1
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Allouba M, Walsh R, Afify A, Hosny M, Halawa S, Galal A, Fathy M, Theotokis PI, Boraey A, Ellithy A, Buchan R, Govind R, Whiffin N, Anwer S, ElGuindy A, Ware JS, Barton PJR, Yacoub M, Aguib Y. Ethnicity, consanguinity, and genetic architecture of hypertrophic cardiomyopathy. Eur Heart J 2023; 44:5146-5158. [PMID: 37431535 PMCID: PMC10733735 DOI: 10.1093/eurheartj/ehad372] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [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: 10/25/2022] [Revised: 03/28/2023] [Accepted: 05/24/2023] [Indexed: 07/12/2023] Open
Abstract
AIMS Hypertrophic cardiomyopathy (HCM) is characterized by phenotypic heterogeneity that is partly explained by the diversity of genetic variants contributing to disease. Accurate interpretation of these variants constitutes a major challenge for diagnosis and implementing precision medicine, especially in understudied populations. The aim is to define the genetic architecture of HCM in North African cohorts with high consanguinity using ancestry-matched cases and controls. METHODS AND RESULTS Prospective Egyptian patients (n = 514) and controls (n = 400) underwent clinical phenotyping and genetic testing. Rare variants in 13 validated HCM genes were classified according to standard clinical guidelines and compared with a prospective HCM cohort of majority European ancestry (n = 684). A higher prevalence of homozygous variants was observed in Egyptian patients (4.1% vs. 0.1%, P = 2 × 10-7), with variants in the minor HCM genes MYL2, MYL3, and CSRP3 more likely to present in homozygosity than the major genes, suggesting these variants are less penetrant in heterozygosity. Biallelic variants in the recessive HCM gene TRIM63 were detected in 2.1% of patients (five-fold greater than European patients), highlighting the importance of recessive inheritance in consanguineous populations. Finally, rare variants in Egyptian HCM patients were less likely to be classified as (likely) pathogenic compared with Europeans (40.8% vs. 61.6%, P = 1.6 × 10-5) due to the underrepresentation of Middle Eastern populations in current reference resources. This proportion increased to 53.3% after incorporating methods that leverage new ancestry-matched controls presented here. CONCLUSION Studying consanguineous populations reveals novel insights with relevance to genetic testing and our understanding of the genetic architecture of HCM.
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Affiliation(s)
- Mona Allouba
- Aswan Heart Centre, Magdi Yacoub Heart Foundation, Kasr El Haggar Street, Aswan 81512, Egypt
- National Heart and Lung Institute, Imperial College London, London, Guy Scadding Building, Dovehouse St, London SW3 6LY, UK
| | - Roddy Walsh
- National Heart and Lung Institute, Imperial College London, London, Guy Scadding Building, Dovehouse St, London SW3 6LY, UK
- Department of Experimental Cardiology, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, Amsterdam 1105 AZ, The Netherlands
| | - Alaa Afify
- Aswan Heart Centre, Magdi Yacoub Heart Foundation, Kasr El Haggar Street, Aswan 81512, Egypt
| | - Mohammed Hosny
- Aswan Heart Centre, Magdi Yacoub Heart Foundation, Kasr El Haggar Street, Aswan 81512, Egypt
- Cardiology Department, Kasr Al Aini Medical School, Cairo University, Kasr Al Aini Street, Cairo 11562, Egypt
| | - Sarah Halawa
- Aswan Heart Centre, Magdi Yacoub Heart Foundation, Kasr El Haggar Street, Aswan 81512, Egypt
| | - Aya Galal
- Aswan Heart Centre, Magdi Yacoub Heart Foundation, Kasr El Haggar Street, Aswan 81512, Egypt
| | - Mariam Fathy
- Aswan Heart Centre, Magdi Yacoub Heart Foundation, Kasr El Haggar Street, Aswan 81512, Egypt
| | - Pantazis I Theotokis
- National Heart and Lung Institute, Imperial College London, London, Guy Scadding Building, Dovehouse St, London SW3 6LY, UK
| | - Ahmed Boraey
- Aswan Heart Centre, Magdi Yacoub Heart Foundation, Kasr El Haggar Street, Aswan 81512, Egypt
- Cardiology Department, Kasr Al Aini Medical School, Cairo University, Kasr Al Aini Street, Cairo 11562, Egypt
| | - Amany Ellithy
- Aswan Heart Centre, Magdi Yacoub Heart Foundation, Kasr El Haggar Street, Aswan 81512, Egypt
| | - Rachel Buchan
- National Heart and Lung Institute, Imperial College London, London, Guy Scadding Building, Dovehouse St, London SW3 6LY, UK
- Royal Brompton & Harefield Hospitals, Guy’s and St. Thomas’ NHS Foundation Trust, London, Sydney St, London SW3 6NP, UK
| | - Risha Govind
- National Heart and Lung Institute, Imperial College London, London, Guy Scadding Building, Dovehouse St, London SW3 6LY, UK
- Royal Brompton & Harefield Hospitals, Guy’s and St. Thomas’ NHS Foundation Trust, London, Sydney St, London SW3 6NP, UK
- Present affiliation: Institute of Psychiatry, Psychology and Neuroscience, King's College London, 16 De Crespigny Park, London SE5 8AF, UK
- Present affiliation: National Institute for Health Research (NIHR) Biomedical Research Centre, South London and Maudsley NHS Foundation Trust and King's College London, 16 De Crespigny Park, London SE5 8AF, UK
| | - Nicola Whiffin
- National Heart and Lung Institute, Imperial College London, London, Guy Scadding Building, Dovehouse St, London SW3 6LY, UK
- Royal Brompton & Harefield Hospitals, Guy’s and St. Thomas’ NHS Foundation Trust, London, Sydney St, London SW3 6NP, UK
- Present affiliation: Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Dr, Headington, Oxford OX3 7BN, UK
| | - Shehab Anwer
- Aswan Heart Centre, Magdi Yacoub Heart Foundation, Kasr El Haggar Street, Aswan 81512, Egypt
| | - Ahmed ElGuindy
- Aswan Heart Centre, Magdi Yacoub Heart Foundation, Kasr El Haggar Street, Aswan 81512, Egypt
| | - James S Ware
- National Heart and Lung Institute, Imperial College London, London, Guy Scadding Building, Dovehouse St, London SW3 6LY, UK
- Royal Brompton & Harefield Hospitals, Guy’s and St. Thomas’ NHS Foundation Trust, London, Sydney St, London SW3 6NP, UK
- MRC London Institute of Medical Sciences, Imperial College London, Du Cane Rd, London W12 0NN, UK
| | - Paul J R Barton
- National Heart and Lung Institute, Imperial College London, London, Guy Scadding Building, Dovehouse St, London SW3 6LY, UK
- Royal Brompton & Harefield Hospitals, Guy’s and St. Thomas’ NHS Foundation Trust, London, Sydney St, London SW3 6NP, UK
- MRC London Institute of Medical Sciences, Imperial College London, Du Cane Rd, London W12 0NN, UK
| | - Magdi Yacoub
- Aswan Heart Centre, Magdi Yacoub Heart Foundation, Kasr El Haggar Street, Aswan 81512, Egypt
- National Heart and Lung Institute, Imperial College London, London, Guy Scadding Building, Dovehouse St, London SW3 6LY, UK
- Harefield Heart Science Centre, Hill End Rd, Harefield, Uxbridge UB9 6JH, UK
| | - Yasmine Aguib
- Aswan Heart Centre, Magdi Yacoub Heart Foundation, Kasr El Haggar Street, Aswan 81512, Egypt
- National Heart and Lung Institute, Imperial College London, London, Guy Scadding Building, Dovehouse St, London SW3 6LY, UK
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2
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McGurk KA, Zhang X, Theotokis P, Thomson K, Harper A, Buchan RJ, Mazaika E, Ormondroyd E, Wright WT, Macaya D, Pua CJ, Funke B, MacArthur DG, Prasad SK, Cook SA, Allouba M, Aguib Y, Yacoub MH, O'Regan DP, Barton PJR, Watkins H, Bottolo L, Ware JS. The penetrance of rare variants in cardiomyopathy-associated genes: A cross-sectional approach to estimating penetrance for secondary findings. Am J Hum Genet 2023; 110:1482-1495. [PMID: 37652022 PMCID: PMC10502871 DOI: 10.1016/j.ajhg.2023.08.003] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 07/21/2023] [Accepted: 08/04/2023] [Indexed: 09/02/2023] Open
Abstract
Understanding the penetrance of pathogenic variants identified as secondary findings (SFs) is of paramount importance with the growing availability of genetic testing. We estimated penetrance through large-scale analyses of individuals referred for diagnostic sequencing for hypertrophic cardiomyopathy (HCM; 10,400 affected individuals, 1,332 variants) and dilated cardiomyopathy (DCM; 2,564 affected individuals, 663 variants), using a cross-sectional approach comparing allele frequencies against reference populations (293,226 participants from UK Biobank and gnomAD). We generated updated prevalence estimates for HCM (1:543) and DCM (1:220). In aggregate, the penetrance by late adulthood of rare, pathogenic variants (23% for HCM, 35% for DCM) and likely pathogenic variants (7% for HCM, 10% for DCM) was substantial for dominant cardiomyopathy (CM). Penetrance was significantly higher for variant subgroups annotated as loss of function or ultra-rare and for males compared to females for variants in HCM-associated genes. We estimated variant-specific penetrance for 316 recurrent variants most likely to be identified as SFs (found in 51% of HCM- and 17% of DCM-affected individuals). 49 variants were observed at least ten times (14% of affected individuals) in HCM-associated genes. Median penetrance was 14.6% (±14.4% SD). We explore estimates of penetrance by age, sex, and ancestry and simulate the impact of including future cohorts. This dataset reports penetrance of individual variants at scale and will inform the management of individuals undergoing genetic screening for SFs. While most variants had low penetrance and the costs and harms of screening are unclear, some individuals with highly penetrant variants may benefit from SFs.
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Affiliation(s)
- Kathryn A McGurk
- National Heart and Lung Institute, Imperial College London, London, UK; MRC London Institute of Medical Sciences, Imperial College London, London, UK
| | - Xiaolei Zhang
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Pantazis Theotokis
- National Heart and Lung Institute, Imperial College London, London, UK; MRC London Institute of Medical Sciences, Imperial College London, London, UK
| | - Kate Thomson
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine and the Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Andrew Harper
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine and the Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Rachel J Buchan
- National Heart and Lung Institute, Imperial College London, London, UK; MRC London Institute of Medical Sciences, Imperial College London, London, UK; Royal Brompton & Harefield Hospitals, Guy's and St. Thomas' NHS Foundation Trust, London, UK
| | - Erica Mazaika
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Elizabeth Ormondroyd
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine and the Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - William T Wright
- Northern Ireland Regional Genetics Centre, Belfast Health and Social Care Trust, Belfast City Hospital, Belfast, Northern Ireland, UK
| | | | - Chee Jian Pua
- National Heart Research Institute Singapore and Duke-National University of Singapore, Singapore, Singapore
| | - Birgit Funke
- Laboratory for Molecular Medicine, Partners Healthcare Center for Personalized Genetic Medicine, Boston, MA, USA
| | - Daniel G MacArthur
- Centre for Population Genomics, Garvan Institute of Medical Research and UNSW, Sydney, NSW, Australia; Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Sanjay K Prasad
- National Heart and Lung Institute, Imperial College London, London, UK; Royal Brompton & Harefield Hospitals, Guy's and St. Thomas' NHS Foundation Trust, London, UK
| | - Stuart A Cook
- MRC London Institute of Medical Sciences, Imperial College London, London, UK; National Heart Research Institute Singapore and Duke-National University of Singapore, Singapore, Singapore
| | - Mona Allouba
- National Heart and Lung Institute, Imperial College London, London, UK; Aswan Heart Centre, Aswan, Egypt
| | - Yasmine Aguib
- National Heart and Lung Institute, Imperial College London, London, UK; Aswan Heart Centre, Aswan, Egypt
| | - Magdi H Yacoub
- National Heart and Lung Institute, Imperial College London, London, UK; Royal Brompton & Harefield Hospitals, Guy's and St. Thomas' NHS Foundation Trust, London, UK; Aswan Heart Centre, Aswan, Egypt
| | - Declan P O'Regan
- MRC London Institute of Medical Sciences, Imperial College London, London, UK
| | - Paul J R Barton
- National Heart and Lung Institute, Imperial College London, London, UK; MRC London Institute of Medical Sciences, Imperial College London, London, UK; Royal Brompton & Harefield Hospitals, Guy's and St. Thomas' NHS Foundation Trust, London, UK
| | - Hugh Watkins
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine and the Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Leonardo Bottolo
- Department of Medical Genetics, University of Cambridge, Cambridge, UK; The Alan Turing Institute, London, UK; MRC Biostatistics Unit, University of Cambridge, Cambridge, UK
| | - James S Ware
- National Heart and Lung Institute, Imperial College London, London, UK; MRC London Institute of Medical Sciences, Imperial College London, London, UK; Royal Brompton & Harefield Hospitals, Guy's and St. Thomas' NHS Foundation Trust, London, UK.
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3
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Sweeney M, O’Fee K, Villanueva-Hayes C, Rahman E, Lee M, Vanezis K, Andrew I, Lim WW, Widjaja A, Barton PJR, Cook SA. Cardiomyocyte-Restricted Expression of IL11 Causes Cardiac Fibrosis, Inflammation, and Dysfunction. Int J Mol Sci 2023; 24:12989. [PMID: 37629170 PMCID: PMC10455677 DOI: 10.3390/ijms241612989] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 07/17/2023] [Revised: 08/10/2023] [Accepted: 08/16/2023] [Indexed: 08/27/2023] Open
Abstract
Cardiac fibrosis is a common pathological process in heart disease, representing a therapeutic target. Transforming growth factor β (TGFβ) is the canonical driver of cardiac fibrosis and was recently shown to be dependent on interleukin 11 (IL11) for its profibrotic effects in fibroblasts. In the opposite direction, recombinant human IL11 has been reported as anti-fibrotic and anti-inflammatory in the mouse heart. In this study, we determined the effects of IL11 expression in cardiomyocytes on cardiac pathobiology and function. We used the Cre-loxP system to generate a tamoxifen-inducible mouse with cardiomyocyte-restricted murine Il11 expression. Using protein assays, bulk RNA-sequencing, and in vivo imaging, we analyzed the effects of IL11 on myocardial fibrosis, inflammation, and cardiac function, challenging previous reports suggesting the cardioprotective potential of IL11. TGFβ stimulation of cardiomyocytes caused Il11 upregulation. Compared to wild-type controls, Il11-expressing hearts demonstrated severe cardiac fibrosis and inflammation that was associated with the upregulation of cytokines, chemokines, complement factors, and increased inflammatory cells. IL11 expression also activated a program of endothelial-to-mesenchymal transition and resulted in left ventricular dysfunction. Our data define species-matched IL11 as strongly profibrotic and proinflammatory when secreted from cardiomyocytes and further establish IL11 as a disease factor.
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Affiliation(s)
- Mark Sweeney
- 1MRC-London Institute of Medical Sciences, Hammersmith Hospital Campus, London W12 0NN, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College, London W12 0NN, UK
- Wellcome Trust/NIHR 4i Clinical Research Fellow, Imperial College, London W12 0NN, UK
| | - Katie O’Fee
- 1MRC-London Institute of Medical Sciences, Hammersmith Hospital Campus, London W12 0NN, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College, London W12 0NN, UK
| | - Chelsie Villanueva-Hayes
- 1MRC-London Institute of Medical Sciences, Hammersmith Hospital Campus, London W12 0NN, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College, London W12 0NN, UK
| | - Ekhlas Rahman
- 1MRC-London Institute of Medical Sciences, Hammersmith Hospital Campus, London W12 0NN, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College, London W12 0NN, UK
| | - Michael Lee
- National Heart and Lung Institute, Imperial College, London W12 0NN, UK
| | - Konstantinos Vanezis
- 1MRC-London Institute of Medical Sciences, Hammersmith Hospital Campus, London W12 0NN, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College, London W12 0NN, UK
- National Heart and Lung Institute, Imperial College, London W12 0NN, UK
| | - Ivan Andrew
- 1MRC-London Institute of Medical Sciences, Hammersmith Hospital Campus, London W12 0NN, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College, London W12 0NN, UK
| | - Wei-Wen Lim
- National Heart Research Institute Singapore, National Heart Centre Singapore, Singapore 169609, Singapore
- Cardiovascular and Metabolic Disorders Program, Duke-National University of Singapore Medical School, Singapore 169857, Singapore
| | - Anissa Widjaja
- Cardiovascular and Metabolic Disorders Program, Duke-National University of Singapore Medical School, Singapore 169857, Singapore
| | - Paul J. R. Barton
- 1MRC-London Institute of Medical Sciences, Hammersmith Hospital Campus, London W12 0NN, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College, London W12 0NN, UK
- National Heart and Lung Institute, Imperial College, London W12 0NN, UK
- Royal Brompton and Harefield Hospitals, Guy’s and St. Thomas’ NHS Foundation Trust, London SW3 6NP, UK
| | - Stuart A. Cook
- 1MRC-London Institute of Medical Sciences, Hammersmith Hospital Campus, London W12 0NN, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College, London W12 0NN, UK
- National Heart Research Institute Singapore, National Heart Centre Singapore, Singapore 169609, Singapore
- Cardiovascular and Metabolic Disorders Program, Duke-National University of Singapore Medical School, Singapore 169857, Singapore
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4
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Quaife NM, Chothani S, Schulz JF, Lindberg EL, Vanezis K, Adami E, O'Fee K, Greiner J, Litviňuková M, van Heesch S, Whiffin N, Hubner N, Schafer S, Rackham O, Cook SA, Barton PJR. LINC01013 Is a Determinant of Fibroblast Activation and Encodes a Novel Fibroblast-Activating Micropeptide. J Cardiovasc Transl Res 2023; 16:77-85. [PMID: 35759180 PMCID: PMC9944705 DOI: 10.1007/s12265-022-10288-z] [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] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 06/09/2022] [Indexed: 10/17/2022]
Abstract
Myocardial fibrosis confers an almost threefold mortality risk in heart disease. There are no prognostic therapies and novel therapeutic targets are needed. Many thousands of unannotated small open reading frames (smORFs) have been identified across the genome with potential to produce micropeptides (< 100 amino acids). We sought to investigate the role of smORFs in myocardial fibroblast activation.Analysis of human cardiac atrial fibroblasts (HCFs) stimulated with profibrotic TGFβ1 using RNA sequencing (RNA-Seq) and ribosome profiling (Ribo-Seq) identified long intergenic non-coding RNA LINC01013 as TGFβ1 responsive and containing an actively translated smORF. Knockdown of LINC01013 using siRNA reduced expression of profibrotic markers at baseline and blunted their response to TGFβ1. In contrast, overexpression of a codon-optimised smORF invoked a profibrotic response comparable to that seen with TGFβ1 treatment, whilst FLAG-tagged peptide associated with the mitochondria.Together, these data support a novel LINC01013 smORF micropeptide-mediated mechanism of fibroblast activation. TGFβ1 stimulation of atrial fibroblasts induces expression of LINC01013, whose knockdown reduces fibroblast activation. Overexpression of a smORF contained within LINC01013 localises to mitochondria and activates fibroblasts.
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Affiliation(s)
- N M Quaife
- National Heart and Lung Institute, Imperial College London, London, UK
- MRC London Institute of Medical Sciences, London, UK
| | - S Chothani
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore, Singapore, 169857, Singapore
| | - J F Schulz
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- DZHK (German Center for Cardiovascular Research), partner site Berlin, Berlin, Germany
| | - E L Lindberg
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - K Vanezis
- National Heart and Lung Institute, Imperial College London, London, UK
- MRC London Institute of Medical Sciences, London, UK
| | - E Adami
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore, Singapore, 169857, Singapore
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - K O'Fee
- MRC London Institute of Medical Sciences, London, UK
| | - J Greiner
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - M Litviňuková
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - S van Heesch
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - N Whiffin
- National Heart and Lung Institute, Imperial College London, London, UK
- Cardiovascular Research Centre, Royal Brompton and Harefield Hospitals, Guy's and St Thomas NHS Foundation Trust, London, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - N Hubner
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- DZHK (German Center for Cardiovascular Research), partner site Berlin, Berlin, Germany
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - S Schafer
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore, Singapore, 169857, Singapore
| | - O Rackham
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore, Singapore, 169857, Singapore
| | - S A Cook
- MRC London Institute of Medical Sciences, London, UK
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore, Singapore, 169857, Singapore
- National Heart Centre Singapore, Singapore, Singapore
| | - P J R Barton
- National Heart and Lung Institute, Imperial College London, London, UK.
- MRC London Institute of Medical Sciences, London, UK.
- Cardiovascular Research Centre, Royal Brompton and Harefield Hospitals, Guy's and St Thomas NHS Foundation Trust, London, UK.
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5
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Reichart D, Lindberg EL, Maatz H, Miranda AMA, Viveiros A, Shvetsov N, Gärtner A, Nadelmann ER, Lee M, Kanemaru K, Ruiz-Orera J, Strohmenger V, DeLaughter DM, Patone G, Zhang H, Woehler A, Lippert C, Kim Y, Adami E, Gorham JM, Barnett SN, Brown K, Buchan RJ, Chowdhury RA, Constantinou C, Cranley J, Felkin LE, Fox H, Ghauri A, Gummert J, Kanda M, Li R, Mach L, McDonough B, Samari S, Shahriaran F, Yapp C, Stanasiuk C, Theotokis PI, Theis FJ, van den Bogaerdt A, Wakimoto H, Ware JS, Worth CL, Barton PJR, Lee YA, Teichmann SA, Milting H, Noseda M, Oudit GY, Heinig M, Seidman JG, Hubner N, Seidman CE. Pathogenic variants damage cell composition and single cell transcription in cardiomyopathies. Science 2022; 377:eabo1984. [PMID: 35926050 PMCID: PMC9528698 DOI: 10.1126/science.abo1984] [Citation(s) in RCA: 57] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Pathogenic variants in genes that cause dilated cardiomyopathy (DCM) and arrhythmogenic cardiomyopathy (ACM) convey high risks for the development of heart failure through unknown mechanisms. Using single-nucleus RNA sequencing, we characterized the transcriptome of 880,000 nuclei from 18 control and 61 failing, nonischemic human hearts with pathogenic variants in DCM and ACM genes or idiopathic disease. We performed genotype-stratified analyses of the ventricular cell lineages and transcriptional states. The resultant DCM and ACM ventricular cell atlas demonstrated distinct right and left ventricular responses, highlighting genotype-associated pathways, intercellular interactions, and differential gene expression at single-cell resolution. Together, these data illuminate both shared and distinct cellular and molecular architectures of human heart failure and suggest candidate therapeutic targets.
