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Ba Y, Gu X. Using single-cell RNA sequencing and bulk RNA sequencing data to reveal a correlation between smoking and neutrophil activation in esophageal carcinoma patients. ENVIRONMENTAL TOXICOLOGY 2024. [PMID: 38700434 DOI: 10.1002/tox.24312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 03/31/2024] [Accepted: 04/22/2024] [Indexed: 05/05/2024]
Abstract
BACKGROUND Cigarette smoking is considered as a major risk factor for esophageal carcinoma (ESCA) patients. Neutrophil activation plays a key role in cancer development and progression. However, the relationship between cigarette smoking and neutrophils in ESCA patients remained unclear. METHODS Single-cell RNA sequencing (scRNA-seq) and bulk RNA sequencing data were obtained from public databases. Uniform manifold approximation and projection (UMAP) was used to perform downscaling and clustering based on scRNA-seq data. The module genes associated with smoking in ESCA patients were filtered by weighted gene co-expression network analysis (WGCNA). Using the "AUCell" package, the enrichment of different cell subpopulations and gene collections were assessed. "CellChat" and "CellphoneDB" were used to infer the probability and significance of ligand-receptor interactions between different cell subpopulations. RESULTS WGCNA was performed to screened module genes associated with smoking in ESCA patients from MEdarkquosie, MEturquoise, and MEgreenyellow. Next, eight cell clusters were identified, and using the AUCell score, we determined that neutrophil clusters were more active in the gene modules associated with smoking in ESCA patients. Two neutrophil subtypes, Neutrophils 1 and Neutrophils 2, exhibited greater enrichment in inflammatory response regulation, intercellular adhesion, and regulation of T cell activation. Furthermore, we found that neutrophils may pass through AMPT-(ITGA5 + ITGB1) and ICAM1-AREG in order to promote the development of ESCA, and that the expression levels of the receptor genes insulin-degrading enzyme and ITGB1 were significantly and positively correlated with cigarette smoking per day. CONCLUSION Combining smoking-related gene modules and scRNA-seq, the current findings revealed the heterogeneity of neutrophils in ESCA and a tumor-promoting role of neutrophils in the tumor microenvironment of smoking ESCA patients.
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Affiliation(s)
- Yunhuan Ba
- Department of Laboratory Medicine, Xinxiang Central Hospital, the Fourth Clinical College of Xinxiang Medical University, Xinxiang, China
| | - Xinyu Gu
- Department of Oncology, The First Affiliated Hospital, College of Clinical Medicine, Henan University of Science and Technology, Luoyang, China
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Yang K, Li S, Ding Y, Meng X, Zhang C, Sun X. Effect of smoking-related features and 731 immune cell phenotypes on esophageal cancer: a two-sample and mediated Mendelian randomized study. Front Immunol 2024; 15:1336817. [PMID: 38601154 PMCID: PMC11004242 DOI: 10.3389/fimmu.2024.1336817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Accepted: 03/18/2024] [Indexed: 04/12/2024] Open
Abstract
Introduction Numerous observational studies have indicated that smoking is a substantial risk factor for esophageal cancer. However, there is a shortage of research that delves into the specific causal relationship and potential mediators between the two. Our study aims to validate the correlation between smoking-related traits and esophageal cancer while exploring the possible mediating effects of immune factors. Methods Initially, we conducted bidirectional univariate Mendelian Randomization (MR) analyses to forecast the causal effects linking smoking-related traits and esophageal cancer. Subsequently, we employed a two-step MR analysis to scrutinize immune cell phenotypes that could mediate these effects. Finally, the coefficient product method was employed to determine the precise mediating impact. Additionally, we have refined our sensitivity analysis to ensure the reliability of the outcomes. Results After analysis, Smoking status: Never had a significant negative association with the incidence of esophageal cancer (inverse-variance weighted (IVW) method, p=1.82e-05, OR=0.10, 95%CI=0.04~0.29). Ever smoked (IVW, p=1.49e-02, OR=4.31, 95%CI=1.33~13.94) and Current tobacco smoking (IVW, p=1.49e-02, OR=4.31, 95%CI=1.33~13.94) showed the promoting effect on the pathogenesis of esophageal cancer. Through further examination, researchers discovered 21 immune cell phenotypes that have a causal relationship with esophageal cancer. After careful screening, two immune cell phenotypes were found to have potential mediating effects. In particular, it was observed that in the case of the preventive effect of Smoking status: Never on esophageal cancer, the absolute count of CD62L plasmacytoid dendritic cells mediated a reduction of 4.21%, while the mediating effect of CD27 in CD20-CD38-B cells was -4.12%. In addition, sensitivity analyses did not reveal significant heterogeneity or level pleiotropy. Conclusion The study provides new evidence for the causal relationship between smoking-related features and esophageal cancer and proposes immune factors with potential mediating effects. However, this finding needs to be further demonstrated by more extensive clinical studies.
