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Li JY, Hu CJ, Peng H, Chen EQ. A novel immune-related long noncoding RNA (lncRNA) pair model to predict the prognosis of triple-negative breast cancer. Transl Cancer Res 2024; 13:1252-1267. [PMID: 38617505 PMCID: PMC11009803 DOI: 10.21037/tcr-23-1975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 02/08/2024] [Indexed: 04/16/2024]
Abstract
Background Breast cancer (BC) is the most prevalent cancer type and is the principal cause of cancer-related death in women. Anti-programmed cell death protein 1/programmed cell death ligand 1 (PD-1/PD-L1) immunotherapy has shown promising effects in metastatic triple-negative breast cancer (TNBC), but the potential factors affecting its efficacy have not been elucidated. Immune-related long noncoding RNAs (irlncRNAs) have been reported to be involved in immune escape to influence the carcinogenic process through the PD-1/PD-L1 signaling pathway. Therefore, exploring the potential regulatory mechanism of irlncRNAs in PD-1/PD-L1 immunotherapy in TNBC is of great importance. Methods We retrieved transcriptome profiling data from The Cancer Genome Atlas (TCGA) and identified differentially expressed irlncRNA (DEirlncRNA) pairs. Least absolute shrinkage and selection operator (LASSO) regression analysis was performed to construct a risk assessment model. Results Receiver operating characteristic (ROC) curve analysis indicated that the risk model may serve as a potential prediction tool in TNBC patients. Clinical stage and risk score were proved to be independent prognostic predictors by univariate and multivariate Cox regression analyses. Subsequently, we investigated the correlation between the risk model and tumor-infiltrating immune cells and immune checkpoints. Finally, we identified USP30-AS1 through the StarBase and Multi Experiment Matrix (MEM) databases, predicted the potential target genes of USP30-AS1, and then discovered that these target genes were closely associated with immune responses. Conclusions Our study constructed a risk assessment model by irlncRNA pairs regardless of expression levels, which contributed to predicting the efficacy of immunotherapy in TNBC. Furthermore, the lncRNA USP30-AS1 in the model was positively correlated with the expression of PD-L1 and provided a potential therapeutic target for TNBC.
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Affiliation(s)
- Jing-Ying Li
- Department of Pharmacy, West China Hospital, Sichuan University, Chengdu, China
| | - Chen-Ji Hu
- Department of Pharmacy, West China Hospital, Sichuan University, Chengdu, China
| | - Hui Peng
- Department of Pharmacy, West China Hospital, Sichuan University, Chengdu, China
| | - En-Qiang Chen
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China
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2
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Saperstein R, Goel S, Maitra R. Noncoding RNA Profile in Reovirus Treated KRAS-Mutated Colorectal Cancer Patients. Diseases 2023; 11:142. [PMID: 37873786 PMCID: PMC10594459 DOI: 10.3390/diseases11040142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 09/26/2023] [Accepted: 10/07/2023] [Indexed: 10/25/2023] Open
Abstract
PURPOSE To investigate the alterations in the expression of noncoding, micro, and small RNA expression during treatment with oncolytic reovirus in KRAS-mutated colorectal cancer. METHODS Oncolytic reovirus treatment was administered in phase 1 clinical trial (NCT01274624) for 5 days every 28 days, and blood samples were collected before the administration of the reovirus and 48 h, 8 days, and 15 days after its administration on day 1. Data from the blood samples were sorted using Transcriptome Analysis Software (TAC) 4.0, where a two-tailed t-test and a fold change filter were used to ascertain which sample signals had a statistically significant relative fold change of greater than 2 at multiple timepoints before or after oncolytic reovirus administration. RESULTS The long noncoding RNA's RP11-332M2.1 (-6.1 x), LINC01506 (-16.18 x), and LINC00534 (-1.94 x) were downregulated at 48 h after reovirus administration [p < 0.05]. ncRNA's EPB41L4A-AS1 (-6.34 x, 48 h; 11.99 x, day 8), JAK2 (2.2 x, 48 h; -2.23 x, day 8), ANXA4 (20.47 x, day 8; -7.54 x, day 15), and PCDH9 (-2.09, day 8; 1.82 x, day 15) were affected by the reovirus treatment and reflected the progress of the treatment [p < 0.05]. The small RNA SNORA26 (-1.59 x, day 8) was downregulated 48 h after the reovirus administration [p < 0.05]. The microRNA MIR-4461 (6.18 x, day 8; -3.76 x, day 15) was also affected by the reovirus administration [p < 0.05]. CONCLUSION The administration of oncolytic reovirus to treat KRAS-mutated colorectal cancer is reflected in a noncoding RNA profile, and expression levels of the ncRNAs in that profile may thus be able to be used as a potential predictive marker for reovirus-treated colorectal cancer.
