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Liu Y, Yao Y, Zhang Y, Xu C, Yang T, Qu M, Lu B, Song X, Pan X, Zhou W, Cui X. Identification of prognostic stemness-related genes in kidney renal papillary cell carcinoma. BMC Med Genomics 2024; 17:121. [PMID: 38702698 PMCID: PMC11067181 DOI: 10.1186/s12920-024-01870-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 04/09/2024] [Indexed: 05/06/2024] Open
Abstract
BACKGROUND Kidney renal papillary cell carcinoma (KIRP) is the second most prevalent malignant cancer originating from the renal epithelium. Nowadays, cancer stem cells and stemness-related genes (SRGs) are revealed to play important roles in the carcinogenesis and metastasis of various tumors. Consequently, we aim to investigate the underlying mechanisms of SRGs in KIRP. METHODS RNA-seq profiles of 141 KIRP samples were downloaded from the TCGA database, based on which we calculated the mRNA expression-based stemness index (mRNAsi). Next, we selected the differentially expressed genes (DEGs) between low- and high-mRNAsi groups. Then, we utilized weighted gene correlation network analysis (WGCNA) and univariate Cox analysis to identify prognostic SRGs. Afterwards, SRGs were included in the multivariate Cox regression analysis to establish a prognostic model. In addition, a regulatory network was constructed by Pearson correlation analysis, incorporating key genes, upstream transcription factors (TFs), and downstream signaling pathways. Finally, we used Connectivity map analysis to identify the potential inhibitors. RESULTS In total, 1124 genes were characterized as DEGs between low- and high-RNAsi groups. Based on six prognostic SRGs (CCKBR, GPR50, GDNF, SPOCK3, KC877982.1, and MYO15A), a prediction model was established with an area under curve of 0.861. Furthermore, among the TFs, genes, and signaling pathways that had significant correlations, the CBX2-ASPH-Notch signaling pathway was the most significantly correlated. Finally, resveratrol might be a potential inhibitor for KIRP. CONCLUSIONS We suggested that CBX2 could regulate ASPH through activation of the Notch signaling pathway, which might be correlated with the carcinogenesis, development, and unfavorable prognosis of KIRP.
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Affiliation(s)
- Yifan Liu
- Department of Urology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, No.1665 Kongjiang Road, Shanghai, 200092, China
| | - Yuntao Yao
- Department of Urology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, No.1665 Kongjiang Road, Shanghai, 200092, China
| | - Yu Zhang
- Tongji University School of Medicine, Shanghai, 200092, China
| | - Chengdang Xu
- Tongji University School of Medicine, Shanghai, 200092, China
| | - Tianyue Yang
- Department of Urology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, No.1665 Kongjiang Road, Shanghai, 200092, China
| | - Mingyu Qu
- Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Bingnan Lu
- Department of Urology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, No.1665 Kongjiang Road, Shanghai, 200092, China
| | - Xu Song
- Department of Urology, Shanghai Seventh People's Hospital, Shanghai, Shandong, 200137, China.
| | - Xiuwu Pan
- Department of Urology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, No.1665 Kongjiang Road, Shanghai, 200092, China.
| | - Wang Zhou
- Department of Urology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, No.1665 Kongjiang Road, Shanghai, 200092, China.
| | - Xingang Cui
- Department of Urology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, No.1665 Kongjiang Road, Shanghai, 200092, China.
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Wang Y, Song Y, Liu Z, Li J, Wang G, Pan H, Zheng Z. miR‑149‑3p suppresses the proliferation and metastasis of glioma cells by targeting the CBX2/Wnt/β‑catenin pathway. Exp Ther Med 2023; 26:562. [PMID: 37954123 PMCID: PMC10632954 DOI: 10.3892/etm.2023.12261] [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: 04/23/2023] [Accepted: 09/11/2023] [Indexed: 11/14/2023] Open
Abstract
The present study aimed to investigate the role of miR-149-3p/chromobox 2 (CBX2)/Wnt/β-catenin pathway in the proliferation and metastasis of glioma cells. The expression and clinical significance of miR-149-3p and CBX2 were analyzed using data from public databases. Cell Counting Kit-8 and colony formation assays were performed to measure cell proliferation. Transwell assays were used to assess cell invasion. The results showed that miR-149-3p was downregulated and CBX2 was upregulated in glioma, and that the downregulated expression of miR-149-3p promoted the proliferation and invasion of glioma cells. In addition, downregulated expression of CBX2 suppressed the proliferation and invasion of glioma cells. Dual-luciferase assay indicated that CBX2 is a target gene of miR149-3p. The possible molecular mechanism of CBX2 was probed by western blotting, which showed that it may further affect the Wnt/β-catenin pathway. These present findings demonstrated that miR-149-3p may function as a tumor suppressor miRNA by directly regulating CBX2 and serve important roles in the malignancy of glioma.
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Affiliation(s)
- Yanjun Wang
- Department of Neurosurgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 250021, P.R. China
- Department of Neurosurgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250021, P.R. China
| | - Yanqun Song
- Department of Neurosurgery, The Third People's Hospital of Heze City, Heze, Shandong 274031, P.R. China
| | - Zhongcheng Liu
- Department of Neurosurgery, The First People's Hospital of Tai'an, Tai'an, Shandong 271000, P.R. China
| | - Junmin Li
- Department of Obstetrics and Gynecology, Jinan Maternity and Child Care Hospital, Jinan, Shandong 250021, P.R. China
| | - Guodong Wang
- Department of Neurosurgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 250021, P.R. China
- Department of Neurosurgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250021, P.R. China
| | - Hong Pan
- Department of Ophthalmology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 250021, P.R. China
- Department of Ophthalmology, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250021, P.R. China
| | - Zhiming Zheng
- Department of Neurosurgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 250021, P.R. China
- Department of Neurosurgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250021, P.R. China
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Taghehchian N, Samsami Y, Maharati A, Zangouei AS, Boroumand-Noughabi S, Moghbeli M. Molecular biology of microRNA-342 during tumor progression and invasion. Pathol Res Pract 2023; 248:154672. [PMID: 37413875 DOI: 10.1016/j.prp.2023.154672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 07/02/2023] [Indexed: 07/08/2023]
Abstract
Cancer is considered as one of the main causes of human deaths and health challenges in the world. Various factors are involved in the high death rate of cancer patients, including late diagnosis and drug resistance that result in treatment failure and tumor recurrence. Invasive diagnostic methods are one of the main reasons of late tumor detection in cancer patients. Therefore, it is necessary to investigate the molecular tumor biology to introduce efficient non-invasive markers. MicroRNAs (miRNAs) are involved in regulation of the cellular mechanisms such as cell proliferation, apoptosis, and migration. MiRNAs deregulations have been also frequently shown in different tumor types. Here, we discussed the molecular mechanisms of miR-342 during tumor growth. MiR-342 mainly functions as a tumor suppressor by the regulation of transcription factors and signaling pathways such as WNT, PI3K/AKT, NF-kB, and MAPK. Therefore, miR-342 mimics can be used as a reliable therapeutic strategy to inhibit the tumor cells growth. The present review can also pave the way to introduce the miR-342 as a non-invasive diagnostic/prognostic marker in cancer patients.