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Affiliation(s)
| | | | | | | | | | - Xiujing Sun
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, National Clinical Research Center for Digestive Disease, Beijing Digestive Disease Center, Beijing Key Laboratory for Precancerous Lesion of Digestive Disease, Beijing, China
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Yang C, Wang H, Shao M, Chu F, He Y, Chen X, Fan J, Chen J, Cai Q, Wu C. Brain-Type Glycogen Phosphorylase (PYGB) in the Pathologies of Diseases: A Systematic Review. Cells 2024; 13:289. [PMID: 38334681 PMCID: PMC10854662 DOI: 10.3390/cells13030289] [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: 11/23/2023] [Revised: 12/27/2023] [Accepted: 01/05/2024] [Indexed: 02/10/2024] Open
Abstract
Glycogen metabolism is a form of crucial metabolic reprogramming in cells. PYGB, the brain-type glycogen phosphorylase (GP), serves as the rate-limiting enzyme of glycogen catabolism. Evidence is mounting for the association of PYGB with diverse human diseases. This review covers the advancements in PYGB research across a range of diseases, including cancer, cardiovascular diseases, metabolic diseases, nervous system diseases, and other diseases, providing a succinct overview of how PYGB functions as a critical factor in both physiological and pathological processes. We present the latest progress in PYGB in the diagnosis and treatment of various diseases and discuss the current limitations and future prospects of this novel and promising target.
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Affiliation(s)
- Caiting Yang
- Institutes of Biomedical Sciences, Shanxi University, Taiyuan 030006, China; (C.Y.); (H.W.); (F.C.); (Y.H.); (X.C.); (J.F.); (J.C.)
| | - Haojun Wang
- Institutes of Biomedical Sciences, Shanxi University, Taiyuan 030006, China; (C.Y.); (H.W.); (F.C.); (Y.H.); (X.C.); (J.F.); (J.C.)
| | - Miaomiao Shao
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China;
| | - Fengyu Chu
- Institutes of Biomedical Sciences, Shanxi University, Taiyuan 030006, China; (C.Y.); (H.W.); (F.C.); (Y.H.); (X.C.); (J.F.); (J.C.)
| | - Yuyu He
- Institutes of Biomedical Sciences, Shanxi University, Taiyuan 030006, China; (C.Y.); (H.W.); (F.C.); (Y.H.); (X.C.); (J.F.); (J.C.)
| | - Xiaoli Chen
- Institutes of Biomedical Sciences, Shanxi University, Taiyuan 030006, China; (C.Y.); (H.W.); (F.C.); (Y.H.); (X.C.); (J.F.); (J.C.)
| | - Jiahui Fan
- Institutes of Biomedical Sciences, Shanxi University, Taiyuan 030006, China; (C.Y.); (H.W.); (F.C.); (Y.H.); (X.C.); (J.F.); (J.C.)
| | - Jingwen Chen
- Institutes of Biomedical Sciences, Shanxi University, Taiyuan 030006, China; (C.Y.); (H.W.); (F.C.); (Y.H.); (X.C.); (J.F.); (J.C.)
| | - Qianqian Cai
- Shanghai Key Laboratory of Molecular Imaging, Shanghai University of Medicine and Health Sciences, Shanghai 201318, China
| | - Changxin Wu
- Institutes of Biomedical Sciences, Shanxi University, Taiyuan 030006, China; (C.Y.); (H.W.); (F.C.); (Y.H.); (X.C.); (J.F.); (J.C.)
