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Su M, Liang Z, Shan S, Gao Y, He L, Liu X, Wang A, Wang H, Cai H. Long non-coding RNA NEAT1 promotes aerobic glycolysis and progression of cervical cancer through WNT/β-catenin/PDK1 axis. Cancer Med 2024; 13:e7221. [PMID: 38733179 PMCID: PMC11087816 DOI: 10.1002/cam4.7221] [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: 02/12/2024] [Revised: 03/07/2024] [Accepted: 04/15/2024] [Indexed: 05/13/2024] Open
Abstract
BACKGROUND Cervical cancer is one of the most common gynecological cancers. Accumulated evidence shows that long non-coding RNAs (lncRNAs) play essential roles in cervical cancer occurrence and progression, but their specific functions and mechanisms remain to be further explored. METHODS The RT-qPCR assay was used to detect the expression of NEAT1 in cervical cancer tissues and cell lines. CCK-8, colony formation, flow cytometry, western blotting, and Transwell assays were used to evaluate the impact of NEAT1 on the malignant behavior of cervical cancer cells. Glucose consumption, lactate production, ATP levels, ROS levels, MMP levels, and the mRNA expressions of glycolysis-related genes and tricarboxylic acid cycle-related genes were detected to analyze the effect of NEAT1 on metabolism reprograming in cervical cancer cells. The expressions of PDK1, β-catenin and downstream molecules of the WNT/β-catenin signaling pathway in cervical cancer cells and tissues were detected by western blotting, RT-qPCR, immunofluorescence and immunohistochemistry assays. RESULTS This study investigated the role and possible molecular mechanism of lncRNA nuclear paraspeckle assembly transcript 1 (NEAT1) in cervical cancer. Our results showed that NEAT1 was highly expressed in cervical cancer tissues and cell lines. Downregulation of NEAT1 inhibited the proliferation, migration, invasion and glycolysis of cervical cancer cells, while overexpression of NEAT1 led to the opposite effects. Mechanistically, NEAT1 upregulated pyruvate dehydrogenase kinase (PDK1) through the WNT/β-catenin signaling pathway, which enhanced glycolysis and then facilitated cervical cancer metastasis. Furthermore, NEAT1 maintained the protein stability of β-catenin but did not affect its mRNA level. We also excluded the direct binding of NEAT1 to the β-catenin protein via RNA pull-down assay. The suppressive impact of NEAT1 knockdown on cell proliferation, invasion, and migration was rescued by β-catenin overexpression. The WNT inhibitor iCRT3 attenuated the carcinogenic effect induced by NEAT1 overexpression. CONCLUSION In summary, these findings indicated that NEAT1 may contribute to the progression of cervical cancer by activating the WNT/β-catenin/PDK1 signaling axis.
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Affiliation(s)
- Min Su
- Department of Gynecological Oncology, Zhongnan HospitalWuhan UniversityWuhanPeople's Republic of China
- Hubei Key Laboratory of Tumor Biological BehaviorsWuhanPeople's Republic of China
- Hubei Cancer Clinical Study CenterWuhanPeople's Republic of China
| | - Ziyan Liang
- Department of Gynecological Oncology, Zhongnan HospitalWuhan UniversityWuhanPeople's Republic of China
- Hubei Key Laboratory of Tumor Biological BehaviorsWuhanPeople's Republic of China
- Hubei Cancer Clinical Study CenterWuhanPeople's Republic of China
| | - Shidong Shan
- Hubei Key Laboratory of Tumor Biological BehaviorsWuhanPeople's Republic of China
- Department of Urology, Zhongnan HospitalWuhan UniversityWuhanPeople's Republic of China
| | - Yang Gao
- Department of Gynecological Oncology, Zhongnan HospitalWuhan UniversityWuhanPeople's Republic of China
- Hubei Key Laboratory of Tumor Biological BehaviorsWuhanPeople's Republic of China
- Hubei Cancer Clinical Study CenterWuhanPeople's Republic of China
| | - Li He
- Hubei Key Laboratory of Tumor Biological BehaviorsWuhanPeople's Republic of China
- Department of Radiation and Medical Oncology, Zhongnan HospitalWuhan UniversityWuhanPeople's Republic of China
| | - Xuelian Liu
- Department of Gynecological Oncology, Zhongnan HospitalWuhan UniversityWuhanPeople's Republic of China
- Hubei Key Laboratory of Tumor Biological BehaviorsWuhanPeople's Republic of China
- Hubei Cancer Clinical Study CenterWuhanPeople's Republic of China
| | - Anjin Wang
- Department of Gynecological Oncology, Zhongnan HospitalWuhan UniversityWuhanPeople's Republic of China
- Hubei Key Laboratory of Tumor Biological BehaviorsWuhanPeople's Republic of China
- Hubei Cancer Clinical Study CenterWuhanPeople's Republic of China
| | - Hua Wang
- Department of Gynecological Oncology, Zhongnan HospitalWuhan UniversityWuhanPeople's Republic of China
- Hubei Key Laboratory of Tumor Biological BehaviorsWuhanPeople's Republic of China
