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Mehrotra M, Phadte P, Shenoy P, Chakraborty S, Gupta S, Ray P. Drug-Resistant Epithelial Ovarian Cancer: Current and Future Perspectives. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1452:65-96. [PMID: 38805125 DOI: 10.1007/978-3-031-58311-7_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Epithelial ovarian cancer (EOC) is a complex disease with diverse histological subtypes, which, based on the aggressiveness and course of disease progression, have recently been broadly grouped into type I (low-grade serous, endometrioid, clear cell, and mucinous) and type II (high-grade serous, high-grade endometrioid, and undifferentiated carcinomas) categories. Despite substantial differences in pathogenesis, genetics, prognosis, and treatment response, clinical diagnosis and management of EOC remain similar across the subtypes. Debulking surgery combined with platinum-taxol-based chemotherapy serves as the initial treatment for High Grade Serous Ovarian Carcinoma (HGSOC), the most prevalent one, and for other subtypes, but most patients exhibit intrinsic or acquired resistance and recur in short duration. Targeted therapies, such as anti-angiogenics (e.g., bevacizumab) and PARP inhibitors (for BRCA-mutated cancers), offer some success, but therapy resistance, through various mechanisms, poses a significant challenge. This comprehensive chapter delves into emerging strategies to address these challenges, highlighting factors like aberrant miRNAs, metabolism, apoptosis evasion, cancer stem cells, and autophagy, which play pivotal roles in mediating resistance and disease relapse in EOC. Beyond standard treatments, the focus of this study extends to alternate targeted agents, including immunotherapies like checkpoint inhibitors, CAR T cells, and vaccines, as well as inhibitors targeting key oncogenic pathways in EOC. Additionally, this chapter covers disease classification, diagnosis, resistance pathways, standard treatments, and clinical data on various emerging approaches, and advocates for a nuanced and personalized approach tailored to individual subtypes and resistance mechanisms, aiming to enhance therapeutic outcomes across the spectrum of EOC subtypes.
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Affiliation(s)
- Megha Mehrotra
- Imaging Cell Signalling & Therapeutics Lab, Advanced Centre for Treatment, Research and Education in Cancer-Tata Memorial Centre, Navi Mumbai, India
- Homi Bhabha National Institute, Mumbai, India
| | - Pratham Phadte
- Imaging Cell Signalling & Therapeutics Lab, Advanced Centre for Treatment, Research and Education in Cancer-Tata Memorial Centre, Navi Mumbai, India
- Homi Bhabha National Institute, Mumbai, India
| | - Priti Shenoy
- Imaging Cell Signalling & Therapeutics Lab, Advanced Centre for Treatment, Research and Education in Cancer-Tata Memorial Centre, Navi Mumbai, India
- Homi Bhabha National Institute, Mumbai, India
| | - Sourav Chakraborty
- Imaging Cell Signalling & Therapeutics Lab, Advanced Centre for Treatment, Research and Education in Cancer-Tata Memorial Centre, Navi Mumbai, India
- Homi Bhabha National Institute, Mumbai, India
| | - Sudeep Gupta
- Homi Bhabha National Institute, Mumbai, India
- Department of Medical Oncology, Tata Memorial Centre, Mumbai, India
| | - Pritha Ray
- Imaging Cell Signalling & Therapeutics Lab, Advanced Centre for Treatment, Research and Education in Cancer-Tata Memorial Centre, Navi Mumbai, India.
- Homi Bhabha National Institute, Mumbai, India.
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Yue C, Lin B, Sun X, Xu X, Zhou C, Fan J. Autophagy-related risk signature based on CDNK2A to facilitate survival prediction of patients with endometrial cancer. J Gene Med 2024; 26:e3648. [PMID: 38282156 DOI: 10.1002/jgm.3648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Revised: 11/05/2023] [Accepted: 11/13/2023] [Indexed: 01/30/2024] Open
Abstract
BACKGROUND Autophagy plays an important role in immunity and inflammation. The present study aimed to explore the prognostic significance of autophagy-related genes (ARGs) in endometrial cancer (EC) using bioinformatics. METHODS The list of ARGs was obtained from the Human Autophagy Database. The differentially expressed ARGs (DEARGs) between the EC and normal endometrial tissue samples were screened from The Cancer Genome Atlas database. Cox regression analysis was performed on the DEARGs to screen the prognostic ARGs and construct risk signatures for overall survival (OS) and progression-free survival (PFS). The hub ARGs were identified from a protein-protein interaction network, and CDKN2A was obtained from the intersection of prognostic ARGs and hub ARGs. The association of CDKN2A expression with clinical characteristics and immune infiltration were analyzed. Finally, the role of CDKN2A in autophagy was confirmed in EC cell lines. RESULTS CDKN2A, PTK6 and DLC1 were used to establish risk signatures for predicting the survival of EC patients. Receiver operating characteristic curve analysis indicated that the risk signatures can accurately predict both OS and PFS. CDKN2A was the only hub prognostic ARG, and showed significant association with the age, survival status, grade, histological type, body mass index and FIGO (i.e. International Federation of Gynecology and Obstetrics) stage (p < 0.05). Furthermore, CDKN2A expression was also correlated with the infiltration of immune cells, indicating that CDKN2A might play a critical role in regulating the immune microenvironment and immune responses in EC. In addition, silencing of CDKN2A gene promoted autophagy in the HEC-1A cell line and upregulated the expression levels of autophagy-related proteins. CONCLUSIONS CDKN2A is a prognostic factor and therapeutic target in EC, and is likely associated with the tumor immune landscape and autophagy.
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Affiliation(s)
- Chaomin Yue
- Department of Obstetrics and Gynaecology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Baohua Lin
- Department of Obstetrics and Gynaecology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Xiang Sun
- Department of Obstetrics and Gynaecology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Xindi Xu
- China Medical University, Shenyang, Liaoning, China
| | - Chufan Zhou
- Department of Obstetrics and Gynaecology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Jiaying Fan
- Department of Obstetrics and Gynaecology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
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Zhao B, Pei L. A macrophage related signature for predicting prognosis and drug sensitivity in ovarian cancer based on integrative machine learning. BMC Med Genomics 2023; 16:230. [PMID: 37784081 PMCID: PMC10544447 DOI: 10.1186/s12920-023-01671-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 09/22/2023] [Indexed: 10/04/2023] Open
Abstract
BACKGROUND Ovarian cancer ranks the leading cause of gynecologic cancer-related death in the United States and the fifth most common cause of cancer-related mortality among American women. Increasing evidences have highlighted the vital role of macrophages M2/M1 proportion in tumor progression, prognosis and immunotherapy. METHODS Weighted gene co-expression network analysis (WGCNA) was performed to identify macrophages related markers. Integrative procedure including 10 machine learning algorithms were performed to develop a prognostic macrophage related signature (MRS) with TCGA, GSE14764, GSE140082 datasets. The role of MRS in tumor microenvironment (TME) and therapy response was evaluated with the data of CIBERSORT, MCPcounter, QUANTISEQ, XCELL, CIBERSORT-ABS, TIMER and EPIC, GSE91061 and IMvigor210 dataset. RESULTS The optimal MRS developed by the combination of CoxBoost and StepCox[forward] algorithm served as an independent risk factor in ovarian cancer. Compared with stage, grade and other established prognostic signatures, the current MRS had a better performance in predicting the overall survival rate of ovarian cancer patients. Low risk score indicated a higher TME score, higher level of immune cells, higher immunophenoscore, higher tumor mutational burden, lower TIDE score and lower IC50 value in ovarian cancer. The survival prediction nomogram had a good potential for clinical application in predicting the 1-, 3-, and 5-year overall survival rate of ovarian cancer patients. CONCLUSION All in all, the current study constructed a powerful prognostic MRS for ovarian cancer patients using 10 machine learning algorithms. This MRS could predict the prognosis and drug sensitivity in ovarian cancer.
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Affiliation(s)
- Bo Zhao
- Department of Obstetrics and Gynecology, General Hospital of Northern Theater Command, Shenyang, 110016, China
| | - Lipeng Pei
- Department of Obstetrics and Gynecology, General Hospital of Northern Theater Command, Shenyang, 110016, China.
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Abstract
Autophagy is a self-digestion process by which misfolded proteins and damaged organelles in eukaryotic cells are degraded to maintain cellular homeostasis. This process is involved in the tumorigenesis, metastasis, and chemoresistance of various tumors such as ovarian cancer (OC). Noncoding RNAs (ncRNAs), mainly including microRNAs, long noncoding RNAs, and circular RNAs, have been extensively investigated in cancer research for their roles in the regulation of autophagy. Recent studies have shown that in OC cells, ncRNAs can modulate the formation of autophagosomes, which affect tumor progression and chemoresistance. An understanding of the role of autophagy in OC progression, treatment, and prognosis is important, and the identification of the regulatory roles of ncRNAs in autophagy leads to intervention strategies for OC therapy. This review summarizes the role of autophagy in OC and discusses the role of ncRNA-mediated autophagy in OC, as an understanding of these roles may contribute to the development of potential therapeutic strategies for this disease.
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Affiliation(s)
- Cong Feng
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Heilongjiang University of Chinese Medicine, Harbin 150040, P.R. China
- Heilongjiang University of Chinese Medicine, Harbin 150040, P.R. China
| | - Xingxing Yuan
- Heilongjiang University of Chinese Medicine, Harbin 150040, P.R. China
- Department of Gastroenterology, Heilongjiang Academy of Traditional Chinese Medicine, Harbin 150001, P.R. China
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Wang RA, Zhang MY, Jiang YX, Wang XD, Qu JJ, Yue YL, Qu YQ. Autophagy-related tumor subtypes associated with significant gene expression profiles and immune cell infiltration signatures to reveal the prognosis of non-small cell lung cancer. J Cancer 2023; 14:1427-1442. [PMID: 37283800 PMCID: PMC10240669 DOI: 10.7150/jca.83097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 05/06/2023] [Indexed: 06/08/2023] Open
Abstract
Autophagy plays an important role in non-small cell lung cancer (NSCLC). We aimed to establish novel autophagy-related tumor subtypes to distinguish the prognosis of NSCLC. In this study, gene expression profiles, mutation data and clinical information obtained from the Cancer Genome Atlas. Kaplan Meier-plotter could evaluate prognostic value of autophagy-related genes. Consensus clustering revealed autophagy-related tumor subtypes. Gene expression profiles, mutation data and immune infiltration signatures were identified, oncogenic pathways and gene-drug interactions were performed according to the clusters. Finally, a total of 23 prognostic genes were screened and consensus clustering analysis divided the NSCLC into 2 clusters. The mutation signature showed that 6 genes are special. Immune infiltration signatures showed that higher fraction of immune cells was associated with cluster 1. The oncogenic pathways and gene-drug interactions also showed different patterns. In conclusion, autophagy-related tumor subtypes have different prognosis. Understanding the subtypes of NSCLC are helpful to accurately identify the NSCLC and personalized treatment.
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Affiliation(s)
- Rong-Ai Wang
- The Second Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
- Qilu Hospital of Shandong University, Jinan, Shandong, China
| | - Meng-Yu Zhang
- Department of Pulmonary and Critical Care Medicine, Laboratory of Basic Medical Sciences, Qilu Hospital of Shandong University, Jinan, Shandong, China
| | - Ying-Xiao Jiang
- Department of Pulmonary and Critical Care Medicine, Laboratory of Basic Medical Sciences, Qilu Hospital of Shandong University, Jinan, Shandong, China
| | - Xiao-Dong Wang
- Department of Pulmonary and Critical Care Medicine, Laboratory of Basic Medical Sciences, Qilu Hospital of Shandong University, Jinan, Shandong, China
| | - Jia-Jia Qu
- Department of Pulmonary and Critical Care Medicine, Laboratory of Basic Medical Sciences, Qilu Hospital of Shandong University, Jinan, Shandong, China
| | - Yue-Liang Yue
- Department of Pulmonary and Critical Care Medicine, Laboratory of Basic Medical Sciences, Qilu Hospital of Shandong University, Jinan, Shandong, China
| | - Yi-Qing Qu
- Department of Pulmonary and Critical Care Medicine, Laboratory of Basic Medical Sciences, Qilu Hospital of Shandong University, Jinan, Shandong, China
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Identification of an Individualized Prognostic Biomarker for Serous Ovarian Cancer: A Qualitative Model. Diagnostics (Basel) 2022; 12:diagnostics12123128. [PMID: 36553135 PMCID: PMC9777083 DOI: 10.3390/diagnostics12123128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 12/03/2022] [Accepted: 12/09/2022] [Indexed: 12/14/2022] Open
Abstract
Serous ovarian cancer is the most common type of ovarian epithelial cancer and usually has a poor prognosis. The objective of this study was to construct an individualized prognostic model for predicting overall survival in serous ovarian cancer. Based on the relative expression orderings (Ea > Eb/Ea ≤ Eb) of gene pairs closely associated with serous ovarian prognosis, we tried constructing a potential individualized qualitative biomarker by the greedy algorithm and evaluated the performance in independent validation datasets. We constructed a prognostic biomarker consisting of 20 gene pairs (SOV-P20). The overall survival between high- and low-risk groups stratified by SOV-P20 was statistically significantly different in the training and independent validation datasets from other platforms (p < 0.05, Wilcoxon test). The average area under the curve (AUC) values of the training and three validation datasets were 0.756, 0.590, 0.630, and 0.680, respectively. The distribution of most immune cells between high- and low-risk groups was quite different (p < 0.001, Wilcoxon test). The low-risk patients tended to show significantly better tumor response to chemotherapy than the high-risk patients (p < 0.05, Fisher’s exact test). SOV-P20 achieved the highest mean index of concordance (C-index) (0.624) compared with the other seven existing prognostic signatures (ranging from 0.511 to 0.619). SOV-P20 is a promising prognostic biomarker for serous ovarian cancer, which will be applicable for clinical predictive risk assessment.
