Single Nucleotide Polymorphisms Research Articles

Principles of CRISPR-Cas13 mismatch intolerance enable selective silencing of point-mutated oncogenic RNA with single-base precision.

Single-nucleotide variants (SNVs) are extremely prevalent in human cancers, although most of these remain clinically unactionable. The programmable RNA nuclease CRISPR-Cas13 has been deployed to specifically target oncogenic RNAs. However, silencing oncogenic SNVs with single-base precision remains extremely challenging due to the intrinsic mismatch tolerance of Cas13. Here, we show that introducing synthetic mismatches at precise positions of the spacer sequence enables de novo design of guide RNAs [CRISPR RNAs (crRNAs)] with strong preferential silencing of point-mutated transcripts. We applied these design principles to effectively silence the oncogenic KRAS G12 hotspot, NRAS G12D and BRAF V600E transcripts with minimal off-target silencing of the wild-type transcripts, underscoring the adaptability of this platform to silence various SNVs. Unexpectedly, the SNV-selective crRNAs harboring mismatched nucleotides reduce the promiscuous collateral activity of the RfxCas13d ortholog. These findings demonstrate that the CRISPR-Cas13 system can be reprogrammed to target mutant transcripts with single-base precision, showcasing the tremendous potential of this tool in personalized transcriptome editing.

Updated analysis of the pharmacogenomics of pediatric bronchodilator response.

This short communication serves as an update to previously published pilot study results on bronchodilator response (BDR) in children with asthma. We expanded our cohort from 54 to 165 pediatric patients seeking emergency department care for an asthma exacerbation. We obtained measured BDR before and after albuterol administration using the Pediatric Asthma Severity Score and collected genomic DNA. Based on a literature review, we analyzed whether 21 candidate single-nucleotide polymorphisms (SNPs) were associated with BDR. Among the three SNPs initially reported in our pilot study as significantly associated with BDR (rs912142, rs7081864, and rs7903366), we confirmed that rs7081864 was still significantly associated with suboptimal BDR (odds ratio, 0.47; confidence interval, 0.24-0.92). If externally validated in broader studies, simple outpatient testing for that SNP variant could help guide pharmacologic therapy for acute asthma symptoms.

Up Regulation of ZNF76 rs10947540 and SCUBE3 rs1888822 Single Nucleotide Polymorphisms as a Genetic Risk Factor in Egyptian Patients with Rheumatoid Arthritis.

The protein SCUBE3has been observed to exhibit an association with various autoimmune conditions, including psoriasis and rheumatoid arthritis. Genetic experiments have revealed that changes in Zinc finger protein-coding sequences correlate with an increased vulnerability to developing autoimmune diseases, so we aimed to study investigates the involvement of ZNF76 rs10947540 and SCUBE3 rs1888822 gene expression in individuals diagnosed with Rheumatoid Arthritis. In a case-control study conducted from January 2022 to March 2023, 80 adults with RA from Menoufia University Hospital were compared with 80 age- and gender-matched healthy controls. Single nucleotide polymorphisms (SNPs) ZNF76 rs10947540 and SCUBE3 rs1888822 were analysed using real-time polymerase chain reaction (PCR). ZNF76 rs10947540 demonstrated a 7.125-fold increased risk for RA in CC genotype individuals and a 2.958-fold risk associated with the C allele. Those with the TC genotype had a 2.523-fold increased risk. Similarly, SCUBE3 rs1888822 showed a 6.364-fold risk for RA in TT genotype individuals and a 3.065-fold risk for T allele carriers. GT genotype individuals had a 2.765-fold risk. Our study suggests that ZNF76 rs10947540 and SCUBE3 rs1888822 polymorphisms may be risk factors for RA in Egyptian patients. Understanding the genetic variations associated with higher risk underscores the role of genetics in RA progression.

Emergence and clonal dissemination of KPC-2- and NDM-1-coharboring Citrobacter freundii in China with an IncR plasmid.

