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Zhang J, Wang Y, Hou S, Chi X, Ding D, Xue M, Zhang M, Wang J, Shuai J, Sun H, Gao Q, Kang C. Overexpression of ZNF169 promotes the growth and proliferation of colorectal cancer cells via the upregulation of ANKZF1. Oncol Rep 2024; 51:82. [PMID: 38666541 PMCID: PMC11063753 DOI: 10.3892/or.2024.8741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 04/05/2024] [Indexed: 05/01/2024] Open
Abstract
Colorectal cancer (CRC) is one of the most common malignancies worldwide. The 5‑year survival rate of patients diagnosed with the early stages of the disease is markedly higher than that of patients in the advanced stages. Therefore, identifying novel biomarkers and drug targets for CRC is critical for clinical practice. Zinc finger protein 169 (ZNF169) is a crucial transcription factor, and its role in CRC remains to be explored. The present study aimed to investigate the clinical relevance, function and underlying mechanisms of ZNF169 in CRC growth and proliferation. The Cancer Genome Atlas (TCGA) database was utilized to analyze the clinical relevance of ZNF169 in patients with CRC. Immunohistochemical staining was performed on tissue samples from patients with CRC to detect the expression of ZNF169. The HCT‑116, HT‑29 and RKO cell lines were employed for in vitro experiments. The overexpression and knockdown of ZNF169 were achieved by transfecting the cells with lentivirus and small interfering RNAs, respectively. Cell Counting Kit‑8, colony formation and EdU staining assays were applied to investigate the function of ZNF169 in CRC cells. Dual luciferase activity and chromatin immunoprecipitation (ChIP)‑quantitative PCR (qPCR) assays were performed to identify the regulatory effects of ZNF169 on the ankyrin repeat and zinc‑finger domain‑containing 1 (ANKZF1; also known as ZNF744) gene. Reverse transcription‑quantitative PCR and western blot analysis were performed to measure mRNA and protein expression, respectively. The analysis of TCGA data revealed a positive correlation between ZNF169 and ANKZF1, with the overexpression of ANKZF1 being associated with a poor prognosis of patients with CRC. The experimental results demonstrated that ZNF169 was expression upregulated in CRC tissue compared with that in normal colon tissue. Gain‑of‑function and loss‑of‑function experiments revealed that ZNF169 enhanced the intensity of EdU staining, promoting the growth and proliferation of CRC cells. Furthermore, the overexpression of ZNF169 potentiated the transcriptional activity of the ANKZF1 gene, while the knockdown of ZNF169 produced the opposite results. ChIP‑qPCR confirmed the interaction between ZNF169 and the promoter sequence of ANKZF1. Rescue experiments revealed that ZNF169 accelerated CRC cell growth and proliferation through the upregulation of ANKZF1. Furthermore, there was a positive correlation identified between ZNF169 and ANKZF1, and upregulation of ANKZF1 expression was associated with the poor prognosis of patients with CRC. On the whole, the present study demonstrates that ZNF169 contributes to CRC malignancy by potentiating the expression of ANKZF1. Thus, the regulation of ZNF169 and/or ANKZF1 expression may represent a viable strategy for the treatment patients with CRC with a high expression of ZNF169.
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Affiliation(s)
- Jie Zhang
- Department of Surgery, Center of Gastrointestinal Rehabilitation, Beijing Rehabilitation Hospital, Capital Medical University, Beijing 100144, P.R. China
| | - Ye Wang
- Department of Surgery, Center of Gastrointestinal Rehabilitation, Beijing Rehabilitation Hospital, Capital Medical University, Beijing 100144, P.R. China
| | - Shiyang Hou
- Department of Surgery, Center of Gastrointestinal Rehabilitation, Beijing Rehabilitation Hospital, Capital Medical University, Beijing 100144, P.R. China
| | - Xiaoqian Chi
- Department of Surgery, Center of Gastrointestinal Rehabilitation, Beijing Rehabilitation Hospital, Capital Medical University, Beijing 100144, P.R. China
| | - Danyang Ding
- Department of Surgery, Center of Gastrointestinal Rehabilitation, Beijing Rehabilitation Hospital, Capital Medical University, Beijing 100144, P.R. China
| | - Mei Xue
- Department of Gastroenterology and Hepatology, Center of Gastrointestinal Rehabilitation, Beijing Rehabilitation Hospital, Capital Medical University, Beijing 100144, P.R. China
| | - Mengqiao Zhang
- Department of Gastroenterology and Hepatology, Center of Gastrointestinal Rehabilitation, Beijing Rehabilitation Hospital, Capital Medical University, Beijing 100144, P.R. China
| | - Jing Wang
- Department of Gastroenterology and Hepatology, Center of Gastrointestinal Rehabilitation, Beijing Rehabilitation Hospital, Capital Medical University, Beijing 100144, P.R. China
| | - Junfang Shuai
- Department of Gastroenterology and Hepatology, Center of Gastrointestinal Rehabilitation, Beijing Rehabilitation Hospital, Capital Medical University, Beijing 100144, P.R. China
| | - Haiying Sun
- Department of Gastroenterology and Hepatology, Center of Gastrointestinal Rehabilitation, Beijing Rehabilitation Hospital, Capital Medical University, Beijing 100144, P.R. China
| | - Qiang Gao
- Department of Gastroenterology and Hepatology, Center of Gastrointestinal Rehabilitation, Beijing Rehabilitation Hospital, Capital Medical University, Beijing 100144, P.R. China
| | - Chunbo Kang
- Department of Surgery, Center of Gastrointestinal Rehabilitation, Beijing Rehabilitation Hospital, Capital Medical University, Beijing 100144, P.R. China
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Zhu Q, Zhao X, Zhang Y, Li Y, Liu S, Han J, Sun Z, Wang C, Deng D, Wang S, Tang Y, Huang Y, Jiang S, Tian C, Chen X, Yuan Y, Li Z, Yang T, Lai T, Liu Y, Yang W, Zou X, Zhang M, Cui H, Liu C, Jin X, Hu Y, Chen A, Xu X, Li G, Hou Y, Liu L, Liu S, Fang L, Chen W, Wu L. Single cell multi-omics reveal intra-cell-line heterogeneity across human cancer cell lines. Nat Commun 2023; 14:8170. [PMID: 38071219 PMCID: PMC10710513 DOI: 10.1038/s41467-023-43991-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 11/27/2023] [Indexed: 12/18/2023] Open
Abstract
Human cancer cell lines have long served as tools for cancer research and drug discovery, but the presence and the source of intra-cell-line heterogeneity remain elusive. Here, we perform single-cell RNA-sequencing and ATAC-sequencing on 42 and 39 human cell lines, respectively, to illustrate both transcriptomic and epigenetic heterogeneity within individual cell lines. Our data reveal that transcriptomic heterogeneity is frequently observed in cancer cell lines of different tissue origins, often driven by multiple common transcriptional programs. Copy number variation, as well as epigenetic variation and extrachromosomal DNA distribution all contribute to the detected intra-cell-line heterogeneity. Using hypoxia treatment as an example, we demonstrate that transcriptomic heterogeneity could be reshaped by environmental stress. Overall, our study performs single-cell multi-omics of commonly used human cancer cell lines and offers mechanistic insights into the intra-cell-line heterogeneity and its dynamics, which would serve as an important resource for future cancer cell line-based studies.
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Affiliation(s)
- Qionghua Zhu
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, China.
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, China.
| | - Xin Zhao
- BGI Research, 518083, Shenzhen, China
- College of Life Sciences, University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Yuanhang Zhang
- BGI Research, 518083, Shenzhen, China
- College of Life Sciences, University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Yanping Li
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, China
| | - Shang Liu
- BGI Research, 518083, Shenzhen, China
| | - Jingxuan Han
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, China
| | - Zhiyuan Sun
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, China
| | - Chunqing Wang
- BGI Research, 518083, Shenzhen, China
- College of Life Sciences, University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Daqi Deng
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, China
| | | | - Yisen Tang
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, China
| | | | - Siyuan Jiang
- BGI Research, 518083, Shenzhen, China
- College of Life Sciences, University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Chi Tian
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, China
| | - Xi Chen
- BGI Research, 518083, Shenzhen, China
| | - Yue Yuan
- BGI Research, 518083, Shenzhen, China
| | - Zeyu Li
- BGI Research, 518083, Shenzhen, China
- College of Life Sciences, University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Tao Yang
- China National GeneBank, 518120, Shenzhen, China
| | - Tingting Lai
- China National GeneBank, 518120, Shenzhen, China
| | - Yiqun Liu
- China National GeneBank, 518120, Shenzhen, China
| | - Wenzhen Yang
- China National GeneBank, 518120, Shenzhen, China
| | - Xuanxuan Zou
- BGI Research, 518083, Shenzhen, China
- College of Life Sciences, University of Chinese Academy of Sciences, 100049, Beijing, China
| | | | - Huanhuan Cui
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, China
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, China
- Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, 518055, Shenzhen, China
| | | | - Xin Jin
- BGI Research, 518083, Shenzhen, China
| | - Yuhui Hu
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, China
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, China
- Department of Pharmacology, School of Medicine, Southern University of Science and Technology, 518055, Shenzhen, China
| | - Ao Chen
- BGI Research, 518083, Shenzhen, China
- JFL-BGI STOmics Center, Jinfeng Laboratory, 401329, Chongqing, China
- The Guangdong-Hong Kong Joint Laboratory on Immunological and Genetic Kidney Diseases, Guangdong, China
| | - Xun Xu
- BGI Research, 518083, Shenzhen, China
| | - Guipeng Li
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, China
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, China
- Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, 518055, Shenzhen, China
| | - Yong Hou
- BGI Research, 518083, Shenzhen, China
- Shenzhen Key Laboratory of Single-Cell Omics, BGI-Shenzhen, 518100, Shenzhen, China
| | - Longqi Liu
- BGI Research, 518083, Shenzhen, China.
- BGI Research, 310012, Hangzhou, China.
- Shenzhen Bay Laboratory, 518000, Shenzhen, China.
| | - Shiping Liu
- BGI Research, 518083, Shenzhen, China.
- The Guangdong-Hong Kong Joint Laboratory on Immunological and Genetic Kidney Diseases, Guangdong, China.
- Shenzhen Key Laboratory of Single-Cell Omics, BGI-Shenzhen, 518100, Shenzhen, China.
- BGI Research, 310012, Hangzhou, China.
- Shenzhen Bay Laboratory, 518000, Shenzhen, China.
| | - Liang Fang
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, China.
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, China.
- Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, 518055, Shenzhen, China.
| | - Wei Chen
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, China.
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, China.
| | - Liang Wu
- BGI Research, 518083, Shenzhen, China.
- JFL-BGI STOmics Center, Jinfeng Laboratory, 401329, Chongqing, China.
- BGI Research, 401329, Chongqing, China.
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Fischer AD, Veronese Paniagua DA, Swaminathan S, Kashima H, Rubin DC, Madison BB. The oncogenic function of PLAGL2 is mediated via ASCL2 and IGF2 and a Wnt-independent mechanism in colorectal cancer. Am J Physiol Gastrointest Liver Physiol 2023; 325:G196-G211. [PMID: 37310750 PMCID: PMC10396286 DOI: 10.1152/ajpgi.00058.2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 06/05/2023] [Accepted: 06/06/2023] [Indexed: 06/14/2023]
Abstract
Colorectal cancer (CRC) tumorigenesis and progression are linked to common oncogenic mutations, especially in the tumor suppressor APC, whose loss triggers the deregulation of TCF4/β-Catenin activity. CRC tumorigenesis is also driven by multiple epimutational modifiers such as transcriptional regulators. We describe the common (and near-universal) activation of the zinc finger transcription factor and Let-7 target PLAGL2 in CRC and find that it is a key driver of intestinal epithelial transformation. PLAGL2 drives proliferation, cell cycle progression, and anchorage-independent growth in CRC cell lines and nontransformed intestinal cells. Investigating effects of PLAGL2 on downstream pathways revealed very modest effects on canonical Wnt signaling. Alternatively, we find pronounced effects on the direct PLAGL2 target genes IGF2, a fetal growth factor, and ASCL2, an intestinal stem cell-specific bHLH transcription factor. Inactivation of PLAGL2 in CRC cell lines has pronounced effects on ASCL2 reporter activity. Furthermore, ASCL2 expression can partially rescue deficits of proliferation and cell cycle progression caused by depletion of PLAGL2 in CRC cell lines. Thus, the oncogenic effects of PLAGL2 appear to be mediated via core stem cell and onco-fetal pathways, with minimal effects on downstream Wnt signaling.NEW & NOTEWORTHY A Let-7 target called PLAGL2 drives oncogenic transformation via Wnt-independent pathways. This work illustrates the robust effects of this zinc finger transcription factor in colorectal cancer (CRC) cell lines and nontransformed intestinal epithelium, with effects mediated, in part, via the direct target genes ASCL2 and IGF2. This has implications for the role of PLAGL2 in activation of onco-fetal and onco-stem cell pathways, contributing to immature and highly proliferative phenotypes in CRC.
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Affiliation(s)
- Anthony D Fischer
- Department of Genetics, Washington University School of Medicine, Saint Louis, Missouri, United States
| | - Daniel A Veronese Paniagua
- Washington University School of Medicine, Saint Louis, Missouri, United States
- Division of Endocrinology, Metabolism and Lipid Research, Department of Medicine, Washington University School of Medicine, United States
| | - Shriya Swaminathan
- Washington University School of Medicine, Saint Louis, Missouri, United States
| | - Hajime Kashima
- Division of Gastroenterology, Department of Medicine, Washington University School of Medicine, Saint Louis, Missouri, United States
| | - Deborah C Rubin
- Division of Gastroenterology, Department of Medicine, Washington University School of Medicine, Saint Louis, Missouri, United States
| | - Blair B Madison
- Division of Gastroenterology, Department of Medicine, Washington University School of Medicine, Saint Louis, Missouri, United States
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4
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A β-Catenin-TCF-Sensitive Locus Control Region Mediates GUCY2C Ligand Loss in Colorectal Cancer. Cell Mol Gastroenterol Hepatol 2021; 13:1276-1296. [PMID: 34954189 PMCID: PMC9073733 DOI: 10.1016/j.jcmgh.2021.12.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 12/14/2021] [Accepted: 12/15/2021] [Indexed: 12/13/2022]
Abstract
BACKGROUND & AIMS Sporadic colorectal cancers arise from initiating mutations in APC, producing oncogenic β-catenin/TCF-dependent transcriptional reprogramming. Similarly, the tumor suppressor axis regulated by the intestinal epithelial receptor GUCY2C is among the earliest pathways silenced in tumorigenesis. Retention of the receptor, but loss of its paracrine ligands, guanylin and uroguanylin, is an evolutionarily conserved feature of colorectal tumors, arising in the earliest dysplastic lesions. Here, we examined a mechanism of GUCY2C ligand transcriptional silencing by β-catenin/TCF signaling. METHODS We performed RNA sequencing analysis of 4 unique conditional human colon cancer cell models of β-catenin/TCF signaling to map the core Wnt-transcriptional program. We then performed a comparative analysis of orthogonal approaches, including luciferase reporters, chromatin immunoprecipitation sequencing, CRISPR/Cas9 (clustered regularly interspaced short palindromic repeats) knockout, and CRISPR epigenome editing, which were cross-validated with human tissue chromatin immunoprecipitation sequencing datasets, to identify functional gene enhancers mediating GUCY2C ligand loss. RESULTS RNA sequencing analyses reveal the GUCY2C hormones as 2 of the most sensitive targets of β-catenin/TCF signaling, reflecting transcriptional repression. The GUCY2C hormones share an insulated genomic locus containing a novel locus control region upstream of the guanylin promoter that mediates the coordinated silencing of both genes. Targeting this region with CRISPR epigenome editing reconstituted GUCY2C ligand expression, overcoming gene inactivation by mutant β-catenin/TCF signaling. CONCLUSIONS These studies reveal DNA elements regulating corepression of GUCY2C ligand transcription by β-catenin/TCF signaling, reflecting a novel pathophysiological step in tumorigenesis. They offer unique genomic strategies that could reestablish hormone expression in the context of canonical oncogenic mutations to reconstitute the GUCY2C axis and oppose transformation.
