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Asghariazar V, Kadkhodayi M, Sarailoo M, Jolfayi AG, Baradaran B. MicroRNA-143 as a potential tumor suppressor in cancer: An insight into molecular targets and signaling pathways. Pathol Res Pract 2023; 250:154792. [PMID: 37689002 DOI: 10.1016/j.prp.2023.154792] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Revised: 08/25/2023] [Accepted: 09/02/2023] [Indexed: 09/11/2023]
Abstract
MicroRNAs (MiRNAs), which are highly conserved and small noncoding RNAs, negatively regulate gene expression and influence signaling pathways involved in essential biological activities, including cell proliferation, differentiation, apoptosis, and cell invasion. MiRNAs have received much attention in the past decade due to their significant roles in cancer development. In particular, microRNA-143 (miR-143) is recognized as a tumor suppressor and is downregulated in most cancers. However, it seems that miR-143 is upregulated in rare cases, such as prostate cancer stem cells, and acts as an oncogene. The present review will outline the current studies illustrating the impact of miR-143 expression levels on cancer progression and discuss its target genes and their relevant signaling pathways to discover a potential therapeutic way for cancer.
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Affiliation(s)
- Vahid Asghariazar
- Cancer Immunology and Immunotherapy Research Center, Ardabil University of Medical Sciences, Ardabil, Iran; Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Deputy of Research and Technology, Ardabil University of Medical Sciences, Ardabil, Iran.
| | - Mahtab Kadkhodayi
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Department of Animal Biology, Faculty of Natural Sciences, The University of Tabriz, Tabriz, Iran
| | - Mehdi Sarailoo
- Students Research Committee, School of Medicine, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Amir Ghaffari Jolfayi
- Student Research Committee, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Behzad Baradaran
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
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Aktar A, Heit B. Role of the pioneer transcription factor GATA2 in health and disease. J Mol Med (Berl) 2023; 101:1191-1208. [PMID: 37624387 DOI: 10.1007/s00109-023-02359-8] [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: 01/09/2023] [Revised: 08/04/2023] [Accepted: 08/14/2023] [Indexed: 08/26/2023]
Abstract
The transcription factor GATA2 is involved in human diseases ranging from hematopoietic disorders, to cancer, to infectious diseases. GATA2 is one of six GATA-family transcription factors that act as pioneering transcription factors which facilitate the opening of heterochromatin and the subsequent binding of other transcription factors to induce gene expression from previously inaccessible regions of the genome. Although GATA2 is essential for hematopoiesis and lymphangiogenesis, it is also expressed in other tissues such as the lung, prostate gland, gastrointestinal tract, central nervous system, placenta, fetal liver, and fetal heart. Gene or transcriptional abnormalities of GATA2 causes or predisposes patients to several diseases including the hematological cancers acute myeloid leukemia and acute lymphoblastic leukemia, the primary immunodeficiency MonoMAC syndrome, and to cancers of the lung, prostate, uterus, kidney, breast, gastric tract, and ovaries. Recent data has also linked GATA2 expression and mutations to responses to infectious diseases including SARS-CoV-2 and Pneumocystis carinii pneumonia, and to inflammatory disorders such as atherosclerosis. In this article we review the role of GATA2 in the etiology and progression of these various diseases.
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Affiliation(s)
- Amena Aktar
- Department of Microbiology and Immunology; the Western Infection, Immunity and Inflammation Centre, The University of Western Ontario, London, ON, N6A 5C1, Canada
| | - Bryan Heit
- Department of Microbiology and Immunology; the Western Infection, Immunity and Inflammation Centre, The University of Western Ontario, London, ON, N6A 5C1, Canada.
- Robarts Research Institute, London, ON, N6A 3K7, Canada.
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Kim K, Kim M, Lee AJ, Song SH, Kang JK, Eom J, Kang GH, Bae JM, Min S, Kim Y, Lim Y, Kim HS, Kim YJ, Kim TY, Jung I. Spatial and clonality-resolved 3D cancer genome alterations reveal enhancer-hijacking as a potential prognostic marker for colorectal cancer. Cell Rep 2023; 42:112778. [PMID: 37453058 DOI: 10.1016/j.celrep.2023.112778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 05/04/2023] [Accepted: 06/23/2023] [Indexed: 07/18/2023] Open
Abstract
The regulatory effect of non-coding large-scale structural variations (SVs) on proto-oncogene activation remains unclear. This study investigated SV-mediated gene dysregulation by profiling 3D cancer genome maps from 40 patients with colorectal cancer (CRC). We developed a machine learning-based method for spatial characterization of the altered 3D cancer genome. This revealed a frequent establishment of "de novo chromatin contacts" that can span multiple topologically associating domains (TADs) in addition to the canonical TAD fusion/shuffle model. Using this information, we precisely identified super-enhancer (SE)-hijacking and its clonal characteristics. Clonal SE-hijacking genes, such as TOP2B, are recurrently associated with cell-cycle/DNA-processing functions, which can potentially be used as CRC prognostic markers. Oncogene activation and increased drug resistance due to SE-hijacking were validated by reconstructing the patient's SV using CRISPR-Cas9. Collectively, the spatial and clonality-resolved analysis of the 3D cancer genome reveals regulatory principles of large-scale SVs in oncogene activation and their clinical implications.
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Affiliation(s)
- Kyukwang Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
| | - Mooyoung Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
| | - Andrew J Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
| | - Sang-Hyun Song
- Cancer Genomics Research Laboratory, Cancer Research Institute, Seoul National University, Seoul 03080, Korea; Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul 03080, Korea
| | - Jun-Kyu Kang
- Cancer Genomics Research Laboratory, Cancer Research Institute, Seoul National University, Seoul 03080, Korea; Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul 03080, Korea
| | - Junghyun Eom
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
| | - Gyeong Hoon Kang
- Department of Pathology, Seoul National University Hospital, Seoul 03080, Korea
| | - Jeong Mo Bae
- Department of Pathology, Seoul National University Hospital, Seoul 03080, Korea
| | - Sunwoo Min
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
| | - Yeonsoo Kim
- Cancer Genomics Research Laboratory, Cancer Research Institute, Seoul National University, Seoul 03080, Korea; Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul 03080, Korea
| | - Yoojoo Lim
- Cancer Genomics Research Laboratory, Cancer Research Institute, Seoul National University, Seoul 03080, Korea; Department of Internal Medicine, Seoul National University Hospital, Seoul 03080, Korea
| | - Han Sang Kim
- Yonsei Cancer Center, Division of Medical Oncology, Department of Internal Medicine, Graduate School of Medical Science, Brain Korea 21 Project, Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Young-Joon Kim
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea
| | - Tae-You Kim
- Cancer Genomics Research Laboratory, Cancer Research Institute, Seoul National University, Seoul 03080, Korea; Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul 03080, Korea; Department of Internal Medicine, Seoul National University Hospital, Seoul 03080, Korea; IMBdx, Inc., Seoul 08506, Korea.
| | - Inkyung Jung
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea.
