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Wang Y, Xie Q, Yu H, Zhou B, Guo X, Wu B, Hu J. Establishment and validation of the autophagy-related ceRNA network in irreversible pulpitis. BMC Genomics 2023; 24:268. [PMID: 37208635 DOI: 10.1186/s12864-023-09363-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 05/06/2023] [Indexed: 05/21/2023] Open
Abstract
BACKGROUND The molecular mechanisms underlying the onset and progression of irreversible pulpitis have been studied for decades. Many studies have indicated a potential correlation between autophagy and this disease. Against the background of the competing endogenous RNA (ceRNA) theory, protein-coding RNA functions are linked with long noncoding RNAs (lncRNAs) and microRNAs (miRNAs). This mechanism has been widely studied in various fields but has rarely been reported in the context of irreversible pulpitis. The hub genes selected under this theory may represent the key to the interaction between autophagy and irreversible pulpitis. RESULTS Filtering and differential expression analyses of the GSE92681 dataset, which contains data from 7 inflamed and 5 healthy pulp tissue samples, were conducted. The results were intersected with autophagy-related genes (ARGs), and 36 differentially expressed ARGs (DE-ARGs) were identified. Functional enrichment analysis and construction of the protein‒protein interaction (PPI) network of DE-ARGs were performed. Coexpression analysis was conducted between differentially expressed lncRNAs (DElncRNAs) and DE-ARGs, and 151 downregulated and 59 upregulated autophagy-related DElncRNAs (AR-DElncRNAs) were identified. StarBase and multiMiR were then used to predict related microRNAs of AR-DElncRNAs and DE-ARGs, respectively. We established ceRNA networks including 9 hub lncRNAs (HCP5 and AC112496.1 ↑; FENDRR, AC099850.1, ZSWIM8-AS1, DLX6-AS1, LAMTOR5-AS1, TMEM161B-AS1 and AC145207.5 ↓), which were validated by a qRT‒PCR analysis of pulp tissue from patients with irreversible pulpitis. CONCLUSION We constructed two networks consisting of 9 hub lncRNAs based on the comprehensive identification of autophagy-related ceRNAs. This study may provide novel insights into the interactive relationship between autophagy and irreversible pulpitis and identifies several lncRNAs that may serve as potential biological markers.
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Affiliation(s)
- Ye Wang
- Shenzhen Stomatology Hospital (Pingshan) of Southern Medical University, Shenzhen, 518118, China
| | - Qiuyan Xie
- Department of Stomatology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Hongwen Yu
- Department of Stomatology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Bangyi Zhou
- Department of Stomatology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Xiaolan Guo
- Department of Stomatology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Buling Wu
- Shenzhen Stomatology Hospital (Pingshan) of Southern Medical University, Shenzhen, 518118, China
- Department of Stomatology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Jiao Hu
- Changsha Stomatological Hospital, Changsha, 410000, China.
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Ghafouri-Fard S, Gholami L, Sadeghpour S, Nazer N, Hussen BM, Sayad A, Taheri M. Altered expression of SOCS genes periodontitis. BMC Oral Health 2022; 22:551. [PMID: 36456933 PMCID: PMC9713975 DOI: 10.1186/s12903-022-02602-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 11/16/2022] [Indexed: 12/03/2022] Open
Abstract
Suppressor of cytokine signalling (SOCS) family comprises a group of proteins that impede JAK/STAT signalling, thus being involved in the pathogenesis of immune-related conditions. In the present work, we aimed at identification of the role of SOCS genes in the pathogenesis of periodontitis through evaluation of their expression levels both in the circulation and in the affected tissues of patients. Thus, we measured expression levels of SOCS1-3 and SOCS5 transcripts in the blood and gingival samples of patients with periodontitis in comparison with control samples obtained during dental crown lengthening. Expressions of SOCS1, SOCS2, SOCS3 and SOCS5 genes were similar between gingival tissues of patients and controls. However, our results demonstrated under-expression of SOCS1 in blood samples of patients compared with controls (Ratio of mean expression (RME) = 0.47, P value = 0.04). The same pattern was observed among female subjects (RME = 0.38, P value = 0.04). SOCS2 was down-regulated in blood samples of female patients compared with female controls (RME = 0.22, P value = 0.04). SOCS3 was also under-expressed in the circulation of total cases versus total controls (RME = 0.29, P value = 0.02) and in female patients compared with female controls (RME = 0.19, P value = 0.04). Expression of SOCS5 was not different between blood samples two study groups. SOCS2 had the best function in separation of affected tissues from unaffected ones (AUC = 0.66, sensitivity = 0.39, specificity = 0.83). SOCS3 was superior to other transcripts in differentiation of blood samples of patients from normal blood samples (AUC = 0.69, sensitivity = 0.81, specificity = 0.68). Combination of transcript levels of SOCS1, SOCS2, SOCS3 and SOCS5 genes enhanced the AUC values to 0.64 and 0.67 in tissue and blood specimens, respectively. Taken together, certain SOCS genes have been found to be dysregulated in the circulation of patients with periodontitis.
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Affiliation(s)
- Soudeh Ghafouri-Fard
- grid.411600.2Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Leila Gholami
- grid.411950.80000 0004 0611 9280Department of Periodontics, Dental Research Center, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Saba Sadeghpour
- grid.411600.2Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Naghme Nazer
- grid.412553.40000 0001 0740 9747Department of Electrical Engineering, Sharif University of Technology, Tehran, Iran
| | - Bashdar Mahmud Hussen
- grid.412012.40000 0004 0417 5553Department of Pharmacognosy, College of Pharmacy, Hawler Medical University, Kurdistan Region, Erbil, Iraq ,grid.448554.c0000 0004 9333 9133Center of Research and Strategic Studies, Lebanese French University, Kurdistan Region, Erbil, Iraq
| | - Arezou Sayad
- grid.411600.2Dental Research Center, Research Institute for Dental Sciences, Dental School, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Taheri
- grid.275559.90000 0000 8517 6224Institute of Human Genetics, Jena University Hospital, Jena, Germany ,grid.411600.2Urology and Nephrology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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Zhang J, Zhang Z, Wu X. Long non-coding RNA DIRC3 suppresses trophoblast invasion in preeclampsia via upregulating HOXD10. Mol Cell Toxicol 2022. [DOI: 10.1007/s13273-022-00297-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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