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Díaz-López YE, Cázares-Domínguez V, Arenas-Huertero F, Gutierrez-Aguilar R. ETV5 Silencing Produces Mesenchymal to Epithelial Transition in INS-1 (832/13) Cell Line. Horm Metab Res 2024; 56:235-243. [PMID: 38335994 DOI: 10.1055/a-2246-4778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/12/2024]
Abstract
ETV5 has been described to be involved in the epithelial to mesenchymal transition (EMT) mainly in cancer. It is known that EMT provokes cytoskeleton remodeling, improving cellular migratory, and invasive capabilities. Moreover, overexpression of ETV5 has been correlated to cancer development and this gene has been implicated in cell proliferation. However, little is known about the downregulation of ETV5 expression in a pancreatic cell line and the inverse mesenchymal to epithelial transition (MET). Therefore, we studied the implications of ETV5 silencing over the phenotype of the insulinoma INS-1 (832/13) cell line and described the MET by partial ETV5 silencing in the INS-1 (832/13) cell line. The downregulation of ETV5 expression was obtained by using ETV5 siRNA in the insulinoma rat cell line, INS-1 (832/13). Then, ETV5 knockdown provoked a MET phenotype observed by crystal violet staining and verified by immunohistochemistry against E-cadherin. Wound healing assay showed no migration, and F-actin stain revealed rearrangement of actin microfilaments. In addition, TGFβ1 and TGFβ3 were downregulated in the absence of ETV5. ETV5 silencing induces epithelial phenotype by downregulating TGFβ1 and TGFβ3 in INS-1 (832/13) cell line.
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Affiliation(s)
- Yael Efrén Díaz-López
- División de Investigación, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Laboratorio de Investigación en Enfermedades Metabólicas, Obesidad y Diabetes, Hospital Infantil de México Federico Gomez, Mexico City, Mexico
| | - Vicenta Cázares-Domínguez
- Laboratorio de Investigación en Enfermedades Metabólicas, Obesidad y Diabetes, Hospital Infantil de México Federico Gomez, Mexico City, Mexico
| | - Francisco Arenas-Huertero
- Laboratorio de Investigación en Patología Experimental, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
| | - Ruth Gutierrez-Aguilar
- División de Investigación, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Laboratorio de Investigación en Enfermedades Metabólicas, Obesidad y Diabetes, Hospital Infantil de México Federico Gomez, Mexico City, Mexico
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2
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Weng C, Gu A, Zhang S, Lu L, Ke L, Gao P, Liu X, Wang Y, Hu P, Plummer D, MacDonald E, Zhang S, Xi J, Lai S, Leskov K, Yuan K, Jin F, Li Y. Single cell multiomic analysis reveals diabetes-associated β-cell heterogeneity driven by HNF1A. Nat Commun 2023; 14:5400. [PMID: 37669939 PMCID: PMC10480445 DOI: 10.1038/s41467-023-41228-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 08/29/2023] [Indexed: 09/07/2023] Open
Abstract
Broad heterogeneity in pancreatic β-cell function and morphology has been widely reported. However, determining which components of this cellular heterogeneity serve a diabetes-relevant function remains challenging. Here, we integrate single-cell transcriptome, single-nuclei chromatin accessibility, and cell-type specific 3D genome profiles from human islets and identify Type II Diabetes (T2D)-associated β-cell heterogeneity at both transcriptomic and epigenomic levels. We develop a computational method to explicitly dissect the intra-donor and inter-donor heterogeneity between single β-cells, which reflect distinct mechanisms of T2D pathogenesis. Integrative transcriptomic and epigenomic analysis identifies HNF1A as a principal driver of intra-donor heterogeneity between β-cells from the same donors; HNF1A expression is also reduced in β-cells from T2D donors. Interestingly, HNF1A activity in single β-cells is significantly associated with lower Na+ currents and we nominate a HNF1A target, FXYD2, as the primary mitigator. Our study demonstrates the value of investigating disease-associated single-cell heterogeneity and provides new insights into the pathogenesis of T2D.
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Affiliation(s)
- Chen Weng
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
- The Biomedical Sciences Training Program (BSTP), School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Anniya Gu
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
- Medical Scientist Training Program (MSTP), School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Shanshan Zhang
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
- The Biomedical Sciences Training Program (BSTP), School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Leina Lu
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Luxin Ke
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
- The Biomedical Sciences Training Program (BSTP), School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Peidong Gao
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Xiaoxiao Liu
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Yuntong Wang
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Peinan Hu
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
- The Biomedical Sciences Training Program (BSTP), School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Dylan Plummer
- Department of Computer and Data Sciences, School of Engineering, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Elise MacDonald
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Saixian Zhang
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Jiajia Xi
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Sisi Lai
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
- The Biomedical Sciences Training Program (BSTP), School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Konstantin Leskov
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Kyle Yuan
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
- Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Fulai Jin
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA.
- Department of Computer and Data Sciences, School of Engineering, Case Western Reserve University, Cleveland, OH, 44106, USA.
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, 44106, USA.
- Department of Population and Quantitative Health Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA.
| | - Yan Li
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA.
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Long Non-Coding RNAs Associated with Mitogen-Activated Protein Kinase in Human Pancreatic Cancer. Cancers (Basel) 2023; 15:cancers15010303. [PMID: 36612299 PMCID: PMC9818929 DOI: 10.3390/cancers15010303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 12/26/2022] [Accepted: 12/29/2022] [Indexed: 01/03/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) have emerged as a significant player in various cancers, including pancreatic cancer. However, how lncRNAs are aberrantly expressed in cancers is largely unknown. We hypothesized that lncRNAs would be regulated by signaling pathways and contribute to malignant phenotypes of cancer. In this study, to understand the significance of mitogen-activated protein kinase/extracellular signal-regulated kinase (MAPK/ERK), which is a major aberrant signaling pathway in pancreatic cancer, for the expression of lncRNAs, we performed comparative transcriptome analyses between pancreatic cancer cell lines with or without activation of MAPK. We identified 45 lncRNAs presumably associated with MAPK in pancreatic cancer cells; among these, LINC00941 was consistently upregulated by MAPK. The immediate genomic upstream region flanking LINC00941 was identified as a promoter region, the activity of which was found to be preferentially associated with MAPK activity via ETS-1 binding site. LINC00941 promoted cell proliferation in vitro. Moreover, TCGA data analysis indicated that high expression of LINC00941 was associated with poor prognosis of patients with pancreatic cancer. Transcriptomes comparing transcriptions between cells with and without LINC00941 knockdown revealed 3229 differentially expressed genes involved in 44 biological processes, including the glycoprotein biosynthetic process, beta-catenin-TCF complex assembly, and histone modification. These results indicate that MAPK mediates the aberrant expression of lncRNAs. LINC00941 is the lncRNA by MAPK most consistently promoted, and is implicated in the dismal prognosis of pancreatic cancer. MAPK-associated lncRNAs may play pivotal roles in malignant phenotypes of pancreatic cancer, and as such might represent both potentially valid therapeutic targets and diagnostic biomarkers.
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Wang X, Lv JL, Cheng S, Su ZH, Qin S, Sun X, Tang XD, Liu QN, Li MW, Wang XY. Bombyx mori transcription factor, E74A, beneficially affects BmNPV infection through direct interaction. PEST MANAGEMENT SCIENCE 2022; 78:5302-5312. [PMID: 36054174 DOI: 10.1002/ps.7152] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Revised: 08/21/2022] [Accepted: 08/27/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Nucleopolyhedrovirus (NPV), one of the baculoviruses, is a promising biopesticide for pest control. Lepidopteran account for 70% of pests, therefore investigation on highly conserved genes associated with viral infections in the lepidopteran model, the silkworm, will serve as a valuable reference for improving the effectiveness of pest management. BmE74A is a member of the erythroblast transformation-specific (ETS) family of transcription factors in Bombyx mori, which we previously found to be highly conserved and closely associated with BmNPV. This study aimed to elucidate the role of BmE74A in viral infection. RESULTS A significantly high expression of BmE74A in eggs indicated its important role in embryonic development, as did relatively high expressions in the hemolymph and midgut. Significant differences in BmE74A expression in different resistant strains after BmNPV infection suggested its involvement as a response to viral infection. Moreover, RNA interference (RNAi) and overexpression experiments confirmed the important role of BmE74A in promoting viral infection. BmNPV infection was significantly suppressed and enhanced by BmE74A knockdown and overexpression, respectively. Besides, BmE74A was found to regulate the expression of BmMdm2 and Bmp53. Furthermore, the binding of ETS, the functional domain of BmE74A, to occlusion-derived virus proteins was confirmed by far-western blotting, and four viral proteins that may interact with ETS proteins were identified by mass spectrometry. Similarly, a homolog of BmE74A in Spodoptera litura was also found to be involved in larval susceptibility to BmNPV. CONCLUSION BmE74A promotes BmNPV proliferation by directly interacting with the virus, which may be related to the suppression of the p53 pathway. © 2022 Society of Chemical Industry.
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Affiliation(s)
- Xin Wang
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Jun-Li Lv
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Shuang Cheng
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Zhi-Hao Su
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Sheng Qin
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, Sericultural Research Institute, Chinese Academy of Agricultural Science, Zhenjiang, China
| | - Xia Sun
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, Sericultural Research Institute, Chinese Academy of Agricultural Science, Zhenjiang, China
| | - Xu-Dong Tang
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, Sericultural Research Institute, Chinese Academy of Agricultural Science, Zhenjiang, China
| | - Qiu-Ning Liu
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Wetland, Yancheng Teachers University, Yancheng, China
| | - Mu-Wang Li
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, Sericultural Research Institute, Chinese Academy of Agricultural Science, Zhenjiang, China
| | - Xue-Yang Wang
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, Sericultural Research Institute, Chinese Academy of Agricultural Science, Zhenjiang, China
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Fetal Programming of the Endocrine Pancreas: Impact of a Maternal Low-Protein Diet on Gene Expression in the Perinatal Rat Pancreas. Int J Mol Sci 2022; 23:ijms231911057. [PMID: 36232358 PMCID: PMC9569808 DOI: 10.3390/ijms231911057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 09/08/2022] [Accepted: 09/10/2022] [Indexed: 11/26/2022] Open
Abstract
In rats, the time of birth is characterized by a transient rise in beta cell replication, as well as beta cell neogenesis and the functional maturation of the endocrine pancreas. However, the knowledge of the gene expression during this period of beta cell expansion is incomplete. The aim was to characterize the perinatal rat pancreas transcriptome and to identify regulatory pathways differentially regulated at the whole organ level in the offspring of mothers fed a regular control diet (CO) and of mothers fed a low-protein diet (LP). We performed mRNA expression profiling via the microarray analysis of total rat pancreas samples at embryonic day (E) 20 and postnatal days (P) 0 and 2. In the CO group, pancreas metabolic pathways related to sterol and lipid metabolism were highly enriched, whereas the LP diet induced changes in transcripts involved in RNA transcription and gene regulation, as well as cell migration and apoptosis. Moreover, a number of individual transcripts were markedly upregulated at P0 in the CO pancreas: growth arrest specific 6 (Gas6), legumain (Lgmn), Ets variant gene 5 (Etv5), alpha-fetoprotein (Afp), dual-specificity phosphatase 6 (Dusp6), and angiopoietin-like 4 (Angptl4). The LP diet induced the downregulation of a large number of transcripts, including neurogenin 3 (Neurog3), Etv5, Gas6, Dusp6, signaling transducer and activator of transcription 3 (Stat3), growth hormone receptor (Ghr), prolactin receptor (Prlr), and Gas6 receptor (AXL receptor tyrosine kinase; Axl), whereas upregulated transcripts were related to inflammatory responses and cell motility. We identified differentially regulated genes and transcriptional networks in the perinatal pancreas. These data revealed marked adaptations of exocrine and endocrine in the pancreas to the low-protein diet, and the data can contribute to identifying novel regulators of beta cell mass expansion and functional maturation and may provide a valuable tool in the generation of fully functional beta cells from stem cells to be used in replacement therapy.