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Matani H, Sahu D, Paskewicz M, Gorbunova A, Omstead AN, Wegner R, Finley GG, Jobe BA, Kelly RJ, Zaidi AH, Goel A. Prognostic and predictive biomarkers for response to neoadjuvant chemoradiation in esophageal adenocarcinoma. Biomark Res 2022; 10:81. [PMCID: PMC9664643 DOI: 10.1186/s40364-022-00429-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Accepted: 10/31/2022] [Indexed: 11/16/2022] Open
Abstract
Abstract
Background
Esophageal adenocarcinoma is a lethal disease. For locally advanced patients, neoadjuvant chemoradiotherapy followed by surgery is the standard of care. Risk stratification relies heavily on clinicopathologic features, particularly pathologic response, which is inadequate, therefore establishing the need for new and reliable biomarkers for risk stratification.
Methods
Thirty four patients with locally advanced esophageal adenocarcinoma were analyzed, of which 21 received a CROSS regimen with carboplatin, paclitaxel, and radiation. Capture-based targeted sequencing was performed on the paired baseline and post-treatment samples. Differentially mutated gene analysis between responders and non-responders of treatment was performed to determine predictors of response. A univariate Cox proportional hazard regression was used to examine associations between gene mutation status and overall survival.
Results
A 3-gene signature, based on mutations in EPHA5, BCL6, and ERBB2, was identified that robustly predicts response to the CROSS regimen. For this model, sensitivity was 84.6% and specificity was 100%. Independently, a 9 gene signature was created using APC, MAP3K6, ETS1, CSF3R, PDGFRB, GATA2, ARID1A, PML, and FGF6, which significantly stratifies patients into risk categories, prognosticating for improved relapse-free (p = 4.73E-03) and overall survival (p = 3.325E-06). The sensitivity for this model was 73.33% and the specificity was 94.74%.
Conclusion
We have identified a 3-gene signature (EPHA5, BCL6, and ERBB2) that is predictive of response to neoadjuvant chemoradiotherapy and a separate prognostic 9-gene classifier that predicts survival outcomes. These panels provide significant potential for personalized management of locally advanced esophageal cancer.
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Yeh SJ, Chen BS. Systems Medicine Design based on Systems Biology Approaches and Deep Neural Network for Gastric Cancer. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2022; 19:3019-3031. [PMID: 34232888 DOI: 10.1109/tcbb.2021.3095369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Gastric cancer (GC) is the third leading cause of cancer death in the world. It is associated with the stimulation of microenvironment, aberrant epigenetic modification, and chronic inflammation. However, few researches discuss the GC molecular progression mechanisms from the perspective of the system level. In this study, we proposed a systems medicine design procedure to identify essential biomarkers and find corresponding drugs for GC. At first, we did big database mining to construct candidate protein-protein interaction network (PPIN) and candidate gene regulation network (GRN). Second, by leveraging the next-generation sequencing (NGS) data, we performed system modeling and applied system identification and model selection to obtain real genome-wide genetic and epigenetic networks (GWGENs). To make the real GWGENs easy to analyze, the principal network projection method was used to extract the core signaling pathways denoted by KEGG pathways. Subsequently, based on the identified biomarkers, we trained a deep neural network of drug-target interaction (DeepDTI) with supervised learning and filtered our candidate drugs considering drug regulation ability and drug sensitivity. With the proposed systematic strategy, we not only shed the light on the progression of GC but also suggested potential multiple-molecule drugs efficiently.
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Lin H, Hu P, Zhang H, Deng Y, Yang Z, Zhang L. GATA2-Mediated Transcriptional Activation of Notch3 Promotes Pancreatic Cancer Liver Metastasis. Mol Cells 2022; 45:329-342. [PMID: 35534193 PMCID: PMC9095506 DOI: 10.14348/molcells.2022.2176] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 11/08/2021] [Accepted: 12/24/2021] [Indexed: 12/04/2022] Open
Abstract
The liver is the predominant metastatic site for pancreatic cancer. However, the factors that determine the liver metastasis and the specific molecular mechanisms are still unclear. In this study, we used human pancreatic cancer cell line Hs766T to establish Hs766T-L3, a subline of Hs766T with stable liver metastatic ability. We performed RNA sequencing of Hs766T-L3 and its parental cell line Hs766T, and revealed huge differences in gene expression patterns and pathway activation between these two cell lines. We correlated the difference in pathway activation with the expression of the four core transcriptional factors including STAT1, NR2F2, GATA2, and SMAD4. Using the TCGA database, we examined the relative expression of these transcription factors (TFs) in pan-cancer and their relationship with the prognosis of the pancreatic cancer. Among these TFs, we considered GATA2 is closely involved in tumor metastasis and may serve as a potential metastatic driver. Further in vitro and in vivo experiments confirmed that GATA2-mediated transcriptional activation of Notch3 promotes the liver metastasis of Hs766T-L3, and knockdown of either GATA2 or Notch3 reduces the metastatic ability of Hs766T-L3. Therefore, we claim that GATA2 may serve as a metastatic driver of pancreatic cancer and a potential therapeutic target to treat liver metastasis of pancreatic cancer.
