1
|
Andrade R, Ribeiro IP, Carreira IM, Tralhão JG. The Diagnostic and Prognostic Potentials of Non-Coding RNA in Cholangiocarcinoma. Int J Mol Sci 2024; 25:6002. [PMID: 38892191 PMCID: PMC11172565 DOI: 10.3390/ijms25116002] [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: 04/17/2024] [Revised: 05/13/2024] [Accepted: 05/28/2024] [Indexed: 06/21/2024] Open
Abstract
Cholangiocarcinoma (CCA) is a rare biliary tract tumor with high malignancy. CCA is the second most common primary hepatobiliary cancer after hepatocarcinoma. Despite its rarity, the incidence of CCA is steadily increasing globally. Most patients with CCA are asymptomatic in the early stages, resulting in a late-stage diagnosis and poor prognosis. Finding reliable biomarkers is essential to improve CCA's early diagnosis and survival rate. Non-coding RNAs (ncRNAs) are non-protein coding RNAs produced by genomic transcription. This includes microRNAs, long non-coding RNAs, and circular RNAs. ncRNAs have multiple functions in regulating gene expression and are crucial for maintaining normal cell function and developing diseases. Many studies have shown that aberrantly expressed ncRNAs can regulate the occurrence and development of CCA. ncRNAs can be easily extracted and detected through tumor tissue and liquid biopsies, representing a potential tool for diagnosing and prognosis CCA. This review will provide a detailed update on the diagnostic and prognostic potentials of lncRNAs and cirRNAs as biomarkers in CCA.
Collapse
Affiliation(s)
- Rita Andrade
- Surgery Department, Centro Hospitalar e Universitario de Coimbra EPE (CHUC), 3000-075 Coimbra, Portugal;
- Clinical Academic Center of Coimbra, Faculty of Medicine, University of Coimbra, 3000-548 Coimbra, Portugal
| | - Ilda Patrícia Ribeiro
- Clinical Academic Center of Coimbra, Faculty of Medicine, University of Coimbra, 3000-548 Coimbra, Portugal
- Cytogenetics and Genomics Laboratory, Institute of Cellular and Molecular Biology, Faculty of Medicine, University of Coimbra, 3000-548 Coimbra, Portugal
- Coimbra Institute for Clinical and Biomedical Research (CBR) and Center of Investigation on Environment Genetics and Oncobiology (CIMAGO), Faculty of Medicine, University of Coimbra, 3000-548 Coimbra, Portugal
- Center for Innovative Biomedicine and Biotechnology (CIBB), University of Coimbra, 3000-548 Coimbra, Portugal
| | - Isabel Marques Carreira
- Clinical Academic Center of Coimbra, Faculty of Medicine, University of Coimbra, 3000-548 Coimbra, Portugal
- Cytogenetics and Genomics Laboratory, Institute of Cellular and Molecular Biology, Faculty of Medicine, University of Coimbra, 3000-548 Coimbra, Portugal
- Coimbra Institute for Clinical and Biomedical Research (CBR) and Center of Investigation on Environment Genetics and Oncobiology (CIMAGO), Faculty of Medicine, University of Coimbra, 3000-548 Coimbra, Portugal
- Center for Innovative Biomedicine and Biotechnology (CIBB), University of Coimbra, 3000-548 Coimbra, Portugal
| | - José Guilherme Tralhão
- Surgery Department, Centro Hospitalar e Universitario de Coimbra EPE (CHUC), 3000-075 Coimbra, Portugal;
- Clinical Academic Center of Coimbra, Faculty of Medicine, University of Coimbra, 3000-548 Coimbra, Portugal
- Coimbra Institute for Clinical and Biomedical Research (CBR) and Center of Investigation on Environment Genetics and Oncobiology (CIMAGO), Faculty of Medicine, University of Coimbra, 3000-548 Coimbra, Portugal
- Center for Innovative Biomedicine and Biotechnology (CIBB), University of Coimbra, 3000-548 Coimbra, Portugal
| |
Collapse
|
2
|
Mao R, Xu C, Zhang Q, Wang Z, Liu Y, Peng Y, Li M. Predictive significance of glycolysis-associated lncRNA profiles in colorectal cancer progression. BMC Med Genomics 2024; 17:112. [PMID: 38685060 PMCID: PMC11057184 DOI: 10.1186/s12920-024-01862-2] [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: 09/09/2023] [Accepted: 04/03/2024] [Indexed: 05/02/2024] Open
Abstract
BACKGROUND The Warburg effect is a hallmark characteristic of colorectal cancer (CRC). Despite extensive research, the role of long non-coding RNAs (lncRNAs) in influencing the Warburg effect remains incompletely understood. Our study aims to identify lncRNAs that may modulate the Warburg effect by functioning as competing endogenous RNAs (ceRNAs). METHODS Utilizing bioinformatics approaches, we extracted glycolysis-associated gene data from the Kyoto Encyclopedia of Genes and Genomes (KEGG) and identified 101 glycolysis-related lncRNAs in CRC. We employed Univariable Cox regression, Least Absolute Shrinkage and Selection Operator (LASSO) regression analysis, and Multivariable Cox regression to develop a prognostic model comprising four glycolysis-linked lncRNAs. We then constructed a prognostic nomogram integrating this lncRNA model with other relevant clinical parameters. RESULTS The prognostic efficacy of our four-lncRNA signature and its associated nomogram was validated in both training and validation cohorts. Functional assays demonstrated significant glycolysis and hexokinase II (HK2) inhibition following the silencing of RUNDC3A - AS1, a key lncRNA in our prognostic signature, highlighting its regulatory importance in the Warburg effect. CONCLUSIONS Our research illuminates the critical role of glycolysis-centric lncRNAs in CRC. The developed prognostic model and nomogram underscore the pivotal prognostic and regulatory significance of the lncRNA RUNDC3A - AS1 in the Warburg effect in colorectal cancer.
Collapse
Affiliation(s)
- Rui Mao
- Hunan Key Laboratory of Aging Biology, Xiangya Hospital, Central South University, Changsha, China
| | - Chenxin Xu
- Center of Gastrointestinal and Minimally Invasive Surgery, Department of General Surgery, The Second Affiliated Hospital of Chengdu, The Third People's Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University, Chongqing Medical University, NO.82 Qinglong Road, Chengdu, Sichuan, 610031, China
- Center of Obesity and Metabolism disease, Department of General surgery, The Second Affiliated Hospital of Chengdu, The Third People's Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University, Chongqing Medical University, Chengdu, 610031, China
| | - Quanzheng Zhang
- Department of Critical Care Medicine, Chengdu Third People's Hospital, Chengdu, 610031, China
| | - Zheng Wang
- Department of Colorectal Surgery, National Clinical Research Center for Cancer, Cancer Hospital, National Cancer Center, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yanjun Liu
- Center of Gastrointestinal and Minimally Invasive Surgery, Department of General Surgery, The Second Affiliated Hospital of Chengdu, The Third People's Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University, Chongqing Medical University, NO.82 Qinglong Road, Chengdu, Sichuan, 610031, China.
- Center of Obesity and Metabolism disease, Department of General surgery, The Second Affiliated Hospital of Chengdu, The Third People's Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University, Chongqing Medical University, Chengdu, 610031, China.
| | - Yurui Peng
- Center of Gastrointestinal and Minimally Invasive Surgery, Department of General Surgery, The Second Affiliated Hospital of Chengdu, The Third People's Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University, Chongqing Medical University, NO.82 Qinglong Road, Chengdu, Sichuan, 610031, China.
- Center of Obesity and Metabolism disease, Department of General surgery, The Second Affiliated Hospital of Chengdu, The Third People's Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University, Chongqing Medical University, Chengdu, 610031, China.
| | - Ming Li
- Department of hepatobiliary surgery, The Second Affiliated Hospital of Chengdu, The Third People's Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University, Chongqing Medical University, NO.82 Qinglong Road, Chengdu, Sichuan, 610031, China.
| |
Collapse
|
3
|
Wan P, Huang J, Liu W, Su X, Zhao B, Wang X, Zhao L. lncRNA GHET1 regulates extravillous trophoblastic phenotype via EZH2/LSD1-mediated MT2A epigenetic suppression in pre-eclampsia. Mol Reprod Dev 2023; 90:758-770. [PMID: 37548351 DOI: 10.1002/mrd.23693] [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: 03/09/2023] [Revised: 05/17/2023] [Accepted: 06/06/2023] [Indexed: 08/08/2023]
Abstract
Pre-eclampsia (PE) is usually defined as new-onset hypertension with albuminuria or other organ damage. Herein, the role and mechanism of long noncoding RNA (lncRNA) gastric carcinoma high expressed transcript 1 (GHET1) during PE are investigated. Expression of GHET1 in PE pregnancies was evaluated using quantitative real-time polymerase chain reaction (qRT-PCR). Proliferation and cell cycle of extravillous trophoblasts were assessed by Cell Counting Kit-8 (CCK-8), colony formation, 5-Ethynyl-2'-deoxyuridine (EdU) assays, and flow cytometry, respectively. Migration, invasion, and network formation of trophoblasts were measured by wound healing, transwell system, and tube formation assays. RNA immunoprecipitation (RIP), RNA pull-down, and chromatin immunoprecipitation (ChIP) assays were used to confirm the molecular interaction. GHET1 was markedly decreased in the placenta of PE patients. GHET1 promoted the proliferation and cell cycle of extravillous trophoblasts, as well as migration, invasion, and network formation in vitro. Metallothionein 2A (MT2A) functioned as a downstream effector of GHET1, which was negatively correlated with GHET1 in PE. GHET1 directly bound with zeste 2 polycomb repressive complex 2/lysine-specific demethylase 1 (EZH2/LSD1). Knockdown of GHET1 reduced the occupancies of H3K27me3 and H3K4me2 in the MT2A promoter region by recruiting EZH2 and LSD1. MT2A knockdown reversed GHET1 inhibition mediated biological functions. GHET1 regulates extravillous trophoblastic phenotype via EZH2/LSD1-mediated MT2A epigenetic suppression in PE.
