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Liu J, Qu Y, Zhao Y, Liang F, Ji L, Wang Z, Li J, Zang Z, Huang H, Zhang J, Gu W, Dai L, Yang R. CCDC12 gene methylation in peripheral blood as a potential biomarker for breast cancer detection. Biomarkers 2024; 29:265-275. [PMID: 38776382 DOI: 10.1080/1354750x.2024.2358302] [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: 03/12/2024] [Accepted: 05/16/2024] [Indexed: 05/25/2024]
Abstract
BACKGROUND Aberrant DNA methylation has been identified as biomarkers for breast cancer detection. Coiled-coil domain containing 12 gene (CCDC12) implicated in tumorigenesis. This study aims to investigate the potential of blood-based CCDC12 methylation for breast cancer detection. METHODS DNA methylation level of CpG sites (Cytosine-phosphate Guanine dinucleotides) in CCDC12 gene was measured by mass spectrometry in 255 breast cancer patients, 155 patients with benign breast nodules and 302 healthy controls. The association between CCDC12 methylation and breast cancer risk was evaluated by logistic regression and receiver operating characteristic curve analysis. RESULTS A total of eleven CpG sites were analyzed. The CCDC12 methylation levels were higher in breast cancer patients. Compared to the lowest tertile of methylation level in CpG_6,7, CpG_10 and CpG_11, the highest quartile was associated with 82, 91 and 95% increased breast cancer risk, respectively. The CCDC12 methylation levels were associated with estrogen receptor (ER) and human epidermal growth factor 2 (HER2) status. In ER-negative and HER2-positive (ER-/HER2+) breast cancer subtype, the combination of four sites CpG_2, CpG_5, CpG_6,7 and CpG_11 methylation levels could distinguish ER-/HER2+ breast cancer from the controls (AUC = 0.727). CONCLUSION The hypermethylation levels of CCDC12 in peripheral blood could be used for breast cancer detection.
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Affiliation(s)
- Jingjing Liu
- Henan Institute of Medical and Pharmaceutical Sciences & Henan Key Medical Laboratory of Tumor Molecular Biomarkers, Zhengzhou University, Zhengzhou, China
| | - Yunhui Qu
- Department of Clinical Laboratory in the First Affiliated Hospital & Key Clinical Laboratory of Henan Province, Zhengzhou University, Zhengzhou, Henan, China
| | - Yutong Zhao
- Henan Institute of Medical and Pharmaceutical Sciences & Henan Key Medical Laboratory of Tumor Molecular Biomarkers, Zhengzhou University, Zhengzhou, China
| | - Feifei Liang
- BGI College, Zhengzhou University, Zhengzhou, China
| | - Longtao Ji
- BGI College, Zhengzhou University, Zhengzhou, China
| | - Zhi Wang
- BGI College, Zhengzhou University, Zhengzhou, China
| | - Jinyu Li
- Department of Otology, the First Affiliated Hospital, Zhengzhou University, Zhengzhou, Henan, China
| | - Zishan Zang
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Haixia Huang
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Jie Zhang
- Department of Clinical Laboratory, Jiangsu Province Hospital of Chinese Medicine, Nanjing, China
| | - Wanjian Gu
- Department of Clinical Laboratory, Jiangsu Province Hospital of Chinese Medicine, Nanjing, China
| | - Liping Dai
- Henan Institute of Medical and Pharmaceutical Sciences & Henan Key Medical Laboratory of Tumor Molecular Biomarkers, Zhengzhou University, Zhengzhou, China
| | - Rongxi Yang
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China
