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Flynn J, Ahmadi MM, McFarland CT, Kubal MD, Taylor MA, Cheng Z, Torchia EC, Edwards MG. Crowdsourcing temporal transcriptomic coronavirus host infection data: Resources, guide, and novel insights. Biol Methods Protoc 2023; 8:bpad033. [PMID: 38107402 PMCID: PMC10723038 DOI: 10.1093/biomethods/bpad033] [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: 08/09/2023] [Revised: 10/07/2023] [Accepted: 11/13/2023] [Indexed: 12/19/2023] Open
Abstract
The emergence of severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) reawakened the need to rapidly understand the molecular etiologies, pandemic potential, and prospective treatments of infectious agents. The lack of existing data on SARS-CoV-2 hampered early attempts to treat severe forms of coronavirus disease-2019 (COVID-19) during the pandemic. This study coupled existing transcriptomic data from severe acute respiratory syndrome-related coronavirus 1 (SARS-CoV-1) lung infection animal studies with crowdsourcing statistical approaches to derive temporal meta-signatures of host responses during early viral accumulation and subsequent clearance stages. Unsupervised and supervised machine learning approaches identified top dysregulated genes and potential biomarkers (e.g. CXCL10, BEX2, and ADM). Temporal meta-signatures revealed distinct gene expression programs with biological implications to a series of host responses underlying sustained Cxcl10 expression and Stat signaling. Cell cycle switched from G1/G0 phase genes, early in infection, to a G2/M gene signature during late infection that correlated with the enrichment of DNA damage response and repair genes. The SARS-CoV-1 meta-signatures were shown to closely emulate human SARS-CoV-2 host responses from emerging RNAseq, single cell, and proteomics data with early monocyte-macrophage activation followed by lymphocyte proliferation. The circulatory hormone adrenomedullin was observed as maximally elevated in elderly patients who died from COVID-19. Stage-specific correlations to compounds with potential to treat COVID-19 and future coronavirus infections were in part validated by a subset of twenty-four that are in clinical trials to treat COVID-19. This study represents a roadmap to leverage existing data in the public domain to derive novel molecular and biological insights and potential treatments to emerging human pathogens.
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Affiliation(s)
- James Flynn
- Illumina Corporation, San Diego, CA 92122, United States
| | - Mehdi M Ahmadi
- Gates Center for Regenerative Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, United States
| | | | | | - Mark A Taylor
- Bioinfo Solutions LLC, Parker, CO 80134, United States
| | - Zhang Cheng
- Illumina Corporation, San Diego, CA 92122, United States
| | - Enrique C Torchia
- Gates Center for Regenerative Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, United States
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Wang Q, Bode AM, Zhang T. Targeting CDK1 in cancer: mechanisms and implications. NPJ Precis Oncol 2023; 7:58. [PMID: 37311884 DOI: 10.1038/s41698-023-00407-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 05/25/2023] [Indexed: 06/15/2023] Open
Abstract
Cyclin dependent kinases (CDKs) are serine/threonine kinases that are proposed as promising candidate targets for cancer treatment. These proteins complexed with cyclins play a critical role in cell cycle progression. Most CDKs demonstrate substantially higher expression in cancer tissues compared with normal tissues and, according to the TCGA database, correlate with survival rate in multiple cancer types. Deregulation of CDK1 has been shown to be closely associated with tumorigenesis. CDK1 activation plays a critical role in a wide range of cancer types; and CDK1 phosphorylation of its many substrates greatly influences their function in tumorigenesis. Enrichment of CDK1 interacting proteins with Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis was conducted to demonstrate that the associated proteins participate in multiple oncogenic pathways. This abundance of evidence clearly supports CDK1 as a promising target for cancer therapy. A number of small molecules targeting CDK1 or multiple CDKs have been developed and evaluated in preclinical studies. Notably, some of these small molecules have also been subjected to human clinical trials. This review evaluates the mechanisms and implications of targeting CDK1 in tumorigenesis and cancer therapy.
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Affiliation(s)
- Qiushi Wang
- The Hormel Institute, University of Minnesota, 801 16th Ave NE, Austin, MN, 55912, USA
| | - Ann M Bode
- The Hormel Institute, University of Minnesota, 801 16th Ave NE, Austin, MN, 55912, USA.
| | - Tianshun Zhang
- The Hormel Institute, University of Minnesota, 801 16th Ave NE, Austin, MN, 55912, USA.
