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Shi L, Han X, Liu F, Long J, Jin Y, Chen S, Duan G, Yang H. Review on Long Non-Coding RNAs as Biomarkers and Potentially Therapeutic Targets for Bacterial Infections. Curr Issues Mol Biol 2024; 46:7558-7576. [PMID: 39057090 PMCID: PMC11276060 DOI: 10.3390/cimb46070449] [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: 06/19/2024] [Revised: 07/13/2024] [Accepted: 07/15/2024] [Indexed: 07/28/2024] Open
Abstract
The confrontation between humans and bacteria is ongoing, with strategies for combating bacterial infections continually evolving. With the advancement of RNA sequencing technology, non-coding RNAs (ncRNAs) associated with bacterial infections have garnered significant attention. Recently, long ncRNAs (lncRNAs) have been identified as regulators of sterile inflammatory responses and cellular defense against live bacterial pathogens. They are involved in regulating host antimicrobial immunity in both the nucleus and cytoplasm. Increasing evidence indicates that lncRNAs are critical for the intricate interactions between host and pathogen during bacterial infections. This paper emphatically elaborates on the potential applications of lncRNAs in clinical hallmarks, cellular damage, immunity, virulence, and drug resistance in bacterial infections in greater detail. Additionally, we discuss the challenges and limitations of studying lncRNAs in the context of bacterial infections and highlight clear directions for this promising field.
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Affiliation(s)
| | | | | | | | | | | | | | - Haiyan Yang
- Department of Epidemiology, School of Public Health, Zhengzhou University, Zhengzhou 450001, China; (L.S.); (X.H.); (F.L.); (J.L.); (Y.J.); (S.C.); (G.D.)
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2
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Qattan A. Genomic Alterations Affecting Competitive Endogenous RNAs (ceRNAs) and Regulatory Networks (ceRNETs) with Clinical Implications in Triple-Negative Breast Cancer (TNBC). Int J Mol Sci 2024; 25:2624. [PMID: 38473871 DOI: 10.3390/ijms25052624] [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: 01/16/2024] [Revised: 02/18/2024] [Accepted: 02/20/2024] [Indexed: 03/14/2024] Open
Abstract
The concept of competitive endogenous RNA regulation has brought on a change in the way we think about transcriptional regulation by miRNA-mRNA interactions. Rather than the relatively simple idea of miRNAs negatively regulating mRNA transcripts, mRNAs and other non-coding RNAs can regulate miRNAs and, therefore, broad networks of gene products through competitive interactions. While this concept is not new, its significant roles in and implications on cancer have just recently come to light. The field is now ripe for the extrapolation of technologies with a substantial clinical impact on cancer. With the majority of the genome consisting of non-coding regions encoding regulatory RNAs, genomic alterations in cancer have considerable effects on these networks that have been previously unappreciated. Triple-negative breast cancer (TNBC) is characterized by high mutational burden, genomic instability and heterogeneity, making this aggressive breast cancer subtype particularly relevant to these changes. In the past few years, much has been learned about the roles of competitive endogenous RNA network regulation in tumorigenesis, disease progression and drug response in triple-negative breast cancer. In this review, we present a comprehensive view of the new knowledge and future perspectives on competitive endogenous RNA networks affected by genomic alterations in triple-negative breast cancer. An overview of the competitive endogenous RNA (ceRNA) hypothesis and its bearing on cellular function and disease is provided, followed by a thorough review of the literature surrounding key competitive endogenous RNAs in triple-negative breast cancer, the genomic alterations affecting them, key disease-relevant molecular and functional pathways regulated by them and the clinical implications and significance of their dysregulation. New knowledge of the roles of these regulatory mechanisms and the current acceleration of research in the field promises to generate insights into the diagnosis, classification and treatment of triple-negative breast cancer through the elucidation of new molecular mechanisms, therapeutic targets and biomarkers.
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Affiliation(s)
- Amal Qattan
- Department of Molecular Oncology, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia
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3
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Yi D, Wang Z, Yang H, Wang R, Shi X, Liu Z, Xu F, Lu Q, Chu X, Sang J. Long non-coding RNA MEG3 acts as a suppressor in breast cancer by regulating miR-330/CNN1. Aging (Albany NY) 2024; 16:1318-1335. [PMID: 38240701 PMCID: PMC10866439 DOI: 10.18632/aging.205419] [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: 07/07/2023] [Accepted: 11/10/2023] [Indexed: 02/06/2024]
Abstract
BACKGROUND The current study aimed to investigate the molecular mechanism of long non-coding RNA (lncRNA) MEG3 in the development of breast cancer. METHODS The regulating relationships among lncRNA MEG3, miRNA-330 and CNN1 were predicted by bioinformatics analysis of breast cancer samples in the Cancer Genome Atlas database. The differential expression of lncRNA MEG3, miRNA-330 and CNN1 was first validated in breast cancer tissues and cells. The effects of lncRNA MEG3 on breast cancer malignant properties were evaluated by manipulating its expression in MCF-7 and BT-474 cells. Rescue experiments, dual-luciferase assays, and RNA immunoprecipitation (RIP) experiments were further used to validate the relationships among lncRNA MEG3, miRNA-330 and CNN1. RESULTS Bioinformatics analysis showed that lncRNA MEGs and CNN1 were significantly downregulated in breast cancer tissues, while miR-330 was upregulated. These differential expressions were further validated in our cohort of breast cancer samples. High expression levels of lncRNA MEG3 and CNN1 as well as low expression of miR-330 were significantly associated with favorable overall survival. Overexpression of lncRNA MEG3 significantly inhibited cell viability, migration and invasion, decreased cells in S stage and promoted cell apoptosis. Dual-luciferase reporter gene assay and RIP experiments showed that lncRNA MEG3 could directly bind to miR-330. Moreover, miR-330 mimics on the basis of lncRNA MEG3 overexpression ameliorated the tumor-suppressing effects of lncRNA MEG3 in breast cancer malignant properties by decreasing CNN1 expression. CONCLUSION Our study indicated lncRNA MEG3 is a breast cancer suppressor by regulating miR-330/CNN1 axis.
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Affiliation(s)
- Dandan Yi
- Department of General Surgery, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing 210008, China
| | - Zetian Wang
- Department of Trauma-Emergency and Critical Care Medicine, Shanghai Fifth People’s Hospital, Fudan University, Shanghai 200240, China
| | - Haojie Yang
- Department of Coloproctology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 200437, China
| | - Ru Wang
- Department of General Surgery, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing 210008, China
| | - Xianbiao Shi
- Department of General Surgery, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing 210008, China
| | - Zhijian Liu
- Department of General Surgery, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing 210008, China
| | - Fazhan Xu
- Department of General Surgery, Nanjing Drum Tower Hospital, Clinical College of Nanjing Medical University, Nanjing 210008, China
| | - Qing Lu
- Department of Breast Surgery, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 200437, China
| | - Xiao Chu
- Department of Thoracic Surgery, The Fifth People’s Hospital of Shanghai, Fudan University, Shanghai 200240, China
| | - Jianfeng Sang
- Department of General Surgery, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing 210008, China
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4
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Cisneros-Villanueva M, Fonseca-Montaño MA, Ríos-Romero M, López-Camarillo C, Jiménez-Morales S, Langley E, Rosette-Rueda AS, Cedro-Tanda A, Hernández-Sotelo D, Hidalgo-Miranda A. LncRNA SOX9-AS1 triggers a transcriptional program involved in lipid metabolic reprogramming, cell migration and invasion in triple-negative breast cancer. Sci Rep 2024; 14:1483. [PMID: 38233470 PMCID: PMC10794186 DOI: 10.1038/s41598-024-51947-2] [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: 04/25/2023] [Accepted: 01/11/2024] [Indexed: 01/19/2024] Open
Abstract
At the molecular level, triple-negative breast cancer (TNBC) is frequently categorized as PAM50 basal-like subtype, but despite the advances in molecular analyses, the clinical outcome for these subtypes is uncertain. Long non-coding RNAs (lncRNAs) are master regulators of genes involved in hallmarks of cancer, which makes them suitable biomarkers for breast cancer (BRCA) diagnosis and prognosis. Here, we evaluated the regulatory role of lncRNA SOX9-AS1 in these subtypes. Using the BRCA-TCGA cohort, we observed that SOX9-AS1 was significantly overexpressed in basal-like and TNBC in comparison with other BRCA subtypes. Survival analyzes showed that SOX9-AS1 overexpression was associated with a favorable prognosis in TNBC and basal-like patients. To study the functions of SOX9-AS1, we determined the expression levels in a panel of nine BRCA cell lines finding increased levels in MDA-MB-468 and HCC1187 TNBC. Using subcellular fractionation in these cell lines, we ascertained that SOX9-AS1 was located in the cytoplasmic compartment. In addition, we performed SOX9-AS1 gene silencing using two short-harping constructs, which were transfected in both cell models and performed a genome-wide RNA-seq analysis. Data showed that 351 lncRNAs and 740 mRNAs were differentially expressed in MDA-MB-468 while 56 lncRNAs and 100 mRNAs were modulated in HCC1187 cells (Log2FC < - 1.5 and > 1.5, p.adj value < 0.05). Pathway analysis revealed that the protein-encoding genes potentially regulate lipid metabolic reprogramming, and epithelial-mesenchymal transition (EMT). Expression of lipid metabolic-related genes LIPE, REEP6, GABRE, FBP1, SCD1, UGT2B11, APOC1 was confirmed by RT-qPCR. Functional analysis demonstrated that the knockdown of SOX9-AS1 increases the triglyceride synthesis, cell migration and invasion in both two TNBC cell lines. In conclusion, high SOX9-AS1 expression predicts an improved clinical course in patients, while the loss of SOX9-AS1 expression enhances the aggressiveness of TNBC cells.
