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Chang F, Xi B, Chai X, Wang X, Ma M, Fan Y. Molecular mechanism of radiation tolerance in lung adenocarcinoma cells using single-cell RNA sequencing. J Cell Mol Med 2024; 28:e18378. [PMID: 38760895 PMCID: PMC11101670 DOI: 10.1111/jcmm.18378] [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: 02/04/2024] [Revised: 04/15/2024] [Accepted: 04/18/2024] [Indexed: 05/20/2024] Open
Abstract
The efficacy of radiotherapy, a cornerstone in the treatment of lung adenocarcinoma (LUAD), is profoundly undermined by radiotolerance. This resistance not only poses a significant clinical challenge but also compromises patient survival rates. Therefore, it is important to explore this mechanism for the treatment of LUAD. Multiple public databases were used for single-cell RNA sequencing (scRNA-seq) data. We filtered, normalized and downscaled scRNA-seq data based on the Seurat package to obtain different cell subpopulations. Subsequently, the ssGSEA algorithm was used to assess the enrichment scores of the different cell subpopulations, and thus screen the cell subpopulations that are most relevant to radiotherapy tolerance based on the Pearson method. Finally, pseudotime analysis was performed, and a preliminary exploration of gene mutations in different cell subpopulations was performed. We identified HIST1H1D+ A549 and PIF1+ A549 as the cell subpopulations related to radiotolerance. The expression levels of cell cycle-related genes and pathway enrichment scores of these two cell subpopulations increased gradually with the extension of radiation treatment time. Finally, we found that the proportion of TP53 mutations in patients who had received radiotherapy was significantly higher than that in patients who had not received radiotherapy. We identified two cellular subpopulations associated with radiotherapy tolerance, which may shed light on the molecular mechanisms of radiotherapy tolerance in LUAD and provide new clinical perspectives.
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Affiliation(s)
- Feiyun Chang
- Department of Thoracic Surgery, Shanxi Province Cancer Hospital/Shanxi Hospital Affiliated to Cancer HospitalChinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical UniversityTaiyuanChina
| | - Bozhou Xi
- The Second Clinical Medical SchoolShanxi Medical UniversityTaiyuanChina
| | - Xinchun Chai
- Department of Thoracic Surgery, Shanxi Province Cancer Hospital/Shanxi Hospital Affiliated to Cancer HospitalChinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical UniversityTaiyuanChina
| | - Xiuyan Wang
- Shenzhen Engineering Center for Translational Medicine of Precision Cancer Immunodiagnosis and Therapy, Shenzhen YuceBioTechnology Co., LtdShenzhenChina
| | - Manyuan Ma
- Shenzhen Engineering Center for Translational Medicine of Precision Cancer Immunodiagnosis and Therapy, Shenzhen YuceBioTechnology Co., LtdShenzhenChina
| | - Yafeng Fan
- Department of Respiration, Shanxi Province Cancer Hospital/Shanxi Hospital Affiliated to Cancer HospitalChinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical UniversityTaiyuanChina
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Zhong J, Kong Y, Li R, Feng M, Li L, Zhu X, Chen L. Identification and Functional Characterization of PI3K/Akt/mTOR Pathway-Related lncRNAs in Lung Adenocarcinoma: A Retrospective Study. CELL JOURNAL 2024; 26:13-27. [PMID: 38351726 PMCID: PMC10864771 DOI: 10.22074/cellj.2023.2007918.1378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 10/08/2023] [Accepted: 11/18/2023] [Indexed: 02/18/2024]
Abstract
OBJECTIVE This paper aimed to investigate the PI3K/Akt/mTOR signal-pathway regulator factor-related lncRNA signatures (PAM-SRFLncSigs), associated with regulators of the indicated signaling pathway in patients with lung adenocarcinoma (LUAD) undergoing immunotherapy. MATERIALS AND METHODS In this retrospective study, we employed univariate Cox, multivariate Cox, and least absolute shrinkage and selection operator (LASSO) regression analyses to identify prognostically relevant long non-coding RNAs (lncRNAs), construct prognostic models, and perform Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses. Subsequently, immunoassay and chemotherapy drug screening were conducted. Finally, the prognostic model was validated using the Imvigor210 cohort, and tumor stem cells were analyzed. RESULTS We identified seven prognosis-related lncRNAs (AC084757.3, AC010999.2, LINC02802, AC026979.2, AC024896.1, LINC00941 and LINC01312). We also developed prognostic models to predict survival in patients with LUAD. KEGG enrichment analysis confirmed association of LUAD with the PI3K/Akt/mTOR signaling pathway. In the analysis of immune function pathways, we discovered three good prognostic pathways (Cytolytic_activity, Inflammation-promoting, T_cell_co-inhibition) in LUAD. Additionally, we screened 73 oncology chemotherapy drugs using the "pRRophetic" algorithm. CONCLUSION Identification of seven lncRNAs linked to regulators of the PI3K/Akt/mTOR signaling pathway provided valuable insights into predicting the prognosis of LUAD, understanding the immune microenvironment and optimizing immunotherapy strategies.
