Identification of genes for bone mineral density variation by computational disease gene identification strategy

Molecular characterization of physis tissue and hormonal profiles of female rats neonatally exposed to low-dose bisphenol A

Physis is a complex cartilaginous structure that is critical for longitudinal bone growth. As one of the endocrine-disrupting chemicals, bisphenol A (BPA) can interfere with the physis by deranging the complex networks of nutritional, cellular, paracrine, and endocrine factors, and this affects longitudinal bone growth, leading to different growth outcomes. However, the exact mechanisms underlying these phenomena remain unclear. Therefore, understanding the molecular pathways involved in the physis after neonatal exposure to low-dose BPA may permit the identification of research targets for therapeutics, which may aid in modulating the process of growth plate closure. In the present study, female Sprague-Dawley rats were exposed to 0.05 mg·kg^-1·day^-1 of BPA and corn oil vehicle from postnatal day 1 (PND1) to 15 via subcutaneous injection. Next-generation RNA sequencing was performed for the mRNA isolated from the physis. The levels of osteocalcin (OC), growth hormone (GH), and insulin-like growth factor 1 (IGF-1) were measured on PND30 (BPA0.05mg vs. Vehicle; n = 5 for each group). We observed statistically significant enrichment of gene sets in the BPA0.05mg tissues compared with the Vehicle tissues. Further analysis of the differentially expressed genes (DEGs) identified BPA0.05mg-specific networks of secreted proteins (LEP, NPY, AGT, ACE2, C4B, and C4BPA) as well as those of local matrix and protease proteins (FBN2, LAMC2, ADAMTS16, and ADAMTS19). Furthermore, the levels of OC and GH were affected by BPA exposure. Our results revealed the specific molecular characteristics of physis contaminated with BPA and may provide new clues for physis maturation and supervision of industrial products and occupational exposure.

Sexual differences in bone porosity, osteocyte density, and extracellular matrix organization due to osteoblastic-specific Bmp2 deficiency in mice

Clinical studies have come to conflicting conclusions regarding BMP2 deficiency's link to regulating bone mass and increasing fracture risk. This may be due to the signaling protein having sex- or age-dependent effects. Previous pre-clinical studies have supported a role, but have not adequately determined the physical mechanism causing altered bulk material properties. This study investigated the physical effects of Bmp2 ablation from osteogenic lineage cells (Osx-Cre; Bmp2^fl/fl) in 10- and 15-week-old male and female mice. Bones collected post-mortem were subjected to fracture toughness testing, reference point indentation testing, microCT, and histological analysis to determine the multi-scale relationships between mechanical/material behavior and collagen production, collagen organization, and bone architecture. BMP2-deficient bones were smaller, more brittle, and contained more lacunae-scale voids and cortical pores. The cellular density was significantly increased and there were material-level differences measured by reference point indentation, independently of collagen fiber alignment or organization. The disparities in bone size and in bone fracture toughness between genotypes were especially striking in males at 15-weeks-old. Together, this study suggests that there are sex- and age-dependent effects of BMP2 deficiency. The results from both sexes also warrant further investigation into BMP2 deficiency's role in osteoblasts' transition to osteocytes and overall bone porosity.

Investigation of Genetic Polymorphisms in BMP2, BMP4, SMAD6, and RUNX2 and Persistent Apical Periodontitis

INTRODUCTION

This study aimed to evaluate the interplay among single-nucleotide polymorphisms (SNPs) in the encoding genes BMP2, BMP4, SMAD6, and RUNX2 in persistent apical periodontitis (PAP).

METHODS

In this multicentric study, 272 patients diagnosed with pulp necrosis with apical periodontitis before root canal therapy who attended regular follow-up visits for at least 1 year were screened. Periapical radiographs and clinical aspects were evaluated, and the participants were classified as PAP (n = 110) or repaired (n = 162). Genomic DNA was used for the genotyping of the following SNPs: rs1005464 and rs235768 in bone morphogenetic protein 2 (BMP2), rs17563 in bone morphogenetic protein 4 (BMP4), rs2119261 and rs3934908 in SMAD family member 6 (SMAD6), and rs59983488 and rs1200425 in runt-related transcription factor 2 (RUNX2). The chi-square test was used to compare genotype distributions between groups. The multifactor dimensionality reduction method was applied to identify SNP-SNP interactions. The alpha for all the analysis was 5%.

