Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2024 Apr 15;16(4):1306-1321.
doi: 10.62347/TAYD3318. eCollection 2024.

Unveiling the unexplored novel signatures for osteoporosis via a detailed bioinformatics and molecular experiments based approach

Huan Zhou  1 , Yousaf Gul  2 , Yasir Hameed  3 , Majid Alhomrani  4   5 , Saleh A Alghamdi  4 , Abdulraheem Ali Almalki  4 , Meshari A Alsuwat  4 , Naif ALSuhaymi  6 , Rida Naz  7 , Guang Chen  8
Affiliations

Unveiling the unexplored novel signatures for osteoporosis via a detailed bioinformatics and molecular experiments based approach

Huan Zhou et al. Am J Transl Res. .

Abstract

Background: Osteoporosis (OP) stands as a prevalent bone ailment affecting the elderly, globally. The identification of reliable diagnostic markers crucially aids OP clinical management.

Methods: Utilizing the GEO database (GSE35959), we acquired expression profiles for OP and normal samples. Differential expression genes (DEGs) and hub genes were pinpointed through STRING, GEO2R, and Cytoscape. The competing endogenous RNA (ceRNA) network was constructed using miRTarBase, miRDB, and MiRcode databases. Gene Ontology (GO) and KEGG pathway enrichment analyses were performed via DAVID. Validation involved clinical OP samples from the Pakistani population, with Real-Time Quantitative Polymerase Chain Reaction (RT-qPCR) assessing hub gene expression.

Results: A total of 2124 differentially expressed genes (DEGs) were identified between OP and normal samples in GSE35959. The selected hub genes among these DEGs were Splicing Factor 3a Subunit 1 (SF3A1), Ataxin 2 Like (ATXN2L), Heat Shock Protein 90 Beta Family Member 1 (HSP90B1), Cluster of Differentiation 74 (CD74), DExH-Box Helicase 29 (DHX29), ALG5 Dolichyl-Phosphate Beta-Glucosyltransferase (ALG5), NudC Domain Containing 2 (NUDCD2), and Ras-related protein Rab-2A (RAB2A). Expression validation of these genes on the Pakistani OP patients revealed significant up-regulation of SF3A1, ATXN2L, and CD74 and significant (P < 0.05) down-regulation of HSP90B1, DHX29, ALG5, NUDCD2, and RAB2A in OP patients. Receiver operating characteristic (ROC) analysis demonstrated that these hub genes displayed considerable diagnostic accuracy for detecting OP. The ceRNA network analysis of the hub genes revealed some important hub genes' regulatory miRNAs and lncRNAs. Via KEGG analysis, hub genes were found to be enriched in N-Glycan biosynthesis, Thyroid hormone synthesis, IL-17 signaling pathway, Prostate cancer, AMPK signaling pathway, Spliceosome, Estrogen signaling pathway, and Fluid shear stress and atherosclerosis, etc., pathways.

Conclusion: The identified eight hub genes in the present study could reliably distinguish OP patients from normal individuals, which may provide novel insight into the diagnostic research of OP.

Keywords: AMPK signaling pathway; Osteoporosis (OP); diagnostic signatures.

PubMed Disclaimer

Conflict of interest statement

None.

