1
|
Jiang L, Wang P, Su M, Yang L, Wang Q. Identification of mRNA Signature for Predicting Prognosis Risk of Rectal Adenocarcinoma. Front Genet 2022; 13:880945. [PMID: 35664306 PMCID: PMC9159392 DOI: 10.3389/fgene.2022.880945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 04/14/2022] [Indexed: 11/13/2022] Open
Abstract
Background: The immune system plays a crucial role in rectal adenocarcinoma (READ). Immune-related genes may help predict READ prognoses. Methods: The Cancer Genome Atlas dataset and GSE56699 were used as the training and validation datasets, respectively, and differentially expressed genes (DEGs) were identified. The optimal DEG combination was determined, and the prognostic risk model was constructed. The correlation between optimal DEGs and immune infiltrating cells was evaluated. Results: Nine DEGs were selected for analysis. Moreover, ADAMDEC1 showed a positive correlation with six immune infiltrates, most notably with B cells and dendritic cells. F13A1 was also positively correlated with six immune infiltrates, particularly macrophage and dendritic cells, whereas LGALS9C was negatively correlated with all immune infiltrates except B cells. Additionally, the prognostic risk model was strongly correlated with the actual situation. We retained only three prognosis risk factors: age, pathologic stage, and prognostic risk model. The stratified analysis revealed that lower ages and pathologic stages have a better prognosis with READ. Age and mRNA prognostic factors were the most important factors in determining the possibility of 3- and 5-year survival. Conclusion: In summary, we identified a nine-gene prognosis risk model that is applicable to the treatment of READ. Altogether, characteristics such as the gene signature and age have a strong predictive value for prognosis risk.
Collapse
Affiliation(s)
- Linlin Jiang
- Department of Chemotherapy, The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, China
| | - Peng Wang
- Department of General Surgery, The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, China
| | - Mu Su
- Department of Chemotherapy, The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, China
| | - Lili Yang
- Department of Chemotherapy, The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, China
| | - Qingbo Wang
- Department of Chemotherapy, The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, China
| |
Collapse
|
2
|
Shafabakhsh R, Arianfar F, Vosough M, Mirzaei HR, Mahjoubin-Tehran M, Khanbabaei H, Kowsari H, Shojaie L, Azar MEF, Hamblin MR, Mirzaei H. Autophagy and gastrointestinal cancers: the behind the scenes role of long non-coding RNAs in initiation, progression, and treatment resistance. Cancer Gene Ther 2021; 28:1229-1255. [PMID: 33432087 DOI: 10.1038/s41417-020-00272-7] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 10/06/2020] [Accepted: 11/23/2020] [Indexed: 02/07/2023]
Abstract
Gastrointestinal (GI) cancers comprise a heterogeneous group of complex disorders that affect different organs, including esophagus, stomach, gallbladder, liver, biliary tract, pancreas, small intestine, colon, rectum, and anus. Recently, an explosion in nucleic acid-based technologies has led to the discovery of long non-coding RNAs (lncRNAs) that have been found to possess unique regulatory functions. This class of RNAs is >200 nucleotides in length, and is characterized by their lack of protein coding. LncRNAs exert regulatory effects in GI cancer development by affecting different functions such as the proliferation and metastasis of cancer cells, apoptosis, glycolysis and angiogenesis. Over the past few decades, considerable evidence has revealed the important role of autophagy in both GI cancer progression and suppression. In addition, recent studies have confirmed a significant correlation between lncRNAs and the regulation of autophagy. In this review, we summarize how lncRNAs play a behind the scenes role in the pathogenesis of GI cancers through regulation of autophagy.
Collapse
Affiliation(s)
- Rana Shafabakhsh
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Iran
| | - Farzaneh Arianfar
- Department of Biochemistry, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Massoud Vosough
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, 1665659911, Iran
| | - Hamid Reza Mirzaei
- Department of Medical Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Maryam Mahjoubin-Tehran
- Student Research Committee, Mashhad University of Medical Sciences, Mashhad, Iran.,Department of Medical Biotechnology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Hashem Khanbabaei
- Medical Physics Department, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Hamed Kowsari
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Iran
| | - Layla Shojaie
- Research Center for Liver Diseases, Keck School of Medicine, Department of Medicine, University of Southern California, Los Angeles, CA, USA
| | | | - Michael R Hamblin
- Laser Research Centre, Faculty of Health Science, University of Johannesburg, Doornfontein, 2028, South Africa.
| | - Hamed Mirzaei
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Iran.
| |
Collapse
|
3
|
Identification of Novel CircRNA-miRNA-mRNA Regulatory Network and Its Prognostic Prediction in Breast Cancer. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2021; 2021:2916398. [PMID: 34745276 PMCID: PMC8570857 DOI: 10.1155/2021/2916398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 10/15/2021] [Indexed: 11/18/2022]
Abstract
Aim This study aimed to investigate the expression profiles of circRNAs and candidate circRNA-miRNA-mRNA network in BC. Methods Differentially expressed circRNAs, miRNAs, and mRNAs (DEcircRNAs, DEmiRNAs, and DEmRNAs) between BC and normal breast tissue samples were screened by analyzing raw data of the RNA sequencing profile. The expression levels of hub genes in 48 pairs of cancerous and tumor-free breast tissues surgically resected from BC patients were determined by RT-qPCR analysis. Results A total of 145 DEcircRNAs, 140 DEmiRNAs, and 2451 DEmRNAs between BC and normal breast tissue samples were screened out. There were 5 pairs of upcircRNA-downmiRNA-upmRNA network and 20 pairs of downcircRNA-upmiRNA-downmRNA network. EIF4EBP1, DUSP1, EGR2, EZH1, and CBX7 were found to be correlated with overall survival of the patients with BC. The expression level of EIF4EBP1 was increased and the expression levels of DUSP1, EGR2, EZH1, and CBX7 were decreased in cancerous breast tissues compared to tumor-free breast tissues (p < 0.0001). The RT-qPCR results from 48 BC patients were consistent with the bioinformatics results. Conclusion This study provides a novel perspective to study circRNA-miRNA-mRNA network in BC and assists in the identification of new potential biomarkers to be used for diagnostic and prognostic purposes.