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Gao Y, Liu S, Yang J, Su M, Xu J, Wang H, Zhang J. The Comprehensive Analysis Illustrates the Role of CDCA5 in Breast Cancer: An Effective Diagnosis and Prognosis Biomarker. Int J Genomics 2023; 2023:7150141. [PMID: 37287817 PMCID: PMC10243952 DOI: 10.1155/2023/7150141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 04/26/2023] [Accepted: 05/10/2023] [Indexed: 06/09/2023] Open
Abstract
Background Several studies have been conducted to investigate the role of cell division cycle-associated 5 (CDCA5) in cancer. Its role in breast cancer, however, remains unknown. Methods The Gene Expression Omnibus and Cancer Genome Atlas Program databases provided the open-access information needed for the research. The CCK8 and colony formation assays were used to measure cell proliferation. The capacity of breast cancer cells to invade and migrate was assessed using the transwell assay. Results In our study, CDCA5 was identified as the interested gene through a series of bioinformatics analysis. We found a higher CDCA5 expression level in tissue and cells of breast cancer. Meanwhile, CDCA5 has been linked to increased proliferation, invasion, and migration of breast cancer cells, which was also associated with worse clinical features. The biochemical pathways, in which CDCA5 was engaged, were identified using biological enrichment analysis. Immune infiltration research revealed that CDCA5 was linked to enhanced activity of several immune function terms. Meanwhile, DNA methylation might be responsible for the aberrant level of CDCA5 in tumor tissue. In addition, CDCA5 could significantly increase the paclitaxel and docetaxel sensitivity, indicating that it has the potential for clinical application. Also, we found that CDCA5 is mainly localized in cell nucleoplasm. Moreover, in the breast cancer microenvironment, we found that CDCA5 is mainly expressed in malignant cells, proliferation T cells, and neutrophils. Conclusion Overall, our findings suggest that CDCA5 is a potential prognostic indicator and target for breast cancer, which can indicate the direction of the relevant research.
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Affiliation(s)
- Yang Gao
- Department of Gynecological Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China
- Hubei Key Laboratory of Tumor Biological Behaviors, Wuhan, China
- Hubei Cancer Clinical Study Center, Wuhan, China
| | - Shuting Liu
- Hubei Key Laboratory of Tumor Biological Behaviors, Wuhan, China
- Hubei Cancer Clinical Study Center, Wuhan, China
- Department of Breast and Thyroid Surgery, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
| | - Junyuan Yang
- Department of Gynecological Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China
- Hubei Key Laboratory of Tumor Biological Behaviors, Wuhan, China
- Hubei Cancer Clinical Study Center, Wuhan, China
| | - Min Su
- Department of Gynecological Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China
- Hubei Key Laboratory of Tumor Biological Behaviors, Wuhan, China
- Hubei Cancer Clinical Study Center, Wuhan, China
| | - Jingjing Xu
- Hubei Key Laboratory of Tumor Biological Behaviors, Wuhan, China
- Hubei Cancer Clinical Study Center, Wuhan, China
- Department of Breast and Thyroid Surgery, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
| | - Hua Wang
- Department of Gynecological Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China
- Hubei Key Laboratory of Tumor Biological Behaviors, Wuhan, China
- Hubei Cancer Clinical Study Center, Wuhan, China
| | - Jingwei Zhang
- Hubei Key Laboratory of Tumor Biological Behaviors, Wuhan, China
- Hubei Cancer Clinical Study Center, Wuhan, China
- Department of Breast and Thyroid Surgery, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
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Kariri YA, Joseph C, Alsaleem MA, Elsharawy KA, Alsaeed S, Toss MS, Mongan NP, Green AR, Rakha EA. Mechanistic and Clinical Evidence Supports a Key Role for Cell Division Cycle Associated 5 (CDCA5) as an Independent Predictor of Outcome in Invasive Breast Cancer. Cancers (Basel) 2022; 14:cancers14225643. [PMID: 36428736 PMCID: PMC9688237 DOI: 10.3390/cancers14225643] [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: 08/11/2022] [Revised: 11/12/2022] [Accepted: 11/15/2022] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Cell Division Cycle Associated 5 (CDCA5) plays a role in the phosphoinositide 3-kinase (PI3K)/AKT/mTOR signalling pathway involving cell division, cancer cell migration and apoptosis. This study aims to assess the prognostic and biological value of CDCA5 in breast cancer (BC). METHODS The biological and prognostic value of CDCA5 were evaluated at mRNA (n = 5109) and protein levels (n = 614) utilizing multiple well-characterized early stage BC cohorts. The effects of CDCA5 knockdown (KD) on multiple oncogenic assays were assessed in vitro using a panel of BC cell lines. RESULTS this study examined cohorts showed that high CDCA5 expression was correlated with features characteristic of aggressive behavior and poor prognosis, including the presence of high grade, large tumor size, lymphovascular invasion (LVI), hormone receptor negativity and HER2 positivity. High CDCA5 expression, at both mRNA and protein levels, was associated with shorter BC-specific survival independent of other variables (p = 0.034, Hazard ratio (HR) = 1.6, 95% CI; 1.1-2.3). In line with the clinical data, in vitro models indicated that CDCA5 depletion results in a marked decrease in BC cell invasion and migration abilities and a significant accumulation of the BC cells in the G2/M-phase. CONCLUSIONS These results provide evidence that CDCA5 plays an important role in BC development and metastasis and could be used as a potential biomarker to predict disease progression in BC.
