1
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Gibson JT, Huang M, Shenelli Croos Dabrera M, Shukla K, Rothe H, Hilbert P, Deltas C, Storey H, Lipska-Ziętkiewicz BS, Chan MMY, Sadeghi-Alavijeh O, Gale DP, Cerkauskaite A, Savige J. Genotype-phenotype correlations for COL4A3-COL4A5 variants resulting in Gly substitutions in Alport syndrome. Sci Rep 2022; 12:2722. [PMID: 35177655 PMCID: PMC8854626 DOI: 10.1038/s41598-022-06525-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 01/24/2022] [Indexed: 12/21/2022] Open
Abstract
Alport syndrome is the commonest inherited kidney disease and nearly half the pathogenic variants in the COL4A3-COL4A5 genes that cause Alport syndrome result in Gly substitutions. This study examined the molecular characteristics of Gly substitutions that determine the severity of clinical features. Pathogenic COL4A5 variants affecting Gly in the Leiden Open Variation Database in males with X-linked Alport syndrome were correlated with age at kidney failure (n = 157) and hearing loss diagnosis (n = 80). Heterozygous pathogenic COL4A3 and COL4A4 variants affecting Gly (n = 304) in autosomal dominant Alport syndrome were correlated with the risk of haematuria in the UK 100,000 Genomes Project. Gly substitutions were stratified by exon location (1 to 20 or 21 to carboxyl terminus), being adjacent to a non-collagenous region (interruption or terminus), and the degree of instability caused by the replacement residue. Pathogenic COL4A5 variants that resulted in a Gly substitution with a highly destabilising residue reduced the median age at kidney failure by 7 years (p = 0.002), and age at hearing loss diagnosis by 21 years (p = 0.004). Substitutions adjacent to a non-collagenous region delayed kidney failure by 19 years (p = 0.014). Heterozygous pathogenic COL4A3 and COL4A4 variants that resulted in a Gly substitution with a highly destabilising residue (Arg, Val, Glu, Asp, Trp) were associated with an increased risk of haematuria (p = 0.018), and those adjacent to a non-collagenous region were associated with a reduced risk (p = 0.046). Exon location had no effect. In addition, COL4A5 variants adjacent to non-collagenous regions were over-represented in the normal population in gnomAD (p < 0.001). The nature of the substitution and of nearby residues determine the risk of haematuria, early onset kidney failure and hearing loss for Gly substitutions in X-linked and autosomal dominant Alport syndrome.
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Affiliation(s)
- Joel T Gibson
- Department of Medicine (Melbourne Health and Northern Health), Royal Melbourne Hospital, The University of Melbourne, Parkville, VIC, 3050, Australia
| | - Mary Huang
- Department of Medicine (Melbourne Health and Northern Health), Royal Melbourne Hospital, The University of Melbourne, Parkville, VIC, 3050, Australia
| | - Marina Shenelli Croos Dabrera
- Department of Medicine (Melbourne Health and Northern Health), Royal Melbourne Hospital, The University of Melbourne, Parkville, VIC, 3050, Australia
| | - Krushnam Shukla
- Department of Medicine (Melbourne Health and Northern Health), Royal Melbourne Hospital, The University of Melbourne, Parkville, VIC, 3050, Australia
| | - Hansjörg Rothe
- Centre for Nephrology and Metabolic Disorders, 02943, Weisswasser, Germany
| | - Pascale Hilbert
- Departement de Biologie Moleculaire, Institute de Pathologie et de Genetique ASBL, Gosselies, Belgium
| | - Constantinos Deltas
- Center of Excellence in Biobanking and Biomedical Research, University of Cyprus Medical School, Nicosia, Cyprus
| | - Helen Storey
- Molecular Genetics, Viapath Laboratories, 5th Floor Tower Wing, Guy's Hospital, London, SE1 9RT, UK
| | | | - Melanie M Y Chan
- Department of Renal Medicine, University College London, London, UK
| | | | - Daniel P Gale
- Department of Renal Medicine, University College London, London, UK
| | - Agne Cerkauskaite
- Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, Vilnius, Lithuania
| | - Judy Savige
- Department of Medicine (Melbourne Health and Northern Health), Royal Melbourne Hospital, The University of Melbourne, Parkville, VIC, 3050, Australia.