The rise of carbapenem-resistant Enterobacteriaceae coharboring KPC-2 and NDM-1 poses a significant public health threat. KPC-2-NDM-1-Citrobacter freundii is rarely reported in clinical settings. In this study, we report the largest cohort of eight KPC-2-NDM-1-C. freundii isolated from children with urinary tract infections. Comprehensive characterization, including antimicrobial susceptibility testing, plasmid conjugation, whole-genome sequencing, and comparative genomics, was conducted for these clinical strains. Antimicrobial susceptibility testing indicated that all strains were resistant to meropenem [minimal inhibitory concentration (MICs) ≥ 8 µg/mL] and imipenem (MICs > 8 µg/mL). Genotyping and comparative genomics analyses identified the eight KPC-2-NDM-1- C. freundii belonging to ST523, exhibiting a close relationship characterized by 45 single nucleotide polymorphisms. Whole-genome sequencing and plasmid analysis confirmed the presence of blaKPC-2 and blaNDM-1 on an IncR plasmid named pC275-2 with 46,050 bp. The blaNDM-1 was integrated within the blaNDM-1 related region, which includes ΔISAba125, blaNDM-1, ble-MBL, trpF, dsbD, and ISCR1, while the blaKPC-2 gene was located on a novel non-Tn4401 genetic element. The blaKPC-2 genetic architectures containing blaKPC-2 differed from classical structures, underscoring the ongoing evolution of these genetic elements.IMPORTANCEOur study described the largest cohort to date of eight ST523 KPC-2-NDM-1-C. freundii isolated from children with urinary tract infections. The cooccurrence of KPC-2, a serine β-lactamases, and NDM-1, a metallo-β-lactamase on an IncR plasmid pC275-2 from a clinical carbapenem-resistant C. freundii. The conserved insertion structure mediated the blaNDM-1, and the propagation of blaKPC-2 gene with a new genetic background using IncR plasmid in clinical settings promotes the emergence of superbugs necessitating vigilant monitoring. Our research detected that ST523 KPC-2- NDM-1-C. freundii were disseminated in a children's hospital. The potential spread of an IncR plasmid within the hospital raises concerns about the pandemic potential of this clone that produces two carbapenemases: KPC-2 and NDM-1. Further investigations will be necessary to control and prevent the spread of KPC-2-NDM-1-C. freundiis.

The Utility of Long-Read Sequencing in Diagnosing Early Onset Parkinson's Disease.

Variants in PRKN and PINK1 are the leading cause of early-onset autosomal recessive Parkinson's disease, yet many cases remain genetically unresolved. We previously identified a 7 megabases complex structural variant in a pair of monozygotic twins using Oxford Nanopore Technologies (ONT) long-read sequencing. This study aims to determine if ONT long-read sequencing can detect a second variant in other unresolved early-onset Parkinson's disease (EOPD) cases with 1 heterozygous PRKN or PINK1 variant. ONT long-read sequencing was performed on EOPD patients with 1 reported PRKN/PINK1 pathogenic variant, with onset age under 50. Positive controls included EOPD patients with 2 known PRKN pathogenic variants. Initial testing involved short-read targeted panel sequencing for single nucleotide variants and multiplex ligation-dependent probe amplification for copy number variants. A total of 47 patients were studied (PRKN "one-variant," n = 23; PINK1 "one-variant," n = 12; PRKN "two-variants," n = 12). ONT long-read sequencing identified a second pathogenic variant in 26% of PRKN "one-variant" patients (6/23), but none in PINK1 "one-variant" patients (0/12). Detected variants included 1 complex inversion, 2 structural variant overlaps, and 3 duplications. In the PRKN "two-variants" group, both variants were identified in all patients (100%, 12/12). ONT long-read sequencing effectively identifies pathogenic structural variants in the PRKN locus missed by conventional methods. It should be considered for unresolved EOPD cases when a second variant is not detected through conventional approaches. ANN NEUROL 2024.

Genetic Linkage Map Construction and QTL Mapping for Juvenile Leaf and Growth Traits in Camellia oleifera

Advancement of the oil tea industry requires the development of high-yielding and superior-quality varieties of Camellia oleifera, a major oilseed crop. However, traditional breeding methods, hampered by lengthy cycles and low selection accuracy, significantly constrain the breeding process. Identifying single nucleotide polymorphisms (SNPs) associated with target traits, and applying molecular marker-assisted selection (MAS) for these traits, can thereby shorten the breeding cycles and amplify the breeding efficiency. In this study, we utilized the hexaploid C. oleifera as the reference genome to identify high-quality SNPs and constructed a high-density genetic linkage map of C. oleifera that spanned 1566.733 cM, included 3097 SNPs, and was anchored to 15 linkage groups. Using interval mapping, we localized quantitative trait loci (QTLs) for 11 juvenile traits in C. oleifera, identifying 15 QTLs for growth traits and 24 QTLs for leaf traits, including 4 stable QTLs. The logarithm of odds (LOD) scores for individual QTLs ranged from 3.48 to 14.62, explaining 9.86–48.61% of the phenotypic variance. We further identified 2 SNPs associated with growth traits (marker11-951 and marker12-68) and 10 SNPs associated with leaf traits (marker11-276, marker11-410, marker11-560, marker13-16, marker13-39, marker13-110, marker13-731, marker14-701, marker14-910, and marker14-1331). These results provide valuable insights into the genetic mapping of key traits in C. oleifera and will contribute to the development of new varieties with high yield and superior quality in the future.

