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Rafiullah R, Albalawi AM, Alaradi SR, Alluqmani M, Mushtaq M, Wali A, Basit S. An expansion of phenotype: novel homozygous variant in the MED17 identified in patients with progressive microcephaly and global developmental delay. J Neurogenet 2022; 36:108-114. [PMID: 36508181 DOI: 10.1080/01677063.2022.2149748] [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: 12/14/2022]
Abstract
Global developmental delay (GDD) is a lifelong disability that affects 1-3% of the population around the globe. It is phenotypically variable and highly heterogeneous in terms of the underlying genetics. Patients with GDD are intellectually disabled (ID) manifesting cognitive impairment and deficient adaptive behavior. Here, we investigated a two-looped consanguineous family segregating severe ID, seizure, and progressive microcephaly. Magnetic resonance imaging (MRI) of the brain showed mild brain atrophy and myelination defect. Whole exome sequencing (WES) was performed on the DNA samples of two patients and a novel homozygous missense variant (Chr11:g0.93528085; NM_004268.5_c.871T > C; p. Trp291Gly) was identified in the MED17 gene. Sanger sequencing revealed that the identified variant is heterozygous in both parents and healthy siblings. This variant is conserved among different species, causes a non-conserved amino acid change, and is predicted deleterious by various in silico tools. The variant is not reported in population variant databases. MED17 (OMIM: 613668) encodes for the mediator of RNA polymerase II transcription complex subunit 17. Structure modeling of MED17 protein revealed that Trp291 is involved in different inter-helical interactions, providing structural stability. Replacement of Trp291Gly, a less hydrophobic amino acid loses the inter-helical interaction leading to a perturb variant of MED17 protein.
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Affiliation(s)
- Rafiullah Rafiullah
- Department of Biotechnology, Faculty of Life Sciences & Informatics, BUITEMS, Quetta, Pakistan
| | - Alia M Albalawi
- Center for Genetics and Inherited Diseases, Taibah University, Madinah, Saudi Arabia
| | - Sultan R Alaradi
- Department of Laboratory and Blood Bank, Alwajh General Hospital, Ministry of Health, Alwajh, Saudi Arabia
| | - Majed Alluqmani
- College of Medicine, Taibah University, Madinah, Saudi Arabia
| | - Muhammad Mushtaq
- Department of Biotechnology, Faculty of Life Sciences & Informatics, BUITEMS, Quetta, Pakistan
| | - Abdul Wali
- Department of Biotechnology, Faculty of Life Sciences & Informatics, BUITEMS, Quetta, Pakistan
| | - Sulman Basit
- Center for Genetics and Inherited Diseases, Taibah University, Madinah, Saudi Arabia.,Department of Biochemistry and Molecular Medicine, College of Medicine, Taibah University, Madinah, Saudi Arabia
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152
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Dixon PH, Levine AP, Cebola I, Chan MMY, Amin AS, Aich A, Mozere M, Maude H, Mitchell AL, Zhang J, Chambers J, Syngelaki A, Donnelly J, Cooley S, Geary M, Nicolaides K, Thorsell M, Hague WM, Estiu MC, Marschall HU, Gale DP, Williamson C. GWAS meta-analysis of intrahepatic cholestasis of pregnancy implicates multiple hepatic genes and regulatory elements. Nat Commun 2022; 13:4840. [PMID: 35977952 PMCID: PMC9385867 DOI: 10.1038/s41467-022-29931-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 04/08/2022] [Indexed: 12/15/2022] Open
Abstract
Intrahepatic cholestasis of pregnancy (ICP) is a pregnancy-specific liver disorder affecting 0.5-2% of pregnancies. The majority of cases present in the third trimester with pruritus, elevated serum bile acids and abnormal serum liver tests. ICP is associated with an increased risk of adverse outcomes, including spontaneous preterm birth and stillbirth. Whilst rare mutations affecting hepatobiliary transporters contribute to the aetiology of ICP, the role of common genetic variation in ICP has not been systematically characterised to date. Here, we perform genome-wide association studies (GWAS) and meta-analyses for ICP across three studies including 1138 cases and 153,642 controls. Eleven loci achieve genome-wide significance and have been further investigated and fine-mapped using functional genomics approaches. Our results pinpoint common sequence variation in liver-enriched genes and liver-specific cis-regulatory elements as contributing mechanisms to ICP susceptibility.
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Affiliation(s)
- Peter H Dixon
- Department of Women and Children's Health, School of Life Course Sciences, King's College London, London, UK
| | - Adam P Levine
- Department of Renal Medicine, University College London, London, UK
- Research Department of Pathology, University College London, London, UK
| | - Inês Cebola
- Section of Genetics and Genomics, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Melanie M Y Chan
- Department of Renal Medicine, University College London, London, UK
| | - Aliya S Amin
- Department of Women and Children's Health, School of Life Course Sciences, King's College London, London, UK
| | - Anshul Aich
- Department of Renal Medicine, University College London, London, UK
| | - Monika Mozere
- Department of Renal Medicine, University College London, London, UK
| | - Hannah Maude
- Section of Genetics and Genomics, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Alice L Mitchell
- Department of Women and Children's Health, School of Life Course Sciences, King's College London, London, UK
| | - Jun Zhang
- Department of Renal Medicine, University College London, London, UK
- Division of Nephrology, Department of Medicine, Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Jenny Chambers
- ICP Support, 69 Mere Green Road, Sutton Coldfield, UK
- Women's Health Research Centre, Imperial College London, London, UK
| | - Argyro Syngelaki
- Harris Birthright Research Centre for Fetal Medicine, King's College Hospital, London, UK
| | | | | | | | - Kypros Nicolaides
- Harris Birthright Research Centre for Fetal Medicine, King's College Hospital, London, UK
| | | | - William M Hague
- Robinson Research Institute, The University of Adelaide, Adelaide, SA, Australia
| | | | - Hanns-Ulrich Marschall
- Department of Molecular and Clinical Medicine/Wallenberg Laboratory, University of Gothenburg, Gothenburg, Sweden
| | - Daniel P Gale
- Department of Renal Medicine, University College London, London, UK
| | - Catherine Williamson
- Department of Women and Children's Health, School of Life Course Sciences, King's College London, London, UK.
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153
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Sustar U, Groselj U, Khan SA, Shafi S, Khan I, Kovac J, Bizjan BJ, Battelino T, Sadiq F. A homozygous variant in the GPIHBP1 gene in a child with severe hypertriglyceridemia and a systematic literature review. Front Genet 2022; 13:983283. [PMID: 36051701 PMCID: PMC9424485 DOI: 10.3389/fgene.2022.983283] [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: 06/30/2022] [Accepted: 07/18/2022] [Indexed: 11/13/2022] Open
Abstract
Background: Due to nonspecific symptoms, rare dyslipidaemias are frequently misdiagnosed, overlooked, and undertreated, leading to increased risk for severe cardiovascular disease, pancreatitis and/or multiple organ failures before diagnosis. Better guidelines for the recognition and early diagnosis of rare dyslipidaemias are urgently required. Methods: Genomic DNA was isolated from blood samples of a Pakistani paediatric patient with hypertriglyceridemia, and from his parents and siblings. Next-generation sequencing (NGS) was performed, and an expanded dyslipidaemia panel was employed for genetic analysis. Results: The NGS revealed the presence of a homozygous missense pathogenic variant c.230G>A (NM_178172.6) in exon 3 of the GPIHBP1 (glycosylphosphatidylinositol-anchored high-density lipoprotein-binding protein 1) gene resulting in amino acid change p.Cys77Tyr (NP_835466.2). The patient was 5.5 years old at the time of genetic diagnosis. The maximal total cholesterol and triglyceride levels were measured at the age of 10 months (850.7 mg/dl, 22.0 mmol/L and 5,137 mg/dl, 58.0 mmol/L, respectively). The patient had cholesterol deposits at the hard palate, eruptive xanthomas, lethargy, poor appetite, and mild splenomegaly. Both parents and sister were heterozygous for the familial variant in the GPIHBP1 gene. Moreover, in the systematic review, we present 62 patients with pathogenic variants in the GPIHBP1 gene and clinical findings, associated with hyperlipoproteinemia. Conclusion: In a child with severe hypertriglyceridemia, we identified a pathogenic variant in the GPIHBP1 gene causing hyperlipoproteinemia (type 1D). In cases of severe elevations of plasma cholesterol and/or triglycerides genetic testing for rare dyslipidaemias should be performed as soon as possible for optimal therapy and patient management.
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Affiliation(s)
- Ursa Sustar
- Department of Endocrinology, Diabetes and Metabolism, University Children’s Hospital, University Medical Centre Ljubljana, Ljubljana, Slovenia
- Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Urh Groselj
- Department of Endocrinology, Diabetes and Metabolism, University Children’s Hospital, University Medical Centre Ljubljana, Ljubljana, Slovenia
- Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
- Division of Cardiovascular Medicine, Department of Medicine, Stanford University, Stanford, CA, United States
- *Correspondence: Urh Groselj, ; Fouzia Sadiq,
| | - Sabeen Abid Khan
- Department of Paediatrics, Shifa College of Medicine, Shifa Tameer-e-Millat University, Islamabad, Pakistan
| | - Saeed Shafi
- Department of Anatomy, Shifa Tameer-e-Millat University, Islamabad, Pakistan
| | - Iqbal Khan
- Department of Vascular Surgery, Shifa International Hospital, Islamabad, Pakistan
- Department of Vascular Surgery, Shifa Tameer-e-Millat University, Islamabad, Pakistan
| | - Jernej Kovac
- Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
- Clinical Institute for Special Laboratory Diagnostics, University Children’s Hospital, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Barbara Jenko Bizjan
- Clinical Institute for Special Laboratory Diagnostics, University Children’s Hospital, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Tadej Battelino
- Department of Endocrinology, Diabetes and Metabolism, University Children’s Hospital, University Medical Centre Ljubljana, Ljubljana, Slovenia
- Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Fouzia Sadiq
- Directorate of Research, Shifa Tameer-e-Millat University, Islamabad, Pakistan
- *Correspondence: Urh Groselj, ; Fouzia Sadiq,
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154
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Lombardi S, Testa MF, Pinotti M, Branchini A. Translation termination codons in protein synthesis and disease. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2022; 132:1-48. [PMID: 36088072 DOI: 10.1016/bs.apcsb.2022.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Fidelity of protein synthesis, a process shaped by several mechanisms involving specialized ribosome regions and external factors, ensures the precise reading of sense as well as stop codons (UGA, UAG, UAA), which are usually localized at the 3' of mRNA and drive the release of the polypeptide chain. However, either natural (NTCs) or premature (PTCs) termination codons, the latter arising from nucleotide changes, can undergo a recoding process named ribosome or translational readthrough, which insert specific amino acids (NTCs) or subset(s) depending on the stop codon type (PTCs). This process is particularly relevant for nonsense mutations, a relatively frequent cause of genetic disorders, which impair gene expression at different levels by potentially leading to mRNA degradation and/or synthesis of truncated proteins. As a matter of fact, many efforts have been made to develop efficient and safe readthrough-inducing compounds, which have been challenged in several models of human disease to provide with a therapy. In this view, the dissection of the molecular determinants shaping the outcome of readthrough, namely nucleotide and protein contexts as well as their interplay and impact on protein structure/function, is crucial to identify responsive nonsense mutations resulting in functional full-length proteins. The interpretation of experimental and mechanistic findings is also important to define a possibly clear picture of potential readthrough-favorable features useful to achieve rescue profiles compatible with therapeutic thresholds typical of each targeted disorder, which is of primary importance for the potential translatability of readthrough into a personalized and mutation-specific, and thus patient-oriented, therapeutic strategy.
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Affiliation(s)
- Silvia Lombardi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Maria Francesca Testa
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Mirko Pinotti
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Alessio Branchini
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy.
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155
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A Comprehensive Evaluation of the Performance of Prediction Algorithms on Clinically Relevant Missense Variants. Int J Mol Sci 2022; 23:ijms23147946. [PMID: 35887294 PMCID: PMC9322961 DOI: 10.3390/ijms23147946] [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: 06/08/2022] [Revised: 07/09/2022] [Accepted: 07/15/2022] [Indexed: 12/12/2022] Open
Abstract
The rapid integration of genomic technologies in clinical diagnostics has resulted in the detection of a multitude of missense variants whose clinical significance is often unknown. As a result, a plethora of computational tools have been developed to facilitate variant interpretation. However, choosing an appropriate software from such a broad range of tools can be challenging; therefore, systematic benchmarking with high-quality, independent datasets is critical. Using three independent benchmarking datasets compiled from the ClinVar database, we evaluated the performance of ten widely used prediction algorithms with missense variants from 21 clinically relevant genes, including BRCA1 and BRCA2. A fourth dataset consisting of 1053 missense variants was also used to investigate the impact of type 1 circularity on their performance. The performance of the prediction algorithms varied widely across datasets. Based on Matthews Correlation Coefficient and Area Under the Curve, SNPs&GO and PMut consistently displayed an overall above-average performance across the datasets. Most of the tools demonstrated greater sensitivity and negative predictive values at the expense of lower specificity and positive predictive values. We also demonstrated that type 1 circularity significantly impacts the performance of these tools and, if not accounted for, may confound the selection of the best performing algorithms.
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156
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Maddali M, Venkatraman A, Kulkarni UP, Mani S, Raj S, Sigamani E, Korula A, A FN, Lionel SA, Selvarajan S, Manipadam MT, Abraham A, George B, Mathews V, Balasubramanian P. Molecular characterization of triple-negative myeloproliferative neoplasms by next-generation sequencing. Ann Hematol 2022; 101:1987-2000. [PMID: 35840818 DOI: 10.1007/s00277-022-04920-w] [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: 03/14/2022] [Accepted: 06/27/2022] [Indexed: 11/01/2022]
Abstract
The role of next-generation sequencing (NGS) in identifying mutations in the driver, epigenetic regulator, RNA splicing, and signaling pathway genes in myeloproliferative neoplasms (MPNs) has contributed substantially to our understanding of the disease pathogenesis as well as disease evolution. NGS aids in determining the clonal nature of the disease in a subset of these disorders where mutations in the driver genes are not detected. There is a paucity of real-world data on the utility of this test in the characterization of triple-negative myeloproliferative neoplasms (TN-MPN). In this study, 46 samples of TN-MPN (essential thrombocythemia (ET) = 17; primary myelofibrosis (PMF) = 23; & myeloproliferative neoplasm unclassified (MPN-u) = 6) were screened for markers of clonality using targeted NGS. Among these, 25 (54.3%) patients had mutations that would help determine the clonal nature of the disease. Eight of the 17 TN-ET (47%) and 13 of the 23 TN-PMF (56.5%) patients had noncanonical mutations in the driver genes and mutations in the genes involved in epigenetic regulation. Identification of mutations categorized as high molecular markers (HMR) in 2 patients helped classify them as PMF with high risk according to the MIPSS 70 scoring system. A novel mutation in the MPIG6B (C6orf25) gene associated with childhood myelofibrosis was detected in a 14-year-old girl. The presence of clonal hematopoiesis could be confirmed in four of the six MPN-u patients in this cohort. This study demonstrates the utility of NGS in improving the characterization of TN-MPN by establishing clonality and detecting noncanonical mutations in driver genes, thereby aiding in clinical decision-making.