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Fernandes MT, Yassuda V, Bragança J, Link W, Ferreira BI, De Sousa-Coelho AL. Tribbles Gene Expression Profiles in Colorectal Cancer. GASTROINTESTINAL DISORDERS 2021; 3:218-236. [DOI: https:/doi.org/10.3390/gidisord3040021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 09/01/2023] Open
Abstract
Colorectal cancer (CRC) is the third most common cancer and the second leading cause of death due to cancer in the world. Therefore, the identification of novel druggable targets is urgently needed. Tribbles proteins belong to a pseudokinase family, previously recognized in CRC as oncogenes and potential therapeutic targets. Here, we analyzed the expression of TRIB1, TRIB2, and TRIB3 simultaneously in 33 data sets from CRC based on available GEO profiles. We show that all three Tribbles genes are overrepresented in CRC cell lines and primary tumors, though depending on specific features of the CRC samples. Higher expression of TRIB2 in the tumor microenvironment and TRIB3 overexpression in an early stage of CRC development, unveil a potential and unexplored role for these proteins in the context of CRC. Differential Tribbles expression was also explored in diverse cellular experimental conditions where either genetic or pharmacological approaches were used, providing novel hints for future research. This comprehensive bioinformatic analysis provides new insights into Tribbles gene expression and transcript regulation in CRC.
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6
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Tribbles Gene Expression Profiles in Colorectal Cancer. GASTROINTESTINAL DISORDERS 2021. [DOI: 10.3390/gidisord3040021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Colorectal cancer (CRC) is the third most common cancer and the second leading cause of death due to cancer in the world. Therefore, the identification of novel druggable targets is urgently needed. Tribbles proteins belong to a pseudokinase family, previously recognized in CRC as oncogenes and potential therapeutic targets. Here, we analyzed the expression of TRIB1, TRIB2, and TRIB3 simultaneously in 33 data sets from CRC based on available GEO profiles. We show that all three Tribbles genes are overrepresented in CRC cell lines and primary tumors, though depending on specific features of the CRC samples. Higher expression of TRIB2 in the tumor microenvironment and TRIB3 overexpression in an early stage of CRC development, unveil a potential and unexplored role for these proteins in the context of CRC. Differential Tribbles expression was also explored in diverse cellular experimental conditions where either genetic or pharmacological approaches were used, providing novel hints for future research. This comprehensive bioinformatic analysis provides new insights into Tribbles gene expression and transcript regulation in CRC.
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7
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De Crignis E, Hossain T, Romal S, Carofiglio F, Moulos P, Khalid MM, Rao S, Bazrafshan A, Verstegen MM, Pourfarzad F, Koutsothanassis C, Gehart H, Kan TW, Palstra RJ, Boucher C, IJzermans JN, Huch M, Boj SF, Vries R, Clevers H, van der Laan LJ, Hatzis P, Mahmoudi T. Application of human liver organoids as a patient-derived primary model for HBV infection and related hepatocellular carcinoma. eLife 2021; 10:e60747. [PMID: 34328417 PMCID: PMC8384419 DOI: 10.7554/elife.60747] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 07/29/2021] [Indexed: 02/06/2023] Open
Abstract
The molecular events that drive hepatitis B virus (HBV)-mediated transformation and tumorigenesis have remained largely unclear, due to the absence of a relevant primary model system. Here we propose the use of human liver organoids as a platform for modeling HBV infection and related tumorigenesis. We first describe a primary ex vivo HBV-infection model derived from healthy donor liver organoids after challenge with recombinant virus or HBV-infected patient serum. HBV-infected organoids produced covalently closed circular DNA (cccDNA) and HBV early antigen (HBeAg), expressed intracellular HBV RNA and proteins, and produced infectious HBV. This ex vivo HBV-infected primary differentiated hepatocyte organoid platform was amenable to drug screening for both anti-HBV activity and drug-induced toxicity. We also studied HBV replication in transgenically modified organoids; liver organoids exogenously overexpressing the HBV receptor sodium taurocholate co-transporting polypeptide (NTCP) after lentiviral transduction were not more susceptible to HBV, suggesting the necessity for additional host factors for efficient infection. We also generated transgenic organoids harboring integrated HBV, representing a long-term culture system also suitable for viral production and the study of HBV transcription. Finally, we generated HBV-infected patient-derived liver organoids from non-tumor cirrhotic tissue of explants from liver transplant patients. Interestingly, transcriptomic analysis of patient-derived liver organoids indicated the presence of an aberrant early cancer gene signature, which clustered with the hepatocellular carcinoma (HCC) cohort on The Cancer Genome Atlas Liver Hepatocellular Carcinoma dataset and away from healthy liver tissue, and may provide invaluable novel biomarkers for the development of HCC and surveillance in HBV-infected patients.
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Affiliation(s)
- Elisa De Crignis
- Department of Biochemistry, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Tanvir Hossain
- Department of Biochemistry, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Shahla Romal
- Department of Biochemistry, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Fabrizia Carofiglio
- Department of Biochemistry, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Panagiotis Moulos
- Biomedical Sciences Research Center 'Alexander Fleming', Vari, Greece
| | - Mir Mubashir Khalid
- Department of Biochemistry, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Shringar Rao
- Department of Biochemistry, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Ameneh Bazrafshan
- Department of Biochemistry, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Monique Ma Verstegen
- Department of Surgery, Erasmus University Medical Center, Rotterdam, Netherlands
| | | | | | - Helmuth Gehart
- Hubrecht Institute-KNAW, University Medical Centre Utrecht, Utrecht, Netherlands
| | - Tsung Wai Kan
- Department of Biochemistry, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Robert-Jan Palstra
- Department of Biochemistry, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Charles Boucher
- Department of Viroscience, Erasmus Medical Centre, Rotterdam, Netherlands
| | - Jan Nm IJzermans
- Department of Surgery, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Meritxell Huch
- Max Plank Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Sylvia F Boj
- Foundation Hubrecht Organoid Technology (HUB), Utrecht, Netherlands
| | - Robert Vries
- Foundation Hubrecht Organoid Technology (HUB), Utrecht, Netherlands
| | - Hans Clevers
- Hubrecht Institute-KNAW, University Medical Centre Utrecht, Utrecht, Netherlands
| | - Luc Jw van der Laan
- Department of Surgery, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Pantelis Hatzis
- Biomedical Sciences Research Center 'Alexander Fleming', Vari, Greece
| | - Tokameh Mahmoudi
- Department of Biochemistry, Erasmus University Medical Center, Rotterdam, Netherlands
- Department of Urology, Erasmus University Medical Center, Rotterdam, Netherlands
- Department of Pathology, Erasmus University Medical Center, Rotterdam, Netherlands
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8
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Cvekl A, Eliscovich C. Crystallin gene expression: Insights from studies of transcriptional bursting. Exp Eye Res 2021; 207:108564. [PMID: 33894228 DOI: 10.1016/j.exer.2021.108564] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 03/05/2021] [Accepted: 03/22/2021] [Indexed: 01/26/2023]
Abstract
Cellular differentiation is marked by temporally and spatially regulated gene expression. The ocular lens is one of the most powerful mammalian model system since it is composed from only two cell subtypes, called lens epithelial and fiber cells. Lens epithelial cells differentiate into fiber cells through a series of spatially and temporally orchestrated processes, including massive production of crystallins, cellular elongation and the coordinated degradation of nuclei and other organelles. Studies of transcriptional and posttranscriptional gene regulatory mechanisms in lens provide a wide range of opportunities to understand global molecular mechanisms of gene expression as steady-state levels of crystallin mRNAs reach very high levels comparable to globin genes in erythrocytes. Importantly, dysregulation of crystallin gene expression results in lens structural abnormalities and cataracts. The mRNA life cycle is comprised of multiple stages, including transcription, splicing, nuclear export into cytoplasm, stabilization, localization, translation and ultimate decay. In recent years, development of modern mRNA detection methods with single molecule and single cell resolution enabled transformative studies to visualize the mRNA life cycle to generate novel insights into the sequential regulatory mechanisms of gene expression during embryogenesis. This review is focused on recent major advancements in studies of transcriptional bursting in differentiating lens fiber cells, analysis of nascent mRNA expression from bi-directional promoters, transient nuclear accumulation of specific mRNAs, condensation of chromatin prior lens fiber cell denucleation, and outlines future studies to probe the interactions of individual mRNAs with specific RNA-binding proteins (RBPs) in the cytoplasm and regulation of translation and mRNA decay.
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Affiliation(s)
- Ales Cvekl
- Department of Ophthalmology and VIsual Sciences, Albert Einstein College of Medicine, Bronx, NY, 10461, USA; Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA.
| | - Carolina Eliscovich
- Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, 10461, USA; Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
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9
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Zepecki JP, Karambizi D, Fajardo JE, Snyder KM, Guetta-Terrier C, Tang OY, Chen JS, Sarkar A, Fiser A, Toms SA, Tapinos N. miRNA-mediated loss of m6A increases nascent translation in glioblastoma. PLoS Genet 2021; 17:e1009086. [PMID: 33684100 PMCID: PMC7971852 DOI: 10.1371/journal.pgen.1009086] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 03/18/2021] [Accepted: 02/15/2021] [Indexed: 12/13/2022] Open
Abstract
Within the glioblastoma cellular niche, glioma stem cells (GSCs) can give rise to differentiated glioma cells (DGCs) and, when necessary, DGCs can reciprocally give rise to GSCs to maintain the cellular equilibrium necessary for optimal tumor growth. Here, using ribosome profiling, transcriptome and m6A RNA sequencing, we show that GSCs from patients with different subtypes of glioblastoma share a set of transcripts, which exhibit a pattern of m6A loss and increased protein translation during differentiation. The target sequences of a group of miRNAs overlap the canonical RRACH m6A motifs of these transcripts, many of which confer a survival advantage in glioblastoma. Ectopic expression of the RRACH-binding miR-145 induces loss of m6A, formation of FTO/AGO1/ILF3/miR-145 complexes on a clinically relevant tumor suppressor gene (CLIP3) and significant increase in its nascent translation. Inhibition of miR-145 maintains RRACH m6A levels of CLIP3 and inhibits its nascent translation. This study highlights a critical role of miRNAs in assembling complexes for m6A demethylation and induction of protein translation during GSC state transition.
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Affiliation(s)
- John P. Zepecki
- Laboratory of Cancer Epigenetics and Plasticity, Brown University, Rhode Island Hospital, Providence Rhode Island, United States of America
| | - David Karambizi
- Laboratory of Cancer Epigenetics and Plasticity, Brown University, Rhode Island Hospital, Providence Rhode Island, United States of America
| | - J. Eduardo Fajardo
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Kristin M. Snyder
- University of Minnesota, College of Veterinary Medicine, St. Paul, Minnesota, United States of America
| | - Charlotte Guetta-Terrier
- Laboratory of Cancer Epigenetics and Plasticity, Brown University, Rhode Island Hospital, Providence Rhode Island, United States of America
| | - Oliver Y. Tang
- Laboratory of Cancer Epigenetics and Plasticity, Brown University, Rhode Island Hospital, Providence Rhode Island, United States of America
| | - Jia-Shu Chen
- Laboratory of Cancer Epigenetics and Plasticity, Brown University, Rhode Island Hospital, Providence Rhode Island, United States of America
| | - Atom Sarkar
- Department of Neurosurgery, Drexel Neuroscience Institute, Philadelphia Pennsylvania, United States of America
| | - Andras Fiser
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Steven A. Toms
- Department of Neurosurgery, Brown University, Providence Rhode Island, United States of America
| | - Nikos Tapinos
- Laboratory of Cancer Epigenetics and Plasticity, Brown University, Rhode Island Hospital, Providence Rhode Island, United States of America
- Department of Neurosurgery, Brown University, Providence Rhode Island, United States of America
- Cancer Biology Program, Brown University, Lifespan Cancer Institute, Providence RI, USA
- Carney Institute for Brain Science, Brown University, Providence, RI, USA
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Abstract
The fungal zinc finger transcription factor NsdC is named after, and is best known for, its essential role in sexual reproduction (never in sexual development). In previous studies with Aspergillus nidulans, it was also shown to have roles in promotion of vegetative growth and suppression of asexual conidiation. In this study, the function of the nsdC homologue in the opportunistic human pathogen A. fumigatus was investigated. NsdC was again found to be essential for sexual development, with deletion of the nsdC gene in both MAT1-1 and MAT1-2 mating partners of a cross leading to complete loss of fertility. However, a functional copy of nsdC in one mating partner was sufficient to allow sexual reproduction. Deletion of nsdC also led to decreased vegetative growth and allowed conidiation in liquid cultures, again consistent with previous findings. However, NsdC in A. fumigatus was shown to have additional biological functions including response to calcium stress, correct organization of cell wall structure, and response to the cell wall stressors. Furthermore, virulence and host immune recognition were affected. Gene expression studies involving chromatin immunoprecipitation (ChIP) of RNA polymerase II (PolII) coupled to next-generation sequencing (Seq) revealed that deletion of nsdC resulted in changes in expression of over 620 genes under basal growth conditions. This demonstrated that this transcription factor mediates the activity of a wide variety of signaling and metabolic pathways and indicates that despite the naming of the gene, the promotion of sexual reproduction is just one among multiple roles of NsdC.IMPORTANCE Aspergillus fumigatus is an opportunistic human fungal pathogen and the main causal agent of invasive aspergillosis, a life-threatening infection especially in immunocompromised patients. A. fumigatus can undergo both asexual and sexual reproductive cycles, and the regulation of both cycles involves several genes and pathways. Here, we have characterized one of these genetic determinants, the NsdC transcription factor, which was initially identified in a screen of transcription factor null mutants showing sensitivity when exposed to high concentrations of calcium. In addition to its known essential roles in sexual reproduction and control of growth rate and asexual reproduction, we have shown in the present study that A. fumigatus NsdC transcription factor has additional previously unrecognized biological functions including calcium tolerance, cell wall stress response, and correct cell wall organization and functions in virulence and host immune recognition. Our results indicate that NsdC can play novel additional biological functions not directly related to its role played during sexual and asexual processes.