Vitamin D binding protein and receptor prevalence in a large population with periodontitis: single nucleotide polymorphism and transcriptomic profiling

BackgroundThere is an ongoing controversy regarding the expression of vitamin D receptor (VDR) and binding protein (VDBP) genes, as well as their polymorphisms, in periodontitis. We examined eight single nucleotide polymorphisms (SNPs) and performed a transcriptome-level bioinformatics analysis to clarify their relationship with periodontitis.MethodsTo explore VDR and VDBP polymorphisms, 600 subjects were included, including 307 patients with chronic periodontitis (CP) and 293 healthy controls. Genomic DNA was extracted from peripheral venous blood collected from each subject. A MassARRAY system was used to detect SNPs, including rs1544410G/A (BsmI), rs2228570C/T (FokI), rs7975232G/T (ApaI), rs731236T/C (TaqI), rs739837G/T, rs9729G/T, and rs3847987C/A in the VDR gene, and rs7041A/C in the VDBP gene. Then, we analyzed transcriptome sequencing datas of gingival tissues from two single-cell transcriptome sequencing studies to identify differential expression profiles. The objective was to further explore the potential association between VDR gene and gingival tissues in individuals with CP.ResultsThe regression analysis model revealed a significant relationship between rs739837G/T (P = 0.04) and rs7041A/C (P = 0.03) polymorphisms and CP susceptibility. Subjects carrying the TT genotype of rs739837 showed a decreased risk of developing CP compared to those carrying the GG + GT genotype (OR = 0.53, 95% CI = 0.29–0.99). Individuals carrying the AC + CC genotype of rs7041 showed a reduced risk of developing CP compared to those with the AA genotype (OR = 0.70, 95% CI = 0.51–0.97). Furthermore, allele C of rs7041 was found to have a protective effect against periodontitis (P = 0.03, OR = 0.75, CI = 0.58–0.98). However, no association was found between CP susceptibility and six other 6 SNPs (rs1544410, rs2228570, rs7975232, rs9729, rs731236, and rs3847987). Differential levels of VDR transcription were observed in gingival tissues during CP.ConclusionsVDR genetic variability and transcriptional expression are significant factors affecting susceptibility to CP. These findings suggested that rs739837 TT in VDR and rs7041 A/C in VDBP may be protective against periodontitis.

Post-transplant complications revealed by mycophenolate mofetil related transporters and metabolic enzymes gene polymorphisms in pediatric patients with hematological disorders

BackgroundHaploidentical hematopoietic stem cell transplantation (Haplo-HSCT) serves as an important option for patients without an HLA matched donor in treating hematological disorders, while patients may experience various complications after transplantation. Mycophenolate mofetil (MMF), a cornerstone drug for graft-versus-host disease (GvHD) prophylaxis, effectively reduces the incidence of acute GvHD, and the efficacy of MMF varies among individuals associated with MMF-related transporters and metabolic enzymes single nucleotide polymorphisms (SNPs). However, limited studies have systematically reported the correlations between the MMF-related SNPs and post-transplant complications.MethodsHere, we conducted a retrospective study involving 90 pediatric patients with hematological disorders who underwent haplo-HSCT at a single center. All patients were subjected to MMF-related SNP testing, combined with common clinical characteristics, to be correlated with post-transplant complications.ResultsWe observed that all 15 MMF-related SNPs were in Hardy-Weinberg equilibrium. Based on multivariate Cox regression analysis of post-transplant complications, we discovered that SLCO1B1 (521T > C) variant genotype was an independent protective factor for chronic GvHD (HR = 0.25, 95% confidence interval (CI) (0.08–0.84)). For viral infection, CYP2C8 (1291 + 106T > C) variant genotype was an independent risk factor for cytomegalovirus infection (HR = 2.98, 95% CI (1.18–7.53)). As to hemorrhagic cystitis, SLCO1B1 (1865 + 4846T > C) variant genotype was an independent protective factor, while older age was considered as an independent risk factor (HR = 0.41, 95% CI (0.19–0.85); HR = 2.52, 95% CI (1.14–5.54), respectively). No statistical significance was discovered between common clinical characteristics and MMF-related SNPs with other complications, including grade II-IV/III-IV acute GvHD, Epstein-Barr virus infection, peri-engraftment syndrome, and capillary leak syndrome. We also discovered SLCO1B1 (597 C > T) and SLC29A1 (-162 + 228 A > C) variant genotypes are both independent factors for cumulative incidence of relapse after haplo-HSCT (HR = 4.02, 95% CI (1.42–11.44); HR = 0.18, 95% CI (0.07–0.43), respectively).ConclusionsOur findings highlight the significance of MMF-related transporters and metabolic enzymes SNPs in the development of post-transplant complications, contributing to facilitating personalized risk assessment and improving the clinical management in haplo-HSCT patients.

