1
|
Hou L, Li Z, Guo X, Lv J, Chong Z, Xiao Y, Zhang L, Li Z. ITGAM is a critical gene in ischemic stroke. Aging (Albany NY) 2024; 16:6852-6867. [PMID: 38637126 PMCID: PMC11087101 DOI: 10.18632/aging.205729] [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: 11/22/2023] [Accepted: 03/04/2024] [Indexed: 04/20/2024]
Abstract
BACKGROUND Globally, ischemic stroke (IS) is ranked as the second most prevailing cause of mortality and is considered lethal to human health. This study aimed to identify genes and pathways involved in the onset and progression of IS. METHODS GSE16561 and GSE22255 were downloaded from the Gene Expression Omnibus (GEO) database, merged, and subjected to batch effect removal using the ComBat method. The limma package was employed to identify the differentially expressed genes (DEGs), followed by enrichment analysis and protein-protein interaction (PPI) network construction. Afterward, the cytoHubba plugin was utilized to screen the hub genes. Finally, a ROC curve was generated to investigate the diagnostic value of hub genes. Validation analysis through a series of experiments including qPCR, Western blotting, TUNEL, and flow cytometry was performed. RESULTS The analysis incorporated 59 IS samples and 44 control samples, revealing 226 DEGs, of which 152 were up-regulated and 74 were down-regulated. These DEGs were revealed to be linked with the inflammatory and immune responses through enrichment analyses. Overall, the ROC analysis revealed the remarkable diagnostic potential of ITGAM and MMP9 for IS. Quantitative assessment of these genes showed significant overexpression in IS patients. ITGAM modulation influenced the secretion of critical inflammatory cytokines, such as IL-1β, IL-6, and TNF-α, and had a distinct impact on neuronal apoptosis. CONCLUSIONS The inflammation and immune response were identified as potential pathological mechanisms of IS by bioinformatics and experiments. In addition, ITGAM may be considered a potential therapeutic target for IS.
Collapse
Affiliation(s)
- Lei Hou
- Department of Neurosurgery, Qilu Hospital of Shandong University, Jinan 250012, Shandong Province, P.R. China
- Department of Neurosurgery, Liaocheng People’s Hospital, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Liaocheng 252000, Shandong Province, P.R. China
| | - Zhongchen Li
- Department of Neurosurgery, Liaocheng People’s Hospital, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Liaocheng 252000, Shandong Province, P.R. China
| | - Xiaoli Guo
- Department of Pediatrics, Liaocheng People’s Hospital, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Liaocheng 252000, Shandong Province, P.R. China
| | - Jiatao Lv
- Department of Neurosurgery, Liaocheng People’s Hospital, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Liaocheng 252000, Shandong Province, P.R. China
| | - Zonglei Chong
- Department of Neurosurgery, Liaocheng People’s Hospital, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Liaocheng 252000, Shandong Province, P.R. China
| | - Yilei Xiao
- Department of Neurosurgery, Liaocheng People’s Hospital, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Liaocheng 252000, Shandong Province, P.R. China
| | - Liyong Zhang
- Department of Neurosurgery, Liaocheng People’s Hospital, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Liaocheng 252000, Shandong Province, P.R. China
| | - Zefu Li
- Department of Neurosurgery, Qilu Hospital of Shandong University, Jinan 250012, Shandong Province, P.R. China
- Department of Neurosurgery, Binzhou Medical University Hospital, Binzhou Medical University, Binzhou 256603, Shandong Province, P.R. China
| |
Collapse
|
2
|
Hijazo-Pechero S, Alay A, Marín R, Vilariño N, Muñoz-Pinedo C, Villanueva A, Santamaría D, Nadal E, Solé X. Gene Expression Profiling as a Potential Tool for Precision Oncology in Non-Small Cell Lung Cancer. Cancers (Basel) 2021; 13:4734. [PMID: 34638221 PMCID: PMC8507534 DOI: 10.3390/cancers13194734] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 09/13/2021] [Indexed: 01/20/2023] Open
Abstract
Recent technological advances and the application of high-throughput mutation and transcriptome analyses have improved our understanding of cancer diseases, including non-small cell lung cancer. For instance, genomic profiling has allowed the identification of mutational events which can be treated with specific agents. However, detection of DNA alterations does not fully recapitulate the complexity of the disease and it does not allow selection of patients that benefit from chemo- or immunotherapy. In this context, transcriptional profiling has emerged as a promising tool for patient stratification and treatment guidance. For instance, transcriptional profiling has proven to be especially useful in the context of acquired resistance to targeted therapies and patients lacking targetable genomic alterations. Moreover, the comprehensive characterization of the expression level of the different pathways and genes involved in tumor progression is likely to better predict clinical benefit from different treatments than single biomarkers such as PD-L1 or tumor mutational burden in the case of immunotherapy. However, intrinsic technical and analytical limitations have hindered the use of these expression signatures in the clinical setting. In this review, we will focus on the data reported on molecular classification of non-small cell lung cancer and discuss the potential of transcriptional profiling as a predictor of survival and as a patient stratification tool to further personalize treatments.
