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Dueñas Rey A, Del Pozo Valero M, Bouckaert M, Wood KA, Van den Broeck F, Daich Varela M, Thomas HB, Van Heetvelde M, De Bruyne M, Van de Sompele S, Bauwens M, Lenaerts H, Mahieu Q, Josifova D, Rivolta C, O'Keefe RT, Ellingford J, Webster AR, Arno G, Ayuso C, De Zaeytijd J, Leroy BP, De Baere E, Coppieters F. Combining a prioritization strategy and functional studies nominates 5'UTR variants underlying inherited retinal disease. Genome Med 2024; 16:7. [PMID: 38184646 PMCID: PMC10771650 DOI: 10.1186/s13073-023-01277-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 12/15/2023] [Indexed: 01/08/2024] Open
Abstract
BACKGROUND 5' untranslated regions (5'UTRs) are essential modulators of protein translation. Predicting the impact of 5'UTR variants is challenging and rarely performed in routine diagnostics. Here, we present a combined approach of a comprehensive prioritization strategy and functional assays to evaluate 5'UTR variation in two large cohorts of patients with inherited retinal diseases (IRDs). METHODS We performed an isoform-level re-analysis of retinal RNA-seq data to identify the protein-coding transcripts of 378 IRD genes with highest expression in retina. We evaluated the coverage of their 5'UTRs by different whole exome sequencing (WES) kits. The selected 5'UTRs were analyzed in whole genome sequencing (WGS) and WES data from IRD sub-cohorts from the 100,000 Genomes Project (n = 2397 WGS) and an in-house database (n = 1682 WES), respectively. Identified variants were annotated for 5'UTR-relevant features and classified into seven categories based on their predicted functional consequence. We developed a variant prioritization strategy by integrating population frequency, specific criteria for each category, and family and phenotypic data. A selection of candidate variants underwent functional validation using diverse approaches. RESULTS Isoform-level re-quantification of retinal gene expression revealed 76 IRD genes with a non-canonical retina-enriched isoform, of which 20 display a fully distinct 5'UTR compared to that of their canonical isoform. Depending on the probe design, 3-20% of IRD genes have 5'UTRs fully captured by WES. After analyzing these regions in both cohorts, we prioritized 11 (likely) pathogenic variants in 10 genes (ARL3, MERTK, NDP, NMNAT1, NPHP4, PAX6, PRPF31, PRPF4, RDH12, RD3), of which 7 were novel. Functional analyses further supported the pathogenicity of three variants. Mis-splicing was demonstrated for the PRPF31:c.-9+1G>T variant. The MERTK:c.-125G>A variant, overlapping a transcriptional start site, was shown to significantly reduce both luciferase mRNA levels and activity. The RDH12:c.-123C>T variant was found in cis with the hypomorphic RDH12:c.701G>A (p.Arg234His) variant in 11 patients. This 5'UTR variant, predicted to introduce an upstream open reading frame, was shown to result in reduced RDH12 protein but unaltered mRNA levels. CONCLUSIONS This study demonstrates the importance of 5'UTR variants implicated in IRDs and provides a systematic approach for 5'UTR annotation and validation that is applicable to other inherited diseases.
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Affiliation(s)
- Alfredo Dueñas Rey
- Center for Medical Genetics Ghent (CMGG), Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, Ghent, 9000, Belgium
| | - Marta Del Pozo Valero
- Center for Medical Genetics Ghent (CMGG), Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, Ghent, 9000, Belgium
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz, University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - Manon Bouckaert
- Center for Medical Genetics Ghent (CMGG), Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, Ghent, 9000, Belgium
| | - Katherine A Wood
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicines and Health, University of Manchester, Manchester, UK
| | - Filip Van den Broeck
- Department of Ophthalmology, Ghent University Hospital, Ghent, Belgium
- Department of Head & Skin, Ghent University, Ghent, Belgium
| | - Malena Daich Varela
- UCL Institute of Ophthalmology, University College London, London, UK
- Moorfields Eye Hospital, London, UK
| | - Huw B Thomas
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicines and Health, University of Manchester, Manchester, UK
| | - Mattias Van Heetvelde
- Center for Medical Genetics Ghent (CMGG), Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, Ghent, 9000, Belgium
| | - Marieke De Bruyne
- Center for Medical Genetics Ghent (CMGG), Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, Ghent, 9000, Belgium
| | - Stijn Van de Sompele
- Center for Medical Genetics Ghent (CMGG), Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, Ghent, 9000, Belgium
| | - Miriam Bauwens
- Center for Medical Genetics Ghent (CMGG), Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, Ghent, 9000, Belgium
| | - Hanne Lenaerts
- Center for Medical Genetics Ghent (CMGG), Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, Ghent, 9000, Belgium
| | - Quinten Mahieu
- Center for Medical Genetics Ghent (CMGG), Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, Ghent, 9000, Belgium
| | | | - Carlo Rivolta
- Department of Ophthalmology, University of Basel, Basel, Switzerland
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Raymond T O'Keefe
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicines and Health, University of Manchester, Manchester, UK
| | - Jamie Ellingford
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicines and Health, University of Manchester, Manchester, UK
- Genomics England, London, UK
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | - Andrew R Webster
- UCL Institute of Ophthalmology, University College London, London, UK
- Moorfields Eye Hospital, London, UK
| | - Gavin Arno
- UCL Institute of Ophthalmology, University College London, London, UK
- Moorfields Eye Hospital, London, UK
| | - Carmen Ayuso
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz, University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Julie De Zaeytijd
- Department of Ophthalmology, Ghent University Hospital, Ghent, Belgium
- Department of Head & Skin, Ghent University, Ghent, Belgium
| | - Bart P Leroy
- Center for Medical Genetics Ghent (CMGG), Ghent University Hospital, Ghent, Belgium
- Department of Ophthalmology, Ghent University Hospital, Ghent, Belgium
- Department of Head & Skin, Ghent University, Ghent, Belgium
- Division of Ophthalmology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Elfride De Baere
- Center for Medical Genetics Ghent (CMGG), Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, Ghent, 9000, Belgium
| | - Frauke Coppieters
- Center for Medical Genetics Ghent (CMGG), Ghent University Hospital, Ghent, Belgium.
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, Ghent, 9000, Belgium.
- Department of Pharmaceutics, Ghent University, Ghent, Belgium.
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Wang L, Rossi RM, Chen X, Chen J, Runyon J, Chawla M, Miller D, Forney C, Lynch A, Zhang X, Kong F, Jacobsson B, Kottyan LC, Weirauch MT, Zhang G, Muglia LJ. A functional mechanism for a non-coding variant near AGTR2 associated with risk for preterm birth. BMC Med 2023; 21:258. [PMID: 37455310 PMCID: PMC10351137 DOI: 10.1186/s12916-023-02973-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 07/05/2023] [Indexed: 07/18/2023] Open
Abstract
BACKGROUND Preterm birth (PTB), defined as delivery before 37 gestational weeks, imposes significant public health burdens. A recent maternal genome-wide association study of spontaneous PTB identified a noncoding locus near the angiotensin II receptor type 2 (AGTR2) gene. Genotype-Tissue Expression data revealed that alleles associated with decreased AGTR2 expression in the uterus were linked to an increased risk of PTB and shortened gestational duration. We hypothesized that a causative variant in this locus modifies AGTR2 expression by altering transcription factor (TF) binding. METHODS To investigate this hypothesis, we performed bioinformatics analyses and functional characterizations at the implicated locus. Potential causal single nucleotide polymorphisms (SNPs) were prioritized, and allele-dependent binding of TFs was predicted. Reporter assays were employed to assess the enhancer activity of the top PTB-associated non-coding variant, rs7889204, and its impact on TF binding. RESULTS Our analyses revealed that rs7889204, a top PTB-associated non-coding genetic variant is one of the strongest eQTLs for the AGTR2 gene in uterine tissue samples. We observed differential binding of CEBPB (CCAAT enhancer binding protein beta) and HOXA10 (homeobox A10) to the alleles of rs7889204. Reporter assays demonstrated decreased enhancer activity for the rs7889204 risk "C" allele. CONCLUSION Collectively, these results demonstrate that decreased AGTR2 expression caused by reduced transcription factor binding increases the risk for PTB and suggest that enhancing AGTR2 activity may be a preventative measure in reducing PTB risk.
