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Xue L, Wu P, Zhao X, Jin X, Wang J, Shi Y, Yang X, She Y, Li Y, Li C. Using Immune-Related lncRNA Signature for Prognosis and Response to Immunotherapy in Cutaneous Melanoma. Int J Gen Med 2021; 14:6463-6475. [PMID: 34675614 PMCID: PMC8518697 DOI: 10.2147/ijgm.s335266] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 09/27/2021] [Indexed: 12/16/2022] Open
Abstract
Background Cutaneous melanoma is a highly malignant skin tumor, and most patients have a poor prognosis. In recent years, immunotherapy has assumed an important role in the treatment of advanced cutaneous melanoma, but only a small percentage of patients benefit from immunotherapy. A growing number of studies have demonstrated that the prognosis of patients with cutaneous melanoma is closely related to long non-coding RNA and the tumor immune microenvironment. Methods We downloaded RNA expression data and immune-related gene lists of cutaneous melanoma patients separately from The Cancer Genome Atlas database and ImmPort website and identified immune-related lncRNAs by co-expression analysis. The prognostic model was constructed by applying least absolute shrinkage and selection operator regression, and all patients were classified into high- and low-risk groups according to the risk score of the model. We evaluated the differences between the two groups in terms of survival outcomes, immune infiltration, pathway enrichment, chemotherapeutic drug sensitivity and immune checkpoint gene expression to verify the impact of lncRNA signature on clinical prognosis and immunotherapy efficacy. Results By correlation analysis and LASSO regression analysis, we constructed an immune-related lncRNA prognostic model based on five lncRNA: HLA-DQB1-AS1, MIR205HG, RP11-643G5.6, USP30-AS1 and RP11-415F23.4. Based on this model, we plotted Kaplan-Meier survival curves and time-dependent ROC curves and analyzed its ability as an independent prognostic factor for cutaneous melanoma in combination with clinicopathological features. The results showed that these lncRNA signature was an independent prognostic factor of cutaneous melanoma with favorable prognostic ability. Our results also show a higher degree of immune infiltration, higher expression of immune checkpoint-associated genes, and better outcome of immunotherapy in the low-risk group of the lncRNA signature. Conclusion The 5 immune-related lncRNA signatures constructed in our study can predict the prognosis of cutaneous melanoma and contribute to the selection of immunotherapy.
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Affiliation(s)
- Ling Xue
- College of Basic Medicine, Gansu University of Chinese Medicine, Lanzhou, 730000, People's Republic of China.,Department of Pathology, The 940th Hospital of the Joint Logistic Support of the People's Liberation Army, Lanzhou, 730050, People's Republic of China
| | - Pingfan Wu
- College of Basic Medicine, Gansu University of Chinese Medicine, Lanzhou, 730000, People's Republic of China.,Department of Pathology, The 940th Hospital of the Joint Logistic Support of the People's Liberation Army, Lanzhou, 730050, People's Republic of China
| | - Xiaowen Zhao
- College of Basic Medicine, Gansu University of Chinese Medicine, Lanzhou, 730000, People's Republic of China.,Department of Pathology, The 940th Hospital of the Joint Logistic Support of the People's Liberation Army, Lanzhou, 730050, People's Republic of China
| | - Xiaojie Jin
- Provincial-Level Key Laboratory of Molecular Medicine of Major Diseases and Study on Prevention and Treatment of Traditional Chinese Medicine, Gansu University of Chinese Medicine, Lanzhou, Gansu, People's Republic of China
| | - Jingjing Wang
- College of Basic Medicine, Gansu University of Chinese Medicine, Lanzhou, 730000, People's Republic of China
| | - Yuxiang Shi
- College of Basic Medicine, Gansu University of Chinese Medicine, Lanzhou, 730000, People's Republic of China
| | - Xiaojing Yang
- College of Basic Medicine, Gansu University of Chinese Medicine, Lanzhou, 730000, People's Republic of China
| | - Yali She
- Provincial-Level Key Laboratory of Molecular Medicine of Major Diseases and Study on Prevention and Treatment of Traditional Chinese Medicine, Gansu University of Chinese Medicine, Lanzhou, Gansu, People's Republic of China
| | - Yaling Li
- College of Basic Medicine, Gansu University of Chinese Medicine, Lanzhou, 730000, People's Republic of China.,Provincial-Level Key Laboratory of Molecular Medicine of Major Diseases and Study on Prevention and Treatment of Traditional Chinese Medicine, Gansu University of Chinese Medicine, Lanzhou, Gansu, People's Republic of China
| | - Changtian Li
- College of Basic Medicine, Gansu University of Chinese Medicine, Lanzhou, 730000, People's Republic of China
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Li Y, Wang J, Wang F, Gao C, Cao Y, Wang J. Development and Verification of an Autophagy-Related lncRNA Signature to Predict Clinical Outcomes and Therapeutic Responses in Ovarian Cancer. Front Med (Lausanne) 2021; 8:715250. [PMID: 34671615 PMCID: PMC8521014 DOI: 10.3389/fmed.2021.715250] [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: 05/26/2021] [Accepted: 08/30/2021] [Indexed: 12/13/2022] Open
Abstract
Objective: Long noncoding RNAs (lncRNAs) are key regulators during ovarian cancer initiation and progression and are involved in mediating autophagy. In this study, we aimed to develop a prognostic autophagy-related lncRNA signature for ovarian cancer. Methods: Autophagy-related abnormally expressed lncRNAs were screened in ovarian cancer with the criteria values of |correlation coefficient| > 0.4 and p < 0.001. Based on them, a prognostic lncRNA signature was established. The Kaplan–Meier overall survival analysis was conducted in high- and low-risk samples in the training, verification, and entire sets, followed by receiver operating characteristics (ROCs) of 7-year survival. Multivariate Cox regression analysis was used for assessing the predictive independency of this signature after adjusting other clinical features. The associations between the risk scores and immune cell infiltration, PD-L1 expression, and sensitivity of chemotherapy drugs were assessed in ovarian cancer. Results: A total of 66 autophagy-related abnormally expressed lncRNAs were identified in ovarian cancer. An autophagy-related lncRNA signature was constructed for ovarian cancer. High-risk scores were indicative of poorer prognosis compared with the low-risk scores in the training, verification, and entire sets. ROCs of 7-year survival confirmed the well-predictive efficacy of this model. Following multivariate Cox regression analysis, this model was an independent prognostic factor. There were distinct differences in infiltrations of immune cells, PD-L1 expression, and sensitivity of chemotherapy drugs between high- and low-risk samples. Conclusions: This study constructed an autophagy-related lncRNA signature that was capable of predicting clinical outcomes and also therapeutic responses for ovarian cancer.
