1
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Yu R, Xue H, Lin W, Collins F, Mount S, Cao K. Progerin mRNA expression in non-HGPS patients is correlated with widespread shifts in transcript isoforms. NAR Genom Bioinform 2024; 6:lqae115. [PMID: 39211333 PMCID: PMC11358823 DOI: 10.1093/nargab/lqae115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 08/06/2024] [Accepted: 08/19/2024] [Indexed: 09/04/2024] Open
Abstract
Hutchinson-Gilford Progeria Syndrome (HGPS) is a premature aging disease caused primarily by a C1824T mutation in LMNA. This mutation activates a cryptic splice donor site, producing a lamin variant called progerin. Interestingly, progerin has also been detected in cells and tissues of non-HGPS patients. Here, we investigated progerin expression using publicly available RNA-seq data from non-HGPS patients in the GTEx project. We found that progerin expression is present across all tissue types in non-HGPS patients and correlated with telomere shortening in the skin. Transcriptome-wide correlation analyses suggest that the level of progerin expression is correlated with switches in gene isoform expression patterns. Differential expression analyses show that progerin expression is correlated with significant changes in genes involved in splicing regulation and mitochondrial function. Interestingly, 5' splice sites whose use is correlated with progerin expression have significantly altered frequencies of consensus trinucleotides within the core 5' splice site. Furthermore, introns whose alternative splicing correlates with progerin have reduced GC content. Our study suggests that progerin expression in non-HGPS patients is part of a global shift in splicing patterns.
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Affiliation(s)
- Reynold Yu
- Department of Cell Biology and Molecular Genetics, University of Maryland College Park, MD, USA
| | - Huijing Xue
- Department of Cell Biology and Molecular Genetics, University of Maryland College Park, MD, USA
| | - Wanru Lin
- Department of Cell Biology and Molecular Genetics, University of Maryland College Park, MD, USA
| | - Francis S Collins
- Molecular Genetics Section, Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Stephen M Mount
- Department of Cell Biology and Molecular Genetics, University of Maryland College Park, MD, USA
| | - Kan Cao
- Department of Cell Biology and Molecular Genetics, University of Maryland College Park, MD, USA
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2
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Dao K, Jungers CF, Djuranovic S, Mustoe AM. U-rich elements drive pervasive cryptic splicing in 3' UTR massively parallel reporter assays. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.05.606557. [PMID: 39149310 PMCID: PMC11326173 DOI: 10.1101/2024.08.05.606557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
Non-coding RNA sequences play essential roles in orchestrating gene expression. However, the sequence codes and mechanisms underpinning post-transcriptional regulation remain incompletely understood. Here, we revisit the finding from a prior massively parallel reporter assay (MPRA) that AU-rich (U-rich) elements in 3' untranslated regions (3' UTRs) can drive upregulation or downregulation of mRNA expression depending on 3' UTR context. We unexpectedly discover that this variable regulation arises from widespread cryptic splicing, predominately from an unannotated splice donor in the coding sequence of GFP to diverse acceptor sites in reporter 3' UTRs. Splicing is activated by U-rich sequences, which function as potent position-dependent regulators of 5' and 3' splice site choice and overall splicing efficiency. Splicing has diverse impacts on reporter expression, causing both increases and decreases in reporter expression via multiple mechanisms. We further provide evidence that cryptic splicing impacts between 10 to 50% of measurements made by other published 3' UTR MPRAs. Overall, our work emphasizes U-rich sequences as principal drivers of splicing and provides strategies to minimize cryptic splicing artifacts in reporter assays.
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Affiliation(s)
- Khoa Dao
- Therapeutic Innovation Center (THINC), Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston TX
| | - Courtney F. Jungers
- Department of Cell Biology and Physiology, Washington University School of Medicine in St. Louis, St. Louis MO
| | - Sergej Djuranovic
- Department of Cell Biology and Physiology, Washington University School of Medicine in St. Louis, St. Louis MO
| | - Anthony M. Mustoe
- Therapeutic Innovation Center (THINC), Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston TX
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston TX
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3
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Aguilar C, Williams D, Kurapati R, Bains RS, Mburu P, Parker A, Williams J, Concas D, Tateossian H, Haynes AR, Banks G, Vikhe P, Heise I, Hutchison M, Atkins G, Gillard S, Starbuck B, Oliveri S, Blake A, Sethi S, Kumar S, Bardhan T, Jeng JY, Johnson SL, Corns LF, Marcotti W, Simon M, Wells S, Potter PK, Lad HV. Pleiotropic brain function of whirlin identified by a novel mutation. iScience 2024; 27:110170. [PMID: 38974964 PMCID: PMC11225360 DOI: 10.1016/j.isci.2024.110170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 04/26/2024] [Accepted: 05/31/2024] [Indexed: 07/09/2024] Open
Abstract
Despite some evidence indicating diverse roles of whirlin in neurons, the functional corollary of whirlin gene function and behavior has not been investigated or broadly characterized. A single nucleotide variant was identified from our recessive ENU-mutagenesis screen at a donor-splice site in whirlin, a protein critical for proper sensorineural hearing function. The mutation (head-bob, hb) led to partial intron-retention causing a frameshift and introducing a premature termination codon. Mutant mice had a head-bobbing phenotype and significant hyperactivity across several phenotyping tests. Lack of complementation of head-bob with whirler mutant mice confirmed the head-bob mutation as functionally distinct with compound mutants having a mild-moderate hearing defect. Utilizing transgenics, we demonstrate rescue of the hyperactive phenotype and combined with the expression profiling data conclude whirlin plays an essential role in activity-related behaviors. These results highlight a pleiotropic role of whirlin within the brain and implicate alternative, central mediated pathways in its function.
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Affiliation(s)
- Carlos Aguilar
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Didcot, Oxfordshire OX11 0RD, UK
| | - Debbie Williams
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Didcot, Oxfordshire OX11 0RD, UK
- Mary Lyon Centre at MRC Harwell, Harwell Campus, Didcot, Oxfordshire OX11 0RD, UK
| | - Ramakrishna Kurapati
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Didcot, Oxfordshire OX11 0RD, UK
| | - Rasneer S. Bains
- Mary Lyon Centre at MRC Harwell, Harwell Campus, Didcot, Oxfordshire OX11 0RD, UK
| | - Philomena Mburu
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Didcot, Oxfordshire OX11 0RD, UK
| | - Andy Parker
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Didcot, Oxfordshire OX11 0RD, UK
| | - Jackie Williams
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Didcot, Oxfordshire OX11 0RD, UK
| | - Danilo Concas
- Mary Lyon Centre at MRC Harwell, Harwell Campus, Didcot, Oxfordshire OX11 0RD, UK
| | - Hilda Tateossian
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Didcot, Oxfordshire OX11 0RD, UK
| | - Andrew R. Haynes
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Didcot, Oxfordshire OX11 0RD, UK
| | - Gareth Banks
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Didcot, Oxfordshire OX11 0RD, UK
| | - Pratik Vikhe
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Didcot, Oxfordshire OX11 0RD, UK
| | - Ines Heise
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Didcot, Oxfordshire OX11 0RD, UK
| | - Marie Hutchison
- Mary Lyon Centre at MRC Harwell, Harwell Campus, Didcot, Oxfordshire OX11 0RD, UK
| | - Gemma Atkins
- Mary Lyon Centre at MRC Harwell, Harwell Campus, Didcot, Oxfordshire OX11 0RD, UK
| | - Simon Gillard
- Mary Lyon Centre at MRC Harwell, Harwell Campus, Didcot, Oxfordshire OX11 0RD, UK
| | - Becky Starbuck
- Mary Lyon Centre at MRC Harwell, Harwell Campus, Didcot, Oxfordshire OX11 0RD, UK
| | - Simona Oliveri
- Mary Lyon Centre at MRC Harwell, Harwell Campus, Didcot, Oxfordshire OX11 0RD, UK
| | - Andrew Blake
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Didcot, Oxfordshire OX11 0RD, UK
| | - Siddharth Sethi
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Didcot, Oxfordshire OX11 0RD, UK
| | - Saumya Kumar
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Didcot, Oxfordshire OX11 0RD, UK
| | - Tanaya Bardhan
- School of Biosciences, University of Sheffield, Sheffield, South Yorkshire S10 2TN, UK
| | - Jing-Yi Jeng
- School of Biosciences, University of Sheffield, Sheffield, South Yorkshire S10 2TN, UK
| | - Stuart L. Johnson
- School of Biosciences, University of Sheffield, Sheffield, South Yorkshire S10 2TN, UK
| | - Lara F. Corns
- School of Biosciences, University of Sheffield, Sheffield, South Yorkshire S10 2TN, UK
| | - Walter Marcotti
- School of Biosciences, University of Sheffield, Sheffield, South Yorkshire S10 2TN, UK
- Neuroscience Institute, University of Sheffield, Sheffield, South Yorkshire S10 2TN, UK
| | - Michelle Simon
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Didcot, Oxfordshire OX11 0RD, UK
| | - Sara Wells
- Mary Lyon Centre at MRC Harwell, Harwell Campus, Didcot, Oxfordshire OX11 0RD, UK
| | - Paul K. Potter
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Didcot, Oxfordshire OX11 0RD, UK
| | - Heena V. Lad
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Didcot, Oxfordshire OX11 0RD, UK
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4
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Emilius L, Bremm F, Binder AK, Schaft N, Dörrie J. Tumor Antigens beyond the Human Exome. Int J Mol Sci 2024; 25:4673. [PMID: 38731892 PMCID: PMC11083240 DOI: 10.3390/ijms25094673] [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: 03/27/2024] [Revised: 04/18/2024] [Accepted: 04/22/2024] [Indexed: 05/13/2024] Open
Abstract
With the advent of immunotherapeutics, a new era in the combat against cancer has begun. Particularly promising are neo-epitope-targeted therapies as the expression of neo-antigens is tumor-specific. In turn, this allows the selective targeting and killing of cancer cells whilst healthy cells remain largely unaffected. So far, many advances have been made in the development of treatment options which are tailored to the individual neo-epitope repertoire. The next big step is the achievement of efficacious "off-the-shelf" immunotherapies. For this, shared neo-epitopes propose an optimal target. Given the tremendous potential, a thorough understanding of the underlying mechanisms which lead to the formation of neo-antigens is of fundamental importance. Here, we review the various processes which result in the formation of neo-epitopes. Broadly, the origin of neo-epitopes can be categorized into three groups: canonical, noncanonical, and viral neo-epitopes. For the canonical neo-antigens that arise in direct consequence of somatic mutations, we summarize past and recent findings. Beyond that, our main focus is put on the discussion of noncanonical and viral neo-epitopes as we believe that targeting those provides an encouraging perspective to shape the future of cancer immunotherapeutics.
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Affiliation(s)
- Lisabeth Emilius
- Department of Dermatology, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany; (L.E.); (F.B.); (A.K.B.); (J.D.)
- Comprehensive Cancer Center Erlangen European Metropolitan Area of Nuremberg (CCC ER-EMN), 91054 Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), 91054 Erlangen, Germany
- Bavarian Cancer Research Center (BZKF), 91054 Erlangen, Germany
| | - Franziska Bremm
- Department of Dermatology, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany; (L.E.); (F.B.); (A.K.B.); (J.D.)
- Comprehensive Cancer Center Erlangen European Metropolitan Area of Nuremberg (CCC ER-EMN), 91054 Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), 91054 Erlangen, Germany
- Bavarian Cancer Research Center (BZKF), 91054 Erlangen, Germany
| | - Amanda Katharina Binder
- Department of Dermatology, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany; (L.E.); (F.B.); (A.K.B.); (J.D.)
- Comprehensive Cancer Center Erlangen European Metropolitan Area of Nuremberg (CCC ER-EMN), 91054 Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), 91054 Erlangen, Germany
- Bavarian Cancer Research Center (BZKF), 91054 Erlangen, Germany
| | - Niels Schaft
- Department of Dermatology, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany; (L.E.); (F.B.); (A.K.B.); (J.D.)
- Comprehensive Cancer Center Erlangen European Metropolitan Area of Nuremberg (CCC ER-EMN), 91054 Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), 91054 Erlangen, Germany
- Bavarian Cancer Research Center (BZKF), 91054 Erlangen, Germany
| | - Jan Dörrie
- Department of Dermatology, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany; (L.E.); (F.B.); (A.K.B.); (J.D.)
- Comprehensive Cancer Center Erlangen European Metropolitan Area of Nuremberg (CCC ER-EMN), 91054 Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), 91054 Erlangen, Germany
- Bavarian Cancer Research Center (BZKF), 91054 Erlangen, Germany
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5
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Karimi E, Gohlke J, van der Borgh M, Lindqvist J, Hourani Z, Kolb J, Cossette S, Lawlor MW, Ottenheijm C, Granzier H. Characterization of NEB pathogenic variants in patients reveals novel nemaline myopathy disease mechanisms and omecamtiv mecarbil force effects. Acta Neuropathol 2024; 147:72. [PMID: 38634969 PMCID: PMC11026289 DOI: 10.1007/s00401-024-02726-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: 12/22/2023] [Revised: 03/19/2024] [Accepted: 03/26/2024] [Indexed: 04/19/2024]
Abstract
Nebulin, a critical protein of the skeletal muscle thin filament, plays important roles in physiological processes such as regulating thin filament length (TFL), cross-bridge cycling, and myofibril alignment. Pathogenic variants in the nebulin gene (NEB) cause NEB-based nemaline myopathy (NEM2), a genetically heterogeneous disorder characterized by hypotonia and muscle weakness, currently lacking curative therapies. In this study, we examined a cohort of ten NEM2 patients, each with unique pathogenic variants, aiming to understand their impact on mRNA, protein, and functional levels. Results show that pathogenic truncation variants affect NEB mRNA stability and lead to nonsense-mediated decay of the mutated transcript. Moreover, a high incidence of cryptic splice site activation was found in patients with pathogenic splicing variants that are expected to disrupt the actin-binding sites of nebulin. Determination of protein levels revealed patients with either relatively normal or markedly reduced nebulin. We observed a positive relation between the reduction in nebulin and a reduction in TFL, or reduction in tension (both maximal and submaximal tension). Interestingly, our study revealed a pathogenic duplication variant in nebulin that resulted in a four-copy gain in the triplicate region of NEB and a much larger nebulin protein and longer TFL. Additionally, we investigated the effect of Omecamtiv mecarbil (OM), a small-molecule activator of cardiac myosin, on force production of type 1 muscle fibers of NEM2 patients. OM treatment substantially increased submaximal tension across all NEM2 patients ranging from 87 to 318%, with the largest effects in patients with the lowest level of nebulin. In summary, this study indicates that post-transcriptional or post-translational mechanisms regulate nebulin expression. Moreover, we propose that the pathomechanism of NEM2 involves not only shortened but also elongated thin filaments, along with the disruption of actin-binding sites resulting from pathogenic splicing variants. Significantly, our findings highlight the potential of OM treatment to improve skeletal muscle function in NEM2 patients, especially those with large reductions in nebulin levels.
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Affiliation(s)
- Esmat Karimi
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, AZ, USA
| | - Jochen Gohlke
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, AZ, USA
| | - Mila van der Borgh
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, AZ, USA
| | - Johan Lindqvist
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, AZ, USA
| | - Zaynab Hourani
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, AZ, USA
| | - Justin Kolb
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, AZ, USA
| | - Stacy Cossette
- Department of Pathology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Michael W Lawlor
- Department of Pathology, Medical College of Wisconsin, Milwaukee, WI, USA
- Diverge Translational Science Laboratory, Milwaukee, WI, USA
| | - Coen Ottenheijm
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, AZ, USA
- Department of Physiology, Amsterdam UMC (Location VUMC), Amsterdam, Netherlands
| | - Henk Granzier
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, AZ, USA.
