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Rad A, Bartsch O, Bakhtiari S, Zhu C, Xu Y, Monteiro FP, Kok F, Vulto-van Silfhout AT, Kruer MC, Bowl MR, Vona B. Expanding the spectrum of phenotypes for MPDZ: Report of four unrelated families and review of the literature. Clin Genet 2024; 106:413-426. [PMID: 38857973 DOI: 10.1111/cge.14563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 04/24/2024] [Accepted: 05/13/2024] [Indexed: 06/12/2024]
Abstract
MPDZ, a gene with diverse functions mediating cell-cell junction interactions, receptor signaling, and binding multivalent scaffold proteins, is associated with a spectrum of clinically heterogeneous phenotypes with biallelic perturbation. Despite its clinical relevance, the mechanistic underpinnings of these variants remain elusive, underscoring the need for extensive case series and functional investigations. In this study, we conducted a systematic review of cases in the literature through two electronic databases following the PRISMA guidelines. We selected nine studies, including 18 patients, with homozygous or compound heterozygous variants in MPDZ and added five patients from four unrelated families with novel MPDZ variants. To evaluate the role of Mpdz on hearing, we analyzed available auditory electrophysiology data from a knockout murine model (Mpdzem1(IMPC)J/em1(IMPC)J) generated by the International Mouse Phenotyping Consortium. Using exome and genome sequencing, we identified three families with compound heterozygous variants, and one family with a homozygous frameshift variant. MPDZ-related disease is clinically heterogenous with hydrocephaly, vision impairment, hearing impairment and cardiovascular disease occurring most frequently. Additionally, we describe two unrelated patients with spasticity, expanding the phenotypic spectrum. Our murine analysis of the Mpdzem1(IMPC)J/em1(IMPC)J allele showed severe hearing impairment. Overall, we expand understanding of MPDZ-related phenotypes and highlight hearing impairment and spasticity among the heterogeneous phenotypes.
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Affiliation(s)
- Aboulfazl Rad
- Department of Otolaryngology - Head and Neck Surgery, Tübingen Hearing Research Centre, Eberhard Karls University Tübingen, Tübingen, Germany
| | - Oliver Bartsch
- Medical Care Centre Section Human Genetics and Institute of Human Genetics, University Medical Centre of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Somayeh Bakhtiari
- Barrow Neurological Institute, Phoenix Children's Hospital, Phoenix, Arizona, USA
- Department of Child Health, Cellular and Molecular Medicine, Genetics, and Neurology, University of Arizona College of Medicine-Phoenix, Phoenix, Arizona, USA
| | - Changlian Zhu
- Center for Brain Repair and Rehabilitation, Institute of Neuroscience and Physiology, University of Gothenburg, Göteborg, Sweden
- Henan Key Laboratory of Child Brain Injury and Henan Pediatric Clinical Research Center, Institute of Neuroscience and Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yiran Xu
- Henan Key Laboratory of Child Brain Injury and Henan Pediatric Clinical Research Center, Institute of Neuroscience and Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | | | - Fernando Kok
- Medical Department, Mendelics Genomic Analysis, Sao Paulo, Brazil
- Neurogenetics, Neurology Department, Hospital das Clínicas da Universidade de São Paulo, São Paulo, Brazil
| | - Anneke T Vulto-van Silfhout
- Department of Human Genetics, Radboud University Medical Centre, Nijmegen, the Netherlands
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Michael C Kruer
- Barrow Neurological Institute, Phoenix Children's Hospital, Phoenix, Arizona, USA
- Department of Child Health, Cellular and Molecular Medicine, Genetics, and Neurology, University of Arizona College of Medicine-Phoenix, Phoenix, Arizona, USA
| | - Michael R Bowl
- UCL Ear Institute, University College London, London, UK
| | - Barbara Vona
- Department of Otolaryngology - Head and Neck Surgery, Tübingen Hearing Research Centre, Eberhard Karls University Tübingen, Tübingen, Germany
- Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany
- Institute for Auditory Neuroscience and InnerEarLab, University Medical Center Göttingen, Göttingen, Germany
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Hussain SI, Muhammad N, Shah SA, Rehman AU, Khan SA, Saleha S, Khan YM, Muhammad N, Khan S, Wasif N. Variants in HCFC1 and MN1 genes causing intellectual disability in two Pakistani families. BMC Med Genomics 2024; 17:176. [PMID: 38956580 PMCID: PMC11221130 DOI: 10.1186/s12920-024-01943-2] [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: 03/25/2024] [Accepted: 06/21/2024] [Indexed: 07/04/2024] Open
Abstract
BACKGROUND Intellectual disability (ID) is a neurodevelopmental condition affecting around 2% of children and young adults worldwide, characterized by deficits in intellectual functioning and adaptive behavior. Genetic factors contribute to the development of ID phenotypes, including mutations and structural changes in chromosomes. Pathogenic variants in the HCFC1 gene cause X-linked mental retardation syndrome, also known as Siderius type X-linked mental retardation. The MN1 gene is necessary for palate development, and mutations in this gene result in a genetic condition called CEBALID syndrome. METHODS Exome sequencing was used to identify the disease-causing variants in two affected families, A and B, from various regions of Pakistan. Affected individuals in these two families presented ID, developmental delay, and behavioral abnormalities. The validation and co-segregation analysis of the filtered variant was carried out using Sanger sequencing. RESULTS In an X-linked family A, a novel hemizygous missense variant (c.5705G > A; p.Ser1902Asn) in the HCFC1 gene (NM_005334.3) was identified, while in family B exome sequencing revealed a heterozygous nonsense variant (c.3680 G > A; p. Trp1227Ter) in exon-1 of the MN1 gene (NM_032581.4). Sanger sequencing confirmed the segregation of these variants with ID in each family. CONCLUSIONS The investigation of two Pakistani families revealed pathogenic genetic variants in the HCFC1 and MN1 genes, which cause ID and expand the mutational spectrum of these genes.
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Affiliation(s)
- Syeda Iqra Hussain
- Department of Biotechnology and Genetic Engineering, Kohat University of Science & Technology (KUST), Kohat, Khyber Pakhtunkhwa, Pakistan
| | - Nazif Muhammad
- Department of Biotechnology and Genetic Engineering, Kohat University of Science & Technology (KUST), Kohat, Khyber Pakhtunkhwa, Pakistan
| | - Shahbaz Ali Shah
- Department of Biotechnology and Genetic Engineering, Kohat University of Science & Technology (KUST), Kohat, Khyber Pakhtunkhwa, Pakistan
| | - Adil U Rehman
- Department of Biotechnology and Genetic Engineering, Kohat University of Science & Technology (KUST), Kohat, Khyber Pakhtunkhwa, Pakistan
| | - Sher Alam Khan
- Department of Biotechnology and Genetic Engineering, Kohat University of Science & Technology (KUST), Kohat, Khyber Pakhtunkhwa, Pakistan
- Department of Computer Science and Bioinformatics, Khushal Khan Khatak University, Karak, Pakistan
| | - Shamim Saleha
- Department of Biotechnology and Genetic Engineering, Kohat University of Science & Technology (KUST), Kohat, Khyber Pakhtunkhwa, Pakistan
| | - Yar Muhammad Khan
- Department of Biotechnology, University of Science and Technology, Bannu, Pakistan
| | - Noor Muhammad
- Department of Biotechnology and Genetic Engineering, Kohat University of Science & Technology (KUST), Kohat, Khyber Pakhtunkhwa, Pakistan
| | - Saadullah Khan
- Department of Biotechnology and Genetic Engineering, Kohat University of Science & Technology (KUST), Kohat, Khyber Pakhtunkhwa, Pakistan.
| | - Naveed Wasif
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, 89081, Ulm, Germany.
- Institute of Human Genetics, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany.
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Sandal S, Verma IC, Mahay SB, Dubey S, Sabharwal RK, Kulshrestha S, Saxena R, Suman P, Kumar P, Puri RD. Next-Generation Sequencing in Unexplained Intellectual Disability. Indian J Pediatr 2024; 91:682-695. [PMID: 37804371 DOI: 10.1007/s12098-023-04820-5] [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: 12/11/2022] [Accepted: 06/23/2023] [Indexed: 10/09/2023]
Abstract
OBJECTIVES To determine the diagnostic yield of next generation sequencing (NGS) in patients with moderate/severe/profound intellectual disability (ID) unexplained by conventional tests and to assess the impact of definitive diagnosis on the clinical management and genetic counselling of these families. METHODS This was a ambi-directional study conducted at Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi. The study comprised 227 patients (prospective cohort - 126, retrospective cohort - 101) in whom NGS based tests were performed. RESULTS The mean age of study cohort was 4.5 ± 4.4 y (2.5 mo to 37.3 y). The male: female ratio was 1.6:1. The overall diagnostic yield of NGS was 53.3% (121/227) with causative variants identified in 84 known ID genes. Autosomal recessive intellectual disability (ARID) (23.3%, 53/227) was the most common followed by autosomal dominant intellectual disability (ADID) (20.7%, 47/227) and X-linked intellectual disability (XLID) (9.2%, 21/227). The diagnostic yield was notably higher for ID plus associated condition group (55.6% vs. 20%) (p = 0.0075, Fisher's exact test) compared to isolated ID group. The impact of diagnosis on active or long-term management was observed in 17/121 (14%) and on reproductive outcomes in 26/121 (21.4%) families. CONCLUSIONS There is paucity of data on molecular genetic spectrum of ID from India. The current study identifies extensive genetic heterogeneity and the impact of NGS in patients with ID unexplained by standard genetic tests. The study identified ARID as the most common cause of ID with additional implications for reproductive outcomes. It reiterates the importance of phenotype in genetic testing.
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Affiliation(s)
- Sapna Sandal
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India
| | - Ishwar Chander Verma
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India
| | - Sunita Bijarnia Mahay
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India
| | - Sudhisha Dubey
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India
| | - R K Sabharwal
- Department of Pediatric Neurology, Sir Ganga Ram Hospital, New Delhi, India
| | - Samarth Kulshrestha
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India
| | - Renu Saxena
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India
| | - Praveen Suman
- Department of Developmental Pediatrics, Sir Ganga Ram Hospital, New Delhi, India
| | - Praveen Kumar
- Department of Pediatric Neurology, Sir Ganga Ram Hospital, New Delhi, India
| | - Ratna Dua Puri
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India.
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Li Y, Usman M, Sapp E, Ke Y, Wang Z, Boudi A, DiFiglia M, Li X. Chronic pharmacologic manipulation of dopamine transmission ameliorates metabolic disturbance in Trappc9-linked brain developmental syndrome. JCI Insight 2024; 9:e181339. [PMID: 38889014 PMCID: PMC11383600 DOI: 10.1172/jci.insight.181339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Accepted: 06/14/2024] [Indexed: 06/20/2024] Open
Abstract
Loss-of-function mutations of the gene encoding the trafficking protein particle complex subunit 9 (Trappc9) cause autosomal recessive intellectual disability and obesity by unknown mechanisms. Genome-wide analysis links Trappc9 to nonalcoholic fatty liver disease (NAFLD). Trappc9-deficient mice have been shown to appear overweight shortly after weaning. Here, we analyzed serum biochemistry and histology of adipose and liver tissues to determine the incidence of obesity and NAFLD in Trappc9-deficient mice and combined transcriptomic and proteomic analyses, pharmacological studies, and biochemical and histological examinations of postmortem mouse brains to unveil mechanisms involved. We found that Trappc9-deficient mice presented with systemic glucose homeostatic disturbance, obesity, and NAFLD, which were relieved upon chronic treatment combining dopamine receptor D2 (DRD2) agonist quinpirole and DRD1 antagonist SCH23390. Blood glucose homeostasis in Trappc9-deficient mice was restored upon administering quinpirole alone. RNA-sequencing analysis of DRD2-containing neurons and proteomic study of brain synaptosomes revealed signs of impaired neurotransmitter secretion in Trappc9-deficient mice. Biochemical and histological studies of mouse brains showed that Trappc9-deficient mice synthesized dopamine normally, but their dopamine-secreting neurons had a lower abundance of structures for releasing dopamine in the striatum. Our study suggests that Trappc9 loss of function causes obesity and NAFLD by constraining dopamine synapse formation.
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Affiliation(s)
- Yan Li
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Charlestown, Massachusetts, USA
| | - Muhammad Usman
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Ellen Sapp
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Charlestown, Massachusetts, USA
| | - Yuting Ke
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Charlestown, Massachusetts, USA
| | - Zejian Wang
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Adel Boudi
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Charlestown, Massachusetts, USA
| | - Marian DiFiglia
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Charlestown, Massachusetts, USA
| | - Xueyi Li
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Charlestown, Massachusetts, USA
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Bassani S, Chrast J, Ambrosini G, Voisin N, Schütz F, Brusco A, Sirchia F, Turban L, Schubert S, Abou Jamra R, Schlump JU, DeMille D, Bayrak-Toydemir P, Nelson GR, Wong KN, Duncan L, Mosera M, Gilissen C, Vissers LELM, Pfundt R, Kersseboom R, Yttervik H, Hansen GÅM, Smeland MF, Butler KM, Lyons MJ, Carvalho CMB, Zhang C, Lupski JR, Potocki L, Flores-Gallegos L, Morales-Toquero R, Petit F, Yalcin B, Tuttle A, Elloumi HZ, McCormick L, Kukolich M, Klaas O, Horvath J, Scala M, Iacomino M, Operto F, Zara F, Writzl K, Maver A, Haanpää MK, Pohjola P, Arikka H, Kievit AJA, Calandrini C, Iseli C, Guex N, Reymond A. Variant-specific pathophysiological mechanisms of AFF3 differently influence transcriptome profiles. Genome Med 2024; 16:72. [PMID: 38811945 PMCID: PMC11137988 DOI: 10.1186/s13073-024-01339-y] [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: 12/12/2023] [Accepted: 04/19/2024] [Indexed: 05/31/2024] Open
Abstract
BACKGROUND We previously described the KINSSHIP syndrome, an autosomal dominant disorder associated with intellectual disability (ID), mesomelic dysplasia and horseshoe kidney, caused by de novo variants in the degron of AFF3. Mouse knock-ins and overexpression in zebrafish provided evidence for a dominant-negative mode of action, wherein an increased level of AFF3 resulted in pathological effects. METHODS Evolutionary constraints suggest that other modes-of-inheritance could be at play. We challenged this hypothesis by screening ID cohorts for individuals with predicted-to-be damaging variants in AFF3. We used both animal and cellular models to assess the deleteriousness of the identified variants. RESULTS We identified an individual with a KINSSHIP-like phenotype carrying a de novo partial duplication of AFF3 further strengthening the hypothesis that an increased level of AFF3 is pathological. We also detected seventeen individuals displaying a milder syndrome with either heterozygous Loss-of-Function (LoF) or biallelic missense variants in AFF3. Consistent with semi-dominance, we discovered three patients with homozygous LoF and one compound heterozygote for a LoF and a missense variant, who presented more severe phenotypes than their heterozygous parents. Matching zebrafish knockdowns exhibit neurological defects that could be rescued by expressing human AFF3 mRNA, confirming their association with the ablation of aff3. Conversely, some of the human AFF3 mRNAs carrying missense variants identified in affected individuals did not rescue these phenotypes. Overexpression of mutated AFF3 mRNAs in zebrafish embryos produced a significant increase of abnormal larvae compared to wild-type overexpression further demonstrating deleteriousness. To further assess the effect of AFF3 variation, we profiled the transcriptome of fibroblasts from affected individuals and engineered isogenic cells harboring + / + , KINSSHIP/KINSSHIP, LoF/ + , LoF/LoF or KINSSHIP/LoF AFF3 genotypes. The expression of more than a third of the AFF3 bound loci is modified in either the KINSSHIP/KINSSHIP or the LoF/LoF lines. While the same pathways are affected, only about one third of the differentially expressed genes are common to the homozygote datasets, indicating that AFF3 LoF and KINSSHIP variants largely modulate transcriptomes differently, e.g. the DNA repair pathway displayed opposite modulation. CONCLUSIONS Our results and the high pleiotropy shown by variation at this locus suggest that minute changes in AFF3 function are deleterious.
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Affiliation(s)
- Sissy Bassani
- Center for Integrative Genomics, University of Lausanne, Genopode Building, Lausanne, CH, 1015, Switzerland
- Present address: Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
| | - Jacqueline Chrast
- Center for Integrative Genomics, University of Lausanne, Genopode Building, Lausanne, CH, 1015, Switzerland
| | - Giovanna Ambrosini
- Bioinformatics Competence Center, University of Lausanne, Lausanne, Switzerland
- Bioinformatics Competence Center, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Norine Voisin
- Center for Integrative Genomics, University of Lausanne, Genopode Building, Lausanne, CH, 1015, Switzerland
- Present address: Sophia Genetics, St Sulpice, Switzerland
| | - Frédéric Schütz
- Biostatistics Platform, University of Lausanne, Lausanne, Switzerland
| | - Alfredo Brusco
- Department of Neurosciences Rita Levi-Montalcini, University of Turin, 10126, Turin, Italy
- Medical Genetics Unit, Città Della Salute E Della Scienza University Hospital, 10126, Turin, Italy
| | - Fabio Sirchia
- Department of Neurosciences Rita Levi-Montalcini, University of Turin, 10126, Turin, Italy
- Medical Genetics Unit, Città Della Salute E Della Scienza University Hospital, 10126, Turin, Italy
- Present address: Department of Molecular Medicine, University of Pavia, Pavia, Italy
- Present address: Medical Genetics Unit, IRCCS San Matteo Foundation, Pavia, Italy
| | - Lydia Turban
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Susanna Schubert
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Rami Abou Jamra
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Jan-Ulrich Schlump
- Department of Pediatrics, Centre for Neuromedicine, Gemeinschaftskrankenhaus Herdecke Gerhard-Kienle-Weg, Herdecke, Germany
| | - Desiree DeMille
- Genomics Analysis 396, ARUP Laboratories, Salt Lake City, UT, USA
| | | | - Gary Rex Nelson
- Pediatric Neurology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Kristen Nicole Wong
- Pediatric Neurology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Laura Duncan
- Department of Pediatrics, Medical Center North, Vanderbilt University Medical Center, Nashville, TN, USA
- Present address: Mayo Clinic, Rochester, MN, USA
| | - Mackenzie Mosera
- Department of Pediatrics, Medical Center North, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Christian Gilissen
- Department of Human Genetics, Research Institute for Medical Innovation, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Lisenka E L M Vissers
- Department of Human Genetics, Research Institute for Medical Innovation, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Rolph Pfundt
- Department of Human Genetics, Research Institute for Medical Innovation, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Rogier Kersseboom
- Center for Genetic Developmental Disorders Southwest, Zuidwester, Middelharnis, The Netherlands
| | - Hilde Yttervik
- Department of Medical Genetics, University Hospital of North Norway, Tromsø, Norway
| | | | | | | | | | - Claudia M B Carvalho
- Pacific Northwest Research Institute (PNRI), Broadway, Seattle, WA, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Chaofan Zhang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
- Texas Children's Hospital, Houston, TX, USA
| | - Lorraine Potocki
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Texas Children's Hospital, Houston, TX, USA
| | | | | | | | - Binnaz Yalcin
- Inserm UMR1231, University of Burgundy, 21000, Dijon, France
| | | | | | - Lane McCormick
- Department of Genetics, Cook Children's Medical Center, Cook Children's Health Care System, Fort Worth, TX, USA
| | - Mary Kukolich
- Department of Genetics, Cook Children's Medical Center, Cook Children's Health Care System, Fort Worth, TX, USA
| | - Oliver Klaas
- Institute for Human Genetics, University Hospital Muenster, Muenster, Germany
| | - Judit Horvath
- Institute for Human Genetics, University Hospital Muenster, Muenster, Germany
| | - Marcello Scala
- Department of Neuroscience, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DINOGMI), University of Genoa, Genoa, 16132, Italy
- Medical Genetics Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Michele Iacomino
- Medical Genetics Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Francesca Operto
- Department of Medicine, Child and Adolescent Neuropsychiatry Unit, Surgery and Dentistry, University of Salerno, Salerno, Italy
| | - Federico Zara
- Department of Neuroscience, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DINOGMI), University of Genoa, Genoa, 16132, Italy
- Medical Genetics Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Karin Writzl
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
- Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Aleš Maver
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Maria K Haanpää
- Department of Genomics, Turku University Hospital, Turku, Finland; University of Turku, Turku, Finland
| | - Pia Pohjola
- Department of Genomics, Turku University Hospital, Turku, Finland; University of Turku, Turku, Finland
| | - Harri Arikka
- Department of Pediatric Neurology, Turku University Hospital, Turku, Finland; University of Turku, Turku, Finland
| | - Anneke J A Kievit
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Camilla Calandrini
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Christian Iseli
- Bioinformatics Competence Center, University of Lausanne, Lausanne, Switzerland
- Bioinformatics Competence Center, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Nicolas Guex
- Bioinformatics Competence Center, University of Lausanne, Lausanne, Switzerland
- Bioinformatics Competence Center, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Alexandre Reymond
- Center for Integrative Genomics, University of Lausanne, Genopode Building, Lausanne, CH, 1015, Switzerland.
