1
|
Zhu M, Yuan Z, Wen C, Wei X. DEX Inhibits H/R-induced Cardiomyocyte Ferroptosis by the miR-141-3p/lncRNA TUG1 Axis. Thorac Cardiovasc Surg 2024. [PMID: 38889747 DOI: 10.1055/s-0044-1787691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/20/2024]
Abstract
BACKGROUND Ferroptosis is emerging as a critical pathway in ischemia/reperfusion (I/R) injury, contributing to compromised cardiac function and predisposing individuals to sepsis and myocardial failure. The study investigates the underlying mechanism of dexmedetomidine (DEX) in hypoxia/reoxygenation (H/R)-induced ferroptosis in cardiomyocytes, aiming to identify novel targets for myocardial I/R injury treatment. METHODS H9C2 cells were subjected to H/R and treated with varying concentrations of DEX. Additionally, H9C2 cells were transfected with miR-141-3p inhibitor followed by H/R treatment. Levels of miR-141-3p, long noncoding RNA (lncRNA) taurine upregulated 1 (TUG1), Fe2+, glutathione (GSH), and malondialdehyde were assessed. Reactive oxygen species (ROS) generation was measured via fluorescent labeling. Expression of ferroptosis-related proteins glutathione peroxidase 4 (GPX4) and acyl-CoA synthetase long-chain family member 4 (ACSL4) was determined using Western blot. The interaction between miR-141-3p and lncRNA TUG1 was evaluated through RNA pull-down assay and dual-luciferase reporter gene assays. The stability of lncRNA TUG1 was assessed using actinomycin D. RESULTS DEX ameliorated H/R-induced cardiomyocyte injury and elevated miR-141-3p expression in cardiomyocytes. DEX treatment increased cell viability, Fe2+, and ROS levels while decreasing ACSL4 protein expression. Furthermore, DEX upregulated GSH and GPX4 protein levels. miR-141-3p targeted lncRNA TUG1, reducing its stability and overall expression. Inhibition of miR-141-3p or overexpression of lncRNA TUG1 partially reversed the inhibitory effect of DEX on H/R-induced ferroptosis in cardiomyocytes. CONCLUSION DEX mitigated H/R-induced ferroptosis in cardiomyocytes by upregulating miR-141-3p expression and downregulating lncRNA TUG1 expression, unveiling a potential therapeutic strategy for myocardial I/R injury.
Collapse
Affiliation(s)
- Mei Zhu
- Department of Anesthesiology, Taizhou People's Hospital Affiliated to Nanjing Medical University, Taizhou, People's Republic of China
| | - Zhiguo Yuan
- Department of Anesthesiology, Taizhou People's Hospital Affiliated to Nanjing Medical University, Taizhou, People's Republic of China
| | - Chuanyun Wen
- Department of Anesthesiology, Taizhou People's Hospital Affiliated to Nanjing Medical University, Taizhou, People's Republic of China
| | - Xiaojia Wei
- Department of Anesthesiology, Taizhou People's Hospital Affiliated to Nanjing Medical University, Taizhou, People's Republic of China
| |
Collapse
|
2
|
Qian Z, Wu F, Feng G, Lin W, Cai X, Wu J, Ke K, Ye Z, Xu G. A prognostic risk model based on lactate metabolism and transport-related lncRNAs for gastric adenocarcinoma. Biomarkers 2024; 29:211-221. [PMID: 38629165 DOI: 10.1080/1354750x.2024.2341411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Accepted: 04/04/2024] [Indexed: 05/15/2024]
Abstract
BACKGROUND Increased lactate levels and metastasis in tumours are strongly associated with dismal outcomes. But prognostic value of lactate metabolism and transport-related lncRNAs in gastric adenocarcinoma (GA) patients remains unaddressed. METHODS Gene expression data of GA were provided by The Cancer Genome Atlas. Lactate metabolism and transport-related gene data were accessed from GSEA. LncRNAs related to lactate metabolism and transport were identified by correlation analysis. A prognostic model was built by regression analysis. Validity of prognostic model was confirmed through survival analysis and receiver operating characteristic (ROC) curve. Immunity of each risk group was evaluated by immune correlation analysis .LncRNA-mRNA network was built by correlation analysis using Cytoscape software. RESULTS A 12-gene prognostic model based on lactate metabolism and transport-related lncRNAs was built in GA. Median riskscore was utilized to classify GA samples into high- and low-risk groups. Survival analysis and ROC curves demonstrated validity of prognostic model. Most immune checkpoint molecules and TIDE scores were lower in the low-risk group. LINC01303 and LINC01545 may be the key prognostic factors in patients with GA. CONCLUSION This study successfully built a prognostic model of lactate metabolism and transport-related lncRNAs in GA. The findings guide prognostic management of GA patients.
Collapse
Affiliation(s)
- Zhenyuan Qian
- General Surgery, Cancer Center, Department of Gastrointestinal and Pancreatic Surgery, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Fang Wu
- General Surgery, Cancer Center, Department of Gastrointestinal and Pancreatic Surgery, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Guoqing Feng
- Department of General Surgery, Haining Traditional Chinese Medicine Hospital, Haining, Jiaxing, Zhejiang, China
| | - Wenfa Lin
- Zhejiang Chinese Medicine University, Hangzhou, Zhejiang, China
| | - Xufan Cai
- Zhejiang Chinese Medicine University, Hangzhou, Zhejiang, China
| | - Jianzhang Wu
- General Surgery, Cancer Center, Department of Gastrointestinal and Pancreatic Surgery, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Kun Ke
- General Surgery, Cancer Center, Department of Gastrointestinal and Pancreatic Surgery, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Zaiyuan Ye
- General Surgery, Cancer Center, Department of Gastrointestinal and Pancreatic Surgery, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Guoxi Xu
- Department of Gastrointestinal Surgery, Jinjiang Municipal Hospital, Jinjiang, Quanzhou, Fujian, China
| |
Collapse
|
3
|
Zhang Y, Yu Y, Yuan L, Zhang B. EZH2 Promotes Glioma Cell Proliferation, Invasion, and Migration via Mir-142-3p/KCNQ1OT1/HMGB3 Axis : Running Title: EZH2 Promotes Glioma cell Malignant Behaviors. Mol Neurobiol 2024:10.1007/s12035-024-04080-0. [PMID: 38556567 DOI: 10.1007/s12035-024-04080-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 02/28/2024] [Indexed: 04/02/2024]
Abstract
This study investigates the role and molecular mechanism of EZH2 in glioma cell proliferation, invasion, and migration. EZH2, miR-142-3p, lncRNA KCNQ1OT1, LIN28B, and HMGB3 expressions in glioma tissues and cells were determined using qRT-PCR or Western blot, followed by CCK-8 assay detection of cell viability, Transwell detection of invasion and migration, ChIP analysis of the enrichment of EZH2 and H3K27me3 on miR-142-3p promoter, dual-luciferase reporter assay and RIP validation of the binding of miR-142-3p-KCNQ1OT1 and KCNQ1OT1-LIN28B, and actinomycin D detection of KCNQ1OT1 and HMGB3 mRNA stability. A nude mouse xenograft model and a lung metastasis model were established. EZH2, KCNQ1OT1, LIN28B, and HMGB3 were highly expressed while miR-142-3p was poorly expressed in gliomas. EZH2 silencing restrained glioma cell proliferation, invasion, and migration. EZH2 repressed miR-142-3p expression by elevating the H3K27me3 level. miR-142-3p targeted KCNQ1OT1 expression, and KCNQ1OT1 bound to LIN28B to stabilize HMGB3 mRNA, thereby promoting its protein expression. EZH2 silencing depressed tumor growth and metastasis in nude mice via the miR-142-3p/KCNQ1OT1/HMGB3 axis. In conclusion, EZH2 curbed miR-142-3p expression, thereby relieving the inhibition of KCNQ1OT1 expression by miR-142-3p, enhancing the binding of KCNQ1OT1 to LIN28B, elevating HMGB3 expression, and ultimately accelerating glioma cell proliferation, invasion, and migration.
Collapse
Affiliation(s)
- Yiming Zhang
- Department of Neurosurgery, Beijing Fengtai You'anmen Hospital, Beijing, 100069, China
| | - Yong Yu
- Epilepsy Center, Beijing Fengtai You'anmen Hospital, Beijing, 100069, China
| | - Lei Yuan
- Department of Neurosurgery, PLA Rocket Force Characteristic Medical Center, No. 16, Xin Jie Kou Wai Street, Beijing, 100088, China.
| | - Baozhong Zhang
- Department of Neurosurgery, He Bei Hua Ao Hospital, No. 11, the Changcheng West Street, Zhangjiakou, 075000, Hebei Province, China.
| |
Collapse
|
4
|
Elkahwagy DM, Kiriacos CJ, Sobeih ME, Khorshid OMR, Mansour M. The lncRNAs Gas5, MALAT1 and SNHG8 as diagnostic biomarkers for epithelial malignant pleural mesothelioma in Egyptian patients. Sci Rep 2024; 14:4823. [PMID: 38413635 PMCID: PMC10899637 DOI: 10.1038/s41598-024-55083-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 02/20/2024] [Indexed: 02/29/2024] Open
Abstract
Long noncoding RNAs have been shown to be involved in a myriad of physiological and pathological pathways. To date, malignant pleural mesothelioma (MPM) is considered an extremely aggressive cancer. One reason for this is the late diagnosis of the disease, which can occur within 30-40 years of asbestos exposure. There is an immense need for the development of new, sensitive, inexpensive and easy methods for the early detection of this disease other than invasive methods such as biopsy. The aim of this study was to determine the expression of circulating lncRNAs in mesothelioma patient plasma to identify potential biomarkers. Ten previously identified lncRNAs that were shown to be aberrantly expressed in mesothelioma tissues were selected as candidates for subsequent validation. The expression of the ten selected candidate lncRNAs was verified via quantitative PCR (qPCR) in human plasma samples from mesothelioma patients versus healthy controls. The expression levels of circulating GAS5, SNHG8 and MALAT1 were significantly greater in plasma samples from patients than in those from controls. The ROC analysis of both MALAT1 and SNHG8 revealed 88.89% sensitivity and 66.67% specificity. The sensitivity of these markers was greater than that of GAS5 (sensitivity 72.22% and specificity 66.67%). The regression model for GAS5 was statistically significant, while that for SNHG8 and MALAT1 was not significant due to the small sample size. The area under the curve (AUC) of the three ROC curves was acceptable and significant: 0.7519 for GAS5, 0.7352 for SNHG8 and 0.7185 for MALAT1. This finding confirmed their ability to be used as markers. The three lncRNAs were not affected by age, sex or smoking status. The three lncRNAs showed great potential as independent predictive diagnostic biomarkers. Although the prediction model for MALAT1 did not significantly differ, MALAT1 was significantly expressed in patients more than in controls (p = 0.0266), and the recorded sensitivity and specificity were greater than those of GAS5.
Collapse
Affiliation(s)
- Dina Mohamed Elkahwagy
- Pharmaceutical Biology Department, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo, 11835, Egypt
| | - Caroline Joseph Kiriacos
- Pharmaceutical Biology Department, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo, 11835, Egypt
| | - Mohamed Emam Sobeih
- Department of Medical Oncology, National Cancer Institute, NCI, Cairo University, Cairo, Egypt
| | - Ola M Reda Khorshid
- Department of Medical Oncology, National Cancer Institute, NCI, Cairo University, Cairo, Egypt
| | - Manar Mansour
- Pharmaceutical Biology and Microbiology Department, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo, Egypt.
- Department of Pharmaceutical Biology, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo, 11835, Egypt.
| |
Collapse
|
5
|
Quan ZH, Xu FP, Huang Z, Chen RH, Xu QW, Lin L. LncRNA MYLK antisense RNA 1 activates cell division cycle 42/Neutal Wiskott-Aldrich syndrome protein pathway via microRNA-101-5p to accelerate epithelial-to-mesenchymal transition of colon cancer cells. Kaohsiung J Med Sci 2024; 40:11-22. [PMID: 37950620 DOI: 10.1002/kjm2.12773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 09/13/2023] [Accepted: 09/20/2023] [Indexed: 11/13/2023] Open
Abstract
Long noncoding RNA MYLK antisense RNA 1 (MYLK-AS1) is the crux in multiple diseases. Therefore, the purpose of this study was to investigate the possible mechanism of MYLK-AS1. A total of 62 colon cancer (CC) specimens and paired adjacent normal tissues were collected, and the expression of MYLK-AS1, microRNA (miR)-101-5p/cell division cycle 42 (CDC42) was detected. CC cell lines were transfected with MYLK-AS1, miR-101-5p, CDC42-related plasmids, and the biological functions and markers of epithelial-mesenchymal transition (EMT) were analyzed. The binding relationship between MYLK-AS1, miR-101-5p, and CDC42 was evaluated. In CC tissues and cell lines, MYLK-AS1 and CDC42 were highly expressed, and miR-101-5p was lowly expressed. Inhibition of MYLK-AS1 or upregulation of miR-101-5p can inhibit CC cell growth and EMT. miR-101-5p inhibited CDC42/N-wasp axis activation in CC cells by targeting CDC42. Knockdown of CDC42 or upregulation of miR-101-5p partially reversed the effects caused by upregulation of MYLK-AS1. MYLK-AS1, which is significantly upregulated in CC, may be a molecular sponge for miR-101-5p, and MYLK-AS1 promotes the activation of the CDC42/N-wasp axis in CC cells by targeting CDC42 through miR-101-5p, which in turn promotes tumor development. MYLK-AS1 may be a potential biomarker and target for CC therapy.
Collapse
Affiliation(s)
- Zhen-Hao Quan
- Department of Gastrointestinal Surgery, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong, China
| | - Fei-Peng Xu
- Department of Gastrointestinal Surgery, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong, China
| | - Zhe Huang
- Department of Gastrointestinal Surgery, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong, China
| | - Ri-Hong Chen
- Department of Gastrointestinal Surgery, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong, China
| | - Qing-Wen Xu
- Department of Gastrointestinal Surgery, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong, China
| | - Lin Lin
- Department of Gastrointestinal Surgery, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong, China
| |
Collapse
|
6
|
Chen B, Tan L, Wang Y, Yang L, Liu J, Chen D, Huang S, Mao F, Lian J. LOC102549726/miR-760-3p network is involved in the progression of ISO-induced pathological cardiomyocyte hypertrophy via endoplasmic reticulum stress. J Mol Histol 2023; 54:675-687. [PMID: 37899367 PMCID: PMC10635935 DOI: 10.1007/s10735-023-10166-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Accepted: 09/30/2023] [Indexed: 10/31/2023]
Abstract
Pathological cardiac hypertrophy (CH) is featured by myocyte enlargement and cardiac malfunction. Multiple signaling pathways have been implicated in diverse pathological and physiological processes in CH. However, the function of LOC102549726/miR-760-3p network in CH remains unclear. Here, we characterize the functional role of LOC102549726/miR-760-3p network in CH and delineate the underlying mechanism. The expression of LncRNA LOC102549726 and hypertrophic markers was significantly increased compared to the control, while the level of miR-760-3p was decreased. Next, we examined ER stress response in a hypertrophic cardiomyocyte model. The expression of ER stress markers was greatly enhanced after incubation with ISO. The hypertrophic reaction, ER stress response, and increased potassium and calcium ion channels were alleviated by genetic downregulation of LOC102549726. It has been demonstrated that LOC102549726 functions as a competitive endogenous RNA (ceRNA) of miR-760-3p. Overexpression of miR-760-3p decreased cell surface area and substantially mitigated ER stress response; protein levels of potassium and calcium channels were also significantly up-regulated compared to the NC control. In contrast, miR-760-3p inhibition increased cell size, aggravated CH and ER stress responses, and reduced ion channels. Collectively, in this study we demonstrated that the LOC102549726/miR-760-3p network was a crucial regulator of CH development. Ion channels mediate the ER stress response and may be a downstream sensor of the LOC102549726/miR-760-3p network. Therefore, these findings advance our understanding of pathological CH and provide new insights into therapeutic targets for cardiac remodeling.