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Deng J, Zhang Q, Lv L, Ma P, Zhang Y, Zhao N, Zhang Y. Identification of an autophagy-related gene signature for predicting prognosis and immune activity in pancreatic adenocarcinoma. Sci Rep 2022; 12:7006. [PMID: 35488119 PMCID: PMC9054801 DOI: 10.1038/s41598-022-11050-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 03/10/2022] [Indexed: 12/11/2022] Open
Abstract
Adenocarcinoma of the pancreas (PAAD) is a cancerous growth that deteriorates rapidly and has a poor prognosis. Researchers are investigating autophagy in PAAD to identify a new biomarker and treatment target. An autophagy-related gene (ARG) model for overall survival (OS) was constructed using multivariate Cox regression analyses. A cohort of the Cancer Genome Atlas (TCGA)-PAAD was used as the training group as a basis for model construction. This prediction model was validated with several external datasets. To evaluate model performance, the analysis with receiver operating characteristic curves (ROC) was performed. The Human Protein Atlas (HPA) and Cancer Cell Line Encyclopedia (CCLE) were investigated to validate the effects of ARGs expression on cancer cells. Comparing the levels of immune infiltration between high-risk and low-risk groups was finished through the use of CIBERSORT. The differentially expressed genes (DEGs) between the low-/high-risk groups were analyzed further via Gene Ontology biological process (GO-BP) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses, which were used to identify potential small-molecule compounds in Connectivity Map (CMap), followed by half-maximal inhibitory concentration (IC50) examination with PANC-1 cells. The risk score was finally calculated as follows: BAK1 × 0.34 + ITGA3 × 0.38 + BAG3 × 0.35 + APOL1 × 0.26-RAB24 × 0.67519. ITGA3 and RAB24 both emerged as independent prognostic factors in multivariate Cox regression. Each PAAD cohort had a significantly shorter OS in the high-risk group than in the low-risk group. The high-risk group exhibited infiltration of several immune cell types, including naive B cells (p = 0.003), plasma cells (p = 0.044), and CD8 T cells (nearly significant, p = 0.080). Higher infiltration levels of NK cells (p = 0.025), resting macrophages (p = 0.020), and mast cells (p = 0.007) were found in the high-risk group than the low-risk group. The in vitro and in vivo expression of signature ARGs was consistent in the CCLE and HPA databases. The top 3 enriched Gene Ontology biological processes (GO-BPs) were signal release, regulation of transsynaptic signaling, and modulation of chemical synaptic transmission, and the top 3 enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were MAPK, cAMP, and cell adhesion molecules. Four potential small-molecule compounds (piperacetazine, vinburnine, withaferin A and hecogenin) that target ARGs were also identified. Taking the results together, our research shows that the ARG signature may serve as a useful prognostic indicator and reveal potential therapeutic targets in patients with PAAD.
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Affiliation(s)
- Jiang Deng
- Institute of Health Service and Transfusion Medicine, Beijing, 100850, People's Republic of China
- Beijing Key Laboratory of Blood Safety and Supply Technologies, Beijing, 100850, People's Republic of China
| | - Qian Zhang
- Institute of Health Service and Transfusion Medicine, Beijing, 100850, People's Republic of China
- Beijing Key Laboratory of Blood Safety and Supply Technologies, Beijing, 100850, People's Republic of China
| | - Liping Lv
- Institute of Health Service and Transfusion Medicine, Beijing, 100850, People's Republic of China
- Beijing Key Laboratory of Blood Safety and Supply Technologies, Beijing, 100850, People's Republic of China
| | - Ping Ma
- Institute of Health Service and Transfusion Medicine, Beijing, 100850, People's Republic of China
- Beijing Key Laboratory of Blood Safety and Supply Technologies, Beijing, 100850, People's Republic of China
| | - Yangyang Zhang
- Institute of Health Service and Transfusion Medicine, Beijing, 100850, People's Republic of China
- Beijing Key Laboratory of Blood Safety and Supply Technologies, Beijing, 100850, People's Republic of China
| | - Ning Zhao
- Institute of Health Service and Transfusion Medicine, Beijing, 100850, People's Republic of China
- Beijing Key Laboratory of Blood Safety and Supply Technologies, Beijing, 100850, People's Republic of China
| | - Yanyu Zhang
- Institute of Health Service and Transfusion Medicine, Beijing, 100850, People's Republic of China.
- Beijing Key Laboratory of Blood Safety and Supply Technologies, Beijing, 100850, People's Republic of China.
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Shen W, Jiang W, Ye S, Sun M, Yang H, Shan B. Identification of epigenetic genes for predicting prognosis and immunotherapy response of ovarian cancer. Jpn J Clin Oncol 2022; 52:742-751. [PMID: 35435215 DOI: 10.1093/jjco/hyac051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 03/23/2022] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Epigenetic factors play a critical role in tumour development and progression. The aim of this study was to construct and validate a robust epigenetic gene set-based signature for predicting prognosis of ovarian cancer. METHODS By using LASSO Cox regression model, we screened out the most useful prognostic epigenetic factors and a prognostic signature was developed based on them. Survival receiver operating characteristic was used to test the prognostic accuracy of signature in training and validation sets. The associations between the risk scores and immune cell infiltration, tumour purity, immune checkpoint inhibitor genes expression were also assessed in ovarian cancer . RESULTS A total of 26 epigenetic factors were identified to develop the prognostic signature. In the training set, the prognosis of high-risk patients was strikingly poorer than that of low-risk patients (hazard ratio: 2.11, 95% confidence interval: 1.65-2.72, P < 0.001). Similar results were further observed in the internal validation set (hazard ratio: 1.69, 95% confidence interval: 1.07-2.63, P = 0.020) and external validation set (hazard ratio:1.95, 95% confidence interval: 1.41-2.69; P < 0.001). Survival receiver operating characteristic at 5 year showed the epigenetic signature (area under the curve = 0.700) performed better than other clinical features in predicting prognosis. Distinct difference in immune activation related pathways, immune cells infiltration, tumour purity reflected by immune and stromal score and immune checkpoint inhibitor genes gene expression was observed between high- and low-risk samples. CONCLUSIONS This study constructed an epigenetic signature that was capable of predicting postoperative outcomes and may also serve as potential biomarker for immunotherapy responses for ovarian cancer.
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Affiliation(s)
- Wenbin Shen
- Department of Gynecologic Oncology, Fudan Univeristy Shanghai Cancer Center, Shanghai.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, People's Republic of China
| | - Wei Jiang
- Department of Gynecologic Oncology, Fudan Univeristy Shanghai Cancer Center, Shanghai.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, People's Republic of China
| | - Shuang Ye
- Department of Gynecologic Oncology, Fudan Univeristy Shanghai Cancer Center, Shanghai.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, People's Republic of China
| | - Min Sun
- Department of Gynecologic Oncology, Fudan Univeristy Shanghai Cancer Center, Shanghai.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, People's Republic of China
| | - Huijuan Yang
- Department of Gynecologic Oncology, Fudan Univeristy Shanghai Cancer Center, Shanghai.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, People's Republic of China
| | - Boer Shan
- Department of Gynecologic Oncology, Fudan Univeristy Shanghai Cancer Center, Shanghai.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, People's Republic of China
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Zhang C, Li X, Li F, Li G, Niu G, Chen H, Ying GG, Huang M. Accurate prediction and further dissection of neonicotinoid elimination in the water treatment by CTS@AgBC using multihead attention-based convolutional neural network combined with the time-dependent Cox regression model. JOURNAL OF HAZARDOUS MATERIALS 2022; 423:127029. [PMID: 34479086 DOI: 10.1016/j.jhazmat.2021.127029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 08/17/2021] [Accepted: 08/23/2021] [Indexed: 06/13/2023]
Abstract
Imidacloprid (IMI), as the most widely used neonicotinoid insecticide, poses a serious threat to the water ecosystem due to the inefficient elimination in the traditional water treatment. Chitosan (CTS)-stabilized biochar (BC)-supported Ag nanoparticles (CTS@AgBC) are applied to eliminate the IMI in the water treatment effectively. Batch experiments depict that the modification of BC by CTS and Ag nanoparticles remarkably improve its adsorption performance. The pseudo-second-order and Elovich models have good performance in simulating the adsorption processes of CTS@AgBC and BC. This indicates that the chemical adsorption on real surfaces plays the dominant role in the adsorption of IMI by CTS@AgBC and BC. In addition, the multihead attention (MHA)-based convolutional neural network (CNN) combined with the time-dependent Cox regression model are initially applied to predict and dissect the adsorption elimination processes of IMI by CTS@AgBC. The proposed MHA-CNN model achieves more accurate concentration prediction of IMI than traditional models. According to influence weights by MHA module, biochar category, pH, and treatment temperature are considered the three dominant environmental variables to determine the IMI elimination processes. This study provides insights into roles of environmental variables in the elimination of IMI by CTS@AgBC and the accurate prediction of IMI concentration.
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Affiliation(s)
- Chao Zhang
- School of Civil Engineering & Transportation, South China University of Technology, Guangzhou 510640, PR China
| | - Xiaoyong Li
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, School of Environment, South China Normal University, Guangzhou 510006, PR China
| | - Feng Li
- School of Civil Engineering & Transportation, South China University of Technology, Guangzhou 510640, PR China.
| | - Gugong Li
- School of Civil Engineering & Transportation, South China University of Technology, Guangzhou 510640, PR China
| | - Guoqiang Niu
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, School of Environment, South China Normal University, Guangzhou 510006, PR China
| | - Hongyu Chen
- School of Civil Engineering & Transportation, South China University of Technology, Guangzhou 510640, PR China
| | - Guang-Guo Ying
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, School of Environment, South China Normal University, Guangzhou 510006, PR China
| | - Mingzhi Huang
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, School of Environment, South China Normal University, Guangzhou 510006, PR China; School of Resources and Environmental Sciences, Quanzhou Normal University, Quanzhou, Fujian 362000, PR China; SCNU Qingyuan Institute of Science and Technology Innovation Co, Ltd, Qingyuan 511517, China.
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10
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Bradley ST, Lee YS, Gurel Z, Kimple RJ. Autophagy awakens-the myriad roles of autophagy in head and neck cancer development and therapeutic response. Mol Carcinog 2022; 61:243-253. [PMID: 34780672 PMCID: PMC8799495 DOI: 10.1002/mc.23372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 11/07/2021] [Accepted: 11/08/2021] [Indexed: 02/03/2023]
Abstract
Autophagy is an evolutionarily conserved cell survival mechanism that degrades damaged proteins and organelles to generate cellular energy during times of stress. Recycling of these cellular components occurs in a series of sequential steps with multiple regulatory points. Mechanistic dysfunction can lead to a variety of human diseases and cancers due to the complexity of autophagy and its ability to regulate vital cellular functions. The role that autophagy plays in both the development and treatment of cancer is highly complex, especially given the fact that most cancer therapies modulate autophagy. This review aims to discuss the balance of autophagy in the development, progression, and treatment of head and neck cancer, as well as highlighting the need for a deeper understanding of what is still unknown about autophagy.