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Affiliation(s)
- Heng Lin
- Institute of Hepatobiliary Surgery, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Peng Hu
- Institute of Hepatobiliary Surgery, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Hongyu Zhang
- Institute of Hepatobiliary Surgery, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Yong Deng
- Institute of Hepatobiliary Surgery, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Zhiqing Yang
- Institute of Hepatobiliary Surgery, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Leida Zhang
- Institute of Hepatobiliary Surgery, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China
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Yu B, Dai W, Pang L, Sang Q, Li F, Yu J, Feng H, Li J, Hou J, Yan C, Su L, Zhu Z, Li YY, Liu B. The dynamic alteration of transcriptional regulation by crucial TFs during tumorigenesis of gastric cancer. Mol Med 2022; 28:41. [PMID: 35421923 PMCID: PMC9008954 DOI: 10.1186/s10020-022-00468-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Accepted: 04/04/2022] [Indexed: 11/26/2022] Open
Abstract
Background The mechanisms of Gastric cancer (GC) initiation and progression are complicated, at least partly owing to the dynamic changes of gene regulation during carcinogenesis. Thus, investigations on the changes in regulatory networks can improve the understanding of cancer development and provide novel insights into the molecular mechanisms of cancer. Methods Differential co-expression analysis (DCEA), differential gene regulation network (GRN) modeling and differential regulation analysis (DRA) were integrated to detect differential transcriptional regulation events between gastric normal mucosa and cancer samples based on GSE54129 dataset. Cytological experiments and IHC staining assays were used to validate the dynamic changes of CREB1 regulated targets in different stages. Results A total of 1955 differentially regulated genes (DRGs) were identified and prioritized in a quantitative way. Among the top 1% DRGs, 14 out of 19 genes have been reported to be GC relevant. The four transcription factors (TFs) among the top 1% DRGs, including CREB1, BPTF, GATA6 and CEBPA, were regarded as crucial TFs relevant to GC progression. The differentially regulated links (DRLs) around the four crucial TFs were then prioritized to generate testable hypotheses on the differential regulation mechanisms of gastric carcinogenesis. To validate the dynamic alterations of gene regulation patterns of crucial TFs during GC progression, we took CREB1 as an example to screen its differentially regulated targets by using cytological and IHC staining assays. Eventually, TCEAL2 and MBNL1 were proved to be differentially regulated by CREB1 during tumorigenesis of gastric cancer. Conclusions By combining differential networking information and molecular cell experiments verification, testable hypotheses on the regulation mechanisms of GC around the core TFs and their top ranked DRLs were generated. Since TCEAL2 and MBNL1 have been reported to be potential therapeutic targets in SCLC and breast cancer respectively, their translation values in GC are worthy of further investigation. Supplementary Information The online version contains supplementary material available at 10.1186/s10020-022-00468-7.
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Wu C, Li Z, Feng G, Wang L, Xie J, Jin Y, Wang L, Liu S. Tumor suppressing role of serum-derived exosomal microRNA-15a in osteosarcoma cells through the GATA binding protein 2/murine double minute 2 axis and the p53 signaling pathway. Bioengineered 2021; 12:8378-8395. [PMID: 34592889 PMCID: PMC8806960 DOI: 10.1080/21655979.2021.1987092] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Exosomes are emerging tools for transporting lipids, proteins, microRNAs (miRNAs), or other biomarkers for clinical purposes. They have produced widespread concern in managing human diseases, including osteosarcoma (OS). This study focuses on the function of serum-derived exosomal miR-15a in the growth of OS cells and the mechanism of action. Differentially expressed genes between OS and normal samples were screened using two datasets GSE70367 and GSE65071. miR-15a was poorly expressed, whereas GATA-binding protein 2 (GATA2) and murine double minute 2 (MDM2) were abundantly expressed in OS samples. miR-15a and its target mRNAs, including GATA2, were enriched in the p53 signaling pathway. miR-15a directly targets GATA2 mRNA to inhibit its expression, whereas GATA2 activates the transcription of MDM2, a negative regulator of p53. Overexpression of GATA2 and MDM2 promoted proliferation and cell cycle progression of MG-63 cells, whereas miR-15a blocked this axis and suppressed cell growth. miR-15a was identified as a major cargo of serum-derived exosomes, and exosomes conveying miR-15a were internalized by OS cells. This study demonstrated that miR-15a suppresses the GATA2/MDM2 axis to inhibit the proliferation and invasiveness of OS cells in vitro through the p53 signaling pathway.
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Affiliation(s)
- Chunyu Wu
- Department of Continuing Education, Affiliated Hospital of Heilongjiang University of Chinese Medicine, Harbin, Heilongjiang, P.R. China
| | - Zhigang Li
- Department of the Second Ward Orthopedics, The Second Affiliated Hospital of Heilongjiang University of Chinese Medicine, Harbin, Heilongjiang, P.R. China
| | - Guang Feng
- Department of Youth League Committee, Heilongjiang University of Chinese Medicine, Harbin, Heilongjiang, P.R. China
| | - Liqin Wang
- Department of Vice Director of the Hospital, Affiliated Hospital of Heilongjiang University of Chinese Medicine, Harbin, Heilongjiang, P.R. China
| | - Jingri Xie
- Department of the Liver Spleen and Stomach, Affiliated Hospital of Heilongjiang University of Chinese Medicine, Harbin, Heilongjiang, P.R. China
| | - Yang Jin
- Department of the Graduate School, Heilongjiang University of Chinese Medicine, Harbin, Heilongjiang, P.R. China
| | - Long Wang
- Department of Graduate Division, Affiliated Hospital of Heilongjiang University of Chinese Medicine, Harbin, Heilongjiang, P.R. China
| | - Songjiang Liu
- Department of Oncology, Affiliated Hospital of Heilongjiang University of Chinese Medicine, Harbin, Heilongjiang, P.R. China
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Shang H, Zhang H, Ren Z, Zhao H, Zhang Z, Tong J. Characterization of the Potential Role of NTPCR in Epithelial Ovarian Cancer by Integrating Transcriptomic and Metabolomic Analysis. Front Genet 2021; 12:695245. [PMID: 34539736 PMCID: PMC8442909 DOI: 10.3389/fgene.2021.695245] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 07/27/2021] [Indexed: 11/13/2022] Open
Abstract
Background Epithelial ovarian carcinoma (EOC) is a malignant tumor with high motility in women. Our previous study found that dysregulated nucleoside-triphosphatase cancer-related (NTPCR) was associated with the prognosis of EOC patients, and thus, this present study attempted to explore the potential roles of NTPCR in disease progression. Methods Expressed level of NTPCR was investigated in EOC tissues by RT-qPCR and Western blot analysis. NTPCR shRNA and overexpression vector were generated and transfected into OVCAR-3 or SKOV3 cells to detect the effect of NTPCR on cell proliferation, cell cycle, cell migration, and invasion. Transcriptomic sequencing and metabolite profiling analysis were performed in shNTPCR groups to identify transcriptome or metabolite alteration that might contribute to EOC. Finally, we searched the overlapped signaling pathways correlated with differential metabolites and differentially expressed genes (DEGs) by integrating analysis. Results Comparing para-cancerous tissues, we found that NTPCR is highly expressed in cancer tissues (p < 0.05). Overexpression of NTPCR inhibited cell proliferation, migration, and invasion and reduced the proportion of S- and G2/M-phase cells, while downregulation of NTPCR showed the opposite results. RNA sequencing analysis demonstrated cohorts of DEGs were identified in shNTPCR samples. Protein–protein interaction networks were constructed for DEGs. STAT1 (degree = 43) and OAS2 (degree = 36) were identified as hub genes in the network. Several miRNAs together with target genes were predicted to be crucial genes related to disease progression, including hsa-miR-124-3p, hsa-miR-30a-5p, hsa-miR-146a-5, EP300, GATA2, and STAT3. We also screened the differential metabolites from shNTPCR samples, including 22 upregulated and 22 downregulated metabolites. By integrating transcriptomics and metabolomics analysis, eight overlapped pathways were correlated with these DEGs and differential metabolites, such as primary bile acid biosynthesis, protein digestion, and absorption, pentose, and glucuronate interconversions. Conclusion NTPCR might serve as a tumor suppressor in EOC progression. Our results demonstrated that DEGs and differential metabolites were mainly related to several signaling pathways, which might be a crucial role in the progression of NTPCR regulation of EOC.