Collapse
Affiliation(s)
- Bangsheng Chen
- Emergency Medical Center, Ningbo Yinzhou No. 2 Hospital, Ningbo, Zhejiang, 315192, China
| | - Lian Tan
- Intensive Care Unit, Ningbo Yinzhou No. 2 Hospital, Ningbo, Zhejiang, 315192, China
| | - Ying Wang
- Cadiovascular Department, Ningbo Medical Center LiHuiLi Hospital, Ningbo, Zhejiang, 315100, China
| | - Lei Yang
- Emergency Medical Center, Ningbo Yinzhou No. 2 Hospital, Ningbo, Zhejiang, 315192, China
| | - Jiequan Liu
- Emergency Medical Center, Ningbo Yinzhou No. 2 Hospital, Ningbo, Zhejiang, 315192, China
| | - Danqi Chen
- Intensive Care Unit, Ningbo Yinzhou No. 2 Hospital, Ningbo, Zhejiang, 315192, China
| | - Shuaishuai Huang
- Laboratory of Renal Carcinoma, Ningbo Yinzhou No. 2 Hospital, Ningbo, Zhejiang, 315192, China
| | - Feiyan Mao
- Department of General Surgery, HwaMei Hospital, University of Chinese Academy of Sciences, Ningbo, Zhejiang, 315100, China
| | - Jiangfang Lian
- Cadiovascular Department, Ningbo Medical Center LiHuiLi Hospital, Ningbo, Zhejiang, 315100, China.
| |
Collapse
|
7
|
Li F, Chen X. Contribution and underlying mechanisms of lncRNA TRPM2-AS in the development and progression of human cancers. Pathol Res Pract 2023; 251:154887. [PMID: 37871443 DOI: 10.1016/j.prp.2023.154887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 10/07/2023] [Accepted: 10/11/2023] [Indexed: 10/25/2023]
Abstract
Long-stranded non-coding RNAs (lncRNAs) are RNA molecules that are longer than 200 nucleotides and do not code for proteins. They play a significant role in various biological processes, including epigenetics, cell cycle, and cell differentiation. Many studies have shown that the occurrence of human cancer is closely related to the abnormal expression of lncRNA. In recent years, lncRNAs have been a hot topic in cancer research. TRPM2-AS, a novel lncRNA, is aberrantly expressed in many human cancers, and its overexpression is strongly linked to poor clinical outcomes in patients. It has been demonstrated that TRPM2-AS acts as a ceRNA, participates in signaling pathways, and interacts with biological proteins and other molecular mechanisms to regulate gene expression. In addition, it can regulate the proliferation, migration, invasion, apoptosis, and treatment resistance of cancer cells. As a result, TRPM2-AS may be a potential target for cancer treatment and a possible biomarker for cancer prognosis. This review outlined the expression, biological processes, and molecular mechanisms of TRPM2-AS in various malignancies, and discussed potential therapeutic uses.
Collapse
Affiliation(s)
- Fei Li
- Department of Gynecology, Harbin Medical University Cancer Hospital, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Xiuwei Chen
- Department of Gynecology, Harbin Medical University Cancer Hospital, Harbin Medical University, Harbin, Heilongjiang 150081, China.
| |
Collapse
|
8
|
Jiang W, Chen Y, Sun M, Huang X, Zhang H, Fu Z, Wang J, Zhang S, Lian C, Tang B, Xiang D, Wang Y, Zhang Y, Jian C, Yang C, Zhang J, Zhang D, Chen T, Zhang J. LncRNA DGCR5-encoded polypeptide RIP aggravates SONFH by repressing nuclear localization of β-catenin in BMSCs. Cell Rep 2023; 42:112969. [PMID: 37573506 DOI: 10.1016/j.celrep.2023.112969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 06/21/2023] [Accepted: 07/26/2023] [Indexed: 08/15/2023] Open
Abstract
The differentiation fate of bone marrow mesenchymal stem cells (BMSCs) affects the progression of steroid-induced osteonecrosis of the femoral head (SONFH). We find that lncRNA DGCR5 encodes a 102-amino acid polypeptide, RIP (Rac1 inactivated peptide), which promotes the adipogenic differentiation of BMSCs and aggravates the progression of SONFH. RIP, instead of lncRNA DGCR5, binds to the N-terminal motif of RAC1, and inactivates the RAC1/PAK1 cascade, resulting in decreased Ser675 phosphorylation of β-catenin. Ultimately, the nuclear localization of β-catenin decreases, and the differentiation balance of BMSCs tilts toward the adipogenesis lineage. In the femoral head of rats, overexpression of RIP causes trabecular bone disorder and adipocyte accumulation, which can be rescued by overexpressing RAC1. This finding expands the regulatory role of lncRNAs in BMSCs and suggests RIP as a potential therapeutic target.
Collapse
Affiliation(s)
- Weiqian Jiang
- Department of Orthopedics, the First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Yu Chen
- Department of Orthopedics, the First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Mingjie Sun
- Department of Orthopedics, the First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Xiao Huang
- Department of Orthopedics, the First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Hongrui Zhang
- Department of Orthopedics, the First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Zheng Fu
- Department of Orthopedics, Binzhou People's Hospital, Binzhou, Shandong Province, China
| | - Jingjiang Wang
- Department of Orthopedics, the Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Shichun Zhang
- Department of Orthopedics, the Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Chengjie Lian
- Department of Orthopedics, the First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Boyu Tang
- Department of Orthopedics, the First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Dulei Xiang
- Department of Orthopedics, the First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Yange Wang
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, China
| | - Yulu Zhang
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, China
| | - Changchun Jian
- Department of Orthopedics, the First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Chaohua Yang
- Department of Orthopedics, the First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Jun Zhang
- Department of Orthopedics, the First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Dian Zhang
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, China
| | - Tingmei Chen
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, China
| | - Jian Zhang
- Department of Orthopedics, the First Affiliated Hospital of Chongqing Medical University, Chongqing, China.
| |
Collapse
|
9
|
Wang Q, Long Z, Zhu F, Li H, Xiang Z, Liang H, Wu Y, Dai X, Zhu Z. Integrated analysis of lncRNA/circRNA-miRNA-mRNA in the proliferative phase of liver regeneration in mice with liver fibrosis. BMC Genomics 2023; 24:417. [PMID: 37488484 PMCID: PMC10364436 DOI: 10.1186/s12864-023-09478-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 06/22/2023] [Indexed: 07/26/2023] Open
Abstract
BACKGROUND Non-coding RNAs play important roles in liver regeneration; however, their functions and mechanisms of action in the regeneration of fibrotic liver have not been elucidated. We aimed to clarify the expression patterns and regulatory functions of lncRNAs, circRNAs, miRNAs, and mRNAs in the proliferative phase of fibrotic liver regeneration. METHODS Based on a mouse model of liver fibrosis with 70% hepatectomy, whole-transcriptome profiling was performed using high-throughput sequencing on samples collected at 0, 12, 24, 48, and 72 h after hepatectomy. Hub genes were selected by weighted gene co-expression network analysis and subjected to enrichment analysis. Integrated analysis was performed to reveal the interactions of differentially expressed (DE) lncRNAs, circRNAs, miRNAs, and mRNAs, and to construct lncRNA-mRNA cis- and trans-regulatory networks and lncRNA/circRNA-miRNA-mRNA ceRNA regulatory networks. Real-Time quantitative PCR was used to validate part of the ceRNA network. RESULTS A total of 1,329 lncRNAs, 48 circRNAs, 167 miRNAs, and 6,458 mRNAs were differentially expressed, including 812 hub genes. Based on these DE RNAs, we examined several mechanisms of ncRNA regulatory networks, including lncRNA cis and trans interactions, circRNA parental genes, and ceRNA pathways. We constructed a cis-regulatory core network consisting of 64 lncRNA-mRNA pairs (53 DE lncRNAs and 58 hub genes), a trans-regulatory core network consisting of 103 lncRNA-mRNA pairs (18 DE lncRNAs and 85 hub genes), a lncRNA-miRNA-mRNA ceRNA core regulatory network (20 DE lncRNAs, 12 DE miRNAs, and 33 mRNAs), and a circRNA-miRNA-mRNA ceRNA core regulatory network (5 DE circRNAs, 5 DE miRNAs, and 39 mRNAs). CONCLUSIONS These results reveal the expression patterns of lncRNAs, circRNAs, miRNAs, and mRNAs in the proliferative phase of fibrotic liver regeneration, as well as core regulatory networks of mRNAs and non-coding RNAs underlying liver regeneration. The findings provide insights into molecular mechanisms that may be useful in developing new therapeutic approaches to ameliorate diseases that are characterized by liver fibrosis, which would be beneficial for the prevention of liver failure and treatment of liver cancer.
Collapse
Affiliation(s)
- Qian Wang
- The First Affiliated Hospital, Department of Reproductive Medicine, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
| | - Zhangtao Long
- The First Affiliated Hospital, Department of Hepatobiliary Surgery, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
| | - Fengfeng Zhu
- The First Affiliated Hospital, Department of Hepatobiliary Surgery, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
| | - Huajian Li
- The First Affiliated Hospital, Department of Hepatobiliary Surgery, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
| | - Zhiqiang Xiang
- The First Affiliated Hospital, Department of Hepatobiliary Surgery, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
| | - Hao Liang
- The First Affiliated Hospital, Department of Hepatobiliary Surgery, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
| | - Yachen Wu
- The First Affiliated Hospital, Department of Hepatobiliary Surgery, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
| | - Xiaoming Dai
- The First Affiliated Hospital, Department of Hepatobiliary Surgery, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.
| | - Zhu Zhu
- The First Affiliated Hospital, Department of Hepatobiliary Surgery, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.
- The First Affiliated Hospital, Department of Education and Training, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.
| |
Collapse
|
10
|
Xiang X, Guo Y, Chen Z, Zhang F, Qin Y. Accurate prognostic prediction for patients with clear cell renal cell carcinoma using a ferroptosis-related long non-coding RNA risk model. Cancer Biomark 2023:CBM210445. [PMID: 37248883 DOI: 10.3233/cbm-210445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
INTRODUCTION Ferroptosis is a recently discovered type of programmed cell death that plays a crucial role in tumor occurrence and progression. However, no prognostic model has been established yet for clear cell renal cell carcinoma (ccRCC) using ferroptosis-related long non-coding RNAs (lncRNAs). METHODS In the present study, lncRNA expression profiles, sex, age, TMN stage, and other clinical data of ccRCC samples were extracted from The Cancer Genome Atlas database. In addition, ferroptosis-related lncRNAs were identified using co-expression analysis, and the risk model was established using Cox regression and least absolute shrinkage and selection operator regression analyses. Log-rank test and Kaplan-Meier analysis were performed to evaluate the predictive accuracy of the risk model for the overall survival (OS) of patients with ccRCC. Moreover, the functional enrichment of ferroptosis-related lncRNAs was performed and visualized using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes. RESULTS Eight prognostic ferroptosis-related lncRNAs were identified, such as LINC01615, AC026401.3, LINC00944, AL590094.1, DLGAP1-AS2, AC016773.1, AC147651.1, and AP000439.2, making up the ferroptosis-related lncRNA risk model. The risk model effectively divided patients with ccRCC into high- and low-risk groups, and their survival time was calculated. The high-risk group showed significantly shorter OS compared to the low-risk group. The nomogram to predict the survival rate of the patients revealed that the risk score was the most critical factor affecting OS in patients with ccRCC. The ferroptosis-related lncRNA risk model was an independent predictor of prognostic risk assessment in patients with ccRCC. CONCLUSION The ferroptosis-related lncRNAs risk model and genomic clinicopathological nomogram have the potential to accurately predict the prognosis of patients with ccRCC and could serve as potential therapeutic targets in the future.
Collapse
Affiliation(s)
- Xuebao Xiang
- Department of Urology, Affiliated Hospital of Guilin Medical College Guilin, Guangxi, China
| | - Yi Guo
- Centre for Genomic and Personalized Medicine Guangxi Medical University, Nanning, Guangxi, China
| | - Zhongyuan Chen
- Centre for Genomic and Personalized Medicine Guangxi Medical University, Nanning, Guangxi, China
| | - Fangxin Zhang
- Centre for Genomic and Personalized Medicine Guangxi Medical University, Nanning, Guangxi, China
| | - Yan Qin
- Department of Health Management, The People's Hospital of Guangxi Zhuang Autonomous Region and Research Center of Health Management, Guangxi Academy of Medical Sciences, Nanning, Guangxi, China
| |
Collapse
|
11
|
Xin X, Jia-Yin Y, Jun-Yang H, Rui W, Xiong-Ri K, Long-Rui D, Liu J, Jue-Yu Z. Comprehensive analysis of lncRNA-mRNA co-expression networks in HPV-driven cervical cancer reveals the pivotal function of LINC00511-PGK1 in tumorigenesis. Comput Biol Med 2023; 159:106943. [PMID: 37099974 DOI: 10.1016/j.compbiomed.2023.106943] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Revised: 04/06/2023] [Accepted: 04/14/2023] [Indexed: 04/28/2023]
Abstract
BACKGROUND Mounting evidence suggests that noncoding RNAs (lncRNAs) were involved in various human cancers. However, the role of these lncRNAs in HPV-driven cervical cancer (CC) has not been extensively studied. Considering that HR-HPV infections contribute to cervical carcinogenesis by regulating the expression of lncRNAs, miRNAs and mRNAs, we aim to systematically analyze lncRNAs and mRNAs expression profile to identify novel lncRNAs-mRNAs co-expression networks and explore their potential impact on tumorigenesis in HPV-driven CC. METHODS LncRNA/mRNA microarray technology was utilized to identify the differentially expressed lncRNAs (DElncRNAs) and mRNAs (DEmRNAs) in HPV-16 and HPV-18 cervical carcinogenesis compared to normal cervical tissues. Venn diagram and weighted gene co-expression network analysis (WGCNA) were used to identify the hub DElncRNAs/DEmRNAs that were both significantly correlated with HPV-16 and HPV-18 CC patients. LncRNA-mRNA correlation analysis and functional enrichment pathway analysis were performed on these key DElncRNAs/DEmRNAs in HPV-16 and HPV-18 CC patients to explore their mutual mechanism in HPV-driven CC. A lncRNA-mRNA co-expression score (CES) model was established and validated by using the Cox regression method. Afterward, the clinicopathological characteristics were analyzed between CES-high and CES-low groups. In vitro, functional experiments were performed to evaluate the role of LINC00511 and PGK1 in cell proliferation, migration and invasion in CC cells. To understand whether LINC00511 play as an oncogenic role partially via modulating the expression of PGK1, rescue assays were used. RESULTS We identified 81 lncRNAs and 211 mRNAs that were commonly differentially expressed in HPV-16 and HPV-18 CC tissues compared to normal tissues. The results of lncRNA-mRNA correlation analysis and functional enrichment pathway analysis showed that the LINC00511-PGK1 co-expression network may make an important contribution to HPV-mediated tumorigenesis and be closely associated with metabolism-related mechanisms. Combined with clinical survival data, the prognostic lncRNA-mRNA co-expression score (CES) model based on LINC00511 and PGK1 could precisely predict patients' overall survival (OS). CES-high patients had a worse prognosis than CES-low patients and the enriched pathways and potential targets of applicable drugs were explored in CES-high patients. In vitro experiments confirmed the oncogenic functions of LINC00511 and PGK1 in the progression of CC, and revealed that LINC00511 functions in an oncogenic role in CC cells partially via modulating the expression of PGK1. CONCLUSIONS Together, these data identify co-expression modules that provide valuable information to understand the pathogenesis of HPV-mediated tumorigenesis, which highlights the pivotal function of the LINC00511-PGK1 co-expression network in cervical carcinogenesis. Furthermore, our CES model has a reliable predicting ability that could stratify CC patients into low- and high-risk groups of poor survival. This study provides a bioinformatics method to screen prognostic biomarkers which leads to lncRNA-mRNA co-expression network identification and construction for patients' survival prediction and potential drug applications in other cancers.
Collapse
Affiliation(s)
- Xu Xin
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, Guangdong, China
| | - Yu Jia-Yin
- Department of Radiation Medicine, Guangdong Provincial Key Laboratory for Safety Evaluation of Cosmetics, School of Public Health, Southern Medical University, Guangzhou, 510515, China
| | - Huang Jun-Yang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, Guangdong, China; School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, Guangdong, China
| | - Wang Rui
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, Guangdong, China
| | - Kuang Xiong-Ri
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, Guangdong, China
| | - Dang Long-Rui
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, Guangdong, China
| | - Jie Liu
- Department of Gynaecology and Obstetrics, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, Guangdong, China
| | - Zhou Jue-Yu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, Guangdong, China.
| |
Collapse
|
12
|
Zhang S, Cui Y, Gao X, Wei C, Wang Q, Yang B, Sun W, Luo Y, Jiang Q, Huang Y. Resveratrol inhibits the formation and accumulation of lipid droplets through AdipoQ signal pathway and lipid metabolism lncRNAs. J Nutr Biochem 2023; 117:109351. [PMID: 37087074 DOI: 10.1016/j.jnutbio.2023.109351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 02/01/2023] [Accepted: 04/10/2023] [Indexed: 04/24/2023]
Abstract
Resveratrol (RES) is one of the best-known bioactive polyphenols that has received much attention in recent years because of its importance to anti-obesity. However, the exact mechanism underlying this effect and whether it can improve lipid metabolism by regulating the long-chain non-coding RNA (lncRNA) remains unclear. In this study, twenty-four healthy crossbred castrated boars were fed a basal diet (control) and a basal diet supplemented with 200 mg, 400 mg or 600 mg RES per Kilogram (kg) of feed for 41 days, respectively. We founded that 400mg/kg and 600mg/kg RES-supplemented diet did not affect growth rate, but reduced significantly subcutaneous adipose thickness, carcass fat rate, greater dramatically the serum concentration of adiponectin and high-density lipoprotein in pigs. Further, we verified that RES could inhibit the formation and accumulation of lipid droplets by AdipoQ-AdipoR1-AMPKα and AdipoQ-AdipoR2-PPARα signal pathway in vivo and vitro (3T3-L1 preadipocytes). Transcriptome analyses founded that 5 differently expressed (DE) lncRNAs and 77 mRNAs in subcutaneous adipose between control group and 400 mg/kg RES group, which mainly involved in "adipocytokine signaling pathway", "Wnt signaling pathway", "PI3K-Akt signaling pathway" and "MAPK signaling pathway". In conclusion, RES can inhibit the formation and accumulation of lipid droplets through AdipoQ signal pathway and lipid metabolism-related lncRNAs. Our results provide a new insight on the molecular mechanism of RES as a nutritional agents to the prevention and treatment for obesity.
