Single Nucleotide Polymorphism Loci Research Articles

Two genetic variants in the SRD5A2 gene are found to be associated with sex differences in the disease characteristics of patients with chronic hepatitis B virus infection

BackgroundTo examine the expression characteristics of single nucleotide polymorphisms (SNPs) in the SRD5A2 gene and investigate their potential association with differences in the clinical characteristics between sexes in patients with chronic hepatitis B virus (HBV) infection.MethodsA total of 30 loci in six genes primarily involved in the metabolism and signaling of sex hormones/sex hormone receptors, namely AKR1C2, AKR1C3, HSD17B6, SRD5A1, SRD5A2, and ESR1, were genotyped in 1007 patients from eight counties (cities) in Northeastern China with chronic HBV infection and 1040 healthy controls, and their association with viral replication characteristics and the differences in disease severity between sexes was assessed. Western blotting was conducted to determine the hepatic SRD5A2 protein level and its relationship with the inflammatory activity and fibrosis degree in male and female patients.ResultsTwo SNP loci in the SRD5A2 gene (rs12470143 and rs7594951) exhibited significant differences in genotype and allele frequencies between sexes, with the proportion of T alleles significantly higher in males than in females. It was found that the incidence and severity of HBV-related liver fibrosis were significantly higher in patients with the T/T genotype in SRD5A2 rs12470143 and rs7594951 than those with the non-T/T genotype. Additionally, serum HBV DNA levels were significantly elevated in T/T patients compared to non-T/T patients. Female patients exhibited significantly lower serum DNA levels compared to male patients. Western blot analysis indicated that greater hepatic SRD5A2 protein levels were associated with higher METAVIR inflammation and fibrosis scores. Furthermore, multivariate analysis showed that the two genetic variants in the SRD5A2 gene (rs12470143 C > T, r7594951 C > T), together with the male sex, age > 50 years old, HBeAg positive status, elevated serum HBsAg load, high serum HBV DNA load, and HBV genotype C, were independent risk factors for HBV-related liver fibrosis.ConclusionsThis study demonstrated that two genetic variants in the SRD5A2 gene (rs12470143 C > T, r7594951 C > T) are associated with sex differences in the clinical characteristics of patients with chronic HBV infection.

Genetics and Ischemic Heart Disease: Should We Opt for Genetic Testing for Primary Prevention?

Cardiovascular diseases (CVD) are a prevalent health concern within the general population of Pakistan, where the average lifespan is notably lower than the global average, with men typically living to 67 years and women to 69 years. According to the 2019 Global Burden of Disease study, Pakistan had an estimated age-standardized incidence rate of CVD at 918.18 per 100,000 (compared to the global rate of 684.33 per 100,000), along with an age-standardized death rate of 357.88 per 100,000 (globally, this rate is 239.85 per 100,000).1 Coronary heart disease (CHD), as revealed by the Framingham Heart Study focusing on individuals aged 40 to 94 without prior heart disease, displayed a lifetime risk of 49% for men and 32% for women when reaching the age of 40.2 There has been a declining trend in death rates in the United States attributed to CVD, CHD, and stroke since 1975. Data from 2000 to 2008 also indicate a decline in CHD mortality.3 Worryingly, the World Health Organization (WHO) reports a concerning rise in CHD-related fatalities in Pakistan. In 2020, 240,720 individuals died due to CHD, accounting for 16.49% of all deaths. This highlights an escalating trend of CHD-related mortality in Pakistan. It's important to note that most individuals presenting with cardiac events have one or more established or borderline risk factors aside from age and gender.4-6 While some essential risk factors are discernible, others may remain elusive. The screening of these risk factors and the evidence for targeted therapeutic interventions are still emerging and require further exploration.7 The starting point for assessing CVD risk factors is variables used to predict major cardiovascular events. These include age, sex, blood pressure, cholesterol levels, diabetes mellitus, and smoking status. Although risk assessment tools like the Pooled Cohort Equation in 2014 and Astro-CHARM have been developed, they have yet to provide satisfactory assessments for potential new CVD risk factors.8 CHD is recognized as a multifactorial disorder resulting from genetic and environmental factors interplay. Environmental risk factors have been identified in approximately 80% of CHD cases.9 Several risk scores, such as the Framingham Risk Score, PROCAM, Reynolds Risk Score, and QRISK 2, have been proposed to guide the use of statins in high-risk groups.10-14 Yet, these risk scores often lack precision and may either overestimate or underestimate future CHD events.15,16 The variation in disease susceptibility among individuals with similar environmental factors and conventional coronary artery disease risk factors (CRFs) may be attributed to genetic variations.17 Genetic analysis can potentially enhance risk discrimination beyond the consideration of CRFs alone. Family history of heart disease, accounting for more than 40% of risk estimation, has long been considered a part of CRFs.18 Candidate gene studies have been conducted to identify common variants in genes associated with disease pathways.19 Single-nucleotide polymorphisms (SNPs) have been employed as markers of genetic diversity. Among these SNPs, those located on the 9p21 locus have shown the strongest association with CHD risk to date.20,21 However, despite the clear link between these variants and incident CHD, 9p21 locus SNPs have not definitively improved the prediction or classification of CHD risk compared to traditional risk factors.22-24 It is important to note that most genetic studies on CHD have predominantly focused on European/Caucasian populations, and their applicability to the South Asian population, including Pakistan, requires further investigation.25,26 In this context, the Pakistani population, much like other Asian countries, is underrepresented in genetic research on CHD. Shahid SU et al. did some work in this respect,27 showing 21 SNPs risk score for genetic risk analysis in the Pakistani population. In conclusion, while different risk assessment tools have been developed for the Pakistani population aged 40 years and above, there is an urgent need to expand cardiac risk evaluation by identifying genetic markers related to CHD, particularly in the younger population. This will be crucial for advancing our understanding of CHD risk factors and developing more effective prevention and intervention strategies.

