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Zhang Y, Tang J, Wang C, Zhang Q, Zeng A, Song L. Autophagy-related lncRNAs in tumor progression and drug resistance: A double-edged sword. Genes Dis 2024; 11:367-381. [PMID: 37588204 PMCID: PMC10425854 DOI: 10.1016/j.gendis.2023.04.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 04/21/2023] [Accepted: 04/23/2023] [Indexed: 08/18/2023] Open
Abstract
The incidence and mortality rates of cancer are increasing every year worldwide but the survival rate of cancer patients is still unsatisfactory. Therefore, it is necessary to further elucidate the molecular mechanisms involved in tumor development and drug resistance to improve cancer cure or survival rates. In recent years, autophagy has become a hot topic in the field of oncology research, which plays a double-edged role in tumorigenesis, progression, and drug resistance. Meanwhile, long non-coding RNA (lncRNA) has also been shown to regulate autophagy, and the two-sided nature of autophagy determines the dual regulatory role of autophagy-related lncRNAs (ARlncRNAs). Therefore, ARlncRNAs can be effective therapeutic targets for various cancers. Furthermore, the high abundance and stability of ARlncRNAs in tumor tissues make them promising biomarkers. In this review, we summarized the roles and mechanisms of ARlncRNAs in tumor cell proliferation, apoptosis, migration, invasion, drug resistance, angiogenesis, radiation resistance, and immune regulation. In addition, we described the clinical significance of these ARlncRNAs, including as biomarkers/therapeutic targets and their association with clinical drugs.
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Affiliation(s)
- Yunchao Zhang
- School of Medical and Life Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan 611137, China
| | - Jiayu Tang
- School of Medical and Life Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan 611137, China
| | - Cheng Wang
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan 611137, China
| | - Qinxiu Zhang
- School of Medical and Life Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan 611137, China
| | - Anqi Zeng
- Institute of Translational Pharmacology and Clinical Application, Sichuan Academy of Chinese Medical Science, Chengdu, Sichuan 610041, China
| | - Linjiang Song
- School of Medical and Life Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan 611137, China
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Li N, Chen J, Yu W, Huang X. Construction of a novel signature based on immune-related lncRNA to identify high and low risk pancreatic adenocarcinoma patients. BMC Gastroenterol 2023; 23:312. [PMID: 37710166 PMCID: PMC10503173 DOI: 10.1186/s12876-023-02916-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 08/06/2023] [Indexed: 09/16/2023] Open
Abstract
BACKGROUND Pancreatic adenocarcinoma is one of the most lethal tumors in the world with a poor prognosis. Thus, an accurate prediction model, which identify patients within high risk of pancreatic adenocarcinoma is needed to adjust the treatment and elevate the prognosis of these patients. METHODS We obtained RNAseq data of The Cancer Genome Atlas (TCGA) pancreatic adenocarcinoma (PAAD) from UCSC Xena database, identified immune-related lncRNAs (irlncRNAs) by correlation analysis, and identified differential expressed irlncRNAs (DEirlncRNAs) between pancreatic adenocarcinoma tissues from TCGA and normal pancreatic tissues from TCGA and Genotype-Tissue Expression (GTEx). Further univariate and lasso regression analysis were performed to construct prognostic signature model. Then, we calculated the areas under curve and identified the best cut-off value to identify high- and low-risk patients with pancreatic adenocarcinoma. The clinical characteristics, immune cell infiltration, immunosuppressive microenvironment, and chemoresistance were compared between high- and low-risk patients with pancreatic adenocarcinoma. RESULTS We identified 20 DEirlncRNA pairs and grouped the patients by the best cut-off value. We proved that our prognostic signature model possesses a remarkable efficiency to predict prognosis of PAAD patients. The AUC for ROC curve was 0.905 for 1-year prediction, 0.942 for 2-year prediction, and 0.966 for 3-year prediction. Patients in high-risk group have poor survival rate and worse clinical characteristics. We also proved that patients in high-risk groups were in immunosuppressive status and may be resistant to immunotherapy. Anti-cancer drug evaluation was performed based on in-silico predated tool, such as paclitaxel, sorafenib, and erlotinib, may be suitable for PAAD patients in high-risk group. CONCLUSIONS Overall, our study constructed a novel prognostic risk model based on pairing irlncRNAs, exhibited a promising prediction value in patients with pancreatic adenocarcinoma. Our prognostic risk model may help distinguish PAAD patients suitable for medical treatments.