Collapse
Affiliation(s)
- Sanbao Zhang
- College of Animal Science and Technology, Guangxi University, Nanning Guangxi 530004, China.
| | - Yueyue Cui
- College of Animal Science and Technology, Guangxi University, Nanning Guangxi 530004, China.
| | - Xiaotong Gao
- College of Animal Science and Technology, Guangxi University, Nanning Guangxi 530004, China.
| | - Chongwan Wei
- College of Animal Science and Technology, Guangxi University, Nanning Guangxi 530004, China.
| | - Qian Wang
- College of Animal Science and Technology, Guangxi University, Nanning Guangxi 530004, China.
| | - Bao Yang
- College of Animal Science and Technology, Guangxi University, Nanning Guangxi 530004, China.
| | - Wenyue Sun
- College of Animal Science and Technology, Guangxi University, Nanning Guangxi 530004, China.
| | - Yunyan Luo
- College of Animal Science and Technology, Guangxi University, Nanning Guangxi 530004, China.
| | - Qinyang Jiang
- College of Animal Science and Technology, Guangxi University, Nanning Guangxi 530004, China.
| | - Yanna Huang
- College of Animal Science and Technology, Guangxi University, Nanning Guangxi 530004, China.
| |
Collapse
|
13
|
Feng H, Wang S, Wang Y, Ni X, Yang Z, Hu X, Sen Yang. LncCat: An ORF attention model to identify LncRNA based on ensemble learning strategy and fused sequence information. Comput Struct Biotechnol J 2023; 21:1433-1447. [PMID: 36824229 PMCID: PMC9941877 DOI: 10.1016/j.csbj.2023.02.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 02/06/2023] [Accepted: 02/06/2023] [Indexed: 02/10/2023] Open
Abstract
Background Long non-coding RNA (lncRNA) is one of the most essential forms of transcripts, playing crucial regulatory roles in the development of cancers and diseases without protein-coding ability. It was assumed that short ORFs (sORFs) in lncRNA were weak to translate proteins. However, recent research has shown that sORFs can encode peptides, which increases the difficulty to identify lncRNA. Therefore, identifying lncRNAs with sORFs facilitates finding novel regulatory factors. Results In this paper, we propose LncCat for identifying lncRNA based on category boosting (CatBoost) and ORF-attention features. LncCat combines five types of features to encode transcript sequences and employs CatBoost to build a prediction model. In addition, the visualization comparison reveals that the ORF-attention features between lncRNAs and protein-coding transcripts are significantly distinct. The comparison results show that LncCat outperforms competing methods on several benchmark datasets. For Matthew's Correlation Coefficient (MCC), LncCat achieves 0.9503, 0.9219, 0.8591, 0.8672, and 0.9047 on the human, mouse, zebrafish, wheat, and chicken datasets, with improvements ranging from 1.90% to 7.82%, 1.49-17.63%, 6.11-21.50%, 3.02-51.64% and 5.35-26.90%, respectively. Moreover, LncCat dramatically improves the MCC by at least 11.90%, 12.96% and 42.61% on sORF test datasets of human, mouse, and zebrafish, respectively. Conclusions Experiments indicate that LncCat performs better both on long ORF and sORF datasets, and ORF-attention features show positive effects on predicting lncRNA. In brief, LncCat is a reliable method for identifying lncRNA. Additionally, a user-friendly web server is developed for academics at http://cczubio.top/lnccat.
Collapse
Affiliation(s)
- Hongqi Feng
- School of Computer Science and Artificial Intelligence Aliyun School of Big Data School of Software, Changzhou University, Changzhou 213164, China
| | - Shaocong Wang
- School of Computer Science and Artificial Intelligence Aliyun School of Big Data School of Software, Changzhou University, Changzhou 213164, China
| | - Yan Wang
- Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, Changchun 130012, China
- School of Artificial Intelligence, Jilin University, Changchun 130012, China
| | - Xinye Ni
- The Affiliated Changzhou No.2 People’s Hospital of Nanjing Medical University, Changzhou 213164, China
| | - Zexi Yang
- School of Computer Science and Artificial Intelligence Aliyun School of Big Data School of Software, Changzhou University, Changzhou 213164, China
| | - Xuemei Hu
- Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, Changchun 130012, China
| | - Sen Yang
- School of Computer Science and Artificial Intelligence Aliyun School of Big Data School of Software, Changzhou University, Changzhou 213164, China
- The Affiliated Changzhou No.2 People’s Hospital of Nanjing Medical University, Changzhou 213164, China
| |
Collapse
|
14
|
Yang J, Huang Q, Liao P, Zhang P, Sun S, Xu Q. Mechanism of miR-338-3p in sepsis-induced acute lung injury via indirectly modulating ATF4. Transpl Immunol 2023; 76:101681. [PMID: 35926799 DOI: 10.1016/j.trim.2022.101681] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 07/29/2022] [Accepted: 07/30/2022] [Indexed: 01/31/2023]
Abstract
Sepsis is recognized as an inflammation-related syndrome in response to invading pathogens. Many patients suffer from sepsis including transplant recipients. Lipopolysaccharide (LPS) is known to trigger sepsis-related organ dysfunction. This study expounded on the possible effect of microRNA (miR)-338-3p in sepsis-induced acute lung injury (ALI). Firstly, human bronchial epithelial cell line 16HBE received LPS treatment to establish the cell models of sepsis-induced ALI. The expression patterns of miR-338-3p, long non-coding RNA OPA-interacting protein 5 antisense transcript 1 (lncRNA OIP5-AS1), and activating transcription factor 4 (ATF4) in 16HBE cells were examined. Afterwards, 16HBE cell viability, the apoptosis rate, and the levels of inflammation and lactate dehydrogenase (LDH) were determined to assess the degree of cell injury. We disclosed that LPS treatment triggered 16HBE cell injury, downregulated miR-338-3p, and upregulated OIP5-AS1 and ATF4. miR-338-3p overexpression repressed LPS-induced 16HBE cell injury. miR-338-3p diminished OIP5-AS1 stability via binding to OIP5-AS1 and downregulated OIP5-AS1 expression and OIP5-AS1 can enhance ATF4 mRNA stability and upregulate ATF4 mRNA level. The rescue experiments showed that ATF4 overexpression aggravated LPS-induced 16HBE cell injury. Overall, miR-338-3p overexpression decreased OIP5-AS1 expression and stability and further downregulated ATF4 mRNA level, thereby mitigating LPS-induced 16HBE cell injury.
Collapse
Affiliation(s)
- Jing Yang
- Department of Pediatric, Qilu Hospital (Qingdao), Cheeloo College of Medicine, Shandong University, Qingdao 266035, Shandong, China.
| | - Qikun Huang
- Department of Pediatric, Qilu Hospital (Qingdao), Cheeloo College of Medicine, Shandong University, Qingdao 266035, Shandong, China
| | - Peiyuan Liao
- Department of Pediatric, Qilu Hospital (Qingdao), Cheeloo College of Medicine, Shandong University, Qingdao 266035, Shandong, China
| | - Pingli Zhang
- Department of Pediatric, Qilu Hospital (Qingdao), Cheeloo College of Medicine, Shandong University, Qingdao 266035, Shandong, China
| | - Shijing Sun
- Department of Pediatric, Qilu Hospital (Qingdao), Cheeloo College of Medicine, Shandong University, Qingdao 266035, Shandong, China
| | - Qianwen Xu
- Department of Pediatric, Qilu Hospital (Qingdao), Cheeloo College of Medicine, Shandong University, Qingdao 266035, Shandong, China
| |
Collapse
|
15
|
Zhu C, Zhong W, Gong C, Chen B, Guo J. Global research trends on epigenetics and neuropathic pain: A bibliometric analysis. Front Mol Neurosci 2023; 16:1145393. [PMID: 37152435 PMCID: PMC10155611 DOI: 10.3389/fnmol.2023.1145393] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 03/24/2023] [Indexed: 05/09/2023] Open
Abstract
Objective Neuropathic pain (NP) is a common disease that manifests with pathological changes in the somatosensory system. In recent years, the interactions of NP with the epigenetic mechanism have been increasingly elucidated. However, only a few studies have used bibliometric tools to systematically analyze knowledge in this field. The objective of this study is to visually analyze the trends, hotspots, and frontiers in epigenetics and NP research by using a bibliometric method. Methods Studies related to epigenetics and NP were searched from the Science Citation Index-Expanded of the Web of Science Core Collection database. Search time is from inception to November 30, 2022. No restrictions were placed on language. Only articles and reviews were included as document types. Data on institutions, countries, authors, journal distribution, and keywords were imported into CiteSpace software for visual analysis. Results A total of 867 publications met the inclusion criteria, which spanned the period from 2000 to 2022. Over the years, the number of publications and the frequency of citations exhibited a clear upward trend in general, reaching a peak in 2021. The major contributing countries in terms of the number of publications were China, the United States, and Japan. The top three institutions were Rutgers State University, Xuzhou Medical University, and Nanjing Medical University. Molecular Pain, Pain, and Journal of Neuroinflammation contributed significantly to the volume of issues. Among the top 10 authors in terms of the number of publications, Tao Yuan-Xiang contributed 30 entries, followed by Zhang Yi with 24 and Wu Shao-Gen with 20. On the basis of the burst and clusters of keywords, "DNA methylation," "Circular RNA," "acetylation," "long non-coding RNA," and "microglia" are global hotspots in the field. Conclusion The bibliometric analysis indicates that the number of publications related to epigenetics and NP is exhibiting a rapid increase. Keyword analysis shows that "DNA methylation," "Circular RNA," "acetylation," "long non-coding RNA" and "microglia" are the most interesting terms for researchers in the field. More rigorous clinical trials and additional studies that explore relevant mechanisms are required in the future.
Collapse
|
16
|
Li J, Wang Y, Zhang X, Yang X, Qi Q, Mi Q, Feng M, Wang Y, Wang C, Li P, Du L. Characterisation of a novel transcript LNPPS acting as tumour suppressor in bladder cancer via PDCD5-mediated p53 degradation blockage. Clin Transl Med 2023; 13:e1149. [PMID: 36578176 PMCID: PMC9797767 DOI: 10.1002/ctm2.1149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Revised: 11/30/2022] [Accepted: 12/05/2022] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Long non-coding RNAs (lncRNAs) play a crucial role in tumour initiation and progression. However, little is known about their contributions to p53-related bladder cancer (BC) inhibition. METHODS By using high-throughput sequencing, we screened the expression profiles of lncRNAs in BC and adjacent non-tumour tissues. The roles of a novel lncRNA, named LNPPS [a lncRNA for programmed cell death 5 (PDCD5) and p53 stability], were determined by gain- and loss-of-function assays. RNA pull-down followed by mass spectrometry analysis, RNA immunoprecipitation assays and other immunoprecipitation assays were performed to reveal the interactions among LNPPS, PDCD5 and p53, and the regulatory effect of LNPPS on the complex ubiquitination network comprising PDCD5, p53 and mouse double minute 2 homologue (MDM2). RESULTS LNPPS was downregulated in BC and markedly inhibited the viability of BC cells by inducing PDCD5/p53-related apoptosis in vivo and in vitro. Mechanistically, LNPPS, serving as a scaffold, connected PDCD5 and p53 with nucleotides (nt) located at 121-251 nt and 251-306 nt of LNPPS, respectively. This process allowed LNPPS to protect PDCD5 from proteasomal degradation by blocking its K20 site ubiquitination. On the other hand, the increased interaction between PDCD5 and p53 displaced p53 from the MDM2-p53 ubiquitination complex, resulting in an increase in p53 expression and related apoptosis levels. Moreover, LNPPS could induce the accumulation of PDCD5 and p53 in the nucleus and exert a synergistic effect on the prevention of protein degradation. In addition, we confirmed that the downregulation of LNPPS in BC was mediated by the decreased N6-methyladenosine (m6 A) modification. CONCLUSION Our findings highlight a novel cross-talk between LNPPS and the PDCD5/p53/MDM2 ubiquitination axis in BC development, indicating its potential as a therapeutic target for BC patients.
Collapse
Affiliation(s)
- Juan Li
- Department of Clinical LaboratoryThe Second HospitalCheeloo College of MedicineShandong UniversityJinanShandongChina
- Shandong Engineering & Technology Research Center for Tumor Marker DetectionJinanShandongChina
| | - Yifan Wang
- Department of Clinical LaboratoryThe Second HospitalCheeloo College of MedicineShandong UniversityJinanShandongChina
| | - Xinya Zhang
- Department of Clinical LaboratoryThe Second HospitalCheeloo College of MedicineShandong UniversityJinanShandongChina
| | - Xuemei Yang
- Department of Clinical LaboratoryThe Second HospitalCheeloo College of MedicineShandong UniversityJinanShandongChina
- Shandong Engineering & Technology Research Center for Tumor Marker DetectionJinanShandongChina
| | - Qiuchen Qi
- Department of Clinical LaboratoryThe Second HospitalCheeloo College of MedicineShandong UniversityJinanShandongChina
- Shandong Engineering & Technology Research Center for Tumor Marker DetectionJinanShandongChina
| | - Qi Mi
- Department of Clinical LaboratoryThe Second HospitalCheeloo College of MedicineShandong UniversityJinanShandongChina
| | - Maoxiao Feng
- Department of Clinical LaboratoryThe Second HospitalCheeloo College of MedicineShandong UniversityJinanShandongChina
| | - Yunshan Wang
- Department of Clinical LaboratoryThe Second HospitalCheeloo College of MedicineShandong UniversityJinanShandongChina
- Shandong Engineering & Technology Research Center for Tumor Marker DetectionJinanShandongChina
- Shandong Provincial Clinical Medicine Research Center for Clinical LaboratoryJinanShandongChina
| | - Chuanxin Wang
- Department of Clinical LaboratoryThe Second HospitalCheeloo College of MedicineShandong UniversityJinanShandongChina
- Shandong Engineering & Technology Research Center for Tumor Marker DetectionJinanShandongChina
- Shandong Provincial Clinical Medicine Research Center for Clinical LaboratoryJinanShandongChina
| | - Peilong Li
- Department of Clinical LaboratoryThe Second HospitalCheeloo College of MedicineShandong UniversityJinanShandongChina
- Shandong Engineering & Technology Research Center for Tumor Marker DetectionJinanShandongChina
| | - Lutao Du
- Department of Clinical LaboratoryThe Second HospitalCheeloo College of MedicineShandong UniversityJinanShandongChina
- Shandong Engineering & Technology Research Center for Tumor Marker DetectionJinanShandongChina
- Shandong Provincial Clinical Medicine Research Center for Clinical LaboratoryJinanShandongChina
| |
Collapse
|
17
|
Kovaleva O, Sorokin M, Egorova A, Petrenko A, Shelekhova K, Gratchev A. Macrophage - tumor cell interaction beyond cytokines. Front Oncol 2023; 13:1078029. [PMID: 36910627 PMCID: PMC9995642 DOI: 10.3389/fonc.2023.1078029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Accepted: 02/07/2023] [Indexed: 02/25/2023] Open
Abstract
Tumor cells communication with tumor associated macrophages is a highly important factor of tumor malignant potential development. For a long time, studies of this interaction were focused on a cytokine- and other soluble factors -mediated processes. Discovery of exosomes and regulatory RNAs as their cargo opened a broad field of research. Non-coding RNAs (ncRNAs) were demonstrated to contribute significantly to the development of macrophage phenotype, not only by regulating expression of certain genes, but also by providing for feedback loops of macrophage activation. Being a usual cargo of macrophage- or tumor cell-derived exosomes ncRNAs provide an important mechanism of tumor-stromal cell interaction that contributes significantly to the pathogenesis of various types of tumors. Despite the volume of ongoing research there are still many gaps that must be filled before the practical use of ncRNAs will be possible. In this review we discuss the role of regulatory RNAs in the development of macrophage phenotype. Further we review recent studies supporting the hypothesis that macrophages may affect the properties of tumor cells and vice versa tumor cells influence macrophage phenotype by miRNA and lncRNA transported between these cells by exosomes. We suggest that this mechanism of tumor cell - macrophage interaction is highly promising for the development of novel diagnostic and therapeutic strategies, though many problems are still to be solved.