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Affiliation(s)
- Mireya Cisneros-Villanueva
- Laboratorio Genómica del Cáncer, Instituto Nacional de Medicina Genómica (INMEGEN), 14610, Mexico, México
- Programa de Doctorado en Ciencias Biomédicas, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero (UAGro), Chilpancingo de los Bravo, Guerrero, México
- Laboratorio de Epigenética del Cáncer, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero (UAGro), Chilpancingo de los Bravo, Guerrero, México
| | - Marco Antonio Fonseca-Montaño
- Laboratorio Genómica del Cáncer, Instituto Nacional de Medicina Genómica (INMEGEN), 14610, Mexico, México
- Programa de Doctorado, Posgrado en Ciencias Biológicas, Unidad de Posgrado, Universidad Nacional Autónoma de México (UNAM), 04510, Mexico, México
| | - Magdalena Ríos-Romero
- Laboratorio Genómica del Cáncer, Instituto Nacional de Medicina Genómica (INMEGEN), 14610, Mexico, México
| | - César López-Camarillo
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, Mexico, México
| | - Silvia Jiménez-Morales
- Laboratorio Genómica del Cáncer, Instituto Nacional de Medicina Genómica (INMEGEN), 14610, Mexico, México
| | - Elizabeth Langley
- Laboratorio de Cáncer Hormono Regulado, Instituto Nacional de Cancerología (INCan), 14080, Mexico, México
| | - Alan Sajid Rosette-Rueda
- Laboratorio Genómica del Cáncer, Instituto Nacional de Medicina Genómica (INMEGEN), 14610, Mexico, México
| | | | - Daniel Hernández-Sotelo
- Laboratorio de Epigenética del Cáncer, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero (UAGro), Chilpancingo de los Bravo, Guerrero, México.
| | - Alfredo Hidalgo-Miranda
- Laboratorio Genómica del Cáncer, Instituto Nacional de Medicina Genómica (INMEGEN), 14610, Mexico, México.
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5
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Zhao Y, Song Y, Zhang Y, Ji M, Hou P, Sui F. Screening protective miRNAs and constructing novel lncRNAs/miRNAs/mRNAs networks and prognostic models for triple-negative breast cancer. Mol Cell Probes 2023; 72:101940. [PMID: 37871689 DOI: 10.1016/j.mcp.2023.101940] [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: 09/21/2023] [Revised: 10/20/2023] [Accepted: 10/20/2023] [Indexed: 10/25/2023]
Abstract
Triple-negative breast cancer (TNBC) represents 10-20 % of all breast cancer (BC) cases and is characterized by poor prognosis. Given the urgent need to improve prognostication and develop specific therapies for TNBC, the identification of new molecular targets is of great importance. MicroRNA (miRNA) has been reported as a valuable and novel molecular target in the progression of TNBC. However, the expression and function of miRNAs in different tumors are heterogeneous. Herein, we first analyzed miRNA data from The Cancer Genome Atlas (TCGA) and surprisedly found that overexpressed miRNAs were associated with poor survival in all breast cancer patients, but the overexpressed miRNAs were associated with better survival in TNBC patients. Based on the heterogeneity of miRNA expression in TNBC, we conducted further analysis using univariate Cox proportional hazard regression models and identified 17 miRNAs with prognostic potential. Subsequently, a multivariate Cox model was employed to create a 3-miRNA prognostic model for predicting overall survival in TNBC patients. The diagnostic model exhibited an area under the curve (AUC) of 0.727, and multivariable Cox regression indicated that each covariate was associated with survival. These data indicate that this model is relatively accurate and robust for risk assessment, which have a certain value for clinical application. In order to explore the network behind the overexpressed miRNAs in TNBC, we established a novel network consisting of lncRNAs, miRNAs, and mRNAs through complete transcriptome data from matched samples in the TCGA database. In this network, IRS-1 appeared to be the top hub gene. Experimental results demonstrated that miR-15b-5p and miR-148a-3p effectively target IRS-1 in vitro, shedding light on the intricate regulatory mechanisms in TNBC mediated by the heterogeneous miRNAs. Besides, miR-148a-3p significantly inhibited cell migration and viability. Overall, this study may add valuable insights into the molecular landscape of TNBC based on miRNAs and have the potential to contribute to the development of targeted therapies and improved prognostic strategies of TNBC.
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Affiliation(s)
- Yuelei Zhao
- Department of Endocrinology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, Shaanxi Province, PR China
| | - Yichen Song
- Department of Endocrinology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, Shaanxi Province, PR China
| | - Yan Zhang
- Department of Endocrinology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, Shaanxi Province, PR China
| | - Meiju Ji
- Center for Translational Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, Shaanxi Province, PR China
| | - Peng Hou
- Department of Endocrinology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, Shaanxi Province, PR China
| | - Fang Sui
- Department of Otorhinolaryngology-Head and Neck Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, 277 Yan-ta West Road, Xi'an, Shaanxi, 710061, PR China.
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6
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Moallemi Rad L, Safarzadeh A, Taheri M, Ghafouri-Fard S, Eghbali A. Construction of ceRNA network and identification of hub differentially expressed genes associated with breast cancer using reanalysis of microarray dataset: A systems biology approach. Pathol Res Pract 2023; 251:154838. [PMID: 37804544 DOI: 10.1016/j.prp.2023.154838] [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: 08/01/2023] [Revised: 09/30/2023] [Accepted: 09/30/2023] [Indexed: 10/09/2023]
Abstract
The interaction between long non-coding RNAs (lncRNAs), miRNAs and mRNAs has implications in the pathogenesis of different cancer, including breast cancer. In the current study, we developed an in-silico approach to ascertain the competing endogenous RNA (ceRNA) network in breast cancer. Our approach led to identification of 1816 differentially expressed (DE) mRNAs, including 1039 downregulated DEmRNAs (such as LEP and ADIPOQ) and 777 upregulated DEmRNAs (such as COL11A1 and COL10A1), 19 DElncRNAs, including 15 downregulated DElncRNAs (such as CARMN and COPG2IT1) and 4 upregulated DElncRNAs (such as MALAT1 and NRAV) and 27 DEmiRNAs, including 15 downregulated DEmiRNAs (such as MIR452 and MIR224) and 12 upregulated DEmiRNAs (such as MIR6787 and MIR21). Pathway analysis revealed down-regulation of PPAR, Fatty acid metabolism, Adipocytokine, Vascular smooth muscle contraction and Metabolism of xenobiotics by cytochrome P450, while up-regulation of Pyrimidine metabolism, p53 signaling pathway, Cell cycle, Oocyte meiosis and RNA transport pathways in breast cancer. Finally, we constructed an lncRNA/miRNA/mRNA ceRNA network consisted of 2 lncRNAs, 15 mRNAs, and 4 miRNAs. This network represents an appropriate target for design of anti-cancer modalities and documentation of novel markers for breast cancer.
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Affiliation(s)
- Lina Moallemi Rad
- Department of Molecular and Cell Biology, Faculty of Basic Sciences, University of Mazandaran, Babolsar, Iran
| | - Arash Safarzadeh
- Photochemistry Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Taheri
- Institute of Human Genetics, Jena University Hospital, Jena, Germany; Urology and Nephrology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Soudeh Ghafouri-Fard
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Ahmad Eghbali
- Anesthesiology Research Center, Mofid Children Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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7
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Hussen BM, Hidayat HJ, Abdullah SR, Mohamadtahr S, Rasul MF, Samsami M, Taheri M. Role of long non-coding RNAs and TGF-β signaling in the regulation of breast cancer pathogenesis and therapeutic targets. Cytokine 2023; 170:156351. [PMID: 37657235 DOI: 10.1016/j.cyto.2023.156351] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 08/22/2023] [Accepted: 08/25/2023] [Indexed: 09/03/2023]
Abstract
The cytokine known as transforming growth factor (TGF) is essential for cell development, differentiation, and apoptosis in BC. TGF-β dysregulation can either promote or inhibit tumor development, and it is a key signaling pathway in BC spread. A recently identified family of ncRNAs known as lncRNAs has received a great deal of effort and is an important regulator of many cellular processes, including transcription of genes, chromatin remodeling, progression of the cell cycle, and posttranscriptional processing. Furthermore, both TGF-β signaling and lncRNAs serve as important early-stage biomarkers for BC diagnosis and prognosis and also play a significant role in BC drug resistance. According to recent studies, lncRNAs can regulate TGF-β by modulating its cofactors in BC. However, the particular functions of lncRNAs and the TGF-β pathway in controlling BC progression are not well understood yet. This review explores the lncRNAs' functional properties in BC as tumor suppressors or oncogenes in the regulation of genes, with a focus on dysregulated TGF-β signaling. Further, we emphasize the functional roles of lncRNAs and TGF-β pathway in the progression of BC to discover new treatment strategies and better comprehend the fundamental cellular pathways.