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Xin R, Cheng Q, Chi X, Feng X, Zhang H, Wang Y, Duan M, Xie T, Song X, Yu Q, Fan Y, Huang L, Zhou F. Computational Characterization of Undifferentially Expressed Genes with Altered Transcription Regulation in Lung Cancer. Genes (Basel) 2023; 14:2169. [PMID: 38136991 PMCID: PMC10742656 DOI: 10.3390/genes14122169] [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: 10/01/2023] [Revised: 11/19/2023] [Accepted: 11/27/2023] [Indexed: 12/24/2023] Open
Abstract
A transcriptome profiles the expression levels of genes in cells and has accumulated a huge amount of public data. Most of the existing biomarker-related studies investigated the differential expression of individual transcriptomic features under the assumption of inter-feature independence. Many transcriptomic features without differential expression were ignored from the biomarker lists. This study proposed a computational analysis protocol (mqTrans) to analyze transcriptomes from the view of high-dimensional inter-feature correlations. The mqTrans protocol trained a regression model to predict the expression of an mRNA feature from those of the transcription factors (TFs). The difference between the predicted and real expression of an mRNA feature in a query sample was defined as the mqTrans feature. The new mqTrans view facilitated the detection of thirteen transcriptomic features with differentially expressed mqTrans features, but without differential expression in the original transcriptomic values in three independent datasets of lung cancer. These features were called dark biomarkers because they would have been ignored in a conventional differential analysis. The detailed discussion of one dark biomarker, GBP5, and additional validation experiments suggested that the overlapping long non-coding RNAs might have contributed to this interesting phenomenon. In summary, this study aimed to find undifferentially expressed genes with significantly changed mqTrans values in lung cancer. These genes were usually ignored in most biomarker detection studies of undifferential expression. However, their differentially expressed mqTrans values in three independent datasets suggested their strong associations with lung cancer.
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Affiliation(s)
- Ruihao Xin
- Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, Changchun 130012, China; (R.X.); (Y.W.); (M.D.); (L.H.)
- Jilin Institute of Chemical Technology, College of Information and Control Engineering, Jilin 132000, China; (Q.C.); (X.C.); (H.Z.)
| | - Qian Cheng
- Jilin Institute of Chemical Technology, College of Information and Control Engineering, Jilin 132000, China; (Q.C.); (X.C.); (H.Z.)
| | - Xiaohang Chi
- Jilin Institute of Chemical Technology, College of Information and Control Engineering, Jilin 132000, China; (Q.C.); (X.C.); (H.Z.)
| | - Xin Feng
- School of Science, Jilin Institute of Chemical Technology, Jilin 132000, China;
- Department of Epidemiology and Biostatistics, School of Public Health, Jilin University, Changchun 130012, China;
| | - Hang Zhang
- Jilin Institute of Chemical Technology, College of Information and Control Engineering, Jilin 132000, China; (Q.C.); (X.C.); (H.Z.)
| | - Yueying Wang
- Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, Changchun 130012, China; (R.X.); (Y.W.); (M.D.); (L.H.)
| | - Meiyu Duan
- Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, Changchun 130012, China; (R.X.); (Y.W.); (M.D.); (L.H.)
| | - Tunyang Xie
- Centre for Mathematical Sciences, University of Cambridge, Wilberforce Road, Cambridge CB3 0WA, UK;
| | - Xiaonan Song
- Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, College of Software, Jilin University, Changchun 130012, China;
| | - Qiong Yu
- Department of Epidemiology and Biostatistics, School of Public Health, Jilin University, Changchun 130012, China;
| | - Yusi Fan
- Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, College of Software, Jilin University, Changchun 130012, China;
| | - Lan Huang
- Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, Changchun 130012, China; (R.X.); (Y.W.); (M.D.); (L.H.)
| | - Fengfeng Zhou
- Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, Changchun 130012, China; (R.X.); (Y.W.); (M.D.); (L.H.)
- School of Biology and Engineering, Guizhou Medical University, Guiyang 550025, China
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Song GQ, Wu HM, Ji KJ, He TL, Duan YM, Zhang JW, Hu GQ. The necroptosis signature and molecular mechanism of lung squamous cell carcinoma. Aging (Albany NY) 2023; 15:12907-12926. [PMID: 37976123 DOI: 10.18632/aging.205210] [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: 04/27/2023] [Accepted: 10/15/2023] [Indexed: 11/19/2023]
Abstract
BACKGROUND Given the poor prognosis of lung squamous cell carcinoma (LUSC), the aim of this study was to screen for new prognostic biomarkers. METHODS The TGCA_LUSC dataset was used as the training set, and GSE73403 was used as the validation set. The genes involved in necroptosis-related pathways were acquired from the KEGG database, and the differential genes between the LUSC and normal samples were identified using the GSEA. A necroptosis signature was constructed by survival analysis, and its correlation with patient prognosis and clinical features was evaluated. The molecular characteristics and drug response associated with the necroptosis signature were also identified. The drug candidates were then validated at the cellular level. RESULTS The TCGA_LUSC dataset included 51 normal samples and 502 LUSC samples. The GSE73403 dataset included 69 samples. 159 genes involved in necroptosis pathways were acquired from the KEGG database, of which most showed significant differences between two groups in terms of genomic, transcriptional and methylation alterations. In particular, CHMP4C, IL1B, JAK1, PYGB and TNFRSF10B were significantly associated with the survival (p < 0.05) and were used to construct the necroptosis signature, which showed significant correlation with patient prognosis and clinical features in univariate and multivariate analyses (p < 0.05). Furthermore, CHMP4C, IL1B, JAK1 and PYGB were identified as potential targets of trametinib, selumetinib, SCH772984, PD 325901 and dasatinib. Finally, knockdown of these genes in LUSC cells increased chemosensitivity to those drugs. CONCLUSION We identified a necroptosis signature in LUSC that can predict prognosis and identify patients who can benefit from targeted therapies.