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Affiliation(s)
- Rafael Saperstein
- Department of Biology, Yeshiva University, 500 W 185th St, New York, NY 10033, USA;
| | - Sanjay Goel
- Department of Oncology, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08901, USA;
| | - Radhashree Maitra
- Department of Biology, Yeshiva University, 500 W 185th St, New York, NY 10033, USA;
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Liu Y, Zhang H, Hu D, Liu S. New algorithms based on autophagy-related lncRNAs pairs to predict the prognosis of skin cutaneous melanoma patients. Arch Dermatol Res 2023; 315:1511-1526. [PMID: 36624362 DOI: 10.1007/s00403-022-02522-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 12/12/2022] [Accepted: 12/27/2022] [Indexed: 01/11/2023]
Abstract
Skin cutaneous melanoma (SKCM) is the most malignant skin tumor for it is enormously easy to develop invasion and metastasis. Autophagy is a process by which cellular material is degraded by lysosomes or vacuoles and recycled. Autophagy-related long non-coding RNAs (lncRNAs) have been thought to correlate with SKCM. This study aims to explore the prognostic significance of autophagy-related lncRNAs and establish a prognostic model of autophagy-related lncRNA pairs in SKCM. Firstly, the RNA-seq data and related clinical information were downloaded from the TCGA database. 446 qualified samples were enrolled. 222 autophagy-related genes were obtained from the HADb database. Pearson correlation analysis was conducted to identify autophagy-related lncRNAs (ARLs). After that, we obtained prognosis-related ARLs and autophagy-related lncRNA pairs (ARLPs). Using Lasso-Cox regression analysis, an autophagy-related lncRNA-pair prognostic signature was established. The accuracy of the signature were confirmed through a series of validations in terms of mutation profiles, immunity infiltration, and cellular pathways. And we used the random forest method to find USP30-AS1 as a key mediating factor in SKCM.
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Affiliation(s)
- Yuyao Liu
- Department of Burns, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui Province, China
| | - Haoxue Zhang
- Department of Dermatovenerology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui Province, China
- Key Laboratory of Dermatology, Ministry of Education, Hefei , Anhui Province, China
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Medical University, Hefei, Anhui Province, China
| | - Delin Hu
- Department of Burns, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui Province, China.
| | - Shengxiu Liu
- Department of Dermatovenerology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui Province, China.
- Key Laboratory of Dermatology, Ministry of Education, Hefei , Anhui Province, China.
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Medical University, Hefei, Anhui Province, China.
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Distefano R, Ilieva M, Madsen JH, Ishii H, Aikawa M, Rennie S, Uchida S. T2DB: A Web Database for Long Non-Coding RNA Genes in Type II Diabetes. Noncoding RNA 2023; 9:30. [PMID: 37218990 PMCID: PMC10204529 DOI: 10.3390/ncrna9030030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 05/01/2023] [Accepted: 05/04/2023] [Indexed: 05/24/2023] Open
Abstract
Type II diabetes (T2D) is a growing health problem worldwide due to increased levels of obesity and can lead to other life-threatening diseases, such as cardiovascular and kidney diseases. As the number of individuals diagnosed with T2D rises, there is an urgent need to understand the pathogenesis of the disease in order to prevent further harm to the body caused by elevated blood glucose levels. Recent advances in long non-coding RNA (lncRNA) research may provide insights into the pathogenesis of T2D. Although lncRNAs can be readily detected in RNA sequencing (RNA-seq) data, most published datasets of T2D patients compared to healthy donors focus only on protein-coding genes, leaving lncRNAs to be undiscovered and understudied. To address this knowledge gap, we performed a secondary analysis of published RNA-seq data of T2D patients and of patients with related health complications to systematically analyze the expression changes of lncRNA genes in relation to the protein-coding genes. Since immune cells play important roles in T2D, we conducted loss-of-function experiments to provide functional data on the T2D-related lncRNA USP30-AS1, using an in vitro model of pro-inflammatory macrophage activation. To facilitate lncRNA research in T2D, we developed a web application, T2DB, to provide a one-stop-shop for expression profiling of protein-coding and lncRNA genes in T2D patients compared to healthy donors or subjects without T2D.
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Affiliation(s)
- Rebecca Distefano
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark;
| | - Mirolyuba Ilieva
- Center for RNA Medicine, Department of Clinical Medicine, Aalborg University, DK-2450 Copenhagen, Denmark; (M.I.); (J.H.M.)
| | - Jens Hedelund Madsen
- Center for RNA Medicine, Department of Clinical Medicine, Aalborg University, DK-2450 Copenhagen, Denmark; (M.I.); (J.H.M.)
| | - Hideshi Ishii
- Center of Medical Innovation and Translational Research, Department of Medical Data Science, Graduate School of Medicine, Osaka University, Suita 565-0871, Japan;
| | - Masanori Aikawa
- Center for Interdisciplinary Cardiovascular Sciences, Cardiovascular Division, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA;
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Center for Excellence in Vascular Biology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Sarah Rennie
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark;
| | - Shizuka Uchida
- Center for RNA Medicine, Department of Clinical Medicine, Aalborg University, DK-2450 Copenhagen, Denmark; (M.I.); (J.H.M.)