Genome-wide association study identifies candidate SNPs and genes associated with red-spotted grouper nervous necrosis virus infection of the giant grouper (Epinephelus lanceolatus)

The giant grouper is one of the most important farmed marine animals worldwide; however, red-spotted grouper nervous necrosis virus (RGNNV) has seriously affected its survival. Here, we performed a genome-wide association study on the same pedigree population of 202 giant grouper individuals for full-genome screening to identify markers and candidate genes for RGNNV resistance. The results were used to screen for single-nucleotide polymorphism (SNP) loci and candidate genes that significantly correlated with RGNNV traits. We detected 2,360,340 SNP loci and used a general linear model to identify 54 SNP loci with significant anti-RGNNV associations. We screened for candidate genes in a 100-kb zone (50 kb upstream and 50 kb downstream) around each SNP locus and detected 25 candidate genes. Of these, G protein-coupled receptor 143 (gpr143) was a candidate gene for disease resistance in giant groupers. RT-qPCR was used to examine the expression of gpr143 in various tissues of healthy groupers and was found to be highly expressed in the eye and brain. Following RGNNV infection, gene expression analysis revealed that gpr143 mRNA expression was significantly upregulated in the brains of susceptible fish, suggesting that GPR143 plays a role in viral invasion. GPR143 overexpression in giant grouper cells significantly promoted RGNNV replication, accelerated the cytopathic effects of RGNNV infection, and increased viral gene transcription. Our results suggest that markers linked to RGNNV disease resistance, including SNP markers and genes, could be useful for marker-assisted introgression, allowing for the development of highly RGNNV-resistant giant groupers.

Genetic loci associated with Fusarium wilt resistance in tomato (Solanum lycopersicum L.) discovered by genome‐wide association study

AbstractFusarium wilt (FW), caused by Fusarium oxysporum f. sp. lycopersici (Fol), has impacted global tomato production. This study aims to identify single nucleotide polymorphisms (SNPs) and candidate genes associated with FW resistance against different Fol isolates in tomato accessions using genome‐wide association studies (GWAS). Ninety‐four tomato accessions were evaluated for FW resistance and subjected to GWAS analysis. Broad‐spectrum tomato accessions demonstrated resistance to Fol in at least two isolates, exhibiting a disease severity index (DSI) of 0%. Thirty‐two SNP loci were significantly linked to the DSI of Fol isolates TFPK401, BK2269 and NP‐T4, clustering on chromosome 6. Among these, 12 common significant SNPs were associated with the DSI of at least two Fol isolates, while four unique SNPs were specific to TFPK401 or NP‐T4. Furthermore, candidate genes associated with disease response to Fol infection were identified within a 37.9–41 Mb region flanking the SNPs. These findings contribute to a deeper understanding of resistance mechanisms against Fol infection in tomatoes, potentially aiding the development of effective breeding strategies for Fusarium wilt resistance.

