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Chen B, Xie K, Zhang J, Yang L, Zhou H, Zhang L, Peng R. Comprehensive analysis of mitochondrial dysfunction and necroptosis in intracranial aneurysms from the perspective of predictive, preventative, and personalized medicine. Apoptosis 2023; 28:1452-1468. [PMID: 37410216 PMCID: PMC10425526 DOI: 10.1007/s10495-023-01865-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/14/2023] [Indexed: 07/07/2023]
Abstract
Mitochondrial dysfunction and necroptosis are closely associated, and play vital roles in the medical strategy of multiple cardiovascular diseases. However, their implications in intracranial aneurysms (IAs) remain unclear. In this study, we aimed to explore whether mitochondrial dysfunction and necroptosis could be identified as valuable starting points for predictive, preventive, and personalized medicine for IAs. The transcriptional profiles of 75 IAs and 37 control samples were collected from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs), weighted gene co-expression network analysis, and least absolute shrinkage and selection operator (LASSO) regression were used to screen key genes. The ssGSEA algorithm was performed to establish phenotype scores. The correlation between mitochondrial dysfunction and necroptosis was evaluated using functional enrichment crossover, phenotype score correlation, immune infiltration, and interaction network construction. The IA diagnostic values of key genes were identified using machine learning. Finally, we performed the single-cell sequencing (scRNA-seq) analysis to explore mitochondrial dysfunction and necroptosis at the cellular level. In total, 42 IA-mitochondrial DEGs and 15 IA-necroptosis DEGs were identified. Screening revealed seven key genes invovled in mitochondrial dysfunction (KMO, HADH, BAX, AADAT, SDSL, PYCR1, and MAOA) and five genes involved in necroptosis (IL1B, CAMK2G, STAT1, NLRP3, and BAX). Machine learning confirmed the high diagnostic value of these key genes for IA. The IA samples showed higher expression of mitochondrial dysfunction and necroptosis. Mitochondrial dysfunction and necroptosis exhibited a close association. Furthermore, scRNA-seq indicated that mitochondrial dysfunction and necroptosis were preferentially up-regulated in monocytes/macrophages and vascular smooth muscle cells (VSMCs) within IA lesions. In conclusion, mitochondria-induced necroptosis was involved in IA formation, and was mainly up-regulated in monocytes/macrophages and VSMCs within IA lesions. Mitochondria-induced necroptosis may be a novel potential target for diagnosis, prevention, and treatment of IA.
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Affiliation(s)
- Bo Chen
- Department of Neurosurgery, Xiangya Hospital, Central South University, No. 87 Xiangya Rd., Changsha, 410008 Hunan People’s Republic of China
- Hypothalamic-Pituitary Research Center, Xiangya Hospital, Central South University, Changsha, Hunan China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan China
- Department of Surgery, LKS Faculty of Medicine, Queen Mary Hospital, The University of Hong Kong, Hong Kong, China
| | - Kang Xie
- Department of Neurosurgery, Xiangya Hospital, Central South University, No. 87 Xiangya Rd., Changsha, 410008 Hunan People’s Republic of China
- Hypothalamic-Pituitary Research Center, Xiangya Hospital, Central South University, Changsha, Hunan China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan China
| | - Jianzhong Zhang
- Department of Neurosurgery, Xiangya Hospital, Central South University (Jiangxi Branch), Nanchang, 330000 Jiangxi China
| | - Liting Yang
- Department of Neurosurgery, Xiangya Hospital, Central South University, No. 87 Xiangya Rd., Changsha, 410008 Hunan People’s Republic of China
- Hypothalamic-Pituitary Research Center, Xiangya Hospital, Central South University, Changsha, Hunan China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan China
| | - Hongshu Zhou
- Department of Neurosurgery, Xiangya Hospital, Central South University, No. 87 Xiangya Rd., Changsha, 410008 Hunan People’s Republic of China
- Hypothalamic-Pituitary Research Center, Xiangya Hospital, Central South University, Changsha, Hunan China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan China
| | - Liyang Zhang
- Department of Neurosurgery, Xiangya Hospital, Central South University, No. 87 Xiangya Rd., Changsha, 410008 Hunan People’s Republic of China
- Hypothalamic-Pituitary Research Center, Xiangya Hospital, Central South University, Changsha, Hunan China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan China