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Affiliation(s)
- Samantha T Bradley
- Department of Human Oncology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Yong-Syu Lee
- Department of Human Oncology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Zafer Gurel
- Department of Human Oncology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Randall J Kimple
- Department of Human Oncology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
- UW Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
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11
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Belotti Y, Lim EH, Lim CT. The Role of the Extracellular Matrix and Tumor-Infiltrating Immune Cells in the Prognostication of High-Grade Serous Ovarian Cancer. Cancers (Basel) 2022; 14:404. [PMID: 35053566 PMCID: PMC8773831 DOI: 10.3390/cancers14020404] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 01/05/2022] [Accepted: 01/11/2022] [Indexed: 12/12/2022] Open
Abstract
Ovarian cancer is the eighth global leading cause of cancer-related death among women. The most common form is the high-grade serous ovarian carcinoma (HGSOC). No further improvements in the 5-year overall survival have been seen over the last 40 years since the adoption of platinum- and taxane-based chemotherapy. Hence, a better understanding of the mechanisms governing this aggressive phenotype would help identify better therapeutic strategies. Recent research linked onset, progression, and response to treatment with dysregulated components of the tumor microenvironment (TME) in many types of cancer. In this study, using bioinformatic approaches, we identified a 19-gene TME-related HGSOC prognostic genetic panel (19 prognostic genes (PLXNB2, HMCN2, NDNF, NTN1, TGFBI, CHAD, CLEC5A, PLXNA1, CST9, LOXL4, MMP17, PI3, PRSS1, SERPINA10, TLL1, CBLN2, IL26, NRG4, and WNT9A) by assessing the RNA sequencing data of 342 tumors available in the TCGA database. Using machine learning, we found that specific patterns of infiltrating immune cells characterized each risk group. Furthermore, we demonstrated the predictive potential of our risk score across different platforms and its improved prognostic performance compared with other gene panels.
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Affiliation(s)
- Yuri Belotti
- Institute for Health Innovation and Technology, National University of Singapore, 14 Medical Drive, Singapore 117599, Singapore;
| | - Elaine Hsuen Lim
- Division of Medical Oncology, National Cancer Center Singapore, 11 Hospital Drive, Singapore 169610, Singapore;
| | - Chwee Teck Lim
- Institute for Health Innovation and Technology, National University of Singapore, 14 Medical Drive, Singapore 117599, Singapore;
- Department of Biomedical Engineering, National University of Singapore, 4 Engineering Drive 3, Singapore 117583, Singapore
- Mechanobiology Institute, National University of Singapore, 5A Engineering Drive 1, Singapore 117411, Singapore
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Zhang MY, Huo C, Liu JY, Shi ZE, Zhang WD, Qu JJ, Yue YL, Qu YQ. Identification of a Five Autophagy Subtype-Related Gene Expression Pattern for Improving the Prognosis of Lung Adenocarcinoma. Front Cell Dev Biol 2021; 9:756911. [PMID: 34869345 PMCID: PMC8636677 DOI: 10.3389/fcell.2021.756911] [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: 08/11/2021] [Accepted: 10/27/2021] [Indexed: 12/21/2022] Open
Abstract
Background: Autophagy plays an important role in lung adenocarcinoma (LUAD). In this study, we aimed to explore the autophagy-related gene (ARG) expression pattern and to identify promising autophagy-related biomarkers to improve the prognosis of LUAD. Methods: The gene expression profiles and clinical information of LUAD patients were downloaded from the Cancer Genome Atlas (TCGA), and validation cohort information was extracted from the Gene Expression Omnibus database. The Human Autophagy Database (HADb) was used to extract ARGs. Gene expression data were analyzed using the limma package and visualized using the ggplot2 package as well as the pheatmap package in R software. Functional enrichment analysis was also performed for the differentially expressed ARGs (DEARGs). Then, consensus clustering revealed autophagy-related tumor subtypes, and differentially expressed genes (DEGs) were screened according to the subtypes. Next, the univariate Cox and multivariate Cox regression analyses were used to identify independent prognostic ARGs. After overlapping DEGs and the independent prognostic ARGs, the predictive risk model was established and validated. Correlation analyses between ARGs and clinicopathological variables were also explored. Finally, the TIMER and TISIDB databases were used to further explore the correlation analysis between immune cell infiltration levels and the risk score as well as clinicopathological variables in the predictive risk model. Results: A total of 222 genes from the HADb were identified as ARGs, and 28 of the 222 genes were pooled as DEARGs. The most significant GO term was autophagy (p = 3.05E-07), and KEGG analysis results indicated that 28 DEARGs were significantly enriched in the ErbB signaling pathway (p < 0.001). Then, consensus clustering analysis divided the LUAD into two clusters, and a total of 168 DEGs were identified according to cluster subtypes. Then univariate and multivariate Cox regression analyses were used to identify 12 genes that could serve as independent prognostic indicators. After overlapping 168 DEGs and 12 genes, 10 genes (ATG4A, BAK1, CAPNS1, CCR2, CTSD, EIF2AK3, ITGB1, MBTPS2, SPHK1, ST13) were selected for the further exploration of the prognostic pattern. Survival analysis results indicated that this risk model identified the prognosis (p = 4.379E-10). Combined with the correlation analysis results between ARGs and clinicopathological variables, five ARGs were screened as prognostic genes. Among them, SPHK1 expression levels were positively correlated with CD4+ T cells and dendritic cell infiltration levels. Conclusions: In this study, we constructed a predictive risk model and identified a five autophagy subtype-related gene expression pattern to improve the prognosis of LUAD. Understanding the subtypes of LUAD is helpful to accurately characterize the LUAD and develop personalized treatment.
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Affiliation(s)
- Meng-Yu Zhang
- Department of Pulmonary and Critical Care Medicine, Qilu Hospital, Cheeloo College of Medicine, Shandong University; Shandong Key Laboratory of Infectious Respiratory Diseases, Jinan, China
| | - Chen Huo
- Department of Pulmonary and Critical Care Medicine, Qilu Hospital, Cheeloo College of Medicine, Shandong University; Shandong Key Laboratory of Infectious Respiratory Diseases, Jinan, China
| | - Jian-Yu Liu
- Department of Pulmonary and Critical Care Medicine, Qilu Hospital, Cheeloo College of Medicine, Shandong University; Shandong Key Laboratory of Infectious Respiratory Diseases, Jinan, China
| | - Zhuang-E Shi
- Department of Pulmonary and Critical Care Medicine, Qilu Hospital, Cheeloo College of Medicine, Shandong University; Shandong Key Laboratory of Infectious Respiratory Diseases, Jinan, China
| | - Wen-Di Zhang
- Department of Pulmonary and Critical Care Medicine, Qilu Hospital, Cheeloo College of Medicine, Shandong University; Shandong Key Laboratory of Infectious Respiratory Diseases, Jinan, China
| | - Jia-Jia Qu
- Department of Pulmonary and Critical Care Medicine, Qilu Hospital, Cheeloo College of Medicine, Shandong University; Shandong Key Laboratory of Infectious Respiratory Diseases, Jinan, China
| | - Yue-Liang Yue
- Department of Pulmonary and Critical Care Medicine, Qilu Hospital, Cheeloo College of Medicine, Shandong University; Shandong Key Laboratory of Infectious Respiratory Diseases, Jinan, China
| | - Yi-Qing Qu
- Department of Pulmonary and Critical Care Medicine, Qilu Hospital of Shandong University; Shandong Key Laboratory of Infectious Respiratory Diseases, Jinan, China
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Duan L, Cao L, Zhang R, Niu L, Yang W, Feng W, Zhou W, Chen J, Wang X, Li Y, Zhang Y, Liu J, Zhao Q, Fan D, Hong L. Development and validation of a survival model for esophageal adenocarcinoma based on autophagy-associated genes. Bioengineered 2021; 12:3434-3454. [PMID: 34252349 PMCID: PMC8806464 DOI: 10.1080/21655979.2021.1946235] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 06/16/2021] [Indexed: 12/15/2022] Open
Abstract
Autophagy is a highly conserved catabolic process which has been implicated in esophageal adenocarcinoma (EAC). We sought to investigate the biological functions and prognostic value of autophagy-related genes (ARGs) in EAC. A total of 21 differentially expressed ARGs were identified between EAC and normal samples. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis were then applied for the differentially expressed ARGs in EAC, and the protein-protein interaction (PPI) network was established. Cox survival analysis and Lasso regression analysis were performed to establish a prognostic prediction model based on nine overall survival (OS)-related ARGs (CAPN1, GOPC, TBK1, SIRT1, ARSA, BNIP1, ERBB2, NRG2, PINK1). The 9-gene prognostic signature significantly stratified patient outcomes in The Cancer Genome of Atlas (TCGA)-EAC cohort and was considered as an independently prognostic predictor for EAC patients. Moreover, Gene set enrichment analysis (GSEA) analyses revealed several important cellular processes and signaling pathways correlated with the high-risk group in EAC. This prognostic prediction model was confirmed in an independent validation cohort (GSE13898) from The Gene Expression Omnibus (GEO) database. We also developed a nomogram with a concordance index of 0.78 to predict the survival possibility of EAC patients by integrating the risk signature and clinicopathological features. The calibration curves substantiated favorable concordance between actual observation and nomogram prediction. Last but not least, Erb-B2 Receptor Tyrosine Kinase 2 (ERBB2), a member of the prognostic gene signature, was identified as a potential therapeutic target for EAC patients. To sum up, we established and verified a novel prognostic prediction model based on ARGs which could optimize the individualized survival prediction in EAC.
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Affiliation(s)
- Lili Duan
- Division of Digestive Surgery, State Key Laboratory of Cancer Biology and National Clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi’an, Shaanxi Province, China
| | - Lu Cao
- Department of Biomedical Engineering, Fourth Military Medical University, Xi’an, Shaanxi Province, China
| | - Rui Zhang
- Division of Digestive Surgery, State Key Laboratory of Cancer Biology and National Clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi’an, Shaanxi Province, China
| | - Liaoran Niu
- Division of Digestive Surgery, State Key Laboratory of Cancer Biology and National Clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi’an, Shaanxi Province, China
| | - Wanli Yang
- Division of Digestive Surgery, State Key Laboratory of Cancer Biology and National Clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi’an, Shaanxi Province, China
| | - Weibo Feng
- Division of Digestive Surgery, State Key Laboratory of Cancer Biology and National Clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi’an, Shaanxi Province, China
| | - Wei Zhou
- Division of Digestive Surgery, State Key Laboratory of Cancer Biology and National Clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi’an, Shaanxi Province, China
| | - Junfeng Chen
- Division of Digestive Surgery, State Key Laboratory of Cancer Biology and National Clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi’an, Shaanxi Province, China
| | - Xiaoqian Wang
- Division of Digestive Surgery, State Key Laboratory of Cancer Biology and National Clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi’an, Shaanxi Province, China
| | - Yiding Li
- Division of Digestive Surgery, State Key Laboratory of Cancer Biology and National Clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi’an, Shaanxi Province, China
| | - Yujie Zhang
- Division of Digestive Surgery, State Key Laboratory of Cancer Biology and National Clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi’an, Shaanxi Province, China
| | - Jinqiang Liu
- Division of Digestive Surgery, State Key Laboratory of Cancer Biology and National Clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi’an, Shaanxi Province, China
| | - Qingchuan Zhao
- Division of Digestive Surgery, State Key Laboratory of Cancer Biology and National Clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi’an, Shaanxi Province, China
| | - Daiming Fan
- Division of Digestive Surgery, State Key Laboratory of Cancer Biology and National Clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi’an, Shaanxi Province, China
| | - Liu Hong
- Division of Digestive Surgery, State Key Laboratory of Cancer Biology and National Clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi’an, Shaanxi Province, China
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Shen S, Wang R, Qiu H, Li C, Wang J, Xue J, Tang Q. Development of an Autophagy-Based and Stemness-Correlated Prognostic Model for Hepatocellular Carcinoma Using Bulk and Single-Cell RNA-Sequencing. Front Cell Dev Biol 2021; 9:743910. [PMID: 34820373 PMCID: PMC8606524 DOI: 10.3389/fcell.2021.743910] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 10/11/2021] [Indexed: 01/10/2023] Open
Abstract
Accumulating evidence has proved that autophagy serves as a tumor promoter in formed malignancies, and the autophagy-related prognostic signatures have been constructed as clinical tools to predict prognosis in many high-mortality cancers. Autophagy-related genes have participated in the development and metastasis of hepatocellular carcinoma (HCC), but the understanding of their prognostic value is limited. Thereafter, LIMMA and survival analysis were conducted in both ICGC and TCGA databases and a total of 10 hub autophagy-related genes, namely, NPC1, CDKN2A, RPTOR, SPHK1, HGS, BIRC5, SPNS1, BAK1, ATIC, and MAPK3, were collected. Then, GO, KEGG, correlation, consensus, and PCA analyses were utilized to reveal their potential targeted role in HCC treatment. Single-cell RNA-seq of cancer stem cells also indicated that there was a positive correlation between these genes and stemness. In parallel, we applied univariate, LASSO, and multivariate regression analyses to study the autophagy-related genes and finally proposed that ATIC and BIRC5 were the valuable prognostic indicators of HCC. The signature based on ATIC and BIRC5 exhibited moderate power for predicting the survival of HCC in the ICGC cohort, and its efficacy was further validated in the TCGA cohort. Taken together, we suggested that 10 aforementioned hub genes are promising therapeutic targets of HCC and the ATIC/BIRC5 prognostic signature is a practical prognostic indicator for HCC patients.
