Genetic Variants Research Articles

Discovery of a cryptic founder variant in MYBPC3 associated with hypertrophic cardiomyopathy by promoting the most frequent natural missplicing events

Abstract Introduction MYBPC3 splicing errors are a common cause of hypertrophic cardiomyopathy (HCM). Most known actionable intronic variants are located near exons. However, genetic variants in deep intronic regions are also emerging as casuals factors of HCM. The previously undescribed variant MYBPC3 (NM_000256.3):c.2308+227G>A is not reported in gnomAD or dbSNP but is overrepresented in a cohort of probands with HCM from the same geographical area. This led us to suspect its clinical relevance despite the very low probability of being splice-altering as assigned by SpliceAI (Δ score = 0.03). Purpose To conduct a phenotypic and clinical description of the cohort, ascertain the pathogenicity of the variant, and investigate the existence of a common ancestor. Methods (1) Observational analysis of clinical data and familial evaluation results, (2) Functional study involving mRNA expression analysis in peripheral blood, along with in silico analysis of the splicing disruption mechanism, and (3) Haplotype analysis to evaluate the founder effect and assess the age of the mutation. Results MYBPC3:c.2308+227G>A was identified in 26 probands with HCM (69% male; mean age at diagnosis 53±10 years). Eighty relatives from 20 families were screened resulting in 17 cases diagnosed (mean age 49±19 years; 53% males), 19 positive genotype/negative phenotype and 38 non-carriers. The greatest cosegregation involved three cases carrying the variant, confirmed in four different families. Males were diagnosed at a younger age but without significant differences in clinical features or events during follow-up (table). RT-PCR expression analysis in patients' blood revealed that this variant disrupts pre-mRNA splicing by promoting the use of cryptic donor and acceptor splice sites, located downstream and upstream of the variant, respectively, which are already present in the intron 23 reference sequence. Strikingly, these cryptic splice sites represent one of the most frequent natural unannotated missplicing events in MYBPC3, as evidenced by SpliceVault analysis of high-throughput RNA sequencing databases. The direct primary event induced by the variant is expected to disrupt a regulatory RNA-protein binding site, thereby unblocking the use of preexisting cryptic splice sites and amplifying natural exonification missplicing events within intron 23 (figure). Finally, the haplotype analysis, based on the copy number of nine STRs covering a total of 29.2 Mb surrounding MYBPC3:c.2308+227G>A, revealed that 17 unrelated carriers shared a DNA segment of 10 Mb (10,067,150 bp). The origin of this mutation is estimated to be at least 82 generations ago and roughly 1649 years in the past (IC95%:1180-2300). Conclusions MYBPC3:c.2308+227G>A is an elusive novel deep intronic variant causing HCM by a molecular mechanism not previously described in this context. The founder effect of this variant is confirmed in our geographical area.Phenotypic and clinical characteristics

Genetic Variants at PRKCG Splice and UTR Sites Promote Cancer Susceptibility by Disrupting Epigenetic and miRNA Regulatory Network

Genetic Variants at PRKCG Splice and UTR Sites Promote Cancer Susceptibility by Disrupting Epigenetic and miRNA Regulatory Network

Progress in understanding the genetic underpinning of coronary artery disease: from genotype to phenotype

Abstract Background The functional dissection of genetic risk opens the door to strategies for pharmacological manipulation of molecular and cellular processes implicated in human diseases, including coronary artery disease (CAD). Aim To assess the relationship between a set of single nucleotide polymorphisms previously associated with CAD and coronary artery calcium (CAC) score in an asymptomatic population from Portugal. Methods Prospective study in a cohort of 1,284 subjects aged 59.3±8.9 years, 73.6% males without apparent CAD. The CAC score was performed by cardiac computed tomography and reported as Agatston units according to the Hoff nomogram. Anthropometric, conventional, and biochemical risk factors were evaluated. Thirty-three single nucleotide polymorphisms were genotyped by TaqMan real-time PCR. Bivariate and multivariate logistic regression analysis estimated variables associated with the CAC score. Results After bivariate analysis, PHACTR1 rs1332844 C>T, a downstream regulator of the endothelin-1 gene, showed a significant association with CAC score (p=0.015), together with CDKN2B-AS1 variants rs4977574 A>G in the locus 9p21.3 (p=0.002) and rs1333049 G>C (p=0.010). MTHFD1L gene encodes a mitochondrial enzyme responsible for homocysteine remethylating in methionine, and rs6922269 G>A showed protection against artery calcification (p=0.013). After multivariate logistic regression, PHACTR1 rs1332844 (CT+TT) (p=0.009) and CDKN2B-AS1 rs4977574 A>G (GG) (p=0.002) remained in the equation as independently associated with arterial calcification, together with male sex (p=0.039), age (p<0.0001), hypertension (p=0.001), diabetes (p<0.0001), smoking status (p<0.0001) and obesity (p=0.020). MTHFD1L rs6922269 AA also remained as significant protection from arterial calcification (p=0.027). Conclusion The present work showed two genetic variants, PHACTR1 and CDKN2B-AS1, linked to arterial wall calcification, herewith clinical and environmental risk factors. MTHFD1L showed protection. Understanding the genetic basis of vessel calcification can enable lifestyle changes or pharmacologic therapy to attenuate risk before the disease becomes clinic. More research in this field is critical to understanding the genetic basis of CAD through an intermediate phenotype, coronary arterial wall calcification.