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Affiliation(s)
- Guo-Qiang Song
- Department of Pulmonary, Changxing County Hospital of Traditional Chinese Medicine, Huzhou, China
| | - Hua-Man Wu
- Department of Pulmonary and Critical Care Medicine, Zigong First People’s Hospital, Zigong, China
| | - Ke-Jie Ji
- Department of Pulmonary, Changxing County Hospital of Traditional Chinese Medicine, Huzhou, China
| | - Tian-Li He
- Department of Radiotherapy, Changxing People’s Hospital, Huzhou, China
| | - Yi-Meng Duan
- Department of Pulmonary, Changxing County Hospital of Traditional Chinese Medicine, Huzhou, China
| | - Jia-Wen Zhang
- Department of Pulmonary, Changxing County Hospital of Traditional Chinese Medicine, Huzhou, China
| | - Guo-Qiang Hu
- Department of Pulmonary, Changxing County Hospital of Traditional Chinese Medicine, Huzhou, China
- Department of Cancer Center, Changxing County Hospital of Traditional Chinese Medicine, Huzhou, China
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Identification of Clinical Prognostic Regulators and Analysis of Ferroptosis-Related Signatures in the Tumor Immune Microenvironment in Lung Squamous Cell Carcinoma. DISEASE MARKERS 2023; 2023:9155944. [PMID: 36845013 PMCID: PMC9946749 DOI: 10.1155/2023/9155944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 10/21/2022] [Accepted: 11/24/2022] [Indexed: 02/17/2023]
Abstract
Objective Lung squamous cell carcinoma (LUSC) is a common respiratory malignancy and presents an increasing prevalence. Ferroptosis is a newly identified controlled cell death that has captured clinical attention worldwide. However, the ferroptosis-related lncRNA expression in LUSC and its relevance to prognosis remain elusive. Methods The research measured predictive ferroptosis-related lncRNAs in LUSC samples from the TCGA datasets. Data on the stemness indices (mRNAsi) and corresponding clinical characteristics were obtained from TCGA. A prognosis model was established using the LASSO regression. Changes within the neoplasm microenvironment (TME) and medicine association were examined to grasp higher immune cell infiltration in numerous risk teams. In line with coexpression studies, the expression of lncRNAs is closely associated with that of ferroptosis. They were overexpressed in unsound people in the absence of alternative clinical symptoms. Results The low-risk and speculative teams were considered to have substantial differences in CCR and inflammation-promoting genes. C10orf55, AC016924.1, AL161431.1, LUCAT1, AC104248.1, and MIR3945HG were highly expressed in the high-risk group, suggesting their involvement in the oncology process of LUSC. Moreover, AP006545.2 and AL122125.1 were considerably higher in the low-risk group, implying the potential of these genes as LUSC tumor suppressor genes. The biomarkers listed above may serve as therapeutic targets for LUSC. lncRNAs were also linked to patient outcomes in the LUSC trial. Conclusion lncRNAs of ferroptosis were overexpressed in the high-risk cohort without other clinical signs, implying their potential to predict BLCA prognosis. GSEA highlighted immunological and tumor-related pathways in the high-risk group. LUSC occurrence and progression are linked to lncRNAs of ferroptosis. Corresponding prognostic models help forecast the prognosis of LUSC patients. lncRNAs of ferroptosis and associated immune cell infiltration in the tumor microenvironment (TME) may serve as potential therapeutic targets in LUSC, which requires further trials. In addition, the lncRNAs of ferroptosis signature offer a viable alternative to predict LUSC, and these ferroptosis-lncRNAs show a prospective research area for LUSC-targeted treatment in the future.
