Single Nucleotide Polymorphisms Research Articles

Single Nucleotide Polymorphisms (SNPs) in the Shadows: Uncovering their Function in Non-Coding Region of Esophageal Cancer.

Esophageal cancer is a complex disease influenced by genetic and environmental factors. Single nucleotide polymorphisms (SNPs) in non-coding regions of the genome have emerged as crucial contributors to esophageal cancer susceptibility. This review provides a comprehensive overview of the role of SNPs in non-coding regions and their association with esophageal cancer. The accumulation of SNPs in the genome has been implicated in esophageal cancer risk. Various studies have identified specific locations in the genome where SNPs are more likely to occur, suggesting a location-specific response. Chromatin conformational studies have shed light on the localization of SNPs and their impact on gene transcription, posttranscriptional modifications, gene expression regulation, and histone modification. Furthermore, miRNA-related SNPs have been found to play a significant role in esophageal squamous cell carcinoma (ESCC). These SNPs can affect miRNA binding sites, thereby altering target gene regulation and contributing to ESCC development. Additionally, the risk of ESCC has been linked to base excision repair, suggesting that SNPs in this pathway may influence disease susceptibility. Somatic DNA segment alterations and modified expression quantitative trait loci (eQTL) have also been associated with ESCC. These alterations can lead to disrupted gene expression and cellular processes, ultimately contributing to cancer development and progression. Moreover, SNPs have been found to be associated with the long non-coding RNA HOTAIR, which plays a crucial role in ESCC pathogenesis. This review concludes with a discussion of the current and future perspectives in the field of SNPs in non-coding regions and their relevance to esophageal cancer. Understanding the functional implications of these SNPs may lead to the identification of novel therapeutic targets and the development of personalized approaches for esophageal cancer prevention and treatment.

Impact of CCR5Δ32 on the risk of infection, Staphylococcus aureus carriage, and plasma concentrations of chemokines in Danish blood donors

The CC chemokine receptor 5 (CCR5) is a suggested receptor for Staphylococcus aureus leukotoxin ED. Homozygosity for the Δ32 deletion (CCR5Δ32) protects against human immunodeficiency virus infection and possibly also against leukotoxin ED. We examined the impact of CCR5Δ32 on the susceptibility to S.aureus infection, all-cause infections, and S.aureus nasal carriage, respectively, and on the concentrations of circulating chemokines in blood donors. We included 95,406 participants from the Danish Blood Donor Study (DBDS) genotyped for >650,000 single nucleotide polymorphisms. The CCR5Δ32 (rs333, MAF: 0.12) was imputed from a reference panel and validated. Infectious outcomes were identified by diagnosis codes and redeemed prescription of antibiotics in national health registers. Data on S.aureus nasal carriage and forty-seven inflammatory biomarkers were available for 6721 and 7811 participants, respectively. Cox, logistic, and linear regression models adjusted for relevant confounders were used to explore said associations. During more than 700,000 person-years of observation, we found that CCR5Δ32 was associated with neither an increased risk of redeemed dicloxacillin, hospital-treated S.aureus-associated infection (replicated in 345,996 Icelanders), redeemed antibiotics, all-cause infection, and nor with S.aureus nasal carriage. We discovered an association between CCR5Δ32 and elevated CCL4 concentrations, which were 1.26-fold higher in Δ32-heterozygotes (95%-CI: 1.23-1.30) and 2.64-fold higher in Δ32-homozygotes (95%-CI: 2.41-2.90) compared with wildtype homozygotes. Conversely, concentrations of CCL2, CXCL-10, and CCL11 were slightly lower among Δ32-heterozygotes. Results from this CCR5Δ32 high-prevalent cohort do not support the idea that CCR5Δ32 affects the risk of S.aureus carriage or infection to any relevant degree, in this northern European context. CCL4 was the main chemokine affected by CCR5Δ32 and was observed in higher concentration among Δ32-carriers. This study cannot rule out that S.aureus is a previous driver of CCR5Δ32 selection. The Health Research Fund of Central Denmark Region, Aarhus University, Danish Administrative Regions, Bio- and Genome Bank Denmark, Danish Blood Donor Research Foundation, Aase & Ejnar Danielsens Foundation, Højmosegård Grant, National Institute of Allergy and Infectious Diseases, and A.P. Møller Foundation for the Advancement of Medical Science.