Collapse
Affiliation(s)
- Pengyun Wan
- Department of Obstetrics and Gynecology, Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province, People's Republic of China
| | - Jia Huang
- Reproductive Health Department, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang, Jiangxi Province, People's Republic of China
| | - Wenting Liu
- Department of Obstetrics and Gynecology, Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province, People's Republic of China
| | - Xiaoyan Su
- Pathology Department, Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province, People's Republic of China
| | - Bei Zhao
- Traditional Chinese Medicine Department, Duchang County People's Hospital, Jiujiang, Jiangxi Province, People's Republic of China
| | - Xianggang Wang
- Medical Examination Department, Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province, People's Republic of China
| | - Lu Zhao
- Department of Obstetrics and Gynecology, Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province, People's Republic of China
| |
Collapse
|
4
|
Gao X, Zhang W, Jia Y, Xu H, Zhu Y, Pei X. Identification of a prognosis-related ceRNA network in cholangiocarcinoma and potentially therapeutic molecules using a bioinformatic approach and molecular docking. Sci Rep 2022; 12:16247. [PMID: 36171401 PMCID: PMC9519560 DOI: 10.1038/s41598-022-20362-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Accepted: 09/12/2022] [Indexed: 11/20/2022] Open
Abstract
Cholangiocarcinoma (CCA) is a highly malignant disease with a poor prognosis, and mechanisms of initiation and development are not well characterized. It is long noncoding RNAs (lncRNAs) acting as miRNA decoys to regulate cancer-related RNAs in competing endogenous RNA (ceRNA) networks that suggest a possible molecular mechanism in CCA. The current study aims to find potential prognosis biomarkers and small molecule therapeutic targets based on the construction of a CCA prognosis-related ceRNA network. A transcriptome dataset for CCA was downloaded from the TCGA database. Differentially expressed lncRNAs (DElncRNAs), DEmiRNAs and DEmRNAs were identified based on the differential expression and a DEceRNA network was constructed using predicted miRNA-lncRNA and miRNA-mRNA interactions. Heat maps, PCA analysis, and Pathway enrichment analysis and GO enrichment analysis were conducted. The prognostic risk model and molecular docking were constructed based on identified key ceRNA networks. A DElncRNA-miRNA-mRNAs network consisting of 434 lncRNA-miRNA pairs and 284 miRNA-mRNA pairs with 200 lncRNAs, 21 miRNAs, and 245 mRNAs was constructed. There were three lncRNAs (AC090772.1, LINC00519, and THAP7-AS1) and their downstream mRNAs (MECOM, MBNL3, RCN2) screened out as prognostic factors in CAA. Three key networks (LINC00519/ hsa-mir-22/ MECOM, THAP7-AS1/hsa-mir-155/MBNL3, and THAP7-AS1/hsa-mir-155/RCN2) were identified based on binding sites prediction and survival analysis. A prognostic risk model was established with a good predictive ability (AUC = 0.66–0.83). Four anticancer small molecules, MECOM and 17-alpha-estradiol (−7.1 kcal/mol), RCN2 and emodin (−8.3 kcal/mol), RCN2 and alpha-tocopherol (−5.6 kcal/mol), and MBNL3 and 17-beta-estradiol (−7.1 kcal/mol) were identified. Based on the DEceRNA network and Kaplan–Meier survival analysis, we identified three important ceRNA networks associated with the poor prognosis of CCA. Four anti-cancer small molecules were screened out by computer-assisted drug screening as potential small molecules for the treatment of CCA. This study provides theoretical support for the development of ceRNA network-based drugs to improve the prognosis of CCA.
Collapse
Affiliation(s)
- Xiaoling Gao
- The Medical Laboratory Center, Hainan General Hospital, Haikou, 570311, China.
| | - Wenhao Zhang
- The First School of Clinical Medicine, Lanzhou University, Lanzhou, 730000, China
| | - Yanjuan Jia
- NHC Key Laboratory of Diagnosis and Therapy of Gastrointestinal Tumor, Gansu Provincial Hospital, Lanzhou, 730000, China.,The Institute of Clinical Research and Translational Medicine, Gansu Provincial Hospital, Lanzhou, 730000, China.,Gansu University of Chinese Medicine, Lanzhou, 730000, China
| | - Hui Xu
- NHC Key Laboratory of Diagnosis and Therapy of Gastrointestinal Tumor, Gansu Provincial Hospital, Lanzhou, 730000, China.,The Institute of Clinical Research and Translational Medicine, Gansu Provincial Hospital, Lanzhou, 730000, China
| | - Yuchen Zhu
- The Second Clinical Medical College, Lanzhou University, Lanzhou, 730000, China
| | - Xiong Pei
- The Second Clinical Medical College, Lanzhou University, Lanzhou, 730000, China
| |
Collapse
|
5
|
lncRNA TM4SF1-AS1 predicts dismal outcomes and promotes cholangiocarcinoma progression via modulating miR-744-3p. Clin Res Hepatol Gastroenterol 2022; 46:101915. [PMID: 35346892 DOI: 10.1016/j.clinre.2022.101915] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 03/02/2022] [Accepted: 03/21/2022] [Indexed: 02/04/2023]
Abstract
BACKGROUND Cholangiocarcinoma (CCA) is of great malignancy and high mortality. Identification of effective biomarkers could improve the monitoring of CCA development and attenuate patients' outcomes. OBJECTIVE The potential of lncRNA TM4SF1-AS1 (TM4SF1-AS1) serving biomarker of CCA was estimated and the underlying mechanism was also investigated. METHODS A total of 107 pairs of tumor and paracancer tissues were collected from CCA patients. The expression levels of TM4SF1-AS1 and miR-744-3p were analyzed in CCA by PCR, and their clinical significance was estimated by a series of statistical analyses. CCK8 and Transwell assays were used to assess the development-related cellular processes of CCA. The interaction between TM4SF1-AS1 and miR-774-3p was evaluated by cell transfection and dual-luciferase reporter assay. RESULTS The elevated expression of TM4SF1-AS1 and the declined expression of miR-744-3p were observed in CCA. Both TM4SF1-AS1 and miR-744-3p were found to possess a close association with the malignant progression and poor prognosis of CCA patients. TM4SF1-AS1 was suggested to act as a tumor promoter of CCA, where miR-744-3p was found to mediate the function of TM4SF1-AS1. CONCLUSION Both TM4SF1-AS1 and miR-744-3p were identified as prognostic biomarkers of CCA. TM4SF1-AS1 served as tumor promoter of CCA via modulating miR-744-3p.
Collapse
|
6
|
Shi Q, Ma Y, Zhang X, Yin C. Circ_0060551 promotes the migration and invasion of cervical cancer by Up-regulating TPD52. Am J Reprod Immunol 2022; 88:e13586. [PMID: 35716110 DOI: 10.1111/aji.13586] [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: 11/30/2021] [Revised: 04/28/2022] [Accepted: 06/13/2022] [Indexed: 11/29/2022] Open
Abstract
PROBLEM Cervical cancer has been recognized as the second most common cancer in women worldwide. Previous studies have reported that some circular RNAs (circRNAs) can influence the progression of cervical cancer. However, more researches are still required to unveil the underlying mechanism of how circRNAs regulate the progression of such cancer. We aimed at unveiling the mechanism of how circ_0060551 effected the progression of cervical cancer. METHOD OF STUDY RT-qPCR and western blot assays were used to detect the expression and protein levels. Mechanism experiments were conducted to investigate the relationship among circ_0060551, TPD52, miR-520a-5p and ELAVL1. Rescue assays were mainly carried out to verify how circ_0060551 influenced the migration and invasion of cervical cancer cells. RESULTS According to the results, circ_0060551 was up-regulated in cervical cancer cells and could promote the migration and invasion of cells via TPD52. In addition, circ_0060551 could up-regulate TPD52 expression through a ceRNA model to target miR-520a-5p. Moreover, circ_0060551 could stabilize the mRNA expression of TPD52 via recruiting ELAVL1. CONCLUSION Our study proved that circ_0060551 could promote the migration and invasion of cervical cancer cells. This article is protected by copyright. All rights reserved.
Collapse
Affiliation(s)
- Qi Shi
- Changchun Obstetrics- Gynecology Hospital, No. 555 West Fifth Road, Nanguan District, Changchun, Jilin, 130042, China
| | - Yuanyuan Ma
- Department of Obstetrics and Gynecology, the Third Affiliated Hospital of Heilongjiang University of Chinese Medicine, No. 2 Xiangjiang Road, Xiangfang District, Harbin, Heilongjiang, 150090, China
| | - Xiaojie Zhang
- Changchun Obstetrics- Gynecology Hospital, No. 555 West Fifth Road, Nanguan District, Changchun, Jilin, 130042, China
| | - Chunxia Yin
- Changchun Obstetrics- Gynecology Hospital, No. 555 West Fifth Road, Nanguan District, Changchun, Jilin, 130042, China
| |
Collapse
|
7
|
Wang S, Sun Y, Hu S, Lou C, Pan YB. Construction of a lncRNA-associated competing endogenous RNA regulatory network after traumatic brain injury in mouse. Mol Brain 2022; 15:40. [PMID: 35501920 PMCID: PMC9063179 DOI: 10.1186/s13041-022-00925-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 04/19/2022] [Indexed: 12/19/2022] Open
Abstract
Traumatic brain injury (TBI) is a major public health problem worldwide which causes high mortality and disability. Functioning as microRNA (miRNA) sponges, long non-coding RNA (lncRNA) regulates the expression of protein-coding genes in a competing endogenous RNA (ceRNA) network. However, the lncRNA-associated ceRNA in TBI remains unclear. In this study, we processed the raw SRR files of mice cortex samples of sham injury (n = 3) and TBI groups (n = 3) to count files. Then, the expression profiles of lncRNAs and mRNAs were identified, and 86 differentially expressed (DE) lncRNAs and 1201 DEmRNAs between sham and TBI groups were identified. The DEmRNAs were used to perform enrichment analyses. Next, a lncRNA-miRNA-mRNA regulatory ceRNA network was constructed. The network consisted of 23 mRNAs, 5 miRNAs and 2 lncRNAs. The expression alternations of the 5 miRNAs were validated via qRT-PCR. The subnetwork of hub lncRNA Neat1 was extracted. We identified a potential inflammatory associated regulatory axis: Neat1/miR-31-5p/Myd88 axis. The PPI network based on DEmRNA involved in ceRNA network was constructed PPI networks to identify the hub genes. Finally, DElncRNAs and DEmRNAs were selected randomly and validated by qRT-PCR. In conclusion, with the lncRNA-miRNA-mRNA ceRNA network provided above, we can improve our understanding of the regulatory mechanisms and interaction among lncRNAs, miRNAs and mRNAs in TBI process.
Collapse
|
8
|
Wu Y, Hayat K, Hu Y, Yang J. Long Non-Coding RNAs as Molecular Biomarkers in Cholangiocarcinoma. Front Cell Dev Biol 2022; 10:890605. [PMID: 35573683 PMCID: PMC9093656 DOI: 10.3389/fcell.2022.890605] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Accepted: 04/10/2022] [Indexed: 11/13/2022] Open
Abstract
Cholangiocarcinoma (CCA) is a biliary system cancer that has the characteristics of strong invasiveness, poor prognosis, and few therapy choices. Furthermore, the absence of precise biomarkers for early identification and prognosis makes it hard to intervene in the early phase of initial diagnosis or recurring cholangiocarcinoma following surgery. Encouragingly, previous studies found that long non-coding RNA (lncRNA), a subgroup of RNA that is more than 200 nucleotides long, can affect cell proliferation, migration, apoptosis, and even drug resistance by altering numerous signaling pathways, thus reaching pro-cancer or anti-cancer outcomes. This review will take a retrospective view of the recent investigations on the work of lncRNAs in cholangiocarcinoma progression and the potential of lncRNAs serving as promising clinical biomarkers and therapeutic targets for CCA.
