Identification of genetic risk factors of periodontitis by combined QTL mapping in mice and subsequent genome-wide association analysis, sequencing, and high-throughput genotyping of patients of aggressive periodontitis
Final Report Abstract
Periodontitis (PD) is a chronic inflammatory disease of the oral cavity. A major proportion of the population variance with PD can be attributed to genetic factors but only a proportion of the heritability has been explained. For identification of a comprehensive spectrum of genetic risk loci, we established an unbiased strategy for the de novo generation of hypotheses of candidate gene regions in humans. In a systems genetics approach, we used recombinant inbred mouse lines (RIL) of the Collaborative Cross (CC) and of an F2 cross and mapped risk genes of periodontitis as quantitative trait loci (QTLs). The human orthologous chromosomal regions that correlated to the mouse-QTLs were used as candidate loci for detailed analysis in large human case-control samples of aggressive and chronic PD. We assessed alveolar bone loss in response to experimental periodontal infection in 25 CC lines (286 mice) and of the F2 mouse population using micro–computed tomography analysis. The orthologous human chromosomal regions of the significant QTLs were analyzed for association with imputed genotype data derived from case-control samples of aggressive periodontitis (AgP; 896 cases, 7,104 controls) and chronic periodontitis (CP; 2,746 cases, 1,864 controls) of northwest European and European American descent, respectively. Use of variation data from the genomes of the CC founder strains suggested seven candidate genes. We found no evidence for association of these candidates with the human orthologues. We further hypothesized that expression patterns in mouse models recapitulate those among humans. We examined the transcriptome-wide gene expression differences between mice susceptible and resistant to changes in bone volume after P.G. and F.N. infection by RNA sequencing, to extend the total number of candidate genes beyond the mapped QTLs. And additionally, to also narrow down the number of candidate genes located at the QTLs to reduce the significance threshold of multiple testing. Samples from two susceptible and two resistant lines of the 25 CC lines and from individuals of the F2 cross were collected after infection and at a naïve status. Total RNA from the periodontium was sequenced and differential expression analysis between both groups was performed. Candidate genes were nominated based differential gene expression (DEGs). All human orthologous genes of the mouse DEGs were searched for genetic variants associated with AgP and CP in our case-control samples. Two DEGs that both were not located at a QTL from the CC-RILs, showed association in our pooled samples of AgP and CP, with P<1 x 10E-05. One DEG, which was located at a QTL mapped in the F2 cross was associated with AgP and CP (P = 2.9 × 10-5). A limitation of our study was the comparatively small size of our case-control samples, which may have caused false negative findings and may have precluded more significant p-values of association. However, no larger samples with a homogenous genetic background are currently available. In conclusion, we showed that QTL mapping in the mouse model is appropriate to generate candidate genes for human periodontitis and this approach is strengthened by comparative analysis of transcriptome-wide expression. In accordance to our hypothesis, we identified risk loci that were not identified by GWAS, because the associations did not reach genome-wide significance (P<5 x 10E-08). These genes highlight novel candidate genes of the pathogenesis of PD as a result of bacteria induced inflammation, and are relevant for complementation of GWAS findings.
Publications
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(2017) The PF4/PPBP/CXCL5 Gene Cluster Is Associated with Periodontitis. J Dent Res. Jul;96(8):945-952
Shusterman A, Munz M, Richter G, Jepsen S, Lieb W, Krone B, Hoffman P, Laudes M, Wellmann J, Berger K, Kocher T, Offenbacher S, Divaris K, Franke A, Schreiber S, Dommisch H, Weiss E, Schaefer AS, Houri- Haddad Y, Iraqi FA
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(2018) Integration of Murine and Human Studies for Mapping Periodontitis Susceptibility. J Dent Res. 97(5):537-546
Nashef A, Qabaja R, Salaymeh Y, Botzman M, Munz M, Dommisch H, Krone B, Hoffmann P, Wellmann J, Laudes MO, Berger K, Kocher T, Loos B, van der Velde N, Uitterlinden AG, de Groot LCPGM, Franke A, Offenbacher S, Lieb W, Divaris K, Mott R, Gat-Viks I, Wiess E, Schaefer A, Iraqi FA, Haddad YH