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Affiliation(s)
- Li Wang
- Center for Prevention of Preterm Birth, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.
- March of Dimes Prematurity Research Center Ohio Collaborative, Cincinnati, OH, USA.
- Present Address: Department of Biology, Xavier University, OH, Cincinnati, USA.
| | - Robert M Rossi
- Center for Prevention of Preterm Birth, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- March of Dimes Prematurity Research Center Ohio Collaborative, Cincinnati, OH, USA
- Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Xiaoting Chen
- March of Dimes Prematurity Research Center Ohio Collaborative, Cincinnati, OH, USA
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Jing Chen
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Divisions of Biomedical Informatics and Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Jilian Runyon
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Mehak Chawla
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Daniel Miller
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Carmy Forney
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Arthur Lynch
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Xuzhe Zhang
- Center for Prevention of Preterm Birth, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- March of Dimes Prematurity Research Center Ohio Collaborative, Cincinnati, OH, USA
| | - Fansheng Kong
- Center for Prevention of Preterm Birth, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- March of Dimes Prematurity Research Center Ohio Collaborative, Cincinnati, OH, USA
| | - Bo Jacobsson
- Department of Obstetrics and Gynecology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Obstetrics and Gynecology, Region Västra Götaland, Sahlgrenska University Hospital, Gothenburg, Sweden
- Department of Genetics and Bioinformatics, Domain of Health Data and Digitalisation, Institute of Public Health, Oslo, Norway
| | - Leah C Kottyan
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Matthew T Weirauch
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Divisions of Biomedical Informatics and Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Ge Zhang
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- March of Dimes Prematurity Research Center Ohio Collaborative, Cincinnati, OH, USA
- Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Louis J Muglia
- Center for Prevention of Preterm Birth, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.
- March of Dimes Prematurity Research Center Ohio Collaborative, Cincinnati, OH, USA.
- Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, University of Cincinnati College of Medicine, Cincinnati, OH, USA.
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA.
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Diks AM, Teodosio C, de Mooij B, Groenland RJ, Naber BAE, de Laat IF, Vloemans SA, Rohde S, de Jonge MI, Lorenz L, Horsten D, van Dongen JJM, Berkowska MA, Holstege H. Carriers of the p.P522R variant in PLCγ2 have a slightly more responsive immune system. Mol Neurodegener 2023; 18:25. [PMID: 37081539 PMCID: PMC10116473 DOI: 10.1186/s13024-023-00604-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 02/14/2023] [Indexed: 04/22/2023] Open
Abstract
BACKGROUND The rs72824905 single-nucleotide polymorphism in the PLCG2 gene, encoding the p.P522R residue change in Phospholipase C gamma 2 (PLCγ2), associates with protection against several dementia subtypes and with increased likelihood of longevity. Cell lines and animal models indicated that p.P522R is a functional hypermorph. We aimed to confirm this in human circulating peripheral immune cells. METHODS We compared effects of p.P522R on immune system function between carriers and non-carriers (aged 59-103y), using in-depth immunophenotyping, functional B-cell and myeloid cell assays, and in vivo SARS-CoV-2 vaccination. RESULTS In line with expectations, p.P522R impacts immune cell function only slightly, but it does so across a wide array of immune cell types. Upon B-cell stimulation, we observed increased PLCγ2 phosphorylation and calcium release, suggesting increased B-cell sensitivity upon antigen recognition. Further, p.P522R-carriers had higher numbers of CD20++CD21-CD24+ naive B cells and IgG1+ memory B cells. In myeloid cells, normalized ROS production was higher upon PLCγ2-dependent stimulation. On classical monocytes, CD33 levels were elevated. Furthermore, carriers expressed lower levels of allergy-related FcεRI on several immune cell subsets. Nevertheless, carriers and non-carriers had similar serological responses to SARS-CoV-2 vaccination. CONCLUSION The immune system from p.P522R-carriers is slightly more responsive to stimulation than in non-carriers.
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Affiliation(s)
- Annieck M Diks
- Department of Immunology, Leiden University Medical Center, Albinusdreef 2, Leiden, ZA, 2333, the Netherlands
- Department of Human Genetics, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, the Netherlands
| | - Cristina Teodosio
- Department of Immunology, Leiden University Medical Center, Albinusdreef 2, Leiden, ZA, 2333, the Netherlands
- Translational and Clinical Research Program, Cancer Research Center (IBMCC; University of Salamanca - CSIC), Salamanca, Spain
- Department of Medicine, University of Salamanca and Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain
| | - Bas de Mooij
- Department of Immunology, Leiden University Medical Center, Albinusdreef 2, Leiden, ZA, 2333, the Netherlands
| | - Rick J Groenland
- Department of Immunology, Leiden University Medical Center, Albinusdreef 2, Leiden, ZA, 2333, the Netherlands
| | - Brigitta A E Naber
- Department of Immunology, Leiden University Medical Center, Albinusdreef 2, Leiden, ZA, 2333, the Netherlands
| | - Inge F de Laat
- Department of Immunology, Leiden University Medical Center, Albinusdreef 2, Leiden, ZA, 2333, the Netherlands
| | - Sandra A Vloemans
- Department of Immunology, Leiden University Medical Center, Albinusdreef 2, Leiden, ZA, 2333, the Netherlands
| | - Susan Rohde
- Department of Human Genetics, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, the Netherlands
| | - Marien I de Jonge
- Laboratory of Medical Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Linda Lorenz
- Department of Human Genetics, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, the Netherlands
| | - Debbie Horsten
- Department of Human Genetics, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, the Netherlands
| | - Jacques J M van Dongen
- Department of Immunology, Leiden University Medical Center, Albinusdreef 2, Leiden, ZA, 2333, the Netherlands.
- Translational and Clinical Research Program, Cancer Research Center (IBMCC; University of Salamanca - CSIC), Salamanca, Spain.
- Department of Medicine, University of Salamanca and Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain.
| | - Magdalena A Berkowska
- Department of Immunology, Leiden University Medical Center, Albinusdreef 2, Leiden, ZA, 2333, the Netherlands
| | - Henne Holstege
- Department of Human Genetics, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, the Netherlands.
