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Younsi ME, Achour A, Kraoua L, Nesrine M, Sayari T, Abderrahim E, Laabidi J, Zouaghi MK, Kharrat M, Gargah T, Trabelsi M, M'rad R. Genetic study of Alport syndrome in Tunisia. Pediatr Nephrol 2024:10.1007/s00467-024-06474-7. [PMID: 39138691 DOI: 10.1007/s00467-024-06474-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/24/2024] [Revised: 06/13/2024] [Accepted: 07/11/2024] [Indexed: 08/15/2024]
Abstract
BACKGROUND Alport syndrome is a genetic disorder affecting the kidneys, ears, and eyes, causing chronic kidney disease, sensorineural hearing loss, and ocular abnormalities. It results from pathogenic variants in the COL4A3, COL4A4, or COL4A5 genes, with different inheritance patterns: X-linked from COL4A5 variants, autosomal recessive from homozygous variants in COL4A3 or COL4A4, digenic from variants in both COL4A3 and COL4A4, and autosomal dominant from heterozygous variants in COL4A3 or COL4A4. METHODS We analyzed 45 patients with Alport syndrome from 11 Tunisian families to determine their clinical and genetic characteristics. Clinical data were collected retrospectively, and whole-exome sequencing was conducted on one patient from each family. Sanger sequencing validated pathogenic variants, and cascade screening extended the analysis to 53 individuals. RESULTS We identified nine likely pathogenic variants among 11 index cases: six novel and three known variations. Of these, five were in COL4A3, and four were in COL4A5, with variants including frameshift, nonsense, missense, and alternative splicing. Most variations affected the Gly-XY codon. Among the 45 clinically identified siblings, 30 tested positive for Alport syndrome. The cascade screening identified 3 additional affected individuals, 10 unaffected siblings, and 10 unaffected parents. The mode of inheritance was autosomal recessive in six families and X-linked in four families. CONCLUSIONS This study is the first to screen the mutational spectrum of Alport syndrome in Tunisia. It reveals novel pathogenic variants and suggests that autosomal recessive inheritance may be more common in the Tunisian population than X-linked inheritance, contrary to existing literature.
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Affiliation(s)
- Mariem El Younsi
- Laboratoire de Génétique Humaine, Faculté de Médecine de Tunis, Université de Tunis El Manar, LR99ES101007, Tunis, Tunisia
| | - Ahlem Achour
- Laboratoire de Génétique Humaine, Faculté de Médecine de Tunis, Université de Tunis El Manar, LR99ES101007, Tunis, Tunisia
- Service des Maladies Congénitales Et Héréditaires, Hôpital Charles Nicolle, 1006, Tunis, Tunisia
| | - Lilia Kraoua
- Laboratoire de Génétique Humaine, Faculté de Médecine de Tunis, Université de Tunis El Manar, LR99ES101007, Tunis, Tunisia
- Service des Maladies Congénitales Et Héréditaires, Hôpital Charles Nicolle, 1006, Tunis, Tunisia
| | - Mezzi Nesrine
- Laboratory of Biomedical Genomics and Oncogenetics, Pasteur Institute of Tunis, 1002, Tunis, Tunisia
| | - Taha Sayari
- Service de Néphrologie Pédiatrique, Hôpital Charles Nicolle, 1006, Tunis, Tunisia
| | - Ezzeddine Abderrahim
- Service de Médecine Interne Et de Néphrologie Adulte, Hôpital Charles Nicolle, 1006, Tunis, Tunisia
| | - Janet Laabidi
- Service Néphrologie, L'Hôpital Militaire Principal d'Instruction de Tunis, MontFleury, 1008, Tunis, Tunisia
| | - Mohamed Karim Zouaghi
- Service de Néphrologie, Dialyse Et Transplantation Rénale, Hôpital La Rabta 1007, Tunis, Tunisia
| | - Maher Kharrat
- Laboratoire de Génétique Humaine, Faculté de Médecine de Tunis, Université de Tunis El Manar, LR99ES101007, Tunis, Tunisia
| | - Tahar Gargah
- Service de Néphrologie Pédiatrique, Hôpital Charles Nicolle, 1006, Tunis, Tunisia
| | - Mediha Trabelsi
- Laboratoire de Génétique Humaine, Faculté de Médecine de Tunis, Université de Tunis El Manar, LR99ES101007, Tunis, Tunisia
- Service des Maladies Congénitales Et Héréditaires, Hôpital Charles Nicolle, 1006, Tunis, Tunisia
| | - Ridha M'rad
- Laboratoire de Génétique Humaine, Faculté de Médecine de Tunis, Université de Tunis El Manar, LR99ES101007, Tunis, Tunisia.
- Service des Maladies Congénitales Et Héréditaires, Hôpital Charles Nicolle, 1006, Tunis, Tunisia.
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Bish MD, Ramachandran SR, Wright A, Lincoln LM, Whitham SA, Graham MA, Pedley KF. The Soybean Rpp3 Gene Encodes a TIR-NBS-LRR Protein that Confers Resistance to Phakopsora pachyrhizi. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2024; 37:561-570. [PMID: 38569009 DOI: 10.1094/mpmi-01-24-0007-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/05/2024]
Abstract
Soybean rust is an economically significant disease caused by the fungus Phakopsora pachyrhizi that negatively impacts soybean (Glycine max [L.] Merr.) production throughout the world. Susceptible plants infected by P. pachyrhizi develop tan-colored lesions on the leaf surface that give rise to funnel-shaped uredinia as the disease progresses. While most soybean germplasm is susceptible, seven genetic loci (Rpp1 to Rpp7) that provide race-specific resistance to P. pachyrhizi (Rpp) have been identified. Rpp3 was first discovered and characterized in the soybean accession PI 462312 (Ankur), and it was also determined to be one of two Rpp genes present in PI 506764 (Hyuuga). Genetic crosses with PI 506764 were later used to fine-map the Rpp3 locus to a 371-kb region on chromosome 6. The corresponding region in the susceptible Williams 82 (Wm82) reference genome contains several homologous nucleotide binding site-leucine rich repeat (NBS-LRR) genes. To identify Rpp3, we designed oligonucleotide primers to amplify Rpp3 candidate (Rpp3C) NBS-LRR genes at this locus from PI 462312, PI 506764, and Wm82 using polymerase chain reaction (PCR). Five Rpp3C genes were identified in both Rpp3-resistant soybean lines, and co-silencing these genes compromised resistance to P. pachyrhizi. Gene expression analysis and sequence comparisons of the Rpp3C genes in PI 462312 and PI 506764 suggest that a single candidate gene, Rpp3C3, is responsible for Rpp3-mediated resistance. [Formula: see text] The author(s) have dedicated the work to the public domain under the Creative Commons CC0 "No Rights Reserved" license by waiving all of his or her rights to the work worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law, 2024.
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Affiliation(s)
- Mandy D Bish
- Foreign Disease-Weed Science Research Unit, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Fort Detrick, MD 21702, U.S.A
| | - Sowmya R Ramachandran
- Foreign Disease-Weed Science Research Unit, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Fort Detrick, MD 21702, U.S.A
- Oak Ridge Institute for Science and Education, ARS Research Participation Program, Oak Ridge, TN, U.S.A
| | - Amy Wright
- Foreign Disease-Weed Science Research Unit, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Fort Detrick, MD 21702, U.S.A
| | - Lori M Lincoln
- Corn Insects and Crop Genetics Research Unit, USDA-ARS, Ames, IA 50011, U.S.A
| | - Steven A Whitham
- Department of Plant Pathology, Entomology, and Microbiology, Iowa State University, Ames, IA 50011, U.S.A
| | - Michelle A Graham
- Corn Insects and Crop Genetics Research Unit, USDA-ARS, Ames, IA 50011, U.S.A
- Department of Agronomy, Iowa State University, Ames, IA 50011, U.S.A
| | - Kerry F Pedley
- Foreign Disease-Weed Science Research Unit, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Fort Detrick, MD 21702, U.S.A
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Yuan X, Zhang S, Shang H, Tang Y. A novel mutation in SORD gene associated with distal hereditary motor neuropathies. BMC Med Genomics 2024; 17:169. [PMID: 38915017 PMCID: PMC11194961 DOI: 10.1186/s12920-024-01940-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 06/18/2024] [Indexed: 06/26/2024] Open
Abstract
BACKGROUND Distal hereditary motor neuropathy (dHMN) is a heterogeneous group of hereditary diseases caused by the gradual degeneration of the lower motor neuron. More than 30 genes associated with dHMN have been reported, while 70-80% of those with the condition are still unable to receive a genetic diagnosis. METHODS A 26-year-old man experiencing gradual weakness in his lower limbs was referred to our hospital, and data on clinical features, laboratory tests, and electrophysiological tests were collected. To identify the disease-causing mutation, we conducted whole exome sequencing (WES) and then validated it through Sanger sequencing for the proband and his parents. Silico analysis was performed to predict the pathogenesis of the identified mutations. A literature review of all reported mutations of the related gene for the disease was performed. RESULTS The patient presented with dHMN phenotype harboring a novel homozygous variant c.361G > C (p.Ala121Pro) in SORD, inherited from his parents, respectively. A121 is a highly conserved site and the mutation was categorized as "likely pathogenic" according to the criteria and guidelines of the American College of Medical Genetics and Genomics (ACMG). A total of 13 published articles including 101 patients reported 18 SORD variants. Almost all described cases have the homozygous deletion variant c.757delG (p.A253Qfs*27) or compound heterozygous state of a combination of c.757delG (p.A253Qfs*27) with another variant. The variant c.361G > C (p.Ala121Pro) detected in our patient was the second homozygous variant in SORD-associated hereditary neuropathy. CONCLUSION One novel homozygous variant c.361G > C (p.Ala121Pro) in SORD was identified in a Chinese patient with dHMN phenotype, which expands the mutation spectrum of SORD-associated hereditary neuropathy and underscores the significance of screening for SORD variants in patients with undiagnosed hereditary neuropathy patients.
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Affiliation(s)
- Xiaoqin Yuan
- Department of Neurology, School of Medicine, Mianyang Central Hospital, University of Electronic Science and Technology of China, Mianyang, Sichuan, 621000, China
| | - Shanshan Zhang
- Department of Neurology, School of Medicine, Mianyang Central Hospital, University of Electronic Science and Technology of China, Mianyang, Sichuan, 621000, China
| | - Huifang Shang
- Department of Neurology, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China.
| | - Yufeng Tang
- Department of Neurology, School of Medicine, Mianyang Central Hospital, University of Electronic Science and Technology of China, Mianyang, Sichuan, 621000, China.
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Smith CEL, Laugel-Haushalter V, Hany U, Best S, Taylor RL, Poulter JA, Wortmann SB, Feichtinger RG, Mayr JA, Al Bahlani S, Nikolopoulos G, Rigby A, Black GC, Watson CM, Mansour S, Inglehearn CF, Mighell AJ, Bloch-Zupan A. Biallelic variants in Plexin B2 ( PLXNB2) cause amelogenesis imperfecta, hearing loss and intellectual disability. J Med Genet 2024; 61:689-698. [PMID: 38458752 PMCID: PMC11228227 DOI: 10.1136/jmg-2023-109728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 02/22/2024] [Indexed: 03/10/2024]
Abstract
BACKGROUND Plexins are large transmembrane receptors for the semaphorin family of signalling proteins. Semaphorin-plexin signalling controls cellular interactions that are critical during development as well as in adult life stages. Nine plexin genes have been identified in humans, but despite the apparent importance of plexins in development, only biallelic PLXND1 and PLXNA1 variants have so far been associated with Mendelian genetic disease. METHODS Eight individuals from six families presented with a recessively inherited variable clinical condition, with core features of amelogenesis imperfecta (AI) and sensorineural hearing loss (SNHL), with variable intellectual disability. Probands were investigated by exome or genome sequencing. Common variants and those unlikely to affect function were excluded. Variants consistent with autosomal recessive inheritance were prioritised. Variant segregation analysis was performed by Sanger sequencing. RNA expression analysis was conducted in C57Bl6 mice. RESULTS Rare biallelic pathogenic variants in plexin B2 (PLXNB2), a large transmembrane semaphorin receptor protein, were found to segregate with disease in all six families. The variants identified include missense, nonsense, splicing changes and a multiexon deletion. Plxnb2 expression was detected in differentiating ameloblasts. CONCLUSION We identify rare biallelic pathogenic variants in PLXNB2 as a cause of a new autosomal recessive, phenotypically diverse syndrome with AI and SNHL as core features. Intellectual disability, ocular disease, ear developmental abnormalities and lymphoedema were also present in multiple cases. The variable syndromic human phenotype overlaps with that seen in Plxnb2 knockout mice, and, together with the rarity of human PLXNB2 variants, may explain why pathogenic variants in PLXNB2 have not been reported previously.
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Affiliation(s)
- Claire E L Smith
- Institute of Medical Research, St James's University Hospital, University of Leeds Faculty of Medicine and Health, Leeds, UK
| | - Virginie Laugel-Haushalter
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U1258, CNRS-UMR7104, Université de Strasbourg, Strasbourg, France
| | - Ummey Hany
- Institute of Medical Research, St James's University Hospital, University of Leeds Faculty of Medicine and Health, Leeds, UK
| | - Sunayna Best
- Institute of Medical Research, St James's University Hospital, University of Leeds Faculty of Medicine and Health, Leeds, UK
- Yorkshire Regional Genetics Service, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Rachel L Taylor
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
- Division of Evolution and Genomic Sciences, Manchester Academic Health Science Centre, Faculty of Biology, Medicine and Health, School of Biological Sciences, University of Manchester, Manchester, UK
- EMQN CIC, Manchester, UK
| | - James A Poulter
- Institute of Medical Research, St James's University Hospital, University of Leeds Faculty of Medicine and Health, Leeds, UK
| | - Saskia B Wortmann
- Department of Paediatrics, University Children's Hospital, Salzburger Landesklinken (SALK) and Paracelsus Medical University, Salzburg, Austria
- Amalia Children's Hospital, Radboudumc, Nijmegen, The Netherlands
| | - Rene G Feichtinger
- Department of Paediatrics, University Children's Hospital, Salzburger Landesklinken (SALK) and Paracelsus Medical University, Salzburg, Austria
| | - Johannes A Mayr
- Department of Paediatrics, University Children's Hospital, Salzburger Landesklinken (SALK) and Paracelsus Medical University, Salzburg, Austria
| | - Suhaila Al Bahlani
- Dental & OMFS Clinic, Al Nahdha Hospital, Government of Oman Ministry of Health, Muscat, Oman
| | | | - Alice Rigby
- Institute of Medical Research, St James's University Hospital, University of Leeds Faculty of Medicine and Health, Leeds, UK
- School of Dentistry, University of Leeds Faculty of Medicine and Health, Leeds, UK
| | - Graeme C Black
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
- Division of Evolution and Genomic Sciences, Manchester Academic Health Science Centre, Faculty of Biology, Medicine and Health, School of Biological Sciences, University of Manchester, Manchester, UK
| | - Christopher M Watson
- Institute of Medical Research, St James's University Hospital, University of Leeds Faculty of Medicine and Health, Leeds, UK
- North East and Yorkshire Genomic Laboratory Hub, Central Lab, St James's University Hospital, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Sahar Mansour
- Lymphovascular Research Unit, Molecular and Clinical Sciences Research Institute, St George's Hospital, University of London, London, UK
- SW Thames Regional Centre for Genomics, St George's University Hospitals NHS Foundation Trust, London, UK
| | - Chris F Inglehearn
- Institute of Medical Research, St James's University Hospital, University of Leeds Faculty of Medicine and Health, Leeds, UK
| | - Alan J Mighell
- School of Dentistry, University of Leeds Faculty of Medicine and Health, Leeds, UK
| | - Agnès Bloch-Zupan
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U1258, CNRS-UMR7104, Université de Strasbourg, Strasbourg, France
- Faculté de Chirurgie Dentaire, Université de Strasbourg, Strasbourg, France
- Centre de référence des maladies rares orales et dentaires O-Rares, Filière Santé Maladies rares TETE COU, European Reference Network CRANIO, Pôle de Médecine et Chirurgie Bucco-dentaires, Hôpital Civil, Hôpitaux Universitaires de Strasbourg (HUS), Strasbourg, France
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Shchagina O, Murtazina A, Chausova P, Orlova M, Dadali E, Kurbatov S, Kutsev S, Polyakov A. Genetic Landscape of SH3TC2 variants in Russian patients with Charcot-Marie-Tooth disease. Front Genet 2024; 15:1381915. [PMID: 38903759 PMCID: PMC11187259 DOI: 10.3389/fgene.2024.1381915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Accepted: 05/13/2024] [Indexed: 06/22/2024] Open
Abstract
Introduction Charcot-Marie-Tooth disease type 4C (CMT4C) OMIM#601596 stands out as one of the most prevalent forms of recessive motor sensory neuropathy worldwide. This disorder results from biallelic pathogenic variants in the SH3TC2 gene. Methods Within a cohort comprising 700 unrelated Russian patients diagnosed with Charcot-Marie-Tooth disease, we conducted a gene panel analysis encompassing 21 genes associated with hereditary neuropathies. Among the cohort, 394 individuals exhibited demyelinating motor and sensory neuropathy. Results and discussion Notably, 10 cases of CMT4C were identified within this cohort. The prevalence of CMT4C among Russian demyelinating CMT patients lacking the PMP22 duplication is estimated at 2.5%, significantly differing from observations in European populations. In total, 4 novel and 9 previously reported variants in the SH3TC2 gene were identified. No accumulation of a major variant was detected. Three previously reported variants, c.2860C>T p. (Arg954*), p. (Arg658Cys) and c.279G>A p. (Lys93Lys), recurrently detected in unrelated families. Nucleotide alteration p. (Arg954*) is present in most of our patients (30%).
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Affiliation(s)
| | | | | | - Mariya Orlova
- Research Centre for Medical Genetics, Moscow, Russia
| | - Elena Dadali
- Research Centre for Medical Genetics, Moscow, Russia
| | - Sergei Kurbatov
- Research Institute of Experimental Biology and Medicine, Voronezh State Medical University named After N.N. Burdenko, Voronezh, Russia
- Saratov State Medical University, Saratov, Russia
| | - Sergey Kutsev
- Research Centre for Medical Genetics, Moscow, Russia
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Esposito S, Zollo I, Villella VR, Scialò F, Giordano S, Esposito MV, Salemme N, Di Domenico C, Cernera G, Zarrilli F, Castaldo G, Amato F. Identification of an ultra-rare Alu insertion in the CFTR gene: Pitfalls and challenges in genetic test interpretation. Clin Chim Acta 2024; 558:118317. [PMID: 38580140 DOI: 10.1016/j.cca.2024.118317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 03/28/2024] [Accepted: 04/03/2024] [Indexed: 04/07/2024]
Abstract
Cystic fibrosis (CF) is a life-limiting genetic disorder characterized by defective chloride ion transport due to mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene. Early detection through newborn screening programs significantly improves outcomes for individuals with CF by enabling timely intervention. Here, we report the identification of an Alu element insertion within the exon 15 of CFTR gene, initially overlooked in standard next-generation sequencing analyses. However, using traditional molecular techniques, based on polymerase chain reaction and Sanger sequencing, allowed the identification of the Alu element and the reporting of a correct diagnosis. Our analysis, based on bioinformatics tools and molecular techniques, revealed that the Alu element insertion severely affects the gene expression, splicing patterns, and structure of CFTR protein. In conclusion, this study emphasizes the importance of how the integration of human expertise and modern technologies represents a pivotal step forward in genomic medicine, ensuring the delivery of precision healthcare to individuals affected by genetic diseases.
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Affiliation(s)
- Speranza Esposito
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Naples, Italy; CEINGE- Advanced Biotechnologies Franco Salvatore, Naples, Italy
| | - Immacolata Zollo
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Naples, Italy; CEINGE- Advanced Biotechnologies Franco Salvatore, Naples, Italy
| | - Valeria Rachela Villella
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Naples, Italy; CEINGE- Advanced Biotechnologies Franco Salvatore, Naples, Italy
| | - Filippo Scialò
- CEINGE- Advanced Biotechnologies Franco Salvatore, Naples, Italy; Department of Translational Medical Science, University of Campania Luigi Vanvitelli, Naples, Italy
| | - Sonia Giordano
- AORN Ospedali dei Colli-Monaldi-Cotugno-CTO, Naples, Italy
| | | | - Nunzia Salemme
- San Giuseppe and Melorio Hospital, Santa Maria Capua Vetere, Caserta, Italy
| | | | - Gustavo Cernera
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Naples, Italy; CEINGE- Advanced Biotechnologies Franco Salvatore, Naples, Italy
| | - Federica Zarrilli
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Naples, Italy; CEINGE- Advanced Biotechnologies Franco Salvatore, Naples, Italy
| | - Giuseppe Castaldo
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Naples, Italy; CEINGE- Advanced Biotechnologies Franco Salvatore, Naples, Italy
| | - Felice Amato
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Naples, Italy; CEINGE- Advanced Biotechnologies Franco Salvatore, Naples, Italy.
