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Fattahi Z, Shokouhian E, Peymani F, Babanejad M, Beheshtian M, Edizadeh M, Molaei N, Alagha P, Ghodratpour F, Keshavarzi F, Moghadam MG, Arzhangi S, Kahrizi K, Najmabadi H. Improved Diagnostic Yield in Recessive Intellectual Disability Utilizing Systematic Whole Exome Sequencing Data Reanalysis. Clin Genet 2025; 107:612-619. [PMID: 39748273 DOI: 10.1111/cge.14692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2024] [Revised: 12/13/2024] [Accepted: 12/19/2024] [Indexed: 01/04/2025]
Abstract
Recent advances in next generation sequencing (NGS) have positioned whole exome sequencing (WES) as an efficient first-tier method in genetic diagnosis. However, despite the diagnostic yield of 35%-50% in intellectual disability (ID) many patients still remain undiagnosed due to inherent limitations and bioinformatic short-comings. In this study, we reanalyzed WES data from 159 Iranian families showing recessively inherited ID. The reanalysis was conducted with an initial clinical re-evaluation of the patients and their families, followed by data reanalysis using two updated bioinformatic pipelines. In the first phase, the BWA-GATK pipeline was utilized for alignment and variant calling, with subsequent variant annotation by the ANNOVAR tool. This approach yielded causative variants in 17 families (10.6%). Among these, six genes (MAZ, ACTR5, AKTIP, MIX23, SERPINB12, and CDC25B) were identified as novel candidates potentially associated with ID, supported by bioinformatics functional annotation and segregation analysis. In the second phase, families with negative results were reassessed using the Illumina DRAGEN Bio-IT platform for variant-calling, and Ilyome, a newly developed web-based tool, for annotation. The second phase identified likely pathogenic variants in two additional families, increasing the total diagnostic yield to 11.9% which is consistent with other studies conducted on cohorts of patients with ID. In conclusion, identification of co-segregating variants in six novel candidate genes in this study, emphasizes once more on the potential of WES reanalysis to uncover previously unknown gene-disease associations. Notably, it demonstrates that systematic reanalysis of WES data using updated bioinformatic tools and a thorough review of the literature for new gene-disease associations while performing phenotypic re-evaluation, can improve diagnostic outcome of WES in recessively inherited ID. Consequently, if performed within a 1-3 year period, it can reduce the number of cases that may require other costly diagnostic methods such as whole genome sequencing.
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Affiliation(s)
- Zohreh Fattahi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Ebrahim Shokouhian
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Fatemeh Peymani
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Mojgan Babanejad
- 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
| | - Masoud Edizadeh
- Department of Bioinformatics, Genoks Genetic Diagnosis Center, Ankara, Turkey
| | - Negar Molaei
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Parnian Alagha
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Fatemeh Ghodratpour
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Fatemeh Keshavarzi
- 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
| | - 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
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2
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Zhang J, Yang K, Chen WQ, Sun DL, Hu HY, Li Q, Yan YS, Li YZ, Yin CH, Guo Q. SEC24D depletion induces osteogenic differentiation deficiency by inactivating the ATF6/TGF-β/Runx2 regulatory loop. Commun Biol 2025; 8:758. [PMID: 40374976 PMCID: PMC12081754 DOI: 10.1038/s42003-025-08175-9] [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: 10/09/2024] [Accepted: 05/06/2025] [Indexed: 05/18/2025] Open
Abstract
Protein coat complexes strongly influence intracellular cargo trafficking. Coatopathies represent a wide range of genetic conditions caused by mutations in protein coat components. The SEC24D gene, which encodes a Sec24 isoform that constitutes a cargo-specific capturer in the COPII coat, is responsible for a rare type of autosomal recessive osteogenesis imperfecta. We report an OI patient. Clinical and imaging findings suggested that the patient had OI. Genetic detection by whole-exome sequencing (WES) identified a compound heterozygous SEC24D variants, including c.2609_2610delGA (p. R870fs*10) and c.938G>A (p. R313H). In silico analysis suggested that the missense R313H mutation most likely affects protein stability and secondary structure. In vitro studies showed that knockdown or mutation of SEC24D affected the osteogenic differentiation of mesenchymal stem cells (MSCs) and inducted ER stress. Transcriptomic sequencing suggested that the TGF-β pathway mediated the destructive effect of SEC24D depletion on osteogenic differentiation. Further experiments confirmed that ATF6 participated in regulating the TGF-β pathway and osteogenic biomarkers by SEC24D. This study identified a SEC24D variation causing OI, which expanded the mutation spectrum of this gene. Further studies on the mechanism of action showed that SEC24D defects may induce osteogenic differentiation deficiency by inactivating the ATF6/TGF-β/Runx2 regulatory loop.
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Affiliation(s)
- Jing Zhang
- Prenatal Diagnosis Center, Shijiazhuang Obstetrics and Gynecology Hospital; Hebei Key Laboratory of Maternal and Fetal Medicine; Shijiazhuang Key Laboratory of Reproductive Health, Shijiazhuang, Hebei, China
| | - Kai Yang
- Prenatal Diagnosis Center, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing, China
| | - Wen-Qi Chen
- Prenatal Diagnosis Center, Shijiazhuang Obstetrics and Gynecology Hospital; Hebei Key Laboratory of Maternal and Fetal Medicine; Shijiazhuang Key Laboratory of Reproductive Health, Shijiazhuang, Hebei, China
| | - Dong-Lan Sun
- Prenatal Diagnosis Center, Shijiazhuang Obstetrics and Gynecology Hospital; Hebei Key Laboratory of Maternal and Fetal Medicine; Shijiazhuang Key Laboratory of Reproductive Health, Shijiazhuang, Hebei, China
| | - Hua-Ying Hu
- Medical Innovation Research Division of Chinese, PLA General Hospital, Beijing, China; Jiaen Genetics Laboratory, Beijing Jiaen Hospital, Beijing, China
| | - Qian Li
- Prenatal Diagnosis Center, Department of Obstetrics and Gynaecology, Sixth Medical Center, Chinese PLA General Hospital, Beijing, China
| | - You-Sheng Yan
- Prenatal Diagnosis Center, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing, China
| | - Ya-Zhou Li
- Department of Pediatric Orthopedic, The Third Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Cheng-Hong Yin
- Prenatal Diagnosis Center, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing, China.
| | - Qing Guo
- Prenatal Diagnosis Center, Shijiazhuang Obstetrics and Gynecology Hospital; Hebei Key Laboratory of Maternal and Fetal Medicine; Shijiazhuang Key Laboratory of Reproductive Health, Shijiazhuang, Hebei, China.
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3
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Lu T, Umeshita S, Imanishi K, Wang Y, Liu YS, Nagae M, Senoo Y, Ikeda K, Fujita M, Kinoshita T, Murakami Y. ARV1 is a component of the enzyme initiating glycosylphosphatidylinositol biosynthesis. J Biol Chem 2025:110236. [PMID: 40378954 DOI: 10.1016/j.jbc.2025.110236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2025] [Revised: 04/24/2025] [Accepted: 04/28/2025] [Indexed: 05/19/2025] Open
Abstract
Glycosylphosphatidylinositol (GPI) serves as a membrane anchor of numerous cell surface proteins. It is synthesized in the endoplasmic reticulum from phosphatidylinositol (PI) by stepwise reactions and transferred to the C-terminus of the protein. Defects in genes involved in GPI biosynthesis affect the expression of GPI-anchored proteins (GPI-APs) or their structure, causing the neurological disorder, inherited GPI deficiency (IGD). Individuals with ARV1 deficiency have symptoms resembling IGD, but how ARV1 regulates GPI biosynthesis is poorly understood. Here, we show that ARV1 acts as a component of the enzyme initiating GPI biosynthesis, GPI N-acetylglucosaminyltransferase (GPI-GnT) complex, which forms a ring structure as predicted by AlphaFold3. ARV1 associates with PIGQ, a GPI-GnT component, and ARV1 mutants defective in this association lose their ability to enhance GPI-GnT activity, showing that association with PIGQ is critical for ARV1's function. ARV1-containing GPI-GnT used PI more efficiently than ARV1-less GPI-GnT in an in vitro enzyme assay. Collectively, our results suggest that ARV1 facilitates efficient recruitment of PI to GPI-GnT, thereby playing a critical role in the regulation of GPI-AP expression.
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Affiliation(s)
- TianTian Lu
- Laboratory of Immunoglycobiology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan; Immunology Frontier Research Center, Osaka University, Suita, Osaka 565-0871, Japan
| | - Saori Umeshita
- Laboratory of Immunoglycobiology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan
| | - Kae Imanishi
- Laboratory of Immunoglycobiology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan
| | - Yicheng Wang
- Laboratory of Immunoglycobiology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan; Immunology Frontier Research Center, Osaka University, Suita, Osaka 565-0871, Japan
| | - Yi-Shi Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Masamichi Nagae
- Laboratory of Immunoglycobiology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan; Immunology Frontier Research Center, Osaka University, Suita, Osaka 565-0871, Japan
| | - Yuya Senoo
- Laboratory of Biomolecule Analysis, Department of Applied Genomics, Kazusa DNA Research Institute, Chiba 292-0818, Japan
| | - Kazutaka Ikeda
- Laboratory of Biomolecule Analysis, Department of Applied Genomics, Kazusa DNA Research Institute, Chiba 292-0818, Japan
| | - Morihisa Fujita
- Institute for Glyco-core Research (iGCORE), Gifu University, Gifu 501-1193, Japan
| | - Taroh Kinoshita
- Laboratory of Immunoglycobiology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan; Immunology Frontier Research Center, Osaka University, Suita, Osaka 565-0871, Japan; Center for Infectious Disease Education and Research, Osaka University, Suita, Osaka 565-0871, Japan
| | - Yoshiko Murakami
- Laboratory of Immunoglycobiology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan
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Bonde LD, Hecher L, Alawi M, Forbes KP, Symonds JD, Hamilton MJ, Kutsche K. Novel biallelic NUP107 variants affect the nuclear pore complex and expand the clinical spectrum to include brain malformations. J Med Genet 2025:jmg-2025-110671. [PMID: 40350250 DOI: 10.1136/jmg-2025-110671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2025] [Accepted: 04/28/2025] [Indexed: 05/14/2025]
Abstract
Biallelic variants in NUP107 cause isolated or syndromic steroid-resistant nephrotic syndrome (SRNS), characterised by proteinuria, hypoalbuminaemia and focal segmental glomerulosclerosis that progresses to end-stage renal disease. Patients with syndromic SRNS have microcephaly, developmental delay or intellectual disability and short stature. Simplified gyration is observed in some individuals. We report on a 2-year-old girl with novel biallelic NUP107 variants, c.2606G>T; p.(Gly869Val) and c.1576+1G>A, proteinuria and a severe neurodevelopmental disorder with microcephaly, developmental delay, early-onset seizures, sensorineural hearing loss and brain structural anomalies, including simplified gyral pattern and hypoplasia of the corpus callosum, pons, brainstem and cerebellum. NUP107 is part of the NUP107-160 complex, which, together with other proteins termed nucleoporins, forms the nuclear pore complex (NPC). The NPC regulates nucleocytoplasmic transport and other cellular processes. In patient-derived fibroblasts, we identified aberrantly spliced NUP107 mRNAs with a frameshift and premature stop codon leading to non-sense-mediated mRNA decay, reduced levels of NUP107 transcripts, reduced NUP107 and NUP133 proteins, and a reduced NPC number. In addition, an abnormal nucleolar morphology was found in patient-derived cells. Our functional data support the conclusion that the NUP107 variants underlie the patient's phenotype, thereby broadening the clinical spectrum associated with NUP107 variants to include abnormal brain development.
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Affiliation(s)
- Loisa Dana Bonde
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Laura Hecher
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Department of Pediatrics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- German Center for Child and Adolescent Health (DZKJ), partner site Hamburg, Hamburg, Germany
| | - Malik Alawi
- Bioinformatics Core, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Kirsten P Forbes
- Department of Neuroradiology, Queen Elizabeth University Hospital, Glasgow, Scotland, UK
| | - Joseph D Symonds
- Paediatric Neurology Department, Royal Hospital for Children, Queen Elizabeth University Hospitals, Glasgow, Scotland, UK
- Paediatric Neurosciences Research Group, School of Health and Wellbeing, University of Glasgow, Glasgow, Scotland, UK
| | - Mark J Hamilton
- West of Scotland Clinical Genetics Service, Queen Elizabeth University Hospitals, Glasgow, Scotland, UK
| | - Kerstin Kutsche
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- German Center for Child and Adolescent Health (DZKJ), partner site Hamburg, Hamburg, Germany
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5
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Mastromoro G, Guadagnolo D, Gianno F, Khaleghi Hashemian N, Terracciano A, Bernardini L, Giancotti A, Novelli A, Piacentini G, Di Gioia C, Pizzuti A. Cardiac Involvement and TBCK -Related Neurodevelopmental Disorder: Is It a New Feature of This Condition? Am J Med Genet A 2025; 197:e64001. [PMID: 39865381 DOI: 10.1002/ajmg.a.64001] [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: 01/24/2024] [Revised: 12/26/2024] [Accepted: 01/10/2025] [Indexed: 01/28/2025]
Abstract
TBCK (TBC1 Domain-Containing Kinase) encodes a protein playing a role in actin organization and cell growth/proliferation via the mTOR signaling pathway. Deleterious biallelic TBCK variants cause Hypotonia, infantile, with psychomotor retardation and characteristic facies 3. We report on three affected sibs, also displaying cardiac malformations. The parents, a consanguineous couple of first cousins, were referred to schedule invasive diagnosis for their sixth pregnancy. They were known to carry the pathogenic c.1532G>A TBCK variant. The variant was originally identified in homozygosity in the first and second children of the couple, both affected. One also presented a right-sided aortic arch. The other had Tetralogy of Fallot. Present pregnancy ultrasound revealed cystic hygroma and hypoplastic nasal bone, not previously reported in this condition. Chromosomal microarray analysis found no imbalance and identified 8.6% runs of homozygosity. Whole exome sequencing confirmed the TBCK variant without additional pathogenic or candidate variants. Fetal echocardiography revealed left ventricle and aortic arch hypoplasia. The couple opted for pregnancy termination. Fetopsy confirmed sonographic findings and revealed a hypoplastic aorta arising from right ventricle and corpus callosum agenesis. Interestingly, the cardiac phenotype segregates with variants and cardiac involvement might be considered a new feature of this variant causing Hypotonia, infantile, with psychomotor retardation and characteristic facies 3.
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Affiliation(s)
- Gioia Mastromoro
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Daniele Guadagnolo
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Francesca Gianno
- Department of Radiological, Oncological and Anatomic Pathology, Sapienza University, Rome, Italy
| | | | - Alessandra Terracciano
- Translational Cytogenomics Research Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Laura Bernardini
- Medical Genetics Unit, Fondazione IRCCS Casa Sollievo Della Sofferenza, San Giovanni Rotondo, Italy
| | - Antonella Giancotti
- Maternal and Child Health and Urological Sciences, Sapienza University of Rome, Rome, Italy
| | - Antonio Novelli
- Translational Cytogenomics Research Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Gerardo Piacentini
- Fetal and Neonatal Cardiology Unit, Isola Tiberina Hospital - Gemelli Isola, Roma, Italy
| | - Cira Di Gioia
- Department of Radiological, Oncological and Anatomic Pathology, Sapienza University, Rome, Italy
| | - Antonio Pizzuti
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
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6
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Pappas A, Mooney M, Kohnen K, Owens JW, Zhang W, Hopkin RJ, Shillington A. The phenotypic spectrum of the Cornelia de Lange-like "Alazami-Yuan syndrome": A case report of the 7th diagnosed individual and review of the literature. Clin Case Rep 2025; 13:e9208. [PMID: 40321225 PMCID: PMC12048704 DOI: 10.1002/ccr3.9208] [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: 05/17/2024] [Revised: 06/13/2024] [Accepted: 06/27/2024] [Indexed: 05/08/2025] Open
Abstract
We present a 17-year-old female with a childhood clinical diagnosis of Cornelia de Lange Syndrome (CdLS), however later genetic testing identified compound heterozygous variants in TAF6, consistent with AYS. This case report adds to the phenotypic spectrum observed in AYS, and draws connections to transcriptional pathways between CdLS and AYS.
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Affiliation(s)
- Annie Pappas
- Department of PediatricsUniversity of Cincinnati College of MedicineCincinnatiOhioUSA
| | - Mary Mooney
- Department of PediatricsUniversity of Cincinnati College of MedicineCincinnatiOhioUSA
| | - Katherine Kohnen
- Department of PediatricsUniversity of Cincinnati College of MedicineCincinnatiOhioUSA
| | - Joshua W. Owens
- Division of Human GeneticsCincinnati Children's Hospital Medical CenterCincinnatiOhioUSA
- Department of PediatricsUniversity of Cincinnati College of MedicineCincinnatiOhioUSA
| | - Wenying Zhang
- Division of Human GeneticsCincinnati Children's Hospital Medical CenterCincinnatiOhioUSA
- Department of PediatricsUniversity of Cincinnati College of MedicineCincinnatiOhioUSA
| | - Robert J. Hopkin
- Division of Human GeneticsCincinnati Children's Hospital Medical CenterCincinnatiOhioUSA
- Department of PediatricsUniversity of Cincinnati College of MedicineCincinnatiOhioUSA
| | - Amelle Shillington
- Division of Human GeneticsCincinnati Children's Hospital Medical CenterCincinnatiOhioUSA
- Department of PediatricsUniversity of Cincinnati College of MedicineCincinnatiOhioUSA
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7
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Swan LE. VPS13 and bridge-like lipid transporters, mechanisms, and mysteries. Front Neurosci 2025; 19:1534061. [PMID: 40356703 PMCID: PMC12066543 DOI: 10.3389/fnins.2025.1534061] [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: 11/25/2024] [Accepted: 03/14/2025] [Indexed: 05/15/2025] Open
Abstract
Bridge-like lipid transporters (BLTPs) have recently been revealed as key regulators of intraorganellar lipid trafficking, with their loss being associated with defective synaptic signalling and congenital neurological diseases. This group consists of five protein subfamilies [BLTP1-3, autophagy-related 2 (ATG2), and vacuolar protein sorting 13 (VPS13)], which mediate minimally selective lipid transfer between cellular membranes. Deceptively simple in both structure and presumed function, this review addresses open questions as to how bridge-like transporters work, the functional consequences of bulk lipid transfer on cellular signalling, and summarises some recent studies that have shed light on the surprising level of regulation and specificity found in this family of transporters.
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Affiliation(s)
- Laura Elizabeth Swan
- Department of Biochemistry, Cell and Systems Biology, University of Liverpool, Liverpool, United Kingdom
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Jensen TD, Ni B, Reuter CM, Gorzynski JE, Fazal S, Bonner D, Ungar RA, Goddard PC, Raja A, Ashley EA, Bernstein JA, Zuchner S, Greicius MD, Montgomery SB, Schatz MC, Wheeler MT, Battle A. Integration of transcriptomics and long-read genomics prioritizes structural variants in rare disease. Genome Res 2025; 35:914-928. [PMID: 40113264 PMCID: PMC12047269 DOI: 10.1101/gr.279323.124] [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: 03/15/2024] [Accepted: 01/06/2025] [Indexed: 03/22/2025]
Abstract
Rare structural variants (SVs)-insertions, deletions, and complex rearrangements-can cause Mendelian disease, yet they remain difficult to accurately detect and interpret. We sequenced and analyzed Oxford Nanopore Technologies long-read genomes of 68 individuals from the undiagnosed disease network (UDN) with no previously identified diagnostic mutations from short-read sequencing. Using our optimized SV detection pipelines and 571 control long-read genomes, we detected 716 long-read rare (MAF < 0.01) SV alleles per genome on average, achieving a 2.4× increase from short reads. To characterize the functional effects of rare SVs, we assessed their relationship with gene expression from blood or fibroblasts from the same individuals and found that rare SVs overlapping enhancers were enriched (LOR = 0.46) near expression outliers. We also evaluated tandem repeat expansions (TREs) and found 14 rare TREs per genome; notably, these TREs were also enriched near overexpression outliers. To prioritize candidate functional SVs, we developed Watershed-SV, a probabilistic model that integrates expression data with SV-specific genomic annotations, which significantly outperforms baseline models that do not incorporate expression data. Watershed-SV identified a median of eight high-confidence functional SVs per UDN genome. Notably, this included compound heterozygous deletions in FAM177A1 shared by two siblings, which were likely causal for a rare neurodevelopmental disorder. Our observations demonstrate the promise of integrating long-read sequencing with gene expression toward improving the prioritization of functional SVs and TREs in rare disease patients.