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Affiliation(s)
- Shengwei Shen
- Department of Hepatobiliary and Pancreatic Surgery, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Rui Wang
- Department of Hepatobiliary and Pancreatic Surgery, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Hua Qiu
- The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Chong Li
- Department of Hepatobiliary and Pancreatic Surgery, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Jinghan Wang
- Department of Hepatobiliary and Pancreatic Surgery, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Junli Xue
- Department of Oncology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Qinghe Tang
- Department of Hepatobiliary and Pancreatic Surgery, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
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Liu Z, Liu L, Guo C, Yu S, Meng L, Zhou X, Han X. Tumor suppressor gene mutations correlate with prognosis and immunotherapy benefit in hepatocellular carcinoma. Int Immunopharmacol 2021; 101:108340. [PMID: 34789428 DOI: 10.1016/j.intimp.2021.108340] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 10/29/2021] [Accepted: 10/31/2021] [Indexed: 01/03/2023]
Abstract
INTRODUCTION The tumor microenvironment (TME) has profound impacts on prognosis and immunotherapy. The TME can be altered by the genomic mutations on specific tumor-suppressor genes (TSG), thus, comprehending the association between TME and TSG in hepatocellular carcinoma (HCC) is imperative. METHODS With a total of 1699 HCC patients from 6 international multicenter cohorts, we delineated the mutational landscape of TSG and summarized the proportion of TSG mutated HCC in different countries. Using the genomic and transcriptomic data, we comprehensively explored the impacts of TSG mutations on TME and immunity in HCC. A dataset of 31 HCC patients from the cBioPortal database was utilized to evaluate the predictive value of TSG subtypes for immunotherapy response. RESULTS Interestingly, TSG non-mutated HCC will have more "immune-hot" tumors, and display the infiltration abundance of immune cells such as B cell, CD4+/CD8+T cell, and neutrophil. Moreover, TSG non-mutated HCC was characterized by the higher expression level of three immune checkpoints, including CD40, CD40LG, and TNFRSF4. In line with the TME characterization and immune checkpoint profiles, TSG non-mutated HCC displayed prolonged overall survival and relapse-free survival, notably, are more likely to respond to immune checkpoint inhibitors. CONCLUSIONS Our findings suggested the TSG subtypes could serve as a promising biomarker for guiding surveillance protocol and immunotherapeutic decisions for patients with HCC.
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Affiliation(s)
- Zaoqu Liu
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China; Interventional Institute of Zhengzhou University, Zhengzhou, Henan 450052, China; Interventional Treatment and Clinical Research Center of Henan Province, Zhengzhou, Henan 450052, China.
| | - Long Liu
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - ChunGuang Guo
- Department of Endovascular Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Sun Yu
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Lingfang Meng
- Department of Infection Management, The Second Affiliated Hospital of Zhengzhou University, China
| | - Xueliang Zhou
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China.
| | - Xinwei Han
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China; Interventional Institute of Zhengzhou University, Zhengzhou, Henan 450052, China; Interventional Treatment and Clinical Research Center of Henan Province, Zhengzhou, Henan 450052, China.
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Zhang D, Li Y, Yang S, Wang M, Yao J, Zheng Y, Deng Y, Li N, Wei B, Wu Y, Zhai Z, Dai Z, Kang H. Identification of a glycolysis-related gene signature for survival prediction of ovarian cancer patients. Cancer Med 2021; 10:8222-8237. [PMID: 34609082 PMCID: PMC8607265 DOI: 10.1002/cam4.4317] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 08/22/2021] [Accepted: 08/31/2021] [Indexed: 12/17/2022] Open
Abstract
Background Ovarian cancer (OV) is deemed the most lethal gynecological cancer in women. The aim of this study was to construct an effective gene prognostic model for predicting overall survival (OS) in patients with OV. Methods The expression profiles of glycolysis‐related genes (GRGs) and clinical data of patients with OV were extracted from The Cancer Genome Atlas (TCGA) database. Univariate, multivariate, and least absolute shrinkage and selection operator Cox regression analyses were conducted, and a prognostic signature based on GRGs was constructed. The predictive ability of the signature was analyzed using training and test sets. Results A gene risk signature based on nine GRGs (ISG20, CITED2, PYGB, IRS2, ANGPTL4, TGFBI, LHX9, PC, and DDIT4) was identified to predict the survival outcome of patients with OV. The signature showed a good prognostic ability for OV, particularly high‐grade OV, in the TCGA dataset, with areas under the curve (AUC) of 0.709 and 0.762 for 3‐ and 5‐year survival, respectively. Similar results were found in the test sets, and the AUCs of 3‐, 5‐year OS were 0.714 and 0.772 in the combined test set. And our signature was an independent prognostic factor. Moreover, a nomogram combining the prediction model and clinical factors was developed. Conclusion Our study established a nine‐GRG risk model and nomogram to better predict OS in patients with OV. The risk model represents a promising and independent prognostic predictor for patients with OV. Moreover, our study on GRGs could offer guidance for the elucidation of underlying mechanisms in future studies.
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Affiliation(s)
- Dai Zhang
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China.,Department of Thyroid, Breast and Vascular Surgery, Xijing Hospital, The Air Force Medical University, Xi'an, China
| | - Yiche Li
- Department of Tumor Surgery, Shaanxi Provincial People's Hospital, Xi'an, China
| | - Si Yang
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Meng Wang
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Jia Yao
- Department of Breast Surgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Yi Zheng
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Yujiao Deng
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Na Li
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Bajin Wei
- Department of Breast Surgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Ying Wu
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China.,Department of Breast Surgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Zhen Zhai
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Zhijun Dai
- Department of Breast Surgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Huafeng Kang
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
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Rashidieh B, Molakarimi M, Mohseni A, Tria SM, Truong H, Srihari S, Adams RC, Jones M, Duijf PHG, Kalimutho M, Khanna KK. Targeting BRF2 in Cancer Using Repurposed Drugs. Cancers (Basel) 2021; 13:cancers13153778. [PMID: 34359683 PMCID: PMC8345145 DOI: 10.3390/cancers13153778] [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: 05/31/2021] [Revised: 07/16/2021] [Accepted: 07/21/2021] [Indexed: 11/29/2022] Open
Abstract
Simple Summary BRF2, a subunit of the RNA polymerase III transcription complex, is upregulated in a wide variety of cancers and is a potential therapeutic target; however, no effective drugs are available to target BRF2. The upregulation of BRF2 in cancer cells confers survival via the prevention of oxidative stress-induced apoptosis. In this manuscript, we report the identification of potential BRF2 inhibitors through in silico drug repurposing screening. We further characterized bexarotene as a hit compound for the development of selective BRF2 inhibitors and provide experimental validation to support the repurposing of this FDA-approved drug as an agent to reduce the cellular levels of ROS and consequent BRF2 expression in cancers with elevated levels of oxidative stress. Abstract The overexpression of BRF2, a selective subunit of RNA polymerase III, has been shown to be crucial in the development of several types of cancers, including breast cancer and lung squamous cell carcinoma. Predominantly, BRF2 acts as a central redox-sensing transcription factor (TF) and is involved in rescuing oxidative stress (OS)-induced apoptosis. Here, we showed a novel link between BRF2 and the DNA damage response. Due to the lack of BRF2-specific inhibitors, through virtual screening and molecular dynamics simulation, we identified potential drug candidates that interfere with BRF2-TATA-binding Protein (TBP)-DNA complex interactions based on binding energy, intermolecular, and torsional energy parameters. We experimentally tested bexarotene as a potential BRF2 inhibitor. We found that bexarotene (Bex) treatment resulted in a dramatic decline in oxidative stress and Tert-butylhydroquinone (tBHQ)-induced levels of BRF2 and consequently led to a decrease in the cellular proliferation of cancer cells which may in part be due to the drug pretreatment-induced reduction of ROS generated by the oxidizing agent. Our data thus provide the first experimental evidence that BRF2 is a novel player in the DNA damage response pathway and that bexarotene can be used as a potential inhibitor to treat cancers with the specific elevation of oxidative stress.
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Affiliation(s)
- Behnam Rashidieh
- QIMR Berghofer Medical Research Institute, Herston, QLD 4006, Australia; (S.M.T.); (H.T.); (S.S.); (R.C.A.); (M.K.)
- Correspondence: (B.R.); (K.K.K.)
| | - Maryam Molakarimi
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University (TMU), Nasr Bridge, Tehran 14115-154, Iran; (M.M.); (A.M.)
| | - Ammar Mohseni
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University (TMU), Nasr Bridge, Tehran 14115-154, Iran; (M.M.); (A.M.)
| | - Simon Manuel Tria
- QIMR Berghofer Medical Research Institute, Herston, QLD 4006, Australia; (S.M.T.); (H.T.); (S.S.); (R.C.A.); (M.K.)
- School of Environment and Science, Griffith University, Nathan, QLD 4111, Australia
| | - Hein Truong
- QIMR Berghofer Medical Research Institute, Herston, QLD 4006, Australia; (S.M.T.); (H.T.); (S.S.); (R.C.A.); (M.K.)
| | - Sriganesh Srihari
- QIMR Berghofer Medical Research Institute, Herston, QLD 4006, Australia; (S.M.T.); (H.T.); (S.S.); (R.C.A.); (M.K.)
| | - Rachael C. Adams
- QIMR Berghofer Medical Research Institute, Herston, QLD 4006, Australia; (S.M.T.); (H.T.); (S.S.); (R.C.A.); (M.K.)
| | - Mathew Jones
- The University of Queensland Diamantina Institute, Faculty of Medicine, The University of Queensland, Brisbane, QLD 4102, Australia;
| | - Pascal H. G. Duijf
- Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Faculty of Health, Queensland University of Technology (QUT), Brisbane, QLD 4000, Australia;
- Centre for Data Science, Queensland University of Technology (QUT), Brisbane, QLD 4000, Australia
| | - Murugan Kalimutho
- QIMR Berghofer Medical Research Institute, Herston, QLD 4006, Australia; (S.M.T.); (H.T.); (S.S.); (R.C.A.); (M.K.)
| | - Kum Kum Khanna
- QIMR Berghofer Medical Research Institute, Herston, QLD 4006, Australia; (S.M.T.); (H.T.); (S.S.); (R.C.A.); (M.K.)
- Correspondence: (B.R.); (K.K.K.)
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Identification of autophagy-related risk signatures for the prognosis, diagnosis, and targeted therapy in cervical cancer. Cancer Cell Int 2021; 21:362. [PMID: 34238288 PMCID: PMC8268251 DOI: 10.1186/s12935-021-02073-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 07/02/2021] [Indexed: 12/24/2022] Open
Abstract
Background To rummage autophagy-related prognostic, diagnostic, and therapeutic biomarkers in cervical cancer (CC). Methods The RNA-sequence and clinical information were from the TCGA and GTEx databases. We operated Cox regression to determine signatures related to overall survival (OS) and recurrence-free survival (RFS) respectively. The diagnostic and therapeutic effectiveness of prognostic biomarkers were further explored. Results We identified nine (VAMP7, MTMR14, ATG4D, KLHL24, TP73, NAMPT, CD46, HGS, ATG4C) and three risk signatures (SERPINA1, HSPB8, SUPT20H) with prognostic values for OS and RFS respectively. Six risk signatures (ATG4C, ATG4D, CD46, TP73, SERPINA1, HSPB8) were selected for qPCR. We screened five prognostic signatures(ATG4C, CD46, HSPB8, MTMR14, NAMPT) with diagnostic function through the GEO database. Correlation between our models and treatment targets certificated the prognostic score provided a reference for precision medicine. Conclusions We constructed OS and RFS prognostic models in CC. Autophagy-related risk signatures might serve as diagnostic and therapeutic biomarkers. Supplementary Information The online version contains supplementary material available at 10.1186/s12935-021-02073-w.