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Affiliation(s)
- Na Li
- Nursing Department, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jionghuang Chen
- Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Weihua Yu
- Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.
| | - Xiaoling Huang
- Nursing Department, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.
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Li J, Zhang Y, Li C, Wu H, Feng C, Wang W, Liu X, Zhang Y, Cai Y, Jia Y, Qiao H, Wu F, Zhang S. A lactate-related LncRNA model for predicting prognosis, immune landscape and therapeutic response in breast cancer. Front Genet 2022; 13:956246. [DOI: 10.3389/fgene.2022.956246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 09/20/2022] [Indexed: 11/13/2022] Open
Abstract
Breast cancer (BC) has the highest incidence rate of all cancers globally, with high heterogeneity. Increasing evidence shows that lactate and long non-coding RNA (lncRNA) play a critical role in tumor occurrence, maintenance, therapeutic response, and immune microenvironment. We aimed to construct a lactate-related lncRNAs prognostic signature (LRLPS) for BC patients to predict prognosis, tumor microenvironment, and treatment responses. The BC data download from the Cancer Genome Atlas (TCGA) database was the entire cohort, and it was randomly assigned to the training and test cohorts at a 1:1 ratio. Difference analysis and Pearson correlation analysis identified 196 differentially expressed lactate-related lncRNAs (LRLs). The univariate Cox regression analysis, least absolute shrinkage and selection operator (LASSO), and multivariate Cox regression analysis were used to construct the LRLPS, which consisted of 7 LRLs. Patients could be assigned into high-risk and low-risk groups based on the medium-risk sore in the training cohort. Then, we performed the Kaplan–Meier survival analysis, time-dependent receiver operating characteristic (ROC) curves, and univariate and multivariate analyses. The results indicated that the prognosis prediction ability of the LRLPS was excellent, robust, and independent. Furthermore, a nomogram was constructed based on the LRLPS risk score and clinical factors to predict the 3-, 5-, and 10-year survival probability. The GO/KEGG and GSEA indicated that immune-related pathways differed between the two-risk group. CIBERSORT, ESTIMATE, Tumor Immune Dysfunction and Exclusion (TIDE), and Immunophenoscore (IPS) showed that low-risk patients had higher levels of immune infiltration and better immunotherapeutic response. The pRRophetic and CellMiner databases indicated that many common chemotherapeutic drugs were more effective for low-risk patients. In conclusion, we developed a novel LRLPS for BC that could predict the prognosis, immune landscape, and treatment response.
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Yu-Qing H, Peng-Ping L, Ke S, Ke-Xing Y, Wei-Jun Z, Zhen-Yu W. Comprehensive analysis of liquid-liquid phase separation-related genes in prediction of breast cancer prognosis. Front Genet 2022; 13:834471. [PMID: 36246644 PMCID: PMC9554098 DOI: 10.3389/fgene.2022.834471] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 08/03/2022] [Indexed: 11/13/2022] Open
Abstract
Objective: Liquid-liquid phase separation (LLPS) is a functional unit formed by specific molecules. It lacks a membrane and has been reported to play a crucial role in tumor drug resistance and growth by regulating gene expression and drug distribution. However, whether LLPS could be used to predict cancer prognosis was not clear. This study aimed to construct a prognostic model for breast cancer based on LLPS-correlated genes (LCGs).Methods: LCGs were identified using the PhaSepDB, gene expression profile and clinical characteristics of breast cancer were obtained from TCGA and cBioportal. The PanCancer Atlas (TCGA) cohort was used as the training cohort to construct the prognostic model, while the Nature 2012 and Nat Commun 2016 (TCGA) cohort and GEO data were used as test cohort to perform external verification. Data analysis was performed with R4.2.0 and SPSS20.0.Results: We identified 140 prognosis-related LCGs (pLCGs) (p< 0.01) in all cohorts, 240 pLCGs (p< 0.01) in the luminal cohort, and 28 pLCGs (p< 0.05) in the triple-negative breast cancer (TNBC) cohort. Twelve genes in all cohorts (training cohort: 5/10-year ROC values were 0.76 and 0.77; verification cohort: 5/10-year ROC values were 0.61 and 0.58), eight genes in the luminal cohort (training cohort: 5/10-year ROC values were 0.79 and 0.75; verification cohort: 5/10-year ROC values were 0.62 and 0.62), and four genes in the TNBC cohort (training cohort: 5/10-year ROC values were 0.73 and 0.79; verification cohort: 5/10-year ROC values were 0.55 and 0.54) were screened out to construct the prognostic prediction model. The 17-gene risk-score was constructed in all cohorts (1/3/5-year ROC values were 0.88, 0.83, and 0.81), and the 11-gene risk-score was constructed in the luminal cohort (1/3/5-year ROC values were 0.67, 0.85 and 0.84), and the six-gene risk-score was constructed in the TNBC cohort (1/3/5-year ROC value were 0.87, 0.88 and 0.81). Finally, the risk-score and clinical factors were applied to construct nomograms in all cohorts (1/3/5-year ROC values were 0.89, 0.79 and 0.75, C-index = 0.784), in the luminal cohort (1/3/5-year ROC values were 0.84, 0.83 and 0.85, C-index = 0.803), and in the TNBC cohort (1/3/5-year ROC values were 0.95, 0.84 and 0.77, C-index = 0.847).Discussion: This study explored the roles of LCGs in the prediction of breast cancer prognosis.