Identification, functional analysis of chitin-binding proteins and the association of its single nucleotide polymorphisms with Vibrio parahaemolyticus resistance in Penaeus vannamei

Chitin-binding proteins (CBPs) play pivotal roles in numerous biological processes in arthropods, including growth, molting, reproduction, and immune defense. However, their function in the antibacterial immune defense of crustaceans remains relatively underexplored. In this study, twenty CBPs were identified and characterized in Penaeus vannamei. Expression profiling highlighted that the majority of CBPs were highly expressed in the intestine and hepatopancreas and responded to challenge by Vibrio parahaemolyticus. To explore the role of these CBPs in innate immunity, six CBPs (PvPrg4, PvKrtap16, PvPT-1a, PvPT-1b, PvExtensin and PvCP-AM1159) were selected for RNAi experiments. Silencing of only PvPrg4 and PvKrtap16 significantly decreased the cumulative mortality of V. parahaemolyticus-infected shrimp. Further studies demonstrated that inhibition of PvPrg4 and PvKrtap16 resulted in a marked upregulation of genes associated with the NF-κB and JAK-STAT signaling pathways, as well as antimicrobial peptides (AMPs), in both the intestine and hepatopancreas. These results collectively suggested that PvPrg4 and PvKrtap16 potentially promote V. parahaemolyticus invasion by negatively regulating the JAK-STAT and NF-κB pathways, thereby inhibiting the expression of AMPs. In addition, SNP analysis identified three SNPs in the exons of PvPrg4 that were significantly associated with tolerance to V. parahaemolyticus. Taken together, these findings are expected to assist in the molecular marker-assisted breeding of P. vannamei associated with anti-V. parahaemolyticus traits, as well as expand our understanding of CBP functions within the immune regulatory system of crustaceans.

Homologous recombination deficiency score is an independent prognostic factor in esophageal squamous cell carcinoma.

Homologous recombination deficiency (HRD) represents an impairment in the homologous recombination repair (HRR) pathway, crucial for repairing DNA double-strand breaks and contributing to genomic instability in cancer. The HRD score may be a more reliable biomarker than HRR-related gene mutations for identifying patients sensitive to poly(ADP-ribose) polymerase inhibitors. Despite its relevance in various cancers, the HRD score remains underexplored in esophageal squamous cell carcinoma (ESCC). We retrospectively analyzed HRD scores in 96 ESCC patients, examining correlations with clinical characteristics and survival outcomes, and validated our findings using the TCGA dataset. Genomic sequencing utilized a custom superHRD next-generation sequencing panel, and HRD scores were calculated from 54,000 single-nucleotide polymorphisms using Kruskal-Wallis rank-sum tests and two cut-off points for analysis. Higher HRD scores correlated with advanced tumor stages, recurrence, and mutations in TP53 and ABCB1, while APC mutations were linked to lower HRD scores. Patients with high HRD scores had significantly shorter disease-free survival (p = 0.013) and a trend toward shorter overall survival (OS) (p = 0.005), particularly those not receiving adjuvant therapy. Conversely, HRD-high patients undergoing adjuvant therapy showed a trend toward longer OS (p = 0.015). Multivariate analysis identified HRD as an independent prognostic factor (hazard ratio = 2.814 for recurrence, p = 0.015). Validation with the TCGA dataset supported these findings. This study highlights the associations between HRD scores, clinical characteristics, and genomic mutations in ESCC, suggesting HRD as a potential prognostic biomarker. HRD assessment may aid in patient stratification and personalized treatment strategies, warranting further investigation to validate the therapeutic implications of HRD scores in ESCC.

ANRIL: A Long Noncoding RNA in Age-related Diseases.

The intensification of the aging population is often accompanied by an increase in agerelated diseases, which impair the quality of life of the elderly. The characteristic feature of aging is progressive physiological decline, which is the largest cause of human pathology and death worldwide. However, natural aging interacts in exceptionally complex ways within and between organs, but its underlying mechanisms are still poorly understood. Long non-coding RNA (lncRNA) is a type of noncoding RNA that exceeds 200 nucleotides in length and does not possess protein-coding ability. It plays a crucial role in the occurrence and development of diseases. ANRIL, also known as CDKN2B-AS1, is an antisense ncRNA located at the INK4 site. It can play a crucial role in agerelated disease progression by regulating single nucleotide polymorphism, histone modifications, or post-transcriptional modifications (such as RNA stability and microRNA), such as cardiovascular disease, diabetes, tumor, arthritis, and osteoporosis. Therefore, a deeper understanding of the molecular mechanisms of lncRNA ANRIL in age-related diseases will help provide new diagnostic and therapeutic targets for clinical practice.

The first 2-year prospective audit of prenatal cell-free deoxyribonucleic screening using single nucleotide polymorphisms approach in a single academic laboratory.

