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Zhou HY, Wang YC, Wang T, Wu W, Cao YY, Zhang BC, Wang MD, Mao P. CCNA2 and NEK2 regulate glioblastoma progression by targeting the cell cycle. Oncol Lett 2024; 27:206. [PMID: 38516683 PMCID: PMC10956385 DOI: 10.3892/ol.2024.14339] [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: 09/19/2023] [Accepted: 02/05/2024] [Indexed: 03/23/2024] Open
Abstract
Glioblastoma (GBM) is characterized by significant heterogeneity, leading to poor survival outcomes for patients, despite the implementation of comprehensive treatment strategies. The roles of cyclin A2 (CCNA2) and NIMA related kinase 2 (NEK2) have been extensively studied in numerous cancers, but their specific functions in GBM remain to be elucidated. The present study aimed to investigate the potential molecular mechanisms of CCNA2 and NEK2 in GBM. CCNA2 and NEK2 expression and prognosis in glioma were evaluated by bioinformatics methods. In addition, the distribution of CCNA2 and NEK2 expression in GBM subsets was determined using pseudo-time analysis and tricycle position of single-cell sequencing. Gene Expression Omnibus and Kyoto Encyclopedia of Genes and Genome databases were employed and enrichment analyses were conducted to investigate potential signaling pathways in GBM subsets and a nomogram was established to predict 1-, 2- and 3-year overall survival probability in GBM. CCNA2 and NEK2 expression levels were further validated by western blot analysis and immunohistochemical staining in GBM samples. High expression of CCNA2 and NEK2 in glioma indicates poor clinical outcomes. Single-cell sequencing of GBM revealed that these genes were upregulated in a subset of positive neural progenitor cells (P-NPCs), which showed significant proliferation and progression properties and may activate G2M checkpoint pathways. A comprehensive nomogram predicts 1-, 2- and 3-year overall survival probability in GBM by considering P-NPCs, age, chemotherapy and radiotherapy scores. CCNA2 and NEK2 regulate glioblastoma progression by targeting the cell cycle, thus indicating the potential of novel therapy directed to CCNA2 and NEK2 in GBM.
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Affiliation(s)
- Hao-Yu Zhou
- Department of Neurosurgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
| | - Yi-Chang Wang
- Department of Neurosurgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
| | - Tuo Wang
- Department of Neurosurgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
| | - Wei Wu
- Department of Neurosurgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
| | - Yi-Yang Cao
- Department of Neurosurgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
| | - Bei-Chen Zhang
- Department of Neurosurgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
| | - Mao-De Wang
- Department of Neurosurgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
| | - Ping Mao
- Department of Neurosurgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
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Chen L, Xin G, He Y, Tian Q, Kong X, Fu Y, Wang J, Zhang H, Wang L. Study of molecular patterns associated with ferroptosis in Parkinson's disease and its immune signature. PLoS One 2023; 18:e0295699. [PMID: 38127902 PMCID: PMC10734959 DOI: 10.1371/journal.pone.0295699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Accepted: 11/27/2023] [Indexed: 12/23/2023] Open
Abstract
Parkinson's disease is the second most common neurodegenerative disease in the world. We downloaded data on Parkinson's disease and Ferroptosis-related genes from the GEO and FerrDb databases. We used WCGAN and Random Forest algorithm to screen out five Parkinson's disease ferroptosis-related hub genes. Two genes were identified for the first time as possibly playing a role in Braak staging progression. Unsupervised clustering analysis based on hub genes yielded ferroptosis isoforms, and immune infiltration analysis indicated that these isoforms are associated with immune cells and may represent different immune patterns. FRHGs scores were obtained to quantify the level of ferroptosis modifications in each individual. In addition, differences in interleukin expression were found between the two ferroptosis subtypes. The biological functions involved in the hub gene are analyzed. The ceRNA regulatory network of hub genes was mapped. The disease classification diagnosis model and risk prediction model were also constructed by applying hub genes based on logistic regression. Multiple external datasets validated the hub gene and classification diagnostic model with some accuracy. This study explored hub genes associated with ferroptosis in Parkinson's disease and their molecular patterns and immune signatures to provide new ideas for finding new targets for intervention and predictive biomarkers.