- Department of Neurosurgery, Xiangya Hospital, Central South University (Jiangxi Branch), Nanchang, 330000 Jiangxi China
| | - Renjun Peng
- Department of Neurosurgery, Xiangya Hospital, Central South University, No. 87 Xiangya Rd., Changsha, 410008 Hunan People’s Republic of China
- Hypothalamic-Pituitary Research Center, Xiangya Hospital, Central South University, Changsha, Hunan China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan China
- Department of Neurosurgery, Xiangya Hospital, Central South University (Jiangxi Branch), Nanchang, 330000 Jiangxi China
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Zhang J, Ryu JY, Tirado SR, Dickinson LD, Abosch A, Aziz-Sultan MA, Boulos AS, Barrow DL, Batjer HH, Binyamin TR, Blackburn SL, Chang EF, Chen PR, Colby GP, Cosgrove GR, David CA, Day AL, Folkerth RD, Frerichs KU, Howard BM, Jahromi BR, Niemela M, Ojemann SG, Patel NJ, Richardson RM, Shi X, Valle-Giler EP, Wang AC, Welch BG, Williams Z, Zusman EE, Weiss ST, Du R. A Transcriptomic Comparative Study of Cranial Vasculature. Transl Stroke Res 2023:10.1007/s12975-023-01186-w. [PMID: 37612482 DOI: 10.1007/s12975-023-01186-w] [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: 07/06/2023] [Revised: 07/06/2023] [Accepted: 08/07/2023] [Indexed: 08/25/2023]
Abstract
In genetic studies of cerebrovascular diseases, the optimal vessels to use as controls remain unclear. Our goal is to compare the transcriptomic profiles among 3 different types of control vessels: superficial temporal artery (STA), middle cerebral arteries (MCA), and arteries from the circle of Willis obtained from autopsies (AU). We examined the transcriptomic profiles of STA, MCA, and AU using RNAseq. We also investigated the effects of using these control groups on the results of the comparisons between aneurysms and the control arteries. Our study showed that when comparing pathological cerebral arteries to control groups, all control groups presented similar responses in the activation of immunological processes, the regulation of intracellular signaling pathways, and extracellular matrix productions, despite their intrinsic biological differences. When compared to STA, AU exhibited upregulation of stress and apoptosis genes, whereas MCA showed upregulation of genes associated with tRNA/rRNA processing. Moreover, our results suggest that the matched case-control study design, which involves control STA samples collected from the same subjects of matched aneurysm samples in our study, can improve the identification of non-inherited disease-associated genes. Given the challenges associated with obtaining fresh intracranial arteries from healthy individuals, our study suggests that using MCA, AU, or paired STA samples as controls are feasible strategies for future large-scale studies investigating cerebral vasculopathies. However, the intrinsic differences of each type of control should be taken into consideration when interpreting the results. With the limitations of each control type, it may be most optimal to use multiple tissues as controls.
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Affiliation(s)
- Jianing Zhang
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, 75 Francis Street, Boston, MA, 02115, USA
| | - Jee-Yeon Ryu
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, 75 Francis Street, Boston, MA, 02115, USA
| | - Selena-Rae Tirado
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, 75 Francis Street, Boston, MA, 02115, USA
| | | | - Aviva Abosch
- Department of Neurosurgery, University of Nebraska Medical Center, Omaha, NE, USA
| | - M Ali Aziz-Sultan
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, 75 Francis Street, Boston, MA, 02115, USA
| | - Alan S Boulos
- Department of Neurosurgery, Albany Medical Center, Albany, NY, USA
| | - Daniel L Barrow
- Department of Neurosurgery, Emory University, Atlanta, GA, USA
| | - H Hunt Batjer
- Department of Neurosurgery, University of Texas Southwestern, Dallas, TX, USA
| | | | - Spiros L Blackburn
- Department of Neurosurgery, University of Texas Health Science Center, Houston, TX, USA
| | - Edward F Chang
- Department of Neurosurgery, University of California San Francisco, San Francisco, CA, USA
- Department of Neurosurgery, University of California Los Angeles, Los Angeles, CA, USA
| | - P Roc Chen
- Department of Neurosurgery, University of Texas Health Science Center, Houston, TX, USA
| | - Geoffrey P Colby
- Department of Neurosurgery, University of California Los Angeles, Los Angeles, CA, USA
| | - G Rees Cosgrove