We reported a performance during an implementation of prenatal cell-free (cf) DNA screening using single nucleotide polymorphism (SNP) approach in our accredited laboratory. Prospective audit with prompt intervention was set for the processing of 2,502 samples from singleton pregnancy from August 2017 to July 2019. Risks of trisomy 21 (T21), T18, T13, monosomy X (XO), and other sex chromosome aneuploidies (SCAs) were clarified by a proprietary bioinformatics algorithm. Laboratory failure occurred in 192 samples (7.7 %) as a result of inadequate sequencing (n=144), fundamental limitation of the testing (n=19), and obvious human error (n=29). Faulty setting of the calibration curve was the most common human error (n=22/29). After a redraw (n=110), 79 (71.8 %) were settled. Overall, 2,389/2,502 samples (95.5 %) were reportable. Thirty-five samples were high-risk for T21 (n=19), T18 (n=5), T13 (n=1), XO (n=3), and other SCAs (n=7), respectively. Positive predictive values calculated from either prenatal confirmatory tests or postnatal findings were 93.8 % (n=16), 100 % (n=4), 50 % (n=2), and 83.3 % (n=6) for T21, T18, XO, and other SCAs, respectively, with high sensitivity and specificity (>99.9 %). Vanishing twin was detected from 1 out of 4 samples with detected additional haplotypes. An overall performance of SNP-based prenatal cf-DNA screening during our initial implementation can be optimized with proactive approach. The technical know-how was a significant limiting factor for adopting the technology. The lessons learnt may be of interest to the academic laboratory considering adopting their own test instead of sending blood to a testing service of a supplier.

StSNV: a comprehensive resource of SNVs in spatial transcriptome.

Single nucleotide variants (SNVs), as important componentsof genetic variation, affect gene expression, function and phenotype. Mining and summarizing the spatial distribution of SNVs in diseased and normal tissues for a better understanding of their characteristics and potential roles in cell-lineage determination, aging, or disease occurrence is significant. Herein, we have developed a comprehensive spatial mutation resource stSNV (http://bio-bigdata.hrbmu.edu.cn/stSNV/index.jsp), which provides an atlas of spatial SNVs in major diseased and normal tissues of human and mouse. stSNV documents 42202 spatial mutated genes involving 898908 SNVs called from 730067 spots within 450 slices from 19 diseased and 28 normal tissues. Importantly, potential characteristics of SNVs are explored and provided by analyzing the perturbation of the SNVs to gene expression, spatial communication,biological function, region-specific mutated genes, spatial mutant signatures, SNV-cell co-localizationand mutation core region. All these spatial mutation data and in-depth analyses have been integrated into a user-friendly interface, visualized through intuitive tables and various image formats. Flexible tools are developed to explore co-localization among clusters, genes, cell types and SNVs in the same slice. In summary, stSNV as a valuable resourcehelps to dissect intra-tissue genetic heterogeneity and lays the groundwork for understanding the SNVs' biological regulatory mechanisms.

Exploring mitochondrial blood-based and genetic markers in older adults with mild cognitive impairment and remitted major depressive disorder

Mild cognitive impairment (MCI) is a prodromal stage in aging to possible progression to Alzheimer’s disease and related dementia (ADRD), where co-occurrence of major depressive disorder (MDD) accelerates the progression. Metabolic and mitochondrial abnormalities in ADRD and other neurodegenerative disorders have been widely suggested, while possible mitochondrial dysfunction has been associated with etiopathology of both MCI and MDD. Hence, investigation of mitochondrial markers in MCI, MDD, and presence of both conditions is warranted. In total, 332 older adult participants were included: 168 with MCI, 108 with MCI plus remitted MDD (rMDD), and 56 with rMDD but without MCI. We measured plasma circulating mitochondrial DNA (ccf-mtDNA), lactate, and extracted nuclear mitochondrial encoded (NMt) single-nucleotide variants (SNVs) (n = 312). Non-parametric statistical tests on ccf-mtDNA and lactate levels were performed on the diagnosis, clinical and cardiometabolic variables. Binary sequence kernel association test (SKAT-O) and burden test were performed on NMt-SNV, adjusted for age, race, gender, type II diabetes, and APOE genotype. Lower level of lactate was observed in MCI (KW χ2 = 14.8, P = 0.0024), more specifically, significant differences of lower plasma lactate between MCI only and rMDD, but not between MCI+rMDD and MCI were found, suggesting potential roles in MCI driving lactate lower levels. While higher levels of ccf-mtDNA were observed in APOE-ε4 carrier (χ2 = 5.04, P = 0.05). This relationship was present only in MCI (P = 0.043) and MCI+rMDD groups (P = 0.023). No significant nuclear-encoded mitochondrial gene associations were observed with MCI or MDD. The results suggest decreased level of plasma lactate in individuals with MCI and MCI+rMDD, with inverse correlation with ccf-mtDNA, in addition to effect of APOE-ε4 in further increasing ccf-mtDNA specifically in participants with cognitive impairment. These findings contribute to a deeper understanding of the mitochondrial markers in MCI and MDD, warranting further research to explore the precise roles of mitochondrial abnormalities in the development and progression of MCI.