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Affiliation(s)
- Yousif A. Kariri
- Academic Unit for Translational Medical Sciences, School of Medicine, Biodiscovery Institute, University Park Campus, University of Nottingham, Nottingham NG7 2RD, UK
- Department of Clinical Laboratory Science, Faculty of Applied Medical Science, Shaqra University, Shaqra 11961, Saudi Arabia
- Nottingham Breast Cancer Research Centre, Nottingham NG7 2RD, UK
| | - Chitra Joseph
- School of Medicine, Nottingham City Hospital, Nottingham University Hospitals NHS Trust and The University of Nottingham, Nottingham NG5 1PB, UK
| | - Mansour A. Alsaleem
- Academic Unit for Translational Medical Sciences, School of Medicine, Biodiscovery Institute, University Park Campus, University of Nottingham, Nottingham NG7 2RD, UK
- Nottingham Breast Cancer Research Centre, Nottingham NG7 2RD, UK
- Department of Applied Medical Science, Applied College, Qassim University, Unayzah 56435, Saudi Arabia
| | - Khloud A. Elsharawy
- Academic Unit for Translational Medical Sciences, School of Medicine, Biodiscovery Institute, University Park Campus, University of Nottingham, Nottingham NG7 2RD, UK
- Nottingham Breast Cancer Research Centre, Nottingham NG7 2RD, UK
- Department of Zoology, Faculty of Science, Damietta University, Damietta 34517, Egypt
| | - Sami Alsaeed
- Academic Unit for Translational Medical Sciences, School of Medicine, Biodiscovery Institute, University Park Campus, University of Nottingham, Nottingham NG7 2RD, UK
- Nottingham Breast Cancer Research Centre, Nottingham NG7 2RD, UK
- Department of Clinical Laboratory Science, Faculty of Applied Medical Sciences, Northern Border University, Arar 73244, Saudi Arabia
| | - Michael S. Toss
- Nottingham Breast Cancer Research Centre, Nottingham NG7 2RD, UK
- School of Medicine, Nottingham City Hospital, Nottingham University Hospitals NHS Trust and The University of Nottingham, Nottingham NG5 1PB, UK
| | - Nigel P. Mongan
- Biodiscovery Institute, Faculty of Medicine and Health Sciences, School of Veterinary Medicine and Science, University of Nottingham, Nottingham NG7 2RD, UK
- Department of Pharmacology, Weill Cornell Medicine, New York, NY 10065, USA
| | - Andrew R. Green
- Academic Unit for Translational Medical Sciences, School of Medicine, Biodiscovery Institute, University Park Campus, University of Nottingham, Nottingham NG7 2RD, UK
- Nottingham Breast Cancer Research Centre, Nottingham NG7 2RD, UK
| | - Emad A. Rakha
- Academic Unit for Translational Medical Sciences, School of Medicine, Biodiscovery Institute, University Park Campus, University of Nottingham, Nottingham NG7 2RD, UK
- Nottingham Breast Cancer Research Centre, Nottingham NG7 2RD, UK
- School of Medicine, Nottingham City Hospital, Nottingham University Hospitals NHS Trust and The University of Nottingham, Nottingham NG5 1PB, UK
- Correspondence: or ; Tel.: +44-0115-9691169; Fax: +44-0115-9627768
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Hou W, Li Y, Zhang J, Xia Y, Wang X, Chen H, Lou H. Cohesin in DNA damage response and double-strand break repair. Crit Rev Biochem Mol Biol 2022; 57:333-350. [PMID: 35112600 DOI: 10.1080/10409238.2022.2027336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 01/03/2022] [Accepted: 01/06/2022] [Indexed: 11/03/2022]
Abstract
Cohesin, a four-subunit ring comprising SMC1, SMC3, RAD21 and SA1/2, tethers sister chromatids by DNA replication-coupled cohesion (RC-cohesion) to guarantee correct chromosome segregation during cell proliferation. Postreplicative cohesion, also called damage-induced cohesion (DI-cohesion), is an emerging critical player in DNA damage response (DDR). In this review, we sum up recent progress on how cohesin regulates the DNA damage checkpoint activation and repair pathway choice, emphasizing postreplicative cohesin loading and DI-cohesion establishment in yeasts and mammals. DI-cohesion and RC-cohesion show distinct features in many aspects. DI-cohesion near or far from the break sites might undergo different regulations and execute different tasks in DDR and DSB repair. Furthermore, some open questions in this field and the significance of this new scenario to our understanding of genome stability maintenance and cohesinopathies are discussed.