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11
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Pei J, Harakalova M, Treibel TA, Lumbers RT, Boukens BJ, Efimov IR, van Dinter JT, González A, López B, El Azzouzi H, van den Dungen N, van Dijk CGM, Krebber MM, den Ruijter HM, Pasterkamp G, Duncker DJ, Nieuwenhuis EES, de Weger R, Huibers MM, Vink A, Moore JH, Moon JC, Verhaar MC, Kararigas G, Mokry M, Asselbergs FW, Cheng C. H3K27ac acetylome signatures reveal the epigenomic reorganization in remodeled non-failing human hearts. Clin Epigenetics 2020; 12:106. [PMID: 32664951 PMCID: PMC7362435 DOI: 10.1186/s13148-020-00895-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 06/30/2020] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND H3K27ac histone acetylome changes contribute to the phenotypic response in heart diseases, particularly in end-stage heart failure. However, such epigenetic alterations have not been systematically investigated in remodeled non-failing human hearts. Therefore, valuable insight into cardiac dysfunction in early remodeling is lacking. This study aimed to reveal the acetylation changes of chromatin regions in response to myocardial remodeling and their correlations to transcriptional changes of neighboring genes. RESULTS We detected chromatin regions with differential acetylation activity (DARs; Padj. < 0.05) between remodeled non-failing patient hearts and healthy donor hearts. The acetylation level of the chromatin region correlated with its RNA polymerase II occupancy level and the mRNA expression level of its adjacent gene per sample. Annotated genes from DARs were enriched in disease-related pathways, including fibrosis and cell metabolism regulation. DARs that change in the same direction have a tendency to cluster together, suggesting the well-reorganized chromatin architecture that facilitates the interactions of regulatory domains in response to myocardial remodeling. We further show the differences between the acetylation level and the mRNA expression level of cell-type-specific markers for cardiomyocytes and 11 non-myocyte cell types. Notably, we identified transcriptome factor (TF) binding motifs that were enriched in DARs and defined TFs that were predicted to bind to these motifs. We further showed 64 genes coding for these TFs that were differentially expressed in remodeled myocardium when compared with controls. CONCLUSIONS Our study reveals extensive novel insight on myocardial remodeling at the DNA regulatory level. Differences between the acetylation level and the transcriptional level of cell-type-specific markers suggest additional mechanism(s) between acetylome and transcriptome. By integrating these two layers of epigenetic profiles, we further provide promising TF-encoding genes that could serve as master regulators of myocardial remodeling. Combined, our findings highlight the important role of chromatin regulatory signatures in understanding disease etiology.
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Affiliation(s)
- Jiayi Pei
- Department of Nephrology and Hypertension, DIGD, UMC Utrecht, University of Utrecht, Utrecht, Netherlands
- Department of Cardiology, Division Heart & Lungs, UMC Utrecht, University of Utrecht, Utrecht, Netherlands
- Regenerative Medicine Utrecht (RMU), UMC Utrecht, University of Utrecht, Utrecht, Netherlands
| | - Magdalena Harakalova
- Department of Cardiology, Division Heart & Lungs, UMC Utrecht, University of Utrecht, Utrecht, Netherlands
- Regenerative Medicine Utrecht (RMU), UMC Utrecht, University of Utrecht, Utrecht, Netherlands
- Department of Pathology, UMC Utrecht, University of Utrecht, Utrecht, Netherlands
| | - Thomas A Treibel
- Institute of Cardiovascular Science, University College London, London, UK
| | - R Thomas Lumbers
- Institute of Cardiovascular Science, University College London, London, UK
| | | | - Igor R Efimov
- Department of Biomedical Engineering, GWU, Washington, D.C, USA
| | - Jip T van Dinter
- Department of Cardiology, Division Heart & Lungs, UMC Utrecht, University of Utrecht, Utrecht, Netherlands
| | - Arantxa González
- Program of Cardiovascular Diseases, CIMA Universidad de Navarra and IdiSNA, Pamplona, Spain
- CIBERCV, Carlos III Institute of Health, Madrid, Spain
| | - Begoña López
- Program of Cardiovascular Diseases, CIMA Universidad de Navarra and IdiSNA, Pamplona, Spain
- CIBERCV, Carlos III Institute of Health, Madrid, Spain
| | - Hamid El Azzouzi
- Department of Cardiology, Division Heart & Lungs, UMC Utrecht, University of Utrecht, Utrecht, Netherlands
| | | | - Christian G M van Dijk
- Department of Nephrology and Hypertension, DIGD, UMC Utrecht, University of Utrecht, Utrecht, Netherlands
| | - Merle M Krebber
- Department of Nephrology and Hypertension, DIGD, UMC Utrecht, University of Utrecht, Utrecht, Netherlands
| | - Hester M den Ruijter
- Department of Experimental Cardiology, UMC Utrecht, University of Utrecht, Utrecht, Netherlands
| | - Gerard Pasterkamp
- Laboratory of Clinical Chemistry and Hematology, UMC Utrecht, Utrecht, Netherlands
| | - Dirk J Duncker
- Division of Experimental Cardiology, Department of Cardiology, Erasmus University Medical Center, Rotterdam, Netherlands
| | | | - Roel de Weger
- Department of Pathology, UMC Utrecht, University of Utrecht, Utrecht, Netherlands
| | - Manon M Huibers
- Department of Pathology, UMC Utrecht, University of Utrecht, Utrecht, Netherlands
| | - Aryan Vink
- Department of Pathology, UMC Utrecht, University of Utrecht, Utrecht, Netherlands
| | - Jason H Moore
- Institute for Biomedical Informatics, UPENN, Philadelphia, USA
| | - James C Moon
- Institute of Cardiovascular Science, University College London, London, UK
| | - Marianne C Verhaar
- Department of Nephrology and Hypertension, DIGD, UMC Utrecht, University of Utrecht, Utrecht, Netherlands
| | - Georgios Kararigas
- Charité - Universitätsmedizin Berlin, and DZHK (German Centre for Cardiovascular Research), partner site, Berlin, Germany
| | - Michal Mokry
- Regenerative Medicine Utrecht (RMU), UMC Utrecht, University of Utrecht, Utrecht, Netherlands.
- Laboratory of Clinical Chemistry and Hematology, UMC Utrecht, Utrecht, Netherlands.
- Division of Paediatrics, UMC Utrecht, University of Utrecht, Utrecht, Netherlands.
| | - Folkert W Asselbergs
- Department of Cardiology, Division Heart & Lungs, UMC Utrecht, University of Utrecht, Utrecht, Netherlands.
- Institute of Cardiovascular Science, Faculty of Population Health Science, University College London, London, UK.
- Health Data Research UK and Institute of Health Informatics, University College London, London, UK.
| | - Caroline Cheng
- Department of Nephrology and Hypertension, DIGD, UMC Utrecht, University of Utrecht, Utrecht, Netherlands.
- Regenerative Medicine Utrecht (RMU), UMC Utrecht, University of Utrecht, Utrecht, Netherlands.
- Division of Experimental Cardiology, Department of Cardiology, Erasmus University Medical Center, Rotterdam, Netherlands.
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12
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Kim S, Beltran B, Irnov I, Jacobs-Wagner C. Long-Distance Cooperative and Antagonistic RNA Polymerase Dynamics via DNA Supercoiling. Cell 2020; 179:106-119.e16. [PMID: 31539491 DOI: 10.1016/j.cell.2019.08.033] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 06/14/2019] [Accepted: 08/16/2019] [Indexed: 12/12/2022]
Abstract
Genes are often transcribed by multiple RNA polymerases (RNAPs) at densities that can vary widely across genes and environmental conditions. Here, we provide in vitro and in vivo evidence for a built-in mechanism by which co-transcribing RNAPs display either collaborative or antagonistic dynamics over long distances (>2 kb) through transcription-induced DNA supercoiling. In Escherichia coli, when the promoter is active, co-transcribing RNAPs translocate faster than a single RNAP, but their average speed is not altered by large variations in promoter strength and thus RNAP density. Environmentally induced promoter repression reduces the elongation efficiency of already-loaded RNAPs, causing premature termination and quick synthesis arrest of no-longer-needed proteins. This negative effect appears independent of RNAP convoy formation and is abrogated by topoisomerase I activity. Antagonistic dynamics can also occur between RNAPs from divergently transcribed gene pairs. Our findings may be broadly applicable given that transcription on topologically constrained DNA is the norm across organisms.
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Affiliation(s)
- Sangjin Kim
- Microbial Sciences Institute, Yale University, West Haven, CT 06516, USA; Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA; Howard Hughes Medical Institute, Yale University, New Haven, CT 06536, USA.
| | - Bruno Beltran
- Microbial Sciences Institute, Yale University, West Haven, CT 06516, USA; Howard Hughes Medical Institute, Yale University, New Haven, CT 06536, USA
| | - Irnov Irnov
- Microbial Sciences Institute, Yale University, West Haven, CT 06516, USA; Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA; Howard Hughes Medical Institute, Yale University, New Haven, CT 06536, USA
| | - Christine Jacobs-Wagner
- Microbial Sciences Institute, Yale University, West Haven, CT 06516, USA; Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA; Howard Hughes Medical Institute, Yale University, New Haven, CT 06536, USA; Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT 06536, USA.
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13
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Diwadkar AR, Kan M, Himes BE. Facilitating Analysis of Publicly Available ChIP-Seq Data for Integrative Studies. AMIA ... ANNUAL SYMPOSIUM PROCEEDINGS. AMIA SYMPOSIUM 2020; 2019:371-379. [PMID: 32308830 PMCID: PMC7153109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
ChIP-Seq, a technique that allows for quantification of DNA sequences bound by transcription factors or histones, has been widely used to characterize genome-wide DNA-protein binding at baseline and induced by specific exposures. Integrating results of multiple ChIP-Seq datasets is a convenient approach to identify robust DNA- protein binding sites and determine their cell-type specificity. We developed brocade, a computational pipeline for reproducible analysis of publicly available ChIP-Seq data that creates R markdown reports containing information on datasets downloaded, quality control metrics, and differential binding results. Glucocorticoids are commonly used anti-inflammatory drugs with tissue-specific effects that are not fully understood. We demonstrate the utility of brocade via the analysis of five ChIP-Seq datasets involving glucocorticoid receptor (GR), a transcription factor that mediates glucocorticoid response, to identify cell type-specific and shared GR binding sites across the five cell types. Our results show that brocade facilitates analysis of individual ChIP-Seq datasets and comparative studies involving multiple datasets.
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Affiliation(s)
- Avantika R Diwadkar
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, Philadelphia, PA, US
| | - Mengyuan Kan
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, Philadelphia, PA, US
| | - Blanca E Himes
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, Philadelphia, PA, US
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14
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Blomain ES, Rappaport JA, Pattison AM, Bashir B, Caparosa E, Stem J, Snook AE, Waldman SA. APC-β-catenin-TCF signaling silences the intestinal guanylin-GUCY2C tumor suppressor axis. Cancer Biol Ther 2020; 21:441-451. [PMID: 32037952 PMCID: PMC7515458 DOI: 10.1080/15384047.2020.1721262] [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] [Indexed: 12/11/2022] Open
Abstract
Sporadic colorectal cancer initiates with mutations in APC or its degradation target β-catenin, producing TCF-dependent nuclear transcription driving tumorigenesis. The intestinal epithelial receptor, GUCY2C, with its canonical paracrine hormone guanylin, regulates homeostatic signaling along the crypt-surface axis opposing tumorigenesis. Here, we reveal that expression of the guanylin hormone, but not the GUCY2C receptor, is lost at the earliest stages of transformation in APC-dependent tumors in humans and mice. Hormone loss, which silences GUCY2C signaling, reflects transcriptional repression mediated by mutant APC-β-catenin-TCF programs in the nucleus. These studies support a pathophysiological model of intestinal tumorigenesis in which mutant APC-β-catenin-TCF transcriptional regulation eliminates guanylin expression at tumor initiation, silencing GUCY2C signaling which, in turn, dysregulates intestinal homeostatic mechanisms contributing to tumor progression. They expand the mechanistic paradigm for colorectal cancer from a disease of irreversible mutations in APC and β-catenin to one of guanylin hormone loss whose replacement, and reconstitution of GUCY2C signaling, could prevent tumorigenesis
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Affiliation(s)
- Erik S Blomain
- Department of Pharmacology and Experimental Therapeutics, Thomas Jefferson University, Philadelphia, PA, USA
| | - Jeffrey A Rappaport
- Department of Pharmacology and Experimental Therapeutics, Thomas Jefferson University, Philadelphia, PA, USA
| | - Amanda M Pattison
- Department of Pharmacology and Experimental Therapeutics, Thomas Jefferson University, Philadelphia, PA, USA
| | - Babar Bashir
- Department of Pharmacology and Experimental Therapeutics, Thomas Jefferson University, Philadelphia, PA, USA
| | - Ellen Caparosa
- Department of Pharmacology and Experimental Therapeutics, Thomas Jefferson University, Philadelphia, PA, USA
| | - Jonathan Stem
- Department of Pharmacology and Experimental Therapeutics, Thomas Jefferson University, Philadelphia, PA, USA
| | - Adam E Snook
- Department of Pharmacology and Experimental Therapeutics, Thomas Jefferson University, Philadelphia, PA, USA
| | - Scott A Waldman
- Department of Pharmacology and Experimental Therapeutics, Thomas Jefferson University, Philadelphia, PA, USA
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15
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Alvarez JM, Moyano TC, Zhang T, Gras DE, Herrera FJ, Araus V, O'Brien JA, Carrillo L, Medina J, Vicente-Carbajosa J, Jiang J, Gutiérrez RA. Local Changes in Chromatin Accessibility and Transcriptional Networks Underlying the Nitrate Response in Arabidopsis Roots. MOLECULAR PLANT 2019; 12:1545-1560. [PMID: 31526863 DOI: 10.1016/j.molp.2019.09.002] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 08/27/2019] [Accepted: 09/05/2019] [Indexed: 05/13/2023]
Abstract
Transcriptional regulation, determined by the chromatin structure and regulatory elements interacting at promoter regions, is a key step in plant responses to environmental cues. Nitrate (NO3-) is a nutrient signal that regulates the expression of hundreds of genes in Arabidopsis thaliana. Here, we integrate mRNA sequencing, genome-wide RNA polymerase II (RNPII), chromatin immunoprecipitation sequencing, and DNase sequencing datasets to establish the relationship between RNPII occupancy and chromatin accessibility in response to NO3- treatments in Arabidopsis roots. Genomic footprinting allowed us to identify in vivo regulatory elements controlling gene expression in response to NO3- treatments. NO3--modulated transcription factor (TF) footprints are important for a rapid increase in RNPII occupancy and transcript accumulation over time. We mapped key TF regulatory interactions and functionally validated the role of NAP, an NAC-domain containing TF, as a new regulatory factor in NO3- transport. Taken together, our study provides a comprehensive view of transcriptional networks in response to a nutrient signal in Arabidopsis roots.
