Bone mineral density and genetic markers involved in three connected pathways (focal adhesion, actin cytoskeleton regulation and cell cycle): the CUMAGAS-BMD information system

Analyzing Genome-Wide Association Study Dataset Highlights Immune Pathways in Lip Bone Mineral Density

Osteoporosis is a common complex human disease. Until now, large-scale genome-wide association studies (GWAS) using single genetic variant have reported some novel osteoporosis susceptibility variants. However, these risk variants only explain a small proportion of osteoporosis genetic risk, and most genetic risk is largely unknown. Interestingly, the pathway analysis method has been used in investigation of osteoporosis mechanisms and reported some novel pathways. Until now, it remains unclear whether there are other risk pathways involved in BMD. Here, we selected a lip BMD GWAS with 301,019 SNPs in 5,858 Europeans, and conducted a gene-based analysis (SET SCREEN TEST) and a pathway-based analysis (WebGestalt). On the gene level, BMD susceptibility genes reported by previous GWAS were identified to be the top 10 significant signals. On the pathway level, we identified 27 significant KEGG pathways. Three immune pathways including T cell receptor signaling pathway (hsa04660), complement and coagulation cascades (hsa04610), and intestinal immune network for IgA production (hsa04672) are ranked the top three significant signals. Evidence from the PubMed and Google Scholar databases further supports our findings. In summary, our findings provide complementary information to these nine risk pathways.

Monogene frühmanifeste Osteoporose und Altersosteoporose – ein Kontinuum

Das Risiko für atraumatische/osteoporotische Frakturen nimmt ab einem Alter von 55 Jahren zu und wird zu einem großen Teil durch die individuelle Knochenmineraldichte und -struktur bestimmt. Durch Modeling während des Wachstums und anschließendes Remodeling passen Osteoblasten und Osteoklasten als Teil der sog. „basic multicellular unit“ das Knochengewebe kontinuierlich an die Erfordernisse an. Angeborene Störungen ihrer Funktion und/oder ihres Zusammenspiels durch häufige oder seltene Genvarianten können durch verzögerten Knochenaufbau oder beschleunigten Knochenabbau zu einer pathologisch niedrigen Knochenmineraldichte (BMD) führen. Häufige Varianten in über 500 Genloci erklären zusammen derzeit ca. 20 % der BMD-Varianz und beeinflussen das Risiko der Altersosteoporose. In einem signifikanten Teil der erwachsenen Patienten mit frühmanifester Osteoporose (vor dem 55. Lebensjahr) finden sich hingegen seltene Varianten als monogene Krankheitsursache. Aufgrund der mitunter sehr milden und variablen Manifestation dieser monogenen Krankheiten ist die genetische Diagnostik die zuverlässigste Möglichkeit der molekularen Zuordnung. Die bei der früh- und spätmanifesten Osteoporose involvierten Gene zeigen eine deutliche Überlappung, besonders bei Genen mit Funktion im Wnt-Signalweg. Die Einbeziehung genetischer Varianten in den diagnostischen Prozess erlaubt eine genauere Prognose und möglicherweise auch eine spezifischere Therapie. Auf die Altersosteoporose lässt sich dieser personalisierte Ansatz unter Umständen in einem nächsten Schritt mithilfe polygener Risiko-Scores übertragen.

Multiple analyses of large-scale genome-wide association study highlight new risk pathways in lumbar spine bone mineral density

Osteoporosis is a common human complex disease. It is mainly characterized by low bone mineral density (BMD) and low-trauma osteoporotic fractures (OF). Until now, a large proportion of heritability has yet to be explained. The existing large-scale genome-wide association studies (GWAS) provide strong support for the investigation of osteoporosis mechanisms using pathway analysis. Recent findings showed that different risk pathways may be involved in BMD in different tissues. Here, we conducted multiple pathway analyses of a large-scale lumbar spine BMD GWAS dataset (2,468,080 SNPs and 31,800 samples) using two published gene-based analysis software including ProxyGeneLD and the PLINK. Using BMD genes from ProxyGeneLD, we identified 51 significant KEGG pathways with adjusted P<0.01. Using BMD genes from PLINK, we identified 38 significant KEGG pathways with adjusted P<0.01. Interestingly, 33 pathways are shared in both methods. In summary, we not only identified the known risk pathway such as Wnt signaling, in which the top GWAS variants are significantly enriched, but also highlight some new risk pathways. Interestingly, evidence from further supports the involvement of these pathways in MBD.

Quantitative proteomics and integrative network analysis identified novel genes and pathways related to osteoporosis

Osteoporosis is mainly characterized by low bone mineral density (BMD), and can be attributed to excessive bone resorption by osteoclasts. Migration of circulating monocytes from blood to bone is important for subsequent osteoclast differentiation and bone resorption. Identification of those genes and pathways related to osteoclastogenesis and BMD will contribute to a better understanding of the pathophysiological mechanisms of osteoporosis. In this study, we applied the LC-nano-ESI-MS(E) (Liquid Chromatograph-nano-Electrospray Ionization-Mass Spectrometry) for quantitative proteomic profiling in 33 female Caucasians with discordant BMD levels, with 16 high vs. 17 low BMD subjects. Protein quantitation was accomplished by label-free measurement of total ion currents collected from MS(E) data. Comparison of protein expression in high vs. low BMD subjects showed that ITGA2B (p=0.0063) and GSN (p=0.019) were up-regulated in the high BMD group. Additionally, our protein-RNA integrative analysis showed that RHOA (p=0.00062) differentially expressed between high vs. low BMD groups. Network analysis based on multiple tools revealed two pathways: "regulation of actin cytoskeleton" (p=1.13E-5, FDR=3.34E-4) and "leukocyte transendothelial migration" (p=2.76E-4, FDR=4.71E-3) that are functionally relevant to osteoporosis. Consistently, ITGA2B, GSN and RHOA played crucial roles in these two pathways respectively. All together, our study strongly supported the contribution of the genes ITGA2B, GSN and RHOA and the two pathways to osteoporosis risk.

BIOLOGICAL SIGNIFICANCE

Mass spectrometry based quantitative proteomics study integrated with network analysis identified novel genes and pathways related to osteoporosis. The results were further verified in multiple level studies including protein-RNA integrative analysis and genome wide association studies.