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Affiliation(s)
- Negin Taghehchian
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Yalda Samsami
- Department of Medical Genetics and Molecular Medicine, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Amirhosein Maharati
- Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Amir Sadra Zangouei
- Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Samaneh Boroumand-Noughabi
- Department of Hematology and Blood Bank, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Meysam Moghbeli
- Department of Medical Genetics and Molecular Medicine, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.
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Li X, Li L, Xiong X, Kuang Q, Peng M, Zhu K, Luo P. Identification of the Prognostic Biomarkers CBX6 and CBX7 in Bladder Cancer. Diagnostics (Basel) 2023; 13:diagnostics13081393. [PMID: 37189494 DOI: 10.3390/diagnostics13081393] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 03/22/2023] [Accepted: 04/07/2023] [Indexed: 05/17/2023] Open
Abstract
BACKGROUND Chromobox (CBX) proteins are essential components of polycomb group proteins and perform essential functions in bladder cancer (BLCA). However, research on CBX proteins is still limited, and the function of CBXs in BLCA has not been well illustrated. METHODS AND RESULTS We analyzed the expression of CBX family members in BLCA patients from The Cancer Genome Atlas database. By Cox regression analysis and survival analysis, CBX6 and CBX7 were identified as potential prognostic factors. Subsequently, we identified genes associated with CBX6/7 and performed enrichment analysis, and they were enriched in urothelial carcinoma and transitional carcinoma. Mutation rates of TP53 and TTN correlate with expression of CBX6/7. In addition, differential analysis indicated that the roles played by CBX6 and CBX7 may be related to immune checkpoints. The CIBERSORT algorithm was used to screen out immune cells that play a role in the prognosis of bladder cancer patients. Multiplex immunohistochemistry staining confirmed a negative correlation between CBX6 and M1 macrophages, as well as a consistent alteration in CBX6 and regulatory T cells (Tregs), a positive correlation between CBX7 and resting mast cells, and a negative correlation between CBX7 and M0 macrophages. CONCLUSIONS CBX6 and CBX7 expression levels may assist in predicting the prognosis of BLCA patients. CBX6 may contribute to a poor prognosis in patients by inhibiting M1 polarization and promoting Treg recruitment in the tumor microenvironment, while CBX7 may contribute to a better prognosis in patients by increasing resting mast cell numbers and decreasing macrophage M0 content.
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Affiliation(s)
- Xinxin Li
- Department of Urology, Wuhan Third Hospital and Tongren Hospital of Wuhan University, Wuhan 430060, China
| | - Lili Li
- Central Laboratory, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Xi Xiong
- Department of Urology, Wuhan Third Hospital, School of Medicine, Wuhan University of Science and Technology, Wuhan 430060, China
| | - Qihui Kuang
- Department of Urology, Wuhan Third Hospital and Tongren Hospital of Wuhan University, Wuhan 430060, China
| | - Min Peng
- Department of Oncology, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Kai Zhu
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Pengcheng Luo
- Department of Urology, Wuhan Third Hospital and Tongren Hospital of Wuhan University, Wuhan 430060, China
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5
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Xu Z, Wu Y, Yang M, Wei H, Pu J. CBX2-mediated suppression of SIAH2 triggers WNK1 accumulations to promote glycolysis in hepatocellular carcinoma. Exp Cell Res 2023; 426:113513. [PMID: 36780970 DOI: 10.1016/j.yexcr.2023.113513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Revised: 01/19/2023] [Accepted: 02/10/2023] [Indexed: 02/13/2023]
Abstract
Previous studies have highlighted the poor prognosis of liver cancer, and treatment effects are overall limited. We aimed to confirm the biological roles of SIAH2 in liver cancer and provide potential therapeutic targets. Differential analysis was conducted based on public datasets and found that SIAH2 expressed lowly in HCC samples relative to normal tissues, which was demonstrated in tumor samples via immunohistochemistry (IHC). Besides, SIAH2 overexpression could significantly suppress HCC proliferation. SIAH2 deficiency induced cell proliferation, migration and self-renewal abilities in vitro and in vivo. Mechanistically, SIAH2 could interact with WNK1, and trigger the ubiquitination and degradation of WNK1 proteins. In addition, low SIAH2 depended on elevated WNK1 proteins to drive HCC malignant features, including proliferation, migration and stemness. Meanwhile, we further found that CBX2 could regulate SIAH2 expressions. CBX2 cooperated with EZH2 to mediate the H3K27me3 enrichment on the promoter region of SIAH2 to suppress its transcriptional levels. High CBX2/EZH2 levels in HCC correlated with poor prognosis of patients. Gene set enrichment analysis (GSEA) further implicated that WNK1 correlates tightly with glycolytic process in HCC samples. WNK1 overexpression was found to notably enhance glycolytic activity, whereas WNK1 deficiency could significantly suppress the HCC glycolysis activity. Lastly, the subcutaneous tumor model further demonstrated that targeting WNK1 was effective to inhibit the in vivo tumor growth of SIAH2low HCC. Collectively, down-regulated SIAH2 expressions induced by CBX2/EZH2 could drive progression and glycolysis via accumulating WNK1 proteins, indicating that CBX2/SIAH2/WNK1 axis is a potential prognostic biomarker and therapeutic vulnerability for human HCC.
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Affiliation(s)
- Zuoming Xu
- Department of Hepatobiliary Surgery, Affiliated Hospital of Youjiang Medical University for Nationalities, 533000, China
| | - Yinghong Wu
- Graduate College of Youjiang Medical University for Nationalities, 533000, China
| | - Meng Yang
- Graduate College of Youjiang Medical University for Nationalities, 533000, China
| | - Huamei Wei
- Department of Pathology, Affiliated Hospital of Youjiang Medical University for Nationalitie, 533000, China
| | - Jian Pu
- Department of Hepatobiliary Surgery, Affiliated Hospital of Youjiang Medical University for Nationalities, 533000, China.
