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Luo H, Jing H, Chen W. An extensive overview of the role of lncRNAs generated from immune cells in the etiology of cancer. Int Immunopharmacol 2024; 133:112063. [PMID: 38677091 DOI: 10.1016/j.intimp.2024.112063] [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: 02/03/2024] [Revised: 04/07/2024] [Accepted: 04/08/2024] [Indexed: 04/29/2024]
Abstract
Long non-coding RNAs (lncRNAs) are involved in the control of critical tumor-suppressor and oncogenic pathways in cancer. These types of non-coding RNAs could affect both immune and cancer cells. The thorough analysis of lncRNAs derived from immune cells and the incorporation of new findings significantly advance our understanding of the complex role of lncRNAs in the context of cancer. This work highlights the promise of lncRNAs for translational therapeutic approaches while also establishing a solid foundation for comprehending the complex link between lncRNAs and cancer through a coherent narrative. The main findings of this article are that types of lncRNAs derived from immune cells, such as MM2P and MALAT1, can affect the behaviors of cancer cells, like invasion, angiogenesis, and proliferation. As research in this area grows, the therapeutic potential of targeting these lncRNAs offers promising opportunities for expanding our understanding of cancer biology and developing cutting-edge, precision-based therapies for cancer therapy.
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Affiliation(s)
- Hong Luo
- Department of Oncology, Yancheng Branch of Nanjing Drum Tower Hospital, Yancheng, Jiangsu Province, China.
| | - Hailiang Jing
- Department of Integrative Medicine, Yancheng Branch of Nanjing Drum Tower Hospital, Yancheng, Jiangsu Province, China
| | - Wei Chen
- Department of Oncology, Tumor Hospital Affiliated to Nantong University, Nantong, Jiangsu Province, China
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2
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Vishnubalaji R, Alajez NM. Long non-coding RNA AC099850.4 correlates with advanced disease state and predicts worse prognosis in triple-negative breast cancer. Front Med (Lausanne) 2023; 10:1149860. [PMID: 37727755 PMCID: PMC10505935 DOI: 10.3389/fmed.2023.1149860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 07/25/2023] [Indexed: 09/21/2023] Open
Abstract
Our understanding of the function of long non-coding RNAs (lncRNAs) in health and disease states has evolved over the past decades due to the many advances in genome research. In the current study, we characterized the lncRNA transcriptome enriched in triple-negative breast cancer (TNBC, n = 42) and estrogen receptor (ER+, n = 42) breast cancer compared to normal breast tissue (n = 56). Given the aggressive nature of TNBC, our data revealed selective enrichment of 57 lncRNAs in TNBC. Among those, AC099850.4 lncRNA was chosen for further investigation where it exhibited elevated expression, which was further confirmed in a second TNBC cohort (n = 360) where its expression correlated with a worse prognosis. Network analysis of AC099850.4high TNBC highlighted enrichment in functional categories indicative of cell cycle activation and mitosis. Ingenuity pathway analysis on the differentially expressed genes in AC099850.4high TNBC revealed the activation of the canonical kinetochore metaphase signaling pathway, pyridoxal 5'-phosphate salvage pathway, and salvage pathways of pyrimidine ribonucleotides. Additionally, upstream regulator analysis predicted the activation of several upstream regulator networks including CKAP2L, FOXM1, RABL6, PCLAF, and MITF, while upstream regulator networks of TP53, NUPR1, TRPS1, and CDKN1A were suppressed. Interestingly, elevated expression of AC099850.4 correlated with worse short-term relapse-free survival (log-rank p = 0.01). Taken together, our data are the first to reveal AC099850.4 as an unfavorable prognostic marker in TNBC, associated with more aggressive clinicopathological features, and suggest its potential utilization as a prognostic biomarker and therapeutic target in TNBC.
