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Kamble P, Nagar PR, Bhakhar KA, Garg P, Sobhia ME, Naidu S, Bharatam PV. Cancer pharmacoinformatics: Databases and analytical tools. Funct Integr Genomics 2024; 24:166. [PMID: 39294509 DOI: 10.1007/s10142-024-01445-5] [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: 07/29/2024] [Revised: 08/26/2024] [Accepted: 09/03/2024] [Indexed: 09/20/2024]
Abstract
Cancer is a subject of extensive investigation, and the utilization of omics technology has resulted in the generation of substantial volumes of big data in cancer research. Numerous databases are being developed to manage and organize this data effectively. These databases encompass various domains such as genomics, transcriptomics, proteomics, metabolomics, immunology, and drug discovery. The application of computational tools into various core components of pharmaceutical sciences constitutes "Pharmacoinformatics", an emerging paradigm in rational drug discovery. The three major features of pharmacoinformatics include (i) Structure modelling of putative drugs and targets, (ii) Compilation of databases and analysis using statistical approaches, and (iii) Employing artificial intelligence/machine learning algorithms for the discovery of novel therapeutic molecules. The development, updating, and analysis of databases using statistical approaches play a pivotal role in pharmacoinformatics. Multiple software tools are associated with oncoinformatics research. This review catalogs the databases and computational tools related to cancer drug discovery and highlights their potential implications in the pharmacoinformatics of cancer.
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Affiliation(s)
- Pradnya Kamble
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research, S.A.S. Nagar, Punjab, India
| | - Prinsa R Nagar
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research, S.A.S. Nagar, Punjab, India
| | - Kaushikkumar A Bhakhar
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research, S.A.S. Nagar, Punjab, India
| | - Prabha Garg
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research, S.A.S. Nagar, Punjab, India
| | - M Elizabeth Sobhia
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research, S.A.S. Nagar, Punjab, India
| | - Srivatsava Naidu
- Center of Biomedical Engineering, Indian Institute of Technology Ropar, Rupnagar, Punjab, India
| | - Prasad V Bharatam
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research, S.A.S. Nagar, Punjab, India.
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, S.A.S. Nagar, Punjab, India.
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Zhang Q, An N, Liu Y, Zhu Y, Pan W, Gu P, Zhao J, Pu Q, Zhu W. Alveolar type 2 cells marker gene SFTPC inhibits epithelial-to-mesenchymal transition by upregulating SOX7 and suppressing WNT/β-catenin pathway in non-small cell lung cancer. Front Oncol 2024; 14:1448379. [PMID: 39346732 PMCID: PMC11427448 DOI: 10.3389/fonc.2024.1448379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2024] [Accepted: 08/22/2024] [Indexed: 10/01/2024] Open
Abstract
Introduction Surfactant Protein C gene (SFTPC) is a marker gene of alveolar type 2 cells (AT2), which are the key structures of alveoli. Mutations or deletions in SFTPC cause idiopathic pulmonary fibrosis (IPF). Importantly, IPF is an independent risk factor for non-small cell lung cancer (NSCLC). It suggests that abnormal expression of SFTPC may be relevant to development of NSCLC. However, the function and mechanism of SFTPC in NSCLC are still poor understood until now. Methods The expression of SFTPC and the relationship between SFTPC and prognosis of NSCLC were analyzed in TCGA database and our collected clinical NSCLC tissues. Subsequently, the function and mechanism of SFTPC in NSCLC were explored by RNA-sequence, qRT-PCR, Western blot, Immunohistochemical, Wound-healing, Millicell, Transwell assays and mouse tumor xenograft model. Results SFTPC was dramatically downregulated in NSCLC tissues from TCGA database and 40 out of 46 collected clinical LUAD tissues compared with adjacent non-tumor tissues. Low expression of SFTPC was associated with poor prognosis of LUAD by TCGA database. Importantly, we confirmed that overexpression of SFTPC significantly inhibited Epithelial-to-Mesenchymal Transition (EMT) process of NSCLC cells by upregulating SOX7 and then inactivating WNT/β-catenin pathway in vitro and in vivo. Particularly, we discovered that low expression of SFTPC was associated with EMT process and low expression of SOX7 in NSCLC tissues. Conclusion Our study revealed a novel mechanism of SFTPC in NSCLC development. Meanwhile, it also might provide a new clue for exploring the molecular mechanism about NSCLC development in patients with IPF in the future.
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Affiliation(s)
- Qiongyin Zhang
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Ning An
- Cancer Center, Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Yang Liu
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Ying Zhu
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Wuliang Pan
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Peiling Gu
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Jinzhu Zhao
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Qiang Pu
- Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Wen Zhu
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
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Sun Q, Zheng S, Tang W, Wang X, Wang Q, Zhang R, Zhang N, Ping W. Prediction of lung adenocarcinoma prognosis and diagnosis with a novel model anchored in circadian clock-related genes. Sci Rep 2024; 14:18202. [PMID: 39107445 PMCID: PMC11303802 DOI: 10.1038/s41598-024-68256-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Accepted: 07/22/2024] [Indexed: 08/10/2024] Open
Abstract
Lung adenocarcinoma is the most common primary lung cancer seen in the world, and identifying genetic markers is essential for predicting the prognosis of lung adenocarcinoma and improving treatment outcomes. It is well known that alterations in circadian rhythms are associated with a higher risk of cancer. Moreover, circadian rhythms play a regulatory role in the human body. Therefore, studying the changes in circadian rhythms in cancer patients is crucial for optimizing treatment. The gene expression data and clinical data were sourced from TCGA database, and we identified the circadian clock-related genes. We used the obtained TCGA-LUAD data set to build the model, and the other 647 lung adenocarcinoma patients' data were collected from two GEO data sets for external verification. A risk score model for circadian clock-related genes was constructed, based on the identification of 8 genetically significant genes. Based on ROC analyses, the risk model demonstrated a high level of accuracy in predicting the overall survival times of lung adenocarcinoma patients in training folds, as well as external data sets. This study has successfully constructed a risk model for lung adenocarcinoma prognosis, utilizing circadian rhythm as its foundation. This model demonstrates a dependable capacity to forecast the outcome of the disease, which can further guide the relevant mechanism of lung adenocarcinoma and combine behavioral therapy with treatment to optimize treatment decision-making.
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Affiliation(s)
- Qihang Sun
- Department of Thoracic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Shubin Zheng
- Department of Thoracic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Wei Tang
- Department of Thoracic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Xiaoyu Wang
- Department of Thoracic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Qi Wang
- Department of Thoracic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Ruijie Zhang
- Department of Thoracic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Ni Zhang
- Department of Thoracic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.
| | - Wei Ping
- Department of Thoracic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.
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Zuo B, Wang L, Li X, Li X, Wang J, Xiong Y, Lei J, Zhang X, Chen Y, Liu Q, Jiao J, Sui M, Fan J, Wu N, Song Z, Li G. Abnormal low expression of SFTPC promotes the proliferation of lung adenocarcinoma by enhancing PI3K/AKT/mTOR signaling transduction. Aging (Albany NY) 2023; 15:12451-12475. [PMID: 37955668 PMCID: PMC10683597 DOI: 10.18632/aging.205191] [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: 06/23/2023] [Accepted: 10/03/2023] [Indexed: 11/14/2023]
Abstract
The abnormality of surfactant protein C (SFTPC) has been linked to the development of a number of interstitial lung diseases, according to mounting evidence. Nonetheless, the function and mechanism of SFTPC in the biological progression of lung adenocarcinoma (LUAD) remain unclear. Analysis of public datasets and testing of clinical samples suggested that SFTPC expression was abnormally low in LUAD, which was associated with the onset and poor prognosis of LUAD. The SFTPC-related risk score was derived using least absolute shrinkage and selection operator Cox regression as well as multivariate Cox regression. The risk score was highly correlated with tumor purity and tumor mutation burden, and it could serve as an independent prognostic indicator for LUAD. Low-risk LUAD patients may benefit more from CTLA-4 or/and PD-1 inhibitors. Overall, the risk score is useful for LUAD patient prognostication and treatment guidance. Moreover, in vitro and in vivo experiments demonstrated that SFTPC inhibits the proliferation of LUAD by inhibiting PI3K/AKT/mTOR signaling transduction. These results reveal the molecular mechanism by which SFTPC inhibits the proliferation of LUAD and suggest that SFTPC could be a new therapeutic target for LUAD.
