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Bisson JA, Gordillo M, Kumar R, de Silva N, Yang E, Banks KM, Shi ZD, Lee K, Yang D, Chung WK, Huangfu D, Evans T. GATA6 regulates WNT and BMP programs to pattern precardiac mesoderm during the earliest stages of human cardiogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.09.602666. [PMID: 39026742 PMCID: PMC11257636 DOI: 10.1101/2024.07.09.602666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Haploinsufficiency for GATA6 is associated with congenital heart disease (CHD) with variable comorbidity of pancreatic or diaphragm defects, although the etiology of disease is not well understood. Here, we used cardiac directed differentiation from human embryonic stem cells (hESCs) as a platform to study GATA6 function during early cardiogenesis. GATA6 loss-of-function hESCs had a profound impairment in cardiac progenitor cell (CPC) specification and cardiomyocyte (CM) generation due to early defects during the mesendoderm and lateral mesoderm patterning stages. Profiling by RNA-seq and CUT&RUN identified genes of the WNT and BMP programs regulated by GATA6 during early mesoderm patterning. Furthermore, interactome analysis detected GATA6 binding with developmental transcription factors and chromatin remodelers suggesting cooperative regulation of cardiac lineage gene accessibility. We show that modulating WNT and BMP inputs during the first 48 hours of cardiac differentiation is sufficient to partially rescue CPC and CM defects in GATA6 heterozygous and homozygous mutant hESCs. This study provides evidence of the regulatory functions for GATA6 directing human precardiac mesoderm patterning during the earliest stages of cardiogenesis to further our understanding of haploinsufficiency causing CHD and the co-occurrence of cardiac and other organ defects caused by human GATA6 mutations.
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Affiliation(s)
- Joseph A. Bisson
- Department of Surgery, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Miriam Gordillo
- Department of Surgery, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Ritu Kumar
- Department of Surgery, Weill Cornell Medicine, New York, NY, 10065, USA
- current address: Gladstone Institutes, San Francisco, CA, 94158, USA
| | - Neranjan de Silva
- Department of Surgery, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Ellen Yang
- Department of Surgery, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Kelly M. Banks
- Department of Surgery, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Zhong-Dong Shi
- Developmental Biology Program, Sloan Kettering Institute, New York, NY, 10065, USA
| | - Kihyun Lee
- Developmental Biology Program, Sloan Kettering Institute, New York, NY, 10065, USA
- current address: College of Pharmacy, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Dapeng Yang
- Developmental Biology Program, Sloan Kettering Institute, New York, NY, 10065, USA
| | - Wendy K. Chung
- Childrens Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Danwei Huangfu
- Developmental Biology Program, Sloan Kettering Institute, New York, NY, 10065, USA
| | - Todd Evans
- Department of Surgery, Weill Cornell Medicine, New York, NY, 10065, USA
- Hartman Institute for Therapeutic Organ Regeneration, Weill Cornell Medicine, New York, NY 10065, USA
- Center for Genomic Health, Weill Cornell Medicine, New York, NY 10065, USA
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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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Zhang Q, Yang M, Zhang P, Wu B, Wei X, Li S. Deciphering gastric inflammation-induced tumorigenesis through multi-omics data and AI methods. Cancer Biol Med 2023; 21:j.issn.2095-3941.2023.0129. [PMID: 37589244 PMCID: PMC11033716 DOI: 10.20892/j.issn.2095-3941.2023.0129] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 06/26/2023] [Indexed: 08/18/2023] Open
Abstract
Gastric cancer (GC), the fifth most common cancer globally, remains the leading cause of cancer deaths worldwide. Inflammation-induced tumorigenesis is the predominant process in GC development; therefore, systematic research in this area should improve understanding of the biological mechanisms that initiate GC development and promote cancer hallmarks. Here, we summarize biological knowledge regarding gastric inflammation-induced tumorigenesis, and characterize the multi-omics data and systems biology methods for investigating GC development. Of note, we highlight pioneering studies in multi-omics data and state-of-the-art network-based algorithms used for dissecting the features of gastric inflammation-induced tumorigenesis, and we propose translational applications in early GC warning biomarkers and precise treatment strategies. This review offers integrative insights for GC research, with the goal of paving the way to novel paradigms for GC precision oncology and prevention.
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Affiliation(s)
- Qian Zhang
- Institute for TCM-X, MOE Key Laboratory of Bioinformatics, Bioinformatics Division, BNRIST, Department of Automation, Tsinghua University, Beijing 100084, China
| | - Mingran Yang
- Institute for TCM-X, MOE Key Laboratory of Bioinformatics, Bioinformatics Division, BNRIST, Department of Automation, Tsinghua University, Beijing 100084, China
| | - Peng Zhang
- Institute for TCM-X, MOE Key Laboratory of Bioinformatics, Bioinformatics Division, BNRIST, Department of Automation, Tsinghua University, Beijing 100084, China
| | - Bowen Wu
- Institute for TCM-X, MOE Key Laboratory of Bioinformatics, Bioinformatics Division, BNRIST, Department of Automation, Tsinghua University, Beijing 100084, China
| | - Xiaosen Wei
- Institute for TCM-X, MOE Key Laboratory of Bioinformatics, Bioinformatics Division, BNRIST, Department of Automation, Tsinghua University, Beijing 100084, China
| | - Shao Li
- Institute for TCM-X, MOE Key Laboratory of Bioinformatics, Bioinformatics Division, BNRIST, Department of Automation, Tsinghua University, Beijing 100084, China
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Kar S, Niharika, Roy A, Patra SK. Overexpression of SOX2 Gene by Histone Modifications: SOX2 Enhances Human Prostate and Breast Cancer Progression by Prevention of Apoptosis and Enhancing Cell Proliferation. Oncology 2023; 101:591-608. [PMID: 37549026 DOI: 10.1159/000531195] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 05/02/2023] [Indexed: 08/09/2023]
Abstract
INTRODUCTION SOX2 plays a crucial role in tumor development, cancer stem cell maintenance, and cancer progression. Mechanisms of SOX2 gene regulation in human breast and prostate cancers are not established yet. METHODS SOX2 expression in prostate and breast cancer tissues and cell lines was determined by qRT-PCR, Western blot, and immunochemistry, followed by the investigation of pro-tumorigenic properties like cell proliferation, migration, and apoptosis by gene knockdown and treatment with epigenetic modulators and ChIP. RESULTS Prostate and breast cancer tissues showed very high expression of SOX2. All cancer cell lines DU145 and PC3 (prostate) and MCF7 and MDA-MB-231 (breast) exhibited high expression of SOX2. Inhibition of SOX2 drastically decreased cell proliferation and migration. Epigenetic modulators enhanced SOX2 gene expression in both cancer types. DNA methylation pattern in SOX2 promoter could not be appreciably counted for SOX2 overexpression. Activation of SOX2 gene promoter was due to very high deposition of H3K4me3 and H3K9acS10p and drastic decrease of H3K9me3 and H3K27me3. CONCLUSION Histone modification is crucial for the overexpression of SOX2 during tumor development and cancer progression. These findings show the avenue of co-targeting SOX2 and its active epigenetic modifier enzymes to effectively treat aggressive prostate and breast cancers.
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Affiliation(s)
- Swayamsiddha Kar
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, India
| | - Niharika
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, India
| | - Ankan Roy
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, India
| | - Samir Kumar Patra
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, India
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Abe H, Kamimura K, Okuda S, Watanabe Y, Inoue J, Aoyagi Y, Wakai T, Kominami R, Terai S. BCL11B expression in hepatocellular carcinoma relates to chemosensitivity and clinical prognosis. Cancer Med 2023; 12:15650-15663. [PMID: 37293953 PMCID: PMC10417273 DOI: 10.1002/cam4.6167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 05/14/2023] [Accepted: 05/17/2023] [Indexed: 06/10/2023] Open
Abstract
INTRODUCTION B-cell lymphoma/leukemia 11B (BCL11B) is a subunit of SWI/SNF chromatin remodeling complexes and functions in cell cycle regulation and apoptosis upon DNA replication stress and damages via transcription. Many malignancies were reported to exhibit changes in BCL11B gene expression; however, no study has focused on the relationship between BCL11B and hepatocellular carcinoma, which potentially exhibits DNA replication stress and damages upon its oncogenesis. Thus, in this study, we examined the molecular characterization of BCL11B expression in hepatocellular carcinoma. METHODS AND RESULTS The cumulative progression-free survival and overall survival were significantly longer in the clinical cases of BCL11B-negative hepatocellular carcinoma than BCL11B-positve cases. Microarray and real-time PCR analyses in hepatocellular carcinoma cell lines indicated a correlation between BCL11B and GATA6, a gene reported to be correlated with oncogenic activities and resistance to anthracycline, which is often used for hepatocellular carcinoma chemotherapy. Consequently, BCL11B-overexpressing cell lines exhibited resistance to anthracycline in cell growth assays and the resistance has been evidenced by the increased expression of BCL-xL in cell lines. The results were supported by the analyses of human HCC samples showing the correlation between BCL11B and GATA6 expressions. DISCUSSIONS AND CONCLUSION Our results indicated that overexpression of BCL11B amplifies GATA6 expression in hepatocellular carcinoma in vitro and in vivo that leads to anti-apoptotic signal activation, and induces resistance to chemotherapy, which influenced the postoperative prognosis.
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Affiliation(s)
- Hiroyuki Abe
- Division of Gastroenterology and Hepatology, Graduate School of Medical and Dental SciencesNiigata UniversityNiigataNiigataJapan
| | - Kenya Kamimura
- Division of Gastroenterology and Hepatology, Graduate School of Medical and Dental SciencesNiigata UniversityNiigataNiigataJapan
- Department of General MedicineNiigata University School of MedicineNiigataNiigataJapan
| | - Shujiro Okuda
- Division of Bioinformatics, Graduate School of Medical and Dental SciencesNiigata UniversityNiigataNiigataJapan
| | - Yu Watanabe
- Division of Bioinformatics, Graduate School of Medical and Dental SciencesNiigata UniversityNiigataNiigataJapan
| | - Jun Inoue
- Department of Agricultural Chemistry, Faculty of Applied BiosciencesTokyo University of AgricultureTokyoJapan
| | - Yutaka Aoyagi
- Department of Gastroenterology and HepatologyNiigata Medical CenterNiigataNiigataJapan
| | - Toshifumi Wakai
- Division of Digestive and General Surgery, Graduate School of Medical and Dental SciencesNiigata UniversityNiigataNiigataJapan
| | - Ryo Kominami
- Department of Molecular Genetics, Graduate School of Medical and Dental SciencesNiigata UniversityNiigataNiigataJapan
| | - Shuji Terai
- Division of Gastroenterology and Hepatology, Graduate School of Medical and Dental SciencesNiigata UniversityNiigataNiigataJapan
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de Andrés MP, Jackson RJ, Felipe I, Zagorac S, Pilarsky C, Schlitter AM, Martinez de Villareal J, Jang GH, Costello E, Gallinger S, Ghaneh P, Greenhalf W, Knösel T, Palmer DH, Ruemmele P, Weichert W, Buechler M, Hackert T, Neoptolemos JP, Notta F, Malats N, Martinelli P, Real FX. GATA4 and GATA6 loss-of-expression is associated with extinction of the classical programme and poor outcome in pancreatic ductal adenocarcinoma. Gut 2023; 72:535-548. [PMID: 36109153 DOI: 10.1136/gutjnl-2021-325803] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 08/05/2022] [Indexed: 12/08/2022]
Abstract
OBJECTIVE GATA6 is a key regulator of the classical phenotype in pancreatic ductal adenocarcinoma (PDAC). Low GATA6 expression associates with poor patient outcome. GATA4 is the second most expressed GATA factor in the pancreas. We assessed whether, and how, GATA4 contributes to PDAC phenotype and analysed the association of expression with outcome and response to chemotherapy. DESIGN We analysed PDAC transcriptomic data, stratifying cases according to GATA4 and GATA6 expression and identified differentially expressed genes and pathways. The genome-wide distribution of GATA4 was assessed, as well as the effects of GATA4 knockdown. A multicentre tissue microarray study to assess GATA4 and GATA6 expression in samples (n=745) from patients with resectable was performed. GATA4 and GATA6 levels were dichotomised into high/low categorical variables; association with outcome was assessed using univariable and multivariable Cox regression models. RESULTS GATA4 messenger RNA is enriched in classical, compared with basal-like tumours. We classified samples in 4 groups as high/low for GATA4 and GATA6. Reduced expression of GATA4 had a minor transcriptional impact but low expression of GATA4 enhanced the effects of GATA6 low expression. GATA4 and GATA6 display a partially overlapping genome-wide distribution, mainly at promoters. Reduced expression of both proteins in tumours was associated with the worst patient survival. GATA4 and GATA6 expression significantly decreased in metastases and negatively correlated with basal markers. CONCLUSIONS GATA4 and GATA6 cooperate to maintain the classical phenotype. Our findings provide compelling rationale to assess their expression as biomarkers of poor prognosis and therapeutic response.