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Affiliation(s)
- Hongkai Shang
- Department of the Fourth Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, China.,Department of Gynecology, Hangzhou First People's Hospital, Hangzhou, China.,Department of Gynecology, Zhejiang University School of Medicine, Hangzhou, China
| | - Huizhi Zhang
- Department of the Fourth Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, China.,Department of Gynecology, Hangzhou First People's Hospital, Hangzhou, China
| | - Ziyao Ren
- Department of Gynecology, Hangzhou First People's Hospital, Hangzhou, China.,Department of Gynecology, Zhejiang University School of Medicine, Hangzhou, China
| | - Hongjiang Zhao
- Department of the Fourth Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, China.,Department of Gynecology, Hangzhou First People's Hospital, Hangzhou, China
| | - Zhifen Zhang
- Department of Gynecology, Hangzhou Women's Hospital (Maternity and Child Health Care Hospital), Hangzhou, China
| | - Jinyi Tong
- Department of the Fourth Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, China.,Department of Gynecology, Hangzhou Women's Hospital (Maternity and Child Health Care Hospital), Hangzhou, China
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Gong C, Fan Y, Zhou X, Lai S, Wang L, Liu J. Comprehensive Analysis of Expression and Prognostic Value of GATAs in Lung Cancer. J Cancer 2021; 12:3862-3876. [PMID: 34093794 PMCID: PMC8176258 DOI: 10.7150/jca.52623] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 04/23/2021] [Indexed: 02/07/2023] Open
Abstract
GATAs are a family of transcription factors that play sophisticated and extensive roles in cell fate transitions and tissue morphogenesis during embryonic development. Emerging evidence indicate that GATAs are involved in tumorigenesis of lung cancer (LC). However, the distinct roles, diverse expression patterns and prognostic values of six GATA family members in LC have yet to be elucidated. In the present study, the diverse expression patterns, prognostic values, genetic mutations, protein-protein interaction(PPI) networks of GATAs, Gene Ontology enrichment and Kyoto Encyclopedia of Genes and Genomes pathway in LC patients were analyzed using a serious of databases, including ONCOMINE database, Cancer Cell Line Encyclopedia database, the Human Protein Atlas, the Gene Expression Profiling Interactive Analysis database, the Kaplan-Meier plotter, cBioPortal, String database and database Database for Annotation, Visualization, and Integrated Discovery. The mRNA expression levels of GATA1/2/4/5/6 were downregulated, while GATA3 showed abnormal expressions of up-regulation and down-regulation in patients with LC. Aberrant GATAs mRNA expression was connected with prognosis. Furthermore, genetic alterations mainly appeared in GATA4. Gene Ontology enrichment and network analysis demonstrated that GATAs and their 50 interactors were primarily associated with positive regulation of transcription from RNA polymerase II promoter, transcription factor complex, transcription factor binding Jak-STAT signaling pathway. This comprehensive bioinformatic analysis demonstrated that GATA1/2/3/4/6 may be new prognosis factors, and GATA2/5/6 may be potential targets for personalized therapy for patients with LC, but further studies are requisite to analyze the mechanism of their carcinogenicity and investigate novel drug treatment. Finally, these findings would conduce to a better understanding of the unique roles of GATAs in LC.
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Affiliation(s)
- Chengwu Gong
- Department of Cardiothoracic Surgery, Second Affiliated Hospital, Nanchang University, Nanchang, Jiangxi 330006, China
| | - Yun Fan
- Department of Neurology and National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Xueliang Zhou
- Department of Cardiothoracic Surgery, First Affiliated Hospital, Nanchang University, Nanchang, Jiangxi 330006, China
| | - Songqing Lai
- Department of Cardiothoracic Surgery, First Affiliated Hospital, Nanchang University, Nanchang, Jiangxi 330006, China
| | - Lijun Wang
- Department of Cardiothoracic Surgery, Second Affiliated Hospital, Nanchang University, Nanchang, Jiangxi 330006, China
| | - Jichun Liu
- Department of Cardiothoracic Surgery, Second Affiliated Hospital, Nanchang University, Nanchang, Jiangxi 330006, China
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Greville G, Llop E, Howard J, Madden SF, Perry AS, Peracaula R, Rudd PM, McCann A, Saldova R. 5-AZA-dC induces epigenetic changes associated with modified glycosylation of secreted glycoproteins and increased EMT and migration in chemo-sensitive cancer cells. Clin Epigenetics 2021; 13:34. [PMID: 33579350 PMCID: PMC7881483 DOI: 10.1186/s13148-021-01015-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 01/18/2021] [Indexed: 12/16/2022] Open
Abstract