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Duan J, Lei Y, Lv G, Liu Y, Zhao W, Yang Q, Su X, Song Z, Lu L, Shi Y. Identification of a novel autophagy signature for predicting survival in patients with lung adenocarcinoma. PeerJ 2021; 9:e11074. [PMID: 33976960 PMCID: PMC8067911 DOI: 10.7717/peerj.11074] [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: 05/01/2020] [Accepted: 02/17/2021] [Indexed: 01/22/2023] Open
Abstract
Background Lung adenocarcinoma (LUAD) is the most commonhistological lung cancer subtype, with an overall five-year survivalrate of only 17%. In this study, we aimed to identify autophagy-related genes (ARGs) and develop an LUAD prognostic signature. Methods In this study, we obtained ARGs from three databases and downloaded gene expression profiles from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) database. We used TCGA-LUAD (n = 490) for a training and testing dataset, and GSE50081 (n = 127) as the external validation dataset.The least absolute shrinkage and selection operator (LASSO) Cox and multivariate Cox regression models were used to generate an autophagy-related signature. We performed gene set enrichment analysis (GSEA) and immune cell analysis between the high- and low-risk groups. A nomogram was built to guide the individual treatment for LUAD patients. Results We identified a total of 83 differentially expressed ARGs (DEARGs) from the TCGA-LUAD dataset, including 33 upregulated DEARGs and 50 downregulated DEARGs, both with thresholds of adjusted P < 0.05 and |Fold change| > 1.5. Using LASSO and multivariate Cox regression analyses, we identified 10 ARGs that we used to build a prognostic signature with areas under the curve (AUCs) of 0.705, 0.715, and 0.778 at 1, 3, and 5 years, respectively. Using the risk score formula, the LUAD patients were divided into low- or high-risk groups. Our GSEA results suggested that the low-risk group were enriched in metabolism and immune-related pathways, while the high-risk group was involved in tumorigenesis and tumor progression pathways. Immune cell analysis revealed that, when compared to the high-risk group, the low-risk group had a lower cell fraction of M0- and M1- macrophages, and higher CD4 and PD-L1 expression levels. Conclusion Our identified robust signature may provide novel insight into underlying autophagy mechanisms as well as therapeutic strategies for LUAD treatment.
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Affiliation(s)
- Jin Duan
- Department of Geriatric Thoracic Surgery, The First Hospital of Kunming Medical University, Kunming City, Yunnan Province, P.R. China
| | - Youming Lei
- Department of Geriatric Thoracic Surgery, The First Hospital of Kunming Medical University, Kunming City, Yunnan Province, P.R. China
| | - Guoli Lv
- Department of Geriatric Thoracic Surgery, The First Hospital of Kunming Medical University, Kunming City, Yunnan Province, P.R. China
| | - Yinqiang Liu
- Department of Geriatric Thoracic Surgery, The First Hospital of Kunming Medical University, Kunming City, Yunnan Province, P.R. China
| | - Wei Zhao
- Department of Geriatric Thoracic Surgery, The First Hospital of Kunming Medical University, Kunming City, Yunnan Province, P.R. China
| | - Qingmei Yang
- Department of Geriatric Thoracic Surgery, The First Hospital of Kunming Medical University, Kunming City, Yunnan Province, P.R. China
| | - Xiaona Su
- Department of Cancer Center, Daping Hospital, Army Medical University, Chongqing, China
| | | | - Leilei Lu
- Origimed Co. Ltd., Shanghai, P.R. China
| | - Yunfei Shi
- Department of Geriatric Thoracic Surgery, The First Hospital of Kunming Medical University, Kunming City, Yunnan Province, P.R. China
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Long noncoding RNA GAS8-AS1: A novel biomarker in human diseases. Biomed Pharmacother 2021; 139:111572. [PMID: 33838502 DOI: 10.1016/j.biopha.2021.111572] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 03/21/2021] [Accepted: 03/31/2021] [Indexed: 12/16/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) represent a group of ncRNAs with more than 200 nucleotides. These RNAs can specifically regulate gene expression at both the transcriptional and the post-transcriptional levels, and increasing evidence indicates that they play vital roles in a variety of disease-related cellular processes. The lncRNA GAS8 antisense RNA 1 (GAS8-AS1, also known as C16orf3) is located in the second intron of GAS8 and has been reported to be both abnormally expressed in several diseases and closely correlated with many clinical characteristics. GAS8-AS1 has been shown to affect many biological functions, including cell proliferation, migration, invasiveness, and autophagy using several signaling pathways. In this review, we have summarized current studies on GAS8-AS1 roles in disease and discuss its potential clinical utility. GAS8-AS1 may be a promising biomarker for both diagnoses and prognoses, and a novel target for many disease therapies.
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Li H, Wu N, Liu ZY, Chen YC, Cheng Q, Wang J. Development of a novel transcription factors-related prognostic signature for serous ovarian cancer. Sci Rep 2021; 11:7207. [PMID: 33785763 PMCID: PMC8010122 DOI: 10.1038/s41598-021-86294-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 03/12/2021] [Indexed: 12/20/2022] Open
Abstract
Growing evidence suggest that transcription factors (TFs) play vital roles in serous ovarian cancer (SOC). In the present study, TFs mRNA expression profiles of 564 SOC subjects in the TCGA database, and 70 SOC subjects in the GEO database were screened. A 17-TFs related prognostic signature was constructed using lasso cox regression and validated in the TCGA and GEO cohorts. Consensus clustering analysis was applied to establish a cluster model. The 17-TFs related prognostic signature, risk score and cluster models were effective at accurately distinguishing the overall survival of SOC. Analysis of genomic alterations were used to elaborate on the association between the 17-TFs related prognostic signature and genomic aberrations. The GSEA assay results suggested that there was a significant difference in the inflammatory and immune response pathways between the high-risk and low-risk score groups. The potential immune infiltration, immunotherapy, and chemotherapy responses were analyzed due to the significant difference in the regulation of lymphocyte migration and T cell-mediated cytotoxicity between the two groups. The results indicated that patients with low-risk score were more likely to respond anti-PD-1, etoposide, paclitaxel, and veliparib but not to gemcitabine, doxorubicin, docetaxel, and cisplatin. Also, the prognostic nomogram model revealed that the risk score was a good prognostic indicator for SOC patients. In conclusion, we explored the prognostic values of TFs in SOC and developed a 17-TFs related prognostic signature to predict the survival of SOC patients.
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Affiliation(s)
- He Li
- The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University/Hunan Cancer Hospital, Changsha, Changsha, 410008, Hunan, People's Republic of China
| | - Nayiyuan Wu
- The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University/Hunan Cancer Hospital, Changsha, Changsha, 410008, Hunan, People's Republic of China
| | - Zhao-Yi Liu
- The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University/Hunan Cancer Hospital, Changsha, Changsha, 410008, Hunan, People's Republic of China
| | - Yong-Chang Chen
- The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University/Hunan Cancer Hospital, Changsha, Changsha, 410008, Hunan, People's Republic of China
| | - Quan Cheng
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China.
| | - Jing Wang
- The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University/Hunan Cancer Hospital, Changsha, Changsha, 410008, Hunan, People's Republic of China.
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Development of an Autophagy-Related Gene Prognostic Model and Nomogram for Estimating Renal Clear Cell Carcinoma Survival. JOURNAL OF ONCOLOGY 2021; 2021:8810849. [PMID: 33679977 PMCID: PMC7910047 DOI: 10.1155/2021/8810849] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 12/29/2020] [Accepted: 01/24/2021] [Indexed: 02/06/2023]
Abstract
Background Kidney renal clear cell carcinoma (KIRC) is a fatal malignancy of the urinary system. Autophagy is implicated in KIRC occurrence and development. Here, we evaluated the prognostic value of autophagy-related genes (ARGs) in kidney renal clear cell carcinoma. Materials and Methods We analyzed RNA sequencing and clinical KIRC patient data obtained from TCGA and ICGC to develop an ARG prognostic signature. Differentially expressed ARGs were further evaluated by functional assessment and bioinformatic analysis. Next, ARG score was determined in 215 KIRC patients using univariable Cox and LASSO regression analyses. An ARG nomogram was built based on multivariable Cox analysis. The prognosis nomogram model based on the ARG signatures and clinicopathological information was evaluated for discrimination, calibration, and clinical usefulness. Results A total of 47 differentially expressed ARGs were identified. Of these, 8 candidates that significantly correlated with KIRC overall survival were subjected to LASSO analysis and an ARG score built. Functional enrichment and bioinformatic analysis were used to reveal the differentially expressed ARGs in cancer-related biological processes and pathways. Multivariate Cox analysis was used to integrate the ARG nomogram with the ARG signature and clinicopathological information. The nomogram exhibited proper calibration and discrimination (C-index = 0.75, AUC = >0.7). Decision curve analysis also showed that the nomogram was clinically useful. Conclusions KIRC patients and doctors could benefit from ARG nomogram use in clinical practice.
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Guo Y, Yang PT, Wang ZW, Xu K, Kou WH, Luo H. Identification of Three Autophagy-Related Long Non-Coding RNAs as a Novel Head and Neck Squamous Cell Carcinoma Prognostic Signature. Front Oncol 2021; 10:603864. [PMID: 33575215 PMCID: PMC7871905 DOI: 10.3389/fonc.2020.603864] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 11/09/2020] [Indexed: 01/08/2023] Open
Abstract
Head and neck squamous cell carcinoma (HNSCC) has a poor prognosis. Considerable evidence indicates that autophagy and non-coding RNA play essential roles in the biological processes involved in cancers, but associations between autophagy-related long non-coding RNAs (lncRNAs) and HNSCC remain unclear. In the present study, HNSCC RNA sequences and autophagy-related gene data were extracted from The Cancer Genome Atlas database and the Human Autophagy Database. A total of 1,153 autophagy-related lncRNAs were selected via calculating Pearson’s correlation coefficient. Three prognosis-related autophagy lncRNAs were identified via univariate Cox regression, least absolute shrinkage and selection operator analysis, and multivariate Cox regression analysis. We also constructed a prognostic model based on these autophagy-related lncRNAs and evaluated its ability to accurately and independently predict the prognosis of HNSCC patients. The area under the curve (AUC) was 0.864 (3-year) and 0.836 (5-year), and our model can independently predict the prognosis of HNSCC. The prognostic value of the three autophagy lncRNAs was confirmed via analysis of samples from five databases. To further identify the functions of the three lncRNAs, a co-expression network was constructed and pathway analysis was performed. In that analysis the lncRNAs were correlated with 189 related genes and 20 autophagy-related genes, and these lncRNAs mainly involved homologous recombination, the Fanconi anemia pathway, the autophagy-related pathway, and immune-related pathways. In addition, we validated the expression levels of three lncRNAs and autophagy markers (ATG12, BECN1, and MAP1LC3B) based on TIMER, Oncomine, and HPA database analysis. Our results indicated that TTTY15 was increased in HPV positive and HPV negative HNSCC patients, and three autophagy markers were up-regulated in all HNSCCC patients. Lastly, association between three lncRNAs and autophagy markers was performed, and our results showed that TTTY15 and MIF-AS1 were associated with autophagy markers. Collectively, these results suggested that three autophagy-related lncRNAs have prognostic value in HNSCC patients.