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O'Neill MJ, Muhammad A, Li B, Wada Y, Hall L, Solus JF, Short L, Roden DM, Glazer AM. Dominant negative effects of SCN5A missense variants. Genet Med 2022; 24:1238-1248. [PMID: 35305865 DOI: 10.1016/j.gim.2022.02.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 02/15/2022] [Accepted: 02/15/2022] [Indexed: 10/18/2022] Open
Abstract
PURPOSE Up to 30% of patients with Brugada syndrome (BrS) carry loss-of-function (LoF) variants in the cardiac sodium channel gene SCN5A encoding for the protein NaV1.5. Recent studies suggested that NaV1.5 can dimerize, and some variants exert dominant negative effects. In this study, we sought to explore the generality of missense variant NaV1.5 dominant negative effects and their clinical severity. METHODS We identified 35 LoF variants (<10% of wild type [WT] peak current) and 15 partial LoF variants (10%-50% of WT peak current) that we assessed for dominant negative effects. SCN5A variants were studied in HEK293T cells, alone or in heterozygous coexpression with WT SCN5A using automated patch clamp. To assess the clinical risk, we compared the prevalence of dominant negative vs putative haploinsufficient (frameshift, splice, or nonsense) variants in a BrS consortium and the Genome Aggregation Database population database. RESULTS In heterozygous expression with WT, 32 of 35 LoF and 6 of 15 partial LoF variants showed reduction to <75% of WT-alone peak current, showing a dominant negative effect. Individuals with dominant negative LoF variants had an elevated disease burden compared with the individuals with putative haploinsufficient variants (2.7-fold enrichment in BrS cases, P = .019). CONCLUSION Most SCN5A missense LoF variants exert a dominant negative effect. This class of variant confers an especially high burden of BrS.
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Affiliation(s)
- Matthew J O'Neill
- Vanderbilt University School of Medicine, Medical Scientist Training Program, Vanderbilt University, Nashville, TN
| | - Ayesha Muhammad
- Vanderbilt University School of Medicine, Medical Scientist Training Program, Vanderbilt University, Nashville, TN
| | - Bian Li
- Vanderbilt Center for Arrhythmia Research and Therapeutics (VanCART), Vanderbilt University Medical Center, Nashville, TN
| | - Yuko Wada
- Vanderbilt Center for Arrhythmia Research and Therapeutics (VanCART), Vanderbilt University Medical Center, Nashville, TN
| | - Lynn Hall
- Vanderbilt Center for Arrhythmia Research and Therapeutics (VanCART), Vanderbilt University Medical Center, Nashville, TN
| | - Joseph F Solus
- Vanderbilt Center for Arrhythmia Research and Therapeutics (VanCART), Vanderbilt University Medical Center, Nashville, TN
| | - Laura Short
- Vanderbilt Center for Arrhythmia Research and Therapeutics (VanCART), Vanderbilt University Medical Center, Nashville, TN
| | - Dan M Roden
- Vanderbilt Center for Arrhythmia Research and Therapeutics (VanCART), Vanderbilt University Medical Center, Nashville, TN; Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN; Department of Pharmacology, Vanderbilt University Medical Center, Nashville, TN; Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN
| | - Andrew M Glazer
- Vanderbilt Center for Arrhythmia Research and Therapeutics (VanCART), Vanderbilt University Medical Center, Nashville, TN; Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN.
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Alves AC, Azevedo S, Benito-Vicente A, Graça R, Galicia-Garcia U, Barros P, Jordan P, Martin C, Bourbon M. LDLR variants functional characterization: Contribution to variant classification. Atherosclerosis 2021; 329:14-21. [PMID: 34167030 DOI: 10.1016/j.atherosclerosis.2021.06.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 04/28/2021] [Accepted: 06/02/2021] [Indexed: 12/27/2022]
Abstract
BACKGROUND AND AIMS Familial hypercholesterolaemia (FH) is an autosomal disorder of lipid metabolism presenting with increased cardiovascular risk. LDLR mutations are the cause of disease in 90% of the cases but functional studies have only been performed for about 15% of all LDLR variants. In the Portuguese Familial Hypercholesterolemia Study (PFHS), 142 unique LDLR alterations were identified and 44 (30%) lack functional characterization. The aim of the present work is to increase evidence for variant classification by performing functional characterization of 13 LDLR missense alterations found in Portugal and in 20 other countries. METHODS Different LDLR mutants were generated by site-directed mutagenesis and expressed in CHO-ldlA7 cells lacking endogenous expression of LDLR. To determine the effects of alterations on LDLR function, cell surface expression, binding and uptake of FITC-LDL were assessed by flow cytometry and Western blot. RESULTS Of the 13 variants studied 7 were shown to affect LDLR function - expression, binding or uptake, with rates lower than 60%: p.(Cys184Tyr), p.(Gly207_Ser213del); p.(His211Asp); p.(Asp221Tyr); p.(Glu288Lys); p.(Gly592Glu) and p.(Asp601Val)). The remaining 6 variants do not alter the LDLR function. CONCLUSIONS These studies contributed to an update of these variants classification: from the 9 variants classified as variants of unknown significance, 7 have reached now a final classification and 3 variants have improved classification from likely pathogenic to pathogenic. In Portugal, an additional 55 patients received an FH definite diagnosis thanks to these studies. Since only likely pathogenic and pathogenic variants are clinically actionable, this work shows the importance of functional studies for variant classification.
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Affiliation(s)
- Ana Catarina Alves
- Unidade de I&D, Grupo de Investigação Cardiovascular, Departamento de Promoção da Saúde e Prevenção de Doenças Não Transmissíveis, Instituto Nacional de Saúde Doutor Ricardo Jorge, Lisboa, Portugal; BioISI - Biosystems & Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Sílvia Azevedo
- Unidade de I&D, Grupo de Investigação Cardiovascular, Departamento de Promoção da Saúde e Prevenção de Doenças Não Transmissíveis, Instituto Nacional de Saúde Doutor Ricardo Jorge, Lisboa, Portugal
| | - Asier Benito-Vicente
- Biofisika Institute (UPV/EHU, CSIC) and Departamento de Bioquímica y Biología Molecular, Universidad Del País Vasco, Apdo. 644, 48080, Bilbao, Spain
| | - Rafael Graça
- Unidade de I&D, Grupo de Investigação Cardiovascular, Departamento de Promoção da Saúde e Prevenção de Doenças Não Transmissíveis, Instituto Nacional de Saúde Doutor Ricardo Jorge, Lisboa, Portugal; BioISI - Biosystems & Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Unai Galicia-Garcia
- Biofisika Institute (UPV/EHU, CSIC) and Departamento de Bioquímica y Biología Molecular, Universidad Del País Vasco, Apdo. 644, 48080, Bilbao, Spain; Department of Molecular Biophysics, Fundación Biofísica Bizkaia, 48940, Leioa, Spain
| | - Patrícia Barros
- BioISI - Biosystems & Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal; Departamento de Genética Humana, Instituto Nacional de Saúde Doutor Ricardo Jorge, Lisboa, Portugal
| | - Peter Jordan
- BioISI - Biosystems & Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal; Departamento de Genética Humana, Instituto Nacional de Saúde Doutor Ricardo Jorge, Lisboa, Portugal
| | - Cesar Martin
- Biofisika Institute (UPV/EHU, CSIC) and Departamento de Bioquímica y Biología Molecular, Universidad Del País Vasco, Apdo. 644, 48080, Bilbao, Spain
| | - Mafalda Bourbon
- Unidade de I&D, Grupo de Investigação Cardiovascular, Departamento de Promoção da Saúde e Prevenção de Doenças Não Transmissíveis, Instituto Nacional de Saúde Doutor Ricardo Jorge, Lisboa, Portugal; BioISI - Biosystems & Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal.
