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Fu M, Gu J, Yu D, Wang M, Zhang J, Ji R, Jiang P, Zhang X. Circ1811 suppresses gastric cancer progression by regulating the miR-632/DAPK1 axis. Gene 2024; 910:148331. [PMID: 38438055 DOI: 10.1016/j.gene.2024.148331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 02/23/2024] [Accepted: 02/28/2024] [Indexed: 03/06/2024]
Abstract
Compelling evidence has identified circRNAs as crucial regulators in initiation and progression of various cancers, including gastric cancer (GC). However, the function and regulatory mechanisms of circRNAs in GC remain largely unknown. In this study, attention is paid to a novel circular RNA circ1811, which exerts significant downregulated expression in GC tissues compared with adjacent non-cancerous tissues. The expression of circ1811 in GC tumor tissues is negatively correlated with the extent of lymphatic metastasis in GC patients. Overexpression of circ1811 inhibited GC cell proliferation, migration and invasion while promoting apoptosis, whereas knockdown of circ1811 led to the opposite effects. AGO2 RIP and dual luciferase reporter assays indicated that circ1811 directly sponges miR-632 to upregulate the expression of DAPK1. Collectively, circ1811 acts as a tumor-suppressor for GC progression by regulating the miR-632/DAPK1 axis. Our findings suggest the potential of circ1811 as ideal biomarker and therapeutic target for GC.
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Affiliation(s)
- Min Fu
- Institute of Digestive Diseases, The Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu 212002, China; Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Jianmei Gu
- Departmemt of Clinical Laboratory Medicine, Nantong Tumor Hospital/Affiliated Tumor Hospital of Nantong University, Nantong, Jiangsu 226361, China
| | - Dan Yu
- Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Maoye Wang
- Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Jiahui Zhang
- Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Runbi Ji
- Institute of Digestive Diseases, The Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu 212002, China
| | - Pengcheng Jiang
- Institute of Digestive Diseases, The Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu 212002, China
| | - Xu Zhang
- Institute of Digestive Diseases, The Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu 212002, China; Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013, China.
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Yang ZL, Tian C, He J, Pan H, Ruan GP, Zhao J, Wang K, Pan XH, Zhu XQ. Whole-transcriptome profiling reveals potential biomarkers for the reversal of thymic epithelial cell senescence by umbilical cord mesenchymal stem cells. Aging (Albany NY) 2024; 16:205738. [PMID: 38637117 DOI: 10.18632/aging.205738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 03/18/2024] [Indexed: 04/20/2024]
Abstract
BACKGROUND Reduced numbers and dysfunction of thymic epithelial cells (TECs) are important factors of thymic degeneration. Previous studies have found that umbilical cord mesenchymal stem cells (UCMSCs) reverse the structure and function of the senescent thymus in vivo. However, the transcriptomic regulation mechanism is unclear. METHODS TECs were cultured with H2O2 for 72 hours to induce senescence. UCMSCs were cocultured with senescent TECs for 48 hours to detect SA-β-gal, P16 and Ki67. The cocultured TECs were collected for lncRNA, mRNA and miRNA sequencing to establish a competitive endogenous regulatory network (ceRNA). And RT-qPCR, immunofluorescence staining, and western blot were used to identified key genes. RESULTS Our results showed that H2O2 induced TEC aging and that UCMSCs reversed these changes. Compared with those in aged TECs, 2260 DE mRNAs, 1033 DE lncRNAs and 67 DE miRNAs were differentially expressed, and these changes were reversed by coculturing the cells with UCMSCs. Differential mRNA enrichment analysis of ceRNA regulation revealed that the PI3K-AKT pathway was a significant signaling pathway. UCMSC coculture upregulated VEGFA, which is the upstream factor of the PI3K-AKT signaling pathway, and the expression of the key proteins PI3K and AKT. Thus, the expression of the cell cycle suppressor P27, which is downstream of the PI3K-AKT signaling pathway, was downregulated, while the expression of the cell cycle regulators CDK2 and CCNE was upregulated. CONCLUSION UCMSC coculture upregulated the expression of VEGFA, activated the PI3K-AKT signaling pathway, increased the expression of CDK2 and CCNE, decreased the expression of P27, and promoted the proliferation of TECs.
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Affiliation(s)
- Zai-Ling Yang
- The Basic Medical Laboratory of the 920th Hospital of Joint Logistics Support Force of PLA, The Transfer Medicine Key Laboratory of Cell Therapy Technology of Yunan, The Integrated Engineering Laboratory of Cell Biological Medicine of State and Regions, Kunming 650032, Yunnan, China
- The Second People’s Hospital of Guiyang, Medical Laboratory, Guiyang 550023, Guizhou, China
| | - Chuan Tian
- The Basic Medical Laboratory of the 920th Hospital of Joint Logistics Support Force of PLA, The Transfer Medicine Key Laboratory of Cell Therapy Technology of Yunan, The Integrated Engineering Laboratory of Cell Biological Medicine of State and Regions, Kunming 650032, Yunnan, China
| | - Jie He
- The Basic Medical Laboratory of the 920th Hospital of Joint Logistics Support Force of PLA, The Transfer Medicine Key Laboratory of Cell Therapy Technology of Yunan, The Integrated Engineering Laboratory of Cell Biological Medicine of State and Regions, Kunming 650032, Yunnan, China
| | - Hang Pan
- The Basic Medical Laboratory of the 920th Hospital of Joint Logistics Support Force of PLA, The Transfer Medicine Key Laboratory of Cell Therapy Technology of Yunan, The Integrated Engineering Laboratory of Cell Biological Medicine of State and Regions, Kunming 650032, Yunnan, China
| | - Guang-Ping Ruan
- The Basic Medical Laboratory of the 920th Hospital of Joint Logistics Support Force of PLA, The Transfer Medicine Key Laboratory of Cell Therapy Technology of Yunan, The Integrated Engineering Laboratory of Cell Biological Medicine of State and Regions, Kunming 650032, Yunnan, China
| | - Jing Zhao
- The Basic Medical Laboratory of the 920th Hospital of Joint Logistics Support Force of PLA, The Transfer Medicine Key Laboratory of Cell Therapy Technology of Yunan, The Integrated Engineering Laboratory of Cell Biological Medicine of State and Regions, Kunming 650032, Yunnan, China
| | - Kai Wang
- The Basic Medical Laboratory of the 920th Hospital of Joint Logistics Support Force of PLA, The Transfer Medicine Key Laboratory of Cell Therapy Technology of Yunan, The Integrated Engineering Laboratory of Cell Biological Medicine of State and Regions, Kunming 650032, Yunnan, China
| | - Xing-Hua Pan
- The Basic Medical Laboratory of the 920th Hospital of Joint Logistics Support Force of PLA, The Transfer Medicine Key Laboratory of Cell Therapy Technology of Yunan, The Integrated Engineering Laboratory of Cell Biological Medicine of State and Regions, Kunming 650032, Yunnan, China
| | - Xiang-Qing Zhu
- The Basic Medical Laboratory of the 920th Hospital of Joint Logistics Support Force of PLA, The Transfer Medicine Key Laboratory of Cell Therapy Technology of Yunan, The Integrated Engineering Laboratory of Cell Biological Medicine of State and Regions, Kunming 650032, Yunnan, China
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Wei H, Teng F, Wang X, Hou X, Wang H, Wang H, Sun H, Zhou X. Identification of a prognosis-related gene signature and ceRNA regulatory networks in lung adenocarcinoma. Heliyon 2024; 10:e28084. [PMID: 38601687 PMCID: PMC11004716 DOI: 10.1016/j.heliyon.2024.e28084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 02/23/2024] [Accepted: 03/12/2024] [Indexed: 04/12/2024] Open
Abstract
The ceRNA network, consisting of both noncoding RNA and protein-coding RNA, governs the occurrence, progression, metastasis, and infiltration of lung adenocarcinoma. Signatures comprising multiple genes can effectively determine survival stratification and prognosis of patients with lung adenocarcinoma. To explore the mechanisms of lung adenocarcinoma progression and identify potential biological targets, we carried out systematic bioinformatics analyses of the genetic profiles of lung adenocarcinoma, such as weighted gene co-expression network analysis (WGCNA), differential expression (DE) assessment, univariate and multivariate Cox proportional hazard regression models, ceRNA modulatory networks generated using the ENCORI and miRcode databases, nomogram models, ROC curve assessment, and Kaplan-Meier survival curve analysis. The ceRNA network encompassed 37 nodes, comprising 12 mRNAs, 22 lncRNAs, and three miRNAs. Simultaneously, we performed integration analysis using the 12 genes from the ceRNA network. Our findings revealed that the signature established by these 12 genes serves as an adverse element in lung adenocarcinoma, contributing to unfavorable patient prognosis. To ensure the credibility of our results, we used in vitro experiments for further verification. In conclusion, our study delved into the potential mechanisms underlying lung adenocarcinoma via the ceRNA regulatory network, specifically focusing on the PIF1 and has-miR-125a-5p axis. Additionally, a signature comprising 12 genes was identified as a biomarker related to the prognosis of lung adenocarcinoma.
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Affiliation(s)
- Hong Wei
- In-Patient Ultrasound Department, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150081, China
| | - Fei Teng
- In-Patient Ultrasound Department, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150081, China
| | - XiaoLei Wang
- In-Patient Ultrasound Department, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150081, China
| | - XiuJuan Hou
- In-Patient Ultrasound Department, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150081, China
| | - HongBo Wang
- In-Patient Ultrasound Department, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150081, China
| | - Hong Wang
- In-Patient Ultrasound Department, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150081, China
| | - Hui Sun
- In-Patient Ultrasound Department, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150081, China
| | - XianLi Zhou
- In-Patient Ultrasound Department, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150081, China
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Li R, Liu Y, Liu J, Chen B, Ji Z, Xu A, Zhang T. CCL2 regulated by the CTBP1-AS2/miR-335-5p axis promotes hemangioma progression and angiogenesis. Immunopharmacol Immunotoxicol 2024:1-10. [PMID: 38622049 DOI: 10.1080/08923973.2024.2330651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 03/09/2024] [Indexed: 04/17/2024]
Abstract
Context: Hemangioma (HA) is a benign vascular neoplasm that can lead to permanent scarring. C-C motif chemokine ligand 2 (CCL2) plays a crucial role in facilitating growth and angiogenesis during HA progression. However, the mechanism regulating CCL2 in HA remains poorly elucidated. Objective: To elucidate the mechanism regulating CCL2 in HA. Methods: Quantitative real-time polymerase chain reaction (RT-qPCR) was employed to determine the expression levels of CCL2, long noncoding RNA (lncRNA) CTBP1 divergent transcript (CTBP1-AS2), and microRNAs (miRNAs). Proliferation, migration, invasion, and angiogenic abilities of human HA endothelial cells (HemECs) were assessed using cell counting kit-8 (CCK-8), colony formation, flow cytometry, transwell, and tube formation assays. Bioinformatics analysis, RNA pull-down, and luciferase reporter assays were conducted to investigate whether CCL2 targets miR-335-5p. Additionally, rescue experiments were performed in this study. Results: CCL2 expression was markedly upregulated in HemECs. CCL2 promoted HA cell proliferation, migration, invasion, and angiogenesis while inhibiting apoptosis. CCL2 was directly targeted by miR-335-5p. Additionally, we found that CTBP1-AS2 could function as a competing endogenous RNA (ceRNA) to sponge miR-335-5p, thereby upregulating CCL2. Conclusion: Our findings suggest that targeting the CTBP1-AS2/miR-335-5p/CCL2 axis may hold promise as a therapeutic strategy for HA.
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Affiliation(s)
- Ruixuan Li
- Department of Cardiology, the Third Xiangya Hospital, Central South University, Changsha, PR China
| | - Ying Liu
- Department of Plastic Surgery, the Second Affiliated Hospital of Harbin Medical University, Harbin, PR China
| | - Jianfeng Liu
- Department of Plastic Surgery, the Second Affiliated Hospital of Harbin Medical University, Harbin, PR China
| | - Bo Chen
- Department of Plastic Surgery, the Second Affiliated Hospital of Harbin Medical University, Harbin, PR China
| | - Zhongjie Ji
- Department of Plastic Surgery, the Second Affiliated Hospital of Harbin Medical University, Harbin, PR China
| | - Aixia Xu
- Department of Endocrinology, Changsha Central Hospital, Changsha, PR China
| | - Tianhua Zhang
- Department of Vascular Surgery, the Second Affiliated Hospital of Harbin Medical University, Harbin, PR China
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Kong X, Wu T, Cai H, Chen Z, Wang Y, He P, Liu P, Li L, Peng S, Xu F, Wang J, Zhang H, Wang L. Construction of ceRNA network mediated by circRNAs screening from microarray and identification of novel biomarkers for myasthenia gravis. Gene 2024:148463. [PMID: 38631652 DOI: 10.1016/j.gene.2024.148463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 04/03/2024] [Accepted: 04/10/2024] [Indexed: 04/19/2024]
Abstract
BACKGROUND Recent studies have revealed that circRNA can serve as ceRNA to participate in multiple autoimmune diseases. Our study aims to explore the key circRNA as ceRNA and biomarker for MG. METHODS We used circRNA microarray to explore differentially expressed circRNAs (DECs) from MG and compare with control. Then, we predicted the target miRNA associated with DECs and screened miRNAs by the algorithm of random walk with restart (RWR). Next, we constructed the circRNA-miRNA-mRNA ceRNA regulated network (CMMC) to identify the hub objects. Following, we detected the expression of hub-circRNAs by RT-PCR. We verify has_circ_0004183 (circFRMD4) sponging miR-145-5p regulate cells proliferation using luciferase assay and CCK-8. RESULTS We found that the expression level of circFRMD4 and has_circ_0035381 (circPIGB) were upregulated and has_circ_0089153(circ NUP214) had the lowest expression level in MG. Finally, we proved circFRMD4 sponging miR-145-5p regulate Jurkat cells proliferation. CircFRMD4 take part in the genesis and development of MG via circFRMD4/miR145-5p axis. CONCLUSIONS We found that circFRMD4, circPIGB and circNUP214 can be considered as valuable potential novel biomarkers for AchR + MG. CircFRMD4 participate in the development of AchR + MG via targeting binding with miR-145-5p.
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Affiliation(s)
- Xiaotong Kong
- Department of Neurology, The Second Affiliated Hospital, Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Tao Wu
- Department of Neurology, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Hanlu Cai
- Department of Neurology, The Second Affiliated Hospital, Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Zhimin Chen
- Department of Neurology, The Second Affiliated Hospital, Harbin Medical University, Harbin, Heilongjiang Province, China; Department of Neurology, The Second Hospital of Harbin, Harbin, Heilongjiang Province, China
| | - Yu Wang
- Department of Neurology, The Second Affiliated Hospital, Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Ping He
- Department of Neurology, The First Hospital of Harbin, Harbin, Heilongjiang Province, China
| | - Peifang Liu
- Department of Neurology, The Second Affiliated Hospital, Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Lei Li
- Department of Neurology, The Second Affiliated Hospital, Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Shanshan Peng
- Department of Neurology, The Second Affiliated Hospital, Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Fanfan Xu
- Department of Neurology, The Second Affiliated Hospital, Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Jianjian Wang
- Department of Neurology, The Second Affiliated Hospital, Harbin Medical University, Harbin, Heilongjiang Province, China.
| | - Huixue Zhang
- Department of Neurology, The Second Affiliated Hospital, Harbin Medical University, Harbin, Heilongjiang Province, China.
| | - Lihua Wang
- Department of Neurology, The Second Affiliated Hospital, Harbin Medical University, Harbin, Heilongjiang Province, China.
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Ding Y, Jiang Y, Zeng H, Zhou M, Zhou X, Yu Z, Pan J, Geng X, Zhu Y, Zheng H, Huang S, Gong Y, Huang H, Xiong C, Huang D. Identification of a robust biomarker LAPTM4A for glioma based on comprehensive computational biology and experimental verification. Aging (Albany NY) 2024; 16:205736. [PMID: 38613802 DOI: 10.18632/aging.205736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 03/03/2024] [Indexed: 04/15/2024]
Abstract
BACKGROUND Glioma, a highly invasive and deadly form of human neoplasm, presents a pressing need for the exploration of potential therapeutic targets. While the lysosomal protein transmembrane 4A (LATPM4A) has been identified as a risk factor in pancreatic cancer patients, its role in glioma remains unexplored. METHODS The analysis of differentially expressed genes (DEG) was conducted from The Cancer Genome Atlas (TCGA) glioma dataset and the Genotype Tissue Expression (GTEx) dataset. Through weighted gene co-expression network analysis (WGCNA), the key glioma-related genes were identified. Among these, by using Kaplan-Meier (KM) analysis and univariate/multivariate COX methods, LAPTM4A emerged as the most influential gene. Moreover, the bioinformatics methods and experimental verification were employed to analyze its relationships with diagnosis, clinical parameters, epithelial-mesenchymal transition (EMT), metastasis, immune cell infiltration, immunotherapy, drug sensitivity, and ceRNA network. RESULTS Our findings revealed that LAPTM4A was up-regulated in gliomas and was associated with clinicopathological features, leading to poor prognosis. Furthermore, functional enrichment analysis demonstrated that LATPM4A played a role in the immune system and cancer progression. In vitro experiments indicated that LAPTM4A may influence metastasis through the EMT pathway in glioma. Additionally, we found that LAPTM4A was associated with the tumor microenvironment (TME) and immunotherapy. Notably, drug sensitivity analysis revealed that patients with high LAPTM4A expression were sensitive to doxorubicin, which contributed to a reduction in LAPTM4A expression. Finally, we uncovered the FGD5-AS1-hsa-miR-103a-3p-LAPTM4A axis as a facilitator of glioma progression. CONCLUSIONS In conclusion, our study identifies LATPM4A as a promising biomarker for prognosis and immune characteristics in glioma.
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Affiliation(s)
- Yongqi Ding
- Department of Thyroid Surgery, Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, China
- Second College of Clinical Medicine, Nanchang University, Nanchang, Jiangxi 330006, China
| | - Yike Jiang
- Second College of Clinical Medicine, Nanchang University, Nanchang, Jiangxi 330006, China
| | - Hong Zeng
- Second College of Clinical Medicine, Nanchang University, Nanchang, Jiangxi 330006, China
| | - Minqin Zhou
- Second College of Clinical Medicine, Nanchang University, Nanchang, Jiangxi 330006, China
| | - Xuanrui Zhou
- Second College of Clinical Medicine, Nanchang University, Nanchang, Jiangxi 330006, China
| | - Zichuan Yu
- Second College of Clinical Medicine, Nanchang University, Nanchang, Jiangxi 330006, China
| | - Jingying Pan
- Second College of Clinical Medicine, Nanchang University, Nanchang, Jiangxi 330006, China
| | - Xitong Geng
- Second College of Clinical Medicine, Nanchang University, Nanchang, Jiangxi 330006, China
| | - Yanting Zhu
- Second College of Clinical Medicine, Nanchang University, Nanchang, Jiangxi 330006, China
| | - Hao Zheng
- Second College of Clinical Medicine, Nanchang University, Nanchang, Jiangxi 330006, China
| | - Shuhan Huang
- Second College of Clinical Medicine, Nanchang University, Nanchang, Jiangxi 330006, China
| | - Yiyang Gong
- Second College of Clinical Medicine, Nanchang University, Nanchang, Jiangxi 330006, China
| | - Huabin Huang
- Department of Radiology, Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, China
| | - Chengfeng Xiong
- Department of Thyroid Surgery, Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, China
| | - Da Huang
- Department of Thyroid Surgery, Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, China
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Yin Z, Zhao Q, Lv X, Zhang X, Wu Y. Circular RNA ath-circ032768, a competing endogenous RNA, response the drought stress by targeting miR472-RPS5 module. Plant Biol (Stuttg) 2024. [PMID: 38588338 DOI: 10.1111/plb.13645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 02/21/2024] [Indexed: 04/10/2024]
Abstract
CircRNAs (circular RNAs) reduce the abundance of miRNAs through ceRNA (competing endogenous RNA), to regulate many physiological processes and stress responses in plants. However, the role of circRNA in drought stress is poorly understood. Through ring identification and sequencing verification of ath-circ032768, bioinformatics analysis predicted the interaction of ath-circ032768-miR472-RPS5, and further obtained transgenic plants overexpressing ath-circ032768 and silencing STTM-miR472. The change in drought stress was analysed using biochemical and molecular biological methods. Sequencing and biological analysis confirmed that ath-circ032768, miR472 and RPS5 were responsive to drought stress, and changes in gene expression were consistent with the prediction of ceRNA. The silencing vectors ath-circ032768 and STTM-miR472 were constructed using molecular biology techniques, and stable transgenic plants with drought tolerance obtained. Further physiological and biochemical studies showed that ath-circ032768 could bind to miR472, and that miR472 could bind to the RPS5 gene, resulting in decreased expression of RPS5. Hence, ath-circ032768 can competitively inhibit degradation of RPS5 by miR472 through ceRNA. This process is accompanied by increased expression of DREB2A, RD29A and RD29B genes. Through the ath-circ032768-miR472-RPS5 pathway, the RPS5 stress resistance protein interacts with DREB2A protein to enhance expression of downstream drought resistance genes, RD29A and RD29B, and participate in the regulation mechanism of plant drought resistance, thereby improving drought tolerance of plants.