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Affiliation(s)
- Baile Zuo
- Henan Key Laboratory of Immunology and Targeted Drugs, School of Medical Technology, Xinxiang Medical University, Xinxiang, Henan, China
| | - Lin Wang
- Department of Geriatrics, Xijing Hospital, The Air Force Military Medical University, Xi’an, Shaanxi, China
| | - Xiaoyan Li
- Department of Blood Transfusion, Shanxi Provincial People’s Hospital, Affiliate of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Xin Li
- Department of Geriatric Medicine, Shanxi Provincial People’s Hospital, Affiliate of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Jinping Wang
- Department of Ultrasound, Shanxi Provincial People’s Hospital, Affiliate of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Yanlu Xiong
- Department of Thoracic Surgery, Tangdu Hospital, Fourth Military Medical University, Xi’an, Shaanxi, China
| | - Jie Lei
- Department of Thoracic Surgery, Tangdu Hospital, Fourth Military Medical University, Xi’an, Shaanxi, China
| | - Xi Zhang
- Department of Oncology, The Third Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Yifan Chen
- College of Management, Zhejiang Shuren University, Hangzhou, Zhejiang, China
| | - Qiongwen Liu
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, Henan, China
| | - Jinke Jiao
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, Henan, China
| | - Mengru Sui
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, Henan, China
| | - Jinhan Fan
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, Henan, China
| | - Ningxue Wu
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, Henan, China
| | - Zewen Song
- Department of Oncology, The Third Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Guoyin Li
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, Henan, China
- MOE Key Laboratory of Modern Teaching Technology, Center for Teacher Professional Ability Development, Shaanxi Normal University, Xi’an, Shaanxi, China
- Academy of Medical Science, Zhengzhou University, Zhengzhou, Henan, China
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Zhang L, Guan M, Zhang X, Yu F, Lai F. Machine-learning and combined analysis of single-cell and bulk-RNA sequencing identified a DC gene signature to predict prognosis and immunotherapy response for patients with lung adenocarcinoma. J Cancer Res Clin Oncol 2023; 149:13553-13574. [PMID: 37507593 PMCID: PMC10590321 DOI: 10.1007/s00432-023-05151-w] [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: 06/23/2023] [Accepted: 07/09/2023] [Indexed: 07/30/2023]
Abstract
BACKGROUND Innate immune effectors, dendritic cells (DCs), influence cancer prognosis and immunotherapy significantly. As such, dendritic cells are important in killing tumors and influencing tumor microenvironment, whereas their roles in lung adenocarcinoma (LUAD) are largely unknown. METHODS In this study, 1658 LUAD patients from different cohorts were included. In addition, 724 cancer patients who received immunotherapy were also included. To identify DC marker genes in LUAD, we used single-cell RNAsequencing data for analysis and determined 83 genes as DC marker genes. Following that, integrative machine learning procedure was developed to construct a signature for DC marker genes. RESULTS Using TCGA bulk-RNA sequencing data as the training set, we developed a signature consisting of seven genes and classified patients by their risk status. Another six independent cohorts demonstrated the signature' s prognostic power, and multivariate analysis demonstrated it was an independent prognostic factor. LUAD patients in the high-risk group displayed more advanced features, discriminatory immune-cell infiltrations and immunosuppressive states. Cell-cell communication analysis indicates that tumor cells with lower risk scores communicate more actively with the tumor microenvironment. Eight independent immunotherapy cohorts revealed that patients with low-risk had better immunotherapy responses. Drug sensitivity analysis indicated that targeted therapy agents exhibited greater sensitivity to low-risk patients, while chemotherapy agents displayed greater sensitivity to high-risk patients. In vitro experiments confirmed that CTSH is a novel protective factor for LUAD. CONCLUSIONS An unique signature based on DC marker genes that is highly predictive of LUAD patients' prognosis and response to immunotherapy. CTSH is a new biomarker for LUAD.
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Affiliation(s)
- Liangyu Zhang
- Department of Thoracic Surgery, The First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, China
- Department of Thoracic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350212, China
| | - Maohao Guan
- Department of Thoracic Surgery, The First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, China
- Department of Thoracic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350212, China
| | - Xun Zhang
- Department of Thoracic Surgery, The First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, China
- Department of Thoracic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350212, China
| | - Fengqiang Yu
- Department of Thoracic Surgery, The First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, China.
- Department of Thoracic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350212, China.
| | - Fancai Lai
- Department of Thoracic Surgery, The First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, China.
- Department of Thoracic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350212, China.
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Wang Y, Xu Y, Liu C, Yuan C, Zhang Y. Identification of disulfidptosis-related subgroups and prognostic signatures in lung adenocarcinoma using machine learning and experimental validation. Front Immunol 2023; 14:1233260. [PMID: 37799714 PMCID: PMC10548142 DOI: 10.3389/fimmu.2023.1233260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 09/04/2023] [Indexed: 10/07/2023] Open
Abstract
Background Disulfidptosis is a newly identified variant of cell death characterized by disulfide accumulation, which is independent of ATP depletion. Accordingly, the latent influence of disulfidptosis on the prognosis of lung adenocarcinoma (LUAD) patients and the progression of tumors remains poorly understood. Methods We conducted a multifaceted analysis of the transcriptional and genetic modifications in disulfidptosis regulators (DRs) specific to LUAD, followed by an evaluation of their expression configurations to define DR clusters. Harnessing the differentially expressed genes (DEGs) identified from these clusters, we formulated an optimal predictive model by amalgamating 10 distinct machine learning algorithms across 101 unique combinations to compute the disulfidptosis score (DS). Patients were subsequently stratified into high and low DS cohorts based on median DS values. We then performed an exhaustive comparison between these cohorts, focusing on somatic mutations, clinical attributes, tumor microenvironment, and treatment responsiveness. Finally, we empirically validated the biological implications of a critical gene, KYNU, through assays in LUAD cell lines. Results We identified two DR clusters and there were great differences in overall survival (OS) and tumor microenvironment. We selected the "Least Absolute Shrinkage and Selection Operator (LASSO) + Random Survival Forest (RFS)" algorithm to develop a DS based on the average C-index across different cohorts. Our model effectively stratified LUAD patients into high- and low-DS subgroups, with this latter demonstrating superior OS, a reduced mutational landscape, enhanced immune status, and increased sensitivity to immunotherapy. Notably, the predictive accuracy of DS outperformed the published LUAD signature and clinical features. Finally, we validated the DS expression using clinical samples and found that inhibiting KYNU suppressed LUAD cells proliferation, invasiveness, and migration in vitro. Conclusions The DR-based scoring system that we developed enabled accurate prognostic stratification of LUAD patients and provides important insights into the molecular mechanisms and treatment strategies for LUAD.
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Affiliation(s)
- Yuzhi Wang
- Department of Laboratory Medicine, Deyang People’s Hospital, Deyang, Sichuan, China
| | - Yunfei Xu
- Department of Laboratory Medicine, Chengdu Women’s and Children’s Central Hospital, Chengdu, Sichuan, China
| | - Chunyang Liu
- Department of Ultrasound, The First People’s Hospital of Yibin, Yibin, Sichuan, China
| | - Chengliang Yuan
- Department of Laboratory Medicine, Deyang People’s Hospital, Deyang, Sichuan, China
| | - Yi Zhang
- Department of Blood Transfusion, Deyang People’s Hospital, Deyang, Sichuan, China
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Wang L, Liu W, Liu K, Wang L, Yin X, Bo L, Xu H, Lin S, Feng K, Zhou X, Lin L, Fei M, Zhang C, Ning S, Zhao H. The dynamic dysregulated network identifies stage-specific markers during lung adenocarcinoma malignant progression and metastasis. MOLECULAR THERAPY. NUCLEIC ACIDS 2022; 30:633-647. [PMID: 36514354 PMCID: PMC9722404 DOI: 10.1016/j.omtn.2022.11.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 11/17/2022] [Indexed: 11/23/2022]
Abstract
Brain metastasis occurs in approximately 30% of patients with lung adenocarcinoma (LUAD) and is closely associated with poor prognosis, recurrence, and death. However, dynamic gene regulation and molecular mechanism driving LUAD progression remain poorly understood. In this study, we performed a comprehensive single-cell transcriptome analysis using data from normal, early stage, advanced stage, and brain metastasis LUAD. Our single-cell-level analysis reveals the cellular composition heterogeneity at different stages during LUAD progression. We identified stage-specific risk genes that could contribute to LUAD progression and metastasis by reprogramming immune-related and metabolic-related functions. We constructed an early advanced metastatic dysregulated network and revealed the dynamic changes in gene regulations during LUAD progression. We identified 6 early advanced (HLA-DRB1, HLA-DQB1, SFTPB, SFTPC, PLA2G1B, and FOLR1), 8 advanced metastasis (RPS15, RPS11, RPL13A, RPS24, HLA-DRB5, LYPLA1, KCNJ15, and PSMA3), and 2 common risk genes in different stages (SFTPD and HLA-DRA) as prognostic markers in LUAD. Particularly, decreased expression of HLA-DRA, HLA-DRB1, HLA-DQB1, and HLA-DRB5 refer poor prognosis in LUAD by controlling antigen processing and presentation and T cell activation. Increased expression of PSMA3 and LYPLA1 refer poor prognosis by reprogramming fatty acid metabolism and RNA catabolic process. Our findings will help further understanding the pathobiology of brain metastases in LUAD.
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Affiliation(s)
- Li Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China,Corresponding author Li Wang, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.
| | - Wangyang Liu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Kailai Liu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Lixia Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Xiangzhe Yin
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Lin Bo
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Haotian Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Shihua Lin
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Ke Feng
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Xinyu Zhou
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Lin Lin
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Meiting Fei
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Caiyu Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Shangwei Ning
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China,Corresponding author Shangwei Ning, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.
| | - Hongying Zhao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China,Corresponding author Hongying Zhao, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.