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Mohar NP, Cox EM, Adelizzi E, Moore SA, Mathews KD, Darbro BW, Wallrath LL. The Influence of a Genetic Variant in CCDC78 on LMNA-Associated Skeletal Muscle Disease. Int J Mol Sci 2024; 25:4930. [PMID: 38732148 PMCID: PMC11084688 DOI: 10.3390/ijms25094930] [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: 03/13/2024] [Revised: 04/12/2024] [Accepted: 04/24/2024] [Indexed: 05/13/2024] Open
Abstract
Mutations in the LMNA gene-encoding A-type lamins can cause Limb-Girdle muscular dystrophy Type 1B (LGMD1B). This disease presents with weakness and wasting of the proximal skeletal muscles and has a variable age of onset and disease severity. This variability has been attributed to genetic background differences among individuals; however, such variants have not been well characterized. To identify such variants, we investigated a multigeneration family in which affected individuals are diagnosed with LGMD1B. The primary genetic cause of LGMD1B in this family is a dominant mutation that activates a cryptic splice site, leading to a five-nucleotide deletion in the mature mRNA. This results in a frame shift and a premature stop in translation. Skeletal muscle biopsies from the family members showed dystrophic features of variable severity, with the muscle fibers of some family members possessing cores, regions of sarcomeric disruption, and a paucity of mitochondria, not commonly associated with LGMD1B. Using whole genome sequencing (WGS), we identified 21 DNA sequence variants that segregate with the family members possessing more profound dystrophic features and muscle cores. These include a relatively common variant in coiled-coil domain containing protein 78 (CCDC78). This variant was given priority because another mutation in CCDC78 causes autosomal dominant centronuclear myopathy-4, which causes cores in addition to centrally positioned nuclei. Therefore, we analyzed muscle biopsies from family members and discovered that those with both the LMNA mutation and the CCDC78 variant contain muscle cores that accumulated both CCDC78 and RyR1. Muscle cores containing mislocalized CCDC78 and RyR1 were absent in the less profoundly affected family members possessing only the LMNA mutation. Taken together, our findings suggest that a relatively common variant in CCDC78 can impart profound muscle pathology in combination with a LMNA mutation and accounts for variability in skeletal muscle disease phenotypes.
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Affiliation(s)
- Nathaniel P. Mohar
- Interdisciplinary Graduate Program in Genetics, University of Iowa, Iowa City, IA 52242, USA; (N.P.M.); (E.A.)
- Department of Biochemistry and Molecular Biology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Efrem M. Cox
- Department of Pathology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA (S.A.M.)
- Department of Neurosurgery, UNLV School of Medicine, Las Vegas, NV 89106, USA
| | - Emily Adelizzi
- Interdisciplinary Graduate Program in Genetics, University of Iowa, Iowa City, IA 52242, USA; (N.P.M.); (E.A.)
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Steven A. Moore
- Department of Pathology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA (S.A.M.)
| | - Katherine D. Mathews
- Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA;
| | - Benjamin W. Darbro
- Interdisciplinary Graduate Program in Genetics, University of Iowa, Iowa City, IA 52242, USA; (N.P.M.); (E.A.)
- Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA;
| | - Lori L. Wallrath
- Interdisciplinary Graduate Program in Genetics, University of Iowa, Iowa City, IA 52242, USA; (N.P.M.); (E.A.)
- Department of Biochemistry and Molecular Biology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
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Truong DJJ, Geilenkeuser J, Wendel SV, Wilming JCH, Armbrust N, Binder EMH, Santl TH, Siebenhaar A, Gruber C, Phlairaharn T, Živanić M, Westmeyer GG. Exonuclease-enhanced prime editors. Nat Methods 2024; 21:455-464. [PMID: 38302659 PMCID: PMC10927552 DOI: 10.1038/s41592-023-02162-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 12/19/2023] [Indexed: 02/03/2024]
Abstract
Prime editing (PE) is a powerful gene-editing technique based on targeted gRNA-templated reverse transcription and integration of the de novo synthesized single-stranded DNA. To circumvent one of the main bottlenecks of the method, the competition of the reverse-transcribed 3' flap with the original 5' flap DNA, we generated an enhanced fluorescence-activated cell sorting reporter cell line to develop an exonuclease-enhanced PE strategy ('Exo-PE') composed of an improved PE complex and an aptamer-recruited DNA-exonuclease to remove the 5' original DNA flap. Exo-PE achieved better overall editing efficacy than the reference PE2 strategy for insertions ≥30 base pairs in several endogenous loci and cell lines while maintaining the high editing precision of PE2. By enabling the precise incorporation of larger insertions, Exo-PE complements the growing palette of different PE tools and spurs additional refinements of the PE machinery.
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Affiliation(s)
- Dong-Jiunn Jeffery Truong
- Institute for Synthetic Biomedicine, Helmholtz Munich, Neuherberg, Germany
- Department of Bioscience, TUM School of Natural Sciences and TUM School of Medicine,Technical University of Munich, Munich, Germany
| | - Julian Geilenkeuser
- Institute for Synthetic Biomedicine, Helmholtz Munich, Neuherberg, Germany
- Department of Bioscience, TUM School of Natural Sciences and TUM School of Medicine,Technical University of Munich, Munich, Germany
| | - Stephanie Victoria Wendel
- Institute for Synthetic Biomedicine, Helmholtz Munich, Neuherberg, Germany
- Department of Bioscience, TUM School of Natural Sciences and TUM School of Medicine,Technical University of Munich, Munich, Germany
| | - Julius Clemens Heinrich Wilming
- Institute for Synthetic Biomedicine, Helmholtz Munich, Neuherberg, Germany
- Department of Bioscience, TUM School of Natural Sciences and TUM School of Medicine,Technical University of Munich, Munich, Germany
| | - Niklas Armbrust
- Institute for Synthetic Biomedicine, Helmholtz Munich, Neuherberg, Germany
- Department of Bioscience, TUM School of Natural Sciences and TUM School of Medicine,Technical University of Munich, Munich, Germany
| | - Eva Maria Hildegard Binder
- Institute for Synthetic Biomedicine, Helmholtz Munich, Neuherberg, Germany
- Department of Bioscience, TUM School of Natural Sciences and TUM School of Medicine,Technical University of Munich, Munich, Germany
| | - Tobias Heinrich Santl
- Institute for Synthetic Biomedicine, Helmholtz Munich, Neuherberg, Germany
- Department of Bioscience, TUM School of Natural Sciences and TUM School of Medicine,Technical University of Munich, Munich, Germany
| | - Annika Siebenhaar
- Institute for Synthetic Biomedicine, Helmholtz Munich, Neuherberg, Germany
- Department of Bioscience, TUM School of Natural Sciences and TUM School of Medicine,Technical University of Munich, Munich, Germany
| | - Christoph Gruber
- Institute of Developmental Genetics, Helmholtz Munich, Neuherberg, Germany
| | - Teeradon Phlairaharn
- Institute for Synthetic Biomedicine, Helmholtz Munich, Neuherberg, Germany
- Department of Bioscience, TUM School of Natural Sciences and TUM School of Medicine,Technical University of Munich, Munich, Germany
| | - Milica Živanić
- Institute for Synthetic Biomedicine, Helmholtz Munich, Neuherberg, Germany
- Department of Bioscience, TUM School of Natural Sciences and TUM School of Medicine,Technical University of Munich, Munich, Germany
| | - Gil Gregor Westmeyer
- Institute for Synthetic Biomedicine, Helmholtz Munich, Neuherberg, Germany.
- Department of Bioscience, TUM School of Natural Sciences and TUM School of Medicine,Technical University of Munich, Munich, Germany.
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9
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Tran Van Canh L, Aubourg S. Bioinformatics Methods for Prediction of Gene Families Encoding Extracellular Peptides. Methods Mol Biol 2024; 2731:3-21. [PMID: 38019422 DOI: 10.1007/978-1-0716-3511-7_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2023]
Abstract
Genes encoding small secreted peptides are widely distributed among plant genomes but their detection and annotation remains challenging. The bioinformatics protocol described here aims to identify as exhaustively as possible secreted peptide precursors belonging to a family of interest. First, homology searches are performed at the protein and genome levels. Next, multiple sequence alignments and predictions of a secretion signal are used to define a set of homologous proteins sharing features of secreted peptide precursors. These protein sequences are then used as input of motif detection and profile-based tools to build representative matrices and profiles that are used iteratively as guides to scan again the proteome and genome until family completion.
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Affiliation(s)
- Loup Tran Van Canh
- Institut Agro, INRAE, IRHS, SFR QUASAV, Université d'Angers, Angers, France
| | - Sébastien Aubourg
- Institut Agro, INRAE, IRHS, SFR QUASAV, Université d'Angers, Angers, France
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10
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Shchagina O, Gracheva E, Chukhrova A, Bliznets E, Bychkov I, Kutsev S, Polyakov A. Functional Characterization of Two Novel Intron 4 SERPING1 Gene Splice Site Pathogenic Variants in Families with Hereditary Angioedema. Biomedicines 2023; 12:72. [PMID: 38255179 PMCID: PMC10813231 DOI: 10.3390/biomedicines12010072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 12/20/2023] [Accepted: 12/20/2023] [Indexed: 01/24/2024] Open
Abstract
Variants that affect splice sites comprise 14.3% of all pathogenic variants in the SERPING1 gene; more than half of them are located outside the canonical sites. To make a clinical decision concerning patients with such variants, it is essential to know the exact way in which the effect of the variant would be realized. The optimal approach to determine the consequences is considered to be mRNA analysis. In the current study, we present the results of functional analysis of two previously non-described variants in the SERPING1 gene (NM_000062.3) affecting intron 4: c.686-1G>A and c.685+4dup, which were detected in members of two Russian families with autosomal dominant inheritance of angioedema type 1. Analysis of the patients' mRNA (extracted from whole blood) showed that the SERPING1(NM_000062.3):c.685+4dup variant leads to the loss of the donor splice site and the activation of the cryptic site in exon 4: r.710_745del (p.Gly217_Pro228del), while the SERPING1(NM_000062.3):c.686-1G>A variant leads to the skipping of exon 5: r.746_949del (p.Asp229_Ser296del).
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Affiliation(s)
- Olga Shchagina
- Research Centre for Medical Genetics, 115522 Moscow, Russia (E.B.); (I.B.); (S.K.)
| | - Elena Gracheva
- Department of Health of Vologda Region, Budgetary Healthcare Institution, Vologda Region Regional Clinical Hospital, 160002 Vologda, Russia;
| | - Alyona Chukhrova
- Research Centre for Medical Genetics, 115522 Moscow, Russia (E.B.); (I.B.); (S.K.)
| | - Elena Bliznets
- Research Centre for Medical Genetics, 115522 Moscow, Russia (E.B.); (I.B.); (S.K.)
| | - Igor Bychkov
- Research Centre for Medical Genetics, 115522 Moscow, Russia (E.B.); (I.B.); (S.K.)
| | - Sergey Kutsev
- Research Centre for Medical Genetics, 115522 Moscow, Russia (E.B.); (I.B.); (S.K.)
| | - Aleksander Polyakov
- Research Centre for Medical Genetics, 115522 Moscow, Russia (E.B.); (I.B.); (S.K.)
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11
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Xu Z, Wang X, Meng J, Zhang L, Song B. m5U-GEPred: prediction of RNA 5-methyluridine sites based on sequence-derived and graph embedding features. Front Microbiol 2023; 14:1277099. [PMID: 37937221 PMCID: PMC10627201 DOI: 10.3389/fmicb.2023.1277099] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 10/02/2023] [Indexed: 11/09/2023] Open
Abstract
5-Methyluridine (m5U) is one of the most common post-transcriptional RNA modifications, which is involved in a variety of important biological processes and disease development. The precise identification of the m5U sites allows for a better understanding of the biological processes of RNA and contributes to the discovery of new RNA functional and therapeutic targets. Here, we present m5U-GEPred, a prediction framework, to combine sequence characteristics and graph embedding-based information for m5U identification. The graph embedding approach was introduced to extract the global information of training data that complemented the local information represented by conventional sequence features, thereby enhancing the prediction performance of m5U identification. m5U-GEPred outperformed the state-of-the-art m5U predictors built on two independent species, with an average AUROC of 0.984 and 0.985 tested on human and yeast transcriptomes, respectively. To further validate the performance of our newly proposed framework, the experimentally validated m5U sites identified from Oxford Nanopore Technology (ONT) were collected as independent testing data, and in this project, m5U-GEPred achieved reasonable prediction performance with ACC of 91.84%. We hope that m5U-GEPred should make a useful computational alternative for m5U identification.
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Affiliation(s)
- Zhongxing Xu
- Department of Public Health, School of Medicine and Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
- School of AI and Advanced Computing, Xi'an Jiaotong-Liverpool University, Suzhou, China
| | - Xuan Wang
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, China
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Jia Meng
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, China
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
- AI University Research Centre, Xi'an Jiaotong-Liverpool University, Suzhou, China
| | - Lin Zhang
- School of Information and Control Engineering, China University of Mining and Technology, Xuzhou, China
| | - Bowen Song
- Department of Public Health, School of Medicine and Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
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12
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Karimian M, Yaqubi S, Karimian Z. The eNOS-G894T genetic polymorphism and risk of preeclampsia: A case-control study, an updated meta-analysis, and a bioinformatic assay. Cytokine 2023; 169:156283. [PMID: 37356259 DOI: 10.1016/j.cyto.2023.156283] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 06/18/2023] [Indexed: 06/27/2023]
Abstract
OBJECTIVES Preeclampsia (PE) is a leading cause of maternal death worldwide and involves vascular endothelial dysfunction. The aim of this study was to investigate the association of the G894T polymorphism in the endothelial nitric oxide synthase (eNOS) gene and the risk of preeclampsia in a case-control design in an Iranian population, which was followed by a meta-analysis and an in silico approach. METHODS In the case-control study, 300 people including 135 pregnant women with preeclampsia and 165 healthy pregnant women were included. The genotype of G894T polymorphism was determined by the PCR-RFLP method. We searched authoritative scientific databases to find eligible studies for meta-analysis. The odds ratio with a 95% confidence interval was estimated to find the strength of the association of the mentioned polymorphism with the risk of preeclampsia. In addition, the effect of G894T transversion on eNOS gene function was evaluated by some bioinformatics tools. RESULTS Our case-control data showed that the G894T polymorphism is associated with an increased risk of preeclampsia. In the meta-analysis, 33 eligible studies were included, and the results showed that the G894T polymorphism is associated with an increased risk of preeclampsia in the overall analysis and some stratified analyses. In addition, the structural analysis showed that the G894T variant can affect the splicing process as well as the protein stability. CONCLUSIONS Based on the results, the aforementioned polymorphism may be a risk factor for preeclampsia and could be considered a potential molecular biomarker for screening susceptible individuals.
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Affiliation(s)
- Mohammad Karimian
- Department of Molecular and Cell Biology, Faculty of Basic Sciences, University of Mazandaran, Babolsar, Iran.
| | - Sahar Yaqubi
- Department of Molecular and Cell Biology, Faculty of Basic Sciences, University of Mazandaran, Babolsar, Iran
| | - Zahra Karimian
- Department of Midwifery, Faculty of Nursing and Midwifery, Kashan University of Medical Sciences, Kashan, Iran
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13
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Niggl E, Bouman A, Briere LC, Hoogenboezem RM, Wallaard I, Park J, Admard J, Wilke M, Harris-Mostert EDRO, Elgersma M, Bain J, Balasubramanian M, Banka S, Benke PJ, Bertrand M, Blesson AE, Clayton-Smith J, Ellingford JM, Gillentine MA, Goodloe DH, Haack TB, Jain M, Krantz I, Luu SM, McPheron M, Muss CL, Raible SE, Robin NH, Spiller M, Starling S, Sweetser DA, Thiffault I, Vetrini F, Witt D, Woods E, Zhou D, Elgersma Y, van Esbroeck ACM. HNRNPC haploinsufficiency affects alternative splicing of intellectual disability-associated genes and causes a neurodevelopmental disorder. Am J Hum Genet 2023; 110:1414-1435. [PMID: 37541189 PMCID: PMC10432175 DOI: 10.1016/j.ajhg.2023.07.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 07/04/2023] [Accepted: 07/07/2023] [Indexed: 08/06/2023] Open
Abstract
Heterogeneous nuclear ribonucleoprotein C (HNRNPC) is an essential, ubiquitously abundant protein involved in mRNA processing. Genetic variants in other members of the HNRNP family have been associated with neurodevelopmental disorders. Here, we describe 13 individuals with global developmental delay, intellectual disability, behavioral abnormalities, and subtle facial dysmorphology with heterozygous HNRNPC germline variants. Five of them bear an identical in-frame deletion of nine amino acids in the extreme C terminus. To study the effect of this recurrent variant as well as HNRNPC haploinsufficiency, we used induced pluripotent stem cells (iPSCs) and fibroblasts obtained from affected individuals. While protein localization and oligomerization were unaffected by the recurrent C-terminal deletion variant, total HNRNPC levels were decreased. Previously, reduced HNRNPC levels have been associated with changes in alternative splicing. Therefore, we performed a meta-analysis on published RNA-seq datasets of three different cell lines to identify a ubiquitous HNRNPC-dependent signature of alternative spliced exons. The identified signature was not only confirmed in fibroblasts obtained from an affected individual but also showed a significant enrichment for genes associated with intellectual disability. Hence, we assessed the effect of decreased and increased levels of HNRNPC on neuronal arborization and neuronal migration and found that either condition affects neuronal function. Taken together, our data indicate that HNRNPC haploinsufficiency affects alternative splicing of multiple intellectual disability-associated genes and that the developing brain is sensitive to aberrant levels of HNRNPC. Hence, our data strongly support the inclusion of HNRNPC to the family of HNRNP-related neurodevelopmental disorders.