Insights into genetic determinants of piglet survival during a PRRSV outbreak

Breeding animals to produce more robust and disease-resistant pig populations becomes a complementary strategy to the more conventional methods of biosecurity and vaccination. The objective of this study was to explore the ability of a panel of genetic markers and immunity parameters to predict the survival rates during a natural PRRSV outbreak. Ten-week-old female Duroc pigs (n = 129), obtained from 61 sows and 20 boars, were naturally infected with a highly pathogenic PRRSV genotype 1 strain. Prior to infection, piglets were screened for immunity parameters (IgG levels in plasma and SOX13 mRNA expression in blood) and genetic markers previously associated to PRRSV immune response and immunity traits. Additionally, the 20 boars were genotyped with a panel of 132 single nucleotide polymorphisms (SNPs). Survival analysis showed that mortality was significantly higher for animals with low basal IgG levels in plasma and/or high SOX13 mRNA expression in blood. The genotypes of sires for SNPs associated with IgG plasma levels, CRP in serum, percentage of γδ T cells, lymphocyte phagocytic capacity, total number of lymphocytes and leukocytes, and MCV and MCH were significantly associated with the number of surviving offspring. Furthermore, CD163 and GBP5 markers were also associated to piglet survival. The effects of these SNPs were polygenic and cumulative, survival decreased from 94 to 21% as more susceptible alleles were accumulated for the different markers. Our results confirmed the existence of genetic variability in survival after PRRSV infection and provided a set of genetic markers and immunity traits associated with PRRS resistance.

QTL mapping provides new insights into emamectin benzoate resistance in salmon lice, Lepeophtheirus salmonis

BackgroundThe salmon louse (Lepeophtheirus salmonis) is a parasite of wild and farmed salmonid fish, causing huge economic damage to the commercial farming of Atlantic salmon (Salmo salar) in the northern hemisphere. The avermectin emamectin benzoate (EMB) is widely used for salmon delousing. While resistance to EMB is widespread in Atlantic populations of L. salmonis, the molecular mechanisms of resistance remain to be elucidated. The aim of the present work was to obtain insights into potential EMB resistance mechanisms by identifying genetic and transcriptomic markers associated with EMB resistance.ResultsCrosses were performed between EMB-susceptible and -resistant L. salmonis, sourced from two parental strains isolated in Scotland, producing fully pedigreed families. The EMB susceptibility of individual parasites was characterised using time-to-response bioassays. Parasites of two families were subjected to double digest restriction site-associated DNA sequencing (ddRAD-seq) for simultaneous discovery of single nucleotide polymorphisms (SNPs) and genotyping. Data analysis revealed that EMB resistance is associated with one quantitative trait locus (QTL) region on L. salmonis chromosome 5. Marker-trait association was confirmed by genotyping assays for 7 SNPs in two additional families. Furthermore, the transcriptome of male parasites of the EMB-susceptible and -resistant L. salmonis parental strains was assessed. Among eighteen sequences showing higher transcript expression in EMB-resistant as compared to drug-susceptible lice, the most strongly up-regulated gene is located in the above QTL region and shows high homology to β spectrin, a cytoskeleton protein that has roles in neuron architecture and function. Further genes differentially regulated in EMB-resistant lice include a glutathione S-transferase (GST), and genes coding for proteins with predicted roles in mitochondrial function, intracellular signalling or transcription.ConclusionsMajor determinants of EMB resistance in L. salmonis are located on Chromosome 5. Resistance can be predicted using a limited number of genetic markers. Genes transcriptionally up-regulated in EMB resistant parasites include a β spectrin, a cytoskeletal protein with still incompletely understood roles in neuron structure and function, as well as glutathione S-transferase, an enzyme with potential roles in the biochemical defence against toxicants.