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Affiliation(s)
- Huang Yu-Qing
- The First People’s Hospital of Xiaoshan, Hangzhou, China
- Xaioshan Hospital Affiliated to Wenzhou Medical University, Wenzhou, China
| | - Li Peng-Ping
- The First People’s Hospital of Xiaoshan, Hangzhou, China
- Xaioshan Hospital Affiliated to Wenzhou Medical University, Wenzhou, China
| | - Sun Ke
- The First People’s Hospital of Xiaoshan, Hangzhou, China
- Xaioshan Hospital Affiliated to Wenzhou Medical University, Wenzhou, China
| | - Yin Ke-Xing
- The First People’s Hospital of Xiaoshan, Hangzhou, China
- Xaioshan Hospital Affiliated to Wenzhou Medical University, Wenzhou, China
| | - Zhang Wei-Jun
- The First People’s Hospital of Xiaoshan, Hangzhou, China
- Xaioshan Hospital Affiliated to Wenzhou Medical University, Wenzhou, China
- *Correspondence: Wang Zhen-Yu, ; Zhang Wei-Jun,
| | - Wang Zhen-Yu
- The First People’s Hospital of Xiaoshan, Hangzhou, China
- Xaioshan Hospital Affiliated to Wenzhou Medical University, Wenzhou, China
- *Correspondence: Wang Zhen-Yu, ; Zhang Wei-Jun,
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Lu X, Gou Z, Yu L, Bu H. A novel risk model based on immune response predicts clinical outcomes and characterizes immunophenotypes in triple-negative breast cancer. Am J Cancer Res 2022; 12:3913-3931. [PMID: 36119814 PMCID: PMC9442003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 08/03/2022] [Indexed: 06/15/2023] Open
Abstract
Triple-negative breast cancer (TNBC) is highly heterogeneous in prognosis. The current TNM staging system shows its limitation in accurate risk evaluation. Immune response and immune cell abundances in the tumor immune microenvironment (TIME) are critical for cancer progression, clinical outcome and therapeutic response in TNBC. However, there is a lack of an effective risk model based on the overall transcriptional alterations relevant to different immune responses. In this study, multiple bioinformatics and statistical approaches were used to develop an immune-related risk (IRR) signature based on the differentially expressed genes between the immune-active and immune-inactive samples. The IRR model showed great performance in risk stratification, immune landscape evaluation and immunotherapy response prediction. Compared with the low-IRR group, the high-IRR group exhibited a poorer prognosis, less cytotoxic cell infiltration, higher M2/M1 ratio and upregulated glycolytic activity. Moreover, the high-IRR group showed more resistance to immunotherapy than the low-IRR group. Our study reveals that the IRR model may be a promising tool to help clinicians assess risk and optimize treatment for TNBC patients.