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Naqvi AAT, Rizvi SAM, Hassan MI. Pan-cancer analysis of Chromobox (CBX) genes for prognostic significance and cancer classification. Biochim Biophys Acta Mol Basis Dis 2023; 1869:166561. [PMID: 36183965 DOI: 10.1016/j.bbadis.2022.166561] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Revised: 09/15/2022] [Accepted: 09/20/2022] [Indexed: 11/16/2022]
Abstract
Polycomb group of proteins play a significant role in chromatin remodelling essential for epigenetic regulation of transcription. Chromobox (CBX) gene family is an important part of canonical polycomb repressive complex 1 (PRC1), belonging to the polycomb group involved in chromatin remodelling. Aberrations in CBX expression are linked to various cancers. To assess their biomarker significance, we performed a pan-cancer analysis of CBX mRNA levels in 18 cancer types. We also performed cancer classification using CBX genes as distinctive features for machine learning model development. Logistic regression (L.R.), support vector machine (SVM), random forest (R.F.), decision tree (D.T.), and XGBoost (XGB) algorithms for model training and classification. The expression of CBX genes was significantly changed in four cancer types, i.e., cholangiocarcinoma (CHOL), colon adenocarcinoma (COAD), lung adenocarcinoma (LUAD), and lung squamous cell carcinoma (LUSC). The fold change (FC) values suggest that CBX2 was significantly upregulated in CHOL (FC = 1.639), COAD (FC = 1.734), and LUSC (FC = 1.506). On the other hand, CBX7 was found downregulated in COAD (FC = -1.209), LUAD (FC = -1.190), and LUSC (FC = -1.214). The performance of machine learning models for classification was excellent. L.R., R.F., SVM, and XGB obtained a prediction accuracy of 100 % for most cancers. However, D.T. performed comparatively poorly in prediction accuracy. The results suggest that CBX expression is significantly altered in all the cancers studied; therefore, they might be treated as potential biomarkers for therapeutic intervention of these cancers.
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Affiliation(s)
| | | | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India.
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7
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Fu Y, Yang K, Wu K, Wang H, Li Q, Zhang F, Yang K, Yao Q, Ma X, Deng Y, Zhang J, Liu C, Qu K. Identification of hepatocellular carcinoma subtypes based on PcG-related genes and biological relevance with cancer cells. Clin Epigenetics 2022; 14:184. [PMID: 36566204 PMCID: PMC9790136 DOI: 10.1186/s13148-022-01393-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 11/30/2022] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) is an extensive heterogeneous disease where epigenetic factors contribute to its pathogenesis. Polycomb group (PcG) proteins are a group of subunits constituting various macro-molecular machines to regulate the epigenetic landscape, which contributes to cancer phenotype and has the potential to develop a molecular classification of HCC. RESULTS Here, based on multi-omics data analysis of DNA methylation, mRNA expression, and copy number of PcG-related genes, we established an epigenetic classification system of HCC, which divides the HCC patients into two subgroups with significantly different outcomes. Comparing these two epigenetic subgroups, we identified different metabolic features, which were related to epigenetic regulation of polycomb-repressive complex 1/2 (PRC1/2). Furthermore, we experimentally proved that inhibition of PcG complexes enhanced the lipid metabolism and reduced the capacity of HCC cells against glucose shortage. In addition, we validated the low chemotherapy sensitivity of HCC in Group A and found inhibition of PRC1/2 promoted HCC cells' sensitivity to oxaliplatin in vitro and in vivo. Finally, we found that aberrant upregulation of CBX2 in Group A and upregulation of CBX2 were associated with poor prognosis in HCC patients. Furthermore, we found that manipulation of CBX2 affected the levels of H3K27me3 and H2AK119ub. CONTRIBUTIONS Our study provided a novel molecular classification system based on PcG-related genes data and experimentally validated the biological features of HCC in two subgroups. Our founding supported the polycomb complex targeting strategy to inhibit HCC progression where CBX2 could be a feasible therapeutic target.
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Affiliation(s)
- Yunong Fu
- grid.452438.c0000 0004 1760 8119Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, 710061 Shaanxi China
| | - Kaibo Yang
- grid.452438.c0000 0004 1760 8119Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, 710061 Shaanxi China
| | - Kunjin Wu
- grid.452438.c0000 0004 1760 8119Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, 710061 Shaanxi China
| | - Hai Wang
- grid.452438.c0000 0004 1760 8119Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, 710061 Shaanxi China
| | - Qinglin Li
- grid.452438.c0000 0004 1760 8119Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, 710061 Shaanxi China
| | - Fengping Zhang
- grid.452438.c0000 0004 1760 8119Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, 710061 Shaanxi China
| | - Kun Yang
- grid.452438.c0000 0004 1760 8119Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, 710061 Shaanxi China
| | - Qing Yao
- grid.452438.c0000 0004 1760 8119Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, 710061 Shaanxi China
| | - Xiaohua Ma
- grid.452438.c0000 0004 1760 8119Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, 710061 Shaanxi China
| | - Yujie Deng
- grid.417295.c0000 0004 1799 374XDepartment of Geriatrics, Xijing Hospital, Fourth Military Medical University, Xi’an, Shaanxi China
| | - Jingyao Zhang
- grid.452438.c0000 0004 1760 8119Department of Surgical Intensive Care Units, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, 710061 Shaanxi China
| | - Chang Liu
- grid.452438.c0000 0004 1760 8119Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, 710061 Shaanxi China ,grid.452438.c0000 0004 1760 8119Department of Surgical Intensive Care Units, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, 710061 Shaanxi China
| | - Kai Qu
- grid.452438.c0000 0004 1760 8119Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, 710061 Shaanxi China
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An intersectional analysis of LncRNAs and mRNAs reveals the potential therapeutic targets of Bi Zhong Xiao Decoction in collagen-induced arthritis rats. Chin Med 2022; 17:110. [PMID: 36109779 PMCID: PMC9479270 DOI: 10.1186/s13020-022-00670-z] [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: 05/16/2022] [Accepted: 09/12/2022] [Indexed: 11/12/2022] Open
Abstract
Background Bi Zhong Xiao decoction (BZXD), a traditional Chinese herbal formula, has been used clinically for many years to treat rheumatoid arthritis (RA). Both clinical and experimental studies have revealed that BZXD is effective in treating RA, but the mechanism remains unclear. In this study, we aimed to explore the mechanism of efficacy of BZXD through transcriptomic analysis of lncRNA and mRNA. Methods The combination method of ultra-high performance liquid chromatography-mass spectrometry/mass spectrometry was used to assess the quality of BZXD. The efficacy of BZXD in treating collagen-induced arthritis (CIA) was evaluated by clinical assessment, weight changes, hematoxylin–eosin and safranin o-fast green staining, and Micro-CT. Arraystar rat lncRNA-mRNA chip technology was used to determine the lncRNA and mRNA expression profiles of the Control, CIA and BZXD groups, and to screen gene expression profiles related to the curative effect of BZXD. A lncRNA-mRNA co-expression network was constructed for the therapeutic efficacy genes. Through GO function and KEGG pathway enrichment analysis, the biological functions and signaling pathways of therapeutic efficacy genes were determined. Based on fold change and functional annotation, key differentially expressed lncRNAs and mRNAs were selected for reverse transcription-quantitative polymerase chain reaction (RT-qPCR) validation. The functions of lncRNAs targeting mRNAs were verified in vitro. Results We demonstrated that BZXD could effectively reverse bone erosion. After BZXD treatment, up to 33 lncRNAs and 107 mRNAs differentially expressed genes were reversely regulated by BZXD. These differentially expressed lncRNAs are mainly involved in the biological process of the immune response and are closely related to the ECM-receptor interaction, MAPK signaling pathway, Focal adhesion, Ras signaling pathway, Antigen processing and presentation, and Chemokine signaling pathway. We identified four lncRNAs (uc.361−, ENSRNOT00000092834, ENSRNOT00000089244, ENSRNOT00000084631) and three mRNAs (Acvr2a, Cbx2, Morc4) as potential therapeutic targets for BZXD and their microarray data consistent with the RT-qPCR. In vitro experiments confirmed that silencing the lncRNAs ENSRNOT00000092834 and ENSRNOT00000084631 reversed the expression of target mRNAs. Conclusions This study elucidates the possible mechanism of BZXD reversing bone erosion in CIA rats from the perspective of lncRNA and mRNA. To provide a basis and direction for further exploration of the mechanism of BZXD in treating RA. Supplementary Information The online version contains supplementary material available at 10.1186/s13020-022-00670-z.