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Affiliation(s)
- Z Yin
- College of Life Sciences, Northwest A&F University, Yangling, Shaan Xi, China
| | - Q Zhao
- College of Life Sciences, Northwest A&F University, Yangling, Shaan Xi, China
| | - X Lv
- College of Life Sciences, Northwest A&F University, Yangling, Shaan Xi, China
| | - X Zhang
- College of Life Sciences, Northwest A&F University, Yangling, Shaan Xi, China
| | - Y Wu
- College of Life Sciences, Northwest A&F University, Yangling, Shaan Xi, China
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Chong ZX, Ho WY, Yeap SK. Tumour-regulatory role of long non-coding RNA HOXA-AS3. Prog Biophys Mol Biol 2024; 189:13-25. [PMID: 38593905 DOI: 10.1016/j.pbiomolbio.2024.04.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 03/25/2024] [Accepted: 04/03/2024] [Indexed: 04/11/2024]
Abstract
Dysregulation of long non-coding RNA (lncRNA) HOXA-AS3 has been shown to contribute to the development of multiple cancer types. Several studies have presented the tumour-modulatory role or prognostic significance of this lncRNA in various kinds of cancer. Overall, HOXA-AS3 can act as a competing endogenous RNA (ceRNA) that inhibits the activity of seven microRNAs (miRNAs), including miR-29a-3p, miR-29 b-3p, miR-29c, miR-218-5p, miR-455-5p, miR-1286, and miR-4319. This relieves the downstream messenger RNA (mRNA) targets of these miRNAs from miRNA-mediated translational repression, allowing them to exert their effect in regulating cellular activities. Examples of the pathways regulated by lncRNA HOXA-AS3 and its associated downstream targets include the WNT/β-catenin and epithelial-to-mesenchymal transition (EMT) activities. Besides, HOXA-AS3 can interact with other cellular proteins like homeobox HOXA3 and HOXA6, influencing the oncogenic signaling pathways associated with these proteins. Generally, HOXA-AS3 is overexpressed in most of the discussed human cancers, making this lncRNA a potential candidate to diagnose cancer or predict the clinical outcomes of cancer patients. Hence, targeting HOXA-AS3 could be a new therapeutic approach to slowing cancer progression or as a potential biomarker and therapeutic target. A drawback of using lncRNA HOXA-AS3 as a biomarker or therapeutic target is that most of the studies that have reported the tumour-regulatory roles of lncRNA HOXA-AS3 are single observational, in vitro, or in vivo studies. More in-depth mechanistic and large-scale clinical trials must be conducted to confirm the tumour-modulatory roles of lncRNA HOXA-AS3 further. Besides, no lncRNA HOXA-AS3 inhibitor has been tested preclinically and clinically, and designing such an inhibitor is crucial as it may potentially slow cancer progression.
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Affiliation(s)
- Zhi Xiong Chong
- Faculty of Science and Engineering, University of Nottingham Malaysia, 43500 Semenyih, Selangor, Malaysia.
| | - Wan Yong Ho
- Faculty of Science and Engineering, University of Nottingham Malaysia, 43500 Semenyih, Selangor, Malaysia.
| | - Swee Keong Yeap
- China-ASEAN College of Marine Sciences, Xiamen University Malaysia, 43900 Sepang, Selangor, Malaysia.
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Li W, Cao Z, Xu F, Zhang X, Sun Y, Xie Z, Ning C, Zhang Q, Wang D, Tang H. Whole transcriptome sequencing reveals key genes and ceRNA regulatory networks associated with pimpled eggs in hens. Poult Sci 2024; 103:103715. [PMID: 38652954 DOI: 10.1016/j.psj.2024.103715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Revised: 03/21/2024] [Accepted: 03/31/2024] [Indexed: 04/25/2024] Open
Abstract
Eggshell is one of the most important indicators of egg quality, and due to low shell strength, pimple eggs (PE) are more susceptible to breakage, thus causing huge economic losses to the egg industry. At the current time, the molecular mechanisms that regulate the formation of pimple eggs are poorly understood. In this study, uterine tissues of PE-laying hens (n = 8) and normal egg (NE) -laying hens (n = 8) were analyzed by whole transcriptome sequencing, and a total of 619 differentially expressed mRNAs (DE mRNAs), 122 differentially expressed lncRNAs (DE lncRNAs) and 21 differentially expressed miRNAs (DE miRNAs) were obtained. Based on the targeting relationship among DE mRNAs, DE lncRNAs and DE miRNAs, we constructed a competitive endogenous RNA (ceRNA) network including 12 DE miRNAs, 19 DE lncRNAs, and 128 DE mRNAs. Considering the large amount of information contained in the network, we constructed a smaller ceRNA network to better understand the complex mechanisms of pimple egg formation. The smaller ceRNA network network contains 7 DE lncRNAs (LOC107056551, LOC121109367, LOC121108909, LOC121108862, LOC112530033, LOC121113165, LOC107054145), 5 DE miRNAs (gga-miR-6568-3p, gga-miR-31-5p, gga-miR-18b-3p, gga-miR-1759-3p, gga-miR-12240-3p) and 7 DE mRNAs (CABP1, DNAJC5, HCN3, HPCA, IBSP, KCNT1, OTOP3), and these differentially expressed genes may play key regulatory roles in the formation of pimpled eggs in hens. This study provides the overall expression profiles of mRNAs, lncRNAs and miRNAs in the uterine tissues of hens, which provides a theoretical basis for further research on the molecular mechanisms of pimpled egg formation, and has potential applications in improving eggshell quality.
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Affiliation(s)
- Wenqiang Li
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Key Laboratory of Efficient Utilization of Non-grain Feed Resources (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, College of Animal Science & Technology, Shandong Agricultural University, Taian City, Shandong Province, 271018, China
| | - Zhi Cao
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Key Laboratory of Efficient Utilization of Non-grain Feed Resources (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, College of Animal Science & Technology, Shandong Agricultural University, Taian City, Shandong Province, 271018, China
| | - Fei Xu
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Key Laboratory of Efficient Utilization of Non-grain Feed Resources (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, College of Animal Science & Technology, Shandong Agricultural University, Taian City, Shandong Province, 271018, China
| | - Xuguang Zhang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Key Laboratory of Efficient Utilization of Non-grain Feed Resources (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, College of Animal Science & Technology, Shandong Agricultural University, Taian City, Shandong Province, 271018, China
| | - Yifei Sun
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Key Laboratory of Efficient Utilization of Non-grain Feed Resources (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, College of Animal Science & Technology, Shandong Agricultural University, Taian City, Shandong Province, 271018, China
| | - Zhongbiao Xie
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Key Laboratory of Efficient Utilization of Non-grain Feed Resources (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, College of Animal Science & Technology, Shandong Agricultural University, Taian City, Shandong Province, 271018, China
| | - Chao Ning
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Key Laboratory of Efficient Utilization of Non-grain Feed Resources (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, College of Animal Science & Technology, Shandong Agricultural University, Taian City, Shandong Province, 271018, China
| | - Qin Zhang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Key Laboratory of Efficient Utilization of Non-grain Feed Resources (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, College of Animal Science & Technology, Shandong Agricultural University, Taian City, Shandong Province, 271018, China
| | - Dan Wang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Key Laboratory of Efficient Utilization of Non-grain Feed Resources (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, College of Animal Science & Technology, Shandong Agricultural University, Taian City, Shandong Province, 271018, China
| | - Hui Tang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Key Laboratory of Efficient Utilization of Non-grain Feed Resources (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, College of Animal Science & Technology, Shandong Agricultural University, Taian City, Shandong Province, 271018, China.
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Liu T, Su X, Kong X, Dong H, Wei Y, Wang Y, Wang C. Whole transcriptome sequencing identifies key lncRNAs,circRNAs, and mRNAs for exploring the pathogenesis and therapeutic target of mouse pneumoconiosis. Gene 2024; 901:148169. [PMID: 38242381 DOI: 10.1016/j.gene.2024.148169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Revised: 12/17/2023] [Accepted: 01/15/2024] [Indexed: 01/21/2024]
Abstract
BACKGROUND Pneumoconiosis is a kind of lung dysfunction caused by the inhalation of mineral dust. However, the potential molecular mechanism of pneumoconiosis have not been fully elucidated. METHODS In this study, the silica-treated pneumoconiosis mice model was constructed and the transcriptome sequencing data including lncRNA, circRNA, and mRNA were obtained. Firstly, differentially expressed lncRNA, circRNA, and mRNA (DElncRNA, DEcircRNA, DEGs) between control and pneumoconiosis/silicosis samples were screened, the target miRNAs (co-pre-miRNAs) were obtained by intersecting the miRNAs predicted by DElncRNA and DEcircRNA, respectively, and the target mRNAs (co-mRNA) were obtained by intersecting the mRNAs predicted by target miRNA and DEGs. Then, the lncRNA/circRNA-miRNA-mRNA networks were constructed by Cytoscape. Next, the key mRNAs were obtained by protein-protein interaction (PPI) analysis, and the key lncRNAs/circRNAs were selected by correlation analysis. Moreover, the expression of the key lncRNAs, circRNAs and mRNAs on chromosome were studied by the "circlize" package. Furthermore, the TFs-miRNA-mRNA network was constructed and the function of DEGs were explored by Ingenuity Pathway Analysis (IPA). To demonstrate the feasibility and value of the constructed ceRNA networks, we validated key genes and mmu-miR-682 pathway. Finally, We used the Drug-Gene Interaction database to predict potential drugs that could interfere with key genes,which may help to find promising treatment. RESULTS There were 427 DElncRNAs, 107 DEcircRNAs and 1,597 DEGs between silicosis and control groups. Totals of 77 co-pre-miRNAs and 96 co-mRNA were screened, and the lncRNA/circRNA-miRNA-mRNA networks were constructed with 27 lncRNA/25 circRNAs, 74 miRNAs and 96 mRNAs. Then, 6 key mRNAs including Igf1, Klf4, Ptgs2, Epas1, Gnao1, and Il1a were obtained by PPI, and all of these key mRNAs and 10 key lncRNAs and 8 circRNAs were significantly different between the pneumoconiosis and normal groups, in which 10 lncRNAs and 9 circRNA that have not been previously studied in pneumoconiosis/silicosis can be used as new potential therapeutic targets. Moreover, the TFs-miRNA-mRNA network were constructed with 11 TFs, 1 key miRNA (mmu-miR-682) and 3 key mRNAs (Igf1, Epas1, Ptgs2). And the validation of key genes revealing by RNA-seq through experimental approaches shows the the predictive power of this study. Finally, IPA results indicated that 41 pathways were activated and 2 pathways were suppressed in pneumoconiosis/silicosis groups, and Pathogen Induced Cytokine Storm Signaling Pathway was the most significant pathway affected by pneumoconiosis/silicosis. In addition, 93 drugs were screened out by Drug-Gene Interaction database. Among them, Hydroxychloroquine was a kind of drug which associated with Il1a and Ptgs2, may be a promising treatment. CONCLUSION This study constructed the lncRNA/circRNA-miRNA-mRNA and TFs-miRNA-mRNA networks, which could deepen the potential molecular regulatory mechanism of pneumoconiosis/silicosis.
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Affiliation(s)
- Ting Liu
- NHC Key Laboratory of Pneumoconiosis, Shanxi Key Laboratory of Respiratory, Department of Pulmonary and Critical Care Medicine, The First Hospital of Shanxi Medical University, The First Clinical Medical College of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Xuesen Su
- NHC Key Laboratory of Pneumoconiosis, Shanxi Key Laboratory of Respiratory, Department of Pulmonary and Critical Care Medicine, The First Hospital of Shanxi Medical University, The First Clinical Medical College of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Xiaomei Kong
- NHC Key Laboratory of Pneumoconiosis, Shanxi Key Laboratory of Respiratory, Department of Pulmonary and Critical Care Medicine, The First Hospital of Shanxi Medical University, The First Clinical Medical College of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Hantian Dong
- NHC Key Laboratory of Pneumoconiosis, Shanxi Key Laboratory of Respiratory, Department of Pulmonary and Critical Care Medicine, The First Hospital of Shanxi Medical University, The First Clinical Medical College of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Yangyang Wei
- NHC Key Laboratory of Pneumoconiosis, Shanxi Key Laboratory of Respiratory, Department of Pulmonary and Critical Care Medicine, The First Hospital of Shanxi Medical University, The First Clinical Medical College of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Yan Wang
- Medical School of Shanxi Datong University, Datong, Shanxi Province, China
| | - Chen Wang
- NHC Key Laboratory of Pneumoconiosis, Shanxi Key Laboratory of Respiratory, Department of Pulmonary and Critical Care Medicine, The First Hospital of Shanxi Medical University, The First Clinical Medical College of Shanxi Medical University, Taiyuan, Shanxi, China.
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11
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Sun K, Sun Y, Du X, Zhang X, Ma Z, Gao Y, Liang X. Lnc-Clic5 as a sponge for miR-212-5p to inhibit cow barn PM 2.5-induced apoptosis in rat alveolar macrophages. Toxicology 2024; 504:153797. [PMID: 38583737 DOI: 10.1016/j.tox.2024.153797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 03/17/2024] [Accepted: 04/04/2024] [Indexed: 04/09/2024]
Abstract
Particulate matter 2.5 (PM2.5) is a highly hazardous airborne particulate matter that poses a significant risk to humans and animals. Urban airborne particulate matter contributes to the increased incidence and mortality of respiratory diseases, such as asthma and chronic obstructive pulmonary disease (COPD), in humans. However, the specific mechanism by which PM2.5 affects animals in barn environments is yet to be elucidated. In this study, we investigated the effect of exposure to cow barn PM2.5 on rat alveolar macrophages (NR8383) and found that it induced apoptosis via the miR-212-5p/RASSF1 pathway. We found that lnc-Clic5 expression was downregulated in NR8383 cells exposed to cow barn PM2.5. Lnc-Clic5 plays a competitive endogenous RNA (ceRNA) regulatory role by sponging miR-212-5p to attenuate the regulation of RASSF1. Moreover, lnc-Clic5 overexpression inhibited NR8383 apoptosis by targeting the miR-212-5p/RASSF1 pathway. Co-treatment with miR-212-5p and lnc-Clic5 in the presence of cow barn PM2.5 revealed that lnc-Clic5 reversed NR8383 cell apoptosis induced by PM2.5 when miR-212-5p was overexpressed. These findings contribute to the study of ncRNAs and ceRNAs regulating PM2.5-induced apoptosis in animal farms, provide therapeutic targets for lung macrophage apoptosis, and may be useful for further evaluating the toxicological effects of PM2.5 in farmhouses on the respiratory systems of humans and animals.
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Affiliation(s)
- Ke Sun
- College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China
| | - Yize Sun
- College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China
| | - Xiaohui Du
- College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China
| | - Xiqing Zhang
- College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China
| | - Zhenhua Ma
- College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China
| | - Yunhang Gao
- College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China.
| | - Xiaojun Liang
- Ningxia Academy of Agriculture and Forestry, Yinchuan 750002, China.
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Hu Y, Cao H, Sheng J, Sun Y, Zhu Y, Lin Q, Yi N, He S, Peng L, Li L. The functional role of circRNA CHRC through miR-431-5p/KLF15 signaling axis in the progression of heart failure. J Genet Genomics 2024:S1673-8527(24)00063-8. [PMID: 38575112 DOI: 10.1016/j.jgg.2024.03.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 03/25/2024] [Accepted: 03/26/2024] [Indexed: 04/06/2024]
Abstract
Pathological myocardial hypertrophy is a common early clinical manifestation of heart failure, with non-coding RNAs exerting regulatory influence. However, the molecular function of circular RNAs (circRNAs) in the progression from cardiac hypertrophy to heart failure remains unclear. To uncover functional circRNAs and identify the core circRNA signaling pathway in heart failure, we construct a global triple network (microRNA, circRNA, and mRNA) based on the competitive endogenous RNA (ceRNA) theory. We observe that circRNA CHRC, within the ceRNA network, is down-regulated in both transverse aortic constriction (TAC) mice and Ang-II-treated primary mouse cardiomyocytes. Silencing circRNA CHRC increases cross-sectional cell area, atrial natriuretic peptide, and β-myosin heavy chain levels in primary mouse cardiomyocytes. Further screening reveals that circRNA CHRC targets the miR-431-5p/KLF15 axis implicated in heart failure progression in vivo and in vitro. Immunoprecipitation with anti-Ago2-RNA confirms the interaction between circRNA CHRC and miR-431-5p, while miR-431-5p mimics reverse Klf15 activation caused by circRNA CHRC over-expression. In summary, circRNA CHRC attenuates cardiac hypertrophy via sponging miR-431-5p to maintain the normal level of Klf15 expression.
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Affiliation(s)
- Yi Hu
- State Key Laboratory of Cardiology and Medical Innovation Center, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China; Shanghai Arrhythmias Research Center, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China; Laboratory of Molecular Genetics and Stem Cell Differentiation, Tongji University School of Medicine, Shanghai 200120, China
| | - Huaming Cao
- Department of Cardiology, Shanghai Shibei Hospital, Shanghai 200435, China
| | - Jie Sheng
- State Key Laboratory of Cardiology and Medical Innovation Center, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China; Shanghai Arrhythmias Research Center, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China; Laboratory of Molecular Genetics and Stem Cell Differentiation, Tongji University School of Medicine, Shanghai 200120, China
| | - Yizhuo Sun
- State Key Laboratory of Cardiology and Medical Innovation Center, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China; Shanghai Arrhythmias Research Center, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China; Laboratory of Molecular Genetics and Stem Cell Differentiation, Tongji University School of Medicine, Shanghai 200120, China
| | - Yuping Zhu
- State Key Laboratory of Cardiology and Medical Innovation Center, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China; Shanghai Arrhythmias Research Center, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China; Laboratory of Molecular Genetics and Stem Cell Differentiation, Tongji University School of Medicine, Shanghai 200120, China
| | - Qin Lin
- State Key Laboratory of Cardiology and Medical Innovation Center, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China; Shanghai Arrhythmias Research Center, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China; Laboratory of Molecular Genetics and Stem Cell Differentiation, Tongji University School of Medicine, Shanghai 200120, China
| | - Na Yi
- State Key Laboratory of Cardiology and Medical Innovation Center, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China; Shanghai Arrhythmias Research Center, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China; Laboratory of Molecular Genetics and Stem Cell Differentiation, Tongji University School of Medicine, Shanghai 200120, China
| | - Siyu He
- State Key Laboratory of Cardiology and Medical Innovation Center, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China; Shanghai Arrhythmias Research Center, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China; Laboratory of Molecular Genetics and Stem Cell Differentiation, Tongji University School of Medicine, Shanghai 200120, China
| | - Luying Peng
- State Key Laboratory of Cardiology and Medical Innovation Center, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China; Shanghai Arrhythmias Research Center, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China; Laboratory of Molecular Genetics and Stem Cell Differentiation, Tongji University School of Medicine, Shanghai 200120, China; Research Units of Origin and Regulation of Heart Rhythm, Chinese Academy of Medical Sciences, Shanghai 200120, China.
| | - Li Li
- State Key Laboratory of Cardiology and Medical Innovation Center, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China; Shanghai Arrhythmias Research Center, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China; Laboratory of Molecular Genetics and Stem Cell Differentiation, Tongji University School of Medicine, Shanghai 200120, China; Research Units of Origin and Regulation of Heart Rhythm, Chinese Academy of Medical Sciences, Shanghai 200120, China.