Figures

Figure 1
Figure 1
Analyzing gene expression patterns, sample clustering, quantifying differentially expressed genes (DEGs) and non-DEGs, and creating a volcano plot specifically for DEGs within the GSE35959 dataset. (A) Expression-wise comparison of samples in the GSE35959 dataset, (B) Expression-based clustering of samples in the GSE35959 dataset, (C) A total count of DEGs and non DEGs in GSE35959 dataset, and (D) A volcano graph of DEGs in the GSE35959.
Figure 2
Figure 2
A PPI network of the top 20 DEGs (10 up-regulated and 10 down-regulated) and the selected hub genes. (A) A PPI network of top 20 DEGs, (B) A PPI network of top 20 DEGs highlighting selected hub genes, and (C) A PPI network of the hub genes.
Figure 3
Figure 3
Validation results for the mRNA expression levels of 8 selected hub genes. To validate these genes, we used the GSE56815 and GSE56814 datasets. Each of the selected genes (A) SF3A1, (B) ATXN2L, (C) HNSP90B1, (D) CD74, (E) DHX29, (F) ALG5, (G) NUDCD2, and (H) RAB2A underwent validation. * = P-value < 0.05.
Figure 4
Figure 4
Networks highlighting associations between miRNAs, lncRNAs, and hub genes. (A) A network of overall predicted miRNAs targeting hub genes, (B) A network between meaningful miRNAs and hub genes, (C) A network of six miRNAs and overall lncRNAs targeting miRNAs, and (D) A network of miRNAs and meaningful lncRNAs. The green nodes are the miRNAs, red nodes are hub genes, while purple nodes are lncRNAs.
Figure 5
Figure 5
Gene ontology (GO) enrichment analysis of hub genes utilizing the DAVID tool. (A) Biological Process (BP) Terms: This section focuses on the enrichment analysis results related to biological processes associated with the hub genes, (B) Cellular Component (CC) Terms: This section elaborates on the enrichment analysis results concerning the cellular components linked to the hub genes, and (C) Molecular Function (MF) Terms: Here, the legend provides insights into the enrichment analysis findings related to the molecular functions of the hub genes. A P < 0.05 was regarded as the selection criteria.
Figure 6
Figure 6
Kyoto encyclopedia of genes and genomes (KEGG) enrichment analysis of hub genes conducted with the DAVID tool. (A) KEGG Terms: This section presents the results of the KEGG enrichment analysis, highlighting the specific KEGG pathways associated with the hub genes, and (B) KEGG Terms Phylogram: Here, the legend describes the representation of the KEGG terms in a phylogenetic tree-like structure. A P < 0.01 was regarded as the selection criteria.
Figure 7
Figure 7
Relative expression and ROC curve analysis of the hub genes in Pakistani OP patients and normal controls. (A) Relative expression analysis of the hub genes in Pakistani OP patients and control samples via RT-qPCR, and (B) RT-qPCR expression-based ROC curves of the identified hub genes. * = P-value < 0.05.
See this image and copyright information in PMC

References

    1. Li H, Li T, Fan J, Li T, Fan L, Wang S, Weng X, Han Q, Zhao RC. miR-216a rescues dexamethasone suppression of osteogenesis, promotes osteoblast differentiation and enhances bone formation, by regulating c-Cbl-mediated PI3K/AKT pathway. Cell Death Differ. 2015;22:1935–1945. - PMC - PubMed
    1. Compston J, Cooper A, Cooper C, Gittoes N, Gregson C, Harvey N, Hope S, Kanis JA, McCloskey EV, Poole KES, Reid DM, Selby P, Thompson F, Thurston A, Vine N National Osteoporosis Guideline Group (NOGG) UK clinical guideline for the prevention and treatment of osteoporosis. Arch Osteoporos. 2017;12:43. - PMC - PubMed
    1. Tarantino U, Iolascon G, Cianferotti L, Masi L, Marcucci G, Giusti F, Marini F, Parri S, Feola M, Rao C, Piccirilli E, Zanetti EB, Cittadini N, Alvaro R, Moretti A, Calafiore D, Toro G, Gimigliano F, Resmini G, Brandi ML. Clinical guidelines for the prevention and treatment of osteoporosis: summary statements and recommendations from the Italian Society for Orthopaedics and Traumatology. J Orthop Traumatol. 2017;18(Suppl 1):3–36. - PMC - PubMed
    1. Tanaka KI, Xue Y, Nguyen-Yamamoto L, Morris JA, Kanazawa I, Sugimoto T, Wing SS, Richards JB, Goltzman D. FAM210A is a novel determinant of bone and muscle structure and strength. Proc Natl Acad Sci U S A. 2018;115:E3759–E3768. - PMC - PubMed
    1. Uehara S, Udagawa N, Mukai H, Ishihara A, Maeda K, Yamashita T, Murakami K, Nishita M, Nakamura T, Kato S, Minami Y, Takahashi N, Kobayashi Y. Protein kinase N3 promotes bone resorption by osteoclasts in response to Wnt5a-Ror2 signaling. Sci Signal. 2017;10:eaan0023. - PubMed

LinkOut - more resources