Genetic determinants of risk in pulmonary arterial hypertension: international genome-wide association studies and meta-analysis

Background Rare genetic variants cause pulmonary arterial hypertension, but the contribution of common genetic variation to disease risk and natural history is poorly characterised. We tested for genome-wide association for pulmonary arterial hypertension in large international cohorts and assessed the contribution of associated regions to outcomes. Methods We did two separate genome-wide association studies (GWAS) and a meta-analysis of pulmonary arterial hypertension. These GWAS used data from four international case-control studies across 11744 individuals with European ancestry (including 2085 patients). One GWAS used genotypes from 5895 whole-genome sequences and the other GWAS used genotyping array data from an additional 5849 individuals. Cross-validation of loci reaching genome-wide significance was sought by meta-analysis. Conditional analysis corrected for the most significant variants at each locus was used to resolve signals for multiple associations. We functionally annotated associated variants and tested associations with duration of survival. All-cause mortality was the primary endpoint in survival analyses. Findings A locus near SOX17 (rs10103692, odds ratio 1·80 [95% CI 1·55–2·08], p=5·13×10– ¹⁵) and a second locus in HLA-DPA1 and HLA-DPB1 (collectively referred to as HLA-DPA1/DPB1 here; rs2856830, 1·56 [1·42–1·71], p=7·65×10– ²⁰) within the class II MHC region were associated with pulmonary arterial hypertension. The SOX17 locus had two independent signals associated with pulmonary arterial hypertension (rs13266183, 1·36 [1·25–1·48], p=1·69×10– ¹²; and rs10103692). Functional and epigenomic data indicate that the risk variants near SOX17 alter gene regulation via an enhancer active in endothelial cells. Pulmonary arterial hypertension risk variants determined haplotype-specific enhancer activity, and CRISPR-mediated inhibition of the enhancer reduced SOX17 expression. The HLA-DPA1/DPB1 rs2856830 genotype was strongly associated with survival. Median survival from diagnosis in patients with pulmonary arterial hypertension with the C/C homozygous genotype was double (13·50 years [95% CI 12·07 to >13·50]) that of those with the T/T genotype (6·97 years [6·02–8·05]), despite similar baseline disease severity. Interpretation This is the first study to report that common genetic variation at loci in an enhancer near SOX17 and in HLA-DPA1/DPB1 is associated with pulmonary arterial hypertension. Impairment of SOX17 function might be more common in pulmonary arterial hypertension than suggested by rare mutations in SOX17. Further studies are needed to confirm the association between HLA typing or rs2856830 genotyping and survival, and to determine whether HLA typing or rs2856830 genotyping improves risk stratification in clinical practice or trials. Funding UK NIHR, BHF, UK MRC, Dinosaur Trust, NIH/NHLBI, ERS, EMBO, Wellcome Trust, EU, AHA, ACClinPharm, Netherlands CVRI, Dutch Heart Foundation, Dutch Federation of UMC, Netherlands OHRD and RNAS, German DFG, German BMBF, APH Paris, INSERM, Université Paris-Sud, and French ANR

An insight into Hevea - Phytophthora interaction: The story of Hevea defense and Phytophthora counter defense mediated through molecular signalling

Hevea brasiliensis is the major commercial source of natural rubber in the world accounting for 99% of the world’s total rubber production. Abnormal leaf fall disease caused by Phytophthora spp. is the most destructive, annually recurring disease of rubber tree in India causing a loss of 38–56% in latex yield as most of the major cultivated clones are susceptible to this disease. Conventional breeding programmes aimed at incorporating disease resistance involves complex and time consuming steps especially in perennial tree crops like rubber tree, which warrants the need to identify molecular solutions for developing immunity in plant towards the pathogen. Currently, adopting efficient disease control measures against Phytophthora is a difficult task due to the peculiarities in the pathogen physiological characteristics, broad host range of clonal susceptibility and the unpredictable prevailing environmental conditions. To develop fruitful disease management strategies, it is essential to focus our research on the complex molecular interaction involved in Phytophthora pathogenicity and corresponding Hevea tolerance. In this review an attempt is made to consolidate the available data on host pathogen interaction between Hevea brasiliensis and various Phytophthora species that infect H. brasiliensis. Keywords: Hevea brasiliensis, Phytophthora, Plant defense, Effector, Elicito

Transcriptome profiling reveals genetic basis of disease resistance against Corynespora cassiicola in rubber tree (Hevea brasiliensis)