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Affiliation(s)
- Eva Niggl
- Department of Clinical Genetics, Erasmus MC, 3015 GD Rotterdam, the Netherlands; ENCORE Expertise Center for Neurodevelopmental Disorders, Erasmus MC, 3015 GD Rotterdam, the Netherlands
| | - Arjan Bouman
- Department of Clinical Genetics, Erasmus MC, 3015 GD Rotterdam, the Netherlands.
| | - Lauren C Briere
- Center for Genomic Medicine and Department of Pediatrics, Massachusetts General Hospital, Boston, MA 02114, USA
| | | | - Ilse Wallaard
- Department of Clinical Genetics, Erasmus MC, 3015 GD Rotterdam, the Netherlands; ENCORE Expertise Center for Neurodevelopmental Disorders, Erasmus MC, 3015 GD Rotterdam, the Netherlands
| | - Joohyun Park
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, 72076 Tübingen, Germany
| | - Jakob Admard
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, 72076 Tübingen, Germany; NGS Competence Center Tübingen, Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Martina Wilke
- Department of Clinical Genetics, Erasmus MC, 3015 GD Rotterdam, the Netherlands
| | - Emilio D R O Harris-Mostert
- Department of Clinical Genetics, Erasmus MC, 3015 GD Rotterdam, the Netherlands; ENCORE Expertise Center for Neurodevelopmental Disorders, Erasmus MC, 3015 GD Rotterdam, the Netherlands
| | - Minetta Elgersma
- Department of Clinical Genetics, Erasmus MC, 3015 GD Rotterdam, the Netherlands; ENCORE Expertise Center for Neurodevelopmental Disorders, Erasmus MC, 3015 GD Rotterdam, the Netherlands
| | - Jennifer Bain
- Department of Neurology Division of Child Neurology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Meena Balasubramanian
- Sheffield Clinical Genetics Service, Sheffield Children's NHS Foundation Trust, S5 7AU Sheffield, UK; Department of Oncology & Metabolism, University of Sheffield, S5 7AU Sheffield, UK
| | - Siddharth Banka
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester M13 9WL, UK; Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, M13 9PL Manchester, UK
| | - Paul J Benke
- Division of Clinical Genetics, Joe DiMaggio Children's Hospital, Hollywood, FL 33021, USA
| | - Miriam Bertrand
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, 72076 Tübingen, Germany
| | - Alyssa E Blesson
- Department of Neurogenetics, Kennedy Krieger Institute, Baltimore, MD 21205, USA
| | - Jill Clayton-Smith
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester M13 9WL, UK; Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, M13 9PL Manchester, UK
| | - Jamie M Ellingford
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester M13 9WL, UK; Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, M13 9PL Manchester, UK
| | | | - Dana H Goodloe
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35233, USA
| | - Tobias B Haack
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, 72076 Tübingen, Germany; Center for Rare Diseases, University of Tübingen, 72076 Tübingen, Germany
| | - Mahim Jain
- Department of Neurogenetics, Kennedy Krieger Institute, Baltimore, MD 21205, USA
| | - Ian Krantz
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Sharon M Luu
- Waisman Center, University of Wisconsin Hospitals and Clinics, Madison, WI 53704, USA; Department of Medical and Molecular Genetics, Indiana University, Indianapolis, IN 46202, USA
| | - Molly McPheron
- Department of Medical and Molecular Genetics, Indiana University, Indianapolis, IN 46202, USA
| | - Candace L Muss
- Nemours / AI DuPont Hospital for Children, Wilmington, DE 19803, USA
| | - Sarah E Raible
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Nathaniel H Robin
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35233, USA
| | - Michael Spiller
- Sheffield Diagnostic Genetics Service, Sheffield Children's NHS Foundation Trust, Sheffield, UK
| | - Susan Starling
- Division of Clinical Genetics, Children's Mercy, Kansas City, MO 64108, USA; School of Medicine, University of Missouri- Kansas City, Kansas City, MO 64108, USA
| | - David A Sweetser
- Center for Genomic Medicine and Department of Pediatrics, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Isabelle Thiffault
- Division of Clinical Genetics, Children's Mercy, Kansas City, MO 64108, USA; Genomic Medicine Center, Children's Mercy Research Institute, Kansas City, MO 64108, USA; Department of Pathology and Laboratory Medicine, Children's Mercy Kansas City, Kansas City, MO 64108, USA
| | - Francesco Vetrini
- Department of Medical and Molecular Genetics, Indiana University, Indianapolis, IN 46202, USA; Undiagnosed Rare Disease Clinic (URDC), Indiana University, Indianapolis, IN 46202, USA
| | - Dennis Witt
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, 72076 Tübingen, Germany
| | - Emily Woods
- Sheffield Clinical Genetics Service, Sheffield Children's NHS Foundation Trust, S5 7AU Sheffield, UK
| | - Dihong Zhou
- Division of Clinical Genetics, Children's Mercy, Kansas City, MO 64108, USA; School of Medicine, University of Missouri- Kansas City, Kansas City, MO 64108, USA
| | - Ype Elgersma
- Department of Clinical Genetics, Erasmus MC, 3015 GD Rotterdam, the Netherlands; ENCORE Expertise Center for Neurodevelopmental Disorders, Erasmus MC, 3015 GD Rotterdam, the Netherlands.
| | - Annelot C M van Esbroeck
- Department of Clinical Genetics, Erasmus MC, 3015 GD Rotterdam, the Netherlands; ENCORE Expertise Center for Neurodevelopmental Disorders, Erasmus MC, 3015 GD Rotterdam, the Netherlands
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14
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Saadi SM, Cali E, Khalid LB, Yousaf H, Zafar G, Khan HN, Sher M, Vona B, Abdullah U, Malik NA, Klar J, Efthymiou S, Dahl N, Houlden H, Toft M, Baig SM, Fatima A, Iqbal Z. Genetic Investigation of Consanguineous Pakistani Families Segregating Rare Spinocerebellar Disorders. Genes (Basel) 2023; 14:1404. [PMID: 37510308 PMCID: PMC10379343 DOI: 10.3390/genes14071404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 06/30/2023] [Accepted: 07/03/2023] [Indexed: 07/30/2023] Open
Abstract
Spinocerebellar disorders are a vast group of rare neurogenetic conditions, generally characterized by overlapping clinical symptoms including progressive cerebellar ataxia, spastic paraparesis, cognitive deficiencies, skeletal/muscular and ocular abnormalities. The objective of the present study is to identify the underlying genetic causes of the rare spinocerebellar disorders in the Pakistani population. Herein, nine consanguineous families presenting different spinocerebellar phenotypes have been investigated using whole exome sequencing. Sanger sequencing was performed for segregation analysis in all the available individuals of each family. The molecular analysis of these families identified six novel pathogenic/likely pathogenic variants; ZFYVE26: c.1093del, SACS: c.1201C>T, BICD2: c.2156A>T, ALS2: c.2171-3T>G, ALS2: c.3145T>A, and B4GALNT1: c.334_335dup, and three already reported pathogenic variants; FA2H: c.159_176del, APTX: c.689T>G, and SETX: c.5308_5311del. The clinical features of all patients in each family are concurrent with the already reported cases. Hence, the current study expands the mutation spectrum of rare spinocerebellar disorders and implies the usefulness of next-generation sequencing in combination with clinical investigation for better diagnosis of these overlapping phenotypes.
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Affiliation(s)
- Saadia Maryam Saadi
- Human Molecular Genetics Laboratory, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College (NIBGE-C), Pakistan Institute of Engineering and Applied Sciences (PIEAS), Islamabad 44000, Pakistan
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Elisa Cali
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Lubaba Bintee Khalid
- Department of Biological and Biomedical Sciences, Aga Khan University, Karachi 74000, Pakistan
| | - Hammad Yousaf
- Human Molecular Genetics Laboratory, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College (NIBGE-C), Pakistan Institute of Engineering and Applied Sciences (PIEAS), Islamabad 44000, Pakistan
| | - Ghazala Zafar
- Department of Biological and Biomedical Sciences, Aga Khan University, Karachi 74000, Pakistan
| | - Haq Nawaz Khan
- Department of Biological and Biomedical Sciences, Aga Khan University, Karachi 74000, Pakistan
| | - Muhammad Sher
- Department of Allied Health Sciences, Iqra National University Swat Campus, Swat 19200, Pakistan
| | - Barbara Vona
- Institute of Human Genetics, University Medical Center Göttingen, 37073 Göttingen, Germany
- Institute for Auditory Neuroscience and InnerEarLab, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Uzma Abdullah
- University Institute of Biochemistry and Biotechnology (UIBB), Pir Mehr Ali Shah Arid Agriculture University Rawalpindi (PMAS-AAUR), Rawalpindi 46300, Pakistan
| | - Naveed Altaf Malik
- Human Molecular Genetics Laboratory, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College (NIBGE-C), Pakistan Institute of Engineering and Applied Sciences (PIEAS), Islamabad 44000, Pakistan
| | - Joakim Klar
- Department of Immunology, Genetics and Pathology, Uppsala University and Science for Life Laboratory, P.O. Box 815, 751 08 Uppsala, Sweden
| | - Stephanie Efthymiou
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Niklas Dahl
- Department of Immunology, Genetics and Pathology, Uppsala University and Science for Life Laboratory, P.O. Box 815, 751 08 Uppsala, Sweden
| | - Henry Houlden
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Mathias Toft
- Institute of Clinical Medicine, University of Oslo, P.O. Box 1171, N-0318 Oslo, Norway
- Department of Neurology, Oslo University Hospital, P.O. Box 4950 Nydalen, N-0424 Oslo, Norway
| | - Shahid Mahmood Baig
- Human Molecular Genetics Laboratory, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College (NIBGE-C), Pakistan Institute of Engineering and Applied Sciences (PIEAS), Islamabad 44000, Pakistan
- Department of Biological and Biomedical Sciences, Aga Khan University, Karachi 74000, Pakistan
| | - Ambrin Fatima
- Department of Biological and Biomedical Sciences, Aga Khan University, Karachi 74000, Pakistan
| | - Zafar Iqbal
- Department of Neurology, Oslo University Hospital, P.O. Box 4950 Nydalen, N-0424 Oslo, Norway
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15
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Fabo T, Khavari P. Functional characterization of human genomic variation linked to polygenic diseases. Trends Genet 2023; 39:462-490. [PMID: 36997428 PMCID: PMC11025698 DOI: 10.1016/j.tig.2023.02.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 02/22/2023] [Accepted: 02/23/2023] [Indexed: 03/30/2023]
Abstract
The burden of human disease lies predominantly in polygenic diseases. Since the early 2000s, genome-wide association studies (GWAS) have identified genetic variants and loci associated with complex traits. These have ranged from variants in coding sequences to mutations in regulatory regions, such as promoters and enhancers, as well as mutations affecting mediators of mRNA stability and other downstream regulators, such as 5' and 3'-untranslated regions (UTRs), long noncoding RNA (lncRNA), and miRNA. Recent research advances in genetics have utilized a combination of computational techniques, high-throughput in vitro and in vivo screening modalities, and precise genome editing to impute the function of diverse classes of genetic variants identified through GWAS. In this review, we highlight the vastness of genomic variants associated with polygenic disease risk and address recent advances in how genetic tools can be used to functionally characterize them.
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Affiliation(s)
- Tania Fabo
- Program in Epithelial Biology, Stanford University, Stanford, CA, USA; Stanford Cancer Institute, Stanford University, Stanford, CA, USA; Graduate Program in Genetics, Stanford University, Stanford, CA, USA; Stanford University School of Medicine, Stanford University, Stanford, CA, USA
| | - Paul Khavari
- Program in Epithelial Biology, Stanford University, Stanford, CA, USA; Stanford Cancer Institute, Stanford University, Stanford, CA, USA; Graduate Program in Genetics, Stanford University, Stanford, CA, USA; Stanford University School of Medicine, Stanford University, Stanford, CA, USA; Veterans Affairs Palo Alto Healthcare System, Palo Alto, CA, USA.
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16
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Lin BC, Katneni U, Jankowska KI, Meyer D, Kimchi-Sarfaty C. In silico methods for predicting functional synonymous variants. Genome Biol 2023; 24:126. [PMID: 37217943 PMCID: PMC10204308 DOI: 10.1186/s13059-023-02966-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 05/10/2023] [Indexed: 05/24/2023] Open
Abstract
Single nucleotide variants (SNVs) contribute to human genomic diversity. Synonymous SNVs are previously considered to be "silent," but mounting evidence has revealed that these variants can cause RNA and protein changes and are implicated in over 85 human diseases and cancers. Recent improvements in computational platforms have led to the development of numerous machine-learning tools, which can be used to advance synonymous SNV research. In this review, we discuss tools that should be used to investigate synonymous variants. We provide supportive examples from seminal studies that demonstrate how these tools have driven new discoveries of functional synonymous SNVs.
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Affiliation(s)
- Brian C Lin
- Hemostasis Branch 1, Division of Hemostasis, Office of Plasma Protein Therapeutics CMC, Office of Therapeutic Products, Center for Biologics Evaluation and Research, US FDA, Silver Spring, MD, USA
| | - Upendra Katneni
- Hemostasis Branch 1, Division of Hemostasis, Office of Plasma Protein Therapeutics CMC, Office of Therapeutic Products, Center for Biologics Evaluation and Research, US FDA, Silver Spring, MD, USA
| | - Katarzyna I Jankowska
- Hemostasis Branch 1, Division of Hemostasis, Office of Plasma Protein Therapeutics CMC, Office of Therapeutic Products, Center for Biologics Evaluation and Research, US FDA, Silver Spring, MD, USA
| | - Douglas Meyer
- Hemostasis Branch 1, Division of Hemostasis, Office of Plasma Protein Therapeutics CMC, Office of Therapeutic Products, Center for Biologics Evaluation and Research, US FDA, Silver Spring, MD, USA
| | - Chava Kimchi-Sarfaty
- Hemostasis Branch 1, Division of Hemostasis, Office of Plasma Protein Therapeutics CMC, Office of Therapeutic Products, Center for Biologics Evaluation and Research, US FDA, Silver Spring, MD, USA.
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17
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Burmeister T, Bullinger L, le Coutre P. The Recurrent Atypical e8a2 BCR::ABL1 Transcript with Insertion of an Inverted 55 Base Pair ABL1 Intron 1b Sequence: A Detailed Molecular Analysis. Acta Haematol 2023; 146:413-418. [PMID: 37231781 DOI: 10.1159/000531128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 05/15/2023] [Indexed: 05/27/2023]
Abstract
Atypical BCR::ABL1 transcripts are found in approximately 2% of cases of chronic myeloid leukemia. It is important to detect them since affected patients also benefit from tyrosine kinase inhibitor therapy. In the rare e8a2 atypical BCR::ABL1 transcript, two out-of-frame exons are fused, thus, interposed nucleotides are usually found at the fusion site to restore the reading frame. In approximately half of previously reported e8a2 BCR::ABL1 cases, an inserted 55 bp sequence homologous to an inverted sequence from ABL1 intron 1b was detected. The generation of this recurrent transcript variant is not obvious. This work describes the molecular analysis of such an e8a2 BCR::ABL1 translocation from a CML patient. The genomic chromosomal breakpoint is identified, and the formation of this transcript is theoretically explained. The clinical course of the patient is reported, and recommendations are provided for the molecular analysis of future e8a2 BCR::ABL1 cases.
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MESH Headings
- Humans
- Fusion Proteins, bcr-abl/genetics
- Introns
- Base Pairing
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/diagnosis
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/drug therapy
- Sequence Inversion
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Affiliation(s)
- Thomas Burmeister
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Campus Virchow, Medizinische Klinik für Hämatologie, Onkologie und Tumorimmunologie, Berlin, Germany
- Labor Berlin Charité - Vivantes, Berlin, Germany
| | - Lars Bullinger
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Campus Virchow, Medizinische Klinik für Hämatologie, Onkologie und Tumorimmunologie, Berlin, Germany
| | - Philipp le Coutre
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Campus Mitte, Medizinische Klinik für Hämatologie, Onkologie und Tumorimmunologie, Berlin, Germany
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18
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Novotná Floriančičová K, Baltzis A, Smejkal J, Czerneková M, Kaczmarek Ł, Malý J, Notredame C, Vinopal S. Phylogenetic and functional characterization of water bears (Tardigrada) tubulins. Sci Rep 2023; 13:5194. [PMID: 36997657 PMCID: PMC10063605 DOI: 10.1038/s41598-023-31992-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 03/21/2023] [Indexed: 04/01/2023] Open
Abstract
Tardigrades are microscopic ecdysozoans that can withstand extreme environmental conditions. Several tardigrade species undergo reversible morphological transformations and enter into cryptobiosis, which helps them to survive periods of unfavorable environmental conditions. However, the underlying molecular mechanisms of cryptobiosis are mostly unknown. Tubulins are evolutionarily conserved components of the microtubule cytoskeleton that are crucial in many cellular processes. We hypothesize that microtubules are necessary for the morphological changes associated with successful cryptobiosis. The molecular composition of the microtubule cytoskeleton in tardigrades is unknown. Therefore, we analyzed and characterized tardigrade tubulins and identified 79 tardigrade tubulin sequences in eight taxa. We found three α-, seven β-, one γ-, and one ε-tubulin isoform. To verify in silico identified tardigrade tubulins, we also isolated and sequenced nine out of ten predicted Hypsibius exemplaris tubulins. All tardigrade tubulins were localized as expected when overexpressed in mammalian cultured cells: to the microtubules or to the centrosomes. The presence of a functional ε-tubulin, clearly localized to centrioles, is attractive from a phylogenetic point of view. Although the phylogenetically close Nematoda lost their δ- and ε-tubulins, some groups of Arthropoda still possess them. Thus, our data support the current placement of tardigrades into the Panarthropoda clade.
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Affiliation(s)
- Kamila Novotná Floriančičová
- Department of Biology, Faculty of Science, J. E. Purkyně University (UJEP), Usti Nad Labem, Czech Republic
- Centre for Nanotechnology and Biotechnology, Faculty of Science, UJEP, Usti Nad Labem, Czech Republic
| | | | - Jiří Smejkal
- Centre for Nanotechnology and Biotechnology, Faculty of Science, UJEP, Usti Nad Labem, Czech Republic
| | - Michaela Czerneková
- Department of Biology, Faculty of Science, J. E. Purkyně University (UJEP), Usti Nad Labem, Czech Republic
| | - Łukasz Kaczmarek
- Department of Animal Taxonomy and Ecology, Adam Mickiewicz University in Poznań, Poznań, Poland
| | - Jan Malý
- Centre for Nanotechnology and Biotechnology, Faculty of Science, UJEP, Usti Nad Labem, Czech Republic
| | - Cedric Notredame
- Centre for Genomic Regulation, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Stanislav Vinopal
- Department of Biology, Faculty of Science, J. E. Purkyně University (UJEP), Usti Nad Labem, Czech Republic.
- Centre for Nanotechnology and Biotechnology, Faculty of Science, UJEP, Usti Nad Labem, Czech Republic.
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19
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Sánchez C, Doménech A, Gomez-Lucia E, Méndez JL, Ortiz JC, Benítez L. A Novel Dependoparvovirus Identified in Cloacal Swabs of Monk Parakeet (Myiopsitta monachus) from Urban Areas of Spain. Viruses 2023; 15:v15040850. [PMID: 37112831 PMCID: PMC10145644 DOI: 10.3390/v15040850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 03/19/2023] [Accepted: 03/25/2023] [Indexed: 03/29/2023] Open
Abstract
The introduction of invasive birds into new ecosystems frequently has negative consequences for the resident populations. Accordingly, the increasing population of monk parakeets (Myiopsitta monachus) in Europe may pose a threat because we have little knowledge of the viruses they can transmit to native naïve species. In this study, we describe a new dependoparvovirus detected by metagenomic analysis of cloacal samples from 28 apparently healthy individuals captured in urban areas of Madrid, Spain. The genomic characterization revealed that the genome encoded the NS and VP proteins typical of parvoviruses and was flanked by inverted terminal repeats. No recombination signal was detected. The phylogenetic analysis showed that it was closely related to a parvovirus isolated in a wild psittacid in China. Both viruses share 80% Rep protein sequence identity and only 64% with other dependoparvoviruses identified in Passeriformes, Anseriformes, and Piciformes and are included in a highly supported clade, which could be considered a new species. The prevalence was very low, and none of the additional 73 individuals tested positive by PCR. These results highlight the importance of exploring the viral genome in invasive species to prevent the emergence of novel viral pathogenic species.
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20
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Liu H, Micic N, Miller S, Crocoll C, Bjarnholt N. Species-specific dynamics of specialized metabolism in germinating sorghum grain revealed by temporal and tissue-resolved transcriptomics and metabolomics. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 196:807-820. [PMID: 36863218 DOI: 10.1016/j.plaphy.2023.02.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 02/12/2023] [Accepted: 02/14/2023] [Indexed: 06/19/2023]
Abstract
Seed germination is crucial for plant productivity, and the biochemical changes during germination affect seedling survival, plant health and yield. While the general metabolism of germination is extensively studied, the role of specialized metabolism is less investigated. We therefore analyzed the metabolism of the defense compound dhurrin during sorghum (Sorghum bicolor) grain germination and early seedling development. Dhurrin is a cyanogenic glucoside, which is catabolized into different bioactive compounds at other stages of plant development, but its fate and role during germination is unknown. We dissected sorghum grain into three different tissues and investigated dhurrin biosynthesis and catabolism at the transcriptomic, metabolomic and biochemical level. We further analyzed transcriptional signature differences of cyanogenic glucoside metabolism between sorghum and barley (Hordeum vulgare), which produces similar specialized metabolites. We found that dhurrin is de novo biosynthesized and catabolized in the growing embryonic axis as well as the scutellum and aleurone layer, two tissues otherwise mainly acknowledged for their involvement in release and transport of general metabolites from the endosperm to the embryonic axis. In contrast, genes encoding cyanogenic glucoside biosynthesis in barley are exclusively expressed in the embryonic axis. Glutathione transferase enzymes (GSTs) are involved in dhurrin catabolism and the tissue-resolved analysis of GST expression identified new pathway candidate genes and conserved GSTs as potentially important in cereal germination. Our study demonstrates a highly dynamic tissue- and species-specific specialized metabolism during cereal grain germination, highlighting the importance of tissue-resolved analyses and identification of specific roles of specialized metabolites in fundamental plant processes.
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Affiliation(s)
- Huijun Liu
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, 1871, Denmark; Copenhagen Plant Science Center, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, 1871, Denmark.
| | - Nikola Micic
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, 1871, Denmark; Copenhagen Plant Science Center, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, 1871, Denmark.
| | - Sara Miller
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, 1871, Denmark; Copenhagen Plant Science Center, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, 1871, Denmark.
| | - Christoph Crocoll
- DynaMo Center, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, 1871, Denmark.
| | - Nanna Bjarnholt
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, 1871, Denmark; Copenhagen Plant Science Center, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, 1871, Denmark.
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21
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Cvrčková F, Bezvoda R. Gaining Insight into Large Gene Families with the Aid of Bioinformatic Tools. Methods Mol Biol 2023; 2604:173-191. [PMID: 36773233 DOI: 10.1007/978-1-0716-2867-6_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
Proteins participating in plant cell morphogenesis are often encoded by large gene families, in some cases comprising paralogs with variable (modular) domain organization, as in the case of the formin (FH2 protein) family of actin nucleators that can have also additional functions. Unravelling the phylogeny of such a complex gene family brings a number of specific challenges but may be crucial for predictions of protein function and for experimental design. Here we present an overview of our "cottage industry" semi-manual bioinformatic approach, based mostly, though not exclusively, on freely available software tools, which we used to obtain insight into the evolutionary history of plant FH2 proteins and some other components of the plant cell morphogenesis apparatus.