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Hu DM, Zhang WD, Shi ZE, Zhang MY, Li R, Wang QX, Ji XL, Qu YQ. FOXP family DNA methylation correlates with immune infiltration and prognostic value in NSCLC. Front Genet 2022; 13:937069. [PMID: 36160018 PMCID: PMC9500381 DOI: 10.3389/fgene.2022.937069] [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: 05/05/2022] [Accepted: 08/15/2022] [Indexed: 01/17/2023] Open
Abstract
Background: Forkhead box P (FOXP) family was introduced as a double-edged sword in tumorigenesis and influenced immunotherapy response by modulating host immunity. This study aimed to summarize the involvement of the FOXP family in non-small cell lung cancer (NSCLC).Methods: The UALCAN, Gene Expression Profiling Interactive Analysis (GEPIA), and Reverse transcription-quantitative polymerase chain reaction (RT‒qPCR) were used to analyse the expression levels of the FOXP family in NSCLC. The prognostic impact was evaluated using Kaplan-Meier Plotter. MethSurv, UALCAN, and cBioPortal were applied to analyse the DNA methylation and mutation status of the FOXP family respectively. COEXPEDIA, STRING, and GeneMANIA were used to explore the interaction mechanism. Finally, TISIDB was used to investigate all of the immune-related characteristics regulated by the FOXP family.Results: The expression levels of FOXP1/3/4 were dysregulated in NSCLC tissues than that in normal tissues. Groups with low expression levels of FOXP1/4 and high expression levels of FOXP2/3 were associated with poor prognosis in NSCLC. The transcriptional levels of FOXP2/3/4 were correlated with DNA methylation in NSCLC. FOXP1/3/4 DNA methylation were correlated with prognosis. Pathway enrichment analysis indicated the FOXP family was mainly related to immune-related pathways. After DNA methylation, the correlations between FOXP family and immune factors were opposite to that before alteration in NSCLC.Conclusion: This study elucidated FOXP family could serve as vital diagnostic and prognostic biomarkers in NSCLC. Our study highlighted novel potential functions of FOXP family DNA methylation in regulation of immune-related signatures in NSCLC.
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Affiliation(s)
- Dong-Mei Hu
- Shandong Key Laboratory of Infectious Respiratory Diseases, Department of Pulmonary and Critical Care Medicine, Qilu Hospital of Shandong University, Jinan, China
- Laboratory of Basic Medical Sciences, Qilu Hospital of Shandong University, Jinan, China
| | - Wen-Di Zhang
- Shandong Key Laboratory of Infectious Respiratory Diseases, Department of Pulmonary and Critical Care Medicine, Qilu Hospital of Shandong University, Jinan, China
- Laboratory of Basic Medical Sciences, Qilu Hospital of Shandong University, Jinan, China
| | - Zhuang-E Shi
- Shandong Key Laboratory of Infectious Respiratory Diseases, Department of Pulmonary and Critical Care Medicine, Qilu Hospital of Shandong University, Jinan, China
- Laboratory of Basic Medical Sciences, Qilu Hospital of Shandong University, Jinan, China
| | - Meng-Yu Zhang
- Shandong Key Laboratory of Infectious Respiratory Diseases, Department of Pulmonary and Critical Care Medicine, Qilu Hospital of Shandong University, Jinan, China
- Laboratory of Basic Medical Sciences, Qilu Hospital of Shandong University, Jinan, China
| | - Rui Li
- Shandong Key Laboratory of Infectious Respiratory Diseases, Department of Pulmonary and Critical Care Medicine, Qilu Hospital of Shandong University, Jinan, China
- Laboratory of Basic Medical Sciences, Qilu Hospital of Shandong University, Jinan, China
| | - Qing-Xiang Wang
- Shandong Key Laboratory of Infectious Respiratory Diseases, Department of Pulmonary and Critical Care Medicine, Qilu Hospital of Shandong University, Jinan, China
- Laboratory of Basic Medical Sciences, Qilu Hospital of Shandong University, Jinan, China
| | - Xiu-Li Ji
- Department of Pulmonary Disease, Jinan Traditional Chinese Medicine Hospital, Jinan, China
- *Correspondence: Yi-Qing Qu, ; Xiu-Li Ji,
| | - Yi-Qing Qu
- Shandong Key Laboratory of Infectious Respiratory Diseases, Department of Pulmonary and Critical Care Medicine, Qilu Hospital of Shandong University, Jinan, China
- *Correspondence: Yi-Qing Qu, ; Xiu-Li Ji,
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Role of Long Noncoding RNAs in Smoking-Induced Lung Cancer: An In Silico Study. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2022; 2022:7169353. [PMID: 35529255 PMCID: PMC9070410 DOI: 10.1155/2022/7169353] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 03/13/2022] [Accepted: 04/05/2022] [Indexed: 11/17/2022]