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Wang Y, Wang X, Liu Y, He Y, Duan X, Li Q, Huang Y, Xu G, Lu Q. HPV16-miRNAs exert oncogenic effects through enhancers in human cervical cancer. Cancer Cell Int 2024; 24:172. [PMID: 38750489 PMCID: PMC11097496 DOI: 10.1186/s12935-024-03364-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Accepted: 05/08/2024] [Indexed: 05/18/2024] Open
Abstract
BACKGROUND Cervical cancer is a human papillomavirus (HPV)-related disease. HPV type 16 (HPV16), which is the predominant cause of cervical cancer, can encode miRNAs (HPV16-miRNAs). However, the role of HPV16-miRNAs in the pathogenesis of cervical cancer remains unclear. METHODS Human cervical cancer cell lines SiHa (HPV16-positive) and C33A (HPV-negative), and cervical cancer tissues were collected to investigate the expression levels of two HPV16-miRNAs (HPV16-miR-H1 and HPV16-miR-H6). The overexpression and knockdown of HPV16-miR-H1 and HPV16-miR-H6 were performed using the lentiviral vector system and miRNA inhibitors, respectively. RNA-sequencing (RNA-seq) analysis and H3K27ac chromatin immunoprecipitation and sequencing (CHIP-seq) experiments were utilized to explore the roles of HPV16-miR-H1 and HPV16-miR-H6 facilitated by enhancers. CCK8, EdU, transwell, and wound healing assays were performed to verify the effects of HPV16-miR-H1 and HPV16-miR-H6 on cell proliferation and migration. RESULTS HPV16-miR-H1 and HPV16-miR-H6 were highly expressed in both SiHa cells and tissue samples from HPV16-positive cervical cancer patients. RNA-seq analysis showed that HPV16-miR-H1 and HPV16-miR-H6 induced the upregulation of numerous tumor progression-associated genes. H3K27ac CHIP-seq experiments further revealed that HPV16-miR-H1 and HPV16-miR-H6 modulated the expression of critical genes by regulating their enhancer activity. The functional study demonstrated that HPV16-miR-H1 and HPV16-miR-H6 increased the migratory capacity of SiHa cells. CONCLUSIONS Our data shed light on the role of HPV16-encoded miRNAs in cervical cancer, particularly emphasizing their involvement in the miRNA-enhancer-target gene system. This novel regulatory mechanism of HPV16-miRNAs provides new insights and approaches for the development of therapeutic strategies by targeting HPV16-positive cervical cancer.
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Affiliation(s)
- Yunuan Wang
- Department of Obstetrics and Gynecology, Jinshan Hospital, Fudan University, Shanghai, 201508, China
- Department of Obstetrics and Gynecology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xueying Wang
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai Clinical Research Center for Mental Health, Shanghai Institute of Traditional Chinese Medicine for Mental Health, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yiting Liu
- Department of Obstetrics and Gynecology, Jinshan Hospital, Fudan University, Shanghai, 201508, China
- Department of Obstetrics and Gynecology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yuxin He
- Department of Obstetrics and Gynecology, Jinshan Hospital, Fudan University, Shanghai, 201508, China
| | - Xiaoling Duan
- Department of Obstetrics and Gynecology, Jinshan Hospital, Fudan University, Shanghai, 201508, China
| | - Qinmei Li
- Department of Obstetrics and Gynecology, Jinshan Hospital, Fudan University, Shanghai, 201508, China
| | - Yanchun Huang
- Department of Obstetrics and Gynecology, Jinshan Hospital, Fudan University, Shanghai, 201508, China
| | - Guoxiong Xu
- Research Center for Clinical Medicine, Jinshan Hospital, Fudan University, Shanghai, 201508, China
| | - Qi Lu
- Department of Obstetrics and Gynecology, Jinshan Hospital, Fudan University, Shanghai, 201508, China.