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, 75 Francis Street, Boston, MA, 02115, USA
| | - Carlos A David
- Department of Neurosurgery, University of North Carolina Chapel Hill, Chapel Hill, NC, USA
| | - Arthur L Day
- Department of Neurosurgery, University of Texas Health Science Center, Houston, TX, USA
| | - Rebecca D Folkerth
- Department of Forensic Medicine, New York University Grossman School of Medicine, New York, NY, USA
| | - Kai U Frerichs
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, 75 Francis Street, Boston, MA, 02115, USA
| | - Brian M Howard
- Department of Neurosurgery, Emory University, Atlanta, GA, USA
| | - Behnam R Jahromi
- Department of Neurosurgery, Helsinki University and Helsinki University Hospital, Helsinki, Finland
| | - Mika Niemela
- Department of Neurosurgery, Helsinki University and Helsinki University Hospital, Helsinki, Finland
| | - Steven G Ojemann
- Department of Neurosurgery, University of Colorado, Denver, CO, USA
| | - Nirav J Patel
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, 75 Francis Street, Boston, MA, 02115, USA
| | - R Mark Richardson
- Department of Neurosurgery, Massachusetts General Hospital, Boston, MA, USA
| | - Xiangen Shi
- Department of Neurosurgery, Affiliated Fuxing Hospital, Capital Medical University, Beijing, China
| | | | - Anthony C Wang
- Department of Neurosurgery, University of California Los Angeles, Los Angeles, CA, USA
| | - Babu G Welch
- Department of Neurosurgery, University of Texas Southwestern, Dallas, TX, USA
| | - Ziv Williams
- Department of Neurosurgery, Massachusetts General Hospital, Boston, MA, USA
| | | | - Scott T Weiss
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Rose Du
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, 75 Francis Street, Boston, MA, 02115, USA.
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Ma Z, Zhong P, Yue P, Sun Z. Identification of immune-related molecular markers in intracranial aneurysm (IA) based on machine learning and cytoscape-cytohubba plug-in. BMC Genom Data 2023; 24:20. [PMID: 37041519 PMCID: PMC10088219 DOI: 10.1186/s12863-023-01121-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 03/30/2023] [Indexed: 04/13/2023] Open
Abstract
BACKGROUND Intracranial aneurysm (IA) is a common cerebrovascular disease. The immune mechanism of IA is more complicated, and it is unclear so far. Therefore, it is necessary to continue to explore the immune related molecular mechanism of IA. METHODS All data were downloaded from the public database. Limma package and ssGSEA algorithm was used to identify differentially expressed mRNAs (DEmRNAs) and analyze immune cell infiltration, respectively. Machine learning and cytoscape-cytohubba plug-in was used to identify key immune types and multicentric DEmRNAs of IA, respectively. Multicentric DEmRNAs related to key immune cells were screened out as key DEmRNAs by Spearman correlation analysis. Diagnostic models, competing endogenous RNA (ceRNA) regulatory network and transcription factor regulatory network were constructed based on key DEmRNAs. Meanwhile, drugs related to key DEmRNAs were screened out based on DGIdb database. The expression of key DEmRNAs was also verified by real time-PCR. RESULTS In this study, 7 key DEmRNAs (NRXN1, GRIA2, SLC1A2, SLC17A7, IL6, VEGFA and SYP) associated with key differential immune cell infiltration (CD56bright natural killer cell, Immature B cell and Type 1 T helper cell) were identified. Functional enrichment analysis showed that VEGFA and IL6 may be involved in the regulation of the PI3K-Akt signaling pathway. Moreover, IL6 was also found to be enriched in cytokine-cytokine receptor interaction signaling pathway. In the ceRNA regulatory network, a large number of miRNAs and lncRNAs were found. In the transcription factor regulatory network, the transcription factor SP1 was correlated with VEGFA, SYP and IL6. It is also predicted that drugs related to key DEmRNAs such as CARBOPLATIN, FENTANYL and CILOSTAZOL may contribute to the treatment of IA. In addition, it was also found that SVM and RF models based on key DEmRNAs may be potential markers for diagnosing IA and unruptured intracranial aneurysm (UIA), respectively. The expression trend of key DEmRNAs verified by real-time PCR was consistent with the bioinformatics analysis results. CONCLUSION The identification of molecules and pathways in this study provides a theoretical basis for understanding the immune related molecular mechanism of IA. Meanwhile, the drug prediction and diagnosis model construction may also be helpful for clinical diagnosis and management.
