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Wang Q, Liu J, Chen Z, Zheng J, Wang Y, Dong J. Targeting metabolic reprogramming in hepatocellular carcinoma to overcome therapeutic resistance: A comprehensive review. Biomed Pharmacother 2024; 170:116021. [PMID: 38128187 DOI: 10.1016/j.biopha.2023.116021] [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: 09/18/2023] [Revised: 11/23/2023] [Accepted: 12/14/2023] [Indexed: 12/23/2023] Open
Abstract
Hepatocellular carcinoma (HCC) poses a heavy burden on human health with high morbidity and mortality rates. Systematic therapy is crucial for advanced and mid-term HCC, but faces a significant challenge from therapeutic resistance, weakening drug effectiveness. Metabolic reprogramming has gained attention as a key contributor to therapeutic resistance. Cells change their metabolism to meet energy demands, adapt to growth needs, or resist environmental pressures. Understanding key enzyme expression patterns and metabolic pathway interactions is vital to comprehend HCC occurrence, development, and treatment resistance. Exploring metabolic enzyme reprogramming and pathways is essential to identify breakthrough points for HCC treatment. Targeting metabolic enzymes with inhibitors is key to addressing these points. Inhibitors, combined with systemic therapeutic drugs, can alleviate resistance, prolong overall survival for advanced HCC, and offer mid-term HCC patients a chance for radical resection. Advances in metabolic research methods, from genomics to metabolomics and cells to organoids, help build the HCC metabolic reprogramming network. Recent progress in biomaterials and nanotechnology impacts drug targeting and effectiveness, providing new solutions for systemic therapeutic drug resistance. This review focuses on metabolic enzyme changes, pathway interactions, enzyme inhibitors, research methods, and drug delivery targeting metabolic reprogramming, offering valuable references for metabolic approaches to HCC treatment.
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Affiliation(s)
- Qi Wang
- Department of Hepatobiliary and Pancreatic Surgery, The First Hospital of Jilin University, Jilin University, Changchun 130021, China
| | - Juan Liu
- Research Unit of Precision Hepatobiliary Surgery Paradigm, Chinese Academy of Medical Sciences, Beijing 100021, China; Hepato-Pancreato-Biliary Center, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing 102218, China; Institute for Organ Transplant and Bionic Medicine, Tsinghua University, Beijing 102218, China; Key Laboratory of Digital Intelligence Hepatology (Ministry of Education/Beijing), School of Clinical Medicine, Tsinghua University, Beijing, China.
| | - Ziye Chen
- Clinical Translational Science Center, Beijing Tsinghua Changgung Hospital, Tsinghua University, Beijing 102218, China
| | - Jingjing Zheng
- Hepato-Pancreato-Biliary Center, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing 102218, China
| | - Yunfang Wang
- Research Unit of Precision Hepatobiliary Surgery Paradigm, Chinese Academy of Medical Sciences, Beijing 100021, China; Hepato-Pancreato-Biliary Center, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing 102218, China; Institute for Organ Transplant and Bionic Medicine, Tsinghua University, Beijing 102218, China; Clinical Translational Science Center, Beijing Tsinghua Changgung Hospital, Tsinghua University, Beijing 102218, China; Key Laboratory of Digital Intelligence Hepatology (Ministry of Education/Beijing), School of Clinical Medicine, Tsinghua University, Beijing, China.
| | - Jiahong Dong
- Department of Hepatobiliary and Pancreatic Surgery, The First Hospital of Jilin University, Jilin University, Changchun 130021, China; Research Unit of Precision Hepatobiliary Surgery Paradigm, Chinese Academy of Medical Sciences, Beijing 100021, China; Hepato-Pancreato-Biliary Center, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing 102218, China; Institute for Organ Transplant and Bionic Medicine, Tsinghua University, Beijing 102218, China; Key Laboratory of Digital Intelligence Hepatology (Ministry of Education/Beijing), School of Clinical Medicine, Tsinghua University, Beijing, China.
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2
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ESCCdb: A Comprehensive Database and Key Regulator Exploring Platform Based on Cross Dataset Comparisons for Esophageal Squamous Cell Carcinoma. Comput Struct Biotechnol J 2023; 21:2119-2128. [PMID: 36968016 PMCID: PMC10036886 DOI: 10.1016/j.csbj.2023.03.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 03/15/2023] [Accepted: 03/16/2023] [Indexed: 03/19/2023] Open
Abstract
Esophageal cancer is the seventh most prevalent and the sixth most lethal cancer. Esophageal squamous cell carcinoma (ESCC) is one of the major esophageal cancer subtypes that accounts for 87 % of the total cases. However, its molecular mechanism remains unclear. Here, we present an integrated database for ESCC called ESCCdb, which includes a total of 56 datasets and published studies from the GEO, Xena or SRA databases and related publications. It helps users to explore a particular gene with multiple graphical and interactive views with one click. The results comprise expression changes across 20 datasets, copy number alterations in 11 datasets, somatic mutations from 12 papers, related drugs derived from DGIdb, related pathways, and gene correlations. ESCCdb enables directly cross-dataset comparison of a gene's mutations, expressions and copy number changes in multiple datasets. This allows users to easily assess the alterations in ESCC. Furthermore, survival analysis, drug-gene relationships, and results from whole-genome CRISPR/Cas9 screening can help users determine the clinical relevance, derive functional inferences, and identify potential drugs. Notably, ESCCdb also enables the exploration of the correlation structure and identification of potential key regulators for a process. Finally, we identified 789 consistently differential expressed genes; we summarized recurrently mutated genes and genes affected by significant copy number alterations. These genes may be stable biomarkers or important players during ESCC development. ESCCdb fills the gap between massive omics data and users' needs for integrated analysis and can promote basic and clinical ESCC research. The database is freely accessible at http://cailab.labshare.cn/ESCCdb.
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3
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Jeong JH, Zhong S, Li F, Huang C, Chen X, Liu Q, Peng S, Park H, Lee YM, Dhillon J, Luo JL. Tumor-derived OBP2A promotes prostate cancer castration resistance. J Exp Med 2022; 220:213776. [PMID: 36547668 PMCID: PMC9789742 DOI: 10.1084/jem.20211546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 06/22/2022] [Accepted: 11/17/2022] [Indexed: 12/24/2022] Open
Abstract
Androgen deprivation therapy (ADT) is a systemic therapy for advanced prostate cancer (PCa); although most patients initially respond to ADT, almost all cancers eventually develop castration-resistant PCa (CRPC). Currently, most research focuses on castration-resistant tumors, and the role of tumors in remission is almost completely ignored. Here, we report that odorant-binding protein (OBP2A) released from tumors in remission during ADT catches survival factors, such as CXCL15/IL8, to promote PCa cell androgen-independent growth and enhance the infiltration of myeloid-derived suppressor cells (MDSCs) into tumor microenvironment, leading to the emergence of castration resistance. OBP2A knockdown significantly inhibits CRPC and metastatic CRPC development and improves therapeutic efficacy of CTLA-4/PD-1 antibodies. Treatment with OBP2A-binding ligand α-pinene interrupts the function of OBP2A and suppresses CRPC development. Furthermore, α-pinene-conjugated doxorubicin/docetaxel can be specifically delivered to tumors, resulting in improved anticancer efficacy. Thus, our studies establish a novel concept for the emergence of PCa castration resistance and provide new therapeutic strategies for advanced PCa.
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Affiliation(s)
- Ji-Hak Jeong
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL, USA,Vessel-Organ Interaction Research Center (VOICE, MRC), College of Pharmacy, Kyungpook National University, Daegu, South Korea
| | - Shangwei Zhong
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL, USA,The Cancer Research Institute, Hengyang Medical School, University of South China, Hengyang, China
| | - Fuzhuo Li
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL, USA
| | - Changhao Huang
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL, USA
| | - Xueyan Chen
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL, USA
| | - Qingqing Liu
- The Cancer Research Institute, Hengyang Medical School, University of South China, Hengyang, China
| | - Shoujiao Peng
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL, USA
| | - HaJeung Park
- X-ray Core Facility, The Scripps Research Institute, Jupiter, FL, USA
| | - You Mie Lee
- Vessel-Organ Interaction Research Center (VOICE, MRC), College of Pharmacy, Kyungpook National University, Daegu, South Korea
| | | | - Jun-Li Luo
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL, USA,The Cancer Research Institute, Hengyang Medical School, University of South China, Hengyang, China,Correspondence to Jun-Li Luo:
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4
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Zheng ZJ, Li YS, Zhu JD, Zou HY, Fang WK, Cui YY, Xie JJ. Construction of the Six-lncRNA Prognosis Signature as a Novel Biomarker in Esophageal Squamous Cell Carcinoma. Front Genet 2022; 13:839589. [PMID: 35432441 PMCID: PMC9008717 DOI: 10.3389/fgene.2022.839589] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 02/14/2022] [Indexed: 02/05/2023] Open
Abstract
Esophageal squamous cell carcinoma (ESCC) is a common malignant gastrointestinal tumor threatening global human health. For patients diagnosed with ESCC, determining the prognosis is a huge challenge. Due to their important role in tumor progression, long non-coding RNAs (lncRNAs) may be putative molecular candidates in the survival prediction of ESCC patients. Here, we obtained three datasets of ESCC lncRNA expression profiles (GSE53624, GSE53622, and GSE53625) from the Gene Expression Omnibus (GEO) database. The method of statistics and machine learning including survival analysis and LASSO regression analysis were applied. We identified a six-lncRNA signature composed of AL445524.1, AC109439.2, LINC01273, AC015922.3, LINC00547, and PSPC1-AS2. Kaplan-Meier and Cox analyses were conducted, and the prognostic ability and predictive independence of the lncRNA signature were found in three ESCC datasets. In the entire set, time-dependent ROC curve analysis showed that the prediction accuracy of the lncRNA signature was remarkably greater than that of TNM stage. ROC and stratified analysis indicated that the combination of six-lncRNA signature with the TNM stage has the highest accuracy in subgrouping ESCC patients. Furthermore, experiments subsequently confirmed that one of the lncRNAs LINC01273 may play an oncogenic role in ESCC. This study suggested the six-lncRNA signature could be a valuable survival predictor for patients with ESCC and have potential to be an auxiliary biomarker of TNM stage to subdivide ESCC patients more accurately, which has important clinical significance.