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Circular RNA hsa_circ_0002360 Promotes Proliferation and Invasion and Inhibits Oxidative Stress in Gastric Cancer by Sponging miR-629-3p and Regulating the PDLIM4 Expression. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:2775433. [PMID: 35982735 PMCID: PMC9381216 DOI: 10.1155/2022/2775433] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 05/27/2022] [Accepted: 05/30/2022] [Indexed: 12/18/2022]
Abstract
Many studies have found that circRNA hsa_0002360 (circ0002360) plays an important role in cancer onset and progression. However, its role in gastric cancer (GC) remains uncertain. Circ0002360 was found to be upregulated in GC cells using QRT-PCR. Furthermore, miR-629-3p, a target miRNA of circ0002360, was the most suppressed miRNA following circ0002360 overexpression. RNA immunoprecipitation (RIP), dual-luciferase reporter analyses, clone formation, transwell, DCFH-DA, and ELISA assays demonstrated that circ0002360-targeted miR-629-3p promotes cell proliferation and migration while inhibiting oxidative stress. GC-related mRNA microarrays from the GEO and TCGA databases, including GSE103236, GSE79973, GSE33429, GSE22804, GSE84437, and TCGA-STAD datasets, were used to find hub biomarkers between normal and gastric cancer samples. WGCNA and uni-Cox analysis were used to identify 27 survival-related risk genes, which were then used to build a risk model for prognosis prediction. Following that, all patients from the GSE84437 and TCGA-STAD datasets with 27 survival-related genes and enough data on survival status and time were randomly assigned to train (n = 433) and test (n = 375) cohorts. Furthermore, ROC and Kaplan-Meier (KM) analyses were used to validate the risk model for both cohorts. randomForest analysis indicated that PDLIM4 was the target gene of miR-629-3p, whose level was increased by circ0002360 but reversed by miR-629-3p mimics. Finally, this study confirmed that circ0002360 sponged miR-629-3p and then upregulated PDLIM4 expression. As a result, circ0002360 may be a useful marker for predicting GC prognosis and an anti-GC treatment target.
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Prognostic Risk Signature and Comprehensive Analyses of Endoplasmic Reticulum Stress-Related Genes in Lung Adenocarcinoma. J Immunol Res 2022; 2022:6567916. [PMID: 35571564 PMCID: PMC9096573 DOI: 10.1155/2022/6567916] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 03/29/2022] [Accepted: 04/04/2022] [Indexed: 12/24/2022] Open
Abstract
Lung adenocarcinoma (LUAD) is the main pathological subtype of non-small-cell lung cancer. Endoplasmic reticulum stress (ERS) has been found to be involved in multiple tumor-related biological processes. At present, a comprehensive analysis of ERS-related genes in LUAD is still lacking. A total of 1034 samples from TCGA and GEO were used to screen differentially expressed genes. Further, Random Forest algorithm was utilized to screen characteristic genes related to prognosis. Then, LASSO Cox regression was used to construct a prognostic signature. Taking the median of signature score as the threshold, patients were separated into high-risk (HR) group and low-risk (LR) group. Tumor mutation burden (TMB), immune cell infiltration, cancer stem cell infiltration, expression of HLA, and immune checkpoints of the two risk groups were analyzed. TIDE score was used to evaluate the response of the two risk groups to immunotherapy. Finally, the gene expression was verified in clinical tissues with RT-qPCR. An eight-gene signature (ADRB2, AGER, CDKN3, GJB2, SFTPC, SLC2A1, SLC6A4, and SSR4) was constructed. TMB and cancer stem cell infiltration were higher in the HR group than the LR group. TIDE score and expression level of HLA were higher in the LR group than the HR group. Expression level of immune checkpoints, including CD28, CD27, IDO2, and others, were higher in the LR group. Multiple drugs approved by FAD, targeting ERS-related genes, were available for the treatment of LUAD. In summary, we established a stable prognostic model based on ERS-related genes to help the classification of LUAD patients and looked for new treatment strategies from aspects of immunity, tumor mutation, and tumor stem cell infiltration.
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Kim M, Vu NT, Wang X, Bulut GB, Wang MH, Uram-Tuculescu C, Pillappa R, Kim S, Chalfant CE. Caspase-9b drives cellular transformation, lung inflammation, and lung tumorigenesis. Mol Cancer Res 2022; 20:1284-1294. [PMID: 35412615 DOI: 10.1158/1541-7786.mcr-21-0905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 02/28/2022] [Accepted: 04/08/2022] [Indexed: 11/16/2022]
Abstract
Caspase 9 undergoes alternative splicing to produce two opposing isoforms: pro-apoptotic Caspase-9a (C9a) and pro-survival Caspase-9b (C9b). Previously, our laboratory reported that C9b is expressed in majority of non-small cell lung cancer tumors and directly activates the NF-κB pathway. In this study, the role of C9b in activation of the NF-κB pathway in vivo, lung inflammation and immune responses, and lung tumorigenesis were examined. Specifically, a transgenic mouse model expressing human C9b in the lung pneumocytes developed inflammatory lung lesions, which correlated with enhanced activation of the NF-κB pathway and increased influx of immunosuppressive MDSCs in contrast to wild-type mice. C9b mice presented with facial dermatitis, a thickened and disorganized dermis, enhanced collagen depth, and increased serum levels of IL-6. C9b mice also developed spontaneous lung tumors, and C9b cooperated with oncogenic KRAS in lung tumorigenesis. C9b expression also cooperated with oncogenic KRAS and p53 downregulation to drive the full cell transformation of human bronchial epithelial cells (e.g., tumor formation). Implications: Our findings show that C9b can directly activate NF-κB pathway in vivo to modulate lung inflammation, immune cell influx, and peripheral immune responses, which demonstrates that C9b is key factor in driving cell transformation and lung tumorigenesis.
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Affiliation(s)
- Minjung Kim
- University of South Florida, Tampa, FL, United States
| | - Ngoc T Vu
- University of South Florida, United States
| | - Xue Wang
- University of South Florida, Tampa, Virginia, United States
| | - Gamze B Bulut
- Virginia Commonwealth University-School of Medicine, Richmond, Virginia, United States
| | - Min-Hsuan Wang
- H. Lee Moffitt Cancer Center & Research, Tampa, Florida, United States
| | | | - Raghavendra Pillappa
- Virginia Commonwealth University-School of Medicine, Richmond, Virginia, United States
| | | | - Charles E Chalfant
- University of Virginia School of Medicine, Charlottesville, Virginia, United States
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11
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MicroRNA-629-3p Promotes Interleukin-13-Induced Bronchial Epithelial Cell Injury and Inflammation by Targeting FOXA2. Cell Biochem Biophys 2022; 80:457-466. [DOI: 10.1007/s12013-022-01072-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 02/14/2022] [Indexed: 11/03/2022]
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12
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Ramos B, Pereira T, Silva F, Costa JL, Oliveira HP. Differential Gene Expression Analysis of the Most Relevant Genes for Lung Cancer Prediction and Sub-type Classification. PATTERN RECOGNITION AND IMAGE ANALYSIS 2022. [DOI: 10.1007/978-3-031-04881-4_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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13
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Hayek H, Kosmider B, Bahmed K. The role of miRNAs in alveolar epithelial cells in emphysema. Biomed Pharmacother 2021; 143:112216. [PMID: 34649347 PMCID: PMC9275516 DOI: 10.1016/j.biopha.2021.112216] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 09/13/2021] [Accepted: 09/15/2021] [Indexed: 02/07/2023] Open
Abstract
Chronic obstructive pulmonary disease (COPD) is an inflammatory lung disease becoming one of the leading causes of mortality and morbidity globally. The significant risk factors for COPD are exposure to harmful particles such as cigarette smoke, biomass smoke, and air pollution. Pulmonary emphysema belongs to COPD and is characterized by a unique alveolar destruction pattern resulting in marked airspace enlargement. Alveolar type II (ATII) cells have stem cell potential; they proliferate and differentiate to alveolar type I cells to restore the epithelium after damage. Oxidative stress causes premature cell senescence that can contribute to emphysema development. MiRNAs regulate gene expression, are essential for maintaining ATII cell homeostasis, and their dysregulation contributes to this disease development. They also serve as biomarkers of lung diseases and potential therapeutics. In this review, we summarize recent findings on miRNAs’ role in alveolar epithelial cells in emphysema.
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Affiliation(s)
- Hassan Hayek
- Department of Microbiology, Immunology, and Inflammation, Temple University, Philadelphia, PA 19140, USA; Center for Inflammation and Lung Research, Temple University, Philadelphia, PA 19140, USA
| | - Beata Kosmider
- Department of Microbiology, Immunology, and Inflammation, Temple University, Philadelphia, PA 19140, USA; Center for Inflammation and Lung Research, Temple University, Philadelphia, PA 19140, USA; Department of Biomedical Education and Data Science, Temple University, Philadelphia, PA 19140, USA
| | - Karim Bahmed
- Center for Inflammation and Lung Research, Temple University, Philadelphia, PA 19140, USA; Department of Thoracic Medicine and Surgery, Temple University, Philadelphia, PA 19140, USA.