- Hubei Cancer Clinical Study CenterWuhanPeople's Republic of China
| | - Hongbing Cai
- Department of Gynecological Oncology, Zhongnan HospitalWuhan UniversityWuhanPeople's Republic of China
- Hubei Key Laboratory of Tumor Biological BehaviorsWuhanPeople's Republic of China
- Hubei Cancer Clinical Study CenterWuhanPeople's Republic of China
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Gandhi P, Wang Y, Li G, Wang S. The role of long noncoding RNAs in ocular angiogenesis and vascular oculopathy. Cell Biosci 2024; 14:39. [PMID: 38521951 PMCID: PMC10961000 DOI: 10.1186/s13578-024-01217-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 03/05/2024] [Indexed: 03/25/2024] Open
Abstract
BACKGROUND Long noncoding RNAs (lncRNAs) are RNA transcripts over 200 nucleotides in length that do not code for proteins. Initially considered a genomic mystery, an increasing number of lncRNAs have been shown to have vital roles in physiological and pathological conditions by regulating gene expression through diverse mechanisms depending on their subcellular localization. Dysregulated angiogenesis is responsible for various vascular oculopathies, including diabetic retinopathy, retinopathy of prematurity, age-related macular degeneration, and corneal neovascularization. While anti-VEGF treatment is available, it is not curative, and long-term outcomes are suboptimal, and some patients are unresponsive. To better understand these diseases, researchers have investigated the role of lncRNAs in regulating angiogenesis and models of vascular oculopathies. This review summarizes recent research on lncRNAs in ocular angiogenesis, including the pro-angiogenic lncRNAs ANRIL, HOTAIR, HOTTIP, H19, IPW, MALAT1, MIAT, NEAT1, and TUG1, the anti-angiogenic lncRNAs MEG3 and PKNY, and the human/primate specific lncRNAs lncEGFL7OS, discussing their functions and mechanisms of action in vascular oculopathies.
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Affiliation(s)
- Pranali Gandhi
- Tulane University School of Medicine, New Orleans, LA, 70112, USA
| | - Yuzhi Wang
- Louisiana State University School of Medicine, New Orleans, LA, 70112, USA
| | - Guigang Li
- Department of Ophthalmology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei province, P.R. China.
| | - Shusheng Wang
- Department of Cell and Molecular Biology, Tulane University, New Orleans, LA, 70118, USA.
- Department of Ophthalmology, Tulane University, New Orleans, LA, 70112, USA.
- Tulane Personalized Health Institute, Tulane University, New Orleans, LA, 70112, USA.
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Zabeti Touchaei A, Vahidi S, Samadani AA. Decoding the regulatory landscape of lncRNAs as potential diagnostic and prognostic biomarkers for gastric and colorectal cancers. Clin Exp Med 2024; 24:29. [PMID: 38294554 PMCID: PMC10830721 DOI: 10.1007/s10238-023-01260-5] [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: 08/30/2023] [Accepted: 12/12/2023] [Indexed: 02/01/2024]
Abstract
Colorectal cancer (CRC) and gastric cancer (GC) are major contributors to cancer-related mortality worldwide. Despite advancements in understanding molecular mechanisms and improved drug treatments, the overall survival rate for patients remains unsatisfactory. Metastasis and drug resistance are major challenges contributing to the high mortality rate in both CRC and GC. Recent research has shed light on the role of long noncoding RNAs (lncRNAs) in the development and progression of these cancers. LncRNAs regulate gene expression through various mechanisms, including epigenetic modifications and interactions with microRNAs (miRNAs) and proteins. They can serve as miRNA precursors or pseudogenes, modulating gene expression at transcriptional and post-transcriptional levels. Additionally, circulating lncRNAs have emerged as non-invasive biomarkers for the diagnosis, prognosis, and prediction of drug therapy response in CRC and GC. This review explores the intricate relationship between lncRNAs and CRC/GC, encompassing their roles in cancer development, progression, and chemoresistance. Furthermore, it discusses the potential of lncRNAs as therapeutic targets in these malignancies. The interplay between lncRNAs, miRNAs, and tumor microenvironment is also highlighted, emphasizing their impact on the complexity of cancer biology. Understanding the regulatory landscape and molecular mechanisms governed by lncRNAs in CRC and GC is crucial for the development of effective diagnostic and prognostic biomarkers, as well as novel therapeutic strategies. This review provides a comprehensive overview of the current knowledge and paves the way for further exploration of lncRNAs as key players in the management of CRC and GC.