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Nabeta R, Katselis GS, Chumala P, Dickinson R, Fernandez NJ, Meachem MD. Identification of potential plasma protein biomarkers for feline pancreatic carcinoma by liquid chromatography tandem mass spectrometry. Vet Comp Oncol 2022; 20:720-731. [PMID: 35514180 DOI: 10.1111/vco.12826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 04/14/2022] [Accepted: 04/26/2022] [Indexed: 12/01/2022]
Abstract
In both humans and cats, pancreatic carcinoma is an aggressive cancer with a grave prognosis. Proteomics techniques have successfully identified several blood-based biomarkers of human pancreatic neoplasia. Thus, this study aims to investigate whether similar biomarkers can be identified in the plasma of cats with FePAC by using liquid chromatography tandem mass spectrometry (LC-MS/MS). To facilitate evaluation of the low abundance plasma proteome, a human-based immunodepletion device (MARS-2) was first validated for use with feline plasma. Marked reduction and/or complete removal of albumin and immunoglobulins was confirmed by analysis of electrophoretograms and mass spectral data. Subsequently, plasma collected from 9 cats with pancreatic carcinoma (FePAC), 10 cats with symptomatic pancreatitis, and 10 healthy control cats was immunodepleted and subjected to LC-MS/MS. Thirty-seven plasma proteins were found to be differentially expressed (p < .05 in one-way ANOVA, FC >2 in fold change analysis). Among these proteins, ETS variant transcription factor 4 (p < .05) was overexpressed, while gelsolin (p < .01), tryptophan 2,3-dioxygenase (p < .05), serpin family F member 1 (p < .01), apolipoprotein A-IV (p < .01) and phosphatidylinositol-glycan-specific phospholipase D (p < .05) were down-regulated in cats with FePAC. Further studies on these potential biomarkers are needed to investigate their diagnostic value.
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Affiliation(s)
- Rina Nabeta
- Department of Veterinary Pathology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - George S Katselis
- Department of Medicine, Division of the Canadian Centre for Health and Safety in Agriculture, College of Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Paulos Chumala
- Department of Medicine, Division of the Canadian Centre for Health and Safety in Agriculture, College of Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Ryan Dickinson
- Department of Veterinary Pathology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Nicole J Fernandez
- Department of Veterinary Pathology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Melissa D Meachem
- Department of Veterinary Pathology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
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Li S, Xie K. Ductal metaplasia in pancreas. Biochim Biophys Acta Rev Cancer 2022; 1877:188698. [DOI: 10.1016/j.bbcan.2022.188698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 02/09/2022] [Accepted: 02/09/2022] [Indexed: 02/07/2023]
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Lien YC, Pinney SE, Lu XM, Simmons RA. Identification of Novel Regulatory Regions Induced by Intrauterine Growth Restriction in Rat Islets. Endocrinology 2022; 163:6459683. [PMID: 34894232 PMCID: PMC8743043 DOI: 10.1210/endocr/bqab251] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Indexed: 01/05/2023]
Abstract
Intrauterine growth restriction (IUGR) leads to the development of type 2 diabetes in adulthood, and the permanent alterations in gene expression implicate an epigenetic mechanism. Using a rat model of IUGR, we performed TrueSeq-HELP Tagging to assess the association of DNA methylation changes and gene dysregulation in islets. We identified 511 differentially methylated regions (DMRs) and 4377 significantly altered single CpG sites. Integrating the methylome and our published transcriptome data sets resulted in the identification of pathways critical for islet function. The identified DMRs were enriched with transcription factor binding motifs, such as Elk1, Etv1, Foxa1, Foxa2, Pax7, Stat3, Hnf1, and AR. In silico analysis of 3-dimensional chromosomal interactions using human pancreas and islet Hi-C data sets identified interactions between 14 highly conserved DMRs and 35 genes with significant expression changes at an early age, many of which persisted in adult islets. In adult islets, there were far more interactions between DMRs and genes with significant expression changes identified with Hi-C, and most of them were critical to islet metabolism and insulin secretion. The methylome was integrated with our published genome-wide histone modification data sets from IUGR islets, resulting in further characterization of important regulatory regions of the genome altered by IUGR containing both significant changes in DNA methylation and specific histone marks. We identified novel regulatory regions in islets after exposure to IUGR, suggesting that epigenetic changes at key transcription factor binding motifs and other gene regulatory regions may contribute to gene dysregulation and an abnormal islet phenotype in IUGR rats.
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Affiliation(s)
- Yu-Chin Lien
- Center for Research on Reproduction and Women’s Health, Perelman School of Medicine, the University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Division of Neonatology, Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Sara E Pinney
- Center for Research on Reproduction and Women’s Health, Perelman School of Medicine, the University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Division Endocrinology and Diabetes, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
- Perlman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Xueqing Maggie Lu
- Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Rebecca A Simmons
- Center for Research on Reproduction and Women’s Health, Perelman School of Medicine, the University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Division of Neonatology, Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
- Perlman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Correspondence: Rebecca A. Simmons, MD, Center for Research on Reproduction and Women’s Health, Perelman School of Medicine, the University of Pennsylvania, BRB II/III, 13th Fl, Rm 1308, 421 Curie Blvd, Philadelphia, PA 19104, USA.
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9
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Geusz RJ, Wang A, Lam DK, Vinckier NK, Alysandratos KD, Roberts DA, Wang J, Kefalopoulou S, Ramirez A, Qiu Y, Chiou J, Gaulton KJ, Ren B, Kotton DN, Sander M. Sequence logic at enhancers governs a dual mechanism of endodermal organ fate induction by FOXA pioneer factors. Nat Commun 2021; 12:6636. [PMID: 34789735 PMCID: PMC8599738 DOI: 10.1038/s41467-021-26950-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 10/28/2021] [Indexed: 01/15/2023] Open
Abstract
FOXA pioneer transcription factors (TFs) associate with primed enhancers in endodermal organ precursors. Using a human stem cell model of pancreas differentiation, we here discover that only a subset of pancreatic enhancers is FOXA-primed, whereas the majority is unprimed and engages FOXA upon lineage induction. Primed enhancers are enriched for signal-dependent TF motifs and harbor abundant and strong FOXA motifs. Unprimed enhancers harbor fewer, more degenerate FOXA motifs, and FOXA recruitment to unprimed but not primed enhancers requires pancreatic TFs. Strengthening FOXA motifs at an unprimed enhancer near NKX6.1 renders FOXA recruitment pancreatic TF-independent, induces priming, and broadens the NKX6.1 expression domain. We make analogous observations about FOXA binding during hepatic and lung development. Our findings suggest a dual role for FOXA in endodermal organ development: first, FOXA facilitates signal-dependent lineage initiation via enhancer priming, and second, FOXA enforces organ cell type-specific gene expression via indirect recruitment by lineage-specific TFs.
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Affiliation(s)
- Ryan J. Geusz
- grid.266100.30000 0001 2107 4242Department of Pediatrics, Pediatric Diabetes Research Center, University of California, La Jolla, San Diego, CA 92093 USA ,grid.266100.30000 0001 2107 4242Department of Cellular & Molecular Medicine, University of California, La Jolla, San Diego, CA 92093 USA ,grid.468218.10000 0004 5913 3393Sanford Consortium for Regenerative Medicine, La Jolla, San Diego, CA 92093 USA ,grid.266100.30000 0001 2107 4242Biomedical Graduate Studies Program, University of California San Diego, La Jolla, San Diego, CA 92037 USA
| | - Allen Wang
- grid.266100.30000 0001 2107 4242Department of Pediatrics, Pediatric Diabetes Research Center, University of California, La Jolla, San Diego, CA 92093 USA ,grid.266100.30000 0001 2107 4242Department of Cellular & Molecular Medicine, University of California, La Jolla, San Diego, CA 92093 USA ,grid.468218.10000 0004 5913 3393Sanford Consortium for Regenerative Medicine, La Jolla, San Diego, CA 92093 USA
| | - Dieter K. Lam
- grid.266100.30000 0001 2107 4242Department of Pediatrics, Pediatric Diabetes Research Center, University of California, La Jolla, San Diego, CA 92093 USA ,grid.266100.30000 0001 2107 4242Department of Cellular & Molecular Medicine, University of California, La Jolla, San Diego, CA 92093 USA ,grid.468218.10000 0004 5913 3393Sanford Consortium for Regenerative Medicine, La Jolla, San Diego, CA 92093 USA
| | - Nicholas K. Vinckier
- grid.266100.30000 0001 2107 4242Department of Pediatrics, Pediatric Diabetes Research Center, University of California, La Jolla, San Diego, CA 92093 USA ,grid.266100.30000 0001 2107 4242Department of Cellular & Molecular Medicine, University of California, La Jolla, San Diego, CA 92093 USA ,grid.468218.10000 0004 5913 3393Sanford Consortium for Regenerative Medicine, La Jolla, San Diego, CA 92093 USA
| | - Konstantinos-Dionysios Alysandratos
- grid.239424.a0000 0001 2183 6745Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA 02118 USA ,grid.189504.10000 0004 1936 7558The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA 02118 USA
| | - David A. Roberts
- grid.239424.a0000 0001 2183 6745Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA 02118 USA
| | - Jinzhao Wang
- grid.266100.30000 0001 2107 4242Department of Pediatrics, Pediatric Diabetes Research Center, University of California, La Jolla, San Diego, CA 92093 USA ,grid.266100.30000 0001 2107 4242Department of Cellular & Molecular Medicine, University of California, La Jolla, San Diego, CA 92093 USA ,grid.468218.10000 0004 5913 3393Sanford Consortium for Regenerative Medicine, La Jolla, San Diego, CA 92093 USA
| | - Samy Kefalopoulou
- grid.266100.30000 0001 2107 4242Department of Pediatrics, Pediatric Diabetes Research Center, University of California, La Jolla, San Diego, CA 92093 USA ,grid.266100.30000 0001 2107 4242Department of Cellular & Molecular Medicine, University of California, La Jolla, San Diego, CA 92093 USA ,grid.468218.10000 0004 5913 3393Sanford Consortium for Regenerative Medicine, La Jolla, San Diego, CA 92093 USA
| | - Araceli Ramirez
- grid.266100.30000 0001 2107 4242Department of Pediatrics, Pediatric Diabetes Research Center, University of California, La Jolla, San Diego, CA 92093 USA ,grid.266100.30000 0001 2107 4242Department of Cellular & Molecular Medicine, University of California, La Jolla, San Diego, CA 92093 USA ,grid.468218.10000 0004 5913 3393Sanford Consortium for Regenerative Medicine, La Jolla, San Diego, CA 92093 USA
| | - Yunjiang Qiu
- grid.266100.30000 0001 2107 4242Department of Cellular & Molecular Medicine, University of California, La Jolla, San Diego, CA 92093 USA
| | - Joshua Chiou
- grid.266100.30000 0001 2107 4242Department of Pediatrics, Pediatric Diabetes Research Center, University of California, La Jolla, San Diego, CA 92093 USA ,grid.266100.30000 0001 2107 4242Biomedical Graduate Studies Program, University of California San Diego, La Jolla, San Diego, CA 92037 USA
| | - Kyle J. Gaulton
- grid.266100.30000 0001 2107 4242Department of Pediatrics, Pediatric Diabetes Research Center, University of California, La Jolla, San Diego, CA 92093 USA
| | - Bing Ren
- grid.266100.30000 0001 2107 4242Department of Cellular & Molecular Medicine, University of California, La Jolla, San Diego, CA 92093 USA ,grid.1052.60000000097371625Ludwig Institute for Cancer Research, La Jolla, San Diego, CA 92093-0653 USA
| | - Darrell N. Kotton
- grid.239424.a0000 0001 2183 6745Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA 02118 USA ,grid.189504.10000 0004 1936 7558The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA 02118 USA
| | - Maike Sander
- Department of Pediatrics, Pediatric Diabetes Research Center, University of California, La Jolla, San Diego, CA, 92093, USA. .,Department of Cellular & Molecular Medicine, University of California, La Jolla, San Diego, CA, 92093, USA. .,Sanford Consortium for Regenerative Medicine, La Jolla, San Diego, CA, 92093, USA.