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14
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Huang GH, Zhang YH, Chen L, Li Y, Huang T, Cai YD. Identifying Lung Cancer Cell Markers with Machine Learning Methods and Single-Cell RNA-Seq Data. Life (Basel) 2021; 11:life11090940. [PMID: 34575089 PMCID: PMC8467493 DOI: 10.3390/life11090940] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Revised: 09/03/2021] [Accepted: 09/06/2021] [Indexed: 11/21/2022] Open
Abstract
Non-small cell lung cancer is a major lethal subtype of epithelial lung cancer, with high morbidity and mortality. The single-cell sequencing technique plays a key role in exploring the pathogenesis of non-small cell lung cancer. We proposed a computational method for distinguishing cell subtypes from the different pathological regions of non-small cell lung cancer on the basis of transcriptomic profiles, including a group of qualitative classification criteria (biomarkers) and various rules. The random forest classifier reached a Matthew’s correlation coefficient (MCC) of 0.922 by using 720 features, and the decision tree reached an MCC of 0.786 by using 1880 features. The obtained biomarkers and rules were analyzed in the end of this study.
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Affiliation(s)
- Guo-Hua Huang
- School of Life Sciences, Shanghai University, Shanghai 200444, China;
- Department of Mechanical and Energy Engineering, Shaoyang University, Shaoyang 422000, China;
| | - Yu-Hang Zhang
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA;
| | - Lei Chen
- Department of College of Information Engineering, Shanghai Maritime University, Shanghai 201306, China;
| | - You Li
- Department of Mechanical and Energy Engineering, Shaoyang University, Shaoyang 422000, China;
| | - Tao Huang
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai 200031, China
- Correspondence: (T.H.); (Y.-D.C.); Tel.: +86-21-54923269 (T.H.); +86-21-66136132 (Y.-D.C.)
| | - Yu-Dong Cai
- School of Life Sciences, Shanghai University, Shanghai 200444, China;
- Correspondence: (T.H.); (Y.-D.C.); Tel.: +86-21-54923269 (T.H.); +86-21-66136132 (Y.-D.C.)
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15
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Krasniqi E, Sacconi A, Marinelli D, Pizzuti L, Mazzotta M, Sergi D, Capomolla E, Donzelli S, Carosi M, Bagnato A, Gamucci T, Tomao S, Natoli C, Marchetti P, Grassadonia A, Tinari N, De Tursi M, Vizza E, Ciliberto G, Landi L, Cappuzzo F, Barba M, Blandino G, Vici P. MicroRNA-based signatures impacting clinical course and biology of ovarian cancer: a miRNOmics study. Biomark Res 2021; 9:57. [PMID: 34256855 PMCID: PMC8276429 DOI: 10.1186/s40364-021-00289-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 04/26/2021] [Indexed: 02/06/2023] Open
Abstract
Background In Western countries, ovarian cancer (OC) still represents the leading cause of gynecological cancer-related deaths, despite the remarkable gains in therapeutical options. Novel biomarkers of early diagnosis, prognosis definition and prediction of treatment outcomes are of pivotal importance. Prior studies have shown the potentials of micro-ribonucleic acids (miRNAs) as biomarkers for OC and other cancers. Methods We focused on the prognostic and/or predictive potential of miRNAs in OC by conducting a comprehensive array profiling of miRNA expression levels in ovarian tissue samples from 17 non-neoplastic controls, and 60 tumor samples from OC patients treated at the Regina Elena National Cancer Institute (IRE). A set of 54 miRNAs with differential expression in tumor versus normal samples (T/N-deregulated) was identified in the IRE cohort and validated against data from the Cancer Genoma Atlas (TCGA) related to 563 OC patients and 8 non-neoplastic controls. The prognostic/predictive role of the selected 54 biomarkers was tested in reference to survival endpoints and platinum resistance (P-res). Results In the IRE cohort, downregulation of the 2 miRNA-signature including miR-99a-5p and miR-320a held a negative prognostic relevance, while upregulation of miR-224-5p was predictive of less favorable event free survival (EFS) and P-res. Data from the TCGA showed that downregulation of 5 miRNAs, i.e., miR-150, miR-30d, miR-342, miR-424, and miR-502, was associated with more favorable EFS and overall survival outcomes, while miR-200a upregulation was predictive of P-res. The 9 miRNAs globally identified were all included into a single biologic signature, which was tested in enrichment analysis using predicted/validated miRNA target genes, followed by network representation of the miRNA-mRNA interactions. Conclusions Specific dysregulated microRNA sets in tumor tissue showed predictive/prognostic value in OC, and resulted in a promising biological signature for this disease. Supplementary Information The online version contains supplementary material available at 10.1186/s40364-021-00289-6.
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Affiliation(s)
- E Krasniqi
- Division of Medical Oncology 2, IRCCS Regina Elena National Cancer Institute, Via Elio Chianesi 53, 00144, Rome, Italy
| | - A Sacconi
- UOSD Clinical Trial Center, Biostatistics and Bioinformatics, IRCCS Regina Elena National Cancer Institute, Via Elio Chianesi 53, 00144, Rome, Italy
| | - D Marinelli
- Department of Clinical and Molecular Medicine, Sant'Andrea Hospital, Medical Oncology Unit, Sapienza University, Via di Grottarossa 1035/1039, 00189, Rome, Italy
| | - L Pizzuti
- Division of Medical Oncology 2, IRCCS Regina Elena National Cancer Institute, Via Elio Chianesi 53, 00144, Rome, Italy
| | - M Mazzotta
- Division of Medical Oncology 2, IRCCS Regina Elena National Cancer Institute, Via Elio Chianesi 53, 00144, Rome, Italy
| | - D Sergi
- Division of Medical Oncology 2, IRCCS Regina Elena National Cancer Institute, Via Elio Chianesi 53, 00144, Rome, Italy
| | - E Capomolla
- Division of Medical Oncology 2, IRCCS Regina Elena National Cancer Institute, Via Elio Chianesi 53, 00144, Rome, Italy
| | - S Donzelli
- Oncogenomic and Epigenetic Unit, IRCCS Regina Elena National Cancer Institute, Via Elio Chianesi 53, 00144, Rome, Italy
| | - M Carosi
- Pathology Department IRCCS Regina Elena National Cancer Institute, Via Elio Chianesi 53, 00144, Rome, Italy
| | - A Bagnato
- Preclinical Models and New Therapeutic Agents Unit, IRCCS Regina Elena National Cancer Institute, Via Elio Chianesi 53, 00144, Rome, Italy
| | - T Gamucci
- Medical Oncology, Sandro Pertini Hospital, Via dei Monti Tiburtini 385, 00157, Rome, Italy
| | - S Tomao
- Department of Radiological Oncological and Pathological Sciences, Division of Medical Oncology A, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - C Natoli
- Department of Medical, Oral & Biotechnological Sciences, University G. D'Annunzio, Via dei Vestini, 31, 66100, Chieti, Italy
| | - P Marchetti
- Department of Clinical and Molecular Medicine, Sant'Andrea Hospital, Medical Oncology Unit, Sapienza University, Via di Grottarossa 1035/1039, 00189, Rome, Italy
| | - A Grassadonia
- Department of Medical, Oral & Biotechnological Sciences, University G. D'Annunzio, Via dei Vestini, 31, 66100, Chieti, Italy
| | - N Tinari
- Department of Medical, Oral & Biotechnological Sciences, University G. D'Annunzio, Via dei Vestini, 31, 66100, Chieti, Italy
| | - M De Tursi
- Department of Medical, Oral & Biotechnological Sciences, University G. D'Annunzio, Via dei Vestini, 31, 66100, Chieti, Italy
| | - E Vizza
- Department of Oncological Surgery, Gynecologic Oncologic Unit, IRCCS Regina Elena National Cancer Institute, Via Elio Chianesi 53, 00144, Rome, Italy
| | - G Ciliberto
- Scientific Direction, IRCCS Regina Elena National Cancer Institute, Via Elio Chianesi 53, 00144, Rome, Italy
| | - L Landi
- Division of Medical Oncology 2, IRCCS Regina Elena National Cancer Institute, Via Elio Chianesi 53, 00144, Rome, Italy
| | - F Cappuzzo
- Division of Medical Oncology 2, IRCCS Regina Elena National Cancer Institute, Via Elio Chianesi 53, 00144, Rome, Italy
| | - M Barba
- Division of Medical Oncology 2, IRCCS Regina Elena National Cancer Institute, Via Elio Chianesi 53, 00144, Rome, Italy.
| | - G Blandino
- Oncogenomic and Epigenetic Unit, IRCCS Regina Elena National Cancer Institute, Via Elio Chianesi 53, 00144, Rome, Italy.
| | - P Vici
- Division of Medical Oncology 2, IRCCS Regina Elena National Cancer Institute, Via Elio Chianesi 53, 00144, Rome, Italy
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Niu N, Ma X, Liu H, Zhao J, Lu C, Yang F, Qi W. DLC1 inhibits lung adenocarcinoma cell proliferation, migration and invasion via regulating MAPK signaling pathway. Exp Lung Res 2021; 47:173-182. [PMID: 33678109 DOI: 10.1080/01902148.2021.1885524] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Lung adenocarcinoma (LUAD), one of the most common cancers, is a major threat to people's health due to its high mortality, and the survival of most patients suffering LUAD remains poor. This study aimed to explore the mechanism of Deleted in Liver Cancer 1 (DLC1) as a tumor suppressor underlying the occurrence and progression of LUAD. As revealed by bioinformatics analysis and qRT-PCR, DLC1 was significantly down-regulated in LUAD tumor tissue and cells. A series of cellular experiments including CCK-8, wound healing and Transwell assays were performed to detect the effect of DLC1 on the biological function of LUAD cells. It was found that overexpressing DLC1 significantly inhibited LUAD cell proliferative, migratory and invasive abilities, while knockdown of DLC1 promoted these abilities. Gene Set Enrichment Analysis (GSEA) and dual-luciferase assay were used to explore the downstream signaling pathway of DLC1, finding that DLC1 could remarkably inhibit the activity of mitogen-activated protein kinase (MAPK) signaling pathway. Western blot implemented for MAPK signaling pathway-related proteins further identified that DLC1 restrained the activation of MAPK/ERK signaling pathway. Furthermore, rescue experiments suggested that DLC1 inhibited LUAD cell proliferation and invasion by suppressing the MAPK/ERK signaling pathway. Overall, our study discussed the DLC1-dependent mechanism involved in LUAD. We found that the up-regulation of DLC1 may inhibit the malignant progression of LUAD by suppressing MAPK signaling pathway, which supports the view that DLC1 may serve as a molecular target for the targeted therapy of LUAD patients.