Background Glycosylation, one of the most fundamental post-translational modifications, is altered in cancer and is subject in part, to epigenetic regulation. As there are many epigenetic-targeted therapies currently in clinical trials for the treatment of a variety of cancers, it is important to understand the impact epi-therapeutics have on glycosylation. Results Ovarian and triple negative breast cancer cells were treated with the DNA methyltransferase inhibitor, 5-AZA-2-deoxycytidine (5-AZA-dC). Branching and sialylation were increased on secreted N-glycans from chemo-sensitive/non-metastatic cell lines following treatment with 5-AZA-dC. These changes correlated with increased mRNA expression levels in MGAT5 and ST3GAL4 transcripts in ovarian cancer cell lines. Using siRNA transient knock down of GATA2 and GATA3 transcription factors, we show that these regulate the glycosyltransferases ST3GAL4 and MGAT5, respectively. Moreover, 5-AZA-dC-treated cells displayed an increase in migration, with a greater effect seen in chemo-sensitive cell lines. Western blots showed an increase in apoptotic and senescence (p21) markers in all 5-AZA-dC-treated cells. The alterations seen in N-glycans from secreted glycoproteins in 5-AZA-dC-treated breast and ovarian cancer cells were similar to the N-glycans previously known to potentiate tumour cell survival. Conclusions While the FDA has approved epi-therapeutics for some cancer treatments, their global effect is still not fully understood. This study gives insight into the effects that epigenetic alterations have on cancer cell glycosylation, and how this potentially impacts on the overall fate of those cells. Graphic abstract ![]()
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Affiliation(s)
- Gordon Greville
- GlycoScience Group, the National Institute for Bioprocessing, Research and Training (NIBRT), Fosters Avenue, Mount Merrion, Blackrock, Co Dublin, Ireland.,College of Health and Agricultural Science (CHAS), UCD School of Medicine, University College Dublin (UCD), Belfield, Dublin 4, Ireland
| | - Esther Llop
- Biochemistry and Molecular Biology Unit, Department of Biology, University of Girona, Girona, Spain.,Girona Biomedical Research Institute (IDIBGI), Girona, Spain
| | - Jane Howard
- College of Health and Agricultural Science (CHAS), UCD School of Medicine, University College Dublin (UCD), Belfield, Dublin 4, Ireland.,UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin (UCD), Belfield, Dublin 4, Ireland
| | - Stephen F Madden
- Data Science Centre, Royal College of Surgeons in Ireland (RCSI), Dublin 2, Ireland
| | - Antoinette S Perry
- UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin (UCD), Belfield, Dublin 4, Ireland.,School of Biology and Environmental Science, University College Dublin (UCD), Belfield, Dublin 4, Ireland
| | - Rosa Peracaula
- Biochemistry and Molecular Biology Unit, Department of Biology, University of Girona, Girona, Spain.,Girona Biomedical Research Institute (IDIBGI), Girona, Spain
| | - Pauline M Rudd
- GlycoScience Group, the National Institute for Bioprocessing, Research and Training (NIBRT), Fosters Avenue, Mount Merrion, Blackrock, Co Dublin, Ireland.,UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin (UCD), Belfield, Dublin 4, Ireland
| | - Amanda McCann
- College of Health and Agricultural Science (CHAS), UCD School of Medicine, University College Dublin (UCD), Belfield, Dublin 4, Ireland.,UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin (UCD), Belfield, Dublin 4, Ireland
| | - Radka Saldova
- GlycoScience Group, the National Institute for Bioprocessing, Research and Training (NIBRT), Fosters Avenue, Mount Merrion, Blackrock, Co Dublin, Ireland. .,College of Health and Agricultural Science (CHAS), UCD School of Medicine, University College Dublin (UCD), Belfield, Dublin 4, Ireland.
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12
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GATA6 promotes epithelial-mesenchymal transition and metastasis through MUC1/β-catenin pathway in cholangiocarcinoma. Cell Death Dis 2020; 11:860. [PMID: 33060563 PMCID: PMC7567063 DOI: 10.1038/s41419-020-03070-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 09/24/2020] [Accepted: 09/28/2020] [Indexed: 01/06/2023]
Abstract
GATA6 acts as an oncogene or tumour suppressor in different cancers. Previously, we found that aberrant expression of GATA6 promoted metastasis in cholangiocarcinoma (CCA). However, the mechanism by which GATA6 promotes metastasis in CCA is unclear. In the present study, we aimed to investigate the role of GATA6 in CCA cell epithelial–mesenchymal transition (EMT). Our results showed that GATA6 expression was positively associated with N-cadherin and vimentin expression but negatively associated with E-cadherin expression in 91 CCA samples. GATA6 promoted EMT and metastasis in CCA cells in vitro and in vivo based on knockdown and overexpression analyses. ChIP-sequencing data revealed that MUC1 is a novel downstream target of GATA6. GATA6 upregulated MUC1 expression through binding to both the 1584 and 1456 GATA-motifs in the promoter region and enhancing its transcription by luciferase reporter assays and point-mutant assays. MUC1 expression was positively associated with N-cadherin and vimentin expression but negatively associated with E-cadherin expression in 91 CCA samples. In addition, MUC1 promoted EMT in CCA cells based on knockdown and overexpression analyses. Moreover, MUC1 knockdown significantly abrogated the GATA6-induced EMT in CCA cells, indicating that MUC1 promoted EMT through upregulating MUC1 in CCA cells. β-Catenin is a putative transcriptional coactivator that regulates EMT in cancers. Our data showed that MUC1 expression was positively associated with nuclear β-catenin expression in 91 CCA samples. MUC1 upregulated nuclear β-catenin expression in CCA cells. Moreover, MUC1 bound to β-catenin in CCA cells based on protein immunoprecipitation analyses. MUC1 knockdown significantly decreased the binding of MUC1 to β-catenin, and thereby decreased nuclear β-catenin protein levels in CCA cells, indicating that MUC1 bound to β-catenin and increased its nuclear expression in CCA cells. Together, our results show that GATA6 promotes EMT through MUC1/β-catenin pathway in CCA, indicating potential implications for anti-metastatic therapy.
