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Wang B, Wang X, Du X, Gao S, Liang B, Yao W. Identification and prognostic evaluation of differentially expressed long noncoding RNAs associated with immune infiltration in osteosarcoma. Heliyon 2024; 10:e27023. [PMID: 38463807 PMCID: PMC10920385 DOI: 10.1016/j.heliyon.2024.e27023] [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: 12/09/2023] [Revised: 01/20/2024] [Accepted: 02/22/2024] [Indexed: 03/12/2024] Open
Abstract
Osteosarcoma is a malignant bone cancer that originates from the bone with the strongest invasiveness. Tumor formation strongly correlates with immune cell infiltration into the tumor immune microenvironment (TIME). Therefore, we aimed to identify TIME-related biomarkers as potential prognostic markers of osteosarcoma. The mRNA and long noncoding RNA (lncRNA) transcriptome data of 88 patients with osteosarcoma and the expression profile of GSE99671 were downloaded from The Cancer Genome Atlas and Gene Expression Omnibus, respectively. Immune infiltration scores and types were evaluated using ESTIMATE and CIBERSORT. A linear model was established to identify the differentially expressed genes (DEGs) and lncRNAs (DElncRNAs). Functional enrichment analysis of DEGs was conducted by Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, gene set enrichment analysis, and gene set variation analysis. DElncRNAs were analyzed using a weighted gene co-expression network. Least absolute shrinkage and selection operator regression was applied to screen for prognostic markers. Patient survival was predicted by the risk score and analyzed by receiver operating characteristic curve. Clinical features affecting patient survival were assessed. Immune infiltration positively correlated with osteosarcoma patient survival. Different immune cell infiltrates in patients with osteosarcma may serve as prognostic indicators and targets for immunotherapy. In total, 1125 DEGs, 80 DElncRNAs, and 11 pairs of co-expressed lncRNA-mRNAs were identified. DEGs in the three modules were associated with immune infiltration into the TIME. Four DElncRNAs, namely AC015819.1, AC015911.3, AL365361.1, and USP30-AS1, showed good prognostic ability for osteosarcoma and were positively correlated with the immune score. Tumor metastasis and risk scores alone were good prognostic indicators, and a combination of the two variables can better predict the prognosis of osteosarcoma. We identified four lncRNAs, AC015819.1, AC015911.3, AL365361.1, and USP30-AS1, as potential biomarkers for osteosarcoma prognosis.
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Affiliation(s)
- Bangmin Wang
- Department of Bone Oncology, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, China
| | - Xin Wang
- Department of Bone Oncology, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, China
| | - Xinhui Du
- Department of Bone Oncology, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, China
| | - Shilei Gao
- Department of Bone Oncology, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, China
| | - Bo Liang
- Department of Nephrology, The Key Laboratory for the Prevention and Treatment of Chronic Kidney Disease of Chongqing, Chongqing Clinical Research Center of Kidney and Urology Diseases, Xinqiao Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Weitao Yao
- Department of Bone Oncology, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, China
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Paszkowska A, Kolenda T, Guglas K, Kozłowska-Masłoń J, Podralska M, Teresiak A, Bliźniak R, Dzikiewicz-Krawczyk A, Lamperska K. C10orf55, CASC2, and SFTA1P lncRNAs Are Potential Biomarkers to Assess Radiation Therapy Response in Head and Neck Cancers. J Pers Med 2022; 12:jpm12101696. [PMID: 36294833 PMCID: PMC9605465 DOI: 10.3390/jpm12101696] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/04/2022] [Accepted: 10/08/2022] [Indexed: 11/07/2022] Open
Abstract
Long non-coding RNAs have proven to be important molecules in carcinogenesis. Due to little knowledge about them, the molecular mechanisms of tumorigenesis are still being explored. The aim of this work was to study the effect of ionizing radiation on the expression of lncRNAs in head and neck squamous cell carcinoma (HNSCC) in patients responding and non-responding to radiotherapy. The experimental model was created using a group of patients with response (RG, n = 75) and no response (NRG, n = 75) to radiotherapy based on the cancer genome atlas (TCGA) data. Using the in silico model, statistically significant lncRNAs were defined and further validated on six HNSCC cell lines irradiated at three different doses. Based on the TCGA model, C10orf55, C3orf35, C5orf38, CASC2, MEG3, MYCNOS, SFTA1P, SNHG3, and TMEM105, with the altered expression between the RG and NRG were observed. Analysis of pathways and immune profile indicated that these lncRNAs were associated with changes in processes, such as epithelial-to-mesenchymal transition, regulation of spindle division, and the p53 pathway, and differences in immune cells score and lymphocyte infiltration signature score. However, only C10orf55, CASC2, and SFTA1P presented statistically altered expression after irradiation in the in vitro model. In conclusion, the expression of lncRNAs is affected by ionization radiation in HNSCC, and these lncRNAs are associated with pathways, which are important for radiation response and immune response. Potentially presented lncRNAs could be used as biomarkers for personalized radiotherapy in the future. However, these results need to be verified based on an in vitro experimental model to show a direct net of interactions.
