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Da Z, Guo R, Sun J, Wang A. Identification of osteoarthritis-characteristic genes and immunological micro-environment features through bioinformatics and machine learning-based approaches. BMC Med Genomics 2023; 16:236. [PMID: 37805587 PMCID: PMC10559406 DOI: 10.1186/s12920-023-01672-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 09/23/2023] [Indexed: 10/09/2023] Open
Abstract
BACKGROUND Osteoarthritis (OA) is a multifaceted chronic joint disease characterized by complex mechanisms. It has a detrimental impact on the quality of life for individuals in the middle-aged and elderly population while also imposing a significant socioeconomic burden. At present, there remains a lack of comprehensive understanding regarding the pathophysiology of OA. The objective of this study was to examine the genes, functional pathways, and immune infiltration characteristics associated with the development and advancement of OA. METHODS The Gene Expression Omnibus (GEO) database was utilized to acquire gene expression profiles. The R software was employed to conduct the screening of differentially expressed genes (DEGs) and perform enrichment analysis on these genes. The OA-characteristic genes were identified using the Weighted Gene Co-expression Network Analysis (WGCNA) and the Lasso algorithm. In addition, the infiltration levels of immune cells in cartilage were assessed using single-sample gene set enrichment analysis (ssGSEA). Subsequently, a correlation analysis was conducted to examine the relationship between immune cells and the OA-characteristic genes. RESULTS A total of 80 DEGs were identified. As determined by functional enrichment, these DEGs were associated with chondrocyte metabolism, apoptosis, and inflammation. Three OA-characteristic genes were identified using WGCNA and the lasso algorithm, and their expression levels were then validated using the verification set. Finally, the analysis of immune cell infiltration revealed that T cells and B cells were primarily associated with OA. In addition, Tspan2, HtrA1 demonstrated a correlation with some of the infiltrating immune cells. CONCLUSIONS The findings of an extensive bioinformatics analysis revealed that OA is correlated with a variety of distinct genes, functional pathways, and processes involving immune cell infiltration. The present study has successfully identified characteristic genes and functional pathways that hold potential as biomarkers for guiding drug treatment and facilitating molecular-level research on OA.
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Affiliation(s)
- Zheng Da
- Xingtai People's Hospital Affiliated to Hebei Medical University, Xingtai City, Hebei Province, China
| | - Rui Guo
- Xingtai People's Hospital Affiliated to Hebei Medical University, Xingtai City, Hebei Province, China.
| | - Jianjian Sun
- Ningbo Huamei Hospital, University of Chinese Academy of Sciences, Ningbo City, Zhejiang Province, China
| | - Ai Wang
- Zhongshan Hospital Affiliated to Fudan University, Shanghai City, China
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Li L, Shen FR, Cheng Q, Sun J, Li H, Sun HT, Cai X, Chen M, Yang B, Wang L, Xu L. SLC5A3 is important for cervical cancer cell growth. Int J Biol Sci 2023; 19:2787-2802. [PMID: 37324953 PMCID: PMC10266070 DOI: 10.7150/ijbs.84570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 05/16/2023] [Indexed: 06/17/2023] Open
Abstract
Novel molecular targets for cervical cancer must be identified. This study examined the role of SLC5A3, a myo-inositol transporter, in the pathogenesis of cervical cancer. Through boinformatics analysis, we showed that the SLC5A3 mRNA levels were upregulated in cervical cancer tissues. The upregulated SLC5A3 mRNA levels were negatively correlated with survival and progression-free interval. Genes co-expressed with SLC5A3 were enriched in multiple signaling cascades involved in cancer progression. In primary/established cervical cancer cells, SLC5A3 shRNA/knockout (KO) exerted growth-inhibitory effects and promoted cell death/apoptosis. Furthermore, SLC5A3 knockdown or KO downregulated myo-inositol levels, induced oxidative injury, and decreased Akt-mTOR activation in cervical cancer cells. In contrast, supplementation of myo-inositol or n-acetyl-L-cysteine or transduction of a constitutively active Akt1 construct mitigated SLC5A3 KO-induced cytotoxicity in cervical cancer cells. Lentiviral SLC5A3 overexpression construct transduction upregulated the cellular myo-inositol level and promoted Akt-mTOR activation, enhancing cervical cancer cell proliferation and migration. The binding of TonEBP to the SLC5A3 promoter was upregulated in cervical cancer. In vivo studies showed that intratumoral injection of SLC5A3 shRNA-expressing virus arrested cervical cancer xenograft growth in mice. SLC5A3 KO also inhibited pCCa-1 cervical cancer xenograft growth. The SLC5A3-depleted xenograft tissues exhibited myo-inositol downregulation, Akt-mTOR inactivation, and oxidative injury. Transduction of sh-TonEBP AAV construct downregulated SLC5A3 expression and inhibited pCCa-1 cervical cancer xenograft growth. Together, overexpressed SLC5A3 promotes growth of cervical cancer cells, representing as a novel therapeutic oncotarget for the devastating disease.