Collapse
|
4
|
Vieira LM, Jorge NAN, de Sousa JB, Setubal JC, Stadler PF, Walter MEMT. Competing Endogenous RNA in Colorectal Cancer: An Analysis for Colon, Rectum, and Rectosigmoid Junction. Front Oncol 2021; 11:681579. [PMID: 34178670 PMCID: PMC8222815 DOI: 10.3389/fonc.2021.681579] [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: 03/16/2021] [Accepted: 04/22/2021] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Colorectal cancer (CRC) is a heterogeneous cancer. Its treatment depends on its anatomical site and distinguishes between colon, rectum, and rectosigmoid junction cancer. This study aimed to identify diagnostic and prognostic biomarkers using networks of CRC-associated transcripts that can be built based on competing endogenous RNAs (ceRNA). METHODS RNA expression and clinical information data of patients with colon, rectum, and rectosigmoid junction cancer were obtained from The Cancer Genome Atlas (TCGA). The RNA expression profiles were assessed through bioinformatics analysis, and a ceRNA was constructed for each CRC site. A functional enrichment analysis was performed to assess the functional roles of the ceRNA networks in the prognosis of colon, rectum, and rectosigmoid junction cancer. Finally, to verify the ceRNA impact on prognosis, an overall survival analysis was performed. RESULTS The study identified various CRC site-specific prognosis biomarkers: hsa-miR-1271-5p, NRG1, hsa-miR-130a-3p, SNHG16, and hsa-miR-495-3p in the colon; E2F8 in the rectum and DMD and hsa-miR-130b-3p in the rectosigmoid junction. We also identified different biological pathways that highlight differences in CRC behavior at different anatomical sites, thus reinforcing the importance of correctly identifying the tumor site. CONCLUSIONS Several potential prognostic markers for colon, rectum, and rectosigmoid junction cancer were found. CeRNA networks could provide better understanding of the differences between, and common factors in, prognosis of colon, rectum, and rectosigmoid junction cancer.
Collapse
Affiliation(s)
- Lucas Maciel Vieira
- Departamento de Ciência da Computação, Instituto de Ciência Exatas, University of Brasília, Brasília, Brazil
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Leipzig, Germany
| | | | - João Batista de Sousa
- Division of Coloproctology, Department of Surgery, University of Brasília School of Medicine, Brasília, Brazil
| | - João Carlos Setubal
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| | - Peter F. Stadler
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Leipzig, Germany
- Max Planck Institute for Mathematics in the Science, Leipzig, Germany
- Institute for Theoretical Chemistry, University of Vienna, Wien, Austria
- Facultad de Ciencias, Universidad National de Colombia, Sede Bogotá, Colombia
- Santa Fe Institute, Santa Fe, CA, United States
| | | |
Collapse
|
5
|
Yoon S, Oh Y, Oh SY. Clinical Implications of Combined Lymphocyte and Neutrophil Count in Locally Advanced Rectal Cancer After Preoperative Chemoradiotherapy. World J Surg 2021; 45:2591-2600. [PMID: 33866423 DOI: 10.1007/s00268-021-06126-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/03/2021] [Indexed: 10/21/2022]
Abstract
BACKGROUND There are controversies about the ability of neutrophil to lymphocyte ratio to predict the recurrence and survival in patients with locally advanced rectal cancer (LARC) treated with neoadjuvant chemoradiation. The objective of this study is to investigate the prognostic potential of combined lymphocyte count (LC) and neutrophil count (NC) in LARC patients treated with chemoradiotherapy (CRT) followed by curative surgery. METHODS Patients with LARC who underwent surgical resection between January 2010 and December 2017 were reviewed retrospectively. We divided the patients into three groups: high LC and low NC, low LC and high NC, and the remaining patients. The cut-off values of LC and NC were determined by receiver operating characteristic curve analysis and log-rank test statistics. We compared the disease-free survival (DFS) rate between the groups. RESULTS A total of 176 consecutive patients were included in this study. The 5 year DFS rate was significantly different among the three groups in pathologic node (pN)+ patients (73.2% vs. 61.9% vs. 14.2%; P = 0.025). Cox multivariate analysis for pN+ patients demonstrated that combination of low LC and high NC (hazard ratio, 3.630; 95% confidence interval [CI], 1.306-10.093; P = 0.013) was significantly correlated with decreased DFS. CONCLUSIONS This study showed that the combination of LC and NC is a powerful predictive factor for disease recurrence in pN+ LARC patients who underwent CRT.
Collapse
Affiliation(s)
- Sunseok Yoon
- Department of Surgery, Ajou University School of Medicine, 164, World cup-ro, Yeongtong-gu, Suwon, 16499, Korea
| | - Yoon Oh
- Department of Surgery, Ajou University School of Medicine, 164, World cup-ro, Yeongtong-gu, Suwon, 16499, Korea
| | - Seung Yeop Oh
- Department of Surgery, Ajou University School of Medicine, 164, World cup-ro, Yeongtong-gu, Suwon, 16499, Korea.
| |
Collapse
|
6
|
Zhang Q, Feng Z, Shi S, Zhang Y, Ren S. Comprehensive analysis of lncRNA-associated ceRNA network reveals the novel potential of lncRNA, miRNA and mRNA biomarkers in human rectosigmoid junction cancer. Oncol Lett 2020; 21:144. [PMID: 33552263 PMCID: PMC7798100 DOI: 10.3892/ol.2020.12405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 11/20/2020] [Indexed: 12/24/2022] Open
Abstract
Although accumulating evidence has confirmed the potential biological functions of long non-coding RNAs (lncRNAs) as competitive endogenous RNAs (ceRNAs) in colorectal tumorigenesis and progression, few studies have focused on rectosigmoid junction cancer. In the present study, a comprehensive analysis was conducted to explore lncRNA-mediated ceRNA implications and their potential value for prognosis. lncRNA, microRNA (miR/miRNA) and mRNA expression profiles were downloaded from The Cancer Genome Atlas database. Subsequently, a lncRNA-miRNA-mRNA regulatory network was constructed to evaluate the functions of these differentially expressed genes on overall survival (OS) for rectosigmoid junction cancer. As a result, a rectosigmoid junction cancer-specific ceRNA network was successfully constructed with 7 differentially expressed (DE)lncRNAs, 16 DEmiRNAs and 71 DEmRNAs. Among the network, one DElncRNA (small nucleolar RNA host gene 20) and three mRNAs (sodium- and chloride-dependent taurine transporter, fibroblast growth factor 13 and tubulin polyglutamylase TTLL7) were significantly associated with OS (P<0.05). Additionally, two lncRNAs (KCNQ1OT1 and MIR17HG) interacted with most of the DEmiRNAs. Notably, two top-ranked miRNAs (hsa-miR-374a-5p and hsa-miR-374b-5p) associated networks were identified to be markedly associated with the pathogenesis. Furthermore, four DEmRNAs (caveolin-1, MET, filamin-A and AKT3) were enriched in the Kyoto Encylopedia of Gene and Genomes pathway analysis, as well as being included in the ceRNA network. In summary, the present results revealed that a specific lncRNA-miRNA-mRNA network was associated with rectosigmoid junction cancer, providing several molecules that may be used as novel prognostic biomarkers and therapeutic targets.