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Affiliation(s)
- Yan Li
- Department of Obstetrics and Gynecology, The Yancheng Clinical College of Xuzhou Medical University, The First People's Hospital of Yancheng, Yancheng, China
| | - Juan Wang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Fang Wang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Chengzhen Gao
- Department of Obstetrics and Gynecology, The Yancheng Clinical College of Xuzhou Medical University, The First People's Hospital of Yancheng, Yancheng, China
| | - Yuanyuan Cao
- Department of Obstetrics and Gynecology, The Yancheng Clinical College of Xuzhou Medical University, The First People's Hospital of Yancheng, Yancheng, China
| | - Jianhua Wang
- Department of Gastroenterology, The Yancheng Clinical College of Xuzhou Medical University, The First People's Hospital of Yancheng, Yancheng, China
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53
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Shen L, Li N, Zhou Q, Li Z, Shen L. Development and Validation of an Autophagy-Related LncRNA Prognostic Signature in Head and Neck Squamous Cell Carcinoma. Front Oncol 2021; 11:743611. [PMID: 34660307 PMCID: PMC8517509 DOI: 10.3389/fonc.2021.743611] [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: 07/19/2021] [Accepted: 09/08/2021] [Indexed: 01/23/2023] Open
Abstract
Head and neck squamous cell carcinoma (HNSCC) is one of the greatest public challenges because of delayed diagnosis and poor prognosis. In this study, we established an autophagy-associated long non-coding (Lnc)RNA prognostic signature to assess the prognosis of HNSCC patients. The LncRNA expression profiles and clinical information of 499 HNSCC samples were available in The Cancer Genome Atlas. Autophagic LncRNAs were analyzed using Pearson correlation. A co-expression network showed the interactions between autophagic genes and LncRNAs. An autophagic LncRNAs prognostic signature, consisting of MYOSLID, AL139287.1, AC068580.1, AL022328.2, AC104083.1, AL160006.1, AC116914.2, LINC00958, and AL450992.2, was developed through uni- and multivariate Cox regressions. High- and low-risk groups were classified based on the median risk scores. The high-risk group had significantly worse overall survival according to Kaplan–Meier curve analysis. Multivariate Cox regression demonstrated that risk scores were a significant independent prognostic factor (hazard ratio = 1.739, 95% confidence interval: 1.460–2.072), with an area under the curve of 0.735. Principal component analysis distinguished two categories based on the nine-LncRNA prognostic signature. In conclusion, this novel autophagic LncRNA signature is an independent prognostic factor and may suggest novel therapeutic targets for HNSCC.
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Affiliation(s)
- Lin Shen
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, China
| | - Na Li
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, China
| | - Qin Zhou
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, China
| | - Zhanzhan Li
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, China
| | - Liangfang Shen
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, China
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Huang K, Yue X, Zheng Y, Zhang Z, Cheng M, Li L, Chen Z, Yang Z, Bian E, Zhao B. Development and Validation of an Mesenchymal-Related Long Non-Coding RNA Prognostic Model in Glioma. Front Oncol 2021; 11:726745. [PMID: 34540695 PMCID: PMC8446619 DOI: 10.3389/fonc.2021.726745] [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: 06/17/2021] [Accepted: 08/16/2021] [Indexed: 12/29/2022] Open
Abstract
Glioma is well known as the most aggressive and prevalent primary malignant tumor in the central nervous system. Molecular subtypes and prognosis biomarkers remain a promising research area of gliomas. Notably, the aberrant expression of mesenchymal (MES) subtype related long non-coding RNAs (lncRNAs) is significantly associated with the prognosis of glioma patients. In this study, MES-related genes were obtained from The Cancer Genome Atlas (TCGA) and the Ivy Glioblastoma Atlas Project (Ivy GAP) data sets of glioma, and MES-related lncRNAs were acquired by performing co-expression analysis of these genes. Next, Cox regression analysis was used to establish a prognostic model, that integrated ten MES-related lncRNAs. Glioma patients in TCGA were divided into high-risk and low-risk groups based on the median risk score; compared with the low-risk groups, patients in the high-risk group had shorter survival times. Additionally, we measured the specificity and sensitivity of our model with the ROC curve. Univariate and multivariate Cox analyses showed that the prognostic model was an independent prognostic factor for glioma. To verify the predictive power of these candidate lncRNAs, the corresponding RNA-seq data were downloaded from the Chinese Glioma Genome Atlas (CGGA), and similar results were obtained. Next, we performed the immune cell infiltration profile of patients between two risk groups, and gene set enrichment analysis (GSEA) was performed to detect functional annotation. Finally, the protective factors DGCR10 and HAR1B, and risk factor SNHG18 were selected for functional verification. Knockdown of DGCR10 and HAR1B promoted, whereas knockdown of SNHG18 inhibited the migration and invasion of gliomas. Collectively, we successfully constructed a prognostic model based on a ten MES-related lncRNAs signature, which provides a novel target for predicting the prognosis for glioma patients.
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Affiliation(s)
- Kebing Huang
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Hefei, China.,Cerebral Vascular Disease Research Center, Anhui Medical University, Hefei, China
| | - Xiaoyu Yue
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Hefei, China.,Cerebral Vascular Disease Research Center, Anhui Medical University, Hefei, China
| | - Yinfei Zheng
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Hefei, China.,Cerebral Vascular Disease Research Center, Anhui Medical University, Hefei, China
| | - Zhengwei Zhang
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Hefei, China.,Cerebral Vascular Disease Research Center, Anhui Medical University, Hefei, China
| | - Meng Cheng
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Hefei, China.,Cerebral Vascular Disease Research Center, Anhui Medical University, Hefei, China
| | - Lianxin Li
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Hefei, China.,Cerebral Vascular Disease Research Center, Anhui Medical University, Hefei, China
| | - Zhigang Chen
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Hefei, China.,Cerebral Vascular Disease Research Center, Anhui Medical University, Hefei, China
| | - Zhihao Yang
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Hefei, China.,Cerebral Vascular Disease Research Center, Anhui Medical University, Hefei, China
| | - Erbao Bian
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Hefei, China.,Cerebral Vascular Disease Research Center, Anhui Medical University, Hefei, China
| | - Bing Zhao
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Hefei, China.,Cerebral Vascular Disease Research Center, Anhui Medical University, Hefei, China
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Effect of Aberrant Long Noncoding RNA on the Prognosis of Clear Cell Renal Cell Carcinoma. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2021; 2021:6533049. [PMID: 34512796 PMCID: PMC8433025 DOI: 10.1155/2021/6533049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 08/07/2021] [Indexed: 11/17/2022]
Abstract
Clear cell renal cell carcinoma (ccRCC) is a kind of lethal cancer. Although there are mature treatment methods, there is still a lack of rigorous and scientific means for cancer diagnosis. Long noncoding RNAs (lncRNAs) are a kind of noncoding RNA (ncRNA). Recent studies find that alteration of lncRNA expression is related to the occurrence of many cancers. In order to find lncRNAs which can effectively predict the prognosis of ccRCC, RNA-seq count data and clinical information were downloaded from TCGA-KIRC, and gene expression profiles from 530 patients were included. Then, K-means was used for clustering, and the number of clusters was determined to be 5. The R-package "edgeR" was used to perform differential expression analysis. Subsequently, a risk model composed of 10 lncRNA biomarkers significantly related to prognosis was identified via Cox and LASSO regression analyses. Then, patients were divided into two groups according to the model-based risk score, and then, GSEA pathway enrichment was performed. The results showed that metabolism- and mTOR-related pathways were activated while immune-related pathways were inhibited in the high-risk patients. Combined with previous studies, it is believed that these 10 lncRNAs are potential targets for the treatment of ccRCC. In addition, Cox regression analysis was used to verify the independence of the risk model, and as results revealed, the risk model can be used to independently predict the prognosis of patients. In conclusion, our study found 10 lncRNAs related to the prognosis of ccRCC and provided new ideas for clinical diagnosis and drug development.