Collapse
Affiliation(s)
- Olga Kovaleva
- Laboratory for Tumor Stromal Cell Biology, Institute of Carcinogenesis, Nikolaj Nikolajevich (N.N.) Blokhin National Medical Research Center of Oncology, Moscow, Russia
| | - Maxim Sorokin
- Laboratory for Tumor Stromal Cell Biology, Institute of Carcinogenesis, Nikolaj Nikolajevich (N.N.) Blokhin National Medical Research Center of Oncology, Moscow, Russia
| | - Anastasija Egorova
- Laboratory for Tumor Stromal Cell Biology, Institute of Carcinogenesis, Nikolaj Nikolajevich (N.N.) Blokhin National Medical Research Center of Oncology, Moscow, Russia
| | - Anatoly Petrenko
- Laboratory for Tumor Stromal Cell Biology, Institute of Carcinogenesis, Nikolaj Nikolajevich (N.N.) Blokhin National Medical Research Center of Oncology, Moscow, Russia
| | - Ksenya Shelekhova
- Department of Pathology, Clinical Research and Practical Center for Specialized Oncological Care, St. Petersburg, Russia.,Pathology Department, SPb Medico-Social Institute, St. Petersburg, Russia
| | - Alexei Gratchev
- Laboratory for Tumor Stromal Cell Biology, Institute of Carcinogenesis, Nikolaj Nikolajevich (N.N.) Blokhin National Medical Research Center of Oncology, Moscow, Russia
| |
Collapse
|
18
|
Xiang X, Guo Y, Chen Z, Zhang F, Huang J, Qin Y. A prognostic risk prediction model based on ferroptosis-related long non-coding RNAs in bladder cancer: A bulk RNA-seq research and scRNA-seq validation. Medicine (Baltimore) 2022; 101:e32558. [PMID: 36595859 PMCID: PMC9794272 DOI: 10.1097/md.0000000000032558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND To construct a prognostic risk model of bladder cancer (BC) from the perspective of long non-coding RNAs (lncRNAs) and ferroptosis, in order to guide clinical prognosis and identify potential therapeutic targets. METHODS In-hours BC samples were collected from 4 patients diagnosed with BC, who underwent radical cystectomy. Single cell transcriptome sequencing was performed and Seurat package were used for quality control and secondary analysis. LncRNAs expression profiles of BC samples were extracted from The Cancer Genome Atlas database. And sex, age, tumor, node, metastasis stage and other clinical data was downloaded at the same time. Ferroptosis-related lncRNAs were identified by co-expression analysis. We constructed a risk model by Cox regression and least absolute shrinkage and selection operator regression analyses. The predictive strength of the risk model for overall survival (OS) of patients with BC was evaluated by the log-rank test and Kaplan-Meier method. Finally, the enrichment analysis was performed and visualized. RESULTS We identified and included 15 prognostic ferroptosis-related lncRNAs (AL356740.1, FOXC2AS1, ZNF528AS1, LINC02535, PSMB8AS1, AL590428.1, AP000347.2, OCIAD1-AS1, AP001347.1, AC104986.2, AC018926.2, LINC00867, AC099518.4, USP30-AS1, and ARHGAP5-AS1), to build our ferroptosis-related lncRNAs risk model. Using this risk model, BC patients were divided into high and low-risk groups, and their respective survival lengths were calculated. The results showed that the OS of the low-risk group was significantly longer than that of the high-risk group. A nomogram was utilized to predict the survival rate of BC patients. As indicated in the nomogram, risk score was the most important indicator of OS in patients with BC. The ferroptosis-related lncRNAs risk model is an independent tool for prognostic risk assessment in patients with BC. Single cell transcriptome sequencing suggests that ferroptosis-related lncRNAs express specifically in BC tumor microenvironment. AL356740.1, LINC02535 and LINC00867 were mainly expressed in tumor cells. CONCLUSION The risk model based on the ferroptosis-related lncRNAs and the genomic clinico-pathological nomogram could be used to accurately predict the prognosis of patients with BC. The lncRNAs used to build this model might become potential therapeutic targets in the future.
Collapse
Affiliation(s)
- Xuebao Xiang
- Department of Urology, Affiliated Hospital of Guilin Medical College, Guilin, People’s Republic of China
- Centre for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, People’s Republic of China
| | - Yi Guo
- Centre for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, People’s Republic of China
| | - Zhongyuan Chen
- Centre for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, People’s Republic of China
| | - Fangxin Zhang
- Centre for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, People’s Republic of China
| | - Jiefu Huang
- Department of Urology, Affiliated Hospital of Guilin Medical College, Guilin, People’s Republic of China
| | - Yan Qin
- Department of Health Management, The People’s Hospital of Guangxi Zhuang Autonomous Region & Research center of Health Management, Guangxi Academy of Medical Sciences, Nanning, People’s Republic of China
- * Correspondence: Yan Qin, Department of Health Management, The People’s Hospital of Guangxi Zhuang Autonomous Region & Research center of Health Management, Guangxi Academy of Medical Sciences, Nanning, Guangxi 530021, People’s Republic of China (e-mail: )
| |
Collapse
|
19
|
Wu EY, Huang LP, Bao JH. miR-96-5p regulates cervical cancer cell resistance to cisplatin by inhibiting lncRNA TRIM52-AS1 and promoting IGF2BP2. Kaohsiung J Med Sci 2022; 38:1178-1189. [PMID: 36354205 DOI: 10.1002/kjm2.12593] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 08/02/2022] [Accepted: 08/16/2022] [Indexed: 11/11/2022] Open
Abstract
MicroRNA (miRNA) and long noncoding RNA (lncRNA) are both regulators of cancer progression. This study sought to discuss the functional mechanism of miR-96-5p/lncRNA TRIM52 antisense RNA 1 (head-to-head; TRIM52-AS1) in cervical cancer (CC) cell resistance to cisplatin (DDP). DDP-resistant CC cell line was established using increasing concentrations of DDP, followed by transfection with miR-96-5p inhibitor, or si-TRIM52-AS1, or insulin-like growth factor 2 mRNA binding protein 2 (IGF2BP2) overexpression vector. Expression levels of miR-96-5p, TRIM52-AS1, and IGF2BP2 were determined. Changes in IC50 value to DDP, cell proliferation, and apoptosis rate were evaluated by cell-counting kit-8 assay, colony formation, and flow cytometry. The bindings of miR-96-5p to IGF2BP2 and TRIM52-AS1 to IGF2BP2 were verified by dual-luciferase or RNA pull-down assays. These experiments revealed an up-expression of miR-96-5p and IGF2BP2 while an under-expression of TRIM52-AS1 in CC cells. After DDP treatment, miR-96-5p inhibition increased apoptosis and decreased proliferation and DDP resistance. miR-96-5p bound to TRIM52-AS1 and downregulated TRIM52-AS1 expression, and TRIM52-AS1 bound to IGF2BP2 to inhibit IGF2BP2 expression. TRIM52-AS1 inhibition or IGF2BP2 overexpression neutralized the inhibition of silencing miR-96-5p on CC cell resistance to DDP. Overall, miR-96-5p improved CC cell resistance to DDP by inhibiting TRIM52-AS1 and promoting IGF2BP2.
Collapse
Affiliation(s)
- En Yuesu Wu
- Department of Gynecology II, Affiliated Hospital of Inner Mongolia Minzu University, Tongliao, Inner Mongolia, China
| | - Li-Ping Huang
- Department of Gynecology II, Affiliated Hospital of Inner Mongolia Minzu University, Tongliao, Inner Mongolia, China
| | - Jin-Hua Bao
- Department of Gynecology II, Affiliated Hospital of Inner Mongolia Minzu University, Tongliao, Inner Mongolia, China
| |
Collapse
|
20
|
Zhang H, Wang Y, Pan Z, Sun X, Mou M, Zhang B, Li Z, Li H, Zhu F. ncRNAInter: a novel strategy based on graph neural network to discover interactions between lncRNA and miRNA. Brief Bioinform 2022; 23:6747810. [PMID: 36198065 DOI: 10.1093/bib/bbac411] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 08/04/2022] [Accepted: 08/23/2022] [Indexed: 12/14/2022] Open
Abstract
In recent years, many studies have illustrated the significant role that non-coding RNA (ncRNA) plays in biological activities, in which lncRNA, miRNA and especially their interactions have been proved to affect many biological processes. Some in silico methods have been proposed and applied to identify novel lncRNA-miRNA interactions (LMIs), but there are still imperfections in their RNA representation and information extraction approaches, which imply there is still room for further improving their performances. Meanwhile, only a few of them are accessible at present, which limits their practical applications. The construction of a new tool for LMI prediction is thus imperative for the better understanding of their relevant biological mechanisms. This study proposed a novel method, ncRNAInter, for LMI prediction. A comprehensive strategy for RNA representation and an optimized deep learning algorithm of graph neural network were utilized in this study. ncRNAInter was robust and showed better performance of 26.7% higher Matthews correlation coefficient than existing reputable methods for human LMI prediction. In addition, ncRNAInter proved its universal applicability in dealing with LMIs from various species and successfully identified novel LMIs associated with various diseases, which further verified its effectiveness and usability. All source code and datasets are freely available at https://github.com/idrblab/ncRNAInter.
Collapse
Affiliation(s)
- Hanyu Zhang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China.,Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou 330110, China
| | - Yunxia Wang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Ziqi Pan
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Xiuna Sun
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Minjie Mou
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Bing Zhang
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou 330110, China
| | - Zhaorong Li
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou 330110, China
| | - Honglin Li
- School of Computer Science and Technology, East China Normal University, Shanghai 200062, China.,Shanghai Key Laboratory of New Drug Design, East China University of Science and Technology, Shanghai 200237, China
| | - Feng Zhu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China.,Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou 330110, China
| |
Collapse
|
21
|
Hong Y, Zhang Y, Zhao H, Chen H, Yu QQ, Cui H. The roles of lncRNA functions and regulatory mechanisms in the diagnosis and treatment of hepatocellular carcinoma. Front Cell Dev Biol 2022; 10:1051306. [PMID: 36467404 PMCID: PMC9716033 DOI: 10.3389/fcell.2022.1051306] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 11/07/2022] [Indexed: 10/27/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is the most frequent and deadly type of liver cancer. While the underlying molecular mechanisms are poorly understood, it is documented that lncRNAs may play key roles. Many HCC-associated lncRNAs have been linked to HBV and HCV infection, mediating gene expression, cell growth, development, and death. Studying the regulatory mechanisms and biological functions of HCC-related lncRNAs will assist our understanding of HCC pathogenesis as well as its diagnosis and management. Here, we address the potential of dysregulated lncRNAs in HCC as diagnostic and therapeutic biomarkers, and we evaluate the oncogenic or tumor-suppressive properties of these lncRNAs.
Collapse
Affiliation(s)
- Yuling Hong
- School of Clinical Medicine, Jining Medical University, Jining, China
| | - Yunxing Zhang
- Jining First People’s Hospital, Jining Medical College, Jining, China
| | - Haibo Zhao
- Jining First People’s Hospital, Jining Medical College, Jining, China
| | - Hailing Chen
- School of Clinical Medicine, Jining Medical University, Jining, China
| | - Qing-Qing Yu
- Jining First People’s Hospital, Jining Medical College, Jining, China
| | - Hongxia Cui
- Jining First People’s Hospital, Jining Medical College, Jining, China
| |
Collapse
|
22
|
Rozi R, Zhou Y, Rong K, Chen P. miR-124-3p sabotages lncRNA MALAT1 stability to repress chondrocyte pyroptosis and relieve cartilage injury in osteoarthritis. J Orthop Surg Res 2022; 17:453. [PMID: 36243708 PMCID: PMC9571420 DOI: 10.1186/s13018-022-03334-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 09/21/2022] [Indexed: 11/21/2022] Open
Abstract
Background Osteoarthritis (OA) is a prevalent inflammatory joint disorder. microRNAs (miRNAs) are increasingly involved in OA. Aim Our study is proposed to clarify the role of miR-124-3p in chondrocyte pyroptosis and cartilage injury in OA.
Methods OA mouse model was established via the treatment of destabilization of the medial meniscus (DMM), and the in vitro cell model was also established as mouse chondrocytes were induced by lipopolysaccharide (LPS). Mouse cartilage injury was assessed using safranin-O-fast green staining, hematoxylin–eosin staining, and OARSI grading method. Expressions of miR-124-3p, MALAT1, KLF5, and CXCL11 were determined. Cartilage injury (MMP-13, osteocalcin), inflammation (IL-6, IL-2, TNF-, IL-1β, and IL-18)- and pyroptosis-related factors (Cleaved Caspase-1 and GSDMD-N) levels were detected. Mechanically, MALAT1 subcellular localization was confirmed. The binding relationships of miR-124-3p and MALAT1 and MALAT1 and KLF5 were verified. MALAT1 half-life period was detected. Then, miR-124-3p was overexpressed using agomiR-124-3p to perform the rescue experiments with oe-MALAT1 or oe-CXCL11. Results miR-124-3p was downregulated in DMM mice and LPS-induced chondrocytes where cartilage injury, and increased levels of inflammation- and pyroptosis-related factors were found. miR-124-3p overexpression relieved cartilage injury and repressed chondrocyte pyroptosis. miR-124-3p bounds to MALAT1 to downregulate its stability and expression, and MALAT1 bounds to KLF5 to enhance CXCL11 transcription. Overexpression of MALAT1 or CXCL11 annulled the repressive function of miR-124-3p in chondrocyte pyroptosis. Conclusion miR-124-3p reduced MALAT1 stability and inhibited the binding of MALAT1 and KLF5 to downregulate CXCL11, thereby suppressing chondrocyte pyroptosis and cartilage injury in OA.
Collapse
Affiliation(s)
- Rigbat Rozi
- Department of Fourth Orthopedics, Traditional Chinese Medicine Hospital, Affiliated to Xinjiang Medical University, No. 116, Huanghe Road, Ürümqi, 830000, Xinjiang, People's Republic of China
| | - Yubo Zhou
- Department of Fourth Orthopedics, Traditional Chinese Medicine Hospital, Affiliated to Xinjiang Medical University, No. 116, Huanghe Road, Ürümqi, 830000, Xinjiang, People's Republic of China
| | - Kai Rong
- Department of Fourth Orthopedics, Traditional Chinese Medicine Hospital, Affiliated to Xinjiang Medical University, No. 116, Huanghe Road, Ürümqi, 830000, Xinjiang, People's Republic of China
| | - Pingbo Chen
- Department of Fourth Orthopedics, Traditional Chinese Medicine Hospital, Affiliated to Xinjiang Medical University, No. 116, Huanghe Road, Ürümqi, 830000, Xinjiang, People's Republic of China.
| |
Collapse
|
23
|
Zhang G, Fu L, Wang Y, Liu B, Ma S, Ma H, Zhang H, Zhang F, Yang K, Cai H. Integrative pan-cancer analysis indicates the prognostic importance of long noncoding RNA SNHG17 in human cancers. Pathol Res Pract 2022; 238:154140. [PMID: 36167008 DOI: 10.1016/j.prp.2022.154140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 09/18/2022] [Accepted: 09/19/2022] [Indexed: 11/16/2022]
Abstract
BACKGROUND Cancer is one of the most widespread causes of death today. Early diagnosis can dramatically reduce cancer-related mortality. Studies have shown that the lncRNA Small Nucleolar RNA Host Gene 17 (SNHG17) is aberrantly expressed in various types of solid tumors. Nevertheless, its prognostic value remains to be elucidated. The main objective of this meta-analysis was to elucidate whether SNHG17 can be considered as a potential prognostic biomarker for a variety of cancers. METHODS Correlational studies were screened from Cochrane, Embase, PubMed, and Web of Science. Hazard ratios (HRs) and odds ratios (ORs) with 95% confidence intervals (CIs) were pooled, and the role of SNHG17 in cancer was analyzed. The Cancer Genome Atlas (TCGA) database was employed to verify the results. RESULTS Seventeen original papers including 1451 patients were included in the meta-analysis. SNHG17 expression was upregulated in various cancers. Overexpression of SNHG17 was significantly correlated with worse overall survival (OS) (HR = 1.92, 95% CI 1.55-2.37, P < 0.001) and relapse-free survival (RFS) (HR = 1.87, 95% CI 1.06-3.30, P = 0.030). Furthermore, overexpression of SNHG17 was predictive of earlier lymph node metastasis (LNM) (OR = 2.94, 95% CI 2.29-3.78, P < 0.001), more advanced tumor-node-metastases (TNM) stage (OR = 3.56, 95% CI 2.22-5.68, P < 0.001), larger tumor size (OR = 2.18, 95% CI 1.65-2.88, P < 0.001), worse differentiation grade (OR = 1.69, 95% CI 1.26-2.25, P < 0.001), and earlier distant metastasis (DM) (OR = 1.63, 95% CI 1.03-2.56, P = 0.033) in human cancers. Moreover, further inquiry based on TCGA dataset validated that SNHG17 was high expression in various tumors and foresaw unfavorable clinical prognosis. CONCLUSIONS Overexpression of SNHG17 correlates with poor prognosis and advanced clinicopathological features in cancer patients and may be a potential prognostic indicator and a therapeutic target for cancer treatment.