Collapse
Affiliation(s)
- Qianshi Zhang
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Dalian Medical University, Dalian, Liaoning 116023, P.R. China
| | - Zhen Feng
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Dalian Medical University, Dalian, Liaoning 116023, P.R. China
| | - Shasha Shi
- Department of Ultrasound, The Second Affiliated Hospital of Dalian Medical University, Dalian, Liaoning 116023, P.R. China
| | - Yu Zhang
- Department of Clinical Laboratory, The Second Affiliated Hospital of Dalian Medical University, Dalian, Liaoning 116023, P.R. China
| | - Shuangyi Ren
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Dalian Medical University, Dalian, Liaoning 116023, P.R. China
| |
Collapse
|
7
|
Zhang Z, Chen J, Zhu S, Zhu D, Xu J, He G. Construction and Validation of a Cell Cycle-Related Robust Prognostic Signature in Colon Cancer. Front Cell Dev Biol 2020; 8:611222. [PMID: 33304907 PMCID: PMC7701219 DOI: 10.3389/fcell.2020.611222] [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: 09/28/2020] [Accepted: 10/28/2020] [Indexed: 01/05/2023] Open
Abstract
Colon cancer is one of the most common cancers, great progress was taken place in the treatment of colon cancer, however, the prognostic assessment system remains lagging. Cell cycle plays a vital role in the whole procedure of cancers. In this study, we firstly identified cell cycle-related genes specific in colon cancer. Functional enrichment analysis proved our analysis reliable. Furthermore, we constructed a robust signature based on the cell cycle-related genes. The AUC of the signature to predict the overall survival was 0.808, 0.807, and 0.831 of AUC at 1, 3, and 5 years, respectively. Internal and external validation proved the signature efficient. The 9 genes involved in the signature also showed a great job in molecular subgrouping which indicated the significant value of the 9 genes for further experimental research. In conclusion, the present research provided a novel robust signature predicting the prognosis of colon cancer.
Collapse
Affiliation(s)
- Zhiyuan Zhang
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jingwen Chen
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Shichao Zhu
- Department of Cardiac Surgery, Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Dexiang Zhu
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jianmin Xu
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Guodong He
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| |
Collapse
|
8
|
Identification of circRNA-lncRNA-miRNA-mRNA Competitive Endogenous RNA Network as Novel Prognostic Markers for Acute Myeloid Leukemia. Genes (Basel) 2020; 11:genes11080868. [PMID: 32751923 PMCID: PMC7465400 DOI: 10.3390/genes11080868] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 07/23/2020] [Accepted: 07/29/2020] [Indexed: 12/12/2022] Open
Abstract
Background: Acute myeloid leukemia (AML) is one of the most common malignant and aggressive hematologic tumors, and its pathogenesis is associated with abnormal post-transcriptional regulation. Unbalanced competitive endogenous RNA (ceRNA) promotes tumorigenesis and progression, and greatly contributes to tumor risk classification and prognosis. However, the comprehensive analysis of the circular RNA (circRNA)-long non-coding RNA (lncRNA)-miRNA-mRNA ceRNA network in the prognosis of AML is still rarely reported. Method: We obtained transcriptome data of AML and normal samples from The Cancer Genome Atlas (TCGA), Genotype-tissue Expression (GTEx), and Gene Expression Omnibus (GEO) databases, and identified differentially expressed (DE) mRNAs, lncRNAs, and circRNAs. Then, the targeting relationships among lncRNA-miRNA, circRNA-miRNA, and miRNA-mRNA were predicted, and the survival related hub mRNAs were further screened by univariate and multivariate Cox proportional hazard regression. Finally, the AML prognostic circRNA-lncRNA-miRNA-mRNA ceRNA regulatory network was established. Results: We identified prognostic 6 hub mRNAs (TM6SF1, ZMAT1, MANSC1, PYCARD, SLC38A1, and LRRC4) through Cox regression model, and divided the AML samples into high and low risk groups according to the risk score obtained by multivariate Cox regression. Survival analysis verified that the survival rate of the high-risk group was significantly reduced (p < 0.0001). The prognostic ceRNA network of 6 circRNAs, 32 lncRNAs, 8 miRNAs, and 6 mRNAs was established according to the targeting relationship between 6 hub mRNAs and other RNAs. Conclusion: In this study, ceRNA network jointly participated by circRNAs and lncRNAs was established for the first time. It comprehensively elucidated the post-transcriptional regulatory mechanism of AML, and identified novel AML prognostic biomarkers, which has important guiding significance for the clinical diagnosis, treatment, and further scientific research of AML.
Collapse
|
9
|
Yan WX, Qi XZ, Sun YS, Lin JX, Zhou HZ, Chen L. LncRNA DCST1-AS1 regulates proliferation and apoptosis of rectal cancer cells by targeting miR-874-3p. Shijie Huaren Xiaohua Zazhi 2020; 28:401-409. [DOI: 10.11569/wcjd.v28.i11.401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Some long non-coding RNAs (lncRNAs) have been demonstrated to be abnormally expressed in rectal cancer (RC) and may be involved in tumorigenesis and development. The expression of lncRNA DCST1-AS1 is upregulated in tumors, but its mechanism of action in the development and progression of RC has not been elucidated. It was hypothesized that the expression level of DCST1-AS1 is increased in RC cells and it may promote tumorigenesis and development.