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Affiliation(s)
- Bashdar Mahmud Hussen
- Department of Pharmacognosy, College of Pharmacy, Hawler Medical University, Kurdistan Region, Erbil, Iraq; Department of Biomedical Sciences, Cihan University-Erbil, Erbil, Kurdistan Region 44001, Iraq
| | - Hazha Jamal Hidayat
- Department of Biology, College of Education, Salahaddin University-Erbil, Kurdistan Region, Iraq
| | - Snur Rasool Abdullah
- Department of Medical Laboratory Science, College of Health Sciences, Lebanese French University, Kurdistan Region, Erbil, Iraq
| | - Sayran Mohamadtahr
- Department of Pharmacognosy, College of Pharmacy, Hawler Medical University, Kurdistan Region, Erbil, Iraq
| | - Mohammad Fatih Rasul
- Department of Pharmaceutical Basic Science, Faculty of Pharmacy, Tishk International University, Erbil, Kurdistan Region, Iraq
| | - Majid Samsami
- Cancer Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Mohammad Taheri
- Institute of Human Genetics, Jena University Hospital, Jena, Germany; Urology and Nephrology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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8
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Zhang KX, Ding C, Liu QH, Zhu DM. Knockdown of LINC01087 inhibits gastric cancer malignant behavior by regulating the miR-135a-5p/CAAP1 axis. Funct Integr Genomics 2023; 23:248. [PMID: 37474836 DOI: 10.1007/s10142-023-01157-2] [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: 04/13/2023] [Revised: 06/19/2023] [Accepted: 06/26/2023] [Indexed: 07/22/2023]
Abstract
Long noncoding RNAs play important roles in the occurrence and development of many malignant cancers. This study focuses on the effects of LINC01087 on gastric cancer and its underlying mechanism. In the present study, LINC01087 and CAAP1 were found to be upregulated, and miR-135a-5p was diminished in gastric cancer specimens and cells. Inhibition of LINC01087 resulted in cell proliferation inhibition and induced cell apoptosis through the intrinsic apoptosis signaling pathway, as evidenced by the activation of caspase-3 and caspase-9. An investigation of the signaling pathway revealed that the effects on proliferation and apoptosis following LINC01087 knockdown were mediated by suppression of CAAP1. Furthermore, application of a miR-135a-5p inhibitor or overexpression of CAAP1 could attenuate the apoptotic effect achieved by LINC01087 inhibition, confirming the involvement of miR-135a-5p/CAAP1 signaling in the occurrence of gastric cancer. In conclusion, the LINC01087/miR-135a-5p/CAAP1 axis modulates gastric cancer tumorigenesis and pathogenesis and presents new insight into gastric cancer targeted therapy.
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Affiliation(s)
- Kai-Xin Zhang
- Department of General Surgery, The First Affiliated Hospital of Soochow University, No. 188 Shizi Street, Suzhou, 215600, Jiangsu Province, China
| | - Chuang Ding
- Department of Gastrointestinal Surgery, Suqian Hospital affiliated to Xuzhou Medical University, Suqian, 223800, Jiangsu Province, China
| | - Qiu-Hua Liu
- Department of General Surgery, Zhangjiagang Hospital Affiliated to Soochow University, the First People's Hospital of Zhangjiagang, Zhangjiagang, 215600, Jiangsu Province, China
| | - Dong-Ming Zhu
- Department of General Surgery, The First Affiliated Hospital of Soochow University, No. 188 Shizi Street, Suzhou, 215600, Jiangsu Province, China.
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Jiang J, Zhan X, Wei J, Fan Q, Li H, Li H, Li S, Zhao Y, Yin G, Tang L, Wu Y, Lan M, Qin Y, Guo Q, Xu W, Lu L, Yang Y, Zhang Y, Qu H. Artificial intelligence reveals dysregulation of osteosarcoma and cuproptosis-related biomarkers, PDHA1, CDKN2A and neutrophils. Sci Rep 2023; 13:4927. [PMID: 36967449 PMCID: PMC10040405 DOI: 10.1038/s41598-023-32195-2] [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: 07/24/2022] [Accepted: 03/23/2023] [Indexed: 03/29/2023] Open
Abstract
At present, the impact of cuproptosis-related genes in the study of osteosarcoma is largely unknown. Genome-wide data of osteosarcoma and controls were downloaded from 3 different databases, and specific diagnostic models associated with cuproptosis in osteosarcoma were constructed by support vector machines with artificial intelligence, random forest trees and LASSO regression. Differential analysis of immune cell infiltration was examined using routine blood data from 25,665 cases. Differential expression was examined using immunohistochemistry and PCR. PDHA1 and CDKN2A were obtained as specific cuproptosis-related biomarkers for osteosarcoma after artificial intelligence analysis. PDHA1, CDKN2A and neutrophils were differentially expressed in OS and control groups. PDHA1 and CDKN2A are significantly dysregulated in OS and are able to serve as biomarkers of OS.
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Affiliation(s)
- Jie Jiang
- Orthopedics, Guangxi Academy of Medical Sciences, Guangxi Zhuang Autonomous Region People's Hospital, Nanning, 530016, People's Republic of China
| | - Xinli Zhan
- Spinal Orthopedic Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, People's Republic of China
| | - Jianxun Wei
- Orthopedics, Guangxi Academy of Medical Sciences, Guangxi Zhuang Autonomous Region People's Hospital, Nanning, 530016, People's Republic of China
| | - Qie Fan
- Orthopedics, Guangxi Academy of Medical Sciences, Guangxi Zhuang Autonomous Region People's Hospital, Nanning, 530016, People's Republic of China
| | - Haowen Li
- Orthopedics, Guangxi Academy of Medical Sciences, Guangxi Zhuang Autonomous Region People's Hospital, Nanning, 530016, People's Republic of China
| | - Hao Li
- Orthopedics, Guangxi Academy of Medical Sciences, Guangxi Zhuang Autonomous Region People's Hospital, Nanning, 530016, People's Republic of China
| | - Shuzhen Li
- Orthopedics, Guangxi Academy of Medical Sciences, Guangxi Zhuang Autonomous Region People's Hospital, Nanning, 530016, People's Republic of China
| | - Yong Zhao
- Orthopedics, Guangxi Academy of Medical Sciences, Guangxi Zhuang Autonomous Region People's Hospital, Nanning, 530016, People's Republic of China
| | - Guodong Yin
- Orthopedics, Guangxi Academy of Medical Sciences, Guangxi Zhuang Autonomous Region People's Hospital, Nanning, 530016, People's Republic of China
| | - Lin Tang
- Orthopedics, Guangxi Academy of Medical Sciences, Guangxi Zhuang Autonomous Region People's Hospital, Nanning, 530016, People's Republic of China
| | - Yongxiang Wu
- Orthopedics, Guangxi Academy of Medical Sciences, Guangxi Zhuang Autonomous Region People's Hospital, Nanning, 530016, People's Republic of China
| | - Mindong Lan
- Orthopedics, Guangxi Academy of Medical Sciences, Guangxi Zhuang Autonomous Region People's Hospital, Nanning, 530016, People's Republic of China
| | - Yijue Qin
- Department of Traditional Chinese Medicine, Guangxi Academy of Medical Sciences, Guangxi Zhuang Autonomous Region People's Hospital, Nanning, 530016, People's Republic of China
| | - Quan Guo
- Department of Traditional Chinese Medicine, Guangxi Academy of Medical Sciences, Guangxi Zhuang Autonomous Region People's Hospital, Nanning, 530016, People's Republic of China
| | - Weicheng Xu
- Department of Traditional Chinese Medicine, Guangxi Academy of Medical Sciences, Guangxi Zhuang Autonomous Region People's Hospital, Nanning, 530016, People's Republic of China
| | - Ling Lu
- Department of Traditional Chinese Medicine, Guangxi Academy of Medical Sciences, Guangxi Zhuang Autonomous Region People's Hospital, Nanning, 530016, People's Republic of China
| | - Yanwei Yang
- Department of Traditional Chinese Medicine, Guangxi Academy of Medical Sciences, Guangxi Zhuang Autonomous Region People's Hospital, Nanning, 530016, People's Republic of China
| | - Yitian Zhang
- Department of Traditional Chinese Medicine, Guangxi Academy of Medical Sciences, Guangxi Zhuang Autonomous Region People's Hospital, Nanning, 530016, People's Republic of China
| | - Haishun Qu
- Department of Traditional Chinese Medicine, Guangxi Academy of Medical Sciences, Guangxi Zhuang Autonomous Region People's Hospital, Nanning, 530016, People's Republic of China.
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10
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Huang X, Su B, Wang X, Zhou Y, He X, Liu B. A network-based dynamic criterion for identifying prediction and early diagnosis biomarkers of complex diseases. J Bioinform Comput Biol 2022; 20:2250027. [PMID: 36573886 DOI: 10.1142/s0219720022500275] [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: 12/13/2022]
Abstract
Lung adenocarcinoma (LUAD) seriously threatens human health and generally results from dysfunction of relevant module molecules, which dynamically change with time and conditions, rather than that of an individual molecule. In this study, a novel network construction algorithm for identifying early warning network signals (IEWNS) is proposed for improving the performance of LUAD early diagnosis. To this end, we theoretically derived a dynamic criterion, namely, the relationship of variation (RV), to construct dynamic networks. RV infers correlation [Formula: see text] statistics to measure dynamic changes in molecular relationships during the process of disease development. Based on the dynamic networks constructed by IEWNS, network warning signals used to represent the occurrence of LUAD deterioration can be defined without human intervention. IEWNS was employed to perform a comprehensive analysis of gene expression profiles of LUAD from The Cancer Genome Atlas (TCGA) database and the Gene Expression Omnibus (GEO) database. The experimental results suggest that the potential biomarkers selected by IEWNS can facilitate a better understanding of pathogenetic mechanisms and help to achieve effective early diagnosis of LUAD. In conclusion, IEWNS provides novel insight into the initiation and progression of LUAD and helps to define prospective biomarkers for assessing disease deterioration.