Collapse
Affiliation(s)
- Guangming Zhang
- The First Clinical Medical College of Gansu University of Chinese Medicine (Gansu Provincial Hospital), Lanzhou 730000, China; General Surgery Clinical Medical Center, Gansu Provincial Hospital, Lanzhou 730000, China; Key Laboratory of Molecular Diagnostics and Precision Medicine for Surgical Oncology in Gansu Province, Gansu Provincial Hospital, Lanzhou 730000, China; Gansu Provincial Hospital, Lanzhou 730000, China
| | - Liangyin Fu
- The First Clinical Medical College of Gansu University of Chinese Medicine (Gansu Provincial Hospital), Lanzhou 730000, China; General Surgery Clinical Medical Center, Gansu Provincial Hospital, Lanzhou 730000, China; Key Laboratory of Molecular Diagnostics and Precision Medicine for Surgical Oncology in Gansu Province, Gansu Provincial Hospital, Lanzhou 730000, China; Gansu Provincial Hospital, Lanzhou 730000, China
| | | | - Bin Liu
- Gansu Provincial Hospital, Lanzhou 730000, China
| | - Shixun Ma
- Gansu Provincial Hospital, Lanzhou 730000, China
| | - Haizhong Ma
- Gansu Provincial Hospital, Lanzhou 730000, China
| | - Helin Zhang
- The First Clinical Medical College of Gansu University of Chinese Medicine (Gansu Provincial Hospital), Lanzhou 730000, China
| | - Fan Zhang
- The First Clinical Medical College of Gansu University of Chinese Medicine (Gansu Provincial Hospital), Lanzhou 730000, China
| | - Kehu Yang
- Evidence-Based Medicine Center, School of Basic Medical Sciences, Lanzhou University, Lanzhou 730000, China
| | - Hui Cai
- The First Clinical Medical College of Gansu University of Chinese Medicine (Gansu Provincial Hospital), Lanzhou 730000, China; General Surgery Clinical Medical Center, Gansu Provincial Hospital, Lanzhou 730000, China; Key Laboratory of Molecular Diagnostics and Precision Medicine for Surgical Oncology in Gansu Province, Gansu Provincial Hospital, Lanzhou 730000, China; Gansu Provincial Hospital, Lanzhou 730000, China; NHC Key Laboratory of Diagnosis and Therapy of Gastrointestinal Tumor, Gansu Provincial Hospital, Lanzhou 730000, China.
| |
Collapse
|
24
|
LincRNAs and snoRNAs in Breast Cancer Cell Metastasis: The Unknown Players. Cancers (Basel) 2022; 14:cancers14184528. [PMID: 36139687 PMCID: PMC9496948 DOI: 10.3390/cancers14184528] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 09/10/2022] [Accepted: 09/16/2022] [Indexed: 11/17/2022] Open
Abstract
Recent advances in research have led to earlier diagnosis and targeted therapies against breast cancer, which has resulted in reduced breast cancer-related mortality. However, the majority of breast cancer-related deaths are due to metastasis of cancer cells to other organs, a process that has not been fully elucidated. Among the factors and genes implicated in the metastatic process regulation, non-coding RNAs have emerged as crucial players. This review focuses on the role of long intergenic noncoding RNAs (lincRNAs) and small nucleolar RNAs (snoRNAs) in breast cancer cell metastasis. LincRNAs are transcribed between two protein-coding genes and are longer than 200 nucleotides, they do not code for a specific protein but function as regulatory molecules in processes such as cell proliferation, apoptosis, epithelial-to-mesenchymal transition, migration, and invasion while most of them are highly elevated in breast cancer tissues and seem to function as competing endogenous RNAs (ceRNAs) inhibiting relevant miRNAs that specifically target vital metastasis-related genes. Similarly, snoRNAs are 60-300 nucleotides long and are found in the nucleolus being responsible for the post-transcriptional modification of ribosomal and spliceosomal RNAs. Most snoRNAs are hosted inside intron sequences of protein-coding and non-protein-coding genes, and they also regulate metastasis-related genes affecting related cellular properties.
Collapse
|
25
|
Long Noncoding RNA LINC02249 Is a Prognostic Biomarker and Correlates with Immunosuppressive Microenvironment in Skin Cutaneous Melanoma. JOURNAL OF ONCOLOGY 2022; 2022:2054901. [PMID: 36117849 PMCID: PMC9473915 DOI: 10.1155/2022/2054901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 08/08/2022] [Accepted: 08/11/2022] [Indexed: 11/25/2022]
Abstract
Skin cutaneous melanoma (SKCM) is one of the most aggressive and life-threatening tumors. It has a high incidence rate, as well as significant metastasis and fatality rates. To successfully treat SKCM and to increase the overall survival rate, early identification and risk stratification are both absolutely necessary. Long noncoding RNAs (lncRNAs) play a significant regulatory role in a variety of cancers. However, the expression and function of many lncRNAs have not been investigated. We evaluated the expression profile of the long noncoding RNA LINC02249 (LINC02249) in pan-cancers by using data on gene expression obtained from TCGA and GTEx. The biological function of LINC02249 was determined by gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). The prognostic value of LINC02249 expression in SKCM patients was statistically analyzed. Besides, the ssGSEA approach was utilized in order to investigate the degree to which LINC02249 expression is correlated with tumor immune infiltration. In this study, the expression of LINC02249 was found to be abnormally high in a variety of tumors, according to our findings. When compared with nontumor specimens, the level of expression of LINC02249 was shown to be significantly elevated in SKCM samples. GO and KEGG assays revealed LINC02249 may be involved in tumor progression. High expression of LINC02249 was associated with shorter overall survival and disease-specific survival of SKCM patients. More importantly, multivariate methods revealed that LINC02249 expression was an independent prognostic factor for SKCM cases. Using ssGSEA, we found that the expression of LINC02249 was negatively associated with different tumor-infiltrating immune cells, especially aDC, Treg, and macrophages. Overall, our findings suggested that LINC02249 can serve as a novel biomarker to predict the prognosis and immune infiltration in SKCM.
Collapse
|
26
|
LncPheDB: a genome-wide lncRNAs regulated phenotypes database in plants. ABIOTECH 2022; 3:169-177. [PMID: 36304839 PMCID: PMC9590470 DOI: 10.1007/s42994-022-00084-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 09/12/2022] [Indexed: 11/01/2022]
Abstract
LncPheDB (https://www.lncphedb.com/) is a systematic resource of genome-wide long non-coding RNAs (lncRNAs)-phenotypes associations for multiple species. It was established to display the genome-wide lncRNA annotations, target genes prediction, variant-trait associations, gene-phenotype correlations, lncRNA-phenotype correlations, and the similar non-coding regions of the queried sequence in multiple species. LncPheDB sorted out a total of 203,391 lncRNA sequences, 2000 phenotypes, and 120,271 variants of nine species (Zea mays L., Gossypium barbadense L., Triticum aestivum L., Lycopersicon esculentum Mille, Oryza sativa L., Hordeum vulgare L., Sorghum bicolor L., Glycine max L., and Cucumis sativus L.). By exploring the relationship between lncRNAs and the genomic position of variants in genome-wide association analysis, a total of 68,862 lncRNAs were found to be related to the diversity of agronomic traits. More importantly, to facilitate the study of the functions of lncRNAs, we analyzed the possible target genes of lncRNAs, constructed a blast tool for performing similar fragmentation studies in all species, linked the pages of phenotypic studies related to lncRNAs that possess similar fragments and constructed their regulatory networks. In addition, LncPheDB also provides a user-friendly interface, a genome visualization platform, and multi-level and multi-modal convenient data search engine. We believe that LncPheDB plays a crucial role in mining lncRNA-related plant data. Supplementary Information The online version contains supplementary material available at 10.1007/s42994-022-00084-3.
Collapse
|
27
|
Wang Y, Feng YC, Gan Y, Teng L, Wang L, La T, Wang P, Gu Y, Yan L, Li N, Zhang L, Wang L, Thorne RF, Zhang XD, Cao H, Shao FM. LncRNA MILIP links YBX1 to translational activation of Snai1 and promotes metastasis in clear cell renal cell carcinoma. J Exp Clin Cancer Res 2022; 41:260. [PMID: 36028903 PMCID: PMC9414127 DOI: 10.1186/s13046-022-02452-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 07/28/2022] [Indexed: 12/25/2022] Open
Abstract
Abstract
Background
Distant metastasis is the major cause of clear cell renal cell carcinoma (ccRCC)-associated mortality. However, molecular mechanisms involved in ccRCC metastasis remain to be fully understood. With the increasing appreciation of the role of long non-coding RNAs (lncRNAs) in cancer development, progression, and treatment resistance, the list of aberrantly expressed lncRNAs contributing to ccRCC pathogenesis is expanding rapidly.
Methods
Bioinformatics analysis was carried out to interrogate publicly available ccRCC datasets. In situ hybridization and qRT-PCR assays were used to test lncRNA expression in human ccRCC tissues and cell lines, respectively. Chromatin immunoprecipitation and luciferase reporter assays were used to examine transcriptional regulation of gene expression. Wound healing as well as transwell migration and invasion assays were employed to monitor ccRCC cell migration and invasion in vitro. ccRCC metastasis was also examined using mouse models in vivo. RNA pulldown and RNA immunoprecipitation were performed to test RNA–protein associations, whereas RNA-RNA interactions were tested using domain-specific chromatin isolation by RNA purification.
Results
MILIP expression was upregulated in metastatic compared with primary ccRCC tissues. The increased MILIP expression in metastatic ccRCC cells was driven by the transcription factor AP-2 gamma (TFAP2C). Knockdown of MILIP diminished the potential of ccRCC cell migration and invasion in vitro and reduced the formation of ccRCC metastatic lesions in vivo. The effect of MILIP on ccRCC cells was associated with alterations in the expression of epithelial-to-mesenchymal transition (EMT) hallmark genes. Mechanistically, MILIP formed an RNA-RNA duplex with the snail family transcriptional repressor 1 (Snai1) mRNA and bound to Y-box binding protein 1 (YBX1). This promoted the association between the YBX1 protein and the Snai1 mRNA, leading to increased translation of the latter. Snai1 in turn played an important role in MILIP-driven ccRCC metastasis.
Conclusions
The TFAP2C-responsive lncRNA MILIP drives ccRCC metastasis. Targeting MILIP may thus represent a potential avenue for ccRCC treatment.
Collapse
|
28
|
Lei X, Dai X, Wang Q, Long R, Xiang Z, Li H, Long Z, Zhang C, Zhu Z. RNA-seq transcriptome profiling of liver regeneration in mice identifies the miR-34b-5p/phosphoinositide-dependent protein kinase 1 axis as a potential target for hepatocyte proliferation. Biochem Biophys Res Commun 2022; 627:111-121. [PMID: 36030652 DOI: 10.1016/j.bbrc.2022.08.049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 08/14/2022] [Accepted: 08/17/2022] [Indexed: 11/16/2022]
Abstract
Characterized by compensatory hyperplasia dependent on hepatocyte proliferation, the liver will initiate regeneration after partial hepatectomy (PH) and acute or chronic injuries. A variety of genes and noncoding RNAs play pivotal roles in these cell proliferation and growth processes. However, it is still unclear how competition endogenous RNAs (ceRNAs) modulate cellular activities during each phase of liver regeneration, and the specific mechanisms of posttranscriptional gene expression regulation in hepatocyte proliferation remain to be elucidated. To investigate the mechanism of liver regeneration through RNA-seq profiling and to determine the role of miR-34b-5p/PDK1 on hepatocyte proliferation, we established a 2/3 PH mouse model for whole transcriptome profiling based on high-throughput sequencing techniques. We subsequently constructed a lncRNA-miRNA-mRNA ceRNA regulatory network through integrative analyses of RNA interactions. Finally, plasmid transfection in NCTC 1469 cells, dual luciferase reporter gene assay, quantitative real-time PCR, western blotting, Cell Counting Kit-8, and EdU-DNA synthesis cell proliferation assay were used to demonstrate the role of the miR-34b-5p/PDK1 axis in hepatocyte proliferation in vitro. A total of 1443 mRNAs (962 up, 481 down), 48 miRNAs (35 up, 13 down), and 1955 lncRNAs (986 up, 969 down) were identified as significantly differentially expressed. We then successfully constructed a ceRNA regulatory network consisting of 7 lncRNAs, 15 miRNAs, and 347 mRNAs based on the predicted inverse interactions among ceRNAs. Additionally, miR-34b-5p/PDK1 was predicted to be closely related to hepatocyte proliferation. We further demonstrated that miR-34b-5p could bind specifically to the 3'-untranslated region (3'-UTR) of PDK1 using the dual luciferase reporter assay. Ectopic overexpression of miR-34b-5p significantly reduced the mRNA and protein expression of PDK1, while it markedly inhibited the proliferation of mouse NCTC 1469 cells in vitro. In contrast, knocking down miR-34b-5p exhibited the inverse effects on PDK1 expression and hepatocyte proliferation. Through analyzing the ceRNA network during mouse liver regeneration, this study reveals that miR-34b-5p can inhibit hepatocyte proliferation through negatively regulating PDK1 and may be a potential pharmacological intervention target.
Collapse
Affiliation(s)
- Xiaohua Lei
- The First Affiliated Hospital, Department of Hepatobiliary Surgery, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Xiaoming Dai
- The First Affiliated Hospital, Department of Hepatobiliary Surgery, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Qian Wang
- The First Affiliated Hospital, Department of Reproductive Medicine, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Ruchang Long
- The First Affiliated Hospital, Department of Hepatobiliary Surgery, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Zhiqiang Xiang
- The First Affiliated Hospital, Department of Hepatobiliary Surgery, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Huajian Li
- The First Affiliated Hospital, Department of Hepatobiliary Surgery, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Zhangtao Long
- The First Affiliated Hospital, Department of Hepatobiliary Surgery, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Chao Zhang
- The First Affiliated Hospital, Department of Hepatobiliary Surgery, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Zhu Zhu
- The First Affiliated Hospital, Department of Hepatobiliary Surgery, Hengyang Medical School, University of South China, Hengyang, Hunan, China; The First Affiliated Hospital, Department of Education and Training, Hengyang Medical School, University of South China, Hengyang, Hunan, China.
| |
Collapse
|
29
|
Luo L, Zhen Y, Peng D, Wei C, Zhang X, Liu X, Han L, Zhang Z. The role of N6-methyladenosine-modified non-coding RNAs in the pathological process of human cancer. Cell Death Discov 2022; 8:325. [PMID: 35851061 PMCID: PMC9293946 DOI: 10.1038/s41420-022-01113-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Revised: 06/29/2022] [Accepted: 07/01/2022] [Indexed: 12/13/2022] Open
Abstract
Non-coding RNAs (ncRNAs) account for the majority of the widespread transcripts of mammalian genomes. They rarely encode proteins and peptides, but their regulatory role is crucial in numerous physiological and pathological processes. The m6A (N6-methyladenosine) modification is one of the most common internal RNA modifications in eukaryotes and is associated with all aspects of RNA metabolism. Accumulating researches have indicated a close association between m6A modification and ncRNAs, and suggested m6A-modified ncRNAs played a crucial role in tumor progression. The correlation between m6A modification and ncRNAs offers a novel perspective for investigating the potential mechanisms of cancer pathological processes, which suggests that both m6A modification and ncRNAs are critical prognostic markers and therapeutic targets in numerous malignancies. In the present report, we summarized the interaction between m6A modification and ncRNA, emphasizing how their interaction regulates pathological processes in cancer.