Single nucleotide polymorphisms in the CDH18 gene affect growth traits in Hu sheep

AbstractGrowth traits are critical economic traits in sheep. Genetic polymorphism has a great influence on the improvement of sheep traits. The aim of this study was to analyze the effect of cadherin 18 (CDH18) gene polymorphisms on growth traits in Hu sheep. The single nucleotide polymorphisms (SNPs) of the CDH18 gene in Hu sheep were identified by Illumina Ovine SNP 50K BeadChip. Five SNPs were screened out within the CDH18 gene, where SNP1 (rs423955510) was located in exon and SNP2 (rs412944692), SNP3 (rs416959317), SNP4 (rs398980439) and SNP5 (rs428685044) were located in intron. The expression of the CDH18 gene in Hu sheep tissue was analyzed using quantitative real‐time polymerase chain reaction, and the structure and phylogeny of the gene were analyzed using bioinformatics techniques. The results showed that SNP1, SNP2, SNP4, and SNP5 were significantly associated with body weight and body size (p < 0.05). Meanwhile, there were strong linkage disequilibrium relationships between SNP1 and SNP2 (r2 > 0.33). The CDH18 gene was expressed in the muscle tissues of Hu sheep at different months. The relative expression levels at weaning and 4‐month muscle tissue were higher. Bioinformatic analysis revealed that SNP1 existed in the 5′ untranslated regions, which might affect the efficiency of translation. The above findings suggested that these SNP loci might affect growth traits and could be regarded as potential molecular markers for improving the growth performance of Hu sheep, which lay a molecular foundation for the breeding of sheep and accelerate the pace of sheep breeding.

Mining the candidate genes of rice panicle traits via a genome-wide association study.

Panicle traits are important for improving the panicle architecture and grain yield of rice. Therefore, we performed a genome-wide association study (GWAS) to analyze and determine the genetic determinants of five panicle traits. A total of 1.29 million single nucleotide polymorphism (SNP) loci were detected in 162 rice materials. We carried out a GWAS of panicle length (PL), total grain number per panicle (TGP), filled grain number per panicle (FGP), seed setting rate (SSR) and grain weight per panicle (GWP) in 2019, 2020 and 2021. Four quantitative trait loci (QTLs) for PL were detected on chromosomes 1, 6, and 9; one QTL for TGP, FGP, and GWP was detected on chromosome 4; two QTLs for FGP were detected on chromosomes 4 and 7; and one QTL for SSR was detected on chromosome 1. These QTLs were detected via a general linear model (GLM) and mixed linear model (MLM) in both years of the study period. In this study, the genomic best linear unbiased prediction (BLUP) method was used to verify the accuracy of the GWAS results. There are nine QTLs were both detected by the multi-environment GWAS method and the BLUP method. Moreover, further analysis revealed that three candidate genes, LOC_Os01g43700, LOC_Os09g25784, and LOC_Os04g47890, may be significantly related to panicle traits of rice. Haplotype analysis indicated that LOC_Os01g43700 and LOC_Os09g25784 are highly associated with PL and that LOC_Os04g47890 is highly associated with TGP, FGP, and GWP. Our results offer essential genetic information for the molecular improvement of panicle traits. The identified candidate genes and elite haplotypes could be used in marker-assisted selection to improve rice yield through pyramid breeding.

Machine Learning Study of SNPs in Noncoding Regions to Predict Non-small Cell Lung Cancer Susceptibility

Non-small cell lung cancer (NSCLC) is the most common pathological subtype of lung cancer. Both environmental and genetic factors have been reported to impact the lung cancer susceptibility. We conducted a genome-wide association study (GWAS) of 287 NSCLC patients and 467 healthy controls in a Chinese population using the Illumina Genome-Wide Asian Screening Array Chip on 712,095 SNPs (single nucleotide polymorphisms). Using logistic regression modeling, GWAS identified 17 new noncoding region SNP loci associated with the NSCLC risk, and the top three (rs80040741, rs9568547, rs6010259) were under a stringent p-value (<3.02e-6). Notably, rs80040741 and rs6010259 were annotated from the intron regions of MUC3A and MLC1, respectively. Together with another five SNPs previously reported in Chinese NSCLC patients and another four covariates (e.g., smoking status, age, low dose CT screening, sex), a predictive model by machine learning methods can separate the NSCLC from healthy controls with an accuracy of 86%. This is the first time to apply machine learning method in predicting the NSCLC susceptibility using both genetic and clinical characteristics. Our findings will provide a promising method in NSCLC early diagnosis and improve our understanding of applying machine learning methods in precision medicine.