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Tran NL, Jiang J, Ma M, Gadbois GE, Gulay KCM, Verano A, Zhou H, Huang CT, Scott DA, Bang AG, Tiriac H, Lowy AM, Wang ES, Ferguson FM. ZBTB11 Depletion Targets Metabolic Vulnerabilities in K-Ras Inhibitor Resistant PDAC. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.19.594824. [PMID: 38826238 PMCID: PMC11142081 DOI: 10.1101/2024.05.19.594824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Over 95% of pancreatic ductal adenocarcinomas (PDAC) harbor oncogenic mutations in K-Ras. Upon treatment with K-Ras inhibitors, PDAC cancer cells undergo metabolic reprogramming towards an oxidative phosphorylation-dependent, drug-resistant state. However, direct inhibition of complex I is poorly tolerated in patients due to on-target induction of peripheral neuropathy. In this work, we develop molecular glue degraders against ZBTB11, a C2H2 zinc finger transcription factor that regulates the nuclear transcription of components of the mitoribosome and electron transport chain. Our ZBTB11 degraders leverage the differences in demand for biogenesis of mitochondrial components between human neurons and rapidly-dividing pancreatic cancer cells, to selectively target the K-Ras inhibitor resistant state in PDAC. Combination treatment of both K-Ras inhibitor-resistant cell lines and multidrug resistant patient-derived organoids resulted in superior anti-cancer activity compared to single agent treatment, while sparing hiPSC-derived neurons. Proteomic and stable isotope tracing studies revealed mitoribosome depletion and impairment of the TCA cycle as key events that mediate this response. Together, this work validates ZBTB11 as a vulnerability in K-Ras inhibitor-resistant PDAC and provides a suite of molecular glue degrader tool compounds to investigate its function.
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Affiliation(s)
- Nathan L. Tran
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA
- Cancer Molecular Therapeutics Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA
| | - Jiewei Jiang
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA
| | - Min Ma
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA
| | - Gillian E. Gadbois
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA
| | - Kevin C. M. Gulay
- Department of Surgery, Division of Surgical Oncology, UCSD Moores Cancer Center, University of California San Diego, La Jolla, CA
| | - Alyssa Verano
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02115
| | - Haowen Zhou
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA
| | - Chun-Teng Huang
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA
| | - David A. Scott
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA
| | - Anne G. Bang
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA
| | - Herve Tiriac
- Department of Surgery, Division of Surgical Oncology, UCSD Moores Cancer Center, University of California San Diego, La Jolla, CA
| | - Andrew M. Lowy
- Department of Surgery, Division of Surgical Oncology, UCSD Moores Cancer Center, University of California San Diego, La Jolla, CA
| | - Eric S. Wang
- Cancer Molecular Therapeutics Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA
| | - Fleur M. Ferguson
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA
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7
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Tran H, Le L, Singh BN, Kramer J, Steward R. Tet controls axon guidance in early brain development through glutamatergic signaling. iScience 2024; 27:109634. [PMID: 38655199 PMCID: PMC11035372 DOI: 10.1016/j.isci.2024.109634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 12/18/2023] [Accepted: 03/26/2024] [Indexed: 04/26/2024] Open
Abstract
Mutations in ten-eleven translocation (TET) proteins are associated with human neurodevelopmental disorders. We find a function of Tet in regulating Drosophila early brain development. The Tet DNA-binding domain (TetAXXC) is required for axon guidance in the mushroom body (MB). Glutamine synthetase 2 (Gs2), a key enzyme in glutamatergic signaling, is significantly down-regulated in the TetAXXC brains. Loss of Gs2 recapitulates the TetAXXC phenotype. Surprisingly, Tet and Gs2 act in the insulin-producing cells (IPCs) to control MB axon guidance, and overexpression of Gs2 in IPCs rescues the defects of TetAXXC. Feeding TetAXXC with metabotropic glutamate receptor antagonist MPEP rescues the phenotype while glutamate enhances it. Mutants in Tet and Drosophila Fmr1, the homolog of human FMR1, have similar defects, and overexpression of Gs2 in IPCs also rescues the Fmr1 phenotype. We provide the first evidence that Tet controls the guidance of developing brain axons by modulating glutamatergic signaling.
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Affiliation(s)
- Hiep Tran
- Waksman Institute, Rutgers University, Piscataway, NJ 08854, USA
| | - Le Le
- Waksman Institute, Rutgers University, Piscataway, NJ 08854, USA
| | - Badri Nath Singh
- Waksman Institute, Rutgers University, Piscataway, NJ 08854, USA
| | - Joseph Kramer
- Department of Pathology and Laboratory Medicine, Rutgers Biomedical and Health Sciences, Rutgers University, New Brunswick, NJ 08901, USA
| | - Ruth Steward
- Waksman Institute, Rutgers University, Piscataway, NJ 08854, USA
- Department of Molecular Biology and Biochemistry, Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ 08901, USA
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8
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Garg P, Jamal F, Srivastava P. RNA-Seq data analysis reveals novel nonsense mutations in the NPR3 gene leading to the progression of intellectual disability disorder. Heliyon 2024; 10:e30755. [PMID: 38765165 PMCID: PMC11101858 DOI: 10.1016/j.heliyon.2024.e30755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 05/02/2024] [Accepted: 05/03/2024] [Indexed: 05/21/2024] Open
Abstract
Intellectual disability (ID) is a progressive disorder that affects around 1-3% of the world's population. The heterogeneity of intellectual disability makes it difficult to diagnose as a complete disease. Genetic factors and major mutations play a noticeable role in the development and progression of ID. There is a high need to explore novel variants that may lead to new insights into the progressive aspects of ID. In the current course of study, 31 samples of ID from different studies available on GEO (GSE77742, GSE74263, GSE90682, GSE98476, GSE108887, GSE145710, and PRJEB21964) datasets were taken for the study. These datasets were analyzed for differential gene expression and single nucleotide polymorphism (SNPs). The SNPs of high impact were compared with the differentially expressed genes. Comparison leads to the identification of the priority gene ie NPR3 gene. The identified priority gene further was evaluated for the effect of the mutation using a Mutation Taster. Structure comparison analysis of the wild and mutated proteins of the NPR3 gene was further carried out by UCSF Chimera. Structural analysis reveals the anomalies in protein expression affecting the regulations of the NPR3 gene. These findings identified a novel nonsense mutation (E222*) in the downregulated NPR3 gene that leads to anomalies in the regulation of its protein expression. This missense mutation reveals a major role in causing ID. Our study concludes that the decrease in the expression of the NPR3 gene causes delayed sensory, motor, and physiological functions of the human brain leading to neurodevelopmental delay that causes ID.
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Affiliation(s)
- Prekshi Garg
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow Campus, 226028, India
| | - Farrukh Jamal
- Department of Biochemistry, Dr. Rammanohar Lohia Avadh University, Ayodhya, 224001, UP, India
| | - Prachi Srivastava
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow Campus, 226028, India
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Usmani MA, Ghaffar A, Shahzad M, Akram J, Majeed AI, Malik K, Fatima K, Khan AA, Ahmed ZM, Riazuddin S, Riazuddin S. A Missense Variant in HACE1 Is Associated with Intellectual Disability, Epilepsy, Spasticity, and Psychomotor Impairment in a Pakistani Kindred. Genes (Basel) 2024; 15:580. [PMID: 38790209 PMCID: PMC11121239 DOI: 10.3390/genes15050580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 04/19/2024] [Accepted: 04/23/2024] [Indexed: 05/26/2024] Open
Abstract
Intellectual disability (ID), which affects around 2% to 3% of the population, accounts for 0.63% of the overall prevalence of neurodevelopmental disorders (NDD). ID is characterized by limitations in a person's intellectual and adaptive functioning, and is caused by pathogenic variants in more than 1000 genes. Here, we report a rare missense variant (c.350T>C; p.(Leu117Ser)) in HACE1 segregating with NDD syndrome with clinical features including ID, epilepsy, spasticity, global developmental delay, and psychomotor impairment in two siblings of a consanguineous Pakistani kindred. HACE1 encodes a HECT domain and ankyrin repeat containing E3 ubiquitin protein ligase 1 (HACE1), which is involved in protein ubiquitination, localization, and cell division. HACE1 is also predicted to interact with several proteins that have been previously implicated in the ID phenotype in humans. The p.(Leu117Ser) variant replaces an evolutionarily conserved residue of HACE1 and is predicted to be deleterious by various in silico algorithms. Previously, eleven protein truncating variants of HACE1 have been reported in individuals with NDD. However, to our knowledge, p.(Leu117Ser) is the second missense variant in HACE1 found in an individual with NDD.
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Affiliation(s)
- Muhammad A. Usmani
- Department of Otorhinolaryngology Head & Neck Surgery, School of Medicine, University of Maryland, Baltimore, MD 21201, USA; (M.A.U.); (A.G.)
- Department of Molecular Biology, Shaheed Zulfiqar Ali Bhutto Medical University, Islamabad 44000, Pakistan; (M.S.); (J.A.); (S.R.)
- Jinnah Burn and Reconstructive Surgery Center, Allama Iqbal Medical College, University of Health Sciences, Lahore 54550, Pakistan
| | - Amama Ghaffar
- Department of Otorhinolaryngology Head & Neck Surgery, School of Medicine, University of Maryland, Baltimore, MD 21201, USA; (M.A.U.); (A.G.)
- Center of Excellence in Molecular Biology, University of the Punjab, Lahore 54500, Pakistan
| | - Mohsin Shahzad
- Department of Molecular Biology, Shaheed Zulfiqar Ali Bhutto Medical University, Islamabad 44000, Pakistan; (M.S.); (J.A.); (S.R.)
| | - Javed Akram
- Department of Molecular Biology, Shaheed Zulfiqar Ali Bhutto Medical University, Islamabad 44000, Pakistan; (M.S.); (J.A.); (S.R.)
| | - Aisha I. Majeed
- Department of Radiology, Shaheed Zulfiqar Ali Bhutto Medical University, Islamabad 44000, Pakistan;
| | - Kausar Malik
- Center of Excellence in Molecular Biology, University of the Punjab, Lahore 54500, Pakistan
| | - Khushbakht Fatima
- Department of Applied Health Sciences, University of Management and Technology, Lahore 54500, Pakistan;
| | - Asma A. Khan
- Center of Excellence in Molecular Biology, University of the Punjab, Lahore 54500, Pakistan
| | - Zubair M. Ahmed
- Department of Otorhinolaryngology Head & Neck Surgery, School of Medicine, University of Maryland, Baltimore, MD 21201, USA; (M.A.U.); (A.G.)
- Department of Molecular Biology and Biochemistry, School of Medicine, University of Maryland, Baltimore, MD 21201, USA
| | - Sheikh Riazuddin
- Department of Molecular Biology, Shaheed Zulfiqar Ali Bhutto Medical University, Islamabad 44000, Pakistan; (M.S.); (J.A.); (S.R.)
- Jinnah Burn and Reconstructive Surgery Center, Allama Iqbal Medical College, University of Health Sciences, Lahore 54550, Pakistan
| | - Saima Riazuddin
- Department of Otorhinolaryngology Head & Neck Surgery, School of Medicine, University of Maryland, Baltimore, MD 21201, USA; (M.A.U.); (A.G.)
- Center of Excellence in Molecular Biology, University of the Punjab, Lahore 54500, Pakistan
- Department of Molecular Biology and Biochemistry, School of Medicine, University of Maryland, Baltimore, MD 21201, USA
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10
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Khan H, Harripaul R, Mikhailov A, Herzi S, Bowers S, Ayub M, Shabbir MI, Vincent JB. Biallelic variants identified in 36 Pakistani families and trios with autism spectrum disorder. Sci Rep 2024; 14:9230. [PMID: 38649688 PMCID: PMC11035605 DOI: 10.1038/s41598-024-57942-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 03/22/2024] [Indexed: 04/25/2024] Open
Abstract
With its high rate of consanguineous marriages and diverse ethnic population, little is currently understood about the genetic architecture of autism spectrum disorder (ASD) in Pakistan. Pakistan has a highly ethnically diverse population, yet with a high proportion of endogamous marriages, and is therefore anticipated to be enriched for biallelic disease-relate variants. Here, we attempt to determine the underlying genetic abnormalities causing ASD in thirty-six small simplex or multiplex families from Pakistan. Microarray genotyping followed by homozygosity mapping, copy number variation analysis, and whole exome sequencing were used to identify candidate. Given the high levels of consanguineous marriages among these families, autosomal recessively inherited variants were prioritized, however de novo/dominant and X-linked variants were also identified. The selected variants were validated using Sanger sequencing. Here we report the identification of sixteen rare or novel coding variants in fifteen genes (ARAP1, CDKL5, CSMD2, EFCAB12, EIF3H, GML, NEDD4, PDZD4, POLR3G, SLC35A2, TMEM214, TMEM232, TRANK1, TTC19, and ZNF292) in affected members in eight of the families, including ten homozygous variants in four families (nine missense, one loss of function). Three heterozygous de novo mutations were also identified (in ARAP1, CSMD2, and NEDD4), and variants in known X-linked neurodevelopmental disorder genes CDKL5 and SLC35A2. The current study offers information on the genetic variability associated with ASD in Pakistan, and demonstrates a marked enrichment for biallelic variants over that reported in outbreeding populations. This information will be useful for improving approaches for studying ASD in populations where endogamy is commonly practiced.
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Affiliation(s)
- Hamid Khan
- Molecular Neuropsychiatry and Development (MiND) Lab, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Centre for Addiction and Mental Health, 250 College St, Toronto, ON, M5T 1R8, Canada
- Department of Biological Sciences, International Islamic University Islamabad, Islamabad, Pakistan
| | - Ricardo Harripaul
- Molecular Neuropsychiatry and Development (MiND) Lab, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Centre for Addiction and Mental Health, 250 College St, Toronto, ON, M5T 1R8, Canada
- Institute of Medical Science, University of Toronto, Toronto, ON, Canada
| | - Anna Mikhailov
- Molecular Neuropsychiatry and Development (MiND) Lab, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Centre for Addiction and Mental Health, 250 College St, Toronto, ON, M5T 1R8, Canada
| | - Sumayah Herzi
- Molecular Neuropsychiatry and Development (MiND) Lab, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Centre for Addiction and Mental Health, 250 College St, Toronto, ON, M5T 1R8, Canada
| | - Sonya Bowers
- Molecular Neuropsychiatry and Development (MiND) Lab, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Centre for Addiction and Mental Health, 250 College St, Toronto, ON, M5T 1R8, Canada
| | | | - Muhammad Imran Shabbir
- Department of Biological Sciences, International Islamic University Islamabad, Islamabad, Pakistan
| | - John B Vincent
- Molecular Neuropsychiatry and Development (MiND) Lab, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Centre for Addiction and Mental Health, 250 College St, Toronto, ON, M5T 1R8, Canada.
- Institute of Medical Science, University of Toronto, Toronto, ON, Canada.
- Department of Psychiatry, University of Toronto, Toronto, ON, Canada.
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11
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Asghari Sarfaraz A, Jabbarpour N, Bonyadi M, Khalaj-Kondory M. Identification and bioinformatics analysis of a novel variant in the HERC2 gene in a patient with intellectual developmental disorder. J Neurogenet 2024; 38:19-25. [PMID: 38884635 DOI: 10.1080/01677063.2024.2365634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 06/04/2024] [Indexed: 06/18/2024]
Abstract
HERC2-associated neurodevelopmental-disorders(NDD) encompass a cluster of medical conditions that arise from genetic mutations occurring within the HERC2 gene. These disorders can manifest a spectrum of symptoms that impact the brain and nervous system, including delayed psychomotor development, severe mental retardation, seizures and autistic features. Whole-Exome-Sequencing(WES) was performed on a ten-year-old male patient referred to the genetic center for genetic analysis. Blood samples were collected from the proband, his parents, and his sister to extract DNA. PCR-Sanger-sequencing was utilized to validate the findings obtained from WES. In order to obtain a more thorough understanding of the impact of the mutation, an extensive analysis was conducted using bioinformatics tools. WES data analysis identified a homozygous single nucleotide change(C > T) at position c14215 located in exon ninety-two of the HERC2 gene (NC_000015.10(NM_004667.6):c.14215C > T). The absence of this mutation among our cohort composed of four hundred normal healthy adults from the same ethnic group, and its absence in any other population database, confirms the pathogenicity of the mutation. This study revealed that the substitution of arginine with a stop codon within the Hect domain caused a premature stop codon at position 4739(p.Arg4739Ter). This mutation significantly results in the production of a truncated HERC2 protein with an incomplete HECT domain. In the final stage of ubiquitin attachment, HECT E3 ubiquitin ligases play a catalytic role by creating a thiolester intermediate using their conserved catalytic cysteine (Cys4762). This intermediate is formed before ubiquitin is transferred to a substrate protein. The truncation of the HERC2 protein is expected to disrupt its ability to perform this function, which could potentially hinder important regulatory processes related to the development and maintenance of synapses. The identification of a novel pathogenic variant, NC_000015.10(NM_004667.6):c.14215C > T, located within the ninety-two exon of the HERC2 gene, is notable for its association with an autosomal recessive inheritance pattern in cases of Intellectual Developmental Disorder(IDD). In the end, this variant could potentially play a part in the underlying mechanisms leading to the onset of intellectual developmental disorder.
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Affiliation(s)
- Asal Asghari Sarfaraz
- Animal Biology Department, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran
| | - Neda Jabbarpour
- Animal Biology Department, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran
| | - Mortaza Bonyadi
- Center of Excellence for Biodiversity, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran
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12
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Xu W, Yao H, Wu Z, Yan X, Jiao Z, Liu Y, Zhang M, Wang D. Oncoprotein SET-associated transcription factor ZBTB11 triggers lung cancer metastasis. Nat Commun 2024; 15:1362. [PMID: 38355937 PMCID: PMC10867109 DOI: 10.1038/s41467-024-45585-5] [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: 07/21/2022] [Accepted: 01/29/2024] [Indexed: 02/16/2024] Open
Abstract
Metastasis is the major cause of lung cancer-related death, but the mechanisms governing lung tumor metastasis remain incompletely elucidated. SE translocation (SET) is overexpressed in lung tumors and correlates with unfavorable prognosis. Here we uncover SET-associated transcription factor, zinc finger and BTB domain-containing protein 11 (ZBTB11), as a prometastatic regulator in lung tumors. SET interacts and collaborates with ZBTB11 to promote lung cancer cell migration and invasion, primarily through SET-ZBTB11 complex-mediated transcriptional activation of matrix metalloproteinase-9 (MMP9). Additionally, by transcriptional repression of proline-rich Gla protein 2 (PRRG2), ZBTB11 links Yes-associated protein 1 (YAP1) activation to drive lung tumor metastasis independently of SET-ZBTB11 complex. Loss of ZBTB11 suppresses distal metastasis in a lung tumor mouse model. Overexpression of ZBTB11 is recapitulated in human metastatic lung tumors and correlates with diminished survival. Our study demonstrates ZBTB11 as a key metastatic regulator and reveals diverse mechanisms by which ZBTB11 modulates lung tumor metastasis.