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Zhou Q, Shi R. Shared Genetic Features of Psoriasis and Myocardial Infarction: Insights From a Weighted Gene Coexpression Network Analysis. J Am Heart Assoc 2024; 13:e033893. [PMID: 38533976 DOI: 10.1161/jaha.123.033893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 03/05/2024] [Indexed: 03/28/2024]
Abstract
BACKGROUND Increasing evidence suggests a higher propensity for acute myocardial infarction (MI) in patients with psoriasis. However, the shared mechanisms underlying this comorbidity in these patients remain unclear. This study aimed to explore the shared genetic features of psoriasis and MI and to identify potential biomarkers indicating their coexistence. METHODS AND RESULTS Data sets obtained from the gene expression omnibus were examined using a weighted gene coexpression network analysis approach. Hub genes were identified using coexpression modules and validated in other data sets and through in vitro cellular experiments. Bioinformatics tools, including the Human microRNA Disease Database, StarBase, and miRNet databases, were used to construct a ceRNA network and predict potential regulatory mechanisms. By applying weighted gene coexpression network analysis, we identified 2 distinct modules that were significant for both MI and psoriasis. Inflammatory and immune pathways were highlighted by gene ontology enrichment analysis of the overlapping genes. Three pivotal genes-Src homology and collagen 1, disruptor of telomeric silencing 1-like, and feline leukemia virus subgroup C cellular receptor family member 2-were identified as potential biomarkers. We constructed a ceRNA network that suggested the upstream regulatory roles of these genes in the coexistence of psoriasis and MI. CONCLUSIONS As potential therapeutic targets, Src homology and collagen 1, feline leukemia virus subgroup C cellular receptor family member 2, and disruptor of telomeric silencing 1-like provide novel insights into the shared genetic features between psoriasis and MI. This study paves the way for future studies focusing on the prevention of MI in patients with psoriasis.
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Affiliation(s)
- Qiaoyu Zhou
- Department of Cardiovascular Medicine Third Xiangya Hospital of Central South University Changsha Hunan China
| | - Ruizheng Shi
- Department of Cardiovascular Medicine Xiangya Hospital, Central South University Changsha Hunan China
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Xu W, Mo W, Han D, Dai W, Xu X, Li J, Xu X. Hepatocyte-derived exosomes deliver the lncRNA CYTOR to hepatic stellate cells and promote liver fibrosis. J Cell Mol Med 2024; 28:e18234. [PMID: 38520214 PMCID: PMC10960169 DOI: 10.1111/jcmm.18234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 02/19/2024] [Accepted: 02/28/2024] [Indexed: 03/25/2024] Open
Abstract
Liver fibrosis is characterized by the activation and transformation of hepatic stellate cells (HSCs) induced by various injury factors. The degree of liver fibrosis can be significantly improved, but persistent injury factors present a significant therapeutic challenge. Hepatocytes are the most important parenchymal cell type in the liver. In this study, we explored the molecular mechanisms by which damaged liver cells activate HSCs through extracellular vesicles. We established a coculture model of LO2 and LX2 and validated its exosomal transmission activity. Subsequently, differentially expressed long noncoding RNAs (lncRNAs) were screened through RNA sequencing and their mechanisms of action as competing endogenous RNAs (ceRNAs) further confirmed using biological methods, such as FISH and luciferase assays. Damaged liver cells induced activation of LX2 and upregulation of liver fibrosis-related markers. Exosomes extracted and identified from the supernatant fraction contained differentially expressed lncRNA cytoskeleton regulator RNA (CYTOR) that competed with microRNA-125 (miR-125) for binding to glial cell line-derived neurotrophic factor (GDNF) in HSCs, in turn, promoting LX2 activation. MiR-125 could target and regulate both CYTOR and GDNF and vice versa, as verified using the luciferase assay. In an in vivo model, damaged liver extracellular vesicles induced the formation of liver fibrosis. Notably, downregulation of CYTOR within extracellular vesicles effectively inhibited liver fibrosis. The lncRNA CYTOR in exosomes of damaged liver cells is upregulated and modulates the expression of downstream GDNF through activity as a ceRNA, providing an effective mechanism for activation of HSCs.
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Affiliation(s)
- Wenqiang Xu
- Department of GastroenterologyShidong Hospital of Shanghai, School of Health Science and Engineering, University of Shanghai for Science and TechnologyShanghaiChina
| | - Wenhui Mo
- Department of GastroenterologyShidong Hospital of Shanghai, School of Health Science and Engineering, University of Shanghai for Science and TechnologyShanghaiChina
| | - Dengyu Han
- Department of GastroenterologyShidong Hospital of Shanghai, School of Health Science and Engineering, University of Shanghai for Science and TechnologyShanghaiChina
| | - Weiqi Dai
- Department of GastroenterologyShidong Hospital of Shanghai, School of Health Science and Engineering, University of Shanghai for Science and TechnologyShanghaiChina
| | - Xiaorong Xu
- Department of GastroenterologyShanghai Tenth People's Hospital, Tongji University School of MedicineShanghaiChina
| | - Jingjing Li
- Department of GastroenterologyShidong Hospital of Shanghai, School of Health Science and Engineering, University of Shanghai for Science and TechnologyShanghaiChina
| | - Xuanfu Xu
- Department of GastroenterologyShidong Hospital of Shanghai, School of Health Science and Engineering, University of Shanghai for Science and TechnologyShanghaiChina
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15
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Wang Y, Wang J, Zhang L, He J, Ji B, Wang J, Ding B, Ren M. Unveiling the role of YARS1 in bladder cancer: A prognostic biomarker and therapeutic target. J Cell Mol Med 2024; 28:1-20. [PMID: 38506098 PMCID: PMC10951887 DOI: 10.1111/jcmm.18213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 02/03/2024] [Accepted: 02/16/2024] [Indexed: 03/21/2024] Open
Abstract
YARS is responsible for catalysing the binding of tyrosine to its cognate tRNA and plays a crucial role in basic biosynthesis. However, its biological functions in bladder cancer remains to be proven. We analysed variations in YARS1 expression and survival in bladder cancer using multiple data sets, including TCGA-BLCA, GSE13507 and bladder cancer-specific tissue microarrays. Furthermore, we explored the biological functions of YARS1 using transcriptome data. Our findings revealed a noteworthy correlation between YARS1 and immune infiltration in bladder cancer, as determined using the XCELL algorithm and single-cell analysis. In addition, we employed the TIDE algorithm to evaluate the responsiveness of different cohorts to immune checkpoint therapy. We investigated the regulatory associations between YARS1 and various aspects of bladder cancer, including senescence, ferroptosis and stemness. Finally, we established a ceRNA network that is directly linked to the overall prognosis, YARS1 can serve as a prognostic biomarker for bladder cancer; its interaction with MYC has implications for bladder cancer cell senescence, ferroptosis and stemness. Moreover, the identified ceRNA network has potential as a therapeutic target in bladder cancer.
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Affiliation(s)
- YaXuan Wang
- Department of UrologyThe First Affiliated Hospital of Harbin Medical UniversityHarbinChina
| | - Jinfeng Wang
- Department of UrologyThe First Affiliated Hospital of Harbin Medical UniversityHarbinChina
| | - Lu Zhang
- Department of UrologyThe First Affiliated Hospital of Harbin Medical UniversityHarbinChina
| | - JiaXing He
- Department of UrologyThe First Affiliated Hospital of Harbin Medical UniversityHarbinChina
| | - Bo Ji
- Department of UrologyThe First Affiliated Hospital of Harbin Medical UniversityHarbinChina
| | - JianShe Wang
- Department of UrologyThe First Affiliated Hospital of Harbin Medical UniversityHarbinChina
| | - BeiChen Ding
- Department of UrologyThe First Affiliated Hospital of Harbin Medical UniversityHarbinChina
| | - MingHua Ren
- Department of UrologyThe First Affiliated Hospital of Harbin Medical UniversityHarbinChina
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Li Y, Kan X. Cuproptosis-Related Genes MTF1 and LIPT1 as Novel Prognostic Biomarker in Acute Myeloid Leukemia. Biochem Genet 2024; 62:1136-1159. [PMID: 37561332 DOI: 10.1007/s10528-023-10473-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Accepted: 07/24/2023] [Indexed: 08/11/2023]
Abstract
Acute myeloid leukemia (AML) is a life-threatening hematologic malignant disease with high morbidity and mortality in both adults and children. Cuproptosis, a novel mode of cell death, plays an important role in tumor development, but the functional mechanisms of cuproptosis-related genes (CRGs) in AML are unclear. The differential expression of CRGs between tumors such as AML and normal tissues in UCSC XENA, TCGA and GTEx was verified using R (version: 3.6.3). Lasso regression, Cox regression and Nomogram were used to screen for prognostic biomarkers of AML and to construct corresponding prognostic models. Kaplan-Meier analysis, ROC analysis, clinical correlation analysis, immune infiltration analysis and enrichment analysis were used to further investigate the correlation and functional mechanisms of CRGs with AML. The ceRNA regulatory network was used to identify the mRNA-miRNA-lncRNA regulatory axis. Cuproptosis-related genes LIPT1, MTF1, GLS and CDKN2A were highly expressed in AML, while FDX1, LIAS, DLD, DLAT, PDHA1, SLC31A1 and ATP7B were lowly expressed in AML. Lasso regression, Cox regression, Nomogram and calibration curve finally identified MTF1 and LIPT1 as two novel prognostic biomarkers of AML and constructed the corresponding prognostic models. In addition, all 12 CRGs had predictive power for AML, with MTF1, LIAS, SLC31A1 and CDKN2A showing more reliable results. Further analysis showed that ATP7B was closely associated with mutation types such as FLT3, NPM1, RAS and IDH1 R140 in AML, while the expression of MTF1, LIAS and ATP7B in AML was closely associated with immune infiltration. Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Set Enrichment Analysis (GSEA) revealed that biological functions such as metal ion transmembrane transporter activity, haptoglobin binding and oxygen carrier activity, pathways such as interferon alpha response, coagulation, UV response DN, apoptosis, hypoxia and heme metabolism all play a role in the development of AML. The ceRNA regulatory network revealed that 6 lncRNAs such as MALAT1, interfere with MTF1 expression through 6 miRNAs such as hsa-miR-32-5p, which in turn affect the development and progression of AML. In addition, APTO-253 has the potential to become an AML-targeted drug. The cuproptosis-related genes MTF1 and LIPT1 can be used as prognostic biomarkers in AML. A total of six lncRNAs, including MALAT1, are involved in the expression and regulation of MTF1 in AML through six miRNAs such as hsa-miR-32-5p.
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Affiliation(s)
- Yujian Li
- Department of Pediatrics, General Hospital of Tianjin Medical University, Tianjin, China
| | - Xuan Kan
- Department of Pediatrics, General Hospital of Tianjin Medical University, Tianjin, China.
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Ren X, Wang X, Song H, Zhang C, Yuan J, He J, Li J, Wang Z. Long non-coding RNA LINC01554 overexpression suppresses viability, migration, and invasion of liver cancer cells through regulating miR-148b-3p/EIF4E3. Heliyon 2024; 10:e27319. [PMID: 38501022 PMCID: PMC10945188 DOI: 10.1016/j.heliyon.2024.e27319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 02/27/2024] [Accepted: 02/27/2024] [Indexed: 03/20/2024] Open
Abstract
Background Long non-coding RNAs (lncRNAs) can be severed as competing endogenous RNAs (ceRNAs) to regulate target genes or mRNAs via sponging microRNAs (miRNAs). This study explored the effect of LINC01554 on liver cancer cells through the ceRNA mechanism. Methods Five significantly down-regulated lncRNAs were selected for further verification, and then through bioinformatics, interactive miRNAs and mRNAs of lncRNAs were identified. The relationship between LINC01554, miR-148b-3p and EIF4E3 was detected by the dual luciferase reporter gene assay. Afterwards, HCCLM3 cells were transfected with pCDH-LINC01554, miR-148b-3p inhibitor and miR-148b-3p mimics. Cell viability, apoptosis, migration and invasion were measured by Cell Counting Kit-8, flow cytometer, and Transwell assays. Real-time quantitative PCR (RT-qPCR) and Western blot were used to measure the expressions of related genes and proteins. Results LINC01554 was significantly down-regulated in the liver cancer cell lines, and was expressed in the cytoplasm of HCCLM3 cells. LINC01554 overexpression inhibited proliferation, migration, and invasion of HCCLM3 cells, and promote their apoptosis (P < 0.05). Besides, LINC01554 overexpression also significantly increased the levels of BAX, BCL2/BAX, P53, cleaved-Caspase3, TIMP3, E-cadherin and EIF4E3 (P < 0.05). Through bioinformatics and dual-luciferase reporter gene assay, LINC01554, miR-148b-3p and EIF4E3 were proved to interact with each other. Furthermore, the effects of miR-148b-3p knockdown on HCCLM3 cells were similar with those of LINC01554 overexpression, and miR-148b-3p mimics could reverse the changes of cell viability, apoptosis, migration, and invasion induced by LINC01554 overexpression. Conclusions LINC01554 overexpression could suppress the growth and metastasis of HCCLM3 cells via miR-148b-3p/EIF4E3.
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Affiliation(s)
- Xiaojing Ren
- Radiological & Environment Medicine Dept, China Institute for Radiation Protection, Taiyuan, 030032, China
- Department of Hepatobiliary Surgery, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, Taiyuan, 030032, China
| | - Xiaoxiao Wang
- Department of Hepatobiliary Surgery, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, Taiyuan, 030032, China
| | - Huangqin Song
- Department of Hepatobiliary Surgery, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, Taiyuan, 030032, China
| | - Chao Zhang
- Department of Hepatobiliary Surgery, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, Taiyuan, 030032, China
| | - Junlong Yuan
- Department of Hepatobiliary Surgery, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, Taiyuan, 030032, China
| | - Jiefeng He
- Department of Hepatobiliary Surgery, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, Taiyuan, 030032, China
| | - Jianguo Li
- Radiological & Environment Medicine Dept, China Institute for Radiation Protection, Taiyuan, 030032, China
| | - Zhuangqiang Wang
- Department of Hepatobiliary Surgery, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, Taiyuan, 030032, China
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Mao W, Zhang Z. The Hsa_circ_0105558/miR-182-5p/ATF6 Cascade Affects H 2O 2-Triggered Oxidative Damage and Apoptosis of Human Lens Epithelial Cells. Biochem Genet 2024:10.1007/s10528-024-10753-1. [PMID: 38530576 DOI: 10.1007/s10528-024-10753-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 02/20/2024] [Indexed: 03/28/2024]
Abstract
Age-related cataract (ARC) is the prevalent cause of useful vision loss. Circular RNAs are related to ARC pathogenesis partly through their competing endogenous RNA (ceRNA) activity. Herein, we defined the action of hsa_circ_0105558 in hydrogen peroxide (H2O2)-driven apoptosis and oxidative damage in human lens epithelial SRA01/04 cells. Hsa_circ_0105558, microRNA (miR)-182-5p and activating transcription factor 6 (ATF6) were evaluated by a qRT-PCR or immunoblotting method. The hsa_circ_0105558/miR-182-5p and miR-182-5p/ATF6 relationships were predicted by bioinformatics analysis and confirmed by dual-luciferase reporter assay. Reactive oxygen species level, glutathione peroxidase level, superoxide dismutase activity, and malondialdehyde level were measured using the matched assay kits. Hsa_circ_0105558 was upregulated in human ARC lens and H2O2-exposed SRA01/04 cells. Suppression of hsa_circ_0105558 attenuated H2O2-driven SRA01/04 cell apoptosis and oxidative damage. Hsa_circ_0105558 targeted miR-182-5p, and reduced miR-182-5p expression reversed the influence of hsa_circ_0105558 depletion on H2O2-driven oxidative damage and apoptosis. ATF6 was a target of miR-182-5p, and miR-182-5p-driven downregulation of ATF6 regulated cell oxidative damage and apoptosis under H2O2 insult. Moreover, hsa_circ_0105558 functioned as a ceRNA to post-transcriptionally control ATF6 expression through miR-182-5p competition. Our study demonstrates that hsa_circ_0105558 modulates SRA01/04 cell oxidative damage and apoptosis under H2O2 insult through the miR-182-5p/ATF6 cascade.
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Affiliation(s)
- Wei Mao
- Refractive Surgery Department, Ningbo Eye Hospital, Ningbo, 315010, Zhejiang, China.
| | - Zhe Zhang
- Refractive Surgery Department, Ningbo Eye Hospital, Ningbo, 315010, Zhejiang, China
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Yu M, Feng Y, Yan J, Zhang X, Tian Z, Wang T, Wang J, Shen W. Transcriptomic regulatory analysis of skeletal muscle development in landrace pigs. Gene 2024; 915:148407. [PMID: 38531491 DOI: 10.1016/j.gene.2024.148407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 12/28/2023] [Accepted: 03/21/2024] [Indexed: 03/28/2024]
Abstract
The development of pig skeletal muscle is a complex dynamic regulation process, which mainly includes the formation of primary and secondary muscle fibers, the remodeling of muscle fibers, and the maturation of skeletal muscle; However, the regulatory mechanism of the entire developmental process remains unclear. This study analyzed the whole-transcriptome data of skeletal muscles at 27 developmental nodes (E33-D180) in Landrace pigs, and their key regulatory factors in the development process were identified using the bioinformatics method. Firstly, we constructed a transcriptome expression map of skeletal muscle development from embryo to adulthood in Landrace pig. Subsequently, due to drastic change in gene expression, the perinatal periods including E105, D0 and D9, were focused, and the genes related to the process of muscle fiber remodeling and volume expansion were revealed. Then, though conjoint analysis with miRNA and lncRNA transcripts, a ceRNA network were identified, which consist of 11 key regulatory genes (such as CHAC1, RTN4IP1 and SESN1), 7 miRNAs and 43 lncRNAs, and they potentially play an important role in the process of muscle fiber differentiation, muscle fiber remodeling and volume expansion, intramuscular fat deposition, and other skeletal muscle developmental events. In summary, we reveal candidate genes and underlying molecular regulatory networks associated with perinatal skeletal muscle fiber type remodeling and expansion. These data provide new insights into the molecular regulation of mammalian skeletal muscle development and diversity.
