW, Australia
| | - Velimir Gayevskiy
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, Australia
| | - Ryan L Davis
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, Australia
- Department of Neurogenetics, Kolling Institute, St. Leonards, NSW, Australia
- Sydney Medical School-Northern, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
| | - Marie Wong
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia
- School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Sydney, NSW, Australia
| | - Chelsea Mayoh
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia
- School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Sydney, NSW, Australia
| | - Amali Mallawaarachchi
- Division of Genomics and Epigenetics, Garvan Institute of Medical Research, Sydney, Australia
- Clinical Genetics Unit, Institute of Precision Medicine and Bioinformatics, Sydney Local Health District, Sydney, Australia
| | - Yvonne Hort
- Division of Genomics and Epigenetics, Garvan Institute of Medical Research, Sydney, Australia
| | - Mark J McCabe
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, Australia
| | - Sarah Beecroft
- Centre for Medical Research, University of Western Australia, Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA, Australia
| | - Matilda R Jackson
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, An Alliance Between SA Pathology and the University of South Australia, Adelaide, Australia
- Australian Genomics, Parkville, VIC, Australia
| | - Peer Arts
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, An Alliance Between SA Pathology and the University of South Australia, Adelaide, Australia
| | - Andrew Dubowsky
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, Australia
| | - Nigel Laing
- Centre for Medical Research, University of Western Australia, Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA, Australia
| | - Marcel E Dinger
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, Australia
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - Hamish S Scott
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, An Alliance Between SA Pathology and the University of South Australia, Adelaide, Australia
- Australian Genomics, Parkville, VIC, Australia
- School of Medicine, University of Adelaide, Adelaide, SA, Australia
- ACRF Cancer Genomics Facility, Centre for Cancer Biology, An Alliance Between SA Pathology and the University of South Australia, Adelaide, SA, Australia
| | - Emily Oates
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - Mark Pinese
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia
- School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Sydney, NSW, Australia
| | - Mark J Cowley
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia.
- School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Sydney, NSW, Australia.
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38
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Arizaca Maquera KA, Welden JR, Margvelani G, Miranda Sardón SC, Hart S, Robil N, Hernandez AG, de la Grange P, Nelson PT, Stamm S. Alzheimer's disease pathogenetic progression is associated with changes in regulated retained introns and editing of circular RNAs. Front Mol Neurosci 2023; 16:1141079. [PMID: 37266374 PMCID: PMC10231643 DOI: 10.3389/fnmol.2023.1141079] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 02/20/2023] [Indexed: 06/03/2023] Open
Abstract
Introduction The molecular changes leading to Alzheimer's disease (AD) progression are poorly understood. A decisive factor in the disease occurs when neurofibrillary tangles (NFT) composed of microtubule associated protein tau (MAPT) form in the entorhinal cortex and then spread throughout the brain. Methods We therefore determined mRNA and circular RNA changes during AD progression, comparing Braak NFT stages I-VI. Total RNA was isolated from human brain (entorhinal and frontotemporal cortex). Poly(A)+ RNA was subjected to Nanopore sequencing, and total RNA was analyzed by standard Illumina sequencing. Circular RNAs were sequenced from RNase R treated and rRNA depleted total RNA. The sequences were analyzed using different bioinformatic tools, and expression constructs for circRNAs were analyzed in transfection experiments. Results We detected 11,873 circRNAs of which 276 correlated with Braak NFT stages. Adenosine to inosine RNA editing increased about threefold in circRNAs during AD progression. Importantly, this correlation cannot be detected with mRNAs. CircMAN2A1 expression correlated with AD progression and transfection experiments indicated that RNA editing promoted its translation using start codons out of frame with linear mRNAs, which generates novel proteins. Discussion Thus, we identified novel regulated retained introns that correlate with NFT Braak stages and provide evidence for a role of translated circRNAs in AD development.
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Affiliation(s)
| | - Justin Ralph Welden
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, United States
| | - Giorgi Margvelani
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, United States
| | - Sandra C. Miranda Sardón
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, United States
| | - Samantha Hart
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, United States
| | | | | | | | - Peter T. Nelson
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, United States
- Alzheimer’s Disease Research Center and Department of Pathology and Laboratory Medicine, University of Kentucky, Lexington, KY, United States
| | - Stefan Stamm
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, United States
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Bryen SJ, Zhang K, Dziaduch G, Bommireddipalli S, Naseri T, Reupena MS, Viali S, Minster RL, Waddell LB, Charlton A, O’Grady GL, Evesson FJ, Cooper ST. Compound heterozygous splicing variants expand the genotypic spectrum of EMC1-related disorders. Clin Genet 2023; 103:553-559. [PMID: 36799557 PMCID: PMC10101692 DOI: 10.1111/cge.14311] [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] [Revised: 02/09/2023] [Accepted: 02/13/2023] [Indexed: 02/18/2023]
Abstract
EMC1 encodes subunit 1 of the endoplasmic reticulum (ER) membrane protein complex (EMC), a transmembrane domain insertase involved in membrane protein biosynthesis. Variants in EMC1 are described as a cause of global developmental delay, hypotonia, cortical visual impairment, and commonly, cerebral atrophy on MRI scan. We report an individual with severe global developmental delay and progressive cerebellar atrophy in whom exome sequencing identified a heterozygous essential splice-site variant in intron-3 of EMC1 (NM_015047.3:c.287-1G>A). Whole genome sequencing (WGS) identified a deep intronic variant in intron-20 of EMC1 (NM_015047.3:c.2588-771C>G) that was poorly predicted by in silico programs to disrupt pre-mRNA splicing. Reverse Transcription-PCR (RT-PCR) revealed stochastic activation of a pseudo-exon associated with the c.2588-771C>G variant and mis-splicing arising from the c.287-1G>A variant. This case highlights the utility of WGS and RNA studies to identify and assess likely pathogenicity of deep intronic variants and expands the genotypic and phenotypic spectrum of EMC1-related disorders.