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Affiliation(s)
- Ze-Jun Zheng
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, China
| | - Yan-Shang Li
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, China
- Department of Pathology, Medical College of Jiaying University, Meizhou, China
| | - Jun-De Zhu
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, China
| | - Hai-Ying Zou
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, China
| | - Wang-Kai Fang
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, China
| | - Yi-Yao Cui
- Department of Thoracic Surgery, Beijing Friendship Hospital, Affiliated to the Capital University of Medical Sciences, Beijing, China
| | - Jian-Jun Xie
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, China
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Wang MD, Wang NY, Zhang HL, Sun LY, Xu QR, Liang L, Li C, Huang DS, Zhu H, Yang T. Fatty acid transport protein-5 (FATP5) deficiency enhances hepatocellular carcinoma progression and metastasis by reprogramming cellular energy metabolism and regulating the AMPK-mTOR signaling pathway. Oncogenesis 2021; 10:74. [PMID: 34772914 PMCID: PMC8589992 DOI: 10.1038/s41389-021-00364-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Revised: 09/22/2021] [Accepted: 10/11/2021] [Indexed: 12/11/2022] Open
Abstract
Aberrant lipid metabolism is an essential feature of hepatocellular carcinoma (HCC). Fatty acid transport protein-5 (FATP5) is highly expressed in the liver and is involved in the fatty acid transport pathway. However, the potential role of FATP5 in the pathogenesis of HCC remains largely unknown. Herein, we showed that FATP5 was downregulated in HCC tissues and even much lower in vascular tumor thrombi. Low expression of FATP5 was correlated with multiple aggressive and invasive clinicopathological characteristics and contributed to tumor metastasis and a poor prognosis in HCC patients. FATP5 inhibited the epithelial–mesenchymal transition (EMT) process and suppressed HCC cell migration and invasion, while silencing FATP5 had the opposite effects. Mechanistically, knockdown of FATP5 promoted cellular glycolytic flux and ATP production, thus suppressing AMP-activated protein kinase (AMPK) and activating its downstream signaling mammalian target of rapamycin (mTOR) to support HCC progression and metastasis. Activation of AMPK using metformin reversed the EMT program and impaired the metastatic capacity of FATP5-depleted HCC cells. Collectively, FATP5 served as a novel suppressor of HCC progression and metastasis partly by regulating the AMPK/mTOR pathway in HCC, and targeting the FATP5-AMPK axis may be a promising therapeutic strategy for personalized HCC treatment.
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Affiliation(s)
- Ming-Da Wang
- Department of Hepatobiliary Pancreatic and Minimal Invasive Surgery, Zhejiang Provincial People's Hospital (People's Hospital of Hangzhou Medical College), Hangzhou, Zhejiang, China.,Department of Hepatobiliary Surgery, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University (Navy Medical University), Shanghai, China
| | - Nan-Ya Wang
- The Cancer Center, the First Hospital of Jilin University, Changchun, Jilin, China
| | - Hui-Lu Zhang
- Department of Digestive Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Li-Yang Sun
- Department of Hepatobiliary Pancreatic and Minimal Invasive Surgery, Zhejiang Provincial People's Hospital (People's Hospital of Hangzhou Medical College), Hangzhou, Zhejiang, China
| | - Qiu-Ran Xu
- Department of Hepatobiliary Pancreatic and Minimal Invasive Surgery, Zhejiang Provincial People's Hospital (People's Hospital of Hangzhou Medical College), Hangzhou, Zhejiang, China.,School of Clinical Medicine, Hangzhou Medical College, Hangzhou, China
| | - Lei Liang
- Department of Hepatobiliary Pancreatic and Minimal Invasive Surgery, Zhejiang Provincial People's Hospital (People's Hospital of Hangzhou Medical College), Hangzhou, Zhejiang, China
| | - Chao Li
- Department of Hepatobiliary Surgery, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University (Navy Medical University), Shanghai, China
| | - Dong-Sheng Huang
- Department of Hepatobiliary Pancreatic and Minimal Invasive Surgery, Zhejiang Provincial People's Hospital (People's Hospital of Hangzhou Medical College), Hangzhou, Zhejiang, China. .,School of Clinical Medicine, Hangzhou Medical College, Hangzhou, China.
| | - Hong Zhu
- Department of Medical Oncology, the First Affiliated Hospital of Soochow University, Suzhou, China.
| | - Tian Yang
- Department of Hepatobiliary Pancreatic and Minimal Invasive Surgery, Zhejiang Provincial People's Hospital (People's Hospital of Hangzhou Medical College), Hangzhou, Zhejiang, China. .,Department of Hepatobiliary Surgery, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University (Navy Medical University), Shanghai, China. .,School of Clinical Medicine, Hangzhou Medical College, Hangzhou, China.
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6
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Cheng S, Guo J, Wang D, Fang Q, Liu Y, Xie W, Zhang Y, Li C. A Novel Three-LncRNA Signature Predicting Tumor Recurrence in Nonfunctioning Pituitary Adenomas. Front Genet 2021; 12:754503. [PMID: 34745223 PMCID: PMC8564111 DOI: 10.3389/fgene.2021.754503] [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: 08/06/2021] [Accepted: 10/04/2021] [Indexed: 12/14/2022] Open
Abstract
The nonfunctioning pituitary adenoma (NFPA) recurrence rate is relatively high after surgical resection. Here, we constructed effective long noncoding RNA (lncRNA) signatures to predict NFPA prognosis. LncRNAs expression microarray sequencing profiles were obtained from 66 NFPAs. Sixty-six patients were randomly separated into a training (n = 33) and test group (n = 33). Univariable Cox regression and a machine learning algorithm was used to filter lncRNAs. Time-dependent receiver operating characteristic (ROC) analysis was performed to improve the prediction signature. Three lncRNAs (LOC101927765, RP11-23N2.4 and RP4-533D7.4) were included in a prognostic signature with high prediction accuracy for tumor recurrence, which had the largest area under ROC curve (AUC) value in the training/test group (AUC = 0.87/0.73). The predictive ability of the signature was validated by Kaplan-Meier survival analysis. A signature-based risk score model divied patients into two risk group, and the recurrence-free survival rates of the groups were significantly different (log-rank p < 0.001). In addition, the ROC analysis showed that the lncRNA signature predictive ability was significantly better than that of age in the training/testing/entire group (AUC = 0.87/0.726/0.798 vs. AUC = 0.683/0.676/0.679). We constructed and verified a three-lncRNA signature predictive of recurrence, suggesting potential therapeutic targets for NFPA.
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Affiliation(s)
- Sen Cheng
- Department of Neurosurgery, Beijing Tiantan Hospital Affiliated to Capital Medical University, Beijing, China
| | - Jing Guo
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Dawei Wang
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Qiuyue Fang
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Yulou Liu
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Weiyan Xie
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Yazhuo Zhang
- Department of Neurosurgery, Beijing Tiantan Hospital Affiliated to Capital Medical University, Beijing, China.,Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.,Beijing Institute for Brain Disorders Brain Tumor Center, Beijing, China.,China National Clinical Research Center for Neurological Diseases, Beijing, China
| | - Chuzhong Li
- Department of Neurosurgery, Beijing Tiantan Hospital Affiliated to Capital Medical University, Beijing, China.,Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.,Beijing Institute for Brain Disorders Brain Tumor Center, Beijing, China.,China National Clinical Research Center for Neurological Diseases, Beijing, China
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7
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Zhang Q, Liu W, Luo SB, Xie FC, Liu XJ, Xu RA, Chen L, Su Z. Development of a Prognostic Five-Gene Signature for Diffuse Lower-Grade Glioma Patients. Front Neurol 2021; 12:633390. [PMID: 34295296 PMCID: PMC8291287 DOI: 10.3389/fneur.2021.633390] [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: 11/25/2020] [Accepted: 06/02/2021] [Indexed: 01/07/2023] Open
Abstract
Background: Diffuse lower-grade gliomas (LGGs) are infiltrative and heterogeneous neoplasms. Gene signature including multiple protein-coding genes (PCGs) is widely used as a tumor marker. This study aimed to construct a multi-PCG signature to predict survival for LGG patients. Methods: LGG data including PCG expression profiles and clinical information were downloaded from The Cancer Genome Atlas (TCGA) and the Chinese Glioma Genome Atlas (CGGA). Survival analysis, receiver operating characteristic (ROC) analysis, and random survival forest algorithm (RSFVH) were used to identify the prognostic PCG signature. Results: From the training (n = 524) and test (n = 431) datasets, a five-PCG signature which can classify LGG patients into low- or high-risk group with a significantly different overall survival (log rank P < 0.001) was screened out and validated. In terms of prognosis predictive performance, the five-PCG signature is stronger than other clinical variables and IDH mutation status. Moreover, the five-PCG signature could further divide radiotherapy patients into two different risk groups. GO and KEGG analysis found that PCGs in the prognostic five-PCG signature were mainly enriched in cell cycle, apoptosis, DNA replication pathways. Conclusions: The new five-PCG signature is a reliable prognostic marker for LGG patients and has a good prospect in clinical application.
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Affiliation(s)
- Qiang Zhang
- Department of Clinical Laboratory, The People's Hospital of Lishui, Lishui, China
| | - Wenhao Liu
- Guangdong-Hong Kong-Macao Greater Bay Area (GBA) Research Innovation Institute for Nanotechnology, Guangzhou, China
| | - Shun-Bin Luo
- Department of Clinical Pharmacy, The People's Hospital of Lishui, Lishui, China
| | - Fu-Chen Xie
- Department of Urinary Surgery, The People's Hospital of Lishui, Lishui, China
| | - Xiao-Jun Liu
- Pathology Department, The People's Hospital of Lishui, Lishui, China
| | - Ren-Ai Xu
- The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Lixi Chen
- Department of Gynecology in Xiahe Branch, Xiamen University Affiliated Zhongshan Hospital, Xiamen, China
| | - Zhilin Su
- Department of Laboratory Medicine, The First Affiliated Hospital of Xiamen University, Xiamen, China
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8
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Su X, Yu Z, Zhang Y, Chen J, Wei L, Sun L. Construction and Analysis of the Dysregulated ceRNA Network and Identification of Risk Long Noncoding RNAs in Breast Cancer. Front Genet 2021; 12:664393. [PMID: 34149805 PMCID: PMC8212960 DOI: 10.3389/fgene.2021.664393] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 04/26/2021] [Indexed: 12/26/2022] Open
Abstract
Breast cancer (BRCA) is the second leading cause of cancer-related mortality in women worldwide. However, the molecular mechanism involved in the development of BRCA is not fully understood. In this study, based on the miRNA-mediated long non-coding RNA (lncRNA)-protein coding gene (PCG) relationship and lncRNA-PCG co-expression information, we constructed and analyzed a specific dysregulated lncRNA-PCG co-expression network in BRCA. Then, we performed the random walk with restart (RWR) method to prioritize BRCA-related lncRNAs through comparing their RWR score and significance. As a result, we identified 30 risk lncRNAs for BRCA, which can distinguish normal and tumor samples. Moreover, through gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway analysis, we found that these risk lncRNAs mainly synergistically exerted functions related to cell cycle and DNA separation and replication. At last, we developed a four-lncRNA prognostic signature (including AP000851.1, LINC01977, MAFG-DT, SIAH2-AS1) and assessed the survival accuracy of the signature by performing time-dependent receiver operating characteristic (ROC) analysis. The areas under the ROC curve for 1, 3, 5, and 10 years of survival prediction were 0.68, 0.61, 0.62, and 0.63, respectively. The multivariable Cox regression results verified that the four-lncRNA signature could be used as an independent prognostic biomarker in BRCA. In summary, these results have important reference value for the study of diagnosis, treatment, and prognosis evaluation of BRCA.
