Dataset Information

Screening of differentially expressed genes in male idiopathic osteoporosis via RNA sequencing.

ABSTRACT: As a type of osteoporosis (OP), male idiopathic OP (MIO) is a bone disorder that occurs in young males and is a public health problem worldwide. However, the detailed pathogenesis of MIO remains to be elucidated. In the present study, blood samples of patients with MIO, senile OP, postmenopausal OP and normal controls (NCs) were obtained for RNA sequencing. Compared with the NC group, differentially expressed genes (DEGs) in the three types of OP were identified. DEGs that were common among the three types of OP and the DEGs that were unique to patients with MIO were determined. Gene ontology enrichment analysis and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses were conducted. MIO?specific and OP?specific protein?protein interaction (PPI) networks were constructed. Compared with NCs, a total of 519, 368 and 1,472 DEGs were identified in samples from MIO, senile OP and postmenopausal OP, respectively. Tetraspanin 5 (TSPAN5) and ??synuclein (SNCA) were unique DEGs in MIO that were not identified in the other two types of OP compared with NCs. Furthermore, the expression of carbonic anhydrase 1 (CA1) and S100 calcium?binding protein P (S100P) in MIO was significantly different compared with senile OP, postmenopausal OP and NC samples. 'MAPK signaling pathway', 'type I diabetes mellitus' and 'hematopoietic cell lineage' were among significantly enriched pathways of DEGs in MIO. SNCA and CDC?like kinase 1 were the hub genes in the MIO?specific PPI network. In conclusion, the mitogen?activated protein kinase signaling and type I diabetes mellitus pathways may be involved in bone formation; SNCA and TSPAN5 may be associated with bone resorption. These two pathways and two genes may serve a role in MIO. CA1 and S100P may regulate the process of MIO by modulation of calcification and dysregulation of calcium binding. These findings may have provided an experimental basis for elucidating the underlying mechanisms and developing potential diagnostic biomarkers of MIO.

SUBMITTER: Feng L

PROVIDER: S-EPMC6059696 | biostudies-other | 2018 Jul

REPOSITORIES: biostudies-other

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Screening of differentially expressed genes in male idiopathic osteoporosis via RNA sequencing.

Feng Li L Wang Yan Y Zhou Jing J Tian Baofang B Xia Bo B

Molecular medicine reports 20180507 1

As a type of osteoporosis (OP), male idiopathic OP (MIO) is a bone disorder that occurs in young males and is a public health problem worldwide. However, the detailed pathogenesis of MIO remains to be elucidated. In the present study, blood samples of patients with MIO, senile OP, postmenopausal OP and normal controls (NCs) were obtained for RNA sequencing. Compared with the NC group, differentially expressed genes (DEGs) in the three types of OP were identified. DEGs that were common among the ...[more]

PMID: 29750314

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Project description:In the search for a therapeutic schedule for spinal cord injury, it is necessary to understand key genes and their corresponding regulatory networks involved in the spinal cord injury process. However, ad hoc selection and analysis of one or two genes cannot fully reveal the complex molecular biological mechanisms of spinal cord injury. The emergence of second-generation sequencing technology (RNA sequencing) has provided a better method. In this study, RNA sequencing technology was used to analyze differentially expressed genes at different time points after spinal cord injury in rat models established by contusion of the eighth thoracic segment. The numbers of genes that changed significantly were 944, 1362 and 1421 at 1, 4 and 7 days after spinal cord injury respectively. After gene ontology analysis and temporal expression analysis of the differentially expressed genes, C5ar1, Socs3 and CCL6 genes were then selected and identified by real-time polymerase chain reaction and western blot assay. The mRNA expression trends of C5ar1, Socs3 and CCL6 genes were consistent with the RNA sequencing results. Further verification and analysis of C5ar1 indicate that the level of protein expression of C5ar1 was consistent with its nucleic acid level after spinal cord injury. C5ar1 was mainly expressed in neurons and astrocytes. Finally, the gene Itgb2, which may be related to C5ar1, was found by Chilibot database and literature search. Immunofluorescence histochemical results showed that the expression of Itgb2 was highly consistent with that of C5ar1. Itgb2 was expressed in astrocytes. RNA sequencing technology can screen differentially expressed genes at different time points after spinal cord injury. Through analysis and verification, genes strongly associated with spinal cord injury can be screened. This can provide experimental data for further determining the molecular mechanism of spinal cord injury, and also provide possible targets for the treatment of spinal cord injury. This study was approved ethically by the Laboratory Animal Ethics Committee of Jiangsu Province, China (approval No. 2018-0306-001) on March 6, 2018.

Project description:BackgroundSessile serrated adenomas/polyps (SSA/Ps) may account for 20-30% of colon cancers. Although large SSA/Ps are generally recognized phenotypically, small (<1 cm) or dysplastic SSA/Ps are difficult to differentiate from hyperplastic or small adenomatous polyps by endoscopy and histopathology. Our aim was to define the comprehensive gene expression phenotype of SSA/Ps to better define this cancer precursor.ResultsRNA sequencing was performed on 5' capped RNA from seven SSA/Ps collected from patients with the serrated polyposis syndrome (SPS) versus eight controls. Highly expressed genes were analyzed by qPCR in additional SSA/Ps, adenomas and controls. The cellular localization and level of gene products were examined by immunohistochemistry in syndromic and sporadic SSA/Ps, adenomatous and hyperplastic polyps and controls. We identified 1,294 differentially expressed annotated genes, with 106 increased ≥10-fold, in SSA/Ps compared to controls. Comparing these genes with an array dataset for adenomatous polyps identified 30 protein coding genes uniquely expressed ≥10-fold in SSA/Ps. Biological pathways altered in SSA/Ps included mucosal integrity, cell adhesion, and cell development. Marked increased expression of MUC17, the cell junction protein genes VSIG1 and GJB5, and the antiapoptotic gene REG4 were found in SSA/Ps, relative to controls and adenomas, were verified by qPCR analysis of additional SSA/Ps (n = 21) and adenomas (n = 10). Immunohistochemical staining of syndromic (n≥11) and sporadic SSA/Ps (n≥17), adenomatous (n≥13) and hyperplastic (n≥10) polyps plus controls (n≥16) identified unique expression patterns for VSIG1 and MUC17 in SSA/Ps.ConclusionA subset of genes and pathways are uniquely increased in SSA/Ps, compared to adenomatous polyps, thus supporting the concept that cancer develops by different pathways in these phenotypically distinct polyps with markedly different gene expression profiles. Immunostaining for a subset of these genes differentiates both syndromic and sporadic SSA/Ps from adenomatous and hyperplastic polyps.

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Screening of differentially expressed genes in male idiopathic osteoporosis via RNA sequencing.

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Screening of differentially expressed genes in male idiopathic osteoporosis via RNA sequencing.

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