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Zhang YJ, Zhao LY, He X, Yao RF, Lu F, Lu BN, Pang ZR. CBXs-related prognostic gene signature correlates with immune microenvironment in gastric cancer. Aging (Albany NY) 2022; 14:6227-6254. [PMID: 35969177 PMCID: PMC9417237 DOI: 10.18632/aging.204214] [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: 05/06/2022] [Accepted: 07/12/2022] [Indexed: 12/09/2022]
Abstract
Background: Chromobox (CBX) proteins are important Polycomb family proteins in the development of gastric cancer. Nonetheless, the relationship between CBXs and gastric cancer microenvironment remains unclear. Methods: Multiple databases were used for the analysis of CBXs expression and clinical value in gastric cancer patients. A Cox regression analysis was used to evaluate the prognostic importance of CBXs. Thereafter, regression analysis of LASSO Cox was used to construct the prognostic model. Spearman's correlation between risk score and immune infiltration was analyzed using the McP-counter algorithm. A predicted nomogram was developed to predict the overall survival of gastric cancer patients after 1, 2, and 3 years. Results: In contrast with normal tissues, mRNA and protein expression levels of CBX2/3 were significantly high in gastric cancer tissues, whereas those of CBX6/7 were low. CBXs significantly correlated with immune subtypes and molecular subtypes. A prognostic gene model based on five CBX genes (CBX1, CBX2, CBX3, CBX7, and CBX8) predicted the overall survival of gastric cancer patients. A significant correlation was noted between the risk score of the CBXs-related prognostic gene model and immune-cell infiltration. Low risk patients could achieve a better response to immune checkpoint inhibitors. A predictive nomogram constructed using the above five CBX genes revealed that overall survival rates over 1, 2, and 3 years could be reasonably predicted. Therefore, the roles of CBXs were associated with chromatin modifications and histone methylation, etc. Conclusion: In summary, we identified a prognostic CBXs model comprising five genes (CBX1, CBX2, CBX3, CBX7, and CBX8) for gastric cancer patients through bioinformatics analysis.
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Affiliation(s)
- Yin Jiang Zhang
- School of Pharmacy, Minzu University of China, Beijing, P.R. China
- Key Laboratory of Ethnomedicine (Minzu University of China), Ministry of Education, Beijing, P.R. China
| | - Lin Yi Zhao
- School of Pharmacy, Minzu University of China, Beijing, P.R. China
- Key Laboratory of Ethnomedicine (Minzu University of China), Ministry of Education, Beijing, P.R. China
| | - Xu He
- School of Pharmacy, Minzu University of China, Beijing, P.R. China
- Key Laboratory of Ethnomedicine (Minzu University of China), Ministry of Education, Beijing, P.R. China
| | - Rong Fei Yao
- School of Pharmacy, Minzu University of China, Beijing, P.R. China
- Key Laboratory of Ethnomedicine (Minzu University of China), Ministry of Education, Beijing, P.R. China
| | - Fan Lu
- School of Pharmacy, Minzu University of China, Beijing, P.R. China
- Key Laboratory of Ethnomedicine (Minzu University of China), Ministry of Education, Beijing, P.R. China
| | - Bi Nan Lu
- School of Pharmacy, Minzu University of China, Beijing, P.R. China
- Key Laboratory of Ethnomedicine (Minzu University of China), Ministry of Education, Beijing, P.R. China
| | - Zong Ran Pang
- School of Pharmacy, Minzu University of China, Beijing, P.R. China
- Key Laboratory of Ethnomedicine (Minzu University of China), Ministry of Education, Beijing, P.R. China
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Deng S, Feng Y, Pauklin S. 3D chromatin architecture and transcription regulation in cancer. J Hematol Oncol 2022; 15:49. [PMID: 35509102 PMCID: PMC9069733 DOI: 10.1186/s13045-022-01271-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 04/21/2022] [Indexed: 12/18/2022] Open
Abstract
Chromatin has distinct three-dimensional (3D) architectures important in key biological processes, such as cell cycle, replication, differentiation, and transcription regulation. In turn, aberrant 3D structures play a vital role in developing abnormalities and diseases such as cancer. This review discusses key 3D chromatin structures (topologically associating domain, lamina-associated domain, and enhancer-promoter interactions) and corresponding structural protein elements mediating 3D chromatin interactions [CCCTC-binding factor, polycomb group protein, cohesin, and Brother of the Regulator of Imprinted Sites (BORIS) protein] with a highlight of their associations with cancer. We also summarise the recent development of technologies and bioinformatics approaches to study the 3D chromatin interactions in gene expression regulation, including crosslinking and proximity ligation methods in the bulk cell population (ChIA-PET and HiChIP) or single-molecule resolution (ChIA-drop), and methods other than proximity ligation, such as GAM, SPRITE, and super-resolution microscopy techniques.
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Affiliation(s)
- Siwei Deng
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Old Road, Headington, Oxford, OX3 7LD, UK
| | - Yuliang Feng
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Old Road, Headington, Oxford, OX3 7LD, UK
| | - Siim Pauklin
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Old Road, Headington, Oxford, OX3 7LD, UK.
