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Zhang C, Shen Q, Gao M, Li J, Pang B. The role of Cyclin Dependent Kinase Inhibitor 3 ( CDKN3) in promoting human tumors: Literature review and pan-cancer analysis. Heliyon 2024; 10:e26061. [PMID: 38380029 PMCID: PMC10877342 DOI: 10.1016/j.heliyon.2024.e26061] [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: 08/29/2023] [Revised: 02/01/2024] [Accepted: 02/07/2024] [Indexed: 02/22/2024] Open
Abstract
Background Although many experiments and clinical studies have proved the link between the expression of CDKN3 and human tumors, we have not been able to identify any bioinformatics study in which the extensive tumor-promoting effect of CDKN3 was systematically analyzed. Objective Explore the extensive tumor-promoting effects of CDKN3 and review the research progress of CDKN3 in cancer. Methods We systematically reviewed the literature on CDKN3 and tumors. We explored the potential tumor-promoting effects of CDKN3 on different tumors in the TCGA database and the GTEx database using multiple platforms and websites. We studied the expression level of CDKN3, survival, prognosis, diagnosis, genetic variation, immune infiltration, and enrichment analysis using databases such as TIMER 2.0, GEPIA2, cBioPortal, and STRING. Results We found that CDKN3 is highly expressed in most tumors. The expression of CDKN3 is closely related to the prognosis of some tumors. And CDKN3 may have diagnostic value. The conclusion of our literature review is roughly the same, but there are differences, which are worthy of further study. Moreover, CDKN3 may be related to immune cell infiltration in tumor tissues. The genetic alteration of LUAD, STAD, SARC, PCPG, and ESCA with "Amplification" as the main type. In addition, through enrichment analysis, we found that CDKN3 affects tumors mainly through the control of the cell cycle and mitosis. Conclusion CDKN3 is highly expressed in most tumor tissues and has a statistical correlation with survival prognosis. It has extensive tumor-promoting effects that may be related to mechanisms such as immune infiltration.
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Affiliation(s)
- Chuanlong Zhang
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, 100053, China
| | - Qian Shen
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, 100053, China
| | - Mengqi Gao
- Wangjing Hospital, China Academy of Chinese Medical Sciences, Beijing, 100102, China
| | - Junchen Li
- Tianjin University of Traditional Chinese Medicine, Tianjin, 300000, China
| | - Bo Pang
- International Medical Department of Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, 100053, China
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2
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Gao C, Fan X, Liu Y, Han Y, Liu S, Li H, Zhang Q, Wang Y, Xue F. Comprehensive Analysis Reveals the Potential Roles of CDKN3 in Pancancer and Verification in Endometrial Cancer. Int J Gen Med 2023; 16:5817-5839. [PMID: 38106976 PMCID: PMC10723185 DOI: 10.2147/ijgm.s438479] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 11/29/2023] [Indexed: 12/19/2023] Open
Abstract
Background Cyclin-dependent kinase inhibitor 3 (CDKN3) has been studied in many cancers. However, the comprehensive and systematic pancancer analysis of CDKN3 genes is still lacking. Methods Data were downloaded from online databases. R was used for analysis of the differential expression and gene alteration of CDKN3 and of the associations between CDKN3 expression and survival, signaling pathways, and drug sensitivity. Clinical samples and in vitro experiments were selected for verification. Results CDKN3 expression was higher in most types of cancers, and this phenotype was significantly correlated with poor survival. CDKN3 showed gene alterations and copy number alterations in many cancers and associated with some immune-related pathways and factors. Drug sensitivity analysis elucidated that CDKN3 could be a useful marker for therapy selection. Clinical samples elucidated CDKN3 expressed high in endometrial cancer tissue. In vitro studies showed that CDKN3 induced pro-tumor effect in immune environment and facilitated endometrial cancer cell proliferation and G1/S phase transition. Conclusion CDKN3 has been shown to be highly expressed in most types of cancers and promoted cancer cell progression. CDKN3 may serve as a novel marker in clinical diagnosis, treatment, and prognosis prediction in future.
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Affiliation(s)
- Chao Gao
- Department of Gynecology and Obstetrics, Tianjin Medical University General Hospital, Tianjin, People’s Republic of China
- Tianjin Key Laboratory of Female Reproductive Health and Eugenics, Tianjin Medical University General Hospital, Tianjin, People’s Republic of China
| | - Xiangqin Fan
- Department of Gynecology and Obstetrics, Tianjin Medical University General Hospital, Tianjin, People’s Republic of China
- Tianjin Key Laboratory of Female Reproductive Health and Eugenics, Tianjin Medical University General Hospital, Tianjin, People’s Republic of China
- Department of Obstetrics and Gynecology, Zaozhuang Municipal Hospital, Shandong, People’s Republic of China
| | - Yanyan Liu
- Department of Gynecology and Obstetrics, Tianjin Medical University General Hospital, Tianjin, People’s Republic of China
- Tianjin Key Laboratory of Female Reproductive Health and Eugenics, Tianjin Medical University General Hospital, Tianjin, People’s Republic of China
| | - Yanyan Han
- Department of Pathology, First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, People’s Republic of China
- National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, Tianjin, People’s Republic of China
| | - Shiqi Liu
- Department of Gynecology and Obstetrics, Tianjin Medical University General Hospital, Tianjin, People’s Republic of China
- Tianjin Key Laboratory of Female Reproductive Health and Eugenics, Tianjin Medical University General Hospital, Tianjin, People’s Republic of China
| | - Huanrong Li
- Department of Gynecology and Obstetrics, Tianjin Medical University General Hospital, Tianjin, People’s Republic of China
- Tianjin Key Laboratory of Female Reproductive Health and Eugenics, Tianjin Medical University General Hospital, Tianjin, People’s Republic of China
| | - Qiaoling Zhang
- Department of Gynecology and Obstetrics, Tianjin Medical University General Hospital, Tianjin, People’s Republic of China
- Tianjin Key Laboratory of Female Reproductive Health and Eugenics, Tianjin Medical University General Hospital, Tianjin, People’s Republic of China
| | - Yingmei Wang
- Department of Gynecology and Obstetrics, Tianjin Medical University General Hospital, Tianjin, People’s Republic of China
- Tianjin Key Laboratory of Female Reproductive Health and Eugenics, Tianjin Medical University General Hospital, Tianjin, People’s Republic of China
| | - Fengxia Xue
- Department of Gynecology and Obstetrics, Tianjin Medical University General Hospital, Tianjin, People’s Republic of China
- Tianjin Key Laboratory of Female Reproductive Health and Eugenics, Tianjin Medical University General Hospital, Tianjin, People’s Republic of China
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Al Sharie AH, Abu Zahra AM, El-Elimat T, Darweesh RF, Al-Khaldi AK, Abu Mousa BM, Amer MSB, Al Zu’bi YO, Al-Kammash K, Abu Lil A, Al Malkawi AA, Alazzeh Z, Alali FQ. Cyclin dependent kinase inhibitor 3 (CDKN3) upregulation is associated with unfavorable prognosis in clear cell renal cell carcinoma and shapes tumor immune microenvironment: A bioinformatics analysis. Medicine (Baltimore) 2023; 102:e35004. [PMID: 37682177 PMCID: PMC10489202 DOI: 10.1097/md.0000000000035004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 08/08/2023] [Indexed: 09/09/2023] Open
