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Jain K, McCarley SC, Mukhtar G, Ferlin A, Fleming A, Morris-Rosendahl DJ, Shovlin CL. Pathogenic Variant Frequencies in Hereditary Haemorrhagic Telangiectasia Support Clinical Evidence of Protection from Myocardial Infarction. J Clin Med 2023; 13:250. [PMID: 38202257 PMCID: PMC10779873 DOI: 10.3390/jcm13010250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 12/20/2023] [Accepted: 12/25/2023] [Indexed: 01/12/2024] Open
Abstract
Hereditary haemorrhagic telangiectasia (HHT) is a vascular dysplasia inherited as an autosomal dominant trait, due to a single heterozygous loss-of-function variant, usually in ACVRL1 (encoding activin receptor-like kinase 1 [ALK1]), ENG (encoding endoglin [CD105]), or SMAD4. In a consecutive single-centre series of 37 positive clinical genetic tests performed in 2021-2023, a skewed distribution pattern was noted, with 30 of 32 variants reported only once, but ACVRL1 c.1231C>T (p.Arg411Trp) identified as the disease-causal gene in five different HHT families. In the same centre's non-overlapping 1992-2020 series where 110/134 (82.1%) HHT-causal variants were reported only once, ACVRL1 c.1231C>T (p.Arg411Trp) was identified in nine further families. In a 14-country, four-continent HHT Mutation Database where 181/250 (72.4%) HHT-causal variants were reported only once, ACVRL1 c.1231C>T (p.Arg411Trp) was reported by 12 different laboratories, the adjacent ACVRL1 c.1232G>A (p.Arg411Gln) by 14, and ACVRL1 c.1120C>T (p.Arg374Trp) by 18. Unlike the majority of HHT-causal ACVRL1 variants, these encode ALK1 protein that reaches the endothelial cell surface but fails to signal. Six variants of this type were present in the three series and were reported 6.8-25.5 (mean 8.9) times more frequently than the other ACVRL1 missense variants (all p-values < 0.0039). Noting lower rates of myocardial infarction reported in HHT, we explore potential mechanisms, including a selective paradigm relevant to ALK1's role in the initiating event of atherosclerosis, where a plausible dominant negative effect of these specific variants can be proposed. In conclusion, there is an ~9-fold excess of kinase-inactive, cell surface-expressed ACVRL1/ALK1 pathogenic missense variants in HHT. The findings support further examination of differential clinical and cellular phenotypes by HHT causal gene molecular subtypes.
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Affiliation(s)
- Kinshuk Jain
- National Heart and Lung Institute, Imperial College London, London W12 0NN, UK; (K.J.); (S.C.M.); (G.M.); (D.J.M.-R.)
| | - Sarah C. McCarley
- National Heart and Lung Institute, Imperial College London, London W12 0NN, UK; (K.J.); (S.C.M.); (G.M.); (D.J.M.-R.)
| | - Ghazel Mukhtar
- National Heart and Lung Institute, Imperial College London, London W12 0NN, UK; (K.J.); (S.C.M.); (G.M.); (D.J.M.-R.)
| | - Anna Ferlin
- Clinical Genetics and Genomics Laboratory, Royal Brompton Hospital, Guy’s and St Thomas’ NHS Trust, London SE1 7EH, UK; (A.F.); (A.F.)
| | - Andrew Fleming
- Clinical Genetics and Genomics Laboratory, Royal Brompton Hospital, Guy’s and St Thomas’ NHS Trust, London SE1 7EH, UK; (A.F.); (A.F.)
| | - Deborah J. Morris-Rosendahl
- National Heart and Lung Institute, Imperial College London, London W12 0NN, UK; (K.J.); (S.C.M.); (G.M.); (D.J.M.-R.)
- Clinical Genetics and Genomics Laboratory, Royal Brompton Hospital, Guy’s and St Thomas’ NHS Trust, London SE1 7EH, UK; (A.F.); (A.F.)
| | - Claire L. Shovlin
- National Heart and Lung Institute, Imperial College London, London W12 0NN, UK; (K.J.); (S.C.M.); (G.M.); (D.J.M.-R.)