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Affiliation(s)
- Xiaojie Su
- College of Medical Laboratory Science and Technology, Harbin Medical University, Daqing, China
| | - Zhaoyan Yu
- Department of Otorhinolaryngology, Shandong Provincial Hospital Affiliated to Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - Yuexin Zhang
- School of Medical Informatics, Harbin Medical University, Daqing, China
| | - Jiaxin Chen
- School of Medical Informatics, Harbin Medical University, Daqing, China
| | - Ling Wei
- School of Medical Informatics, Harbin Medical University, Daqing, China
| | - Liang Sun
- College of Artificial Intelligence and Big Data for Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China.,Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, China
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9
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Guo JC, Wei QS, Dong L, Fang SS, Li F, Zhao Y. Prognostic Value of an Autophagy-Related Five-Gene Signature for Lower-Grade Glioma Patients. Front Oncol 2021; 11:644443. [PMID: 33768004 PMCID: PMC7985555 DOI: 10.3389/fonc.2021.644443] [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: 12/21/2020] [Accepted: 02/15/2021] [Indexed: 12/16/2022] Open
Abstract
Background: Molecular characteristics can be good indicators of tumor prognosis and have been introduced into the classification of gliomas. The prognosis of patients with newly classified lower-grade gliomas (LGGs, including grade 2 and grade 3 gliomas) is highly heterogeneous, and new molecular markers are urgently needed. Methods: Autophagy related genes (ATGs) were obtained from Human Autophagy Database (HADb). From the Cancer Genome Atlas (TCGA) and the Chinese Glioma Genome Atlas (CGGA), gene expression profiles including ATG expression information and patient clinical data were downloaded. Cox regression analysis, receiver operating characteristic (ROC) analysis, Kaplan–Meier analysis, random survival forest algorithm (RSFVH) and stratification analysis were performed. Results: Through univariate Cox regression analysis, we found a total of 127 ATGs associated with the prognosis of LGG patients from TCGA dataset and a total of 131 survival-related ATGs from CGGA dataset. Using TCGA dataset as the training group (n = 524), we constructed a five-ATG signature (including BAG1, BID, MAP1LC3C, NRG3, PTK6), which could divide LGG patients into two risk groups with significantly different overall survival (Log Rank P < 0.001). Then we confirmed in the independent CGGA dataset that the five-ATG signature had the ability to predict prognosis (n = 431, Log Rank P < 0.001). We further discovered that the predictive ability of the five-ATG signature was better than the existing clinical indicators and IDH mutation status. In addition, the five-ATG signature could further classify patients after receiving radiotherapy or chemotherapy into groups with different prognosis. Conclusions: We identified a five-ATG signature that could be a reliable prognostic marker and might be therapeutic targets for autophagy therapy for LGG patients.
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Affiliation(s)
- Jin-Cheng Guo
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China
| | - Qing-Shuang Wei
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China
| | - Lei Dong
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China
| | - Shuang-Sang Fang
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China
| | - Feng Li
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China
| | - Yi Zhao
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China
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10
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Wang W, Zhu D, Zhao Z, Sun M, Wang F, Li W, Zhang J, Jiang G. RNA sequencing reveals the expression profiles of circRNA and identifies a four-circRNA signature acts as a prognostic marker in esophageal squamous cell carcinoma. Cancer Cell Int 2021; 21:151. [PMID: 33663506 PMCID: PMC7934454 DOI: 10.1186/s12935-021-01852-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Accepted: 02/24/2021] [Indexed: 12/13/2022] Open
Abstract
Background CircRNAs with tissue-specific expression and stable structure may be good tumor prognostic markers. However, the expression of circRNAs in esophageal squamous cell carcinoma (ESCC) remain unknown. We aim to identify prognostic circRNAs and construct a circRNA-related signature in ESCC. Methods RNA sequencing was used to test the circRNA expression profiles of 73 paired ESCC tumor and normal tissues after RNase R enrichment. Bioinformatics methods, such as principal component analysis (PCA), t-distributed Stochastic Neighbor Embedding (t-SNE) algorithm, unsupervised clustering and hierarchical clustering were performed to analyze the circRNA expression characteristics. Univariate cox regression analysis, random survival forests-variable hunting (RSFVH), Kaplan–Meier analysis, multivariable Cox regression and ROC (receiver operating characteristic) curve analysis were used to screen the prognostic circRNA signature. Real-time quantitative PCR (qPCR) and fluorescence in situ hybridization(FISH) in 125 ESCC tissues were performed. Results Compared with normal tissues, there were 11651 differentially expressed circRNAs in cancer tissues. A total of 1202 circRNAs associated with ESCC prognosis (P < 0.05) were identified. Through bioinformatics analysis, we screened a circRNA signature including four circRNAs (hsa_circ_0000005, hsa_circ_0007541, hsa_circ_0008199, hsa_circ_0077536) which can classify the ESCC patients into two groups with significantly different survival (log rank P < 0.001), and found its predictive performance was better than that of the TNM stage(0.84 vs. 0.66; 0.65 vs. 0.62). Through qPCR and FISH experiment, we validated the existence of the screened circRNAs and the predictive power of the circRNA signature. Conclusion The prognostic four-circRNA signature could be a new prognostic biomarker for ESCC, which has high clinical application value.
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Affiliation(s)
- Weiwei Wang
- Department of Pathology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Jian she Dong Road 1, Zhengzhou, 450052, Henan, China.,Department of Pathology, School of Basic Medicine, Zhengzhou University, Zhengzhou, 450002, China.,Henan Key Laboratory for Tumor Pathology, Zhengzhou University, Zhengzhou, 450052, China
| | - Di Zhu
- Department of Pathology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Jian she Dong Road 1, Zhengzhou, 450052, Henan, China.,Department of Pathology, School of Basic Medicine, Zhengzhou University, Zhengzhou, 450002, China.,Henan Key Laboratory for Tumor Pathology, Zhengzhou University, Zhengzhou, 450052, China
| | - Zhihua Zhao
- Department of Pathology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Jian she Dong Road 1, Zhengzhou, 450052, Henan, China.,Department of Pathology, School of Basic Medicine, Zhengzhou University, Zhengzhou, 450002, China.,Henan Key Laboratory for Tumor Pathology, Zhengzhou University, Zhengzhou, 450052, China
| | - Miaomiao Sun
- Department of Pathology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Jian she Dong Road 1, Zhengzhou, 450052, Henan, China.,Department of Pathology, School of Basic Medicine, Zhengzhou University, Zhengzhou, 450002, China.,Henan Key Laboratory for Tumor Pathology, Zhengzhou University, Zhengzhou, 450052, China
| | - Feng Wang
- Department of Oncology, First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450052, China
| | - Wencai Li
- Department of Pathology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Jian she Dong Road 1, Zhengzhou, 450052, Henan, China.,Department of Pathology, School of Basic Medicine, Zhengzhou University, Zhengzhou, 450002, China.,Henan Key Laboratory for Tumor Pathology, Zhengzhou University, Zhengzhou, 450052, China
| | - Jianying Zhang
- State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, Zhengzhou, 450052, Henan, China.
| | - Guozhong Jiang
- Department of Pathology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Jian she Dong Road 1, Zhengzhou, 450052, Henan, China. .,Department of Pathology, School of Basic Medicine, Zhengzhou University, Zhengzhou, 450002, China. .,Henan Key Laboratory for Tumor Pathology, Zhengzhou University, Zhengzhou, 450052, China.
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11
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Lee N, Xia X, Meng H, Zhu W, Wang X, Zhang T, Zhang C, Zhang J, Luo P. Identification of a novel CpG methylation signature to predict prognosis in lung squamous cell carcinoma. Cancer Biomark 2021; 30:63-73. [PMID: 32924987 DOI: 10.3233/cbm-201564] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
BACKGROUND DNA methylation plays a vital role in modulating genomic function and warrants evaluation as a biomarker for the diagnosis and treatment of lung squamous cell carcinoma (LUSC). OBJECTIVE In this study, we aimed to identify effective potential biomarkers for predicting prognosis and drug sensitivity in LUSC. METHODS A univariate Cox proportional hazards regression analysis, a random survival forests-variable hunting (RSFVH) algorithm, and a multivariate Cox regression analysis were adopted to analyze the methylation profile of patients with LUSC included in public databases: The Cancer Genome Atlas (TCGA), and the Gene Expression Omnibus (GEO). RESULTS A methylated region consisting of 3 sites (cg06675147, cg07064331, cg20429172) was selected. Patients were divided into a high-risk group and a low-risk group in the training dataset. High-risk patients had shorter overall survival (OS) (hazard ratio [HR]: 2.72, 95% confidence interval [CI]: 1.82-4.07, P< 0.001) compared with low-risk patients. The accuracy of the prognostic signature was validated in the test and validation cohorts (TCGA, n= 94; GSE56044, n= 23). Gene set variation analysis (GSVA) showed that activity in the cell cycle/mitotic, ERBB, and ERK/MAPK pathways was higher in the high-risk compared with the low-risk group, which may lead to differences in OS.Interestingly, we observed that patients in the high-risk group were more sensitive to gemcitabine and docetaxel than the low-risk group, which is consistent with results of the GSVA. CONCLUSION We report novel methylation sites that could be used as powerful tools for predicting risk factors for poorer survival in patients with LUSC.