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Affiliation(s)
- Ya Guo
- Department of Radiation Oncology, Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, China
| | - Peng Tao Yang
- Department of Radiation Oncology, Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, China
| | - Zhong Wei Wang
- Department of Radiation Oncology, Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, China
| | - Kun Xu
- Department of Radiation Oncology, Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, China
| | - Wei Hua Kou
- Department of Radiation Oncology, Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, China
| | - Heng Luo
- Department of Radiation Oncology, Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, China
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Xu L, Qiao Y, Zheng Q. Identification of an autophagy-related gene expression signature for colorectal cancer. ALL LIFE 2021. [DOI: 10.1080/26895293.2021.1872716] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Affiliation(s)
- Lijun Xu
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Inflammatory Bowel Disease Research Center, Shanghai Institute of Digestive Disease, Renji Hospital, School of Medicine Shanghai Jiao Tong University, Shanghai, People’s Republic of China
| | - Yuqi Qiao
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Inflammatory Bowel Disease Research Center, Shanghai Institute of Digestive Disease, Renji Hospital, School of Medicine Shanghai Jiao Tong University, Shanghai, People’s Republic of China
| | - Qing Zheng
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Inflammatory Bowel Disease Research Center, Shanghai Institute of Digestive Disease, Renji Hospital, School of Medicine Shanghai Jiao Tong University, Shanghai, People’s Republic of China
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25
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Guo E, Wu C, Ming J, Zhang W, Zhang L, Hu G. The Clinical Significance of DNA Damage Repair Signatures in Clear Cell Renal Cell Carcinoma. Front Genet 2021; 11:593039. [PMID: 33488669 PMCID: PMC7820869 DOI: 10.3389/fgene.2020.593039] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 12/04/2020] [Indexed: 12/16/2022] Open
Abstract
DNA damage repair plays an important role in cancer’s initiation and progression, and in therapeutic resistance. The prognostic potential of damage repair indicators was studied in the case of clear cell renal cell carcinoma (ccRCC). Gene expression profiles of the disease were downloaded from cancer genome databases and gene ontology was applied to the DNA repair-related genes. Twenty-six differentially expressed DNA repair genes were identified, and regression analysis was used to identify those with prognostic potential and to construct a risk model. The model accurately predicted patient outcomes and distinguished among patients with different expression levels of immune evasion genes. The data indicate that DNA repair genes can be valuable for predicting the progression of clear cell renal cell carcinoma and the clinical benefits of immunotherapy.
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Affiliation(s)
- Ergang Guo
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Hubei, Wuhan
| | - Cheng Wu
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Hubei, Wuhan
| | - Jun Ming
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Hubei, Wuhan
| | - Wei Zhang
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Hubei, Wuhan
| | - Linli Zhang
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Hubei, Wuhan
| | - Guoqing Hu
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Hubei, Wuhan
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Zhang Q, Lv L, Ma P, Zhang Y, Deng J, Zhang Y. Identification of an Autophagy-Related Pair Signature for Predicting Prognoses and Immune Activity in Pancreatic Adenocarcinoma. Front Immunol 2021; 12:743938. [PMID: 34956177 PMCID: PMC8695429 DOI: 10.3389/fimmu.2021.743938] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 11/10/2021] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Pancreatic adenocarcinoma (PAAD) spreads quickly and has a poor prognosis. Autophagy research on PAAD could reveal new biomarkers and targets for diagnosis and treatment. METHODS Autophagy-related genes were translated into autophagy-related gene pairs, and univariate Cox regression was performed to obtain overall survival (OS)-related IRGPs (P<0.001). LASSO Cox regression analyses were performed to construct an autophagy-related gene pair (ARGP) model for predicting OS. The Cancer Genome Atlas (TCGA)-PAAD cohort was set as the training group for model construction. The model predictive value was validated in multiple external datasets. Receiver operating characteristic (ROC) curves were used to evaluate model performance. Tumor microenvironments and immune infiltration were compared between low- and high-risk groups with ESTIMATE and CIBERSORT. Differentially expressed genes (DEGs) between the groups were further analyzed by Gene Ontology biological process (GO-BP) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses and used to identify potential small-molecule compounds in L1000FWD. RESULTS Risk scores were calculated as follows: ATG4B|CHMP4C×(-0.31) + CHMP2B|MAP1LC3B×(0.30) + CHMP6|RIPK2 ×(-0.33) + LRSAM1|TRIM5×(-0.26) + MAP1LC3A|PAFAH1B2×(-0.15) + MAP1LC3A|TRIM21×(-0.08) + MET|MFN2×(0.38) + MET|MTDH×(0.47) + RASIP1|TRIM5×(-0.23) + RB1CC1|TPCN1×(0.22). OS was significantly shorter in the high-risk group than the low-risk group in each PAAD cohort. The ESTIMATE analysis showed no difference in stromal scores but a significant difference in immune scores (p=0.0045) and ESTIMATE scores (p=0.014) between the groups. CIBERSORT analysis showed higher naive B cell, Treg cell, CD8 T cell, and plasma cell levels in the low-risk group and higher M1 and M2 macrophage levels in the high-risk group. In addition, the results showed that naive B cells (r=-0.32, p<0.001), Treg cells (r=-0.31, p<0.001), CD8 T cells (r=-0.24, p=0.0092), and plasma cells (r=-0.2, p<0.026) were statistically correlated with the ARGP risk score. The top 3 enriched GO-BPs were signal release, regulation of transsynaptic signaling, and modulation of chemical synaptic transmission, and the top 3 enriched KEGG pathways were the insulin secretion, dopaminergic synapse, and NF-kappa B signaling pathways. Several potential small-molecule compounds targeting ARGs were also identified. CONCLUSION Our results demonstrate that the ARGP-based model may be a promising prognostic indicator for identifying drug targets in patients with PAAD.
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Affiliation(s)
- Qian Zhang
- Institute of Health Service and Transfusion Medicine, Beijing, China
- Beijing Key Laboratory of Blood Safety and Supply Technologies, Beijing, China
| | - Liping Lv
- Institute of Health Service and Transfusion Medicine, Beijing, China
- Beijing Key Laboratory of Blood Safety and Supply Technologies, Beijing, China
| | - Ping Ma
- Institute of Health Service and Transfusion Medicine, Beijing, China
- Beijing Key Laboratory of Blood Safety and Supply Technologies, Beijing, China
| | - Yangyang Zhang
- Institute of Health Service and Transfusion Medicine, Beijing, China
- Beijing Key Laboratory of Blood Safety and Supply Technologies, Beijing, China
| | - Jiang Deng
- Institute of Health Service and Transfusion Medicine, Beijing, China
- Beijing Key Laboratory of Blood Safety and Supply Technologies, Beijing, China
- *Correspondence: Jiang Deng, ; Yanyu Zhang,
| | - Yanyu Zhang
- Institute of Health Service and Transfusion Medicine, Beijing, China
- Beijing Key Laboratory of Blood Safety and Supply Technologies, Beijing, China
- *Correspondence: Jiang Deng, ; Yanyu Zhang,
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Kucuk B, Kibar B, Cacan E. A broad analysis in clinical and in vitro models on regulator of G-protein signalling 10 regulation that is associated with ovarian cancer progression and chemoresistance. Cell Biochem Funct 2020; 39:413-422. [PMID: 33354811 DOI: 10.1002/cbf.3607] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 11/20/2020] [Accepted: 12/13/2020] [Indexed: 12/22/2022]
Abstract
Ovarian cancer is one of the deadliest types of gynaecological cancers and more than half of the patients die within 5 years after diagnosis. Recurrence in advanced staged patients after chemotherapy is associated with increased chemoresistance, which results in poor prognosis. Regulator of G-protein signalling 10 (RGS10) negatively regulates cell proliferation, migration and survival by attenuating G-protein coupled-receptors mediated signalling pathways. Recent studies have shown that loss of RGS10 expression is significantly associated with proliferation and cisplatin resistance in ovarian cancer cells. SIGNIFICANCE OF THE STUDY: In this study, we analysed differential RGS10 expression levels using public microarray datasets from clinical and in vitro ovarian cancer samples. We validated that cancer progression and chemotherapy exposure change RGS10 expression. We enriched our study to evaluate the relationship between chemoresistance and differential RGS10 expression against ovarian cancer potential chemotherapeutic agent, palbociclib. Results showed that palbociclib treatment reduced cell viability, despite significantly decreased RGS10 expression in chemoresistant cells. Overall, the results confirmed that cancer progression and chemoresistance are significantly associated with the down-regulation of RGS10 while some chemotherapeutics seem to be beneficial in decreasing chemoresistance in ovarian cancer.
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Affiliation(s)
- Burak Kucuk
- Department of Molecular Biology and Genetics, Tokat Gaziosmanpasa University, Tokat, Turkey
| | - Beyza Kibar
- Department of Molecular Biology and Genetics, Tokat Gaziosmanpasa University, Tokat, Turkey
| | - Ercan Cacan
- Department of Molecular Biology and Genetics, Tokat Gaziosmanpasa University, Tokat, Turkey
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28
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Chen H, Deng Q, Wang W, Tao H, Gao Y. Identification of an autophagy-related gene signature for survival prediction in patients with cervical cancer. J Ovarian Res 2020; 13:131. [PMID: 33160404 PMCID: PMC7648936 DOI: 10.1186/s13048-020-00730-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 10/12/2020] [Indexed: 12/17/2022] Open
Abstract
Cervical cancer is one of the most common female malignancy that occurs worldwide and is reported to cause over 300,000 deaths in 2018. Autophagy controls the survival and death of cancerous cells by regulating the degradation process of cytoplasm and cellular organelle. In the present study, the differentially expressed autophagy-related genes (ARGs) between healthy and cancerous cervical tissues (squamous cell neoplasms) were obtained using data from GTEx and The Cancer Genome Atlas (TCGA) database. The functionalities of the differentially expressed ARGs were analyzed using Gene Ontology (GO) as well as the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. Next, we conducted univariate Cox regression assay and obtained 12 ARGs that were associated with the prognosis of cervical cancer patients. We carried out a multivariate Cox regression analysis and developed six ARG-related prognostic signature for the survival prediction of patients with squamous cell cervical cancer (Risk score = − 0.63*ATG3–0.42*BCL2 + 0.85*CD46–0.38*IFNG+ 0.23*NAMPT+ 0.82*TM9SF1). Following the calculation of risk score using the signature, the patients were divided into high and low-risk groups according to the median value. Kaplan-Meier curve demonstrated that patients with a high-risk score tend to have a poor prognosis (P < 0.001). The value for area under the curves corresponding to the receiver operating characteristic (ROC) was 0.740. As observed, the expression of IFNG was negatively associated with lymph node metastasis (P = 0.026), while a high-risk score was significantly associated with increased age (P = 0.008). To further validate the prognostic signature, we carried out a permutation test and confirmed the performance of the risk score. In conclusion, our study developed six ARG-related prognostic signature for patients with squamous cell cervical cancer, which might help in improving the prognostic predictions of such patients.
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Affiliation(s)
- Hengyu Chen
- Department of Pancreatic Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.,NHC Key Laboratory of Hormones and Development, Tianjin Institute of Endocrinology, Tianjin Medical University Chu Hsien-I Memorial Hospital, Tianjin, 300070, China.,Department of Gynecology, The Second Affiliated Hospital of Hainan Medical University, Haikou, 570102, China
| | - Qingchun Deng
- Department of Gynecology, The Second Affiliated Hospital of Hainan Medical University, Haikou, 570102, China
| | - Wenwen Wang
- Department of Gynecology and Obstetrics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Huishan Tao
- Department of Gynecology and Obstetrics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.
| | - Ying Gao
- Department of Gynecology and Obstetrics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.
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Esteve JM, Esteve-Esteve M. [Molecular pathways of autophagy regulation by BRCA1: Implications in cancer]. REVISTA ESPAÑOLA DE PATOLOGÍA : PUBLICACIÓN OFICIAL DE LA SOCIEDAD ESPAÑOLA DE ANATOMÍA PATOLÓGICA Y DE LA SOCIEDAD ESPAÑOLA DE CITOLOGÍA 2020; 53:246-253. [PMID: 33012495 DOI: 10.1016/j.patol.2019.08.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 07/30/2019] [Accepted: 08/02/2019] [Indexed: 01/20/2023]
Abstract
The BRCA1 protein contributes to maintain genomic integrity, through transcriptional regulation of proteins that control the cell cycle and DNA repair or by direct interaction with these proteins. The genetic instability caused by mutations that result in a deficit of BRCA1 activity, confers an increased risk of mainly breast and ovarian cancers. In recent years, it has been shown that autophagy has a dual role in tumor development, and chemical agents such as lucanthone, chloroquine, Z-ligustilide, spautin-1, tunicamycin, T-12, and olaparib, regulate tumor survival/death autophagy-dependent. Here we also review the different molecular pathways by which BRCA1 regulates (mostly negatively) autophagy, mainly in breast and ovarian cancers, and where the cellular redox state (ROS, GSH) and proteins mTOR, p53-Mdm2, STAT3, and Parkin, have been shown to play an essential role.