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Affiliation(s)
| | - Sogand Vahidi
- Medical Biology Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran.
| | - Ali Akbar Samadani
- Guilan Road Trauma Research Center, Trauma Institute, Guilan University of Medical Sciences, Rasht, Iran.
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Patruno L, Milite S, Bergamin R, Calonaci N, D’Onofrio A, Anselmi F, Antoniotti M, Graudenzi A, Caravagna G. A Bayesian method to infer copy number clones from single-cell RNA and ATAC sequencing. PLoS Comput Biol 2023; 19:e1011557. [PMID: 37917660 PMCID: PMC10645363 DOI: 10.1371/journal.pcbi.1011557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 11/14/2023] [Accepted: 09/30/2023] [Indexed: 11/04/2023] Open
Abstract
Single-cell RNA and ATAC sequencing technologies enable the examination of gene expression and chromatin accessibility in individual cells, providing insights into cellular phenotypes. In cancer research, it is important to consistently analyze these states within an evolutionary context on genetic clones. Here we present CONGAS+, a Bayesian model to map single-cell RNA and ATAC profiles onto the latent space of copy number clones. CONGAS+ clusters cells into tumour subclones with similar ploidy, rendering straightforward to compare their expression and chromatin profiles. The framework, implemented on GPU and tested on real and simulated data, scales to analyse seamlessly thousands of cells, demonstrating better performance than single-molecule models, and supporting new multi-omics assays. In prostate cancer, lymphoma and basal cell carcinoma, CONGAS+ successfully identifies complex subclonal architectures while providing a coherent mapping between ATAC and RNA, facilitating the study of genotype-phenotype maps and their connection to genomic instability.
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Affiliation(s)
- Lucrezia Patruno
- Department of Informatics, Systems and Communication, Università degli Studi di Milano-Bicocca, Milan, Italy
- Department of Mathematics and Geosciences, Università degli Studi di Trieste, Trieste, Italy
| | - Salvatore Milite
- Department of Mathematics and Geosciences, Università degli Studi di Trieste, Trieste, Italy
- Centre for Computational Biology, Human Technopole, Milan, Italy
| | - Riccardo Bergamin
- Department of Mathematics and Geosciences, Università degli Studi di Trieste, Trieste, Italy
| | - Nicola Calonaci
- Department of Mathematics and Geosciences, Università degli Studi di Trieste, Trieste, Italy
| | - Alberto D’Onofrio
- Department of Mathematics and Geosciences, Università degli Studi di Trieste, Trieste, Italy
| | - Fabio Anselmi
- Department of Mathematics and Geosciences, Università degli Studi di Trieste, Trieste, Italy
| | - Marco Antoniotti
- Department of Informatics, Systems and Communication, Università degli Studi di Milano-Bicocca, Milan, Italy
- B4—Bicocca Bioinformatics Biostatistics and Bioimaging Centre, Università degli Studi di Milano-Bicocca, Milan, Italy
| | - Alex Graudenzi
- Department of Informatics, Systems and Communication, Università degli Studi di Milano-Bicocca, Milan, Italy
- B4—Bicocca Bioinformatics Biostatistics and Bioimaging Centre, Università degli Studi di Milano-Bicocca, Milan, Italy
| | - Giulio Caravagna
- Department of Mathematics and Geosciences, Università degli Studi di Trieste, Trieste, Italy
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Li F, Tang H, Zhao S, Gao X, Yang L, Xu J. Circ-E-Cad encodes a protein that promotes the proliferation and migration of gastric cancer via the TGF-β/Smad/C-E-Cad/PI3K/AKT pathway. Mol Carcinog 2023; 62:360-368. [PMID: 36453704 PMCID: PMC10107598 DOI: 10.1002/mc.23491] [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: 04/27/2022] [Revised: 06/24/2022] [Accepted: 07/07/2022] [Indexed: 12/03/2022]
Abstract
Accumulating studies indicate that circular RNAs (circRNAs) play critical roles in cancer progression. Most of them have been reported to act as microRNA sponges or interact with RNA-binding proteins; however, their full range of functions remains largely unclear. Recently, an increasing number of circRNAs have been found to encode proteins. C-E-Cad, a protein encoded by circular E-cadherin (circ-E-Cad), has been shown to have a great influence in the progression of glioblastoma, but its specific role in gastric cancer (GC) is unclear. Here, we found that both circ-E-Cad and C-E-Cad were upregulated in GC cell lines and GC tissues compared with a human gastric epithelial cell line (GES-1) and normal tissues. Knockdown of circ-E-Cad suppressed GC cell line proliferation and metastasis in vitro and in vivo, whereas overexpression of C-E-Cad had the opposite effects. Immunoblotting revealed that C-E-Cad exerted tumor-promoting functions by regulating the PI3K/AKT pathway. A rescue experiment showed that C-E-Cad but not circ-E-Cad was the executor of protumor biological functions. In addition, we demonstrated that the C-E-Cad expression level could have been increased by the TGF-β/Smad pathway. In summary, our results indicated that the TGF-β/Smad pathway could increase the expression of C-E-Cad to regulate GC cell proliferation, migration, and epithelial-mesenchymal transition by affecting PI3K/AKT signaling.