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Affiliation(s)
- Wenbin Xu
- State Key Laboratory of Common Mechanism Research for Major Diseases & Department of Medical Genetics, Institute of Basic Medical Sciences & School of Basic Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
| | - Han Yao
- State Key Laboratory of Common Mechanism Research for Major Diseases & Department of Medical Genetics, Institute of Basic Medical Sciences & School of Basic Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
| | - Zhen Wu
- State Key Laboratory of Common Mechanism Research for Major Diseases & Department of Medical Genetics, Institute of Basic Medical Sciences & School of Basic Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
| | - Xiaojun Yan
- State Key Laboratory of Common Mechanism Research for Major Diseases & Department of Medical Genetics, Institute of Basic Medical Sciences & School of Basic Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
| | - Zishan Jiao
- State Key Laboratory of Common Mechanism Research for Major Diseases & Department of Medical Genetics, Institute of Basic Medical Sciences & School of Basic Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
| | - Yajing Liu
- State Key Laboratory of Common Mechanism Research for Major Diseases & Department of Medical Genetics, Institute of Basic Medical Sciences & School of Basic Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
| | - Meng Zhang
- State Key Laboratory of Common Mechanism Research for Major Diseases & Department of Medical Genetics, Institute of Basic Medical Sciences & School of Basic Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
| | - Donglai Wang
- State Key Laboratory of Common Mechanism Research for Major Diseases & Department of Medical Genetics, Institute of Basic Medical Sciences & School of Basic Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China.
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13
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Bassani S, Chrast J, Ambrosini G, Voisin N, Schütz F, Brusco A, Sirchia F, Turban L, Schubert S, Jamra RA, Schlump JU, DeMille D, Bayrak-Toydemir P, Nelson GR, Wong KN, Duncan L, Mosera M, Gilissen C, Vissers LE, Pfundt R, Kersseboom R, Yttervik H, Hansen GÅM, Falkenberg Smeland M, Butler KM, Lyons MJ, Carvalho CM, Zhang C, Lupski JR, Potocki L, Flores-Gallegos L, Morales-Toquero R, Petit F, Yalcin B, Tuttle A, Elloumi HZ, Mccormick L, Kukolich M, Klaas O, Horvath J, Scala M, Iacomino M, Operto F, Zara F, Writzl K, Maver A, Haanpää MK, Pohjola P, Arikka H, Iseli C, Guex N, Reymond A. Variant-specific pathophysiological mechanisms of AFF3 differently influence transcriptome profiles. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.01.14.24301100. [PMID: 38293053 PMCID: PMC10827271 DOI: 10.1101/2024.01.14.24301100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Background We previously described the KINSSHIP syndrome, an autosomal dominant disorder associated with intellectual disability (ID), mesomelic dysplasia and horseshoe kidney,caused by de novo variants in the degron of AFF3. Mouse knock-ins and overexpression in zebrafish provided evidence for a dominant-negative (DN) mode-of-action, wherein an increased level of AFF3 resulted in pathological effects. Methods Evolutionary constraints suggest that other mode-of-inheritance could be at play. We challenged this hypothesis by screening ID cohorts for individuals with predicted-to-be deleterious variants in AFF3. We used both animal and cellular models to assess the deleteriousness of the identified variants. Results We identified an individual with a KINSSHIP-like phenotype carrying a de novo partial duplication of AFF3 further strengthening the hypothesis that an increased level of AFF3 is pathological. We also detected seventeen individuals displaying a milder syndrome with either heterozygous LoF or biallelic missense variants in AFF3. Consistent with semi-dominance, we discovered three patients with homozygous LoF and one compound heterozygote for a LoF and a missense variant, who presented more severe phenotypes than their heterozygous parents. Matching zebrafish knockdowns exhibit neurological defects that could be rescued by expressing human AFF3 mRNA, confirming their association with the ablation of aff3. Conversely, some of the human AFF3 mRNAs carrying missense variants identified in affected individuals did not complement. Overexpression of mutated AFF3 mRNAs in zebrafish embryos produced a significant increase of abnormal larvae compared to wild-type overexpression further demonstrating deleteriousness. To further assess the effect of AFF3 variation, we profiled the transcriptome of fibroblasts from affected individuals and engineered isogenic cells harboring +/+, DN/DN, LoF/+, LoF/LoF or DN/LoF AFF3 genotypes. The expression of more than a third of the AFF3 bound loci is modified in either the DN/DN or the LoF/LoF lines. While the same pathways are affected, only about one-third of the differentially expressed genes are common to these homozygote datasets, indicating that AFF3 LoF and DN variants largely modulate transcriptomes differently, e.g. the DNA repair pathway displayed opposite modulation. Conclusions Our results and the high pleiotropy shown by variation at this locus suggest that minute changes in AFF3 function are deleterious.
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Affiliation(s)
- Sissy Bassani
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Jacqueline Chrast
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Giovanna Ambrosini
- Bioinformatics Competence Center, University of Lausanne, Lausanne, Switzerland
- Bioinformatics Competence Center, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Norine Voisin
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Frédéric Schütz
- Biostatistics platform, University of Lausanne, Lausanne, Switzerland
| | - Alfredo Brusco
- Department of Neurosciences Rita Levi-Montalcini, University of Turin, 10126 Turin, Italy
- Medical Genetics Unit, Città della Salute e della Scienza University Hospital, 10126 Turin, Italy
| | - Fabio Sirchia
- Department of Neurosciences Rita Levi-Montalcini, University of Turin, 10126 Turin, Italy
- Medical Genetics Unit, Città della Salute e della Scienza University Hospital, 10126 Turin, Italy
| | - Lydia Turban
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Susanna Schubert
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Rami Abou Jamra
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Jan-Ulrich Schlump
- Department of Pediatrics, Centre for Neuromedicine, Gemeinschaftskrankenhaus Herdecke Gerhard-Kienle-Weg, Herdecke, Germany
| | - Desiree DeMille
- Genomics Analysis 396, ARUP Laboratories, Salt Lake City, Utah, USA
| | - Pinar Bayrak-Toydemir
- Pediatric Neurology, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Gary Rex Nelson
- Pediatric Neurology, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Kristen Nicole Wong
- Pediatric Neurology, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Laura Duncan
- Department of Pediatrics, Medical Center North, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Mackenzie Mosera
- Department of Pediatrics, Medical Center North, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Christian Gilissen
- Department of Human Genetics, Research Institute for Medical Innovation, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Lisenka E.L.M. Vissers
- Department of Human Genetics, Research Institute for Medical Innovation, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Rolph Pfundt
- Department of Human Genetics, Research Institute for Medical Innovation, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Rogier Kersseboom
- Center for genetic developmental disorders southwest, Zuidwester, Middelharnis, The Netherlands
| | - Hilde Yttervik
- Department of Medical Genetics, University Hospital of North Norway, Tromsø, Norway
| | | | | | | | | | - Claudia M.B. Carvalho
- Pacific Northwest Research Institute (PNRI), Broadway, Seattle, Washington, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Chaofan Zhang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - James R. Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
- Texas Children’s Hospital, Houston, Texas, USA
| | - Lorraine Potocki
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Texas Children’s Hospital, Houston, Texas, USA
| | | | | | | | - Binnaz Yalcin
- Inserm UMR1231, University of Burgundy, 21000 Dijon, France
| | | | | | - Lane Mccormick
- Department of Genetics, Cook Children’s Medical Center, Cook Children’s Health Care System, Fort Worth, Texas, USA
| | - Mary Kukolich
- Department of Genetics, Cook Children’s Medical Center, Cook Children’s Health Care System, Fort Worth, Texas, USA
| | - Oliver Klaas
- Institute for Human Genetics, University Hospital Muenster, Muenster, Germany
| | - Judit Horvath
- Institute for Human Genetics, University Hospital Muenster, Muenster, Germany
| | - Marcello Scala
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, 16132, Genoa, Italy
- Medical Genetics Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Michele Iacomino
- Medical Genetics Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Francesca Operto
- Child and Adolescent Neuropsychiatry Unit, Department of Medicine, Surgery and Dentistry, University of Salerno, Salerno, Italy
| | - Federico Zara
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, 16132, Genoa, Italy
- Medical Genetics Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Karin Writzl
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
- Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Ales Maver
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Maria K. Haanpää
- Department of Genomics, Turku University Hospital, Turku, Finland; University of Turku, Turku, Finland
| | - Pia Pohjola
- Department of Genomics, Turku University Hospital, Turku, Finland; University of Turku, Turku, Finland
| | - Harri Arikka
- Department of Pediatric Neurology, Turku University Hospital, Turku, Finland; University of Turku, Turku, Finland
| | - Christian Iseli
- Bioinformatics Competence Center, University of Lausanne, Lausanne, Switzerland
- Bioinformatics Competence Center, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Nicolas Guex
- Bioinformatics Competence Center, University of Lausanne, Lausanne, Switzerland
- Bioinformatics Competence Center, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Alexandre Reymond
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
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Almousa H, Lewis SA, Bakhtiari S, Nordlie SH, Pagnozzi A, Magee H, Efthymiou S, Heim JA, Cornejo P, Zaki MS, Anwar N, Maqbool S, Rahman F, Neilson DE, Vemuri A, Jin SC, Yang XR, Heidari A, van Gassen K, Trimouille A, Thauvin-Robinet C, Liu J, Bruel AL, Tomoum H, Shata MO, Hashem MO, Toosi MB, Karimiani EG, Yeşil G, Lingappa L, Baruah D, Ebrahimzadeh F, Van-Gils J, Faivre L, Zamani M, Galehdari H, Sadeghian S, Shariati G, Mohammad R, van der Smagt J, Qari A, Vincent JB, Innes AM, Dursun A, Özgül RK, Akar HT, Bilguvar K, Mignot C, Keren B, Raveli C, Burglen L, Afenjar A, Kaat LD, van Slegtenhorst M, Alkuraya F, Houlden H, Padilla-Lopez S, Maroofian R, Sacher M, Kruer MC. TRAPPC6B biallelic variants cause a neurodevelopmental disorder with TRAPP II and trafficking disruptions. Brain 2024; 147:311-324. [PMID: 37713627 PMCID: PMC10766242 DOI: 10.1093/brain/awad301] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 07/11/2023] [Accepted: 08/10/2023] [Indexed: 09/17/2023] Open
Abstract
Highly conserved transport protein particle (TRAPP) complexes regulate subcellular trafficking pathways. Accurate protein trafficking has been increasingly recognized to be critically important for normal development, particularly in the nervous system. Variants in most TRAPP complex subunits have been found to lead to neurodevelopmental disorders with diverse but overlapping phenotypes. We expand on limited prior reports on TRAPPC6B with detailed clinical and neuroradiologic assessments, and studies on mechanisms of disease, and new types of variants. We describe 29 additional patients from 18 independent families with biallelic variants in TRAPPC6B. We identified seven homozygous nonsense (n = 12 patients) and eight canonical splice-site variants (n = 17 patients). In addition, we identified one patient with compound heterozygous splice-site/missense variants with a milder phenotype and one patient with homozygous missense variants. Patients displayed non-progressive microcephaly, global developmental delay/intellectual disability, epilepsy and absent expressive language. Movement disorders including stereotypies, spasticity and dystonia were also observed. Brain imaging revealed reductions in cortex, cerebellum and corpus callosum size with frequent white matter hyperintensity. Volumetric measurements indicated globally diminished volume rather than specific regional losses. We identified a reduced rate of trafficking into the Golgi apparatus and Golgi fragmentation in patient-derived fibroblasts that was rescued by wild-type TRAPPC6B. Molecular studies revealed a weakened interaction between mutant TRAPPC6B (c.454C>T, p.Q152*) and its TRAPP binding partner TRAPPC3. Patient-derived fibroblasts from the TRAPPC6B (c.454C>T, p.Q152*) variant displayed reduced levels of TRAPPC6B as well as other TRAPP II complex-specific members (TRAPPC9 and TRAPPC10). Interestingly, the levels of the TRAPPC6B homologue TRAPPC6A were found to be elevated. Moreover, co-immunoprecipitation experiments showed that TRAPPC6A co-precipitates equally with TRAPP II and TRAPP III, while TRAPPC6B co-precipitates significantly more with TRAPP II, suggesting enrichment of the protein in the TRAPP II complex. This implies that variants in TRAPPC6B may preferentially affect TRAPP II functions compared to TRAPP III functions. Finally, we assessed phenotypes in a Drosophila TRAPPC6B-deficiency model. Neuronal TRAPPC6B knockdown impaired locomotion and led to wing posture defects, supporting a role for TRAPPC6B in neuromotor function. Our findings confirm the association of damaging biallelic TRAPPC6B variants with microcephaly, intellectual disability, language impairments, and epilepsy. A subset of patients also exhibited dystonia and/or spasticity with impaired ambulation. These features overlap with disorders arising from pathogenic variants in other TRAPP subunits, particularly components of the TRAPP II complex. These findings suggest that TRAPPC6B is essential for brain development and function, and TRAPP II complex activity may be particularly relevant for mediating this function.
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Affiliation(s)
- Hashem Almousa
- Department of Biology, Concordia University, Montreal, Quebec H4B1R6, Canada
| | - Sara A Lewis
- Barrow Neurological Institute, Phoenix Children’s Hospital, Phoenix, AZ 85016, USA
- Departments of Child Health, Cellular and Molecular Medicine, Genetics, and Neurology, University of Arizona College of Medicine—Phoenix, Phoenix, AZ 85004, USA
| | - Somayeh Bakhtiari
- Barrow Neurological Institute, Phoenix Children’s Hospital, Phoenix, AZ 85016, USA
- Departments of Child Health, Cellular and Molecular Medicine, Genetics, and Neurology, University of Arizona College of Medicine—Phoenix, Phoenix, AZ 85004, USA
| | - Sandra Hinz Nordlie
- Barrow Neurological Institute, Phoenix Children’s Hospital, Phoenix, AZ 85016, USA
- Departments of Child Health, Cellular and Molecular Medicine, Genetics, and Neurology, University of Arizona College of Medicine—Phoenix, Phoenix, AZ 85004, USA
| | - Alex Pagnozzi
- CSIRO Health and Biosecurity, The Australian e-Health Research Centre, Brisbane 4029, Australia
| | - Helen Magee
- Barrow Neurological Institute, Phoenix Children’s Hospital, Phoenix, AZ 85016, USA
- Departments of Child Health, Cellular and Molecular Medicine, Genetics, and Neurology, University of Arizona College of Medicine—Phoenix, Phoenix, AZ 85004, USA
| | - Stephanie Efthymiou
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Jennifer A Heim
- Barrow Neurological Institute, Phoenix Children’s Hospital, Phoenix, AZ 85016, USA
| | - Patricia Cornejo
- Pediatric Neuroradiology Division, Pediatric Radiology, Barrow Neurological Institute, Phoenix Children’s Hospital, Phoenix, AZ 85016, USA
- Department of Child Health, University of Arizona College of Medicine, Phoenix, AZ 85004, USA
- Department of Radiology, Mayo Clinic, Scottsdale, AZ 85259, USA
| | - Maha S Zaki
- Clinical Genetics Department, Human Genetics and Genome Research Division, National Research Centre, Cairo 12622, Egypt
- Genetics Department, Armed Forces College of Medicine (AFCM), Cairo 4460015, Egypt
| | - Najwa Anwar
- Department of Developmental-Behavioural Paediatrics, The Children's Hospital and Institute of Child Health, Lahore 54000, Pakistan
| | - Shazia Maqbool
- Department of Developmental-Behavioural Paediatrics, The Children's Hospital and Institute of Child Health, Lahore 54000, Pakistan
| | - Fatima Rahman
- Department of Developmental-Behavioural Paediatrics, The Children's Hospital and Institute of Child Health, Lahore 54000, Pakistan
| | - Derek E Neilson
- Genetics and Metabolism, Phoenix Children’s Hospital, Phoenix, AZ 85016, USA
| | - Anusha Vemuri
- Department of Pathology, University of Chicago, Chicago, IL 60637, USA
| | - Sheng Chih Jin
- Department of Genetics, Washington University, St.Louis, MO 63110, USA
| | - Xiao-Ru Yang
- Department of Medical Genetics and Alberta Children’s Hospital Research Institute, Cumming School of Medicine, University of Calgary, S.W. Calgary, AB T2N 4N1, Canada
| | - Abolfazl Heidari
- Reference Laboratory, Qazvin Medical University, Qazvin 34148-33245, Iran
| | - Koen van Gassen
- Division of Laboratories, Pharmacy and Biomedical Genetics, Section of Clinical Genetics, University Medical Center Utrecht (UMCU), 3584 CX Utrecht, Netherlands
| | - Aurélien Trimouille
- Laboratoire de Génétique Moléculaire, Service de Génétique Médicale, CHU Bordeaux—Hôpital Pellegrin, Place Amélie Raba Léon, 33000 Bordeaux, France
| | - Christel Thauvin-Robinet
- Department of Genetics and Reference Center for Development Disorders and Intellectual Disabilities, FHU TRANSLAD, CHU Dijon Bourgogne, 21000 Dijon, France
- Unité Fontctionnelle d’Innovation diagnostiques des maladies rares, FHU TRANSLAD, CHU Dijon Bourgogne, 21000 Dijon, France
- GAD ‘Génétique des Anomalies du Développement’, INSERM-Université de Bourgogne UMR1231, 21078 Dijon, France
| | - James Liu
- Barrow Neurological Institute, Phoenix Children’s Hospital, Phoenix, AZ 85016, USA
- Departments of Child Health, Cellular and Molecular Medicine, Genetics, and Neurology, University of Arizona College of Medicine—Phoenix, Phoenix, AZ 85004, USA
| | - Ange-Line Bruel
- Unité Fontctionnelle d’Innovation diagnostiques des maladies rares, FHU TRANSLAD, CHU Dijon Bourgogne, 21000 Dijon, France
- GAD ‘Génétique des Anomalies du Développement’, INSERM-Université de Bourgogne UMR1231, 21078 Dijon, France
| | - Hoda Tomoum
- Department of Pediatrics, Ain Shams University, Cairo 11516, Egypt
| | | | - Mais O Hashem
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Mehran Beiraghi Toosi
- Pediatric Neurology Department, Ghaem Hospital, Mashhad University of Medical Sciences, Mashhad 13944-91388, Iran
- Neuroscience Research Center, Mashhad University of Medical Science, Mashhad 13944-91388, Iran
| | - Ehsan Ghayoor Karimiani
- Molecular and Clinical Sciences Institute, St.George’s, University of London, London SW17 0RE, UK
| | - Gözde Yeşil
- Istanbul Medical Faculty Department of Medical Genetics, Istanbul University, Istanbul 34452, Turkey
| | - Lokesh Lingappa
- Pediatric Neurology, Rainbow Children Hospital, Hyderabad 500034, India
| | - Debangana Baruah
- Pediatric Neurology, Rainbow Children Hospital, Hyderabad 500034, India
| | - Farnoosh Ebrahimzadeh
- Department of Internal Medicine, Mashhad University of Medical Sciences, Mashhad 13944-91388, Iran
| | - Julien Van-Gils
- Division of Laboratories, Pharmacy and Biomedical Genetics, Section of Clinical Genetics, University Medical Center Utrecht (UMCU), 3584 CX Utrecht, Netherlands
| | - Laurence Faivre
- Department of Genetics and Reference Center for Development Disorders and Intellectual Disabilities, FHU TRANSLAD, CHU Dijon Bourgogne, 21000 Dijon, France
| | - Mina Zamani
- Department of Biology, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz 6135783151, Iran
- Narges Medical Genetics and Prenatal Diagnosis Laboratory, Ahvaz 6155889467, Iran
| | - Hamid Galehdari
- Department of Biology, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz 6135783151, Iran
| | - Saeid Sadeghian
- Department of Pediatric Neurology, Golestan Medical, Educational, and Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz 6135733118, Iran
| | - Gholamreza Shariati
- Narges Medical Genetics and Prenatal Diagnosis Laboratory, Ahvaz 6155889467, Iran
- Department of Medical Genetics, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz 6135733118, Iran
| | - Rahema Mohammad
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Jasper van der Smagt
- Division of Laboratories, Pharmacy and Biomedical Genetics, Section of Clinical Genetics, University Medical Center Utrecht (UMCU), 3584 CX Utrecht, Netherlands
| | - Alya Qari
- Medical Genomics Department, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh 11564, Saudi Arabia
| | - John B Vincent
- Molecular Neuropsychiatry & Development (MiND) Lab, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON M6J 1H4, Canada
| | - A Micheil Innes
- Department of Medical Genetics and Alberta Children’s Hospital Research Institute, Cumming School of Medicine, University of Calgary, S.W. Calgary, AB T2N 4N1, Canada
| | - Ali Dursun
- Department of Pediatric Metabolism, Hacettepe University, Faculty of Medicine & Institute of Child Health, Ankara 06800, Turkey
| | - R Köksal Özgül
- Department of Pediatric Metabolism, Hacettepe University, Faculty of Medicine & Institute of Child Health, Ankara 06800, Turkey
| | - Halil Tuna Akar
- Department of Pediatric Metabolism, Hacettepe University, Faculty of Medicine & Institute of Child Health, Ankara 06800, Turkey
| | - Kaya Bilguvar
- Department of Medical Genetics, Acibadem Mehmet Ali Aydinlar University, Istanbul 34752, Turkey
- Department of Neurosurgery and Genetics, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Cyril Mignot
- Département de Génétique, APHP Sorbonne Université, Hôpital Trousseau & Groupe Hospitalier Pitié-Salpêtrière, 75013 Paris, France
- Centre de Référence Déficiences Intellectuelles de Causes Rares, 75012 Paris, France
| | - Boris Keren
- Département de Génétique, APHP Sorbonne Université, Hôpital Trousseau & Groupe Hospitalier Pitié-Salpêtrière, 75013 Paris, France
| | - Claudia Raveli
- APHP Sorbonne Université, Service de Neuropédiatrie, Hôpital Trousseau, 75012 Paris, France
| | - Lydie Burglen
- Département de Génétique, Centre de référence des malformations et maladies congénitales du cervelet, APHP. Sorbonne Université, Hôpital Trousseau, 75012 Paris, France
| | - Alexandra Afenjar
- Département de Génétique, Centre de référence des malformations et maladies congénitales du cervelet, APHP. Sorbonne Université, Hôpital Trousseau, 75012 Paris, France
| | - Laura Donker Kaat
- Department of Clinical Genetics, Erasmus Medical Center, 3000 Rotterdam, The Netherlands
| | | | - Fowzan Alkuraya
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Henry Houlden
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Sergio Padilla-Lopez
- Barrow Neurological Institute, Phoenix Children’s Hospital, Phoenix, AZ 85016, USA
- Departments of Child Health, Cellular and Molecular Medicine, Genetics, and Neurology, University of Arizona College of Medicine—Phoenix, Phoenix, AZ 85004, USA
| | - Reza Maroofian
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Michael Sacher
- Department of Biology, Concordia University, Montreal, Quebec H4B1R6, Canada
- Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec H3A0C7, Canada
| | - Michael C Kruer
- Barrow Neurological Institute, Phoenix Children’s Hospital, Phoenix, AZ 85016, USA
- Departments of Child Health, Cellular and Molecular Medicine, Genetics, and Neurology, University of Arizona College of Medicine—Phoenix, Phoenix, AZ 85004, USA
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15
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Uctepe E, Vona B, Esen FN, Sonmez FM, Smol T, Tümer S, Mancılar H, Geylan Durgun DE, Boute O, Moghbeli M, Ghayoor Karimiani E, Hashemi N, Bakhshoodeh B, Kim HG, Maroofian R, Yesilyurt A. Bi-allelic truncating variants in CASP2 underlie a neurodevelopmental disorder with lissencephaly. Eur J Hum Genet 2024; 32:52-60. [PMID: 37880421 PMCID: PMC10772072 DOI: 10.1038/s41431-023-01461-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 07/24/2023] [Accepted: 09/11/2023] [Indexed: 10/27/2023] Open
Abstract
Lissencephaly (LIS) is a malformation of cortical development due to deficient neuronal migration and abnormal formation of cerebral convolutions or gyri. Thirty-one LIS-associated genes have been previously described. Recently, biallelic pathogenic variants in CRADD and PIDD1, have associated with LIS impacting the previously established role of the PIDDosome in activating caspase-2. In this report, we describe biallelic truncating variants in CASP2, another subunit of PIDDosome complex. Seven patients from five independent families presenting with a neurodevelopmental phenotype were identified through GeneMatcher-facilitated international collaborations. Exome sequencing analysis was carried out and revealed two distinct novel homozygous (NM_032982.4:c.1156delT (p.Tyr386ThrfsTer25), and c.1174 C > T (p.Gln392Ter)) and compound heterozygous variants (c.[130 C > T];[876 + 1 G > T] p.[Arg44Ter];[?]) in CASP2 segregating within the families in a manner compatible with an autosomal recessive pattern. RNA studies of the c.876 + 1 G > T variant indicated usage of two cryptic splice donor sites, each introducing a premature stop codon. All patients from whom brain MRIs were available had a typical fronto-temporal LIS and pachygyria, remarkably resembling the CRADD and PIDD1-related neuroimaging findings. Other findings included developmental delay, attention deficit hyperactivity disorder, hypotonia, seizure, poor social skills, and autistic traits. In summary, we present patients with CASP2-related ID, anterior-predominant LIS, and pachygyria similar to previously reported patients with CRADD and PIDD1-related disorders, expanding the genetic spectrum of LIS and lending support that each component of the PIDDosome complex is critical for normal development of the human cerebral cortex and brain function.