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10
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Rian K, Hidalgo MR, Çubuk C, Falco MM, Loucera C, Esteban-Medina M, Alamo-Alvarez I, Peña-Chilet M, Dopazo J. Genome-scale mechanistic modeling of signaling pathways made easy: A bioconductor/cytoscape/web server framework for the analysis of omic data. Comput Struct Biotechnol J 2021; 19:2968-2978. [PMID: 34136096 PMCID: PMC8170118 DOI: 10.1016/j.csbj.2021.05.022] [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] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 04/21/2021] [Accepted: 05/11/2021] [Indexed: 12/13/2022] Open
Abstract
Genome-scale mechanistic models of pathways are gaining importance for genomic data interpretation because they provide a natural link between genotype measurements (transcriptomics or genomics data) and the phenotype of the cell (its functional behavior). Moreover, mechanistic models can be used to predict the potential effect of interventions, including drug inhibitions. Here, we present the implementation of a mechanistic model of cell signaling for the interpretation of transcriptomic data as an R/Bioconductor package, a Cytoscape plugin and a web tool with enhanced functionality which includes building interpretable predictors, estimation of the effect of perturbations and assessment of the effect of mutations in complex scenarios.
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Affiliation(s)
- Kinza Rian
- Clinical Bioinformatics Area, Fundación Progreso y Salud (FPS), Hospital Virgen del Rocío, Sevilla 41013, Spain
- Laboratory of Innovative Technologies (LTI), National School of Applied Sciences in Tangier, UAE, Morocco
| | - Marta R. Hidalgo
- Bioinformatics and Biostatistics Unit, Centro de Investigación Príncipe Felipe (CIPF), 46012 Valencia, Spain
| | - Cankut Çubuk
- Clinical Bioinformatics Area, Fundación Progreso y Salud (FPS), Hospital Virgen del Rocío, Sevilla 41013, Spain
| | - Matias M. Falco
- Clinical Bioinformatics Area, Fundación Progreso y Salud (FPS), Hospital Virgen del Rocío, Sevilla 41013, Spain
- Bioinformatics in RareDiseases (BiER), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Sevilla 41013, Spain
| | - Carlos Loucera
- Clinical Bioinformatics Area, Fundación Progreso y Salud (FPS), Hospital Virgen del Rocío, Sevilla 41013, Spain
- Computational Systems Medicine. Institute of Biomedicine of Seville (IBiS), Sevilla 41013, Spain
| | - Marina Esteban-Medina
- Clinical Bioinformatics Area, Fundación Progreso y Salud (FPS), Hospital Virgen del Rocío, Sevilla 41013, Spain
- Computational Systems Medicine. Institute of Biomedicine of Seville (IBiS), Sevilla 41013, Spain
| | - Inmaculada Alamo-Alvarez
- Clinical Bioinformatics Area, Fundación Progreso y Salud (FPS), Hospital Virgen del Rocío, Sevilla 41013, Spain
- Computational Systems Medicine. Institute of Biomedicine of Seville (IBiS), Sevilla 41013, Spain
| | - María Peña-Chilet
- Clinical Bioinformatics Area, Fundación Progreso y Salud (FPS), Hospital Virgen del Rocío, Sevilla 41013, Spain
- Bioinformatics in RareDiseases (BiER), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Sevilla 41013, Spain
- Computational Systems Medicine. Institute of Biomedicine of Seville (IBiS), Sevilla 41013, Spain
| | - Joaquín Dopazo
- Clinical Bioinformatics Area, Fundación Progreso y Salud (FPS), Hospital Virgen del Rocío, Sevilla 41013, Spain
- Bioinformatics in RareDiseases (BiER), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Sevilla 41013, Spain
- Computational Systems Medicine. Institute of Biomedicine of Seville (IBiS), Sevilla 41013, Spain
- Functional Genomics Node (INB-ELIXIR-es), Sevilla, Spain
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11
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Suzuki M, Saito-Adachi M, Arai Y, Fujiwara Y, Takai E, Shibata S, Seki M, Rokutan H, Maeda D, Horie M, Suzuki Y, Shibata T, Kiyono T, Yachida S. E74-Like Factor 3 Is a Key Regulator of Epithelial Integrity and Immune Response Genes in Biliary Tract Cancer. Cancer Res 2020; 81:489-500. [PMID: 33293429 DOI: 10.1158/0008-5472.can-19-2988] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 04/28/2020] [Accepted: 11/16/2020] [Indexed: 11/16/2022]
Abstract
The transcription factor E74-like factor 3 (ELF3) is inactivated in a range of cancers, including biliary tract cancer (BTC). Here, we investigated the tumor-suppressive role of ELF3 in bile duct cells by identifying several previously unknown direct target genes of ELF3 that appear to be implicated in biliary duct carcinogenesis. ELF3 directly repressed ZEB2, a key regulator of epithelial-mesenchymal transition, and upregulated the expression of CGN, an integral element in lumen formation. Loss of ELF3 led to decreased cell-cell junctions and enhanced cell motility. ALOX5 and CXCL16 were also identified as additional direct targets of ELF3; their corresponding proteins 5-lipoxygenase and CXCL16 play a role in the immune response. Conditioned medium from cells overexpressing ELF3 significantly enhanced the migration of natural killer cells and CD8+ T cells toward the conditioned medium. Gene expression profiling for BTC expressing high levels of ELF3 revealed significant enrichment of the ELF3-related genes. In a BTC xenograft model, activation of ELF3 increased expression of ELF3-related genes, enhanced the tubular structure of the tumors, and led to a loss of vimentin. Overall, our results indicate that ELF3 is a key regulator of both epithelial integrity and immune responses in BTC. SIGNIFICANCE: Thease finding shows that ELF3 regulates epithelial integrity and host immune responses and functions as a tumor suppressor in biliary tract cancer. GRAPHICAL ABSTRACT: http://cancerres.aacrjournals.org/content/canres/81/2/489/F1.large.jpg.
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Affiliation(s)
- Masami Suzuki
- Department of Cancer Genome Informatics, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Mihoko Saito-Adachi
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Yasuhito Arai
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Yuko Fujiwara
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Erina Takai
- Department of Cancer Genome Informatics, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Shinsuke Shibata
- Electron Microscope Laboratory, Keio University School of Medicine, Tokyo, Japan
| | - Masahide Seki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Hirofumi Rokutan
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Daichi Maeda
- Department of Clinical Genomics, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Masafumi Horie
- Department of Cancer Genome Informatics, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Tatsuhiro Shibata
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan.,Laboratory of Molecular Medicine, Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Tohru Kiyono
- Project for Prevention of HPV-Related Cancer, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Chiba, Japan.
| | - Shinichi Yachida
- Department of Cancer Genome Informatics, Graduate School of Medicine, Osaka University, Osaka, Japan.
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12
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Altered Transcription Factor Binding and Gene Bivalency in Islets of Intrauterine Growth Retarded Rats. Cells 2020; 9:cells9061435. [PMID: 32527043 PMCID: PMC7348746 DOI: 10.3390/cells9061435] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 05/30/2020] [Accepted: 06/04/2020] [Indexed: 12/16/2022] Open
Abstract
Intrauterine growth retardation (IUGR), which induces epigenetic modifications and permanent changes in gene expression, has been associated with the development of type 2 diabetes. Using a rat model of IUGR, we performed ChIP-Seq to identify and map genome-wide histone modifications and gene dysregulation in islets from 2- and 10-week rats. IUGR induced significant changes in the enrichment of H3K4me3, H3K27me3, and H3K27Ac marks in both 2-wk and 10-wk islets, which were correlated with expression changes of multiple genes critical for islet function in IUGR islets. ChIP-Seq analysis showed that IUGR-induced histone mark changes were enriched at critical transcription factor binding motifs, such as C/EBPs, Ets1, Bcl6, Thrb, Ebf1, Sox9, and Mitf. These transcription factors were also identified as top upstream regulators in our previously published transcriptome study. In addition, our ChIP-seq data revealed more than 1000 potential bivalent genes as identified by enrichment of both H3K4me3 and H3K27me3. The poised state of many potential bivalent genes was altered by IUGR, particularly Acod1, Fgf21, Serpina11, Cdh16, Lrrc27, and Lrrc66, key islet genes. Collectively, our findings suggest alterations of histone modification in key transcription factors and genes that may contribute to long-term gene dysregulation and an abnormal islet phenotype in IUGR rats.