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Affiliation(s)
- Madhavi Maddali
- Department of Haematology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Arvind Venkatraman
- Department of Haematology, Christian Medical College, Vellore, Tamil Nadu, India
| | | | - Sathya Mani
- Department of Haematology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Santhosh Raj
- Department of Pathology, Christian Medical College, Vellore, Tamil Nadu, India
| | | | - Anu Korula
- Department of Haematology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Fouzia N A
- Department of Haematology, Christian Medical College, Vellore, Tamil Nadu, India
| | | | - Sushil Selvarajan
- Department of Haematology, Christian Medical College, Vellore, Tamil Nadu, India
| | | | - Aby Abraham
- Department of Haematology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Biju George
- Department of Haematology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Vikram Mathews
- Department of Haematology, Christian Medical College, Vellore, Tamil Nadu, India
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157
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Hunter GA, Ferreira GC. An Extended C-Terminus, the Possible Culprit for Differential Regulation of 5-Aminolevulinate Synthase Isoforms. Front Mol Biosci 2022; 9:920668. [PMID: 35911972 PMCID: PMC9329541 DOI: 10.3389/fmolb.2022.920668] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 05/30/2022] [Indexed: 12/05/2022] Open
Abstract
5-Aminolevulinate synthase (ALAS; E.C. 2.3.1.37) is a pyridoxal 5′-phosphate (PLP)-dependent enzyme that catalyzes the key regulatory step of porphyrin biosynthesis in metazoa, fungi, and α-proteobacteria. ALAS is evolutionarily related to transaminases and is therefore classified as a fold type I PLP-dependent enzyme. As an enzyme controlling the key committed and rate-determining step of a crucial biochemical pathway ALAS is ideally positioned to be subject to allosteric feedback inhibition. Extensive kinetic and mutational studies demonstrated that the overall enzyme reaction is limited by subtle conformational changes of a hairpin loop gating the active site. These findings, coupled with structural information, facilitated early prediction of allosteric regulation of activity via an extended C-terminal tail unique to eukaryotic forms of the enzyme. This prediction was subsequently supported by the discoveries that mutations in the extended C-terminus of the erythroid ALAS isoform (ALAS2) cause a metabolic disorder known as X-linked protoporphyria not by diminishing activity, but by enhancing it. Furthermore, kinetic, structural, and molecular modeling studies demonstrated that the extended C-terminal tail controls the catalytic rate by modulating conformational flexibility of the active site loop. However, the precise identity of any such molecule remains to be defined. Here we discuss the most plausible allosteric regulators of ALAS activity based on divergences in AlphaFold-predicted ALAS structures and suggest how the mystery of the mechanism whereby the extended C-terminus of mammalian ALASs allosterically controls the rate of porphyrin biosynthesis might be unraveled.
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Affiliation(s)
- Gregory A. Hunter
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, United States
- *Correspondence: Gregory A. Hunter, ; Gloria C. Ferreira,
| | - Gloria C. Ferreira
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, United States
- Department of Chemistry, College of Arts and Sciences, University of South Florida, Tampa, FL, United States
- Global and Planetary Health, College of Public Health, University of South Florida, Tampa, FL, United States
- *Correspondence: Gregory A. Hunter, ; Gloria C. Ferreira,
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158
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Elisei R, Ciampi R, Matrone A, Prete A, Gambale C, Ramone T, Simeakis G, Materazzi G, Torregrossa L, Ugolini C, Romei C. Somatic RET Indels in Sporadic Medullary Thyroid Cancer: Prevalence and Response to Selpercatinib. J Clin Endocrinol Metab 2022; 107:2195-2202. [PMID: 35616103 DOI: 10.1210/clinem/dgac325] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Indexed: 11/19/2022]
Abstract
CONTEXT Although the majority of RET alterations are single nucleotide variants (SNV), small deletions and/or insertions have been reported at variable prevalence. No information about the efficacy of RET-specific inhibitors in patients harboring RET indels has been provided. OBJECTIVE We present an update on the prevalence of RET indels in medullary thyroid cancer (MTC) and describe the efficacy of selpercatinib in patients with advanced MTC with RET indels. METHODS The MTC tissues of 287 patients were analyzed using an Ion S5 targeted sequencing. The functional role of the reported indels have been evaluated by MutationTaster. Clinical and pathological data of MTC patients harboring a RET indel were collected and analyzed. Two patients with a RET indel were treated with selpercatinib. RESULTS Among 178 RET-positive cases, 147 (82.6%) harbored a SNV and 31 (17.4%) a RET in-frame indel. Nine indels were not previously reported and were found to be disease causing by MutationTaster. Patients harboring an indel were found to have an aggressive disease and 2 of them were treated with selpercatinib, experiencing a good response to the treatment. CONCLUSION These data show that RET indels are not infrequent and correlate with an aggressive disease. Two RET indel-positive patients showed a partial response to the treatment with a highly selective RET inhibitor; thus, these RET indels can be considered actionable mutations. In order to not miss these alterations, the analysis of the full gene is recommended.
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Affiliation(s)
- Rossella Elisei
- Unit of Endocrinology, Department of Clinical and Experimental Medicine, University-Hospital of Pisa, 56124 Pisa, Italy
| | - Raffaele Ciampi
- Unit of Endocrinology, Department of Clinical and Experimental Medicine, University-Hospital of Pisa, 56124 Pisa, Italy
| | - Antonio Matrone
- Unit of Endocrinology, Department of Clinical and Experimental Medicine, University-Hospital of Pisa, 56124 Pisa, Italy
| | - Alessandro Prete
- Unit of Endocrinology, Department of Clinical and Experimental Medicine, University-Hospital of Pisa, 56124 Pisa, Italy
| | - Carla Gambale
- Unit of Endocrinology, Department of Clinical and Experimental Medicine, University-Hospital of Pisa, 56124 Pisa, Italy
| | - Teresa Ramone
- Unit of Endocrinology, Department of Clinical and Experimental Medicine, University-Hospital of Pisa, 56124 Pisa, Italy
| | - George Simeakis
- Endocrine Dept., 401 General Military Hospital of Athens, Athens 11525, Greece
| | - Gabriele Materazzi
- Department of Surgical, Medical, Molecular Pathology and Critical Area, Surgery Unit, University Hospital of Pisa, 56124 Pisa, Italy
| | - Liborio Torregrossa
- Department of Surgical, Medical, Molecular Pathology and Critical Area, Pathology Unit, University Hospital of Pisa, 56124 Pisa, Italy
| | - Clara Ugolini
- Department of Surgical, Medical, Molecular Pathology and Critical Area, Pathology Unit, University Hospital of Pisa, 56124 Pisa, Italy
| | - Cristina Romei
- Unit of Endocrinology, Department of Clinical and Experimental Medicine, University-Hospital of Pisa, 56124 Pisa, Italy
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159
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Liu L, Zou L, Li K, Hou H, Hu Q, Liu S, Li J, Song C, Chen J, Wang S, Wang Y, Li C, Du H, Li JL, Chen F, Xu Z, Sun W, Sun Q, Xiong W. Template-independent genome editing in the Pcdh15 av-3j mouse, a model of human DFNB23 nonsyndromic deafness. Cell Rep 2022; 40:111061. [PMID: 35830793 DOI: 10.1016/j.celrep.2022.111061] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Revised: 04/15/2022] [Accepted: 06/14/2022] [Indexed: 11/03/2022] Open
Abstract
Although frameshift mutations lead to 22% of inherited Mendelian disorders in humans, there is no efficient in vivo gene therapy strategy available to date, particularly in nondividing cells. Here, we show that nonhomologous end-joining (NHEJ)-mediated nonrandom editing profiles compensate the frameshift mutation in the Pcdh15 gene and restore the lost mechanotransduction function in postmitotic hair cells of Pcdh15av-3J mice, an animal model of human nonsyndromic deafness DFNB23. Identified by an ex vivo evaluation system in cultured cochlear explants, the selected guide RNA restores reading frame in approximately 50% of indel products and recovers mechanotransduction in more than 70% of targeted hair cells. In vivo treatment shows that half of the animals gain improvements in auditory responses, and balance function is restored in the majority of injected mutant mice. These results demonstrate that NHEJ-mediated reading-frame restoration is a simple and efficient strategy in postmitotic systems.
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Affiliation(s)
- Lian Liu
- School of Life Sciences, Tsinghua University, Beijing 100084, China; IDG/McGovern Institute for Brain Research at Tsinghua University, Tsinghua University, Beijing 100084, China
| | - Linzhi Zou
- School of Life Sciences, Tsinghua University, Beijing 100084, China; IDG/McGovern Institute for Brain Research at Tsinghua University, Tsinghua University, Beijing 100084, China
| | - Kuan Li
- School of Life Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Hanqing Hou
- School of Life Sciences, Tsinghua University, Beijing 100084, China; IDG/McGovern Institute for Brain Research at Tsinghua University, Tsinghua University, Beijing 100084, China
| | - Qun Hu
- School of Life Sciences, Tsinghua University, Beijing 100084, China; IDG/McGovern Institute for Brain Research at Tsinghua University, Tsinghua University, Beijing 100084, China
| | - Shuang Liu
- School of Life Sciences, Tsinghua University, Beijing 100084, China; IDG/McGovern Institute for Brain Research at Tsinghua University, Tsinghua University, Beijing 100084, China
| | - Jie Li
- School of Life Sciences, Tsinghua University, Beijing 100084, China; IDG/McGovern Institute for Brain Research at Tsinghua University, Tsinghua University, Beijing 100084, China
| | - Chenmeng Song
- School of Life Sciences, Tsinghua University, Beijing 100084, China; IDG/McGovern Institute for Brain Research at Tsinghua University, Tsinghua University, Beijing 100084, China
| | - Jiaofeng Chen
- School of Life Sciences, Tsinghua University, Beijing 100084, China; IDG/McGovern Institute for Brain Research at Tsinghua University, Tsinghua University, Beijing 100084, China
| | - Shufeng Wang
- School of Life Sciences, Tsinghua University, Beijing 100084, China; IDG/McGovern Institute for Brain Research at Tsinghua University, Tsinghua University, Beijing 100084, China
| | - Yangzhen Wang
- School of Life Sciences, Tsinghua University, Beijing 100084, China; IDG/McGovern Institute for Brain Research at Tsinghua University, Tsinghua University, Beijing 100084, China
| | - Changri Li
- Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Haibo Du
- School of Life Sciences, Shandong University, Qingdao, Shandong 266237, China
| | - Jun-Liszt Li
- Chinese Institute for Brain Research, Beijing 102206, China; Academy for Advanced Interdisciplinary Studies (AAIS), Peking University, Beijing 100871, China
| | - Fangyi Chen
- Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Zhigang Xu
- School of Life Sciences, Shandong University, Qingdao, Shandong 266237, China
| | - Wenzhi Sun
- Chinese Institute for Brain Research, Beijing 102206, China; School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
| | - Qianwen Sun
- School of Life Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Wei Xiong
- School of Life Sciences, Tsinghua University, Beijing 100084, China; IDG/McGovern Institute for Brain Research at Tsinghua University, Tsinghua University, Beijing 100084, China.
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Loss-of-function, gain-of-function and dominant-negative mutations have profoundly different effects on protein structure. Nat Commun 2022; 13:3895. [PMID: 35794153 PMCID: PMC9259657 DOI: 10.1038/s41467-022-31686-6] [Citation(s) in RCA: 73] [Impact Index Per Article: 36.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 06/29/2022] [Indexed: 12/12/2022] Open
Abstract
Most known pathogenic mutations occur in protein-coding regions of DNA and change the way proteins are made. Taking protein structure into account has therefore provided great insight into the molecular mechanisms underlying human genetic disease. While there has been much focus on how mutations can disrupt protein structure and thus cause a loss of function (LOF), alternative mechanisms, specifically dominant-negative (DN) and gain-of-function (GOF) effects, are less understood. Here, we investigate the protein-level effects of pathogenic missense mutations associated with different molecular mechanisms. We observe striking differences between recessive vs dominant, and LOF vs non-LOF mutations, with dominant, non-LOF disease mutations having much milder effects on protein structure, and DN mutations being highly enriched at protein interfaces. We also find that nearly all computational variant effect predictors, even those based solely on sequence conservation, underperform on non-LOF mutations. However, we do show that non-LOF mutations could potentially be identified by their tendency to cluster in three-dimensional space. Overall, our work suggests that many pathogenic mutations that act via DN and GOF mechanisms are likely being missed by current variant prioritisation strategies, but that there is considerable scope to improve computational predictions through consideration of molecular disease mechanisms. Most known pathogenic mutations occur in protein-coding regions of DNA and change the way proteins are made. Here the authors analyse the locations of thousands of human disease mutations and their predicted effects on protein structure and show that,while loss-of-function mutations tend to be highly disruptive, non-loss-of-function mutations are in general much milder at a protein structural level.
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Healy L, O'Shea M, McNulty J, King G, Twomey E, Treacy E, Crushell E, Hughes J, Knerr I, Monavari AA. Glutaric aciduria type 1: Diagnosis, clinical features and long‐term outcome in a large cohort of 34 Irish patients. JIMD Rep 2022; 63:379-387. [PMID: 35822093 PMCID: PMC9259398 DOI: 10.1002/jmd2.12302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 05/09/2022] [Accepted: 05/11/2022] [Indexed: 11/08/2022] Open
Abstract
Glutaric aciduria type 1 (GA1) is a rare neurometabolic disorder that can lead to encephalopathic crises and severe dystonic movement disorders. Adherence to strict dietary restriction, in particular a diet low in lysine, carnitine supplementation and emergency treatment in pre‐symptomatic patients diagnosed by high‐risk screen (HRS) or newborn screen (NBS) leads to a favourable outcome. We present biochemical and clinical characteristics and long‐term outcome data of 34 Irish patients with GA1 aged 1–40 years. Sixteen patients were diagnosed clinically, and 17 patients by HRS, prior to introduction of NBS for GA1 in the Republic of Ireland in 2018. One patient was diagnosed by NBS. Clinical diagnosis was at a median of 1 year (range 1 month to 8 years) and by HRS was at a median of 4 days (range 3 days to 11 years). 14/18 (77.8%) diagnosed by HRS or NBS had neither clinical manifestations nor radiological features of GA1, or had radiological features only, compared to 0/16 (0%) diagnosed clinically (p < 0.001). Patients diagnosed clinically who survived to school‐age were more likely to have significant cerebral palsy and dystonia (7/11; 63.6% vs. 0/13; 0%, p < 0.001). They were less likely to be in mainstream school versus the HRS group (5/10; 50% vs. 12/13; 92.3%; p = 0.012). Clinical events occurring after 6 years of age were unusual, but included spastic diplegia, thalamic haemorrhage, Chiari malformation, pituitary hormone deficiency and epilepsy. The exact aetiology of these events is unclear.