Potential use of pharmacogenetics in cardiology: genome-wide association studies of amiodarone-induced thyroid disorders

Abstract Background Amiodarone is a commonly prescribed antiarrhythmic drug used to manage supraventricular and ventricular arrhythmias. The use of amiodarone is associated with a broad range of adverse effects, including amiodarone-induced hypothyroidism (AIH) or amiodarone-induced thyrotoxicosis (AIT) (1). Both conditions are linked with increased mortality and have no known reliable risk predictors (2). Purpose We investigated the genetic underpinnings of amiodarone-induced thyroid disorders, and the clinical validity and utility of screening for genetic variants. Methods We conducted the first genome-wide association studies (GWAS) of AIH and AIT using data from three large biobanks. We compared the AUCs for SNPs identified through the above GWAS with polygenic risk scores for both hypo- and hyperthyroidism. Finally, we tested the clinical validity and utility of screening for risk variants. Results We found two risk loci for AIH. The lead variant at the first locus, rs1443438, was intronic to FOXE1 (OR 0.39, MAF = 35%, P = 1.59 × 10-42). The other lead variant, rs2209796, was located 93 kb upstream to FOXA2 (OR 0.56, MAF = 29%, P = 2.64 × 10-15: Figure 1). For AIT, we found one risk locus. The lead variant, rs2268803, was intronic to CAPZB (OR 1.81, MAF = 42%, P = 2.43 × 10-8: Figure 1). Next, we added GWAS SNPs or polygenic risk scores to risk prediction models consisting of age, sex and 4 principal components (PCs), and compared AUC estimates between risk models. Using GWAS SNPs, we found that the AIT variant increased the AUC with 6% (95%CI 1.1 – 10.3, AUC: 0.72) and 9% (95%CI 6.2 – 11.2, AUC: 0.75) for AIH, compared to the benchmark model. Both GWAS SNP models were superior to polygenic risk scores in terms of AUC (P for difference <0.05). The positive and negative predictive value (PPV and NPV) for the AIT-variant was 14.6% and 95.7%, respectively. For the AIH-variants combined, we found a PPV of 17% and a NPV of 95%. Conclusions Common genetic variants are associated with both amiodarone-induced hypo- and hyperthyroidism and are at this point, superior to polygenic risk scores in predicting amiodarone-induced thyroid disorders. These findings add to the potentials of pharmacogenetics in cardiology. Figure 1. Double Manhattan plot of amiodarone induced thyroid disorders. The Y-axis is the negative log10 of the P-value for each single nucleotide polymorphism. The X-axis is the chromosome, with positions on each chromosome ranging from lower to higher (left to right). The dotted line marks the threshold for genome-wide significance. Amiodoarone-induced hypothyroidism at the top, and amiodarone-induced thyrotoxicosis at the bottom.Figure 1

Chemoproteogenomic stratification of the missense variant cysteinome

Cancer genomes are rife with genetic variants; one key outcome of this variation is widespread gain-of-cysteine mutations. These acquired cysteines can be both driver mutations and sites targeted by precision therapies. However, despite their ubiquity, nearly all acquired cysteines remain unidentified via chemoproteomics; identification is a critical step to enable functional analysis, including assessment of potential druggability and susceptibility to oxidation. Here, we pair cysteine chemoproteomics—a technique that enables proteome-wide pinpointing of functional, redox sensitive, and potentially druggable residues—with genomics to reveal the hidden landscape of cysteine genetic variation. Our chemoproteogenomics platform integrates chemoproteomic, whole exome, and RNA-seq data, with a customized two-stage false discovery rate (FDR) error controlled proteomic search, which is further enhanced with a user-friendly FragPipe interface. Chemoproteogenomics analysis reveals that cysteine acquisition is a ubiquitous feature of both healthy and cancer genomes that is further elevated in the context of decreased DNA repair. Reference cysteines proximal to missense variants are also found to be pervasive, supporting heretofore untapped opportunities for variant-specific chemical probe development campaigns. As chemoproteogenomics is further distinguished by sample-matched combinatorial variant databases and is compatible with redox proteomics and small molecule screening, we expect widespread utility in guiding proteoform-specific biology and therapeutic discovery.

Myocardial DNA damage is responsible for the relationship between genotype and treatment response in patients with dilated cardiomyopathy