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Affiliation(s)
- Niu Niu
- Department of Cardiothoracic Surgery, Affiliated Hospital of Jiaxing University (The First Hospital of Jiaxing), Jiaxing, Zhejiang, China
| | - Xingjie Ma
- Department of Cardiothoracic Surgery, Affiliated Hospital of Jiaxing University (The First Hospital of Jiaxing), Jiaxing, Zhejiang, China
| | - Haitao Liu
- Department of Cardiothoracic Surgery, Affiliated Hospital of Jiaxing University (The First Hospital of Jiaxing), Jiaxing, Zhejiang, China
| | - Junjie Zhao
- Department of Cardiothoracic Surgery, Affiliated Hospital of Jiaxing University (The First Hospital of Jiaxing), Jiaxing, Zhejiang, China
| | - Chao Lu
- Department of Cardiothoracic Surgery, Affiliated Hospital of Jiaxing University (The First Hospital of Jiaxing), Jiaxing, Zhejiang, China
| | - Fan Yang
- Department of Cardiothoracic Surgery, Affiliated Hospital of Jiaxing University (The First Hospital of Jiaxing), Jiaxing, Zhejiang, China
| | - Weibo Qi
- Department of Cardiothoracic Surgery, Affiliated Hospital of Jiaxing University (The First Hospital of Jiaxing), Jiaxing, Zhejiang, China
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17
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Upregulation of Serum miR-629 Predicts Poor Prognosis for Non-Small-Cell Lung Cancer. DISEASE MARKERS 2021; 2021:8819934. [PMID: 33763157 PMCID: PMC7946467 DOI: 10.1155/2021/8819934] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 01/19/2021] [Accepted: 02/05/2021] [Indexed: 11/29/2022]
Abstract
Non-small-cell lung cancer (NSCLC) is one of the most common types of cancer worldwide. Accumulating evidence has suggested that aberrant expression of microRNAs (miRNAs) is involved in the carcinogenesis and progression of NSCLC. The current study is aimed at investigating the clinical significance of serum miR-629 in NSCLC. The expression levels of serum miR-629 in patients with NSCLC, patients with nonmalignant lung diseases, and healthy controls were assessed by real-time quantitative polymerase chain reaction. Our results showed that serum miR-629 levels were significantly upregulated in NSCLC patients compared to the controls. Serum miR-629 exhibited better performance for discriminating NSCLC patients from healthy controls, compared to the traditional biomarkers CYFRA 21-1 and CEA. In addition, a high serum miR-629 level was positively correlated with adverse clinicopathological parameters including lymph node metastasis, differentiation, and clinical stage. Serum miR-629 was dramatically reduced in the NSCLC cases receiving surgical treatment. Moreover, the patients in the high serum miR-629 group suffered poorer overall survival and disease-free survival than those in the low serum miR-629 group. In conclusion, serum miR-629 might serve as a potential prognostic biomarker for NSCLC.
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18
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Liu H, Ma X, Niu N, Zhao J, Lu C, Yang F, Qi W. MIR-301b-3p Promotes Lung Adenocarcinoma Cell Proliferation, Migration and Invasion by Targeting DLC1. Technol Cancer Res Treat 2021; 20:1533033821990036. [PMID: 33754907 PMCID: PMC8093615 DOI: 10.1177/1533033821990036] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 11/25/2020] [Accepted: 12/29/2020] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND miR-301b-3p is reported in various human cancers for its abnormal expression, while the role and molecular mechanisms in lung adenocarcinoma (LUAD) remain unclear, and this is the focus of the present study. MATERIALS AND METHODS TCGA database was consulted to know gene expression in LUAD tissue. CCK-8, colony formation assay and Transwell assay were applied to identify the role of target genes in regulating LUAD cell biological properties. Bioinformatics analysis plus dual-luciferase assay were performed to validate the potential connection between genes. RESULTS miR-301b-3p and DLC1 were the target genes of this study and respectively differentially up-regulated and down-regulated in LUAD. Functional experiments indicated that miR-301b-3p contributed to cancer cell proliferation, migration and invasion, while this effect was reversed with overexpressed DLC1 which was identified as a direct target of and regulated by miR-301b-3p. CONCLUSIONS Collectively, miR-301b-3p was identified to actively function on LUAD malignant progression by suppressing DLC1 expression. This discovery provides a novel therapeutic strategy for LUAD patients, which helps improve the survival of patients.
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Affiliation(s)
- Haitao Liu
- Department of Cardiothoracic Surgery, The First Hospital of Jiaxing
(Affiliated Hospital of Jiaxing University), Jiaxing, Zhejiang China
| | - Xingjie Ma
- Department of Cardiothoracic Surgery, The First Hospital of Jiaxing
(Affiliated Hospital of Jiaxing University), Jiaxing, Zhejiang China
| | - Niu Niu
- Department of Cardiothoracic Surgery, The First Hospital of Jiaxing
(Affiliated Hospital of Jiaxing University), Jiaxing, Zhejiang China
| | - Junjie Zhao
- Department of Cardiothoracic Surgery, The First Hospital of Jiaxing
(Affiliated Hospital of Jiaxing University), Jiaxing, Zhejiang China
| | - Chao Lu
- Department of Cardiothoracic Surgery, The First Hospital of Jiaxing
(Affiliated Hospital of Jiaxing University), Jiaxing, Zhejiang China
| | - Fan Yang
- Department of Cardiothoracic Surgery, The First Hospital of Jiaxing
(Affiliated Hospital of Jiaxing University), Jiaxing, Zhejiang China
| | - Weibo Qi
- Department of Cardiothoracic Surgery, The First Hospital of Jiaxing
(Affiliated Hospital of Jiaxing University), Jiaxing, Zhejiang China
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Luo X, Yue M, Li C, Sun D, Wang L. Long Non-Coding RNA LINC00239 Functions as a Competitive Endogenous RNA by Sponging microRNA-484 and Enhancing KLF12 Expression to Promote the Oncogenicity of Colorectal Cancer. Onco Targets Ther 2020; 13:12067-12081. [PMID: 33262607 PMCID: PMC7695693 DOI: 10.2147/ott.s278582] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 10/21/2020] [Indexed: 12/24/2022] Open
Abstract
Background Long intergenic non-protein coding RNA 239 (LINC00239) is an oncogenic long non-coding RNA in acute myeloid leukemia. We aimed to determine LINC00239 expression in colorectal cancer (CRC) and examine the influences of LINC00239 on tumor behaviors of CRC cells. Furthermore, the mechanism underlying the actions of LINC00239 in CRC was unveiled in detail. Materials and Methods Quantitative real-time polymerase chain reaction was used to detect LINC00239 expression in CRC tissues and cell lines. CRC cell proliferation, apoptosis, migration, and invasion were investigated by cell counting kit-8 assays, flow cytometry, and cell migration and invasion assays, respectively. Tumor xenograft experiments were performed to evaluate the tumor growth of CRC cells in vivo. The interactions among LINC00239, microRNA-484 (miR-484), and kruppel-like factor 12 (KLF12) were analyzed by bioinformatics prediction, RNA immunoprecipitation and luciferase reporter assay. Results LINC00239 was upregulated in CRC tissues and cell lines. LINC00239 knockdown impaired CRC cell proliferation, migration, and invasion and promoted apoptosis in vitro. Additionally, LINC00239 deficiency inhibited CRC growth in vivo. Mechanistically, LINC00239 functioned as a competing endogenous RNA by directly sponging miR-484, thereby enhancing KLF12 expression. Rescue experiments further corroborated that miR-484 inhibition or KLF12 overexpression reversed the inhibitory actions of LINC00239 knockdown in CRC cells. Conclusion The LINC00239/miR-484/KLF12 pathway executed critical roles in CRC oncogenicity and may provide potential targets for CRC treatments.