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Affiliation(s)
- Tanner D Jensen
- Department of Genetics, Stanford University, Stanford, California 94305, USA
| | - Bohan Ni
- Department of Computer Science, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Chloe M Reuter
- Center for Undiagnosed Diseases, Stanford University, Stanford, California 94305, USA
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, California 94305, USA
| | - John E Gorzynski
- Department of Genetics, Stanford University, Stanford, California 94305, USA
- Center for Undiagnosed Diseases, Stanford University, Stanford, California 94305, USA
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Sarah Fazal
- Dr. John T. Macdonald Foundation Department of Human Genetics and John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida 33136, USA
| | - Devon Bonner
- Center for Undiagnosed Diseases, Stanford University, Stanford, California 94305, USA
- Department of Pediatrics, Division of Medical Genetics, Stanford University School of Medicine, Stanford, California 94304, USA
| | - Rachel A Ungar
- Department of Genetics, Stanford University, Stanford, California 94305, USA
| | - Pagé C Goddard
- Department of Genetics, Stanford University, Stanford, California 94305, USA
| | - Archana Raja
- Center for Undiagnosed Diseases, Stanford University, Stanford, California 94305, USA
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Euan A Ashley
- Center for Undiagnosed Diseases, Stanford University, Stanford, California 94305, USA
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Jonathan A Bernstein
- Center for Undiagnosed Diseases, Stanford University, Stanford, California 94305, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California 94304, USA
| | - Stephan Zuchner
- Dr. John T. Macdonald Foundation Department of Human Genetics and John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida 33136, USA
| | - Michael D Greicius
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Stephen B Montgomery
- Department of Genetics, Stanford University, Stanford, California 94305, USA;
- Department of Pathology, Stanford University, Stanford, California 94305, USA
- Department of Biomedical Data Science, Stanford University, Stanford, California 94305, USA
| | - Michael C Schatz
- Department of Computer Science, Johns Hopkins University, Baltimore, Maryland 21218, USA;
| | - Matthew T Wheeler
- Center for Undiagnosed Diseases, Stanford University, Stanford, California 94305, USA;
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, California 94305, USA
- GREGoR Stanford Site, Stanford University, Stanford, California 94305, USA
| | - Alexis Battle
- Department of Computer Science, Johns Hopkins University, Baltimore, Maryland 21218, USA;
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA
- Department of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland 21218, USA
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9
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Li S, Fang H, Li H, Peng M, Bao J, Cai Y, Chen J, Li Z. Novel Compound Heterozygous Variants in ZNF526 Causing Dentici-Novelli Neurodevelopmental Syndrome: A Case Report and Literature Review. Mol Genet Genomic Med 2025; 13:e70089. [PMID: 40197775 PMCID: PMC11976872 DOI: 10.1002/mgg3.70089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2024] [Revised: 02/10/2025] [Accepted: 03/04/2025] [Indexed: 04/10/2025] Open
Abstract
BACKGROUND The ZNF526 gene encodes a ubiquitously expressed Kruppel-type zinc finger protein crucial in transcriptional regulation. Recent studies suggest that biallelic pathogenic variants in ZNF526 may lead to Dentici-Novelli neurodevelopmental syndrome, characterized by microcephaly, developmental delay, epilepsy, and ocular anomalies. To date, phenotypic details have been reported for only six patients with ZNF526 variants. METHODS This study gathered clinical information and genetic data from a child with neurodevelopmental disorders. A three-dimensional protein model was employed to predict variant effects on protein structure. A literature review was conducted to compare this case with previously reported cases, analyzing clinical features and genetic findings. RESULTS The proband, a 7-month-old girl, exhibited developmental delay, microcephaly, limb hypotonia, abnormal brain imaging, and seizures. Chromosomal karyotype analysis and copy number variation analyses were normal. Whole exome sequencing revealed two heterozygous variants in the ZNF526 gene (NM_133444.3): c.1426del (p.Val476Phefs*9), a de novo frameshift variant, and c.1513T;> C (p.Cys505Arg), inherited from her mother. These previously unreported variants are on separate alleles, forming a compound heterozygous state correlated with the clinical presentation. Ocular anomalies were absent, while café-au-lait spots may represent a novel feature. Among 12 cases of Dentici-Novelli neurodevelopmental syndrome, 11 unique ZNF526 variants have been identified, with loss-of-function variants possibly linked to seizures. CONCLUSION This study describes the youngest patient with Dentici-Novelli neurodevelopmental syndrome, broadening the ZNF526 mutation spectrum and detailing the associated clinical profile. These findings are valuable for genetic diagnosis and family counseling in cases of this syndrome.
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Affiliation(s)
- Shaoxin Li
- Department of RehabilitationAnhui Provincial Children's HospitalHefeiChina
| | - Hui Fang
- Department of RehabilitationAnhui Provincial Children's HospitalHefeiChina
| | - Hong Li
- Department of RehabilitationAnhui Provincial Children's HospitalHefeiChina
| | - Min Peng
- Chigene (Beijing) Translational Medical Research Center Co.BeijingChina
| | - Jinsong Bao
- Department of RehabilitationAnhui Provincial Children's HospitalHefeiChina
| | - Yunfei Cai
- Department of RehabilitationAnhui Provincial Children's HospitalHefeiChina
| | - Jing Chen
- Department of RehabilitationAnhui Provincial Children's HospitalHefeiChina
| | - Zhige Li
- Department of RehabilitationAnhui Provincial Children's HospitalHefeiChina
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10
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Buhusayen FAM, Alashraaf M, Jadah RHSH. Identification of ARV1 Gene Mutations in Three Pediatric Cases of Developmental and Epileptic Encephalopathy. Cureus 2025; 17:e82903. [PMID: 40416165 PMCID: PMC12103100 DOI: 10.7759/cureus.82903] [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] [Accepted: 04/23/2025] [Indexed: 05/27/2025] Open
Abstract
The ARV1 gene produces a protein made up of 271 amino acids that helps transport fats across membranes within the cell's endoplasmic reticulum (ER), a key area involved in processing lipids. This protein is related to an enzyme called ACAT2, which is important for managing cholesterol and fat levels in the body. This protein features an N-terminal zinc-binding motif located in the cytosol, followed by multiple domains that span the ER membrane, and concludes with a C-terminus that terminates in the ER lumen. ARV1 deficiency clinically manifests as autosomal recessive developmental and epileptic encephalopathy 38 (DEE38) in humans. In this report, we share three pediatric cases presenting with early-onset epileptic encephalopathy and significant developmental delay. Whole-exome sequencing (WES) identified two pathogenic ARV1 variants: p.Cys61Tyr (missense) and p.Phe144Argfs5* (frameshift), both predicted to severely disrupt protein structure and function. These findings add to what we know about how mutations in the ARV1 gene can lead to developmental and epileptic encephalopathy (DEE38), and they strengthen our understanding of the gene's role in brain development. The children in our report also show how widely the symptoms of ARV1-related conditions can vary from case to case. Their experiences highlight just how important early genetic testing can be, especially for young patients with unexplained seizures and developmental challenges. Our report contributes to understanding the spectrum of complex neurological conditions. By sharing these cases, we're adding to the growing knowledge about ARV1-related encephalopathies and reinforcing why this gene deserves a place in targeted epilepsy genetic panels.
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Affiliation(s)
| | - Mohamed Alashraaf
- General Surgery, King Hamad University Hospital, Royal Medical Services, Riffa, BHR
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11
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Pettinato F, Marzà V, Ciantia F, Romanello G, Cocuzza MD, Fichera M, Rizzo R, Barone R. Acute neurological regression following fever as presenting sign of pontocerebellar hypoplasia type 2D ( SEPSECS mutation). Biomed Rep 2025; 22:67. [PMID: 40017499 PMCID: PMC11865714 DOI: 10.3892/br.2025.1945] [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: 05/09/2024] [Accepted: 09/10/2024] [Indexed: 03/01/2025] Open
Abstract
Pontocerebellar hypoplasia type 2D (PCH2D) is caused by mutations in the gene encoding O-phosphoseryl-tRNA:selenocysteinyl-tRNA synthase (SEPSECS; chromosome 4p15.2). This is a key enzyme in the biosynthesis of selenoproteins, which act in maintaining antioxidant systems. To date, 26 patients with PCH2D have been reported, all with neurological involvement characterized by progressive pontocerebellar and cerebral atrophy. The present study reports on a patient with compound heterozygosity in the SEPSECS gene, including a novel missense variant, c.440G>A (p.Ser147Asn). The patient exhibited acute neurological regression following a vaccination-related fever, which is reminiscent of primary mitochondrial disease. In addition, the patient displayed severe spastic tetraparesis, convergent strabismus and postnatal onset of microcephaly, as well as recurrent blood lactate elevation. Brain MRI showed multiple alterations in the peri/supraventricular and subcortical white matter and progressive pontocerebellar and cerebral atrophy. A review of the clinical spectrum associated with SEPSECS mutations was conducted and the first report on a patient with SEPSECS mutations of acute neurological regression following a catabolic stressor at the onset of PCH2D was provided. This study broadens the genetic background of PCH2D and associated PCH2D phenotype, supporting the causal link between selenoprotein biosynthesis deficiency and mitochondrial disorders.
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Affiliation(s)
- Fabio Pettinato
- Child and Adolescent Neurology and Psychiatric Section, Azienda Ospedaliera Universitaria Policlinico ‘G.Rodolico-San Marco’, Department of Clinical and Experimental Medicine, University of Catania, I-95124 Catania, Italy
| | - Viviana Marzà
- Child and Adolescent Neurology and Psychiatric Section, Azienda Ospedaliera Universitaria Policlinico ‘G.Rodolico-San Marco’, Department of Clinical and Experimental Medicine, University of Catania, I-95124 Catania, Italy
| | - Fiorella Ciantia
- Child and Adolescent Neurology and Psychiatric Section, Azienda Ospedaliera Universitaria Policlinico ‘G.Rodolico-San Marco’, Department of Clinical and Experimental Medicine, University of Catania, I-95124 Catania, Italy
| | - Giorgia Romanello
- Child and Adolescent Neurology and Psychiatric Section, Azienda Ospedaliera Universitaria Policlinico ‘G.Rodolico-San Marco’, Department of Clinical and Experimental Medicine, University of Catania, I-95124 Catania, Italy
| | - Maria Donatella Cocuzza
- Child and Adolescent Neurology and Psychiatric Section, Azienda Ospedaliera Universitaria Policlinico ‘G.Rodolico-San Marco’, Department of Clinical and Experimental Medicine, University of Catania, I-95124 Catania, Italy
| | - Marco Fichera
- Department of Biomedical and Biotechnological Sciences, Medical Genetics, University of Catania, I-95124 Catania, Italy
- Research Unit of Rare Diseases and Neurodevelopmental Disorders, Oasi Research Institute, I-94018 Troina, Italy
| | - Renata Rizzo
- Child and Adolescent Neurology and Psychiatric Section, Azienda Ospedaliera Universitaria Policlinico ‘G.Rodolico-San Marco’, Department of Clinical and Experimental Medicine, University of Catania, I-95124 Catania, Italy
| | - Rita Barone
- Child and Adolescent Neurology and Psychiatric Section, Azienda Ospedaliera Universitaria Policlinico ‘G.Rodolico-San Marco’, Department of Clinical and Experimental Medicine, University of Catania, I-95124 Catania, Italy
- Research Unit of Rare Diseases and Neurodevelopmental Disorders, Oasi Research Institute, I-94018 Troina, Italy
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12
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Hammad Seroor Jadah R, Al Aghawani JA. When Genes Misfire: ARV1 and the Unseen Battle Against Pediatric Epileptic Encephalopathy. Cureus 2025; 17:e82297. [PMID: 40376369 PMCID: PMC12080507 DOI: 10.7759/cureus.82297] [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] [Accepted: 04/15/2025] [Indexed: 05/18/2025] Open
Abstract
The rare ARV1 gene encodes a protein that is crucial for homeostasis and sterol metabolism. It is vital for maintaining membrane integrity and cellular stability. Given the limited epidemiological data, it is evident that ARV1 mutations are rare, showing significant neurological and systemic manifestations, including developmental delays, epilepsy, or cardiomyopathy. We report a case of a six-month-old female presenting with global developmental delay, hypotonia, and poor fine motor milestones. MRI revealed bifrontal subarachnoid spaces and abnormalities in the right parietal lobe. A homozygous pathogenic variant in the ARV1 gene (p.Phe144Argfs*5) was confirmed through whole exome sequencing (WES), thereby diagnosing autosomal recessive developmental and epileptic encephalopathy-38 (DEE38). Through this report, we aim to highlight the importance of early diagnosis in rare genetic disorders and increase awareness among healthcare professionals.
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Affiliation(s)
| | - Jood A Al Aghawani
- Medicine and Surgery, Royal College of Surgeons in Ireland - Bahrain, Busaiteen, BHR
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13
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Zhang H, Janina N, Ütkür K, Manivannan T, Zhang L, Wang L, Grefen C, Schaffrath R, Krämer U. Diphthamide formation in Arabidopsis requires DPH1-interacting DPH2 for light and oxidative stress resistance. PLANT PHYSIOLOGY 2025; 197:kiaf128. [PMID: 40200557 DOI: 10.1093/plphys/kiaf128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2025] [Accepted: 02/23/2025] [Indexed: 04/10/2025]
Abstract
Diphthamide is a posttranslationally modified histidine residue of eukaryotic TRANSLATION ELONGATION FACTOR 2 (eEF2) and the target of diphtheria toxin in human cells. In yeast and mammals, the 4Fe-4S cluster-containing proteins Dph1 and Dph2 catalyze the first biosynthetic step of diphthamide formation. Here, we identify Arabidopsis (Arabidopsis thaliana) DPH2 and show that it is required for diphthamide biosynthesis, localizes to the cytosol, and interacts physically with AtDPH1. Arabidopsis dph2 mutants form shorter primary roots and smaller rosettes than the wild type, similar to dph1 mutants which we characterized previously. Additionally, increased ribosomal -1 frameshifting error rates and attenuated TARGET OF RAPAMYCIN (TOR) kinase activity in dph2 mutants also phenocopy the dph1 mutant. Beyond the known heavy metal hypersensitivity and heat shock tolerance of dph1, we show here that both dph1 and dph2 mutants are hypersensitive to elevated light intensities and oxidative stress and that wild-type Arabidopsis seedlings accumulate diphthamide-unmodified eEF2 under oxidative stress. Both mutants share the deregulation of 1,186 transcripts associated with several environmental and hormone responses. AtDPH1 and AtDPH2 do not complement the corresponding mutants of Saccharomyces cerevisiae. In summary, DPH2 and DPH1 interact to function inter-dependently in diphthamide formation, the maintenance of translational fidelity, wild-type growth rates, and TOR kinase activation, and they contribute to mitigating damage from elevated light intensities and oxidative stress. Under oxidative stress, a dose-dependent loss of diphthamide could potentiate downstream effects in a feed-forward loop. This work advances our understanding of translation and its interactions with growth regulation and stress responses in plants.
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Affiliation(s)
- Hongliang Zhang
- Molecular Genetics and Physiology of Plants, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum 44801, Germany
| | - Nadežda Janina
- Molecular Genetics and Physiology of Plants, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum 44801, Germany
| | - Koray Ütkür
- Microbiology, Institute for Biology, University of Kassel, Kassel 34132, Germany
| | | | - Lei Zhang
- Molecular and Cellular Botany, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum 44801, Germany
| | - Lizhen Wang
- Molecular Genetics and Physiology of Plants, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum 44801, Germany
| | - Christopher Grefen
- Molecular and Cellular Botany, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum 44801, Germany
| | - Raffael Schaffrath
- Microbiology, Institute for Biology, University of Kassel, Kassel 34132, Germany
| | - Ute Krämer
- Molecular Genetics and Physiology of Plants, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum 44801, Germany
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14
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Gowda VK, Srinivasan VM, Kinhal UV, Srinivas SM, Pandey H, Phani NM, Dhayalan P, Lal D. Expanding the Phenotypic Spectrum of DPH2-Related Disorder. Am J Med Genet A 2025:e64061. [PMID: 40130534 DOI: 10.1002/ajmg.a.64061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2024] [Revised: 01/06/2025] [Accepted: 03/11/2025] [Indexed: 03/26/2025]
Abstract
Biallelic variants in DPH2 have recently been reported to cause the syndrome of developmental delay with short stature, dysmorphic facial features, and sparse hair-2, also known as diphthamide deficiency syndrome-2. Here we report a child with a biallelic loss-of-function variant p.(Arg477*) in DPH2 with clinical features of developmental delay, failure to thrive, sparse hair, seizures that responded to antiepileptics, proportionate short stature, dysmorphism, and hypotonia. Neuroimaging abnormalities were cerebral atrophy, periventricular white matter hyperintensities, and prominent subarachnoid spaces. The electroencephalogram was suggestive of modified hypsarrhythmia. The phenotype of the current case overlaps with the previous cases reported in the literature; however, seizures, behavioral issues, and neuroimaging abnormalities have not been reported to date. This is the third report from the world. The current report gives a detailed account of an Indian child with a DPH2-related disorder.
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Affiliation(s)
- Vykuntaraju K Gowda
- Department of Pediatric Neurology, Indira Gandhi Institute of Child Health, Bangalore, India
| | | | - Uddhava V Kinhal
- Department of Pediatric Neurology, Indira Gandhi Institute of Child Health, Bangalore, India
| | - Sahana M Srinivas
- Department of Pediatric Dermatology, Indira Gandhi Institute of Child Health, Bangalore, India
| | - Himani Pandey
- Department of Molecular Genetics, Redcliffe Labs, Noida, India
| | - Nagaraja M Phani
- Department of Molecular Genetics, Lifecell International, Chennai, India
| | - Pavithra Dhayalan
- Department of Molecular Genetics, Lifecell International, Chennai, India
| | - Devi Lal
- Department of Zoology, Ramjas College, University of Delhi, Delhi, India
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15
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Riffe RM, Downes GB. Neurogenetic disorders associated with mutations in the FERRY complex: a novel disease class? Biol Open 2025; 14:BIO061808. [PMID: 40062705 PMCID: PMC11928052 DOI: 10.1242/bio.061808] [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] [Indexed: 03/23/2025] Open
Abstract
The five-subunit endosomal Rab5 and RNA/ribose intermediary (FERRY) complex is a newly described protein complex consisting of TBCK, PPP1R21, FERRY3 (previously C12orf4), CRYZL1, and GATD1. The FERRY complex is proposed to function as a Rab5 effector to shuttle mRNA to the cell periphery for local translation, a process especially important in cells with far reaching processes. Interestingly, three members of the FERRY complex are associated with ultra-rare neurogenetic disorders. Mutation of TBCK causes TBCK syndrome, mutation of PPP1R21 is associated with PPP1R21-related intellectual disability, and mutation of FERRY3 results in an autosomal recessive intellectual disability. Neurologic disorders have yet to be associated with mutation of GATD1 or CRYZL1. Here, we provide a review of each FERRY complex-related neurologic disorder and draw clinical comparisons between the disease states. We also discuss data from the current cellular and animal models available to study these disorders, which is notably disparate and scattered across different cell types and systems. Taken together, we explore the possibility that these three diseases may represent one shared disease class, which could be further understood by combining and comparing known information about each individual disease. If true, this could have substantial implications on our understanding of the cellular role of the FERRY complex and on treatment strategies for affected individuals, allowing researchers, clinicians, and patient organizations to maximize the utility of research efforts and resources to support patients with these disorders.