Collapse
Affiliation(s)
- Sara Hijazo-Pechero
- Unit of Bioinformatics for Precision Oncology, Catalan Institute of Oncology (ICO), L’Hospitalet de Llobregat, 08908 Barcelona, Spain; (S.H.-P.); (A.A.); (R.M.)
- Preclinical and Experimental Research in Thoracic Tumors (PrETT), Molecular Mechanisms and Experimental Therapy in Oncology Program (Oncobell), Bellvitge Biomedical Research Institute (IDIBELL), L’Hospitalet de Llobregat, 08908 Barcelona, Spain; (N.V.); (C.M.-P.)
| | - Ania Alay
- Unit of Bioinformatics for Precision Oncology, Catalan Institute of Oncology (ICO), L’Hospitalet de Llobregat, 08908 Barcelona, Spain; (S.H.-P.); (A.A.); (R.M.)
- Preclinical and Experimental Research in Thoracic Tumors (PrETT), Molecular Mechanisms and Experimental Therapy in Oncology Program (Oncobell), Bellvitge Biomedical Research Institute (IDIBELL), L’Hospitalet de Llobregat, 08908 Barcelona, Spain; (N.V.); (C.M.-P.)
| | - Raúl Marín
- Unit of Bioinformatics for Precision Oncology, Catalan Institute of Oncology (ICO), L’Hospitalet de Llobregat, 08908 Barcelona, Spain; (S.H.-P.); (A.A.); (R.M.)
- Preclinical and Experimental Research in Thoracic Tumors (PrETT), Molecular Mechanisms and Experimental Therapy in Oncology Program (Oncobell), Bellvitge Biomedical Research Institute (IDIBELL), L’Hospitalet de Llobregat, 08908 Barcelona, Spain; (N.V.); (C.M.-P.)
| | - Noelia Vilariño
- Preclinical and Experimental Research in Thoracic Tumors (PrETT), Molecular Mechanisms and Experimental Therapy in Oncology Program (Oncobell), Bellvitge Biomedical Research Institute (IDIBELL), L’Hospitalet de Llobregat, 08908 Barcelona, Spain; (N.V.); (C.M.-P.)
- Thoracic Oncology Unit, Department of Medical Oncology, Catalan Institute of Oncology (ICO), L’Hospitalet de Llobregat, 08908 Barcelona, Spain
- Neuro-Oncology Unit, Hospital Universitari de Bellvitge-ICO L’Hospitalet (IDIBELL), 08908 Barcelona, Spain
| | - Cristina Muñoz-Pinedo
- Preclinical and Experimental Research in Thoracic Tumors (PrETT), Molecular Mechanisms and Experimental Therapy in Oncology Program (Oncobell), Bellvitge Biomedical Research Institute (IDIBELL), L’Hospitalet de Llobregat, 08908 Barcelona, Spain; (N.V.); (C.M.-P.)
| | - Alberto Villanueva
- Program Against Cancer Therapeutic Resistance (ProCURE), Catalan Institute of Oncology (ICO), Bellvitge Biomedical Research Institute (IDIBELL), L’Hospitalet de Llobregat, 08908 Barcelona, Spain;
| | - David Santamaría
- INSERM U1218, ACTION Laboratory, Institut Européen de Chimie et Biologie (IECB), Université de Bordeaux, F-33607 Pessac, France;
| | - Ernest Nadal
- Preclinical and Experimental Research in Thoracic Tumors (PrETT), Molecular Mechanisms and Experimental Therapy in Oncology Program (Oncobell), Bellvitge Biomedical Research Institute (IDIBELL), L’Hospitalet de Llobregat, 08908 Barcelona, Spain; (N.V.); (C.M.-P.)