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Çubuk H, Yalçın Çapan Ö. A Review of Functional Characterization of Single Amino Acid Change Mutations in HNF Transcription Factors in MODY Pathogenesis. Protein J 2021; 40:348-60. [PMID: 33950347 DOI: 10.1007/s10930-021-09991-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/22/2021] [Indexed: 12/15/2022]
Abstract
Mutations in HNF transcription factor genes cause the most common subtypes of maturity-onset of diabetes of youth (MODY), a monogenic form of diabetes mellitus. Mutations in the HNF1-α, HNF4-α, and HNF1-β genes are primarily considered as the cause of MODY3, MODY1, and MODY5 subtypes, respectively. Although patients with different subtypes display similar symptoms, they may develop distinct diabetes-related complications and require different treatments depending on the type of the mutation. Genetic analysis of MODY patients revealed more than 400 missense/nonsense mutations in HNF1-α, HNF4-α, and HNF1-β genes, however only a small portion of them are functionally characterized. Evaluation of nonsense mutations are more direct as they lead to premature stop codons and mostly in mRNA decay or nonfunctional truncated proteins. However, interpretation of the single amino acid change (missense) mutation is not such definite, as effect of the variant may vary depending on the location and also the substituted amino acid. Mutations with benign effect on the protein function may not be the pathologic variant and further genetic testing may be required. Here, we discuss the functional characterization analysis of single amino acid change mutations identified in HNF1-α, HNF4-α, and HNF1-β genes and evaluate their roles in MODY pathogenesis. This review will contribute to comprehend HNF nuclear family-related molecular mechanisms and to develop more accurate diagnosis and treatment based on correct evaluation of pathologic effects of the variants.
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Cabré N, Luciano-Mateo F, Chapski DJ, Baiges-Gaya G, Fernández-Arroyo S, Hernández-Aguilera A, Castañé H, Rodríguez-Tomàs E, París M, Sabench F, Del Castillo D, Del Bas JM, Tomé M, Bodineau C, Sola-García A, López-Miranda J, Martín-Montalvo A, Durán RV, Vondriska TM, Rosa-Garrido M, Camps J, Menéndez JA, Joven J. Glutaminolysis-induced mTORC1 activation drives non-alcoholic steatohepatitis progression. J Hepatol 2021:S0168-8278(21)00302-0. [PMID: 33961941 DOI: 10.1016/j.jhep.2021.04.037] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 04/21/2021] [Accepted: 04/22/2021] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS A holistic insight on the relationship between obesity and metabolic dysfunction-associated fatty liver disease is an unmet clinical need. Omics investigations can be used to investigate the multifaceted role of altered mitochondrial pathways to promote nonalcoholic steatohepatitis, a major risk factor for liver disease-associated death. There are no specific treatments but remission via surgery might offer an opportunity to examine the signaling processes that govern the complex spectrum of chronic liver diseases observed in extreme obesity. We aim to assess the emerging relationship between metabolism, methylation and liver disease. METHODS We tailed the flow of information, before and after steatohepatitis remission, from biochemical, histological, and multi-omics analyses in liver biopsies from patients with extreme obesity and successful bariatric surgery. Functional studies were performed in HepG2 cells and primary hepatocytes. RESULTS The reversal of hepatic mitochondrial dysfunction and the control of oxidative stress and inflammatory responses revealed the regulatory role of mitogen-activated protein kinases. The reversible metabolic rearrangements leading to steatohepatitis increased the glutaminolysis-induced production of α-ketoglutarate and the hyperactivation of mammalian target of rapamycin complex 1. These changes were crucial for the adenosine monophosphate-activated protein kinase/mammalian target of rapamycin-driven pathways that modulated hepatocyte survival by coordinating apoptosis and autophagy. The signaling activity of α-ketoglutarate and the associated metabolites also affected methylation-related epigenomic remodeling enzymes. Integrative analysis of hepatic transcriptome signatures and differentially methylated genomic regions distinguished patients with and without steatohepatitis. CONCLUSION We provide evidence supporting the multifaceted potential of the increased glutaminolysis-induced α-ketoglutarate production and the mammalian target of rapamycin complex 1 dysregulation as a conceivable source of the inefficient adaptive responses leading to steatohepatitis. LAY SUMMARY Steatohepatitis is a frequent and threatening complication of extreme obesity without specific treatment. Omics technologies can be used to identify therapeutic targets. We highlight increased glutaminolysis-induced α-ketoglutarate production as a potential source of signals promoting and exacerbating steatohepatitis.
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Affiliation(s)
- Noemí Cabré
- Universitat Rovira i Virgili, Department of Medicine and Surgery, Reus, Spain; Unitat de Recerca Biomèdica (URB-CRB), Hospital Universitari de Sant Joan, Institut d'Investigacio Sanitaria Pere Virgili, Universitat Rovira i Virgili, Reus, Spain
| | - Fedra Luciano-Mateo
- Universitat Rovira i Virgili, Department of Medicine and Surgery, Reus, Spain; Unitat de Recerca Biomèdica (URB-CRB), Hospital Universitari de Sant Joan, Institut d'Investigacio Sanitaria Pere Virgili, Universitat Rovira i Virgili, Reus, Spain
| | - Douglas J Chapski
- Department of Anesthesiology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, US
| | - Gerard Baiges-Gaya
- Universitat Rovira i Virgili, Department of Medicine and Surgery, Reus, Spain; Unitat de Recerca Biomèdica (URB-CRB), Hospital Universitari de Sant Joan, Institut d'Investigacio Sanitaria Pere Virgili, Universitat Rovira i Virgili, Reus, Spain
| | - Salvador Fernández-Arroyo
- Universitat Rovira i Virgili, Department of Medicine and Surgery, Reus, Spain; Unitat de Recerca Biomèdica (URB-CRB), Hospital Universitari de Sant Joan, Institut d'Investigacio Sanitaria Pere Virgili, Universitat Rovira i Virgili, Reus, Spain
| | - Anna Hernández-Aguilera
- Universitat Rovira i Virgili, Department of Medicine and Surgery, Reus, Spain; Unitat de Recerca Biomèdica (URB-CRB), Hospital Universitari de Sant Joan, Institut d'Investigacio Sanitaria Pere Virgili, Universitat Rovira i Virgili, Reus, Spain
| | - Helena Castañé
- Universitat Rovira i Virgili, Department of Medicine and Surgery, Reus, Spain; Unitat de Recerca Biomèdica (URB-CRB), Hospital Universitari de Sant Joan, Institut d'Investigacio Sanitaria Pere Virgili, Universitat Rovira i Virgili, Reus, Spain
| | - Elisabet Rodríguez-Tomàs
- Universitat Rovira i Virgili, Department of Medicine and Surgery, Reus, Spain; Unitat de Recerca Biomèdica (URB-CRB), Hospital Universitari de Sant Joan, Institut d'Investigacio Sanitaria Pere Virgili, Universitat Rovira i Virgili, Reus, Spain
| | - Marta París