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Affiliation(s)
- Daniel Reichart
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Cardiovascular Division, Brigham and Women's Hospital, Boston, MA 02115, USA.,Department of Medicine I, University Hospital, LMU Munich, 80336 Munich, Germany
| | - Eric L Lindberg
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Henrike Maatz
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany.,DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, 10785 Berlin, Germany
| | - Antonio M A Miranda
- National Heart and Lung Institute, Imperial College London, London SW3 6LY, UK.,British Heart Foundation Centre for Research Excellence and Centre for Regenerative Medicine, Imperial College London, London WC2R 2LS, UK
| | - Anissa Viveiros
- Division of Cardiology, Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2R3, Canada.,Mazankowski Alberta Heart Institute, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2R3, Canada
| | - Nikolay Shvetsov
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Anna Gärtner
- Erich and Hanna Klessmann Institute, Heart and Diabetes Center NRW, University Hospital of the Ruhr-University Bochum, 32545 Bad Oeynhausen, Germany
| | - Emily R Nadelmann
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Michael Lee
- National Heart and Lung Institute, Imperial College London, London SW3 6LY, UK
| | - Kazumasa Kanemaru
- Cellular Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
| | - Jorge Ruiz-Orera
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Viktoria Strohmenger
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Walter-Brendel-Centre of Experimental Medicine, Ludwig-Maximilian University of Munich, 81377 Munich, Germany
| | - Daniel M DeLaughter
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Bethesda, MD 20815, USA
| | - Giannino Patone
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Hao Zhang
- Division of Cardiology, Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2R3, Canada.,Mazankowski Alberta Heart Institute, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2R3, Canada
| | - Andrew Woehler
- Systems Biology Imaging Platform, Berlin Institute for Medical Systems Biology (BIMSB), Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), 10115 Berlin, Germany
| | - Christoph Lippert
- Digital Health-Machine Learning group, Hasso Plattner Institute for Digital Engineering, University of Potsdam, 14482 Potsdam, Germany.,Hasso Plattner Institute for Digital Health, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Yuri Kim
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Cardiovascular Division, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Eleonora Adami
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Joshua M Gorham
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Sam N Barnett
- National Heart and Lung Institute, Imperial College London, London SW3 6LY, UK
| | - Kemar Brown
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Cardiac Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Rachel J Buchan
- National Heart and Lung Institute, Imperial College London, London SW3 6LY, UK.,Royal Brompton and Harefield Hospitals, Guy's and St. Thomas' NHS Foundation Trust, London SW3 6NR, UK
| | - Rasheda A Chowdhury
- National Heart and Lung Institute, Imperial College London, London SW3 6LY, UK
| | | | - James Cranley
- Cellular Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
| | - Leanne E Felkin
- National Heart and Lung Institute, Imperial College London, London SW3 6LY, UK.,Royal Brompton and Harefield Hospitals, Guy's and St. Thomas' NHS Foundation Trust, London SW3 6NR, UK
| | - Henrik Fox
- Heart and Diabetes Center NRW, Clinic for Thoracic and Cardiovascular Surgery, University Hospital of the Ruhr-University, 32545 Bad Oeynhausen, Germany
| | - Ahla Ghauri
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Jan Gummert
- Heart and Diabetes Center NRW, Clinic for Thoracic and Cardiovascular Surgery, University Hospital of the Ruhr-University, 32545 Bad Oeynhausen, Germany
| | - Masatoshi Kanda
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany.,Department of Rheumatology and Clinical Immunology, Sapporo Medical University School of Medicine, Sapporo 060-8556, Japan
| | - Ruoyan Li
- Cellular Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
| | - Lukas Mach
- National Heart and Lung Institute, Imperial College London, London SW3 6LY, UK.,Royal Brompton and Harefield Hospitals, Guy's and St. Thomas' NHS Foundation Trust, London SW3 6NR, UK
| | - Barbara McDonough
- Cardiovascular Division, Brigham and Women's Hospital, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Bethesda, MD 20815, USA
| | - Sara Samari
- National Heart and Lung Institute, Imperial College London, London SW3 6LY, UK
| | - Farnoush Shahriaran
- Computational Health Center, Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), 85764 Neuherberg, Germany
| | - Clarence Yapp
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Caroline Stanasiuk
- Erich and Hanna Klessmann Institute, Heart and Diabetes Center NRW, University Hospital of the Ruhr-University Bochum, 32545 Bad Oeynhausen, Germany
| | - Pantazis I Theotokis
- National Heart and Lung Institute, Imperial College London, London SW3 6LY, UK.,MRC London Institute of Medical Sciences, Imperial College London, London W12 0NN, UK
| | - Fabian J Theis
- Computational Health Center, Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), 85764 Neuherberg, Germany
| | | | - Hiroko Wakimoto
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - James S Ware
- National Heart and Lung Institute, Imperial College London, London SW3 6LY, UK.,Royal Brompton and Harefield Hospitals, Guy's and St. Thomas' NHS Foundation Trust, London SW3 6NR, UK.,MRC London Institute of Medical Sciences, Imperial College London, London W12 0NN, UK
| | - Catherine L Worth
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Paul J R Barton
- National Heart and Lung Institute, Imperial College London, London SW3 6LY, UK.,Royal Brompton and Harefield Hospitals, Guy's and St. Thomas' NHS Foundation Trust, London SW3 6NR, UK.,MRC London Institute of Medical Sciences, Imperial College London, London W12 0NN, UK
| | - Young-Ae Lee
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany.,Clinic for Pediatric Allergy, Experimental and Clinical Research Center, Charité-Universitätsmedizin Berlin, 13125 Berlin, Germany
| | - Sarah A Teichmann
- Cellular Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK.,Department of Physics, Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, UK
| | - Hendrik Milting
- Erich and Hanna Klessmann Institute, Heart and Diabetes Center NRW, University Hospital of the Ruhr-University Bochum, 32545 Bad Oeynhausen, Germany
| | - Michela Noseda
- National Heart and Lung Institute, Imperial College London, London SW3 6LY, UK.,British Heart Foundation Centre for Research Excellence and Centre for Regenerative Medicine, Imperial College London, London WC2R 2LS, UK
| | - Gavin Y Oudit
- Division of Cardiology, Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2R3, Canada.,Mazankowski Alberta Heart Institute, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2R3, Canada
| | - Matthias Heinig
- Computational Health Center, Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), 85764 Neuherberg, Germany.,Department of Informatics, Technische Universitaet Muenchen (TUM), 85748 Munich, Germany.,DZHK (German Centre for Cardiovascular Research), Munich Heart Association, Partner Site Munich, 10785 Berlin, Germany
| | | | - Norbert Hubner
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany.,DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, 10785 Berlin, Germany.,Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Christine E Seidman
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Cardiovascular Division, Brigham and Women's Hospital, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Bethesda, MD 20815, USA
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6
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Tayal U, Verdonschot JAJ, Hazebroek MR, Howard J, Gregson J, Newsome S, Gulati A, Pua CJ, Halliday BP, Lota AS, Buchan RJ, Whiffin N, Kanapeckaite L, Baruah R, Jarman JWE, O'Regan DP, Barton PJR, Ware JS, Pennell DJ, Adriaans BP, Bekkers SCAM, Donovan J, Frenneaux M, Cooper LT, Januzzi JL, Cleland JGF, Cook SA, Deo RC, Heymans SRB, Prasad SK. Precision Phenotyping of Dilated Cardiomyopathy Using Multidimensional Data. J Am Coll Cardiol 2022; 79:2219-2232. [PMID: 35654493 PMCID: PMC9168440 DOI: 10.1016/j.jacc.2022.03.375] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 03/18/2022] [Accepted: 03/21/2022] [Indexed: 01/08/2023]
Abstract
BACKGROUND Dilated cardiomyopathy (DCM) is a final common manifestation of heterogenous etiologies. Adverse outcomes highlight the need for disease stratification beyond ejection fraction. OBJECTIVES The purpose of this study was to identify novel, reproducible subphenotypes of DCM using multiparametric data for improved patient stratification. METHODS Longitudinal, observational UK-derivation (n = 426; median age 54 years; 67% men) and Dutch-validation (n = 239; median age 56 years; 64% men) cohorts of DCM patients (enrolled 2009-2016) with clinical, genetic, cardiovascular magnetic resonance, and proteomic assessments. Machine learning with profile regression identified novel disease subtypes. Penalized multinomial logistic regression was used for validation. Nested Cox models compared novel groupings to conventional risk measures. Primary composite outcome was cardiovascular death, heart failure, or arrhythmia events (median follow-up 4 years). RESULTS In total, 3 novel DCM subtypes were identified: profibrotic metabolic, mild nonfibrotic, and biventricular impairment. Prognosis differed between subtypes in both the derivation (P < 0.0001) and validation cohorts. The novel profibrotic metabolic subtype had more diabetes, universal myocardial fibrosis, preserved right ventricular function, and elevated creatinine. For clinical application, 5 variables were sufficient for classification (left and right ventricular end-systolic volumes, left atrial volume, myocardial fibrosis, and creatinine). Adding the novel DCM subtype improved the C-statistic from 0.60 to 0.76. Interleukin-4 receptor-alpha was identified as a novel prognostic biomarker in derivation (HR: 3.6; 95% CI: 1.9-6.5; P = 0.00002) and validation cohorts (HR: 1.94; 95% CI: 1.3-2.8; P = 0.00005). CONCLUSIONS Three reproducible, mechanistically distinct DCM subtypes were identified using widely available clinical and biological data, adding prognostic value to traditional risk models. They may improve patient selection for novel interventions, thereby enabling precision medicine.
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Affiliation(s)
- Upasana Tayal
- National Heart Lung Institute, Imperial College London, London, United Kingdom; Royal Brompton Hospital (Guy's and St Thomas's NHS Foundation Trust), London, United Kingdom.
| | - Job A J Verdonschot
- Cardiovascular Research Institute Maastricht (CARIM), Maastricht University Medical Center, Maastricht, the Netherlands; Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Mark R Hazebroek
- Cardiovascular Research Institute Maastricht (CARIM), Maastricht University Medical Center, Maastricht, the Netherlands
| | - James Howard
- National Heart Lung Institute, Imperial College London, London, United Kingdom
| | - John Gregson
- Department of Medical Statistics, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Simon Newsome
- Department of Medical Statistics, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Ankur Gulati
- Royal Brompton Hospital (Guy's and St Thomas's NHS Foundation Trust), London, United Kingdom
| | | | - Brian P Halliday
- National Heart Lung Institute, Imperial College London, London, United Kingdom; Royal Brompton Hospital (Guy's and St Thomas's NHS Foundation Trust), London, United Kingdom
| | - Amrit S Lota
- National Heart Lung Institute, Imperial College London, London, United Kingdom; Royal Brompton Hospital (Guy's and St Thomas's NHS Foundation Trust), London, United Kingdom
| | - Rachel J Buchan
- National Heart Lung Institute, Imperial College London, London, United Kingdom; Royal Brompton Hospital (Guy's and St Thomas's NHS Foundation Trust), London, United Kingdom
| | - Nicola Whiffin
- National Heart Lung Institute, Imperial College London, London, United Kingdom; Medical Research Council London Institute of Medical Sciences, Imperial College London, London, United Kingdom
| | - Lina Kanapeckaite
- Royal Brompton Hospital (Guy's and St Thomas's NHS Foundation Trust), London, United Kingdom
| | - Resham Baruah
- Royal Brompton Hospital (Guy's and St Thomas's NHS Foundation Trust), London, United Kingdom
| | - Julian W E Jarman
- Royal Brompton Hospital (Guy's and St Thomas's NHS Foundation Trust), London, United Kingdom
| | - Declan P O'Regan
- Medical Research Council London Institute of Medical Sciences, Imperial College London, London, United Kingdom
| | - Paul J R Barton
- National Heart Lung Institute, Imperial College London, London, United Kingdom; Royal Brompton Hospital (Guy's and St Thomas's NHS Foundation Trust), London, United Kingdom; Medical Research Council London Institute of Medical Sciences, Imperial College London, London, United Kingdom
| | - James S Ware
- National Heart Lung Institute, Imperial College London, London, United Kingdom; Royal Brompton Hospital (Guy's and St Thomas's NHS Foundation Trust), London, United Kingdom; Medical Research Council London Institute of Medical Sciences, Imperial College London, London, United Kingdom
| | - Dudley J Pennell
- National Heart Lung Institute, Imperial College London, London, United Kingdom; Royal Brompton Hospital (Guy's and St Thomas's NHS Foundation Trust), London, United Kingdom
| | - Bouke P Adriaans
- Cardiovascular Research Institute Maastricht (CARIM), Maastricht University Medical Center, Maastricht, the Netherlands
| | - Sebastiaan C A M Bekkers
- Cardiovascular Research Institute Maastricht (CARIM), Maastricht University Medical Center, Maastricht, the Netherlands
| | - Jackie Donovan
- Royal Brompton Hospital (Guy's and St Thomas's NHS Foundation Trust), London, United Kingdom
| | - Michael Frenneaux
- National Heart Lung Institute, Imperial College London, London, United Kingdom
| | | | - James L Januzzi
- Cardiology Division, Massachusetts General Hospital, Baim Insitute for Clinical Research, Boston, Massachusetts, USA
| | - John G F Cleland
- National Heart Lung Institute, Imperial College London, London, United Kingdom
| | - Stuart A Cook
- National Heart Centre, Singapore; Medical Research Council London Institute of Medical Sciences, Imperial College London, London, United Kingdom
| | - Rahul C Deo
- One Brave Idea and Division of Cardiovascular Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Stephane R B Heymans
- Cardiovascular Research Institute Maastricht (CARIM), Maastricht University Medical Center, Maastricht, the Netherlands; Centre for Molecular and Vascular Biology, Department of Cardiovascular Sciences, KU Leuven, Belgium
| | - Sanjay K Prasad
- National Heart Lung Institute, Imperial College London, London, United Kingdom; Royal Brompton Hospital (Guy's and St Thomas's NHS Foundation Trust), London, United Kingdom.
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7
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de Marvao A, McGurk KA, Zheng SL, Thanaj M, Bai W, Duan J, Biffi C, Mazzarotto F, Statton B, Dawes TJW, Savioli N, Halliday BP, Xu X, Buchan RJ, Baksi AJ, Quinlan M, Tokarczuk P, Tayal U, Francis C, Whiffin N, Theotokis PI, Zhang X, Jang M, Berry A, Pantazis A, Barton PJR, Rueckert D, Prasad SK, Walsh R, Ho CY, Cook SA, Ware JS, O'Regan DP. Phenotypic Expression and Outcomes in Individuals With Rare Genetic Variants of Hypertrophic Cardiomyopathy. J Am Coll Cardiol 2021; 78:1097-1110. [PMID: 34503678 PMCID: PMC8434420 DOI: 10.1016/j.jacc.2021.07.017] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 07/01/2021] [Accepted: 07/06/2021] [Indexed: 01/06/2023]
Abstract
BACKGROUND Hypertrophic cardiomyopathy (HCM) is caused by rare variants in sarcomere-encoding genes, but little is known about the clinical significance of these variants in the general population. OBJECTIVES The goal of this study was to compare lifetime outcomes and cardiovascular phenotypes according to the presence of rare variants in sarcomere-encoding genes among middle-aged adults. METHODS This study analyzed whole exome sequencing and cardiac magnetic resonance imaging in UK Biobank participants stratified according to sarcomere-encoding variant status. RESULTS The prevalence of rare variants (allele frequency <0.00004) in HCM-associated sarcomere-encoding genes in 200,584 participants was 2.9% (n = 5,712; 1 in 35), and the prevalence of variants pathogenic or likely pathogenic for HCM (SARC-HCM-P/LP) was 0.25% (n = 493; 1 in 407). SARC-HCM-P/LP variants were associated with an increased risk of death or major adverse cardiac events compared with controls (hazard ratio: 1.69; 95% confidence interval [CI]: 1.38-2.07; P < 0.001), mainly due to heart failure endpoints (hazard ratio: 4.23; 95% CI: 3.07-5.83; P < 0.001). In 21,322 participants with both cardiac magnetic resonance imaging and whole exome sequencing, SARC-HCM-P/LP variants were associated with an asymmetric increase in left ventricular maximum wall thickness (10.9 ± 2.7 mm vs 9.4 ± 1.6 mm; P < 0.001), but hypertrophy (≥13 mm) was only present in 18.4% (n = 9 of 49; 95% CI: 9%-32%). SARC-HCM-P/LP variants were still associated with heart failure after adjustment for wall thickness (hazard ratio: 6.74; 95% CI: 2.43-18.7; P < 0.001). CONCLUSIONS In this population of middle-aged adults, SARC-HCM-P/LP variants have low aggregate penetrance for overt HCM but are associated with an increased risk of adverse cardiovascular outcomes and an attenuated cardiomyopathic phenotype. Although absolute event rates are low, identification of these variants may enhance risk stratification beyond familial disease.
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Affiliation(s)
- Antonio de Marvao
- MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, London, United Kingdom
| | - Kathryn A McGurk
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Sean L Zheng
- National Heart and Lung Institute, Imperial College London, London, United Kingdom; Cardiovascular Research Centre at Royal Brompton and Harefield Hospitals, London, United Kingdom
| | - Marjola Thanaj
- MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, London, United Kingdom
| | - Wenjia Bai
- Biomedical Image Analysis Group, Department of Computing, Imperial College London, London, United Kingdom; Department of Brain Sciences, Imperial College London, London, United Kingdom
| | - Jinming Duan
- MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, London, United Kingdom; Biomedical Image Analysis Group, Department of Computing, Imperial College London, London, United Kingdom; School of Computer Science, University of Birmingham, Birmingham, United Kingdom
| | - Carlo Biffi
- MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, London, United Kingdom; Biomedical Image Analysis Group, Department of Computing, Imperial College London, London, United Kingdom
| | - Francesco Mazzarotto
- National Heart and Lung Institute, Imperial College London, London, United Kingdom; Cardiovascular Research Centre at Royal Brompton and Harefield Hospitals, London, United Kingdom; Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy; Cardiomyopathy Unit, Careggi University Hospital, Florence, Italy
| | - Ben Statton
- MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, London, United Kingdom
| | - Timothy J W Dawes
- MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, London, United Kingdom; National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Nicolò Savioli
- MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, London, United Kingdom
| | - Brian P Halliday
- National Heart and Lung Institute, Imperial College London, London, United Kingdom; Cardiovascular Research Centre at Royal Brompton and Harefield Hospitals, London, United Kingdom
| | - Xiao Xu
- National Heart and Lung Institute, Imperial College London, London, United Kingdom; Cardiovascular Research Centre at Royal Brompton and Harefield Hospitals, London, United Kingdom
| | - Rachel J Buchan
- National Heart and Lung Institute, Imperial College London, London, United Kingdom; Cardiovascular Research Centre at Royal Brompton and Harefield Hospitals, London, United Kingdom
| | - A John Baksi
- National Heart and Lung Institute, Imperial College London, London, United Kingdom; Cardiovascular Research Centre at Royal Brompton and Harefield Hospitals, London, United Kingdom
| | - Marina Quinlan
- MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, London, United Kingdom
| | - Paweł Tokarczuk
- MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, London, United Kingdom
| | - Upasana Tayal
- National Heart and Lung Institute, Imperial College London, London, United Kingdom; Cardiovascular Research Centre at Royal Brompton and Harefield Hospitals, London, United Kingdom
| | - Catherine Francis
- National Heart and Lung Institute, Imperial College London, London, United Kingdom; Cardiovascular Research Centre at Royal Brompton and Harefield Hospitals, London, United Kingdom
| | - Nicola Whiffin
- National Heart and Lung Institute, Imperial College London, London, United Kingdom; Cardiovascular Research Centre at Royal Brompton and Harefield Hospitals, London, United Kingdom; Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Pantazis I Theotokis
- MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, London, United Kingdom
| | - Xiaolei Zhang
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Mikyung Jang
- National Heart and Lung Institute, Imperial College London, London, United Kingdom; Cardiovascular Research Centre at Royal Brompton and Harefield Hospitals, London, United Kingdom
| | - Alaine Berry
- MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, London, United Kingdom
| | - Antonis Pantazis
- National Heart and Lung Institute, Imperial College London, London, United Kingdom; Cardiovascular Research Centre at Royal Brompton and Harefield Hospitals, London, United Kingdom
| | - Paul J R Barton
- MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, London, United Kingdom; National Heart and Lung Institute, Imperial College London, London, United Kingdom; Cardiovascular Research Centre at Royal Brompton and Harefield Hospitals, London, United Kingdom
| | - Daniel Rueckert
- Biomedical Image Analysis Group, Department of Computing, Imperial College London, London, United Kingdom; Faculty of Informatics and Medicine, Klinikum Rechts der Isar, TU Munich, Munich, Germany
| | - Sanjay K Prasad
- National Heart and Lung Institute, Imperial College London, London, United Kingdom; Cardiovascular Research Centre at Royal Brompton and Harefield Hospitals, London, United Kingdom
| | - Roddy Walsh
- Department of Experimental Cardiology, Amsterdam UMC, AMC Heart Centre, Amsterdam, the Netherlands
| | - Carolyn Y Ho
- Cardiovascular Division, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Stuart A Cook
- MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, London, United Kingdom; National Heart and Lung Institute, Imperial College London, London, United Kingdom; Cardiovascular Research Centre at Royal Brompton and Harefield Hospitals, London, United Kingdom; National Heart Centre Singapore, Singapore; Duke-NUS Graduate Medical School, Singapore
| | - James S Ware
- MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, London, United Kingdom; National Heart and Lung Institute, Imperial College London, London, United Kingdom; Cardiovascular Research Centre at Royal Brompton and Harefield Hospitals, London, United Kingdom.
| | - Declan P O'Regan
- MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, London, United Kingdom.
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8
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Patel PN, Ito K, Willcox JAL, Haghighi A, Jang MY, Gorham JM, DePalma SR, Lam L, McDonough B, Johnson R, Lakdawala NK, Roberts A, Barton PJR, Cook SA, Fatkin D, Seidman CE, Seidman JG. Contribution of Noncanonical Splice Variants to TTN Truncating Variant Cardiomyopathy. Circ Genom Precis Med 2021; 14:e003389. [PMID: 34461741 DOI: 10.1161/circgen.121.003389] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
BACKGROUND Heterozygous TTN truncating variants cause 10% to 20% of idiopathic dilated cardiomyopathy (DCM). Although variants which disrupt canonical splice signals (ie, invariant dinucleotide of the splice donor site, invariant dinucleotide of the splice acceptor site) at exon-intron junctions are readily recognized as TTN truncating variants, the effects of other nearby sequence variations on splicing and their contribution to disease is uncertain. METHODS Rare variants of unknown significance located in the splice regions of highly expressed TTN exons from 203 DCM cases, 3329 normal subjects, and clinical variant databases were identified. The effects of these variants on splicing were assessed using an in vitro splice assay. RESULTS Splice-altering variants of unknown significance were enriched in DCM cases over controls and present in 2% of DCM patients (P=0.002). Application of this method to clinical variant databases demonstrated 20% of similar variants of unknown significance in TTN splice regions affect splicing. Noncanonical splice-altering variants were most frequently located at position +5 of the donor site (P=4.4×107) and position -3 of the acceptor site (P=0.002). SpliceAI, an emerging in silico prediction tool, had a high positive predictive value (86%-95%) but poor sensitivity (15%-50%) for the detection of splice-altering variants. Alternate exons spliced out of most TTN transcripts frequently lacked the consensus base at +5 donor and -3 acceptor positions. CONCLUSIONS Noncanonical splice-altering variants in TTN explain 1-2% of DCM and offer a 10-20% increase in the diagnostic power of TTN sequencing in this disease. These data suggest rules that may improve efforts to detect splice-altering variants in other genes and may explain the low percent splicing observed for many alternate TTN exons.
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Affiliation(s)
- Parth N Patel
- Department of Genetics (P.N.P., K.I., J.A.L.W., A.H., M.Y.J., J.M.G., S.R.D., L.L., B.M., C.E.S., J.G.S.), Harvard Medical School, Boston, MA.,Department of Medicine, Brigham and Women's Hospital (P.N.P., A.H., M.Y.J.), Harvard Medical School, Boston, MA
| | - Kaoru Ito
- Department of Genetics (P.N.P., K.I., J.A.L.W., A.H., M.Y.J., J.M.G., S.R.D., L.L., B.M., C.E.S., J.G.S.), Harvard Medical School, Boston, MA.,Laboratory for Cardiovascular Genomics and Informatics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan (K.I.)
| | - Jon A L Willcox
- Department of Genetics (P.N.P., K.I., J.A.L.W., A.H., M.Y.J., J.M.G., S.R.D., L.L., B.M., C.E.S., J.G.S.), Harvard Medical School, Boston, MA
| | - Alireza Haghighi
- Department of Genetics (P.N.P., K.I., J.A.L.W., A.H., M.Y.J., J.M.G., S.R.D., L.L., B.M., C.E.S., J.G.S.), Harvard Medical School, Boston, MA.,Department of Medicine, Brigham and Women's Hospital (P.N.P., A.H., M.Y.J.), Harvard Medical School, Boston, MA.,Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, MA (A.H.)
| | - Min Young Jang
- Department of Genetics (P.N.P., K.I., J.A.L.W., A.H., M.Y.J., J.M.G., S.R.D., L.L., B.M., C.E.S., J.G.S.), Harvard Medical School, Boston, MA.,Department of Medicine, Brigham and Women's Hospital (P.N.P., A.H., M.Y.J.), Harvard Medical School, Boston, MA
| | - Joshua M Gorham
- Department of Genetics (P.N.P., K.I., J.A.L.W., A.H., M.Y.J., J.M.G., S.R.D., L.L., B.M., C.E.S., J.G.S.), Harvard Medical School, Boston, MA
| | - Steven R DePalma
- Department of Genetics (P.N.P., K.I., J.A.L.W., A.H., M.Y.J., J.M.G., S.R.D., L.L., B.M., C.E.S., J.G.S.), Harvard Medical School, Boston, MA
| | - Lien Lam
- Department of Genetics (P.N.P., K.I., J.A.L.W., A.H., M.Y.J., J.M.G., S.R.D., L.L., B.M., C.E.S., J.G.S.), Harvard Medical School, Boston, MA
| | - Barbara McDonough
- Department of Genetics (P.N.P., K.I., J.A.L.W., A.H., M.Y.J., J.M.G., S.R.D., L.L., B.M., C.E.S., J.G.S.), Harvard Medical School, Boston, MA
| | - Renee Johnson
- Victor Chang Cardiac Research Institute, Darlinghurst (R.J., D.F.).,Faculty of Medicine, UNSW Sydney, Kensington, NSW, Australia (R.J., D.F.)
| | - Neal K Lakdawala
- Division of Cardiovascular Medicine, Brigham and Women's Hospital (N.K.L., C.E.S.)
| | - Amy Roberts
- Department of Cardiology, Boston Children's Hospital, MA (A.R.)
| | - Paul J R Barton
- National Heart and Lung Institute (P.J.R.B., S.A.C.).,Cardiovascular Research Centre, Royal Brompton and Harefield Hospitals, London, United Kingdom (P.J.R.B.)
| | - Stuart A Cook
- National Heart and Lung Institute (P.J.R.B., S.A.C.).,MRC London Institute of Medical Sciences, Imperial College London (S.A.C.).,Cardiovascular and Metabolic Disorders Program, Duke-National University of Singapore Medical School (S.A.C.).,National Heart Research Institute Singapore, National Heart Centre Singapore (S.A.C.)
| | - Diane Fatkin
- Victor Chang Cardiac Research Institute, Darlinghurst (R.J., D.F.).,Faculty of Medicine, UNSW Sydney, Kensington, NSW, Australia (R.J., D.F.).,Cardiology Department, St Vincent's Hospital, Darlinghurst, NSW, Australia (D.F.)
| | - Christine E Seidman
- Department of Genetics (P.N.P., K.I., J.A.L.W., A.H., M.Y.J., J.M.G., S.R.D., L.L., B.M., C.E.S., J.G.S.), Harvard Medical School, Boston, MA.,Howard Hughes Medical Institute (C.E.S.), Harvard Medical School, Boston, MA.,Division of Cardiovascular Medicine, Brigham and Women's Hospital (N.K.L., C.E.S.)