AIM To investigate the effects of DCST1-AS1 on the proliferation and apoptosis of RC cells and the potential mechanism.
METHODS The levels of DCST1-AS1 and miR-874-3p in 30 RC tissues and adjacent tissues were measured by quantitative real-time polymerase chain reaction. RC SW1463 cells were divided into different groups and transfected with si-NC, si-DCST1-AS1, miR-NC, miR-874-3p, pcDNA, pcDNA-DCST1-AS1, si-DCST1-AS1 + anti-miR-NC, and si-DCST1-AS1 + anti-miR-874-3p, respectively. The proliferation and apoptosis of SW1463 cells in each group were measured by MTT assay and flow cytometry, respectively. Western blot analysis was carried out to measure the expression levels of CyclinD1, p21, B-cell lymphoma-2 (Bcl-2), and Bcl-2-associated X protein (Bax) proteins in SW1463 cells. The targeting relationship between DCST1-AS1 and miR-874-3p was validated using a dual-luciferase reporter assay system.
RESULTS Compared with tumor adjacent tissues, the level of lncRNA DCST1-AS1 in RC tissues was remarkably increased (P < 0.05), while the level of miR-874-3p was significantly decreased (P < 0.05). Compared with the si-NC and miR-NC groups, cell proliferation and CyclinD1 and Bcl-2 protein levels were reduced in the si-DCST1-AS1 group and miR-874-3p group, while the apoptosis rate and levels of p21 and Bax were increased. LncRNA DCST1-AS1 targeted and negatively regulated the expression of miR-874-3p. Compared with the si-DCST1-AS1 + anti-miR-NC group, cell proliferation and CyclinD1 and Bcl-2 protein levels in the si-DCST1-AS1 + anti-miR-874-3p group were increased, while cell apoptosis rate and p21 and Bax protein levels were decreased.
CONCLUSION LncRNA DCST1-AS1 regulates the proliferation and apoptosis of SW1463 cells by targeting miR-874-3p. DCST1-AS1 may be a potential molecular target for RC.
Collapse
Affiliation(s)
- Wang-Xin Yan
- Department of Colorectal and Anal Surgery, Wenzhou People's Hospital, Wenzhou 325000, Zhejiang Province, China
| | - Xiao-Zhe Qi
- Department of Colorectal and Anal Surgery, Wenzhou People's Hospital, Wenzhou 325000, Zhejiang Province, China
| | - Yue-Sheng Sun
- Department of General Surgery, Wenzhou People's Hospital, Wenzhou 325000, Zhejiang Province, China
| | - Ji-Xu Lin
- Department of Colorectal and Anal Surgery, Wenzhou People's Hospital, Wenzhou 325000, Zhejiang Province, China
| | - Hui-Zhen Zhou
- Department of Colorectal and Anal Surgery, Wenzhou People's Hospital, Wenzhou 325000, Zhejiang Province, China
| | - Liang Chen
- Department of Colorectal and Anal Surgery, Wenzhou People's Hospital, Wenzhou 325000, Zhejiang Province, China
| |
Collapse
|
10
|
Liu Y, Liu B, Jin G, Zhang J, Wang X, Feng Y, Bian Z, Fei B, Yin Y, Huang Z. An Integrated Three-Long Non-coding RNA Signature Predicts Prognosis in Colorectal Cancer Patients. Front Oncol 2019; 9:1269. [PMID: 31824849 PMCID: PMC6883412 DOI: 10.3389/fonc.2019.01269] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Accepted: 11/04/2019] [Indexed: 01/25/2023] Open
Abstract
Colorectal cancer (CRC) is one of the most common cancers worldwide, whose morbidity and mortality gradually increased. Here, we aimed to identify and access prognostic long non-coding RNAs (lncRNAs) associated with overall survival (OS) in CRC. Firstly, RNA expression profiles were obtained from The Cancer Genome Atlas (TCGA) database, and 439 CRC patients were enrolled as a training set. Univariate Cox analysis and the least absolute shrinkage and selection operator analysis (LASSO) were performed to identify the prognostic lncRNAs. Multivariable Cox regression analysis was used to establish a prognostic risk formula including three lncRNAs (AP003555.2, AP006284.1, and LINC01602). The low-risk group had a better OS than the high-risk group (P < 0.0001), and the areas under the receiver operating characteristic curve (AUCs) of 3- and 5-year OS were 0.712 and 0.674, respectively. Then, we evaluated the signature in a clinical validation set which were collected from the Affiliated Hospital of Jiangnan University. Compared with the low-risk group, patients' OS were found to be significantly worse in the high-risk group (P = 0.0057). The AUCs of 3- and 5-year OS were 0.701 and 0.694, respectively. Finally, we constructed an lncRNA–microRNA (miRNA)–messenger RNA (mRNA) competing endogenous RNA (ceRNA) network to explore the potential function of three differentially expressed lncRNAs (DElncRNAs). The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicated that these DElncRNAs were involved with several cancer-related pathways. In summary, our data provide evidence that the three-lncRNA signature could serve as an independent biomarker to predict prognosis in CRC. This study will also suggest that these three lncRNAs potentially participate in the progression of CRC.
