Microsatellites and SNPs linkage analysis in a Sardinian genetic isolate confirms several essential hypertension loci previously identified in different populations

Background. A multiplicity of study designs such as gene candidate analysis, genome wide search (GWS) and, recently, whole genome association studies have been employed for the identification of the genetic components of essential hypertension (EH). Several genome-wide linkage studies of EH and blood pressure-related phenotypes demonstrate that there is no single locus with a major effect while several genomic regions likely to contain EH-susceptibility loci were validated by multiple studies. Methods. We carried out the clinical assessment of the entire adult population in a Sardinian village (Talana) and we analyzed 16 selected families with 62 hypertensive subjects out of 267 individuals. We carried out a double GWS using a set of 902 uniformly spaced microsatellites and a high-density SNPs map on the same group of families. Results. Three loci were identified by both microsatellites and SNP scans and the obtained linkage results showed a remarkable degree of similarity. These loci were identified on chromosome 2q24, 11q23.1–25 and 13q14.11–21.33. Further support to these findings is their broad description present in literature associated to EH or related phenotypes. Bioinformatic investigation of these loci shows several potential EH candidate genes, several of whom already associated to blood pressure regulation pathways. Conclusion. Our search for major susceptibility EH genetic factors evidences that EH in the genetic isolate of Talana is due to the contribution of several genes contained in loci identified and replicated by earlier findings in different human populations

High Differentiation among Eight Villages in a Secluded Area of Sardinia Revealed by Genome-Wide High Density SNPs Analysis

To better design association studies for complex traits in isolated populations it's important to understand how history and isolation moulded the genetic features of different communities. Population isolates should not “a priori” be considered homogeneous, even if the communities are not distant and part of a small region. We studied a particular area of Sardinia called Ogliastra, characterized by the presence of several distinct villages that display different history, immigration events and population size. Cultural and geographic isolation characterized the history of these communities. We determined LD parameters in 8 villages and defined population structure through high density SNPs (about 360 K) on 360 unrelated people (45 selected samples from each village). These isolates showed differences in LD values and LD map length. Five of these villages show high LD values probably due to their reduced population size and extreme isolation. High genetic differentiation among villages was detected. Moreover population structure analysis revealed a high correlation between genetic and geographic distances. Our study indicates that history, geography and biodemography have influenced the genetic features of Ogliastra communities producing differences in LD and population structure. All these data demonstrate that we can consider each village an isolate with specific characteristics. We suggest that, in order to optimize the study design of complex traits, a thorough characterization of genetic features is useful to identify the presence of sub-populations and stratification within genetic isolates

Agnostic Pathway/Gene Set Analysis of Genome-Wide Association Data Identifies Associations for Pancreatic Cancer

Background Genome-wide association studies (GWAS) identify associations of individual single-nucleotide polymorphisms (SNPs) with cancer risk but usually only explain a fraction of the inherited variability. Pathway analysis of genetic variants is a powerful tool to identify networks of susceptibility genes. Methods We conducted a large agnostic pathway-based meta-analysis of GWAS data using the summary-based adaptive rank truncated product method to identify gene sets and pathways associated with pancreatic ductal adenocarcinoma (PDAC) in 9040 cases and 12 496 controls. We performed expression quantitative trait loci (eQTL) analysis and functional annotation of the top SNPs in genes contributing to the top associated pathways and gene sets. All statistical tests were two-sided. Results We identified 14 pathways and gene sets associated with PDAC at a false discovery rate of less than 0.05. After Bonferroni correction (P Conclusion Our agnostic pathway and gene set analysis integrated with functional annotation and eQTL analysis provides insight into genes and pathways that may be biologically relevant for risk of PDAC, including those not previously identified.Peer reviewe

Three new pancreatic cancer susceptibility signals identified on chromosomes 1q32.1, 5p15.33 and 8q24.21.

Genome-wide association studies (GWAS) have identified common pancreatic cancer susceptibility variants at 13 chromosomal loci in individuals of European descent. To identify new susceptibility variants, we performed imputation based on 1000 Genomes (1000G) Project data and association analysis using 5,107 case and 8,845 control subjects from 27 cohort and case-control studies that participated in the PanScan I-III GWAS. This analysis, in combination with a two-staged replication in an additional 6,076 case and 7,555 control subjects from the PANcreatic Disease ReseArch (PANDoRA) and Pancreatic Cancer Case-Control (PanC4) Consortia uncovered 3 new pancreatic cancer risk signals marked by single nucleotide polymorphisms (SNPs) rs2816938 at chromosome 1q32.1 (per allele odds ratio (OR) = 1.20, P = 4.88x10 -15), rs10094872 at 8q24.21 (OR = 1.15, P = 3.22x10 -9) and rs35226131 at 5p15.33 (OR = 0.71, P = 1.70x10 -8). These SNPs represent independent risk variants at previously identified pancreatic cancer risk loci on chr1q32.1 ( NR5A2), chr8q24.21 ( MYC) and chr5p15.33 ( CLPTM1L- TERT) as per analyses conditioned on previously reported susceptibility variants. We assessed expression of candidate genes at the three risk loci in histologically normal ( n = 10) and tumor ( n = 8) derived pancreatic tissue samples and observed a marked reduction of NR5A2 expression (chr1q32.1) in the tumors (fold change -7.6, P = 5.7x10 -8). This finding was validated in a second set of paired ( n = 20) histologically normal and tumor derived pancreatic tissue samples (average fold change for three NR5A2 isoforms -31.3 to -95.7, P = 7.5x10 -4-2.0x10 -3). Our study has identified new susceptibility variants independently conferring pancreatic cancer risk that merit functional follow-up to identify target genes and explain the underlying biology