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Affiliation(s)
- José M Alvarez
- Pontificia Universidad Catolica de Chile, Santiago, Chile
| | - Tomás C Moyano
- Pontificia Universidad Catolica de Chile, Santiago, Chile
| | - Tao Zhang
- Yangzhou University, Yangzhou, China
| | - Diana E Gras
- Instituto de Agrobiotecnologia del Litoral, CONICET, Santa Fe, Argentina
| | - Francisco J Herrera
- University of California, Berkeley, CA, USA; Trancura Biosciences, Inc., San Francisco, CA 94158, USA
| | - Viviana Araus
- Pontificia Universidad Catolica de Chile, Santiago, Chile
| | - José A O'Brien
- Pontificia Universidad Catolica de Chile, Santiago, Chile
| | - Laura Carrillo
- Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA), Universidad Politécnica de Madrid (UPM), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo, 28223-Pozuelo de Alarcón, Madrid, Spain
| | - Joaquín Medina
- Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA), Universidad Politécnica de Madrid (UPM), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo, 28223-Pozuelo de Alarcón, Madrid, Spain
| | - Jesús Vicente-Carbajosa
- Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA), Universidad Politécnica de Madrid (UPM), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo, 28223-Pozuelo de Alarcón, Madrid, Spain
| | - Jiming Jiang
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Plant Biology and Horticulture, Michigan State University, MI 48824, USA
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16
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Peters JM, Walter V, Patterson AD, Gonzalez FJ. Unraveling the role of peroxisome proliferator-activated receptor-β/δ (PPARβ/δ) expression in colon carcinogenesis. NPJ Precis Oncol 2019; 3:26. [PMID: 31602402 PMCID: PMC6779880 DOI: 10.1038/s41698-019-0098-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 09/17/2019] [Indexed: 01/09/2023] Open
Abstract
The peroxisome proliferator-activated-β/δ (PPARβ/δ) was identified in 1994, but not until 1999 was PPARβ/δ suggested to be involved in carcinogenesis. Initially, it was hypothesized that expression of PPARβ/δ was increased during colon cancer progression, which led to increased transcription of yet-to-be confirmed target genes that promote cell proliferation and tumorigenesis. It was also hypothesized at this time that lipid-metabolizing enzymes generated lipid metabolites that served as ligands for PPARβ/δ. These hypothetical mechanisms were attractive because they potentially explained how non-steroidal anti-inflammatory drugs inhibited tumorigenesis by potentially limiting the concentration of endogenous PPARβ/δ ligands that could activate this receptor that was increased in cancer cells. However, during the last 20 years, considerable research was undertaken describing expression of PPARβ/δ in normal and cancer cells that has led to a significant impact on the mechanisms by which PPARβ/δ functions in carcinogenesis. Whereas results from earlier studies led to much uncertainty about the role of PPARβ/δ in cancer, more recent analyses of large databases have revealed a more consistent understanding. The focus of this review is on the fundamental level of PPARβ/δ expression in normal tissues and cancerous tissue as described by studies during the past two decades and what has been delineated during this timeframe about how PPARβ/δ expression influences carcinogenesis, with an emphasis on colon cancer.
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Affiliation(s)
- Jeffrey M. Peters
- Department of Veterinary and Biomedical Sciences, The Center of Molecular Toxicology and Carcinogenesis, The Pennsylvania State University, University Park, State College, PA 16801 USA
| | - Vonn Walter
- Departments of Public Health Sciences and Biochemistry, The Pennsylvania State University, College of Medicine, Hershey, State College, PA 16801 USA
| | - Andrew D. Patterson
- Department of Veterinary and Biomedical Sciences, The Center of Molecular Toxicology and Carcinogenesis, The Pennsylvania State University, University Park, State College, PA 16801 USA
| | - Frank J. Gonzalez
- Laboratory of Metabolism, National Cancer Institute, Bethesda, MD USA
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17
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Zhao H, He L, Yin D, Song B. Identification of β-catenin target genes in colorectal cancer by interrogating gene fitness screening data. Oncol Lett 2019; 18:3769-3777. [PMID: 31516589 PMCID: PMC6733007 DOI: 10.3892/ol.2019.10724] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 07/12/2019] [Indexed: 11/06/2022] Open
Abstract
β-catenin regulates its target genes which are associated with proliferation, differentiation, migration and angiogenesis, and the dysregulation of Wnt/β-catenin signaling facilitates hallmarks of colorectal cancer (CRC). Identification of β-catenin targets and their potential roles in tumorigenesis has gained increased interest. However, the number of identified targets remains limited. The present study implemented a novel strategy, interrogating gene fitness profiles derived from large-scale RNA interference and CRISPR-CRISPR associated protein 9 screening data to identify β-catenin target genes in CRC cell lines. Using these data sets, pair wise gene fitness similarities were determined which highlighted a total of 13 genes whose functions were highly correlated with β-catenin. It was further demonstrated that the expression of these genes were altered in CRC, illustrating their potential roles in the progression of CRC. The present study further demonstrated that these targets could be used to predict disease-free survival in CRC. In conclusion, the findings provided novel approaches for the identification of β-catenin targets, which may become prognostic biomarkers or drug targets for the management of CRC.
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Affiliation(s)
- Haomin Zhao
- Department of Vascular Surgery, China-Japan Union Hospital of Jilin University, Changchun, Jilin 130033, P.R. China
| | - Liang He
- Department of Gastrointestinal Surgery, First Hospital of Jilin University, Changchun, Jilin 130033, P.R. China
| | - Dexin Yin
- Department of Vascular Surgery, China-Japan Union Hospital of Jilin University, Changchun, Jilin 130033, P.R. China
| | - Bin Song
- Department of Gastrointestinal Surgery, China-Japan Union Hospital of Jilin University, Changchun, Jilin 130033, P.R. China
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18
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Kelly TK, Ahmadiantehrani S, Blattler A, London SE. Epigenetic regulation of transcriptional plasticity associated with developmental song learning. Proc Biol Sci 2019; 285:rspb.2018.0160. [PMID: 29720411 DOI: 10.1098/rspb.2018.0160] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 04/06/2018] [Indexed: 12/19/2022] Open
Abstract
Ethologists discovered over 100 years ago that some lifelong behavioural patterns were acquired exclusively during restricted developmental phases called critical periods (CPs). Developmental song learning in zebra finches is one of the most striking examples of a CP for complex learned behaviour. After post-hatch day 65, whether or not a juvenile male can memorize the song of a 'tutor' depends on his experiences in the month prior. If he experienced a tutor, he can no longer learn, but if he has been isolated from hearing a tutor the learning period is extended. We aimed to identify how tutor experience alters the brain and controls the ability to learn. Epigenetic landscapes are modulated by experience and are able to regulate the transcription of sets of genes, thereby affecting cellular function. Thus, we hypothesized that tutor experiences determine the epigenetic landscape in the auditory forebrain, a region required for tutor song memorization. Using ChIPseq, RNAseq and molecular biology, we provide evidence that naturalistic experiences associated with the ability to learn can induce epigenetic changes, and propose transcriptional plasticity as a mediator of CP learning potential.
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Affiliation(s)
| | - Somayeh Ahmadiantehrani
- Department of Psychology, Institute for Mind and Biology, University of Chicago, Chicago, IL 60637, USA
| | | | - Sarah E London
- Department of Psychology, Institute for Mind and Biology, University of Chicago, Chicago, IL 60637, USA
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19
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van de Lagemaat LN, Flenley M, Lynch MD, Garrick D, Tomlinson SR, Kranc KR, Vernimmen D. CpG binding protein (CFP1) occupies open chromatin regions of active genes, including enhancers and non-CpG islands. Epigenetics Chromatin 2018; 11:59. [PMID: 30292235 PMCID: PMC6173865 DOI: 10.1186/s13072-018-0230-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 09/28/2018] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The mechanism by which protein complexes interact to regulate the deposition of post-translational modifications of histones remains poorly understood. This is particularly important at regulatory regions, such as CpG islands (CGIs), which are known to recruit Trithorax (TrxG) and Polycomb group proteins. The CxxC zinc finger protein 1 (CFP1, also known as CGBP) is a subunit of the TrxG SET1 protein complex, a major catalyst of trimethylation of H3K4 (H3K4me3). RESULTS Here, we used ChIP followed by high-throughput sequencing (ChIP-seq) to analyse genomic occupancy of CFP1 in two human haematopoietic cell types. We demonstrate that CFP1 occupies CGIs associated with active transcription start sites (TSSs), and is mutually exclusive with H3K27 trimethylation (H3K27me3), a marker of polycomb repressive complex 2. Strikingly, rather than being restricted to active CGI TSSs, CFP1 also occupies a substantial fraction of active non-CGI TSSs and enhancers of transcribed genes. However, relative to other TrxG subunits, CFP1 was specialised to TSSs. Finally, we found enrichment of CpG-containing DNA motifs in CFP1 peaks at CGI promoters. CONCLUSIONS We found that CFP1 is not solely recruited to CpG islands as it was originally defined, but also other regions including non-CpG island promoters and enhancers.
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Affiliation(s)
- Louie N. van de Lagemaat
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG UK
| | - Maria Flenley
- MRC Molecular Haematology Unit, Weatherall Institute for Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DS UK
| | - Magnus D. Lynch
- MRC Molecular Haematology Unit, Weatherall Institute for Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DS UK
- Centre for Stem Cells and Regenerative Medicine, 28th Floor Guy’s Tower, Great Maze Pond, London, SE1 9RT UK
- st John’s institute of dermatology, Great Maze Pond, London, SE1 9RT UK
| | - David Garrick
- INSERM, UMRS-1126, Institut Universitaire d’Hématologie, Université Paris Diderot, 75010 Paris, France
| | - Simon R. Tomlinson
- MRC Centre for Regenerative Medicine, University of Edinburgh, 5 Little France Drive, Edinburgh, EH16 4UU UK
| | - Kamil R. Kranc
- MRC Centre for Regenerative Medicine, University of Edinburgh, 5 Little France Drive, Edinburgh, EH16 4UU UK
- Laboratory of Haematopoietic Stem Cell & Leukaemia Biology, Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London, EC1M 6BQ UK
| | - Douglas Vernimmen
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG UK
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20
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Morgan SL, Chang EY, Mariano NC, Bermudez A, Arruda NL, Wu F, Luo Y, Shankar G, Huynh SK, Huang CC, Pitteri SJ, Wang KC. CRISPR-Mediated Reorganization of Chromatin Loop Structure. J Vis Exp 2018:57457. [PMID: 30272647 PMCID: PMC6235177 DOI: 10.3791/57457] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Recent studies have clearly shown that long-range, three-dimensional chromatin looping interactions play a significant role in the regulation of gene expression, but whether looping is responsible for or a result of alterations in gene expression is still unknown. Until recently, how chromatin looping affects the regulation of gene activity and cellular function has been relatively ambiguous, and limitations in existing methods to manipulate these structures prevented in-depth exploration of these interactions. To resolve this uncertainty, we engineered a method for selective and reversible chromatin loop re-organization using CRISPR-dCas9 (CLOuD9). The dynamism of the CLOuD9 system has been demonstrated by successful localization of CLOuD9 constructs to target genomic loci to modulate local chromatin conformation. Importantly, the ability to reverse the induced contact and restore the endogenous chromatin conformation has also been confirmed. Modulation of gene expression with this method establishes the capacity to regulate cellular gene expression and underscores the great potential for applications of this technology in creating stable de novo chromatin loops that markedly affect gene expression in the contexts of cancer and development.
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Affiliation(s)
- Stefanie L Morgan
- Department of Dermatology, Program in Epithelial Biology, Stanford University School of Medicine; Program in Cancer Biology, Stanford University School of Medicine
| | - Erin Y Chang
- Department of Dermatology, Program in Epithelial Biology, Stanford University School of Medicine
| | - Natasha C Mariano
- Department of Dermatology, Program in Epithelial Biology, Stanford University School of Medicine
| | - Abel Bermudez
- Canary Center for Cancer Early Detection, Department of Radiology, Stanford University School of Medicine
| | | | | | - Yunhai Luo
- Department of Dermatology, Program in Epithelial Biology, Stanford University School of Medicine
| | - Gautam Shankar
- Department of Dermatology, Program in Epithelial Biology, Stanford University School of Medicine
| | - Star K Huynh
- Department of Dermatology, Program in Epithelial Biology, Stanford University School of Medicine
| | | | - Sharon J Pitteri
- Canary Center for Cancer Early Detection, Department of Radiology, Stanford University School of Medicine
| | - Kevin C Wang
- Department of Dermatology, Program in Epithelial Biology, Stanford University School of Medicine; Program in Cancer Biology, Stanford University School of Medicine; Veterans Affairs Healthcare System;
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21
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PRSS8 suppresses colorectal carcinogenesis and metastasis. Oncogene 2018; 38:497-517. [DOI: 10.1038/s41388-018-0453-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 07/22/2018] [Accepted: 07/24/2018] [Indexed: 12/13/2022]
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22
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Ewing RM, Song J, Gokulrangan G, Bai S, Bowler EH, Bolton R, Skipp P, Wang Y, Wang Z. Multiproteomic and Transcriptomic Analysis of Oncogenic β-Catenin Molecular Networks. J Proteome Res 2018; 17:2216-2225. [PMID: 29747501 DOI: 10.1021/acs.jproteome.8b00180] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The dysregulation of Wnt signaling is a frequent occurrence in many different cancers. Oncogenic mutations of CTNNB1/β-catenin, the key nuclear effector of canonical Wnt signaling, lead to the accumulation and stabilization of β-catenin protein with diverse effects in cancer cells. Although the transcriptional response to Wnt/β-catenin signaling activation has been widely studied, an integrated understanding of the effects of oncogenic β-catenin on molecular networks is lacking. We used affinity-purification mass spectrometry (AP-MS), label-free liquid chromatography-tandem mass spectrometry, and RNA-Seq to compare protein-protein interactions, protein expression, and gene expression in colorectal cancer cells expressing mutant (oncogenic) or wild-type β-catenin. We generate an integrated molecular network and use it to identify novel protein modules that are associated with mutant or wild-type β-catenin. We identify a DNA methyltransferase I associated subnetwork that is enriched in cells with mutant β-catenin and a subnetwork enriched in wild-type cells associated with the CDKN2A tumor suppressor, linking these processes to the transformation of colorectal cancer cells through oncogenic β-catenin signaling. In summary, multiomics analysis of a defined colorectal cancer cell model provides a significantly more comprehensive identification of functional molecular networks associated with oncogenic β-catenin signaling.
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Affiliation(s)
- Rob M Ewing
- School of Biological Sciences , University of Southampton , Southampton SO17 1BJ , United Kingdom
| | - Jing Song
- School of Medicine , Case Western Reserve University , Cleveland , Ohio 44106 , United States
| | - Giridharan Gokulrangan
- School of Medicine , Case Western Reserve University , Cleveland , Ohio 44106 , United States
| | - Sheldon Bai
- School of Medicine , Case Western Reserve University , Cleveland , Ohio 44106 , United States
| | - Emily H Bowler
- School of Biological Sciences , University of Southampton , Southampton SO17 1BJ , United Kingdom
| | - Rachel Bolton
- School of Biological Sciences , University of Southampton , Southampton SO17 1BJ , United Kingdom
| | - Paul Skipp
- School of Biological Sciences , University of Southampton , Southampton SO17 1BJ , United Kingdom
| | - Yihua Wang
- School of Biological Sciences , University of Southampton , Southampton SO17 1BJ , United Kingdom
| | - Zhenghe Wang
- School of Medicine , Case Western Reserve University , Cleveland , Ohio 44106 , United States
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23
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Global unleashing of transcription elongation waves in response to genotoxic stress restricts somatic mutation rate. Nat Commun 2017; 8:2076. [PMID: 29233992 PMCID: PMC5727188 DOI: 10.1038/s41467-017-02145-4] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 11/08/2017] [Indexed: 01/11/2023] Open
Abstract
Complex molecular responses preserve gene expression accuracy and genome integrity in the face of environmental perturbations. Here we report that, in response to UV irradiation, RNA polymerase II (RNAPII) molecules are dynamically and synchronously released from promoter-proximal regions into elongation to promote uniform and accelerated surveillance of the whole transcribed genome. The maximised influx of de novo released RNAPII correlates with increased damage-sensing, as confirmed by RNAPII progressive accumulation at dipyrimidine sites and by the average slow-down of elongation rates in gene bodies. In turn, this transcription elongation ‘safe’ mode guarantees efficient DNA repair regardless of damage location, gene size and transcription level. Accordingly, we detect low and homogenous rates of mutational signatures associated with UV exposure or cigarette smoke across all active genes. Our study reveals a novel advantage for transcription regulation at the promoter-proximal level and provides unanticipated insights into how active transcription shapes the mutagenic landscape of cancer genomes. Precise orchestration of gene expression regulation upon DNA damage is essential for genome integrity. Here the authors identify a novel widespread stress-triggered defence mechanism that promotes rapid transcription-driven genomic surveillance thus limiting mutagenesis and shaping cancer genomes.
