Single Nucleotide Polymorphism Changes Research Articles

Increasing Knockin Efficiency in Mouse Zygotes by Transient Hypothermia.

Integration of a point mutation to correct or edit a gene requires the repair of the CRISPR-Cas9-induced double-strand break by homology-directed repair (HDR). This repair pathway is more active in late S and G2 phases of the cell cycle, whereas the competing pathway of nonhomologous end-joining (NHEJ) operates throughout the cell cycle. Accordingly, modulation of the cell cycle by chemical perturbation or simply by the timing of gene editing to shift the editing toward the S/G2 phase has been shown to increase HDR rates. Using a traffic light reporter in mouse embryonic stem cells and a fluorescence conversion reporter in human-induced pluripotent stem cells, we confirm that a transient cold shock leads to an increase in the rate of HDR, with a corresponding decrease in the rate of NHEJ repair. We then investigated whether a similar cold shock could lead to an increase in the rate of HDR in the mouse embryo. By analyzing the efficiency of gene editing using single nucleotide polymorphism changes and loxP insertion at three different genetic loci, we found that a transient reduction in temperature after zygote electroporation of CRISPR-Cas9 ribonucleoprotein with a single-stranded oligodeoxynucleotide repair template did indeed increase knockin efficiency, without affecting embryonic development. The efficiency of gene editing with and without the cold shock was first assessed by genotyping blastocysts. As a proof of concept, we then confirmed that the modified embryo culture conditions were compatible with live births by targeting the coat color gene tyrosinase and observing the repair of the albino mutation. Taken together, our data suggest that a transient cold shock could offer a simple and robust way to improve knockin outcomes in both stem cells and zygotes.

A Review of the Epidemiological Evidence for Adducin Family Gene Polymorphisms and Hypertension.

Hypertension is one of the most common cardiovascular diseases that seriously endangers human health and has become a significant public health problem worldwide. In the vast majority of patients, the cause of hypertension is unknown, called essential hypertension (EH), accounting for more than 95% of total hypertension. Epidemiological and genetic studies of humans and animals provide strong evidence of a causal relationship between high salt intake and hypertension. Adducin is one of the important candidate genes for essential hypertension. Adducin is a heterodimeric or heterotetrameric protein that consists of α, β, and γ subunits; the three subunits are encoded by genes (ADD1, ADD2, and ADD3) that map to three different chromosomes. Animal model experiments and clinical studies suggest that changes in single-nucleotide polymorphisms (SNPs) at part of the adducin family gene increase the Na+-K+-ATPase activity of the renal tubular basement membrane and increase the reabsorption of Na+ by renal tubular epithelial cells, which may cause hypertension. This review makes a summary on the structure, function, and mechanism of adducin and the role of adducin on the onset of EH, providing a basis for the early screening, prevention, and treatment of EH.

DNMT1, DNMT3A and DNMT3B Polymorphisms Associated With Gastric Cancer Risk: A Systematic Review and Meta-analysis

BackgroundIncreasing studies showed that abnormal changes in single nucleotide polymorphisms (SNPs) of DNMTs (DNMT1, DNMT3A and DNMT3B) were associated with occurrence or decrease of various tumors. However, the associations between DNMTs variations and gastric cancer (GC) risk were still conflicting. We aimed to assess the effect of DNMTs polymorphisms on the susceptibility to GC. MethodsFirstly, we did a meta-analysis for 7 SNPs (rs16999593, rs2228611, rs8101866 in DNMT1, rs1550117, rs13420827 in DNMT3A, rs1569686, rs2424913 in DNMT3B). Four genetic models (homozygote, heterozygote, dominant and recessive model) were used. Moreover, a meta-sensitivity and subgroup analysis was performed to clarify heterogeneity source. Lastly, 17 SNPs that couldn't be meta-analyzed were presented in a systematic review. Findings20 studies were included, 13 studies could be meta-analyzed and 7 ones could not. Firstly, a meta-analysis on 13 studies (3959 GC cases and 5992 controls) for 7 SNPs showed that GC risk increased in rs16999593 (heterozygote model: OR 1.36, 95%CI 1.14–1.61; dominant model: OR 1.36, 95%CI 1.15–1.60) and rs1550117 (homozygote model: OR 2.03, 95%CI 1.38–3.00; dominant model: OR 1.20, 95%CI 1.01–1.42; recessive model: OR 1.96, 95%CI 1.33–2.89) but decreased in rs1569686 (dominant model: OR 0.74, 95%CI 0.61–0.90). The remaining SNPs were not found associated with GC risk. Furthermore, the subgroup analysis indicated that for rs1550117 and rs1569686, the significant associations were particularly found in people from Chinese Jiangsu province (rs1550117, OR 1.77, 95%CI 1.25–2.51; rs1569686, OR 0.48, 95%CI 0.36–0.64) and that PCR-RFLP was a sensitive method to discover significant associations (rs1550117, OR 1.77, 95%CI 1.25–2.51; rs1569686, OR 0.49, 95%CI 0.37–0.65). Lastly, a systematic review on 7 studies for 17 SNPs suggested that rs36012910, rs7560488 and rs6087990 might have a potential effect on GC initiation. ConclusionThis meta-analysis demonstrated that rs16999593 and rs1550117 could contribute to GC risk and that rs1569686 might be a protective factor against gastric carcinogenesis. By using these SNPs as biomarkers, it is feasible to estimate the risk of acquiring GC and thus formulate timely preventive strategy.