Abstract
Cell cycle regulatory proteins plays a pivotal role in the development and progression of many human malignancies. Identification of their biological functions as well as their prognostic utility presents an active field of research. As a continuation of the ongoing efforts to elucidate the molecular characteristics of clear cell renal cell carcinoma (ccRCC); we present a comprehensive bioinformatics study targeting the prognostic and mechanistic role of cyclin-dependent kinase inhibitor 3 (CDKN3) in ccRCC. The ccRCC cohort from the Cancer Genome Atlas Program was accessed through the UCSC Xena browser to obtain CDKN3 mRNA expression data and their corresponding clinicopathological variables. The independent prognostic signature of CDKN3 was evaluated using univariate and multivariate Cox logistic regression analysis. Gene set enrichment analysis and co-expression gene functional annotations were used to discern CDKN3-related altered molecular pathways. The tumor immune microenvironment was evaluated using TIMER 2.0 and gene expression profiling interactive analysis. CDKN3 upregulation is associated with shortened overall survival (hazard ratio [HR] = 2.325, 95% confident interval [CI]: 1.703-3.173, P < .0001) in the Cancer Genome Atlas Program ccRCC cohort. Univariate (HR: 0.426, 95% CI: 0.316-0.576, P < .001) and multivariate (HR: 0.560, 95% CI: 0.409-0.766, P < .001) Cox logistic regression analyses indicate that CDKN3 is an independent prognostic variable of the overall survival. High CDKN3 expression is associated with enrichment within the following pathways including allograph rejection, epithelial-mesenchymal transition, mitotic spindle, inflammatory response, IL-6/JAK/STAT3 signaling, spermatogenesis, TNF-α signaling via NF-kB pathway, complement activation, KRAS signaling, and INF-γ signaling. CDKN3 is also associated with significant infiltration of a wide spectrum of immune cells and correlates remarkably with immune-related genes. CDKN3 is a poor prognostic biomarker in ccRCC that alters many molecular pathways and impacts the tumor immune microenvironment.
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Affiliation(s)
- Ahmed H. Al Sharie
- Faculty of Medicine, Jordan University of Science & Technology, Irbid, Jordan
| | - Abdulmalek M. Abu Zahra
- Department of Medical Laboratory Sciences, Jordan University of Science and Technology, Irbid, Jordan
| | - Tamam El-Elimat
- Department of Medicinal Chemistry and Pharmacognosy, Faculty of Pharmacy, Jordan University of Science and Technology, Irbid, Jordan
| | - Reem F. Darweesh
- Department of Medical Laboratory Sciences, Jordan University of Science and Technology, Irbid, Jordan
| | - Ayah K. Al-Khaldi
- Department of Medical Laboratory Sciences, Jordan University of Science and Technology, Irbid, Jordan
| | - Balqis M. Abu Mousa
- Faculty of Medicine, Jordan University of Science & Technology, Irbid, Jordan
| | | | - Yazan O. Al Zu’bi
- Faculty of Medicine, Jordan University of Science & Technology, Irbid, Jordan
| | - Kinda Al-Kammash
- Faculty of Medicine, Jordan University of Science & Technology, Irbid, Jordan
| | - Alma Abu Lil
- Faculty of Medicine, Jordan University of Science & Technology, Irbid, Jordan
| | | | - Zainab Alazzeh
- Faculty of Medicine, Jordan University of Science & Technology, Irbid, Jordan
| | - Feras Q. Alali
- College of Pharmacy, QU Health, Qatar University, Doha, Qatar
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Specific Blood RNA Profiles in Individuals with Acute Spinal Cord Injury as Compared with Trauma Controls. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2023; 2023:1485135. [PMID: 36686379 PMCID: PMC9851797 DOI: 10.1155/2023/1485135] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 11/30/2022] [Accepted: 12/22/2022] [Indexed: 01/15/2023]
Abstract
Background Spinal cord injury (SCI) is known to cause a more robust systemic inflammatory response than general trauma without CNS injury, inducing severe secondary organ damage, especially the lung and liver. Related studies are principally focused on the mechanisms underlying repair and regeneration in the injured spinal cord tissue. However, the specific mechanism of secondary injury after acute SCI is widely overlooked, compared with general trauma. Methods Two datasets of GSE151371 and GSE45376 related to the blood samples and spinal cord after acute SCI were selected to identify the differentially expressed genes (DEGs). In GSE151371, functional enrichment analysis on specific DEGs of blood samples was performed. And the top 15 specific hub genes were identified from intersectional genes between the specific upregulated DEGs of blood samples in GSE151371 and the upregulated DEGs of the spinal cord in GSE45376. The specific functional enrichment analysis and the drug candidates of the hub genes and the miRNAs-targeted hub genes were also analyzed and predicted. Results DEGs were identified, and a total of 64 specific genes were the intersection of upregulated genes of the spinal cord in GSE45376 and upregulated genes of human blood samples in GSE151371. The top 15 hub genes including HP, LCN2, DLGAP5, CEP55, HMMR, CDKN3, PRTN3, SKA3, MPO, LTF, CDC25C, MMP9, NEIL3, NUSAP1, and CD163 were calculated from the 64 specific genes. Functional enrichment analysis of the top 15 hub genes revealed inflammation-related pathways. The predicted miRNAs-targeted hub genes and drug candidates of hub genes were also performed to put forward reasonable treatment strategies. Conclusion The specific hub genes of acute SCI as compared with trauma without CNS injury were identified. The functional enrichment analysis of hub genes showed a specific immune response. Several predicted drugs of hub genes were also obtained. The hub genes and the predicted miRNAs may be potential biomarkers and therapeutic targets and require further validation.
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5
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KLF7 promotes preadipocyte proliferation via activation of the Akt signaling pathway by Cis-regulating CDKN3. Acta Biochim Biophys Sin (Shanghai) 2022; 54:1486-1496. [PMID: 36269137 PMCID: PMC9827951 DOI: 10.3724/abbs.2022144] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Krüppel-like transcription factor 7 (KLF7) promotes preadipocyte proliferation; however, its target gene in this process has not yet been identified. Using KLF7 ChIP-seq analysis, we previously showed that a KLF7-binding peak is present upstream of the cyclin-dependent kinase inhibitor 3 gene ( CDKN3) in chicken preadipocytes. In the present study, we identify CDKN3 as a target gene of KLF7 that mediates the effects of KLF7 on preadipocyte proliferation. Furthermore, 5'-truncating mutation analysis shows that the minimal promoter is located between nt -160 and nt -7 (relative to the translation initiation codon ATG) of CDKN3. KLF7 overexpression increases CDKN3 promoter activity in the DF-1 and immortalized chicken preadipocyte (ICP1) cell lines. Deletion of the putative binding site of KLF7 abolishes the promotive effect of KLF7 overexpression on CDKN3 promoter activity. Moreover, CDKN3 knockdown and overexpression assays reveal that CDKN3 enhances ICP1 cell proliferation. Flow cytometry analysis shows that CDKN3 accelerates the G1/S transition. Furthermore, we find that KLF7 promotes ICP1 cell proliferation via Akt phosphorylation by regulating CDKN3. Taken together, our results suggest that KLF7 promotes preadipocyte proliferation by activating the Akt signaling pathway by cis-regulating CDKN3, thus driving the G1/S transition.