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6
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Lauffer MC, van Roon-Mom W, Aartsma-Rus A. Possibilities and limitations of antisense oligonucleotide therapies for the treatment of monogenic disorders. COMMUNICATIONS MEDICINE 2024; 4:6. [PMID: 38182878 PMCID: PMC10770028 DOI: 10.1038/s43856-023-00419-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 11/27/2023] [Indexed: 01/07/2024] Open
Abstract
Antisense oligonucleotides (ASOs) are incredibly versatile molecules that can be designed to specifically target and modify RNA transcripts to slow down or halt rare genetic disease progression. They offer the potential to target groups of patients or can be tailored for individual cases. Nonetheless, not all genetic variants and disorders are amenable to ASO-based treatments, and hence, it is important to consider several factors before embarking on the drug development journey. Here, we discuss which genetic disorders have the potential to benefit from a specific type of ASO approach, based on the pathophysiology of the disease and pathogenic variant type, as well as those disorders that might not be suitable for ASO therapies. We further explore additional aspects, such as the target tissues, intervention time points, and potential clinical benefits, which need to be considered before developing a compound. Overall, we provide an overview of the current potentials and limitations of ASO-based therapeutics for the treatment of monogenic disorders.
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Affiliation(s)
- Marlen C Lauffer
- Dutch Center for RNA Therapeutics, Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Willeke van Roon-Mom
- Dutch Center for RNA Therapeutics, Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Annemieke Aartsma-Rus
- Dutch Center for RNA Therapeutics, Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands.
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7
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Karimi E, van der Borgh M, Lindqvist J, Gohlke J, Hourani Z, Kolb J, Cossette S, Lawlor MW, Ottenheijm C, Granzier H. Characterization of NEB mutations in patients reveals novel nemaline myopathy disease mechanisms and omecamtiv mecarbil force effects. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.20.572678. [PMID: 38187705 PMCID: PMC10769406 DOI: 10.1101/2023.12.20.572678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Nebulin, a critical protein of the skeletal muscle thin filament, plays important roles in physiological processes such as regulating thin filament length (TFL), cross-bridge cycling, and myofibril alignment. Mutations in the nebulin gene ( NEB ) cause NEB-based nemaline myopathy (NEM2), a genetically heterogeneous disorder characterized by hypotonia and muscle weakness, currently lacking therapies targeting the underlying pathological mechanisms. In this study, we examined a cohort of ten NEM2 patients, each with unique mutations, aiming to understand their impact on mRNA, protein, and functional levels. Results show that truncation mutations affect NEB mRNA stability and lead to nonsense-mediated decay of the mutated transcript. Moreover, a high incidence of cryptic splice site activation was found in patients with splicing mutations which is expected to disrupt the actin-binding sites of nebulin. Determination of protein levels revealed patients with relatively normal nebulin levels and others with markedly reduced nebulin. We observed a positive relation between the reduction in nebulin and a reduction in TFL, and a positive relation between the reduction in nebulin level and the reduction in tension (both maximal and submaximal tension). Interestingly, our study revealed a duplication mutation in nebulin that resulted in a larger nebulin protein and longer TFL. Additionally, we investigated the effect of Omecamtiv mecarbil (OM), a small-molecule activator of cardiac myosin, on force production of type I muscle fibers of NEM2 patients. OM treatment substantially increased submaximal tension across all NEM2 patients ranging from 87-318%, with the largest effects in patients with the lowest level of nebulin. In summary, this study indicates that post-transcriptional or post-translational mechanisms regulate nebulin expression. Moreover, we propose that the pathomechanism of NEM2 involves not only shortened but also elongated thin filaments, along with the disruption of actin-binding sites resulting from splicing mutations. Significantly, our findings highlight the potential of OM treatment to improve skeletal muscle function in NEM2 patients, especially those with large reductions in nebulin levels.
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8
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Gonçalves CI, Carriço JN, Omar OM, Abdalla E, Lemos MC. Hypoparathyroidism, deafness and renal dysplasia syndrome caused by a GATA3 splice site mutation leading to the activation of a cryptic splice site. Front Endocrinol (Lausanne) 2023; 14:1207425. [PMID: 37600721 PMCID: PMC10436458 DOI: 10.3389/fendo.2023.1207425] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 07/13/2023] [Indexed: 08/22/2023] Open
Abstract
The HDR syndrome is a rare autosomal dominant disorder characterised by Hypoparathyroidism, Deafness, and Renal dysplasia, and is caused by inactivating heterozygous germline mutations in the GATA3 gene. We report an 11-year-old girl with HDR syndrome caused by a heterozygous mutation located at the splice acceptor site of exon 5 of the GATA3 gene (NM_001002295.2: c.925-1G>T). Functional studies using a minigene assay showed that this splice site mutation abolished the normal splicing of the GATA3 pre-mRNA and led to the use of a cryptic splice acceptor site, resulting in the loss of the first seven nucleotides (TCTGCAG) of exon 5 in the GATA3 mRNA. These findings increase the understanding of the mechanisms by which GATA3 splicing mutations can cause HDR syndrome.
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Affiliation(s)
- Catarina I. Gonçalves
- CICS-UBI, Health Sciences Research Centre, University of Beira Interior, Covilhã, Portugal
| | - Josianne N. Carriço
- CICS-UBI, Health Sciences Research Centre, University of Beira Interior, Covilhã, Portugal
| | - Omneya M. Omar
- Department of Pediatrics, Faculty of Medicine, Alexandria University, Alexandria, Egypt
| | - Ebtesam Abdalla
- Department of Human Genetics, Medical Research Institute, Alexandria University, Alexandria, Egypt
| | - Manuel C. Lemos
- CICS-UBI, Health Sciences Research Centre, University of Beira Interior, Covilhã, Portugal
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9
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Das R, Tu ZJ, Bosler DS, Cheng Y. Identification and interpretation of TET2 noncanonical splicing site intronic variants in myeloid neoplasm patients. EJHAEM 2023; 4:738-744. [PMID: 37601840 PMCID: PMC10435687 DOI: 10.1002/jha2.744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 06/09/2023] [Accepted: 06/14/2023] [Indexed: 08/22/2023]
Abstract
Background: DNA hypermethylation and instability due to inactivation mutations in Ten-eleven translocation 2 (TET2) is a key biomarker of hematological malignancies. This study aims at characterizing two intronic noncanonical splice-site variants, c.3954+5_3954+8delGTTT and c.3954+5G>A. Methods: We used in silico prediction tools, reverse transcription (RT)-PCR, and Sanger sequencing on blood/bone marrow-derived RNA specimens to determine the aberrant splicing. Results: In silico prediction of both variants exhibited reduced splicing strength at the TET2 intron 7 splicing donor site. RT-PCR and Sanger sequencing identified a 62-bp deletion at the exon 7, producing a frameshift mutation, p.Cys1298*. Conclusion: This study provides functional evidence for two intronic TET2 variants that cause alternative splicing and frameshift mutation.
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Affiliation(s)
- Riku Das
- Department of Laboratory Medicine, Robert J. Tomsich Pathology and Laboratory Medicine InstituteCleveland ClinicClevelandOhioUSA
| | - Zheng Jin Tu
- Department of Laboratory Medicine, Robert J. Tomsich Pathology and Laboratory Medicine InstituteCleveland ClinicClevelandOhioUSA
| | - David S. Bosler
- Department of Laboratory Medicine, Robert J. Tomsich Pathology and Laboratory Medicine InstituteCleveland ClinicClevelandOhioUSA
| | - Yu‐Wei Cheng
- Department of Laboratory Medicine, Robert J. Tomsich Pathology and Laboratory Medicine InstituteCleveland ClinicClevelandOhioUSA
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10
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Girardini KN, Olthof AM, Kanadia RN. Introns: the "dark matter" of the eukaryotic genome. Front Genet 2023; 14:1150212. [PMID: 37260773 PMCID: PMC10228655 DOI: 10.3389/fgene.2023.1150212] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 04/28/2023] [Indexed: 06/02/2023] Open
Abstract
The emergence of introns was a significant evolutionary leap that is a major distinguishing feature between prokaryotic and eukaryotic genomes. While historically introns were regarded merely as the sequences that are removed to produce spliced transcripts encoding functional products, increasingly data suggests that introns play important roles in the regulation of gene expression. Here, we use an intron-centric lens to review the role of introns in eukaryotic gene expression. First, we focus on intron architecture and how it may influence mechanisms of splicing. Second, we focus on the implications of spliceosomal snRNAs and their variants on intron splicing. Finally, we discuss how the presence of introns and the need to splice them influences transcription regulation. Despite the abundance of introns in the eukaryotic genome and their emerging role regulating gene expression, a lot remains unexplored. Therefore, here we refer to introns as the "dark matter" of the eukaryotic genome and discuss some of the outstanding questions in the field.
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Affiliation(s)
- Kaitlin N. Girardini
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT, United States
| | - Anouk M. Olthof
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT, United States
- Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Rahul N. Kanadia
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT, United States
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, United States
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11
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García-Ruiz S, Zhang D, Gustavsson EK, Rocamora-Perez G, Grant-Peters M, Fairbrother-Browne A, Reynolds RH, Brenton JW, Gil-Martínez AL, Chen Z, Rio DC, Botia JA, Guelfi S, Collado-Torres L, Ryten M. Splicing accuracy varies across human introns, tissues and age. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.29.534370. [PMID: 37034741 PMCID: PMC10081249 DOI: 10.1101/2023.03.29.534370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Alternative splicing impacts most multi-exonic human genes. Inaccuracies during this process may have an important role in ageing and disease. Here, we investigated mis-splicing using RNA-sequencing data from ~14K control samples and 42 human body sites, focusing on split reads partially mapping to known transcripts in annotation. We show that mis-splicing occurs at different rates across introns and tissues and that these splicing inaccuracies are primarily affected by the abundance of core components of the spliceosome assembly and its regulators. Using publicly available data on short-hairpin RNA-knockdowns of numerous spliceosomal components and related regulators, we found support for the importance of RNA-binding proteins in mis-splicing. We also demonstrated that age is positively correlated with mis-splicing, and it affects genes implicated in neurodegenerative diseases. This in-depth characterisation of mis-splicing can have important implications for our understanding of the role of splicing inaccuracies in human disease and the interpretation of long-read RNA-sequencing data.
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Affiliation(s)
- S García-Ruiz
- Department of Genetics and Genomic Medicine Research & Teaching, UCL GOS Institute of Child Health, London, UK
- NIHR Great Ormond Street Hospital Biomedical Research Centre, University College London, London, UK
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815
| | - D Zhang
- Department of Genetics and Genomic Medicine Research & Teaching, UCL GOS Institute of Child Health, London, UK
| | - E K Gustavsson
- Department of Genetics and Genomic Medicine Research & Teaching, UCL GOS Institute of Child Health, London, UK
- NIHR Great Ormond Street Hospital Biomedical Research Centre, University College London, London, UK
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815
| | - G Rocamora-Perez
- Department of Genetics and Genomic Medicine Research & Teaching, UCL GOS Institute of Child Health, London, UK
| | - M Grant-Peters
- Department of Genetics and Genomic Medicine Research & Teaching, UCL GOS Institute of Child Health, London, UK
- NIHR Great Ormond Street Hospital Biomedical Research Centre, University College London, London, UK
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815
| | - A Fairbrother-Browne
- Department of Genetics and Genomic Medicine Research & Teaching, UCL GOS Institute of Child Health, London, UK
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815
- Department of Medical and Molecular Genetics, School of Basic and Medical Biosciences, King's College London, London, UK
- Department of Neurodegenerative Disease, Queen Square Institute of Neurology, UCL, London, UK
| | - R H Reynolds
- Department of Genetics and Genomic Medicine Research & Teaching, UCL GOS Institute of Child Health, London, UK
- NIHR Great Ormond Street Hospital Biomedical Research Centre, University College London, London, UK
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815
| | - J W Brenton
- Department of Genetics and Genomic Medicine Research & Teaching, UCL GOS Institute of Child Health, London, UK
- NIHR Great Ormond Street Hospital Biomedical Research Centre, University College London, London, UK
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815
| | - A L Gil-Martínez
- Department of Genetics and Genomic Medicine Research & Teaching, UCL GOS Institute of Child Health, London, UK
- Department of Neurodegenerative Disease, Queen Square Institute of Neurology, UCL, London, UK
| | - Z Chen
- Department of Genetics and Genomic Medicine Research & Teaching, UCL GOS Institute of Child Health, London, UK
- Department of Neurodegenerative Disease, Queen Square Institute of Neurology, UCL, London, UK
| | - D C Rio
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720, USA
| | - J A Botia
- Departamento de Ingeniería de la Información y las Comunicaciones, Universidad de Murcia, Murcia, Spain
| | - S Guelfi
- Department of Genetics and Genomic Medicine Research & Teaching, UCL GOS Institute of Child Health, London, UK
- Verge Genomics, South San Francisco, CA, 94080, USA
| | - L Collado-Torres
- Lieber Institute for Brain Development, Baltimore, MD, USA , 21205
| | - M Ryten
- Department of Genetics and Genomic Medicine Research & Teaching, UCL GOS Institute of Child Health, London, UK
- NIHR Great Ormond Street Hospital Biomedical Research Centre, University College London, London, UK
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815
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12
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Rogalska ME, Vafiadaki E, Erpapazoglou Z, Haghighi K, Green L, Mantzoros CS, Hajjar RJ, Tranter M, Karakikes I, Kranias EG, Stillitano F, Kafasla P, Sanoudou D. Isoform changes of action potential regulators in the ventricles of arrhythmogenic phospholamban-R14del humanized mouse hearts. Metabolism 2023; 138:155344. [PMID: 36375644 DOI: 10.1016/j.metabol.2022.155344] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 10/30/2022] [Accepted: 11/01/2022] [Indexed: 11/13/2022]
Abstract
Arrhythmogenic cardiomyopathy (ACM) is characterized by life-threatening ventricular arrhythmias and sudden cardiac death and affects hundreds of thousands of patients worldwide. The deletion of Arginine 14 (p.R14del) in the phospholamban (PLN) gene has been implicated in the pathogenesis of ACM. PLN is a key regulator of sarcoplasmic reticulum (SR) Ca2+ cycling and cardiac contractility. Despite global gene and protein expression studies, the molecular mechanisms of PLN-R14del ACM pathogenesis remain unclear. Using a humanized PLN-R14del mouse model and human induced pluripotent stem cell derived cardiomyocytes (iPSC-CMs), we investigated the transcriptome-wide mRNA splicing changes associated with the R14del mutation. We identified >200 significant alternative splicing (AS) events and distinct AS profiles were observed in the right (RV) and left (LV) ventricles in PLN-R14del compared to WT mouse hearts. Enrichment analysis of the AS events showed that the most affected biological process was associated with "cardiac cell action potential", specifically in the RV. We found that splicing of 2 key genes, Trpm4 and Camk2d, which encode proteins regulating calcium homeostasis in the heart, were altered in PLN-R14del mouse hearts and human iPSC-CMs. Bioinformatical analysis pointed to the tissue-specific splicing factors Srrm4 and Nova1 as likely upstream regulators of the observed splicing changes in the PLN-R14del cardiomyocytes. Our findings suggest that aberrant splicing may affect Ca2+-homeostasis in the heart, contributing to the increased risk of arrythmogenesis in PLN-R14del ACM.
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Affiliation(s)
- Malgorzata E Rogalska
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona 08003, Spain
| | - Elizabeth Vafiadaki
- Molecular Biology Division, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece
| | - Zoi Erpapazoglou
- Institute for Fundamental Biomedical Research, B.S.R.C. "Alexander Fleming", 16672 Athens, Greece
| | - Kobra Haghighi
- Department of Pharmacology and Systems Physiology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Lisa Green
- Department of Medicine, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Christos S Mantzoros
- Division of Endocrinology, Diabetes and Metabolism, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA; Section of Endocrinology, Boston VA Healthcare System, Harvard Medical School, Boston, MA 02215, USA
| | | | - Michael Tranter
- Department of Medicine, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Ioannis Karakikes
- Department of Cardiothoracic Surgery and Cardiovascular Institute, Stanford University School of Medicine, 240 Pasteur Dr, Stanford, CA 94304, USA
| | - Evangelia G Kranias
- Department of Pharmacology and Systems Physiology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Francesca Stillitano
- Division Heart and Lung, Department of Cardiology, University Medical Center Utrecht, 3584, CX, Utrecht, the Netherlands
| | - Panagiota Kafasla
- Institute for Fundamental Biomedical Research, B.S.R.C. "Alexander Fleming", 16672 Athens, Greece
| | - Despina Sanoudou
- Molecular Biology Division, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece; Clinical Genomics and Pharmacogenomics Unit, 4(th) Department of Internal Medicine, Attikon Hospital, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece; Center for New Biotechnologies and Precision Medicine, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece.