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Affiliation(s)
- Lydia Healy
- National Centre of Inherited Metabolic Disorders, Children's Health Ireland at Temple Street Dublin Republic of Ireland
| | - Meabh O'Shea
- National Centre of Inherited Metabolic Disorders, Children's Health Ireland at Temple Street Dublin Republic of Ireland
- European Reference Network for Rare Hereditary Metabolic Disorders (MetabERN) European Reference Network for Rare Hereditary Metabolic Disorders (MetabERN), National Centre for Inherited Metabolic Disorders, Children's Health Ireland at Temple Street and Mater Misericordiae University Hospital Dublin Republic of Ireland
| | - Jennifer McNulty
- National Centre of Inherited Metabolic Disorders, Children's Health Ireland at Temple Street Dublin Republic of Ireland
- European Reference Network for Rare Hereditary Metabolic Disorders (MetabERN) European Reference Network for Rare Hereditary Metabolic Disorders (MetabERN), National Centre for Inherited Metabolic Disorders, Children's Health Ireland at Temple Street and Mater Misericordiae University Hospital Dublin Republic of Ireland
| | - Graham King
- National Centre of Inherited Metabolic Disorders, Children's Health Ireland at Temple Street Dublin Republic of Ireland
| | - Eilish Twomey
- Department of Radiology Children's Health Ireland at Temple Street Dublin Republic of Ireland
| | - Eileen Treacy
- European Reference Network for Rare Hereditary Metabolic Disorders (MetabERN) European Reference Network for Rare Hereditary Metabolic Disorders (MetabERN), National Centre for Inherited Metabolic Disorders, Children's Health Ireland at Temple Street and Mater Misericordiae University Hospital Dublin Republic of Ireland
- National Adult Centre for Inherited Metabolic Disorders Mater Misericordiae University Hospital Dublin Republic of Ireland
- University College Dublin Dublin Republic of Ireland
- University of Dublin Dublin Republic of Ireland
| | - Ellen Crushell
- National Centre of Inherited Metabolic Disorders, Children's Health Ireland at Temple Street Dublin Republic of Ireland
- European Reference Network for Rare Hereditary Metabolic Disorders (MetabERN) European Reference Network for Rare Hereditary Metabolic Disorders (MetabERN), National Centre for Inherited Metabolic Disorders, Children's Health Ireland at Temple Street and Mater Misericordiae University Hospital Dublin Republic of Ireland
- University College Dublin Dublin Republic of Ireland
| | - Joanne Hughes
- National Centre of Inherited Metabolic Disorders, Children's Health Ireland at Temple Street Dublin Republic of Ireland
- European Reference Network for Rare Hereditary Metabolic Disorders (MetabERN) European Reference Network for Rare Hereditary Metabolic Disorders (MetabERN), National Centre for Inherited Metabolic Disorders, Children's Health Ireland at Temple Street and Mater Misericordiae University Hospital Dublin Republic of Ireland
| | - Ina Knerr
- National Centre of Inherited Metabolic Disorders, Children's Health Ireland at Temple Street Dublin Republic of Ireland
- European Reference Network for Rare Hereditary Metabolic Disorders (MetabERN) European Reference Network for Rare Hereditary Metabolic Disorders (MetabERN), National Centre for Inherited Metabolic Disorders, Children's Health Ireland at Temple Street and Mater Misericordiae University Hospital Dublin Republic of Ireland
- University College Dublin Dublin Republic of Ireland
| | - Ahmad Ardeshir Monavari
- National Centre of Inherited Metabolic Disorders, Children's Health Ireland at Temple Street Dublin Republic of Ireland
- European Reference Network for Rare Hereditary Metabolic Disorders (MetabERN) European Reference Network for Rare Hereditary Metabolic Disorders (MetabERN), National Centre for Inherited Metabolic Disorders, Children's Health Ireland at Temple Street and Mater Misericordiae University Hospital Dublin Republic of Ireland
- University College Dublin Dublin Republic of Ireland
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A RAS-Independent Biomarker Panel to Reliably Predict Response to MEK Inhibition in Colorectal Cancer. Cancers (Basel) 2022; 14:cancers14133252. [PMID: 35805024 PMCID: PMC9265111 DOI: 10.3390/cancers14133252] [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: 06/03/2022] [Revised: 06/27/2022] [Accepted: 06/29/2022] [Indexed: 02/04/2023] Open
Abstract
Simple Summary Today, clinical management for the majority of cancer patients is still based on a “one-size-fits-all” approach. To improve the outcomes in the era of personalized medicine, it is essential to stratify patients based on established and novel biomarkers. In the present study, we investigated a SMAD4 loss-of-function mutation, which is associated with chemoresistance and decreased overall survival in colorectal cancer (CRC). To investigate the molecular mechanism behind the impact on drug response, we used CRISPR technology on patient-derived organoid models (PDOs) of CRC. We showed that PDOs with loss-of-function SMAD4 mutations are sensitive to MEK-inhibitors. Using a novel four-gene signature reliably predicts sensitivity towards MEK-inhibitors, regardless of the RAS and BRAF status. The present study is a significant step towards personalized cancer therapy by identifying a new biomarker. Abstract Background: In colorectal cancer (CRC), mutations of genes associated with the TGF-β/BMP signaling pathway, particularly affecting SMAD4, are known to correlate with decreased overall survival and it is assumed that this signaling axis plays a key role in chemoresistance. Methods: Using CRISPR technology on syngeneic patient-derived organoids (PDOs), we investigated the role of a loss-of-function of SMAD4 in sensitivity to MEK-inhibitors. CRISPR-engineered SMAD4R361H PDOs were subjected to drug screening, RNA-Sequencing, and multiplex protein profiling (DigiWest®). Initial observations were validated on an additional set of 62 PDOs with known mutational status. Results: We show that loss-of-function of SMAD4 renders PDOs sensitive to MEK-inhibitors. Multiomics analyses indicate that disruption of the BMP branch within the TGF-β/BMP pathway is the pivotal mechanism of increased drug sensitivity. Further investigation led to the identification of the SFAB-signature (SMAD4, FBXW7, ARID1A, or BMPR2), coherently predicting sensitivity towards MEK-inhibitors, independent of both RAS and BRAF status. Conclusion: We identified a novel mutational signature that reliably predicts sensitivity towards MEK-inhibitors, regardless of the RAS and BRAF status. This finding poses a significant step towards better-tailored cancer therapies guided by the use of molecular biomarkers.
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Marchi M, D'Amato I, Andelic M, Cartelli D, Salvi E, Lombardi R, Gumus E, Lauria G. Congenital insensitivity to pain: a novel mutation affecting a U12-type intron causes multiple aberrant splicing of SCN9A. Pain 2022; 163:e882-e887. [PMID: 34799533 PMCID: PMC9199108 DOI: 10.1097/j.pain.0000000000002535] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 10/19/2021] [Accepted: 11/01/2021] [Indexed: 11/26/2022]
Abstract
ABSTRACT Mutations in the alpha subunit of voltage-gated sodium channel 1.7 (NaV1.7), encoded by SCN9A gene, play an important role in the regulation of nociception and can lead to a wide range of clinical outcomes, ranging from extreme pain syndromes to congenital inability to experience pain. To expand the phenotypic and genotypic spectrum of SCN9A-related channelopathies, we describe the proband, a daughter born from consanguineous parents, who had pain insensitivity, diminished temperature sensation, foot burns, and severe loss of nociceptive nerve fibers in the epidermis. Next-generation sequencing of SCN9A (NM_002977.3) revealed a novel homozygous substitution (c.377+7T>G) in the donor splice site of intron 3. As the RNA functional testing is challenging, the in silico analysis is the first approach to predict possible alterations. In this case, the computational analysis was unable to identify the splicing consensus and could not provide any prediction for splicing defects. The affected intron indeed belongs to the U12 type, a family of introns characterised by noncanonical consensus at the splice sites, accounting only for 0.35% of all human introns, and is not included in most of the training sets for splicing prediction. A functional study on proband RNA showed different aberrant transcripts, where exon 3 was missing and an intron fragment was included. A quantification study using real-time polymerase chain reaction showed a significant reduction of the NaV1.7 canonical transcript. Collectively, these data widen the spectrum of SCN9A-related insensitivity to pain by describing a mutation causing NaV1.7 deficiency, underlying the nociceptor dysfunction, and highlight the importance of molecular investigation of U12 introns' mutations despite the silent prediction.
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Affiliation(s)
- Margherita Marchi
- Neuroalgology Unit, Fondazione IRCCS Istituto Neurologico “Carlo Besta”, Milan, Italy
| | - Ilaria D'Amato
- Neuroalgology Unit, Fondazione IRCCS Istituto Neurologico “Carlo Besta”, Milan, Italy
| | - Mirna Andelic
- Neuroalgology Unit, Fondazione IRCCS Istituto Neurologico “Carlo Besta”, Milan, Italy
- Department of Neurology, School of Mental Health and Neuroscience, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Daniele Cartelli
- Neuroalgology Unit, Fondazione IRCCS Istituto Neurologico “Carlo Besta”, Milan, Italy
| | - Erika Salvi
- Neuroalgology Unit, Fondazione IRCCS Istituto Neurologico “Carlo Besta”, Milan, Italy
| | - Raffaella Lombardi
- Neuroalgology Unit, Fondazione IRCCS Istituto Neurologico “Carlo Besta”, Milan, Italy
| | - Evren Gumus
- Department of Medical Genetics, Faculty of Medicine, University of Harran, Sanliurfa, Turkey
| | - Giuseppe Lauria
- Neuroalgology Unit, Fondazione IRCCS Istituto Neurologico “Carlo Besta”, Milan, Italy
- Department of Medical Biotechnology and Translational Medicine, University of Milan, Milan, Italy
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164
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Das S, Mohammed A, Mandal T, Maji S, Verma J, Ruturaj, Gupta A. Polarized trafficking and copper transport activity of ATP7B: a mutational approach to establish genotype-phenotype correlation in Wilson disease. Hum Mutat 2022; 43:1408-1429. [PMID: 35762218 DOI: 10.1002/humu.24428] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Revised: 06/22/2022] [Accepted: 06/24/2022] [Indexed: 11/07/2022]
Abstract
Mutation in ATP7B gene causes Wilson disease (WD) that is characterized by severe hepatic and neurological symptoms. ATP7B localizes at the trans-Golgi Network (TGN) transporting copper to copper-dependent enzymes and traffics in apically targeted vesicles upon intracellular copper elevation. To decode the cellular underpinnings of WD manifestation we investigated copper-responsive polarized trafficking and copper transport activity of fifteen WD causing point mutations in ATP7B. Amino-terminal mutations Gly85Val, Leu168Pro and Gly591Asp displayed TGN and sub-apical localization whereas, Leu492Ser mislocalized at the basolateral region. The actuator domain mutation Gly875Arg shows retention in the endoplasmic reticulum (ER), Ala874Val and Leu795Phe show partial targeting to TGN and post-Golgi vesicles. The Nucleotide-Binding Domain mutations His1069Gln and Leu1083Phe also display impaired targeting. The C-terminal mutations Leu1373Pro/Arg is arrested at ER but Ser1423Asn shows TGN localization. Transmembrane mutant Arg778Leu resides in ER and TGN while Arg969Gln is exclusively ER localized. Cellular Cu level does not alter the targeting of any of the studied mutations. Mutants that traffic to TGN exhibits biosynthetic function. Finally, we correlated cellular phenotypes with the clinical manifestation of the two most prevalent mutations; the early onset and more aggressive WD caused by Arg778Leu and the milder form of WD caused by mutation His1069Gln. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Santanu Das
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal, 741246, India
| | - Ameena Mohammed
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal, 741246, India
| | - Taniya Mandal
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal, 741246, India
| | - Saptarshi Maji
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal, 741246, India
| | - Jay Verma
- Maulana Azad Medical College, 2 Bahadur Shah Zafar Marg, New Delhi, Delhi, 110002, India
| | - Ruturaj
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal, 741246, India
| | - Arnab Gupta
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal, 741246, India
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165
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Nassisi M, De Bartolo G, Mohand-Said S, Condroyer C, Antonio A, Lancelot ME, Bujakowska K, Smirnov V, Pugliese T, Neidhardt J, Sahel JA, Zeitz C, Audo I. Retrospective Natural History Study of RPGR-Related Cone- and Cone-Rod Dystrophies While Expanding the Mutation Spectrum of the Disease. Int J Mol Sci 2022; 23:7189. [PMID: 35806195 PMCID: PMC9266815 DOI: 10.3390/ijms23137189] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Revised: 06/24/2022] [Accepted: 06/24/2022] [Indexed: 01/06/2023] Open
Abstract
Variants in the X-linked retinitis pigmentosa GTPase regulator gene (RPGR) and, specifically, in its retinal opening reading frame-15 isoform (RPGRORF15) may cause rod-cone (RCD), cone, and cone-rod dystrophies (CDs and CRDs). While RPGR-related RCDs have been frequently evaluated, the characteristics and progression of RPGR-related CD/CRDs are largely unknown. Therefore, the goal of our work was to perform genotype-phenotype correlations specifically in RPGRORF15-related CD/CRDs. This retrospective longitudinal study included 34 index patients and two affected relatives with a molecular diagnosis of RPGR-related CD/CRDs. Patients were recruited at the "Quinze-Vingts" Hospital, Paris, France and screened for mutations in RPGRORF15 at the Institut de la Vision, Paris, France. We identified 29 distinct variants, of which 27 were truncating. All were located in the 3' half of the RPGRORF15 transcript. Twenty of them were novel. Fifteen subjects were affected by CD, the remaining had CRD. When analyzing the longitudinal data, a progressive decline in visual acuity (VA) was noted, with more than 60% of the patients reaching VA ≥ 1 LogMar in the best eye after the fifth decade of life. To our knowledge, this is the largest described study of a cohort of CD/CRD patients affected by RPGRORF15 variants. Longitudinal data showed a rapidly progressive disease, possibly locating an optimal window of intervention for future therapies in younger ages.
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Affiliation(s)
- Marco Nassisi
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, 75012 Paris, France; (M.N.); (G.D.B.); (S.M.-S.); (C.C.); (A.A.); (M.-E.L.); (K.B.); (V.S.); (T.P.); (J.-A.S.)
- Centre Hospitalier National d’Ophtalmologie des Quinze-Vingts, National Rare Disease Center REFERET and INSERM-DGOS CIC 1423, 75012 Paris, France
- Department of Clinical Sciences and Community Health, University of Milan, 20122 Milan, Italy
- Ophthalmology Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico di Milano, 20122 Milan, Italy
| | - Giuseppe De Bartolo
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, 75012 Paris, France; (M.N.); (G.D.B.); (S.M.-S.); (C.C.); (A.A.); (M.-E.L.); (K.B.); (V.S.); (T.P.); (J.-A.S.)
- Centre Hospitalier National d’Ophtalmologie des Quinze-Vingts, National Rare Disease Center REFERET and INSERM-DGOS CIC 1423, 75012 Paris, France
| | - Saddek Mohand-Said
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, 75012 Paris, France; (M.N.); (G.D.B.); (S.M.-S.); (C.C.); (A.A.); (M.-E.L.); (K.B.); (V.S.); (T.P.); (J.-A.S.)
- Centre Hospitalier National d’Ophtalmologie des Quinze-Vingts, National Rare Disease Center REFERET and INSERM-DGOS CIC 1423, 75012 Paris, France
| | - Christel Condroyer
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, 75012 Paris, France; (M.N.); (G.D.B.); (S.M.-S.); (C.C.); (A.A.); (M.-E.L.); (K.B.); (V.S.); (T.P.); (J.-A.S.)
| | - Aline Antonio
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, 75012 Paris, France; (M.N.); (G.D.B.); (S.M.-S.); (C.C.); (A.A.); (M.-E.L.); (K.B.); (V.S.); (T.P.); (J.-A.S.)
- Centre Hospitalier National d’Ophtalmologie des Quinze-Vingts, National Rare Disease Center REFERET and INSERM-DGOS CIC 1423, 75012 Paris, France
| | - Marie-Elise Lancelot
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, 75012 Paris, France; (M.N.); (G.D.B.); (S.M.-S.); (C.C.); (A.A.); (M.-E.L.); (K.B.); (V.S.); (T.P.); (J.-A.S.)
| | - Kinga Bujakowska
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, 75012 Paris, France; (M.N.); (G.D.B.); (S.M.-S.); (C.C.); (A.A.); (M.-E.L.); (K.B.); (V.S.); (T.P.); (J.-A.S.)
- Ocular Genomics Institute, Massachusetts Eye and Ear Infirmary, Department of Ophthalmology, Harvard Medical School, Boston, MA 02114, USA
| | - Vasily Smirnov
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, 75012 Paris, France; (M.N.); (G.D.B.); (S.M.-S.); (C.C.); (A.A.); (M.-E.L.); (K.B.); (V.S.); (T.P.); (J.-A.S.)
- Exploration de la Vision et Neuro-Ophthalmologie, Centre Hospitalier Universitaire de Lille, 59000 Lille, France
- Faculté de Médecine, Université de Lille, 59000 Lille, France
| | - Thomas Pugliese
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, 75012 Paris, France; (M.N.); (G.D.B.); (S.M.-S.); (C.C.); (A.A.); (M.-E.L.); (K.B.); (V.S.); (T.P.); (J.-A.S.)
- Centre Hospitalier National d’Ophtalmologie des Quinze-Vingts, National Rare Disease Center REFERET and INSERM-DGOS CIC 1423, 75012 Paris, France
| | - John Neidhardt
- Human Genetics, Faculty VI, School of Medicine and Health Sciences, University of Oldenburg, 26129 Oldenburg, Germany;
- Research Center Neurosensory Science, University Oldenburg, 26129 Oldenburg, Germany
| | - José-Alain Sahel
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, 75012 Paris, France; (M.N.); (G.D.B.); (S.M.-S.); (C.C.); (A.A.); (M.-E.L.); (K.B.); (V.S.); (T.P.); (J.-A.S.)
- Centre Hospitalier National d’Ophtalmologie des Quinze-Vingts, National Rare Disease Center REFERET and INSERM-DGOS CIC 1423, 75012 Paris, France
- Department of Ophthalmology, University of Pittsburgh Medical School, Pittsburgh, PA 15213, USA
| | - Christina Zeitz
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, 75012 Paris, France; (M.N.); (G.D.B.); (S.M.-S.); (C.C.); (A.A.); (M.-E.L.); (K.B.); (V.S.); (T.P.); (J.-A.S.)
| | - Isabelle Audo
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, 75012 Paris, France; (M.N.); (G.D.B.); (S.M.-S.); (C.C.); (A.A.); (M.-E.L.); (K.B.); (V.S.); (T.P.); (J.-A.S.)