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Affiliation(s)
- Fanying Li
- Department of Neurosurgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Hongxing Tang
- Department of Neurosurgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Shaoji Zhao
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Xinya Gao
- Department of Neurosurgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Lixuan Yang
- Department of Neurosurgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Jianbo Xu
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, People's Republic of China
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Mao Y, Cai F, Jiang T, Zhu X. Identification Invasion-Related Long Non-Coding RNAs in Lung Adenocarcinoma and Analysis of Competitive Endogenous RNA Regulatory Networks. Int J Gen Med 2023; 16:1817-1831. [PMID: 37213476 PMCID: PMC10198273 DOI: 10.2147/ijgm.s407266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Accepted: 05/01/2023] [Indexed: 05/23/2023] Open
Abstract
Background Cell invasion plays a vital role in cancer development and progression. Aberrant expression of long non-coding RNAs (lncRNAs) is also critical in carcinogenesis. However, the prognostic value of invasion-related lncRNAs in lung adenocarcinoma (LUAD) remains unknown. Methods Differentially expressed mRNAs (DEmRNAs), lncRNAs (DElncRNAs), and microRNAs (DEmiRNAs) were between LUAD and control samples. Pearson correlation analyses were performed to screen for invasion-related DElncRNAs (DEIRLs). Univariate and multivariate Cox regression algorithms were applied to identify key genes and construct the risk score model, which was evaluated using receiver operating characteristic (ROC) curves. Gene set enrichment analysis (GSEA) was used to explore the underlying pathways of the risk model. Moreover, an invasion-related competitive endogenous RNA (ceRNA) regulatory network was constructed. Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) was performed to detect the expression of prognostic lncRNAs in the LUAD and control samples. Results A total of 45 DElncRNAs were identified as DEIRLs. RP3-525N10.2, LINC00857, EP300-AS1, PDZRN3-AS1, and RP5-1102E8.3 were potential prognostic lncRNAs, the expression of which was verified by RT-qPCR in LUAD samples. Both the risk score model and nomogram used the prognostic lncRNAs. ROC curves showed the risk score model had moderate accuracy and the nomogram had high accuracy in predicting patient prognosis. GSEA results indicated that the risk score model was associated with many biological processes and pathways relevant to cell proliferation. A ceRNA regulatory network was constructed in which PDZRN3-miR-96-5p-CPEB1, EP300-AS1-miR-93-5p-CORO2B, and RP3-525N10.2-miR-130a-5p-GHR may be key invasion-related regulatory pathways in LUAD. Conclusion Our study identified five novel invasion-related prognostic lncRNAs (RP3-525N10.2, LINC00857, EP300-AS1, PDZRN3-AS1, and RP5-1102E8.3) and established an accurate model for predicting the prognosis of patients with LUAD. These findings enrich our understanding of the relationships between cell invasion, lncRNAs, and LUAD and may provide novel treatment directions.
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Affiliation(s)
- Yuze Mao
- Department of Cardio-Thoracic Surgery, First Affiliated Hospital of Jiamusi University, Jiamusi, Heilongjiang, 154000, People’s Republic of China
| | - Fangyu Cai
- Department of Thoracic Surgery, Beidahuang Industry Group General Hospital, Harbin, Heilongjiang, 150088, People’s Republic of China
| | - Tengjiao Jiang
- Department of Cardio-Thoracic Surgery, First Affiliated Hospital of Jiamusi University, Jiamusi, Heilongjiang, 154000, People’s Republic of China
| | - Xiaofeng Zhu
- Department of Cardio-Thoracic Surgery, First Affiliated Hospital of Jiamusi University, Jiamusi, Heilongjiang, 154000, People’s Republic of China
- Correspondence: Xiaofeng Zhu, Department of Cardio-Thoracic Surgery, First Affiliated Hospital of Jiamusi University, Jiamusi, Heilongjiang, 154000, People’s Republic of China, Tel +86-13845456700, Email
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Wang Y, Liu P, Chen X, Yang W. Circ_CHMP5 aggravates oxidized low-density lipoprotein-induced damage to human umbilical vein endothelial cells through miR-516b-5p/TGFβR2 axis. Clin Hemorheol Microcirc 2023; 85:325-339. [PMID: 37212088 DOI: 10.3233/ch-231722] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
