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Ban R, Huo C, Wang J, Zhang G, Zhao X. Exploration of the Shared Gene Signatures and Molecular Mechanisms Between Ischemic Stroke and Atherosclerosis. Int J Gen Med 2024; 17:2223-2239. [PMID: 38784404 PMCID: PMC11114141 DOI: 10.2147/ijgm.s454336] [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: 12/24/2023] [Accepted: 05/12/2024] [Indexed: 05/25/2024] Open
Abstract
Purpose Atherosclerosis (AS) is a chronic inflammatory vascular disease and the predominant cause of ischemic stroke (IS). AS is a potential pathogenetic factor in IS. However, the processes by which they interact remain unknown. The purpose of this paper was to investigate the shared gene signatures and putative molecular processes in AS and IS. Methods Gene Expression Omnibus (GEO) data for AS and IS microarrays were retrieved. The co-expression modules associated with AS and IS were identified using the Weighted Gene Co-Expression Network Analysis (WGCNA). We constructed an interaction network of shared differentially expressed genes in AS and IS and conducted an enrichment analysis using ClueGO software. We validated the results in a separate cohort through differential gene analysis. Additionally, we retrieved AS and IS-related miRNAs from the Human microRNA Disease Database (HMDD) and predicted their target genes using miRWalk. We then built a network of miRNAs-mRNAs-KEGG pathways using the shared genes. Results Through WGCNA, we identified five modules and six modules as significant in AS and IS, respectively. A ClueGO enrichment analysis of common genes showed that highly active CCR1 chemokine receptor binding is critical to AS and IS pathogenesis. The differential analysis expression results in another cohort closely matched these findings. The miRNA-mRNA network suggested that hsa-miR-330-5p, hsa-miR-143-3p, hsa-miR-16-5p, hsa-miR-152-3p might regulate the shared gene KRAS, which could be a key player in AS and IS. Conclusion We integrated ischemic stroke and carotid atherosclerosis public database data and found that ATF3, CCL3, CCL4, JUNB, KRAS, and ZC3H12A may affect both, making them novel biomarkers or therapeutic target genes. Clinical samples and expression trends supported our analyses of pivotal genes.
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Affiliation(s)
- Ru Ban
- Department of Neurology, Liaocheng People’s Hospital and Liaocheng Hospital Affiliated to Shandong First Medical University, Liaocheng, Shandong, People’s Republic of China
| | - Chengju Huo
- Department of Neurology, Liaocheng People’s Hospital and Liaocheng Hospital Affiliated to Shandong First Medical University, Liaocheng, Shandong, People’s Republic of China
| | - Jingru Wang
- Department of Neurology, Liaocheng People’s Hospital and Liaocheng Hospital Affiliated to Shandong First Medical University, Liaocheng, Shandong, People’s Republic of China
| | - Guifeng Zhang
- Department of Neurology, Liaocheng People’s Hospital and Liaocheng Hospital Affiliated to Shandong First Medical University, Liaocheng, Shandong, People’s Republic of China
| | - Xin Zhao
- Department of Neurology, Liaocheng People’s Hospital and Liaocheng Hospital Affiliated to Shandong First Medical University, Liaocheng, Shandong, People’s Republic of China
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Xie H, Ding C, Li Q, Sheng W, Xu J, Feng R, Cheng H. Identification of shared gene signatures in major depressive disorder and triple-negative breast cancer. BMC Psychiatry 2024; 24:369. [PMID: 38755543 PMCID: PMC11100035 DOI: 10.1186/s12888-024-05795-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 04/26/2024] [Indexed: 05/18/2024] Open
Abstract
BACKGROUND Patients with major depressive disorder (MDD) have an increased risk of breast cancer (BC), implying that these two diseases share similar pathological mechanisms. This study aimed to identify the key pathogenic genes that lead to the occurrence of both triple-negative breast cancer (TNBC) and MDD. METHODS Public datasets GSE65194 and GSE98793 were analyzed to identify differentially expressed genes (DEGs) shared by both datasets. A protein-protein interaction (PPI) network was constructed using STRING and Cytoscape to identify key PPI genes using cytoHubba. Hub DEGs were obtained from the intersection of hub genes from a PPI network with genes in the disease associated modules of the Weighed Gene Co-expression Network Analysis (WGCNA). Independent datasets (TCGA and GSE76826) and RT-qPCR validated hub gene expression. RESULTS A total of 113 overlapping DEGs were identified between TNBC and MDD. The PPI network was constructed, and 35 hub DEGs were identified. Through WGCNA, the blue, brown, and turquoise modules were recognized as highly correlated with TNBC, while the brown, turquoise, and yellow modules were similarly correlated with MDD. Notably, G3BP1, MAF, NCEH1, and TMEM45A emerged as hub DEGs as they appeared both in modules and PPI hub DEGs. Within the GSE65194 and GSE98793 datasets, G3BP1 and MAF exhibited a significant downregulation in TNBC and MDD groups compared to the control, whereas NCEH1 and TMEM45A demonstrated a significant upregulation. These findings were further substantiated by TCGA and GSE76826, as well as through RT-qPCR validation. CONCLUSIONS This study identified G3BP1, MAF, NCEH1 and TMEM45A as key pathological genes in both TNBC and MDD.