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Affiliation(s)
- Xunxi Lu
- Department of Pathology, West China Hospital, Sichuan UniversityChengdu 610041, China
- Institute of Clinical Pathology, West China Hospital, Sichuan UniversityChengdu 610041, China
| | - Zongchao Gou
- Department of Breast Surgery, West China Hospital, Sichuan UniversityChengdu 610041, China
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan UniversityChengdu 610041, China
| | - Luoting Yu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan UniversityChengdu 610041, China
| | - Hong Bu
- Department of Pathology, West China Hospital, Sichuan UniversityChengdu 610041, China
- Institute of Clinical Pathology, West China Hospital, Sichuan UniversityChengdu 610041, China
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Tian J, Fu C, Zeng X, Fan X, Wu Y. An Independent Prognostic Model Based on Ten Autophagy-Related Long Noncoding RNAs in Pancreatic Cancer Patients. Genet Res (Camb) 2022; 2022:3895396. [PMID: 35645615 PMCID: PMC9124146 DOI: 10.1155/2022/3895396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 04/27/2022] [Indexed: 11/17/2022] Open
Abstract
Purpose Pancreatic cancer (PC) is a common, highly lethal cancer with a low survival rate. Autophagy is involved in the occurrence and progression of PC. This study aims to explore the feasibility of using an autophagy-related long noncoding RNA (lncRNA) signature for assessing PC patient survival. Methods We obtained RNA sequencing and clinical data of patients from the TCGA website. Autophagy genes were obtained from the Human Autophagy Database. The prognostic model, generated through univariate and multivariate Cox regression analyses, included 10 autophagy-related lncRNAs. Receiver operating characteristic (ROC) curves and forest plots were generated for univariate and multivariate Cox regression analyses, to examine the predictive feasibility of the risk model. Gene set enrichment analysis (GSEA) was used to screen enriched gene sets. Results Twenty-eight autophagy-related lncRNAs were filtered out through univariate Cox regression analysis (P < 0.001). Ten autophagy-related lncRNAs, including 4 poor prognosis factors and 6 beneficial prognosis factors, were further screened via multivariate Cox regression analysis. The AUC value of the ROC curve was 0.815. GSEA results demonstrated that cancer-related gene sets were significantly enriched. Conclusion A signature based on ten autophagy-related lncRNAs was identified. This signature could be potentially used for evaluating clinical prognosis and might be used for targeted therapy against PC.
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Affiliation(s)
- Jiahui Tian
- Department of Laboratory, The First Affiliated Hospital of Hunan Normal University, Changsha, Hunan 410005, China
- Department of Medicine, Hunan Normal University, Changsha, Hunan 410005, China
| | - Chunyan Fu
- Department of Medicine, Hunan Normal University, Changsha, Hunan 410005, China
| | - Xuan Zeng
- Department of Medicine, Hunan Normal University, Changsha, Hunan 410005, China
| | - Xiaoxiao Fan
- Department of Laboratory, The First Affiliated Hospital of Hunan Normal University, Changsha, Hunan 410005, China
| | - Yi Wu
- Department of Laboratory, The First Affiliated Hospital of Hunan Normal University, Changsha, Hunan 410005, China
- Department of Medicine, Hunan Normal University, Changsha, Hunan 410005, China
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Mascia F, Mazo I, Alterovitz WL, Karagiannis K, Wu WW, Shen RF, Beaver JA, Rao VA. In search of autophagy biomarkers in breast cancer: Receptor status and drug agnostic transcriptional changes during autophagy flux in cell lines. PLoS One 2022; 17:e0262134. [PMID: 34990474 PMCID: PMC8735604 DOI: 10.1371/journal.pone.0262134] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 12/18/2021] [Indexed: 12/15/2022] Open
Abstract
Autophagy drives drug resistance and drug-induced cancer cell cytotoxicity. Targeting the autophagy process could greatly improve chemotherapy outcomes. The discovery of specific inhibitors or activators has been hindered by challenges with reliably measuring autophagy levels in a clinical setting. We investigated drug-induced autophagy in breast cancer cell lines with differing ER/PR/Her2 receptor status by exposing them to known but divergent autophagy inducers each with a unique molecular target, tamoxifen, trastuzumab, bortezomib or rapamycin. Differential gene expression analysis from total RNA extracted during the earliest sign of autophagy flux showed both cell- and drug-specific changes. We analyzed the list of differentially expressed genes to find a common, cell- and drug-agnostic autophagy signature. Twelve mRNAs were significantly modulated by all the drugs and 11 were orthogonally verified with Q-RT-PCR (Klhl24, Hbp1, Crebrf, Ypel2, Fbxo32, Gdf15, Cdc25a, Ddit4, Psat1, Cd22, Ypel3). The drug agnostic mRNA signature was similarly induced by a mitochondrially targeted agent, MitoQ. In-silico analysis on the KM-plotter cancer database showed that the levels of these mRNAs are detectable in human samples and associated with breast cancer prognosis outcomes of Relapse-Free Survival in all patients (RSF), Overall Survival in all patients (OS), and Relapse-Free Survival in ER+ Patients (RSF ER+). High levels of Klhl24, Hbp1, Crebrf, Ypel2, CD22 and Ypel3 were correlated with better outcomes, whereas lower levels of Gdf15, Cdc25a, Ddit4 and Psat1 were associated with better prognosis in breast cancer patients. This gene signature uncovers candidate autophagy biomarkers that could be tested during preclinical and clinical studies to monitor the autophagy process.