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Identification of cell cycle-associated and -unassociated regulators for expression of a hepatocellular carcinoma oncogene cyclin-dependent kinase inhibitor 3. Biochem Biophys Res Commun 2022; 625:46-52. [DOI: 10.1016/j.bbrc.2022.07.088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 07/22/2022] [Indexed: 11/23/2022]
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Celastrol with a Knockdown of miR-9-2, miR-17 and miR-19 Causes Cell Cycle Changes and Induces Apoptosis and Autophagy in Glioblastoma Multiforme Cells. Processes (Basel) 2022. [DOI: 10.3390/pr10030441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Glioblastoma multiforme (GBM) is a cancer with extremely high aggressiveness, malignancy and mortality. Because of all of the poor prognosis features of GBM, new methods should be sought that will effectively cure it. We examined the efficacy of a combination of celastrol and a knockdown of the miR-9-2, miR-17 and miR-19 genes in the human glioblastoma U251MG cell line. U251MG cells were transfected with specific siRNA and exposed to celastrol. The effect of the knockdown of the miRs genes in combination with exposure to celastrol on the cell cycle (flow cytometry) and the expression of selected genes related to its regulation (RT-qPCR) and the regulation of apoptosis and autophagy was investigated. We found a significant reduction in cell viability and proliferation, an accumulation of the subG1-phase cells and a decreased population of cells in the S and G2/M phases, as well as the induction of apoptosis and autophagy. The observed changes were not identical in the case of the silencing of each of the tested miRNAs, which indicates a different mechanism of action of miR9-2, miR-17, miR-19 silencing on GBM cells in combination with celastrol. The multidirectional effects of the silencing of the genes encoding miR-9-2, miR-17 and miR-19 in combination with exposure to celastrol is possible. The studied strategy of silencing the miR overexpressed in GBM could be important in developing more effective treatments for glioblastoma. Additional studies are necessary in order to obtain a more detailed interpretation of the obtained results. The siRNA-induced miR-9-2, miR-17 and miR-19 mRNA knockdowns in combination with celastrol could offer a novel therapeutic strategy to more effectively control the growth of human GBM cells.
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Wang N, Yang Q, Gu Y, Zhen X, Shi Y, Gu W, Wang J, He Y, Wang J. MNSFβ Promotes the Proliferation and Migration of Human Extravillous Trophoblast Cells and the Villus Expression Level of MNSFβ Is Decreased in Recurrent Miscarriage Patients. Gynecol Obstet Invest 2020; 86:27-39. [PMID: 33326956 DOI: 10.1159/000506309] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 01/31/2020] [Indexed: 11/19/2022]
Abstract
AIMS The invasion of extravillous trophoblast (EVT) cells into maternal decidua is essential for the establishment and maintenance of pregnancy. Derangement of EVT cell invasion might cause pregnancy complications including recurrent miscarriage (RM). We previously reported that deficiency of monoclonal nonspecific suppressor factor beta (MNSFβ) led to the early pregnancy failure in mice and the decidual MNSFβ expression level in RM patients was significantly decreased, but the underlying molecular mechanism of the role that MNSFβ played at the maternal-fetal interface remains unclear. Thus, in the present study, we determined effects of downregulated MNSFβ expression on human EVT cell activities. METHODS The MNSFβ expression in first-trimester human decidual and placental villus tissues was detected, respectively, by immunofluorescence or immunohistochemical analyses. The MNSFβ expression level in the immortalized first-trimester human EVT cell line HTR8/SVneo was downregulated by transfecting the small interfering RNA against MNSFβ and upregulated by transfecting the recombinant pDsRed-MNSFβ plasmids. The proliferation, migration, invasion, and apoptosis activities of HTR8/SVneo cells were, respectively, determined by cytometry assay, scratch test, transwell assay, and FITC/PI staining. The expression levels of P53, RhoA, Bcl-2, Bax, and MMP-9 in HTR8/SVneo cells, as well as the expression levels of MNSFβ and RhoA in placental villi of RM patients and physically normal pregnant women (NP), were examined by Western blot analysis. RESULTS MNSFβ protein signals were observed in first-trimester human villus and extravillous trophoblast cells. The downregulated MNSFβ expression significantly attenuated the proliferation, migration, and invasion abilities of HTR8/SVneo cells, accompanied with the obviously decreased expression levels of P53, RhoA, Bcl-2, Bax, and MMP-9, whereas the upregulated MNSFβ expression in HTR8/SVneo cells represented the inverse effects. Furthermore, expression levels of MNSFβ and RhoA in first-trimester human placental villus tissues of RM patients were significantly decreased compared to that of NP women. CONCLUSION These data suggested that MNSFβ promotes proliferation and migration of human EVT cells, probably via the P53 signaling pathway, and the deficiency of MNSFβ in placental villi might lead to early pregnancy loss by reducing proliferation and invasion activities of EVTs.