The association of gene polymorphisms of adenosine and dopamine receptors with the response to caffeine citrate treatment in infants with apnea of prematurity: a prospective nested case-control study

BackgroundTo investigate the potential influence of adenosine and dopamine receptor genes polymorphisms in combination with clinical factors on the response of preterm infants to caffeine citrate treatment in apnea of prematurity (AOP).MethodsA prospective nested case-control study enrolled 221 preterm infants with gestational age < 34 weeks. These infants were divided into the response (n = 160) and the non-response groups (n = 61). 22 single-nucleotide polymorphisms in adenosine and dopamine receptor genes were genotyped. The basic characteristics and clinical outcomes of the two groups were compared. Univariate logistic regression analysis was performed to evaluate the differences in genotype distribution between the groups. Multivariable logistic regression analysis was performed to identify independent risk and protective factors and develop a nomogram to predict caffeine citrate response in preterm infants.ResultsPreterm infants in the non-response group had lower gestational age, lower birth weight, longer periods of oxygen supplementation and caffeine citrate use, and higher incidence of patent ductus arteriosus (PDA), bronchopulmonary dysplasia (BPD), neonatal respiratory distress syndrome (NRDS), retinopathy of prematurity (ROP), and brain injury (P < 0.05 for all). The ADORA1 rs10920573, ADORA2B rs2015353, ADORA3 rs10776728, DRD3 rs7625282, and DRD3 rs6280 gene polymorphisms were associated with caffeine citrate response in preterm infants (PFDR < 0.05 for all). The ADORA1 rs10920573 CC (aOR, 3.51; 95% CI, 1.34–9.25) and DRD3 rs6280 CT genotypes (aOR, 3.19; 95% CI, 1.53–6.65) were independent risk factors for non-response, whereas greater gestational age (aOR, 0.631; 95% CI, 0.53–0.75) was an independent protective factor for response. The concordance index of the nomogram was 0.764 (95% CI, 0.687–0.842), and the calibration and decision curve analysis indicated the nomogram had excellent predict performance.ConclusionsAdenosine receptor gene and dopamine receptor gene polymorphisms influence caffeine citrate treatment response in AOP. By combining genetic and clinical variables, it is possible to predict the response to caffeine citrate treatment in preterm infants.

Multigeographic clinical assessment of a molecular diagnostic assay for detection of key codons to predict decreased susceptibility or resistance to cephalosporins in Neisseria gonorrhoeae.

Cephalosporin resistance in Neisseria gonorrhoeae has severely compromised the efficacy of World Health Organization (WHO)-recommended therapies. This study aimed to methodologically evaluate the optimized Six-CodonPlus assay, and additionally conducted a multicenter evaluation to assess its clinical application, especially for predicting antimicrobial resistance (AMR). For methodological evaluation, 397 sequence-known N. gonorrhoeae isolates were evaluated for specificity, 17 nongonococcal isolates were assessed for cross-reactivity, 159 uncultured urogenital swabs and urine samples were evaluated for sensitivity at the clinical level. For multicenter evaluation, 773 isolates with confirmed phenotypic data and 718 clinical urogenital swabs collected from four geographical cities were, respectively, utilized for the evaluation of AMR-prediction strategies and the clinical application of the assay. The assay accurately identified specific single-nucleotide polymorphisms in resistance-associated genes, the detection limits dropped to 10 copies/reaction for individual targets. The specificity reached 100% and no cross-reactivity occurred with double-target confirmation. The assay could be directly applied to clinical samples containing over 20 copies/reaction. Multicenter evaluation formulated two optimal strategies for decreased susceptibility prediction in specific scenarios, and one tactic for prediction of resistance and identification of FC428-like strains. High sensitivity of 86.84% (95% CI, 71.11-95.05) and specificity of 99.59% (95% CI, 98.71-99.89) for resistance prediction were demonstrated for ceftriaxone (CRO). Regarding N. gonorrhoeae identification among multicenter swabs, specificity reached 97.53% (95% CI, 95.49-98.69), and sensitivity reached 93.77% (95% CI, 90.04-96.22). The Six-CodonPlus assay exhibited excellent detection performance and formulated optimal AMR-related prediction strategy with regional adaptability, providing critical information for population screening and clinical treatment.