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Affiliation(s)
- Wenya Hou
- Shenzhen University General Hospital, Guangdong Key Laboratory for Genome Stability & Disease Prevention, Shenzhen University School of Medicine, Shenzhen, Guangdong, China
| | - Yan Li
- Shenzhen University General Hospital, Guangdong Key Laboratory for Genome Stability & Disease Prevention, Shenzhen University School of Medicine, Shenzhen, Guangdong, China
| | - Jiaxin Zhang
- Shenzhen University General Hospital, Guangdong Key Laboratory for Genome Stability & Disease Prevention, Shenzhen University School of Medicine, Shenzhen, Guangdong, China
| | - Yisui Xia
- Shenzhen University General Hospital, Guangdong Key Laboratory for Genome Stability & Disease Prevention, Shenzhen University School of Medicine, Shenzhen, Guangdong, China
| | - Xueting Wang
- Shenzhen University General Hospital, Guangdong Key Laboratory for Genome Stability & Disease Prevention, Shenzhen University School of Medicine, Shenzhen, Guangdong, China
- Union Shenzhen Hospital, Department of Dermatology, Huazhong University of Science and Technology (Nanshan Hospital), Shenzhen, Guangdong, China
| | - Hongxiang Chen
- Union Shenzhen Hospital, Department of Dermatology, Huazhong University of Science and Technology (Nanshan Hospital), Shenzhen, Guangdong, China
| | - Huiqiang Lou
- Shenzhen University General Hospital, Guangdong Key Laboratory for Genome Stability & Disease Prevention, Shenzhen University School of Medicine, Shenzhen, Guangdong, China
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Zhong L, Shu HB. Mitotic inactivation of the cGAS‒MITA/STING pathways. J Mol Cell Biol 2021; 13:721-727. [PMID: 34609492 PMCID: PMC8718187 DOI: 10.1093/jmcb/mjab061] [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: 05/23/2021] [Revised: 08/12/2021] [Accepted: 08/23/2021] [Indexed: 11/13/2022] Open
Abstract
The cyclic guanosine monophosphate‒adenosine monophosphate synthase (cGAS)‒mediator of interferon response factor 3 activation/stimulator of interferon genes (MITA/STING) axis has emerged as a major pathway, which senses microbial or mislocated cellular DNA in the cytosol to trigger innate immune responses. cGAS senses cytosolic DNA without a preference of self- or nonself-DNA. How the cGAS‒MITA/STING axis is inactivated upon nuclear envelope breakdown (NEBD) at mitotic entry in vertebrate cells to avoid self-DNA sensing remains unclear until very recently. In this review, we summarize the recent advances on how cGAS responds to chromosomes upon NEBD and the mechanisms involved in the inactivation of the cGAS‒MITA/STING pathways in mitosis.
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Affiliation(s)
- Li Zhong
- Department of Infectious Diseases, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Research Unit of Innate Immune and Inflammatory Diseases of the Chinese Academy of Medical Sciences, Wuhan 430071, China
| | - Hong-Bing Shu
- Department of Infectious Diseases, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Research Unit of Innate Immune and Inflammatory Diseases of the Chinese Academy of Medical Sciences, Wuhan 430071, China
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Antony J, Chin CV, Horsfield JA. Cohesin Mutations in Cancer: Emerging Therapeutic Targets. Int J Mol Sci 2021; 22:6788. [PMID: 34202641 PMCID: PMC8269296 DOI: 10.3390/ijms22136788] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 06/08/2021] [Accepted: 06/18/2021] [Indexed: 12/12/2022] Open
Abstract
The cohesin complex is crucial for mediating sister chromatid cohesion and for hierarchal three-dimensional organization of the genome. Mutations in cohesin genes are present in a range of cancers. Extensive research over the last few years has shown that cohesin mutations are key events that contribute to neoplastic transformation. Cohesin is involved in a range of cellular processes; therefore, the impact of cohesin mutations in cancer is complex and can be cell context dependent. Candidate targets with therapeutic potential in cohesin mutant cells are emerging from functional studies. Here, we review emerging targets and pharmacological agents that have therapeutic potential in cohesin mutant cells.