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Affiliation(s)
- Lixia Chen
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, City Harbin, Province Heilongjiang, China
| | - Guanghao Xin
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, City Harbin, Province Heilongjiang, China
| | - Yijie He
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, City Harbin, Province Heilongjiang, China
| | - Qinghua Tian
- Department of Neurology, The 962 Hospital of the Chinese People’s Liberation Army Joint Logistic Support Force, City Harbin, Province Heilongjiang, China
| | - Xiaotong Kong
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, City Harbin, Province Heilongjiang, China
| | - Yanchi Fu
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, City Harbin, Province Heilongjiang, China
| | - Jianjian Wang
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, City Harbin, Province Heilongjiang, China
| | - Huixue Zhang
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, City Harbin, Province Heilongjiang, China
| | - Lihua Wang
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, City Harbin, Province Heilongjiang, China
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Martins S, Coletti R, Lopes MB. Disclosing transcriptomics network-based signatures of glioma heterogeneity using sparse methods. BioData Min 2023; 16:26. [PMID: 37752578 PMCID: PMC10523751 DOI: 10.1186/s13040-023-00341-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 08/13/2023] [Indexed: 09/28/2023] Open
Abstract
Gliomas are primary malignant brain tumors with poor survival and high resistance to available treatments. Improving the molecular understanding of glioma and disclosing novel biomarkers of tumor development and progression could help to find novel targeted therapies for this type of cancer. Public databases such as The Cancer Genome Atlas (TCGA) provide an invaluable source of molecular information on cancer tissues. Machine learning tools show promise in dealing with the high dimension of omics data and extracting relevant information from it. In this work, network inference and clustering methods, namely Joint Graphical lasso and Robust Sparse K-means Clustering, were applied to RNA-sequencing data from TCGA glioma patients to identify shared and distinct gene networks among different types of glioma (glioblastoma, astrocytoma, and oligodendroglioma) and disclose new patient groups and the relevant genes behind groups' separation. The results obtained suggest that astrocytoma and oligodendroglioma have more similarities compared with glioblastoma, highlighting the molecular differences between glioblastoma and the others glioma subtypes. After a comprehensive literature search on the relevant genes pointed our from our analysis, we identified potential candidates for biomarkers of glioma. Further molecular validation of these genes is encouraged to understand their potential role in diagnosis and in the design of novel therapies.
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Affiliation(s)
- Sofia Martins
- NOVA School of Science and Technology, NOVA University of Lisbon, Caparica, 2829-516, Portugal
| | - Roberta Coletti
- Center for Mathematics and Applications (NOVA Math), NOVA School of Science and Technology, Caparica, 2829-516, Portugal.
| | - Marta B Lopes
- NOVA School of Science and Technology, NOVA University of Lisbon, Caparica, 2829-516, Portugal.
- Center for Mathematics and Applications (NOVA Math), NOVA School of Science and Technology, Caparica, 2829-516, Portugal.
- NOVA Laboratory for Computer Science and Informatics (NOVA LINCS), NOVA School of Science and Technology, Caparica, 2829-516, Portugal.
- UNIDEMI, Department of Mechanical and Industrial Engineering, NOVA School of Science and Technology, Caparica, 2829-516, Portugal.