| | - J G Seidman
- Department of Genetics (P.N.P., K.I., J.A.L.W., A.H., M.Y.J., J.M.G., S.R.D., L.L., B.M., C.E.S., J.G.S.), Harvard Medical School, Boston, MA
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9
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Aguib Y, Allouba M, Walsh R, Ibrahim AM, Halawa S, Afify A, Hosny M, Theotokis PI, Galal A, Elshorbagy S, Roshdy M, Kassem HS, Ellithy A, Buchan R, Whiffin N, Anwer S, Cook SA, Moustafa A, ElGuindy A, Ware JS, Barton PJR, Yacoub M. New Variant With a Previously Unrecognized Mechanism of Pathogenicity in Hypertrophic Cardiomyopathy. Circulation 2021; 144:754-757. [PMID: 34460321 PMCID: PMC8389346 DOI: 10.1161/circulationaha.120.048295] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Yasmine Aguib
- Aswan Heart Centre, Egypt (Y.A., M.A., A.M.I., S.H., A.A., M.H., A.G., S.E., M.R., A.E., S.A., A. ElGuindy, M.Y.).,National Heart and Lung Institute, Imperial College London, United Kingdom (Y.A., M.A., P.I.T., R.B., N.W., A. ElGuindy, J.S.W., P.J.R.B., M.Y.)
| | - Mona Allouba
- Aswan Heart Centre, Egypt (Y.A., M.A., A.M.I., S.H., A.A., M.H., A.G., S.E., M.R., A.E., S.A., A. ElGuindy, M.Y.).,National Heart and Lung Institute, Imperial College London, United Kingdom (Y.A., M.A., P.I.T., R.B., N.W., A. ElGuindy, J.S.W., P.J.R.B., M.Y.)
| | - Roddy Walsh
- Department of Experimental Cardiology, Amsterdam UMC, the Netherlands (R.W.)
| | - Ayman M Ibrahim
- Aswan Heart Centre, Egypt (Y.A., M.A., A.M.I., S.H., A.A., M.H., A.G., S.E., M.R., A.E., S.A., A. ElGuindy, M.Y.).,Faculty of Science, Cairo University, Egypt (A.M.I.)
| | - Sarah Halawa
- Aswan Heart Centre, Egypt (Y.A., M.A., A.M.I., S.H., A.A., M.H., A.G., S.E., M.R., A.E., S.A., A. ElGuindy, M.Y.).,Biotechnology Graduate Program (S.H., A.M.), American University in Cairo, New Cairo, Egypt
| | - Alaa Afify
- Aswan Heart Centre, Egypt (Y.A., M.A., A.M.I., S.H., A.A., M.H., A.G., S.E., M.R., A.E., S.A., A. ElGuindy, M.Y.)
| | - Mohammed Hosny
- Aswan Heart Centre, Egypt (Y.A., M.A., A.M.I., S.H., A.A., M.H., A.G., S.E., M.R., A.E., S.A., A. ElGuindy, M.Y.).,Cardiology Department, Faculty of Medicine, Cairo University, Egypt (M.H.)
| | - Pantazis I Theotokis
- National Heart and Lung Institute, Imperial College London, United Kingdom (Y.A., M.A., P.I.T., R.B., N.W., A. ElGuindy, J.S.W., P.J.R.B., M.Y.)
| | - Aya Galal
- Aswan Heart Centre, Egypt (Y.A., M.A., A.M.I., S.H., A.A., M.H., A.G., S.E., M.R., A.E., S.A., A. ElGuindy, M.Y.)
| | - Sara Elshorbagy
- Aswan Heart Centre, Egypt (Y.A., M.A., A.M.I., S.H., A.A., M.H., A.G., S.E., M.R., A.E., S.A., A. ElGuindy, M.Y.)
| | - Mohamed Roshdy
- Aswan Heart Centre, Egypt (Y.A., M.A., A.M.I., S.H., A.A., M.H., A.G., S.E., M.R., A.E., S.A., A. ElGuindy, M.Y.)
| | - Heba S Kassem
- Clinical Genomics Center, Alexandria Faculty of Medicine, Egypt (H.S.K.)
| | - Amany Ellithy
- Aswan Heart Centre, Egypt (Y.A., M.A., A.M.I., S.H., A.A., M.H., A.G., S.E., M.R., A.E., S.A., A. ElGuindy, M.Y.)
| | - Rachel Buchan
- National Heart and Lung Institute, Imperial College London, United Kingdom (Y.A., M.A., P.I.T., R.B., N.W., A. ElGuindy, J.S.W., P.J.R.B., M.Y.).,Royal Brompton and Harefield Hospitals, London, United Kingdom (R.B., N.W., J.S.W., P.J.R.B.)
| | - Nicola Whiffin
- National Heart and Lung Institute, Imperial College London, United Kingdom (Y.A., M.A., P.I.T., R.B., N.W., A. ElGuindy, J.S.W., P.J.R.B., M.Y.).,Royal Brompton and Harefield Hospitals, London, United Kingdom (R.B., N.W., J.S.W., P.J.R.B.).,Wellcome Centre for Human Genetics, University of Oxford, United Kingdom (N.W.)
| | - Shehab Anwer
- Aswan Heart Centre, Egypt (Y.A., M.A., A.M.I., S.H., A.A., M.H., A.G., S.E., M.R., A.E., S.A., A. ElGuindy, M.Y.)
| | - Stuart A Cook
- Duke-National University of Singapore Medical School (S.A.C.).,National Heart Centre Singapore (S.A.C.).,MRC London Institute of Medical Sciences, United Kingdom (S.A.C., J.S.W., P.J.R.B.)
| | - Ahmed Moustafa
- Biotechnology Graduate Program (S.H., A.M.), American University in Cairo, New Cairo, Egypt.,Department of Biology (A.M.), American University in Cairo, New Cairo, Egypt
| | - Ahmed ElGuindy
- Aswan Heart Centre, Egypt (Y.A., M.A., A.M.I., S.H., A.A., M.H., A.G., S.E., M.R., A.E., S.A., A. ElGuindy, M.Y.).,National Heart and Lung Institute, Imperial College London, United Kingdom (Y.A., M.A., P.I.T., R.B., N.W., A. ElGuindy, J.S.W., P.J.R.B., M.Y.)
| | - James S Ware
- National Heart and Lung Institute, Imperial College London, United Kingdom (Y.A., M.A., P.I.T., R.B., N.W., A. ElGuindy, J.S.W., P.J.R.B., M.Y.).,Royal Brompton and Harefield Hospitals, London, United Kingdom (R.B., N.W., J.S.W., P.J.R.B.).,MRC London Institute of Medical Sciences, United Kingdom (S.A.C., J.S.W., P.J.R.B.)
| | - Paul J R Barton
- National Heart and Lung Institute, Imperial College London, United Kingdom (Y.A., M.A., P.I.T., R.B., N.W., A. ElGuindy, J.S.W., P.J.R.B., M.Y.).,Royal Brompton and Harefield Hospitals, London, United Kingdom (R.B., N.W., J.S.W., P.J.R.B.).,MRC London Institute of Medical Sciences, United Kingdom (S.A.C., J.S.W., P.J.R.B.)
| | - Magdi Yacoub
- Aswan Heart Centre, Egypt (Y.A., M.A., A.M.I., S.H., A.A., M.H., A.G., S.E., M.R., A.E., S.A., A. ElGuindy, M.Y.).,National Heart and Lung Institute, Imperial College London, United Kingdom (Y.A., M.A., P.I.T., R.B., N.W., A. ElGuindy, J.S.W., P.J.R.B., M.Y.).,Harefield Heart Science Centre, United Kingdom (M.Y.)
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10
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Wright CF, Quaife NM, Ramos-Hernández L, Danecek P, Ferla MP, Samocha KE, Kaplanis J, Gardner EJ, Eberhardt RY, Chao KR, Karczewski KJ, Morales J, Gallone G, Balasubramanian M, Banka S, Gompertz L, Kerr B, Kirby A, Lynch SA, Morton JEV, Pinz H, Sansbury FH, Stewart H, Zuccarelli BD, Cook SA, Taylor JC, Juusola J, Retterer K, Firth HV, Hurles ME, Lara-Pezzi E, Barton PJR, Whiffin N. Non-coding region variants upstream of MEF2C cause severe developmental disorder through three distinct loss-of-function mechanisms. Am J Hum Genet 2021; 108:1083-1094. [PMID: 34022131 PMCID: PMC8206381 DOI: 10.1016/j.ajhg.2021.04.025] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [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: 02/08/2021] [Accepted: 04/29/2021] [Indexed: 02/08/2023] Open
Abstract
Clinical genetic testing of protein-coding regions identifies a likely causative variant in only around half of developmental disorder (DD) cases. The contribution of regulatory variation in non-coding regions to rare disease, including DD, remains very poorly understood. We screened 9,858 probands from the Deciphering Developmental Disorders (DDD) study for de novo mutations in the 5' untranslated regions (5' UTRs) of genes within which variants have previously been shown to cause DD through a dominant haploinsufficient mechanism. We identified four single-nucleotide variants and two copy-number variants upstream of MEF2C in a total of ten individual probands. We developed multiple bespoke and orthogonal experimental approaches to demonstrate that these variants cause DD through three distinct loss-of-function mechanisms, disrupting transcription, translation, and/or protein function. These non-coding region variants represent 23% of likely diagnoses identified in MEF2C in the DDD cohort, but these would all be missed in standard clinical genetics approaches. Nonetheless, these variants are readily detectable in exome sequence data, with 30.7% of 5' UTR bases across all genes well covered in the DDD dataset. Our analyses show that non-coding variants upstream of genes within which coding variants are known to cause DD are an important cause of severe disease and demonstrate that analyzing 5' UTRs can increase diagnostic yield. We also show how non-coding variants can help inform both the disease-causing mechanism underlying protein-coding variants and dosage tolerance of the gene.
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Affiliation(s)
- Caroline F Wright
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Royal Devon & Exeter Hospital, Exeter EX2 5DW, UK
| | - Nicholas M Quaife
- National Heart & Lung Institute and MRC London Institute of Medical Sciences, Imperial College London, London W12 0NN, UK; Cardiovascular Research Centre, Royal Brompton & Harefield Hospitals NHS Trust, London SW3 6NP, UK
| | - Laura Ramos-Hernández
- Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), 28029 Madrid, Spain
| | - Petr Danecek
- Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1RQ, UK
| | - Matteo P Ferla
- National Institute for Health Research Oxford Biomedical Research Centre, Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Kaitlin E Samocha
- Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1RQ, UK
| | - Joanna Kaplanis
- Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1RQ, UK
| | - Eugene J Gardner
- Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1RQ, UK
| | - Ruth Y Eberhardt
- Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1RQ, UK
| | - Katherine R Chao
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Konrad J Karczewski
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Joannella Morales
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge CB10 1SD, UK
| | - Giuseppe Gallone
- Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1RQ, UK
| | - Meena Balasubramanian
- Sheffield Clinical Genetics Service, Sheffield Children's NHS Foundation Trust, Sheffield S10 2TH, UK; Academic Unit of Child Health, Department of Oncology & Metabolism, University of Sheffield, Sheffield S10 2TH, UK
| | - Siddharth Banka
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University Hospitals NHS Foundation Trust, Health Innovation Manchester, Manchester M13 9WL, UK; Division of Evolution and Genomic Sciences, School of Biological Sciences, University of Manchester, Oxford Road, Manchester M13 9PL, UK
| | - Lianne Gompertz
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University Hospitals NHS Foundation Trust, Health Innovation Manchester, Manchester M13 9WL, UK
| | - Bronwyn Kerr
- Division of Evolution and Genomic Sciences, School of Biological Sciences, University of Manchester, Oxford Road, Manchester M13 9PL, UK
| | - Amelia Kirby
- Department of Pediatrics, Wake Forest School of Medicine, Winston-Salem, NC 27101, USA
| | - Sally A Lynch
- UCD Academic Centre on Rare Diseases, School of Medicine and Medical Sciences, University College Dublin, and Clinical Genetics, Temple Street Children's University Hospital, Dublin D01 XD99, Ireland
| | - Jenny E V Morton
- West Midlands Regional Clinical Genetics Service and Birmingham Health Partners, Birmingham Women's and Children's Hospitals NHS Foundation Trust, Birmingham B4 6NH, UK
| | - Hailey Pinz
- Department of Pediatrics, Saint Louis University School of Medicine, Saint Louis, MO 63104, USA
| | - Francis H Sansbury
- All Wales Medical Genomics Service, NHS Wales Cardiff and Vale University Health Board, Institute of Medical Genetics, University Hospital of Wales, Cardiff CF14 4AY, UK
| | - Helen Stewart
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 7LE, UK
| | - Britton D Zuccarelli
- Department of Neurology, University of Kansas School of Medicine-Salina Campus, Salina, KS 67401, USA
| | - Stuart A Cook
- National Heart & Lung Institute and MRC London Institute of Medical Sciences, Imperial College London, London W12 0NN, UK
| | - Jenny C Taylor
- National Institute for Health Research Oxford Biomedical Research Centre, Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | | | | | - Helen V Firth
- Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1RQ, UK; East Anglian Medical Genetics Service, Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
| | - Matthew E Hurles
- Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1RQ, UK
| | - Enrique Lara-Pezzi
- Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), 28029 Madrid, Spain; CIBER de enfermedades CardioVasculares (CIBERCV), 28029 Madrid, Spain
| | - Paul J R Barton
- National Heart & Lung Institute and MRC London Institute of Medical Sciences, Imperial College London, London W12 0NN, UK; Cardiovascular Research Centre, Royal Brompton & Harefield Hospitals NHS Trust, London SW3 6NP, UK
| | - Nicola Whiffin
- Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1RQ, UK; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK.
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11
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Tadros R, Francis C, Xu X, Vermeer AMC, Harper AR, Huurman R, Kelu Bisabu K, Walsh R, Hoorntje ET, Te Rijdt WP, Buchan RJ, van Velzen HG, van Slegtenhorst MA, Vermeulen JM, Offerhaus JA, Bai W, de Marvao A, Lahrouchi N, Beekman L, Karper JC, Veldink JH, Kayvanpour E, Pantazis A, Baksi AJ, Whiffin N, Mazzarotto F, Sloane G, Suzuki H, Schneider-Luftman D, Elliott P, Richard P, Ader F, Villard E, Lichtner P, Meitinger T, Tanck MWT, van Tintelen JP, Thain A, McCarty D, Hegele RA, Roberts JD, Amyot J, Dubé MP, Cadrin-Tourigny J, Giraldeau G, L'Allier PL, Garceau P, Tardif JC, Boekholdt SM, Lumbers RT, Asselbergs FW, Barton PJR, Cook SA, Prasad SK, O'Regan DP, van der Velden J, Verweij KJH, Talajic M, Lettre G, Pinto YM, Meder B, Charron P, de Boer RA, Christiaans I, Michels M, Wilde AAM, Watkins H, Matthews PM, Ware JS, Bezzina CR. Shared genetic pathways contribute to risk of hypertrophic and dilated cardiomyopathies with opposite directions of effect. Nat Genet 2021; 53:128-134. [PMID: 33495596 PMCID: PMC7611259 DOI: 10.1038/s41588-020-00762-2] [Citation(s) in RCA: 122] [Impact Index Per Article: 40.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 12/10/2020] [Indexed: 01/29/2023]
Abstract
The heart muscle diseases hypertrophic (HCM) and dilated (DCM) cardiomyopathies are leading causes of sudden death and heart failure in young, otherwise healthy, individuals. We conducted genome-wide association studies and multi-trait analyses in HCM (1,733 cases), DCM (5,521 cases) and nine left ventricular (LV) traits (19,260 UK Biobank participants with structurally normal hearts). We identified 16 loci associated with HCM, 13 with DCM and 23 with LV traits. We show strong genetic correlations between LV traits and cardiomyopathies, with opposing effects in HCM and DCM. Two-sample Mendelian randomization supports a causal association linking increased LV contractility with HCM risk. A polygenic risk score explains a significant portion of phenotypic variability in carriers of HCM-causing rare variants. Our findings thus provide evidence that polygenic risk score may account for variability in Mendelian diseases. More broadly, we provide insights into how genetic pathways may lead to distinct disorders through opposing genetic effects.
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Affiliation(s)
- Rafik Tadros
- Cardiovascular Genetics Center, Montreal Heart Institute, Faculty of Medicine, Université de Montréal, Montreal, Québec, Canada.
- Department of Clinical and Experimental Cardiology, Heart Center, Amsterdam Cardiovascular Sciences, University of Amsterdam, Amsterdam UMC, Amsterdam, the Netherlands.
| | - Catherine Francis
- Cardiovascular Research Centre, Royal Brompton and Harefield National Health Service Foundation Trust, London, UK
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Xiao Xu
- MRC London Institute of Medical Sciences, Imperial College London, London, UK
| | - Alexa M C Vermeer
- Department of Clinical and Experimental Cardiology, Heart Center, Amsterdam Cardiovascular Sciences, University of Amsterdam, Amsterdam UMC, Amsterdam, the Netherlands
- Department of Clinical Genetics, University of Amsterdam, Amsterdam UMC, Amsterdam, the Netherlands
- European Reference Network for Rare and Low Prevalence Complex Diseases of the Heart (ERN GUARD-HEART)
| | - Andrew R Harper
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- Wellcome Centre for Human Genetics, Oxford, UK
| | - Roy Huurman
- Department of Cardiology, Thoraxcenter, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Ken Kelu Bisabu
- Cardiovascular Genetics Center, Montreal Heart Institute, Faculty of Medicine, Université de Montréal, Montreal, Québec, Canada
| | - Roddy Walsh
- Department of Clinical and Experimental Cardiology, Heart Center, Amsterdam Cardiovascular Sciences, University of Amsterdam, Amsterdam UMC, Amsterdam, the Netherlands
| | - Edgar T Hoorntje
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Netherlands Heart Institute, Utrecht, the Netherlands
| | - Wouter P Te Rijdt
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Netherlands Heart Institute, Utrecht, the Netherlands
| | - Rachel J Buchan
- Cardiovascular Research Centre, Royal Brompton and Harefield National Health Service Foundation Trust, London, UK
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Hannah G van Velzen
- Department of Cardiology, Thoraxcenter, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Marjon A van Slegtenhorst
- Department of Clinical Genetics, Thoraxcenter, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Jentien M Vermeulen
- Department of Psychiatry, University of Amsterdam, Amsterdam UMC, Amsterdam, the Netherlands
| | - Joost Allard Offerhaus
- Department of Clinical and Experimental Cardiology, Heart Center, Amsterdam Cardiovascular Sciences, University of Amsterdam, Amsterdam UMC, Amsterdam, the Netherlands
| | - Wenjia Bai
- Data Science Institute, Imperial College London, London, UK
- Department of Brain Sciences and UK Dementia Research Institute at Imperial College London, Hammersmith Hospital, Imperial College London, London, UK
| | - Antonio de Marvao
- MRC London Institute of Medical Sciences, Imperial College London, London, UK
| | - Najim Lahrouchi
- Department of Clinical and Experimental Cardiology, Heart Center, Amsterdam Cardiovascular Sciences, University of Amsterdam, Amsterdam UMC, Amsterdam, the Netherlands
| | - Leander Beekman
- Department of Clinical and Experimental Cardiology, Heart Center, Amsterdam Cardiovascular Sciences, University of Amsterdam, Amsterdam UMC, Amsterdam, the Netherlands
| | - Jacco C Karper
- Department of Cardiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Jan H Veldink
- Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Elham Kayvanpour
- Institute for Cardiomyopathies, Heidelberg Heart Center, University of Heidelberg, Heidelberg, Germany
- DZHK (German Center for Cardiovascular Research), Berlin, Germany
| | - Antonis Pantazis
- Cardiovascular Research Centre, Royal Brompton and Harefield National Health Service Foundation Trust, London, UK
| | - A John Baksi
- Cardiovascular Research Centre, Royal Brompton and Harefield National Health Service Foundation Trust, London, UK
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Nicola Whiffin
- Cardiovascular Research Centre, Royal Brompton and Harefield National Health Service Foundation Trust, London, UK
- National Heart and Lung Institute, Imperial College London, London, UK
- MRC London Institute of Medical Sciences, Imperial College London, London, UK
| | - Francesco Mazzarotto
- Cardiovascular Research Centre, Royal Brompton and Harefield National Health Service Foundation Trust, London, UK
- National Heart and Lung Institute, Imperial College London, London, UK
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
- Cardiomyopathy Unit, Careggi University Hospital, Florence, Italy
| | - Geraldine Sloane
- Cardiovascular Research Centre, Royal Brompton and Harefield National Health Service Foundation Trust, London, UK
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Hideaki Suzuki
- Department of Brain Sciences and UK Dementia Research Institute at Imperial College London, Hammersmith Hospital, Imperial College London, London, UK
- Department of Cardiovascular Medicine, Tohoku University Hospital, Seiryo, Aoba, Sendai, Japan
- Tohoku Medical Megabank Organization, Tohoku University, Seiryo, Aoba, Sendai, Japan
| | - Deborah Schneider-Luftman
- The Francis Crick Institute, London, UK
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK
| | - Paul Elliott
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK
| | - Pascale Richard
- Service de biochimie métabolique, UF de cardiogénétique et myogénétique moléculaire et cellulaire, APHP, Hôpital Pitié-Salpêtrière, Paris, France
- INSERM, UMR_S 1166 and ICAN Institute for Cardiometabolism and Nutrition, Faculté de Médecine, Sorbonne Université, Paris, France
| | - Flavie Ader
- Service de biochimie métabolique, UF de cardiogénétique et myogénétique moléculaire et cellulaire, APHP, Hôpital Pitié-Salpêtrière, Paris, France
- INSERM, UMR_S 1166 and ICAN Institute for Cardiometabolism and Nutrition, Faculté de Médecine, Sorbonne Université, Paris, France
- Faculté de Pharmacie, Université de Paris, Paris, France
| | - Eric Villard
- INSERM, UMR_S 1166 and ICAN Institute for Cardiometabolism and Nutrition, Faculté de Médecine, Sorbonne Université, Paris, France
| | - Peter Lichtner
- Institute of Human Genetics, Helmholtz Zentrum Muenchen, Neuherberg, Germany
| | - Thomas Meitinger
- Institute of Human Genetics, Helmholtz Zentrum Muenchen, Neuherberg, Germany
- Klinikum rechts der Isar der TU Muenchen School of Medicine, Institute of Human Genetics, Munich, Germany
- DZHK (German Center for Cardiovascular Research), partner site Munich Heart Alliance, Munich, Germany
| | - Michael W T Tanck
- Department of Clinical Epidemiology, Biostatistics and Bioinformatics, University of Amsterdam, Amsterdam Public Health (APH), Amsterdam UMC, Amsterdam, the Netherlands
| | - J Peter van Tintelen
- Department of Clinical Genetics, University of Amsterdam, Amsterdam UMC, Amsterdam, the Netherlands
- Department of Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Andrew Thain
- Department of Medicine and Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - David McCarty
- Department of Medicine and Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - Robert A Hegele
- Department of Medicine and Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - Jason D Roberts
- Department of Medicine and Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - Julie Amyot
- Cardiovascular Genetics Center, Montreal Heart Institute, Faculty of Medicine, Université de Montréal, Montreal, Québec, Canada
| | - Marie-Pierre Dubé
- Montreal Heart Institute Research Center, Faculty of Medicine, Université de Montréal, Montreal, Québec, Canada
| | - Julia Cadrin-Tourigny
- Cardiovascular Genetics Center, Montreal Heart Institute, Faculty of Medicine, Université de Montréal, Montreal, Québec, Canada
| | - Geneviève Giraldeau
- Cardiovascular Genetics Center, Montreal Heart Institute, Faculty of Medicine, Université de Montréal, Montreal, Québec, Canada
| | - Philippe L L'Allier
- Cardiovascular Genetics Center, Montreal Heart Institute, Faculty of Medicine, Université de Montréal, Montreal, Québec, Canada
| | - Patrick Garceau
- Cardiovascular Genetics Center, Montreal Heart Institute, Faculty of Medicine, Université de Montréal, Montreal, Québec, Canada
| | - Jean-Claude Tardif
- Montreal Heart Institute Research Center, Faculty of Medicine, Université de Montréal, Montreal, Québec, Canada
| | - S Matthijs Boekholdt
- Department of Cardiology, University of Amsterdam, Heartcenter, Amsterdam UMC, Amsterdam, the Netherlands
| | - R Thomas Lumbers
- Institute of Health Informatics, University College London, London, UK
- Health Data Research UK, Gibbs Building, London, UK
- Barts Heart Centre, Saint Bartholomew's Hospital, London, UK
| | - Folkert W Asselbergs
- Department of Cardiology, Division Heart and Lungs, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
- Institute of Cardiovascular Science and Institute of Health Informatics, Faculty of Population Health Sciences, University College London, London, UK
| | - Paul J R Barton
- Cardiovascular Research Centre, Royal Brompton and Harefield National Health Service Foundation Trust, London, UK
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Stuart A Cook
- National Heart and Lung Institute, Imperial College London, London, UK
- MRC London Institute of Medical Sciences, Imperial College London, London, UK
- National Heart Research Institute Singapore, National Heart Center Singapore, Singapore, Singapore
- Cardiovascular and Metabolic Disorders Program, Duke-National University of Singapore Medical School, Singapore, Singapore
| | - Sanjay K Prasad
- Cardiovascular Research Centre, Royal Brompton and Harefield National Health Service Foundation Trust, London, UK
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Declan P O'Regan
- MRC London Institute of Medical Sciences, Imperial College London, London, UK
| | - Jolanda van der Velden
- Department of Physiology, Amsterdam Cardiovascular Sciences, Amsterdam UMC, Amsterdam, the Netherlands
| | - Karin J H Verweij
- Department of Psychiatry, University of Amsterdam, Amsterdam UMC, Amsterdam, the Netherlands
| | - Mario Talajic
- Cardiovascular Genetics Center, Montreal Heart Institute, Faculty of Medicine, Université de Montréal, Montreal, Québec, Canada
| | - Guillaume Lettre
- Montreal Heart Institute Research Center, Faculty of Medicine, Université de Montréal, Montreal, Québec, Canada
| | - Yigal M Pinto
- Department of Clinical and Experimental Cardiology, Heart Center, Amsterdam Cardiovascular Sciences, University of Amsterdam, Amsterdam UMC, Amsterdam, the Netherlands
- European Reference Network for Rare and Low Prevalence Complex Diseases of the Heart (ERN GUARD-HEART)
| | - Benjamin Meder
- Institute for Cardiomyopathies, Heidelberg Heart Center, University of Heidelberg, Heidelberg, Germany
| | - Philippe Charron
- European Reference Network for Rare and Low Prevalence Complex Diseases of the Heart (ERN GUARD-HEART)
- INSERM, UMR_S 1166 and ICAN Institute for Cardiometabolism and Nutrition, Faculté de Médecine, Sorbonne Université, Paris, France
- Département de Génétique, Centre de référence des maladies cardiaques héréditaires ou rares, APHP, Hôpital Pitié-Salpêtrière, Paris, France
| | - Rudolf A de Boer
- Department of Cardiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Imke Christiaans
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Michelle Michels
- Department of Cardiology, Thoraxcenter, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Arthur A M Wilde
- Department of Clinical and Experimental Cardiology, Heart Center, Amsterdam Cardiovascular Sciences, University of Amsterdam, Amsterdam UMC, Amsterdam, the Netherlands
- European Reference Network for Rare and Low Prevalence Complex Diseases of the Heart (ERN GUARD-HEART)
| | - Hugh Watkins
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- Wellcome Centre for Human Genetics, Oxford, UK
| | - Paul M Matthews
- Department of Brain Sciences and UK Dementia Research Institute at Imperial College London, Hammersmith Hospital, Imperial College London, London, UK
| | - James S Ware
- Cardiovascular Research Centre, Royal Brompton and Harefield National Health Service Foundation Trust, London, UK.
