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Jones LK, Lam R, McKee KK, Aleksandrova M, Dowling J, Alexander SI, Mallawaarachchi A, Cottle DL, Short KM, Pais L, Miner JH, Mallett AJ, Simons C, McCarthy H, Yurchenco PD, Smyth IM. A mutation affecting laminin alpha 5 polymerisation gives rise to a syndromic developmental disorder. Development 2020; 147:dev189183. [PMID: 32439764 PMCID: PMC7540250 DOI: 10.1242/dev.189183] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 04/30/2020] [Indexed: 12/15/2022]
Abstract
Laminin alpha 5 (LAMA5) is a member of a large family of proteins that trimerise and then polymerise to form a central component of all basement membranes. Consequently, the protein plays an instrumental role in shaping the normal development of the kidney, skin, neural tube, lung and limb, and many other organs and tissues. Pathogenic mutations in some laminins have been shown to cause a range of largely syndromic conditions affecting the competency of the basement membranes to which they contribute. We report the identification of a mutation in the polymerisation domain of LAMA5 in a patient with a complex syndromic disease characterised by defects in kidney, craniofacial and limb development, and by a range of other congenital defects. Using CRISPR-generated mouse models and biochemical assays, we demonstrate the pathogenicity of this variant, showing that the change results in a failure of the polymerisation of α/β/γ laminin trimers. Comparing these in vivo phenotypes with those apparent upon gene deletion in mice provides insights into the specific functional importance of laminin polymerisation during development and tissue homeostasis.
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Affiliation(s)
- Lynelle K Jones
- Department of Anatomy and Developmental Biology, Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Monash University, Melbourne 3800, Australia
| | - Rachel Lam
- Department of Anatomy and Developmental Biology, Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Monash University, Melbourne 3800, Australia
| | - Karen K McKee
- Department of Pathology and Laboratory Medicine, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ 08901, USA
| | - Maya Aleksandrova
- Department of Pathology and Laboratory Medicine, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ 08901, USA
| | | | - Stephen I Alexander
- Nephrology Department, Centre for Kidney Research, The Children's Hospital at Westmead, Sydney 2145, New South Wales, Australia
| | - Amali Mallawaarachchi
- Department of Medical Genomics, Royal Prince Alfred Hospital; Garvan Institute of Medical Research, Sydney 2010, New South Wales, Australia
| | - Denny L Cottle
- Department of Anatomy and Developmental Biology, Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Monash University, Melbourne 3800, Australia
| | - Kieran M Short
- Department of Anatomy and Developmental Biology, Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Monash University, Melbourne 3800, Australia
| | - Lynn Pais
- Broad Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jeffery H Miner
- Division of Nephrology, Department of Medicine and Department of Cell Biology and Physiology, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Andrew J Mallett
- Kidney Health Service, Royal Brisbane and Women's Hospital and the Institute for Molecular Bioscience and Faculty of Medicine, The University of Queensland, Brisbane 4072, Queensland, Australia
| | - Cas Simons
- Murdoch Children's Research Institute, The Royal Children's Hospital Melbourne, Melbourne 3052, Victoria, Australia
| | - Hugh McCarthy
- The Sydney Children's Hospitals Network and the Children's Hospital Westmead Clinical School, University of Sydney, Sydney 2145, New South Wales, Australia
| | - Peter D Yurchenco
- Department of Pathology and Laboratory Medicine, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ 08901, USA
| | - Ian M Smyth
- Department of Anatomy and Developmental Biology, Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Monash University, Melbourne 3800, Australia
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Mallett AJ, Quinlan C, Patel C, Fowles L, Crawford J, Gattas M, Baer R, Bennetts B, Ho G, Holman K, Simons C. Precision Medicine Diagnostics for Rare Kidney Disease: Twitter as a Tool in Clinical Genomic Translation. Kidney Med 2019; 1:315-318. [PMID: 32734212 PMCID: PMC7380393 DOI: 10.1016/j.xkme.2019.06.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
New technologies such as genomics present opportunities to deliver precision medicine, including in the diagnosis of rare kidney disorders. Simultaneously, social media platforms such as Twitter can provide rapid and wide-reaching information dissemination in health care and science. We present 2 cases in which the reporting of a novel genetic cause for human kidney disease was communicated through Twitter and then subsequently noted by treating clinicians, thereby resulting in rapid clinical diagnostic translation. In 1 family, this involved the reporting of heterozygous variants in GREB1L relating to autosomal dominant unilateral or bilateral renal agenesis, and in the other family, this involved biallelic variants in CLDN10 relating to autosomal recessive hypokalemic renal tubular phenotypes. The times from Twitter notification to clinical diagnostic genetic report for these families were 111 and 200 days, respectively. Although caution is required, these cases show that social media platforms can contribute to rapid and accessible academic communication that may benefit clinicians, genomics-based researchers, and patients and families affected by rare kidney diseases.