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Affiliation(s)
- Nan Lee
- Department of Oncology, Zhu Jiang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Xuelian Xia
- Department of Anesthesiology, Luo He Central Hospital, Henan, China
| | - Hui Meng
- Department of Oncology, Zhu Jiang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Weiliang Zhu
- Department of Oncology, Zhu Jiang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Xiankai Wang
- Department of Oncology, Zhu Jiang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Tianyuan Zhang
- Department of Oncology, Zhu Jiang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Chanyuan Zhang
- Department of Oncology, Zhu Jiang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Jian Zhang
- Department of Oncology, Zhu Jiang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Peng Luo
- Department of Oncology, Zhu Jiang Hospital, Southern Medical University, Guangzhou, Guangdong, China
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12
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Zhang L, Li P, Liu E, Xing C, Zhu D, Zhang J, Wang W, Jiang G. Prognostic value of a five-lncRNA signature in esophageal squamous cell carcinoma. Cancer Cell Int 2020; 20:386. [PMID: 32831646 PMCID: PMC7419219 DOI: 10.1186/s12935-020-01480-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 08/03/2020] [Indexed: 12/22/2022] Open
Abstract
Background The aim of this study was to identify prognostic long non-coding RNAs (lncRNAs) and develop a multi-lncRNA signature for suvival prediction in esophageal squamous cell carcinoma (ESCC). Methods The clinical and gene expression data from Gene Expression Omnibus database (GSE53624, n = 119) were obtianed as training set. A total of 98 paired ESCC tumor and normal tissues were detected by RNA sequencing and used as test set. Another 84 ESCC tissues were used for real-time quantitative PCR(qRT-PCR) and as an independent validation cohort. Survival analysis, Cox regression and Kaplan–Meier analysis were performed. Results We screened a prognostic marker of ESCC from the GSE53624 dataset and named it as the five-lncRNA signature including AC007179.1, MORF4L2-AS1, RP11-488I20.9, RP13-30A9.2, RP4-735C1.6, which could classify patients into high- and low-risk groups with significantly different survival(median survival: 1.75 years vs. 4.01 years, log rank P < 0.05). Then test dataset and validation dataset confirmed that the five-lncRNA signature can determine the prognosis of ESCC patients. Predictive independence of the prognostic marker was proved by multivariable Cox regression analyses in the three datasets (P < 0.05). In addition, the signature was found to be better than TNM stage in terms of prognosis. Conclusion The five-lncRNA signature could be a good prognostic biomarker for ESCC patients and has important clinical value.
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Affiliation(s)
- Lan Zhang
- Department of Pathology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450052 Henan China
| | - Pan Li
- Department of Pathology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450052 Henan China
| | - Enjie Liu
- Department of Pathology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450052 Henan China
| | - Chenju Xing
- Department of Pathology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450052 Henan China
| | - Di Zhu
- Department of Pathology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450052 Henan China
| | - Jianying Zhang
- State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, Zhengzhou, 450052 Henan China
| | - Weiwei Wang
- Department of Pathology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450052 Henan China
| | - Guozhong Jiang
- Department of Pathology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450052 Henan China
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13
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Ling B, Yao M, Li G, Liu J, Liu B, Wang W, Jiang B. Clinical significance of ring finger protein 2 high expression in skin squamous cell carcinoma. Oncol Lett 2020; 20:1111-1118. [PMID: 32724350 PMCID: PMC7377046 DOI: 10.3892/ol.2020.11666] [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: 08/18/2019] [Accepted: 03/18/2020] [Indexed: 12/17/2022] Open
Abstract
Although ring finger protein 2 (RNF2) serves an important role in the occurrence, development and regulation of various types of cancer, RNF2 expression in skin squamous cell carcinoma (SCC) remains unknown. The aim of the present study was to investigate the role of RNF2 expression in SCC and adjacent tissues from patients. The protein and gene expression levels of RNF2 in SCC and adjacent tissues were detected by immunohistochemistry (IHC), western blot analysis and semi-quantitative reverse transcription (RT) PCR. Single factor analysis was used to study the association between RNF2 expression level and the clinicopathological characteristics of patients with SCC. Multifactor Cox survival analysis was used to examine the association between RNF2 expression and the overall survival rate of postoperative patients with SCC. The results from IHC staining demonstrated that the positive expression rate of RNF2 was 84.68% (210/248) and 56.05% (139/248) in SCC and in adjacent tissues, respectively. Furthermore, results from western blot analysis demonstrated that RNF2 protein expression in SCC tissues was significantly higher compared with that in the adjacent tissues (P<0.05). The positive rate of RNF2 mRNA in SCC was 81.05% (201/248), which was significantly higher compared with that in the adjacent tissues 54.44% (135/248; P<0.05). Furthermore, RNF2 protein and gene expression levels were associated with tumor diameter, tumor stage, tumor metastasis and the degree of tumor differentiation in patients with SCC. Patients exhibiting higher RNF2 protein expression in SCC tissues had a significantly shorter disease-specific survival rate compared with patients with low RNF2 expression. In addition, RNF2 protein expression, tumor diameter, tumors site and tumor stage were independent factors affecting the overall survival rate of postoperative patients. High protein and gene expression levels of RNF2 in SCC tissues may be associated with the occurrence and development of SCC and prognosis of patients. The results form this study may serve the development of novel therapeutic options and diagnostic strategies for patients with SCC.
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Affiliation(s)
- Bai Ling
- Department of Pharmacy, The First People's Hospital of Yancheng City, Yancheng, Jiangsu 224005, P.R. China
| | - Ming Yao
- Department of Dermatology, Yancheng Hospital of Traditional Chinese Medicine, Affiliated to Nanjing University of Traditional Chinese Medicine, Yancheng, Jiangsu 224000, P.R. China
| | - Gongqi Li
- Department of Clinical Laboratory, Linyi Traditional Hospital, Linyi, Shandong 276003, P.R. China
| | - Jun Liu
- Department of Laboratory Medicine, The Fifth People's Hospital of Wuxi, Wuxi, Jiangsu 214005, P.R. China
| | - Bin Liu
- Department of Laboratory Medicine, The Fifth People's Hospital of Wuxi, Wuxi, Jiangsu 214005, P.R. China
| | - Wei Wang
- Department of Laboratory Medicine, The First People's Hospital of Yancheng City, Yancheng, Jiangsu 224005, P.R. China
| | - Bin Jiang
- Department of Laboratory Medicine, The Central Blood Station of Yancheng City, Yancheng, Jiangsu 224000, P.R. China
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14
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Zhang JH, Hou R, Pan Y, Gao Y, Yang Y, Tian W, Zhu YB. A five-microRNA signature for individualized prognosis evaluation and radiotherapy guidance in patients with diffuse lower-grade glioma. J Cell Mol Med 2020; 24:7504-7514. [PMID: 32412186 PMCID: PMC7339211 DOI: 10.1111/jcmm.15377] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 04/20/2020] [Accepted: 04/22/2020] [Indexed: 12/14/2022] Open
Abstract
Despite the prognostic value of IDH and other gene mutations found in diffuse glioma, markers that judge individual prognosis of patients with diffuse lower‐grade glioma (LGG) are still lacking. This study aims to develop an expression‐based microRNA signature to provide survival and radiotherapeutic response prediction for LGG patients. MicroRNA expression profiles and relevant clinical information of LGG patients were downloaded from The Cancer Genome Atlas (TCGA; the training group) and the Chinese Glioma Genome Atlas (CGGA; the test group). Cox regression analysis, random survival forests‐variable hunting (RSFVH) screening and receiver operating characteristic (ROC) were used to identify the prognostic microRNA signature. ROC and TimeROC curves were plotted to compare the predictive ability of IDH mutation and the signature. Stratification analysis was conducted in patients with radiotherapy information. Gene ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were performed to explore the biological function of the signature. We identified a five‐microRNA signature that can classify patients into low‐risk or high‐risk group with significantly different survival in the training and test datasets (P < 0.001). The five‐microRNA signature was proved to be superior to IDH mutation in survival prediction (AUCtraining = 0.688 vs 0.607). Stratification analysis found the signature could further divide patients after radiotherapy into two risk groups. GO and KEGG analyses revealed that microRNAs from the prognostic signature were mainly enriched in cancer‐associated pathways. The newly discovered five‐microRNA signature could predict survival and radiotherapeutic response of LGG patients based on individual microRNA expression.
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Affiliation(s)
- Jian-Hua Zhang
- Department of Blood Transfusion, Peking University People's Hospital, Beijing, China
| | - Ruiqin Hou
- Department of Blood Transfusion, Peking University People's Hospital, Beijing, China
| | - Yuhualei Pan
- Experimental and Translational Research Center, Beijing Friendship Hospital, Affiliated to the Capital University of Medical Sciences, Beijing, China
| | - Yuhan Gao
- Department of Blood Transfusion, Peking University People's Hospital, Beijing, China
| | - Ying Yang
- Department of Blood Transfusion, Peking University People's Hospital, Beijing, China
| | - Wenqin Tian
- Department of Blood Transfusion, Peking University People's Hospital, Beijing, China
| | - Yan-Bing Zhu
- Experimental and Translational Research Center, Beijing Friendship Hospital, Affiliated to the Capital University of Medical Sciences, Beijing, China
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15
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Ye Y, Guo J, Xiao P, Ning J, Zhang R, Liu P, Yu W, Xu L, Zhao Y, Yu J. Macrophages-induced long noncoding RNA H19 up-regulation triggers and activates the miR-193b/MAPK1 axis and promotes cell aggressiveness in hepatocellular carcinoma. Cancer Lett 2020; 469:310-322. [PMID: 31705929 DOI: 10.1016/j.canlet.2019.11.001] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 10/13/2019] [Accepted: 11/01/2019] [Indexed: 02/05/2023]
Abstract
Dysregulation of long noncoding RNA (lncRNA) H19 has been implicated in hepatocellular carcinoma (HCC), but the concrete regulatory mechanism is lack of research. We mined gene expression profiles of 457 HCC samples from TCGA and TJMUCH cohorts and further validated in 64 FFPE HCC tissues. LncRNA H19 overexpression in situ was significantly correlated with poor prognosis of HCC patients, which induced EMT, promoted stemness and accelerated invasion of HCC cells in vitro. Co-expression network analysis indicated lncRNA H19 negatively correlated with miR-193b and positively correlated with MAPK1 gene, which implicated that lncRNA H19 served as a sponge molecule to hijack miR-193b and protect MAPK1. Forced overexpression of H19 attenuated miR-193b-mediated inhibition on multiple driver oncogenes (EGFR, KRAS, PTEN and IGF1R) and MAPK1 gene, thus triggered EMT and stem cell transformation in HCC. LncRNA H19 positively correlated with CD68 + TAMs in situ. TAMs-induced lncRNA H19 promotes HCC aggressiveness via triggering and activating the miR-193b/MAPK1 axis, mediates the crosstalk between HCC and immunological microenvironment, and causes poor clinical outcomes. LncRNA H19 is a valuable predictive biomarker and potential therapeutic target in HCC.