Prokariotic expression of major autoantigens from Diabetes Mellitus fused to thioredoxin: IA-2 and ZnT8

Prokariotic expression of major autoantigens from Diabetes Mellitus fused to thioredoxin: IA-2 and ZnT8

Clinical genomics: when whole genome sequencing is like a whole-body CT scan.

Although we have witnessed major improvements in genomic testing in the past 5 years, multiple challenges need to be solved before clinical genomic testing becomes routine (1). The clinical implementation of genomic testing parallels the challenges we have faced with other transformative technologies. For the past decade, the medical community has been discussing the impact on healthcare and society of direct-to-consumer marketed whole-body computed tomography (CT)8 scanning (2). The CT scan is a technology that uses X-rays to produce cross-sectional images of the human body. There are clinical scenarios in which the CT scan is invaluable: disease diagnosis, evaluation after trauma, and monitoring response to oncologic therapy. However, CT scan is also being marketed as a preventive diagnostic for healthy individuals (3). Genomics can parallel CT scanning in scenarios of ( a ) first line diagnostic testing, ( b ) last ditch diagnosis, and ( c ) inappropriate clinical use. Genomic testing implies the examination of the nucleic acid sequence of multiple, if not all, known genes. Broadly, this includes microarray tests that survey changes in single nucleotide polymorphisms (SNPs) and copy-number variation across the entire genome, sequencing the exome or whole genome by next-generation sequencing, and sequencing large panels of clinically significant genes. Genomic testing is currently moving from academic research practice to commercialization and direct-to-consumer marketing. Although genomic testing is not yet routine, DNA testing targeted to single genes, viruses, or bacteria is commonplace and performed in many clinical laboratories. The use of genetic information has evolved over the past decade from targeted single-gene tests to broader genomic tests that encompass thousands of genes. Numerous ethical, economic, and …

Relationship between increased albendazole systemic exposure and changes in single nucleotide polymorphisms on the β-tubulin isotype 1 encoding gene in Haemonchus contortus

Resistance to benzimidazole anthelmintics in the nematode Haemonchus contortus has been correlated with single nucleotide polymorphisms (SNPs) on the β-tubulin isotype 1 gene. Three mutations can be used as markers for the detection of resistance, namely SNPs at position 200 and 167 (both TTC to TAC) or at position 198 (GAA to GCA). Harbouring a resistance genotype at any one of these codons can lead to a resistant phenotype. Our objective in this study was to analyse the frequencies of the three mutations when the albendazole dose rate and selection pressure were increased. We used adult H. contortus (males and females) collected directly from the abomasum of untreated lambs, or lambs treated with the manufacturer's recommended dose rate (5mg/kg), three times the recommended dose rate (15mg/kg), or nine times the recommended dose rate (45mg/kg). Anthelmintic efficacy was determined by worm and egg count reductions. For the surviving worms of the four treatment groups, the frequencies of each resistance SNP at codons 167, 200 and 198 were measured using pyrosequencing. Our results showed a strong relationship between an increasing dose rate and an increase in the frequency of the (TAC)200 SNP and a decrease in the (TAC)167 SNP. All worms genotyped were GAA at codon 198.

Reflections

Genomics is affecting all areas of medicine. In transfusion medicine, DNA-based genotyping is being used as an alternative to serological antibody-based methods to determine blood groups for matching donor to recipient. Most antigenic polymorphisms are due to single nucleotide polymorphism changes in the respective genes, and DNA arrays that target these changes have been validated by comparison with antibody-based typing. Importantly, the ability to test for antigens for which there are no serologic reagents is a major medical advance to identify antibodies and find compatible donor units, and can be life-saving. This review summarizes the evolving use and applications of genotyping for red cell and platelet blood group antigens affecting several areas of medicine. These include prenatal medicine for evaluating risk of fetal or neonatal disease and candidates for Rh-immune globulin; transplantation for bone marrow donor selection and transfusion support for highly alloimmunized patients and for confirmation of A2 status of kidney donors; hematology for comprehensive typing for patients with anemia requiring chronic transfusion; and oncology for patients receiving monoclonal antibody therapies that interfere with pretransfusion testing. A genomics approach allows, for the first time, the ability to routinely select donor units antigen matched to recipients for more than ABO/RhD to reduce complications. Of relevance, the growth of whole-genome sequencing in chronic disease and for general health will provide patients' comprehensive extended blood group profile as part of their medical record to be used to inform selection of the optimal transfusion therapy.