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Affiliation(s)
- Eyyup Uctepe
- Acibadem Ankara Tissue Typing Laboratory, Ankara, Türkiye
| | - Barbara Vona
- Institute of Human Genetics, University Medical Center Göttingen, Heinrich-Düker-Weg 12, 37073, Göttingen, Germany
- Institute for Auditory Neuroscience and InnerEarLab, University Medical Center Göttingen, Robert-Koch-Str. 40, 37075, Göttingen, Germany
| | | | - F Mujgan Sonmez
- Department of Child Neurology, Faculty of Medicine, Retired lecturer, Karadeniz Technical University, Trabzon, Türkiye
- Private Office, Ankara, Türkiye
| | - Thomas Smol
- Institut de Génétique Médicale, Université de Lille, ULR7364 RADEME, CHU Lille, F-59000, Lille, France
| | - Sait Tümer
- Acibadem Labgen Genetic Diagnosis Center, Istanbul, Türkiye
| | | | | | - Odile Boute
- Clinique de Génétique, Université de Lille, ULR7364 RADEME, CHU Lille, F-59000, Lille, France
| | - Meysam Moghbeli
- Department of Medical Genetics and Molecular Medicine, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Ehsan Ghayoor Karimiani
- Molecular and Clinical Sciences Institute, St. George's, University of London, Cranmer Terrace, London, SW17 0RE, UK
- Department of Medical Genetics, Next Generation Genetic Polyclinic, Mashhad, Iran
| | - Narges Hashemi
- Department of Pediatrics, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | | | - Hyung Goo Kim
- Neurological Disorders Research Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Doha, Qatar
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
| | - Reza Maroofian
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, University College London, London, UK
| | - Ahmet Yesilyurt
- Acibadem Labgen Genetic Diagnosis Center, Istanbul, Türkiye.
- Acibadem Maslak Hospital, Istanbul, Türkiye.
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16
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Volik PI, Kopeina GS, Zhivotovsky B, Zamaraev AV. Total recall: the role of PIDDosome components in neurodegeneration. Trends Mol Med 2023; 29:996-1013. [PMID: 37716905 DOI: 10.1016/j.molmed.2023.08.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 08/23/2023] [Accepted: 08/25/2023] [Indexed: 09/18/2023]
Abstract
The PIDDosome is a multiprotein complex that includes p53-induced protein with a death domain 1 (PIDD1), receptor-interacting protein-associated ICH-1/CED-3 homologous protein with a death domain (RAIDD), and caspase-2, the activation of which is driven by PIDDosome assembly. In addition to the key role of the PIDDosome in the regulation of cell differentiation, tissue homeostasis, and organogenesis and regeneration, caspase-2, RAIDD and PIDD1 engagement in neuronal development was shown. Here, we focus on the involvement of PIDDosome components in neurodegenerative disorders, including retinal neuropathies, different types of brain damage, and Alzheimer's disease (AD), Huntington's disease (HD), and Lewy body disease. We also discuss pathogenic variants of PIDD1, RAIDD, and caspase-2 that are associated with intellectual, behavioral, and psychological abnormalities, together with prospective PIDDosome inhibition strategies and their potential clinical application.
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Affiliation(s)
- Pavel I Volik
- Facuty of Medicine, MV Lomonosov Moscow State University, 119991 Moscow, Russia; Engelhardt Institute of Molecular Biology, RAS, 119991 Moscow, Russia
| | - Gelina S Kopeina
- Facuty of Medicine, MV Lomonosov Moscow State University, 119991 Moscow, Russia; Engelhardt Institute of Molecular Biology, RAS, 119991 Moscow, Russia
| | - Boris Zhivotovsky
- Facuty of Medicine, MV Lomonosov Moscow State University, 119991 Moscow, Russia; Engelhardt Institute of Molecular Biology, RAS, 119991 Moscow, Russia; Division of Toxicology, Institute of Environmental Medicine, Karolinska Institutet, Box 210, 17177 Stockholm, Sweden.
| | - Alexey V Zamaraev
- Facuty of Medicine, MV Lomonosov Moscow State University, 119991 Moscow, Russia; Engelhardt Institute of Molecular Biology, RAS, 119991 Moscow, Russia.
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17
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Cao H, Naik SH, Amann-Zalcenstein D, Hickey P, Salim A, Cao B, Nilsson SK, Keightley MC, Lieschke GJ. Late fetal hematopoietic failure results from ZBTB11 deficiency despite abundant HSC specification. Blood Adv 2023; 7:6506-6519. [PMID: 37567157 PMCID: PMC10632610 DOI: 10.1182/bloodadvances.2022009580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 07/17/2023] [Accepted: 07/18/2023] [Indexed: 08/13/2023] Open
Abstract
Hematopoiesis produces diverse blood cell lineages to meet the basal needs and sudden demands of injury or infection. A rapid response to such challenges requires the expansion of specific lineages and a prompt return to balanced steady-state levels, necessitating tightly coordinated regulation. Previously we identified a requirement for the zinc finger and broad complex, tramtrak, bric-a-brac domain-containing 11 (ZBTB11) transcription factor in definitive hematopoiesis using a forward genetic screen for zebrafish myeloid mutants. To understand its relevance to mammalian systems, we extended these studies to mice. When Zbtb11 was deleted in the hematopoietic compartment, embryos died at embryonic day (E) 18.5 with hematopoietic failure. Zbtb11 hematopoietic knockout (Zbtb11hKO) hematopoietic stem cells (HSCs) were overabundantly specified from E14.5 to E17.5 compared with those in controls. Overspecification was accompanied by loss of stemness, inability to differentiate into committed progenitors and mature lineages in the fetal liver, failure to seed fetal bone marrow, and total hematopoietic failure. The Zbtb11hKO HSCs did not proliferate in vitro and were constrained in cell cycle progression, demonstrating the cell-intrinsic role of Zbtb11 in proliferation and cell cycle regulation in mammalian HSCs. Single-cell RNA sequencing analysis identified that Zbtb11-deficient HSCs were underrepresented in an erythroid-primed subpopulation and showed downregulation of oxidative phosphorylation pathways and dysregulation of genes associated with the hematopoietic niche. We identified a cell-intrinsic requirement for Zbtb11-mediated gene regulatory networks in sustaining a pool of maturation-capable HSCs and progenitor cells.
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Affiliation(s)
- Huimin Cao
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC, Australia
- Biomedical Manufacturing, Commonwealth Scientific and Industrial Research Organisation, Clayton, VIC, Australia
| | - Shalin H. Naik
- Department of Immunology, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Single Cell Open Research Endeavour, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Daniela Amann-Zalcenstein
- Single Cell Open Research Endeavour, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
- Advanced Genomics Facility, Advanced Technology and Biology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Peter Hickey
- Single Cell Open Research Endeavour, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
- Advanced Genomics Facility, Advanced Technology and Biology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Agus Salim
- Mathematics and Statistics, La Trobe University, Bundoora, VIC, Australia
- Melbourne School of Population and Global Health, School of Mathematics and Statistics, University of Melbourne, Parkville, VIC, Australia
| | - Benjamin Cao
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC, Australia
- Biomedical Manufacturing, Commonwealth Scientific and Industrial Research Organisation, Clayton, VIC, Australia
| | - Susan K. Nilsson
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC, Australia
- Biomedical Manufacturing, Commonwealth Scientific and Industrial Research Organisation, Clayton, VIC, Australia
| | - M. Cristina Keightley
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC, Australia
- La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC, Australia
- Rural Clinical Sciences, La Trobe Rural Health School, Bendigo, VIC, Australia
| | - Graham J. Lieschke
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC, Australia
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18
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Wu Z, Chen H, Ke S, Mo L, Qiu M, Zhu G, Zhu W, Liu L. Identifying potential biomarkers of idiopathic pulmonary fibrosis through machine learning analysis. Sci Rep 2023; 13:16559. [PMID: 37783761 PMCID: PMC10545744 DOI: 10.1038/s41598-023-43834-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 09/28/2023] [Indexed: 10/04/2023] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is the most common and serious type of idiopathic interstitial pneumonia, characterized by chronic, progressive, and low survival rates, while unknown disease etiology. Until recently, patients with idiopathic pulmonary fibrosis have a poor prognosis, high mortality, and limited treatment options, due to the lack of effective early diagnostic and prognostic tools. Therefore, we aimed to identify biomarkers for idiopathic pulmonary fibrosis based on multiple machine-learning approaches and to evaluate the role of immune infiltration in the disease. The gene expression profile and its corresponding clinical data of idiopathic pulmonary fibrosis patients were downloaded from Gene Expression Omnibus (GEO) database. Next, the differentially expressed genes (DEGs) with the threshold of FDR < 0.05 and |log2 foldchange (FC)| > 0.585 were analyzed via R package "DESeq2" and GO enrichment and KEGG pathways were run in R software. Then, least absolute shrinkage and selection operator (LASSO) logistic regression, support vector machine-recursive feature elimination (SVM-RFE) and random forest (RF) algorithms were combined to screen the key potential biomarkers of idiopathic pulmonary fibrosis. The diagnostic performance of these biomarkers was evaluated through receiver operating characteristic (ROC) curves. Moreover, the CIBERSORT algorithm was employed to assess the infiltration of immune cells and the relationship between the infiltrating immune cells and the biomarkers. Finally, we sought to understand the potential pathogenic role of the biomarker (SLAIN1) in idiopathic pulmonary fibrosis using a mouse model and cellular model. A total of 3658 differentially expressed genes of idiopathic pulmonary fibrosis were identified, including 2359 upregulated genes and 1299 downregulated genes. FHL2, HPCAL1, RNF182, and SLAIN1 were identified as biomarkers of idiopathic pulmonary fibrosis using LASSO logistic regression, RF, and SVM-RFE algorithms. The ROC curves confirmed the predictive accuracy of these biomarkers both in the training set and test set. Immune cell infiltration analysis suggested that patients with idiopathic pulmonary fibrosis had a higher level of B cells memory, Plasma cells, T cells CD8, T cells follicular helper, T cells regulatory (Tregs), Macrophages M0, and Mast cells resting compared with the control group. Correlation analysis demonstrated that FHL2 was significantly associated with the infiltrating immune cells. qPCR and western blotting analysis suggested that SLAIN1 might be a signature for the diagnosis of idiopathic pulmonary fibrosis. In this study, we identified four potential biomarkers (FHL2, HPCAL1, RNF182, and SLAIN1) and evaluated the potential pathogenic role of SLAIN1 in idiopathic pulmonary fibrosis. These findings may have great significance in guiding the understanding of disease mechanisms and potential therapeutic targets in idiopathic pulmonary fibrosis.
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Affiliation(s)
- Zenan Wu
- The Clinical Medical School, Jiangxi University of Traditional Chinese Medicine, Nanchang, Jiangxi, China
| | - Huan Chen
- The Eighth Affiliated Hospital of Sun Yat-sen University, Shenzhen, China
| | - Shiwen Ke
- The Affiliated Hospital of Jiangxi University of Traditional Chinese Medicine, Nanchang, China
| | - Lisha Mo
- The Affiliated Hospital of Jiangxi University of Traditional Chinese Medicine, Nanchang, China
| | - Mingliang Qiu
- The Affiliated Hospital of Jiangxi University of Traditional Chinese Medicine, Nanchang, China
| | - Guoshuang Zhu
- The Clinical Medical School, Jiangxi University of Traditional Chinese Medicine, Nanchang, Jiangxi, China
| | - Wei Zhu
- The Second Clinical Medical School, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Liangji Liu
- The Affiliated Hospital of Jiangxi University of Traditional Chinese Medicine, Nanchang, China.
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19
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Almenabawy N, Ramadan M, Kamel M, Mahmoud IG, Amer F, Shaheen Y, Elnaggar W, Selim L. Clinical, biochemical, and molecular characterization of mucopolysaccharidosis type III in 34 Egyptian patients. Am J Med Genet A 2023; 191:2354-2363. [PMID: 37596900 DOI: 10.1002/ajmg.a.63342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 06/09/2023] [Accepted: 06/20/2023] [Indexed: 08/21/2023]
Abstract
Mucopolysaccharidosis type III (MPS III) is a rare autosomal recessive lysosomal storage disorder characterized by progressive neurocognitive deterioration. There are four MPS III subtypes (A, B, C, and D) that are clinically indistinguishable with variable rates of progression. A retrospective analysis was carried out on 34 patients with MPS III types at Cairo University Children's Hospital. We described the clinical, biochemical, and molecular spectrum of MPS III patients. Of 34 patients, 22 patients had MPS IIIB, 7/34 had MPS IIIC, 4/34 had MPS IIIA, and only 1 had MPS IIID. All patients presented with developmental delay/intellectual disability, and speech delay. Ataxia was reported in a patient with MPS IIIC, and cerebellar atrophy in a patient with MPS IIIA. We reported 25 variants in the 4 MPS III genes, 11 of which were not previously reported. This is the first study to analyze the clinical and genetic spectrum of MPS III patients in Egypt. This study explores the genetic map of MPS III in the Egyptian population. It will pave the way for a national registry for rare diseases in Egypt, a country with a high rate of consanguineous marriage and consequently a high rate of autosomal recessive disorders.
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Affiliation(s)
- Nihal Almenabawy
- Pediatric Department, Pediatric Neurology and Metabolic Division, Cairo University Children's Hospital, Cairo, Egypt
| | - Manal Ramadan
- Pediatric Department, Ahmed Maher Teaching Hospital, Cairo, Egypt
| | - Mona Kamel
- Pediatric Department, Pediatric Neurology and Metabolic Division, Cairo University Children's Hospital, Cairo, Egypt
| | - Iman G Mahmoud
- Pediatric Department, Pediatric Neurology and Metabolic Division, Cairo University Children's Hospital, Cairo, Egypt
| | - Fawzia Amer
- Pediatric Department, Pediatric Neurology and Metabolic Division, Cairo University Children's Hospital, Cairo, Egypt
| | - Yara Shaheen
- Pediatric Department, Pediatric Neurology and Metabolic Division, Cairo University Children's Hospital, Cairo, Egypt
| | - Walaa Elnaggar
- Pediatric Department, Pediatric Neurology and Metabolic Division, Cairo University Children's Hospital, Cairo, Egypt
| | - Laila Selim
- Pediatric Department, Pediatric Neurology and Metabolic Division, Cairo University Children's Hospital, Cairo, Egypt
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20
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Zarrei M, Burton CL, Engchuan W, Higginbotham EJ, Wei J, Shaikh S, Roslin NM, MacDonald JR, Pellecchia G, Nalpathamkalam T, Lamoureux S, Manshaei R, Howe J, Trost B, Thiruvahindrapuram B, Marshall CR, Yuen RKC, Wintle RF, Strug LJ, Stavropoulos DJ, Vorstman JAS, Arnold P, Merico D, Woodbury-Smith M, Crosbie J, Schachar RJ, Scherer SW. Gene copy number variation and pediatric mental health/neurodevelopment in a general population. Hum Mol Genet 2023; 32:2411-2421. [PMID: 37154571 PMCID: PMC10360394 DOI: 10.1093/hmg/ddad074] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 04/27/2023] [Accepted: 05/02/2023] [Indexed: 05/10/2023] Open
Abstract
We assessed the relationship of gene copy number variation (CNV) in mental health/neurodevelopmental traits and diagnoses, physical health and cognition in a community sample of 7100 unrelated children and youth of European or East Asian ancestry (Spit for Science). Clinically significant or susceptibility CNVs were present in 3.9% of participants and were associated with elevated scores on a continuous measure of attention-deficit/hyperactivity disorder (ADHD) traits (P = 5.0 × 10-3), longer response inhibition (a cognitive deficit found in several mental health and neurodevelopmental disorders; P = 1.0 × 10-2) and increased prevalence of mental health diagnoses (P = 1.9 × 10-6, odds ratio: 3.09), specifically ADHD, autism spectrum disorder anxiety and learning problems/learning disorder (P's < 0.01). There was an increased burden of rare deletions in gene-sets related to brain function or expression in brain associated with more ADHD traits. With the current mental health crisis, our data established a baseline for delineating genetic contributors in pediatric-onset conditions.
