Effect of 1022C>T and 1222A>G genetic polymorphisms of SLC22A1 gene on substrates binding to human organic cation transporter 1

Human organic cation transporter 1 (hOCT1) is a transmembrane influx transporter protein encoded by the SLC22A1gene. hOCT1 plays a pivotal role in the hepatocellular and renal uptake of several xenobiotics and endogenoussubstrates. The human SLC22A1 gene is highly polymorphic. Non-synonymous single nucleotide polymorphisms(SNPs) of the human SLC22A1 gene tend to impair the transmembrane conductance of substrates by hOCT1. Herein,we describe the effect of 1022C>T and 1222A>G variations in the human SLC22A1 gene on hOCT1 structure andsubstrate binding. The three-dimensional (3D) structures of hOCT1 variants were ab initio models using the iTASSERserver, and drug-binding residues of the transmembrane domain were predicted using the Prankweb server. Substratebinding was analyzed by molecular docking using AutoDock 4.2.6. Amino acid residues, crucial for substrate bindingand transport, were altered in Met408Val and Pro341Leu variants and were suggestive of conformational changeinduced by 1022C>T and 1222A>G SNPs. Moreover, a statistically significant difference was observed betweenthe binding affinities of substrates to wild and mutant variants. Therefore, it is evident that 1022C>T and 1222A>Gnon-synonymous SNPs impair the drug uptake process of hOCT1, and hence patients with the former variants need tobe closely monitored for idiosyncratic adverse drug reactions or sub-therapeutic responses while being initiated intotherapy with hOCT1 substrates.

Novel non-synonymous mutations of PAX8 in a cohort of Chinese with congenital hypothyroidism / 中华医学杂志(英文版)

Background@#The transcription factor paired box 8 (PAX8) was associated with type 2 congenital non-goitrous hypothyroidism (CHNG2), a clinical phenotype of congenital hypothyroidism (CH). Though studied in a few regions with different ethnicities, the incidence of PAX8 mutations varied, even among Chinese cohorts in different regions. This study aimed to identify and characterize PAX8 mutations and explore the prevalence of its mutations in another cohort of CH.@*Methods@#The 105 unrelated Chinese patients with CH were collected from four major hospitals. Exomes of the 105 samples were sequenced by Hiseq 2000 platform to identify mutations of PAX8 on genomic DNAs extracted from peripheral blood samples. Luciferase reporter assays were used to assess the effects of mutations on the transcription of thyroid peroxidase (TPO).@*Results@#Three PAX8 mutations in four subjects were identified in 105 samples. One variant, rs189229644, was detected in two subjects, and categorized as uncertain significance. The other two missense mutations (275T>C/Ile92Thr and 398G>A/Arg133Gln) were not detected in three large-scale genotyping projects, namely 1000 Genome Project, Exome Aggregation Consortium and GO Exome Sequencing Project. Functional studies for the two mutations revealed that they could impair the transcription ability of PAX8 on one of its target genes, TPO. Therefore, the two mutations were causative for the pathogenesis of CHNG2. After combining the studies of PAX8 mutations, an average frequency of 1.74% (21/1209) could be obtained in Chinese patients with CH.@*Conclusion@#The study specifically demonstrates the role of two mutations in impairing the transcription ability of PAX8, which should be considered as pathogenic variants for CH.

Comprehensive Analysis of Non-Synonymous Natural Variants of G Protein-Coupled Receptors