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Affiliation(s)
- Mubin Yu
- Key Laboratory of Animal Reproduction and Biotechnology in Universities of Shandong, College of Life Sciences, Qingdao Agricultural University, Qingdao 266109, China
| | - Yanqin Feng
- Key Laboratory of Animal Reproduction and Biotechnology in Universities of Shandong, College of Life Sciences, Qingdao Agricultural University, Qingdao 266109, China
| | - Jiamao Yan
- Key Laboratory of Animal Reproduction and Biotechnology in Universities of Shandong, College of Life Sciences, Qingdao Agricultural University, Qingdao 266109, China
| | - Xiaoyuan Zhang
- Key Laboratory of Animal Reproduction and Biotechnology in Universities of Shandong, College of Life Sciences, Qingdao Agricultural University, Qingdao 266109, China
| | - Zhe Tian
- Key Laboratory of Animal Reproduction and Biotechnology in Universities of Shandong, College of Life Sciences, Qingdao Agricultural University, Qingdao 266109, China
| | - Tao Wang
- Key Laboratory of Animal Reproduction and Biotechnology in Universities of Shandong, College of Life Sciences, Qingdao Agricultural University, Qingdao 266109, China
| | - Junjie Wang
- Key Laboratory of Animal Reproduction and Biotechnology in Universities of Shandong, College of Life Sciences, Qingdao Agricultural University, Qingdao 266109, China.
| | - Wei Shen
- Key Laboratory of Animal Reproduction and Biotechnology in Universities of Shandong, College of Life Sciences, Qingdao Agricultural University, Qingdao 266109, China.
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20
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Guo Y, Geng W, Chen Z, Zhi Y, Zhang K, Li Z, Li G, Kang X, Tian W, Li H, Liu X. LncRNA lncMGR regulates skeletal muscle development and regeneration by recruiting CDK9 and sponging miRNAs. Int J Biol Macromol 2024; 266:131049. [PMID: 38522687 DOI: 10.1016/j.ijbiomac.2024.131049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 01/31/2024] [Accepted: 03/02/2024] [Indexed: 03/26/2024]
Abstract
Long non-coding RNAs (lncRNAs) play an essential role in vertebrate myogenesis and muscle diseases. However, the dynamic expression patterns, biological functions, and mechanisms of lncRNAs in skeletal muscle development and regeneration remain largely unknown. In this study, a novel lncRNA (named lncMGR) was differentially expressed during breast muscle development in fast- and slow-growing chickens. Functionally, lncMGR promoted myoblast differentiation, inhibited myoblast proliferation in vitro, and promoted myofiber hypertrophy and injury repair in vivo. Mechanistically, lncMGR increased the mRNA and protein expression of skeletal muscle myosin heavy chain 1 A (MYH1A) via both transcriptional and post-transcriptional regulation. Nuclear lncMGR recruited cyclin-dependent kinase 9 (CDK9) to the core transcriptional activation region of the MYH1A gene to activate MYH1A transcription. Cytoplasmic lncMGR served as a competitive endogenous RNA (ceRNA) to competitively absorb miR-2131-5p away from MYH1A and subsequently protected the MYH1A from miR-2131-5p-mediated degradation. Besides miR-2131-5p, cytoplasmic lncMGR could also sponge miR-143-3p to reconcile the antagonist between the miR-2131-5p/MYH1A-mediated inhibition effects and miR-143-3p-mediated promotion effects on myoblast proliferation, thereby inhibiting myoblast proliferation. Collectively, lncMGR could recruit CDK9 and sponge multiple miRNAs to regulate skeletal muscle development and regeneration, and could be a therapeutic target for muscle diseases.
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Affiliation(s)
- Yulong Guo
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China
| | - Wanzhuo Geng
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China
| | - Zhimin Chen
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China
| | - Yihao Zhi
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China
| | - Ke Zhang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China
| | - Zhuanjian Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China; Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou 450046, China; International Joint Research Laboratory for Poultry Breeding of Henan, Zhengzhou 450002, China
| | - Guoxi Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China; Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou 450046, China; International Joint Research Laboratory for Poultry Breeding of Henan, Zhengzhou 450002, China
| | - Xiangtao Kang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China; Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou 450046, China; International Joint Research Laboratory for Poultry Breeding of Henan, Zhengzhou 450002, China
| | - Weihua Tian
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China; Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou 450046, China; International Joint Research Laboratory for Poultry Breeding of Henan, Zhengzhou 450002, China.
| | - Hong Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China; Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou 450046, China; International Joint Research Laboratory for Poultry Breeding of Henan, Zhengzhou 450002, China.
| | - Xiaojun Liu
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China; Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou 450046, China; International Joint Research Laboratory for Poultry Breeding of Henan, Zhengzhou 450002, China.
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Ahmadi M, Fathi M, Malmir A, Ghafouri-Fard S. Role of circular RNA/miRNA axes in the pathophysiology of polycystic ovary syndrome. Mol Biol Rep 2024; 51:437. [PMID: 38520572 DOI: 10.1007/s11033-024-09376-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 02/23/2024] [Indexed: 03/25/2024]
Abstract
Polycystic ovary syndrome (PCOS) is a disorder resulted from interactions between genetic and environmental factors. Based on the importance of epigenetic factors in the pathoetiology of PCOS, the current review focused on identification of circular RNAs (circRNAs) that are involved in PCOS through acting as molecular sponges for microRNAs (miRNAs). The literature search led to identification of circ_0043533/miR-1179, circ_0030018/miR-136, circ_FURIN/miR-423-5p, circ-FURIN/miR-195-5p, circ_0043532/miR-182, circ_RANBP9/miR-136-5p, circRHBG/miR-515-5p, circMTO1/miR-320b, circASPH/miR-375, circPSMC3/miR-296-3p, circLDLR/miR-1294, circPUM1/miR-760, and hsa_circ_0118530/miR-136 as molecular axes contributing to the pathogenesis of PCOS. To set the stage for future research on the role of the ceRNA network in PCOS, in-silico analyses were performed using miRWalk, miRNet, and miRDIP databases. miRWalk identified 80 genes regulated by 5 miRNAs, miRNet revealed 6449 circRNAs potentially controlling 11 miRNAs, and miRDIP identified 11 miRNAs associated with 35 human pathways. These targets can be used in the treatment options, design of personalized medicine and prediction of prognosis of PCOS.
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Affiliation(s)
- Mohsen Ahmadi
- Student Research Committee, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohadeseh Fathi
- Student Research Committee, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Ali Malmir
- Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Soudeh Ghafouri-Fard
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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Lin Y, Sun L, Dai J, Lv Y, Liao R, Shen X, Gao J. Characterization and Comparative Analysis of Whole-Transcriptome Sequencing in High- and Low-Fecundity Chongming White Goat Ovaries during the Estrus Phase. Animals (Basel) 2024; 14:988. [PMID: 38612227 PMCID: PMC11010919 DOI: 10.3390/ani14070988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 03/14/2024] [Accepted: 03/20/2024] [Indexed: 04/14/2024] Open
Abstract
Reproductive performance is one of the most important economic traits in the goat industry. Increasing the number of goats is an effective measure to improve production efficiency and reduce production costs. Ovaries are important reproductive organs in female mammals that directly affect the estrous cycle and reproductive abilities. Understanding the complex transcription network of non-coding RNAs (lncRNAs, circRNAs, and miRNAs) and messenger RNA (mRNA) could lead to significant insights into the ovarian regulation of the reproductive processes of animals. However, the whole-transcriptome analysis of the non-coding RNAs and mRNA of the ovaries in Chongming white goats between high-fecundity (HP) and low-fecundity (LP) groups is limited. In this study, a whole-transcriptome sequencing approach was used to identify lncRNA, circRNA, miRNA, and mRNA expression in the ovaries of Chongming white goats during the estrus phase using RNA-Seq technology. More than 20,000 messenger RNAs (mRNAs), 10,000 long non-coding RNAs (lncRNAs), 3500 circular RNAs (circRNAs), and 1000 micro RNAs (miRNAs) were identified. A total of 1024 differential transcripts (724 mRNAs, 112 lncRNAs, 178 circRNAs, and 10 miRNAs) existing between the HP and the LP groups were revealed through a bioinformatics analysis. They were enriched in the prolactin signaling pathway, the Jak-STAT signaling pathway, and the GnRH signaling pathway, as well as various metabolic pathways. Differentially expressed mRNAs (such as LYPD6, VEGFA, NOS3, TNXB, and EPHA2) and miRNAs (such as miR-10a-5p) play key roles in the regulation of goat ovaries during the estrus phase. The enrichment of pathways related to reproduction, such as the Hippo, Hedgehog, PI3K-AKT, and MAPK signaling pathways, suggests that they might be involved in the prolificacy of goat ovaries. Overall, we identified several gene modules associated with goat fecundity and provided a basis for a molecular mechanism in the ovaries of Chongming white goats.
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Affiliation(s)
- Yuexia Lin
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China; (Y.L.); (L.S.); (J.D.); (Y.L.); (R.L.)
| | - Lingwei Sun
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China; (Y.L.); (L.S.); (J.D.); (Y.L.); (R.L.)
- Division of Animal Genetic Engineering, Shanghai Municipal Key Laboratory of Agri-Genetics and Breeding, Shanghai 201106, China
- Key Laboratory of Livestock and Poultry Resources (Pig) Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai 201106, China
| | - Jianjun Dai
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China; (Y.L.); (L.S.); (J.D.); (Y.L.); (R.L.)
- Division of Animal Genetic Engineering, Shanghai Municipal Key Laboratory of Agri-Genetics and Breeding, Shanghai 201106, China
- Key Laboratory of Livestock and Poultry Resources (Pig) Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai 201106, China
| | - Yuhua Lv
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China; (Y.L.); (L.S.); (J.D.); (Y.L.); (R.L.)
| | - Rongrong Liao
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China; (Y.L.); (L.S.); (J.D.); (Y.L.); (R.L.)
| | - Xiaohui Shen
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China; (Y.L.); (L.S.); (J.D.); (Y.L.); (R.L.)
| | - Jun Gao
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China; (Y.L.); (L.S.); (J.D.); (Y.L.); (R.L.)
- Division of Animal Genetic Engineering, Shanghai Municipal Key Laboratory of Agri-Genetics and Breeding, Shanghai 201106, China
- Key Laboratory of Livestock and Poultry Resources (Pig) Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai 201106, China
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Li Y, Fu Q, Fang J, Xu Z, Zhang C, Tan L, Liao X, Wu Y. Analysis of ceRNA Network and Identification of Potential Treatment Target and Biomarkers of Endothelial Cell Injury in Sepsis. Genet Test Mol Biomarkers 2024. [PMID: 38501698 DOI: 10.1089/gtmb.2023.0143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/20/2024] Open
Abstract
Background: Sepsis is a complex clinical syndrome caused by a dysregulated host immune response to infection. This study aimed to identify a competing endogenous RNA (ceRNA) network that can greatly contribute to understanding the pathophysiological process of sepsis and determining sepsis biomarkers. Methods: The GSE100159, GSE65682, GSE167363, and GSE94717 datasets were obtained from the Gene Expression Omnibus (GEO) database. Weighted gene coexpression network analysis was performed to find modules possibly involved in sepsis. A long noncoding RNA-microRNA-messenger RNA (lncRNA-miRNA-mRNA) network was constructed based on the findings. Single-cell analysis was performed. Human umbilical vein endothelial cells were treated with lipopolysaccharide (LPS) to create an in vitro model of sepsis for network verification. Reverse transcription-polymerase chain reaction, fluorescence in situ hybridization, and luciferase reporter genes were used to verify the bioinformatic analysis. Result: By integrating data from three GEO datasets, we successfully constructed a ceRNA network containing 18 lncRNAs, 7 miRNAs, and 94 mRNAs based on the ceRNA hypothesis. The lncRNA ZFAS1 was found to be highly expressed in LPS-stimulated endothelial cells and may thus play a role in endothelial cell injury. Univariate and multivariate Cox analyses showed that only SLC26A6 was an independent predictor of prognosis in sepsis. Overall, our findings indicated that the ZFAS1/hsa-miR-449c-5p/SLC26A6 ceRNA regulatory axis may play a role in the progression of sepsis. Conclusion: The sepsis ceRNA network, especially the ZFAS1/hsa-miR-449c-5p/SLC26A6 regulatory axis, is expected to reveal potential biomarkers and therapeutic targets for sepsis management.
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Affiliation(s)
- Yulin Li
- The Department of Emergency, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China
| | - Qinghui Fu
- The Department of SICU, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China
| | - Junjun Fang
- The Department of SICU, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China
| | - Zhipeng Xu
- The Department of SICU, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China
| | - Chunhu Zhang
- The Department of SICU, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China
| | - Longwei Tan
- The Department of SICU, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China
| | - Xin Liao
- The Department of SICU, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China
| | - Yao Wu
- The Department of SICU, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China
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Xu K, Wang X, Hu S, Tang J, Liu S, Chen H, Zhang X, Dai P. LINC00540 promotes sorafenib resistance and functions as a ceRNA for miR-4677-3p to regulate AKR1C2 in hepatocellular carcinoma. Heliyon 2024; 10:e27322. [PMID: 38463802 PMCID: PMC10920722 DOI: 10.1016/j.heliyon.2024.e27322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Revised: 01/24/2024] [Accepted: 02/27/2024] [Indexed: 03/12/2024] Open
Abstract
Sorafenib resistance is one of the main causes of poor prognosis in patients with advanced hepatocellular carcinoma (HCC). Long noncoding RNAs (lncRNAs) function as suppressors or oncogenic factors during tumor progression and drug resistance. Here, to identify therapeutic targets for HCC, the biological mechanisms of abnormally expressed lncRNAs were examined in sorafenib-resistant HCC cells. Specifically, we established sorafenib-resistant HCC cell lines (Huh7-S and SMMC7721-S), which displayed an epithelial-mesenchymal transition (EMT) phenotype. Transcriptome sequencing (RNA-Seq) was performed to established differential lncRNA expression profiles for sorafenib-resistant cells. Through this analysis, we identified LINC00540 as significantly up-regulated in sorafenib-resistant cells and a candidate lncRNA for further mechanistic investigation. Functionally, LINC00540 knockdown promoted sorafenib sensitivity and suppressed migration, invasion, EMT and the activation of PI3K/AKT signaling pathway in sorafenib-resistant HCC cells, whereas overexpression of LINC00540 resulted in the opposite effects in parental cells. LINC00540 functions as a competing endogenous RNA (ceRNA) by competitively binding to miR-4677-3p , thereby promoting AKR1C2 expression. This is the first study that demonstrates a role for LINC00540 in enhancing sorafenib resistance, migration and invasion of HCC cells through the LINC00540/miR-4677-3p/AKR1C2 axis, suggesting that LINC00540 may represent a potential therapeutic target and prognosis biomarker for HCC.
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Affiliation(s)
- Kaixuan Xu
- National Engineering Research Center for Miniaturized Detection Systems, College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Xinxin Wang
- National Engineering Research Center for Miniaturized Detection Systems, College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Shuwei Hu
- National Engineering Research Center for Miniaturized Detection Systems, College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Jiaxuan Tang
- National Engineering Research Center for Miniaturized Detection Systems, College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Shihui Liu
- National Engineering Research Center for Miniaturized Detection Systems, College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Hui Chen
- The University Hospital of Northwest University, Xi'an, 710069, China
| | - Xiaobin Zhang
- The University Hospital of Northwest University, Xi'an, 710069, China
| | - Penggao Dai
- National Engineering Research Center for Miniaturized Detection Systems, College of Life Sciences, Northwest University, Xi'an, 710069, China
- Shaanxi Lifegen Co., Ltd, Xi'an, 712000, China
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Shao ZC, Sun WK, Deng QQ, Cheng L, Huang X, Hu LK, Li HN. Identification of Key lncRNAs in Gout Under Copper Death and Iron Death Mechanisms: A Study Based on ceRNA Network Analysis and Random Forest Algorithm. Mol Biotechnol 2024:10.1007/s12033-024-01099-5. [PMID: 38472694 DOI: 10.1007/s12033-024-01099-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 01/17/2024] [Indexed: 03/14/2024]
Abstract
This study focused on identifying potential key lncRNAs associated with gout under the mechanisms of copper death and iron death through ceRNA network analysis and Random Forest (RF) algorithm, which aimed to provide new insights into the molecular mechanisms of gout, and potential molecular targets for future therapeutic strategies of gout. Initially, we conducted an in-depth bioinformatics analysis of gout microarray chips to screen the key cuproptosis-related genes (CRGs) and key ferroptosis-related genes (FRGs). Using these data, we constructed a key ceRNA network for gout. Finally, key lncRNAs associated with gout were identified through the RF algorithm combined with ROC curves, and validated using the Comparative Toxicogenomics Database (CTD). We successfully identified NLRP3, LIPT1, and DBT as key CRGs associated with gout, and G6PD, PRKAA1, LIG3, PHF21A, KLF2, PGRMC1, JUN, PANX2, and AR as key FRGs associated with gout. The key ceRNA network identified four downregulated key lncRNAs (SEPSECS-AS1, LINC01054, REV3L-IT1, and ZNF883) along with three downregulated mRNAs (DBT, AR, and PRKAA1) based on the ceRNA theory. According to CTD validation inference scores and biological functions of target mRNAs, we identified a potential gout-associated lncRNA ZNF883/hsa-miR-539-5p/PRKAA1 regulatory axis. This study identified the key lncRNA ZNF883 in the context of copper death and iron death mechanisms related to gout for the first time through the application of ceRNA network analysis and the RF algorithm, thereby filling a research gap in this field and providing new insights into the molecular mechanisms of gout. We further found that lncRNA ZNF883 might function in gout patients by regulating PRKAA1, the mechanism of which was potentially related to uric acid reabsorption in the proximal renal tubules and inflammation regulation. The proposed lncRNA ZNF883/hsa-miR-539-5p/PRKAA1 regulatory axis might represent a potential RNA regulatory pathway for controlling the progression of gout disease. This discovery offered new molecular targets for the treatment of gout, and had significant implications for future therapeutic strategies in managing the gout.
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Affiliation(s)
- Zi-Chen Shao
- Jiangxi University of Chinese Medicine, Nanchang, 330004, Jiangxi, China
| | - Wei-Kang Sun
- Jiangxi University of Chinese Medicine, Nanchang, 330004, Jiangxi, China
| | - Qin-Qin Deng
- Jiangxi University of Chinese Medicine, Nanchang, 330004, Jiangxi, China
| | - Ling Cheng
- Jiangxi University of Chinese Medicine, Nanchang, 330004, Jiangxi, China
| | - Xin Huang
- Jiangxi University of Chinese Medicine, Nanchang, 330004, Jiangxi, China
| | - Lie-Kui Hu
- Jiangxi University of Chinese Medicine, Nanchang, 330004, Jiangxi, China
| | - Hua-Nan Li
- Affiliated Hospital of Jiangxi University of Chinese Medicine, No.445, Bayi Avenue, Nanchang, 330006, Jiangxi, China.