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Affiliation(s)
- Andrew J Mallett
- Department of Renal Medicine, Royal Brisbane and Women's Hospital, Herston, QLD, Australia.,KidGen Collaborative, Australian Genomics Health Alliance, Parkville, VIC, Australia.,Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD, Australia.,Murdoch Children's Research Institute, The Royal Children's Hospital Melbourne, Parkville, Melbourne, VIC, Australia.,Faculty of Medicine, The University of Queensland, Herston, QLD, Australia
| | - Catherine Quinlan
- KidGen Collaborative, Australian Genomics Health Alliance, Parkville, VIC, Australia.,Murdoch Children's Research Institute, The Royal Children's Hospital Melbourne, Parkville, Melbourne, VIC, Australia.,Department of Paediatric Nephrology, Royal Children's Hospital, Parkville, VIC, Australia.,Department of Paediatrics, University of Melbourne, VIC, Australia
| | - Chirag Patel
- KidGen Collaborative, Australian Genomics Health Alliance, Parkville, VIC, Australia.,Genetic Health Queensland, Royal Brisbane and Women's Hospital, Herston, QLD, Australia
| | - Lindsay Fowles
- KidGen Collaborative, Australian Genomics Health Alliance, Parkville, VIC, Australia.,Genetic Health Queensland, Royal Brisbane and Women's Hospital, Herston, QLD, Australia
| | - Joanna Crawford
- KidGen Collaborative, Australian Genomics Health Alliance, Parkville, VIC, Australia.,Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD, Australia
| | - Michael Gattas
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Herston, QLD, Australia
| | - Richard Baer
- Department of Nephrology, Mater Public Hospital, South Brisbane, QLD, Australia
| | - Bruce Bennetts
- KidGen Collaborative, Australian Genomics Health Alliance, Parkville, VIC, Australia.,Department of Molecular Genetics, Children's Hospital at Westmead, Westmead, NSW, Australia.,Discipline of Genetic Medicine and Discipline of Child & Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Gladys Ho
- KidGen Collaborative, Australian Genomics Health Alliance, Parkville, VIC, Australia.,Department of Molecular Genetics, Children's Hospital at Westmead, Westmead, NSW, Australia.,Discipline of Genetic Medicine and Discipline of Child & Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Katherine Holman
- KidGen Collaborative, Australian Genomics Health Alliance, Parkville, VIC, Australia.,Department of Molecular Genetics, Children's Hospital at Westmead, Westmead, NSW, Australia.,Discipline of Genetic Medicine and Discipline of Child & Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Cas Simons
- KidGen Collaborative, Australian Genomics Health Alliance, Parkville, VIC, Australia.,Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD, Australia.,Murdoch Children's Research Institute, The Royal Children's Hospital Melbourne, Parkville, Melbourne, VIC, Australia
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Jayasinghe K, Quinlan C, Stark Z, Patel C, Mallawaarachchi A, Wardrop L, Kerr PG, Trnka P, Mallett AJ. Renal genetics in Australia: Kidney medicine in the genomic age. Nephrology (Carlton) 2018; 24:279-286. [PMID: 30239064 PMCID: PMC6587832 DOI: 10.1111/nep.13494] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/10/2018] [Indexed: 12/17/2022]
Abstract
There have been few new therapies for patients with chronic kidney disease in the last decade. However, the management of patients affected by genetic kidney disease is rapidly evolving. Inherited or genetic kidney disease affects around 10% of adults with end‐stage kidney disease and up to 70% of children with early onset kidney disease. Advances in next‐generation sequencing have enabled rapid and cost‐effective sequencing of large amounts of DNA. Next‐generation sequencing‐based diagnostic tests now enable identification of a monogenic cause in around 20% of patients with early‐onset chronic kidney disease. A definitive diagnosis through genomic testing may negate the need for prolonged diagnostic investigations and surveillance, facilitate reproductive planning and provide accurate counselling for at‐risk relatives. Genomics