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Affiliation(s)
- Francesca Mascia
- Laboratory of Applied Biochemistry, Division of Biotechnology Review and Research III, Office of Biotechnology Products, CDER, FDA, Silver Spring, Maryland, United States of America
| | - Ilya Mazo
- HIVE Bioinformatics Group, Office of Biostatistics and Epidemiology, CBER, FDA, Silver Spring, Maryland, United States of America
| | - Wei-Lun Alterovitz
- HIVE Bioinformatics Group, Office of Biostatistics and Epidemiology, CBER, FDA, Silver Spring, Maryland, United States of America
| | - Konstantinos Karagiannis
- HIVE Bioinformatics Group, Office of Biostatistics and Epidemiology, CBER, FDA, Silver Spring, Maryland, United States of America
| | - Wells W. Wu
- Facility for Biotechnology Resource CBER, FDA, Silver Spring, Maryland, United States of America
| | - Rong-Fong Shen
- Facility for Biotechnology Resource CBER, FDA, Silver Spring, Maryland, United States of America
| | - Julia A. Beaver
- Oncology Center of Excellence, FDA, Silver Spring, Maryland, United States of America
| | - V. Ashutosh Rao
- Laboratory of Applied Biochemistry, Division of Biotechnology Review and Research III, Office of Biotechnology Products, CDER, FDA, Silver Spring, Maryland, United States of America
- * E-mail:
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Over Fifty Years of Life, Death, and Cannibalism: A Historical Recollection of Apoptosis and Autophagy. Int J Mol Sci 2021; 22:ijms222212466. [PMID: 34830349 PMCID: PMC8618802 DOI: 10.3390/ijms222212466] [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: 10/21/2021] [Revised: 11/02/2021] [Accepted: 11/03/2021] [Indexed: 01/18/2023] Open
Abstract
Research in biomedical sciences has changed dramatically over the past fifty years. There is no doubt that the discovery of apoptosis and autophagy as two highly synchronized and regulated mechanisms in cellular homeostasis are among the most important discoveries in these decades. Along with the advancement in molecular biology, identifying the genetic players in apoptosis and autophagy has shed light on our understanding of their function in physiological and pathological conditions. In this review, we first describe the history of key discoveries in apoptosis with a molecular insight and continue with apoptosis pathways and their regulation. We touch upon the role of apoptosis in human health and its malfunction in several diseases. We discuss the path to the morphological and molecular discovery of autophagy. Moreover, we dive deep into the precise regulation of autophagy and recent findings from basic research to clinical applications of autophagy modulation in human health and illnesses and the available therapies for many diseases caused by impaired autophagy. We conclude with the exciting crosstalk between apoptosis and autophagy, from the early discoveries to recent findings.