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Affiliation(s)
- Xiaofan Luo
- Department of Colorectal and Anal Surgery, First Hospital of Jilin University, Changchun, Jilin 130021, People's Republic of China
| | - Meng Yue
- Department of Colorectal and Anal Surgery, First Hospital of Jilin University, Changchun, Jilin 130021, People's Republic of China
| | - Chenguang Li
- Department of Colorectal and Anal Surgery, First Hospital of Jilin University, Changchun, Jilin 130021, People's Republic of China
| | - Di Sun
- Department of Colorectal and Anal Surgery, First Hospital of Jilin University, Changchun, Jilin 130021, People's Republic of China
| | - Lei Wang
- Department of Colorectal and Anal Surgery, First Hospital of Jilin University, Changchun, Jilin 130021, People's Republic of China
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Liu Y, Ye G, Huang L, Zhang C, Sheng Y, Wu B, Han L, Wu C, Dong B, Qi Y. Single-cell transcriptome analysis demonstrates inter-patient and intra-tumor heterogeneity in primary and metastatic lung adenocarcinoma. Aging (Albany NY) 2020; 12:21559-21581. [PMID: 33170151 PMCID: PMC7695431 DOI: 10.18632/aging.103945] [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: 04/21/2020] [Accepted: 08/08/2020] [Indexed: 12/15/2022]
Abstract
In this study, we performed single-cell transcriptome data analysis of fifty primary and metastatic lung adenocarcinoma (LUAD) samples from the GSE123902 and GSE131907 datasets to determine the landscape of inter-patient and intra-tumoral heterogeneity. The gene expression profiles and copy number variations (CNV) showed significant heterogeneity in the primary and metastatic LUAD samples. We observed upregulation of pathways related to translational initiation, endoplasmic reticulum stress, exosomes, and unfolded protein response in the brain metastasis samples as compared to the primary tumor samples. Pathways related to exosomes, cell adhesion and metabolism were upregulated and the epithelial-to-mesenchymal-transition (EMT) pathway was downregulated in brain metastasis samples from chemotherapy-treated LUAD patients as compared to those from the untreated LUAD patients. Tumor cell subgroups in the brain metastasis samples showed differential expression of genes related to type II alveolar cells, chemoresistance, glycolysis and oxidative phosphorylation (metabolic reprogramming), and EMT. Thus, single-cell transcriptome analysis demonstrated intra-patient and intra-tumor heterogeneity in the regulation of pathways related to tumor progression, chemoresistance and metabolism in the primary and metastatic LUAD tissues. Moreover, our study demonstrates that single cell transcriptome analysis is a potentially useful tool for accurate diagnosis and personalized targeted treatment of LUAD patients.
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Affiliation(s)
- Yafei Liu
- Department of Thoracic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Guanchao Ye
- Department of Thoracic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Lan Huang
- Biotherapy Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Chunyang Zhang
- Department of Thoracic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Yinliang Sheng
- Department of Thoracic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Bin Wu
- Department of Thoracic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Lu Han
- Department of Thoracic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Chunli Wu
- Department of Thoracic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Bo Dong
- Department of Thoracic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Yu Qi
- Department of Thoracic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
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Yue PJ, Sun YY, Li YH, Xu ZM, Fu WN. MYCT1 inhibits the EMT and migration of laryngeal cancer cells via the SP1/miR-629-3p/ESRP2 pathway. Cell Signal 2020; 74:109709. [PMID: 32659265 DOI: 10.1016/j.cellsig.2020.109709] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 07/02/2020] [Accepted: 07/07/2020] [Indexed: 12/14/2022]
Abstract
MYCT1 has an inhibitory effect on the migration of laryngeal cancer cells, although the underlying molecular mechanism remains unknown. In this study, we aimed to explore the mechanism of MYCT1 in the epithelial-mesenchymal transition (EMT) and migration of laryngeal cancer cells. We found that MYCT1 significantly decreased the expression of miR-629-3p but increased the expression of ESRP2 in laryngeal cancer cells. The expression of miR-629-3p and ESRP2 in laryngeal cancer tissues showed significantly positive and negative correlations with patient metastasis, respectively. miR-629-3p was confirmed to repress the expression of ESRP2 by targeting its 3'UTR. SP1 was verified to be a direct transcription factor for miR-629-3p and a downstream target of MYCT1. Moreover, MYCT1 inhibited the EMT and migration of laryngeal cancer cells through the SP1/miR-629-3p/ESRP2 pathway. Taken together, our results establish a novel MYCT1 signaling pathway in the EMT and migration of laryngeal cancer cells, thus providing important insights for further studying the pathway in the diagnosis and treatment of laryngeal cancer.
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Affiliation(s)
- Peng-Jie Yue
- Department of Medical Genetics, China Medical University, Shenyang 110122, PR China
| | - Yuan-Yuan Sun
- Department of Medical Genetics, China Medical University, Shenyang 110122, PR China
| | - Yun-Hui Li
- Department of Laboratory Medicine, General Hospital of Northern Theater Command (Heping Campus), Shenyang 110001, PR China.
| | - Zhen-Ming Xu
- Department of Otolaryngology, the Fourth People's Hospital of Shenyang City, Shenyang 110031, PR China.
| | - Wei-Neng Fu
- Department of Medical Genetics, China Medical University, Shenyang 110122, PR China.
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22
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Al-Marsoummi S, Pacella J, Dockter K, Soderberg M, Singhal SK, Vomhof-DeKrey EE, Basson MD. Schlafen 12 Is Prognostically Favorable and Reduces C-Myc and Proliferation in Lung Adenocarcinoma but Not in Lung Squamous Cell Carcinoma. Cancers (Basel) 2020; 12:E2738. [PMID: 32987632 PMCID: PMC7650563 DOI: 10.3390/cancers12102738] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 09/21/2020] [Indexed: 02/06/2023] Open
Abstract
Schlafen 12 (SLFN12) is an intermediate human Schlafen that induces differentiation in enterocytes, prostate, and breast cancer. We hypothesized that SLFN12 influences lung cancer biology. We investigated survival differences in high versus low SLFN12-expressing tumors in two databases. We then adenovirally overexpressed SLFN12 (AdSLFN12) in HCC827, H23, and H1975 cells to model lung adenocarcinoma (LUAD), and in H2170 and HTB-182 cells representing lung squamous cell carcinoma (LUSC). We analyzed proliferation using a colorimetric assay, mRNA expression by RT-qPCR, and protein by Western blot. To further explore the functional relevance of SLFN12, we correlated SLFN12 with seventeen functional oncogenic gene signatures in human tumors. Low tumoral SLFN12 expression predicted worse survival in LUAD patients, but not in LUSC. AdSLFN12 modulated expression of SCGB1A1, SFTPC, HOPX, CK-5, CDH1, and P63 in a complex fashion in these cells. AdSLFN12 reduced proliferation in all LUAD cell lines, but not in LUSC cells. SLFN12 expression inversely correlated with expression of a myc-associated gene signature in LUAD, but not LUSC tumors. SLFN12 overexpression reduced c-myc protein in LUAD cell lines but not in LUSC, by inhibiting c-myc translation. Our results suggest SLFN12 improves prognosis in LUAD in part via a c-myc-dependent slowing of proliferation.
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Affiliation(s)
- Sarmad Al-Marsoummi
- Department of Biomedical Sciences, School of Medicine and the Health Sciences, University of North Dakota, Grand Forks, ND 58202, USA; (S.A.-M.); (J.P.); (K.D.); (M.S.); (E.E.V.-D.)
| | - Jonathan Pacella
- Department of Biomedical Sciences, School of Medicine and the Health Sciences, University of North Dakota, Grand Forks, ND 58202, USA; (S.A.-M.); (J.P.); (K.D.); (M.S.); (E.E.V.-D.)
| | - Kaylee Dockter
- Department of Biomedical Sciences, School of Medicine and the Health Sciences, University of North Dakota, Grand Forks, ND 58202, USA; (S.A.-M.); (J.P.); (K.D.); (M.S.); (E.E.V.-D.)
| | - Matthew Soderberg
- Department of Biomedical Sciences, School of Medicine and the Health Sciences, University of North Dakota, Grand Forks, ND 58202, USA; (S.A.-M.); (J.P.); (K.D.); (M.S.); (E.E.V.-D.)
| | - Sandeep K. Singhal
- Department of Pathology, School of Medicine and the Health Sciences, University of North Dakota, Grand Forks, ND 58202, USA;
| | - Emilie E. Vomhof-DeKrey
- Department of Biomedical Sciences, School of Medicine and the Health Sciences, University of North Dakota, Grand Forks, ND 58202, USA; (S.A.-M.); (J.P.); (K.D.); (M.S.); (E.E.V.-D.)
- Department of Surgery, School of Medicine and the Health Sciences, University of North Dakota, Grand Forks, ND 58202, USA
| | - Marc D. Basson
- Department of Biomedical Sciences, School of Medicine and the Health Sciences, University of North Dakota, Grand Forks, ND 58202, USA; (S.A.-M.); (J.P.); (K.D.); (M.S.); (E.E.V.-D.)