- National Heart and Lung Institute, Imperial College London, London, UK.
- MRC London Institute of Medical Sciences, Imperial College London, London, UK.
| | - Connie R Bezzina
- Department of Clinical and Experimental Cardiology, Heart Center, Amsterdam Cardiovascular Sciences, University of Amsterdam, Amsterdam UMC, Amsterdam, the Netherlands.
- European Reference Network for Rare and Low Prevalence Complex Diseases of the Heart (ERN GUARD-HEART), .
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12
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Zhang X, Walsh R, Whiffin N, Buchan R, Midwinter W, Wilk A, Govind R, Li N, Ahmad M, Mazzarotto F, Roberts A, Theotokis PI, Mazaika E, Allouba M, de Marvao A, Pua CJ, Day SM, Ashley E, Colan SD, Michels M, Pereira AC, Jacoby D, Ho CY, Olivotto I, Gunnarsson GT, Jefferies JL, Semsarian C, Ingles J, O'Regan DP, Aguib Y, Yacoub MH, Cook SA, Barton PJR, Bottolo L, Ware JS. Disease-specific variant pathogenicity prediction significantly improves variant interpretation in inherited cardiac conditions. Genet Med 2021; 23:69-79. [PMID: 33046849 PMCID: PMC7790749 DOI: 10.1038/s41436-020-00972-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Revised: 09/08/2020] [Accepted: 09/09/2020] [Indexed: 11/18/2022] Open
Abstract
PURPOSE Accurate discrimination of benign and pathogenic rare variation remains a priority for clinical genome interpretation. State-of-the-art machine learning variant prioritization tools are imprecise and ignore important parameters defining gene-disease relationships, e.g., distinct consequences of gain-of-function versus loss-of-function variants. We hypothesized that incorporating disease-specific information would improve tool performance. METHODS We developed a disease-specific variant classifier, CardioBoost, that estimates the probability of pathogenicity for rare missense variants in inherited cardiomyopathies and arrhythmias. We assessed CardioBoost's ability to discriminate known pathogenic from benign variants, prioritize disease-associated variants, and stratify patient outcomes. RESULTS CardioBoost has high global discrimination accuracy (precision recall area under the curve [AUC] 0.91 for cardiomyopathies; 0.96 for arrhythmias), outperforming existing tools (4-24% improvement). CardioBoost obtains excellent accuracy (cardiomyopathies 90.2%; arrhythmias 91.9%) for variants classified with >90% confidence, and increases the proportion of variants classified with high confidence more than twofold compared with existing tools. Variants classified as disease-causing are associated with both disease status and clinical severity, including a 21% increased risk (95% confidence interval [CI] 11-29%) of severe adverse outcomes by age 60 in patients with hypertrophic cardiomyopathy. CONCLUSIONS A disease-specific variant classifier outperforms state-of-the-art genome-wide tools for rare missense variants in inherited cardiac conditions ( https://www.cardiodb.org/cardioboost/ ), highlighting broad opportunities for improved pathogenicity prediction through disease specificity.
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Affiliation(s)
- Xiaolei Zhang
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
- Cardiovascular Research Centre, Royal Brompton and Harefield NHS, Foundation Trust London, London, United Kingdom
| | - Roddy Walsh
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
- Cardiovascular Research Centre, Royal Brompton and Harefield NHS, Foundation Trust London, London, United Kingdom
| | - Nicola Whiffin
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
- Cardiovascular Research Centre, Royal Brompton and Harefield NHS, Foundation Trust London, London, United Kingdom
| | - Rachel Buchan
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
- Cardiovascular Research Centre, Royal Brompton and Harefield NHS, Foundation Trust London, London, United Kingdom
| | - William Midwinter
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
- Cardiovascular Research Centre, Royal Brompton and Harefield NHS, Foundation Trust London, London, United Kingdom
| | - Alicja Wilk
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
- Cardiovascular Research Centre, Royal Brompton and Harefield NHS, Foundation Trust London, London, United Kingdom
| | - Risha Govind
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
- Cardiovascular Research Centre, Royal Brompton and Harefield NHS, Foundation Trust London, London, United Kingdom
| | - Nicholas Li
- Cardiovascular Research Centre, Royal Brompton and Harefield NHS, Foundation Trust London, London, United Kingdom
- MRC London Institute of Medical Sciences, Imperial College London, London, United Kingdom
| | - Mian Ahmad
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
- Cardiovascular Research Centre, Royal Brompton and Harefield NHS, Foundation Trust London, London, United Kingdom
| | - Francesco Mazzarotto
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
- Cardiomyopathy Unit, Careggi University Hospital, Florence, Italy
- Department of Clinical and Experimental Medicine, University of Florence, Florence, Italy
| | - Angharad Roberts
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
- Cardiovascular Research Centre, Royal Brompton and Harefield NHS, Foundation Trust London, London, United Kingdom
| | - Pantazis I Theotokis
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
- Cardiovascular Research Centre, Royal Brompton and Harefield NHS, Foundation Trust London, London, United Kingdom
| | - Erica Mazaika
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
- Cardiovascular Research Centre, Royal Brompton and Harefield NHS, Foundation Trust London, London, United Kingdom
| | - Mona Allouba
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
- Aswan Heart Centre, Magdi Yacoub Heart Foundation, Aswan, Egypt
| | - Antonio de Marvao
- MRC London Institute of Medical Sciences, Imperial College London, London, United Kingdom
| | | | - Sharlene M Day
- Division of Cardiovascular Medicine and Penn Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA
| | - Euan Ashley
- Division of Cardiovascular Medicine, Stanford University Medical Center, Stanford, CA, USA
| | - Steven D Colan
- Department of Cardiology, Boston Children's Hospital, Boston, MA, USA
| | - Michelle Michels
- Department of Cardiology, Thoraxcenter, Erasmus MC Rotterdam, Rotterdam, Netherlands
| | - Alexandre C Pereira
- Heart Institute (InCor), University of Sao Paulo Medical School, Sao Paulo, Brazil
| | - Daniel Jacoby
- Department of Internal Medicine, Yale University, New Haven, CT, USA
| | - Carolyn Y Ho
- Cardiovascular Division, Brigham and Women's Hospital, Boston, MA, USA
| | - Iacopo Olivotto
- Cardiomyopathy Unit, Careggi University Hospital, Florence, Italy
| | | | - John L Jefferies
- The Cardiovascular Institute, University of Tennessee, Memphis, TN, USA
| | - Chris Semsarian
- Centenary Institute, The University of Sydney, Sydney, Australia
- Department of Cardiology, Royal Prince Alfred Hospital, Sydney, Australia
| | - Jodie Ingles
- Centenary Institute, The University of Sydney, Sydney, Australia
| | - Declan P O'Regan
- MRC London Institute of Medical Sciences, Imperial College London, London, United Kingdom
| | - Yasmine Aguib
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
- Aswan Heart Centre, Magdi Yacoub Heart Foundation, Aswan, Egypt
| | - Magdi H Yacoub
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
- Aswan Heart Centre, Magdi Yacoub Heart Foundation, Aswan, Egypt
| | - Stuart A Cook
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
- Cardiovascular Research Centre, Royal Brompton and Harefield NHS, Foundation Trust London, London, United Kingdom
- National Heart Centre, Singapore, Singapore
- Duke-National University of Singapore, Singapore, Singapore
| | - Paul J R Barton
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
- Cardiovascular Research Centre, Royal Brompton and Harefield NHS, Foundation Trust London, London, United Kingdom
| | - Leonardo Bottolo
- Department of Medical Genetics, University of Cambridge, Cambridge, United Kingdom.
- Alan Turing Institute, London, United Kingdom.
- MRC Biostatistics Unit, University of Cambridge, Cambridge, United Kingdom.
| | - James S Ware
- National Heart and Lung Institute, Imperial College London, London, United Kingdom.
- Cardiovascular Research Centre, Royal Brompton and Harefield NHS, Foundation Trust London, London, United Kingdom.
- MRC London Institute of Medical Sciences, Imperial College London, London, United Kingdom.
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13
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Whiffin N, Karczewski KJ, Zhang X, Chothani S, Smith MJ, Evans DG, Roberts AM, Quaife NM, Schafer S, Rackham O, Alföldi J, O'Donnell-Luria AH, Francioli LC, Cook SA, Barton PJR, MacArthur DG, Ware JS. Characterising the loss-of-function impact of 5' untranslated region variants in 15,708 individuals. Nat Commun 2020; 11:2523. [PMID: 32461616 PMCID: PMC7253449 DOI: 10.1038/s41467-019-10717-9] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 05/23/2019] [Indexed: 01/17/2023] Open
Abstract
Upstream open reading frames (uORFs) are tissue-specific cis-regulators of protein translation. Isolated reports have shown that variants that create or disrupt uORFs can cause disease. Here, in a systematic genome-wide study using 15,708 whole genome sequences, we show that variants that create new upstream start codons, and variants disrupting stop sites of existing uORFs, are under strong negative selection. This selection signal is significantly stronger for variants arising upstream of genes intolerant to loss-of-function variants. Furthermore, variants creating uORFs that overlap the coding sequence show signals of selection equivalent to coding missense variants. Finally, we identify specific genes where modification of uORFs likely represents an important disease mechanism, and report a novel uORF frameshift variant upstream of NF2 in neurofibromatosis. Our results highlight uORF-perturbing variants as an under-recognised functional class that contribute to penetrant human disease, and demonstrate the power of large-scale population sequencing data in studying non-coding variant classes.
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Affiliation(s)
- Nicola Whiffin
- National Heart and Lung Institute and MRC London Institute of Medical Sciences, Imperial College London, Du Cane Road, London, W12 0NN, UK.
- NIHR Royal Brompton Cardiovascular Research Centre, Royal Brompton and Harefield National Health Service Foundation Trust, Sydney Street, London, SW3 6NP, UK.
- Medical and Population Genetics, Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA, 02142, USA.
| | - Konrad J Karczewski
- Medical and Population Genetics, Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA, 02142, USA
- Analytical and Translational Genetics Unit, Massachusetts General Hospital, 55 Fruit Street, Boston, MA, 02114, USA
| | - Xiaolei Zhang
- National Heart and Lung Institute and MRC London Institute of Medical Sciences, Imperial College London, Du Cane Road, London, W12 0NN, UK
- NIHR Royal Brompton Cardiovascular Research Centre, Royal Brompton and Harefield National Health Service Foundation Trust, Sydney Street, London, SW3 6NP, UK
| | - Sonia Chothani
- Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
| | - Miriam J Smith
- NW Genomic Laboratory Hub, Centre for Genomic Medicine, Division of Evolution and Genomic Science, St Mary's Hospital, University of Manchester, Oxford Road, Manchester, M13 9WL, UK
| | - D Gareth Evans
- NW Genomic Laboratory Hub, Centre for Genomic Medicine, Division of Evolution and Genomic Science, St Mary's Hospital, University of Manchester, Oxford Road, Manchester, M13 9WL, UK
| | - Angharad M Roberts
- National Heart and Lung Institute and MRC London Institute of Medical Sciences, Imperial College London, Du Cane Road, London, W12 0NN, UK
- NIHR Royal Brompton Cardiovascular Research Centre, Royal Brompton and Harefield National Health Service Foundation Trust, Sydney Street, London, SW3 6NP, UK
| | - Nicholas M Quaife
- National Heart and Lung Institute and MRC London Institute of Medical Sciences, Imperial College London, Du Cane Road, London, W12 0NN, UK
- NIHR Royal Brompton Cardiovascular Research Centre, Royal Brompton and Harefield National Health Service Foundation Trust, Sydney Street, London, SW3 6NP, UK
| | - Sebastian Schafer
- Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
- National Heart Centre Singapore, 5 Hospital Drive, Singapore, 169609, Singapore
| | - Owen Rackham
- Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
| | - Jessica Alföldi
- Medical and Population Genetics, Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA, 02142, USA
- Analytical and Translational Genetics Unit, Massachusetts General Hospital, 55 Fruit Street, Boston, MA, 02114, USA
| | - Anne H O'Donnell-Luria
- Medical and Population Genetics, Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA, 02142, USA
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
| | - Laurent C Francioli
- Medical and Population Genetics, Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA, 02142, USA
- Analytical and Translational Genetics Unit, Massachusetts General Hospital, 55 Fruit Street, Boston, MA, 02114, USA
| | - Stuart A Cook
- National Heart and Lung Institute and MRC London Institute of Medical Sciences, Imperial College London, Du Cane Road, London, W12 0NN, UK
- Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
- National Heart Centre Singapore, 5 Hospital Drive, Singapore, 169609, Singapore
| | - Paul J R Barton
- National Heart and Lung Institute and MRC London Institute of Medical Sciences, Imperial College London, Du Cane Road, London, W12 0NN, UK
- NIHR Royal Brompton Cardiovascular Research Centre, Royal Brompton and Harefield National Health Service Foundation Trust, Sydney Street, London, SW3 6NP, UK
| | - Daniel G MacArthur
- Medical and Population Genetics, Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA, 02142, USA
- Analytical and Translational Genetics Unit, Massachusetts General Hospital, 55 Fruit Street, Boston, MA, 02114, USA
- Centre for Population Genomics, Garvan Institute of Medical Research, and UNSW Sydney, Sydney, Australia
- Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, Australia
| | - James S Ware
- National Heart and Lung Institute and MRC London Institute of Medical Sciences, Imperial College London, Du Cane Road, London, W12 0NN, UK
- NIHR Royal Brompton Cardiovascular Research Centre, Royal Brompton and Harefield National Health Service Foundation Trust, Sydney Street, London, SW3 6NP, UK
- Medical and Population Genetics, Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA, 02142, USA
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14
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Mazzarotto F, Olivotto I, Boschi B, Girolami F, Poggesi C, Barton PJR, Walsh R. Contemporary Insights Into the Genetics of Hypertrophic Cardiomyopathy: Toward a New Era in Clinical Testing? J Am Heart Assoc 2020; 9:e015473. [PMID: 32306808 PMCID: PMC7428545 DOI: 10.1161/jaha.119.015473] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Genetic testing for hypertrophic cardiomyopathy (HCM) is an established clinical technique, supported by 30 years of research into its genetic etiology. Although pathogenic variants are often detected in patients and used to identify at-risk relatives, the effectiveness of genetic testing has been hampered by ambiguous genetic associations (yielding uncertain and potentially false-positive results), difficulties in classifying variants, and uncertainty about genotype-negative patients. Recent case-control studies on rare variation, improved data sharing, and meta-analysis of case cohorts contributed to new insights into the genetic basis of HCM. In particular, although research into new genes and mechanisms remains essential, reassessment of Mendelian genetic associations in HCM argues that current clinical genetic testing should be limited to a small number of validated disease genes that yield informative and interpretable results. Accurate and consistent variant interpretation has benefited from new standardized variant interpretation guidelines and innovative approaches to improve classification. Most cases lacking a pathogenic variant are now believed to indicate non-Mendelian HCM, with more benign prognosis and minimal risk to relatives. Here, we discuss recent advances in the genetics of HCM and their application to clinical genetic testing together with practical issues regarding implementation. Although this review focuses on HCM, many of the issues discussed are also relevant to other inherited cardiac diseases.
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Affiliation(s)
- Francesco Mazzarotto
- Cardiomyopathy UnitCareggi University HospitalFlorenceItaly
- Cardiovascular Research CenterRoyal Brompton and Harefield NHS Foundation TrustLondonUnited Kingdom
- National Heart and Lung InstituteImperial College LondonUnited Kingdom
- Department of Clinical and Experimental MedicineUniversity of FlorenceItaly
| | - Iacopo Olivotto
- Cardiomyopathy UnitCareggi University HospitalFlorenceItaly
- Department of Clinical and Experimental MedicineUniversity of FlorenceItaly
| | - Beatrice Boschi
- Cardiomyopathy UnitCareggi University HospitalFlorenceItaly
- Genetic UnitCareggi University HospitalFlorenceItaly
| | - Francesca Girolami
- Cardiomyopathy UnitCareggi University HospitalFlorenceItaly
- Department of Paediatric CardiologyMeyer Children's HospitalFlorenceItaly
| | - Corrado Poggesi
- Department of Clinical and Experimental MedicineUniversity of FlorenceItaly
| | - Paul J. R. Barton
- Cardiovascular Research CenterRoyal Brompton and Harefield NHS Foundation TrustLondonUnited Kingdom
- National Heart and Lung InstituteImperial College LondonUnited Kingdom
| | - Roddy Walsh
- Department of Clinical and Experimental CardiologyHeart CenterAcademic Medical CenterAmsterdamthe Netherlands
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15
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Chen H, Moreno-Moral A, Pesce F, Devapragash N, Mancini M, Heng EL, Rotival M, Srivastava PK, Harmston N, Shkura K, Rackham OJL, Yu WP, Sun XM, Tee NGZ, Tan ELS, Barton PJR, Felkin LE, Lara-Pezzi E, Angelini G, Beltrami C, Pravenec M, Schafer S, Bottolo L, Hubner N, Emanueli C, Cook SA, Petretto E. Author Correction: WWP2 regulates pathological cardiac fibrosis by modulating SMAD2 signaling. Nat Commun 2019; 10:4085. [PMID: 31501434 PMCID: PMC6733793 DOI: 10.1038/s41467-019-12060-5] [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] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Affiliation(s)
- Huimei Chen
- Programme in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, 169857, Republic of Singapore
| | - Aida Moreno-Moral
- Programme in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, 169857, Republic of Singapore
| | - Francesco Pesce
- Department of Emergency and Organ Transplantation (DETO), University of Bari, 70124, Bari, Italy
| | - Nithya Devapragash
- Programme in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, 169857, Republic of Singapore
| | - Massimiliano Mancini
- SOC di Anatomia Patologica, Ospedale San Giovanni di Dio, 50123, Florence, Italy
| | - Ee Ling Heng
- National Heart and Lung Institute, Imperial College London, London, SW7 2AZ, UK
| | - Maxime Rotival
- Unit of Human Evolutionary Genetics, Institute Pasteur, 75015, Paris, France
| | - Prashant K Srivastava
- Division of Brain Sciences, Imperial College Faculty of Medicine, London, W12 0NN, UK
| | - Nathan Harmston
- Programme in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, 169857, Republic of Singapore
| | - Kirill Shkura
- Division of Brain Sciences, Imperial College Faculty of Medicine, London, W12 0NN, UK
| | - Owen J L Rackham
- Programme in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, 169857, Republic of Singapore
| | - Wei-Ping Yu
- Animal Gene Editing Laboratory, BRC, A*STAR20 Biopolis Way, Singapore, 138668, Republic of Singapore
- Institute of Molecular and Cell Biology, A*STAR, 61 Biopolis Drive, Singapore, 138673, Republic of Singapore
| | - Xi-Ming Sun
- MRC London Institute of Medical Sciences (LMC), Imperial College, London, W12 0NN, UK
| | | | - Elisabeth Li Sa Tan
- Programme in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, 169857, Republic of Singapore
| | - Paul J R Barton
- National Heart and Lung Institute, Imperial College London, London, SW7 2AZ, UK
- Cardiovascular Research Centre, Royal Brompton and Harefield NHS Trust, London, SW3 6NP, UK
| | - Leanne E Felkin
- National Heart and Lung Institute, Imperial College London, London, SW7 2AZ, UK
- Cardiovascular Research Centre, Royal Brompton and Harefield NHS Trust, London, SW3 6NP, UK
| | - Enrique Lara-Pezzi
- Centro Nacional de Investigaciones Cardiovasculares - CNIC, 28029, Madrid, Spain
| | - Gianni Angelini
- National Heart and Lung Institute, Imperial College London, London, SW7 2AZ, UK
- Bristol Heart Institute, Bristol Medical School, University of Bristol, Bristol, BS2 89HW, UK
| | - Cristina Beltrami
- National Heart and Lung Institute, Imperial College London, London, SW7 2AZ, UK
| | - Michal Pravenec
- Institute of Physiology, Czech Academy of Sciences, 142 00, Praha 4, Czech Republic
| | - Sebastian Schafer
- Programme in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, 169857, Republic of Singapore
- National Heart Centre Singapore, Singapore, 169609, Republic of Singapore
| | - Leonardo Bottolo
- Department of Medical Genetics, University of Cambridge, Cambridge, CB2 0QQ, UK
- The Alan Turing Institute, London, NW1 2DB, UK
- MRC Biostatistics Unit, University of Cambridge, Cambridge, CB2 0SR, UK
| | - Norbert Hubner
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125, Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, 13347, Berlin, Germany
- Charité-Universitätsmedizin, 10117, Berlin, Germany
- Berlin Institute of Health (BIH), 10178, Berlin, Germany
| | - Costanza Emanueli
- National Heart and Lung Institute, Imperial College London, London, SW7 2AZ, UK
- Cardiovascular Research Centre, Royal Brompton and Harefield NHS Trust, London, SW3 6NP, UK
| | - Stuart A Cook
- Programme in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, 169857, Republic of Singapore
- MRC London Institute of Medical Sciences (LMC), Imperial College, London, W12 0NN, UK
- National Heart Centre Singapore, Singapore, 169609, Republic of Singapore
| | - Enrico Petretto
- Programme in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, 169857, Republic of Singapore.
- MRC London Institute of Medical Sciences (LMC), Imperial College, London, W12 0NN, UK.
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16
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Chen H, Moreno-Moral A, Pesce F, Devapragash N, Mancini M, Heng EL, Rotival M, Srivastava PK, Harmston N, Shkura K, Rackham OJL, Yu WP, Sun XM, Tee NGZ, Tan ELS, Barton PJR, Felkin LE, Lara-Pezzi E, Angelini G, Beltrami C, Pravenec M, Schafer S, Bottolo L, Hubner N, Emanueli C, Cook SA, Petretto E. WWP2 regulates pathological cardiac fibrosis by modulating SMAD2 signaling. Nat Commun 2019; 10:3616. [PMID: 31399586 PMCID: PMC6689010 DOI: 10.1038/s41467-019-11551-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 07/19/2019] [Indexed: 01/03/2023] Open
Abstract
Cardiac fibrosis is a final common pathology in inherited and acquired heart diseases that causes cardiac electrical and pump failure. Here, we use systems genetics to identify a pro-fibrotic gene network in the diseased heart and show that this network is regulated by the E3 ubiquitin ligase WWP2, specifically by the WWP2-N terminal isoform. Importantly, the WWP2-regulated pro-fibrotic gene network is conserved across different cardiac diseases characterized by fibrosis: human and murine dilated cardiomyopathy and repaired tetralogy of Fallot. Transgenic mice lacking the N-terminal region of the WWP2 protein show improved cardiac function and reduced myocardial fibrosis in response to pressure overload or myocardial infarction. In primary cardiac fibroblasts, WWP2 positively regulates the expression of pro-fibrotic markers and extracellular matrix genes. TGFβ1 stimulation promotes nuclear translocation of the WWP2 isoforms containing the N-terminal region and their interaction with SMAD2. WWP2 mediates the TGFβ1-induced nucleocytoplasmic shuttling and transcriptional activity of SMAD2.