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Yang S, Yi L, Xia X, Chen X, Hou X, Zhang L, Yang F, Liao J, Han Z, Fu Y. Transcriptome comparative analysis of amygdala-hippocampus in depression: A rat model induced by chronic unpredictable mild stress (CUMS). J Affect Disord 2023; 334:258-270. [PMID: 37105469 DOI: 10.1016/j.jad.2023.04.074] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 04/11/2023] [Accepted: 04/16/2023] [Indexed: 04/29/2023]
Abstract
BACKGROUND Depression is a common and complex mental disease, and its pathogenesis involves several brain regions. Abnormalities in the amygdala-hippocampal neural circuits have been shown to be involved in depression. However, the underlying molecular mechanisms remain unclear. METHODS A rat model was used to determine the transcriptome changes in the amygdala-hippocampal neural network under chronic unpredictable mild stress (CUMS). Depression-related modules in this neural network were identified using weighted gene co-expression network analysis (WGCNA). Difference and enrichment analyses were used to determine differential gene expression in the two brain regions. RESULTS The modules in the amygdala and hippocampus associated with depression-like behavior contained 363 and 225 genes, respectively. Forty-two differentially expressed genes were identified in the amygdala candidate module and 37 in the hippocampus. Enrichment analysis showed that candidate genes in the amygdala were associated with neuronal myelination and candidate genes in the hippocampus were associated with synaptic transmission. Finally, based on module hub gene statistics, differential gene expression, and protein-protein interaction networks, 11 central genes were found in the amygdala candidate module, and one central gene was found in the hippocampal module. LIMITATIONS Our study was based on a rat CUMS model. Further evidence is needed to prove that our results are applicable to patients with depression. CONCLUSION This study identified critical modules and central genes involved in the amygdala-hippocampal circuit in the context of depression, and may provide further understanding of the pathogenesis of depression and help identify potential targets for antidepressant therapy.
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Affiliation(s)
- Shu Yang
- Department of Psychiatry, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Li Yi
- Department of Psychiatry, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Xiaodi Xia
- Department of Psychiatry, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Xiaolu Chen
- The First Branch, the First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Xiao Hou
- Department of Clinical Medicine, Chongqing Medical and Pharmaceutical College, Chongqing 401331, China
| | - Longjie Zhang
- Department of Pharmacy, School of Pharmacy, Chongqing Medical University, Chongqing 400016, China
| | - Fang Yang
- Department of pharmacology, School of Pharmacy, Chongqing Medical University, Chongqing 400016, China
| | - Jiaxin Liao
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Zhijie Han
- Department of Bioinformatics, School of Basic Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Yixiao Fu
- Department of Psychiatry, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China.
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Han S, Zhang Z, Ma W, Gao J, Li Y. Nucleotide-Binding Oligomerization Domain (NOD)-Like Receptor Subfamily C (NLRC) as a Prognostic Biomarker for Glioblastoma Multiforme Linked to Tumor Microenvironment: A Bioinformatics, Immunohistochemistry, and Machine Learning-Based Study. J Inflamm Res 2023; 16:523-537. [PMID: 36798872 PMCID: PMC9926983 DOI: 10.2147/jir.s397305] [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: 11/19/2022] [Accepted: 02/03/2023] [Indexed: 02/12/2023] Open
Abstract
Purpose Glioblastoma multiforme (GBM) remains the deadliest primary brain tumor. We aimed to illuminate the role of nucleotide-binding oligomerization domain (NOD)-like receptor subfamily C (NLRC) in GBM. Patients and Methods Based on public database data (mainly The Cancer Genome Atlas [TCGA]), we performed bioinformatics analysis to visually evaluate the role and mechanism of NLRCs in GBM. Then, we validated our findings in a glioma tissue microarray (TMA) by immunohistochemistry (IHC), and the prognostic value of NOD1 was assessed via random forest (RF) models. Results In GBM tissues, the expression of NLRC members was significantly increased, which was related to the low survival rate of GBM. Additionally, Cox regression analysis revealed that the expression of NOD1 (among NLRCs) served as an independent prognostic marker. A nomogram based on multivariate analysis proved the effective predictive performance of NOD1 in GBM. Enrichment analysis showed that high expression of NOD1 could regulate extracellular structure, cell adhesion, and immune response to promote tumor progression. Then, immune infiltration analysis showed that NOD1 overexpression correlated with an enhanced immune response. Then, in a glioma TMA, the results of IHC revealed that the increase in NOD1 expression indicated high recurrence and poor prognosis of human glioma. Furthermore, the expression level of NOD1 showed good prognostic value in the TMA cohort via RF. Conclusion The value of NOD1 as a biomarker for GBM was demonstrated. The possible mechanisms may lie in the regulatory role of NLRC-related pathways in the tumor microenvironment.