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Affiliation(s)
- Jisha Antony
- Department of Pathology, Otago Medical School, University of Otago, Dunedin 9016, New Zealand;
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Auckland 1010, New Zealand
| | - Chue Vin Chin
- Department of Pathology, Otago Medical School, University of Otago, Dunedin 9016, New Zealand;
| | - Julia A. Horsfield
- Department of Pathology, Otago Medical School, University of Otago, Dunedin 9016, New Zealand;
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Auckland 1010, New Zealand
- Genetics Otago Research Centre, University of Otago, Dunedin 9016, New Zealand
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Gui T, Yao C, Jia B, Shen K. Identification and analysis of genes associated with epithelial ovarian cancer by integrated bioinformatics methods. PLoS One 2021; 16:e0253136. [PMID: 34143800 PMCID: PMC8213194 DOI: 10.1371/journal.pone.0253136] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 05/31/2021] [Indexed: 12/24/2022] Open
Abstract
Background Though considerable efforts have been made to improve the treatment of epithelial ovarian cancer (EOC), the prognosis of patients has remained poor. Identifying differentially expressed genes (DEGs) involved in EOC progression and exploiting them as novel biomarkers or therapeutic targets is of great value. Methods Overlapping DEGs were screened out from three independent gene expression omnibus (GEO) datasets and were subjected to Gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) pathway enrichment analyses. The protein-protein interactions (PPI) network of DEGs was constructed based on the STRING database. The expression of hub genes was validated in GEPIA and GEO. The relationship of hub genes expression with tumor stage and overall survival and progression-free survival of EOC patients was investigated using the cancer genome atlas data. Results A total of 306 DEGs were identified, including 265 up-regulated and 41 down-regulated. Through PPI network analysis, the top 20 genes were screened out, among which 4 hub genes, which were not researched in depth so far, were selected after literature retrieval, including CDC45, CDCA5, KIF4A, ESPL1. The four genes were up-regulated in EOC tissues compared with normal tissues, but their expression decreased gradually with the continuous progression of EOC. Survival curves illustrated that patients with a lower level of CDCA5 and ESPL1 had better overall survival and progression-free survival statistically. Conclusion Two hub genes, CDCA5 and ESPL1, identified as probably playing tumor-promotive roles, have great potential to be utilized as novel therapeutic targets for EOC treatment.
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Affiliation(s)
- Ting Gui
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Chenhe Yao
- Department of R&D Technology Center, Beijing Zhicheng Biomedical Technology Co, Ltd, Beijing, China
| | - Binghan Jia
- Department of R&D Technology Center, Beijing Zhicheng Biomedical Technology Co, Ltd, Beijing, China
| | - Keng Shen
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
- * E-mail:
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Identification of Potentially Therapeutic Target Genes of Hepatocellular Carcinoma. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 17:ijerph17031053. [PMID: 32046048 PMCID: PMC7037431 DOI: 10.3390/ijerph17031053] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 02/05/2020] [Accepted: 02/05/2020] [Indexed: 12/14/2022]
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) is a major threat to public health. However, few effective therapeutic strategies exist. We aimed to identify potentially therapeutic target genes of HCC by analyzing three gene expression profiles. METHODS The gene expression profiles were analyzed with GEO2R, an interactive web tool for gene differential expression analysis, to identify common differentially expressed genes (DEGs). Functional enrichment analyses were then conducted followed by a protein-protein interaction (PPI) network construction with the common DEGs. The PPI network was employed to identify hub genes, and the expression level of the hub genes was validated via data mining the Oncomine database. Survival analysis was carried out to assess the prognosis of hub genes in HCC patients. RESULTS A total of 51 common up-regulated DEGs and 201 down-regulated DEGs were obtained after gene differential expression analysis of the profiles. Functional enrichment analyses indicated that these common DEGs are linked to a series of cancer events. We finally identified 10 hub genes, six of which (OIP5, ASPM, NUSAP1, UBE2C, CCNA2, and KIF20A) are reported as novel HCC hub genes. Data mining the Oncomine database validated that the hub genes have a significant high level of expression in HCC samples compared normal samples (t-test, p < 0.05). Survival analysis indicated that overexpression of the hub genes is associated with a significant reduction (p < 0.05) in survival time in HCC patients. CONCLUSIONS We identified six novel HCC hub genes that might be therapeutic targets for the development of drugs for some HCC patients.
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Meng J, Gao L, Zhang M, Gao S, Fan S, Liang C. Systematic investigation of the prognostic value of cell division cycle-associated proteins for clear cell renal cell carcinoma patients. Biomark Med 2020; 14:223-238. [PMID: 31955607 DOI: 10.2217/bmm-2019-0498] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Aim: To explore the prognostic value of the cell division cycle-associated proteins (CDCA) family in clear cell renal cell carcinoma. Methods: Gene profiles were collected from the The Cancer Genome Atlas-Kidney Renal Clear Cell Carcinoma (TCGA-KIRC), the GSE29609 and GSE22541 datasets. Genetic alteration and DNA methylation data were downloaded from the cBioPortal and MethSurv. The functional enrichment data were analyzed by Metascape. Results: The mRNA expression of the CDCAs, except CBX2, was significantly increased in clear cell renal cell carcinoma patients. Genetic alterations might affect the expression of CDCAs, but promotor methylation does not affect CDCA gene expression. The overall expression of the CDCAs, according to the The Cancer Genome Atlas-KIRC database (hazard ratio [HR]: 2.18), the GSE29609 (HR: 6.08) and GSE22541 (HR: 6.73), was significantly associated with unfavorable overall survival. In addition, genes co-expressed with CDCAs (R2 ≥0.3) were highly associated with cell division and the FOXM1 pathway. Conclusion: Our study demonstrated that the aberrant expression of CDCA gene family members plays an indispensable role in tumorigenesis.