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11
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Hu K, Yao L, Zhou L, Li J. Diverse Chromobox Family Members: Potential Prognostic Biomarkers and Therapeutic Targets in Head and Neck Squamous Cell Carcinoma. Int J Gen Med 2022; 15:2463-2474. [PMID: 35282653 PMCID: PMC8904945 DOI: 10.2147/ijgm.s350783] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 02/09/2022] [Indexed: 12/25/2022] Open
Abstract
Background The Chromobox (CBX) family members were involved in a variety of physiological and oncological processes through the regulation of the epigenetic modification of chromatin. However, the comprehensive analysis of the CBX family in head and neck squamous cell carcinoma (HNSC) is lacking. Methods In this work, we used multiple online databases and tools to investigate the roles of CBX family in aspects of gene expression, prognostic evaluation, genetic alteration, immune micro-environment of tumor, and status of methylation. Results The mRNA expression levels of CBX1, CBX3, and CBX5 were aberrantly increased in patients with HNSC, while CBX7 was aberrantly decreased. Higher expression of CBX7 was significantly associated with longer OS. Within the 5–11% of genetic alteration rate of CBXs, CBX3 ranked the highest and CBX5/7 ranked the lowest. SPRR1B, S100A7, CASP14, CDSN, LCE3D were the top 5 neighbor genes with the strongest association with CBXs in HNSC patients. Signaling pathways such as epidermal cell differentiation, cornification, and peptide cross-linking were demonstrated to have a strong association with CBX genes. The profiles of immune cell infiltration had high similarity for the group of HNSC patients stratified by expression of CBXs. The methylation levels of CBX1 and CBX5 significantly decreased, while that of CBX7 significantly increased in HNSC samples when compared with normal tissue. Conclusion In conclusion, the CBX family showed its valuation for further investigation in HNSC. Our research highlighted that CBX7 had the potential to be a novel diagnostic and prognostic biomarker for patients with HNSC.
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Affiliation(s)
- Kuan Hu
- Department of Hepatobiliary Surgery, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People’s Republic of China
| | - Lei Yao
- Department of Hepatobiliary Surgery, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People’s Republic of China
| | - Lei Zhou
- Department of Anesthesiology, Third Xiangya Hospital of Central South University, Changsha, 410008, Hunan, People’s Republic of China
| | - Juanni Li
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People’s Republic of China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People’s Republic of China
- Correspondence: Juanni Li, Department of Pathology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People’s Republic of China, Email
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12
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Choi BH, Colon TM, Lee E, Kou Z, Dai W. CBX8 interacts with chromatin PTEN and is involved in regulating mitotic progression. Cell Prolif 2021; 54:e13110. [PMID: 34592789 PMCID: PMC8560621 DOI: 10.1111/cpr.13110] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 07/14/2021] [Accepted: 07/27/2021] [Indexed: 02/06/2023] Open
Abstract
OBJECTIVES Besides its role in regulating phosphatidylinositol-3 kinase (PI3K) signalling in the cytosol, PTEN also has a nuclear function. In this study, we attempted to understand the mechanism of chromatin PTEN in suppressing chromosomal instability during cell division. MATERIALS AND METHODS Immunocoprecipitation, ectopic expression, and deletional analyses were used to identify the physical interaction between Chromobox Homolog protein 8 (CBX8) and PTEN, as well as the functional domain(s) of PTEN mediating the interaction. Cell synchronization followed by immunoblotting was employed to study cell cycle regulation of CBX8 and the functional interaction between chromatin PTEN and CBX8. Small interfering RNAs (siRNAs) were used to study the role of PTEN and CBX8 in modulating histone epigenetic markers during the cell cycle. RESULTS Polycomb group (PcG) proteins including CBXs function to repress gene expression in a wide range of organisms including mammals. We recently showed that PTEN interacted with CBX8, a component of Polycomb Repressing Complex 1 (PRC1), and that CBX8 co-localized with PTEN in the nucleus. CBX8 levels were high, coinciding with its phosphorylation in mitosis. Phosphorylation of CBX8 was associated with monoubiquitinated PTEN and phosphorylated-BubR1 on chromatin. Moreover, CBX8 played an important role in cell proliferation and mitotic progression. Significantly, downregulation of either PTEN or CBX8 induced H3K27Me3 epigenetic marker in mitotic cells. CONCLUSION CBX8 is a new component that physically interacts with chromatin PTEN, playing an important role in regulating mitotic progression.
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Affiliation(s)
- Byeong Hyeok Choi
- Department of Environmental MedicineNew York University Grossman School of MedicineNew YorkNYUSA
| | - Tania Marlyn Colon
- Department of Environmental MedicineNew York University Grossman School of MedicineNew YorkNYUSA
| | - Eunji Lee
- Department of Environmental MedicineNew York University Grossman School of MedicineNew YorkNYUSA
| | - Ziyue Kou
- Department of Environmental MedicineNew York University Grossman School of MedicineNew YorkNYUSA
| | - Wei Dai
- Department of Environmental MedicineNew York University Grossman School of MedicineNew YorkNYUSA
- Department of Biochemistry and Molecular PharmacologyNew York University Langone Medical CenterNew YorkNYUSA
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13
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Li J, Ouyang T, Li M, Hong T, Alriashy M, Meng W, Zhang N. CBX7 is Dualistic in Cancer Progression Based on its Function and Molecular Interactions. Front Genet 2021; 12:740794. [PMID: 34659360 PMCID: PMC8517511 DOI: 10.3389/fgene.2021.740794] [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: 07/22/2021] [Accepted: 09/17/2021] [Indexed: 12/12/2022] Open
Abstract
Chromobox protein homolog 7 (CBX7) is a member of the Chromobox protein family and participates in the formation of the polycomb repressive complex 1(PRC1). In cells, CBX7 often acts as an epigenetic regulator to regulate gene expression. However, pathologically, abnormal expression of CBX7 can lead to an imbalance of gene expression, which is closely related to the occurrence and progression of cancers. In cancers, CBX7 plays a dual role; On the one hand, it contributes to cancer progression in some cancers by inhibiting oncosuppressor genes. On the other hand, it suppresses cancer progression by interacting with different molecules to regulate the synthesis of cell cycle-related proteins. In addition, CBX7 protein may interact with different RNAs (microRNAs, long noncoding RNAs, circular RNAs) in different cancer environments to participate in a variety of pathways, affecting the development of cancers. Furthermore, CBX7 is involved in cancer-related immune response and DNA repair. In conclusion, CBX7 expression is a key factor in the occurrence and progression of cancers.