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Affiliation(s)
- Radhakrishnan Vishnubalaji
- Translational Cancer and Immunity Center (TCIC), Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), Doha, Qatar
| | - Nehad M. Alajez
- Translational Cancer and Immunity Center (TCIC), Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), Doha, Qatar
- College of Health and Life Sciences, Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), Doha, Qatar
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Wu X, Zhang Y, Liang G, Ye H. Cuproptosis-related lncRNAs potentially predict prognosis and therapy sensitivity of breast cancer. Front Pharmacol 2023; 14:1199883. [PMID: 37529698 PMCID: PMC10390311 DOI: 10.3389/fphar.2023.1199883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 07/03/2023] [Indexed: 08/03/2023] Open
Abstract
Background: Cuproptosis-related lncRNAs regulate the biological functions of various cancers. However, the role of cuproptosis-related lncRNAs in breast cancer remains unclear. In this study, we investigated the biological functions and clinical applications of cuproptosis-related lncRNAs in breast cancer. Methods: The Cancer Genome Atlas (TCGA) database and the GSE20685 dataset were used for screening cuproptosis-related lncRNAs. Colony formation and CCK-8 kit assays were performed for detecting the proliferative function of cuproptosis-related lncRNAs, whereas wound healing, migration, and invasion assays were performed for detecting the metastatic regulation of cuproptosis-related lncRNAs in breast cancer. Finally, a prognostic cuproptosis-related lncRNA model was constructed using LASSO Cox regression analysis for detecting survival and sensitivity to conventional treatment (endocrine therapy, chemotherapy, and radiotherapy) and novel therapy (PARP and CDK4/6 inhibitors). Results: In this study, we screened six cuproptosis-related lncRNAs associated with the survival of patients with breast cancer. Biofunctional experiments indicated that cuproptosis-related lncRNAs play essential roles in regulating the proliferation and metastasis of breast cancer cells. Finally, we applied a model of six cuproptosis-related lncRNAs to classify the patients into high- and low-risk groups. High-risk group patients exhibited worse survival rates (p < 0.001) and lower sensitivity to chemotherapy, endocrine therapy, and radiation therapy. Compared with high-risk patients, low-risk patients exhibited a lower expression of CDK4/6 inhibitor-resistant biomarkers (CCNE1, E2F1, and E2F2) and PARP inhibitor-resistant biomarkers (BRCA1/BRCA2), indicating that patients in the low-risk group were more suitable for PARP inhibitor and CDK4/6 inhibitor application. Conclusion: Cuproptosis-related lncRNAs are essential for regulating the biological functions of breast cancer, and they have the potential to predict prognosis and sensitivity of breast cancer to various therapies.
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Affiliation(s)
- Xiwen Wu
- Department of Clinical Nutrition, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Ying Zhang
- Staff and Faculty Clinic, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Gehao Liang
- Department of Breast Surgery, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Huizhen Ye
- Staff and Faculty Clinic, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
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Hou Y, Tang Y, Ma C, Yu J, Jia Y. Overexpression of CASC19 contributes to tumor progression and predicts poor prognosis after radical resection in hepatocellular carcinoma. Dig Liver Dis 2023; 55:799-806. [PMID: 36805849 DOI: 10.1016/j.dld.2022.12.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 11/29/2022] [Accepted: 12/04/2022] [Indexed: 02/23/2023]
Abstract
BACKGROUND Long non-coding RNAs (lncRNAs) have been implicated as functional molecules in hepatocellular carcinoma (HCC) progression. The present research aimed to investigate the levels of LncRNA cancer susceptibility candidate gene 19 (CASC19) in HCC tissues and cell lines and to explore its potential role in the diagnosis and prognosis of HCC. METHODS HCC tissues and cell lines were collected to assess the levels of CASC19 by real-time quantitative reverse transcription PCR (RT-qPCR). The prognostic value of CASC19 was evaluated using the Kaplan-Meier method and Cox regression analysis. The functional role of CASC19 in regulating HCC cell proliferation, migration, and invasion was evaluated by Cell Counting Kit-8 (CCK-8) and Transwell analysis. The potential targeted miR-140-5p of CASC19 was confirmed by a dual-luciferase reporter assay. RESULTS High CASC19 expression positively correlated with tumor size, differentiation, and TNM stage in HCC patients (P < 0.05). Patients with high CASC19 expression have a poorer survival prognosis and are prone to relapse compared to those with low CASC19. miR-140-5p, a target miRNA for CASC19, negatively correlated with CASC19 levels in tumor tissues. Reduced CASC19 levels attenuated cell proliferation, migration, and invasion, but this attenuation was reversed by suppression of miR-140-5p. CONCLUSION Up-regulated CASC19 may serve as a biomarker for predicting poor prognosis in HCC patients. In vitro, overexpressed CASC19 promoted the progression of HCC, indicating that CASC19 may be a possible therapeutic target for the treatment of HCC.