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Affiliation(s)
- Huimei Chen
- Programme in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, 169857, Republic of Singapore
| | - Aida Moreno-Moral
- Programme in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, 169857, Republic of Singapore
| | - Francesco Pesce
- Department of Emergency and Organ Transplantation (DETO), University of Bari, 70124, Bari, Italy
| | - Nithya Devapragash
- Programme in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, 169857, Republic of Singapore
| | - Massimiliano Mancini
- SOC di Anatomia Patologica, Ospedale San Giovanni di Dio, 50123, Florence, Italy
| | - Ee Ling Heng
- National Heart and Lung Institute, Imperial College London, London, SW7 2AZ, UK
| | - Maxime Rotival
- Unit of Human Evolutionary Genetics, Institute Pasteur, 75015, Paris, France
| | - Prashant K Srivastava
- Division of Brain Sciences, Imperial College Faculty of Medicine, London, W12 0NN, UK
| | - Nathan Harmston
- Programme in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, 169857, Republic of Singapore
| | - Kirill Shkura
- Division of Brain Sciences, Imperial College Faculty of Medicine, London, W12 0NN, UK
| | - Owen J L Rackham
- Programme in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, 169857, Republic of Singapore
| | - Wei-Ping Yu
- Animal Gene Editing Laboratory, BRC, A*STAR20 Biopolis Way, Singapore, 138668, Republic of Singapore
- Institute of Molecular and Cell Biology, A*STAR, 61 Biopolis Drive, Singapore, 138673, Republic of Singapore
| | - Xi-Ming Sun
- MRC London Institute of Medical Sciences (LMC), Imperial College, London, W12 0NN, UK
| | | | - Elisabeth Li Sa Tan
- Programme in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, 169857, Republic of Singapore
| | - Paul J R Barton
- National Heart and Lung Institute, Imperial College London, London, SW7 2AZ, UK
- Cardiovascular Research Centre, Royal Brompton and Harefield NHS Trust, London, SW3 6NP, UK
| | - Leanne E Felkin
- National Heart and Lung Institute, Imperial College London, London, SW7 2AZ, UK
- Cardiovascular Research Centre, Royal Brompton and Harefield NHS Trust, London, SW3 6NP, UK
| | - Enrique Lara-Pezzi
- Centro Nacional de Investigaciones Cardiovasculares - CNIC, 28029, Madrid, Spain
| | - Gianni Angelini
- National Heart and Lung Institute, Imperial College London, London, SW7 2AZ, UK
- Bristol Heart Institute, Bristol Medical School, University of Bristol, Bristol, BS2 89HW, UK
| | - Cristina Beltrami
- National Heart and Lung Institute, Imperial College London, London, SW7 2AZ, UK
| | - Michal Pravenec
- Institute of Physiology, Czech Academy of Sciences, 142 00, Praha 4, Czech Republic
| | - Sebastian Schafer
- Programme in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, 169857, Republic of Singapore
- National Heart Centre Singapore, Singapore, 169609, Republic of Singapore
| | - Leonardo Bottolo
- Department of Medical Genetics, University of Cambridge, Cambridge, CB2 0QQ, UK
- The Alan Turing Institute, London, NW1 2DB, UK
- MRC Biostatistics Unit, University of Cambridge, Cambridge, CB2 0SR, UK
| | - Norbert Hubner
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125, Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, 13347, Berlin, Germany
- Charité-Universitätsmedizin, 10117, Berlin, Germany
- Berlin Institute of Health (BIH), 10178, Berlin, Germany
| | - Costanza Emanueli
- National Heart and Lung Institute, Imperial College London, London, SW7 2AZ, UK
- Cardiovascular Research Centre, Royal Brompton and Harefield NHS Trust, London, SW3 6NP, UK
| | - Stuart A Cook
- Programme in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, 169857, Republic of Singapore
- MRC London Institute of Medical Sciences (LMC), Imperial College, London, W12 0NN, UK
- National Heart Centre Singapore, Singapore, 169609, Republic of Singapore
| | - Enrico Petretto
- Programme in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, 169857, Republic of Singapore.
- MRC London Institute of Medical Sciences (LMC), Imperial College, London, W12 0NN, UK.
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17
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Chothani S, Schäfer S, Adami E, Viswanathan S, Widjaja AA, Langley SR, Tan J, Wang M, Quaife NM, Jian Pua C, D'Agostino G, Guna Shekeran S, George BL, Lim S, Yiqun Cao E, van Heesch S, Witte F, Felkin LE, Christodoulou EG, Dong J, Blachut S, Patone G, Barton PJR, Hubner N, Cook SA, Rackham OJL. Widespread Translational Control of Fibrosis in the Human Heart by RNA-Binding Proteins. Circulation 2019; 140:937-951. [PMID: 31284728 PMCID: PMC6749977 DOI: 10.1161/circulationaha.119.039596] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Supplemental Digital Content is available in the text. Fibrosis is a common pathology in many cardiac disorders and is driven by the activation of resident fibroblasts. The global posttranscriptional mechanisms underlying fibroblast-to-myofibroblast conversion in the heart have not been explored.
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Affiliation(s)
- Sonia Chothani
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore Medical School, Singapore (S.C., S.S., E.A., S.V., A.W., S.L., M.W., G.D., S.G.S., B.L.G., S.L., E.Y.C., E.C., J.D., S.A.C., O.J.L.R.)
| | - Sebastian Schäfer
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore Medical School, Singapore (S.C., S.S., E.A., S.V., A.W., S.L., M.W., G.D., S.G.S., B.L.G., S.L., E.Y.C., E.C., J.D., S.A.C., O.J.L.R.).,National Heart Centre Singapore, Singapore (S.S., S.L., J.T., C.J.P., S.A.C.)
| | - Eleonora Adami
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore Medical School, Singapore (S.C., S.S., E.A., S.V., A.W., S.L., M.W., G.D., S.G.S., B.L.G., S.L., E.Y.C., E.C., J.D., S.A.C., O.J.L.R.).,Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany (E.A., S.v.H., F.W., S.B., G.P., N.H.)
| | - Sivakumar Viswanathan
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore Medical School, Singapore (S.C., S.S., E.A., S.V., A.W., S.L., M.W., G.D., S.G.S., B.L.G., S.L., E.Y.C., E.C., J.D., S.A.C., O.J.L.R.)
| | - Anissa A Widjaja
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore Medical School, Singapore (S.C., S.S., E.A., S.V., A.W., S.L., M.W., G.D., S.G.S., B.L.G., S.L., E.Y.C., E.C., J.D., S.A.C., O.J.L.R.)
| | - Sarah R Langley
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore Medical School, Singapore (S.C., S.S., E.A., S.V., A.W., S.L., M.W., G.D., S.G.S., B.L.G., S.L., E.Y.C., E.C., J.D., S.A.C., O.J.L.R.)
| | - Jessie Tan
- National Heart Centre Singapore, Singapore (S.S., S.L., J.T., C.J.P., S.A.C.)
| | - Mao Wang
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore Medical School, Singapore (S.C., S.S., E.A., S.V., A.W., S.L., M.W., G.D., S.G.S., B.L.G., S.L., E.Y.C., E.C., J.D., S.A.C., O.J.L.R.)
| | - Nicholas M Quaife
- National Heart and Lung Institute, Imperial College London, United Kingdom (N.M.Q., L.E.F., P.J.R.B., S.A.C.).,Medical Research Council-London Institute of Medical Sciences, Hammersmith Hospital Campus, United Kingdom (N.M.Q, S.A.C.).,Cardiovascular Research Centre, Royal Brompton and Harefield National Health Serfice Trust, London, United Kingdom (N.M.Q, P.J.R.B.)
| | - Chee Jian Pua
- National Heart Centre Singapore, Singapore (S.S., S.L., J.T., C.J.P., S.A.C.)
| | - Giuseppe D'Agostino
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore Medical School, Singapore (S.C., S.S., E.A., S.V., A.W., S.L., M.W., G.D., S.G.S., B.L.G., S.L., E.Y.C., E.C., J.D., S.A.C., O.J.L.R.)
| | - Shamini Guna Shekeran
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore Medical School, Singapore (S.C., S.S., E.A., S.V., A.W., S.L., M.W., G.D., S.G.S., B.L.G., S.L., E.Y.C., E.C., J.D., S.A.C., O.J.L.R.)
| | - Benjamin L George
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore Medical School, Singapore (S.C., S.S., E.A., S.V., A.W., S.L., M.W., G.D., S.G.S., B.L.G., S.L., E.Y.C., E.C., J.D., S.A.C., O.J.L.R.)
| | - Stella Lim
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore Medical School, Singapore (S.C., S.S., E.A., S.V., A.W., S.L., M.W., G.D., S.G.S., B.L.G., S.L., E.Y.C., E.C., J.D., S.A.C., O.J.L.R.).,National Heart Centre Singapore, Singapore (S.S., S.L., J.T., C.J.P., S.A.C.)
| | - Elaine Yiqun Cao
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore Medical School, Singapore (S.C., S.S., E.A., S.V., A.W., S.L., M.W., G.D., S.G.S., B.L.G., S.L., E.Y.C., E.C., J.D., S.A.C., O.J.L.R.)
| | - Sebastiaan van Heesch
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany (E.A., S.v.H., F.W., S.B., G.P., N.H.)
| | - Franziska Witte
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany (E.A., S.v.H., F.W., S.B., G.P., N.H.)
| | - Leanne E Felkin
- National Heart and Lung Institute, Imperial College London, United Kingdom (N.M.Q., L.E.F., P.J.R.B., S.A.C.)
| | - Eleni G Christodoulou
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore Medical School, Singapore (S.C., S.S., E.A., S.V., A.W., S.L., M.W., G.D., S.G.S., B.L.G., S.L., E.Y.C., E.C., J.D., S.A.C., O.J.L.R.)
| | - Jinrui Dong
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore Medical School, Singapore (S.C., S.S., E.A., S.V., A.W., S.L., M.W., G.D., S.G.S., B.L.G., S.L., E.Y.C., E.C., J.D., S.A.C., O.J.L.R.)
| | - Susanne Blachut
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany (E.A., S.v.H., F.W., S.B., G.P., N.H.)
| | - Giannino Patone
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany (E.A., S.v.H., F.W., S.B., G.P., N.H.)
| | - Paul J R Barton
- National Heart and Lung Institute, Imperial College London, United Kingdom (N.M.Q., L.E.F., P.J.R.B., S.A.C.).,Cardiovascular Research Centre, Royal Brompton and Harefield National Health Serfice Trust, London, United Kingdom (N.M.Q, P.J.R.B.)
| | - Norbert Hubner
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany (E.A., S.v.H., F.W., S.B., G.P., N.H.).,German Centre for Cardiovascular Research, partner site Berlin, Germany (N.H.).,Charité-Universitätsmedizin, Berlin, Germany (N.H.).,Berlin Institute of Health, Germany (N.H.)
| | - Stuart A Cook
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore Medical School, Singapore (S.C., S.S., E.A., S.V., A.W., S.L., M.W., G.D., S.G.S., B.L.G., S.L., E.Y.C., E.C., J.D., S.A.C., O.J.L.R.).,National Heart Centre Singapore, Singapore (S.S., S.L., J.T., C.J.P., S.A.C.).,National Heart and Lung Institute, Imperial College London, United Kingdom (N.M.Q., L.E.F., P.J.R.B., S.A.C.).,Medical Research Council-London Institute of Medical Sciences, Hammersmith Hospital Campus, United Kingdom (N.M.Q, S.A.C.)
| | - Owen J L Rackham
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore Medical School, Singapore (S.C., S.S., E.A., S.V., A.W., S.L., M.W., G.D., S.G.S., B.L.G., S.L., E.Y.C., E.C., J.D., S.A.C., O.J.L.R.)
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18
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Walsh R, Mazzarotto F, Whiffin N, Buchan R, Midwinter W, Wilk A, Li N, Felkin L, Ingold N, Govind R, Ahmad M, Mazaika E, Allouba M, Zhang X, de Marvao A, Day SM, Ashley E, Colan SD, Michels M, Pereira AC, Jacoby D, Ho CY, Thomson KL, Watkins H, Barton PJR, Olivotto I, Cook SA, Ware JS. Quantitative approaches to variant classification increase the yield and precision of genetic testing in Mendelian diseases: the case of hypertrophic cardiomyopathy. Genome Med 2019; 11:5. [PMID: 30696458 PMCID: PMC6350371 DOI: 10.1186/s13073-019-0616-z] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [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: 11/26/2018] [Accepted: 01/14/2019] [Indexed: 12/29/2022] Open
Abstract
Background International guidelines for variant interpretation in Mendelian disease set stringent criteria to report a variant as (likely) pathogenic, prioritising control of false-positive rate over test sensitivity and diagnostic yield. Genetic testing is also more likely informative in individuals with well-characterised variants from extensively studied European-ancestry populations. Inherited cardiomyopathies are relatively common Mendelian diseases that allow empirical calibration and assessment of this framework. Methods We compared rare variants in large hypertrophic cardiomyopathy (HCM) cohorts (up to 6179 cases) to reference populations to identify variant classes with high prior likelihoods of pathogenicity, as defined by etiological fraction (EF). We analysed the distribution of variants using a bespoke unsupervised clustering algorithm to identify gene regions in which variants are significantly clustered in cases. Results Analysis of variant distribution identified regions in which variants are significantly enriched in cases and variant location was a better discriminator of pathogenicity than generic computational functional prediction algorithms. Non-truncating variant classes with an EF ≥ 0.95 were identified in five established HCM genes. Applying this approach leads to an estimated 14–20% increase in cases with actionable HCM variants, i.e. variants classified as pathogenic/likely pathogenic that might be used for predictive testing in probands’ relatives. Conclusions When found in a patient confirmed to have disease, novel variants in some genes and regions are empirically shown to have a sufficiently high probability of pathogenicity to support a “likely pathogenic” classification, even without additional segregation or functional data. This could increase the yield of high confidence actionable variants, consistent with the framework and recommendations of current guidelines. The techniques outlined offer a consistent and unbiased approach to variant interpretation for Mendelian disease genetic testing. We propose adaptations to ACMG/AMP guidelines to incorporate such evidence in a quantitative and transparent manner. Electronic supplementary material The online version of this article (10.1186/s13073-019-0616-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Roddy Walsh
- Cardiovascular Research Centre, Cardiovascular Genetics and Genomics group at Royal Brompton Hospital and Harefield NHS Foundation Trust, Sydney Street, London, SW3 6NP, UK. .,National Heart and Lung Institute, Imperial College London, London, UK. .,Department of Experimental Cardiology, Amsterdam Cardiovascular Sciences, Amsterdam UMC, Amsterdam, Netherlands.
| | - Francesco Mazzarotto
- Cardiovascular Research Centre, Cardiovascular Genetics and Genomics group at Royal Brompton Hospital and Harefield NHS Foundation Trust, Sydney Street, London, SW3 6NP, UK.,Cardiomyopathy Unit, Careggi University Hospital, Florence, Italy.,Department of Clinical and Experimental Medicine, University of Florence, Florence, Italy
| | - Nicola Whiffin
- Cardiovascular Research Centre, Cardiovascular Genetics and Genomics group at Royal Brompton Hospital and Harefield NHS Foundation Trust, Sydney Street, London, SW3 6NP, UK.,National Heart and Lung Institute, Imperial College London, London, UK.,MRC London Institute of Medical Sciences, Imperial College London, London, UK
| | - Rachel Buchan
- Cardiovascular Research Centre, Cardiovascular Genetics and Genomics group at Royal Brompton Hospital and Harefield NHS Foundation Trust, Sydney Street, London, SW3 6NP, UK.,National Heart and Lung Institute, Imperial College London, London, UK
| | - William Midwinter
- Cardiovascular Research Centre, Cardiovascular Genetics and Genomics group at Royal Brompton Hospital and Harefield NHS Foundation Trust, Sydney Street, London, SW3 6NP, UK.,National Heart and Lung Institute, Imperial College London, London, UK
| | - Alicja Wilk
- Cardiovascular Research Centre, Cardiovascular Genetics and Genomics group at Royal Brompton Hospital and Harefield NHS Foundation Trust, Sydney Street, London, SW3 6NP, UK.,National Heart and Lung Institute, Imperial College London, London, UK
| | - Nicholas Li
- Cardiovascular Research Centre, Cardiovascular Genetics and Genomics group at Royal Brompton Hospital and Harefield NHS Foundation Trust, Sydney Street, London, SW3 6NP, UK.,MRC London Institute of Medical Sciences, Imperial College London, London, UK
| | - Leanne Felkin
- Cardiovascular Research Centre, Cardiovascular Genetics and Genomics group at Royal Brompton Hospital and Harefield NHS Foundation Trust, Sydney Street, London, SW3 6NP, UK.,National Heart and Lung Institute, Imperial College London, London, UK
| | - Nathan Ingold
- Cardiovascular Research Centre, Cardiovascular Genetics and Genomics group at Royal Brompton Hospital and Harefield NHS Foundation Trust, Sydney Street, London, SW3 6NP, UK
| | - Risha Govind
- Cardiovascular Research Centre, Cardiovascular Genetics and Genomics group at Royal Brompton Hospital and Harefield NHS Foundation Trust, Sydney Street, London, SW3 6NP, UK.,National Heart and Lung Institute, Imperial College London, London, UK
| | - Mian Ahmad
- Cardiovascular Research Centre, Cardiovascular Genetics and Genomics group at Royal Brompton Hospital and Harefield NHS Foundation Trust, Sydney Street, London, SW3 6NP, UK.,National Heart and Lung Institute, Imperial College London, London, UK
| | - Erica Mazaika
- Cardiovascular Research Centre, Cardiovascular Genetics and Genomics group at Royal Brompton Hospital and Harefield NHS Foundation Trust, Sydney Street, London, SW3 6NP, UK.,National Heart and Lung Institute, Imperial College London, London, UK
| | - Mona Allouba
- National Heart and Lung Institute, Imperial College London, London, UK.,Aswan Heart Centre, Aswan, Egypt
| | - Xiaolei Zhang
- Cardiovascular Research Centre, Cardiovascular Genetics and Genomics group at Royal Brompton Hospital and Harefield NHS Foundation Trust, Sydney Street, London, SW3 6NP, UK.,National Heart and Lung Institute, Imperial College London, London, UK
| | - Antonio de Marvao
- MRC London Institute of Medical Sciences, Imperial College London, London, UK
| | - Sharlene M Day
- Division of Cardiovascular Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Euan Ashley
- Division of Cardiovascular Medicine, Stanford University Medical Center, Stanford, CA, USA
| | - Steven D Colan
- Department of Cardiology, Boston Children's Hospital, Boston, MA, USA
| | - Michelle Michels
- Department of Cardiology, Thoraxcenter, Erasmus MC Rotterdam, Rotterdam, Netherlands
| | - Alexandre C Pereira
- Heart Institute (InCor), University of Sao Paulo Medical School, Sao Paulo, Brazil
| | | | - Carolyn Y Ho
- Cardiovascular Division, Brigham and Women's Hospital, Boston, MA, USA
| | - Kate L Thomson
- Oxford Medical Genetics Laboratory, Oxford University Hospitals NHS Foundation Trust, The Churchill Hospital, Oxford, UK.,Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Hugh Watkins
- Radcliffe Department of Medicine, University of Oxford, Oxford, UK.,The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Paul J R Barton
- Cardiovascular Research Centre, Cardiovascular Genetics and Genomics group at Royal Brompton Hospital and Harefield NHS Foundation Trust, Sydney Street, London, SW3 6NP, UK.,National Heart and Lung Institute, Imperial College London, London, UK
| | - Iacopo Olivotto
- Cardiomyopathy Unit, Careggi University Hospital, Florence, Italy
| | - Stuart A Cook
- Cardiovascular Research Centre, Cardiovascular Genetics and Genomics group at Royal Brompton Hospital and Harefield NHS Foundation Trust, Sydney Street, London, SW3 6NP, UK.,National Heart and Lung Institute, Imperial College London, London, UK.,National Heart Centre Singapore, Singapore, Singapore.,Duke-National University of Singapore, Singapore, Singapore
| | - James S Ware
- Cardiovascular Research Centre, Cardiovascular Genetics and Genomics group at Royal Brompton Hospital and Harefield NHS Foundation Trust, Sydney Street, London, SW3 6NP, UK. .,National Heart and Lung Institute, Imperial College London, London, UK. .,MRC London Institute of Medical Sciences, Imperial College London, London, UK.
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19
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Affiliation(s)
- Leanne E Felkin
- National Heart and Lung Institute, Imperial College London, England
| | - Roddy Walsh
- National Institute for Health Research Biomedical Research Unit in Cardiovascular Disease at Royal Brompton and Harefield National Health Service Foundation Trust and Imperial College London, London, England
| | - James S Ware
- National Heart and Lung Institute, Imperial College London, England
| | - Magdi H Yacoub
- National Heart and Lung Institute, Imperial College London, England
| | | | - Paul J R Barton
- National Institute for Health Research Biomedical Research Unit in Cardiovascular Disease at Royal Brompton and Harefield National Health Service Foundation Trust and Imperial College London, London, England
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20
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Whiffin N, Walsh R, Govind R, Edwards M, Ahmad M, Zhang X, Tayal U, Buchan R, Midwinter W, Wilk AE, Najgebauer H, Francis C, Wilkinson S, Monk T, Brett L, O'Regan DP, Prasad SK, Morris-Rosendahl DJ, Barton PJR, Edwards E, Ware JS, Cook SA. CardioClassifier: disease- and gene-specific computational decision support for clinical genome interpretation. Genet Med 2018; 20:1246-1254. [PMID: 29369293 DOI: 10.1038/gim.2017.258] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [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: 09/01/2017] [Accepted: 12/05/2017] [Indexed: 11/10/2022] Open
Abstract
PURPOSE Internationally adopted variant interpretation guidelines from the American College of Medical Genetics and Genomics (ACMG) are generic and require disease-specific refinement. Here we developed CardioClassifier ( http://www.cardioclassifier.org ), a semiautomated decision-support tool for inherited cardiac conditions (ICCs). METHODS CardioClassifier integrates data retrieved from multiple sources with user-input case-specific information, through an interactive interface, to support variant interpretation. Combining disease- and gene-specific knowledge with variant observations in large cohorts of cases and controls, we refined 14 computational ACMG criteria and created three ICC-specific rules. RESULTS We benchmarked CardioClassifier on 57 expertly curated variants and show full retrieval of all computational data, concordantly activating 87.3% of rules. A generic annotation tool identified fewer than half as many clinically actionable variants (64/219 vs. 156/219, Fisher's P = 1.1 × 10-18), with important false positives, illustrating the critical importance of disease and gene-specific annotations. CardioClassifier identified putatively disease-causing variants in 33.7% of 327 cardiomyopathy cases, comparable with leading ICC laboratories. Through addition of manually curated data, variants found in over 40% of cardiomyopathy cases are fully annotated, without requiring additional user-input data. CONCLUSION CardioClassifier is an ICC-specific decision-support tool that integrates expertly curated computational annotations with case-specific data to generate fast, reproducible, and interactive variant pathogenicity reports, according to best practice guidelines.
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Affiliation(s)
- Nicola Whiffin
- National Heart & Lung Institute, Imperial College London, London, UK. .,Cardiovascular Research Centre at Royal Brompton and Harefield NHS Foundation Trust, London, UK. .,MRC London Institute of Medical Sciences, Imperial College London, London, UK.
| | - Roddy Walsh
- National Heart & Lung Institute, Imperial College London, London, UK.,Cardiovascular Research Centre at Royal Brompton and Harefield NHS Foundation Trust, London, UK
| | - Risha Govind
- National Heart & Lung Institute, Imperial College London, London, UK.,Cardiovascular Research Centre at Royal Brompton and Harefield NHS Foundation Trust, London, UK
| | - Matthew Edwards
- Clinical Genetics and Genomics Laboratory, Royal Brompton and Harefield NHS Foundation Trust, London, UK
| | - Mian Ahmad
- National Heart & Lung Institute, Imperial College London, London, UK.,Cardiovascular Research Centre at Royal Brompton and Harefield NHS Foundation Trust, London, UK
| | - Xiaolei Zhang
- National Heart & Lung Institute, Imperial College London, London, UK.,Cardiovascular Research Centre at Royal Brompton and Harefield NHS Foundation Trust, London, UK
| | - Upasana Tayal
- National Heart & Lung Institute, Imperial College London, London, UK.,Cardiovascular Research Centre at Royal Brompton and Harefield NHS Foundation Trust, London, UK
| | - Rachel Buchan
- National Heart & Lung Institute, Imperial College London, London, UK.,Cardiovascular Research Centre at Royal Brompton and Harefield NHS Foundation Trust, London, UK
| | - William Midwinter
- National Heart & Lung Institute, Imperial College London, London, UK.,Cardiovascular Research Centre at Royal Brompton and Harefield NHS Foundation Trust, London, UK
| | - Alicja E Wilk
- National Heart & Lung Institute, Imperial College London, London, UK.,Cardiovascular Research Centre at Royal Brompton and Harefield NHS Foundation Trust, London, UK
| | - Hanna Najgebauer
- National Heart & Lung Institute, Imperial College London, London, UK.,Cardiovascular Research Centre at Royal Brompton and Harefield NHS Foundation Trust, London, UK
| | - Catherine Francis
- National Heart & Lung Institute, Imperial College London, London, UK.,Cardiovascular Research Centre at Royal Brompton and Harefield NHS Foundation Trust, London, UK
| | - Sam Wilkinson
- Clinical Genetics and Genomics Laboratory, Royal Brompton and Harefield NHS Foundation Trust, London, UK
| | - Thomas Monk
- Clinical Genetics and Genomics Laboratory, Royal Brompton and Harefield NHS Foundation Trust, London, UK
| | - Laura Brett
- Clinical Genetics and Genomics Laboratory, Royal Brompton and Harefield NHS Foundation Trust, London, UK
| | - Declan P O'Regan
- MRC London Institute of Medical Sciences, Imperial College London, London, UK
| | - Sanjay K Prasad
- National Heart & Lung Institute, Imperial College London, London, UK.,Cardiovascular Research Centre at Royal Brompton and Harefield NHS Foundation Trust, London, UK
| | - Deborah J Morris-Rosendahl
- National Heart & Lung Institute, Imperial College London, London, UK.,Clinical Genetics and Genomics Laboratory, Royal Brompton and Harefield NHS Foundation Trust, London, UK
| | - Paul J R Barton
- National Heart & Lung Institute, Imperial College London, London, UK.,Cardiovascular Research Centre at Royal Brompton and Harefield NHS Foundation Trust, London, UK
| | - Elizabeth Edwards
- National Heart & Lung Institute, Imperial College London, London, UK.,Cardiovascular Research Centre at Royal Brompton and Harefield NHS Foundation Trust, London, UK
| | - James S Ware
- National Heart & Lung Institute, Imperial College London, London, UK.,Cardiovascular Research Centre at Royal Brompton and Harefield NHS Foundation Trust, London, UK.,MRC London Institute of Medical Sciences, Imperial College London, London, UK
| | - Stuart A Cook
- National Heart & Lung Institute, Imperial College London, London, UK.,Cardiovascular Research Centre at Royal Brompton and Harefield NHS Foundation Trust, London, UK.,National Heart Centre Singapore, Singapore, Singapore.,Duke-National University of Singapore, Singapore, Singapore
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21
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Whiffin N, Minikel E, Walsh R, O'Donnell-Luria AH, Karczewski K, Ing AY, Barton PJR, Funke B, Cook SA, MacArthur D, Ware JS. Using high-resolution variant frequencies to empower clinical genome interpretation. Genet Med 2017; 19:1151-1158. [PMID: 28518168 PMCID: PMC5563454 DOI: 10.1038/gim.2017.26] [Citation(s) in RCA: 280] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Accepted: 02/02/2017] [Indexed: 02/06/2023] Open
Abstract
Purpose Whole-exome and whole-genome sequencing have transformed the discovery of genetic variants that cause human Mendelian disease, but discriminating pathogenic from benign variants remains a daunting challenge. Rarity is recognized as a necessary, although not sufficient, criterion for pathogenicity, but frequency cutoffs used in Mendelian analysis are often arbitrary and overly lenient. Recent very large reference datasets, such as the Exome Aggregation Consortium (ExAC), provide an unprecedented opportunity to obtain robust frequency estimates even for very rare variants. Methods We present a statistical framework for the frequency-based filtering of candidate disease-causing variants, accounting for disease prevalence, genetic and allelic heterogeneity, inheritance mode, penetrance, and sampling variance in reference datasets. Results Using the example of cardiomyopathy, we show that our approach reduces by two-thirds the number of candidate variants under consideration in the average exome, without removing true pathogenic variants (false-positive rate<0.001). Conclusion We outline a statistically robust framework for assessing whether a variant is “too common” to be causative for a Mendelian disorder of interest. We present precomputed allele frequency cutoffs for all variants in the ExAC dataset.