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Affiliation(s)
- Hua Xie
- Department of Oncology, The Second Affiliated Hospital of Anhui Medical University, Furong Road 678, Shushan District, Hefei, 230601, Anhui, China
- Xuancheng People's Hospital, Affiliated Xuancheng Hospital of Wannan Medical College, Dabatang Road 51, Xuanzhou District, Xuancheng, Anhui, 242000, China
| | - Chenxiang Ding
- Bengbu Medical College, Donghaida Road 2600, Longzihu District, Bengbu, Anhui, 233030, China
| | - Qianwen Li
- Xuancheng People's Hospital, Affiliated Xuancheng Hospital of Wannan Medical College, Dabatang Road 51, Xuanzhou District, Xuancheng, Anhui, 242000, China
| | - Wei Sheng
- Mental Health center of Xuancheng City, Changqiaocun Jinba Road, Economic and Technological Development Zone, Xuancheng, Anhui, 242000, China
| | - Jie Xu
- Xuancheng People's Hospital, Affiliated Xuancheng Hospital of Wannan Medical College, Dabatang Road 51, Xuanzhou District, Xuancheng, Anhui, 242000, China
| | - Renjian Feng
- Xuancheng People's Hospital, Affiliated Xuancheng Hospital of Wannan Medical College, Dabatang Road 51, Xuanzhou District, Xuancheng, Anhui, 242000, China
| | - Huaidong Cheng
- Department of Oncology, The Second Affiliated Hospital of Anhui Medical University, Furong Road 678, Shushan District, Hefei, 230601, Anhui, China.
- Department of Oncology, Shenzhen Hospital of Southern Medical University, Xinhu Road 1333, Bao'an District, Shenzhen, Guangdong, 518000, China.
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Hiraide S, Takahashi M, Yoshida Y, Yamada H, Komine K, Ishioka C. Tumor suppressor miR-193a-3p enhances efficacy of BRAF/MEK inhibitors in BRAF-mutated colorectal cancer. Cancer Sci 2021; 112:3856-3870. [PMID: 34288281 PMCID: PMC8409311 DOI: 10.1111/cas.15075] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Revised: 06/04/2021] [Accepted: 07/15/2021] [Indexed: 12/11/2022] Open
Abstract
Patients with BRAF‐mutated colorectal cancer (CRC) have a poor prognosis despite recent therapeutic advances such as combination therapy with BRAF, MEK, and epidermal growth factor receptor (EGFR) inhibitors. To identify microRNAs (miRNAs) that can improve the efficacy of BRAF inhibitor dabrafenib (DAB) and MEK inhibitor trametinib (TRA), we screened 240 miRNAs in BRAF‐mutated CRC cells and identified five candidate miRNAs. Overexpression of miR‐193a‐3p, one of the five screened miRNAs, in CRC cells inhibited cell proliferation by inducing apoptosis. Reverse‐phase protein array analysis revealed that proteins with altered phosphorylation induced by miR‐193a‐3p were involved in several oncogenic pathways including MAPK‐related pathways. Furthermore, overexpression of miR‐193a‐3p in BRAF‐mutated cells enhanced the efficacy of DAB and TRA through inhibiting reactivation of MAPK signaling and inducing inhibition of Mcl1. Inhibition of Mcl1 by siRNA or by Mcl1 inhibitor increased the antiproliferative effect of combination therapy with DAB, TRA, and anti‐EGFR antibody cetuximab. Collectively, our study demonstrated the possibility that miR‐193a‐3p acts as a tumor suppressor through regulating multiple proteins involved in oncogenesis and affects cellular sensitivity to MAPK‐related pathway inhibitors such as BRAF inhibitors, MEK inhibitors, and/or anti‐EGFR antibodies. Addition of miR‐193a‐3p and/or modulation of proteins involved in the miR‐193a‐3p–mediated pathway, such as Mcl1, to EGFR/BRAF/MEK inhibition may be a potential therapeutic strategy against BRAF‐mutated CRC.