Abstract Background Dilated cardiomyopathy (DCM) is one of the leading causes of heart transplantation. Our group and others have previously reported that DNA damage accumulation in myocardial tissue and certain genetic variants such as those in LMNA are associated with treatment response and prognosis (ref 1-5). However, the potential association between myocardial DNA damage and genotype, and their contribution when combined to predicting treatment response, remains unclear. Methods We identified the deleterious variants in cardiomyopathy-related genes by analyzing the whole exome sequencing data from 89 patients with DCM who were recruited from two participating facilities. Immunostaining of γ-H2A.X, a DNA damage marker, was performed on endomyocardial biopsy specimens from the same patients, from which the percentage of nuclei positive for γ-H2A.X signals (%γ-H2A.X) was calculated. Left ventricular reverse remodeling (LVRR) was assessed by transthoracic echocardiography at 1 year after biopsy. We examined the associations among genotype, myocardial DNA damage, and the achievement of LVRR. Results Among the 89 patients with DCM, 11 (12.4%) carried pathogenic or likely pathogenic (P/LP) variants in sarcomere genes such as TTN, and 21 (23.6%) carried P/LP variants in non-sarcomere genes such as LMNA, while the rest had no P/LP variants in cardiomyopathy-related genes (Figure A). Patients with P/LP variants in sarcomere genes had a lower %γ-H2A.X [21.2 (10.7–29.0)% vs. 7.0 (4.3–12.4)%, P = 0.002] (Figure B), and a higher probability to achieve LVRR at 1-year (81.8% vs. 23.8%, P = 0.003) (Figure C) when compared to those with P/LP variants in non-sarcomere genes. The odds ratio for carriers of P/LP variants in sarcomere genes to achieve LVRR was 14.40 (95%CI 2.31–89.94) compared to that for carriers of P/LP variants in non-sarcomere genes. However, this effect was markedly attenuated after adjusting for the proportion of γ-H2A.X-positive nuclei [adjusted odds ratio 6.05 (95%CI 0.86–42.53)] (Table). Conclusions Among patients with DCM, carriers of P/LP variants in sarcomere genes showed less DNA damage and a favorable treatment response, when compared with carriers of P/LP variants in non-sarcomere genes. Our results suggest that myocardial DNA damage was partially responsible for the relationship between genotype and treatment response in patients with DCM.Figure, panels A-C

UGT1A1 and BLVRA allele and genotype variants in neonatal patients with hyperbilirubinemia in southern China

We explore the allele and genotype distribution of UGT1A1 and BLVRA variants in individuals affected by neonatal hyperbilirubinemia in southern China. Blood specimens were collected from 240 neonates: 126 cases of hyperbilirubinemia and 114 healthy controls. Serum levels of total protein, albumin, bilirubin (total and direct), urea nitrogen, creatinine, and other biochemical parameters were quantified using a biochemical analyzer. Nine UGT1A1 and five BLVRA genetic variants were genotyped using flight time mass spectrometry. The allele and genotype frequencies of these variants and their associations with neonatal hyperbilirubinemia were analyzed. The genotype frequencies of CC and CG for the UGT1A1 variant rs11888492 in the hyperbilirubinemia group were 90.48% and 9.52%, respectively (P = 0.001), in comparison with the control group. The C and G allele frequencies of rs11888492 in the hyperbilirubinemia group were 95.24% and 4.76%, respectively (P = 0.023). Similarly, in the hyperbilirubinemia group, the genotype frequencies for the UGT1A1 variant rs4148325 were 90.48% CC, 8.73% CT, and 0.79% TT (P = 0.001), with corresponding allele frequencies of 94.84% for C and 5.16% for T (P = 0.002). No notable distinctions were detected for other variants. Newborns carrying the CC genotype of rs11888492 exhibited higher total bilirubin (TBIL) levels than those carrying the GG genotype (P = 0.034), whereas newborns carrying the CC genotype of rs4148325 displayed higher TBIL levels than those carrying the CT genotype (P = 0.003). The presence of the G allele at rs11888492 was found to be significantly correlated with a decreased likelihood of developing neonatal hyperbilirubinemia (odds ratio [OR]: 0.363; 95% confidence interval [CI] 0.169–0.777). Furthermore, a substantial reduction in the risk of neonatal hyperbilirubinemia associated with the CT genotype of rs4148325 were revealed (OR = 0.242; 95% CI 0.102–0.574). Additionally, an inverse relationship was identified between TBIL concentration and the quantity of genetic variants. The UGT1A1 variants rs11888492 and rs4148325 are strongly associated with neonatal hyperbilirubinemia in southern China.

Blood pressure polygenic risk scores associate with resistant hypertension in individuals with type 1 diabetes

Abstract Background Hypertension is a major risk factor of global disease burden, but treatment goals are often not met. A subset of individuals with hypertension is affected by treatment-resistant hypertension (RHTN), and they suffer from increased cardiovascular morbidity and mortality. Early identification of individuals at risk of RHTN could lead to more efficient antihypertensive drug treatment. Purpose The aim of this study was to investigate whether polygenic risk scores (PRS) for systolic (SBP) and diastolic blood pressure (DBP) predict RHTN in individuals with or without type 1 diabetes (T1D). Methods We performed association analyses between PRSs and RHTN in two Finnish cohorts: The Finnish Diabetic Nephropathy Study (FinnDiane) and the Finnish individuals of the LIFE Study (LIFE-Fin). FinnDiane is an ongoing, observational nationwide study aiming to identify genetic and clinical risk factors for complications of T1D. We included data from 778 adults (476 with RHTN and 302 with controlled hypertension). LIFE is a randomized, double-blind study evaluating long-term effects of losartan compared with atenolol in patients with signs of left ventricular hypertrophy. We used SBP and DBP data from 378 Finnish individuals (173 with RHTN and 205 with controlled hypertension) at the four-year visit of the study. In FinnDiane, RHTN was defined as SBP ≥130 or DBP ≥85 mmHg and the use of three or more antihypertensive drugs, or SBP <130 and DBP <85 mmHg and the use of four or more antihypertensive drugs. In LIFE-Fin, RHTN was defined as SBP ≥140 or DBP ≥90 mmHg and the use of three or more antihypertensive drugs. Controlled hypertension was defined as the use of three or fewer antihypertensive drugs and SBP <130 and DBP <85 mmHg in FinnDiane, and as SBP <140 and DBP <90 mmHg in LIFE-Fin. We calculated a PRS for each participant using genome-wide association study data for 1,098,015 genetic variants; the variant-specific data were derived from UK Biobank based PRS-CS-method computed PRSs (1). Results We observed significant associations of SBP and DBP PRSs with RHTN in FinnDiane (OR 1.56 [1.30; 1.87], P = 1.8e-6, and OR 1.25 [1.04; 1.50], P = 0.02, per one-SD increase of the PRS value) when adjusted for age, sex, estimated glomerular filtration rate and body mass index. The association between SBP PRS and RHTN remained significant when T1D individuals with or without albuminuria were analysed separately. Neither SBP nor DBP PRSs were significantly associated with RHTN in LIFE-Fin. Conclusion Higher SBP PRSs associate with higher risk of RHTN in individuals with T1D, with or without albuminuria, but not in nondiabetic individuals with hypertension. It remains to be investigated whether general blood pressure genetics contribute to RHTN in the general population.