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24
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Zhou Y, Zhang B, Li G, Tong T, Wan X. GD-RDA: A New Regularized Discriminant Analysis for High-Dimensional Data. J Comput Biol 2017; 24:1099-1111. [DOI: 10.1089/cmb.2017.0029] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Affiliation(s)
- Yan Zhou
- College of Mathematics and Statistics, Institute of Statistical Sciences, Shenzhen University, ShenZhen, China
| | - Baoxue Zhang
- School of Statistics, Capital University of Economics and Business, Beijing, China
| | - Gaorong Li
- Beijing Institute for Scientific and Engineering Computing, Beijing University of Technology, Beijing, China
| | - Tiejun Tong
- Department of Mathematics, Hong Kong Baptist University, Hong Kong, China
| | - Xiang Wan
- Department of Computer Science, Hong Kong Baptist University, Hong Kong, China
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25
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Brandt MM, Meddens CA, Louzao-Martinez L, van den Dungen NAM, Lansu NR, Nieuwenhuis EES, Duncker DJ, Verhaar MC, Joles JA, Mokry M, Cheng C. Chromatin Conformation Links Distal Target Genes to CKD Loci. J Am Soc Nephrol 2017; 29:462-476. [PMID: 29093029 DOI: 10.1681/asn.2016080875] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 09/09/2017] [Indexed: 11/03/2022] Open
Abstract
Genome-wide association studies (GWASs) have identified many genetic risk factors for CKD. However, linking common variants to genes that are causal for CKD etiology remains challenging. By adapting self-transcribing active regulatory region sequencing, we evaluated the effect of genetic variation on DNA regulatory elements (DREs). Variants in linkage with the CKD-associated single-nucleotide polymorphism rs11959928 were shown to affect DRE function, illustrating that genes regulated by DREs colocalizing with CKD-associated variation can be dysregulated and therefore, considered as CKD candidate genes. To identify target genes of these DREs, we used circular chromosome conformation capture (4C) sequencing on glomerular endothelial cells and renal tubular epithelial cells. Our 4C analyses revealed interactions of CKD-associated susceptibility regions with the transcriptional start sites of 304 target genes. Overlap with multiple databases confirmed that many of these target genes are involved in kidney homeostasis. Expression quantitative trait loci analysis revealed that mRNA levels of many target genes are genotype dependent. Pathway analyses showed that target genes were enriched in processes crucial for renal function, identifying dysregulated geranylgeranyl diphosphate biosynthesis as a potential disease mechanism. Overall, our data annotated multiple genes to previously reported CKD-associated single-nucleotide polymorphisms and provided evidence for interaction between these loci and target genes. This pipeline provides a novel technique for hypothesis generation and complements classic GWAS interpretation. Future studies are required to specify the implications of our dataset and further reveal the complex roles that common variants have in complex diseases, such as CKD.
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Affiliation(s)
- Maarten M Brandt
- Experimental Cardiology, Department of Cardiology, Thoraxcenter Erasmus University Medical Center, Rotterdam, The Netherlands; and
| | - Claartje A Meddens
- Department of Pediatrics, Wilhelmina Children's Hospital.,Regenerative Medicine Center Utrecht, Department of Pediatrics
| | - Laura Louzao-Martinez
- Department of Nephrology and Hypertension, Division of Internal Medicine and Dermatology
| | - Noortje A M van den Dungen
- Department of Cardiology, Division Heart and Lungs, and.,Epigenomics Facility, Department of Cardiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Nico R Lansu
- Department of Pediatrics, Wilhelmina Children's Hospital.,Regenerative Medicine Center Utrecht, Department of Pediatrics.,Epigenomics Facility, Department of Cardiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | - Dirk J Duncker
- Experimental Cardiology, Department of Cardiology, Thoraxcenter Erasmus University Medical Center, Rotterdam, The Netherlands; and
| | - Marianne C Verhaar
- Department of Nephrology and Hypertension, Division of Internal Medicine and Dermatology
| | - Jaap A Joles
- Department of Nephrology and Hypertension, Division of Internal Medicine and Dermatology
| | - Michal Mokry
- Department of Pediatrics, Wilhelmina Children's Hospital.,Regenerative Medicine Center Utrecht, Department of Pediatrics.,Epigenomics Facility, Department of Cardiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Caroline Cheng
- Experimental Cardiology, Department of Cardiology, Thoraxcenter Erasmus University Medical Center, Rotterdam, The Netherlands; and .,Department of Nephrology and Hypertension, Division of Internal Medicine and Dermatology
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26
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Hu Z, Dong K, Dai W, Tong T. A Comparison of Methods for Estimating the Determinant of High-Dimensional Covariance Matrix. Int J Biostat 2017; 13:/j/ijb.ahead-of-print/ijb-2017-0013/ijb-2017-0013.xml. [PMID: 28953454 DOI: 10.1515/ijb-2017-0013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 08/16/2017] [Indexed: 11/15/2022]
Abstract
The determinant of the covariance matrix for high-dimensional data plays an important role in statistical inference and decision. It has many real applications including statistical tests and information theory. Due to the statistical and computational challenges with high dimensionality, little work has been proposed in the literature for estimating the determinant of high-dimensional covariance matrix. In this paper, we estimate the determinant of the covariance matrix using some recent proposals for estimating high-dimensional covariance matrix. Specifically, we consider a total of eight covariance matrix estimation methods for comparison. Through extensive simulation studies, we explore and summarize some interesting comparison results among all compared methods. We also provide practical guidelines based on the sample size, the dimension, and the correlation of the data set for estimating the determinant of high-dimensional covariance matrix. Finally, from a perspective of the loss function, the comparison study in this paper may also serve as a proxy to assess the performance of the covariance matrix estimation.
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27
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Xie JL, Qin L, Miao Z, Grys BT, Diaz JDLC, Ting K, Krieger JR, Tong J, Tan K, Leach MD, Ketela T, Moran MF, Krysan DJ, Boone C, Andrews BJ, Selmecki A, Ho Wong K, Robbins N, Cowen LE. The Candida albicans transcription factor Cas5 couples stress responses, drug resistance and cell cycle regulation. Nat Commun 2017; 8:499. [PMID: 28894103 PMCID: PMC5593949 DOI: 10.1038/s41467-017-00547-y] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 07/06/2017] [Indexed: 12/16/2022] Open
Abstract
The capacity to coordinate environmental sensing with initiation of cellular responses underpins microbial survival and is crucial for virulence and stress responses in microbial pathogens. Here we define circuitry that enables the fungal pathogen Candida albicans to couple cell cycle dynamics with responses to cell wall stress induced by echinocandins, a front-line class of antifungal drugs. We discover that the C. albicans transcription factor Cas5 is crucial for proper cell cycle dynamics and responses to echinocandins, which inhibit β-1,3-glucan synthesis. Cas5 has distinct transcriptional targets under basal and stress conditions, is activated by the phosphatase Glc7, and can regulate the expression of target genes in concert with the transcriptional regulators Swi4 and Swi6. Thus, we illuminate a mechanism of transcriptional control that couples cell wall integrity with cell cycle regulation, and uncover circuitry governing antifungal drug resistance.Cas5 is a transcriptional regulator of responses to cell wall stress in the fungal pathogen Candida albicans. Here, Xie et al. show that Cas5 also modulates cell cycle dynamics and responses to antifungal drugs.
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Affiliation(s)
- Jinglin L Xie
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada, M5G 1M1
| | - Longguang Qin
- Faculty of Health Sciences, University of Macau, Macau SAR, 999078, China
| | - Zhengqiang Miao
- Faculty of Health Sciences, University of Macau, Macau SAR, 999078, China
| | - Ben T Grys
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada, M5G 1M1
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada, M5S 3E1
| | - Jacinto De La Cruz Diaz
- Department of Microbiology and Immunology, University of Rochester, Rochester, NY, 14642, USA
| | - Kenneth Ting
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada, M5G 1M1
| | - Jonathan R Krieger
- The Hospital for Sick Children, SPARC Biocentre, Toronto, ON, Canada, M5G 0A4
| | - Jiefei Tong
- The Hospital for Sick Children, Program in Cell Biology, Peter Gilgan Centre for Research and Learning, Toronto, ON, Canada, M5G 0A4
| | - Kaeling Tan
- Faculty of Health Sciences, University of Macau, Macau SAR, 999078, China
| | - Michelle D Leach
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada, M5G 1M1
- Aberdeen Fungal Group, School of Medical Sciences, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Abderdeen, AB252ZD, UK
| | - Troy Ketela
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada, M5G 1M1
| | - Michael F Moran
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada, M5G 1M1
- The Hospital for Sick Children, SPARC Biocentre, Toronto, ON, Canada, M5G 0A4
- The Hospital for Sick Children, Program in Cell Biology, Peter Gilgan Centre for Research and Learning, Toronto, ON, Canada, M5G 0A4
| | - Damian J Krysan
- Department of Microbiology and Immunology, University of Rochester, Rochester, NY, 14642, USA
- Department of Pediatrics and Microbiology/Immunology, University of Rochester, Rochester, NY, 14642, USA
| | - Charles Boone
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada, M5G 1M1
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada, M5S 3E1
| | - Brenda J Andrews
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada, M5G 1M1
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada, M5S 3E1
| | - Anna Selmecki
- Department of Medical Microbiology and Immunology, Creighton University School of Medicine, Omaha, NE, 68178, USA
| | - Koon Ho Wong
- Faculty of Health Sciences, University of Macau, Macau SAR, 999078, China
| | - Nicole Robbins
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada, M5G 1M1
| | - Leah E Cowen
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada, M5G 1M1.
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28
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Manipulation of nuclear architecture through CRISPR-mediated chromosomal looping. Nat Commun 2017; 8:15993. [PMID: 28703221 PMCID: PMC5511349 DOI: 10.1038/ncomms15993] [Citation(s) in RCA: 179] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 05/16/2017] [Indexed: 01/01/2023] Open
Abstract
Chromatin looping is key to gene regulation, yet no broadly applicable methods to selectively modify chromatin loops have been described. We have engineered a method for chromatin loop reorganization using CRISPR-dCas9 (CLOuD9) to selectively and reversibly establish chromatin loops. We demonstrate the power of this technology to selectively modulate gene expression at targeted loci.
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29
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Massart R, Suderman M, Mongrain V, Szyf M. DNA methylation and transcription onset in the brain. Epigenomics 2017; 9:797-809. [DOI: 10.2217/epi-2016-0184] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim: The goal of this study was to test the state of methylation of transcription start positions in DNA that are actively involved in transcription. Materials & methods: We used sequential ChIP-bisulfite-sequencing with an antibody to RNpolII-PS5 to map the state of methylation of actively transcribing transcription start sites (TSS). Results: TSS that RNApolII-PS5 physically bind to, are ubiquitously unmethylated. TSS that appear to be both heavily methylated and transcriptionally active are truly a mixture of unmethylated TSS with bound RNApolII-PS5 in some nuclei and unbound methylated TSS in other nuclei. Conclusion: TSS DNA methylation is universally inconsistent with transcription onset and could therefore serve as a digital count of the fraction of nuclei with methylation-silenced TSS.
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Affiliation(s)
- Renaud Massart
- Department of Pharmacology & Therapeutics, McGill University, Montreal, Quebec, Canada
- Inserm U955 Interventional NeuroPsychology Team, Ecole Normale Supérieure, PSL Research University
| | - Matthew Suderman
- Department of Pharmacology & Therapeutics, McGill University, Montreal, Quebec, Canada
- McGill Centre for Bioinformatics, McGill University, 3649 Promenade Sir William Osler, Montreal, Quebec H3G 0B1, Canada
- MRC Integrative Epidemiology Unit, School of Social & Community Medicine, University of Bristol, Bristol, UK
| | - Valerie Mongrain
- Department of Neuroscience, Université de Montréal & Research Center, Hôpital du Sacré-Coeur de Montréal, 5400 Gouin West blvd., Montreal, Quebec H4J1C5, Canada
| | - Moshe Szyf
- Department of Pharmacology & Therapeutics, McGill University, Montreal, Quebec, Canada
- Sackler Program for Epigenetics & Psychobiology, McGill University, Montreal, Quebec, Canada
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30
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Cheishvili D, Christiansen S, Stochinsky R, Pepin AS, Sapozhnikov DM, Zhou R, Schmeltzer L, Dymov S, Szyf M. DNA methylation controls unmethylated transcription start sites in the genome in trans. Epigenomics 2017; 9:611-633. [PMID: 28470094 DOI: 10.2217/epi-2016-0141] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
AIM DNA methylation downregulates transcription. However, a large number of genes, which are unmethylated in the promoter region, are inactive. We tested the hypothesis that these genes are regulated by DNA methylation of upstream regulators. METHODS We inhibited DNMT1 with 5-aza-2'-deoxycytidine or depleted it with shRNA to map the transcription initiation positions controlled by DNMT1 using ChIPseq with RNApolIIser5 antibody. Ingenuity pathway analysis identified potential methylated upstream regulators. Their functional role in controlling unmethylated promoters was determined by CRISPR/Cas9 gene editing. RESULTS We show that a large group of unmethylated promoters is regulated by DNMT1 through DNA methylation dependent silencing of upstream regulators such as transcription factor HNF4A. CONCLUSION The landscape of genes regulated by DNA methylation is more wide-ranging than genes downregulated by methylation of their own cis-regulatory sequences; regulation of unmethylated promoters is dependent on the methylation state of upstream trans regulators.
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Affiliation(s)
- David Cheishvili
- Department of Pharmacology & Therapeutics, McGill University, Montreal, Quebec, Canada
| | - Steffan Christiansen
- Department of Pharmacology & Therapeutics, McGill University, Montreal, Quebec, Canada.,Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Rebecca Stochinsky
- Department of Pharmacology & Therapeutics, McGill University, Montreal, Quebec, Canada
| | - Anne-Sophie Pepin
- Department of Pharmacology & Therapeutics, McGill University, Montreal, Quebec, Canada
| | - Daniel M Sapozhnikov
- Department of Pharmacology & Therapeutics, McGill University, Montreal, Quebec, Canada
| | - Rudy Zhou
- Department of Pharmacology & Therapeutics, McGill University, Montreal, Quebec, Canada
| | - Lauren Schmeltzer
- Department of Pharmacology & Therapeutics, McGill University, Montreal, Quebec, Canada
| | - Sergey Dymov
- Department of Pharmacology & Therapeutics, McGill University, Montreal, Quebec, Canada
| | - Moshe Szyf
- Department of Pharmacology & Therapeutics, McGill University, Montreal, Quebec, Canada.,Department of Pharmacology & Therapeutics, Sackler Program for Epigenetics & Developmental Psychobiology, McGill University Medical School, Montreal, Quebec, Canada.,Department of Pharmacology & Therapeutics, Canadian Institute for Advanced Research, Montreal, Quebec, Canada
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31
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Ohtsuka M, Ling H, Ivan C, Pichler M, Matsushita D, Goblirsch M, Stiegelbauer V, Shigeyasu K, Zhang X, Chen M, Vidhu F, Bartholomeusz GA, Toiyama Y, Kusunoki M, Doki Y, Mori M, Song S, Gunther JR, Krishnan S, Slaby O, Goel A, Ajani JA, Radovich M, Calin GA. H19 Noncoding RNA, an Independent Prognostic Factor, Regulates Essential Rb-E2F and CDK8-β-Catenin Signaling in Colorectal Cancer. EBioMedicine 2016; 13:113-124. [PMID: 27789274 PMCID: PMC5264449 DOI: 10.1016/j.ebiom.2016.10.026] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 10/16/2016] [Accepted: 10/18/2016] [Indexed: 02/06/2023] Open
Abstract
High H19 expression in primary tumors is an independent predictor of short overall survival in CRC patients. RB1-E2F and CDK8-β-catenin signaling are essential in mediating the oncogenic activity of H19 in CRC. Combined analysis of H19 and its targets further improved the prediction power on overall survival of CRC patients.