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Affiliation(s)
- Nan Wang
- NHC Key Lab of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), Pharmacy School, Fudan University, Shanghai, China
| | - Qian Yang
- NHC Key Lab of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), Pharmacy School, Fudan University, Shanghai, China
| | - Yan Gu
- The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Xingxing Zhen
- NHC Key Lab of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), Pharmacy School, Fudan University, Shanghai, China
| | - Yan Shi
- NHC Key Lab of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), Pharmacy School, Fudan University, Shanghai, China
| | - Wenwen Gu
- NHC Key Lab of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), Pharmacy School, Fudan University, Shanghai, China
| | - Jianmei Wang
- The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Yaping He
- NHC Key Lab of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), Pharmacy School, Fudan University, Shanghai, China,
| | - Jian Wang
- NHC Key Lab of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), Pharmacy School, Fudan University, Shanghai, China
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9
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Identification of NCAPH as a biomarker for prognosis of breast cancer. Mol Biol Rep 2020; 47:7831-7842. [DOI: 10.1007/s11033-020-05859-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 09/23/2020] [Indexed: 12/23/2022]
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10
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Jiang CH, Yuan X, Li JF, Xie YF, Zhang AZ, Wang XL, Yang L, Liu CX, Liang WH, Pang LJ, Zou H, Cui XB, Shen XH, Qi Y, Jiang JF, Gu WY, Li F, Hu JM. Bioinformatics-based screening of key genes for transformation of liver cirrhosis to hepatocellular carcinoma. J Transl Med 2020; 18:40. [PMID: 32000807 PMCID: PMC6993496 DOI: 10.1186/s12967-020-02229-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 01/14/2020] [Indexed: 02/06/2023] Open
Abstract
Background Hepatocellular carcinoma (HCC) is the most common type of liver tumour, and is closely related to liver cirrhosis. Previous studies have focussed on the pathogenesis of liver cirrhosis developing into HCC, but the molecular mechanism remains unclear. The aims of the present study were to identify key genes related to the transformation of cirrhosis into HCC, and explore the associated molecular mechanisms. Methods GSE89377, GSE17548, GSE63898 and GSE54236 mRNA microarray datasets from Gene Expression Omnibus (GEO) were analysed to obtain differentially expressed genes (DEGs) between HCC and liver cirrhosis tissues, and network analysis of protein–protein interactions (PPIs) was carried out. String and Cytoscape were used to analyse modules and identify hub genes, Kaplan–Meier Plotter and Oncomine databases were used to explore relationships between hub genes and disease occurrence, development and prognosis of HCC, and the molecular mechanism of the main hub gene was probed using Kyoto Encyclopedia of Genes and Genomes(KEGG) pathway analysis. Results In total, 58 DEGs were obtained, of which 12 and 46 were up- and down-regulated, respectively. Three hub genes (CDKN3, CYP2C9 and LCAT) were identified and associated prognostic information was obtained. CDKN3 may be correlated with the occurrence, invasion, and recurrence of HCC. Genes closely related to changes in the CDKN3 hub gene were screened, and Kyoto Encyclopedia of Genes and Genomes (KEGGs) pathway analysis identified numerous cell cycle-related genes. Conclusion CDKN3 may affect the transformation of liver cirrhosis into HCC, and represents a new candidate molecular marker of the occurrence and progression of HCC.
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Affiliation(s)
- Chen Hao Jiang
- Department of Pathology and Key Laboratory for Xinjiang Endemic and Ethnic Diseases (Ministry of Education), Shihezi University School of Medicine, Xinjiang, 832002, China.,Department of Pathology, The First Affiliated Hospital, Shihezi University School of Medicine, Xinjiang, 832002, China
| | - Xin Yuan
- Department of Pathology and Key Laboratory for Xinjiang Endemic and Ethnic Diseases (Ministry of Education), Shihezi University School of Medicine, Xinjiang, 832002, China.,Department of Pathology, The First Affiliated Hospital, Shihezi University School of Medicine, Xinjiang, 832002, China
| | - Jiang Fen Li
- Department of Pathology and Key Laboratory for Xinjiang Endemic and Ethnic Diseases (Ministry of Education), Shihezi University School of Medicine, Xinjiang, 832002, China.,Department of Pathology, The First Affiliated Hospital, Shihezi University School of Medicine, Xinjiang, 832002, China
| | - Yu Fang Xie
- Department of Pathology and Key Laboratory for Xinjiang Endemic and Ethnic Diseases (Ministry of Education), Shihezi University School of Medicine, Xinjiang, 832002, China.,Department of Pathology, The First Affiliated Hospital, Shihezi University School of Medicine, Xinjiang, 832002, China
| | - An Zhi Zhang
- Department of Pathology and Key Laboratory for Xinjiang Endemic and Ethnic Diseases (Ministry of Education), Shihezi University School of Medicine, Xinjiang, 832002, China.,Department of Pathology, The First Affiliated Hospital, Shihezi University School of Medicine, Xinjiang, 832002, China
| | - Xue Li Wang
- Department of Pathology and Key Laboratory for Xinjiang Endemic and Ethnic Diseases (Ministry of Education), Shihezi University School of Medicine, Xinjiang, 832002, China.,Department of Pathology, The First Affiliated Hospital, Shihezi University School of Medicine, Xinjiang, 832002, China
| | - Lan Yang
- Department of Pathology and Key Laboratory for Xinjiang Endemic and Ethnic Diseases (Ministry of Education), Shihezi University School of Medicine, Xinjiang, 832002, China.,Department of Pathology, The First Affiliated Hospital, Shihezi University School of Medicine, Xinjiang, 832002, China
| | - Chun Xia Liu
- Department of Pathology and Key Laboratory for Xinjiang Endemic and Ethnic Diseases (Ministry of Education), Shihezi University School of Medicine, Xinjiang, 832002, China.,Department of Pathology, The First Affiliated Hospital, Shihezi University School of Medicine, Xinjiang, 832002, China
| | - Wei Hua Liang
- Department of Pathology and Key Laboratory for Xinjiang Endemic and Ethnic Diseases (Ministry of Education), Shihezi University School of Medicine, Xinjiang, 832002, China.,Department of Pathology, The First Affiliated Hospital, Shihezi University School of Medicine, Xinjiang, 832002, China
| | - Li Juan Pang
- Department of Pathology and Key Laboratory for Xinjiang Endemic and Ethnic Diseases (Ministry of Education), Shihezi University School of Medicine, Xinjiang, 832002, China.,Department of Pathology, The First Affiliated Hospital, Shihezi University School of Medicine, Xinjiang, 832002, China
| | - Hong Zou
- Department of Pathology and Key Laboratory for Xinjiang Endemic and Ethnic Diseases (Ministry of Education), Shihezi University School of Medicine, Xinjiang, 832002, China.,Department of Pathology, The First Affiliated Hospital, Shihezi University School of Medicine, Xinjiang, 832002, China
| | - Xiao Bin Cui
- Department of Pathology and Key Laboratory for Xinjiang Endemic and Ethnic Diseases (Ministry of Education), Shihezi University School of Medicine, Xinjiang, 832002, China.,Department of Pathology, The First Affiliated Hospital, Shihezi University School of Medicine, Xinjiang, 832002, China
| | - Xi Hua Shen
- Department of Pathology and Key Laboratory for Xinjiang Endemic and Ethnic Diseases (Ministry of Education), Shihezi University School of Medicine, Xinjiang, 832002, China.,Department of Pathology, The First Affiliated Hospital, Shihezi University School of Medicine, Xinjiang, 832002, China
| | - Yan Qi
- Department of Pathology and Key Laboratory for Xinjiang Endemic and Ethnic Diseases (Ministry of Education), Shihezi University School of Medicine, Xinjiang, 832002, China.,Department of Pathology, The First Affiliated Hospital, Shihezi University School of Medicine, Xinjiang, 832002, China
| | - Jin Fang Jiang
- Department of Pathology and Key Laboratory for Xinjiang Endemic and Ethnic Diseases (Ministry of Education), Shihezi University School of Medicine, Xinjiang, 832002, China.,Department of Pathology, The First Affiliated Hospital, Shihezi University School of Medicine, Xinjiang, 832002, China
| | - Wen Yi Gu
- Australian Institute of Bioengineering and Nanotechnology, University of Queensland, Brisbane, QLD, 4072, Australia
| | - Feng Li
- Department of Pathology and Key Laboratory for Xinjiang Endemic and Ethnic Diseases (Ministry of Education), Shihezi University School of Medicine, Xinjiang, 832002, China.,Department of Pathology, The First Affiliated Hospital, Shihezi University School of Medicine, Xinjiang, 832002, China.,Department of Pathology, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
| | - Jian Ming Hu
- Department of Pathology and Key Laboratory for Xinjiang Endemic and Ethnic Diseases (Ministry of Education), Shihezi University School of Medicine, Xinjiang, 832002, China. .,Department of Pathology, The First Affiliated Hospital, Shihezi University School of Medicine, Xinjiang, 832002, China.