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Affiliation(s)
- Fatima Cvrčková
- Department of Experimental Plant Biology, Faculty of Science, Charles University, CZ, Prague, Czechia.
| | - Radek Bezvoda
- Department of Experimental Plant Biology, Faculty of Science, Charles University, CZ, Prague, Czechia
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22
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Sun R, Wang Z, Zhao J, Ren P, Ma J, Guo Y. Optimized Detection of Unknown MET Exon 14 Skipping Mutations in Routine Testing for Patients With Non-Small-Cell Lung Cancer. JCO Precis Oncol 2023; 7:e2200482. [PMID: 36848606 DOI: 10.1200/po.22.00482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023] Open
Abstract
PURPOSE MET exon 14 (METex14) skipping is an actionable biomarker in non-small-cell lung cancer. However, MET variants are highly complex and diverse, and not all variants lead to exon 14 skipping. Assessing the skipping effect of unknown variants is still a key issue in molecular diagnosis. MATERIALS AND METHODS We retrospectively collected MET variants around exon 14 from 4,233 patients with non-small-cell lung cancer who underwent next-generation sequencing testing using DNA, as well as two published data sets. RESULTS Among the 4,233 patients, 44 unique variants including 29 novel variants (65.9%) were discovered from 53 patients. Notably, 31 samples (58.5%) failed RNA verification. Using RNA verification, nine novel skipping variants and five nonskipping variants were confirmed. We further used SpliceAI with the delta score cutoff of 0.315 to aid the classification of novel variants (sensitivity = 98.88% and specificity = 100%). When applied to the reported variants, we also found three wrongly classified nonskipping variants. Finally, an optimized knowledge-based interpretation procedure for clinical routine was built according to the mutation type and location, and five more skipping mutations from the 13 unknown variants were determined, which improved the population determination rate to 0.92%. CONCLUSION This study discovered more METex14 skipping variants and optimized an innovative approach that could be adapted for the interpretation of infrequent or novel METex14 variants timely without experimental validation.
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Affiliation(s)
- Rui Sun
- Department of Molecular Pathology, the Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou, Henan Province, China.,Henan Key Laboratory of Molecular Pathology, Zhengzhou, Henan Province, China
| | - Zhizhong Wang
- Department of Molecular Pathology, the Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou, Henan Province, China.,Henan Key Laboratory of Molecular Pathology, Zhengzhou, Henan Province, China
| | - Jiuzhou Zhao
- Department of Molecular Pathology, the Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou, Henan Province, China.,Henan Key Laboratory of Molecular Pathology, Zhengzhou, Henan Province, China
| | - Pengfei Ren
- Department of Molecular Pathology, the Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou, Henan Province, China
| | - Jie Ma
- Department of Molecular Pathology, the Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou, Henan Province, China
| | - Yongjun Guo
- Department of Molecular Pathology, the Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou, Henan Province, China.,Henan Key Laboratory of Molecular Pathology, Zhengzhou, Henan Province, China
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23
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Zhong V, Archibald BN, Brophy JAN. Transcriptional and post-transcriptional controls for tuning gene expression in plants. CURRENT OPINION IN PLANT BIOLOGY 2023; 71:102315. [PMID: 36462457 DOI: 10.1016/j.pbi.2022.102315] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 10/22/2022] [Accepted: 10/27/2022] [Indexed: 06/17/2023]
Abstract
Plant biotechnologists seek to modify plants through genetic reprogramming, but our ability to precisely control gene expression in plants is still limited. Here, we review transcription and translation in the model plants Arabidopsis thaliana and Nicotiana benthamiana with an eye toward control points that may be used to predictably modify gene expression. We highlight differences in gene expression requirements between these plants and other species, and discuss the ways in which our understanding of gene expression has been used to engineer plants. This review is intended to serve as a resource for plant scientists looking to achieve precise control over gene expression.
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Affiliation(s)
- Vivian Zhong
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Bella N Archibald
- Department of Bioengineering, Stanford University, Stanford, CA, USA
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24
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Dong Z, Wang Y, Zhang J, Zhu F, Liu Z, Kang Y, Lin M, Shi H. Analyzing the effects of BRCA1/2 variants on mRNA splicing by minigene assay. J Hum Genet 2023; 68:65-71. [PMID: 36446827 DOI: 10.1038/s10038-022-01077-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 08/15/2022] [Accepted: 08/23/2022] [Indexed: 11/30/2022]
Abstract
As BRCA1/2 gene sequencing become more extensive, a large number VUS (variants of uncertain significance) emerge rapidly. Verifying the splicing effect is an effective means for VUS reclassification. The Minigene Assay platform was established and its reliability was verified in this article. 47 BRCA1 or BRCA2 variants were selected and performed to validate their effect on mRNA splicing. The results showed that, a total of 16 variants were experimentally proved to have effects on mRNA splicing, among which 14 variants were shown to cause truncated proteins by Sanger sequencing. While the other two variants, BRCA2 c.7976 + 3 A > G and BRCA1 c.5152 + 3_5152 + 4insT was analyzed to cause 57 bp and 26 bp base in-frame deletion, respectively. The remaining 31 variants were not shown to cause mRNA splicing abnormity, including several sites at the edge of exons, which were predicted to affect splicing of mRNA by multiple bioinformatic software. Based on our experimental results, 37 variants were reclassified by ACMG rules. Our study showed that experimental splicing analysis was effectual for variants classification, and multiple functional assay or clinical data were also necessary for comprehensive judgment of variants.
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Affiliation(s)
- Zhouhuan Dong
- The First Medical Center, Chinese PLA General Hospital & PLA Medical School, Beijing, 100853, PR China
| | - Yun Wang
- The First Medical Center, Chinese PLA General Hospital & PLA Medical School, Beijing, 100853, PR China
| | - Jing Zhang
- The First Medical Center, Chinese PLA General Hospital & PLA Medical School, Beijing, 100853, PR China
| | - Fengwei Zhu
- The First Medical Center, Chinese PLA General Hospital & PLA Medical School, Beijing, 100853, PR China
| | - Zhiyuan Liu
- Amoy Diagnostics Co., Ltd., Xiamen, 361027, PR China
| | - Yajun Kang
- Amoy Diagnostics Co., Ltd., Xiamen, 361027, PR China
| | - Mingyuan Lin
- Amoy Diagnostics Co., Ltd., Xiamen, 361027, PR China
| | - Huaiyin Shi
- The First Medical Center, Chinese PLA General Hospital & PLA Medical School, Beijing, 100853, PR China.
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25
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Garcia-Pelaez J, Barbosa-Matos R, Lobo S, Dias A, Garrido L, Castedo S, Sousa S, Pinheiro H, Sousa L, Monteiro R, Maqueda JJ, Fernandes S, Carneiro F, Pinto N, Lemos C, Pinto C, Teixeira MR, Aretz S, Bajalica-Lagercrantz S, Balmaña J, Blatnik A, Benusiglio PR, Blanluet M, Bours V, Brems H, Brunet J, Calistri D, Capellá G, Carrera S, Colas C, Dahan K, de Putter R, Desseignés C, Domínguez-Garrido E, Egas C, Evans DG, Feret D, Fewings E, Fitzgerald RC, Coulet F, Garcia-Barcina M, Genuardi M, Golmard L, Hackmann K, Hanson H, Holinski-Feder E, Hüneburg R, Krajc M, Lagerstedt-Robinson K, Lázaro C, Ligtenberg MJL, Martínez-Bouzas C, Merino S, Michils G, Novaković S, Patiño-García A, Ranzani GN, Schröck E, Silva I, Silveira C, Soto JL, Spier I, Steinke-Lange V, Tedaldi G, Tejada MI, Woodward ER, Tischkowitz M, Hoogerbrugge N, Oliveira C. Genotype-first approach to identify associations between CDH1 germline variants and cancer phenotypes: a multicentre study by the European Reference Network on Genetic Tumour Risk Syndromes. Lancet Oncol 2023; 24:91-106. [PMID: 36436516 PMCID: PMC9810541 DOI: 10.1016/s1470-2045(22)00643-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Revised: 10/11/2022] [Accepted: 10/12/2022] [Indexed: 11/27/2022]
Abstract
BACKGROUND Truncating pathogenic or likely pathogenic variants of CDH1 cause hereditary diffuse gastric cancer (HDGC), a tumour risk syndrome that predisposes carrier individuals to diffuse gastric and lobular breast cancer. Rare CDH1 missense variants are often classified as variants of unknown significance. We conducted a genotype-phenotype analysis in families carrying rare CDH1 variants, comparing cancer spectrum in carriers of pathogenic or likely pathogenic variants (PV/LPV; analysed jointly) or missense variants of unknown significance, assessing the frequency of families with lobular breast cancer among PV/LPV carrier families, and testing the performance of lobular breast cancer-expanded criteria for CDH1 testing. METHODS This genotype-first study used retrospective diagnostic and clinical data from 854 carriers of 398 rare CDH1 variants and 1021 relatives, irrespective of HDGC clinical criteria, from 29 institutions in ten member-countries of the European Reference Network on Tumour Risk Syndromes (ERN GENTURIS). Data were collected from Oct 1, 2018, to Sept 20, 2022. Variants were classified by molecular type and clinical actionability with the American College of Medical Genetics and Association for Molecular Pathology CDH1 guidelines (version 2). Families were categorised by whether they fulfilled the 2015 and 2020 HDGC clinical criteria. Genotype-phenotype associations were analysed by Student's t test, Kruskal-Wallis, χ2, and multivariable logistic regression models. Performance of HDGC clinical criteria sets were assessed with an equivalence test and Youden index, and the areas under the receiver operating characteristic curves were compared by Z test. FINDINGS From 1971 phenotypes (contributed by 854 probands and 1021 relatives aged 1-93 years), 460 had gastric and breast cancer histology available. CDH1 truncating PV/LPVs occurred in 176 (21%) of 854 families and missense variants of unknown significance in 169 (20%) families. Multivariable logistic regression comparing phenotypes occurring in families carrying PV/LPVs or missense variants of unknown significance showed that lobular breast cancer had the greatest positive association with the presence of PV/LPVs (odds ratio 12·39 [95% CI 2·66-57·74], p=0·0014), followed by diffuse gastric cancer (8·00 [2·18-29·39], p=0·0017) and gastric cancer (7·81 [2·03-29·96], p=0·0027). 136 (77%) of 176 families carrying PV/LPVs fulfilled the 2015 HDGC criteria. Of the remaining 40 (23%) families, who did not fulfil the 2015 criteria, 11 fulfilled the 2020 HDGC criteria, and 18 had lobular breast cancer only or lobular breast cancer and gastric cancer, but did not meet the 2020 criteria. No specific CDH1 variant was found to predispose individuals specifically to lobular breast cancer, although 12 (7%) of 176 PV/LPV carrier families had lobular breast cancer only. Addition of three new lobular breast cancer-centred criteria improved testing sensitivity while retaining high specificity. The probability of finding CDH1 PV/LPVs in patients fulfilling the lobular breast cancer-expanded criteria, compared with the 2020 criteria, increased significantly (AUC 0·92 vs 0·88; Z score 3·54; p=0·0004). INTERPRETATION CDH1 PV/LPVs were positively associated with HDGC-related phenotypes (lobular breast cancer, diffuse gastric cancer, and gastric cancer), and no evidence for a positive association with these phenotypes was found for CDH1 missense variants of unknown significance. CDH1 PV/LPVs occurred often in families with lobular breast cancer who did not fulfil the 2020 HDGC criteria, supporting the expansion of lobular breast cancer-centred criteria. FUNDING European Reference Network on Genetic Tumour Risk Syndromes, European Regional Development Fund, Fundação para a Ciência e a Tecnologia (Portugal), Cancer Research UK, and European Union's Horizon 2020 research and innovation programme.
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Affiliation(s)
- José Garcia-Pelaez
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal,Faculty of Medicine, University of Porto, Porto, Portugal,Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal,Porto Comprehensive Cancer Center Raquel Seruca, Porto, Portugal
| | - Rita Barbosa-Matos
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal,Institute of Biomedical Sciences Abel Salazar, University of Porto, Porto, Portugal,Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal,Porto Comprehensive Cancer Center Raquel Seruca, Porto, Portugal
| | - Silvana Lobo
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal,Institute of Biomedical Sciences Abel Salazar, University of Porto, Porto, Portugal,Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal,Porto Comprehensive Cancer Center Raquel Seruca, Porto, Portugal
| | - Alexandre Dias
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal,Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal,Porto Comprehensive Cancer Center Raquel Seruca, Porto, Portugal
| | - Luzia Garrido
- Centro Hospitalar Universitário São João, Porto, Portugal
| | - Sérgio Castedo
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal,Faculty of Medicine, University of Porto, Porto, Portugal,Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal,Centro Hospitalar Universitário São João, Porto, Portugal,Porto Comprehensive Cancer Center Raquel Seruca, Porto, Portugal,European Reference Network on Genetic Tumour Risk Syndromes (ERN GENTURIS), Porto, Portugal
| | - Sónia Sousa
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal,Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal,Porto Comprehensive Cancer Center Raquel Seruca, Porto, Portugal
| | - Hugo Pinheiro
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal,Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal,Serviço de Medicina Interna, Centro Hospitalar Tâmega e Sousa, Penafiel, Portugal,Porto Comprehensive Cancer Center Raquel Seruca, Porto, Portugal
| | - Liliana Sousa
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal,Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal,Escola de Economia e Gestão, Universidade do Minho, Braga, Portugal,Porto Comprehensive Cancer Center Raquel Seruca, Porto, Portugal
| | - Rita Monteiro
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal,Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal
| | - Joaquin J Maqueda
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal,Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal,Bioinf2Bio, Porto, Portugal
| | - Susana Fernandes
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal
| | - Fátima Carneiro
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal,Faculty of Medicine, University of Porto, Porto, Portugal,Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal,Centro Hospitalar Universitário São João, Porto, Portugal,Porto Comprehensive Cancer Center Raquel Seruca, Porto, Portugal,European Reference Network on Genetic Tumour Risk Syndromes (ERN GENTURIS), Porto, Portugal
| | - Nádia Pinto
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal,Center of Mathematics, University of Porto, Porto, Portugal,Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal,Porto Comprehensive Cancer Center Raquel Seruca, Porto, Portugal
| | - Carolina Lemos
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal,Institute of Biomedical Sciences Abel Salazar, University of Porto, Porto, Portugal,Institute for Molecular and Cell Biology, University of Porto, Porto, Portugal,Porto Comprehensive Cancer Center Raquel Seruca, Porto, Portugal
| | - Carla Pinto
- Department of Laboratory Genetics, Portuguese Oncology Institute of Porto, Porto, Portugal,Porto Comprehensive Cancer Center Raquel Seruca, Porto, Portugal
| | - Manuel R Teixeira
- Institute of Biomedical Sciences Abel Salazar, University of Porto, Porto, Portugal,Department of Laboratory Genetics, Portuguese Oncology Institute of Porto, Porto, Portugal,Porto Comprehensive Cancer Center Raquel Seruca, Porto, Portugal,European Reference Network on Genetic Tumour Risk Syndromes (ERN GENTURIS), Porto, Portugal
| | - Stefan Aretz
- Institute of Human Genetics, Medical Faculty, University of Bonn, Bonn, Germany,National Center for Hereditary Tumor Syndromes, University Hospital Bonn, Bonn, Germany,ERN GENTURIS, Bonn, Germany
| | - Svetlana Bajalica-Lagercrantz
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden,Department of Clinical Genetics, Cancer Genetic Unit, Karolinska University Hospital Solna, Stockholm, Sweden,Cancer Theme, Karolinska University Hospital Solna, Stockholm, Sweden,ERN GENTURIS, Stockholm, Sweden
| | - Judith Balmaña
- Hospital Vall d'Hebron, Universitat Autonoma de Barcelona, Barcelona, Spain,ERN GENTURIS, Barcelona, Spain
| | - Ana Blatnik
- Department of Clinical Cancer Genetics, Institute of Oncology Ljubljana, Ljubljana, Slovenia,ERN GENTURIS, Ljubljana, Slovenia
| | - Patrick R Benusiglio
- Medical Genetics Department, Pitié-Salpêtrière Hospital, AP-HP and Sorbonne University, Paris, France
| | - Maud Blanluet
- Service de Génétique Oncologique, Institut Curie, Paris, France
| | - Vincent Bours
- Laboratory of Human Genetics, GIGA Institute, University of Liège, Liège, Belgium,Center of Genetics, University Hospital, Liège, Belgium,ERN GENTURIS, Liège, Belgium
| | - Hilde Brems
- Department of Human Genetics, University of Leuven, Leuven, Belgium
| | - Joan Brunet
- Hereditary Cancer Programme, Catalan Institute of Oncology, Bellvitge Institute for Biomedical Research and Girona Biomedical Research Institute, Barcelona-Girona, Spain,ERN GENTURIS, Barcelona, Spain
| | - Daniele Calistri
- Laboratorio di Bioscienze, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, Meldola, Italy
| | - Gabriel Capellá
- Hereditary Cancer Program, Catalan Institute of Oncology, Bellvitge Institute for Biomedical Research, Barcelona, Spain,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain,ERN GENTURIS, Barcelona, Spain
| | - Sergio Carrera
- Oncology Service, Biocruces Bizkaia Health Research Institute, Cruces University Hospital, Cruces-Barakaldo, Bizkaia, Spain
| | - Chrystelle Colas
- Service de Génétique Oncologique, Institut Curie, Paris, France,ERN GENTURIS, Paris, France
| | - Karin Dahan
- Center of Human Genetics, IPG, Gosselies, Belgium
| | - Robin de Putter
- Clinical Genetics Department, University Hospital of Ghent, Ghent, Belgium,ERN GENTURIS, Ghent, Belgium
| | - Camille Desseignés
- Medical Genetics Department, Pitié-Salpêtrière Hospital, AP-HP and Sorbonne University, Paris, France
| | | | - Conceição Egas
- CNC—Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
| | - D Gareth Evans
- Division of Evolution and Genomic Sciences, University of Manchester, Manchester, UK,Manchester Centre for Genomic Medicine, Manchester, UK
| | - Damien Feret
- Center of Human Genetics, IPG, Gosselies, Belgium
| | - Eleanor Fewings
- Department of Medical Genetics, National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge, Cambridge, UK
| | | | - Florence Coulet
- Medical Genetics Department, Pitié-Salpêtrière Hospital, AP-HP and Sorbonne University, Paris, France
| | - María Garcia-Barcina
- Genetics Unit, Biocruces Bizkaia Health Research Institute, Basurto University Hospital, Bilbao, Bizkaia, Spain
| | - Maurizio Genuardi
- Sezione di Medicina Genomica, Dipartimento di Scienze della Vita e Salute Pubblica, Università Cattolica del Sacro Cuore, Rome, Italy,UOC Genetica Medica, Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario A Gemelli IRCCS, Rome, Italy,ERN GENTURIS, Rome, Italy
| | - Lisa Golmard
- Service de Génétique Oncologique, Institut Curie, Paris, France
| | - Karl Hackmann
- Institute for Clinical Genetics, University Hospital Carl Gustav Carus and Faculty of Medicine, Technische Universität Dresden, Dresden, Germany,National Center for Tumor Diseases, Dresden, Germany: German Cancer Research Center, Heidelberg, Germany,Helmholtz-Zentrum Dresden-Rossendorf, Dresden, Germany,German Cancer Consortium, Dresden, Germany
| | - Helen Hanson
- SouthWest Thames Regional Genetics Service, St George's University Hospitals NHS Foundation Trust, London, UK
| | - Elke Holinski-Feder
- Medizinische Klinik und Poliklinik IV, Klinikum der Universität München, Munich, Germany,Medizinisch Genetisches Zentrum, Munich, Germany,ERN GENTURIS, Munich, Germany
| | - Robert Hüneburg
- Department of Internal Medicine I, University Hospital Bonn, Bonn, Germany,National Center for Hereditary Tumor Syndromes, University Hospital Bonn, Bonn, Germany,ERN GENTURIS, Bonn, Germany
| | - Mateja Krajc
- Department of Clinical Cancer Genetics, Institute of Oncology Ljubljana, Ljubljana, Slovenia,ERN GENTURIS, Ljubljana, Slovenia
| | - Kristina Lagerstedt-Robinson
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden,Department of Clinical Genetics, Cancer Genetic Unit, Karolinska University Hospital Solna, Stockholm, Sweden,ERN GENTURIS, Stockholm, Sweden
| | - Conxi Lázaro
- Hereditary Cancer Program, Catalan Institute of Oncology, Bellvitge Institute for Biomedical Research, Barcelona, Spain,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain,ERN GENTURIS, Barcelona, Spain
| | - Marjolijn J L Ligtenberg
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands,Department of Pathology, Radboud University Medical Center, Nijmegen, Netherlands,Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands,ERN GENTURIS, Nijmegen, Netherlands
| | - Cristina Martínez-Bouzas
- Genetics Service, Biocruces Bizkaia Health Research Institute, Cruces University Hospital, Cruces-Barakaldo, Bizkaia, Spain
| | - Sonia Merino
- Genetics Unit, Biocruces Bizkaia Health Research Institute, Basurto University Hospital, Bilbao, Bizkaia, Spain
| | | | - Srdjan Novaković
- Department of Molecular Diagnostics, Institute of Oncology Ljubljana, Ljubljana, Slovenia
| | - Ana Patiño-García
- Unidad de Medicina Genómica y Pediatría, Clínica Universidad de Navarra, Programa de Tumores Sólidos, Centro de Investigación Médica Aplicada, Instituto de Investigación Sanitaria de Navarra, Pamplona, Navarra, Spain
| | | | - Evelin Schröck
- Institute for Clinical Genetics, University Hospital Carl Gustav Carus and Faculty of Medicine, Technische Universität Dresden, Dresden, Germany,National Center for Tumor Diseases, Dresden, Germany: German Cancer Research Center, Heidelberg, Germany,Helmholtz-Zentrum Dresden-Rossendorf, Dresden, Germany,German Cancer Consortium, Dresden, Germany,Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany,ERN GENTURIS, Dresden, Germany
| | - Inês Silva
- GenoMed—Diagnósticos de Medicina Molecular, Lisbon, Portugal
| | | | - José L Soto
- Molecular Genetics Laboratory, Elche University Hospital, Elche, Spain
| | - Isabel Spier
- Institute of Human Genetics, Medical Faculty, University of Bonn, Bonn, Germany,National Center for Hereditary Tumor Syndromes, University Hospital Bonn, Bonn, Germany,ERN GENTURIS, Bonn, Germany
| | - Verena Steinke-Lange
- Medizinische Klinik und Poliklinik IV, Klinikum der Universität München, Munich, Germany,Medizinisch Genetisches Zentrum, Munich, Germany,ERN GENTURIS, Munich, Germany
| | - Gianluca Tedaldi
- Laboratorio di Bioscienze, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, Meldola, Italy
| | - María-Isabel Tejada
- Genetics Service, Biocruces Bizkaia Health Research Institute, Cruces University Hospital, Cruces-Barakaldo, Bizkaia, Spain
| | - Emma R Woodward
- Division of Evolution and Genomic Sciences, University of Manchester, Manchester, UK,Manchester Centre for Genomic Medicine, Manchester, UK
| | - Marc Tischkowitz
- Department of Medical Genetics, National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge, Cambridge, UK
| | - Nicoline Hoogerbrugge
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands,Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands,ERN GENTURIS, Nijmegen, Netherlands
| | - Carla Oliveira
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal; Faculty of Medicine, University of Porto, Porto, Portugal; Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal; Porto Comprehensive Cancer Center Raquel Seruca, Porto, Portugal; European Reference Network on Genetic Tumour Risk Syndromes (ERN GENTURIS), Porto, Portugal.