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13
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He B, Zhang Y, Zhou Z, Wang B, Liang Y, Lang J, Lin H, Bing P, Yu L, Sun D, Luo H, Yang J, Tian G. A Neural Network Framework for Predicting the Tissue-of-Origin of 15 Common Cancer Types Based on RNA-Seq Data. Front Bioeng Biotechnol 2020; 8:737. [PMID: 32850691 PMCID: PMC7419649 DOI: 10.3389/fbioe.2020.00737] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 06/10/2020] [Indexed: 12/19/2022] Open
Abstract
Sequencing-based identification of tumor tissue-of-origin (TOO) is critical for patients with cancer of unknown primary lesions. Even if the TOO of a tumor can be diagnosed by clinicopathological observation, reevaluations by computational methods can help avoid misdiagnosis. In this study, we developed a neural network (NN) framework using the expression of a 150-gene panel to infer the tumor TOO for 15 common solid tumor cancer types, including lung, breast, liver, colorectal, gastroesophageal, ovarian, cervical, endometrial, pancreatic, bladder, head and neck, thyroid, prostate, kidney, and brain cancers. To begin with, we downloaded the RNA-Seq data of 7,460 primary tumor samples across the above mentioned 15 cancer types, with each type of cancer having between 142 and 1,052 samples, from the cancer genome atlas. Then, we performed feature selection by the Pearson correlation method and performed a 150-gene panel analysis; the genes were significantly enriched in the GO:2001242 Regulation of intrinsic apoptotic signaling pathway and the GO:0009755 Hormone-mediated signaling pathway and other similar functions. Next, we developed a novel NN model using the 150 genes to predict tumor TOO for the 15 cancer types. The average prediction sensitivity and precision of the framework are 93.36 and 94.07%, respectively, for the 7,460 tumor samples based on the 10-fold cross-validation; however, the prediction sensitivity and precision for a few specific cancers, like prostate cancer, reached 100%. We also tested the trained model on a 20-sample independent dataset with metastatic tumor, and achieved an 80% accuracy. In summary, we present here a highly accurate method to infer tumor TOO, which has potential clinical implementation.
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Affiliation(s)
- Binsheng He
- Academician Workstation, Changsha Medical University, Changsha, China
| | | | - Zhen Zhou
- Department of Radiology, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Bo Wang
- Geneis (Beijing) Co., Ltd., Beijing, China
| | | | | | - Huixin Lin
- Geneis (Beijing) Co., Ltd., Beijing, China
| | - Pingping Bing
- Academician Workstation, Changsha Medical University, Changsha, China
| | - Lan Yu
- Inner Mongolia People's Hospital, Huhhot, China
| | - Dejun Sun
- Inner Mongolia People's Hospital, Huhhot, China
| | - Huaiqing Luo
- Academician Workstation, Changsha Medical University, Changsha, China
| | - Jialiang Yang
- Academician Workstation, Changsha Medical University, Changsha, China.,Geneis (Beijing) Co., Ltd., Beijing, China
| | - Geng Tian
- Geneis (Beijing) Co., Ltd., Beijing, China
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14
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Greville G, Llop E, Huang C, Creagh-Flynn J, Pfister S, O'Flaherty R, Madden SF, Peracaula R, Rudd PM, McCann A, Saldova R. Hypoxia Alters Epigenetic and N-Glycosylation Profiles of Ovarian and Breast Cancer Cell Lines in-vitro. Front Oncol 2020; 10:1218. [PMID: 32850359 PMCID: PMC7405916 DOI: 10.3389/fonc.2020.01218] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 06/15/2020] [Indexed: 12/14/2022] Open
Abstract
Background: Glycosylation is one of the most fundamental post-translational modifications. Importantly, glycosylation is altered in many cancers. These alterations have been proven to impact on tumor progression and to promote tumor cell survival. From the literature, it is known that there is a clear link between chemoresistance and hypoxia, hypoxia and epigenetics and more recently glycosylation and epigenetics. Methods and Results: Our objective was to investigate these differential parameters, in an in vitro model of ovarian and breast cancer. Ovarian (A2780, A2780cis, PEO1, PEO4) and triple negative breast cancer (TNBC) (MDA-MB-231 and MDA-MB-436) cells were exposed to differential hypoxic conditions (0.5-2% O2) and compared to normoxia (21% O2). Results demonstrated that in hypoxic conditions some significant changes in glycosylation on the secreted N-glycans from the ovarian and breast cancer cell lines were observed. These included, alterations in oligomannosylated, bisected glycans, glycans with polylactosamine extensions, in branching, galactosylation and sialylation in all cell lines except for PEO1. In general, hypoxia exposed ovarian and TNBC cells also displayed increased epithelial to mesenchymal transition (EMT) and migration, with a greater effect seen in the 0.5% hypoxia exposed samples compared to 1 and 2% hypoxia (p ≤ 0.05). SiRNA transient knock down of GATA2/3 transcription factors resulted in a decrease in the expression of glycosyltransferases ST3GAL4 and MGAT5, which are responsible for sialylation and branching, respectively. Conclusions: These glycan changes are known to be integral to cancer cell survival and metastases, suggesting a possible mechanism of action, linking GATA2 and 3, and invasiveness of both ovarian and TNBC cells in vitro.
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Affiliation(s)
- Gordon Greville
- GlycoScience Group, The National Institute for Bioprocessing Research and Training (NIBRT), Dublin, Ireland.,UCD School of Medicine, College of Health and Agricultural Science (CHAS), University College Dublin (UCD), Dublin, Ireland
| | - Esther Llop
- Biochemistry and Molecular Biology Unit, Department of Biology, University of Girona, Girona, Spain.,Biochemistry of Cancer Group, Girona Biomedical Research Institute (IDIBGI), Girona, Spain
| | - Chengnan Huang
- GlycoScience Group, The National Institute for Bioprocessing Research and Training (NIBRT), Dublin, Ireland
| | - Jack Creagh-Flynn
- UCD School of Medicine, College of Health and Agricultural Science (CHAS), University College Dublin (UCD), Dublin, Ireland
| | - Stephanie Pfister
- UCD School of Medicine, College of Health and Agricultural Science (CHAS), University College Dublin (UCD), Dublin, Ireland
| | - Roisin O'Flaherty
- GlycoScience Group, The National Institute for Bioprocessing Research and Training (NIBRT), Dublin, Ireland
| | - Stephen F Madden
- Data Science Centre, Division of Population Health Sciences, Royal College of Surgeons in Ireland (RCSI), Dublin, Ireland
| | - Rosa Peracaula
- Biochemistry and Molecular Biology Unit, Department of Biology, University of Girona, Girona, Spain.,Biochemistry of Cancer Group, Girona Biomedical Research Institute (IDIBGI), Girona, Spain