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Savige J, Storey H, Watson E, Hertz JM, Deltas C, Renieri A, Mari F, Hilbert P, Plevova P, Byers P, Cerkauskaite A, Gregory M, Cerkauskiene R, Ljubanovic DG, Becherucci F, Errichiello C, Massella L, Aiello V, Lennon R, Hopkinson L, Koziell A, Lungu A, Rothe HM, Hoefele J, Zacchia M, Martic TN, Gupta A, van Eerde A, Gear S, Landini S, Palazzo V, al-Rabadi L, Claes K, Corveleyn A, Van Hoof E, van Geel M, Williams M, Ashton E, Belge H, Ars E, Bierzynska A, Gangemi C, Lipska-Ziętkiewicz BS. Consensus statement on standards and guidelines for the molecular diagnostics of Alport syndrome: refining the ACMG criteria. Eur J Hum Genet 2021; 29:1186-1197. [PMID: 33854215 PMCID: PMC8384871 DOI: 10.1038/s41431-021-00858-1] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 02/13/2021] [Accepted: 03/02/2021] [Indexed: 02/06/2023] Open
Abstract
The recent Chandos House meeting of the Alport Variant Collaborative extended the indications for screening for pathogenic variants in the COL4A5, COL4A3 and COL4A4 genes beyond the classical Alport phenotype (haematuria, renal failure; family history of haematuria or renal failure) to include persistent proteinuria, steroid-resistant nephrotic syndrome, focal and segmental glomerulosclerosis (FSGS), familial IgA glomerulonephritis and end-stage kidney failure without an obvious cause. The meeting refined the ACMG criteria for variant assessment for the Alport genes (COL4A3-5). It identified 'mutational hotspots' (PM1) in the collagen IV α5, α3 and α4 chains including position 1 Glycine residues in the Gly-X-Y repeats in the intermediate collagenous domains; and Cysteine residues in the carboxy non-collagenous domain (PP3). It considered that 'well-established' functional assays (PS3, BS3) were still mainly research tools but sequencing and minigene assays were commonly used to confirm splicing variants. It was not possible to define the Minor Allele Frequency (MAF) threshold above which variants were considered Benign (BA1, BS1), because of the different modes of inheritances of Alport syndrome, and the occurrence of hypomorphic variants (often Glycine adjacent to a non-collagenous interruption) and local founder effects. Heterozygous COL4A3 and COL4A4 variants were common 'incidental' findings also present in normal reference databases. The recognition and interpretation of hypomorphic variants in the COL4A3-COL4A5 genes remains a challenge.
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Affiliation(s)
- Judy Savige
- grid.1008.90000 0001 2179 088XDepartment of Medicine (MH and NH), The University of Melbourne, Parkville, VIC Australia
| | - Helen Storey
- grid.239826.40000 0004 0391 895XMolecular Genetics, Viapath Laboratories, Guy’s Hospital, London, UK
| | - Elizabeth Watson
- Elizabeth Watson, South West Genomic Laboratory Hub, North Bristol Trust, Bristol, UK
| | - Jens Michael Hertz
- grid.7143.10000 0004 0512 5013Jens Michael Hertz, Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | - Constantinos Deltas
- grid.6603.30000000121167908Center of Excellence in Biobanking and Biomedical Research and Molecule Medicine Center, University of Cyprus, Nicosia, Cyprus
| | - Alessandra Renieri
- grid.9024.f0000 0004 1757 4641Medical Genetics, University of Siena, Siena, Italy
| | - Francesca Mari
- Institute de Pathologie et de Genetique ASBL, Departement de Biologie Moleculaire, Gosselies, Belgium
| | - Pascale Hilbert
- Institute de Pathologie et de Genetique ASBL, Departement de Biologie Moleculaire, Gosselies, Belgium
| | - Pavlina Plevova
- grid.412727.50000 0004 0609 0692Department of Medical Genetics, and Department of Biomedical Sciences, University Hospital of Ostrava, Ostrava, Czech Republic
| | - Peter Byers
- grid.34477.330000000122986657Departments of Pathology and Medicine (Medical Genetics), University of Washington, Seattle, WA USA