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Affiliation(s)
- Zhengfei Ma
- Department of Neurology, The First Affiliated Hospital of Anhui Medical University, Anhui Province, No. 299, Bianhe Zhong Lu District, Suzhou City, Hefei, 234000, China
- Department of Neurology, Suzhou Hospital of Anhui Medical University, Suzhou, China
| | - Ping Zhong
- Department of Neurology, Suzhou Hospital of Anhui Medical University, Suzhou, China
| | - Peidong Yue
- Department of Neurosurgery, Suzhou Hospital of Anhui Medical University, Suzhou, China
| | - Zhongwu Sun
- Department of Neurology, The First Affiliated Hospital of Anhui Medical University, Anhui Province, No. 299, Bianhe Zhong Lu District, Suzhou City, Hefei, 234000, China.
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Banaganapalli B, Mallah B, Alghamdi KS, Albaqami WF, Alshaer DS, Alrayes N, Elango R, Shaik NA. Integrative weighted molecular network construction from transcriptomics and genome wide association data to identify shared genetic biomarkers for COPD and lung cancer. PLoS One 2022; 17:e0274629. [PMID: 36194576 PMCID: PMC9531836 DOI: 10.1371/journal.pone.0274629] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 09/01/2022] [Indexed: 11/05/2022] Open
Abstract
Chronic obstructive pulmonary disease (COPD) is a multifactorial progressive airflow obstruction in the lungs, accounting for high morbidity and mortality across the world. This study aims to identify potential COPD blood-based biomarkers by analyzing the dysregulated gene expression patterns in blood and lung tissues with the help of robust computational approaches. The microarray gene expression datasets from blood (136 COPD and 6 controls) and lung tissues (16 COPD and 19 controls) were analyzed to detect shared differentially expressed genes (DEGs). Then these DEGs were used to construct COPD protein network-clusters and functionally enrich them against gene ontology annotation terms. The hub genes in the COPD network clusters were then queried in GWAS catalog and in several cancer expression databases to explore their pathogenic roles in lung cancers. The comparison of blood and lung tissue datasets revealed 63 shared DEGs. Of these DEGs, 12 COPD hub gene-network clusters (SREK1, TMEM67, IRAK2, MECOM, ASB4, C1QTNF2, CDC42BPA, DPF3, DET1, CCDC74B, KHK, and DDX3Y) connected to dysregulations of protein degradation, inflammatory cytokine production, airway remodeling, and immune cell activity were prioritized with the help of protein interactome and functional enrichment analysis. Interestingly, IRAK2 and MECOM hub genes from these COPD network clusters are known for their involvement in different pulmonary diseases. Additional COPD hub genes like SREK1, TMEM67, CDC42BPA, DPF3, and ASB4 were identified as prognostic markers in lung cancer, which is reported in 1% of COPD patients. This study identified 12 gene network- clusters as potential blood based genetic biomarkers for COPD diagnosis and prognosis.