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Affiliation(s)
- Yingnan Ye
- Cancer Molecular Diagnostics Core, Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center of Caner, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, PR China.
| | - Jincheng Guo
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, PR China; Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou, PR China.
| | - Pei Xiao
- Cancer Molecular Diagnostics Core, Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center of Caner, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, PR China; Department of Immunology, Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center of Caner, Key Laboratory of Cancer Immunology and Biotherapy, Tianjin's Clinical Research Center for Cancer, Tianjin, PR China.
| | - Junya Ning
- Cancer Molecular Diagnostics Core, Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center of Caner, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, PR China; Department of Immunology, Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center of Caner, Key Laboratory of Cancer Immunology and Biotherapy, Tianjin's Clinical Research Center for Cancer, Tianjin, PR China.
| | - Rui Zhang
- Cancer Molecular Diagnostics Core, Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center of Caner, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, PR China.
| | - Pengpeng Liu
- Cancer Molecular Diagnostics Core, Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center of Caner, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, PR China.
| | - Wenwen Yu
- Department of Immunology, Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center of Caner, Key Laboratory of Cancer Immunology and Biotherapy, Tianjin's Clinical Research Center for Cancer, Tianjin, PR China.
| | - Liyan Xu
- Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou, PR China.
| | - Yi Zhao
- Cancer Molecular Diagnostics Core, Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center of Caner, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, PR China; Key Laboratory of Intelligent Information Processing, Advanced Computer Research Center, State Key Laboratory of Computer Architecture, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, PR China; School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, PR China.
| | - Jinpu Yu
- Cancer Molecular Diagnostics Core, Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center of Caner, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, PR China; Department of Immunology, Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center of Caner, Key Laboratory of Cancer Immunology and Biotherapy, Tianjin's Clinical Research Center for Cancer, Tianjin, PR China.
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16
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Fang S, Guo J, Zhang J, Liu J, Hong S, Yu B, Gao Y, Hu S, Liu H, Sun L, Zhao Y. A P53‐related microRNA model for predicting the prognosis of hepatocellular carcinoma patients. J Cell Physiol 2019; 235:3569-3578. [PMID: 31556110 DOI: 10.1002/jcp.29245] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 08/26/2019] [Indexed: 12/31/2022]
Affiliation(s)
- Shuang‐Sang Fang
- Hwa Mei Hospital University of Chinese Academy of Sciences Ningbo China
- School of Traditional Chinese Medicine Beijing University of Chinese Medicine Beijing China
- Key Laboratory of Intelligent Information Processing, State Key Laboratory of Computer Architecture, Institute of Computing Technology Chinese Academy of Sciences Beijing China
| | - Jin‐Cheng Guo
- Hwa Mei Hospital University of Chinese Academy of Sciences Ningbo China
- School of Traditional Chinese Medicine Beijing University of Chinese Medicine Beijing China
- Key Laboratory of Intelligent Information Processing, State Key Laboratory of Computer Architecture, Institute of Computing Technology Chinese Academy of Sciences Beijing China
| | - Jian‐Hua Zhang
- Department of Blood Transfusion Peking University People's Hospital Beijing China
| | - Jin‐Na Liu
- Key Laboratory of Intelligent Information Processing, State Key Laboratory of Computer Architecture, Institute of Computing Technology Chinese Academy of Sciences Beijing China
| | - Shuai Hong
- Key Laboratory of Intelligent Information Processing, State Key Laboratory of Computer Architecture, Institute of Computing Technology Chinese Academy of Sciences Beijing China
| | - Bo Yu
- Key Laboratory of Intelligent Information Processing, State Key Laboratory of Computer Architecture, Institute of Computing Technology Chinese Academy of Sciences Beijing China
| | - Yuhan Gao
- Department of Blood Transfusion Peking University People's Hospital Beijing China
| | - Su‐Pei Hu
- Hwa Mei Hospital University of Chinese Academy of Sciences Ningbo China
| | - Hai‐Zhong Liu
- Hwa Mei Hospital University of Chinese Academy of Sciences Ningbo China
| | - Liang Sun
- Hwa Mei Hospital University of Chinese Academy of Sciences Ningbo China
- Key Laboratory of Intelligent Information Processing, State Key Laboratory of Computer Architecture, Institute of Computing Technology Chinese Academy of Sciences Beijing China
| | - Yi Zhao
- Hwa Mei Hospital University of Chinese Academy of Sciences Ningbo China
- School of Traditional Chinese Medicine Beijing University of Chinese Medicine Beijing China
- Key Laboratory of Intelligent Information Processing, State Key Laboratory of Computer Architecture, Institute of Computing Technology Chinese Academy of Sciences Beijing China
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17
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Prognostic Significance of CIP2A in Esophagogastric Junction Adenocarcinoma: A Study of 65 Patients and a Meta-Analysis. DISEASE MARKERS 2019; 2019:2312439. [PMID: 31534561 PMCID: PMC6724434 DOI: 10.1155/2019/2312439] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 05/28/2019] [Accepted: 07/16/2019] [Indexed: 12/28/2022]
Abstract
Background The expression of the cancerous inhibitor protein phosphatase 2A (CIP2A) appears to be predictive of the prognosis of various solid tumors. However, the association between this protein and the risk of esophagogastric junction adenocarcinoma (EGJA) remains unclear. We investigated CIP2A expression and its clinical significance in EGJA and conducted a meta-analysis to explore the relationship between CIP2A and the prognosis of patients with solid tumors. Methods Immunohistochemistry (IHC) was performed to detect the expression of CIP2A in EGJA. Kaplan-Meier estimation, Cox analysis, and ROC curves were performed to analyze the survival of patients and the prognostic factors. In the meta-analysis, we searched relevant publications in several widely used databases and used 15 studies (2348 patients). Results IHC demonstrated that CIP2A was elevated in EGJA and correlated with poor survival as an independent indicator. It could forecast the survival more precisely when combined with the grade, which is another independent prognosis marker of EGJA. Meta-analysis demonstrated that the associations between the expression of CIP2A and the prognosis were detected for overall survival (HR = 1.98, 95%CI = 1.69‐2.32), disease-specific survival (HR = 1.72, 95%CI = 1.50‐1.97), and time to tumor progression (pooled HR = 1.95, 95%CI = 1.56‐2.43). Conclusion High expression of CIP2A was a poor indicator of the prognosis of EGJA, and CIP2A may be a new biomarker for the diagnosis and treatment of EGJA. The meta-analysis suggested that CIP2A expression can be a predictive marker of overall survival, disease-specific survival, and time to tumor progression in patients with solid tumors.
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18
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Ruffalo M, Bar-Joseph Z. Protein interaction disruption in cancer. BMC Cancer 2019; 19:370. [PMID: 31014259 PMCID: PMC6823625 DOI: 10.1186/s12885-019-5532-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 03/27/2019] [Indexed: 12/18/2022] Open
Abstract
Background Most methods that integrate network and mutation data to study cancer focus on the effects of genes/proteins, quantifying the effect of mutations or differential expression of a gene and its neighbors, or identifying groups of genes that are significantly up- or down-regulated. However, several mutations are known to disrupt specific protein-protein interactions, and network dynamics are often ignored by such methods. Here we introduce a method that allows for predicting the disruption of specific interactions in cancer patients using somatic mutation data and protein interaction networks. Methods We extend standard network smoothing techniques to assign scores to the edges in a protein interaction network in addition to nodes. We use somatic mutations as input to our modified network smoothing method, producing scores that quantify the proximity of each edge to somatic mutations in individual samples. Results Using breast cancer mutation data, we show that predicted edges are significantly associated with patient survival and known ligand binding site mutations. In-silico analysis of protein binding further supports the ability of the method to infer novel disrupted interactions and provides a mechanistic explanation for the impact of mutations on key pathways. Conclusions Our results show the utility of our method both in identifying disruptions of protein interactions from known ligand binding site mutations, and in selecting novel clinically significant interactions.Supporting website with software and data: https://www.cs.cmu.edu/~mruffalo/mut-edge-disrupt/. Electronic supplementary material The online version of this article (10.1186/s12885-019-5532-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Matthew Ruffalo
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, PA, 15213, USA
| | - Ziv Bar-Joseph
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, PA, 15213, USA. .,Machine Learning Department, School of Computer Science, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, PA, 15213, USA.
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19
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Zhao J, Li X, Guo J, Li M, Zhang J, Ding J, Li S, Tang Z, Qian F, Li Y, Wang Q, Li C, Li E, Xu L. ReCirc: prediction of circRNA expression and function through probe reannotation of non-circRNA microarrays. Mol Omics 2019; 15:150-163. [PMID: 30916068 DOI: 10.1039/c8mo00252e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Growing evidence shows that circular RNAs (circRNAs) play important roles in physiological and pathological processes, but our knowledge about the function of circRNAs in diseases is still limited. CircRNA functions are closely related to their expression levels. We developed a probe reannotating program named ReCirc, which is based on sequence alignment between microarray probes and circRNAs, to reannotate circRNAs from non-circRNA microarrays (any microarray that was not designed to profile circRNAs) with microarray probe sequences that were aligned to the body and back-spliced junction sequences of circRNAs to identify circRNAs. Through ReCirc, we obtained 39 818 reannotated probe set-circRNA pairs, which involved 5388 circRNAs, from an Affymetrix human exon array. We evaluated our method by comparing circRNAs obtained by us with golden standard RNase R-resistant (RNase R+) circRNAs, predicted by an RNA-seq-based method find_circ, in the HeLa cell line. The results showed that ReCirc circRNAs, especially those with higher expression level, were partially present in RNase R+ data. In addition to RNA-seq, a circRNA microarray, such as the Agilent-069978 Arraystar Human CircRNA microarray, was also applied to predict and profile circRNAs. Thus, we compared the circRNA profile obtained from ReCirc with that from the circRNA microarray. The results showed that circRNA expression is similar between ReCirc and circRNA microarray in samples from the same tissue. We also evaluated ReCirc, by comparing ReCirc with the find_circ program, in their abilities to compute circRNA expression variation in multiple cell lines and performed molecular verification in the HeLaS3 cell line for those circRNAs that got good performance. As a result, 5 of the 9 randomly selected circRNAs were successfully verified. Functional analysis of identified circRNAs in 4 different cancers indicated that circRNAs may be crucial biomarkers for cancer diagnosis and prognosis. Thus, ReCirc allows us to identify circRNAs from any non-circRNA microarray, and to back-annotate old microarray data from public data sets, which would facilitate re-utilization of the wealth of microarray data sets, to enable the characterization of circRNAs in tissues and cell lines. Here we state that our method is designed only for microarrays and cannot be used for RNAseq data.
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Affiliation(s)
- Jianmei Zhao
- School of Medical Informatics, Harbin Medical University, Daqing Campus, Daqing, China. and The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou, China.
| | - Xuecang Li
- School of Medical Informatics, Harbin Medical University, Daqing Campus, Daqing, China.
| | - Jincheng Guo
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou, China.
| | - Meng Li
- School of Medical Informatics, Harbin Medical University, Daqing Campus, Daqing, China.
| | - Jian Zhang
- School of Medical Informatics, Harbin Medical University, Daqing Campus, Daqing, China.
| | - Jiyu Ding
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou, China.
| | - Shang Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Zhidong Tang
- School of Medical Informatics, Harbin Medical University, Daqing Campus, Daqing, China.
| | - Fengcui Qian
- School of Medical Informatics, Harbin Medical University, Daqing Campus, Daqing, China.
| | - Yanyu Li
- School of Medical Informatics, Harbin Medical University, Daqing Campus, Daqing, China.
| | - Qiuyu Wang
- School of Medical Informatics, Harbin Medical University, Daqing Campus, Daqing, China. and The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou, China.
| | - Chunquan Li
- School of Medical Informatics, Harbin Medical University, Daqing Campus, Daqing, China. and The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou, China.
| | - Enmin Li
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou, China.
| | - Liyan Xu
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou, China.