- Specialist Medicine, Hammersmith Hospital, Imperial College Healthcare NHS Trust, London W12 0HS, UK
- Social, Genetic and Environmental Determinants of Health, NIHR Imperial Biomedical Research Centre, London W2 1NY, UK
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Xiao S, Kai Z, Murphy D, Li D, Patel D, Bielowka AM, Bernabeu-Herrero ME, Abdulmogith A, Mumford AD, Westbury SK, Aldred MA, Vargesson N, Caulfield MJ, Shovlin CL. Functional filter for whole-genome sequencing data identifies HHT and stress-associated non-coding SMAD4 polyadenylation site variants >5 kb from coding DNA. Am J Hum Genet 2023; 110:1903-1918. [PMID: 37816352 PMCID: PMC10645545 DOI: 10.1016/j.ajhg.2023.09.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Revised: 09/01/2023] [Accepted: 09/08/2023] [Indexed: 10/12/2023] Open
Abstract
Despite whole-genome sequencing (WGS), many cases of single-gene disorders remain unsolved, impeding diagnosis and preventative care for people whose disease-causing variants escape detection. Since early WGS data analytic steps prioritize protein-coding sequences, to simultaneously prioritize variants in non-coding regions rich in transcribed and critical regulatory sequences, we developed GROFFFY, an analytic tool that integrates coordinates for regions with experimental evidence of functionality. Applied to WGS data from solved and unsolved hereditary hemorrhagic telangiectasia (HHT) recruits to the 100,000 Genomes Project, GROFFFY-based filtration reduced the mean number of variants/DNA from 4,867,167 to 21,486, without deleting disease-causal variants. In three unsolved cases (two related), GROFFFY identified ultra-rare deletions within the 3' untranslated region (UTR) of the tumor suppressor SMAD4, where germline loss-of-function alleles cause combined HHT and colonic polyposis (MIM: 175050). Sited >5.4 kb distal to coding DNA, the deletions did not modify or generate microRNA binding sites, but instead disrupted the sequence context of the final cleavage and polyadenylation site necessary for protein production: By iFoldRNA, an AAUAAA-adjacent 16-nucleotide deletion brought the cleavage site into inaccessible neighboring secondary structures, while a 4-nucleotide deletion unfolded the downstream RNA polymerase II roadblock. SMAD4 RNA expression differed to control-derived RNA from resting and cycloheximide-stressed peripheral blood mononuclear cells. Patterns predicted the mutational site for an unrelated HHT/polyposis-affected individual, where a complex insertion was subsequently identified. In conclusion, we describe a functional rare variant type that impacts regulatory systems based on RNA polyadenylation. Extension of coding sequence-focused gene panels is required to capture these variants.
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Affiliation(s)
- Sihao Xiao
- National Heart and Lung Institute, Imperial College London, W12 ONN London, UK; National Institute for Health Research (NIHR) Imperial Biomedical Research Centre, W2 1NY London, UK.
| | - Zhentian Kai
- Topgen Biopharm Technology Co. Ltd., Shanghai 201203, China
| | - Daniel Murphy
- National Institute for Health Research (NIHR) Imperial Biomedical Research Centre, W2 1NY London, UK; Women's, Children's & Clinical Support (Pharmacy), Imperial College Healthcare NHS Trust, W2 1NY London, UK
| | - Dongyang Li
- National Heart and Lung Institute, Imperial College London, W12 ONN London, UK; National Institute for Health Research (NIHR) Imperial Biomedical Research Centre, W2 1NY London, UK
| | - Dilip Patel
- National Heart and Lung Institute, Imperial College London, W12 ONN London, UK; National Institute for Health Research (NIHR) Imperial Biomedical Research Centre, W2 1NY London, UK
| | - Adrianna M Bielowka
- National Heart and Lung Institute, Imperial College London, W12 ONN London, UK; National Institute for Health Research (NIHR) Imperial Biomedical Research Centre, W2 1NY London, UK
| | - Maria E Bernabeu-Herrero
- National Heart and Lung Institute, Imperial College London, W12 ONN London, UK; National Institute for Health Research (NIHR) Imperial Biomedical Research Centre, W2 1NY London, UK
| | - Awatif Abdulmogith
- National Heart and Lung Institute, Imperial College London, W12 ONN London, UK; National Institute for Health Research (NIHR) Imperial Biomedical Research Centre, W2 1NY London, UK
| | - Andrew D Mumford
- School of Cellular and Molecular Medicine, University of Bristol, BS8 1QU Bristol, UK
| | - Sarah K Westbury
- School of Cellular and Molecular Medicine, University of Bristol, BS8 1QU Bristol, UK
| | - Micheala A Aldred
- Division of Pulmonary, Critical Care, Sleep & Occupational Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Neil Vargesson
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, AB25 2ZD Aberdeen, UK
| | - Mark J Caulfield
- William Harvey Research Institute, Queen Mary University of London, E1 4NS London, UK
| | - Claire L Shovlin
- National Heart and Lung Institute, Imperial College London, W12 ONN London, UK; National Institute for Health Research (NIHR) Imperial Biomedical Research Centre, W2 1NY London, UK; Specialist Medicine, Imperial College Healthcare NHS Trust, W12 OHS London, UK.
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