A genome-wide association study identifies nucleotide variants at SIGLEC5 and DEFA1A3 as risk loci for periodontitis
HUMAN MOLECULAR GENETICS
Authors: Munz, Matthias; Willenborg, Christina; Richter, Gesa M.; Jockel-Schneider, Yvonne; Graetz, Christian; Staufenbiel, Ingmar; Wellmann, Juergen; Berger, Klaus; Krone, Bastian; Hoffmann, Per; van der Velde, Nathalie; Uitterlinden, Andre G.; de Groot, Lisette C. P. G. M.; Sawalha, Amr H.; Direskeneli, Haner; Saruhan-Direskeneli, Guher; Guzeldemir-Akcakanat, Esra; Keceli, Gencay; Laudes, Matthias; Noack, Barbara; Teumer, Alexander; Holtfreter, Birte; Kocher, Thomas; Eickholz, Peter; Meyle, Joerg; Doerfer, Christof; Bruckmann, Corinna; Lieb, Wolfgang; Franke, Andre; Schreiber, Stefan; Nohutcu, Rahime M.; Erdmann, Jeanette; Loos, Bruno G.; Jepsen, Soeren; Dommisch, Henrik; Schaefer, Arne S.
Abstract
Periodontitis is one of the most common inflammatory diseases, with a prevalence of 11% worldwide for the severe forms and an estimated heritability of 50%. The disease is characterized by destruction of the alveolar bone due to an aberrant host inflammatory response to a dysbiotic oral microbiome. Previous genome-wide association studies (GWAS) have reported several suggestive susceptibility loci. Here, we conducted a GWAS using a German and Dutch case-control sample of aggressive periodontitis (AgP, 896 cases, 7,104 controls), a rare but highly severe and early-onset form of periodontitis, validated the associations in a German sample of severe forms of the more moderate phenotype chronic periodontitis (CP) (993 cases, 1,419 controls). Positive findings were replicated in a Turkish sample of AgP (223 cases, 564 controls). A locus at SIGLEC5 (sialic acid binding Ig-like lectin 5) and a chromosomal region downstream of the DEFA1A3 locus (defensin alpha 1-3) showed association with both disease phenotypes and were associated with periodontitis at a genome-wide significance level in the pooled samples, with P = 1.09E-08 (rs4284742,-G; OR = 1.34, 95% CI = 1.21-1.48) and P = 5.48E-10 (rs2738058,-T; OR = 1.28, 95% CI = 1.18-1.38), respectively. SIGLEC5 is expressed in various myeloid immune cells and classified as an inhibitory receptor with the potential tomediate tyrosine phosphatases SHP-1/-2 dependent signaling. Alpha defensins are antimicrobial peptides with expression in neutrophils andmucosal surfaces and a role in phagocyte-mediated host defense. This study identifies the first shared genetic risk loci of AgP and CP with genome-wide significance and highlights the role of innate and adaptive immunity in the etiology of periodontitis.
Gene co-expression network analysis identifies porcine genes associated with variation in Salmonella shedding
BMC GENOMICS
Authors: Kommadath, Arun; Bao, Hua; Arantes, Adriano S.; Plastow, Graham S.; Tuggle, Christopher K.; Bearson, Shawn M. D.; Guan, Le Luo; Stothard, Paul
Abstract
Background: Salmonella enterica serovar Typhimurium is a gram-negative bacterium that can colonise the gut of humans and several species of food producing farm animals to cause enteric or septicaemic salmonellosis. While many studies have looked into the host genetic response to Salmonella infection, relatively few have used correlation of shedding traits with gene expression patterns to identify genes whose variable expression among different individuals may be associated with differences in Salmonella clearance and resistance. Here, we aimed to identify porcine genes and gene co-expression networks that differentiate distinct responses to Salmonella challenge with respect to faecal Salmonella shedding. Results: Peripheral blood transcriptome profiles from 16 pigs belonging to extremes of the trait of faecal Salmonella shedding counts recorded up to 20 days post-inoculation (low shedders (LS), n = 8; persistent shedders (PS), n = 8) were generated using RNA-sequencing from samples collected just before (day 0) and two days after (day 2) Salmonella inoculation. Weighted gene co-expression network analysis (WGCNA) of day 0 samples identified four modules of co-expressed genes significantly correlated with Salmonella shedding counts upon future challenge. Two of those modules consisted largely of innate immunity related genes, many of which were significantly up-regulated at day 2 post-inoculation. The connectivity at both days and the mean gene-wise expression levels at day 0 of the genes within these modules were higher in networks constructed using LS samples alone than those using PS alone. Genes within these modules include those previously reported to be involved in Salmonella resistance such as SLC11A1 (formerly NRAMP1), TLR4, CD14 and CCR1 and those for which an association with Salmonella is novel, for example, SIGLEC5, IGSF6 and TNFSF13B. Conclusions: Our analysis integrates gene co-expression network analysis, gene-trait correlations and differential expression to provide new candidate regulators of Salmonella shedding in pigs. The comparatively higher expression (also confirmed in an independent dataset) and the significantly higher connectivity of genes within the Salmonella shedding associated modules in LS compared to PS even before Salmonella challenge may be factors that contribute to the decreased faecal Salmonella shedding observed in LS following challenge.