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Affiliation(s)
- Samantha J. Bryen
- Kids Neuroscience Centre, The Children’s Hospital at Westmead, NSW, Australia
- School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, NSW, Australia
| | - Katharine Zhang
- Kids Neuroscience Centre, The Children’s Hospital at Westmead, NSW, Australia
- Functional Neuromics, Children’s Medical Research Institute, Westmead, NSW, Australia
| | - Gregory Dziaduch
- Kids Neuroscience Centre, The Children’s Hospital at Westmead, NSW, Australia
- Functional Neuromics, Children’s Medical Research Institute, Westmead, NSW, Australia
| | - Shobhana Bommireddipalli
- Kids Neuroscience Centre, The Children’s Hospital at Westmead, NSW, Australia
- School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, NSW, Australia
| | - Take Naseri
- Ministry of Health, Apia, Samoa
- International Health Institute, School of Public Health, Brown University, Providence, RI, USA
| | | | | | | | - Leigh B. Waddell
- Kids Neuroscience Centre, The Children’s Hospital at Westmead, NSW, Australia
- School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, NSW, Australia
| | | | - Gina L. O’Grady
- Kids Neuroscience Centre, The Children’s Hospital at Westmead, NSW, Australia
- School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, NSW, Australia
- Paediatric Neuroservices, Starship Child Health, Auckland, New Zealand
| | - Frances J. Evesson
- Kids Neuroscience Centre, The Children’s Hospital at Westmead, NSW, Australia
- Functional Neuromics, Children’s Medical Research Institute, Westmead, NSW, Australia
| | - Sandra T. Cooper
- Kids Neuroscience Centre, The Children’s Hospital at Westmead, NSW, Australia
- School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, NSW, Australia
- Functional Neuromics, Children’s Medical Research Institute, Westmead, NSW, Australia
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Rajcsanyi LS, Hoffmann A, Ghosh A, Matrisch-Dinkler B, Zheng Y, Peters T, Sun W, Dong H, Noé F, Wolfrum C, Herpertz-Dahlmann B, Seitz J, de Zwaan M, Herzog W, Ehrlich S, Zipfel S, Giel K, Egberts K, Burghardt R, Föcker M, Tsai LT, Müller TD, Blüher M, Hebebrand J, Hirtz R, Hinney A. Genetic variants in genes involved in creatine biosynthesis in patients with severe obesity or anorexia nervosa. Front Genet 2023; 14:1128133. [PMID: 37101650 PMCID: PMC10123275 DOI: 10.3389/fgene.2023.1128133] [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: 12/20/2022] [Accepted: 03/27/2023] [Indexed: 04/28/2023] Open
Abstract
Increased thermogenesis in brown adipose tissue might have an obesity-reducing effect in humans. In transgenic mice, depletion of genes involved in creatine metabolism results in disrupted thermogenic capacity and altered effects of high-fat feeding on body weight. Data analyses of a sex-stratified genome-wide association study (GWAS) for body mass index (BMI) within the genomic regions of genes of this pathway (CKB, CKMT1B, and GATM) revealed one sex-dimorphic BMI-associated SNP in CKB (rs1136165). The effect size was larger in females than in males. A mutation screen of the coding regions of these three candidate genes in a screening group (192 children and adolescents with severe obesity, 192 female patients with anorexia nervosa, and 192 healthy-lean controls) identified five variants in each, CKB and GATM, and nine variants in the coding sequence of CKMT1B. Non-synonymous variants identified in CKB and CKMT1B were genotyped in an independent confirmation study group (781 families with severe obesity (trios), 320 children and adolescents with severe obesity, and 253 healthy-lean controls). In silico tools predicted mainly benign yet protein-destabilizing potentials. A transmission disequilibrium test in trios with severe obesity indicated an obesity-protective effect of the infrequent allele at rs149544188 located in CKMT1B. Subsequent correlation analyses in 1,479 individuals of the Leipzig Obesity BioBank revealed distinct correlations of CKB with the other two genes in omental visceral adipose tissue (VAT) and abdominal subcutaneous adipose tissue (SAT). Furthermore, between-subject comparisons of gene expression levels showed generally higher expressions of all three genes of interest in VAT than in SAT. Future in vitro analyses are needed to assess the functional implications of these findings.