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Janjua D, Thakur K, Aggarwal N, Chaudhary A, Yadav J, Chhokar A, Tripathi T, Joshi U, Senrung A, Bharti AC. Prognostic and therapeutic potential of STAT3: Opportunities and challenges in targeting HPV-mediated cervical carcinogenesis. Crit Rev Oncol Hematol 2024; 197:104346. [PMID: 38608913 DOI: 10.1016/j.critrevonc.2024.104346] [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: 02/09/2024] [Revised: 03/28/2024] [Accepted: 04/04/2024] [Indexed: 04/14/2024] Open
Abstract
Cervical cancer (CaCx) ranks as the fourth most prevalent cancer among women globally. Persistent infection of high-risk human papillomaviruses (HR-HPVs) is major etiological factor associated with CaCx. Signal Transducer and Activator of Transcription 3 (STAT3), a prominent member of the STAT family, has emerged as independent oncogenic driver. It is a target of many oncogenic viruses including HPV. How STAT3 influences HPV viral gene expression or gets affected by HPV is an area of active investigation. A better understanding of host-virus interaction will provide a prognostic and therapeutic window for CaCx control and management. In this comprehensive review, we delve into carcinogenic role of STAT3 in development of HPV-induced CaCx. With an emphasis on fascinating interplay between STAT3 and HPV genome, the review explores the diverse array of opportunities and challenges associated with this field to harness the prognostic and therapeutic potential of STAT3 in CaCx.
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Affiliation(s)
- Divya Janjua
- Molecular Oncology Laboratory, Department of Zoology, University of Delhi (North Campus), New Delhi, India
| | - Kulbhushan Thakur
- Molecular Oncology Laboratory, Department of Zoology, University of Delhi (North Campus), New Delhi, India
| | - Nikita Aggarwal
- Molecular Oncology Laboratory, Department of Zoology, University of Delhi (North Campus), New Delhi, India
| | - Apoorva Chaudhary
- Molecular Oncology Laboratory, Department of Zoology, University of Delhi (North Campus), New Delhi, India
| | - Joni Yadav
- Molecular Oncology Laboratory, Department of Zoology, University of Delhi (North Campus), New Delhi, India
| | - Arun Chhokar
- Molecular Oncology Laboratory, Department of Zoology, University of Delhi (North Campus), New Delhi, India; Department of Zoology, Deshbandhu College, University of Delhi, Delhi, India
| | - Tanya Tripathi
- Molecular Oncology Laboratory, Department of Zoology, University of Delhi (North Campus), New Delhi, India
| | - Udit Joshi
- Molecular Oncology Laboratory, Department of Zoology, University of Delhi (North Campus), New Delhi, India
| | - Anna Senrung
- Molecular Oncology Laboratory, Department of Zoology, University of Delhi (North Campus), New Delhi, India; Department of Zoology, Daulat Ram College, University of Delhi, Delhi, India
| | - Alok Chandra Bharti
- Molecular Oncology Laboratory, Department of Zoology, University of Delhi (North Campus), New Delhi, India.
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Li J, Wang X, Li Z, Li M, Zheng X, Zheng D, Wang Y, Xi M. SULF1 Activates the VEGFR2/PI3K/AKT Pathway to Promote the Development of Cervical Cancer. Curr Cancer Drug Targets 2024; 24:820-834. [PMID: 37539927 DOI: 10.2174/1568009623666230804161607] [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: 02/08/2023] [Revised: 06/14/2023] [Accepted: 06/23/2023] [Indexed: 08/05/2023]
Abstract
BACKGROUND AND PURPOSE Sulfatase 1 (SULF1) can regulate the binding of numerous signaling molecules by removing 6-O-sulfate from heparan sulfate proteoglycans (HSPGs) to affect numerous physiological and pathological processes. Our research aimed to investigate the effect of the SULF1-mediated VEGFR2/PI3K/AKT signaling pathway on tumorigenesis and development of cervical cancer (CC). METHODS The expression and prognostic values of SULF1 in patients with CC were analyzed through bioinformatics analysis, qRT-PCR, immunohistochemistry, and western blot. The function and regulatory mechanism of SULF1 in proliferation, migration, and invasion of cervical cancer cells were examined through lentivirus transduction, CCK8, flow cytometry analysis, plate colony formation assay, scratch assay, transwell assay, western blot, VEGFR2 inhibitor (Ki8751), and mouse models. RESULTS SULF1 expression was significantly upregulated in CC tissues, which was significantly associated with poor prognosis of patients with CC. In vitro, the upregulation of SULF1 expression in HeLa cells promoted cell proliferation, colony formation, migration, and invasion while inhibiting apoptosis. Conversely, the downregulation of SULF1 expression had the opposite effect. In vivo, the upregulation of SULF1 expression resulted in a significant increase in both tumor growth and angiogenesis, while its downregulation had the opposite effect. Furthermore, western blot detection and cell function rescue assay confirmed that the upregulation of SULF1 in HeLa cells promoted the tumorigenic behaviors of cancer cells by activating the VEGFR2/PI3K/AKT signaling pathway. CONCLUSION SULF1 plays an oncogenic role in the tumorigenesis and development of CC, indicating its potential as a novel molecular target for gene-targeted therapy in patients with CC.