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Affiliation(s)
- R. Madison Riffe
- Neuroscience and Behavior Graduate Program, University of Massachusetts Amherst, Amherst, MA, 01003, USA
- Biology Department, University of Massachusetts Amherst, Amherst, MA, 01003, USA
| | - Gerald B. Downes
- Neuroscience and Behavior Graduate Program, University of Massachusetts Amherst, Amherst, MA, 01003, USA
- Biology Department, University of Massachusetts Amherst, Amherst, MA, 01003, USA
- Molecular and Cellular Biology Graduate Program, University of Massachusetts Amherst, Amherst, MA, 01003, USA
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16
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AlAbdi L, Maddirevula S, Aljamal B, Hamid H, Almulhim A, Hashem MO, Algoos Y, Alqahtani M, Albaloshi S, Alghamdi M, Alduaylij M, Shamseldin HE, Nadeef S, Patel N, Abdulwahab F, Abouyousef O, Alshidi T, Jaafar A, Abouelhoda M, Alhazzani A, Alfares A, Qudair A, Alsulaiman A, Alhashem A, Khan AO, Chedrawi A, Alebdi B, AlAjlan F, Alotaibi F, Alzaidan H, Banjar H, Abdelraouf H, Alkuraya H, Abumansour I, Alfayez K, Tulbah M, Alowain M, Alqahtani M, El-Kalioby M, Shboul M, Sulaiman R, Al Tala S, Khan S, Coskun S, Mrouge S, Alenazi W, Rahbeeni Z, Alkuraya FS. Arab founder variants: Contributions to clinical genomics and precision medicine. MED 2025; 6:100528. [PMID: 39504961 DOI: 10.1016/j.medj.2024.10.005] [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: 06/17/2024] [Revised: 08/16/2024] [Accepted: 10/07/2024] [Indexed: 11/08/2024]
Abstract
BACKGROUND Founder variants are ancestral variants shared by individuals who are not closely related. The large effect size of some of these variants in the context of Mendelian disorders offers numerous precision medicine opportunities. METHODS Using one of the largest datasets on Mendelian disorders in the Middle East, we identified 2,908 medically relevant founder variants derived from 18,360 exomes and genomes and investigated their contribution to the clinical annotation of the human genome. FINDINGS Strikingly, ∼34% of Arab founder variants are absent in gnomAD. We found a strong contribution of Arab founder variants to the identification of novel gene-disease links (n = 224) and the support/dispute (n = 81 support, n = 101 dispute) of previously reported candidate gene-disease links. The powerful segregation evidence generated by Arab founder variants allowed many ClinVar and Human Gene Mutation Database variants to be reclassified. Overall, 39.5% of diagnostic reports from our clinical lab are based on founder variants, and 19.41% of tested individuals carry at least one pathogenic founder variant. The presumptive loss-of-function mechanism that typically underlies autosomal recessive diseases means that Arab founder variants also offer unique opportunities in "druggable genome" research. Arab founder variants were also informative of migration patterns in the Middle East consistent with documented historical accounts. CONCLUSIONS We highlight the contribution of founder variants from an under-represented population group to precision medicine and inform future prevention programs. Our study also sheds light on the added value of these variants in supplementing other lines of research in tracing population history. FUNDING There is no funding for this work.
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Affiliation(s)
- Lama AlAbdi
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh 11564, Saudi Arabia
| | - Sateesh Maddirevula
- Department of Clinical Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh 11564, Saudi Arabia
| | - Bayan Aljamal
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh 11564, Saudi Arabia
| | - Halima Hamid
- Department of Zoology, College of Science, King Saud University, Riyadh 11362, Saudi Arabia
| | - Aisha Almulhim
- Department of Zoology, College of Science, King Saud University, Riyadh 11362, Saudi Arabia
| | - Mais O Hashem
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh 11564, Saudi Arabia
| | - Yusra Algoos
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh 11564, Saudi Arabia
| | - Mashael Alqahtani
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh 11564, Saudi Arabia
| | - Shahad Albaloshi
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh 11564, Saudi Arabia
| | - Mohammed Alghamdi
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh 11564, Saudi Arabia
| | - Mohammed Alduaylij
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh 11564, Saudi Arabia
| | - Hanan E Shamseldin
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh 11564, Saudi Arabia
| | - Seba Nadeef
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh 11564, Saudi Arabia
| | - Nisha Patel
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh 11564, Saudi Arabia
| | - Firdous Abdulwahab
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh 11564, Saudi Arabia
| | - Omar Abouyousef
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh 11564, Saudi Arabia
| | - Tarfa Alshidi
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh 11564, Saudi Arabia
| | - Amal Jaafar
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh 11564, Saudi Arabia
| | - Mohamed Abouelhoda
- Department of Computational Science, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh 11564, Saudi Arabia
| | - Adel Alhazzani
- Neuroscience Center, King Faisal Specialist Hospital and Research Center, Riyadh 11564, Saudi Arabia
| | - Ahmed Alfares
- Department of Clinical Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh 11564, Saudi Arabia
| | - Ahmad Qudair
- Department of Pediatrics, King Faisal Specialist Hospital and Research Center, Jeddah 23433, Saudi Arabia
| | - Ahood Alsulaiman
- Department of Medical Genomics, Centre for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh 11564, Saudi Arabia
| | - Amal Alhashem
- Department of Pediatrics, Prince Sultan Military Medical Center, Riyadh 12233, Saudi Arabia; College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia; Seha Virtual Hospital, Ministry of Health, Riyadh 12382, Saudi Arabia
| | - Arif O Khan
- Eye Institute, Cleveland Clinic, Abu Dhabi, UAE; Department of Ophthalmology, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, OH 44195, USA
| | - Aziza Chedrawi
- Department of Medical Genomics, Centre for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh 11564, Saudi Arabia
| | - Basel Alebdi
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh 11564, Saudi Arabia
| | - Fahad AlAjlan
- Neuroscience Center, King Faisal Specialist Hospital and Research Center, Riyadh 11564, Saudi Arabia
| | - Fawaz Alotaibi
- Neuroscience Center, King Faisal Specialist Hospital and Research Center, Riyadh 11564, Saudi Arabia
| | - Hamad Alzaidan
- Department of Medical Genomics, Centre for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh 11564, Saudi Arabia
| | - Hanaa Banjar
- Department of Pediatrics, King Faisal Specialist Hospital and Research Center, Riyadh 11564, Saudi Arabia
| | - Hanem Abdelraouf
- Department of Pediatrics, Prince Sultan Military Medical Center, Riyadh 12233, Saudi Arabia
| | - Hisham Alkuraya
- Global Eye Care, Specialized Medical Center Hospital, Riyadh 13215, Saudi Arabia
| | - Iman Abumansour
- Department of Pediatrics, King Faisal Specialist Hospital and Research Center, Jeddah 23433, Saudi Arabia; Department of Medical Genetics, Faculty of Medicine, Umm Al-Qura University, Makkah 24382, Saudi Arabia
| | - Khowlah Alfayez
- Department of Pediatrics, Prince Sultan Military Medical Center, Riyadh 12233, Saudi Arabia
| | - Maha Tulbah
- Department of Obstetrics and Gynecology, King Faisal Specialist Hospital and Research Center, Riyadh 11564, Saudi Arabia
| | - Mohammed Alowain
- Department of Medical Genomics, Centre for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh 11564, Saudi Arabia; College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia
| | - Mohammed Alqahtani
- Neuroscience Center, King Faisal Specialist Hospital and Research Center, Riyadh 11564, Saudi Arabia
| | - Mohammed El-Kalioby
- Department of Computational Science, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh 11564, Saudi Arabia
| | - Mohammad Shboul
- Department of Medical Laboratory Sciences, Faculty of Medical Sciences, Jordan University of Science and Technology, Irbid 22110, Jordan
| | - Raashda Sulaiman
- Department of Medical Genomics, Centre for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh 11564, Saudi Arabia
| | - Saed Al Tala
- Department of Pediatrics, Armed Forces Hospital, Khamis Mushayt 62413, Saudi Arabia
| | - Sameena Khan
- Neuroscience Center, King Faisal Specialist Hospital and Research Center, Riyadh 11564, Saudi Arabia
| | - Serdar Coskun
- Department of Pathology and Laboratory Medicine, King Faisal Specialist Hospital and Research Center and College of Medicine, Riyadh 11564, Saudi Arabia
| | - Sobaihi Mrouge
- Department of Pediatrics, King Faisal Specialist Hospital and Research Center, Jeddah 23433, Saudi Arabia
| | - Walaa Alenazi
- Department of Computational Science, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh 11564, Saudi Arabia
| | - Zuhair Rahbeeni
- Department of Medical Genomics, Centre for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh 11564, Saudi Arabia
| | - Fowzan S Alkuraya
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh 11564, Saudi Arabia; Department of Pediatrics, Prince Sultan Military Medical Center, Riyadh 12233, Saudi Arabia.
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17
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Flores-Mendez M, Tintos-Hernández JA, Ramos-Rodriguez L, Miles L, Lo TY, Song Y, Ortiz-González XR. TBCK-deficiency leads to compartment-specific mRNA and lysosomal trafficking defects in patient-derived neurons. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.03.02.641041. [PMID: 40093117 PMCID: PMC11908138 DOI: 10.1101/2025.03.02.641041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 03/19/2025]
Abstract
Monogenic pediatric neurodegenerative disorders can reveal fundamental cellular mechanisms that underlie selective neuronal vulnerability. TBCK-Encephaloneuronopathy (TBCKE) is a rare autosomal recessive disorder caused by stop-gain variants in the TBCK gene. Clinically, patients show evidence of profound neurodevelopmental delays, but also symptoms of progressive encephalopathy and motor neuron disease. Yet, the physiological role of TBCK protein remains unclear. We report a human neuronal TBCKE model, derived from iPSCs homozygous for the Boricua variant (p.R126X). Using unbiased proteomic analyses of human neurons, we find TBCK interacts with PPP1R21, C12orf4, and Cryzl1, consistent with TBCK being part of the FERRY mRNA transport complex. Loss of TBCK leads to depletion of C12ORF4 protein levels across multiple cell types, suggesting TBCK may also play a role regulating at least some members of the FERRY complex. We find that TBCK preferentially, but not exclusively, localizes to the surface of endolysosomal vesicles and can colocalize with mRNA in lysosomes. Furthermore, TBCK-deficient neurons have reduced mRNA content in the axonal compartment relative to the soma. TBCK-deficient neurons show reduced levels of the lysosomal dynein/dynactin adapter protein JIP4, which functionally leads to TBCK-deficient neurons exhibiting striking lysosomal axonal retrograde trafficking defects. Hence, our work reveals that TBCK can mediate endolysosomal trafficking of mRNA, particularly along lysosomes in human axonal compartments. TBCK-deficiency leads to compartment-specific mRNA and lysosomal trafficking defects in neurons, which likely contribute to the preferential susceptibility to neurodegeneration.
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Affiliation(s)
- Marco Flores-Mendez
- Department of Pediatrics, Division of Neurology, The Children's of Philadelphia, Philadelphia, PA
- Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Jesus A Tintos-Hernández
- Department of Pediatrics, Division of Neurology, The Children's of Philadelphia, Philadelphia, PA
- Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Leonardo Ramos-Rodriguez
- Department of Biomedical Graduate Studies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Leann Miles
- Department of Biomedical Graduate Studies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Tsz Y Lo
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Yuanquan Song
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, PA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA
| | - Xilma R Ortiz-González
- Department of Pediatrics, Division of Neurology, The Children's of Philadelphia, Philadelphia, PA
- Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA
- Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
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18
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Chekroun I, Shenbagam S, Almarri MA, Mokrab Y, Uddin M, Alkhnbashi OS, Zaki MS, Najmabadi H, Kahrizi K, Fakhro KA, Almontashiri NAM, Ali FR, Özbek U, Reversade B, Alkuraya FS, Alsheikh-Ali A, Abou Tayoun AN. Genomics of rare diseases in the Greater Middle East. Nat Genet 2025; 57:505-514. [PMID: 39901015 DOI: 10.1038/s41588-025-02075-8] [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: 09/23/2024] [Accepted: 01/06/2025] [Indexed: 02/05/2025]
Abstract
The Greater Middle East (GME) represents a concentrated region of unparalleled genetic diversity, characterized by an abundance of distinct alleles, founder mutations and extensive autozygosity driven by high consanguinity rates. These genetic hallmarks present a unique, yet vastly untapped resource for genomic research on Mendelian diseases. Despite this immense potential, the GME continues to face substantial challenges in comprehensive data collection and analysis. This Perspective highlights the region's unique position as a natural laboratory for genetic discovery and explores the challenges that have stifled progress thus far. Importantly, we propose strategic solutions, advocating for an all-inclusive research approach. With targeted investment and focused efforts, the latent genetic wealth in the GME can be transformed into a global hub for genomic research that will redefine and advance our understanding of the human genome.
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Affiliation(s)
- Ikram Chekroun
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai Health, Dubai, UAE
| | - Shruti Shenbagam
- Al Jalila Genomics Center of Excellence, Al Jalila Children's Specialty Hospital, Dubai, UAE
| | - Mohamed A Almarri
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai Health, Dubai, UAE
| | - Younes Mokrab
- Research Branch, Sidra Medicine, Doha, Qatar
- Department of Genetic Medicine, Weill Cornell Medicine-Qatar, Doha, Qatar
- College of Health Sciences, Qatar University, Doha, Qatar
| | - Mohammed Uddin
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai Health, Dubai, UAE
- Center for Applied and Translational Genomics, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai Health, Dubai, UAE
| | - Omer S Alkhnbashi
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai Health, Dubai, UAE
- Center for Applied and Translational Genomics, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai Health, Dubai, UAE
| | - Maha S Zaki
- Department of Clinical Genetics, Human Genetics and Genome Research Institute, National Research Centre, Cairo, Egypt
| | - Hossein Najmabadi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
- Kariminejad-Najmabadi Pathology and Genetics Center, Tehran, Iran
| | - Kimia Kahrizi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
- Kariminejad-Najmabadi Pathology and Genetics Center, Tehran, Iran
| | - Khalid A Fakhro
- Research Branch, Sidra Medicine, Doha, Qatar
- Department of Genetic Medicine, Weill Cornell Medicine-Qatar, Doha, Qatar
| | - Naif A M Almontashiri
- College of Applied Medical Sciences and Center for Genetics and Inherited Diseases, Taibah University, Madinah, Kingdom of Saudi Arabia
| | - Fahad R Ali
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai Health, Dubai, UAE
- Center for Genomic Discovery, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai Health, Dubai, UAE
| | - Uğur Özbek
- Rare and Undiagnosed Disease Platform, IBG-Izmir Biomedicine and Genome Center, Izmir, Türkiye
| | - Bruno Reversade
- Laboratory of Human Genetics and Therapeutics, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
| | - Fowzan S Alkuraya
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Kingdom of Saudi Arabia
- Lifera Omics, Riyadh, Kingdom of Saudi Arabia
| | - Alawi Alsheikh-Ali
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai Health, Dubai, UAE
- Dubai Health, Dubai, UAE
| | - Ahmad N Abou Tayoun
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai Health, Dubai, UAE.
- Al Jalila Genomics Center of Excellence, Al Jalila Children's Specialty Hospital, Dubai, UAE.
- Center for Genomic Discovery, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai Health, Dubai, UAE.
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19
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Lesage S, Salih MA. Editorial: Consanguinity and rare genetic neurological diseases. Front Neurol 2025; 16:1494253. [PMID: 39995785 PMCID: PMC11847681 DOI: 10.3389/fneur.2025.1494253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2024] [Accepted: 01/22/2025] [Indexed: 02/26/2025] Open
Affiliation(s)
- Suzanne Lesage
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Institut National de la Recherche Médicale-U1127, Centre National de la Recherche Scientifique-UMR7225, APHP, Paris, France
| | - Mustafa A. Salih
- King Abdulaziz City for Science and Technology (KACST), Riyadh, Saudi Arabia
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20
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Novis LE, Silva TYT, Pedroso JL, Barsottini OGP. Demystifying the Etiology of ILOCA in the Genomic Era: A Narrative Review. CEREBELLUM (LONDON, ENGLAND) 2025; 24:45. [PMID: 39920364 DOI: 10.1007/s12311-025-01798-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 02/03/2025] [Indexed: 02/09/2025]
Abstract
BACKGROUND Idiopathic Late-Onset Cerebellar Ataxia (ILOCA) is a challenging and heterogeneous disorder characterized by progressive cerebellar ataxia beginning after the age of 40 without a family history of cerebellar ataxia. Despite extensive investigations, many cases remain undiagnosed. The advent Next Generation Sequencing (NGS) has significantly advanced the identification of genetic causes associated with ILOCA. OBJECTIVE This study aims to review the concept of ILOCA, its historical perspective, epidemiology, diagnostic criteria, and the impact of the new era of genetic diagnosis facilitated by NGS technologies. METHODS A comprehensive literature review was conducted, focusing on the genetic advancements in diagnosing ILOCA. RESULTS ILOCA accounts for a significant proportion of late-onset cerebellar ataxias. The prevalence of late-onset cerebellar ataxias ranges from 2.2 to 12.4 per 100,000 individuals, with genetic causes identified in up to 30-50% of cases using NGS. Key genetic findings include repeat expansion disorders such as Spinocerebellar Ataxia type 27 B, Cerebellar Ataxia, Neuropathy and Vestibular Areflexia Syndrome and Friedreich Ataxia. SCAs and Autosomal Recessive Cerebellar Ataxia caused by point mutations are also frequently observed in large cohorts. Advances in NGS have increased the diagnostic yield for ILOCA. CONCLUSION ILOCA represents a significant diagnostic challenge due to its heterogeneous nature and the overlap with other neurodegenerative and genetic conditions. The use of NGS technologies has revolutionized the diagnostic approach, uncovering genetic causes in a substantial number of previously undiagnosed cases. Routine investigation of specific genes associated with ILOCA is recommended to improve diagnostic accuracy and patient management.
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Affiliation(s)
- Luiz Eduardo Novis
- Setor de Neurologia Geral e Ataxias, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil.
- Department of Neurology and Neurosurgery, Escola Paulista de Medicina, Universidade Federal de São Paulo (UNIFESP), Pedro Toledo Street, 650, 04039-002, Vila Clementino, São Paulo, SP, Brazil.
| | | | - José Luiz Pedroso
- Setor de Neurologia Geral e Ataxias, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Orlando Graziani Póvoas Barsottini
- Department of Neurology and Neurosurgery, Escola Paulista de Medicina, Universidade Federal de São Paulo (UNIFESP), Pedro Toledo Street, 650, 04039-002, Vila Clementino, São Paulo, SP, Brazil
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21
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Hochman L, Drummond A, Morgan K. Cerebellar Ataxia, Impaired Intellectual Development, and Disequilibrium Syndrome-2: A Case Report. Cureus 2025; 17:e78066. [PMID: 40013199 PMCID: PMC11864093 DOI: 10.7759/cureus.78066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/27/2025] [Indexed: 02/28/2025] Open
Abstract
Pathogenic variants in the WDR81 gene on chromosome 17p13.3 have been linked to cerebellar ataxia, impaired intellectual development, and disequilibrium syndrome-2 (CAMRQ2), a rare disorder characterized by congenital cerebellar ataxia (a condition causing impaired coordination and balance due to cerebellar dysfunction), intellectual disability, and gait abnormalities. Additional features include thoracic kyphosis, scoliosis, short stature, intention tremor, and cerebellar atrophy. We present a case of a mildly affected female from a non-consanguineous family, expanding the clinical spectrum of this disorder. The patient, born at term as part of a dizygotic-diamniotic twin pregnancy, exhibited developmental delays, feeding difficulties, and unsteady gait. This case highlights the importance of iterative genetic testing, as initial evaluations, including brain MRI and genetic testing, were nondiagnostic. However, reanalysis at age five identified a homozygous pathogenic variant in WDR81, demonstrating how periodic re-evaluation of genetic data can aid in diagnosing rare disorders that may have been previously unrecognized. The patient continues to experience cerebellar ataxia and hypotonia, characterized by decreased muscle tone and reduced strength, with no other major medical conditions. She receives physical and occupational therapies and is academically at grade level with tutoring support. This case highlights the phenotypic variability of CAMRQ2 and underscores the importance of considering WDR81 variants in patients with cerebellar ataxia, even in the absence of consanguinity.