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Affiliation(s)
- Mehdi Zarrei
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - Christie L Burton
- Neurosciences and Mental Health Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Worrawat Engchuan
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - Edward J Higginbotham
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - John Wei
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Sabah Shaikh
- Neurosciences and Mental Health Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Nicole M Roslin
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
- Neurosciences and Mental Health Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Jeffrey R MacDonald
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Giovanna Pellecchia
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Thomas Nalpathamkalam
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Sylvia Lamoureux
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Roozbeh Manshaei
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Ted Rogers Centre for Heart Research, Cardiac Genome Clinic, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Jennifer Howe
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Brett Trost
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | | | - Christian R Marshall
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Genome Diagnostics, Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Ryan K C Yuen
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - Richard F Wintle
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Lisa J Strug
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
- Departments of Statistical Sciences, Computer Science and Biostatistics, University of Toronto, Toronto, ON M5G 1Z5, Canada
| | - Dimitri J Stavropoulos
- Genome Diagnostics, Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Jacob A S Vorstman
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
- Department of Psychiatry, University of Toronto, Toronto, ON M5T 1R8, Canada
- Autism Research Unit, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Paul Arnold
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
- Mathison Centre for Mental Health Research and Education, University of Calgary, Calgary, AB T2N 1N4, Canada
- Departments of Psychiatry & Medical Genetics, Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Daniele Merico
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Deep Genomics Inc., Toronto, ON M5G 1M1, Canada
| | - Marc Woodbury-Smith
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Institute of Neuroscience, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Jennifer Crosbie
- Neurosciences and Mental Health Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Department of Psychiatry, University of Toronto, Toronto, ON M5T 1R8, Canada
| | - Russell J Schachar
- Neurosciences and Mental Health Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Department of Psychiatry, University of Toronto, Toronto, ON M5T 1R8, Canada
- Institute of Medical Science, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Stephen W Scherer
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
- Department of Molecular Genetics, McLaughlin Centre, University of Toronto, Toronto, ON M5S 1A8, Canada
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21
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Lu Y, Zhou Y, Guo J, Qi M, Lin Y, Zhang X, Xiang Y, Fu Q, Wang B. Integrated analysis of copy number variation-associated lncRNAs identifies candidates contributing to the etiologies of congenital kidney anomalies. Commun Biol 2023; 6:735. [PMID: 37460814 DOI: 10.1038/s42003-023-05101-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 07/05/2023] [Indexed: 07/20/2023] Open
Abstract
Congenital anomalies of the kidney and urinary tract (CAKUT) are disorders resulting from defects in the development of the kidneys and their outflow tract. Copy number variations (CNVs) have been identified as important genetic variations leading to CAKUT, whereas most CAKUT-associated CNVs cannot be attributed to a specific pathogenic gene. Here we construct coexpression networks involving long noncoding RNAs (lncRNAs) within these CNVs (CNV-lncRNAs) using human kidney developmental transcriptomic data. The results show that CNV-lncRNAs encompassed in recurrent CAKUT associated CNVs have highly correlated expression with CAKUT genes in the developing kidneys. The regulatory effects of two hub CNV-lncRNAs (HSALNG0134318 in 22q11.2 and HSALNG0115943 in 17q12) in the module most significantly enriched in known CAKUT genes (CAKUT_sig1, P = 1.150 × 10-6) are validated experimentally. Our results indicate that the reduction of CNV-lncRNAs can downregulate CAKUT genes as predicted by our computational analyses. Furthermore, knockdown of HSALNG0134318 would downregulate HSALNG0115943 and affect kidney development related pathways. The results also indicate that the CAKUT_sig1 module has function significance involving multi-organ development. Overall, our findings suggest that CNV-lncRNAs play roles in regulating CAKUT genes, and the etiologies of CAKUT-associated CNVs should take account of effects on the noncoding genome.
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Affiliation(s)
- Yibo Lu
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Yiyang Zhou
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Jing Guo
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Ming Qi
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Yuwan Lin
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Xingyu Zhang
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Ying Xiang
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China.
- Shanghai Key Laboratory of Clinical Molecular Diagnostics for Pediatrics, Shanghai, 200127, China.
| | - Qihua Fu
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China.
- Shanghai Key Laboratory of Clinical Molecular Diagnostics for Pediatrics, Shanghai, 200127, China.
| | - Bo Wang
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China.
- Shanghai Key Laboratory of Clinical Molecular Diagnostics for Pediatrics, Shanghai, 200127, China.
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22
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Tran H, Le L, Singh BN, Kramer J, Steward R. Tet Controls Axon Guidance in Early Brain Development through Glutamatergic Signaling. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.02.539069. [PMID: 37398066 PMCID: PMC10312521 DOI: 10.1101/2023.05.02.539069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Mutations in human TET proteins have been found in individuals with neurodevelopmental disorders. Here we report a new function of Tet in regulating Drosophila early brain development. We found that mutation in the Tet DNA-binding domain ( Tet AXXC ) resulted in axon guidance defects in the mushroom body (MB). Tet is required in early brain development during the outgrowth of MB β axons. Transcriptomic study shows that glutamine synthetase 2 (Gs2), a key enzyme in glutamatergic signaling, is significantly downregulated in the Tet AXXC mutant brains. CRISPR/Cas9 mutagenesis or RNAi knockdown of Gs2 recapitulates the Tet AXXC mutant phenotype. Surprisingly, Tet and Gs2 act in the insulin-producing cells (IPCs) to control MB axon guidance, and overexpression of Gs2 in these cells rescues the axon guidance defects of Tet AXXC . Treating Tet AXXC with the metabotropic glutamate receptor antagonist MPEP can rescue while treating with glutamate enhances the phenotype confirming Tet function in regulating glutamatergic signaling. Tet AXXC and the Drosophila homolog of Fragile X Messenger Ribonucleoprotein protein mutant ( Fmr1 3 ) have similar axon guidance defects and reduction in Gs2 mRNA levels. Interestingly, overexpression of Gs2 in the IPCs also rescues the Fmr1 3 phenotype, suggesting functional overlapping of the two genes. Our studies provide the first evidence that Tet can control the guidance of axons in the developing brain by modulating glutamatergic signaling and the function is mediated by its DNA-binding domain.
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23
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Streubel JMS, Pereira G. Control of centrosome distal appendages assembly and disassembly. Cells Dev 2023; 174:203839. [PMID: 37062431 DOI: 10.1016/j.cdev.2023.203839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 03/29/2023] [Accepted: 04/08/2023] [Indexed: 04/18/2023]
Abstract
Centrosomes are microtubule organizing centers involved in chromosome segregation, spindle orientation, cell motility and cilia formation. In recent years, they have also emerged as key modulators of asymmetric cell division. Centrosomes are composed of two centrioles that initiate duplication in S phase. The conservative nature of centriole duplication means that the two centrioles of a G1 cell are of different ages. They are also structurally different as only the older centriole carry appendages, an assembly of a subset of proteins primarily required for cilia formation. In a growing tissue, the non-motile, primary cilium acts as a mechano- and sensory organelle that influences cell behavior via modulation of signaling pathways. Here, we discuss the most recent findings about distal appendage composition and function, as well as cell cycle-specific regulation and their implications in various diseases.
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Affiliation(s)
- Johanna M S Streubel
- Centre for Organismal Studies (COS), University of Heidelberg, Heidelberg, Germany; German Cancer Research Centre (DKFZ), DKFZ-ZMBH Alliance, Heidelberg, Germany; Centre for Molecular Biology (ZMBH), University of Heidelberg, Heidelberg, Germany
| | - Gislene Pereira
- Centre for Organismal Studies (COS), University of Heidelberg, Heidelberg, Germany; German Cancer Research Centre (DKFZ), DKFZ-ZMBH Alliance, Heidelberg, Germany; Centre for Molecular Biology (ZMBH), University of Heidelberg, Heidelberg, Germany.
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24
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Yahia A, Hamed AAA, Mohamed IN, Elseed MA, Salih MA, El-Sadig SM, Siddig HE, Nasreldien AEM, Abdullah MA, Elzubair M, Omer FY, Bakhiet AM, Abubaker R, Abozar F, Adil R, Emad S, Musallam MA, Eltazi IZM, Omer Z, Malik H, Mohamed MOE, Elhassan AA, Mohamed EOE, Ahmed AKMA, Ahmed EAA, Eltaraifee E, Hussein BK, Abd Allah ASI, Salah L, Nimir M, Tag Elseed OM, Elhassan TEA, Elbashier A, Alfadul ESA, Fadul M, Ali KF, Taha SOMA, Bushara EE, Amin M, Koko M, Ibrahim ME, Ahmed AE, Elsayed LEO, Stevanin G. Clinical phenotyping and genetic diagnosis of a large cohort of Sudanese families with hereditary spinocerebellar degenerations. Eur J Hum Genet 2023:10.1038/s41431-023-01344-6. [PMID: 37012327 DOI: 10.1038/s41431-023-01344-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 02/12/2023] [Accepted: 03/13/2023] [Indexed: 04/05/2023] Open
Abstract
Hereditary spinocerebellar degenerations (SCDs) is an umbrella term that covers a group of monogenic conditions that share common pathogenic mechanisms and include hereditary spastic paraplegia (HSP), cerebellar ataxia, and spinocerebellar ataxia. They are often complicated with axonal neuropathy and/or intellectual impairment and overlap with many neurological conditions, including neurodevelopmental disorders. More than 200 genes and loci inherited through all modes of Mendelian inheritance are known. Autosomal recessive inheritance predominates in consanguineous communities; however, autosomal dominant and X-linked inheritance can also occur. Sudan is inhabited by genetically diverse populations, yet it has high consanguinity rates. We used next-generation sequencing, genotyping, bioinformatics analysis, and candidate gene approaches to study 90 affected patients from 38 unrelated Sudanese families segregating multiple forms of SCDs. The age-at-onset in our cohort ranged from birth to 35 years; however, most patients manifested childhood-onset diseases (the mean and median ages at onset were 7.5 and 3 years, respectively). We reached the genetic diagnosis in 63% and possibly up to 73% of the studied families when considering variants of unknown significance. Combining the present data with our previous analysis of 25 Sudanese HSP families, the success rate reached 52-59% (31-35/59 families). In this article we report candidate variants in genes previously known to be associated with SCDs or other phenotypically related monogenic disorders. We also highlight the genetic and clinical heterogeneity of SCDs in Sudan, as we did not identify a major causative gene in our cohort, and the potential for discovering novel SCD genes in this population.
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Affiliation(s)
- Ashraf Yahia
- Faculty of Medicine, University of Khartoum, Khartoum, Sudan.
- Paris Brain Institute - ICM, CNRS UMR7225, INSERM 1127, Sorbonne University, F-75000, Paris, France.
- Center of Neurodevelopmental Disorders (KIND), Centre for Psychiatry Research, Department of Women's and Children's Health, Karolinska Institutet and Stockholm Health Care Services, Region Stockholm, Stockholm, Sweden.
- Astrid Lindgren Children's Hospital, Karolinska University Hospital, Solna, Sweden.
| | - Ahlam A A Hamed
- Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - Inaam N Mohamed
- Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - Maha A Elseed
- Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - Mustafa A Salih
- Division of Pediatric Neurology, Department of Pediatrics, College of Medicine, King Saud University, Riyadh, Saudi Arabia
- College of Medicine, AlMughtaribeen University, Khartoum, Sudan
| | | | | | - Ali Elsir Musa Nasreldien
- Pediatric Neurology Department, Red Cross Memorial Children Hospital (RCWMCH), University of Cape Town (UCT), Cape Town, South Africa
| | | | - Maha Elzubair
- Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | | | | | - Rayan Abubaker
- Sudanese Neurogenetics Research group, Faculty of Medicine, University of Khartoum, Khartoum, Sudan
- National University Biomedical Research Institute, National University, Khartoum, Sudan
| | - Fatima Abozar
- Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - Rawaa Adil
- Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - Sara Emad
- Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | | | - Isra Z M Eltazi
- Neurology Department, Hamad Medical Corporation, Doha, Qatar
| | - Zulfa Omer
- Department of Hematology and Medical Oncology, University of Cincinnati Medical Center, Ohio, USA
| | - Hiba Malik
- Department of Neurology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
| | - Mayada O E Mohamed
- Division of Emergency Medicine, Sudan Medical Specialization Board, Khartoum, Sudan
| | - Ali A Elhassan
- Sudan Neuroscience Projects, University of Khartoum, Khartoum, Sudan
| | | | - Ahmed K M A Ahmed
- Department of Molecular Neuroscience, Graduate school of Medicine, Osaka University, 2-2, Yamadaoka, Suita, Osaka, 565-0871, Japan
- WPI Immunology Frontier Research Center, Osaka University, 3-1, Yamadaoka, Suita, Osaka, 565-0871, Japan
| | | | | | - Bidour K Hussein
- Institute of Endemic Diseases, University of Khartoum, Khartoum, Sudan
| | | | - Lina Salah
- Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - Mohamed Nimir
- Department of Pathology, University Hospitals Coventry and Warwickshire NHS Trust, Coventry, UK
- Warwick Medical School, University of Warwick, Coventry, UK
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK
| | | | | | | | | | - Moneeb Fadul
- Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - Khalil F Ali
- Department of Cardiology, Royal Derby Hospital, Derby, UK
| | | | | | - Mutaz Amin
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Al-Neelain University, Khartoum, Sudan
| | - Mahmoud Koko
- Institute of Endemic Diseases, University of Khartoum, Khartoum, Sudan
| | | | - Ammar E Ahmed
- Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - Liena E O Elsayed
- Department of Basic Sciences, College of Medicine, Princess Nourah bint Abdulrahman University, Riyadh, P.O.Box 84428, Riyadh, 11671, Saudi Arabia
| | - Giovanni Stevanin
- Paris Brain Institute - ICM, CNRS UMR7225, INSERM 1127, Sorbonne University, F-75000, Paris, France.
- Univ. Bordeaux, CNRS, INCIA, UMR 5287, F-33000, Bordeaux, France.
- EPHE, PSL Research university, CNRS, INCIA, UMR 5287, F-75000, Paris, France.
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25
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Rasool IG, Zahoor MY, Ahmed I, Iqbal M, Shafqat S, Anjum AA, Shehzad W. Description of novel variants in consanguineous Pakistani families affected with intellectual disability. Genes Genomics 2023; 45:457-465. [PMID: 35150401 DOI: 10.1007/s13258-022-01219-y] [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: 08/21/2021] [Accepted: 01/16/2022] [Indexed: 11/04/2022]
Abstract
BACKGROUND Intellectual disability (ID) is a neurodevelopmental condition, affecting 1-3% of the population. Genetic factors play a key role causing the limitation in intellectual functioning and adaptive behavior. The heterogeneity of ID makes it more difficult for genetic and clinical diagnosis. Mapping of variants through next generation DNA sequencing in consanguineous families would help to understand the molecular parthenogenesis of ID. OBJECTIVE The aim of this study was to describe the genetic variants of ID in consanguineous Pakistani families. METHODS We analyzed four unrelated consanguineous Pakistani families having an intellectual disability through whole exome sequencing (WES). Data was analyzed using different bioinformatics tools and software. RESULTS We mapped four novel variants in different ID genes. Each variant is found in different family, co-segregating with a recessive pattern of inheritance. The variants found are; c.1437delG:p.Asn480Thrfs*10, mapped in FKRP, c.2041 C>A:p.Leu681Met in HIRA, c.382 C>T:p.Arg128Cys in BDH1 and c.267+1G>A:p.? identified in TRAPPC6B. CONCLUSIONS These variants help in demonstration of status and molecular basis of intellectual disability in Pakistani population leading to provision of genetic counseling services and a contribution in disease variant database.
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Affiliation(s)
- Iqra Ghulam Rasool
- Molecular Biology and Biotechnology Section, Institute of Biochemistry and Biotechnology, University of Veterinary and Animal Sciences, Lahore, 54000, Pakistan
| | - Muhammad Yasir Zahoor
- Molecular Biology and Biotechnology Section, Institute of Biochemistry and Biotechnology, University of Veterinary and Animal Sciences, Lahore, 54000, Pakistan.
| | - Irfan Ahmed
- Molecular Biology and Biotechnology Section, Institute of Biochemistry and Biotechnology, University of Veterinary and Animal Sciences, Lahore, 54000, Pakistan
| | - Muhammad Iqbal
- Department of Biotechnology, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Shehla Shafqat
- Department of Biotechnology, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Aftab Ahmad Anjum
- Institute of Microbiology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Wasim Shehzad
- Molecular Biology and Biotechnology Section, Institute of Biochemistry and Biotechnology, University of Veterinary and Animal Sciences, Lahore, 54000, Pakistan
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26
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Zare Ashrafi F, Akhtarkhavari T, Fattahi Z, Asadnezhad M, Beheshtian M, Arzhangi S, Najmabadi H, Kahrizi K. Emerging Epidemiological Data on Rare Intellectual Disability Syndromes from Analyzing the Data of a Large Iranian Cohort. ARCHIVES OF IRANIAN MEDICINE 2023; 26:186-197. [PMID: 38301078 PMCID: PMC10685746 DOI: 10.34172/aim.2023.29] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Accepted: 02/25/2023] [Indexed: 02/03/2024]
Abstract
BACKGROUND Intellectual disability (ID) is a genetically heterogeneous condition, and so far, 1679 human genes have been identified for this phenotype. Countries with a high rate of parental consanguinity, such as Iran, provide an excellent opportunity to identify the remaining novel ID genes, especially those with an autosomal recessive (AR) mode of inheritance. This study aimed to investigate the most prevalent ID genes identified via next-generation sequencing (NGS) in a large ID cohort at the Genetics Research Center (GRC) of the University of Social Welfare and Rehabilitation Sciences. METHODS First, we surveyed the epidemiological data of 619 of 1295 families in our ID cohort, who referred to the Genetics Research Center from all over the country between 2004 and 2021 for genetic investigation via the NGS pipeline. We then compared our data with those of several prominent studies conducted in consanguineous countries. Data analysis, including cohort data extraction, categorization, and comparison, was performed using the R program version 4.1.2. RESULTS We categorized the most common ID genes that were mutated in more than two families into 17 categories. The most common syndromic ID in our cohort was AP4 deficiency syndrome, and the most common non-syndromic autosomal recessive intellectual disability (ARID) gene was ASPM. We identified two unrelated families for the 36 ID genes. We found 14 genes in common between our cohort and the Arab and Pakistani groups, of which three genes (AP4M1, AP4S1, and ADGRG1) were repeated more than once. CONCLUSION To date, there has been no comprehensive targeted NGS platform for the detection of ID genes in our country. Due to the large sample size of our study, our data may provide the initial step toward designing an indigenously targeted NGS platform for the diagnosis of ID, especially common ARID in our population.