BACKGROUND Atherosclerosis (AS) was one of the main causes of death in the elderly, and lesions in human umbilical vein endothelial cells (HUVECs) could lead to AS. CircRNA-charged multivesicular body protein 5 (circ_CHMP5) was reported to participate in the progression of AS. METHODS Quantitative real-time polymerase chain reaction (qRT-PCR) was used to analyze the levels of circ_CHMP5, miR-516b-5p, and transforming growth factor beta receptor 2 (TGFβR2) in AS patients or ox-LDL-induced HUVECs. 5-Ethynyl-2'-deoxyuridine and cell counting kit-8 assays were performed to detect cell proliferation. Proteins expression was assessed by western blot assay. Cell apoptosis was examined by flow cytometry. Tube formation assay was utilized to measure the tube formation ability of HUVCEs. The targeting relationships between miR-516b-5p and circ_CHMP5 or TGFβR2 were confirmed by dual-luciferase reporter assay and RNA-pull down assay. RESULTS Circ_CHMP5 was enhanced in the serum of AS patients and ox-LDL-exposure HUVECs. Ox-LDL blocked proliferation and tube formation of HUVECs and induced cell apoptosis, and circ_CHMP5 knockdown reversed these effects. In addition, circ_CHMP5 regulated the growth of ox-LDL-induced HUVECs through miR-516b-5p and TGFβR2. Moreover, the effects of circ_CHMP5 knockdown on ox-LDL-induced HUVECs were obviously recovered by downregulation of miR-516b-5p, and overexpression of TGFβR2 restored the effects of miR-516b-5p upregulation on ox-LDL-stimulated HUVECs. CONCLUSION Silence of circ_CHMP5 overturned ox-LDL-treated inhibition of HUVECs proliferation and angiogenesis by miR-516b-5p and TGFβR2. These results provided new solutions for the treatment of AS.
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Affiliation(s)
- Yueru Wang
- Department of Internal Medicine-Cardiovascular, Shanxi Provincial People's Hospital, Taiyuan City, Shanxi, China
| | - Ping Liu
- Shanxi Provincial Medical Service Evaluation Center, Taiyuan City, Shanxi, China
| | - Xiaoyan Chen
- Department of Ultrasound, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, Taiyuan, China
| | - Wuxiao Yang
- Department of Cardiology, Shanxi Provincial People's Hospital, Taiyuan City, Shanxi, China
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Qiao Z, Xing Y, Zhang Q, Tang Y, Feng R, Pang W. Tamoxifen resistance-related ceRNA network for breast cancer. Front Cell Dev Biol 2022; 10:1023079. [PMID: 36506097 PMCID: PMC9733938 DOI: 10.3389/fcell.2022.1023079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 11/14/2022] [Indexed: 11/27/2022] Open
Abstract
Background: Tamoxifen (TMX) is one of the most widely used drugs to treat breast cancer (BC). However, acquired drug resistance is still a major obstacle to its application, rendering it crucial to explore the mechanisms of TMX resistance in BC. This aims of this study were to identify the mechanisms of TMX resistance and construct ceRNA regulatory networks in breast cancer. Methods: GEO2R was used to screen for differentially expressed mRNAs (DEmRNAs) leading to drug resistance in BC cells. MiRTarbase and miRNet were used to predict miRNAs and lncRNAs upstream, and the competing endogenous RNA (ceRNA) regulatory network of BC cell resistance was constructed by starBase. We used the Kaplan-Meier plotter and Gene Expression Profiling Interactive Analysis (GEPIA) to analyze the expression and prognostic differences of genes in the ceRNA network with core axis, and qRT-PCR was used to further verify the above conclusions. Results: We found that 21 DEmRNAs were upregulated and 43 DEmRNA downregulated in drug-resistant BC cells. DEmRNAs were noticeably enriched in pathways relevant to cancer. We then constructed a protein-protein interaction (PPI) network based on the STRING database and defined 10 top-ranked hub genes among the upregulated and downregulated DEmRNAs. The 20 DEmRNAs were predicted to obtain 113 upstream miRNAs and 501 lncRNAs. Among them, 7 mRNAs, 22 lncRNAs, and 11 miRNAs were used to structure the ceRNA regulatory network of drug resistance in BC cells. 4 mRNAs, 4 lncRNAs, and 3 miRNAs were detected by GEPIA and the Kaplan-Meier plotter to be significantly associated with BC expression and prognosis. The differential expression of the genes in BC cells was confirmed by qRT-PCR. Conclusion: The ceRNA regulatory network of TMX-resistant BC was successfully constructed and confirmed. This will provide an important resource for finding therapeutic targets for TMX resistance, where the discovery of candidate conventional mechanisms can aid clinical decision-making. In addition, this resource will help discover the mechanisms behind this type of resistance.