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Affiliation(s)
- Xin Huang
- School of Mathematics and Information Science, Anshan Normal University, Anshan, Liaoning 114007, P. R. China
| | - Benzhe Su
- School of Computer Science and Technology, Dalian University of Technology, Dalian, Liaoning 116024, P. R. China
| | - Xingyu Wang
- School of Mathematics and Information Science, Anshan Normal University, Anshan, Liaoning 114007, P. R. China
| | - Yang Zhou
- Liaoning Clinical Research Center for Lung Cancer, The Second Hospital of Dalian Medical University Dalian, Liaoning 116023, P. R. China
| | - Xinyu He
- School of Computer and Information Technology, Liaoning Normal University, Dalian, Liaoning 116029, P. R. China
| | - Bing Liu
- School of Mathematics and Information Science, Anshan Normal University, Anshan, Liaoning 114007, P. R. China
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Wu L, Yang J, Ke RS, Liu Y, Guo P, Feng L, Li Z, Li Z. Impact of lncRNA SOX9-AS1 overexpression on the prognosis and progression of intrahepatic cholangiocarcinoma. Clin Res Hepatol Gastroenterol 2022; 46:101999. [PMID: 35870795 DOI: 10.1016/j.clinre.2022.101999] [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: 05/20/2022] [Revised: 07/06/2022] [Accepted: 07/19/2022] [Indexed: 02/04/2023]
Abstract
BACKGROUND Intrahepatic cholangiocarcinoma (ICC) is a latent and malignant tumor with a dismal prognosis. This study was to evaluate the clinical relevance and therapeutic potential of SOX9-AS1 expression in ICC. METHODS The cancerous tissues and adjacent normal tissues were collected from ICC patients. Blood samples from ICC, hepatocellular carcinoma (HCC) group, the extrahepatic cholangiocarcinoma (ECC) group and the healthy controls were collected. SOX9-AS1 levels were evaluated in tissues (versus normal tissues) and plasma samples (versus plasma from HCC and ECC by quantitative real-time RT-PCR. The diagnostic value of SOX9-AS1 for ICC was estimated using receiver operating characteristic (ROC) curves. The relevancy between SOX9-AS1 expression and overall survival or recurrence-free survival was assessed by Kaplan-Meier curves multivariate analyses. The overexpression and knockdown of SOX9-AS1 on cell behavior were assessed by CCK-8 and transwell assay. RESULTS SOX9-AS1 levels were increased in ICC, both in the tissues and the cell lines. The upregulation of SOX9-AS1 showed a highly discriminative profile, distinguishing ICC patients from healthy subjects or HCC or ECC patients. Upregulation of SOX9-AS1 was related to shorter overall survival and recurrence-free survival. Muli-variate analysis revealed that SOX9-AS1 expression was an independent prognostic purpose factor of worst overall survival and recurrence-free survival. CONCLUSIONS SOX9-AS1 drives tumor growth and metastasis in ICC. SOX9-AS1 may be applied as a new diagnostic and prognostic purposed marker, in addition to a promising therapeutic target in ICC.
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Affiliation(s)
- Lupeng Wu
- Department of Hepatobiliary Pancreatic Vascular Surgery, The First Affiliated Hospital of Xiamen University, Xiamen, Fujian, 361003, China
| | - Jingrui Yang
- Department of Hepatobiliary Pancreatic Vascular Surgery, The First Affiliated Hospital of Xiamen University, Xiamen, Fujian, 361003, China
| | - Rui-Sheng Ke
- Department of General Surgery, The First Affiliated Hospital of Xiamen University, Xiamen, Fujian, 361003, China
| | - Yujian Liu
- Department of Hepatobiliary Pancreatic Vascular Surgery, The First Affiliated Hospital of Xiamen University, Xiamen, Fujian, 361003, China
| | - Ping Guo
- Department of Hepatobiliary Pancreatic Vascular Surgery, The First Affiliated Hospital of Xiamen University, Xiamen, Fujian, 361003, China
| | - Liuxing Feng
- Department of Hepatobiliary Pancreatic Vascular Surgery, The First Affiliated Hospital of Xiamen University, Xiamen, Fujian, 361003, China
| | - Zhimin Li
- Department of Hepatobiliary Pancreatic Vascular Surgery, The First Affiliated Hospital of Xiamen University, Xiamen, Fujian, 361003, China.
| | - Zhimin Li
- Department of Hepatobiliary Pancreatic Vascular Surgery, The First Affiliated Hospital of Xiamen University, Xiamen, Fujian, 361003, China.
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12
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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.
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Di S, Bai R, Lu D, Chen C, Ma T, Zou Z, Zhang Z. Long non-coding RNA MAFG-AS1 promotes proliferation and metastasis of breast cancer by modulating STC2 pathway. Cell Death Discov 2022; 8:249. [PMID: 35513366 PMCID: PMC9072673 DOI: 10.1038/s41420-022-01043-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 04/21/2022] [Accepted: 04/25/2022] [Indexed: 12/22/2022] Open
Abstract
Breast cancer is the most common cancer worldwide. A number of studies proposed that long non-coding RNA plays an essential role in the regulation of invasion and metastasis of various forms of malignancy, including lung cancer, gastric cancer, and bladder cancer. In this study, a long non-coding RNA(LncRNA) MAFG-AS1 was explored in detail to understand the significance in the etiology of breast cancer. The results indicated that expression of LncRNA MAFG-AS1 in the breast cancer tissues was significantly higher than the adjacent normal breast tissues and elevated expression level of LncRNA MAFG-AS1 was correlated to the larger tumor size, negative expression of ER, PR and lymph node metastasis. The potency of breast cancer proliferation, invasion, and metastasis was inhibited in the absence of LncRNA MAFG-AS1. Mechanically, LncRNA MAFG-AS1 was mainly located in the cytoplasm. The downstream target gene of LncRNA MAFG-AS1 was STC2 which might promote cell proliferation and metastasis in breast cancer and this study provides a new potential therapeutic target for breast cancer.
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Affiliation(s)
- Shihao Di
- Department of Pathology, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou road, 210029, Nanjing, China
| | - Rumeng Bai
- Department of Pathology, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou road, 210029, Nanjing, China
| | - Die Lu
- Department of Pathology, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou road, 210029, Nanjing, China
- Department of Pathology, The First Affiliated Hospital of Soochow University, 899 Pinghai Road, 215006, Suzhou, China
| | - Chunni Chen
- Department of Pathology, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou road, 210029, Nanjing, China
- Department of Pathology, The Second Affiliated Hospital of Xi'an Jiaotong University (Xibei Hospital), 157 West 5th Road, 710004, Xi'an, China
| | - Tianshi Ma
- Department of Pathology, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou road, 210029, Nanjing, China
- Department of Pathology, Zhejiang Provincial People's Hospital & People's Hospital of Hangzhou Medical College, 158 Shangtang Road, 310014, Hangzhou, China
| | - Zigui Zou
- Department of Pathology, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou road, 210029, Nanjing, China
- Department of Pathology, The First Affiliated Hospital of Soochow University, 899 Pinghai Road, 215006, Suzhou, China
| | - Zhihong Zhang
- Department of Pathology, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou road, 210029, Nanjing, China.
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Li Y, Wu M, Xu S, Huang H, Yan L, Gu Y. Colorectal cancer stem cell-derived exosomal long intergenic noncoding RNA 01315 (LINC01315) promotes proliferation, migration, and stemness of colorectal cancer cells. Bioengineered 2022; 13:10827-10842. [PMID: 35470736 PMCID: PMC9161962 DOI: 10.1080/21655979.2022.2065800] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
The effect of long intergenic noncoding RNA 01315 (LINC01315) on colorectal cancer has widely been proved. Nevertheless, how LINC01315 functions in the stemness of colorectal cancer and whether LINC01315 exists in colorectal cancer stem-like cell-derived exosomes remain dim, which are thus investigated in this research. CD133+/CD44+ colorectal cancer stem cells were sorted and verified through flow cytometry. Exosomes derived from CD133+/CD44+ colorectal cancer stem cells were collected. The viability, proliferation, stemness and migration of CD133+/CD44+, CD133−/CD44−, and colorectal cancer cells after transfection or the co-culture with exosomes were detected by MTT, colony formation, spheroid, and wound healing assays, respectively. Expressions of LINC01315, BCL-2, Bax, cleaved caspase-3, MMP-9, E-cadherin, and vimentin in cells or exosomes were analyzed using western blot or qRT-PCR. Genes interacted with LINC01315 in colorectal cancer were predicted by bioinformatics analysis. The results showed that LINC01315 was high-expressed in CD133+/CD44+ colorectal cancer stem cells and exosomes. Compared with colorectal cancer cells, the viability, proliferation, stemness, and migration of CD133+/CD44+ cancer cells were stronger, while these of CD133−/CD44− cancer cells were weaker. Besides, LINC01315 silencing decreased the viability, proliferation, stemness, and migration of CD133+/CD44+ cancer cells, while sh-LINC01315 inhibited the promotive effects of CD133+/CD44+ cancer cell-derived exosomes on the viability, proliferation, stemness, and migration of colorectal cancer cells. LINC01315 was also found to be correlated with DPEP1, KRT23, ASCL2, AXIN2, and DUSP4 in colorectal cancer. In conclusion, colorectal cancer stem cell-derived exosomal LINC01315 promotes the proliferation, migration, and stemness of colorectal cancer cells.
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Affiliation(s)
- Youran Li
- Department of Colorectal Surgery, Jiangsu Province Hospital of Chinese Medicine, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Minna Wu
- Department of Colorectal Surgery, Jiangsu Province Hospital of Chinese Medicine, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Shanshan Xu
- Department of Colorectal Surgery, Jiangsu Province Hospital of Chinese Medicine, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Hua Huang
- Department of Anorectal, Changshu Hospital Affiliated to Nanjing University of Chinese Medicine, Changshu, Suzhou, Jiangsu, China
| | - Lei Yan
- Department of Colorectal Surgery, Jiangsu Province Hospital of Chinese Medicine, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Yunfei Gu
- Department of Colorectal Surgery, Jiangsu Province Hospital of Chinese Medicine, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
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Xiu Y, Cao S, Jiang R, Zhou Y. lncRNA LINC01315 promotes malignancy of triple-negative breast cancer and predicts poor outcomes by modulating microRNA-876-5p/GRK5. Bioengineered 2022; 13:10001-10009. [PMID: 35412954 PMCID: PMC9161853 DOI: 10.1080/21655979.2022.2062536] [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] [Indexed: 11/15/2022] Open
Abstract
Triple-negative breast cancer (TNBC) is a malignant tumor that threatens women’s health. Exploring novel development-associated biomarkers could help improve the survival rate of TNBC. This study evaluated the significance and mechanism of LINC01315 in TNBC progression aiming to identify a potential biomarker. There were 103 TNBC patients that provided clinical tissues in this study. The expression of LINC01315 was assessed by PCR and its association with clinical data was evaluated by statistical analyses. The in vitro cell experiments were conducted to estimate the biological effect of LINC01315 and its molecular mechanism. A significant upregulation of LINC01315 was observed in TNBC, which was associated with disease development and severity of patients. The upregulation of LINC01315 could be a symptom of the poor prognosis of patients. The knockdown of LINC01315 suppressed the main cellular processes of TNBC progression. Additionally, miR-876-5p was demonstrated to be a target of LINC01315 and regulate the expression of GRK5, through which LINC01315 modulated the progression of TNBC. Upregulated LINC01315 in TNBC indicated the malignant development and poor survival rate of patients. Inhibition of LINC01315 might be a potential therapeutic strategy of TNBC.
