A genome-wide association study identifies a novel candidate locus at the DLGAP1 gene with susceptibility to resistant hypertension in the Japanese population

Numerous genetic variants associated with hypertension and blood pressure are known, but there is a paucity of evidence from genetic studies of resistant hypertension, especially in Asian populations. To identify novel genetic loci associated with resistant hypertension in the Japanese population, we conducted a genome-wide association study with 2705 resistant hypertension cases and 21,296 mild hypertension controls, all from BioBank Japan. We identified one novel susceptibility candidate locus, rs1442386 on chromosome 18p11.3 (DLGAP1), achieving genome-wide significance (odds ratio (95% CI) = 0.85 (0.81–0.90), P = 3.75 × 10−8) and 18 loci showing suggestive association, including rs62525059 of 8q24.3 (CYP11B2) and rs3774427 of 3p21.1 (CACNA1D). We further detected biological processes associated with resistant hypertension, including chemical synaptic transmission, regulation of transmembrane transport, neuron development and neurological system processes, highlighting the importance of the nervous system. This study provides insights into the etiology of resistant hypertension in the Japanese population.

The Protein Tyrosine Phosphatase Non-receptor Type N22 (PTPN22) Gene Functional Polymorphism (1858T) is not Associated with Rheumatoid Arthritis in Kuwaiti Patients

Background: Rheumatoid Arthritis (RA) is a chronic disorder characterized by an inflammation of synovial tissue in joints resulting in pain, deformities and affects the quality of life. The gene for protein tyrosine phosphatase non-receptor type 22 (PTPN22) encodes a lymphoid specific phosphatase (LYP), which serves as a negative regulator of T lymphocyte activation and is associated with a number of autoimmune/chronic diseases in various ethnic groups. Objective: This study was undertaken to investigate an association between PTPN22 gene functional polymorphism (C1858T; rs2476601) and rheumatoid arthritis (RA) in Kuwaiti Arabs. The frequency of this candidate locus was compared between Kuwaiti RA patients and the controls and with that reported from other populations. Methods: The study was carried out in 191 Kuwaiti RA patients and 214 healthy controls. The diagnosis of RA was carried out according to the guidelines of the American College of Rheumatology (ACR). The genotypes of PTPN22 gene (C1858T) polymorphism were detected by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and confirmed by DNA sequence analysis in RA patients and controls. Results: The TT genotype of PTPN22 gene functional polymorphism C1858T was found in 2/191 (1%) in RA patients compared to 2/214 (1%) in the controls (P = 1.0). In contrast, heterozygous CT genotype was detected in 3/191 (1.57%) RA patients compared to 32/214 (14.9%) in the controls. The CC genotype was detected in 186/191 (97.38%), RA patients while it was detected in 180/214 (84.1%) of the controls. The two RA patients who carried the homozygous variant (TT) genotype were both positive for rheumatoid factor (RF) and did not have any extra-articular manifestations. Amongst the Kuwaiti RA patients, 27% had a family history of RA. No correlation was found between the activity/severity of the disease and PTPN22 gene polymorphism genotypes. Conclusion: This study did not find an association between the PTPN22 gene functional polymorphism (C1858T) and clinical manifestation and activity/severity of RA in Kuwaiti Arabs. This is in sharp contrast to previous reports from Caucasian and some other populations in which a positive association of PTPN22 gene (C1858T) polymorphism with genetic susceptibility to RA has been reported.

Genes underlying species differences in CHC production between Drosophila melanogaster and D. simulans.

Surface chemical compounds are key components of survival and reproduction in many species. Cuticular hydrocarbons (CHCs) are chemical compounds produced by all insects that are used for both desiccation resistance and chemical communication, including communication related to mating. In the species pair of Drosophila melanogaster and D. simulans, female CHCs stimulate conspecific males to mate and repel heterospecific males. While CHCs are a critical contributor to both reproductive success within a species and isolation between species, few genes underlying species variation in CHC profiles are known. Here, we use genetic mapping of the 3rd chromosome to test a suite of candidate genes for interspecies variation in CHCs. Candidate gene CG5946 was found to be involved in species differences in the production of 7,11-heptacosadiene and 7-tricosene between D. melanogaster and D. simulans. This is therefore a new candidate locus contributing to species-specific variation in the CHC profile. In the process of mapping genes for CHCs, we also identified 29 candidate genes for the reduced survival or inviability of interspecies hybrids.

Abstract MP175: Disruption of the Genome Architecture at the PRRX1 Locus is Associated With the Pathogenesis of LMNA -related Dilated Cardiomyopathy