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Identification of a Nomogram from Ferroptosis-Related Long Noncoding RNAs Signature to Analyze Overall Survival in Patients with Bladder Cancer. JOURNAL OF ONCOLOGY 2021; 2021:8533464. [PMID: 34484338 PMCID: PMC8413054 DOI: 10.1155/2021/8533464] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 07/09/2021] [Accepted: 08/13/2021] [Indexed: 12/13/2022]
Abstract
Purpose This study aimed to establish a nomogram to predict the overall survival (OS) of patients with bladder cancer (BC) by ferroptosis-related long noncoding RNAs (FRlncRNAs) signature. Methods We obtained FRlncRNAs expression profiles and clinical data of patients with BC from the Cancer Genome Atlas database. The patients were divided into the training set, testing set, and overall set. Lasso regression and multivariate Cox regression were used to establish the FRlncRNAs signature, the prognosis of each group was compared by Kaplan–Meier (K-M) analysis, and the receiver operating characteristic (ROC) curve evaluated the accuracy of the model. The Gene Set Enrichment Analysis (GSEA) was used for the visualization of the functional enrichment for FRlncRNAs. The databases of GEPIA and K-M Plotter were used for subsequent functional analysis of major FRlncRNAs. Results Thirteen prognostic FRlncRNAs (LINC00942, MAFG-DT, AL049840.3, AL136084.3, OCIAD1-AS1, AC062017.1, AC008074.2, AC018653.3, AL031775.1, USP30-AS1, LINC01767, AC132807.2, and AL354919.2) were identified to be significantly different, constituting an FRlncRNAs signature. Patients with BC were divided into low-risk group and high-risk group by this signature in the training, testing, and overall sets. K-M analysis showed that the prognosis of patients in the high-risk group was poor and the difference in the subgroup analyses was statistically significant. ROC analysis revealed that the predictive ability of the model was more accurate than traditional assessment methods. A risk score based on FRlncRNAs signature was an independent prognostic factor for the patients with BC (HR = 1.388, 95%CI = 1.228–1.568, P < 0.001). Combining the FRlncRNAs signature and clinicopathological factors, a predictive nomogram was constructed. The nomogram can accurately predict the overall survival of patients and had high clinical practicability. The GSEA analysis showed that the primary pathways were WNT, MAPK, and cell-matrix adhesion signaling pathways. The major FRlncRNAs (MAFG-DT) were associated with poor prognosis in the GEPIA and K-M Plotter database. Conclusion Thirteen prognostic FRlncRNAs and their nomogram were accurate tools for predicting the OS of BC, which might be molecular biomarkers and therapeutic targets.
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Xiang Z, Chen X, Lv Q, Peng X. A Novel Inflammatory lncRNAs Prognostic Signature for Predicting the Prognosis of Low-Grade Glioma Patients. Front Genet 2021; 12:697819. [PMID: 34408772 PMCID: PMC8365518 DOI: 10.3389/fgene.2021.697819] [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: 05/05/2021] [Accepted: 07/05/2021] [Indexed: 11/13/2022] Open
Abstract
Background As immunotherapy has received attention as new treatments for brain cancer, the role of inflammation in the process of glioma is of particular importance. Increasing studies have further shown that long non-coding RNAs (lncRNAs) are important factors that promote the development of glioma. However, the relationship between inflammation-related lncRNAs and the prognosis of glioma patients remains unclear. The purpose of this study is to construct and validate an inflammation-related lncRNA prognostic signature to predict the prognosis of low-grade glioma patients. Methods By downloading and analyzing the gene expression data and clinical information of the Cancer Genome Atlas (TCGA) and Chinese Glioma Genome Atlas (CGGA) patients with low-grade gliomas, we could screen for inflammatory gene-related lncRNAs. Furthermore, through Cox and the Least Absolute Shrinkage and Selection Operator regression analyses, we established a risk model and divided patients into high- and low-risk groups based on the median value of the risk score to analyze the prognosis. In addition, we analyzed the tumor mutation burden (TMB) between the two groups based on somatic mutation data, and explored the difference in copy number variations (CNVs) based on the GISTIC algorithm. Finally, we used the MCPCounter algorithm to study the relationship between the risk model and immune cell infiltration, and used gene set enrichment analysis (GSEA), Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses to explore the enrichment pathways and biological processes of differentially expressed genes between the high- and low-risk groups. Results A novel prognostic signature was constructed including 11 inflammatory lncRNAs. This risk model could be an independent prognostic predictor. The patients in the high-risk group had a poor prognosis. There were significant differences in TMB and CNVs for patients in the high- and low-risk groups. In the high-risk group, the immune system was activated more significantly, and the expression of immune checkpoint-related genes was also higher. The GSEA, GO, and KEGG analyses showed that highly expressed genes in the high-risk group were enriched in immune-related processes, while lowly expressed genes were enriched in neuromodulation processes. Conclusion The risk model of 11 inflammation-related lncRNAs can serve as a promising prognostic biomarker for low-grade gliomas patients.