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26
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Fan K, Guo Y, Song Z, Yuan L, Zheng W, Hu X, Gong L, Deng H. The TSC2 c.2742+5G>A variant causes variable splicing changes and clinical manifestations in a family with tuberous sclerosis complex. Front Mol Neurosci 2023; 16:1091323. [PMID: 37152430 PMCID: PMC10157042 DOI: 10.3389/fnmol.2023.1091323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 03/16/2023] [Indexed: 05/09/2023] Open
Abstract
Background Tuberous sclerosis complex (TSC) is a genetic, variably expressed, multisystem disease characterized by benign tumors. It is caused by pathogenic variants of the TSC complex subunit 1 gene (TSC1) and the TSC complex subunit 2 gene (TSC2). Genetic testing allows for early diagnosis, genetic counseling, and improved outcomes, but it did not identify a pathogenic variant in up to 25% of all TSC patients. This study aimed to identify the disease-causing variant in a Han-Chinese family with TSC. Methods A six-member, three-generation Han-Chinese family with TSC and three unrelated healthy women were recruited. A comprehensive medical examination, a 3-year follow-up, whole exome sequencing, Sanger sequencing, and segregation analysis were performed in the family. The splicing analysis results obtained from six in silico tools, minigene assay, and patients' lymphocyte messenger RNA were compared, and quantitative reverse transcription PCR was used to confirm the pathogenicity of the variant. Results Two affected family members had variable clinical manifestations including a rare bilateral cerebellar ataxia symptom. The 3-year follow-up results suggest the effects of a combined treatment of anti-epilepsy drugs and sirolimus for TSC-related epilepsy and cognitive deficits. Whole exome sequencing, Sanger sequencing, segregation analysis, splicing analysis, and quantitative reverse transcription PCR identified the TSC2 gene c.2742+5G>A variant as the genetic cause. This variant inactivated the donor splice site, a cryptic non-canonical splice site was used for different splicing changes in two affected subjects, and the resulting mutant messenger RNA may be degraded by nonsense-mediated decay. The defects of in silico tools and minigene assay in predicting cryptic splice sites were suggested. Conclusions This study identified a TSC2 c.2742+5G>A variant as the genetic cause of a Han-Chinese family with TSC and first confirmed its pathogenicity. These findings expand the phenotypic and genetic spectrum of TSC and may contribute to its diagnosis and treatment, as well as a better understanding of the splicing mechanism.
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Affiliation(s)
- Kuan Fan
- Department of Health Management, The Third Xiangya Hospital, Central South University, Changsha, China
- Center for Experimental Medicine, The Third Xiangya Hospital, Central South University, Changsha, China
- Department of Neurology, Guizhou Provincial People's Hospital, Guiyang, China
| | - Yi Guo
- Center for Experimental Medicine, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Zhi Song
- Department of Neurology, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Lamei Yuan
- Center for Experimental Medicine, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Wen Zheng
- Department of Neurology, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Xiao Hu
- Department of Neurology, Guizhou Provincial People's Hospital, Guiyang, China
| | - Lina Gong
- Department of Neurology, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Hao Deng
- Department of Health Management, The Third Xiangya Hospital, Central South University, Changsha, China
- Center for Experimental Medicine, The Third Xiangya Hospital, Central South University, Changsha, China
- Department of Neurology, The Third Xiangya Hospital, Central South University, Changsha, China
- *Correspondence: Hao Deng
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27
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Pan-Lizcano R, Mariñas-Pardo L, Núñez L, Rebollal-Leal F, López-Vázquez D, Pereira A, Molina-Nieto A, Calviño R, Vázquez-Rodríguez JM, Hermida-Prieto M. Rare Variants in Genes of the Cholesterol Pathway Are Present in 60% of Patients with Acute Myocardial Infarction. Int J Mol Sci 2022; 23:ijms232416127. [PMID: 36555767 PMCID: PMC9786046 DOI: 10.3390/ijms232416127] [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: 11/04/2022] [Revised: 12/06/2022] [Accepted: 12/12/2022] [Indexed: 12/24/2022] Open
Abstract
Acute myocardial infarction (AMI) is a pandemic in which conventional risk factors are inadequate to detect who is at risk early in the asymptomatic stage. Although gene variants in genes related to cholesterol, which may increase the risk of AMI, have been identified, no studies have systematically screened the genes involved in this pathway. In this study, we included 105 patients diagnosed with AMI with an elevation of the ST segment (STEMI) and treated with primary percutaneous coronary intervention (PPCI). Using next-generation sequencing, we examined the presence of rare variants in 40 genes proposed to be involved in lipid metabolism and we found that 60% of AMI patients had a rare variant in the genes involved in the cholesterol pathway. Our data show the importance of considering the wide scope of the cholesterol pathway in order to assess the genetic risk related to AMI.
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Affiliation(s)
- Ricardo Pan-Lizcano
- Grupo de Investigación en Cardiología, Instituto de Investigación Biomédica de A Coruña (INIBIC), Complexo Hospitalario Universitario de A Coruña (CHUAC-SERGAS), GRINCAR-Universidade da Coruña (UDC), 15006 A Coruña, Spain
| | - Luis Mariñas-Pardo
- Facultad de Ciencias de la Salud, Universidad Internacional de Valencia (VIU), 46002 Valencia, Spain
| | - Lucía Núñez
- Grupo de Investigación en Cardiología, Instituto de Investigación Biomédica de A Coruña (INIBIC), Complexo Hospitalario Universitario de A Coruña (CHUAC-SERGAS), GRINCAR-Universidade da Coruña (UDC), 15006 A Coruña, Spain
- Departamento de Ciencias de la Salud, GRINCAR Research Group, Universidade da Coruña, 15403 A Coruña, Spain
- Correspondence: ; Tel.: +34-981-178-150
| | - Fernando Rebollal-Leal
- Servicio de Cardiología, Complexo Hospitalario Universitario de A Coruña (CHUAC-SERGAS), Instituto de Investigación Biomédica de A Coruña (INIBIC), Universidade da Coruña (UDC), 15006 A Coruña, Spain
| | - Domingo López-Vázquez
- Servicio de Cardiología, Complexo Hospitalario Universitario de A Coruña (CHUAC-SERGAS), Instituto de Investigación Biomédica de A Coruña (INIBIC), Universidade da Coruña (UDC), 15006 A Coruña, Spain
| | - Ana Pereira
- Servicio de Cardiología, Complexo Hospitalario Universitario de A Coruña (CHUAC-SERGAS), Instituto de Investigación Biomédica de A Coruña (INIBIC), Universidade da Coruña (UDC), 15006 A Coruña, Spain
| | - Aranzazu Molina-Nieto
- Servicio de Cardiología, Complexo Hospitalario Universitario de A Coruña (CHUAC-SERGAS), Instituto de Investigación Biomédica de A Coruña (INIBIC), Universidade da Coruña (UDC), 15006 A Coruña, Spain
| | - Ramón Calviño
- Servicio de Cardiología, Complexo Hospitalario Universitario de A Coruña (CHUAC-SERGAS), Instituto de Investigación Biomédica de A Coruña (INIBIC), Universidade da Coruña (UDC), 15006 A Coruña, Spain
- CIBERCV (Centro de Investigación Biomédica en Red Enfermedades Cardiovasculares), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Jose Manuel Vázquez-Rodríguez
- Servicio de Cardiología, Complexo Hospitalario Universitario de A Coruña (CHUAC-SERGAS), Instituto de Investigación Biomédica de A Coruña (INIBIC), Universidade da Coruña (UDC), 15006 A Coruña, Spain
- CIBERCV (Centro de Investigación Biomédica en Red Enfermedades Cardiovasculares), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Manuel Hermida-Prieto
- Grupo de Investigación en Cardiología, Instituto de Investigación Biomédica de A Coruña (INIBIC), Complexo Hospitalario Universitario de A Coruña (CHUAC-SERGAS), GRINCAR-Universidade da Coruña (UDC), 15006 A Coruña, Spain
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Chen YL, Ho CL, Hung CY, Chen WL, Chang C, Hou YH, Chen JR, Chen PJ, Chow NH, Huang W, Hsu YT, Chen TY, Liu T. Enhancing diagnosis of T-cell lymphoma using non-recombined T-cell receptor sequences. Front Oncol 2022; 12:1014132. [PMID: 36568146 PMCID: PMC9772823 DOI: 10.3389/fonc.2022.1014132] [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: 08/08/2022] [Accepted: 11/25/2022] [Indexed: 12/13/2022] Open
Abstract
Clonality assessment, which can detect neoplastic T cells by identifying the uniquely recombined T-cell receptor (TCR) genes, provides important support in the diagnosis of T-cell lymphoma (TCL). BIOMED-2 is the gold standard clonality assay and has proven to be effective in European TCL patients. However, we failed to prove its sensitivity in Taiwanese TCL patients, especially based on the TCRβ gene. To explore potential impact of genetic background in the BIOMED-2 test, we analyzed TCRβ sequences of 21 healthy individuals and two TCL patients. This analysis suggests that genetic variations in the BIOMED-2 primer sites could not explain the difference in sensitivity. The BIOMED-2 test results of the two TCL patients were positive and negative, respectively. Interestingly, a higher percentage (>81%) of non-recombined TCRβ sequences was observed in the test-negative patient than those of the test-positive patient and all healthy individuals (13~66%). The result suggests a new TCR target for enhancing TCL diagnosis. To further explore the hypothesis, we proposed a cost-effective digital PCR assay that quantifies the relative abundance of non-recombined TCRβ sequences containing a J2-2P~J2-3 segment. With the digital PCR assay, bone marrow specimens from TCL patients (n=9) showed a positive outcome (i.e., the relative abundance of the J2-2P~J2-3 sequences ≧5%), whereas non-TCL patients (n=6) gave a negative result. As five of nine TCL patients had a negative BIOMED-2 test result, the J2-2P~J2-3 sequences may improve TCL detection. This is the first report showing the capability of characterizing non-recombined TCR sequences as a supplementary strategy for the BIOMED-2 clonality test.
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Affiliation(s)
- Yi-Lin Chen
- Department of Pathology, National Cheng Kung University Hospital, Tainan, Taiwan,Molecular Medicine Core Laboratory, Research Center of Clinical Medicine, National Cheng Kung University Hospital, Tainan, Taiwan,Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Chung-Liang Ho
- Department of Pathology, National Cheng Kung University Hospital, Tainan, Taiwan,Molecular Medicine Core Laboratory, Research Center of Clinical Medicine, National Cheng Kung University Hospital, Tainan, Taiwan,Institute of Molecular Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Chen-Yan Hung
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan, Taiwan
| | - Wan-Li Chen
- Department of Pathology, National Cheng Kung University Hospital, Tainan, Taiwan,Molecular Medicine Core Laboratory, Research Center of Clinical Medicine, National Cheng Kung University Hospital, Tainan, Taiwan
| | - Chen Chang
- Department of Pathology, National Cheng Kung University Hospital, Tainan, Taiwan
| | - Yi-Hsin Hou
- Department of Pathology, National Cheng Kung University Hospital, Tainan, Taiwan,Molecular Medicine Core Laboratory, Research Center of Clinical Medicine, National Cheng Kung University Hospital, Tainan, Taiwan
| | - Jian-Rong Chen
- Department of Pathology, National Cheng Kung University Hospital, Tainan, Taiwan,Molecular Medicine Core Laboratory, Research Center of Clinical Medicine, National Cheng Kung University Hospital, Tainan, Taiwan
| | - Pin-Jun Chen
- Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Nan-Haw Chow
- Department of Pathology, National Cheng Kung University Hospital, Tainan, Taiwan,Molecular Medicine Core Laboratory, Research Center of Clinical Medicine, National Cheng Kung University Hospital, Tainan, Taiwan,Institute of Molecular Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Wenya Huang
- Department of Pathology, National Cheng Kung University Hospital, Tainan, Taiwan,Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Ya-Ting Hsu
- Section of Hematology/Oncology, Department of Internal Medicine, National Cheng Kung University Hospital, Tainan, Taiwan
| | - Tsai-Yun Chen
- Section of Hematology/Oncology, Department of Internal Medicine, National Cheng Kung University Hospital, Tainan, Taiwan
| | - Tsunglin Liu
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan, Taiwan,*Correspondence: Tsunglin Liu,
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Rahmani N, Ahmadvand M, Khakpour G. Use of expanded carrier screening for retrospective diagnosis of two deceased siblings with Van Maldergem syndrome 2: case report. ASIAN BIOMED 2022; 16:322-328. [PMID: 37551355 PMCID: PMC10392142 DOI: 10.2478/abm-2022-0036] [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] [Indexed: 08/09/2023]
Abstract
Van Maldergem syndrome (VMLDS) is a recessive disease which affects multiple organs including the face, ear, and limb extremities. It can be caused by pathogenic variants in either the gene DCHS1 or FAT4. Diagnosis of VMLDS is complicated, especially regarding its similarity of symptoms to Hennekam syndrome, another disorder caused by FAT4 variants. Reported patients are two infantile siblings with multiple congenital anomalies, who deceased without clinical diagnosis. Whole exome sequencing was exploited for expanded carrier screening (ECS) of their parents, which revealed a novel splicing variant in the gene FAT4, NM_024582.6: c.7018+1G>A. In silico analysis of the variant indicates loss of canonical donor splice site of intron 6. This variant is classified as pathogenic based on ACMG criteria. Reverse phenotyping of patients resulted in likely diagnosis of VMLDS2. This study reaffirms the possibility of using ECS, leading to the genetic diagnosis of a rare disease with complicated clinical features.
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Affiliation(s)
- Nasim Rahmani
- Department of Medical Genetics and Molecular Biology, School of Medicine, Iran University of Medical Sciences, Tehran1449614535, Iran
| | - Mohammad Ahmadvand
- Department of Oncology and Stem Cell Transplantation, Shariati Hospital, School of Medicine, Tehran University of Medical Sciences, Tehran1411713135, Iran
| | - Golnaz Khakpour
- Department of Medical Genetics and Molecular Biology, School of Medicine, Iran University of Medical Sciences, Tehran1449614535, Iran
- Department of Eye Research Center, The Five Senses Institute, Rassoul Akram Hospital, School of Medicine, Iran University of Medical Sciences, Tehran1445613131, Iran
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30
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Hopkins CE, Brock T, Caulfield TR, Bainbridge M. Phenotypic screening models for rapid diagnosis of genetic variants and discovery of personalized therapeutics. Mol Aspects Med 2022; 91:101153. [PMID: 36411139 PMCID: PMC10073243 DOI: 10.1016/j.mam.2022.101153] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/22/2022] [Accepted: 10/23/2022] [Indexed: 11/19/2022]
Abstract
Precision medicine strives for highly individualized treatments for disease under the notion that each individual's unique genetic makeup and environmental exposures imprints upon them not only a disposition to illness, but also an optimal therapeutic approach. In the realm of rare disorders, genetic predisposition is often the predominant mechanism driving disease presentation. For such, mostly, monogenic disorders, a causal gene to phenotype association is likely. As a result, it becomes important to query the patient's genome for the presence of pathogenic variations that are likely to cause the disease. Determining whether a variant is pathogenic or not is critical to these analyses and can be challenging, as many disease-causing variants are novel and, ergo, have no available functional data to help categorize them. This problem is exacerbated by the need for rapid evaluation of pathogenicity, since many genetic diseases present in young children who will experience increased morbidity and mortality without rapid diagnosis and therapeutics. Here, we discuss the utility of animal models, with a focus mainly on C. elegans, as a contrast to tissue culture and in silico approaches, with emphasis on how these systems are used in determining pathogenicity of variants with uncertain significance and then used to screen for novel therapeutics.
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Affiliation(s)
| | | | - Thomas R Caulfield
- Mayo Clinic, Department of Neuroscience, Department of Computational Biology, Department of Clinical Genomics, Jacksonville, FL, 32224, Rochester, MN, 55905, USA
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31
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Cormier MJ, Pedersen BS, Bayrak-Toydemir P, Quinlan AR. Combining genetic constraint with predictions of alternative splicing to prioritize deleterious splicing in rare disease studies. BMC Bioinformatics 2022; 23:482. [PMID: 36376793 PMCID: PMC9664736 DOI: 10.1186/s12859-022-05041-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 11/07/2022] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Despite numerous molecular and computational advances, roughly half of patients with a rare disease remain undiagnosed after exome or genome sequencing. A particularly challenging barrier to diagnosis is identifying variants that cause deleterious alternative splicing at intronic or exonic loci outside of canonical donor or acceptor splice sites. RESULTS Several existing tools predict the likelihood that a genetic variant causes alternative splicing. We sought to extend such methods by developing a new metric that aids in discerning whether a genetic variant leads to deleterious alternative splicing. Our metric combines genetic variation in the Genome Aggregate Database with alternative splicing predictions from SpliceAI to compare observed and expected levels of splice-altering genetic variation. We infer genic regions with significantly less splice-altering variation than expected to be constrained. The resulting model of regional splicing constraint captures differential splicing constraint across gene and exon categories, and the most constrained genic regions are enriched for pathogenic splice-altering variants. Building from this model, we developed ConSpliceML. This ensemble machine learning approach combines regional splicing constraint with multiple per-nucleotide alternative splicing scores to guide the prediction of deleterious splicing variants in protein-coding genes. ConSpliceML more accurately distinguishes deleterious and benign splicing variants than state-of-the-art splicing prediction methods, especially in "cryptic" splicing regions beyond canonical donor or acceptor splice sites. CONCLUSION Integrating a model of genetic constraint with annotations from existing alternative splicing tools allows ConSpliceML to prioritize potentially deleterious splice-altering variants in studies of rare human diseases.
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Affiliation(s)
- Michael J Cormier
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
- Utah Center for Genetic Discovery, University of Utah, Salt Lake City, UT, USA
| | - Brent S Pedersen
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
- Utah Center for Genetic Discovery, University of Utah, Salt Lake City, UT, USA
| | | | - Aaron R Quinlan
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA.
- Utah Center for Genetic Discovery, University of Utah, Salt Lake City, UT, USA.