A Genome-Wide Association Study (GWAS) of Takotsubo syndrome

Abstract Background Takotsubo syndrome (TS) is an acute cardiac condition of unknown etiology characterized by transient regional systolic dysfunction of the left and/or right ventricle. Several studies have suggested the importance of genetics; however, studies are limited and have presented conflicting results. Purpose To identify potential genetic risk variants associated with TS. Methods A case-control GWAS in three steps; I) A discovery study with Swedish takotsubo cases (n=260) and age- and sex-matched controls without heart disease from the UK Biobank (n=3034), II) A replication study of Swedish takotsubo cases (n=250) and sex- and age-matched Swedish controls without myocardial infarction from the Swedish coronary angiography and angioplasty register (n=229), III) A Meta-analysis of study I-II with extended controls from the UK-biobank (n=5161). Genotyping was performed using the Axiom® UK Biobank Genotyping Array including 820 000 single nucleotide polymorphisms (SNPs). After applying filters and QC control around 480 000 SNPs remained with a Bonferroni corrected p-value 1*10^-7, minor allele frequency (MAF 1.5-2%), Hardy-Weinberg (HWE) 10^-6. QC, filtering and analysis were performed in PLINK 1.9 and R v 4.0. Results In the discovery (I) 1490 SNP:s fulfilled a significance level of &amp;lt;10^-4, of which 36 SNP:s replicated (II) with a significance level of &amp;lt;10^-2, 11 reached a significance level of 10^-7 in the meta-analysis (III). One of the 36 SNP:s, rs1614887, replicated (II) with a significance level of 10^-3. This SNP is an intron variant in the butyrophilin subfamily 2 member A2 gene, a glycoprotein receptor involved in lipid, fatty-acid and sterol metabolism highly expressed in the heart. Of the 11 SNP:s with a significance level of 10^-7 in the meta-analysis (III) several risk variants were associated with psoriasis. Conclusions This is the largest GWAS of takotsubo syndrome performed so far, identifying one candidate gene and several potential risk variants. Further research of genetic risk variants in TS is warranted.

Protein quantitative trait loci identifies genetic biomarkers of proteins associated with measures of myocardial fibrosis in new-onset, treatment naive rheumatoid arthritis

Abstract Introduction The excess risk of cardiovascular disease (CVD) in patients with rheumatoid arthritis (RA) compared to the general population is attributed to chronic inflammation. Identifying the underlying mechanisms and shared inflammatory pathways more precisely would enable tailored treatment. Purpose To identify genetic variants associated with the cardio-metabolic-inflammatory proteomic signature in patients with early, treatment-naïve RA and low CVD risk. Methods The Coronary Artery Disease Evaluation in RA (CADERA) study was a bolt-on to a RCT of patients with early, treatment-naïve RA and low CVD risk profile (maximum of 1 traditional CVD risk factor and no diabetes mellitus). Normalised expression of 334 proteins from 75 CADERA patients who underwent cardiovascular magnetic resonance imaging (CMR) was measured using the Olink Proximity Extension Immunoassay across Inflammation, Cardiovascular II, III and Cardiometabolic panels. Genome-wide single nucleotide polymorphism (SNP) data were generated using the Illumina Global Screening Array and was imputed and checked for data quality using standard approaches. Proteins associated with CMR parameters were identified using Bayesian mixed effects linear regression. Protein quantitative trait locus (pQTL) analysis was then performed using linear regression models adjusted for age, gender, and systolic blood pressure. Cis-pQTLs were defined as SNPs within 1Mb of the protein-encoding gene, and significance threshold was set at 1e-5. Due to sample size, trans-pQTLs were not considered in this analysis. Linkage disequilibrium (LD) clumping was performed using PLINK software to identify index SNPs defined as the most significant variant in LD (r2 &amp;lt;0.5) within a region of +/- 250Kb. Results Following quality control 318 proteins and 5,971,781 SNPs were available for analysis in 75 CADERA patients. The median age was 51 years [inter-quartile range (IQR) 40 - 61] with 52/75 (69%) females, 40/75 (53%) current/ex-smokers, and median body mass index (BMI) 26.4kg/m2 (IQR 23.3 - 28). Participants had a median RA symptom duration of 21.9 weeks (IQR 14.4 - 32.7). Only 8/75 (10%) reported a history of hypertension, hypercholesteroaemia or family history of CVD. 54 out of 318 proteins were associated with CMR measures of myocardial fibrosis and/or vascular stiffness. 460 cis-pQTLs were identified for 20 out of the 318 proteins. LD clumping revealed 40 cis-pQTLs independently associated with these 20 proteins. Of these, NOTCH3 (rs34763630) was positively associated with extracellular volume, and SELPLG (rs7980427) was negatively associated with late gadolinium enhancement as detected on CMR (table 1). No other proteins with genetic support were associated with CMR measures. Conclusion This study for the first time, implicates genetic markers associated with two proteins as putative candidate biomarkers of CMR-identified myocardial fibrosis in new-onset RA that now warrant validation in an independent cohort.

