The Polymorphism at PLCB4 Promoter (rs6086746) Changes the Binding Affinity of RUNX2 and Affects Osteoporosis Susceptibility: An Analysis of Bioinformatics-Based Case-Control Study and Functional Validation

Abstract

PurposeGenome-wide association studies have identified numerous genetic variants that are associated with osteoporosis risk; however, most of them are present in the non-coding regions of the genome and the functional mechanisms are unknown. In this study, we aimed to investigate the potential variation in runt domain transcription factor 2 (RUNX2), which is an osteoblast-specific transcription factor that normally stimulates bone formation and osteoblast differentiation, regarding variants within RUNX2 binding sites and risk of osteoporosis in postmenopausal osteoporosis (PMOP).MethodsWe performed bioinformatics-based prediction by combining whole genome sequencing and chromatin immunoprecipitation sequencing to screen functional SNPs in the RUNX2 binding site using data from the database of Taiwan Biobank; Case-control studies with 651 postmenopausal women comprising 107 osteoporosis patients, 290 osteopenia patients, and 254 controls at Tri-Service General Hospital between 2015 and 2019 were included. The subjects were examined for bone mass density and classified into normal and those with osteopenia or osteoporosis by T-scoring with dual-energy X-ray absorptiometry. Furthermore, mRNA expression and luciferase reporter assay were used to provide additional evidence regarding the associations identified in the association analyses. Chi-square tests and logistic regression were mainly used for statistical assessment.ResultsThrough candidate gene approaches, 3 SNPs in the RUNX2 binding site were selected. A novel SNP rs6086746 in the PLCB4 promoter was identified to be associated with osteoporosis in Chinese populations. Patients with AA allele had higher risk of osteoporosis than those with GG+AG (adjusted OR = 6.89; 95% confidence intervals: 2.23–21.31, p = 0.001). Moreover, the AA genotype exhibited lower bone mass density (p < 0.05). Regarding mRNA expression, there were large differences in the correlation between PLCB4 and different RUNX2 alleles (Cohen’s q = 0.91). Functionally, the rs6086746 A allele reduces the RUNX2 binding affinity, thus enhancing the suppression of PLCB4 expression (p < 0.05).ConclusionsOur results provide further evidence to support the important role of the SNP rs6086746 in the etiology of osteopenia/osteoporosis, thereby enhancing the current understanding of the susceptibility to osteoporosis. We further studied the mechanism underlying osteoporosis regulation by PLCB4.

Combined Therapy of Yishen Zhuanggu Decoction and Caltrate D600 Alleviates Postmenopausal Osteoporosis by Targeting FoxO3a and Activating the Wnt/β-Catenin Pathway

“…. BALP is an important biomarker for bone formation, and Runx2 is a critical transcription regulator in osteoblast differentiation [23,24]. As shown in Figures 2(a) and 2(b), the levels of BALP and Runx2 in PMO rats were evidently lower than that in sham rats (P < 0.01).…”

Identification of key genes and biological pathways in chronic obstructive pulmonary disease using bioinformatics and next generation sequencing data analysis

“…Signaling pathways include immune system [109], signal transduction [110], extracellular matrix organization [111], adaptive immune system [112], neutrophil degranulation [113], innate immune system [114], metabolism [115], diseases of metabolism [116] and Hemostasis [117] were responsible for advancement of COPD. MPO (myeloperoxidase) [190], CTSD (cathepsin D) [1389], KLF10 [1390], FRZB (frizzled related protein) [1391], DUSP1 [1392], IL1B [1393], CCL11 [1394], LMNA (lamin A/C) [1395], WIF1 [1396], IL1RN [1397], IFNG (interferon gamma) [1398], CX3CL1 [1399], BMP2 [1400], CDKN1A [1401], BMP4 [1402], ICAM1 [1403], CD34 [1404], IL33 [1405], FASLG (Fas ligand) [1406], KDM6B [1407], TNF (tumor necrosis factor) [1408], GDF15 [1409], IL2 [1410], INPP4B [1411], FABP4 [1412], CYP2C19 [1413], CXCR4 [1414], DKK2 [1415], PLCB4 [1416], ANXA1 [1417], DUSP6 [1418], CORIN (corin, serine peptidase) [1419], F8 [1420], DDIT4 [1421], IL1R2 [1422], S100A4…”

Interaction between MARK3 (rs11623869), PLCB4 (rs6086746) and GEMIN2 (rs2277458) variants with bone mineral density and serum 25-hidroxivitamin D levels in Mexican Mestizo women

“…PLCB4 plays an essential role in signal transduction ( 34 ). Genetic variants in PLCB4 have been identified as cause of the Auriculocondylar syndrome 2 (ARCND2), a disease characterized by craniofacial malformations ( 13 ), PLCB4 acts as a direct signaling effector of the endothelin receptor type A (EDNRA)-Gq/11 pathway. Kanai et al, 2022 demonstrated that variants in PLCB4 gene interfere with the EDNRA signaling pathway, leading to the development of ARCND2 ( 35 ).…”

“…PLCB4 encodes a phospholipase C which participates in the phosphoinositide cycle signaling pathway, transmitting information from the extracellular environment into the cell, influencing several cellular processes. It has been reported that rs6086746 may affect the binding of the transcription factor RUNX2 to the promoter region of PLCB4 , this might be part of the mechanisms contributing to the development of OP ( 13 ). RUNX2 is a key transcription regulatory factor in osteoblast differentiation, it plays an important role in regulating osteoblast maturation and balance ( 14 ).…”