Collapse
Affiliation(s)
- Yanhua Wu
- Department of Gastroenterology, The Fourth School of Clinical Medicine, Zhejiang Chinese Medical University, Hangzhou, China
| | - Khizar Hayat
- Department of Gastroenterology, International Education College of Zhejiang Chinese Medical University, Hangzhou, China
| | - Yufei Hu
- Department of Gastroenterology, The Fourth School of Clinical Medicine, Zhejiang Chinese Medical University, Hangzhou, China
| | - Jianfeng Yang
- Department of Gastroenterology, Affiliated Hangzhou First People’s Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Integrated Traditional Chinese and Western Medicine for Biliary and Pancreatic Diseases of Zhejiang Province, Hangzhou, China
- *Correspondence: Jianfeng Yang,
| |
Collapse
|
9
|
Identification of Novel Prognostic Signatures for Clear Cell Renal Cell Carcinoma Based on ceRNA Network Construction and Immune Infiltration Analysis. DISEASE MARKERS 2022; 2022:4033583. [PMID: 35320950 PMCID: PMC8938059 DOI: 10.1155/2022/4033583] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 02/20/2022] [Accepted: 03/02/2022] [Indexed: 12/11/2022]
Abstract
Objective. Clear cell renal cell carcinoma (ccRCC) carries significant morbidity and mortality globally and is often resistant to conventional radiotherapy and chemotherapy. Immune checkpoint blockade (ICB) has received attention in ccRCC patients as a promising anticancer treatment. Furthermore, competitive endogenous RNA (ceRNA) networks are crucial for the occurrence and progression of various tumors. This study was aimed at identifying reliable prognostic signatures and exploring potential mechanisms between ceRNA regulation and immune cell infiltration in ccRCC patients. Methods and Results. Gene expression profiling and clinical information of ccRCC samples were obtained from The Cancer Genome Atlas (TCGA) database. Through comprehensive bioinformatic analyses, differentially expressed mRNAs (DEmRNAs;
), lncRNAs (DElncRNAs;
), and miRNAs (DEmiRNAs;
) were identified to establish ceRNA networks. The CIBERSORT algorithm was applied to calculate the proportion of 22 types of tumor-infiltrating immune cells (TIICs) in ccRCC tissues. Subsequently, univariate Cox, Lasso, and multivariate Cox regression analyses were employed to construct ceRNA-related and TIIC-related prognostic signatures. In addition, we explored the relationship between the crucial genes and TIICs via coexpression analysis, which revealed that the interactions between MALAT1, miR-1271-5p, KIAA1324, and follicular helper T cells might be closely correlated with the progression of ccRCC. Ultimately, we preliminarily validated that the potential MALAT1/miR-1271-5p/KIAA1324 axis was consistent with the ceRNA theory by qRT-PCR in the ccRCC cell lines. Conclusion. On the basis of the ceRNA networks and TIICs, we constructed two prognostic signatures with excellent predictive value and explored possible molecular regulatory mechanisms, which might contribute to the improvement of prognosis and individualized treatment for ccRCC patients.
Collapse
|
10
|
The mmu_circRNA_37492/hsa_circ_0012138 function as potential ceRNA to attenuate obstructive renal fibrosis. Cell Death Dis 2022; 13:207. [PMID: 35246505 PMCID: PMC8897503 DOI: 10.1038/s41419-022-04612-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 01/21/2022] [Accepted: 02/04/2022] [Indexed: 12/11/2022]
Abstract
Circular RNAs (circRNAs) are involved in the pathogenesis of certain renal diseases, however, the function and mechanism of them in renal fibrosis remains largely unknown. In the present study, RNA expression data in unilateral ureteral obstruction (UUO) kidneys was obtained from our previous circRNA Microarray and public Gene Expression Omnibus datasets to construct a ceRNA network. The effects of target circRNA as long as the homologous human circRNA on renal fibrosis was examined in vitro and in vivo. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis was further performed among genes regulated by the human circRNA. We found that circRNA_37492, showing well connection degree in the ceRNA network, was abundant expression and high sequence conservation. We observed that the expression of circRNA_37492 was induced by the TGF-β1 or UUO in BUMPT cells and C57BL/6 mice, respectively. In vitro, cytoplasmic circRNA_37492 inhibited type I, III collagen and fibronectin deposition by sponging miR-7682-3p and then upregulated its downstream target Fgb. In vivo, overexpression of circRNA_37492 attenuated fibrotic lesions in the kidneys of UUO mice via targeting miR-7682-3p/Fgb axis. Furthermore, hsa_circ_0012138, homologous with circRNA_37492, may potentially target miR-651-5p/FGB axis in human renal fibrosis. Not only that, GO and KEGG enrichment revealed that hsa_circ_0012138-regulated genes were previously demonstrated to related to the fibrosis. In conclusion, we for the first time demonstrated that circRNA_37492 attenuated renal fibrosis via targeting miR-7682-3p/Fgb axis, and the homologous hsa_circRNA_0012138 was speculated as a possible ceRNA to regulate multiple gene expressions and involve in human renal fibrosis, suggesting that circRNA_37492/hsa_circ_0012138 may serve as potent therapy target for obstructive renal fibrosis disease.
Collapse
|
11
|
Liu Y, Sun J, Qi P, Liu Y. Long non-coding RNA titin-antisense RNA1 contributes to growth and metastasis of cholangiocarcinoma by suppressing microRNA-513a-5p to upregulate stratifin. Bioengineered 2021; 12:12611-12624. [PMID: 34903127 PMCID: PMC8810091 DOI: 10.1080/21655979.2021.2011014] [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] [Indexed: 12/20/2022] Open
Abstract
Cholangiocarcinoma (CCA) is one of the most common histological types of primary hepatic malignancy and is associated with poor overall prognosis, causing a ponderous burden on human life. Hence, it is necessary to elucidate the pathogenesis of CCA. The objective of our research was to shed light on the mechanism through which long non-coding RNA titin-antisense RNA1 (lncRNA TTN-AS1) is involved in the development of CCA. Reverse transcription quantitative polymerase chain reaction was used to detect TTN-AS1 expression in CCA samples and cells. Functional experiments were performed using the Cell Counting Kit-8, 5-ethynyl-2'-deoxyuridine, transwell, and in vivo tumor growth assays. The relationship between TTN-AS1, miR-513a-5p, and stratifin (SFN) was explored using a dual luciferase reporter assay, RNA immunoprecipitation (RIP) experiment, and Pearson correlation analysis. The result showed that TTN-AS1 and SFN are highly expressed in CCA tissues. Bioinformatics analysis, luciferase reporter and RIP experiments revealed the correlation between TTN-AS1, miR-513a-5p, and SFN. In addition, silencing TTN-AS1 mitigated CCA cell proliferation and migration. Mechanistically, miR-513a-5p is sponged by TTN-AS1. The miR-513a-5p inhibitor abolished the effect of TTN-AS1 silencing on the aggressive behaviors of CCA cells. Furthermore, we showed that miR-513a-5p is a regulator of CCA by targeting SFN. TTN-AS1 induced CCA cell growth and metastasis via the miR-513a-5p/SFN pathway, which offers a new strategy for therapeutic interventions for CCA.
Collapse
Affiliation(s)
- Yang Liu
- Department of Hepatobiliary Surgery, Huanggang Center Hospital, Huanggang, Hubei, China
| | - Jiangyang Sun
- Department of Hepatobiliary Surgery, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Peng Qi
- Department of General Surgery, Hubei No. 3 People's Hospital of Jianghan University, Wuhan, Hubei, China
| | - Yang Liu
- Department of General Surgery, Hubei No. 3 People's Hospital of Jianghan University, Wuhan, Hubei, China
| |
Collapse
|
12
|
Liu C, Liu L, Gao J, Wang J, Liu Y. Identification of Two Long Non-Coding RNAs AC010082.1 and AC011443.1 as Biomarkers of Coronary Heart Disease Based on Logistic Stepwise Regression Prediction Model. Front Genet 2021; 12:780431. [PMID: 34868268 PMCID: PMC8637336 DOI: 10.3389/fgene.2021.780431] [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: 09/21/2021] [Accepted: 11/01/2021] [Indexed: 12/23/2022] Open
Abstract
Coronary heart disease (CHD) is a global health concern with high morbidity and mortality rates. This study aimed to identify the possible long non-coding RNA (lncRNA) biomarkers of CHD. The lncRNA- and mRNA-related data of patients with CHD were downloaded from the Gene Expression Omnibus database (GSE113079). The limma package was used to identify differentially expressed lncRNAs and mRNAs (DElncRNAs and DEmRNAs, respectively). Then, miRcode, TargetScan, miRDB, and miRTarBase databases were used to form the competing endogenous RNA (ceRNA) network. Furthermore, SPSS Modeler 18.0 was used to construct a logistic stepwise regression prediction model for CHD diagnosis based on DElncRNAs. Of the microarray data, 70% was used as a training set and 30% as a test set. Moreover, a validation cohort including 30 patients with CHD and 30 healthy controls was used to verify the hub lncRNA expression through real-time reverse transcription-quantitative PCR (RT-qPCR). A total of 185 DElncRNAs (114 upregulated and 71 downregulated) and 382 DEmRNAs (162 upregulated and 220 downregulated) between CHD and healthy controls were identified from the microarray data. Furthermore, through bioinformatics prediction, a 38 lncRNA-21miRNA-40 mRNA ceRNA network was constructed. Next, by constructing a logistic stepwise regression prediction model for 38 DElncRNAs, we screened two hub lncRNAs AC010082.1 and AC011443.1 (p < 0.05). The sensitivity, specificity, and area under the curve were 98.41%, 100%, and 0.995, respectively, for the training set and 93.33%, 91.67%, and 0.983, respectively, for the test set. We further verified the significant upregulation of AC010082.1 (p < 0.01) and AC011443.1 (p < 0.05) in patients with CHD using RT-qPCR in the validation cohort. Our results suggest that lncRNA AC010082.1 and AC011443.1 are potential biomarkers of CHD. Their pathological mechanism in CHD requires further validation.