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Affiliation(s)
- Jialin Meng
- Department of Urology, The First Affiliated Hospital of Anhui Medical University; Institute of Urology & Anhui Province Key Laboratory of Genitourinary Diseases, Anhui Medical University, Hefei, Anhui, P.R. China
| | - Lei Gao
- Department of Urology, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, PR China
| | - Meng Zhang
- Department of Urology, The First Affiliated Hospital of Anhui Medical University; Institute of Urology & Anhui Province Key Laboratory of Genitourinary Diseases, Anhui Medical University, Hefei, Anhui, P.R. China
| | - Shenglin Gao
- Department of Urology, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, Changzhou, Jiangsu, P.R. China
| | - Song Fan
- Department of Urology, The First Affiliated Hospital of Anhui Medical University; Institute of Urology & Anhui Province Key Laboratory of Genitourinary Diseases, Anhui Medical University, Hefei, Anhui, P.R. China
| | - Chaozhao Liang
- Department of Urology, The First Affiliated Hospital of Anhui Medical University; Institute of Urology & Anhui Province Key Laboratory of Genitourinary Diseases, Anhui Medical University, Hefei, Anhui, P.R. China
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Liu J, Meng H, Li S, Shen Y, Wang H, Shan W, Qiu J, Zhang J, Cheng W. Identification of Potential Biomarkers in Association With Progression and Prognosis in Epithelial Ovarian Cancer by Integrated Bioinformatics Analysis. Front Genet 2019; 10:1031. [PMID: 31708970 PMCID: PMC6822059 DOI: 10.3389/fgene.2019.01031] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 09/25/2019] [Indexed: 02/03/2023] Open
Abstract
Epithelial ovarian cancer (EOC) is one of the malignancies in women, which has the highest mortality. However, the microlevel mechanism has not been discussed in detail. The expression profiles GSE27651, GSE38666, GSE40595, and GSE66957 including 188 tumor and 52 nontumor samples were downloaded from the Gene Expression Omnibus database. The differentially expressed genes (DEGs) were filtered using R software, and we performed functional analysis using the clusterProfiler. Cytoscape software, the molecular complex detection plugin and database STRING analyzed DEGs to construct protein-protein interaction network. We identified 116 DEGs including 81 upregulated and 35 downregulated DEGs. Functional analysis revealed that they were significantly enriched in the extracellular region and biosynthesis of amino acids. We next identified four bioactive compounds (vorinostat, LY-294002,trichostatin A, and tanespimycin) based on ConnectivityMap. Then 114 nodes were obtained in protein-protein interaction. The three most relevant modules were detected. In addition, according to degree ≥ 10, 14 core genes including FOXM1, CXCR4, KPNA2, NANOG, UBE2C, KIF11, ZWINT, CDCA5, DLGAP5, KIF15, MCM2, MELK, SPP1, and TRIP13 were identified. Kaplan-Meier analysis, Oncomine, and Gene Expression Profiling Interactive Analysis showed that overexpression of FOXM1, SPP1, UBE2C, KIF11, ZWINT, CDCA5, UBE2C, and KIF15 was related to bad prognosis of EOC patients. CDCA5, FOXM1, KIF15, MCM2, and ZWINT were associated with stage. Receiver operating characteristic (ROC) curve showed that messenger RNA levels of these five genes exhibited better diagnostic efficiency for normal and tumor tissues. The Human Protein Atlas database was performed. The protein levels of these five genes were significantly higher in tumor tissues compared with normal tissues. Functional enrichment analysis suggested that all the hub genes played crucial roles in citrate cycle tricarboxylic acid cycle. Furthermore, the univariate and multivariate Cox proportional hazards regression showed that ZWINT was independent prognostic indictor among EOC patients. The genes and pathways discovered in the above studies may open a new direction for EOC treatment.