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Affiliation(s)
- Juan Li
- Department of Gynecology and Obstetrics, Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
- Department of Diagnosis and Treatment for Cervical Diseases, Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, 611731, China
| | - Xihao Wang
- Department of Pathology, Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, 611731, China
| | - Zhilong Li
- Laboratory of Molecular Translational Medicine, Center for Translational Medicine, Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Minzhen Li
- Department of Gynecology and Obstetrics, Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Xuelian Zheng
- Department of Gynecology and Obstetrics, Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Danxi Zheng
- Department of Gynecology and Obstetrics, Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Yanyun Wang
- Laboratory of Molecular Translational Medicine, Center for Translational Medicine, Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Mingrong Xi
- Department of Gynecology and Obstetrics, Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
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Thakur K, Janjua D, Aggarwal N, Chhokar A, Yadav J, Tripathi T, Chaudhary A, Senrung A, Shrivastav A, Bharti AC. Physical interaction between STAT3 and AP1 in cervical carcinogenesis: Implications in HPV transcription control. Biochim Biophys Acta Mol Basis Dis 2023; 1869:166817. [PMID: 37532113 DOI: 10.1016/j.bbadis.2023.166817] [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: 07/05/2022] [Revised: 07/07/2023] [Accepted: 07/19/2023] [Indexed: 08/04/2023]
Abstract
The constitutive activation and aberrant expression of Signal Transducer and Activator of Transcription 3 (STAT3) plays a key role in initiation and progression of cervical cancer (CaCx). How STAT3 influences HPV transcription is poorly defined. In the present study, we probed direct and indirect interactions of STAT3 with HPV16/18 LCR. In silico assessment of cis-elements present on LCR revealed the presence of potential STAT3 binding motifs. However, experimental validation by ChIP-PCR could not confirm any specific STAT3 binding on HPV16 LCR. Protein-protein interaction (PPI) network analysis of STAT3 with other host transcription factors that bind LCR, highlighted the physical association of STAT3 with c-FOS and c-JUN. This was further confirmed in vitro by co-immunoprecipitation, where STAT3 co-immunoprecipitated with c-FOS and c-JUN in CaCx cells. The result was supported by immunocytochemical analysis and colocalization of STAT3 with c-FOS and c-JUN. Positive signals in proximity ligation assay validated physical interaction and colocalization of STAT3 with AP1. Colocalization of STAT3 with c-FOS and c-JUN increased upon IL-6 treatment and decreased post-Stattic treatment. Alteration of STAT3 expression affected the subcellular localization of c-FOS and c-JUN, along with the expression of viral oncoproteins (E6 and E7) in CaCx cells. High expression of c-JUN in tumor tissues correlated with poor prognosis in both HPV16 and HPV18 CaCx cohort whereas high expression of STAT3 correlated with poor prognosis in HPV18 CaCx lesions only. Overall, the data suggest an indirect interaction of STAT3 with HPV LCR via c-FOS and c-JUN and potentiate transcription of viral oncoproteins.
