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Zhi FH, Liu W, Yang HS, Luo HH, Feng YF, Lei YY. Exploring the relationship between the interleukin family and lung adenocarcinoma through Mendelian randomization and RNA sequencing analysis. Discov Oncol 2024; 15:436. [PMID: 39264458 PMCID: PMC11393260 DOI: 10.1007/s12672-024-01325-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Accepted: 09/06/2024] [Indexed: 09/13/2024] Open
Abstract
BACKGROUND Lung adenocarcinoma (LUAD) is still one of the most prevalent malignancies. Interleukin factors are closely associated with the initiation and progression of cancer. However, the relationship between interleukin factors and LUAD has not been fully elucidated. This study aimed to use Mendelian randomization (MR) and RNA sequencing (RNA-seq) analyses to identify the interleukin factors associated with the onset and progression of LUAD. METHODS Exposure-related instrumental variables were selected from interleukin factor summary datasets. The LUAD summary dataset from FINGENE served as the outcome. MR and sensitivity analyses were conducted to screen for interleukin factors associated with LUAD occurrence. Transcriptome analyses revealed the role of interleukin factors in lung tissues. The results were validated through Western blotting and further confirmed with driver gene-negative patients from multiple centers. Potential mechanisms influencing LUAD occurrence and development were explored using bulk RNA-seq and single-cell RNA-seq data. RESULTS MR analysis indicated that elevated plasma levels of IL6RB, IL27RA, IL22RA1, and IL16 are causally associated with increased LUAD risk, while IL18R1 and IL11RA exhibit the opposite effect. Transcriptome analyses revealed that IL11RA, IL18R1, and IL16 were downregulated in tumor tissues compared with normal lung tissue, but only higher expression of IL11RA correlated with improved prognosis in patients with LUAD from different centers and persisted even in driver-gene negative patients. The IL11RA protein level was lower in various LUAD cell lines than in human bronchial epithelial cells. The genes co-expressed with IL11RA were enriched in the Ras signaling pathway and glycosylation processes. Fibroblasts were the primary IL11RA-expressing cell population, with IL11RA+fibroblasts exhibiting a more immature state. The genes differentially expressed between IL11RA+and IL11RA- fibroblasts were involved in the PI3K-Akt/TNF signaling pathway. CONCLUSION According to the MR and transcriptome analyses, the downregulation of IL11RA was closely related to the occurrence and development of LUAD.
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Affiliation(s)
- Fei-Hang Zhi
- Department of Thoracic Surgery, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510080, Guangdong, China
| | - Wei Liu
- Department of Thoracic Surgery, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510080, Guangdong, China
| | - Hao-Shuai Yang
- Department of Thoracic Surgery, China-Japan Friendship Hospital, Beijing, China
| | - Hong-He Luo
- Department of Thoracic Surgery, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510080, Guangdong, China
| | - Yan-Fen Feng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, Guangdong, China.
- Department of Pathology, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, Guangdong, China.
| | - Yi-Yan Lei
- Department of Thoracic Surgery, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510080, Guangdong, China.
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He J, Li F, Jing Z, Ren X, Jia D, Zeng Y, Yu Y. GNPNAT1 Serves as a Prognostic Biomarker Correlated with Immune Infiltration and Promotes Cancer Cell Metastasis through Stabilization of Snai2 in Lung Adenocarcinoma. Biomedicines 2024; 12:1477. [PMID: 39062049 PMCID: PMC11274686 DOI: 10.3390/biomedicines12071477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2024] [Revised: 06/21/2024] [Accepted: 06/27/2024] [Indexed: 07/28/2024] Open
Abstract
BACKGROUND Lung cancer is a common malignant tumor with high morbidity and mortality rate. Glucosamine 6-phosphate N-acetyltransferase (GNPNAT1), which serves as a critical enzyme in hexosamine biosynthetic pathway (HBP), has been identified as a metastasis-associated gene and is upregulated in lung adenocarcinoma (LUAD). However, the exact role and related mechanism of GNPNAT1 in LUAD metastasis remain unknown. METHODS We analyzed the expression of GNPNAT1 in the public databases and confirmed the results by immunohistochemistry (IHC). The biological functions of GNPNAT1 in LUAD were investigated based on The Cancer Genome Atlas (TCGA). Correlations between GNPNAT1 and cancer immune characteristics were analyzed via the Estimation of Stromal and Immune cells in Malignant Tumor tissues using Expression data (ESTIMATE) and Cell-type Identification by Estimating Relative Subsets of RNA Transcript (CIBERSORT) R package. The underlying mechanisms of altered GNPNAT1 expression on LUAD cell tumorigenesis, proliferation, migration, invasion, and metastasis were explored in vitro and in vivo. RESULTS We demonstrated that GNPNAT1 expression was significantly increased in LUAD and negatively associated with the overall survival (OS) of patients. hsa-miR-1-3p and hsa-miR-26a-5p were identified as upstream miRNA targets of GNPNAT1. GNPNAT1 was associated with the infiltration levels of CD8 T cells, memory-activated CD4 T cells, NK cells resting, macrophages M0, macrophages M1, neutrophils, gamma delta T cells, and eosinophils, while it was negatively correlated with memory-resting CD4 T cells, regulatory T cells (Tregs), resting NK cells, monocytes, resting dendritic cells, and resting mast cells. GNPNAT1 knockdown significantly inhibited proliferation, migration, invasion, epithelial-mesenchymal transition (EMT) process, and metastasis of LUAD cells, while overexpression of GNPNAT1 revealed the opposite effects. Rescue assay showed that Snai2 knockdown reversed GNPNAT1-induced LUAD cells migration, invasion, and EMT. Mechanistically, GNPNAT1 promoted cancer cell metastasis via repressing ubiquitination degradation of Snai2 in LUAD. CONCLUSIONS Taken together, these data indicate that GNPNAT1 serves as a prognostic biomarker for LUAD patient. Additionally, GNPNAT1 is critical for promoting tumorigenesis and metastasis of LUAD cells and may be a potential therapeutic target for preventing LUAD metastasis.
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Affiliation(s)
- Jinqi He
- Department of Medical Oncology, Harbin Medical University Cancer Hospital, Harbin 150040, China; (J.H.); (Z.J.); (X.R.); (D.J.); (Y.Z.)
| | - Faxiang Li
- Department of Medical Oncology, The Central Hospital of Shaoyang, Shaoyang 422000, China;
| | - Zihan Jing
- Department of Medical Oncology, Harbin Medical University Cancer Hospital, Harbin 150040, China; (J.H.); (Z.J.); (X.R.); (D.J.); (Y.Z.)
| | - Xingmei Ren
- Department of Medical Oncology, Harbin Medical University Cancer Hospital, Harbin 150040, China; (J.H.); (Z.J.); (X.R.); (D.J.); (Y.Z.)
| | - Dexin Jia
- Department of Medical Oncology, Harbin Medical University Cancer Hospital, Harbin 150040, China; (J.H.); (Z.J.); (X.R.); (D.J.); (Y.Z.)
| | - Yuan Zeng
- Department of Medical Oncology, Harbin Medical University Cancer Hospital, Harbin 150040, China; (J.H.); (Z.J.); (X.R.); (D.J.); (Y.Z.)
| | - Yan Yu
- Department of Medical Oncology, Harbin Medical University Cancer Hospital, Harbin 150040, China; (J.H.); (Z.J.); (X.R.); (D.J.); (Y.Z.)
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Shu M, Huang L, Chen Y, Wang Y, Xie Z, Li S, Zhou J, Wei L, Fu T, Liu B, Chen H, Tang K, Ke Z. Identification of a DNA-methylome-based signature for prognosis prediction in driver gene-negative lung adenocarcinoma. Cancer Lett 2024; 593:216835. [PMID: 38548216 DOI: 10.1016/j.canlet.2024.216835] [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: 11/30/2023] [Revised: 03/22/2024] [Accepted: 03/22/2024] [Indexed: 06/01/2024]
Abstract
"Driver gene-negative" lung adenocarcinoma (LUAD) was of rare treatment options and a poor prognosis. Presently, for them, few biomarkers are available for stratification analysis to make appropriate treatment strategy. This study aimed to develop a DNA-methylome-based signature to realize the precise risk-stratifying. Here, an Illumina MethylationEPIC Beadchip was applied to obtain differentially methylated CpG sites (DMCs). A four-CpG-based signature, named as TLA, was successfully established, whose prognosis-predicting power was well verified in one internal (n = 78) and other external (n = 110) validation cohorts. Patients with high-risk scores had shorter overall survival (OS) in all cohorts [hazard ratio (HR): 11.79, 5.16 and 2.99, respectively]. Additionally, it can effectively divide patients into low-risk and high-risk groups, with significantly different OS in the diverse subgroups stratified by the standard clinical parameters. As an independent prognostic factor, TLA may assist in improving the nomogram's 5-year OS-predicting ability (AUC 0.756, 95% CI:0.695-0.816), superior to TNM alone (AUC 0.644, 95% CI: 0.590-0.698). Additionally, the relationship of TLA-related genes, TAC1, LHX9, and ALX1, with prognosis and tumour invasion made them serve as potential therapy targets for driver gene-negative LUAD.
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Affiliation(s)
- Man Shu
- Department of Pathology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, PR China
| | - Leilei Huang
- Department of Pathology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, PR China
| | - Yu Chen
- Department of Pathology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, PR China; Department of Pathology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, PR China
| | - Yanxia Wang
- Department of Pathology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, PR China
| | - Zhongpeng Xie
- Department of Pathology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, PR China
| | - Shuhua Li
- Molecular Diagnosis and Gene Test Centre, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, PR China
| | - Jianwen Zhou
- Molecular Diagnosis and Gene Test Centre, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, PR China
| | - Lihong Wei
- Department of Pathology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, PR China
| | - Tongze Fu
- Department of Pathology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, PR China; Molecular Diagnosis and Gene Test Centre, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, PR China
| | - Bixia Liu
- Molecular Diagnosis and Gene Test Centre, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, PR China
| | - Honglei Chen
- Department of Pathology, School of Basic Medical Science, Wuhan University, Wuhan, Hubei, PR China.
| | - Kejing Tang
- Division of Pulmonary and Critical Care Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, PR China; Institute of Pulmonary Diseases, Sun Yat-sen University, Guangzhou, PR China.
| | - Zunfu Ke
- Department of Pathology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, PR China; Molecular Diagnosis and Gene Test Centre, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, PR China.
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Cen W, Yan Q, Zhou W, Mao M, Huang Q, Lin Y, Jiang N. miR-4739 promotes epithelial-mesenchymal transition and angiogenesis in "driver gene-negative" non-small cell lung cancer via activating the Wnt/β-catenin signaling. Cell Oncol (Dordr) 2023; 46:1821-1835. [PMID: 37500965 DOI: 10.1007/s13402-023-00848-z] [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] [Accepted: 07/21/2023] [Indexed: 07/29/2023] Open
Abstract
PURPOSE "Driver gene-negative" non-small cell lung cancer (NSCLC) currently has no approved targeted drug, due to the lack of common actionable driver molecules. Even though miRNAs play crucial roles in various malignancies, their roles in "driver gene-negative" NSCLC keep unclear. METHODS miRNA expression microarrays were utilized to screen miRNAs associated with "driver gene-negative" NSCLC malignant progression. Quantitative real-time PCR (RT-qPCR) and in situ hybridization (ISH) were employed to validate the expression of miR-4739, and its correlation with clinicopathological characteristics was analyzed in tumor specimens using univariate and multivariate analyses. The biological functions and underlying mechanisms of miR-4739 were investigated both in vitro and in vivo. RESULTS our research demonstrated, for the first time, that miR-4739 was substantially increased in "driver gene-negative" NSCLC tumor tissues and cell lines, and overexpression of miR-4739 was related to clinical staging, metastasis, and unfavorable outcomes. Functional experiments discovered that miR-4739 dramatically enhanced tumor cell proliferation, migration, and metastasis by promoting the epithelial-to-mesenchymal transition (EMT). Meanwhile, miR-4739 can be transported from cancer cells to the site of vascular epithelial cells through exosomes, consequently facilitating the proliferation and migration of vascular epithelial cells and inducing angiogenesis. Mechanistically, miR-4739 can activate Wnt/β-catenin signaling both in tumor cells and vascular epithelial cells by targeting Wnt/β-catenin signaling antagonists APC2 and DKK3, respectively. CONCLUSION Our work identifies a valuable oncogene, miR-4739, that accelerates malignant progression in "driver gene-negative" NSCLC and serves as a potential therapeutic target for this group of tumors.
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Affiliation(s)
- Wenjian Cen
- State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, 510060, P. R. China
- Department of Molecular Diagnostics, Sun Yat-sen University Cancer Center, Guangzhou, 510060, P. R. China
| | - Qin Yan
- State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, 510060, P. R. China
- Department of Pathology, Sun Yat-sen University Cancer Center, Guangzhou, 510060, Guangdong, P. R. China
| | - Wenpeng Zhou
- Department of Gastroenterology and Hepatology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, P. R. China
| | - Minjie Mao
- State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, 510060, P. R. China
- Department of Laboratory Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510060, P. R. China
| | - Qitao Huang
- State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, 510060, P. R. China
- Department of Pathology, Sun Yat-sen University Cancer Center, Guangzhou, 510060, Guangdong, P. R. China
| | - Yaobin Lin
- State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, 510060, P. R. China.