Collapse
Affiliation(s)
- Lin Luo
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 480082, China.,Academy of medical sciences, Zhengzhou University, Zhengzhou, Henan, 450001, China
| | - Yingwei Zhen
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 480082, China
| | - Dazhao Peng
- Tianjin Neurological Institute, Key Laboratory of Post-Neuroinjury Neuro-repair and Regeneration in Central Nervous System, Ministry of Education and Tianjin City, Tianjin Medical University General Hospital, Tianjin, 300052, China
| | - Cheng Wei
- Tianjin Neurological Institute, Key Laboratory of Post-Neuroinjury Neuro-repair and Regeneration in Central Nervous System, Ministry of Education and Tianjin City, Tianjin Medical University General Hospital, Tianjin, 300052, China
| | - Xiaoyang Zhang
- Tianjin Neurological Institute, Key Laboratory of Post-Neuroinjury Neuro-repair and Regeneration in Central Nervous System, Ministry of Education and Tianjin City, Tianjin Medical University General Hospital, Tianjin, 300052, China
| | - Xianzhi Liu
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 480082, China.
| | - Lei Han
- Tianjin Neurological Institute, Key Laboratory of Post-Neuroinjury Neuro-repair and Regeneration in Central Nervous System, Ministry of Education and Tianjin City, Tianjin Medical University General Hospital, Tianjin, 300052, China.
| | - Zhenyu Zhang
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 480082, China.
| |
Collapse
|
30
|
Zheng YJ, Liang TS, Wang J, Zhao JY, Zhai SN, Yang DK, Wang LD. Long non-coding RNA ZNF667-AS1 retards the development of esophageal squamous cell carcinoma via modulation of microRNA-1290-mediated PRUNE2. Transl Oncol 2022; 21:101371. [PMID: 35504176 PMCID: PMC9079108 DOI: 10.1016/j.tranon.2022.101371] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 01/14/2022] [Accepted: 02/11/2022] [Indexed: 11/28/2022] Open
|
31
|
Liu P, Wang Y, Zhang N, Zhao X, Li R, Wang Y, Chen C, Wang D, Zhang X, Chen L, Zhao D. Comprehensive identification of RNA transcripts and construction of RNA network in chronic obstructive pulmonary disease. Respir Res 2022; 23:154. [PMID: 35690768 PMCID: PMC9188256 DOI: 10.1186/s12931-022-02069-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Accepted: 05/24/2022] [Indexed: 12/15/2022] Open
Abstract
Background Chronic obstructive pulmonary disease (COPD) is one of the world’s leading causes of death and a major chronic disease, highly prevalent in the aging population exposed to tobacco smoke and airborne pollutants, which calls for early and useful biomolecular predictors. Roles of noncoding RNAs in COPD have been proposed, however, not many studies have systematically investigated the crosstalk among various transcripts in this context. The construction of RNA functional networks such as lncRNA-mRNA, and circRNA-miRNA-mRNA interaction networks could therefore facilitate our understanding of RNA interactions in COPD. Here, we identified the expression of RNA transcripts in RNA sequencing from COPD patients, and the potential RNA networks were further constructed. Methods All fresh peripheral blood samples of three patients with COPD and three non-COPD patients were collected and examined for mRNA, miRNA, lncRNA, and circRNA expression followed by qRT-PCR validation. We also examined mRNA expression to enrich relevant biological pathways. lncRNA-mRNA coexpression network and circRNA-miRNA-mRNA network in COPD were constructed. Results In this study, we have comprehensively identified and analyzed the differentially expressed mRNAs, lncRNAs, miRNAs, and circRNAs in peripheral blood of COPD patients with high-throughput RNA sequencing. 282 mRNAs, 146 lncRNAs, 85 miRNAs, and 81 circRNAs were differentially expressed. GSEA analysis showed that these differentially expressed RNAs correlate with several critical biological processes such as “ncRNA metabolic process”, “ncRNA processing”, “ribosome biogenesis”, “rRNAs metabolic process”, “tRNA metabolic process” and “tRNA processing”, which might be participating in the progression of COPD. RT-qPCR with more clinical COPD samples was used for the validation of some differentially expressed RNAs, and the results were in high accordance with the RNA sequencing. Given the putative regulatory function of lncRNAs and circRNAs, we have constructed the co-expression network between lncRNA and mRNA. To demonstrate the potential interactions between circRNAs and miRNAs, we have also constructed a competing endogenous RNA (ceRNA) network of differential expression circRNA-miRNA-mRNA in COPD. Conclusions In this study, we have identified and analyzed the differentially expressed mRNAs, lncRNAs, miRNAs, and circRNAs, providing a systematic view of the differentially expressed RNA in the context of COPD. We have also constructed the lncRNA-mRNA co-expression network, and for the first time constructed the circRNA-miRNA-mRNA in COPD. This study reveals the RNA involvement and potential regulatory roles in COPD, and further uncovers the interactions among those RNAs, which will assist the pathological investigations of COPD and shed light on therapeutic targets exploration for COPD. Supplementary Information The online version contains supplementary material available at 10.1186/s12931-022-02069-8.
Collapse
Affiliation(s)
- Pengcheng Liu
- Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital, Anhui Medical University, 678 Furong Road, Hefei, 230601, Anhui Province, China
| | - Yucong Wang
- Department of Clinical Laboratory, The First Affiliated Hospital of USTC, The CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Ningning Zhang
- Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital, Anhui Medical University, 678 Furong Road, Hefei, 230601, Anhui Province, China
| | - Xiaomin Zhao
- Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital, Anhui Medical University, 678 Furong Road, Hefei, 230601, Anhui Province, China
| | - Renming Li
- Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital, Anhui Medical University, 678 Furong Road, Hefei, 230601, Anhui Province, China
| | - Yu Wang
- Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital, Anhui Medical University, 678 Furong Road, Hefei, 230601, Anhui Province, China
| | - Chen Chen
- Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital, Anhui Medical University, 678 Furong Road, Hefei, 230601, Anhui Province, China
| | - Dandan Wang
- Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital, Anhui Medical University, 678 Furong Road, Hefei, 230601, Anhui Province, China
| | - Xiaoming Zhang
- School of Basic Medicine, Anhui Medical University, Hefei, 230601, China
| | - Liang Chen
- Department of Clinical Laboratory, The First Affiliated Hospital of USTC, The CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, 230027, China.
| | - Dahai Zhao
- Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital, Anhui Medical University, 678 Furong Road, Hefei, 230601, Anhui Province, China.
| |
Collapse
|
32
|
The Intersection of Non-Coding RNAs Contributes to Forest Trees' Response to Abiotic Stress. Int J Mol Sci 2022; 23:ijms23126365. [PMID: 35742808 PMCID: PMC9223653 DOI: 10.3390/ijms23126365] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 05/15/2022] [Accepted: 06/01/2022] [Indexed: 12/10/2022] Open
Abstract
Non-coding RNAs (ncRNAs) play essential roles in plants by modulating the expression of genes at the transcriptional or post-transcriptional level. In recent years, ncRNAs have been recognized as crucial regulators for growth and development in forest trees, and ncRNAs that respond to various abiotic stresses are now under intense study. In this review, we summarized recent advances in the understanding of abiotic stress-responsive microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs) in forest trees. Furthermore, we analyzed the intersection of miRNAs, and epigenetic modified ncRNAs of forest trees in response to abiotic stress. In particular, the abiotic stress-related lncRNA/circRNA-miRNA-mRNA regulatory network of forest trees was explored.
Collapse
|
33
|
Xu T, Liu CC, Xin WJ. The Epigenetic Mechanisms Involved in Chronic Pain in Rodents: A Mini- Review. Curr Neuropharmacol 2022; 20:1011-1021. [PMID: 34561983 PMCID: PMC9886825 DOI: 10.2174/1570159x19666210924104757] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 08/20/2021] [Accepted: 09/17/2021] [Indexed: 11/22/2022] Open
Abstract
Chronic pain is a common distressing neurological disorder and about 30% of the global population suffers from it. In addition to being highly prevalent, chronic pain causes a heavy economic and social burden. Although substantial progress has been achieved to dissect the underlying mechanism of chronic pain in the past few decades, the incidence and treatment of this neurological illness is yet not properly managed in clinical practice. While nerve injury-, chemotherapy- or inflammation-induced functional regulation of gene expression in the dorsal root ganglion and spinal cord are extensively reported to be involved in the pathogenic process of chronic pain, the specific mechanism of these altered transcriptional profile still remains unclear. Recent studies have shown that epigenetic mechanisms, including DNA/RNA methylation, histone modification and circular RNAs regulation, are involved in the occurrence and development of chronic pain. In this review, we provide a description of research on the role of epigenetic mechanism in chronic pain, summarize the latest clinical and preclinical advance in this field, and propose the potential directions for further research to elucidate the molecular mechanism underlying the pathogenesis of chronic pain.
Collapse
Affiliation(s)
- Ting Xu
- Guangdong Province Key Laboratory of Brain Function and Disease, Department of Physiology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China; ,These authors contributed equally.
| | - Cui-Cui Liu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Department of Rehabilitation Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China,These authors contributed equally.
| | - Wen-Jun Xin
- Guangdong Province Key Laboratory of Brain Function and Disease, Department of Physiology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China; ,Address correspondence to this author at the Guangdong Province Key Laboratory of Brain Function and Disease, Department of Physiology, Zhongshan School of Medicine, Sun Yat-Sen University, 74 Zhongshan Rd. 2, Guangzhou, China; E-mail:
| |
Collapse
|
34
|
Mechanism of miR-340-5p in laryngeal cancer cell proliferation and invasion through the lncRNA NEAT1/MMP11 axis. Pathol Res Pract 2022; 236:153912. [PMID: 35700579 DOI: 10.1016/j.prp.2022.153912] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Revised: 04/07/2022] [Accepted: 04/22/2022] [Indexed: 02/06/2023]
Abstract
OBJECTIVES Laryngeal cancer (LC), with a relatively rare diagnosis, is a primary malignancy originating from laryngeal mucosa. This study investigated the mechanisms of microRNA (miR)- 340-5p in LC cell proliferation and invasion. METHODS The expression patterns of miR-340-5p, long non-coding RNA (lncRNA) nuclear paraspeckle assembly transcript 1 (NEAT1), and matrix metallopeptidase 11 (MMP11) in LC cells, tissues, and para-carcinoma tissues, and human bronchial epithelial cells (HBEC) were examined via RT-qPCR. The effects of elevating or silencing miR-340-5p on LC cell proliferation and invasion were examined. The subcellular localization of lncRNA NEAT1 was determined. The binding relations among miR-340-5p, lncRNA NEAT1, and MMP11 were verified. Functional rescue experiments were designed to verify the functions of lncRNA NEAT1 and MMP11 on LC cell proliferation and invasion. Nude-mouse tumor models were established to assess the role of miR-340-5p in LC in vivo. RESULTS miR-340-5p was under-expressed in LC, and miR-340-5p overexpression repressed LC cell proliferation and invasion. Mechanically, miR-340-5p decreased lncRNA NEAT1 stability via directly binding to lncRNA NEAT1 and thus declined lncRNA NEAT1 expression in LC cells, while lncRNA NEAT1 accelerated MMP11 transcription via binding to heat shock factor 1 (HSF1). Overexpression of lncRNA NEAT1 or MMP11 reversed the repression of miR-340-5p overexpression on LC cell proliferation and invasion. In vivo, miR-340-5p overexpression repressed the tumor growth. CONCLUSION miR-340-5p overexpression reduced lncRNA NEAT1 stability via binding to lncRNA NEAT1, which declined lncRNA NEAT1 expression and reduced the binding of lncRNA NEAT1 to HSF1 to further inhibit MMP11 transcription, thus repressing LC cell proliferation and invasion.
Collapse
|
35
|
Wang M, Liu W, Liu W, Wang C. Diagnostic and prognostic significance of long noncoding RNA LINC00173 in patients with melanoma. Rev Assoc Med Bras (1992) 2022; 68:170-175. [PMID: 35239877 DOI: 10.1590/1806-9282.20210822] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Accepted: 10/23/2021] [Indexed: 12/24/2022] Open
Abstract
OBJECTIVE A growing volume of literature has suggested long noncoding RNAs (lncRNAs) as important players in tumor progression. In this study, we aimed to investigate the expression and prognostic value of lncRNA LINC00173 (LINC00173) in melanoma. METHODS LINC00173 expression was measured in 163 paired cancerous and noncancerous specimen samples by real-time polymerase chain reaction. The correlations between LINC00173 expression with clinicopathological characteristics and prognosis were analyzed by chi-square test, log-rank test, and multivariate survival analysis. Receiver-operating characteristic curves were used for the assessment of the diagnostic value of LINC00173 for melanoma patients. RESULTS The expression level of LINC00173 in melanoma specimens was distinctly higher than that in adjacent non-neoplasm specimens (p<0.01). Besides, LINC00173 was expressed more frequently in patients with advanced melanoma than in patients with early melanoma. Multivariate assays confirmed that LINC00173 expression level was an independent prognostic predictor of melanoma patients (p<0.05). CONCLUSION Our data indicated that LINC00173 expression could serve as an unfavorable prognostic biomarker for melanoma patients.
Collapse
Affiliation(s)
- Mujun Wang
- The First People's Hospital of Jinan City, Department of Surgery - Jinan, China
| | - Wei Liu
- The First Affiliated Hospital of Shandong First Medical University, Department of Medical Ultrasound - Jinan, China
| | - Wenxing Liu
- Shizhong District People's Hospital of Jinan, Department of Surgery - Jinan, China
| | - Chao Wang
- The First People's Hospital of Jinan City, Department of Surgery - Jinan, China
| |
Collapse
|
36
|
Zhao Z, Gao J, Huang S. LncRNA SNHG7 Promotes the HCC Progression Through miR-122-5p/FOXK2 Axis. Dig Dis Sci 2022; 67:925-935. [PMID: 33738672 DOI: 10.1007/s10620-021-06918-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 02/22/2021] [Indexed: 01/31/2023]
Abstract
Hepatocellular carcinoma (HCC) is a malignant tumor with high mortality and severe complication in China. Numerous studies have shown that long noncoding RNAs (lncRNAs) are involved in the regulation of various processes in cancer cells. Our research aimed to investigate the underlying mechanism of the lncRNA small nucleolar RNA host gene 7 (SNHG7) in HCC development. The expression of SNHG7, microRNA-122-5p (miR-122-5p), and Forkhead box K2 (FOXK2) was assessed via quantitative real-time polymerase chain reaction. 3-(4,5) -dimethylthiahiazo (-z-y1)-3,5-di-phenytetrazoliumromide (MTT) and transwell assays were performed to measure cell viability, migration, and invasion, respectively. The relative protein levels were detected by Western blot. The relationships between miR-122-5p and SNHG7 or FOXK2 were predicted by online software and then confirmed by dual-luciferase reporter assay. Animal experiments were conducted to clarify the effects of SNHG7 on proliferation in vivo. To begin with, SNHG7 was upregulated, while miR-122-5p was downregulated in HCC tissues and cells. Downregulation of SNHG7 inhibited cell growth and metastasis. Interestingly, SNHG7 could abolish the effects of miR-122-5p on HCC cells. Furthermore, miR-122-5p targeted FOXK2 and miR-122-5p recovered the effects of FOXK2 downregulation on cell growth and metastasis in HCC cells. Besides, SNHG7 facilitated HCC tumor growth in vivo through the miR-122-5p/FOXK2 axis. The lncRNA SNHG7 boosted the development of HCC by regulating FOXK2 through sponging miR-122-5p.
Collapse
Affiliation(s)
- Zhengbin Zhao
- Department of Infectious Diseases, The First Hospital of Lanzhou University, No. 1 Donggang West Road, Chengguan District, Lanzhou City, Gansu, China.
| | - Jing Gao
- Department of Laboratory, Hospital of Northwest Minzu University, Lanzhou, 730030, Gansu, China
| | - Shuangsheng Huang
- Medical College of Northwest Minzu University, Lanzhou, 730030, Gansu, China
| |
Collapse
|
37
|
Hu C, He M, Xu Q, Tian W. Advances With Non-coding RNAs in Neuropathic Pain. Front Neurosci 2022; 15:760936. [PMID: 35002601 PMCID: PMC8733285 DOI: 10.3389/fnins.2021.760936] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 10/29/2021] [Indexed: 12/22/2022] Open
Abstract
Neuropathic pain (NP) is one of the most common types of clinical pain. The common causes of this syndrome include injury to the central or peripheral nervous systems and pathological changes. NP is characterized by spontaneous pain, hyperalgesia, abnormal pain, and paresthesia. Because of its diverse etiology, the pathogenesis of NP has not been fully elucidated and has become one of the most challenging problems in clinical medicine. This kind of pain is extremely resistant to conventional treatment and is accompanied by serious complications. Non-coding RNAs (ncRNAs), such as microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs), contribute to diverse biological processes by regulating the expression of various mRNAs involved in pain-related pathways, at the posttranscriptional level. Abnormal regulation of ncRNAs is closely related to the occurrence and development of NP. In this review, we summarize the current state of understanding of the roles of different ncRNAs in the development of NP. Understanding these mechanisms can help develop novel therapeutic strategies to prevent or treat chronic pain.