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Affiliation(s)
- Farzane Zare Ashrafi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Tara Akhtarkhavari
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Zohreh Fattahi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Maryam Asadnezhad
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Maryam Beheshtian
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Sanaz Arzhangi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Hossein Najmabadi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Kimia Kahrizi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
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A Biallelic Truncating Variant in the TPR Domain of GEMIN5 Associated with Intellectual Disability and Cerebral Atrophy. Genes (Basel) 2023; 14:genes14030707. [PMID: 36980979 PMCID: PMC10048441 DOI: 10.3390/genes14030707] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 03/06/2023] [Accepted: 03/08/2023] [Indexed: 03/17/2023] Open
Abstract
GEMIN5 is a multifunctional RNA-binding protein required for the assembly of survival motor neurons. Several bi-allelic truncating and missense variants in this gene are reported to cause a neurodevelopmental disorder characterized by cerebellar atrophy, intellectual disability (ID), and motor dysfunction. Whole exome sequencing of a Pakistani consanguineous family with three brothers affected by ID, cerebral atrophy, mobility, and speech impairment revealed a novel homozygous 3bp-deletion NM_015465.5:c.3162_3164del that leads to the loss of NM_015465.5 (NP_056280.2):p. (Asp1054_Ala1055delinsGlu) amino acid in one of the α-helixes of the tetratricopeptide repeats of GEMIN5. In silico 3D representations of the GEMIN5 dimerization domain show that this variant likely affects the orientation of the downstream sidechains out of the helix axis, which would affect the packing with neighboring helices. The phenotype of all affected siblings overlaps well with previously reported patients, suggesting that NM_015465.5: c.3162_3164del (NP_056280.2):p. (Asp1054_Ala1055delinsGlu) is a novel GEMIN5 pathogenic variant. Overall, our data expands the molecular and clinical phenotype of the recently described neurodevelopmental disorder with cerebellar atrophy and motor dysfunction (NEDCAM) syndrome.
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28
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Shen J, Lin X, Dai F, Chen G, Lin H, Fang B, Liu H. Ubiquitin-specific peptidases: Players in bone metabolism. Cell Prolif 2023:e13444. [PMID: 36883930 PMCID: PMC10392067 DOI: 10.1111/cpr.13444] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 02/22/2023] [Accepted: 02/28/2023] [Indexed: 03/09/2023] Open
Abstract
Osteoporosis is an ageing-related disease, that has become a major public health problem and its pathogenesis has not yet been fully elucidated. Substantial evidence suggests a strong link between overall age-related disease progression and epigenetic modifications throughout the life cycle. As an important epigenetic modification, ubiquitination is extensively involved in various physiological processes, and its role in bone metabolism has attracted increasing attention. Ubiquitination can be reversed by deubiquitinases, which counteract protein ubiquitination degradation. As the largest and most structurally diverse cysteinase family of deubiquitinating enzymes, ubiquitin-specific proteases (USPs), comprising the largest and most structurally diverse cysteine kinase family of deubiquitinating enzymes, have been found to be important players in maintaining the balance between bone formation and resorption. The aim of this review is to explore recent findings highlighting the regulatory functions of USPs in bone metabolism and provide insight into the molecular mechanisms governing their actions during bone loss. An in-deep understanding of USPs-mediated regulation of bone formation and bone resorption will provide a scientific rationale for the discovery and development of novel USP-targeted therapeutic strategies for osteoporosis.
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Affiliation(s)
- Jianlin Shen
- Department of Orthopaedics, Affiliated Hospital of Putian University, Putian, China
| | - Xiaoning Lin
- Department of Orthopaedics, Affiliated Hospital of Putian University, Putian, China
| | - Feifei Dai
- School of Medicine, Putian Universtiy, Putian, China
| | - Guoli Chen
- Department of Orthopaedics, Affiliated Hospital of Putian University, Putian, China
| | - Haibin Lin
- Department of Orthopaedics, Affiliated Hospital of Putian University, Putian, China
| | - Bangjiang Fang
- Department of Emergency, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Institute of Emergency and Critical Care Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Huan Liu
- Department of Orthopaedics, Affiliated Hospital of Putian University, Putian, China
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29
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Genome-Wide Sequencing Modalities for Children with Unexplained Global Developmental Delay and Intellectual Disabilities—A Narrative Review. CHILDREN 2023; 10:children10030501. [PMID: 36980059 PMCID: PMC10047410 DOI: 10.3390/children10030501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 02/25/2023] [Accepted: 03/01/2023] [Indexed: 03/06/2023]
Abstract
Unexplained global developmental delay (GDD) and intellectual disabilities (ID) together affect nearly 2% of the pediatric population. Establishing an etiologic diagnosis is crucial for disease management, prognostic evaluation, and provision of physical and psychological support for both the patient and the family. Advancements in genome sequencing have allowed rapid accumulation of gene–disorder associations and have accelerated the search for an etiologic diagnosis for unexplained GDD/ID. We reviewed recent studies that utilized genome-wide analysis technologies, and we discussed their diagnostic yield, strengths, and limitations. Overall, exome sequencing (ES) and genome sequencing (GS) outperformed chromosomal microarrays and targeted panel sequencing. GS provides coverage for both ES and chromosomal microarray regions, providing the maximal diagnostic potential, and the cost of ES and reanalysis of ES-negative results is currently still lower than that of GS alone. Therefore, singleton or trio ES is the more cost-effective option for the initial investigation of individuals with GDD/ID in clinical practice compared to a staged approach or GS alone. Based on these updated evidence, we proposed an evaluation algorithm with ES as the first-tier evaluation for unexplained GDD/ID.
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Evaluation of Individuals with Non-Syndromic Global Developmental Delay and Intellectual Disability. CHILDREN 2023; 10:children10030414. [PMID: 36979972 PMCID: PMC10047567 DOI: 10.3390/children10030414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 02/11/2023] [Accepted: 02/16/2023] [Indexed: 02/24/2023]
Abstract
Global Developmental Delay (GDD) and Intellectual Disability (ID) are two of the most common presentations encountered by physicians taking care of children. GDD/ID is classified into non-syndromic GDD/ID, where GDD/ID is the sole evident clinical feature, or syndromic GDD/ID, where there are additional clinical features or co-morbidities present. Careful evaluation of children with GDD and ID, starting with detailed history followed by a thorough examination, remain the cornerstone for etiologic diagnosis. However, when initial history and examination fail to identify a probable underlying etiology, further genetic testing is warranted. In recent years, genetic testing has been shown to be the single most important diagnostic modality for clinicians evaluating children with non-syndromic GDD/ID. In this review, we discuss different genetic testing currently available, review common underlying copy-number variants and molecular pathways, explore the recent evidence and recommendations for genetic evaluation and discuss an approach to the diagnosis and management of children with non-syndromic GDD and ID.
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The exploration of genetic aetiology and diagnostic strategy for 321 Chinese individuals with intellectual disability. Clin Chim Acta 2023; 538:94-103. [PMID: 36368352 DOI: 10.1016/j.cca.2022.10.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/08/2022] [Accepted: 10/28/2022] [Indexed: 11/09/2022]
Abstract
BACKGROUND Intellectual disability is a heterogeneous neurodevelopmental disorder with complex genetic architectures. Different sequential methodologies are usually applied to identify the genetic aetiologies of ID patients. METHODS We collected 321 consecutive ID patients. All patients underwent karyotyping, while 293 and 164 cases further received copy number variation sequencing (CNV-seq) and whole-exome sequencing (WES). The updated WES technology can detect CNVs simultaneously. The diagnostic data from 137 patients who received WES and CNV-seq were used to define the approach that could be recommended as the first-tier test. RESULTS WES obtains the highest diagnostic yield of 50% (82/164), compared with karyotyping (7.79%, 25/321) and CNV-seq (19.80%, 58/293). Among the variants detected by WES, 66.67% (44/66) de novo and 57.58% (38/66) novel pathogenic/likely pathogenic (P/LP) variants were identified in patients with ID. Besides, 24 out of 25P/LP CNVs discovered by CNV-seq can also be accurately identified using WES in 137 patients who received WES and CNV-seq. Thus, genetic abnormalities found through karyotyping, CNV-seq, and WES can be completely detected by combined karyotyping and WES. CONCLUSIONS This study illustrates the genetic aberrations of a Chinese ID cohort and expands the mutation spectrum of ID-related genes. Compared with the conventional diagnostic strategy, a combination of karyotype analysis and WES could be recommended as the first-tier diagnostic strategy for ID patients.
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Wang J, Liu Y, Gao Y, Liang J, Wang B, Xia Q, Xie Y, Shan F, Xia Q. Comprehensive bioinformatics analysis and molecular validation of lncRNAs-mediated ceRNAs network in schizophrenia. Life Sci 2022; 312:121205. [PMID: 36410410 DOI: 10.1016/j.lfs.2022.121205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 10/31/2022] [Accepted: 11/14/2022] [Indexed: 11/19/2022]
Abstract
AIMS The present study aimed to investigate how Schizophrenia (SCZ)-specific long non-coding RNAs (lncRNAs) served as competing endogenous RNAs (ceRNAs) to modulate the biological functions and pathways involved in the pathogenesis of SCZ. MAIN METHODS Microarray dataset (GSE54913) was obtained from Gene Expression Omnibus (GEO) database. Differently expressed (DE) lncRNAs and mRNAs were identified by "limma" package. The binding miRNAs of lncRNAs and target mRNAs of shared miRNAs were predicted by miRcode, miRDB, miRTarbase and targetscan databases. Following the ceRNAs theory, interaction network was established and visualized with the cytoscape. Functional enrichment analysis uncovered the concentrated functions and signaling pathways that may be associated with SCZ progression. Protein-protein interaction (PPI) analysis was utilized to determine hub genes. Quantitative real-time PCR (qRT-PCR) and receiver operating characteristic curve (ROC) were performed to evaluate the expression and diagnostic value of ceRNAs members, respectively. KEY FINDINGS DElncRNAs and DEmRNAs were initially screened from GSE54913 to construct the SCZ-related ceRNAs network with 42 nodes and 53 edges. Functional enrichment analysis revealed that ceRNAs members appeared to be highly correlated with transcription factor activation, cell replication and tumor-related pathways. Once validated, a significant ceRNAs subnetwork was proposed as being implicated in the pathogenesis of SCZ. ROC analysis indicated that SCZ-related ceRNAs members may be sensitive diagnostic biomarkers for SCZ. SIGNIFICANCE The significant SCZ-related ceRNAs subnetworks (lncRNA-C2orf48A/hsa-miR-20b-5p,-17-5p/KIF23, FOXJ2) may represent promising predictive and diagnostic biomarkers and provide novel insights into the mechanism by which lncRNAs act as microRNA sponges and contribute to the pathogenesis of SCZ.
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Affiliation(s)
- Jiequan Wang
- Department of Pharmacy, Affiliated Psychological Hospital of Anhui Medical University, Hefei, Anhui 230000, China; Department of Pharmacy, Anhui Mental Health Center, Hefei, Anhui 230000, China; Department of Pharmacy, Hefei Fourth People's Hospital, Hefei, Anhui 230000, China
| | - Yaru Liu
- Department of Pharmacy, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, China; The Grade 3 Pharmaceutical Chemistry Laboratory of State Administration of Traditional Chinese Medicine, Hefei, Anhui 230022, China
| | - Yejun Gao
- Anhui Province Key Laboratory of Major Autoimmune Diseases, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, Anhui 230032, China
| | - Jun Liang
- Department of Pharmacy, Affiliated Psychological Hospital of Anhui Medical University, Hefei, Anhui 230000, China; Department of Pharmacy, Anhui Mental Health Center, Hefei, Anhui 230000, China; Department of Pharmacy, Hefei Fourth People's Hospital, Hefei, Anhui 230000, China
| | - Baoshi Wang
- Department of Pharmacy, Affiliated Psychological Hospital of Anhui Medical University, Hefei, Anhui 230000, China; Department of Pharmacy, Anhui Mental Health Center, Hefei, Anhui 230000, China; Department of Pharmacy, Hefei Fourth People's Hospital, Hefei, Anhui 230000, China
| | - Quan Xia
- Department of Pharmacy, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, China; The Grade 3 Pharmaceutical Chemistry Laboratory of State Administration of Traditional Chinese Medicine, Hefei, Anhui 230022, China
| | - Yawen Xie
- Department of Pharmacy, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, China; The Grade 3 Pharmaceutical Chemistry Laboratory of State Administration of Traditional Chinese Medicine, Hefei, Anhui 230022, China; Anhui Province Key Laboratory of Major Autoimmune Diseases, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, Anhui 230032, China
| | - Feng Shan
- Department of Pharmacy, Affiliated Psychological Hospital of Anhui Medical University, Hefei, Anhui 230000, China; Department of Pharmacy, Anhui Mental Health Center, Hefei, Anhui 230000, China; Department of Pharmacy, Hefei Fourth People's Hospital, Hefei, Anhui 230000, China
| | - Qingrong Xia
- Department of Pharmacy, Affiliated Psychological Hospital of Anhui Medical University, Hefei, Anhui 230000, China; Department of Pharmacy, Anhui Mental Health Center, Hefei, Anhui 230000, China; Department of Pharmacy, Hefei Fourth People's Hospital, Hefei, Anhui 230000, China.
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Chhetri G, Ke Y, Wang P, Usman M, Li Y, Sapp E, Wang J, Ghosh A, Islam MA, Wang X, Boudi A, DiFiglia M, Li X. Impaired XK recycling for importing manganese underlies striatal vulnerability in Huntington's disease. J Cell Biol 2022; 221:213461. [PMID: 36099524 PMCID: PMC9475296 DOI: 10.1083/jcb.202112073] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 06/15/2022] [Accepted: 07/29/2022] [Indexed: 02/08/2023] Open
Abstract
Mutant huntingtin, which causes Huntington's disease (HD), is ubiquitously expressed but induces preferential loss of striatal neurons by unclear mechanisms. Rab11 dysfunction mediates homeostatic disturbance of HD neurons. Here, we report that Rab11 dysfunction also underscores the striatal vulnerability in HD. We profiled the proteome of Rab11-positive endosomes of HD-vulnerable striatal cells to look for protein(s) linking Rab11 dysfunction to striatal vulnerability in HD and found XK, which triggers the selective death of striatal neurons in McLeod syndrome. XK was trafficked together with Rab11 and was diminished on the surface of immortalized HD striatal cells and striatal neurons in HD mouse brains. We found that XK participated in transporting manganese, an essential trace metal depleted in HD brains. Introducing dominantly active Rab11 into HD striatal cells improved XK dynamics and increased manganese accumulation in an XK-dependent manner. Our study suggests that impaired Rab11-based recycling of XK onto cell surfaces for importing manganese is a driver of striatal dysfunction in Huntington's disease.
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Affiliation(s)
- Gaurav Chhetri
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Yuting Ke
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China.,Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA
| | - Ping Wang
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA.,Department of Neurology, The Second Hospital, Cheeloo College of Medicine, Shandong University, Ji'nan, China
| | - Muhammad Usman
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Yan Li
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Ellen Sapp
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA
| | - Jing Wang
- Instrumental Analysis Center, Shanghai Jiao Tong University, Shanghai, China
| | - Arabinda Ghosh
- Department of Botany, Microbiology Division, Gauhati University, Guwahati, Assam, India
| | - Md Ariful Islam
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaolong Wang
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Adel Boudi
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA
| | - Marian DiFiglia
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA
| | - Xueyi Li
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China.,Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA
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Dong X, Liang Z, Zhang J, Zhang Q, Xu Y, Zhang Z, Zhang L, Zhang B, Zhao Y. Trappc1 deficiency impairs thymic epithelial cell development by breaking endoplasmic reticulum homeostasis. Eur J Immunol 2022; 52:1789-1804. [PMID: 35908180 DOI: 10.1002/eji.202249915] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 06/28/2022] [Accepted: 07/26/2022] [Indexed: 11/05/2022]
Abstract
Thymic epithelial cells (TECs) are important for T cell development and immune tolerance establishment. Although comprehensive molecular regulation of TEC development has been studied, the role of transport protein particle complexes (Trappcs) in TECs is not clear. Using TEC-specific homozygous or heterozygous Trappc1 deleted mice model, we found that Trappc1 deficiency caused severe thymus atrophy with decreased cell number and blocked maturation of TECs. Mice with a TEC-specific Trappc1 deletion show poor thymic T cell output and have a greater percentage of activated/memory T cells, suffered from spontaneous autoimmune disorders. Our RNA-seq and molecular studies indicated that the decreased endoplasmic reticulum (ER) and Golgi apparatus, enhanced unfolded protein response (UPR) and subsequent Atf4-CHOP-mediated apoptosis, and reactive oxygen species (ROS)-mediated ferroptosis coordinately contributed to the reduction of Trappc1-deleted TECs. Additionally, reduced Aire+ mTECs accompanied by the decreased expression of Irf4, Irf8, and Tbx21 in Trappc1 deficiency mTECs, may further coordinately block the tissue-restricted antigen expression. In this study, we reveal that Trappc1 plays an indispensable role in TEC development and maturation and provide evidence for the importance of inter-organelle traffic and ER homeostasis in TEC development. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Xue Dong
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences.,University of Chinese Academy of Sciences
| | - Zhanfeng Liang
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences.,University of Chinese Academy of Sciences.,Beijing Institute for Stem Cell and Regeneration
| | - Jiayu Zhang
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences.,University of Chinese Academy of Sciences
| | - Qian Zhang
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences.,University of Chinese Academy of Sciences
| | - Yanan Xu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences.,University of Chinese Academy of Sciences
| | - Zhaoqi Zhang
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences.,University of Chinese Academy of Sciences
| | - Lianfeng Zhang
- Key Laboratory of Human Diseases and Comparative Medicine, Ministry of Health, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences
| | - Baojun Zhang
- Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University
| | - Yong Zhao
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences.,University of Chinese Academy of Sciences.,Beijing Institute for Stem Cell and Regeneration
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Cai T, Huang J, Ma X, Hu S, Zhu L, Zhu J, Feng Z. Case Report: Identification of Two Variants of ALG13 in Families With or Without Seizure and Binocular Strabismus: Phenotypic Spectrum Analysis. Front Genet 2022; 13:892940. [PMID: 35899201 PMCID: PMC9310169 DOI: 10.3389/fgene.2022.892940] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 06/07/2022] [Indexed: 11/28/2022] Open
Abstract
Background: Genetic causes in most affected children with intellectual disability and/or development delay remain unknown. Methods: To identify potential variants responsible for these disorders, we recruited 161 affected families and performed whole-exome sequencing and associated bioinformatics analysis. Results: In the present study, we report the identification of variants in the ALG13 gene in two of the families. In family 1, a known pathogenic missense variant (c.23T > C; p.V8A) of ALG13 was identified in a boy and his mother. In family 2, a novel missense variant (c.862C > G; p.L288V) of the same gene was identified in the affected boy and his phenotypically normal mother. Genotype-phenotype correlation analysis by comparing reported 28 different variants (HGMD) showed that three major phenotypes, including various seizures/epilepsy, intellectual disability, and development delay (such as growth, speech, motor, etc.), are present in most affected individuals. However, other phenotypes, such as strabismus and absence of seizure in our second patient, are not reported if any, which may represent a unique case of X-linked recessive nonsyndromic disorder caused by a mutation in ALG13. Conclusion: We identified two missense variants in ALG13 in a cohort of 161 families with affected individuals diagnosed as intellectual disability and/or development delay. A novel c.862C > G mutation may represent a case of X-linked recessive.