Abstract
The prevalence of lung cancer induced by cigarette smoking has increased over time. Long noncoding (lnc) RNAs, regulatory factors that play a role in human diseases, are commonly dysregulated in lung cancer. Cigarette smoking is closely related to changes in lncRNA expression, which can affect lung cancer. Herein, we assess the mechanism of lung cancer initiation induced by smoking. To calculate the impact of smoking on the survival of patients with lung cancer, we extracted data from The Cancer Genome Atlas and Gene Expression Omnibus databases and identified the differentially expressed genes in the lung cancer tissue compared to the normal lung tissue. Genes positively and negatively associated with smoking were identified. Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, and Cytoscape analyses were performed to determine the function of the genes and the effects of smoking on the immune microenvironment. lncRNAs corresponding to smoking-associated genes were identified, and a smoking-related lncRNA model was constructed using univariate and multivariate Cox analyses. This model was used to assess the survival of and potential risk in patients who smoked. During screening, 562 differentially expressed genes were identified, and we elucidated that smoking affected the survival of patients 4.5 years after the diagnosis of lung cancer. Furthermore, genes negatively associated with smoking were closely associated with immunity. Twelve immune cell types were also found to infiltrate differentially in smokers and nonsmokers. Thus, the smoking-associated lncRNA model is a good predictor of survival and risk in smokers and may be used as an independent prognostic factor for lung cancer.
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Sasa GBK, Xuan C, Chen M, Jiang Z, Ding X. Clinicopathological implications of lncRNAs, immunotherapy and DNA methylation in lung squamous cell carcinoma: a narrative review. Transl Cancer Res 2022; 10:5406-5429. [PMID: 35116387 PMCID: PMC8799054 DOI: 10.21037/tcr-21-1607] [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: 08/11/2021] [Accepted: 11/16/2021] [Indexed: 11/06/2022]
Abstract
Objective To explore the clinicopathological impact of lncRNAs, immunotherapy, and DNA methylation in lung squamous cell carcinoma (LUSC), emphasizing their exact roles in carcinogenesis and modes of action. Background LUSC is the second most prevalent form, accounting for around 30% of non-small cell lung cancer (NSCLC). To date, molecular-targeted treatments have significantly improved overall survival in lung adenocarcinoma patients but have had little effect on LUSC therapy. As a result, there is an urgent need to discover new treatments for LUSC that are based on existing genomic methods. Methods In this review, we summarized and analyzed recent research on the biological activities and processes of lncRNA, immunotherapy, and DNA methylation in the formation of LUSC. The relevant studies were retrieved using a thorough search of Pubmed, Web of Science, Science Direct, Google Scholar, and the university's online library, among other sources. Conclusions LncRNAs are the primary components of the mammalian transcriptome and are emerging as master regulators of a number of cellular processes, including the cell cycle, differentiation, apoptosis, and growth, and are implicated in the pathogenesis of a variety of cancers, including LUSC. Understanding their role in LUSC in detail may help develop innovative treatment methods and tactics for LUSC. Meanwhile, immunotherapy has transformed the LUSC treatment and is now considered the new standard of care. To get a better knowledge of LUSC biology, it is critical to develop superior modeling systems. Preclinical models, particularly those that resemble human illness by preserving the tumor immune environment, are essential for studying cancer progression and evaluating novel treatment targets. DNA methylation, similarly, is a component of epigenetic alterations that regulate cellular function and contribute to cancer development. By methylating the promoter regions of tumor suppressor genes, abnormal DNA methylation silences their expression. DNA methylation indicators are critical in the early detection of lung cancer, predicting therapy efficacy, and tracking treatment resistance. As such, this review seeks to explore the clinicopathological impact of lncRNAs, immunotherapy, and DNA methylation in LUSC, emphasizing their exact roles in carcinogenesis and modes of action.