Development of a tetra-primer ARMS–PCR for identification of sika and red deer and their hybrids

Accurate identification of deer-derived components is significant in food and drug authenticity. Over the years, several methods have been developed to authenticate these products; however, identifying whether female deer products are hybrids is challenging. In this study, the zinc finger protein X-linked (ZFX) gene sequences of sika deer (Cervus nippon), red deer (Cervus elaphus) and their hybrid offspring were amplified and sequenced, the X221 and X428 species-specific single nucleotide polymorphisms (SNP) loci were verified, and a tetra-primer amplification refractory mutation system (T-ARMS–PCR) assay was developed to identify the parent-of-origin of female sika deer, red deer, and their hybrid deer. The T-ARMS–PCR developed based on the X221 locus could identify sika deer, red deer, and their hybrid offspring according to the presence or absence of PCR product sizes of 486 bp, 352 bp, and 179 bp, respectively, just as X428 locus could identify sika deer, red deer, and their hybrid offspring according to the presence or absence of PCR product sizes of 549 bp, 213 bp, and 383 bp, respectively. Forty products labeled deer-derived ingredients randomly purchased were tested using this assay, and the results showed that the identification results based on the two SNP loci were utterly consistent with the actual sources. In addition, this method was found to be accurate, simple, convenient, and with high specificity, thus providing an essential technical reference for deer product species identification. It is also an important supplement to the identification methods of the original ingredients of existing deer products.Graphical abstract

Genome-wide association study reveals genomic loci of sex differentiation and gonadal development in Plectropomus leopardus.

Introduction: Plectropomus leopardus, a commercially significant marine fish, is primarily found in the Western Pacific regions and along the coast of Southeast Asia. A thorough analysis of the molecular mechanisms involved in sex differentiation is crucial for gaining a comprehensive understanding of gonadal development and improving sex control breeding. However, the relevant fundamental studies of P. leopardus are relatively lacking. Methods: In this study, a genome-wide association study (GWAS) was conducted to investigate the genetic basis mechanism of sex differentiation and gonadal developmental traits in P. leopardus utilizing about 6,850,000 high-quality single-nucleotide polymorphisms (SNPs) derived from 168 individuals (including 126 females and 42 males) by the genome-wide efficient mixed-model association (GEMMA) algorithm. Results: The results of these single-trait GWASs showed that 46 SNP loci (-log10 p > 7) significantly associated with sex differentiation, and gonadal development traits were distributed in multiple different chromosomes, which suggested the analyzed traits were all complex traits under multi-locus control. A total of 1,838 potential candidate genes were obtained by considering a less-stringent threshold (-log10 p > 6) and ±100kb regions surrounding the significant genomic loci. Moreover, 31 candidate genes were identified through a comprehensive analysis of significant GWAS peaks, gene ontology (GO) annotations, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses, including taf7, ddx6, apoeb, sgk1, a2m, usf1, hsd3b7, dll4, xbp1, tet3, esr1, and gli3. These trait-associated genes have been shown to be involved in germline development, male sex differentiation, gonad morphogenesis, hormone receptor binding, oocyte development, male gonad development, steroidogenesis, estrogen-synthetic pathway, etc. Discussion: In the present study, multiple genomic loci of P. leopardus associated with sex differentiation and gonadal development traits were identified for the first time by using GWAS, providing a valuable resource for further research on the molecular genetic mechanism and sex control in P. leopardus. Our results also can contribute to understanding the genetic basis of the sex differentiation mechanism and gonadal development process in grouper fish.