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Liu Z, Ren C, Cai J, Yin B, Yuan J, Ding R, Ming W, Sun Y, Li Y. A Novel Aging-Related Prognostic lncRNA Signature Correlated with Immune Cell Infiltration and Response to Immunotherapy in Breast Cancer. Molecules 2023; 28:molecules28083283. [PMID: 37110517 PMCID: PMC10141963 DOI: 10.3390/molecules28083283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 03/15/2023] [Accepted: 03/21/2023] [Indexed: 04/29/2023] Open
Abstract
Breast cancer (BC) is among the most universal malignant tumors in women worldwide. Aging is a complex phenomenon, caused by a variety of factors, that plays a significant role in tumor development. Consequently, it is crucial to screen for prognostic aging-related long non-coding RNAs (lncRNAs) in BC. The BC samples from the breast-invasive carcinoma cohort were downloaded from The Cancer Genome Atlas (TCGA) database. The differential expression of aging-related lncRNAs (DEarlncRNAs) was screened by Pearson correlation analysis. Univariate Cox regression, LASSO-Cox analysis, and multivariate Cox analysis were performed to construct an aging-related lncRNA signature. The signature was validated in the GSE20685 dataset from the Gene Expression Omnibus (GEO) database. Subsequently, a nomogram was constructed to predict survival in BC patients. The accuracy of prediction performance was assessed through the time-dependent receiver operating characteristic (ROC) curves, Kaplan-Meier analysis, principal component analyses, decision curve analysis, calibration curve, and concordance index. Finally, differences in tumor mutational burden, tumor-infiltrating immune cells, and patients' response to chemotherapy and immunotherapy between the high- and low-risk score groups were explored. Analysis of the TCGA cohort revealed a six aging-related lncRNA signature consisting of MCF2L-AS1, USP30-AS1, OTUD6B-AS1, MAPT-AS1, PRR34-AS1, and DLGAP1-AS1. The time-dependent ROC curve proved the optimal predictability for prognosis in BC patients with areas under curves (AUCs) of 0.753, 0.772, and 0.722 in 1, 3, and 5 years, respectively. Patients in the low-risk group had better overall survival and significantly lower total tumor mutational burden. Meanwhile, the high-risk group had a lower proportion of tumor-killing immune cells. The low-risk group could benefit more from immunotherapy and some chemotherapeutics than the high-risk group. The aging-related lncRNA signature can provide new perspectives and methods for early BC diagnosis and therapeutic targets, especially tumor immunotherapy.
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Affiliation(s)
- Zhixin Liu
- Department of Biochemistry and Molecular Biology, Binzhou Medical University, Yantai 264003, China
- Department of Orthopedics, Qilu Hospital of Shandong University, Jinan 250012, China
| | - Chongkang Ren
- Department of Biochemistry and Molecular Biology, Binzhou Medical University, Yantai 264003, China
| | - Jinyi Cai
- Department of Biochemistry and Molecular Biology, Binzhou Medical University, Yantai 264003, China
| | - Baohui Yin
- Department of Pediatrics, Yantai Affiliated Hospital of Binzhou Medical University, Yantai 264100, China
| | - Jingjie Yuan
- Department of Biochemistry and Molecular Biology, Binzhou Medical University, Yantai 264003, China
| | - Rongjuan Ding
- Department of Biochemistry and Molecular Biology, Binzhou Medical University, Yantai 264003, China
| | - Wenzhuo Ming
- Department of Biochemistry and Molecular Biology, Binzhou Medical University, Yantai 264003, China
| | - Yunxiao Sun
- Department of Pediatrics, Yantai Affiliated Hospital of Binzhou Medical University, Yantai 264100, China
| | - Youjie Li
- Department of Biochemistry and Molecular Biology, Binzhou Medical University, Yantai 264003, China
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Xiang X, Guo Y, Chen Z, Zhang F, Huang J, Qin Y. A prognostic risk prediction model based on ferroptosis-related long non-coding RNAs in bladder cancer: A bulk RNA-seq research and scRNA-seq validation. Medicine (Baltimore) 2022; 101:e32558. [PMID: 36595859 PMCID: PMC9794272 DOI: 10.1097/md.0000000000032558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND To construct a prognostic risk model of bladder cancer (BC) from the perspective of long non-coding RNAs (lncRNAs) and ferroptosis, in order to guide clinical prognosis and identify potential therapeutic targets. METHODS In-hours BC samples were collected from 4 patients diagnosed with BC, who underwent radical cystectomy. Single cell transcriptome sequencing was performed and Seurat package were used for quality control and secondary analysis. LncRNAs expression profiles of BC samples were