- Department of Surgery, Hospital Universitari de Sant Joan, Institut d'Investigació Sanitaria Pere Virgili, Universitat Rovira i Virgili, Reus, Spain
| | - Fàtima Sabench
- Department of Surgery, Hospital Universitari de Sant Joan, Institut d'Investigació Sanitaria Pere Virgili, Universitat Rovira i Virgili, Reus, Spain
| | - Daniel Del Castillo
- Department of Surgery, Hospital Universitari de Sant Joan, Institut d'Investigació Sanitaria Pere Virgili, Universitat Rovira i Virgili, Reus, Spain
| | - Josep M Del Bas
- Technological Unit of Nutrition and Health, EURECAT-Technology Centre of Catalonia, Reus, Spain
| | - Mercedes Tomé
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Consejo Superior de Investigaciones Científicas - Universidad Pablo de Olavide, Avda. Américo Vespucio 24, 41092 Sevilla, Spain
| | - Clément Bodineau
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Consejo Superior de Investigaciones Científicas - Universidad Pablo de Olavide, Avda. Américo Vespucio 24, 41092 Sevilla, Spain; Institut Européen de Chimie et Biologie, INSERM U1218, Université de Bordeaux, 2 Rue Robert Escarpit, Pessac 33607, France
| | - Alejandro Sola-García
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Consejo Superior de Investigaciones Científicas - Universidad Pablo de Olavide, Avda. Américo Vespucio 24, 41092 Sevilla, Spain
| | - José López-Miranda
- Lipids and Atherosclerosis Unit, IMIBIC/Reina Sofia University Hospital. University of Cordoba, Cordoba, Spain; CIBER Fisiopatología de la Obesidad y Nutrición (CIBEROBN), Instituto de Salud Carlos III, Cordoba, Spain
| | - Alejandro Martín-Montalvo
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Consejo Superior de Investigaciones Científicas - Universidad Pablo de Olavide, Avda. Américo Vespucio 24, 41092 Sevilla, Spain
| | - Raúl V Durán
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Consejo Superior de Investigaciones Científicas - Universidad Pablo de Olavide, Avda. Américo Vespucio 24, 41092 Sevilla, Spain; Institut Européen de Chimie et Biologie, INSERM U1218, Université de Bordeaux, 2 Rue Robert Escarpit, Pessac 33607, France
| | - Thomas M Vondriska
- Department of Anesthesiology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, US
| | - Manuel Rosa-Garrido
- Department of Anesthesiology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, US
| | - Jordi Camps
- Universitat Rovira i Virgili, Department of Medicine and Surgery, Reus, Spain; Unitat de Recerca Biomèdica (URB-CRB), Hospital Universitari de Sant Joan, Institut d'Investigacio Sanitaria Pere Virgili, Universitat Rovira i Virgili, Reus, Spain.
| | - Javier A Menéndez
- Program Against Cancer Therapeutic Resistance (ProCURE), Metabolism and Cancer Group , Catalan Institute of Oncology, Girona , Spain; Girona Biomedical Research Institute (IDIBGI), Girona, Spain
| | - Jorge Joven
- Universitat Rovira i Virgili, Department of Medicine and Surgery, Reus, Spain; Unitat de Recerca Biomèdica (URB-CRB), Hospital Universitari de Sant Joan, Institut d'Investigacio Sanitaria Pere Virgili, Universitat Rovira i Virgili, Reus, Spain; The Campus of International Excellence Southern Catalonia, Tarragona, Spain.
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Ricci C, Cerase A, Riolo G, Manasse G, Battistini S. KRIT1 Gene in Patients with Cerebral Cavernous Malformations: Clinical Features and Molecular Characterization of Novel Variants. J Mol Neurosci 2021; 71:1876-1883. [PMID: 33651268 PMCID: PMC8421287 DOI: 10.1007/s12031-021-01814-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 02/09/2021] [Indexed: 11/24/2022]
Abstract
Cerebral cavernous malformations (CCMs) are vascular malformations that may result in headaches, seizures, focal neurological deficits, and hemorrhage. CCMs occur sporadically (80%) or in familial form (20%), with autosomal dominant inheritance. Among the three CCM-related genes, mutations in KRIT1 account for 53–65% of familial cases and more than 100 different mutations have been identified so far. In the present work, we describe the clinical, neuroradiological, and genetic findings of sixteen CCM Italian patients, 13 belonging to 4 unrelated families and 3 sporadic cases. Six distinct KRIT1 gene variants, two novel (c.1730+1_1730+3del, c.1664 C>T) and four previously described (c.966G>A, c.1255-1G>A c.1197_1200del, c.1255-1_1256del), were identified, including a possible de novo mutation. All the variants resulted in a premature stop codon. Cerebral 1.5 T magnetic resonance imaging showed multiple CCMs in all the mutation carriers for whom it was available, including sporadic cases. One patient had also cutaneous angiomas. Among the mutation carriers, symptomatic patients constituted 66% and a variable phenotypic expression was observed. Our data confirms phenotypic variability and incomplete penetrance of neurological symptoms in KRIT1-positive families, expands the mutational spectrum of this gene, and highlights how sporadic cases with multiple lesions need an approach similar to individuals with familial CCM.
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Affiliation(s)
- Claudia Ricci
- Department of Medical, Surgical and Neurological Sciences, University of Siena, Siena, Italy
| | - Alfonso Cerase
- Neuroimaging Unit - Diagnostic and Functional Neuroradiology, Department of Neurological and Motor Sciences, Azienda ospedaliero-universitaria Senese University Hospital, Siena, Italy
| | - Giulia Riolo
- Department of Medical, Surgical and Neurological Sciences, University of Siena, Siena, Italy
| | - Giuditta Manasse
- Department of Medical, Surgical and Neurological Sciences, University of Siena, Siena, Italy
| | - Stefania Battistini
- Department of Medical, Surgical and Neurological Sciences, University of Siena, Siena, Italy.
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Chemi F, Mohan S, Brady G. Circulating Tumour Cells in Lung Cancer. Recent Results Cancer Res 2020; 215:105-25. [PMID: 31605226 DOI: 10.1007/978-3-030-26439-0_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/25/2023]
Abstract
Circulating tumour cells (CTCs) constitute a potential tumour surrogate that could serve as "liquid biopsy" with the advantage to be a minimally invasive approach compared to traditional tissue biopsies. As CTCs are thought to be the source of metastatic lesions, their analysis represents a potential means of tracking cancer cells from the primary tumour en route to distant sites, thus providing valuable insights into the metastatic process. However, several problems, such as their rarity in the peripheral blood, the technical limitations of single-cell downstream analysis and their phenotypic variability, make CTC detection and molecular characterisation very challenging. Nevertheless, in the last decade, there has been an exponential increase of interest in the development of powerful cellular and molecular methodologies applied to CTCs. In this chapter, we focus on the recent advances of functional studies and molecular profiling of CTCs. We will also highlight the clinical relevance of CTC detection and enumeration, and discuss their potential as tumour biomarkers with special focus on lung cancer.