- Department of Pathology, School of Medicine and the Health Sciences, University of North Dakota, Grand Forks, ND 58202, USA;
- Department of Surgery, School of Medicine and the Health Sciences, University of North Dakota, Grand Forks, ND 58202, USA
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Zhao JW, Jiao L, Guo MM, Zheng L, Wang XB, Gao SH, Ying BW, Ming L. SFTPC genetic polymorphisms are associated with tuberculosis susceptibility and clinical phenotype in a Western Chinese Han population. Exp Ther Med 2020; 20:100. [PMID: 32973949 PMCID: PMC7507020 DOI: 10.3892/etm.2020.9230] [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: 01/30/2020] [Accepted: 08/19/2020] [Indexed: 02/05/2023] Open
Abstract
Tuberculosis (TB) is one of the most common infectious diseases globally. The surfactant protein C (SFTPC), which is involved in innate immunity and surfactant function in the lung, may contribute toward the progression of TB. The aim of the present study was to preliminarily investigate the possible association of single nucleotide polymorphisms (SNPs) in the SFTPC gene with TB susceptibility and clinical phenotypes in a Western Chinese Han population. The improved multiplex ligation detection reaction method was used to genotype 6 SNPs in SFTPC, in 900 patients with TB and 1,534 healthy control subjects. It was found that the A allele for rs1124 and the C allele for rs8192313 were associated with increased susceptibility to TB, P=0.024 and P=0.045, respectively. However, these two P-values were not significant following Bonferroni correction. In all samples, the haplotype [CGA], representing three SFTPC variants, was revealed to increase the risk of TB (P=0.001 and P=0.005, following Bonferroni correction). Furthermore, patients with the AA genotype for rs1124 and with the CC genotype for rs8192313 were associated with higher levels of C-reactive protein (P=0.001 and P=0.005, respectively). The results of the present study indicated that the SFTPC SNPs may increase the susceptibility to TB and the immune response of the host to Mycobacterium tuberculosis and may potentially be novel biomarkers for the pathogenesis of TB.
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Affiliation(s)
- Jun-Wei Zhao
- Department of Laboratory Medicine, The First Affiliated Hospital of Zhengzhou University, Key Clinical Laboratory of Henan Province, Zhengzhou, Henan 450052, P.R. China
| | - Lin Jiao
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Man-Man Guo
- Department of Laboratory Medicine, The First Affiliated Hospital of Zhengzhou University, Key Clinical Laboratory of Henan Province, Zhengzhou, Henan 450052, P.R. China
| | - Lei Zheng
- Department of Laboratory Medicine, The First Affiliated Hospital of Zhengzhou University, Key Clinical Laboratory of Henan Province, Zhengzhou, Henan 450052, P.R. China
| | - Xue-Bin Wang
- Department of Laboratory Medicine, The First Affiliated Hospital of Zhengzhou University, Key Clinical Laboratory of Henan Province, Zhengzhou, Henan 450052, P.R. China
| | - Shu-Hui Gao
- Department of Laboratory Medicine, The First Affiliated Hospital of Zhengzhou University, Key Clinical Laboratory of Henan Province, Zhengzhou, Henan 450052, P.R. China
| | - Bin-Wu Ying
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Liang Ming
- Department of Laboratory Medicine, The First Affiliated Hospital of Zhengzhou University, Key Clinical Laboratory of Henan Province, Zhengzhou, Henan 450052, P.R. China
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24
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Wang T, Zhai R, Lv X, Wang K, Xu J. LINC02418 promotes malignant behaviors in lung adenocarcinoma cells by sponging miR-4677-3p to upregulate KNL1 expression. BMC Pulm Med 2020; 20:217. [PMID: 32795273 PMCID: PMC7427971 DOI: 10.1186/s12890-020-01229-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 07/08/2020] [Indexed: 12/12/2022] Open
Abstract
Background Lung adenocarcinoma (LAD) is a prevalent type of bronchogenic malignant tumor and one of the most critical factors related to human death. Long noncoding RNAs (lncRNAs) are involved in many complex biological processes and have been emerged as extremely important regulators of various cancers. LINC02418, a novel lncRNA, hasn’t been mentioned in previous studies on cancer development. Therefore, it’s important to define the potential function of LINC02418 in LAD. Methods Gene expression was examined by RT-qPCR or western blot. CCK-8, colony formation, TUNEL, and transwell assays were utilized to study the role of LINC02418 in LAD. The interaction of miR-4677-3p with LINC02418 (or KNL1) was verified through luciferase reporter, RIP and RNA pull-down assays. Results High expression of LINC02418 was observed in LAD specimens and cells. Downregulation of LINC02418 obstructed the proliferation and motility of LAD cells. Moreover, LINC02418 negatively modulated miR-4677-3p expression and miR-4677-3p overexpression could repress cell proliferation and migration. Moreover, kinetochore scaffold 1 (KNL1) expression was negatively modulated by miR-4677-3p but positively regulated by LINC02418. Furthermore, miR-4677-3p could bind with LINC02418 (or KNL1). Finally, KNL1 overexpression reversed the inhibitory function of LINC02418 deficiency in the malignant behaviors of LAD cells. Conclusions LINC02418 contributes to the malignancy in LAD via miR-4677-3p/KNL1 signaling, providing a probable therapeutic direction for LAD.
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Affiliation(s)
- Tao Wang
- Department of Thoracic Surgery, The Second Affiliated Hospital of Air Force Medical University, Xi'an, 710038, Shaanxi, China
| | - Ruiren Zhai
- Department of Tumor Center, Sunshine Union Hospital, Weifang, 261000, Shandong, China
| | - Xiuhua Lv
- Department of Radiology, Xijing Hospital, Fourth Military Medical University, Xi'an, 710032, Shaanxi, China.
| | - Ke Wang
- Department of Radiology, Xijing Hospital, Fourth Military Medical University, Xi'an, 710032, Shaanxi, China
| | - Junqing Xu
- Department of Radiology, Shenzhen University General Hospital, Shenzhen University Clinical Medical Academy, No.1098 Xueyuan Avenue, Nanshan District, Shenzhen, 518055, Guangdong, China.
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25
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Li X, Ma N, Zhang Y, Wei H, Zhang H, Pang X, Li X, Wu D, Wang D, Yang Z, Zhang S. Circular RNA circNRIP1 promotes migration and invasion in cervical cancer by sponging miR-629-3p and regulating the PTP4A1/ERK1/2 pathway. Cell Death Dis 2020; 11:399. [PMID: 32457332 PMCID: PMC7251091 DOI: 10.1038/s41419-020-2607-9] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 05/13/2020] [Accepted: 05/14/2020] [Indexed: 01/14/2023]
Abstract
Emerging evidence indicates that circRNAs play essential roles in tumorigenesis and development. However, the role of circRNAs in cervical cancer (CC) remains unclear. CircRNA microarrays performed on the immortal cervical cell line H8 and the cervical cancer cell line SiHa were used to identify a circRNA, termed circNRIP1 (hsa_circ_0004771), which was upregulated in SiHa. QRT-PCR confirmed that circNRIP1 was upregulated in CC tissues, where its expression was correlated with lymphovascular space invasion. Besides, both in vitro and in vivo experiments demonstrated that circNRIP1 promotes cell proliferation, migration, and invasion. Additionally, we found that miR-629-3p induced tumor suppression by regulating PTP4A1 and the ERK1/2 pathway. Finally, we confirmed that circNRIP1 exerts its effect, at least partially, by sponging miR-629-3p and thereby regulating the PTP4A1/ERK1/2 pathway. Therefore, circNRIP1 may be useful as a potential prognostic biomarker and therapeutic target in CC patients.
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Affiliation(s)
- Xinhui Li
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, No. 36, Sanhao Street, Shenyang, Liaoning Province, China
| | - Ningye Ma
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, No. 36, Sanhao Street, Shenyang, Liaoning Province, China
| | - Yao Zhang
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, No. 36, Sanhao Street, Shenyang, Liaoning Province, China
| | - Heng Wei
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, No. 36, Sanhao Street, Shenyang, Liaoning Province, China
| | - Huijie Zhang
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, No. 36, Sanhao Street, Shenyang, Liaoning Province, China
| | - Xiaoao Pang
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, No. 36, Sanhao Street, Shenyang, Liaoning Province, China
| | - Xiang Li
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, No. 36, Sanhao Street, Shenyang, Liaoning Province, China
| | - Dan Wu
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, No. 36, Sanhao Street, Shenyang, Liaoning Province, China
| | - Dian Wang
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, No. 36, Sanhao Street, Shenyang, Liaoning Province, China
| | - Zhuo Yang
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, No. 36, Sanhao Street, Shenyang, Liaoning Province, China
| | - Shulan Zhang
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, No. 36, Sanhao Street, Shenyang, Liaoning Province, China.
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Chikuda J, Otsuka K, Shimomura I, Ito K, Miyazaki H, Takahashi RU, Nagasaki M, Mukudai Y, Ochiya T, Shimane T, Shirota T, Yamamoto Y. CD44s Induces miR-629-3p Expression in Association with Cisplatin Resistance in Head and Neck Cancer Cells. Cancers (Basel) 2020; 12:cancers12040856. [PMID: 32244823 PMCID: PMC7226407 DOI: 10.3390/cancers12040856] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 03/31/2020] [Indexed: 01/06/2023] Open
Abstract
Cisplatin (cis-diamminedichloroplatinum II [CDDP] ) is a well-known chemotherapeutic drug that has been used for the treatment of various types of human cancers, including head and neck cancer. Cisplatin exerts anticancer effects by causing DNA damage, replication defects, transcriptional inhibition, cell cycle arrest, and the induction of apoptosis. However, drug resistance is one of the most serious problems with cancer chemotherapy, and it causes expected therapeutic effects to not always be achieved. Here, we analyzed global microRNA (miRNA) expression in CD44 standard form (CD44s)-expressing SAS cells, and we identified miR-629-3p as being responsible for acquiring anticancer drug resistance in head and neck cancer. The introduction of miR-629-3p expression inhibited apoptotic cell death under cisplatin treatment conditions, and it promoted cell migration. Among the computationally predicted target genes of miR-629-3p, we found that a number of gene expressions were suppressed by the transfection with miR-629-3p. Using a xenografting model, we showed that miR-629-3p conferred cisplatin resistance to SAS cells. Clinically, increased miR-629-3p expression tended to be associated with decreased survival in head and neck cancer patients. In conclusion, our data suggest that the increased expression of miR-629-3p provides a mechanism of cisplatin resistance in head and neck cancer and may serve as a therapeutic target to reverse chemotherapy resistance.