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Affiliation(s)
- Luisa S. Rajcsanyi
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
- Center for Translational Neuro- and Behavioral Sciences, University Hospital Essen, Essen, Germany
| | - Anne Hoffmann
- Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Zentrum München at the University of Leipzig and University Hospital Leipzig, Leipzig, Germany
| | - Adhideb Ghosh
- Institute of Food, Nutrition and Health, ETH Zurich, Schwerzenbach, Switzerland
| | - Birgit Matrisch-Dinkler
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Yiran Zheng
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
- Center for Translational Neuro- and Behavioral Sciences, University Hospital Essen, Essen, Germany
| | - Triinu Peters
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
- Center for Translational Neuro- and Behavioral Sciences, University Hospital Essen, Essen, Germany
| | - Wenfei Sun
- Institute of Food, Nutrition and Health, ETH Zurich, Schwerzenbach, Switzerland
| | - Hua Dong
- Institute of Food, Nutrition and Health, ETH Zurich, Schwerzenbach, Switzerland
| | - Falko Noé
- Institute of Food, Nutrition and Health, ETH Zurich, Schwerzenbach, Switzerland
| | - Christian Wolfrum
- Institute of Food, Nutrition and Health, ETH Zurich, Schwerzenbach, Switzerland
| | - Beate Herpertz-Dahlmann
- Department of Child and Adolescent Psychiatry and Psychotherapy, University Hospital of the RWTH Aachen, Aachen, Germany
| | - Jochen Seitz
- Department of Child and Adolescent Psychiatry and Psychotherapy, University Hospital of the RWTH Aachen, Aachen, Germany
| | - Martina de Zwaan
- Department of Psychosomatic Medicine and Psychotherapy, Hannover Medical School, Hannover, Germany
| | - Wolfgang Herzog
- Department of Internal Medicine II, General Internal and Psychosomatic Medicine, University of Heidelberg, Heidelberg, Germany
| | - Stefan Ehrlich
- Translational Developmental Neuroscience Section, Division of Psychological and Social Medicine and Developmental Neurosciences, Faculty of Medicine, TU Dresden, Dresden, Germany
- Eating Disorders Research and Treatment Center, Department of Child and Adolescent Psychiatry, Faculty of Medicine, TU Dresden, Dresden, Germany
| | - Stephan Zipfel
- Department of Psychosomatic Medicine and Psychotherapy, Medical University Hospital Tübingen, Tübingen, Germany
- Center of Excellence in Eating Disorders KOMET, Tübingen, Germany
| | - Katrin Giel
- Department of Psychosomatic Medicine and Psychotherapy, Medical University Hospital Tübingen, Tübingen, Germany
- Center of Excellence in Eating Disorders KOMET, Tübingen, Germany
| | - Karin Egberts
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, University Würzburg, Würzburg, Germany
| | - Roland Burghardt
- Child and Adolescent Psychiatry Clinic, Oberberg Fachklinik Fasanenkiez Berlin, Berlin, Germany
| | - Manuel Föcker
- Department of Child and Adolescent Psychiatry, University Hospital Münster, Münster, Germany
| | - Linus T. Tsai
- Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, United States
| | - Timo D. Müller
- Institute for Diabetes and Obesity, Helmholtz Diabetes Center, Helmholtz Zentrum München, München, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Matthias Blüher
- Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Zentrum München at the University of Leipzig and University Hospital Leipzig, Leipzig, Germany
| | - Johannes Hebebrand
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
- Center for Translational Neuro- and Behavioral Sciences, University Hospital Essen, Essen, Germany
| | - Raphael Hirtz
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
- Department of Pediatrics, Division of Rare Diseases, and CeSER, Ruhr-University Bochum, Bochum, Germany
- Department of Pediatric Endocrinology and Diabetology, Clinic for Pediatrics II, University Hospital Essen, Essen, Germany
| | - Anke Hinney
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
- Center for Translational Neuro- and Behavioral Sciences, University Hospital Essen, Essen, Germany
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Identification and in silico characterization of CSRP3 synonymous variants in dilated cardiomyopathy. Mol Biol Rep 2023; 50:4105-4117. [PMID: 36877346 DOI: 10.1007/s11033-023-08314-7] [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: 10/12/2021] [Accepted: 01/31/2023] [Indexed: 03/07/2023]
Abstract
BACKGROUND Synonymous variations have always been ignored while studying the underlying genetic mechanisms for most of the human diseases. However, recent studies have suggested that these silent changes in the genome can alter the protein expression and folding. METHODS AND RESULTS CSRP3, which is a well-known candidate gene associated with dilated cardiomyopathy (DCM) and hypertrophic cardiomyopathy (HCM), was screened for 100 idiopathic DCM cases and 100 controls. Three synonymous variations were identified viz., c.96G > A, p.K32=; c.336G > A, p.A112=; c.354G > A, p.E118=. A comprehensive in silico analysis was performed using various web based widely accepted tools, Mfold, Codon Usage, HSF3.1 and RNA22. Mfold predicted structural changes in all the variants except c.96 G > A (p.K32=), however it predicted changes in the stability of mRNA due to all the synonymous variants. Codon bias was observed as evident by the Relative Synonymous Codon Usage and Log Ratio of Codon Usage Frequencies. The Human Splicing Finder also predicted remarkable changes in the regulatory elements in the variants c.336G > A and c.354 G > A. The miRNA target prediction using varied modes available in RNA22 revealed that 70.6% of the target sites of miRNAs in CSRP3 were altered due to variant c.336G > A while 29.41% sites were completely lost. CONCLUSION Findings of the present study suggest that synonymous variants revealed striking deviations in the structural conformation of mRNA, stability of mRNA, relative synonymous codon usage, splicing and miRNA binding sites from the wild type suggesting their possible role in the pathogenesis of DCM, either by destabilizing the mRNA structure, or codon usage bias or else altering the cis-acting regulatory elements during splicing.