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13
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Huang W, Zhang L, Zhu Y, Chen J, Zhu Y, Lin F, Chen X, Huang J. A genetic screen in Arabidopsis reveals the identical roles for RBP45d and PRP39a in 5' cryptic splice site selection. FRONTIERS IN PLANT SCIENCE 2022; 13:1086506. [PMID: 36618610 PMCID: PMC9813592 DOI: 10.3389/fpls.2022.1086506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 12/02/2022] [Indexed: 06/17/2023]
Abstract
Cryptic splice sites in eukaryotic genome are generally dormant unless activated by mutation of authentic splice sites or related splicing factors. How cryptic splice sites are used remains unclear in plants. Here, we identified two cryptic splicing regulators, RBP45d and PRP39a that are homologs of yeast U1 auxiliary protein Nam8 and Prp39, respectively, via genetic screening for suppressors of the virescent sot5 mutant, which results from a point mutation at the 5' splice site (5' ss) of SOT5 intron 7. Loss-of-function mutations in RBP45d and PRP39a significantly increase the level of a cryptically spliced variant that encodes a mutated but functional sot5 protein, rescuing sot5 to the WT phenotype. We furtherly demonstrated that RBP45d and PRP39a interact with each other and also with the U1C, a core subunit of U1 snRNP. We found that RBP45d directly binds to the uridine (U)-rich RNA sequence downstream the 5' ss of SOT5 intron 7. However, other RBP45/47 members do not function redundantly with RBP45d, at least in regulation of cryptic splicing. Taken together, RBP45d promotes U1 snRNP to recognize the specific 5' ss via binding to intronic U-rich elements in plants.
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Affiliation(s)
- Weihua Huang
- Shanghai Key Laboratory of Plant Molecular Sciences, Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Liqun Zhang
- Shanghai Key Laboratory of Plant Molecular Sciences, Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Yajuan Zhu
- Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Jingli Chen
- Shanghai Key Laboratory of Plant Molecular Sciences, Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Yawen Zhu
- Shanghai Key Laboratory of Plant Molecular Sciences, Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Fengru Lin
- Shanghai Key Laboratory of Plant Molecular Sciences, Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Xiaomei Chen
- Shanghai Key Laboratory of Plant Molecular Sciences, Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Jirong Huang
- Shanghai Key Laboratory of Plant Molecular Sciences, Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, China
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14
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Molina MF, Pio MG, Scheps KG, Adrover E, Abelleyro MM, Targovnik HM, Rivolta CM. Curating the gnomAD database: Report of novel variants in the thyroid peroxidase gene using in silico bioinformatics algorithms and a literature review. Mol Cell Endocrinol 2022; 558:111748. [PMID: 35995307 DOI: 10.1016/j.mce.2022.111748] [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: 06/22/2022] [Revised: 07/31/2022] [Accepted: 08/01/2022] [Indexed: 12/15/2022]
Abstract
Thyroid peroxidase (TPO) is a membrane-bound glycoprotein located at the apical side of the thyroid follicular cells that catalyzes both iodination and coupling of iodotyrosine residues within the thyroglobulin molecule, leading to the synthesis of thyroid hormone. Variants in TPO cause congenital hypothyroidism (CH) by iodide organification defect and are commonly inherited in an autosomal recessive fashion. In the present work, we report a detailed population analysis and bioinformatic prediction of the TPO variants indexed in the Genome Aggregation Database (gnomAD) v2.1.1. The proportion of missense cysteine variants and nonsense, frameshift, and splice acceptor/donor variants were analyzed in each ethnic group (European (Non-Finnish), European (Finnish), African/African Americans, Latino/Admixed American, East Asian, South Asian, Ashkenazi Jewish, Other). The results showed a clear predominance of frameshift variants in the East Asian (82%) and European (Finnish) (75%) population, whereas the splice site variants predominate in African/African Americans (99.46%), Other (96%), Latino/Admixed American (94%), South Asian (86%), European (Non-Finnish) (56%) and Ashkenazi Jewish (56%) populations. The analysis of the distribution of the variants indexed in gnomAD v2.1.1 database revealed that most missense variants identified in the An peroxidase domain map in exon 8, followed by exons 11, 7 and 9, and finally in descending order by exons 10, 6, 12 and 5. In total, 183 novel TPO variants were described (13 missense cysteine's variants, 158 missense variants involving the An peroxidase domain and 12 splicing acceptor or donor sites variants) which were not reported in the literature and that would have deleterious effects on prediction programs. In the gnomAD v2.1.1 population, the estimated prevalence of heterozygous carriers of the potentially damaging variants was 1:77. In conclusion, we provide an updated and curated reference source of new TPO variants for application in clinical diagnosis and genetic counseling. Also, this work contributes to elucidating the molecular basis of CH associated with TPO defects.
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Affiliation(s)
- Maricel F Molina
- Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Departamento de Microbiología, Inmunología, Biotecnología y Genética/Cátedra de Genética, Buenos Aires, Argentina; CONICET-Universidad de Buenos Aires, Instituto de Inmunología, Genética y Metabolismo (INIGEM), Buenos Aires, Argentina
| | - Mauricio Gomes Pio
- Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Departamento de Microbiología, Inmunología, Biotecnología y Genética/Cátedra de Genética, Buenos Aires, Argentina; CONICET-Universidad de Buenos Aires, Instituto de Inmunología, Genética y Metabolismo (INIGEM), Buenos Aires, Argentina
| | - Karen G Scheps
- Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Departamento de Microbiología, Inmunología, Biotecnología y Genética/Cátedra de Genética, Buenos Aires, Argentina; CONICET-Universidad de Buenos Aires, Instituto de Inmunología, Genética y Metabolismo (INIGEM), Buenos Aires, Argentina
| | - Ezequiela Adrover
- Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Departamento de Microbiología, Inmunología, Biotecnología y Genética/Cátedra de Genética, Buenos Aires, Argentina; CONICET-Universidad de Buenos Aires, Instituto de Inmunología, Genética y Metabolismo (INIGEM), Buenos Aires, Argentina
| | - Miguel M Abelleyro
- CONICET-Academia Nacional de Medicina, Instituto de Medicina Experimental (IMEX), Buenos Aires, Argentina
| | - Héctor M Targovnik
- Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Departamento de Microbiología, Inmunología, Biotecnología y Genética/Cátedra de Genética, Buenos Aires, Argentina; CONICET-Universidad de Buenos Aires, Instituto de Inmunología, Genética y Metabolismo (INIGEM), Buenos Aires, Argentina
| | - Carina M Rivolta
- Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Departamento de Microbiología, Inmunología, Biotecnología y Genética/Cátedra de Genética, Buenos Aires, Argentina; CONICET-Universidad de Buenos Aires, Instituto de Inmunología, Genética y Metabolismo (INIGEM), Buenos Aires, Argentina.
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15
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Saha K, Ghosh G. Cooperative engagement and subsequent selective displacement of SR proteins define the pre-mRNA 3D structural scaffold for early spliceosome assembly. Nucleic Acids Res 2022; 50:8262-8278. [PMID: 35871302 PMCID: PMC9371905 DOI: 10.1093/nar/gkac636] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 07/04/2022] [Accepted: 07/13/2022] [Indexed: 11/13/2022] Open
Abstract
Abstract
We recently reported that serine–arginine-rich (SR) protein-mediated pre-mRNA structural remodeling generates a pre-mRNA 3D structural scaffold that is stably recognized by the early spliceosomal components. However, the intermediate steps between the free pre-mRNA and the assembled early spliceosome are not yet characterized. By probing the early spliceosomal complexes in vitro and RNA-protein interactions in vivo, we show that the SR proteins bind the pre-mRNAs cooperatively generating a substrate that recruits U1 snRNP and U2AF65 in a splice signal-independent manner. Excess U1 snRNP selectively displaces some of the SR protein molecules from the pre-mRNA generating the substrate for splice signal-specific, sequential recognition by U1 snRNP, U2AF65 and U2AF35. Our work thus identifies a novel function of U1 snRNP in mammalian splicing substrate definition, explains the need for excess U1 snRNP compared to other U snRNPs in vivo, demonstrates how excess SR proteins could inhibit splicing, and provides a conceptual basis to examine if this mechanism of splicing substrate definition is employed by other splicing regulatory proteins.
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Affiliation(s)
- Kaushik Saha
- Department of Chemistry and Biochemistry, University of California San Diego , 9500 Gilman Drive , La Jolla , CA 92093-0375, USA
| | - Gourisankar Ghosh
- Department of Chemistry and Biochemistry, University of California San Diego , 9500 Gilman Drive , La Jolla , CA 92093-0375, USA
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16
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Schlautmann LP, Lackmann JW, Altmüller J, Dieterich C, Boehm V, Gehring N. Exon junction complex-associated multi-adapter RNPS1 nucleates splicing regulatory complexes to maintain transcriptome surveillance. Nucleic Acids Res 2022; 50:5899-5918. [PMID: 35640609 PMCID: PMC9178013 DOI: 10.1093/nar/gkac428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 05/05/2022] [Accepted: 05/10/2022] [Indexed: 12/04/2022] Open
Abstract
The exon junction complex (EJC) is an RNA-binding multi-protein complex with critical functions in post-transcriptional gene regulation. It is deposited on the mRNA during splicing and regulates diverse processes including pre-mRNA splicing and nonsense-mediated mRNA decay (NMD) via various interacting proteins. The peripheral EJC-binding protein RNPS1 was reported to serve two insufficiently characterized functions: suppressing mis-splicing of cryptic splice sites and activating NMD in the cytoplasm. The analysis of transcriptome-wide effects of EJC and RNPS1 knockdowns in different human cell lines supports the conclusion that RNPS1 can moderately influence NMD activity, but is not a globally essential NMD factor. However, numerous aberrant splicing events strongly suggest that the main function of RNPS1 is splicing regulation. Rescue analyses revealed that the RRM and C-terminal domain of RNPS1 both contribute partially to regulate RNPS1-dependent splicing events. We defined the RNPS1 core interactome using complementary immunoprecipitations and proximity labeling, which identified interactions with splicing-regulatory factors that are dependent on the C-terminus or the RRM domain of RNPS1. Thus, RNPS1 emerges as a multifunctional splicing regulator that promotes correct and efficient splicing of different vulnerable splicing events via the formation of diverse splicing-promoting complexes.
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Affiliation(s)
- Lena P Schlautmann
- Institute for Genetics, University of Cologne, 50674 Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50937 Cologne, Germany
| | - Jan-Wilm Lackmann
- CECAD Research Center, University of Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany
| | - Janine Altmüller
- Cologne Center for Genomics (CCG), University of Cologne, 50931 Cologne, Germany
| | - Christoph Dieterich
- Section of Bioinformatics and Systems Cardiology, Department of Internal Medicine III and Klaus Tschira Institute for Integrative Computational Cardiology, Heidelberg University Hospital, 69120 Heidelberg, Germany
- DZHK (German Centre for Cardiovascular Research), Partner site Heidelberg/Mannheim, 69120 Heidelberg, Germany
| | - Volker Boehm
- Institute for Genetics, University of Cologne, 50674 Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50937 Cologne, Germany
| | - Niels H Gehring
- Institute for Genetics, University of Cologne, 50674 Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50937 Cologne, Germany
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17
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Tran TT, Linga VG, Al-Obaide MAI, Bello-Germino D, Hoda M, Adesanya O, Vasylyeva TL. Congenital nephrotic syndrome in a Hispanic Guatemalan newborn associated with a NPHS1 variant: A case report. Biomed Rep 2021; 16:4. [PMID: 34900253 PMCID: PMC8652645 DOI: 10.3892/br.2021.1487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 11/05/2021] [Indexed: 11/06/2022] Open
Abstract
Congenital nephrotic syndrome (CNS) is an autosomal recessive disorder usually detected in the first 3 months of life when the syndromes effects manifest, including edema and a failure to gain weight. A baby boy was admitted to the Neonatal Intensive Care Unit for prematurity (35 weeks) with unremarkable maternal prenatal laboratory tests. The patient had persistent systemic hypertension, hypoproteinemia, hypoalbuminemia and nephrotic range proteinuria. CNS was diagnosed, and genetic testing showed a homozygous variant, c.3024A>G (AGA>AGG) in exon 22 of the nephrin locus. Bioinformatics analysis suggested the genetic condition was likely a result of malfunctional DNA binding sites of transcription factors FOXL1 and FOXC1.
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Affiliation(s)
- Thu T Tran
- Department of Pediatrics, Texas Tech University Health Sciences Center, Amarillo, TX 79106, USA
| | - Vijay G Linga
- Department of Pediatrics, Texas Tech University Health Sciences Center, Amarillo, TX 79106, USA
| | - Mohammed A I Al-Obaide
- Department of Pediatrics, Texas Tech University Health Sciences Center, Amarillo, TX 79106, USA
| | - Daniella Bello-Germino
- Department of Pediatrics, Texas Tech University Health Sciences Center, Amarillo, TX 79106, USA
| | - Mehar Hoda
- Department of Pediatrics, Texas Tech University Health Sciences Center, Amarillo, TX 79106, USA
| | - Olubukunola Adesanya
- Department of Pediatrics, Texas Tech University Health Sciences Center, Amarillo, TX 79106, USA
| | - Tetyana L Vasylyeva
- Department of Pediatrics, Texas Tech University Health Sciences Center, Amarillo, TX 79106, USA
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18
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Tang H, Shi X, Zhang G. Novel compound heterozygous mutations in the CYP4F22 gene in a patient with autosomal recessive congenital ichthyosis. Clin Case Rep 2021; 9:e05082. [PMID: 34917360 PMCID: PMC8645175 DOI: 10.1002/ccr3.5082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 10/27/2021] [Accepted: 10/31/2021] [Indexed: 11/30/2022] Open
Abstract
Autosomal recessive congenital ichthyosis (ARCI) is a rare form of keratinization disorder of the skin, which can be caused by mutations in 14 ARCI genes. We present a rare case of ARCI that carried a novel null mutation and a novel splice site mutation in the CYP4F22 gene.
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Affiliation(s)
- Haiyan Tang
- Department of Medical GeneticsThe Second Xiangya HospitalCentral South UniversityChangshaChina
- Center for Medical GeneticsSchool of Life SciencesCentral South UniversityChangshaChina
| | - Xiaoliu Shi
- Department of Medical GeneticsThe Second Xiangya HospitalCentral South UniversityChangshaChina
| | - Guiying Zhang
- Department of DermatologyThe Second Xiangya HospitalCentral South UniversityChangshaChina
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19
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Pio MG, Siffo S, Scheps KG, Molina MF, Adrover E, Abelleyro MM, Rivolta CM, Targovnik HM. Curating the gnomAD database: Report of novel variants in the thyrogobulin gene using in silico bioinformatics algorithms. Mol Cell Endocrinol 2021; 534:111359. [PMID: 34119605 DOI: 10.1016/j.mce.2021.111359] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 06/01/2021] [Accepted: 06/02/2021] [Indexed: 01/09/2023]
Abstract
Thyroglobulin (TG) is a large glycosylated protein of 2767 amino acids, secreted by the thyrocytes into the follicular lumen. It plays an essential role in the process of thyroid hormone synthesis. TG gene variants lead to permanent congenital hypothyroidism. In the present work, we report a detailed population and bioinformatic prediction analyses of the TG variants indexed in the Genome Aggregation Database (gnomAD). The results showed a clear predominance of nonsense variants in the European (Finnish), European (Non-Finnish) and Ashkenazi Jewish ethnic groups, whereas the splice site variants predominate in South Asian and African/African-American populations. In total, 282 novel TG variants were described (47 missense involving the wild-type cysteine residues, 177 missense located in the ChEL domain and 58 splice site variants) which were not reported in the literature and that would have deleterious effects in prediction programs. In the gnomAD population, the estimated prevalence of heterozygous carriers of the potentially damaging variants was 1:320. In conclusion, we provide an updated and curated reference source for the diagnosis of thyroid disease, mainly to congenital hypothyroidism due to TG deficiency. The identification and characterization of TG variants is undoubtedly a valuable approach to study the TG structure/function relations and an important tool for clinical diagnosis and genetic counseling.