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Affiliation(s)
- Zijin Xiang
- Department of Pharmacy, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Xueru Chen
- Department of Pharmacy, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Qiaoli Lv
- Jiangxi Key Laboratory of Translational Cancer Research, Jiangxi Cancer Hospital of Nanchang University, Nanchang, China
| | - Xiangdong Peng
- Department of Pharmacy, The Third Xiangya Hospital, Central South University, Changsha, China
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Zhang F, Wang X, Hu H, Yang Y, Wang J, Tang Y, Li D, Bai Y, Han P. A hypoxia related long non-coding RNA signature could accurately predict survival outcomes in patients with bladder cancer. Bioengineered 2021; 12:3802-3823. [PMID: 34281486 PMCID: PMC8806425 DOI: 10.1080/21655979.2021.1948781] [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] [Indexed: 02/08/2023] Open
Abstract
Hypoxia plays a significant role in tumor progression. This study aimed to develop a hypoxia-related long noncoding RNA (lncRNA) signature for predicting survival outcomes of patients with bladder cancer (BC). The transcriptome and clinicopathologic data were downloaded from The Cancer Genome Atlas (TCGA) database. Univariate Cox regression analysis and Lasso regression analysis were used to screened lncRNAs. Ten lncRNAs were screened out and included into the hypoxia lncRNA signature. The risk score based on hypoxia lncRNA signature could accurately predict the survival outcomes of BC patients. Immune infiltration analysis showed that six types of immune cells had significant different infiltration. Tumor mutation burden (TMB) analysis showed that the risk scores between the wild types and the mutation types of TP53, FGFR3, and RB1 were significantly different. Gene Set Enrichment Analysis (GSEA) showed that cancer-associated pathways belonged to the high risk groups and immune-related signal pathways were enriched into the low risk group. Then, we constructed a predictive model with the risk score, age, and clinical stage, which showed a robust prognostic performance. An lncRNA-mRNA coexpression network was constructed, which contained 62 lncRNA-mRNA links among 10 lncRNAs and 40 related mRNAs. In summary, the hypoxia lncRNA signature could accurately predict prognosis, chemotherapy and immunotherapy response in patients with BC and was relevant to clinicopathologic parameters and immune cell infiltration.
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Affiliation(s)
- Facai Zhang
- Department of Urology/Institute of Urology, West China Hospital, Sichuan University, Sichuan Province, China.,Department of Urology, The Affiliated Hospital of Guizhou Medical University, Guizhou Province, China
| | - Xiaoming Wang
- Department of Urology/Institute of Urology, West China Hospital, Sichuan University, Sichuan Province, China
| | - Huan Hu
- School of Clinical Medicine, Guizhou Medical University, Guizhou Province, China
| | - Yubo Yang
- Department of Urology/Institute of Urology, West China Hospital, Sichuan University, Sichuan Province, China
| | - Jiahao Wang
- Department of Urology/Institute of Urology, West China Hospital, Sichuan University, Sichuan Province, China
| | - Yin Tang
- Department of Urology/Institute of Urology, West China Hospital, Sichuan University, Sichuan Province, China
| | - Dengxiong Li
- Department of Urology/Institute of Urology, West China Hospital, Sichuan University, Sichuan Province, China
| | - Yunjin Bai
- Department of Urology/Institute of Urology, West China Hospital, Sichuan University, Sichuan Province, China
| | - Ping Han
- Department of Urology/Institute of Urology, West China Hospital, Sichuan University, Sichuan Province, China.,Department of Urology, The Second People's Hospital of Yibin, Sichuan Province, China
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Zhao C, Wang Y, Tu F, Zhao S, Ye X, Liu J, Zhang J, Wang Z. A Prognostic Autophagy-Related Long Non-coding RNA (ARlncRNA) Signature in Acute Myeloid Leukemia (AML). Front Genet 2021; 12:681867. [PMID: 34276784 PMCID: PMC8278057 DOI: 10.3389/fgene.2021.681867] [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: 03/17/2021] [Accepted: 05/10/2021] [Indexed: 12/20/2022] Open
Abstract
Background Some studies have proven that autophagy and lncRNA play important roles in AML. Several autophagy related lncRNA signatures have been shown to affect the survival of patients in some other cancers. However, the role of autophagy related lncRNA in AML has not been explored yet. Hence, this study aims to find an autophagy related lncRNA signature that can affect survival for AML patients. Method A Pearson correlation analysis, a Kaplan–Meier survival curve, a univariate cox regression, and a multivariate cox regression were performed to establish an autophagy related lncRNA signature. A univariate cox regression, a multivariate cox regression, a Kaplan–Meier survival curve, and a ROC curve were applied to confirm if the signature is an independent prognosis for AML patients. The relationship between the signature and the clinical features was explored by using a T test. Gene Set Enrichment Analysis (GSEA) was used to investigate the potential tumor related pathways. Results A four-autophagy related lncRNA (MIR133A1HG, AL359715.1, MIRLET7BHG, and AL356752.1) signature was established. The high risk score based on signature was related to the short survival time of AML patients. The signature was an independent factor for the prognosis for AML patients (HR = 1.684, 95% CI = 1.324–2.142, P < 0.001). The signature was correlated with age, leukocyte numbers, and FAB (M3 or non-M3). The P53, IL6/JAK/STAT3, TNF-α, INF-γ, and IL2/STAT5 pathways might contribute to the differences between the risk groups based on signature in AML. Conclusion The four autophagy related lncRNAs and their signature might be novel biomarkers for predicting the survival of AML patients. Some biological pathways might be the potential mechanisms of the signature for the survival of AML patients.
