Browsing by Author "Shaboodien, Gasnat"

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    Analysis of desmoplakin in arrythmogenic right ventricular cardiomyopathy
    (2010) Fish, Maryam; Mayosi, Bongani; Shaboodien, Gasnat
    It has been shown that all forms of cardiomyopathy, including the dilated, hypertrophic, restrictive, and right ventricular arrhythmogenic forms, are found in African populations. Arrhythmogenic right ventricular cardiomyopathy (ARVC) is a rare muscle disease characterised by fibrofatty replacement of the right ventricular myocardium, leading to electrical instability and eventual heart failure. Dilated cardiomyopathy (DCM) is a disease characterised by a reduction in ventricular wall thickness which leads to reduced contractility and impaired ventricular function. Mutations that cause ARVC have been reported in five desmosomal and three non-desmosomal genes.
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    Analysis of genetic variations associated with arrhythmogenic right ventricular cardiomyopathy
    (2016) Fish, Maryam; Mayosi, Bongani M; Shaboodien, Gasnat
    Cardiomyopathy accounts for 20-30% of acute heart failure cases in adult Africans. Several types of cardiomyopathy have been identified; this study focused primarily on the genetic causes of arrhythmogenic right ventricular cardiomyopathy (ARVC). Many genes are implicated in ARVC pathogenesis, but many remain to be identified. We investigated a South African family (ACM2) with autosomal dominant ARVC, for whom the genetic cause of disease was unknown. Extensive genetic analysis was previously performed using genome-wide linkage analysis, but no disease-causing genetic variant was identified. We subsequently performed candidate gene screening of the phospholamban (PLN) gene, genome-wide copy number variant (CNV) analysis and whole exome sequencing to identify the causal genetic variant. The ACM2 family harboured no disease-causing PLN variants. However, on screening all cardiomyopathy cases in our registry (ARVC, dilated cardiomyopathy (DCM), hypertrophic cardiomyopathy and peripartum cardiomyopathy), we identified a known pathogenic PLN variant (c.25C>T; p.R9C) in a DCM family of European descent. This variant was reported in an American DCM family of European descent. Haplotype analysis revealed independent variant origins in these families. CNV analysis revealed no disease-causing variants in the ACM2 family. Whole exome sequencing of two affected ACM2 family members revealed 38 variants shared by these individuals. Variants were verified in family members and population controls by high resolution melt analysis and Sanger sequencing, and by bioinformatics analysis to predict variant pathogenicity. A novel N-cadherin (CDH2) c.686A>C (p.Q229P) variant segregated with ARVC in the ACM2 family and was bioinformatically predicted to be deleterious. An additional pathogenic CDH2 variant (c.1219G>A (p.D407N)) was identified in another individual with ARVC after screening 85 cases. These CDH2 variants were absent in normal population controls. Furthermore, alterations in Cdh2 are known to cause cardiomyopathy in rodent models. Taken together, these findings support the causal role of N-cadherin gene variants in human cardiomyopathy.
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    Genetics of Peripartum Cardiomyopathy: Current Knowledge, Future Directions and Clinical Implications
    (2021-01-15) Spracklen, Timothy F; Chakafana, Graham; Schwartz, Peter J; Kotta, Maria-Christina; Shaboodien, Gasnat; Ntusi, Ntobeko A B; Sliwa, Karen
    Peripartum cardiomyopathy (PPCM) is a condition in which heart failure and systolic dysfunction occur late in pregnancy or within months following delivery. Over the last decade, genetic advances in heritable cardiomyopathy have provided new insights into the role of genetics in PPCM. In this review, we summarise current knowledge of the genetics of PPCM and potential avenues for further research, including the role of molecular chaperone mutations in PPCM. Evidence supporting a genetic basis for PPCM has emanated from observations of familial disease, overlap with familial dilated cardiomyopathy, and sequencing studies of PPCM cohorts. Approximately 20% of PPCM patients screened for cardiomyopathy genes have an identified pathogenic mutation, with TTN truncations most commonly implicated. As a stress-associated condition, PPCM may be modulated by molecular chaperones such as heat shock proteins (Hsps). Recent studies have led to the identification of Hsp mutations in a PPCM model, suggesting that variation in these stress-response genes may contribute to PPCM pathogenesis. Although some Hsp genes have been implicated in dilated cardiomyopathy, their roles in PPCM remain to be determined. Additional areas of future investigation may include the delineation of genotype-phenotype correlations and the screening of newly-identified cardiomyopathy genes for their roles in PPCM. Nevertheless, these findings suggest that the construction of a family history may be advised in the management of PPCM and that genetic testing should be considered. A better understanding of the genetics of PPCM holds the potential to improve treatment, prognosis, and family management.