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42
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Ben Rhouma B, Kley M, Kallabi F, Kacem FH, Kammoun T, Safi W, Keskes L, Mnif M, Odermatt A, Belguith N. Molecular mechanisms underlying the defects of two novel mutations in the HSD17B3 gene found in the Tunisian population. J Steroid Biochem Mol Biol 2023; 227:106235. [PMID: 36563763 DOI: 10.1016/j.jsbmb.2022.106235] [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: 11/19/2022] [Revised: 12/18/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022]
Abstract
17β-hydroxysteroid dehydrogenase type 3 (17β-HSD3) converts Δ4-androstene-3,17-dione (androstenedione) to testosterone. It is expressed almost exclusively in the testes and is essential for appropriate male sexual development. More than 70 mutations in the HSD17B3 gene that cause 17β-HSD3 deficiency and result in 46,XY Disorders of Sex Development (46,XY DSD) have been reported. This study describes three novel Tunisian cases with mutations in HSD17B3. The first patient is homozygous for the previously reported mutation p.C206X. The inheritance of this mutation seemed to be independent of consanguineous marriage, which can be explained by its high frequency in the Tunisian population. The second patient has a novel splice site mutation in intron 6 at position c.490 -6 T > C. A splicing assay revealed a complete omission of exon 7 in the resulting HSD17B3 mRNA transcript. Skipping of exon 7 in HSD17B3 is predicted to cause a frame shift in exon 8 that affects the catalytic site and results in a truncation in exon 9, leading to an inactive enzyme. The third patient is homozygous for the novel missense mutation p.K202M, representing the first mutation identified in the catalytic tetrad of 17β-HSD3. Site-directed mutagenesis and enzyme activity measurements revealed a completely abolished 17β-HSD3 activity of the p.K202M mutant, despite unaffected protein expression, compared to the wild-type enzyme. Furthermore, the present study emphasizes the importance of genetic counselling, detabooization of 46,XY DSD, and a sensitization of the Tunisian population for the risks of consanguineous marriage.
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Affiliation(s)
- Bochra Ben Rhouma
- Human Molecular Genetics Laboratory, Faculty of Medicine, 3029 Sfax, Tunisia; Higher Institute of Nursing, M. Ali Street, 4000 Gabes, Tunisia.
| | - Manuel Kley
- Division of Molecular and Systems Toxicology, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland; Swiss Centre for Applied Human Toxicology and Department of Pharmaceutical Sciences, University of Basel, Missionsstrasse 64, 4055 Basel, Switzerland.
| | - Fakhri Kallabi
- Human Molecular Genetics Laboratory, Faculty of Medicine, 3029 Sfax, Tunisia.
| | - Faten Hadj Kacem
- Department of Endocrinology, Hedi Chaker Hospital, 3029 Sfax, Tunisia.
| | - Thouraya Kammoun
- Department of Pediatrics, Hedi Chaker Hospital, 3029 Sfax, Tunisia.
| | - Wajdi Safi
- Department of Endocrinology, Hedi Chaker Hospital, 3029 Sfax, Tunisia.
| | - Leila Keskes
- Human Molecular Genetics Laboratory, Faculty of Medicine, 3029 Sfax, Tunisia.
| | - Mouna Mnif
- Department of Endocrinology, Hedi Chaker Hospital, 3029 Sfax, Tunisia.
| | - Alex Odermatt
- Division of Molecular and Systems Toxicology, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland; Swiss Centre for Applied Human Toxicology and Department of Pharmaceutical Sciences, University of Basel, Missionsstrasse 64, 4055 Basel, Switzerland.
| | - Neila Belguith
- Human Molecular Genetics Laboratory, Faculty of Medicine, 3029 Sfax, Tunisia; Department of Congenital and Hereditary Diseases, 1010 Charles Nicolles Hospital, Tunis, Tunisia.
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Fedets OM, Dmytruk KV, Adaszek L, Kurlyak IM, Dmytruk OV, Lisiecka U, Winiarczyk S. Polymorphism of glutathione S-transferase P1 of dogs with mammary tumours. Vet Comp Oncol 2023; 21:270-278. [PMID: 36808425 DOI: 10.1111/vco.12885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 01/21/2023] [Accepted: 01/23/2023] [Indexed: 02/23/2023]
Abstract
Mammary tumours constitute more than half of neoplasms in female dogs from different countries. Genome sequences are associated with cancer susceptibility but there is little information available about genetic polymorphisms of glutathione S-transferase P1 (GSTP1) in canine cancers. The aim of this study was to find single nucleotide polymorphisms (SNPs) in GSTP1 of dogs (Canis lupus familiaris) with mammary tumours compared to healthy dogs and to determine the association between GSTP1 polymorphisms and the occurrence of these tumours. The study population included 36 client-owned female dogs with mammary tumours and 12 healthy female dogs, with no previous diagnosis of cancer. DNA was extracted from blood and amplified by PCR assay. PCR-products were sequenced by Sanger method and analysed manually. The 33 polymorphisms were found in GSTP1: 1 coding SNP (exon 4), 24 non-coding SNPs (9 in exon 1), 7 deletions and 1 insertion. The 17 polymorphisms have been found in introns 1, 4, 5 and 6. The dogs with mammary tumours have significant difference from healthy in SNPs I4 c.1018 + 123 T > C (OR 13.412, 95%CI 1.574-114.267, P = .001), I5 c.1487 + 27 T > C (OR 10.737, 95%CI 1.260-91.477, P = .004), I5 c.1487 + 842 G > C (OR 4.714, 95% CI 1.086-20.472, P = .046) and I6 c.2481 + 50 A > G (OR 12.000, 95% CI 1.409-102.207, P = .002). SNP E5 c.1487 T > C and I5 c.1487 + 829 delG also differed significantly (P = .03) but not to the confidence interval. The study, for the first time, showed a positive association of SNPs in GSTP1 with mammary tumours of dogs, that can possibly be used to predict the occurrence of this pathology.