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26
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Wang Y, Wang X, Sun H, Zhang Z, Gu J. LncRNA MCM3AP-AS1 promotes chemoresistance in triple-negative breast cancer through the miR-524-5p/RBM39 axis. Mol Cell Biochem 2024:10.1007/s11010-023-04908-8. [PMID: 38472681 DOI: 10.1007/s11010-023-04908-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 11/25/2023] [Indexed: 03/14/2024]
Abstract
Triple-negative breast cancer (TNBC) is the most lethal subtype of BC, with unfavorable treatment outcomes. Evidence suggests the engagement of lncRNA MCM3AP-AS1 in BC development. This study investigated the action of MCM3AP-AS1 in chemoresistance of TNBC cells. Drug-resistant TNBC cell lines SUM159PTR and MDA-MB-231R were constructed by exposure to increasing concentrations of doxorubicin/docetaxel (DOX/DXL). MCM3AP-AS1 and miR-524-5p expression levels were determined by RT-qPCR. RNA binding motif 39 (RBM39) level was measured using Western blot. Cell viability and apoptosis were assessed by CCK-8 assay and flow cytometry. The targeted binding of miR-524-5p with MCM3AP-AS1 or RBM39 was predicted by ECORI database and validated by dual-luciferase assays. The gain-and-loss of function assays were conducted in cells to investigate the interactions among MCM3AP-AS1, miR-524-5p, and RBM39. TNBC xenograft mouse models were established through subcutaneous injection of MCM3AP-AS1-silencing MDA-MB-231R cells and intraperitoneally administrated with DOX/DXL to verify the role of MCM3AP-AS1 in vivo. MCM3AP-AS1 was upregulated in drug-resistant TNBC cells, and MCM3AP-AS1 silencing could sensitize drug-resistant TNBC cells to chemotherapeutic drugs by promoting apoptosis. MCM3AP-AS1 targeted miR-524-5p. After DOX/DXL treatment, miR-524-5p inhibition partially reversed the effect of MCM3AP-AS1 silencing on inhibiting chemoresistance and promoting apoptosis of drug-resistant TNBC cells. miR-524-5p targeted RBM39. Silencing MCM3AP-AS1 promoted apoptosis via the miR-524-5p/RBM39 axis, thereby enhancing chemosensitivity of drug-resistant TNBC cells. MCM3AP-AS1 knockdown upregulated miR-524-5p, downregulated RBM39, and restrained tumor development in vivo. MCM3AP-AS1 silencing potentiates apoptosis of drug-resistant TNBC cells by upregulating miR-524-5p and downregulating RBM39, thereby suppressing chemoresistance in TNBC.
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Affiliation(s)
- Yueping Wang
- Department of Medical Laboratory Science, Anhui No. 2 Provincial People's Hospital, 1868 #Dangshan Road, North 2nd Ring, Hefei, 230041, Anhui, China
- Department of Molecular and Cellular Biology, University of Connecticut, Storrs, CT, 06269, USA
| | - Xuedong Wang
- Department of Medical Laboratory Science, Anhui No. 2 Provincial People's Hospital, 1868 #Dangshan Road, North 2nd Ring, Hefei, 230041, Anhui, China.
| | - Haiyi Sun
- School of Clinical Medicine, Anhui Medical University, Hefei, 230032, Anhui, China
| | - Ziyun Zhang
- Department of Medical Laboratory Science, Anhui No. 2 Provincial People's Hospital, 1868 #Dangshan Road, North 2nd Ring, Hefei, 230041, Anhui, China
| | - Juan Gu
- Department of Medical Laboratory Science, Anhui No. 2 Provincial People's Hospital, 1868 #Dangshan Road, North 2nd Ring, Hefei, 230041, Anhui, China
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Zhang N, Song GY, Yu QH, Fan XM, Zhang WS, Hu YJ, Chao TZ, Wu YY, Duan SY, Wang F, Du RP, Xu P. Evaluation of the lncRNA-miRNA-mRNA ceRNA network in lungs of miR-147 -/- mice. Front Pharmacol 2024; 15:1335374. [PMID: 38510653 PMCID: PMC10953689 DOI: 10.3389/fphar.2024.1335374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 02/20/2024] [Indexed: 03/22/2024] Open
Abstract
Background: Previous studies have documented important roles for microRNA-147 (miR-147) in inflammation, radiation-induced injury, cancer, and a range of other diseases. Murine lungs exhibit high levels of miRNA, mRNA, and lncRNA expression. However, very little research to date has focused on the lncRNA-miRNA-mRNA competing endogenous RNA (ceRNA) networks associated with miR-147, and the regulation of lncRNAs and miRNAs in this setting remains poorly understood. Methods: After establishing a miR-147-/- model mouse, samples of lung tissue were harvested for RNA-sequencing, and differentially expressed lncRNAs, miRNAs, and mRNAs were identified. The miRNA targets of these lncRNAs and the identified miRNAs were first overlapped to facilitate the prediction of target mRNAs, with analyses then examining the overlap between these targets and mRNAs that were differentially expressed. Then, these target mRNAs were subjected to pathway enrichment analyses. These results were ultimately used to establish a miR-147-related ceRNA network. Results: Relative to wild-type mice, the lungs of miR-147-/- mice exhibited 91, 43, and 71 significantly upregulated lncRNAs, miRNAs, and mRNAs, respectively, together with 114, 31, and 156 that were significantly downregulated. The lncRNA-miRNA-mRNA network established based on these results led to the identification of Kcnh6 as a differentially expressed hub gene candidate and enabled the identification of a range of regulatory relationships. KEGG pathway enrichment showed that the mRNA targets of differentially expressed lncRNAs and miRNAs in the mice were associated with tumor-related signaling, endometrial cancer, bladder cancer, and ErbB signaling. Conclusion: These results suggest that the identified ceRNA network in miR-147-/- mice shapes tumor-associated signaling activity, with miR-147 potentially regulating various lncRNAs and miRNAs through Kcnh6, ultimately influencing tumorigenesis. Future studies of the lncRNA, miRNA, and mRNA regulatory targets shown to be associated with miR-147 in the present study may ultimately lead to the identification of novel clinically relevant targets through which miR-147 shapes the pathogenesis of cancer and other diseases.
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Affiliation(s)
- Nan Zhang
- Laboratory of Radiation-Induced Diseases and Molecule-Targeted Drugs, School of Food and Biomedicine, Zaozhuang University, Zaozhuang, Shandong, China
| | - Gui-Yuan Song
- Laboratory of Radiation-Induced Diseases and Molecule-Targeted Drugs, School of Food and Biomedicine, Zaozhuang University, Zaozhuang, Shandong, China
- School of Pharmacy, Weifang Medical University, Weifang, Shandong, China
| | - Qing-Hua Yu
- Laboratory of Radiation-Induced Diseases and Molecule-Targeted Drugs, School of Food and Biomedicine, Zaozhuang University, Zaozhuang, Shandong, China
- School of Public Health, Weifang Medical University, Weifang, Shandong, China
| | - Xin-Ming Fan
- Department of Radiotherapy, Zaozhuang Municipal Hospital, Zaozhuang, Shandong, China
| | - Wen-Shuo Zhang
- Department of Radiotherapy, Zaozhuang Municipal Hospital, Zaozhuang, Shandong, China
| | - Yong-Jian Hu
- Henan Key Laboratory of Medical Tissue Regeneration, Xinxiang Medical University, Xinxiang, Henan, China
| | - Tian-Zhu Chao
- Laboratory of Radiation-Induced Diseases and Molecule-Targeted Drugs, School of Food and Biomedicine, Zaozhuang University, Zaozhuang, Shandong, China
| | - Yao-Yao Wu
- Laboratory of Radiation-Induced Diseases and Molecule-Targeted Drugs, School of Food and Biomedicine, Zaozhuang University, Zaozhuang, Shandong, China
| | - Shu-Yan Duan
- Laboratory of Radiation-Induced Diseases and Molecule-Targeted Drugs, School of Food and Biomedicine, Zaozhuang University, Zaozhuang, Shandong, China
| | - Fei Wang
- Laboratory of Radiation-Induced Diseases and Molecule-Targeted Drugs, School of Food and Biomedicine, Zaozhuang University, Zaozhuang, Shandong, China
| | - Rui-Peng Du
- Laboratory of Radiation-Induced Diseases and Molecule-Targeted Drugs, School of Food and Biomedicine, Zaozhuang University, Zaozhuang, Shandong, China
| | - Ping Xu
- Laboratory of Radiation-Induced Diseases and Molecule-Targeted Drugs, School of Food and Biomedicine, Zaozhuang University, Zaozhuang, Shandong, China
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Xiong Y, Kong X, Tu S, Xin W, Wei Y, Yi S, Wan R, Xiao W. LINC02086 inhibits ferroptosis and promotes malignant phenotypes of pancreatic cancer via miR-342-3p/CA9 axis. Funct Integr Genomics 2024; 24:49. [PMID: 38438595 DOI: 10.1007/s10142-024-01329-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Revised: 02/22/2024] [Accepted: 02/27/2024] [Indexed: 03/06/2024]
Abstract
Long noncoding RNAs (lncRNAs) play important roles in modulating the tumorigenesis and progression of malignant tumors. LINC02086 is a newly identified oncogene associated with tumorigenesis, but its role in pancreatic cancer (PC) has not been fully elucidated. In this study we examined the expression levels of LINC02086, miR-342-3p, and CA9 in PC. The relationship of ferroptosis with these factors was analyzed by detecting the expression levels of Fe2+, reactive oxygen species (ROS), and ferroptosis marker proteins. The expression of these genes was altered to observe their effects on cell proliferation, migration, and invasion ability. Bioinformatics was used to predict target genes, and the binding relationship was verified luciferase reporter assay. Finally, the function of LINC02086 was evaluated in vivo. The findings suggest that LINC02086 is highly expressed in PC tissues and cell lines and is correlated with a poor prognosis. In vitro experiments demonstrated that LINC02086 knockdown promoted ferroptosis in PC cells to suppress their malignant phenotype. LINC02086 acts as a competitive endogenous RNA that adsorbed miR-342-3p. miR-342-3p hinders the malignant progression of PC by promoting ferroptosis. In addition, miR-342-3p targets CA9 and affects its function. Further mechanistic studies revealed that LINC02086 inhibits ferroptosis and promotes PC progression by acting as a sponge for miR-342-3p to upregulate CA9 expression. In vivo experiments further confirmed this mechanism. Taken together, LINC02086 upregulates CA9 expression by competitively binding with miR-342-3p, thereby inhibiting ferroptosis in PC cells and promoting their malignant phenotype. The results of our study provide new insights into how LINC02086 contributes to the progression of PC.
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Affiliation(s)
- Yuanpeng Xiong
- Department of General Surgery, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, 330006, Jiangxi, China
| | - Xiaoyu Kong
- Department of Clinical Microbiology, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, 330006, Jiangxi, China
| | - Shuju Tu
- Department of General Surgery, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, 330006, Jiangxi, China
| | - Wanpeng Xin
- Department of General Surgery, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, 330006, Jiangxi, China
| | - Yongyang Wei
- Department of General Surgery, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, 330006, Jiangxi, China
| | - Siqing Yi
- Department of General Surgery, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, 330006, Jiangxi, China
| | - Renhua Wan
- Department of General Surgery, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, 330006, Jiangxi, China
| | - Weidong Xiao
- Department of General Surgery, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, 330006, Jiangxi, China.
- Institute of Digestive Surgery, Nanchang University, Nanchang, 330006, Jiangxi, China.
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Wang P, Liu Z, Zhang X, Huo H, Wang L, Dai H, Yang F, Zhao G, Huo J. Integrated analysis of lncRNA, miRNA and mRNA expression profiles reveals regulatory pathways associated with pig testis function. Genomics 2024; 116:110819. [PMID: 38432498 DOI: 10.1016/j.ygeno.2024.110819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 02/12/2024] [Accepted: 02/28/2024] [Indexed: 03/05/2024]
Abstract
Long noncoding RNA (lncRNA) and microRNA (miRNA) are known to play pivotal roles in mammalian testicular function and spermatogenesis. However, their impact on porcine male reproduction has yet to be well unraveled. Here, we sequenced and identified lncRNA and miRNA expressed in the testes of Chinese indigenous Banna mini-pig inbred line (BMI) and introduced Western Duroc (DU) and Large White (LW) pigs. By pairwise comparison (BMI vs DU, BMI vs LW, and DU vs LW), we found the gene expression differences in the testes between Chinese local pigs and introduced Western commercial breeds were more striking than those between introduced commercial breeds. Furthermore, we found 1622 co-differentially expressed genes (co-DEGs), 122 co-differentially expressed lncRNAs (co-DELs), 39 co-differentially expressed miRNAs (co-DEMs) in BMI vs introduced commercial breeds (DU and LW). Functional analysis revealed that these co-DEGs and co-DELs/co-DEMs target genes were enriched in male sexual function pathways, including MAPK, AMPK, TGF-β/Smad, Hippo, NF-kappa B, and PI3K/Akt signaling pathways. Additionally, we established 10,536 lncRNA-mRNA, 11,248 miRNA-mRNA pairs, and 62 ceRNA (lncRNA-miRNA-mRNA) networks. The ssc-miR-1343 had the most interactive factors in the ceRNA network, including 20 mRNAs and 3 lncRNAs, consisting of 56 ceRNA pairs. These factors played extremely important roles in the regulation of testis function as key nodes in the interactive regulatory network. Our results provide insight into the functional roles of lncRNAs and miRNAs in porcine testis and offer a valuable resource for understanding the differences between Chinese indigenous and introduced Western pigs.
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Affiliation(s)
- Pei Wang
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Zhipeng Liu
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Xia Zhang
- College of Life Science, Lyuliang University, Lvliang 033001, China
| | - Hailong Huo
- Yunnan Open University, Kunming 650500, China
| | - Lina Wang
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Hongmei Dai
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Fuhua Yang
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Guiying Zhao
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China.
| | - Jinlong Huo
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China.
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Wang D, Zhao X, Li S, Guo H, Li S, Yu D. The impact of LncRNA-SOX2-OT/let-7c-3p/SKP2 Axis on head and neck squamous cell carcinoma progression: Insights from bioinformatics analysis and experimental validation. Cell Signal 2024; 115:111018. [PMID: 38110167 DOI: 10.1016/j.cellsig.2023.111018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 12/01/2023] [Accepted: 12/15/2023] [Indexed: 12/20/2023]
Abstract
BACKGROUND LncRNA SRY-box transcription factor 2 overlapping transcript (SOX2-OT) is linked to multiple cancers, but its specific role and mechanism in head and neck squamous cell carcinoma (HNSCC) remain poorly understood. METHODS We harnessed clinical data and HNSCC transcriptome profiles from UCSC Xena, TCGA, and GEO databases. Employing various algorithms, we assessed the correlation between SOX2-OT expression and the HNSCC immune microenvironment. Differential expression analysis identified immune-enriched miRNAs (DEmiRNAs) and mRNAs (DEmRNAs). Utilizing miRanda, miRWalk, and Cytoscape, we constructed a ceRNA network encompassing SOX2-OT, DEmiRNAs, and DEmRNAs. A Sankey diagram visualized pivotal SOX2-OT-miRNA-mRNA-pathways. Functional assays validated SOX2-OT silencing effects in HNSCC cells. Luciferase reporter assays verified SOX2-OT/let-7c-3p/SKP2 relationships. Additionally, a xenograft mouse model revealed SOX2-OT's impact on xenograft growth and lung metastasis. RESULTS SOX2-OT expression demonstrated a predominantly positive correlation with B lineage and VTCN1, while manifesting a negative correlation with Neutrophil and CD47 in HNSCC tissues. We discerned a ceRNA network comprising 65 DEmiRNAs and 116 DEmRNAs, while a protein-protein interaction (PPI) network revealed 97 protein nodes among DEmRNAs. Notably, the Sankey diagram spotlighted six key DEmRNAs intricately linked to the SOX2-OT-regulated DEmiRNAs immune-related pathway. Experimental assays established that SOX2-OT silencing exerted inhibitory effects on cell proliferation, migration, tumor growth, and lung metastasis within HNSCC cells, both in vitro and in vivo. We identified let-7c-3p as a target miRNA of SOX2-OT and SKP2 as a target mRNA of let-7c-3p. CONCLUSIONS Our study establishes the critical SOX2-OT/let-7c-3p/SKP2 axis as a pivotal regulator of HNSCC tumorigenesis and metastasis.
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Affiliation(s)
- Di Wang
- Department of Otolaryngology Head and Neck Surgery, The Second Hospital of Jilin University, People's Republic of China
| | - Xue Zhao
- Department of Otolaryngology Head and Neck Surgery, The Second Hospital of Jilin University, People's Republic of China
| | - Shuang Li
- Department of Otolaryngology Head and Neck Surgery, The Second Hospital of Jilin University, People's Republic of China
| | - Haixian Guo
- Department of Otolaryngology Head and Neck Surgery, The Second Hospital of Jilin University, People's Republic of China
| | - Shaonan Li
- Department of Otolaryngology Head and Neck Surgery, The Second Hospital of Jilin University, People's Republic of China
| | - Dan Yu
- Department of Otolaryngology Head and Neck Surgery, The Second Hospital of Jilin University, People's Republic of China.
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Cai Z, Cai Y, Huang J, Zhang J. Circ_0027446 promotes malignant development of glioblastoma by interacting with miR-346 to up-regulate PGK1. Metab Brain Dis 2024; 39:361-371. [PMID: 38091240 DOI: 10.1007/s11011-023-01332-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 11/27/2023] [Indexed: 03/22/2024]
Abstract
Circular RNAs (circRNAs) can play essential roles in tumor development, including glioblastoma (GBM). The current study was performed to explore the function and mechanism of circ_0027446 in GBM progression. Circ_0027446, microRNA-346 (miR-346) and Phosphoglycerate kinase 1 (PGK1) levels were detected using reverse transcription-quantitative polymerase chain reaction assay. Cell behaviors were examined using Cell Counting Kit-8 assay, colony formation assay, EdU assay, flow cytometry, and transwell assay. Glycolytic metabolism was analyzed by commercial kits. The protein level was determined via western blot. The target interaction was analyzed by dual-luciferase reporter assay. Circ_0027446 function in vivo was explored by tumor xenograft assay. Circ_0027446 expression was significantly up-regulated in GBM samples and cells. Circ_0027446 down-regulation suppressed proliferation, invasion, glycolytic metabolism and enhanced apoptosis of GBM cells. MiR-346 was a target of circ_0027446, and circ_0027446 promoted GBM progression by sponging miR-346. PGK1 acted as a target gene of miR-346, and circ_0027446 interacted with miR-346 to regulate PGK1 expression. Overexpression of miR-346 inhibited malignant behaviors of GBM cells through down-regulating PGK1. Circ_0027446 contributed to tumor growth in vivo via miR-346/PGK1 axis. The current evidences demonstrated that circ_0027446 facilitated malignant progression of GBM through binding to miR-346 to up-regulate PGK1.
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Affiliation(s)
- Zifeng Cai
- Inpatient Department District N22, Quanzhou First Hospital Affiliated to Fujian Medical University, Chendong Branch of Quanzhou 1st Hospital, No. 7, Row 11, Qian Yi Shan Zhuang Shi Wai Yuan, Fengze District, Quanzhou, 362000, China
| | - Yonghui Cai
- Inpatient Department District N22, Quanzhou First Hospital Affiliated to Fujian Medical University, Chendong Branch of Quanzhou 1st Hospital, No. 7, Row 11, Qian Yi Shan Zhuang Shi Wai Yuan, Fengze District, Quanzhou, 362000, China
| | - Jincong Huang
- Inpatient Department District N22, Quanzhou First Hospital Affiliated to Fujian Medical University, Chendong Branch of Quanzhou 1st Hospital, No. 7, Row 11, Qian Yi Shan Zhuang Shi Wai Yuan, Fengze District, Quanzhou, 362000, China
| | - Jinning Zhang
- Inpatient Department District N22, Quanzhou First Hospital Affiliated to Fujian Medical University, Chendong Branch of Quanzhou 1st Hospital, No. 7, Row 11, Qian Yi Shan Zhuang Shi Wai Yuan, Fengze District, Quanzhou, 362000, China.