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Construction of a Novel Immune-Related lncRNA Pair Signature with Prognostic Significance for Kidney Clear Cell Renal Cell Carcinoma. DISEASE MARKERS 2021; 2021:8800358. [PMID: 34512816 PMCID: PMC8429034 DOI: 10.1155/2021/8800358] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Revised: 08/07/2021] [Accepted: 08/10/2021] [Indexed: 02/07/2023]
Abstract
Background Renal cell carcinoma (RCC) is one of the most common aggressive malignant tumors in the urinary system, among which the clear cell renal cell carcinoma (ccRCC) is the most common subtype. The immune-related long noncoding ribonucleic acids (irlncRNAs) which are abundant in immune cells and immune microenvironment (IME) have potential significance in evaluating the prognosis and effects of immunotherapy. The signature based on irlncRNA pairs and independent of the exact expression level seems to have a latent predictive significance for the prognosis of patients with malignant tumors but has not been applied in ccRCC yet. Method In this article, we retrieved The Cancer Genome Atlas (TCGA) database for the transcriptome profiling data of the ccRCC and performed coexpression analysis between known immune-related genes (ir-genes) and lncRNAs to find differently expressed irlncRNA (DEirlncRNA). Then, we adopted a single-factor test and a modified LASSO regression analysis to screen out ideal DEirlncRNAs and constructed a Cox proportional hazard model. We have sifted 28 DEirlncRNA pairs, 12 of which were included in this model. Next, we compared the area under the curve (AUC), found the cutoff point by using the Akaike information criterion (AIC) value, and distinguished the patients with ccRCC into a high-risk group and a low-risk group using this value. Finally, we tested this model by investigating the relationship between risk score and survival, clinical pathological characteristics, cells in tumor immune microenvironment, chemotherapy, and targeted checkpoint biomarkers. Results A novel immune-related lncRNA pair signature consisting of 12 DEirlncRNA pairs was successfully constructed and tightly associated with overall survival, clinical pathological characteristics, cells in tumor immune microenvironment, and reactiveness to immunotherapy and chemotherapy in patients with ccRCC. Besides, the efficacy of this signature was verified in some commonly used clinicopathological subgroups and could serve as an independent prognostic factor in patients with ccRCC. Conclusions This signature was proven to have a potential predictive significance for the prognosis of patients with ccRCC and the efficacy of immunotherapy.
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Li Z, Qian Z, Chen F, Jiang S, Meng L, Chen J. Identification of Key lncRNA-mRNA Pairs and Functional lncRNAs in Breast Cancer by Integrative Analysis of TCGA Data. Front Genet 2021; 12:709514. [PMID: 34490040 PMCID: PMC8417727 DOI: 10.3389/fgene.2021.709514] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 07/16/2021] [Indexed: 01/14/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) play an important role in many diseases and are involved in the post-transcriptional regulatory network of tumors. The purpose of this study is to mine new lncRNA–mRNA regulatory pairs and analyze the new mechanism of lncRNA involvement in breast cancer progression. Using breast cancer miRNA and mRNA expression profiling from The Cancer Genome Atlas (TCGA), we identified 59 differentially expressed lncRNAs, 88 differentially expressed miRNAs, and 1,465 differentially expressed mRNAs between breast cancer tissue and adjacent normal breast cancer. Whereafter, four candidate lncRNAs (FGF14-AS2, LINC01235, AC055854.1, and AC124798.1) were identified by the Kaplan–Meier (K–M) plotter. Furthermore, we screened the hub lncRNA (LINC01235) through univariate Cox analysis, multivariate Cox analysis, and qPCR validation, which was significantly correlated with breast cancer stage, ER status, and pathological N. Subsequently, 107 LINC01235-related mRNAs were obtained by combining differentially expressed miRNAs, differentially expressed mRNAs, and LINC01235 targeting miRNAs and mRNAs. The protein–protein interaction (PPI) network was established by Cytoscape software, and 53 key genes were screened. Function and pathway enrichment showed that LINC01235-related key genes might be involved in the process of cell differentiation, cell proliferation, and p53 signal pathway. In addition, LINC01235 has been confirmed to regulate the proliferation, migration, and invasion of MCF-7 cells in in vitro experiments. Furthermore, we screened three mRNAs (ESR1, ADRA2A, and DTL) associated with breast cancer drug resistance from key genes. Through RNA interference experiments in vitro and correlation analysis, we found that there was a negative feedback mechanism between LINC01235 and ESR1/ADRA2A. In conclusion, our results suggest that LINC01235-ESR1 and LINC01235-ADRA2A could serve as important co-expression pairs in the progression of breast cancer, and LINC01235 plays a key role as an independent prognostic factor in patients with breast cancer. The findings of this work greatly increase our understanding of the molecular regulatory mechanisms of lncRNA in breast cancer.
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Affiliation(s)
- Zhe Li
- Department of Breast Surgery, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Zheng Qian
- Department of Breast Surgery, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Fei Chen
- Department of Breast Surgery, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Shujun Jiang
- Department of Breast Surgery, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Lingjia Meng
- Department of General Surgery, Putuo Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Jinzhong Chen
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
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