Genomic-Wide Association Studies For Resistance to Anthracnose in a Pseudo-F2 Mango Population

Goal: This study aimed to apply genome-wide association studies (GWAS) to identify single nucleotide polymorphisms (SNPs) associated with resistance to mango anthracnose. Theoretical Framework: The statistical methods of GWAS aim to identify associations among genotypes with phenotypes for marker-assisted selection (MAS) or genome dissection of important traits. Method: Ninety-four plants of a ‘Haden’ × ‘Tommy Atkins’ pseudo-F2 population were genotyped with 705 SNPs and phenotyped for resistance to Colletotrichum siamense, anthracnose causal agent, by spraying young leaves, three times at different periods, with 103 conidia/mL. Qualitative GWAS, with Plink Fisher’s exact test and Cochran-Armitage trend genotypic test, and quantitative GWAS, with Tassel general (GLM) and mixed linear models (MLM) were applied. F2 plants with symptoms mean absence &gt;75% were considered moderately resistant to the fungus. Results and discussion: Qualitative and quantitative GWAS methods combined enable the identification of two consensus SNP loci controlling 24.76% of total variance to mango anthracnose resistance. Other four SNPs, identified, exclusively in quantitative or qualitative analysis, explained 28.55% of total variance to mango anthracnose. These SNPs loci are promising candidate for further PCR primers design in order to apply MAS in mango. Research implications: This study facilitates the identification of consensus chromosomal regions associated with mango anthracnose resistance. The application of MAS in mango breeding will accelerate the development of new cultivars. Originality/Value: To our knowledge, this a pioneering GWAS study applied to anthracnose, which is the most significant and widespread fungal disease affecting mango fruit globally.

Pharmacogenomics of CRP response to statins: a GIST consortium study

Abstract Introduction Statins are first line treatments in the primary and secondary prevention of cardiovascular disease. Prior clinical studies have shown that statins act independently of lipid lowering mechanisms to decrease C-reactive protein (CRP), a marker of inflammation. Purpose To elucidate genetic loci associated with CRP response to statins. Methods CRP response was specified as the change from baseline in log CRP after at least 4 weeks of statin therapy. Cohort level Genome-wide Association Studies (GWAS) of this CRP response was performed by linear regression analysis adjusted for baseline CRP, age, sex and BMI covariates using genetic data imputed to 1000 Genomes, testing ~10 million single nucleotide polymorphisms (SNPs) of minor allele frequency (MAF) &amp;gt;2%. Following quality control with EasyQC, a meta-analysis was conducted with METAL to combine GWAS results from six different cohorts of European ancestry (CARDS, FHS, JUPITER, MESA, PARC, PROSPER) within the GIST consortium. 1Mb loci regions were defined, centred +/-500kb around the lead SNP. Conditional analysis was performed using GCTA. Results There were 11,075 statin-treated individuals. The meta-analysis results revealed two loci achieving genome wide significance (P&amp;lt;5e-8): APOE (chr 19) and HNF1A (chr 12) (Figure 1). A signal at the CRP locus was highly suggestive (P=2.3e-7). All three loci are known to be associated with CRP levels in the absence of statin. Conditional analysis did not reveal secondary signals. The most associated variant at the APOE locus was the missense SNP rs429358, which contributes to the APOE E4 haplotype and is a risk locus for both dyslipidaemia and Alzheimer’s dementia. It is a C&amp;gt;T missense variant of MAF 0.12 leading to a R/C amino acid change, more common in African ancestry populations (MAF 0.27), and least common in Asian populations (MAF 0.09). A nominally significant association (P=0.09) for interaction with randomized allocation to statin v. placebo within samples derived from clinical trials supports this pharmacogenetic effect at APOE beyond genetic effects on baseline CRP levels. The most associated variant at the HNF1A locus was the intronic SNP rs11065384, which is in strong LD with the HNF1A missense SNP (rs1169288). The HNF1A locus is associated with diabetes, cholesterol levels, and coronary artery disease. There was no between-study heterogeneity at the top three loci (P&amp;gt;0.1), and forest plots show contribution to these signals from all 6 studies within the meta-analysis (Figure 2 A,B,C). Conclusions APOE and HNF1A are associated with CRP response to statins at the level of genome-wide significance. TheAPOE E4 signal is also known to be associated with LDL-Cholesterol response to statins, whereas the HNF1A locus is identified here for the first time as a pharmacogenetic determinant of statin response. The effect of this interindividual variability in CRP response on non-cardiovascular clinical outcomes should be elucidated.Figure 1Figure 2 A,B,C