A high polygenic risk score is associated with SSA/SSB antibody positivity and early onset in primary Sjögren's disease.

To calculate a polygenic risk score (PRS) based on single nucleotide variants (SNVs) previously associated with primary Sjögren's disease (SjD) with genome-wide significance, and determine the genetic risk for SjD stratified by antibodies, sex and age at diagnosis. Patients with SjD (n = 1065) were genotyped using Illumina OmniExpressExome chip. Control genotype data were available (n = 7742). Two PRSs were constructed, one including HLA gene variants (n = 21 SNVs), and one without HLA (n = 18 SNVs). High PRS quartile (Q4) individuals were compared with low PRS (Q1-3). A high PRS was associated with SSA antibody positive SjD (OR 9.16, 95% CI 7.75-10.85, p= 3.7x10-146), and strengthened in SjD positive for both SSA/SSB antibodies (OR 13.67, 95% CI 10.88-17.32, p= 4.6x10-108). High PRS classified SSA/SSB antibody positive SjD with very good accuracy (AUC 0.86). PRS without HLA showed a weaker association with SSA/SSB positive SjD (OR 2.09, 95% CI 1.71-2.55, p= 6.4x10-13). Antibody negative SjD displayed a PRS similar to controls. Patients in the high PRS quartile were significantly younger at diagnosis, 48.9 ± 14.9 vs 53.4 ± 13.4 years in the low PRS quartiles (Q1-3), p= 2.2x10-6, and presented higher frequencies of ANA, SSA and SSA/SSB antibodies, p < 1x10-5. A high PRS is associated with SSA/SSB antibody positivity and early disease onset, both largely attributed to the weight of the HLA alleles. Integration of PRS with other biomarkers applied to clinical phenotypes, could be a useful tool for disease risk stratification and treatment decisions.

Advanced Ligase Chain Reaction Strategy to Generate a Circular DNA Walker for Electrochemiluminescent Detection of Single Nucleotide Polymorphism.

Single nucleotide polymorphism (SNP) primarily refers to DNA sequence polymorphism caused by variations in a single nucleotide, which is closely associated with many diseases such as genetic disorders and tumors. However, trace DNA mutants typically exist in a large pool of wild-type DNA, making it challenging to establish accurate and sensitive approaches for SNP detection. Herein, we developed an advanced ligase chain reaction (LCR) strategy to output the circular DNA walker for signal amplification, which realized accuracy and sensitive SNP detection based on the electrochemiluminescent (ECL) platform. Unlike the general LCR system that utilizes two sets of short single-stranded DNA (ssDNA) primers to generate double-stranded DNA amplification products, we ingeniously designed a long single-stranded DNA primer to replace one set of short ssDNA primers, allowing for the generation of circular DNA products upon complementing the target. Noticeably, the circular DNA serves as a DNA walker that can be easily purified by nucleases to eliminate unreacted primers and byproducts, significantly improving accuracy and sensitivity. Then, the circular DNA walker moved along a linearly ordered DNA quenching probe track modified on the ECL sensing interface, restoring the ECL signals by cleaving the quenching probes labeled on the DNA track with the help of apurinic/apyrimidinic endonuclease 1. Employing the p53 gene as a model, we realized the sensitive detection of mutant p53 in the range from 10 aM to 10 pM, with a detection limit of 6 aM, providing a promising platform for SNP detection.

Comprehensive Mendelian randomization analysis of low-density lipoprotein cholesterol and multiple cancers