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Affiliation(s)
- Jun Li
- Department of the Second Clinical Medical College of Nanchang University, Jiangxi Province, China
| | - Taohui Ouyang
- Department of Neurosurgery, the First Affiliated Hospital of Nanchang University, Jiangxi Province, China
| | - Meihua Li
- Department of Neurosurgery, the First Affiliated Hospital of Nanchang University, Jiangxi Province, China
| | - Tao Hong
- Department of Neurosurgery, the First Affiliated Hospital of Nanchang University, Jiangxi Province, China
| | - Mhs Alriashy
- Department of Neurosurgery, Huashan Hospital of Fudan University, Shanghai, China
| | - Wei Meng
- Department of Neurosurgery, the First Affiliated Hospital of Nanchang University, Jiangxi Province, China
| | - Na Zhang
- Department of Neurology, the First Affiliated Hospital of Nanchang University, Jiangxi Province, China
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14
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Zhu J, Luo JE, Chen Y, Wu Q. Circ_0061140 knockdown inhibits tumorigenesis and improves PTX sensitivity by regulating miR-136/CBX2 axis in ovarian cancer. J Ovarian Res 2021; 14:136. [PMID: 34649611 PMCID: PMC8518226 DOI: 10.1186/s13048-021-00888-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 09/29/2021] [Indexed: 02/07/2023] Open
Abstract
Background Ovarian cancer is an aggressive tumor in women with high mortality. Paclitaxel (PTX) can be used for the chemotherapy of ovarian cancer. Here, the roles of circular_0061140 (circ_0061140) in PTX sensitivity and malignant progression of ovarian cancer are unveiled. Methods The expressions of circ_0061140, microRNA-136 (miR-136) and chromobox 2 (CBX2) mRNA were detected by quantitative real-time polymerase chain reaction (qRT-PCR). Protein expression was determined by western blot. The half maximal inhibitory concentration (IC50) of PTX was determined by 3-(4,5-Dimethylthazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay. Cell proliferation was investigated by cell counting kit-8 (CCK-8) and colony formation assays. Cell apoptosis was demonstrated by flow cytometry analysis. Cell migration and invasion were evaluated by transwell assay. The binding relationship between miR-136 and circ_0061140 or CBX2 was predicted by interactome or starbase online database, and identified by dual-luciferase reporter assay. The effects of circ_0061140 on tumor formation and PTX sensitivity in vivo were disclosed by tumor formation assay. Results Circ_0061140 and CBX2 expressions were upregulated, while miR-136 expression was downregulated in PTX-resistant tissues and cells compared with control groups. Circ_0061140 knockdown repressed cell proliferation, migration and invasion, and promoted cell apoptosis and PTX sensitivity; however, these effects were restrained by miR-136 RNAi. Additionally, circ_0061140 was a sponge of miR-136, and miR-136 bound to CBX2. Furthermore, circ_0061140 knockdown inhibited tumor formation and improved PTX sensitivity in vivo. Conclusions Circ_0061140 silencing repressed the progression and PTX resistance of ovarian cancer by downregulating CBX2 expression via sponging miR-136, which provided novel insight into studying the therapy of ovarian cancer with PTX. Supplementary Information The online version contains supplementary material available at 10.1186/s13048-021-00888-9.
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Affiliation(s)
- Jun Zhu
- Department of Obstetrics and Gynecology, Suizhou Hospital, Hubei University of Medicine, Suizhou Central Hospital, No. 60 Longmen Street, Dongcheng District, Suizhou, 441300, China
| | - Jun-E Luo
- Department of Gynecology, Suizhou Hospital, Hubei University of Medicine, Suizhou Central Hospital, Suizhou, 441300, China
| | - Yurong Chen
- Department of Obstetrics and Gynecology, Suizhou Maternal and Child Health Hospital, Suizhou, 441300, China
| | - Qiong Wu
- Department of Obstetrics and Gynecology, Suizhou Hospital, Hubei University of Medicine, Suizhou Central Hospital, No. 60 Longmen Street, Dongcheng District, Suizhou, 441300, China.
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15
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Zhou H, Xiong Y, Liu Z, Hou S, Zhou T. Expression and prognostic significance of CBX2 in colorectal cancer: database mining for CBX family members in malignancies and vitro analyses. Cancer Cell Int 2021; 21:402. [PMID: 34321009 PMCID: PMC8317347 DOI: 10.1186/s12935-021-02106-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Accepted: 07/21/2021] [Indexed: 11/23/2022] Open
Abstract
Background The Chromobox (CBX) domain protein family, a core component of polycomb repressive complexes 1, is involved in transcriptional repression, cell differentiation, and program development by binding to methylated histone tails. Each CBX family member plays a distinct role in various biological processes through their own specific chromatin domains, due to differences in conserved sequences of the CBX proteins. It has been demonstrated that colorectal cancer (CRC) is a multiple-step biological evolutionary process, whereas the roles of the CBX family in CRC remain largely unclear. Methods In the present study, the expression and prognostic significance of the CBX family in CRC were systematically analyzed through a series of online databases, including Cancer Cell Line Encyclopedia (CCLE), Oncomine, Human Protein Atlas (HPA), and Gene Expression Profiling Interactive Analysis (GEPIA). For in vitro verification, we performed cell cloning, flow cytometry and transwell experiments to verify the proliferation and invasion ability of CRC cells after knocking down CBX2. Results Most CBX proteins were found to be highly expressed in CRC, but only the elevated expression of CBX2 could be associated with poor prognosis in patients with CRC. Further examination of the role of CBX2 in CRC was performed through several in vitro experiments. CBX2 was overexpressed in CRC cell lines via the CCLE database and the results were verified by RT-qPCR. Moreover, the knockdown of CBX2 significantly suppressed CRC cell proliferation and invasion. Furthermore, the downregulation of CBX2 was found to promote CRC cell apoptosis. Conclusions Based on these findings, CBX2 may function as an oncogene and potential prognostic biomarker. Thus, the association between the abnormal expression of CBX2 and the initiation of CRC deserves further exploration.