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Affiliation(s)
- Juan M Esteve
- Facultad de Ciencias de la Salud, Universidad CEU Cardenal Herrera, Castellón de la Plana, España.
| | - Miguel Esteve-Esteve
- Servicio de Medicina Preventiva, Hospital Universitario Dr. Peset, Valencia, España
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Jin Y, Qin X. Development of a Prognostic Signature Based on Autophagy-related Genes for Head and Neck Squamous Cell Carcinoma. Arch Med Res 2020; 51:860-867. [PMID: 32948377 DOI: 10.1016/j.arcmed.2020.09.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 08/06/2020] [Accepted: 09/08/2020] [Indexed: 12/24/2022]
Abstract
BACKGROUND Head and neck squamous cell carcinoma (HNSCC) is a malignant tumor with relative low survival rate. Increasingly evidences have emphasized the importance of autophagy in cancer initiation, progression, and the responses to cancer treatment. AIM OF THE STUDY This study aimed to investigate the potential biological and prognostic significance of autophagy-related genes (ARGs) in HNSCC patients. METHODS We collected a list of ARGs from Human Autophagy Database and obtained expression profiles and clinical information of HNSCC samples from the Cancer Genome Atlas (TCGA) portal. Differential expression analysis and functional enrichment analysis were performed by R software. The prognostic value of differentially expressed ARGs was detected by Cox regression analysis and prognosis-related ARGs were subjected to LASSO regression analysis. Univariate and multivariate Cox regression analysis were applied to identify promising independent prognosticators for HNSCC. RESULTS A total of 35 differentially expressed ARGs were screened out and functional enrichment analysis results indicated these genes were mainly associated with autophagy-related biological processes and pathways. Seven prognosis-related ARGs (ITGA3, CDKN2A, FADD, NKX2-3, BAK1, CXCR4, and HSPB8) were selected to construct a risk signature, which proved to be effective in predicting the survival rate of HNSCC patients. Moreover, univariate analysis showed risk score, tumor stage, T stage, and N stage were negatively correlated with patient overall survival and the multivariate Cox regression analysis results indicated risk score, age, and N stage was significantly associated with patient prognosis. CONCLUSIONS Our findings may provide novel evidences for the diagnosis and prognosis evaluation for HNSCC.
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Affiliation(s)
- Yu Jin
- Department of General Dentistry, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, PR China; Shanghai Key Laboratory of Stomatology and Shanghai Research Institute of Stomatology, National Clinical Research Center of Stomatology, PR China
| | - Xing Qin
- Shanghai Key Laboratory of Stomatology and Shanghai Research Institute of Stomatology, National Clinical Research Center of Stomatology, PR China; Department of Oral and Maxillofacial-Head and Neck Oncology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, PR China.
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31
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Ding H, Fan GL, Yi YX, Zhang W, Xiong XX, Mahgoub OK. Prognostic Implications of Immune-Related Genes' (IRGs) Signature Models in Cervical Cancer and Endometrial Cancer. Front Genet 2020; 11:725. [PMID: 32793281 PMCID: PMC7385326 DOI: 10.3389/fgene.2020.00725] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 06/15/2020] [Indexed: 01/30/2023] Open
Abstract
Cervical cancer and endometrial cancer remain serious threats to women's health. Even though some patients can be treated with surgery plus chemoradiotherapy as a conventional option, the overall efficacy is deemed unsatisfactory. As such, the development for new treatment approaches is truly necessary. In recent years, immunotherapy has been widely used in clinical practice and it is an area of great interest that researchers are keeping attention on. However, a thorough immune-related genes (IRGs) study for cervical cancer and endometrial cancer is still lacking. We therefore aim to make a comprehensive evaluation of IRGs through bioinformatics and large databases, and also investigate the relationship between the two types of cancer. We reviewed the transcriptome RNAs of IRGs and clinical data based on the TCGA database. Survival-associated IRGs in cervical/endometrial cancer were identified using univariable and multivariable Cox proportional-hazard regression analysis for developing an IRG signature model to evaluate the risk of patients. In the end, this model was validated based on the enrichment analyses through GO, KEGG, and GSEA pathways, Kaplan-Meier survival curve, ROC curves, and immune cell infiltration. Our results showed that out of 25/23 survival-associated IRGs for cervical/endometrial cancer, 13/12 warranted further examination by multivariate Cox proportional-hazard regression analysis and were selected to develop an IRGs signature model. As a result, enrichment analyses for high-risk groups indicated main enriched pathways were associated with tumor development and progression, and statistical differences were found between high-risk and low-risk groups as shown by Kaplan-Meier survival curve. This model could be used as an independent measure for risk assessment and was considered relevant to immune cell infiltration, but it had nothing to do with clinicopathological characteristics. In summary, based on comprehensive analysis, we obtained the IRGs signature model in cervical cancer (LTA, TFRC, TYK2, DLL4, CSK, JUND, NFATC4, SBDS, FLT1, IL17RD, IL3RA, SDC1, PLAU) and endometrial cancer (LTA, PSMC4, KAL1, TNF, SBDS, HDGF, LTB, HTR3E, NR2F1, NR3C1, PGR, CBLC), which can effectively evaluate the prognosis and risk of patients and provide justification in immunology for further researches.
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Affiliation(s)
- Hao Ding
- Department of Gynecology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Guan-Lan Fan
- Department of Gynecology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Yue-Xiong Yi
- Department of Gynecology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Wei Zhang
- Department of Gynecology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Xiao-Xing Xiong
- Central Laboratory, Renmin Hospital of Wuhan University, Wuhan, China
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Wang H, Ma X, Liu J, Wan Y, Jiang Y, Xia Y, Cheng W. Prognostic value of an autophagy-related gene expression signature for endometrial cancer patients. Cancer Cell Int 2020; 20:306. [PMID: 32684843 PMCID: PMC7359499 DOI: 10.1186/s12935-020-01413-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 07/09/2020] [Indexed: 12/20/2022] Open
Abstract
Background Autophagy is associated with cancer development. Autophagy-related genes play significant roles in endometrial cancer (EC), a major gynecological malignancy worldwide, but little was known about their value as prognostic markers. Here we evaluated the value of a prognostic signature based on autophagy-related genes for EC. Methods First, various autophagy-related genes were obtained via the Human Autophagy Database and their expression profiles were downloaded from The Cancer Genome Atlas. Second, key prognostic autophagy-related genes were identified via univariate, LASSO and multivariate Cox regression analyses. Finally, a risk score to predict the prognosis of EC was calculated and validated by using the test and the entire data sets. Besides, the key genes mRNA expression were validated using quantitative real-time PCR in clinical tissue samples. Results A total of 40 differentially expressed autophagy-related genes in EC were screened and five of them were prognosis-related (CDKN1B, DLC1, EIF4EBP1, ERBB2 and GRID1). A prognostic signature was constructed based on these five genes using the train set, which stratified EC patients into high-risk and low-risk groups (p < 0.05). In terms of overall survival, the analyses of the test set and the entire set yielded consistent results (test set: p < 0.05; entire set: p < 0.05). Time-dependent ROC analysis suggested that the risk score predicted EC prognosis accurately and independently (0.674 at 1 year, 0.712 at 3 years and 0.659 at 5 years). A nomogram with clinical utility was built. Patients in the high-risk group displayed distinct mutation signatures compared with those in the low-risk group. For clinical sample validation, we found that EIF4EBP1and ERBB2 had higher level in EC than that in normal tissues while CDKN1B, DLC1 and GRID1 had lower level, which was consistent with the results predicted. Conclusions Based on five autophagy-related genes (CDKN1B, DLC1, EIF4EBP1, ERBB2 and GRID1), our model can independently predict the OS of EC patients by combining molecular signature and clinical characteristics.
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Affiliation(s)
- Hui Wang
- Department of Gynecology, The First Affiliated Hospital of Nanjing Medical University, 368 North Jiangdong Road, Nanjing, 210029 Jiangsu People's Republic of China.,State Key Laboratory of Reproductive Medicine, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166 China.,State Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, 101 Longmian Avenue, Nanjing, Jiangsu 211166 China
| | - Xiaoling Ma
- Department of Gynecology, The First Affiliated Hospital of Nanjing Medical University, 368 North Jiangdong Road, Nanjing, 210029 Jiangsu People's Republic of China.,State Key Laboratory of Reproductive Medicine, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166 China.,State Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, 101 Longmian Avenue, Nanjing, Jiangsu 211166 China
| | - Jinhui Liu
- Department of Gynecology, The First Affiliated Hospital of Nanjing Medical University, 368 North Jiangdong Road, Nanjing, 210029 Jiangsu People's Republic of China
| | - Yicong Wan
- Department of Gynecology, The First Affiliated Hospital of Nanjing Medical University, 368 North Jiangdong Road, Nanjing, 210029 Jiangsu People's Republic of China
| | - Yi Jiang
- Department of Gynecology, The First Affiliated Hospital of Nanjing Medical University, 368 North Jiangdong Road, Nanjing, 210029 Jiangsu People's Republic of China
| | - Yankai Xia
- State Key Laboratory of Reproductive Medicine, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166 China.,State Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, 101 Longmian Avenue, Nanjing, Jiangsu 211166 China
| | - Wenjun Cheng
- Department of Gynecology, The First Affiliated Hospital of Nanjing Medical University, 368 North Jiangdong Road, Nanjing, 210029 Jiangsu People's Republic of China
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Wang L, Li X. Identification of an energy metabolism‑related gene signature in ovarian cancer prognosis. Oncol Rep 2020; 43:1755-1770. [PMID: 32186777 PMCID: PMC7160557 DOI: 10.3892/or.2020.7548] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 01/17/2020] [Indexed: 01/08/2023] Open
Abstract
Changes in energy metabolism may be potential biomarkers and therapeutic targets for cancer as they frequently occur within cancer cells. However, basic cancer research has failed to reach a consistent conclusion on the function(s) of mitochondria in energy metabolism. The significance of energy metabolism in the prognosis of ovarian cancer remains unclear; thus, there remains an urgent need to systematically analyze the characteristics and clinical value of energy metabolism in ovarian cancer. Based on gene expression patterns, the present study aimed to analyze energy metabolism‑associated characteristics to evaluate the prognosis of patients with ovarian cancer. A total of 39 energy metabolism‑related genes significantly associated with prognosis were obtained, and three molecular subtypes were identified by nonnegative matrix factorization clustering, among which the C1 subtype was associated with poor clinical outcomes of ovarian cancer. The immune response was enhanced in the tumor microenvironment. A total of 888 differentially expressed genes were identified in C1 compared with the other subtypes, and the results of the pathway enrichment analysis demonstrated that they were enriched in the 'PI3K‑Akt signaling pathway', 'cAMP signaling pathway', 'ECM‑receptor interaction' and other pathways associated with the development and progression of tumors. Finally, eight characteristic genes (tolloid‑like 1 gene, type XVI collagen, prostaglandin F2α, cartilage intermediate layer protein 2, kinesin family member 26b, interferon inducible protein 27, growth arrest‑specific gene 1 and chemokine receptor 7) were obtained through LASSO feature selection; and a number of them have been demonstrated to be associated with ovarian cancer progression. In addition, Cox regression analysis was performed to establish an 8‑gene signature, which was determined to be an independent prognostic factor for patients with ovarian cancer and could stratify sample risk in the training, test and external validation datasets (P<0.01; AUC >0.8). Gene Set Enrichment Analysis results revealed that the 8‑gene signature was involved in important biological processes and pathways of ovarian cancer. In conclusion, the present study established an 8‑gene signature associated with metabolic genes, which may provide new insights into the effects of energy metabolism on ovarian cancer. The 8‑gene signature may serve as an independent prognostic factor for ovarian cancer patients.