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Tu H, Wu M, Huang W, Wang L. Screening of potential biomarkers and their predictive value in early stage non-small cell lung cancer: a bioinformatics analysis. Transl Lung Cancer Res 2019; 8:797-807. [PMID: 32010558 PMCID: PMC6976355 DOI: 10.21037/tlcr.2019.10.13] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 10/12/2019] [Indexed: 12/29/2022]
Abstract
BACKGROUND Non-small cell lung cancer (NSCLC) remains the first leading cause of death in malignancies worldwide. Despite the early screening of NSCLC by low-dose spiral computed tomography (CT) in high-risk individuals caused a 20% reduction in the mortality, there still exists imperative needs for the identification of novel biomarkers for the diagnosis and treatment of lung cancer. METHODS mRNA microarray datasets GSE19188, GSE33532, and GSE44077 were searched, and the differentially expressed genes (DEGs) were obtained using GEO2R. Functional and pathway enrichment analyses were performed for the DEGs using DAVID database. Protein-protein interaction (PPI) network was plotted with STRING and visualized by Cytoscape. Module analysis of the PPI network was done through MCODE. The overall survival (OS) analysis of genes from MCODE was performed with the Kaplan Meier-plotter. RESULTS A total of 221 DEGs were obtained, which were mainly enriched in the terms related to cell division, cell proliferation, and signal transduction. A PPI network was constructed, consisting of 221 nodes and 739 edges. A significant module including 27 genes was identified in the PPI network. Elevated expression of these genes was associated with poor OS of NSCLC patients, including UBE2T, UNF2, CDKN3, ANLN, CCNB2, and CKAP2L. The enriched functions and pathways included protein binding, ATP binding, cell cycle, and p53 signaling pathway. CONCLUSIONS The DEGs in NSCLC have the potential to become useful targets for the diagnosis and treatment of NSCLC.
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Affiliation(s)
- Hongbin Tu
- Department of Integrated TCM & Western Medicine, Shanghai Pulmonary Hospital Affiliated to Tongji University, Shanghai 200433, China
| | - Meihong Wu
- Department of Oncology, Changhai Hospital Affiliated to Second Military Medical University, Shanghai 200438, China
| | - Weiling Huang
- Department of Integrated TCM & Western Medicine, Shanghai Pulmonary Hospital Affiliated to Tongji University, Shanghai 200433, China
| | - Lixin Wang
- Department of Integrated TCM & Western Medicine, Shanghai Pulmonary Hospital Affiliated to Tongji University, Shanghai 200433, China
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12
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Yu H, Yao J, Du M, Ye J, He X, Yin L. CDKN3 promotes cell proliferation, invasion and migration by activating the AKT signaling pathway in esophageal squamous cell carcinoma. Oncol Lett 2019; 19:542-548. [PMID: 31897169 DOI: 10.3892/ol.2019.11077] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 09/26/2019] [Indexed: 01/25/2023] Open
Abstract
In China, esophageal squamous cell carcinoma (ESCC), capable of direct invasion and early metastasis, exhibits high mortality. Identification of the molecular basis driving ESCC progression and development of new diagnostic biomarkers are urgently needed. Cyclin-dependent kinase inhibitor 3 (CDKN3) performs crucial roles in the modulation of tumor development. The present study aimed to explore the functions and underlying mechanism of CDKN3 in regulating ESCC cell proliferation and invasion. The expression levels of CDKN3 in ESCC cells were evaluated by reverse transcription-quantitative PCR. Cell counting kit-8 and colony forming assays were used to evaluate cell viability. Wound-healing assay was performed to explore cell migration. Transwell invasion analysis was conducted to investigate the invasive capacity of ESCC cells. Protein levels were detected by western blot assay. The results demonstrated that the expression of CDKN3 was significantly upregulated in ESCC tissues, as predicted using the UALCAN and Gene Expression Omnibus databases. PCR and western blot assays confirmed that CDKN3 was upregulated in ESCC cell lines. Functional assays revealed that CDKN3 knockdown with small interfering RNA decreased the ability of ESCC cells to proliferate, invade and migrate and suppressed G1/S transition. Further mechanistic analyses demonstrated that CDKN3 promoted cell proliferation and invasion by activating the AKT signaling pathway in ESCC cells. To the best of our knowledge, the present study is the first to identify the functions of CDKN3 in ESCC and provide evidence that CDKN3 regulates tumor progression by activating the AKT signaling pathway. Therefore, CDKN3 may serve as a potential effective therapeutic target for ESCC treatment.
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Affiliation(s)
- Hanxu Yu
- Department of Radiotherapy, The Affiliated Cancer Hospital of Nanjing Medical University, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing, Jiangsu 210000, P.R. China.,Department of Radiotherapy, Lianshui County People's Hospital, Lianshui, Jiangsu 223001, P.R. China
| | - Jun Yao
- Department of Radiotherapy, Yancheng Second People's Hospital, Yancheng, Jiangsu 22400, P.R. China
| | - Mingyu Du
- Department of Radiotherapy, The Affiliated Cancer Hospital of Nanjing Medical University, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing, Jiangsu 210000, P.R. China
| | - Jinjun Ye
- Department of Radiotherapy, The Affiliated Cancer Hospital of Nanjing Medical University, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing, Jiangsu 210000, P.R. China
| | - Xia He
- Department of Radiotherapy, The Affiliated Cancer Hospital of Nanjing Medical University, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing, Jiangsu 210000, P.R. China
| | - Li Yin
- Department of Radiotherapy, The Affiliated Cancer Hospital of Nanjing Medical University, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing, Jiangsu 210000, P.R. China
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13
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Caccuri F, Sommariva M, Marsico S, Giordano F, Zani A, Giacomini A, Fraefel C, Balsari A, Caruso A. Inhibition of DNA Repair Mechanisms and Induction of Apoptosis in Triple Negative Breast Cancer Cells Expressing the Human Herpesvirus 6 U94. Cancers (Basel) 2019; 11:cancers11071006. [PMID: 31323788 PMCID: PMC6679437 DOI: 10.3390/cancers11071006] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 07/01/2019] [Accepted: 07/11/2019] [Indexed: 12/18/2022] Open
Abstract
Triple-negative breast cancer (TNBC) accounts for 15–20% of all breast cancers. In spite of initial good response to chemotherapy, the prognosis of TNBC remains poor and no effective specific targeted therapy is readily available. Recently, we demonstrated the ability of U94, the latency gene of human herpes virus 6 (HHV-6), to interfere with proliferation and with crucial steps of the metastatic cascade by using MDA-MB 231 TNBC breast cancer cell line. U94 expression was also associated with a partial mesenchymal-to-epithelial transition (MET) of cells, which displayed a less aggressive phenotype. In this study, we show the ability of U94 to exert its anticancer activity on three different TNBC cell lines by inhibiting DNA damage repair genes, cell cycle and eventually leading to cell death following activation of the intrinsic apoptotic pathway. Interestingly, we found that U94 acted synergistically with DNA-damaging drugs. Overall, we provide evidence that U94 is able to combat tumor cells with different mechanisms, thus attesting for the great potential of this molecule as a multi-target drug in cancer therapy.