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Fairclough SR, Kiedrowski LA, Lin JJ, Zelichov O, Tarcic G, Stinchcombe TE, Odegaard JI, Lanman RB, Shaw AT, Nagy RJ. Identification of osimertinib-resistant EGFR L792 mutations by cfDNA sequencing: oncogenic activity assessment and prevalence in large cfDNA cohort. Exp Hematol Oncol 2019; 8:24. [PMID: 31632838 PMCID: PMC6788107 DOI: 10.1186/s40164-019-0148-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 09/23/2019] [Indexed: 12/20/2022] Open
Abstract
Cell-free DNA (cfDNA) next-generation sequencing has the potential to capture tumor heterogeneity and genomic evolution under treatment pressure in a non-invasive manner. Here, we report the detection of EGFR L792 mutations, a non-covalent mechanism of osimertinib resistance, using Guardant360 cfDNA testing in a patient with metastatic EGFR-mutant non-small cell lung cancer (NSCLC) whose disease progressed on osimertinib. We subsequently analyzed a large cohort of over 1800 additional patient samples harboring an EGFR T790M mutation and identified a concomitant L792 mutation in a total of 22 (1.2%) cases. In vitro functional assays demonstrated that the EGFR L858R/T790M/L792F/H mutations conferred intermediate-level resistance to osimertinib. Further understanding of potential acquired resistance mechanisms to targeted therapy may help inform treatment strategy in EGFR-mutant NSCLC.
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Affiliation(s)
| | | | - Jessica J Lin
- 2Massachusetts General Hospital Cancer Center and Department of Medicine, Massachusetts General Hospital, 55 Fruit St, Boston, MA 02114 USA
| | - Ori Zelichov
- NovellusDx, Jerusalem Biopark, Hadassah Ein-Kerem Medical Center Campus, Jerusalem, Israel
| | - Gabi Tarcic
- NovellusDx, Jerusalem Biopark, Hadassah Ein-Kerem Medical Center Campus, Jerusalem, Israel
| | | | | | - Richard B Lanman
- Guardant Health, Inc., 505 Penobscot Dr, Redwood City, CA 94063 USA
| | - Alice T Shaw
- 2Massachusetts General Hospital Cancer Center and Department of Medicine, Massachusetts General Hospital, 55 Fruit St, Boston, MA 02114 USA
| | - Rebecca J Nagy
- Guardant Health, Inc., 505 Penobscot Dr, Redwood City, CA 94063 USA
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Karlsson L, de Paula Michelatto D, Lusa ALG, D'Almeida Mgnani Silva C, Östberg LJ, Persson B, Guerra-Júnior G, Valente de Lemos-Marini SH, Baldazzi L, Menabó S, Balsamo A, Greggio NA, Palandi de Mello M, Barbaro M, Lajic S. Novel non-classic CYP21A2 variants, including combined alleles, identified in patients with congenital adrenal hyperplasia. Clin Biochem 2019; 73:50-56. [PMID: 31344365 DOI: 10.1016/j.clinbiochem.2019.07.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 07/19/2019] [Accepted: 07/19/2019] [Indexed: 11/18/2022]
Abstract
OBJECTIVE Congenital adrenal hyperplasia (CAH) is an inborn error of metabolism and a common disorder of sex development where >90% of all cases are due to 21-hydroxylase deficiency. Novel and rare pathogenic variants account for 5% of all clinical cases. Here, we sought to investigate the functional and structural effects of four novel (p.Val358Ile, p.Arg369Gln, p.Asp377Tyr, and p.Leu461Pro) and three combinations of CYP21A2 variants (i.e. one allele containing two variants p.[Ile172Asn;Val358Ile], p.[Val281Leu;Arg369Gln], or p.[Asp377Tyr;Leu461Pro]) identified in patients with CAH. METHODS All variants were reconstructed by in vitro site-directed mutagenesis, the proteins were transiently expressed in COS-1 cells and enzyme activities directed toward the two natural substrates (17-hydroxyprogesterone and progesterone) were determined. In parallel, in silico prediction of the pathogenicity of the variants based on the human CYP21 X-ray structure was performed. RESULTS The novel variants, p.Val358Ile, p.Arg369Gln, p.Asp377Tyr, and p.Leu461Pro exhibited residual enzymatic activities within the range of non-classic (NC) CAH variants (40-82%). An additive effect on the reduction of enzymatic activity (1-17%) was observed when two variants were expressed together, as identified in several patients, resulting in either NC or more severe phenotypes. In silico predictions were in line with the in vitro data except for p.Leu461Pro. CONCLUSIONS Altogether, the combination of clinical data, in silico prediction, and data from in vitro studies are important for establishing a correct genotype and phenotype correlation in patients with CAH.
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Affiliation(s)
- Leif Karlsson
- Department of Women's and Children's Health, Karolinska Institutet, Pediatric Endocrinology Unit (Q2:08), Karolinska University Hospital, Stockholm, Sweden
| | - Débora de Paula Michelatto
- Department of Women's and Children's Health, Karolinska Institutet, Pediatric Endocrinology Unit (Q2:08), Karolinska University Hospital, Stockholm, Sweden; Laboratório de Genética Molecular Humana, Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, SP, Brazil
| | - Ana Letícia Gori Lusa
- Laboratório de Genética Molecular Humana, Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, SP, Brazil
| | | | - Linus J Östberg
- Science for Life Laboratory and eSSENCE, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Bengt Persson
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Gil Guerra-Júnior
- Departamento de Pediatria, Faculdade de Ciências Médicas, Universidade Estadual de Campinas, Campinas, SP, Brazil
| | | | - Lilia Baldazzi
- Department of Woman, Child and Urological Diseases, Centre for Rare Endocrine Conditions (CARENDO BO; Endo-ERN), S.Orsola-Malpighi University Hospital, Bologna, Italy
| | - Soara Menabó
- Department of Woman, Child and Urological Diseases, Centre for Rare Endocrine Conditions (CARENDO BO; Endo-ERN), S.Orsola-Malpighi University Hospital, Bologna, Italy
| | - Antonio Balsamo
- Department of Woman, Child and Urological Diseases, Centre for Rare Endocrine Conditions (CARENDO BO; Endo-ERN), S.Orsola-Malpighi University Hospital, Bologna, Italy
| | - Nella Augusta Greggio
- Department of Women's and Children's Health of Padua, Pediatric Endocrinology Unit, Italy
| | - Maricilda Palandi de Mello
- Laboratório de Genética Molecular Humana, Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, SP, Brazil
| | - Michela Barbaro
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Center for Inherited Metabolic Diseases (CMMS L7:05), Karolinska University Hospital, Stockholm, Sweden
| | - Svetlana Lajic
- Department of Women's and Children's Health, Karolinska Institutet, Pediatric Endocrinology Unit (Q2:08), Karolinska University Hospital, Stockholm, Sweden.
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Abstract
A major strength of zebrafish as a model organism is their rapid, in vitro development. The easy access to embryos compared to mammals, allows larval molecular and cellular composition to be manipulated by microinjection, providing a powerful avenue for biological and translational studies. Here, we describe the essential steps and different applications of microinjection in zebrafish for genome editing and functional studies, along with some experimental tips that are critical for microinjection success.
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Zhan L, Li J, Wei B. Autophagy therapeutics: preclinical basis and initial clinical studies. Cancer Chemother Pharmacol. 2018;82:923-934. [PMID: 30225602 DOI: 10.1007/s00280-018-3688-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2018] [Accepted: 09/10/2018] [Indexed: 12/12/2022]
Abstract
Autophagy captures and degrades intracellular components such as proteins and organelles to sustain metabolism and homeostasis. Rapidly accumulating attention is being paid to the role of autophagy in the development of cancer, which makes autophagy attractive tools and targets for novel therapeutic approaches. Functional studies have confirmed that autophagy dysregulation is causal in many cases of cancer, with autophagy acting as tumor suppressors or tumor promoters, and autophagy inhibitor or promoter has shown promise in preclinical studies. The autophagy-targeted therapeutics using chloroquine/hydroxychloroquine have reached clinical development for treating cancer, but these drugs are actually not efficient probably because of a reduced penetration within the tumor. In this review, we first discuss the discoveries related to dual function of autophagy in cancer. Then, we provide an overview of preclinical studies and clinical trials involved in the development of autophagy therapeutics and finally discuss the future of such therapies.