- Department of Thoracic Surgery, Sun Yat-sen University Cancer Center, Guangzhou, 510060, Guangdong, P. R. China.
| | - Neng Jiang
- State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, 510060, P. R. China.
- Department of Pathology, Sun Yat-sen University Cancer Center, Guangzhou, 510060, Guangdong, P. R. China.
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Fick CN, Dunne EG, Lankadasari MB, Mastrogiacomo B, Asao T, Vanstraelen S, Liu Y, Sanchez-Vega F, Jones DR. Genomic profiling and metastatic risk in early-stage non-small cell lung cancer. JTCVS OPEN 2023; 16:9-16. [PMID: 38204702 PMCID: PMC10775106 DOI: 10.1016/j.xjon.2023.10.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 10/02/2023] [Accepted: 10/11/2023] [Indexed: 01/12/2024]
Affiliation(s)
- Cameron N. Fick
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Elizabeth G. Dunne
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Manendra B. Lankadasari
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
- Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Brooke Mastrogiacomo
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
- Computational Oncology Service, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Tetsuhiko Asao
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Stijn Vanstraelen
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Yuan Liu
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
- Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Francisco Sanchez-Vega
- Computational Oncology Service, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - David R. Jones
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
- Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY
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Zhang Y, Zhu Y, Wang S, Feng YC, Li H. Erythropoietin receptor is a risk factor for prognosis: A potential biomarker in lung adenocarcinoma. Pathol Res Pract 2023; 251:154891. [PMID: 37844485 DOI: 10.1016/j.prp.2023.154891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Revised: 10/10/2023] [Accepted: 10/12/2023] [Indexed: 10/18/2023]
Abstract
Lung cancer has the highest mortality rate of all cancers, and LUAD's survival rate is particularly poor. Erythropoietin receptor (EPOR) can be detected in lung adenocarcinoma (LUAD), however, the expression levels and prognostic value of EPOR in LUAD are still unclear. In our study, clinicopathological data of 92 LUAD patients between January 2008 and June 2016, multiple bioinformatics databases and immunohistochemistry were used to explore the EPOR expression, the mutant genes affecting EPOR expression, and the correlation of EPOR expression with oxidative stress - related genes, prognosis, immune microenvironment. All statistical analyses were performed in the R version 4.1.1. The study found that EPOR expression might be down-regulated at the mRNA levels and significantly up-regulated at the protein levels in LUAD, which indicates that the mRNA and protein levels of EPOR are inconsistent. The muTarget showed that the expression of EPOR was significantly different between the mutant group and the wild group of 15 genes, including DDX60L and C1orf168. Importantly, we found that EPOR was associated with VEGF and HIF family members, and had significant positive correlation with oxidative stress - related genes such as CCS, EPX and TXNRD2. This suggests that EPOR may be involved in the regulation of oxidative stress. The Kaplan-Meier Plotter and PrognoScan databases consistently concluded that EPOR was associated with prognosis in LUAD patients. Our clinicopathological data showed that high EPOR expression was associated with poorer overall survival (29.5 vs 46 months) and had a good predictive ability for 4-year and 5-year survival probability. EPOR is expected to be a potential new prognostic marker for LUAD.
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Affiliation(s)
- Yajing Zhang
- Clinical Laboratory Center, The First Affiliated Hospital of Xinjiang Medical University, Xinjiang, China; Xinjiang Key Laboratory of Oncology, Tumor Hospital Affiliated to Xinjiang Medical University, Xinjiang, China
| | - Yousen Zhu
- Clinical Laboratory Center, The First Affiliated Hospital of Xinjiang Medical University, Xinjiang, China
| | - Senyu Wang
- Xinjiang Key Laboratory of Oncology, Tumor Hospital Affiliated to Xinjiang Medical University, Xinjiang, China
| | - Yang Chun Feng
- Xinjiang Key Laboratory of Oncology, Tumor Hospital Affiliated to Xinjiang Medical University, Xinjiang, China.
| | - Hui Li
- Clinical Laboratory Center, The First Affiliated Hospital of Xinjiang Medical University, Xinjiang, China.
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Li Z, Guo M, Lin W, Huang P. Machine Learning-Based Integration Develops a Macrophage-Related Index for Predicting Prognosis and Immunotherapy Response in Lung Adenocarcinoma. Arch Med Res 2023; 54:102897. [PMID: 37865004 DOI: 10.1016/j.arcmed.2023.102897] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 08/06/2023] [Accepted: 10/06/2023] [Indexed: 10/23/2023]
Abstract
BACKGROUND Macrophages play a critical role in tumor immune microenvironment (TIME) formation and cancer progression in lung adenocarcinoma (LUAD). However, few studies have comprehensively and systematically described the characteristics of macrophages in LUAD. METHODS This study identified macrophage-related markers with single-cell RNA sequencing data from the GSE189487 dataset. An integrative machine learning-based procedure based on 10 algorithms was developed to construct a macrophage-related index (MRI) in The Cancer Genome Atlas (TCGA), GSE30219, GSE31210, and GSE72094 datasets. Several algorithms were used to evaluate the associations of MRI with TIME and immunotherapy-related biomarkers. The role of MRI in predicting the immunotherapy response was evaluated with the GSE91061 dataset. RESULTS The optimal MRI constructed by the combination of the Lasso algorithm and plsRCox was an independent risk factor in LUAD and showed a stable and powerful performance in predicting the overall survival rate of patients with LUAD. Those with low MRI scores had a higher TIME score, a higher level of immune cells, a higher immunophenoscore, and a lower Tumor Immune Dysfunction and Exclusion (TIDE) score, indicating a better response to immunotherapy. The IC50 value of common drugs for chemotherapy and target therapy with low MRI scores was higher compared to high MRI scores. Moreover, the survival prediction nomogram, developed from MRI, had good potential for clinical application in predicting the 1-, 3-, and 5-year overall survival rate of LUAD. CONCLUSION Our study constructed for the first time a consensus MRI for LUAD with 10 machine learning algorithms. The MRI could be helpful for risk stratification, prognosis, and selection of treatment approach in LUAD.
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Affiliation(s)
- Zuwei Li
- Department of Thoracic Surgery and Institute of Thoracic Oncology, West China Hospital, Sichuan University, Chengdu, China
| | - Minzhang Guo
- Department of Thoracic Surgery and Institute of Thoracic Oncology, West China Hospital, Sichuan University, Chengdu, China
| | - Wanli Lin
- Department of Thoracic Surgery, Gaozhou People's Hospital, Maoming, China
| | - Peiyuan Huang
- Department of Pharmacy, Gaozhou People's Hospital, Maoming, China.
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Li L, Zhang F, Zhang J, Shi X, Wu H, Chao X, Ma S, Lang J, Wu M, Zhang D, Liang Z. Identifying Serum Small Extracellular Vesicle MicroRNA as a Noninvasive Diagnostic and Prognostic Biomarker for Ovarian Cancer. ACS NANO 2023; 17:19197-19210. [PMID: 37750402 DOI: 10.1021/acsnano.3c05694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/27/2023]
Abstract
There remains a lack of effective and noninvasive methods for the diagnosis and prognosis prediction of epithelial ovarian carcinoma (EOC). Here, we investigated the possibility of serum-derived small extracellular vesicle (sEV) microRNAs (miRNAs) as potential biomarkers for distinguishing between benign and malignant adnexal masses and predicting the prognosis of EOC patients. A serum sEV miRNA model for identifying the EOC (sEVmiR-EOC) was successfully established in the training cohort. Furthermore, the sEVmiR-EOC model was confirmed in the testing cohort and validation cohort, demonstrating robust diagnostic accuracy. The sEVmiR-EOC model showed better performance than carbohydrate antigen 125 (CA125) in discriminating patients with stage I EOC from benign patients. Using EOC samples and follow-up data, we identified miR-141-3p and miR-200c-3p as potential prognostic predictors. Finally, we confirmed the change of the sEVmiR-EOC RiskScore between the preoperative and postoperative samples and found that the sEVmiR-EOC model could predict the prognosis of EOC patients.
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Affiliation(s)
- Lei Li
- Department of Obstetrics and Gynecology, National Clinical Research Center for Obstetric & Gynecologic Diseases, Peking Union Medical College Hospital, Beijing 100730, China
| | - Fuchuang Zhang
- Department of Translational Medicine, 3D Medicines Inc., Shanghai 201114, China
| | - Jiyang Zhang
- Department of Translational Medicine, 3D Medicines Inc., Shanghai 201114, China
| | - Xiaohua Shi
- Department of Pathology, Molecular Pathology Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, China
| | - Huanwen Wu
- Department of Pathology, Molecular Pathology Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, China
| | - Xiaopei Chao
- Department of Obstetrics and Gynecology, National Clinical Research Center for Obstetric & Gynecologic Diseases, Peking Union Medical College Hospital, Beijing 100730, China
| | - Shuiqing Ma
- Department of Obstetrics and Gynecology, National Clinical Research Center for Obstetric & Gynecologic Diseases, Peking Union Medical College Hospital, Beijing 100730, China
| | - Jinghe Lang
- Department of Obstetrics and Gynecology, National Clinical Research Center for Obstetric & Gynecologic Diseases, Peking Union Medical College Hospital, Beijing 100730, China
| | - Ming Wu
- Department of Obstetrics and Gynecology, National Clinical Research Center for Obstetric & Gynecologic Diseases, Peking Union Medical College Hospital, Beijing 100730, China
| | - Dadong Zhang
- Department of Translational Medicine, 3D Medicines Inc., Shanghai 201114, China
| | - Zhiyong Liang
- Department of Pathology, Molecular Pathology Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, China
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Xiao G, Xu X, Chen Z, Zeng J, Xie J. SPAG5 Expression Predicts Poor Prognosis and is Associated With Adverse Immune Infiltration in Lung Adenocarcinomas. Clin Med Insights Oncol 2023; 17:11795549231199915. [PMID: 37744424 PMCID: PMC10517604 DOI: 10.1177/11795549231199915] [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: 03/31/2023] [Accepted: 08/21/2023] [Indexed: 09/26/2023] Open
Abstract
Background Sperm-associated antigen 5 (SPAG5) has been identified as a novel driver oncogene involved in multiple cancers; however, its role in lung adenocarcinoma (LUAD) needs further investigation. Our study aims to elucidate the potential significance of SPAG5 in LUAD prognosis and its implications for the efficacy of immunotherapy. Methods In this study, we used bioinformatics analysis and tissue microarray (TMA) staining to examine the potential role of SPAG5 in LUAD survival and response to immunotherapy. We used the Oncomine, TIMER2.0, Gene Expression Profiling Interactive Analysis (GEPIA), Sangerbox, PredicScan, and Kaplan-Meier Plotter databases to examine the expression and prognostic role of SPAG5 in the LUAD of The Cancer Genome Atlas (TCGA), Gene Expression Omnibus (GEO), and other databases. We also used Cancer Single-cell State Atlas (CancerSEA) and Tumor Immune Estimation Resource (TIMER2.0) to analyze the association of SPAG5 with malignant phenotype and tumor immune microenvironment. Furthermore, Immune Cell Abundance Identifier (ImmuCellAI) analysis of TCGA sequencing data was used to predict the role of SPAG5 in determining the response to immune checkpoint blockade (ICB) treatment in LUAD. Co-expression analysis of programmed death-ligand 1 (PD-L1) and SPAG5 was performed using LUAD TMA immunohistochemistry (IHC) analysis. Results Our findings indicate that SPAG5 is overexpressed in LUAD and is positively correlated with advanced clinical stage, poor overall survival, relapse-free survival, and progression-free survival outcomes. SPAG5 may be involved in regulating the cell cycle, proliferation, invasion, DNA damage and repair, and tumor immunosuppression. Furthermore, TMA IHC analysis showed a positive correlation between PD-L1 expression in LUAD and SPAG5 which suggests that SPAG5 may serve as a potential predictor of response to ICB therapy in LUAD. Conclusions Our results highlight the role of SAPG5 in promoting a tumor malignancy phenotype and immunosuppression in LUAD and suggest that SPAG5 may serve as a potential response marker for ICB therapy.