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Affiliation(s)
- Babajan Banaganapalli
- Department of Genetic Medicine, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
- Princess Al-Jawhara Al-Brahim Center of Excellence in Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia
- * E-mail: (BB); (NAS)
| | - Bayan Mallah
- Department of Genetic Medicine, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
- Princess Al-Jawhara Al-Brahim Center of Excellence in Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Kawthar Saad Alghamdi
- Department of Biology, Faculty of Science, University of Hafr Al Batin, Hafr Al Batin, Saudi Arabia
| | - Walaa F. Albaqami
- Department of Science, Prince Sultan Military College of Health Sciences, Dhahran, Saudi Arabia
| | - Dalal Sameer Alshaer
- Department of Genetic Medicine, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Nuha Alrayes
- Princess Al-Jawhara Al-Brahim Center of Excellence in Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ramu Elango
- Department of Genetic Medicine, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
- Princess Al-Jawhara Al-Brahim Center of Excellence in Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Noor A. Shaik
- Department of Genetic Medicine, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
- Princess Al-Jawhara Al-Brahim Center of Excellence in Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia
- * E-mail: (BB); (NAS)
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Li Y, Zhang Z, Liu D. Intracranial Aneurysms Induced by RUNX1 Through Regulation of NFKB1 in Patients With Hypertension-An Integrated Analysis Based on Multiple Datasets and Algorithms. Front Neurol 2022; 13:877801. [PMID: 35655614 PMCID: PMC9152011 DOI: 10.3389/fneur.2022.877801] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 04/22/2022] [Indexed: 11/13/2022] Open
Abstract
Objective The purpose of this study was to identify potential therapeutic targets by examining the hub genes contributing to progression of intracranial aneurysm (IA) in patients with hypertension. Methods The bulk RNA sequencing (RNA-seq) datasets of hypertension and IA were obtained from the Gene Expression Omnibus (www.ncbi.nlm.nih.gov/geo) database. These data were then used to calculate disease-related differentially expressed genes (DEGs) at the individual level. An scRNA-seq dataset of patients with abdominal aortic aneurysms (AAA) was used to analyze monocyte/macrophage-related DEGs. On the basis of the DEG data related to monocytes and macrophages, a TF-genes network has been developed. Hub genes and core sub-networks have also been identified. Furthermore, the key genes have been validated in an external cohort. Results From combined monocyte and macrophage-derived DEGs from abdominal aortic aneurysms, five hub DEGs were detected, including IFI30, SERPINE1, HMOX1, IL24, and RUNX1. A total of 57 genes were found in the IA bulk RNA-seq dataset. A support vector machine-recursive feature elimination algorithm (SVM-RFE) was applied to further screen the seven genes (RPS4Y1, DDX3Y, RUNX1, CLEC10A, PLAC8, SLA, and LILRB3). RUNX1 was the hub gene that regulated NFKB1 in the monocyte/macrophage-related network. And RUNX1 is implicated in IA progression by regulating hematopoietic stem cell differentiation and abnormal platelet production, according to gene set enrichment analysis. Conclusion Among patients with hypertension, RUNX1 in monocytes and macrophages was associated with a higher risk of IA through its regulation of NFKB1.
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Affiliation(s)
- Yang Li
- Department of Neurosurgery, The First People's Hospital of Yinchuan, Yinchuan, China
| | - Zhen Zhang
- Department of Neurosurgery, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, China
| | - Donghua Liu
- Department of Neurosurgery, The Second People's Hospital of Yinchuan, Yinchuan, China
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Li Q, Aishwarya S, Li JP, Pan DX, Shi JP. Gene Expression Profiling of Glioblastoma to Recognize Potential Biomarker Candidates. Front Genet 2022; 13:832742. [PMID: 35571016 PMCID: PMC9091202 DOI: 10.3389/fgene.2022.832742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 03/23/2022] [Indexed: 01/09/2023] Open
Abstract
Glioblastoma is an aggressive malignant tumor of the brain and spinal cord. Due to the blood–brain barrier, the accessibility of its treatments still remains significantly challenging. Unfortunately, the recurrence rates of glioblastoma upon surgery are very high too. Hence, understanding the molecular drivers of disease progression is valuable. In this study, we aimed to investigate the molecular drivers responsible for glioblastoma progression and identify valid biomarkers. Three microarray expression profiles GSE90604, GSE50601, and GSE134470 containing healthy and glioblastoma-affected samples revealed overlapping differentially expressed genes (DEGs). The interrelational pathway enrichment analysis elucidated the halt of cell cycle checkpoints and activation of signaling pathways and led to the identification of 6 predominant hub genes. Validation of hub genes in comparison with The Cancer Genome Atlas datasets identified the potential biomarkers of glioblastoma. The study evaluated two significantly upregulated genes, SPARC (secreted protein acidic and rich in cysteine) and VIM (vimentin) for glioblastoma. The genes CACNA1E (calcium voltage-gated channel subunit alpha1 e), SH3GL2 (SH3 domain-containing GRB2-like 2, endophilin A1), and DDN (dendrin) were identified as under-expressed genes as compared to the normal and pan-cancer tissues along with prominent putative prognostic biomarker potentials. The genes DDN and SH3GL2 were found to be upregulated in the proneural subtype, while CACNA1E in the mesenchymal subtype of glioblastoma exhibits good prognostic potential. The mutational analysis also revealed the benign, possibly, and probably damaging substitution mutations. The correlation between the DEG and survival in glioblastoma was evaluated using the Kaplan–Meier plots, and VIM had a greater life expectancy of 60.25 months. Overall, this study identified key candidate genes that might serve as predictive biomarkers for glioblastoma.