Diabetes Mellitus influence in Lipoprotein(a) gene expression and association to coronary artery disease

Abstract Introduction Lp(a) and type 2 diabetes mellitus are both known and established risk factors for the development of coronary artery disease (CAD). Lp(a) levels are 75% to 95% heritable and predominately determined by single-nucleotide variants at the LPA gene; rs3798220 is one of the most studied variants and accounts for a significant portion of Lp(a) levels. Whether diabetes could influence the LPA rs3798220 account for Lp(a) levels is unknown. Aim Evaluate whether there is a different association between polymorphism LPA rs3798220 T>C and Lp(a) levels and their association with CAD in diabetic and non-diabetic populations. Methods 3,209 subjects (mean age 59.3±8.9 years, 76.3% male were selected from the data set of the Research Center. The LPA rs3798220 T>C was genotyped with the TaqMan PCR assay (Applied Biosystems 7300 Real-Time). This genetic variant has a minor allele frequency (MAF) <2%; hence, the risk homozygous CC is a rare genotype, and we used the heterozygous CT in our analysis. Lp(a) biochemical levels were measured in all participants. From the 3,209 participants, 810 had diabetes, and 2399 were no diabetics. For each group, chi-squared tests were used to determine the association of CAD prevalence by genotype, and t-tests were used to evaluate differences in CAD prevalence by Lp(a) levels. Results In non-diabetic subjects, LPA TC was significantly associated with CAD in non-diabetic subjects compared with TT (p<0.0001). Similarly, Lp(a) was higher in the CAD population (37.2±39.7) compared to the healthy population (25.6±30.0) (p<0.0001). In diabetic group, Lp(a) was higher in the CAD population (38.5±41.4) compared to the population without CAD (23.9±29.2) (p<0.0001). Nevertheless, there was no difference in genotype between CAD and non-CAD patients (p=0.710). Conclusion The LPA rs3798220 T>C variant in non-diabetic group can explain high Lp(a) levels and their association with CAD. However, in patients with diabetes, Lp(a) is elevated in CAD patients besides the fact that no significant genotype differences were displayed. Non-genetic influences like behavioural factors or even epigenetic changes may probably explain high Lp(a) levels in this population.

Prevalence of pathogenic variants in cardiomyopathy-associated genes in acute myocarditis: a systematic review and meta-analysis

Abstract Background Acute myocarditis is an inflammatory condition that may precede the development of dilated or arrhythmogenic cardiomyopathy. Objectives To investigate the reported prevalence of pathogenic/likely pathogenic (P/LP) variants in cardiomyopathy-associated genes in patients with acute myocarditis. Methods For this systematic review and meta-analysis, we searched Pubmed and Embase databases on March 04, 2023. Observational studies evaluating the prevalence of P/LP variants in cardiomyopathy-associated genes in patients with acute myocarditis were included. Studies were stratified into adult and pediatric age groups and for the following scenarios: (a) complicated myocarditis (i.e., presenting with acute heart failure, reduced left ventricular ejection fraction, or life-threatening ventricular arrhythmias); (b) uncomplicated myocarditis. The study followed PRISMA guidelines. Results Of 732 studies identified, 8 met the inclusion criteria, providing data for 586 patients with acute myocarditis. A total of 89 P/LP variants in cardiomyopathy-associated genes were reported in 85 patients. In uncomplicated myocarditis the pooled prevalence was 4.2% (95% CI 1.8-7.4%, I2 1.4%), while in complicated myocarditis pooled prevalence was 21.9% (95% CI 14.3-30.5%, I2 38.8%) and 44.5% (95% CI 22.7-67.4%, I2 52.8%) in adults and children, respectively. P/LP variants in desmosomal genes were predominant in uncomplicated myocarditis (64%), while sarcomeric gene variants were more prevalent in complicated myocarditis (58% in adults and 71% in children). Conclusions Genetic variants are present in a large proportion of patients with acute myocarditis. The prevalence of genetic variants and the genes involved vary according to age and clinical presentation.Central Illustration

Metabolomic profiling of the entire UK Biobank enables interpretation of familial hypercholesterolemia mutations and prediction of severe cardiovascular outcomes