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Affiliation(s)
- Nicola Whiffin
- Cardiovascular Genetics and Genomics, National Heart and Lung Institute, Imperial College London, London, UK.,NIHR Royal Brompton Cardiovascular Biomedical Research Unit, Royal Brompton &Harefield Hospitals &Imperial College London, London, UK
| | - Eric Minikel
- Analytic &Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts, USA.,Program in Medical and Population Genetics, Broad Institute of MIT &Harvard, Cambridge, Massachusetts, USA
| | - Roddy Walsh
- Cardiovascular Genetics and Genomics, National Heart and Lung Institute, Imperial College London, London, UK.,NIHR Royal Brompton Cardiovascular Biomedical Research Unit, Royal Brompton &Harefield Hospitals &Imperial College London, London, UK
| | - Anne H O'Donnell-Luria
- Analytic &Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts, USA.,Program in Medical and Population Genetics, Broad Institute of MIT &Harvard, Cambridge, Massachusetts, USA
| | - Konrad Karczewski
- Analytic &Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts, USA.,Program in Medical and Population Genetics, Broad Institute of MIT &Harvard, Cambridge, Massachusetts, USA
| | - Alexander Y Ing
- Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine, Cambridge, Massachusetts, USA.,Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Paul J R Barton
- Cardiovascular Genetics and Genomics, National Heart and Lung Institute, Imperial College London, London, UK.,NIHR Royal Brompton Cardiovascular Biomedical Research Unit, Royal Brompton &Harefield Hospitals &Imperial College London, London, UK
| | - Birgit Funke
- Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine, Cambridge, Massachusetts, USA.,Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Stuart A Cook
- Cardiovascular Genetics and Genomics, National Heart and Lung Institute, Imperial College London, London, UK.,NIHR Royal Brompton Cardiovascular Biomedical Research Unit, Royal Brompton &Harefield Hospitals &Imperial College London, London, UK.,National Heart Centre Singapore, Singapore, Singapore.,Duke-National University of Singapore, Singapore, Singapore
| | - Daniel MacArthur
- Analytic &Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts, USA.,Program in Medical and Population Genetics, Broad Institute of MIT &Harvard, Cambridge, Massachusetts, USA.,Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - James S Ware
- Cardiovascular Genetics and Genomics, National Heart and Lung Institute, Imperial College London, London, UK.,NIHR Royal Brompton Cardiovascular Biomedical Research Unit, Royal Brompton &Harefield Hospitals &Imperial College London, London, UK.,Program in Medical and Population Genetics, Broad Institute of MIT &Harvard, Cambridge, Massachusetts, USA.,MRC London Institute of Medical Sciences, Imperial College London, London, UK
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22
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Rea G, Homfray T, Till J, Roses-Noguer F, Buchan RJ, Wilkinson S, Wilk A, Walsh R, John S, McKee S, Stewart FJ, Murday V, Taylor RW, Ashworth M, Baksi AJ, Daubeney P, Prasad S, Barton PJR, Cook SA, Ware JS. Histiocytoid cardiomyopathy and microphthalmia with linear skin defects syndrome: phenotypes linked by truncating variants in NDUFB11. Cold Spring Harb Mol Case Stud 2017; 3:a001271. [PMID: 28050600 PMCID: PMC5171697 DOI: 10.1101/mcs.a001271] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Accepted: 10/20/2016] [Indexed: 12/30/2022] Open
Abstract
Variants in NDUFB11, which encodes a structural component of complex I of the mitochondrial respiratory chain (MRC), were recently independently reported to cause histiocytoid cardiomyopathy (histiocytoid CM) and microphthalmia with linear skin defects syndrome (MLS syndrome). Here we report an additional case of histiocytoid CM, which carries a de novo nonsense variant in NDUFB11 (ENST00000276062.8: c.262C > T; p.[Arg88*]) identified using whole-exome sequencing (WES) of a family trio. An identical variant has been previously reported in association with MLS syndrome. The case we describe here lacked the diagnostic features of MLS syndrome, but a detailed clinical comparison of the two cases revealed significant phenotypic overlap. Heterozygous variants in HCCS (which encodes an important mitochondrially targeted protein) and COX7B, which, like NDUFB11, encodes a protein of the MRC, have also previously been identified in MLS syndrome including a case with features of both MLS syndrome and histiocytoid CM. However, a systematic review of WES data from previously published histiocytoid CM cases, alongside four additional cases presented here for the first time, did not identify any variants in these genes. We conclude that NDUFB11 variants play a role in the pathogenesis of both histiocytoid CM and MLS and that these disorders are allelic (genetically related).
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Affiliation(s)
- Gillian Rea
- NIHR Cardiovascular Biomedical Research Unit at Royal Brompton and Harefield NHS Foundation Trust and Imperial College London, London SW3 6NP, United Kingdom
- National Heart and Lung Institute, Imperial College London, London SW3 6NP, United Kingdom
- Northern Ireland Regional Genetics Service, Belfast City Hospital, Belfast, BT9 7AB, United Kingdom
| | - Tessa Homfray
- Royal Brompton and Harefield NHS Foundation Trust, London SW3 6NP, United Kingdom
| | - Jan Till
- Royal Brompton and Harefield NHS Foundation Trust, London SW3 6NP, United Kingdom
| | - Ferran Roses-Noguer
- Royal Brompton and Harefield NHS Foundation Trust, London SW3 6NP, United Kingdom
| | - Rachel J Buchan
- NIHR Cardiovascular Biomedical Research Unit at Royal Brompton and Harefield NHS Foundation Trust and Imperial College London, London SW3 6NP, United Kingdom
- National Heart and Lung Institute, Imperial College London, London SW3 6NP, United Kingdom
| | - Sam Wilkinson
- NIHR Cardiovascular Biomedical Research Unit at Royal Brompton and Harefield NHS Foundation Trust and Imperial College London, London SW3 6NP, United Kingdom
- National Heart and Lung Institute, Imperial College London, London SW3 6NP, United Kingdom
| | - Alicja Wilk
- NIHR Cardiovascular Biomedical Research Unit at Royal Brompton and Harefield NHS Foundation Trust and Imperial College London, London SW3 6NP, United Kingdom
- National Heart and Lung Institute, Imperial College London, London SW3 6NP, United Kingdom
| | - Roddy Walsh
- NIHR Cardiovascular Biomedical Research Unit at Royal Brompton and Harefield NHS Foundation Trust and Imperial College London, London SW3 6NP, United Kingdom
- National Heart and Lung Institute, Imperial College London, London SW3 6NP, United Kingdom
| | - Shibu John
- NIHR Cardiovascular Biomedical Research Unit at Royal Brompton and Harefield NHS Foundation Trust and Imperial College London, London SW3 6NP, United Kingdom
- National Heart and Lung Institute, Imperial College London, London SW3 6NP, United Kingdom
| | - Shane McKee
- Northern Ireland Regional Genetics Service, Belfast City Hospital, Belfast, BT9 7AB, United Kingdom
| | - Fiona J Stewart
- Northern Ireland Regional Genetics Service, Belfast City Hospital, Belfast, BT9 7AB, United Kingdom
| | - Victoria Murday
- Department of Clinical Genetics, Laboratory Medicine, The Queen Elizabeth University Hospital, Glasgow G51 4TF, United Kingdom
| | - Robert W Taylor
- Wellcome Trust Centre for Mitochondrial Research, Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, NE2 4HH, United Kingdom
| | - Michael Ashworth
- Histopathology Department, Camelia Botnar Laboratories, Great Ormond Street Hospital for Children NHS Trust, London WC1N 3JH, United Kingdom
| | - A John Baksi
- Royal Brompton and Harefield NHS Foundation Trust, London SW3 6NP, United Kingdom
| | - Piers Daubeney
- National Heart and Lung Institute, Imperial College London, London SW3 6NP, United Kingdom
- Royal Brompton and Harefield NHS Foundation Trust, London SW3 6NP, United Kingdom
| | - Sanjay Prasad
- NIHR Cardiovascular Biomedical Research Unit at Royal Brompton and Harefield NHS Foundation Trust and Imperial College London, London SW3 6NP, United Kingdom
- Royal Brompton and Harefield NHS Foundation Trust, London SW3 6NP, United Kingdom
| | - Paul J R Barton
- NIHR Cardiovascular Biomedical Research Unit at Royal Brompton and Harefield NHS Foundation Trust and Imperial College London, London SW3 6NP, United Kingdom
- National Heart and Lung Institute, Imperial College London, London SW3 6NP, United Kingdom
| | - Stuart A Cook
- National Heart and Lung Institute, Imperial College London, London SW3 6NP, United Kingdom
- MRC Clinical Sciences Centre, Imperial College London, London W12 0NN, United Kingdom
- National Heart Centre Singapore, Singapore 169609, Singapore
| | - James S Ware
- NIHR Cardiovascular Biomedical Research Unit at Royal Brompton and Harefield NHS Foundation Trust and Imperial College London, London SW3 6NP, United Kingdom
- National Heart and Lung Institute, Imperial College London, London SW3 6NP, United Kingdom
- MRC Clinical Sciences Centre, Imperial College London, London W12 0NN, United Kingdom
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23
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Gómez-Salinero JM, López-Olañeta MM, Ortiz-Sánchez P, Larrasa-Alonso J, Gatto A, Felkin LE, Barton PJR, Navarro-Lérida I, Del Pozo MÁ, García-Pavía P, Sundararaman B, Giovinazo G, Yeo GW, Lara-Pezzi E. The Calcineurin Variant CnAβ1 Controls Mouse Embryonic Stem Cell Differentiation by Directing mTORC2 Membrane Localization and Activation. Cell Chem Biol 2016; 23:1372-1382. [PMID: 27746127 DOI: 10.1016/j.chembiol.2016.09.010] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [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: 03/17/2016] [Revised: 08/28/2016] [Accepted: 09/02/2016] [Indexed: 12/11/2022]
Abstract
Embryonic stem cells (ESC) have the potential to generate all the cell lineages that form the body. However, the molecular mechanisms underlying ESC differentiation and especially the role of alternative splicing in this process remain poorly understood. Here, we show that the alternative splicing regulator MBNL1 promotes generation of the atypical calcineurin Aβ variant CnAβ1 in mouse ESCs (mESC). CnAβ1 has a unique C-terminal domain that drives its localization mainly to the Golgi apparatus by interacting with Cog8. CnAβ1 regulates the intracellular localization and activation of the mTORC2 complex. CnAβ1 knockdown results in delocalization of mTORC2 from the membrane to the cytoplasm, inactivation of the AKT/GSK3β/β-catenin signaling pathway, and defective mesoderm specification. In summary, here we unveil the structural basis for the mechanism of action of CnAβ1 and its role in the differentiation of mESCs to the mesodermal lineage.
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Affiliation(s)
- Jesús M Gómez-Salinero
- Myocardial Pathophysiology Program, Fundación Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), 28029 Madrid, Spain
| | - Marina M López-Olañeta
- Myocardial Pathophysiology Program, Fundación Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), 28029 Madrid, Spain
| | - Paula Ortiz-Sánchez
- Myocardial Pathophysiology Program, Fundación Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), 28029 Madrid, Spain
| | - Javier Larrasa-Alonso
- Myocardial Pathophysiology Program, Fundación Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), 28029 Madrid, Spain
| | - Alberto Gatto
- Myocardial Pathophysiology Program, Fundación Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), 28029 Madrid, Spain
| | - Leanne E Felkin
- National Heart and Lung Institute, Imperial College London, London SW7 2AZ, UK
| | - Paul J R Barton
- National Heart and Lung Institute, Imperial College London, London SW7 2AZ, UK; NIHR Cardiovascular Biomedical Research Unit, Royal Brompton and Harefield NHS Foundation Trust, London SW7 2AZ, UK
| | - Inmaculada Navarro-Lérida
- Vascular Pathophysiology Program, Fundación Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), 28029 Madrid, Spain
| | - Miguel Ángel Del Pozo
- Vascular Pathophysiology Program, Fundación Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), 28029 Madrid, Spain
| | - Pablo García-Pavía
- Heart Failure and Inherited Cardiac Diseases Unit, Department of Cardiology, Hospital Universitario Puerta de Hierro Majadahonda, 28222 Madrid, Spain
| | - Balaji Sundararaman
- Sanford Consortium for Regenerative Medicine, University of California San Diego (UCSD), La Jolla, CA 92037, USA
| | - Giovanna Giovinazo
- Pluripotent Cell Technology Unit, Fundación Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), 28029 Madrid, Spain
| | - Gene W Yeo
- Sanford Consortium for Regenerative Medicine, University of California San Diego (UCSD), La Jolla, CA 92037, USA
| | - Enrique Lara-Pezzi
- Myocardial Pathophysiology Program, Fundación Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), 28029 Madrid, Spain; National Heart and Lung Institute, Imperial College London, London SW7 2AZ, UK.
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24
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Roberts AM, Ware JS, Herman DS, Schafer S, Baksi J, Bick AG, Buchan RJ, Walsh R, John S, Wilkinson S, Mazzarotto F, Felkin LE, Gong S, MacArthur JAL, Cunningham F, Flannick J, Gabriel SB, Altshuler DM, Macdonald PS, Heinig M, Keogh AM, Hayward CS, Banner NR, Pennell DJ, O'Regan DP, San TR, de Marvao A, Dawes TJW, Gulati A, Birks EJ, Yacoub MH, Radke M, Gotthardt M, Wilson JG, O'Donnell CJ, Prasad SK, Barton PJR, Fatkin D, Hubner N, Seidman JG, Seidman CE, Cook SA. Integrated allelic, transcriptional, and phenomic dissection of the cardiac effects of titin truncations in health and disease. Sci Transl Med 2015; 7:270ra6. [PMID: 25589632 DOI: 10.1126/scitranslmed.3010134] [Citation(s) in RCA: 321] [Impact Index Per Article: 35.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The recent discovery of heterozygous human mutations that truncate full-length titin (TTN, an abundant structural, sensory, and signaling filament in muscle) as a common cause of end-stage dilated cardiomyopathy (DCM) promises new prospects for improving heart failure management. However, realization of this opportunity has been hindered by the burden of TTN-truncating variants (TTNtv) in the general population and uncertainty about their consequences in health or disease. To elucidate the effects of TTNtv, we coupled TTN gene sequencing with cardiac phenotyping in 5267 individuals across the spectrum of cardiac physiology and integrated these data with RNA and protein analyses of human heart tissues. We report diversity of TTN isoform expression in the heart, define the relative inclusion of TTN exons in different isoforms (using the TTN transcript annotations available at http://cardiodb.org/titin), and demonstrate that these data, coupled with the position of the TTNtv, provide a robust strategy to discriminate pathogenic from benign TTNtv. We show that TTNtv is the most common genetic cause of DCM in ambulant patients in the community, identify clinically important manifestations of TTNtv-positive DCM, and define the penetrance and outcomes of TTNtv in the general population. By integrating genetic, transcriptome, and protein analyses, we provide evidence for a length-dependent mechanism of disease. These data inform diagnostic criteria and management strategies for TTNtv-positive DCM patients and for TTNtv that are identified as incidental findings.
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Affiliation(s)
- Angharad M Roberts
- Clinical Sciences Centre, Medical Research Council (MRC), Imperial College London, London W12 0NN, UK. National Institute for Health Research (NIHR) Cardiovascular Biomedical Research Unit at Royal Brompton & Harefield National Health Service (NHS) Foundation Trust and Imperial College London, London SW3 6NP, UK
| | - James S Ware
- National Institute for Health Research (NIHR) Cardiovascular Biomedical Research Unit at Royal Brompton & Harefield National Health Service (NHS) Foundation Trust and Imperial College London, London SW3 6NP, UK. National Heart & Lung Institute, Imperial College London, London SW3 6NP, UK. Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Daniel S Herman
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA 02142, USA. Department of Laboratory Medicine, University of Washington, Seattle, WA 98195, USA
| | - Sebastian Schafer
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany
| | - John Baksi
- National Institute for Health Research (NIHR) Cardiovascular Biomedical Research Unit at Royal Brompton & Harefield National Health Service (NHS) Foundation Trust and Imperial College London, London SW3 6NP, UK
| | - Alexander G Bick
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Rachel J Buchan
- National Institute for Health Research (NIHR) Cardiovascular Biomedical Research Unit at Royal Brompton & Harefield National Health Service (NHS) Foundation Trust and Imperial College London, London SW3 6NP, UK
| | - Roddy Walsh
- National Institute for Health Research (NIHR) Cardiovascular Biomedical Research Unit at Royal Brompton & Harefield National Health Service (NHS) Foundation Trust and Imperial College London, London SW3 6NP, UK
| | - Shibu John
- National Institute for Health Research (NIHR) Cardiovascular Biomedical Research Unit at Royal Brompton & Harefield National Health Service (NHS) Foundation Trust and Imperial College London, London SW3 6NP, UK
| | - Samuel Wilkinson
- National Institute for Health Research (NIHR) Cardiovascular Biomedical Research Unit at Royal Brompton & Harefield National Health Service (NHS) Foundation Trust and Imperial College London, London SW3 6NP, UK
| | - Francesco Mazzarotto
- National Institute for Health Research (NIHR) Cardiovascular Biomedical Research Unit at Royal Brompton & Harefield National Health Service (NHS) Foundation Trust and Imperial College London, London SW3 6NP, UK. National Heart & Lung Institute, Imperial College London, London SW3 6NP, UK
| | - Leanne E Felkin
- National Institute for Health Research (NIHR) Cardiovascular Biomedical Research Unit at Royal Brompton & Harefield National Health Service (NHS) Foundation Trust and Imperial College London, London SW3 6NP, UK. National Heart & Lung Institute, Imperial College London, London SW3 6NP, UK
| | - Sungsam Gong
- National Institute for Health Research (NIHR) Cardiovascular Biomedical Research Unit at Royal Brompton & Harefield National Health Service (NHS) Foundation Trust and Imperial College London, London SW3 6NP, UK
| | - Jacqueline A L MacArthur
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK
| | - Fiona Cunningham
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK
| | - Jason Flannick
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA 02142, USA. Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Stacey B Gabriel
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - David M Altshuler
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA 02142, USA. Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Peter S Macdonald
- Cardiology Department, St Vincent's Hospital, Darlinghurst, New South Wales 2010, Australia. Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales 2010, Australia. Faculty of Medicine, University of New South Wales, Kensington, New South Wales 2052, Australia
| | - Matthias Heinig
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany
| | - Anne M Keogh
- Cardiology Department, St Vincent's Hospital, Darlinghurst, New South Wales 2010, Australia. Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales 2010, Australia. Faculty of Medicine, University of New South Wales, Kensington, New South Wales 2052, Australia
| | - Christopher S Hayward
- Cardiology Department, St Vincent's Hospital, Darlinghurst, New South Wales 2010, Australia. Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales 2010, Australia. Faculty of Medicine, University of New South Wales, Kensington, New South Wales 2052, Australia
| | - Nicholas R Banner
- National Heart & Lung Institute, Imperial College London, London SW3 6NP, UK. Royal Brompton & Harefield NHS Foundation Trust, Harefield Hospital, Hill End Road, Harefield, Middlesex UB9 6JH, UK
| | - Dudley J Pennell
- National Institute for Health Research (NIHR) Cardiovascular Biomedical Research Unit at Royal Brompton & Harefield National Health Service (NHS) Foundation Trust and Imperial College London, London SW3 6NP, UK. National Heart & Lung Institute, Imperial College London, London SW3 6NP, UK
| | - Declan P O'Regan
- Clinical Sciences Centre, Medical Research Council (MRC), Imperial College London, London W12 0NN, UK
| | - Tan Ru San
- National Heart Centre Singapore, Singapore 169609, Singapore
| | - Antonio de Marvao
- Clinical Sciences Centre, Medical Research Council (MRC), Imperial College London, London W12 0NN, UK
| | - Timothy J W Dawes
- Clinical Sciences Centre, Medical Research Council (MRC), Imperial College London, London W12 0NN, UK
| | - Ankur Gulati
- National Institute for Health Research (NIHR) Cardiovascular Biomedical Research Unit at Royal Brompton & Harefield National Health Service (NHS) Foundation Trust and Imperial College London, London SW3 6NP, UK
| | - Emma J Birks
- National Heart & Lung Institute, Imperial College London, London SW3 6NP, UK. Department of Medicine, University of Louisville and Jewish Hospital, Louisville, KY 40202, USA
| | - Magdi H Yacoub
- National Heart & Lung Institute, Imperial College London, London SW3 6NP, UK
| | - Michael Radke
- Neuromuscular and Cardiovascular Cell Biology, Max Delbrück Center for Molecular Medicine, 13092 Berlin, Germany
| | - Michael Gotthardt
- Neuromuscular and Cardiovascular Cell Biology, Max Delbrück Center for Molecular Medicine, 13092 Berlin, Germany. German Centre for Cardiovascular Research, 13347 Berlin, Germany
| | - James G Wilson
- Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Christopher J O'Donnell
- National Heart, Lung, and Blood Institute's Framingham Heart Study, Framingham, MA 01702, USA. Division of Intramural Research, National Heart, Lung, and Blood Institute, Bethesda, MD 20892, USA
| | - Sanjay K Prasad
- National Institute for Health Research (NIHR) Cardiovascular Biomedical Research Unit at Royal Brompton & Harefield National Health Service (NHS) Foundation Trust and Imperial College London, London SW3 6NP, UK
| | - Paul J R Barton
- National Institute for Health Research (NIHR) Cardiovascular Biomedical Research Unit at Royal Brompton & Harefield National Health Service (NHS) Foundation Trust and Imperial College London, London SW3 6NP, UK. National Heart & Lung Institute, Imperial College London, London SW3 6NP, UK
| | - Diane Fatkin
- Cardiology Department, St Vincent's Hospital, Darlinghurst, New South Wales 2010, Australia. Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales 2010, Australia. Faculty of Medicine, University of New South Wales, Kensington, New South Wales 2052, Australia
| | - Norbert Hubner
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany. German Centre for Cardiovascular Research, 13347 Berlin, Germany. Charité-Universitätsmedizin, 10117 Berlin, Germany
| | | | - Christine E Seidman
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA 02142, USA. Cardiovascular Division, Brigham and Women's Hospital, Boston, MA 02115, USA. Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.
| | - Stuart A Cook
- Clinical Sciences Centre, Medical Research Council (MRC), Imperial College London, London W12 0NN, UK. National Heart & Lung Institute, Imperial College London, London SW3 6NP, UK. National Heart Centre Singapore, Singapore 169609, Singapore. Duke-National University of Singapore, Singapore 169857, Singapore.
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25
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Buyandelger B, Mansfield C, Kostin S, Choi O, Roberts AM, Ware JS, Mazzarotto F, Pesce F, Buchan R, Isaacson RL, Vouffo J, Gunkel S, Knöll G, McSweeney SJ, Wei H, Perrot A, Pfeiffer C, Toliat MR, Ilieva K, Krysztofinska E, López-Olañeta MM, Gómez-Salinero JM, Schmidt A, Ng KE, Teucher N, Chen J, Teichmann M, Eilers M, Haverkamp W, Regitz-Zagrosek V, Hasenfuss G, Braun T, Pennell DJ, Gould I, Barton PJR, Lara-Pezzi E, Schäfer S, Hübner N, Felkin LE, O'Regan DP, Brand T, Milting H, Nürnberg P, Schneider MD, Prasad S, Petretto E, Knöll R. ZBTB17 (MIZ1) Is Important for the Cardiac Stress Response and a Novel Candidate Gene for Cardiomyopathy and Heart Failure. ACTA ACUST UNITED AC 2015; 8:643-52. [PMID: 26175529 DOI: 10.1161/circgenetics.113.000690] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Accepted: 07/02/2015] [Indexed: 12/30/2022]
Abstract
BACKGROUND Mutations in sarcomeric and cytoskeletal proteins are a major cause of hereditary cardiomyopathies, but our knowledge remains incomplete as to how the genetic defects execute their effects. METHODS AND RESULTS We used cysteine and glycine-rich protein 3, a known cardiomyopathy gene, in a yeast 2-hybrid screen and identified zinc-finger and BTB domain-containing protein 17 (ZBTB17) as a novel interacting partner. ZBTB17 is a transcription factor that contains the peak association signal (rs10927875) at the replicated 1p36 cardiomyopathy locus. ZBTB17 expression protected cardiac myocytes from apoptosis in vitro and in a mouse model with cardiac myocyte-specific deletion of Zbtb17, which develops cardiomyopathy and fibrosis after biomechanical stress. ZBTB17 also regulated cardiac myocyte hypertrophy in vitro and in vivo in a calcineurin-dependent manner. CONCLUSIONS We revealed new functions for ZBTB17 in the heart, a transcription factor that may play a role as a novel cardiomyopathy gene.