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Affiliation(s)
- Qiang Li
- Department of Neurosurgery, Hwa Mei Hospital, University of Chinese Academy of Sciences (Ningbo No. 2 Hospital), Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo, China
| | - S. Aishwarya
- Department of Bioinformatics, Stella Maris College (Autonomous), Chennai, India
| | - Ji-Ping Li
- Department of Neurosurgery, Hwa Mei Hospital, University of Chinese Academy of Sciences (Ningbo No. 2 Hospital), Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo, China
| | - Dong-Xiao Pan
- Department of Neurosurgery, Hwa Mei Hospital, University of Chinese Academy of Sciences (Ningbo No. 2 Hospital), Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo, China
| | - Jia-Pei Shi
- Department of Radiology, Hwa Mei Hospital, University of Chinese Academy of Sciences (Ningbo No. 2 Hospital), Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo, China
- *Correspondence: Jia-Pei Shi,
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Zhong A, Ding N, Zhou Y, Yang G, Peng Z, Zhang H, Chai X. Identification of Hub Genes Associated with the Pathogenesis of Intracranial Aneurysm via Integrated Bioinformatics Analysis. Int J Gen Med 2021; 14:4039-4050. [PMID: 34354366 PMCID: PMC8331219 DOI: 10.2147/ijgm.s320396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 07/09/2021] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND At present, the pathogenesis of intracranial aneurysms (IA) remains unclear, which significantly hinders the development of novel strategies for the clinical treatment. In this study, bioinformatics methods were used to identify the potential hub genes and pathways associated with the pathogenesis of IA. METHODS The gene expression datasets of patients with intracranial aneurysm were downloaded from the Gene Expression Database (GEO), and the different data sets were integrated by the robust rank aggregation (RRA) method to identify the differentially expressed genes between patients with intracranial aneurysm and the controls. The functional enrichment analyses of the significant differentially expressed genes (DEGs) were performed and the protein-protein interaction (PPI) network was constructed; thereafter, the hub genes were screened by cytoHubba plug-in of Cytoscape, and finally sequencing dataset GSE122897 was used to verify the hub genes. RESULTS The GSE15629, GSE75436, GSE26969, and GSE6551 expression profiles have been included in this study, including 34 intracranial aneurysm samples and 26 control samples. The four datasets obtained 136 significant DEGs (45 up-regulated, 91 down-regulated). Enrichment analysis showed that the extracellular matrix structural constituent and the ECM-receptor interaction were closely related to the occurrence of IA. It was finally determined that eight hub genes associated with the development of IA, including VCAN, COL1A1, COL11A1, COL5A1, COL5A2, POSTN, THBS2, and CDH2. CONCLUSION The discovery of potential hub genes and pathways could enhance the understanding of the molecular mechanisms associated with the development of IA. These hub genes may be potential therapeutic targets for the management and new biomarker for the diagnosis of IA.