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Huang B, Ou G, Zhang N. Identification of key regulatory molecules in the early development stage of Alzheimer's disease. J Cell Mol Med 2024; 28:e18151. [PMID: 38429903 PMCID: PMC10907834 DOI: 10.1111/jcmm.18151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Revised: 12/19/2023] [Accepted: 01/05/2024] [Indexed: 03/03/2024] Open
Abstract
Alzheimer's disease (AD) is one of the most common neurodegenerative diseases, the incidence of which increases with age, and the pathological changes in the brain are irreversible. Recent studies have highlighted the essential role of long noncoding RNAs (lncRNAs) in AD by acting as competing endogenous RNAs (ceRNAs). Our aim was to construct lncRNA-associated ceRNA regulatory networks composed of potential biomarkers for the early stage of AD. AD related datasets come from AlzData and GEO databases. The R package 'Limma' identifies differentially expressed genes (DEGs), Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) databases for functional enrichment analysis. Protein-protein interactions (PPIs) in DEGs were constructed in the STRING database, and Cytoscape software identified DEGs. Convergent functional genomics (CFG) analysis of differentially expressed hub genes (referred to as early-DEGs) in the brain before the development of AD pathology. The AlzData database analyses the expression levels of early-DEGs in different nerve cells. The lncRNA-miRNA-mRNA regulatory network was established according to the ceRNA hypothesis. We identified four lncRNAs (XIST, NEAT1, KCNQ1OT1 and HCG18) and four miRNAs (hsa-let-7c-5p, hsa-miR-107, hsa-miR-129-2-3p and hsa-miR-214-3p) were preliminarily identified as potential biomarkers for early AD, competitively regulating Atp6v0b, Atp6v1e1 Atp6v1f and Syt1. This study indicates that NEAT1, XIST, HCG18 and KCNQ1OT1 act as ceRNAs in competitive binding with miRNAs to regulate the expression of Atp6v0b, Atp6v1e1, Atp6v1f and Syt1 before the occurrence of pathological changes in AD.
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Affiliation(s)
- Bin Huang
- Clinical LaboratoryFifth Affiliated Hospital of Southern Medical UniversityGuangzhouChina
| | - Guan‐yong Ou
- School of MedicineSouthern University of Science and TechnologyShenzhenChina
| | - Ni Zhang
- Department of PhysiologyShantou University Medical CollegeShantouChina
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Jiang T, Xu L, Qu X, Li R, Cheng Y, He H. Hsa_circ_0014606 Derived from Exosomes Promotes Gastric Carcinoma Tumorigenesis and Proliferation by Sponging miR-514b-3p to Upregulate HNRNPC. Dig Dis Sci 2024; 69:811-820. [PMID: 38217675 DOI: 10.1007/s10620-023-08254-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 12/14/2023] [Indexed: 01/15/2024]
Abstract
Gastric cancer is a common malignant tumor, and due to its insidious onset and limited screening methods, most patients are diagnosed with advanced disease and have a poor prognosis. The circRNA in exosomes has an essential role in cancer diagnosis and treatment. However, the part of hsa_circ_0014606 within exosomes in gastric cancer progression is unclear. Firstly, we extracted exosomes from the serum of gastric cancer patients and healthy individuals by ultracentrifugation and analyzed the expression of hsa_circ_0014606 in both exosomes; then knocked down hsa_circ_0014606 in vivo and in vitro, respectively, to observe its effect on the physiological function of gastric cancer cells; finally, we used bioinformatics to screen hsa_circ_0014606 targeting miRNAs and mRNAs, and experiments were performed to verify the interrelationship between the three. The results showed that the level of hsa_circ_0014606 in the serum exosomes of gastric cancer patients was significantly higher than that of the healthy population. The knockdown of hsa_circ_0014606 slowed the proliferation of gastric cancer cells, significantly reduced migration and invasion ability, accelerated apoptosis, and reduced tumor size in mice. In addition, the expression of hsa_circ_0014606 was negatively correlated with the expression of miR-514b-3p and positively correlated with the expression of heterogeneous nuclear ribonucleoprotein C (HNRNPC). In conclusion, hsa_circ_0014606 exerted a pro-cancer effect indirectly through miR-514b-3p targeting gene HNRNPC, and this study provides a new potential target for treating gastric cancer.
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Affiliation(s)
- Tao Jiang
- Department of Otolaryngology, Affiliated Zhongshan Hospital of Dalian University, Dalian, Liaoning, China
| | - Lingling Xu
- Department of Medical Oncology, The Second Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Xiaona Qu
- Department of Medical Oncology, The Second Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Rui Li
- Department of Otolaryngology, Affiliated Zhongshan Hospital of Dalian University, Dalian, Liaoning, China
| | - Ye Cheng
- Department of Medical Oncology, The Second Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Hongmei He
- Department of Medical Oncology, The Second Hospital of Dalian Medical University, Dalian, Liaoning, China.
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Liu X, Zhang Y, Liu Z, Gao Y, Yuan L, Zeng D, Tan F, Wan H, Pei Z. METTL3 as a novel diagnosis and treatment biomarker and its association with glycolysis, cuproptosis and ceRNA in oesophageal carcinoma. J Cell Mol Med 2024; 28:e18195. [PMID: 38429907 PMCID: PMC10907846 DOI: 10.1111/jcmm.18195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 11/22/2023] [Accepted: 02/09/2024] [Indexed: 03/03/2024] Open
Abstract
METTL3 has been shown to be involved in regulating a variety of biological processes. However, the relationship between METTL3 expression and glycolysis, cuproptosis-related genes and the ceRNA network in oesophageal carcinoma (ESCA) remains unclear. ESCA expression profiles from databases were obtained, and target genes were identified using differential analysis and visualization. Immunohistochemistry (IHC) staining assessed METTL3 expression differences. Functional enrichment analysis using GO, KEGG and GSEA was conducted on the co-expression profile of METTL3. Cell experiments were performed to assess the effect of METTL3 interference on tumour cells. Correlation and differential analyses were carried out to assess the relationship between METTL3 with glycolysis and cuproptosis. qRT-PCR was used to validate the effects of METTL3 interference on glycolysis-related genes. Online tools were utilized to screen and construct ceRNA networks based on the ceRNA theory. METTL3 expression was significantly higher in ESCA compared to the controls. The IHC results were consistent with the above results. Enrichment analysis revealed that METTL3 is involved in multiple pathways associated with tumour development. Significant correlations were observed between METTL3 and glycolysis-related genes and cuproptosis-related gene. Experiments confirmed that interfered with METTL3 significantly inhibited glucose uptake and lactate production in tumour cells, and affected the expression of glycolytic-related genes. Finally, two potential ceRNA networks were successfully predicted and constructed. Our study establishes the association between METTL3 overexpression and ESCA progression. Additionally, we propose potential links between METTL3 and glycolysis, cuproptosis and ceRNA, presenting a novel targeted therapy strategy for ESCA.
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Affiliation(s)
- Xu‐Sheng Liu
- Department of Nuclear Medicine, Hubei Provincial Clinical Research Center for precision Diagnosis and Treatment of liver cancerTaihe Hospital, Hubei University of MedicineShiyanChina
- Hubei Provincial Clinical Research Center for Umbilical Cord Blood Hematopoietic Stem CellsTaihe Hospital, Hubei University of MedicineShiyanChina
| | - Yu Zhang
- Department of Nuclear Medicine, Hubei Provincial Clinical Research Center for precision Diagnosis and Treatment of liver cancerTaihe Hospital, Hubei University of MedicineShiyanChina
| | - Zi‐Yue Liu
- Department of Nuclear Medicine, Hubei Provincial Clinical Research Center for precision Diagnosis and Treatment of liver cancerTaihe Hospital, Hubei University of MedicineShiyanChina
| | - Yan Gao
- Department of Nuclear Medicine, Hubei Provincial Clinical Research Center for precision Diagnosis and Treatment of liver cancerTaihe Hospital, Hubei University of MedicineShiyanChina
| | - Ling‐Ling Yuan
- Department of PathologyTaihe Hospital, Hubei University of MedicineShiyanChina
| | - Dao‐Bing Zeng
- Department of Nuclear Medicine, Hubei Provincial Clinical Research Center for precision Diagnosis and Treatment of liver cancerTaihe Hospital, Hubei University of MedicineShiyanChina
| | - Fan Tan
- Department of Nuclear Medicine, Hubei Provincial Clinical Research Center for precision Diagnosis and Treatment of liver cancerTaihe Hospital, Hubei University of MedicineShiyanChina
| | - Hua‐Bing Wan
- Department of Nuclear Medicine, Hubei Provincial Clinical Research Center for precision Diagnosis and Treatment of liver cancerTaihe Hospital, Hubei University of MedicineShiyanChina
| | - Zhi‐Jun Pei
- Department of Nuclear Medicine, Hubei Provincial Clinical Research Center for precision Diagnosis and Treatment of liver cancerTaihe Hospital, Hubei University of MedicineShiyanChina
- Hubei Provincial Clinical Research Center for Umbilical Cord Blood Hematopoietic Stem CellsTaihe Hospital, Hubei University of MedicineShiyanChina
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Hao W, Yang W, Yang Y, Cheng T, Wei T, Tang L, Qian N, Yang Y, Li X, Jiang H, Wang M. Identification of lncRNA-miRNA-mRNA Networks in the Lenticular Nucleus Region of the Brain Contributes to Hepatolenticular Degeneration Pathogenesis and Therapy. Mol Neurobiol 2024; 61:1673-1686. [PMID: 37759104 PMCID: PMC10896925 DOI: 10.1007/s12035-023-03631-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 08/31/2023] [Indexed: 09/29/2023]
Abstract
Long non-coding RNAs (lncRNAs) are a recently discovered group of non-coding RNAs that play a crucial role in the regulation of various human diseases, especially in the study of nervous system diseases which has garnered significant attention. However, there is limited knowledge on the identification and function of lncRNAs in hepatolenticular degeneration (HLD). The objective of this study was to identify novel lncRNAs and determine their involvement in the networks associated with HLD. We conducted a comprehensive analysis of RNA sequencing (RNA-seq) data, reverse transcription-quantitative polymerase chain reaction (RT-qPCR), and computational biology to identify novel lncRNAs and explore their potential mechanisms in HLD. We identified 212 differently expressed lncRNAs, with 98 upregulated and 114 downregulated. Additionally, 32 differently expressed mRNAs were found, with 15 upregulated and 17 downregulated. We obtained a total of 1131 pairs of co-expressed lncRNAs and mRNAs by Pearson correlation test and prediction and annotation of the lncRNA-targeted miRNA-mRNA network. The differential lncRNAs identified in this study were found to be involved in various biological functions and signaling pathways. These include translational initiation, motor learning, locomotors behavior, dioxygenase activity, integral component of postsynaptic membrane, neuroactive ligand-receptor interaction, nuclear factor-kappa B (NF-κB) signaling pathway, cholinergic synapse, sphingolipid signaling pathway, and Parkinson's disease signaling pathway, as revealed by the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses. Six lncRNAs, including XR_001782921.1 (P < 0.01), XR_ 001780581.1 (P < 0.01), ENSMUST_00000207119 (P < 0.01), XR_865512.2 (P < 0.01), TCONS_00005916 (P < 0.01), and TCONS_00020683 (P < 0.01), showed significant differences in expression levels between the model group and normal group by RT-qPCR. Among these, four lncRNAs (TCONS_00020683, XR_865512.2, XR_001780581.1, and ENSMUST00000207119) displayed a high degree of conservation. This study provides a unique perspective for the pathogenesis and therapy of HLD by constructing the lncRNA-miRNA-mRNA network. This insight provides a foundation for future exploration in this field.
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Affiliation(s)
- Wenjie Hao
- Department of Neurology, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, China
- Center for Xin'an Medicine and Modernization of Traditional Chinese Medicine of IHM, Anhui University of Chinese Medicine, Hefei, China
- Key Laboratory of Xin'an Medicine of the Ministry of Education, Anhui University of Chinese Medicine, Hefei, China
| | - Wenming Yang
- Department of Neurology, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, China.
- Center for Xin'an Medicine and Modernization of Traditional Chinese Medicine of IHM, Anhui University of Chinese Medicine, Hefei, China.
- Key Laboratory of Xin'an Medicine of the Ministry of Education, Anhui University of Chinese Medicine, Hefei, China.
| | - Yue Yang
- Department of Neurology, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, China
| | - Ting Cheng
- Department of Graduate, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Taohua Wei
- Department of Neurology, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, China
- Center for Xin'an Medicine and Modernization of Traditional Chinese Medicine of IHM, Anhui University of Chinese Medicine, Hefei, China
| | - Lulu Tang
- Department of Neurology, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, China
- Center for Xin'an Medicine and Modernization of Traditional Chinese Medicine of IHM, Anhui University of Chinese Medicine, Hefei, China
| | - Nannan Qian
- Key Laboratory of Xin'an Medicine of the Ministry of Education, Anhui University of Chinese Medicine, Hefei, China
| | - Yulong Yang
- Key Laboratory of Xin'an Medicine of the Ministry of Education, Anhui University of Chinese Medicine, Hefei, China
| | - Xiang Li
- Department of Neurology, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, China
| | - Hailin Jiang
- Center for Xin'an Medicine and Modernization of Traditional Chinese Medicine of IHM, Anhui University of Chinese Medicine, Hefei, China
| | - Meixia Wang
- Department of Neurology, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, China
- Center for Xin'an Medicine and Modernization of Traditional Chinese Medicine of IHM, Anhui University of Chinese Medicine, Hefei, China
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Zhang R, Liu W, Zhang Z. miR-306-5p is involved in chitin metabolism in Aedes albopictus pupae via linc8338-miR-306-5p-XM_019678125.2 axis. Pestic Biochem Physiol 2024; 200:105811. [PMID: 38582583 DOI: 10.1016/j.pestbp.2024.105811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 01/31/2024] [Accepted: 02/02/2024] [Indexed: 04/08/2024]
Abstract
Aedes albopictus can transmit several lethal arboviruses. This mosquito has become a sever public health threat due to its rapidly changing global distribution. Chitin, which is the major component of the cuticle and peritrophic membrane (PM), is crucial for the growth and development of insect. microRNAs (miRNAs) play important roles in the posttranscriptional level regulation of gene expression, thereby influencing many biological processes in insects. In this study, an attempt was made to evaluate the role of miR-306-5p in regulating chitin metabolism in Ae. albopictus pupae. Overexpression of miR-306-5p resulted in a significantly reduced survival rate in pupae and an increased malformation rate in adults. Both in vivo and in vitro evidence confirmed the presence of the competing endogenous RNA (ceRNA) regulatory axis (linc8338-miR-306-5p-XM_019678125.2). RNAi of linc8338 and XM_019678125.2 had effects on pupae similar to those of miR-306-5p. The highest expression level of miR-306-5p was found in the midgut, and alteration in the expression of miR-306-5p, XM_019678125.2 and linc8338 induced increased transcript levels of chitin synthase 2 (AaCHS2) and decreased chitinase 10 (AaCht10); as well as increased thickness of the midgut and enlarged midgut epithelial cells. The results of this study highlight the potential of miR-306-5p as a prospective target in mosquito control and confirm that the ceRNA mechanism is involved in chitin metabolism. These findings will provide a basis for further studies to uncover the molecular mechanisms through which ncRNAs regulate chitin metabolism.
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Affiliation(s)
- Ruiling Zhang
- School of Clinical and Basic Medical Science, Shandong First Medical University (Shandong Academy of Medical Sciences), Jinan 250117, China; School of Laboratory Animal & Shandong Laboratory Animal Center, Shandong First Medical University (Shandong Academy of Medical Sciences), Jinan 250117, China.
| | - Wenjuan Liu
- School of Clinical and Basic Medical Science, Shandong First Medical University (Shandong Academy of Medical Sciences), Jinan 250117, China
| | - Zhong Zhang
- School of Clinical and Basic Medical Science, Shandong First Medical University (Shandong Academy of Medical Sciences), Jinan 250117, China.
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Ma Z, Wang N, Meng T, Zhang R, Huang Y, Li T. Integrated analysis of ceRNA-miRNA changes in paraquat-induced pulmonary epithelial-mesenchymal transition via high-throughput sequencing. J Biochem Mol Toxicol 2024; 38:e23681. [PMID: 38444083 DOI: 10.1002/jbt.23681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 09/13/2023] [Accepted: 02/23/2024] [Indexed: 03/07/2024]
Abstract
Recent studies have shown that epithelial-mesenchymal transition (EMT) plays an important role in paraquat (PQ)-induced tissue fibrosis, which is the main cause of death in patients with PQ poisoning. However, no effective treatment for pulmonary interstitial fibrosis caused by PQ poisoning exists. It is of great significance for us to find new therapeutic targets through bioinformatics in PQ-induced EMT. We conducted transcriptome sequencing to determine the expression profiles of 1210 messenger RNAs (mRNAs), 558 long noncoding RNAs, 28 microRNAs (miRNAs), including 18 known-miRNAs, 10 novel-miRNAs and 154 circular RNAs in the PQ-exposed EMT group mice. Using gene ontology and Kyoto Encyclopaedia of Genes and Genomes analyses, we identified the pathways associated with signal transduction, cancers, endocrine systems and immune systems were involved in PQ-induced EMT. Furthermore, we constructed long noncoding RNA-miRNA-mRNA interrelated networks and found that upregulated genes included Il22ra2, Mdm4, Slc35e2 and Angptl4, and downregulated genes included RGS2, Gabpb2, Acvr1, Prkd3, Sp100, Tlr12, Syt15 and Camk2d. Thirteen new potential competitive endogenous RNA targets were also identified for further treatment of PQ-induced pulmonary tissue fibrosis. Through further study of the pathway and networks, we may identify new molecular targets in PQ-induced pulmonary EMT.
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Affiliation(s)
- Zhiyu Ma
- Department of Emergency Medicine, Shengjing Hospital of China Medical University, Shengyang, China
| | - Nana Wang
- Endocrinology Department, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Tingting Meng
- Department of Emergency Medicine, Shengjing Hospital of China Medical University, Shengyang, China
| | - Ruoying Zhang
- Department of Emergency Medicine, Shengjing Hospital of China Medical University, Shengyang, China
| | - Yang Huang
- Department of Emergency Medicine, Shengjing Hospital of China Medical University, Shengyang, China
| | - Tiegang Li
- Department of Emergency Medicine, Shengjing Hospital of China Medical University, Shengyang, China
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Yan S, Fu P, Li H, Huang Z, Shan R, Gong B. Comprehensive Analysis of circRNA, lncRNA, miRNA and mRNA Expression Profiles and Their Competing Endogenous RNA Networks in Hepatitis B Virus-Related Hepatocellular Carcinoma. Mol Biotechnol 2024:10.1007/s12033-024-01056-2. [PMID: 38411789 DOI: 10.1007/s12033-024-01056-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 01/02/2024] [Indexed: 02/28/2024]
Abstract
Pursuing knowledge about circular RNA (circRNA), long non-coding RNA (lncRNA), microRNA (miRNA), and messenger RNA (mRNA) expression profiles and their competing endogenous RNA (ceRNA) networks in hepatitis B virus-related hepatocellular carcinoma (HBV-related HCC) was the focus of this research. Expression patterns of circRNAs, lncRNAs, miRNAs, and mRNAs were searched for in relation to HBV-related HCC using whole-transcriptome sequencing. The expression levels of chosen circRNA, lncRNA, miRNA, and mRNA were analyzed using quantitative reverse transcription-polymerase chain reaction (qRT-PCR). The potential connections and roles of ceRNA were deduced via bioinformatics research. The sum of 284 circRNAs, 2,927 lncRNAs, 693 miRNAs, and 5566 mRNAs were discovered to be expressed at considerably different levels in HBV-related HCC tissue and adjacent normal tissue. And the most significantly up- and down-regulated circRNAs, lncRNAs, miRNAs, and mRNAs were verified in HBV-related HCC by qRT-PCR. The circRNA/miRNA/mRNA and lncRNA/miRNA/mRNA networks of HBV-related HCC were established, and the ceRNA regulatory networks revealed the gene expression mechanisms controlled by ncRNAs. Collectively, we revealed the contribution of various circRNA, lncRNA, miRNA, and mRNA expression profiles and identified their ceRNA regulatory networks in HBV-related HCC, providing a theoretical basis for further exploration.