Long noncoding RNAs (lncRNAs) are transcripts at least 200 nucleotides long that do not code for proteins. The clinical relevance of lncRNAs in colorectal cancer (CRC) is largely unknown. Here we identified that H19 expression in primary tumors is an independent prognostic predictor of poor prognosis of CRC patients and further proved its oncogenic role. To characterize the mechanisms, we profiled gene expression changes following H19 modulation in CRC cell lines and analyzed gene expression association in clinical datasets. Our data revealed important cancer-signaling pathways, including the RB1-E2F and the CDK8-β-catenin signaling, underlying H19 function. The clinical significance of long noncoding RNAs (lncRNAs) in colorectal cancer (CRC) remains largely unexplored. Here, we analyzed a large panel of lncRNA candidates with The Cancer Genome Atlas (TCGA) CRC dataset, and identified H19 as the most significant lncRNA associated with CRC patient survival. We further validated such association in two independent CRC cohorts. H19 silencing blocked G1-S transition, reduced cell proliferation, and inhibited cell migration. We profiled gene expression changes to gain mechanism insight of H19 function. Transcriptome data analysis revealed not only previously identified mechanisms such as Let-7 regulation by H19, but also RB1-E2F1 function and β-catenin activity as essential upstream regulators mediating H19 function. Our experimental data showed that H19 affects phosphorylation of RB1 protein by regulating gene expression of CDK4 and CCND1. We further demonstrated that reduced CDK8 expression underlies changes of β-catenin activity, and identified that H19 interacts with macroH2A, an essential regulator of CDK8 gene transcription. However, the relevance of H19-macroH2A interaction in CDK8 regulation remains to be experimentally determined. We further explored the clinical relevance of above mechanisms in clinical samples, and showed that combined analysis of H19 with its targets improved prognostic value of H19 in CRC.
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Affiliation(s)
- Masahisa Ohtsuka
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Hui Ling
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Cristina Ivan
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Martin Pichler
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; Research Unit for non-coding RNA and genome editing, Division of Oncology, Medical University of Graz, Austria
| | - Daisuke Matsushita
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Matthew Goblirsch
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Verena Stiegelbauer
- Research Unit for non-coding RNA and genome editing, Division of Oncology, Medical University of Graz, Austria
| | - Kunitoshi Shigeyasu
- Center for Gastrointestinal Research, Baylor Research Institute and Charles A. Sammons Cancer Center, Baylor University Medical Center, Dallas, TX, USA
| | - Xinna Zhang
- Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Meng Chen
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Fnu Vidhu
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Geoffrey A Bartholomeusz
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yuji Toiyama
- Department of Gastrointestinal and Pediatric Surgery, Division of Reparative Medicine, Institute of Life Sciences, Mie University Graduate School of Medicine, Mie, Japan
| | - Masato Kusunoki
- Department of Gastrointestinal and Pediatric Surgery, Division of Reparative Medicine, Institute of Life Sciences, Mie University Graduate School of Medicine, Mie, Japan
| | - Yuichiro Doki
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Masaki Mori
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Shumei Song
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jillian R Gunther
- Department of Radiation Oncology, Division of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sunil Krishnan
- Department of Radiation Oncology, Division of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ondrej Slaby
- Central European Institute of Technology, Molecular Oncology II, Masaryk University, Brno, Czech Republic
| | - Ajay Goel
- Center for Gastrointestinal Research, Baylor Research Institute and Charles A. Sammons Cancer Center, Baylor University Medical Center, Dallas, TX, USA
| | - Jaffer A Ajani
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Milan Radovich
- Department of Surgery, Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - George A Calin
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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Btg2 is a Negative Regulator of Cardiomyocyte Hypertrophy through a Decrease in Cytosolic RNA. Sci Rep 2016; 6:28592. [PMID: 27346836 PMCID: PMC4921833 DOI: 10.1038/srep28592] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 06/06/2016] [Indexed: 12/27/2022] Open
Abstract
Under hypertrophic stimulation, cardiomyocytes enter a hypermetabolic state and accelerate biomass accumulation. Although the molecular pathways that regulate protein levels are well-studied, the functional implications of RNA accumulation and its regulatory mechanisms in cardiomyocytes remain elusive. Here, we have elucidated the quantitative kinetics of RNA in cardiomyocytes through single cell imaging and c-Myc (Myc)-mediated hypermetabolic analytical model using cultured cardiomyocytes. Nascent RNA labeling combined with single cell imaging demonstrated that Myc protein significantly increased the amount of global RNA production per cardiomyocyte. Chromatin immunoprecipitation with high-throughput sequencing clarified that overexpressed Myc bound to a specific set of genes and recruits RNA polymerase II. Among these genes, we identified Btg2 as a novel target of Myc. Btg2 overexpression significantly reduced cardiomyocyte surface area. Conversely, shRNA-mediated knockdown of Btg2 accelerated adrenergic stimulus-induced hypertrophy. Using mass spectrometry analysis, we determined that Btg2 binds a series of proteins that comprise mRNA deadenylation complexes. Intriguingly, Btg2 specifically suppresses cytosolic, but not nuclear, RNA levels. Btg2 knockdown further enhances cytosolic RNA accumulation in cardiomyocytes under adrenergic stimulation, suggesting that Btg2 negatively regulates reactive hypertrophy by negatively regulating RNA accumulation. Our findings provide insight into the functional significance of the mechanisms regulating RNA levels in cardiomyocytes.
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A Positive Regulatory Loop between a Wnt-Regulated Non-coding RNA and ASCL2 Controls Intestinal Stem Cell Fate. Cell Rep 2016; 15:2588-96. [DOI: 10.1016/j.celrep.2016.05.038] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Revised: 04/04/2016] [Accepted: 05/06/2016] [Indexed: 12/21/2022] Open
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Chen X, Jung JG, Shajahan-Haq AN, Clarke R, Shih IM, Wang Y, Magnani L, Wang TL, Xuan J. ChIP-BIT: Bayesian inference of target genes using a novel joint probabilistic model of ChIP-seq profiles. Nucleic Acids Res 2016; 44:e65. [PMID: 26704972 PMCID: PMC4838354 DOI: 10.1093/nar/gkv1491] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Revised: 11/16/2015] [Accepted: 12/09/2015] [Indexed: 11/16/2022] Open
Abstract
Chromatin immunoprecipitation with massively parallel DNA sequencing (ChIP-seq) has greatly improved the reliability with which transcription factor binding sites (TFBSs) can be identified from genome-wide profiling studies. Many computational tools are developed to detect binding events or peaks, however the robust detection of weak binding events remains a challenge for current peak calling tools. We have developed a novel Bayesian approach (ChIP-BIT) to reliably detect TFBSs and their target genes by jointly modeling binding signal intensities and binding locations of TFBSs. Specifically, a Gaussian mixture model is used to capture both binding and background signals in sample data. As a unique feature of ChIP-BIT, background signals are modeled by a local Gaussian distribution that is accurately estimated from the input data. Extensive simulation studies showed a significantly improved performance of ChIP-BIT in target gene prediction, particularly for detecting weak binding signals at gene promoter regions. We applied ChIP-BIT to find target genes from NOTCH3 and PBX1 ChIP-seq data acquired from MCF-7 breast cancer cells. TF knockdown experiments have initially validated about 30% of co-regulated target genes identified by ChIP-BIT as being differentially expressed in MCF-7 cells. Functional analysis on these genes further revealed the existence of crosstalk between Notch and Wnt signaling pathways.
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Affiliation(s)
- Xi Chen
- Bradley Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, 900 North Glebe Road, Arlington, VA 22203, USA
| | - Jin-Gyoung Jung
- Department of Pathology, Johns Hopkins Medical Institutions, 1550 Orleans Street, CRB-II, Baltimore, MD 21231, USA
| | - Ayesha N Shajahan-Haq
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, 3970 Reservoir Road NW, Washington, DC 20057, USA
| | - Robert Clarke
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, 3970 Reservoir Road NW, Washington, DC 20057, USA
| | - Ie-Ming Shih
- Department of Pathology, Johns Hopkins Medical Institutions, 1550 Orleans Street, CRB-II, Baltimore, MD 21231, USA
| | - Yue Wang
- Bradley Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, 900 North Glebe Road, Arlington, VA 22203, USA
| | - Luca Magnani
- Department of Surgery and Cancer, Imperial College London, ICTEM building, Hammersmith Hospital, DuCane Road, London W120NN, UK
| | - Tian-Li Wang
- Department of Pathology, Johns Hopkins Medical Institutions, 1550 Orleans Street, CRB-II, Baltimore, MD 21231, USA
| | - Jianhua Xuan
- Bradley Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, 900 North Glebe Road, Arlington, VA 22203, USA
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Dong K, Pang H, Tong T, Genton MG. Shrinkage-based diagonal Hotelling’s tests for high-dimensional small sample size data. J MULTIVARIATE ANAL 2016. [DOI: 10.1016/j.jmva.2015.08.022] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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36
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Dale T, Clarke PA, Esdar C, Waalboer D, Adeniji-Popoola O, Ortiz-Ruiz MJ, Mallinger A, Samant RS, Czodrowski P, Musil D, Schwarz D, Schneider K, Stubbs M, Ewan K, Fraser E, TePoele R, Court W, Box G, Valenti M, de Haven Brandon A, Gowan S, Rohdich F, Raynaud F, Schneider R, Poeschke O, Blaukat A, Workman P, Schiemann K, Eccles SA, Wienke D, Blagg J. A selective chemical probe for exploring the role of CDK8 and CDK19 in human disease. Nat Chem Biol 2015; 11:973-980. [PMID: 26502155 PMCID: PMC4677459 DOI: 10.1038/nchembio.1952] [Citation(s) in RCA: 105] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Accepted: 10/01/2015] [Indexed: 12/31/2022]
Abstract
There is unmet need for chemical tools to explore the role of the Mediator complex in human pathologies ranging from cancer to cardiovascular disease. Here we determine that CCT251545, a small-molecule inhibitor of the WNT pathway discovered through cell-based screening, is a potent and selective chemical probe for the human Mediator complex-associated protein kinases CDK8 and CDK19 with >100-fold selectivity over 291 other kinases. X-ray crystallography demonstrates a type 1 binding mode involving insertion of the CDK8 C terminus into the ligand binding site. In contrast to type II inhibitors of CDK8 and CDK19, CCT251545 displays potent cell-based activity. We show that CCT251545 and close analogs alter WNT pathway-regulated gene expression and other on-target effects of modulating CDK8 and CDK19, including expression of genes regulated by STAT1. Consistent with this, we find that phosphorylation of STAT1(SER727) is a biomarker of CDK8 kinase activity in vitro and in vivo. Finally, we demonstrate in vivo activity of CCT251545 in WNT-dependent tumors.
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Affiliation(s)
- Trevor Dale
- School of Bioscience, Cardiff University, Cardiff, UK
| | - Paul A. Clarke
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, SW7 3RP
| | | | - Dennis Waalboer
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, SW7 3RP
| | | | - Maria-Jesus Ortiz-Ruiz
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, SW7 3RP
| | - Aurélie Mallinger
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, SW7 3RP
| | - Rahul S. Samant
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, SW7 3RP
| | | | | | | | | | - Mark Stubbs
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, SW7 3RP
| | - Ken Ewan
- School of Bioscience, Cardiff University, Cardiff, UK
| | | | - Robert TePoele
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, SW7 3RP
| | - Will Court
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, SW7 3RP
| | - Gary Box
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, SW7 3RP
| | - Melanie Valenti
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, SW7 3RP
| | - Alexis de Haven Brandon
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, SW7 3RP
| | - Sharon Gowan
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, SW7 3RP
| | | | - Florence Raynaud
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, SW7 3RP
| | | | | | | | - Paul Workman
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, SW7 3RP
| | | | - Suzanne A. Eccles
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, SW7 3RP
| | - Dirk Wienke
- Merck KGaA, Merck Serono, Darmstadt, Germany
| | - Julian Blagg
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, SW7 3RP
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Furlan-Magaril M, Recillas-Targa F. Individual and Sequential Chromatin Immunoprecipitation Protocols. Methods Mol Biol 2015; 1334:205-18. [PMID: 26404152 DOI: 10.1007/978-1-4939-2877-4_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
DNA regulatory elements nucleate the interaction of several transcription factors in conjunction with ubiquitous and/or tissue-specific cofactors in order to regulate gene expression making it relevant to determine the profiles of cohabitation of several proteins on the chromatin fiber. Chromatin immunoprecipitation (ChIP) has been broadly used to determine the profile of several histone posttranslational modifications as well as transcription factor occupancy in vivo. However, individual ChIP does not resolve whether the epitope under study is present at the same time on a given genomic location. Here we describe the ChIP-re-ChIP assay that represents a direct strategy to determine the in vivo co-localization of proteins or histone posttranslational modifications in a chromatinized template on the basis of double and independent rounds of immunoprecipitation with high-quality ChIP-grade antibodies.
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Affiliation(s)
- Mayra Furlan-Magaril
- Nuclear Dynamics Programme, The Babraham Institute, Cambridge, CB22 3AT, UK.,Instituto de Fisiología Celular, Departamento de Genética Molecular, Universidad Nacional Autónoma de México, Mexico City, USA
| | - Félix Recillas-Targa
- Instituto de Fisiología Celular, Departamento de Genética Molecular, Universidad Nacional Autónoma de México, Mexico City, USA.
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He X, Zhang P. Serine/arginine-rich splicing factor 3 (SRSF3) regulates homologous recombination-mediated DNA repair. Mol Cancer 2015; 14:158. [PMID: 26282282 PMCID: PMC4539922 DOI: 10.1186/s12943-015-0422-1] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Accepted: 07/28/2015] [Indexed: 12/20/2022] Open
Abstract
Background Our previous work found that serine/arginine-rich splicing factor 3 (SRSF3) was overexpressed in human ovarian cancer and the overexpression of SRSF3 was required for ovarian cancer cell growth and survival. The mechanism underlying the role of SRSF3 in ovarian cancer remains to be addressed. Methods We conducted microarray analysis to profile the gene expression and splicing in SRSF3-knockdown cells and employed quantitative PCR and western blotting to validate the profiling results. We used chromatin immunoprecipitation to study transcription and the direct repeat green fluorescent protein reporter assay to study homologous recombination-mediated DNA repair (HRR). Results We identified 687 genes with altered expression and 807 genes with altered splicing in SRSF3-knockdown cells. Among expression-altered genes, those involved in HRR, including BRCA1, BRIP1 and RAD51, were enriched and were all downregulated. We demonstrated that the downregulation of BRCA1, BRIP1 and RAD51 expression was caused by decreased transcription and not due to increased nonsense-mediated mRNA decay. Further, we found that SRSF3 knockdown impaired HRR activity in the cell and increased the level of γ-H2AX, a biomarker for double-strand DNA breaks. Finally, we observed that SRSF3 knockdown changed splicing pattern of KMT2C, a H3K4-specific histone methyltransferase, and reduced the levels of mono- and trimethylated H3K4. Conclusion These results suggest that SRSF3 is a new regulator of HRR process, which possibly regulates the expression of HRR-related genes indirectly through an epigenetic pathway. This new function of SRSF3 not only explains why overexpression of SRSF3 is required for ovarian cancer cell growth and survival but also offers a new insight into the mechanism of the neoplastic transformation. Electronic supplementary material The online version of this article (doi:10.1186/s12943-015-0422-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xiaolong He
- Department of Biopharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago-Rockford Campus, 1601 Parkview Avenue, Room N308, Rockford, IL, 61107, USA. .,University of Illinois Cancer Center, University of Illinois at Chicago, Chicago, IL, USA.
| | - Pei Zhang
- Department of Biopharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago-Rockford Campus, 1601 Parkview Avenue, Room N308, Rockford, IL, 61107, USA.