- Centre Hospitalier National d’Ophtalmologie des Quinze-Vingts, National Rare Disease Center REFERET and INSERM-DGOS CIC 1423, 75012 Paris, France
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166
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Guo R, Du P, Pei Y, Yang J, Li S, Chang S, Sun H, He X, Dong J, Zhou J, Jing Z. Whole-Exome Sequencing Identified Genes Responsible for Thoracic Aortic Aneurysms and Dissections in three Chinese Families. Front Genet 2022; 13:910932. [PMID: 35754816 PMCID: PMC9215720 DOI: 10.3389/fgene.2022.910932] [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: 04/01/2022] [Accepted: 04/25/2022] [Indexed: 11/23/2022] Open
Abstract
Thoracic aortic aneurysms and dissections are precarious conditions that often cannot be diagnosed with fatal outcomes. Over the last few years, pathogenic variants in numerous genes have been identified that predispose to heritable presentations of TAAD. An evidence-based strategy for the selection of genes to test in familial TAAD helps inform family screening and intervention to prevent life-threatening events. Using whole-exome sequencing, four members of three unrelated families clinically diagnosed with TAAD were used to identify the genetic origin of the disorder. Variant evaluation was carried out to detect the pathogenic mutation. Our studies suggest that mutations of COL3A1 and ACTA2 are responsible for familial TAAD. In addition, we highlight FBLN5, FBN1, SLC2A10, FBN2, and NOTCH1 as candidate genes. Future studies of crosstalk among the pathways may provide us a step toward understanding the pathogenic mechanism. This finding indicates the necessity of obtaining family medical history and screening of extended relatives of patients with TAAD for the early identification and treatment of TAAD.
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Affiliation(s)
- Renle Guo
- Department of Vascular Surgery, Changhai Hospital, Naval Military Medical University, Shanghai, China.,Department of Vascular Surgery, Taian Central Hospital, Taian, China
| | - Pengcheng Du
- Department of Vascular Surgery, Changhai Hospital, Naval Military Medical University, Shanghai, China
| | - Yifei Pei
- Department of Vascular Surgery, Changhai Hospital, Naval Military Medical University, Shanghai, China
| | - Jin Yang
- Department of Vascular Surgery, Suining Central Hostpital, Suining, China
| | - Shuangshuang Li
- Department of Vascular Surgery, Changhai Hospital, Naval Military Medical University, Shanghai, China
| | - Sheng Chang
- Department of Vascular Surgery, Changhai Hospital, Naval Military Medical University, Shanghai, China
| | - Huiying Sun
- Department of Vascular Surgery, Changhai Hospital, Naval Military Medical University, Shanghai, China
| | - Xiaomin He
- Department of Vascular Surgery, Changhai Hospital, Naval Military Medical University, Shanghai, China
| | - Jian Dong
- Department of Vascular Surgery, Changhai Hospital, Naval Military Medical University, Shanghai, China.,Department of Vascular Surgery, Shanghai TCM-Integrated Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Jian Zhou
- Department of Vascular Surgery, Changhai Hospital, Naval Military Medical University, Shanghai, China
| | - Zaiping Jing
- Department of Vascular Surgery, Changhai Hospital, Naval Military Medical University, Shanghai, China
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167
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Kumar J, Lackey L, Waldern JM, Dey A, Mustoe AM, Weeks KM, Mathews DH, Laederach A. Quantitative prediction of variant effects on alternative splicing in MAPT using endogenous pre-messenger RNA structure probing. eLife 2022; 11:73888. [PMID: 35695373 PMCID: PMC9236610 DOI: 10.7554/elife.73888] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 06/12/2022] [Indexed: 11/29/2022] Open
Abstract
Splicing is highly regulated and is modulated by numerous factors. Quantitative predictions for how a mutation will affect precursor mRNA (pre-mRNA) structure and downstream function are particularly challenging. Here, we use a novel chemical probing strategy to visualize endogenous precursor and mature MAPT mRNA structures in cells. We used these data to estimate Boltzmann suboptimal structural ensembles, which were then analyzed to predict consequences of mutations on pre-mRNA structure. Further analysis of recent cryo-EM structures of the spliceosome at different stages of the splicing cycle revealed that the footprint of the Bact complex with pre-mRNA best predicted alternative splicing outcomes for exon 10 inclusion of the alternatively spliced MAPT gene, achieving 74% accuracy. We further developed a β-regression weighting framework that incorporates splice site strength, RNA structure, and exonic/intronic splicing regulatory elements capable of predicting, with 90% accuracy, the effects of 47 known and 6 newly discovered mutations on inclusion of exon 10 of MAPT. This combined experimental and computational framework represents a path forward for accurate prediction of splicing-related disease-causing variants.
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Affiliation(s)
- Jayashree Kumar
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, United States.,Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Lela Lackey
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, United States.,Department of Genetics and Biochemistry, Center for Human Genetics, Clemson University, Greenwood, United States
| | - Justin M Waldern
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Abhishek Dey
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Anthony M Mustoe
- Verna and Marrs McClean Department of Biochemistry and Molecular Biology, Therapeutic Innovation Center (THINC), and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, United States
| | - Kevin M Weeks
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - David H Mathews
- Department of Biochemistry & Biophysics and Center for RNA Biology, School of Medicine and Dentistry, University of Rochester, Rochester, United States
| | - Alain Laederach
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, United States.,Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, United States
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168
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Rare and population-specific functional variation across pig lines. Genet Sel Evol 2022; 54:39. [PMID: 35659233 PMCID: PMC9164375 DOI: 10.1186/s12711-022-00732-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 05/17/2022] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND It is expected that functional, mainly missense and loss-of-function (LOF), and regulatory variants are responsible for most phenotypic differences between breeds and genetic lines of livestock species that have undergone diverse selection histories. However, there is still limited knowledge about the existing missense and LOF variation in commercial livestock populations, in particular regarding population-specific variation and how it can affect applications such as across-breed genomic prediction. METHODS We re-sequenced the whole genome of 7848 individuals from nine commercial pig lines (average sequencing coverage: 4.1×) and imputed whole-genome genotypes for 440,610 pedigree-related individuals. The called variants were categorized according to predicted functional annotation (from LOF to intergenic) and prevalence level (number of lines in which the variant segregated; from private to widespread). Variants in each category were examined in terms of their distribution along the genome, alternative allele frequency, per-site Wright's fixation index (FST), individual load, and association to production traits. RESULTS Of the 46 million called variants, 28% were private (called in only one line) and 21% were widespread (called in all nine lines). Genomic regions with a low recombination rate were enriched with private variants. Low-prevalence variants (called in one or a few lines only) were enriched for lower allele frequencies, lower FST, and putatively functional and regulatory roles (including LOF and deleterious missense variants). On average, individuals carried fewer private deleterious missense alleles than expected compared to alleles with other predicted consequences. Only a small subset of the low-prevalence variants had intermediate allele frequencies and explained small fractions of phenotypic variance (up to 3.2%) of production traits. The significant low-prevalence variants had higher per-site FST than the non-significant ones. These associated low-prevalence variants were tagged by other more widespread variants in high linkage disequilibrium, including intergenic variants. CONCLUSIONS Most low-prevalence variants have low minor allele frequencies and only a small subset of low-prevalence variants contributed detectable fractions of phenotypic variance of production traits. Accounting for low-prevalence variants is therefore unlikely to noticeably benefit across-breed analyses, such as the prediction of genomic breeding values in a population using reference populations of a different genetic background.
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169
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Bomba L, Walter K, Guo Q, Surendran P, Kundu K, Nongmaithem S, Karim MA, Stewart ID, Langenberg C, Danesh J, Di Angelantonio E, Roberts DJ, Ouwehand WH, Dunham I, Butterworth AS, Soranzo N. Whole-exome sequencing identifies rare genetic variants associated with human plasma metabolites. Am J Hum Genet 2022; 109:1038-1054. [PMID: 35568032 PMCID: PMC9247822 DOI: 10.1016/j.ajhg.2022.04.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 04/13/2022] [Indexed: 12/11/2022] Open
Abstract
Metabolite levels measured in the human population are endophenotypes for biological processes. We combined sequencing data for 3,924 (whole-exome sequencing, WES, discovery) and 2,805 (whole-genome sequencing, WGS, replication) donors from a prospective cohort of blood donors in England. We used multiple approaches to select and aggregate rare genetic variants (minor allele frequency [MAF] < 0.1%) in protein-coding regions and tested their associations with 995 metabolites measured in plasma by using ultra-high-performance liquid chromatography-tandem mass spectrometry. We identified 40 novel associations implicating rare coding variants (27 genes and 38 metabolites), of which 28 (15 genes and 28 metabolites) were replicated. We developed algorithms to prioritize putative driver variants at each locus and used mediation and Mendelian randomization analyses to test directionality at associations of metabolite and protein levels at the ACY1 locus. Overall, 66% of reported associations implicate gene targets of approved drugs or bioactive drug-like compounds, contributing to drug targets' validating efforts.
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Affiliation(s)
- Lorenzo Bomba
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK; Open Targets, Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - Klaudia Walter
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
| | - Qi Guo
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK; National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics, University of Cambridge, Cambridge CB1 8RN, UK
| | - Praveen Surendran
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK; Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Puddicombe Way, Cambridge CB2 0AW, UK
| | - Kousik Kundu
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK; Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Puddicombe Way, Cambridge CB2 0AW, UK
| | - Suraj Nongmaithem
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
| | - Mohd Anisul Karim
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK; Open Targets, Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - Isobel D Stewart
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0SL, UK
| | - Claudia Langenberg
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0SL, UK; Computational Medicine, Berlin Institute of Health at Charité - Utniversitätsmedizin Berlin, Berlin 10117, Germany
| | - John Danesh
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK; British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK; British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge CB2 0QQ, UK; National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics, University of Cambridge, Cambridge CB1 8RN, UK; Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge CB10 1SA, UK
| | - Emanuele Di Angelantonio
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK; British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge CB2 0QQ, UK; National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics, University of Cambridge, Cambridge CB1 8RN, UK; Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge CB10 1SA, UK; Human Technopole, Palazzo Italia, Viale Rita Levi-Montalcini 1, 20157 Milan, Italy
| | - David J Roberts
- National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics, University of Cambridge, Cambridge CB1 8RN, UK; NHS Blood and Transplant-Oxford Centre, Level 2, John Radcliffe Hospital, Oxford OX3 9BQ, UK; Radcliffe Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9BQ, UK
| | - Willem H Ouwehand
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK; Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Puddicombe Way, Cambridge CB2 0AW, UK
| | | | - Ian Dunham
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK; Open Targets, Wellcome Genome Campus, Hinxton CB10 1SD, UK; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - Adam S Butterworth
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK; British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge CB2 0QQ, UK; National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics, University of Cambridge, Cambridge CB1 8RN, UK; Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge CB10 1SA, UK
| | - Nicole Soranzo
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK; Open Targets, Wellcome Genome Campus, Hinxton CB10 1SD, UK; Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Puddicombe Way, Cambridge CB2 0AW, UK; British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge CB2 0QQ, UK; National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics, University of Cambridge, Cambridge CB1 8RN, UK; Human Technopole, Palazzo Italia, Viale Rita Levi-Montalcini 1, 20157 Milan, Italy.
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170
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A novel missense variant in the LMNB2 gene causes progressive myoclonus epilepsy. Acta Neurol Belg 2022; 122:659-667. [PMID: 33783721 DOI: 10.1007/s13760-021-01650-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 03/08/2021] [Indexed: 12/18/2022]
Abstract
Progressive myoclonus epilepsies (PMEs) are a group of disorders embracing myoclonus, seizures, and neurological dysfunctions. Because of the genetic and clinical heterogeneity, a large proportion of PMEs cases have remained molecularly undiagnosed. The present study aimed to determine the underlying genetic factors that contribute to the PME phenotype in an Iranian female patient. We describe a consanguineous Iranian family with autosomal recessive PME that had remained undiagnosed despite extensive genetic and pathological tests. After performing neuroimaging and clinical examinations, due to heterogeneity of PMEs, the proband was subjected to paired-end whole-exome sequencing and the candidate variant was confirmed by Sanger sequencing. Various in-silico tools were also used to predict the pathogenicity of the variant. In this study, we identified a novel homozygous missense variant (NM_032737.4:c.472C > T; p.(Arg158Trp)) in the LMNB2 gene (OMIM: 150341) as the most likely disease-causing variant. Neuroimaging revealed a progressive significant generalized atrophy in the cerebral and cerebellum without significant white matter signal changes. Video-electroencephalography monitoring showed a generalized pattern of high-voltage sharp waves in addition to multifocal spikes and waves compatible with mixed type seizures and epileptic encephalopathic pattern. Herein, we introduce the second case of PME caused by a novel variant in the LMNB2 gene. This study also underscores the potentiality of next-generation sequencing in the genetic diagnosis of patients with neurologic diseases with an unknown cause.
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171
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Livesey BJ, Marsh JA. Interpreting protein variant effects with computational predictors and deep mutational scanning. Dis Model Mech 2022; 15:275742. [PMID: 35736673 PMCID: PMC9235876 DOI: 10.1242/dmm.049510] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Computational predictors of genetic variant effect have advanced rapidly in recent years. These programs provide clinical and research laboratories with a rapid and scalable method to assess the likely impacts of novel variants. However, it can be difficult to know to what extent we can trust their results. To benchmark their performance, predictors are often tested against large datasets of known pathogenic and benign variants. These benchmarking data may overlap with the data used to train some supervised predictors, which leads to data re-use or circularity, resulting in inflated performance estimates for those predictors. Furthermore, new predictors are usually found by their authors to be superior to all previous predictors, which suggests some degree of computational bias in their benchmarking. Large-scale functional assays known as deep mutational scans provide one possible solution to this problem, providing independent datasets of variant effect measurements. In this Review, we discuss some of the key advances in predictor methodology, current benchmarking strategies and how data derived from deep mutational scans can be used to overcome the issue of data circularity. We also discuss the ability of such functional assays to directly predict clinical impacts of mutations and how this might affect the future need for variant effect predictors.
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Affiliation(s)
- Benjamin J Livesey
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Joseph A Marsh
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
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172
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Huong NTM, Hoa NPA, Ngoc ND, Mai NTP, Yen PH, Anh HTV, Hoa G, Dien TM. Mutation spectrum of ATP7B gene in pediatric patients with Wilson disease in Vietnam. Mol Genet Metab Rep 2022; 31:100861. [PMID: 35782615 PMCID: PMC9248214 DOI: 10.1016/j.ymgmr.2022.100861] [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: 11/30/2021] [Revised: 03/08/2022] [Accepted: 03/09/2022] [Indexed: 12/08/2022] Open
Abstract
Background Wilson disease (WD) is caused by mutations in the copper-transporting P-type adenosine triphosphatase encoded by the ATP7B gene. In this study, we screened and identified the ATP7B mutations among unrelated Vietnamese pediatric patients. Methods One-hundred-thirteen pediatric patients with clinically diagnosed WD were recruited. DNA samples were extracted from peripheral blood. Mutations in the ATP7B gene were identified by Sanger sequencing. Results Approximately 98% of the clinically diagnosed WD patients carried ATP7B mutations. A total of 35 different ATP7B variants were detected, including five novel mutations (L658P, L792P, T977K, IVS4 + 1G > A and IVS20 + 4A > G). Remarkably, this study revealed that S105* was the most prevalent variant (32.27%), followed by L1371P (9.09%), I1148T (7.27%), R778L (6.36%), T850I (5.45%), V176Sfs*28 and IVS14-2A > G (4.55%). Most ATP7B mutations were located in the exon 2 (37.73%), exon 16 (10.00%), exon 8 (9.55%), exon 20 (9.09%), exon 10 and exon 18 (5.45%), exon 14 (5.00%), exon 13 and intron 14 (4.55%). We developed a streamlined procedure to quickly characterize mutations in the ATP7B gene in the Vietnamese children, starting with sequencing exon 2 and subsequently to exons 8,10,13-16,18, and 20 to allow quick diagnosis of clinically suspected patients. Conclusion The mutational spectrum and hotspots of ATP7B gene in the Vietnamese population were fairly different from other East Asian populations. A streamlined procedure was developed to screen exon 2 in ATP7B gene among suspected WD patients to reduce genetically diagnostic cost, to facilitate early detection and intervention in countries with limited resources.