Collapse
Affiliation(s)
- Chao Liu
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China.,Graduate School, Beijing University of Chinese Medicine, Beijing, China
| | - Lanchun Liu
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China.,Graduate School, Beijing University of Chinese Medicine, Beijing, China
| | - Jialiang Gao
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Jie Wang
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China.,Key Technology Laboratory of Cardiovascular Disease-Syndrome Combination, Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yongmei Liu
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China.,Key Technology Laboratory of Cardiovascular Disease-Syndrome Combination, Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| |
Collapse
|
13
|
Liu Z, Weng S, Xu H, Wang L, Liu L, Zhang Y, Guo C, Dang Q, Xing Z, Lu T, Han X. Computational Recognition and Clinical Verification of TGF-β-Derived miRNA Signature With Potential Implications in Prognosis and Immunotherapy of Intrahepatic Cholangiocarcinoma. Front Oncol 2021; 11:757919. [PMID: 34760703 PMCID: PMC8573406 DOI: 10.3389/fonc.2021.757919] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 10/11/2021] [Indexed: 12/20/2022] Open
Abstract
MicroRNAs (miRNAs) were recently implicated in modifying the transforming growth factor β (TGF-β) signaling in multiple cancers. However, TGF-β-derived miRNAs and their potential clinical significance remain largely unexplored in intrahepatic cholangiocarcinoma (ICC). In this study, we proposed an integrated framework that enables the identification of TGF-β-derived miRNAs in ICC (termed “TGFmitor”). A total of 36 TGF-β-derived miRNAs were identified, of which nine significantly correlated with overall survival (OS) and aberrantly expressed in ICC. According to these miRNAs, we discovered and validated a TGF-β associated miRNA signature (TAMIS) in GSE53870 (n =63) and TCGA-CHOL (n =32). To further confirm the clinical interpretation of TAMIS, another validation based on qRT-PCR results from 181 ICC tissues was performed. TAMIS was proven to be an independent risk indicator for both OS and relapse-free survival (RFS). TAMIS also displayed robust performance in three cohorts, with satisfactory AUCs and C-index. Besides, patients with low TAMIS were characterized by superior levels of CD8+ T cells infiltration and PD-L1 expression, while patients with high TAMIS possessed enhanced CMTM6 expression. Kaplan-Meier analysis suggested CMTM6 could further stratify TAMIS. The TAMIShighCMTM6high subtype had the worst prognosis and lowest levels of CD8A and PD-L1 expression relative to the other subtypes, indicating this subtype might behave as “super-cold” tumors. Notably, the improved discrimination was observed when CMTM6 was combined with TAMIS. Overall, our signature could serve as a powerful tool to help improve prognostic management and immunotherapies of ICC patients.
Collapse
Affiliation(s)
- Zaoqu Liu
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Interventional Institute of Zhengzhou University, Zhengzhou, China.,Interventional Treatment and Clinical Research Center of Henan Province, Zhengzhou, China
| | - Siyuan Weng
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Interventional Institute of Zhengzhou University, Zhengzhou, China.,Interventional Treatment and Clinical Research Center of Henan Province, Zhengzhou, China
| | - Hui Xu
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Interventional Institute of Zhengzhou University, Zhengzhou, China.,Interventional Treatment and Clinical Research Center of Henan Province, Zhengzhou, China
| | - Libo Wang
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Long Liu
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yuyuan Zhang
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - ChunGuang Guo
- Department of Endovascular Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Qin Dang
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Zhe Xing
- Department of Neurosurgery, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Taoyuan Lu
- Department of Cerebrovascular Disease, Zhengzhou University People's Hospital, Zhengzhou, China
| | - Xinwei Han
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Interventional Institute of Zhengzhou University, Zhengzhou, China.,Interventional Treatment and Clinical Research Center of Henan Province, Zhengzhou, China
| |
Collapse
|
14
|
Protein profiling reveals potential isomiR-associated cross-talks among RNAs in cholangiocarcinoma. Comput Struct Biotechnol J 2021; 19:5722-5734. [PMID: 34745457 PMCID: PMC8551523 DOI: 10.1016/j.csbj.2021.10.014] [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: 07/03/2021] [Revised: 09/29/2021] [Accepted: 10/10/2021] [Indexed: 12/04/2022] Open
Abstract
Protein profiling identified crucial genes that were used to screen related ncRNAs. Both miRNAs and isomiRs were involved in coding-non-coding RNA regulatory network. IsomiR-associated ceRNA networks implied the complex interactions among RNAs.
Cholangiocarcinomas (CCAs) are tumors that arise from the cholangiocytes. Although some genes have been shown with important roles in pathological process, interactions or cross-talks among different RNAs are important to understand the detailed molecular mechanisms in cancer development, especially discussing cross-talks among isomiRs and other RNAs. Herein, to characterize crucial genes in CCA, the protein expression profile was performed to survey potential crucial mRNAs and related non-coding RNAs (ncRNAs) in mRNA-ncRNA network, mainly including miRNAs/isomiRs and lncRNAs. Deregulated mRNAs were firstly obtained if consistent expression patterns were found at protein and mRNA levels, and related miRNAs/isomiRs were screened according to regulatory relationships. Diverse isomiRs from a given miRNA locus also contributed to interactions between the small RNAs and target mRNAs, and miRNAs were further used to survey related lncRNAs to expand the interactions. Thus, several groups of RNAs were constructed as candidate competitive endogenous RNA (ceRNA) networks. Finally, we found that RAB11FIP1:miR-101-3p:MIR3142HG may be a potential ceRNA network, and the interactions among them may be more complex due to variety of isomiRs. Simultaneously, RAB11FIP1 and miR-194-5p were also detected other related lncRNAs (FBXL19-AS1, SNHG1 and PVT1) that may be crucial in coding-non-coding RNA regulatory network. Our results show that diverse isomiRs with sequence and expression heterogeneities contribute to ceRNA regulatory network that may have crucial roles in CCA, which will expand our understanding of interactions among diverse RNAs and their contributions in cancer development.
Collapse
Key Words
- BLCA, bladder urothelial carcinoma
- BRCA, breast invasive carcinoma
- CHOL, cholangiocarcinoma
- COAD, colon adenocarcinoma
- Cholangiocarcinoma (CCA)
- Cross-talk
- ESCA, esophageal carcinoma
- HNSC, head and neck squamous cell carcinoma
- KICH, kidney chromophobe
- KIRC, Kidney renal clear cell carcinoma
- KIRP, kidney renal papillary cell carcinoma
- LIHC, liver hepatocellular carcinoma
- LUAD, lung adenocarcinoma
- LUSC, lung squamous cell carcinoma
- Long non-coding RNA (lncRNA)
- PRAD, prostate adenocarcinoma
- Protein profiling
- STAD, stomach adenocarcinoma
- THCA, thyroid carcinoma
- UCEC, uterine corpus endometrial carcinoma
- isomiR
- microRNA (miRNA)
Collapse
|
15
|
Song Y, Nie L, Zhang YT. LncRNAs specifically overexpressed in endocervical adenocarcinoma are associated with an unfavorable recurrence prognosis and the immune response. PeerJ 2021; 9:e12116. [PMID: 34616607 PMCID: PMC8462375 DOI: 10.7717/peerj.12116] [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: 02/26/2021] [Accepted: 08/15/2021] [Indexed: 12/20/2022] Open
Abstract
Background Cervical cancer is the fourth most common gynecological tumor in terms of both the incidence and mortality of females worldwide. Cervical squamous cell carcinoma (CSCC) accounts for 70–80% of cervical cancers, and endocervical adenocarcinoma (EAC) accounts for 20–25%. Unlike CSCC, EAC has worse clinical outcomes and prognosis. In this study, we explored the relationship between various types of long noncoding RNAs (lncRNAs) and pathological types of cervical cancer. Methods RNA sequencing (RNA-Seq) and clinical data from The Cancer Genome Atlas (TCGA) were used in this study. A single-sample gene set enrichment analysis (ssGSEA) and the ESTIMATE package were used to assess lncRNA activity and immune responses, respectively. RT-qPCR was performed to verify our findings. Results We explored the relationship between various types of lncRNAs and pathological types of cervical cancer. A series of long intergenic noncoding RNAs (lincRNAs) and antisense RNAs, which are the major types of lncRNAs, were identified to be specifically expressed in EAC and associated with a poor recurrence prognosis in patients with cervical cancer, suggesting that they might serve as independent prognostic markers of recurrence in patients with cervical cancer. RT-qPCR was performed to verify the 10 EAC-specific lncRNAs in cervical cancer samples we collected. Furthermore, the overexpression of these lncRNAs was positively correlated with EAC pathology levels but negatively correlated with immune responses in the microenvironment of cervical cancer. Conclusions These lncRNAs potentially represent new biomarkers for the prediction of the recurrence prognosis and help obtain deeper insights into potential immunotherapeutic approaches for treating cervical cancer.
Collapse
Affiliation(s)
- Yong Song
- Department of Public Health, Maternal and Child Health Hospital of Hubei Province, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.,School of Health Sciences, Wuhan University, Wuhan, Hubei, China
| | - Long Nie
- Department of Oncology, Suizhou Hospital, Hubei University of Medicine, Suizhou, Hubei, China
| | - Yu-Ting Zhang
- School of Nursing, Health Science Center, Shenzhen University, Shenzhen, Guangdong, China
| |
Collapse
|
16
|
Yu H, Wang X, Cao H. Construction and investigation of a circRNA-associated ceRNA regulatory network in Tetralogy of Fallot. BMC Cardiovasc Disord 2021; 21:437. [PMID: 34521346 PMCID: PMC8442392 DOI: 10.1186/s12872-021-02217-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 08/20/2021] [Indexed: 12/14/2022] Open
Abstract
Background As the most frequent type of cyanotic congenital heart disease (CHD), tetralogy of Fallot (TOF) has a relatively poor prognosis without corrective surgery. Circular RNAs (circRNAs) represent a novel class of endogenous noncoding RNAs that regulate target gene expression posttranscriptionally in heart development. Here, we investigated the potential role of the ceRNA network in the pathogenesis of TOF. Methods To identify circRNA expression profiles in TOF, microarrays were used to screen the differentially expressed circRNAs between 3 TOF and 3 control human myocardial tissue samples. Then, a dysregulated circRNA-associated ceRNA network was constructed using the established multistep screening strategy. Results In summary, a total of 276 differentially expressed circRNAs were identified, including 214 upregulated and 62 downregulated circRNAs in TOF samples. By constructing the circRNA-associated ceRNA network based on bioinformatics data, a total of 19 circRNAs, 9 miRNAs, and 34 mRNAs were further screened. Moreover, by enlarging the sample size, the qPCR results validated the positive correlations between hsa_circ_0007798 and HIF1A. Conclusions The findings in this study provide a comprehensive understanding of the ceRNA network involved in TOF biology, such as the hsa_circ_0007798/miR-199b-5p/HIF1A signalling axis, and may offer candidate diagnostic biomarkers or potential therapeutic targets for TOF. In addition, we propose that the ceRNA network regulates TOF progression. Supplementary Information The online version contains supplementary material available at 10.1186/s12872-021-02217-w.