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Affiliation(s)
- Chunxia Zhao
- School of Nursing, Nanchang University, Nanchang, China
| | - Yulu Wang
- Department of Integrated Oncology, Center for Integrated Oncology, University Hospital Bonn, Bonn, Germany
| | - Famei Tu
- Department of Nursing, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Shuai Zhao
- Department of Anesthesiology, University Hospital Bonn, Bonn, Germany
| | - Xiaoying Ye
- Department of Hematology, Shangrao People's Hospital, Shangrao, China
| | - Jing Liu
- Department of Hematology, Shangrao People's Hospital, Shangrao, China
| | - Juan Zhang
- Department of Hematology, Shangrao People's Hospital, Shangrao, China
| | - Zifeng Wang
- Department of Hematology, Shangrao People's Hospital, Shangrao, China
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Yan X, Wu HH, Chen Z, Du GW, Bai XJ, Tuoheti K, Liu TZ. Construction and Validation of an Autophagy-Related Prognostic Signature and a Nomogram for Bladder Cancer. Front Oncol 2021; 11:632387. [PMID: 34221960 PMCID: PMC8252967 DOI: 10.3389/fonc.2021.632387] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 05/05/2021] [Indexed: 12/13/2022] Open
Abstract
Objective Bladder cancer (BC) is one of the top ten cancers endangering human health but we still lack accurate tools for BC patients’ risk stratification. This study aimed to develop an autophagy-related signature that could predict the prognosis of BC. In order to provide clinical doctors with a visual tool that could precisely predict the survival probability of BC patients, we also attempted to establish a nomogram based on the risk signature. Methods We screened out autophagy-related genes (ARGs) combining weighted gene co-expression network analysis (WGCNA) and differentially expressed gene (DEG) in BC. Based on the screened ARGs, we performed survival analysis and Cox regression analysis to identify potential prognostic biomarkers. A risk signature based on the prognostic ARGs by multivariate Cox regression analysis was established, which was validated by using seven datasets. To provide clinical doctors with a useful tool for survival possibility prediction, a nomogram assessed by the ARG-based signature and clinicopathological features was constructed, verified using four independent datasets. Results Three prognostic biomarkers including BOC (P = 0.008, HR = 1.104), FGF7(P = 0.030, HR = 1.066), and MAP1A (P = 0.001, HR = 1.173) were identified and validated. An autophagy-related risk signature was established and validated. This signature could act as an independent prognostic feature in patients with BC (P = 0.047, HR = 1.419). We then constructed two nomograms with and without ARG-based signature and subsequent analysis indicated that the nomogram with ARG signature showed high accuracy for overall survival probability prediction of patients with BC (C-index = 0.732, AUC = 0.816). These results proved that the ARG signature improved the clinical net benefit of the standard model based on clinicopathological features (age, pathologic stage). Conclusions Three ARGs were identified as prognosis biomarkers in BC. An ARG-based signature was established for the first time, showing strong potential for prognosis prediction in BC. This signature was proven to improve the clinical net benefit of the standard model. A nomogram was established using this signature, which could lead to more effective prognosis prediction for BC patients.
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Affiliation(s)
- Xin Yan
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Hua-Hui Wu
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Zhao Chen
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Guo-Wei Du
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Xiao-Jie Bai
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Kurerban Tuoheti
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Tong-Zu Liu
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China
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A Novel Autophagy-Related lncRNA Gene Signature to Improve the Prognosis of Patients with Melanoma. BIOMED RESEARCH INTERNATIONAL 2021; 2021:8848227. [PMID: 34250091 PMCID: PMC8238568 DOI: 10.1155/2021/8848227] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Accepted: 05/20/2021] [Indexed: 01/04/2023]
Abstract
Objective Autophagy and long noncoding RNAs (lncRNAs) have been the focus of research on the pathogenesis of melanoma. However, the autophagy network of lncRNAs in melanoma has not been reported. The purpose of this study was to investigate the lncRNA prognostic markers related to melanoma autophagy and predict the prognosis of patients with melanoma. Methods We downloaded RNA sequencing data and clinical information of melanoma from the Cancer Genome Atlas. The coexpression of autophagy-related genes (ARGs) and lncRNAs was analyzed. The risk model of autophagy-related lncRNAs was established by univariate and multivariate Cox regression analyses, and the best prognostic index was evaluated combined with clinical data. Finally, gene set enrichment analysis was performed on patients in the high- and low-risk groups. Results According to the results of the univariate Cox analysis, only the overexpression of LINC00520 was associated with poor overall survival, unlike HLA-DQB1-AS1, USP30-AS1, AL645929, AL365361, LINC00324, and AC055822. The results of the multivariate Cox analysis showed that the overall survival of patients in the high-risk group was shorter than that recorded in the low-risk group (p < 0.001). Moreover, in the receiver operating characteristic curve of the risk model we constructed, the area under the curve (AUC) was 0.734, while the AUC of T and N was 0.707 and 0.658, respectively. The Gene Ontology was mainly enriched with the positive regulation of autophagy and the activation of the immune system. The results of the Kyoto Encyclopedia of Genes and Genomes enrichment were mostly related to autophagy, immunity, and melanin metabolism. Conclusion The positive regulation of autophagy may slow the transition from low-risk patients to high-risk patients in melanoma. Furthermore, compared with clinical information, the autophagy-related lncRNA risk model may better predict the prognosis of patients with melanoma and provide new treatment ideas.
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Li J, Du H, Chen W, Qiu M, He P, Ma Z. Identification of potential autophagy-associated lncRNA in prostate cancer. Aging (Albany NY) 2021; 13:13153-13165. [PMID: 33971627 PMCID: PMC8148478 DOI: 10.18632/aging.202997] [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: 12/22/2020] [Accepted: 03/14/2021] [Indexed: 12/17/2022]
Abstract
Background: Long non-coding RNAs (lncRNAs) have been linked to autophagy. It is urgent to identify and assess the hub autophagy-associated lncRNA in prostate cancer. Methods: Differentially expressed lncRNAs associated with autophagy were identified in prostate cancer based on The Cancer Genome Atlas Prostate Adenocarcinoma (TCGA-PRAD) data. An autophagy-mediated competing endogenous RNA network was constructed to screen for autophagy-associated lncRNA, and the preselected lncRNAs were further validated using Gene Expression Omnibus (GEO) datasets. Furthermore, a prognostic lncRNA signature was established and assessed. Additionally, Gene Set Enrichment Analysis (GSEA) revealed the underlying molecular mechanisms. Results: Using a competing endogenous RNA network, 66 differentially expressed lncRNAs associated with autophagy were identified, and the differential expression of 7 lncRNAs were verified using the TCGA-PRAD, GSE21034, and GSE94767 datasets. Additionally, a lncRNA signature associated with autophagy, including MKNK1-AS1 and INE1, was identified as an independent indicator of survival with a C-index of 0.882. The GSEA analysis indicated that several autophagy-related signaling pathways were enriched in different risk groups. Conclusions: The lncRNAs associated with autophagy were identified, and a prediction model was developed that could be used as a prognostic predictor for prostate cancer, indicating the critical role of lncRNA in the regulation of prostate cancer autophagy regulation.