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173
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Iosifidis C, Liu J, Gale T, Ellingford JM, Campbell C, Ingram S, Chandler K, Parry NRA, Black GC, Sergouniotis PI. Clinical and genetic findings in TRPM1-related congenital stationary night blindness. Acta Ophthalmol 2022; 100:e1332-e1339. [PMID: 35633130 DOI: 10.1111/aos.15186] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 05/05/2022] [Indexed: 11/27/2022]
Abstract
PURPOSE Congenital stationary night blindness (CSNB) is a heterogeneous group of Mendelian retinal disorders that present in childhood. Biallelic variants altering the protein-coding region of the TRPM1 gene are one of the commonest causes of CSNB. Here, we report the clinical and genetic findings in 10 unrelated individuals with TRPM1-retinopathy. METHODS Study subjects were recruited through a tertiary clinical ophthalmic genetic service at Manchester, UK. All participants underwent visual electrodiagnostic testing and panel-based genetic analysis. RESULTS Study subjects had a median age of 8 years (range: 3-20 years). All probands were myopic and had electroretinographic findings in keeping with complete CSNB. Notably, three probands reported no night vision problems. Fourteen different disease-associated TRPM1 variants were detected. One individual was homozygous for the NM_001252024.2 (TRPM1):c.965 + 29G>A variant and a mini-gene assay highlighted that this change results in mis-splicing and premature protein termination. Additionally, two unrelated probands who had CSNB and mild neurodevelopmental abnormalities were found to carry a 15q13.3 microdeletion. This copy number variant encompasses seven genes, including TRPM1, and was encountered in the heterozygous state and in trans with a missense TRPM1 variant in each case. CONCLUSION Our findings highlight the importance of comprehensive genomic analysis, beyond the exons and protein-coding regions of genes, for individuals with CSNB. When this characteristic retinal phenotype is accompanied by extraocular findings (including learning and/or behavioural difficulties), a 15q13.3 microdeletion should be suspected. Focused analysis (e.g. microarray testing) is recommended to look for large-scale deletions encompassing TRPM1 in patients with CSNB and neurodevelopmental abnormalities.
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Affiliation(s)
- Christos Iosifidis
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicines and Health University of Manchester Manchester UK
- Manchester Centre for Genomic Medicine, Saint Mary's Hospital Manchester University NHS Foundation Trust Manchester UK
- Manchester Royal Eye Hospital Manchester University NHS Foundation Trust Manchester UK
| | - Jingshu Liu
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicines and Health University of Manchester Manchester UK
| | - Theodora Gale
- Manchester Centre for Genomic Medicine, Saint Mary's Hospital Manchester University NHS Foundation Trust Manchester UK
| | - Jamie M. Ellingford
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicines and Health University of Manchester Manchester UK
- Manchester Centre for Genomic Medicine, Saint Mary's Hospital Manchester University NHS Foundation Trust Manchester UK
| | - Christopher Campbell
- Manchester Centre for Genomic Medicine, Saint Mary's Hospital Manchester University NHS Foundation Trust Manchester UK
| | - Stuart Ingram
- Manchester Centre for Genomic Medicine, Saint Mary's Hospital Manchester University NHS Foundation Trust Manchester UK
| | - Kate Chandler
- Manchester Centre for Genomic Medicine, Saint Mary's Hospital Manchester University NHS Foundation Trust Manchester UK
| | - Neil R. A. Parry
- Manchester Royal Eye Hospital Manchester University NHS Foundation Trust Manchester UK
- Division of Pharmacy and Optometry, School of Health Sciences, Faculty of Biology, Medicines and Health University of Manchester Manchester UK
| | - Graeme C. Black
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicines and Health University of Manchester Manchester UK
- Manchester Centre for Genomic Medicine, Saint Mary's Hospital Manchester University NHS Foundation Trust Manchester UK
| | - Panagiotis I. Sergouniotis
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicines and Health University of Manchester Manchester UK
- Manchester Centre for Genomic Medicine, Saint Mary's Hospital Manchester University NHS Foundation Trust Manchester UK
- Manchester Royal Eye Hospital Manchester University NHS Foundation Trust Manchester UK
- Institute of Biochemistry and Molecular Genetics, Faculty of Medicine University of Ljubljana Ljubljana Slovenia
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174
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Lin D, Du H, Zhao S, Liu B, Song H, Wang G, Zhang W, Liang H, Liu P, Liu C, Han W, Li Z, Yang Y, Chen S, Zhao L, Li X, Wu Z, Qiu G, Wu Z, Zhang TJ, Wu N, Wang S, Liu J, Liu S, Zuo Y, Liu G, Yu C, Liu L, Shao J, Zhao S, Yan Z, Zhao H, Niu Y, Li X, Wang H, Ma C, Chen Z, Liu B, Cheng X, Lin J, Du H, Li Y, Song S, Tian W, Xie Z, Zhao Z, Zhao L, Zhao Z, Zheng Z, Huang Y, Sun N, Wu N. Phenotype expansion of variants affecting p38 MAPK signaling in hypospadias patients. Orphanet J Rare Dis 2022; 17:209. [PMID: 35606856 PMCID: PMC9128137 DOI: 10.1186/s13023-022-02334-5] [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: 09/10/2021] [Accepted: 04/26/2022] [Indexed: 11/10/2022] Open
Abstract
Background Hypospadias is a congenital anomaly of the male urogenital system. Genetics factors play an important role in its pathogenesis. To search for potential causal genes/variants for hypospadias, we performed exome sequencing in a pedigree with three patients across two generations and a cohort of 49 sporadic patients with hypospadias. Results A novel BRAF variant (NM_004333.6: c.362C > A) was found to co-segregate with the hypospadias phenotype in the disease pedigree. In cells overexpressing the BRAF mutant, the phosphorylation level of p38 MAPK was significantly increased as compared with the cells overexpressing the wild-type BRAF or RASopathy-related BRAF mutant. This variant further led to a reduced transcription level of the SRY gene, which is essential for the normal development of the male reproductive system. In the cohort of sporadic patients, we identified two additional variants in p38 MAPK signaling-related genes (TRIM67 and DAB2IP) potentially associated with hypospadias. Conclusion Our study expands the phenotypic spectrum of variants affecting p38 MAPK signaling toward the involvement of hypospadias.
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175
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Giovannetti A, Bianco SD, Traversa A, Panzironi N, Bruselles A, Lazzari S, Liorni N, Tartaglia M, Carella M, Pizzuti A, Mazza T, Caputo V. MiRLog and dbmiR: prioritization and functional annotation tools to study human microRNA sequence variants. Hum Mutat 2022; 43:1201-1215. [PMID: 35583122 PMCID: PMC9546175 DOI: 10.1002/humu.24399] [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: 01/27/2022] [Revised: 05/03/2022] [Accepted: 05/11/2022] [Indexed: 11/22/2022]
Abstract
The recent identification of noncoding variants with pathogenic effects suggests that these variations could underlie a significant number of undiagnosed cases. Several computational methods have been developed to predict the functional impact of noncoding variants, but they exhibit only partial concordance and are not integrated with functional annotation resources, making the interpretation of these variants still challenging. MicroRNAs (miRNAs) are small noncoding RNA molecules that act as fine regulators of gene expression and play crucial functions in several biological processes, such as cell proliferation and differentiation. An increasing number of studies demonstrate a significant impact of miRNA single nucleotide variants (SNVs) both in Mendelian diseases and complex traits. To predict the functional effect of miRNA SNVs, we implemented a new meta‐predictor, MiRLog, and we integrated it into a comprehensive database, dbmiR, which includes a precompiled list of all possible miRNA allelic SNVs, providing their biological annotations at nucleotide and miRNA levels. MiRLog and dbmiR were used to explore the genetic variability of miRNAs in 15,708 human genomes included in the gnomAD project, finding several ultra‐rare SNVs with a potentially deleterious effect on miRNA biogenesis and function representing putative contributors to human phenotypes.
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Affiliation(s)
- Agnese Giovannetti
- Laboratory of Clinical Genomics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo (FG), Italy
| | - Salvatore Daniele Bianco
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy.,Unit of Bioinformatics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo (FG), Italy
| | - Alice Traversa
- Laboratory of Clinical Genomics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo (FG), Italy
| | - Noemi Panzironi
- Laboratory of Clinical Genomics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo (FG), Italy
| | - Alessandro Bruselles
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Sara Lazzari
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Niccolò Liorni
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy.,Unit of Bioinformatics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo (FG), Italy
| | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Massimo Carella
- Medical Genetics Unit, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo (FG), Italy
| | - Antonio Pizzuti
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Tommaso Mazza
- Unit of Bioinformatics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo (FG), Italy
| | - Viviana Caputo
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
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176
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Tawfik CA, Elbagoury NM, Khater NI, Essawi ML. Mutation analysis reveals novel and known mutations in SAG gene in first two Egyptian families with Oguchi disease. BMC Ophthalmol 2022; 22:217. [PMID: 35549688 PMCID: PMC9103117 DOI: 10.1186/s12886-022-02444-5] [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: 01/10/2022] [Accepted: 05/04/2022] [Indexed: 11/29/2022] Open
Abstract
Background Oguchi disease is a rare type of congenital stationary night blindness associated with an abnormal fundus appearance. It is inherited in an autosomal recessive manner where two types exist according to the gene affected; type 1 associated with S-antigen (SAG) gene mutations and type 2 associated with rhodopsin kinase (GRK1) gene mutations. Purpose The aim of this work was to describe the clinical and genetic findings of the first two reported families of Oguchi disease in Egypt and African region. Methods Four members of two consanguineous Egyptian families with history of night blindness since childhood underwent complete ophthalmological examination, standard automated static perimetry, fundus color photography, fundus autofluorescence (FAF), fundus fluorescein angiography (FFA) in light-adapted state and spectral-domain optical coherence tomography (SD-OCT) of both the macula and the optic nerve head as well as central corneal thickness with repeated fundus photography following prolonged dark adaptation. Mutation screening of 7 coding exons of GRK1 gene and 15 coding exons of SAG gene as well as some flanking regions were performed using Sanger sequencing technique. The variants were tested for pathogenicity using different in silico functional analysis tools. Results The clinical examination and investigations confirmed Oguchi disease phenotype. One patient showed p.R193* (c.577C > T) which is a previously reported SAG gene mutation in a homozygous form. The other three patients from a different family showed (c.649–1 G > C), a novel canonical splice site SAG gene mutation in a homozygous form. Conclusion The identification of the novel canonical splice site SAG gene variant in three members of the same family with clinically confirmed Oguchi disease reinforces its pathogenicity. A fourth patient from another family carried a previously reported mutation in the same gene. SAG gene variants may be the underlying genetic cause for Oguchi disease in Egypt. Our findings have expanded the spectrum of Oguchi disease-associated mutations in SAG gene and may serve as a basis for genetic diagnosis for Oguchi disease.
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Affiliation(s)
- Caroline Atef Tawfik
- Department of Ophthalmology, Ain Shams University, 38 Abbasseya, Nour Mosque, El-Mohamady, Al Waili, Cairo, 11566, Egypt.
| | - Nagham Maher Elbagoury
- Medical Molecular Genetics Department, Human Genetics and Genome Research Institute, National Research Centre, Cairo, Egypt.,Center of Excellence for Human Genetics, National Research Centre, Cairo, Egypt
| | - Noha Ibrahim Khater
- Department of Ophthalmology, Cairo University, Giza, Egypt.,Al Mouneer Diabetic Eye Center, Dokki, Giza, Egypt
| | - Mona Lotfi Essawi
- Medical Molecular Genetics Department, Human Genetics and Genome Research Institute, National Research Centre, Cairo, Egypt.,Center of Excellence for Human Genetics, National Research Centre, Cairo, Egypt
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177
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Yang M, Huang L, Huang H, Tang H, Zhang N, Yang H, Wu J, Mu F. Integrating convolution and self-attention improves language model of human genome for interpreting non-coding regions at base-resolution. Nucleic Acids Res 2022; 50:e81. [PMID: 35536244 PMCID: PMC9371931 DOI: 10.1093/nar/gkac326] [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: 09/22/2021] [Revised: 02/22/2022] [Accepted: 05/09/2022] [Indexed: 12/12/2022] Open
Abstract
Interpretation of non-coding genome remains an unsolved challenge in human genetics due to impracticality of exhaustively annotating biochemically active elements in all conditions. Deep learning based computational approaches emerge recently to help interpret non-coding regions. Here, we present LOGO (Language of Genome), a self-attention based contextualized pre-trained language model containing only two self-attention layers with 1 million parameters as a substantially light architecture that applies self-supervision techniques to learn bidirectional representations of the unlabelled human reference genome. LOGO is then fine-tuned for sequence labelling task, and further extended to variant prioritization task via a special input encoding scheme of alternative alleles followed by adding a convolutional module. Experiments show that LOGO achieves 15% absolute improvement for promoter identification and up to 4.5% absolute improvement for enhancer-promoter interaction prediction. LOGO exhibits state-of-the-art multi-task predictive power on thousands of chromatin features with only 3% parameterization benchmarking against the fully supervised model, DeepSEA and 1% parameterization against a recent BERT-based DNA language model. For allelic-effect prediction, locality introduced by one dimensional convolution shows improved sensitivity and specificity for prioritizing non-coding variants associated with human diseases. In addition, we apply LOGO to interpret type 2 diabetes (T2D) GWAS signals and infer underlying regulatory mechanisms. We make a conceptual analogy between natural language and human genome and demonstrate LOGO is an accurate, fast, scalable, and robust framework to interpret non-coding regions for global sequence labeling as well as for variant prioritization at base-resolution.
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Affiliation(s)
- Meng Yang
- MGI, BGI-Shenzhen, Shenzhen 518083, China.,Department of Biology, University of Copenhagen, Copenhagen DK-2200, Denmark
| | | | | | - Hui Tang
- MGI, BGI-Shenzhen, Shenzhen 518083, China
| | - Nan Zhang
- MGI, BGI-Shenzhen, Shenzhen 518083, China
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen 518083, China.,Guangdong Provincial Academician Workstation of BGI Synthetic Genomics, BGI-Shenzhen, Shenzhen, 518120, China
| | - Jihong Wu
- Department of Ophthalmology, Eye & ENT Hospital, Shanghai Medical College, Fudan University, Shanghai, China.,Shanghai Key Laboratory of Visual Impairment and Restoration, Science and Technology Commission of Shanghai Municipality, Shanghai, China.,Key Laboratory of Myopia (Fudan University), Chinese Academy of Medical Sciences, National Health Commission, Shanghai, China
| | - Feng Mu
- MGI, BGI-Shenzhen, Shenzhen 518083, China
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178
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Mahalapbutr P, Klaewkla M, Charoenwongpaiboon T. Unraveling the effect of A143T, P205T and D244N mutations in α-galactosidase A on its catalytic activity and susceptibility to globotriaosylceramide and iminosugar 1-deoxygalactonojirimycin chaperone. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.118790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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179
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Laver TW, Wakeling MN, Knox O, Colclough K, Wright CF, Ellard S, Hattersley AT, Weedon MN, Patel KA. Evaluation of Evidence for Pathogenicity Demonstrates That BLK, KLF11, and PAX4 Should Not Be Included in Diagnostic Testing for MODY. Diabetes 2022; 71:1128-1136. [PMID: 35108381 PMCID: PMC9044126 DOI: 10.2337/db21-0844] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 01/30/2022] [Indexed: 12/05/2022]
Abstract
Maturity-onset diabetes of the young (MODY) is an autosomal dominant form of monogenic diabetes, reported to be caused by variants in 16 genes. Concern has been raised about whether variants in BLK (MODY11), KLF11 (MODY7), and PAX4 (MODY9) cause MODY. We examined variant-level genetic evidence (cosegregation with diabetes and frequency in population) for published putative pathogenic variants in these genes and used burden testing to test gene-level evidence in a MODY cohort (n = 1,227) compared with a control population (UK Biobank [n = 185,898]). For comparison we analyzed well-established causes of MODY, HNF1A, and HNF4A. The published variants in BLK, KLF11, and PAX4 showed poor cosegregation with diabetes (combined logarithm of the odds [LOD] scores ≤1.2), compared with HNF1A and HNF4A (LOD scores >9), and are all too common to cause MODY (minor allele frequency >4.95 × 10-5). Ultra-rare missense and protein-truncating variants (PTV) were not enriched in a MODY cohort compared with the UK Biobank population (PTV P > 0.05, missense P > 0.1 for all three genes) while HNF1A and HNF4A were enriched (P < 10-6). Findings of sensitivity analyses with different population cohorts supported our results. Variant and gene-level genetic evidence does not support BLK, KLF11, or PAX4 as a cause of MODY. They should not be included in MODY diagnostic genetic testing.