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Affiliation(s)
- Mauricio Gomes Pio
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Microbiología, Inmunología, Biotecnología y Genética/Cátedra de Genética, Buenos Aires, Argentina; CONICET-Universidad de Buenos Aires, Instituto de Inmunología, Genética y Metabolismo (INIGEM), Buenos Aires, Argentina
| | - Sofia Siffo
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Microbiología, Inmunología, Biotecnología y Genética/Cátedra de Genética, Buenos Aires, Argentina; CONICET-Universidad de Buenos Aires, Instituto de Inmunología, Genética y Metabolismo (INIGEM), Buenos Aires, Argentina
| | - Karen G Scheps
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Microbiología, Inmunología, Biotecnología y Genética/Cátedra de Genética, Buenos Aires, Argentina; CONICET-Universidad de Buenos Aires, Instituto de Inmunología, Genética y Metabolismo (INIGEM), Buenos Aires, Argentina
| | - Maricel F Molina
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Microbiología, Inmunología, Biotecnología y Genética/Cátedra de Genética, Buenos Aires, Argentina; CONICET-Universidad de Buenos Aires, Instituto de Inmunología, Genética y Metabolismo (INIGEM), Buenos Aires, Argentina
| | - Ezequiela Adrover
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Microbiología, Inmunología, Biotecnología y Genética/Cátedra de Genética, Buenos Aires, Argentina; CONICET-Universidad de Buenos Aires, Instituto de Inmunología, Genética y Metabolismo (INIGEM), Buenos Aires, Argentina
| | - Miguel M Abelleyro
- CONICET-Academia Nacional de Medicina, Instituto de Medicina Experimental (IMEX), Buenos Aires, Argentina
| | - Carina M Rivolta
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Microbiología, Inmunología, Biotecnología y Genética/Cátedra de Genética, Buenos Aires, Argentina; CONICET-Universidad de Buenos Aires, Instituto de Inmunología, Genética y Metabolismo (INIGEM), Buenos Aires, Argentina
| | - Héctor M Targovnik
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Microbiología, Inmunología, Biotecnología y Genética/Cátedra de Genética, Buenos Aires, Argentina; CONICET-Universidad de Buenos Aires, Instituto de Inmunología, Genética y Metabolismo (INIGEM), Buenos Aires, Argentina.
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20
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Mishra A, Siwach P, Misra P, Dhiman S, Pandey AK, Srivastava P, Jayaram B. Intron exon boundary junctions in human genome have in-built unique structural and energetic signals. Nucleic Acids Res 2021; 49:2674-2683. [PMID: 33621338 PMCID: PMC7969029 DOI: 10.1093/nar/gkab098] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Revised: 01/21/2021] [Accepted: 02/22/2021] [Indexed: 11/13/2022] Open
Abstract
Precise identification of correct exon–intron boundaries is a prerequisite to analyze the location and structure of genes. The existing framework for genomic signals, delineating exon and introns in a genomic segment, seems insufficient, predominantly due to poor sequence consensus as well as limitations of training on available experimental data sets. We present here a novel concept for characterizing exon–intron boundaries in genomic segments on the basis of structural and energetic properties. We analyzed boundary junctions on both sides of all the exons (3 28 368) of protein coding genes from human genome (GENCODE database) using 28 structural and three energy parameters. Study of sequence conservation at these sites shows very poor consensus. It is observed that DNA adopts a unique structural and energy state at the boundary junctions. Also, signals are somewhat different for housekeeping and tissue specific genes. Clustering of 31 parameters into four derived vectors gives some additional insights into the physical mechanisms involved in this biological process. Sites of structural and energy signals correlate well to the positions playing important roles in pre-mRNA splicing.
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Affiliation(s)
- Akhilesh Mishra
- Supercomputing Facility for Bioinformatics & Computational Biology, Indian Institute of Technology Delhi, India.,Kusuma School of Biological Sciences, Indian Institute of Technology, Delhi, India
| | - Priyanka Siwach
- Supercomputing Facility for Bioinformatics & Computational Biology, Indian Institute of Technology Delhi, India.,Department of Biotechnology, Chaudhary Devi Lal University, Sirsa, Haryana, India
| | - Pallavi Misra
- Supercomputing Facility for Bioinformatics & Computational Biology, Indian Institute of Technology Delhi, India
| | - Simran Dhiman
- Supercomputing Facility for Bioinformatics & Computational Biology, Indian Institute of Technology Delhi, India
| | | | - Parul Srivastava
- Supercomputing Facility for Bioinformatics & Computational Biology, Indian Institute of Technology Delhi, India
| | - B Jayaram
- Supercomputing Facility for Bioinformatics & Computational Biology, Indian Institute of Technology Delhi, India.,Kusuma School of Biological Sciences, Indian Institute of Technology, Delhi, India.,Department of Chemistry, Indian Institute of Technology, Delhi, India
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21
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Pio MG, Molina MF, Siffo S, Chiesa A, Rivolta CM, Targovnik HM. A novel mutation in intron 11 donor splice site, responsible of a rare genotype in thyroglobulin gene by altering the pre-mRNA splincing process. Cell expression and bioinformatic analysis. Mol Cell Endocrinol 2021; 522:111124. [PMID: 33321114 DOI: 10.1016/j.mce.2020.111124] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 12/08/2020] [Accepted: 12/10/2020] [Indexed: 01/09/2023]
Abstract
Thyroglobulin (TG) is a homodimeric glycoprotein synthesized by the thyroid gland. To date, two hundred twenty-seven variations of the TG gene have been identified in humans. Thyroid dyshormonogenesis due to TG gene mutations have an estimated incidence of approximately 1 in 100,000 newborns. The clinical spectrum ranges from euthyroid to mild or severe hypothyroidism. The purpose of the present study was to identify and characterize new variants in the TG gene. We report an Argentine patient with congenital hypothyroidism, enlarged thyroid gland and low levels of serum TG. Sequencing of DNA, expression of chimeric minigenes as well as bioinformatics analysis were performed. DNA sequencing identified the presence of compound heterozygous mutations in the TG gene: the maternal mutation consists of a c.3001+5G > A, whereas the paternal mutation consists of p.Arg296*. Minigen analysis of the variant c.3001+5A performed in HeLa, CV1 and Hek293T cell lines, showed a total lack of transcript expression. So, in order to validate that the loss of expression was caused by such variation, site-directed mutagenesis was performed on the mutated clone, which previously had a pSPL3 vector change, to give rise to a wild-type clone c.3001+5G, endorsing that the mutation c.3001+5G > A is the cause of the total lack of expression. In conclusion, we demonstrate that the c.3001+5G > A mutation causes a rare genotype, altering the splicing of the pre-mRNA. This work contributes to elucidating the molecular bases of TG defects associated with congenital hypothyroidism and expands our knowledge in relation to the pathologic roles of the position 5 in the donor splice site.
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Affiliation(s)
- Mauricio Gomes Pio
- Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Departamento de Microbiología, Inmunología, Biotecnología y Genética/Cátedra de Genética, Buenos Aires, Argentina; CONICET-Universidad de Buenos Aires. Instituto de Inmunología, Genética y Metabolismo (INIGEM), Buenos Aires, Argentina
| | - Maricel F Molina
- Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Departamento de Microbiología, Inmunología, Biotecnología y Genética/Cátedra de Genética, Buenos Aires, Argentina; CONICET-Universidad de Buenos Aires. Instituto de Inmunología, Genética y Metabolismo (INIGEM), Buenos Aires, Argentina
| | - Sofia Siffo
- Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Departamento de Microbiología, Inmunología, Biotecnología y Genética/Cátedra de Genética, Buenos Aires, Argentina; CONICET-Universidad de Buenos Aires. Instituto de Inmunología, Genética y Metabolismo (INIGEM), Buenos Aires, Argentina
| | - Ana Chiesa
- Centro de Investigaciones Endocrinológicas, CEDIE-CONICET, División Endocrinología, Hospital de Niños "Ricardo Gutiérrez", Buenos Aires, Argentina
| | - Carina M Rivolta
- Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Departamento de Microbiología, Inmunología, Biotecnología y Genética/Cátedra de Genética, Buenos Aires, Argentina; CONICET-Universidad de Buenos Aires. Instituto de Inmunología, Genética y Metabolismo (INIGEM), Buenos Aires, Argentina
| | - Héctor M Targovnik
- Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Departamento de Microbiología, Inmunología, Biotecnología y Genética/Cátedra de Genética, Buenos Aires, Argentina; CONICET-Universidad de Buenos Aires. Instituto de Inmunología, Genética y Metabolismo (INIGEM), Buenos Aires, Argentina.
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22
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Alvarez MEV, Chivers M, Borovska I, Monger S, Giannoulatou E, Kralovicova J, Vorechovsky I. Transposon clusters as substrates for aberrant splice-site activation. RNA Biol 2020; 18:354-367. [PMID: 32965162 PMCID: PMC7951965 DOI: 10.1080/15476286.2020.1805909] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Transposed elements (TEs) have dramatically shaped evolution of the exon-intron structure and significantly contributed to morbidity, but how recent TE invasions into older TEs cooperate in generating new coding sequences is poorly understood. Employing an updated repository of new exon-intron boundaries induced by pathogenic mutations, termed DBASS, here we identify novel TE clusters that facilitated exon selection. To explore the extent to which such TE exons maintain RNA secondary structure of their progenitors, we carried out structural studies with a composite exon that was derived from a long terminal repeat (LTR78) and AluJ and was activated by a C > T mutation optimizing the 5ʹ splice site. Using a combination of SHAPE, DMS and enzymatic probing, we show that the disease-causing mutation disrupted a conserved AluJ stem that evolved from helix 3.3 (or 5b) of 7SL RNA, liberating a primordial GC 5ʹ splice site from the paired conformation for interactions with the spliceosome. The mutation also reduced flexibility of conserved residues in adjacent exon-derived loops of the central Alu hairpin, revealing a cross-talk between traditional and auxilliary splicing motifs that evolved from opposite termini of 7SL RNA and were approximated by Watson-Crick base-pairing already in organisms without spliceosomal introns. We also identify existing Alu exons activated by the same RNA rearrangement. Collectively, these results provide valuable TE exon models for studying formation and kinetics of pre-mRNA building blocks required for splice-site selection and will be useful for fine-tuning auxilliary splicing motifs and exon and intron size constraints that govern aberrant splice-site activation.
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Affiliation(s)
| | - Martin Chivers
- School of Medicine, University of Southampton, Southampton, UK
| | - Ivana Borovska
- Slovak Academy of Sciences, Institute of Molecular Physiology and Genetics, Bratislava, Slovak Republic
| | - Steven Monger
- Computational Genomics Laboratory, Victor Chang Cardiac Research Institute, Darlinghurst, Australia
| | - Eleni Giannoulatou
- Computational Genomics Laboratory, Victor Chang Cardiac Research Institute, Darlinghurst, Australia.,St. Vincent's Clinical School, University of New South Wales, Sydney, Australia
| | - Jana Kralovicova
- School of Medicine, University of Southampton, Southampton, UK.,Slovak Academy of Sciences, Institute of Molecular Physiology and Genetics, Bratislava, Slovak Republic
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23
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Wang TY, Guo X. Expression vector cassette engineering for recombinant therapeutic production in mammalian cell systems. Appl Microbiol Biotechnol 2020; 104:5673-5688. [PMID: 32372203 DOI: 10.1007/s00253-020-10640-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 04/13/2020] [Accepted: 04/20/2020] [Indexed: 12/16/2022]
Abstract
Human tissue plasminogen activator was the first recombinant therapy protein that successfully produced in Chinese hamster ovary cells in 1986 and approved for clinical use. Since then, more and more therapeutic proteins are being manufactured in mammalian cells, and the technologies for recombinant protein production in this expression system have developed rapidly, with the optimization of both upstream and downstream processes. One of the most promising strategies is expression vector cassette optimization based on the expression vector cassette. In this review paper, these approaches and developments are summarized, and the future strategy on the utilizing of expression cassettes for the production of recombinant therapeutic proteins in mammalian cells is discussed.
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Affiliation(s)
- Tian-Yun Wang
- Department of Biochemistry and Molecular Biology, Xinxiang Medical University, Xinxiang, 453003, Henan, China.
- International Joint Research Laboratory for Recombinant Pharmaceutical Protein Expression System of Henan, Xinxiang Medical University, Xinxiang, 453003, Henan, China.
| | - Xiao Guo
- International Joint Research Laboratory for Recombinant Pharmaceutical Protein Expression System of Henan, Xinxiang Medical University, Xinxiang, 453003, Henan, China
- Perildicals Publishing House, Xinxiang Medical University, Xinxiang, Henan, China
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24
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Yang YM, Yan K, Liu B, Chen M, Wang LY, Huang YZ, Qian YQ, Sun YX, Li HG, Dong MY. Comprehensive genetic diagnosis of patients with Duchenne/Becker muscular dystrophy (DMD/BMD) and pathogenicity analysis of splice site variants in the DMD gene. J Zhejiang Univ Sci B 2020; 20:753-765. [PMID: 31379145 DOI: 10.1631/jzus.b1800541] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Duchenne muscular dystrophy (DMD) and Becker muscular dystrophy (BMD) are caused by mutations in the DMD gene. The aim of this study is to identify pathogenic DMD variants in probands and reduce the risk of recurrence of the disease in affected families. Variations in 100 unrelated DMD/BMD patients were detected by multiplex ligation-dependent probe amplification (MLPA) and next-generation sequencing (NGS). Pathogenic variants in DMD were successfully identified in all cases, and 11 of them were novel. The most common mutations were intragenic deletions (69%), with two hotspots located in the 5' end (exons 2-19) and the central of the DMD gene (exons 45-55), while point mutations were observed in 22% patients. Further, c.1149+1G>A and c.1150-2A>G were confirmed by hybrid minigene splicing assay (HMSA). This two splice site mutations would lead to two aberrant DMD isoforms which give rise to severely truncated protein. Therefore, the clinical use of MLPA, NGS, and HMSA is an effective strategy to identify variants. Importantly, eight embryos were terminated pregnancies according to prenatal diagnosis and a healthy boy was successfully delivered by preimplantation genetic diagnosis (PGD). Early and accurate genetic diagnosis is essential for prenatal diagnosis/PGD to reduce the risk of recurrence of DMD in affected families.