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Affiliation(s)
- Livia Hochman
- Medicine, Florida State University College of Medicine, Tallahassee, USA
| | - Alrick Drummond
- Pediatrics, Florida State University College of Medicine, Tallahassee, USA
| | - Kara Morgan
- Genetics, University of South Florida Health, Tampa, USA
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22
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Waskow ER, Undiagnosed Diseases Network, Emrick LT, Rosenfeld JA, Ketkar S, Burrage LC, Scott DA. Recessive loss-of-function variants in DPH1 identified as the molecular cause in a sibling pair previously diagnosed with Fine-Lubinsky syndrome. Am J Med Genet A 2025; 197:e63845. [PMID: 39166428 PMCID: PMC11637968 DOI: 10.1002/ajmg.a.63845] [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] [Revised: 07/04/2024] [Accepted: 07/31/2024] [Indexed: 08/22/2024]
Abstract
Fine-Lubinsky syndrome is a rare clinically defined syndrome sometimes referred to as brachycephaly, deafness, cataract, microstomia, and impaired intellectual development syndrome. Here we provide a clinical and molecular update for a sibling pair diagnosed with Fine-Lubinsky syndrome. An extensive genetic work-up, including chromosomal microarray analysis and quad exome sequencing, was nondiagnostic. However, a research reanalysis of their exome sequencing data revealed that both were homozygous for an intronic c.749+39G>A [NM_001383.6] variant in DPH1. RNAseq analysis performed on RNA from fibroblasts revealed significantly reduced expression of DPH1 transcripts suggestive of abnormal splicing followed by nonsense mediated mRNA decay. Since the phenotypes of this sibling pair were consistent with those associated with the inheritance of biallelic pathogenic variants in DPH1, they were given a diagnosis of developmental delay with short stature, dysmorphic facial features, and sparse hair 1 (DEDSSH1). This leads us to recommend that all individuals with a clinical diagnosis of Fine-Lubinsky syndrome be screened for variants in DPH1. The clinical histories of this sibling pair emphasize that hearing loss associated with DEDSSH1 may remit over time and that individuals with DEDSSH1 should be monitored for the development of cardiomyopathy. This case also demonstrates the clinical utility of RNAseq as a means of functionally validating the effects of intronic variants that may affect splicing.
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Affiliation(s)
- Emily R. Waskow
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030
- Texas Children’s Hospital, Houston, TX, 77030
| | | | - Lisa T. Emrick
- Texas Children’s Hospital, Houston, TX, 77030
- Department of Pediatrics, Division of Pediatric Neurology and Developmental Neuroscience, Baylor College of Medicine, Houston, TX 77030
| | - Jill A. Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030
| | - Shamika Ketkar
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030
| | - Lindsay C. Burrage
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030
- Texas Children’s Hospital, Houston, TX, 77030
| | - Daryl A. Scott
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030
- Texas Children’s Hospital, Houston, TX, 77030
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23
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Corbalan JJ, Frietze KK, Nickels J, Sturley SL. Arv1; a "Mover and Shaker" of Subcellular Lipids. CONTACT (THOUSAND OAKS (VENTURA COUNTY, CALIF.)) 2025; 8:25152564251314601. [PMID: 39845563 PMCID: PMC11748065 DOI: 10.1177/25152564251314601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2025] [Accepted: 01/06/2025] [Indexed: 01/24/2025]
Abstract
The composition of eukaryotic membranes reflects a varied but precise amalgam of lipids. The genetic underpinning of how such diversity is achieved or maintained is surprisingly obscure, despite its clear metabolic and pathophysiological impact. The Arv1 protein is represented in all eukaryotes and was initially identified in the model eukaryote Sacccharomyces cerevisiae as a candidate transporter of lipids from the endoplasmic reticulum. Human Arv1 has been shown to directly bind cholesterol and fatty acid affinity probes. Murine in vivo studies point to a role for ARV1 in regulating obesity, glucose tolerance, insulin sensitivity and brain function. Multiple human ARV1 variants have been associated with epileptic encephalopathy, cerebellar ataxia, and severe intellectual deficits. We hypothesize that Arv1 acts as an energy independent, lipid scramblase at the endoplasmic reticulum thereby modulating membrane lipid asymmetry and thus the trafficking of sterols and the substituents of glycosyl-phosphatidylinositol and sphingolipid biosynthesis.
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Affiliation(s)
- J. Jose Corbalan
- Institute of Metabolic Disorders, Genesis Biotechnology Group, 1000 Waterview Drive, Hamilton, NJ 08691, USA
| | - Karla K. Frietze
- Institute of Metabolic Disorders, Genesis Biotechnology Group, 1000 Waterview Drive, Hamilton, NJ 08691, USA
| | - Joseph Nickels
- Institute of Metabolic Disorders, Genesis Biotechnology Group, 1000 Waterview Drive, Hamilton, NJ 08691, USA
- Rutgers Center for Lipid Research, New Jersey Institute for Food, Nutrition, and Health, Rutgers University, New Brunswick, New Jersey 08901, USA
| | - Stephen L. Sturley
- Department of Biology, Barnard College at Columbia University, 3009 Broadway, New York, NY 10023, USA
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24
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Kim JI, Miura Y, Li MY, Revah O, Selvaraj S, Birey F, Meng X, Thete MV, Pavlov SD, Andersen J, Pașca AM, Porteus MH, Huguenard JR, Pașca SP. Human assembloids reveal the consequences of CACNA1G gene variants in the thalamocortical pathway. Neuron 2024; 112:4048-4059.e7. [PMID: 39419023 DOI: 10.1016/j.neuron.2024.09.020] [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: 04/03/2023] [Revised: 08/15/2024] [Accepted: 09/19/2024] [Indexed: 10/19/2024]
Abstract
Abnormalities in thalamocortical crosstalk can lead to neuropsychiatric disorders. Variants in CACNA1G, which encodes the α1G subunit of the thalamus-enriched T-type calcium channel, are associated with absence seizures, intellectual disability, and schizophrenia, but the cellular and circuit consequences of these genetic variants in humans remain unknown. Here, we developed a human assembloid model of the thalamocortical pathway to dissect the contribution of genetic variants in T-type calcium channels. We discovered that the M1531V CACNA1G variant associated with seizures led to changes in T-type currents in thalamic neurons, as well as correlated hyperactivity of thalamic and cortical neurons in assembloids. By contrast, CACNA1G loss, which has been associated with risk of schizophrenia, resulted in abnormal thalamocortical connectivity that was related to both increased spontaneous thalamic activity and aberrant axonal projections. These results illustrate the utility of multi-cellular systems for interrogating human genetic disease risk variants at both cellular and circuit level.
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Affiliation(s)
- Ji-Il Kim
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA 94305, USA; Stanford Brain Organogenesis, Wu Tsai Neuroscience Institute, Stanford, CA 94305, USA
| | - Yuki Miura
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA 94305, USA; Stanford Brain Organogenesis, Wu Tsai Neuroscience Institute, Stanford, CA 94305, USA
| | - Min-Yin Li
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA 94305, USA; Stanford Brain Organogenesis, Wu Tsai Neuroscience Institute, Stanford, CA 94305, USA
| | - Omer Revah
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA 94305, USA; Stanford Brain Organogenesis, Wu Tsai Neuroscience Institute, Stanford, CA 94305, USA; Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA 94305, USA
| | - Sridhar Selvaraj
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - Fikri Birey
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA 94305, USA; Stanford Brain Organogenesis, Wu Tsai Neuroscience Institute, Stanford, CA 94305, USA
| | - Xiangling Meng
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA 94305, USA; Stanford Brain Organogenesis, Wu Tsai Neuroscience Institute, Stanford, CA 94305, USA
| | - Mayuri Vijay Thete
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA 94305, USA; Stanford Brain Organogenesis, Wu Tsai Neuroscience Institute, Stanford, CA 94305, USA
| | - Sergey D Pavlov
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA 94305, USA; Stanford Brain Organogenesis, Wu Tsai Neuroscience Institute, Stanford, CA 94305, USA
| | - Jimena Andersen
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA 94305, USA; Stanford Brain Organogenesis, Wu Tsai Neuroscience Institute, Stanford, CA 94305, USA
| | - Anca M Pașca
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - Matthew H Porteus
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - John R Huguenard
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA 94305, USA
| | - Sergiu P Pașca
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA 94305, USA; Stanford Brain Organogenesis, Wu Tsai Neuroscience Institute, Stanford, CA 94305, USA.
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25
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Ma X, Li J, Liu N, Banerjee S, Hu X, Wang X, Dong J, Liu K, Yang C, Dong Z. Insights into the distinct membrane targeting mechanisms of WDR91 family proteins. Structure 2024; 32:2287-2300.e4. [PMID: 39426373 DOI: 10.1016/j.str.2024.09.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 07/15/2024] [Accepted: 09/24/2024] [Indexed: 10/21/2024]
Abstract
WDR91 and SORF1, members of the WD repeat-containing protein 91 family, control phosphoinositide conversion by inhibiting phosphatidylinositol 3-kinase activity on endosomes, which promotes endosome maturation. Here, we report the crystal structure of the human WDR91 WD40 domain complexed with Rab7 that has an unusual interface at the C-terminus of the Rab7 switch II region. WDR91 is highly selective for Rab7 among the tested GTPases. A LIS1 homology (LisH) motif within the WDR91 N-terminal domain (NTD) mediates self-association and may contribute partly to the augmented interaction between full-length WDR91 and Rab7. Both the Rab7 binding site and the LisH motif are indispensable for WDR91 function in endocytic trafficking. For the WDR91 orthologue SORF1 lacking the C-terminal WD40 domain, a C-terminal amphipathic helix (AH) mediates strong interactions with liposomes containing acidic lipids. During evolution the human WDR91 ancestor gene might have acquired a WD40 domain to replace the AH for endosomal membrane targeting.
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Affiliation(s)
- Xinli Ma
- China-US (Henan) Hormel Cancer Institute, Zhengzhou, Henan 450003, China
| | - Jian Li
- China-US (Henan) Hormel Cancer Institute, Zhengzhou, Henan 450003, China
| | - Nan Liu
- State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan and Center for Life Science, School of Life Sciences, Yunnan University, Kunming 650091, China
| | - Surajit Banerjee
- Northeastern Collaborative Access Team, Argonne National Laboratory, Argonne, Illinois 60439, USA
| | - Xiaotong Hu
- China-US (Henan) Hormel Cancer Institute, Zhengzhou, Henan 450003, China
| | - Xiaoyu Wang
- China-US (Henan) Hormel Cancer Institute, Zhengzhou, Henan 450003, China
| | - Jianshu Dong
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan 450001, China
| | - Kangdong Liu
- China-US (Henan) Hormel Cancer Institute, Zhengzhou, Henan 450003, China; College of Medicine, Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Chonglin Yang
- State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan and Center for Life Science, School of Life Sciences, Yunnan University, Kunming 650091, China
| | - Zigang Dong
- China-US (Henan) Hormel Cancer Institute, Zhengzhou, Henan 450003, China; College of Medicine, Zhengzhou University, Zhengzhou, Henan 450052, China.
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26
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Tanabe H, Koshizuka Y, Tanaka K, Takahashi K, Ijiri M, Takahashi K, Ando K, Ueno N, Kashima S, Sarashina T, Moriichi K, Mitsube K, Mizukami Y, Fujiya M, Makita Y. High-resolution genetic analysis of whole APC gene deletions: a report of two cases and patient characteristics. Hum Genome Var 2024; 11:46. [PMID: 39632802 PMCID: PMC11618449 DOI: 10.1038/s41439-024-00301-z] [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: 09/11/2024] [Revised: 11/04/2024] [Accepted: 11/09/2024] [Indexed: 12/07/2024] Open
Abstract
Familial adenomatous polyposis (FAP) is an autosomal dominant syndrome caused by germline variants in the APC gene, leading to the development of numerous colorectal polyps and significantly increases the risk of colorectal cancer. A diagnosis is typically made using colonoscopy, and genetic testing can assist in patient surveillance and carrier identification. Recent advances include the use of whole-genome array comparative genomic hybridization (a-CGH), which provides better resolution of genetic imbalances. We aimed to explore the specific features of FAP patients with whole APC gene deletions using high-resolution a-CGH and to compare patient characteristics. Two polyposis patients with whole APC deletions were identified, and the lost genetic sizes ranged from 0.3-1.1 Mb. Nervous abnormalities were a characteristic symptom in a patient with a 1.1 Mb loss. A patient with an approximately 0.3 Mb loss, which included the entire APC gene, presented a polyposis phenotype without intellectual disability. The comparison of genetic losses, with or without intellectual disability, revealed 7 genetic changes. Consequently, EPB41L4A is a candidate gene associated with the neurogenic phenotype.
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Affiliation(s)
- Hiroki Tanabe
- Oncology Center, Asahikawa Medical University Hospital, Asahikawa, Japan.
- Genetic Oncology Department, Asahikawa Medical University Hospital, Asahikawa, Japan.
- Department of Genetic Counseling, Asahikawa Medical University Hospital, Asahikawa, Japan.
- Division of Gastroenterology, Department of Internal Medicine, Asahikawa Medical University, Asahikawa, Japan.
| | - Yasuyuki Koshizuka
- Department of Surgery, Asahikawa-Kosei general Hospital, Asahikawa, Japan
| | - Kazuyuki Tanaka
- Department of Gastroenterology, Asahikawa-Kosei General Hospital, Asahikawa, Japan
| | - Kenji Takahashi
- Genetic Oncology Department, Asahikawa Medical University Hospital, Asahikawa, Japan
- Division of Gastroenterology, Department of Internal Medicine, Asahikawa Medical University, Asahikawa, Japan
| | - Masami Ijiri
- Department of Gastroenterology, Japanese Red Cross Asahikawa Hospital, Asahikawa, Japan
| | - Keitaro Takahashi
- Division of Gastroenterology, Department of Internal Medicine, Asahikawa Medical University, Asahikawa, Japan
| | - Katsuyoshi Ando
- Genetic Oncology Department, Asahikawa Medical University Hospital, Asahikawa, Japan
- Division of Gastroenterology, Department of Internal Medicine, Asahikawa Medical University, Asahikawa, Japan
| | - Nobuhiro Ueno
- Division of Gastroenterology, Department of Internal Medicine, Asahikawa Medical University, Asahikawa, Japan
| | - Shin Kashima
- Division of Gastroenterology, Department of Internal Medicine, Asahikawa Medical University, Asahikawa, Japan
| | - Takeo Sarashina
- Oncology Center, Asahikawa Medical University Hospital, Asahikawa, Japan
| | - Kentaro Moriichi
- Division of Gastroenterology, Department of Internal Medicine, Asahikawa Medical University, Asahikawa, Japan
| | - Kenrokuro Mitsube
- Department of Obstetrics and Gynecology, Asahikawa-Kosei General Hospital, Asahikawa, Japan
| | - Yusuke Mizukami
- Department of Genetic Counseling, Asahikawa Medical University Hospital, Asahikawa, Japan
- Division of Gastroenterology, Department of Internal Medicine, Asahikawa Medical University, Asahikawa, Japan
| | - Mikihiro Fujiya
- Division of Gastroenterology, Department of Internal Medicine, Asahikawa Medical University, Asahikawa, Japan
| | - Yoshio Makita
- Department of Genetic Counseling, Asahikawa Medical University Hospital, Asahikawa, Japan
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27
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Ugur B, Schueder F, Shin J, Hanna MG, Wu Y, Leonzino M, Su M, McAdow AR, Wilson C, Postlethwait J, Solnica-Krezel L, Bewersdorf J, De Camilli P. VPS13B is localized at the interface between Golgi cisternae and is a functional partner of FAM177A1. J Cell Biol 2024; 223:e202311189. [PMID: 39331042 PMCID: PMC11451052 DOI: 10.1083/jcb.202311189] [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: 12/05/2023] [Revised: 05/31/2024] [Accepted: 08/05/2024] [Indexed: 09/28/2024] Open
Abstract
Mutations in VPS13B, a member of a protein family implicated in bulk lipid transport between adjacent membranes, cause Cohen syndrome. VPS13B is known to be concentrated in the Golgi complex, but its precise location within this organelle and thus the site(s) where it achieves lipid transport remains unclear. Here, we show that VPS13B is localized at the interface between proximal and distal Golgi subcompartments and that Golgi complex reformation after Brefeldin A (BFA)-induced disruption is delayed in VPS13B KO cells. This delay is phenocopied by the loss of FAM177A1, a Golgi complex protein of unknown function reported to be a VPS13B interactor and whose mutations also result in a developmental disorder. In zebrafish, the vps13b ortholog, not previously annotated in this organism, genetically interacts with fam177a1. Collectively, these findings raise the possibility that bulk lipid transport by VPS13B may play a role in the dynamics of Golgi membranes and that VPS13B may be assisted in this function by FAM177A1.
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Affiliation(s)
- Berrak Ugur
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, USA
- Program in Cellular Neuroscience, Neurodegeneration, and Repair, Yale University School of Medicine, New Haven, CT, USA
- Aligning Science Across Parkinson’s Collaborative Research Network, Chevy Chase, MD, USA
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT, USA
| | - Florian Schueder
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, USA
| | - Jimann Shin
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Michael G. Hanna
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, USA
- Program in Cellular Neuroscience, Neurodegeneration, and Repair, Yale University School of Medicine, New Haven, CT, USA
- Aligning Science Across Parkinson’s Collaborative Research Network, Chevy Chase, MD, USA
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT, USA
| | - Yumei Wu
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, USA
- Program in Cellular Neuroscience, Neurodegeneration, and Repair, Yale University School of Medicine, New Haven, CT, USA
- Aligning Science Across Parkinson’s Collaborative Research Network, Chevy Chase, MD, USA
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT, USA
| | - Marianna Leonzino
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, USA
- Program in Cellular Neuroscience, Neurodegeneration, and Repair, Yale University School of Medicine, New Haven, CT, USA
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT, USA
| | - Maohan Su
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
| | - Anthony R. McAdow
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Catherine Wilson
- Institute of Neuroscience, University of Oregon, Eugene, OR, USA
| | | | - Lilianna Solnica-Krezel
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Joerg Bewersdorf
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
- Nanobiology Institute, Yale University, West Haven, CT, USA
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
- Department of Physics, Yale University, New Haven, CT, USA
| | - Pietro De Camilli
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, USA
- Program in Cellular Neuroscience, Neurodegeneration, and Repair, Yale University School of Medicine, New Haven, CT, USA
- Aligning Science Across Parkinson’s Collaborative Research Network, Chevy Chase, MD, USA
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT, USA
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28
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Mu C, Liu P, Liu L, Wang Y, Liu K, Li X, Li G, Cheng J, Bu M, Chen H, Tang M, Yao Y, Guan J, Ma T, Zhou Z, Wu Q, Li J, Guo H, Xia K, Hu Z, Peng X, Lang B, Li F, Chen XW, Xu Z, Yuan L. KCTD10 p.C124W variant contributes to schizophrenia by attenuating LLPS-mediated synapse formation. Proc Natl Acad Sci U S A 2024; 121:e2400464121. [PMID: 39565307 PMCID: PMC11621769 DOI: 10.1073/pnas.2400464121] [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: 01/26/2024] [Accepted: 10/23/2024] [Indexed: 11/21/2024] Open
Abstract
KCTD10, a member of the potassium channel tetramerization domain (KCTD) family, is implicated in neuropsychiatric disorders and functions as a substrate recognition component within the RING-type ubiquitin ligase complex. A rare de novo variant of KCTD10, p.C124W, was identified in schizophrenia cases, yet its underlying pathogenesis remains unexplored. Here, we demonstrate that heterozygous KCTD10 C124W mice display pronounced synaptic abnormalities and exhibit schizophrenia-like behaviors. Mechanistically, we reveal that KCTD10 undergoes liquid-liquid phase separation (LLPS), a process orchestrated by its intrinsically disordered region (IDR). p.C124W mutation disrupts this LLPS capability, leading to diminished degradation of RHOB and subsequent excessive accumulation in the postsynaptic density fractions. Notably, neither IDR deletion nor p.C124W mutation in KCTD10 mitigates the synaptic abnormalities caused by Kctd10 deficiency. Thus, our findings implicate that LLPS may be associated with the pathogenesis of KCTD10-associated brain disorders and highlight the potential of targeting RHOB as a therapeutic strategy for diseases linked to mutations in KCTD10 or RHOB.