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Affiliation(s)
- Kulbhushan Thakur
- Molecular Oncology Laboratory, Department of Zoology, University of Delhi (North Campus), New Delhi, India
| | - Divya Janjua
- Molecular Oncology Laboratory, Department of Zoology, University of Delhi (North Campus), New Delhi, India
| | - Nikita Aggarwal
- Molecular Oncology Laboratory, Department of Zoology, University of Delhi (North Campus), New Delhi, India
| | - Arun Chhokar
- Molecular Oncology Laboratory, Department of Zoology, University of Delhi (North Campus), New Delhi, India; Department of Zoology, Deshbandhu College, University of Delhi, Delhi, India
| | - Joni Yadav
- Molecular Oncology Laboratory, Department of Zoology, University of Delhi (North Campus), New Delhi, India
| | - Tanya Tripathi
- Molecular Oncology Laboratory, Department of Zoology, University of Delhi (North Campus), New Delhi, India
| | - Apoorva Chaudhary
- Molecular Oncology Laboratory, Department of Zoology, University of Delhi (North Campus), New Delhi, India
| | - Anna Senrung
- Molecular Oncology Laboratory, Department of Zoology, University of Delhi (North Campus), New Delhi, India
| | - Anuraag Shrivastav
- Department of Biology, The University of Winnipeg, 515 Portage Avenue, Winnipeg, Manitoba, Canada; Paul Albrechtsen Research Institute CCMB, 675 McDermot Ave, Winnipeg, Manitoba, Canada
| | - Alok Chandra Bharti
- Molecular Oncology Laboratory, Department of Zoology, University of Delhi (North Campus), New Delhi, India.
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Fu J, Si L, Zhou Y, Li D, Wang R. Distinct N7-methylguanosine profiles of circular RNAs in drug-resistant acute myeloid leukemia. Sci Rep 2023; 13:14704. [PMID: 37679400 PMCID: PMC10485064 DOI: 10.1038/s41598-023-41974-w] [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: 05/15/2023] [Accepted: 09/04/2023] [Indexed: 09/09/2023] Open
Abstract
Post-transcriptional methylation modifications, such as the N7-methylguanosine (m7G) modification, are increasingly acknowledged for their role in the development and resistance to chemotherapy in acute myeloid leukemia (AML). This study employed MeRIP-seq technology to investigate the m7G sites within circular RNAs (circRNAs) derived from human AML cells and drug-resistant AML cells, in order to identify these sites more comprehensively. In addition, a detailed analysis of the relationship between m7G and drug-resistant AML was conducted. The bioinformatics analysis was utilized to predict the functions of specific methylated transcripts. The findings revealed a significant difference in m7G level between AML cells and drug-resistant AML cells, suggesting a potentially critical role of m7G in circRNAs in drug-resistant AML development. The methylation of M7G could affect the circRNA-miRNA-mRNA co-expression during the development of AML resistance, which could further influence the regulation of resistance-associated target genes in AML. Furthermore, gene ontology analysis indicated that the distinct distribution pattern of circRNAs with m7G methylation in drug-resistant AML cells was correlated with metabolism-related pathways. These results suggested a potential association between drug-resistant AML and m7G methylation of circRNAs. Moreover, the results revealed a novel role of m7G RNA methylation in circRNAs in the progression of AML chemoresistance.
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Affiliation(s)
- Jinqiu Fu
- Department of Pediatrics, Qilu Hospital of Shandong University, Jinan, China
| | - Libo Si
- Department of Thoracic Surgery, Qilu Hospital of Shandong University, Jinan, China
| | - Yao Zhou
- Department of Pediatrics, Qilu Hospital of Shandong University, Jinan, China
| | - Dong Li
- Department of Pediatrics, Qilu Hospital of Shandong University, Jinan, China
| | - Ran Wang
- Department of Hematology, Qilu Hospital of Shandong University, Jinan, Shandong Province, China.
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Liu Z, Yan W, Liu S, Liu Z, Xu P, Fang W. Regulatory network and targeted interventions for CCDC family in tumor pathogenesis. Cancer Lett 2023; 565:216225. [PMID: 37182638 DOI: 10.1016/j.canlet.2023.216225] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 05/03/2023] [Accepted: 05/10/2023] [Indexed: 05/16/2023]
Abstract
CCDC (coiled-coil domain-containing) is a coiled helix domain that exists in natural proteins. There are about 180 CCDC family genes, encoding proteins that are involved in intercellular transmembrane signal transduction and genetic signal transcription, among other functions. Alterations in expression, mutation, and DNA promoter methylation of CCDC family genes have been shown to be associated with the pathogenesis of many diseases, including primary ciliary dyskinesia, infertility, and tumors. In recent studies, CCDC family genes have been found to be involved in regulation of growth, invasion, metastasis, chemosensitivity, and other biological behaviors of malignant tumor cells in various cancer types, including nasopharyngeal carcinoma, lung cancer, colorectal cancer, and thyroid cancer. In this review, we summarize the involvement of CCDC family genes in tumor pathogenesis and the relevant upstream and downstream molecular mechanisms. In addition, we summarize the potential of CCDC family genes as tumor therapy targets. The findings discussed here help us to further understand the role and the therapeutic applications of CCDC family genes in tumors.