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Affiliation(s)
- Yan-Mei Yang
- Department of Reproductive Genetics, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou 310006, China.,Key Laboratory of Reproductive Genetics (Zhejiang University), Ministry of Education, Hangzhou 310006, China.,Key Laboratory of Women's Reproductive Health of Zhejiang Province, Hangzhou 310006, China
| | - Kai Yan
- Department of Reproductive Genetics, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou 310006, China.,Key Laboratory of Reproductive Genetics (Zhejiang University), Ministry of Education, Hangzhou 310006, China.,Key Laboratory of Women's Reproductive Health of Zhejiang Province, Hangzhou 310006, China
| | - Bei Liu
- Department of Reproductive Genetics, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou 310006, China.,Key Laboratory of Reproductive Genetics (Zhejiang University), Ministry of Education, Hangzhou 310006, China.,Key Laboratory of Women's Reproductive Health of Zhejiang Province, Hangzhou 310006, China
| | - Min Chen
- Department of Reproductive Genetics, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou 310006, China.,Key Laboratory of Reproductive Genetics (Zhejiang University), Ministry of Education, Hangzhou 310006, China.,Key Laboratory of Women's Reproductive Health of Zhejiang Province, Hangzhou 310006, China
| | - Li-Ya Wang
- Department of Reproductive Genetics, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou 310006, China.,Key Laboratory of Reproductive Genetics (Zhejiang University), Ministry of Education, Hangzhou 310006, China.,Key Laboratory of Women's Reproductive Health of Zhejiang Province, Hangzhou 310006, China
| | - Ying-Zhi Huang
- Department of Reproductive Genetics, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou 310006, China.,Key Laboratory of Reproductive Genetics (Zhejiang University), Ministry of Education, Hangzhou 310006, China.,Key Laboratory of Women's Reproductive Health of Zhejiang Province, Hangzhou 310006, China
| | - Ye-Qing Qian
- Department of Reproductive Genetics, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou 310006, China.,Key Laboratory of Reproductive Genetics (Zhejiang University), Ministry of Education, Hangzhou 310006, China.,Key Laboratory of Women's Reproductive Health of Zhejiang Province, Hangzhou 310006, China
| | - Yi-Xi Sun
- Department of Reproductive Genetics, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou 310006, China.,Key Laboratory of Reproductive Genetics (Zhejiang University), Ministry of Education, Hangzhou 310006, China.,Key Laboratory of Women's Reproductive Health of Zhejiang Province, Hangzhou 310006, China
| | - Hong-Ge Li
- Department of Reproductive Genetics, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou 310006, China.,Key Laboratory of Reproductive Genetics (Zhejiang University), Ministry of Education, Hangzhou 310006, China.,Key Laboratory of Women's Reproductive Health of Zhejiang Province, Hangzhou 310006, China
| | - Min-Yue Dong
- Department of Reproductive Genetics, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou 310006, China.,Key Laboratory of Reproductive Genetics (Zhejiang University), Ministry of Education, Hangzhou 310006, China.,Key Laboratory of Women's Reproductive Health of Zhejiang Province, Hangzhou 310006, China
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25
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Boehm V, Britto-Borges T, Steckelberg AL, Singh KK, Gerbracht JV, Gueney E, Blazquez L, Altmüller J, Dieterich C, Gehring NH. Exon Junction Complexes Suppress Spurious Splice Sites to Safeguard Transcriptome Integrity. Mol Cell 2018; 72:482-495.e7. [DOI: 10.1016/j.molcel.2018.08.030] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 07/24/2018] [Accepted: 08/20/2018] [Indexed: 12/14/2022]
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26
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El Wafi M, El Housse H, Zaid N, Zouine S, Nourichafi N, Bouisk K, Benajiba M, Habti N. Novel intronic RHD variants identified in serologically D-negative blood donors. Vox Sang 2017; 112:796-802. [DOI: 10.1111/vox.12570] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 07/05/2017] [Accepted: 07/17/2017] [Indexed: 01/28/2023]
Affiliation(s)
- M. El Wafi
- Laboratory of Hematology; Cellular and Genetic Engineering; Faculty of Medicine and Pharmacy Casablanca; Hassan II University of Casablanca; Casablanca Morocco
- Laboratory of Biotechnology and Experimental Medicine; Faculty of Medicine and Pharmacy Casablanca; Hassan II University of Casablanca; Casablanca Morocco
| | - H. El Housse
- Laboratory of Hematology; Cellular and Genetic Engineering; Faculty of Medicine and Pharmacy Casablanca; Hassan II University of Casablanca; Casablanca Morocco
- Laboratory of Biotechnology and Experimental Medicine; Faculty of Medicine and Pharmacy Casablanca; Hassan II University of Casablanca; Casablanca Morocco
| | - N. Zaid
- Beaulieu-Saucier Pharmacogenomics Center; Montreal Heart Institute; Montreal QC Canada
| | - S. Zouine
- Laboratory of Hematology; Cellular and Genetic Engineering; Faculty of Medicine and Pharmacy Casablanca; Hassan II University of Casablanca; Casablanca Morocco
- Laboratory of Biotechnology and Experimental Medicine; Faculty of Medicine and Pharmacy Casablanca; Hassan II University of Casablanca; Casablanca Morocco
| | - N. Nourichafi
- Regional Blood Transfusion Center in Casablanca; Casablanca Morocco
| | - K. Bouisk
- Regional Blood Transfusion Center in Casablanca; Casablanca Morocco
| | - M. Benajiba
- National Blood Transfusion and Hematology Center; Rabat Morocco
| | - N. Habti
- Laboratory of Hematology; Cellular and Genetic Engineering; Faculty of Medicine and Pharmacy Casablanca; Hassan II University of Casablanca; Casablanca Morocco
- Laboratory of Biotechnology and Experimental Medicine; Faculty of Medicine and Pharmacy Casablanca; Hassan II University of Casablanca; Casablanca Morocco
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27
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Brillen AL, Schöneweis K, Walotka L, Hartmann L, Müller L, Ptok J, Kaisers W, Poschmann G, Stühler K, Buratti E, Theiss S, Schaal H. Succession of splicing regulatory elements determines cryptic 5΄ss functionality. Nucleic Acids Res 2017; 45:4202-4216. [PMID: 28039323 PMCID: PMC5397162 DOI: 10.1093/nar/gkw1317] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 12/19/2016] [Indexed: 12/25/2022] Open
Abstract
A critical step in exon definition is the recognition of a proper splice donor (5΄ss) by the 5’ end of U1 snRNA. In the selection of appropriate 5΄ss, cis-acting splicing regulatory elements (SREs) are indispensable. As a model for 5΄ss recognition, we investigated cryptic 5΄ss selection within the human fibrinogen Bβ-chain gene (FGB) exon 7, where we identified several exonic SREs that simultaneously acted on up- and downstream cryptic 5΄ss. In the FGB exon 7 model system, 5΄ss selection iteratively proceeded along an alternating sequence of U1 snRNA binding sites and interleaved SREs which in principle supported different 3’ exon ends. Like in a relay race, SREs either suppressed a potential 5΄ss and passed the splicing baton on or splicing actually occurred. From RNA-Seq data, we systematically selected 19 genes containing exons with silent U1 snRNA binding sites competing with nearby highly used 5΄ss. Extensive SRE analysis by different algorithms found authentic 5΄ss significantly more supported by SREs than silent U1 snRNA binding sites, indicating that our concept may permit generalization to a model for 5΄ss selection and 3’ exon end definition.
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Affiliation(s)
- Anna-Lena Brillen
- Institute for Virology, Heinrich-Heine-University Düsseldorf, 40225 Düsseldorf, Germany
| | - Katrin Schöneweis
- Department of Infectious Diseases, Molecular Virology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Lara Walotka
- Institute for Virology, Heinrich-Heine-University Düsseldorf, 40225 Düsseldorf, Germany
| | - Linda Hartmann
- Institute for Virology, Heinrich-Heine-University Düsseldorf, 40225 Düsseldorf, Germany
| | - Lisa Müller
- Institute for Virology, Heinrich-Heine-University Düsseldorf, 40225 Düsseldorf, Germany
| | - Johannes Ptok
- Institute for Virology, Heinrich-Heine-University Düsseldorf, 40225 Düsseldorf, Germany
| | - Wolfgang Kaisers
- Department of Anesthesiology, University Hospital Düsseldorf, Heinrich-Heine-University Düsseldorf, 40225 Düsseldorf, Germany
| | - Gereon Poschmann
- Molecular Proteomics Laboratory, BMFZ, Heinrich-Heine-University Düsseldorf, 40225 Düsseldorf, Germany
| | - Kai Stühler
- Molecular Proteomics Laboratory, BMFZ, Heinrich-Heine-University Düsseldorf, 40225 Düsseldorf, Germany.,Institute for Molecular Medicine, University Hospital Düsseldorf, Heinrich-Heine-University Düsseldorf, 40225 Düsseldorf, Germany
| | - Emanuele Buratti
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Area Science Park, 34149 Trieste, Italy
| | - Stephan Theiss
- Institute of Clinical Neuroscience and Medical Psychology, Heinrich-Heine-University Düsseldorf, 40225
| | - Heiner Schaal
- Institute for Virology, Heinrich-Heine-University Düsseldorf, 40225 Düsseldorf, Germany
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28
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Ahmad Z, Xing C, Panach K, Kittler R, McPhaul MJ, Wilson JD. Identification of the Underlying Androgen Receptor Defect in the Dallas Reifenstein Family. J Endocr Soc 2017; 1:836-842. [PMID: 29264534 PMCID: PMC5686667 DOI: 10.1210/js.2017-00124] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 05/16/2017] [Indexed: 11/19/2022] Open
Abstract
CONTEXT The Dallas Reifenstein family - first described in 1965 - includes 14 known members with partial androgen insensitivity syndrome (PAIS). However, the underlying molecular defect was never identified. OBJECTIVE To identify the underlying genetic defect for PAIS in the Dallas Reifenstein family. DESIGN DNA was purified from scrotal skin fibroblasts, and whole exome sequencing was then performed in four affected men in the family. Additional family members - both affected and unaffected - were subsequently recruited to confirm segregation of the candidate mutations with the PAIS phenotype. PATIENTS The affected men have PAIS with infertility associated with azoospermia, hypospadias, and gynecomastia. RESULTS All four men harbored an intronic variant NC_000023.10:g.66788676A>C between exon 1 and exon 2 of the androgen receptor (AR) canonical transcript NM_000044 (complementary DNA position NM_000044: c.1616+22072A>C) predicted to cause an alternatively spliced AR transcript. Reverse transcription (RT) polymerase chain (PCR) experiments detected the predicted PCR product of the alternatively spliced AR transcript, and the mutation segregated with the PAIS phenotype in this family. The transcript includes the insertion of 185 nucleotides with a premature stop codon at chrX:66863131-66863133, likely resulting in a reduction in AR protein expression due to nonsense-mediated decay. CONCLUSIONS An intronic AR mutation was identified in the Dallas Reifenstein family. The findings suggest that in cases of PAIS without identifiable AR mutations in coding regions, intronic AR mutations should be considered.
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Affiliation(s)
- Zahid Ahmad
- Division of Nutrition and Metabolic Diseases, Center for Human Nutrition, UT Southwestern Medical Center, Dallas, Texas 75390
| | - Chao Xing
- McDermott Center for Human Growth and Development, UT Southwestern Medical Center, Dallas, Texas 75390
| | - Kamaldeep Panach
- Division of Endocrinology and Department of Internal Medicine, UT Southwestern Medical Center, Dallas, Texas 75390
| | - Ralf Kittler
- McDermott Center for Human Growth and Development, UT Southwestern Medical Center, Dallas, Texas 75390
| | - Michael J. McPhaul
- Division of Endocrinology and Department of Internal Medicine, UT Southwestern Medical Center, Dallas, Texas 75390
- Quest Diagnostics Nichols Institute, San Juan Capistrano, California 92665
| | - Jean D. Wilson
- Division of Endocrinology and Department of Internal Medicine, UT Southwestern Medical Center, Dallas, Texas 75390
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29
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Deep intronic mutations and human disease. Hum Genet 2017; 136:1093-1111. [DOI: 10.1007/s00439-017-1809-4] [Citation(s) in RCA: 178] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 05/05/2017] [Indexed: 12/22/2022]
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30
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Tian Q, Li Y, Kousar R, Guo H, Peng F, Zheng Y, Yang X, Long Z, Tian R, Xia K, Lin H, Pan Q. A novel NHS mutation causes Nance-Horan Syndrome in a Chinese family. BMC MEDICAL GENETICS 2017; 18:2. [PMID: 28061824 PMCID: PMC5219716 DOI: 10.1186/s12881-016-0360-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 12/02/2016] [Indexed: 11/21/2022]
Abstract
Background Nance-Horan Syndrome (NHS) (OMIM: 302350) is a rare X-linked developmental disorder characterized by bilateral congenital cataracts, with occasional dental anomalies, characteristic dysmorphic features, brachymetacarpia and mental retardation. Carrier females exhibit similar manifestations that are less severe than in affected males. Methods Here, we report a four-generation Chinese family with multiple affected individuals presenting Nance-Horan Syndrome. Whole-exome sequencing combined with RT-PCR and Sanger sequencing was used to search for a genetic cause underlying the disease phenotype. Results Whole-exome sequencing identified in all affected individuals of the family a novel donor splicing site mutation (NM_198270: c.1045 + 2T > A) in intron 4 of the gene NHS, which maps to chromosome Xp22.13. The identified mutation results in an RNA processing defect causing a 416-nucleotide addition to exon 4 of the mRNA transcript, likely producing a truncated NHS protein. Conclusions The donor splicing site mutation NM_198270: c.1045 + 2T > A of the NHS gene is the causative mutation in this Nance-Horan Syndrome family. This research broadens the spectrum of NHS gene mutations, contributing to our understanding of the molecular genetics of NHS. Electronic supplementary material The online version of this article (doi:10.1186/s12881-016-0360-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Qi Tian
- State Key Laboratory of Medical Genetics & School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Yunping Li
- Department of Ophthalmology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Rizwana Kousar
- State Key Laboratory of Medical Genetics & School of Life Sciences, Central South University, Changsha, Hunan, China.,Department of Biology, Allama Iqbal Open University, Islamabad, Pakistan
| | - Hui Guo
- State Key Laboratory of Medical Genetics & School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Fenglan Peng
- ChangSha Health Vocational Collage, Changsha, Hunan, China
| | - Yu Zheng
- State Key Laboratory of Medical Genetics & School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Xiaohua Yang
- Shenzhen Baoan District Maternal and Child Health Hospital, Shenzhen, Guangdong, China
| | - Zhigao Long
- State Key Laboratory of Medical Genetics & School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Runyi Tian
- State Key Laboratory of Medical Genetics & School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Kun Xia
- State Key Laboratory of Medical Genetics & School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Haiying Lin
- Shenzhen Baoan District Maternal and Child Health Hospital, Shenzhen, Guangdong, China.
| | - Qian Pan
- State Key Laboratory of Medical Genetics & School of Life Sciences, Central South University, Changsha, Hunan, China.
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Schleit J, Bailey SS, Tran T, Chen D, Stowers S, Schwarze U, Byers PH. Molecular Outcome, Prediction, and Clinical Consequences of Splice Variants in COL1A1, Which Encodes the proα1(I) Chains of Type I Procollagen. Hum Mutat 2016; 36:728-39. [PMID: 25963598 DOI: 10.1002/humu.22812] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Accepted: 04/28/2015] [Indexed: 11/09/2022]
Abstract
Approximately 10%-20% of germline pathogenic variants alter mRNA splicing, with phenotypes often dependent on the stability of the mRNA produced by the mutant allele. To better understand the relationships between genotype, mRNA splicing, and phenotype, we examined clinical and molecular data from 243 probands with osteogenesis imperfecta (OI) representing 145 unique splicing variants within the type I procollagen gene, COL1A1. All individuals with IVSX-1G>A mutations had OI type I because the substitution shifted the splice acceptor site 1 nt downstream and destabilized the mRNA. OI phenotypes were not consistent for any other splice variant identified. We sequenced all cDNA species from cultured dermal fibroblasts from 40 individuals to identify splice outcome and compared those results to splice predictions from Human Splice Finder (HSF), Spliceport (SP), and Automatic Splice Site and Exon Definition Analyses (ASSEDA). Software-based splice predictions were correct in 42%, 55%, and 74% instances for HSF, SP, and ASSEDA, respectively. As molecular diagnostics move increasingly to DNA sequence analysis, the need to understand the effects of splice site variants will increase. These data demonstrate that caution must be exercised when using splice prediction software to predict splice outcome.