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Affiliation(s)
- Shaoying Yan
- Department of Clinical Laboratory, Medical Center of Burn Plastic and Wound Repair, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
- Nanchang Key Laboratory of Diagnosis of Infectious Diseases, Nanchang, Jiangxi, China
| | - Peng Fu
- Department of Clinical Laboratory, Medical Center of Burn Plastic and Wound Repair, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Huiming Li
- Department of Clinical Laboratory, Medical Center of Burn Plastic and Wound Repair, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Zikun Huang
- Department of Clinical Laboratory, Medical Center of Burn Plastic and Wound Repair, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
- Nanchang Key Laboratory of Diagnosis of Infectious Diseases, Nanchang, Jiangxi, China
| | - Renfeng Shan
- Department of General Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China.
| | - Binbin Gong
- Department of Urology, The First Affiliated Hospital of Nanchang University, No.17, Yongwaizheng Street, Nanchang, 330006, Jiangxi, China.
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Teng Y, Li S, Wei L, Zhang C, Li L, Wang S, Zhang J, Huang J, Zhang H, Wu N, Liu J. LncRNA DGUOK-AS1 Promotes Cell Progression in Lung Squamous Cell Carcinoma by Regulation of miR-653-5p/SLC6A15 Axis. Mol Biotechnol 2024:10.1007/s12033-024-01088-8. [PMID: 38407689 DOI: 10.1007/s12033-024-01088-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 01/24/2024] [Indexed: 02/27/2024]
Abstract
Long noncoding RNA (lncRNA) plays a key role in regulating cancer development. LncRNA deoxyguanosine kinase antisense RNA 1 (DGUOK-AS1) has been reported as a promoter in tumor. The work was designed to further investigate the mechanism of action of DGUOK-AS1 in lung squamous cell carcinoma (LUSC). DGUOK-AS1 level in LUSC cells was measured using RT-qPCR. Counting Kit-8 assays and colony forming assays were performed to evaluate LUSC cell viability and proliferation. Transwell assays were performed to detect cell migration and invasion. Luciferase reporter and RNA pulldown assays were used to verify the binding capacity of DGUOK-AS1 and miR-653-5p. RNA immunoprecipitation assays were performed to verify the relationship of DGUOK-AS1, miR-653-5p, and SLC6A15. DGUOK-AS1 was highly expressed in LUSC cells. DGUOK-AS1 knockdown suppressed LUSC cell proliferation, migration, and invasion. SLC6A15 was demonstrated to be targeted by miR-653-5p, and DGUOK-AS1 interacted with miR-653-5p to modulate SLC6A15 level in LUSC cells. Overexpression of SLC6A15 reversed the suppressive effects of DGUOK-AS1 knockdown on LUSC cell processes. In conclusion, DGUOK-AS1 promotes malignant behaviors of LUSC cells by upregulating SLC6A15 level through interaction with miR-653-5p.
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Affiliation(s)
- Yan Teng
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, Tianjin's Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center for Cancer, Tianjin, 300060, China
| | - Shixia Li
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, Tianjin's Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center for Cancer, Tianjin, 300060, China
| | - Lijuan Wei
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, Tianjin's Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center for Cancer, Tianjin, 300060, China
| | - Chi Zhang
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, Tianjin's Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center for Cancer, Tianjin, 300060, China
| | - Lijuan Li
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, Tianjin's Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center for Cancer, Tianjin, 300060, China
| | - Shuang Wang
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, Tianjin's Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center for Cancer, Tianjin, 300060, China
| | - Jing Zhang
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, Tianjin's Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center for Cancer, Tianjin, 300060, China
| | - Jinchao Huang
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, Tianjin's Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center for Cancer, Tianjin, 300060, China
| | - Huan Zhang
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, Tianjin's Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center for Cancer, Tianjin, 300060, China
| | - Nan Wu
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, Tianjin's Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center for Cancer, Tianjin, 300060, China
| | - Juntian Liu
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, Tianjin's Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center for Cancer, Tianjin, 300060, China.
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Ma X, Guo X, Yongfu L, Wang T, Bao P, Chu M, Wu X, Yan P, Liang C. Identification of circRNA-associated ceRNA networks in the longissimus dorsi of yak under different feeding systems. BMC Vet Res 2024; 20:67. [PMID: 38395831 PMCID: PMC10893644 DOI: 10.1186/s12917-024-03926-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Accepted: 02/09/2024] [Indexed: 02/25/2024] Open
Abstract
BACKGROUND Yaks (Bos grunniens), prized for their ability to thrive in high-altitude environments, are indispensable livestock in the plateau region. Modifying their feeding systems holds significant promise for improving their growth and meat quality. Tenderness, a key determinant of yak meat quality and consumer appeal, is demonstrably influenced by dietary regimen. Indoor feeding regimes have been shown to enhance tenderness by lowering shear stress and optimizing pH values. CircRNAs, well-known modulators of circulatory function, also play a crucial role in skeletal muscle development across various animal species. However, their functional significance in yak skeletal muscle remains largely unexplored. RESULTS In this study, we identified a total of 5,534 circRNAs within the longissimus dorsi muscle, and we found 51 differentially expressed circRNAs (20 up-regulated and 31 down-regulated) between the two feeding groups. Constructing a comprehensive ceRNA network illuminated intricate regulatory mechanisms, with PGP and circRNA_0617 converging on bta-miR-2285q, mirrored by KLF15/circRNA_0345/bta-miR-20b and CTSF/circRNA_0348/bta-miR-146a. These findings shed light on the potential of circRNAs to influence yak muscle development and meat quality, offering valuable insights for future research. CONCLUSIONS This investigation unraveled a complex interaction network between circRNAs、mRNAs and miRNAs in yak skeletal muscle. We further elucidated the target genes regulated by these target genes within the network, offering valuable insights into the potential regulatory mechanisms governing muscle development and meat quality-related traits in yaks.
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Affiliation(s)
- Xiaoming Ma
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Xian Guo
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - La Yongfu
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Tong Wang
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Pengjia Bao
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Min Chu
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Xiaoyun Wu
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Ping Yan
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China.
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Chinese Academy of Agricultural Sciences, Lanzhou, China.
- Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Chinese Academy of Agricultural Sciences, Lanzhou, China.
- Institute of Western Agriculture, the Chinese Academy of Agricultural sciences, Changji, China.
| | - Chunnian Liang
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China.
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Chinese Academy of Agricultural Sciences, Lanzhou, China.
- Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Chinese Academy of Agricultural Sciences, Lanzhou, China.
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Huang J, Yang X, Xu S, Li P. The Analysis of ceRNA Networks and Tumor Microenvironment in Endometrial Cancer. J Cancer 2024; 15:2147-2159. [PMID: 38495486 PMCID: PMC10937290 DOI: 10.7150/jca.93364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 01/31/2024] [Indexed: 03/19/2024] Open
Abstract
Background: Endometrial carcinoma is a life-threatening and aggressive tumor that affects women worldwide. ceRNAs and carcinoma-infiltrating immunocytes can be associated with tumor formation and progression. Therefore, investigating the unique mechanisms underlying endometrial carcinoma is crucial. Methods: Prognostic nomograms were constructed based on the differentially expressed genes between normal and tumor tissues. Twenty types of tumor immune infiltrating cells in uterine corpus endometrial carcinoma (UCEC) were examined using CIBERSORT. To identify the potential signaling pathways, the associations among essential ceRNA network genes and important immunocytes were investigated using the co-expression assay. Results: Differential analysis identified 3636 mRNAs, 249 miRNAs, and 252 lncRNAs unique to UCEC. The ceRNA network was constructed using the interplays between 19 lncRNA-miRNA pairs and 434 miRNA-mRNA pairs. Furthermore, CIBERSORT and ceRNA integration analysis revealed that immune cells, including dendritic cells and natural killer cells, and associated ceRNAs such as LRP8, HDGF, PPARGC1B, and TEAD1 can appropriately predict prognosis. A receiver operating characteristic curve was constructed to predict patient outcomes. Conclusions: Using a nomogram, we predicted the outcomes of patients with UCEC Furthermore, we revealed its significance in improving clinical management.
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Affiliation(s)
- Jian Huang
- Clinical and Translational Research Center, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, China
| | - Xiaoyue Yang
- The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200030, China
- Shanghai Key Laboratory of Embryo Original Diseases, Shanghai 200030, China
| | - Shen Xu
- Blood Transfusion Department, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ping Li
- Department of Gynecology, Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
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Zhang F, Pei S, Xiao M. Identification of functional genes in liver fibrosis based on bioinformatics analysis of a lncRNA-mediated ceRNA network. BMC Med Genomics 2024; 17:56. [PMID: 38378545 PMCID: PMC10877760 DOI: 10.1186/s12920-024-01813-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 01/20/2024] [Indexed: 02/22/2024] Open
Abstract
BACKGROUND Liver fibrosis is a major global healths problem; nevertheless, its molecular mechanism are not completely clear. This study aimed to build a lncRNA-miRNA-mRNA network, identify potentially related lncRNAs, and explore the pathogenesis of liver fibrosis. MATERIALS AND METHODS We used the Gene Expression Omnibus databases and bioinformatics analysis to identify differentially expressed genes (DEGs) between liver fibrosis and normal tissues. The ceRNA network was constructed according to the interactions between DElncRNA, miRNA, and DEmRNA. Then, these DEGs were identified using functional enrichment analysis, and a protein-protein interaction (PPI) network was established. The critical lncRNAs were verified using the quantitative real-time polymerase chain reaction (qRT-PCR). RESULTS The ceRNA network was composed of three lncRNAs, five miRNAs, and 93 mRNAs. Gene Ontology functional enrichment analysis revealed significant enhancement in cell components, molecular function, and biological process. Kyoto Encyclopedia of Genes and Genomes pathway analysis revealed pathways associated with transcriptional misregulation in cancer, including the Rap1 signaling pathway, proteoglycans in cancer, mineral absorption, HTLV-l infection, and central carbon metabolism in cancer. According to the PPI network and the GSE84044 database, seven hub genes associated with liver fibrosis were identified. In addition, qRT-PCR revealed that lncRNA AC100861 (lncRNA TNFRSF10A-DT) was explicitly decreased in liver fibrosis tissues and activated hepatic stellate cells. CONCLUSIONS In summary, this study preliminarily found that lncRNA TNFRSF10A-DT may be a biomarker for the diagnosis and outcome of liver fibrosis. We uncovered a novel lncRNA-mediated ceRNA regulatory mechanism in the pathogenesis of liver fibrosis.
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Affiliation(s)
- Feng Zhang
- Department of Cardiovascular Medicine, Xiangya Hospital, Central South University, Hunan, Changsha, 410008, People's Republic of China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Hunan, Changsha, 410008, People's Republic of China
| | - Siya Pei
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Hunan, Changsha, 410008, People's Republic of China
- Department of Infection Diseases, Xiangya Hospital, Central South University, Hunan, Changsha, 410008, People's Republic of China
| | - Meifang Xiao
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Hunan, Changsha, 410008, People's Republic of China.
- Department of Health Management Center, Xiangya Hospital, Central South University, Hunan, Changsha, 410008, People's Republic of China.
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Liu XS, Liu ZY, Zeng DB, Hu J, Chen XL, Gu JL, Gao Y, Pei ZJ. Functional enrichment analysis reveals the involvement of DARS2 in multiple biological pathways and its potential as a therapeutic target in esophageal carcinoma. Aging (Albany NY) 2024; 16:3934-3954. [PMID: 38382106 DOI: 10.18632/aging.205569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 01/17/2024] [Indexed: 02/23/2024]
Abstract
OBJECTIVE The enzyme Aspartyl tRNA synthetase 2 (DARS2) is a crucial enzyme in the mitochondrial tRNA synthesis pathway, playing a critical role in maintaining normal mitochondrial function and protein synthesis. However, the role of DARS2 in ESCA is unclear. MATERIALS AND METHODS Transcriptional data of pan-cancer and ESCA were downloaded from UCSC XENA, TCGA, and GEO databases to analyze the differential expression of DARS2 between tumor samples and normal samples, and its correlation with clinicopathological features of ESCA patients. R was used for GO, KEGG, and GSEA functional enrichment analysis of DARS2 co-expression and to analyze the connection of DARS2 with glycolysis and m6A-related genes. In vitro experiments were performed to assess the effects of interfering with DARS2 expression on ESCA cells. TarBase v.8, mirDIP, miRTarBase, ENCORI, and miRNet databases were used to analyze and construct a ceRNA network containing DARS2. RESULTS DARS2 was overexpressed in various types of tumors. In vitro experiments confirmed that interfering with DARS2 expression significantly affected the proliferation, migration, apoptosis, cell cycle, and glycolysis of ESCA cells. DARS2 may be involved in multiple biological pathways related to tumor development. Furthermore, correlation and differential analysis revealed that DARS2 may regulate ESCA m6A modification through its interaction with METTL3 and YTHDF1. A ceRNA network containing DARS2, DLEU2/has-miR-30a-5p/DARS2, was successfully predicted and constructed. CONCLUSIONS Our findings reveal the upregulation of DARS2 in ESCA and its association with clinical features, glycolysis pathway, m6A modification, and ceRNA network. These discoveries provide valuable insights into the molecular mechanisms underlying ESCA.
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Affiliation(s)
- Xu-Sheng Liu
- Department of Nuclear Medicine, Hubei Provincial Clinical Research Center for Umbilical Cord Blood Hematopoietic Stem Cells, Taihe Hospital, Hubei University of Medicine, Shiyan 442000, Hubei, China
| | - Zi-Yue Liu
- Department of Nuclear Medicine, Hubei Provincial Clinical Research Center for Umbilical Cord Blood Hematopoietic Stem Cells, Taihe Hospital, Hubei University of Medicine, Shiyan 442000, Hubei, China
| | - Dao-Bing Zeng
- Department of Nuclear Medicine, Hubei Provincial Clinical Research Center for Umbilical Cord Blood Hematopoietic Stem Cells, Taihe Hospital, Hubei University of Medicine, Shiyan 442000, Hubei, China
| | - Jian Hu
- Department of Critical Care Medicine, Danjiangkou First Hospital, Danjiangkou 420381, Hubei, China
| | - Xuan-Long Chen
- Department of Medical Ultrasound, Taihe Hospital, Hubei University of Medicine, Shiyan 442000, Hubei, China
| | - Jiao-Long Gu
- Department of Obstetrics and Gynecology, Taihe Hospital, Hubei University of Medicine, Shiyan 442000, Hubei, China
| | - Yan Gao
- Department of Nuclear Medicine, Hubei Provincial Clinical Research Center for Umbilical Cord Blood Hematopoietic Stem Cells, Taihe Hospital, Hubei University of Medicine, Shiyan 442000, Hubei, China
| | - Zhi-Jun Pei
- Department of Nuclear Medicine, Hubei Provincial Clinical Research Center for Umbilical Cord Blood Hematopoietic Stem Cells, Taihe Hospital, Hubei University of Medicine, Shiyan 442000, Hubei, China
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Chen X, Wang T, Guo W, Yan X, Kou H, Yu Y, Liu C, Gao W, Wang W, Wang R. Transcriptome reveals the roles and potential mechanisms of lncRNAs in the regulation of albendazole resistance in Haemonchus contortus. BMC Genomics 2024; 25:188. [PMID: 38368335 PMCID: PMC10873934 DOI: 10.1186/s12864-024-10096-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 02/07/2024] [Indexed: 02/19/2024] Open
Abstract
BACKGROUND Haemonchus contortus (H. contortus) is the most common parasitic nematode in ruminants and is prevalent worldwide. H. contortus resistance to albendazole (ABZ) hinders the efficacy of anthelmintic drugs, but little is known about the molecular mechanisms that regulate this of drug resistance. Recent research has demonstrated that long noncoding RNAs (lncRNAs) can exert significant influence as pivotal regulators of the emergence of drug resistance. RESULTS In this study, transcriptome sequencing was conducted on both albendazole-sensitive (ABZ-sensitive) and albendazole-resistant (ABZ-resistant) H. contortus strains, with three biological replicates for each group. The analysis of lncRNA in the transcriptomic data revealed that there were 276 differentially expressed lncRNA (DElncRNA) between strains with ABZ-sensitive and ABZ-resistant according to the criteria of |log2Foldchange|≥ 1 and FDR < 0.05. Notably, MSTRG.12969.2 and MSTRG.9827.1 exhibited the most significant upregulation and downregulation, respectively, in the resistant strains. The potential roles of the DElncRNAs included catalytic activity, stimulus response, regulation of drug metabolism, and modulation of the immune response. Moreover, we investigated the interactions between DElncRNAs and other RNAs, specifically MSTRG.12741.1, MSTRG.11848.1, MSTRG.5895.1, and MSTRG.14070.1, involved in regulating drug stimulation through cis/trans/antisense/lncRNA‒miRNA-mRNA interaction networks. This regulation leads to a decrease (or increase) in the expression of relevant genes, consequently enhancing the resistance of H. contortus to albendazole. Furthermore, through comprehensive analysis of competitive endogenous RNAs (ceRNAs) involved in drug resistance-related pathways, such as the mTOR signalling pathway and ABC transporter signalling pathway, the relevance of the MSTRG.2499.1-novel-m0062-3p-HCON_00099610 interaction was identified to mainly involve the regulation of catalytic activity, metabolism, ubiquitination and transcriptional regulation of gene promoters. Additionally, quantitative real-time polymerase chain reaction (qRT-PCR) validation indicated that the transcription profiles of six DElncRNAs and six DEmRNAs were consistent with those obtained by RNA-seq. CONCLUSIONS The results of the present study allowed us to better understand the changes in the lncRNA expression profile of ABZ-resistant H. contortus. In total, these results suggest that the lncRNAs MSTRG.963.1, MSTRG.12741.1, MSTRG.11848.1 and MSTRG.2499.1 play important roles in the development of ABZ resistance and can serve as promising biomarkers for further study.
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Affiliation(s)
- Xindi Chen
- Key Laboratory of Animal Disease Clinical Diagnosis and Treatment Technology, College of Veterinary Medicine, Inner Mongolia Agricultural University, Ordos Street, Hohhot, 010018, Inner Mongolia Municipality, China
| | - Tengyu Wang
- Key Laboratory of Animal Disease Clinical Diagnosis and Treatment Technology, College of Veterinary Medicine, Inner Mongolia Agricultural University, Ordos Street, Hohhot, 010018, Inner Mongolia Municipality, China
| | - Wenrui Guo
- Key Laboratory of Animal Disease Clinical Diagnosis and Treatment Technology, College of Veterinary Medicine, Inner Mongolia Agricultural University, Ordos Street, Hohhot, 010018, Inner Mongolia Municipality, China
| | - Xu Yan
- Key Laboratory of Animal Disease Clinical Diagnosis and Treatment Technology, College of Veterinary Medicine, Inner Mongolia Agricultural University, Ordos Street, Hohhot, 010018, Inner Mongolia Municipality, China
| | - Huilin Kou
- Key Laboratory of Animal Disease Clinical Diagnosis and Treatment Technology, College of Veterinary Medicine, Inner Mongolia Agricultural University, Ordos Street, Hohhot, 010018, Inner Mongolia Municipality, China
| | - Yu Yu
- Key Laboratory of Animal Disease Clinical Diagnosis and Treatment Technology, College of Veterinary Medicine, Inner Mongolia Agricultural University, Ordos Street, Hohhot, 010018, Inner Mongolia Municipality, China
| | - Chunxia Liu
- Key Laboratory of Animal Disease Clinical Diagnosis and Treatment Technology, College of Life Science, Inner Mongolia Agricultural University, Hohhot, 010018, Inner Mongolia Municipality, China
| | - Wa Gao
- Inner Mongolia Key Laboratory of Tick-Borne Zoonotic Infectious Disease, Department of Medicine, Hetao College, Bayan Nur, 015000, Inner Mongolia Autonomous Region, China
| | - Wenlong Wang
- Key Laboratory of Animal Disease Clinical Diagnosis and Treatment Technology, College of Veterinary Medicine, Inner Mongolia Agricultural University, Ordos Street, Hohhot, 010018, Inner Mongolia Municipality, China.
| | - Rui Wang
- Key Laboratory of Animal Disease Clinical Diagnosis and Treatment Technology, College of Veterinary Medicine, Inner Mongolia Agricultural University, Ordos Street, Hohhot, 010018, Inner Mongolia Municipality, China.