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Affiliation(s)
- Mónica P de Andrés
- Epithelial Carcinogenesis Group, Spanish National Cancer Research Centre-CNIO, Madrid, Spain
| | - Richard J Jackson
- Institute of Translational Medicine, University of Liverpool, Liverpool, UK
| | - Irene Felipe
- Epithelial Carcinogenesis Group, Spanish National Cancer Research Centre-CNIO, Madrid, Spain
- CIBERONC, Madrid, Spain
| | - Sladjana Zagorac
- Epithelial Carcinogenesis Group, Spanish National Cancer Research Centre-CNIO, Madrid, Spain
| | | | - Anna Melissa Schlitter
- Institute of Pathology, School of Medicine, Technische Universitat Munchen, Munchen, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jaime Martinez de Villareal
- Epithelial Carcinogenesis Group, Spanish National Cancer Research Centre-CNIO, Madrid, Spain
- CIBERONC, Madrid, Spain
| | - Gun Ho Jang
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Eithne Costello
- Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool, UK
| | - Steve Gallinger
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Department of Surgery, University of Toronto, Toronto, Ontario, Canada
- Wallace McCain Centre for Pancreatic Cancer, Princess Margaret Cancer Centre, University, Toronto, Ontario, Canada
- Health Network, Toronto, Ontario, Canada
- Hepatobiliary/Pancreatic Surgical Oncology Program, University Health Network, Toronto, Ontario, Canada
| | - Paula Ghaneh
- Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool, UK
| | - William Greenhalf
- Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool, UK
| | - Thomas Knösel
- Institute of Pathology, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Daniel H Palmer
- Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool, UK
| | - Petra Ruemmele
- Pathologisches Institute, Erlangen University Hospital, Erlangen, Germany
| | - Wilko Weichert
- Institute of Pathology, School of Medicine, Technische Universitat Munchen, Munchen, Germany
| | - Markus Buechler
- Department of General, Visceral, and Transplantation Surgery, University of Heidelberg, Heidelberg, Germany
| | - Thilo Hackert
- Department of General, Visceral, and Transplantation Surgery, University of Heidelberg, Heidelberg, Germany
| | - John P Neoptolemos
- Department of General, Visceral, and Transplantation Surgery, University of Heidelberg, Heidelberg, Germany
| | - Faiyaz Notta
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Division of Research, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Núria Malats
- CIBERONC, Madrid, Spain
- Genetic and Molecular Epidemiology Group, Spanish National Cancer Research Centre-CNIO, Madrid, Spain
| | - Paola Martinelli
- Institute of Cancer Research, Clinic for Internal Medicine I, Medical University of Vienna, Vienna, Austria
| | - Francisco X Real
- Departament de Medicina i Ciències de la Vida, Universitt Pompeu Fabra, Barcelona, Spain
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GATA6 regulates expression of annexin A10 (ANXA10) associated with epithelial–mesenchymal transition of oral squamous cell carcinoma. Arch Oral Biol 2022; 144:105569. [DOI: 10.1016/j.archoralbio.2022.105569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 10/03/2022] [Accepted: 10/07/2022] [Indexed: 11/16/2022]
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Taherkhani A, Dehto SS, Jamshidi S, Shojaei S. Pathogenesis and prognosis of primary oral squamous cell carcinoma based on microRNAs target genes: a systems biology approach. Genomics Inform 2022; 20:e27. [PMID: 36239104 PMCID: PMC9576470 DOI: 10.5808/gi.22038] [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: 06/17/2022] [Accepted: 08/30/2022] [Indexed: 11/20/2022] Open
Abstract
Oral squamous cell carcinoma (OSCC) is the most prevalent head and neck malignancy, with frequent cervical lymph-node metastasis, leading to a poor prognosis in OSCC patients. The present study aimed to identify potential markers, including microRNAs (miRNAs) and genes, significantly involved in the etiology of early-stage OSCC. Additionally, the main OSCC's dysregulated Gene Ontology annotations and significant signaling pathways were identified. The dataset GSE45238 underwent multivariate statistical analysis in order to distinguish primary OSCC tissues from healthy oral epithelium. Differentially expressed miRNAs (DEMs) with the criteria of p-value < 0.001 and |Log2 fold change| > 1.585 were identified in the two groups, and subsequently, validated targets of DEMs were identified. A protein interaction map was constructed, hub genes were identified, significant modules within the network were illustrated, and significant pathways and biological processes associated with the clusters were demonstrated. Using the GEPI2 database, the hub genes' predictive function was assessed. Compared to the healthy controls, main OSCC had a total of 23 DEMs. In patients with head and neck squamous cell carcinoma (HNSCC), upregulation of CALM1, CYCS, THBS1, MYC, GATA6, and SPRED3 was strongly associated with a poor prognosis. In HNSCC patients, overexpression of PIK3R3, GIGYF1, and BCL2L11 was substantially correlated with a good prognosis. Besides, “proteoglycans in cancer” was the most significant pathway enriched in the primary OSCC. The present study results revealed more possible mechanisms mediating primary OSCC and may be useful in the prognosis of the patients with early-stage OSCC.
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Affiliation(s)
- Amir Taherkhani
- Research Center for Molecular Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Shahab Shahmoradi Dehto
- Department of Oral and Maxillofacial Pathology, Faculty of Dentistry, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Shokoofeh Jamshidi
- Dental Research Center, Department of Oral and Maxillofacial Pathology, School of Dentistry, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Setareh Shojaei
- Department of Oral and Maxillofacial Pathology, Faculty of Dentistry, Hamadan University of Medical Sciences, Hamadan, Iran
- Corresponding author E-mail:
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Zhong Z, Harmston N, Wood KC, Madan B, Virshup DM. A p300/GATA6 axis determines differentiation and Wnt dependency in pancreatic cancer models. J Clin Invest 2022; 132:e156305. [PMID: 35536676 PMCID: PMC9197518 DOI: 10.1172/jci156305] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 05/04/2022] [Indexed: 11/17/2022] Open
Abstract
Wnt signaling regulates the balance between stemness and differentiation in multiple tissues and in cancer. RNF43-mutant pancreatic cancers are dependent on Wnt production, and pharmacologic blockade of the pathway, e.g., by PORCN inhibitors, leads to tumor differentiation. However, primary resistance to these inhibitors has been observed. To elucidate potential mechanisms, we performed in vivo CRISPR screens in PORCN inhibitor-sensitive RNF43-mutant pancreatic cancer xenografts. As expected, genes in the Wnt pathway whose loss conferred drug resistance were identified, including APC, AXIN1, and CTNNBIP1. Unexpectedly, the screen also identified the histone acetyltransferase EP300 (p300), but not its paralog, CREBBP (CBP). We found that EP300 is silenced due to genetic alterations in all the existing RNF43-mutant pancreatic cancer cell lines that are resistant to PORCN inhibitors. Mechanistically, loss of EP300 directly downregulated GATA6 expression, thereby silencing the GATA6-regulated differentiation program and leading to a phenotypic transition from the classical subtype to the dedifferentiated basal-like/squamous subtype of pancreatic cancer. EP300 mutation and loss of GATA6 function bypassed the antidifferentiation activity of Wnt signaling, rendering these cancer cells resistant to Wnt inhibition.
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Affiliation(s)
- Zheng Zhong
- Program in Cancer and Stem Cell Biology, Duke–NUS Medical School, Singapore
- Department of Physiology, National University of Singapore, Singapore
| | - Nathan Harmston
- Program in Cancer and Stem Cell Biology, Duke–NUS Medical School, Singapore
- Science Division, Yale–NUS College, Singapore
| | - Kris C. Wood
- Department of Pharmacology and Cancer Biology and
| | - Babita Madan
- Program in Cancer and Stem Cell Biology, Duke–NUS Medical School, Singapore
| | - David M. Virshup
- Program in Cancer and Stem Cell Biology, Duke–NUS Medical School, Singapore
- Department of Pediatrics, Duke University, Durham, North Carolina, USA
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Ma J, Zhan Z, Li N, Huang Y, Li Y, Liu L, Shen Q, Chu Q, Wang X, Wu B, Zhang H. Preliminary Interpretations of Epigenetic Profiling of Cord Blood in Preeclampsia. Genes (Basel) 2022; 13:888. [PMID: 35627272 PMCID: PMC9141867 DOI: 10.3390/genes13050888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 05/01/2022] [Accepted: 05/14/2022] [Indexed: 12/04/2022] Open
Abstract
Preeclampsia (PE) is characterized by new-onset hypertension after 20 weeks of pregnancy and results in high maternal and fetal mortality worldwide. It has been reported that PE is associated with abnormalities in the umbilical cord and cord blood. However, previous studies were focused primarily on the transcriptomics level, while the underlying gene regulatory landscapes are still unclear. Thus, we performed the Assay for Transposase-Accessible Chromatin with high-throughput sequencing (ATAC-seq) using the umbilical cord blood samples collected from a patient with superimposed PE and three healthy donors to uncover the chromatin accessibility changes attributed to PE. We have identified genes associated with immunomodulation and hypoxia response that have higher chromatin accessibility close to their transcription start sites. Motif analysis indicated that the GATA family transcription factor binding was enriched in PE and may play an essential regulatory role in the disease progression. Overall, our findings provide an overview of gene regulatory programs and the corresponding downstream pathways associated with PE that may influence the placenta function and fetal growth.
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Affiliation(s)
- Junrui Ma
- School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; (J.M.); (Q.C.); (X.W.)
- Faculty of Medical Laboratory Science, College of Health Science and Technology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Zhongqun Zhan
- Institute of Translational Medicine, University of Chinese Academy of Sciences Shenzhen Hospital, Shenzhen 518106, China; (Z.Z.); (Q.S.)
| | - Ning Li
- Cytotherapy Laboratory, The First Affiliated Hospital (Shenzhen People’s Hospital) Southern University of Science and Technology, Shenzhen 518020, China;
| | - Yanli Huang
- Department of Obstetrics, University of Chinese Academy of Sciences Shenzhen Hospital, Shenzhen 518106, China; (Y.H.); (Y.L.); (L.L.)
| | - Yan Li
- Department of Obstetrics, University of Chinese Academy of Sciences Shenzhen Hospital, Shenzhen 518106, China; (Y.H.); (Y.L.); (L.L.)
| | - Lu Liu
- Department of Obstetrics, University of Chinese Academy of Sciences Shenzhen Hospital, Shenzhen 518106, China; (Y.H.); (Y.L.); (L.L.)
| | - Qi Shen
- Institute of Translational Medicine, University of Chinese Academy of Sciences Shenzhen Hospital, Shenzhen 518106, China; (Z.Z.); (Q.S.)
| | - Qiao Chu
- School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; (J.M.); (Q.C.); (X.W.)
| | - Xiaonan Wang
- School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; (J.M.); (Q.C.); (X.W.)
| | - Benqing Wu
- Institute of Translational Medicine, University of Chinese Academy of Sciences Shenzhen Hospital, Shenzhen 518106, China; (Z.Z.); (Q.S.)
- Department of Neonatology, Shenzhen Guangming Maternity & Child Healthcare Hospital, Shenzhen 518107, China
| | - Hui Zhang
- Institute of Translational Medicine, University of Chinese Academy of Sciences Shenzhen Hospital, Shenzhen 518106, China; (Z.Z.); (Q.S.)
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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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Abstract
Gastric cancer (GC) is a leading contributor to global cancer incidence and mortality. Pioneering genomic studies, focusing largely on primary GCs, revealed driver alterations in genes such as ERBB2, FGFR2, TP53 and ARID1A as well as multiple molecular subtypes. However, clinical efforts targeting these alterations have produced variable results, hampered by complex co-alteration patterns in molecular profiles and intra-patient genomic heterogeneity. In this Review, we highlight foundational and translational advances in dissecting the genomic cartography of GC, including non-coding variants, epigenomic aberrations and transcriptomic alterations, and describe how these alterations interplay with environmental influences, germline factors and the tumour microenvironment. Mapping of these alterations over the GC life cycle in normal gastric tissues, metaplasia, primary carcinoma and distant metastasis will improve our understanding of biological mechanisms driving GC development and promoting cancer hallmarks. On the translational front, integrative genomic approaches are identifying diverse mechanisms of GC therapy resistance and emerging preclinical targets, enabled by technologies such as single-cell sequencing and liquid biopsies. Validating these insights will require specifically designed GC cohorts, converging multi-modal genomic data with longitudinal data on therapeutic challenges and patient outcomes. Genomic findings from these studies will facilitate 'next-generation' clinical initiatives in GC precision oncology and prevention.
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Affiliation(s)
- Khay Guan Yeoh
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Department of Gastroenterology and Hepatology, National University Health System, Singapore, Singapore
- Singapore Gastric Cancer Consortium, Singapore, Singapore
| | - Patrick Tan
- Singapore Gastric Cancer Consortium, Singapore, Singapore.
- Cancer and Stem Cell Biology, Duke-NUS Medical School Singapore, Singapore, Singapore.
- Genome Institute of Singapore, Singapore, Singapore.
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.
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13
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Zhai J, Luo G. GATA6‑induced FN1 activation promotes the proliferation, invasion and migration of oral squamous cell carcinoma cells. Mol Med Rep 2022; 25:102. [PMID: 35088888 PMCID: PMC8822886 DOI: 10.3892/mmr.2022.12618] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 08/12/2021] [Indexed: 12/28/2022] Open
Abstract
GATA binding protein 6 (GATA6) is a transcription factor involved in cell fate decision making and tissue morphogenesis and serves a significant role in the progression of a number of types of cancer. The present study aimed to investigate the role and mechanisms underlying the effects of GATA6 in oral squamous cell carcinoma (OSCC). The expression levels of GATA6 were determined in a number of OSCC cell lines and the expression of GATA6 was knocked down to evaluate its role in the proliferation, invasion and migration of OSCC cells. Subsequently, the association between GATA6 and fibronectin 1 (FN1) was investigated using bioinformatics and further verified using dual‑luciferase reporter and chromosomal immunoprecipitation assays. Following the overexpression of FN1 in OSCC cells with GATA6 silencing, functional assays were performed to assess the mechanisms underlying GATA6 in OSCC progression. The results of the present study indicated that OSCC cells exhibited markedly upregulated expression levels of GATA6, while knockdown of GATA6 inhibited the proliferation, colony formation, invasion and migration of OSCC cells. In addition, GATA6 regulated FN1 expression levels by binding to the FN1 promoter. The suppressive effects of GATA6 knockdown on the proliferation, colony formation, invasion and migration of OSCC cells were abolished following FN1 overexpression. In conclusion, the findings of the present study demonstrated that GATA6 promoted the malignant development of OSCC cells by binding to the FN1 promotor. These results may contribute to further understanding the pathogenesis of OSCC and provide potential therapeutic targets for the clinical treatment of OSCC.