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Affiliation(s)
- Francesca Caccuri
- Department of Molecular and Translational Medicine, University of Brescia, Brescia 25123, Italy
| | - Michele Sommariva
- Dipartimento di Scienze Biomediche per la Salute, Università degli Studi di Milano, Milan 20133, Italy
| | - Stefania Marsico
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Arcavacata di Rende, Cosenza 87036, Italy
| | - Francesca Giordano
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Arcavacata di Rende, Cosenza 87036, Italy
| | - Alberto Zani
- Department of Molecular and Translational Medicine, University of Brescia, Brescia 25123, Italy
| | - Arianna Giacomini
- Department of Molecular and Translational Medicine, University of Brescia, Brescia 25123, Italy
| | - Cornel Fraefel
- Institute of Virology, University of Zurich, Zurich 8057, Switzerland
| | - Andrea Balsari
- Dipartimento di Scienze Biomediche per la Salute, Università degli Studi di Milano, Milan 20133, Italy
| | - Arnaldo Caruso
- Department of Molecular and Translational Medicine, University of Brescia, Brescia 25123, Italy.
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14
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Wu M, Liu Z, Li X, Zhang A, Lin D, Li N. Analysis of potential key genes in very early hepatocellular carcinoma. World J Surg Oncol 2019; 17:77. [PMID: 31043166 PMCID: PMC6495517 DOI: 10.1186/s12957-019-1616-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 04/14/2019] [Indexed: 02/07/2023] Open
Abstract
Background Hepatocellular carcinoma (HCC) is the major pathological type of primary liver cancer, one of the leading causes of cancer death worldwide. In addition, the long-term survival rates of HCC still remain low. Therefore, we attempted to identify the potential key genes in the occurrence of HCC by comparing the expression profiles of very early HCC tissue samples with that of chronic cirrhotic tissue samples by integrating the bioinformatics analysis in this study. Methods Gene expression profiles of 19 very early HCC and 19 cirrhotic tissue samples were selected from GSE63898. Differentially expressed genes (DEGs) were also identified by using online tool GEO2R. Furthermore, the GO and KEGG enrichment analysis of the DGEs were conducted on DAVID datasets. Then a protein–protein interaction (PPI) network was constructed and the modules were analyzed based on STRING database and Cytoscape software. The hub genes were screened by applying the cytoHubba plugin and then analyzed with the Kaplan Meier plotter. Results A total of 118 DEGs were identified between very early HCC and cirrhotic tissue samples. These DGEs were strongly associated with several biological processes, such as negative regulation of growth and p53 signaling pathway. A PPI network was constructed and top eight hub genes, including CDKN3, CDK1, CCNB1, TOP2A, CCNA2, CCNB2, PRC1, and RRM2, were determined. High expressions of CDK1, CCNB1, TOP2A, CCNA2, PRC1, RRM2, CDKN3, and CCNB2 were associated with poorer overall survivals (OS) in HCC patients. Conclusion We had compared the expression profiles between the very early HCC and cirrhotic tissue samples by using bioinformatics analysis tools, which might help us better to understand the molecular mechanism of the initiation of HCC and even to find novel targets for HCC therapy.
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Affiliation(s)
- Min Wu
- Department of General Surgery, Beijing Youan Hospital, Capital Medical University, 8 Xitoutiao, Youanmenwai, Feng-tai District, Beijing, 100069, China
| | - Zhaobo Liu
- Department of General Surgery, Beijing Youan Hospital, Capital Medical University, 8 Xitoutiao, Youanmenwai, Feng-tai District, Beijing, 100069, China
| | - Xin Li
- Department of General Surgery, Beijing Youan Hospital, Capital Medical University, 8 Xitoutiao, Youanmenwai, Feng-tai District, Beijing, 100069, China
| | - Aiying Zhang
- Beijing Institute of Hepatology, Beijing YouAn Hospital, Capital Medical University, 8 Xitoutiao, Youanmenwai, Feng-tai District, Beijing, 100069, China
| | - Dongdong Lin
- Department of General Surgery, Beijing Youan Hospital, Capital Medical University, 8 Xitoutiao, Youanmenwai, Feng-tai District, Beijing, 100069, China
| | - Ning Li
- Department of General Surgery, Beijing Youan Hospital, Capital Medical University, 8 Xitoutiao, Youanmenwai, Feng-tai District, Beijing, 100069, China.
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15
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Liu J, Min L, Zhu S, Guo Q, Li H, Zhang Z, Zhao Y, Xu C, Zhang S. Cyclin-Dependent Kinase Inhibitor 3 Promoted Cell Proliferation by Driving Cell Cycle from G1 to S Phase in Esophageal Squamous Cell Carcinoma. J Cancer 2019; 10:1915-1922. [PMID: 31205550 PMCID: PMC6547974 DOI: 10.7150/jca.27053] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 01/12/2019] [Indexed: 12/19/2022] Open
Abstract
Background and aims. Cyclin-dependent kinase inhibitor 3 (CDKN3) has been found playing a varying role in carcinogenesis, but its biological function in esophageal squamous cell carcinoma (ESCC) is unclear. The aim of this study was to demonstrate the role of CDKN3 in ESCC. Materials and Methods: Real-time PCR and Western blot was performed in 15 pairs of ESCC tissues and adjacent normal esophageal tissues. Then cell proliferation ability, cloning ability, cell cycle status and migration and invasion ability were explored in CDKN3 overexpressed TE1 cell line and CDKN3 siRNA transfected TE1 and KYSE70 cell lines. Finally, cell cycle related proteins CyclinD1, CDK4, pAKT, P53, P21, and P27 were tested by Western blot. Results: mRNA level was higher in 11 ESCC tissues compared to adjacent normal tissues, and an increased protein expression was further detected in 8 of those 11 ESCC tissues. Functional assays showed that CDKN3 overexpression promoted ESCC cell proliferation, colony formation, migration and invasion, and facilitated G1/S transition. Opposite results were also got after transfected with CDKN3 siRNA. Cell cycle associated protein pAKT, CyclinD1, CDK4 and P27 were upregulated and P53, P21 and were downregulated under CDKN3 overexpression. All the protein levels were found changed in the opposite direction when CDKN3 expression was disturbed by siRNA. Conclusions: Our study suggested that CDKN3 acted as an oncogene in human ESCC and may accelerate the G1/S transition by affecting CyclinD-CDK4 complex via regulating pAKT-p53-p21 axis and p27 independent of AKT.