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Affiliation(s)
- Yan Xiu
- Medical Clinical Laboratory, Yantai Affiliated Hospital of Binzhou Medical University, Yantai, Shandong, China
| | - Shannan Cao
- Medical Clinical Laboratory, Yantai Affiliated Hospital of Binzhou Medical University, Yantai, Shandong, China
| | - Ru Jiang
- Medical Clinical Laboratory, Yantai Affiliated Hospital of Binzhou Medical University, Yantai, Shandong, China
| | - Yuming Zhou
- Medical Clinical Laboratory, Yantai Affiliated Hospital of Binzhou Medical University, Yantai, Shandong, China
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Li Y, Wang W, Wu M, Zhu P, Zhou Z, Gong Y, Gu Y. LncRNA LINC01315 silencing modulates cancer stem cell properties and epithelial-to-mesenchymal transition in colorectal cancer via miR-484/DLK1 axis. Cell Cycle 2022; 21:851-873. [PMID: 35156543 PMCID: PMC8973332 DOI: 10.1080/15384101.2022.2033415] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Long non-coding RNA long intergenic non-protein coding RNA 01315 (LncRNA LINC01315) has been found to be implicated in various cancers, but its role and functions in colorectal cancer (CRC) remain to be addressed. Data on LINC01315 expression in CRC were gathered using bioinformatics analysis, and cancer stem cells (CSCs) were sorted by aldehyde dehydrogenase (ALDH) assay and flow cytometry. Migration, invasion, and stemness of CSCs isolated from CRC cells after transfection were determined by scratch, Transwell, and sphere-formation assays, respectively. Tumor xenograft model was constructed. Target genes and potential-binding sites were predicted using online databases and further confirmed via dual-luciferase reporter assay. Relative factors expressions were determined via quantitative real-time polymerase-chain reaction and Western blot as needed. LINC01315 was high-expressed in CRC and ALDH+ cells. LINC01315 silencing suppressed the migration, invasion, and sphere formation of CRC cells and tumor growth, and downregulated expressions of CSC molecules (ALDH, cluster of difference 44 (CD44), Prominin, and sex determining region Y-box 2 (SOX2)), Zinc Finger E-Box Binding Homeobox 1 (ZEB1) and Vimentin but upregulated E-Cadherin expression. MiR-484 could competitively bind with LINC01315, and LINC01315 silencing promoted miR-484 expression. The level of Delta Like Non-Canonical Notch Ligand 1 (DLK1), the target gene of miR-484, was enhanced by overexpressed LINC01315 yet was suppressed by LINC01315 silencing. Also, DLK1 silencing reversed the effects of downregulated miR-484 on migration, invasion, sphere formation, and CSC molecules expressions in CRC cells. LINC01315 silencing modulated CSC properties and epithelial-to-mesenchymal transition via miR-484/DLK1 axis.
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Affiliation(s)
- Youran Li
- Department of Colorectal Surgery, Jiangsu Province Hospital of Chinese Medicine, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing City, China
| | - Wei Wang
- Department of Colorectal Surgery, Jiangsu Province Hospital of Chinese Medicine, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing City, China
| | - Minna Wu
- Department of Colorectal Surgery, Jiangsu Province Hospital of Chinese Medicine, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing City, China
| | - Ping Zhu
- Department of Colorectal Surgery, Jiangsu Province Hospital of Chinese Medicine, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing City, China
| | - Zailong Zhou
- Department of Colorectal Surgery, Jiangsu Province Hospital of Chinese Medicine, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing City, China
| | - Yuxia Gong
- Department of Colorectal Surgery, Jiangsu Province Hospital of Chinese Medicine, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing City, China
| | - Yunfei Gu
- Department of Colorectal Surgery, Jiangsu Province Hospital of Chinese Medicine, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing City, China,CONTACT Yunfei GuJiangsu Province Hospital of Chinese Medicine, Affiliated Hospital of Nanjing University of Chinese Medicine, No. 155 Hanzhong Road, Qinhuai District, Nanjing City, Jiangsu Province210029, China. +86-02586617141-71116
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Development of a Prognostic Model Based on the Identification of EMT-Related lncRNAs in Triple-Negative Breast Cancer. JOURNAL OF ONCOLOGY 2021; 2021:9219961. [PMID: 34873403 PMCID: PMC8643262 DOI: 10.1155/2021/9219961] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 11/08/2021] [Indexed: 12/29/2022]
Abstract
Background Triple-negative breast cancer (TNBC) remains the most incurable subtype of breast cancer owing to high heterogeneity, aggressive nature, and lack of treatment options. It is generally acknowledged that epithelial-mesenchymal transition (EMT) is the key step in tumor metastasis. Methods With the application of TCGA and GEO databases, we identified EMT-related lncRNAs by the Cox univariate regression analysis. Optimum risk scores were calculated and used to divide TNBC patients into high-/low-risk subgroups by the median value using the Lasso regression analysis. The Kaplan–Meier and ROC curve analyses were applied for model validation. Then, we assessed the risk model from multi-omic aspects including immune infiltration, drug sensitivity, mutability spectrum, signaling pathways, and clinical indicators. We also analyzed the expression pattern of lncRNAs involved in the model using qRT-PCR in TNBC cell lines and constructed the ceRNA network. Results The risk model was composed of EMT-related long noncoding RNAs (lncRNAs), which seemed to be valuable in the prognostic prediction of TNBC patients. The model could act as an independent prognostic factor of TNBC and showed a robust prognostic ability in the stratification analysis. Further investigation demonstrated that the expression of lncRNAs was different between high aggressive and low aggressive TNBC cell lines, as well as TNBC patients. Conclusions Together, our study successfully established a risk model with great accuracy and efficacy in the prognostic prediction of TNBC patients.
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Han C, Zhang C, Wang H, Li K, Zhao L. Angiogenesis-related lncRNAs predict the prognosis signature of stomach adenocarcinoma. BMC Cancer 2021; 21:1312. [PMID: 34876056 PMCID: PMC8653638 DOI: 10.1186/s12885-021-08987-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 11/09/2021] [Indexed: 12/29/2022] Open
Abstract
Background Stomach adenocarcinoma (STAD), which accounts for approximately 95% of gastric cancer types, is a malignancy cancer with high morbidity and mortality. Tumor angiogenesis plays important roles in the progression and pathogenesis of STAD, in which long noncoding RNAs (lncRNAs) have been verified to be crucial for angiogenesis. Our study sought to construct a prognostic signature of angiogenesis-related lncRNAs (ARLncs) to accurately predict the survival time of STAD. Methods The RNA-sequencing dataset and corresponding clinical data of STAD were acquired from The Cancer Genome Atlas (TCGA). ARLnc sets were obtained from the Ensemble genome database and Molecular Signatures Database (MSigDB, Angiogenesis M14493, INTegrin pathway M160). A ARLnc-related prognostic signature was then constructed via univariate Cox and multivariate Cox regression analysis in the training cohort. Survival analysis and Cox regression were performed to assess the performance of the prognostic signature between low- and high-risk groups, which was validated in the validation cohort. Furthermore, a nomogram that combined the clinical pathological characteristics and risk score conducted to predict the overall survival (OS) of STAD. In addition, ARLnc-mRNA coexpression pairs were constructed with Pearson’s correlation analysis and visualized to infer the functional annotation of the ARLncs by gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. The expression of four ARLncs in STAD and their correlation with the angiogenesis markers, CD34 and CD105, were also validated by RT–qPCR in a clinical cohort. Results A prognostic prediction signature including four ARLncs (PVT1, LINC01315, AC245041.1, and AC037198.1) was identified and constructed. The OS of patients in the high-risk group was significantly lower than that of patients in the low-risk group (p < 0.001). The values of the time-dependent area under the curve (AUC) for the ARLnc signature for 1-, 3-, and 5- year OS were 0.683, 0.739, and 0.618 in the training cohort and 0.671, 0.646, and 0.680 in the validation cohort, respectively. Univariate and multivariate Cox regression analyses indicated that the ARLnc signature was an independent prognostic factor for STAD patients (p < 0.001). Furthermore, the nomogram and calibration curve showed accurate prediction of the survival time based on the risk score. In addition, 262 mRNAs were screened for coexpression with four ARLncs, and GO analysis showed that mRNAs were mainly involved in biological processes, including angiogenesis, cell adhesion, wound healing, and extracellular matrix organization. Furthermore, correlation analysis showed that there was a positive correlation between risk score and the expression of the angiogenesis markers, CD34 and CD105, in TCGA datasets and our clinical sample cohort. Conclusion Our study constructed a prognostic signature consisting of four ARLnc genes, which was closely related to the survival of STAD patients, showing high efficacy of the prognostic signature. Thus, the present study provided a novel biomarker and promising therapeutic strategy for patients with STAD. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-021-08987-y.
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Affiliation(s)
- Chen Han
- Research Center, The Fourth Hospital of Hebei Medical University, 050011, Shijiazhuang, China
| | - Cong Zhang
- Research Center, The Fourth Hospital of Hebei Medical University, 050011, Shijiazhuang, China
| | - Huixia Wang
- Research Center, The Fourth Hospital of Hebei Medical University, 050011, Shijiazhuang, China
| | - Kexin Li
- Research Center, The Fourth Hospital of Hebei Medical University, 050011, Shijiazhuang, China
| | - Lianmei Zhao
- Research Center, The Fourth Hospital of Hebei Medical University, 050011, Shijiazhuang, China.