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Affiliation(s)
- Jun Li
- Department of Urology, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Hong Du
- Department of Urology, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Wenqiang Chen
- Department of Urology, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Mingxing Qiu
- Department of Urology, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Peng He
- Department of Urology, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Zhiwei Ma
- Department of Urology, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China
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Chen M, Chi Y, Chen H, Zhao L. Long non-coding RNA USP30-AS1 aggravates the malignant progression of cervical cancer by sequestering microRNA-299-3p and thereby overexpressing PTP4A1. Oncol Lett 2021; 22:505. [PMID: 33986866 PMCID: PMC8114562 DOI: 10.3892/ol.2021.12766] [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: 12/19/2020] [Accepted: 04/08/2021] [Indexed: 12/12/2022] Open
Abstract
USP30 antisense RNA 1 (USP30-AS1) has been studied in bladder urothelial carcinoma. However, the detailed role of USP30-AS1 in cervical cancer remains to be elucidated. Therefore, the present study determined whether USP30-AS1 is implicated in cervical cancer malignancy, and investigated relevant molecular mechanisms. USP30-AS1 expression was measured via reverse transcription-quantitative PCR. Functional experiments, including the Cell Counting Kit-8 assay, flow cytometry, Transwell migration and invasion assays, and mouse tumour model, were performed in order to elucidate the roles of USP30-AS1. The target of USP30-AS1 was predicted using bioinformatics analysis, which was further verified via RNA immunoprecipitation and luciferase reporter assays. Herein, USP30-AS1 overexpression was detected in cervical cancer sample data from The Cancer Genome Atlas and our cohort. Patients with cervical cancer expressing high levels of USP30-AS1 exhibited shorter overall survival than those with low USP30-AS1 expression. In vitro and in vivo experiments revealed that USP30-AS1 interference promoted cell apoptosis; restrained cell proliferation, migration and invasion in vitro, and hindered tumour growth in vivo. Mechanistically, USP30-AS1 competed for microRNA-299-3p (miR-299-3p) in cervical cancer and lowered the regulatory actions of miR-299-3p on protein tyrosine phosphatase type IVA (PTP4A1), resulting in PTP4A1 overexpression. Furthermore, rescue experiments confirmed that miR-299-3p interventions or exogenous PTP4A1 could counteract the cancer-inhibiting actions of USP30-AS1 silencing on cervical cancer cells. In conclusion, the miR-299-3p/PTP4A1 axis is the downstream effector of USP30-AS1 in cervical cancer, forming the USP30-AS1/miR-299-3p/PTP4A1 pathway. This newly identified competing endogenous RNA pathway may offer a novel theoretical and experimental basis for developing promising new strategies for the targeted therapy of cervical cancer.
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Affiliation(s)
- Mengyue Chen
- Department of Gynaecology, The First People's Hospital of Chongqing Liangjiang New Area, Chongqing 401120, P.R. China
| | - Yugang Chi
- Department of Gynaecology and Obstetrics, Chongqing Health Center for Women and Children, Chongqing 400021, P.R. China
| | - Hongwei Chen
- Department of Gynaecology, The First People's Hospital of Chongqing Liangjiang New Area, Chongqing 401120, P.R. China
| | - Limei Zhao
- Department of Gynaecology, The First People's Hospital of Chongqing Liangjiang New Area, Chongqing 401120, P.R. China
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An angiogenesis-related long noncoding RNA signature correlates with prognosis in patients with hepatocellular carcinoma. Biosci Rep 2021; 41:228144. [PMID: 33764367 PMCID: PMC8026853 DOI: 10.1042/bsr20204442] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 03/18/2021] [Accepted: 03/24/2021] [Indexed: 12/12/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the most prevalent and lethal cancers worldwide. Neovascularization is closely related to the malignancy of tumors. We constructed a signature of angiogenesis-related long noncoding RNA (lncRNA) to predict the prognosis of patients with HCC. The lncRNA expression matrix of 424 HCC patients was downloaded from The Cancer Genome Atlas (TCGA). First, gene set enrichment analysis (GSEA) was used to distinguish the differentially expressed genes of the angiogenesis genes in liver cancer and adjacent tissues. Next, a signature of angiogenesis-related lncRNAs was constructed using univariate and multivariate analyses, and receiver operating characteristic (ROC) curves were used to assess the accuracy. The signature and relevant clinical information were used to construct the nomogram. A 5-lncRNA signature was highly correlated with overall survival (OS) in HCC patients and performed well in evaluations using the C-index, areas under the curve, and calibration curves. In summary, the 5-lncRNA model can serve as an accurate signature to predict the prognosis of patients with liver cancer, but its mechanism of action must be further elucidated by experiments.
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Cao H, Tong H, Zhu J, Xie C, Qin Z, Li T, Liu X, He W. A Glycolysis-Based Long Non-coding RNA Signature Accurately Predicts Prognosis in Renal Carcinoma Patients. Front Genet 2021; 12:638980. [PMID: 33868376 PMCID: PMC8047215 DOI: 10.3389/fgene.2021.638980] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 03/16/2021] [Indexed: 12/18/2022] Open
Abstract
Background The prognosis of renal cell carcinoma (RCC) varies greatly among different risk groups, and the traditional indicators have limited effect in the identification of risk grade in patients with RCC. The purpose of our study is to explore a glycolysis-based long non-coding RNAs (lncRNAs) signature and verify its potential clinical significance in prognostic prediction of RCC patients. Methods In this study, RNA data and clinical information were downloaded from The Cancer Genome Atlas (TCGA) database. Univariate and multivariate cox regression displayed six significantly related lncRNAs (AC124854.1, AC078778.1, EMX2OS, DLGAP1-AS2, AC084876.1, and AC026401.3) which were utilized in construction of risk score by a formula. The accuracy of risk score was verified by a series of statistical methods such as receiver operating characteristic (ROC) curves, nomogram and Kaplan-Meier curves. Its potential clinical significance was excavated by gene enrichment analysis. Results Kaplan-Meier curves and ROC curves showed reliability of the risk score to predict the prognosis of RCC patients. Stratification analysis indicated that the risk score was independent predictor compare to other traditional clinical parameters. The clinical nomogram showed highly rigorous with index of 0.73 and precisely predicted 1-, 3-, and 5-year survival time of RCC patients. Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene set enrichment analysis (GSEA) depicted the top ten correlated pathways in both high-risk group and low-risk group. There are 6 lncRNAs and 25 related mRNAs including 36 lncRNA-mRNA links in lncRNA-mRNA co-expression network. Conclusion This research demonstrated that glycolysis-based lncRNAs possessed an important value in survival prediction of RCC patients, which would be a potential target for future treatment.