has allowed the better understanding of disease pathogenesis, providing prognostic information and facilitating development of targeted treatments for patients with inherited or genetic kidney disease. Although genomic testing is becoming more readily available, there are many challenges to implementation in clinical practice. Multidisciplinary renal genetics clinics serve as a model of how some of these challenges may be overcome. Such clinics are already well established in most parts of Australia, with more to follow in future. With the rapid pace of new technology and gene discovery, collaboration between expert clinicians, laboratory and research scientists is of increasing importance to maximize benefits to patients and health‐care systems. The authors reckoned the importance of genomic testing as it allows better understanding of disease pathogenesis, provides prognostic information and facilitates development of targeted treatment, particularly for patients with inherited or genetic kidney disease.
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Affiliation(s)
- Kushani Jayasinghe
- Department of Nephrology, Monash Medical Centre, Melbourne, Victoria, Australia.,KidGen Renal Genetics Flagship, Australian Genomic Health Alliance, Melbourne, Victoria, Australia.,Monash University, Melbourne, Victoria, Australia
| | - Catherine Quinlan
- KidGen Renal Genetics Flagship, Australian Genomic Health Alliance, Melbourne, Victoria, Australia.,Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Department of Paediatric Nephrology, Royal Children's Hospital, Melbourne, Victoria, Australia
| | - Zornitza Stark
- KidGen Renal Genetics Flagship, Australian Genomic Health Alliance, Melbourne, Victoria, Australia.,Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
| | - Chirag Patel
- KidGen Renal Genetics Flagship, Australian Genomic Health Alliance, Melbourne, Victoria, Australia.,Genetic Health Queensland, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia
| | - Amali Mallawaarachchi
- Department of Medical Genomics, Royal Prince Alfred Hospital, Sydney, New South Wales, Australia
| | - Louise Wardrop
- KidGen Renal Genetics Flagship, Australian Genomic Health Alliance, Melbourne, Victoria, Australia.,Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Peter G Kerr
- Department of Nephrology, Monash Medical Centre, Melbourne, Victoria, Australia.,Monash University, Melbourne, Victoria, Australia
| | - Peter Trnka
- KidGen Renal Genetics Flagship, Australian Genomic Health Alliance, Melbourne, Victoria, Australia.,Queensland Child and Adolescent Renal Service, Queensland Children's Hospital, South Brisbane, Queensland, Australia.,Institute for Molecular Bioscience and Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia.,Kidney Health Service and Conjoint Renal Research Laboratory, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia
| | - Andrew J Mallett
- KidGen Renal Genetics Flagship, Australian Genomic Health Alliance, Melbourne, Victoria, Australia.,Institute for Molecular Bioscience and Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia.,Kidney Health Service and Conjoint Renal Research Laboratory, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia
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Jin YY, Feng BY, Mao JH. The status quo and challenges of genetic diagnosis in children with steroid-resistant nephrotic syndrome. World J Pediatr 2018; 14:105-109. [PMID: 29644498 DOI: 10.1007/s12519-018-0156-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 03/28/2018] [Indexed: 01/12/2023]
Affiliation(s)
- Yan-Yan Jin
- Department of Nephrology, Children's Hospital, Zhejiang University School of Medicine, #57 Zhugan Lane, Hangzhou, 310003, China
| | - Bing-Yu Feng
- Department of Nephrology, Children's Hospital, Zhejiang University School of Medicine, #57 Zhugan Lane, Hangzhou, 310003, China.,Department of Paediatrics, The First People's Hospital of Huzhou, Huzhou, 313000, China
| | - Jian-Hua Mao
- Department of Nephrology, Children's Hospital, Zhejiang University School of Medicine, #57 Zhugan Lane, Hangzhou, 310003, China.