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Maubant S, Tesson B, Maire V, Ye M, Rigaill G, Gentien D, Cruzalegui F, Tucker GC, Roman-Roman S, Dubois T. Transcriptome analysis of Wnt3a-treated triple-negative breast cancer cells. PLoS One 2015; 10:e0122333. [PMID: 25848952 PMCID: PMC4388387 DOI: 10.1371/journal.pone.0122333] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Accepted: 02/10/2015] [Indexed: 12/31/2022] Open
Abstract
The canonical Wnt/β-catenin pathway is activated in triple-negative breast cancer (TNBC). The activation of this pathway leads to the expression of specific target genes depending on the cell/tissue context. Here, we analyzed the transcriptome of two different TNBC cell lines to define a comprehensive list of Wnt target genes. The treatment of cells with Wnt3a for 6h up-regulated the expression (fold change > 1.3) of 59 genes in MDA-MB-468 cells and 241 genes in HCC38 cells. Thirty genes were common to both cell lines. Beta-catenin may also be a transcriptional repressor and we found that 18 and 166 genes were down-regulated in response to Wnt3a treatment for 6h in MDA-MB-468 and HCC38 cells, respectively, of which six were common to both cell lines. Only half of the activated and the repressed transcripts have been previously described as Wnt target genes. Therefore, our study reveals 137 novel genes that may be positively regulated by Wnt3a and 104 novel genes that may be negatively regulated by Wnt3a. These genes are involved in the Wnt pathway itself, and also in TGFβ, p53 and Hedgehog pathways. Thorough characterization of these novel potential Wnt target genes may reveal new regulators of the canonical Wnt pathway. The comparison of our list of Wnt target genes with those published in other cellular contexts confirms the notion that Wnt target genes are tissue-, cell line- and treatment-specific. Genes up-regulated in Wnt3a-stimulated cell lines were more strongly expressed in TNBC than in luminal A breast cancer samples. These genes were also overexpressed, but to a much lesser extent, in HER2+ and luminal B tumors. We identified 72 Wnt target genes higher expressed in TNBCs (17 with a fold change >1.3) which may reflect the chronic activation of the canonical Wnt pathway that occurs in TNBC tumors.
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Affiliation(s)
- Sylvie Maubant
- Breast Cancer Biology Group, Translational Research Department, Institut Curie, Centre de Recherche, Paris, France
| | - Bruno Tesson
- Breast Cancer Biology Group, Translational Research Department, Institut Curie, Centre de Recherche, Paris, France
- INSERM U900, Bioinformatics, Biostatistics, Epidemiology and Computational Systems Biology of Cancer, Institut Curie, Centre de Recherche, Paris, France
- Mines ParisTech, Fontainebleau, France
| | - Virginie Maire
- Breast Cancer Biology Group, Translational Research Department, Institut Curie, Centre de Recherche, Paris, France
| | - Mengliang Ye
- Breast Cancer Biology Group, Translational Research Department, Institut Curie, Centre de Recherche, Paris, France
| | - Guillem Rigaill
- Unité de Recherche en Génomique Végétale, INRA-CNRS-Université d'Evry Val d'Essonne, Evry, France
| | - David Gentien
- Platform of Molecular Biology Facilities, Translational Research Department, Institut Curie, Centre de Recherche, Paris, France
| | - Francisco Cruzalegui
- Institut de Recherches SERVIER, Pôle Innovation Thérapeutique Oncologie, Croissy-sur-Seine, France
| | - Gordon C. Tucker
- Institut de Recherches SERVIER, Pôle Innovation Thérapeutique Oncologie, Croissy-sur-Seine, France
| | - Sergio Roman-Roman
- Translational Research Department, Institut Curie, Centre de Recherche, Paris, France
| | - Thierry Dubois
- Breast Cancer Biology Group, Translational Research Department, Institut Curie, Centre de Recherche, Paris, France
- * E-mail:
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Madsen JGS, Schmidt SF, Larsen BD, Loft A, Nielsen R, Mandrup S. iRNA-seq: computational method for genome-wide assessment of acute transcriptional regulation from total RNA-seq data. Nucleic Acids Res 2015; 43:e40. [PMID: 25564527 PMCID: PMC4381047 DOI: 10.1093/nar/gku1365] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Accepted: 12/19/2014] [Indexed: 11/21/2022] Open
Abstract
RNA-seq is a sensitive and accurate technique to compare steady-state levels of RNA between different cellular states. However, as it does not provide an account of transcriptional activity per se, other technologies are needed to more precisely determine acute transcriptional responses. Here, we have developed an easy, sensitive and accurate novel computational method, iRNA-seq, for genome-wide assessment of transcriptional activity based on analysis of intron coverage from total RNA-seq data. Comparison of the results derived from iRNA-seq analyses with parallel results derived using current methods for genome-wide determination of transcriptional activity, i.e. global run-on (GRO)-seq and RNA polymerase II (RNAPII) ChIP-seq, demonstrate that iRNA-seq provides similar results in terms of number of regulated genes and their fold change. However, unlike the current methods that are all very labor-intensive and demanding in terms of sample material and technologies, iRNA-seq is cheap and easy and requires very little sample material. In conclusion, iRNA-seq offers an attractive novel alternative to current methods for determination of changes in transcriptional activity at a genome-wide level.
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Affiliation(s)
- Jesper Grud Skat Madsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M 5230, Denmark NNF Center of Basic Metabolic Research, University of Copenhagen, Copenhagen 2200, Denmark
| | - Søren Fisker Schmidt
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M 5230, Denmark
| | - Bjørk Ditlev Larsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M 5230, Denmark
| | - Anne Loft
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M 5230, Denmark
| | - Ronni Nielsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M 5230, Denmark
| | - Susanne Mandrup
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M 5230, Denmark
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Sinha S. Reproducibility of parameter learning with missing observations in naive Wnt Bayesian network trained on colorectal cancer samples and doxycycline-treated cell lines. ACTA ACUST UNITED AC 2015; 11:1802-19. [DOI: 10.1039/c5mb00117j] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Moulos P, Hatzis P. Systematic integration of RNA-Seq statistical algorithms for accurate detection of differential gene expression patterns. Nucleic Acids Res 2014; 43:e25. [PMID: 25452340 PMCID: PMC4344485 DOI: 10.1093/nar/gku1273] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
RNA-Seq is gradually becoming the standard tool for transcriptomic expression studies in biological research. Although considerable progress has been recorded in the development of statistical algorithms for the detection of differentially expressed genes using RNA-Seq data, the list of detected genes can differ significantly between algorithms. We present a new method (PANDORA) that combines multiple algorithms toward a summarized result, more efficiently reflecting true experimental outcomes. This is achieved through the systematic combination of several analysis algorithms, by weighting their outcomes according to their performance with realistically simulated data sets generated from real data. Results supported by the analysis of both simulated and real data from different organisms as well as correlation with PolII occupancy demonstrate that PANDORA improves the detection of differential expression. It accomplishes this by optimizing the tradeoff between standard performance measurements, such as precision and sensitivity.
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Affiliation(s)
- Panagiotis Moulos
- Biomedical Sciences Research Center 'Alexander Fleming', 34 Fleming str, 16672, Vari, Greece
| | - Pantelis Hatzis
- Biomedical Sciences Research Center 'Alexander Fleming', 34 Fleming str, 16672, Vari, Greece
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43
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Rai R, Zhu L, Chen H, Gupta AP, Sze SK, Zheng J, Ruedl C, Bozdech Z, Featherstone M. Genome-wide analysis in Plasmodium falciparum reveals early and late phases of RNA polymerase II occupancy during the infectious cycle. BMC Genomics 2014; 15:959. [PMID: 25373614 PMCID: PMC4232647 DOI: 10.1186/1471-2164-15-959] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Accepted: 10/23/2014] [Indexed: 01/06/2023] Open
Abstract
Background Over the course of its intraerythrocytic developmental cycle (IDC), the malaria parasite Plasmodium falciparum tightly orchestrates the rise and fall of transcript levels for hundreds of genes. Considerable debate has focused on the relative importance of transcriptional versus post-transcriptional processes in the regulation of transcript levels. Enzymatically active forms of RNAPII in other organisms have been associated with phosphorylation on the serines at positions 2 and 5 of the heptad repeats within the C-terminal domain (CTD) of RNAPII. We reasoned that insight into the contribution of transcriptional mechanisms to gene expression in P. falciparum could be obtained by comparing the presence of enzymatically active forms of RNAPII at multiple genes with the abundance of their associated transcripts. Results We exploited the phosphorylation state of the CTD to detect enzymatically active forms of RNAPII at most P. falciparum genes across the IDC. We raised highly specific monoclonal antibodies against three forms of the parasite CTD, namely unphosphorylated, Ser5-P and Ser2/5-P, and used these in ChIP-on-chip type experiments to map the genome-wide occupancy of RNAPII. Our data reveal that the IDC is divided into early and late phases of RNAPII occupancy evident from simple bi-phasic RNAPII binding profiles. By comparison to mRNA abundance, we identified sub-sets of genes with high occupancy by enzymatically active forms of RNAPII and relatively low transcript levels and vice versa. We further show that the presence of active and repressive histone modifications correlates with RNAPII occupancy over the IDC. Conclusions The simple early/late occupancy by RNAPII cannot account for the complex dynamics of mRNA accumulation over the IDC, suggesting a major role for mechanisms acting downstream of RNAPII occupancy in the control of gene expression in this parasite. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-959) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | | | - Zbynek Bozdech
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore.
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Sycheva AM, Kel A, Nikolaev EN, Moshkovskii SA. Equal impact of diffusion and DNA binding rates on the potential spatial distribution of nuclear factor κB transcription factor inside the nucleus. BIOCHEMISTRY (MOSCOW) 2014; 79:577-80. [PMID: 25100017 DOI: 10.1134/s0006297914060121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
There are two physical processes that influence the spatial distribution of transcription factor molecules entering the nucleus of a eukaryotic cell, the binding to genomic DNA and the diffusion throughout the nuclear volume. Comparison of the DNA-protein association rate constant and the protein diffusion constant may determine which one is the limiting factor. If the process is diffusion-limited, transcription factor molecules are captured by DNA before their even distribution in the nuclear volume. Otherwise, if the reaction rate is limiting, these molecules diffuse evenly and then find their binding sites. Using well-studied human NF-κB dimer as an example, we calculated its diffusion constant using the Debye-Smoluchowski equation. The value of diffusion constant was about 10(-15) cm(3)/s, and it was comparable to the NF-κB association rate constant for DNA binding known from previous studies. Thus, both diffusion and DNA binding play an equally important role in NF-κB spatial distribution. The importance of genome 3D-structure in gene expression regulation and possible dependence of gene expression on the local concentration of open chromatin can be hypothesized from our theoretical estimate.
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Affiliation(s)
- A M Sycheva
- Orekhovich Institute of Biomedical Chemistry, Russian Academy of Medical Sciences, Moscow, 119121, Russia.
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45
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Whissell G, Montagni E, Martinelli P, Hernando-Momblona X, Sevillano M, Jung P, Cortina C, Calon A, Abuli A, Castells A, Castellvi-Bel S, Nacht AS, Sancho E, Stephan-Otto Attolini C, Vicent GP, Real FX, Batlle E. The transcription factor GATA6 enables self-renewal of colon adenoma stem cells by repressing BMP gene expression. Nat Cell Biol 2014; 16:695-707. [PMID: 24952462 DOI: 10.1038/ncb2992] [Citation(s) in RCA: 98] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Accepted: 05/20/2014] [Indexed: 02/07/2023]
Abstract
Aberrant activation of WNT signalling and loss of BMP signals represent the two main alterations leading to the initiation of colorectal cancer (CRC). Here we screen for genes required for maintaining the tumour stem cell phenotype and identify the zinc-finger transcription factor GATA6 as a key regulator of the WNT and BMP pathways in CRC. GATA6 directly drives the expression of LGR5 in adenoma stem cells whereas it restricts BMP signalling to differentiated tumour cells. Genetic deletion of Gata6 from mouse colon adenomas increases the levels of BMP factors, which signal to block self-renewal of tumour stem cells. In human tumours, GATA6 competes with β-catenin/TCF4 for binding to a distal regulatory region of the BMP4 locus that has been linked to increased susceptibility to development of CRC. Hence, GATA6 creates an environment permissive for CRC initiation by lowering the threshold of BMP signalling required for tumour stem cell expansion.
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Affiliation(s)
- Gavin Whissell
- Institute for Research in Biomedicine (IRB Barcelona), 08028 Barcelona, Spain
| | - Elisa Montagni
- 1] Institute for Research in Biomedicine (IRB Barcelona), 08028 Barcelona, Spain [2]
| | - Paola Martinelli
- 1] Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain [2]
| | | | - Marta Sevillano
- Institute for Research in Biomedicine (IRB Barcelona), 08028 Barcelona, Spain
| | - Peter Jung
- Institute for Research in Biomedicine (IRB Barcelona), 08028 Barcelona, Spain
| | - Carme Cortina
- Institute for Research in Biomedicine (IRB Barcelona), 08028 Barcelona, Spain
| | - Alexandre Calon
- Institute for Research in Biomedicine (IRB Barcelona), 08028 Barcelona, Spain
| | - Anna Abuli
- 1] Department of Gastroenterology, Hospital Clínic, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona, 08036 Barcelona, Catalonia, Spain [2] Department of Gastroenterology, Hospital del Mar-IMIM (Hospital del Mar Medical Research Centre), Pompeu Fabra University, 08003 Barcelona, Catalonia, Spain
| | - Antoni Castells
- Department of Gastroenterology, Hospital Clínic, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona, 08036 Barcelona, Catalonia, Spain
| | - Sergi Castellvi-Bel
- Department of Gastroenterology, Hospital Clínic, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona, 08036 Barcelona, Catalonia, Spain
| | - Ana Silvina Nacht
- Centre de Regulació Genòmica (CRG), Universitat Pompeu Fabra (UPF), E-08003 Barcelona, Spain
| | - Elena Sancho
- Institute for Research in Biomedicine (IRB Barcelona), 08028 Barcelona, Spain
| | | | - Guillermo P Vicent
- Centre de Regulació Genòmica (CRG), Universitat Pompeu Fabra (UPF), E-08003 Barcelona, Spain
| | - Francisco X Real
- 1] Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain [2] Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Eduard Batlle
- 1] Institute for Research in Biomedicine (IRB Barcelona), 08028 Barcelona, Spain [2] Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
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Verhaegh W, van Ooijen H, Inda MA, Hatzis P, Versteeg R, Smid M, Martens J, Foekens J, van de Wiel P, Clevers H, van de Stolpe A. Selection of personalized patient therapy through the use of knowledge-based computational models that identify tumor-driving signal transduction pathways. Cancer Res 2014; 74:2936-45. [PMID: 24695361 DOI: 10.1158/0008-5472.can-13-2515] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Increasing knowledge about signal transduction pathways as drivers of cancer growth has elicited the development of "targeted drugs," which inhibit aberrant signaling pathways. They require a companion diagnostic test that identifies the tumor-driving pathway; however, currently available tests like estrogen receptor (ER) protein expression for hormonal treatment of breast cancer do not reliably predict therapy response, at least in part because they do not adequately assess functional pathway activity. We describe a novel approach to predict signaling pathway activity based on knowledge-based Bayesian computational models, which interpret quantitative transcriptome data as the functional output of an active signaling pathway, by using expression levels of transcriptional target genes. Following calibration on only a small number of cell lines or cohorts of patient data, they provide a reliable assessment of signaling pathway activity in tumors of different tissue origin. As proof of principle, models for the canonical Wnt and ER pathways are presented, including initial clinical validation on independent datasets from various cancer types.