Genome-wide meta-analysis identifies five new susceptibility loci for pancreatic cancer.

In 2020, 146,063 deaths due to pancreatic cancer are estimated to occur in Europe and the United States combined. To identify common susceptibility alleles, we performed the largest pancreatic cancer GWAS to date, including 9040 patients and 12,496 controls of European ancestry from the Pancreatic Cancer Cohort Consortium (PanScan) and the Pancreatic Cancer Case-Control Consortium (PanC4). Here, we find significant evidence of a novel association at rs78417682 (7p12/TNS3, P = 4.35 × 10-8). Replication of 10 promising signals in up to 2737 patients and 4752 controls from the PANcreatic Disease ReseArch (PANDoRA) consortium yields new genome-wide significant loci: rs13303010 at 1p36.33 (NOC2L, P = 8.36 × 10-14), rs2941471 at 8q21.11 (HNF4G, P = 6.60 × 10-10), rs4795218 at 17q12 (HNF1B, P = 1.32 × 10-8), and rs1517037 at 18q21.32 (GRP, P = 3.28 × 10-8). rs78417682 is not statistically significantly associated with pancreatic cancer in PANDoRA. Expression quantitative trait locus analysis in three independent pancreatic data sets provides molecular support of NOC2L as a pancreatic cancer susceptibility gene

Identifying pancreatic cancer risk genetic variants

Tesis doctoral inédita leída en la Universidad Autónoma de Madrid, Facultad de Medicina, Departamento de Medicina Preventiva, Salud pública y Microbiología. Fecha de lectura: 12-12-2018Esta tesis tiene embargado el acceso al texto completo hasta el 12-06-202

Genes linked with inflammatory processes are differentially expressed in patients with chronic heart failure and pain

Background and Aims Pain is a significant problem among patients with chronic heart failure (HF). The mechanisms underlying pain in HF remain poorly understood. Gene expression analysis using mRNA sequencing can highlight mechanistic underpinnings of complex symptoms such as pain. The aim of this study was to identify differentially expressed genes linked with pain in patients with HF with pain compared with patients with HF but without pain. The research question was: what genes linked with pain are differentially expressed between patients with HF and pain compared to patients with HF without pain? Methods Data were collected as part of a parent randomized controlled trial to test the efficacy of a computerized cognitive intervention for memory among patients with chronic HF (R01 NR016116). Blood specimens, pain measures, and sociodemographic characteristics were collected during the baseline visit in the parent trial. Data from 40 patients with HF: 20 with pain and 20 without pain, were analyzed in the current study. Pain presence (yes/no) was assessed using 1 item of the Health Utilities Index Mark-3 questionnaire. Sociodemographic data collected were age, self-reported gender, race and ethnicity, years of education, marital status, depressive symptoms (Patient Health Questionnaire-8), and health-related quality of life (Minnesota Living with Heart Failure Questionnaire). Clinical characteristics included body mass index, left ventricular ejection fraction (LVEF), and New York Heart Association heart failure class. Differences in demographic and clinical variables between the pain and no pain groups were examined using independent samples t-tests and chi square. The mRNA was isolated from whole blood and sequenced using a 150bppaired-end read configuration. Genes were tested for differential expression between HF patients with pain and without pain using DESeq2. Genes were considered differentially expressed if the log fold change between groups was ≥ ± 0.58 with a false discovery p-value < 0.05. Differentially expressed genes were examined using protein-protein interactions analysis, disease-related biological pathways, and existing pain literature. Independent samples t-tests were used to identify statistically significant differences in gene expression between the pain and no pain groups. Target genes of interest were validated through real-time polymerase chain reaction in a different sample of 24 patients: 10 with pain and 14 without pain, selected from the parent study and matched to the discovery sample on age and gender. Results Among the patients with pain, the mean age was 66.45 ± 6.21 years compared to 62.65 ± 13.87 years in the patients with pain. Most patients were men (60% in the pain group vs. 70% in the no pain group) and White(75% vs. 60%, respectively). The sample was primarily New York Heart Association class II (42.5%), with an average LVEF of 42.56% ± 13.58%. There were no statistically significant differences in demographic or clinical status variables between patients with and without pain. A total of 334 differentially expressed genes were identified (279 upregulated and 55 downregulated); they were mostly involved in neutrophil degranulation pathways (n = 57, false discovery p-value = 7.9e-17), followed by extracellular matrix organization pathways (n = 19, false discovery p-value = 4.5e-03). The protein-protein interactions analysis produced a network of 288 nodes and 497 edges, compared to the expected number of 182 edges(enrichment p-value < 1.0e-16), with a core network consisting of 15 co-expressed genes. From this core network of 15 genes, 7 target genes of interest were identified: (1) cathepsin G (CTSG), (2) lactotransferrin(LTF), (3) lipocalin-2 (LCN2), (4) matrix metallopeptidase 8 (MMP8), (5) matrix metallopeptidase 9 (MMP9), (6)proprotein convertase subtilisin/kexin type 9 (PCSK9), and (7) neutrophil defensin 3 (DEFA3). All 7 genes were connected to inflammatory pathways and inflammatory pain conditions (e.g., arthritis) in existing pain literature. All 7 genes were upregulated in patients with HF and pain compared to those with HF and without pain. Three of these 7 genes (MMP8,PCSK9,andDEFA3) were also validated in the second sample of 24patients with HF. Conclusions This study identified 7 genes that were differentially expressed in patients with chronic HF and pain compared to patients with HF but no pain. Of these, 3 were validated in an additional sample which further strengthens the proposed connection of these genes with pain. The genes were significantly enriched in inflammatory and extracellular matrix organization and may play a role in development of chronic pain among patients with HF. This study is novel in that the biologic mechanisms underlying pain in this population have not been previously examined using gene expression analysis. Further research is needed with a more ethnically diverse sample and more robust pain measures, particularly regarding severity and locations of pain.The parent study was funded by the National Institute of Nursing Research (R01 NR016116). This current study was funded by an Advancing Early Research Opportunities (AERO) Grant from the Rita and Alex Hillman Foundation. This study was supported by a T32 postdoctoral Fellowship from the National Institute of Nursing Research (T32 NR018407)