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Affiliation(s)
- Tao Cai
- Senior Department of Pediatrics, the Seventh Medical Center of PLA General Hospital, Beijing, China,Experimental Medicine Section, National Institutes of Health/National Institute of Dental and Craniofacial Research, Bethesda, MD, United States,*Correspondence: Tao Cai, ; Zhichun Feng,
| | - Jieting Huang
- Senior Department of Pediatrics, the Seventh Medical Center of PLA General Hospital, Beijing, China,Beijing Key Laboratory of Pediatric Organ Failure, Beijing, China
| | - Xiuwei Ma
- Senior Department of Pediatrics, the Seventh Medical Center of PLA General Hospital, Beijing, China
| | - Siqi Hu
- Senior Department of Pediatrics, the Seventh Medical Center of PLA General Hospital, Beijing, China,The National Engineering Laboratory for Birth Defects Prevention and Control of Key Technology, Beijing, China
| | - Lina Zhu
- Senior Department of Pediatrics, the Seventh Medical Center of PLA General Hospital, Beijing, China
| | - Jinwen Zhu
- Angen Gene Medicine Technology, Beijing, China
| | - Zhichun Feng
- Senior Department of Pediatrics, the Seventh Medical Center of PLA General Hospital, Beijing, China,Beijing Key Laboratory of Pediatric Organ Failure, Beijing, China,The National Engineering Laboratory for Birth Defects Prevention and Control of Key Technology, Beijing, China,*Correspondence: Tao Cai, ; Zhichun Feng,
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Sánchez-Luquez KY, Carpena MX, Karam SM, Tovo-Rodrigues L. The contribution of whole-exome sequencing to intellectual disability diagnosis and knowledge of underlying molecular mechanisms: A systematic review and meta-analysis. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2022; 790:108428. [PMID: 35905832 DOI: 10.1016/j.mrrev.2022.108428] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 07/21/2022] [Accepted: 07/23/2022] [Indexed: 01/01/2023]
Abstract
Whole-exome sequencing (WES) is useful for molecular diagnosis, family genetic counseling, and prognosis of intellectual disability (ID). However, ID molecular diagnosis ascertainment based on WES is highly dependent on de novo mutations (DNMs) and variants of uncertain significance (VUS). The quantification of DNM frequency in ID molecular diagnosis ascertainment and the biological mechanisms common to genes with VUS may provide objective information about WES use in ID diagnosis and etiology. We aimed to investigate and estimate the rate of ID molecular diagnostic assessment by WES, quantify the contribution of DNMs to this rate, and biologically and functionally characterize the genes whose mutations were identified through WES. A PubMed/Medline, Web of Science, Scopus, Science Direct, BIREME, and PsycINFO systematic review and meta-analysis was performed, including studies published between 2010 and 2022. Thirty-seven articles with data on ID molecular diagnostic yield using the WES approach were included in the review. WES testing accounted for an overall diagnostic rate of 42% (Confidence interval (CI): 35-50%), while the estimate restricted to DNMs was 11% (CI: 6-18%). Genetic information on mutations and genes was extracted and split into two groups: (1) genes whose mutation was used for positive molecular diagnosis, and (2) genes whose mutation led to uncertain molecular diagnosis. After functional enrichment analysis, in addition to their expected roles in neurodevelopment, genes from the first group were enriched in epigenetic regulatory mechanisms, immune system regulation, and circadian rhythm control. Genes from uncertain diagnosis cases were enriched in the renin angiotensin pathway. Taken together, our results support WES as an important approach to the molecular diagnosis of ID. The results also indicated relevant pathways that may underlie the pathogenesis of ID with the renin-angiotensin pathway being suggested to be a potential pathway underlying the pathogenesis of ID.
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Affiliation(s)
| | - Marina Xavier Carpena
- Postgraduate Program in Epidemiology, Universidade Federal de Pelotas, Pelotas, Brazil.
| | - Simone M Karam
- Postgraduate Program in Public Health, Universidade Federal do Rio Grande, Rio Grande, Brazil.
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Covaceuszach S, Peche LY, Konarev PV, Grdadolnik J, Cattaneo A, Lamba D. Untangling the Conformational Plasticity of V66M Human proBDNF Polymorphism as a Modifier of Psychiatric Disorder Susceptibility. Int J Mol Sci 2022; 23:ijms23126596. [PMID: 35743044 PMCID: PMC9224406 DOI: 10.3390/ijms23126596] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 06/10/2022] [Accepted: 06/11/2022] [Indexed: 01/27/2023] Open
Abstract
The human genetic variant BDNF (V66M) represents the first example of neurotrophin family member that has been linked to psychiatric disorders. In order to elucidate structural differences that account for the effects in cognitive function, this hproBDNF polymorph was expressed, refolded, purified, and compared directly to the WT variant for the first time for differences in their 3D structures by DSF, limited proteolysis, FT-IR, and SAXS measurements in solution. Our complementary studies revealed a deep impact of V66M polymorphism on hproBDNF conformations in solution. Although the mean conformation in solution appears to be more compact in the V66M variant, overall, we demonstrated a large increase in flexibility in solution upon V66M mutation. Thus, considering that plasticity in IDR is crucial for protein function, the observed alterations may be related to the functional alterations in hproBDNF binding to its receptors p75NTR, sortilin, HAP1, and SorCS2. These effects can provoke altered intracellular neuronal trafficking and/or affect proBDNF physiological functions, leading to many brain-associated diseases and conditions such as cognitive impairment and anxiety. The structural alterations highlighted in the present study may pave the way to the development of drug discovery strategies to provide greater therapeutic responses and of novel pharmacologic strategy in human populations with this common polymorphism, ultimately guiding personalized medicine for neuropsychiatric disorders.
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Affiliation(s)
- Sonia Covaceuszach
- Istituto di Cristallografia, Consiglio Nazionale delle Ricerche, 34149 Trieste, Italy;
- Correspondence: (S.C.); (D.L.)
| | - Leticia Yamila Peche
- Istituto di Cristallografia, Consiglio Nazionale delle Ricerche, 34149 Trieste, Italy;
| | - Petr Valeryevich Konarev
- A.V. Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics” of Russian Academy of Sciences, 119333 Moscow, Russia;
| | - Joze Grdadolnik
- Laboratory for Molecular Structural Dynamics, Theory Department, National Institute of Chemistry, Hajdrihova 19, 1001 Ljubljana, Slovenia;
| | - Antonino Cattaneo
- European Brain Research Institute, 00161 Roma, Italy;
- Scuola Normale Superiore, 56126 Pisa, Italy
| | - Doriano Lamba
- Istituto di Cristallografia, Consiglio Nazionale delle Ricerche, 34149 Trieste, Italy;
- Consorzio Interuniversitario “Istituto Nazionale Biostrutture e Biosistemi”, 00136 Roma, Italy
- Correspondence: (S.C.); (D.L.)
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38
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Heseding HM, Jahn K, Eberlein CK, Wieting J, Maier HB, Proskynitopoulos PJ, Glahn A, Bleich S, Frieling H, Deest M. Distinct promoter regions of the oxytocin receptor gene are hypomethylated in Prader-Willi syndrome and in Prader-Willi syndrome associated psychosis. Transl Psychiatry 2022; 12:246. [PMID: 35688807 PMCID: PMC9187685 DOI: 10.1038/s41398-022-02014-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 05/23/2022] [Accepted: 05/30/2022] [Indexed: 11/12/2022] Open
Abstract
Prader-Willi syndrome (PWS) is a rare neurodevelopmental disorder caused by a loss of usually paternally expressed, maternally imprinted genes located on chromosome 15q11-q13. Individuals with PWS display a specific behavioral phenotype and have a higher susceptibility than the general population for certain psychiatric conditions, especially psychosis. An impairment of the oxytocin system has been described in Prader-Willi syndrome, but has not yet been investigated in detail on the epigenetic level. Recent studies have pointed out altered methylation patterns of the oxytocin receptor gene (OXTR) in various psychiatric disorders, including psychosis. In this study, we investigated methylation rates of CpG dinucleotides in the promoter region of the oxytocin receptor gene via bisulfite-sequencing using DNA extracted from peripheral blood samples of 31 individuals with PWS and 14 controls matched for age, sex, and BMI. Individuals with PWS show significantly lower methylation in the intron 1 region of the OXTR than neurotypical controls (p = 0.012). Furthermore, male PWS subjects with psychosis show significantly lower methylation of the OXTR exon 1 region than those without psychosis (p = 0.002). Transcription factor binding site analysis revealed E2F1 as a transcription factor potentially binding to the exon 1 region. E2F1 is physiologically regulated by Necdin, an anti-apoptotic protein whose corresponding gene is located within the PWS locus. This study provides evidence of a disruption of the Oxytocin system on an epigenetic level in PWS in general and in individuals with PWS and psychosis.
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Affiliation(s)
- Hannah M. Heseding
- grid.10423.340000 0000 9529 9877Department of Psychiatry, Social Psychiatry and Psychotherapy, Hannover Medical School, Hannover, Germany
| | - Kirsten Jahn
- grid.10423.340000 0000 9529 9877Department of Psychiatry, Social Psychiatry and Psychotherapy, Hannover Medical School, Hannover, Germany
| | - Christian K. Eberlein
- grid.10423.340000 0000 9529 9877Department of Psychiatry, Social Psychiatry and Psychotherapy, Hannover Medical School, Hannover, Germany
| | - Jelte Wieting
- grid.10423.340000 0000 9529 9877Department of Psychiatry, Social Psychiatry and Psychotherapy, Hannover Medical School, Hannover, Germany
| | - Hannah B. Maier
- grid.10423.340000 0000 9529 9877Department of Psychiatry, Social Psychiatry and Psychotherapy, Hannover Medical School, Hannover, Germany
| | - Phileas J. Proskynitopoulos
- grid.10423.340000 0000 9529 9877Department of Psychiatry, Social Psychiatry and Psychotherapy, Hannover Medical School, Hannover, Germany
| | - Alexander Glahn
- grid.10423.340000 0000 9529 9877Department of Psychiatry, Social Psychiatry and Psychotherapy, Hannover Medical School, Hannover, Germany
| | - Stefan Bleich
- grid.10423.340000 0000 9529 9877Department of Psychiatry, Social Psychiatry and Psychotherapy, Hannover Medical School, Hannover, Germany
| | - Helge Frieling
- grid.10423.340000 0000 9529 9877Department of Psychiatry, Social Psychiatry and Psychotherapy, Hannover Medical School, Hannover, Germany
| | - Maximilian Deest
- Department of Psychiatry, Social Psychiatry and Psychotherapy, Hannover Medical School, Hannover, Germany.
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Bauer G, Buchert R, Haack TB, Harting I, Gutschalk A. CCDC82 frameshift mutation associated with intellectual disability, spastic paraparesis, and dysmorphic features. Clin Genet 2022; 102:80-81. [PMID: 35373332 DOI: 10.1111/cge.14135] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 03/23/2022] [Accepted: 03/24/2022] [Indexed: 11/29/2022]
Affiliation(s)
- Gregor Bauer
- Department of Neurology, University of Heidelberg, Heidelberg, Germany
| | - Rebecca Buchert
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Tobias B Haack
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Inga Harting
- Department of Neuroradiology, University of Heidelberg, Heidelberg, Germany
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40
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PIDD1 in cell cycle control, sterile inflammation and cell death. Biochem Soc Trans 2022; 50:813-824. [PMID: 35343572 PMCID: PMC9162469 DOI: 10.1042/bst20211186] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 03/06/2022] [Accepted: 03/08/2022] [Indexed: 02/06/2023]
Abstract
The death fold domain-containing protein PIDD1 has recently attracted renewed attention as a regulator of the orphan cell death-related protease, Caspase-2. Caspase-2 can activate p53 to promote cell cycle arrest in response to centrosome aberrations, and its activation requires formation of the PIDDosome multi-protein complex containing multimers of PIDD1 and the adapter RAIDD/CRADD at its core. However, PIDD1 appears to be able to engage with multiple client proteins to promote an even broader range of biological responses, such as NF-κB activation, translesion DNA synthesis or cell death. PIDD1 shows features of inteins, a class of self-cleaving proteins, to create different polypeptides from a common precursor protein that allow it to serve these diverse functions. This review summarizes structural information and molecular features as well as recent experimental advances that highlight the potential pathophysiological roles of this unique death fold protein to highlight its drug-target potential.
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41
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Pastore SF, Ko SY, Frankland PW, Hamel PA, Vincent JB. PTCHD1: Identification and Neurodevelopmental Contributions of an Autism Spectrum Disorder and Intellectual Disability Susceptibility Gene. Genes (Basel) 2022; 13:527. [PMID: 35328080 PMCID: PMC8953913 DOI: 10.3390/genes13030527] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 03/01/2022] [Accepted: 03/03/2022] [Indexed: 11/24/2022] Open
Abstract
Over the last one and a half decades, copy number variation and whole-genome sequencing studies have illuminated the considerable genetic heterogeneity that underlies the etiologies of autism spectrum disorder (ASD) and intellectual disability (ID). These investigations support the idea that ASD may result from complex interactions between susceptibility-related genetic variants (single nucleotide variants or copy number variants) and the environment. This review outlines the identification and neurobiological characterization of two such genes located in Xp22.11, Patched domain-containing 1 (PTCHD1), and its antisense lncRNA PTCHD1-AS. Animal models of Ptchd1 disruption have recapitulated a subset of clinical symptoms related to ASD as well as to ID. Furthermore, these Ptchd1 mouse knockout studies implicate the expression of Ptchd1 in both the thalamic and the hippocampal brain regions as being crucial for proper neurodevelopment and cognitive function. Altered kynurenine metabolic signalling has been postulated as a disease mechanism in one of these animal studies. Additionally, ASD patient-derived induced pluripotent stem cells (iPSCs) carrying a copy number loss impacting the antisense non-coding RNA PTCHD1-AS have been used to generate 2D neuronal cultures. While copy number loss of PTCHD1-AS does not affect the transcription of PTCHD1, the neurons exhibit diminished miniature excitatory postsynaptic current frequency, supporting its role in ASD etiology. A more thorough understanding of risk factor genes, such as PTCHD1 and PTCHD1-AS, will help to clarify the intricate genetic and biological mechanisms that underlie ASD and ID, providing a foundation for meaningful therapeutic interventions to enhance the quality of life of individuals who experience these conditions.
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Affiliation(s)
- Stephen F. Pastore
- Molecular Neuropsychiatry and Development (MiND) Lab, Molecular Brain Science Research Department, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON M5T 1RS, Canada;
- Institute of Medical Science, University of Toronto, Toronto, ON M5S 1A8, Canada;
| | - Sangyoon Y. Ko
- Program in Neurosciences and Mental Health, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada;
- Department of Physiology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Paul W. Frankland
- Institute of Medical Science, University of Toronto, Toronto, ON M5S 1A8, Canada;
- Program in Neurosciences and Mental Health, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada;
- Department of Physiology, University of Toronto, Toronto, ON M5S 1A8, Canada
- Department of Psychology, University of Toronto, Toronto, ON M5S 3G3, Canada
| | - Paul A. Hamel
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada;
| | - John B. Vincent
- Molecular Neuropsychiatry and Development (MiND) Lab, Molecular Brain Science Research Department, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON M5T 1RS, Canada;
- Institute of Medical Science, University of Toronto, Toronto, ON M5S 1A8, Canada;
- Department of Psychiatry, University of Toronto, Toronto, ON M5T 1R8, Canada
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42
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Catino G, Genovese S, Di Tommaso S, Orlando V, Petti MT, De Bernardi ML, Dallapiccola B, Novelli A, Ulgheri L, Piscopo C, Alesi V. Reciprocal Xp11.4p11.3 microdeletion/microduplication spanning USP9X, DDX3X, and CASK genes in two patients with syndromic intellectual disability. Am J Med Genet A 2022; 188:1836-1847. [PMID: 35238482 DOI: 10.1002/ajmg.a.62694] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 02/02/2022] [Accepted: 02/05/2022] [Indexed: 12/13/2022]
Abstract
Only a few patients with deletions or duplications at Xp11.4, bridging USP9X, DDX3X, and CASK genes, have been described so far. Here, we report on a female harboring a de novo Xp11.4p11.3 deletion and a male with an overlapping duplication inherited from an unaffected mother, presenting with syndromic intellectual disability. We discuss the role of USP9X, DDX3X, and CASK genes in human development and describe the effects of Xp11.4 deletion and duplications in female and male patients, respectively.
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Affiliation(s)
- Giorgia Catino
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children Hospital, IRCCS, Rome, Italy
| | - Silvia Genovese
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children Hospital, IRCCS, Rome, Italy
| | - Silvia Di Tommaso
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children Hospital, IRCCS, Rome, Italy
| | - Valeria Orlando
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children Hospital, IRCCS, Rome, Italy
| | - Maria Teresa Petti
- Department of Molecular Medicine and Medical Biotechnology, University Federico II, Naples, Italy
| | | | - Bruno Dallapiccola
- Genetics and Rare Disease Research Division, Bambino Gesu Children Hospital, IRCCS, Rome, Italy
| | - Antonio Novelli
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children Hospital, IRCCS, Rome, Italy
| | - Lucia Ulgheri
- Department of Biomedical Sciences, Clinical Genetics Service, Azienda Ospedaliero-Universitaria, Sassari, Italy
| | - Carmelo Piscopo
- Department of Molecular Medicine and Medical Biotechnology, University Federico II, Naples, Italy
| | - Viola Alesi
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children Hospital, IRCCS, Rome, Italy
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43
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Wen J, Chai H, Grommisch B, DiAdamo A, Dykas D, Ma D, Popa A, Zhao C, Spencer-Manzon M, Jiang YH, McGrath J, Li P, Bale A, Zhang H. Detecting regions of homozygosity improves the diagnosis of pathogenic variants and uniparental disomy in pediatric patients. Am J Med Genet A 2022; 188:1728-1738. [PMID: 35199448 DOI: 10.1002/ajmg.a.62693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 01/12/2022] [Accepted: 01/28/2022] [Indexed: 11/10/2022]
Abstract
Chromosomal microarray analysis using single nucleotide polymorphism probes can detect regions of homozygosity (ROH). This confers a potential utility in revealing autosomal recessive (AR) diseases and uniparental disomy (UPD). Results of genetic testing among pediatric patients from 2015 to 2019 were evaluated. Diagnostic findings with detected ROH from large consecutive case series in the literature were reviewed. Of 2050 pediatric patients, 65 (3%) had one or more ROH and 31 (53%) had follow-up whole exome sequencing (WES) and methylation studies. Seven homozygous variants were detected and four of them from three patients (9.6%) were within the detected ROH and classified as pathogenic or likely pathogenic variants for AR diseases. One patient (3%) had segmental UPD15q for a diagnosis of Prader-Willi syndrome. Additive diagnostic yield from ROH reporting was at least 0.2% (4/2050) of pediatric patients. These results were consistent with findings from several large case series reported in the literature. Detecting ROH had an estimated baseline predictive value of 10% for AR diseases and 3% for UPD. Consanguinity revealed by multiple ROH was a strong predictor for AR diseases. These results provide evidence for genetic counseling and recommendation of follow-up WES and methylation studies for pediatric patients reported with ROH.
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Affiliation(s)
- Jiadi Wen
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Hongyan Chai
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Brittany Grommisch
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Autumn DiAdamo
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Daniel Dykas
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Deqiong Ma
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Andreea Popa
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Chen Zhao
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
| | | | - Yong-Hui Jiang
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - James McGrath
- Department of Comparative medicine, Yale University, New Haven, Connecticut, USA
| | - Peining Li
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Allen Bale
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Hui Zhang
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
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Yahia A, Ayed IB, Hamed AA, Mohammed IN, Elseed MA, Bakhiet AM, Guillot-Noel L, Abozar F, Adil R, Emad S, Abubaker R, Musallam MA, Eltazi IZM, Omer Z, Maaroof OM, Soussi A, Bouzid A, Kmiha S, Kamoun H, Salih MA, Ahmed AE, Elsayed L, Masmoudi S, Stevanin G. Genetic diagnosis in Sudanese and Tunisian families with syndromic intellectual disability through exome sequencing. Ann Hum Genet 2022; 86:181-194. [PMID: 35118659 DOI: 10.1111/ahg.12460] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 11/24/2021] [Accepted: 01/17/2022] [Indexed: 12/20/2022]
Abstract
BACKGROUND Intellectual disability is a form of neurodevelopmental disorders that begin in childhood and is characterized by substantial intellectual difficulties as well as difficulties in conceptual, social, and practical areas of living. Several genetic and nongenetic factors contribute to its development; however, its most severe forms are generally attributed to single-gene defects. High-throughput technologies and data sharing contributed to the diagnosis of hundreds of single-gene intellectual disability subtypes. METHOD We applied exome sequencing to identify potential variants causing syndromic intellectual disability in six Sudanese patients from four unrelated families. Data sharing through the Varsome portal corroborated the diagnosis of one of these patients and a Tunisian patient investigated through exome sequencing. Sanger sequencing validated the identified variants and their segregation with the phenotypes in the five studied families. RESULT We identified three pathogenic/likely pathogenic variants in CCDC82, ADAT3, and HUWE1 and variants of uncertain significance in HERC2 and ATP2B3. The patients with the CCDC82 variants had microcephaly and spasticity, two signs absent in the two previously reported families with CCDC82-related intellectual disability. CONCLUSION In conclusion, we report new patients with pathogenic mutations in the genes CCDC82, ADAT3, and HUWE1. We also highlight the possibility of extending the CCDC82-linked phenotype to include spastic paraplegia and microcephaly.