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13
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Chhatriya B, Mukherjee M, Ray S, Sarkar P, Chatterjee S, Nath D, Das K, Goswami S. Comparison of tumour and serum specific microRNA changes dissecting their role in pancreatic ductal adenocarcinoma: a meta-analysis. BMC Cancer 2019; 19:1175. [PMID: 31795960 PMCID: PMC6891989 DOI: 10.1186/s12885-019-6380-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 11/20/2019] [Indexed: 02/07/2023] Open
Abstract
Background Pancreatic ductal adenocarcinoma (PDAC) is considered as one of the most aggressive cancers lacking efficient early detection biomarkers. Circulating miRNAs are now being considered to have potency to be used as diagnostic and prognostic biomarkers in different diseases as well as cancers. In case of cancer, a fraction of the circulating miRNAs is actually derived from the tumour tissue. This fraction would function as stable biomarker for the disease and also would contribute to the understanding of the disease development. There are not many studies exploring this aspect in pancreatic cancer and even there is not much overlap of results between existing studies. Methods In order to address that gap, we performed a miRNA microarray analysis to identify differentially expressed circulating miRNAs between PDAC patients and normal healthy individuals and also found two more similar datasets to perform a meta-analysis using a total of 182 PDAC patients and 170 normal, identifying a set of miRNAs significantly altered in patient serum. Next, we found five datasets studying miRNA expression profile in tumour tissues of PDAC patients as compared to normal pancreas and performed a second meta-analysis using data from a total of 183 pancreatic tumour and 47 normal pancreas to detect significantly deregulated miRNAs in pancreatic carcinoma. Comparison of these two lists and subsequent search for their target genes which were also deregulated in PDAC in inverse direction to miRNAs was done followed by investigation of their role in disease development. Results We identified 21 miRNAs altered in both pancreatic tumour tissue and serum. While deciphering the functions of their target genes, we characterized key miR-Gene interactions perturbing the biological pathways. We identified important cancer related pathways, pancreas specific pathways, AGE-RAGE signaling, prolactin signaling and insulin resistance signaling pathways among the most affected ones. We also reported the possible involvement of crucial transcription factors in the process. Conclusions Our study identified a unique meta-signature of 21 miRNAs capable of explaining pancreatic carcinogenesis and possibly holding the potential to act as biomarker for the disease detection which could be explored further.
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Affiliation(s)
| | - Moumita Mukherjee
- National Institute of Biomedical Genomics, Kalyani, West Bengal, India
| | - Sukanta Ray
- School of Digestive and Liver Diseases, Institute of Post Graduate Medical Education and Research, Kolkata, West Bengal, India
| | - Piyali Sarkar
- Present Address: Tata Medical Centre, Kolkata, West Bengal, India
| | | | - Debashis Nath
- Indira Gandhi Memorial Hospital, Agartala, Tripura, India
| | - Kshaunish Das
- School of Digestive and Liver Diseases, Institute of Post Graduate Medical Education and Research, Kolkata, West Bengal, India
| | - Srikanta Goswami
- National Institute of Biomedical Genomics, Kalyani, West Bengal, India.
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14
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Yang L, Zhu Y, Kong D, Gong J, Yu W, Liang Y, Nie Y, Teng CB. EGF suppresses the expression of miR-124a in pancreatic β cell lines via ETS2 activation through the MEK and PI3K signaling pathways. Int J Biol Sci 2019; 15:2561-2575. [PMID: 31754329 PMCID: PMC6854373 DOI: 10.7150/ijbs.34985] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 08/11/2019] [Indexed: 12/11/2022] Open
Abstract
Diabetes mellitus is characterized by pancreatic β cell dysfunction. Previous studies have indicated that epidermal growth factor (EGF) and microRNA-124a (miR-124a) play opposite roles in insulin biosynthesis and secretion by beta cells. However, the underlying mechanisms remain poorly understood. In the present study, we demonstrated that EGF could inhibit miR-124a expression in beta cell lines through downstream signaling pathways, including mitogen-activated protein kinase kinase (MEK) and phosphatidylinositol 3-kinase (PI3K) cascades. Further, the transcription factor ETS2, a member of the ETS (E26 transformation-specific) family, was identified to be responsible for the EGF-mediated suppression of miR-124a expression, which was dependent on ETS2 phosphorylation at threonine 72. Activation of ETS2 decreased miR-124a promoter transcriptional activity through the putative conserved binding sites AGGAANA/TN in three miR-124a promoters located in different chromosomes. Of note, ETS2 played a positive role in regulating beta cell function-related genes, including miR-124a targets, Forkhead box a2 (FOXA2) and Neurogenic differentiation 1 (NEUROD1), which may have partly been through the inhibition of miR-124 expression. Knockdown and overexpression of ETS2 led to the prevention and promotion of insulin biosynthesis respectively, while barely affecting the secretion ability. These results suggest that EGF may induce the activation of ETS2 to inhibit miR-124a expression to maintain proper beta cell functions and that ETS2, as a novel regulator of insulin production, is a potential therapeutic target for diabetes mellitus treatment.
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Affiliation(s)
- Lin Yang
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Yuansen Zhu
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Delin Kong
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Jiawei Gong
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Wen Yu
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Yang Liang
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Yuzhe Nie
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Chun-Bo Teng
- College of Life Science, Northeast Forestry University, Harbin, China
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15
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Das KK, Heeg S, Pitarresi JR, Reichert M, Bakir B, Takano S, Kopp JL, Wahl-Feuerstein A, Hicks P, Sander M, Rustgi AK. ETV5 regulates ductal morphogenesis with Sox9 and is critical for regeneration from pancreatitis. Dev Dyn 2018. [PMID: 29532564 DOI: 10.1002/dvdy.24626] [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: 12/16/2022] Open
Abstract
BACKGROUND The plasticity of pancreatic acinar cells to undergo acinar to ductal metaplasia (ADM) has been demonstrated to contribute to the regeneration of the pancreas in response to injury. Sox9 is critical for ductal cell fate and important in the formation of ADM, most likely in concert with a complex hierarchy of, as yet, not fully elucidated transcription factors. RESULTS By using a mouse model of acute pancreatitis and three dimensional organoid culture of primary pancreatic ductal cells, we herein characterize the Ets-transcription factor Etv5 as a pivotal regulator of ductal cell identity and ADM that acts upstream of Sox9 and is essential for Sox9 expression in ADM. Loss of Etv5 is associated with increased severity of acute pancreatitis and impaired ADM formation leading to delayed tissue regeneration and recovery in response to injury. CONCLUSIONS Our data provide new insights in the regulation of ADM with implications in our understanding of pancreatic homeostasis, pancreatitis and epithelial plasticity. Developmental Dynamics 247:854-866, 2018. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- Koushik K Das
- Division of Gastroenterology, University of Pennsylvania, Philadelphia, Pennsylvania.,Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.,Abramson Cancer Center, University of Pennsylvania, Philadelphia, Pennsylvania.,Division of Gastroenterology, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Steffen Heeg
- Division of Gastroenterology, University of Pennsylvania, Philadelphia, Pennsylvania.,Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.,Abramson Cancer Center, University of Pennsylvania, Philadelphia, Pennsylvania.,Department of Medicine II, Medical Center, University of Freiburg, Freiburg, Germany
| | - Jason R Pitarresi
- Division of Gastroenterology, University of Pennsylvania, Philadelphia, Pennsylvania.,Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.,Abramson Cancer Center, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Maximilian Reichert
- Division of Gastroenterology, University of Pennsylvania, Philadelphia, Pennsylvania.,Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.,Abramson Cancer Center, University of Pennsylvania, Philadelphia, Pennsylvania.,II. Medizinische Klinik, Technical University of Munich, Munich, Germany
| | - Basil Bakir
- Division of Gastroenterology, University of Pennsylvania, Philadelphia, Pennsylvania.,Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.,Abramson Cancer Center, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Shigetsugu Takano
- Division of Gastroenterology, University of Pennsylvania, Philadelphia, Pennsylvania.,Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.,Abramson Cancer Center, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Janel L Kopp
- Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, Canada
| | - Anja Wahl-Feuerstein
- Department of Medicine II, Medical Center, University of Freiburg, Freiburg, Germany
| | - Philip Hicks
- Division of Gastroenterology, University of Pennsylvania, Philadelphia, Pennsylvania.,Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.,Abramson Cancer Center, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Maike Sander
- Department of Pediatrics, Department of Cellular and Molecular Medicine, University of California San Diego School of Medicine, San Diego, California
| | - Anil K Rustgi
- Division of Gastroenterology, University of Pennsylvania, Philadelphia, Pennsylvania.,Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.,Abramson Cancer Center, University of Pennsylvania, Philadelphia, Pennsylvania.,Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
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16
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Ndlovu R, Deng LC, Wu J, Li XK, Zhang JS. Fibroblast Growth Factor 10 in Pancreas Development and Pancreatic Cancer. Front Genet 2018; 9:482. [PMID: 30425728 PMCID: PMC6219204 DOI: 10.3389/fgene.2018.00482] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Accepted: 09/28/2018] [Indexed: 01/03/2023] Open
Abstract
The tenacious prevalence of human pancreatic diseases such as diabetes mellitus and adenocarcinoma has prompted huge research interest in better understanding of pancreatic organogenesis. The plethora of signaling pathways involved in pancreas development is activated in a highly coordinated manner to assure unmitigated development and morphogenesis in vertebrates. Therefore, a complex mesenchymal-epithelial signaling network has been implicated to play a pivotal role in organogenesis through its interactions with other germ layers, specifically the endoderm. The Fibroblast Growth Factor Receptor FGFR2-IIIb splicing isoform (FGFR2b) and its high affinity ligand Fibroblast Growth Factor 10 (FGF10) are expressed in the epithelium and mesenchyme, respectively, and therefore are well positioned to transmit mesenchymal to epithelial signaling. FGF10 is a typical paracrine FGF and chiefly mediates biological responses by activating FGFR2b with heparin/heparan sulfate (HS) as cofactor. A substantial number of studies using genetically engineered mouse models have demonstrated an essential role of FGF10 in the development of many organs and tissues including the pancreas. During mouse embryonic development, FGF10 signaling is crucial for epithelial cell proliferation, maintenance of progenitor cell fate and branching morphogenesis in the pancreas. FGF10 is also implicated in pancreatic cancer, and that overexpression of FGFR2b is associated with metastatic invasion. A thorough understanding of FGF10 signaling machinery and its crosstalk with other pathways in development and pathological states may provide novel opportunities for pancreatic cancer targeted therapy and regenerative medicine.