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20
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Qiao GJ, Chen L, Wu JC, Li ZR. Identification of an eight-gene signature for survival prediction for patients with hepatocellular carcinoma based on integrated bioinformatics analysis. PeerJ 2019; 7:e6548. [PMID: 30918751 PMCID: PMC6431139 DOI: 10.7717/peerj.6548] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 01/25/2019] [Indexed: 11/25/2022] Open
Abstract
Background Hepatocellular carcinoma (HCC) remains one of the leading causes of cancer-related death worldwide. Despite recent advances in imaging techniques and therapeutic intervention for HCC, the low overall 5-year survival rate of HCC patients remains unsatisfactory. This study aims to find a gene signature to predict clinical outcomes in HCC. Methods Bioinformatics analysis including Cox’s regression analysis, Kaplan-Meier (KM) and receiver operating characteristic curve (ROC) analysis and the random survival forest algorithm were performed to mine the expression profiles of 553 hepatocellular carcinoma (HCC) patients from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) public database. Results We selected a signature comprising eight protein-coding genes (DCAF13, FAM163A, GPR18, LRP10, PVRIG, S100A9, SGCB, and TNNI3K) in the training dataset (AUC = 0.77 at five years, n = 332). The signature stratified patients into high- and low-risk groups with significantly different survival in the training dataset (median 2.20 vs. 8.93 years, log-rank test P < 0.001) and in the test dataset (median 2.68 vs. 4.24 years, log-rank test P = 0.004, n = 221, GSE14520). Further multivariate Cox regression analysis showed that the signature was an independent prognostic factor for patients with HCC. Compared with TNM stage and another reported three-gene model, the signature displayed improved survival prediction power in entire dataset (AUC signature = 0.66 vs. AUC TNM = 0.64 vs. AUC gene model = 0.60, n = 553). Stratification analysis shows that it can be used as an auxiliary marker for many traditional staging models. Conclusions We constructed an eight-gene signature that can be a novel prognostic marker to predict the survival of HCC patients.
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Affiliation(s)
- Guo-Jie Qiao
- Institute of Tropical Agriculture and Forestry, Hainan University, Hainkou, China.,Department of Hepatobiliary Surgery, Hainan Provincial People's Hospital, Hainan Medical College, Hainkou, China
| | - Liang Chen
- Department of Hepatobiliary Surgery, Hainan Provincial People's Hospital, Hainan Medical College, Hainkou, China
| | - Jin-Cai Wu
- Department of Hepatobiliary Surgery, Hainan Provincial People's Hospital, Hainan Medical College, Hainkou, China
| | - Zhou-Ri Li
- Institute of Tropical Agriculture and Forestry, Hainan University, Hainkou, China.,Department of Hepatobiliary Surgery, Hainan Provincial People's Hospital, Hainan Medical College, Hainkou, China
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21
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Peng L, Guo JC, Long L, Pan F, Zhao JM, Xu LY, Li EM. A Novel Clinical Six-Flavoprotein-Gene Signature Predicts Prognosis in Esophageal Squamous Cell Carcinoma. BIOMED RESEARCH INTERNATIONAL 2019; 2019:3869825. [PMID: 31815134 PMCID: PMC6878914 DOI: 10.1155/2019/3869825] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 08/23/2019] [Accepted: 10/04/2019] [Indexed: 02/05/2023]
Abstract
Flavoproteins and their interacting proteins play important roles in mitochondrial electron transport, fatty acid degradation, and redox regulation. However, their clinical significance and function in esophageal squamous cell carcinoma (ESCC) are little known. Here, using survival analysis and machine learning, we mined 179 patient expression profiles with ESCC in GSE53625 from the Gene Expression Omnibus (GEO) database and constructed a signature consisting of two flavoprotein genes (GPD2 and PYROXD2) and four flavoprotein interacting protein genes (CTTN, GGH, SRC, and SYNJ2BP). Kaplan-Meier analysis revealed the signature was significantly associated with the survival of ESCC patients (mean survival time: 26.77 months in the high-risk group vs. 54.97 months in the low-risk group, P < 0.001, n = 179), and time-dependent ROC analysis demonstrated that the six-gene signature had good predictive ability for six-year survival for ESCC (AUC = 0.86, 95% CI: 0.81-0.90). We then validated its prediction performance in an independent set by RT-PCR (mean survival: 15.73 months in the high-risk group vs. 21.1 months in the low-risk group, P=0.032, n = 121). Furthermore, RNAi-mediated knockdown of genes in the flavoprotein signature led to decreased proliferation and migration of ESCC cells. Taken together, CTTN, GGH, GPD2, PYROXD2, SRC, and SYNJ2BP have an important clinical significance for prognosis of ESCC patients, suggesting they are efficient prognostic markers and potential targets for ESCC therapy.
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Affiliation(s)
- Liu Peng
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou 515041, Guangdong, China
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou 515041, Guangdong, China
| | - Jin-Cheng Guo
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou 515041, Guangdong, China
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou 515041, Guangdong, China
| | - Lin Long
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou 515041, Guangdong, China
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou 515041, Guangdong, China
| | - Feng Pan
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou 515041, Guangdong, China
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou 515041, Guangdong, China
| | - Jian-Mei Zhao
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou 515041, Guangdong, China
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou 515041, Guangdong, China
| | - Li-Yan Xu
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou 515041, Guangdong, China
- Institute of Oncologic Pathology, Shantou University Medical College, Shantou 515041, Guangdong, China
| | - En-Min Li
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou 515041, Guangdong, China
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou 515041, Guangdong, China
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22
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Tian S, Meng G, Zhang W. A six-mRNA prognostic model to predict survival in head and neck squamous cell carcinoma. Cancer Manag Res 2018; 11:131-142. [PMID: 30588115 PMCID: PMC6305138 DOI: 10.2147/cmar.s185875] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Transcriptional dysregulation is one of the most important features of cancer genesis and progression. Applying gene expression dysregulation information to predict the development of cancers is useful for cancer diagnosis. However, previous studies mainly focused on the relationship between a single gene and cancer. Prognostic prediction using combined gene models remains limited. MATERIALS AND METHODS Gene expression profiles were downloaded from The Cancer Genome Atlas and the data sets were randomly divided into training data sets and test data sets. A six-gene signature associated with head and neck squamous cell carcinoma (HNSCC) and overall survival (OS) was identified according to a training cohort by using weighted gene correlation network analysis and least absolute shrinkage and selection operator Cox regression. The test data set and gene expression omnibus (GEO) data set were used to validate this signature. RESULTS We identified six candidate genes, namely, FOXL2NB, PCOLCE2, SPINK6, ULBP2, KCNJ18, and RFPL1, and, using a six-gene model, predicted the risk of death of head and neck squamous cell carcinoma in The Cancer Genome Atlas. At a selected cutoff, patients were clustered into low- and high-risk groups. The OS curves of the two groups of patients had significant differences, and the time-dependent receiver operating characteristics of OS, disease-specific survival (DSS), and progression-free survival (PFS) were as high as 0.766, 0.731, and 0.623, respectively. Then, the test data set and the GEO data set were used to evaluate our model, and we found that the OS time in the high-risk group was significantly shorter than in the low-risk group in both data sets, and the receiver operating characteristics of test data set were 0.669, 0.675, and 0.614, respectively. Furthermore, univariate and multivariate Cox regression analyses showed that the risk score was independent of clinicopathological features. CONCLUSION The six-gene model could predict the OS of HNSCC patients and improve therapeutic decision-making.
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Affiliation(s)
- Saisai Tian
- Department of Phytochemistry, School of Pharmacy, Second Military Medical University, Shanghai 200433, People's Republic of China,
| | - Guofeng Meng
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, People's Republic of China,
| | - Weidong Zhang
- Department of Phytochemistry, School of Pharmacy, Second Military Medical University, Shanghai 200433, People's Republic of China,
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, People's Republic of China,
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23
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Wang L, Dong G, Xia W, Mao Q, Wang A, Chen B, Ma W, Wu Y, Xu L, Jiang F. Integrative analysis of differential genes and identification of a "2-gene score" associated with survival in esophageal squamous cell carcinoma. Thorac Cancer 2018; 10:60-70. [PMID: 30421504 PMCID: PMC6312844 DOI: 10.1111/1759-7714.12902] [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: 08/26/2018] [Revised: 09/27/2018] [Accepted: 09/28/2018] [Indexed: 02/01/2023] Open
Abstract
Background Developments in high‐throughput genomic technologies have led to improved understanding of the molecular underpinnings of esophageal squamous cell carcinoma (ESCC). However, there is currently no model that combines the clinical features and gene expression signatures to predict outcomes. Methods We obtained data from the GSE53625 database of Chinese ESCC patients who had undergone surgical treatment. The R packages, Limma and WGCNA, were used to identify and construct a co‐expression network of differentially expressed genes, respectively. The Cox regression model was used, and a nomogram prediction model was constructed. Results A total of 3654 differentially expressed genes were identified. Bioinformatics enrichment analysis was conducted. Multivariate analysis of the clinical cohort revealed that age and adjuvant therapy were independent factors for survival, and these were entered into the clinical nomogram. After integrating the gene expression profiles, we identified a “2‐gene score” associated with overall survival. The combinational model is composed of clinical data and gene expression profiles. The C‐index of the combined nomogram for predicting survival was statistically higher than the clinical nomogram. The calibration curve revealed that the combined nomogram and actual observation showed better prediction accuracy than the clinical nomogram alone. Conclusions The integration of gene expression signatures and clinical variables produced a predictive model for ESCC that performed better than those based exclusively on clinical variables. This approach may provide a novel prediction model for ESCC patients after surgery.