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Affiliation(s)
- Zhen Liu
- Cancer Center, Integrated Hospital of Traditional Chinese Medicine, Southern Medical University, 510315, Guangzhou, China.
| | - Weiwei Yan
- Cancer Center, Integrated Hospital of Traditional Chinese Medicine, Southern Medical University, 510315, Guangzhou, China
| | - Shaohua Liu
- Department of General Surgery, Pingxiang People's Hospital, Pingxiang, Jiangxi, 337000, China
| | - Zhan Liu
- Department of Gastroenterology and Clinical Nutrition, The First Affiliated Hospital (People's Hospital of Hunan Province), Hunan Normal University, Changsha, 410002, China
| | - Ping Xu
- Cancer Center, Integrated Hospital of Traditional Chinese Medicine, Southern Medical University, 510315, Guangzhou, China; Respiratory Department, Peking University Shenzhen Hospital, Shenzhen, 518034, China.
| | - Weiyi Fang
- Cancer Center, Integrated Hospital of Traditional Chinese Medicine, Southern Medical University, 510315, Guangzhou, China.
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Sokolowski DJ, Ahn J, Erdman L, Hou H, Ellis K, Wang L, Goldenberg A, Wilson M. Differential Expression Enrichment Tool (DEET): an interactive atlas of human differential gene expression. NAR Genom Bioinform 2023; 5:lqad003. [PMID: 36694664 PMCID: PMC9869326 DOI: 10.1093/nargab/lqad003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 12/14/2022] [Accepted: 01/19/2023] [Indexed: 01/24/2023] Open
Abstract
Differential gene expression analysis using RNA sequencing (RNA-seq) data is a standard approach for making biological discoveries. Ongoing large-scale efforts to process and normalize publicly available gene expression data enable rapid and systematic reanalysis. While several powerful tools systematically process RNA-seq data, enabling their reanalysis, few resources systematically recompute differentially expressed genes (DEGs) generated from individual studies. We developed a robust differential expression analysis pipeline to recompute 3162 human DEG lists from The Cancer Genome Atlas, Genotype-Tissue Expression Consortium, and 142 studies within the Sequence Read Archive. After measuring the accuracy of the recomputed DEG lists, we built the Differential Expression Enrichment Tool (DEET), which enables users to interact with the recomputed DEG lists. DEET, available through CRAN and RShiny, systematically queries which of the recomputed DEG lists share similar genes, pathways, and TF targets to their own gene lists. DEET identifies relevant studies based on shared results with the user's gene lists, aiding in hypothesis generation and data-driven literature review.