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Affiliation(s)
- Rodrick Ndlovu
- College of Life and Environmental Sciences, Wenzhou University, Wenzhou, China
| | - Lian-Cheng Deng
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Jin Wu
- College of Life and Environmental Sciences, Wenzhou University, Wenzhou, China
| | - Xiao-Kun Li
- College of Life and Environmental Sciences, Wenzhou University, Wenzhou, China
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, China
- *Correspondence: Xiao-Kun Li, Jin-San Zhang, ;
| | - Jin-San Zhang
- College of Life and Environmental Sciences, Wenzhou University, Wenzhou, China
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, China
- Centre for Precision Medicine, the First Affiliated Hospital, Wenzhou Medical University, Wenzhou, China
- *Correspondence: Xiao-Kun Li, Jin-San Zhang, ;
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17
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Heeg S, Das KK, Reichert M, Bakir B, Takano S, Caspers J, Aiello NM, Wu K, Neesse A, Maitra A, Iacobuzio-Donahue CA, Hicks P, Rustgi AK. ETS-Transcription Factor ETV1 Regulates Stromal Expansion and Metastasis in Pancreatic Cancer. Gastroenterology 2016; 151:540-553.e14. [PMID: 27318148 PMCID: PMC5002361 DOI: 10.1053/j.gastro.2016.06.005] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/17/2015] [Revised: 05/13/2016] [Accepted: 06/06/2016] [Indexed: 12/18/2022]
Abstract
BACKGROUND & AIMS The ETS-transcription factor ETV1 is involved in epithelial-mesenchymal transition during pancreatic development and is induced in mouse pancreatic intraepithelial neoplasia (PanIN) and pancreatic ductal adenocarcinoma (PDAC). We investigated the function of ETV1 in stromal expansion of PDAC and metastasis, as well as its effects on a novel downstream target Sparc, which encodes a matricellular protein found in PDAC stroma that has been associated with invasiveness, metastasis and poor patient outcomes. METHODS Pancreatic ductal cells were isolated from Pdx1Cre;Kras(G12D/+) mice (PanIN), Pdx1Cre;Kras(G12D/+);p53(fl/+) and Pdx1Cre;Kras(G12D/+);p53(fl/+);Rosa26(YFP) mice (PDAC), and Pdx1Cre;Kras(G12D/+);p53(fl/+);Sparc(-/-) mice. Cells were grown in 3-dimensional organoid culture to analyze morphology, proliferation, and invasion. Human PanIN and PDAC tissues were evaluated for ETV1 expression. Orthotopic pancreatic transplants of ETV1-overexpressing PDAC and respective control cells were performed. RESULTS ETV1 expression was significantly increased in human PanINs and, even more so, in primary and metastatic PDAC. Analyses of mouse orthotopic xenografts revealed that ETV1 induced significantly larger primary tumors than controls, with significantly increased stromal expansion, ascites and metastases. In 3-dimensional organoids, ETV1 disrupted cyst architecture, induced EMT, and increased invasive capacity. Furthermore, we identified Sparc as a novel functional gene target of Etv1 by luciferase assays, and SPARC and ETV1 proteins co-localized in vivo. Disruption of Sparc abrogates the phenotype of stromal expansion and metastasis found with ETV1 overexpression in vivo. We identified hyaluronan synthase 2 (Has2) as another novel downstream factor of Etv1; that may mediate ETV1's significant expansion of hyaluronic acid in PDAC stroma. Conversely, disruption of Etv1 in PDAC mice (Pdx1Cre;Kras(G12D/+);p53(fl/+);Rosa26(YFP);Cre;Etv1(fl/fl)) reduced levels of SPARC and hyaluronic acid in the stroma. CONCLUSIONS ETV1 is critical in the desmoplastic stromal expansion and metastatic progression of pancreatic cancer in mice, mediated functionally in part through Sparc and Has2.
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Affiliation(s)
- Steffen Heeg
- Division of Gastroenterology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Department of Medicine II, Medical Center, University of Freiburg; Freiburg, Germany
| | - Koushik K Das
- Division of Gastroenterology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Maximilian Reichert
- Division of Gastroenterology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; II. Medizinische Klinik, Technical University of Munich, Munich, Germany
| | - Basil Bakir
- Division of Gastroenterology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Shigetsugu Takano
- Division of Gastroenterology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Julia Caspers
- Department of Medicine II, Medical Center, University of Freiburg; Freiburg, Germany
| | - Nicole M Aiello
- Division of Gastroenterology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Katherine Wu
- Division of Gastroenterology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Albrecht Neesse
- Division of Gastroenterology and Gastrointestinal Oncology, University Medical Centre Goettingen, Goettingen, Germany
| | - Anirban Maitra
- University of Texas, MD Anderson Cancer Center, Houston, Texas
| | - Christine A Iacobuzio-Donahue
- David M. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Philip Hicks
- Division of Gastroenterology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Anil K Rustgi
- Division of Gastroenterology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.
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18
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Yachida S, Wood LD, Suzuki M, Takai E, Totoki Y, Kato M, Luchini C, Arai Y, Nakamura H, Hama N, Elzawahry A, Hosoda F, Shirota T, Morimoto N, Hori K, Funazaki J, Tanaka H, Morizane C, Okusaka T, Nara S, Shimada K, Hiraoka N, Taniguchi H, Higuchi R, Oshima M, Okano K, Hirono S, Mizuma M, Arihiro K, Yamamoto M, Unno M, Yamaue H, Weiss MJ, Wolfgang CL, Furukawa T, Nakagama H, Vogelstein B, Kiyono T, Hruban RH, Shibata T. Genomic Sequencing Identifies ELF3 as a Driver of Ampullary Carcinoma. Cancer Cell 2016; 29:229-40. [PMID: 26806338 PMCID: PMC5503303 DOI: 10.1016/j.ccell.2015.12.012] [Citation(s) in RCA: 134] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Revised: 09/16/2015] [Accepted: 12/21/2015] [Indexed: 02/07/2023]
Abstract
Ampullary carcinomas are highly malignant neoplasms that can have either intestinal or pancreatobiliary differentiation. To characterize somatic alterations in ampullary carcinomas, we performed whole-exome sequencing and DNA copy-number analysis on 60 ampullary carcinomas resected from clinically well-characterized Japanese and American patients. We next selected 92 genes and performed targeted sequencing to validate significantly mutated genes in an additional 112 cancers. The prevalence of driver gene mutations in carcinomas with the intestinal phenotype is different from those with the pancreatobiliary phenotype. We identified a characteristic significantly mutated driver gene (ELF3) as well as previously known driver genes (TP53, KRAS, APC, and others). Functional studies demonstrated that ELF3 silencing in normal human epithelial cells enhances their motility and invasion.
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Affiliation(s)
- Shinichi Yachida
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo 1040045, Japan; Division of Cancer Genomics, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 1040045, Japan.
| | - Laura D Wood
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Masami Suzuki
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo 1040045, Japan
| | - Erina Takai
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo 1040045, Japan
| | - Yasushi Totoki
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo 1040045, Japan
| | - Mamoru Kato
- Department of Bioinformatics, National Cancer Center Research Institute, Tokyo 1040045, Japan
| | - Claudio Luchini
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Yasuhito Arai
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo 1040045, Japan
| | - Hiromi Nakamura
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo 1040045, Japan
| | - Natsuko Hama
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo 1040045, Japan
| | - Asmaa Elzawahry
- Department of Bioinformatics, National Cancer Center Research Institute, Tokyo 1040045, Japan
| | - Fumie Hosoda
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo 1040045, Japan
| | - Tomoki Shirota
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo 1040045, Japan
| | - Nobuhiko Morimoto
- Division of Medical Elemental Technology Development, Department of Advanced Analysis Technology, R&D Group, Olympus Corporation, Tokyo 1630914, Japan
| | - Kunio Hori
- Division of Medical Elemental Technology Development, Department of Advanced Analysis Technology, R&D Group, Olympus Corporation, Tokyo 1630914, Japan
| | - Jun Funazaki
- Division of Medical Elemental Technology Development, Department of Advanced Analysis Technology, R&D Group, Olympus Corporation, Tokyo 1630914, Japan
| | - Hikaru Tanaka
- Division of Virology, National Cancer Center Research Institute, Tokyo 1040045, Japan
| | - Chigusa Morizane
- Department of Hepatobiliary and Pancreatic Oncology, National Cancer Center Hospital, Tokyo 1040045, Japan
| | - Takuji Okusaka
- Department of Hepatobiliary and Pancreatic Oncology, National Cancer Center Hospital, Tokyo 1040045, Japan
| | - Satoshi Nara
- Hepatobiliary and Pancreatic Surgery Division, National Cancer Center Hospital, Tokyo 1040045, Japan
| | - Kazuaki Shimada
- Hepatobiliary and Pancreatic Surgery Division, National Cancer Center Hospital, Tokyo 1040045, Japan
| | - Nobuyoshi Hiraoka
- Department of Pathology and Clinical Laboratories, National Cancer Center Hospital, Tokyo 1040045, Japan
| | - Hirokazu Taniguchi
- Department of Pathology and Clinical Laboratories, National Cancer Center Hospital, Tokyo 1040045, Japan
| | - Ryota Higuchi
- Department of Surgery, Institute of Gastroenterology, Tokyo Women's Medical University, Tokyo 1628666, Japan
| | - Minoru Oshima
- Department of Gastroenterological Surgery, Kagawa University, Kagawa 7610793, Japan
| | - Keiichi Okano
- Department of Gastroenterological Surgery, Kagawa University, Kagawa 7610793, Japan
| | - Seiko Hirono
- Second Department of Surgery, Wakayama Medical University, Wakayama 6418509, Japan
| | - Masamichi Mizuma
- Department of Surgery, Tohoku University Graduate School of Medicine, Sendai Miyagi 9808575, Japan
| | - Koji Arihiro
- Department of Anatomical Pathology, Hiroshima University Hospital, Hiroshima 7348551, Japan
| | - Masakazu Yamamoto
- Department of Surgery, Institute of Gastroenterology, Tokyo Women's Medical University, Tokyo 1628666, Japan
| | - Michiaki Unno
- Department of Surgery, Tohoku University Graduate School of Medicine, Sendai Miyagi 9808575, Japan
| | - Hiroki Yamaue
- Second Department of Surgery, Wakayama Medical University, Wakayama 6418509, Japan
| | - Matthew J Weiss
- Department of Surgery, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Christopher L Wolfgang
- Department of Surgery, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Toru Furukawa
- Institute for Integrated Medical Science, Tokyo Women's Medical University, Tokyo 1628666, Japan
| | - Hitoshi Nakagama
- Division of Carcinogenesis and Cancer Prevention, National Cancer Center Research Institute, Tokyo 1040045, Japan
| | - Bert Vogelstein
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Ludwig Center and The Howard Hughes Medical Institute at Johns Hopkins Kimmel Cancer Center, Baltimore, MD 21287, USA
| | - Tohru Kiyono
- Division of Carcinogenesis and Cancer Prevention, National Cancer Center Research Institute, Tokyo 1040045, Japan
| | - Ralph H Hruban
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; Department of Oncology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Tatsuhiro Shibata
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo 1040045, Japan; Laboratory of Molecular Medicine, Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo 1088639, Japan
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19
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Chen F, Sha M, Wang Y, Wu T, Shan W, Liu J, Zhou W, Zhu Y, Sun Y, Shi Y, Bleich D, Han X. Transcription factor Ets-1 links glucotoxicity to pancreatic beta cell dysfunction through inhibiting PDX-1 expression in rodent models. Diabetologia 2016; 59:316-24. [PMID: 26564177 DOI: 10.1007/s00125-015-3805-3] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/20/2015] [Accepted: 10/14/2015] [Indexed: 02/07/2023]
Abstract
AIMS/HYPOTHESIS 'Glucotoxicity' is a term used to convey the negative effect of hyperglycaemia on beta cell function; however, the underlying molecular mechanisms that impair insulin secretion and gene expression are poorly defined. Our objective was to define the role of transcription factor v-ets avian erythroblastosis virus E26 oncogene homologue 1 (Ets-1) in beta cell glucotoxicity. METHODS Primary islets and Min6 cells were exposed to high glucose and Ets-1 expression was measured. Recombinant adenovirus and transgenic mice were used to upregulate Ets-1 expression in beta cells in vitro and in vivo, and insulin secretion was assessed. The binding activity of H3/H4 histone on the Ets-1 promoter, and that of forkhead box (FOX)A2, FOXO1 and Ets-1 on the Pdx-1 promoter was measured by chromatin immunoprecipitation and quantitative real-time PCR assay. RESULTS High glucose induced upregulation of Ets-1 expression and hyperacetylation of histone H3 and H4 at the Ets-1 gene promoter in beta cells. Ets-1 overexpression dramatically suppressed insulin secretion and biosynthesis both in vivo and in vitro. Besides, Ets-1 overexpression increased the activity of FOXO1 but decreased that of FOXA2 binding to the pancreatic and duodenal homeobox 1 (PDX-1) homology region 2 (PH2), resulting in inhibition of Pdx-1 promoter activity and downregulation of PDX-1 expression and activity. In addition, high glucose promoted the interaction of Ets-1 and FOXO1, and the activity of Ets-1 binding to the Pdx-1 promoter. Importantly, PDX-1 overexpression reversed the defect in pancreatic beta cells induced by Ets-1 excess, while knockdown of Ets-1 prevented hyperglycaemia-induced dysfunction of pancreatic beta cells. CONCLUSIONS/INTERPRETATION Our observations suggest that Ets-1 links glucotoxicity to pancreatic beta cell dysfunction through inhibiting PDX-1 expression in type 2 diabetes.