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Affiliation(s)
- Shiyuan Han
- Department of Neurosurgery, Chinese Academy of Medical Sciences and Peking Union Medical College, Peking Union Medical College Hospital (Dongdan Campus), Beijing, People’s Republic of China
| | - Zimu Zhang
- Department of General Surgery, Chinese Academy of Medical Sciences and Peking Union Medical College, Peking Union Medical College Hospital (Dongdan Campus), Beijing, People’s Republic of China
| | - Wenbin Ma
- Department of Neurosurgery, Chinese Academy of Medical Sciences and Peking Union Medical College, Peking Union Medical College Hospital (Dongdan Campus), Beijing, People’s Republic of China
| | - Jun Gao
- Department of Neurosurgery, Chinese Academy of Medical Sciences and Peking Union Medical College, Peking Union Medical College Hospital (Dongdan Campus), Beijing, People’s Republic of China
| | - Yongning Li
- Department of Neurosurgery, Chinese Academy of Medical Sciences and Peking Union Medical College, Peking Union Medical College Hospital (Dongdan Campus), Beijing, People’s Republic of China,Department of International Medical Service, Chinese Academy of Medical Sciences and Peking Union Medical College, Peking Union Medical College Hospital (Dongdan campus), Beijing, People’s Republic of China,Correspondence: Yongning Li, Department of Neurosurgery and Department of International Medical Service, Chinese Academy of Medical Sciences and Peking Union Medical College, Peking Union Medical College Hospital (Dongdan campus), No. 1 Shuaifuyuan Wangfujing Dongcheng District, Beijing, People’s Republic of China, Tel +86 13901074129, Fax +86 1069152530, Email
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Investigating Key Targets of Dajianzhong Decoction for Treating Crohn’s Disease Using Weighted Gene Co-Expression Network. Processes (Basel) 2022. [DOI: 10.3390/pr11010112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Background: Crohn’s disease (CD) is an inflammatory bowel disease, cases of which have substantially increased in recent years. The classical formula Dajianzhong decoction (DD, Japanese: Daikenchuto) is often used to treat CD, but few studies have evaluated related therapeutic mechanisms. In this study, we investigated the potential targets and mechanisms of DD used for treating CD at the molecular level through the weighted gene co-expression network. Methods: The main chemical components of the three DD herbs (Zanthoxylum bungeanum Maxim., Zingiber officinale (Willd.) Rosc., and Ginseng Radix et Rhizoma) were searched for using the HERB database. The targets for each component were identified using the SwissTargetPrediction and HERB databases, whereas the disease targets for CD were retrieved from the GeneCards and DisGeNET databases. The functional enrichment analysis was performed on the common targets of DD and CD. High-throughput sequencing data for CD patients were retrieved from the Gene Expression Omnibus database, and WGCNA was performed to identify the key targets. The association between the key targets and DD ingredients was verified using molecular docking. Results: By analyzing the interaction targets between DD and CD, 196 overlapping genes were identified. The enrichment results indicated that the PI3K-AKT, TNF, MAPK, and IL-17 signaling pathways influenced the mechanism of action of DD in counteracting CD. Combined with WGCNA, four differentially expressed genes (SLC6A4, NOS2, SHBG, and ABCB1) and their corresponding 24 compounds were closely related to the occurrence of CD. Conclusions: By integrating gene co-expression network analysis, this study preliminarily reveals the internal molecular mechanism of DD in treating CD from a systematic perspective, validated by molecular docking. However, these findings require further validation.
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