Relationship between cancer stem cell-related SNPs and survival outcomes in patients with primary lung cancer

BackgroundCancer stem cells may be the source of cancer-causing mutant cells and are closely related to the prognosis of cancer. Our study aimed to investigate the potential association between single-nucleotide polymorphisms (SNPs) of cancer stem cell-related genes and the prognosis of lung cancer patients.MethodsThe SNP loci were genotyped by matrix-assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF–MS), and the overall survival of subjects was analyzed by log-rank test after stratifying and adjusting their demographic data, clinical data, and genotypes. The correlation between survival time and quality of life of lung cancer under codominant, dominant, recessive, and additive genetic models was analyzed by the Cox regression model. The association between SNP polymorphism and the prognosis of lung cancer was analyzed by Stata16.0 software, and their heterogeneity was tested. Interaction analysis was performed using R software (version 4.2.0).ResultsStratified analysis unveiled that rs3740535 had recessive AA genotype and additive GG genotype; Rs3130932 dominant GT + GG genotype, additive TT genotype; Rs13409 additive TT genotype; Rs6815391 recessive CC genotype and additional TT genotype were associated with increased risk of lung cancer death. Rs3130932 recessive GG genotype was associated with a reduced risk of lung cancer death.ConclusionRs3740535, rs3130932, rs13409, and rs6815391 are associated with the overall survival of lung cancer patients and may be valuable for the prognosis of lung cancer patients.

Development of a POCT detection platform based on a locked nucleic acid-enhanced ARMS-RPA-GoldMag lateral flow assay

In this study, a novel genotyping point-of-care testing (POCT) rapid detection device, the locked nucleic acid (LNA)-amplification refractory mutation system (ARMS)-recombinase polymerase amplification (RPA)-GoldMag lateral flow assay (LFA) platform, was provided by mining and synthesis based on prior technology. Research methods based on system-integrated innovation and knowledge-integrated generation have become a new trend in technology development. Here, we exploit the combination of LNA-coupled ARMS-RPA and gold nanoparticle probe technology for detection signal amplification, thus pioneering a new tool for accurate, rapid, and cost-effective genotyping. We also performed SNP typing detection and clinical validation of this new assay platform using common glucose-6-phosphate dehydrogenase (G6PD) gene single nucleotide polymorphism (SNP) loci, and the results demonstrated the high sensitivity, specificity, stability, accuracy and feasibility of the LNA-ARMS-RPA-GoldMag lateral flow assay platform. It is hoped that this new technology will make a significant contribution to the field of POCT rapid diagnosis and aim to expand the application space, reflecting its clinical application value and development prospects.

Genome-Wide Association Study of Lactation Traits in Chinese Holstein Cows in Southern China.

Lactation traits are economically important for dairy cows. Southern China has a high-temperature and high-humidity climate, and environmental and genetic interactions greatly impact dairy cattle performance. The aim of this study was to identify novel single-nucleotide polymorphism sites and novel candidate genes associated with lactation traits in Chinese Holstein cows under high-temperature and humidity conditions in southern China. A genome-wide association study was performed for the lactation traits of 392 Chinese Holstein cows, using GGP Bovine 100 K SNP gene chips. Some 23 single nucleotide polymorphic loci significantly associated with lactation traits were screened. Among them, 16 were associated with milk fat rate, 7 with milk protein rate, and 3 with heat stress. A quantitative trait locus that significantly affects milk fat percentage in Chinese Holstein cows was identified within a window of approximately 0.5 Mb in the region of 0.4-0.9 Mb on Bos taurus autosome 14. According to Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses, ten genes (DGAT1, IDH2, CYP11B1, GFUS, CYC1, GPT, PYCR3, OPLAH, ALDH1A3, and NAPRT) associated with lactation fat percentage, milk yield, antioxidant activity, stress resistance, and inflammation and immune response were identified as key candidates for lactation traits. The results of this study will help in the development of an effective selection and breeding program for Chinese Holstein cows in high-temperature and humidity regions.