- Department of Biomedical Informatics, University of Utah, Salt Lake City, UT, USA.
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32
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García-Cruz C, Aragón J, Lourdel S, Annan A, Roger JE, Montanez C, Vaillend C. Tissue- and cell-specific whole-transcriptome meta-analysis from brain and retina reveals differential expression of dystrophin complexes and new dystrophin spliced isoforms. Hum Mol Genet 2022; 32:659-676. [PMID: 36130212 PMCID: PMC9896479 DOI: 10.1093/hmg/ddac236] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 09/13/2022] [Accepted: 09/14/2022] [Indexed: 02/07/2023] Open
Abstract
The large DMD gene encodes a group of dystrophin proteins in brain and retina, produced from multiple promoters and alternative splicing events. Dystrophins are core components of different scaffolding complexes in distinct cell types. Their absence may thus alter several cellular pathways, which might explain the heterogeneous genotype-phenotype relationships underlying central comorbidities in Duchenne muscular dystrophy (DMD). However, the cell-specific expression of dystrophins and associated proteins (DAPs) is still largely unknown. The present study provides a first RNA-Seq-based reference showing tissue- and cell-specific differential expression of dystrophins, splice variants and DAPs in mouse brain and retina. We report that a cell type may express several dystrophin complexes, perhaps due to expression in separate cell subdomains and/or subpopulations, some of which with differential expression at different maturation stages. We also identified new splicing events in addition to the common exon-skipping events. These include a new exon within intron 51 (E51b) in frame with the flanking exons in retina, as well as inclusions of intronic sequences with stop codons leading to the presence of transcripts with elongated exons 40 and/or 41 (E40e, E41e) in both retina and brain. PCR validations revealed that the new exons may affect several dystrophins. Moreover, immunoblot experiments using a combination of specific antibodies and dystrophin-deficient mice unveiled that the transcripts with stop codons are translated into truncated proteins lacking their C-terminus, which we called N-Dp427 and N-Dp260. This study thus uncovers a range of new findings underlying the complex neurobiology of DMD.
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Affiliation(s)
| | | | - Sophie Lourdel
- Institut des Neurosciences Paris Saclay, Université Paris-Saclay, CNRS, 91400 Saclay, France
| | - Ahrmad Annan
- Institut des Neurosciences Paris Saclay, Université Paris-Saclay, CNRS, 91400 Saclay, France
| | - Jérôme E Roger
- To whom correspondence should be addressed. E-mail: (C.V.); (C.M.); (J.E.R.)
| | - Cecilia Montanez
- To whom correspondence should be addressed. E-mail: (C.V.); (C.M.); (J.E.R.)
| | - Cyrille Vaillend
- To whom correspondence should be addressed. E-mail: (C.V.); (C.M.); (J.E.R.)
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33
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Bartoletti-Stella A, Tarozzi M, Mengozzi G, Asirelli F, Brancaleoni L, Mometto N, Stanzani-Maserati M, Baiardi S, Linarello S, Spallazzi M, Pantieri R, Ferriani E, Caffarra P, Liguori R, Parchi P, Capellari S. Dementia-related genetic variants in an Italian population of early-onset Alzheimer’s disease. Front Aging Neurosci 2022; 14:969817. [PMID: 36133075 PMCID: PMC9484406 DOI: 10.3389/fnagi.2022.969817] [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: 06/15/2022] [Accepted: 08/02/2022] [Indexed: 11/13/2022] Open
Abstract
Early-onset Alzheimer’s disease (EOAD) is the most common form of early-onset dementia. Although three major genes have been identified as causative, the genetic contribution to the disease remains unsolved in many patients. Recent studies have identified pathogenic variants in genes representing a risk factor for developing Alzheimer’s disease (AD) and in causative genes for other degenerative dementias as responsible for EOAD. To study them further, we investigated a panel of candidate genes in 102 Italian EOAD patients, 45.10% of whom had a positive family history and 21.74% with a strong family history of dementia. We found that 10.78% of patients carried pathogenic or likely pathogenic variants, including a novel variant, in PSEN1, PSEN2, or APP, and 7.84% showed homozygosity for the ε4 APOE allele. Additionally, 7.84% of patients had a moderate risk allele in PSEN1, PSEN2, or TREM2 genes. Besides, we observed that 12.75% of our patients carried only a variant in genes associated with other neurodegenerative diseases. The combination of these variants contributes to explain 46% of cases with a definite familiarity and 32% of sporadic forms. Our results confirm the importance of extensive genetic screening in EOAD for clinical purposes, to select patients for future treatments and to contribute to the definition of overlapping pathogenic mechanisms between AD and other forms of dementia.
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Affiliation(s)
- Anna Bartoletti-Stella
- Department of Experimental Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
| | - Martina Tarozzi
- Department of Experimental Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
| | - Giacomo Mengozzi
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bellaria Hospital, Bologna, Italy
| | - Francesca Asirelli
- Department of Medical Science and Surgery (DIMEC), University of Bologna, Bologna, Italy
| | - Laura Brancaleoni
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bellaria Hospital, Bologna, Italy
- Neurologia e Rete Stroke Metropolitana, Ospedale Maggiore, Bologna, Italy
| | - Nicola Mometto
- UOC Neurologia, Ospedale Guglielmo da Saliceto, Piacenza, Italy
| | | | - Simone Baiardi
- Department of Experimental Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bellaria Hospital, Bologna, Italy
| | - Simona Linarello
- Programma Cure Intermedie - Azienda USL di Bologna, Bologna, Italy
| | - Marco Spallazzi
- U.O. di Neurologia, Azienda Ospedaliero-Universitaria, Parma, Italy
| | - Roberta Pantieri
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bellaria Hospital, Bologna, Italy
| | - Elisa Ferriani
- UOC Psicologia Clinica Ospedaliera, Ospedale Bellaria, Azienda USL di Bologna, Bologna, Italy
| | - Paolo Caffarra
- Unità di Neuroscienze, Università di Parma, Parma, Italy
| | - Rocco Liguori
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bellaria Hospital, Bologna, Italy
- Department of Biomedical and NeuroMotor Sciences (DIBINEM), University of Bologna, Bologna, Italy
| | - Piero Parchi
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bellaria Hospital, Bologna, Italy
- Department of Biomedical and NeuroMotor Sciences (DIBINEM), University of Bologna, Bologna, Italy
| | - Sabina Capellari
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bellaria Hospital, Bologna, Italy
- Department of Biomedical and NeuroMotor Sciences (DIBINEM), University of Bologna, Bologna, Italy
- *Correspondence: Sabina Capellari,
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34
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Li K, Luo T, Zhu Y, Huang Y, Wang A, Zhang D, Dong L, Wang Y, Wang R, Tang D, Yu Z, Shen Q, Lv M, Ling Z, Fang Z, Yuan J, Li B, Xia K, He X, Li J, Zhao G. Performance evaluation of differential splicing analysis methods and splicing analytics platform construction. Nucleic Acids Res 2022; 50:9115-9126. [PMID: 35993808 PMCID: PMC9458456 DOI: 10.1093/nar/gkac686] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 07/01/2022] [Accepted: 08/01/2022] [Indexed: 12/24/2022] Open
Abstract
A proportion of previously defined benign variants or variants of uncertain significance in humans, which are challenging to identify, may induce an abnormal splicing process. An increasing number of methods have been developed to predict splicing variants, but their performance has not been completely evaluated using independent benchmarks. Here, we manually sourced ∼50 000 positive/negative splicing variants from > 8000 studies and selected the independent splicing variants to evaluate the performance of prediction methods. These methods showed different performances in recognizing splicing variants in donor and acceptor regions, reminiscent of different weight coefficient applications to predict novel splicing variants. Of these methods, 66.67% exhibited higher specificities than sensitivities, suggesting that more moderate cut-off values are necessary to distinguish splicing variants. Moreover, the high correlation and consistent prediction ratio validated the feasibility of integration of the splicing prediction method in identifying splicing variants. We developed a splicing analytics platform called SPCards, which curates splicing variants from publications and predicts splicing scores of variants in genomes. SPCards also offers variant-level and gene-level annotation information, including allele frequency, non-synonymous prediction and comprehensive functional information. SPCards is suitable for high-throughput genetic identification of splicing variants, particularly those located in non-canonical splicing regions.
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Affiliation(s)
| | | | - Yan Zhu
- Centre for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Yuanfeng Huang
- Bioinformatics Center & National Clinical Research Centre for Geriatric Disorders & Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China,Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - An Wang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei 230022, China,NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract (Anhui Medical University), No 81 Meishan Road, Hefei 230032, Anhui, China,Key Laboratory of Population Health Across Life Cycle (Anhui Medical University), Ministry of Education of the People's Republic of China, No 81 Meishan Road, Hefei 230032, Anhui, China
| | - Di Zhang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei 230022, China,NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract (Anhui Medical University), No 81 Meishan Road, Hefei 230032, Anhui, China,Key Laboratory of Population Health Across Life Cycle (Anhui Medical University), Ministry of Education of the People's Republic of China, No 81 Meishan Road, Hefei 230032, Anhui, China
| | - Lijie Dong
- Centre for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Yujian Wang
- Bioinformatics Center & National Clinical Research Centre for Geriatric Disorders & Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China,Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Rui Wang
- Centre for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Dongdong Tang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei 230022, China,NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract (Anhui Medical University), No 81 Meishan Road, Hefei 230032, Anhui, China,Key Laboratory of Population Health Across Life Cycle (Anhui Medical University), Ministry of Education of the People's Republic of China, No 81 Meishan Road, Hefei 230032, Anhui, China
| | - Zhen Yu
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei 230022, China,NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract (Anhui Medical University), No 81 Meishan Road, Hefei 230032, Anhui, China,Key Laboratory of Population Health Across Life Cycle (Anhui Medical University), Ministry of Education of the People's Republic of China, No 81 Meishan Road, Hefei 230032, Anhui, China
| | - Qunshan Shen
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei 230022, China,NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract (Anhui Medical University), No 81 Meishan Road, Hefei 230032, Anhui, China,Key Laboratory of Population Health Across Life Cycle (Anhui Medical University), Ministry of Education of the People's Republic of China, No 81 Meishan Road, Hefei 230032, Anhui, China
| | - Mingrong Lv
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei 230022, China,NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract (Anhui Medical University), No 81 Meishan Road, Hefei 230032, Anhui, China,Key Laboratory of Population Health Across Life Cycle (Anhui Medical University), Ministry of Education of the People's Republic of China, No 81 Meishan Road, Hefei 230032, Anhui, China
| | - Zhengbao Ling
- Centre for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Zhenghuan Fang
- Centre for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Jing Yuan
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei 230022, China,NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract (Anhui Medical University), No 81 Meishan Road, Hefei 230032, Anhui, China,Key Laboratory of Population Health Across Life Cycle (Anhui Medical University), Ministry of Education of the People's Republic of China, No 81 Meishan Road, Hefei 230032, Anhui, China
| | - Bin Li
- Bioinformatics Center & National Clinical Research Centre for Geriatric Disorders & Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China,Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Kun Xia
- Centre for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China,Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Xiaojin He
- Correspondence may also be addressed to Xiaojin He. Tel: +86 731 8975 2406; Fax: +86 731 8432 7332;
| | - Jinchen Li
- To whom correspondence should be addressed. Tel: +86 731 8975 2406; Fax: +86 731 8432 7332;
| | - Guihu Zhao
- Correspondence may also be addressed to Guihu Zhao. Tel: +86 731 8975 2406; Fax: +86 731 8432 7332;
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35
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An Intron c.103-3T>C Variant of the AMELX Gene Causes Combined Hypomineralized and Hypoplastic Type of Amelogenesis Imperfecta: Case Series and Review of the Literature. Genes (Basel) 2022; 13:genes13071272. [PMID: 35886055 PMCID: PMC9321068 DOI: 10.3390/genes13071272] [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: 06/21/2022] [Revised: 07/07/2022] [Accepted: 07/09/2022] [Indexed: 02/04/2023] Open
Abstract
Amelogenesis imperfecta (AI) is a heterogeneous group of genetic disorders of dental enamel. X-linked AI results from disease-causing variants in the AMELX gene. In this paper, we characterise the genetic aetiology and enamel histology of female AI patients from two unrelated families with similar clinical and radiographic findings. All three probands were carefully selected from 40 patients with AI. In probands from both families, scanning electron microscopy confirmed hypoplastic and hypomineralised enamel. A neonatal line separated prenatally and postnatally formed enamel of distinctly different mineralisation qualities. In both families, whole exome analysis revealed the intron variant NM_182680.1: c.103-3T>C, located three nucleotides before exon 4 of the AMELX gene. In family I, an additional variant, c.2363G>A, was found in exon 5 of the FAM83H gene. This report illustrates a variant in the AMELX gene that was not previously reported to be causative for AI as well as an additional variant in the FAM83H gene with probably limited clinical significance.
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36
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Hoffman MJ, Takizawa A, Jensen ES, Schilling R, Grzybowski M, Geurts AM, Dwinell MR. Btg2 mutation induces renal injury and impairs blood pressure control in female rats. Physiol Genomics 2022; 54:231-241. [PMID: 35503009 DOI: 10.1152/physiolgenomics.00167.2021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Hypertension (HTN) is a complex disease influenced by heritable genetic elements and environmental interactions. Dietary salt is among the most influential modifiable factors contributing to increased blood pressure (BP). It is well established that men and women develop BP impairment in different patterns and a recent emphasis has been placed on identifying mechanisms leading to the differences observed between the sexes in HTN development. The current work reported here builds on an extensive genetic mapping experiment which sought to identify genetic determinants of salt sensitive (SS) HTN using the Dahl SS rat. BTG anti-proliferation factor 2 (Btg2) was previously identified by our group as a candidate gene contributing to SS HTN in female rats. In the current study, Btg2 was mutated using TALEN targeted gene disruption on the SSBN congenic rat background. The Btg2 mutated rats exhibited impaired BP and proteinuria responses to a high salt diet compared to wild type rats. Differences in body weight, mutant pup viability, skeletal morphology, and adult nephron density suggest a potential role for Btg2 in developmental signaling pathways. Subsequent cell cycle gene expression assessment provides several additional signaling pathways that Btg2 may function through during salt handling in the kidney. The expression analysis also identified several potential upstream targets that can be explored to further isolate therapeutic approaches for SS HTN.
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Affiliation(s)
- Matthew J Hoffman
- Genomic Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, WI, United States.,Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Akiko Takizawa
- Genomic Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, WI, United States.,Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Eric S Jensen
- Biomedical Research Center, Medical College of Wisconsin, Milwaukee, WI, United States.,Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Rebecca Schilling
- Genomic Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, WI, United States.,Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Michael Grzybowski
- Genomic Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, WI, United States.,Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Aron M Geurts
- Genomic Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, WI, United States.,Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Melinda R Dwinell
- Genomic Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, WI, United States.,Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, United States
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37
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Zhu L, Li W. Roles of Physicochemical and Structural Properties of RNA-Binding Proteins in Predicting the Activities of Trans-Acting Splicing Factors with Machine Learning. Int J Mol Sci 2022; 23:ijms23084426. [PMID: 35457243 PMCID: PMC9030803 DOI: 10.3390/ijms23084426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 04/13/2022] [Accepted: 04/14/2022] [Indexed: 02/06/2023] Open
Abstract
Trans-acting splicing factors play a pivotal role in modulating alternative splicing by specifically binding to cis-elements in pre-mRNAs. There are approximately 1500 RNA-binding proteins (RBPs) in the human genome, but the activities of these RBPs in alternative splicing are unknown. Since determining RBP activities through experimental methods is expensive and time consuming, the development of an efficient computational method for predicting the activities of RBPs in alternative splicing from their sequences is of great practical importance. Recently, a machine learning model for predicting the activities of splicing factors was built based on features of single and dual amino acid compositions. Here, we explored the role of physicochemical and structural properties in predicting their activities in alternative splicing using machine learning approaches and found that the prediction performance is significantly improved by including these properties. By combining the minimum redundancy–maximum relevance (mRMR) method and forward feature searching strategy, a promising feature subset with 24 features was obtained to predict the activities of RBPs. The feature subset consists of 16 dual amino acid compositions, 5 physicochemical features, and 3 structural features. The physicochemical and structural properties were as important as the sequence composition features for an accurate prediction of the activities of splicing factors. The hydrophobicity and distribution of coil are suggested to be the key physicochemical and structural features, respectively.
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Affiliation(s)
| | - Wenjin Li
- Correspondence: ; Tel.: +86-0755-26942336
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38
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Stephenson SE, Costain G, Blok LE, Silk MA, Nguyen TB, Dong X, Alhuzaimi DE, Dowling JJ, Walker S, Amburgey K, Hayeems RZ, Rodan LH, Schwartz MA, Picker J, Lynch SA, Gupta A, Rasmussen KJ, Schimmenti LA, Klee EW, Niu Z, Agre KE, Chilton I, Chung WK, Revah-Politi A, Au PB, Griffith C, Racobaldo M, Raas-Rothschild A, Ben Zeev B, Barel O, Moutton S, Morice-Picard F, Carmignac V, Cornaton J, Marle N, Devinsky O, Stimach C, Wechsler SB, Hainline BE, Sapp K, Willems M, Bruel AL, Dias KR, Evans CA, Roscioli T, Sachdev R, Temple SE, Zhu Y, Baker JJ, Scheffer IE, Gardiner FJ, Schneider AL, Muir AM, Mefford HC, Crunk A, Heise EM, Millan F, Monaghan KG, Person R, Rhodes L, Richards S, Wentzensen IM, Cogné B, Isidor B, Nizon M, Vincent M, Besnard T, Piton A, Marcelis C, Kato K, Koyama N, Ogi T, Goh ESY, Richmond C, Amor DJ, Boyce JO, Morgan AT, Hildebrand MS, Kaspi A, Bahlo M, Friðriksdóttir R, Katrínardóttir H, Sulem P, Stefánsson K, Björnsson HT, Mandelstam S, Morleo M, Mariani M, Scala M, Accogli A, Torella A, Capra V, Wallis M, Jansen S, Waisfisz Q, de Haan H, Sadedin S, Lim SC, White SM, Ascher DB, Schenck A, Lockhart PJ, Christodoulou J, Tan TY, Christodoulou J, Tan TY. Germline variants in tumor suppressor FBXW7 lead to impaired ubiquitination and a neurodevelopmental syndrome. Am J Hum Genet 2022; 109:601-617. [PMID: 35395208 DOI: 10.1016/j.ajhg.2022.03.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 02/28/2022] [Indexed: 11/01/2022] Open
Abstract
Neurodevelopmental disorders are highly heterogenous conditions resulting from abnormalities of brain architecture and/or function. FBXW7 (F-box and WD-repeat-domain-containing 7), a recognized developmental regulator and tumor suppressor, has been shown to regulate cell-cycle progression and cell growth and survival by targeting substrates including CYCLIN E1/2 and NOTCH for degradation via the ubiquitin proteasome system. We used a genotype-first approach and global data-sharing platforms to identify 35 individuals harboring de novo and inherited FBXW7 germline monoallelic chromosomal deletions and nonsense, frameshift, splice-site, and missense variants associated with a neurodevelopmental syndrome. The FBXW7 neurodevelopmental syndrome is distinguished by global developmental delay, borderline to severe intellectual disability, hypotonia, and gastrointestinal issues. Brain imaging detailed variable underlying structural abnormalities affecting the cerebellum, corpus collosum, and white matter. A crystal-structure model of FBXW7 predicted that missense variants were clustered at the substrate-binding surface of the WD40 domain and that these might reduce FBXW7 substrate binding affinity. Expression of recombinant FBXW7 missense variants in cultured cells demonstrated impaired CYCLIN E1 and CYCLIN E2 turnover. Pan-neuronal knockdown of the Drosophila ortholog, archipelago, impaired learning and neuronal function. Collectively, the data presented herein provide compelling evidence of an F-Box protein-related, phenotypically variable neurodevelopmental disorder associated with monoallelic variants in FBXW7.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - John Christodoulou
- Murdoch Children's Research Institute, Melbourne, VIC 3052, Australia; Department of Paediatrics, University of Melbourne, Melbourne, VIC 3052, Australia; Victorian Clinical Genetics Services, Melbourne, VIC 3052, Australia
| | - Tiong Yang Tan
- Murdoch Children's Research Institute, Melbourne, VIC 3052, Australia; Department of Paediatrics, University of Melbourne, Melbourne, VIC 3052, Australia; Victorian Clinical Genetics Services, Melbourne, VIC 3052, Australia.