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Affiliation(s)
- Gabriel B K Sasa
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Cheng Xuan
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Meiyue Chen
- The fourth affiliated hospital, Zhejiang University of Medicine, Hangzhou, China
| | - Zhenggang Jiang
- Department of Science Research and Information Management, Zhejiang Provincial Centers for Disease Control and Prevention, Hangzhou, China
| | - Xianfeng Ding
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
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Wang G, Pan C, Cao K, Zhang J, Geng H, Wu K, Wen J, Liu C. Impacts of Cigarette Smoking on the Tumor Immune Microenvironment in Esophageal Squamous Cell Carcinoma. J Cancer 2022; 13:413-425. [PMID: 35069891 PMCID: PMC8771511 DOI: 10.7150/jca.65400] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 11/23/2021] [Indexed: 02/05/2023] Open
Abstract
Objective: Cigarette smoking is a carcinogenic factor for esophageal cancer and evidence also indicates its effects on tumor microenvironment in patients with esophageal squamous cell carcinoma (ESCC). Materials and Methods: In our study, we demonstrated nine immune infiltrating cells and markers in non-smokers and smokers of 189 non-drinking ESCC patients with multiplex fluorescent immunohistochemistry (mflHC) staining and multispectral imaging. The impacts of cigarette smoking on tumor microenvironment and patient prognosis were also analyzed. Results: Among 189 ESCC patients of non-drinker, 86 patients was current smokers, while 34 males and 59 females were non-smokers and 10 former-smokers. Among 34 male non-smokers and 83 smokers, distinct immune infiltrating cells, with increased DCs in stromal regions (P=0.033), elevated infiltration of Treg cells in intraepithelial regions (P=0.010) and reduced activate cytotoxic T lymphocytes (aCTLs) in both intraepithelial (P=0.021) and stromal regions (P=0.017), were observed in tumor specimens of smoking males, implying an immune suppressed response during cigarette smoke exposure. For smoking characters, the level of stromal tumor-associated macrophages (TAMs) infiltration was correlated with smoking year after age adjusted (rs =0.352, P=0.002). Though cigarette smoking did not alter the expression of programmed death ligand 1 (PD-L1) in epithelial cells or TAMs in tumor specimens, higher expression of PD-L1 predicted a worse survival in non-smokers but not smokers. Conclusions: Our findings indicated smoking may impair T cell-mediated immune response and supported the possible impacts of cigarette smoking in PD-L1 related research and therapy of ESCC.
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Affiliation(s)
- Geng Wang
- Department of Thoracic Surgery, Cancer Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Chuqing Pan
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Kexin Cao
- Department of Preventive Medicine, Shantou University Medical College, Shantou, Guangdong, China
| | - Jingbing Zhang
- Department of Preventive Medicine, Shantou University Medical College, Shantou, Guangdong, China
| | - Hui Geng
- Department of Preventive Medicine, Shantou University Medical College, Shantou, Guangdong, China
| | - Kusheng Wu
- Department of Preventive Medicine, Shantou University Medical College, Shantou, Guangdong, China
| | - Jing Wen
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
- Guangdong Esophageal Cancer Research Institute, Guangzhou, China
| | - Caixia Liu
- Department of Preventive Medicine, Shantou University Medical College, Shantou, Guangdong, China
- Department of Preventive Medicine, Shantou University Medical College, No.22, Xinling Road. Shantou 515041, Guangdong, People's Republic of China
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Yu X, Liu J, Xie R, Chang M, Xu B, Zhu Y, Xie Y, Yang S. Construction of a prognostic model for lung squamous cell carcinoma based on seven N6-methylandenosine-related autophagy genes. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2021; 18:6709-6723. [PMID: 34517553 DOI: 10.3934/mbe.2021333] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
OBJECTIVE We aimed to construct a novel prognostic model based on N6-methyladenosine (m6A)-related autophagy genes for predicting the prognosis of lung squamous cell carcinoma (LUSC). METHODS Gene expression profiles and clinical information of Patients with LUSC were downloaded from The Cancer Genome Atlas (TCGA) database. In addition, m6A- and autophagy-related gene profiles were obtained from TCGA and Human Autophagy Database, respectively. Pearson correlation analysis was performed to identify the m6A-related autophagy genes, and univariate Cox regression analysis was conducted to screen for genes associated with prognosis. Based on these genes, LASSO Cox regression analysis was used to construct a prognostic model. The corresponding prognostic score (PS) was calculated, and patients with LUSC were assigned to low- and high-risk groups according to the median PS value. An independent dataset (GSE37745) was used to validate the prognostic ability of the model. CIBERSORT was used to calculate the differences in immune cell infiltration between the high- and low-risk groups. RESULTS Seven m6A-related autophagy genes were screened to construct a prognostic model: CASP4, CDKN1A, DLC1, ITGB1, PINK1, TP63, and EIF4EBP1. In the training and validation sets, patients in the high-risk group had worse survival times than those in the low-risk group; the areas under the receiver operating characteristic curves were 0.958 and 0.759, respectively. There were differences in m6A levels and immune cell infiltration between the high- and low-risk groups. CONCLUSIONS Our prognostic model of the seven m6A-related autophagy genes had significant predictive value for LUSC; thus, these genes may serve as autophagy-related therapeutic targets in clinical practice.