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Affiliation(s)
- Anna Paszkowska
- Laboratory of Cancer Genetics, Greater Poland Cancer Center, Garbary Street 15, 61-866 Poznan, Poland
- Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland
- Research and Implementation Unit, Greater Poland Cancer Center, Garbary Street 15, 61-866 Poznan, Poland
| | - Tomasz Kolenda
- Laboratory of Cancer Genetics, Greater Poland Cancer Center, Garbary Street 15, 61-866 Poznan, Poland
- Research and Implementation Unit, Greater Poland Cancer Center, Garbary Street 15, 61-866 Poznan, Poland
- Correspondence: (T.K.); (K.L.)
| | - Kacper Guglas
- Laboratory of Cancer Genetics, Greater Poland Cancer Center, Garbary Street 15, 61-866 Poznan, Poland
- Research and Implementation Unit, Greater Poland Cancer Center, Garbary Street 15, 61-866 Poznan, Poland
- Postgraduate School of Molecular Medicine, Medical University of Warsaw, Zwirki and Wigury Street 61, 02-091 Warsaw, Poland
| | - Joanna Kozłowska-Masłoń
- Laboratory of Cancer Genetics, Greater Poland Cancer Center, Garbary Street 15, 61-866 Poznan, Poland
- Research and Implementation Unit, Greater Poland Cancer Center, Garbary Street 15, 61-866 Poznan, Poland
- Institute of Human Biology and Evolution, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznańskiego 6, 61-614 Poznan, Poland
| | - Marta Podralska
- Institute of Human Genetics, Polish Academy of Sciences, Strzeszynska 32, 60-479 Poznan, Poland
| | - Anna Teresiak
- Laboratory of Cancer Genetics, Greater Poland Cancer Center, Garbary Street 15, 61-866 Poznan, Poland
- Research and Implementation Unit, Greater Poland Cancer Center, Garbary Street 15, 61-866 Poznan, Poland
| | - Renata Bliźniak
- Laboratory of Cancer Genetics, Greater Poland Cancer Center, Garbary Street 15, 61-866 Poznan, Poland
| | | | - Katarzyna Lamperska
- Laboratory of Cancer Genetics, Greater Poland Cancer Center, Garbary Street 15, 61-866 Poznan, Poland
- Research and Implementation Unit, Greater Poland Cancer Center, Garbary Street 15, 61-866 Poznan, Poland
- Correspondence: (T.K.); (K.L.)
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Jin Q, Gong Q, Le X, He J, Zhuang L. Bioinformatics and Experimental Analyses Reveal Immune-Related LncRNA-mRNA Pair AC011483.1- CCR7 as a Biomarker and Therapeutic Target for Ischemic Cardiomyopathy. Int J Mol Sci 2022; 23:ijms231911994. [PMID: 36233294 PMCID: PMC9569729 DOI: 10.3390/ijms231911994] [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] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 09/28/2022] [Accepted: 10/02/2022] [Indexed: 11/16/2022] Open
Abstract
Ischemic cardiomyopathy (ICM), which increases along with aging, is the leading cause of heart failure. Currently, immune response is believed to be critical in ICM whereas the roles of immune-related lncRNAs remain vague. In this study, we aimed to systematically analyze immune-related lncRNAs in the aging-related disease ICM. Here, we downloaded publicly available RNA-seq data from ischemic cardiomyopathy patients and non-failing controls (GSE116250). Weighted gene co-expression network analysis (WGCNA) was performed to identify key ICM-related modules. The immune-related lncRNAs of key modules were screened by co-expression analysis of immune-related mRNAs. Then, a competing endogenous RNA (ceRNA) network, including 5 lncRNAs and 13 mRNAs, was constructed using lncRNA-mRNA pairs which share regulatory miRNAs and have significant correlation. Among the lncRNA-mRNA pairs, one pair (AC011483.1-CCR7) was verified in another publicly available ICM dataset (GSE46224) and ischemic cell model. Further, the immune cell infiltration analysis of the GSE116250 dataset revealed that the proportions of monocytes and CD8+ T cells were negatively correlated with the expression of AC011483.1-CCR7, while plasma cells were positively correlated, indicating that AC011483.1-CCR7 may participate in the occurrence and development of ICM through immune cell infiltration. Together, our findings revealed that lncRNA-mRNA pair AC011483.1-CCR7 may be a novel biomarker and therapeutic target for ICM.
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Affiliation(s)
- Qiao Jin
- Department of Veterinary Medicine, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Qian Gong
- Department of Veterinary Medicine, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Xuan Le
- Department of Veterinary Medicine, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jin He
- Institute of Genetics and Reproduction, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Lenan Zhuang
- Department of Veterinary Medicine, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
- Institute of Genetics and Reproduction, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
- Correspondence: ; Tel.: +86-158-3612-8207
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