Background: LMNA , a gene encoding A-type lamin proteins (abbreviated as lamin A), is one of the most frequently mutated genes in dilated cardiomyopathy (DCM). The molecular mechanisms underlying cardiomyocyte dysfunction in LMNA -related DCM remain elusive, translating to the lack of disease-specific therapies. Lamin A has been shown to play a critical role in genome organization via interactions with the chromatin at specific regions called lamina-associated domains (LADs). However, little is known about whether DCM-causing LMNA mutations rearrange the genome conformation and chromosome accessibility. The overarching goal of this study is to define the role of genome organization in LMNA -related DCM. Methods: LMNA -related DCM was modeled in vitro using cardiomyocytes derived from induced pluripotent stem cells (iPSC-CMs) from DCM patients carrying a frameshift mutation in the LMNA gene (c. 348_349insG; p. K117fs) and isogenic controls. We combined genome-wide single cell functional genomic and epigenomic mapping analyses to define the gene regulation and cis-regulatory interactions in isogenic iPSC-CMs. Results: Single-cell RNA-seq revealed global gene dysregulation in LMNA mutant compared to isogenic control iPSC-CMs. The homeodomain transcription factor PRRX1 was significantly upregulated in mutant cells. We showed that LAD integrity is disrupted at the PRRX1 locus in mutant iPSC-CMs. In agreement, DNA fluorescence in situ hybridization (FISH) revealed that the PRRX1 locus loses peripheral association and relocates towards the transcriptionally active nuclear interior in mutant iPSC-CMs. Correspondingly, single-cell assay for transposase accessible chromatin (ATAC)-seq showed increased chromatin co-accessibility at the PRRX1 locus, providing a plausible explanation for ectopic activation of PRRX1 in LMNA mutant iPSC-CMs. Conclusion: Our data suggest that LMNA haploinsufficiency disrupts the structure of LADs, leading to ectopic promoter interactions and altered gene expression in LMNA -related DCM iPSC-CMs. We identified PRRX1 as a promising candidate locus linking changes in LAD organization with gene dysregulation in LMNA -related DCM.

Super-MSI: CfDNA-based pan-cancer microsatellite instability detection.

e13672 Background: Microsatellite instability (MSI) is a molecular subtype found in many cancers, which is often associated with the benefits of immunotherapy. However, the application of traditional testing strategies (such as PCR or IHC) is largely limited due to their dependencies on sufficient tumor tissues. Here, we introduced Super-MSI, a cfDNA-based pan-cancer MSI detection method using next-generation sequencing (NGS). Methods: 5500 detectable microsatellite loci from 250 white blood cells (WBCs) and 29 PCR-validated MSI-H tissue samples were sequenced and characterized, while the former represented for MSS pattern, and the later, for MSI-H. 91 microsatellite loci with the most variable motif repeat numbers between patterns were filtered and the Super-MSI method was established. Plasma samples were collected from 608 patients with known MSI status assessed by PCR (593 MSS and 15 MSI-H) to validate the method. All samples were sequenced with a 642-gene panel, and initial microsatellite reads count distributions were profiled by MSIsensor. Results: We characterized each microsatellite locus by REF alleles (MSI-H:WBC ratio less than 1) and ALT alleles (MSI-H:WBC ratio more than 20), then defined the sum of ALT alleles frequency in WBC group as the baseline for each candidate locus. For plasma samples with unknown MSI status, hypergeometric distribution and FDR calibration were employed to assess the difference of ALT alleles frequency between the WBC baseline and plasma samples. Locus with FDR adjusted p-value less than 0.05 was defined as an unstable locus based on prior knowledge, and negative log-transformed FDR-p was defined as MSscore for the locus. The plasma sample with both unstable microsatellite proportion larger than 20% and total MSscore larger than 270 was defined as MSI-H, and contrariwise, MSS. For all evaluable samples in the validation cohort, Super-MSI showed high sensitivity and specificity of 60% (9/15) and 100% (593/593) for an overall accuracy of 99.0% (602/608), superior to its kind bMSISEA (83.5%, 106/127) and Guardant360 (98.4%, 934/949). Within LOD of 0.5% maxAF (approximately 1% ctDNA fraction), Super-MSI was able to detect 81.8% (9/11) of MSI-H samples, demonstrating high concordance with tissue-based PCR tests. Conclusions: Super-MSI can genotype pan-cancer patients with blood cfDNA samples and give highly accurate MSI evaluation with 81.8% sensitivity and 100% specificity above 1% ctDNA fraction.

QTL analysis for rice salinity tolerance and fine mapping of a candidate locus qSL7 for shoot length under salt stress

Salinity is one of the major abiotic stresses limiting rice production worldwide. Understanding the genetic basis of salinity tolerance is key for rice breeding. In this study, a recombinant inbred line (RIL) population derived from a super hybrid rice Liang–You–Pei–Jiu (LYP9) parents 93-11 and PA64s, exhibited variation in phenotypes including shoot length (SL), root length (RL), shoot fresh weight (SFW), root fresh weight (RFW), shoot dry weight (SDW), and root dry weight (RDW) under 50 and 100 mM NaCl stress. QTL analysis identified a total of 38 QTLs for these 6 traits under two distinct concentrations of salt, distributing on chromosomes 1, 2, 3, 4, 5, 6, 7 and 10. A total of 21 QTLs were found in 6 stable loci. A novel major QTL, qSL7 for shoot length on chromosome 7 was identified in two distinct concentrations. A chromosome segment substitution line (CSSL) harboring the qSL7 locus from PA64s with 93-11 background was developed and exhibited higher SL value, higher K+ concentration, and lower Na+ concentration compared to 93-11. With BC5F2:3 derived from CSSL-qSL7/93-11, the qSL7 was fine mapped within a 252.9 kb region on chromosome 7 where 40 annotated genes located including, LOC_Os07g43530, which encodes a DNA-binding domain containing protein reported previously as a transcription factor playing a positive role in salt stress tolerance. Our study provides new genetic resources for improvement of salinity tolerance in rice breeding.