High-Density Genetic Map and QTL Analysis in Cunninghamia lanceolate: Insights into Growth and Wood-Color Traits

Cunninghamia lanceolata is one of the most important tree species in China due to its significance both in economy and ecology. The aims of the present study were to construct a high-density genetic map and identify a quantitative trait locus (QTL) for C. lanceolata. In this study, an F1 population comprising 81 individuals was developed. Using specific length amplified fragment sequencing (SLAF-seq) technology, a total of 254,899 loci were found to be polymorphic. After linkage analysis, 2574 markers were used to construct genetic linkage maps. Specifically, 1632 markers were allocated to 11 linkage groups (LGs) for the female map, 1038 for the male map, and 2574 for the integrated map. The integrated map consisted of 4596 single-nucleotide polymorphisms (SNPs) loci, resulting in an average of 1.79 SNP loci per SLAF marker. The marker coverage was 1665.76 cM for the female map, 1436.39 cM for the male map, and 1748.40 cM for the integrated map. The average interval between two adjacent mapped markers was 1.03 cM, 1.40 cM, and 0.68 cM for the female map, male map, and integrated map, respectively. Using the integrated map, we performed interval mapping (logarithm of odds, LOD &gt; 2.0) to detect traits of interest. We identified a total of 2, 1, 2, 5, 1, 2, 1, and 3 QTLs for diameter at breast height, heartwood diameter, heartwood proportion, heartwood a*, heartwood b*, heartwood L*, sapwood a*, and sapwood L*, respectively. The number of markers associated with each QTL ranged from 1 to 14, and each marker explained phenotypic variances ranging from 12.70% to 23.60%. Furthermore, a common QTL was identified for diameter at breast height and heartwood color a*, while another common QTL was observed for heartwood color L* and heartwood color a*. These findings suggest possible pleiotropic effects of the same genes on these traits. In conclusion, we successfully constructed high-density genetic maps for C. lanceolata using the SLAF-seq method with an F1 population. Notably, these linkage maps represent the most comprehensive and densest ones available to date for C. lanceolata and will facilitate future chromosome assignments for C. lanceolata whole-genome sequencing. These identified QTLs will serve as a valuable resource for conducting fine-scale QTL mapping and implementing marker-assisted selection in C. lanceolata, particularly for growth and wood-color traits.

Selection signatures and population dynamics of transposable elements in lima bean

The domestication process in lima bean (Phaseolus lunatus L.) involves two independent events, within the Mesoamerican and Andean gene pools. This makes lima bean an excellent model to understand convergent evolution. The mechanisms of adaptation followed by Mesoamerican and Andean landraces are largely unknown. Genes related to these adaptations can be selected by identification of selective sweeps within gene pools. Previous genetic analyses in lima bean have relied on Single Nucleotide Polymorphism (SNP) loci, and have ignored transposable elements (TEs). Here we show the analysis of whole-genome sequencing data from 61 lima bean accessions to characterize a genomic variation database including TEs and SNPs, to associate selective sweeps with variable TEs and to predict candidate domestication genes. A small percentage of genes under selection are shared among gene pools, suggesting that domestication followed different genetic avenues in both gene pools. About 75% of TEs are located close to genes, which shows their potential to affect gene functions. The genetic structure inferred from variable TEs is consistent with that obtained from SNP markers, suggesting that TE dynamics can be related to the demographic history of wild and domesticated lima bean and its adaptive processes, in particular selection processes during domestication.

CHDH, a key mitochondrial enzyme, plays a diagnostic role in metabolic disorders diseases and tumor progression.

Human choline dehydrogenase (CHDH) is a transmembrane protein located in mitochondria. CHDH has been shown to be one of the important catalytic enzymes that catalyze the oxidation of choline to betaine and is involved in mitochondrial autophagy after mitochondrial damage. In recent years, an increasing number of studies have focused on CHDH and found a close association with the pathogenesis of various diseases, including tumor prognosis. Here we summarized the genomic localization, protein structure and basic functions of CHDH and discuss the progress of CHDH research in metabolic disorders and other diseases. Moreover, we described the regulatory role of CHDH on the progression of different types of malignant tumors. In addition, major pathogenic mechanisms of CHDH in multiple diseases may be associated with single nucleotide polymorphism (SNP). We look forward to providing new strategies and basis for clinical diagnosis and prognosis prediction of diseases by diagnosing SNP loci of CHDH genes. Our work evaluates the feasibility of CHDH as a molecular marker relevant to the diagnosis of some metabolic disorders diseases and tumors, which may provide new targets for the treatment of related diseases and tumors.