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Affiliation(s)
- Gang Xiao
- Department of Thoracic Surgery, Guangzhou First People’s Hospital, South China University of Technology, Guangzhou, China
- Center for Medical Research on Innovation and Translation, Guangzhou First People’s Hospital, South China University of Technology, Guangzhou, China
| | - Xie Xu
- Department of Thoracic Surgery, Guangzhou First People’s Hospital, South China University of Technology, Guangzhou, China
| | - Zhibo Chen
- Department of Thoracic Surgery, Guangzhou First People’s Hospital, South China University of Technology, Guangzhou, China
| | - Jie Zeng
- Department of Thoracic Surgery, Guangzhou First People’s Hospital, South China University of Technology, Guangzhou, China
| | - Jianjiang Xie
- Department of Thoracic Surgery, Guangzhou First People’s Hospital, South China University of Technology, Guangzhou, China
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Deng X, Chen X, Luo Y, Que J, Chen L. Intratumor microbiome derived glycolysis-lactate signatures depicts immune heterogeneity in lung adenocarcinoma by integration of microbiomic, transcriptomic, proteomic and single-cell data. Front Microbiol 2023; 14:1202454. [PMID: 37664112 PMCID: PMC10469687 DOI: 10.3389/fmicb.2023.1202454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Accepted: 08/07/2023] [Indexed: 09/05/2023] Open
Abstract
Introduction Microbiome plays roles in lung adenocarcinoma (LUAD) development and anti-tumor treatment efficacy. Aberrant glycolysis in tumor might promote lactate production that alter tumor microenvironment, affecting microbiome, cancer cells and immune cells. We aimed to construct intratumor microbiome score to predict prognosis of LUAD patients and thoroughly investigate glycolysis and lactate signature's association with LUAD immune cell infiltration. Methods The Cancer Genome Atlas-LUAD (TCGA-LUAD) microbiome data was downloaded from cBioPortal and analyzed to examine its association with overall survival to create a prognostic scoring model. Gene Set Enrichment Analysis (GSEA) was used to find each group's major mechanisms involved. Our study then investigated the glycolysis and lactate pattern in LUAD patients based on 19 genes, which were correlated with the tumor microenvironment (TME) phenotypes and immunotherapy outcomes. We developed a glycolysis-lactate risk score and signature to accurately predict TME phenotypes, prognosis, and response to immunotherapy. Results Using the univariate Cox regression analysis, the abundance of 38 genera were identified with prognostic values and a lung-resident microbial score (LMS) was then developed from the TCGA-LUAD-microbiome dataset. Glycolysis hallmark pathway was significantly enriched in high-LMS group and three distinct glycolysis-lactate patterns were generated. Patients in Cluster1 exhibited unfavorable outcomes and might be insensitive to immunotherapy. Glycolysis-lactate score was constructed for predicting prognosis with high accuracy and validated in external cohorts. Gene signature was developed and this signature was elevated in epithelial cells especially in tumor mass on single-cell level. Finally, we found that the glycolysis-lactate signature levels were consistent with the malignancy of histological subtypes. Discussion Our study demonstrated that an 18-microbe prognostic score and a 19-gene glycolysis-lactate signature for predicting prognosis of LUAD patients. Our LMS, glycolysis-lactate score and glycolysis-lactate signature have potential roles in precision therapy of LUAD patients.
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Affiliation(s)
| | | | | | - Jun Que
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Liang Chen
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
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Guo QK, Yang HS, Shan SC, Chang DD, Qiu LJ, Luo HH, Li HP, Ke ZF, Zhu Y. A radiomics nomogram prediction for survival of patients with "driver gene-negative" lung adenocarcinomas (LUAD). LA RADIOLOGIA MEDICA 2023:10.1007/s11547-023-01643-4. [PMID: 37219740 DOI: 10.1007/s11547-023-01643-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 04/26/2023] [Indexed: 05/24/2023]
Abstract
BACKGROUND To study the role of computed tomography (CT)-derived radiomics features and clinical characteristics on the prognosis of "driver gene-negative" lung adenocarcinoma (LUAD) and to explore the potential molecular biological which may be helpful for patients' individual postoperative care. METHODS A total of 180 patients with stage I-III "driver gene-negative" LUAD in the First Affiliated Hospital of Sun Yat-Sen University from September 2003 to June 2015 were retrospectively collected. The Least Absolute Shrinkage and Selection Operator (LASSO) Cox regression model was used to screen radiomics features and calculated the Rad-score. The prediction performance of the nomogram model based on radiomics features and clinical characteristics was validated and then assessed with respect to calibration. Gene set enrichment analysis (GSEA) was used to explore the relevant biological pathways. RESULTS The radiomics and the clinicopathological characteristics were combined to construct a nomogram resulted in better performance for the estimation of OS (C-index: 0.815; 95% confidence interval [CI]: 0.756-0.874) than the clinicopathological nomogram (C-index: 0.765; 95% CI: 0.692-0.837). Decision curve analysis demonstrated that in terms of clinical usefulness, the radiomics nomogram outperformed the traditional staging system and the clinicopathological nomogram. The clinical prognostic risk score of each patient was calculated based on the radiomics nomogram and divided by X-tile into high-risk (> 65.28) and low-risk (≤ 65.28) groups. GSEA results showed that the low-risk score group was directly related to amino acid metabolism, and the high-risk score group was related to immune and metabolism pathways. CONCLUSIONS The radiomics nomogram was promising to predict the prognosis of patients with "driver gene-negative" LUAD. The metabolism and immune-related pathways may provide new treatment orientation for this genetically unique subset of patients, which may serve as a potential tool to guide individual postoperative care for those patients.
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Affiliation(s)
- Qi-Kun Guo
- Department of Oncology, The Affiliated He Xian Memorial Hospital of Southern Medical University, Guangzhou, 510080, Province Guangdong, People's Republic of China
- Department of Interventional Radiology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510080, Province Guangdong, People's Republic of China
| | - Hao-Shuai Yang
- Department of Thoracic Surgery, China-Japan Friendship Hospital, Beijing, China
| | - Shi-Chao Shan
- Department of Thoracic Surgery, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510080, Province Guangdong, People's Republic of China
| | - Dan-Dan Chang
- Department of Radiology, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510080, Province Guangdong, People's Republic of China
| | - Li-Jie Qiu
- Department of Interventional Radiology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510080, Province Guangdong, People's Republic of China
| | - Hong-He Luo
- Department of Thoracic Surgery, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510080, Province Guangdong, People's Republic of China
| | - He-Ping Li
- Department of Medical Oncology of the Eastern Hospital, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510080, People's Republic of China.
| | - Zun-Fu Ke
- Department of Pathology, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510080, Province Guangdong, People's Republic of China.
- Institution of Precision Medicine, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510080, Province Guangdong, People's Republic of China.
| | - Ying Zhu
- Department of Radiology, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510080, Province Guangdong, People's Republic of China.
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Ullah MA, Alam S, Moin AT, Ahamed T, Shohael AM. Risk factors and actionable molecular signatures in COVID-19-associated lung adenocarcinoma and lung squamous cell carcinoma patients. Comput Biol Med 2023; 158:106855. [PMID: 37040675 PMCID: PMC10072980 DOI: 10.1016/j.compbiomed.2023.106855] [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: 12/02/2022] [Revised: 02/05/2023] [Accepted: 03/30/2023] [Indexed: 04/08/2023]
Abstract
The molecular mechanism of COVID-19's pathogenic effect on lung cancer patients is yet unknown. In this study, we used differential gene expression pattern analysis to try to figure out the possible disease mechanism of COVID-19 and its associated risk factors in patients with the two most common types of non-small-cell lung cancer, lung adenocarcinoma and lung squamous cell carcinoma. We also used network-based approaches to identify potential diagnostic and molecular targets for COVID-19-infected lung cancer patients. Our study showed that lung cancer and COVID-19 patients share 36 genes that are expressed differently and in common. Most of these genes are expressed in lung tissues and are mostly involved in the pathogenesis of different respiratory tract diseases. Additionally, we also found that COVID-19 may affect the expression of several cancer-associated genes in lung cancer patients, such as the oncogenes JUN, TNC, and POU2AF1. Moreover, we also reported that COVID-19 may predispose lung cancer patients to other diseases like acute liver failure and respiratory distress syndrome. Also, our findings in concert with published literature suggest that molecular signatures like hsa-mir-93-5p, CCNB2, IRF1, CD163, and different immune cell-based approaches could help both diagnose and treat this group of patients. Overall, the scientific results of this research will aid in the formulation of suitable management strategies as well as the development of diagnostic and therapeutic methods for COVID-19-infected lung cancer patients.
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Affiliation(s)
- Md Asad Ullah
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Jahangirnagar University, Dhaka, Bangladesh
| | - Sayka Alam
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Jahangirnagar University, Dhaka, Bangladesh
| | - Abu Tayab Moin
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chattogram, Bangladesh
| | - Tanvir Ahamed
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Jahangirnagar University, Dhaka, Bangladesh
| | - Abdullah Mohammad Shohael
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Jahangirnagar University, Dhaka, Bangladesh.
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Fan B, Zheng C, Wang N, Chang Z, Liu Y, Wang C, Xiang J, Tao Y, Wang G, Zhang Q. CircSTK3 drives the metastasis of colorectal cancer by regulating epithelial-mesenchymal transition. iScience 2023; 26:106170. [PMID: 36922993 PMCID: PMC10009203 DOI: 10.1016/j.isci.2023.106170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 11/24/2022] [Accepted: 02/06/2023] [Indexed: 02/11/2023] Open
Abstract
Circular RNAs (circRNAs) play crucial roles in malignancies. We aimed to delineate the functions and clinical importance of dysregulated circRNAs in colorectal cancer (CRC). We determined the circRNA expression profile from five CRC and paired adjacent normal tissues using circRNA microarray. We found that a novel circRNA, hsa_circ_0004592 (named circSTK3), was significantly upregulated in CRC tissues and correlated with decreased survival. Loss- and gain-of-function assays revealed that circSTK3 promoted the migration and invasion but not proliferation of cells. Whole genome expression microarray identified potential downstream targets and the regulatory networks of circSTK3; Gene Ontology analysis confirmed circSTK3 involvement in the CRC metastasis phenotype. Abnormal circSTK3 expression affected a subset of genes associated with CRC metastasis and triggered epithelial-mesenchymal transition programming, maintaining a tumor-promoting signature. Moreover, circSTK3 was transcriptionally regulated by CTCF. These findings reveal the functional and prognostic roles of circSTK3 and expose circRNAs as key players in metastasis.
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Affiliation(s)
- Boyang Fan
- Department of Colorectal Cancer Surgery, the Second Affiliated Hospital of Harbin Medical University, Harbin 150086, China
| | - Chaojing Zheng
- Department of Colorectal Cancer Surgery, the Second Affiliated Hospital of Harbin Medical University, Harbin 150086, China
| | - Ning Wang
- Department of Pharmacology (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Medicine Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin 150081, China
| | - Zewen Chang
- Department of Colorectal Cancer Surgery, the Second Affiliated Hospital of Harbin Medical University, Harbin 150086, China
| | - Yunxiao Liu
- Department of Colorectal Cancer Surgery, the Second Affiliated Hospital of Harbin Medical University, Harbin 150086, China
| | - Chunlin Wang
- Department of Colorectal Cancer Surgery, the Second Affiliated Hospital of Harbin Medical University, Harbin 150086, China
| | - Jun Xiang
- Department of Colorectal Cancer Surgery, the Second Affiliated Hospital of Harbin Medical University, Harbin 150086, China
| | - Yangbao Tao
- Department of Colorectal Cancer Surgery, the Second Affiliated Hospital of Harbin Medical University, Harbin 150086, China
| | - Guiyu Wang
- Department of Colorectal Cancer Surgery, the Second Affiliated Hospital of Harbin Medical University, Harbin 150086, China
| | - Qian Zhang
- Department of Colorectal Surgery, Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou 310000, China
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Sun L, Li W, Zhao Z, Zuo Y, Han Z. Identification of a Necroptosis-Related Prognostic Signature and Associated Regulatory Axis in Lung Adenocarcinoma. Int J Genomics 2023; 2023:8766311. [PMID: 37965055 PMCID: PMC10643042 DOI: 10.1155/2023/8766311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Revised: 12/20/2022] [Accepted: 02/03/2023] [Indexed: 11/16/2023] Open
Abstract
Background Lung cancer is considered to be the second most aggressive and rapidly fatal cancer after breast cancer. Necroptosis, a novel discovered pattern of cell death, is mediated by Receptor-interacting serine/threonine-protein kinase 1 (RIPK1), Receptor-interacting serine/threonine-protein kinase 3 (RIPK3), and Mixed Lineage Kinase Domain Like Pseudokinase (MLKL). Methods For the purpose of developing a prognostic model, Least absolute shrinkage and selection operator (LASSO) Cox regression analysis was conducted. Using Pearson's correlation analysis, we evaluated the correlation between necroptosis-related markers and tumor immune infiltration. A bioinformatics analysis was conducted to construct a necroptosis-related regulatory axis. Results There was a downregulation of most of necroptosis-related genes in lung adenocarcinoma (LUAD) versus lung tissues but an increase in PGAM5, HMGB1, TRAF2, EZH2 levels. We also summarized the Single Nucleotide Variant (SNV) and copy number variation (CNV) of necroptosis-related genes in LUAD. Consensus clustering identified two clusters in LUAD with distinct immune cell infiltration and ESTIMATEScore. Genes related to necroptosis were associated with necroptosis, Tumor necrosis factor (TNF) signaling pathway, and apoptosis according to Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Four prognostic genes (ALDH2, HMGB1, NDRG2, TLR2) were combined to develop a prognostic gene signature for LUAD patients, which was highly accurate in predicting prognosis. Univariate and multivariate analysis identified HMGB1, pT stage, and pN stage as independent factors impacting on LUAD patients' prognosis. A significant correlation was found between the level of TLR2 and NDRG2 and clinical stage, immunity infiltration, and drug resistance. Additionally, the progression of LUAD might be regulated by lncRNA C5orf64/miR-582-5p/NDRG2/TLR2. Conclusion The current bioinformatics analysis identified a necroptosis-related prognostic signature for LUAD and their relation to immunity infiltration. This result requires further investigation.