Association of PCSK6 rs1531817(C/A) polymorphism with the prognosis and coronary stenosis in premature myocardial infarction patients: a prospective cohort study

Abstract Background An increasing proportion of younger patients are currently hospitalized for acute myocardial infarction. Exploring the factors affecting coronary artery lesions and prognosis in patients with premature myocardial infarction (PMI) from a genetic perspective is of great significance to clinical management. Proprotein convertase subtilisins/kexins 6(PCSK6), a member of the PCSK family, functions in protein hydrolytic cleavage. It has been shown that PCSK6 polymorphisms are associated with carotid atherosclerosis. Purpose This research intended to evaluate the relationship between the PCSK6 rs1531817 polymorphism and the prognosis of PMI patients and their coronary stenosis. Methods This study was a prospective cohort study, which consecutively included 605 patients with PMI who underwent emergency PCI from January 2017 to August 2022 at X Hospital. Using the Massarray technique, the single nucleotide polymorphisms(SNPs) of PCSK6 rs1531817 were identified, and the patients underwent follow-up for 12 to 72 months, with major adverse cardiovascular events (MACEs) as the outcome. Analyze the relationship between patients' SNPs, Gensini score(GS), Triple vessel diseases(TVD), and MACEs. Results In PMI patients with PCSK6 rs1531817 CA+AA genotypes, ApoA1/ApoB levels were higher than in patients with CC genotype, and TC/HDL levels were lower (p &amp;lt; 0.05). Logistic regression analysis showed that the PCSK6 rs1531817 polymorphism (Dominant model: CA+AA vs.CC) was significantly correlated with the GS (high vs. low GS, adjOR=0.297, 95%CI:0.139-0.632, p=0.002; high vs. medium GS, adjOR=0.449, 95%CI:0.211-0.956, p=0.038), and it was correlated with the number of coronary artery lesions (TVD vs. SVD, adjOR=0.420, 95%CI:0.226-0.782, p=0.006; TVD vs. DVD, adjOR=0.406, 95%CI:0.214-0.773, p=0.006). According to multivariate Cox regression analysis, the PCSK6 rs1531817 dominant model was associated with the MACEs in PMI patients (adjHR=0.454, 95%CI:0.269-0.766, p=0.003). The mediation effect results showed that ApoA1/ApoB played a partially mediating role in the association between PCSK6 rs1531817 polymorphism and the severity of coronary stenosis (the effect leading to high GS and TVD accounted for 14.6% and 8.3% respectively), TC/HDL and TVD partially parallel mediated the association between PCSK6 rs1531817 polymorphism and MACEs (effect proportions were 8.1% and 17.1%, respectively). Conclusion Carrying the PCSK6 rs1531817 mutant A allele is an independent protective predictor of severe coronary stenosis and long-term prognosis in patients with PMI. Patients with the PCSK6 CA+AA genotypes have milder coronary stenosis partially because they have higher levels of ApoA1/ApoB; in addition, these patients have a better long-term prognosis partially because they have lower TC/HDL levels and fewer TVD patients.Figure 1.ApoA1/ApoB and TC/HDL were compareFigure 2.Correlation of PCSK6 rs1531817 pol

A genome-wide association study identifies genetic determinants of hemoglobin glycation index with implications across sex and ethnicity

IntroductionWe investigated the genetic determinants of variation in the hemoglobin glycation index (HGI), an emerging biomarker for the risk of diabetes complications.MethodsWe conducted a genome-wide association study (GWAS) for HGI in the Action to Control Cardiovascular Risk in Diabetes (ACCORD) trial (N = 7,913) using linear regression and additive genotype encoding on variants with minor allele frequency greater than 3%. We conducted replication analyses of top findings in the Atherosclerosis Risk in Communities (ARIC) study with inverse variance-weighted meta-analysis. We followed up with stratified GWAS analyses by sex and self-reported race.ResultsIn ACCORD, we identified single nucleotide polymorphisms (SNPs) associated with HGI, including a peak with the strongest association at the intergenic SNP rs73407935 (7q11.22) (P = 5.8e−10) with a local replication in ARIC. In black individuals, the variant rs10739419 on chromosome 9 in the Whirlin (WHRN) gene formally replicated (meta-P = 2.2e−9). The SNP-based heritability of HGI was 0.39 (P&amp;lt; 1e−10). HGI had significant sex-specific associations with SNPs in or near GALNT11 in women and HECW2 in men. Finally, in Hispanic participants, we observed genome-wide significant associations with variants near USF1 and NXNL2/SPIN1.DiscussionMany HGI-associated SNPs were distinct from those associated with fasting plasma glucose or HbA1c, lending further support for HGI as a distinct biomarker of diabetes complications. The results of this first evaluation of the genetic etiology of HGI indicate that it is highly heritable and point to heterogeneity by sex and race.