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Affiliation(s)
- Jennifer Schleit
- Departments of Pathology and Medicine (Medical Genetics), University of Washington, Seattle, Washington
| | - Samuel S Bailey
- Departments of Pathology and Medicine (Medical Genetics), University of Washington, Seattle, Washington
| | - Thao Tran
- Departments of Pathology and Medicine (Medical Genetics), University of Washington, Seattle, Washington
| | - Diana Chen
- Departments of Pathology and Medicine (Medical Genetics), University of Washington, Seattle, Washington
| | - Susan Stowers
- Departments of Pathology and Medicine (Medical Genetics), University of Washington, Seattle, Washington
| | - Ulrike Schwarze
- Departments of Pathology and Medicine (Medical Genetics), University of Washington, Seattle, Washington
| | - Peter H Byers
- Departments of Pathology and Medicine (Medical Genetics), University of Washington, Seattle, Washington
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Belforte FS, Citterio CE, Testa G, Olcese MC, Sobrero G, Miras MB, Targovnik HM, Rivolta CM. Compound heterozygous DUOX2 gene mutations (c.2335-1G>C/c.3264_3267delCAGC) associated with congenital hypothyroidism. Characterization of complex cryptic splice sites by minigene analysis. Mol Cell Endocrinol 2016; 419:172-84. [PMID: 26506010 DOI: 10.1016/j.mce.2015.10.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/19/2015] [Revised: 09/25/2015] [Accepted: 10/19/2015] [Indexed: 12/11/2022]
Abstract
Iodide Organification defects (IOD) represent 10% of cases of congenital hypothyroidism (CH) being the main genes affected that of TPO (thyroid peroxidase) and DUOX2 (dual oxidasa 2). From a patient with clinical and biochemical criteria suggestive with CH associated with IOD, TPO and DUOX2 genes were analyzed by means of PCR-Single Strand Conformation Polymorphism analysis and sequencing. A novel heterozygous compound to the mutations c.2335-1G>C (paternal mutation, intron 17) and c.3264_3267delCAGC (maternal mutation, exon 24) was identified in the DUOX2 gene. Ex-vivo splicing assays and subsequent RT-PCR and sequencing analyses were performed on mRNA isolated from the HeLa cells transfected with wild-type and mutant pSPL3 expression vectors. The wild-type and c.2335-1G>C mutant alleles result in the complete inclusion or exclusion of exon 18, or in the activation of an exonic cryptic 5' ss with the consequent deletion of 169 bp at the end of this exon. However, we observed only a band of the expected size in normal thyroid tissue by RT-PCR. Additionally, the c.2335-1G>C mutation activates an unusual cryptic donor splice site in intron 17, located at position -14 of the authentic intron 17/exon 18 junction site, with an insertion of the last 14 nucleotides of the intron 17 in mutant transcripts with complete and partial inclusion of exon 18. The theoretical consequences of splice site mutation, predicted with the bioinformatics NNSplice, Fsplice, SPL, SPLM and MaxEntScan programs were investigated and evaluated in relation with the experimental evidence. These analyses confirm that c.2335-1G>C mutant allele would result in the abolition of the authentic splice acceptor site. The results suggest the coexistence in our patient of four putative truncated proteins of 786, 805, 806 and 1105 amino acids, with conservation of peroxidase-like domain and loss of gp91(phox)/NOX2-like domain. In conclusion a novel heterozygous compound was identified being responsible of IOD. Cryptic splicing sites have been characterized in DUOX2 gene for the first time. The use of molecular biology techniques is a valuable tool for understanding the molecular pathophysiology of this type of thyroid defects.
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Affiliation(s)
- Fiorella S Belforte
- Laboratorio de Genética Molecular Tiroidea, Instituto de Inmunología, Genética y Metabolismo (INIGEM, CONICET-UBA), Hospital de Clínicas "José de San Martín", C1120AAR Buenos Aires, Argentina; Cátedra de Genética (FFyB-UBA), C1113AAD Buenos Aires, Argentina
| | - Cintia E Citterio
- Laboratorio de Genética y Biología Molecular, Instituto de Inmunología, Genética y Metabolismo (INIGEM, CONICET-UBA), Hospital de Clínicas "José de San Martín", C1120AAR Buenos Aires, Argentina; Cátedra de Genética (FFyB-UBA), C1113AAD Buenos Aires, Argentina
| | - Graciela Testa
- Servicio de Endocrinología, Hospital de Niños Santísima Trinidad, 5000 Córdoba, Argentina
| | - María Cecilia Olcese
- Laboratorio de Genética Molecular Tiroidea, Instituto de Inmunología, Genética y Metabolismo (INIGEM, CONICET-UBA), Hospital de Clínicas "José de San Martín", C1120AAR Buenos Aires, Argentina; Cátedra de Genética (FFyB-UBA), C1113AAD Buenos Aires, Argentina
| | - Gabriela Sobrero
- Servicio de Endocrinología, Hospital de Niños Santísima Trinidad, 5000 Córdoba, Argentina
| | - Mirta B Miras
- Servicio de Endocrinología, Hospital de Niños Santísima Trinidad, 5000 Córdoba, Argentina
| | - Héctor M Targovnik
- Laboratorio de Genética y Biología Molecular, Instituto de Inmunología, Genética y Metabolismo (INIGEM, CONICET-UBA), Hospital de Clínicas "José de San Martín", C1120AAR Buenos Aires, Argentina; Cátedra de Genética (FFyB-UBA), C1113AAD Buenos Aires, Argentina
| | - Carina M Rivolta
- Laboratorio de Genética Molecular Tiroidea, Instituto de Inmunología, Genética y Metabolismo (INIGEM, CONICET-UBA), Hospital de Clínicas "José de San Martín", C1120AAR Buenos Aires, Argentina; Cátedra de Genética (FFyB-UBA), C1113AAD Buenos Aires, Argentina.
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Infante JB, Alvelos MI, Bastos M, Carrilho F, Lemos MC. Complete androgen insensitivity syndrome caused by a novel splice donor site mutation and activation of a cryptic splice donor site in the androgen receptor gene. J Steroid Biochem Mol Biol 2016; 155:63-6. [PMID: 26435450 DOI: 10.1016/j.jsbmb.2015.09.042] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Revised: 09/26/2015] [Accepted: 09/28/2015] [Indexed: 01/01/2023]
Abstract
The androgen insensitivity syndrome is an X-linked recessive genetic disorder characterized by resistance to the actions of androgens in an individual with a male karyotype. We evaluated a 34-year-old female with primary amenorrhea and a 46,XY karyotype, with normal secondary sex characteristics, absence of uterus and ovaries, intra-abdominal testis, and elevated testosterone levels. Sequence analysis of the androgen receptor (AR) gene revealed a novel splice donor site mutation in intron 4 (c.2173+2T>C). RT-PCR analysis showed that this mutation resulted in the activation of a cryptic splice donor site located in the second half of exon 4 and in the synthesis of a shorter mRNA transcript and an in-frame deletion of 41 amino acids. This novel mutation associated with a rare mechanism of abnormal splicing further expands the spectrum of mutations associated with the androgen insensitivity syndrome and may contribute to the understanding of the molecular mechanisms involved in splicing defects.
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Affiliation(s)
- Joana B Infante
- CICS-UBI, Health Sciences Research Centre, University of Beira Interior, 6200-506 Covilhã, Portugal
| | - Maria I Alvelos
- CICS-UBI, Health Sciences Research Centre, University of Beira Interior, 6200-506 Covilhã, Portugal
| | - Margarida Bastos
- Serviço de Endocrinologia, Diabetes e Metabolismo, Centro Hospitalar Universitário de Coimbra, 3000-075 Coimbra, Portugal
| | - Francisco Carrilho
- Serviço de Endocrinologia, Diabetes e Metabolismo, Centro Hospitalar Universitário de Coimbra, 3000-075 Coimbra, Portugal
| | - Manuel C Lemos
- CICS-UBI, Health Sciences Research Centre, University of Beira Interior, 6200-506 Covilhã, Portugal.
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34
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Novel mutations in EVC cause aberrant splicing in Ellis-van Creveld syndrome. Mol Genet Genomics 2015; 291:863-72. [PMID: 26621368 DOI: 10.1007/s00438-015-1151-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 11/20/2015] [Indexed: 01/15/2023]
Abstract
Ellis-van Creveld syndrome (EvC) is a rare autosomal recessive disorder characterized by disproportionate chondrodysplasia, postaxial polydactyly, nail dystrophy, dental abnormalities and in a proportion of patients, congenital cardiac malformations. Weyers acrofacial dysostosis (Weyers) is another dominantly inherited disorder allelic to EvC syndrome but with milder phenotypes. Both disorders can result from loss-of-function mutations in either EVC or EVC2 gene, and phenotypes associated with the two gene mutations are clinically indistinguishable. We present here a clinical and molecular analysis of a Chinese family manifested specific features of EvC syndrome. Sequencing of both EVC and EVC2 identified two novel heterozygous splice site mutations c.384+5G>C in intron 3 and c.1465-1G>A in intron 10 in EVC, which were inherited from mother and father, respectively. In vitro minigene expression assay, RT-PCR and sequencing analysis demonstrated that c.384+5G>C mutation abolished normal splice site and created a new cryptic acceptor site within exon 4, whereas c.1465-1G>A mutation affected consensus splice junction site and resulted in full exon 11 skipping. These two aberrant pre-mRNA splicing processes both produced in-frame abnormal transcripts that possibly led to abolishment of important functional domains. To our knowledge, this is the first report of EVC mutations that cause EvC syndrome in Chinese population. Our data revealed that EVC splice site mutations altered splicing pattern and helped elucidate the pathogenesis of EvC syndrome.
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35
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Salas PC, Rosales JML, Milla CP, Montiel JL, Siles JL. A novel mutation in the β-spectrin gene causes the activation of a cryptic 5'-splice site and the creation of a de novo 3'-splice site. Hum Genome Var 2015; 2:15029. [PMID: 27081538 PMCID: PMC4785562 DOI: 10.1038/hgv.2015.29] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2015] [Revised: 06/18/2015] [Accepted: 06/19/2015] [Indexed: 11/16/2022] Open
Abstract
The analysis of genes involved in hereditary spherocytosis, by next-generation sequencing in two patients with clinical diagnosis of the disease, showed the presence of the c.1795+1G>A mutation in the SPTB gene. cDNA amplification then revealed the occurrence of a consequent aberrant mRNA isoform produced from the activation of a cryptic 5′-splice site and the creation of a newly 3′-splice site. The mechanisms by which these two splice sites are used as a result of the same mutation should be analyzed in depth in further studies.
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36
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Abstract
Exitrons are exon-like introns located within protein-coding exons. Removal or retention of exitrons through alternative splicing increases proteome complexity and thus adds to phenotypic diversity.
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Affiliation(s)
- Dorothee Staiger
- Molecular Cell Physiology, Faculty of Biology, Bielefeld University, Bielefeld, Germany.
| | - Gordon G Simpson
- Division of Plant Sciences, Life Sciences, University of Dundee at The James Hutton Institute, Invergowrie, DD2 5DA, UK. .,Cell & Molecular Sciences, The James Hutton Institute, Invergowrie, DD2 5DA, UK.
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Generation and Characterization of a Transgenic Mouse Carrying a Functional Human β -Globin Gene with the IVSI-6 Thalassemia Mutation. BIOMED RESEARCH INTERNATIONAL 2015; 2015:687635. [PMID: 26097845 PMCID: PMC4434229 DOI: 10.1155/2015/687635] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Revised: 12/03/2014] [Accepted: 12/03/2014] [Indexed: 11/17/2022]
Abstract
Mouse models that carry mutations causing thalassemia represent a suitable tool to test in vivo new mutation-specific therapeutic approaches. Transgenic mice carrying the β-globin IVSI-6 mutation (the most frequent in Middle-Eastern regions and recurrent in Italy and Greece) are, at present, not available. We report the production and characterization of a transgenic mouse line (TG-β-IVSI-6) carrying the IVSI-6 thalassemia point mutation within the human β-globin gene. In the TG-β-IVSI-6 mouse (a) the transgenic integration region is located in mouse chromosome 7; (b) the expression of the transgene is tissue specific; (c) as expected, normally spliced human β-globin mRNA is produced, giving rise to β-globin production and formation of a human-mouse tetrameric chimeric hemoglobin muα-globin2/huβ-globin2 and, more importantly, (d) the aberrant β-globin-IVSI-6 RNAs are present in blood cells. The TG-β-IVSI-6 mouse reproduces the molecular features of IVSI-6 β-thalassemia and might be used as an in vivo model to characterize the effects of antisense oligodeoxynucleotides targeting the cryptic sites responsible for the generation of aberrantly spliced β-globin RNA sequences, caused by the IVSI-6 mutation. These experiments are expected to be crucial for the development of a personalized therapy for β-thalassemia.
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38
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Unmasking alternative splicing inside protein-coding exons defines exitrons and their role in proteome plasticity. Genome Res 2015; 25:995-1007. [PMID: 25934563 PMCID: PMC4484396 DOI: 10.1101/gr.186585.114] [Citation(s) in RCA: 113] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 04/30/2015] [Indexed: 11/25/2022]
Abstract
Alternative splicing (AS) diversifies transcriptomes and proteomes and is widely recognized as a key mechanism for regulating gene expression. Previously, in an analysis of intron retention events in Arabidopsis, we found unusual AS events inside annotated protein-coding exons. Here, we also identify such AS events in human and use these two sets to analyse their features, regulation, functional impact, and evolutionary origin. As these events involve introns with features of both introns and protein-coding exons, we name them exitrons (exonic introns). Though exitrons were detected as a subset of retained introns, they are clearly distinguishable, and their splicing results in transcripts with different fates. About half of the 1002 Arabidopsis and 923 human exitrons have sizes of multiples of 3 nucleotides (nt). Splicing of these exitrons results in internally deleted proteins and affects protein domains, disordered regions, and various post-translational modification sites, thus broadly impacting protein function. Exitron splicing is regulated across tissues, in response to stress and in carcinogenesis. Intriguingly, annotated intronless genes can be also alternatively spliced via exitron usage. We demonstrate that at least some exitrons originate from ancestral coding exons. Based on our findings, we propose a “splicing memory” hypothesis whereby upon intron loss imprints of former exon borders defined by vestigial splicing regulatory elements could drive the evolution of exitron splicing. Altogether, our studies show that exitron splicing is a conserved strategy for increasing proteome plasticity in plants and animals, complementing the repertoire of AS events.
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Morrison A, Chekaluk Y, Bacares R, Ladanyi M, Zhang L. BAP1 missense mutation c.2054 A>T (p.E685V) completely disrupts normal splicing through creation of a novel 5' splice site in a human mesothelioma cell line. PLoS One 2015; 10:e0119224. [PMID: 25830670 PMCID: PMC4382119 DOI: 10.1371/journal.pone.0119224] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Accepted: 01/12/2015] [Indexed: 12/11/2022] Open
Abstract
BAP1 is a tumor suppressor gene that is lost or deleted in diverse cancers, including uveal mela¬noma, malignant pleural mesothelioma (MPM), clear cell renal carcinoma, and cholangiocarcinoma. Recently, BAP1 germline mutations have been reported in families with combinations of these same cancers. A particular challenge for mutation screening is the classification of non-truncating BAP1 sequence variants because it is not known whether these subtle changes can affect the protein function sufficiently to predispose to cancer development. Here we report mRNA splicing analysis on a homozygous substitution mutation, BAP1 c. 2054 A&T (p.Glu685Val), identified in an MPM cell line derived from a mesothelioma patient. The mutation occurred at the 3rd nucleotide from the 3' end of exon 16. RT-PCR, cloning and subsequent sequencing revealed several aberrant splicing products not observed in the controls: 1) a 4 bp deletion at the end of exon 16 in all clones derived from the major splicing product. The BAP1 c. 2054 A&T mutation introduced a new 5' splice site (GU), which resulted in the deletion of 4 base pairs and presumably protein truncation; 2) a variety of alternative splicing products that led to retention of different introns: introns 14-16; introns 15-16; intron 14 and intron 16; 3) partial intron 14 and 15 retentions caused by activation of alternative 3' splice acceptor sites (AG) in the introns. Taken together, we were unable to detect any correctly spliced mRNA transcripts in this cell line. These results suggest that aberrant splicing caused by this mutation is quite efficient as it completely abolishes normal splicing through creation of a novel 5' splice site and activation of cryptic splice sites. These data support the conclusion that BAP1 c.2054 A&T (p.E685V) variant is a pathogenic mutation and contributes to MPM through disruption of normal splicing.