RESULTS

The multifactor dimensionality reduction suggested the rs235768 in BMP2 and rs59983488 in RUNX2 as the best SNP-SNP interaction model (cross-validation = 10/10, testing balanced accuracy = 0.584, P = .026) followed by rs17563 in BMP4 and rs2119261 in SMAD6 (cross validation = 10/10, testing balanced accuracy = 0.580, P = .031). In the rs235768 in BMP2 and rs59983488 in RUNX2 model, the high-risk genotype was TT + TT (odds ratio = 4.36; 95% confidence interval, 0.44-42.1). In model rs17563 in BMP4 and rs2119261 in SMAD6, GG + TT (odds ratio = 2.63; 95% confidence interval, 0.71-11.9) was the high-risk genotype.

CONCLUSIONS

The interactions between rs235768 in BMP2 and rs59983488 in RUNX2 and between rs17563 in BMP4 and rs2119261 in SMAD6 are associated with PAP, suggesting that an interplay of these SNPs is involved in the higher risk of developing PAP.

Spina bifida-predisposing heterozygous mutations in Planar Cell Polarity genes and Zic2 reduce bone mass in young mice

Fractures are a common comorbidity in children with the neural tube defect (NTD) spina bifida. Mutations in the Wnt/planar cell polarity (PCP) pathway contribute to NTDs in humans and mice, but whether this pathway independently determines bone mass is poorly understood. Here, we first confirmed that core Wnt/PCP components are expressed in osteoblasts and osteoclasts in vitro. In vivo, we performed detailed µCT comparisons of bone structure in tibiae from young male mice heterozygous for NTD-associated mutations versus WT littermates. PCP signalling disruption caused by Vangl2 (Vangl2Lp/+) or Celsr1 (Celsr1Crsh/+) mutations significantly reduced trabecular bone mass and distal tibial cortical thickness. NTD-associated mutations in non-PCP transcription factors were also investigated. Pax3 mutation (Pax3Sp2H/+) had minimal effects on bone mass. Zic2 mutation (Zic2Ku/+) significantly altered the position of the tibia/fibula junction and diminished cortical bone in the proximal tibia. Beyond these genes, we bioinformatically documented the known extent of shared genetic networks between NTDs and bone properties. 46 genes involved in neural tube closure are annotated with bone-related ontologies. These findings document shared genetic networks between spina bifida risk and bone structure, including PCP components and Zic2. Genetic variants which predispose to spina bifida may therefore independently diminish bone mass.

Novel hedgehog agonists promote osteoblast differentiation in mesenchymal stem cells

Hedgehog (Hh) family members are involved in multiple cellular processes including proliferation, migration, differentiation, and cell fate determination. Recently, the novel Hh agonists Hh-Ag 1.3 and 1.7 were identified in a high-throughput screening of small molecule compounds that activate the expression of Gli1, a target of Hh signaling. This study demonstrates that Hh-Ag 1.3 and 1.7 strongly activate the expression of endogenous Gli1 and promote osteoblast differentiation in the mesenchymal stem cell line C3H10T1/2. Both compounds stimulated alkaline phosphatase activity in a dose-dependent manner, and induced osteoblast marker gene expression in C3H10T1/2 cells, which indicated that they had acquired an osteoblast identity. Of the markers, the expression of osterix/Sp7, a downstream target of runt-related transcription factor (Runx)2, was induced by Hh-Ag 1.7, which also rescued the osteoblast differentiation defect of RD-127, a mesenchymal cell line from Runx2-deficient mice. Hh-Ags also activated canonical Wnt signaling and synergized with low doses of BMP-2 to enhance osteoblastic potential. Thus, Hh-Ag 1.7 could be useful for bone healing in individuals with abnormalities in osteogenesis, such as osteoporosis patients and the elderly, and can contribute to the development of novel therapeutics for the treatment of bone fractures and defects.

Computational approaches to disease-gene prediction: rationale, classification and successes

The identification of genes involved in human hereditary diseases often requires the time-consuming and expensive examination of a great number of possible candidate genes, since genome-wide techniques such as linkage analysis and association studies frequently select many hundreds of 'positional' candidates. Even considering the positive impact of next-generation sequencing technologies, the prioritization of candidate genes may be an important step for disease-gene identification. In this paper we develop a basic classification scheme for computational approaches to disease-gene prediction and apply it to exhaustively review bioinformatics tools that have been developed for this purpose, focusing on conceptual aspects rather than technical detail and performance. Finally, we discuss some past successes obtained by computational approaches to illustrate their beneficial contribution to medical research.