| | - Agne Cerkauskaite
- grid.6441.70000 0001 2243 2806Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, Vilnius, Lithuania
| | - Martin Gregory
- grid.223827.e0000 0001 2193 0096Division of Nephrology, Department of Medicine, University of Utah Health, Salt Lake City, UT USA
| | - Rimante Cerkauskiene
- grid.6441.70000 0001 2243 2806Clinic of Pediatrics, Institute of Clinical Medicine, Faculty of Medicine, Vilnius University, Vilnius, Lithuania
| | - Danica Galesic Ljubanovic
- grid.412095.b0000 0004 0631 385XDepartment of Pathology, University of Zagreb, School of Medicine, Dubrava University Hospital, Zagreb, Croatia
| | - Francesca Becherucci
- grid.411477.00000 0004 1759 0844Nephrology Unit and Meyer Children’s University Hospital, Firenze, Italy
| | - Carmela Errichiello
- grid.411477.00000 0004 1759 0844Nephrology Unit and Meyer Children’s University Hospital, Firenze, Italy
| | - Laura Massella
- grid.414125.70000 0001 0727 6809Division of Nephrology and Dialysis, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Valeria Aiello
- grid.6292.f0000 0004 1757 1758Department of Experimental Diagnostic and Specialty Medicine (DIMES), Nephrology, Dialysis and Renal Transplant Unit, S. Orsola Hospital, University of Bologna, Bologna, Italy
| | - Rachel Lennon
- grid.5379.80000000121662407Wellcome Centre for Cell-Matrix Research, Division of Cell-Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology Medicine and Health, The University of Manchester, Manchester, UK
| | - Louise Hopkinson
- grid.5379.80000000121662407Wellcome Centre for Cell-Matrix Research, Division of Cell-Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology Medicine and Health, The University of Manchester, Manchester, UK
| | - Ania Koziell
- grid.13097.3c0000 0001 2322 6764School of Immunology and Microbial Sciences, Faculty of Life Sciences, King’s College London, London, UK
| | - Adrian Lungu
- grid.415180.90000 0004 0540 9980Fundeni Clinical Institute, Pediatric Nephrology Department, Bucharest, Romania
| | | | - Julia Hoefele
- grid.6936.a0000000123222966Institute of Human Genetics, Technical University of Munich, München, Germany
| | | | - Tamara Nikuseva Martic
- grid.4808.40000 0001 0657 4636Department of Biology, School of Medicine University of Zagreb, Zagreb, Croatia
| | - Asheeta Gupta
- grid.415246.00000 0004 0399 7272Birmingham Children’s Hospital, Birmingham, UK
| | - Albertien van Eerde
- grid.5477.10000000120346234Departments of Genetics and Center for Molecular Medicine, University Medical Center, Utrecht University, Utrecht, The Netherlands
| | | | - Samuela Landini
- grid.8404.80000 0004 1757 2304Medical Genetics Unit, Department of Clinical and Experimental Biomedical Sciences “Mario Serio”, University of Florence, Florence, Italy
| | - Viviana Palazzo
- grid.411477.00000 0004 1759 0844Medical Genetics Unit, Meyer Children’s University Hospital, Florence, Italy
| | - Laith al-Rabadi
- grid.223827.e0000 0001 2193 0096Health Sciences Centre, University of UTAH, Salt Lake City, UT USA
| | - Kathleen Claes
- grid.410569.f0000 0004 0626 3338Department of Nephrology and Renal Transplantation, University Hospitals Leuven, Leuven, Belgium
| | - Anniek Corveleyn
- grid.410569.f0000 0004 0626 3338Center for Human Genetics, University Hospitals and KU Leuven, Leuven, Belgium
| | - Evelien Van Hoof
- grid.410569.f0000 0004 0626 3338Center for Human Genetics, University Hospitals and KU Leuven, Leuven, Belgium
| | - Micheel van Geel
- grid.412966.e0000 0004 0480 1382Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Maggie Williams
- grid.416201.00000 0004 0417 1173Bristol Genetics Laboratory Pathology Sciences, Southmead Hospital, Bristol, UK
| | - Emma Ashton
- grid.420468.cNorth East Thames Regional Genetics Laboratory, Great Ormond Street Hospital, London, UK
| | - Hendica Belge
- grid.10417.330000 0004 0444 9382Department of Physiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Elisabeth Ars