extracted from The Cancer Genome Atlas database. And sex, age, tumor, node, metastasis stage and other clinical data was downloaded at the same time. Ferroptosis-related lncRNAs were identified by co-expression analysis. We constructed a risk model by Cox regression and least absolute shrinkage and selection operator regression analyses. The predictive strength of the risk model for overall survival (OS) of patients with BC was evaluated by the log-rank test and Kaplan-Meier method. Finally, the enrichment analysis was performed and visualized. RESULTS We identified and included 15 prognostic ferroptosis-related lncRNAs (AL356740.1, FOXC2AS1, ZNF528AS1, LINC02535, PSMB8AS1, AL590428.1, AP000347.2, OCIAD1-AS1, AP001347.1, AC104986.2, AC018926.2, LINC00867, AC099518.4, USP30-AS1, and ARHGAP5-AS1), to build our ferroptosis-related lncRNAs risk model. Using this risk model, BC patients were divided into high and low-risk groups, and their respective survival lengths were calculated. The results showed that the OS of the low-risk group was significantly longer than that of the high-risk group. A nomogram was utilized to predict the survival rate of BC patients. As indicated in the nomogram, risk score was the most important indicator of OS in patients with BC. The ferroptosis-related lncRNAs risk model is an independent tool for prognostic risk assessment in patients with BC. Single cell transcriptome sequencing suggests that ferroptosis-related lncRNAs express specifically in BC tumor microenvironment. AL356740.1, LINC02535 and LINC00867 were mainly expressed in tumor cells. CONCLUSION The risk model based on the ferroptosis-related lncRNAs and the genomic clinico-pathological nomogram could be used to accurately predict the prognosis of patients with BC. The lncRNAs used to build this model might become potential therapeutic targets in the future.
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Affiliation(s)
- Xuebao Xiang
- Department of Urology, Affiliated Hospital of Guilin Medical College, Guilin, People’s Republic of China
- Centre for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, People’s Republic of China
| | - Yi Guo
- Centre for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, People’s Republic of China
| | - Zhongyuan Chen
- Centre for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, People’s Republic of China
| | - Fangxin Zhang
- Centre for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, People’s Republic of China
| | - Jiefu Huang
- Department of Urology, Affiliated Hospital of Guilin Medical College, Guilin, People’s Republic of China
| | - Yan Qin
- Department of Health Management, The People’s Hospital of Guangxi Zhuang Autonomous Region & Research center of Health Management, Guangxi Academy of Medical Sciences, Nanning, People’s Republic of China
- * Correspondence: Yan Qin, Department of Health Management, The People’s Hospital of Guangxi Zhuang Autonomous Region & Research center of Health Management, Guangxi Academy of Medical Sciences, Nanning, Guangxi 530021, People’s Republic of China (e-mail: )
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Dai L, Liang W, Shi Z, Li X, Zhou S, Hu W, Yang Z, Wang X. Systematic characterization and biological functions of non-coding RNAs in glioblastoma. Cell Prolif 2022; 56:e13375. [PMID: 36457281 PMCID: PMC9977673 DOI: 10.1111/cpr.13375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 11/02/2022] [Accepted: 11/22/2022] [Indexed: 12/05/2022] Open
Abstract
Glioblastoma multiforme (GBM) is the most malignant and aggressive type of glioma. Non-coding RNAs (ncRNAs) are RNAs that do not encode proteins but widely exist in eukaryotic cells. The common characteristics of these RNAs are that they can all be transcribed from the genome without being translated into proteins, thus performing biological functions, particularly microRNAs (miRNAs), long non-coding RNAs (lncRNAs) and circular RNAs. Studies have found that ncRNAs are associated with the occurrence and development of GBM, and there is a complex regulatory network among ncRNAs, which can regulate cell proliferation, migration, apoptosis and differentiation, thus provide a basis for the development of highly specific diagnostic tools and therapeutic strategies in the future. The present review aimed to comprehensively describe the biogenesis, general features and functions of regulatory ncRNAs in GBM, and to interpret the potential biological functions of these ncRNAs in GBM as well as their impact on clinical diagnosis, treatment and prognosis and discusses the potential mechanisms of these RNA subtypes leading to cancer in order to contribute to the better design of personalized GBM therapies in the future.