Abstract Background Familial hypercholesterolemia (FH) is an inherited disorder resulting in high levels of LDL-C from birth. Premeature coronary heart disease occurs in half of affected men by age 50 years(1). While many genetic variants that cause FH are well understood, there are also many variants in FH genes that are of uncertain clinical significance. Furthermore, the variability in residual cardiovascular risk of FH carriers after statin treatment is not fully understood. We here investigate whether metabolomic and genomic data from the 500,000 person UK Biobank cohort can aid in interpretation of candidate pathogenic variants for FH, and characterise future risk of severe cardiac events in the carriers of such variants. Methods We have quantified 249 metabolomic parameters in 490,830 blood samples from UK Biobank cohort. Among 186,483 participants with exome sequence data we identified 896 who carried known pathogenic FH variants and 405 who carried variants of unknown significance in an established FH gene. We fitted a logistic predictive model to identify pathogenic mutations using LDL levels, statin use and 17 principal components of the metabolomic parameters. We further tested whether metabolomic and genomic scores for predicting future risk of myocardial infarction (MI), that were trained in the general population (i.e. individuals without FH), could predict risk in FH carriers. Results A model including all metabolites had a higher accuracy at identifying known pathogenic FH variants (36/56 at FDR < 0.05), compared to LDL and statin use alone (30/56). Our model also identified 8 FH variants marked as uncertain significance in ClinVar with significant (FDR < 0.05) evidence of predicted pathogenicity. We found that our metabolomic risk score predicted 10-year risk of MI among FH carriers (HR=1.96 per SD, p = 0.0011). This was indeed stronger than the effect in the general population (HR = 1.64 per SD, p = 2.5e-168). A combined metabolomic and polygenic risk score had an even larger effect at predicting MI in FH carriers (HR = 3.06 per SD, p = 2.0e-6), and this score was significantly better at predicting MI in FH carriers than in non-carriers (HR = 3.06 vs 1.88 per SD, interaction p = 0.042). Conclusion Familial hypercholesterolemia is an important source of risk for early cardiovascular disease. Population-scale metabolomics can help distinguish pathogenic from benign variants that have not yet been characterised. Metabolomic and genomic scores can also identify individuals at most elevated risk, and provide even more information to FH individuals than in the general population.

Prognostic role of gene variants in sudden cardiac death risk associated to paediatric hypertrophic cardiomyopathy

Abstract Introduction Genetic testing plays an important role in diagnosis of hypertrophic cardiomyopathy (HCM), being sarcomeric genes commonly involved, particularly MYBPC3. However, arrhythmic risk related to genotype remains unclear in adults and almost unexplored in children. Hence, current sudden cardiac death (SCD) risk calculators do not include genetic information. Purpose To analyse risk of arrhythmic events associated with causal variants in MYBPC3 respecting to other genes in a paediatric cohort with non-syndromic HCM from a cardiomyopathy referral centre. Methods This retrospective study included patients with non-syndromic HCM 0-18 years old between 2009-2022. Demographic, clinical, and genetic data were collected. Genetic variants pathogenicity followed American College of Medical Genetics criteria. A positive genetic test was considered if a likely pathogenic or pathogenic variant in HCM related genes was found. Considered outcomes were SCD or a major arrhythmic cardiac event (MACE) within 5 years follow-up: recovered SCD, appropriate ICD therapy, or sustained ventricular tachycardia. Some SCD-risk estimation models (in 5 years) as HCM Risk-SCD model for patients >=15 y.o and/or 55 kg, ESC Guidelines paediatric algorithm, and HCM Risk-Kids model were applied. Results 77 patients were diagnosed with non-syndromic HCM. A causal variant was found in 45/73 (62%). No significant differences in cardiac phenotype were found related to genes. 10/77 patients (13%) presented a MACE in 5 years follow-up. A positive genetic study was significantly associated with having an event (p=0.011). Most patients with a positive genetic test harboured MYBPC3 variants (21/45, 47%), however only 2 patients who suffered a MACE had a causal variant in MYBPC3. Those with causal variants in genes other than MYBPC3 presented more and earlier events (p=0.022). Risk of having a MACE during follow-up was higher when presenting causal variants in genes other than MYBPC3: Hazard Ratio 18.5 (95% CI 2.31, 148), p=0.006. Applying HCM Risk-SCD calculator, model had better predictive discrimination when variable "causal variant in gene other than MYBPC3" was added in multivariate analysis, with high-risk category >=6% (C-statistic =0.931 vs 0.844) and intermediate-risk category 4-6% (C-statistic =0.845 vs 0.514). Same occurred with ESC Guidelines algorithm, adding that variable to 2 risk factors category (C-statistic =0.881 vs 0.742) or 1 risk factor (C-statistic =0.844 vs 0.635). HCM Risk-Kids also improved its predictive discrimination adding the genetic value to high-risk category >=6% (C-statistic =0.896 vs 0.796) and intermediate-risk (C-statistic =0.821 vs 0.506). Conclusions Genotype may have prognostic value in SCD risk in HCM in children. Our results suggests that causal genetic variants in genes other than MYBPC3 can lead to higher risk of SCD. Genetic information might be considered for future models of arrhythmic risk in children with HCM.