- Thoracic Oncology Unit, Department of Medical Oncology, Catalan Institute of Oncology (ICO), L’Hospitalet de Llobregat, 08908 Barcelona, Spain
| | - Xavier Solé
- Unit of Bioinformatics for Precision Oncology, Catalan Institute of Oncology (ICO), L’Hospitalet de Llobregat, 08908 Barcelona, Spain; (S.H.-P.); (A.A.); (R.M.)
- Preclinical and Experimental Research in Thoracic Tumors (PrETT), Molecular Mechanisms and Experimental Therapy in Oncology Program (Oncobell), Bellvitge Biomedical Research Institute (IDIBELL), L’Hospitalet de Llobregat, 08908 Barcelona, Spain; (N.V.); (C.M.-P.)
- CIBER (Consorcio de Investigación Biomédica en Red) Epidemiologia y Salud Pública (CIBERESP), 28029 Madrid, Spain
| |
Collapse
|
3
|
Chen H, Lu C, Lin C, Li L, Wang Y, Han R, Hu C, He Y. VPS34 suppression reverses osimertinib resistance via simultaneously inhibiting glycolysis and autophagy. Carcinogenesis 2021; 42:880-890. [PMID: 33848354 DOI: 10.1093/carcin/bgab030] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 03/24/2021] [Accepted: 04/09/2021] [Indexed: 12/11/2022] Open
Abstract
Autophagy and glycolysis are associated with osimertinib resistance. The energy complement and dynamic balance between these two processes make it difficult to block the process of drug resistance; breaking the complementary relationship between them may effectively overcome drug resistance. However, the exact mechanisms and the key players for regulating autophagy and glycolysis remain unclear. In this study, we demonstrate that autophagy and glycolysis levels in osimertinib-resistant cells were markedly higher than parental cells, and a dynamic balance existed between them. Inhibition of the class III phosphoinositide 3-kinase vacuolar protein sorting 34 (VPS34) with 3-methyladenine or small interfering RNA can not only inhibit abnormally enhanced autophagy but also inhibit glycolysis by inhibiting the location of epidermal growth factor receptor (EGFR) and the expression of hexokinase II. By demonstrating that VPS34 is the key player controlling autophagy and glycolysis simultaneously, our study may provide a new strategy for overcoming osimertinib resistance for treatment of EGFR-mutant non-small cell lung cancer patients.
Collapse
Affiliation(s)
- Hengyi Chen
- Department of Respiratory Disease, Daping Hospital, Army Medical University, Chongqing, China
| | - Conghua Lu
- Department of Respiratory Disease, Daping Hospital, Army Medical University, Chongqing, China
| | - Caiyu Lin
- Department of Respiratory Disease, Daping Hospital, Army Medical University, Chongqing, China
| | - Li Li
- Department of Respiratory Disease, Daping Hospital, Army Medical University, Chongqing, China
| | - Yubo Wang
- Department of Respiratory Disease, Daping Hospital, Army Medical University, Chongqing, China
| | - Rui Han
- Department of Respiratory Disease, Daping Hospital, Army Medical University, Chongqing, China
| | - Chen Hu
- Department of Respiratory Disease, Daping Hospital, Army Medical University, Chongqing, China
| | - Yong He
- Department of Respiratory Disease, Daping Hospital, Army Medical University, Chongqing, China
| |
Collapse
|
4
|
Wu L, Wan S, Li J, Xu Y, Lou X, Sun M, Wang S. Expression and prognostic value of E2F3 transcription factor in non-small cell lung cancer. Oncol Lett 2021; 21:411. [PMID: 33841572 PMCID: PMC8020386 DOI: 10.3892/ol.2021.12672] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 01/20/2021] [Indexed: 12/20/2022] Open
Abstract
E2F transcription factor 3 (E2F3) plays a vital role in the development of various types of cancer. To verify whether E2F3 is a suitable biomarker for the prognosis of lung cancer, bioinformatics analysis was performed to determine the differential expression level of E2F3 in lung cancer and the surrounding non-tumor tissues, and the results were confirmed in a NSCLC cell line and a tissue microarray (TMA). The relevance of E2F3 in non-small cell lung cancer (NSCLC) was investigated in 19 studies from the Oncomine database and confirmed in The Cancer Genome Atlas database. In the lung cancer cell line A549, the inhibition of E2F3 mRNA expression level led to