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Affiliation(s)
- Oleh M Fedets
- Department of Biological and General Chemistry, Stepan Gzhytskyi National University of Veterinary Medicine and Biotechnologies Lviv, Lviv, Ukraine
| | - Kostyantyn V Dmytruk
- Department of Molecular Genetics and Biotechnology, Institute of Cell Biology National Academy of Sciences of Ukraine, Lviv, Ukraine
| | - Lukasz Adaszek
- Department of Epizootiology and Clinic of Infectious Diseases, Faculty of Veterinary Medicine, University of Life Sciences in Lublin, Lublin, Poland
| | - Iryna M Kurlyak
- Department of Biological and General Chemistry, Stepan Gzhytskyi National University of Veterinary Medicine and Biotechnologies Lviv, Lviv, Ukraine
| | - Olena V Dmytruk
- Department of Molecular Genetics and Biotechnology, Institute of Cell Biology National Academy of Sciences of Ukraine, Lviv, Ukraine
- Department of Biotechnology and Microbiology, University of Rzeszow, Rzeszów, Poland
| | - Urszula Lisiecka
- Department of Epizootiology and Clinic of Infectious Diseases, Faculty of Veterinary Medicine, University of Life Sciences in Lublin, Lublin, Poland
| | - Stanislaw Winiarczyk
- Department of Epizootiology and Clinic of Infectious Diseases, Faculty of Veterinary Medicine, University of Life Sciences in Lublin, Lublin, Poland
- National Veterinary Research Institute, Pulawy, Poland
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44
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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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45
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Panneman DM, Hitti-Malin RJ, Holtes LK, de Bruijn SE, Reurink J, Boonen EGM, Khan MI, Ali M, Andréasson S, De Baere E, Banfi S, Bauwens M, Ben-Yosef T, Bocquet B, De Bruyne M, de la Cerda B, Coppieters F, Farinelli P, Guignard T, Inglehearn CF, Karali M, Kjellström U, Koenekoop R, de Koning B, Leroy BP, McKibbin M, Meunier I, Nikopoulos K, Nishiguchi KM, Poulter JA, Rivolta C, Rodríguez de la Rúa E, Saunders P, Simonelli F, Tatour Y, Testa F, Thiadens AAHJ, Toomes C, Tracewska AM, Tran HV, Ushida H, Vaclavik V, Verhoeven VJM, van de Vorst M, Gilissen C, Hoischen A, Cremers FPM, Roosing S. Cost-effective sequence analysis of 113 genes in 1,192 probands with retinitis pigmentosa and Leber congenital amaurosis. Front Cell Dev Biol 2023; 11:1112270. [PMID: 36819107 PMCID: PMC9936074 DOI: 10.3389/fcell.2023.1112270] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 01/20/2023] [Indexed: 02/05/2023] Open
Abstract
Introduction: Retinitis pigmentosa (RP) and Leber congenital amaurosis (LCA) are two groups of inherited retinal diseases (IRDs) where the rod photoreceptors degenerate followed by the cone photoreceptors of the retina. A genetic diagnosis for IRDs is challenging since >280 genes are associated with these conditions. While whole exome sequencing (WES) is commonly used by diagnostic facilities, the costs and required infrastructure prevent its global applicability. Previous studies have shown the cost-effectiveness of sequence analysis using single molecule Molecular Inversion Probes (smMIPs) in a cohort of patients diagnosed with Stargardt disease and other maculopathies. Methods: Here, we introduce a smMIPs panel that targets the exons and splice sites of all currently known genes associated with RP and LCA, the entire RPE65 gene, known causative deep-intronic variants leading to pseudo-exons, and part of the RP17 region associated with autosomal dominant RP, by using a total of 16,812 smMIPs. The RP-LCA smMIPs panel was used to screen 1,192 probands from an international cohort of predominantly RP and LCA cases. Results and discussion: After genetic analysis, a diagnostic yield of 56% was obtained which is on par with results from WES analysis. The effectiveness and the reduced costs compared to WES renders the RP-LCA smMIPs panel a competitive approach to provide IRD patients with a genetic diagnosis, especially in countries with restricted access to genetic testing.