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Affiliation(s)
- Ying Hou
- Blood Transfusion Department, Dalian Municipal Central Hospital, Dalian, Liaoning 116033, China
| | - Yipeng Tang
- Hepatobiliary Surgery Department, Dalian Municipal Central Hospital, No. 826 Southwest Road, Dalian, Liaoning 116033, China
| | - Chi Ma
- Hepatobiliary Surgery Department, Dalian Municipal Central Hospital, No. 826 Southwest Road, Dalian, Liaoning 116033, China
| | - Jingbo Yu
- Hepatobiliary Surgery Department, Dalian Municipal Central Hospital, No. 826 Southwest Road, Dalian, Liaoning 116033, China
| | - Youpeng Jia
- Hepatobiliary Surgery Department, Dalian Municipal Central Hospital, No. 826 Southwest Road, Dalian, Liaoning 116033, China.
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Qin J, Sharma A, Wang Y, Tobar-Tosse F, Dakal TC, Liu H, Liu H, Ke B, Kong C, Liu T, Zhao C, Schmidt-Wolf IGH, Jin C. Systematic discrimination of the repetitive genome in proximity of ferroptosis genes and a novel prognostic signature correlating with the oncogenic lncRNA CRNDE in multiple myeloma. Front Oncol 2022; 12:1026153. [PMID: 36605450 PMCID: PMC9808058 DOI: 10.3389/fonc.2022.1026153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 12/05/2022] [Indexed: 01/07/2023] Open
Abstract
Emerging insights into iron-dependent form of regulated cell death ferroptosis in cancer have opened a perspective for its use in cancer therapy. Of interest, a systematic profiling of ferroptosis gene signatures as prognostic factors has gained special attention in several cancers. Herein, we sought to investigate the presence of repetitive genomes in the vicinity of ferroptosis genes that may influence their expression and to establish a prognostic gene signature associated with multiple myeloma (MM). Our analysis showed that genes associated with ferroptosis were enriched with the repetitive genome in their vicinity, with a strong predominance of the SINE family, followed by LINE, of which the most significant discriminant values were SINE/Alu and LINE/L1, respectively. In addition, we examined in detail the performance of these genes as a cancer risk prediction model and specified fourteen ferroptosis-related gene signatures, which identified MM high-risk patients with lower immune/stromal scores with higher tumor purity in their immune microenvironment. Of interest, we also found that lncRNA CRNDE correlated with a risk score and was highly associated with the majority of genes comprising the signature. Taken together, we propose to investigate the molecular impact of the repetitive genome we have highlighted on the local transcriptome of ferroptosis genes in cancer. Furthermore, we revealed a genomic signature/biomarker related to ferroptosis that can be used to predict the risk of survival in MM patients.