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Affiliation(s)
- Ashraf Yahia
- Department of Biochemistry, Faculty of Medicine, University of Khartoum, Khartoum, Sudan.,Department of Biochemistry, Faculty of Medicine, National University, Khartoum, Sudan.,Institut du Cerveau - Paris Brain Institute, ICM, Sorbonne Université, INSERM, CNRS, APHP, Paris, France.,Ecole Pratique des Hautes Etudes, EPHE, PSL Research University, Paris, France
| | - Ikhlas Ben Ayed
- Laboratory of Molecular and Cellular Screening Processes (LPCMC), LR15CBS07, Center of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia.,Medical Genetic Department, Hedi Chaker Hospital, Sfax, Tunisia
| | - Ahlam A Hamed
- Department of Pediatrics, Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - Inaam N Mohammed
- Department of Pediatrics, Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - Maha A Elseed
- Department of Pediatrics, Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - Aisha M Bakhiet
- Department of Psychiatry, Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - Lena Guillot-Noel
- Institut du Cerveau - Paris Brain Institute, ICM, Sorbonne Université, INSERM, CNRS, APHP, Paris, France.,Ecole Pratique des Hautes Etudes, EPHE, PSL Research University, Paris, France
| | - Fatima Abozar
- Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - Rawaa Adil
- Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - Sara Emad
- Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - Rayan Abubaker
- Institute of Endemic Diseases, University of Khartoum, Khartoum, Sudan.,National University Biomedical Research Institute (NUBRI), National University, Khartoum, Sudan
| | | | - Isra Z M Eltazi
- Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - Zulfa Omer
- Department of Hematology and Medical Oncology, University of Cincinnati Medical Center, Cincinnati, Ohio, USA
| | - Omer M Maaroof
- Council of Diagnostic Radiology, Sudan Medical Specialization Board, Khartoum, Sudan
| | - Amal Soussi
- Laboratory of Molecular and Cellular Screening Processes (LPCMC), LR15CBS07, Center of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Amal Bouzid
- Laboratory of Molecular and Cellular Screening Processes (LPCMC), LR15CBS07, Center of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Sana Kmiha
- Laboratory of Human Molecular Genetics, LR33ES99, Faculty of Medicine of Sfax, University of Sfax, Sfax, Tunisia.,Department of pediatrics, Hedi Chaker Hospital, Sfax, Tunisia
| | - Hassen Kamoun
- Medical Genetic Department, Hedi Chaker Hospital, Sfax, Tunisia.,Laboratory of Human Molecular Genetics, LR33ES99, Faculty of Medicine of Sfax, University of Sfax, Sfax, Tunisia
| | - Mustafa A Salih
- Division of Pediatric Neurology, Department of Pediatrics, College of Medicine, King Saud University, Riyadh, Saudi Arabia.,Department of Pediatrics, College of Medicine, AlMughtaribeen University, Khartoum, Sudan
| | - Ammar E Ahmed
- Department of Physiology, Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - Liena Elsayed
- Department of Biochemistry, Faculty of Medicine, University of Khartoum, Khartoum, Sudan.,Department of Basic Sciences, College of Medicine, Princess Nourah bint Abdulrahman University, Riyadh, 11671, Saudi Arabia
| | - Saber Masmoudi
- Laboratory of Molecular and Cellular Screening Processes (LPCMC), LR15CBS07, Center of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Giovanni Stevanin
- Institut du Cerveau - Paris Brain Institute, ICM, Sorbonne Université, INSERM, CNRS, APHP, Paris, France.,Ecole Pratique des Hautes Etudes, EPHE, PSL Research University, Paris, France
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45
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Fatumo S, Chikowore T, Choudhury A, Ayub M, Martin AR, Kuchenbaecker K. A roadmap to increase diversity in genomic studies. Nat Med 2022; 28:243-250. [PMID: 35145307 PMCID: PMC7614889 DOI: 10.1038/s41591-021-01672-4] [Citation(s) in RCA: 213] [Impact Index Per Article: 106.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Accepted: 12/21/2021] [Indexed: 12/12/2022]
Abstract
Two decades ago, the sequence of the first human genome was published. Since then, advances in genome technologies have resulted in whole-genome sequencing and microarray-based genotyping of millions of human genomes. However, genetic and genomic studies are predominantly based on populations of European ancestry. As a result, the potential benefits of genomic research-including better understanding of disease etiology, early detection and diagnosis, rational drug design and improved clinical care-may elude the many underrepresented populations. Here, we describe factors that have contributed to the imbalance in representation of different populations and, leveraging our experiences in setting up genomic studies in diverse global populations, we propose a roadmap to enhancing inclusion and ensuring equal health benefits of genomics advances. Our Perspective highlights the importance of sincere, concerted global efforts toward genomic equity to ensure the benefits of genomic medicine are accessible to all.
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Affiliation(s)
- Segun Fatumo
- The African Computational Genomics (TACG) Research Group, MRC/UVRI and LSHTM, Entebbe, Uganda.
- The Department of Non-communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK.
| | - Tinashe Chikowore
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- MRC/Wits Developmental Pathways for Health Research Unit, Department of Paediatrics, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Ananyo Choudhury
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Muhammad Ayub
- Division of Psychiatry, University College London, London, UK
| | - Alicia R Martin
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Karoline Kuchenbaecker
- Division of Psychiatry, University College London, London, UK
- UCL Genetics Institute, University College London, London, UK
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46
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Ropers HH, van Karnebeek CD. Rare diseases: human genome research is coming home. Cold Spring Harb Mol Case Stud 2022; 8:a006210. [PMID: 35332074 PMCID: PMC8958923 DOI: 10.1101/mcs.a006210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
After a long and largely disappointing detour, Genome Research has reidentified Rare Diseases as a major opportunity for improving health care and a clue to understanding gene and genome function. In this Special Issue of CSH Molecular Case Studies on Rare Diseases, several invited Perspectives, numerous Case Reports, and this Editorial itself address recent breakthroughs as well as unsolved problems in this wide field. These range from exciting prospects for gap-free diagnostic whole-genome sequencing to persisting problems related to identifying and distinguishing pathogenic and benign variants; and from the good news that soon, the United Kingdom will no longer be the only country to have introduced whole-genome sequencing into health care to the sobering conclusion that in many countries the clinical infrastructure for bringing Genome Medicine to the patient is still lacking. With less than 5000 genes firmly implicated in disease, the identification of at least twice as many disease genes is a major challenge, and the elucidation of their function is an even larger task. But given the renewed interest in rare diseases, their importance for health care, and the vast and growing spectrum of concepts and methods for studying them, the future of Human Genome Research is bright.
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Affiliation(s)
- Hans-Hilger Ropers
- Max Planck Institute for Molecular Genetics, Berlin D-14195, and Institute of Human Genetics, University Medicine, Mainz D-55131, Germany
| | - Clara D van Karnebeek
- Departments of Pediatrics and Human Genetics, Emma Children's Hospital, Amsterdam University Medical Centers, NL-1105 AZ Amsterdam, The Netherlands
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AlQudairy H, AlDhalaan H, AlRuways S, AlMutairi N, AlNakiyah M, AlGhofaili R, AlBakheet A, Alomrani A, Alharbi OA, Tous E, AlSayed M, AlZaidan H, AlRasheed MM, AlOdaib A, Kaya N. Clinical, radiological, and genetic characterization of SLC13A5 variants in Saudi families: Genotype phenotype correlation and brief review of the literature. Front Pediatr 2022; 10:1051534. [PMID: 36923948 PMCID: PMC10008858 DOI: 10.3389/fped.2022.1051534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 12/14/2022] [Indexed: 03/03/2023] Open
Abstract
Background SLC13A5 (solute carrier family 13, member 5) encodes sodium/citrate cotransporter, which mainly localizes in cellular plasma membranes in the frontal cortex, retina, and liver. Pathogenic variants of the gene cause an autosomal recessive syndrome known as "developmental and epileptic encephalopathy 25 with amelogenesis imperfecta." Results Here, we have investigated six patients from three different consanguineous Saudi families. The affected individuals presented with neonatal seizures, developmental delay, and significant defects in tooth development. Some patients showed other clinical features such as muscle weakness, motor difficulties, intellectual disability, microcephaly, and speech problems in addition to additional abnormalities revealed by electroencephalography (EEGs) and magnetic resonance imaging (MRI). One of the MRI findings was related to cortical thickening in the frontal lobe. To diagnose and study the genetic defects of the patients, whole exome sequencing (WES) coupled with confirmatory Sanger sequencing was utilized. Iterative filtering identified two variants of SLC13A5, one of which is novel, in the families. Families 1 and 2 had the same insertion (a previously reported mutation), leading to a frameshift and premature stop codon. The third family had a novel splice site variant. Confirmatory Sanger sequencing corroborated WES results and indicated full segregation of the variants in the corresponding families. The patients' conditions were poorly controlled by multiple antiepileptics as they needed constant care. Conclusion Considering that recessive mutations are common in the Arab population, SLC13A5 screening should be prioritized in future patients harboring similar symptoms including defects in molar development.
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Affiliation(s)
- Hanan AlQudairy
- Translational Genomic Department, Center for Genomic Medicine, King Faisal Specialist Hospital, and Research Centre (KFSHRC), Riyadh, Saudi Arabia
| | | | - Sarah AlRuways
- Translational Genomic Department, Center for Genomic Medicine, King Faisal Specialist Hospital, and Research Centre (KFSHRC), Riyadh, Saudi Arabia.,College of Pharmacy, King Saud University (KSU), Riyadh, Saudi Arabia
| | - Nouf AlMutairi
- Translational Genomic Department, Center for Genomic Medicine, King Faisal Specialist Hospital, and Research Centre (KFSHRC), Riyadh, Saudi Arabia.,College of Pharmacy, King Saud University (KSU), Riyadh, Saudi Arabia
| | - Maha AlNakiyah
- Translational Genomic Department, Center for Genomic Medicine, King Faisal Specialist Hospital, and Research Centre (KFSHRC), Riyadh, Saudi Arabia.,College of Pharmacy, King Saud University (KSU), Riyadh, Saudi Arabia
| | - Reema AlGhofaili
- Translational Genomic Department, Center for Genomic Medicine, King Faisal Specialist Hospital, and Research Centre (KFSHRC), Riyadh, Saudi Arabia.,College of Pharmacy, King Saud University (KSU), Riyadh, Saudi Arabia
| | | | | | - Omar A Alharbi
- Department of Neurosciences, KFSHRC, Riyadh, Saudi Arabia
| | - Ehab Tous
- Department of Neurosciences, KFSHRC, Riyadh, Saudi Arabia
| | - Moeen AlSayed
- Department of Medical Genomics, Center for Genomic Medicine, KFSHRC, Riyadh, Saudi Arabia
| | - Hamad AlZaidan
- Department of Medical Genomics, Center for Genomic Medicine, KFSHRC, Riyadh, Saudi Arabia
| | - Maha M AlRasheed
- College of Pharmacy, King Saud University (KSU), Riyadh, Saudi Arabia.,Department of Clinical Pharmacy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Ali AlOdaib
- Training and Education Department, Research Centre, KFSHRC, Riyadh, Saudi Arabia
| | - Namik Kaya
- Translational Genomic Department, Center for Genomic Medicine, King Faisal Specialist Hospital, and Research Centre (KFSHRC), Riyadh, Saudi Arabia
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Rashvand Z, Kahrizi K, Najmabadi H, Najafipour R, Omrani MD. A novel variant of C12orf4 linked to autosomal recessive intellectual disability type 66 with phenotype expansion. J Gene Med 2021; 24:e3406. [PMID: 34967075 DOI: 10.1002/jgm.3406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 12/05/2021] [Accepted: 12/08/2021] [Indexed: 11/07/2022] Open
Abstract
BACKGROUND Intellectual disability (ID) is a hallmark of many rare disorders that are highly heterogeneous and complex. A large number of specific genes are involved in development of this heterogeneity, and each of these genes is only found in a small number of patients. This weakens the definition of the predominant genotype and the phenotypic characteristics associated with that gene. Autosomal recessive ID type 66 (OMIM # 618221) is one of these very rare diseases created by defects in C12orf4 gene. METHODS The researchers in the current study included two patients from an Iranian family with initial diagnosis of non-syndromic ID to identify the possible genetic cause(s), and whole-exome sequencing (WES) was performed for the proband. The obtained variant was confirmed by Sanger sequencing and co-segregated in the family. RESULT The patients carried a novel pathogenic splicing variant called c.1441-1G>A in exon 12 of C12orf4 gene (NM_001304811). They predominantly manifested ID, behavioral problems, speech impairment, and dysmorphic facial features, some of which had not been reported in previous studies. CONCLUSION A novel pathogenic splicing variant was identified named c.1441-1G>A in C12orf4 gene. So far, only seven families have been reported with defects in this gene. Previous studies have not highlighted the exact clinical manifestations of these patients, thus, this study could contribute to better delineation of the genotype-phenotype correlation and interpretation of very rare variants of the gene.
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Affiliation(s)
- Zahra Rashvand
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Kimia Kahrizi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Hossein Najmabadi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Reza Najafipour
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Mir Davood Omrani
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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Sheikh TI, Harripaul R, Vasli N, Ghadami M, Santangelo SL, Ayub M, Sasanfar R, Vincent JB. Heterozygous De Novo Truncating Mutation of Nucleolin in an ASD Individual Disrupts Its Nucleolar Localization. Genes (Basel) 2021; 13:51. [PMID: 35052391 PMCID: PMC8774667 DOI: 10.3390/genes13010051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 12/10/2021] [Accepted: 12/14/2021] [Indexed: 11/16/2022] Open
Abstract
Nucleolin (NCL/C23; OMIM: 164035) is a major nucleolar protein that plays a critical role in multiple processes, including ribosome assembly and maturation, chromatin decondensation, and pre-rRNA transcription. Due to its diverse functions, nucleolin has frequently been implicated in pathological processes, including cancer and viral infection. We recently identified a de novo frameshifting indel mutation of NCL, p.Gly664Glufs*70, through whole-exome sequencing of autism spectrum disorder trios. Through the transfection of constructs encoding either a wild-type human nucleolin or a mutant nucleolin with the same C-terminal sequence predicted for the autism proband, and by using co-localization with the nucleophosmin (NPM; B23) protein, we have shown that the nucleolin mutation leads to mislocalization of the NCL protein from the nucleolus to the nucleoplasm. Moreover, a construct with a nonsense mutation at the same residue, p.Gly664*, shows a very similar effect on the location of the NCL protein, thus confirming the presence of a predicted nucleolar location signal in this region of the NCL protein. Real-time fluorescence recovery experiments show significant changes in the kinetics and mobility of mutant NCL protein in the nucleoplasm of HEK293Tcells. Several other studies also report de novoNCL mutations in ASD or neurodevelopmental disorders. The altered mislocalization and dynamics of mutant NCL (p.G664Glufs*70/p.G664*) may have relevance to the etiopathlogy of NCL-related ASD and other neurodevelopmental phenotypes.
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Affiliation(s)
- Taimoor I. Sheikh
- Molecular Neuropsychiatry & Development (MiND) Lab, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON M5T 1R8, Canada; (T.I.S.); (R.H.)
| | - Ricardo Harripaul
- Molecular Neuropsychiatry & Development (MiND) Lab, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON M5T 1R8, Canada; (T.I.S.); (R.H.)
- Institute of Medical Science, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Nasim Vasli
- Department of Pediatric Laboratory Medicine, Hospital for Sick Children, Toronto, ON M5G 1X8, Canada;
| | - Majid Ghadami
- Department of Educational Sciences, Farhangian University, Tehran 19989-63341, Iran;
| | - Susan L. Santangelo
- Center for Psychiatric Research, Maine Medical Center Research Institute, Portland, ME 04101, USA;
- Department of Psychiatry, Tufts University School of Medicine, Boston, MA 02110, USA
- Department of Psychiatry, Maine Medical Center, Portland, ME 04102, USA
| | - Muhammad Ayub
- Department of Psychiatry, Queen’s University, Kingston, ON K7L 7X3, Canada;
- Department of Academic Psychiatry, University College London, London WC1E 6BT, UK
| | - Roksana Sasanfar
- Department of Psychiatry, Harvard Medical School, Boston, MA 02215, USA;
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA 02114, USA
| | - John B. Vincent
- Molecular Neuropsychiatry & Development (MiND) Lab, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON M5T 1R8, Canada; (T.I.S.); (R.H.)
- Institute of Medical Science, University of Toronto, Toronto, ON M5S 1A8, Canada
- Department of Psychiatry, University of Toronto, Toronto, ON M5T 1R8, Canada
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50
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Li J, Lin SM, Qiao JD, Liu XR, Wang J, Jiang M, Zhang J, Zhong M, Chen XQ, Zhu J, He N, Su T, Shi YW, Yi YH, Liao WP. CELSR3 variants are associated with febrile seizures and epilepsy with antecedent febrile seizures. CNS Neurosci Ther 2021; 28:382-389. [PMID: 34951123 PMCID: PMC8841303 DOI: 10.1111/cns.13781] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 09/27/2021] [Accepted: 11/27/2021] [Indexed: 11/30/2022] Open
Abstract
Aims To identify novel pathogenic gene of febrile seizures (FS)/epilepsy with antecedent FS (EFS+). Methods The trio‐based whole‐exome sequencing was performed in a cohort of 462 cases with FS/EFS+. Silico programs, sequence alignment, and protein modeling were used to predict the damaging of variants. Statistical testing was performed to analyze gene‐based burden of variants. Results Five heterozygous missense variants in CELSR3 were detected in five cases (families) with eight individuals (five females, three males) affected. Two variants were de novo, and three were identified in families with more than one individual affected. All the variants were predicted to be damaging in silico tools. Protein modeling showed that the variants resulted in disappearance of multiple hydrogen bonds and one disulfide bond, which potentially caused functional impairments of protein. The frequency of CELSR3 variants identified in this study was significantly higher than that in controls. All affected individuals were diagnosed with FS/EFS+, including six patients with FS and two patients with EFS+. All cases presented favorable outcomes without neurodevelopmental disorders. Conclusions CELSR3 variants are potentially associated with FS/EFS+.
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Affiliation(s)
- Jia Li
- Institute of Neuroscience and Department of Neurology of the Second Affiliated Hospital of Guangzhou Medical University, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, Guangzhou, China
| | - Si-Mei Lin
- Institute of Neuroscience and Department of Neurology of the Second Affiliated Hospital of Guangzhou Medical University, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, Guangzhou, China
| | - Jing-Da Qiao
- Institute of Neuroscience and Department of Neurology of the Second Affiliated Hospital of Guangzhou Medical University, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, Guangzhou, China
| | - Xiao-Rong Liu
- Institute of Neuroscience and Department of Neurology of the Second Affiliated Hospital of Guangzhou Medical University, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, Guangzhou, China
| | - Jie Wang
- Institute of Neuroscience and Department of Neurology of the Second Affiliated Hospital of Guangzhou Medical University, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, Guangzhou, China
| | - Mi Jiang
- Institute of Neuroscience and Department of Neurology of the Second Affiliated Hospital of Guangzhou Medical University, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, Guangzhou, China
| | - Jing Zhang
- Department of Pediatrics, Xiangya Changde Hospital, Changde, China
| | - Min Zhong
- Department of Neurology, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Xu-Qin Chen
- Department of Neurology, Children's Hospital of Soochow University, Suzhou, China
| | - Jing Zhu
- Department of Pediatrics, The First Hospital of Anhui Medical University, Hefei, China
| | - Na He
- Institute of Neuroscience and Department of Neurology of the Second Affiliated Hospital of Guangzhou Medical University, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, Guangzhou, China
| | - Tao Su
- Institute of Neuroscience and Department of Neurology of the Second Affiliated Hospital of Guangzhou Medical University, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, Guangzhou, China
| | - Yi-Wu Shi
- Institute of Neuroscience and Department of Neurology of the Second Affiliated Hospital of Guangzhou Medical University, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, Guangzhou, China
| | - Yong-Hong Yi
- Institute of Neuroscience and Department of Neurology of the Second Affiliated Hospital of Guangzhou Medical University, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, Guangzhou, China
| | - Wei-Ping Liao
- Institute of Neuroscience and Department of Neurology of the Second Affiliated Hospital of Guangzhou Medical University, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, Guangzhou, China
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