- grid.7080.f0000 0001 2296 0625Inherited Kidney Disorders, Fundacio Puigvert, Universitat Autonoma de Barcelona, Barcelona, Spain
| | - Agnieszka Bierzynska
- grid.5337.20000 0004 1936 7603Bristol Renal Unit, Bristol Medical School, University of Bristol, Bristol, UK
| | - Concetta Gangemi
- grid.411475.20000 0004 1756 948XDivision of Nephrology and Dialysis, University Hospital of Verona, Verona, Italy
| | - Beata S. Lipska-Ziętkiewicz
- grid.11451.300000 0001 0531 3426Centre for Rare Diseases, and Clinical Genetics Unit, Medical University of Gdansk, Gdansk, Poland
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Nozu K, Takaoka Y, Kai H, Takasato M, Yabuuchi K, Yamamura T, Horinouchi T, Sakakibara N, Ninchoji T, Nagano C, Iijima K. Genetic background, recent advances in molecular biology, and development of novel therapy in Alport syndrome. Kidney Res Clin Pract 2020; 39:402-413. [PMID: 33214343 PMCID: PMC7771000 DOI: 10.23876/j.krcp.20.111] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 08/06/2020] [Accepted: 08/08/2020] [Indexed: 12/18/2022] Open
Abstract
Alport syndrome (AS) is a progressive inherited kidney disease characterized by hearing loss and ocular abnormalities. There are three forms of AS depending on inheritance mode: X-linked Alport syndrome (XLAS), autosomal recessive AS (ARAS), and autosomal dominant AS (ADAS). XLAS is caused by pathogenic variants in COL4A5, which encodes type IV collagen α5 chain, while ADAS and ARAS are caused by variants in COL4A3 or COL4A4, which encode type IV collagen α3 or α4 chain, respectively. In male XLAS or ARAS cases, end-stage kidney disease (ESKD) develops around a median age of 20 to 30 years old, while female XLAS or ADAS cases develop ESKD around a median age of 60 to 70 years old. The diagnosis of AS is dependent on either genetic or pathological findings. However, determining the pathogenicity of the variants detected by gene tests can be difficult. Recently, we applied the following molecular investigation tools to determine pathogenicity: 1) in silico and in vitro trimer formation assay of α345 chains to assess triple helix formation ability, 2) kidney organoids constructed from patients’ induced pluripotent stem cells to identify α5 chain expression on the glomerular basement membrane, and 3) in vitro splicing assay to detect aberrant splicing to determine the pathogenicity of variants. In this review article, we discuss the genetic background and novel assays for determining the pathogenicity of variants. We also discuss the current treatment approaches and introduce exon skipping therapy as one potential treatment option.
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Affiliation(s)
- Kandai Nozu
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Yutaka Takaoka
- Division of Medical Informatics and Bioinformatics, Kobe University Hospital, Kobe, Japan
| | - Hirofumi Kai
- Department of Molecular Medicine, Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto, Japan
| | - Minoru Takasato
- Laboratory for Human Organogenesis, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan.,Laboratory of Molecular Cell Biology and Development, Department of Animal Development and Physiology, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Kensuke Yabuuchi
- Laboratory for Human Organogenesis, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
| | - Tomohiko Yamamura
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Tomoko Horinouchi
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Nana Sakakibara
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Takeshi Ninchoji
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - China Nagano
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Kazumoto Iijima
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
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