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Affiliation(s)
- Jiading Qin
- Medical College of Nanchang University, Nanchang, China,Department of Hematology, Jiangxi Provincial People’s Hospital, Nanchang, China,National Clinical Research Center for Hematologic Diseases, The First Affiliated Hospital of Soochow University, Soochow, China
| | - Amit Sharma
- Department of Integrated Oncology, Center for Integrated Oncology, University Hospital of Bonn, Bonn, Germany,Department of Neurosurgery, University Hospital of Bonn, Bonn, Germany
| | - Yulu Wang
- Department of Integrated Oncology, Center for Integrated Oncology, University Hospital of Bonn, Bonn, Germany
| | - Fabian Tobar-Tosse
- Department of Basic Sciences for Health, Pontificia Universidad Javeriana Cali, Cali, Colombia
| | - Tikam Chand Dakal
- Genome and Computational Biology Lab, Department of Biotechnology, Mohanlal Sukhadia University, Udaipur, India
| | - Hongde Liu
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing, China
| | - Hongjia Liu
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing, China
| | - Bo Ke
- Department of Hematology, Jiangxi Provincial People’s Hospital, Nanchang, China
| | - Chunfang Kong
- Department of Hematology, Jiangxi Provincial People’s Hospital, Nanchang, China
| | - Tingting Liu
- Department of Hematology, Jiangxi Provincial People’s Hospital, Nanchang, China
| | - Chunxia Zhao
- School of Nursing, Nanchang University, Nanchang, China
| | - Ingo G. H. Schmidt-Wolf
- Department of Integrated Oncology, Center for Integrated Oncology, University Hospital of Bonn, Bonn, Germany
| | - Chenghao Jin
- Medical College of Nanchang University, Nanchang, China,Department of Hematology, Jiangxi Provincial People’s Hospital, Nanchang, China,National Clinical Research Center for Hematologic Diseases, The First Affiliated Hospital of Soochow University, Soochow, China,*Correspondence: Chenghao Jin,
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Su Y, Xie R, Xu Q. LncRNA THAP9-AS1 highly expressed in tissues of hepatocellular carcinoma and accelerates tumor cell proliferation. Clin Res Hepatol Gastroenterol 2022; 46:102025. [PMID: 36170961 DOI: 10.1016/j.clinre.2022.102025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 09/09/2022] [Accepted: 09/24/2022] [Indexed: 02/04/2023]
Abstract
BACKGROUND Long noncoding RNAs (lncRNAs) are emerging as significant regulators of cancer development. The purposes of study were to analyze the expression levels of long noncoding RNA THAP9-AS1 (THAP9-AS1) in hepatocellular carcinoma (HCC) tissue samples and cell lines, evaluate the clinical significance of THAP9-AS1 in predicting the survival prognosis of HCC patients, and explore the biological function of THAP9-AS1 in regulating tumor progression of HCC. METHODS The expression of THAP9-AS1 was determined by quantitative real-time PCR. The determination of HCC cell proliferation was performed using cell counting kit-8 assay. Chi-square test was used to reveal the relationship between THAP9-AS1 and clinicopathological data of HCC patients. Kaplan-Meier method, log-rank test were used to perform analyze the relationship between THAP9-AS1 and prognostic survival in HCC patients. Cox regression was used to evaluate the abilities of THAP9-AS1 to predict survival outcomes in HCC patients. RESULTS The expression of THAP9-AS1 were markedly upregulated in HCC tissue and cells. THAP9-AS1 expression was correlated with tumor size, tumor node metastasis (TNM) stage. High THAP9-AS1 expression was associated with poor prognostic survival in HCC patients. THAP9-AS1 was an independent prognostic factor for HCC patients. Overexpression of THAP9-AS1 promoted HCC cell proliferation, silencing THAP9-AS1 inhibited HCC cell proliferation. CONCLUSION Aberrantly highly expressed THAP9-AS1 in HCC tissues and cells was associated with tumor size, TNM stage and poor survival prognosis, and promoted HCC cell proliferation. THAP9-AS1 had the potential to serve as independent prognostic biomarker for HCC patients and provide a novel target for HCC patients' prognostic treatment.
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Affiliation(s)
- Yan Su
- Department of Infectious Diseases, Affiliated Hospital of Weifang Medical University, Weifang 261031 Shandong, China
| | - Ruizhu Xie
- Department of Infectious Diseases, Affiliated Hospital of Weifang Medical University, Weifang 261031 Shandong, China
| | - Qinyan Xu
- Imaging Center, Affiliated Hospital of Weifang Medical University, Weifang 261031 Shandong, China.