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Zirkelbach E, Hashmi S, Ramdaney A, Dunnington L, Ashfaq M, Nugent EK, Wilson K. Managing Variant Interpretation Discrepancies in Hereditary Cancer: Clinical Practice, Concerns, and Desired Resources. J Genet Couns 2018; 27:761-9. [PMID: 29260485 DOI: 10.1007/s10897-017-0184-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 11/27/2017] [Indexed: 12/23/2022]
Abstract
Variant interpretation is a complex process, and classification may vary between sources. This study aimed to determine the practice of cancer genetic counselors regarding discrepancies in variant interpretation and to identify concerns when counseling these discrepancies. An electronic survey was sent to genetic counselors in the NSGC Cancer Special Interest Group. The vast majority of counselors (93%) had seen a variant interpretation discrepancy in practice. A large majority (96%) of respondents indicated that they conducted their own research on reported variants. Most respondents cited variant databases as the most common resource utilized in researching variants. Approximately 33% of counselors spent 45 min or more of extra time researching a discrepancy compared to researching a variant with a single classification. When asked how they approached counseling sessions involving variant interpretation discrepancies, the free responses emphasized that counselors considered family history, clinical information, and psychosocial concerns, showing that genetic counselors tailored the session to each individual. Discrepancies in variant interpretation are an ongoing concern for clinical cancer genetic counselors, as demonstrated by the fact that counselors desired further resources to aid in addressing these discrepancies, including a centralized database (89%), guidelines from a major organization (88%), continuing education about the issue (74%), and functional studies (58%). Additionally, most respondents reported that the ideal database would be owned by a non-profit organization (59%) and obtain information directly from laboratories (91%). This investigation was the first to address these discrepancies from a clinical point of view. The study demonstrates that discrepancies in variant interpretation are a concern for clinical cancer genetic counselors and outlines the need for additional support.
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Grabowski JM, Gulia-Nuss M, Kuhn RJ, Hill CA. RNAi reveals proteins for metabolism and protein processing associated with Langat virus infection in Ixodes scapularis (black-legged tick) ISE6 cells. Parasit Vectors 2017; 10:24. [PMID: 28086865 PMCID: PMC5237174 DOI: 10.1186/s13071-016-1944-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2016] [Accepted: 12/16/2016] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Tick-borne flaviviruses (TBFs) cause thousands of human cases of encephalitis worldwide each year, with some TBF infections progressing to hemorrhagic fever. TBFs are of medical and veterinary importance and strategies to reduce flavivirus transmission by the tick vector may have significant application. Analyses of the proteome of ISE6 cells derived from the black legged tick, Ixodes scapularis infected with the TBF, Langat virus (LGTV), have provided insights into proteins and cellular processes involved with LGTV infection. METHODS RNA interference (RNAi)-induced knockdown of transcripts was used to investigate the role of ten tick proteins in the LGTV infection cycle in ISE6 cells. LGTV-infected cells were separately transfected with dsRNA corresponding to each gene of interest and the effect on LGTV genome replication and release of infectious virus was assessed by RT-qPCR and plaque assays, respectively. RESULTS RNAi-induced knockdown of transcripts for two enzymes that likely function in amino acid, carbohydrate, lipid, terpenoid/polykeytide and vitamin metabolism, and a transcript for one protein of unknown function were associated with decreased replication of the LGTV genome and release of infectious virus from cells. The knockdown of transcripts for five enzymes predicted to function in metabolism, a protein likely associated with folding, sorting and degradation, and a protein of unknown function was associated with a decrease only in the amount of infectious LGTV released from cells. CONCLUSIONS These data suggest tick proteins potentially associated with metabolism and protein processing may be involved in LGTV infection of ISE6 cells. Our study provides information to begin to elucidate the function of these proteins and identify targets for the development of new interventions aimed at controlling the transmission of TBFs.
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Affiliation(s)
- Jeffrey M Grabowski
- Department of Entomology, College of Agriculture, Purdue University, 901 W State Street, West Lafayette, IN, 47907, USA.,Markey Center for Structural Biology, Department of Biological Sciences, College of Science, Purdue University, 915 W State Street, West Lafayette, IN, 47907, USA.,Current Address: NIH/NIAID, Rocky Mountain Laboratories, Laboratory of Virology, Biology of Vector-Borne Viruses Section, 903 S 4th St, Hamilton, MT, 59840, USA
| | - Monika Gulia-Nuss
- Department of Entomology, College of Agriculture, Purdue University, 901 W State Street, West Lafayette, IN, 47907, USA.,Current Address: Department of Biochemistry and Molecular Biology, College of Agriculture, Biotechnology, and Natural Resources, University of Nevada-Reno, 1664 N Virginia Street, Reno, NV, 89503, USA
| | - Richard J Kuhn
- Markey Center for Structural Biology, Department of Biological Sciences, College of Science, Purdue University, 915 W State Street, West Lafayette, IN, 47907, USA.,Purdue Institute for Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN, 47907, USA
| | - Catherine A Hill
- Department of Entomology, College of Agriculture, Purdue University, 901 W State Street, West Lafayette, IN, 47907, USA. .,Purdue Institute for Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN, 47907, USA.
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Lee BP, Lloyd-Laney HO, Locke JM, McCulloch LJ, Knight B, Yaghootkar H, Cory G, Kos K, Frayling TM, Harries LW. Functional characterisation of ADIPOQ variants using individuals recruited by genotype. Mol Cell Endocrinol 2016; 428:49-57. [PMID: 26996131 DOI: 10.1016/j.mce.2016.03.020] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Revised: 02/18/2016] [Accepted: 03/15/2016] [Indexed: 12/30/2022]
Abstract
Four non-coding GWAS variants in or near the ADIPOQ gene (rs17300539, rs17366653, rs3821799 and rs56354395) together explain 4% of the variation in circulating adiponectin. The functional basis for this is unknown. We tested the effect of these variants on ADIPOQ transcription, splicing and stability respectively in adipose tissue samples from participants recruited by rs17366653 genotype. Transcripts carrying rs17300539 demonstrated a 17% increase in expression (p = 0.001). Variant rs17366653 was associated with disruption of ADIPOQ splicing leading to a 7 fold increase in levels of a non-functional transcript (p = 0.002). Transcripts carrying rs56354395 demonstrated a 59% decrease in expression (p = <0.0001). No effects of rs3821799 genotype on expression was observed. Association between variation in the ADIPOQ gene and serum adiponectin may arise from effects on mRNA transcription, splicing or stability. These studies illustrate the utility of recruit-by-genotype studies in relevant human tissues in functional interpretation of GWAS signals.