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Affiliation(s)
- Junichiro Chikuda
- Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo 104-0045, Japan; (J.C.); or (I.S.); (K.I.); (H.M.); (T.O.)
- Department of Oral and Maxillofacial Surgery, Showa University School of Dentistry, Tokyo 145-8515, Japan; (M.N.); (Y.M.); (T.S.)
| | - Kurataka Otsuka
- Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo 104-0045, Japan; (J.C.); or (I.S.); (K.I.); (H.M.); (T.O.)
- R&D Division, Kewpie Corporation Sengawa Kewport, Choufu-shi, Tokyo 180-0002, Japan
| | - Iwao Shimomura
- Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo 104-0045, Japan; (J.C.); or (I.S.); (K.I.); (H.M.); (T.O.)
| | - Kagenori Ito
- Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo 104-0045, Japan; (J.C.); or (I.S.); (K.I.); (H.M.); (T.O.)
| | - Hiroaki Miyazaki
- Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo 104-0045, Japan; (J.C.); or (I.S.); (K.I.); (H.M.); (T.O.)
| | - Ryou-u Takahashi
- Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo 104-0045, Japan; (J.C.); or (I.S.); (K.I.); (H.M.); (T.O.)
- Department of Molecular Pathology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima 734-8553, Japan
| | - Masahiro Nagasaki
- Department of Oral and Maxillofacial Surgery, Showa University School of Dentistry, Tokyo 145-8515, Japan; (M.N.); (Y.M.); (T.S.)
| | - Yoshiki Mukudai
- Department of Oral and Maxillofacial Surgery, Showa University School of Dentistry, Tokyo 145-8515, Japan; (M.N.); (Y.M.); (T.S.)
| | - Takahiro Ochiya
- Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo 104-0045, Japan; (J.C.); or (I.S.); (K.I.); (H.M.); (T.O.)
- Department of Molecular and Cellular Medicine, Institute of Medical Science, Tokyo Medical University, Tokyo 160-0023, Japan
| | - Toshikazu Shimane
- Head and Neck Oncology Center, Showa University, Tokyo 142-8555, Japan;
| | - Tatsuo Shirota
- Department of Oral and Maxillofacial Surgery, Showa University School of Dentistry, Tokyo 145-8515, Japan; (M.N.); (Y.M.); (T.S.)
| | - Yusuke Yamamoto
- Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo 104-0045, Japan; (J.C.); or (I.S.); (K.I.); (H.M.); (T.O.)
- Correspondence: ; Tel.: +81-3-3542-2511
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Niemira M, Collin F, Szalkowska A, Bielska A, Chwialkowska K, Reszec J, Niklinski J, Kwasniewski M, Kretowski A. Molecular Signature of Subtypes of Non-Small-Cell Lung Cancer by Large-Scale Transcriptional Profiling: Identification of Key Modules and Genes by Weighted Gene Co-Expression Network Analysis (WGCNA). Cancers (Basel) 2019; 12:E37. [PMID: 31877723 PMCID: PMC7017323 DOI: 10.3390/cancers12010037] [Citation(s) in RCA: 165] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 12/16/2019] [Accepted: 12/19/2019] [Indexed: 12/11/2022] Open
Abstract
Non-small-cell lung cancer (NSCLC) represents a heterogeneous group of malignancies consisting essentially of adenocarcinoma (ADC) and squamous cell carcinoma (SCC). Although the diagnosis and treatment of ADC and SCC have been greatly improved in recent decades, there is still an urgent need to identify accurate transcriptome profile associated with the histological subtypes of NSCLC. The present study aims to identify the key dysregulated pathways and genes involved in the development of lung ADC and SCC and to relate them with the clinical traits. The transcriptional changes between tumour and normal lung tissues were investigated by RNA-seq. Gene ontology (GO), canonical pathways analysis with the prediction of upstream regulators, and weighted gene co-expression network analysis (WGCNA) to identify co-expressed modules and hub genes were used to explore the biological functions of the identified dysregulated genes. It was indicated that specific gene signatures differed significantly between ADC and SCC related to the distinct pathways. Of identified modules, four and two modules were the most related to clinical features in ADC and SCC, respectively. CTLA4, MZB1, NIP7, and BUB1B in ADC, as well as GNG11 and CCNB2 in SCC, are novel top hub genes in modules associated with tumour size, SUVmax, and recurrence-free survival. Our research provides a more effective understanding of the importance of biological pathways and the relationships between major genes in NSCLC in the perspective of searching for new molecular targets.
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Affiliation(s)
- Magdalena Niemira
- Clinical Research Centre, Medical University of Bialystok, 15-276 Bialystok, Poland; (A.S.); (A.B.); (A.K.)
| | - Francois Collin
- Centre for Bioinformatics and Data Analysis, Medical University of Bialystok, 15-276 Bialystok, Poland; (F.C.); (K.C.); (M.K.)
| | - Anna Szalkowska
- Clinical Research Centre, Medical University of Bialystok, 15-276 Bialystok, Poland; (A.S.); (A.B.); (A.K.)
| | - Agnieszka Bielska
- Clinical Research Centre, Medical University of Bialystok, 15-276 Bialystok, Poland; (A.S.); (A.B.); (A.K.)
| | - Karolina Chwialkowska
- Centre for Bioinformatics and Data Analysis, Medical University of Bialystok, 15-276 Bialystok, Poland; (F.C.); (K.C.); (M.K.)
| | - Joanna Reszec
- Department of Medical Pathomorphology, Medical University of Bialystok, 15-276 Bialystok, Poland;
| | - Jacek Niklinski
- Department of Clinical Molecular Biology, Medical University of Bialystok, 15-276 Bialystok, Poland;
| | - Miroslaw Kwasniewski
- Centre for Bioinformatics and Data Analysis, Medical University of Bialystok, 15-276 Bialystok, Poland; (F.C.); (K.C.); (M.K.)
| | - Adam Kretowski
- Clinical Research Centre, Medical University of Bialystok, 15-276 Bialystok, Poland; (A.S.); (A.B.); (A.K.)
- Department of Endocrinology, Diabetology and Internal Medicine, Medical University of Bialystok, 15-276 Bialystok, Poland
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Lv X, Shen J, Guo Z, Kong L, Zhou G, Ning H. Aberrant Expression of miR-592 Is Associated with Prognosis and Progression of Renal Cell Carcinoma. Onco Targets Ther 2019; 12:11231-11239. [PMID: 31908489 PMCID: PMC6927226 DOI: 10.2147/ott.s227834] [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: 08/19/2019] [Accepted: 11/05/2019] [Indexed: 01/17/2023] Open
Abstract
Purpose MicroRNAs have recently reported playing a vital role in the development of cancers. However, the role of miR-592 in renal cell carcinoma (RCC) has not been explored. In this study, the potential role of miR-592 was investigated in RCC. Patients and methods The expression of miR-592 was evaluated in RCC tissues and cell lines using qRT-PCR assays. The Kaplan-Meier analysis and Cox proportional hazards model analysis was used to analyze the prognostic value of miR-592 in RCC. The effects of miR-592 on cell proliferation, migration, and invasion were determined by cell counting kit-8 (CCK-8) and Transwell assays in vitro. Results The results showed that miR-592 was significantly increased both in RCC tissues and cell lines. Overexpression of miR-592 was significantly associated with lymph node metastasis, TNM stage, and poor overall survival. And functional studies in two RCC cell lines (786-O and Caki-1) have shown that overexpression of miR-592 promoted cell proliferation, migration, and invasion, while silence of miR-592 inhibited cell proliferation, migration, and invasion. SPRY2 was a direct target of miR-592. Conclusion Overall, overexpression of miR-592 may be a prognostic biomarker and therapeutic strategy for patients with RCC, which is correlated with the progression of RCC.
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Affiliation(s)
- Xianbao Lv
- Department of Urology, Chengwu People's Hospital, Heze, Shandong, 274200, People's Republic of China
| | - Jingang Shen
- Department of Urology, Chengwu People's Hospital, Heze, Shandong, 274200, People's Republic of China
| | - Zhen Guo
- Department of Urology, Central Hospital Affiliated Shandong First Medical University, Jinan, Shandong, 250033, People's Republic of China
| | - Lingwei Kong
- Department of Urology, Chengwu People's Hospital, Heze, Shandong, 274200, People's Republic of China
| | - Guangchun Zhou
- Department of Urology, Chengwu People's Hospital, Heze, Shandong, 274200, People's Republic of China
| | - Hao Ning
- Department of Urology, Shandong Provincial Hospital, Jinan, Shandong, 250021, People's Republic of China
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