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Affiliation(s)
- Lin Wang
- Department of Thoracic Surgery, Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & Nanjing Medical University Affiliated Cancer Hospital, Nanjing, China.,Department of The Fourth Clinical College, Nanjing Medical University, Nanjing, China.,Department of Hematology and Oncology, Department of Geriatric Lung Cancer Laboratory, The Affiliated Geriatric Hospital of Nanjing Medical University, Nanjing, China
| | - Gaochao Dong
- Department of Thoracic Surgery, Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & Nanjing Medical University Affiliated Cancer Hospital, Nanjing, China
| | - Wenjie Xia
- Department of Thoracic Surgery, Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & Nanjing Medical University Affiliated Cancer Hospital, Nanjing, China.,Department of The Fourth Clinical College, Nanjing Medical University, Nanjing, China
| | - Qixing Mao
- Department of Thoracic Surgery, Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & Nanjing Medical University Affiliated Cancer Hospital, Nanjing, China.,Department of The Fourth Clinical College, Nanjing Medical University, Nanjing, China
| | - Anpeng Wang
- Department of Thoracic Surgery, Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & Nanjing Medical University Affiliated Cancer Hospital, Nanjing, China.,Department of The Fourth Clinical College, Nanjing Medical University, Nanjing, China
| | - Bing Chen
- Department of Thoracic Surgery, Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & Nanjing Medical University Affiliated Cancer Hospital, Nanjing, China.,Department of The Fourth Clinical College, Nanjing Medical University, Nanjing, China
| | - Weidong Ma
- Department of Thoracic Surgery, Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & Nanjing Medical University Affiliated Cancer Hospital, Nanjing, China.,Department of The Fourth Clinical College, Nanjing Medical University, Nanjing, China
| | - Yaqin Wu
- Department of Thoracic Surgery, Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & Nanjing Medical University Affiliated Cancer Hospital, Nanjing, China.,Department of The Fourth Clinical College, Nanjing Medical University, Nanjing, China
| | - Lin Xu
- Department of Thoracic Surgery, Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & Nanjing Medical University Affiliated Cancer Hospital, Nanjing, China
| | - Feng Jiang
- Department of Thoracic Surgery, Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & Nanjing Medical University Affiliated Cancer Hospital, Nanjing, China
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Guo J, Wang Z, Miao Y, Shen Y, Li M, Gong L, Wang H, He Y, Gao H, Liu Q, Li C, Zhang Y. A two‑circRNA signature predicts tumour recurrence in clinical non‑functioning pituitary adenoma. Oncol Rep 2018; 41:113-124. [PMID: 30542712 PMCID: PMC6278571 DOI: 10.3892/or.2018.6851] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 10/11/2018] [Indexed: 02/06/2023] Open
Abstract
Clinical non‑functioning pituitary adenoma (NFPA) accounts for >30% of all pituitary adenomas, and the recurrence rate is notably high. The ability to predict tumour recurrence during initial surgery will aid in determining if adjunctive therapy is required to reduce recurrence. With the aim of developing a circular RNA (circRNA) signature to improve prognosis prediction in NFPA, the present study examined the circRNA expression profiles in 73 patients with NFPA from Beijing Tiantan Hospital using high‑throughput RNA chip technology. The dataset was randomly separated into a training group and a test group using an R program. In the training group (n=37), a Cox proportional hazards regression model was used to analyse the genes associated with the recurrence and progression‑free survival (PFS) of patients with NFPA. Meanwhile, a random survival forest algorithm, Kaplan‑Meier and receiver operating characteristic curve (ROC) analyses were used to determine the multi‑circRNA signature with the largest area under the ROC curve (AUROC) and verify its efficacy in the test group (n=36). In the training and test groups, the signatures of two circRNAs (hsa_circ_0000066 and hsa_circ_0069707) were specifically associated with the PFS of patients with NFPA (log‑rank P<0.05). Furthermore, the two‑circRNA signature had a high prediction accuracy for tumour recurrence, with an AUROC of 0.87 and 0.67 in the training and test groups, respectively; and the discriminative power of the signature was greater compared with that of age. The present study is the first to suggest a circRNA signature with a clinical application value for predicting recurrence/progression in patients with NFPA.
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Affiliation(s)
- Jing Guo
- Department of Cell Biology, Beijing Neurosurgical Institute, Capital Medical University, Beijing 100050, P.R. China
| | - Zhuang Wang
- Department of Cell Biology, Beijing Neurosurgical Institute, Capital Medical University, Beijing 100050, P.R. China
| | - Yazhou Miao
- Department of Cell Biology, Beijing Neurosurgical Institute, Capital Medical University, Beijing 100050, P.R. China
| | - Yutao Shen
- Department of Cell Biology, Beijing Neurosurgical Institute, Capital Medical University, Beijing 100050, P.R. China
| | - Mingxuan Li
- Department of Cell Biology, Beijing Neurosurgical Institute, Capital Medical University, Beijing 100050, P.R. China
| | - Lei Gong
- Department of Cell Biology, Beijing Neurosurgical Institute, Capital Medical University, Beijing 100050, P.R. China
| | - Hongyun Wang
- Department of Cell Biology, Beijing Neurosurgical Institute, Capital Medical University, Beijing 100050, P.R. China
| | - Yue He
- Department of Cell Biology, Beijing Neurosurgical Institute, Capital Medical University, Beijing 100050, P.R. China
| | - Hua Gao
- Department of Cell Biology, Beijing Neurosurgical Institute, Capital Medical University, Beijing 100050, P.R. China
| | - Qian Liu
- Department of Cell Biology, Beijing Neurosurgical Institute, Capital Medical University, Beijing 100050, P.R. China
| | - Chuzhong Li
- Department of Cell Biology, Beijing Neurosurgical Institute, Capital Medical University, Beijing 100050, P.R. China
| | - Yazhuo Zhang
- Department of Cell Biology, Beijing Neurosurgical Institute, Capital Medical University, Beijing 100050, P.R. China
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25
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Kang K, Huang YH, Li HP, Guo SM. Expression of UCA1 and MALAT1 long-chain non-coding RNAs in esophageal squamous cell carcinoma tissues is predictive of patient prognosis. Arch Med Sci 2018; 14:752-759. [PMID: 30002691 PMCID: PMC6040126 DOI: 10.5114/aoms.2018.73713] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/10/2016] [Accepted: 02/18/2017] [Indexed: 12/25/2022] Open
Abstract
INTRODUCTION The long non-coding RNAs (lncRNAs) urothelial cancer associated 1 (UCA1) and metastasis associated lung adenocarcinoma transcript 1 (MALAT1) are known to impact cancer cell regulation. The aim of the present study was to determine the relationship between the expression of these lncRNAs in esophageal squamous cell carcinoma (ESCC) tissues and disease prognosis. MATERIAL AND METHODS The expression of UCA1 and MALAT1 lncRNAs was assessed in ESCC and adjacent carcinoma tissues (5 cm away from the tumor) and evaluated in relation to overall survival (OS) and disease-free survival (DFS) of patients. This prospective study included 100 ESCC patients who were admitted to the First Hospital of Yulin City between January 2007 and January 2014. RESULTS The expression levels of UCA1 and MALAT1 lncRNAs in ESCC tissues were significantly higher than those in adjacent carcinoma tissues, and there were statistically significant differences in TNM staging between the patients with high lncRNA expression and low lncRNA expression. The OS and DFS of patients with high UCA1 and MALAT1 lncRNA expression levels were significantly shorter than those with low expression levels. Furthermore, the OS and DFS of ESCC patients appeared to be correlated with TNM staging. CONCLUSIONS These results imply that the up-regulation of UCA1 and MALAT1 lncRNAs in ESCC tissues can impact the degree of tumor progression and is predictive of postoperative survival. Therefore, the expression levels of these lncRNAs can be used as measurement indexes to determine the prognosis of ESCC patients.
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Affiliation(s)
- Kai Kang
- Department of Gastroenterology, the First Hospital of Yulin City, Yulin, Shaanxi Province, China
| | - Yong-Hua Huang
- Department of Gastroenterology, Xingyuan Hospital of Yulin City, Shaanxi Province, Yulin, Shaanxi Province, China
| | - Hai-Peng Li
- Department of Gastroenterology, Xingyuan Hospital of Yulin City, Shaanxi Province, Yulin, Shaanxi Province, China
| | - Shu-Mei Guo
- Department of Gastroenterology, the First Hospital of Yulin City, Yulin, Shaanxi Province, China
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26
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Guo JC, Wu Y, Chen Y, Pan F, Wu ZY, Zhang JS, Wu JY, Xu XE, Zhao JM, Li EM, Zhao Y, Xu LY. Protein-coding genes combined with long noncoding RNA as a novel transcriptome molecular staging model to predict the survival of patients with esophageal squamous cell carcinoma. Cancer Commun (Lond) 2018; 38:4. [PMID: 29784063 PMCID: PMC5993132 DOI: 10.1186/s40880-018-0277-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 12/18/2017] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Esophageal squamous cell carcinoma (ESCC) is the predominant subtype of esophageal carcinoma in China. This study was to develop a staging model to predict outcomes of patients with ESCC. METHODS Using Cox regression analysis, principal component analysis (PCA), partitioning clustering, Kaplan-Meier analysis, receiver operating characteristic (ROC) curve analysis, and classification and regression tree (CART) analysis, we mined the Gene Expression Omnibus database to determine the expression profiles of genes in 179 patients with ESCC from GSE63624 and GSE63622 dataset. RESULTS Univariate cox regression analysis of the GSE63624 dataset revealed that 2404 protein-coding genes (PCGs) and 635 long non-coding RNAs (lncRNAs) were associated with the survival of patients with ESCC. PCA categorized these PCGs and lncRNAs into three principal components (PCs), which were used to cluster the patients into three groups. ROC analysis demonstrated that the predictive ability of PCG-lncRNA PCs when applied to new patients was better than that of the tumor-node-metastasis staging (area under ROC curve [AUC]: 0.69 vs. 0.65, P < 0.05). Accordingly, we constructed a molecular disaggregated model comprising one lncRNA and two PCGs, which we designated as the LSB staging model using CART analysis in the GSE63624 dataset. This LSB staging model classified the GSE63622 dataset of patients into three different groups, and its effectiveness was validated by analysis of another cohort of 105 patients. CONCLUSIONS The LSB staging model has clinical significance for the prognosis prediction of patients with ESCC and may serve as a three-gene staging microarray.