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Affiliation(s)
- Jinhui Liu
- Department of Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Huangyang Meng
- Department of Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Siyue Li
- Department of Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yujie Shen
- Department of Otorhinolaryngology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Hui Wang
- Department of Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Wu Shan
- Department of Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jiangnan Qiu
- Department of Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jie Zhang
- Department of Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Wenjun Cheng
- Department of Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
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Xu J, Zhu C, Yu Y, Wu W, Cao J, Li Z, Dai J, Wang C, Tang Y, Zhu Q, Wang J, Wen W, Xue L, Zhen F, Liu J, Huang C, Zhao F, Zhou Y, He Z, Pan X, Wei H, Zhu Y, He Y, Que J, Luo J, Chen L, Wang W. Systematic cancer-testis gene expression analysis identified CDCA5 as a potential therapeutic target in esophageal squamous cell carcinoma. EBioMedicine 2019; 46:54-65. [PMID: 31324603 PMCID: PMC6710982 DOI: 10.1016/j.ebiom.2019.07.030] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2019] [Revised: 06/21/2019] [Accepted: 07/10/2019] [Indexed: 12/28/2022] Open
Abstract
Background Esophageal squamous cell carcinoma (ESCC) is one of the most lethal malignancies with poor prognosis. Cancer-testis genes (CTGs) have been vigorously pursued as targets for cancer immunotherapy, but the expressive patterns and functional roles of CTGs remain unclear in ESCC. Methods A systematic screening strategy was adopted to screen CTGs in ESCC by integrating multiple public databases and RNA expression microarray data from 119 ESCC subjects. For the newly identified ESCC prognosis-associated CTGs, an independent cohort of 118 patients with ESCC was recruited to validate the relationship via immunohistochemistry. Furthermore, functional assays were performed to determine the underlying mechanisms. Findings 21 genes were recognized as CTGs, in particular, CDCA5 was aberrantly upregulated in ESCC tissues and significantly associated with poor prognosis (HR = 1.85, 95%CI: 1.14–3.01, P = .013). Immunohistochemical staining confirmed that positive CDCA5 expression was associated with advanced TNM staging and a shorter overall survival rate (45.59% vs 28.00% for CDCA5−/+ subjects, P = 1.86 × 10−3). H3K27 acetylation in CDCA5 promoter might lead to the activation of CDCA5 during ESCC tumorigenesis. Functionally, in vitro assay of gain- and loss-of-function of CDCA5 suggested that CDCA5 could promote ESCC cells proliferation, invasion, migration, apoptosis resistance and reduce chemosensitivity to cisplatin. Moreover, in vivo assay showed that silenced CDCA5 could inhibit tumor growth. Mechanistically, CDCA5 knockdown led to an arrest in G2/M phase and changes in the expression of factors that played fundamental roles in the cell cycle pathway. Interpretation CDCA5 contributed to ESCC progression and might serve as an attractive target for ESCC immunotherapy. Fund This work was supported by the Natural Science Foundation of Jiangsu Province (No. BK20181083 and BK20181496), Jiangsu Top Expert Program in Six Professions (No. WSW-003 and WSW-007), Major Program of Science and Technology Foundation of Jiangsu Province (No. BE2016790 and BE2018746), Jiangsu Medical Young Talent Project (No. QNRC2016566), the Program of Jiangsu Medical Innovation Team (No. CXTDA2017006), Postgraduate Research & Practice Innovation Program of Jiangsu Province (KYCX18_1487) and Jiangsu Province 333 Talents Project (No. BRA2017545).
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Affiliation(s)
- Jing Xu
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Chengxiang Zhu
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yue Yu
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China; Department of Thoracic Surgery, Cancer Institute and Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Weibing Wu
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jing Cao
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Zhihua Li
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China; Department of Epidemiology and Biostatistics, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Juncheng Dai
- Department of Epidemiology and Biostatistics, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Cheng Wang
- Department of Epidemiology and Biostatistics, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Yu Tang
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Quan Zhu
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jun Wang
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Wei Wen
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Lei Xue
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Fuxi Zhen
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jinyuan Liu
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Chenjun Huang
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Fei Zhao
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yue Zhou
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Zhicheng He
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Xianglong Pan
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Haixing Wei
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yining Zhu
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yaozhou He
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jun Que
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jinghua Luo
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.
| | - Liang Chen
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.
| | - Wei Wang
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.