Genetic variations in PEAR1 are associated with progression of coronary artery disease

Abstract Aim Platelet endothelial aggregation receptor 1 (PEAR1) is a newly discovered membrane protein mainly expressed in endothelial cells and platelets. Previous researches have indicated the effect PEAR1 had on inflammation. This study aims to investigate the association between PEAR1 genetic variations and coronary artery disease (CAD) progression, which was regarded as a chronic inflammatory procedure. Methods We genotyped twelve common single nucleotide polymorphisms (SNPs) (rs2768759, rs2768762, rs12566888, rs12041331, rs11264579, rs77235035, rs57731889, rs822441, rs822442, rs11264581, rs56260937, and rs4661012) and detected the DNA methylation level of fourteen CpG loci in the promoter of PEAR1 in 162 Chinese patients with CAD. We accessed the association between PEAR1 genetic variants and the progression status of CAD, separated into stable angina, unstable angina, non-ST-elevation myocardial infarction (NSTEMI), and ST-elevation myocardial infarction (STEMI). Results This CAD cohort included 40 (24.7%) with stable angina, 85 (52.5%) with unstable angina, 33 (20.4%) with NSTEMI, and 4 (2.5%) with STEMI. After adjusting for age, sex, hyperlipidemia, and diabetes mellitus as covariates in multiple logistic regression, rs12041331 was the only SNP that significantly associated with CAD type. Carriers of the A allele in rs12041331 were more likely to develop an unstable state (RR=1.996, 95%CI=1.075~3.710, p-value=0.029, Fig. 1). Carriers of A allele in rs11264579 is a potential risk factor of progression of atherosclerosis (RR=2.84, 95%CI=0.99~8.10, p-value=0.051, Fig. 1). Compared with other sites, SNPs of intron 1 were more likely to be associated with the risk of atherosclerosis progression (Fig.2). Conclusion Carriers of A allele in rs12041331 may lead to an increased risk of CAD progression. Region-specific genetic variant reinforces the association between PEAR1 and the risk of atherosclerosis progression.Effect of PEAR1 genetic variants.Correlation between PEAR1 SNPs and risk.

The Molecular Classification of Pheochromocytomas and Paragangliomas: Discovering the Genomic and Immune Landscape of Metastatic Disease.

Pheochromocytomas (PCCs) and paragangliomas (PGLs, together PPGLs) are the most hereditary tumors known. PPGLs were considered benign, but the fourth edition of the World Health Organisation (WHO) classification redefined all PPGLs as malignant neoplasms with variable metastatic potential. The metastatic rate differs based on histopathology, genetic background, size, and location of the tumor. The challenge in predicting metastatic disease lies in the absence of a clear genotype-phenotype correlation among the more than 20 identified genetic driver variants. Recent advances in molecular clustering based on underlying genetic alterations have paved the way for improved cluster-specific personalized treatments. However, despite some clusters demonstrating a higher propensity for metastatic disease, cluster-specific therapies have not yet been widely adopted in clinical practice. Comprehensive genomic profiling and transcriptomic analyses of large PPGL cohorts have identified potential new biomarkers that may influence metastatic potential. It appears that no single biomarker alone can reliably predict metastatic risk; instead, a combination of these biomarkers may be necessary to develop an effective prediction model for metastatic disease. This review evaluates current guidelines and recent genomic and transcriptomic findings, with the aim of accurately identifying novel biomarkers that could contribute to a predictive model for mPPGLs, thereby enhancing patient care and outcomes.

Barriers in translating existing nutrigenetics insights to precision nutrition for cardiometabolic health in ethnically diverse populations.

Cardiometabolic diseases pose a significant threat to global public health, with a substantial majority of cardiovascular disease mortality (more than three-quarters) occurring in low- and middle-income countries. There have been remarkable advances in recent years in identifying genetic variants that alter disease susceptibility by interacting with dietary factors. Despite the remarkable progress, several factors need to be considered before the translation of nutrigenetics insights to personalised and precision nutrition in ethnically diverse populations. Some of these factors include variations in genetic predispositions, cultural and lifestyle factors as well as socioeconomic factors. This review aims to explore the factors that need to be considered in bridging the gap between existing nutrigenetics insights and the implementation of personalised and precision nutrition across diverse ethnicities. Several factors might influence variations among individuals with regards to dietary exposures and metabolic responses and these include genetic diversity, cultural and lifestyle factors as well as socioeconomic factors. A multi-omics approach involving disciplines such as metabolomics, epigenetics and the gut microbiome might contribute to improved understanding of the underlying mechanisms of gene-diet interactions and the implementation of precision nutrition although more research is needed to confirm the practicality and effectiveness of this approach. Conducting gene-diet interaction studies in diverse populations is essential and studies utilising large sample sizes are required as this improves the power to detect interactions with minimal effect sizes. Future studies should focus on replicating initial findings to enhance reliability and promote comparison across studies. Once findings have been replicated in independent samples, dietary intervention studies will be required to further strengthen the evidence and facilitate their application in clinical practice. Nutrigenetics has a potential role to play in the prevention and management of cardiometabolic diseases. Conducting gene-diet interaction studies in diverse populations is essential giving the genetic diversity and variations in dietary patterns. Integrating data from disciplines such as metabolomics, epigenetics and the gut microbiome could help in early identification of individuals at risk of cardiometabolic diseases as well as the implementation of precise dietary interventions for preventing and managing cardiometabolic diseases.

