Identification Of Genetic Pleiotropic Variants For Osteoporosis And Related Complex Diseases And Investigating Of Potential Co-morbidity Mechanism

Osteoporosis is a metabolic bone disease and characterized by reduced bone mineral density(BMD)and quality of bone,deficiencies in the structure of bone tissue,damage of bone microstructure and increased risk of low trauma fractures.Osteoporosis is a kind of disease with complex genetic mode,which is influenced by multiple genes,environment and their interactions.BMD is the most common measurement for predicting the risk of osteoporosis and is a highly heritable trait with heritability as high as 0.85.Hundreds of genome-wide association studies(GWASs)have been conducted to study the genetic determinants of complex human traits.Results of GWASs only explain a small portion of genetic contributions to complex traits/diseases.Clinical and epidemiological findings point to an association between osteoporosis and obesity/T2D.More importantly,some genetic overlap for osteoporosis with obesity and T2D were also found in previous meta-analysis.A novel genetic pleiotropy-informed conditional false discovery rate(cFDR)method leverage pleiotropy to detect pleiotropic genetic variants for two related traits by using existing GWAS summary statistics data of osteoporosis,obesity and T2D.1.The summary statistics used for osteoporosis and obesity were taken from femoral neck BMD(FN BMD),body mass index(BMI)and waist-hip ratio(WHR),which are among the largest and/or the latest meta-analysis results in the osteoporosis and obesity fields.Using conditional Q-Q plots to graphically assess the pleiotropic enrichment,polygenic pleiotropic enrichment was found from conditional Q-Q plots for FN BMD,BMI and WHR across different significance thresholds.Using cFDR method,we identified 7 potentially pleiotropic loci,that is rs3759579(MARK3),rs2178950(TRPS1),rs1473(PUM1),rs9825174(XXYLT1),rs2047937(ZNF423),rsl7277372(DNM3),and rs335170(PRDM6),associated with osteoporosis and obesity,in which 4 loci were associated with FN BMD and BMI and 3 loci were associated with FN BMD and WHR.Of these loci,PUM1 gene differentially expressed in osteoporosis related cells(B lymphocytes)and obesity related cells(adipocytes).WGCNA in bone biopsies showed that PUM1 positively interacted with several known osteoporosis genes(AKAP11,JAG1 and SPTBN1).ZNF423 was the highly connected intramodular hub gene and interconnected with 21 known osteoporosis related genes,including JAG1,EN1 and FAM3C.Combining with biological functions,our study highlights PUM1 as an important potentially pleiotropic gene for osteoporosis and obesity.2.The summary statistics used for osteoporosis and T2D were taken from FN BMD and T2D,which are among the largest and/or the latest meta-analysis results in the osteoporosis and T2D fields.We used conditional Q-Q plots to graphically assess the pleiotropic enrichment and conditional Q-Q plot for FN BMD and T2D showed polygenic pleiotropic enrichment across different significance thresholds.Using cFDR method of GWAS summary data of FN BMD and T2D,we identified 27 significant SNPs with cFDR<0.05 for FN BMD and 61 SNPs for T2D,respectively.Four loci,rs7068487(PLEKHA1),rs10885421(TCF7L2),rs944082(GNG12-AS1(WLS))and rs2065929(PIFO||PGCP1),were found to be potentially pleiotropic and shared between FN BMD and T2D(ccFDR<0.05).PLEKHA1 was found differentially expressed in circulating monocytes between high and low BMD subjects,and PBMCs between diabetic and non-diabetic conditions.WGCNA showed that PLEKHA1 and TCF7L2 were interconnected with multiple osteoporosis and T2D associated genes in bone biopsy and pancreatic islets,such as JAG,EN1 and CPE.Fine mapping showed that rs 11200594 was a potentially causal variant in the locus of PLEKHA1.rs11200594 is also an eQTL of PLEKHA1 in multiple tissue(e.g.peripheral blood cells,adipose and ovary)and is in strong LD with a number of functional variants,especially rs71486610 with multiple functions(promotor,DHS,eQTL and transcription factor binding site).Our results highlight PLEKHA1 as an important potentially pleiotropic gene for osteoporosis and T2D.We identified multiple variants associated with FN BMD,BMI,WHR and T2D,7 potentially pleiotropic loci associated with FN BMD and BMI/WHR and 4 potentially pleiotropic loci associated with FN BMD and T2D.Our study for the first time suggested their potentially pleiotropic roles.The findings may give us new insights into genetic determination and co-determination mechanism of these complex diseases and enable us to gain a better understanding of the shared genetic determination between them.The findings suggest a possible research direction for subsequent functional studies of these potentially implicated genes in the joint pathophysiology of both diseases.