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26
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Smolenski RT, Rybakowska I, Turyn J, Romaszko P, Zabielska M, Taegtmeyer A, Słomińska EM, Kaletha KK, Barton PJR. AMP deaminase 1 gene polymorphism and heart disease-a genetic association that highlights new treatment. Cardiovasc Drugs Ther 2014; 28:183-9. [PMID: 24431031 PMCID: PMC3955129 DOI: 10.1007/s10557-013-6506-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Nucleotide metabolism and signalling is directly linked to myocardial function. Therefore analysis how diversity of genes coding nucleotide metabolism related proteins affects clinical progress of heart disease could provide valuable information for development of new treatments. Several studies identified that polymorphism of AMP deaminase 1 gene (AMPD1), in particular the common C34T variant of this gene was found to benefit patients with heart failure and ischemic heart disease. However, these findings were inconsistent in subsequent studies. This prompted our detailed analysis of heart transplant recipients that revealed diverse effect: improved early postoperative cardiac function associated with C34T mutation in donors, but worse 1-year survival. Our other studies on the metabolic impact of AMPD1 C34T mutation revealed decrease in AMPD activity, increased production of adenosine and de-inhibition of AMP regulated protein kinase. Thus, genetic, clinical and biochemical studies revealed that while long term attenuation of AMPD activity could be deleterious, transient inhibition of AMPD activity before acute cardiac injury is protective. We suggest therefore that pharmacological inhibition of AMP deaminase before transient ischemic event such as during ischemic heart disease or cardiac surgery could provide therapeutic benefit.
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Affiliation(s)
- Ryszard T Smolenski
- Department of Biochemistry, Medical University of Gdansk, Debinki 1, 80-211, Gdansk, Poland,
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27
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Maatz H, Jens M, Liss M, Schafer S, Heinig M, Kirchner M, Adami E, Rintisch C, Dauksaite V, Radke MH, Selbach M, Barton PJR, Cook SA, Rajewsky N, Gotthardt M, Landthaler M, Hubner N. RNA-binding protein RBM20 represses splicing to orchestrate cardiac pre-mRNA processing. J Clin Invest 2014; 124:3419-30. [PMID: 24960161 DOI: 10.1172/jci74523] [Citation(s) in RCA: 144] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Accepted: 05/13/2014] [Indexed: 12/26/2022] Open
Abstract
Mutations in the gene encoding the RNA-binding protein RBM20 have been implicated in dilated cardiomyopathy (DCM), a major cause of chronic heart failure, presumably through altering cardiac RNA splicing. Here, we combined transcriptome-wide crosslinking immunoprecipitation (CLIP-seq), RNA-seq, and quantitative proteomics in cell culture and rat and human hearts to examine how RBM20 regulates alternative splicing in the heart. Our analyses revealed the presence of a distinct RBM20 RNA-recognition element that is predominantly found within intronic binding sites and linked to repression of exon splicing with RBM20 binding near 3' and 5' splice sites. Proteomic analysis determined that RBM20 interacts with both U1 and U2 small nuclear ribonucleic particles (snRNPs) and suggested that RBM20-dependent splicing repression occurs through spliceosome stalling at complex A. Direct RBM20 targets included several genes previously shown to be involved in DCM as well as genes not typically associated with this disease. In failing human hearts, reduced expression of RBM20 affected alternative splicing of several direct targets, indicating that differences in RBM20 expression may affect cardiac function. Together, these findings identify RBM20-regulated targets and provide insight into the pathogenesis of human heart failure.
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28
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Gatto A, Torroja-Fungairiño C, Mazzarotto F, Cook SA, Barton PJR, Sánchez-Cabo F, Lara-Pezzi E. FineSplice, enhanced splice junction detection and quantification: a novel pipeline based on the assessment of diverse RNA-Seq alignment solutions. Nucleic Acids Res 2014; 42:e71. [PMID: 24574529 PMCID: PMC4005686 DOI: 10.1093/nar/gku166] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Alternative splicing is the main mechanism governing protein diversity. The recent developments in RNA-Seq technology have enabled the study of the global impact and regulation of this biological process. However, the lack of standardized protocols constitutes a major bottleneck in the analysis of alternative splicing. This is particularly important for the identification of exon–exon junctions, which is a critical step in any analysis workflow. Here we performed a systematic benchmarking of alignment tools to dissect the impact of design and method on the mapping, detection and quantification of splice junctions from multi-exon reads. Accordingly, we devised a novel pipeline based on TopHat2 combined with a splice junction detection algorithm, which we have named FineSplice. FineSplice allows effective elimination of spurious junction hits arising from artefactual alignments, achieving up to 99% precision in both real and simulated data sets and yielding superior F1 scores under most tested conditions. The proposed strategy conjugates an efficient mapping solution with a semi-supervised anomaly detection scheme to filter out false positives and allows reliable estimation of expressed junctions from the alignment output. Ultimately this provides more accurate information to identify meaningful splicing patterns. FineSplice is freely available at https://sourceforge.net/p/finesplice/.
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Affiliation(s)
- Alberto Gatto
- Cardiovascular Development and Repair Department, Centro Nacional de Investigaciones Cardiovasculares, Madrid, 28029, Spain, Bioinformatics Unit, Centro Nacional de Investigaciones Cardiovasculares, Madrid, 28029, Spain, National Heart and Lung Institute, Imperial College London, London SW7 2AZ, UK, Cardiovascular Biomedical Research Unit, NIHR Royal Brompton and Harefield NHS Foundation Trust, London SW3 6NP, UK, Department of Cardiology, National Heart Centre Singapore, Singapore 168752, Singapore and Cardiovascular and Metabolic Disorders Program, Duke-NUS Graduate Medical School, Singapore 169857, Singapore
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Zhou W, Suntharalingam K, Brand NJ, Barton PJR, Vilar R, Ying L. Possible regulatory roles of promoter g-quadruplexes in cardiac function-related genes - human TnIc as a model. PLoS One 2013; 8:e53137. [PMID: 23326389 PMCID: PMC3541360 DOI: 10.1371/journal.pone.0053137] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2012] [Accepted: 11/23/2012] [Indexed: 12/15/2022] Open
Abstract
G-quadruplexes (G4s) are four-stranded DNA secondary structures, which are involved in a diverse range of biological processes. Although the anti-cancer potential of G4s in oncogene promoters has been thoroughly investigated, the functions of promoter G4s in non-cancer-related genes are not well understood. We have explored the possible regulatory roles of promoter G4s in cardiac function-related genes using both computational and a wide range of experimental approaches. According to our bioinformatics results, it was found that potential G4-forming sequences are particularly enriched in the transcription regulatory regions (TRRs) of cardiac function-related genes. Subsequently, the promoter of human cardiac troponin I (TnIc) was chosen as a model, and G4s found in this region were subjected to biophysical characterisations. The chromosome 19 specific minisatellite G4 sequence (MNSG4) and near transcription start site (TSS) G4 sequence (−80 G4) adopt anti-parallel and parallel structures respectively in 100 mM KCl, with stabilities comparable to those of oncogene G4s. It was also found that TnIc G4s act cooperatively as enhancers in gene expression regulation in HEK293 cells, when stabilised by a synthetic G4-binding ligand. This study provides the first evidence of the biological significance of promoter G4s in cardiac function-related genes. The feasibility of using a single ligand to target multiple G4s in a particular gene has also been discussed.
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Affiliation(s)
- Wenhua Zhou
- Molecular Medicine, National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | | | - Nigel J. Brand
- Harefield Heart Science Centre, National Heart and Lung Institute, Imperial College London, Middlesex, United Kingdom
| | - Paul J. R. Barton
- Harefield Heart Science Centre, National Heart and Lung Institute, Imperial College London, Middlesex, United Kingdom
- NIHR Cardiovascular Biomedical Research Unit, Royal Brompton and Harefield NHS Trust, London, United Kingdom
| | - Ramon Vilar
- Department of Chemistry, Imperial College London, London, United Kingdom
| | - Liming Ying
- Molecular Medicine, National Heart and Lung Institute, Imperial College London, London, United Kingdom
- * E-mail:
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Panse KD, Felkin LE, López-Olañeta MM, Gómez-Salinero J, Villalba M, Muñoz L, Nakamura K, Shimano M, Walsh K, Barton PJR, Rosenthal N, Lara-Pezzi E. Follistatin-like 3 mediates paracrine fibroblast activation by cardiomyocytes. J Cardiovasc Transl Res 2012; 5:814-26. [PMID: 22915069 DOI: 10.1007/s12265-012-9400-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/21/2012] [Accepted: 08/09/2012] [Indexed: 11/28/2022]
Abstract
Follistatins are extracellular inhibitors of the TGF-β family ligands including activin A, myostatin and bone morphogenetic proteins. Follistatin-like 3 (FSTL3) is a potent inhibitor of activin signalling and antagonises the cardioprotective role of activin A in the heart. FSTL3 expression is elevated in patients with heart failure and is upregulated in cardiomyocytes by hypertrophic stimuli, but its role in cardiac remodelling is largely unknown. Here, we show that the production of FSTL3 by cardiomyocytes contributes to the paracrine activation of cardiac fibroblasts, inducing changes in cell adhesion, promoting proliferation and increasing collagen production. We found that FSTL3 is necessary for this response and for the induction of cardiac fibrosis. However, full activation requires additional factors, and we identify connective tissue growth factor as a FSTL3 binding partner in this process. Together, our data unveil a novel mechanism of paracrine communication between cardiomyocytes and fibroblasts that may provide potential as a therapeutic target in heart remodelling.
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Affiliation(s)
- Kalyani D Panse
- Heart Science Centre, Imperial College London, Hill End Road, Middlesex, UB9 6JH, UK
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Herman DS, Lam L, Taylor MRG, Wang L, Teekakirikul P, Christodoulou D, Conner L, DePalma SR, McDonough B, Sparks E, Teodorescu DL, Cirino AL, Banner NR, Pennell DJ, Graw S, Merlo M, Di Lenarda A, Sinagra G, Bos JM, Ackerman MJ, Mitchell RN, Murry CE, Lakdawala NK, Ho CY, Barton PJR, Cook SA, Mestroni L, Seidman JG, Seidman CE. Truncations of titin causing dilated cardiomyopathy. N Engl J Med 2012; 366:619-28. [PMID: 22335739 PMCID: PMC3660031 DOI: 10.1056/nejmoa1110186] [Citation(s) in RCA: 935] [Impact Index Per Article: 77.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
BACKGROUND Dilated cardiomyopathy and hypertrophic cardiomyopathy arise from mutations in many genes. TTN, the gene encoding the sarcomere protein titin, has been insufficiently analyzed for cardiomyopathy mutations because of its enormous size. METHODS We analyzed TTN in 312 subjects with dilated cardiomyopathy, 231 subjects with hypertrophic cardiomyopathy, and 249 controls by using next-generation or dideoxy sequencing. We evaluated deleterious variants for cosegregation in families and assessed clinical characteristics. RESULTS We identified 72 unique mutations (25 nonsense, 23 frameshift, 23 splicing, and 1 large tandem insertion) that altered full-length titin. Among subjects studied by means of next-generation sequencing, the frequency of TTN mutations was significantly higher among subjects with dilated cardiomyopathy (54 of 203 [27%]) than among subjects with hypertrophic cardiomyopathy (3 of 231 [1%], P=3×10(-16)) or controls (7 of 249 [3%], P=9×10(-14)). TTN mutations cosegregated with dilated cardiomyopathy in families (combined lod score, 11.1) with high (>95%) observed penetrance after the age of 40 years. Mutations associated with dilated cardiomyopathy were overrepresented in the titin A-band but were absent from the Z-disk and M-band regions of titin (P≤0.01 for all comparisons). Overall, the rates of cardiac outcomes were similar in subjects with and those without TTN mutations, but adverse events occurred earlier in male mutation carriers than in female carriers (P=4×10(-5)). CONCLUSIONS TTN truncating mutations are a common cause of dilated cardiomyopathy, occurring in approximately 25% of familial cases of idiopathic dilated cardiomyopathy and in 18% of sporadic cases. Incorporation of sequencing approaches that detect TTN truncations into genetic testing for dilated cardiomyopathy should substantially increase test sensitivity, thereby allowing earlier diagnosis and therapeutic intervention for many patients with dilated cardiomyopathy. Defining the functional effects of TTN truncating mutations should improve our understanding of the pathophysiology of dilated cardiomyopathy. (Funded by the Howard Hughes Medical Institute and others.).
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Affiliation(s)
- Daniel S Herman
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
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Hall JL, Fermin DR, Birks EJ, Barton PJR, Slaughter M, Eckman P, Baba HA, Wohlschlaeger J, Miller LW. Clinical, molecular, and genomic changes in response to a left ventricular assist device. J Am Coll Cardiol 2011; 57:641-52. [PMID: 21292124 DOI: 10.1016/j.jacc.2010.11.010] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/24/2010] [Revised: 10/25/2010] [Accepted: 11/08/2010] [Indexed: 12/20/2022]
Abstract
The use of left ventricular assist devices in treating patients with end-stage heart failure has increased significantly in recent years, both as a bridge to transplantation and as destination therapy in those who are ineligible for cardiac transplantation. This increase is based largely on the results of several recently completed clinical trials with the new second-generation continuous-flow devices that showed significant improvements in survival, functional capacity, and quality of life. Additional information on the use of the first- and second-generation left ventricular assist devices has come from a recently released report spanning the years 2006 to 2009, from the Interagency Registry for Mechanically Assisted Circulatory Support, a National Heart, Lung, and Blood Institute-sponsored collaboration between the U.S. Food and Drug Administration, the Centers for Medicare and Medicaid Services, and the scientific community. The authors review the latest clinical trials and data from the registry, with tight integration of the landmark molecular, cellular, and genomic research that accompanies the reverse remodeling of the human heart in response to a left ventricular assist device and functional recovery that has been reported in a subset of these patients.
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Affiliation(s)
- Jennifer L Hall
- Division of Cardiology, Department of Medicine, University of Minnesota, Minneapolis, 55455, USA.
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McDermott-Roe C, Ye J, Ahmed R, Sun XM, Serafín A, Ware J, Bottolo L, Muckett P, Cañas X, Zhang J, Rowe GC, Buchan R, Lu H, Braithwaite A, Mancini M, Hauton D, Martí R, García-Arumí E, Hubner N, Jacob H, Serikawa T, Zidek V, Papousek F, Kolar F, Cardona M, Ruiz-Meana M, García-Dorado D, Comella JX, Felkin LE, Barton PJR, Arany Z, Pravenec M, Petretto E, Sanchis D, Cook SA. Endonuclease G is a novel determinant of cardiac hypertrophy and mitochondrial function. Nature 2011; 478:114-8. [PMID: 21979051 PMCID: PMC3189541 DOI: 10.1038/nature10490] [Citation(s) in RCA: 115] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2011] [Accepted: 08/17/2011] [Indexed: 12/31/2022]
Abstract
Left ventricular mass (LVM) is a highly heritable trait and an independent risk factor for all-cause mortality. So far, genome-wide association studies have not identified the genetic factors that underlie LVM variation, and the regulatory mechanisms for blood-pressure-independent cardiac hypertrophy remain poorly understood. Unbiased systems genetics approaches in the rat now provide a powerful complementary tool to genome-wide association studies, and we applied integrative genomics to dissect a highly replicated, blood-pressure-independent LVM locus on rat chromosome 3p. Here we identified endonuclease G (Endog), which previously was implicated in apoptosis but not hypertrophy, as the gene at the locus, and we found a loss-of-function mutation in Endog that is associated with increased LVM and impaired cardiac function. Inhibition of Endog in cultured cardiomyocytes resulted in an increase in cell size and hypertrophic biomarkers in the absence of pro-hypertrophic stimulation. Genome-wide network analysis unexpectedly implicated ENDOG in fundamental mitochondrial processes that are unrelated to apoptosis. We showed direct regulation of ENDOG by ERR-α and PGC1α (which are master regulators of mitochondrial and cardiac function), interaction of ENDOG with the mitochondrial genome and ENDOG-mediated regulation of mitochondrial mass. At baseline, the Endog-deleted mouse heart had depleted mitochondria, mitochondrial dysfunction and elevated levels of reactive oxygen species, which were associated with enlarged and steatotic cardiomyocytes. Our study has further established the link between mitochondrial dysfunction, reactive oxygen species and heart disease and has uncovered a role for Endog in maladaptive cardiac hypertrophy.
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Affiliation(s)
- Chris McDermott-Roe
- Medical Research Council Clinical Sciences Centre, Faculty of Medicine, Imperial College London, Hammersmith Hospital, Du Cane Road, London W12 ONN, UK
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Knöll R, Linke WA, Zou P, Miocic S, Kostin S, Buyandelger B, Ku CH, Neef S, Bug M, Schäfer K, Knöll G, Felkin LE, Wessels J, Toischer K, Hagn F, Kessler H, Didié M, Quentin T, Maier LS, Teucher N, Unsöld B, Schmidt A, Birks EJ, Gunkel S, Lang P, Granzier H, Zimmermann WH, Field LJ, Faulkner G, Dobbelstein M, Barton PJR, Sattler M, Wilmanns M, Chien KR. Telethonin deficiency is associated with maladaptation to biomechanical stress in the mammalian heart. Circ Res 2011; 109:758-69. [PMID: 21799151 DOI: 10.1161/circresaha.111.245787] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
RATIONALE Telethonin (also known as titin-cap or t-cap) is a 19-kDa Z-disk protein with a unique β-sheet structure, hypothesized to assemble in a palindromic way with the N-terminal portion of titin and to constitute a signalosome participating in the process of cardiomechanosensing. In addition, a variety of telethonin mutations are associated with the development of several different diseases; however, little is known about the underlying molecular mechanisms and telethonin's in vivo function. OBJECTIVE Here we aim to investigate the role of telethonin in vivo and to identify molecular mechanisms underlying disease as a result of its mutation. METHODS AND RESULTS By using a variety of different genetically altered animal models and biophysical experiments we show that contrary to previous views, telethonin is not an indispensable component of the titin-anchoring system, nor is deletion of the gene or cardiac specific overexpression associated with a spontaneous cardiac phenotype. Rather, additional titin-anchorage sites, such as actin-titin cross-links via α-actinin, are sufficient to maintain Z-disk stability despite the loss of telethonin. We demonstrate that a main novel function of telethonin is to modulate the turnover of the proapoptotic tumor suppressor p53 after biomechanical stress in the nuclear compartment, thus linking telethonin, a protein well known to be present at the Z-disk, directly to apoptosis ("mechanoptosis"). In addition, loss of telethonin mRNA and nuclear accumulation of this protein is associated with human heart failure, an effect that may contribute to enhanced rates of apoptosis found in these hearts. CONCLUSIONS Telethonin knockout mice do not reveal defective heart development or heart function under basal conditions, but develop heart failure following biomechanical stress, owing at least in part to apoptosis of cardiomyocytes, an effect that may also play a role in human heart failure.
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Affiliation(s)
- Ralph Knöll
- Imperial College, National Heart & Lung Institute, British Heart Foundation, Centre for Research Excellence, Myocardial Genetics, London, UK.
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Felkin LE, Narita T, Germack R, Shintani Y, Takahashi K, Sarathchandra P, López-Olañeta MM, Gómez-Salinero JM, Suzuki K, Barton PJR, Rosenthal N, Lara-Pezzi E. Calcineurin splicing variant calcineurin Aβ1 improves cardiac function after myocardial infarction without inducing hypertrophy. Circulation 2011; 123:2838-47. [PMID: 21632490 DOI: 10.1161/circulationaha.110.012211] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
BACKGROUND Calcineurin is a calcium-regulated phosphatase that plays a major role in cardiac hypertrophy. We previously described that alternative splicing of the calcineurin Aβ (CnAβ) gene generates the CnAβ1 isoform, with a unique C-terminal region that is different from the autoinhibitory domain present in all other CnA isoforms. In skeletal muscle, CnAβ1 is necessary for myoblast proliferation and stimulates regeneration, reducing fibrosis and accelerating the resolution of inflammation. Its role in the heart is currently unknown. METHODS AND RESULTS We generated transgenic mice overexpressing CnAβ1 in postnatal cardiomyocytes under the control of the α-myosin heavy chain promoter. In contrast to previous studies using an artificially truncated calcineurin, CnAβ1 overexpression did not induce cardiac hypertrophy. Moreover, transgenic mice showed improved cardiac function and reduced scar formation after myocardial infarction, with reduced neutrophil and macrophage infiltration and decreased expression of proinflammatory cytokines. Immunoprecipitation and Western blot analysis showed interaction of CnAβ1 with the mTOR complex 2 and activation of the Akt/SGK cardioprotective pathway in a PI3K-independent manner. In addition, gene expression profiling revealed that CnAβ1 activated the transcription factor ATF4 downstream of the Akt/mTOR pathway to promote the amino acid biosynthesis program, to reduce protein catabolism, and to induce the antifibrotic and antiinflammatory factor growth differentiation factor 15, which protects the heart through Akt activation. CONCLUSIONS Calcineurin Aβ1 shows a unique mode of action that improves cardiac function after myocardial infarction, activating different cardioprotective pathways without inducing maladaptive hypertrophy. These features make CnAβ1 an attractive candidate for the development of future therapeutic approaches.
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Affiliation(s)
- Leanne E Felkin
- Heart Science Centre, National Heart and Lung Institute, Imperial College London, London, UK
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Villard E, Perret C, Gary F, Proust C, Dilanian G, Hengstenberg C, Ruppert V, Arbustini E, Wichter T, Germain M, Dubourg O, Tavazzi L, Aumont MC, DeGroote P, Fauchier L, Trochu JN, Gibelin P, Aupetit JF, Stark K, Erdmann J, Hetzer R, Roberts AM, Barton PJR, Regitz-Zagrosek V, Aslam U, Duboscq-Bidot L, Meyborg M, Maisch B, Madeira H, Waldenström A, Galve E, Cleland JG, Dorent R, Roizes G, Zeller T, Blankenberg S, Goodall AH, Cook S, Tregouet DA, Tiret L, Isnard R, Komajda M, Charron P, Cambien F. A genome-wide association study identifies two loci associated with heart failure due to dilated cardiomyopathy. Eur Heart J 2011; 32:1065-76. [PMID: 21459883 DOI: 10.1093/eurheartj/ehr105] [Citation(s) in RCA: 240] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
AIMS Dilated cardiomyopathy (DCM) is a major cause of heart failure with a high familial recurrence risk. So far, the genetics of DCM remains largely unresolved. We conducted the first genome-wide association study (GWAS) to identify loci contributing to sporadic DCM. METHODS AND RESULTS One thousand one hundred and seventy-nine DCM patients and 1108 controls contributed to the discovery phase. Pools of DNA stratified on disease status, population, age, and gender were constituted and used for testing association of DCM with 517 382 single nucleotide polymorphisms (SNPs). Three DCM-associated SNPs were confirmed by individual genotyping (P < 5.0 10(-7)), and two of them, rs10927875 and rs2234962, were replicated in independent samples (1165 DCM patients and 1302 controls), with P-values of 0.002 and 0.009, respectively. rs10927875 maps to a region on chromosome 1p36.13 which encompasses several genes among which HSPB7 has been formerly suggested to be implicated in DCM. The second identified locus involves rs2234962, a non-synonymous SNP (c.T757C, p. C151R) located within the sequence of BAG3 on chromosome 10q26. To assess whether coding mutations of BAG3 might cause monogenic forms of the disease, we sequenced BAG3 exons in 168 independent index cases diagnosed with familial DCM and identified four truncating and two missense mutations. Each mutation was heterozygous, present in all genotyped relatives affected by the disease and absent in a control group of 347 healthy individuals, strongly suggesting that these mutations are causing the disease. CONCLUSION This GWAS identified two loci involved in sporadic DCM, one of them probably implicates BAG3. Our results show that rare mutations in BAG3 contribute to monogenic forms of the disease, while common variant(s) in the same gene are implicated in sporadic DCM.
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Felkin LE, Lara-Pezzi EA, Hall JL, Birks EJ, Barton PJR. Reverse Remodelling and Recovery from Heart Failure Are Associated with Complex Patterns of Gene Expression. J Cardiovasc Transl Res 2011; 4:321-31. [DOI: 10.1007/s12265-011-9267-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/07/2010] [Accepted: 02/15/2011] [Indexed: 11/30/2022]
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Breckenridge RA, Zuberi Z, Gomes J, Orford R, Dupays L, Felkin LE, Clark JE, Magee AI, Ehler E, Birks EJ, Barton PJR, Tinker A, Mohun TJ. Overexpression of the transcription factor Hand1 causes predisposition towards arrhythmia in mice. J Mol Cell Cardiol 2009; 47:133-41. [PMID: 19376125 DOI: 10.1016/j.yjmcc.2009.04.007] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/12/2008] [Revised: 03/30/2009] [Accepted: 04/01/2009] [Indexed: 11/28/2022]
Abstract
Elevated levels of the cardiac transcription factor Hand1 have been reported in several adult cardiac diseases but it is unclear whether this change is itself maladaptive with respect to heart function. To test this possibility, we have developed a novel, inducible transgenic system, and used it to overexpress Hand1 in adult mouse hearts. Overexpression of Hand1 in the adult mouse heart leads to mild cardiac hypertrophy and a reduction in life expectancy. Treated mice show no significant fibrosis, myocyte disarray or congestive heart failure, but have a greatly reduced threshold for induced ventricular tachycardia, indicating a predisposition to cardiac arrhythmia. Within 48 h, they show a significant loss of connexin43 protein from cardiac intercalated discs, with increased intercalated disc beta-catenin expression at protein and RNA levels. These changes are sustained during prolonged Hand1 overexpression. We propose that cardiac overexpression of Hand1 offers a useful mouse model of arrhythmogenesis and elevated HAND1 may provide one of the molecular links between the failing heart and arrhythmia.