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Affiliation(s)
- Honghao Cao
- Department of Urology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China.,Department of Urology, Rongchang Traditional Chinese Medicine Hospital, Chongqing, China
| | - Hang Tong
- Department of Urology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China.,Central Laboratory, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Junlong Zhu
- Department of Urology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China.,Central Laboratory, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Chenchen Xie
- Central Laboratory, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Zijia Qin
- Department of Urology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China.,Central Laboratory, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Tinghao Li
- Department of Urology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China.,Central Laboratory, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Xudong Liu
- Department of Urology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Weiyang He
- Department of Urology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
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66
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Wu Q, Li Q, Zhu W, Zhang X, Li H. Identification of autophagy-related long non-coding RNA prognostic signature for breast cancer. J Cell Mol Med 2021; 25:4088-4098. [PMID: 33694315 PMCID: PMC8051719 DOI: 10.1111/jcmm.16378] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 01/24/2021] [Accepted: 02/04/2021] [Indexed: 12/14/2022] Open
Abstract
Autophagy-related long non-coding RNAs (lncRNAs) disorders are related to the occurrence and development of breast cancer. The purpose of this study is to explore whether autophagy-related lncRNA can predict the prognosis of breast cancer patients. The autophagy-related lncRNAs prognostic signature was constructed by Least Absolute Shrinkage and Selection Operator (LASSO) Cox regression. We identified five autophagy-related lncRNAs (MAPT-AS1, LINC01871, AL122010.1, AC090912.1, AC061992.1) associated with prognostic value, and they were used to construct an autophagy-related lncRNA prognostic signature (ALPS) model. ALPS model offered an independent prognostic value (HR = 1.664, 1.381-2.006), where this risk score of the model was significantly related to the TNM stage, ER, PR and HER2 status in breast cancer patients. Nomogram could be utilized to predict survival for patients with breast cancer. Principal component analysis and Sankey Diagram results indicated that the distribution of five lncRNAs from the ALPS model tends to be low-risk. Gene set enrichment analysis showed that the high-risk group was enriched in autophagy and cancer-related pathways, and the low-risk group was enriched in regulatory immune-related pathways. These results indicated that the ALPS model composed of five autophagy-related lncRNAs could predict the prognosis of breast cancer patients.
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Affiliation(s)
- Qianxue Wu
- Department of the Endocrine and Breast SurgeryThe First Affiliated Hospital of Chongqing Medical UniversityChongqing Medical UniversityChongqingChina
| | - Qing Li
- Department of the Endocrine and Breast SurgeryThe First Affiliated Hospital of Chongqing Medical UniversityChongqing Medical UniversityChongqingChina
| | - Wenming Zhu
- Department of the Endocrine and Breast SurgeryThe First Affiliated Hospital of Chongqing Medical UniversityChongqing Medical UniversityChongqingChina
| | - Xiang Zhang
- Department of the Endocrine and Breast SurgeryThe First Affiliated Hospital of Chongqing Medical UniversityChongqing Medical UniversityChongqingChina
| | - Hongyuan Li
- Department of the Endocrine and Breast SurgeryThe First Affiliated Hospital of Chongqing Medical UniversityChongqing Medical UniversityChongqingChina
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Yu J, Mao W, Xu B, Chen M. Construction and validation of an autophagy-related long noncoding RNA signature for prognosis prediction in kidney renal clear cell carcinoma patients. Cancer Med 2021; 10:2359-2369. [PMID: 33650306 PMCID: PMC7982638 DOI: 10.1002/cam4.3820] [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: 11/29/2020] [Revised: 01/30/2021] [Accepted: 02/18/2021] [Indexed: 12/18/2022] Open
Abstract
Purpose The purpose of this study was to identify autophagy‐associated long noncoding RNAs (ARlncRNAs) using the kidney renal clear cell carcinoma (KIRC) patient data from The Cancer Genome Atlas (TCGA) database and to construct a prognostic risk‐related ARlncRNAs signature to accurately predict the prognosis of KIRC patients. Methods The KIRC patient data were originated from TCGA database and were classified into a training set and testing set. Seven prognostic risk‐related ARlncRNAs, identified using univariate, lasso, and multivariate Cox regression analysis, were used to construct prognostic risk‐related signatures. Kaplan–Meier curves and receiver operating characteristic (ROC) curves as well as independent prognostic factor analysis and correlation analysis with clinical characteristics were utilized to evaluate and verify the specificity and sensitivity of the signature in training set and testing set, respectively. Two nomograms were established to predict the probable 1‐, 3‐, and 5‐year survival of the KIRC patients. In addition, the lncRNA‐mRNA co‐expression network was constructed and Gene Ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) were used to identify biological functions of ARlncRNAs. Results We constructed and verified a prognostic risk‐related ARlncRNAs signature in training set and testing set, respectively. We found the survival time of KIRC patients with low‐risk scores was significantly better than those with high‐risk scores in training set and testing set. ROC curves suggested that the area under the ROC (AUC) value for prognostic risk score signature was 0.81 in training set and 0.705 in testing set. And AUC values corresponding to 1‐, 3‐, and 5 years of OS were 0.809, 0.753, and 0.794 in training set and 0.698, 0.682, and 0.754 in testing set, respectively. We established the two nomograms that confirmed high C‐index and accomplished good prediction accuracy. Conclusions We constructed a prognostic risk‐related ARlncRNAs signature that could accurately predict the prognosis of KIRC patients.
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Affiliation(s)
- JunJie Yu
- Department of medical college, Southeast University, Nanjing, China
| | - WeiPu Mao
- Department of medical college, Southeast University, Nanjing, China
| | - Bin Xu
- Department of Urology, Southeast University Zhongda hospital, Nanjing, China
| | - Ming Chen
- Department of Urology, Southeast University Zhongda hospital, Nanjing, China
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Mao X, Chen S, Li G. Identification of a ten-long noncoding RNA signature for predicting the survival and immune status of patients with bladder urothelial carcinoma based on the GEO database: a superior machine learning model. Aging (Albany NY) 2021; 13:6957-6981. [PMID: 33621953 PMCID: PMC7993680 DOI: 10.18632/aging.202553] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 12/18/2020] [Indexed: 02/05/2023]
Abstract
Bladder urothelial carcinoma (BLCA) is recognized to be immunogenic and tumorigenic. This study identified a novel long noncoding RNA (lncRNA) signature for predicting survival for patients with BLCA. A univariate Cox regression model and the random survival forest-variable hunting (RSF-VH) algorithm were employed to achieve variable selection. Ten lncRNAs (LOC105375787, CYTOR, URB1-AS1, C21orf91-OT1, CASC15, LOC101928433, FLJ45139, LINC00960, HOTAIR and TTTY19) with the highest prognostic values were identified to establish the prognostic model. The nomogram integrating the signature and clinical factors showed high concordance index values of 0.94, 0.7 and 0.90 in the three datasets, and the calibration curves showed concordance between the predicted and observed 3- and 5-year survival rates. The risk score based on the 10-lncRNA signature accurately distinguished high- and low-risk BLCA patients with different disease-specific survival(DSS) or overall survival(OS) outcomes, which were stratified according to clinical factors, including T stage and tumour grade. Gene set enrichment analysis identified BLCA-specific biological pathways and enriched functional categories, such as the cell cycle, DNA repair and immune system. Furthermore, the increased infiltration of immune cells in the high-risk group indicated that lncRNA-related inflammation may reduce the survival of BLCA patients.