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Affiliation(s)
- Lirui Dai
- Department of NeurosurgeryThe Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou UniversityZhengzhouChina,Institute of Neuroscience, Zhengzhou UniversityZhengzhouChina,Henan International Joint Laboratory of Glioma Metabolism and Microenvironment ResearchZhengzhouHenanChina
| | - Wulong Liang
- Department of NeurosurgeryThe Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou UniversityZhengzhouChina,Henan International Joint Laboratory of Glioma Metabolism and Microenvironment ResearchZhengzhouHenanChina
| | - Zimin Shi
- Department of NeurosurgeryThe Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou UniversityZhengzhouChina,Institute of Neuroscience, Zhengzhou UniversityZhengzhouChina,Henan International Joint Laboratory of Glioma Metabolism and Microenvironment ResearchZhengzhouHenanChina
| | - Xiang Li
- Department of NeurosurgeryThe Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou UniversityZhengzhouChina,Institute of Neuroscience, Zhengzhou UniversityZhengzhouChina,Henan International Joint Laboratory of Glioma Metabolism and Microenvironment ResearchZhengzhouHenanChina
| | - Shaolong Zhou
- Department of NeurosurgeryThe Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou UniversityZhengzhouChina,Henan International Joint Laboratory of Glioma Metabolism and Microenvironment ResearchZhengzhouHenanChina
| | - Weihua Hu
- Department of NeurosurgeryThe Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou UniversityZhengzhouChina,Henan International Joint Laboratory of Glioma Metabolism and Microenvironment ResearchZhengzhouHenanChina
| | - Zhuo Yang
- Department of NeurosurgeryThe Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou UniversityZhengzhouChina,Henan International Joint Laboratory of Glioma Metabolism and Microenvironment ResearchZhengzhouHenanChina
| | - Xinjun Wang
- Department of NeurosurgeryThe Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou UniversityZhengzhouChina,Institute of Neuroscience, Zhengzhou UniversityZhengzhouChina,Henan International Joint Laboratory of Glioma Metabolism and Microenvironment ResearchZhengzhouHenanChina
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Li W, Liu J, Zhu W, Jin X, Yang Z, Gao W, Sun J, Zhu H. Identification of biomarkers for hepatocellular carcinoma based on single cell sequencing and machine learning algorithms. Front Genet 2022; 13:873218. [PMID: 36353113 PMCID: PMC9638064 DOI: 10.3389/fgene.2022.873218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 08/12/2022] [Indexed: 11/30/2022] Open
Abstract
Hepatocellular carcinoma (HCC) remains one of the most lethal cancers around the world. Precision oncology will be crucial for further improving the prognosis of HCC patients. Compared with traditional bulk RNA-seq, single-cell RNA sequencing (scRNA-seq) enables the transcriptomes of a great deal of individual cells assayed in an unbiased manner, showing the potential to deeply reveal tumor heterogeneity. In this study, based on the scRNA-seq results of primary neoplastic cells and paired normal liver cells from eight HCC patients, a new strategy of machine learning algorithms was applied to screen core biomarkers that distinguished HCC tumor tissues from the adjacent normal liver. Expression profiles of HCC cells and normal liver cells were first analyzed by maximum relevance minimum redundancy (mRMR) to get a top 50 signature gene feature. For further analysis, the incremental feature selection (IFS) method and leave-one-out cross validation (LOOCV) were conducted to build an optimal classification model and to extract 21 potentially essential biomarkers for HCC cells. Our results provided new insights into HCC pathogenesis that might be valuable for HCC diagnosis and therapy.
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Affiliation(s)
- Weimin Li
- Department of Hepatobiliary and Pancreatic Surgery, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
- School of Information, Hunan University of Humanities, Science and Technology, Loudi, China
| | - Jixing Liu
- Department of Hepatobiliary and Pancreatic Surgery, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Wenjuan Zhu
- Division of Nephrology, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong, China
| | - Xiaoxin Jin
- The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Zhi Yang
- Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Wenzhe Gao
- Department of Hepatobiliary and Pancreatic Surgery, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
- *Correspondence: Wenzhe Gao, ; Jichun Sun, ; Hongwei Zhu,
| | - Jichun Sun
- Department of Hepatobiliary and Pancreatic Surgery, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
- *Correspondence: Wenzhe Gao, ; Jichun Sun, ; Hongwei Zhu,
| | - Hongwei Zhu
- Department of Hepatobiliary and Pancreatic Surgery, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
- *Correspondence: Wenzhe Gao, ; Jichun Sun, ; Hongwei Zhu,
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Xie J, Tian W, Tang Y, Zou Y, Zheng S, Wu L, Zeng Y, Wu S, Xie X, Xie X. Establishment of a Cell Necroptosis Index to Predict Prognosis and Drug Sensitivity for Patients With Triple-Negative Breast Cancer. Front Mol Biosci 2022; 9:834593. [PMID: 35601830 PMCID: PMC9117653 DOI: 10.3389/fmolb.2022.834593] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 04/04/2022] [Indexed: 12/25/2022] Open
Abstract
Background: Necroptosis has been an alternatively identified mechanism of programmed cancer cell death, which plays a significant role in cancer. However, research about necroptosis-related long noncoding RNAs (lncRNAs) in cancer are still few. Moreover, the potentially prognostic value of necroptosis-related lncRNAs and their correlation with the immune microenvironment remains unclear. The present study aimed to explore the potential prognostic value of necroptosis-related lncRNAs and their relationship to immune microenvironment in triple-negative breast cancer (TNBC). Methods: The RNA expression matrix of patients with TNBC was obtained from The Cancer Genome Atlas (TCGA) and the Gene Expression Omnibus (GEO) databases. Finally, 107 patients of GSE58812, 159 patients of TCGA, and 143 patients of GSE96058 were included. Necroptosis-related lncRNAs were screened by Cox regression and Pearson correlation analysis with necroptosis-related genes. By LASSO regression analysis, nine necroptosis-related lncRNAs were employed, and a cell necroptosis index (CNI) was