Corynespora leaf disease caused by Corynespora cassiicola (Berk. & Curt.) is one of the major diseases responsible for significant yield loss in rubber trees (Hevea brasiliensis). Next-generation sequencing based transcriptomic study of two rubber clones: RRII 105 (susceptible) and GT 1 (moderately resistant) were performed to understand the molecular basis of host tolerance to fungal diseases. Genes encoding disease resistance proteins, leucine-rich repeat proteins and genes involved in carbohydrate metabolic processes were significantly up-regulated in GT 1 upon infection, but were either completely suppressed or down-regulated in RRII 105. Transcription factor activity was a major molecular function triggered in both inoculated clones. Gene Ontology analysis revealed that majority of the transcripts was enriched for defense response, response to stimulus and stress. Higher expression of 118 transcripts with complete ORFs was identified in inoculated GT 1, indicating their possible role in disease resistance. In addition, both unique and common simple sequence repeats (SSRs) were identified. In silico analysis revealed 191 informative SSRs differentiating the two clones. Variant calling in control and disease GT 1 transcriptomes with reference to RRII 105 revealed over one lakh putative base substitutions. Microarray was used to validate the results obtained on transcriptional responses. Biotic stress overview from MapMan analysis revealed stronger activation of defense-related genes, receptor-like kinases and transcription factors. This study presents the first comprehensive transcriptome of resistant and susceptible rubber clones in response to C. cassiicola. The newly identified differentially regulated genes and sequence variation provide critical knowledge for understanding the genetic basis of disease resistance and marker development. Keywords: Corynespora leaf disease, Rubber tree, RNA-Seq analysis, Digital gene expression, Disease resistance protein

Analysis of Genetic Diversity and Resistance to Foliar Pathogens Based on Genotyping-by-Sequencing of a Para Rubber Diversity Panel and Progeny of an Interspecific Cross

Para rubber trees (Hevea brasiliensis) are the largest major source of natural rubber in the world. Its major pathogens are Phytophthora spp., Corynespora cassiicola, and Colletotrichum spp. A rubber diversity panel of 116 clones using over 12,000 single nucleotide polymorphisms (SNPs) from DArTSeq genotyping revealed clear phylogenetic differences in clones that originated from different geographical regions of the world. An integrated linkage map constructed with an F1 progeny of 86 from an interspecific cross between H. brasiliensis and H. benthamiana using 23,978 markers [10,323 SNPs and 13,655 SilicoDArTs] spanned 3947.83 cM with 0.83 cM average marker-interval. The genome scaffolds that were anchored to the linkage map, covering 1.44 Gb of H. brasiliensis reference genome, revealed a high level of collinearity between the genetic map and reference genome. Association analysis identified 12 SNPs significantly associated with the resistance against Phytophthora, Corynespora, and Colletotrichum in six linkage groups: 2, 6, 12, 14, 17, and 18. Kompetitive Allele-Specific PCR marker assays were developed for those 12 SNPs, screened with 178 individuals, and detected clear separation between two genotypes. Within the proximity to those SNPs, 41 potentially key genes that have previously been reported to associate with plant disease resistance were predicted with high confidence

Murraya <it>koenigii</it> leaf extract inhibits proteasome activity and induces cell death in breast cancer cells

<p>Abstract</p> <p>Background</p> <p>Inhibition of the proteolytic activity of 26S proteasome, the protein-degrading machine, is now considered a novel and promising approach for cancer therapy. Interestingly, proteasome inhibitors have been demonstrated to selectively kill cancer cells and also enhance the sensitivity of tumor cells to chemotherapeutic agents. Recently, polyphenols/flavonoids have been reported to inhibit proteasome activity. Murraya <it>koenigii</it> Spreng, a medicinally important herb of Indian origin, has been used for centuries in the Ayurvedic system of medicine. Here we show that Murraya <it>koenigii</it> leaves (curry leaves), a rich source of polyphenols, inhibit the proteolytic activity of the cancer cell proteasome, and cause cell death.</p> <p>Methods</p> <p>Hydro-methanolic extract of curry leaves (CLE) was prepared and its total phenolic content [TPC] determined by, the Folin-Ciocalteau’s method. Two human breast carcinoma cell lines: MCF-7 and MDA-MB-231 and a normal human lung fibroblast cell line, WI-38 were used for the studies. Cytotoxicity of the CLE was assessed by the MTT assay. We studied the effect of CLE on growth kinetics using colony formation assay. Growth arrest was assessed by cell cycle analysis and apoptosis by Annexin-V binding using flow cytometry. Inhibition of the endogenous 26S proteasome was studied in intact cells and cell extracts using substrates specific to 20S proteasomal enzymes.</p> <p>Results</p> <p>CLE decreased cell viability and altered the growth kinetics in both the breast cancer cell lines in a dose-dependent manner. It showed a significant arrest of cells in the S phase albeit in cancer cells only. Annexin V binding data suggests that cell death was via the apoptotic pathway in both the cancer cell lines. CLE treatment significantly decreased the activity of the 26S proteasome in the cancer but not normal cells.</p> <p>Conclusions</p> <p>Our study suggests M. <it>koenigii</it> leaves to be a potent source of proteasome inhibitors that lead to cancer cell death. Therefore, identification of active component(s) from the leaf extract could lead to the development of anti-cancer agents which could be useful in the treatment of different types of cancers.</p