Comparative Study on the Genetic Architecture of Type 2 Diabetes in Indian and Other Ethnic Groups: A Review

Type 2 diabetes mellitus (T2DM) is a condition of metabolism that impacts people worldwide regardless of country, age group, and gender. In addition to a sedentary lifestyle, genetic susceptibility, specifically single nucleotide polymorphisms, is implicated in the emergence and progression of T2DM. This study compares the genetic variants of the Indian population with three other ethnic cohorts: African, European, and Chinese. Based on the literature survey, common and unique Single Nucleotide Polymorphisms (SNPs) and genes were explored in different Populations, including PPARG, TCF7L2, THADA, CDKN2A, IGF2BP2, SLC30A8, HHEX and CDKAL1. Identifying common and specific markers may help in risk prediction and early detection of T2DM. In conclusion, this comparative study of T2DM-susceptible SNPs in Indian and other ethnic groups highlights the complexity and diversity of genetic factors contributing to T2DM. By shedding light on the similarities and disparities in genetic predisposition across populations, this review contributes to the ongoing efforts to develop more effective and tailored approaches for managing and avoiding T2DM in diverse global populations.

Pathogenic cardiomyopathy gene variants inform prognosis in atrial fibrillation: results from exome sequencing in over 17,000 patients in TIMI trials

Abstract Background Rare genetic variants in cardiomyopathy genes are associated with risk of atrial fibrillation (AF), even in the absence of overt ventricular dysfunction. Data on clinical outcomes for rare genetic variant carriers among patients with AF remain sparse. Purpose We aimed to study the prognostic implication of rare pathogenic/likely pathogenic (PLP) variants for dilated cardiomyopathy (DCM), hypertrophic cardiomyopathy (HCM) and arrhythmogenic right ventricular cardiomyopathy (ARVC) in patients with AF from large, well-phenotyped randomized clinical trials. Methods and results Rare variants were called using exome sequencing data in 5 large clinical trials from the TIMI study group (ENGAGE-AF, FOURIER, SAVOR, PEGASUS, DECLARE). PLP variants for cardiomyopathy were identified using phenotype- and gene-specific curation of protein-truncating variants and high-confidence variant classifications from the ClinVar database. In 17,190 patients with a history of AF, we identified 421 (2.4%) PLP variant carriers (age 67±10, 35% women) and 16,769 (97.6%) pts without PLP variants (age 70±9, 36% women). Among these individuals, we identified 265 DCM carriers (1.5%), 106 (0.6%) HCM carriers and 54 (0.3%) ARVC carriers. In this cohort, 9,275 (54%) had a history of heart failure (HF) and 2,991 (17.4%) prior ischemic stroke. Over 2.5 years median follow-up, 1,365 pts (7.9%) were hospitalized for HF, 599 (3.5%) had an ischemic stroke, and 1147 (6.7%) died of cardiovascular causes. In logistic regression analyses adjusting for age, sex, trial, and principal components of ancestry, PLP variants were significantly associated with a history of HF (OR 1.66, p<0.0001), most notably for DCM variants (OR 1.97, 1.48-2.62, p<0.0001). PLP variants were independently associated with incident HF admissions (adj HR 1.75, 1.39-2.29, p<0.0001), most notably for HCM (adj HR 2.59, 1.68-3.99, p<0.0001) and ARVC variants (adj HR 2.50, 1.34-4.66, p=0.004). The increased risk of HF admissions remained consistent in patients with (adj HR 1.49, 1.11-2.00, p=0.009) and those without (adj HR 1.88, 1.00-3.54, p=0.049) a history of HF. PLP variants were also associated with higher risk of cardiovascular death (adj HR 1.46, 1.06-2.02, p=0.02), most notably for DCM variants (adj HR 1.77, 1.21-2.58, p=0.003). In contrast, PLP variants were not associated with history of ischemic stroke at baseline (adj OR 0.99, p=0.96) nor with incident ischemic stroke (adj HR 0.95, p=0.84). Conclusion In patients with AF, rare cardiomyopathy gene variants are associated with increased risks of HF and of cardiovascular death, but not stroke. These results, collected from large well-phenotyped randomized clinical trials, demonstrate an important prognostic implication for rare genetic variants for CMP in pts with AF.

Redefining genotype-phenotype correlation among patients with arrhythmogenic cardiomyopathy: a CMR cohort study

Abstract Background and purpose Arrhythmogenic cardiomyopathy (ACM) is a poorly defined, life-threatening condition. We aimed at identifying the patterns of regional wall motion abnormalities, fibrosis, and fatty infiltration seen on Cardiac Magnetic Resonance (CMR) and correlate them with the different genetic backgrounds. Methods We retrospectively identified ACM patients who underwent CMR and genetic test analysis. We collected data on CMR-derived cardiac volumes, function and tissue characterization. Results Seventy-eight patients with a clinical diagnosis of ACM were enrolled. Genetic tests were performed in 65 (83%) and identified a pathogenetic/likely pathogenetic variant in 51 (78%) patients (38% plakophilin-2, 23% desmoplakin, 5% desmoglein, 5% desmocollin and 8% filamin-C). Imaging features varied according to the genetic background, with subepicardial or mid-wall fibrosis distribution affecting predominantly the lateral and inferior segments of the left ventricle (LV) among the different groups and the septal segments in patients with the filamin-C variant. A characteristic LV subepicardial circumferential LGE pattern ("ring-like") was distinctively and almost exclusively associated with the desmoplakin variant. Conclusions Genetic variants of ACM present some common but also distinctive CMR phenotypes that can help in further characterizing the specific disease signatures associated with different genes. Further studies should investigate the prognostic value of these CMR findings.