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Affiliation(s)
- Juan Liu
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, National Clinical Research Center for Digestive Disease, Beijing Digestive Disease Center, Beijing Key Laboratory for Precancerous Lesion of Digestive Disease, Beijing, 100050, P. R. China
| | - Li Min
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, National Clinical Research Center for Digestive Disease, Beijing Digestive Disease Center, Beijing Key Laboratory for Precancerous Lesion of Digestive Disease, Beijing, 100050, P. R. China
| | - Shengtao Zhu
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, National Clinical Research Center for Digestive Disease, Beijing Digestive Disease Center, Beijing Key Laboratory for Precancerous Lesion of Digestive Disease, Beijing, 100050, P. R. China
| | - Qingdong Guo
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, National Clinical Research Center for Digestive Disease, Beijing Digestive Disease Center, Beijing Key Laboratory for Precancerous Lesion of Digestive Disease, Beijing, 100050, P. R. China
| | - Hengcun Li
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, National Clinical Research Center for Digestive Disease, Beijing Digestive Disease Center, Beijing Key Laboratory for Precancerous Lesion of Digestive Disease, Beijing, 100050, P. R. China
| | - Zheng Zhang
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, National Clinical Research Center for Digestive Disease, Beijing Digestive Disease Center, Beijing Key Laboratory for Precancerous Lesion of Digestive Disease, Beijing, 100050, P. R. China
| | - Yu Zhao
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, National Clinical Research Center for Digestive Disease, Beijing Digestive Disease Center, Beijing Key Laboratory for Precancerous Lesion of Digestive Disease, Beijing, 100050, P. R. China
| | - Changqin Xu
- Shandong Provincial Hospital affiliated to Shandong university
| | - Shutian Zhang
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, National Clinical Research Center for Digestive Disease, Beijing Digestive Disease Center, Beijing Key Laboratory for Precancerous Lesion of Digestive Disease, Beijing, 100050, P. R. China
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16
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Wu M, Liu Z, Zhang A, Li N. Identification of key genes and pathways in hepatocellular carcinoma: A preliminary bioinformatics analysis. Medicine (Baltimore) 2019; 98:e14287. [PMID: 30702595 PMCID: PMC6380748 DOI: 10.1097/md.0000000000014287] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) is one of the most prevalent cancers worldwide. However, the precise mechanisms of the development and progression of HCC remain unclear. The present study attempted to identify and functionally analyze the differentially expressed genes between HCC and cirrhotic tissues by using comprehensive bioinformatics analyses. METHODS The GSE63898 gene expression profile was downloaded from the Gene Expression Omnibus (GEO) and analyzed using the online tool GEO2R to identify differentially expressed genes (DEGs). Gene ontology (GO) functional analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of the DEGs were performed in DAVID. The STRING database was used to evaluate the interactions of DEGs and to construct a protein-protein interaction (PPI) network using Cytoscape software. Hub genes were selected using the cytoHubba plugin and were validated with the cBioPortal database. RESULTS A total of 301 DEGs were identified between HCC and cirrhotic tissues. The GO analysis results showed that these DEGs were significantly enriched in certain biological processes including negative regulation of growth and cell chemotaxis. Several significant pathways, including the p53 signaling pathway, were identified as being closely associated with these DEGs. The top 12 hub genes were screened and included TTK, NCAPG, TOP2A, CCNB1, CDK1, PRC1, RRM2, UBE2C, ZWINT, CDKN3, AURKA, and RACGAP1. The cBioPortal analysis found that alterations in hub genes could result in significantly reduced disease-free survival in HCC. CONCLUSION The present study identified a series of key genes and pathways that may be involved in the tumorigenicity and progression of HCC, providing a new understanding of the underlying molecular mechanisms of carcinogenesis in HCC.
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Affiliation(s)
- Min Wu
- Department of General surgery
| | | | - Aiying Zhang
- Beijing Institute of Hepatology, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Ning Li
- Department of General surgery
- Beijing Institute of Hepatology, Beijing Youan Hospital, Capital Medical University, Beijing, China
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17
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D'Alesio C, Punzi S, Cicalese A, Fornasari L, Furia L, Riva L, Carugo A, Curigliano G, Criscitiello C, Pruneri G, Pelicci PG, Faretta M, Bossi D, Lanfrancone L. RNAi screens identify CHD4 as an essential gene in breast cancer growth. Oncotarget 2018; 7:80901-80915. [PMID: 27779108 PMCID: PMC5348363 DOI: 10.18632/oncotarget.12646] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 09/29/2016] [Indexed: 12/15/2022] Open
Abstract
Epigenetic regulation plays an essential role in tumor development and epigenetic modifiers are considered optimal potential druggable candidates. In order to identify new breast cancer vulnerabilities and improve therapeutic chances for patients, we performed in vivo and in vitro shRNA screens in a human breast cancer cell model (MCF10DCIS.com cell line) using epigenetic libraries. Among the genes identified in our screening, we deeply investigated the role of Chromodomain Helicase DNA binding Protein 4 (CHD4) in breast cancer tumorigenesis. CHD4 silencing significantly reduced tumor growth in vivo and proliferation in vitro of MCF10DCIS.com cells. Similarly, in vivo breast cancer growth was decreased in a spontaneous mouse model of breast carcinoma (MMTV-NeuT system) and in metastatic patient-derived xenograft models. Conversely, no reduction in proliferative ability of non-transformed mammary epithelial cells (MCF10A) was detected. Moreover, we showed that CHD4 depletion arrests proliferation by inducing a G0/G1 block of cell cycle associated with up-regulation of CDKN1A (p21). These results highlight the relevance of genetic screens in the identification of tumor frailties and the role of CHD4 as a potential pharmacological target to inhibit breast cancer growth.