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    Investigation of Copy Number Variation in South African Patients with Congenital Heart Defects
    (2020) Saacks, Nicole Aimee; Shaboodien, Gasnat; Zühlke, Liesl
    Background: Congenital heart disease (CHD) is the leading non-infectious cause of paediatric morbidity and mortality worldwide and a significant social and healthcare burden. The aetiology of CHD is poorly understood, though heritable genetic factors including copy number variants (CNVs) have been shown to contribute to the risk of CHD in individuals of European ancestry. However, the role of rare CNVs in the development of CHD in African populations including South Africa is unknown. This study aims to identify pathogenic and likely pathogenic CNVs in South African cases of CHD. To our knowledge, this is the first study to investigate the genetic basis of CHD in a South African cohort. Methods: The study cohort included 105 patients presenting to the cardiac clinics at Red Cross War Memorial Children's Hospital and Groote Schuur Hospital with non-syndromic isolated CHD (n = 76), nonsyndromic CHD with additional extra-cardiac anomalies (n = 17), and positive controls with syndromic CHD (n = 12). Genotyping was performed using the Affymetrix CytoScan HD platform. Rare CNVs were filtered using stringent criteria for their size and algorithm-specific quality score and were compared against a gene panel of known CHD-associated genes. Candidate genes were considered based on pLI scores and reported CHD phenotypes in mouse models. The identified CNVs were validated by quantifying the read-coverage of available whole-exome sequencing data of a similar overlapping cohort. Results: Chromosomal microarray analysis was successful for 101 participants (including 89 non-syndromic CHD cases and 12 control cases) and led to the identification of eight CNVs overlapping genes known to be causal for CHD (GATA4, TBX1, FLT4, CRKL, NSD1, and B3GAT3), and four CNVs encompassing candidate genes likely to play a role in the development of CHD (DGCR8, JARID2, KDM2A, and FSTL1). The CNVs were identified in nine unrelated individuals: five of the CNVs were classified as pathogenic or likely pathogenic (5.6% of the cohort) and four were classified as variants of unknown significance (4.6%). CNVs of interest were validated using the available whole-exome sequencing data. Conclusions: In this study, we show that chromosomal microarray analysis is an effective technique for identifying CNVs in patients diagnosed with CHD and that this approach can be performed locally in South Africa, producing results similar to those seen in international CHD studies. The findings of this thesis highlight the wide genetic heterogeneity of CHD and the growing importance of CHD genetic studies for both research and clinical purposes. Advancing our understanding of CHD aetiology will help define disease risk in South Africa and improve the way we care for and assess our cardiac patients.
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    The mitochondrial DNA T16189C polymorphism and HIV-associated cardiomyopathy: a genotype-phenotype association study
    (BioMed Central Ltd, 2009) Shaboodien, Gasnat; Engel, Mark E; Syed, Faisal; Poulton, Joanna; Badri, Motasim; Mayosi, Bongani
    BACKGROUND: The mitochondrial DNA (mtDNA) T16189C polymorphism, with a homopolymeric C-tract of 10-12 cytosines, is a putative genetic risk factor for idiopathic dilated cardiomyopathy in the African and British populations. We hypothesized that this variant may predispose to dilated cardiomyopathy in people who are infected with the human immunodeficiency virus (HIV). METHODS: A case-control study of 30 HIV-positive cases with dilated cardiomyopathy and 37 HIV-positive controls without dilated cardiomyopathy was conducted. The study was confined to persons of black African ancestry to minimize confounding of results by population admixture. HIV-positive patients with an echocardiographically confirmed diagnosis of dilated cardiomyopathy and HIV-positive controls with echocardiographically normal hearts were studied. Patients with secondary causes of cardiomyopathy (such as hypertension, diabetes, pregnancy, alcoholism, valvular heart disease, and opportunistic infection) were excluded from the study. DNA samples were sequenced for the mtDNA T16189C polymorphism with a homopolymeric C-tract in the forward and reverse directions on an ABI3100 sequencer. RESULTS: The cases and controls were well matched for age (median 35 years versus 34 years, P = 0.93), gender (males 60% vs 53%, P = 0.54), and stage of HIV disease (mean CD4 T cell count 260.7/muL vs. 176/muL, P = 0.21). The mtDNA T16189C variant with a homopolymeric C-tract was detected at a frequency of 26.7% (8/30) in the HIV-associated cardiomyopathy cases and 13.5% (5/37) in the HIV-positive controls. There was no significant difference between cases and controls (Odds Ratio 2.33, 95% Confidence Interval 0.67-8.06, p = 0.11). CONCLUSION: The mtDNA T16189C variant with a homopolymeric C-tract is not associated with dilated cardiomyopathy in black African people infected with HIV.