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MESH Headings
- Animals
- Blood Glucose/physiology
- Cells, Cultured
- Diabetes Mellitus, Experimental/blood
- Diabetes Mellitus, Experimental/complications
- Diabetes Mellitus, Experimental/genetics
- Diabetes Mellitus, Experimental/physiopathology
- Diabetes Mellitus, Type 2/complications
- Diabetes Mellitus, Type 2/genetics
- Diabetes Mellitus, Type 2/metabolism
- Diabetes Mellitus, Type 2/physiopathology
- Gene Expression Regulation
- Homeodomain Proteins/genetics
- Homeodomain Proteins/metabolism
- Hyperglycemia/blood
- Hyperglycemia/genetics
- Hyperglycemia/physiopathology
- Insulin-Secreting Cells/metabolism
- Insulin-Secreting Cells/physiology
- Male
- Mice
- Mice, Inbred C57BL
- Mice, Transgenic
- Proto-Oncogene Protein c-ets-1/physiology
- Rats
- Rats, Sprague-Dawley
- Trans-Activators/genetics
- Trans-Activators/metabolism
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Affiliation(s)
- Fang Chen
- Key Laboratory of Human Functional Genomics of Jiangsu Province, Nanjing Medical University, 140 Hanzhong Road, Nanjing, 210029, People's Republic of China
| | - Min Sha
- Key Laboratory of Human Functional Genomics of Jiangsu Province, Nanjing Medical University, 140 Hanzhong Road, Nanjing, 210029, People's Republic of China
| | - Yanyang Wang
- Key Laboratory of Human Functional Genomics of Jiangsu Province, Nanjing Medical University, 140 Hanzhong Road, Nanjing, 210029, People's Republic of China
| | - Tijun Wu
- Key Laboratory of Human Functional Genomics of Jiangsu Province, Nanjing Medical University, 140 Hanzhong Road, Nanjing, 210029, People's Republic of China
| | - Wei Shan
- Key Laboratory of Human Functional Genomics of Jiangsu Province, Nanjing Medical University, 140 Hanzhong Road, Nanjing, 210029, People's Republic of China
| | - Jia Liu
- Key Laboratory of Human Functional Genomics of Jiangsu Province, Nanjing Medical University, 140 Hanzhong Road, Nanjing, 210029, People's Republic of China
| | - Wenbo Zhou
- Key Laboratory of Human Functional Genomics of Jiangsu Province, Nanjing Medical University, 140 Hanzhong Road, Nanjing, 210029, People's Republic of China
| | - Yunxia Zhu
- Key Laboratory of Human Functional Genomics of Jiangsu Province, Nanjing Medical University, 140 Hanzhong Road, Nanjing, 210029, People's Republic of China
| | - Yujie Sun
- Key Laboratory of Human Functional Genomics of Jiangsu Province, Nanjing Medical University, 140 Hanzhong Road, Nanjing, 210029, People's Republic of China
| | - Yuguang Shi
- Barshop Institute for Longevity and Aging Studies, University of Texas Health Science Center, San Antonio, TX, USA
| | - David Bleich
- Rutgers New Jersey Medical School, Newark, NJ, USA
| | - Xiao Han
- Key Laboratory of Human Functional Genomics of Jiangsu Province, Nanjing Medical University, 140 Hanzhong Road, Nanjing, 210029, People's Republic of China.
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20
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Marra AN, Wingert RA. Epithelial cell fate in the nephron tubule is mediated by the ETS transcription factors etv5a and etv4 during zebrafish kidney development. Dev Biol 2016; 411:231-245. [PMID: 26827902 DOI: 10.1016/j.ydbio.2016.01.035] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Revised: 01/19/2016] [Accepted: 01/27/2016] [Indexed: 02/06/2023]
Abstract
Kidney development requires the differentiation and organization of discrete nephron epithelial lineages, yet the genetic and molecular pathways involved in these events remain poorly understood. The embryonic zebrafish kidney, or pronephros, provides a simple and useful model to study nephrogenesis. The pronephros is primarily comprised of two types of epithelial cells: transportive and multiciliated cells (MCCs). Transportive cells occupy distinct tubule segments and are characterized by the expression of various solute transporters, while MCCs function in fluid propulsion and are dispersed in a "salt-and-pepper" fashion within the tubule. Epithelial cell identity is reliant on interplay between the Notch signaling pathway and retinoic acid (RA) signaling, where RA promotes MCC fate by inhibiting Notch activity in renal progenitors, while Notch acts downstream to trigger transportive cell formation and block adoption of an MCC identity. Previous research has shown that the transcription factor ets variant 5a (etv5a), and its closely related ETS family members, are required for ciliogenesis in other zebrafish tissues. Here, we mapped etv5a expression to renal progenitors that occupy domains where MCCs later emerge. Thus, we hypothesized that etv5a is required for normal development of MCCs in the nephron. etv5a loss of function caused a decline of MCC number as indicated by the reduced frequency of cells that expressed the MCC-specific markers outer dense fiber of sperm tails 3b (odf3b) and centrin 4 (cetn4), where rescue experiments partially restored MCC incidence. Interestingly, deficiency of ets variant 4 (etv4), a related gene that is broadly expressed in the posterior mesoderm during somitogenesis stages, also led to reduced MCC numbers, which were further reduced by dual etv5a/4 deficiency, suggesting that both of these ETS factors are essential for MCC formation and that they also might have redundant activities. In epistatic studies, exogenous RA treatment expanded the etv5a domain within the renal progenitor field and RA inhibition blocked etv5a in this populace, indicating that etv5a acts downstream of RA. Additionally, treatment with exogenous RA partially rescued the reduced MCC phenotype after loss of etv5a. Further, abrogation of Notch with the small molecule inhibitor DAPT increased the renal progenitor etv5a expression domain as well as MCC density in etv5a deficient embryos, suggesting Notch acts upstream to inhibit etv5a. In contrast, etv4 levels in renal progenitors were unaffected by changes in RA or Notch signaling levels, suggesting a possible non-cell autonomous role during pronephros formation. Taken together, these findings have revealed new insights about the genetic mechanisms of epithelial cell development during nephrogenesis.
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Affiliation(s)
- Amanda N Marra
- Department of Biological Sciences, Center for Zebrafish Research, Center for Stem Cells and Regenerative Medicine, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Rebecca A Wingert
- Department of Biological Sciences, Center for Zebrafish Research, Center for Stem Cells and Regenerative Medicine, University of Notre Dame, Notre Dame, IN 46556, USA.
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21
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Manyes L, Arribas M, Gomez C, Calzada N, Fernandez-Medarde A, Santos E. Transcriptional profiling reveals functional links between RasGrf1 and Pttg1 in pancreatic beta cells. BMC Genomics 2014; 15:1019. [PMID: 25421944 PMCID: PMC4301450 DOI: 10.1186/1471-2164-15-1019] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Accepted: 11/06/2014] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Our prior characterization of RasGrf1 deficient mice uncovered significant defects in pancreatic islet count and size as well as beta cell development and signaling function, raising question about the mechanisms linking RasGrf1 to the generation of those "pancreatic" phenotypes. RESULTS Here, we compared the transcriptional profile of highly purified pancreatic islets from RasGrf1 KO mice to that of WT control animals using commercial oligonucleotide microarrays. RasGrf1 elimination resulted in differential gene expression of numerous components of MAPK- and Calcium-signaling pathways, suggesting a relevant contribution of this GEF to modulation of cellular signaling in the cell lineages integrating the pancreatic islets. Whereas the overall transcriptional profile of pancreatic islets was highly specific in comparison to other organs of the same KO mice, a significant specific repression of Pttg1 was a common transcriptional alteration shared with other tissues of neuroectodermal origin. This observation, together with the remarkable pancreatic phenotypic similarities between RasGrf1 KO and Pttg1 KO mice suggested the possibility of proximal functional regulatory links between RasGrf1 and Pttg1 in pancreatic cell lineages expressing these proteins.Analysis of the mPttg1 promoter region identified specific recognition sites for numerous transcription factors which were also found to be differentially expressed in RasGrf1 KO pancreatic islets and are known to be relevant for Ras-ERK signaling as well as beta cell function. Reporter luciferase assays in BT3 insulinoma cells demonstrated the ability of RasGrf1 to modulate mPttg1 promoter activity through ERK-mediated signals. Analysis of the phenotypic interplay between RasGrf1 and Pttg1 in double knockout RasGrf1/Pttg1 mice showed that combined elimination of the two loci resulted in dramatically reduced values of islet and beta cell count and glucose homeostasis function which neared those measured in single Pttg1 KO mice and were significantly lower than those observed in individual RasGrf1 KO mice. CONCLUSIONS The specific transcriptional profile and signaling behavior of RasgGrf1 KO pancreatic islets, together with the dominance of Pttg1 over RasGrf1 with regards to the generation of these phenotypes in mouse pancreas, suggest that RasGrf1 is an important upstream component of signal transduction pathways regulating Pttg1 expression and controlling beta cell development and physiological responses.