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Mallett AJ, McCarthy HJ, Ho G, Holman K, Farnsworth E, Patel C, Fletcher JT, Mallawaarachchi A, Quinlan C, Bennetts B, Alexander SI. Massively parallel sequencing and targeted exomes in familial kidney disease can diagnose underlying genetic disorders. Kidney Int 2017; 92:1493-1506. [PMID: 28844315 DOI: 10.1016/j.kint.2017.06.013] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 06/06/2017] [Accepted: 06/08/2017] [Indexed: 10/19/2022]
Abstract
Inherited kidney disease encompasses a broad range of disorders, with both multiple genes contributing to specific phenotypes and single gene defects having multiple clinical presentations. Advances in sequencing capacity may allow a genetic diagnosis for familial renal disease, by testing the increasing number of known causative genes. However, there has been limited translation of research findings of causative genes into clinical settings. Here, we report the results of a national accredited diagnostic genetic service for familial renal disease. An expert multidisciplinary team developed a targeted exomic sequencing approach with ten curated multigene panels (207 genes) and variant assessment individualized to the patient's phenotype. A genetic diagnosis (pathogenic genetic variant[s]) was identified in 58 of 135 families referred in two years. The genetic diagnosis rate was similar between families with a pediatric versus adult proband (46% vs 40%), although significant differences were found in certain panels such as atypical hemolytic uremic syndrome (88% vs 17%). High diagnostic rates were found for Alport syndrome (22 of 27) and tubular disorders (8 of 10), whereas the monogenic diagnostic rate for congenital anomalies of the kidney and urinary tract was one of 13. Quality reporting was aided by a strong clinical renal and genetic multidisciplinary committee review. Importantly, for a diagnostic service, few variants of uncertain significance were found with this targeted, phenotype-based approach. Thus, use of targeted massively parallel sequencing approaches in inherited kidney disease has a significant capacity to diagnose the underlying genetic disorder across most renal phenotypes.
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Affiliation(s)
- Andrew J Mallett
- Kidney Health Service and Conjoint Renal Research Laboratory, Royal Brisbane and Women's Hospital, Brisbane, Australia; Faculty of Medicine, University of Queensland, Brisbane, Australia; KidGen Renal Genetics Flagship, Australian Genomics Health Alliance, Australia.
| | - Hugh J McCarthy
- KidGen Renal Genetics Flagship, Australian Genomics Health Alliance, Australia; Department of Pediatric Nephrology, The Children's Hospital at Westmead, Sydney, Australia; Discipline of Pediatrics and Child Health, University of Sydney, Sydney, Australia
| | - Gladys Ho
- KidGen Renal Genetics Flagship, Australian Genomics Health Alliance, Australia; Department of Molecular Genetics, The Children's Hospital at Westmead, Sydney, Australia
| | - Katherine Holman
- KidGen Renal Genetics Flagship, Australian Genomics Health Alliance, Australia; Department of Molecular Genetics, The Children's Hospital at Westmead, Sydney, Australia
| | - Elizabeth Farnsworth
- KidGen Renal Genetics Flagship, Australian Genomics Health Alliance, Australia; Department of Molecular Genetics, The Children's Hospital at Westmead, Sydney, Australia
| | - Chirag Patel
- KidGen Renal Genetics Flagship, Australian Genomics Health Alliance, Australia; Genetic Health Queensland, Royal Brisbane and Women's Hospital, Brisbane, Australia
| | - Jeffery T Fletcher
- KidGen Renal Genetics Flagship, Australian Genomics Health Alliance, Australia; Department of Pediatrics, The Canberra Hospital, Canberra, Australia
| | - Amali Mallawaarachchi
- KidGen Renal Genetics Flagship, Australian Genomics Health Alliance, Australia; Department of Clinical Genetics, Liverpool Hospital, Sydney, Australia; Discipline of Genetic Medicine, University of Sydney, Sydney, Australia