Collapse
Affiliation(s)
- Yuhang Liu
- Wuxi Cancer Institute, Affiliated Hospital of Jiangnan University, Wuxi, China.,Laboratory of Cancer Epigenetics, Wuxi School of Medicine, Jiangnan University, Wuxi, China
| | - Bingxin Liu
- Wuxi Cancer Institute, Affiliated Hospital of Jiangnan University, Wuxi, China.,Laboratory of Cancer Epigenetics, Wuxi School of Medicine, Jiangnan University, Wuxi, China
| | - Guoying Jin
- Wuxi Cancer Institute, Affiliated Hospital of Jiangnan University, Wuxi, China.,Laboratory of Cancer Epigenetics, Wuxi School of Medicine, Jiangnan University, Wuxi, China
| | - Jia Zhang
- Wuxi Cancer Institute, Affiliated Hospital of Jiangnan University, Wuxi, China.,Laboratory of Cancer Epigenetics, Wuxi School of Medicine, Jiangnan University, Wuxi, China
| | - Xue Wang
- Laboratory of Cancer Epigenetics, Wuxi School of Medicine, Jiangnan University, Wuxi, China
| | - Yuyang Feng
- Laboratory of Cancer Epigenetics, Wuxi School of Medicine, Jiangnan University, Wuxi, China
| | - Zehua Bian
- Wuxi Cancer Institute, Affiliated Hospital of Jiangnan University, Wuxi, China.,Laboratory of Cancer Epigenetics, Wuxi School of Medicine, Jiangnan University, Wuxi, China
| | - Bojian Fei
- Department of Surgical Oncology, Affiliated Hospital of Jiangnan University, Wuxi, China
| | - Yuan Yin
- Wuxi Cancer Institute, Affiliated Hospital of Jiangnan University, Wuxi, China.,Laboratory of Cancer Epigenetics, Wuxi School of Medicine, Jiangnan University, Wuxi, China
| | - Zhaohui Huang
- Wuxi Cancer Institute, Affiliated Hospital of Jiangnan University, Wuxi, China.,Laboratory of Cancer Epigenetics, Wuxi School of Medicine, Jiangnan University, Wuxi, China
| |
Collapse
|
11
|
Kalmár A, Nagy ZB, Galamb O, Csabai I, Bodor A, Wichmann B, Valcz G, Barták BK, Tulassay Z, Igaz P, Molnár B. Genome-wide expression profiling in colorectal cancer focusing on lncRNAs in the adenoma-carcinoma transition. BMC Cancer 2019; 19:1059. [PMID: 31694571 PMCID: PMC6836529 DOI: 10.1186/s12885-019-6180-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 09/20/2019] [Indexed: 02/07/2023] Open
Abstract
Background Long non-coding RNAs (lncRNAs) play a fundamental role in colorectal cancer (CRC) development, however, lncRNA expression profiles in CRC and its precancerous stages remain to be explored. We aimed to study whole genomic lncRNA expression patterns in colorectal adenoma–carcinoma transition and to analyze the underlying functional interactions of aberrantly expressed lncRNAs. Methods LncRNA expression levels of colonic biopsy samples (20 CRCs, 20 adenomas (Ad), 20 healthy controls (N)) were analyzed with Human Transcriptome Array (HTA) 2.0. Expression of a subset of candidates was verified by qRT-PCR and in situ hybridization (ISH) analyses. Furthermore, in silico validation was performed on an independent HTA 2.0, on HGU133Plus 2.0 array data and on the TCGA COAD dataset. MiRNA targets of lncRNAs were predicted with miRCODE and lncBase v2 algorithms and miRNA expression was analyzed on miRNA3.0 Array data. MiRNA-mRNA target prediction was performed using miRWALK and c-Met protein levels were analyzed by immunohistochemistry. Comprehensive lncRNA-mRNA-miRNA co-expression pattern analysis was also performed. Results Based on our HTA results, a subset of literature-based CRC-associated lncRNAs showed remarkable expression changes already in precancerous colonic lesions. In both Ad vs. normal and CRC vs. normal comparisons 16 lncRNAs, including downregulated LINC02023, MEG8, AC092834.1, and upregulated CCAT1, CASC19 were identified showing differential expression during early carcinogenesis that persisted until CRC formation (FDR-adjusted p < 0.05). The intersection of CRC vs. N and CRC vs. Ad comparisons defines lncRNAs characteristic of malignancy in colonic tumors, where significant downregulation of LINC01752 and overexpression of UCA1 and PCAT1 were found. Two candidates with the greatest increase in expression in the adenoma-carcinoma transition were further confirmed by qRT-PCR (UCA1, CCAT1) and by ISH (UCA1). In line with aberrant expression of certain lncRNAs in tumors, the expression of miRNA and mRNA targets showed systematic alterations. For example, UCA1 upregulation in CRC samples occurred in parallel with hsa-miR-1 downregulation, accompanied by c-Met target mRNA overexpression (p < 0.05). Conclusion The defined lncRNA sets may have a regulatory role in the colorectal adenoma-carcinoma transition. A subset of CRC-associated lncRNAs showed significantly differential expression in precancerous samples, raising the possibility of developing adenoma-specific markers for early detection of colonic lesions.
Collapse
Affiliation(s)
- Alexandra Kalmár
- 2nd Department of Internal Medicine, Semmelweis University, Szentkirályi str. 46, Budapest, 1088, Hungary. .,Molecular Medicine Research Unit, Hungarian Academy of Sciences, Budapest, Hungary.