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    The pathogenesis of HIV-associated cardiomyopathy : a histological, virological, and genetic study
    (2008) Shaboodien, Gasnat; Mayisi, Bongani M
    Includes abstract. Includes bibliographical references (leaves 115-136).
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    Preliminary genealogical evidence for the Plakophilin-2 gene, PKP2 c.1162C>T founder mutation in cases with Arrhythmogenic Right Ventricular Cardiomyopathy (ARVC)
    (2016) Machipisa, Tafadzwa; Shaboodien, Gasnat; Mayosi, Bongani M
    Introduction: Arrhythmogenic right ventricular cardiomyopathy (ARVC) is a progressive form of inherited heart muscle disease characterized by ventricular arrhythmias and sudden cardiac death. Often the pathogenesis is linked to deleterious mutations in the desmosomal gene plakophilin-2 (PKP2). We extended investigations of the pathogenic PKP2 c.1162C>T founder mutation which had previously been reported to occur within four 'unrelated' probands (6.2%) who selfidentified as Afrikaners and who also carried a common haplotype. Common evolutionary history suggests common haplotypes are linked to a common founder and today the Afrikaner populations are a unique ethnic group in South Africa identified with various founder effects for a range of heritable disorders. Aim: This study aimed to identify the common founder using genealogical and molecular methods for the PKP2 c.1162C>T mutation in ARVC families of Afrikaner descent in South Africa. Methods and results: DNA was collected from 46 participants (7 probands and 39 relatives) from the ARVC Registry of South Africa. Probands and relatives were screened for the PKP2 c.1162C>T mutation using High Resolution Melt and Sanger sequencing. The genetic results indicated that 65.2% (30/46) of the family members harbored this mutation. High Resolution Melt, Sanger sequencing and microsatellite typing were used to create a haplotype which encompassed the c.1162C>T mutation and three microsatellite markers (M1, D12S1692 and M2) spanning the PKP2 gene. A common haplotype emerged that segregated amongst all of the affected members of the seven Afrikaner families. Genealogical tracing went back, through multiple generations, into the implicated ancestral lines of the present day Afrikaner families. Four of the seven families attained their 17th century progenitors. Through genealogical analyses of the two largest families, ACM 19 and ACM 38, we identified 116 couples which we reduced to ten candidate South African founder couples who were then subjected to further analyses. After the ACM 12 family was added to the analysis there were five candidate founder couples. Unfortunately, the ACM 71 family did not progress past the 20th century due to tracing difficulties associated with poor record keeping of mixed ancestry data in South Africa and hence, could not be linked back to any other family tree without finding ACM71.5's grandparents. Additionally, ACM 8 and 57 families were recent finds and completion of their genealogical tracing still has to done. Conclusions: Our genetic data showed that not only were 30/46 individuals positive for the PKP2 c.1162C>T mutation but that all 30 individuals also shared the same common haplotype. Our preliminary genealogy tracing data suggests that the PKP2 c.1162C>T mutation segregates at a higher frequency in the Afrikaner population possibly due to a founder effect. The genealogical evidence supports the hypothesis that the PKP2 c.1162C>T mutation is a founder mutation and that descendants of the common founders are at risk of developing ARVC. At least three more families need to be recruited to make a clear conclusion and achieve genealogical evidence based saturation, ideally, a common founder.