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Affiliation(s)
- Libo Sun
- Department of Pharmacy, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Wenwen Li
- Department of Hematology, Qingdao Women and children's Hospital, Qingdao, China
| | - Zhenhuan Zhao
- Department of Pharmacy, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Yanhua Zuo
- Department of Pharmacy, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Zhiwu Han
- Department of Pharmacy, The Affiliated Hospital of Qingdao University, Qingdao, China
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15
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Yang H, Cai H, Shan S, Chen T, Zou J, Abudurufu M, Luo H, Lei Y, Ke Z, Zhu Y. Methylation of N6 adenosine-related long noncoding RNA: effects on prognosis and treatment in 'driver-gene-negative' lung adenocarcinoma. Mol Oncol 2023; 17:365-377. [PMID: 36221911 PMCID: PMC9892826 DOI: 10.1002/1878-0261.13323] [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: 02/18/2022] [Revised: 08/25/2022] [Accepted: 10/11/2022] [Indexed: 02/04/2023] Open
Abstract
The improvement of treatment for patients with 'driver-gene-negative' lung adenocarcinoma (LUAD) remains a critical problem to be solved. We aimed to explore the role of methylation of N6 adenosine (m6A)-related long noncoding RNA (lncRNA) in stratifying 'driver-gene-negative' LUAD risk. Patients negative for mutations in EGFR, KRAS, BRAF, HER2, MET, ALK, RET, and ROS1 were identified as 'driver-gene-negative' cases. RNA sequencing was performed in 46 paired tumors and adjacent normal tissues from patients with 'driver-gene-negative' LUAD. Twenty-three m6A regulators and relevant lncRNAs were identified using Pearson's correlation analysis. K-means cluster analysis was used to stratify patients, and a prognostic nomogram was developed. The CIBERSORT and pRRophetic algorithms were employed to quantify the immune microenvironment and chemosensitivity. We identified two clusters highly consistent with the prognosis based on their unique expression profiles for 46 m6AlncRNAs. A risk model constructed from nine m6A lncRNAs could stratify patients into high- and low-risk groups with promising predictive power (C-index = 0.824), and the risk score was an independent prognostic factor. The clusters and risk models were closely related to immune characteristics and chemosensitivity. Additional pan-cancer analysis using the nine m6AlncRNAs showed that the expression of DIO3 opposite strand upstream RNA (DIO3OS) is closely related to the immune/stromal score and tumor stemness in a variety of cancers. Our results show that m6AlncRNAs are a reliable prognostic tool and can aid treatment decision-making in 'driver-gene-negative' LUAD. DIO3OS is associated with the development of various cancers and has potential clinical applications.
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Affiliation(s)
- Hao‐Shuai Yang
- Department of Thoracic SurgeryThe First Affiliated Hospital, Sun Yat‐sen UniversityGuangzhouChina
| | - He‐Yuan Cai
- Department of Thoracic SurgeryThe First Affiliated Hospital, Sun Yat‐sen UniversityGuangzhouChina
| | - Shi‐Chao Shan
- Department of Thoracic SurgeryThe First Affiliated Hospital, Sun Yat‐sen UniversityGuangzhouChina
| | - Ting‐Fei Chen
- Department of Thoracic SurgeryThe First Affiliated Hospital, Sun Yat‐sen UniversityGuangzhouChina
| | - Jian‐Yong Zou
- Department of Thoracic SurgeryThe First Affiliated Hospital, Sun Yat‐sen UniversityGuangzhouChina
| | - Maimaiti Abudurufu
- Department of Thoracic SurgeryThe First Affiliated Hospital, Sun Yat‐sen UniversityGuangzhouChina
| | - Hong‐He Luo
- Department of Thoracic SurgeryThe First Affiliated Hospital, Sun Yat‐sen UniversityGuangzhouChina
| | - Yi‐Yan Lei
- Department of Thoracic SurgeryThe First Affiliated Hospital, Sun Yat‐sen UniversityGuangzhouChina
| | - Zun‐Fu Ke
- Department of Pathology & Institution of Precision MedicineThe First Affiliated Hospital, Sun Yat‐sen UniversityGuangzhouChina
| | - Ying Zhu
- Department of RadiologyThe First Affiliated Hospital, Sun Yat‐sen UniversityGuangzhouChina
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Zuo Y, Leng G, Leng P. Identification and validation of molecular subtype and prognostic signature for lung adenocarcinoma based on neutrophil extracellular traps. Pathol Oncol Res 2023; 29:1610899. [PMID: 37143472 PMCID: PMC10151567 DOI: 10.3389/pore.2023.1610899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 03/27/2023] [Indexed: 05/06/2023]
Abstract
Background: Neutrophil Extracellular Traps (NETs) are fibrous networks made of DNA-histone complexes and proteins protruded from activated neutrophils. Accumulating evidences have highlighted the vital role of NETs in tumor progression and diffusion. However, limited systematic studies regarding the role of NETs in LUAD have been performed. Methods: Differentially expressed NETs-related genes and their mutation landscape were identified with TCGA database. Consensus clustering analysis was performed to determine the NETs-related subtypes of LUAD. LASSO algorithm was employed to construct a prognostic signature. Moreover, GSE30219 and GSE31210 were used as independent validation. We also constructed a lncRNA-miRNA-mRNA regulatory axis with several miRNA and lncRNA databases. Results: Consensus clustering identified two NETs-related clusters in LUAD. High NETs score was correlated with a favorable overall survival, abundant immune cell infiltration, and high activity of immune response signal pathways. Six NET-related genes (G0S2, KCNJ15, S100A12, AKT2, CTSG, and HMGB1) with significant prognostic value were screened to develop a prognostic signature. LUAD patients with low-risk had a significantly favorable overall survival both in the training set and validation set. Moreover, NETs-related risk score and clinical stage could act as an independent prognostic factor for LUAD patients. Significant correlation was obtained between risk score and tumor immune microenvironment. We also identified lncRNA BCYRN1/miR-3664-5p/CTSG regulatory axis that may be involved in the progression of LUAD. Conclusion: We developed two molecular subtypes and a prognostic signature for LUAD based on NETs-related genes. This stratification could provide more evidences for estimating the prognosis and immunotherapy of LAUD patients.
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Affiliation(s)
- Yanhua Zuo
- Department of Pharmacy, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Guangyi Leng
- Laboratory of Drug Metabolism and Pharmacokinetics, Shenyang Pharmaceutical University, Shenyang, China
| | - Ping Leng
- Department of Pharmacy, The Affiliated Hospital of Qingdao University, Qingdao, China
- *Correspondence: Ping Leng,
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Pan YQ, Xiao Y, Li Z, Tao L, Chen G, Zhu JF, Lv L, Liu JC, Qi JQ, Shao A. Comprehensive analysis of the significance of METTL7A gene in the prognosis of lung adenocarcinoma. Front Oncol 2022; 12:1071100. [PMID: 36620541 PMCID: PMC9817104 DOI: 10.3389/fonc.2022.1071100] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Accepted: 11/18/2022] [Indexed: 12/25/2022] Open
Abstract
Background The most common subtype of lung cancer, called lung adenocarcinoma (LUAD), is also the largest cause of cancer death in the world. The aim of this study was to determine the importance of the METTL7A gene in the prognosis of patients with LUAD. Methods This particular study used a total of four different LUAD datasets, namely TCGA-LUAD, GSE32863, GSE31210 and GSE13213. Using RT-qPCR, we were able to determine METTL7A expression levels in clinical samples. Univariate and multivariate Cox regression analyses were used to identify factors with independent effects on prognosis in patients with LUAD, and nomograms were designed to predict survival in these patients. Using gene set variation analysis (GSVA), we investigated differences in enriched pathways between METTL7A high and low expression groups. Microenvironmental cell population counter (MCP-counter) and single-sample gene set enrichment analysis (ssGSEA) methods were used to study immune infiltration in LUAD samples. Using the ESTIMATE technique, we were able to determine the immune score, stromal score, and estimated score for each LUAD patient. A competing endogenous RNA network, also known as ceRNA, was established with the help of the Cytoscape program. Results We detected that METTL7A was down-regulated in pan-cancer, including LUAD. The survival study indicates that METTL7A was a protective factor in the prognosis of LUAD. The univariate and multivariate Cox regression analyses revealed that METTL7A was a robust independent prognostic indicator in survival prediction. Through the use of GSVA, several immune-related pathways were shown to be enriched in both the high-expression and low-expression groups of METTL7A. Analysis of the tumor microenvironment revealed that the immune microenvironment of the group with low expression was suppressed, which may be connected to the poor prognosis. To explore the ceRNA regulatory mechanism of METTL7A, we finally constructed a regulatory network containing 1 mRNA, 2 miRNAs, and 5 long non-coding RNAs (lncRNAs). Conclusion In conclusion, we presented METTL7A as a potential and promising prognostic indicator of LUAD. This biomarker has the potential to offer us with a comprehensive perspective of the prediction of prognosis and treatment for LUAD patients.
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Affiliation(s)
- Ya-Qiang Pan
- Department of Cardiothoracic Surgery, Affiliated People’s Hospital of Jiangsu University, Zhenjiang, China
| | - Ying Xiao
- Department of Radiation Oncology, The Fourth Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Zhenhua Li
- Department of Thoracic Surgery, Yan’an Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Long Tao
- Department of Cardiothoracic Surgery, Affiliated People’s Hospital of Jiangsu University, Zhenjiang, China
| | - Ge Chen
- Department of Cardiothoracic Surgery, Affiliated People’s Hospital of Jiangsu University, Zhenjiang, China
| | - Jing-Feng Zhu
- Department of Cardiothoracic Surgery, Affiliated People’s Hospital of Jiangsu University, Zhenjiang, China
| | - Lu Lv
- Department of Cardiothoracic Surgery, Affiliated People’s Hospital of Jiangsu University, Zhenjiang, China
| | - Jian-Chao Liu
- Department of Cardiothoracic Surgery, Affiliated People’s Hospital of Jiangsu University, Zhenjiang, China
| | - Jun-Qing Qi
- Department of Cardiothoracic Surgery, Affiliated People’s Hospital of Jiangsu University, Zhenjiang, China
| | - AiZhong Shao
- Department of Cardiothoracic Surgery, Affiliated People’s Hospital of Jiangsu University, Zhenjiang, China,*Correspondence: AiZhong Shao,
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Qian C, Jiang Z, Zhou T, Wu T, Zhang Y, Huang J, Ouyang J, Dong Z, Wu G, Cao J. Vesicle-mediated transport-related genes are prognostic predictors and are associated with tumor immunity in lung adenocarcinoma. Front Immunol 2022; 13:1034992. [PMID: 36524130 PMCID: PMC9745133 DOI: 10.3389/fimmu.2022.1034992] [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: 09/02/2022] [Accepted: 11/14/2022] [Indexed: 12/03/2022] Open
Abstract
Background Globally, lung adenocarcinoma (LUAD) is the leading cause of cancer-related deaths. It is a progressive disorder that arises from multiple genetic and environmental factors. Dysregulated expression of vesicle-mediated transport-related genes (VMTRGs) have been reported in several cancers. However, the prognostic significance of VMTRGs in LUAD has yet to be established. Methods The VMTRG profiling data for 482 LUAD patients and 59 normal controls were downloaded from The Cancer Genome Altas (TCGA). Univariate Cox regression and Least Absolute Shrinkage and Selection Operator (LASSO) regression analyses were performed to construct and optimize the risk model. Several GEO datasets were used to validate the risk model. The roles of these genes were investigated via the Kyoto Encyclopedia of Genes and Genomes (KEGG) and gene ontology (GO) enrichment analyses. Differences in immune cell infiltrations between risk groups were evaluated using five algorithms. "pRRophetic" was used to investigate anti-cancer drug sensitivities in two groups. Expression of these five genes in LUAD samples and adjacent normal tissues were evaluated by qRT-PCR. Colony formation and wound healing assays were performed to assess the significance of CNIH1 and AP3S1 in LUAD cells. Results We identified 85 prognosis-associated VMTRGs that could be constructed a risk model for LUAD patients, indicating their potential importance in LUAD development. The risk model including the five VMTRGs (CNIH1, KIF20A, GALNT2, GRIA1, and AP3S1) was associated with clinical outcomes. Tumor stage and risk score were found to be independent prognostic factors for LUAD patients. The five VMTRGs were also correlated with activation of the Notch and p53 signaling pathways. The risk model was significantly associated with immune responses and with high-level expression of immune checkpoints. High-risk group patients were more sensitive to several chemotherapeutic drugs and Lapatinib. Furthermore, CNIH1 and AP3S1 promoted LUAD cell growth and migration in vitro. Conclusion We constructed a VMTRG-based risk model for effective prediction of prognostic outcomes for LUAD patients. The risk model was associated with immune infiltration levels. These five hub genes are potential targets for immune therapy combined with chemotherapy in LUAD.