| | - Zsófia Brigitta Nagy
- 2nd Department of Internal Medicine, Semmelweis University, Szentkirályi str. 46, Budapest, 1088, Hungary
| | - Orsolya Galamb
- 2nd Department of Internal Medicine, Semmelweis University, Szentkirályi str. 46, Budapest, 1088, Hungary.,Molecular Medicine Research Unit, Hungarian Academy of Sciences, Budapest, Hungary
| | - István Csabai
- Department of Physics of Complex Systems, Eötvös Loránd University, Budapest, Hungary
| | - András Bodor
- Department of Physics of Complex Systems, Eötvös Loránd University, Budapest, Hungary
| | - Barnabás Wichmann
- 2nd Department of Internal Medicine, Semmelweis University, Szentkirályi str. 46, Budapest, 1088, Hungary.,Molecular Medicine Research Unit, Hungarian Academy of Sciences, Budapest, Hungary
| | - Gábor Valcz
- 2nd Department of Internal Medicine, Semmelweis University, Szentkirályi str. 46, Budapest, 1088, Hungary.,Molecular Medicine Research Unit, Hungarian Academy of Sciences, Budapest, Hungary
| | - Barbara Kinga Barták
- 2nd Department of Internal Medicine, Semmelweis University, Szentkirályi str. 46, Budapest, 1088, Hungary
| | - Zsolt Tulassay
- 2nd Department of Internal Medicine, Semmelweis University, Szentkirályi str. 46, Budapest, 1088, Hungary.,Molecular Medicine Research Unit, Hungarian Academy of Sciences, Budapest, Hungary
| | - Peter Igaz
- 2nd Department of Internal Medicine, Semmelweis University, Szentkirályi str. 46, Budapest, 1088, Hungary.,Molecular Medicine Research Unit, Hungarian Academy of Sciences, Budapest, Hungary
| | - Béla Molnár
- 2nd Department of Internal Medicine, Semmelweis University, Szentkirályi str. 46, Budapest, 1088, Hungary.,Molecular Medicine Research Unit, Hungarian Academy of Sciences, Budapest, Hungary
| |
Collapse
|
12
|
Chen F, Li Z, Deng C, Yan H. Integration analysis for novel lncRNA markers predicting tumor recurrence in human colon adenocarcinoma. J Transl Med 2019; 17:299. [PMID: 31470869 PMCID: PMC6717325 DOI: 10.1186/s12967-019-2049-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 08/25/2019] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Numerous evidence has suggested that long non-coding RNA (lncRNA) acts an important role in tumor biology. This study focuses on the identification of novel prognostic lncRNA biomarkers predicting tumor recurrence in human colon adenocarcinoma. METHODS We obtained the research data from The Cancer Genome Atlas (TCGA) database. The interaction among different expressed lncRNA, miRNA and mRNA markers between colon adenocarcinoma patients with and without tumor recurrence were verified with miRcode, starBase and miRTarBase databases. We established the lncRNA-miRNA-mRNA competing endogenous RNA (ceRNA) network based on the verified association between the selected markers. We performed the functional enrichment analysis to obtain better understanding of the selected lncRNAs. Then we use multivariate logistic regression to identify the prognostic lncRNA markers with covariates. We also generated a nomogram predicting tumor recurrence risk based on the identified lncRNA biomarkers and clinical covariates. RESULTS We included 12,727 lncRNA, 1881 miRNA and 47,761 mRNA profiling and clinical features for 113 colon adenocarcinoma patients obtained from the TCGA database. After filtration, we used 37 specific lncRNAs, 60 miRNAs and 148 mRNAs in the ceRNA network analysis. We identified five lncRNAs as prognostic lncRNA markers predicting tumor recurrence in colon adenocarcinoma, in which four of them were identified for the first time. Finally, we generated a nomogram illustrating the association between the identified lncRNAs and the tumor recurrence risk in colon adenocarcinoma. CONCLUSIONS The four newly identified lncRNA biomarkers might be potential prognostic biomarkers predicting tumor recurrence in colon adenocarcinoma. We recommend that further clinical and fundamental researches be conducted on the identified lncRNA markers.
Collapse
Affiliation(s)
- Fangyao Chen
- Department of Epidemiology and Biostatistics, School of Public Health, Xi’an Jiaotong University Health Science Center, 76 Yanta Xilu Road, Xi’an, 710061 Shaanxi China
| | - Zhe Li
- First Affiliated Hospital of Xi’an Jiaotong University, 277 Yanta Xilu Road, Xi’an, 710061 Shaanxi China
| | - Changyu Deng
- Department of Preventive Medicine, Shantou University Medical College, 22 Xinling Road, Jinping District, Shantou, 515041 Guangdong China
| | - Hong Yan
- Department of Epidemiology and Biostatistics, School of Public Health, Xi’an Jiaotong University Health Science Center, 76 Yanta Xilu Road, Xi’an, 710061 Shaanxi China
| |
Collapse
|
13
|
Hu J, Wang T, Chen Q. Competitive endogenous RNA network identifies four long non-coding RNA signature as a candidate prognostic biomarker for lung adenocarcinoma. Transl Cancer Res 2019; 8:1046-1064. [PMID: 35116848 PMCID: PMC8798056 DOI: 10.21037/tcr.2019.06.09] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 06/07/2019] [Indexed: 11/06/2022]
Abstract
BACKGROUND Lung adenocarcinoma (LUAD) is the most commonly histological subtype of lung cancer (LC) and the prognoses of the majority of LUAD patients are still very poor. The present study aimed at integrating long non-coding RNA (lncRNA), microRNA (miRNA) and messenger RNA (mRNA) expression data to construct lncRNA-miRNA-mRNA competitive endogenous RNA (ceRNA) network and identify importantly potential lncRNA signature in ceRNA network as a candidate prognostic biomarker for LUAD patients. METHODS lncRNA, miRNA and mRNA expression data as well as clinical characteristics of LUAD patients were retrieved from The Cancer Genome Atlas (TCGA) database. Differentially expressed lncRNAs (DElncRNAs), differentially expressed mRNAs (DEmRNAs) and differentially expressed miRNA (DEmiRNA) between LUAD and normal lung tissues samples were analyzed. A lncRNA-miRNA-mRNA ceRNA network was constructed and the biological functions of DEmRNAs in ceRNA network were analyzed using gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses. Univariate and multivariate Cox regression analyses of DElncRNAs in ceRNA network were implemented to predict the overall survival (OS) in LUAD patients. The receiver operating characteristic (ROC) analysis was used to evaluate the performance of multivariate Cox regression model. RESULTS A total of 1,664 DElncRNAs, 120 DEmiRNAs and 2,503 DEmRNAs was identified between LUAD and normal lung tissues samples. A lncRNA-miRNA-mRNA ceRNA network including 140 DElncRNAs, 33 DEmiRNAs and 57 DEmRNAs was established. Kaplan-Meier (KM) [Log-rank (LR) test] and univariate regression analysis of those 140 DElncRNAs revealed that 7 DElncRNAs (LINC00518, UCA1, NAV2-AS2, MED4-AS1, SYNPR-AS1, AC011483.1, AP002478.1) were simultaneously identified to be associated with OS of LUAD patients. A multivariate Cox regression analysis of those 7 DElncRNAs showed that a group of 4 DElncRNAs including AP002478.1 (Cox P=4.66E-03), LINC00518 (Cox P=2.34E-04), MED4-AS1 (Cox P=6.42E-03) and NAV2-AS2 (Cox P=6.66E-02) had significantly prognostic value in OS of LUAD patients. The cumulative risk score indicated that the 4-lncRNA signature was significantly associated with OS of LUAD patients (P=0). The area under the curve (AUC) of the 4-lncRNA signature related with 3-year survival was 0.669. CONCLUSIONS The present study provides novel insights into the lncRNA-related regulatory mechanisms in LUAD, and identifying 4-lncRNA signature may serve as a candidate prognostic biomarker in predicting the OS of LUAD patients.