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Lara-Pezzi E, Terracciano CMN, Soppa GKR, Smolenski RT, Felkin LE, Yacoub MH, Barton PJR. A gene expression profile of the myocardial response to clenbuterol. J Cardiovasc Transl Res 2009; 2:191-7. [PMID: 20559987 DOI: 10.1007/s12265-009-9097-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/23/2009] [Accepted: 02/25/2009] [Indexed: 01/08/2023]
Abstract
Clenbuterol is currently being used as part of a clinical trial into a novel therapeutic approach for the treatment of end-stage heart failure. The purpose of this study was to determine the global pattern of myocardial gene expression in response to clenbuterol and to identify novel targets and pathways involved. Rats were treated with clenbuterol (n = 6) or saline (n = 6) for periods of 1, 3, 9, or 28 days. Rats treated for 28 days were also subject to continuous electrocardiogram analysis using implantable telemetry. RNA was extracted from rats at days 1 and 28 and used from microarray analysis, and further samples from rats at days 1, 3, 9, and 28 were used for analysis by real-time polymerase chain reaction. Clenbuterol treatment induced rapid development of cardiac hypertrophy with increased muscle mass at day 1 and elevated heart rate and QT interval throughout the 28-day period. Microarray analysis revealed a marked but largely transitory change in gene expression with 1,423 genes up-regulated and 964 genes down-regulated at day 1. Up-regulated genes revealed an unexpected association with angiogenesis and integrin-mediated cell adhesion and signaling. Moreover, direct treatment of endothelial cells cultured in vitro resulted in increased cell proliferation and tube formation. Our data show that clenbuterol treatment is associated with rapid cardiac hypertrophy and identify angiogenesis and integrin signaling as novel pathways of clenbuterol action. The data have implications both for our understanding of the physiologic hypertrophy induced by clenbuterol and for treatment of heart failure.
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Affiliation(s)
- Enrique Lara-Pezzi
- Harefield Heart Science Centre, National Heart and Lung Institute, Imperial College, Hill End Road, Harefield, Middlesex, UB9 6JH, UK
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Lara-Pezzi E, Felkin LE, Birks EJ, Sarathchandra P, Panse KD, George R, Hall JL, Yacoub MH, Rosenthal N, Barton PJR. Expression of follistatin-related genes is altered in heart failure. Endocrinology 2008; 149:5822-7. [PMID: 18617621 DOI: 10.1210/en.2008-0151] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Follistatins play roles in diverse biological processes including cell proliferation, wound healing, inflammation, and skeletal muscle growth, yet their role in the heart is currently unknown. We have investigated the myocardial expression profile and cellular distribution of follistatin (FST) and the FST-like genes FSTL1 and FSTL3 in the normal and failing heart. Expression was further analyzed in the novel setting of recovery from heart failure in myocardium obtained from patients who received combined mechanical (left ventricular assist device) and pharmacological therapy. Real-time PCR revealed that FSTL1 and FSTL3 expression was elevated in heart failure but returned to normal after recovery. FSTL3 expression levels correlated with molecular markers of disease severity and FSTL1 with the endothelial cell marker CD31, suggesting a potential link with vascularization. FSTL1 levels before treatment correlated with cardiac function after recovery, suggesting initial levels may influence long-term outcome. Immunohistochemistry revealed that FST was primarily localized to fibroblasts and vascular endothelium within the heart, whereas FSTL1 was localized to myocytes, endothelium, and smooth muscle cells and FSLT3 to myocytes and endothelium. Microarray analysis revealed that FST and FSTL1 were associated with extracellular matrix-related and calcium-binding proteins, whereas FSTL3 was associated mainly with cell signaling and transcription. These data show for the first time that elevated myocardial expression of FST-like genes is a feature of heart failure and may be linked to both disease severity and mechanisms underlying recovery, revealing new insight into the pathogenesis of heart failure and offering novel therapeutic targets.
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Affiliation(s)
- Enrique Lara-Pezzi
- Harefield Heart Science Centre, Hill End Road, Harefield, Middlesex UB9 6JH, United Kingdom
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Fukushima S, Coppen SR, Lee J, Yamahara K, Felkin LE, Terracciano CMN, Barton PJR, Yacoub MH, Suzuki K. Choice of cell-delivery route for skeletal myoblast transplantation for treating post-infarction chronic heart failure in rat. PLoS One 2008; 3:e3071. [PMID: 18728781 PMCID: PMC2516937 DOI: 10.1371/journal.pone.0003071] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2008] [Accepted: 07/28/2008] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Intramyocardial injection of skeletal myoblasts (SMB) has been shown to be a promising strategy for treating post-infarction chronic heart failure. However, insufficient therapeutic benefit and occurrence of ventricular arrhythmias are concerns. We hypothesised that the use of a retrograde intracoronary route for SMB-delivery might favourably alter the behaviour of the grafted SMB, consequently modulating the therapeutic effects and arrhythmogenicity. METHODS AND RESULTS Three weeks after coronary artery ligation in female wild-type rats, 5x10(6) GFP-expressing SMB or PBS only (control) were injected via either the intramyocardial or retrograde intracoronary routes. Injection of SMB via either route similarly improved cardiac performance and physical activity, associated with reduced cardiomyocyte-hypertrophy and fibrosis. Grafted SMB via either route were only present in low numbers in the myocardium, analysed by real-time PCR for the Y-chromosome specific gene, Sry. Cardiomyogenic differentiation of grafted SMB was extremely rare. Continuous ECG monitoring by telemetry revealed that only intramyocardial injection of SMB produced spontaneous ventricular tachycardia up to 14 days, associated with local myocardial heterogeneity generated by clusters of injected SMB and accumulated inflammatory cells. A small number of ventricular premature contractions with latent ventricular tachycardia were detected in the late-phase of SMB injection regardless of the injection-route. CONCLUSION Retrograde intracoronary injection of SMB provided significant therapeutic benefits with attenuated early-phase arrhythmogenicity in treating ischaemic cardiomyopathy, indicating the promising utility of this route for SMB-delivery. Late-phase arrhythmogenicity remains a concern, regardless of the delivery route.
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Affiliation(s)
- Satsuki Fukushima
- Harefield Heart Science Centre, National Heart & Lung Institute, Imperial College London, Harefield, Middlesex, United Kingdom
| | - Steven R. Coppen
- Translational Cardiovascular Therapeutics, William Harvey Research Institute, Barts and The London, Queen Mary's School of Medicine and Dentistry, London, United Kingdom
| | - Joon Lee
- Harefield Heart Science Centre, National Heart & Lung Institute, Imperial College London, Harefield, Middlesex, United Kingdom
| | - Kenichi Yamahara
- Harefield Heart Science Centre, National Heart & Lung Institute, Imperial College London, Harefield, Middlesex, United Kingdom
| | - Leanne E. Felkin
- Harefield Heart Science Centre, National Heart & Lung Institute, Imperial College London, Harefield, Middlesex, United Kingdom
| | - Cesare M. N. Terracciano
- Harefield Heart Science Centre, National Heart & Lung Institute, Imperial College London, Harefield, Middlesex, United Kingdom
| | - Paul J. R. Barton
- Harefield Heart Science Centre, National Heart & Lung Institute, Imperial College London, Harefield, Middlesex, United Kingdom
| | - Magdi H. Yacoub
- Harefield Heart Science Centre, National Heart & Lung Institute, Imperial College London, Harefield, Middlesex, United Kingdom
| | - Ken Suzuki
- Harefield Heart Science Centre, National Heart & Lung Institute, Imperial College London, Harefield, Middlesex, United Kingdom
- Translational Cardiovascular Therapeutics, William Harvey Research Institute, Barts and The London, Queen Mary's School of Medicine and Dentistry, London, United Kingdom
- * E-mail:
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Yamahara K, Fukushima S, Coppen SR, Felkin LE, Varela-Carver A, Barton PJR, Yacoub MH, Suzuki K. Heterogeneic nature of adult cardiac side population cells. Biochem Biophys Res Commun 2008; 371:615-20. [PMID: 18413147 DOI: 10.1016/j.bbrc.2008.04.021] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2008] [Accepted: 04/02/2008] [Indexed: 10/22/2022]
Abstract
Side population cells have been found in various types of adult tissue including heart and are presumed to be tissue-specific stem/progenitor cells. In the present study, we confirmed the presence of cardiac side population (cSP) cells, which showed both the Hoechst 33342 efflux ability and ABCG2 expression, in adult murine heart. Flow cytometric analysis showed that more than half of cSP cells expressed the endothelial marker VE-cadherin or the smooth muscle markers, alpha-smooth muscle actin and desmin. In addition, immunohistochemical analysis demonstrated that ABCG2(+) cells were mainly localized within vascular walls. Quantitative RT-PCR analysis demonstrated that VE-cadherin(-) cSP cells progressively expressed Nkx2.5 and cardiac troponin T with time in culture. VE-cadherin(-) cSP cells also expressed mesodermal-mesenchymal-associated markers and differentiated into osteocytes and adipocytes. These results highlight the heterogeneic nature of cSP cells, consisting of vascular endothelial cells, smooth muscle cells, and mesenchymal stem/progenitor cells including potential cardiomyogenic cells.
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Affiliation(s)
- Kenichi Yamahara
- Harefield Heart Science Centre, Imperial College London, Middlesex, UK
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Birks EJ, Latif N, Enesa K, Folkvang T, Luong LA, Sarathchandra P, Khan M, Ovaa H, Terracciano CM, Barton PJR, Yacoub MH, Evans PC. Elevated p53 expression is associated with dysregulation of the ubiquitin-proteasome system in dilated cardiomyopathy. Cardiovasc Res 2008; 79:472-80. [PMID: 18375498 DOI: 10.1093/cvr/cvn083] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
AIMS The molecular mechanisms that regulate cardiomyocyte apoptosis and their role in human heart failure (HF) are uncertain. Expression of the apoptosis regulator p53 is governed by minute double minute 2 (MDM2), an E3 enzyme that targets p53 for ubiquitination and proteasomal processing, and by the deubiquitinating enzyme, herpesvirus-associated ubiquitin-specific protease (HAUSP), which rescues p53 by removing ubiquitin chains from it. Here, we examined whether elevated expression of p53 was associated with dysregulation of ubiquitin-proteasome system (UPS) components and activation of downstream effectors of apoptosis in human dilated cardiomyopathy (DCM). METHODS AND RESULTS Left ventricular myocardial samples were obtained from patients with DCM (n = 12) or from non-failing (donor) hearts (n = 17). Western blotting and immunohistochemistry revealed that DCM tissues contained elevated levels of p53 and its regulators MDM2 and HAUSP (all P < 0.01) compared with non-failing hearts. DCM tissues also contained elevated levels of polyubiquitinated proteins and possessed enhanced 20S-proteasome chymotrypsin-like activities (P < 0.04) as measured in vitro using a fluorogenic substrate. DCM tissues contained activated caspases-9 and -3 (P < 0.001) and reduced expression of the caspase substrate PARP-1 (P < 0.05). Western blotting and immunohistochemistry revealed that DCM tissues contained elevated expression levels of caspase-3-activated DNAse (CAD; P < 0.001), which is a key effector of DNA fragmentation in apoptosis and also contained elevated expression of a potent inhibitor of CAD (ICAD-S; P < 0.01). CONCLUSION Expression of p53 in human DCM is associated with dysregulation of UPS components, which are known to regulate p53 stability. Elevated p53 expression and caspase activation in DCM was not associated with activation of both CAD and its inhibitor, ICAD-S. Our findings are consistent with the concept that apoptosis may be interrupted and therefore potentially reversible in human HF.
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Affiliation(s)
- Emma J Birks
- Heart Science Centre, National Heart and Lung Institute, Imperial College London, Harefield Hospital, Harefield, UK
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Soppa GKR, Lee J, Stagg MA, Felkin LE, Barton PJR, Siedlecka U, Youssef S, Yacoub MH, Terracciano CMN. Role and possible mechanisms of clenbuterol in enhancing reverse remodelling during mechanical unloading in murine heart failure. Cardiovasc Res 2008; 77:695-706. [PMID: 18178572 PMCID: PMC5436743 DOI: 10.1093/cvr/cvm106] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Aims Combined left ventricular assist device (LVAD) and pharmacological therapy has been proposed to favour myocardial recovery in patients with end-stage heart failure (HF). Clenbuterol (Clen), a β2-adrenoceptor (β2-AR) agonist, has been used as a part of this strategy. In this study, we investigated the direct effects of clenbuterol on unloaded myocardium in HF. Methods and results Left coronary artery ligation or sham operation was performed in male Lewis rats. After 4–6 weeks, heterotopic abdominal transplantation of the failing hearts into normal recipients was performed to induce LV unloading (UN). Recipient rats were treated with saline (Sal) or clenbuterol (2 mg/kg/day) via osmotic minipumps (HF + UN + Sal or HF + UN + Clen) for 7 days. Non-transplanted HF animals were treated with Sal (Sham + Sal, HF + Sal) or clenbuterol (HF + Clen). LV myocytes were isolated and studied using optical, fluorescence, and electrophysiological techniques. Clenbuterol treatment improved in vivo LV function measured with echocardiography (LVEF (%): HF 35.9 ± 2 [16], HF + Clen 52.1 ± 1.4 [16]; P < 0.001; mean ± SEM [n]). In combination with unloading, clenbuterol increased sarcomere shortening (amplitude (µm): HF + UN + Clen 0.1 ± 0.01 [50], HF + UN + Sal 0.07 ± 0.01 [38]; P < 0.001) by normalizing the depressed myofilament sensitivity to Ca2+ (slope of the linear relationship between Ca2+ transient and sarcomere shortening hysteresis loop during relaxation (μm/ratio unit): HF + UN + Clen 2.13 ± 0.2 [52], HF + UN + Sal 1.42 ± 0.13 [38]; P < 0.05). Conclusion Clenbuterol treatment of failing rat hearts, alone or in combination with mechanical unloading, improves LV function at the whole-heart and cellular levels by affecting cell morphology, excitation–contraction coupling, and myofilament sensitivity to calcium. This study supports the use of this drug in the strategy to enhance recovery in HF patients treated with LVADs and also begins to elucidate some of the possible cellular mechanisms responsible for the improvement in LV function.
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Affiliation(s)
- Gopal K R Soppa
- Heart Science Centre, Imperial College London, National Heart and Lung Institute, Laboratory of Cellular Electrophysiology, Harefield Hospital, Harefield, Middlesex, UK
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Fukushima S, Varela-Carver A, Coppen SR, Yamahara K, Felkin LE, Lee J, Barton PJR, Terracciano CMN, Yacoub MH, Suzuki K. Direct intramyocardial but not intracoronary injection of bone marrow cells induces ventricular arrhythmias in a rat chronic ischemic heart failure model. Circulation 2007; 115:2254-61. [PMID: 17438152 DOI: 10.1161/circulationaha.106.662577] [Citation(s) in RCA: 152] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
BACKGROUND Therapeutic efficacy of bone marrow (BM) cell injection for treating ischemic chronic heart failure has not been established. In addition, experimental data are lacking on arrhythmia occurrence after BM cell injection. We hypothesized that therapeutic efficacy and arrhythmia occurrence induced by BM cell injection may be affected by the cell delivery route. METHODS AND RESULTS Three weeks after left coronary artery ligation, wild-type female rats were injected with 1x10(7) mononuclear BM cells derived from green fluorescent protein-transgenic male rats through either a direct intramyocardial or a retrograde intracoronary route. Both intramyocardial and intracoronary injection of BM cells demonstrated similar improvement in left ventricular ejection fraction measured by echocardiography and a similar graft size analyzed by real-time polymerase chain reaction for the Y chromosome-specific Sry gene. Noticeably, intramyocardial injection of BM cells induced frequent ventricular premature contractions (108+/-73 per hour at 7 days after BM cell injection), including multiform, consecutive ventricular premature contractions and ventricular tachycardia for the initial 14 days; intracoronary injection of BM cells and intramyocardial injection of phosphate-buffered saline rarely induced arrhythmias. Immunohistochemistry demonstrated that intramyocardial BM cell injection formed distinct cell clusters containing donor-derived cells and accumulated host-derived inflammatory cells in the infarct border zone, whereas intracoronary BM cell injection provided more homogeneous donor cell dissemination with less inflammation and without disrupting the native myocardial structure. CONCLUSIONS BM cell injection is able to improve cardiac function in ischemic chronic heart failure but has a risk of arrhythmia occurrence when the intramyocardial route is used. Such arrhythmias may be prevented by using the intracoronary route.
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Affiliation(s)
- Satsuki Fukushima
- Harefield Heart Science Centre, National Heart and Lung Institute, Faculty of Medicine, Imperial College London, UK
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Latif N, Yacoub MH, George R, Barton PJR, Birks EJ. Changes in sarcomeric and non-sarcomeric cytoskeletal proteins and focal adhesion molecules during clinical myocardial recovery after left ventricular assist device support. J Heart Lung Transplant 2007; 26:230-5. [PMID: 17346624 DOI: 10.1016/j.healun.2006.08.011] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2006] [Revised: 04/21/2006] [Accepted: 08/14/2006] [Indexed: 10/23/2022] Open
Abstract
BACKGROUND Reverse remodeling can occur after left ventricular assist device (LVAD) support, which is sufficient in some cases to allow explantation of the device without cardiac transplantation. The molecular mechanisms involved remain unknown. A specific pattern of expression of sarcomeric and non-sarcomeric proteins in the myocardium is thought to be essential for normal myocardial function. However, a detailed protein analysis of their role in recovery has not been performed previously. METHODS Myocardial samples were collected at implantation and explantation in 7 patients with dilated cardiomyopathy who had sufficient recovery for device explantation. Western blotting and immunoprobing were used to quantitate changes in the expression of sarcomeric and cytoskeletal proteins. RESULTS At implantation, all patients (6 men and 1 woman, age [mean +/- SD] 36.1 +/- 10.4 years) were inotrope-dependent; ejection fraction (EF) was 12.6 +/- 4.6%, cardiac index (CI) was 1.66 +/- 0.5 liters/min/m2 and pulmonary capillary wedge pressure (PCWP) was 26 +/- 6 mm Hg. Mean duration of LVAD support was 333 +/- 235 days. Prior to explantation, EF (pump off for 15 minutes) was 62.7 +/- 11.4%, CI was 2.7 +/- 0.7 liters/min/m2 and PCWP was 10.9 +/- 3.5 mm Hg. At explantation, the following statistically significant increases were noted: myosin heavy chain, 1.90-fold (p < 0.05); sarcomeric actin, 1.80-fold (p < 0.05); alphaII spectrin, 1.40-fold (p = 0.05); troponin C, 1.34-fold (p < 0.05); troponin T, 2.10-fold (p < 0.05); cytoskeletal actinin, 5.16-fold (p < 0.05); and smooth muscle alpha-actin, 4.10-fold (p = 0.05). Although not significant (NS), increases were also seen for: troponin I, 1.27-fold; myosin light chain 1, 1.28-fold; tropomyosin, 1.28-fold; and sarcomeric actinin at 3.24-fold. There was a decrease in talin of 2.01-fold (p = NS) between implant and explant. Vimentin was unchanged. CONCLUSIONS Our data suggest that reverse remodeling of the myocardium parallels improvements in hemodynamic function in LVAD patients showing clinical myocardial recovery.
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Affiliation(s)
- Najma Latif
- Imperial College London, National Heart and Lung Institute, Heart Science Centre, Harefield Hospital, Harefield, Middlesex, UK.
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Cullen ME, Barton PJR. Mapping transcriptional start sites and in silico DNA footprinting. Methods Mol Biol 2007; 366:203-16. [PMID: 17568126 DOI: 10.1007/978-1-59745-030-0_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Determination of a gene's transcriptional start site underlies the identification of the proximal promoter region and thus facilitates the subsequent analysis of components controlling its expression, namely, cis-acting regulatory elements and their cognate binding proteins. It also enables assembly of meaningful reporter constructs to examine promoter function in different cellular contexts. In this chapter, basic protocols for two experimental approaches to transcriptional start site determination are described: primer extension analysis and the ribonuclease protection assay. Consideration is also given to RNA sources, RNA purification, and primer design. The explosion in genomic DNA and mRNA sequence information derived from genomic sequencing projects, expressed sequence tags and microarrays, combined with in silico analysis, such as automated sequence annotation and gene identification algorithms, now provides an alternative source of detailed information on gene structure and expression. Two approaches to the in silico identification of transcription factor binding sites are described.
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Affiliation(s)
- Martin E Cullen
- Heart Science Centre, National Heart and Lung Institute, Imperial College London, Harefield, Middlesex, UK
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Felkin LE, Birks EJ, George R, Wong S, Khaghani A, Yacoub MH, Barton PJR. A quantitative gene expression profile of matrix metalloproteinases (MMPS) and their inhibitors (TIMPS) in the myocardium of patients with deteriorating heart failure requiring left ventricular assist device support. J Heart Lung Transplant 2006; 25:1413-9. [PMID: 17178334 DOI: 10.1016/j.healun.2006.09.006] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2006] [Revised: 07/26/2006] [Accepted: 09/09/2006] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND Mechanisms underlying the rapid deterioration of heart failure patients who subsequently require left ventricular assist device (LVAD) support are poorly understood. Matrix metalloproteinases (MMPs) and the tissue inhibitors of metalloproteinases (TIMPs) play a key role in myocardial remodelling and heart failure. We hypothesized that MMP and TIMP expression would be altered in these patients. METHODS Quantitative polymerase chain reaction was used to measure myocardial messenger RNA levels of MMP1 to MMP14, TIMP1 to TIMP4, collagen I and collagen III in 24 dilated cardiomyopathy (DCM) patients with deteriorating clinical status who required LVAD support (LVAD Group) and in 7 stable DCM patients undergoing transplantation without need for LVAD support (Tx Group). RESULTS Levels of MMP1, MMP8 and TIMP4 were higher in the LVAD Group compared with the Tx Group (188% +/- 141%, 646% +/- 432%, and 66% +/- 33% higher, respectively, p < 0.05) whereas MMP2, MMP9, MMP10, MMP11, and MMP14 levels were similar. MMP3, MMP7, MMP12, and MMP13 were undetectable. All TIMPs were generally higher in the LVAD group, but only TIMP4 reached significance. Collagen I and III were not altered. We tested for correlations between MMP and TIMP expression with myocardial cytokine levels. MMP8 correlated positively with interleukin-6 and interleukin-1beta, suggesting a link between cytokines and MMPs in these patients. CONCLUSIONS The data show that high myocardial collagenase (MMP1 and MMP8) expression without compensatory changes in collagen or TIMP expression is a feature of patients requiring LVAD support. This may be linked in part to elevated cytokine expression and suggests collagenase activity may be an important therapeutic target in deteriorating heart failure.
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Affiliation(s)
- Leanne E Felkin
- National Heart and Lung Institute, Imperial College London, Heart Science Centre, Harefield, Middlesex
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Cullen ME, Yuen AHY, Felkin LE, Smolenski RT, Hall JL, Grindle S, Miller LW, Birks EJ, Yacoub MH, Barton PJR. Myocardial expression of the arginine:glycine amidinotransferase gene is elevated in heart failure and normalized after recovery: potential implications for local creatine synthesis. Circulation 2006; 114:I16-20. [PMID: 16820567 DOI: 10.1161/circulationaha.105.000448] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
BACKGROUND Combination therapy consisting of mechanical unloading using a left ventricular assist device (LVAD) and pharmacological intervention can promote recovery from end-stage heart failure, but the mechanism is unknown. Preliminary microarray analysis revealed a significant and unexpected decrease in myocardial arginine:glycine amidinotransferase (AGAT) gene expression during recovery in these patients. The aim of this study was to evaluate the expression and role of AGAT expression in heart failure and recovery. METHODS AND RESULTS We used quantitative real time (TaqMan) polymerase chain reaction to examine myocardial AGAT mRNA expression in implant and explant samples from recovering patients after combination therapy (n=12), end-stage heart failure (ESHF) samples from stable patients undergoing transplantation without LVAD support (n=10), and donor hearts with normal hemodynamic function (n=8). AGAT mRNA expression was significantly elevated in all heart failure patients relative to donors (4.3-fold [P<0.001] and 2.7-fold [P<0.005] in LVAD and ESHF relative to donors, respectively) and returned to normal levels after recovery. AGAT enzyme activity was detectable in both human and rat myocardia and was elevated in heart failure. CONCLUSIONS Our data highlight local and potentially regulated expression of AGAT activity in the myocardium and suggest a specific response to heart failure involving elevated local creatine synthesis. These findings have implications both for the management of recovery patients undergoing combination therapy and for heart failure in general.
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Affiliation(s)
- Martin E Cullen
- National Heart and Lung Institute, Imperial College London, Heart Science Centre, Harefield, Middlesex, UB9 6JH, UK
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Abstract
The real-time quantitative polymerase chain reaction (PCR), an increasingly popular technique for the detection of DNA, combines a high degree of accuracy with extreme sensitivity. In this chapter we describe the use of real-time quantitative PCR in transplantation research in two areas in which this method is commonly applied: the accurate quantification of mRNA in tissue samples and genotyping of DNA. These are described in the context of cardiac transplantation, but they are of equal relevance to other areas of transplant biology.
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Affiliation(s)
- Leanne E Felkin
- National Heart and Lung Institute, Imperial College London, Heart Science Centre, Harefield Hospital, Harefield, Middlesex, England
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