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Affiliation(s)
- Chenjun Mu
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics, Key Lab of Rare Pediatric Diseases of Ministry of Education, School of Life Science, Central South University, Changsha, Hunan410078, China
| | - Pan Liu
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics, Key Lab of Rare Pediatric Diseases of Ministry of Education, School of Life Science, Central South University, Changsha, Hunan410078, China
| | - Liang Liu
- Department of Neurology, Xuanwu Hospital, Capital Medical University, Beijing100053, China
| | - Yaqing Wang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Beijing100101, China
| | - Kefu Liu
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics, Key Lab of Rare Pediatric Diseases of Ministry of Education, School of Life Science, Central South University, Changsha, Hunan410078, China
| | - Xiangyu Li
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics, Key Lab of Rare Pediatric Diseases of Ministry of Education, School of Life Science, Central South University, Changsha, Hunan410078, China
| | - Guozhong Li
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics, Key Lab of Rare Pediatric Diseases of Ministry of Education, School of Life Science, Central South University, Changsha, Hunan410078, China
| | - Jianbo Cheng
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics, Key Lab of Rare Pediatric Diseases of Ministry of Education, School of Life Science, Central South University, Changsha, Hunan410078, China
| | - Mengyao Bu
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics, Key Lab of Rare Pediatric Diseases of Ministry of Education, School of Life Science, Central South University, Changsha, Hunan410078, China
| | - Han Chen
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics, Key Lab of Rare Pediatric Diseases of Ministry of Education, School of Life Science, Central South University, Changsha, Hunan410078, China
| | - Manpei Tang
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics, Key Lab of Rare Pediatric Diseases of Ministry of Education, School of Life Science, Central South University, Changsha, Hunan410078, China
| | - Yuanhang Yao
- Center for Life Sciences, Institute of Molecular Medicine, School of Future Technology, Peking University, Beijing100871, China
| | - Jun Guan
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics, Key Lab of Rare Pediatric Diseases of Ministry of Education, School of Life Science, Central South University, Changsha, Hunan410078, China
| | - Tiantian Ma
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Beijing100101, China
| | - Zhengrong Zhou
- Department of Basic Medical Sciences, Neuroscience Center, Shantou University Medical College, Shantou, Guangdong515041, China
| | - Qingfeng Wu
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Beijing100101, China
| | - Jiada Li
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics, Key Lab of Rare Pediatric Diseases of Ministry of Education, School of Life Science, Central South University, Changsha, Hunan410078, China
- Hunan Key Laboratory of Animal Models for Human Diseases, School of Life Science, Central South University, Changsha, Hunan410078, China
| | - Hui Guo
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics, Key Lab of Rare Pediatric Diseases of Ministry of Education, School of Life Science, Central South University, Changsha, Hunan410078, China
- Hunan Key Laboratory of Animal Models for Human Diseases, School of Life Science, Central South University, Changsha, Hunan410078, China
| | - Kun Xia
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics, Key Lab of Rare Pediatric Diseases of Ministry of Education, School of Life Science, Central South University, Changsha, Hunan410078, China
- Hunan Key Laboratory of Animal Models for Human Diseases, School of Life Science, Central South University, Changsha, Hunan410078, China
| | - Zhengmao Hu
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics, Key Lab of Rare Pediatric Diseases of Ministry of Education, School of Life Science, Central South University, Changsha, Hunan410078, China
- Hunan Key Laboratory of Animal Models for Human Diseases, School of Life Science, Central South University, Changsha, Hunan410078, China
| | - Xiaoqing Peng
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics, Key Lab of Rare Pediatric Diseases of Ministry of Education, School of Life Science, Central South University, Changsha, Hunan410078, China
- Hunan Key Laboratory of Animal Models for Human Diseases, School of Life Science, Central South University, Changsha, Hunan410078, China
| | - Bing Lang
- Department of Psychiatry, The Second Xiangya Hospital of Central South University, Changsha, Hunan410011, China
| | - Faxiang Li
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics, Key Lab of Rare Pediatric Diseases of Ministry of Education, School of Life Science, Central South University, Changsha, Hunan410078, China
- Hunan Key Laboratory of Animal Models for Human Diseases, School of Life Science, Central South University, Changsha, Hunan410078, China
| | - Xiao-wei Chen
- Center for Life Sciences, Institute of Molecular Medicine, School of Future Technology, Peking University, Beijing100871, China
| | - Zhiheng Xu
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Beijing100101, China
| | - Ling Yuan
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics, Key Lab of Rare Pediatric Diseases of Ministry of Education, School of Life Science, Central South University, Changsha, Hunan410078, China
- Hunan Key Laboratory of Animal Models for Human Diseases, School of Life Science, Central South University, Changsha, Hunan410078, China
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Sharkia R, Vuillaume ML, Jain S, Mahajnah M, Stoeva R, Guichet A, Colin E, Champ J, Derive N, Chefdor A, Zalan A. An Update of Phenotypic-Genotypic IMNEPD Cases and a Bioinformatics Analysis of the New PTRH2 Gene Variants. Genes (Basel) 2024; 15:1508. [PMID: 39766776 PMCID: PMC11675358 DOI: 10.3390/genes15121508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2024] [Revised: 11/16/2024] [Accepted: 11/19/2024] [Indexed: 01/11/2025] Open
Abstract
BACKGROUND/OBJECTIVES Biallelic mutations in the PTRH2 gene are associated with a rare genetic disease known as infantile-onset multisystem neurologic, endocrine, and pancreatic disease (IMNEPD). In this study, we describe a new case carrying a previously identified mutation, provide an updated analysis of the relative frequencies of the clinical features across all published cases (including the three latest studies), and perform a bioinformatics analysis of the newly identified PTRH2 protein variants from a structural perspective. METHODS Clinical examination of the patients was carried out, and genetic testing was performed using a genome sequencing strategy. A bioinformatics analysis was carried out for the newly reported mutations using PYMOL that was utilized to view the structure and analyze the mutations. Additionally, the ThermoMPNN webserver was employed to check the effect of point mutations on the overall stability of the protein. RESULTS Our findings indicate that motor delay, neuropathy, intellectual disability, distal weakness, hearing impairment, and ataxia are the most common symptoms, while the other clinical features fall into two frequency categories: moderately common ones and the least common ones. The bioinformatics analysis revealed that the Q85 residue is highly conserved, suggesting that mutations at this position could disrupt key signaling pathways or cellular functions. Indeed, the Q85R mutation was shown to significantly impair the stability and functionality of the protein. CONCLUSIONS The clinical presentation of IMNEPD remains highly variable in terms of both severity and progression. Mutations at the Q85 residue have been identified in nearly 50% of reported cases, highlighting this position as a potential mutational hotspot in the PTRH2 protein.
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Affiliation(s)
- Rajech Sharkia
- Unit of Human Biology and Genetics, The Triangle Regional Research and Development Center, Kafr Qari 3007500, Israel;
- Unit of Natural Sciences, Beit-Berl Academic College, Beit-Berl 4490500, Israel
| | - Marie-Laure Vuillaume
- Genetics Department, Tours University Hospital, 37044 Tours, France
- INSERM, Imaging Brain & Neuropsychiatry iBraiN U12523, University of Tours, 37032 Tours, France
| | - Sahil Jain
- Bioinformatics Centre, Dr. D.Y. Patil Biotechnology and Bioinformatics Institute, Dr. D.Y. Patil Vidyapeeth, Pune 411033, India
| | - Muhammad Mahajnah
- The Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa 3109600, Israel
- Child Neurology and Development Center, Hillel Yaffe Medical Center, Hadera 3810000, Israel
| | - Radka Stoeva
- Department of Medical Genetics, Le Mans Hospital, 72037 Le Mans, France
| | - Agnès Guichet
- Genetics Department CHU 4 Rue Larrey, 49933 Angers, France
- Miotvasc, UMR CNRS 6015, INSERM U1083, Angers University, 49933 Angers, France
| | - Estelle Colin
- Genetics Department CHU 4 Rue Larrey, 49933 Angers, France
- Miotvasc, UMR CNRS 6015, INSERM U1083, Angers University, 49933 Angers, France
| | | | | | - Arnaud Chefdor
- Department of Pediatrics, Le Mans Hospital, 72037 Le Mans, France
| | - Abdelnaser Zalan
- Unit of Human Biology and Genetics, The Triangle Regional Research and Development Center, Kafr Qari 3007500, Israel;
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Tirelli M, Bonfiglio F, Cantalupo S, Montella A, Avitabile M, Maiorino T, Diskin SJ, Iolascon A, Capasso M. Integrative genomic analyses identify neuroblastoma risk genes involved in neuronal differentiation. Hum Genet 2024; 143:1293-1309. [PMID: 39192051 PMCID: PMC11522082 DOI: 10.1007/s00439-024-02700-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2024] [Accepted: 08/14/2024] [Indexed: 08/29/2024]
Abstract
Genome-Wide Association Studies (GWAS) have been decisive in elucidating the genetic predisposition of neuroblastoma (NB). The majority of genetic variants identified in GWAS are found in non-coding regions, suggesting that they can be causative of pathogenic dysregulations of gene expression. Nonetheless, pinpointing the potential causal genes within implicated genetic loci remains a major challenge. In this study, we integrated NB GWAS and expression Quantitative Trait Loci (eQTL) data from adrenal gland to identify candidate genes impacting NB susceptibility. We found that ZMYM1, CBL, GSKIP and WDR81 expression was dysregulated by NB predisposing variants. We further investigated the functional role of the identified genes through computational analysis of RNA sequencing (RNA-seq) data from single-cell and whole-tissue samples of NB, neural crest, and adrenal gland tissues, as well as through in vitro differentiation assays in NB cell cultures. Our results indicate that dysregulation of ZMYM1, CBL, GSKIP, WDR81 may lead to malignant transformation by affecting early and late stages of normal program of neuronal differentiation. Our findings enhance the understanding of how specific genes contribute to NB pathogenesis by highlighting their influence on neuronal differentiation and emphasizing the impact of genetic risk variants on the regulation of genes involved in critical biological processes.
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Affiliation(s)
- Matilde Tirelli
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, 80131, Naples, Italy
- CEINGE Biotecnologie Avanzate Franco Salvatore, 80145, Naples, Italy
| | - Ferdinando Bonfiglio
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, 80131, Naples, Italy
- CEINGE Biotecnologie Avanzate Franco Salvatore, 80145, Naples, Italy
| | - Sueva Cantalupo
- CEINGE Biotecnologie Avanzate Franco Salvatore, 80145, Naples, Italy
| | - Annalaura Montella
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, 80131, Naples, Italy
- CEINGE Biotecnologie Avanzate Franco Salvatore, 80145, Naples, Italy
| | | | - Teresa Maiorino
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, 80131, Naples, Italy
- CEINGE Biotecnologie Avanzate Franco Salvatore, 80145, Naples, Italy
| | - Sharon J Diskin
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, 19104, Philadelphia, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, 19104, Philadelphia, USA
| | - Achille Iolascon
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, 80131, Naples, Italy
- CEINGE Biotecnologie Avanzate Franco Salvatore, 80145, Naples, Italy
| | - Mario Capasso
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, 80131, Naples, Italy.
- CEINGE Biotecnologie Avanzate Franco Salvatore, 80145, Naples, Italy.
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Zhang Y, Bi C, Nadeef S, Maddirevula S, Alqahtani M, Alkuraya FS, Li M. NanoRanger enables rapid single-base-pair resolution of genomic disorders. MED 2024; 5:1307-1325.e3. [PMID: 39047733 DOI: 10.1016/j.medj.2024.07.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Revised: 04/13/2024] [Accepted: 07/01/2024] [Indexed: 07/27/2024]
Abstract
BACKGROUND Delineating base-resolution breakpoints of complex rearrangements is crucial for an accurate clinical understanding of pathogenic variants and for carrier screening within family networks or the broader population. However, despite advances in genetic testing using short-read sequencing (SRS), this task remains costly and challenging. METHODS This study addresses the challenges of resolving missing disease-causing breakpoints in complex genomic disorders with suspected homozygous rearrangements by employing multiple long-read sequencing (LRS) strategies, including a novel and efficient strategy named nanopore-based rapid acquisition of neighboring genomic regions (NanoRanger). NanoRanger does not require large amounts of ultrahigh-molecular-weight DNA and stands out for its ease of use and rapid acquisition of large genomic regions of interest with deep coverage. FINDINGS We describe a cohort of 16 familial cases, each harboring homozygous rearrangements that defied breakpoint determination by SRS and optical genome mapping (OGM). NanoRanger identified the breakpoints with single-base-pair resolution, enabling accurate determination of the carrier status of unaffected family members as well as the founder nature of these genomic lesions and their frequency in the local population. The resolved breakpoints revealed that repetitive DNA, gene regulatory elements, and transcription activity contribute to genome instability in these novel recessive rearrangements. CONCLUSIONS Our data suggest that NanoRanger greatly improves the success rate of resolving base-resolution breakpoints of complex genomic disorders and expands access to LRS for the benefit of patients with Mendelian disorders. FUNDING M.L. is supported by KAUST Baseline Award no. BAS/1/1080-01-01 and KAUST Research Translation Fund Award no. REI/1/4742-01.
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Affiliation(s)
- Yingzi Zhang
- Bioscience Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Chongwei Bi
- Bioscience Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Seba Nadeef
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Sateesh Maddirevula
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Mashael Alqahtani
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Fowzan S Alkuraya
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia; Department of Pediatrics, Prince Sultan Military Medical City, Riyadh, Saudi Arabia.
| | - Mo Li
- Bioscience Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia; Bioengineering Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
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32
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Rice SM, Varotsis DF, Wodoslawsky S, Critchlow E, Liu R, McLaren RA, Makhamreh MM, Firman B, Berger SI, Al-Kouatly HB. Prenatal Phenotype of Alkuraya-Kučinskas Syndrome: A Novel Case and Systematic Literature Review. Prenat Diagn 2024; 44:1381-1397. [PMID: 39228063 DOI: 10.1002/pd.6637] [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: 04/12/2024] [Revised: 06/06/2024] [Accepted: 07/12/2024] [Indexed: 09/05/2024]
Abstract
Alkuraya-Kučinskas syndrome (AKS) is an autosomal recessive multisystem disorder resulting from mutations in the BLTP1 gene, formerly known as KIAA1109. Primary manifestations include brain malformations, arthrogryposis, and clubfeet. Cardiac, renal, and ophthalmologic abnormalities may also be observed, while nonimmune hydrops is rare. We present a case of two novel BLTP1 canonical splice-site variants in a fetus with multiple congenital anomalies, including hydrops, a kinked brainstem, and joint contractures. A systematic literature review was conducted to describe the prenatal phenotype of AKS, which was inspired by our case. Our systematic literature review of the prenatal phenotype in 19 cases, including our additional case, demonstrated joint contractures in 90% (18/20), ventriculomegaly in 60% (12/20), brainstem dysgenesis in 50% (10/20), cerebellar hypoplasia in 50% (10/20), parenchymal thinning with lissencephalic aspect in 60% (12/20), and facial dysmorphism in 70% (14/20) of reported AKS cases. In addition to our case, hydrops was reported in two other families. AKS should be considered in fetal presentations with characteristic features, especially brainstem kinking and joint contractures. Exome sequencing, including coverage of canonical intronic splice-site variants, can clarify the diagnosis. TRIAL REGISTRATION: ClinicalTrials.gov registration: NCT03911531.
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Affiliation(s)
- Stephanie M Rice
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Dante F Varotsis
- Department of Obstetrics and Gynecology, Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Sascha Wodoslawsky
- Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Elizabeth Critchlow
- Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Ruby Liu
- Revvity Omics, Inc., Waltham, Massachusetts, USA
| | - Rodney A McLaren
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Mona M Makhamreh
- Department of Obstetrics and Gynecology, Maimonides Medical Center, Brooklyn, New York, USA
| | - Brandy Firman
- Department of Obstetrics and Gynecology, Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Seth I Berger
- Center for Genetic Medicine Research at Children's National Hospital, Washington, DC, USA
| | - Huda B Al-Kouatly
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
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33
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Berling E, Latour P, Loiselet K, Guémy C, Vidoni L, Romero NB, Lacene E, Evangelista T, Stojkovic T. Severe Respiratory and Swallowing Disorders in Infantile-Onset Multisystem Neurologic, Endocrine, and Pancreatic Disease Type 1: Two Cases. Neurol Genet 2024; 10:e200178. [PMID: 39176129 PMCID: PMC11341004 DOI: 10.1212/nxg.0000000000200178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 07/16/2024] [Indexed: 08/24/2024]
Abstract
Objectives The objective of this study was to expand the phenotypic spectrum of infantile-onset multisystem neurologic, endocrine, and pancreatic disease type 1 (IMNEPD1) and highlight the importance of analyzing the PTRH2 gene in patients with neuropathy presenting with pancreatic lipomatosis. Methods Two sisters, aged 73 and 71 years, respectively, presented a severe, length-dependent sensorimotor axonal neuropathy, associated with deafness and intellectual deficiency. Results They both needed a wheelchair from the fourth decade. They developed a severe respiratory dysfunction, requiring nocturnal noninvasive ventilation from around 50 years of age. The younger sister developed severe dysphagia complicated by aspiration pneumonia. A muscle biopsy of the younger sister was suggestive of mitochondrial myopathy. The youngest presented a complete pancreatic lipomatosis. A biallelic novel likely pathogenic variant within PTRH2, c.254A>G (p.Gln85Arg), was evidenced in both patients. Discussion IMNEPD1 is a rare autosomal recessive disorder caused by sequence variant in the PTRH2 gene and characterized by a peripheral neuropathy, cerebellar atrophy, intellectual disability, hearing loss, pancreatic insufficiency, hypothyroidism, and dysmorphic features. In addition to these classic manifestations of the disorder, severe dysphagia and respiratory insufficiency may develop over the course of the disease and should be systematically screened. PTRH2 gene should be considered in patients with pancreatic lipomatosis and neuropathy.