Collapse
Affiliation(s)
- Cheng Hu
- Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Province Hospital of Chinese Medicine, Nanjing, China
| | - Menglin He
- Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Province Hospital of Chinese Medicine, Nanjing, China
| | - Qian Xu
- Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Province Hospital of Chinese Medicine, Nanjing, China
| | - Weiqian Tian
- Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Province Hospital of Chinese Medicine, Nanjing, China
| |
Collapse
|
38
|
Abstract
Most of the transcribed human genome codes for noncoding RNAs (ncRNAs), and long noncoding RNAs (lncRNAs) make for the lion's share of the human ncRNA space. Despite growing interest in lncRNAs, because there are so many of them, and because of their tissue specialization and, often, lower abundance, their catalog remains incomplete and there are multiple ongoing efforts to improve it. Consequently, the number of human lncRNA genes may be lower than 10,000 or higher than 200,000. A key open challenge for lncRNA research, now that so many lncRNA species have been identified, is the characterization of lncRNA function and the interpretation of the roles of genetic and epigenetic alterations at their loci. After all, the most important human genes to catalog and study are those that contribute to important cellular functions-that affect development or cell differentiation and whose dysregulation may play a role in the genesis and progression of human diseases. Multiple efforts have used screens based on RNA-mediated interference (RNAi), antisense oligonucleotide (ASO), and CRISPR screens to identify the consequences of lncRNA dysregulation and predict lncRNA function in select contexts, but these approaches have unresolved scalability and accuracy challenges. Instead-as was the case for better-studied ncRNAs in the past-researchers often focus on characterizing lncRNA interactions and investigating their effects on genes and pathways with known functions. Here, we focus most of our review on computational methods to identify lncRNA interactions and to predict the effects of their alterations and dysregulation on human disease pathways.
Collapse
|
39
|
Chen X, Song J, Wang X, Sun D, Liu Y, Jiang Y. LncRNA LINC00460: Function and mechanism in human cancer. Thorac Cancer 2022; 13:3-14. [PMID: 34821482 PMCID: PMC8720622 DOI: 10.1111/1759-7714.14238] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 11/01/2021] [Accepted: 11/03/2021] [Indexed: 12/15/2022] Open
Abstract
Long non-coding RNAs (LncRNAs), which are more than 200 nucleotides in length and with limited protein-coding potential, play vital roles in the pathogenesis, tumorigenesis, and angiogenesis of cancers. Aberrant expression of lncRNAs has been detected in various carcinomas and may be correlated with oncogenesis by affecting related genes expression. Recently, an increasing number of studies have reported on long intergenic non-protein coding RNA 460 (LINC00460) in human tumor fields. LINC00460 is upregulated in diverse cancer tissues and cells. The upregulated expression level of LINC00460 is correlated with larger tumor size, tumor node metastasis (TNM) stage, lymph node metastasis, and shorter overall survival. The regulatory mechanism of LINC00460 was complex and diverse. LINC00460 could act as a competitive endogenous RNA (ceRNA), directly bind with proteins or regulate multiple pathways, which affected tumor progression. Moreover, LINC00460 was also identified to increase drug resistance, and therefore, weaken the effectiveness of tumor treatment. It has become increasingly important to investigate the roles of LINC00460 in various cancers by different mechanisms. Therefore, a more comprehensive understanding of LINC00460 is crucial to expound on the cellular function and molecular mechanism of human cancers. In this review, we refer to studies concerning LINC00460 and provide the basis for the evaluation of LINC00460 as a predicted biomarker or potential therapeutic target in malignancies, and also provide ideas for the future research of lncRNAs similar to LINC00460.
Collapse
Affiliation(s)
- Xi Chen
- School of StomatologyWeifang Medical UniversityWeifangShandongChina
| | - Jiwu Song
- Department of StomatologyWeifang People's Hospital, First Affiliated Hospital of Weifang Medical UniversityWeifangShandongChina
| | - Xiaoxiao Wang
- School of StomatologyWeifang Medical UniversityWeifangShandongChina
- Department of DentistryAffiliated Hospital of Weifang Medical UniversityWeifangShandongChina
| | - Dongyuan Sun
- School of StomatologyWeifang Medical UniversityWeifangShandongChina
- Department of DentistryAffiliated Hospital of Weifang Medical UniversityWeifangShandongChina
| | - Yunxia Liu
- School of StomatologyWeifang Medical UniversityWeifangShandongChina
- Department of DentistryAffiliated Hospital of Weifang Medical UniversityWeifangShandongChina
| | - Yingying Jiang
- School of StomatologyWeifang Medical UniversityWeifangShandongChina
- Department of DentistryAffiliated Hospital of Weifang Medical UniversityWeifangShandongChina
| |
Collapse
|
40
|
Zhang Y, Long Y, Kwoh CK. Class similarity network for coding and long non-coding RNA classification. BMC Bioinformatics 2021; 22:609. [PMID: 34930120 PMCID: PMC8691036 DOI: 10.1186/s12859-021-04517-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 12/06/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Long non-coding RNAs (lncRNAs) play significant roles in varieties of physiological and pathological processes.The premise of the lncRNA functional study is that the lncRNAs are identified correctly. Recently, deep learning method like convolutional neural network (CNN) has been successfully applied to identify the lncRNAs. However, the traditional CNN considers little relationships among samples via an indirect way. RESULTS Inspired by the Siamese Neural Network (SNN), here we propose a novel network named Class Similarity Network in coding RNA and lncRNA classification. Class Similarity Network considers more relationships among input samples in a direct way. It focuses on exploring the potential relationships between input samples and samples from both the same class and the different classes. To achieve this, Class Similarity Network trains the parameters specific to each class to obtain the high-level features and represents the general similarity to each class in a node. The comparison results on the validation dataset under the same conditions illustrate the superiority of our Class Similarity Network to the baseline CNN. Besides, our method performs effectively and achieves state-of-the-art performances on two test datasets. CONCLUSIONS We construct Class Similarity Network in coding RNA and lncRNA classification, which is shown to work effectively on two different datasets by achieving accuracy, precision, and F1-score as 98.43%, 0.9247, 0.9374, and 97.54%, 0.9990, 0.9860, respectively.
Collapse
Affiliation(s)
- Yu Zhang
- School of Computer Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore, 639798, Singapore.,Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, CB2 0AW, UK
| | - Yahui Long
- College of Computer Science and Electronic Engineering, Hunan University, Changsha, 410000, China
| | - Chee Keong Kwoh
- School of Computer Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore, 639798, Singapore.
| |
Collapse
|
41
|
Duarte MJ, Mascarenhas RS, Assis AF, Tanaka PP, Speck-Hernandez CA, Passos GA. Autoimmune regulator act in synergism with thymocyte adhesion in the control of lncRNAs in medullary thymic epithelial cells. Mol Immunol 2021; 140:127-135. [PMID: 34700158 DOI: 10.1016/j.molimm.2021.10.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 05/30/2021] [Accepted: 10/07/2021] [Indexed: 12/06/2022]
Abstract
The autoimmune regulator (Aire) gene in medullary thymic epithelial cells (mTECs) encodes the AIRE protein, which interacts with its partners within the nucleus. This "Aire complex" induces stalled RNA Pol II on chromatin to proceed with transcription elongation of a large set of messenger RNAs and microRNAs. Considering that RNA Pol II also transcribes long noncoding RNAs (lncRNAs), we hypothesized that Aire might be implicated in the upstream control of this RNA species. To test this, we employed a loss-of-function approach in which Aire knockout mTECs were compared to Aire wild-type mTECs for lncRNA transcriptional profiling both in vitro and in vivo model systems. RNA sequencing enables the differential expression profiling of lncRNAs when these cells adhere in vitro to thymocytes or do not adhere to them as a way to test the effect of cell adhesion. Sets of lncRNAs that are unique and that are shared in vitro and in vivo were identified. Among these, we found the Aire-dependent lncRNAs as for example, Platr28, Ifi30, Morrbid, Malat1, and Xist. This finding represents the first evidence that Aire mediates the transcription of lncRNAs in mTECs. Microarray hybridizations enabled us to observe that temporal thymocyte adhesion modulates the expression levels of such lncRNAs as Morrbid, Xist, and Fbxl12o after 36 h of adhesion. This finding shows the existence of a synergistic mechanism involving a link between thymocyte adhesion, Aire, and lncRNAs in mTECs that might be important for immune self-representation.
Collapse
Affiliation(s)
- Max Jordan Duarte
- Molecular Immunogenetics Group, Department of Genetics, Ribeirão Preto Medical School, University of São Paulo (USP), Ribeirão Preto, SP, Brazil
| | - Romário S Mascarenhas
- Molecular Immunogenetics Group, Department of Genetics, Ribeirão Preto Medical School, University of São Paulo (USP), Ribeirão Preto, SP, Brazil
| | - Amanda Freire Assis
- Molecular Immunogenetics Group, Department of Genetics, Ribeirão Preto Medical School, University of São Paulo (USP), Ribeirão Preto, SP, Brazil
| | - Pedro Paranhos Tanaka
- Molecular Immunogenetics Group, Department of Genetics, Ribeirão Preto Medical School, University of São Paulo (USP), Ribeirão Preto, SP, Brazil
| | - Cesar A Speck-Hernandez
- Program in Basic and Applied Immunology, Ribeirão Preto Medical School, University of São Paulo (USP), Ribeirão Preto, SP, Brazil
| | - Geraldo Aleixo Passos
- Molecular Immunogenetics Group, Department of Genetics, Ribeirão Preto Medical School, University of São Paulo (USP), Ribeirão Preto, SP, Brazil; Program in Basic and Applied Immunology, Ribeirão Preto Medical School, University of São Paulo (USP), Ribeirão Preto, SP, Brazil; Laboratory of Genetics and Molecular Biology, Department of Basic and Oral Biology, School of Dentistry of Ribeirão Preto, USP, Ribeirão Preto, SP, Brazil; Center for Cell-Based Therapy in Dentistry, USP, Ribeirão Preto, SP, Brazil.
| |
Collapse
|
42
|
Wei J, Gao Y, Li Z, Jia H, Han B. LncRNA SNHG6 facilitates cell proliferation, migration, invasion and EMT by upregulating UCK2 and activating the Wnt/β-catenin signaling in cervical cancer. Bioorg Chem 2021; 120:105488. [PMID: 35033815 DOI: 10.1016/j.bioorg.2021.105488] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 09/24/2021] [Accepted: 11/09/2021] [Indexed: 01/21/2023]
Abstract
Cervical cancer is a most prevalent gynecological malignancy around the world. Long non-coding RNAs (lncRNAs) are recognized as crucial players in the cellular activities of diverse cancers including cervical cancer. We aimed to reveal the biological function of lncRNA small nucleolar RNA host gene 6 (SNHG6) in cervical cancer. Our findings illuminated that SNHG6 expression was elevated in cervical cancer tissues and cell lines, and highly expressed SNHG6 was associated with poor outcome in patients with cervical cancer. Moreover, knockdown of SNHG6 repressed cervical cancer development via inhibiting cell proliferation and migration and accelerating cell apoptosis. Further, SNHG6 was a sponge of miR-485-3p and uridine-cytidine kinase 2 (UCK2) was the functional target of miR-485-3p. SNHG6 increased UCK2 expression by binding with miR-485-3p in cervical cancer cells. The rescue experiments showed that SNHG6 contributed to malignant phenotypes of cervical cancer cells by the miR-485-3p/UCK2 axis. Additionally, SNHG6 activated the Wnt/β-catenin pathway to enhance the proliferative and migratory ability of cervical cancer cells. Overall, this work revealed that SNHG6 promoted malignant behaviors of cervical cancer cells by binding with miR-485-3p to regulate UCK2 and activating the Wnt/β-catenin pathway, which may offer a beneficial direction to treat cervical cancer.
Collapse
Affiliation(s)
- Jing Wei
- Department of Gynecology, Cancer Hospital and Institute, China Medical University, Shenyang 110042, Liaoning, China
| | - YuHua Gao
- Department of Gynecology, Cancer Hospital and Institute, China Medical University, Shenyang 110042, Liaoning, China
| | - Zhuo Li
- Department of Gynecology, Cancer Hospital and Institute, China Medical University, Shenyang 110042, Liaoning, China
| | - HaiQing Jia
- Department of Gynecology, Cancer Hospital and Institute, China Medical University, Shenyang 110042, Liaoning, China
| | - Bing Han
- Department of The Sixth General Surgery, Shengjing Hospital of China Medical University, Shenyang 110004, Liaoning, China.
| |
Collapse
|
43
|
Expression Patterns and Regulation of Non-Coding RNAs during Synthesis of Cellulose in Eucalyptus grandis Hill. FORESTS 2021. [DOI: 10.3390/f12111565] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Cellulose, an essential structural component in the plant cell wall and a renewable biomass resource, plays a significant role in nature. Eucalyptus’s excellent timber tree species (including Eucalyptus grandis Hill) provide many raw materials for the paper and wood industries. The synthesis of cellulose is a very complex process involving multiple genes and regulated by various biological networks. However, research on regulating associated genes and non-coding RNAs during cellulose synthesis in E. grandis remains lacking. In this study, the wood anatomical characteristics and chemical indexes of E. grandis were analyzed by taking three different parts (diameter at breast height (DBH), middle and upper part of the trunk) from the main stem of E. grandis as raw materials. The role of non-coding RNAs (Long non-coding RNA, lncRNA; Micro RNA, miRNA; Circle RNA, circRNA) on regulating candidate genes was presented, and the network map of ceRNA (Competing endogenous RNA) regulation during wood cellulose biosynthesis of E. grandis was constructed. The transcriptome sequencing of nine samples obtained from the trunk of the immature xylem in E. grandis at DBH, middle and upper parts had a 95.81 G clean reading, 57,480 transcripts, 7365 lncRNAs, and 5180 circRNAs. Each sample had 172–306 known miRNAs and 1644–3508 new miRNAs. A total of 190 DE-lncRNAs (Differentially expressed long non-coding RNAs), 174 DE-miRNAs (Differentially expressed micro RNAs), and 270 DE-circRNAs (Differentially expressed circle RNAs) were obtained by comparing transcript expression levels. Four lncRNAs and nine miRNAs were screened out, and the ceRNA regulatory network was constructed. LncRNA1 and lncRNA4 regulated the genes responsible for cellulose synthesis in E. grandis, which were overexpressed in 84K (Populus Alba × Populus glandulosa) poplar. The cellulose and lignin content in lncRNA4-oe were significantly higher than wild type 84K poplar and lncRNA1-oe. The average plant height, middle and basal part of the stem diameter in lncRNA4-oe were significantly higher than the wild type. However, there was no significant difference between the growth of lncRNA1-oe and the wild type. Further studies are warranted to explore the molecular regulatory mechanism of cellulose biosynthesis in Eucalyptus species.
Collapse
|
44
|
Olajide JS, Olopade B, Cai J. Functional Intricacy and Symmetry of Long Non-Coding RNAs in Parasitic Infections. Front Cell Infect Microbiol 2021; 11:751523. [PMID: 34692567 PMCID: PMC8531492 DOI: 10.3389/fcimb.2021.751523] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Accepted: 09/20/2021] [Indexed: 12/11/2022] Open
Abstract
RNAs are a class of molecules and the majority in eukaryotes are arbitrarily termed non- coding transcripts which are broadly classified as short and long non-coding RNAs. Recently, knowledge of the identification and functions of long non-coding RNAs have continued to accumulate and they are being recognized as important molecules that regulate parasite-host interface, parasite differentiation, host responses, and disease progression. Herein, we present and integrate the functions of host and parasite long non-coding RNAs during infections within the context of epigenetic re-programming and molecular crosstalk in the course of host-parasite interactions. Also, the modular range of parasite and host long non-coding RNAs in coordinated parasite developmental changes and host immune dynamic landscapes are discussed. We equally canvass the prospects of long non-coding RNAs in disease diagnosis and prognosis. Hindsight and suggestions are offered with the aim that it will bolster our understanding for future works on host and parasite long non-coding RNAs.
Collapse
Affiliation(s)
- Joshua Seun Olajide
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Institute of Veterinary Research Chinese Academy of Agricultural Sciences, Lanzhou, China.,Centre for Distance Learning, Obafemi Awolowo University, Ile-Ife, Nigeria.,Jiangsu Co-Innovation Center for Prevention and Control of Animal Infectious Diseases and Zoonoses, Yangzhou, China
| | - Bolatito Olopade
- Department of Medical Microbiology and Parasitology, College of Health Sciences, Obafemi Awolowo University, Ile-Ife, Nigeria
| | - Jianping Cai
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Institute of Veterinary Research Chinese Academy of Agricultural Sciences, Lanzhou, China.,Jiangsu Co-Innovation Center for Prevention and Control of Animal Infectious Diseases and Zoonoses, Yangzhou, China
| |
Collapse
|
45
|
Zhang RN, Wu DM, Wu LP, Gao GW. LncRNA LINC00337 sponges mir-1285-3p to promote proliferation and metastasis of lung adenocarcinoma cells by upregulating YTHDF1. Cancer Cell Int 2021; 21:550. [PMID: 34663343 PMCID: PMC8524958 DOI: 10.1186/s12935-021-02253-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Accepted: 10/07/2021] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Emerging studies have shown that long noncoding RNAs (lncRNAs) predominantly function in the carcinogenesis of multiple developing human tumors. The current study aimed to investigate the underlying mechanisms of LINC00337 in lung adenocarcinoma. METHODS We analyzed TCGA and GTEx datasets and chose LINC00337 as the research object. Cell proliferation, cell apoptosis, cell cycle, migration, and invasion were detected in the gain and loss experiments of LINC00337 both in vitro and in vivo. Moreover, RNA pull-down, luciferase reporter assays, western blotting analysis, and rescue experiments were performed to investigate the underlying molecular mechanisms of LINC00337 function. RESULTS LINC00337 expression was remarkably upregulated in lung adenocarcinoma. In addition, LINC00337 knockdown was shown to repress cell migration, invasion, and proliferation, as well as the cell cycle, and gear up apoptosis in lung adenocarcinoma in vitro and in vivo. With respect to the mechanism, LINC00337 knockdown boosted miR-1285-3p expression and then restrained YTHDF1 expression post-transcriptionally. Crucially, both miR-1285-3p decrement and YTHDF1 overexpression successfully reversed the influence on cell proliferation, migration, invasion, and apoptosis caused by LINC00337 shRNA. CONCLUSIONS These results suggest that LINC00337 acts as an oncogenic lncRNA, targeting miR-1285-3p and regulating YTHDF1 expression, to promote the progression of lung adenocarcinoma.