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Affiliation(s)
| | | | | | | | - Alberto Fernandez-Medarde
- Centro de Investigación del Cáncer, IBMCC (CSIC-USAL), University of Salamanca, Campus Unamuno, 37007 Salamanca, Spain.
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22
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Hale MA, Swift GH, Hoang CQ, Deering TG, Masui T, Lee YK, Xue J, MacDonald RJ. The nuclear hormone receptor family member NR5A2 controls aspects of multipotent progenitor cell formation and acinar differentiation during pancreatic organogenesis. Development 2014; 141:3123-33. [PMID: 25063451 DOI: 10.1242/dev.109405] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The orphan nuclear receptor NR5A2 is necessary for the stem-like properties of the epiblast of the pre-gastrulation embryo and for cellular and physiological homeostasis of endoderm-derived organs postnatally. Using conditional gene inactivation, we show that Nr5a2 also plays crucial regulatory roles during organogenesis. During the formation of the pancreas, Nr5a2 is necessary for the expansion of the nascent pancreatic epithelium, for the subsequent formation of the multipotent progenitor cell (MPC) population that gives rise to pre-acinar cells and bipotent cells with ductal and islet endocrine potential, and for the formation and differentiation of acinar cells. At birth, the NR5A2-deficient pancreas has defects in all three epithelial tissues: a partial loss of endocrine cells, a disrupted ductal tree and a >90% deficit of acini. The acinar defects are due to a combination of fewer MPCs, deficient allocation of those MPCs to pre-acinar fate, disruption of acinar morphogenesis and incomplete acinar cell differentiation. NR5A2 controls these developmental processes directly as well as through regulatory interactions with other pancreatic transcriptional regulators, including PTF1A, MYC, GATA4, FOXA2, RBPJL and MIST1 (BHLHA15). In particular, Nr5a2 and Ptf1a establish mutually reinforcing regulatory interactions and collaborate to control developmentally regulated pancreatic genes by binding to shared transcriptional regulatory regions. At the final stage of acinar cell development, the absence of NR5A2 affects the expression of Ptf1a and its acinar specific partner Rbpjl, so that the few acinar cells that form do not complete differentiation. Nr5a2 controls several temporally distinct stages of pancreatic development that involve regulatory mechanisms relevant to pancreatic oncogenesis and the maintenance of the exocrine phenotype.
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Affiliation(s)
- Michael A Hale
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9148, USA
| | - Galvin H Swift
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9148, USA
| | - Chinh Q Hoang
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9148, USA
| | - Tye G Deering
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9148, USA
| | - Toshi Masui
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9148, USA
| | - Youn-Kyoung Lee
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9041, USA
| | - Jumin Xue
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9148, USA
| | - Raymond J MacDonald
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9148, USA
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23
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Gutierrez-Aguilar R, Kim DH, Casimir M, Dai XQ, Pfluger PT, Park J, Haller A, Donelan E, Park J, D’Alessio D, Woods SC, MacDonald PE, Seeley RJ. The role of the transcription factor ETV5 in insulin exocytosis. Diabetologia 2014; 57:383-91. [PMID: 24190582 PMCID: PMC3947344 DOI: 10.1007/s00125-013-3096-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Accepted: 10/09/2013] [Indexed: 12/15/2022]
Abstract
AIMS/HYPOTHESIS Genome-wide association studies have revealed an association of the transcription factor ETS variant gene 5 (ETV5) with human obesity. However, its role in glucose homeostasis and energy balance is unknown. METHODS Etv5 knockout (KO) mice were monitored weekly for body weight (BW) and food intake. Body composition was measured at 8 and 16 weeks of age. Glucose metabolism was studied, and glucose-stimulated insulin secretion was measured in vivo and in vitro. RESULTS Etv5 KO mice are smaller and leaner, and have a reduced BW and lower fat mass than their wild-type controls on a chow diet. When exposed to a high-fat diet, KO mice are resistant to diet-induced BW gain. Despite a greater insulin sensitivity, KO mice have profoundly impaired glucose tolerance associated with impaired insulin secretion. Morphometric analysis revealed smaller islets and a reduced beta cell size in the pancreatic islets of Etv5 KO mice. Knockdown of ETV5 in an insulin-secreting cell line or beta cells from human donors revealed intact mitochondrial and Ca(2+) channel activity, but reduced insulin exocytosis. CONCLUSION/INTERPRETATION This work reveals a critical role for ETV5 in specifically regulating insulin secretion both in vitro and in vivo.
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Affiliation(s)
- Ruth Gutierrez-Aguilar
- Department of Internal Medicine, University of Cincinnati, 2170 East Galbraith Road, Cincinnati, OH 45237, USA
| | - Dong-Hoon Kim
- Department of Pharmacology, Korea University College of Medicine, Seoul, South Korea
| | - Marina Casimir
- Department of Pharmacology, University of Alberta, Edmonton, AB, Canada
- Alberta Diabetes Institute, University of Alberta, Edmonton, AB, Canada
| | - Xiao-Qing Dai
- Department of Pharmacology, University of Alberta, Edmonton, AB, Canada
- Alberta Diabetes Institute, University of Alberta, Edmonton, AB, Canada
| | - Paul T. Pfluger
- Institute for Diabetes and Obesity, Helmholtz Centre Munich, Neuherberg, Germany
| | - Jongsun Park
- Department of Pharmacology, College of Medicine, Chungnam National University, Daejeon, South Korea
| | - April Haller
- Department of Internal Medicine, University of Cincinnati, 2170 East Galbraith Road, Cincinnati, OH 45237, USA
| | - Elizabeth Donelan
- Department of Internal Medicine, University of Cincinnati, 2170 East Galbraith Road, Cincinnati, OH 45237, USA
| | - Jisoo Park
- Department of Pharmacology, College of Medicine, Chungnam National University, Daejeon, South Korea
| | - David D’Alessio
- Department of Internal Medicine, University of Cincinnati, 2170 East Galbraith Road, Cincinnati, OH 45237, USA
| | - Stephen C. Woods
- Department of Psychiatry and Behavioral Neuroscience, University of Cincinnati, Cincinnati, OH, USA
| | - Patrick E. MacDonald
- Department of Pharmacology, University of Alberta, Edmonton, AB, Canada
- Alberta Diabetes Institute, University of Alberta, Edmonton, AB, Canada
| | - Randy J. Seeley
- Department of Internal Medicine, University of Cincinnati, 2170 East Galbraith Road, Cincinnati, OH 45237, USA
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24
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Ching ST, Cunha GR, Baskin LS, Basson MA, Klein OD. Coordinated activity of Spry1 and Spry2 is required for normal development of the external genitalia. Dev Biol 2013; 386:1-11. [PMID: 24361260 DOI: 10.1016/j.ydbio.2013.12.014] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2013] [Revised: 12/05/2013] [Accepted: 12/10/2013] [Indexed: 11/16/2022]
Abstract
Development of the mammalian external genitalia is controlled by a network of signaling molecules and transcription factors. Because FGF signaling plays a central role in this complicated morphogenetic process, we investigated the role of Sprouty genes, which are important intracellular modulators of FGF signaling, during embryonic development of the external genitalia in mice. We found that Sprouty genes are expressed by the urethral epithelium during embryogenesis, and that they have a critical function during urethral canalization and fusion. Development of the genital tubercle (GT), the anlage of the prepuce and glans penis in males and glans clitoris in females, was severely affected in male embryos carrying null alleles of both Spry1 and Spry2. In Spry1(-/-);Spry2(-/-) embryos, the internal tubular urethra was absent, and urothelial morphology and organization was abnormal. These effects were due, in part, to elevated levels of epithelial cell proliferation in Spry1(-/-);Spry2(-/-) embryos. Despite changes in overall organization, terminal differentiation of the urothelium was not significantly affected. Characterization of the molecular pathways that regulate normal GT development confirmed that deletion of Sprouty genes leads to elevated FGF signaling, whereas levels of signaling in other cascades were largely preserved. Together, these results show that levels of FGF signaling must be tightly regulated during embryonic development of the external genitalia in mice, and that this regulation is mediated in part through the activity of Sprouty gene products.
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Affiliation(s)
- Saunders T Ching
- Department of Orofacial Sciences, University of California, San Francisco, United States; Department of Urology, University of California, San Francisco, United States
| | - Gerald R Cunha
- Department of Urology, University of California, San Francisco, United States
| | - Laurence S Baskin
- Department of Urology, University of California, San Francisco, United States
| | - M Albert Basson
- Department of Craniofacial Development and Stem Cell Biology, King's College, London, UK
| | - Ophir D Klein
- Department of Orofacial Sciences, University of California, San Francisco, United States; Program in Craniofacial and Mesenchymal Biology, University of California, San Francisco, United States; Institute for Human Genetics, University of California, San Francisco, United States; Department of Pediatrics, University of California, San Francisco, United States.