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Affiliation(s)
- Jin-Cheng Guo
- Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Chaoshan Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou, Guangdong 515041 P. R. China
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, Guangdong 515041 P. R. China
| | - Yang Wu
- Key Laboratory of Intelligent Information Processing, Advanced Computer Research Center, State Key Laboratory of Computer Architecture, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, 100190 P. R. China
| | - Yang Chen
- Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Chaoshan Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou, Guangdong 515041 P. R. China
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, Guangdong 515041 P. R. China
| | - Feng Pan
- Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Chaoshan Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou, Guangdong 515041 P. R. China
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, Guangdong 515041 P. R. China
| | - Zhi-Yong Wu
- Departments of Oncology Surgery, Shantou Central Hospital, Affiliated Shantou Hospital of Sun Yat-Sen University, Shantou, Guangdong 515041 P. R. China
| | - Jia-Sheng Zhang
- Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Chaoshan Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou, Guangdong 515041 P. R. China
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, Guangdong 515041 P. R. China
| | - Jian-Yi Wu
- Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Chaoshan Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou, Guangdong 515041 P. R. China
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, Guangdong 515041 P. R. China
| | - Xiu-E Xu
- Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Chaoshan Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou, Guangdong 515041 P. R. China
- Institute of Oncologic Pathology, Shantou University Medical College, Shantou, Guangdong 515041 P. R. China
| | - Jian-Mei Zhao
- Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Chaoshan Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou, Guangdong 515041 P. R. China
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, Guangdong 515041 P. R. China
| | - En-Min Li
- Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Chaoshan Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou, Guangdong 515041 P. R. China
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, Guangdong 515041 P. R. China
| | - Yi Zhao
- Key Laboratory of Intelligent Information Processing, Advanced Computer Research Center, State Key Laboratory of Computer Architecture, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, 100190 P. R. China
| | - Li-Yan Xu
- Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Chaoshan Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou, Guangdong 515041 P. R. China
- Institute of Oncologic Pathology, Shantou University Medical College, Shantou, Guangdong 515041 P. R. China
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27
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Huang GW, Xue YJ, Wu ZY, Xu XE, Wu JY, Cao HH, Zhu Y, He JZ, Li CQ, Li EM, Xu LY. A three-lncRNA signature predicts overall survival and disease-free survival in patients with esophageal squamous cell carcinoma. BMC Cancer 2018; 18:147. [PMID: 29409459 PMCID: PMC5801805 DOI: 10.1186/s12885-018-4058-6] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 01/28/2018] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Increasing evidence shows that dysregulated long non-coding RNAs (lncRNAs) can serve as potential biomarkers for cancer prognosis. However, lncRNA signatures, as potential prognostic biomarkers for esophageal squamous cell carcinoma (ESCC), have been seldom reported. METHODS Based on our previous transcriptome RNA sequencing analysis from 15 paired ESCC tissues and adjacent normal tissues, we selected 10 lncRNAs with high score rank and characterized the expression of those lncRNAs, by qRT-PCR, in 138 ESCC and paired adjacent normal samples. These 138 patients were divided randomly into training (n = 77) and test (n = 59) groups. A prognostic signature of lncRNAs was identified in the training group and validated in the test group and in an independent cohort (n = 119). Multivariable Cox regression analysis evaluated the independence of the signature in overall survival (OS) and disease-free survival (DFS) prediction. GO and KEGG pathway analysis, combined with cell transwell and proliferation assays, are applied to explore the function of the three lncRNAs. RESULTS A novel three-lncRNA signature, comprised of RP11-366H4.1.1 (ENSG00000248370), LINC00460 (ENSG00000233532) and AC093850.2 (ENSG00000230838), was identified. The signature classified patients into high-risk and low-risk groups with different overall survival (OS) and disease-free survival (DFS). For the training group, median OS: 23.1 months vs. 39.1 months, P < 0.001; median DFS: 15.2 months vs. 33.3 months, P < 0.001. For the test group, median OS: 23 months vs. 59 months, P < 0.001; median DFS: 16.4 months vs. 50.8 months, P < 0.001. For the independent cohort, median OS: 22.4 months vs. 60.4 months, P < 0.001). The signature indicates that patients in the high-risk group show poor OS and DFS, whereas patients with a low-risk group show significantly better outcome. The independence of the signature was validated by multivariable Cox regression analysis. GO and KEGG pathway analysis for 588 protein-coding genes-associated with the three lncRNAs indicated that the three lncRNAs were involved in tumorigenesis. In vitro assays further demonstrated that the three lncRNAs promoted the migration and proliferation of ESCC cells. CONCLUSIONS The three-lncRNA signature is a novel and potential predictor of OS and DFS for patients with ESCC.
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Affiliation(s)
- Guo-Wei Huang
- Institute of Oncologic Pathology, Shantou University Medical College, No. 22, Xinling Road, Shantou, Guangdong, 515041, China
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou, 515041, Guangdong, People's Republic of China
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, 515041, Guangdong, People's Republic of China
| | - Yu-Jie Xue
- Institute of Oncologic Pathology, Shantou University Medical College, No. 22, Xinling Road, Shantou, Guangdong, 515041, China
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, 515041, Guangdong, People's Republic of China
| | - Zhi-Yong Wu
- Institute of Oncologic Pathology, Shantou University Medical College, No. 22, Xinling Road, Shantou, Guangdong, 515041, China
- Departments of Oncology Surgery, Shantou Central Hospital, Affiliated Shantou Hospital of Sun Yat-sen University, Shantou, 515041, Guangdong, People's Republic of China
| | - Xiu-E Xu
- Institute of Oncologic Pathology, Shantou University Medical College, No. 22, Xinling Road, Shantou, Guangdong, 515041, China
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou, 515041, Guangdong, People's Republic of China
| | - Jian-Yi Wu
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou, 515041, Guangdong, People's Republic of China
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, 515041, Guangdong, People's Republic of China
| | - Hui-Hui Cao
- Institute of Oncologic Pathology, Shantou University Medical College, No. 22, Xinling Road, Shantou, Guangdong, 515041, China
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou, 515041, Guangdong, People's Republic of China
| | - Ying Zhu
- Institute of Oncologic Pathology, Shantou University Medical College, No. 22, Xinling Road, Shantou, Guangdong, 515041, China
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou, 515041, Guangdong, People's Republic of China
| | - Jian-Zhong He
- Institute of Oncologic Pathology, Shantou University Medical College, No. 22, Xinling Road, Shantou, Guangdong, 515041, China
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou, 515041, Guangdong, People's Republic of China
| | - Chun-Quan Li
- Institute of Oncologic Pathology, Shantou University Medical College, No. 22, Xinling Road, Shantou, Guangdong, 515041, China
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou, 515041, Guangdong, People's Republic of China
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing, 163319, Heilongjiang, People's Republic of China
| | - En-Min Li
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou, 515041, Guangdong, People's Republic of China.
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, 515041, Guangdong, People's Republic of China.
| | - Li-Yan Xu
- Institute of Oncologic Pathology, Shantou University Medical College, No. 22, Xinling Road, Shantou, Guangdong, 515041, China.
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou, 515041, Guangdong, People's Republic of China.
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Cai B, Zheng Y, Ma S, Xing Q, Wang X, Yang B, Yin G, Guan F. Long non‑coding RNA regulates hair follicle stem cell proliferation and differentiation through PI3K/AKT signal pathway. Mol Med Rep 2018; 17:5477-5483. [PMID: 29393477 DOI: 10.3892/mmr.2018.8546] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 12/15/2017] [Indexed: 11/06/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are defined as non-coding transcripts (>200 nucleotides) that serve important roles in the proliferation and differentiation of stem cells. Hair follicle stem cells (HFTs) have multidirectional differentiation potential and are able to differentiate into skin, hair follicles and sebaceous glands, serving a role in skin wound healing. The aim of the present study was to analyze the regulatory role of lncRNA AK015322 (IncRNA5322) in HFTs and the potential mechanism of IncRNA5322‑mediated differentiation of HFTs. The results demonstrated that lncRNA5322 transfection promoted proliferation and differentiation in HFTs. It was identified that lncRNA5322 transfection upregulated the expression and phosphorylation of phosphoinositide 3‑kinase (PI3K) and protein kinase B (AKT) in HFTs. It was also observed that lncRNA5322 transfection upregulated microRNA (miR)‑21 and miR‑21 agonist (agomir‑21) eliminated lncRNA5322‑induced expression and phosphorylation of PI3K and AKT. The present study also demonstrated that agomir‑21 blocked IncRNA5322‑induced expression and phosphorylation of PI3K and AKT in HFTs. The results indicated that agomir‑21 transfection also suppressed the IncRNA5322‑induced proliferation and differentiation of HFTs. In conclusion, the results of the present study suggest that lncRNA5322 is able to promote the proliferation and differentiation of HFTs by targeting the miR‑21‑mediated PI3K‑AKT signaling pathway in HFTs.
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Affiliation(s)
- Bingjie Cai
- Department of Dermatology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
| | - Yunpeng Zheng
- Department of Dermatology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
| | - Shanshan Ma
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan 450001, P.R. China
| | - Qu Xing
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan 450001, P.R. China
| | - Xinxin Wang
- Department of Dermatology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
| | - Bo Yang
- Department of Dermatology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
| | - Guangwen Yin
- Department of Dermatology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
| | - Fangxia Guan
- Department of Dermatology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
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Meng X, Jin-Cheng G, Jue Z, Quan-Fu M, Bin Y, Xu-Feng W. Protein-coding genes, long non-coding RNAs combined with microRNAs as a novel clinical multi-dimension transcriptome signature to predict prognosis in ovarian cancer. Oncotarget 2017; 8:72847-72859. [PMID: 29069830 PMCID: PMC5641173 DOI: 10.18632/oncotarget.20457] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Accepted: 07/11/2017] [Indexed: 02/05/2023] Open
Abstract
Ovarian cancer is prevalent in women which is usually diagnosed at an advanced stage with a high mortality rate. The aim of this study is to investigate protein-coding gene, long non-coding RNA, and microRNA associated with the prognosis of patients with ovarian serous carcinoma by mining data from TCGA (The Cancer Genome Atlas) public database. The clinical data of ovarian serous carcinoma patients was downloaded from TCGA database in September, 2016. The mean age and survival time of 407 patients with ovarian serous carcinoma were 59.71 ± 11.54 years and 32.98 ± 26.66 months. Cox's proportional hazards regression analysis was conducted to analyze genes that were significantly associated with the survival of ovarian serous carcinoma patients in the training group. Using the random survival forest algorithm, Kaplan-Meier and ROC analysis, we kept prognostic genes to construct the multi-dimensional transcriptome signature with max area under ROC curve (AUC) (0.69 in the training group and 0.62 in the test group). The selected signature composed by VAT1L, CALR, LINC01456, RP11-484L8.1, MIR196A1 and MIR148A, separated the training group patients into high-risk or low-risk subgroup with significantly different survival time (median survival: 35.3 months vs. 64.9 months, P < 0.001). The signature was validated in the test group showing similar prognostic values (median survival: 41.6 months in high-risk vs. 57.4 months in low-risk group, P=0.018). Chi-square test and multivariable Cox regression analysis showed that the signature was an independent prognostic factor for patients with ovarian serous carcinoma. Finally, we validated the expression of the genes experimentally.
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Affiliation(s)
- Xu Meng
- Department of Gynecology, Maternal and Child Health Hospital of Hubei Province, Wuhan, China
| | - Guo Jin-Cheng
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, China
| | - Zhang Jue
- Department of Gynecology, Maternal and Child Health Hospital of Hubei Province, Wuhan, China
| | - Ma Quan-Fu
- Department of Gynecology, Maternal and Child Health Hospital of Hubei Province, Wuhan, China
| | - Yan Bin
- Department of Gynecology, Maternal and Child Health Hospital of Hubei Province, Wuhan, China
| | - Wu Xu-Feng
- Department of Gynecology, Maternal and Child Health Hospital of Hubei Province, Wuhan, China
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