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    Targeted re-sequencing of a large South African cardiomyopathy cohort
    (2024) Ndibangwi, Polycarp; Shaboodien, Gasnat; Ntusi, Ntobeko
    Introduction: Cardiomyopathy is a major cause of heart failure and transplantation globally. In sub Saharan Africa, cardiomyopathies are ranked as the third greatest contributing cause of cardiovascular diseases and account for about 30% of adults hospitalised with heart failure. The prevalence of heart failure due to cardiomyopathies is not well established in the South African population. To address this knowledge gap, we aimed to study the genetic cause of the disease in a large cohort of South African patients with cardiomyopathy. Design: We recruited participants from multiple centres in South Africa and Mozambique between 2015 and 2022. Cases were classified according to phenotypes by a team of experts. Using the Illumina platform, we used targeted sequencing on a panel of 38 known genes that cause primary cardiomyopathies. We used the ACMG classification to investigate class 3, 4 and 5 variants. Variants were validated using Sanger sequencing. Result: We recruited 690 cardiomyopathy probands (594 adults and 96 paediatrics). The 594 adults include dilated cardiomyopathy (n=450), hypertrophic cardiomyopathy (n=60), restrictive cardiomyopathy (n=43) and arrhythmogenic cardiomyopathy (n=41) probands. The adult DCMs constituted 75.8% (450/594) of the IMHOTEP study. The DCM probands had a mean age of 35.6 years at diagnosis, and a 56% preponderance of females were seen; the dominant populations recruited were Black-African (58%) and Mixed ancestry (33%). We reported a diagnostic yield of 16.9% (76/450) for the DCM probands, where 68.4% of the probands had pathogenic TTN truncating variants. The adult HCM cohort constituted 10.1% (60/594) of the IMHOTEP study probands, with a mean age of 41.3 years at diagnosis and a male preponderance of 65%. The dominant populations recruited were 57% Mixed and 25% Black-African. The diagnostic yield for the adult HCM cohort was 23.3% (14/60), with MYH7 (40%) and MYBPC3 (27%) found to be the predominant genes. The adult RCM cohort constituted 7.2% (43/594) of the IMHOTEP study probands, with a mean age of 33.0 years at diagnosis and a 65% female preponderance. The dominant populations recruited were 81% Black-African and 12% Mixed ancestry. We reported a diagnostic yield of 9.3% (4/43) for the RCM probands. The adult ACM cohort constituted 6.9% (41/594) of the IMHOTEP study probands, with a mean age of 40.6 years at diagnosis and a 65.9% male preponderance. The dominant populations recruited were 66% White and 20% Mixed ancestry. We reported a diagnostic yield of 29.3% (12/41), with PKP2 accounting for 62% of the variants. Meanwhile, paediatric probands constituted 13.9% (96/690) of the IMHOTEP study, and 70% were Black-Africans. The diagnostic yield for the paediatric cohort was 2.1% (2/96). Conclusion: This study summarises the findings of the largest cardiomyopathy cohort in Africa. We show a very low genetic yield across all cohorts and that most probands are younger than reported internationally. We also report that DCM has emerged as the dominant phenotype in South Africa. EMF and RCM were categorised as restrictive cardiomyopathies; however, this study identified no single genetic cause in the Mozambique cohort. This study highlights that there is still much work to be done as we have only identified the genetic cause of disease in a small proportion of cardiomyopathy patients.
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    The molecular genetics of familial cardiomyopathy
    (2023) Kamuli, Stephen Nzeki; Shaboodien, Gasnat; Ntusi, Ntobeko
    Introduction The cardiomyopathies are responsible for approximately 5.9 of 100,000 deaths in the general global population and in sub-Saharan Africa (SSA), these myocardial diseases are observed in 21.4% of patients with heart failure. The precise etiology of the cardiomyopathies is currently not well known and through our research we aim to contribute to the genetic landscape and bridge the gaps in knowledge for the different cardiomyopathies as SSA could provide some very important insights into the cardiomyopathies and identify other possible disease mechanisms. Methods Through next generation sequencing techniques such as whole exome sequencing and targeted resequencing we studied three South African families with severe cardiomyopathy. Clinical diagnosis and recruitment of cardiomyopathy patients into the study was done at Groote Schuur Hospital, Cape Town by a panel of experts. Next generation sequencing data was analysed and filtered through various stringent criteria and the final list of variants were validated through Sanger sequencing. Results In the first multi-generational family with severe dilated cardiomyopathy (DCM) (DCM 334), we identified a pathogenic DMPK c.1067C>T(p.P356L) variant in the proband and her affected father. We also screened a cohort of 542 cardiomyopathy probands though Sanger sequencing of the DMPK gene and identified the DMPK