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Affiliation(s)
- Changrui Qian
- Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China,School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Zewei Jiang
- Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Tong Zhou
- Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Tao Wu
- Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Yi Zhang
- Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Ju Huang
- Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Jinglin Ouyang
- Department of Ultrasound Medicine, The Second Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, China
| | - Zhixiong Dong
- Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China,*Correspondence: Zhixiong Dong, ; Guang Wu, ; Jiawei Cao,
| | - Guang Wu
- Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China,*Correspondence: Zhixiong Dong, ; Guang Wu, ; Jiawei Cao,
| | - Jiawei Cao
- Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China,*Correspondence: Zhixiong Dong, ; Guang Wu, ; Jiawei Cao,
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Yu M, Zhao Q, Li J, Xu F, Zhang Z, Liu Y, Dai L, Zhang B, Zhang J, Zhang J. BCAT1 promotes lung adenocarcinoma progression through enhanced mitochondrial function and NF-κB pathway activation. J Zhejiang Univ Sci B 2022; 23:760-769. [PMID: 36111572 DOI: 10.1631/jzus.b2100985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Lung cancer is one of the most prevalent and malignant cancers, among which lung adenocarcinoma (LUAD) accounts for the majority and remains a major cause of cancer-related mortality worldwide (Cui et al., 2019). Despite the growing intensity of research on the pathobiology and progression of lung cancer and the fact that many genes have been identified as potential drivers and targets for therapy (Luo et al., 2019; Zhang et al., 2019), the treatment and prognosis of lung cancer patients have hardly improved. Therefore, this study aimed to investigate the precise mechanism of lung cancer development and explore efficient diagnostic and therapeutic methods for clinical treatment.
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Affiliation(s)
- Mengdan Yu
- Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450052, China.,School of Basic Medical Sciences, Academy of Medical Science, Zhengzhou University, Zhengzhou 450052, China
| | - Qianwei Zhao
- Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450052, China
| | - Jinxia Li
- School of Basic Medical Sciences, Academy of Medical Science, Zhengzhou University, Zhengzhou 450052, China
| | - Fang Xu
- Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450052, China
| | - Zhibiao Zhang
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Yixian Liu
- Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450052, China
| | - Liping Dai
- Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450052, China.,Henan Key Laboratory of Tumor Epidemiology, State Key Laboratory of Esophageal Cancer Prevention and Treatment, Zhengzhou University, Zhengzhou 450052, China
| | - Bingxia Zhang
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Jianying Zhang
- Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450052, China. , .,Henan Key Laboratory of Tumor Epidemiology, State Key Laboratory of Esophageal Cancer Prevention and Treatment, Zhengzhou University, Zhengzhou 450052, China. ,
| | - Jintao Zhang
- Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450052, China. .,Henan Key Laboratory of Tumor Epidemiology, State Key Laboratory of Esophageal Cancer Prevention and Treatment, Zhengzhou University, Zhengzhou 450052, China.
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20
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Shu L, Liu S, Tao Y. Development and validation of a prognosis prediction model based on 18 endoplasmic reticulum stress-related genes for patients with lung adenocarcinoma. Front Oncol 2022; 12:902353. [PMID: 36110953 PMCID: PMC9469654 DOI: 10.3389/fonc.2022.902353] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 07/12/2022] [Indexed: 11/25/2022] Open
Abstract
Background Endoplasmic reticulum (ER) stress had a crucial impact on cell survival, proliferation, and metastasis in various cancers. However, the role of ER stress in lung adenocarcinoma remains unclear. Method Gene expression and clinical data of lung adenocarcinoma (LUAD) samples were extracted from The Cancer Genome Atlas (TCGA) and three Gene Expression Omnibus (GEO) datasets. ER stress score (ERSS) was constructed based on hub genes selected from 799 ER stress-related genes by least absolute shrinkage and selection operator (LASSO) regression. A Cox regression model, integrating ERSS and the TNM stage, was developed to predict overall survival (OS) in TCGA cohort and was validated in GEO cohorts. Gene set enrichment analysis (GSEA), single-sample GSEA (ssGSEA), and gene mutation analyses were performed to further understand the molecular features of ERSS. The tumor immune infiltration was evaluated by ESTIMATE, CIBERSORT, and xCell algorithms. The receiver operating characteristic (ROC) curves were used to evaluate the predictive value of the risk model. p< 0.05 was considered statistically significant. Results One hundred fifty-seven differentially expressed genes (DEGs) were identified between tumor and para-carcinoma tissues, and 45 of them significantly correlated with OS. Next, we identified 18 hub genes and constructed ERSS by LASSO regression. Multivariate analysis demonstrated that higher ERSS (p< 0.0001, hazard ratio (HR) = 3.8, 95%CI: 2.8–5.2) and TNM stage (p< 0.0001, HR = 1.55, 95%CI: 1.34–1.8) were independent predictors for worse OS. The prediction model integrating ERSS and TNM stage performed well in TCGA cohort (area under the curve (AUC) at five years = 0.748) and three GEO cohorts (AUC at 5 years = 0.658, 0.717, and 0.739). Pathway enrichment analysis showed that ERSS significantly correlated with unfolded protein response. Meanwhile, pathways associated with the cell cycle, growth, and metabolism were significantly enriched in the high ERSS group. Patients with SMARCA4, TP53, and EGFR mutations showed significantly higher ERSS (p = 4e−04, 0.0027, and 0.035, respectively). Tissues with high ERSS exhibited significantly higher infiltration of M1 macrophages, activated dendritic cells, and lower infiltration of CD8+ T cells and B cells, which indicate an activated tumor antigen-presenting but suppressive immune response status. Conclusion We developed and validated an ER stress-related risk model that exhibited great predictive value for OS in patients with LUAD. Our work also expanded the understanding of the role of ER stress in LUAD.
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Affiliation(s)
- Long Shu
- NHC Key Laboratory of Carcinogenesis (Central South University), Cancer Research Institute School of Basic Medicine, Central South University, Changsha, China
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
| | - Shuang Liu
- Department of Oncology, Institute of Medical Sciences, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
- *Correspondence: Yongguang Tao, ; Shuang Liu,
| | - Yongguang Tao
- NHC Key Laboratory of Carcinogenesis (Central South University), Cancer Research Institute School of Basic Medicine, Central South University, Changsha, China
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
- Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Department of Pathology, Xiangya Hospital, School of Basic Medicine, Central South University, Changsha, China
- Hunan Key Laboratory of Early Diagnosis and Precision Therapy in Lung Cancer, Department of Thoracic Surgery, Second Xiangya Hospital, Central South University, Changsha, China
- *Correspondence: Yongguang Tao, ; Shuang Liu,
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21
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Signature and Molecular Mechanism of Mitochondrial Energy Metabolism Pathway-Related Genes in Lung Adenocarcinoma. DISEASE MARKERS 2022; 2022:3201600. [PMID: 36046378 PMCID: PMC9423994 DOI: 10.1155/2022/3201600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 08/01/2022] [Indexed: 11/18/2022]
Abstract
Objective The mitochondrial energy metabolic pathway (MEMP) is the primary energy metabolism of tumor cells, and its disruption may promote cancer emergence, spreading, and immune escape. However, there is a lack of studies to determine the relationship between relevant functional mechanisms and lung adenocarcinoma (LUAD) prognosis. Methods Gene set enrichment analysis (GSEA) was employed to determine MEMP pathway-related genes. Then, a prognostic model was created using the MEMP key genes that were found by LASSO-Cox regression analysis. The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases provided the training and validation sets. Furthermore, the infiltration of immune cells was examined by ssGSEA. Finally, a screening of candidate therapeutic compounds for LUAD patients was performed using DrugBank, Protein Data Bank (PDB), and AutoDock Vina databases. Results First, 266 MEMP pathway-related genes that exhibited aberrant activity in tumors were identified. Then, 19 MEMP key genes were used to build a prognostic model, which can successfully predict the survival rates of LUAD patients after 1, 3, and 5 years, respectively. The Kaplan-Meier curve showed that patients in the high-risk group had considerably lower survival outcomes than those in the low-risk group. Furthermore, it was discovered that the high-risk group had the majority of activated T cells, while the low-risk group tended to have more other activated immune cells. The majority of immunological checkpoints expressed themselves more strongly in the high-risk group as well. Finally, 11 prospective medication small molecules were obtained from the projected potential therapeutic drugs, with DB0980 being regarded as the most promising of them for the treatment of LUAD. Conclusion This current study developed reliable prognostic signature, called MEMP score, which provides new guidance for prognostic assessment, immunotherapy, and drug development in LUAD. Thereby, DB0980 appears to be the most likely approach for the treatment of LUAD.
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Liu W, Qiu W, Huang Z, Zhang K, Wu K, Deng K, Chen Y, Guo R, Wu B, Chen T, Fang F. Identification of nine signature proteins involved in periodontitis by integrated analysis of TMT proteomics and transcriptomics. Front Immunol 2022; 13:963123. [PMID: 36016933 PMCID: PMC9397367 DOI: 10.3389/fimmu.2022.963123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 07/15/2022] [Indexed: 11/21/2022] Open
Abstract
Recently, there are many researches on signature molecules of periodontitis derived from different periodontal tissues to determine the disease occurrence and development, and deepen the understanding of this complex disease. Among them, a variety of omics techniques have been utilized to analyze periodontitis pathology and progression. However, few accurate signature molecules are known and available. Herein, we aimed to screened and identified signature molecules suitable for distinguishing periodontitis patients using machine learning models by integrated analysis of TMT proteomics and transcriptomics with the purpose of finding novel prediction or diagnosis targets. Differential protein profiles, functional enrichment analysis, and protein–protein interaction network analysis were conducted based on TMT proteomics of 15 gingival tissues from healthy and periodontitis patients. DEPs correlating with periodontitis were screened using LASSO regression. We constructed a new diagnostic model using an artificial neural network (ANN) and verified its efficacy based on periodontitis transcriptomics datasets (GSE10334 and GSE16134). Western blotting validated expression levels of hub DEPs. TMT proteomics revealed 5658 proteins and 115 DEPs, and the 115 DEPs are closely related to inflammation and immune activity. Nine hub DEPs were screened by LASSO, and the ANN model distinguished healthy from periodontitis patients. The model showed satisfactory classification ability for both training (AUC=0.972) and validation (AUC=0.881) cohorts by ROC analysis. Expression levels of the 9 hub DEPs were validated and consistent with TMT proteomics quantitation. Our work reveals that nine hub DEPs in gingival tissues are closely related to the occurrence and progression of periodontitis and are potential signature molecules involved in periodontitis.
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Affiliation(s)
- Wei Liu
- Shenzhen Stomatology Hospital (Pingshan), Southern Medical University, Shenzhen, China
| | - Wei Qiu
- Department of Stomatology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Zhendong Huang
- Department of Stomatology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Kaiying Zhang
- Department of Stomatology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Keke Wu
- Department of Histology and Embryology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Ke Deng
- Shanghai Key Laboratory of Stomatology, Department of Oral Implantology, Shanghai Ninth People Hospital, National Center of Stomatology, National Clinical Research Center of Oral Diseases, School of Medicine, College of Stomatology, Shanghai Jiao Tong University, Shanghai, China
| | - Yuanting Chen
- Department of Stomatology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Ruiming Guo
- Department of Stomatology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Buling Wu
- Shenzhen Stomatology Hospital (Pingshan), Southern Medical University, Shenzhen, China
- Department of Stomatology, Nanfang Hospital, Southern Medical University, Guangzhou, China
- *Correspondence: Fuchun Fang, ; Ting Chen, ; Buling Wu,
| | - Ting Chen
- Department of Stomatology, Nanfang Hospital, Southern Medical University, Guangzhou, China
- *Correspondence: Fuchun Fang, ; Ting Chen, ; Buling Wu,
| | - Fuchun Fang
- Department of Stomatology, Nanfang Hospital, Southern Medical University, Guangzhou, China
- *Correspondence: Fuchun Fang, ; Ting Chen, ; Buling Wu,
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Zhou D, Wang J, Liu X. Development of six immune-related lncRNA signature prognostic model for smoking-positive lung adenocarcinoma. J Clin Lab Anal 2022; 36:e24467. [PMID: 35561270 PMCID: PMC9169227 DOI: 10.1002/jcla.24467] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 04/10/2022] [Accepted: 04/22/2022] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND Smoking is one of the most hazardous risk factors for the development of lung adenocarcinoma (LUAD). Many survival and prognosis-related biomarkers were discovered using database mining. However, the precision of immune-related long noncoding RNAs (lncRNAs) predictions is insufficient. We identified a novel signature to improve the estimate of smoking-related LUAD prognosis. METHODS The Cancer Genome Atlas database (TCGA) was used to obtain the LUAD lncRNA expression profiles. The smoking-related LUAD cohort was randomly split into discovery and validation cohorts. To determine the risk score, use the LASSO Cox regression technique on the prognostic immune-related lncRNA. The risk signature has been developed. RESULTS A total of 643 immune-related lncRNAs were identified as potential candidates for a risk signature. Finally, six immune-related lncRNAs (AL359915.2, AP000695.1, HSPC324, TGFB2-AS1, AC026355.1, and AC002128.2) were identified and used to carry out risk signature, which showed a close association with overall survival in the discovery cohort. We classified patients as high risk or low risk based on a median risk score of 1.0783. In the discovery cohort, overall survival was marginally longer in the low-risk group than in the high-risk category (p = 2.28e08). The area under the curves (AUC) for 1-, 3-, and 5-year survival was 0.67, 0.7, and 0.82, respectively. Furthermore, we successfully validated and combined cohorts using this risk profile. We discovered a strong positive connection between HSPC324 and VIPR1 as a possible novel biomarker for smoking-related LUAD development in our study. CONCLUSIONS Our research has established a six immune-lncRNA signature that may be used to predict the prognosis of smoking-related LUAD with great accuracy.