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LINC01087 indicates a poor prognosis of glioma patients with preoperative MRI. Funct Integr Genomics 2021; 22:55-64. [PMID: 34817752 PMCID: PMC8770444 DOI: 10.1007/s10142-021-00812-w] [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: 09/09/2021] [Revised: 09/09/2021] [Accepted: 10/08/2021] [Indexed: 01/19/2023]
Abstract
Long intergenic non-coding RNA 01,087 (LINC01087) has been concerned as an oncogene in breast cancer, while its mechanism in glioma has been little surveyed. Thus, we searched the prognostic value and functional action of LINC01087 in glioma. Glioma patients after preoperative MRI diagnosis were enrolled, and LINC01087, microRNA (miR)-1277-5p, and alkaline ceramidase 3 (ACER3) levels were tested in glioma cancer tissue. The correlation between LINC01087 expression and the survival of patients were analyzed. LINC01087, miR-1277-5p, and ACER3 levels in U251 cells were altered via transfection, and cell malignant phenotypes were monitored. The relationship between miR-1277-5p and LINC01087 or ACER3 was detected. The LINC01087 and ACER3 expression was in up-regulation and the miR-1277-5p expression was in down-regulation in clinical glioma samples. High expression of LINC01087 was associated with poor prognosis of glioma patients with preoperative MRI. LINC01087 silencing restrained tumor malignancy in glioma cells. Mechanistically, LINC01087 directly interacted with miR-1277-5p. ACER3 was a known target of miR-1277-5p. Moreover, rescue assays reveal that miR-1277-5p overexpression (or ACER3 overexpression) reversed the effects of LINC01087 upregulation (or miR-1277-5p upregulation) on glioma cells. LINC01087 has prognostic significance in glioma and silencing LINC01087 deters glioma development through elevating miR-1277-5p to reduce ACER3 expression.
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Xue J, Huang S, Chen J, Chen YZ, Shao ZM, Wu J, Chi Y. Overexpression of Long Non-Coding RNA Linc01315 Predicts Poor Prognosis in Breast Cancer. Front Oncol 2021; 11:562378. [PMID: 34676156 PMCID: PMC8524084 DOI: 10.3389/fonc.2021.562378] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 09/16/2021] [Indexed: 01/27/2023] Open
Abstract
Background LncRNAs have been shown to play critical roles in regulating tumorigenesis and tumor progression. Using LncRNAs to predict prognosis and therapeutic response to cancer treatment has been caused for concern, but the predictive value of lncRNAs remains to be explored and underlying mechanisms have not been completely understood. Methods The Linc01315 expression level was detected in 282 breast cancer tissues by using quantitative RT-PCR. The association between Linc01315 expression level and clinicopathological features of these breast cancer patients was further analyzed. Multiple regression analysis was used to evaluate Linc01315 predictive value of patients’ prognosis. Results Our study revealed that Linc01315 expression level was significantly correlated with vessel invasion (P = 0.028) and tumor subtype (P = 0.039). The Kaplan–Meier survival curves demonstrated that patients with lower Linc01315 expression level had significantly longer disease free survival (DFS) (P = 0.002) and overall survival (OS) (P=0.019). Multiple regression analysis showed that Linc01315 level could be an independent predictive factor for DFS (hazards ratio = 0.613, 95% confidence interval = 0.375-1.003; P = 0.049) and OS (hazards ratio = 0.439, 95% confidence interval = 0.228-0.845; P = 0.014). Further analysis showed that low Linc01315 level patients with endocrine therapy could benefit patients DFS (P=0.037) and OS (P=0.025). Conclusion Our results demonstrate that Linc01315 expression level is significantly correlated with breast cancer patients’ prognosis. Linc01315 may represent an independent prognostic marker and therapeutic target in breast cancer.
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Affiliation(s)
- Jingyan Xue
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Sheng Huang
- The 2nd Department of Breast Surgery, Breast Cancer Center of the Third Affiliated Hospital of Kunming Medical University, Tumor Hospital of Yunnan Province, Kunming, China
| | - Jiaying Chen
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Yi-Zuo Chen
- Department of Thyroid and Breast Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Zhi-Min Shao
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jiong Wu
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Collaborative Innovation Center for Cancer Medicine, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yayun Chi
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
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21
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Tian YH, Jia LW, Liu ZF, Chen YH. LINC01087 inhibits glioma cell proliferation and migration, and increases cell apoptosis via miR-384/Bcl-2 axis. Aging (Albany NY) 2021; 13:20808-20819. [PMID: 34459789 PMCID: PMC8436897 DOI: 10.18632/aging.203478] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 08/02/2021] [Indexed: 01/22/2023]
Abstract
BACKGROUND Long non-coding RNA (LncRNA) is associated with disease progression. It is reported that LINC01087 is highly expressed in cancer and participates in tumorigenesis. However, whether it regulates the development of glioma has not been studied. So, the goal of this research is to determine the role of LINC01087 in gliomas and to provide potential targets for clinical treatment. METHODS The gene expression was detected by quantitative reverse transcriptase polymerase chain reaction (QRT-PCR) and Western blotting (WB). Cell proliferation was analyzed by CCK8 and colony formation test, and apoptosis was detected by flow cytometry. Luciferase report experiment and RNA Binding Protein Immunoprecipitation confirmed the interaction between LINC01087, miR-384 and Bcl-2. The effect of regulating LINC01087 on the growth of glioma was confirmed in vitro. RESULTS The LINC01087 expression was up-regulated in clinical glioma samples (n = 35). Furthermore, LINC01087 silencing can obviously suppress the proliferation of glioma cells and induce apoptosis. Mechanically, we found that LINC01087 was the molecular sponge of miR-384. LINC01087 could inhibit the miR-384 expression and boost the Bcl-2 expression through sponge expression of miR-384. The repair of Bcl-2 effectively saved the proliferation and apoptosis of glioma cells lacking LINC01087. CONCLUSION LINC01087 is highly expressed in glioma and can participate in the growth of glioma through miR-384/Bcl-2 axis. So, it is a potential therapeutic target.
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Affiliation(s)
- Yao-Hui Tian
- Department of Neurosurgery, Cangzhou Central Hospital, Cangzhou, Hebei Province, China
| | - Lin-Wei Jia
- Department of Neurosurgery, Cangzhou Central Hospital, Cangzhou, Hebei Province, China
| | - Zhi-Feng Liu
- Department of Neurosurgery, Cangzhou Central Hospital, Cangzhou, Hebei Province, China
| | - Yong-Han Chen
- Department of Neurosurgery, Cangzhou Central Hospital, Cangzhou, Hebei Province, China
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22
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Pei J, Zhang S, Yang X, Han C, Pan Y, Li J, Wang Z, Sun C, Zhang J. Long non-coding RNA RP11-283G6.5 confines breast cancer development through modulating miR-188-3p/TMED3/Wnt/β-catenin signalling. RNA Biol 2021; 18:287-302. [PMID: 34130584 DOI: 10.1080/15476286.2021.1941608] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The contributions of long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) to breast cancer are critical areas of investigation. In this study, we identified a novel lncRNA RP11-283G6.5 which was lowly expressed in breast cancer and whose low expression was correlated with poor overall survival and disease-free survival of breast cancer patients. Functional experiments revealed that ectopic expression of RP11-283G6.5 confined breast cancer cellular growth, migration, and invasion, and promoted cellular apoptosis. Conversely, RP11-283G6.5 silencing facilitated breast cancer cellular growth, migration, and invasion, and repressed cellular apoptosis. Moreover, RP11-283G6.5 was found to confine breast cancer tumour growth and metastasis in vivo. Mechanistically, RP11-283G6.5 competitively bound to ILF3, reduced the binding of ILF3to primary miR-188 (pri-miR-188), abolished the suppressive effect of ILF3 on pri-miR-188 processing, and therefore promoted pri-miR-188 processing, leading to the reduction of pri-miR-188 and the upregulation of mature miR-188-3p. The expression of RP11-283G6.5 was significantly positively correlated with that of miR-188-3p in breast cancer tissues. Through increasing miR-188-3p, RP11-283G6.5 decreased TMED3, a target of miR-188-3p. RP11-283G6.5 further suppressed Wnt/β-catenin signalling via decreasing TMED3. Rescue assays revealed that inhibition of miR-188-3p, overexpression of TMED3 or blocking Wnt/β-catenin signalling all attenuated the roles of RP11-283G6.5 in breast cancer. Collectively, these findings demonstrated that RP11-283G6.5 is a tumour suppressive lncRNA in breast cancer via modulating miR-188-3p/TMED3/Wnt/β-catenin signalling. This study indicated that RP11-283G6.5 might be a promising prognostic biomarker and therapeutic target for breast cancer.
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Affiliation(s)
- Jing Pei
- Department of Breast Surgery, Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Shengquan Zhang
- Department of Biochemistry and Molecular Biology, Anhui Medical University, Hefei, China
| | - Xiaowei Yang
- Department of Breast Surgery, Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Chunguang Han
- Department of Breast Surgery, Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Yubo Pan
- Department of Breast Surgery, Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Jun Li
- Department of Breast Surgery, Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Zhaorui Wang
- Department of Breast Surgery, Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Chenyu Sun
- Department of Internal Medicine, AMITA Health Saint Joseph Hospital Chicago, Chicago, Illinois, USA
| | - Jing Zhang
- Department of Breast Surgery, The Tumor Hospital of Xuzhou, Xuzhou, China
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23
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Thakur KK, Kumar A, Banik K, Verma E, Khatoon E, Harsha C, Sethi G, Gupta SC, Kunnumakkara AB. Long noncoding RNAs in triple-negative breast cancer: A new frontier in the regulation of tumorigenesis. J Cell Physiol 2021; 236:7938-7965. [PMID: 34105151 DOI: 10.1002/jcp.30463] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 05/11/2021] [Accepted: 05/20/2021] [Indexed: 12/16/2022]
Abstract
In recent years, triple-negative breast cancer (TNBC) has emerged as the most aggressive subtype of breast cancer and is usually associated with increased mortality worldwide. The severity of TNBC is primarily observed in younger women, with cases ranging from approximately 12%-24% of all breast cancer cases. The existing hormonal therapies offer limited clinical solutions in completely circumventing the TNBC, with chemoresistance and tumor recurrences being the common hurdles in the path of TNBC treatment. Accumulating evidence has correlated the dysregulation of long noncoding RNAs (lncRNAs) with increased cell proliferation, invasion, migration, tumor growth, chemoresistance, and decreased apoptosis in TNBC. Various clinical studies have revealed that aberrant expression of lncRNAs in TNBC tissues is associated with poor prognosis, lower overall survival, and disease-free survival. Due to these specific characteristics, lncRNAs have emerged as novel diagnostic and prognostic biomarkers for TNBC treatment. However, the underlying mechanism through which lncRNAs perform their actions remains unclear, and extensive research is being carried out to reveal it. Therefore, understanding of mechanisms regulating the modulation of lncRNAs will be a substantial breakthrough in effective treatment therapies for TNBC. This review highlights the association of several lncRNAs in TNBC progression and treatment, along with their possible functions and mechanisms.
