RNA-Binding Proteins as Novel Effectors in Osteoblasts and Osteoclasts: A Systems Biology Approach to Dissect the Transcriptional Landscape.

Publisher: MDPI Country of Publication: Switzerland NLM ID: 101092791 Publication Model: Electronic Cited Medium: Internet ISSN: 1422-0067 (Electronic) Linking ISSN: 14220067 NLM ISO Abbreviation: Int J Mol Sci Subsets: MEDLINE

Original Publication: Basel, Switzerland : MDPI, [2000-

Osteoclasts*/metabolism ; Osteoclasts*/cytology ; Osteoblasts*/metabolism ; Osteoblasts*/cytology ; RNA-Binding Proteins*/metabolism ; RNA-Binding Proteins*/genetics ; Gene Regulatory Networks*; Humans ; Systems Biology/methods ; Animals ; Gene Expression Profiling/methods ; Transcriptome ; MicroRNAs/genetics ; MicroRNAs/metabolism ; Gene Expression Regulation

Bone health is ensured by the coordinated action of two types of cells-the osteoblasts that build up bone structure and the osteoclasts that resorb the bone. The loss of balance in their action results in pathological conditions such as osteoporosis. Central to this study is a class of RNA-binding proteins (RBPs) that regulates the biogenesis of miRNAs. In turn, miRNAs represent a critical level of regulation of gene expression and thus control multiple cellular and biological processes. The impact of miRNAs on the pathobiology of various multifactorial diseases, including osteoporosis, has been demonstrated. However, the role of RBPs in bone remodeling is yet to be elucidated. The aim of this study is to dissect the transcriptional landscape of genes encoding the compendium of 180 RBPs in bone cells. We developed and applied a multi-modular integrative analysis algorithm. The core methodology is gene expression analysis using the GENEVESTIGATOR platform, which is a database and analysis tool for manually curated and publicly available transcriptomic data sets, and gene network reconstruction using the Ingenuity Pathway Analysis platform. In this work, comparative insights into gene expression patterns of RBPs in osteoblasts and osteoclasts were obtained, resulting in the identification of 24 differentially expressed genes. Furthermore, the regulation patterns upon different treatment conditions revealed 20 genes as being significantly up- or down-regulated. Next, novel gene-gene associations were dissected and gene networks were reconstructed. Additively, a set of osteoblast- and osteoclast-specific gene signatures were identified. The consolidation of data and information gained from each individual analytical module allowed nominating novel promising candidate genes encoding RBPs in osteoblasts and osteoclasts and will significantly enhance the understanding of potential regulatory mechanisms directing intracellular processes in the course of (patho)physiological bone turnover.

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grant number 23065 Medical Scientific Fund of the Mayor of the City of Vienna (Medizinisch-Wissenschaftlicher Fond des Bürgermeisters der Bundeshauptstadt Wien) Vienna, Austria

Keywords: RNA-binding proteins; bone homeostasis; bone remodeling; osteoblasts; osteoclasts; systems biology; transcriptional profile; transcriptomics

0 (RNA-Binding Proteins)
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Date Created: 20241016 Date Completed: 20241016 Latest Revision: 20241019

20241019

PMC11476634

10.3390/ijms251910417

39408753