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Zhu H, Mao F, Wang K, Feng J, Cheng S. Cuproptosis-related lncRNAs predict the clinical outcome and immune characteristics of hepatocellular carcinoma. Front Genet 2022; 13:972212. [PMID: 36212138 PMCID: PMC9538148 DOI: 10.3389/fgene.2022.972212] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Accepted: 09/09/2022] [Indexed: 12/16/2022] Open
Abstract
Cuproptosis, as a novel copper-dependent and non-apoptotic form of cell death, is induced by aggregation of lipoylated mitochondrial proteins and the instability of Fe-S cluster proteins. However, the role of cuproptosis-related long noncoding RNAs (CRLncRNAs) in hepatocellular carcinoma (HCC) has not been clearly elucidated. In this study, we identified and characterized cuproptosis-related lncRNAs in HCC. 343 HCC cases from The Cancer Genome Atlas (TCGA) with gene transcriptome data and clinical data were obtained for analysis after the screening. Univariate and multivariate Cox proportional hazards analyses were performed to establish a prognostic cuproptosis-related lncRNA signature (CRlncSig). We established a prognosis-related model consisting of nine cuproptosis-related lncRNAs: GSEC, AL158166.1, AC005479.2, AL365361.1, AC026412.3, AL031985.3, LINC00426, AC009974.2, AC245060.7, which was validated in the internal cohort. High-risk group stratified by the CRlncSig was significantly related to poor prognosis (p < 0.001). The area under the receiver operating characteristic curve (AUC) of 1 year, 3 years, and 5 years of survival were 0.813, 0.789, and 0.752, respectively. Furthermore, a prognostic nomogram including CRlncSig with clinicopathologic factors was built with favorable predictive power. In addition, GO and KEGG enrichment analysis suggested that CRlncSig was involved in many carcinogenesis and immune-related pathways. Additionally, we found that tumor microenvironment, immune infiltration, immune function, and drug response were significantly different between the high-risk and low-risk groups based on the risk model. These results highlight the value of cuproptosis-related lncRNAs on prognosis for HCC patients and provide insight into molecular and immune features underlying cuproptosis-related lncRNAs, which might play an important role in patient management and immunotherapy.
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Affiliation(s)
- Hongfei Zhu
- Tongji University Cancer Center, Shanghai 10th People’s Hospital, School of Medicine, Tongji University, Shanghai, China
- Department of Hepatic Surgery VI, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, China
| | - Feifei Mao
- Tongji University Cancer Center, Shanghai 10th People’s Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Kang Wang
- Department of Hepatic Surgery VI, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, China
| | - Jinkai Feng
- Department of Hepatic Surgery VI, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, China
| | - Shuqun Cheng
- Tongji University Cancer Center, Shanghai 10th People’s Hospital, School of Medicine, Tongji University, Shanghai, China
- Department of Hepatic Surgery VI, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, China
- *Correspondence: Shuqun Cheng,
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Cui G, Liu J, Wang C, Gu R, Wang M, Sun Z, Wei F. Comprehensive analysis of the prognostic signature and tumor microenvironment infiltration characteristics of cuproptosis-related lncRNAs for patients with colon adenocarcinoma. Front Oncol 2022; 12:1007918. [PMID: 36212459 PMCID: PMC9539748 DOI: 10.3389/fonc.2022.1007918] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Accepted: 08/23/2022] [Indexed: 12/24/2022] Open
Abstract
Background Cuproptosis, a newly described method of regulatory cell death (RCD), may be a viable new therapy option for cancers. Long noncoding RNAs (lncRNAs) have been confirmed to be correlated with epigenetic controllers and regulate histone protein modification or DNA methylation during gene transcription. The roles of cuproptosis-related lncRNAs (CRLs) in Colon adenocarcinoma (COAD), however, remain unknown. Methods COAD transcriptome data was obtained from the TCGA database. Thirteen genes associated to cuproptosis were identified in published papers. Following that, correlation analysis was used to identify CRLs. The cuproptosis associated prognostic signature was built and evaluated using Lasso regression and COX regression analysis. A prognostic signature comprising six CRLs was established and the expression patterns of these CRLs were analyzed by qRT-PCR. To assess the clinical utility of prognostic signature, we performed tumor microenvironment (TME) analysis, mutation analysis, nomogram generation, and medication sensitivity analysis. Results We identified 49 prognosis-related CRLs in COAD and constructed a prognostic signature consisting of six CRLs. Each patient can be calculated for a risk score and the calculation formula is: Risk score =TNFRSF10A-AS1 * (-0.2449) + AC006449.3 * 1.407 + AC093382.1 *1.812 + AC099850.3 * (-0.0899) + ZEB1-AS1 * 0.4332 + NIFK-AS1 * 0.3956. Six CRLs expressions were investigated by qRT-PCR in three colorectal cancer cell lines. In three cohorts, COAD patients were identified with different risk groups, with the high-risk group having a worse prognosis than the low-risk group. Furthermore, there were differences in immune cell infiltration and tumor mutation burden (TMB) between the two risk groups. We also identified certain drugs that were more sensitive to the high-risk group: Paclitaxel, Vinblastine, Sunitinib and Elescloml. Conclusions Our findings may be used to further investigate RCD, comprehension of the prognosis and tumor microenvironment infiltration characteristics in COAD.