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Affiliation(s)
- Daan M. Panneman
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands,Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, Netherlands,*Correspondence: Daan M. Panneman,
| | - Rebekkah J. Hitti-Malin
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands,Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, Netherlands
| | - Lara K. Holtes
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Suzanne E. de Bruijn
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands,Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, Netherlands
| | - Janine Reurink
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands,Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, Netherlands
| | - Erica G. M. Boonen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Muhammad Imran Khan
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Manir Ali
- Division of Molecular Medicine, Leeds Institute of Medical Research, St. James’s University Hospital, University of Leeds, Leeds, United Kingdom
| | - Sten Andréasson
- Department of Ophthalmology and Clinical Sciences Lund, Lund University, Skane University Hospital, Lund, Sweden
| | - Elfride De Baere
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium,Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Sandro Banfi
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy,Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, Naples, Italy
| | - Miriam Bauwens
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium,Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Tamar Ben-Yosef
- Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Béatrice Bocquet
- National Reference Centre for Inherited Sensory Diseases, University of Montpellier, Montpellier University Hospital, Sensgene Care Network, ERN-EYE Network, Montpellier, France,Institute for Neurosciences of Montpellier (INM), L’Institut National de la Santé et de la Recherche Médicale, University of Montpellier, L’Institut National de la Santé et de la Recherche Médicale, Montpellier, France
| | - Marieke De Bruyne
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium,Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Berta de la Cerda
- Andalusian Center for Molecular Biology and Regenerative Medicine (CABIMER), Seville, Spain
| | - Frauke Coppieters
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium,Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium,Department of Pharmaceutics, Ghent University, Ghent, Belgium
| | - Pietro Farinelli
- Department of Computational Biology, Unit of Medical Genetics, University of Lausanne, Lausanne, Switzerland
| | - Thomas Guignard
- Chromosomal Genetics Unit, University Hospital of Montpellier, Montpellier, France
| | - Chris F. Inglehearn
- Division of Molecular Medicine, Leeds Institute of Medical Research, St. James’s University Hospital, University of Leeds, Leeds, United Kingdom
| | - Marianthi Karali
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, Naples, Italy,Eye Clinic, Multidisciplinary Department of Medical, Surgical and Dental Sciences, University of Campania Luigi Vanvitelli, Naples, Italy
| | - Ulrika Kjellström
- Department of Ophthalmology and Clinical Sciences Lund, Lund University, Skane University Hospital, Lund, Sweden
| | - Robert Koenekoop
- McGill University Health Center (MUHC) Research Institute, Montreal, QC, Canada,Departments of Paediatric Surgery, Human Genetics, and Adult Ophthalmology, McGill University Health Center, Montreal, QC, Canada
| | - Bart de Koning
- Department of Clinical Genetics, Maastricht University Medical Center+ (MUMC+), Maastricht, Netherlands
| | - Bart P. Leroy
- Department of Ophthalmology, Ghent University Hospital, Ghent, Belgium,Department of Head & Skin, Ghent University, Ghent, Belgium,Division of Ophthalmology & Center for Cellular & Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA, United States,Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Martin McKibbin
- Division of Molecular Medicine, Leeds Institute of Medical Research, St. James’s University Hospital, University of Leeds, Leeds, United Kingdom,Department of Ophthalmology, St. James’s University Hospital, Leeds, United Kingdom
| | - Isabelle Meunier
- National Reference Centre for Inherited Sensory Diseases, University of Montpellier, Montpellier University Hospital, Sensgene Care Network, ERN-EYE Network, Montpellier, France,Institute for Neurosciences of Montpellier (INM), L’Institut National de la Santé et de la Recherche Médicale, University of Montpellier, L’Institut National de la Santé et de la Recherche Médicale, Montpellier, France
| | | | - Koji M. Nishiguchi
- Department of Ophthalmology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - James A. Poulter
- Division of Molecular Medicine, Leeds Institute of Medical Research, St. James’s University Hospital, University of Leeds, Leeds, United Kingdom
| | - Carlo Rivolta
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland,Department of Ophthalmology, University of Basel, Basel, Switzerland,Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Enrique Rodríguez de la Rúa
- Department of Ophthalmology, Retics Patologia Ocular, OFTARED, Instituto de Salud Carlos III, University Hospital Virgen Macarena, Madrid, Spain
| | | | - Francesca Simonelli
- Eye Clinic, Multidisciplinary Department of Medical, Surgical and Dental Sciences, University of Campania Luigi Vanvitelli, Naples, Italy
| | - Yasmin Tatour
- Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Francesco Testa
- Eye Clinic, Multidisciplinary Department of Medical, Surgical and Dental Sciences, University of Campania Luigi Vanvitelli, Naples, Italy
| | | | - Carmel Toomes
- Division of Molecular Medicine, Leeds Institute of Medical Research, St. James’s University Hospital, University of Leeds, Leeds, United Kingdom
| | - Anna M. Tracewska
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Hoai Viet Tran
- Oculogenetic Unit, University Eye Hospital Jules Gonin, Geneva, Switzerland
| | - Hiroaki Ushida
- Department of Ophthalmology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Veronika Vaclavik
- Oculogenetic Unit, University Eye Hospital Jules Gonin, Geneva, Switzerland
| | - Virginie J. M. Verhoeven
- Department of Ophthalmology, Erasmus, Rotterdam, Netherlands,Department of Clinical Genetics, Erasmus, Rotterdam, Netherlands
| | - Maartje van de Vorst
