Comparisons of gene expression between peripheral blood mononuclear cells and bone tissue in osteoporosis

Abstract

Osteoporosis (OP) is one of the major public health problems in the world. However, the biomarkers between the peripheral blood mononuclear cells (PBMs) and bone tissue for prognosis of OP have not been well characterized. This study aimed to explore the similarities and differences of the gene expression profiles between the PBMs and bone tissue and identify potential genes, transcription factors (TFs) and hub proteins involved in OP. The patients were enrolled as an experimental group, and healthy subjects served as normal controls. Human whole-genome expression chips were used to analyze gene expression profiles from PBMs and bone tissue. And the differentially expressed genes (DEGs) were subsequently studied using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analysis. The above DEGs were constructed into protein-protein interaction network. Finally, TF-DEGs regulation networks were constructed. Microarray analysis revealed that 226 DEGs were identified between OP and normal controls in the PBMs, while 2295 DEGs were identified in the bone tissue. And 13 common DEGs were obtained by comparing the 2 tissues. The Gene Ontology analysis indicated that DEGs in the PBMs were more involved in immune response, while DEGs in bone were more involved in renal response and urea transmembrane transport. And the Kyoto Encyclopedia of Genes and Genomes analysis indicated almost all of the pathways in the PBMs were overlapped with those in the bone tissue. Furthermore, protein-protein interaction network presented 6 hub proteins: PI3K1, APP, GNB5, FPR2, GNG13, and PLCG1. APP has been found to be associated with OP. Finally, 5 key TFs were identified by TF-DEGs regulation networks analysis (CREB1, RUNX1, STAT3, CREBBP, and GLI1) and were supposed to be associated with OP. This study enhanced our understanding of the pathogenesis of OP. PI3K1, GNB5, FPR2, GNG13, and PLCG1 might be the potential targets of OP.

Figure 1.

DEGs and overlaps. (A) Heatmaps of DEGs in PBMs between OP and control groups. Red represents upregulated genes, whereas blue represents downregulated genes. (B) Heatmaps of DEGs in bone between OP and control groups. Red represents upregulated genes, whereas blue represents downregulated genes. (C)Volcano maps of DEGs in PBMs between OP and control groups. Red represents upregulated genes, whereas blue represents downregulated genes. (D)Volcano maps of DEGs in bone between OP and control groups. Red represents upregulated genes, whereas blue represents downregulated genes. (E) Diagram of overlapped DEGs. Blue circular represents DEGs in PBMs, yellow circular represents DEGs in bone. DEGs = differentially expressed genes, OP = osteoporosis, PBM = peripheral mononuclear blood cell.

Figure 2.

GO and KEGG pathway analysis of DEGs and overlapped pathways. (A) BP of DEGs in PBMs between OP and control groups. (B) BP of DEGs in bone between OP and control groups. (C) KEGG pathway of DEGs in PBMs between OP and control groups. (D) KEGG pathway of DEGs in bone between OP and control groups. (E) Blue circular represents pathways in PBMs. Yellow circular represents pathways in bone. DEGs = differentially expressed genes, GO = Gene Ontology, KEGG = Kyoto Encyclopedia of Genes and Genomes, OP = osteoporosis, PBM = peripheral mononuclear blood cell.

Figure 3.

PPI network of DEGs. Circular nodes represent DEGs. Increasing degrees is indicated by larger nodes, labels and darker color. Red represents that the nodes degree > 20, yellow represents that the nodes degree >10 and <20, blue represents that the nodes degree >2 and <10, green represents that the nodes degree = 1. DEGs = differentially expressed genes, PPI = protein-protein interaction.

Figure 4.

Diagram of TF and TF-DEGs regulation networks. (A) Diagram of TF. List 1 represents all TFs, list 2 represents 352 DEGs. (B) TF-DEGs regulation networks. The red diamond represents TF, and the green circle represents DEGs. DEGs = differentially expressed genes, TFs = transcription factors.

Figure 5.

Confirmation of microarray results by quantitative PCR. Based on the overlapped genes in PBMs and bone tissue, we selected 4 common DEGs (RNF215, SULT1B1, ALCAM, KRAS) randomly for further qPCR validation. The PBMs were collected from OP patients (n = 3) and NC patients (n = 3). The expression of RNF215, SULT1B1, ALCAM, KRAS in PBMs was consistent with the results of microarray analysis in PBMs. DEGs = differentially expressed genes, NC = normal control, OP = osteoporosis, PBM = peripheral mononuclear blood cell, qPCR = quantitative polymerase chain reaction.