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Affiliation(s)
- Jianbo Zhai
- Welle Dental, Jingan, Shanghai 200040, P.R. China
| | - Gang Luo
- Welle Dental, Jingan, Shanghai 200040, P.R. China
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14
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Maderazo D, Flegg JA, Algama M, Ramialison M, Keith J. Detection and identification of cis-regulatory elements using change-point and classification algorithms. BMC Genomics 2022; 23:78. [PMID: 35078412 PMCID: PMC8790847 DOI: 10.1186/s12864-021-08190-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 11/19/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Transcriptional regulation is primarily mediated by the binding of factors to non-coding regions in DNA. Identification of these binding regions enhances understanding of tissue formation and potentially facilitates the development of gene therapies. However, successful identification of binding regions is made difficult by the lack of a universal biological code for their characterisation. RESULTS We extend an alignment-based method, changept, and identify clusters of biological significance, through ontology and de novo motif analysis. Further, we apply a Bayesian method to estimate and combine binary classifiers on the clusters we identify to produce a better performing composite. CONCLUSIONS The analysis we describe provides a computational method for identification of conserved binding sites in the human genome and facilitates an alternative interrogation of combinations of existing data sets with alignment data.
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Affiliation(s)
- Dominic Maderazo
- School of Mathematics and Statistics, The University of Melbourne, Melbourne, 3010, VIC, Australia.
| | - Jennifer A Flegg
- School of Mathematics and Statistics, The University of Melbourne, Melbourne, 3010, VIC, Australia
| | - Manjula Algama
- School of Mathematics, Monash University, Melbourne, 3800, VIC, Australia
| | - Mirana Ramialison
- Australian Regenerative Medicine Institute, Monash University, Melbourne, 3800, VIC, Australia
| | - Jonathan Keith
- School of Mathematics, Monash University, Melbourne, 3800, VIC, Australia
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15
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Wu Z, Zhou J, Zhang X, Zhang Z, Xie Y, Liu JB, Ho ZV, Panda A, Qiu X, Cejas P, Cañadas I, Akarca FG, McFarland JM, Nagaraja AK, Goss LB, Kesten N, Si L, Lim K, Liu Y, Zhang Y, Baek JY, Liu Y, Patil DT, Katz JP, Hai J, Bao C, Stachler M, Qi J, Ishizuka JJ, Nakagawa H, Rustgi AK, Wong KK, Meyerson M, Barbie DA, Brown M, Long H, Bass AJ. Reprogramming of the esophageal squamous carcinoma epigenome by SOX2 promotes ADAR1 dependence. Nat Genet 2021; 53:881-894. [PMID: 33972779 PMCID: PMC9124436 DOI: 10.1038/s41588-021-00859-2] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 03/29/2021] [Indexed: 01/28/2023]
Abstract
Esophageal squamous cell carcinomas (ESCCs) harbor recurrent chromosome 3q amplifications that target the transcription factor SOX2. Beyond its role as an oncogene in ESCC, SOX2 acts in development of the squamous esophagus and maintenance of adult esophageal precursor cells. To compare Sox2 activity in normal and malignant tissue, we developed engineered murine esophageal organoids spanning normal esophagus to Sox2-induced squamous cell carcinoma and mapped Sox2 binding and the epigenetic and transcriptional landscape with evolution from normal to cancer. While oncogenic Sox2 largely maintains actions observed in normal tissue, Sox2 overexpression with p53 and p16 inactivation promotes chromatin remodeling and evolution of the Sox2 cistrome. With Klf5, oncogenic Sox2 acquires new binding sites and enhances activity of oncogenes such as Stat3. Moreover, oncogenic Sox2 activates endogenous retroviruses, inducing expression of double-stranded RNA and dependence on the RNA editing enzyme ADAR1. These data reveal SOX2 functions in ESCC, defining targetable vulnerabilities.
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Affiliation(s)
- Zhong Wu
- Division of Molecular and Cellular Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Cancer Program, The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA.,These authors contributed equally: Zhong Wu, Jin Zhou, Xiaoyang Zhang
| | - Jin Zhou
- Division of Molecular and Cellular Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Cancer Program, The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA.,These authors contributed equally: Zhong Wu, Jin Zhou, Xiaoyang Zhang
| | - Xiaoyang Zhang
- Division of Molecular and Cellular Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Cancer Program, The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA.,Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA.,These authors contributed equally: Zhong Wu, Jin Zhou, Xiaoyang Zhang
| | - Zhouwei Zhang
- Division of Molecular and Cellular Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Cancer Program, The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Yingtian Xie
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Jie bin Liu
- Division of Molecular and Cellular Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Zandra V. Ho
- Cancer Program, The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Arpit Panda
- Division of Molecular and Cellular Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Committee on Immunology, The University of Chicago, Chicago, IL, USA
| | - Xintao Qiu
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Paloma Cejas
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Israel Cañadas
- Division of Molecular and Cellular Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Present address: Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Fahire Goknur Akarca
- Division of Molecular and Cellular Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - James M. McFarland
- Cancer Program, The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Ankur K. Nagaraja
- Division of Molecular and Cellular Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Cancer Program, The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA.,Present address: Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Louisa B. Goss
- Division of Molecular and Cellular Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Nikolas Kesten
- Division of Molecular and Cellular Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Longlong Si
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Klothilda Lim
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Yanli Liu
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Yanxi Zhang
- Division of Molecular and Cellular Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Ji Yeon Baek
- Division of Molecular and Cellular Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Yang Liu
- Division of Molecular and Cellular Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Cancer Program, The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Deepa T. Patil
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, USA
| | - Jonathan P. Katz
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Josephine Hai
- Division of Molecular and Cellular Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Chunyang Bao
- Division of Molecular and Cellular Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Cancer Program, The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Matthew Stachler
- Division of Molecular and Cellular Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Department of Pathology, Brigham and Women’s Hospital, Boston, MA, USA
| | - Jun Qi
- Cancer Biology Department, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Jeffrey J. Ishizuka
- Division of Molecular and Cellular Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Cancer Program, The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Hiroshi Nakagawa
- Herbert Irving Comprehensive Cancer Center, Division of Digestive and Liver Diseases, Department of Medicine, Columbia University, New York, NY, USA
| | - Anil K. Rustgi
- Herbert Irving Comprehensive Cancer Center, Division of Digestive and Liver Diseases, Department of Medicine, Columbia University, New York, NY, USA
| | - Kwok-Kin Wong
- Division of Hematology and Medical Oncology, Laura and Isaac Perlmutter Cancer Center, New York University Langone Medical Center, New York, NY, USA
| | - Matthew Meyerson
- Division of Molecular and Cellular Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Cancer Program, The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - David A. Barbie
- Division of Molecular and Cellular Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Cancer Program, The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Myles Brown
- Division of Molecular and Cellular Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Henry Long
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Adam J. Bass
- Division of Molecular and Cellular Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Cancer Program, The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA.,Herbert Irving Comprehensive Cancer Center, Division of Hematology and Oncology, Department of Medicine, Columbia University, New York, NY, USA
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16
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Dittrich GM, Froese N, Wang X, Kroeger H, Wang H, Szaroszyk M, Malek-Mohammadi M, Cordero J, Keles M, Korf-Klingebiel M, Wollert KC, Geffers R, Mayr M, Conway SJ, Dobreva G, Bauersachs J, Heineke J. Fibroblast GATA-4 and GATA-6 promote myocardial adaptation to pressure overload by enhancing cardiac angiogenesis. Basic Res Cardiol 2021; 116:26. [PMID: 33876316 PMCID: PMC8055639 DOI: 10.1007/s00395-021-00862-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 03/15/2021] [Indexed: 12/14/2022]
Abstract
Heart failure due to high blood pressure or ischemic injury remains a major problem for millions of patients worldwide. Despite enormous advances in deciphering the molecular mechanisms underlying heart failure progression, the cell-type specific adaptations and especially intercellular signaling remain poorly understood. Cardiac fibroblasts express high levels of cardiogenic transcription factors such as GATA-4 and GATA-6, but their role in fibroblasts during stress is not known. Here, we show that fibroblast GATA-4 and GATA-6 promote adaptive remodeling in pressure overload induced cardiac hypertrophy. Using a mouse model with specific single or double deletion of Gata4 and Gata6 in stress activated fibroblasts, we found a reduced myocardial capillarization in mice with Gata4/6 double deletion following pressure overload, while single deletion of Gata4 or Gata6 had no effect. Importantly, we confirmed the reduced angiogenic response using an in vitro co-culture system with Gata4/6 deleted cardiac fibroblasts and endothelial cells. A comprehensive RNA-sequencing analysis revealed an upregulation of anti-angiogenic genes upon Gata4/6 deletion in fibroblasts, and siRNA mediated downregulation of these genes restored endothelial cell growth. In conclusion, we identified a novel role for the cardiogenic transcription factors GATA-4 and GATA-6 in heart fibroblasts, where both proteins act in concert to promote myocardial capillarization and heart function by directing intercellular crosstalk.
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Affiliation(s)
- Gesine M Dittrich
- Department of Cardiology and Angiology, Hannover Medical School, 30625, Hannover, Germany
- Department of Cardiovascular Physiology, European Center for Angioscience (ECAS), Medical Faculty Mannheim of Heidelberg University, 68167, Mannheim, Germany
- German Center for Cardiovascular Research (DZHK), Partner site Heidelberg/Mannheim, Germany
| | - Natali Froese
- Department of Cardiology and Angiology, Hannover Medical School, 30625, Hannover, Germany
| | - Xue Wang
- Department of Cardiology and Angiology, Hannover Medical School, 30625, Hannover, Germany
- Shanghai Tianyou Hospital Affiliated To Tongji University, Shanghai, 200333, China
| | - Hannah Kroeger
- Department of Cardiology and Angiology, Hannover Medical School, 30625, Hannover, Germany
| | - Honghui Wang
- Department of Cardiology and Angiology, Hannover Medical School, 30625, Hannover, Germany
| | - Malgorzata Szaroszyk
- Department of Cardiology and Angiology, Hannover Medical School, 30625, Hannover, Germany
| | - Mona Malek-Mohammadi
- Department of Cardiovascular Physiology, European Center for Angioscience (ECAS), Medical Faculty Mannheim of Heidelberg University, 68167, Mannheim, Germany
- German Center for Cardiovascular Research (DZHK), Partner site Heidelberg/Mannheim, Germany
| | - Julio Cordero
- Department of Anatomy and Developmental Biology, European Center for Angioscience (ECAS), Medical Faculty Mannheim of Heidelberg University, 68167, Mannheim, Germany
| | - Merve Keles
- Department of Cardiovascular Physiology, European Center for Angioscience (ECAS), Medical Faculty Mannheim of Heidelberg University, 68167, Mannheim, Germany
| | | | - Kai C Wollert
- Department of Cardiology and Angiology, Hannover Medical School, 30625, Hannover, Germany
| | - Robert Geffers
- Genome Analytics, Helmholtz Center for Infection Research, 38124, Braunschweig, Germany
| | - Manuel Mayr
- King's British Heart Foundation Centre, King's College London, London, UK
| | - Simon J Conway
- HB Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Gergana Dobreva
- Department of Anatomy and Developmental Biology, European Center for Angioscience (ECAS), Medical Faculty Mannheim of Heidelberg University, 68167, Mannheim, Germany
- German Center for Cardiovascular Research (DZHK), Partner site Heidelberg/Mannheim, Germany
| | - Johann Bauersachs
- Department of Cardiology and Angiology, Hannover Medical School, 30625, Hannover, Germany
| | - Joerg Heineke
- Department of Cardiology and Angiology, Hannover Medical School, 30625, Hannover, Germany.
- Department of Cardiovascular Physiology, European Center for Angioscience (ECAS), Medical Faculty Mannheim of Heidelberg University, 68167, Mannheim, Germany.
- German Center for Cardiovascular Research (DZHK), Partner site Heidelberg/Mannheim, Germany.
- Cardiovascular Physiology, European Center for Angioscience (ECAS), Medizinische Fakultät Mannheim, Universität Heidelberg, Ludolf-Krehl-Str. 7-11, 68167, Mannheim, Germany.
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17
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Molinari C, Tedaldi G, Rebuzzi F, Morgagni P, Capelli L, Ravaioli S, Tumedei MM, Scarpi E, Tomezzoli A, Bernasconi R, Ambrosio MR, D'Ignazio A, Solaini L, Limarzi F, Ercolani G, Martinelli G, Ulivi P, Saragoni L. Early Gastric Cancer: identification of molecular markers able to distinguish submucosa-penetrating lesions with different prognosis. Gastric Cancer 2021; 24:392-401. [PMID: 33156452 DOI: 10.1007/s10120-020-01135-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 10/18/2020] [Indexed: 02/06/2023]
Abstract
BACKGROUND Early Gastric Cancer (EGC) reaches 25% of the gastric cancers surgically treated in some areas of Northeastern Italy and is usually characterized by a good prognosis. However, among EGCs classified according to Kodama's criteria, Pen A subgroup is characterized by extensive submucosal invasion, lymph node metastases and worse prognosis, whereas Pen B subgroup by better prognosis. The aim of the study was to characterize the differences between Pen A, Pen B and locally advanced gastric cancer (T3N0) in order to identify biomarkers involved in aggressiveness and clinical outcome. METHODS We selected 33 Pen A, 34 Pen B and 20 T3N0 tumors and performed immunohistochemistry of mucins, copy number variation analysis of a gene panel, microsatellite instability (MSI), TP53 mutation and loss of heterozygosity (LOH) analyses. RESULTS Pen A subgroup was characterized by MUC6 overexpression (p = 0.021). Otherwise, the Pen B subgroup was significantly associated with the amplification of GATA6 gene (p = 0.002). The higher percentage of MSI tumors was observed in T3N0 group (p = 0.002), but no significant differences between EGC types were found. Finally, TP53 gene analysis showed that 32.8% of Pen tumors have a mutation in exons 5-8 and 50.0% presented LOH. Co-occurrence of TP53 mutation and LOH mainly characterized Pen A tumors (p = 0.022). CONCLUSIONS Our analyses revealed that clinico-pathological parameters, microsatellite status and frequency of TP53 mutations do not seem to distinguish Pen subgroups. Conversely, the amplification of GATA6 was associated with Pen B, as well as the overexpression of MUC6 and the TP53mut/LOH significantly characterized Pen A.