Impact of high intensity and long duration exercise in genetic arrhythmogenic left ventricular cardiomyopathy

Abstract Background Arrhythmogenic left ventricular (LV) cardiomyopathy (ALVC) is a genetic disease associating extensive LV myocardial fibrosis with or without dysfunction and no or mild right ventricle (RV) involvement, at risk of life-threatening ventricular arrhythmias (VA). While high intensity (HI) and long duration (LD) exercise has been identified as a precipitating factor of RV dysfunction and VA in arrhythmogenic RV cardiomyopathy including in asymptomatic genetic variant carriers, the impact of exercise on disease phenotype and risk is not known in ALVC. Objective To study the relationship between practicing HI and LD exercise and the risk of developing an ALVC phenotype and its severity. Methods In a monocentric retrospective observational study, patients with a pathogenic variant in common ALVC genes (DSP, FLNC, DES, PLN, RBM20, TMEM43), including asymptomatic carriers without ALVC phenotype, were interviewed about their physical practice from age 7 to the time of genetic or disease diagnosis. Intensity and weekly duration of each activity were reported. HI and LD exercise were defined as having practiced at least 1 sport with an intensity ≥ 6 METs and ≥ 2.5 hours/week respectively. We studied the association of HI and LD exercise practice with the risk of ALVC phenotype occurrence and its severity, derived from clinical, ECG and imaging data. Results 114 out of 128 eligible patients answered the questionnaire and were included (85 (74.6%) with a DSP variant, 22 FLNC (19.3%), 6 DES (5.3%), 1 RBM20 (0.9%)). 35 were probands (31%) and 79 relatives (69%) among 46 families. 31 (27%) had no ALVC phenotype at the time of genetic diagnosis. Mean age at diagnosis was 41±18. 62 (54%) patients were women. 97 (85%) had practiced at least one sport, among which 81 (83.5%) at HI and 79 (81.4%) of LD. Median lifetime exercise dose was 18.5 MET.h/week. There were no differences in HI and LD exercise practice between probands and relatives (74.3% vs 69.6%, p=0.6 and 74.3% vs 67.1%, p=0.4 respectively), as well as between patients with and patients without ALVC phenotype at the time of diagnosis (74.7% vs 61.3%, p=0.2 and 72.3% vs 61.3%, p=0.3 respectively). Phenotypic features at diagnosis did not differ between patients with and without HI and LD practice (Table 1). Multivariate analysis adjusted on age and gender showed that HI and LD exercise were not significantly associated with an increased risk of developing an ALVC phenotype (Odds Ratio [95% confidence interval] for age, gender, HI and LD exercise were 1.03 [1.01-1.06] (p=0.013), 1.41 [0.58 ; 3.47] (p=0.45), 2.15 [0.63 ; 7.27] (p=0.22) and 1.17 [0.35 ; 3.87] (p=0.79) respectively). Phenotypic features at diagnosis did not differ across observed quartiles of lifetime exercise dose (Table 2). Conclusion Practicing HI and LD exercise was not associated with an increased risk of developing an ALVC phenotype and its severity at the time of diagnosis in genetic ALVC variant carriers.

Subclinical myocardial phenotype in genotype-positive relatives attending clinical and genetic screening for familial dilated cardiomyopathy

Abstract Aim To investigate if asymptomatic relatives carrying genetic variants associated with familial dilated cardiomyopathy (DCM) show early signs of myocardial disease assessed by echocardiography. Methods and Results Asymptomatic relatives without a DCM-phenotype (n=176, 46% males, mean age 39 years ± 16) of 111 DCM index patients carrying likely pathogenic or pathogenetic variants in TTN, RBM20, and FLNC genes were recruited from two tertiary referral centers for inherited cardiac diseases. All participants underwent echocardiographic examinations focusing on left ventricular (LV) ejection fraction (LVEF), LV global longitudinal strain (LVGLS), and LV end-diastolic diameter (LVEDD), with operators blinded to genetic results. The participants were grouped into genotype positive ([G+], n=82) or genotype negative relatives ([G-], n=94) carrying or not carrying the disease-causing variant. The G+ group had significantly lower systolic LV parameters compared to G- individuals with a mean LVGLS of -18.7% ± 2.4 versus -20.1% ± 2.8, p: 0.0029; and a mean ejection fraction of 57.8% ± 3.7 versus 59.7% ± 2.4, p: <0.0001. The proportion of G+ individuals with an abnormal LVGLS (defined as less than -18%) was 46% compared to 18% in the G- group. 26 % of G+ individuals had an LVEF in the interval between 50 - 55% compared to of 5% G- individuals[MOU1] . Mean LVEDD did not differ significantly between G+ and G-groups (49.7 mm ± 4.9 versus 48.8 mm ± 4.7). However, LVEDD indexed to BSA were significantly increased in G+ individuals (26.7 mm/m2 ± 2.8 versus 25.4 mm/m2 ± 2.5, p-value 0.001). Conclusion Overall, the absolute mean values of LVGLS, LVEF, and LVEDD were within normal ranges in both G+ and G- groups of individuals. However, compared to non-carrier relatives, almost half of the asymptomatic G+ DCM relatives had signs of subclinical myocardial dysfunction with significantly lower values of LVGLS, LVEF, and larger left ventricular dimensions.