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Affiliation(s)
- Aifang Zhong
- Department of Emergency Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan, People’s Republic of China
- Trauma center, The Second Xiangya Hospital, Central South University, Changsha, Hunan, People’s Republic of China
| | - Ning Ding
- Department of Emergency Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan, People’s Republic of China
- Trauma center, The Second Xiangya Hospital, Central South University, Changsha, Hunan, People’s Republic of China
| | - Yang Zhou
- Department of Emergency Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan, People’s Republic of China
- Trauma center, The Second Xiangya Hospital, Central South University, Changsha, Hunan, People’s Republic of China
| | - Guifang Yang
- Department of Emergency Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan, People’s Republic of China
- Trauma center, The Second Xiangya Hospital, Central South University, Changsha, Hunan, People’s Republic of China
| | - Zhenyu Peng
- Department of Emergency Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan, People’s Republic of China
- Emergency Medicine and Difficult Disease Institute, The Second Xiangya Hospital, Central South University, Changsha, Hunan, People’s Republic of China
| | - Hongliang Zhang
- Department of Emergency Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan, People’s Republic of China
- Emergency Medicine and Difficult Disease Institute, The Second Xiangya Hospital, Central South University, Changsha, Hunan, People’s Republic of China
| | - Xiangping Chai
- Department of Emergency Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan, People’s Republic of China
- Trauma center, The Second Xiangya Hospital, Central South University, Changsha, Hunan, People’s Republic of China
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8
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Liu Z, Liao Z, Chen Y, Zhou L, Huangting W, Xiao H. Research on CRISPR/system in major cancers and its potential in cancer treatments. Clin Transl Oncol 2020; 23:425-433. [PMID: 32671729 DOI: 10.1007/s12094-020-02450-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 07/02/2020] [Indexed: 12/24/2022]
Abstract
Cancer is a serious public health problem in the world and the prevention and control of cancer has become one of the health strategies of governments around the world. According to the data of the International Agency for Research on Cancer (IARC), about 8 million people die of cancer every year in the world. With the continuous progress of medical technology, there are many methods to treat cancer at present. However, many treatment methods have achieved different therapeutic effects, some of them have obvious toxic and side effects. Therefore, it is necessary to study simpler and more effective new therapies for alleviating pain and prolonging lifetime of patients. In this view, we focus on the application progress of CRISPR system in some major cancers and its potential in cancer treatments.
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Affiliation(s)
- Z Liu
- Department of Clinical Pharmacy, Sichuan Cancer Hospital and Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, No. 55, Section 4, South Renmin Road, Chengdu, 610041, Sichuan, China.,Personalized Drug Therapy Key Laboratory of Sichuan Province, Chengdu, China
| | - Z Liao
- Department of Gynecology and Obstetrics, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Chengdu, China
| | - Y Chen
- Department of Clinical Pharmacy, Sichuan Cancer Hospital and Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, No. 55, Section 4, South Renmin Road, Chengdu, 610041, Sichuan, China
| | - L Zhou
- Department of Clinical Pharmacy, Sichuan Cancer Hospital and Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, No. 55, Section 4, South Renmin Road, Chengdu, 610041, Sichuan, China.,Personalized Drug Therapy Key Laboratory of Sichuan Province, Chengdu, China
| | - W Huangting
- Department of Clinical Pharmacy, Sichuan Cancer Hospital and Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, No. 55, Section 4, South Renmin Road, Chengdu, 610041, Sichuan, China.,Personalized Drug Therapy Key Laboratory of Sichuan Province, Chengdu, China
| | - H Xiao
- Department of Clinical Pharmacy, Sichuan Cancer Hospital and Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, No. 55, Section 4, South Renmin Road, Chengdu, 610041, Sichuan, China. .,Personalized Drug Therapy Key Laboratory of Sichuan Province, Chengdu, China.
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9
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Tang H, Lu Z, Xue G, Li S, Xu F, Yan Y, Liu J, Zuo Q, Luo Y, Huang Q. The development and understanding of intracranial aneurysm based on rabbit model. Neuroradiology 2020; 62:1219-1230. [PMID: 32594185 DOI: 10.1007/s00234-020-02475-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 06/10/2020] [Indexed: 10/24/2022]
Abstract
In modern society, intracranial aneurysms have seriously affected people's life. To better study and treat intracranial aneurysm, animal models are ideal candidates to perform biological research and preclinical endovascular device testing. Rabbit aneurysm model is one of the most commonly used animal models, and the rabbit aneurysms share similarities in histology, morphology, and hemodynamic aspects with human intracranial aneurysms, which is an ideal model for intracranial aneurysm pre-clinical and basic research. In this review, we will summarize the main methods of establishing rabbit aneurysms model and will further discuss the current biological mechanisms of intracranial aneurysms based on rabbit model. Further improvements of rabbit aneurysm model and more deep studies based on this model are needed to provide new insights into studying and clinical treating intracranial aneurysm.