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Affiliation(s)
- Krishan K Thakur
- Department of Biosciences and Bioengineering, Cancer Biology Laboratory, Indian Institute of Technology (IIT) Guwahati, Guwahati, Assam, India
| | - Aviral Kumar
- Department of Biosciences and Bioengineering, Cancer Biology Laboratory, Indian Institute of Technology (IIT) Guwahati, Guwahati, Assam, India
| | - Kishore Banik
- Department of Biosciences and Bioengineering, Cancer Biology Laboratory, Indian Institute of Technology (IIT) Guwahati, Guwahati, Assam, India
| | - Elika Verma
- Department of Biosciences and Bioengineering, Cancer Biology Laboratory, Indian Institute of Technology (IIT) Guwahati, Guwahati, Assam, India
| | - Elina Khatoon
- Department of Biosciences and Bioengineering, Cancer Biology Laboratory, Indian Institute of Technology (IIT) Guwahati, Guwahati, Assam, India
| | - Choudhary Harsha
- Department of Biosciences and Bioengineering, Cancer Biology Laboratory, Indian Institute of Technology (IIT) Guwahati, Guwahati, Assam, India
| | - Gautam Sethi
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Subash C Gupta
- Department of Biochemistry, Laboratory for Translational Cancer Research, Banaras Hindu University (BHU), Varanasi, Uttar Pradesh, India
| | - Ajaikumar B Kunnumakkara
- Department of Biosciences and Bioengineering, Cancer Biology Laboratory, Indian Institute of Technology (IIT) Guwahati, Guwahati, Assam, India
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24
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Liu ZQ, Zhang GT, Jiang L, Li CQ, Chen QT, Luo DQ. Construction and Comparison of ceRNA Regulatory Network for Different Age Female Breast Cancer. Front Genet 2021; 12:603544. [PMID: 33968126 PMCID: PMC8097183 DOI: 10.3389/fgene.2021.603544] [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: 09/09/2020] [Accepted: 03/15/2021] [Indexed: 01/14/2023] Open
Abstract
Studies have shown the difference appearing among the prognosis of patients in different age groups. However, the molecular mechanism implicated in this disparity have not been elaborated. In this study, expression profiles of female breast cancer (BRCA) associated mRNAs, lncRNAs and miRNAs were downloaded from the TCGA database. The sample were manually classified into three groups according to their age at initial pathological diagnosis: young (age ≤ 39 years), elderly (age ≥ 65 years), and intermediate (age 40-64 years). lncRNA-miRNA-mRNA competitive endogenous RNA (ceRNA) network was respectively constructed for different age BRCA. Then, the biological functions of differentially expressed mRNAs (DEmRNAs) in ceRNA network were further investigated by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. Finally, survival analysis was used to identify prognostic biomarkers for different age BRCA patients. We identified 13 RNAs, 38 RNAs and 40 RNAs specific to patients aged ≤ 39 years, aged 40-64 years, and aged ≥ 65 years, respectively. Furthermore, the unique pathways were mainly enriched in cytokine-cytokine receptor interaction in patients aged 40-64 years, and were mainly enriched in TGF-beta signaling pathway in patients aged ≥ 65 years. According to the survival analysis, AGAP11, has-mir-301b, and OSR1 were respectively functioned as prognostic biomarkers in young, intermediate, and elderly group. In summary, our study identified the differences in the ceRNA regulatory networks and provides an effective bioinformatics basis for further understanding of the pathogenesis and predicting outcomes for different age BRCA.
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Affiliation(s)
- Zhi-Qin Liu
- Key Laboratory of Pharmaceutical Quality Control of Hebei Province, Institute of Life Science and Green Development, College of Pharmaceutical Science, Hebei University, Baoding, China
| | - Gao-Tao Zhang
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis of Ministry of Education, College of Life Science, Hebei University, Baoding, China
| | - Li Jiang
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis of Ministry of Education, College of Life Science, Hebei University, Baoding, China
| | - Chun-Qing Li
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis of Ministry of Education, College of Life Science, Hebei University, Baoding, China
| | - Que-Ting Chen
- Department of Breast Surgery, Affiliated Hospital of Hebei University, Hebei University, Baoding, China
| | - Du-Qiang Luo
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis of Ministry of Education, College of Life Science, Hebei University, Baoding, China
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25
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Bai X, Zhang S, Qiao J, Xing X, Li W, Zhang H, Xie J. Long non‑coding RNA SChLAP1 regulates the proliferation of triple negative breast cancer cells via the miR‑524‑5p/HMGA2 axis. Mol Med Rep 2021; 23:446. [PMID: 33846810 PMCID: PMC8060801 DOI: 10.3892/mmr.2021.12085] [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: 08/16/2020] [Accepted: 02/10/2021] [Indexed: 12/27/2022] Open
Abstract
Long non-coding RNA (lncRNA) second chromosome locus associated with prostate-1 (SChLAP1), also named LINC00913, has been reported to accelerate the carcinogenesis of prostate cancer. The aim of this study was to explore the role and mechanism of SChLAP1 in triple negative breast cancer (TNBC). The expression of SChLAP1 in TNBC tissues and cells was determined by reverse transcription quantitative PCR. The effects of SChLAP1 on the growth of TNBC cells was evaluated by detecting cell viability, colony formation and apoptosis. The present study determined that SChLAP1 was upregulated in TNBC tissues and was associated with the long-distant lymph node metastasis of patients with TNBC. Knockdown of SChLAP1 significantly inhibited cell viability and colony formation, and triggered apoptosis of TNBC cells. Bioinformatics analysis suggested that SChLAP1 acted as a sponge of microRNA (miR)-524-5p and negatively modulated the expression of miR-524-5p. An inverse correlation was also identified between the expression levels of SChLAP1 and miR-524-5p in TNBC tissues. Furthermore, the results demonstrated that SChLAP1 interacted with miR-524-5p, and subsequently regulated the expression level of High Mobility Group AT-Hook 2 (HMGA2) in TNBC cells. It was also found that the overexpression of HMGA2 rescued the suppressed viability of TNBC cells induced by SChLAP1 knockdown. In conclusion, the present findings demonstrated that SChLAP1 modulated the malignant tumor behaviors of TNBC cells by regulating HMGA2 and subsequently restraining miR-524-5p.
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Affiliation(s)
- Xiangdong Bai
- Department of Breast Surgery, Shanxi Provincial Cancer Hospital, Shanxi Medical University, Taiyuan, Shanxi 030013, P.R. China
| | - Shengxiao Zhang
- Department of Rheumatism and Immunology, Second Clinical Medical College, Shanxi Medical University, Taiyuan, Shanxi 030001, P.R. China
| | - Jun Qiao
- Department of Rheumatism and Immunology, Second Clinical Medical College, Shanxi Medical University, Taiyuan, Shanxi 030001, P.R. China
| | - Xiaolong Xing
- Research and Development Division, Shanxi Immune Medical Technology Co., Ltd., Taiyuan, Shanxi 030001, P.R. China
| | - Weina Li
- Department of Radiotherapy, Shanxi Provincial Cancer Hospital, Shanxi Medical University, Taiyuan, Shanxi 030001, P.R. China
| | - Huanhu Zhang
- Department of Gastroenterology, Shanxi Provincial Cancer Hospital, Shanxi Medical University, Taiyuan, Shanxi 030013, P.R. China
| | - Jun Xie
- Department of Biochemistry and Molecular Biology, Shanxi Provincial Cancer Hospital, Shanxi Medical University, Taiyuan, Shanxi 030001, P.R. China
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26
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Ren J, Zhang FJ, Wang JH, Tang JD. LINC01315 promotes the aggressive phenotypes of papillary thyroid cancer cells by sponging miR-497-5p. Kaohsiung J Med Sci 2021; 37:459-467. [PMID: 33611825 DOI: 10.1002/kjm2.12369] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 12/05/2020] [Accepted: 12/22/2020] [Indexed: 12/29/2022] Open
Abstract
Dysregulation of the long intergenic noncoding RNA 01315 (LINC01315) has recently been demonstrated in cancer. However, the role of LINC01315 in papillary thyroid cancer (PTC) has not been determined. We attempted to determine the function of LINC01315 in PTC. The levels of LINC01315 were higher in thyroid carcinoma tissues and cell lines compared with that in noncancerous tissues or normal cells, respectively. LINC01315 knockdown significantly inhibited the in vitro colony formation and invasion of PTC cells. Upregulation of LINC01315 produced opposite effects. Bioinformatic analysis and luciferase reporter assays indicated direct binding of miR-497-5p to LINC01315. Gain- and loss-of-function assays indicated that miR-497-5p acts as a suppressive miRNA in PTC. Furthermore, LINC01315 facilitated the growth and invasion of PTC cells by sponging miR-497-5p. Our results demonstrated the critical role of the LINC01315-miR-497-5p axis in the growth and invasion of PTC cells.