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39
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Chan ER, Mehlotra RK, Pirani KA, Ratsimbasoa AC, Williams SM, Gaedigk A, Zimmerman PA. CYP2D6 gene resequencing in the Malagasy, a population at the crossroads between Asia and Africa: a pilot study. Pharmacogenomics 2022; 23:315-325. [PMID: 35230160 PMCID: PMC8965795 DOI: 10.2217/pgs-2021-0146] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Background: Plasmodium vivax malaria is endemic in Madagascar, where populations have genetic inheritance from Southeast Asia and East Africa. Primaquine, a drug of choice for vivax malaria, is metabolized principally via CYP2D6. CYP2D6 variation was characterized by locus-specific gene sequencing and was compared with TaqMan™ genotype data. Materials & methods: Long-range PCR amplicons were generated from 96 Malagasy samples and subjected to next-generation sequencing. Results: The authors observed high concordance between TaqMan™-based CYP2D6 genotype calls and the base calls from sequencing. In addition, there are new variants and haplotypes present in the Malagasy. Conclusion: Sequencing unique admixed populations provides more detailed and accurate insights regarding CYP2D6 variability, which may help optimize primaquine treatment across human genetic diversity.
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Affiliation(s)
- E Ricky Chan
- Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, OH 44106, USA.,Population & Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Rajeev K Mehlotra
- Center for Global Health & Diseases, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Karim A Pirani
- Division of Clinical Pharmacology, Toxicology & Therapeutic Innovation, Children's Mercy Kansas City, Kansas City, MO 64108, USA
| | - Arsene C Ratsimbasoa
- University of Fianarantsoa, Fianarantsoa, Madagascar.,CNARP (Centre National d'Application de Recherche Pharmaceutique), Antananarivo, Madagascar
| | - Scott M Williams
- Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, OH 44106, USA.,Population & Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Andrea Gaedigk
- Division of Clinical Pharmacology, Toxicology & Therapeutic Innovation, Children's Mercy Kansas City, Kansas City, MO 64108, USA
| | - Peter A Zimmerman
- Center for Global Health & Diseases, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
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40
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Canpolat N, Liu D, Atayar E, Saygili S, Kara NS, Westfall TA, Ding Q, Brown BJ, Braun TA, Slusarski D, Oguz KK, Ozluk Y, Tuysuz B, Ozturk TT, Sever L, Sezerman OU, Topaloglu R, Caliskan S, Attanasio M, Ozaltin F. A splice site mutation in the TSEN2 causes a new syndrome with craniofacial and central nervous system malformations, and atypical hemolytic uremic syndrome. Clin Genet 2022; 101:346-358. [PMID: 34964109 PMCID: PMC10357464 DOI: 10.1111/cge.14105] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 12/19/2021] [Accepted: 12/26/2021] [Indexed: 07/22/2023]
Abstract
Recessive mutations in the genes encoding the four subunits of the tRNA splicing endonuclease complex (TSEN54, TSEN34, TSEN15, and TSEN2) cause various forms of pontocerebellar hypoplasia, a disorder characterized by hypoplasia of the cerebellum and the pons, microcephaly, dysmorphisms, and other variable clinical features. Here, we report an intronic recessive founder variant in the gene TSEN2 that results in abnormal splicing of the mRNA of this gene, in six individuals from four consanguineous families affected with microcephaly, multiple craniofacial malformations, radiological abnormalities of the central nervous system, and cognitive retardation of variable severity. Remarkably, unlike patients with previously described mutations in the components of the TSEN complex, all the individuals that we report developed atypical hemolytic uremic syndrome (aHUS) with thrombotic microangiopathy, microangiopathic hemolytic anemia, thrombocytopenia, proteinuria, severe hypertension, and end-stage kidney disease (ESKD) early in life. Bulk RNA sequencing of peripheral blood cells of four affected individuals revealed abnormal tRNA transcripts, indicating an alteration of the tRNA biogenesis. Morpholino-mediated skipping of exon 10 of tsen2 in zebrafish produced phenotypes similar to human patients. Thus, we have identified a novel syndrome accompanied by aHUS suggesting the existence of a link between tRNA biology and vascular endothelium homeostasis, which we propose to name with the acronym TRACK syndrome (TSEN2 Related Atypical hemolytic uremic syndrome, Craniofacial malformations, Kidney failure).
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Affiliation(s)
- Nur Canpolat
- Department of Pediatric Nephrology, Istanbul University-Cerrahpasa, Cerrahpasa Faculty of Medicine, Istanbul, Turkey
| | - Dingxiao Liu
- Department of Internal Medicine, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
- Department of Vascular Surgery, Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Emine Atayar
- Nephrogenetics Laboratory, Department of Pediatric Nephrology, Hacettepe University, Faculty of Medicine, Ankara, Turkey
| | - Seha Saygili
- Department of Pediatric Nephrology, Istanbul University-Cerrahpasa, Cerrahpasa Faculty of Medicine, Istanbul, Turkey
| | - Nazli Sila Kara
- Biostatistics and Medical Informatics Program, Faculty of Medicine, Graduate School of Health Sciences, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | | | - Qiong Ding
- Department of Internal Medicine, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Bartley J. Brown
- Center for Bioinformatics and Computational Biology, University of Iowa, Iowa City, Iowa, USA
| | - Terry A. Braun
- Center for Bioinformatics and Computational Biology, University of Iowa, Iowa City, Iowa, USA
| | - Diane Slusarski
- Center for Bioinformatics and Computational Biology, University of Iowa, Iowa City, Iowa, USA
| | - Kader Karli Oguz
- Department of Radiology, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Yasemin Ozluk
- Department of Pathology, Istanbul University Faculty of Medicine, Istanbul, Turkey
| | - Beyhan Tuysuz
- Department of Pediatric Genetics, Istanbul University-Cerrahpasa, Cerrahpasa Faculty of Medicine, Istanbul, Turkey
| | - Tugba Tastemel Ozturk
- Department of Pediatric Nephrology, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Lale Sever
- Department of Pediatric Nephrology, Istanbul University-Cerrahpasa, Cerrahpasa Faculty of Medicine, Istanbul, Turkey
| | - Osman Ugur Sezerman
- Biostatistics and Medical Informatics Program, Faculty of Medicine, Graduate School of Health Sciences, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - Rezan Topaloglu
- Department of Pediatric Nephrology, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Salim Caliskan
- Department of Pediatric Nephrology, Istanbul University-Cerrahpasa, Cerrahpasa Faculty of Medicine, Istanbul, Turkey
| | - Massimo Attanasio
- Department of Internal Medicine, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Fatih Ozaltin
- Nephrogenetics Laboratory, Department of Pediatric Nephrology, Hacettepe University, Faculty of Medicine, Ankara, Turkey
- Department of Pediatric Nephrology, Hacettepe University Faculty of Medicine, Ankara, Turkey
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41
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Chan NCN, Wong THY, Cheng KCK, Chan NPH, Ng MHL. An Evaluation for the Causes of Reduced Hb A 2 and the Molecular Characterization of HBD Variants in Hong Kong. Hemoglobin 2022; 45:387-391. [PMID: 35168445 DOI: 10.1080/03630269.2021.1965619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Prenatal screening of β-thalassemia (β-thal) carriers is based on the hallmark phenotype of microcytosis and raised Hb A2. The unanticipated birth of β-thal major (β-TM) offspring to β-thal carriers who were misdiagnosed during prenatal screening have been reported. A subset of these resulted from the masked phenotype due to the coinheritance of HBD variants. In a broader sense, the causes of reduced Hb A2 in thalassemia screening, the prevalence and spectrum of HBD variants in Hong Kong remain to be characterized. Over a 13-month period, a total of 2982 samples were referred for thalassemia screening. Surplus samples with reduced Hb A2 levels (2.0%) were evaluated. HBD variations were assessed by direct sequencing. Sixty-six samples were tested. Hb H disease, HBD variants, α-thalassemia (α-thal) trait and iron deficiency were detected in 40 (60.6%), 12 (18.2%), eight (12.1%) and seven (10.6%) samples, respectively. Seven samples carried more than one of the mentioned conditions. The cause remained elusive in seven samples. Thirteen HBD variants were detected and two were recurrent, including HBD: c.-127T>C [-77 (T>C)] and HBD: c.314G>A (Hb Chori-Burnaby). A novel nonsense variant HBD: c.262C>T [codon 87 (C>T)] was detected in cis with HBD: c.-127T>C. Overall, the prevalence of HBD variants was 0.4%. This study advanced our understanding of the causes of reduced Hb A2 in clinical practice and identified hereditary disorders of α- and δ-globin genes as the prevailing causes. It established the landscape of HBD variations in our locality and highlighted the pitfall of phenotypic screening of β-thal carriers.
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Affiliation(s)
- Nelson C N Chan
- Department of Pathology, Hong Kong Children's Hospital, Kowloon Bay, Hong Kong
| | - Terry H Y Wong
- Department of Anatomical and Cellular Pathology, Prince of Wales Hospital, Shatin, New Territories, Hong Kong
| | - Kelvin C K Cheng
- Department of Anatomical and Cellular Pathology, Prince of Wales Hospital, Shatin, New Territories, Hong Kong
| | - Natalie P H Chan
- Department of Anatomical and Cellular Pathology, Prince of Wales Hospital, Shatin, New Territories, Hong Kong
| | - Margaret H L Ng
- Hematology, Genetics and Genomics Laboratory, Prince of Wales Hospital, Shatin, New Territories, affiliated to The Chinese University of Hong Kong, Hong Kong
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42
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Kobayashi A, Ohtaka R, Toki T, Hara J, Muramatsu H, Kanezaki R, Takahashi Y, Sato T, Kamio T, Kudo K, Sasaki S, Yoshida T, Utsugisawa T, Kanno H, Yoshida K, Nannya Y, Takahashi Y, Kojima S, Miyano S, Ogawa S, Terui K, Ito E. Dyserythropoietic anaemia with an intronic GATA1 splicing mutation in patients suspected to have Diamond-Blackfan anaemia. EJHAEM 2022; 3:163-167. [PMID: 35846220 PMCID: PMC9175706 DOI: 10.1002/jha2.374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 12/08/2021] [Accepted: 12/10/2021] [Indexed: 11/30/2022]
Abstract
Diamond-Blackfan anaemia (DBA) shares clinical features with two recently reported sporadic cases of dyserythropoietic anaemia with a cryptic GATA1 splicing mutation (c.871-24 C>T). We hypothesized that some patients clinically diagnosed with DBA but whose causative genes were unknown may carry the intronic GATA1 mutation. Here, we examined 79 patients in our DBA cohort, who had no detectable causative genes. The intronic GATA1 mutation was identified in two male patients sharing the same pedigree that included multiple cases with anaemia. Cosegregation of this mutation and disease in multiple family members provide evidence to support the pathogenicity of the intronic GATA1 mutation.
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Affiliation(s)
- Akie Kobayashi
- Department of PediatricsHirosaki University Graduate School of MedicineHirosakiJapan
| | - Ryusei Ohtaka
- Department of PediatricsHirosaki University Graduate School of MedicineHirosakiJapan
| | - Tsutomu Toki
- Department of PediatricsHirosaki University Graduate School of MedicineHirosakiJapan
| | - Junichi Hara
- Department of Pediatric Hematology and OncologyOsaka City General HospitalOsakaJapan
| | - Hideki Muramatsu
- Department of PediatricsNagoya University Graduate School of MedicineNagoyaJapan
| | - Rika Kanezaki
- Department of PediatricsHirosaki University Graduate School of MedicineHirosakiJapan
| | - Yuka Takahashi
- Department of PediatricsHirosaki University Graduate School of MedicineHirosakiJapan
| | - Tomohiko Sato
- Department of PediatricsHirosaki University Graduate School of MedicineHirosakiJapan
| | - Takuya Kamio
- Department of PediatricsHirosaki University Graduate School of MedicineHirosakiJapan
| | - Ko Kudo
- Department of PediatricsHirosaki University Graduate School of MedicineHirosakiJapan
| | - Shinya Sasaki
- Department of PediatricsHirosaki University Graduate School of MedicineHirosakiJapan
| | - Taro Yoshida
- Department of PediatricsNagoya University Graduate School of MedicineNagoyaJapan
| | - Taiju Utsugisawa
- Department of Transfusion Medicine and Cell ProcessingFaculty of MedicineTokyo Women's Medical UniversityTokyoJapan
| | - Hitoshi Kanno
- Department of Transfusion Medicine and Cell ProcessingFaculty of MedicineTokyo Women's Medical UniversityTokyoJapan
| | - Kenichi Yoshida
- Department of Pathology and Tumor BiologyGraduate School of MedicineKyoto UniversityKyotoJapan
| | - Yasuhito Nannya
- Department of Pathology and Tumor BiologyGraduate School of MedicineKyoto UniversityKyotoJapan
- Division of Hematopoietic Disease ControlInstitute of Medical ScienceThe University of TokyoTokyoJapan
| | - Yoshiyuki Takahashi
- Department of PediatricsNagoya University Graduate School of MedicineNagoyaJapan
| | - Seiji Kojima
- Department of PediatricsNagoya University Graduate School of MedicineNagoyaJapan
| | - Satoru Miyano
- M&D Data Science CenterTokyo Medical and Dental UniversityTokyoJapan
| | - Seishi Ogawa
- Department of Pathology and Tumor BiologyGraduate School of MedicineKyoto UniversityKyotoJapan
- Department of MedicineCenter for Hematology and Regenerative MedicineKarolinska InstituteStockholmSweden
| | - Kiminori Terui
- Department of PediatricsHirosaki University Graduate School of MedicineHirosakiJapan
| | - Etsuro Ito
- Department of PediatricsHirosaki University Graduate School of MedicineHirosakiJapan
- Department of Community MedicineHirosaki University Graduate School of MedicineHirosakiJapan
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43
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White LA, Bisom TC, Grimes HL, Hayashi M, Lanchy JM, Lodmell JS. Tra2beta-Dependent Regulation of RIO Kinase 3 Splicing During Rift Valley Fever Virus Infection Underscores the Links Between Alternative Splicing and Innate Antiviral Immunity. Front Cell Infect Microbiol 2022; 11:799024. [PMID: 35127560 PMCID: PMC8807687 DOI: 10.3389/fcimb.2021.799024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 12/28/2021] [Indexed: 12/14/2022] Open
Abstract
Rift Valley fever virus (RVFV) is an emerging pathogen that has potential to cause severe disease in humans and domestic livestock. Propagation of RVFV strain MP-12 is negatively impacted by the actions of RIOK3, a protein involved in the cellular immune response to viral infection. During RVFV infection, RIOK3 mRNA is alternatively spliced to produce an isoform that correlates with the inhibition of interferon β signaling. Here, we identify splicing factor TRA2-β (also known as TRA2beta and hTRA2-β) as a key regulator governing the relative abundance of RIOK3 splicing isoforms. Using RT-PCR and minigenes, we determined that TRA2-β interaction with RIOK3 pre-mRNA was necessary for constitutive splicing of RIOK3 mRNA, and conversely, lack of TRA2-β engagement led to increased alternative splicing. Expression of TRA2-β was found to be necessary for RIOK3's antiviral effect against RVFV. Intriguingly, TRA2-β mRNA is also alternatively spliced during RVFV infection, leading to a decrease in cellular TRA2-β protein levels. These results suggest that splicing modulation serves as an immune evasion strategy by RVFV and/or is a cellular mechanism to prevent excessive immune response. Furthermore, the results suggest that TRA2-β can act as a key regulator of additional steps of the innate immune response to viral infection.
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Affiliation(s)
- Luke Adam White
- Division of Biological Sciences, University of Montana, Missoula, MT, United States
| | - Thomas C. Bisom
- Department of Chemistry and Biochemistry, University of Montana, Missoula, MT, United States
| | - Hunter L. Grimes
- Division of Biological Sciences, University of Montana, Missoula, MT, United States
| | - Miyuki Hayashi
- Department of Chemistry and Biochemistry, University of Montana, Missoula, MT, United States
| | - Jean-Marc Lanchy
- Division of Biological Sciences, University of Montana, Missoula, MT, United States
| | - J. Stephen Lodmell
- Division of Biological Sciences, University of Montana, Missoula, MT, United States,Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, MT, United States,*Correspondence: J. Stephen Lodmell,
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44
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Han Q, Liu S, Cui Z, Wang Q, Ma T, Jiang L, Li X, Dai G. Case Report and Literature Review: Diagnosis, Tailored Genetic Counseling and Cancer Prevention for a Locally Advanced dMMR/MSI-H/TMB-H Lung Cancer Patient With Concurrent Lynch Syndrome Mediated by a Rare PMS2 Splicing Variant (c.1144+1G>A). Front Genet 2022; 12:799807. [PMID: 35116055 PMCID: PMC8804326 DOI: 10.3389/fgene.2021.799807] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 12/20/2021] [Indexed: 11/24/2022] Open
Abstract
Lynch syndrome (LS) is a cancer-predisposing genetic disease mediated by pathogenic mutations in DNA mismatch repair (MMR) genes MLH1, MSH2, MSH6, and PMS2. Accumulating evidence demonstrates that there is significant biological heterogeneity across MMR genes. Compared to MLH1 and MSH2, PMS2 variant carriers have a much lower risk for LS-related cancers. Tumors in MLH1 and MSH2 variant carriers often display MMR deficiency (dMMR) and/or high microsatellite instability (MSI-H), two predictive biomarkers for immunotherapy efficacy. However, tumors in PMS2 variant carriers are largely microsatellite stable (MSS) instead of MSI. Therefore, the optimal management of cancer patients with LS requires the integration of disease stage, MMR gene penetrance, dMMR/MSI status, and tumor mutational burden (TMB). In this work, we presented a locally advanced lung cancer patient with dMMR/MSI-H/TMB-H tumor and selective loss of PMS2 by immunohistochemistry. Germline testing revealed a rare PMS2 splicing variant (c.1144+1G>A) in the proband and his healthy daughter. The diagnosis of LS was made based on genetic analysis of this variant and literature review. Given the incomplete penetrance of PMS2, the proband and the carrier received tailored genetic counseling. To reduce cancer risk, the proband received four cycles of nivolumab plus chemotherapy and achieved a disease-free survival of sixteen months.
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Affiliation(s)
- Quanli Han
- Department of Medical Oncology, the First Medical Center of Chinese People’s Liberation Army (PLA) General Hospital, Beijing, China
| | - Si Liu
- Genetron Health (Beijing) Technology, Co. Ltd., Beijing, China
| | - Zhi Cui
- Department of Medical Oncology, the First Medical Center of Chinese People’s Liberation Army (PLA) General Hospital, Beijing, China
| | - Qi Wang
- Department of Medical Oncology, the First Medical Center of Chinese People’s Liberation Army (PLA) General Hospital, Beijing, China
| | - Tonghui Ma
- Genetron Health (Beijing) Technology, Co. Ltd., Beijing, China
| | - Liwen Jiang
- Genetron Health (Beijing) Technology, Co. Ltd., Beijing, China
| | - Xiaomo Li
- Genetron Health (Beijing) Technology, Co. Ltd., Beijing, China
- *Correspondence: Guanghai Dai, ; Xiaomo Li,
| | - Guanghai Dai
- Department of Medical Oncology, the First Medical Center of Chinese People’s Liberation Army (PLA) General Hospital, Beijing, China
- *Correspondence: Guanghai Dai, ; Xiaomo Li,
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45
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Truong DJJ, Armbrust N, Geilenkeuser J, Lederer EM, Santl TH, Beyer M, Ittermann S, Steinmaßl E, Dyka M, Raffl G, Phlairaharn T, Greisle T, Živanić M, Grosch M, Drukker M, Westmeyer GG. Intron-encoded cistronic transcripts for minimally invasive monitoring of coding and non-coding RNAs. Nat Cell Biol 2022; 24:1666-1676. [PMID: 36344775 PMCID: PMC9643161 DOI: 10.1038/s41556-022-00998-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Accepted: 08/19/2022] [Indexed: 11/09/2022]
Abstract
Despite their fundamental role in assessing (patho)physiological cell states, conventional gene reporters can follow gene expression but leave scars on the proteins or substantially alter the mature messenger RNA. Multi-time-point measurements of non-coding RNAs are currently impossible without modifying their nucleotide sequence, which can alter their native function, half-life and localization. Thus, we developed the intron-encoded scarless programmable extranuclear cistronic transcript (INSPECT) as a minimally invasive transcriptional reporter embedded within an intron of a gene of interest. Post-transcriptional excision of INSPECT results in the mature endogenous RNA without sequence alterations and an additional engineered transcript that leaves the nucleus by hijacking the nuclear export machinery for subsequent translation into a reporter or effector protein. We showcase its use in monitoring interleukin-2 (IL2) after T cell activation and tracking the transcriptional dynamics of the long non-coding RNA (lncRNA) NEAT1 during CRISPR interference-mediated perturbation. INSPECT is a method for monitoring gene transcription without altering the mature lncRNA or messenger RNA of the target of interest.