Collapse
Affiliation(s)
- Haifei Yu
- Department of Cardiac Surgery, Fujian Maternity and Child Health Hospital Affiliated to Fujian Medical University, Fuzhou, Fujian, People's Republic of China.,Key Laboratory of Technical Evaluation of Fertility Regulation for Non-human Primates, National Health and Family Planning Commission, Fuzhou, Fujian, People's Republic of China
| | - Xinrui Wang
- Key Laboratory of Technical Evaluation of Fertility Regulation for Non-human Primates, National Health and Family Planning Commission, Fuzhou, Fujian, People's Republic of China. .,Medical Research Centre, Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, People's Republic of China.
| | - Hua Cao
- Department of Cardiac Surgery, Fujian Maternity and Child Health Hospital Affiliated to Fujian Medical University, Fuzhou, Fujian, People's Republic of China. .,Key Laboratory of Technical Evaluation of Fertility Regulation for Non-human Primates, National Health and Family Planning Commission, Fuzhou, Fujian, People's Republic of China. .,Medical Research Centre, Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, People's Republic of China.
| |
Collapse
|
17
|
Abedalthagafi M. Editorial: Genomics and Epigenomics of Cancer Immunotherapy: Challenges and Clinical Implications. Front Oncol 2021; 11:704397. [PMID: 34367989 PMCID: PMC8339285 DOI: 10.3389/fonc.2021.704397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Accepted: 05/26/2021] [Indexed: 11/13/2022] Open
Affiliation(s)
- Malak Abedalthagafi
- King Fahd Medical City, Saudi Genome Project, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| |
Collapse
|
18
|
Wang X, Dong Y, Zheng Y, Chen Y. Multiomics metabolic and epigenetics regulatory network in cancer: A systems biology perspective. J Genet Genomics 2021; 48:520-530. [PMID: 34362682 DOI: 10.1016/j.jgg.2021.05.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 05/07/2021] [Accepted: 05/11/2021] [Indexed: 12/21/2022]
Abstract
Genetic, epigenetic, and metabolic alterations are all hallmarks of cancer. However, the epigenome and metabolome are both highly complex and dynamic biological networks in vivo. The interplay between the epigenome and metabolome contributes to a biological system that is responsive to the tumor microenvironment and possesses a wealth of unknown biomarkers and targets of cancer therapy. From this perspective, we first review the state of high-throughput biological data acquisition (i.e. multiomics data) and analysis (i.e. computational tools) and then propose a conceptual in silico metabolic and epigenetic regulatory network (MER-Net) that is based on these current high-throughput methods. The conceptual MER-Net is aimed at linking metabolomic and epigenomic networks through observation of biological processes, omics data acquisition, analysis of network information, and integration with validated database knowledge. Thus, MER-Net could be used to reveal new potential biomarkers and therapeutic targets using deep learning models to integrate and analyze large multiomics networks. We propose that MER-Net can serve as a tool to guide integrated metabolomics and epigenomics research or can be modified to answer other complex biological and clinical questions using multiomics data.
Collapse
Affiliation(s)
- Xuezhu Wang
- The State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, School of Basic Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, China
| | - Yucheng Dong
- The State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, School of Basic Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, China
| | - Yongchang Zheng
- Department of Liver Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Yang Chen
- The State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, School of Basic Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, China.
| |
Collapse
|
19
|
Zhang Y, Han P, Guo Q, Hao Y, Qi Y, Xin M, Zhang Y, Cui B, Wang P. Oncogenic Landscape of Somatic Mutations Perturbing Pan-Cancer lncRNA-ceRNA Regulation. Front Cell Dev Biol 2021; 9:658346. [PMID: 34079798 PMCID: PMC8166229 DOI: 10.3389/fcell.2021.658346] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 04/19/2021] [Indexed: 12/12/2022] Open
Abstract
Competing endogenous RNAs (ceRNA) are transcripts that communicate with and co-regulate each other by competing for the binding of shared microRNAs (miRNAs). Long non-coding RNAs (lncRNAs) as a type of ceRNA constitute a competitive regulatory network determined by miRNA response elements (MREs). Mutations in lncRNA MREs destabilize their original regulatory pathways. Study of the effects of lncRNA somatic mutations on ceRNA mechanisms can clarify tumor mechanisms and contribute to the development of precision medicine. Here, we used somatic mutation profiles collected from TCGA to characterize the role of lncRNA somatic mutations in the ceRNA regulatory network in 33 cancers. The 31,560 mutation sites identified by TargetScan and miRanda affected the balance of 70,811 ceRNA regulatory pathways. Putative mutations were categorized as high or low based on mutation frequencies. Multivariate multiple regression revealed a significant effect of 162 high-frequency mutations in six cancer types on the expression levels of target mRNAs (ceMs) through the ceRNA mechanism. Low-frequency mutations in multiple cancers perturbing 1624 ceM have been verified by Student’s t-test, indicating a significant mechanism of changes in the expression level of oncogenic genes. Oncogenic signaling pathway studies involving ceMs indicated functional heterogeneity of multiple cancers. Furthermore, we identified that lncRNA, perturbing ceMs associated with patient survival, have potential as biomarkers. Our collective findings revealed individual differences in somatic mutations perturbing ceM expression and impacting tumor heterogeneity.
Collapse
Affiliation(s)
- Yuanfu Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Peng Han
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin, China.,Heilongjiang Cancer Research Institute, Harbin, China
| | - Qiuyan Guo
- Department of Gynecology, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yangyang Hao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Yue Qi
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Mengyu Xin
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Yafang Zhang
- Department of Anatomy, Harbin Medical University, Harbin, China
| | - Binbin Cui
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Peng Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| |
Collapse
|
20
|
Liu TJ, Hu S, Qiu ZD, Liu D. Anti-Tumor Mechanisms Associated With Regulation of Non-Coding RNA by Active Ingredients of Chinese Medicine: A Review. Front Oncol 2021; 10:634936. [PMID: 33680956 PMCID: PMC7930492 DOI: 10.3389/fonc.2020.634936] [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: 11/29/2020] [Accepted: 12/31/2020] [Indexed: 02/06/2023] Open
Abstract
Cancer has become the second leading cause of death worldwide; however, its complex pathogenesis remains largely unclear. Previous research has shown that cancer development and progression are closely associated with various non-coding RNAs, including long non-coding RNAs and microRNAs, which regulate gene expression. Target gene abnormalities are regulated and engaged in the complex mechanism underlying tumor formation, thereby controlling apoptosis, invasion, and migration of tumor cells and providing potentially effective targets for the treatment of malignant tumors. Chemotherapy is a commonly used therapeutic strategy for cancer; however, its effectiveness is limited by general toxicity and tumor cell drug resistance. Therefore, increasing attention has been paid to developing new cancer treatment modalities using traditional Chinese medicines, which exert regulatory effects on multiple components, targets, and pathways. Several active ingredients in Chinese medicine, including ginsenoside, baicalin, and matrine have been found to regulate ncRNA expression levels, thus, exerting anti-tumor effects. This review summarizes the scientific progress made regarding the anti-tumor mechanisms elicited by various active ingredients of Chinese medicine in regulating non-coding RNAs, to provide a theoretical foundation for treating tumors using traditional Chinese medicine.
Collapse
Affiliation(s)
- Tian-Jia Liu
- School of Pharmacy, Changchun University of Chinese Medicine, Changchun, China
| | - Shuang Hu
- School of Pharmacy, Changchun University of Chinese Medicine, Changchun, China
| | - Zhi-Dong Qiu
- School of Pharmacy, Changchun University of Chinese Medicine, Changchun, China
| | - Da Liu
- School of Pharmacy, Changchun University of Chinese Medicine, Changchun, China
| |
Collapse
|
21
|
Tu J, Wu F, Chen L, Zheng L, Yang Y, Ying X, Song J, Chen C, Hu X, Zhao Z, Ji J. Long Non-Coding RNA PCAT6 Induces M2 Polarization of Macrophages in Cholangiocarcinoma via Modulating miR-326 and RhoA-ROCK Signaling Pathway. Front Oncol 2021; 10:605877. [PMID: 33552977 PMCID: PMC7859434 DOI: 10.3389/fonc.2020.605877] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Accepted: 11/30/2020] [Indexed: 12/20/2022] Open
Abstract
LncRNAs can act crucial roles in multiple tumors including cholangiocarcinoma (CCA). M2 polarization of macrophages is crucial for their biological roles in immunologic tolerance, which is able to induce tumorigenesis. Given that increasing evidence have suggested that lncRNAs could participate in modulating immune cell differentiation and function. Our current study was aimed to identify the underlying mechanism of lncRNA prostate cancer-associated transcript 6 (PCAT6) in CCA progression via regulating M2 macrophage polarization. PCAT6 has been reported as an oncogene in many cancers. In our work, we observed increased expression of PCAT6 in CCA patients. PCAT6 expression in various types of immune cells derived from CCA patients was tested by quantitative real-time PCR (qRT-PCR). It was revealed that PCAT6 was highly expressed in macrophages, which indicated that PCAT6 might regulate the function of macrophages to promote CCA progression. Then, via establishing CCA xenograft mouse model, we found loss of PCAT6 obviously triggered the immune response and reduced the in vivo tumor growth. In addition, overexpression of PCAT6 led to the M2 polarization of THP-1-differentiated macrophages. Moreover, miR-326 was predicted and proved as a target for PCAT6. In addition, down-regulation of PCAT6 repressed M2 polarization of macrophages, which was reversed by miR-326 inhibitors. The increase of PCAT6 induced the accumulation of ROS, mitochondrial and metabolic dysfunction in macrophages and mimics of miR-326 exhibited an opposite process. RohA has been recognized as a significant regulator of immune cell function. In our current work, we observed that RohA function as a downstream target for miR-326. In conclusion, our study highlighted a significant role of PCAT6/miR-326/RohA in immune response of macrophages in CCA and indicated PCAT6 as a potential target of immunotherapy in CCA.