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Affiliation(s)
- Chiara Molinari
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, via P. Maroncelli 40, 47014, Meldola, FC, Italy
| | - Gianluca Tedaldi
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, via P. Maroncelli 40, 47014, Meldola, FC, Italy.
| | - Francesca Rebuzzi
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, via P. Maroncelli 40, 47014, Meldola, FC, Italy
| | - Paolo Morgagni
- Department of Surgery, Morgagni-Pierantoni Hospital, Forlì, Italy
| | - Laura Capelli
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, via P. Maroncelli 40, 47014, Meldola, FC, Italy
| | - Sara Ravaioli
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, via P. Maroncelli 40, 47014, Meldola, FC, Italy
| | - Maria Maddalena Tumedei
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, via P. Maroncelli 40, 47014, Meldola, FC, Italy
| | - Emanuela Scarpi
- Biostatistics and Clinical Trials Unit, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy
| | - Anna Tomezzoli
- Department of Pathology, University of Verona, Verona, Italy
| | | | - Maria Raffaella Ambrosio
- Pathology Unit, University of Siena, Siena, Italy.,Pathology Unit, Azienda USL Toscana Nord-Ovest, Pisa, Italy
| | | | - Leonardo Solaini
- Department of Surgery, Morgagni-Pierantoni Hospital, Forlì, Italy.,Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | - Francesco Limarzi
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, via P. Maroncelli 40, 47014, Meldola, FC, Italy
| | - Giorgio Ercolani
- Department of Surgery, Morgagni-Pierantoni Hospital, Forlì, Italy
| | - Giovanni Martinelli
- Department of Medical Oncology, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy
| | - Paola Ulivi
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, via P. Maroncelli 40, 47014, Meldola, FC, Italy
| | - Luca Saragoni
- Pathology Unit, Morgagni-Pierantoni Hospital, Forlì, Italy
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18
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Chang J, Wang Q, Bhetuwal A, Liu W. Metabolic pathways underlying GATA6 regulating Trastuzumab resistance in Gastric Cancer cells based on untargeted metabolomics. Int J Med Sci 2020; 17:3146-3164. [PMID: 33173435 PMCID: PMC7646115 DOI: 10.7150/ijms.50563] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Accepted: 10/09/2020] [Indexed: 12/02/2022] Open
Abstract
Trastuzumab has proven its effectiveness in gastric cancer with HER-2 gene-amplification, which has now developed resistance while the mechanism of which is not fully elucidated. Our previous studies demonstrated that the activity of GATA6 binding protein 6 (GATA6) enhanced prominently in trastuzumab resistant gastric cancer cell lines (NCI N87R and MKN45R). In the present study, we further confirmed the re-sensitization to trastuzumab and inhibition of mitochondrial functions of GATA6 knockout sublines (NCI N87R/ΔGATA6 and MKN45R/ΔGATA6). Moreover, we applied untargeted metabolomic profiling to investigate the potential roles of GATA6 in metabolism of NCI N87R and MKN45R. The UPLC system coupled with Q-Exactive Focus Orbitrap mass spectrometry, multivariate in combination with univariate analysis were performed for the screening of differential metabolites between resistant cells and GATA6 knockout sublines. A total of 68 and 59 endogenous metabolites were found to be altered significantly in NCI N87R/ΔGATA6 and MKN45R/ΔGATA6 cells compared with NCI N87R and MKN45R, respectively. Pathway analyses indicated disturbance of metabolic pathways after GATA6 knockout including tricarboxylic acid (TCA) cycle, glycolysis and energy-related amino acid pathways. An integrated proteomics-metabolomics revealed that sub-networks were closely related to TCA cycle, glycolysis, multiple amino acid and nucleotide metabolism. Western blot showed that TCA cycle and glycolysis-related molecules, including PKM, GLS, GLUL and LDHA, were downregulated in GATA6 knockout sublines. Taken together, these findings demonstrate that GATA6 is involved in metabolism reprogramming which might contribute to trastuzumab resistance in gastric cancer.
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Affiliation(s)
- Jinxia Chang
- School of Basic Medical Sciences, North Sichuan Medical College, Nanchong, Sichuan 637100, China
| | - Qiang Wang
- Department of Laboratory Medicine, Affiliated Hospital of North Sichuan Medical College; Faculty of Laboratory Medicine, Center for Translational Medicine, North Sichuan Medical College, Nanchong, Sichuan 637000, China
| | - Anup Bhetuwal
- Sichuan Key Laboratory of Medical Imaging and Department of Radiology, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan 637000, China
| | - Wenhu Liu
- School of Basic Medical Sciences, North Sichuan Medical College, Nanchong, Sichuan 637100, China
- School of Pharmacy, North Sichuan Medical College, Nanchong, Sichuan 637100, China
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19
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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: 22] [Impact Index Per Article: 5.5] [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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20
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Sharma A, Wasson LK, Willcox JA, Morton SU, Gorham JM, DeLaughter DM, Neyazi M, Schmid M, Agarwal R, Jang MY, Toepfer CN, Ward T, Kim Y, Pereira AC, DePalma SR, Tai A, Kim S, Conner D, Bernstein D, Gelb BD, Chung WK, Goldmuntz E, Porter G, Tristani-Firouzi M, Srivastava D, Seidman JG, Seidman CE. GATA6 mutations in hiPSCs inform mechanisms for maldevelopment of the heart, pancreas, and diaphragm. eLife 2020; 9:53278. [PMID: 33054971 PMCID: PMC7593088 DOI: 10.7554/elife.53278] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 10/14/2020] [Indexed: 12/18/2022] Open
Abstract
Damaging GATA6 variants cause cardiac outflow tract defects, sometimes with pancreatic and diaphragmic malformations. To define molecular mechanisms for these diverse developmental defects, we studied transcriptional and epigenetic responses to GATA6 loss of function (LoF) and missense variants during cardiomyocyte differentiation of isogenic human induced pluripotent stem cells. We show that GATA6 is a pioneer factor in cardiac development, regulating SMYD1 that activates HAND2, and KDR that with HAND2 orchestrates outflow tract formation. LoF variants perturbed cardiac genes and also endoderm lineage genes that direct PDX1 expression and pancreatic development. Remarkably, an exon 4 GATA6 missense variant, highly associated with extra-cardiac malformations, caused ectopic pioneer activities, profoundly diminishing GATA4, FOXA1/2, and PDX1 expression and increasing normal retinoic acid signaling that promotes diaphragm development. These aberrant epigenetic and transcriptional signatures illuminate the molecular mechanisms for cardiovascular malformations, pancreas and diaphragm dysgenesis that arise in patients with distinct GATA6 variants.
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Affiliation(s)
- Arun Sharma
- Department of Genetics, Harvard Medical School, Boston, United States.,Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, United States.,Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, United States
| | - Lauren K Wasson
- Department of Genetics, Harvard Medical School, Boston, United States.,Howard Hughes Medical Institute, Harvard Medical School, Boston, United States
| | - Jon Al Willcox
- Department of Genetics, Harvard Medical School, Boston, United States
| | - Sarah U Morton
- Department of Genetics, Harvard Medical School, Boston, United States.,Division of Newborn Medicine, Boston Children's Hospital, Boston, United States
| | - Joshua M Gorham
- Department of Genetics, Harvard Medical School, Boston, United States
| | | | - Meraj Neyazi
- Department of Genetics, Harvard Medical School, Boston, United States.,Hannover Medical School, Hannover, Germany
| | - Manuel Schmid
- Department of Genetics, Harvard Medical School, Boston, United States.,Deutsches Herzzentrum München, Technische Universität München, Munich, Germany
| | - Radhika Agarwal
- Department of Genetics, Harvard Medical School, Boston, United States
| | - Min Young Jang
- Department of Genetics, Harvard Medical School, Boston, United States
| | - Christopher N Toepfer
- Department of Genetics, Harvard Medical School, Boston, United States.,Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom.,Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Tarsha Ward
- Department of Genetics, Harvard Medical School, Boston, United States
| | - Yuri Kim
- Department of Genetics, Harvard Medical School, Boston, United States
| | - Alexandre C Pereira
- Department of Genetics, Harvard Medical School, Boston, United States.,Laboratory of Genetics and Molecular Cardiology, Heart Institute, Medical School of University of Sao Paulo, Sao Paulo, Brazil
| | - Steven R DePalma
- Department of Genetics, Harvard Medical School, Boston, United States
| | - Angela Tai
- Department of Genetics, Harvard Medical School, Boston, United States
| | - Seongwon Kim
- Department of Genetics, Harvard Medical School, Boston, United States
| | - David Conner
- Department of Genetics, Harvard Medical School, Boston, United States
| | - Daniel Bernstein
- Department of Pediatrics, Stanford University School of Medicine, Stanford, United States
| | - Bruce D Gelb
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Wendy K Chung
- Department of Medicine, Columbia University Medical Center, New York, United States
| | - Elizabeth Goldmuntz
- Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
| | - George Porter
- Department of Pediatrics, University of Rochester Medical Center, Rochester, United States
| | - Martin Tristani-Firouzi
- Division of Pediatric Cardiology, University of Utah School of Medicine, Salt Lake City, United States
| | | | | | - Christine E Seidman
- Department of Genetics, Harvard Medical School, Boston, United States.,Howard Hughes Medical Institute, Harvard Medical School, Boston, United States.,Cardiovascular Division, Department of Medicine, Brigham and Women's Hospital, Boston, United States
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21
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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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22
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Expression patterns of seven key genes, including β-catenin, Notch1, GATA6, CDX2, miR-34a, miR-181a and miR-93 in gastric cancer. Sci Rep 2020; 10:12342. [PMID: 32704077 PMCID: PMC7378835 DOI: 10.1038/s41598-020-69308-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 06/01/2020] [Indexed: 02/08/2023] Open
Abstract
Gastric cancer (GC) is one of the most prevalent cancers and a major cause of cancer related mortality worldwide. Incidence of GC is affected by various factors, including genetic and environmental factors. Despite extensive research has been done for molecular characterization of GC, it remains largely unknown. Therefore, further studies specially conducted among various ethnicities in different geographic locations, are required to know the precise molecular mechanisms leading to tumorigenesis and progression of GC. The expression patterns of seven candidate genes, including β-catenin, Notch1, GATA6, CDX2, miR-34a, miR-181a, and miR-93 were determined in 24 paired GC tissues and corresponding non-cancerous tissues by quantitative Real-Time PCR. The association between the expression of these genes and clinicopathologic factors were also investigated. Our results demonstrated that overall mRNA levels of GATA6 were significantly decreased in the tumor samples in comparison with the non-cancerous tissues (median fold change (FC) = 0.3143; P = 0.0003). Overall miR-93 levels were significantly increased in the tumor samples relative to the non-cancerous gastric tissues (FC = 2.441; P = 0.0002). β-catenin mRNA expression showed a strong positive correlation with miR-34a (r = 0.5784; P = 0.0031), and miR-181a (r = 0.5652; P = 0.004) expression. miR-34a and miR-181a expression showed a significant positive correlation (r = 0.4862; P = 0.016). Moreover, lower expression of Notch1 was related to distant metastasis in GC patients with a borderline statistical significance (p = 0.0549). These data may advance our understanding of the molecular biology that drives GC as well as provide potential targets for defining novel therapeutic strategies for GC treatment.
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23
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Gu E, Song W, Liu A, Wang H. SCDb: an integrated database of stomach cancer. BMC Cancer 2020; 20:490. [PMID: 32487193 PMCID: PMC7265634 DOI: 10.1186/s12885-020-06869-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 04/15/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Stomach cancer (SC) is a type of cancer, which is derived from the stomach mucous membrane. As there are non-specific symptoms or no noticeable symptoms observed at the early stage, newly diagnosed SC cases usually reach an advanced stage and are thus difficult to cure. Therefore, in this study, we aimed to develop an integrated database of SC. METHODS SC-related genes were identified through literature mining and by analyzing the publicly available microarray datasets. Using the RNA-seq, miRNA-seq and clinical data downloaded from The Cancer Genome Atlas (TCGA), the Kaplan-Meier (KM) survival curves for all the SC-related genes were generated and analyzed. The miRNAs (miRanda, miRTarget2, PicTar, PITA and TargetScan databases), SC-related miRNAs (HMDD and miR2Disease databases), single nucleotide polymorphisms (SNPs, dbSNP database), and SC-related SNPs (ClinVar database) were also retrieved from the indicated databases. Moreover, gene_disease (OMIM and GAD databases), copy number variation (CNV, DGV database), methylation (PubMeth database), drug (WebGestalt database), and transcription factor (TF, TRANSFAC database) analyses were performed for the differentially expressed genes (DEGs). RESULTS In total, 9990 SC-related genes (including 8347 up-regulated genes and 1643 down-regulated genes) were identified, among which, 65 genes were further confirmed as SC-related genes by performing enrichment analysis. Besides this, 457 miRNAs, 20 SC-related miRNAs, 1570 SNPs, 108 SC-related SNPs, 419 TFs, 44,605 CNVs, 3404 drug-associated genes, 63 genes with methylation, and KM survival curves of 20,264 genes were obtained. By integrating these datasets, an integrated database of stomach cancer, designated as SCDb, (available at http://www.stomachcancerdb.org/) was established. CONCLUSIONS As a comprehensive resource for human SC, SCDb database will be very useful for performing SC-related research in future, and will thus promote the understanding of the pathogenesis of SC.
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Affiliation(s)
- Erli Gu
- Department of Gastroenterology, Jing'An District Centre Hospital of Shanghai (Huashan Hospital Fudan University Jing'An Branch), Shanghai, 200040, People's Republic of China
| | - Wei Song
- Yuanzi (Shanghai) Information Technology Co., Ltd, No. 259 Xikang Road, Jing'An District, Shanghai, 200040, People's Republic of China
| | - Ajing Liu
- Yuanzi (Shanghai) Information Technology Co., Ltd, No. 259 Xikang Road, Jing'An District, Shanghai, 200040, People's Republic of China
| | - Hong Wang
- Department of Gastroenterology, Jing'An District Centre Hospital of Shanghai (Huashan Hospital Fudan University Jing'An Branch), Shanghai, 200040, People's Republic of China.