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Affiliation(s)
- Thomas W. Laver
- Institute of Biomedical and Clinical Science, University of Exeter, Exeter, U.K
| | - Matthew N. Wakeling
- Institute of Biomedical and Clinical Science, University of Exeter, Exeter, U.K
| | - Olivia Knox
- Institute of Biomedical and Clinical Science, University of Exeter, Exeter, U.K
| | - Kevin Colclough
- Exeter Genomics Laboratory, Royal Devon and Exeter NHS Foundation Trust, Exeter, U.K
| | - Caroline F. Wright
- Institute of Biomedical and Clinical Science, University of Exeter, Exeter, U.K
| | - Sian Ellard
- Institute of Biomedical and Clinical Science, University of Exeter, Exeter, U.K
| | | | - Michael N. Weedon
- Institute of Biomedical and Clinical Science, University of Exeter, Exeter, U.K
| | - Kashyap A. Patel
- Institute of Biomedical and Clinical Science, University of Exeter, Exeter, U.K
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180
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Markova TV, Kenis V, Melchenko E, Guseva D, Osipova D, Galeeva N, Nagornova T, Dadali EL. Clinical and genetic characterization of three Russian patients with pycnodysostosis due to pathogenic variants in the CTSK gene. Mol Genet Genomic Med 2022; 10:e1904. [PMID: 35315254 PMCID: PMC9034671 DOI: 10.1002/mgg3.1904] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 01/22/2022] [Accepted: 01/31/2022] [Indexed: 11/07/2022] Open
Abstract
BACKGROUND Pycnodysostosis (PD, OMIM # 265800) is a rare variant of skeletal dysplasia with an autosomal recessive type of inheritance, characterized by a combination of specific features such as disproportionate nanism, generalized osteosclerosis, and distinct craniofacial dysmorphism. Radiographic features include acro-osteolysis of the distal phalanges in association with sclerosing bone lesions with multiple fractures. The polymorphism of the clinical manifestations of pycnodysostosis and low prevalence of the disorder lead to the difficulties with early. METHODS The following tests were used for diagnostics: genealogical analysis, clinical examination, neurological examination according to the standard method with an assessment of the psychoemotional sphere, radiological analysis, searching for pathogenic variants in the CTSK gene by the automated Sanger sequencing. RESULTS We describe first clinical and genetic characteristics of three Russian patients with pycnodysostosis from unrelated families. Two patients have a novel homozygous nucleotide substitution c.746T>A (p. Ile249Asn), and one has a previously described homozygous pathogenic variant c.746T>C (p.Ile249Thr) in the CTSK gene. In all three cases, a transition or transversion was found at nucleotide position 746 in exon 6 of the CTSK gene, leading to two different amino acid substitutions in the polypeptide chain. The obtained results may indicate the presence of a major pathogenic variant in the CTSK gene, leading to the typical manifestation of the disease. CONCLUSION The data presented in the study enlarge the clinical, radiological, and mutational spectrum of pycnodysostosis. Typical clinical manifestations and the small size of the CTSK gene make the automated Sanger sequencing the optimal method for diagnosis of pycnodysostosis.
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Affiliation(s)
| | - Vladimir Kenis
- H.Turner National Medical Research Center for Сhildren's Orthopedics and Trauma SurgeryPushkinRussia
| | - Evgeniy Melchenko
- H.Turner National Medical Research Center for Сhildren's Orthopedics and Trauma SurgeryPushkinRussia
| | - Darya Guseva
- Research Centre for Medical GeneticsMoscowRussia
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Computational Saturation Mutagenesis to Investigate the Effects of Neurexin-1 Mutations on AlphaFold Structure. Genes (Basel) 2022; 13:genes13050789. [PMID: 35627176 PMCID: PMC9141173 DOI: 10.3390/genes13050789] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 04/20/2022] [Accepted: 04/23/2022] [Indexed: 02/05/2023] Open
Abstract
Neurexin-1 (NRXN1) is a membrane protein essential in synapse formation and cell signaling as a cell-adhesion molecule and cell-surface receptor. NRXN1 and its binding partner neuroligin have been associated with deficits in cognition. Recent genetics research has linked NRXN1 missense mutations to increased risk for brain disorders, including schizophrenia (SCZ) and autism spectrum disorder (ASD). Investigation of the structure-function relationship in NRXN1 has proven difficult due to a lack of the experimental full-length membrane protein structure. AlphaFold, a deep learning-based predictor, succeeds in high-quality protein structure prediction and offers a solution for membrane protein model construction. In the study, we applied a computational saturation mutagenesis method to analyze the systemic effects of missense mutations on protein functions in a human NRXN1 structure predicted from AlphaFold and an experimental Bos taurus structure. The folding energy changes were calculated to estimate the effects of the 29,540 mutations of AlphaFold model on protein stability. The comparative study on the experimental and computationally predicted structures shows that these energy changes are highly correlated, demonstrating the reliability of the AlphaFold structure for the downstream bioinformatics analysis. The energy calculation revealed that some target mutations associated with SCZ and ASD could make the protein unstable. The study can provide helpful information for characterizing the disease-causing mutations and elucidating the molecular mechanisms by which the variations cause SCZ and ASD. This methodology could provide the bioinformatics protocol to investigate the effects of target mutations on multiple AlphaFold structures.
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182
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The Contribution of Rare Copy Number Variants in FAS Towards Pathogenesis of Autoimmune Lymphoproliferative Syndrome. Blood Adv 2022; 6:3974-3978. [PMID: 35476126 PMCID: PMC9278309 DOI: 10.1182/bloodadvances.2021005835] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 04/07/2022] [Indexed: 12/02/2022] Open
Abstract
Rare copy number variants in FAS can cause ALPS by method of haploinsufficiency. CNV analysis can provide a molecular diagnosis for patients with ALPS when whole exome sequencing or panel-based testing are inconclusive.
Autoimmune lymphoproliferative syndrome (ALPS) is characterized by chronic nonmalignant lymphadenopathy, splenomegaly, cytopenias, and other autoimmune manifestations. ALPS is caused by lymphocyte accumulation from defects in FAS-mediated apoptosis. Heterozygous germline or somatic pathogenic single nucleotide variants in FAS are the most common molecular etiology of ALPS. Through the Centralized Sequencing Program at the National Institute of Allergy and Infectious Diseases, we performed exome sequencing on subjects with a clinical diagnosis of ALPS, with a subset receiving copy number variant (CNV) analysis. In this cohort, we identified 3 subjects from unrelated families with CNVs at the FAS locus. One subject had a de novo ∼0.828 Mb copy number loss encompassing all of FAS. The second subject had a maternally inherited ∼1.004 Mb copy number loss encompassing all of FAS. The third subject had a paternally inherited ∼0.044 Mb copy number loss encompassing exons 7 through 9 of FAS. Subjects with deletions in FAS had clinical presentations and biomarker profiles similar to those with ALPS and with germline and somatic FAS variants. We demonstrate that CNV analysis should be pursued if there is clinical and biomarker evidence of ALPS because it can lead to a molecular diagnosis and appropriate treatment when FAS sequencing is inconclusive.
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183
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Ferroptosis and Apoptosis Are Involved in the Formation of L-Selenomethionine-Induced Ocular Defects in Zebrafish Embryos. Int J Mol Sci 2022; 23:ijms23094783. [PMID: 35563172 PMCID: PMC9100823 DOI: 10.3390/ijms23094783] [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: 04/05/2022] [Revised: 04/22/2022] [Accepted: 04/25/2022] [Indexed: 12/16/2022] Open
Abstract
Selenium is an essential trace element for humans and other vertebrates, playing an important role in antioxidant defense, neurobiology and reproduction. However, the toxicity of excessive selenium has not been thoroughly evaluated, especially for the visual system of vertebrates. In this study, fertilized zebrafish embryos were treated with 0.5 µM L-selenomethionine to investigate how excessive selenium alters zebrafish eye development. Selenium-stressed zebrafish embryos showed microphthalmia and altered expression of genes required for retinal neurogenesis. Moreover, ectopic proliferation, disrupted mitochondrial morphology, elevated ROS-induced oxidative stress, apoptosis and ferroptosis were observed in selenium-stressed embryos. Two antioxidants—reduced glutathione (GSH) and N-acetylcysteine (NAC)—and the ferroptosis inhibitor ferrostatin (Fer-1) were unable to rescue selenium-induced eye defects, but the ferroptosis and apoptosis activator cisplatin (CDDP) was able to improve microphthalmia and the expression of retina-specific genes in selenium-stressed embryos. In summary, our results reveal that ferroptosis and apoptosis might play a key role in selenium-induced defects of embryonic eye development. The findings not only provide new insights into selenium-induced cellular damage and death, but also important implications for studying the association between excessive selenium and ocular diseases in the future.
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184
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Abstract
Parathyroid hormone (PTH) and PTH-related peptide (PTHrP) regulate extracellular phosphate and calcium homeostasis as well as bone remodeling. PTH is a classic endocrine peptide hormone whose synthesis and negative feedback by multiple factors control release from the parathyroid glands. PTHrP is ubiquitously expressed (pre- and postnatally) and acts in an autocrine/paracrine manner. This review considers the structural pharmacology and actions of PTH and PTHrP, biological consequences of inherited mutations, engineered analogs that illuminate similarities and differences in physiologic actions, and targeted therapeutic opportunities.
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Affiliation(s)
- Larry J Suva
- Department of Veterinary Physiology and Pharmacology, College of Veterinary Medicine and Biomedical Sciences, Texas Veterinary Medical Center 4466 Texas A&M University, College Station, TX, United States
| | - Peter A Friedman
- Department of Pharmacology and Chemical Biology, Laboratory for GPCR Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States.
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185
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Muzammal M, Di Cerbo A, Almusalami EM, Farid A, Khan MA, Ghazanfar S, Al Mohaini M, Alsalman AJ, Alhashem YN, Al Hawaj MA, Alsaleh AA. In Silico Analysis of the L-2-Hydroxyglutarate Dehydrogenase Gene Mutations and Their Biological Impact on Disease Etiology. Genes (Basel) 2022; 13:genes13040698. [PMID: 35456504 PMCID: PMC9028441 DOI: 10.3390/genes13040698] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 04/08/2022] [Accepted: 04/12/2022] [Indexed: 02/04/2023] Open
Abstract
The L-2-hydroxyglutarate dehydrogenase (L2HGDH) gene encodes an important mitochondrial enzyme. However, its altered activity results in excessive levels of L-2-hydroxyglutarate, which results in diverse psychiatric features of intellectual disability. In the current study, we executed an in-silico analysis of all reported L2HGDH missense and nonsense variants in order to investigate their biological significance. Among the superimposed 3D models, the highest similarity index for a wild-type structure was shown by the mutant Glu336Lys (87.26%), while the lowest similarity index value was shown by Arg70* (10.00%). Three large active site pockets were determined using protein active site prediction, in which the 2nd largest pocket was shown to encompass the substrate L-2-hydroxyglutarate (L2HG) binding residues, i.e., 89Gln, 195Tyr, 402Ala, 403Gly and 404Val. Moreover, interactions of wild-type and mutant L2HGDH variants with the close functional interactor D2HGDH protein resulted in alterations in the position, number and nature of networking residues. We observed that the binding of L2HG with the L2HGDH enzyme is affected by the nature of the amino acid substitution, as well as the number and nature of bonds between the substrate and protein molecule, which are able to affect its biological activity.
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Affiliation(s)
- Muhammad Muzammal
- Gomal Centre of Biochemistry and Biotechnology, Gomal University, Dera Ismail Khan 29050, Pakistan; (M.M.); (M.A.K.)
| | - Alessandro Di Cerbo
- School of Biosciences and Veterinary Medicine, University of Camerino, 62024 Matelica, Italy
- Correspondence: (A.D.C.); (A.F.)
| | | | - Arshad Farid
- Gomal Centre of Biochemistry and Biotechnology, Gomal University, Dera Ismail Khan 29050, Pakistan; (M.M.); (M.A.K.)
- Correspondence: (A.D.C.); (A.F.)
| | - Muzammil Ahmad Khan
- Gomal Centre of Biochemistry and Biotechnology, Gomal University, Dera Ismail Khan 29050, Pakistan; (M.M.); (M.A.K.)
- Department of Human Genetics, Precision Medicine Program, Sidra Medicine, Doha 26999, Qatar
| | - Shakira Ghazanfar
- National Institute for Genomics Advanced Biotechnology, National Agricultural Research Centre, Park Road, Islamabad 45500, Pakistan;
| | - Mohammed Al Mohaini
- Basic Sciences Department, College of Applied Medical Sciences, King Saud bin Abdulaziz University for Health Sciences, Alahsa 31982, Saudi Arabia;
- King Abdullah International Medical Research Center, Alahsa 31982, Saudi Arabia
| | - Abdulkhaliq J. Alsalman
- Department of Clinical Pharmacy, Faculty of Pharmacy, Northern Border University, Rafha 91911, Saudi Arabia;
| | - Yousef N. Alhashem
- Clinical Laboratory Sciences Department, Mohammed Al-Mana College for Medical Sciences, Dammam 34222, Saudi Arabia; (Y.N.A.); (A.A.A.)
| | - Maitham A. Al Hawaj
- Department of Pharmacy Practice, College of Clinical Pharmacy, King Faisal University, Al-Ahsa 31982, Saudi Arabia;
| | - Abdulmonem A. Alsaleh
- Clinical Laboratory Sciences Department, Mohammed Al-Mana College for Medical Sciences, Dammam 34222, Saudi Arabia; (Y.N.A.); (A.A.A.)
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186
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Esfandiary A, Finkelstein DI, Voelcker NH, Rudd D. Clinical Sphingolipids Pathway in Parkinson’s Disease: From GCase to Integrated-Biomarker Discovery. Cells 2022; 11:cells11081353. [PMID: 35456032 PMCID: PMC9028315 DOI: 10.3390/cells11081353] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 04/11/2022] [Accepted: 04/13/2022] [Indexed: 02/01/2023] Open
Abstract
Alterations in the sphingolipid metabolism of Parkinson’s Disease (PD) could be a potential diagnostic feature. Only around 10–15% of PD cases can be diagnosed through genetic alterations, while the remaining population, idiopathic PD (iPD), manifest without validated and specific biomarkers either before or after motor symptoms appear. Therefore, clinical diagnosis is reliant on the skills of the clinician, which can lead to misdiagnosis. IPD cases present with a spectrum of non-specific symptoms (e.g., constipation and loss of the sense of smell) that can occur up to 20 years before motor function loss (prodromal stage) and formal clinical diagnosis. Prodromal alterations in metabolites and proteins from the pathways underlying these symptoms could act as biomarkers if they could be differentiated from the broad values seen in a healthy age-matched control population. Additionally, these shifts in metabolites could be integrated with other emerging biomarkers/diagnostic tests to give a PD-specific signature. Here we provide an up-to-date review of the diagnostic value of the alterations in sphingolipids pathway in PD by focusing on the changes in definitive PD (postmortem confirmed brain data) and their representation in “probable PD” cerebrospinal fluid (CSF) and blood. We conclude that the trend of holistic changes in the sphingolipid pathway in the PD brain seems partly consistent in CSF and blood, and could be one of the most promising pathways in differentiating PD cases from healthy controls, with the potential to improve early-stage iPD diagnosis and distinguish iPD from other Parkinsonism when combined with other pathological markers.
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Affiliation(s)
- Ali Esfandiary
- Drug Delivery, Disposition and Dynamics, Monash University, Parkville, VIC 3052, Australia; (A.E.); (N.H.V.)
- Melbourne Centre for Nanofabrication, Victorian Node of the Australian National Fabrication Facility, Clayton, VIC 3168, Australia
| | | | - Nicolas Hans Voelcker
- Drug Delivery, Disposition and Dynamics, Monash University, Parkville, VIC 3052, Australia; (A.E.); (N.H.V.)
- Melbourne Centre for Nanofabrication, Victorian Node of the Australian National Fabrication Facility, Clayton, VIC 3168, Australia
- Commonwealth Scientific and Industrial Research Organization (CSIRO), Clayton, VIC 3168, Australia
- Materials Science and Engineering, Monash University, Clayton, VIC 3168, Australia
| | - David Rudd
- Drug Delivery, Disposition and Dynamics, Monash University, Parkville, VIC 3052, Australia; (A.E.); (N.H.V.)