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.

Multivariate Bayesian variable selection for multi-trait genetic fine mapping

Abstract Genome-wide association studies (GWAS) have identified thousands of single-nucleotide polymorphisms (SNPs) associated with complex traits, but determining the underlying causal variants remains challenging. Fine mapping aims to pinpoint the potentially causal variants from a large number of correlated SNPs possibly with group structure in GWAS-enriched genomic regions using variable selection approaches. In multi-trait fine mapping, we are interested in identifying the causal variants for multiple related traits. Existing multivariate variable selection methods for fine mapping select variables for all responses without considering the possible heterogeneity across different responses. Here, we develop a novel multivariate Bayesian variable selection method for multi-trait fine mapping to select causal variants from a large number of grouped SNPs that target at multiple correlated and possibly heterogeneous traits. Our new method is featured by its selection at multiple levels, incorporation of prior biological knowledge to guide selection and identification of best subset of traits the variants target at. We showed the advantage of our method over existing methods via comprehensive simulations that mimic typical fine-mapping settings and a real-world fine-mapping example in UK Biobank, where we identified critical causal variants potentially targeting at different subsets of addictive behaviours and risk factors.

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&amp;gt;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&amp;gt;G in the locus 9p21.3 (p=0.002) and rs1333049 G&amp;gt;C (p=0.010). MTHFD1L gene encodes a mitochondrial enzyme responsible for homocysteine remethylating in methionine, and rs6922269 G&amp;gt;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&amp;gt;G (GG) (p=0.002) remained in the equation as independently associated with arterial calcification, together with male sex (p=0.039), age (p&amp;lt;0.0001), hypertension (p=0.001), diabetes (p&amp;lt;0.0001), smoking status (p&amp;lt;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.

Elevated risk for stroke in genetically predisposed bicuspid aortic valve disease: evidences from a mendelian randomization study

Abstract Background Patients with bicuspid aortic valve (BAV) have been recognized to have an elevated risk for stroke. However, the exact causal association between BAV and stroke remains elusive due to stroke-related comorbidities, residual confounding bias and sample size limitations of observational studies. Purpose To identify the causal relationship between genetically predisposed BAV and 15 cardiovascular diseases (CVDs), and whether calcific aortic valve stenosis (CAVS) or atrial fibrillation (AF) could serve as the mediator on the pathway from BAV to stroke by mendelian randomization (MR) approach. Methods Uncorrelated (r² &amp;lt; 0.001) and genome-wide significant (P &amp;lt; 5×10^-8) single nucleotide polymorphisms were extracted from the largest genome-wide association study statistics (2,236 patients and 11,604 controls) of BAV by Gehlen et al. Summary-level statistics for 15 CVDs were obtained from the UK Biobank study, FinnGen study, HERMES consortium, CARDIoGRAMplusC4D consortium and GIGASTROKE consortium. We used 2-sample MR to estimate the causal association between BAV and 15 CVDs, evaluated 12 potential mediators and mediated proportions within 2-step MR framework. Inverse variance weighted was utilized as primary MR analyses method. Results for each outcome from different sources were pooled using the random effect meta-analysis. False discovery rate (FDR) was calculated by Benjamini-Hochberg method to account for multiple comparisons. Results Genetically predicted per log-odds liability increase of BAV was significantly associated with aortic aneurysm (OR, 1.26; 95% CI, 1.13-1.40; FDR-adjusted P = 3.54 × 10^-4), any stroke (OR, 1.06; 95% CI, 1.02-1.09; FDR-adjusted P = 0.004), ischemic stroke (IS) (OR, 1.17; 95% CI, 1.03-1.11; FDR-adjusted P = 0.001) and cardioembolic stroke (CES) (OR, 1.15; 95% CI, 1.06-1.25; FDR-adjusted P = 0.004). No significant association were observed between BAV and another 11 CVD outcomes. Instead of CAVS, genetic liability to AF mediated the total effect of BAV on any stroke (proportion mediated = 13.2% [95% CI, 3.1% - 23.2%]), IS (proportion mediated = 10.8% [95% CI, 2.5% - 19.1%]) and CES (proportion mediated = 21.5% [95% CI, 5.3% - 37.7%]). Conclusions Genetically predisposed BAV is associated with a higher risk of any stroke, IS and CES, which could be mediated by AF. This study implies the pathophysiological processes from BAV towards stroke and highlights the clinical significance of AF intervention in reducing the incidence of stroke for BAV patients.Causal association between BAV and CVDs