Combined CRISPRi and proteomics screening reveal a cohesin-CTCF-bound allele contributing to increased expression of RUVBL1 and prostate cancer progression

Genome-wide association studies along with expression quantitative trait locus (eQTL) mapping have identified hundreds of single-nucleotide polymorphisms (SNPs) and their target genes in prostate cancer (PCa), yet functional characterization of these risk loci remains challenging. To screen for potential regulatory SNPs, we designed a CRISPRi library containing 9,133 guide RNAs (gRNAs) to cover 2,166 candidate SNP loci implicated in PCa and identified 117 SNPs that could regulate 90 genes for PCa cell growth advantage. Among these, rs60464856 was covered by multiple gRNAs significantly depleted in screening (FDR<0.05). Pooled SNP association analysis in the PRACTICAL and FinnGen cohorts showed significantly higher PCa risk for the rs60464856G allele (p value= 1.2×10-16 and 3.2×10-7, respectively). Subsequent eQTL analysis revealed that the G allele is associated with increased RUVBL1 expression in multiple datasets. Further CRISPRi and xCas9 base editing confirmed that the rs60464856G allele leads to elevated RUVBL1 expression. Furthermore, SILAC-based proteomic analysis demonstrated allelic binding of cohesin subunits at the rs60464856 region, where the HiC dataset showed consistent chromatin interactions in prostate cell lines. RUVBL1 depletion inhibited PCa cell proliferation and tumor growth in a xenograft mouse model. Gene-set enrichment analysis suggested an association of RUVBL1 expression with cell-cycle-related pathways. Increased expression of RUVBL1 and activation of cell-cycle pathways were correlated with poor PCa survival in TCGA datasets. Our CRISPRi screening prioritized about one hundred regulatory SNPs essential for prostate cell proliferation. In combination with proteomics and functional studies, we characterized the mechanistic role of rs60464856 and RUVBL1 in PCa progression.

Relationship between IL-17A gene polymorphism and susceptibility to Kawasaki disease.

Kawasaki disease (KD) is the most common autoimmune vasculitis syndrome in children, which supposed be a complex polygenic disorder. Interleukin-17 (IL-17) is a member of the pro-inflammatory cytokine family, which has a strong pro-inflammatory effect and can participate in various acute and chronic inflammatory responses. This study aims to investigate the relationship between the single-nucleotide polymorphism (SNP) locus rs3819025 in the IL-17A gene and the susceptibility to KD. A total of 120 patients with KD who met the diagnostic criteria (the KD group) and 120 healthy children (the control group) were enrolled retrospectively in this study. Polymerase chain reaction (PCR) and DNA direct sequencing were used to detect the SNPs of children in the 2 groups. The frequencies of GG, GA, and AA genotypes of rs3819025 locus in the IL-17A gene in the KD group were 82.5%, 17.5%, and 0, respectively, and the frequencies of GG, GA, and AA genotypes in the control group were 72.5%, 22.5%, and 5.0%, respectively. There were significant differences in both genotype (χ2=7.524, P=0.023). The allele frequencies G and A of rs3819025 locus in the KD group were 91.25% and 8.75%, respectively, while those in the control group were 83.75% and 16.25%, respectively. There was significant difference between the 2 groups (χ2=6.171, P=0.013). The distribution frequencies of GG or GA genotype and G or A allele were 88.46% or 11.54% and 94.23% or 5.77% in the KD group with coronary artery lesion, respectively. The distribution frequencies of GG or GA genotype and G or A allele were 78.72% or 21.28% and 89.36% or 10.64% in the KD group without coronary artery lesion, respectively. There were no significant differences in genotype and allele frequencies of rs3819025 between the KD with coronary artery lesion group and the KD group without coronary artery lesion (both P>0.05). Besides, children with the allele A had a 2.023 times higher risk of KD than those without the allele A (χ2=6.171, P=0.013; OR=2.023, 95% CI 1.151 to 3.557). The locus rs3819025 in the IL-17A gene is associated with the pathogenesis of KD. The allele A of the locus rs3819025 in the IL-17A gene may be a risk factor for KD.

Alternative life-history strategy contributions to effective population size in a naturally spawning salmon population.