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Affiliation(s)
- He Zhou
- The Second Department of Gastrointestinal Surgery, Affiliated Hospital of North Sichuan Medical College, 63 Wenhua Road, Nanchong, 637000, Sichuan Province, China.,Institute of Hepatobiliary, Pancreatic and Intestinal Disease, North Sichuan Medical College, Nanchong, 637000, Sichuan, China
| | - Yongfu Xiong
- The First Department of Hepatobiliary Surgery, Affiliated Hospital of North Sichuan Medical College, Nanchong, 637000, Sichuan, China.,Institute of Hepatobiliary, Pancreatic and Intestinal Disease, North Sichuan Medical College, Nanchong, 637000, Sichuan, China
| | - Zuoliang Liu
- The Second Department of Gastrointestinal Surgery, Affiliated Hospital of North Sichuan Medical College, 63 Wenhua Road, Nanchong, 637000, Sichuan Province, China.,Institute of Hepatobiliary, Pancreatic and Intestinal Disease, North Sichuan Medical College, Nanchong, 637000, Sichuan, China
| | - Songlin Hou
- The Second Department of Gastrointestinal Surgery, Affiliated Hospital of North Sichuan Medical College, 63 Wenhua Road, Nanchong, 637000, Sichuan Province, China.,Institute of Hepatobiliary, Pancreatic and Intestinal Disease, North Sichuan Medical College, Nanchong, 637000, Sichuan, China
| | - Tong Zhou
- The Second Department of Gastrointestinal Surgery, Affiliated Hospital of North Sichuan Medical College, 63 Wenhua Road, Nanchong, 637000, Sichuan Province, China. .,Institute of Hepatobiliary, Pancreatic and Intestinal Disease, North Sichuan Medical College, Nanchong, 637000, Sichuan, China.
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16
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Li Z, Liu Z, Li C, Liu Q, Tan B, Liu Y, Zhang Y, Li Y. CDCA1/2/3/5/7/8 as novel prognostic biomarkers and CDCA4/6 as potential targets for gastric cancer. Transl Cancer Res 2021; 10:3404-3417. [PMID: 35116645 PMCID: PMC8798863 DOI: 10.21037/tcr-20-1050] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 05/10/2021] [Indexed: 01/09/2023]
Abstract
Background Increasing evidence had suggested that cell division cycle-associated (CDCA) family proteins play prominent roles in multiple types of cancer. However, the expression pattern and prognostic value of CDCAs in gastric cancer were still poorly understood. Methods In this study, bioinformatics was used for the first time to comprehensively discuss the expression changes of the CDCA protein family in gastric cancer. We studied the transcription and survival data of CDCAs in patients with gastric cancer in Oncomine, GEPIA, DAVID, cBioportal, and other databases. Results We identified that the CDCA 1/2/3/4/5/6/7/8 were overexpressed gastric cancer than in normal tissues. There was no significant difference in CDCAs expression among different gastric cancer stages. High expression of CDCA4/6 in patients with gastric cancer was closely related to low overall survival (OS), first progression survival (FPS), and post-progression survival (PPS). In contrast, high CDCA1/2/3/5/7/8 expression predicted a better prognosis. The genetic mutation rate of CDCA2 and CDCA4 was 4%, ranking first. The main biological process of CDCAs protein family enrichment was cell division, the main cell component involved was centromeres of chromosomes, and the main molecular function involved was protein binding. Conclusions The study suggested that CDCA1/2/3/5/7/8 were expected to be new prognostic markers for gastric cancer, and CDCA4/6 might be potential targets for the treatment of gastric cancer.
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Affiliation(s)
- Zhaoxing Li
- Department of General Surgery, The Fourth Affiliated Hospital of Hebei Medical University, Shijiazhuang, China
| | - Zhao Liu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Gastrointestinal Surgery, Peking University Cancer Hospital and Institute, Beijing, China
| | - Chuang Li
- The Second Hospital of Shijiazhuang, Shijiazhuang, China
| | - Qingwei Liu
- Department of General Surgery, The Fourth Affiliated Hospital of Hebei Medical University, Shijiazhuang, China
| | - Bibo Tan
- Department of General Surgery, The Fourth Affiliated Hospital of Hebei Medical University, Shijiazhuang, China
| | - Yu Liu
- Department of General Surgery, The Fourth Affiliated Hospital of Hebei Medical University, Shijiazhuang, China
| | | | - Yong Li
- Department of General Surgery, The Fourth Affiliated Hospital of Hebei Medical University, Shijiazhuang, China
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17
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Zhou J, Chen Z, Zou M, Wan R, Wu T, Luo Y, Wu G, Wang W, Liu T. Prognosis and Immune Infiltration of Chromobox Family Genes in Sarcoma. Front Oncol 2021; 11:657595. [PMID: 34046352 PMCID: PMC8147558 DOI: 10.3389/fonc.2021.657595] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 04/13/2021] [Indexed: 12/16/2022] Open
Abstract
Background Chromobox family genes (CBXs) are known to play roles in numerous modifications of the chromatin in order to inhibit the transcription of target genes. CBXs have been shown to be expressed at high levels in many types of cancer and can also serve as a target gene for therapeutic purposes. However, little is known about the expression and prognostic value of CBXs in human sarcomas. Methods The transcription level of CBXs was analyzed using the Oncomine dataset, and the differential expression of CBXs in sarcoma was reported by the Gene Expression Profiling Interactive Analysis (GEPIA) dataset. We also used the CCLE dataset to evaluate the expression of CBXs in a sarcoma cell line. The prognostic value of CBXs was analyzed using GEPIA and Kaplan–Meier analysis. In addition, the corrections between CBXs and their co-expressed genes were reported using Oncomine and GEPIA datasets. DAVID was used to perform GO function enrichment analysis for the CBXs and their co-expression genes. Finally, TIMER was used to analyze the immune cell infiltration of CBXs in patients with sarcoma. Results HP1-α/β/γ (CBX1/3/5) and CBX4/6/8 were found to be overexpressed in human sarcoma, and CBXs were upregulated in almost all the sarcoma cell line. The expression levels of HP1-α/β/γ (CBX1/3/5) and CBX7 were associated with overall survival (OS) in patients with sarcoma, while high expression levels of CBX7 were related to disease-free survival (DFS). In addition, the expression levels of CBX2/6/7 were related to recurrence-free survival (RFS). We also found that the CBX family was positively correlated with the infiltration of immune cells, including CD8+ T cells, CD4+ T cells, B cells, macrophages, neutrophils, and dendritic cells, in sarcoma. Conclusions The results from the present study indicated that CBXs were significantly associated with prognosis and immunological status in sarcoma. These data suggest that CBXs could serve as potential biomarkers for prognosis and immune infiltration in human sarcoma.