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Affiliation(s)
- Zipeng Qiao
- Guangxi Key Laboratory of Environmental Exposomics and Entire Lifecycle Heath, Guilin Medical University, Guilin, Guangxi, China,School of Public Health, Guilin Medical University, Guilin, Guangxi, China
| | - Yu Xing
- Guangxi Key Laboratory of Environmental Exposomics and Entire Lifecycle Heath, Guilin Medical University, Guilin, Guangxi, China,School of Public Health, Guilin Medical University, Guilin, Guangxi, China
| | - Qingquan Zhang
- Guangxi Key Laboratory of Environmental Exposomics and Entire Lifecycle Heath, Guilin Medical University, Guilin, Guangxi, China,School of Public Health, Guilin Medical University, Guilin, Guangxi, China
| | - Yongjun Tang
- Guangxi Key Laboratory of Environmental Exposomics and Entire Lifecycle Heath, Guilin Medical University, Guilin, Guangxi, China,School of Public Health, Guilin Medical University, Guilin, Guangxi, China
| | - Ruifa Feng
- The Second Affiliated Hospital of Guilin Medical University, Guilin, Guangxi, China,*Correspondence: Ruifa Feng, ; Weiyi Pang,
| | - Weiyi Pang
- Guangxi Key Laboratory of Environmental Exposomics and Entire Lifecycle Heath, Guilin Medical University, Guilin, Guangxi, China,School of Public Health, Guilin Medical University, Guilin, Guangxi, China,School of Humanities and Management, Guilin Medical University, Guilin, Guangxi, China,*Correspondence: Ruifa Feng, ; Weiyi Pang,
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Construction of a Prognostic Model Based on Cuproptosis-Related lncRNA Signatures in Pancreatic Cancer. Can J Gastroenterol Hepatol 2022; 2022:4661929. [PMID: 36406148 PMCID: PMC9674419 DOI: 10.1155/2022/4661929] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 09/12/2022] [Accepted: 10/28/2022] [Indexed: 11/13/2022] Open
Abstract
Aim The aim of this study is to identify cuproptosis-related lncRNAs and construct a prognostic model for pancreatic cancer patients for clinical use. Methods The expression profile of lncRNAs was downloaded from The Cancer Genome Atlas database, and cuproptosis-related lncRNAs were identified. The prognostic cuproptosis-related lncRNAs were obtained and used to establish and validate a prognostic risk score model in pancreatic cancer. Results In total, 181 cuproptosis-related lncRNAs were obtained. The prognostic risk score model was constructed based on five lncRNAs (AC025257.1, TRAM2-AS1, AC091057.1, LINC01963, and MALAT1). Patients were assigned to two groups according to the median risk score. Kaplan-Meier survival curves showed that the difference in the prognosis between the high- and low-risk groups was statistically significant. Multivariate Cox analysis showed that our risk score was an independent risk factor for pancreatic cancer patients. Receiver operator characteristic curves revealed that the cuproptosis-related lncRNA model can effectively predict the prognosis of pancreatic cancer. The principal component analysis showed a difference between the high- and low-risk groups intuitively. Functional enrichment analysis showed that different genes were involved in cancer-related pathways in patients in the high- and low-risk groups. Conclusion The risk model based on five prognostic cuproptosis-related lncRNAs can well predict the prognosis of pancreatic cancer patients. Cuproptosis-related lncRNAs could be potential biomarkers for pancreatic cancer diagnosis and treatment.
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Oxidative stress-induced endothelial cells-derived exosomes accelerate skin flap survival through Lnc NEAT1-mediated promotion of endothelial progenitor cell function. Stem Cell Res Ther 2022; 13:325. [PMID: 35850692 PMCID: PMC9290268 DOI: 10.1186/s13287-022-03013-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 06/08/2022] [Indexed: 12/14/2022] Open
Abstract
Background Flap transplantation is commonly used in reconstructive surgery. A prerequisite for skin flap survival is sufficient blood supply. However, such approaches remain unclear. This study aimed to explore the underlying mechanisms of exosomes derived from human umbilical vascular endothelial cells (HUVECs) exposed to oxidative stress on endothelial progenitor cells (EPCs) and their subsequent influence on the survival of skin flaps. Methods HUVECs were treated with various concentrations of H2O2 to establish an oxidative stress model. To investigate the effects of H2O2-HUVEC-Exos and HUVEC-Exos, Cell Counting Kit-8, tube formation, invasion assays, and quantitative real-time polymerase chain reaction (qRT-PCR) were performed in EPCs. Microarray analysis was used to reveal the differentially expressed long non-coding RNAs (lncRNAs) in the H2O2-HUVEC-Exos and HUVEC-Exos. In addition, gene silencing and western blotting were employed to determine the mechanism behind lncRNA nuclear enrichment enriched transcript 1 (Lnc NEAT1) in EPCs. Further, a rat skin flap model was used to determine the role of the exosomes in skin flap survival in vivo. Results HUVECs were stimulated with 100 μmol/L H2O2 for 12 h to establish an oxidative stress model. H2O2-HUVEC-Exos promoted the proliferation, tube formation, and invasion of EPCs and remarkably increased skin flap survival compared to the HUVEC-Exos and control groups. Sequencing of exosome RNAs revealed that the Lnc NEAT1 level was dramatically increased in the H2O2-HUVEC-Exos, leading to activation of the Wnt/β-catenin signaling pathway. Comparatively, knockdown of Lnc NEAT1 in HUVEC-Exos and H2O2-HUVEC-Exos significantly inhibits the angiogenic capacity of EPCs, reduced the survival area of skin flap and downregulated the expression levels of Wnt/β-catenin signaling pathway proteins, whereas Wnt agonist partly reversed the negative effect of NEAT1 downregulation on EPCs through the Wnt/β-catenin signaling pathway. Conclusions Exosomes derived from HUVECs stimulated by oxidative stress significantly promoted the pro-angiogenic ability of EPCs through the Wnt/β-catenin signaling pathway mediated by Lnc NEAT1 and hence enhanced random flap survival in vivo. Therefore, the application of H2O2-HUVEC-Exos may serve as an alternative therapy for improving random skin flap survival. Supplementary Information The online version contains supplementary material available at 10.1186/s13287-022-03013-9.