Differential Gene Expression Among Patients With Heart Failure Experiencing Pain

Background: Chronic pain is frequently experienced by patients with heart failure (HF) and is associated with higher mortality, higher symptom burden, and worsened health-related quality of life. However, the genomic mechanisms underlying chronic pain in HF are understudied. Building an understanding of the mechanistic underpinnings of pain may inform novel interventions. Objective: The objective was to identify genes associated with pain from mRNA sequence data collected from patients with HF with and without pain. Methods: The current study analyzed data from 40 patients with HF previously enrolled in a clinical trial. Pain presence was measured using the Health Utilities Index Mark-3. Genes were tested for differential expression using DESeq2, and differentially expressed genes were analyzed for protein–protein interaction (PPI) and relevant ontological pathways using Metascape. Genes located within the core of the PPI network were considered key in disease-relevant biological pathways. Differentially expressed genes within this PPI network were reviewed in existing literature to narrow down candidate genes of interest. These target genes of interest were reanalyzed in a second sample of 24 patients with HF using validation quantitative polymerase chain reaction. Results: A total of 334 genes (279 upregulated, 55 downregulated) were differentially expressed between patients with and without pain in the primary sample of 40. These genes were largely aligned with neutrophil degranulation pathways. Seven genes of interest were identified from a core network of 15 co-expressed genes in the PPI network and existing literature. Three of these seven genes: matrix metallopeptidase 8 (MMP8), proprotein convertase subtilisin/kexin type 9 (PCSK9), and neutrophil defensin 3 (DEFA3) were upregulated in patients with pain versus without pain in both the primary and validation samples. All seven genes of interest are involved in immune, inflammatory, and atherosclerotic processes. Discussion: These results identify potential genes that may play a mechanistic role in chronic pain in HF. Further research is needed to evaluate these potential genes among clearly delineated pain phenotypes.The parent study was funded by the National Institute of Nursing Research (NR016116). The current study was funded by an Advancing Early Research Opportunities (AERO) Grant from the Rita and Alex Hillman Foundation. This study was supported by a T32 postdoctoral Fellowship from the National Institute of Nursing Research (T32 NR018407: Program Director, Miller & Robb); Advanced Training in Self-Management Interventions for Serious Chronic Conditions

Ball-milling and cheap reagents breathe green life into the one hundred-year-old Hofmann reaction

The Hofmann carbylamine reaction is a very attractive route for preparing isocyanides directly from primary amines. However, its environmentally friendly potential is reduced by the use of hazardous chloroform in large excess. Herein, we report an innovative and very efficient mechanically activated synthesis of isocyanides based on the reaction of amines with chloroform in the presence of solid NaOH and without extra-solvent addition