PurposeThe aim of this study was to investigate the causal relationship between low-density lipoprotein cholesterol (LDL-C) and five cancers (breast, cervical, thyroid, prostate and colorectal) using the Mendelian Randomization (MR) method, with a view to revealing the potential role of LDL-C in the development of these cancers.MethodsWe used gene variant data and disease data from the Genome-Wide Association Study (GWAS) database to assess the causal relationship between LDL-C and each cancer by Mendelian randomisation analysis methods such as inverse variance weighting and MR-Egger. Specifically, we selected Proprotein convertase subtilisin/kexin type 9 (PCSK9) and 3-hydroxy-3-methylglutaryl-CoA reductase (HMGCR), genes associated with LDL-C levels, as instrumental variables, extracted the corresponding single nucleotide polymorphism (SNP) data and analysed the associations of these SNPs with five cancers.In addition, sensitivity analyses and heterogeneity tests were performed to ensure the reliability of the results.ResultsThe analyses showed that when using HMGCR gene, LDL-C were significantly and positively associated with breast (OR:1.200, 95% CI:1.082–1.329, p = 0.001), prostate (OR:1.198, 95% CI:1.050–1.366, p = 0.007), and thyroid cancers (OR:8.291, 95% CI:3.189- 21.555, p = 0.00001) were significantly positively correlated, whereas they were significantly negatively correlated with colorectal cancer (OR:0.641, 95% CI:0.442–0.928, p = 0.019); the results for cervical cancer were not significant (p = 0.050). When using the PCSK9 gene, LDL-C levels were significantly and positively associated with breast (OR:1.107, 95%:CI 1.031–1.187, p = 0.005) and prostate (OR:1.219, 95%:CI 1.101–1.349, p = 0.0001) cancers, but not with cervical (p = 0.294), thyroid cancer (p = 0.759) and colorectal cancer ( p = 0.572).ConclusionAnalyses using both the HMGCR and PCSK9 genes have shown that LDL-C may be a potential risk factor for breast and prostate cancer, while analyses of the HMGCR gene have also suggested that LDL-C may increase the risk of thyroid cancer and decrease the risk of colorectal cancer.

The association between type 1 diabetes mellitus and the risk of immunoglobulin A nephropathy: a Mendelian randomization study

ObjectiveTo investigate the potential causal relationship between type 1 diabetes mellitus (T1DM) and IgA nephropathy (IgAN) to deepen understanding of the association between these two conditions and to provide a scientific basis for future preventive and therapeutic strategies.MethodsThis study employed Mendelian randomization (MR) analysis, using single nucleotide polymorphisms (SNPs) derived from genome-wide association studies (GWAS) as genetic instrumental variables (IVs), to assess the association between T1DM and IgAN. The analytical approaches included univariable and multivariable MR, along with sensitivity analyses such as Mendelian randomization-Egger (MR-Egger) and Mendelian Randomization Pleiotropy RESidual Sum and Outlier (MR-PRESSO), to evaluate the impact of heterogeneity and pleiotropy.ResultsUnivariable MR analysis using the IVW method revealed an odds ratio (OR) of 1.009 [95% confidence interval (CI): 1.032–1.206] for the association between T1DM and IgAN. Adjusted results from multivariable MR analysis indicated a significant relationship between T1DM and increased risk of IgAN; for example, after adjusting for triglycerides (TG), the OR was 1.534 (CI: 1.213–1.543). After adjustment for HOMA-IR, the OR was 1.303 (CI: 1.149–1.198). Sensitivity analyses, including MR-Egger regression intercept testing (p = 0.476), suggested no pleiotropy, and MR-PRESSO did not detect any influence from outlier SNPs.ConclusionThe findings suggest that T1DM is a factor in increasing the risk of IgAN, enhancing our understanding of the potential relationship between T1DM and IgAN and providing possible biological pathways for future disease prevention and intervention.

Microglial CD2AP deficiency exerts protection in an Alzheimer’s disease model of amyloidosis

BackgroundThe CD2-associated protein (CD2AP) was initially identified in peripheral immune cells and regulates cytoskeleton and protein trafficking. Single nucleotide polymorphisms (SNPs) in the CD2AP gene have been associated with Alzheimer’s disease (AD). However, the functional role of CD2AP, especially its role in microglia during AD onset, remains elusive.MethodsCD2AP protein levels in cultured primary cells and in 5xFAD mice was studied. Microglial CD2AP-deficient mice were crossed with 5xFAD mice and the offspring were subjected to neuropathological assessment, behavioral tests, electrophysiology, RNA-seq, Golgi staining, and biochemistry analysis. Primary microglia were also isolated for assessing their uptake and morphology changes.ResultsWe find that CD2AP is abundantly expressed in microglia and its levels are elevated in the brain of AD patients and the 5xFAD model mice at pathological stages. We demonstrate that CD2AP haploinsufficiency in microglia significantly attenuates cognitive and synaptic deficits, weakens the response of microglia to Aβ and the formation of disease-associated microglia (DAM), and alleviates synapse loss in 5xFAD mice. We show that CD2AP-deficient microglia exhibit compromised uptake ability. In addition, we find that CD2AP expression is positively correlated with the expression of the complement C1q that is important for synapse phagocytosis and the formation of DAM in response to Aβ deposition. Moreover, we reveal that CD2AP interacts with colony stimulating factor 1 receptor (CSF1R) and regulates CSF1R cell surface levels, which may further affect C1q expression.ConclusionsOur results demonstrate that CD2AP regulates microgliosis and identify a protective function of microglial CD2AP deficiency against Aβ deposition, suggesting the importance of detailed investigation of AD-associated genes in different brain cells for thoroughly understanding their exact contribution to AD.