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Christian Gilissen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands,Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Alexander Hoischen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands,Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands,Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands
| | - Frans P. M. Cremers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands,Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, Netherlands
| | - Susanne Roosing
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands,Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, Netherlands
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Web-accessible application for identifying pathogenic transcripts with RNA-seq: Increased sensitivity in diagnosis of neurodevelopmental disorders. Am J Hum Genet 2023; 110:251-272. [PMID: 36669495 PMCID: PMC9943747 DOI: 10.1016/j.ajhg.2022.12.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 12/21/2022] [Indexed: 01/20/2023] Open
Abstract
For neurodevelopmental disorders (NDDs), a molecular diagnosis is key for management, predicting outcome, and counseling. Often, routine DNA-based tests fail to establish a genetic diagnosis in NDDs. Transcriptome analysis (RNA sequencing [RNA-seq]) promises to improve the diagnostic yield but has not been applied to NDDs in routine diagnostics. Here, we explored the diagnostic potential of RNA-seq in 96 individuals including 67 undiagnosed subjects with NDDs. We performed RNA-seq on single individuals' cultured skin fibroblasts, with and without cycloheximide treatment, and used modified OUTRIDER Z scores to detect gene expression outliers and mis-splicing by exonic and intronic outliers. Analysis was performed by a user-friendly web application, and candidate pathogenic transcriptional events were confirmed by secondary assays. We identified intragenic deletions, monoallelic expression, and pseudoexonic insertions but also synonymous and non-synonymous variants with deleterious effects on transcription, increasing the diagnostic yield for NDDs by 13%. We found that cycloheximide treatment and exonic/intronic Z score analysis increased detection and resolution of aberrant splicing. Importantly, in one individual mis-splicing was found in a candidate gene nearly matching the individual's specific phenotype. However, pathogenic splicing occurred in another neuronal-expressed gene and provided a molecular diagnosis, stressing the need to customize RNA-seq. Lastly, our web browser application allowed custom analysis settings that facilitate diagnostic application and ranked pathogenic transcripts as top candidates. Our results demonstrate that RNA-seq is a complementary method in the genomic diagnosis of NDDs and, by providing accessible analysis with improved sensitivity, our transcriptome analysis approach facilitates wider implementation of RNA-seq in routine genome diagnostics.
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Zhang X, Cai M, Ma Y, Chen J, Huang S, Cai M, Ding Y, Ma D, Gao Q, Hu X, Zhu C, Yi L. Minigene Assay as an Effective Molecular Diagnostic Strategy in Determining the Pathogenicity of Noncanonical Splice-Site Variants in FLCN. J Mol Diagn 2023; 25:110-120. [PMID: 36410626 DOI: 10.1016/j.jmoldx.2022.10.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 10/24/2022] [Accepted: 10/27/2022] [Indexed: 11/23/2022] Open
Abstract
Primary spontaneous pneumothorax (PSP) or pulmonary cyst is one of the manifestations of Birt-Hogg-Dubé syndrome, which is caused by pathogenic variants in FLCN gene. Genetic testing in patients with PSP identifies a certain number of missense or intronic variants. These variants are usually considered as variants of uncertain significance, whose functional interpretations pose a challenge in clinical genetics. To improve recognition of pathogenic splice-altering variants in FLCN gene, computational tools are used to prioritize potential splice-altering variants and then a hybrid minigene assay is performed to verify the RNA splicing pattern. Herein, variants in FLCN exon 11 and its flanking sequence are focused. Eight variants detected in 11 patients with PSP are evaluated, and six variants are prioritized by in silico tools as potential splice-altering variants of uncertain significance. Four variants (c.1177-5_1177-3delCTC, c.1292_1300+4del, c.1300+4C>T, and c.1300+5G>A) are demonstrated by minigene assay to alter RNA splicing of FLCN, and the last three of them are novel. RT-PCR of patient-derived RNA gives consistent results. Genotype-phenotype correlation analysis in patients with PSP with these variants demonstrates good concordance. Our results underline the importance of RNA analysis, which could provide molecular evidence for pathogenicity of a variant, and provide essential information for the clinical interpretation of variants. Combining the clinical information, a definitive diagnosis could be made.
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Affiliation(s)
- Xinxin Zhang
- Department of Histology and Embryology, School of Medicine, Southeast University, Nanjing, China
| | - Minghui Cai
- Department of Cardiothoracic Surgery, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Linhai, China
| | - Yuanchun Ma
- Jiangsu Key Laboratory for Molecular Medicine, School of Medicine, Nanjing University, Nanjing, China
| | - Jie Chen
- Jiangsu Key Laboratory for Molecular Medicine, School of Medicine, Nanjing University, Nanjing, China
| | - Shaoping Huang
- Department of Histology and Embryology, School of Medicine, Southeast University, Nanjing, China
| | - Mengru Cai
- Jiangsu Key Laboratory for Molecular Medicine, School of Medicine, Nanjing University, Nanjing, China
| | - Yibing Ding
- Jiangsu Key Laboratory for Molecular Medicine, School of Medicine, Nanjing University, Nanjing, China
| | - Dehua Ma
- Department of Cardiothoracic Surgery, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Linhai, China
| | - Qian Gao
- Jiangsu Key Laboratory for Molecular Medicine, School of Medicine, Nanjing University, Nanjing, China
| | - Xiaowen Hu
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Chengchu Zhu
- Department of Cardiothoracic Surgery, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Linhai, China.
| | - Long Yi
- Department of Cardiothoracic Surgery, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Linhai, China; Jiangsu Key Laboratory for Molecular Medicine, School of Medicine, Nanjing University, Nanjing, China.