established; then, we evaluated its prognostic value, clinical significance, pathways, immune infiltration, and chemotherapeutics efficacy. Results: Based on the CNI value, the TNBC patients were divided into high- and low-CNI groups, and the patients with high CNI had worse prognosis, more lymph node metastasis, and larger tumor (p < 0.05). The receiver operating characteristic (ROC) analysis showed that the signature performed well. The result of the infiltration proportion of different immune cell infiltration further explained that TNBC patients with high CNI had low immunogenicity, leading to poor therapeutic outcomes. Moreover, we found significant differences of the IC50 values of various chemotherapeutic drugs in the two CNI groups, which might provide a reference to make a personalized chemotherapy for them. Conclusion: The novel prognostic marker CNI could not only precisely predict the survival probability of patients with TNBC but also demonstrate a potential role in antitumor immunity and drug sensitivity.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Xinhua Xie
- *Correspondence: Xinhua Xie, ; Xiaoming Xie,
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10
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Li C, Liang X, Liu Y. lncRNA USP30-AS1 sponges miR-765 and modulates the progression of colon cancer. World J Surg Oncol 2022; 20:73. [PMID: 35260141 PMCID: PMC8905834 DOI: 10.1186/s12957-022-02529-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 02/15/2022] [Indexed: 11/30/2022] Open
Abstract
Background The incidence and mortality of colon cancer is increasing recently. It is necessary to identify effective biomarkers for the progression and prognosis of colon cancer. To assess the potential of lncRNA USP30-AS1 (USP30-AS1) in serving as the biomarker of colon cancer and unearth the underlying mechanism. Methods There were 123 colon cancer patients enrolled. The expression of USP30-AS1 was evaluated with PCR in tissue and cell samples. The clinical significance of USP30-AS1 was assessed with a series of statistical methods, while the CCK8 and Transwell assay were conducted to estimate its biological effect on the colon cancer cellular processes. In mechanism, the interaction of USP30-AS1 with miR-765 was evaluated with the dual-luciferase reporter assay. Results In colon cancer tissues, the USP30-AS1 downregulation and the miR-765 upregulation were observed, and there was a negative correlation between the USP30-AS1 expression level and the miR-765 expression level. The downregulation of USP30-AS1 related to the malignant progression and served as an adverse prognostic indicator of colon cancer. The overexpression of USP30-AS1 dramatically suppressed colon cancer cellular processes, which was alleviated by miR-765. Conclusions USP30-AS1 predicts the malignancy and prognosis of colon cancer patients. USP30-AS1 suppressed the progression of colon cancer through modulating miR-765.
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Affiliation(s)
- Chengren Li
- Department of Anorectal Surgery, Weifang People's Hospital, No.151, Guangwen Street, Weifang, 261000, Shandong, China
| | - Xu Liang
- Department of Anorectal Surgery, Weifang People's Hospital, No.151, Guangwen Street, Weifang, 261000, Shandong, China
| | - Yongguang Liu
- Department of Anorectal Surgery, Weifang People's Hospital, No.151, Guangwen Street, Weifang, 261000, Shandong, China.
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Peng Y, Wang H, Huang Q, Wu J, Zhang M. A prognostic model based on immune-related long noncoding RNAs for patients with epithelial ovarian cancer. J Ovarian Res 2022; 15:8. [PMID: 35031063 PMCID: PMC8760785 DOI: 10.1186/s13048-021-00930-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 11/29/2021] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Long noncoding RNAs (lncRNAs) are important regulators of gene expression and can affect a variety of physiological processes. Recent studies have shown that immune-related lncRNAs play an important role in the tumour immune microenvironment and may have potential application value in the treatment and prognosis prediction of tumour patients. Epithelial ovarian cancer (EOC) is characterized by a high incidence and poor prognosis. However, there are few studies on immune-related lncRNAs in EOC. In this study, we focused on immune-related lncRNAs associated with survival in EOC. METHODS We downloaded mRNA data for EOC patients from The Cancer Genome Atlas (TCGA) database and mRNA data for normal ovarian tissue from the Genotype-Tissue Expression (GTEx) database and identified differentially expressed genes through differential expression analysis. Immune-related lncRNAs were obtained through intersection and coexpression analysis of differential genes and immune-related genes from the Immunology Database and Analysis Portal (ImmPort). Samples in the TCGA EOC cohort were randomly divided into a training set, validation set and combination set. In the training set, Cox regression analysis and LASSO regression were performed to construct an immune-related lncRNA signature. Kaplan-Meier survival analysis, time-dependent ROC curve analysis, Cox regression analysis and principal component analysis were performed for verification in the training set, validation set and combination set. Further studies of pathways and immune cell infiltration were conducted through Gene Set Enrichment Analysis (GSEA) and the Timer data portal. RESULTS An immune-related lncRNA signature was identified in EOC, which was composed of six immune-related lncRNAs (KRT7-AS, USP30-AS1, AC011445.1, AP005205.2, DNM3OS and AC027348.1). The signature was used to divide patients into high-risk and low-risk groups. The overall survival of the high-risk group was lower than that of the low-risk group and was verified to be robust in both the validation set and the combination set. The signature was confirmed to be an independent prognostic biomarker. Principal component analysis showed the different distribution patterns of high-risk and low-risk groups. This signature may be related to immune cell infiltration (mainly macrophages) and differential expression of immune checkpoint-related molecules (PD-1, PDL1, etc.). CONCLUSIONS We identified and established a prognostic signature of immune-related lncRNAs in EOC, which will be of great value in predicting the prognosis of clinical patients and may provide a new perspective for immunological research and individualized treatment in EOC.
