1
|
Engal E, Zhang Z, Geminder O, Jaffe-Herman S, Kay G, Ben-Hur A, Salton M. The spectrum of pre-mRNA splicing in autism. WILEY INTERDISCIPLINARY REVIEWS. RNA 2024; 15:e1838. [PMID: 38509732 DOI: 10.1002/wrna.1838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 02/26/2024] [Accepted: 02/27/2024] [Indexed: 03/22/2024]
Abstract
Disruptions in spatiotemporal gene expression can result in atypical brain function. Specifically, autism spectrum disorder (ASD) is characterized by abnormalities in pre-mRNA splicing. Abnormal splicing patterns have been identified in the brains of individuals with ASD, and mutations in splicing factors have been found to contribute to neurodevelopmental delays associated with ASD. Here we review studies that shed light on the importance of splicing observed in ASD and that explored the intricate relationship between splicing factors and ASD, revealing how disruptions in pre-mRNA splicing may underlie ASD pathogenesis. We provide an overview of the research regarding all splicing factors associated with ASD and place a special emphasis on five specific splicing factors-HNRNPH2, NOVA2, WBP4, SRRM2, and RBFOX1-known to impact the splicing of ASD-related genes. In the discussion of the molecular mechanisms influenced by these splicing factors, we lay the groundwork for a deeper understanding of ASD's complex etiology. Finally, we discuss the potential benefit of unraveling the connection between splicing and ASD for the development of more precise diagnostic tools and targeted therapeutic interventions. This article is categorized under: RNA in Disease and Development > RNA in Disease RNA Evolution and Genomics > RNA and Ribonucleoprotein Evolution RNA Evolution and Genomics > Computational Analyses of RNA RNA-Based Catalysis > RNA Catalysis in Splicing and Translation.
Collapse
Affiliation(s)
- Eden Engal
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel Canada, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Zhenwei Zhang
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Ophir Geminder
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel Canada, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Shiri Jaffe-Herman
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel Canada, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Gillian Kay
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel Canada, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Asa Ben-Hur
- Department of Computer Science, Colorado State University, Fort Collins, Colorado, USA
| | - Maayan Salton
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel Canada, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| |
Collapse
|
2
|
Sapir T, Kshirsagar A, Gorelik A, Olender T, Porat Z, Scheffer IE, Goldstein DB, Devinsky O, Reiner O. Heterogeneous nuclear ribonucleoprotein U (HNRNPU) safeguards the developing mouse cortex. Nat Commun 2022; 13:4209. [PMID: 35864088 PMCID: PMC9304408 DOI: 10.1038/s41467-022-31752-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 06/30/2022] [Indexed: 11/20/2022] Open
Abstract
HNRNPU encodes the heterogeneous nuclear ribonucleoprotein U, which participates in RNA splicing and chromatin organization. Microdeletions in the 1q44 locus encompassing HNRNPU and other genes and point mutations in HNRNPU cause brain disorders, including early-onset seizures and severe intellectual disability. We aimed to understand HNRNPU’s roles in the developing brain. Our work revealed that HNRNPU loss of function leads to rapid cell death of both postmitotic neurons and neural progenitors, with an apparent higher sensitivity of the latter. Further, expression and alternative splicing of multiple genes involved in cell survival, cell motility, and synapse formation are affected following Hnrnpu’s conditional truncation. Finally, we identified pharmaceutical and genetic agents that can partially reverse the loss of cortical structures in Hnrnpu mutated embryonic brains, ameliorate radial neuronal migration defects and rescue cultured neural progenitors’ cell death. HNRNPU is an RNA splicing protein associated with brain disorders such as early onset seizures. Here they show that HNRNPU functions to maintain neural progenitors and their progeny by regulating splicing of key neuronal genes.
Collapse
Affiliation(s)
- Tamar Sapir
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Aditya Kshirsagar
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Anna Gorelik
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Tsviya Olender
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Ziv Porat
- Flow Cytometry Unit, Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Ingrid E Scheffer
- The University of Melbourne, Austin Health and Royal Children's Hospital, Florey and Murdoch Children's Research Institutes, Melbourne, VIC, Australia
| | - David B Goldstein
- Institute for Genomic Medicine, Columbia University, New York, NY, USA
| | | | - Orly Reiner
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel.