Association between thyroid dysfunction and diabetic retinopathy: a two-sample bidirectional Mendelian randomization study

ObjectivesTo assess the association between thyroid dysfunction and diabetic retinopathy (DR), a two-sample bidirectional Mendelian randomization (MR) study utilizing the Genome-wide Association Study (GWAS) database was conducted to investigate the causal relationship between these two variables.MethodsIn this study, GWAS of 48,328,151 single nucleotide polymorphisms(SNP) in the European population from the IEU open GWAS database were utilized as genetic tools for investigating thyroid dysfunction. The total sample size for the study on hyperthyroidism was 460,499 (case group: 3557; control group: 456,942). The total sample size for hypothyroidism was 410,141 (case group: 30,155; control group: 37,986). In addition, the data on DR were extracted from the FinnGen Biobank, comprising a total sample size of 319,046 individuals (10,413 cases and 308,633 controls). For the forward MR analysis, hyperthyroidism and hypothyroidism were considered as exposures with DR as the outcome. Reverse MR analysis was conducted using DR as exposure and hyperthyroidism and hypothyroidism as outcomes. Methods: The main analytical approach employed inverse variance weighting(IVW), supplemented by MR-Egger, Weighted mode method, weighted median, and Simple mode. Cochran's Q test, MR-PRESSO, MR-Egger and leave-one-out analysis were used to evaluate the sensitivity and pleiotropy.ResultsTwo-sample bidirectional MR analysis revealed a significant association between the presence of hyperthyroidism and hypothyroidism and an increased risk of DR in the forward MR analysis (IVW: OR = 1.29, 95% [CI] = 1.12–1.49, P < 0.001; OR = 1.17, 95% CI = 1.10–1.25, P < 0.001). In the reverse MR analysis, DR was found to be associated with an elevated risk of developing hyperthyroidism and hypothyroidism (IVW: OR = 1.56, 95% CI 1.38–1.76, P < 0.001; OR = 1.41, 95% CI 1.25–1.59, P < 0.001). Furthermore, most supplementary MR methods also demonstrated statistically significant differences and exhibited effect sizes consistent with those obtained from IVW. The sensitivity analysis confirmed the relative reliability of our causal findings.ConclusionsOur findings provide genetic evidence supporting a bidirectional causal relationship between thyroid function and DR.

ScEccDNAdb: an integrated single-cell eccDNA resource for human and mouse.

Extrachromosomal circular DNA (eccDNA), an extrachromosomal circular structured DNA, is extensively found in eukaryotes. Investigating eccDNA at the single-cell level is crucial for understanding cellular heterogeneity, evolution, development, and specific cellular functions. However, high-throughput identification methods for single-cell eccDNA are complex, and the lack of mature, widely applicable technologies has resulted in limited resources. To address this gap, we built scEccDNAdb, a database based on single-cell whole-genome sequencing data. It contains 3 195 464 single-cell eccDNA entries from human and mouse samples, with annotations including oncogenes, typical enhancers, super-enhancers, CCCTC-binding factor-binding sites, single nucleotide polymorphisms, chromatin accessibility, expression quantitative trait loci, transcription factor binding sites, motifs, and structural variants. Additionally, it provides nine online analysis and visualization tools, which enable the creation of publication-quality figures through user-uploaded files. Overall, scEccDNAdb is a comprehensive database for analyzing single-cell eccDNA data across diverse cell types, tissues, and species. Database URL: https://lcbb.swjtu.edu.cn/scEccDNAdb/.

CLOCK gene 3’UTR and exon 9 polymorphisms show a strong association with essential hypertension in a North Indian population