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Affiliation(s)
- Li Li
- Department of Obstetrics and Gynecology, Minhang Hospital, Fudan University, Shanghai, China
| | - Fang-rong Shen
- Obstetrics and Gynecology Department, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Qunxian Cheng
- Department of Obstetrics and Gynecology, Minhang Hospital, Fudan University, Shanghai, China
| | - Jing Sun
- Department of Obstetrics and Gynecology, Minhang Hospital, Fudan University, Shanghai, China
| | - Hang Li
- Department of Obstetrics and Gynecology, Minhang Hospital, Fudan University, Shanghai, China
| | - Hua-ting Sun
- Obstetrics and Gynecology Department, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Xia Cai
- Department of Obstetrics and Gynecology, Minhang Hospital, Fudan University, Shanghai, China
| | - Mengting Chen
- Department of Obstetrics and Gynecology, Minhang Hospital, Fudan University, Shanghai, China
| | - Baohua Yang
- Department of Obstetrics and Gynecology, Minhang Hospital, Fudan University, Shanghai, China
| | - Lifeng Wang
- Department of Obstetrics and Gynecology, Minhang Hospital, Fudan University, Shanghai, China
| | - Ling Xu
- Department of Obstetrics and Gynecology, Minhang Hospital, Fudan University, Shanghai, China
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Lv Y, Zhang J, Li C, Wang L, Lei L, Huang X. Network pharmacological analysis to reveal the mechanism governing the effect of Qin Xi Tong on osteoarthritis and rheumatoid arthritis. Clin Rheumatol 2023:10.1007/s10067-023-06625-5. [PMID: 37162694 DOI: 10.1007/s10067-023-06625-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Revised: 04/03/2023] [Accepted: 05/03/2023] [Indexed: 05/11/2023]
Abstract
INTRODUCTION Qin Xi Tong (QXT), produced by water extracts of Caulis Sinomenii, is clinically effective in the therapy of rheumatoid arthritis (RA). It is also a complementary agent for osteoarthritis (OA). This study aimed to screen the candidate targets and identify the potential mechanisms of QXT against RA and OA. METHOD The active ingredients contained in QXT were queried from the TCMSP database. Their predicted targets were obtained through web-based databases, including TCMSP, BATMAN-TCM, CTD, and PharmMapper. The OA and RA targets were collected from the Genecards database and the GSE55235 dataset. Based on the DAVID database, GO and KEGG enrichment analyses of disease-drug common targets predicted potential signaling pathways for QXT. In addition, core targets were identified by mapping component-target-disease interaction networks with Cytoscape 3.9.1 and STRING. The Swissdock and Pymol tools further validate the predicted results. RESULTS A total of 161 genes were put forward as potential targets for treating RA and OA. These genes might be involved in joint inflammation, including the IL-17 signaling pathway, MAPK signaling pathway, and TNF signaling pathway. They also regulated the progression of joint injuries, such as apoptosis, Th17 cell differentiation, and osteoclast differentiation. In addition, we identified 12 core targets of QXT. Molecular docking results showed that QXT has a high affinity with these core targets. CONCLUSIONS This study reveals the mechanism governing the effect of QXT on RA and OA, predicts the direct target, and provides new ideas for clinical treatment. Key Points • Our study reveals the underlying mechanism of QXT in the treatment of RA and OA. • Further research into the effects of compounds in QXT alone would be of interest.
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Affiliation(s)
- Yanyan Lv
- Department of Rheumatology and Immunology, Xi'an No. 5 Hospital, No. 112 Xi Guan Zheng Jie, Xi'an, China
| | - Jie Zhang
- Department of Rheumatology and Immunology, Xi'an No. 5 Hospital, No. 112 Xi Guan Zheng Jie, Xi'an, China
| | - Chao Li
- Department of Rheumatology and Immunology, Xi'an No. 5 Hospital, No. 112 Xi Guan Zheng Jie, Xi'an, China
| | - Li Wang
- Department of Rheumatology and Immunology, Xi'an No. 5 Hospital, No. 112 Xi Guan Zheng Jie, Xi'an, China
| | - Lei Lei
- School of Life Sciences and Medicine, Northwest University, No. 229 Taibai North Road, Xi'an, China
| | - Xiaoqiang Huang
- Department of Orthopedics, Xi'an No.5 Hospital, No. 112 Xi Guan Zheng Jie, Xi'an, China.