| |
Collapse
|
3
|
Blackwell DL, Fraser SD, Caluseriu O, Vivori C, Tyndall AV, Lamont RE, Parboosingh JS, Innes AM, Bernier FP, Childs SJ. Hnrnpul1 controls transcription, splicing, and modulates skeletal and limb development in vivo. G3 GENES|GENOMES|GENETICS 2022; 12:6553027. [PMID: 35325113 PMCID: PMC9073674 DOI: 10.1093/g3journal/jkac067] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 03/15/2022] [Indexed: 11/17/2022]
Abstract
Mutations in RNA-binding proteins can lead to pleiotropic phenotypes including craniofacial, skeletal, limb, and neurological symptoms. Heterogeneous nuclear ribonucleoproteins (hnRNPs) are involved in nucleic acid binding, transcription, and splicing through direct binding to DNA and RNA, or through interaction with other proteins in the spliceosome. We show a developmental role for Hnrnpul1 in zebrafish, resulting in reduced body and fin growth and missing bones. Defects in craniofacial tendon growth and adult-onset caudal scoliosis are also seen. We demonstrate a role for Hnrnpul1 in alternative splicing and transcriptional regulation using RNA-sequencing, particularly of genes involved in translation, ubiquitination, and DNA damage. Given its cross-species conservation and role in splicing, it would not be surprising if it had a role in human development. Whole-exome sequencing detected a homozygous frameshift variant in HNRNPUL1 in 2 siblings with congenital limb malformations, which is a candidate gene for their limb malformations. Zebrafish Hnrnpul1 mutants suggest an important developmental role of hnRNPUL1 and provide motivation for exploring the potential conservation of ancient regulatory circuits involving hnRNPUL1 in human development.
Collapse
Affiliation(s)
- Danielle L Blackwell
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB T2N 4N1, Canada
- Alberta Children’s Hospital Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Sherri D Fraser
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB T2N 4N1, Canada
- Alberta Children’s Hospital Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Oana Caluseriu
- Department of Medical Genetics, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Claudia Vivori
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona 08002, Spain
| | - Amanda V Tyndall
- Alberta Children’s Hospital Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada
- Department of Medical Genetics, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Ryan E Lamont
- Alberta Children’s Hospital Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada
- Department of Medical Genetics, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Jillian S Parboosingh
- Alberta Children’s Hospital Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada
- Department of Medical Genetics, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - A Micheil Innes
- Alberta Children’s Hospital Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada
- Department of Medical Genetics, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - François P Bernier
- Alberta Children’s Hospital Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada
- Department of Medical Genetics, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Sarah J Childs
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB T2N 4N1, Canada
- Alberta Children’s Hospital Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada
| |
Collapse
|
4
|
Salazar R, Beenders S, LaMarca NM, Thornburg O, Rubin-Thompson L, Snow A, Goldman S, Chung WK, Bain JM. Cross-sectional, quantitative analysis of motor function in females with HNRNPH2-related disorder. RESEARCH IN DEVELOPMENTAL DISABILITIES 2021; 119:104110. [PMID: 34794115 DOI: 10.1016/j.ridd.2021.104110] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 08/12/2021] [Accepted: 10/05/2021] [Indexed: 06/13/2023]
Abstract
AIMS To describe the gross motor function of individuals with HNRNPH2-related disorder (OMIM 300986, Mental Retardation, X-linked, Syndrome, Bain Type; MRXSB) and determine the associations between clinician-measured motor function and caregiver-reported mobility scores. METHODS Developmental histories of 17 female participants with HNRNPH2-related disorder (mean age 11.2 years, range 2.7-37.1 years) with various genotypes within and adjacent to the nuclear localization sequence (NLS) were analyzed. Participants performed the Gross Motor Function Measure-88 (GMFM-88) and caregivers completed developmental histories and the Pediatric Evaluation of Disability Inventory-Computer Adaptive Test (PEDI-CAT). RESULTS All participants had measurable and quantifiable motor impairments. A strong positive correlation between the clinician-measured GMFM-88 total score and the caregiver-reported PEDI-CAT mobility domain score was established. Motor deficits were noted more often in individuals who were nonverbal. The 2 participants with genotypes adjacent to the NLS appear to have milder motor phenotypes. CONCLUSIONS The GMFM-88 and PEDI-CAT are useful and feasible measures of mobility in individuals with HNRNPH2-related disorders. Convergent validity was established between the clinician-measured GMFM-88 raw scores and caregiver-reported PEDI-CAT mobility domain scores. Factors including verbal status and genotype may impact motor abilities.