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Affiliation(s)
- Dong-Jiunn Jeffery Truong
- grid.4567.00000 0004 0483 2525Institute for Synthetic Biomedicine, Helmholtz Zentrum München, Neuherberg, Germany ,grid.6936.a0000000123222966Department of Chemistry and TUM School of Medicine, Technical University of Munich, Munich, Germany
| | - Niklas Armbrust
- grid.4567.00000 0004 0483 2525Institute for Synthetic Biomedicine, Helmholtz Zentrum München, Neuherberg, Germany ,grid.6936.a0000000123222966Department of Chemistry and TUM School of Medicine, Technical University of Munich, Munich, Germany
| | - Julian Geilenkeuser
- grid.4567.00000 0004 0483 2525Institute for Synthetic Biomedicine, Helmholtz Zentrum München, Neuherberg, Germany ,grid.6936.a0000000123222966Department of Chemistry and TUM School of Medicine, Technical University of Munich, Munich, Germany
| | - Eva-Maria Lederer
- grid.4567.00000 0004 0483 2525Institute for Synthetic Biomedicine, Helmholtz Zentrum München, Neuherberg, Germany ,grid.6936.a0000000123222966Department of Chemistry and TUM School of Medicine, Technical University of Munich, Munich, Germany
| | - Tobias Heinrich Santl
- grid.4567.00000 0004 0483 2525Institute for Synthetic Biomedicine, Helmholtz Zentrum München, Neuherberg, Germany ,grid.6936.a0000000123222966Department of Chemistry and TUM School of Medicine, Technical University of Munich, Munich, Germany
| | - Maren Beyer
- grid.4567.00000 0004 0483 2525Institute for Synthetic Biomedicine, Helmholtz Zentrum München, Neuherberg, Germany ,grid.6936.a0000000123222966Department of Chemistry and TUM School of Medicine, Technical University of Munich, Munich, Germany
| | - Sebastian Ittermann
- grid.4567.00000 0004 0483 2525Institute of Stem Cell Research, Helmholtz Zentrum München, Neuherberg, Germany
| | - Emily Steinmaßl
- grid.4567.00000 0004 0483 2525Institute for Synthetic Biomedicine, Helmholtz Zentrum München, Neuherberg, Germany ,grid.6936.a0000000123222966Department of Chemistry and TUM School of Medicine, Technical University of Munich, Munich, Germany
| | - Mariya Dyka
- grid.4567.00000 0004 0483 2525Institute for Synthetic Biomedicine, Helmholtz Zentrum München, Neuherberg, Germany ,grid.6936.a0000000123222966Department of Chemistry and TUM School of Medicine, Technical University of Munich, Munich, Germany
| | - Gerald Raffl
- grid.4567.00000 0004 0483 2525Institute for Synthetic Biomedicine, Helmholtz Zentrum München, Neuherberg, Germany ,grid.6936.a0000000123222966Department of Chemistry and TUM School of Medicine, Technical University of Munich, Munich, Germany
| | - Teeradon Phlairaharn
- grid.4567.00000 0004 0483 2525Institute for Synthetic Biomedicine, Helmholtz Zentrum München, Neuherberg, Germany ,grid.6936.a0000000123222966Department of Chemistry and TUM School of Medicine, Technical University of Munich, Munich, Germany
| | - Tobias Greisle
- grid.4567.00000 0004 0483 2525Institute of Stem Cell Research, Helmholtz Zentrum München, Neuherberg, Germany
| | - Milica Živanić
- grid.4567.00000 0004 0483 2525Institute for Synthetic Biomedicine, Helmholtz Zentrum München, Neuherberg, Germany ,grid.6936.a0000000123222966Department of Chemistry and TUM School of Medicine, Technical University of Munich, Munich, Germany
| | - Markus Grosch
- grid.4567.00000 0004 0483 2525Institute of Stem Cell Research, Helmholtz Zentrum München, Neuherberg, Germany
| | - Micha Drukker
- grid.4567.00000 0004 0483 2525Institute of Stem Cell Research, Helmholtz Zentrum München, Neuherberg, Germany
| | - Gil Gregor Westmeyer
- grid.4567.00000 0004 0483 2525Institute for Synthetic Biomedicine, Helmholtz Zentrum München, Neuherberg, Germany ,grid.6936.a0000000123222966Department of Chemistry and TUM School of Medicine, Technical University of Munich, Munich, Germany
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Lado S, Futas J, Plasil M, Loney T, Weidinger P, Camp JV, Kolodziejek J, Kannan DO, Horin P, Nowotny N, Burger PA. Crimean-Congo Hemorrhagic Fever Virus Past Infections Are Associated with Two Innate Immune Response Candidate Genes in Dromedaries. Cells 2021; 11:8. [PMID: 35011568 PMCID: PMC8750074 DOI: 10.3390/cells11010008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 12/15/2021] [Indexed: 12/16/2022] Open
Abstract
Dromedaries are an important livestock, used as beasts of burden and for meat and milk production. However, they can act as an intermediate source or vector for transmitting zoonotic viruses to humans, such as the Middle East respiratory syndrome coronavirus (MERS-CoV) or Crimean-Congo hemorrhagic fever virus (CCHFV). After several outbreaks of CCHFV in the Arabian Peninsula, recent studies have demonstrated that CCHFV is endemic in dromedaries and camel ticks in the United Arab Emirates (UAE). There is no apparent disease in dromedaries after the bite of infected ticks; in contrast, fever, myalgia, lymphadenopathy, and petechial hemorrhaging are common symptoms in humans, with a case fatality ratio of up to 40%. We used the in-solution hybridization capture of 100 annotated immune genes to genotype 121 dromedaries from the UAE tested for seropositivity to CCHFV. Through univariate linear regression analysis, we identified two candidate genes belonging to the innate immune system: FCAR and CLEC2B. These genes have important functions in the host defense against viral infections and in stimulating natural killer cells, respectively. This study opens doors for future research into immune defense mechanisms in an enzootic host against an important zoonotic disease.
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Affiliation(s)
- Sara Lado
- Research Institute of Wildlife Ecology, Department of Interdisciplinary Life Sciences, University of Veterinary Medicine Vienna, 1160 Vienna, Austria;
- Division of Infectious Diseases and Tropical Medicine, Department of Medicine I, Medical University of Vienna, 1090 Vienna, Austria
| | - Jan Futas
- Department of Animal Genetics, University of Veterinary Sciences Brno, 61242 Brno, Czech Republic; (J.F.); (M.P.); (P.H.)
- RG Animal Immunogenomics, CEITEC VETUNI Brno, 61242 Brno, Czech Republic
| | - Martin Plasil
- Department of Animal Genetics, University of Veterinary Sciences Brno, 61242 Brno, Czech Republic; (J.F.); (M.P.); (P.H.)
- RG Animal Immunogenomics, CEITEC VETUNI Brno, 61242 Brno, Czech Republic
| | - Tom Loney
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai 505055, United Arab Emirates; (T.L.); (N.N.)
| | - Pia Weidinger
- Viral Zoonoses, Emerging and Vector-Borne Infections Group, Institute of Virology, University of Veterinary Medicine Vienna, 1210 Vienna, Austria; (P.W.); (J.V.C.); (J.K.)
| | - Jeremy V. Camp
- Viral Zoonoses, Emerging and Vector-Borne Infections Group, Institute of Virology, University of Veterinary Medicine Vienna, 1210 Vienna, Austria; (P.W.); (J.V.C.); (J.K.)
- Center for Virology, Medical University of Vienna, 1090 Vienna, Austria
| | - Jolanta Kolodziejek
- Viral Zoonoses, Emerging and Vector-Borne Infections Group, Institute of Virology, University of Veterinary Medicine Vienna, 1210 Vienna, Austria; (P.W.); (J.V.C.); (J.K.)
| | | | - Petr Horin
- Department of Animal Genetics, University of Veterinary Sciences Brno, 61242 Brno, Czech Republic; (J.F.); (M.P.); (P.H.)
- RG Animal Immunogenomics, CEITEC VETUNI Brno, 61242 Brno, Czech Republic
| | - Norbert Nowotny
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai 505055, United Arab Emirates; (T.L.); (N.N.)
- Viral Zoonoses, Emerging and Vector-Borne Infections Group, Institute of Virology, University of Veterinary Medicine Vienna, 1210 Vienna, Austria; (P.W.); (J.V.C.); (J.K.)
| | - Pamela A. Burger
- Research Institute of Wildlife Ecology, Department of Interdisciplinary Life Sciences, University of Veterinary Medicine Vienna, 1160 Vienna, Austria;
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47
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Hake L, Süßmuth K, Komlosi K, Kopp J, Drerup C, Metze D, Traupe H, Hausser I, Eckl KM, Hennies HC, Fischer J, Oji V. Quality of life and clinical characteristics of self-improving congenital ichthyosis within the disease spectrum of autosomal recessive congenital ichthyosis. J Eur Acad Dermatol Venereol 2021; 36:582-591. [PMID: 34908195 DOI: 10.1111/jdv.17873] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 11/10/2021] [Indexed: 11/29/2022]
Abstract
BACKGROUND Autosomal recessive congenital ichthyosis (ARCI) is a heterogeneous group of ichthyoses presenting at birth. Self-improving congenital ichthyosis (SICI) is a subtype of ARCI and is diagnosed when skin condition improves remarkably (within years) after birth. So far, there is sparse data on SICI and quality of life (QoL) in this ARCI subtype. This study aims to further delineate the clinical spectrum of SICI as a rather unique subtype of ARCI. OBJECTIVES This prospective study included 78 patients (median age: 15 years) with ARCI who were subdivided in SICI (n=18) and non-SICI patients (nSICI, n=60) by their ARCI phenotype. METHODS Quality of life (QoL) was assessed using the (Children's) Dermatology Life Quality Index. Statistical analysis was performed with Chi-square- and t-tests. RESULTS The genetically confirmed SICI patients presented causative mutations in the following genes: ALOXE3 (8/16; 50.0%), ALOX12B (6/16; 37.5%), PNPLA1 (1/16; 6.3%) and CYP4F22 (1/16; 6.3%). Hypo-/anhidrosis and insufficient Vitamin D levels (< 30 ng/ml) were often seen in SICI patients. Brachydactyly (a shortening of the 4th and 5th finger) was statistically more frequent in SICI (p=0.023) than nSICI patients. A kink of the ear's helix was seen in half of the SICI patients and tends to occur more frequently in patients with ALOX12B mutations (p=0.005). QoL was less impaired in patients under the age of 16, regardless of ARCI type. CONCLUSIONS SICI is an underestimated, milder clinical variant of ARCI including distinct features such as brachydactyly and kinking of the ears. Clinical experts should be aware of these features when seeing neonates with a collodion membrane. SICI patients should be regularly checked for clinical parameters such as hypo-/anhidrosis or vitamin D levels and monitored for changes in quality of life.
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Affiliation(s)
- L Hake
- Department of Dermatology, Elbe Klinikum Buxtehude, Buxtehude, Germany
| | - K Süßmuth
- Department of Dermatology, University Hospital Münster, Münster, Germany
| | - K Komlosi
- Institute of Human Genetics, Medical Center, University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - J Kopp
- Institute of Human Genetics, Medical Center, University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - C Drerup
- Department of Dermatology, University Hospital Münster, Münster, Germany
| | - D Metze
- Department of Dermatology, University Hospital Münster, Münster, Germany
| | - H Traupe
- Department of Dermatology, University Hospital Münster, Münster, Germany
| | - I Hausser
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - K M Eckl
- Department of Biological and Geographical Sciences, University of Huddersfield, Huddersfield, United Kingdom.,Division of Human Genetics, Medical University of Innsbruck, Innsbruck, Austria.,Department of Biology, Edge Hill University, Ormskirk, UK
| | - H C Hennies
- Department of Biological and Geographical Sciences, University of Huddersfield, Huddersfield, United Kingdom.,Cologne Center for Genomics, University Hospital Cologne, Cologne, Germany
| | - J Fischer
- Institute of Human Genetics, Medical Center, University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - V Oji
- Department of Dermatology, University Hospital Münster, Münster, Germany
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Patel CK, Broadgate S, Shalaby A, Yu J, Nemeth AH, Downes SM, Halford S. Whole genome sequencing in a Knobloch syndrome family confirms the molecular diagnosis. Ophthalmic Genet 2021; 43:201-209. [PMID: 34751625 DOI: 10.1080/13816810.2021.1998554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
BACKGROUND To establish the molecular diagnosis in two brothers presenting with the ocular features of Knobloch Syndrome using whole genome sequencing (WGS). METHODS Clinical examination and ophthalmological phenotyping were completed under general anaesthesia. DNA samples were tested on a targeted retinal dystrophy next-generation sequencing panel. Subsequently, WGS was performed to identify additional variants. RESULTS Clinical examination confirmed the diagnosis of Knobloch Syndrome. Targeted sequencing identified a novel heterozygous frameshift pathogenic variant in COL18A1, c.2864dupC; p.(Gly956ArgfsX20), inherited from their mother. A second paternally inherited heterozygous missense variant was identified in both brothers, c.5014 G > A; p.(Asp1672Asn), which was initially considered to have too high frequency to be pathogenic (MAF 8.8%). This led to an in-depth analysis of the COL18A1 locus using WGS data, which confirmed that Asp1672Asn is a likely pathogenic hypomorphic allele. CONCLUSION To date, all confirmed genetic diagnoses of Knobloch syndrome are attributable to variants in COL18A1. The family described here has a heterozygous novel loss of function variant. Detailed analysis of WGS data combined with family segregation studies concluded that although Asp1672Asn has a high population frequency, it is the most likely second pathogenic variant in our family. This supports the hypothesis that this is a hypomorphic allele, which, in combination with a loss of function pathogenic variant, leads to Knobloch syndrome.To our knowledge, this is the first time that WGS has been used to confirm a molecular diagnosis of Knobloch syndrome in this way and has provided further insight into the molecular mechanisms in this rare disorder.
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Affiliation(s)
| | - Suzanne Broadgate
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Ahmed Shalaby
- Oxford Eye Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, UK.,Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Jing Yu
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Andrea H Nemeth
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK.,Oxford Centre for Genomic Medicine, Oxford, UK
| | - Susan M Downes
- Oxford Eye Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, UK.,Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Stephanie Halford
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
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Diagnostic Yield of Targeted Hearing Loss Gene Panel Sequencing in a Large German Cohort With a Balanced Age Distribution from a Single Diagnostic Center: An Eight-year Study. Ear Hear 2021; 43:1049-1066. [PMID: 34753855 PMCID: PMC9007094 DOI: 10.1097/aud.0000000000001159] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Objectives: Hereditary hearing loss exhibits high degrees of genetic and clinical heterogeneity. To elucidate the population-specific and age-related genetic and clinical spectra of hereditary hearing loss, we investigated the sequencing data of causally associated hearing loss genes in a large cohort of hearing-impaired probands with a balanced age distribution from a single center in Southwest Germany. Design: Genetic testing was applied to 305 hearing-impaired probands/families with a suspected genetic hearing loss etiology and a balanced age distribution over a period of 8 years (2011–2018). These individuals were representative of the regional population according to age and sex distributions. The genetic testing workflow consisted of single-gene screening (n = 21) and custom-designed hearing loss gene panel sequencing (n = 284) targeting known nonsyndromic and syndromic hearing loss genes in a diagnostic setup. Retrospective reanalysis of sequencing data was conducted by applying the current American College of Medical Genetics and Genomics/Association for Molecular Pathology guidelines. Results: A genetic diagnosis was established for 75 (25%) of the probands that involved 75 causal variants in 35 genes, including 16 novel causal variants and 9 medically significant variant reclassifications. Nearly half of the solved cases (47%; n = 35) were related to variants in the five most frequently affected genes: GJB2 (25%), MYO15A, WFS1, SLC26A4, and COL11A1 (all 5%). Nearly one-quarter of the cases (23%; n = 17) were associated with variants in seven additional genes (TMPRSS3, COL4A3, LOXHD1, EDNRB, MYO6, TECTA, and USH2A). The remaining one-third of single cases (33%; n = 25) were linked to variants in 25 distinct genes. Diagnostic rates and gene distribution were highly dependent on phenotypic characteristics. A positive family history of autosomal-recessive inheritance in combination with early onset and higher grades of hearing loss significantly increased the solve rate up to 60%, while late onset and lower grades of hearing loss yielded significantly fewer diagnoses. Regarding genetic diagnoses, autosomal-dominant genes accounted for 37%, autosomal-recessive genes for 60%, and X-linked genes for 3% of the solved cases. Syndromic/nonsyndromic hearing loss mimic genes were affected in 27% of the genetic diagnoses. Conclusions: The genetic epidemiology of the largest German cohort subjected to comprehensive targeted sequencing for hereditary hearing loss to date revealed broad causal gene and variant spectra in this population. Targeted hearing loss gene panel analysis proved to be an effective tool for ensuring an appropriate diagnostic yield in a routine clinical setting including the identification of novel variants and medically significant reclassifications. Solve rates were highly sensitive to phenotypic characteristics. The unique population-adapted and balanced age distribution of the cohort favoring late hearing loss onset uncovered a markedly large contribution of autosomal-dominant genes to the diagnoses which may be a representative for other age balanced cohorts in other populations.
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Alicandri E, Covino S, Sebastiani B, Paolacci AR, Badiani M, Manti F, Bonsignore CP, Sorgonà A, Ciaffi M. Diterpene Resin Acids and Olefins in Calabrian Pine ( Pinus nigra subsp. laricio (Poiret) Maire) Oleoresin: GC-MS Profiling of Major Diterpenoids in Different Plant Organs, Molecular Identification and Expression Analysis of Diterpene Synthase Genes. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10112391. [PMID: 34834754 PMCID: PMC8622628 DOI: 10.3390/plants10112391] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 10/28/2021] [Accepted: 11/04/2021] [Indexed: 05/04/2023]
Abstract
A quali-quantitative analysis of diterpenoid composition in tissues obtained from different organs of Pinus nigra subsp. laricio (Poiret) Maire (Calabrian pine) was carried out. Diterpene resin acids were the most abundant diterpenoids across all the examined tissues. The same nine diterpene resin acids were always found, with the abietane type prevailing on the pimarane type, although their quantitative distribution was found to be remarkably tissue-specific. The scrutiny of the available literature revealed species specificity as well. A phylogeny-based approach allowed us to isolate four cDNAs coding for diterpene synthases in Calabrian pine, each of which belonging to one of the four groups into which the d3 clade of the plants' terpene synthases family can be divided. The deduced amino acid sequences allowed predicting that both monofunctional and bifunctional diterpene synthases are involved in the biosynthesis of diterpene resin acids in Calabrian pine. Transcript profiling revealed differential expression across the different tissues and was found to be consistent with the corresponding diterpenoid profiles. The isolation of the complete genomic sequences and the determination of their exon/intron structures allowed us to place the diterpene synthase genes from Calabrian pine on the background of current ideas on the functional evolution of diterpene synthases in Gymnosperms.
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Affiliation(s)
- Enrica Alicandri
- Dipartimento di Agraria, Università Mediterranea di Reggio Calabria, Loc. Feo di Vito, 89129 Reggio Calabria, Italy; (E.A.); (M.B.); (A.S.)
| | - Stefano Covino
- Dipartimento per la Innovazione nei Sistemi Biologici, Agroalimentari e Forestali, Università della Tuscia, Via S. Camillo De Lellis, s.n.c., 01100 Viterbo, Italy; (S.C.); (A.R.P.)
| | - Bartolomeo Sebastiani
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, Via Elce di Sotto 8, 06123 Perugia, Italy;
| | - Anna Rita Paolacci
- Dipartimento per la Innovazione nei Sistemi Biologici, Agroalimentari e Forestali, Università della Tuscia, Via S. Camillo De Lellis, s.n.c., 01100 Viterbo, Italy; (S.C.); (A.R.P.)
| | - Maurizio Badiani
- Dipartimento di Agraria, Università Mediterranea di Reggio Calabria, Loc. Feo di Vito, 89129 Reggio Calabria, Italy; (E.A.); (M.B.); (A.S.)
| | - Francesco Manti
- Dipartimento di Patrimonio, Architettura e Urbanistica, Università Mediterranea di Reggio Calabria, Salita Melissari, 89124 Reggio Calabria, Italy; (F.M.); (C.P.B.)
| | - Carmelo Peter Bonsignore
- Dipartimento di Patrimonio, Architettura e Urbanistica, Università Mediterranea di Reggio Calabria, Salita Melissari, 89124 Reggio Calabria, Italy; (F.M.); (C.P.B.)
| | - Agostino Sorgonà
- Dipartimento di Agraria, Università Mediterranea di Reggio Calabria, Loc. Feo di Vito, 89129 Reggio Calabria, Italy; (E.A.); (M.B.); (A.S.)
| | - Mario Ciaffi
- Dipartimento per la Innovazione nei Sistemi Biologici, Agroalimentari e Forestali, Università della Tuscia, Via S. Camillo De Lellis, s.n.c., 01100 Viterbo, Italy; (S.C.); (A.R.P.)
- Correspondence: ; Tel.: +39-0761-357-424; Fax: +39-0761-357-389
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