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Tian Y, Wu J, Chagas C, Du Y, Lyu H, He Y, Qi S, Peng Y, Hu J. CDCA5 overexpression is an Indicator of poor prognosis in patients with hepatocellular carcinoma (HCC). BMC Cancer 2018; 18:1187. [PMID: 30497429 PMCID: PMC6267780 DOI: 10.1186/s12885-018-5072-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 11/09/2018] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Accurate and early prognosis of disease is essential to clinical decision making, particularly in diseases, such as HCC, that are typically diagnosed at a late stage in the course of disease and therefore carry a poor prognosis. CDCA5 is a cell cycle regulatory protein that has shown prognostic value in several cancers. METHODS We retrospectively evaluated 178 patients with HCC treated with curative liver resection between September 2009 and September 2012 at Nanchong Central Hospital in Nanchong, Sichuan Province, China. Patients were screened for their CDCA5 expression levels and assigned to either the high or low expression group. Patient demographics, comorbidities, clinicopathologic data, such as tumor microvascular invasion status and size, and long-term outcomes were compared between the two groups. The effect of CDCA5 on the proliferation of liver cancer cells was analyzed using in vitro and in vivo assays. RESULTS The present study found that increased CDCA5 expression was associated with increased tumor diameter and microvascular invasion in HCC. It was also found that CDCA5 overexpression may be associated with liver cancer cells. Additionally, this study confirmed that CDCA5 expression was increased in HCC tissue versus normal liver tissue, that CDCA5 expression was associated with decreased survival and that CDCA5 knockdown using shRNA led to cell cycle arrest in the G2/M phase. CONCLUSIONS These findings suggest that CDCA5 expression is associated with poor prognosis in patients with hepatocellular carcinoma.
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Affiliation(s)
- Yunhong Tian
- Department of General Surgery, Nanchong Central Hospital, The second Clinical College of North Sichuan Medical College, Nanchong, 637000, Sichuan, China
| | - Jianlin Wu
- Department of Radiology, Affiliated Zhongshan Hospital of Dalian University, 116011, No.6 of JieFang Road, Dalian, China
| | - Cristian Chagas
- Department of Radiology, Wayne State University, Detroit, MI, 48201, USA
| | - Yichao Du
- Department of Hepatobiliary Surgery of the Affiliated Hospital, Southwest Medical University, Luzhou, Sichuan, China
| | - Huan Lyu
- Department of General Surgery, Nanchong Central Hospital, The second Clinical College of North Sichuan Medical College, Nanchong, 637000, Sichuan, China
| | - Yunhong He
- Department of General Surgery, Nanchong Central Hospital, The second Clinical College of North Sichuan Medical College, Nanchong, 637000, Sichuan, China
| | - Shouliang Qi
- The Sino-Dutch Biomedical and Information Engineering School of Northeastern University, Shenyang, China
| | - Yong Peng
- Department of General Surgery, Nanchong Central Hospital, The second Clinical College of North Sichuan Medical College, Nanchong, 637000, Sichuan, China.
| | - Jiani Hu
- Department of Radiology, Wayne State University, Detroit, MI, 48201, USA.
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Abstract
The mitotic checkpoint ensures proper chromosome segregation; defects in this checkpoint can lead to aneuploidy, a hallmark of cancer. The mitotic checkpoint blocks progression through mitosis as long as chromosomes remain unattached to spindle microtubules. Unattached kinetochores induce the formation of a mitotic checkpoint complex (MCC) composed of Mad2, BubR1, Bub1 and Bub3 which inhibits anaphase onset. Spindle toxins induce prolonged mitotic arrest by creating persistently unattached kinetochores which trigger MCC formation. We find that the multifunctional ser/thr kinase, glycogen synthase kinase 3 (GSK3) is required for a strong mitotic checkpoint. Spindle toxin-induced mitotic arrest is relieved by GSK3 inhibitors SB 415286 (SB), RO 318220 (RO) and lithium chloride. Similarly, targeting GSK3β with knockout or RNAi reduced mitotic arrest in the presence of Taxol. GSK3 was required for optimal localization of Mad2, BubR1, and Bub1 at kinetochores and for optimal assembly of the MCC in spindle toxin-arrested cells. The WNT- and PI3K/Akt signaling pathways negatively regulate GSK3β activity. Inhibition of WNT and PI3K/Akt signaling, in the presence of Taxol, induced a longer mitotic arrest compared to Taxol alone. Our observations provide novel insight into the regulation of the mitotic checkpoint and its connection to growth-signaling pathways.
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DNA replication stress and its impact on chromosome segregation and tumorigenesis. Semin Cancer Biol 2018; 55:61-69. [PMID: 29692334 DOI: 10.1016/j.semcancer.2018.04.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 04/13/2018] [Accepted: 04/16/2018] [Indexed: 01/11/2023]
Abstract
Genome instability and cell cycle dysregulation are commonly associated with cancer. DNA replication stress driven by oncogene activation during tumorigenesis is now well established as a source of genome instability. Replication stress generates DNA damage not only during S phase, but also in the subsequent mitosis, where it impacts adversely on chromosome segregation. Some regions of the genome seem particularly sensitive to replication stress-induced instability; most notably, chromosome fragile sites. In this article, we review some of the important issues that have emerged in recent years concerning DNA replication stress and fragile site expression, as well as how chromosome instability is minimized by a family of ring-shaped protein complexes known as SMC proteins. Understanding how replication stress impacts on S phase and mitosis in cancer should provide opportunities for the development of novel and tumour-specific treatments.
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