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Affiliation(s)
- Wim Verhaegh
- Authors' Affiliations: Molecular Diagnostics, Philips Research, Eindhoven; Hubrecht Institute, Utrecht; Human Genetics, AMC, Amsterdam; and Medical Oncology, Erasmus MC, Rotterdam, the Netherlands
| | - Henk van Ooijen
- Authors' Affiliations: Molecular Diagnostics, Philips Research, Eindhoven; Hubrecht Institute, Utrecht; Human Genetics, AMC, Amsterdam; and Medical Oncology, Erasmus MC, Rotterdam, the Netherlands
| | - Márcia A Inda
- Authors' Affiliations: Molecular Diagnostics, Philips Research, Eindhoven; Hubrecht Institute, Utrecht; Human Genetics, AMC, Amsterdam; and Medical Oncology, Erasmus MC, Rotterdam, the Netherlands
| | - Pantelis Hatzis
- Authors' Affiliations: Molecular Diagnostics, Philips Research, Eindhoven; Hubrecht Institute, Utrecht; Human Genetics, AMC, Amsterdam; and Medical Oncology, Erasmus MC, Rotterdam, the Netherlands
| | - Rogier Versteeg
- Authors' Affiliations: Molecular Diagnostics, Philips Research, Eindhoven; Hubrecht Institute, Utrecht; Human Genetics, AMC, Amsterdam; and Medical Oncology, Erasmus MC, Rotterdam, the Netherlands
| | - Marcel Smid
- Authors' Affiliations: Molecular Diagnostics, Philips Research, Eindhoven; Hubrecht Institute, Utrecht; Human Genetics, AMC, Amsterdam; and Medical Oncology, Erasmus MC, Rotterdam, the Netherlands
| | - John Martens
- Authors' Affiliations: Molecular Diagnostics, Philips Research, Eindhoven; Hubrecht Institute, Utrecht; Human Genetics, AMC, Amsterdam; and Medical Oncology, Erasmus MC, Rotterdam, the Netherlands
| | - John Foekens
- Authors' Affiliations: Molecular Diagnostics, Philips Research, Eindhoven; Hubrecht Institute, Utrecht; Human Genetics, AMC, Amsterdam; and Medical Oncology, Erasmus MC, Rotterdam, the Netherlands
| | - Paul van de Wiel
- Authors' Affiliations: Molecular Diagnostics, Philips Research, Eindhoven; Hubrecht Institute, Utrecht; Human Genetics, AMC, Amsterdam; and Medical Oncology, Erasmus MC, Rotterdam, the Netherlands
| | - Hans Clevers
- Authors' Affiliations: Molecular Diagnostics, Philips Research, Eindhoven; Hubrecht Institute, Utrecht; Human Genetics, AMC, Amsterdam; and Medical Oncology, Erasmus MC, Rotterdam, the Netherlands
| | - Anja van de Stolpe
- Authors' Affiliations: Molecular Diagnostics, Philips Research, Eindhoven; Hubrecht Institute, Utrecht; Human Genetics, AMC, Amsterdam; and Medical Oncology, Erasmus MC, Rotterdam, the Netherlands
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Mokry M, Middendorp S, Wiegerinck CL, Witte M, Teunissen H, Meddens CA, Cuppen E, Clevers H, Nieuwenhuis EES. Many inflammatory bowel disease risk loci include regions that regulate gene expression in immune cells and the intestinal epithelium. Gastroenterology 2014; 146:1040-7. [PMID: 24333384 DOI: 10.1053/j.gastro.2013.12.003] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Revised: 11/30/2013] [Accepted: 12/03/2013] [Indexed: 12/12/2022]
Abstract
BACKGROUND & AIMS The contribution of genetic factors to the pathogenesis of inflammatory bowel disease (IBD) has been established by twin, targeted-sequencing, and genome-wide association studies. These studies identified many risk loci, and research is underway to identify causal variants. These studies have focused mainly on protein-coding genes. We investigated other functional elements in the human genome, such as regulatory regions. METHODS Using acetylated histone 3 lysine 27 chromatin immunoprecipitation and sequencing, we identified tens of thousands of potential regulatory regions that are active in intestinal epithelium (primary intestinal crypts and cultured organoids) isolated from resected material and from biopsies collected during ileo-colonoscopies and immune cells (monocytes, macrophages, CD34(+), CD4(+), and CD8(+)). We correlated these regions with susceptibility loci for IBD. RESULTS We have generated acetylated histone 3 lysine 27 profiles from primary intestinal epithelium and cultured organoids, which we have made publically available. We found that 45 of 163 single nucleotide polymorphisms (SNPs) associated with IBD overlap specifically with active regulatory elements. In addition, by taking strong linkage disequilibrium into account, another 47 IBD-associated SNPs colocalized with active regulatory elements through other SNPs in their vicinity. Altogether, 92 of 163 IBD-associated SNPs correlated with distinct active regulatory elements-a frequency 2.5- to 3.5-fold greater than that expected from random sampling. The variations in these SNPs often create or disrupt known binding motifs; they might affect the binding of transcriptional regulators to alter expression of regulated genes. CONCLUSIONS In addition to variants in protein coding genes, variants in noncoding DNA regulatory regions that are active in intestinal epithelium and immune cells are potentially involved in the pathogenesis of IBD.
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Affiliation(s)
- Michal Mokry
- Division of Pediatrics, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Sabine Middendorp
- Division of Pediatrics, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Caroline L Wiegerinck
- Division of Pediatrics, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Merlijn Witte
- Division of Pediatrics, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, The Netherlands; Hubrecht Institute for Stem Cell Research, Utrecht, The Netherlands
| | - Hans Teunissen
- Division of Pediatrics, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, The Netherlands; Hubrecht Institute for Stem Cell Research, Utrecht, The Netherlands
| | - Claartje A Meddens
- Division of Pediatrics, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Edwin Cuppen
- Hubrecht Institute for Stem Cell Research, Utrecht, The Netherlands; Department of Medical Genetics, Medical Center Utrecht, Utrecht, The Netherlands
| | - Hans Clevers
- Hubrecht Institute for Stem Cell Research, Utrecht, The Netherlands
| | - Edward E S Nieuwenhuis
- Division of Pediatrics, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, The Netherlands.
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González-González M, Fontanillo C, Abad MM, Gutiérrez ML, Mota I, Bengoechea O, Santos-Briz Á, Blanco O, Fonseca E, Ciudad J, Fuentes M, De Las Rivas J, Alcazar JA, García J, Muñoz-Bellvis L, Orfao A, Sayagués JM. Identification of a characteristic copy number alteration profile by high-resolution single nucleotide polymorphism arrays associated with metastatic sporadic colorectal cancer. Cancer 2014; 120:1948-59. [DOI: 10.1002/cncr.28681] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Revised: 01/07/2014] [Accepted: 02/12/2014] [Indexed: 01/16/2023]
Affiliation(s)
- María González-González
- General Cytometry Service-Nucleus; Department of Medicine and Cancer Research Center; Institute of Molecular Biology and Cellular Oncology of the University of Salamanca and Salamanca Institute of Biomedical Research; University of Salamanca; Salamanca Spain
| | - Celia Fontanillo
- Bioinformatics and Functional Genomics Unit; Institute of Molecular Biology and Cellular Oncology/Spanish National Research Council; University of Salamanca; Salamanca Spain
- Celgene Institute for Translational Research Europe (CITRE); Seville Spain
| | - María M. Abad
- Department of Pathology; University Hospital of Salamanca-Salamanca Institute of Biomedical Research; Salamanca Spain
| | - María L. Gutiérrez
- General Cytometry Service-Nucleus; Department of Medicine and Cancer Research Center; Institute of Molecular Biology and Cellular Oncology of the University of Salamanca and Salamanca Institute of Biomedical Research; University of Salamanca; Salamanca Spain
| | - Ines Mota
- General Cytometry Service-Nucleus; Department of Medicine and Cancer Research Center; Institute of Molecular Biology and Cellular Oncology of the University of Salamanca and Salamanca Institute of Biomedical Research; University of Salamanca; Salamanca Spain
| | - Oscar Bengoechea
- Department of Pathology; University Hospital of Salamanca-Salamanca Institute of Biomedical Research; Salamanca Spain
| | - Ángel Santos-Briz
- Department of Pathology; University Hospital of Salamanca-Salamanca Institute of Biomedical Research; Salamanca Spain
| | - Oscar Blanco
- Department of Pathology; University Hospital of Salamanca-Salamanca Institute of Biomedical Research; Salamanca Spain
| | - Emilio Fonseca
- Service of Medical Oncology; University Hospital of Salamanca-Salamanca Institute of Biomedical Research; Salamanca Spain
| | - Juana Ciudad
- General Cytometry Service-Nucleus; Department of Medicine and Cancer Research Center; Institute of Molecular Biology and Cellular Oncology of the University of Salamanca and Salamanca Institute of Biomedical Research; University of Salamanca; Salamanca Spain
| | - Manuel Fuentes
- General Cytometry Service-Nucleus; Department of Medicine and Cancer Research Center; Institute of Molecular Biology and Cellular Oncology of the University of Salamanca and Salamanca Institute of Biomedical Research; University of Salamanca; Salamanca Spain
| | - Javier De Las Rivas
- Bioinformatics and Functional Genomics Unit; Institute of Molecular Biology and Cellular Oncology/Spanish National Research Council; University of Salamanca; Salamanca Spain
| | - José A. Alcazar
- Department of General and Digestive Surgery; University Hospital of Salamanca-Salamanca Institute of Biomedical Research; Salamanca Spain
| | - Jacinto García
- Department of General and Digestive Surgery; University Hospital of Salamanca-Salamanca Institute of Biomedical Research; Salamanca Spain
| | - Luís Muñoz-Bellvis
- Department of General and Digestive Surgery; University Hospital of Salamanca-Salamanca Institute of Biomedical Research; Salamanca Spain
| | - Alberto Orfao
- General Cytometry Service-Nucleus; Department of Medicine and Cancer Research Center; Institute of Molecular Biology and Cellular Oncology of the University of Salamanca and Salamanca Institute of Biomedical Research; University of Salamanca; Salamanca Spain
| | - José M. Sayagués
- General Cytometry Service-Nucleus; Department of Medicine and Cancer Research Center; Institute of Molecular Biology and Cellular Oncology of the University of Salamanca and Salamanca Institute of Biomedical Research; University of Salamanca; Salamanca Spain
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49
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Comprehensive analysis of β-catenin target genes in colorectal carcinoma cell lines with deregulated Wnt/β-catenin signaling. BMC Genomics 2014; 15:74. [PMID: 24467841 PMCID: PMC3909937 DOI: 10.1186/1471-2164-15-74] [Citation(s) in RCA: 168] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Accepted: 01/17/2014] [Indexed: 12/12/2022] Open
Abstract
Background Deregulation of Wnt/β-catenin signaling is a hallmark of the majority of sporadic forms of colorectal cancer and results in increased stability of the protein β-catenin. β-catenin is then shuttled into the nucleus where it activates the transcription of its target genes, including the proto-oncogenes MYC and CCND1 as well as the genes encoding the basic helix-loop-helix (bHLH) proteins ASCL2 and ITF-2B. To identify genes commonly regulated by β-catenin in colorectal cancer cell lines, we analyzed β-catenin target gene expression in two non-isogenic cell lines, DLD1 and SW480, using DNA microarrays and compared these genes to β-catenin target genes published in the PubMed database and DNA microarray data presented in the Gene Expression Omnibus (GEO) database. Results Treatment of DLD1 and SW480 cells with β-catenin siRNA resulted in differential expression of 1501 and 2389 genes, respectively. 335 of these genes were regulated in the same direction in both cell lines. Comparison of these data with published β-catenin target genes for the colon carcinoma cell line LS174T revealed 193 genes that are regulated similarly in all three cell lines. The overlapping gene set includes confirmed β-catenin target genes like AXIN2, MYC, and ASCL2. We also identified 11 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways that are regulated similarly in DLD1 and SW480 cells and one pathway – the steroid biosynthesis pathway – was regulated in all three cell lines. Conclusions Based on the large number of potential β-catenin target genes found to be similarly regulated in DLD1, SW480 and LS174T cells as well as the large overlap with confirmed β-catenin target genes, we conclude that DLD1 and SW480 colon carcinoma cell lines are suitable model systems to study Wnt/β-catenin signaling and associated colorectal carcinogenesis. Furthermore, the confirmed and the newly identified potential β-catenin target genes are useful starting points for further studies.
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50
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Eijkelenboom A, Mokry M, Smits LM, Nieuwenhuis EE, Burgering BMT. FOXO3 selectively amplifies enhancer activity to establish target gene regulation. Cell Rep 2013; 5:1664-78. [PMID: 24360957 DOI: 10.1016/j.celrep.2013.11.031] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2013] [Revised: 08/29/2013] [Accepted: 11/15/2013] [Indexed: 12/22/2022] Open
Abstract
Forkhead box O (FOXO) transcription factors regulate diverse cellular processes, affecting tumorigenesis, metabolism, stem cell maintenance, and lifespan. We show that FOXO3 transcription regulation mainly proceeds through the most active subset of enhancers. In addition to the general distinction between "open" and "closed" chromatin, we show that the level of activity marks (H3K27ac, RNAPII, enhancer RNAs) of these open chromatin regions prior to FOXO3 activation largely determines FOXO3 DNA binding. Consequently, FOXO3 amplifies the levels of these activity marks and their absolute rather than relative changes associate best with FOXO3 target gene regulation. The importance of preexisting chromatin state in directing FOXO3 gene regulation, as shown here, provides a mechanism whereby FOXO3 can regulate cell-specific homeostasis. Genetic variation is reported to affect these chromatin signatures in a quantitative manner, and, in agreement, we observe a correlation between cancer-associated genetic variations and the amplitude of FOXO3 enhancer binding.
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Affiliation(s)
- Astrid Eijkelenboom
- Department of Molecular Cancer Research, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG Utrecht, the Netherlands
| | - Michal Mokry
- Division of Pediatrics, Wilhelmina Children's Hospital, University Medical Center Utrecht, Lundlaan 6, 3584 EA Utrecht, the Netherlands
| | - Lydia M Smits
- Department of Molecular Cancer Research, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG Utrecht, the Netherlands
| | - Edward E Nieuwenhuis
- Division of Pediatrics, Wilhelmina Children's Hospital, University Medical Center Utrecht, Lundlaan 6, 3584 EA Utrecht, the Netherlands
| | - Boudewijn M T Burgering
- Department of Molecular Cancer Research, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG Utrecht, the Netherlands.
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