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24
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Lai HT, Chiang CT, Tseng WK, Chao TC, Su Y. GATA6 enhances the stemness of human colon cancer cells by creating a metabolic symbiosis through upregulating LRH-1 expression. Mol Oncol 2020; 14:1327-1347. [PMID: 32037723 PMCID: PMC7266275 DOI: 10.1002/1878-0261.12647] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 01/09/2020] [Accepted: 02/07/2020] [Indexed: 12/13/2022] Open
Abstract
Cancer stem cells play critical roles in tumor initiation, progression, and relapse. Since we previously found that GATA6 promotes the stemness in HCT‐116 and HT‐29 human colorectal cancer (CRC) cells, we aimed to identify the downstream mediator(s) of the stemness‐stimulating effect of GATA6 herein. LRH‐1 was found as a direct target of GATA6 and its upregulation promoted the stemness in both HCT‐116 and HT‐29 cells. Subsequently, hypoxia‐inducible factor‐1α (HIF‐1α) was identified as a direct target of LRH‐1 and its expression level and activity were significantly elevated in the LRH‐1‐overexpressing clones established from the aforementioned two CRC lines. Accordingly, the expression levels of several HIF‐1α targets were also markedly increased, resulting in a stronger glycolysis associated with dramatic elevations of the lactate levels in these cells. Strikingly, higher mitochondrial activities were also found in these clones which might be attributed to the increase of PGC‐1α stimulated by the lactate uptaken through the upregulated MCT‐1. Finally, significant increases in the self‐renewal ability, intracellular radical oxygen species levels and mitochondrial mass were detected in the CD133+/CD44+ subpopulations isolated from CRC cells regardless of their LRH‐1 expression levels. Together, our results suggest a novel metabolic symbiosis between different colorectal cancer stem cell subpopulations critical for maintaining their mutual stemness.
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Affiliation(s)
- Hung-Tzu Lai
- Institute of Biopharmaceutical Sciences, School of Pharmaceutical Sciences, National Yang-Ming University, Taipei, Taiwan, R.O.C
| | - Chin-Ting Chiang
- Institute of Biopharmaceutical Sciences, School of Pharmaceutical Sciences, National Yang-Ming University, Taipei, Taiwan, R.O.C
| | - Wen-Ko Tseng
- Program in Molecular Medicine, School of Life Sciences, National Yang-Ming University, Taipei, Taiwan, R.O.C.,Colorectal Surgery Department, Chung-Gung Memorial Hospital, Keelung Branch, Taiwan, R.O.C
| | - Ta-Chung Chao
- Division of Medical Oncology, Department of Oncology, Taipei Veterans General Hospital, Taiwan, R.O.C.,Faculty of Medicine, School of Medicine, National Yang-Ming University, Taipei, Taiwan, R.O.C
| | - Yeu Su
- Institute of Biopharmaceutical Sciences, School of Pharmaceutical Sciences, National Yang-Ming University, Taipei, Taiwan, R.O.C
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25
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Romano O, Miccio A. GATA factor transcriptional activity: Insights from genome-wide binding profiles. IUBMB Life 2019; 72:10-26. [PMID: 31574210 DOI: 10.1002/iub.2169] [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: 07/31/2019] [Accepted: 09/05/2019] [Indexed: 01/07/2023]
Abstract
The members of the GATA family of transcription factors have homologous zinc fingers and bind to similar sequence motifs. Recent advances in genome-wide technologies and the integration of bioinformatics data have led to a better understanding of how GATA factors regulate gene expression; GATA-factor-induced transcriptional and epigenetic changes have now been analyzed at unprecedented levels of detail. Here, we review the results of genome-wide studies of GATA factor occupancy in human and murine cell lines and primary cells (as determined by chromatin immunoprecipitation sequencing), and then discuss the molecular mechanisms underlying the mediation of transcriptional and epigenetic regulation by GATA factors.
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Affiliation(s)
- Oriana Romano
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Annarita Miccio
- Laboratory of chromatin and gene regulation during development, Imagine Institute, INSERM UMR, Paris, France.,Paris Descartes, Sorbonne Paris Cité University, Imagine Institute, Paris, France
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26
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Lai HT, Tseng WK, Huang SW, Chao TC, Su Y. MicroRNA-203 diminishes the stemness of human colon cancer cells by suppressing GATA6 expression. J Cell Physiol 2019; 235:2866-2880. [PMID: 31544978 DOI: 10.1002/jcp.29192] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 09/03/2019] [Indexed: 12/27/2022]
Abstract
The interaction between hyaluronan and CD44, an important cancer stem-cell marker, stimulates various tumor cell-specific functions such as the stemness of tumor cells. microRNA-203 (miR-203) can be downregulated by this interaction in human colorectal cancer (CRC) cells, which increases their stemness; however, the underlying mechanism is not yet defined. Here, we show that overexpression and sequestration of miR-203 in HCT-116 and HT-29 human CRC cells reduces and enhances their stemness, respectively. We also show that GATA-binding factor 6 (GATA6) is a direct target of miR-203. Our results indicate that upregulated expression of this transcription factor not only restores the self-renewal abilities of miR-203-overexpressing HCT-116 and HT-29 cells but also promotes the stemness properties of their parental counterparts. More important, we show that silencing the expression of either LRH-1 or Hes-1 is sufficient to diminish the stemness-promoting effects of GATA6 in human CRC cells. Together, our findings delineate the stemness-inhibitory mechanism of miR-203 in human CRC cells and suggest that this miR is a potential therapeutic agent for colorectal cancer.
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Affiliation(s)
- Hung-Tzi Lai
- Institute of Biopharmaceutical Sciences, School of Pharmaceutical Sciences, National Yang-Ming University, Shi-Pai, Taipei, Taiwan, R.O.C
| | - Wen-Ko Tseng
- Program in Molecular Medicine, School of Life Sciences, National Yang-Ming University, Shi-Pai, Taipei, Taiwan, R.O.C.,Colorectal Surgery Department, Chung-Gung Memorial Hospital, Keelung Branch, Keelung, Taipei, Taiwan, R.O.C
| | - Shi-Wei Huang
- Institute of Biopharmaceutical Sciences, School of Pharmaceutical Sciences, National Yang-Ming University, Shi-Pai, Taipei, Taiwan, R.O.C
| | - Ta-Chung Chao
- Division of Medical Oncology, Department of Oncology, Taipei Veterans General Hospital, Taipei, Taiwan, R.O.C.,Faculty of Medicine, School of Medicine, National Yang-Ming University, Shi-Pai, Taipei, Taiwan, R.O.C
| | - Yeu Su
- Institute of Biopharmaceutical Sciences, School of Pharmaceutical Sciences, National Yang-Ming University, Shi-Pai, Taipei, Taiwan, R.O.C.,Program in Molecular Medicine, School of Life Sciences, National Yang-Ming University, Shi-Pai, Taipei, Taiwan, R.O.C
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27
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Li X, Cai H, Wang X, Ao L, Guo Y, He J, Gu Y, Qi L, Guan Q, Lin X, Guo Z. A rank-based algorithm of differential expression analysis for small cell line data with statistical control. Brief Bioinform 2019; 20:482-491. [PMID: 29040359 PMCID: PMC6433897 DOI: 10.1093/bib/bbx135] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 09/21/2017] [Indexed: 12/25/2022] Open
Abstract
To detect differentially expressed genes (DEGs) in small-scale cell line experiments, usually with only two or three technical replicates for each state, the commonly used statistical methods such as significance analysis of microarrays (SAM), limma and RankProd (RP) lack statistical power, while the fold change method lacks any statistical control. In this study, we demonstrated that the within-sample relative expression orderings (REOs) of gene pairs were highly stable among technical replicates of a cell line but often widely disrupted after certain treatments such like gene knockdown, gene transfection and drug treatment. Based on this finding, we customized the RankComp algorithm, previously designed for individualized differential expression analysis through REO comparison, to identify DEGs with certain statistical control for small-scale cell line data. In both simulated and real data, the new algorithm, named CellComp, exhibited high precision with much higher sensitivity than the original RankComp, SAM, limma and RP methods. Therefore, CellComp provides an efficient tool for analyzing small-scale cell line data.
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Affiliation(s)
| | - Hao Cai
- Fujian Medical University, China
| | | | - Lu Ao
- Fujian Medical University, China
| | - You Guo
- Fujian Medical University, China
| | - Jun He
- Fujian Medical University, China
| | | | | | | | - Xu Lin
- Fujian Medical University, China
| | - Zheng Guo
- Fujian Medical University and Harbin Medical University
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28
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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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29
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Peng T, Deng X, Tian F, Li Z, Jiang P, Zhao X, Chen G, Chen Y, Zheng P, Li D, Wang S. The interaction of LOXL2 with GATA6 induces VEGFA expression and angiogenesis in cholangiocarcinoma. Int J Oncol 2019; 55:657-670. [PMID: 31322171 PMCID: PMC6685595 DOI: 10.3892/ijo.2019.4837] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 06/27/2019] [Indexed: 12/15/2022] Open
Abstract
Cholangiocarcinoma (CCA) is the second most common hepatobiliary cancer after hepatocellular carcinoma. Antiangiogenic therapy has been administered to patients with CCA, but the benefits of this therapy remain unsatisfactory. Improved understanding of the molecular mechanisms underlying angiogenesis in CCA is required. In the present study, the expression of GATA-binding protein 6 (GATA6), lysyl oxidase-like 2 (LOXL2) and vascular endothelial growth factor A (VEGFA), in addition to the microvessel density (MVD), were evaluated by performing immunohistochemical staining of human CCA microarrays. The expression of GATA6/LOXL2 was associated with poor overall survival (P=0.01) and disease-free survival (P=0.02), and was positively associated with VEGFA expression (P=0.02) and MVD (P=0.04). In vitro, western blotting, reverse transcription-quantitative PCR analysis and ELISAs revealed that altered GATA6 and LOXL2 expression regulated the expression levels of secreted VEGFA. Co-immunoprecipitation demonstrated a physical interaction between GATA6 and LOXL2 in CCA cell lines, and the scavenger receptor cysteine-rich domain of LOXL2 interacted with GATA6, which regulated VEGFA mRNA expression and protein secretion, and promoted tube formation. In vivo analyses further revealed that GATA6/LOXL2 promoted VEGFA expression, angiogenesis and tumor growth. The GATA6/LOXL2 complex represents a novel candidate prognostic marker for stratifying patients with CCA. Drugs targeting this complex may possess great therapeutic value in the treatment of CCA.
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Affiliation(s)
- Tao Peng
- Hepatobiliary Surgery Institute, Southwest Hospital, Army Medical University, Chongqing 400038, P.R. China
| | - Xiang Deng
- Hepatobiliary Surgery Institute, Southwest Hospital, Army Medical University, Chongqing 400038, P.R. China
| | - Feng Tian
- Hepatobiliary Surgery Institute, Southwest Hospital, Army Medical University, Chongqing 400038, P.R. China
| | - Zhonghu Li
- Hepatobiliary Surgery Institute, Southwest Hospital, Army Medical University, Chongqing 400038, P.R. China
| | - Peng Jiang
- Hepatobiliary Surgery Institute, Southwest Hospital, Army Medical University, Chongqing 400038, P.R. China
| | - Xin Zhao
- Hepatobiliary Surgery Institute, Southwest Hospital, Army Medical University, Chongqing 400038, P.R. China
| | - Guangyu Chen
- Hepatobiliary Surgery Institute, Southwest Hospital, Army Medical University, Chongqing 400038, P.R. China
| | - Yan Chen
- Hepatobiliary Surgery Institute, Southwest Hospital, Army Medical University, Chongqing 400038, P.R. China
| | - Ping Zheng
- Hepatobiliary Surgery Institute, Southwest Hospital, Army Medical University, Chongqing 400038, P.R. China
| | - Dajiang Li
- Hepatobiliary Surgery Institute, Southwest Hospital, Army Medical University, Chongqing 400038, P.R. China
| | - Shuguang Wang
- Hepatobiliary Surgery Institute, Southwest Hospital, Army Medical University, Chongqing 400038, P.R. China
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30
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Rogerson C, Britton E, Withey S, Hanley N, Ang YS, Sharrocks AD. Identification of a primitive intestinal transcription factor network shared between esophageal adenocarcinoma and its precancerous precursor state. Genome Res 2019; 29:723-736. [PMID: 30962179 PMCID: PMC6499311 DOI: 10.1101/gr.243345.118] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 04/03/2019] [Indexed: 02/07/2023]
Abstract
Esophageal adenocarcinoma (EAC) is one of the most frequent causes of cancer death, and yet compared to other common cancers, we know relatively little about the molecular composition of this tumor type. To further our understanding of this cancer, we have used open chromatin profiling to decipher the transcriptional regulatory networks that are operational in EAC. We have uncovered a transcription factor network that is usually found in primitive intestinal cells during embryonic development, centered on HNF4A and GATA6. These transcription factors work together to control the EAC transcriptome. We show that this network is activated in Barrett's esophagus, the putative precursor state to EAC, thereby providing novel molecular evidence in support of stepwise malignant transition. Furthermore, we show that HNF4A alone is sufficient to drive chromatin opening and activation of a Barrett's-like chromatin signature when expressed in normal human epithelial cells. Collectively, these data provide a new way to categorize EAC at a genome scale and implicate HNF4A activation as a potential pivotal event in its malignant transition from healthy cells.