| | - Pauline M Rudd
- GlycoScience Group, The National Institute for Bioprocessing Research and Training (NIBRT), Dublin, Ireland.,Analytics Group, Bioprocessing Technology Institute, Astar, Singapore
| | - Amanda McCann
- UCD School of Medicine, College of Health and Agricultural Science (CHAS), University College Dublin (UCD), Dublin, Ireland.,UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin (UCD), Dublin, Ireland
| | - Radka Saldova
- GlycoScience Group, The National Institute for Bioprocessing Research and Training (NIBRT), Dublin, Ireland.,UCD School of Medicine, College of Health and Agricultural Science (CHAS), University College Dublin (UCD), Dublin, Ireland
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15
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CircPIP5K1A facilitates gastric cancer progression via miR-376c-3p/ZNF146 axis. Cancer Cell Int 2020; 20:81. [PMID: 32190005 PMCID: PMC7071687 DOI: 10.1186/s12935-020-1122-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Accepted: 01/23/2020] [Indexed: 02/07/2023] Open
Abstract
Background Recently, many emerging circular RNAs (circRNAs) have been studied in human malignancies, including gastric cancer (GC). Researches concerning cancers have revealed that aberrant expression of circRNAs play a big part in tumorigenesis and development of diverse malignant tumors. Although hsa_circ_0014130 (circPIP5K1A) has been confirmed to be closely related to non-small cell lung cancer (NSCLC) progression, the knowledge of its function on GC progression remains unclear. Therefore, it is of great interest to uncover the underlying role of circPIP5K1A in GC. Methods The expression and characteristic of circPIP5K1A were separately analyzed by RT-qPCR, nucleic acid electrophoresis, RNase R and Actinomycin D treatment. CCK-8, colony formation, EdU, transwell, TUNEL, flow cytometry, luciferase reporter, RIP and RNA pull-down assays were employed to testify the regulatory role of circPIP5K1A in GC. Results In current study, circPIP5K1A, featured with closed-loop structure, was proved to be highly expressed in tissues and cells of GC. Loss-of-function assays depicted that silencing circPIP5K1A suppressed GC development. Follow-up mechanism tests unveiled that circPIP5K1A bound with miR-376c-3p and inhibition of miR-376c-3p reversed circPIP5K1A downregulation-mediated effect on GC progression. Additionally, ZNF146 was verified to be the downstream molecule of circPIP5K1A/miR-376c-3p axis in modulating GC progression. Conclusions circPIP5K1A stimulates GC progression by sponging miR-376c-3p to upregulate ZNF146 expression.
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16
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Sun Z, Yan B. Multiple roles and regulatory mechanisms of the transcription factor GATA6 in human cancers. Clin Genet 2019; 97:64-72. [PMID: 31437305 DOI: 10.1111/cge.13630] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 08/13/2019] [Accepted: 08/20/2019] [Indexed: 12/24/2022]
Abstract
Cancer is a common type of non-communicable disease, and its morbidity and mortality are rapidly increasing. It is expected to become the largest obstacle to the promotion of global human health in the future. Some transcription factors that play important regulatory roles in embryogenesis and subsequent tissue maintenance can be selectively amplified during tumorigenesis. Due to its high expression in the embryonic endoderm and mesoderm, GATA6 plays a crucial role in the normal development of early human heart, lung, digestive system, adrenal glands, breasts, ovaries, retina, skin, and nervous system. Up to now, overexpression of the GATA6 gene has been shown to play an important role in several cancers, including lung cancer, digestive system tumors, breast cancer, and ovarian cancer. However, the human body is a complex organism, which causes the transcription factor GATA6 to have multiple roles in cancer. In this review, we summarize the multiple roles of transcription factor GATA6 in various cancers and its regulatory mechanisms. The aim is to better understand the relationship between GATA6 gene expression and cancer development and to provide new insights for exploring potential therapeutic targets.
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Affiliation(s)
- Zhaoqing Sun
- Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Bo Yan
- Shandong Provincial Key Laboratory of Cardiac Disease Diagnosis and Treatment, Affiliated Hospital of Jining Medical University, Jining Medical University, Jining, Shandong, China.,The Center for Molecular Genetics of Cardiovascular Diseases, Affiliated Hospital of Jining Medical University, Jining Medical University, Jining, Shandong, China.,Shandong Provincial Sino-US Cooperation Research Center for Translational Medicine, Affiliated Hospital of Jining Medical University, Jining Medical University, Jining, Shandong, China
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17
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Comprehensive analysis of gene expression and DNA methylation for human nasopharyngeal carcinoma. Eur Arch Otorhinolaryngol 2019; 276:2565-2576. [PMID: 31240455 DOI: 10.1007/s00405-019-05525-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 06/18/2019] [Indexed: 12/16/2022]
Abstract
PURPOSE Nasopharyngeal carcinoma (NPC) is one of the most malignant head and neck carcinomas with unique epidemiological features. In this study, we aimed to identify the novel NPC-related genes and biological pathways, shedding light on the potential molecular mechanisms of NPC. METHODS Based on Gene Expression Omnibus (GEO) database, an integrated analysis of microarrays studies was performed to identify differentially expressed genes (DEGs) and differentially methylated genes (DMGs) in NPC compared to normal control. The genes which were both differentially expressed and differentially methylated were identified. Functional annotation and protein-protein interaction (PPI) network construction were used to uncover biological functions of DEGs. RESULTS Two DNA methylation and five gene expression datasets were incorporated. A total of 1074 genes were up-regulated and 939 genes were down-regulated in NPC were identified. A total of 719 differential methylation CpG sites (DMCs) including 1 hypermethylated sites and 718 hypomethylated sites were identified. Among which, 11 genes were both DEGs and DMGs in NPC. Pathways in cancer, p53 signaling pathway and Epstein-Barr virus infection were three pathways significantly enriched pathways in DEmRNAs of NPC. The PPI network of top 50 DEGs were consisted of 191 nodes and 191 edges. CONCLUSIONS Our study was helpful to elucidate the underlying mechanism of NPC and provide clues for therapeutic methods.