Collapse
Affiliation(s)
- Rachel Salazar
- Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA
| | - Sara Beenders
- Department of Physical Therapy and Rehabilitation Sciences, Drexel University, Philadelphia, PA, USA
| | - Nicole M LaMarca
- Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA
| | - Olivia Thornburg
- Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA
| | | | - Arielle Snow
- Queens College, City University of New York, New York, USA
| | - Sylvie Goldman
- Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA
| | - Wendy K Chung
- Department of Pediatrics and Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Jennifer M Bain
- Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA.
| |
Collapse
|
5
|
Puvvula PK, Moon AM. Novel Cell-Penetrating Peptides Derived From Scaffold-Attachment- Factor A Inhibits Cancer Cell Proliferation and Survival. Front Oncol 2021; 11:621825. [PMID: 33859938 PMCID: PMC8042391 DOI: 10.3389/fonc.2021.621825] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 02/18/2021] [Indexed: 12/12/2022] Open
Abstract
Scaffold-attachment-factor A (SAFA) has important roles in many normal and pathologic cellular processes but the scope of its function in cancer cells is unknown. Here, we report dominant-negative activity of novel peptides derived from the SAP and RGG-domains of SAFA and their effects on proliferation, survival and the epigenetic landscape in a range of cancer cell types. The RGG-derived peptide dysregulates SAFA binding and regulation of alternatively spliced targets and decreases levels of key spliceosome proteins in a cell-type specific manner. In contrast, the SAP-derived peptide reduces active histone marks, promotes chromatin compaction, and activates the DNA damage response and cell death in a subset of cancer cell types. Our findings reveal an unprecedented function of SAFA-derived peptides in regulating diverse SAFA molecular functions as a tumor suppressive mechanism and demonstrate the potential therapeutic utility of SAFA-peptides in a wide range of cancer cells.
Collapse
Affiliation(s)
- Pavan Kumar Puvvula
- Department of Molecular and Functional Genomics, Weis Center for Research, Geisinger Clinic, Danville, PA, United States
| | - Anne M Moon
- Department of Molecular and Functional Genomics, Weis Center for Research, Geisinger Clinic, Danville, PA, United States.,Department of Human Genetics, University of Utah, Salt Lake City, UT, United States.,The Mindich Child Health and Development Institute, Hess Center for Science and Medicine at Mount Sinai, New York, NY, United States
| |
Collapse
|
6
|
Spagnoli C, Rizzi S, Salerno GG, Frattini D, Koskenvuo J, Fusco C. Pharmacological Treatment of Severe Breathing Abnormalities in a Case of HNRNPU Epileptic Encephalopathy. Mol Syndromol 2021; 12:101-105. [PMID: 34012379 DOI: 10.1159/000512566] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 10/26/2020] [Indexed: 11/19/2022] Open
Abstract
Abnormal breathing patterns are a typical feature of Rett and Pitt-Hopkins syndrome and their variants. Their treatment can be challenging, with a risk of long-term detrimental consequences. Early infantile epileptic encephalopathy (EIEE) type 54 is a rare epileptic encephalopathy caused by pathogenic variants in the heterogeneous nuclear ribonucleoprotein U (HNRNPU) gene. Only one case has been described in the literature with episodes of hyperventilation and apnea, but treatment was not discussed. We describe the clinical and genetic features and treatment strategies in a case of EIEE type 54 and severely abnormal breathing pattern. A novel and likely pathogenic c.2277dup, p.(Pro760Serfs*5) variant in the HNRNPU gene was found in a male patient with severe episodes of hyperventilation and apnea, leading to syncope. Combination therapy with acetazolamide, alprazolam and aripiprazole led to significant clinical improvement. Although HNRNPU has not been implicated in breathing control, pathogenic variants in this gene can be associated with the development of abnormal breathing patterns reminiscent of Rett and Pitt-Hopkins syndrome. Its function as a gene expression regulator and its interaction with transcription factors offers a potential pathogenetic link between these 3 disorders. Based on our experience, treatment strategies can be similar to those already applied for patients with Pitt-Hopkins and Rett syndrome.
Collapse
Affiliation(s)
- Carlotta Spagnoli
- Child Neurology Unit, Department of Pediatrics, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Susanna Rizzi
- Child Neurology Unit, Department of Pediatrics, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Grazia Gabriella Salerno
- Child Neurology Unit, Department of Pediatrics, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Daniele Frattini
- Child Neurology Unit, Department of Pediatrics, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | | | - Carlo Fusco
- Child Neurology Unit, Department of Pediatrics, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy.,Pediatric Neurophysiology Laboratory, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| |
Collapse
|