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Wang XJ, Gao J, Yu Q, Zhang M, Hu WD. Multi-Omics Integration-Based Prioritisation of Competing Endogenous RNA Regulation Networks in Small Cell Lung Cancer: Molecular Characteristics and Drug Candidates. Front Oncol 2022; 12:904865. [PMID: 35860558 PMCID: PMC9291301 DOI: 10.3389/fonc.2022.904865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Accepted: 06/02/2022] [Indexed: 11/13/2022] Open
Abstract
BackgroundThe competing endogenous RNA (ceRNA) network-mediated regulatory mechanisms in small cell lung cancer (SCLC) remain largely unknown. This study aimed to integrate multi-omics profiles, including the transcriptome, regulome, genome and pharmacogenome profiles, to elucidate prioritised ceRNA characteristics, pathways and drug candidates in SCLC.MethodWe determined the plasma messenger RNA (mRNA), microRNA (miRNA), long noncoding RNA (lncRNA) and circular RNA (circRNA) expression levels using whole-transcriptome sequencing technology in our SCLC plasma cohort. Significantly expressed plasma mRNAs were then overlapped with the Gene Expression Omnibus (GEO) tissue mRNA data (GSE 40275, SCLC tissue cohort). Next, we applied a multistep multi-omics (transcriptome, regulome, genome and pharmacogenome) integration analysis to first construct the network and then to identify the lncRNA/circRNA-miRNA-mRNA ceRNA characteristics, genomic alterations, pathways and drug candidates in SCLC.ResultsThe multi-omics integration-based prioritisation of SCLC ceRNA regulatory networks consisted of downregulated mRNAs (CSF3R/GAA), lncRNAs (AC005005.4-201/DLX6-AS1-201/NEAT1-203) and circRNAs (hsa_HLA-B_1/hsa_VEGFC_8) as well as upregulated miRNAs (hsa-miR-4525/hsa-miR-6747-3p). lncRNAs (lncRNA-AC005005.4-201 and NEAT1-203) and circRNAs (circRNA-hsa_HLA-B_1 and hsa_VEGFC_8) may regulate the inhibited effects of hsa-miR-6747-3p for CSF3R expression in SCLC, while lncRNA-DLX6-AS1-201 or circRNA-hsa_HLA-B_1 may neutralise the negative regulation of hsa-miR-4525 for GAA in SCLC. CSF3R and GAA were present in the genomic alteration, and further identified as targets of FavId and Trastuzumab deruxtecan, respectively. In the SCLC-associated pathway analysis, CSF3R was involved in the autophagy pathways, while GAA was involved in the glucose metabolism pathways.ConclusionsWe identified potential lncRNA/cirRNA-miRNA-mRNA ceRNA regulatory mechanisms, pathways and promising drug candidates in SCLC, providing novel potential diagnostics and therapeutic targets in SCLC.