Collapse
Affiliation(s)
- Ru-Nan Zhang
- Department of Radiation Oncology, Xinxiang Central Hospital, No.56 Jinsui Road, Xinxiang, 453000, Henan, People's Republic of China.
| | - Dong-Mei Wu
- Department of Radiation Oncology, Xinxiang Central Hospital, No.56 Jinsui Road, Xinxiang, 453000, Henan, People's Republic of China
| | - Li-Ping Wu
- Department of Radiation Oncology, Xinxiang Central Hospital, No.56 Jinsui Road, Xinxiang, 453000, Henan, People's Republic of China
| | - Guo-Wei Gao
- Department of Radiation Oncology, Xinxiang Central Hospital, No.56 Jinsui Road, Xinxiang, 453000, Henan, People's Republic of China
| |
Collapse
|
46
|
Gao G, Liu C, Li X, Guan X, Yang X, Qin P. Growth arrest-specific 5 (GAS5) insertion/deletion polymorphism and cancer susceptibility in Asian populations: A meta-analysis. Medicine (Baltimore) 2021; 100:e27415. [PMID: 34731115 PMCID: PMC8519240 DOI: 10.1097/md.0000000000027415] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 09/14/2021] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Previous studies have reported the association of an insertion/deletion (Ins/Del) polymorphism (rs145204276 AGGCA/-) in the promoter region of growth arrest-specific 5 (GAS5) with the risk of cancer, such as breast cancer, gastric cancer, and hepatocellular carcinoma. However, the results are still controversial. We aimed to clarify the association of GAS5 rs145204276 polymorphism with cancer risk by meta-analysis. METHODS PubMed, Embase, Web of Science, China National Knowledge Infrastructure, Wanfang, and Cochrane Library were searched for studies concerning GAS5 and cancer published up to November 25, 2019. Pooled odds ratios (ORs) and 95% confidence intervals (CIs) were used to evaluate cancer risk. RESULTS A total of 12 case-control studies with 8729 cases and 10,807 controls were included in this meta-analysis. We found that the GAS5 rs145204276 polymorphism was not significantly associated with cancer risk (Del vs Ins: OR = 0.96, 95% CI: 0.81-1.13; Del/Del vs Ins/Ins: OR = 1.00, 95% CI: 0.70-1.43; Ins/Del vs Ins/Ins: OR = 0.92, 95% CI: 0.78-1.08; Ins/Del and Del/Del vs Ins/Ins: OR = 0.93, 95% CI: 0.76-1.13; Del/Del vs Ins/Del and Ins/Ins: OR = 1.04, 95% CI: 0.78-1.38). In the stratified analyses, significant effects on gastric cancer were found (Del vs Ins: OR = 0.79, 95% CI: 0.72-0.86; Del/Del vs Ins/Ins: OR = 0.65, 95% CI: 0.52-0.82; Ins/Del vs Ins/Ins: OR = 0.76, 95% CI: 0.68-0.86; Ins/Del + Del/Del vs Ins/Ins: OR = 0.74, 95% CI: 0.66-0.83; Del/Del vs Ins/Ins + Ins/Del: OR = 0.74, 95% CI: 0.59-0.91). CONCLUSION Our meta-analysis showed that GAS5 rs145204276 polymorphisms were not related to overall cancer risk. However, the GAS5 rs145204276 polymorphism may be a protective factor for gastric cancer in the stratification analyses.
Collapse
Affiliation(s)
- Gan Gao
- Liuzhou Maternity and Child Healthcare Hospital, Affiliated Maternity Hospital and Affiliated Children's Hospital of Guangxi University of Science and Technology, LiuZhou, China
| | - Chunming Liu
- Liuzhou Maternity and Child Healthcare Hospital, Affiliated Maternity Hospital and Affiliated Children's Hospital of Guangxi University of Science and Technology, LiuZhou, China
| | - Xueli Li
- Liuzhou Maternity and Child Healthcare Hospital, Affiliated Maternity Hospital and Affiliated Children's Hospital of Guangxi University of Science and Technology, LiuZhou, China
| | - Xiaoyong Guan
- Department of Laboratory, The First Affiliated Hospital of Guangxi University of Science and Technology, LiuZhou, China
| | - Xingxing Yang
- Liuzhou Maternity and Child Healthcare Hospital, Affiliated Maternity Hospital and Affiliated Children's Hospital of Guangxi University of Science and Technology, LiuZhou, China
| | - Peixu Qin
- Liuzhou Maternity and Child Healthcare Hospital, Affiliated Maternity Hospital and Affiliated Children's Hospital of Guangxi University of Science and Technology, LiuZhou, China
| |
Collapse
|
47
|
Rong H, Li Y, Hu S, Gao L, Yi T, Xie Y, Cai P, Li J, Dai X, Ye M, Liao Q. Prognostic signatures and potential pathogenesis of eRNAs-related genes in colon adenocarcinoma. Mol Carcinog 2021; 61:59-72. [PMID: 34622496 DOI: 10.1002/mc.23359] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 09/17/2021] [Accepted: 09/29/2021] [Indexed: 12/23/2022]
Abstract
Enhancer RNAs (eRNAs) are a subclass of long noncoding RNAs (lncRNAs) that have a wide effect in human tumors. However, the systematic analysis of potential functions of eRNAs-related genes (eRGs) in colon cancer (CC) remains unexplored. In this study, a total of 8231 eRGs including 6236 protein-coding genes and 1995 lncRNAs were identified in CC based on the multiple resources. These eRGs showed higher expression level and stability compared to other genes. What's more, the functions of these eRGs were closely related to cancer. Then a prognostic prediction model with 12 eRGs signatures were obtained for colon adenocarcinoma (COAD) patients. ROC curves showed the AUCs were 0.81, 0.77, and 0.78 for 1-, 3-, and 5-year survival prediction, respectively. And the prognostic model also manifested good performance in the validation datasets. Besides, the expression levels of two prognostic signatures, TMEM220 and LRRN2, were verified to be significantly lower in CC tissues than in adjacent noncancerous tissues (p < .05). Finally, the distinct molecular features were characterized between the high- and low-risk group through multiomics analysis including DNA mutation and methylation. Our results show eRGs signatures based prognostic model has high accuracy and may provide innovative biomarkers in COAD.
Collapse
Affiliation(s)
- Hao Rong
- The Affiliated Hospital of Medical School of Ningbo University, Ningbo, China.,Department of Preventive Medicine, Zhejiang Provincial Key Laboratory of Pathological and Physiological Technology, School of Medicine, Ningbo, China
| | - Yanguo Li
- Institute of Drug Discovery Technology, Ningbo University, Ningbo, China
| | - Shiyun Hu
- The Affiliated Hospital of Medical School of Ningbo University, Ningbo, China
| | - Liuying Gao
- The Affiliated People's Hospital of Ningbo University, Ningbo, China
| | - Tianfei Yi
- Department of Preventive Medicine, Zhejiang Provincial Key Laboratory of Pathological and Physiological Technology, School of Medicine, Ningbo, China
| | - Yangyang Xie
- Hua Mei Hospital, University of Chinese Academy of Science, Ningbo, China
| | - Ping Cai
- Hua Mei Hospital, University of Chinese Academy of Science, Ningbo, China
| | - Jianjiong Li
- Hua Mei Hospital, University of Chinese Academy of Science, Ningbo, China
| | - Xiaoyu Dai
- Hua Mei Hospital, University of Chinese Academy of Science, Ningbo, China
| | - Meng Ye
- The Affiliated Hospital of Medical School of Ningbo University, Ningbo, China
| | - Qi Liao
- The Affiliated Hospital of Medical School of Ningbo University, Ningbo, China.,Department of Preventive Medicine, Zhejiang Provincial Key Laboratory of Pathological and Physiological Technology, School of Medicine, Ningbo, China
| |
Collapse
|
48
|
Chen R, He P. Long noncoding RNA HOXA-AS2 accelerates cervical cancer by the miR-509-3p/BTN3A1 axis. J Pharm Pharmacol 2021; 73:1387-1396. [PMID: 34240204 DOI: 10.1093/jpp/rgab090] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 05/28/2021] [Indexed: 01/13/2023]
Abstract
OBJECTIVES Cervical cancer is an aggressive malignant tumour and causes high mortality in women. LncRNA HOXA-AS2 is a tumour promoter in many cancers. The current work was designed to elucidate the functions of HOXA-AS2 in cervical cancer and the underlying regulatory mechanism. METHODS qRT-PCR was conducted to reveal RNA levels. A FISH assay was conducted for the identification of the subcellular location of HOXA-AS2. MTT, EdU, Transwell and tube formation were used for detection of cell growth, migration and angiogenesis, respectively. In-vivo studies were conducted to reveal the role of HOXA-AS2 on transplanted tumour growth in mice. KEY FINDINGS The HOXA-AS2 level was found high in tissues and cells of cervical cancer. Silencing of HOXA-AS2 restrained cell proliferation, migration and invasion. Angiogenesis of HUVECs was restrained after silencing HOXA-AS2. Additionally, HOXA-AS2 upregulated the BTN3A1 by interaction with miR-509-3p. BTN3A1 overexpression rescues the inhibitory effect of silenced HOXA-AS2 on cell phenotypes in cervical cancer. Moreover, xenograft tumour growth in mice was suppressed by HOXA-AS2 depletion and was facilitated by BTN3A1 overexpression. CONCLUSIONS HOXA-AS2 accelerates cellular progression in cervical cancer by the miR-509-3p/BTN3A1 axis.
Collapse
Affiliation(s)
| | - Ping He
- Department of Obstetrics, Guangzhou Women and Children's Medical Center, Guangzhou, Guangdong, China
| |
Collapse
|
49
|
Cui G, Zhao M, Tan H, Wang Z, Meng M, Sun F, Zhang C, Xi Y. RNA Sequencing Reveals Dynamic Carbohydrate Metabolism and Phytohormone Signaling Accompanying Post-mowing Regeneration of Forage Winter Wheat ( Triticum aestivum L.). FRONTIERS IN PLANT SCIENCE 2021; 12:664933. [PMID: 34394136 PMCID: PMC8358837 DOI: 10.3389/fpls.2021.664933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Accepted: 07/05/2021] [Indexed: 06/13/2023]
Abstract
Winter wheat (Triticum aestivum L.) is used as fresh green winter forage worldwide, and its ability to regenerate after mowing determines whether it can be used for forage production; however, the molecular mechanism of regeneration is poorly understood. This study identified long-chain coding and non-coding RNAs in the wheat cultivar "XN9106," which is cultivated for forage and grain production separately in winter and summer, and analyzed their function during post-mowing regeneration. The results showed that the degradation of carbohydrate plays an important role in regeneration, as demonstrated by decreased carbohydrate content. The increased gene expression of enzymes including β-amylase, β-fructofuranosidase, sucrose synthase, sucrose-6-phosphate synthase, trehalose-6-phosphate synthase, and trehalose-6-phosphate phosphatase in mowed seedlings suggests regeneration is fueled by degraded carbohydrates that provide energy and carbon skeletons for the Krebs cycle and amino acid synthesis. The decreased auxin content relieved the inhibition of cytokinin synthesis, that controls the transition from cell division to cell expansion and stimulates cell expansion and differentiation during the cell expansion phase, and eventually accelerate post-mowing regeneration of seedlings. Additionally, differentially expressed long-chain non-coding RNAs (lncRNAs) might participate in the regulation of gene expression related to carbohydrate metabolism and hormone signal transduction. This study demonstrated the responses of key mRNAs and lncRNAs during post-mowing regeneration of winter wheat and revealed the importance of carbohydrate and hormone during regeneration, providing valuable information for genetic improvement of forage wheat.
Collapse
Affiliation(s)
- Guibin Cui
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
- Key Laboratory of Wheat Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Yangling, China
| | - Mei Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
- Key Laboratory of Wheat Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Yangling, China
| | - Hongbin Tan
- Shaanxi Province Seed Industry Group Co., Ltd., Xi’an, China
| | - Zhulin Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
- Key Laboratory of Wheat Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Yangling, China
| | - Min Meng
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
- Key Laboratory of Wheat Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Yangling, China
| | - Fengli Sun
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
- Key Laboratory of Wheat Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Yangling, China
| | - Chao Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
- Key Laboratory of Wheat Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Yangling, China
| | - Yajun Xi
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
- Key Laboratory of Wheat Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Yangling, China
| |
Collapse
|
50
|
Zhang Y, Bu D, Huo P, Wang Z, Rong H, Li Y, Liu J, Ye M, Wu Y, Jiang Z, Liao Q, Zhao Y. ncFANs v2.0: an integrative platform for functional annotation of non-coding RNAs. Nucleic Acids Res 2021; 49:W459-W468. [PMID: 34050762 PMCID: PMC8262724 DOI: 10.1093/nar/gkab435] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 04/18/2021] [Accepted: 05/05/2021] [Indexed: 02/01/2023] Open
Abstract
Increasing evidence proves the essential regulatory roles of non-coding RNAs (ncRNAs) in biological processes. However, characterizing the specific functions of ncRNAs remains a challenging task, owing to the intensive consumption of the experimental approaches. Here, we present an online platform ncFANs v2.0 that is a significantly enhanced version of our previous ncFANs to provide multiple computational methods for ncRNA functional annotation. Specifically, ncFANs v2.0 was updated to embed three functional modules, including ncFANs-NET, ncFANs-eLnc and ncFANs-CHIP. ncFANs-NET is a new module designed for data-free functional annotation based on four kinds of pre-built networks, including the co-expression network, co-methylation network, long non-coding RNA (lncRNA)-centric regulatory network and random forest-based network. ncFANs-eLnc enables the one-stop identification of enhancer-derived lncRNAs from the de novo assembled transcriptome based on the user-defined or our pre-annotated enhancers. Moreover, ncFANs-CHIP inherits the original functions for microarray data-based functional annotation and supports more chip types. We believe that our ncFANs v2.0 carries sufficient convenience and practicability for biological researchers and facilitates unraveling the regulatory mechanisms of ncRNAs. The ncFANs v2.0 server is freely available at http://bioinfo.org/ncfans or http://ncfans.gene.ac.
Collapse
Affiliation(s)
- Yuwei Zhang
- The Affiliated Hospital of Medical School of Ningbo University, Ningbo, Zhejiang, 315000, China.,Department of Preventative Medicine, Zhejiang Provincial Key Laboratory of Pathological and Physiological Technology, School of Medicine, Ningbo University, Ningbo, Zhejiang, 315000, China
| | - Dechao Bu
- Pervasive Computing Research Center, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, 100190, China
| | - Peipei Huo
- Luoyang Branch of Institute of Computing Technology, Chinese Academy of Sciences, Henan, 471000, China
| | - Zhihao Wang
- Luoyang Branch of Institute of Computing Technology, Chinese Academy of Sciences, Henan, 471000, China
| | - Hao Rong
- The Affiliated Hospital of Medical School of Ningbo University, Ningbo, Zhejiang, 315000, China.,Department of Preventative Medicine, Zhejiang Provincial Key Laboratory of Pathological and Physiological Technology, School of Medicine, Ningbo University, Ningbo, Zhejiang, 315000, China
| | - Yanguo Li
- Institute of Drug Discovery Technology, Ningbo University, Ningbo, Zhejiang, 315000, China
| | - Jingjia Liu
- Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo, Zhejiang, 315000, China
| | - Meng Ye
- The Affiliated Hospital of Medical School of Ningbo University, Ningbo, Zhejiang, 315000, China
| | - Yang Wu
- Pervasive Computing Research Center, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, 100190, China
| | - Zheng Jiang
- Department of Colorectal Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Qi Liao
- The Affiliated Hospital of Medical School of Ningbo University, Ningbo, Zhejiang, 315000, China.,Department of Preventative Medicine, Zhejiang Provincial Key Laboratory of Pathological and Physiological Technology, School of Medicine, Ningbo University, Ningbo, Zhejiang, 315000, China
| | - Yi Zhao
- Pervasive Computing Research Center, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, 100190, China
| |
Collapse
|