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Affiliation(s)
| | - Jedid Ahn
- Genetics and Genome Biology, SickKids Research Institute, Toronto, ON, Canada,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada,Department of Computer Science, University of Toronto, Toronto, ON, Canada
| | - Lauren Erdman
- Genetics and Genome Biology, SickKids Research Institute, Toronto, ON, Canada,Department of Computer Science, University of Toronto, Toronto, ON, Canada
| | - Huayun Hou
- Genetics and Genome Biology, SickKids Research Institute, Toronto, ON, Canada
| | - Kai Ellis
- Genetics and Genome Biology, SickKids Research Institute, Toronto, ON, Canada,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Liangxi Wang
- Genetics and Genome Biology, SickKids Research Institute, Toronto, ON, Canada,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Anna Goldenberg
- Genetics and Genome Biology, SickKids Research Institute, Toronto, ON, Canada,Department of Computer Science, University of Toronto, Toronto, ON, Canada,Vector Institute, Toronto, ON, Canada,CIFAR, Toronto, ON, Canada
| | - Michael D Wilson
- To whom correspondence should be addressed. Tel: +1 416 813 7654 (Ext 328699); Fax: +1 416 813 4931;
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Uchendu I, Zhilenkova A, Pirogova Y, Basova M, Bagmet L, Kohanovskaia I, Ngaha Y, Ikebunwa O, Sekacheva M. Cytokines as Potential Therapeutic Targets and their Role in the Diagnosis and Prediction of Cancers. Curr Pharm Des 2023; 29:2552-2567. [PMID: 37916493 DOI: 10.2174/0113816128268111231024054240] [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: 06/19/2023] [Accepted: 09/26/2023] [Indexed: 11/03/2023]
Abstract
The death rate from cancer is declining as a result of earlier identification and more advanced treatments. Nevertheless, a number of unfavourable adverse effects, including prolonged, long-lasting inflammation and reduced immune function, usually coexist with anti-cancer therapies and lead to a general decline in quality of life. Improvements in standardized comprehensive therapy and early identification of a variety of aggressive tumors remain the main objectives of cancer research. Tumor markers in those with cancer are tumor- associated proteins that are clinically significant. Even while several tumor markers are routinely used, they don't always provide reliable diagnostic information. Serum cytokines are promising markers of tumor stage, prognosis, and responsiveness to therapy. In fact, several cytokines are currently proposed as potential biomarkers in a variety of cancers. It has actually been proposed that the study of circulatory cytokines together with biomarkers that are particular to cancer can enhance and accelerate cancer diagnosis and prediction, particularly via blood samples that require minimal to the absence of invasion. The purpose of this review was to critically examine relevant primary research literature in order to elucidate the role and importance of a few identified serum cytokines as prospective therapeutic targets in oncological diseases.
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Affiliation(s)
- Ikenna Uchendu
- Institute for Personalized Oncology, Center for Digital Biodesign and Personalized Healthcare, First Moscow State Medical University of the Ministry of Health of Russia (Sechenov University), Moscow, Russia
- Department of Medical Laboratory Science, Faculty of Health Science and Technology, University of Nigeria, Enugu Campus, Enugu, Nigeria
| | - Angelina Zhilenkova
- Institute for Personalized Oncology, Center for Digital Biodesign and Personalized Healthcare, First Moscow State Medical University of the Ministry of Health of Russia (Sechenov University), Moscow, Russia
| | - Yuliya Pirogova
- Institute for Personalized Oncology, Center for Digital Biodesign and Personalized Healthcare, First Moscow State Medical University of the Ministry of Health of Russia (Sechenov University), Moscow, Russia
| | - Maria Basova
- Institute for Personalized Oncology, Center for Digital Biodesign and Personalized Healthcare, First Moscow State Medical University of the Ministry of Health of Russia (Sechenov University), Moscow, Russia
| | - Leonid Bagmet
- Institute for Personalized Oncology, Center for Digital Biodesign and Personalized Healthcare, First Moscow State Medical University of the Ministry of Health of Russia (Sechenov University), Moscow, Russia
| | - Iana Kohanovskaia
- Institute for Personalized Oncology, Center for Digital Biodesign and Personalized Healthcare, First Moscow State Medical University of the Ministry of Health of Russia (Sechenov University), Moscow, Russia
| | - Yvan Ngaha
- Institute for Personalized Oncology, Center for Digital Biodesign and Personalized Healthcare, First Moscow State Medical University of the Ministry of Health of Russia (Sechenov University), Moscow, Russia