| | - Catherine Quinlan
- KidGen Renal Genetics Flagship, Australian Genomics Health Alliance, Australia; Murdoch Children's Research Institute, Melbourne, Australia; Department of Pediatric Nephrology, Royal Children's Hospital, Melbourne, Australia
| | - Bruce Bennetts
- KidGen Renal Genetics Flagship, Australian Genomics Health Alliance, Australia; Department of Molecular Genetics, The Children's Hospital at Westmead, Sydney, Australia; Discipline of Genetic Medicine, University of Sydney, Sydney, Australia
| | - Stephen I Alexander
- KidGen Renal Genetics Flagship, Australian Genomics Health Alliance, Australia; Department of Pediatric Nephrology, The Children's Hospital at Westmead, Sydney, Australia; Discipline of Pediatrics and Child Health, University of Sydney, Sydney, Australia; Centre for Kidney Research, University of Sydney, Sydney, Australia.
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Onyido EK, Sweeney E, Nateri AS. Wnt-signalling pathways and microRNAs network in carcinogenesis: experimental and bioinformatics approaches. Mol Cancer 2016; 15:56. [PMID: 27590724 PMCID: PMC5010773 DOI: 10.1186/s12943-016-0541-3] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 08/26/2016] [Indexed: 02/02/2023] Open
Abstract
Over the past few years, microRNAs (miRNAs) have not only emerged as integral regulators of gene expression at the post-transcriptional level but also respond to signalling molecules to affect cell function(s). miRNAs crosstalk with a variety of the key cellular signalling networks such as Wnt, transforming growth factor-β and Notch, control stem cell activity in maintaining tissue homeostasis, while if dysregulated contributes to the initiation and progression of cancer. Herein, we overview the molecular mechanism(s) underlying the crosstalk between Wnt-signalling components (canonical and non-canonical) and miRNAs, as well as changes in the miRNA/Wnt-signalling components observed in the different forms of cancer. Furthermore, the fundamental understanding of miRNA-mediated regulation of Wnt-signalling pathway and vice versa has been significantly improved by high-throughput genomics and bioinformatics technologies. Whilst, these approaches have identified a number of specific miRNA(s) that function as oncogenes or tumour suppressors, additional analyses will be necessary to fully unravel the links among conserved cellular signalling pathways and miRNAs and their potential associated components in cancer, thereby creating therapeutic avenues against tumours. Hence, we also discuss the current challenges associated with Wnt-signalling/miRNAs complex and the analysis using the biomedical experimental and bioinformatics approaches.
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Affiliation(s)
- Emenike K Onyido
- Cancer Genetics & Stem Cell Group, Cancer Biology Unit, Division of Cancer & Stem Cells, School of Medicine, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Eloise Sweeney
- Cancer Genetics & Stem Cell Group, Cancer Biology Unit, Division of Cancer & Stem Cells, School of Medicine, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Abdolrahman Shams Nateri
- Cancer Genetics & Stem Cell Group, Cancer Biology Unit, Division of Cancer & Stem Cells, School of Medicine, University of Nottingham, Nottingham, NG7 2UH, UK.
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Mallett A, Fowles LF, McGaughran J, Healy H, Patel C. A multidisciplinary renal genetics clinic improves patient diagnosis. Med J Aust 2016; 204:58-9. [DOI: 10.5694/mja15.01157] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 11/25/2015] [Indexed: 11/17/2022]
Affiliation(s)
| | | | | | - Helen Healy
- Royal Brisbane and Women's Hospital, Brisbane, QLD
| | - Chirag Patel
- Royal Brisbane and Women's Hospital, Brisbane, QLD
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