Collapse
Affiliation(s)
- Jianfei Tu
- Key Laboratory of Imaging Diagnosis and Minimally Invasive Intervention Research, the Fifth Affiliated Hospital of Wenzhou Medical University/Affiliated Lishui Hospital of Zhejiang University/Clinical College of The Affiliated Central Hospital of Lishui University, Lishui, China.,Department of Interventional Diagnosis and Treatment, The Central Hospital of Zhejiang Lishui, Lishui, China
| | - Fazong Wu
- Key Laboratory of Imaging Diagnosis and Minimally Invasive Intervention Research, the Fifth Affiliated Hospital of Wenzhou Medical University/Affiliated Lishui Hospital of Zhejiang University/Clinical College of The Affiliated Central Hospital of Lishui University, Lishui, China.,Department of Interventional Diagnosis and Treatment, The Central Hospital of Zhejiang Lishui, Lishui, China
| | - Li Chen
- Key Laboratory of Imaging Diagnosis and Minimally Invasive Intervention Research, the Fifth Affiliated Hospital of Wenzhou Medical University/Affiliated Lishui Hospital of Zhejiang University/Clinical College of The Affiliated Central Hospital of Lishui University, Lishui, China.,Department of Interventional Diagnosis and Treatment, The Central Hospital of Zhejiang Lishui, Lishui, China
| | - Liyun Zheng
- Key Laboratory of Imaging Diagnosis and Minimally Invasive Intervention Research, the Fifth Affiliated Hospital of Wenzhou Medical University/Affiliated Lishui Hospital of Zhejiang University/Clinical College of The Affiliated Central Hospital of Lishui University, Lishui, China.,Department of Interventional Diagnosis and Treatment, The Central Hospital of Zhejiang Lishui, Lishui, China
| | - Yang Yang
- Key Laboratory of Imaging Diagnosis and Minimally Invasive Intervention Research, the Fifth Affiliated Hospital of Wenzhou Medical University/Affiliated Lishui Hospital of Zhejiang University/Clinical College of The Affiliated Central Hospital of Lishui University, Lishui, China.,Department of Interventional Diagnosis and Treatment, The Central Hospital of Zhejiang Lishui, Lishui, China
| | - Xihui Ying
- Key Laboratory of Imaging Diagnosis and Minimally Invasive Intervention Research, the Fifth Affiliated Hospital of Wenzhou Medical University/Affiliated Lishui Hospital of Zhejiang University/Clinical College of The Affiliated Central Hospital of Lishui University, Lishui, China.,Department of Interventional Diagnosis and Treatment, The Central Hospital of Zhejiang Lishui, Lishui, China
| | - Jingjing Song
- Key Laboratory of Imaging Diagnosis and Minimally Invasive Intervention Research, the Fifth Affiliated Hospital of Wenzhou Medical University/Affiliated Lishui Hospital of Zhejiang University/Clinical College of The Affiliated Central Hospital of Lishui University, Lishui, China.,Department of Interventional Diagnosis and Treatment, The Central Hospital of Zhejiang Lishui, Lishui, China
| | - Chunmiao Chen
- Key Laboratory of Imaging Diagnosis and Minimally Invasive Intervention Research, the Fifth Affiliated Hospital of Wenzhou Medical University/Affiliated Lishui Hospital of Zhejiang University/Clinical College of The Affiliated Central Hospital of Lishui University, Lishui, China
| | - Xianghua Hu
- Key Laboratory of Imaging Diagnosis and Minimally Invasive Intervention Research, the Fifth Affiliated Hospital of Wenzhou Medical University/Affiliated Lishui Hospital of Zhejiang University/Clinical College of The Affiliated Central Hospital of Lishui University, Lishui, China
| | - Zhongwei Zhao
- Key Laboratory of Imaging Diagnosis and Minimally Invasive Intervention Research, the Fifth Affiliated Hospital of Wenzhou Medical University/Affiliated Lishui Hospital of Zhejiang University/Clinical College of The Affiliated Central Hospital of Lishui University, Lishui, China.,Department of Interventional Diagnosis and Treatment, The Central Hospital of Zhejiang Lishui, Lishui, China
| | - Jiansong Ji
- Key Laboratory of Imaging Diagnosis and Minimally Invasive Intervention Research, the Fifth Affiliated Hospital of Wenzhou Medical University/Affiliated Lishui Hospital of Zhejiang University/Clinical College of The Affiliated Central Hospital of Lishui University, Lishui, China.,Department of Interventional Diagnosis and Treatment, The Central Hospital of Zhejiang Lishui, Lishui, China
| |
Collapse
|
22
|
Wang P, Guo Q, Hao Y, Liu Q, Gao Y, Zhi H, Li X, Shang S, Guo S, Zhang Y, Ning S, Li X. LnCeCell: a comprehensive database of predicted lncRNA-associated ceRNA networks at single-cell resolution. Nucleic Acids Res 2021; 49:D125-D133. [PMID: 33219686 PMCID: PMC7778920 DOI: 10.1093/nar/gkaa1017] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 10/03/2020] [Accepted: 11/09/2020] [Indexed: 12/13/2022] Open
Abstract
Within the tumour microenvironment, cells exhibit different behaviours driven by fine-tuning of gene regulation. Identification of cellular-specific gene regulatory networks will deepen the understanding of disease pathology at single-cell resolution and contribute to the development of precision medicine. Here, we describe a database, LnCeCell (http://www.bio-bigdata.net/LnCeCell/ or http://bio-bigdata.hrbmu.edu.cn/LnCeCell/), which aims to document cellular-specific long non-coding RNA (lncRNA)-associated competing endogenous RNA (ceRNA) networks for personalised characterisation of diseases based on the ‘One Cell, One World’ theory. LnCeCell is curated with cellular-specific ceRNA regulations from >94 000 cells across 25 types of cancers and provides >9000 experimentally supported lncRNA biomarkers, associated with tumour metastasis, recurrence, prognosis, circulation, drug resistance, etc. For each cell, LnCeCell illustrates a global map of ceRNA sub-cellular locations, which have been manually curated from the literature and related data sources, and portrays a functional state atlas for a single cancer cell. LnCeCell also provides several flexible tools to infer ceRNA functions based on a specific cellular background. LnCeCell serves as an important resource for investigating the gene regulatory networks within a single cell and can help researchers understand the regulatory mechanisms underlying complex microbial ecosystems and individual phenotypes.
Collapse
Affiliation(s)
- Peng Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Qiuyan Guo
- Department of Gynecology, the First Affiliated Hospital of Harbin Medical University, Harbin 150081, China
| | - Yangyang Hao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Qian Liu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Yue Gao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Hui Zhi
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Xin Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Shipeng Shang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Shuang Guo
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Yunpeng Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Shangwei Ning
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Xia Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| |
Collapse
|
23
|
Zhou H, He Y, Li L, Wu C, Hu G. Identification novel prognostic signatures for Head and Neck Squamous Cell Carcinoma based on ceRNA network construction and immune infiltration analysis. Int J Med Sci 2021; 18:1297-1311. [PMID: 33526991 PMCID: PMC7847625 DOI: 10.7150/ijms.53531] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 01/04/2021] [Indexed: 12/20/2022] Open
Abstract
Background: Head and neck squamous cell carcinoma (HNSCC) is a common malignancy with high mortality and morbidity worldwide, but the underlying biological mechanisms of molecules and tumor infiltrating-immune cells (TIICs) are still unknown. Methods and Results: We obtained mRNAs, lncRNAs, and miRNAs expression profiles of 546 HNSCC from The Cancer Genome Atlas (TCGA) database to develop a ceRNA network. CIBERSORT was employed to estimate the fraction of 22 types of TIICs in HNSCC. Univariate and multivariate Cox regression and lasso regression analyses were used to develop prognostic signatures. Then, two novel risk signatures were constructed respectively based on six ceRNAs (ANLN, KIT, PRKAA2, NFIA, PTX3 and has-miR-148a-3p) and three immune cells (naïve B cells, regulatory T cells and Neutrophils). Kaplan-Meier (K-M) analysis and Cox regression analysis further proved that these two signatures were significant prognostic factors independent of multiple clinicopathological characteristics. Two nomograms were built based on ceRNAs-riskScore and TIICs-riskScore that could be used to predict the prognosis of HNSCC. Co-expression analysis showed significant correlations between miR-148a-3p and naive B cells, naive B cells and plasmas cells. Conclusion: Through construction of the ceRNA network and estimation of TIICs, we established two risk signatures and their nomograms with excellent utility, which indicated the potential molecular and cellular mechanisms, and predicted the prognosis of HNSCC.
Collapse
Affiliation(s)
- Haiting Zhou
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, P.R. China
| | - Yi He
- Department of Orthopedics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, P.R. China
| | - Lingling Li
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, P.R. China
| | - Cheng Wu
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, P.R. China
| | - Guoqing Hu
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, P.R. China
| |
Collapse
|
24
|
Song H, Sun J, Kong W, Ji Y, Xu D, Wang J. Construction of a circRNA-Related ceRNA Prognostic Regulatory Network in Breast Cancer. Onco Targets Ther 2020; 13:8347-8358. [PMID: 32922032 PMCID: PMC7455596 DOI: 10.2147/ott.s266507] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 08/04/2020] [Indexed: 12/12/2022] Open
Abstract
Purpose Accumulating evidence has indicated that circRNAs are closely involved in tumorigenesis and progression of human cancers. However, the molecular mechanism underlying function of circRNAs in breast cancer has not been thoroughly elucidated. Currently, we aimed to characterize the circRNA-related competing endogenous RNA (ceRNA) regulatory network in breast cancer and to construct prognostic model. Materials and Methods First, we constructed circRNA expression profiles for paired breast cancer in a Chinese population using a human circRNA microarray. Expression profiles of circRNAs, miRNAs, and mRNAs were retrieved from our circRNA dataset, the Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) databases. We applied the limma and edgeR packages to identify differentially expressed RNAs. Weighted gene correlation network analysis (WGCNA) was used to identify critical modules of mRNAs. Next, a ceRNA network was established based on circRNA-miRNA and miRNA-mRNA intersections. Both Cox regression analysis and ROC curve analysis were performed to generate prognostic model. Additionally, we performed Gene Set Enrichment Analysis (GSEA) on prognostic signatures. Results Total of 59 circRNAs, 98 miRNAs and 3966 mRNAs were identified as differentially expressed RNAs. We first identified 38 miRNA-mRNA pairs and 38 circRNA-miRNA pairs to construct the circRNA-miRNA-mRNA regulatory network and then generated a prognostic model based on 7 signatures (MMD, SLC29A4, CREB5, FOS, ANKRD29, MYOCD, and PIGR), and patients with high-risk scores presented poor prognosis. Several cancer-related pathways were enriched, including the TGF-β pathway, the focal adhesion pathway, and the JAK-STAT signaling pathway, and 20 prognostic ceRNA regulatory networks were subsequently identified. Conclusion In all, we screened a series of dysregulated circRNAs, miRNAs, and mRNAs, and constructed circRNA-related ceRNA network in breast cancer. Our findings may help to deepen the understanding of circRNA-related regulatory mechanisms. Moreover, we generated a prognostic model that provided new insight into postoperative management for breast cancer.