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Affiliation(s)
- Jian Ren
- Department of Endocrinology, Zhengzhou Central Hospital Affiliated to ZhengZhou University, Zhengzhou, China
| | - Feng-Jiao Zhang
- Department of Endocrinology, Zhengzhou Central Hospital Affiliated to ZhengZhou University, Zhengzhou, China
| | - Jing-Hong Wang
- Department of Endocrinology, Zhengzhou Central Hospital Affiliated to ZhengZhou University, Zhengzhou, China
| | - Jian-Dong Tang
- Department of Endocrinology, Zhengzhou Central Hospital Affiliated to ZhengZhou University, Zhengzhou, China
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27
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Integrated meta-analysis and machine learning approach identifies acyl-CoA thioesterase with other novel genes responsible for biofilm development in Staphylococcus aureus. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2021; 88:104702. [PMID: 33388440 DOI: 10.1016/j.meegid.2020.104702] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 12/24/2020] [Accepted: 12/29/2020] [Indexed: 02/08/2023]
Abstract
Biofilm forming Staphylococcus aureus is a major threat to the health-care industry. It is important to understand the differences between planktonic and biofilm growth forms in the pathogen since conventional treatments targeting the planktonic forms are not effective against biofilms. The current study conducts a meta-analysis of three public transcriptomic profiles to examine the differences in gene expression between the planktonic and biofilm states of S. aureus using random-effects modeling. Mean effect sizes were calculated for 2847 genes among which 726 differentially expressed genes were taken for further analysis. Major genes that are discriminatory between the two conditions were mined using supervised learning techniques and validated by high-accuracy classifiers. Ten different feature selection algorithms were applied and used to rank the most important genes in S. aureus biofilms. Finally, an optimal set of 36 genes are presented as candidate genes in biofilm formation or development while throwing light on the novel roles of an acyl-CoA thioesterase enzyme and 10 hypothetical proteins in biofilms. The relevance of the identified gene set was further validated by building five different classification models using SVM, RF, kNN, NB and DT algorithms that were compared with models built from other relevant gene sets and by reviewing the functional role of 25 previously known genes in biofilm development. The study combines meta-analysis of differential expression with supervised machine learning strategies and feature selection for the first time to identify and validate a discriminatory set of genes important in biofilms of S. aureus. The functional roles of the identified genes predicted to be important in biofilms are further scrutinized and can be considered as a signature target list to develop anti-biofilm therapeutics in S. aureus.
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28
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Liang R, Zhang J, Zhang RM, Qiu H. LINC01315 silencing inhibits the aggressive phenotypes of colorectal carcinoma by sponging miR-205-3p. Biochem Biophys Res Commun 2021; 534:1033-1039. [PMID: 33162032 DOI: 10.1016/j.bbrc.2020.10.041] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 10/17/2020] [Indexed: 12/13/2022]
Abstract
Long non-coding RNAs (lncRNAs) are important regulatory factors in the progression of cancers. In this study, we investigated the molecular mechanism of long intergenic non-coding 01315 (LINC01315) in inhibiting the aggressive characteristics of colorectal carcinoma (CRC) cells. We proved that LINC01315 was significantly upregulated in CRC. Knockdown of LINC01315 decreased CRC cell growth and invasion in vitro. Bioinformatics analysis and a luciferase reporter experiment showed direct binding between LINC01315 and miR-205-3p. Furthermore, LINC01315 positively modulated protein kinase AMP-activated catalytic subunit α 1 (PRKAA1) expression by serving as a "sponge" for miR-205-3p. Moreover, LINC01315 regulated the growth and invasive phenotypes of CRC cells by sponging miR-205-3p. Downregulation of LINC01315 remarkedly impaired the tumorigenicity of CRC cells in vivo in a transplanted tumour model. Altogether, our results demonstrated that downregulation of LINC01315 suppresses CRC progression by sponging miR-205-3p.
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Affiliation(s)
- Rong Liang
- Department of Anorectal Center, Qilu Hospital (Qingdao), Cheeloo College of Medicine, Shandong University, Qingdao, Shandong, China
| | - Jun Zhang
- Department of Gastroenterology Surgery, Jimo District People's Hospital, Qingdao, Shandong, China
| | - Ru Meng Zhang
- Department of Gastrointestinal Surgery, Qingdao Central Hospital, Qingdao, Shandong, China
| | - Hui Qiu
- Department of Anorectal Center, Qilu Hospital (Qingdao), Cheeloo College of Medicine, Shandong University, Qingdao, Shandong, China.
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29
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De Palma FDE, Del Monaco V, Pol JG, Kremer M, D’Argenio V, Stoll G, Montanaro D, Uszczyńska-Ratajczak B, Klein CC, Vlasova A, Botti G, D’Aiuto M, Baldi A, Guigó R, Kroemer G, Maiuri MC, Salvatore F. The abundance of the long intergenic non-coding RNA 01087 differentiates between luminal and triple-negative breast cancers and predicts patient outcome. Pharmacol Res 2020; 161:105249. [DOI: 10.1016/j.phrs.2020.105249] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 10/08/2020] [Accepted: 10/08/2020] [Indexed: 02/07/2023]
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30
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Zhang K, Zhang L, Mi Y, Tang Y, Ren F, Liu B, Zhang Y, Zheng P. A ceRNA network and a potential regulatory axis in gastric cancer with different degrees of immune cell infiltration. Cancer Sci 2020; 111:4041-4050. [PMID: 32860283 PMCID: PMC7648034 DOI: 10.1111/cas.14634] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 08/16/2020] [Accepted: 08/20/2020] [Indexed: 12/12/2022] Open
Abstract
Immune cell infiltration is an important indicator of whether tumor patients will benefit from immunotherapy. Gastric cancer is one of the most common tumors in the world, and new indicators of immunotherapy are urgently needed. The aim of this study was to construct ceRNA networks in gastric cancer with different degrees of immune cell infiltration. We analyzed the expression profiles of different gastric cancer with different degrees of immune cell infiltration retrieved from The Cancer Genome Atlas (TCGA) database and found differentially expressed lncRNAs, mRNAs, and miRNAs. A ceRNA regulatory network of gastric cancer with different degrees of immune cell infiltration was constructed using functional annotation, RNA‐RNA interaction prediction, correlation analysis, survival analysis, and other comprehensive bioinformatics methods. The interaction and correlation between ceRNAs were verified using experiments on tumor tissues and cell lines. Cell line experiments showed a potential RP11‐1094M14.8/miR‐1269a/CXCL9 axis that was consistent with the ceRNA theory. qRT‐PCR results showed that RP11‐1094M14.8 knockdown significantly reduced the expression of CXCL9, and RP11‐1094M14.8 overexpression had the opposite effect. The results of clinical analysis of gastric cancer samples showed that RP11‐1094M14.8 and CXCL9 were highly expressed in hot tumors, and CXCL9 was positively correlated with a better prognosis for patients. The constructed novel ceRNA network and the potential regulatory axis may provide a comprehensive understanding of the potential mechanisms of development in gastric cancer with different degrees of immune cell infiltration. The RP11‐1094M14.8/miR‐1269a/CXCL9 axis may serve as a potential immune‐therapeutic target for gastric cancer with different degrees of immune cell infiltration.
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Affiliation(s)
- Kai Zhang
- Henan Key Laboratory for Helicobacter pylori & Microbiota and GI Cancer, Marshall Medical Research Center, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Department of Gastroenterology, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Biotherapy Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Lei Zhang
- Department of Pediatric Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yang Mi
- Henan Key Laboratory for Helicobacter pylori & Microbiota and GI Cancer, Marshall Medical Research Center, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Department of Gastroenterology, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - YouCai Tang
- Henan Key Laboratory for Helicobacter pylori & Microbiota and GI Cancer, Marshall Medical Research Center, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Department of Gastroenterology, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - FeiFei Ren
- Henan Key Laboratory for Helicobacter pylori & Microbiota and GI Cancer, Marshall Medical Research Center, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Department of Gastroenterology, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Bin Liu
- Henan Key Laboratory for Helicobacter pylori & Microbiota and GI Cancer, Marshall Medical Research Center, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Department of Gastroenterology, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yi Zhang
- Biotherapy Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - PengYuan Zheng
- Henan Key Laboratory for Helicobacter pylori & Microbiota and GI Cancer, Marshall Medical Research Center, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Department of Gastroenterology, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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31
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Ala U. Competing Endogenous RNAs, Non-Coding RNAs and Diseases: An Intertwined Story. Cells 2020; 9:E1574. [PMID: 32605220 PMCID: PMC7407898 DOI: 10.3390/cells9071574] [Citation(s) in RCA: 91] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 06/18/2020] [Accepted: 06/23/2020] [Indexed: 01/17/2023] Open
Abstract
MicroRNAs (miRNAs), a class of small non-coding RNA molecules, are responsible for RNA silencing and post-transcriptional regulation of gene expression. They can mediate a fine-tuned crosstalk among coding and non-coding RNA molecules sharing miRNA response elements (MREs). In a suitable environment, both coding and non-coding RNA molecules can be targeted by the same miRNAs and can indirectly regulate each other by competing for them. These RNAs, otherwise known as competing endogenous RNAs (ceRNAs), lead to an additional post-transcriptional regulatory layer, where non-coding RNAs can find new significance. The miRNA-mediated interplay among different types of RNA molecules has been observed in many different contexts. The analyses of ceRNA networks in cancer and other pathologies, as well as in other physiological conditions, provide new opportunities for interpreting omics data for the field of personalized medicine. The development of novel computational tools, providing putative predictions of ceRNA interactions, is a rapidly growing field of interest. In this review, I discuss and present the current knowledge of the ceRNA mechanism and its implications in a broad spectrum of different pathologies, such as cardiovascular or autoimmune diseases, cancers and neurodegenerative disorders.
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Affiliation(s)
- Ugo Ala
- Department of Veterinary Sciences, University of Turin, 10124 Turin, Italy
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