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Affiliation(s)
- Edouard Berling
- From the APHP (E.B., C.G.), Service de Neurologie, Hôpital Raymond Poincaré, Garches; APHP (E.B., C.G.), Centre de référence Nord-Est-Ile-de-France, FHU PHENIX; Université de Versailles Saint-Quentin-en-Yvelines (E.B.), U 1179 INSERM, Paris-Saclay; Centre de Biologie Est (P.L., L.V.), Hospices Civils, Lyon; Department of Pediatric Radiology (K.L.), Hôpital Necker-Enfants Malades, Paris; Sorbonne Université (N.B.R., T.E.), UMRS974, - INSERM, Centre de Recherche en Myologie, Institut de Myologie Paris; APHP (N.B.R., E.L., T.E.), Unité de Morphologie neuromusculaire, Centre de référence des maladies neuromusculaires Nord-Est-Ile-de-France; and APHP (T.S.), Sorbonne Université, Service de Neuromyologie, Centre de référence Nord-Est-Ile-de-France, Institut de Myologie, Hôpital Pitié-Salpêtrière, Paris, France
| | - Philippe Latour
- From the APHP (E.B., C.G.), Service de Neurologie, Hôpital Raymond Poincaré, Garches; APHP (E.B., C.G.), Centre de référence Nord-Est-Ile-de-France, FHU PHENIX; Université de Versailles Saint-Quentin-en-Yvelines (E.B.), U 1179 INSERM, Paris-Saclay; Centre de Biologie Est (P.L., L.V.), Hospices Civils, Lyon; Department of Pediatric Radiology (K.L.), Hôpital Necker-Enfants Malades, Paris; Sorbonne Université (N.B.R., T.E.), UMRS974, - INSERM, Centre de Recherche en Myologie, Institut de Myologie Paris; APHP (N.B.R., E.L., T.E.), Unité de Morphologie neuromusculaire, Centre de référence des maladies neuromusculaires Nord-Est-Ile-de-France; and APHP (T.S.), Sorbonne Université, Service de Neuromyologie, Centre de référence Nord-Est-Ile-de-France, Institut de Myologie, Hôpital Pitié-Salpêtrière, Paris, France
| | - Klervie Loiselet
- From the APHP (E.B., C.G.), Service de Neurologie, Hôpital Raymond Poincaré, Garches; APHP (E.B., C.G.), Centre de référence Nord-Est-Ile-de-France, FHU PHENIX; Université de Versailles Saint-Quentin-en-Yvelines (E.B.), U 1179 INSERM, Paris-Saclay; Centre de Biologie Est (P.L., L.V.), Hospices Civils, Lyon; Department of Pediatric Radiology (K.L.), Hôpital Necker-Enfants Malades, Paris; Sorbonne Université (N.B.R., T.E.), UMRS974, - INSERM, Centre de Recherche en Myologie, Institut de Myologie Paris; APHP (N.B.R., E.L., T.E.), Unité de Morphologie neuromusculaire, Centre de référence des maladies neuromusculaires Nord-Est-Ile-de-France; and APHP (T.S.), Sorbonne Université, Service de Neuromyologie, Centre de référence Nord-Est-Ile-de-France, Institut de Myologie, Hôpital Pitié-Salpêtrière, Paris, France
| | - Clément Guémy
- From the APHP (E.B., C.G.), Service de Neurologie, Hôpital Raymond Poincaré, Garches; APHP (E.B., C.G.), Centre de référence Nord-Est-Ile-de-France, FHU PHENIX; Université de Versailles Saint-Quentin-en-Yvelines (E.B.), U 1179 INSERM, Paris-Saclay; Centre de Biologie Est (P.L., L.V.), Hospices Civils, Lyon; Department of Pediatric Radiology (K.L.), Hôpital Necker-Enfants Malades, Paris; Sorbonne Université (N.B.R., T.E.), UMRS974, - INSERM, Centre de Recherche en Myologie, Institut de Myologie Paris; APHP (N.B.R., E.L., T.E.), Unité de Morphologie neuromusculaire, Centre de référence des maladies neuromusculaires Nord-Est-Ile-de-France; and APHP (T.S.), Sorbonne Université, Service de Neuromyologie, Centre de référence Nord-Est-Ile-de-France, Institut de Myologie, Hôpital Pitié-Salpêtrière, Paris, France
| | - Léo Vidoni
- From the APHP (E.B., C.G.), Service de Neurologie, Hôpital Raymond Poincaré, Garches; APHP (E.B., C.G.), Centre de référence Nord-Est-Ile-de-France, FHU PHENIX; Université de Versailles Saint-Quentin-en-Yvelines (E.B.), U 1179 INSERM, Paris-Saclay; Centre de Biologie Est (P.L., L.V.), Hospices Civils, Lyon; Department of Pediatric Radiology (K.L.), Hôpital Necker-Enfants Malades, Paris; Sorbonne Université (N.B.R., T.E.), UMRS974, - INSERM, Centre de Recherche en Myologie, Institut de Myologie Paris; APHP (N.B.R., E.L., T.E.), Unité de Morphologie neuromusculaire, Centre de référence des maladies neuromusculaires Nord-Est-Ile-de-France; and APHP (T.S.), Sorbonne Université, Service de Neuromyologie, Centre de référence Nord-Est-Ile-de-France, Institut de Myologie, Hôpital Pitié-Salpêtrière, Paris, France
| | - Norma B Romero
- From the APHP (E.B., C.G.), Service de Neurologie, Hôpital Raymond Poincaré, Garches; APHP (E.B., C.G.), Centre de référence Nord-Est-Ile-de-France, FHU PHENIX; Université de Versailles Saint-Quentin-en-Yvelines (E.B.), U 1179 INSERM, Paris-Saclay; Centre de Biologie Est (P.L., L.V.), Hospices Civils, Lyon; Department of Pediatric Radiology (K.L.), Hôpital Necker-Enfants Malades, Paris; Sorbonne Université (N.B.R., T.E.), UMRS974, - INSERM, Centre de Recherche en Myologie, Institut de Myologie Paris; APHP (N.B.R., E.L., T.E.), Unité de Morphologie neuromusculaire, Centre de référence des maladies neuromusculaires Nord-Est-Ile-de-France; and APHP (T.S.), Sorbonne Université, Service de Neuromyologie, Centre de référence Nord-Est-Ile-de-France, Institut de Myologie, Hôpital Pitié-Salpêtrière, Paris, France
| | - Emmanuelle Lacene
- From the APHP (E.B., C.G.), Service de Neurologie, Hôpital Raymond Poincaré, Garches; APHP (E.B., C.G.), Centre de référence Nord-Est-Ile-de-France, FHU PHENIX; Université de Versailles Saint-Quentin-en-Yvelines (E.B.), U 1179 INSERM, Paris-Saclay; Centre de Biologie Est (P.L., L.V.), Hospices Civils, Lyon; Department of Pediatric Radiology (K.L.), Hôpital Necker-Enfants Malades, Paris; Sorbonne Université (N.B.R., T.E.), UMRS974, - INSERM, Centre de Recherche en Myologie, Institut de Myologie Paris; APHP (N.B.R., E.L., T.E.), Unité de Morphologie neuromusculaire, Centre de référence des maladies neuromusculaires Nord-Est-Ile-de-France; and APHP (T.S.), Sorbonne Université, Service de Neuromyologie, Centre de référence Nord-Est-Ile-de-France, Institut de Myologie, Hôpital Pitié-Salpêtrière, Paris, France
| | - Teresinha Evangelista
- From the APHP (E.B., C.G.), Service de Neurologie, Hôpital Raymond Poincaré, Garches; APHP (E.B., C.G.), Centre de référence Nord-Est-Ile-de-France, FHU PHENIX; Université de Versailles Saint-Quentin-en-Yvelines (E.B.), U 1179 INSERM, Paris-Saclay; Centre de Biologie Est (P.L., L.V.), Hospices Civils, Lyon; Department of Pediatric Radiology (K.L.), Hôpital Necker-Enfants Malades, Paris; Sorbonne Université (N.B.R., T.E.), UMRS974, - INSERM, Centre de Recherche en Myologie, Institut de Myologie Paris; APHP (N.B.R., E.L., T.E.), Unité de Morphologie neuromusculaire, Centre de référence des maladies neuromusculaires Nord-Est-Ile-de-France; and APHP (T.S.), Sorbonne Université, Service de Neuromyologie, Centre de référence Nord-Est-Ile-de-France, Institut de Myologie, Hôpital Pitié-Salpêtrière, Paris, France
| | - Tanya Stojkovic
- From the APHP (E.B., C.G.), Service de Neurologie, Hôpital Raymond Poincaré, Garches; APHP (E.B., C.G.), Centre de référence Nord-Est-Ile-de-France, FHU PHENIX; Université de Versailles Saint-Quentin-en-Yvelines (E.B.), U 1179 INSERM, Paris-Saclay; Centre de Biologie Est (P.L., L.V.), Hospices Civils, Lyon; Department of Pediatric Radiology (K.L.), Hôpital Necker-Enfants Malades, Paris; Sorbonne Université (N.B.R., T.E.), UMRS974, - INSERM, Centre de Recherche en Myologie, Institut de Myologie Paris; APHP (N.B.R., E.L., T.E.), Unité de Morphologie neuromusculaire, Centre de référence des maladies neuromusculaires Nord-Est-Ile-de-France; and APHP (T.S.), Sorbonne Université, Service de Neuromyologie, Centre de référence Nord-Est-Ile-de-France, Institut de Myologie, Hôpital Pitié-Salpêtrière, Paris, France
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34
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Kinoshita T. Towards a thorough understanding of mammalian glycosylphosphatidylinositol-anchored protein biosynthesis. Glycobiology 2024; 34:cwae061. [PMID: 39129667 DOI: 10.1093/glycob/cwae061] [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: 07/01/2024] [Revised: 08/01/2024] [Accepted: 08/10/2024] [Indexed: 08/13/2024] Open
Abstract
Glycosylphosphatidylinositols (GPIs) are glycolipids found ubiquitously in eukaryotes. They consist of a glycan and an inositol phospholipid, and act as membrane anchors of many cell-surface proteins by covalently linking to their C-termini. GPIs also exist as unlinked, free glycolipids on the cell surface. In human cells, at least 160 proteins with various functions are GPI-anchored proteins. Because the attachment of GPI is required for the cell-surface expression of GPI-anchored proteins, a thorough knowledge of the molecular basis of mammalian GPI-anchored protein biosynthesis is important for understanding the basic biochemistry and biology of GPI-anchored proteins and their medical significance. In this paper, I review our previous knowledge of the biosynthesis of mammalian GPI-anchored proteins and then examine new findings made since 2020.
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Affiliation(s)
- Taroh Kinoshita
- Center for Infectious Disease Education and Research, Osaka University, 2-8 Yamada-oka, Suita, Osaka, Japan
- Research Institute for Microbial Diseases, Osaka University, 3-1 Yamada-oka, Suita, Osaka, Japan
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35
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Uśpieński T, Niewiadomski P. The Proteasome and Cul3-Dependent Protein Ubiquitination Is Required for Gli Protein-Mediated Activation of Gene Expression in the Hedgehog Pathway. Cells 2024; 13:1496. [PMID: 39273066 PMCID: PMC11394618 DOI: 10.3390/cells13171496] [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: 04/30/2024] [Revised: 09/02/2024] [Accepted: 09/03/2024] [Indexed: 09/15/2024] Open
Abstract
Many cellular processes are regulated by proteasome-mediated protein degradation, including regulation of signaling pathways and gene expression. Among the pathways regulated by the ubiquitin-proteasome system is the Hedgehog pathway and its downstream effectors, the Gli transcription factors. Here we provide evidence that proteasomal activity is necessary for maintaining the activation of the Hedgehog pathway, and this crucial event takes place at the level of Gli proteins. We undertook extensive work to demonstrate the specificity of the observed phenomenon by ruling out the involvement of primary cilium, impaired nuclear import, failed dissociation from Sufu, microtubule stabilization, and stabilization of Gli repressor forms. Moreover, we showed that proteasomal-inhibition-mediated Hedgehog pathway downregulation is not restricted to the NIH-3T3 cell line. We demonstrated, using CRISPR/Ca9 mutagenesis, that neither Gli1, Gli2, nor Gli3 are solely responsible for the Hedgehog pathway downregulation upon proteasome inhibitor treatment, and that Cul3 KO renders the same phenotype. Finally, we report two novel E3 ubiquitin ligases, Btbd9 and Kctd3, known Cul3 interactors, as positive Hedgehog pathway regulators. Our data pave the way for a better understanding of the regulation of gene expression and the Hedgehog signaling pathway.
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Affiliation(s)
- Tomasz Uśpieński
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
| | - Paweł Niewiadomski
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
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36
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Mayfield JM, Hitefield NL, Czajewski I, Vanhye L, Holden L, Morava E, van Aalten DMF, Wells L. O-GlcNAc transferase congenital disorder of glycosylation (OGT-CDG): Potential mechanistic targets revealed by evaluating the OGT interactome. J Biol Chem 2024; 300:107599. [PMID: 39059494 PMCID: PMC11381892 DOI: 10.1016/j.jbc.2024.107599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 07/10/2024] [Accepted: 07/11/2024] [Indexed: 07/28/2024] Open
Abstract
O-GlcNAc transferase (OGT) is the sole enzyme responsible for the post-translational modification of O-GlcNAc on thousands of target nucleocytoplasmic proteins. To date, nine variants of OGT that segregate with OGT Congenital Disorder of Glycosylation (OGT-CDG) have been reported and characterized. Numerous additional variants have been associated with OGT-CDG, some of which are currently undergoing investigation. This disorder primarily presents with global developmental delay and intellectual disability (ID), alongside other variable neurological features and subtle facial dysmorphisms in patients. Several hypotheses aim to explain the etiology of OGT-CDG, with a prominent hypothesis attributing the pathophysiology of OGT-CDG to mutations segregating with this disorder disrupting the OGT interactome. The OGT interactome consists of thousands of proteins, including substrates as well as interactors that require noncatalytic functions of OGT. A key aim in the field is to identify which interactors and substrates contribute to the primarily neural-specific phenotype of OGT-CDG. In this review, we will discuss the heterogenous phenotypic features of OGT-CDG seen clinically, the variable biochemical effects of mutations associated with OGT-CDG, and the use of animal models to understand this disorder. Furthermore, we will discuss how previously identified OGT interactors causal for ID provide mechanistic targets for investigation that could explain the dysregulated gene expression seen in OGT-CDG models. Identifying shared or unique altered pathways impacted in OGT-CDG patients will provide a better understanding of the disorder as well as potential therapeutic targets.
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Affiliation(s)
- Johnathan M Mayfield
- Department of Biochemistry and Molecular Biology, Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA
| | - Naomi L Hitefield
- Department of Biochemistry and Molecular Biology, Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA
| | | | - Lotte Vanhye
- Department of Clinical Genomics and Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Laura Holden
- Department of Biochemistry and Molecular Biology, Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA
| | - Eva Morava
- Department of Clinical Genomics and Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Daan M F van Aalten
- School of Life Sciences, University of Dundee, Dundee, UK; Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark.
| | - Lance Wells
- Department of Biochemistry and Molecular Biology, Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA.
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37
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He XD, Phillips S, Hioki K, Majhi PD, Babbitt C, Tremblay KD, Pobezinsky LA, Mager J. TATA-binding associated factors have distinct roles during early mammalian development. Dev Biol 2024; 511:53-62. [PMID: 38593904 PMCID: PMC11143476 DOI: 10.1016/j.ydbio.2024.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 03/06/2024] [Accepted: 04/04/2024] [Indexed: 04/11/2024]
Abstract
Early embryonic development is a finely orchestrated process that requires precise regulation of gene expression coordinated with morphogenetic events. TATA-box binding protein-associated factors (TAFs), integral components of transcription initiation coactivators like TFIID and SAGA, play a crucial role in this intricate process. Here we show that disruptions in TAF5, TAF12 and TAF13 individually lead to embryonic lethality in the mouse, resulting in overlapping yet distinct phenotypes. Taf5 and Taf12 mutant embryos exhibited a failure to implant post-blastocyst formation, and Taf5 mutants have aberrant lineage specification within the inner cell mass. In contrast, Taf13 mutant embryos successfully implant and form egg-cylinder stages but fail to initiate gastrulation. Strikingly, we observed a depletion of pluripotency factors in TAF13-deficient embryos, including OCT4, NANOG and SOX2, highlighting an indispensable role of TAF13 in maintaining pluripotency. Transcriptomic analysis revealed distinct gene targets affected by the loss of TAF5, TAF12 and TAF13. Thus, we propose that TAF5, TAF12 and TAF13 convey locus specificity to the TFIID complex throughout the mouse genome.
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Affiliation(s)
- Xinjian Doris He
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, MA, USA
| | - Shelby Phillips
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, MA, USA
| | - Kaito Hioki
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, MA, USA
| | - Prabin Dhangada Majhi
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, MA, USA
| | - Courtney Babbitt
- Department of Biology, University of Massachusetts, Amherst, MA, USA
| | - Kimberly D Tremblay
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, MA, USA
| | - Leonid A Pobezinsky
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, MA, USA
| | - Jesse Mager
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, MA, USA.
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38
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Kamate M, Basavanagowda T. ARV1 Gene: A Novel Cause of Autosomal Recessive Cerebellar Ataxia with Elevated Alpha Fetoprotein. CEREBELLUM (LONDON, ENGLAND) 2024; 23:1239-1244. [PMID: 37749428 DOI: 10.1007/s12311-023-01606-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 09/14/2023] [Indexed: 09/27/2023]
Abstract
ARV1 mutation is known to present as developmental and epileptic encephalopathy (DEE)-38. However, the phenotypic spectrum has been expanding ever since it was reported in 2016. Along with seizures and developmental delay, other unique clinical features include ophthalmological abnormalities and movement disorders in the form of ataxia and dystonia, especially in those with missense mutation. These manifestations closely mimic ataxia telangiectasia. Elevation of alpha-fetoprotein levels is an important investigative marker in the diagnosis of ataxia telangiectasia and ataxia with oculomotor apraxia syndromes. ARV1 can also be associated with increased alpha-fetoprotein. There are no reports evaluating alpha-fetoprotein levels in cases with ARV1 mutation, which is significant in the context of ocular abnormalities with ataxia. We report a case of ARV1 mutation presenting with ataxia, ocular abnormalities, and elevated alpha-fetoprotein levels, thus mimicking autosomal recessive cerebellar ataxias. This study provides a comprehensive literature review of the cases reported so far, thus expanding the understanding of the spectrum of presentation, and helps in correlating the clinical picture with the underlying causative genetic mutation. ARV1 gene is another example of one gene with phenotypic pleiotropy. Though presentation with DEE is common, a few, especially those with missense mutations, can present with ataxia and ocular abnormalities. All cases presenting with ataxia who have increased alpha-fetoprotein levels and seizures should be tested for the ARV1 gene, when testing for ataxia genes is negative. The underlying genetic mechanism can explain the varying clinical manifestations of the ARV1 gene.
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Affiliation(s)
- Mahesh Kamate
- Department of Pediatric Neurology, Jawaharlal Nehru Medical College, KLE Academy of Higher Education and Research, Room No. 25, KLE's PK Hospital, Belagavi, Karnataka, 590010, India.
| | - Thanuja Basavanagowda
- Department of Pediatric Neurology, Jawaharlal Nehru Medical College, KLE Academy of Higher Education and Research, Room No. 25, KLE's PK Hospital, Belagavi, Karnataka, 590010, India
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39
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Shi Y, Huang D, Song C, Cao R, Wang Z, Wang D, Zhao L, Xu X, Lu C, Xiong F, Zhao H, Li S, Zhou Q, Luo S, Hu D, Zhang Y, Wang C, Shen Y, Su W, Wu Y, Schmitz K, Wei S, Song W. Diphthamide deficiency promotes association of eEF2 with p53 to induce p21 expression and neural crest defects. Nat Commun 2024; 15:3301. [PMID: 38671004 PMCID: PMC11053169 DOI: 10.1038/s41467-024-47670-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 04/08/2024] [Indexed: 04/28/2024] Open
Abstract
Diphthamide is a modified histidine residue unique for eukaryotic translation elongation factor 2 (eEF2), a key ribosomal protein. Loss of this evolutionarily conserved modification causes developmental defects through unknown mechanisms. In a patient with compound heterozygous mutations in Diphthamide Biosynthesis 1 (DPH1) and impaired eEF2 diphthamide modification, we observe multiple defects in neural crest (NC)-derived tissues. Knockin mice harboring the patient's mutations and Xenopus embryos with Dph1 depleted also display NC defects, which can be attributed to reduced proliferation in the neuroepithelium. DPH1 depletion facilitates dissociation of eEF2 from ribosomes and association with p53 to promote transcription of the cell cycle inhibitor p21, resulting in inhibited proliferation. Knockout of one p21 allele rescues the NC phenotypes in the knockin mice carrying the patient's mutations. These findings uncover an unexpected role for eEF2 as a transcriptional coactivator for p53 to induce p21 expression and NC defects, which is regulated by diphthamide modification.
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Affiliation(s)
- Yu Shi
- Department of Clinical Laboratory, Children's Hospital of Chongqing Medical University, Chongqing Key Laboratory of Child Neurodevelopment and Cognitive Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, National Clinical Research Center for Child Health and Disorders, 136 Zhongshan 2nd Rd, Chongqing, 400014, China.