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Affiliation(s)
- Connor Rogerson
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, United Kingdom
| | - Edward Britton
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, United Kingdom
| | - Sarah Withey
- School of Medical Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Sciences Centre, University of Manchester, Manchester M13 9PT, United Kingdom
| | - Neil Hanley
- School of Medical Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Sciences Centre, University of Manchester, Manchester M13 9PT, United Kingdom.,Endocrinology Department, Central Manchester University Hospitals NHS Foundation Trust, Manchester M13 9WU, United Kingdom
| | - Yeng S Ang
- School of Medical Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Sciences Centre, University of Manchester, Manchester M13 9PT, United Kingdom.,GI Science Centre, Salford Royal NHS FT, University of Manchester, Salford M6 8HD, United Kingdom
| | - Andrew D Sharrocks
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, United Kingdom
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31
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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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32
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Dai W, Li Q, Liu BY, Li YX, Li YY. Differential networking meta-analysis of gastric cancer across Asian and American racial groups. BMC SYSTEMS BIOLOGY 2018; 12:51. [PMID: 29745833 PMCID: PMC5998874 DOI: 10.1186/s12918-018-0564-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Background Gastric Carcinoma is one of the most lethal cancer around the world, and is also the most common cancers in Eastern Asia. A lot of differentially expressed genes have been detected as being associated with Gastric Carcinoma (GC) progression, however, little is known about the underlying dysfunctional regulation mechanisms. To address this problem, we previously developed a differential networking approach that is characterized by involving differential coexpression analysis (DCEA), stage-specific gene regulatory network (GRN) modelling and differential regulation networking (DRN) analysis. Result In order to implement differential networking meta-analysis, we developed a novel framework which integrated the following steps. Considering the complexity and diversity of gastric carcinogenesis, we first collected three datasets (GSE54129, GSE24375 and TCGA-STAD) for Chinese, Korean and American, and aimed to investigate the common dysregulation mechanisms of gastric carcinogenesis across racial groups. Then, we constructed conditional GRNs for gastric cancer corresponding to normal and carcinoma, and prioritized differentially regulated genes (DRGs) and gene links (DRLs) from three datasets separately by using our previously developed differential networking method. Based on our integrated differential regulation information from three datasets and prior knowledge (e.g., transcription factor (TF)-target regulatory relationships and known signaling pathways), we eventually generated testable hypotheses on the regulation mechanisms of two genes, XBP1 and GIF, out of 16 common cross-racial DRGs in gastric carcinogenesis. Conclusion The current cross-racial integrative study from the viewpoint of differential regulation networking provided useful clues for understanding the common dysfunctional regulation mechanisms of gastric cancer progression and discovering new universal drug targets or biomarkers for gastric cancer. Electronic supplementary material The online version of this article (10.1186/s12918-018-0564-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Wentao Dai
- Shanghai Center for Bioinformation Technology, 1278 Keyuan Road, Shanghai, 201203, People's Republic of China.,Shanghai Engineering Research Center of Pharmaceutical Translation & Shanghai Industrial Technology Institute, 1278 Keyuan Road, Shanghai, 201203, People's Republic of China
| | - Quanxue Li
- Shanghai Center for Bioinformation Technology, 1278 Keyuan Road, Shanghai, 201203, People's Republic of China.,School of biotechnology, East China University of Science and Technology, Shanghai, 200237, China
| | - Bing-Ya Liu
- Shanghai Key Laboratory of Gastric Neoplasms, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, People's Republic of China
| | - Yi-Xue Li
- Shanghai Center for Bioinformation Technology, 1278 Keyuan Road, Shanghai, 201203, People's Republic of China. .,School of biotechnology, East China University of Science and Technology, Shanghai, 200237, China. .,Shanghai Engineering Research Center of Pharmaceutical Translation & Shanghai Industrial Technology Institute, 1278 Keyuan Road, Shanghai, 201203, People's Republic of China. .,Key Lab of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China.
| | - Yuan-Yuan Li
- Shanghai Center for Bioinformation Technology, 1278 Keyuan Road, Shanghai, 201203, People's Republic of China. .,School of biotechnology, East China University of Science and Technology, Shanghai, 200237, China. .,Shanghai Engineering Research Center of Pharmaceutical Translation & Shanghai Industrial Technology Institute, 1278 Keyuan Road, Shanghai, 201203, People's Republic of China. .,Key Lab of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China.
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33
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Aberrant GATA2 epigenetic dysregulation induces a GATA2/GATA6 switch in human gastric cancer. Oncogene 2017; 37:993-1004. [PMID: 29106391 DOI: 10.1038/onc.2017.397] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 08/08/2017] [Accepted: 09/15/2017] [Indexed: 02/07/2023]
Abstract
Six GATA transcription factors play important roles in eukaryotic development. Among these, GATA2, an essential factor for the hematopoietic cell lineage, exhibits low expression in human gastric tissues, whereas GATA6, which is crucial for gastrointestinal development and differentiation, is frequently amplified and/or overexpressed in human gastric cancer. Interestingly, we found that GATA6 was overexpressed in human gastric cancer cells only when GATA2 expression was completely absent, thereby showing an inverse correlation between GATA2 and GATA6. In gastric cancer cells that express high GATA6 levels, a GATA2 CpG island is hypermethylated, repressing expression in these cells. In contrast, GATA6 expression is undetectable in GATA2-overexpressing gastric cancer cells, which lack GATA2 DNA methylation. Furthermore, PRC2 complex-mediated transcriptional silencing of GATA6 was observed in the GATA2-overexpressing cells. We also show that the GATA2 and PRC2 complexes are enriched within the GATA6 locus, and that the recruitment of the PRC2 complex is impaired by disrupting GATA2 expression, resulting in GATA6 upregulation. In addition, ectopic GATA2 expression significantly downregulates GATA6 expression, suggesting GATA2 directly represses GATA6. Furthermore, GATA6 downregulation showed antitumor activity by inducing growth arrest. Finally, we show that aberrant GATA2 methylation occurs early during the multistep process of gastric carcinogenesis regardless of Helicobacter pylori infection. Taken together, GATA2 dysregulation by epigenetic modification is associated with unfavorable phenotypes in human gastric cancer cells by allowing GATA6 expression.
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34
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Clinical study of genomic drivers in pancreatic ductal adenocarcinoma. Br J Cancer 2017; 117:572-582. [PMID: 28720843 PMCID: PMC5558689 DOI: 10.1038/bjc.2017.209] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Revised: 05/18/2017] [Accepted: 06/12/2017] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Pancreatic ductal adenocarcinoma (PDA) is a lethal cancer with complex genomes and dense fibrotic stroma. This study was designed to identify clinically relevant somatic aberrations in pancreatic cancer genomes of patients with primary and metastatic disease enrolled and treated in two clinical trials. METHODS Tumour nuclei were flow sorted prior to whole genome copy number variant (CNV) analysis. Targeted or whole exome sequencing was performed on most samples. We profiled biopsies from 68 patients enrolled in two Stand Up to Cancer (SU2C)-sponsored clinical trials. These included 38 resected chemoradiation naïve tumours (SU2C 20206-003) and metastases from 30 patients who progressed on prior therapies (SU2C 20206-001). Patient outcomes including progression-free survival (PFS) and overall survival (OS) were observed. RESULTS We defined: (a) CDKN2A homozygous deletions that included the adjacent MTAP gene, only its' 3' region, or excluded MTAP; (b) SMAD4 homozygous deletions that included ME2; (c) a pancreas-specific MYC super-enhancer region; (d) DNA repair-deficient genomes; and (e) copy number aberrations present in PDA patients with long-term (⩾ 40 months) and short-term (⩽ 12 months) survival after surgical resection. CONCLUSIONS We provide a clinically relevant framework for genomic drivers of PDA and for advancing novel treatments.
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35
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Park J, Yoo HM, Jang W, Shin S, Kim M, Kim Y, Lee SW, Kim JG. Distribution of somatic mutations of cancer-related genes according to microsatellite instability status in Korean gastric cancer. Medicine (Baltimore) 2017; 96:e7224. [PMID: 28640116 PMCID: PMC5484224 DOI: 10.1097/md.0000000000007224] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
In studies of the molecular basis of gastric cancer (GC), microsatellite instability (MSI) is one of the key factors. Somatic mutations found in GC are expected to contribute to MSI-high (H) tumorigenesis. We estimated somatic mutation distribution according to MSI status in 52 matched pair GC samples using the Ion Torrent Ion S5 XL with the AmpliSeq Cancer Hotspot panel.Seventy-five (9.8%) somatic variants consisting of 34 hotspot mutations and 41 other likely pathogenic variants were identified in 34 GC samples. The TP53 mutations was most common (35%, 26/75), followed by EGFR (8%, 6/75), HNF1A (8%, 6/75), PIK3CA (8%, 6/75), and ERBB2 (5%, 4/75). To determine MSI status, 52 matched pair samples were estimated using 15 MSI markers. Thirty-nine MS stable (S), 5 MSI-low (L), and 8 MSI-H were classified. GCs with MSI-H tended to have more variants significantly compared with GCs with MS stable (MSS) and MSI-L (standardized J-T statistic = 3.161 for number of variants; P = .002). The mean number of all variants and hotspot mutations per tumor samples only in GCs with MSI-H were 3.9 (range, 1-6) and 1.1 (range, 0-3), respectively. Whereas, the mean number of all variants and hotspot mutations per tumor samples only in GCs with MSS/MSI-L were 1 (0-5)/0.8 (0-1) and 0.5 (0-3)/0.8 (0-1), respectively.In conclusion, GC with MSI-H harbored more mutations in genes that act as a tumor suppressor or oncogene compared to GC with MSS/MSI-L. This finding suggests that the accumulation of MSIs contributes to the genetic diversity and complexities of GC. In addition, targeted NGS approach allows for detection of common and also rare clinically actionable mutations and profiles of comutations in multiple patients simultaneously. Because GC shows distinctive patterns related to ethnics, further studies pertaining to different racial/ethnic groups or cancer types may reinforce our investigations.
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Affiliation(s)
| | - Han Mo Yoo
- Division of Gastrointestinal Surgery, Department of Surgery
| | | | | | | | | | - Seung-Woo Lee
- Division of Gastroenterology, Department of Internal Medicine, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Jeong Goo Kim
- Division of Gastrointestinal Surgery, Department of Surgery
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36
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Ciucci S, Ge Y, Durán C, Palladini A, Jiménez-Jiménez V, Martínez-Sánchez LM, Wang Y, Sales S, Shevchenko A, Poser SW, Herbig M, Otto O, Androutsellis-Theotokis A, Guck J, Gerl MJ, Cannistraci CV. Enlightening discriminative network functional modules behind Principal Component Analysis separation in differential-omic science studies. Sci Rep 2017; 7:43946. [PMID: 28287094 PMCID: PMC5347127 DOI: 10.1038/srep43946] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 02/06/2017] [Indexed: 01/08/2023] Open
Abstract
Omic science is rapidly growing and one of the most employed techniques to explore differential patterns in omic datasets is principal component analysis (PCA). However, a method to enlighten the network of omic features that mostly contribute to the sample separation obtained by PCA is missing. An alternative is to build correlation networks between univariately-selected significant omic features, but this neglects the multivariate unsupervised feature compression responsible for the PCA sample segregation. Biologists and medical researchers often prefer effective methods that offer an immediate interpretation to complicated algorithms that in principle promise an improvement but in practice are difficult to be applied and interpreted. Here we present PC-corr: a simple algorithm that associates to any PCA segregation a discriminative network of features. Such network can be inspected in search of functional modules useful in the definition of combinatorial and multiscale biomarkers from multifaceted omic data in systems and precision biomedicine. We offer proofs of PC-corr efficacy on lipidomic, metagenomic, developmental genomic, population genetic, cancer promoteromic and cancer stem-cell mechanomic data. Finally, PC-corr is a general functional network inference approach that can be easily adopted for big data exploration in computer science and analysis of complex systems in physics.