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Affiliation(s)
- Jiaqi Zhong
- The Marine Biomedical Research Institute of Guangdong Zhanjiang, School of Ocean and Tropical Medicine, Guangdong Medical University, Zhanjiang, China
| | - Ying Kong
- Department of Clinical Laboratory, The Third People's Hospital of Hubei Province, Wuhan, China
| | - Ruming Li
- The Marine Biomedical Research Institute of Guangdong Zhanjiang, School of Ocean and Tropical Medicine, Guangdong Medical University, Zhanjiang, China
| | - Minghan Feng
- The Marine Biomedical Research Institute of Guangdong Zhanjiang, School of Ocean and Tropical Medicine, Guangdong Medical University, Zhanjiang, China
| | - Liming Li
- The Marine Biomedical Research Institute of Guangdong Zhanjiang, School of Ocean and Tropical Medicine, Guangdong Medical University, Zhanjiang, China
| | - Xiao Zhu
- The Marine Biomedical Research Institute of Guangdong Zhanjiang, School of Ocean and Tropical Medicine, Guangdong Medical University, Zhanjiang, China.
| | - Lianzhou Chen
- Laboratory of General Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.
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Dong J, Tao T, Yu J, Shan H, Liu Z, Zheng G, Li Z, Situ W, Zhu X, Li Z. A ferroptosis-related LncRNAs signature for predicting prognoses and screening potential therapeutic drugs in patients with lung adenocarcinoma: A retrospective study. Cancer Rep (Hoboken) 2024; 7:e1925. [PMID: 38043920 PMCID: PMC10809199 DOI: 10.1002/cnr2.1925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 09/22/2023] [Accepted: 10/16/2023] [Indexed: 12/05/2023] Open
Abstract
BACKGROUND Lung adenocarcinoma (LUAD) has a high mortality rate. Ferroptosis is linked to tumor initiation and progression. AIMS This study aims to develop prognostic models of ferroptosis-related lncRNAs, evaluate the correlation between differentially expressed genes and tumor microenvironment, and identify prospective drugs for managing LUAD. METHODS AND RESULTS In this study, transcriptomic and clinical data were downloaded from the TCGA database, and ferroptosis-related genes were obtained from the FerrDb database. Through correlation analysis, Cox analysis, and the LASSO algorithm for constructing a prognostic model, we found that ferroptosis-related lncRNA-based gene signatures (FLncSig) had a strong prognostic predicting ability in the LUAD patients. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichments reconfirmed that ferroptosis is related to receptor-ligand activity, enzyme inhibitor activity, and the IL-17 signaling pathway. Next, tumor mutation burden (TMB), tumor immune dysfunction and exclusion (TIDE) algorithms, and pRRophetic were used to predict immunotherapy response and chemotherapy sensitivity. The IMvigor210 cohort was also used to validate the prognostic model. In the tumor microenvironment, Type_II_IFN_Response and HLA were found to be a group of low-risk pathways, while MHC_class_I was a group of high-risk pathways. Patients in the high-risk subgroup had lower TIDE scores. Exclusion, MDSC, CAF, and TAMM2 were significantly and positively correlated with risk scores. In addition, we found 15 potential therapeutic drugs for LUAD. Finally, differential analysis of stemness index based on mRNA expression (mRNAsi) indicated that mRNAsi was correlated with gender, primary tumor (T), distant metastasis (M), and the tumor, node, and metastasis (TNM) stage in LUAD patients. CONCLUSIONS In conclusion, the prognostic model based on FLncSig can alleviate the difficulty in predicting the prognosis and immunotherapy of LUAD patients. The identified FLncSig and the screened drugs exhibit potential for clinical application and provide references for the treatment of LUAD.