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Affiliation(s)
- Jian Zhou
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Ziyuan Chen
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Ming Zou
- Department of Orthopedics, Brain Hospital of Hunan Province (The Second People's Hospital of Hunan Province), Changsha, China
| | - Rongjun Wan
- Department of Respiratory and Critical Care Medicine, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, China
| | - Tong Wu
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Yingquan Luo
- Department of General Medicine, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Gen Wu
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, China.,Clinical Medicine Eight-Year Program, Central South University, Changsha, China
| | - Wanchun Wang
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Tang Liu
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital, Central South University, Changsha, China
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18
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Chetverina DA, Lomaev DV, Erokhin MM. Polycomb and Trithorax Group Proteins: The Long Road from Mutations in Drosophila to Use in Medicine. Acta Naturae 2020; 12:66-85. [PMID: 33456979 PMCID: PMC7800605 DOI: 10.32607/actanaturae.11090] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 09/30/2020] [Indexed: 12/12/2022] Open
Abstract
Polycomb group (PcG) and Trithorax group (TrxG) proteins are evolutionarily conserved factors responsible for the repression and activation of the transcription of multiple genes in Drosophila and mammals. Disruption of the PcG/TrxG expression is associated with many pathological conditions, including cancer, which makes them suitable targets for diagnosis and therapy in medicine. In this review, we focus on the major PcG and TrxG complexes, the mechanisms of PcG/TrxG action, and their recruitment to chromatin. We discuss the alterations associated with the dysfunction of a number of factors of these groups in oncology and the current strategies used to develop drugs based on small-molecule inhibitors.
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Affiliation(s)
- D. A. Chetverina
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334 Russia
| | - D. V. Lomaev
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334 Russia
| | - M. M. Erokhin
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334 Russia
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19
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Xie X, Ning Y, Long J, Wang H, Chen X. Diverse CBX family members as potential prognostic biomarkers in non-small-cell lung cancer. FEBS Open Bio 2020; 10:2206-2215. [PMID: 32894652 PMCID: PMC7530393 DOI: 10.1002/2211-5463.12971] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 08/19/2020] [Accepted: 09/01/2020] [Indexed: 12/11/2022] Open
Abstract
Chromobox (CBX) family members are vital epigenetic regulators that repress the transcription of target genes through chromatin modification. Several studies have investigated the role of CBX family members in cancer. However, the function and prognostic value of diverse CBX family members in non‐small‐cell lung cancer remain largely unknown. In this study, we reveal that CBX family members are overexpressed in non‐small‐cell lung cancer tissue compared with normal lung tissue, with the exception of CBX6. Kaplan–Meier analysis demonstrated that high expressions of CBX1 and CBX3 are correlated with overall survival, disease‐specific survival, disease‐free interval, and progression‐free interval for patients with lung adenocarcinoma (LUAD). Furthermore, regression model analysis suggests that CBX3 may be suitable as an independent prediction factor for overall survival and progression‐free interval in patients with LUAD. In addition, CBX3 mRNA expression was found to be associated with tumor diameter and lymph node metastasis. Gene enrichment analysis suggests that CBX3 is involved in the cell cycle and P53 signaling pathways. Aberrant expression of CBX3 in LUAD is correlated with DNA copy number alteration. In summary, our data imply that CBX3 plays an important role in the promotion of LUAD and may thus have potential as a prognostic biomarker and molecular therapeutic target for the disease.
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Affiliation(s)
- Xiaobin Xie
- School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, China
| | - Yue Ning
- Department of Pathology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Jie Long
- School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, China
| | - Hongyan Wang
- School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, China
| | - Xiaowei Chen
- Department of Hematology, Guangzhou First People's Hospital, South China University of Technology School of Medicine, Guangzhou, China
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20
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Dou Y, Chen F, Lu Y, Qiu H, Zhang H. Effects of Wnt/β-Catenin Signal Pathway Regulated by miR-342-5p Targeting CBX2 on Proliferation, Metastasis and Invasion of Ovarian Cancer Cells. Cancer Manag Res 2020; 12:3783-3794. [PMID: 32547214 PMCID: PMC7247607 DOI: 10.2147/cmar.s250208] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 04/20/2020] [Indexed: 12/12/2022] Open
Abstract
Objective This study aimed to investigate the effect of Wnt/β-catenin signal pathway mediated by miR-342-5p targeting CBX2 gene on the proliferation, metastasis, invasion and apoptosis of ovarian cancer cells, and to explore its related regulatory mechanism. Methods Human normal ovarian epithelial cell line IOSE80, human ovarian cancer cell line SKOV3 and OVCAR3 were the subjects. Software were used to predict the binding site of miR-342-5p targeting CBX2 gene. The proliferation rate of ovarian cancer cells was detected by MTT method; the cell viability of each group was observed by colony formation test; the apoptosis of cells in each group was detected by flow cytometry; the invasive ability of cells was determined by transwell test, and the migration ability of cells was detected by scratch test. The mRNA expression levels of miR-342-5p, CBX2, Wnt1, β-catenin, C-myc and Cyclin D1 were measured by qRT-PCR. Also, Western blot was used to determine the protein expression levels of CBX2, Wnt1, β-catenin, C-myc and Cyclin D1. Results CBX2 was identified as the target gene of miR-342-5p. MTT test results showed that miR-342-5p could significantly inhibit the proliferation of SKOV3 and OVCAR3 cells, colony formation assay results indicated that the viability of SKOV3 and OVCAR3 cells transfected with miR-342-5p decreased significantly, and flow cytometry results suggested that miR-342-5p could promote the apoptosis of SKOV3 and OVCAR3 cells. Also, the results of transwell showed that miR-342-5p could significantly inhibit the invasive ability of SKOV3 and OVCAR3 cells, and the results of scratch assay suggested that miR-342-5p could significantly inhibit the migration of SKOV3 and OVCAR3 cells. Moreover, qRT-PCR and Western blot results indicated that the mRNA and protein expression levels of CBX2, Wnt1, β-catenin, C-myc and Cyclin D1 decreased in SKOV3 and OVCAR3 cells transfected with miR-342-5p, while the mRNA expression levels of miR-342-5p increased significantly (P<0.05). Conclusion MiR-342-5p targeted gene is CBX2, which can significantly reduce the proliferation, invasion, migration and viability of ovarian cancer cell lines SKOV3 and OVCAR3, and promote their apoptosis. The mechanism may be related to the mediation of Wnt/β-catenin signal pathway and down-regulation of the related genes expression.
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Affiliation(s)
- Yan Dou
- Department of Oncology, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, School of Clinical Medicine, Henan University, Zhengzhou, Henan 450003, People's Republic of China
| | - Fengxia Chen
- Department of Oncology, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, School of Clinical Medicine, Henan University, Zhengzhou, Henan 450003, People's Republic of China
| | - Yawan Lu
- Department of Oncology, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, School of Clinical Medicine, Henan University, Zhengzhou, Henan 450003, People's Republic of China
| | - Huanhuan Qiu
- Department of Oncology, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, School of Clinical Medicine, Henan University, Zhengzhou, Henan 450003, People's Republic of China
| | - Hongmei Zhang
- Department of Nursing, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, School of Clinical Medicine, Henan University, Zhengzhou, Henan 450003, People's Republic of China
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