- Department of Biological Sciences, University of Delaware, Newark, DE, 19716, USA.
| | - Daochao Huang
- Department of Pediatric Research Institute, Children's Hospital of Chongqing Medical University, 136 Zhongshan 2nd Rd, Chongqing, 400014, China
| | - Cui Song
- Department of Endocrinology and Genetic Metabolism Disease, Children's Hospital of Chongqing Medical University, 136 Zhongshan 2nd Rd, Chongqing, 400014, China
| | - Ruixue Cao
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Institute of Aging, Key Laboratory of Alzheimer's Disease of Zhejiang Province, School of Mental Health and Kangning Hospital, The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Zhao Wang
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Institute of Aging, Key Laboratory of Alzheimer's Disease of Zhejiang Province, School of Mental Health and Kangning Hospital, The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Dan Wang
- Department of Pediatric Research Institute, Children's Hospital of Chongqing Medical University, 136 Zhongshan 2nd Rd, Chongqing, 400014, China
| | - Li Zhao
- Department of Pediatric Research Institute, Children's Hospital of Chongqing Medical University, 136 Zhongshan 2nd Rd, Chongqing, 400014, China
| | - Xiaolu Xu
- Department of Biological Sciences, University of Delaware, Newark, DE, 19716, USA
| | - Congyu Lu
- Department of Biological Sciences, University of Delaware, Newark, DE, 19716, USA
| | - Feng Xiong
- Department of Endocrinology and Genetic Metabolism Disease, Children's Hospital of Chongqing Medical University, 136 Zhongshan 2nd Rd, Chongqing, 400014, China
| | - Haowen Zhao
- Department of Clinical Laboratory, Children's Hospital of Chongqing Medical University, Chongqing Key Laboratory of Child Neurodevelopment and Cognitive Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, National Clinical Research Center for Child Health and Disorders, 136 Zhongshan 2nd Rd, Chongqing, 400014, China
- Department of Pediatric Research Institute, Children's Hospital of Chongqing Medical University, 136 Zhongshan 2nd Rd, Chongqing, 400014, China
| | - Shuxiang Li
- Department of Pediatric Research Institute, Children's Hospital of Chongqing Medical University, 136 Zhongshan 2nd Rd, Chongqing, 400014, China
- Department of Endocrinology and Genetic Metabolism Disease, Children's Hospital of Chongqing Medical University, 136 Zhongshan 2nd Rd, Chongqing, 400014, China
| | - Quansheng Zhou
- Department of Pediatric Research Institute, Children's Hospital of Chongqing Medical University, 136 Zhongshan 2nd Rd, Chongqing, 400014, China
- Department of Endocrinology and Genetic Metabolism Disease, Children's Hospital of Chongqing Medical University, 136 Zhongshan 2nd Rd, Chongqing, 400014, China
| | - Shuyue Luo
- Department of Pediatric Research Institute, Children's Hospital of Chongqing Medical University, 136 Zhongshan 2nd Rd, Chongqing, 400014, China
| | - Dongjie Hu
- Department of Pediatric Research Institute, Children's Hospital of Chongqing Medical University, 136 Zhongshan 2nd Rd, Chongqing, 400014, China
| | - Yun Zhang
- Department of Radiology, Children's Hospital of Chongqing Medical University, 136 Zhongshan 2nd Rd, Chongqing, 400014, China
| | - Cui Wang
- Department of Radiology, Children's Hospital of Chongqing Medical University, 136 Zhongshan 2nd Rd, Chongqing, 400014, China
| | - Yiping Shen
- Division of Genetics and Genomics, Boston Children's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Weiting Su
- Kunming Institute of Zoology, Chinese Academy of Science, Kunming, 650223, Yunnan, China
| | - Yili Wu
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Institute of Aging, Key Laboratory of Alzheimer's Disease of Zhejiang Province, School of Mental Health and Kangning Hospital, The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Karl Schmitz
- Department of Biological Sciences, University of Delaware, Newark, DE, 19716, USA
| | - Shuo Wei
- Department of Biological Sciences, University of Delaware, Newark, DE, 19716, USA.
| | - Weihong Song
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Institute of Aging, Key Laboratory of Alzheimer's Disease of Zhejiang Province, School of Mental Health and Kangning Hospital, The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China.
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Frankhouser DE, Rockne RC, Uechi L, Zhao D, Branciamore S, O'Meally D, Irizarry J, Ghoda L, Ali H, Trent JM, Forman S, Fu YH, Kuo YH, Zhang B, Marcucci G. State-transition modeling of blood transcriptome predicts disease evolution and treatment response in chronic myeloid leukemia. Leukemia 2024; 38:769-780. [PMID: 38307941 PMCID: PMC10997512 DOI: 10.1038/s41375-024-02142-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 12/22/2023] [Accepted: 01/05/2024] [Indexed: 02/04/2024]
Abstract
Chronic myeloid leukemia (CML) is initiated and maintained by BCR::ABL which is clinically targeted using tyrosine kinase inhibitors (TKIs). TKIs can induce long-term remission but are also not curative. Thus, CML is an ideal system to test our hypothesis that transcriptome-based state-transition models accurately predict cancer evolution and treatment response. We collected time-sequential blood samples from tetracycline-off (Tet-Off) BCR::ABL-inducible transgenic mice and wild-type controls. From the transcriptome, we constructed a CML state-space and a three-well leukemogenic potential landscape. The potential's stable critical points defined observable disease states. Early states were characterized by anti-CML genes opposing leukemia; late states were characterized by pro-CML genes. Genes with expression patterns shaped similarly to the potential landscape were identified as drivers of disease transition. Re-introduction of tetracycline to silence the BCR::ABL gene returned diseased mice transcriptomes to a near healthy state, without reaching it, suggesting parts of the transition are irreversible. TKI only reverted the transcriptome to an intermediate disease state, without approaching a state of health; disease relapse occurred soon after treatment. Using only the earliest time-point as initial conditions, our state-transition models accurately predicted both disease progression and treatment response, supporting this as a potentially valuable approach to time clinical intervention, before phenotypic changes become detectable.
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Affiliation(s)
- David E Frankhouser
- Department of Computational and Quantitative Medicine, Beckman Research Institute, City of Hope National Medical Center, Duarte, CAL, 91010, USA.
| | - Russell C Rockne
- Department of Computational and Quantitative Medicine, Beckman Research Institute, City of Hope National Medical Center, Duarte, CAL, 91010, USA.
| | - Lisa Uechi
- Department of Computational and Quantitative Medicine, Beckman Research Institute, City of Hope National Medical Center, Duarte, CAL, 91010, USA
| | - Dandan Zhao
- Department of Hematologic Malignancies Translational Science, Beckman Research Institute and Division of Leukemia, City of Hope National Medical Center, Duarte, CAL, 91010, USA
| | - Sergio Branciamore
- Department of Computational and Quantitative Medicine, Beckman Research Institute, City of Hope National Medical Center, Duarte, CAL, 91010, USA
| | - Denis O'Meally
- Department of Diabetes and & Cancer Discovery Science, Beckman Research Institute, City of Hope National Medical Center, Duarte, CAL, 91010, USA
| | - Jihyun Irizarry
- Department of Hematologic Malignancies Translational Science, Beckman Research Institute and Division of Leukemia, City of Hope National Medical Center, Duarte, CAL, 91010, USA
| | - Lucy Ghoda
- Department of Hematologic Malignancies Translational Science, Beckman Research Institute and Division of Leukemia, City of Hope National Medical Center, Duarte, CAL, 91010, USA
| | - Haris Ali
- Department of Hematologic Malignancies Translational Science, Beckman Research Institute and Division of Leukemia, City of Hope National Medical Center, Duarte, CAL, 91010, USA
| | | | - Stephen Forman
- Department of Hematologic Malignancies Translational Science, Beckman Research Institute and Division of Leukemia, City of Hope National Medical Center, Duarte, CAL, 91010, USA
| | - Yu-Hsuan Fu
- Department of Hematologic Malignancies Translational Science, Beckman Research Institute and Division of Leukemia, City of Hope National Medical Center, Duarte, CAL, 91010, USA
| | - Ya-Huei Kuo
- Department of Hematologic Malignancies Translational Science, Beckman Research Institute and Division of Leukemia, City of Hope National Medical Center, Duarte, CAL, 91010, USA
| | - Bin Zhang
- Department of Hematologic Malignancies Translational Science, Beckman Research Institute and Division of Leukemia, City of Hope National Medical Center, Duarte, CAL, 91010, USA.
| | - Guido Marcucci
- Department of Hematologic Malignancies Translational Science, Beckman Research Institute and Division of Leukemia, City of Hope National Medical Center, Duarte, CAL, 91010, USA.
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41
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Gefen AM, Zaritsky JJ. Review of childhood genetic nephrolithiasis and nephrocalcinosis. Front Genet 2024; 15:1381174. [PMID: 38606357 PMCID: PMC11007102 DOI: 10.3389/fgene.2024.1381174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Accepted: 03/04/2024] [Indexed: 04/13/2024] Open
Abstract
Nephrolithiasis (NL) is a common condition worldwide. The incidence of NL and nephrocalcinosis (NC) has been increasing, along with their associated morbidity and economic burden. The etiology of NL and NC is multifactorial and includes both environmental components and genetic components, with multiple studies showing high heritability. Causative gene variants have been detected in up to 32% of children with NL and NC. Children with NL and NC are genotypically heterogenous, but often phenotypically relatively homogenous, and there are subsequently little data on the predictors of genetic childhood NL and NC. Most genetic diseases associated with NL and NC are secondary to hypercalciuria, including those secondary to hypercalcemia, renal phosphate wasting, renal magnesium wasting, distal renal tubular acidosis (RTA), proximal tubulopathies, mixed or variable tubulopathies, Bartter syndrome, hyperaldosteronism and pseudohyperaldosteronism, and hyperparathyroidism and hypoparathyroidism. The remaining minority of genetic diseases associated with NL and NC are secondary to hyperoxaluria, cystinuria, hyperuricosuria, xanthinuria, other metabolic disorders, and multifactorial etiologies. Genome-wide association studies (GWAS) in adults have identified multiple polygenic traits associated with NL and NC, often involving genes that are involved in calcium, phosphorus, magnesium, and vitamin D homeostasis. Compared to adults, there is a relative paucity of studies in children with NL and NC. This review aims to focus on the genetic component of NL and NC in children.
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Affiliation(s)
- Ashley M. Gefen
- Phoenix Children’s Hospital, Department of Pediatrics, Division of Nephrology, Phoenix, AZ, United States
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Cheng J, Wang Z, Tang M, Zhang W, Li G, Tan S, Mu C, Hu M, Zhang D, Jia X, Wen Y, Guo H, Xu D, Liu L, Li J, Xia K, Li F, Duan R, Xu Z, Yuan L. KCTD10 regulates brain development by destabilizing brain disorder-associated protein KCTD13. Proc Natl Acad Sci U S A 2024; 121:e2315707121. [PMID: 38489388 PMCID: PMC10963008 DOI: 10.1073/pnas.2315707121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Accepted: 02/02/2024] [Indexed: 03/17/2024] Open
Abstract
KCTD10 belongs to the KCTD (potassiumchannel tetramerization domain) family, many members of which are associated with neuropsychiatric disorders. However, the biological function underlying the association with brain disorders remains to be explored. Here, we reveal that Kctd10 is highly expressed in neuronal progenitors and layer V neurons throughout brain development. Kctd10 deficiency triggers abnormal proliferation and differentiation of neuronal progenitors, reduced deep-layer (especially layer V) neurons, increased upper-layer neurons, and lowered brain size. Mechanistically, we screened and identified a unique KCTD10-interacting protein, KCTD13, associated with neurodevelopmental disorders. KCTD10 mediated the ubiquitination-dependent degradation of KCTD13 and KCTD10 ablation resulted in a considerable increase of KCTD13 expression in the developing cortex. KCTD13 overexpression in neuronal progenitors led to reduced proliferation and abnormal cell distribution, mirroring KCTD10 deficiency. Notably, mice with brain-specific Kctd10 knockout exhibited obvious motor deficits. This study uncovers the physiological function of KCTD10 and provides unique insights into the pathogenesis of neurodevelopmental disorders.
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Affiliation(s)
- Jianbo Cheng
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics, Key Lab of Rare Pediatric Diseases of Ministry of Education, School of Life Sciences, Central South University, Changsha, Hunan410078, China
| | - Zhen Wang
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics, Key Lab of Rare Pediatric Diseases of Ministry of Education, School of Life Sciences, Central South University, Changsha, Hunan410078, China
| | - Manpei Tang
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics, Key Lab of Rare Pediatric Diseases of Ministry of Education, School of Life Sciences, Central South University, Changsha, Hunan410078, China
| | - Wen Zhang
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics, Key Lab of Rare Pediatric Diseases of Ministry of Education, School of Life Sciences, Central South University, Changsha, Hunan410078, China
| | - Guozhong Li
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics, Key Lab of Rare Pediatric Diseases of Ministry of Education, School of Life Sciences, Central South University, Changsha, Hunan410078, China
| | - Senwei Tan
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics, Key Lab of Rare Pediatric Diseases of Ministry of Education, School of Life Sciences, Central South University, Changsha, Hunan410078, China
| | - Chenjun Mu
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics, Key Lab of Rare Pediatric Diseases of Ministry of Education, School of Life Sciences, Central South University, Changsha, Hunan410078, China
| | - Mengyuan Hu
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics, Key Lab of Rare Pediatric Diseases of Ministry of Education, School of Life Sciences, Central South University, Changsha, Hunan410078, China
| | - Dan Zhang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing100101, China
| | - Xiangbin Jia
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics, Key Lab of Rare Pediatric Diseases of Ministry of Education, School of Life Sciences, Central South University, Changsha, Hunan410078, China
| | - Yangxuan Wen
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics, Key Lab of Rare Pediatric Diseases of Ministry of Education, School of Life Sciences, Central South University, Changsha, Hunan410078, China
| | - Hui Guo
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics, Key Lab of Rare Pediatric Diseases of Ministry of Education, School of Life Sciences, Central South University, Changsha, Hunan410078, China
- Hunan Key Laboratory of Animal Models for Human Diseases, Central South University, Changsha, Hunan410078, China
| | - Dan Xu
- Fujian Key Laboratory of Molecular Neurology, Institute of Neuroscience, Fujian Medical University, Fuzhou350005, China
| | - Liang Liu
- Department of Neurology, Xuanwu Hospital, Capital Medical University, Beijing100053, China
| | - Jiada Li
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics, Key Lab of Rare Pediatric Diseases of Ministry of Education, School of Life Sciences, Central South University, Changsha, Hunan410078, China
- Hunan Key Laboratory of Animal Models for Human Diseases, Central South University, Changsha, Hunan410078, China
| | - Kun Xia
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics, Key Lab of Rare Pediatric Diseases of Ministry of Education, School of Life Sciences, Central South University, Changsha, Hunan410078, China
- Hunan Key Laboratory of Animal Models for Human Diseases, Central South University, Changsha, Hunan410078, China
| | - Faxiang Li
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics, Key Lab of Rare Pediatric Diseases of Ministry of Education, School of Life Sciences, Central South University, Changsha, Hunan410078, China
- Hunan Key Laboratory of Animal Models for Human Diseases, Central South University, Changsha, Hunan410078, China
| | - Ranhui Duan
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics, Key Lab of Rare Pediatric Diseases of Ministry of Education, School of Life Sciences, Central South University, Changsha, Hunan410078, China
- Hunan Key Laboratory of Animal Models for Human Diseases, Central South University, Changsha, Hunan410078, China
| | - Zhiheng Xu
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing100101, China
| | - Ling Yuan
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics, Key Lab of Rare Pediatric Diseases of Ministry of Education, School of Life Sciences, Central South University, Changsha, Hunan410078, China
- Hunan Key Laboratory of Animal Models for Human Diseases, Central South University, Changsha, Hunan410078, China
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Hale AT, Boudreau H, Devulapalli R, Duy PQ, Atchley TJ, Dewan MC, Goolam M, Fieggen G, Spader HL, Smith AA, Blount JP, Johnston JM, Rocque BG, Rozzelle CJ, Chong Z, Strahle JM, Schiff SJ, Kahle KT. The genetic basis of hydrocephalus: genes, pathways, mechanisms, and global impact. Fluids Barriers CNS 2024; 21:24. [PMID: 38439105 PMCID: PMC10913327 DOI: 10.1186/s12987-024-00513-z] [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: 12/13/2023] [Accepted: 01/25/2024] [Indexed: 03/06/2024] Open
Abstract
Hydrocephalus (HC) is a heterogenous disease characterized by alterations in cerebrospinal fluid (CSF) dynamics that may cause increased intracranial pressure. HC is a component of a wide array of genetic syndromes as well as a secondary consequence of brain injury (intraventricular hemorrhage (IVH), infection, etc.) that can present across the age spectrum, highlighting the phenotypic heterogeneity of the disease. Surgical treatments include ventricular shunting and endoscopic third ventriculostomy with or without choroid plexus cauterization, both of which are prone to failure, and no effective pharmacologic treatments for HC have been developed. Thus, there is an urgent need to understand the genetic architecture and molecular pathogenesis of HC. Without this knowledge, the development of preventive, diagnostic, and therapeutic measures is impeded. However, the genetics of HC is extraordinarily complex, based on studies of varying size, scope, and rigor. This review serves to provide a comprehensive overview of genes, pathways, mechanisms, and global impact of genetics contributing to all etiologies of HC in humans.
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Affiliation(s)
- Andrew T Hale
- Department of Neurosurgery, University of Alabama at Birmingham, FOT Suite 1060, 1720 2ndAve, Birmingham, AL, 35294, UK.
| | - Hunter Boudreau
- Department of Neurosurgery, University of Alabama at Birmingham, FOT Suite 1060, 1720 2ndAve, Birmingham, AL, 35294, UK
| | - Rishi Devulapalli
- Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, UK
| | - Phan Q Duy
- Department of Neurosurgery, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Travis J Atchley
- Department of Neurosurgery, University of Alabama at Birmingham, FOT Suite 1060, 1720 2ndAve, Birmingham, AL, 35294, UK
| | - Michael C Dewan
- Division of Pediatric Neurosurgery, Monroe Carell Jr. Children's Hospital, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Mubeen Goolam
- Neuroscience Institute, University of Cape Town, Cape Town, South Africa
| | - Graham Fieggen
- Neuroscience Institute, University of Cape Town, Cape Town, South Africa
- Division of Pediatric Neurosurgery, Red Cross War Memorial Children's Hospital, University of Cape Town, Cape Town, South Africa
| | - Heather L Spader
- Department of Neurosurgery, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Anastasia A Smith
- Division of Pediatric Neurosurgery, Children's of Alabama, University of Alabama at Birmingham, Birmingham, AL, UK
| | - Jeffrey P Blount
- Division of Pediatric Neurosurgery, Children's of Alabama, University of Alabama at Birmingham, Birmingham, AL, UK
| | - James M Johnston
- Division of Pediatric Neurosurgery, Children's of Alabama, University of Alabama at Birmingham, Birmingham, AL, UK
| | - Brandon G Rocque
- Division of Pediatric Neurosurgery, Children's of Alabama, University of Alabama at Birmingham, Birmingham, AL, UK
| | - Curtis J Rozzelle
- Division of Pediatric Neurosurgery, Children's of Alabama, University of Alabama at Birmingham, Birmingham, AL, UK
| | - Zechen Chong
- Heflin Center for Genomics, University of Alabama at Birmingham, Birmingham, AL, UK
| | - Jennifer M Strahle
- Division of Pediatric Neurosurgery, St. Louis Children's Hospital, Washington University in St. Louis, St. Louis, MO, USA
| | - Steven J Schiff
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT, USA
| | - Kristopher T Kahle
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
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Coban-Akdemir Z, Song X, Ceballos FC, Pehlivan D, Karaca E, Bayram Y, Mitani T, Gambin T, Bozkurt-Yozgatli T, Jhangiani SN, Muzny DM, Lewis RA, Liu P, Boerwinkle E, Hamosh A, Gibbs RA, Sutton VR, Sobreira N, Carvalho CM, Shaw CA, Posey JE, Valle D, Lupski JR. The impact of the Turkish population variome on the genomic architecture of rare disease traits. GENETICS IN MEDICINE OPEN 2024; 2:101830. [PMID: 39669594 PMCID: PMC11613692 DOI: 10.1016/j.gimo.2024.101830] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 02/03/2024] [Accepted: 02/07/2024] [Indexed: 12/14/2024]
Abstract
Purpose The variome of the Turkish (TK) population, a population with a considerable history of admixture and consanguinity, has not been deeply investigated for insights on the genomic architecture of disease. Methods We generated and analyzed a database of variants derived from exome sequencing data of 773 TK unrelated, clinically affected individuals with various suspected Mendelian disease traits and 643 unaffected relatives. Results Using uniform manifold approximation and projection, we showed that the TK genomes are more similar to those of Europeans and consist of 2 main subpopulations: clusters 1 and 2 (N = 235 and 1181, respectively), which differ in admixture proportion and variome (https://turkishvariomedb.shinyapps.io/tvdb/). Furthermore, the higher inbreeding coefficient values observed in the TK affected compared with unaffected individuals correlated with a larger median span of long-sized (>2.64 Mb) runs of homozygosity (ROH) regions (P value = 2.09e-18). We show that long-sized ROHs are more likely to be formed on recently configured haplotypes enriched for rare homozygous deleterious variants in the TK affected compared with TK unaffected individuals (P value = 3.35e-11). Analysis of genotype-phenotype correlations reveals that genes with rare homozygous deleterious variants in long-sized ROHs provide the most comprehensive set of molecular diagnoses for the observed disease traits with a systematic quantitative analysis of Human Phenotype Ontology terms. Conclusion Our findings support the notion that novel rare variants on newly configured haplotypes arising within the recent past generations of a family or clan contribute significantly to recessive disease traits in the TK population.