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Affiliation(s)
- Carolina D'Alesio
- Department of Experimental Oncology, European Institute of Oncology, Milan 20141, Italy
| | - Simona Punzi
- Department of Experimental Oncology, European Institute of Oncology, Milan 20141, Italy
| | - Angelo Cicalese
- Department of Experimental Oncology, European Institute of Oncology, Milan 20141, Italy
| | - Lorenzo Fornasari
- Department of Experimental Oncology, European Institute of Oncology, Milan 20141, Italy
| | - Laura Furia
- Department of Experimental Oncology, European Institute of Oncology, Milan 20141, Italy
| | - Laura Riva
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia, Milan 20139, Italy
| | - Alessandro Carugo
- Department of Experimental Oncology, European Institute of Oncology, Milan 20141, Italy.,Department of Molecular and Cellular Oncology, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Giuseppe Curigliano
- Division of Experimental Therapeutics, European Institute of Oncology, Milan 20141, Italy
| | - Carmen Criscitiello
- Division of Experimental Therapeutics, European Institute of Oncology, Milan 20141, Italy
| | - Giancarlo Pruneri
- School of Medicine, University of Milan, Milan 20122, Italy.,Biobank for Translational Medicine Unit, Department of Pathology, European Institute of Oncology, Milan 20141, Italy
| | - Pier Giuseppe Pelicci
- Department of Experimental Oncology, European Institute of Oncology, Milan 20141, Italy.,Department of Oncology, University of Milan, Milan 20139, Italy
| | - Mario Faretta
- Department of Experimental Oncology, European Institute of Oncology, Milan 20141, Italy
| | - Daniela Bossi
- Department of Experimental Oncology, European Institute of Oncology, Milan 20141, Italy
| | - Luisa Lanfrancone
- Department of Experimental Oncology, European Institute of Oncology, Milan 20141, Italy
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18
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Chang SL, Chen TJ, Lee YE, Lee SW, Lin LC, He HL. CDKN3 expression is an independent prognostic factor and associated with advanced tumor stage in nasopharyngeal carcinoma. Int J Med Sci 2018; 15:992-998. [PMID: 30013440 PMCID: PMC6036165 DOI: 10.7150/ijms.25065] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/21/2018] [Accepted: 05/27/2018] [Indexed: 12/12/2022] Open
Abstract
Background: Through data mining from the public transcriptome of NPC, cyclin-dependent kinase inhibitor 3 (CDKN3) was identified as a significantly upregulated gene in NPC. CDKN3 functions as a key factor in cell cycle regulation. This study was aimed to investigate the expression of CDKN3 in NPC tissues and its prognostic significance. Methods: Immunohistochemistry was performed for 124 NPC patients to assess the protein expression of CDKN3. The stainings of CDKN3 were scored by using H-score method. The relationships between CDKN3 expression status and clinicopathological parameters, disease-specific survival (DSS), distant metastasis-free survival (DMeFS), and local recurrence-free survival (LRFS) were statistically analyzed. Results: High expression of CDKN3 was significantly associated with higher primary nodal status (P=0.030) and higher TNM stage (P=0.019). In univariate analysis, high expression of CDKN3 predicted worse DSS (P<0.0001), DMeFS (P<0.0001), and LRFS (P<0.0001). In multivariate analysis, CDKN3 overexpression still acted as an independent prognostic factor for worse DSS (P<0.001; hazard ratio [HR]=11.999, 95% CI: 5.378-26.771), DMeFS (P<0.001; HR=15.069, 95% CI: 5.884-38.592), and LRFS (P<0.001; HR=5.000, 95% CI: 2.312-10.815). Conclusion: High expression of CDKN3 was an independent negative prognostic factor for NPC and was associated with advanced disease status. It might serve as potential therapeutic target and aid in risk stratification for patients with NPC.
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Affiliation(s)
- Shih-Lun Chang
- Department of Otolaryngology, Chi Mei Medical Center, Tainan, Taiwan.,Department of Optometry, Chung Hwa University of Medical Technology, Tainan, Taiwan
| | - Tzu-Ju Chen
- Department of Optometry, Chung Hwa University of Medical Technology, Tainan, Taiwan.,Department of Pathology, Chi-Mei Medical Center, Tainan, Taiwan
| | - Ying-En Lee
- Department of Anesthesiology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Sung-Wei Lee
- Department of Radiation Oncology, Chi Mei Medical Center, Liouying, Tainan, Taiwan
| | - Li-Ching Lin
- Department of Radiation Oncology, Chi Mei Medical Center, Tainan, Taiwan
| | - Hong-Lin He
- Department of Pathology, Chi-Mei Medical Center, Tainan, Taiwan
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19
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Wang H, Chen H, Zhou H, Yu W, Lu Z. Cyclin-Dependent Kinase Inhibitor 3 Promotes Cancer Cell Proliferation and Tumorigenesis in Nasopharyngeal Carcinoma by Targeting p27. Oncol Res 2017; 25:1431-1440. [PMID: 28109073 PMCID: PMC7840971 DOI: 10.3727/096504017x14835311718295] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Nasopharyngeal carcinoma (NPC) is a common malignancy of the head and neck that arises from the nasopharynx epithelium and is highly invasive. Cyclin-dependent kinase inhibitor 3 (CDKN3) belongs to the dual-specificity protein phosphatase family, which plays a key role in regulating cell division. Abnormal expression of CDKN3 has been found in numerous types of cancer. In the current study, we explored the possible role of CDKN3 in cell proliferation, ability to invade, and radiosensitivity in NPC cells. We reported that CDKN3 was upregulated and p27 was downregulated in NPC tissues and is associated with a worse prognosis for patients. In addition, downregulation of CDKN3 and upregulation of p27 decreased cell proliferation, induced cell cycle arrest, increased apoptosis, decreased cell invasion, and enhanced radiosensitivity. Silencing of p27 significantly inhibited the effects of the knockdown of CDKN3. Moreover, downregulation of CDKN3 and upregulation of p27 inhibited the increase in tumor volume and weight in implanted tumors, decreased the phosphorylation of Akt, and increased the expression of cleaved caspase 3 in tumors. CDKN3 expression was also inversely correlated with p27 expression in NPC patients. Knockdown of CDKN3 increased p27 expression. Silencing of p27 markedly inhibited the effects of CDKN3 on cell proliferation, cell cycle progression, apoptosis, invasion, and radiosensitivity. These results demonstrate that upregulation of p27 is involved in the knockdown of CDKN3-induced decrease in cell proliferation, increase in cell cycle arrest and apoptosis, decrease in invasion, and increase in radiosensitivity. The results demonstrate that the CDKN3/p27 axis may be a novel target in the treatment of NPC.
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20
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Li Y, Ji S, Fu LY, Jiang T, Wu D, Meng FD. Knockdown of Cyclin-Dependent Kinase Inhibitor 3 Inhibits Proliferation and Invasion in Human Gastric Cancer Cells. Oncol Res 2016; 25:721-731. [PMID: 27983933 PMCID: PMC7841180 DOI: 10.3727/096504016x14772375848616] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Cyclin-dependent kinase inhibitor 3 (CDKN3) has been reported to promote tumorigenesis. Since it is unclear whether CDKN3 participates in the development of human gastric cancer, this study assessed the association between CDKN3 expression and cell biological function and demonstrated the clinical significance and prognosis of CDKN3 in human gastric cancer. In this study, we found that CDKN3 showed a high expression in 35 paired human gastric cancer tissues and was correlated with poor patient survival, AJCC clinical staging, and recurrence. Silencing of CDKN3 in human gastric cancer cells can significantly reduce proliferation, migration, invasion, and adhesion abilities. Also, silencing of CDKN3 in human gastric cancer cells can induce G0-G1 cell cycle arrest and apoptosis. Detection of cell cycle marker expression showed that CDKN3 knockdown promotes cell cycle arrest by decreasing the expression of CDK2, CDC25A, CCNB1, and CCNB2 in human gastric cancer cells. The results of this study will help elucidate the oncogene function of CDKN3 in human gastric cancer.
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