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Affiliation(s)
- Dajie Zhou
- Department of Clinical Laboratory CenterYantai Yuhuangding HospitalYantaiChina
| | - Jing Wang
- Department of Clinical Laboratory CenterYantai Yuhuangding HospitalYantaiChina
| | - Xiangdong Liu
- Department of Clinical LaboratoryShandong Provincial Hospital Affiliated to Shandong First Medical UniversityJinanChina
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Zhang T, Cheng G, Chen P, Peng Y, Liu L, Li R, Qiu B. RS1
gene is a novel prognostic biomarker for lung adenocarcinoma. Thorac Cancer 2022; 13:1850-1861. [PMID: 35569920 PMCID: PMC9200886 DOI: 10.1111/1759-7714.14471] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 04/28/2022] [Accepted: 04/29/2022] [Indexed: 12/23/2022] Open
Abstract
Background Although it has a poor prognosis, patients with lung adenocarcinoma (LUAD) have a relatively higher 5‐year survival period. Thus, it is necessary to identify effective prognostic markers to evaluate the effect of early treatment. RS1 gene encodes retinoschisin, a key protein in congenital retinoschisis, while few studies have been reported on the association between RS1 and cancer prognosis. Methods We performed bioinformatic analyses based on the data obtained from The Cancer Genome Atlas and Gene Expression Omnibus databases to demonstrate the expression level of RS1 was related to the LUAD prognosis and our findings were verified in‐vitro and clinical samples. Then, we explored the potential mechanism of how RS1 expression influenced the prognosis of LUAD. Results Compared with normal tissues, the RS1 expression was significantly lower in tumor tissues. The Multivariate Cox regression model showed that RS1 could be used as an independent prognostic indicator. Furthermore, we found significant differences in immune cell infiltration between RS1 high and low expression groups, and the proteasome pathway was found enriched in RS1 low expression samples. Conclusion In conclusion, our study suggests that RS1 is a novel prognostic biomarker for LUAD. Differences in immune cell infiltration and signaling pathways may contribute to the poor prognosis of LUAD caused by low RS1 expression.
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Affiliation(s)
- Tao Zhang
- Department of Radiation Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital Chinese Academy of Medical Science and Peking Union Medical College Beijing People's Republic of China
| | - Guowei Cheng
- Department of Radiation Oncology Cancer Hospital of HuanXing ChaoYang District Beijing Beijing People's Republic of China
| | - Ping Chen
- Department of Radiation Oncology Cancer Hospital of HuanXing ChaoYang District Beijing Beijing People's Republic of China
| | - Yue Peng
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital Chinese Academy of Medical Science and Peking Union Medical College Beijing People's Republic of China
| | - Lei Liu
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital Chinese Academy of Medical Science and Peking Union Medical College Beijing People's Republic of China
| | - Runze Li
- Department of Clinical Medicine, The 2nd Clinical School Tongji Meidical College of Huazhong University of Science and Technology Wuhan People's Republic of China
| | - Bin Qiu
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital Chinese Academy of Medical Science and Peking Union Medical College Beijing People's Republic of China
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Cai HY, Yang HS, Shan SC, Lei YY, Zou JY, Zhu Y, Luo HH. A novel signature based on immune-related gene pairs and clinical features to predict prognosis and treatment effect in "driver gene negative" lung adenocarcinoma. Cancer Med 2022; 11:2259-2270. [PMID: 35246970 PMCID: PMC9160806 DOI: 10.1002/cam4.4577] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 01/06/2022] [Accepted: 01/07/2022] [Indexed: 12/17/2022] Open
Abstract
OBJECTIVE Examining the role of immune-related genes (IRGs) in "driver gene negative" lung adenocarcinoma (LUAD) may provide new ideas for the treatment and study for this LUAD subgroup. We aimed to find the hub immune-related gene pairs can stratify the risk of "driver-gene-negative" LUAD. MATERIALS AND METHODS IRGs were identified according to ImmPort database based on RNA sequencing results of tumors and normal tissues from 46 patients with "driver gene negative" LUAD at The First Affiliated Hospital of Sun Yat-sen University and cyclically singly paired as immune-related gene pairs (IRGPs). Multivariate Cox analysis was used to construct an immune risk model and a prognostic nomogram combining was also been developed. Immune microenvironment landscape described by CIBERSORT and drug sensitivity calculated by pRRophetic algorithm were used to explore possible treatment improvements. RESULTS A novel immune risk model with 5-IRGPs (CD1A|CXCL135, CD1A|S100A7L2, IFNA7|CMTM2, IFNA7|CSF3, CAMP|TFR2) can accurately distinguish patients in the high- and low-risk groups. Risk score act as an independent prognostic factor and is related to clinical stage. There are significant differences in tumor immune microenvironment and PD-1/PD-L1/CTLA-4 expression between groups. The low-risk patient may benefit more from the commonly used chemotherapy regimens such as gemcitabine and paclitaxel. CONCLUSION This study constructed 5-IRGPs as a reliable prognostic tool and may represent genes pairs that are potential rationale for choice of treatment for "driver gene negative" LUAD.
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Affiliation(s)
- He-Yuan Cai
- Department of Thoracic Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Hao-Shuai Yang
- Department of Thoracic Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Shi-Chao Shan
- Department of Thoracic Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yi-Yan Lei
- Department of Thoracic Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Jian-Yong Zou
- Department of Thoracic Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Ying Zhu
- Department of Radiology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Hong-He Luo
- Department of Thoracic Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
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Qiao C, Qiao T, Yang S, Liu L, Zheng M. SNHG17/miR-384/ELF1 axis promotes cell growth by transcriptional regulation of CTNNB1 to activate Wnt/β-catenin pathway in oral squamous cell carcinoma. Cancer Gene Ther 2022; 29:122-132. [PMID: 33531646 DOI: 10.1038/s41417-021-00294-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 10/29/2020] [Accepted: 01/05/2021] [Indexed: 01/29/2023]
Abstract
Increasing evidence proved the abnormal expression of long non-coding RNAs (lncRNAs) in various human malignancies, including oral squamous cell carcinoma (OSCC). Nevertheless, limited explorations concern the role of lncRNA small nucleolar RNA host gene 17 (SNHG17) in OSCC. Herein, SNHG17 was disclosed to be remarkably upregulated in OSCC cell lines and promoted OSCC cell growth. Further mechanistic studies, including DNA/RNA pull down, RIP, ChIP, and luciferase reporter gene assays, were conducted. It was confirmed that Wnt/β-catenin signaling pathway was involved in the SNHG17-mediated OSCC cell growth. Moreover, E74 like ETS transcription factor 1 (ELF1) was identified as the transcription activator of CTNNB1 (β-catenin mRNA) in OSCC. Inspired by competing for endogenous RNAs (ceRNAs) network, we were pleasantly surprised to find that SNHG17 and ELF1 functioned as ceRNAs in OSCC via competitively binding to microRNA-384 (miR-384). By using rescue assays, we revealed that SNHG17 facilitated OSCC cell growth through modulating miR-384/ELF1 axis. Importantly, we certified that ELF1 was indispensable for SNHG17-affected OSCC progression. Collectively, it can be concluded that SNHG17/miR-384/ELF1 axis contributed to OSCC cell growth via promoting CTNNB1 expression, thus activating Wnt/β-catenin signaling pathway.
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Affiliation(s)
- Chunyan Qiao
- Department of Pathology, School and Hospital of Stomatology, Jilin University, Changchun, 130012, Jilin, China.
| | - Tianyi Qiao
- Department of Gastroenterology, the First Clinical Medical College and Hospital of Jilin University, Changchun, 130012, Jilin, China
| | - Shihui Yang
- Department of Dental Implantology, School and Hospital of Stomatology, Jilin University, Changchun, 130012, Jilin, China
| | - Lili Liu
- Department of Pathology, School and Hospital of Stomatology, Jilin University, Changchun, 130012, Jilin, China
| | - Mengdan Zheng
- Department of Pathology, School and Hospital of Stomatology, Jilin University, Changchun, 130012, Jilin, China
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27
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Ma Y, Zhang H. Genomics and Prognosis Analysis of N 6-Methyladenosine Regulators in Lung Adenocarcinoma. Front Genet 2021; 12:746666. [PMID: 34956315 PMCID: PMC8697852 DOI: 10.3389/fgene.2021.746666] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Accepted: 10/11/2021] [Indexed: 12/09/2022] Open
Abstract
Objective: N6-methyladenosine (m6A) modification is involved in modulating various biological processes in human cancers. But the implication of m6A modification in lung adenocarcinoma (LUAD) is still unclear. Hence, this study conducted a comprehensive analysis of the expression and clinical implication of m6A regulators in LUAD. Methods: Consensus clustering analysis of 502 LUAD samples in the TCGA dataset was presented based on the expression profiles of 20 m6A regulators using ConsensusClusterPlus package. Overall survival (OS), activation of signaling pathways and tumor immunity (immune/stromal score, tumor purity, expression of HLA and immune checkpoints, and immune cell infiltration) were compared between m6A modification patterns. The m6A-related genes between patterns were identified and prognostic m6A-related genes were imported into LASSO-cox regression analysis. The m6A risk score was developed and its prognostic implication was evaluated and externally verified in the GSE30219 and GSE72094 dataset. Furthermore, a nomogram that contained independent prognostic indicators was established, followed by external verification. Results: Two m6A modification patterns were clustered across LUAD based on the expression similarity of the m6A regulators via consensus clustering analysis, with distinct OS, activation of signaling pathways and tumor immunity. Totally, 213 m6A-related genes that were identified by comparing two patterns were significantly related to LUAD prognosis. By LASSO method, we constructed the m6A risk score that was a reliable and independent prognostic factor for LUAD. Patients with low m6A risk score displayed a prominent survival advantage. After incorporating independent clinical features, we developed the prognostic nomogram that exhibited high predictive accuracy and the best clinical net benefit for OS. Conclusion: Collectively, our study may provide a clinically useful tool for precise prognostic management and optimization of immunotherapeutic strategies for LUAD patients.
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Affiliation(s)
- Yanpin Ma
- Department of Oncology, The First Affiliated Hospital, and College of Clinical Medicine of Henan University of Science and Technology, Luoyang, China
| | - Huping Zhang
- Department of Infectious Diseases, The First Affiliated Hospital, and College of Clinical Medicine of Henan University of Science and Technology, Luoyang, China
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28
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Li N, Wang J, Zhan X. Identification of Immune-Related Gene Signatures in Lung Adenocarcinoma and Lung Squamous Cell Carcinoma. Front Immunol 2021; 12:752643. [PMID: 34887858 PMCID: PMC8649721 DOI: 10.3389/fimmu.2021.752643] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 10/22/2021] [Indexed: 12/25/2022] Open
Abstract
Accumulating evidence indicates that immunotherapy helped to improve the survival and quality-of-life of patients with lung adenocarcinoma (LUAD) or lung squamous cell carcinoma (LUSC) besides chemotherapy and gene targeting treatment. This study aimed to develop immune-related gene signatures in LUAD and LUSC subtypes, respectively. LUAD and LUSC samples were divided into high- and low-abundance groups of immune cell infiltration (Immunity_H and Immunity_L) based on the abundance of immune cell infiltrations. The distribution of immune cells was significantly different between the high- and low-immunity subtypes in LUAD and LUSC samples. The differentially expressed genes (DEGs) between those two groups in LUAD and LUSC contain some key immune-related genes, such as PDL1, PD1, CTLA-4, and HLA families. The DEGs were enriched in multiple immune-related pathways. Furthermore, the seven-immune-related-gene-signature (CD1B, CHRNA6, CLEC12B, CLEC17A, CLNK, INHA, and SLC14A2) prognostic model-based high- and low-risk groups were significantly associated with LUAD overall survival and clinical characteristics. The eight-immune-related-gene-signature (C4BPB, FCAMR, GRAPL, MAP1LC3C, MGC2889, TRIM55, UGT1A1, and VIPR2) prognostic model-based high- and low-risk groups were significantly associated with LUSC overall survival and clinical characteristics. The prognostic models were tested as good ones by receiver operating characteristic, principal component analysis, univariate and multivariate analysis, and nomogram. The verifications of these two immune-related-gene-signature prognostic models showed consistency in the train and test cohorts of LUAD and LUSC. In addition, patients with LUAD in the low-risk group responded better to immunotherapy than those in the high-risk group. This study revealed two reliable immune-related-gene-signature models that were significantly associated with prognosis and tumor microenvironment cell infiltration in LUAD and LUSC, respectively. Evaluation of the integrated characterization of multiple immune-related genes and pathways could help to predict the response to immunotherapy and monitor immunotherapy strategies.