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Affiliation(s)
- Jiaxin Dong
- Computational Systems Biology Lab (CSBL), The Marine Biomedical Research InstituteGuangdong Medical UniversityZhanjiangChina
| | - Tao Tao
- Medical Research Center, Department of GastroenterologyZibo Central HospitalZiboChina
| | - Jiaao Yu
- Computational Systems Biology Lab (CSBL), The Marine Biomedical Research InstituteGuangdong Medical UniversityZhanjiangChina
| | - Huisi Shan
- Computational Systems Biology Lab (CSBL), The Marine Biomedical Research InstituteGuangdong Medical UniversityZhanjiangChina
| | - Ziyu Liu
- Computational Systems Biology Lab (CSBL), The Marine Biomedical Research InstituteGuangdong Medical UniversityZhanjiangChina
| | - Guangzhao Zheng
- Computational Systems Biology Lab (CSBL), The Marine Biomedical Research InstituteGuangdong Medical UniversityZhanjiangChina
| | - Zhihong Li
- Computational Systems Biology Lab (CSBL), The Marine Biomedical Research InstituteGuangdong Medical UniversityZhanjiangChina
| | - Wanyi Situ
- Computational Systems Biology Lab (CSBL), The Marine Biomedical Research InstituteGuangdong Medical UniversityZhanjiangChina
| | - Xiao Zhu
- Computational Systems Biology Lab (CSBL), The Marine Biomedical Research InstituteGuangdong Medical UniversityZhanjiangChina
| | - Zesong Li
- Guangdong Provincial Key Laboratory of Systems Biology and Synthetic Biology for Urogenital Tumors, Shenzhen Key Laboratory of Genitourinary Tumor, Department of UrologyThe First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital (Shenzhen Institute of Translational Medicine)ShenzhenChina
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Zhang J, Song L, Li G, Liang A, Cai X, Huang Y, Zhu X, Zhou X. Comprehensive assessment of base excision repair (BER)-related lncRNAs as prognostic and functional biomarkers in lung adenocarcinoma: implications for personalized therapeutics and immunomodulation. J Cancer Res Clin Oncol 2023; 149:17199-17213. [PMID: 37789154 DOI: 10.1007/s00432-023-05435-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Accepted: 09/17/2023] [Indexed: 10/05/2023]
Abstract
BACKGROUND Lung adenocarcinoma (LUAD) is the most prevalent subtype of lung cancer, and comprehending its molecular mechanisms is pivotal for advancing treatment efficacy. This study aims to explore the prognostic and functional significance of base excision repair (BER)-related long non-coding RNAs (BERLncs) in LUAD. METHODS A risk score model for BERLncs was developed using the least absolute shrinkage and selection operator regression and Cox regression analysis. Model validation and prognostic evaluation were performed using Kaplan-Meier and receiver-operating characteristic curve analyses. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses were conducted to elucidate the potential biological functions of BERLncs. Comparative analyses were carried out to investigate disparities in tumor mutation burden (TMB), immune infiltration, tumor immune dysfunction and exclusion (TIDE) score, chemosensitivity, and immune checkpoint gene expression between the two risk groups. RESULTS A predictive risk score model comprising 19 BERLncs was successfully developed. Patients were divided into high-risk and low-risk groups according to the median risk score. The high-risk subgroup exhibited significantly inferior overall survival. Functional enrichment analysis revealed pathways associated with lung cancer development, notably the neuroactive ligand-receptor interaction pathway. High-risk patients demonstrated elevated TMB, diminished TIDE scores, and an immunosuppressive tumor microenvironment, while low-risk patients displayed potential benefits from immunotherapy. Additionally, the risk model identified potential anticancer agents. CONCLUSION The risk score model based on BERLncs shows promise as a prognostic biomarker for LUAD patients, providing valuable insights for clinical decision-making, therapeutic strategies, and understanding of underlying biological mechanisms.
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Affiliation(s)
- Junzheng Zhang
- Department of Immunology, School of Medicine, Nantong University, Nantong, China
- Computational Systems Biology Lab (CSBL), The Marine Biomedical Research Institute, Guangdong Medical University, Zhanjiang, China
| | - Lu Song
- Department of Clinical Laboratory, Qingdao City Sixth People's Hospital, Qingdao, China
| | - Guanrong Li
- Computational Systems Biology Lab (CSBL), The Marine Biomedical Research Institute, Guangdong Medical University, Zhanjiang, China
| | - Anqi Liang
- Computational Systems Biology Lab (CSBL), The Marine Biomedical Research Institute, Guangdong Medical University, Zhanjiang, China
| | - Xiaoting Cai
- Computational Systems Biology Lab (CSBL), The Marine Biomedical Research Institute, Guangdong Medical University, Zhanjiang, China
| | - Yaqi Huang
- Computational Systems Biology Lab (CSBL), The Marine Biomedical Research Institute, Guangdong Medical University, Zhanjiang, China
| | - Xiao Zhu
- Computational Systems Biology Lab (CSBL), The Marine Biomedical Research Institute, Guangdong Medical University, Zhanjiang, China.
- Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou Medical College, Hangzhou, China.
| | - Xiaorong Zhou
- Department of Immunology, School of Medicine, Nantong University, Nantong, China.
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Zou Z, Zhang M, Xu S, Zhang Y, Zhang J, Li Z, Zhu X. Computational identification of long non-coding RNAs associated with graphene therapy in glioblastoma multiforme. Brain Commun 2023; 6:fcad293. [PMID: 38162904 PMCID: PMC10754320 DOI: 10.1093/braincomms/fcad293] [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: 04/20/2023] [Revised: 08/26/2023] [Accepted: 10/24/2023] [Indexed: 01/03/2024] Open
Abstract
Glioblastoma multiforme represents the most prevalent primary malignant brain tumour, while long non-coding RNA assumes a pivotal role in the pathogenesis and progression of glioblastoma multiforme. Nonetheless, the successful delivery of long non-coding RNA-based therapeutics to the tumour site has encountered significant obstacles attributable to inadequate biocompatibility and inefficient drug delivery systems. In this context, the use of a biofunctional surface modification of graphene oxide has emerged as a promising strategy to surmount these challenges. By changing the surface of graphene oxide, enhanced biocompatibility can be achieved, facilitating efficient transport of long non-coding RNA-based therapeutics specifically to the tumour site. This innovative approach presents the opportunity to exploit the therapeutic potential inherent in long non-coding RNA biology for treating glioblastoma multiforme patients. This study aimed to extract relevant genes from The Cancer Genome Atlas database and associate them with long non-coding RNAs to identify graphene therapy-related long non-coding RNA. We conducted a series of analyses to achieve this goal, including univariate Cox regression, least absolute shrinkage and selection operator regression and multivariate Cox regression. The resulting graphene therapy-related long non-coding RNAs were utilized to develop a risk score model. Subsequently, we conducted Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses on the identified graphene therapy-related long non-coding RNAs. Additionally, we employed the risk model to construct the tumour microenvironment model and analyse drug sensitivity. To validate our findings, we referenced the IMvigor210 immunotherapy model. Finally, we investigated differences in the tumour stemness index. Through our investigation, we identified four promising graphene therapy-related long non-coding RNAs (AC011405.1, HOXC13-AS, LINC01127 and LINC01574) that could be utilized for treating glioblastoma multiforme patients. Furthermore, we identified 16 compounds that could be utilized in graphene therapy. Our study offers novel insights into the treatment of glioblastoma multiforme, and the identified graphene therapy-related long non-coding RNAs and compounds hold promise for further research in this field. Furthermore, additional biological experiments will be essential to validate the clinical significance of our model. These experiments can help confirm the potential therapeutic value and efficacy of the identified graphene therapy-related long non-coding RNAs and compounds in treating glioblastoma multiforme.
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Affiliation(s)
- Zhuoheng Zou
- Computational Systems Biology Lab (CSBL), The Marine Biomedical Research Institute, Guangdong Medical University, Zhanjiang 524023, China
| | - Ming Zhang
- Department of Physical Medicine and Rehabilitation, Zibo Central Hospital, Zibo 255000, China
| | - Shang Xu
- Computational Systems Biology Lab (CSBL), The Marine Biomedical Research Institute, Guangdong Medical University, Zhanjiang 524023, China
| | - Youzhong Zhang
- Computational Systems Biology Lab (CSBL), The Marine Biomedical Research Institute, Guangdong Medical University, Zhanjiang 524023, China
| | - Junzheng Zhang
- Computational Systems Biology Lab (CSBL), The Marine Biomedical Research Institute, Guangdong Medical University, Zhanjiang 524023, China
| | - Zesong Li
- Guangdong Provincial Key Laboratory of Systems Biology and Synthetic Biology for Urogenital Tumors, Shenzhen Key Laboratory of Genitourinary Tumor, Department of Urology, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People’s Hospital (Shenzhen Institute of Translational Medicine), Shenzhen 518035, China
| | - Xiao Zhu
- Computational Systems Biology Lab (CSBL), The Marine Biomedical Research Institute, Guangdong Medical University, Zhanjiang 524023, China
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