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18
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Tan HW, Leung CON, Chan KKS, Ho DWH, Leung MS, Wong CM, Ng IOL, Lo RCL. Deregulated GATA6 modulates stem cell-like properties and metabolic phenotype in hepatocellular carcinoma. Int J Cancer 2019; 145:1860-1873. [PMID: 30834518 DOI: 10.1002/ijc.32248] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 02/10/2019] [Accepted: 02/27/2019] [Indexed: 12/11/2022]
Abstract
Accumulating evidence illustrates the significance of cell plasticity in the molecular biology of liver cancer. Reprogramming of mature parenchymal cells to a less differentiated state by key molecular targets contributes to the pathogenesis of hepatocellular carcinoma (HCC). Hereby, we investigated the role of GATA6, a transcription factor implicated in hepatocyte lineage specification, in HCC. Our results demonstrated a lower expression of GATA6 in HCC tissues compared to the corresponding nontumoral liver tissues. Moreover, GATA6 underexpression, as observed in about 50% cases in our clinical cohort, was associated with a poorer degree of tumor cell differentiation and worse disease-free survival outcome. In vitro, silencing of GATA6 in HCC cells augmented cell migration and invasion abilities of HCC cells by activating epithelial-mesenchymal transition. Self-renewal was also enhanced in vitro. Consistently, in vivo tumorigenicity and self-renewal was promoted upon GATA6 knockdown. Notably, suppression of GATA6 converts HCC cells to a metabolic phenotype recapitulating stem-cell state. Expression of glycolytic markers was elevated in GATA6-knockdown clones accompanied by increased glucose uptake; while overexpression of GATA6 resulted in opposite effects. Further to this, we identified that GATA6 bound to the promoter region of PKM gene and regulated PKM2 transcription. Taken together, downregulation of GATA6 directs HCC cells to glycolytic metabolism and fosters tumorigenicity, self-renewal and metastasis. GATA6 is a transcriptional regulator and a genetic switch that converts the phenotypic reprogramming of HCC cells. It is a potential prognostic biomarker and therapeutic target for liver cancer.
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Affiliation(s)
- Han-Wei Tan
- Department of Pathology, The University of Hong Kong, Pokfulam, Hong Kong
| | - Carmen Oi-Ning Leung
- Department of Pathology, The University of Hong Kong, Pokfulam, Hong Kong.,Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Hong Kong
| | | | - Daniel Wai-Hung Ho
- Department of Pathology, The University of Hong Kong, Pokfulam, Hong Kong
| | - Ming-Sum Leung
- Department of Pathology, The University of Hong Kong, Pokfulam, Hong Kong
| | - Chun-Ming Wong
- Department of Pathology, The University of Hong Kong, Pokfulam, Hong Kong.,State Key Laboratory of Liver Research, The University of Hong Kong, Pokfulam, Hong Kong
| | - Irene Oi-Lin Ng
- Department of Pathology, The University of Hong Kong, Pokfulam, Hong Kong.,State Key Laboratory of Liver Research, The University of Hong Kong, Pokfulam, Hong Kong
| | - Regina Cheuk-Lam Lo
- Department of Pathology, The University of Hong Kong, Pokfulam, Hong Kong.,State Key Laboratory of Liver Research, The University of Hong Kong, Pokfulam, Hong Kong
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19
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Hsa_circ_0000673 is down-regulated in gastric cancer and inhibits the proliferation and invasion of tumor cells by targetting miR-532-5p. Biosci Rep 2018; 38:BSR20180538. [PMID: 30061181 PMCID: PMC6146288 DOI: 10.1042/bsr20180538] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2018] [Revised: 07/13/2018] [Accepted: 07/30/2018] [Indexed: 12/12/2022] Open
Abstract
Circular RNAs (circRNAs), a new class of endogenous non-coding RNAs, have recently been known to play critical roles in various cellular biological processes, including tumorigenesis, in which they act as an miRNA sponge that regulates gene expression. Thus, revealing the functions of circRNAs in carcinogenesis and cancer development has been of great interest. However, their expression and functions in gastric cancer (GC) development are still largely unknown. Therefore, the present study aimed to identify novel deregulated circRNAs in GC and reveal their biological functions and molecular mechanisms in GC. Quantitative real-time PCR (qRT-PCR) was performed to measure the expression levels of circRNAs in GC tissues, cell lines, and plasma. The MTT assay, colony formation assay, transwell assay, and tumor xenografts in vivo were used to evaluate the effects of circRNAs on the proliferation and invasion of GC. The abovementioned methods coupled with Western blotting were used to investigate the molecular mechanisms. The current study showed that hsa_circ_0000673 was significantly down-regulated in GC. Overexpression of hsa_circ_0000673 inhibited the proliferation and invasion of GC cells. In contrast, hsa_circ_0000673 down-regulation promoted the proliferation and invasion of GC cells. Further studies revealed that hsa_circ_0000673 targetted miR-532-5p and up-regulated the expression of RUNX3. The present study showed that hsa_circ_0000673 was decreased in GC and it exerted tumor-suppressing effects by targetting miR-532-5p and up-regulating RUNX3 expression level. Hsa_circ_0000673 may be a promising diagnosis biomarker and therapeutic target in GC.
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20
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Vaziri F, Tarashi S, Fateh A, Siadat SD. New insights of Helicobacter pylori host-pathogen interactions: The triangle of virulence factors, epigenetic modifications and non-coding RNAs. World J Clin Cases 2018; 6:64-73. [PMID: 29774218 PMCID: PMC5955730 DOI: 10.12998/wjcc.v6.i5.64] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/14/2018] [Revised: 02/09/2018] [Accepted: 03/07/2018] [Indexed: 02/05/2023] Open
Abstract
Helicobacter pylori (H. pylori) is a model organism for understanding host-pathogen interactions and infection-mediated carcinogenesis. Gastric cancer and H. pylori colonization indicates the strong correlation. The progression and exacerbation of H. pylori infection are influenced by some factors of pathogen and host. Several virulence factors involved in the proper adherence and attenuation of immune defense to contribute the risk of emerging gastric cancer, therefore analysis of them is very important. H. pylori also modulates inflammatory and autophagy process to intensify its pathogenicity. From the host regard, different genetic factors particularly affect the development of gastric cancer. Indeed, epigenetic modifications, MicroRNA and long non-coding RNA received more attention. Generally, various factors related to pathogen and host that modulate gastric cancer development in response to H. pylori need more attention due to develop an efficacious therapeutic intervention. Therefore, this paper will present a brief overview of host-pathogen interaction especially emphases on bacterial virulence factors, interruption of host cellular signaling, the role of epigenetic modifications and non-coding RNAs.
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Affiliation(s)
- Farzam Vaziri
- Microbiology Research Center, Pasteur Institute of Iran, Tehran 1316943551, Iran
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran 1316943551, Iran
| | - Samira Tarashi
- Microbiology Research Center, Pasteur Institute of Iran, Tehran 1316943551, Iran
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran 1316943551, Iran
| | - Abolfazl Fateh
- Microbiology Research Center, Pasteur Institute of Iran, Tehran 1316943551, Iran
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran 1316943551, Iran
| | - Seyed Davar Siadat
- Microbiology Research Center, Pasteur Institute of Iran, Tehran 1316943551, Iran
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran 1316943551, Iran
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