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Affiliation(s)
- Lei Wang
- Department of Obstetrics and Gynecology, ShengJing Hospital of China Medical University, Shenyang, Liaoning 110004, P.R. China
| | - Xiuqin Li
- Department of Obstetrics and Gynecology, ShengJing Hospital of China Medical University, Shenyang, Liaoning 110004, P.R. China
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Qiu J, Sun M, Wang Y, Chen B. Identification and validation of an individualized autophagy-clinical prognostic index in gastric cancer patients. Cancer Cell Int 2020; 20:178. [PMID: 32477008 PMCID: PMC7240997 DOI: 10.1186/s12935-020-01267-y] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 05/14/2020] [Indexed: 12/24/2022] Open
Abstract
Background The purpose of this study is to perform bioinformatics analysis of autophagy-related genes in gastric cancer, and to construct a multi-gene joint signature for predicting the prognosis of gastric cancer. Methods GO and KEGG analysis were applied for differentially expressed autophagy-related genes in gastric cancer, and PPI network was constructed in Cytoscape software. In order to optimize the prognosis evaluation system of gastric cancer, we established a prognosis model integrating autophagy-related genes. We used single factor Cox proportional risk regression analysis to screen genes related to prognosis from 204 autophagy-related genes in The Atlas Cancer Genome (TCGA) gastric cancer cohort. Then, the generated genes were applied to the Least Absolute Shrinkage and Selection Operator (LASSO). Finally, the selected genes were further included in the multivariate Cox proportional hazard regression analysis to establish the prognosis model. According to the median risk score, patients were divided into high-risk group and low-risk group, and survival analysis was conducted to evaluate the prognostic value of risk score. Finally, by combining clinic-pathological features and prognostic gene signatures, a nomogram was established to predict individual survival probability. Results GO analysis showed that the 28 differently expressed autophagy-related genes was enriched in cell growth, neuron death, and regulation of cell growth. KEGG analysis showed that the 28 differently expressed autophagy-related genes were related to platinum drug resistance, apoptosis and p53 signaling pathway. The risk score was constructed based on 4 genes (GRID2, ATG4D,GABARAPL2, CXCR4), and gastric cancer patients were significantly divided into high-risk and low-risk groups according to overall survival. In multivariate Cox regression analysis, risk score was still an independent prognostic factor (HR = 1.922, 95% CI = 1.573–2.349, P < 0.001). Cumulative curve showed that the survival time of patients with low-risk score was significantly longer than that of patients with high-risk score (P < 0.001). The external data GSE62254 proved that nomograph had a great ability to evaluate the prognosis of individual gastric cancer patients. Conclusions This study provides a potential prognostic marker for predicting the prognosis of GC patients and the molecular biology of GC autophagy.
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Affiliation(s)
- Jieping Qiu
- 1Department of Clinical Medicine, The First Clinical College, Anhui Medical University, Hefei, China
| | - Mengyu Sun
- 1Department of Clinical Medicine, The First Clinical College, Anhui Medical University, Hefei, China
| | - Yaoqun Wang
- 1Department of Clinical Medicine, The First Clinical College, Anhui Medical University, Hefei, China
| | - Bo Chen
- 2Department of Gastrointestinal Surgery Center, The First Affiliated Hospital of Anhui Medical University, NO. 218 Jixi Road, Hefei, Anhui 230000 China
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Zhao H, Gu S, Bao S, Yan C, Zhang Z, Hou P, Zhou M, Sun J. Mechanistically derived patient-level framework for precision medicine identifies a personalized immune prognostic signature in high-grade serous ovarian cancer. Brief Bioinform 2020; 22:5840066. [PMID: 32436954 DOI: 10.1093/bib/bbaa069] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 03/24/2020] [Accepted: 04/02/2020] [Indexed: 12/16/2022] Open
Abstract
An accurate prognosis assessment for cancer patients could aid in guiding clinical decision-making. Reliance on traditional clinical features alone in a complex clinical environment is challenging and unsatisfactory in the era of precision medicine; thus, reliable prognostic biomarkers are urgently required to improve a patient staging system. In this study, we proposed a patient-level computational framework from mechanistic and translational perspectives to establish a personalized prognostic signature (named PLPPS) in high-grade serous ovarian carcinoma (HGSOC). The PLPPS composed of 68 immune genes achieved accurate prognostic risk stratification for 1190 patients in the meta-training cohort and was rigorously validated in multiple cross-platform independent cohorts comprising 792 HGSOC patients. Furthermore, the PLPPS was shown to be the better prognostic factor compared with clinical parameters in the univariate analysis and retained a significant independent association with prognosis after adjusting for clinical parameters in the multivariate analysis. In benchmark comparisons, the performance of PLPPS (hazard ratio (HR), 1.371; concordance index (C-index), 0.604 and area under the curve (AUC), 0.637) is comparable to or better than other published gene signatures (HR, 0.972 to 1.340; C-index, 0.495 to 0.592 and AUC, 0.48-0.624). With further validation in prospective clinical trials, we hope that the PLPPS might become a promising genomic tool to guide personalized management and decision-making of HGSOC in clinical practice.
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Chen C, Chen S, Hu X, Wang J, Wen T, Fu J, Li H. Effects of autophagy-associated genes on the prognosis for lung adenocarcinoma. Transl Cancer Res 2020; 9:1947-1959. [PMID: 35117541 PMCID: PMC8798140 DOI: 10.21037/tcr.2020.02.07] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 02/04/2020] [Indexed: 12/29/2022]
Abstract
Background Several studies show that autophagy plays an important part in the biological processes of lung adenocarcinoma. Therefore, this work aimed to establish one scoring system on the basis of the expression profiles of differentially expressed autophagy-related genes (DEARGs) in patients with lung adenocarcinoma. Methods The Cancer Genome Atlas (TCGA) was applied to retrieve lung adenocarcinoma data. The overall survival (OS)-associated DEARGs were selected for the DEARG scoring scale. Moreover, the online database Kaplan-Meier Plotter (www.Kmplot.com) was employed to verify the accuracy of our results. Results The expression patterns of DEARG were detected in lung adenocarcinoma as well as normal lung tissues. A gene set related to autophagy was identified, along with 9 genes that showed marked significance in predicting the lung adenocarcinoma prognosis. According to the cox regression results, DEARGs (including ITGB4, BIRC5, ERO1A, and NLRC4) were applied to calculate the DEARGs risk score. Patients with lower DEARGs risk scores were associated with better OS. Moreover, based on analysis with the receiver operating characteristic (ROC) curve, DEARGs accurately distinguished the healthy tissues from lung adenocarcinoma tissues [area under the curve (AUC) value of >0.6]. Conclusions A scoring system is constructed based on the primary DEARGs, which accurately predicts the outcomes of lung adenocarcinoma.
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Affiliation(s)
- Chongxiang Chen
- Department of Intensive Care Unit, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China.,Guangzhou Institute of Respiratory Diseases, State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510120, China
| | - Siliang Chen
- Department of Hematology, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
| | - Xiaochun Hu
- Department of Hematology, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
| | - Jiaojiao Wang
- Department of Tuberculosis, Fuzhou Pulmonary Hospital of Fujian, Teaching Hospital of Fujian Medical University, Fuzhou 350008, China
| | - Tianmeng Wen
- School of Public Health, Sun Yat-sen University, Guangzhou 510080, China
| | - Juan Fu
- Department of Ultrasound and Electrocardiogram, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
| | - Huan Li
- Department of Intensive Care Unit, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
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Prognostic implications of autophagy-associated gene signatures in non-small cell lung cancer. Aging (Albany NY) 2019; 11:11440-11462. [PMID: 31811814 PMCID: PMC6932887 DOI: 10.18632/aging.102544] [Citation(s) in RCA: 104] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Accepted: 11/19/2019] [Indexed: 02/07/2023]
Abstract
Autophagy, a highly conserved cellular proteolysis process, has been involved in non-small cell lung cancer (NSCLC). We tried to develop a prognostic prediction model for NSCLC patients based on the expression profiles of autophagy-associated genes. Univariate Cox regression analysis was used to determine autophagy-associated genes significantly correlated with overall survival (OS) of the TCGA lung cancer cohort. LASSO regression was performed to build multiple-gene prognostic signatures. We found that the 22-gene and 11-gene signatures could dichotomize patients with significantly different OS and independently predict the OS in TCGA lung adenocarcinoma (HR=2.801, 95% CI=2.252-3.486, P<0.001) and squamous cell carcinoma (HR=1.105, 95% CI=1.067-1.145, P<0.001), respectively. The prognostic performance of the 22-gene signature was validated in four GEO lung cancer cohorts. Moreover, GO, KEGG, and GSEA analyses unveiled several fundamental signaling pathways and cellular processes associated with the 22-gene signature in lung adenocarcinoma. We also constructed a clinical nomogram with a concordance index of 0.71 to predict the survival possibility of NSCLC patients by integrating clinical characteristics and the autophagy gene signature. The calibration curves substantiated fine concordance between nomogram prediction and actual observation. Overall, we constructed and verified a novel autophagy-associated gene signature that could improve the individualized outcome prediction in NSCLC.
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Ho CJ, Gorski SM. Molecular Mechanisms Underlying Autophagy-Mediated Treatment Resistance in Cancer. Cancers (Basel) 2019; 11:E1775. [PMID: 31717997 PMCID: PMC6896088 DOI: 10.3390/cancers11111775] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 10/30/2019] [Accepted: 10/31/2019] [Indexed: 12/13/2022] Open
Abstract
Despite advances in diagnostic tools and therapeutic options, treatment resistance remains a challenge for many cancer patients. Recent studies have found evidence that autophagy, a cellular pathway that delivers cytoplasmic components to lysosomes for degradation and recycling, contributes to treatment resistance in different cancer types. A role for autophagy in resistance to chemotherapies and targeted therapies has been described based largely on associations with various signaling pathways, including MAPK and PI3K/AKT signaling. However, our current understanding of the molecular mechanisms underlying the role of autophagy in facilitating treatment resistance remains limited. Here we provide a comprehensive summary of the evidence linking autophagy to major signaling pathways in the context of treatment resistance and tumor progression, and then highlight recently emerged molecular mechanisms underlying autophagy and the p62/KEAP1/NRF2 and FOXO3A/PUMA axes in chemoresistance.
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Affiliation(s)
- Cally J. Ho
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 1L3, Canada;
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - Sharon M. Gorski
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 1L3, Canada;
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
- Centre for Cell Biology, Development, and Disease, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
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Niu Y, Sun W, Chen K, Fu Z, Chen Y, Zhu J, Chen H, Shi Y, Zhang H, Wang L, Shen HM, Xia D, Wu Y. A Novel Scoring System for Pivotal Autophagy-Related Genes Predicts Outcomes after Chemotherapy in Advanced Ovarian Cancer Patients. Cancer Epidemiol Biomarkers Prev 2019; 28:2106-2114. [PMID: 31533939 DOI: 10.1158/1055-9965.epi-19-0359] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 06/30/2019] [Accepted: 09/12/2019] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND In the clinical practice of ovarian cancer, the application of autophagy, an important regulator of carcinogenesis and chemoresistance, is still limited. This study aimed to establish a scoring system based on expression profiles of pivotal autophagy-related (ATG) genes in patients with stage III/IV ovarian cancer who received chemotherapy. METHODS Data of ovarian serous cystadenocarcinoma in The Cancer Genome Atlas (TCGA-OV) were used as training dataset. Two validation datasets comprised patients in a Chinese local database and a dataset from the Gene Expression Omnibus (GEO). ATG genes significantly (P < 0.1) associated with overall survival (OS) were selected and aggregated into an ATG scoring scale, of which the abilities to predict OS and recurrence-free survival (RFS) were examined. RESULTS Forty-three ATG genes were selected to develop the ATG score. In TCGA-OV, patients with lower ATG scores had better OS [HR = 0.41; 95% confidence interval (CI), 0.26-0.65; P < 0.001] and RFS [HR = 0.47; 95% CI, 0.27-0.82; P = 0.007]. After complete or partial remission to primary therapy, the rate of recurrence was 47.2% in the low-score group and 68.3% in the high-score group (odds ratio = 0.42; 95% CI, 0.18-0.92; P = 0.03). Such findings were verified in the two validation datasets. CONCLUSIONS We established a novel scoring system based on pivotal ATG genes, which accurately predicts the outcomes of patients with advanced ovarian cancer after chemotherapy. IMPACT The present ATG scoring system may provide a novel perspective and a promising tool for the development of personalized therapy in the future.
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Affiliation(s)
- Yuequn Niu
- Department of Toxicology of School of Public Health, and Department of Gynecologic Oncology of Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Wenjie Sun
- Department of Pathology, Zhejiang University School of Medicine, Hangzhou, China
| | - Kelie Chen
- Department of Toxicology of School of Public Health, and Department of Gynecologic Oncology of Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Zhiqin Fu
- Department of Gynecological Oncology, Zhejiang Cancer Hospital, Hangzhou, China
| | - Yaqing Chen
- Department of Gynecological Oncology, Zhejiang Cancer Hospital, Hangzhou, China
| | - Jianqing Zhu
- Department of Gynecological Oncology, Zhejiang Cancer Hospital, Hangzhou, China
| | - Hanwen Chen
- Department of Toxicology of School of Public Health, and Department of Gynecologic Oncology of Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Department of Gastroenterology, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yu Shi
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Honghe Zhang
- Department of Pathology, Zhejiang University School of Medicine, Hangzhou, China
| | - Liming Wang
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Han-Ming Shen
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Dajing Xia
- Department of Toxicology of School of Public Health, and Department of Gynecologic Oncology of Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China.
| | - Yihua Wu
- Department of Toxicology of School of Public Health, and Department of Gynecologic Oncology of Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China.
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