decreased tumor cell viability and cell migration, which was determined by a Cell Counting Kit-8 and wound healing assays, respectively. Immunohistochemistry analyses of E2F3, Bcl-2, Bax and caspase-3 were performed in the NSCLC TMA (n=50). The assessment of TMA detected the increase of E2F3 protein expression level in the tumor tissues, as compared with that in the non-tumor tissues, which was also correlated with the increase in expression of Bcl-2 in tumors. Analysis of the clinical data from patients with NSCLC revealed that the overexpression of E2F3 was associated with early lymphatic spreading, and poor patient survival time. The OncomiR website was used to predict the E2F3 upstream microRNAs and determine their prognostic value in patients with NSCLC. The results from the present study revealed that E2F3 was overexpressed at both the transcriptional and translational levels in NSCLC tissues, as compared with that in non-tumor tissues. The overexpression of E2F3 was associated with the upregulation of the anti-apoptotic factor, Bcl-2, which may contribute to uncontrolled tumor growth. Thus, E2F3 was shown to have important oncogenic properties in the development of NSCLC, and it may become a potential biomarker for patients with NSCLC.
Collapse
Affiliation(s)
- Lei Wu
- Department of Pathology, School of Biology and Basic Medical Sciences, Soochow University, Suzhou, Jiangsu 215123, P.R. China
| | - Shan Wan
- Department of Pathology, School of Biology and Basic Medical Sciences, Soochow University, Suzhou, Jiangsu 215123, P.R. China
| | - Jinfan Li
- Department of Pathology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, P.R. China.,Department of Collaborative Innovation Center of Clinical Immunology between Soochow University and Sihong People's Hospital, Sihong, Jiangsu 223900, P.R. China
| | - Yiying Xu
- Department of Pathology, School of Biology and Basic Medical Sciences, Soochow University, Suzhou, Jiangsu 215123, P.R. China
| | - Xiaoli Lou
- Department of Pathology, School of Biology and Basic Medical Sciences, Soochow University, Suzhou, Jiangsu 215123, P.R. China
| | - Maomin Sun
- Laboratory Animal Research Center, Soochow University School of Medicine, Suzhou, Jiangsu 215123, P.R. China
| | - Shouli Wang
- Department of Pathology, School of Biology and Basic Medical Sciences, Soochow University, Suzhou, Jiangsu 215123, P.R. China.,Department of Collaborative Innovation Center of Clinical Immunology between Soochow University and Sihong People's Hospital, Sihong, Jiangsu 223900, P.R. China
| |
Collapse
|
5
|
Bommu U, Konidala KK, Pabbaraju N, Yeguvapalli S. Gene microarray expression profile analysis of differentially expressed genes of potential alternative pathways in non–small cell lung cancer: In search of biomarkers. GENE REPORTS 2020. [DOI: 10.1016/j.genrep.2020.100633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
|
6
|
Shah RR, Shah DR. Safety and Tolerability of Epidermal Growth Factor Receptor (EGFR) Tyrosine Kinase Inhibitors in Oncology. Drug Saf 2019; 42:181-198. [PMID: 30649743 DOI: 10.1007/s40264-018-0772-x] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Tyrosine kinase inhibitors (TKIs) that target epidermal growth factor receptor (EGFR) have dramatically improved progression-free survival in non-small-cell lung cancer (NSCLC) patients who carry sensitizing EGFR-activating mutations and in patients with breast and pancreatic cancers. However, EGFR-TKIs are associated with significant and disabling undesirable effects that adversely impact on quality of life and compliance. These effects include dermatological reactions, diarrhoea, hepatotoxicity, stomatitis, interstitial lung disease and ocular toxicity. Each individual EGFR-TKI is also associated with additional adverse effect(s) that are not shared widely by the other members of its class. Often, these effects call for dose reduction, treatment discontinuation or pharmacotherapeutic intervention. Since dermatological effects result from on-target effects on wild-type EGFR, rash is often considered to be a biomarker of efficacy. A number of studies have reported better outcomes in