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Affiliation(s)
- Sakura Hiraide
- Department of Clinical Oncology, Tohoku University Graduate School of Medicine, Miyagi, Japan.,Department of Clinical Oncology, Institute of Development, Aging and Cancer, Tohoku University, Miyagi, Japan
| | - Masanobu Takahashi
- Department of Clinical Oncology, Institute of Development, Aging and Cancer, Tohoku University, Miyagi, Japan.,Department of Medical Oncology, Tohoku University Hospital, Miyagi, Japan
| | - Yuya Yoshida
- Department of Clinical Oncology, Tohoku University Graduate School of Medicine, Miyagi, Japan.,Department of Clinical Oncology, Institute of Development, Aging and Cancer, Tohoku University, Miyagi, Japan
| | - Hideharu Yamada
- Department of Clinical Oncology, Tohoku University Graduate School of Medicine, Miyagi, Japan
| | - Keigo Komine
- Department of Clinical Oncology, Institute of Development, Aging and Cancer, Tohoku University, Miyagi, Japan.,Department of Medical Oncology, Tohoku University Hospital, Miyagi, Japan
| | - Chikashi Ishioka
- Department of Clinical Oncology, Tohoku University Graduate School of Medicine, Miyagi, Japan.,Department of Clinical Oncology, Institute of Development, Aging and Cancer, Tohoku University, Miyagi, Japan.,Department of Medical Oncology, Tohoku University Hospital, Miyagi, Japan
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Lou W, Ding B, Wang J, Xu Y. The Involvement of the hsa_circ_0088494-miR-876-3p-CTNNB1/CCND1 Axis in Carcinogenesis and Progression of Papillary Thyroid Carcinoma. Front Cell Dev Biol 2020; 8:605940. [PMID: 33363164 PMCID: PMC7755655 DOI: 10.3389/fcell.2020.605940] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Accepted: 11/11/2020] [Indexed: 12/16/2022] Open
Abstract
Recently, growing studies have demonstrated that circular RNAs (circRNAs) function as critical players in multiple human tumors, including papillary thyroid carcinoma (PTC). However, the expression and underlying potential mechanism of circRNAs in PTC are still not fully elucidated. In this study, 14 candidate differentially expressed circRNAs (DECs) between normal thyroid tissues and benign thyroid tissues or PTC were first screened using the GSE93522 dataset by the GEO2R online tool. Then, the structural loop graphs of these 14 circRNAs were obtained through the CSCD database. After performing miRNA co-prediction by combination of CSCD and CRI databases, a potential circRNA-miRNA sub-network, consisting of 9 circRNAs and 21 miRNAs, was successfully constructed. Subsequently, the expression and prognostic values of these miRNAs were further determined by starBase, and two miRNAs, namely, miR-605-5p and miR-876-3p, were identified as key miRNAs in PTC. Then, their downstream target genes were predicted by the miRNet database. CTNNB1 and CCND1 were found to be two most potential targets of miR-876-3p by combination of multiple in silico analyses, including protein–protein interaction (PPI), hub gene screening, correlation analysis, and expression analysis. Conclusively, we established a key hsa_circ_0088494-miR-876-3p-CTNNB1/CCND1 axis linked to carcinogenesis and progression of PTC, which may provide promising therapeutic targets in treating PTC in the future.
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Affiliation(s)
- Weiyang Lou
- Department of Breast Surgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Bisha Ding
- Key Laboratory of Combined Multi-Organ Transplantation, Division of Hepatobiliary and Pancreatic Surgery, Program of Innovative Cancer Therapeutics, Department of Surgery, First Affiliated Hospital, College of Medicine, Zhejiang University, Ministry of Public Health, Hangzhou, China.,Key Laboratory of Organ Transplantation, Zhejiang University, Hangzhou, China
| | - Jiannan Wang
- Department of Breast Surgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Yongfang Xu
- Department of Respiratory Medicine, Thoracic Disease Center, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
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