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Affiliation(s)
- Guoliang Cui
- Department of Gastroenterology, The Second Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
| | - Jinhui Liu
- Department of Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Can Wang
- Department of Colorectal Surgery, Jiangsu Province Hospital of Chinese Medicine, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
| | - Renjun Gu
- School of Traditional Chinese Medicine and School of Integrated Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Manli Wang
- The First Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing, China
| | - Zhiguang Sun
- Department of Gastroenterology, The Second Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
- *Correspondence: Fei Wei, ; Zhiguang Sun,
| | - Fei Wei
- Department of Physiology, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
- *Correspondence: Fei Wei, ; Zhiguang Sun,
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A Ferroptosis-Related LncRNA Signature Associated with Prognosis, Tumor Immune Environment, and Genome Instability in Hepatocellular Carcinoma. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2022; 2022:6284540. [PMID: 36035299 PMCID: PMC9410853 DOI: 10.1155/2022/6284540] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Revised: 07/13/2022] [Accepted: 07/25/2022] [Indexed: 11/18/2022]
Abstract
Background Ferroptosis is an iron-dependent form of cell death. In this study, we identified ferroptosis-related long noncoding RNAs (FRlncRNAs) to investigate their association with hepatocellular carcinoma (HCC) in prognosis, tumor immune environment, and genome instability. Methods Transcriptome profile data of HCC were retrieved from a public database. FRlncRNAs were identified by co-expression analysis. Patients were randomly divided into training and test cohorts. Univariate Cox analysis and Least Absolute Shrinkage and Selection Operator (LASSO) Cox regression were performed to construct a risk model. Patients were divided into high- and low-risk groups based on the risk model. AUC and C index were used to assess the risk model. Survival analysis, immune status, and genome instability were compared between the two groups. Results Sixteen FRlncRNAs were identified and used to construct an FRlncRNA signature for the risk model. The Kaplan-Meier analysis revealed that patients in the high-risk group had poorer overall survival than patients in the low-risk group. The area under curve of the risk model was 0.879, 0.809, and 0.757 in the training cohort and 0.635, 0.688, and 0.739 in the test cohort at 1, 2, and 3 years, respectively. The risk model was an independent prognostic predictor and showed excellent prediction of prognosis compared with clinicopathological features. For the differentially expressed ferroptosis-related genes, many enriched metabolic pathways were identified in the functional enrichment analysis. Immune cells such as CD8+ T cells, macrophages M1, natural killer cells, and B cells, which may be associated with antitumor immune responses, differed between the high- and low-risk groups. Genome instability based on the risk model was also explored. A total of 61 genes were differently mutated between the two risk groups, and among them, TP53, HECW2, TRIM66, MCTP2, and KIAA1551 had the most significant mutation frequency differences. Conclusion The FRlncRNA signature is closely related with overall survival, tumor immune environment, and genome instability in HCC.