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Affiliation(s)
- Zeynep Coban-Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX
| | - Xiaofei Song
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL
| | | | - Davut Pehlivan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
- Section of Neurology, Department of Pediatrics, Baylor College of Medicine, Houston, TX
| | - Ender Karaca
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
- Department of Pathology, Baylor University Medical Center, Dallas, TX
- Texas A&M School of Medicine, Texas A&M University, Dallas, TX
| | - Yavuz Bayram
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Tadahiro Mitani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Tomasz Gambin
- Institute of Computer Science, Warsaw University of Technology, Warsaw, Poland
| | - Tugce Bozkurt-Yozgatli
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX
- Department of Biostatistics and Bioinformatics, Institute of Health Sciences, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | | | - Donna M. Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
| | - Richard A. Lewis
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
- Department of Pediatrics, Baylor College of Medicine, Houston, TX
- Department of Ophthalmology, Cullen Eye Institute, Baylor College of Medicine, Houston, TX
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Eric Boerwinkle
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
| | - Ada Hamosh
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Richard A. Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
| | - V. Reid Sutton
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
- Texas Children’s Hospital, Houston, TX
| | - Nara Sobreira
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Claudia M.B. Carvalho
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
- Pacific Northwest Research Institute, Seattle, WA
| | - Chad A. Shaw
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
- Baylor Genetics, Houston, TX
| | - Jennifer E. Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - David Valle
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
| | - James R. Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
- Department of Pediatrics, Baylor College of Medicine, Houston, TX
- Texas Children’s Hospital, Houston, TX
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Allison K, Maletic-Savatic M, Pehlivan D. MECP2-related disorders while gene-based therapies are on the horizon. Front Genet 2024; 15:1332469. [PMID: 38410154 PMCID: PMC10895005 DOI: 10.3389/fgene.2024.1332469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 01/23/2024] [Indexed: 02/28/2024] Open
Abstract
The emergence of new genetic tools has led to the discovery of the genetic bases of many intellectual and developmental disabilities. This creates exciting opportunities for research and treatment development, and a few genetic disorders (e.g., spinal muscular atrophy) have recently been treated with gene-based therapies. MECP2 is found on the X chromosome and regulates the transcription of thousands of genes. Loss of MECP2 gene product leads to Rett Syndrome, a disease found primarily in females, and is characterized by developmental regression, motor dysfunction, midline hand stereotypies, autonomic nervous system dysfunction, epilepsy, scoliosis, and autistic-like behavior. Duplication of MECP2 causes MECP2 Duplication Syndrome (MDS). MDS is found mostly in males and presents with developmental delay, hypotonia, autistic features, refractory epilepsy, and recurrent respiratory infections. While these two disorders share several characteristics, their differences (e.g., affected sex, age of onset, genotype/phenotype correlations) are important to distinguish in the light of gene-based therapy because they require opposite solutions. This review explores the clinical features of both disorders and highlights these important clinical differences.
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Affiliation(s)
- Katherine Allison
- Royal College of Surgeons in Ireland, School of Medicine, Dublin, Ireland
| | - Mirjana Maletic-Savatic
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX, United States
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX, United States
| | - Davut Pehlivan
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX, United States
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX, United States
- Blue Bird Circle Rett Center, Texas Children's Hospital, Houston, TX, United States
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46
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Schaffrath R, Brinkmann U. Diphthamide - a conserved modification of eEF2 with clinical relevance. Trends Mol Med 2024; 30:164-177. [PMID: 38097404 DOI: 10.1016/j.molmed.2023.11.008] [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: 09/28/2023] [Revised: 11/03/2023] [Accepted: 11/09/2023] [Indexed: 02/17/2024]
Abstract
Diphthamide, a complex modification on eukaryotic translation elongation factor 2 (eEF2), assures reading-frame fidelity during translation. Diphthamide and enzymes for its synthesis are conserved in eukaryotes and archaea. Originally identified as target for diphtheria toxin (DT) in humans, its clinical relevance now proves to be broader than the link to pathogenic bacteria. Diphthamide synthesis enzymes (DPH1 and DPH3) are associated with cancer, and DPH gene mutations can cause diphthamide deficiency syndrome (DDS). Finally, new analyses provide evidence that diphthamide may restrict propagation of viruses including SARS-CoV-2 and HIV-1, and that DPH enzymes are targeted by viruses for degradation to overcome this restriction. This review describes how diphthamide is synthesized and functions in translation, and covers its clinical relevance in human development, cancer, and infectious diseases.
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Affiliation(s)
- Raffael Schaffrath
- Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, Kassel, Germany.
| | - Ulrich Brinkmann
- Roche Pharma Research and Early Development (pRED), Large Molecule Research, Roche Innovation Center Munich, Penzberg, Germany.
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47
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Alshammari MJ, Shamseldin HE, Essbaiheen F, Eltahir SH, Alruwaili AR, Abdulwahab F, Alkuraya FS. Genomic analysis of presumed perinatal stroke in Saudi Arabia reveals a strong monogenic contribution. Hum Genet 2024; 143:59-69. [PMID: 38180561 DOI: 10.1007/s00439-023-02621-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 11/10/2023] [Indexed: 01/06/2024]
Abstract
Perinatal stroke is associated with significant short- and long-term morbidity and has been recognized as the most common cause of cerebral palsy in term infants. The diagnosis of presumed perinatal stroke (PPS) is made in children who present with neurological deficit and/or seizures attributable to focal chronic infarction on neuroimaging and have uneventful neonatal history. The underlying mechanism of presumed perinatal stroke remains unknown and thorough investigation of potential monogenic causes has not been conducted to date. Here, we describe the use of untargeted exome sequencing to investigate a cohort of eight patients from six families with PPS. A likely deleterious variant was identified in four families. These include the well-established risk genes COL4A2 and JAM3. In addition, we report the first independent confirmation of the recently described link between ESAM and perinatal stroke. Our data also highlight NID1 as a candidate gene for the condition. This study suggests that monogenic disorders are important contributors to the pathogenesis of PPS and should be investigated by untargeted sequencing especially when traditional risk factors are excluded.
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Affiliation(s)
- Muneera J Alshammari
- Department of Pediatrics, King Saud University Medical City, King Saud University, Riyadh, Saudi Arabia
| | - Hanan E Shamseldin
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Fahad Essbaiheen
- Department of Diagnostic Imaging, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Sara H Eltahir
- Department of Pediatrics, King Saud University Medical City, King Saud University, Riyadh, Saudi Arabia
| | - Ashwag R Alruwaili
- Radiological Sciences Department, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Firdous Abdulwahab
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Fowzan S Alkuraya
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.
- Department of Pediatrics, Prince Sultan Military Medical City, Riyadh, Saudi Arabia.
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48
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Mir YR, Agrahari AK, Hassan A, Choudhary A, Asthana S, Taneja AK, Nawaz S, Ilyas M, Scotti C, Kuchay RAH. Identification and structural characterization of a pathogenic ARSA missense variant in two consanguineous families from Jammu and Kashmir (India) with late infantile metachromatic leukodystrophy. Mol Biol Rep 2023; 51:30. [PMID: 38153581 DOI: 10.1007/s11033-023-09072-2] [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: 07/08/2023] [Accepted: 11/01/2023] [Indexed: 12/29/2023]
Abstract
BACKGROUND Metachromatic leukodystrophy (MLD) is a rare lysosomal storage disorder caused by a deficiency of Arylsulfatase A (ARSA) enzyme activity. Its clinical manifestations include progressive motor and cognitive decline. ARSA gene mutations are frequent in MLD. METHODS AND RESULTS In the present study, whole exome sequencing (WES) was employed to decipher the genetic cause of motor and cognitive decline in proband's of two consanguineous families from J&K (India). Clinical investigations using radiological and biochemical analysis revealed MLD-like features. WES confirmed a pathogenic variant in the ARSA gene. Molecular simulation dynamics was applied for structural characterization of the variant. CONCLUSION We report the identification of a pathogenic missense variant (c.1174 C > T; p.Arg390Trp) in the ARSA gene in two cases of late infantile MLD from consanguineous families in Jammu and Kashmir, India. Our study utilized genetic analysis and molecular dynamics simulations to identify and investigate the structural consequences of this mutation. The molecular dynamics simulations revealed significant alterations in the structural dynamics, residue interactions, and stability of the ARSA protein harbouring the p.Arg390Trp mutation. These findings provide valuable insights into the molecular mechanisms underlying the pathogenicity of this variant in MLD.
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Affiliation(s)
- Yaser Rafiq Mir
- Department of Biotechnology, Baba Ghulam Shah Badshah University, Rajouri, J&K, 185234, India
| | - Ashish Kumar Agrahari
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, India
| | - Asima Hassan
- Department of Ophthalmology GMC Srinagar, Srinagar, J&K, India
| | | | - Shailendra Asthana
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, India
| | - Atul Kumar Taneja
- Department of Radiology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Shah Nawaz
- Department of Pediatrics, GMC Jammu, Jammu, J&K, India
| | | | - Claudia Scotti
- Department of Molecular Medicine, Unit of Immunology and General Pathology, University of Pavia, Pavia, Italy
| | - Raja A H Kuchay
- Department of Biotechnology, Baba Ghulam Shah Badshah University, Rajouri, J&K, 185234, India.
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Ugur B, Schueder F, Shin J, Hanna MG, Wu Y, Leonzino M, Su M, McAdow AR, Wilson C, Postlethwait J, Solnica-Krezel L, Bewersdorf J, De Camilli P. VPS13B is localized at the cis-trans Golgi complex interface and is a functional partner of FAM177A1. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.18.572081. [PMID: 38187698 PMCID: PMC10769246 DOI: 10.1101/2023.12.18.572081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Mutations in VPS13B, a member of a protein family implicated in bulk lipid transport between adjacent membranes, cause Cohen syndrome. VPS13B is known to be concentrated in the Golgi complex, but its precise location within this organelle and thus the site(s) where it achieves lipid transport remains unclear. Here we show that VPS13B is localized at the interface between cis and trans Golgi sub-compartments and that Golgi complex re-formation after Brefeldin A (BFA) induced disruption is delayed in VPS13B KO cells. This delay is phenocopied by loss of FAM177A1, a Golgi complex protein of unknown function reported to be a VPS13B interactor and whose mutations also result in a developmental disorder. In zebrafish, the vps13b orthologue, not previously annotated in this organism, genetically interacts with fam177a1. Collectively, these findings raise the possibility that bulk lipid transport by VPS13B may play a role in expanding Golgi membranes and that VPS13B may be assisted in this function by FAM177A1.
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Affiliation(s)
- Berrak Ugur
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, USA
- Program in Cellular Neuroscience, Neurodegeneration, and Repair, Yale University School of Medicine, New Haven, CT, USA
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
- HHMI, Yale University School of Medicine, New Haven, CT, USA
| | - Florian Schueder
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, USA
| | - Jimann Shin
- Department of Developmental Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Michael G. Hanna
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, USA
- Program in Cellular Neuroscience, Neurodegeneration, and Repair, Yale University School of Medicine, New Haven, CT, USA
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
- HHMI, Yale University School of Medicine, New Haven, CT, USA
| | - Yumei Wu
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, USA
- Program in Cellular Neuroscience, Neurodegeneration, and Repair, Yale University School of Medicine, New Haven, CT, USA
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
- HHMI, Yale University School of Medicine, New Haven, CT, USA
| | - Marianna Leonzino
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, USA
- Program in Cellular Neuroscience, Neurodegeneration, and Repair, Yale University School of Medicine, New Haven, CT, USA
- HHMI, Yale University School of Medicine, New Haven, CT, USA
| | - Maohan Su
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
| | - Anthony R. McAdow
- Department of Developmental Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Catherine Wilson
- Institute of Neuroscience, University of Oregon, Eugene, OR, USA
| | | | - Lilianna Solnica-Krezel
- Department of Developmental Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Joerg Bewersdorf
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
- Nanobiology Institute, Yale University, West Haven, CT, USA
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
- Department of Physics, Yale University, New Haven, CT, USA
| | - Pietro De Camilli
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, USA
- Program in Cellular Neuroscience, Neurodegeneration, and Repair, Yale University School of Medicine, New Haven, CT, USA
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
- HHMI, Yale University School of Medicine, New Haven, CT, USA
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, USA
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50
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AlAbdi L, Shamseldin HE, Khouj E, Helaby R, Aljamal B, Alqahtani M, Almulhim A, Hamid H, Hashem MO, Abdulwahab F, Abouyousef O, Jaafar A, Alshidi T, Al-Owain M, Alhashem A, Al Tala S, Khan AO, Mardawi E, Alkuraya H, Faqeih E, Afqi M, Alkhalifi S, Rahbeeni Z, Hagos ST, Al-Ahmadi W, Nadeef S, Maddirevula S, Khabar KSA, Putra A, Angelov A, Park C, Reyes-Ramos AM, Umer H, Ullah I, Driguez P, Fukasawa Y, Cheung MS, Gallouzi IE, Alkuraya FS. Beyond the exome: utility of long-read whole genome sequencing in exome-negative autosomal recessive diseases. Genome Med 2023; 15:114. [PMID: 38098057 PMCID: PMC10720148 DOI: 10.1186/s13073-023-01270-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 12/05/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Long-read whole genome sequencing (lrWGS) has the potential to address the technical limitations of exome sequencing in ways not possible by short-read WGS. However, its utility in autosomal recessive Mendelian diseases is largely unknown. METHODS In a cohort of 34 families in which the suspected autosomal recessive diseases remained undiagnosed by exome sequencing, lrWGS was performed on the Pacific Bioscience Sequel IIe platform. RESULTS Likely causal variants were identified in 13 (38%) of the cohort. These include (1) a homozygous splicing SV in TYMS as a novel candidate gene for lethal neonatal lactic acidosis, (2) a homozygous non-coding SV that we propose impacts STK25 expression and causes a novel neurodevelopmental disorder, (3) a compound heterozygous SV in RP1L1 with complex inheritance pattern in a family with inherited retinal disease, (4) homozygous deep intronic variants in LEMD2 and SNAP91 as novel candidate genes for neurodevelopmental disorders in two families, and (5) a promoter SNV in SLC4A4 causing non-syndromic band keratopathy. Surprisingly, we also encountered causal variants that could have been identified by short-read exome sequencing in 7 families. The latter highlight scenarios that are especially challenging at the interpretation level. CONCLUSIONS Our data highlight the continued need to address the interpretation challenges in parallel with efforts to improve the sequencing technology itself. We propose a path forward for the implementation of lrWGS sequencing in the setting of autosomal recessive diseases in a way that maximizes its utility.
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Affiliation(s)
- Lama AlAbdi
- Department of Zoology, Collage of Science, King Saud University, Riyadh, Saudi Arabia
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Hanan E Shamseldin
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Ebtissal Khouj
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Rana Helaby
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Bayan Aljamal
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Mashael Alqahtani
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Aisha Almulhim
- Department of Zoology, Collage of Science, King Saud University, Riyadh, Saudi Arabia
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Halima Hamid
- Department of Zoology, Collage of Science, King Saud University, Riyadh, Saudi Arabia
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Mais O Hashem
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Firdous Abdulwahab
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Omar Abouyousef
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Amal Jaafar
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Tarfa Alshidi
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Mohammed Al-Owain
- Department of Medical Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
- Collage of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Amal Alhashem
- Collage of Medicine, Alfaisal University, Riyadh, Saudi Arabia
- Pediatric Department, Division of Genetic and Metabolic Medicine, Prince Sultan Medical Military City, Riyadh, Saudi Arabia
| | - Saeed Al Tala
- Pediatric Department, Neonatal Unit, Armed Forces Hospital, Khamis Mushayt, Saudi Arabia
| | - Arif O Khan
- Eye Institute, Cleveland Clinic Abu Dhabi, Abu Dhabi, United Arab Emirates
- Department of Ophthalmology, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, OH, USA
| | - Elham Mardawi
- Maternal Fetal Medicine, Security Forces Hospital Program, Riyadh, Saudi Arabia
| | - Hisham Alkuraya
- Vitreoretinal Surgery and Ocular Genetics, Global Eye Care/Specialized Medical Center Hospital, Riyadh, Saudi Arabia
| | - Eissa Faqeih
- Section of Medical Genetics, King Fahad Medical City, Children's Specialist Hospital, Riyadh, Saudi Arabia
| | - Manal Afqi
- Metabolic and Genetic Center, King Salman Bin Abdulaziz Medical City, Almadinah Almunwarah, Saudi Arabia
| | - Salwa Alkhalifi
- Newborn Screening, Ministry of Health, Eastern Province, Saudi Arabia
| | - Zuhair Rahbeeni
- Department of Medical Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Samya T Hagos
- Department of Clinical Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Wijdan Al-Ahmadi
- Department of Molecular Biomedicine, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Seba Nadeef
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Sateesh Maddirevula
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Khalid S A Khabar
- Department of Molecular Biomedicine, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Alexander Putra
- King Abdullah University of Science and Technology (KAUST), Core Labs, Thuwal, Saudi Arabia
| | - Angel Angelov
- King Abdullah University of Science and Technology (KAUST), Core Labs, Thuwal, Saudi Arabia
| | - Changsook Park
- King Abdullah University of Science and Technology (KAUST), Core Labs, Thuwal, Saudi Arabia
| | - Ana M Reyes-Ramos
- King Abdullah University of Science and Technology (KAUST), Core Labs, Thuwal, Saudi Arabia
| | - Husen Umer
- King Abdullah University of Science and Technology (KAUST), Core Labs, Thuwal, Saudi Arabia
| | - Ikram Ullah
- King Abdullah University of Science and Technology (KAUST), Core Labs, Thuwal, Saudi Arabia
| | - Patrick Driguez
- King Abdullah University of Science and Technology (KAUST), Core Labs, Thuwal, Saudi Arabia
| | - Yoshinori Fukasawa
- King Abdullah University of Science and Technology (KAUST), Core Labs, Thuwal, Saudi Arabia
| | - Ming Sin Cheung
- King Abdullah University of Science and Technology (KAUST), Core Labs, Thuwal, Saudi Arabia
| | - Imed Eddine Gallouzi
- KAUST Smart-Health Initiative King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Fowzan S Alkuraya
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.
- KAUST Smart-Health Initiative King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
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