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Affiliation(s)
- Arianne Morrison
- School of Medicine, Wake Forest University, Winston Salem, North Carolina, United States of America
| | - Yvonne Chekaluk
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Ruben Bacares
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Marc Ladanyi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Liying Zhang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
- * E-mail:
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Citterio CE, Morales CM, Bouhours-Nouet N, Machiavelli GA, Bueno E, Gatelais F, Coutant R, González-Sarmiento R, Rivolta CM, Targovnik HM. Novel compound heterozygous Thyroglobulin mutations c.745+1G>A/c.7036+2T>A associated with congenital goiter and hypothyroidism in a Vietnamese family. Identification of a new cryptic 5' splice site in the exon 6. Mol Cell Endocrinol 2015; 404:102-12. [PMID: 25633667 DOI: 10.1016/j.mce.2015.01.032] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/30/2014] [Revised: 12/17/2014] [Accepted: 01/21/2015] [Indexed: 10/24/2022]
Abstract
Several patients were identified with dyshormonogenesis caused by mutations in the thyroglobulin (TG) gene. These defects are inherited in an autosomal recessive manner and affected individuals are either homozygous or compound heterozygous for the mutations. The aim of the present study was to identify new TG mutations in a patient of Vietnamese origin affected by congenital hypothyroidism, goiter and low levels of serum TG. DNA sequencing identified the presence of compound heterozygous mutations in the TG gene: the maternal mutation consists of a novel c.745+1G>A (g.IVS6 + 1G>A), whereas the hypothetical paternal mutation consists of a novel c.7036+2T>A (g.IVS40 + 2T>A). The father was not available for segregation analysis. Ex-vivo splicing assays and subsequent RT-PCR analyses were performed on mRNA isolated from the eukaryotic-cells transfected with normal and mutant expression vectors. Minigene analysis of the c.745+1G>A mutant showed that the exon 6 is skipped during pre-mRNA splicing or partially included by use of a cryptic 5' splice site located to 55 nucleotides upstream of the authentic exon 6/intron 6 junction site. The functional analysis of c.7036+2T>A mutation showed a complete skipping of exon 40. The theoretical consequences of splice site mutations, predicted with the bioinformatics tool NNSplice, Fsplice, SPL, SPLM and MaxEntScan programs were investigated and evaluated in relation with the experimental evidence. These analyses predicted that both mutant alleles would result in the abolition of the authentic splice donor sites. The c.745+1G>A mutation originates two putative truncated proteins of 200 and 1142 amino acids, whereas c.7036+2T>A mutation results in a putative truncated protein of 2277 amino acids. In conclusion, we show that the c.745+1G>A mutation promotes the activation of a new cryptic donor splice site in the exon 6 of the TG gene. The functional consequences of these mutations could be structural changes in the protein molecule that alter the biosynthesis of thyroid hormones.
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Affiliation(s)
- Cintia E Citterio
- Laboratorio de Genética y Biología Molecular, Instituto de Inmunología, Genética y Metabolismo (INIGEM, CONICET-UBA), Hospital de Clínicas "José de San Martín", C1120AAR Buenos Aires, Argentina; Cátedra de Genética y Biología Molecular (FFyB-UBA), C1113AAD Buenos Aires, Argentina
| | - Cecilia M Morales
- Laboratorio de Genética y Biología Molecular, Instituto de Inmunología, Genética y Metabolismo (INIGEM, CONICET-UBA), Hospital de Clínicas "José de San Martín", C1120AAR Buenos Aires, Argentina; Cátedra de Genética y Biología Molecular (FFyB-UBA), C1113AAD Buenos Aires, Argentina
| | - Natacha Bouhours-Nouet
- Unité Endocrinologie Diabétologie Pédiatrique and Centre des Maladies Rares de la Réceptivité Hormonale, CHU-Angers, 49933 Angers CEDEX 9, France
| | - Gloria A Machiavelli
- Laboratorio de Genética y Biología Molecular, Instituto de Inmunología, Genética y Metabolismo (INIGEM, CONICET-UBA), Hospital de Clínicas "José de San Martín", C1120AAR Buenos Aires, Argentina; Cátedra de Genética y Biología Molecular (FFyB-UBA), C1113AAD Buenos Aires, Argentina
| | - Elena Bueno
- Unidad de Medicina Molecular, Departamento de Medicina, Facultad de Medicina, Universidad de Salamanca, 37007 Salamanca, España
| | - Frédérique Gatelais
- Unité Endocrinologie Diabétologie Pédiatrique and Centre des Maladies Rares de la Réceptivité Hormonale, CHU-Angers, 49933 Angers CEDEX 9, France
| | - Regis Coutant
- Unité Endocrinologie Diabétologie Pédiatrique and Centre des Maladies Rares de la Réceptivité Hormonale, CHU-Angers, 49933 Angers CEDEX 9, France
| | - Rogelio González-Sarmiento
- Unidad de Medicina Molecular, Departamento de Medicina, Facultad de Medicina, Universidad de Salamanca, 37007 Salamanca, España
| | - Carina M Rivolta
- Laboratorio de Genética y Biología Molecular, Instituto de Inmunología, Genética y Metabolismo (INIGEM, CONICET-UBA), Hospital de Clínicas "José de San Martín", C1120AAR Buenos Aires, Argentina; Cátedra de Genética y Biología Molecular (FFyB-UBA), C1113AAD Buenos Aires, Argentina; Unidad de Medicina Molecular, Departamento de Medicina, Facultad de Medicina, Universidad de Salamanca, 37007 Salamanca, España
| | - Héctor M Targovnik
- Laboratorio de Genética y Biología Molecular, Instituto de Inmunología, Genética y Metabolismo (INIGEM, CONICET-UBA), Hospital de Clínicas "José de San Martín", C1120AAR Buenos Aires, Argentina; Cátedra de Genética y Biología Molecular (FFyB-UBA), C1113AAD Buenos Aires, Argentina; Unidad de Medicina Molecular, Departamento de Medicina, Facultad de Medicina, Universidad de Salamanca, 37007 Salamanca, España.
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Alsina L, Colobran R, de Sevilla MF, Català A, Viñas L, Ricart S, Plaza AM, Lois S, Juan M, Pujol-Borrell R, Martinez-Gallo M. Novel and atypical splicing mutation in a compound heterozygous UNC13D defect presenting in Familial Hemophagocytic Lymphohistiocytosis triggered by EBV infection. Clin Immunol 2014; 153:292-7. [PMID: 24825797 DOI: 10.1016/j.clim.2014.04.019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2013] [Revised: 04/28/2014] [Accepted: 04/30/2014] [Indexed: 11/19/2022]
Abstract
Familial Hemophagocytic Lymphohistiocytosis type 3 (FHL3) is a genetic disorder caused by mutations in UNC13D gene, coding the granule priming factor Munc13-4 that intervenes in NK and T cell cytotoxic function. Here we report the case of a 17-month-old girl with prolonged symptomatic EBV infectious mononucleosis and clinical symptoms of hemophagocytic syndrome. In vitro functional analysis pointed to a degranulation defect. The genetic analysis of UNC13D gene identified initially a heterozygous mutation (c.753+1G>T) in the donor splice-site that resulted in exon 9 skipping (maternal allele). Mutations in other genes were considered, but additional analysis of UNC13D cDNA revealed in the paternal allele a heterozygous transition from G to A (c.2448-13G>A) at the 3' acceptor splice-site in intron 25, generating a new acceptor splice-site that leads to a frameshift and a premature STOP codon. Allele specific amplification of the cDNA confirmed the absence of a functional mRNA from the paternal allele. This case illustrates an atypical compound heterozygous UNC13D mutation affecting the RNA splicing that generates a typical FHL3 phenotype.
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Affiliation(s)
- L Alsina
- Allergy and Clinical Immunology, Universitat de Barcelona, Barcelona, Spain; Immunology Functional Unit, SJD-Clínic, Barcelona, Spain
| | - R Colobran
- Deparment of Cell Biology, Physiology and Immunology, Universitat Autònoma de Barcelona, Barcelona, Spain; Immunology Division Hospital Universitari Vall d'Hebron, Barcelona, Spain; Vall d'Hebron Institut de Recerca, Barcelona, Spain
| | - M F de Sevilla
- Paediatric Department, Universitat de Barcelona, Barcelona, Spain
| | - A Català
- Hematology Department, Hospital Sant Joan de Déu., Universitat de Barcelona, Barcelona, Spain
| | - L Viñas
- Deparment of Cell Biology, Physiology and Immunology, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - S Ricart
- Paediatric Department, Universitat de Barcelona, Barcelona, Spain
| | - A M Plaza
- Allergy and Clinical Immunology, Universitat de Barcelona, Barcelona, Spain; Immunology Functional Unit, SJD-Clínic, Barcelona, Spain
| | - S Lois
- Research Unit in Translational Bioinformatics in Neurosciences, Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - M Juan
- Immunology Functional Unit, SJD-Clínic, Barcelona, Spain; Immunology Department, Hospital Clinic, Universitat de Barcelona - IDIBAPS, Barcelona, Spain
| | - R Pujol-Borrell
- Deparment of Cell Biology, Physiology and Immunology, Universitat Autònoma de Barcelona, Barcelona, Spain; Immunology Division Hospital Universitari Vall d'Hebron, Barcelona, Spain; Vall d'Hebron Institut de Recerca, Barcelona, Spain.
| | - M Martinez-Gallo
- Deparment of Cell Biology, Physiology and Immunology, Universitat Autònoma de Barcelona, Barcelona, Spain; Immunology Division Hospital Universitari Vall d'Hebron, Barcelona, Spain; Vall d'Hebron Institut de Recerca, Barcelona, Spain
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Gillis E, Kempers M, Salemink S, Timmermans J, Cheriex EC, Bekkers SCAM, Fransen E, De Die-Smulders CEM, Loeys BL, Van Laer L. An FBN1 deep intronic mutation in a familial case of Marfan syndrome: an explanation for genetically unsolved cases? Hum Mutat 2014; 35:571-4. [PMID: 24610719 DOI: 10.1002/humu.22540] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2013] [Accepted: 02/21/2014] [Indexed: 11/08/2022]
Abstract
Marfan syndrome (MFS) is caused by mutations in the FBN1 (fibrillin-1) gene, but approximately 10% of MFS cases remain genetically unsolved. Here, we report a new FBN1 mutation in an MFS family that had remained negative after extensive molecular genomic DNA FBN1 testing, including denaturing high-performance liquid chromatography, Sanger sequencing, and multiplex ligation-dependent probe amplification. Linkage analysis in the family and cDNA sequencing of the proband revealed a deep intronic point mutation in intron 56 generating a new splice donor site. This mutation results in the integration of a 90-bp pseudo-exon between exons 56 and 57 containing a stop codon, causing nonsense-mediated mRNA decay. Although more than 90% of FBN1 mutations can be identified with regular molecular testing at the genomic level, deep intronic mutations will be missed and require cDNA sequencing or whole-genome sequencing.
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Affiliation(s)
- Elisabeth Gillis
- Center for Medical Genetics, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
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Jantzen RR, Truelson SN, Choy FY. Human α-N-acetylglucosaminidase: cDNA cryptic site removal and native secretion signal addition significantly enhance enzyme expression and secretion. Process Biochem 2013. [DOI: 10.1016/j.procbio.2013.05.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Geahlen JH, Lapid C, Thorell K, Nikolskiy I, Huh WJ, Oates EL, Lennerz JKM, Tian X, Weis VG, Khurana SS, Lundin SB, Templeton AR, Mills JC. Evolution of the human gastrokine locus and confounding factors regarding the pseudogenicity of GKN3. Physiol Genomics 2013; 45:667-83. [PMID: 23715263 DOI: 10.1152/physiolgenomics.00169.2012] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
In a screen for genes expressed specifically in gastric mucous neck cells, we identified GKN3, the recently discovered third member of the gastrokine family. We present confirmatory mouse data and novel porcine data showing that mouse GKN3 expression is confined to mucous cells of the corpus neck and antrum base and is prominently expressed in metaplastic lesions. GKN3 was proposed originally to be expressed in some human populations and a pseudogene in others. To investigate that hypothesis, we studied human GKN3 evolution in the context of its paralogous genomic neighbors, GKN1 and GKN2. Haplotype analysis revealed that GKN3 mimics GKN2 in patterns of exonic SNP allocation, whereas GKN1 appeared to be more stringently selected. GKN3 showed signatures of both directional selection and population based selective sweeps in humans. One such selective sweep includes SNP rs10187256, originally identified as an ancestral tryptophan to premature STOP codon mutation. The derived (nonancestral) allele went to fixation in Asia. We show that another SNP, rs75578132, identified 5 bp downstream of rs10187256, exhibits a second selective sweep in almost all Europeans, some Latinos, and some Africans, possibly resulting from a reintroduction of European genes during African colonization. Finally, we identify a mutation that would destroy the splice donor site in the putative exon3-intron3 boundary, which occurs in all human genomes examined to date. Our results highlight a stomach-specific human genetic locus, which has undergone various selective sweeps across European, Asian, and African populations and thus reflects geographic and ethnic patterns in genome evolution.
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Affiliation(s)
- Jessica H Geahlen
- Division of Gastroenterology, Department of Medicine, School of Medicine, Washington University, St. Louis, Missouri 63110, USA
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Havens MA, Duelli DM, Hastings ML. Targeting RNA splicing for disease therapy. WILEY INTERDISCIPLINARY REVIEWS. RNA 2013; 4:247-66. [PMID: 23512601 PMCID: PMC3631270 DOI: 10.1002/wrna.1158] [Citation(s) in RCA: 128] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Splicing of pre-messenger RNA into mature messenger RNA is an essential step for the expression of most genes in higher eukaryotes. Defects in this process typically affect cellular function and can have pathological consequences. Many human genetic diseases are caused by mutations that cause splicing defects. Furthermore, a number of diseases are associated with splicing defects that are not attributed to overt mutations. Targeting splicing directly to correct disease-associated aberrant splicing is a logical approach to therapy. Splicing is a favorable intervention point for disease therapeutics, because it is an early step in gene expression and does not alter the genome. Significant advances have been made in the development of approaches to manipulate splicing for therapy. Splicing can be manipulated with a number of tools including antisense oligonucleotides, modified small nuclear RNAs (snRNAs), trans-splicing, and small molecule compounds, all of which have been used to increase specific alternatively spliced isoforms or to correct aberrant gene expression resulting from gene mutations that alter splicing. Here we describe clinically relevant splicing defects in disease states, the current tools used to target and alter splicing, specific mutations and diseases that are being targeted using splice-modulating approaches, and emerging therapeutics.
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Affiliation(s)
- Mallory A. Havens
- Department of Cell Biology and Anatomy, Chicago Medical School, Rosalind Franklin University of Medicine and Science. North Chicago, IL, 60064, USA. No conflicts of interest
| | - Dominik M. Duelli
- Department of Cellular and Molecular Pharmacology, Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, IL, 60064, USA. No conflicts of interest
| | - Michelle L. Hastings
- Department of Cell Biology and Anatomy, Chicago Medical School, Rosalind Franklin University of Medicine and Science. North Chicago, IL, 60064, USA, Phone: 847-578-8517 Fax: 847-578-3253. No conflicts of interest
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Juan-Mateu J, González-Quereda L, Rodríguez MJ, Verdura E, Lázaro K, Jou C, Nascimento A, Jiménez-Mallebrera C, Colomer J, Monges S, Lubieniecki F, Foncuberta ME, Pascual-Pascual SI, Molano J, Baiget M, Gallano P. Interplay between DMD point mutations and splicing signals in Dystrophinopathy phenotypes. PLoS One 2013; 8:e59916. [PMID: 23536893 PMCID: PMC3607557 DOI: 10.1371/journal.pone.0059916] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2012] [Accepted: 02/19/2013] [Indexed: 12/12/2022] Open
Abstract
DMD nonsense and frameshift mutations lead to severe Duchenne muscular dystrophy while in-frame mutations lead to milder Becker muscular dystrophy. Exceptions are found in 10% of cases and the production of alternatively spliced transcripts is considered a key modifier of disease severity. Several exonic mutations have been shown to induce exon-skipping, while splice site mutations result in exon-skipping or activation of cryptic splice sites. However, factors determining the splicing pathway are still unclear. Point mutations provide valuable information regarding the regulation of pre-mRNA splicing and elements defining exon identity in the DMD gene. Here we provide a comprehensive analysis of 98 point mutations related to clinical phenotype and their effect on muscle mRNA and dystrophin expression. Aberrant splicing was found in 27 mutations due to alteration of splice sites or splicing regulatory elements. Bioinformatics analysis was performed to test the ability of the available algorithms to predict consequences on mRNA and to investigate the major factors that determine the splicing pathway in mutations affecting splicing signals. Our findings suggest that the splicing pathway is highly dependent on the interplay between splice site strength and density of regulatory elements.