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Li S, Yao W, Liu R, Gao L, Lu Y, Zhang H, Liang X. Long non-coding RNA LINC00152 in cancer: Roles, mechanisms, and chemotherapy and radiotherapy resistance. Front Oncol 2022; 12:960193. [PMID: 36033524 PMCID: PMC9399773 DOI: 10.3389/fonc.2022.960193] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 07/20/2022] [Indexed: 11/13/2022] Open
Abstract
Long non-coding RNA LINC00152 (cytoskeleton regulator, or LINC00152) is an 828-bp lncRNA located on chromosome 2p11.2. LINC00152 was originally discovered during research on hepatocarcinogenesis and has since been regarded as a crucial oncogene that regulates gene expression in many cancer types. LINC00152 is aberrantly expressed in various cancers, including gastric, breast, ovarian, colorectal, hepatocellular, and lung cancer, and glioma. Several studies have indicated that LINC00152 is correlated with cell proliferation, apoptosis, migration, invasion, cell cycle, epithelial-mesenchymal transition (EMT), chemotherapy and radiotherapy resistance, and tumor growth and metastasis. High LINC00152 expression in most tumors is significantly associated with poor patient prognosis. Mechanistic analysis has demonstrated that LINC00152 can serve as a competing endogenous RNA (ceRNA) by sponging miRNA, regulating the abundance of the protein encoded by a particular gene, or modulating gene expression at the epigenetic level. LINC00152 can serve as a diagnostic or prognostic biomarker, as well as a therapeutic target for most cancer types. In the present review, we discuss the roles and mechanisms of LINC00152 in human cancer, focusing on its functions in chemotherapy and radiotherapy resistance.
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Affiliation(s)
- Shuang Li
- Cancer Center, Department of Affiliated People’ Radiation Oncology, Zhejiang Provincial People’s Hospital, Affiliated People’s Hospital, Hangzhou Medical College, Hangzhou, China
- Graduate Department, Jinzhou Medical University, Jinzhou, China
| | - Weiping Yao
- Cancer Center, Department of Affiliated People’ Radiation Oncology, Zhejiang Provincial People’s Hospital, Affiliated People’s Hospital, Hangzhou Medical College, Hangzhou, China
- Graduate Department, Bengbu Medical College, Bengbu, China
| | - Ruiqi Liu
- Cancer Center, Department of Affiliated People’ Radiation Oncology, Zhejiang Provincial People’s Hospital, Affiliated People’s Hospital, Hangzhou Medical College, Hangzhou, China
- Graduate Department, Bengbu Medical College, Bengbu, China
| | - Liang Gao
- Cancer Center, Department of Medical Oncology, Zhejiang Provincial People’s Hospital, Affiliated People’s Hospital, Hangzhou Medical College, Hangzhou, China
| | - Yanwei Lu
- Cancer Center, Department of Affiliated People’ Radiation Oncology, Zhejiang Provincial People’s Hospital, Affiliated People’s Hospital, Hangzhou Medical College, Hangzhou, China
| | - Haibo Zhang
- Cancer Center, Department of Affiliated People’ Radiation Oncology, Zhejiang Provincial People’s Hospital, Affiliated People’s Hospital, Hangzhou Medical College, Hangzhou, China
- *Correspondence: Xiaodong Liang, ; Haibo Zhang,
| | - Xiaodong Liang
- Cancer Center, Department of Affiliated People’ Radiation Oncology, Zhejiang Provincial People’s Hospital, Affiliated People’s Hospital, Hangzhou Medical College, Hangzhou, China
- Graduate Department, Jinzhou Medical University, Jinzhou, China
- *Correspondence: Xiaodong Liang, ; Haibo Zhang,
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Regulator of G Protein Signaling 20 Correlates with Long Intergenic Non-Coding RNA (lincRNAs) Harboring Oncogenic Potential and Is Markedly Upregulated in Hepatocellular Carcinoma. BIOLOGY 2022; 11:biology11081174. [PMID: 36009801 PMCID: PMC9405539 DOI: 10.3390/biology11081174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 07/14/2022] [Accepted: 07/28/2022] [Indexed: 11/17/2022]
Abstract
Hepatocellular carcinoma (HCC) is at the forefront of the global cancer burden, and biomarkers for HCC are constantly being sought. Interestingly, RGS (Regulators of G protein signaling) proteins, which negatively regulate GPCR signaling, have been associated with various cancers, with some members of the RGS family being associated with liver cancer as well. Considering this, we investigated the role of RGS20 as a potential prognostic marker in 28 different cancer types with special emphasis on HCC. By using the Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) data, our analysis revealed that (a) RGS20 was strongly upregulated in tumor tissue compared with adjacent normal tissue of HCC patients; (b) RGS20 was strongly associated with some important clinical parameters such as alpha-fetoprotein and tumor grade in the HCC patients; (c) besides HCC (p < 0.001), RGS20 was found to be an important factor for survival in four other cancers (clear renal cell carcinoma: p < 0.001, lung adenocarcinoma: p = 0.004, mesothelioma: p = 0.039, ovarian serous cystadenocarcinoma: p = 0.048); (d) RGS20 was found to be significantly associated with some tumor-related signaling pathways and long intergenic non-coding RNAs (lincRNAs: LINC00511, PVT1, MIR4435-2HG, BCYRN1, and MAPKAPK5-AS1) that exhibit oncogenic potential. Taken together, we showed that RGS20 correlates with a few HCC-associated lincRNAs harboring oncogenic potential and is markedly upregulated in HCC patients. Our analysis further supports the putative function of RGS proteins, particularly RGS20, in cancer.