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Li T, Yuan J, Xu P, Jia J, Zhao J, Zhang J, Ding R, Zhao X, He D, Wu T, Cheng X. PMAIP1, a novel diagnostic and potential therapeutic biomarker in osteoporosis. Aging (Albany NY) 2024; 16:3694-3715. [PMID: 38372699 DOI: 10.18632/aging.205553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 12/26/2023] [Indexed: 02/20/2024]
Abstract
BACKGROUND Osteoporosis is a common endocrine metabolic bone disease, which may lead to severe consequences. However, the unknown molecular mechanism of osteoporosis, the observable side effects of present treatments and the inability to fundamentally improve bone metabolism seriously restrict the impact of prevention and treatment. The study aims to identify potential biomarkers from osteoclast progenitors, specifically peripheral blood monocytes on predicting the osteoporotic phenotype. METHODS Datasets were obtained from Gene Expression Omnibus (GEO). Based on the differentially expressed genes (DEGs) and GSEA results, GO and KEGG analyses were performed using the DAVID database and Metascape database. PPI network, TF network, drug-gene interaction network, and ceRNA network were established to determine the hub genes. Its osteogenesis, migration, and proliferation abilities in bone marrow mesenchymal stem cells (BMSCs) were validated through RT-qPCR, WB, ALP staining, VK staining, wound healing assay, transwell assay, and CCK-8 assay. RESULTS A total of 63 significant DEGs were screened. Functional and pathway enrichment analysis discovered that the functions of the significant DEGs (SDEGs) are mainly related to immunity and metal ions. A comprehensive evaluation of all the network analyses, PMAIP1 was defined as osteoporosis's core gene. This conclusion was further confirmed in clinical cohort data. A series of experiments demonstrated that the PMAIP1 gene can promote the osteogenesis, migration and proliferation of BMSC cells. CONCLUSIONS All of these outcomes showed a new theoretical basis for further research in the treatment of osteoporosis, and PMAIP1 was identified as a potential biomarker for osteoporosis diagnosis and treatment.
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Affiliation(s)
- Tao Li
- Institute of Orthopaedics of Jiangxi Province, Nanchang, Jiangxi, China
| | - Jinghong Yuan
- Institute of Orthopaedics of Jiangxi Province, Nanchang, Jiangxi, China
- Department of Osteoporosis, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Peichuan Xu
- Institute of Orthopaedics of Jiangxi Province, Nanchang, Jiangxi, China
| | - Jingyu Jia
- Institute of Orthopaedics of Jiangxi Province, Nanchang, Jiangxi, China
- Department of Osteoporosis, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Jiangminghao Zhao
- Department of Osteoporosis, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Jian Zhang
- Institute of Orthopaedics of Jiangxi Province, Nanchang, Jiangxi, China
- Department of Osteoporosis, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Rui Ding
- Institute of Orthopaedics of Jiangxi Province, Nanchang, Jiangxi, China
- Department of Orthopaedics, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Xiaokun Zhao
- Department of Osteoporosis, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Dingwen He
- Institute of Orthopaedics of Jiangxi Province, Nanchang, Jiangxi, China
| | - Tianlong Wu
- Institute of Orthopaedics of Jiangxi Province, Nanchang, Jiangxi, China
- Department of Orthopaedics, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Xigao Cheng
- Institute of Orthopaedics of Jiangxi Province, Nanchang, Jiangxi, China
- Department of Osteoporosis, The Second Affiliated Hospital of Nanchang University, Nanchang, China
- Department of Orthopaedics, The Second Affiliated Hospital of Nanchang University, Nanchang, China
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Zheng H, Wu D, Chen X, He W, Hua J, Li Q, Ji Y. Endothelial downregulation of nuclear m6A reader YTHDC1 promotes pulmonary vascular remodeling in sugen hypoxia model of pulmonary hypertension. Heliyon 2024; 10:e24963. [PMID: 38318069 PMCID: PMC10838804 DOI: 10.1016/j.heliyon.2024.e24963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 01/15/2024] [Accepted: 01/17/2024] [Indexed: 02/07/2024] Open
Abstract
Background Pulmonary hypertension (PH) is characterized with vascular remodeling, which is intiated by vascular endothelial dysfunction. N6-methyladenosine (m6A) modification mediates gene expression in many ways including mediating RNA degradation, splicing, nuclear export et al. m6A modification have been found to be associated with the development of PH. However, the role of m6A regulators in pulmonary artery endothelial cells (PAECs) dysfunction of PH is still under research. Methods The expression levels of m6A regulators in PAECs were analyzed with the single-cell sequencing Data(scRNA). Next, the target differentially expressed genes (DEGs) of m6A regulators in PAECs were functionally annotated. The analysis of cellular interactions included the examination of receptor-ligand pairs regulated by m6A regulators. Pseudo-time trajectory analyses and a ceRNA network involving lncRNAs, miRNAs, and mRNAs were conducted in PAECs. Furthermore, microarray data (GSE180169) for Sugen Hypoxia PH (SuHx PH) mouse models was screened for DEGs and m6A regulators in PAECs. Moreover, the expression of YTHDC1 in the lung samples of SuHx PH models was determined using immunofluorescence. In vitro, the mRNA expression of YTHDC1 in HPAECs under hypoxia conditions was detected. The effect of YTHDC1 recombinant protein on HPAEC proliferation was detected by Cell Counting Kit-8 (CCK8). Results Dysregulation of m6A regulators was observed in mouse PAECs. The m6A reader of YTHDC1 was decreased in PAECs in scRNA data and RNAseq data of isolated PAECs of SuHx PH models. Downregulation of YTHDC1 was caused by hypoxia in PAECs in vitro and similar results was observed in PAECs of SuHx PH mouse models. Next, YTHDC1 recombinant protein was found to inhibit HPAECs proliferation. The DEGs targeted by YTHDC1 were enriched in angiogenesis, endothelial cell migration, fluid shear stress, and stem cell maintenance. Analysis indicates that interactions among endothelial cells, smooth muscle cells, fibroblasts, and immune cells, mediated by specific YTHDC1 target genes (e.g., PTPRC-MRC1, ITBG2-ICAM1, COL4A1-CD44), contribute to PH development. Also, the YTHDC1 expression were consistent with Thioredoxin interacting protein (TXNIP). What's more, the predicted transcription factors showed that NFKB1, Foxd3 may be involved in the regulation of YTHDC1. Lastly, our data suggest that YTHDC1 may be involved in regulating PAECs dysfunction through lncRNA/miRNA/mRNA network. Conclusion For the first time, we analyzed changes in the expression and biological functions of m6A regulators in SuHx PH mouse models. We causatively linked YTHDC1 to PAECs dysfunction, providing novel insight into and opportunities to diagnose and treat PH.
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Affiliation(s)
| | | | - Xiangyu Chen
- Department of Critical Care Medicine, Zhongda Hospital, School of Medicine, Southeast University, No.87, Dingjiaqiao, Gulou District, Nanjing, 210009, China
| | - Wenjuan He
- Department of Critical Care Medicine, Zhongda Hospital, School of Medicine, Southeast University, No.87, Dingjiaqiao, Gulou District, Nanjing, 210009, China
| | - Jing Hua
- Department of Critical Care Medicine, Zhongda Hospital, School of Medicine, Southeast University, No.87, Dingjiaqiao, Gulou District, Nanjing, 210009, China
| | - Qiang Li
- Department of Critical Care Medicine, Zhongda Hospital, School of Medicine, Southeast University, No.87, Dingjiaqiao, Gulou District, Nanjing, 210009, China
| | - YingQun Ji
- Department of Critical Care Medicine, Zhongda Hospital, School of Medicine, Southeast University, No.87, Dingjiaqiao, Gulou District, Nanjing, 210009, China
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Chen YN, Fu XR, Guo H, Fu XY, Shi KS, Gao T, Yu HQ. YY1-induced lncRNA00511 promotes melanoma progression via the miR-150-5p/ADAM19 axis. Am J Cancer Res 2024; 14:809-831. [PMID: 38455406 PMCID: PMC10915319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 01/07/2024] [Indexed: 03/09/2024] Open
Abstract
Increasing evidence indicates that long noncoding RNAs (lncRNAs) are therapeutic targets and key regulators of tumors development and progression, including melanoma. Long intergenic non-protein-coding RNA 511 (LINC00511) has been demonstrated as an oncogenic molecule in breast, stomach, colorectal, and lung cancers. However, the precise role and functional mechanisms of LINC00511 in melanoma remain unknown. This study confirmed that LINC00511 was highly expressed in melanoma cells (A375 and SK-Mel-28 cells) and tissues, knockdown of LINC00511 could inhibit melanoma cell migration and invasion, as well as the growth of subcutaneous tumor xenografts in vivo. By using Chromatin immunoprecipitation (ChIP) assay, it was demonstrated that the transcription factor Yin Yang 1 (YY1) is capable of binding to the LINC00511 promoter and enhancing its expression in cis. Further mechanistic investigation showed that LINC00511 was mainly enriched in the cytoplasm of melanoma cells and interacted directly with microRNA-150-5p (miR-150-5p). Consistently, the knockdown of miR-150-5p could recover the effects of LINC00511 knockdown on melanoma cells. Furthermore, ADAM metallopeptidase domain expression 19 (ADAM19) was identified as a downstream target of miR-150-5p, and overexpression of ADAM19 could promote melanoma cell proliferation. Rescue assays indicated that LINC00511 acted as a competing endogenous RNA (ceRNA) to sponge miR-150-5p and increase the expression of ADAM19, thereby activating the PI3K/AKT pathway. In summary, we identified LINC00511 as an oncogenic lncRNA in melanoma and defined the LINC00511/miR-150-5p/ADAM19 axis, which might be considered a potential therapeutic target and novel molecular mechanism the treatment of patients with melanoma.
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Affiliation(s)
- Ya-Ni Chen
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University Hohhot 010020, Inner Mongolia, China
| | - Xin-Rui Fu
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University Hohhot 010020, Inner Mongolia, China
| | - Hua Guo
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University Hohhot 010020, Inner Mongolia, China
| | - Xin-Yao Fu
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University Hohhot 010020, Inner Mongolia, China
| | - Ke-Song Shi
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University Hohhot 010020, Inner Mongolia, China
| | - Tian Gao
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University Hohhot 010020, Inner Mongolia, China
| | - Hai-Quan Yu
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University Hohhot 010020, Inner Mongolia, China
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Liu Y, Wu J, Chen L, Zou J, Yang Q, Tian H, Zheng D, Ji Z, Cai J, Li Z, Chen Y. ncRNAs-mediated overexpression of TET3 predicts unfavorable prognosis and correlates with immunotherapy efficacy in breast cancer. Heliyon 2024; 10:e24855. [PMID: 38318018 PMCID: PMC10838756 DOI: 10.1016/j.heliyon.2024.e24855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 01/07/2024] [Accepted: 01/16/2024] [Indexed: 02/07/2024] Open
Abstract
Breast cancer is the most frequent form of cancer in women and the primary cause of cancer-related deaths globally. DNA methylation and demethylation are important processes in human tumorigenesis. Ten-eleven translocation 3 (TET3) is a DNA demethylase. Prior research has demonstrated that TET3 is highly expressed in various human malignant tumors. However, the exact function and mechanism of TET3 in breast cancer remain unclear. In this study, we investigated TET3 expression in breast cancer and its correlation with clinicopathological characteristics of breast cancer patients. The results presented that TET3 expression was significantly increased in breast cancer and associated with the PAM50 subtype. Subsequently, we performed receiver operating characteristic, survival, and Cox hazard regression analyses. These results suggest that TET3 expression is associated with a poor prognosis and may be an indirect independent prognostic indicator in breast cancer. We also established a protein-protein interaction (PPI) network of TET3 and executed enrichment analyses of TET3 co-expressed genes, revealing their primary association with the cell cycle. Moreover, we identified noncoding RNAs (ncRNAs) contributing to TET3 overexpression using expression, correlation, and survival analyses. We identified the LINC01521/hsa-miR-29a-3p axis as the primary TET3 upstream ncRNA-related pathway in breast cancer. Furthermore, TET3 expression was positively associated with immune cell infiltration, immune cell biomarkers, and eight immune checkpoint gene expressions in breast cancer. TET3 expression also correlated with patient responses to immunotherapy. Finally, we conducted subcellular localization and immunohistochemical staining analysis of TET3 in breast cancer. We found that TET3 localized to the nucleoplasm, vesicles, and cytosol in the MCF-7 cell line, and TET3 expression was significantly upregulated in breast cancer tissues compared to para-tumor tissues. Our findings indicate that ncRNA-mediated overexpression of TET3 predicts an unfavorable prognosis and correlates with immunotherapy efficacy in breast cancer.
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Affiliation(s)
| | | | | | - Juan Zou
- Department of Thyroid, Breast and Hernia Surgery, The Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Qiuping Yang
- Department of Thyroid, Breast and Hernia Surgery, The Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Huiting Tian
- Department of Thyroid, Breast and Hernia Surgery, The Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Daitian Zheng
- Department of Thyroid, Breast and Hernia Surgery, The Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Zeqi Ji
- Department of Thyroid, Breast and Hernia Surgery, The Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Jiehui Cai
- Department of Thyroid, Breast and Hernia Surgery, The Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Zhiyang Li
- Department of Thyroid, Breast and Hernia Surgery, The Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Yexi Chen
- Department of Thyroid, Breast and Hernia Surgery, The Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
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Wu J, Fu G, Luo C, Chen L, Liu Q. Cuproptosis-related ceRNA axis triggers cell proliferation and cell cycle through CBX2 in lung adenocarcinoma. BMC Pulm Med 2024; 24:85. [PMID: 38355480 PMCID: PMC10865584 DOI: 10.1186/s12890-024-02887-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 01/27/2024] [Indexed: 02/16/2024] Open
Abstract
BACKGROUND Lung adenocarcinoma (LUAD) has high morbidity and mortality. Despite substantial advances in treatment, the prognosis of patients with LUAD remains unfavorable. The ceRNA axis has been reported to play an important role in the pathogenesis of LUAD. In addition, cuproptosis is considered an important factor in tumorigenesis. The expression of CBX2 has been associated with the development of multiple tumors, including LUAD. However, the precise molecular mechanisms through which the cuproptosis-related ceRNA network regulates CBX2 remain unclear. METHODS The DEGs between tumor and normal samples of LUAD were identified in TCGA database. The "ConsensusClusterPlus" R package was used to perform consensus clustering based on the mRNA expression matrix and cuproptosis-related gene expression profile. Then, LASSO-COX regression analysis was performed to identify potential prognostic biomarkers associated with cuproptosis, and the ceRNA network was constructed. Finally, the mechanisms of ceRNA in LUAD was studied by cell experiments. RESULTS In this study, the AC144450.1/miR-424-5p axis was found to promote the progression of LUAD by acting on CBX2. The expression of AC144450.1 and miR-424-5p can be altered to regulate CBX2 and is correlated with cell proliferation and cell cycle of LUAD. Mechanistically, AC144450.1 affects the expression of CBX2 by acting as the ceRNA of miR-424-5p. In addition, a cuproptosis-related model were constructed in this study to predict the prognosis of LUAD. CONCLUSIONS This study is the first to demonstrate that the AC144450.1/miR-424-5p/CBX2 axis is involved in LUAD progression and may serve as a novel target for its diagnosis and treatment.
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Affiliation(s)
- Jiang Wu
- Department of Thoracic Surgery, Xinqiao Hospital, Army Medical University, 400037, Chongqing, China
| | - Guang Fu
- Department of Thoracic Surgery, Xinqiao Hospital, Army Medical University, 400037, Chongqing, China
| | - Chao Luo
- Department of Thoracic Surgery, Xinqiao Hospital, Army Medical University, 400037, Chongqing, China
| | - Liang Chen
- Department of Thoracic Surgery, Xinqiao Hospital, Army Medical University, 400037, Chongqing, China
| | - Quanxing Liu
- Department of Thoracic Surgery, Xinqiao Hospital, Army Medical University, 400037, Chongqing, China.
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Li X, Sun S, Zhang H. RNA sequencing reveals differential long noncoding RNA expression profiles in bacterial and viral meningitis in children. BMC Med Genomics 2024; 17:50. [PMID: 38347610 PMCID: PMC10863080 DOI: 10.1186/s12920-024-01820-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 01/26/2024] [Indexed: 02/15/2024] Open
Abstract
BACKGROUND We aimed to investigate the involvement of long non-coding RNA (lncRNA) in bacterial and viral meningitis in children. METHODS The peripheral blood of five bacterial meningitis patients, five viral meningitis samples, and five healthy individuals were collected for RNA sequencing. Then, the differentially expressed lncRNA and mRNA were detected in bacterial meningitis vs. controls, viral meningitis vs. healthy samples, and bacterial vs. viral meningitis patients. Besides, co-expression and the competing endogenous RNA (ceRNA) networks were constructed. Receiver operating characteristic curve (ROC) analysis was performed. RESULTS Compared with the control group, 2 lncRNAs and 32 mRNAs were identified in bacterial meningitis patients, and 115 lncRNAs and 54 mRNAs were detected in viral meningitis. Compared with bacterial meningitis, 165 lncRNAs and 765 mRNAs were identified in viral meningitis. 2 lncRNAs and 31 mRNAs were specific to bacterial meningitis, and 115 lncRNAs and 53 mRNAs were specific to viral meningitis. The function enrichment results indicated that these mRNAs were involved in innate immune response, inflammatory response, and immune system process. A total of 8 and 1401 co-expression relationships were respectively found in bacterial and viral meningitis groups. The ceRNA networks contained 1 lncRNA-mRNA pair and 4 miRNA-mRNA pairs in viral meningitis group. GPR68 and KIF5C, identified in bacterial meningitis co-expression analysis, had an area under the curve (AUC) of 1.00, while the AUC of OR52K2 and CCR5 is 0.883 and 0.698, respectively. CONCLUSIONS Our research is the first to profile the lncRNAs in bacterial and viral meningitis in children and may provide new insight into understanding meningitis regulatory mechanisms.
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Affiliation(s)
- Xin Li
- Department of Pediatrics, The Second Hospital of Hebei Medical University, Hebei Medical University, No. 215 West Heping Street, Shijiazhuang, Hebei, 050000, China
- First Department of Neurology, Hebei Children's Hospital, Hebei Children's Hospital Affiliated to Hebei Medical University, Shijiazhuang, 050000, China
| | - Suzhen Sun
- First Department of Neurology, Hebei Children's Hospital, Hebei Children's Hospital Affiliated to Hebei Medical University, Shijiazhuang, 050000, China
| | - Huifeng Zhang
- Department of Pediatrics, The Second Hospital of Hebei Medical University, Hebei Medical University, No. 215 West Heping Street, Shijiazhuang, Hebei, 050000, China.
- First Department of Neurology, Hebei Children's Hospital, Hebei Children's Hospital Affiliated to Hebei Medical University, Shijiazhuang, 050000, China.
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