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Affiliation(s)
- Benjamin P Lee
- Institute of Biomedical & Clinical Science, University of Exeter Medical School, Exeter, Devon, EX2 5DW, UK
| | - Henry O Lloyd-Laney
- Institute of Biomedical & Clinical Science, University of Exeter Medical School, Exeter, Devon, EX2 5DW, UK
| | - Jonathan M Locke
- Institute of Biomedical & Clinical Science, University of Exeter Medical School, Exeter, Devon, EX2 5DW, UK
| | - Laura J McCulloch
- Institute of Biomedical & Clinical Science, University of Exeter Medical School, Exeter, Devon, EX2 5DW, UK
| | - Bridget Knight
- Institute of Biomedical & Clinical Science, University of Exeter Medical School, Exeter, Devon, EX2 5DW, UK
| | - Hanieh Yaghootkar
- Institute of Biomedical & Clinical Science, University of Exeter Medical School, Exeter, Devon, EX2 5DW, UK
| | - Giles Cory
- Institute of Biomedical & Clinical Science, University of Exeter Medical School, Exeter, Devon, EX2 5DW, UK
| | - Katarina Kos
- Institute of Biomedical & Clinical Science, University of Exeter Medical School, Exeter, Devon, EX2 5DW, UK
| | - Timothy M Frayling
- Institute of Biomedical & Clinical Science, University of Exeter Medical School, Exeter, Devon, EX2 5DW, UK
| | - Lorna W Harries
- Institute of Biomedical & Clinical Science, University of Exeter Medical School, Exeter, Devon, EX2 5DW, UK.
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Abstract
Osteoarthritis (OA) is the most common age-related arthritic disorder and is characterized by aberrant extracellular matrix (ECM) content and surface disruptions that range from fibrillation, clefting and delamination, leading to articular surface erosion. Worldwide, over 20% of the population is affected with OA and 80% of these patients have limitations in movement, whereas 25% experience inhibition in major daily activities of life. OA is the most common disabling arthritic disease; nevertheless, no disease-modifying treatment is available except for the expensive total joint replacement surgery at end-stage disease. Lack of insight into the underlying pathophysiological mechanisms of OA has considerably contributed to the inability of the scientific community to develop disease-modifying drugs. To overcome this critical barrier, focus should be on translation of identified robust gene deviations towards the underlying biological mechanisms.
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Affiliation(s)
- Nils Bomer
- Dept. Medical Statistics and Bioinformatics, Section Molecular Epidemiology, Leiden University Medical Centre, LUMC Post-zone S-05-P, P.O. Box 9600, 2300 RC Leiden, The Netherlands.
| | - Wouter den Hollander
- Dept. Medical Statistics and Bioinformatics, Section Molecular Epidemiology, Leiden University Medical Centre, LUMC Post-zone S-05-P, P.O. Box 9600, 2300 RC Leiden, The Netherlands.
| | - Yolande F M Ramos
- Dept. Medical Statistics and Bioinformatics, Section Molecular Epidemiology, Leiden University Medical Centre, LUMC Post-zone S-05-P, P.O. Box 9600, 2300 RC Leiden, The Netherlands.
| | - Ingrid Meulenbelt
- Dept. Medical Statistics and Bioinformatics, Section Molecular Epidemiology, Leiden University Medical Centre, LUMC Post-zone S-05-P, P.O. Box 9600, 2300 RC Leiden, The Netherlands.
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Pupavac M, Tian X, Chu J, Wang G, Feng Y, Chen S, Fenter R, Zhang VW, Wang J, Watkins D, Wong LJ, Rosenblatt DS. Added value of next generation gene panel analysis for patients with elevated methylmalonic acid and no clinical diagnosis following functional studies of vitamin B12 metabolism. Mol Genet Metab 2016; 117:363-8. [PMID: 26827111 DOI: 10.1016/j.ymgme.2016.01.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 01/22/2016] [Indexed: 12/13/2022]
Abstract
Next generation sequencing (NGS) based gene panel testing is increasingly available as a molecular diagnostic approach for inborn errors of metabolism. Over the past 40 years patients have been referred to the Vitamin B12 Clinical Research Laboratory at McGill University for diagnosis of inborn errors of cobalamin metabolism by functional studies in cultured fibroblasts. DNA samples from patients in which no diagnosis was made by these studies were tested by a NGS gene panel to determine whether any molecular diagnoses could be made. 131 DNA samples from patients with elevated methylmalonic acid and no diagnosis following functional studies of cobalamin metabolism were analyzed using the 24 gene extended cobalamin metabolism NGS based panel developed by Baylor Miraca Genetics Laboratories. Gene panel testing identified two or more variants in a single gene in 16/131 patients. Eight patients had pathogenic findings, one had a finding of uncertain significance, and seven had benign findings. Of the patients with pathogenic findings, five had mutations in ACSF3, two in SUCLG1 and one in TCN2. Thus, the NGS gene panel allowed for the presumptive diagnosis of 8 additional patients for which a diagnosis was not made by the functional assays.
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Affiliation(s)
- Mihaela Pupavac
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Xia Tian
- Baylor Miraca Genetics Laboratories, Houston, TX, United States
| | - Jordan Chu
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Guoli Wang
- Baylor Miraca Genetics Laboratories, Houston, TX, United States
| | - Yanming Feng
- Baylor Miraca Genetics Laboratories, Houston, TX, United States
| | - Stella Chen
- Baylor Miraca Genetics Laboratories, Houston, TX, United States
| | | | - Victor W Zhang
- Baylor Miraca Genetics Laboratories, Houston, TX, United States; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
| | - Jing Wang
- Baylor Miraca Genetics Laboratories, Houston, TX, United States; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
| | - David Watkins
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Lee-Jun Wong
- Baylor Miraca Genetics Laboratories, Houston, TX, United States; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
| | - David S Rosenblatt
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.
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20
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Liu Y, Sidhu A, Bean LH, Conway RL, Fridovich-Keil JL. Genetic and functional studies reveal a novel noncoding variant in GALT associated with a false positive newborn screening result for galactosemia. Clin Chim Acta 2015; 446:171-4. [PMID: 25920691 DOI: 10.1016/j.cca.2015.04.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Revised: 04/14/2015] [Accepted: 04/14/2015] [Indexed: 10/23/2022]
Abstract
BACKGROUND Classic galactosemia (CG) is a potentially lethal genetic disorder that results from profound loss of galactose-1-phosphate uridylyltransferase (GALT). CG is detected by newborn screening (NBS) in many countries; however, conclusive diagnosis can be complex due to broad and overlapping ranges of GALT activity. Molecular studies can also be complex due to allelic heterogeneity at the GALT locus. METHODS We conducted both biochemical and molecular follow-up studies for an infant flagged by NBS for possible galactosemia. To clarify the diagnosis we also conducted biochemical and RNA studies of lymphoblasts prepared from the child and one parent. RESULTS We identified a novel noncoding GALT variant, c.377+17C>T, that was homozygous in the child and heterozygous in both parents. The child and both parents also showed diminished GALT activity in red blood cells, and transformed lymphoblasts from the child and one parent further showed diminished GALT activity. However, qRT-PCR studies demonstrated apparently normal GALT mRNA levels in lymphoblasts, and Gal-1P values measured in the child following galactose exposure in infancy and at 1 year were normal. CONCLUSIONS These results highlight the existence of rare but apparently benign variants in GALT and underscore the need for functional studies to distinguish pathogenic from benign variants.
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Affiliation(s)
- Ying Liu
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Alpa Sidhu
- Children's Hospital of Michigan Metabolic Clinic, Wayne State University, Detroit, MI 48201, USA
| | - Lora H Bean
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Robert L Conway
- Children's Hospital of Michigan Metabolic Clinic, Wayne State University, Detroit, MI 48201, USA
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