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Jiang H, Sun J, Liu F, Wu X, Wen Z. An Immune-Related Long Noncoding RNA Pair as a New Biomarker to Predict the Prognosis of Patients in Breast Cancer. Front Genet 2022; 13:895200. [PMID: 35812755 PMCID: PMC9257047 DOI: 10.3389/fgene.2022.895200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 05/30/2022] [Indexed: 11/13/2022] Open
Abstract
Background: Immune-related long non-coding RNAs (irlncRNAs) might remodel the tumor immune microenvironment by changing the inherent properties of tumor cells and the expression of immune genes, which have been used to predict the efficacy of immunotherapy and the prognosis of various tumors. However, the value of irlncRNAs in breast cancer (BRCA) remains unclear.Materials and Methods: Initially, transcriptome data and immune-related gene sets were downloaded from The Cancer Genome Atlas (TCGA) database. The irlncRNAs were extracted from the Immunology Database and Analysis Portal (ImmPort) database. Differently expressed irlncRNAs (DEirlncRNAs) were further identified by utilizing the limma R package. Then, univariate and multivariate Cox regression analyses were conducted to select the DEirlncRNAs associated with the prognosis of BRCA patients. In addition, the univariate and least absolute shrinkage and selection operator (LASSO) Cox regression analyses were performed to determine the DEirlncRNA pairs with the independent prediction capability of prognosis in BRCA patients. Finally, the chosen DEirlncRNA pair would be evaluated in terms of survival time, clinicopathological characteristics, tumor-infiltrating immune cells, immune checkpoints (ICs), signaling pathways, and potential small-molecule drugs.Results: A total of 21 DEirlncRNA pairs were extracted, and among them, lncRNA MIR4435-2HG and lncRNA U62317.1 were chosen to establish a risk signature that served as an independent prognostic biomarker in BRCA patients. Patients in the high-risk group had a worse prognosis than those in the low-risk group, and they also had an abundance of infiltration of CD4+ T and CD8+ T cells to enhance the immune response to tumor cells. Furthermore, the risk signature showed a strong correlation with ICs, signaling pathways, and potential small-molecule drugs.Conclusion: Our research revealed that the risk signature independent of specific DEirlncRNA pair expression was closely associated with the prognosis and tumor immune microenvironment in BRCA patients and had the potential to function as an independent prognostic biomarker and a predictor of immunotherapy for BRCA patients, which would provide new insights for BRCA accurate treatment.
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Affiliation(s)
- Hanwen Jiang
- Department of Neurology, Brain Ultrasound, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Jingxian Sun
- Department of Neurosurgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Fucong Liu
- Department of Neurology, Brain Ultrasound, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Xincai Wu
- Department of Neurology, Brain Ultrasound, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Zhaohui Wen
- Department of Neurology, Brain Ultrasound, The First Affiliated Hospital of Harbin Medical University, Harbin, China
- *Correspondence: Zhaohui Wen,
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