Genome Wide Association Metanalysis Of Skull Bone Mineral Density Identifies Loci Relevant For Osteoporosis And Craniosynostosis

Abstract

Skull bone mineral density (SK-BMD) provides a suitable trait for the discovery of genes important to bone biology in general, and particularly for identifying components unique to intramembranous ossification, which cannot be captured at other skeletal sites. We assessed genetic determinants of SK-BMD in 43,800 individuals, identifying 59 genome-wide significant loci (4 novel), explaining 12.5% of its variance. Pathway and enrichment analyses of the association signals resulted in clustering within gene-sets involved in regulating the development of the skeleton; overexpressed in the musculoskeletal system; and enriched in enhancer and transcribed regions in osteoblasts. From the four novel loci (mapping to ZIC1, PRKAR1A, ATP6V1C1, GLRX3), two (ZIC1 and PRKAR1A) have previously been related to craniofacial developmental defects. Functional validation of skull development in zebrafish revealed abnormal cranial bone initiation that culminated in ectopic sutures and reduced BMD in mutated zic1 and atp6v1c1 fish and asymmetric bone growth and elevated BMD in mutated prkar1a fish. We confirmed a role of ZIC1 loss-of-function in suture patterning and discovered ATP6V1C1 gene associated with suture development. In light of the evidence presented suggesting that SK-BMD is genetically related to craniofacial abnormalities, our study opens new avenues to the understanding of the pathophysiology of craniofacial defects and towards the effective pharmacological treatment of bone diseases.

Functional Validation of Osteoporosis Genetic Findings Using Small Fish Models

“…Still, the function for many of these genes is unknown, especially whether it is relevant to bone homeostasis. Very recently, Medina-Gomez et al performed the largest skull-BMD-GWAS meta-analysis involving 43,800 individuals, identifying 59 loci, from which four loci were novel [ 7 ]. Using functional studies in zebrafish, the authors demonstrated that skull-BMD GWAS has great potential to help uncover genes important in developmental craniofacial conditions, such as craniosynostosis [ 7 ].…”

“…Very recently, Medina-Gomez et al performed the largest skull-BMD-GWAS meta-analysis involving 43,800 individuals, identifying 59 loci, from which four loci were novel [ 7 ]. Using functional studies in zebrafish, the authors demonstrated that skull-BMD GWAS has great potential to help uncover genes important in developmental craniofacial conditions, such as craniosynostosis [ 7 ]. Remarkably, this work showed that the majority of genes involved in skull homeostasis and intramembranous ossification also play a role in the maintenance of the remaining skeleton and are equally important to understanding the biology of osteoporosis.…”

“…Furthermore, zebrafish were recently used to validate new BMD candidate genes identified from the recent skull-BMD-GWAS, providing functional evidence that skull-BMD loci provide a repertoire of genes to be tested for involvement in craniofacial malformation and BMD regulation. Medina-Gomez et al performed the largest skull-BMD-GWAS meta-analysis identifying 59 loci, from which 4 loci were novel [ 7 ]. The group tested zic1 , atp6v1c1a , atp6v1c1b , prkar1a, and prkar1b in zebrafish, unprecedently showing that loss-of-function of each of these genes could lead to craniofacial malformation and abnormal BMD, thus, exemplifying the use of zebrafish to elucidate genes playing a role also in developmental craniofacial conditions.…”

“…The skull has been of recent interest, due to the possibility of enrichment and discoveries of intramembranous ossification-associated genes in the etiology of OP. In addition, given the relatively lower mechanical load on the skull, osteocytes are highly mechanosensitive, opening opportunities for the identification of genes involved in fine-tuning mechanical regulation of osteocytes [ 7 , 8 ]. Bone geometry and bone size/shape GWAS was also performed over the recent decades [ 9 , 10 ].…”

Mechanical-Stress-Related Epigenetic Regulation of ZIC1 Transcription Factor in the Etiology of Postmenopausal Osteoporosis

“…Previously, ZIC1 had been related to craniofacial developmental defects [ 3 ]. Its function was further assessed in a large-scale GWAS meta-analysis focusing specifically on BMD variation in the skull, finding 4 novel loci among 59 with genome-wide significance, including ZIC1 [ 4 ]. The gene was further screened in zebrafish crispants that displayed low skull BMD and abnormal suture patterning [ 4 ].…”