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Affiliation(s)
- Xin Yu
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and PeKing Union Medical College, Shenzhen 518116, China
| | - Jun Liu
- Department of Chemotherapy, Affiliated Hospital of Nantong University, Nantong 226001, China
| | - Ruiwen Xie
- Department of Cardiothoracic Surgery, Dongguan People's Hospital, Dongguan, Guangzhou 523000, China
| | - Mengling Chang
- Department of Chemotherapy, Affiliated Hospital of Nantong University, Nantong 226001, China
| | - Bichun Xu
- Department of Oncology Radiotherapy, The Second Affiliated Hospital of Soochow University, Suzhou 215000, China
| | - Yangqing Zhu
- Department of Chemotherapy, Affiliated Hospital of Nantong University, Nantong 226001, China
| | - Yuancai Xie
- Department of Thoracic Surgery, Peking University Shenzhen Hospital, Shenzhen 518036, China
| | - Shengli Yang
- Department of Thoracic Surgery, Foshan First people's Hospital, Affiliated Hospital of Sun Yat sen University, Foshan 528000, China
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Chen C, Cheng X, Li S, Chen H, Cui M, Bian L, Jin H. A Novel Signature for Predicting Prognosis of Smoking-Related Squamous Cell Carcinoma. Front Genet 2021; 12:666371. [PMID: 33968141 PMCID: PMC8100348 DOI: 10.3389/fgene.2021.666371] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 03/23/2021] [Indexed: 12/31/2022] Open
Abstract
Tobacco smoking is an established risk factor for squamous cell carcinoma (SCC). We obtained smoking-related SCC, including cervical SCC (CSCC), esophageal SCC (ESCC), head and neck SCC (HNSC), and lung SCC (LUSC), from The Cancer Genome Atlas (TCGA) database to investigate the association between smoking status (reformed and current smoking) and prognosis. We found that reformed smokers had a better prognosis than current smokers in CSCC (p = 0.003), HNSC (p = 0.019), and LUSC (p < 0.01) cohorts. Then, we selected LUSC cohorts as the training cohort and other SCC cohorts as the test cohorts. Function analysis revealed that homologous recombination (HR) was the most significant pathway involved in smoking-induced LUSC. Moreover, the effect of cross-talk between the smoking status and HR deficiency (HRD) on the prognosis was further evaluated, revealing that quitting smoking with high HRD scores could significantly improve patients’ prognosis (p < 0.01). To improve prognosis prediction and more effectively screen suitable populations for platinum drugs and poly-ADP-ribose polymerase (PARP) inhibitors, we constructed a risk score model using smoking- and HRD-related genes in LUSC. The risk score model had high power for predicting 2-, 3-, and 5-year survival (p < 0.01, AUC = 0.67, 0.66, and 0.66). In addition, the risk scores were an independent risk factor for LUSC (HR = 2.34, 95%CI = 1.70–3.23). The practical nomogram was also built using the risk score, smoking status, and other clinical information with a good c-index (0.72, 95%CI = 0.70–0.74). Finally, we used other TCGA SCC cohorts to confirm the reliability and validity of the risk score model (p < 0.01 and AUC > 0.6 at 2, 3, and 5 years in CSCC and HNSC cohorts). In conclusion, the present study suggested that smoking cessation should be a part of smoking-related SCC treatment, and also provided a risk score model to predict prognosis and improve the effectiveness of screening the platinum/PARP population.
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Affiliation(s)
- Chang Chen
- Department of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing, China
| | - Xiaoqing Cheng
- Jiangsu Provincial Center for Disease Control and Prevention (Jiangsu Institution of Public Health), Nanjing, China
| | - Shuyan Li
- Anhui Province Veterans Hospital, Bengbu, China
| | - Huanghui Chen
- Department of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing, China
| | - Mengjing Cui
- Department of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing, China
| | - Linlin Bian
- Jiangsu Provincial Center for Disease Control and Prevention (Jiangsu Institution of Public Health), Nanjing, China
| | - Hui Jin
- Department of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing, China
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