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Affiliation(s)
- Jonàs Juan-Mateu
- Servei de Genètica, Hospital de la Santa Creu i Sant Pau and CIBERER U705, Barcelona, Spain
- Universitat de Barcelona (UB), Barcelona, Spain
| | - Lidia González-Quereda
- Servei de Genètica, Hospital de la Santa Creu i Sant Pau and CIBERER U705, Barcelona, Spain
| | - Maria José Rodríguez
- Servei de Genètica, Hospital de la Santa Creu i Sant Pau and CIBERER U705, Barcelona, Spain
| | - Edgard Verdura
- Servei de Genètica, Hospital de la Santa Creu i Sant Pau and CIBERER U705, Barcelona, Spain
| | - Kira Lázaro
- Servei de Genètica, Hospital de la Santa Creu i Sant Pau and CIBERER U705, Barcelona, Spain
| | - Cristina Jou
- Servei d'Anatomia Patològica Hospital Sant Joan de Déu, Barcelona, Spain
| | - Andrés Nascimento
- Unitat de Patologia Neuromuscular, Servei de Neurologia, Hospital Sant Joan de Déu, Barcelona, Spain
| | | | - Jaume Colomer
- Unitat de Patologia Neuromuscular, Servei de Neurologia, Hospital Sant Joan de Déu, Barcelona, Spain
| | - Soledad Monges
- Servicio de Neuropediatría, Hospital Nacional Pediátrico Garrahan, Buenos Aires, Argentina
| | - Fabiana Lubieniecki
- Servicio de Patología, Hospital Nacional Pediátrico Garrahan, Buenos Aires, Argentina
| | | | | | - Jesús Molano
- Unidad de Genética Molecular and CIBERER U753, Hospital Universitario Materno Infantil La Paz, Madrid, Spain
| | - Montserrat Baiget
- Servei de Genètica, Hospital de la Santa Creu i Sant Pau and CIBERER U705, Barcelona, Spain
| | - Pia Gallano
- Servei de Genètica, Hospital de la Santa Creu i Sant Pau and CIBERER U705, Barcelona, Spain
- * E-mail:
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Moran CJ, Walters TD, Guo CH, Kugathasan S, Klein C, Turner D, Wolters VM, Bandsma RH, Mouzaki M, Langer JC, Cutz E, Benseler SM, Roifman CM, Silverberg MS, Griffiths AM, Snapper SB, Muise AM. IL-10R polymorphisms are associated with very-early-onset ulcerative colitis. Inflamm Bowel Dis 2013; 19:115-23. [PMID: 22550014 PMCID: PMC3744177 DOI: 10.1002/ibd.22974] [Citation(s) in RCA: 178] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
BACKGROUND Interleukin-10 (IL-10) signaling genes are attractive inflammatory bowel disease (IBD) candidate genes as IL-10 restricts intestinal inflammation, IL-10 polymorphisms have been associated with IBD in genome-wide association studies, and mutations in IL-10 and IL-10 receptor (IL-10R) genes have been reported in immunodeficient children with severe infantile-onset IBD. Our objective was to determine if IL-10R polymorphisms were associated with early-onset IBD (EO-IBD) and very-early-onset IBD (VEO-IBD). METHODS Candidate-gene analysis of IL10RA and IL10RB was performed after initial sequencing of an infantile onset-IBD patient identified a novel homozygous mutation. The discovery cohort included 188 EO-IBD subjects and 188 healthy subjects. Polymorphisms associated with IBD in the discovery cohort were genotyped in an independent validation cohort of 422 EO-IBD subjects and 480 healthy subjects. RESULTS We identified a homozygous, splice-site point mutation in IL10RA in an infantile-onset IBD patient causing a premature stop codon (P206X) and IL-10 insensitivity. IL10RA and IL10RB sequencing in the discovery cohort identified five IL10RA polymorphisms associated with ulcerative colitis (UC) and two IL10RB polymorphisms associated with Crohn's disease (CD). Of these polymorphisms, two IL10RA single nucleotide polymorphisms, rs2228054 and rs2228055, were associated with VEO-UC in the discovery cohort and replicated in an independent validation cohort (odds ratio [OR] 3.08, combined P = 2 x 10(-4); and OR 2.93, P = 6 x 10(-4), respectively). CONCLUSIONS We identified IL10RA polymorphisms that confer risk for developing VEO-UC. Additionally, we identified the first splice site mutation in IL10RA resulting in infantile-onset IBD. This study expands the phenotype of IL10RA polymorphisms to include both severe arthritis and VEO-UC.
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Affiliation(s)
- Christopher J Moran
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, MassGeneral Hospital for Children,
,Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Children’s Hospital Boston
,Department of Pediatrics, Harvard Medical School, Boston, MA
| | - Thomas D Walters
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Paediatrics, The Hospital for Sick Children
| | - Cong-Hui Guo
- Program in Cell Biology at University of Toronto
| | - Subra Kugathasan
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Emory University School of Medicine
| | - Christoph Klein
- Department of Pediatrics, Dr. von Hauner Children’s Hospital, Ludwig-Maximilians University, Munich, Germany
| | - Dan Turner
- Pediatric Gastroenterology Unit, Shaare Zedek Medical Center, The Hebrew University of Jerusalem
| | - Victorien M Wolters
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Paediatrics, The Hospital for Sick Children
,Program in Cell Biology at University of Toronto
| | | | - Robert H Bandsma
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Paediatrics, The Hospital for Sick Children
| | - Marialena Mouzaki
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Paediatrics, The Hospital for Sick Children
| | | | - Ernest Cutz
- Department of Pathology, The Hospital for Sick Children
| | | | - Chaim M Roifman
- Division of Immunology and Allergy, The Hospital for Sick Children
| | - Mark S Silverberg
- Division of Gastroenterology, Mount Sinai Hospital, Toronto, Ontario
| | - Anne M Griffiths
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Paediatrics, The Hospital for Sick Children
| | - Scott B Snapper
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Children’s Hospital Boston
,Department of Pediatrics, Harvard Medical School, Boston, MA
,Division of Gastroenterology and Hepatology, Brigham & Women’s Hospital
,Department of Medicine, Harvard Medical School, Boston, MA
,Corresponding authors: Scott B Snapper, M.D., Ph.D. Center for Inflammatory Bowel Disease Treatment and Research Division of Gastroenterology & Nutrition Children’s Hospital Boston 300 Longwood Ave, Boston, MA 02115 Phone: 617-919-4973 FAX: 617-730-0498 Aleixo M Muise Division of Gastroenterology, Program in Cell Biology Department of Pediatrics Hospital for Sick Children 555 University Ave, Toronto, Ontario M5G 1X8, Canada Phone: 416-813-6171 FAX: 416-813-4972
| | - Aleixo M Muise
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Paediatrics, The Hospital for Sick Children
,Program in Cell Biology at University of Toronto
,Corresponding authors: Scott B Snapper, M.D., Ph.D. Center for Inflammatory Bowel Disease Treatment and Research Division of Gastroenterology & Nutrition Children’s Hospital Boston 300 Longwood Ave, Boston, MA 02115 Phone: 617-919-4973 FAX: 617-730-0498 Aleixo M Muise Division of Gastroenterology, Program in Cell Biology Department of Pediatrics Hospital for Sick Children 555 University Ave, Toronto, Ontario M5G 1X8, Canada Phone: 416-813-6171 FAX: 416-813-4972
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Ng CS, Wu P, Foley J, Foley A, McDonald ML, Juan WT, Huang CJ, Lai YT, Lo WS, Chen CF, Leal SM, Zhang H, Widelitz RB, Patel PI, Li WH, Chuong CM. The chicken frizzle feather is due to an α-keratin (KRT75) mutation that causes a defective rachis. PLoS Genet 2012; 8:e1002748. [PMID: 22829773 PMCID: PMC3400578 DOI: 10.1371/journal.pgen.1002748] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2011] [Accepted: 04/19/2012] [Indexed: 12/15/2022] Open
Abstract
Feathers have complex forms and are an excellent model to study the development and evolution of morphologies. Existing chicken feather mutants are especially useful for identifying genetic determinants of feather formation. This study focused on the gene F, underlying the frizzle feather trait that has a characteristic curled feather rachis and barbs in domestic chickens. Our developmental biology studies identified defects in feather medulla formation, and physical studies revealed that the frizzle feather curls in a stepwise manner. The frizzle gene is transmitted in an autosomal incomplete dominant mode. A whole-genome linkage scan of five pedigrees with 2678 SNPs revealed association of the frizzle locus with a keratin gene-enriched region within the linkage group E22C19W28_E50C23. Sequence analyses of the keratin gene cluster identified a 69 bp in-frame deletion in a conserved region of KRT75, an α-keratin gene. Retroviral-mediated expression of the mutated F cDNA in the wild-type rectrix qualitatively changed the bending of the rachis with some features of frizzle feathers including irregular kinks, severe bending near their distal ends, and substantially higher variations among samples in comparison to normal feathers. These results confirmed KRT75 as the F gene. This study demonstrates the potential of our approach for identifying genetic determinants of feather forms. With the availability of a sequenced chicken genome, the reservoir of variant plumage genes found in domestic chickens can provide insight into the molecular mechanisms underlying the diversity of feather forms. In this paper, we identify the molecular basis of the distinctive frizzle (F) feather phenotype that is caused by a single autosomal incomplete dominant gene in which heterozygous individuals show less severe phenotypes than homozygous individuals. Feathers in frizzle chickens curve backward. We used computer-assisted analysis to establish that the rachis of the frizzle feather was irregularly kinked and more severely bent than normal. Moreover, microscopic evaluation of regenerating feathers found reduced proliferating cells that give rise to the frizzle rachis. Analysis of a pedigree of frizzle chickens showed that the phenotype is linked to two single-nucleotide polymorphisms in a cluster of keratin genes within the linkage group E22C19W28_E50C23. Sequencing of the gene cluster identified a 69-base pair in-frame deletion of the protein coding sequence of the α-keratin-75 gene. Forced expression of the mutated gene in normal chickens produced a twisted rachis. Although chicken feathers are primarily composed of beta-keratins, our findings indicate that alpha-keratins have an important role in establishing the structure of feathers.
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Affiliation(s)
- Chen Siang Ng
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Ping Wu
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - John Foley
- Department of Anatomy and Cell Biology, Indiana University School of Medicine, Bloomington, Indiana, United States of America
- Department of Dermatology, Indiana University School of Medicine, Bloomington, Indiana, United States of America
| | - Anne Foley
- Department of Anatomy and Cell Biology, Indiana University School of Medicine, Bloomington, Indiana, United States of America
- Department of Dermatology, Indiana University School of Medicine, Bloomington, Indiana, United States of America
| | - Merry-Lynn McDonald
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Wen-Tau Juan
- Institute of Physics, Academia Sinica, Taipei, Taiwan
| | - Chih-Jen Huang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
- Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan
| | - Yu-Ting Lai
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Wen-Sui Lo
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Chih-Feng Chen
- Department of Animal Sciences, National Chung Hsing University, Taichung, Taiwan
| | - Suzanne M. Leal
- Department of Dermatology, Indiana University School of Medicine, Bloomington, Indiana, United States of America
| | - Huanmin Zhang
- Avian Disease and Oncology Laboratory, Agriculture Research Service, United States Department of Agriculture, East Lansing, Michigan, United States of America
| | - Randall B. Widelitz
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Pragna I. Patel
- Institute for Genetic Medicine and Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, California, United States of America
| | - Wen-Hsiung Li
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
- Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, United States of America
- * E-mail: (W-HL); (C-MC)
| | - Cheng-Ming Chuong
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
- Research Center for Developmental Biology and Regenerative Medicine, National Taiwan University, Taipei, Taiwan
- * E-mail: (W-HL); (C-MC)
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Kameyama T, Suzuki H, Mayeda A. Re-splicing of mature mRNA in cancer cells promotes activation of distant weak alternative splice sites. Nucleic Acids Res 2012; 40:7896-906. [PMID: 22675076 PMCID: PMC3439910 DOI: 10.1093/nar/gks520] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Transcripts of the human tumor susceptibility gene 101 (TSG101) are aberrantly spliced in many cancers. A major aberrant splicing event on the TSG101 pre-mRNA involves joining of distant alternative 5′ and 3′ splice sites within exon 2 and exon 9, respectively, resulting in the extensive elimination of the mRNA. The estimated strengths of the alternative splice sites are much lower than those of authentic splice sites. We observed that the equivalent aberrant mRNA could be generated from an intron-less TSG101 gene expressed ectopically in breast cancer cells. Remarkably, we identified a pathway-specific endogenous lariat RNA consisting solely of exonic sequences, predicted to be generated by a re-splicing between exon 2 and exon 9 on the spliced mRNA. Our results provide evidence for a two-step splicing pathway in which the initial constitutive splicing removes all 14 authentic splice sites, thereby bringing the weak alternative splice sites into close proximity. We also demonstrate that aberrant multiple-exon skipping of the fragile histidine triad (FHIT) pre-mRNA in cancer cells occurs via re-splicing of spliced FHIT mRNA. The re-splicing of mature mRNA can potentially generate mutation-independent diversity in cancer transcriptomes. Conversely, a mechanism may exist in normal cells to prevent potentially deleterious mRNA re-splicing events.
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Affiliation(s)
- Toshiki Kameyama
- Division of Gene Expression Mechanism, Institute for Comprehensive Medical Science, Fujita Health University, Toyoake, Aichi 470-1192, Japan
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50
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De Conti L, Skoko N, Buratti E, Baralle M. Complexities of 5'splice site definition: implications in clinical analyses. RNA Biol 2012; 9:911-23. [PMID: 22617876 DOI: 10.4161/rna.20386] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
In higher eukaryotes, the 5' splice site (5'ss) is initially recognized through an RNA-RNA interaction by U1 small nuclear ribonucleoprotein (U1 snRNP). This event represents one of the key steps in initial spliceosomal assembly and many disease-associated mutations in humans often disrupt this process. Beside base pair complementarity, 5'ss recognition can also be modified by additional factors such as RNA secondary structures or the specific binding of other nuclear proteins. In this work, we have focused on investigating a few examples of changes detected within the 5'ss in patients, that would not be immediately considered "disease causing mutations". We show that the splicing outcome of very similar mutations can be very different due to variations in trans-acting factor(s) interactions and specific context influences. Using several NF1 donor sites and SELEX approaches as experimental models, we have examined the binding properties of particular sequence motifs such as GGGU found in donor sites, and how the sequence context can change their interaction with hnRNPs such as H/F and A1/A2. Our results clearly show that even minor differences in local nucleotide context can differentially affect the binding ability of these factors to the GGGU core. Finally, using a previously identified mutation in KCNH2 that resulted in intron retention we show how very similar 5'ss mutations found in patients can have a very different splicing outcome due to the neighbouring sequence context, thus highlighting the general need to approach splicing problems with suitable experimental approaches.
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Affiliation(s)
- Laura De Conti
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
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