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Affiliation(s)
- Na Li
- Shandong Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University, Jinan, China.,Medical Science and Technology Innovation Center, Shandong First Medical University, Jinan, China
| | - Jiahong Wang
- Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Xianquan Zhan
- Shandong Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University, Jinan, China.,Medical Science and Technology Innovation Center, Shandong First Medical University, Jinan, China.,Gastroenterology Research Institute and Clinical Center, Shandong First Medical University, Jinan, China
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Lamort AS, Kaiser JC, Pepe MAA, Lilis I, Ntaliarda G, Somogyi K, Spella M, Behrend SJ, Giotopoulou GA, Kujawa W, Lindner M, Koch I, Hatz RA, Behr J, Sotillo R, Schamberger AC, Stathopoulos GT. Prognostic phenotypes of early-stage lung adenocarcinoma. Eur Respir J 2021; 60:13993003.01674-2021. [PMID: 34887322 DOI: 10.1183/13993003.01674-2021] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 11/11/2021] [Indexed: 11/05/2022]
Abstract
BACKGROUND Survival after curative resection of early-stage lung adenocarcinoma (LUAD) varies and prognostic biomarkers are urgently needed. METHODS Large-format tissue samples from a prospective cohort of 200 patients with resected LUAD were immunophenotyped for cancer hallmarks TP53, NF1, CD45, PD-1, PCNA, TUNEL, and FVIII, and were followed for median (95%CI)=2.34 (1.71-3.49) years. RESULTS Unsupervised hierarchical clustering revealed two patient subgroups with similar clinicopathologic features and genotype, but with markedly different survival: "proliferative" patients (60%) with elevated TP53, NF1, CD45, and PCNA expression had 50% 5-year overall survival while "apoptotic" patients (40%) with high TUNEL had 70% 5-year survival [HR95%CI=2.23 (1.33-3.80); p=0.0069]. Cox regression and machine learning algorithms including random forests built clinically useful models: a score to predict overall survival and a formula and nomogram to predict tumour phenotype. The distinct LUAD phenotypes were validated in TCGA and KMplotter data and showed prognostic power supplementary to IASLC TNM stage and WHO histologic classification. CONCLUSIONS Two molecular subtypes of LUAD exist and their identification provides important prognostic information.
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Affiliation(s)
- Anne-Sophie Lamort
- Comprehensive Pneumology Center (CPC) and Institute for Lung Biology and Disease (iLBD), Helmholtz Center Munich-German Research Center for Environmental Health (HMGU), Munich, Bavaria, Germany.,German Center for Lung Research, Gießen, Hesse, Germany.,Equally contributing authors
| | - Jan Christian Kaiser
- Institute of Radiation Medicine (IRM), Helmholtz Center Munich-German Research Center for Environmental Health (HMGU), Neuherberg, Bavaria, Germany.,Equally contributing authors
| | - Mario A A Pepe
- Comprehensive Pneumology Center (CPC) and Institute for Lung Biology and Disease (iLBD), Helmholtz Center Munich-German Research Center for Environmental Health (HMGU), Munich, Bavaria, Germany.,German Center for Lung Research, Gießen, Hesse, Germany
| | - Ioannis Lilis
- Department of Physiology, Faculty of Medicine, University of Patras, Rio, Achaia, Greece
| | - Giannoula Ntaliarda
- Department of Physiology, Faculty of Medicine, University of Patras, Rio, Achaia, Greece
| | - Kalman Somogyi
- German Center for Lung Research, Gießen, Hesse, Germany.,Division of Molecular Thoracic Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Magda Spella
- Department of Physiology, Faculty of Medicine, University of Patras, Rio, Achaia, Greece
| | - Sabine J Behrend
- Comprehensive Pneumology Center (CPC) and Institute for Lung Biology and Disease (iLBD), Helmholtz Center Munich-German Research Center for Environmental Health (HMGU), Munich, Bavaria, Germany.,German Center for Lung Research, Gießen, Hesse, Germany
| | - Georgia A Giotopoulou
- Comprehensive Pneumology Center (CPC) and Institute for Lung Biology and Disease (iLBD), Helmholtz Center Munich-German Research Center for Environmental Health (HMGU), Munich, Bavaria, Germany.,German Center for Lung Research, Gießen, Hesse, Germany
| | - Willem Kujawa
- Comprehensive Pneumology Center (CPC) and Institute for Lung Biology and Disease (iLBD), Helmholtz Center Munich-German Research Center for Environmental Health (HMGU), Munich, Bavaria, Germany.,German Center for Lung Research, Gießen, Hesse, Germany
| | - Michael Lindner
- German Center for Lung Research, Gießen, Hesse, Germany.,Center for Thoracic Surgery Munich, Ludwig-Maximilian-University of Munich and Asklepios Medical Center, Gauting, Bavaria, Germany
| | - Ina Koch
- German Center for Lung Research, Gießen, Hesse, Germany.,Center for Thoracic Surgery Munich, Ludwig-Maximilian-University of Munich and Asklepios Medical Center, Gauting, Bavaria, Germany
| | - Rudolf A Hatz
- German Center for Lung Research, Gießen, Hesse, Germany.,Center for Thoracic Surgery Munich, Ludwig-Maximilian-University of Munich and Asklepios Medical Center, Gauting, Bavaria, Germany
| | - Juergen Behr
- German Center for Lung Research, Gießen, Hesse, Germany.,Department of Medicine V, University Hospital, Ludwig-Maximilians-University of Munich, Munich, Bavaria, Germany
| | - Rocio Sotillo
- German Center for Lung Research, Gießen, Hesse, Germany.,Division of Molecular Thoracic Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Translational Lung Research Center Heidelberg (TRLC), German Center for Lung Research (DZL), Heidelberg, Germany
| | - Andrea C Schamberger
- Comprehensive Pneumology Center (CPC) and Institute for Lung Biology and Disease (iLBD), Helmholtz Center Munich-German Research Center for Environmental Health (HMGU), Munich, Bavaria, Germany.,German Center for Lung Research, Gießen, Hesse, Germany
| | - Georgios T Stathopoulos
- Comprehensive Pneumology Center (CPC) and Institute for Lung Biology and Disease (iLBD), Helmholtz Center Munich-German Research Center for Environmental Health (HMGU), Munich, Bavaria, Germany .,German Center for Lung Research, Gießen, Hesse, Germany.,Equally contributing authors
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Meng J, Cao L, Song H, Chen L, Qu Z. Integrated analysis of gene expression and DNA methylation datasets identified key genes and a 6-gene prognostic signature for primary lung adenocarcinoma. Genet Mol Biol 2021; 44:e20200465. [PMID: 34787244 PMCID: PMC8596225 DOI: 10.1590/1678-4685-gmb-2020-0465] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 08/20/2021] [Indexed: 12/13/2022] Open
Abstract
Lung adenocarcinoma (LUAD) is the main subtype of non-small cell lung cancer with a poor survival prognosis. In our study, gene expression, DNA methylation, and clinicopathological data of primary LUAD were utilized to identify potential prognostic markers for LUAD, which were recruited from The Cancer Genome Atlas (TCGA) database. Univariate regression analysis showed that there were 21 methylation-associated DEGs related to overall survival (OS), including 9 down- and 12 up-regulated genes. The 12 up-regulated genes with hypomethylation may be risky genes, whereas the other 9 down-regulated genes with hypermethylation might be protective genes. By using the Step-wise multivariate Cox analysis, a methylation-associated 6-gene (consisting of CCL20, F2, GNPNAT1, NT5E, B3GALT2, and VSIG2) prognostic signature was constructed and the risk score based on this gene signature classified patients into high- or low-risk groups. Patients of the high-risk group had shorter OS than those of the low-risk group in both the training and validation cohort. Multivariate Cox analysis and the stratified analysis revealed that the risk score was an independent prognostic factor for LUAD patients. The methylation-associated gene signature may serve as a prognostic factor for LUAD patients and the represent hypermethylated or hypomethylated genes might be potential targets for LUAD therapy.
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Affiliation(s)
- Jing Meng
- Inner Mongolia People's Hospital, Department of Stomatology, Hohhot, China
| | - Lei Cao
- Inner Mongolia People's Hospital, Department of Clinical Medical Research Center, Hohhot, China
| | - Huifang Song
- Inner Mongolia People's Hospital, Department of Respiratory and Critical Care Medicine, Hohhot, China
| | - Lichun Chen
- Inner Mongolia People's Hospital, Department of Stomatology, Hohhot, China
| | - Zhiguo Qu
- Inner Mongolia People's Hospital, Department of Stomatology, Hohhot, China
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31
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Zhong H, Wang J, Zhu Y, Shen Y. Comprehensive Analysis of a Nine-Gene Signature Related to Tumor Microenvironment in Lung Adenocarcinoma. Front Cell Dev Biol 2021; 9:700607. [PMID: 34540825 PMCID: PMC8440811 DOI: 10.3389/fcell.2021.700607] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 08/04/2021] [Indexed: 01/29/2023] Open
Abstract
Lung adenocarcinoma (LUAD) is the most common malignancy, leading to more than 1 million related deaths each year. Due to low long-term survival rates, the exploration of molecular mechanisms underlying LUAD progression and novel prognostic predictors is urgently needed to improve LUAD treatment. In our study, cancer-specific differentially expressed genes (DEGs) were identified using the robust rank aggregation (RRA) method between tumor and normal tissues from six Gene Expression Omnibus databases (GSE43458, GSE62949, GSE68465, GSE115002, GSE116959, and GSE118370), followed by a selection of prognostic modules using weighted gene co-expression network analysis. Univariate Cox regression, least absolute shrinkage and selection operator (LASSO), and multivariate Cox regression analyses were applied to identify nine hub genes (CBFA2T3, CR2, SEL1L3, TM6SF1, TSPAN32, ITGA6, MAPK11, RASA3, and TLR6) that constructed a prognostic risk model. The RNA expressions of nine hub genes were validated in tumor and normal tissues by RNA-sequencing and single-cell RNA-sequencing, while immunohistochemistry staining from the Human Protein Atlas database showed consistent results in the protein levels. The risk model revealed that high-risk patients were associated with poor prognoses, including advanced stages and low survival rates. Furthermore, a multivariate Cox regression analysis suggested that the prognostic risk model could be an independent prognostic factor for LUAD patients. A nomogram that incorporated the signature and clinical features was additionally built for prognostic prediction. Moreover, the levels of hub genes were related to immune cell infiltration in LUAD microenvironments. A CMap analysis identified 13 small molecule drugs as potential agents based on the risk model for LUAD treatment. Thus, we identified a prognostic risk model including CBFA2T3, CR2, SEL1L3, TM6SF1, TSPAN32, ITGA6, MAPK11, RASA3, and TLR6 as novel biomarkers and validated their prognostic and predicted values for LUAD.
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Affiliation(s)
- Haihui Zhong
- Department of Thoracic Surgery, Meizhou People's Hospital (Huangtang Hospital), Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou Academy of Medical Sciences, Meizhou, China
| | - Jie Wang
- Institute for Pathology, University Hospital of Cologne, Cologne, Germany
| | - Yaru Zhu
- Department of Critical Care Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Yefeng Shen
- Institute for Pathology, University Hospital of Cologne, Cologne, Germany
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The Emerging Importance of Tumor Genomics in Operable Non-Small Cell Lung Cancer. Cancers (Basel) 2021; 13:cancers13153656. [PMID: 34359558 PMCID: PMC8345160 DOI: 10.3390/cancers13153656] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 07/14/2021] [Accepted: 07/19/2021] [Indexed: 12/25/2022] Open
Abstract
During the last two decades, next-generation sequencing (NGS) has played a key role in enhancing non-small cell lung cancer treatment paradigms through the application of "targeted therapy" in advanced and metastatic disease. The use of specific tyrosine kinase inhibitors in patients with oncogenic driver alterations, such as EGFR, ALK, ROS1, BRAF V600E, MET, and NTRK mutations, among others, has changed treatment approaches and improved outcomes in patients with late-stage disease. Although NGS technology has mostly been used in the setting of systemic therapy to identify targets, response to therapy, and mechanisms of resistance, it has multiple potential applications for patients with earlier-stage disease, as well. In this review, we discuss the emerging role of NGS technologies to better understand tumor biology in patients with non-small cell lung cancer who are undergoing surgery with curative intent. In this patient cohort, we examine tumor heterogeneity, the underlying tumor genomics associated with lung adenocarcinoma subtypes, the prediction of recurrence after complete surgical resection, the use of plasma circulating tumor DNA for detection of early cancers and monitoring for minimal residual disease, the differentiation of separate primaries from intrapulmonary metastases, and the use of NGS to guide induction and adjuvant therapies.