Collapse
Affiliation(s)
- Jing Hu
- Department of Medical Oncology, The Affiliated Hospital of Kunming University of Science and Technology, Kunming 650032, China;,Department of Medical Oncology, The First People’s Hospital of Yunnan Province, Kunming 650032, China
| | - Tonglian Wang
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Qiang Chen
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| |
Collapse
|
14
|
Liao X, Wang X, Huang K, Han C, Deng J, Yu T, Yang C, Huang R, Liu X, Yu L, Zhu G, Su H, Qin W, Zeng X, Han B, Han Q, Liu Z, Zhou X, Gong Y, Liu Z, Huang J, Winkler CA, O'Brien SJ, Ye X, Peng T. Integrated analysis of competing endogenous RNA network revealing potential prognostic biomarkers of hepatocellular carcinoma. J Cancer 2019; 10:3267-3283. [PMID: 31289599 PMCID: PMC6603367 DOI: 10.7150/jca.29986] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2018] [Accepted: 04/03/2019] [Indexed: 12/15/2022] Open
Abstract
Objective: The goal of our study is to identify a competing endogenous RNA (ceRNA) network using dysregulated RNAs between HCC tumors and the adjacent normal liver tissues from The Cancer Genome Atlas (TCGA) datasets, and to investigate underlying prognostic indicators in hepatocellular carcinoma (HCC) patients. Methods: All of the RNA- and miRNA-sequencing datasets of HCC were obtained from TCGA, and dysregulated RNAs between HCC tumors and the adjacent normal liver tissues were investigated by DESeq and edgeR algorithm. Survival analysis was used to confirm underlying prognostic indicators. Results: In the present study, we constructed a ceRNA network based on 16 differentially expressed genes (DEGs), 7 differentially expressed microRNAs and 34 differentially expressed long non-coding RNAs (DELs). Among these dysregulated RNAs, three DELs (AP002478.1, HTR2A-AS1, and ERVMER61-1) and six DEGs (enhancer of zeste homolog 2 [EZH2], kinesin family member 23 [KIF23], chromobox 2 [CBX2], centrosomal protein 55 [CEP55], cell division cycle 25A [CDC25A], and claspin [CLSPN]) were used for construct a prognostic signature for HCC overall survival (OS), and performed well in HCC OS (adjusted P<0.0001, adjusted hazard ratio = 2.761, 95% confidence interval = 1.838-4.147). Comprehensive survival analysis demonstrated that this prognostic signature may be act as an independent prognostic indicator of HCC OS. Functional assessment of these dysregulated DEGs in the ceRNA network and gene set enrichment of this prognostic signature suggest that both were enriched in the biological processes and pathways of the cell cycle, cell division and cell proliferation. Conclusions: Our current study constructed a ceRNA network for HCC, and developed a prognostic signature that may act as an independent indicator for HCC OS.
Collapse
Affiliation(s)
- Xiwen Liao
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Xiangkun Wang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Ketuan Huang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Chuangye Han
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Jianlong Deng
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi Zhuang Autonomous Region, People's Republic of China.,Department of Hepatobiliary Surgery, The Sixth Affiliated Hospital of Guangxi Medical University, Yulin, 537000, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Tingdong Yu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Chengkun Yang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Rui Huang
- Department of Hematology, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Xiaoguang Liu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi Zhuang Autonomous Region, People's Republic of China.,Department of Hepatobiliary Surgery, Affiliated Hospital of Guangdong Medical University, Zhanjiang, 524001, Guangdong Province, China
| | - Long Yu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi Zhuang Autonomous Region, People's Republic of China.,Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450000, Henan Province, China
| | - Guangzhi Zhu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Hao Su
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Wei Qin
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Xianmin Zeng
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Bowen Han
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Quanfa Han
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Zhengqian Liu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Xin Zhou
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Yizhen Gong
- Department of Colorectal and Anal Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi Zhuang Autonomous Region, People's Republic of China.,Department of Evidence-based Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Zhengtao Liu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi Zhuang Autonomous Region, People's Republic of China.,Key Laboratory of Combined Multi-Organ Transplantation, Ministry of Public Health and Key Laboratory of Organ Transplantation of Zhejiang Province, Hangzhou, 310003, Zhejiang Province, People's Republic of China.,Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, SE-171 21, Sweden
| | - Jianlv Huang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi Zhuang Autonomous Region, People's Republic of China.,Department of Hepatobiliary Surgery, The Third Affiliated Hospital of Guangxi Medical University, Nanning 530031, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Cheryl A Winkler
- Basic Research Laboratory, CCR, NCI and Leidos Biomedical Research, Frederick National Laboratory, Frederick MD. 21702, USA
| | - Stephen J O'Brien
- Theodosius Dobzhansky Center for Genome Bioinformatics, Saint-Petersburg State University, Saint-Petersburg, 199004, Russia.,Oceanographic Center, Nova Southeastern University, Ft Lauderdale, 33004, FL, USA
| | - Xinping Ye
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Tao Peng
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi Zhuang Autonomous Region, People's Republic of China
| |
Collapse
|
15
|
Wang Y, Lu T, Wo Y, Sun X, Li S, Miao S, Dong Y, Leng X, Jiao W. Identification of a putative competitive endogenous RNA network for lung adenocarcinoma using TCGA datasets. PeerJ 2019; 7:e6809. [PMID: 31065463 PMCID: PMC6485208 DOI: 10.7717/peerj.6809] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Accepted: 03/18/2019] [Indexed: 12/11/2022] Open
Abstract
The mechanisms underlying the oncogenesis and progression of lung adenocarcinoma (LUAD) are currently unclear. The discovery of competitive endogenous RNA (ceRNA) regulatory networks has provided a new direction for the treatment and prognosis of patients with LUAD. However, the mechanism of action of ceRNA in LUAD remains elusive. In the present study, differentially expressed mRNAs, microRNAs (miRs) and long non-coding RNAs from the cancer genome atlas database were screened. CeRNAs for LUAD were then identified using online prediction software. Among the ceRNAs identified, family with sequence similarity 83 member A (FAM83A), miR-34c-5p, KCNQ1OT1 and FLJ26245 were observed to be significantly associated with the overall survival of patients with LUAD. Of note, FAM83A has potential significance in drug resistance, and may present a candidate biomarker for the prognosis and treatment of patients with LUAD.