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48
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Che XQ, Lin GZ, Liu XH, Wang G, Zhao QH, Ren RJ. Genetic and Neuroimaging Analysis of SIGMAR1 for Frontotemporal Dementia. J Alzheimers Dis 2023; 95:469-475. [PMID: 37545231 DOI: 10.3233/jad-221195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
BACKGROUND Recently, Sigma nonopioid intracellular receptor 1 (SIGMAR1) variants have been shown harboring C9orf72 pathogenic repeat expansions in some frontotemporal dementia (FTD) cases. However, no SIGMAR1 genotype analysis has been reported in a cohort absent of C9orf72 pathogenic repeat expansions to date. OBJECTIVE The present study investigated the contribution of SIGMAR1 independent of C9orf72 gene status to FTD spectrum syndromes. METHODS We directly sequencing the entire coding region and a minimum of 50 bp from each of the flanking introns of SIGMAR1 gene in 82 sporadic FTD patients (female: male = 42 : 40) and 417 controls. For the patient carrying SIGMAR1 variant, a follow-up 3T MR imaging was performed in the study. RESULTS Gene sequencing of SIGMAR1 revealed a rare 3'UTR nucleotide variation rs192856872 in a male patient with semantic dementia independent of C9orf72 gene status. The MR imaging showed asymmetrical atrophy in the anterior temporal lobes and the degeneration extends caudally into the posterior temporal lobes as the disease progresses. ESEFinder analysis showed new SRSF1 and SRSF1-IgM-BRCA1 binding sites with significant scores, which is predicted to affect normal splicing. CONCLUSION We found a novel SIGMAR1 variant independent of C9orf72 gene status associated with semantic dementia phenotype.
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Affiliation(s)
- Xiang-Qian Che
- Department of Neurology & Neuroscience Institute, Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Guo-Zhen Lin
- Department of Psychiatry, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiao-Hong Liu
- Department of Neurology, Shanghai Putuo District People's Hospital, Shanghai, China
| | - Gang Wang
- Department of Neurology & Neuroscience Institute, Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qian-Hua Zhao
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China
- MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China
| | - Ru-Jing Ren
- Department of Neurology & Neuroscience Institute, Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
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49
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Sundaresan Y, Banin E, Sharon D. Exonic Variants that Affect Splicing - An Opportunity for "Hidden" Mutations Causing Inherited Retinal Diseases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1415:183-187. [PMID: 37440032 DOI: 10.1007/978-3-031-27681-1_27] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/14/2023]
Abstract
Inherited retinal diseases (IRDs) are an extremely diverse group of ocular disorders characterized by progressive loss of photoreceptors leading to blindness. So far, pathogenic variants in over 300 genes are reported to structurally and functionally affect the retina resulting in visual impairment. Around 15% of all IRD mutations are known to affect an essential regulatory mechanism, pre-mRNA splicing, which contributes to the transcriptomic diversity. These variants disrupt potential donor and acceptor splice sites as well as other crucial cis-acting elements resulting in aberrant splicing. One group of these elements, the exonic splicing enhancers (ESEs), are involved in promoting exon definition and are likely to harbor "hidden" mutations since sequence-analyzing pipelines cannot identify them efficiently. The main focus of this review is to discuss the molecular mechanisms behind various exonic variants affecting splice sites and ESEs that lead to impaired splicing which in turn result in an IRD pathology.
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Affiliation(s)
- Yogapriya Sundaresan
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Eyal Banin
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Dror Sharon
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel.
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50
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Barbosa P, Savisaar R, Carmo-Fonseca M, Fonseca A. Computational prediction of human deep intronic variation. Gigascience 2022; 12:giad085. [PMID: 37878682 PMCID: PMC10599398 DOI: 10.1093/gigascience/giad085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 06/07/2023] [Accepted: 09/20/2023] [Indexed: 10/27/2023] Open
Abstract
BACKGROUND The adoption of whole-genome sequencing in genetic screens has facilitated the detection of genetic variation in the intronic regions of genes, far from annotated splice sites. However, selecting an appropriate computational tool to discriminate functionally relevant genetic variants from those with no effect is challenging, particularly for deep intronic regions where independent benchmarks are scarce. RESULTS In this study, we have provided an overview of the computational methods available and the extent to which they can be used to analyze deep intronic variation. We leveraged diverse datasets to extensively evaluate tool performance across different intronic regions, distinguishing between variants that are expected to disrupt splicing through different molecular mechanisms. Notably, we compared the performance of SpliceAI, a widely used sequence-based deep learning model, with that of more recent methods that extend its original implementation. We observed considerable differences in tool performance depending on the region considered, with variants generating cryptic splice sites being better predicted than those that potentially affect splicing regulatory elements. Finally, we devised a novel quantitative assessment of tool interpretability and found that tools providing mechanistic explanations of their predictions are often correct with respect to the ground - information, but the use of these tools results in decreased predictive power when compared to black box methods. CONCLUSIONS Our findings translate into practical recommendations for tool usage and provide a reference framework for applying prediction tools in deep intronic regions, enabling more informed decision-making by practitioners.
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Affiliation(s)
- Pedro Barbosa
- LASIGE, Departamento de Informática, Faculdade de Ciências, Universidade de Lisboa, 1749-016,, Lisboa, Portugal
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028, Lisboa, Portugal
| | | | - Maria Carmo-Fonseca
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028, Lisboa, Portugal
| | - Alcides Fonseca
- LASIGE, Departamento de Informática, Faculdade de Ciências, Universidade de Lisboa, 1749-016,, Lisboa, Portugal
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