c.1477C>T(p.R493C) variant as a variant of unknown significance. We then investigated a three-generation family with four affected family members who were also affected with severe DCM (DCM343). We used whole exome sequencing and identified the pathogenic BAG3 c.925C>T (p.R309Ter) variant as the cause of disease within this family. Viral infection, anti-hypertensive medication and genetic modifiers in RYR1 and NEB contributed to the variable phenotype among the individuals with the BAG3 variant. Through targeted resequencing we also identified the same pathogenic BAG3 variant in 2 of the 634 cardiomyopathy probands screened. In the third family, we investigated a South African family affected with severe arrhythmogenic cardiomyopathy (ACM). We used whole exome sequencing and targeted resequencing in combination and identified the pathogenic PKP2 c.2197_2202InsGdelCACACC (p.H733Afs*8) as the cause of disease in the proband and his father. We also present evidence of the ALPK3 c.2701C>T(p.Q901Ter) variant modifying the phenotypic manifestation which correlates with the variable penetrance that is seen among ACM families. Conclusion Through this project, we have identified many firsts. To the best of our knowledge, we are the first to show that DMPK is associated with primary DCM in severely affected young patients. As a first for South Africa, we not only identified the pathogenic BAG3 variant in a family with severe DCM, but we also identified the same variant in two additional probands, raising the possibility of a founder effect. In the third and final family with ACM, we identified the pathogenic PKP2 variant as the cause of disease within this family with the novel ALPK3 variant acting as a possible modifier. Our research has added to what is currently known about the cardiomyopathies in Africa but there is still much work to be done as we believe we have just scratched the tip of the iceberg.
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    Validation of the PARVA c.392A>T variant in a South African family with severe Arrhythmogenic Right Ventricular Cardiomyopathy
    (2016) Kamuli, Stephen; Shaboodien, Gasnat; Mayosi, Bongani M
    Introduction: Cardiomyopathy is an endemic disease in Africa that is a major contributor to the clinical syndrome of heart failure. The various forms of cardiomyopathies pose a great challenge in Africa for many reasons, including the difficulty of diagnosis and the scarcity of interventions such as heart transplantations in resource-poor environments. The aetiology of the cardiomyopathies had been unknown but various genetic abnormalities associated with cardiomyopathy have been unraveled. A previous whole exome sequencing project conducted in the United Kingdom (UK) had identified parvin alpha (PARVA) as a candidate gene in a South African family, ACM 8, with several members affected with arrhythmogenic right ventricular cardiomyopathy (ARVC). Hypothesis: We hypothesize that PARVA harbors novel genetic mutations that cause ARVC and other forms of cardiomyopathy. Aim: To screen the PARVA gene for mutations in a large panel of probands with ARVC and other cardiomyopathies and to validate the whole exome sequencing results obtained in the UK on a different sequencing platform. Methods and Results: We investigated the ACM 8 family with three affected individuals (two severely affected children and the mother) for whom the genetic cause of the disease was unknown. Genetic analysis was previously performed at Newcastle in the UK using whole exome sequencing on an Illumina platform. In this analysis, the PARVA c.392A>T variant was identified as a possible cause of ARVC in this family. We expanded on this work by using high resolution melt (HRM) analysis and Sanger sequencing to screen all the available ACM 8 family members to determine segregation of the PARVA c.392A>T variant within this family. We observed that the phenotypic variability seen within this family cannot be explained by the PARVA c.392A>T variant alone and called into question the causative role of PARVA within this family We also screened the cardiomyopathy cohort consisting of 180 probands diagnosed with ARVC, dilated cardiomyopathy (DCM), hypertrophic cardiomyopathy (HCM) and restrictive cardiomyopathy (RCM) in the Cardiovascular Genetics Laboratory. No definitive evidence of pathogenic PARVA variants was found any of the cardiomyopathy probands screened. We subsequently performed whole exome sequencing on this family to validate the UK findings ( Ion Torrent platform). We found that both affected individuals were homozygous for the PKP2 c.1162C>T mutation. PKP2 is a gene known to cause ARVC, and the c.1162C>T mutation has been described as a founder mutation for autosomal dominant ARVC families of Afrikaner decent in South Africa. Conclusion: While this study set out to validate the whole exome sequencing experiments conducted in family ACM 8 in the UK, we instead found the causal variant to be the previously reported PKP2 c.1162C>T mutation. We also explored the possibility of PARVA as a causal gene for ARVC but no pathogenic PARVA mutations were identified.