BackgroundHypertension (HTN) is a medical condition characterized by persistent systolic and diastolic blood pressures of ≥ 140 mmHg and ≥ 90 mmHg, respectively. With more than 1200 million adult patients aged 30–79 years worldwide according to the latest WHO data, HTN is a major health risk factor; more importantly, 46% of patients are unaware of this condition. Essential hypertension (EH), also known as primary hypertension, is the predominant subtype and has a complex etiology that involves both genetic and non-genetic factors. Majority of living organisms are influenced by the light and dark cycle of a day and respond to these changes through an intricate clock referred to as the “biological clock” or “circadian rhythm”. The connection between circadian rhythm and blood pressure is well established, with many studies supporting the role of circadian rhythm gene mutation(s)/polymorphism(s) in EH. To date, no such data are available from any Indian population.MethodsThis case‒control study was conducted on 405 EH patients and 505 healthy controls belonging to the Jammu region of North India after an informed consent was obtained from the participants. A total of three single nucleotide variants, two in the CLOCK gene (rs1801260 and rs34789226) and one in the BMAL1/ARNTL gene (rs6486121), were selected for genotyping. Genotyping was performed via the RFLP technique, and the applicable statistical analyses were performed via the SPSS and SNPStats programs.ResultsLogistic regression analysis revealed a statistically significant association of both CLOCK gene variants rs1801260 (T > C 3’UTR) and rs34789226 (C > T Exon 9) and a nonsignificant association of the BMAL1/ARNTL intronic variant rs6486121 (C > T) with EH. The 3’UTR variant showed a statistically significant association under the codominant (p < 0.0001), dominant (p < 0.0001), and recessive (p = 0.0004) models. In contrast, the exon 9 variant showed a statistically significant negative association under the codominant (p = 0.003) and dominant (p = 0.015) models only. The rs6486121/rs1801260 and rs1801260/rs34789226/rs6486121 haplotypes showed significant differences in their distribution between cases and controls (p < 0.0001). Certain genotypes and haplotypes were found more common in hypertensive males than females.ConclusionThis is a first report linking circadian rhythm gene polymorphisms with EH in any Indian population. The statistically significant association of the CLOCK gene 3’UTR and exon 9 polymorphisms with EH, highlight the potential role of this gene and probably other genes of the circadian pathway in the etiology of EH in the study population. Additionally, our study also revealed that certain genotypes are making males more susceptible to EH.

The F204S mutation in adrenodoxin oxidoreductase drives salinomycin resistance in Eimeria tenella

Salinomycin is a polyether ionophore widely used for the treatment of coccidiosis in poultry. However, the emergence of coccidia strains resistant to salinomycin presents challenges for control efforts, and the mechanisms underlying this resistance in Eimeria remain inadequately understood. In this study, 78 stable salinomycin-resistant strains were generated through experimental evolution approaches. Whole-genome sequencing of salinomycin-resistant Eimeria tenella isolates revealed single nucleotide polymorphisms (SNPs), with 12 candidate genes harboring nonsynonymous mutations identified. To confirm the candidate gene responsible for conferring salinomycin resistance, we leveraged reverse genetic strategies and identified a key amino acid substitution (F204S) in adrenodoxin oxidoreductase (EtADR), which markedly reduced susceptibility to salinomycin. Our results elucidate the complex interactions among salinomycin resistance, parasite fitness, point mutations, and the structure of EtADR, laying the foundation for future studies on drug resistance in Eimeria and contributing to the development of targeted control strategies.

Genome-wide association study reveals the advantaged genes regulating japonica rice grain shape traits in northern China

Background Rice, a staple food for over half of the global population, exhibits significant diversity in grain shape characteristics, which impact not only appearance and milling quality but also grain weight and yield. Identifying genes and loci underlying these traits is crucial for improving rice breeding programs. Previous studies have identified multiple quantitative trait loci (QTLs) and genes regulating grain length, width, and length-width ratio; however, further investigation is necessary to elucidate their regulatory pathways and their practical application in crop improvement. Methods This study employed a genome-wide association study (GWAS) on 280 japonica rice varieties from northern China to decipher the genetic basis of grain shape traits. Phenotyping included measurements of 11 grain-related traits, such as grain length, width, and area, along with their brown and white rice counterparts. High-density single nucleotide polymorphism (SNP) markers (33,579) were utilized for genotyping, and GWAS was performed using a mixed linear model (MLM) incorporating principal component analysis (PCA) and kinship (K) matrix to account for population structure and relatedness. Results Our analysis detected 15 QTLs associated with the 11 grain shape traits, of which five major QTL clusters emerged as crucial. Candidate genes, including LOC_Os01g50720 (qGL1), OsMKK4 (LOC_Os02g54600, influencing qBA2, qWL2, and qWA2), GW5 (LOC_Os05g09520, controlling qGW5, qBW5, qBR5, qWW5, and qWR5), GW6a (LOC_Os06g44100, associated with qGW6, qBW6, qBR6, qWW6, and qWR6), and FZP (LOC_Os07g47330, linked to qWL7), were identified based on functional annotations and haplotype analysis. These findings offer valuable insights into the genetic mechanisms underlying rice grain shape and suggest promising targets for marker-assisted selection to enhance rice quality and yield.