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33
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Zhang Z, Yang S, Ma Y, Zhou H, Wu X, Han J, Hou J, Hao L, Spicer JD, Koh YW, Provencio M, Reguart N, Mitsudomi T, Wang Q. Consistency of recommendations for the diagnosis and treatment of non-small cell lung cancer: a systematic review. Transl Lung Cancer Res 2021; 10:2715-2732. [PMID: 34295672 PMCID: PMC8264323 DOI: 10.21037/tlcr-21-423] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 06/04/2021] [Indexed: 01/09/2023]
Abstract
BACKGROUND To systematically assess the consistency of recommendations regarding diagnosis and treatment of non-small cell lung cancer (NSCLC) in clinical practice guidelines (CPGs). METHODS We systematically searched relevant literature databases and websites to identify CPGs related to NSCLC. We extracted the general characteristics of the included guidelines and their recommendations and descriptively compared and analyzed the consistency of recommendations across the guidelines. RESULTS A total of 28 NSCLC guidelines were retrieved. The recommendations covered mainly diagnosis and treatment. The recommendations in the guidelines differed substantially in various topics, such as the application of positron emission tomography (PET) and the classification of stage III. Fourteen guidelines divided stage III into two types: operable and inoperable; and the remaining 14 guidelines into three sub-stages IIIA, IIIB and IIIC. Recommendations regarding the treatment in stage III were relatively inconsistent. In driver gene (EGFR, ALK, ROS1) positive patients, targeted therapy was the most common recommendation for first-line treatment, but recommendations regarding second-line treatment varied according to the site of the mutation. In driver gene negative patients, immunotherapy was the most frequently recommended option as both first- and second-line treatment, followed by chemotherapy. DISCUSSION A number of countries are devoting themselves to develop NSCLC guidelines and the process of updating guidelines is accelerating, yet recommendations between guidelines are not consistent. We adopted a systematic review method to systematically search and analyze the NSCLC guidelines worldwide. We objectively reviewed the differences in recommendations for NSCLC diagnosis and treatment between the guidelines. Inconsistency of recommendations across guidelines can result from multiple potential reasons. Such as, the guidelines developed time, different countries and regions and many more. Poor consistency across CPGs can confuse the guideline users, and we therefore advocate paying more attention to examining the controversies and updating guidelines timely to improve the consistency among CPGs. Our study had also several limitations, we limited the search to CPGs published in Chinese or English, the interpretation of recommendations is inherently subjective, we did not evaluate the details of the clinical content of the CPG recommendations. Our research presents the current status of NSCLC guidelines worldwide and give the opportunity to pay more attention to the existing gaps. Further investigations should determine the reasons for inconsistency, the implications for recommendation development, and the role of synthesis across recommendations for optimal guidance of clinical care treatment. With the continuous revision and update of the guidelines, we are confident that future guidelines will be formulated with higher quality to form clear, definite and consistent recommendations for NSCLC diagnosis and treatment.
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Affiliation(s)
- Zhe Zhang
- Department of Internal Medicine, The Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, China
| | - Sen Yang
- Department of Internal Medicine, The Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, China
| | - Yanfang Ma
- School of Chinese Medicine of Hong Kong Baptist University, Kowloon Tong, Hong Kong, China
| | - Hanqiong Zhou
- Department of Internal Medicine, The Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, China
| | - Xuan Wu
- Department of Internal Medicine, The Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, China
| | - Jing Han
- Department of Internal Medicine, The Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, China
| | - Jiabao Hou
- Department of Internal Medicine, The Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, China
| | - Lidan Hao
- Department of Internal Medicine, The Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, China
| | - Jonathan D. Spicer
- Division of Thoracic and Upper Gastrointestinal Surgery, Department of Surgery, McGill University Health Centre, McGill University, Montreal, QC, Canada
| | - Young Wha Koh
- Department of Pathology, Ajou University School of Medicine, Suwon, Republic of Korea
| | - Mariano Provencio
- Medical Oncology Department, Hospital Universitario Puerta de Hierro Majadahonda, Majadahonda, Madrid, Spain
| | - Noemi Reguart
- Thoracic Oncology Unit, Department of Medical Oncology, IDIPAPS, Hospital Clinic Barcelona, Villarroel, Spain
| | - Tetsuya Mitsudomi
- Division of Thoracic Surgery, Department of Surgery, Kindai University Faculty of Medicine, Osaka, Japan
| | - Qiming Wang
- Department of Internal Medicine, The Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, China
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34
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Establishment of a Gene Signature to Predict Prognosis for Patients with Lung Adenocarcinoma. Int J Mol Sci 2020; 21:ijms21228479. [PMID: 33187219 PMCID: PMC7697394 DOI: 10.3390/ijms21228479] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 10/31/2020] [Accepted: 11/04/2020] [Indexed: 12/11/2022] Open
Abstract
Accumulating evidence indicates that the reliable gene signature may serve as an independent prognosis factor for lung adenocarcinoma (LUAD) diagnosis. Here, we sought to identify a risk score signature for survival prediction of LUAD patients. In the Gene Expression Omnibus (GEO) database, GSE18842, GSE75037, GSE101929, and GSE19188 mRNA expression profiles were downloaded to screen differentially expressed genes (DEGs), which were used to establish a protein-protein interaction network and perform clustering module analysis. Univariate and multivariate proportional hazards regression analyses were applied to develop and validate the gene signature based on the TCGA dataset. The signature genes were then verified on GEPIA, Oncomine, and HPA platforms. Expression levels of corresponding genes were also measured by qRT-PCR and Western blotting in HBE, A549, and PC-9 cell lines. The prognostic signature based on eight genes (TTK, HMMR, ASPM, CDCA8, KIF2C, CCNA2, CCNB2, and MKI67) was established, which was independent of other clinical factors. The risk model offered better discrimination between risk groups, and patients with high-risk scores tended to have poor survival rate at 1-, 3- and 5-year follow-up. The model also presented better survival prediction in cancer-specific cohorts of age, gender, clinical stage III/IV, primary tumor 1/2, and lymph node metastasis 1/2. The signature genes, moreover, were highly expressed in A549 and PC-9 cells. In conclusion, the risk score signature could be used for prognostic estimation and as an independent risk factor for survival prediction in patients with LUAD.
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35
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Zheng P, Li L. FANCI Cooperates with IMPDH2 to Promote Lung Adenocarcinoma Tumor Growth via a MEK/ERK/MMPs Pathway. Onco Targets Ther 2020; 13:451-463. [PMID: 32021289 PMCID: PMC6970268 DOI: 10.2147/ott.s230333] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 12/12/2019] [Indexed: 01/15/2023] Open
Abstract
Purpose Fanconi anemia complementation group I (FANCI) is a key protein in ribosome biogenesis and DNA repair. Here, we aimed to determine the clinical significance, prognostic value and biology functions of FANCI in lung adenocarcinoma (LUAD). Methods The expression of FANCI in LUAD tissue and its relationship with patient outcomes were assessed using bioinformatics analysis, as well as quantitative reverse-transcription PCR (qRT-PCR) and Western blot analysis of LUAD tissue and adjacent normal lung tissue. The chi-squared test and Cox regression analysis were used to analyze the clinical significance of FANCI expression. The biological effects of FANCI knockdown in human LUAD cell lines were investigated by analysis of proliferation, colony formation, cell cycle distribution, migration, and invasion in vitro, and monitoring of tumor xenograft growth in vivo. FANCI interactions with IMPDH2 and involvement in MEK/ERK/MMPs signaling were analyzed using co-immunoprecipitation assays, immunofluorescence microscopy, and Western blotting. Results FANCI was identified as a hub gene for LUAD. FANCI expression was upregulated in LUAD tissues compared with normal lung tissues and was positively associated with lymphatic metastasis, distant metastasis, and poor outcome. FANCI was also an independent prognostic factor in LUAD patients. Knockdown of FANCI in LUAD cell lines decreased their proliferation, migration, invasion, and cell cycle progression in vitro, and decreased the growth of xenografts in mice. Direct binding of FANCI to IMPDH2 decreased IMPDH2 degradation, regulated activation of MEK/ERK/MMPs signaling. Overexpression of IMPDH2 reversed the inhibitory effects of FANCI knockdown. Conclusion FANCI may act as an oncogene in LUAD by cooperating with IMPDH2 to promote cell proliferation via the MEK/ERK/MMPs pathway. These results identify FANCI as a potential prognostic biomarker and therapeutic target for LUAD.
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Affiliation(s)
- Pengchao Zheng
- Department of Cardio-Thoracic Surgery, Second People's Hospital of Jinmen, Jingmen, Hubei 448000, People's Republic of China.,Department of Cardio-Thoracic Surgery, Jingchu Center Hospital Affiliated to the Institute of Technology, Jingmen, Hubei 448000, People's Republic of China
| | - Lei Li
- Department of Cardio-Thoracic Surgery, Second People's Hospital of Jinmen, Jingmen, Hubei 448000, People's Republic of China.,Department of Cardio-Thoracic Surgery, Jingchu Center Hospital Affiliated to the Institute of Technology, Jingmen, Hubei 448000, People's Republic of China
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Chen Y, Sun Y, Cui Y, Lei Y, Jiang N, Jiang W, Wang H, Chen L, Luo J, Chen Y, Tang K, Zhou C, Ke Z. High CTHRC1 expression may be closely associated with angiogenesis and indicates poor prognosis in lung adenocarcinoma patients. Cancer Cell Int 2019; 19:318. [PMID: 31798347 PMCID: PMC6884781 DOI: 10.1186/s12935-019-1041-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 11/18/2019] [Indexed: 01/02/2023] Open
Abstract
Background This study aimed to investigate the prognostic value of the potential biomarker collagen triple helix repeat containing 1 (CTHRC1) in lung adenocarcinoma (LUAD) patients. Methods A total of 210 LUAD patients diagnosed between 2003 and 2016 in the Department of Pathology of the First Affiliated Hospital of Sun Yat-sen University were included in this study. The expression of CTHRC1 and vascular endothelial growth factor (VEGF), and microvessel density (MVD, determined by CD34 immunostaining) were evaluated by immunohistochemistry in LUAD tissues. The association between the expression of these proteins and clinicopathological features or clinical outcomes was analyzed. Results Here, we confirmed that CTHRC1 expression was associated with prognosis and can serve as a significant predictor for overall survival (OS) and progression-free survival (PFS) in LUAD. Additionally, we observed that CTHRC1 expression was positively associated with tumor angiogenesis markers, such as VEGF expression (P < 0.001) and MVD (P < 0.01). Then, we performed gene set enrichment analysis (GESA) and cell experiments to confirm that enhanced CTHRC1 expression can promote VEGF levels. Based on and cox regression analysis, a predictive model that included CTHRC1, VEGF and MVD was constructed and confirmed as a more accurate independent predictor for OS (P = 0.001) and PFS (P < 0.001) in LUAD than other parameters. Conclusions These results demonstrated that high CTHRC1 expression may be closely related to tumor angiogenesis and poor prognosis in LUAD. The predictive model based on the CTHRC1 level and tumor angiogenesis markers can be used to predict LUAD patient prognosis more accurately.
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Affiliation(s)
- Yangshan Chen
- 1Department of Pathology, The First Affiliated Hospital, Sun Yat-sen University, No. 58, Zhongshan Second Road, Guangzhou, 510080 Guangdong People's Republic of China
| | - Yu Sun
- 1Department of Pathology, The First Affiliated Hospital, Sun Yat-sen University, No. 58, Zhongshan Second Road, Guangzhou, 510080 Guangdong People's Republic of China
| | - Yongmei Cui
- 1Department of Pathology, The First Affiliated Hospital, Sun Yat-sen University, No. 58, Zhongshan Second Road, Guangzhou, 510080 Guangdong People's Republic of China
| | - Yiyan Lei
- 2Department of Thoracic Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080 Guangdong People's Republic of China
| | - Neng Jiang
- 1Department of Pathology, The First Affiliated Hospital, Sun Yat-sen University, No. 58, Zhongshan Second Road, Guangzhou, 510080 Guangdong People's Republic of China
| | - Wenting Jiang
- 1Department of Pathology, The First Affiliated Hospital, Sun Yat-sen University, No. 58, Zhongshan Second Road, Guangzhou, 510080 Guangdong People's Republic of China
| | - Han Wang
- 1Department of Pathology, The First Affiliated Hospital, Sun Yat-sen University, No. 58, Zhongshan Second Road, Guangzhou, 510080 Guangdong People's Republic of China
| | - Lili Chen
- 1Department of Pathology, The First Affiliated Hospital, Sun Yat-sen University, No. 58, Zhongshan Second Road, Guangzhou, 510080 Guangdong People's Republic of China
| | - Jiping Luo
- 1Department of Pathology, The First Affiliated Hospital, Sun Yat-sen University, No. 58, Zhongshan Second Road, Guangzhou, 510080 Guangdong People's Republic of China
| | - Yanyang Chen
- 1Department of Pathology, The First Affiliated Hospital, Sun Yat-sen University, No. 58, Zhongshan Second Road, Guangzhou, 510080 Guangdong People's Republic of China
| | - Kejing Tang
- 3Department of Respiratory Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080 Guangdong People's Republic of China
| | - Chengzhi Zhou
- 4State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510080 Guangdong People's Republic of China
| | - Zunfu Ke
- 1Department of Pathology, The First Affiliated Hospital, Sun Yat-sen University, No. 58, Zhongshan Second Road, Guangzhou, 510080 Guangdong People's Republic of China.,5Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080 Guangdong People's Republic of China
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