Collapse
Affiliation(s)
- Huan Song
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, People's Republic of China
| | - Jian Sun
- Department of Thoracic Surgery, The First People's Hospital of Yancheng City, Yancheng 224006, People's Republic of China
| | - Weimin Kong
- Department of Thoracic Surgery, The First People's Hospital of Yancheng City, Yancheng 224006, People's Republic of China
| | - Ye Ji
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, People's Republic of China
| | - Dian Xu
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, People's Republic of China
| | - Jianming Wang
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, People's Republic of China
| |
Collapse
|
25
|
Loeffler MA, Hu J, Kirchner M, Wei X, Xiao Y, Albrecht T, De La Torre C, Sticht C, Banales JM, Vogel MN, Pathil-Warth A, Mehrabi A, Hoffmann K, Rupp C, Köhler B, Springfeld C, Schirmacher P, Ji J, Roessler S, Goeppert B. miRNA profiling of biliary intraepithelial neoplasia reveals stepwise tumorigenesis in distal cholangiocarcinoma via the miR-451a/ATF2 axis. J Pathol 2020; 252:239-251. [PMID: 32710569 DOI: 10.1002/path.5514] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 05/30/2020] [Accepted: 07/17/2020] [Indexed: 12/14/2022]
Abstract
Distal cholangiocarcinoma (dCCA) is a biliary tract cancer with a dismal prognosis and is often preceded by biliary intraepithelial neoplasia (BilIN), representing the most common biliary non-invasive precursor lesion. BilIN are histologically well defined but have not so far been characterised systematically at the molecular level. The aim of this study was to determine miRNA-regulated genes in cholangiocarcinogenesis via BilIN. We used a clinicopathologically well-characterised cohort of 12 dCCA patients. Matched samples of non-neoplastic biliary epithelia, BilIN and invasive tumour epithelia of each patient were isolated from formalin-fixed paraffin-embedded tissue sections by laser microdissection. The resulting 36 samples were subjected to total RNA extraction and the expression of 798 miRNAs was assessed using the Nanostring® technology. Candidate miRNAs were validated by RT-qPCR and functionally investigated following lentiviral overexpression in dCCA-derived cell lines. Potential direct miRNA target genes were identified by microarray and prediction algorithms and were confirmed by luciferase assay. We identified 49 deregulated miRNAs comparing non-neoplastic and tumour tissue. Clustering of these miRNAs corresponded to the three stages of cholangiocarcinogenesis, supporting the concept of BilIN as a tumour precursor. Two downregulated miRNAs, i.e. miR-451a (-10.9-fold down) and miR-144-3p (-6.3-fold down), stood out by relative decrease. Functional analyses of these candidates revealed a migration inhibitory effect in dCCA cell lines. Activating transcription factor 2 (ATF2) and A disintegrin and metalloproteinase domain-containing protein 10 (ADAM10) were identified as direct miR-451a target genes. Specific ATF2 inhibition by pooled siRNAs reproduced the inhibitory impact of miR-451a on cancer cell migration. Thus, our data support the concept of BilIN as a direct precursor of invasive dCCA at the molecular level. In addition, we identified miR-451a and miR-144-3p as putative tumour suppressors attenuating cell migration by inhibiting ATF2 in the process of dCCA tumorigenesis. © The Authors. The Journal of Pathology published by John Wiley & Sons, Ltd. on behalf of The Pathological Society of Great Britain and Ireland.
Collapse
Affiliation(s)
- Moritz A Loeffler
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Jun Hu
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Martina Kirchner
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Xiyang Wei
- Life Sciences Institute, Zhejiang University, Hangzhou, PR China
| | - Yi Xiao
- Life Sciences Institute, Zhejiang University, Hangzhou, PR China
| | - Thomas Albrecht
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | | | - Carsten Sticht
- Medical Research Centre, University of Heidelberg, Mannheim, Germany
| | - Jesus M Banales
- Department of Liver and Gastrointestinal Diseases, Biodonostia Health Research Institute, Donostia University Hospital, San Sebastian, Spain
| | - Monika N Vogel
- Diagnostic and Interventional Radiology, Thoraxklinik at University Hospital Heidelberg, Heidelberg, Germany
| | - Anita Pathil-Warth
- Department of Internal Medicine IV, Gastroenterology and Hepatology, University Hospital Heidelberg, Heidelberg, Germany
| | - Arianeb Mehrabi
- Department of General, Visceral and Transplantation Surgery, University Hospital Heidelberg, Heidelberg, Germany.,Liver Cancer Center Heidelberg (LCCH), Heidelberg, Germany
| | - Katrin Hoffmann
- Department of General, Visceral and Transplantation Surgery, University Hospital Heidelberg, Heidelberg, Germany.,Liver Cancer Center Heidelberg (LCCH), Heidelberg, Germany
| | - Christian Rupp
- Department of Internal Medicine IV, Gastroenterology and Hepatology, University Hospital Heidelberg, Heidelberg, Germany.,Liver Cancer Center Heidelberg (LCCH), Heidelberg, Germany
| | - Bruno Köhler
- Liver Cancer Center Heidelberg (LCCH), Heidelberg, Germany.,Department of Medical Oncology, University Hospital Heidelberg, National Center for Tumor Diseases, Heidelberg, Germany
| | - Christoph Springfeld
- Liver Cancer Center Heidelberg (LCCH), Heidelberg, Germany.,Department of Medical Oncology, University Hospital Heidelberg, National Center for Tumor Diseases, Heidelberg, Germany
| | - Peter Schirmacher
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany.,Liver Cancer Center Heidelberg (LCCH), Heidelberg, Germany
| | - Junfang Ji
- Life Sciences Institute, Zhejiang University, Hangzhou, PR China
| | - Stephanie Roessler
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany.,Liver Cancer Center Heidelberg (LCCH), Heidelberg, Germany
| | - Benjamin Goeppert
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany.,Liver Cancer Center Heidelberg (LCCH), Heidelberg, Germany
| |
Collapse
|
26
|
Dong G, Wang X, Jia Y, Jia Y, Zhao W, Zhang J, Tong Z. HAND2-AS1 Works as a ceRNA of miR-3118 to Suppress Proliferation and Migration in Breast Cancer by Upregulating PHLPP2. BIOMED RESEARCH INTERNATIONAL 2020; 2020:8124570. [PMID: 33015182 PMCID: PMC7512048 DOI: 10.1155/2020/8124570] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 08/05/2020] [Indexed: 02/06/2023]
Abstract
Large quantities of long noncoding RNAs (lncRNAs) have been verified to exert vital functions in the process of breast cancer (BC). lncRNA heart and neural crest derivatives expressed 2-antisense RNA 1 (HAND2-AS1) was reported to suppress the development of several cancers. However, its detailed function in BC remained unclear. In the current study, HAND2-AS1 was discovered to be low expressed in BC cell lines, and overexpression of HAND2-AS1 could repress proliferation, migration, and invasion but facilitate apoptosis in BC cells. Moreover, HAND2-AS1 was found to act as a sponge of miR-3118 which was detected to be upregulated in BC cell lines. miR-3118 depletion could constrict the progression of BC. HAND-AS1 hindered the course of BC by reducing the expression of miR-3118. Besides, PHLPP2 was treated as a downstream target of miR-3118 under the selection of RNA pull-down assays. HAND2-AS1 inhibited the process of BC by enhancing expression of PHLPP2. In summary, our study testified that HAND2-AS1 suppressed BC growth by targeting the miR-3118/PHLPP2 axis, indicating that HAND2-AS1 could be regarded as a potential target for BC treatment.
Collapse
Affiliation(s)
- Guolei Dong
- Department of Breast Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Cancer, Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Key Laboratory of Cancer Prevention and Therapy, Tianjin, Tianjin's Clinical Research Center for Cancer, Tianjin 300060, China
| | - Xiaorui Wang
- Department of Breast Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Cancer, Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Key Laboratory of Cancer Prevention and Therapy, Tianjin, Tianjin's Clinical Research Center for Cancer, Tianjin 300060, China
| | - Yan Jia
- Department of Breast Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Cancer, Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Key Laboratory of Cancer Prevention and Therapy, Tianjin, Tianjin's Clinical Research Center for Cancer, Tianjin 300060, China
| | - Yongsheng Jia
- Department of Breast Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Cancer, Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Key Laboratory of Cancer Prevention and Therapy, Tianjin, Tianjin's Clinical Research Center for Cancer, Tianjin 300060, China
| | - Weipeng Zhao
- Department of Breast Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Cancer, Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Key Laboratory of Cancer Prevention and Therapy, Tianjin, Tianjin's Clinical Research Center for Cancer, Tianjin 300060, China
| | - Jin Zhang
- The 3rd Department of Breast Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Cancer, Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Key Laboratory of Cancer Prevention and Therapy, Tianjin, Tianjin's Clinical Research Center for Cancer, Tianjin 300060, China
| | - Zhongsheng Tong
- Department of Breast Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Cancer, Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Key Laboratory of Cancer Prevention and Therapy, Tianjin, Tianjin's Clinical Research Center for Cancer, Tianjin 300060, China
| |
Collapse
|
27
|
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.
Collapse
Affiliation(s)
- Ugo Ala
- Department of Veterinary Sciences, University of Turin, 10124 Turin, Italy
| |
Collapse
|
28
|
Chen J, Chen JG, Sun B, Wu JH, Du CY. Integrative analysis of immune microenvironment-related CeRNA regulatory axis in gastric cancer. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2020; 17:3953-3971. [PMID: 32987562 DOI: 10.3934/mbe.2020219] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
This study aimed to identify significant immune microenvironment-related competing endogenous RNA (CeRNA) regulatory axis in gastric cancer (GC). Analysis of differentially expressed mRNAs (DEmRNAs), miRNAs (DEmiRNAs), and lncRNAs (DElncRNAs) was performed for the microarray datasets. After abundance analysis of immune cell's infiltration, immune-related mRNAs and lncRNAs were obtained. Meanwhile, according to the Pearson correlation coefficient between immune-related mRNAs and lncRNAs, the co-expression mRNA-lncRNA pairs were screened. Furthermore, the target genes of co-existance miRNAs were predicted, and miRNA-lncRNA pairs were identified. Finally, the lncRNA-miRNA and miRNA-mRNA relationship regulated by the same miRNA was screened. Combining with the co-expression relationship between lncRNA and mRNA, the CeRNA network was constructed. In abundance analysis of immune cell's infiltration, a total of eight immune cells were obtained, in addition, 83 immune-related DElncRNAs and 705 immune-related DEmRNAs were screened. KEGG pathway enrichment analysis showed that these mRNAs were mainly involved in PI3K-Akt signaling pathway and human papillomavirus infection, while lncRNA were relevant to gastric acid secretion. A total of 25 miRNAs were significantly associated with immune-related mRNAs, such as hsa-miR-148a-3p, hsa-miR-17-5p, and hsa-miR-25-3p. From the mRNA-miRNA-lncRNA CeRNA network, we observed that AC104389.28─miR-17-5─SMAD5 axis and LINC01133─miR-17-5p─PBLD axis played a crucial role in the development of GC. Furthermore, resting memory CD4 T cells and plasma cells were closely associated with the pathogenesis of GC, and these immune cells might be affected by the key genes. The present study identified key genes that associated with immune microenvironment in GC, providing potential molecular targets for immunotherapy of GC.