| | - Obinna Ikebunwa
- Department of Medical Laboratory Science, Faculty of Health Science and Technology, University of Nigeria, Enugu Campus, Enugu, Nigeria
- Department of Biotechnology, First Moscow State Medical University of The Ministry of Health of Russia (Sechenov University), Moscow, Russia
| | - Marina Sekacheva
- Institute for Personalized Oncology, Center for Digital Biodesign and Personalized Healthcare, First Moscow State Medical University of the Ministry of Health of Russia (Sechenov University), Moscow, Russia
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Hao Z, Pan Z, Qian W. Atractylenolide I Inhibits Triple-Negative Breast Cancer Cell Proliferation and Promotes Apoptosis via Blocking the Janus Kinase 2/Signal Transducer and Activator of Transcription 3 Signaling Pathway. J BIOMATER TISS ENG 2022. [DOI: 10.1166/jbt.2022.3105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Bioactive agent Atractylenolide I (AT-1) has been shown to possess therapeutic value for treating various malignancies. The purpose of the current study is to clarify the potential effect of AT-1 on the development of triple-negative breast cancer (TNBC) and to investigate relevant
signaling pathways involved in its mechanism. MTT assay was used to assess the effect of different concentrations of AT-1 on cell survival rate in MCF-10A normal breast epithelial cell line and MDA-MB-231 TNBC cell line. Exogenous IL-6 and WP1066 respectively acted as the agonist and the inhibitor
of JAK2/STAT3. Determination of MDA-MB-231 cell viability, proliferation and apoptosis employed MTT, colony formation assay and TUNEL. Western blotting was conducted to measure the expression of proliferation- and apoptosis-related proteins. The viability of MCF-10A cells was unaffected by
AT-1, whereas in MDA-MB-231 cells the proliferation level was decreased and the apoptosis level was increased after AT-1 treatment. IL-6 partially restored the expression of AT-1-blocked JAK2/STAT3, and WP1066 inhibited JAK2/STAT3 expression in combination with IL-6 and AT-1. Furthermore,
compared with the AT-1 group, co-incubation of IL-6 and AT-1 partially restored the proliferative capacity and reduced the apoptosis of MDA-MB-231 cells, while WP1066 reversed these effects in combination with IL-6 and AT-1. AT-1 suppressed proliferation and promoted apoptosis in TNBC cells
likely through inhibiting the activation of JAK2/STAT3 signaling pathway. The findings from this study may provide guidance for future studies on AT-1 and theoretical basis of AT-1 pharmacological activities.
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Affiliation(s)
- Zhiye Hao
- Department of Oncology, Southern Branch of Guang’anmen Hospital, China Academy of Chinese Medical Sciences, Beijing Province, 102618, China
| | - Zheng Pan
- Department of Respiratory Medicine, The Characteristic Medical Center of Chinese People’s Armed Police Force, Tianjin Province, 300162, China
| | - Wei Qian
- Department of Intensive Care Unit, Southern Branch of Guang’anmen Hospital, China Academy of Chinese Medical Sciences, Huangcun Town, Daxing District, Beijing, 102618, China
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Priyanka PP, Yenugu S. Coiled-Coil Domain-Containing (CCDC) Proteins: Functional Roles in General and Male Reproductive Physiology. Reprod Sci 2021; 28:2725-2734. [PMID: 33942254 DOI: 10.1007/s43032-021-00595-2] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 04/22/2021] [Indexed: 01/10/2023]
Abstract
The coiled-coil domain-containing (CCDC) proteins have been implicated in a variety of physiological and pathological processes. Their functional roles vary from their interaction with molecular components of signaling pathways to determining the physiological functions at the cellular and organ level. Thus, they govern important functions like gametogenesis, embryonic development, hematopoiesis, angiogenesis, and ciliary development. Further, they are implicated in the pathogenesis of a large number of cancers. Polymorphisms in CCDC genes are associated with the risk of lifetime diseases. Because of their role in many biological processes, they have been extensively studied. This review concisely presents the functional role of CCDC proteins that have been studied in the last decade. Studies on CCDC proteins continue to be an active area of investigation because of their indispensable functions. However, there is ample opportunity to further understand the involvement of CCDC proteins in many more functions. It is anticipated that basing on the available literature, the functional role of CCDC proteins will be explored much further.
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Affiliation(s)
| | - Suresh Yenugu
- Department of Animal Biology, University of Hyderabad, Hyderabad, 500046, India.
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