patients with skin reactions compared with those without. This has led to a 'dosing-to-rash' strategy to optimize therapeutic outcomes. Although conceptually attractive, there is currently insufficient evidence-based support for this strategy. While skin reactions following EGFR-TKIs are believed to result from an effect on wild-type EGFR, their efficacy is related to effects on mutant variants of EGFR. It is noteworthy that newer EGFR-TKIs that spare wild-type EGFR are associated with fewer dermatological reactions. Furthermore, secondary mutations such as T790M in exon 20 often lead to development of resistance to the clinical activity and efficacy of first- and second-generation EGFR-TKIs. This has stimulated the search for later-generations of EGFR-TKIs with the ability to overcome this resistance and with greater target selectivity to spare wild-type EGFR in expectations of an improved safety profile. However, available data reviewed herein indicate that not only are these newer agents associated with the aforementioned adverse effects typical of earlier agents, but they are also susceptible to resistance due to tertiary mutations, most frequently C797S. At least three later-generation EGFR-TKIs, canertinib, naquotinib and rociletinib, have been discontinued from further development in NSCLC following concerns about their safety and risk/benefit.
Collapse
|
7
|
Wang H, Xie Q, Ou-Yang W, Zhang M. Integrative analyses of genes associated with idiopathic pulmonary fibrosis. J Cell Biochem 2019; 120:8648-8660. [PMID: 30506760 DOI: 10.1002/jcb.28153] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 11/09/2018] [Indexed: 01/24/2023]
Abstract
Idiopathic pulmonary fibrosis (IPF), characterized by irreversible scarring and progressive destruction of the lung tissue, is one of the most common types of idiopathic interstitial pneumonia worldwide. However, there are no reliable candidates for curative therapies. Hence, elucidation of the mechanisms of IPF genesis and exploration of potential biomarkers and prognostic indicators are essential for accurate diagnosis and treatment of IPF. Recently, efficient microarray and bioinformatics analyses have promoted an understanding of the molecular mechanisms of disease occurrence and development, which is necessary to explore genetic alternations and identify potential diagnostic biomarkers. However, high false-positive rates results have been observed based on single microarray datasets. In the current study, we performed a comprehensive analysis of the differential expression, biological functions, and interactions of IPF-related genes. Three publicly available microarray datasets including 54 IPF samples and 34 normal samples were integrated by performing gene set enrichment analysis and analyzing differentially expressed genes (DEGs). Our results identified 350 DEGs genetically associated with IPF. Gene ontology analyses revealed that the changes in the modules were mostly enriched in the positive regulation of smooth muscle cell proliferation, positive regulation of inflammatory responses, and the extracellular space. Kyoto encyclopedia of genes and genomes enrichment analysis of DEGs revealed that IPF involves the TNF signaling pathway, NOD-like receptor signaling pathway, and PPAR signaling pathway. To identify key genes related to IPF in the protein-protein interaction network, 20 hub genes were screened out with highest scores. Our results provided a framework for developing new pathological molecular networks related to specific diseases in silico.
Collapse
Affiliation(s)
- Huimei Wang
- Department of Integrative Medicine and Neurobiology, State Key Laboratory of Medical Neurobiology, Institute of Brain Science, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, PR China
| | - Qiqi Xie
- Department of Orthopaedics, Second Hospital of Lanzhou University, Lanzhou, Gansu, PR China
| | - Wen Ou-Yang
- The Second Clinical Medical College, Zhujiang Hospital, Southern Medical University, Guangzhou, PR China
| | - Mingwei Zhang
- Department of Radiotherapy, First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, PR China
| |
Collapse
|