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Pan J, Purev C, Zhao H, Zhang Z, Wang F, Wendoule N, Qi G, Liu Y, Zhou H. Discovery of exercise-related genes and pathway analysis based on comparative genomes of Mongolian originated Abaga and Wushen horse. Open Life Sci 2022; 17:1269-1281. [PMID: 36249530 PMCID: PMC9518662 DOI: 10.1515/biol-2022-0487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 07/21/2022] [Accepted: 07/28/2022] [Indexed: 11/17/2022] Open
Abstract
The Mongolian horses have excellent endurance and stress resistance to adapt to the cold and harsh plateau conditions. Intraspecific genetic diversity is mainly embodied in various genetic advantages of different branches of the Mongolian horse. Since people pay progressive attention to the athletic performance of horse, we expect to guide the exercise-oriented breeding of horses through genomics research. We obtained the clean data of 630,535,376,400 bp through the entire genome second-generation sequencing for the whole blood of four Abaga horses and ten Wushen horses. Based on the data analysis of single nucleotide polymorphism, we severally detected that 479 and 943 positively selected genes, particularly exercise related, were mainly enriched on equine chromosome 4 in Abaga horses and Wushen horses, which implied that chromosome 4 may be associated with the evolution of the Mongolian horse and athletic performance. Four hundred and forty genes of positive selection were enriched in 12 exercise-related pathways and narrowed in 21 exercise-related genes in Abaga horse, which were distinguished from Wushen horse. So, we speculated that the Abaga horse may have oriented genes for the motorial mechanism and 21 exercise-related genes also provided a molecular genetic basis for exercise-directed breeding of the Mongolian horse.
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Affiliation(s)
- Jing Pan
- Faculty of Life Sciences, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia Autonomous Region, People’s Republic of China
- Department of Reproductive Medicine, Inner Mongolia Maternal and Child Health Care Hospitaly, Hohhot, Inner Mongolia Autonomous Region, People’s Republic of China
| | - Chimge Purev
- Mongolia-China Joint Laboratory of Applied Molecular Biology, “Administration of the Science Park” CSTI, Ulaanbaatar, Mongolia
| | - Hongwei Zhao
- Beijing 8omics Gene Technology Co. Ltd, Beijing, People’s Republic of China
| | - Zhipeng Zhang
- Faculty of Life Sciences, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia Autonomous Region, People’s Republic of China
| | - Feng Wang
- Faculty of Life Sciences, Nankai University, Tianjin, People’s Republic of China
| | - Nashun Wendoule
- Animal Husbandry Workstation of Ewenki Autonomous County, Hulun Buir, Inner Mongolia Autonomous Region, People’s Republic of China
| | - Guichun Qi
- Bayanta Village of Animal Husbandry and Veterinary Station of Ewenki Autonomous County, Hulun Buir, Inner Mongolia Autonomous Region, People’s Republic of China
| | - Yongbin Liu
- Sheep Collaboration and Innovation Center, Inner Mongolia Universityy, Hohhot, Inner Mongolia Autonomous Region, People’s Republic of China
| | - Huanmin Zhou
- Faculty of Life Sciences, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia Autonomous Region, People’s Republic of China
- Sheep Collaboration and Innovation Center, Inner Mongolia Universityy, Hohhot, Inner Mongolia Autonomous Region, People’s Republic of China
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The sodium/myo-inositol co-transporter SLC5A3 promotes non-small cell lung cancer cell growth. Cell Death Dis 2022; 13:569. [PMID: 35760803 PMCID: PMC9237060 DOI: 10.1038/s41419-022-05017-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 06/07/2022] [Accepted: 06/09/2022] [Indexed: 01/21/2023]
Abstract
Identification of novel molecular signaling targets for non-small cell lung cancer (NSCLC) is important. The present study examined expression, functions and possible underlying mechanisms of the sodium/myo-inositol co-transporter SLC5A3 in NSCLC. The Cancer Genome Atlas (TCGA) database and local NSCLC tissue results demonstrated that SLC5A3 expression in NSCLC tissues (including patient-derived primary NSCLC cells) was significantly higher than that in normal lung tissues and lung epithelial cells. In primary NSCLC cells and immortalized lines, SLC5A3 depletion, using small hairpin RNA (shRNA) and CRSIRP/Cas9 methods, robustly impeded cell proliferation and migration, simultaneously provoking cell cycle arrest and apoptosis. Conversely, ectopic overexpression of SLC5A3 further enhanced proliferation and migration in primary NSCLC cells. The intracellular myo-inositol contents and Akt-mTOR activation were largely inhibited by SLC5A3 silencing or knockout (KO), but were augmented following SLC5A3 overexpression in primary NSCLC cells. Significantly, SLC5A3 KO-induced anti-NSCLC cell activity was largely ameliorated by exogenously adding myo-inositol or by a constitutively-active Akt construct. By employing the patient-derived xenograft (PDX) model, we found that the growth of subcutaneous NSCLC xenografts in nude mice was largely inhibited by intratumoral injection SLC5A3 shRNA adeno-associated virus (AAV). SLC5A3 silencing, myo-inositol depletion, Akt-mTOR inactivation and apoptosis induction were detected in SLC5A3 shRNA virus-injected NSCLC xenograft tissues. Together, elevated SLC5A3 promotes NSCLC cell growth possibly by maintaining myo-inositol contents and promoting Akt-mTOR activation.
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