Collapse
Affiliation(s)
- Jie Chen
- Department of Gastric Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China
| | - Jing Gui Chen
- Department of Gastric Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China
| | - Bo Sun
- Department of Gastric Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China
| | - Jiang Hong Wu
- Department of Gastric Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China
| | - Chun Yan Du
- Department of Gastric Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China
| |
Collapse
|
29
|
Comprehensive analysis of competitive endogenous RNAs network reveals potential prognostic lncRNAs in gastric cancer. Heliyon 2020; 6:e03978. [PMID: 32455175 PMCID: PMC7235626 DOI: 10.1016/j.heliyon.2020.e03978] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 04/13/2020] [Accepted: 05/11/2020] [Indexed: 01/17/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) are key regulators of a range of human diseases, including various cancers, with multiple previous studies having explored lncRNA dysregulation in the context of gastric cancer (GC). The present study sought to expand upon these previous results by downloading lncRNA, mRNA, and microRNA (miRNA) expression profiles derived from 180 GC tissues and 24 normal control tissues within the Cancer Genome Atlas (TCGA) database. These datasets were then interrogated to identify GC-related differentially expressed (DE) RNAs (|fold change| ≥ 2, FDR< 0.01), leading to the identification of 1946 DE lncRNAs, 123 DE miRNAs, and 3159 DE mRNAs. These results were then used to generate a putative GC-related competitive endogenous RNA (ceRNA) network composed of 131 lncRNAs, 9 miRNAs, and 78 mRNAs. Subsequent survival analyses based upon this network revealed 17 of these lncRNAs to be significantly associated with GC patient survival (P < 0.05). Further multivariable Cox regression and lasso analyses allowed for the construction of an 8-lncRNA risk score that was able to effectively predict GC patient survival with good discriminative ability. The Kaplan-Meier Plotter database further confirmed that network hub genes that were related to these 8 lncRNAs were associated with GC patient prognosis (P < 0.05). As the ceRNA network in the present study was constructed with a focus on both disease stage and differential gene expression, it represents a key resource that will offer valuable insights into the mechanistic roles of ceRNA pathways in GC development and progression.
Collapse
|
30
|
Liu S, Zhang D, Chen L, Gao S, Huang X. Long non-coding RNA BRM promotes proliferation and invasion of papillary thyroid carcinoma by regulating the microRNA-331-3p/SLC25A1 axis. Oncol Lett 2020; 19:3071-3078. [PMID: 32218861 PMCID: PMC7068577 DOI: 10.3892/ol.2020.11418] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 08/30/2019] [Indexed: 12/12/2022] Open
Abstract
Long non-coding RNA BRM (lncBRM) was first identified in liver cancer stem cells and was reported to promote multiple cancer types. However, the function of lncBRM in papillary thyroid carcinoma (PTC) remains unclear. The primary focus of the present study was to determine the biological role of lncBRM in PTC. Reverse transcription-quantitative PCR assays revealed that lncBRM was upregulated in PTC tissues and cells. Cell Counting Kit-8, Transwell invasion and colony-formation assays were performed to assess cell proliferation, invasion and migration, respectively. Furthermore, high expression of lncBRM was associated with poor overall survival time in patients with PTC. lncBRM knockout significantly suppressed cell proliferation, migration and invasion. lncBRM was predicted to bind to microRNA (miR)-331-3p and targets SLC25A1. Overexpression of miR-331-3p or inhibition of SLC25A1 resulted in significantly suppressed proliferation, migration and invasion of PTC cells. Rescue assays demonstrated that inhibition of miR-331-3p significantly abrogated the effects of lncBRM knockout on PTC cell proliferation, migration and invasion. In conclusion, the present study suggests that lncBRM promotes PTC by regulating miR-331-3p and targeting SLC25A1.
Collapse
Affiliation(s)
- Shihong Liu
- Department of Nuclear Medicine, The People's Hospital of Tong Liang District, Chongqing 402560, P.R. China
| | - Deping Zhang
- Department of Nuclear Medicine, The People's Hospital of Tong Liang District, Chongqing 402560, P.R. China
| | - Li Chen
- Department of Nuclear Medicine, The People's Hospital of Tong Liang District, Chongqing 402560, P.R. China
| | - Shangfang Gao
- Department of Nuclear Medicine, The People's Hospital of Tong Liang District, Chongqing 402560, P.R. China
| | - Xiu Huang
- Department of Radiography, The People's Hospital of Tong Liang District, Chongqing 402560, P.R. China
| |
Collapse
|
31
|
Wu F, Sui Y, Wang Y, Xu T, Fan L, Zhu H. Long Noncoding RNA SNHG7, a Molecular Sponge for microRNA-485, Promotes the Aggressive Behavior of Cervical Cancer by Regulating PAK4. Onco Targets Ther 2020; 13:685-699. [PMID: 32158221 PMCID: PMC6986251 DOI: 10.2147/ott.s232542] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 11/22/2019] [Indexed: 12/19/2022] Open
Abstract
Purpose A long noncoding RNA called small nucleolar RNA host gene 7 (SNHG7) is known to be a key regulator of biological processes in multiple human cancer types. In this study, our aims were to determine the expression status of SNHG7 in cervical cancer, to figure out the detailed roles of SNHG7 in cervical cancer cells, and to identify the mechanism underlying the activity of SNHG7 in cervical cancer. Methods Reverse-transcription quantitative PCR was performed to measure SNHG7 expression in cervical cancer. A Cell Counting Kit-8 assay, flow-cytometric analysis, cell migration and invasion assays, and a tumor xenograft experiment were conducted to respectively determine the effects of SNHG7 on cervical cancer cell proliferation, apoptosis, migration, and invasion in vitro and tumor growth in vivo. Results SNHG7 was found to be markedly upregulated in cervical cancer tissues and cell lines. Higher SNHG7 expression significantly correlated with FIGO stage, lymph node metastasis, the depth of cervical invasion, and shorter overall survival in patients with cervical cancer. Functional experiments indicated that a SNHG7 knockdown attenuated proliferation, migration, and invasiveness and promoted apoptosis of cervical cancer cells in vitro. The SNHG7 knockdown also slowed tumor growth in vivo. Further investigation showed that SNHG7 acts as a competing endogenous RNA for microRNA-485 (miR-485) in cervical cancer cells, and the inhibitory actions of the SNHG7 knockdown on the malignant phenotype were reversed by miR-485 inhibition. P21-activated kinase 4 (PAK4) was identified as a direct target gene of miR-485 in cervical cancer, and PAK4 expression was promoted by SNHG7. Conclusion SNHG7 functions as an oncogenic RNA in cervical cancer, competitively binds to miR-485, and thereby upregulates PAK4. This SNHG7–miR-485–PAK4 regulatory network may provide insights into the pathogenesis of cervical cancer, and can help in the identification of novel diagnostic and therapeutic approaches for cervical cancer.
Collapse
Affiliation(s)
- Fei Wu
- Department of Gynecology and Obstetrics, The Second Hospital of Jilin University, Changchun 130041, People's Republic of China
| | - Yujie Sui
- Medical Research Center, The Second Hospital of Jilin University, Changchun 130041, People's Republic of China
| | - Yinhuai Wang
- Department of Gynecology and Obstetrics, The Second Hospital of Jilin University, Changchun 130041, People's Republic of China
| | - Tianmin Xu
- Department of Gynecology and Obstetrics, The Second Hospital of Jilin University, Changchun 130041, People's Republic of China
| | - Limei Fan
- Department of Gynecology and Obstetrics, The Second Hospital of Jilin University, Changchun 130041, People's Republic of China
| | - He Zhu
- Department of Gynecology and Obstetrics, The Second Hospital of Jilin University, Changchun 130041, People's Republic of China
| |
Collapse
|
32
|
Liu H, Chen R, Kang F, Lai H, Wang Y. KCNQ1OT1 promotes ovarian cancer progression via modulating MIR-142-5p/CAPN10 axis. Mol Genet Genomic Med 2020; 8:e1077. [PMID: 31909901 PMCID: PMC7005641 DOI: 10.1002/mgg3.1077] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 11/09/2019] [Accepted: 11/17/2019] [Indexed: 12/11/2022] Open
Abstract
Background Long non‐coding RNA (lncRNA) has been regarded as crucial regulator for cancer progression. Roles of KCNQ1 opposite strand/antisense transcript 1 (KCNQ1OT1) in cancers including osteosarcoma and colon cancer have been previously reported. However, its role in ovarian cancer (OC) remains unclear. Methods Expression level of KCNQ1OT1 on OC cells and normal cell was analyzed with quantitative real‐time PCR. Gain and loss‐of‐function experiments were performed to analyze the biological roles of KCNQ1OT1 in OC. Moreover, whether KCNQ1OT1 functions its role via mediating MICRORNA‐142‐5p (MIR‐142‐5p)/calpain 10 (CAPN10) axis was analyzed. In addition, effects of KCNQ1OT1, MIR‐142‐5p, and CAPN10 on overall survival of OC patients were analyzed at Kaplan–Meier plotter website. Results We showed KCNQ1OT1 was elevated expression in OC cells and indicated poorer overall survival of OC patients. Besides, we found KCNQ1OT1 could promote OC cell proliferation and migration in vitro. Moreover, MIR‐142‐5p was found reduced expression, while CAPN10 was found elevated expression in OC cells compared with normal cell. Kaplan–Meier curve analysis showed low MIR‐142‐5p or high CAPN10 expression were indicators for poorer overall survival of OC patients. At length, we showed KCNQ1OT1 could regulate OC development via MIR‐142‐5p/CAPN10 axis. Conclusions Taken together, KCNQ1OT1 upregulates CAPN10 expression via sponging MIR‐142‐5p, thus promoting the proliferation and migration of OC.
Collapse
Affiliation(s)
- Hongli Liu
- Department of Gynecology, Women and Children's Hospital, School of Medicine, Xiamen University, Fujian, China
| | - Ruixin Chen
- Department of Gynecology, Women and Children's Hospital, School of Medicine, Xiamen University, Fujian, China
| | - Fenhong Kang
- Department of Gynecology, Women and Children's Hospital, School of Medicine, Xiamen University, Fujian, China
| | - Haiqing Lai
- Department of Gynecology, Women and Children's Hospital, School of Medicine, Xiamen University, Fujian, China
| | - Yanlong Wang
- Department of Gynecology, Women and Children's Hospital, School of Medicine, Xiamen University, Fujian, China
| |
Collapse
|