Alternative life-history tactics are predicted to affect within-population genetic processes but have received little attention. For example, the impact of precocious males on effective population size (N e) has not been quantified directly in Pacific salmon Oncorhynchus spp., even though they can make up a large percentage of the total male spawners. We investigated the contribution of precocial males ("jacks") to N e in a naturally spawning population of Coho Salmon O. kisutch from the Auke Creek watershed in Juneau, Alaska. Mature adults that returned from 2009 to 2019 (~8000 individuals) were genotyped at 259 single-nucleotide polymorphism (SNP) loci for parentage analysis. We used demographic and genetic methods to estimate the effective number of breeders per year (N b). Jack contribution to N b was assessed by comparing values of N b calculated with and without jacks and their offspring. Over a range of N b values (108-406), the average jack contribution to N b from 2009 to 2015 was 12.9% (SE = 3.8%). Jacks consistently made up over 20% of the total male spawners. The presence of jacks did not seem to influence N b/N. The linkage disequilibrium N e estimate was lower than the demographic estimate, possibly due to immigration effects on population genetic processes: based on external marks and parentage data, we estimated that immigrant spawners produced 4.5% of all returning offspring. Our results demonstrate that jacks can influence N b and N e and can make a substantial contribution to population dynamics and conservation of threatened stocks.

Genetic mapping identified major main-effect and three co-localized quantitative trait loci controlling high iron and zinc content in groundnut.

Malnutrition is a major challenge globally, and groundnut is a highly nutritious self-pollinated legume crop blessed with ample genomic resources, including the routine deployment of genomic-assisted breeding. This study aimed to identify genomic regions and candidate genes for high iron (Fe) and zinc (Zn) content, utilizing a biparental mapping population (ICGV 00440×ICGV 06040;). Genetic mapping and quantitative trait locus (QTL) analysis (474 mapped single-nucleotide polymorphism loci; 1536.33cM) using 2 seasons of phenotypic data together with genotypic data identified 5 major main-effect QTLs for Fe content. These QTLs exhibited log-of-odds (LOD) scores ranging from 6.5 to 7.4, explaining phenotypic variation (PVE) ranging from 22% (qFe-Ah01) to 30.0% (qFe-Ah14). Likewise, four major main effect QTLs were identified for Zn content, with LOD score ranging from 4.4 to 6.8 and PVE ranging from 21.8% (qZn-Ah01) to 32.8% (qZn-Ah08). Interestingly, three co-localized major and main effect QTLs (qFe-Ah01, qZn-Ah03, and qFe-Ah11) were identified for both Fe and Zn contents. These genomic regions harbored key candidate genes, including zinc/iron permease transporter, bZIP transcription factor, and vacuolar iron transporter which likely play pivotal roles in the accumulation of Fe and Zn contents in seeds. The findings of this study hold potential for fine mapping and diagnostic marker development for high Fe and Zn contents in groundnut.

Genome-wide association study of dilated cardiomyopathy-induced heart failure associated with renal insufficiency in a Chinese population

BackgroundAs it is unclear whether there is genetic susceptibility to cardiorenal syndrome (CRS), we conducted a genome-wide association study of dilated cardiomyopathy (DCM)-induced heart failure (HF) associated with renal insufficiency (RI) in a Chinese population to identify putative susceptibility variants and culprit genes.MethodsA total of 99 Han Chinese patients with DCM-induced chronic HF were selected and divided into one of three groups, namely, HF with normal renal function (Group 1), HF with mild RI (Group 2) and HF with moderate to severe RI (Group 3). Genomic DNA was extracted from each subject for genotyping.ResultsAccording to Gene Ontology (GO) function and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, top 10 lists of molecular function, cell composition and biological process of differential target genes and 15 signalling pathways were discriminated among the three groups. Additionally, sequencing results identified 26 significantly different single-nucleotide polymorphisms (SNPs) in the 15 signalling pathways, including three SNPs (rs57938337, rs6683225 and rs6692782) in ryanodine receptor 2 (RYR2) and two SNPs (rs12439006 and rs16958069) in RYR3. The genotype and allele frequencies of the five SNPs in RYR2 and RYR3 were significantly differential between HF (Group 1) and CRS (Group 2 + 3) patients.ConclusionTwenty-six significantly different SNP loci in 17 genes of the 15 KEGG pathways were found in the three patient groups. Among these variants, rs57938337, rs6683225 and rs6692782 in RYR2 and rs12439006 and rs16958069 in RYR3 are associated with RI in Han Chinese patients with heart failure, suggesting that these variants may be used to identify patients susceptible to CRS in the future.