Collapse
Affiliation(s)
- Yuanyong Wang
- Department of Thoracic Surgery, Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
| | - Tong Lu
- Department of Thoracic Surgery, Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
| | - Yang Wo
- Department of Thoracic Surgery, Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
| | - Xiao Sun
- Department of Thoracic Surgery, Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
| | - Shicheng Li
- Department of Thoracic Surgery, Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
| | - Shuncheng Miao
- Department of Thoracic Surgery, Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
| | - Yanting Dong
- Department of Thoracic Surgery, Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
| | - Xiaoliang Leng
- Department of Thoracic Surgery, Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
| | - Wenjie Jiao
- Department of Thoracic Surgery, Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
| |
Collapse
|
16
|
Yue C, Ren Y, Ge H, Liang C, Xu Y, Li G, Wu J. Comprehensive analysis of potential prognostic genes for the construction of a competing endogenous RNA regulatory network in hepatocellular carcinoma. Onco Targets Ther 2019; 12:561-576. [PMID: 30679912 PMCID: PMC6338110 DOI: 10.2147/ott.s188913] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) is an extremely common malignant tumor with worldwide prevalence. The aim of this study was to identify potential prognostic genes and construct a competing endogenous RNA (ceRNA) regulatory network to explore the mechanisms underlying the development of HCC. METHODS Integrated analysis was used to identify potential prognostic genes in HCC with R software based on the GSE14520, GSE17548, GSE19665, GSE29721, GSE60502, and the Cancer Genome Atlas databases. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway-enrichment analyses were performed to explore the molecular mechanisms of potential prognostic genes. Differentially expressed miRNAs (DEMs) and lncRNAs (DELs) were screened based on the Cancer Genome Atlas database. An lncRNA-miRNA-mRNA ceRNA regulatory network was constructed based on information about interactions derived from the miRcode, TargetScan, miRTarBase, and miRDB databases. RESULTS A total of 152 potential prognostic genes were screened that were differentially expressed in HCC tissue and significantly associated with overall survival of HCC patients. There were 13 key potential prognostic genes in the ceRNA regulatory network: eleven upregulated genes (CCNB1, CEP55, CHEK1, EZH2, KPNA2, LRRC1, PBK, RRM2, SLC7A11, SUCO, and ZWINT) and two downregulated genes (ACSL1 and CDC37L1) whose expression might be regulated by eight DEMs and 61 DELs. Kaplan-Meier curve analysis showed that nine DELs (AL163952.1, AL359878.1, AP002478.1, C2orf48, C10orf91, CLLU1, CLRN1-AS1, ERVMER61-1, and WARS2-IT1) in the ceRNA regulatory network were significantly associated with HCC-patient prognoses. CONCLUSION This study identified potential prognostic genes and constructed an lncRNA- miRNA-mRNA ceRNA regulatory network of HCC, which not only has important clinical significance for early diagnoses but also provides effective targets for HCC treatments and could provide new insights for HCC-interventional strategies.
Collapse
Affiliation(s)
- Chaosen Yue
- Department of General Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, People's Republic of China, ;
| | - Yaoyao Ren
- Department of Anesthesiology, Beijing Tongren Hospital, Capital Medical University, Beijing, People's Republic of China
| | - Hua Ge
- Department of General Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, People's Republic of China, ;
| | - Chaojie Liang
- Department of General Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, People's Republic of China, ;
| | - Yingchen Xu
- Department of General Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, People's Republic of China, ;
| | - Guangming Li
- Department of General Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, People's Republic of China, ;
| | - Jixiang Wu
- Department of General Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, People's Republic of China, ;
| |
Collapse
|
17
|
Ye Y, Yang S, Han Y, Sun J, Xv L, Wu L, Wang Y, Ming L. Linc00472 suppresses proliferation and promotes apoptosis through elevating PDCD4 expression by sponging miR-196a in colorectal cancer. Aging (Albany NY) 2018; 10:1523-1533. [PMID: 29930217 PMCID: PMC6046238 DOI: 10.18632/aging.101488] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 06/16/2018] [Indexed: 12/19/2022]
Abstract
Long intergenic non-coding RNA Linc00472 has been considered as a tumor suppressor in some cancers. However, the function and mechanism of Linc00472 in colorectal cancer has not been well elucidated. In this study, we found that Linc00472 was down-regulated in colorectal cancer tissues and cells. Elevated Linc00472 expression suppressed proliferation and induced apoptosis in colorectal cancer cells. Moreover, Linc00472 acted as a competing endogenous RNA (ceRNA) of miR-196a to release programmed cell death 4 (PDCD4). Furthermore, miR-196a overexpression or PDCD4 knockdown reversed Linc00472-mediated proliferation inhibition and apoptosis induction in colorectal cancer cells. Ectopic Linc00472 expression hindered tumor growth in vivo. Our study demonstrated that Linc00472 suppressed proliferation and induced apoptosis through up-regulating PDCD4 by decoying miR-196a, which may be an effective therapeutic target for colorectal cancer.
Collapse
Affiliation(s)
- Yafei Ye
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Henan, Zhengzhou 450000, China
| | - Shengnan Yang
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Henan, Zhengzhou 450000, China
| | - Yanping Han
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Henan, Zhengzhou 450000, China
| | - Jingjing Sun
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Henan, Zhengzhou 450000, China
| | - Lijuan Xv
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Henan, Zhengzhou 450000, China
| | - Lina Wu
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Henan, Zhengzhou 450000, China
| | - Yongfeng Wang
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Henan, Zhengzhou 450000, China
| | - Liang Ming
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Henan, Zhengzhou 450000, China
| |
Collapse
|