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Affiliation(s)
- Haishuang Tang
- Department of Neurosurgery, Changhai Hospital, Second Military Medical University, Shanghai, 200433, People's Republic of China.,Naval Medical Center of PLA, Second Military Medical University, Shanghai, 200050, People's Republic of China
| | - Zhiwen Lu
- Department of Neurosurgery, Changhai Hospital, Second Military Medical University, Shanghai, 200433, People's Republic of China
| | - Gaici Xue
- Department of Neurosurgery, Changhai Hospital, Second Military Medical University, Shanghai, 200433, People's Republic of China
| | - Sisi Li
- Department of Neurosurgery, Changhai Hospital, Second Military Medical University, Shanghai, 200433, People's Republic of China
| | - Fengfeng Xu
- Naval Medical Center of PLA, Second Military Medical University, Shanghai, 200050, People's Republic of China
| | - Yazhou Yan
- Department of Neurosurgery, Changhai Hospital, Second Military Medical University, Shanghai, 200433, People's Republic of China
| | - Jianmin Liu
- Department of Neurosurgery, Changhai Hospital, Second Military Medical University, Shanghai, 200433, People's Republic of China
| | - Qiao Zuo
- Department of Neurosurgery, Changhai Hospital, Second Military Medical University, Shanghai, 200433, People's Republic of China
| | - Yin Luo
- Department of Neurosurgery, Changhai Hospital, Second Military Medical University, Shanghai, 200433, People's Republic of China
| | - Qinghai Huang
- Department of Neurosurgery, Changhai Hospital, Second Military Medical University, Shanghai, 200433, People's Republic of China.
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Guo T, Hou D, Yu D. Bioinformatics analysis of gene expression profile data to screen key genes involved in intracranial aneurysms. Mol Med Rep 2019; 20:4415-4424. [PMID: 31545495 PMCID: PMC6797989 DOI: 10.3892/mmr.2019.10696] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 04/17/2019] [Indexed: 01/10/2023] Open
Abstract
Intracranial aneurysm (IA) is a cerebrovascular disease with a high mortality rate. The pathogenesis of IA remains unclear and the treatment limited. The purpose of the present study was to identify the key genes expressed in IAs and provide the basis for further research and treatment. The raw dataset GSE75436 was downloaded from Gene Expression Omnibus, including 15 IA samples and 15 matched superficial temporal artery (STA) samples. Then, differentially expressed genes (DEGs) were identified using the limma package in R software. Hierarchical clustering analysis was performed on the DEGs using the gplot2 package in R. Database for Annotation, Visualization, and Integrated Discovery (DAVID) online tools were used to perform gene ontology (GO) functional enrichment analysis. DAVID and gene set enrichment analysis were separately used to perform the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses. The intersections of the two results were selected as common KEGG pathways. Protein-protein interaction (PPI) analysis among the DEGs involved in the common KEGG pathways was performed using Search Tool for the Retrieval of Interacting Genes online tools, and visualized with Cytoscape software. A total of 782 DEGs were identified, comprising 392 upregulated and 390 downregulated DEGs. Hierarchical clustering demonstrated that the DEGs could precisely distinguish the IAs from the STAs. The GO enrichment analysis demonstrated that the upregulated DEGs were mainly involved in the inflammatory response and the management of extracellular matrix, and the downregulated DEGs were mainly involved in the process of vascular smooth muscle contraction. The KEGG pathway enrichment analysis demonstrated that the common pathways were ‘leishmaniasis’, ‘Toll-like receptor signaling pathway’ and ‘vascular smooth muscle contraction’. In the PPI network, tumor necrosis factor (TNF), interleukin 8 and Toll-like receptor 4 had the highest degrees; they were associated with the inflammatory response. The Toll-like receptor signaling pathway and TNF gene may serve as targets for future research and treatment.
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Affiliation(s)
- Tie Guo
- Department of Neurology, Haikou Hospital Affiliated to Xiangya School of Medicine, Central South University, Haikou, Hainan 570208, P.R. China
| | - Dan Hou
- Department of Neurology, Haikou Hospital Affiliated to Xiangya School of Medicine, Central South University, Haikou, Hainan 570208, P.R. China
| | - Dan Yu
- Department of Neurology, Haikou Hospital Affiliated to Xiangya School of Medicine, Central South University, Haikou, Hainan 570208, P.R. China
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