G protein-coupled receptors (GPCRs) are the largest superfamily of transmembrane receptors and have vital signaling functions in various organs. Because of their critical roles in physiology and pathology, GPCRs are the most commonly used therapeutic target. It has been suggested that GPCRs undergo massive genetic variations such as genetic polymorphisms and DNA insertions or deletions. Among these genetic variations, non-synonymous natural variations change the amino acid sequence and could thus alter GPCR functions such as expression, localization, signaling, and ligand binding, which may be involved in disease development and altered responses to GPCR-targeting drugs. Despite the clinical importance of GPCRs, studies on the genotype-phenotype relationship of GPCR natural variants have been limited to a few GPCRs such as β-adrenergic receptors and opioid receptors. Comprehensive understanding of non-synonymous natural variations within GPCRs would help to predict the unknown genotype-phenotype relationship and yet-to-be-discovered natural variants. Here, we analyzed the non-synonymous natural variants of all non-olfactory GPCRs available from a public database, UniProt. The results suggest that non-synonymous natural variations occur extensively within the GPCR superfamily especially in the N-terminus and transmembrane domains. Within the transmembrane domains, natural variations observed more frequently in the conserved residues, which leads to disruption of the receptor function. Our analysis also suggests that only few non-synonymous natural variations have been studied in efforts to link the variations with functional consequences.

Microevolutionary trends of dengue virus-3 in Kerala, India.

Envelope gene is of great evolutionary significance and had been targeted as the vaccine candidate for dengue virus. We analyzed partial sequences of this gene to understand its genetic variability among viral isolates from Kerala state, India, if any. The current study focused on the evolutionary trends of this phylogenetically important gene among DENV-3 isolates through 2008 to 2010 outbreaks. The results gave an insight into the microevolutionary trends of the dengue viral genome. A unique mutation was recorded in the Domain II of the Envelope gene (EDII) of the viral genome at the amino acid position 219 (A219T). The evolutionary implication of this non-synonymous mutation near the EDI/EDII hinge remains to be explored. The study also provided knowledge on the genetic ancestral history of the viral isolates. Two variants of different phylogenetic origin were recorded in Kerala State. The findings in the study have significant implications on the development of dengue vaccines based on the Envelope gene of the virus.

Prediction of Genes Related to Positive Selection Using Whole-Genome Resequencing in Three Commercial Pig Breeds

Selective sweep can cause genetic differentiation across populations, which allows for the identification of possible causative regions/genes underlying important traits. The pig has experienced a long history of allele frequency changes through artificial selection in the domestication process. We obtained an average of 329,482,871 sequence reads for 24 pigs from three pig breeds: Yorkshire (n = 5), Landrace (n = 13), and Duroc (n = 6). An average read depth of 11.7 was obtained using whole-genome resequencing on an Illumina HiSeq2000 platform. In this study, cross-population extended haplotype homozygosity and cross-population composite likelihood ratio tests were implemented to detect genes experiencing positive selection for the genome-wide resequencing data generated from three commercial pig breeds. In our results, 26, 7, and 14 genes from Yorkshire, Landrace, and Duroc, respectively were detected by two kinds of statistical tests. Significant evidence for positive selection was identified on genes ST6GALNAC2 and EPHX1 in Yorkshire, PARK2 in Landrace, and BMP6, SLA-DQA1, and PRKG1 in Duroc.These genes are reportedly relevant to lactation, reproduction, meat quality, and growth traits. To understand how these single nucleotide polymorphisms (SNPs) related positive selection affect protein function, we analyzed the effect of non-synonymous SNPs. Three SNPs (rs324509622, rs80931851, and rs80937718) in the SLA-DQA1 gene were significant in the enrichment tests, indicating strong evidence for positive selection in Duroc. Our analyses identified genes under positive selection for lactation, reproduction, and meat-quality and growth traits in Yorkshire, Landrace, and Duroc, respectively.

A family-based transmission disequilibrium test of single nucleotide polymorphisms in exon 4 of ZNF804A gene in Han Chinese patients with schizophrenia / 第二军医大学学报

Objective To investigate the association of the single nucleotide polymorphisms (SNPs) in exon 4 of ZNF804A gene with schizophrenia in a family-trios sample. Methods MassARRAY genotyping technique and the transmission disequilibrium test (TDT) were employed to study the association of SNPs (seven nonsynonymous and two intronic) encompassing exon 4 of ZNF804A gene with schizophrenia in 69 nuclear families. Results (1) Four SNPs (rs79776875, rs78816540, rs79082132 and rs62198467) in this study were found to be rare variants (0