- Melbourne Centre for Nanofabrication, Victorian Node of the Australian National Fabrication Facility, Clayton, VIC 3168, Australia
- Correspondence: ; Tel.: +61-3-9903-9581
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187
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Bender C, Woo EG, Guan B, Ullah E, Feng E, Turriff A, Tumminia SJ, Sieving PA, Cukras CA, Hufnagel RB. Predominant Founder Effect among Recurrent Pathogenic Variants for an X-Linked Disorder. Genes (Basel) 2022; 13:genes13040675. [PMID: 35456481 PMCID: PMC9029724 DOI: 10.3390/genes13040675] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 04/06/2022] [Accepted: 04/06/2022] [Indexed: 02/05/2023] Open
Abstract
For disorders with X-linked inheritance, variants may be transmitted through multiple generations of carrier females before an affected male is ascertained. Pathogenic RS1 variants exclusively cause X-linked retinoschisis (XLRS). While RS1 is constrained to variation, recurrent variants are frequently observed in unrelated probands. Here, we investigate recurrent pathogenic variants to determine the relative burden of mutational hotspot and founder allele events to this phenomenon. A cohort RS1 variant analysis and standardized classification, including variant enrichment in the XLRS cohort and in RS1 functional domains, were performed on 332 unrelated XLRS probands. A total of 108 unique RS1 variants were identified. A subset of 19 recurrently observed RS1 variants were evaluated in 190 probands by a haplotype analysis, using microsatellite and single nucleotide polymorphisms. Fourteen variants had at least two probands with common variant-specific haplotypes over ~1.95 centimorgans (cM) flanking RS1. Overall, 99/190 of reportedly unrelated probands had 25 distinct shared haplotypes. Examination of this XLRS cohort for common RS1 haplotypes indicates that the founder effect plays a significant role in this disorder, including variants in mutational hotspots. This improves the accuracy of clinical variant classification and may be generalizable to other X-linked disorders.
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Affiliation(s)
- Chelsea Bender
- National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA; (C.B.); (E.G.W.); (B.G.); (E.U.); (E.F.); (A.T.); (S.J.T.); (P.A.S.); (C.A.C.)
| | - Elizabeth Geena Woo
- National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA; (C.B.); (E.G.W.); (B.G.); (E.U.); (E.F.); (A.T.); (S.J.T.); (P.A.S.); (C.A.C.)
| | - Bin Guan
- National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA; (C.B.); (E.G.W.); (B.G.); (E.U.); (E.F.); (A.T.); (S.J.T.); (P.A.S.); (C.A.C.)
| | - Ehsan Ullah
- National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA; (C.B.); (E.G.W.); (B.G.); (E.U.); (E.F.); (A.T.); (S.J.T.); (P.A.S.); (C.A.C.)
| | - Eric Feng
- National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA; (C.B.); (E.G.W.); (B.G.); (E.U.); (E.F.); (A.T.); (S.J.T.); (P.A.S.); (C.A.C.)
| | - Amy Turriff
- National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA; (C.B.); (E.G.W.); (B.G.); (E.U.); (E.F.); (A.T.); (S.J.T.); (P.A.S.); (C.A.C.)
| | - Santa J. Tumminia
- National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA; (C.B.); (E.G.W.); (B.G.); (E.U.); (E.F.); (A.T.); (S.J.T.); (P.A.S.); (C.A.C.)
| | - Paul A. Sieving
- National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA; (C.B.); (E.G.W.); (B.G.); (E.U.); (E.F.); (A.T.); (S.J.T.); (P.A.S.); (C.A.C.)
- UC Davis Medical Center, Ophthalmology & Vision Sciences, University of California, Davis, CA 95817, USA
| | - Catherine A. Cukras
- National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA; (C.B.); (E.G.W.); (B.G.); (E.U.); (E.F.); (A.T.); (S.J.T.); (P.A.S.); (C.A.C.)
| | - Robert B. Hufnagel
- National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA; (C.B.); (E.G.W.); (B.G.); (E.U.); (E.F.); (A.T.); (S.J.T.); (P.A.S.); (C.A.C.)
- Correspondence:
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188
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Identification, function, and biological relevance of POGLUT2 and POGLUT3. Biochem Soc Trans 2022; 50:1003-1012. [PMID: 35411374 DOI: 10.1042/bst20210850] [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: 02/24/2022] [Revised: 03/25/2022] [Accepted: 03/28/2022] [Indexed: 11/17/2022]
Abstract
O-glycosylation of Epidermal Growth Factor-like (EGF) repeats plays crucial roles in protein folding, trafficking and function. The Notch extracellular domain has been used as a model to study these mechanisms due to its many O-glycosylated EGF repeats. Three enzymes were previously known to O-glycosylate Notch EGF repeats: Protein O-Glucosyltransferase 1 (POGLUT1), Protein O-Fucosyltransferase 1 (POFUT1), and EGF Domain Specific O-Linked N-Acetylglucosamine Transferase (EOGT). All of these modifications affect Notch activity. Recently, POGLUT2 and POGLUT3 were identified as two novel O-glucosyltransferases that modify a few Notch EGF repeats at sites distinct from those modified by POGLUT1. Comparison of these modification sites revealed a putative consensus sequence which predicted modification of many extracellular matrix proteins including fibrillins (FBNs) and Latent TGFβ-binding proteins (LTBPs). Glycoproteomic analysis revealed that approximately half of the 47 EGF repeats in FBN1 and FBN2, and half of the 18 EGF repeats in LTBP1, are modified by POGLUT2 and/or POGLUT3. Cellular assays showed that loss of modifications by POGLUT2 and/or POGLUT3 significantly reduces FBN1 secretion. There is precedent for EGF modifications to affect protein-protein interactions, as has been demonstrated by research of POGLUT1 and POFUT1 modifications on Notch. Here we discuss the identification and characterization of POGLUT2 and POGLUT3 and the ongoing research that continues to elucidate the biological significance of these novel enzymes.
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Chaker-Margot M, Werten S, Dunzendorfer-Matt T, Lechner S, Ruepp A, Scheffzek K, Maier T. Structural basis of activation of the tumor suppressor protein neurofibromin. Mol Cell 2022; 82:1288-1296.e5. [PMID: 35353986 DOI: 10.1016/j.molcel.2022.03.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 01/14/2022] [Accepted: 03/03/2022] [Indexed: 12/15/2022]
Abstract
Mutations in the NF1 gene cause the familial genetic disease neurofibromatosis type I, as well as predisposition to cancer. The NF1 gene product, neurofibromin, is a GTPase-activating protein and acts as a tumor suppressor by negatively regulating the small GTPase, Ras. However, structural insights into neurofibromin activation remain incompletely defined. Here, we provide cryoelectron microscopy (cryo-EM) structures that reveal an extended neurofibromin homodimer in two functional states: an auto-inhibited state with occluded Ras-binding site and an asymmetric open state with an exposed Ras-binding site. Mechanistically, the transition to the active conformation is stimulated by nucleotide binding, which releases a lock that tethers the catalytic domain to an extended helical repeat scaffold in the occluded state. Structure-guided mutational analysis supports functional relevance of allosteric control. Disease-causing mutations are mapped and primarily impact neurofibromin stability. Our findings suggest a role for nucleotides in neurofibromin regulation and may lead to therapeutic modulation of Ras signaling.
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Affiliation(s)
| | - Sebastiaan Werten
- Institute of Biological Chemistry, Biocenter, Medical University of Innsbruck, Innsbruck 6020, Austria
| | | | - Stefan Lechner
- Institute of Biological Chemistry, Biocenter, Medical University of Innsbruck, Innsbruck 6020, Austria
| | - Angela Ruepp
- Institute of Biological Chemistry, Biocenter, Medical University of Innsbruck, Innsbruck 6020, Austria
| | - Klaus Scheffzek
- Institute of Biological Chemistry, Biocenter, Medical University of Innsbruck, Innsbruck 6020, Austria.
| | - Timm Maier
- Biozentrum, University of Basel, 4056 Basel, Switzerland.
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190
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Gholizadeh MA, Mohammadi-Sarband M, Fardanesh F, Garshasbi M. Neurodevelopmental disorder with microcephaly, hypotonia, and variable brain anomalies in a consanguineous Iranian family is associated with a homozygous start loss variant in the PRUNE1 gene. BMC Med Genomics 2022; 15:78. [PMID: 35379233 PMCID: PMC8981834 DOI: 10.1186/s12920-022-01228-6] [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: 08/07/2021] [Accepted: 03/30/2022] [Indexed: 11/24/2022] Open
Abstract
Background Homozygous or compound heterozygous PRUNE1 mutations cause a neurodevelopmental disorder with microcephaly, hypotonia, and variable brain malformations (NMIHBA) (OMIM #617481). The PRUNE1 gene encodes a member of the phosphoesterase (DHH) protein superfamily that is involved in the regulation of cell migration. To date, most of the described mutations in the PRUNE1 gene are clustered in DHH domain. Methods We subjected 4 members (two affected and two healthy) of a consanguineous Iranian family in the study. The proband underwent whole-exome sequencing and a start loss identified variant was confirmed by Sanger sequencing. Co-segregation of the detected variant with the disease in family was confirmed. Results By whole-exome sequencing, we identified the a start loss variant, NM_021222.3:c.3G>A; p.(Met1?), in the PRUNE1 in two patients of a consanguineous Iranian family with spastic quadriplegic cerebral palsy (CP), hypotonia, developmental regression, and cerebellar atrophy. Sanger sequencing confirmed the segregation of the variant with the disease in the family. Protein structure analysis also revealed that the variant probably leads to the deletion of DHH (Asp-His-His) domain, the active site of the protein, and loss of PRUNE1 function. Conclusion We identified a start loss variant, NM_021222.3:c.3G>A; p.(Met1?) in the PRUNE1 gene in two affected members as a possible cause of NMIHBA in an Iranian family. We believe that the study adds a new pathogenic variant in spectrum of mutations in the PRUNE1 gene as a cause of PRUNE1-related syndrome.
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Affiliation(s)
- Mehdi Agha Gholizadeh
- Department of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran.,PardisGene Company, Tehran, Iran
| | | | - Fatemeh Fardanesh
- Shemiranat Genetic Counselling Center, State Welfare Organization, Tehran, Iran
| | - Masoud Garshasbi
- Department of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran. .,Department of Medical Genetics, DeNA Laboratory, Tehran, Iran.
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191
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Ose NJ, Butler BM, Kumar A, Kazan IC, Sanderford M, Kumar S, Ozkan SB. Dynamic coupling of residues within proteins as a mechanistic foundation of many enigmatic pathogenic missense variants. PLoS Comput Biol 2022; 18:e1010006. [PMID: 35389981 PMCID: PMC9017885 DOI: 10.1371/journal.pcbi.1010006] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 04/19/2022] [Accepted: 03/09/2022] [Indexed: 01/07/2023] Open
Abstract
Many pathogenic missense mutations are found in protein positions that are neither well-conserved nor fall in any known functional domains. Consequently, we lack any mechanistic underpinning of dysfunction caused by such mutations. We explored the disruption of allosteric dynamic coupling between these positions and the known functional sites as a possible mechanism for pathogenesis. In this study, we present an analysis of 591 pathogenic missense variants in 144 human enzymes that suggests that allosteric dynamic coupling of mutated positions with known active sites is a plausible biophysical mechanism and evidence of their functional importance. We illustrate this mechanism in a case study of β-Glucocerebrosidase (GCase) in which a vast majority of 94 sites harboring Gaucher disease-associated missense variants are located some distance away from the active site. An analysis of the conformational dynamics of GCase suggests that mutations on these distal sites cause changes in the flexibility of active site residues despite their distance, indicating a dynamic communication network throughout the protein. The disruption of the long-distance dynamic coupling caused by missense mutations may provide a plausible general mechanistic explanation for biological dysfunction and disease.
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Affiliation(s)
- Nicholas J. Ose
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe, Arizona, United States of America
| | - Brandon M. Butler
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe, Arizona, United States of America
| | - Avishek Kumar
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe, Arizona, United States of America
| | - I. Can Kazan
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe, Arizona, United States of America
| | - Maxwell Sanderford
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, Pennsylvania, United States of America
- Department of Biology, Temple University, Philadelphia, Pennsylvania, United States of America
| | - Sudhir Kumar
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, Pennsylvania, United States of America
- Department of Biology, Temple University, Philadelphia, Pennsylvania, United States of America
- Center for Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia
| | - S. Banu Ozkan
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe, Arizona, United States of America
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192
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Usami SI, Isaka Y, Miyagawa M, Nishio SY. Variants in CDH23 cause a broad spectrum of hearing loss: from non-syndromic to syndromic hearing loss as well as from congenital to age-related hearing loss. Hum Genet 2022; 141:903-914. [PMID: 35020051 PMCID: PMC9034991 DOI: 10.1007/s00439-022-02431-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 01/06/2022] [Indexed: 11/28/2022]
Abstract
Variants in the CDH23 gene are known to be responsible for both syndromic hearing loss (Usher syndrome type ID: USH1D) and non-syndromic hearing loss (DFNB12). Our series of studies demonstrated that CDH23 variants cause a broad range of phenotypes of non-syndromic hearing loss (DFNB12); from congenital profound hearing loss to late-onset high-frequency-involved progressive hearing loss. In this study, based on the genetic and clinical data from more than 10,000 patients, the mutational spectrum, clinical characteristics and genotype/phenotype correlations were evaluated. The present results reconfirmed that the variants in CDH23 are an important cause of non-syndromic sensorineural hearing loss. In addition, we showed that the mutational spectrum in the Japanese population, which is probably representative of the East Asian population in general, as well as frequent CDH23 variants that might be due to some founder effects. The present study demonstrated CDH23 variants cause a broad range of phenotypes, from non-syndromic to syndromic hearing loss as well as from congenital to age-related hearing loss. Genotype (variant combinations) and phenotype (association with retinal pigmentosa, onset age) are shown to be well correlated and are thought to be related to the residual function defined by the CDH23 variants.
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Affiliation(s)
- Shin-Ichi Usami
- Department of Hearing Implant Sciences, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto, 390-8621, Japan.
| | - Yuichi Isaka
- Department of Hearing Implant Sciences, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto, 390-8621, Japan
| | - Maiko Miyagawa
- Department of Hearing Implant Sciences, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto, 390-8621, Japan
| | - Shin-Ya Nishio
- Department of Hearing Implant Sciences, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto, 390-8621, Japan
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193
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Alawneh RJ, Johnson AL, Hoover-Fong JE, Jackson EM, Steinberg JP, MacCarrick G. Postnatal Progressive Craniosynostosis in Syndromic Conditions: Two Patients With Saethre-Chotzen Due to TWIST1 Gene Deletions and Review of the Literature. Cleft Palate Craniofac J 2022:10556656221090844. [PMID: 35354337 DOI: 10.1177/10556656221090844] [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: 11/15/2022] Open
Abstract
Saethre-Chotzen syndrome (SCS) is a known craniosynostosis syndrome with a variable presentation of craniofacial and somatic involvement. Congenital coronal craniosynostosis is most commonly observed in SCS; however, progressive postnatal craniosynostosis of other sutures has been reported. The authors present 2 infants with progressive postnatal craniosynostosis and SCS caused by chromosome 7p deletions including the TWIST1 gene. The evolution of their clinical features and a literature review of patients with syndromic, postnatal progressive craniosynostosis illustrate the importance of longitudinal observation and management of these patients.
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Affiliation(s)
- Rama J Alawneh
- Faculty of Medicine, King Abdullah University Hospital, 37251Jordan University of Science and Technology, Irbid, Jordan
| | - Andrea L Johnson
- Department of Cellular Biology and Molecular Genetics, 1068University of Maryland College Park, College Park, MD, USA
| | - Julie Elizabeth Hoover-Fong
- Greenberg Center for Skeletal Dysplasias, Department of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Eric M Jackson
- Department of Neurosurgery, 1500Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jordan P Steinberg
- Division of Plastic Surgery, Nicklaus Children's Hospital, Miami, FL, USA
| | - Gretchen MacCarrick
- Department of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
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194
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A Type 3 Gaucher-Like Disease Due To Saposin C Deficiency in Two Emirati Families Caused by a Novel Splice Site Variant in the PSAP Gene. J Mol Neurosci 2022; 72:1322-1333. [DOI: 10.1007/s12031-022-01987-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 02/20/2022] [Indexed: 10/18/2022]
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195
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Chahine Karam F, Loi TH, Ma A, Nash BM, Grigg JR, Parekh D, Riley LG, Farnsworth E, Bennetts B, Gonzalez-Cordero A, Jamieson RV. Human iPSC-Derived Retinal Organoids and Retinal Pigment Epithelium for Novel Intronic RPGR Variant Assessment for Therapy Suitability. J Pers Med 2022; 12:jpm12030502. [PMID: 35330501 PMCID: PMC8951517 DOI: 10.3390/jpm12030502] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 03/16/2022] [Accepted: 03/17/2022] [Indexed: 02/04/2023] Open
Abstract
The RPGR gene encodes Retinitis Pigmentosa GTPase Regulator, a known interactor with ciliary proteins, which is involved in maintaining healthy photoreceptor cells. Variants in RPGR are the main contributor to X-linked rod-cone dystrophy (RCD), and RPGR gene therapy approaches are in clinical trials. Hence, elucidation of the pathogenicity of novel RPGR variants is important for a patient therapy opportunity. Here, we describe a novel intronic RPGR variant, c.1415 − 9A>G, in a patient with RCD, which was classified as a variant of uncertain significance according to current clinical diagnostic criteria. The variant lay several base pairs intronic to the canonical splice acceptor site, raising suspicion of an RPGR RNA splicing abnormality and consequent protein dysfunction. To investigate disease causation in an appropriate disease model, induced pluripotent stem cells were generated from patient fibroblasts and differentiated to retinal pigment epithelium (iPSC-RPE) and retinal organoids (iPSC-RO). Abnormal RNA splicing of RPGR was demonstrated in patient fibroblasts, iPSC-RPE and iPSC-ROs, leading to a predicted frameshift and premature stop codon. Decreased RPGR expression was demonstrated in these cell types, with a striking loss of RPGR localization at the ciliary transitional zone, critically in the photoreceptor cilium of the patient iPSC-ROs. Mislocalisation of rhodopsin staining was present in the patient’s iPSC-RO rod photoreceptor cells, along with an abnormality of L/M opsin staining affecting cone photoreceptor cells and increased photoreceptor apoptosis. Additionally, patient iPSC-ROs displayed an increase in F-actin expression that was consistent with an abnormal actin regulation phenotype. Collectively, these studies indicate that the splicing abnormality caused by the c.1415 − 9A>G variant has an impact on RPGR function. This work has enabled the reclassification of this variant to pathogenic, allowing the consideration of patients with this variant having access to gene therapy clinical trials. In addition, we have identified biomarkers of disease suitable for the interrogation of other RPGR variants of uncertain significance.