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Affiliation(s)
- Yao Peng
- Department of Oncology, The Second Affiliated Hospital of Anhui Medical University, No. 678, Furong Road, Hefei, 230601, Anhui, P.R. China.,Anhui Medical University, No. 81, Meishan Road, Hefei, 230032, Anhui, P.R. China
| | - Hui Wang
- Department of Oncology, Lu'an People's Hospital of Anhui Province, No. 21, West Anhui Road, Lu'an, 237006, Anhui, P.R. China
| | - Qi Huang
- Department of Oncology, The Second Affiliated Hospital of Anhui Medical University, No. 678, Furong Road, Hefei, 230601, Anhui, P.R. China
| | - Jingjing Wu
- Department of Oncology, The Second Affiliated Hospital of Anhui Medical University, No. 678, Furong Road, Hefei, 230601, Anhui, P.R. China
| | - Mingjun Zhang
- Department of Oncology, The Second Affiliated Hospital of Anhui Medical University, No. 678, Furong Road, Hefei, 230601, Anhui, P.R. China. .,Anhui Medical University, No. 81, Meishan Road, Hefei, 230032, Anhui, P.R. China.
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12
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Wu Q, Zhang Z, Ji M, Yan T, Jiang Y, Chen Y, Chang J, Zhang J, Tang D, Zhu D, Wei Y. The Establishment and Experimental Verification of an lncRNA-Derived CD8+ T Cell Infiltration ceRNA Network in Colorectal Cancer. Clin Med Insights Oncol 2022; 16:11795549221092218. [PMID: 35479766 PMCID: PMC9036385 DOI: 10.1177/11795549221092218] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 03/17/2022] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Long noncoding RNAs (LncRNA) lead a vital role in colorectal cancer (CRC) development. The infiltrating CD8+ T cell is the main target of immunotherapy. Our study aimed to figure out the potential mechanism of lncRNAs regulating the function of CD8+ T cells in CRC. METHODS We collected bulk RNA-seq, miRNA-seq, and single-cell RNA-seq (scRNA-seq) data from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) database. The cibersort algorithm and correlation analysis were used to estimate the abundance of CD8+ T cells and screened out the most relevant lncRNAs. We used scRNA-seq data to identify the main cell lncRNA expressed. Furthermore, one competing endogenous RNA (ceRNA) network focusing on the potential mechanism of lncRNA-derived CD8+ T cell infiltration was constructed. We established a co-culture system to assess the immunosuppressive function of the lncRNA. And we evaluated the effects of the lncRNA on CD8+ T cell cytotoxicity by flow cytometry, qPCR, and clone formation assay. RESULTS Three CD8+ T cell infiltration-related lncRNAs were identified, and LINC00657 was expressed mainly in tumor cells, negatively associated with CD8+ T cell infiltration. Hsa-miRNA-1224-3p and hsa-miRNA-338-5p and SCD, ETS2, UBE2H, and YY1 were identified to construct the ceRNA network. Immunosuppression-related tumor marker CD155 was proved to be positively correlated with LINC00657 and mRNAs in the ceRNA network. In addition, we proved that LINC00657 could impair the cytotoxicity of CD8+ T cells, and its expression was positively associated with CD155 in vitro. CONCLUSIONS We successfully constructed an lncRNA-derived CD8+ T cell infiltration ceRNA network in CRC. LINC00657 may play a leading role in the CRC immune escape and could be a novel immunotherapy target.