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Affiliation(s)
- Sara Ciucci
- Biomedical Cybernetics Group, Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering (CMCB), Department of Physics, Technische Universität Dresden, Tatzberg 47/49, 01307 Dresden, Germany.,Lipotype GmbH, Tatzberg 47, 01307 Dresden, Germany
| | - Yan Ge
- Biomedical Cybernetics Group, Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering (CMCB), Department of Physics, Technische Universität Dresden, Tatzberg 47/49, 01307 Dresden, Germany
| | - Claudio Durán
- Biomedical Cybernetics Group, Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering (CMCB), Department of Physics, Technische Universität Dresden, Tatzberg 47/49, 01307 Dresden, Germany
| | - Alessandra Palladini
- Biomedical Cybernetics Group, Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering (CMCB), Department of Physics, Technische Universität Dresden, Tatzberg 47/49, 01307 Dresden, Germany.,Lipotype GmbH, Tatzberg 47, 01307 Dresden, Germany.,Membrane Biochemistry Group, DZD Paul Langerhans Institute, Technische Universität Dresden, Tatzberg 47/49, 01307 Dresden, Germany
| | - Víctor Jiménez-Jiménez
- Integrin Signalling Group, Fundación Centro Nacional de Investigaciones Cardiovasculares Carlos III, Melchor Fernández Almagro 3, 28029 Madrid, Spain
| | - Luisa María Martínez-Sánchez
- Biomedical Cybernetics Group, Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering (CMCB), Department of Physics, Technische Universität Dresden, Tatzberg 47/49, 01307 Dresden, Germany
| | - Yuting Wang
- MPI of Molecular Cell Biology and Genetics, Pfotenhauerstrstraße 108, 01307 Dresden, Germany.,Center for Regenerative Therapies Dresden (CRTD), Center for Molecular and Cellular Bioengineering (CMCB), Technische Universität Dresden, Fetscherstraße 105, 01307 Dresden, Germany
| | - Susanne Sales
- MPI of Molecular Cell Biology and Genetics, Pfotenhauerstrstraße 108, 01307 Dresden, Germany
| | - Andrej Shevchenko
- MPI of Molecular Cell Biology and Genetics, Pfotenhauerstrstraße 108, 01307 Dresden, Germany
| | - Steven W Poser
- Department of Internal Medicine III, University Hospital Carl Gustav Carus at the Technische Universität Dresden, Fetscherstr.74, 01307 Dresden, Germany
| | - Maik Herbig
- Cellular Machines Group, Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering (CMCB), Technische Universität Dresden, Tatzberg 47/49, 01307 Dresden, Germany
| | - Oliver Otto
- Cellular Machines Group, Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering (CMCB), Technische Universität Dresden, Tatzberg 47/49, 01307 Dresden, Germany
| | - Andreas Androutsellis-Theotokis
- Center for Regenerative Therapies Dresden (CRTD), Center for Molecular and Cellular Bioengineering (CMCB), Technische Universität Dresden, Fetscherstraße 105, 01307 Dresden, Germany.,Department of Internal Medicine III, University Hospital Carl Gustav Carus at the Technische Universität Dresden, Fetscherstr.74, 01307 Dresden, Germany.,Department of Stem Cell Biology, Centre for Biomolecular Sciences, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham NG7 2RD, U.K
| | - Jochen Guck
- Cellular Machines Group, Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering (CMCB), Technische Universität Dresden, Tatzberg 47/49, 01307 Dresden, Germany
| | | | - Carlo Vittorio Cannistraci
- Biomedical Cybernetics Group, Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering (CMCB), Department of Physics, Technische Universität Dresden, Tatzberg 47/49, 01307 Dresden, Germany
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37
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Li Q, Li J, Dai W, Li YX, Li YY. Differential regulation analysis reveals dysfunctional regulatory mechanism involving transcription factors and microRNAs in gastric carcinogenesis. Artif Intell Med 2017; 77:12-22. [PMID: 28545608 DOI: 10.1016/j.artmed.2017.02.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Revised: 02/23/2017] [Accepted: 02/23/2017] [Indexed: 12/12/2022]
Abstract
Gastric cancer (GC) is one of the most incident malignancies in the world. Although lots of featured genes and microRNAs (miRNAs) have been identified to be associated with gastric carcinogenesis, underlying regulatory mechanisms still remain unclear. In order to explore the dysfunctional mechanisms of GC, we developed a novel approach to identify carcinogenesis relevant regulatory relationships, which is characterized by quantifying the difference of regulatory relationships between stages. Firstly, we applied the strategy of differential coexpression analysis (DCEA) to transcriptomic datasets including paired mRNA and miRNA of gastric samples to identify a set of genes/miRNAs related to gastric cancer progression. Based on these genes/miRNAs, we constructed conditional combinatorial gene regulatory networks (cGRNs) involving both transcription factors (TFs) and miRNAs. Enrichment of known cancer genes/miRNAs and predicted prognostic genes/miRNAs was observed in each cGRN. Then we designed a quantitative method to measure differential regulation level of every regulatory relationship between normal and cancer, and the known cancer genes/miRNAs proved to be ranked significantly higher. Meanwhile, we defined differentially regulated link (DRL) by combining differential regulation, differential expression and the regulation contribution of the regulator to the target. By integrating survival analysis and DRL identification, three master regulators TCF7L1, TCF4, and MEIS1 were identified and testable hypotheses of dysfunctional mechanisms underlying gastric carcinogenesis related to them were generated. The fine-tuning effects of miRNAs were also observed. We propose that this differential regulation network analysis framework is feasible to gain insights into dysregulated mechanisms underlying tumorigenesis and other phenotypic changes.
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Affiliation(s)
- Quanxue Li
- School of biotechnology, East China University of Science and Technology, Shanghai, China; Shanghai Center for Bioinformation Technology, Shanghai, China
| | - Junyi Li
- Shanghai Center for Bioinformation Technology, Shanghai, China; Key Lab of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Wentao Dai
- Shanghai Center for Bioinformation Technology, Shanghai, China; Shanghai Industrial Technology Institute, Shanghai, China; Shanghai Engineering Research Center of Pharmaceutical Translation, Shanghai, China
| | - Yi-Xue Li
- School of biotechnology, East China University of Science and Technology, Shanghai, China; Shanghai Center for Bioinformation Technology, Shanghai, China; Key Lab of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China; Shanghai Industrial Technology Institute, Shanghai, China; Shanghai Engineering Research Center of Pharmaceutical Translation, Shanghai, China.
| | - Yuan-Yuan Li
- Shanghai Center for Bioinformation Technology, Shanghai, China; Shanghai Industrial Technology Institute, Shanghai, China; Shanghai Engineering Research Center of Pharmaceutical Translation, Shanghai, China.
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38
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Wang AB, Zhang YV, Tumbar T. Gata6 promotes hair follicle progenitor cell renewal by genome maintenance during proliferation. EMBO J 2016; 36:61-78. [PMID: 27908934 DOI: 10.15252/embj.201694572] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2016] [Revised: 09/30/2016] [Accepted: 10/28/2016] [Indexed: 01/29/2023] Open
Abstract
Cell proliferation is essential to rapid tissue growth and repair, but can result in replication-associated genome damage. Here, we implicate the transcription factor Gata6 in adult mouse hair follicle regeneration where it controls the renewal of rapidly proliferating epithelial (matrix) progenitors and hence the extent of production of terminally differentiated lineages. We find that Gata6 protects against DNA damage associated with proliferation, thus preventing cell cycle arrest and apoptosis. Furthermore, we show that in vivo Gata6 stimulates EDA-receptor signaling adaptor Edaradd level and NF-κB pathway activation, known to be important for DNA damage repair and stress response in general and for hair follicle growth in particular. In cultured keratinocytes, Edaradd rescues DNA damage, cell survival, and proliferation of Gata6 knockout cells and restores MCM10 expression. Our data add to recent evidence in embryonic stem and neural progenitor cells, suggesting a model whereby developmentally regulated transcription factors protect from DNA damage associated with proliferation at key stages of rapid tissue growth. Our data may add to understanding why Gata6 is a frequent target of amplification in cancers.
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Affiliation(s)
- Alex B Wang
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Ying V Zhang
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Tudorita Tumbar
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
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39
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Cejas P, Cavazza A, Yandava CN, Moreno V, Horst D, Moreno-Rubio J, Burgos E, Mendiola M, Taing L, Goel A, Feliu J, Shivdasani RA. Transcriptional Regulator CNOT3 Defines an Aggressive Colorectal Cancer Subtype. Cancer Res 2016; 77:766-779. [PMID: 27899379 DOI: 10.1158/0008-5472.can-16-1346] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Revised: 10/26/2016] [Accepted: 11/05/2016] [Indexed: 01/05/2023]
Abstract
Cancer cells exhibit dramatic alterations of chromatin organization at cis-regulatory elements, but the molecular basis, extent, and impact of these alterations are still being unraveled. Here, we identify extensive genome-wide modification of sites bearing the active histone mark H3K4me2 in primary human colorectal cancers, as compared with corresponding benign precursor adenomas. Modification of certain colorectal cancer sites highlighted the activity of the transcription factor CNOT3, which is known to control self-renewal of embryonic stem cells (ESC). In primary colorectal cancer cells, we observed a scattered pattern of CNOT3 expression, as might be expected for a tumor-initiating cell marker. Colorectal cancer cells exhibited nuclear and cytoplasmic expression of CNOT3, suggesting possible roles in both transcription and mRNA stability. We found that CNOT3 was bound primarily to genes whose expression was affected by CNOT3 loss, and also at sites modulated in certain types of colorectal cancers. These target genes were implicated in ESC and cancer self-renewal and fell into two distinct groups: those dependent on CNOT3 and MYC for optimal transcription and those repressed by CNOT3 binding and promoter hypermethylation. Silencing CNOT3 in colorectal cancer cells resulted in replication arrest. In clinical specimens, early-stage tumors that included >5% CNOT3+ cells exhibited a correlation to worse clinical outcomes compared with tumors with little to no CNOT3 expression. Together, our findings implicate CNOT3 in the coordination of colonic epithelial cell self-renewal, suggesting this factor as a new biomarker for molecular and prognostic classification of early-stage colorectal cancer. Cancer Res; 77(3); 766-79. ©2016 AACR.
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Affiliation(s)
- Paloma Cejas
- Department of Medical Oncology and Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts.,Department of Medical Oncology, Hospital La Paz Institute for Health Research CIBERONC, Madrid, Spain
| | - Alessia Cavazza
- Department of Medical Oncology and Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - C N Yandava
- Department of Medical Oncology and Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Victor Moreno
- Department of Medical Oncology, Hospital La Paz Institute for Health Research CIBERONC, Madrid, Spain
| | - David Horst
- Pathology Institute, Ludwig-Maximilians-Universitat, Munich, Germany
| | - Juan Moreno-Rubio
- Department of Medical Oncology, Hospital La Paz Institute for Health Research CIBERONC, Madrid, Spain
| | - Emilio Burgos
- Department of Pathology, Hospital La Paz Institute for Health Research, Madrid, Spain
| | - Marta Mendiola
- Department of Medical Oncology, Hospital La Paz Institute for Health Research CIBERONC, Madrid, Spain.,Department of Pathology, Hospital La Paz Institute for Health Research, Madrid, Spain
| | - Len Taing
- Department of Medical Oncology and Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Ajay Goel
- Center for Gastrointestinal Cancer Research, Baylor University Medical Center, Dallas, Texas
| | - Jaime Feliu
- Department of Medical Oncology, Hospital La Paz Institute for Health Research CIBERONC, Madrid, Spain
| | - Ramesh A Shivdasani
- Department of Medical Oncology and Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts. .,Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
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40
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Sarkar A, Huebner AJ, Sulahian R, Anselmo A, Xu X, Flattery K, Desai N, Sebastian C, Yram MA, Arnold K, Rivera M, Mostoslavsky R, Bronson R, Bass AJ, Sadreyev R, Shivdasani RA, Hochedlinger K. Sox2 Suppresses Gastric Tumorigenesis in Mice. Cell Rep 2016; 16:1929-41. [PMID: 27498859 DOI: 10.1016/j.celrep.2016.07.034] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Revised: 03/22/2016] [Accepted: 07/14/2016] [Indexed: 01/10/2023] Open
Abstract
Sox2 expression marks gastric stem and progenitor cells, raising important questions regarding the genes regulated by Sox2 and the role of Sox2 itself during stomach homeostasis and disease. By using ChIP-seq analysis, we have found that the majority of Sox2 targets in gastric epithelial cells are tissue specific and related to functions such as endoderm development, Wnt signaling, and gastric cancer. Unexpectedly, we found that Sox2 itself is dispensable for gastric stem cell and epithelial self-renewal, yet Sox2(+) cells are highly susceptible to tumorigenesis in an Apc/Wnt-driven mouse model. Moreover, Sox2 loss enhances, rather than impairs, tumor formation in Apc-deficient gastric cells in vivo and in vitro by inducing Tcf/Lef-dependent transcription and upregulating intestinal metaplasia-associated genes, providing a mechanistic basis for the observed phenotype. Together, these data identify Sox2 as a context-dependent tumor suppressor protein that is dispensable for normal tissue regeneration but restrains stomach adenoma formation through modulation of Wnt-responsive and intestinal genes.
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Affiliation(s)
- Abby Sarkar
- Cancer Center and Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Howard Hughes Medical Institute and Department of Stem Cell and Regenerative Biology, 7 Divinity Avenue, Harvard University, Cambridge, MA 02138, USA
| | - Aaron J Huebner
- Cancer Center and Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Howard Hughes Medical Institute and Department of Stem Cell and Regenerative Biology, 7 Divinity Avenue, Harvard University, Cambridge, MA 02138, USA
| | - Rita Sulahian
- Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Anthony Anselmo
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Xinsen Xu
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Kyle Flattery
- Cancer Center and Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Howard Hughes Medical Institute and Department of Stem Cell and Regenerative Biology, 7 Divinity Avenue, Harvard University, Cambridge, MA 02138, USA
| | - Niyati Desai
- Division of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Carlos Sebastian
- Cancer Center and Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Mary Anna Yram
- Cancer Center and Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Howard Hughes Medical Institute and Department of Stem Cell and Regenerative Biology, 7 Divinity Avenue, Harvard University, Cambridge, MA 02138, USA
| | - Katrin Arnold
- Cancer Center and Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Howard Hughes Medical Institute and Department of Stem Cell and Regenerative Biology, 7 Divinity Avenue, Harvard University, Cambridge, MA 02138, USA
| | - Miguel Rivera
- Division of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Raul Mostoslavsky
- Cancer Center and Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Roderick Bronson
- Department of Pathology, Harvard Medical School, Boston, MA 02115, USA
| | - Adam J Bass
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Ruslan Sadreyev
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Ramesh A Shivdasani
- Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Konrad Hochedlinger
- Cancer Center and Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Howard Hughes Medical Institute and Department of Stem Cell and Regenerative Biology, 7 Divinity Avenue, Harvard University, Cambridge, MA 02138, USA.
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41
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Mori F, Sacconi A, Canu V, Ganci F, Novello M, Anelli V, Covello R, Ferraresi V, Muti P, Biagini R, Blandino G, Strano S. miR-181c associates with tumor relapse of high grade osteosarcoma. Oncotarget 2016; 6:13946-61. [PMID: 26062442 PMCID: PMC4546443 DOI: 10.18632/oncotarget.3539] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Accepted: 02/17/2015] [Indexed: 11/25/2022] Open
Abstract
High-grade osteosarcoma (OS) is characterized by low incidence, high aggressiveness and moderate 5-years survival rate after aggressive poly-chemotherapy and surgery. Here we used miRNA profiling as a tool to possibly predict and monitor OS's development and therapeutic outcome. First, we evaluated the altered expression of selected miRNAs from a case of Giant Cell Tumor (GCT) apparently evolved into an OS. We found that most of modulated miRs were associated with pathways of bone resorption and osteogenesis. miRNA expression also revealed that GCT and OS were distinct tumors. Second, we validated the observed miRNA profile in two independent casuistries of ten GCT (not evolved into malignant tumors) and sixteen OS patients. Interestingly, we found that miR-181c and other three miRNAs identified in the first step of the study were also consistently de-regulated in all OS patients. Ectopic expression of miR-181c reduced cell viability and enhanced chemotherapeutic-induced cell death of U2OS and SAOS2 cells. These findings indicate that: i) miRNAs aberrantly modulated in GCT could be predictive of its development into OS and ii) miRNAs expression could be useful to monitor the OS therapeutic outcome.
