Systems genetics and bioinformatics analyses using ESR1-correlated genes identify potential candidates underlying female bone development

Estrogen receptor α (ESR1) is involved in E2 signaling and plays a major role in postmenopausal bone loss. However, the molecular network underlying ESR1 has not been explored. We used systems genetics and bioinformatics to identify important genes associated with Esr1 in postmenopausal bone loss. We identified ~2300 Esr1-coexpressed genes in female BXD bone femur, functional analysis of which revealed ‘osteoblast signaling’ as the most enriched pathway. PPI network led to the identification of 25 ‘female bone candidates’. The gene-regulatory analysis revealed RUNX2 as a key TF. ANKRD1 and RUNX2 were significantly different between osteoporosis patients and healthy controls. Sp7, Col1a1 and Pth1r correlated with multiple femur bone phenotypes in BXD mice. miR-3121-3p targeted Csf1, Ankrd1, Sp7 and Runx2. β-estradiol treatment markedly increased the expression of these candidates in mouse osteoblast. Our study revealed that Esr1-correlated genes Ankrd1, Runx2, Csf1 and Sp7 may play important roles in female bone development. •Systems genetics and bioinformatics analyses using BXD mice identified female bone candidates.•Protein-protein interaction network led to the identification of 25 ‘female bone candidates’.•Ankrd1, Runx2, Csf1 and Sp7 may play important roles in female bone development.•β-estradiol treatment markedly increased the expression of candidates in mouse osteoblast.