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Affiliation(s)
- XuDong Mao
- Department of Urology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, People's Republic of China
| | - ShiHan Chen
- Department of Endocrinology and Metabolism, West China Hospital, Sichuan University, Chengdu, Sichuan, People's Republic of China
| | - GongHui Li
- Department of Urology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, People's Republic of China
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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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An epithelial-mesenchymal transition-related long noncoding RNA signature correlates with the prognosis and progression in patients with bladder cancer. Biosci Rep 2021; 41:227198. [PMID: 33289830 PMCID: PMC7786330 DOI: 10.1042/bsr20203944] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Revised: 12/05/2020] [Accepted: 12/08/2020] [Indexed: 12/22/2022] Open
Abstract
Bladder cancer is a common malignant tumour worldwide. Epithelial-mesenchymal transition (EMT)-related biomarkers can be used for early diagnosis and prognosis of cancer patients. To explore, accurate prediction models are essential to the diagnosis and treatment for bladder cancer. In the present study, an EMT-related long noncoding RNA (lncRNA) model was developed to predict the prognosis of patients with bladder cancer. Firstly, the EMT-related lncRNAs were identified by Pearson correlation analysis, and a prognostic EMT-related lncRNA signature was constructed through univariate and multivariate Cox regression analyses. Then, the diagnostic efficacy and the clinically predictive capacity of the signature were assessed. Finally, Gene set enrichment analysis (GSEA) and functional enrichment analysis were carried out with bioinformatics. An EMT-related lncRNA signature consisting of TTC28-AS1, LINC02446, AL662844.4, AC105942.1, AL049840.3, SNHG26, USP30-AS1, PSMB8-AS1, AL031775.1, AC073534.1, U62317.2, C5orf56, AJ271736.1, and AL139385.1 was constructed. The diagnostic efficacy of the signature was evaluated by the time-dependent receiver-operating characteristic (ROC) curves, in which all the values of the area under the ROC (AUC) were more than 0.73. A nomogram established by integrating clinical variables and the risk score confirmed that the signature had a good clinically predict capacity. GSEA analysis revealed that some cancer-related and EMT-related pathways were enriched in high-risk groups, while immune-related pathways were enriched in low-risk groups. Functional enrichment analysis showed that EMT was associated with abundant GO terms or signaling pathways. In short, our research showed that the 14 EMT-related lncRNA signature may predict the prognosis and progression of patients with bladder cancer.
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Li X, Jin F, Li Y. A novel autophagy-related lncRNA prognostic risk model for breast cancer. J Cell Mol Med 2020; 25:4-14. [PMID: 33216456 PMCID: PMC7810925 DOI: 10.1111/jcmm.15980] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 09/14/2020] [Indexed: 12/28/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are well known as crucial regulators to breast cancer development and are implicated in controlling autophagy. LncRNAs are also emerging as valuable prognostic factors for breast cancer patients. It is critical to identify autophagy-related lncRNAs with prognostic value in breast cancer. In this study, we identified autophagy-related lncRNAs in breast cancer by constructing a co-expression network of autophagy-related mRNAs-lncRNAs from The Cancer Genome Atlas (TCGA). We evaluated the prognostic value of these autophagy-related lncRNAs by univariate and multivariate Cox proportional hazards analyses and eventually obtained a prognostic risk model consisting of 11 autophagy-related lncRNAs (U62317.4, LINC01016, LINC02166, C6orf99, LINC00992, BAIAP2-DT, AC245297.3, AC090912.1, Z68871.1, LINC00578 and LINC01871). The risk model was further validated as a novel independent prognostic factor for breast cancer patients based on the calculated risk score by Kaplan-Meier analysis, univariate and multivariate Cox regression analyses and time-dependent receiver operating characteristic (ROC) curve analysis. Moreover, based on the risk model, the low-risk and high-risk groups displayed different autophagy and oncogenic statues by principal component analysis (PCA) and Gene Set Enrichment Analysis (GSEA) functional annotation. Taken together, these findings suggested that the risk model of the 11 autophagy-related lncRNAs has significant prognostic value for breast cancer and might be autophagy-related therapeutic targets in clinical practice.
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Affiliation(s)
- Xiaoying Li
- Department of Breast Surgery, The First Affiliated Hospital of China Medical University, Shenyang, China.,Department of Cell Biology, Key Laboratory of Cell Biology, Ministry of Public Health, and Key Laboratory of Medical Cell Biology, Ministry of Education, China Medical University, Shenyang, China
| | - Feng Jin
- Department of Breast Surgery, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Yang Li
- Department of Cell Biology, Key Laboratory of Cell Biology, Ministry of Public Health, and Key Laboratory of Medical Cell Biology, Ministry of Education, China Medical University, Shenyang, China
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Tamargo-Gómez I, Fernández ÁF, Mariño G. Pathogenic Single Nucleotide Polymorphisms on Autophagy-Related Genes. Int J Mol Sci 2020; 21:ijms21218196. [PMID: 33147747 PMCID: PMC7672651 DOI: 10.3390/ijms21218196] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 10/28/2020] [Accepted: 10/30/2020] [Indexed: 02/06/2023] Open
Abstract
In recent years, the study of single nucleotide polymorphisms (SNPs) has gained increasing importance in biomedical research, as they can either be at the molecular origin of a determined disorder or directly affect the efficiency of a given treatment. In this regard, sequence variations in genes involved in pro-survival cellular pathways are commonly associated with pathologies, as the alteration of these routes compromises cellular homeostasis. This is the case of autophagy, an evolutionarily conserved pathway that counteracts extracellular and intracellular stressors by mediating the turnover of cytosolic components through lysosomal degradation. Accordingly, autophagy dysregulation has been extensively described in a wide range of human pathologies, including cancer, neurodegeneration, or inflammatory alterations. Thus, it is not surprising that pathogenic gene variants in genes encoding crucial effectors of the autophagosome/lysosome axis are increasingly being identified. In this review, we present a comprehensive list of clinically relevant SNPs in autophagy-related genes, highlighting the scope and relevance of autophagy alterations in human disease.
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Affiliation(s)
- Isaac Tamargo-Gómez
- Instituto de Investigación Sanitaria del Principado de Asturias, 33011 Oviedo, Spain;
- Departamento de Biología Funcional, Universidad de Oviedo, 33011 Oviedo, Spain
| | - Álvaro F. Fernández
- Instituto de Investigación Sanitaria del Principado de Asturias, 33011 Oviedo, Spain;
- Departamento de Biología Funcional, Universidad de Oviedo, 33011 Oviedo, Spain
- Correspondence: (Á.F.F.); (G.M.); Tel.: +34-985652416 (G.M.)
| | - Guillermo Mariño
- Instituto de Investigación Sanitaria del Principado de Asturias, 33011 Oviedo, Spain;
- Departamento de Biología Funcional, Universidad de Oviedo, 33011 Oviedo, Spain
- Correspondence: (Á.F.F.); (G.M.); Tel.: +34-985652416 (G.M.)
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