Screening and functional microarray analysis of differentially expressed genes related to osteoporosis

Chen, Y.; Xia, Ronggang

doi:10.4238/2014.april.25.8

Cited by 13 publications

(9 citation statements)

References 43 publications

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“…6 , spectrin beta, non-erythrocytic 1 (SPTBN1), shared by 2 groups, was a hub connected with other 25 nodes including estrogen receptor 1 (ESR1), neurotrophic receptor tyrosine kinase 1 (NTRK1) and phosphatase and tensin homolog (PTEN), etc. ESR1 is related to low bone mineral density (BMD) in AS 35 , 36 . NTRK1 is involved in the pain mechanism 35 while PTEN could active PI3K/Akt signaling which is related to the bone metabolism of AS patients 37 .…”

Section: Resultsmentioning

confidence: 99%

Dissecting the Underlying Pharmaceutical Mechanism of Chinese Traditional Medicine Yun-Pi-Yi-Shen-Tong-Du-Tang Acting on Ankylosing Spondylitis through Systems Biology Approaches

Xie

Huang

Zhao

et al. 2017

Sci Rep

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Traditional Chinese Medicine (TCM) has been served as complementary medicine for Ankylosing Spondylitis (AS) treatment for a long time. Yun-Pi-Yi-Shen-Tong-Du-Tang (Y-Y-T) is a novel empirical formula designed by Prof. Chengping Wen. In this study, a retrospective investigation supported efficacy of Y-Y-T and then we deciphered the underlying molecular mechanism of the efficacy. Herbal ingredients and targeting proteins were collected from TCMID. PPI networks were constructed to further infer the relationship among Y-Y-T, drugs used for treating AS, differentially expressed genes of AS patients and AS disease proteins. Finally, it was suggested that TLR signaling pathway and T cell receptor signaling pathway may involve in the biological processes of AS progression and contribute to the curative effect and proteins such as JAK2, STAT3, HSP90AA1, TNF and PTEN were the key targets. Our systemic investigation to infer therapeutic mechanism of Y-Y-T for AS treatment provides a new insight in understanding TCM pharmacology.

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Section: Resultsmentioning

confidence: 99%

Dissecting the Underlying Pharmaceutical Mechanism of Chinese Traditional Medicine Yun-Pi-Yi-Shen-Tong-Du-Tang Acting on Ankylosing Spondylitis through Systems Biology Approaches

Xie

Huang

Zhao

et al. 2017

Sci Rep

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“…The single-nucleotide polymorphisms (SNPs) of the NRIP1 gene which modulates transcriptional activity of the oestrogen receptor, were correlative with postmenopausal osteoporosis. 36,37 Chen and Xia 38 showed that there was a close relationship between NRIP1 and BMD in B cells in a microarray study. The expression of IRAK3 is predominantly in peripheral blood leukocytes and induced strongly upon the maturation of macrophages.…”

Section: Discussionmentioning

confidence: 99%

Identification of candidate genes in osteoporosis by integrated microarray analysis

Wang

Fei

et al. 2016

Bone & Joint Research

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ObjectivesIn order to screen the altered gene expression profile in peripheral blood mononuclear cells of patients with osteoporosis, we performed an integrated analysis of the online microarray studies of osteoporosis.MethodsWe searched the Gene Expression Omnibus (GEO) database for microarray studies of peripheral blood mononuclear cells in patients with osteoporosis. Subsequently, we integrated gene expression data sets from multiple microarray studies to obtain differentially expressed genes (DEGs) between patients with osteoporosis and normal controls. Gene function analysis was performed to uncover the functions of identified DEGs.ResultsA total of three microarray studies were selected for integrated analysis. In all, 1125 genes were found to be signiﬁcantly differentially expressed between osteoporosis patients and normal controls, with 373 upregulated and 752 downregulated genes. Positive regulation of the cellular amino metabolic process (gene ontology (GO): 0033240, false discovery rate (FDR) = 1.00E + 00) was significantly enriched under the GO category for biological processes, while for molecular functions, flavin adenine dinucleotide binding (GO: 0050660, FDR = 3.66E-01) and androgen receptor binding (GO: 0050681, FDR = 6.35E-01) were significantly enriched. DEGs were enriched in many osteoporosis-related signalling pathways, including those of mitogen-activated protein kinase (MAPK) and calcium. Protein-protein interaction (PPI) network analysis showed that the significant hub proteins contained ubiquitin specific peptidase 9, X-linked (Degree = 99), ubiquitin specific peptidase 19 (Degree = 57) and ubiquitin conjugating enzyme E2 B (Degree = 57).ConclusionAnalysis of gene function of identified differentially expressed genes may expand our understanding of fundamental mechanisms leading to osteoporosis. Moreover, significantly enriched pathways, such as MAPK and calcium, may involve in osteoporosis through osteoblastic differentiation and bone formation.Cite this article: J. J. Li, B. Q. Wang, Q. Fei, Y. Yang, D. Li. Identification of candidate genes in osteoporosis by integrated microarray analysis. Bone Joint Res 2016;5:594–601. DOI: 10.1302/2046-3758.512.BJR-2016-0073.R1.

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“…HGS encodes a protein that regulates endosomal sorting and plays a critical role in the lysosomal transport, recycling, and degradation of ubiquitinated membrane proteins in the multivesicular body, which may be a key machinery for autophagic regulation [ 40 ]. ESR1 is essential for sexual development and reproductive function and is involved in the induction of autophagy in response to toxins [ 41 , 42 ]. Autophagy inhibition can reduce intracellular SNCA aggregation and enhance SNCA secretion, which leads to an exacerbation of the microenvironmental response, including inflammation and cellular damage [ 43 ].…”

Section: Discussionmentioning

confidence: 99%

Altered Autophagy-Associated Genes Expression in T Cells of Oral Lichen Planus Correlated with Clinical Features

Tan

Zhang

et al. 2016

Mediators of Inflammation

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Oral lichen planus (OLP) is a T cell-mediated inflammatory autoimmune disease. Autophagy has emerged as a fundamental trafficking event in mediating T cell response, which plays crucial roles in innate and adaptive immunity. The present study mainly investigated the mRNA expression of autophagy-associated genes in peripheral blood T cells of OLP patients and evaluated correlations between their expression and the clinical features of OLP. Five differentially expressed autophagy-associated genes were identified by autophagy array. Quantitative real-time RT-PCR results confirmed that IGF1 expression in the peripheral blood T cells of OLP patients was significantly higher than that in controls, especially in female and middle-aged (30–50 years old) OLP patients. In addition, ATG9B mRNA levels were significantly lower in nonerosive OLP patients. However, no significant differences were found in the expression of HGS, ESR1, and SNCA between OLP patients and controls. Taken together, dysregulation of T cell autophagy may be involved in immune response of OLP and may be correlated with clinical patterns.

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Screening and functional microarray analysis of differentially expressed genes related to osteoporosis

Cited by 13 publications

References 43 publications

Dissecting the Underlying Pharmaceutical Mechanism of Chinese Traditional Medicine Yun-Pi-Yi-Shen-Tong-Du-Tang Acting on Ankylosing Spondylitis through Systems Biology Approaches

Dissecting the Underlying Pharmaceutical Mechanism of Chinese Traditional Medicine Yun-Pi-Yi-Shen-Tong-Du-Tang Acting on Ankylosing Spondylitis through Systems Biology Approaches

Identification of candidate genes in osteoporosis by integrated microarray analysis

Altered Autophagy-Associated Genes Expression in T Cells of Oral Lichen Planus Correlated with Clinical Features

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