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Affiliation(s)
- Xiao-Jun Wang
- Department of Respiratory Medicine, Gansu Provincial Hospital, Lanzhou, China
- The First School of Clinical Medicine, Lanzhou University, Lanzhou, China
| | - Jing Gao
- Department of Respiratory Medicine, Gansu Provincial Hospital, Lanzhou, China
- The First School of Clinical Medicine, Lanzhou University, Lanzhou, China
- Respiratory Medicine Unit, Department of Medicine, Karolinska Institute, Stockholm, Sweden
- Department of Pulmonary Medicine, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- *Correspondence: Wei-Dong Hu, ; Min Zhang, ; Jing Gao,
| | - Qin Yu
- The First School of Clinical Medicine, Lanzhou University, Lanzhou, China
| | - Min Zhang
- Department of Pathology, Gansu Provincial Hospital, Lanzhou, China
- *Correspondence: Wei-Dong Hu, ; Min Zhang, ; Jing Gao,
| | - Wei-Dong Hu
- Department of Respiratory Medicine, Gansu Provincial Hospital, Lanzhou, China
- *Correspondence: Wei-Dong Hu, ; Min Zhang, ; Jing Gao,
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Tang SY, Zhou PJ, Meng Y, Zeng FR, Deng GT. Gastric cancer: An epigenetic view. World J Gastrointest Oncol 2022; 14:90-109. [PMID: 35116105 PMCID: PMC8790429 DOI: 10.4251/wjgo.v14.i1.90] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 05/17/2021] [Accepted: 12/23/2021] [Indexed: 02/06/2023] Open
Abstract
Gastric cancer (GC) poses a serious threat worldwide with unfavorable prognosis mainly due to late diagnosis and limited therapies. Therefore, precise molecular classification and search for potential targets are required for diagnosis and treatment, as GC is complicated and heterogeneous in nature. Accumulating evidence indicates that epigenetics plays a vital role in gastric carcinogenesis and progression, including histone modifications, DNA methylation and non-coding RNAs. Epigenetic biomarkers and drugs are currently under intensive evaluations to ensure efficient clinical utility in GC. In this review, key epigenetic alterations and related functions and mechanisms are summarized in GC. We focus on integration of existing epigenetic findings in GC for the bench-to-bedside translation of some pivotal epigenetic alterations into clinical practice and also describe the vacant field waiting for investigation.
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Affiliation(s)
- Si-Yuan Tang
- Department of Gastroenterology, Xiangya Hospital, Central South University, Changsha 410008, Hunan Province, China
| | - Pei-Jun Zhou
- Cancer Research Institute, School of Basic Medicine Science, Central South University, School of Basic Medicine Science, Central South University 410008, Hunan Province, China
| | - Yu Meng
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha 410008, Hunan Province, China
| | - Fu-Rong Zeng
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha 410008, Hunan Province, China
| | - Guang-Tong Deng
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha 410008, Hunan Province, China
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Huang J, Huang B, Kong Y, Yang Y, Tian C, Chen L, Liao Y, Ma L. Polycystic ovary syndrome: Identification of novel and hub biomarkers in the autophagy-associated mRNA-miRNA-lncRNA network. Front Endocrinol (Lausanne) 2022; 13:1032064. [PMID: 36523600 PMCID: PMC9745174 DOI: 10.3389/fendo.2022.1032064] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 11/14/2022] [Indexed: 12/03/2022] Open
Abstract
INTRODUCTION Polycystic ovary syndrome (PCOS) is a common metabolic and endocrine disorder prevalent among women of reproductive age. Recent studies show that autophagy participated in the pathogenesis of PCOS, including anovulation, hyperandrogenism, and metabolic disturbances. This study was designed to screen autophagy-related genes (ATGs) that may play a pivotal role in PCOS, providing potential biomarkers and identifying new molecular subgroups for therapeutic intervention. METHODS Gene expression profiles of the PCOS and control samples were obtained from the publicly available Gene Expression Omnibus database. The gene lists of ATGs from databases were integrated. Then, the weighted gene co-expression network analysis was conducted to obtain functional modules and construct a multifactorial co-expression network. Gene Ontology and KEGG pathway enrichment analyses were performed for further exploration of ATG's function in the key modules. Differentially expressed ATGs were identified and validated in external datasets with the Limma R package. To provide guidance on PCOS phenotyping, the dysfunction module consists of a co-expression network mapped to PCOS patients. A PCOS-Autophagy-related co-expression network was established using Cytoscape, followed by identifying molecular subgroups using the Limma R package. ps. RNA-sequencing analysis was used to confirm the differential expression of hub ATGs, and the diagnostic value of hub ATGs was assessed by receiver operating characteristic curve analysis. RESULTS Three modules (Brown, Turquoise, and Green) in GSE8157, three modules (Blue, Red, and Green) in GSE43264, and four modules (Blue, Green, Black, and Yellow) in GSE106724 were identified to be PCOS-related by WGCNA analysis. 29 ATGs were found to be the hub genes that strongly correlated with PCOS. These hub ATGs were mainly enriched in autophagy-related functions and pathways such as autophagy, endocytosis, apoptosis, and mTOR signaling pathways. The mRNA-miRNA-lncRNA multifactorial network was successfully constructed. And three new molecular subgroups were identified via the K-means algorithm. DISCUSSION We provide a novel insight into the mechanisms behind autophagy in PCOS. BRCA1, LDLR, MAP1B, hsa-miR-92b-3p, hsa-miR-20b-5p, and NEAT1 might play a considerably important role in PCOS dysfunction. As a result, new potential biomarkers can be evaluated for use in PCOS diagnosis and treatment in the future.
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