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Affiliation(s)
- Federica Mori
- Molecular Chemoprevention Unit, Regina Elena National Cancer Institute, Rome, Italy
| | - Andrea Sacconi
- Translational Oncogenomics, Regina Elena National Cancer Institute, Rome, Italy
| | - Valeria Canu
- Translational Oncogenomics, Regina Elena National Cancer Institute, Rome, Italy
| | - Federica Ganci
- Translational Oncogenomics, Regina Elena National Cancer Institute, Rome, Italy
| | | | - Vincenzo Anelli
- UOC Radiology, Regina Elena National Cancer Institute, Rome, Italy
| | - Renato Covello
- UOC Department of Pathology, Regina Elena National Cancer Institute, Rome, Italy
| | | | - Paola Muti
- Department of Oncology, McMaster University, Hamilton, ON, Canada
| | - Roberto Biagini
- UOC Orthopedic Surgery, Regina Elena National Cancer Institute, Rome, Italy
| | - Giovanni Blandino
- Translational Oncogenomics, Regina Elena National Cancer Institute, Rome, Italy.,Department of Oncology, McMaster University, Hamilton, ON, Canada
| | - Sabrina Strano
- Molecular Chemoprevention Unit, Regina Elena National Cancer Institute, Rome, Italy.,Department of Oncology, McMaster University, Hamilton, ON, Canada
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42
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Hayakawa Y, Sethi N, Sepulveda AR, Bass AJ, Wang TC. Oesophageal adenocarcinoma and gastric cancer: should we mind the gap? Nat Rev Cancer 2016; 16:305-18. [PMID: 27112208 DOI: 10.1038/nrc.2016.24] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Over recent decades we have witnessed a shift in the anatomical distribution of gastric cancer (GC), which increasingly originates from the proximal stomach near the junction with the oesophagus. In parallel, there has been a dramatic rise in the incidence of oesophageal adenocarcinoma (OAC) in the lower oesophagus, which is associated with antecedent Barrett oesophagus (BO). In this context, there has been uncertainty regarding the characterization of adenocarcinomas spanning the area from the lower oesophagus to the distal stomach. Most relevant to this discussion is the distinction, if any, between OAC and intestinal-type GC of the proximal stomach. It is therefore timely to review our current understanding of OAC and intestinal-type GC, integrating advances from cell-of-origin studies and comprehensive genomic alteration analyses, ultimately enabling better insight into the relationship between these two cancers.
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Affiliation(s)
- Yoku Hayakawa
- Division of Digestive and Liver Diseases and Herbert Irving Cancer Research Center, Columbia University College of Physicians and Surgeons, 1130 St Nicholas Avenue, New York, New York 10032, USA
| | - Nilay Sethi
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215, USA
| | - Antonia R Sepulveda
- Division of Clinical Pathology and Cell Biology, Department of Pathology, Columbia University College of Physicians and Surgeons, New York, New York 10032, USA
| | - Adam J Bass
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215, USA
| | - Timothy C Wang
- Division of Digestive and Liver Diseases and Herbert Irving Cancer Research Center, Columbia University College of Physicians and Surgeons, 1130 St Nicholas Avenue, New York, New York 10032, USA
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43
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Abstract
The Database of Human Gastric Cancer (DBGC) is a comprehensive database that integrates various human gastric cancer-related data resources. Human gastric cancer-related transcriptomics projects, proteomics projects, mutations, biomarkers and drug-sensitive genes from different sources were collected and unified in this database. Moreover, epidemiological statistics of gastric cancer patients in China and clinicopathological information annotated with gastric cancer cases were also integrated into the DBGC. We believe that this database will greatly facilitate research regarding human gastric cancer in many fields. DBGC is freely available at http://bminfor.tongji.edu.cn/dbgc/index.do
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44
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A loss-of-function and H2B-Venus transcriptional reporter allele for Gata6 in mice. BMC DEVELOPMENTAL BIOLOGY 2015; 15:38. [PMID: 26498761 PMCID: PMC4619391 DOI: 10.1186/s12861-015-0086-5] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Accepted: 10/09/2015] [Indexed: 12/03/2022]
Abstract
Background The GATA-binding factor 6 (Gata6) gene encodes a zinc finger transcription factor that often functions as a key regulator of lineage specification during development. It is the earliest known marker of the primitive endoderm lineage in the mammalian blastocyst. During gastrulation, GATA6 is expressed in early cardiac mesoderm and definitive endoderm progenitors, and is necessary for development of specific mesoderm and endoderm-derived organs including the heart, liver, and pancreas. Furthermore, reactivation or silencing of the Gata6 locus has been associated with certain types of cancer affecting endodermal organs. Results We have generated a Gata6H2B-Venus knock-in reporter mouse allele for the purpose of labeling GATA6-expressing cells with a bright nuclear-localized fluorescent marker that is suitable for live imaging at single-cell resolution. Conclusions Expression of the Venus reporter was characterized starting from embryonic stem (ES) cells, through mouse embryos and adult animals. The Venus reporter was not expressed in ES cells, but was activated upon endoderm differentiation. Gata6H2B-Venus/H2B-Venus homozygous embryos did not express GATA6 protein and failed to specify the primitive endoderm in the blastocyst. However, null blastocysts continued to express high levels of Venus in the absence of GATA6 protein, suggesting that early Gata6 transcription is independent of GATA6 protein expression. At early post-implantation stages of embryonic development, there was a strong correlation of Venus with endogenous GATA6 protein in endoderm and mesoderm progenitors, then later in the heart, midgut, and hindgut. However, there were discrepancies in reporter versus endogenous protein expression in certain cells, such as the body wall and endocardium. During organogenesis, detection of Venus in specific organs recapitulated known sites of endogenous GATA6 expression, such as in the lung bud epithelium, liver, pancreas, gall bladder, stomach epithelium, and vascular endothelium. In adults, Venus was observed in the lungs, pancreas, liver, gall bladder, ovaries, uterus, bladder, skin, adrenal glands, small intestine and corpus region of the stomach. Overall, Venus fluorescent protein under regulatory control of the Gata6 locus was expressed at levels that were easily visualized directly and could endure live and time-lapse imaging techniques. Venus is co-expressed with endogenous GATA6 throughout development to adulthood, and should provide an invaluable tool for examining the status of the Gata6 locus during development, as well as its silencing or reactivation in cancer or other disease states. Electronic supplementary material The online version of this article (doi:10.1186/s12861-015-0086-5) contains supplementary material, which is available to authorized users.
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45
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Tan P, Yeoh KG. Genetics and Molecular Pathogenesis of Gastric Adenocarcinoma. Gastroenterology 2015; 149:1153-1162.e3. [PMID: 26073375 DOI: 10.1053/j.gastro.2015.05.059] [Citation(s) in RCA: 324] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Revised: 05/18/2015] [Accepted: 05/20/2015] [Indexed: 02/07/2023]
Abstract
Gastric cancer (GC) is globally the fifth most common cancer and third leading cause of cancer death. A complex disease arising from the interaction of environmental and host-associated factors, key contributors to GC's high mortality include its silent nature, late clinical presentation, and underlying biological and genetic heterogeneity. Achieving a detailed molecular understanding of the various genomic aberrations associated with GC will be critical to improving patient outcomes. The recent years has seen considerable progress in deciphering the genomic landscape of GC, identifying new molecular components such as ARID1A and RHOA, cellular pathways, and tissue populations associated with gastric malignancy and progression. The Cancer Genome Atlas (TCGA) project is a landmark in the molecular characterization of GC. Key challenges for the future will involve the translation of these molecular findings to clinical utility, by enabling novel strategies for early GC detection, and precision therapies for individual GC patients.
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Affiliation(s)
- Patrick Tan
- Cancer and Stem Cell Biology Program, Duke-National University of Singapore Graduate Medical School, Singapore; Genome Institute of Singapore, Agency for Science, Technology, and Research, Singapore; Cancer Science Institute of Singapore, National University of Singapore, Singapore; Cellular and Molecular Research, National Cancer Centre Singapore, Singapore; Singapore Gastric Cancer Consortium, Singapore.
| | - Khay-Guan Yeoh
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Department of Gastroenterology and Hepatology, National University Health System, Singapore; Singapore Gastric Cancer Consortium, Singapore.
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46
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Cao MS, Liu BY, Dai WT, Zhou WX, Li YX, Li YY. Differential network analysis reveals dysfunctional regulatory networks in gastric carcinogenesis. Am J Cancer Res 2015; 5:2605-2625. [PMID: 26609471 PMCID: PMC4633893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Accepted: 08/04/2015] [Indexed: 06/05/2023] Open
Abstract
Gastric Carcinoma is one of the most common cancers in the world. A large number of differentially expressed genes have been identified as being associated with gastric cancer progression, however, little is known about the underlying regulatory mechanisms. To address this problem, we developed a differential networking approach that is characterized by including a nascent methodology, differential coexpression analysis (DCEA), and two novel quantitative methods for differential regulation analysis. We first applied DCEA to a gene expression dataset of gastric normal mucosa, adenoma and carcinoma samples to identify gene interconnection changes during cancer progression, based on which we inferred normal, adenoma, and carcinoma-specific gene regulation networks by using linear regression model. It was observed that cancer genes and drug targets were enriched in each network. To investigate the dynamic changes of gene regulation during carcinogenesis, we then designed two quantitative methods to prioritize differentially regulated genes (DRGs) and gene pairs or links (DRLs) between adjacent stages. It was found that known cancer genes and drug targets are significantly higher ranked. The top 4% normal vs. adenoma DRGs (36 genes) and top 6% adenoma vs. carcinoma DRGs (56 genes) proved to be worthy of further investigation to explore their association with gastric cancer. Out of the 16 DRGs involved in two top-10 DRG lists of normal vs. adenoma and adenoma vs. carcinoma comparisons, 15 have been reported to be gastric cancer or cancer related. Based on our inferred differential networking information and known signaling pathways, we generated testable hypotheses on the roles of GATA6, ESRRG and their signaling pathways in gastric carcinogenesis. Compared with established approaches which build genome-scale GRNs, or sub-networks around differentially expressed genes, the present one proved to be better at enriching cancer genes and drug targets, and prioritizing disease-related genes on the dataset we considered. We propose this extendable differential networking framework as a promising way to gain insights into gene regulatory mechanisms underlying cancer progression and other phenotypic changes.
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Affiliation(s)
- Mu-Shui Cao
- School of Life Science and Technology, Tongji UniversityShanghai 200092, P. R. China
- Shanghai Center for Bioinformation TechnologyShanghai 200235, P. R. China
- Shanghai Industrial Technology Institute1278 Keyuan Road, Shanghai 201203, P. R. China
| | - Bing-Ya Liu
- Shanghai Key Laboratory of Gastric Neoplasms, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of MedicineShanghai 200025, P. R. China
| | - Wen-Tao Dai
- Shanghai Center for Bioinformation TechnologyShanghai 200235, P. R. China
- Shanghai Industrial Technology Institute1278 Keyuan Road, Shanghai 201203, P. R. China
| | - Wei-Xin Zhou
- Shanghai Center for Bioinformation TechnologyShanghai 200235, P. R. China
- Shanghai Industrial Technology Institute1278 Keyuan Road, Shanghai 201203, P. R. China
- Shanghai Engineering Research Center of Pharmaceutical Translation1278 Keyuan Road, Shanghai 201203, P. R. China
| | - Yi-Xue Li
- School of Life Science and Technology, Tongji UniversityShanghai 200092, P. R. China
- Shanghai Center for Bioinformation TechnologyShanghai 200235, P. R. China
- Shanghai Industrial Technology Institute1278 Keyuan Road, Shanghai 201203, P. R. China
- Shanghai Engineering Research Center of Pharmaceutical Translation1278 Keyuan Road, Shanghai 201203, P. R. China
| | - Yuan-Yuan Li
- Shanghai Center for Bioinformation TechnologyShanghai 200235, P. R. China
- Shanghai Industrial Technology Institute1278 Keyuan Road, Shanghai 201203, P. R. China
- Shanghai Engineering Research Center of Pharmaceutical Translation1278 Keyuan Road, Shanghai 201203, P. R. China
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47
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Deng L, Liu H. MicroRNA-506 suppresses growth and metastasis of oral squamous cell carcinoma via targeting GATA6. Int J Clin Exp Med 2015; 8:1862-1870. [PMID: 25932114 PMCID: PMC4402761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Accepted: 02/28/2015] [Indexed: 06/04/2023]
Abstract
Oral squamous cell carcinoma (OSCC) remains the main cause of cancer mortality, accounts for 90% of oral cancers. Increasing evidence reveals that aberrant expression of microRNA contributes to the development and progression of OSCC, but the roles of microRNA-506 (miR-506) in OSCC remain elusive. Here, we found that the expression of miR-506 was decreased in 21 OSCC tissues and SCC-4 and SCC-9 cells. miR-506 overexpression suppressed proliferation, migration and invasion capabilities of OSCC cells. Moreover, miR-506 overexpression suppressed the luciferase activity of the GATA6-Wt 3'-UTR and decreased the mRNA and protein levels of GATA6. GATA6 overexpression attenuated the suppressive effects of miR-506. Furthermore, GATA6 was increased in OSCC tissues compared with the adjacent normal tissues and inversely associated with miR-506. Taken together, these results suggest that miR-506 is an important suppressor and could be a novel prognostic factor and therapeutic target for OSCC patients.
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Affiliation(s)
- Li Deng
- Department of Stomatology, Jining NO. 1 People's Hospital Jining 272011, Shandong, China
| | - Hui Liu
- Department of Stomatology, Jining NO. 1 People's Hospital Jining 272011, Shandong, China
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48
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Gautier EL, Yvan-Charvet L. Understanding macrophage diversity at the ontogenic and transcriptomic levels. Immunol Rev 2014; 262:85-95. [DOI: 10.1111/imr.12231] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Emmanuel L. Gautier
- Institut National de la Sante et de la Recherche Médicale UMR_S 1166; Paris France
- Pierre & Marie Curie University Paris 6; Paris France
- ICAN Institute of CArdiometabolism & Nutrition; Paris France
| | - Laurent Yvan-Charvet
- Institut National de la Sante et de la Recherche Médicale U1065; Centre Méditerranéen de Médecine Moléculaire (C3M); Nice France
- Atip-Avenir; Nice France
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