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Affiliation(s)
- Qi Wu
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
- Shanghai Engineering Research Center of Colorectal Cancer Minimally Invasive Technology, Shanghai, China
- Cancer Center, Zhongshan Hospital, Shanghai, China
| | - Zhiyuan Zhang
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
- Shanghai Engineering Research Center of Colorectal Cancer Minimally Invasive Technology, Shanghai, China
- Cancer Center, Zhongshan Hospital, Shanghai, China
| | - Meiling Ji
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
- Shanghai Engineering Research Center of Colorectal Cancer Minimally Invasive Technology, Shanghai, China
- Cancer Center, Zhongshan Hospital, Shanghai, China
| | - Tao Yan
- Department of Cardiovascular Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yudong Jiang
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
- Shanghai Engineering Research Center of Colorectal Cancer Minimally Invasive Technology, Shanghai, China
- Cancer Center, Zhongshan Hospital, Shanghai, China
| | - Yijiao Chen
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
- Shanghai Engineering Research Center of Colorectal Cancer Minimally Invasive Technology, Shanghai, China
- Cancer Center, Zhongshan Hospital, Shanghai, China
| | - Jiang Chang
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
- Shanghai Engineering Research Center of Colorectal Cancer Minimally Invasive Technology, Shanghai, China
- Cancer Center, Zhongshan Hospital, Shanghai, China
| | - Jicheng Zhang
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
- Shanghai Engineering Research Center of Colorectal Cancer Minimally Invasive Technology, Shanghai, China
- Cancer Center, Zhongshan Hospital, Shanghai, China
| | - Dong Tang
- Department of General Surgery, Institute of General Surgery, Northern Jiangsu People’s Hospital, Clinical Medical College, Yangzhou University, Yangzhou, China
| | - Dexiang Zhu
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
- Shanghai Engineering Research Center of Colorectal Cancer Minimally Invasive Technology, Shanghai, China
- Cancer Center, Zhongshan Hospital, Shanghai, China
| | - Ye Wei
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
- Shanghai Engineering Research Center of Colorectal Cancer Minimally Invasive Technology, Shanghai, China
- Cancer Center, Zhongshan Hospital, Shanghai, China
- Ye Wei, Department of General Surgery, Zhongshan Hospital, Fudan University, 180 Fenglin Road, 200030, Shanghai, China.
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Mathias C, Muzzi JCD, Antunes BB, Gradia DF, Castro MAA, Carvalho de Oliveira J. Unraveling Immune-Related lncRNAs in Breast Cancer Molecular Subtypes. Front Oncol 2021; 11:692170. [PMID: 34136413 PMCID: PMC8202402 DOI: 10.3389/fonc.2021.692170] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 05/06/2021] [Indexed: 12/15/2022] Open
Abstract
Breast cancer (BRCA) is the most leading cause of cancer worldwide. It is a heterogeneous disease with at least five molecular subtypes including luminal A, luminal B, basal-like, HER2-enriched, and normal-like. These five molecular subtypes are usually stratified according to their mRNA profile patterns; however, ncRNAs are increasingly being used for this purpose. Among the ncRNAs class, the long non-coding RNAs (lncRNAs) are molecules with more than 200 nucleotides with versatile regulatory roles; and high tissue-specific expression profiles. The heterogeneity of BRCA can also be reflected regarding tumor microenvironment immune cells composition, which can directly impact a patient's prognosis and therapy response. Using BRCA immunogenomics data from a previous study, we propose here a bioinformatics approach to include lncRNAs complexity in BRCA molecular and immune subtype. RNA-seq data from The Cancer Genome Atlas (TCGA) BRCA cohort was analyzed, and signal-to-noise ratio metrics were applied to create these subtype-specific signatures. Five immune-related signatures were generated with approximately ten specific lncRNAs, which were then functionally analyzed using GSEA enrichment and survival analysis. We highlighted here some lncRNAs in each subtype. LINC01871 is related to immune response activation and favorable overall survival in basal-like samples; EBLN3P is related to immune response suppression and progression in luminal B, MEG3, XXYLT1-AS2, and LINC02613 were related with immune response activation in luminal A, HER2-enriched and normal-like subtypes, respectively. In this way, we emphasize the need to know better the role of lncRNAs as regulators of immune response to provide new perspectives regarding diagnosis, prognosis and therapeutical targets in BRCA molecular subtypes.
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Affiliation(s)
- Carolina Mathias
- Department of Genetics, Federal University of Parana, Post-graduation Program in Genetics, Curitiba, Brazil
| | - João Carlos Degraf Muzzi
- Bioinformatics and Systems Biology Lab, Federal University of Parana (UFPR), Polytechnic Center, Curitiba, Brazil.,Immunochemistry Laboratory (LIMQ), Federal University of Parana, Post-graduation Program in Microbiology, Parasitology and Pathology, Curitiba, Brazil.,Instituto de Pesquisa Pelé Pequeno Príncipe, Oncology Division, Curitiba, Brazil
| | - Bruna Borba Antunes
- Department of Genetics, Federal University of Parana, Post-graduation Program in Genetics, Curitiba, Brazil.,Bioinformatics and Systems Biology Lab, Federal University of Parana (UFPR), Polytechnic Center, Curitiba, Brazil
| | - Daniela F Gradia
- Department of Genetics, Federal University of Parana, Post-graduation Program in Genetics, Curitiba, Brazil
| | - Mauro A A Castro
- Bioinformatics and Systems Biology Lab, Federal University of Parana (UFPR), Polytechnic Center, Curitiba, Brazil
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