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Affiliation(s)
- Fidelle Chahine Karam
- Eye Genetics Research Unit, Children’s Medical Research Institute, Sydney Children’s Hospitals Network, Save Sight Institute, University of Sydney, Westmead, Sydney 2145, Australia; (F.C.K.); (T.H.L.); (A.M.); (B.M.N.); (J.R.G.)
| | - To Ha Loi
- Eye Genetics Research Unit, Children’s Medical Research Institute, Sydney Children’s Hospitals Network, Save Sight Institute, University of Sydney, Westmead, Sydney 2145, Australia; (F.C.K.); (T.H.L.); (A.M.); (B.M.N.); (J.R.G.)
| | - Alan Ma
- Eye Genetics Research Unit, Children’s Medical Research Institute, Sydney Children’s Hospitals Network, Save Sight Institute, University of Sydney, Westmead, Sydney 2145, Australia; (F.C.K.); (T.H.L.); (A.M.); (B.M.N.); (J.R.G.)
- Department of Clinical Genetics, Western Sydney Genetics Program, Sydney Children’s Hospitals Network, Westmead, Sydney 2145, Australia
- Specialty of Genomic Medicine, Faculty of Medicine and Health, University of Sydney, Westmead, Sydney 2145, Australia; (E.F.); (B.B.)
| | - Benjamin M. Nash
- Eye Genetics Research Unit, Children’s Medical Research Institute, Sydney Children’s Hospitals Network, Save Sight Institute, University of Sydney, Westmead, Sydney 2145, Australia; (F.C.K.); (T.H.L.); (A.M.); (B.M.N.); (J.R.G.)
- Specialty of Genomic Medicine, Faculty of Medicine and Health, University of Sydney, Westmead, Sydney 2145, Australia; (E.F.); (B.B.)
- Sydney Genome Diagnostics, Western Sydney Genetics Program, Sydney Children’s Hospitals Network, Westmead, Sydney 2145, Australia
| | - John R. Grigg
- Eye Genetics Research Unit, Children’s Medical Research Institute, Sydney Children’s Hospitals Network, Save Sight Institute, University of Sydney, Westmead, Sydney 2145, Australia; (F.C.K.); (T.H.L.); (A.M.); (B.M.N.); (J.R.G.)
- Specialty of Ophthalmology, Faculty of Medicine and Health, University of Sydney, Sydney 2006, Australia
| | - Darshan Parekh
- Rare Diseases Functional Genomics Laboratory, Sydney Children’s Hospitals Network and Children’s Medical Research Institute, Westmead, Sydney 2145, Australia; (D.P.); (L.G.R.)
| | - Lisa G. Riley
- Rare Diseases Functional Genomics Laboratory, Sydney Children’s Hospitals Network and Children’s Medical Research Institute, Westmead, Sydney 2145, Australia; (D.P.); (L.G.R.)
- Specialty of Child and Adolescent Health, University of Sydney, Westmead, Sydney 2145, Australia
| | - Elizabeth Farnsworth
- Specialty of Genomic Medicine, Faculty of Medicine and Health, University of Sydney, Westmead, Sydney 2145, Australia; (E.F.); (B.B.)
- Sydney Genome Diagnostics, Western Sydney Genetics Program, Sydney Children’s Hospitals Network, Westmead, Sydney 2145, Australia
| | - Bruce Bennetts
- Specialty of Genomic Medicine, Faculty of Medicine and Health, University of Sydney, Westmead, Sydney 2145, Australia; (E.F.); (B.B.)
- Sydney Genome Diagnostics, Western Sydney Genetics Program, Sydney Children’s Hospitals Network, Westmead, Sydney 2145, Australia
| | - Anai Gonzalez-Cordero
- Stem Cell Medicine Group, Children’s Medical Research Institute, University of Sydney, Westmead, Sydney 2145, Australia;
- School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney 2006, Australia
| | - Robyn V. Jamieson
- Eye Genetics Research Unit, Children’s Medical Research Institute, Sydney Children’s Hospitals Network, Save Sight Institute, University of Sydney, Westmead, Sydney 2145, Australia; (F.C.K.); (T.H.L.); (A.M.); (B.M.N.); (J.R.G.)
- Department of Clinical Genetics, Western Sydney Genetics Program, Sydney Children’s Hospitals Network, Westmead, Sydney 2145, Australia
- Specialty of Genomic Medicine, Faculty of Medicine and Health, University of Sydney, Westmead, Sydney 2145, Australia; (E.F.); (B.B.)
- Correspondence: ; Tel.: +61-2-9687-2800; Fax: +61-2-9687-2120
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Screening of OTULIN gene mutation with targeted next generation sequencing in Turkish populations and in silico analysis of these mutations. Mol Biol Rep 2022; 49:4643-4652. [PMID: 35294702 DOI: 10.1007/s11033-022-07312-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 03/01/2022] [Indexed: 10/18/2022]
Abstract
BACKGROUND OTULIN-related autoinflammatory syndrome (ORAS) is an autosomal recessive disease characterized by systemic inflammation, recurrent fever. Due to limited knowledge about the OTULIN DNA variants that cause ORAS, the diagnosis and treatment of this disease is difficult. In this study, we aim to identify OTULIN DNA variants responsible for the genetic pathology of ORAS and observe the effects of these variants on the OTULIN protein structure and the function with different bioinformatics approaches. METHODS The present study included 3230 individuals with the suspicion of an autoinflammatory disease who were referred to Ege University Children's Hospital Molecular Medicine Laboratory. OTULIN variants were detected using a panel consisting of 37 different autoinflammatory diseases (AID) genes via targeted Next-Generation Sequencing. RESULTS As a result of the study, DNA variants associated with various AID were detected in 65% of the individuals to whom the panel was applied. Among these variants, only three different OTULIN variants (p.Val82Ile, p.Gln115His and p.Leu131_Arg132insLeuCysThrGlu) were detected. The pathogenic effects of the variants detected in the OTULIN gene were determined by using Polyphen2 as "Probably Pathogenic" for the p.Val82Ile and "benign" for the p.Gln115His. At the same time, the effects of these variants on the structure and function of the OTULIN protein were investigated by in silico approaches. Both variants reduce protein stability and binding affinity. CONCLUSION The results of the current study suggest that the evaluation of OTULIN variants with in silico approaches will contribute to the development of personalized treatments by diagnosing the disease specific to the variant.
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197
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LIM domain-wide comprehensive virtual mutagenesis provides structural rationale for cardiomyopathy mutations in CSRP3. Sci Rep 2022; 12:3562. [PMID: 35241752 PMCID: PMC8894373 DOI: 10.1038/s41598-022-07553-1] [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: 11/17/2021] [Accepted: 02/11/2022] [Indexed: 11/29/2022] Open
Abstract
Cardiomyopathies are a severe and chronic cardiovascular burden worldwide, affecting a large cohort in the general population. Cysteine and glycine-rich protein 3 (CSRP3) is one of key proteins implicated in dominant dilated cardiomyopathy (DCM) and hypertrophic cardiomyopathy (HCM). In this study, we device a rapid in silico screening protocol that creates a mutational landscape map for all possible allowed and disallowed substitutions in the protein of interest. This map provides the structural and functional insights on the stability of LIM domains of CSRP3. Further, the sequence analysis delineates the eukaryotic CSRP3 protein orthologs which complements the mutational map, but provide limited information of amino acid exchanges. Next, we also evaluated the effect of HCM/DCM mutations on these domains. One of highly destabilising mutations—L44P (also disease causing) and a neutral mutation—L44M were further subjected to molecular dynamics (MD) simulations. The results establish that L44P substitution affects the LIM domain structure by altering secondary structure and due to loss of hydrophobic interaction with Phenylananine 35. The present study provides a useful perspective to our understanding of the role of mutations in the CSRP3 LIM domains and their evolution. This study provides a novel computational screening method for quick identification of key mutation sites for specific protein structures that can reduce the burden on experimental research.
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198
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Safgren SL, Olson RJ, Pinto E Vairo F, Bothun ED, Hanna C, Klee EW, Schimmenti LA. De novo PBX1 variant in a patient with glaucoma, kidney anomalies, and developmental delay: An expansion of the CAKUTHED phenotype. Am J Med Genet A 2022; 188:919-925. [PMID: 34797033 DOI: 10.1002/ajmg.a.62576] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 10/05/2021] [Accepted: 11/02/2021] [Indexed: 01/22/2023]
Abstract
An infant was referred for evaluation of congenital glaucoma and corneal clouding. In addition, he had a pelvic kidney, hypotonia, patent ductus arteriosus, abnormal pinnae, and developmental delay. Exome sequencing identified a previously unpublished de novo single nucleotide insertion in PBX1 c.400dupG (NM_002585.3), predicted to cause a frameshift resulting in a truncated protein with loss of function (p.Ala134Glyfs*65). Identification of this loss of function variant supports the diagnosis of congenital anomalies of the kidney and urinary tract syndrome with or without hearing loss, abnormal ears, or developmental delay (CAKUTHED). Here, we propose glaucoma as an extra-renal manifestation associated with PBX1-related disease due to the relationship of PBX1 with MEIS1, MEIS2, and FOXC1 transcription factors associated with eye development.
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Affiliation(s)
- Stephanie L Safgren
- Department of Quantitative Health Sciences, Division of Computational Biology, Mayo Clinic, Rochester, Minnesota, USA
| | - Rory J Olson
- Center of Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Filippo Pinto E Vairo
- Center of Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA
- Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota, USA
| | - Erick D Bothun
- Department of Ophthalmology, Mayo Clinic, Rochester, Minnesota, USA
| | - Christian Hanna
- Department of Pediatric Nephrology and Hypertension, Mayo Clinic, Rochester, Minnesota, USA
| | - Eric W Klee
- Department of Quantitative Health Sciences, Division of Computational Biology, Mayo Clinic, Rochester, Minnesota, USA
- Center of Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA
- Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota, USA
| | - Lisa A Schimmenti
- Department of Ophthalmology, Mayo Clinic, Rochester, Minnesota, USA
- Department of Otorhinolaryngology, Mayo Clinic, Rochester, Minnesota, USA
- Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota, USA
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota, USA
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Molecular Diagnostic Outcomes from 700 Cases: What Can We Learn from a Retrospective Analysis of Clinical Exome Sequencing? J Mol Diagn 2022; 24:274-286. [PMID: 35065284 PMCID: PMC9904168 DOI: 10.1016/j.jmoldx.2021.12.002] [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: 01/18/2021] [Revised: 11/29/2021] [Accepted: 12/10/2021] [Indexed: 01/19/2023] Open
Abstract
Clinical exome sequencing (CES) aids in the diagnosis of rare genetic disorders. Herein, we report the molecular diagnostic yield and spectrum of genetic alterations contributing to disease in 700 pediatric cases analyzed at the Children's Hospital of Philadelphia. The overall diagnostic yield was 23%, with three cases having more than one molecular diagnosis and 2.6% having secondary/additional findings. A candidate gene finding was reported in another 8.4% of cases. The clinical indications with the highest diagnostic yield were neurodevelopmental disorders (including seizures), whereas immune- and oncology-related indications were negatively associated with molecular diagnosis. The rapid expansion of knowledge regarding the genome's role in human disease necessitates reanalysis of CES samples. To capture these new discoveries, a subset of cases (n = 240) underwent reanalysis, with an increase in diagnostic yield. We describe our experience reporting CES results in a pediatric setting, including reporting of secondary findings, reporting newly discovered genetic conditions, and revisiting negative test results. Finally, we highlight the challenges associated with implementing critical updates to the CES workflow. Although these updates are necessary, they demand an investment of time and resources from the laboratory. In summary, these data demonstrate the clinical utility of exome sequencing and reanalysis, while highlighting the critical considerations for continuous improvement of a CES test in a clinical laboratory.
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200
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Ullah I, Murtaza K, Ammara H, Misbah, Bhinder MA, Riaz A, Shehzad W, Zahoor MY. Association study of CLDN14 variations in patients with kidney stones. Open Life Sci 2022; 17:81-92. [PMID: 35291565 PMCID: PMC8886595 DOI: 10.1515/biol-2021-0134] [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: 05/27/2021] [Revised: 10/08/2021] [Accepted: 10/10/2021] [Indexed: 11/28/2022] Open
Abstract
Claudin-14 protein plays an essential role in regulating calcium ions in the kidney and ear. Two phenotypes, hearing loss and kidney stones, were reportedly associated with variations in the CLDN14 gene. This study aimed to understand CLDN14 mutations’ contribution to hearing loss and renal stone formation in a Pakistani cohort. We analyzed CLDN14 sequence variations in 100 patients, along with healthy individuals, to assess whether specific polymorphisms were associated with the disease. Also, we performed an in silico analysis using a mutation database and protein annotation. The rs219779’s genotype CT (p = 0.0020) and rs219780’s genotype AG (p = 0.0012) were significantly associated with kidney stones. We also found that a novel haplotype, “TA” associated with kidney stone formation, has moderate linkage disequilibrium. The TA haplotype was significantly correlated with a kidney stone risk formation of 3.76-fold (OR (CI 95%) = 3.76 (1.83–7.72)) and p = 0.0016 compared to other haplotypes. In silico analysis revealed that mutations associated with hearing loss were not correlated with renal stone formation but affected claudin-14 protein stability. We structurally mapped a novel TA haplotype of CLDN14 that, based on our analysis, likely contributes to the pathogenesis of renal stones.
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Affiliation(s)
- Ihsan Ullah
- Molecular Biology and Biotechnology Section, Institute of Biochemistry & Biotechnology, University of Veterinary & Animal Sciences , Syed Abdul Qadir Jillani (Out Fall) Road , Lahore 54000 , Pakistan
| | - Khadijah Murtaza
- Molecular Biology and Biotechnology Section, Institute of Biochemistry & Biotechnology, University of Veterinary & Animal Sciences , Syed Abdul Qadir Jillani (Out Fall) Road , Lahore 54000 , Pakistan
| | - Hafiza Ammara
- Molecular Biology and Biotechnology Section, Institute of Biochemistry & Biotechnology, University of Veterinary & Animal Sciences , Syed Abdul Qadir Jillani (Out Fall) Road , Lahore 54000 , Pakistan
| | - Misbah
- Department of Medicine, Services Hospital , Lahore 54000 , Pakistan
| | - Munir Ahmad Bhinder
- Department of Human Genetics and Molecular Biology, University of Health Sciences , Lahore 54000 , Pakistan
| | - Amjad Riaz
- Department of Theriogenology, University of Veterinary & Animal Sciences , Lahore 54000 , Pakistan
| | - Wasim Shehzad
- Molecular Biology and Biotechnology Section, Institute of Biochemistry & Biotechnology, University of Veterinary & Animal Sciences , Syed Abdul Qadir Jillani (Out Fall) Road , Lahore 54000 , Pakistan
| | - Muhammad Yasir Zahoor
- Molecular Biology and Biotechnology Section, Institute of Biochemistry & Biotechnology, University of Veterinary & Animal Sciences , Syed Abdul Qadir Jillani (Out Fall) Road , Lahore 54000 , Pakistan
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