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25
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Lombaert IMA, Abrams SR, Li L, Eswarakumar VP, Sethi AJ, Witt RL, Hoffman MP. Combined KIT and FGFR2b signaling regulates epithelial progenitor expansion during organogenesis. Stem Cell Reports 2013; 1:604-19. [PMID: 24371813 PMCID: PMC3871401 DOI: 10.1016/j.stemcr.2013.10.013] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2013] [Revised: 10/30/2013] [Accepted: 10/31/2013] [Indexed: 11/14/2022] Open
Abstract
Organ formation and regeneration require epithelial progenitor expansion to engineer, maintain, and repair the branched tissue architecture. Identifying the mechanisms that control progenitor expansion will inform therapeutic organ (re)generation. Here, we discover that combined KIT and fibroblast growth factor receptor 2b (FGFR2b) signaling specifically increases distal progenitor expansion during salivary gland organogenesis. FGFR2b signaling upregulates the epithelial KIT pathway so that combined KIT/FGFR2b signaling, via separate AKT and mitogen-activated protein kinase (MAPK) pathways, amplifies FGFR2b-dependent transcription. Combined KIT/FGFR2b signaling selectively expands the number of KIT+K14+SOX10+ distal progenitors, and a genetic loss of KIT signaling depletes the distal progenitors but also unexpectedly depletes the K5+ proximal progenitors. This occurs because the distal progenitors produce neurotrophic factors that support gland innervation, which maintains the proximal progenitors. Furthermore, a rare population of KIT+FGFR2b+ cells is present in adult glands, in which KIT signaling also regulates epithelial-neuronal communication during homeostasis. Our findings provide a framework to direct regeneration of branched epithelial organs. Combined KIT and FGFR2b signaling amplifies FGFR2b-dependent transcription KIT/FGFR2b signaling during organogenesis expands distal KIT+ epithelial progenitors Distal progenitors communicate with proximal progenitors via the neuronal niche KIT+ progenitors maintain epithelial-neuronal communication during adult homeostasis
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Affiliation(s)
- Isabelle M A Lombaert
- Matrix and Morphogenesis Section, Laboratory of Cell and Developmental Biology, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD 20892, USA
| | - Shaun R Abrams
- Matrix and Morphogenesis Section, Laboratory of Cell and Developmental Biology, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD 20892, USA
| | - Li Li
- Department of Orthopedics & Rehabilitation, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Veraragavan P Eswarakumar
- Department of Orthopedics & Rehabilitation, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Aditya J Sethi
- Developmental Mechanisms Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD 20892, USA
| | - Robert L Witt
- Head & Neck Multidisciplinary Clinic, Helen F. Graham Cancer Center of Christiana Care, Newark, DE 19713, USA
| | - Matthew P Hoffman
- Matrix and Morphogenesis Section, Laboratory of Cell and Developmental Biology, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD 20892, USA
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Stephens DN, Klein RH, Salmans ML, Gordon W, Ho H, Andersen B. The Ets transcription factor EHF as a regulator of cornea epithelial cell identity. J Biol Chem 2013; 288:34304-24. [PMID: 24142692 DOI: 10.1074/jbc.m113.504399] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
The cornea is the clear, outermost portion of the eye composed of three layers: an epithelium that provides a protective barrier while allowing transmission of light into the eye, a collagen-rich stroma, and an endothelium monolayer. How cornea development and aging is controlled is poorly understood. Here we characterize the mouse cornea transcriptome from early embryogenesis through aging and compare it with transcriptomes of other epithelial tissues, identifying cornea-enriched genes, pathways, and transcriptional regulators. Additionally, we profiled cornea epithelium and stroma, defining genes enriched in these layers. Over 10,000 genes are differentially regulated in the mouse cornea across the time course, showing dynamic expression during development and modest expression changes in fewer genes during aging. A striking transition time point for gene expression between postnatal days 14 and 28 corresponds with completion of cornea development at the transcriptional level. Clustering classifies co-expressed, and potentially co-regulated, genes into biologically informative categories, including groups that exhibit epithelial or stromal enriched expression. Based on these findings, and through loss of function studies and ChIP-seq, we show that the Ets transcription factor EHF promotes cornea epithelial fate through complementary gene activating and repressing activities. Furthermore, we identify potential interactions between EHF, KLF4, and KLF5 in promoting cornea epithelial differentiation. These data provide insights into the mechanisms underlying epithelial development and aging, identifying EHF as a regulator of cornea epithelial identity and pointing to interactions between Ets and KLF factors in promoting epithelial fate. Furthermore, this comprehensive gene expression data set for the cornea is a powerful tool for discovery of novel cornea regulators and pathways.
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Hoffman GE, Logsdon BA, Mezey JG. PUMA: a unified framework for penalized multiple regression analysis of GWAS data. PLoS Comput Biol 2013; 9:e1003101. [PMID: 23825936 PMCID: PMC3694815 DOI: 10.1371/journal.pcbi.1003101] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2012] [Accepted: 05/02/2013] [Indexed: 01/25/2023] Open
Abstract
Penalized Multiple Regression (PMR) can be used to discover novel disease associations in GWAS datasets. In practice, proposed PMR methods have not been able to identify well-supported associations in GWAS that are undetectable by standard association tests and thus these methods are not widely applied. Here, we present a combined algorithmic and heuristic framework for PUMA (Penalized Unified Multiple-locus Association) analysis that solves the problems of previously proposed methods including computational speed, poor performance on genome-scale simulated data, and identification of too many associations for real data to be biologically plausible. The framework includes a new minorize-maximization (MM) algorithm for generalized linear models (GLM) combined with heuristic model selection and testing methods for identification of robust associations. The PUMA framework implements the penalized maximum likelihood penalties previously proposed for GWAS analysis (i.e. Lasso, Adaptive Lasso, NEG, MCP), as well as a penalty that has not been previously applied to GWAS (i.e. LOG). Using simulations that closely mirror real GWAS data, we show that our framework has high performance and reliably increases power to detect weak associations, while existing PMR methods can perform worse than single marker testing in overall performance. To demonstrate the empirical value of PUMA, we analyzed GWAS data for type 1 diabetes, Crohns's disease, and rheumatoid arthritis, three autoimmune diseases from the original Wellcome Trust Case Control Consortium. Our analysis replicates known associations for these diseases and we discover novel etiologically relevant susceptibility loci that are invisible to standard single marker tests, including six novel associations implicating genes involved in pancreatic function, insulin pathways and immune-cell function in type 1 diabetes; three novel associations implicating genes in pro- and anti-inflammatory pathways in Crohn's disease; and one novel association implicating a gene involved in apoptosis pathways in rheumatoid arthritis. We provide software for applying our PUMA analysis framework.
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Affiliation(s)
- Gabriel E. Hoffman
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, United States of America
- * E-mail: (GEH); (JGM)
| | - Benjamin A. Logsdon
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, United States of America
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Jason G. Mezey
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, United States of America
- Department of Genetic Medicine, Weill Cornell Medical College, New York, New York, United States of America
- * E-mail: (GEH); (JGM)
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Zhang JS, Koenig A, Harrison A, Ugolkov AV, Fernandez-Zapico ME, Couch FJ, Billadeau DD. Mutant K-Ras increases GSK-3β gene expression via an ETS-p300 transcriptional complex in pancreatic cancer. Oncogene 2011; 30:3705-15. [PMID: 21441955 DOI: 10.1038/onc.2011.90] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Glycogen synthase kinase-3 beta (GSK-3β) is overexpressed in a number of human malignancies and has been shown to contribute to tumor cell proliferation and survival. Although regulation of GSK-3β activity has been extensively studied, the mechanisms governing GSK-3β gene expression are still unknown. Using pancreatic cancer as a model, we find that constitutively active Ras signaling increases GSK-3β gene expression via the canonical mitogen-activated protein kinase signaling pathway. Analysis of the mechanism revealed that K-Ras regulates the expression of this kinase through two highly conserved E-twenty six (ETS) binding elements within the proximal region. Furthermore, we demonstrate that mutant K-Ras enhances ETS2 loading onto the promoter, and ETS requires its transcriptional activity to increase GSK-3β gene transcription in pancreatic cancer cells. Lastly, we show that ETS2 cooperates with p300 histone acetyltransferase to remodel chromatin and promote GSK-3β expression. Taken together, these results provide a general mechanism for increased expression of GSK-3β in pancreatic cancer and perhaps other cancers, where Ras signaling is deregulated.
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Affiliation(s)
- J-S Zhang
- Department of Immunology and Division of Oncology Research, Schulze Center for Novel Therapeutics, College of Medicine, Mayo Clinic, Rochester, MN, USA.
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Nyeng P, Bjerke MA, Norgaard GA, Qu X, Kobberup S, Jensen J. Fibroblast growth factor 10 represses premature cell differentiation during establishment of the intestinal progenitor niche. Dev Biol 2010; 349:20-34. [PMID: 20883684 DOI: 10.1016/j.ydbio.2010.09.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2010] [Revised: 08/29/2010] [Accepted: 09/20/2010] [Indexed: 11/30/2022]
Abstract
Spatio-temporal regulation of the balance between cell renewal and cell differentiation is of vital importance for embryonic development and adult homeostasis. Fibroblast growth factor signaling relayed from the mesenchyme to the epithelium is necessary for progenitor maintenance during organogenesis of most endoderm-derived organs, but it is still ambiguous whether the signal is exclusively mitogenic. Furthermore, the downstream mechanisms are largely unknown. In order to elucidate these questions we performed a complementary analysis of fibroblast growth factor 10 (Fgf10), gain-of-function and loss-of-function in the embryonic mouse duodenum, where the progenitor niche is clearly defined and differentiation proceeds in a spatially organized manner. In agreement with a role in progenitor maintenance, FGF10 is expressed in the duodenal mesenchyme during early development while the cognate receptor FGFR2b is expressed in the epithelial progenitor niche. Fgf10 gain-of-function in the epithelium leads to spatial expansion of the progenitor niche and repression of cell differentiation, while loss-of-function results in premature cell differentiation and subsequent epithelial hypoplasia. We conclude that FGF10 mediated mesenchymal-to-epithelial signaling maintains the progenitor niche in the embryonic duodenum primarily by repressing cell differentiation, rather than through mitogenic signaling. Furthermore, we demonstrate that FGF10-signaling targets include ETS-family transcription factors, which have previously been shown to regulate epithelial maturation and tumor progression.
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Affiliation(s)
- Pia Nyeng
- Barbara Davis Center for Childhood Diabetes, University of Colorado Health Sciences Center, 1775 N Ursula St. B140, 80045 Aurora, CO, USA.
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Lombaert IMA, Hoffman MP. Epithelial stem/progenitor cells in the embryonic mouse submandibular gland. FRONTIERS OF ORAL BIOLOGY 2010; 14:90-106. [PMID: 20428013 PMCID: PMC3375329 DOI: 10.1159/000313709] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Salivary gland organogenesis involves the specification, maintenance, lineage commitment, and differentiation of epithelial stem/progenitor cells. Identifying how stem/progenitor cells are directed along a series of cell fate decisions to form a functional salivary gland will be necessary for future stem cell regenerative therapy. The identification of stem/progenitor cells within the salivary gland has focused on their role in postnatal glands and little is known about them in embryonic glands. Here, we have reviewed the information available for other developing organ systems and used it to determine whether similar cell populations exist in the mouse submandibular gland. Additionally, using growth factors that influence salivary gland epithelial morphogenesis during development, we have taken a simple experimental approach asking whether any of these growth factors influence early developmental lineages within the salivary epithelium on a transcriptional level. These preliminary findings show that salivary epithelial stem/progenitor populations exist within the gland, and that growth factors that are reported to control epithelial morphogenesis may also impact cell fate decisions. Further investigation of the signaling networks that influence stem/progenitor cell behavior will allow us to hypothesize how we might induce autologous stem cells to regenerate damaged salivary tissue in a therapeutic context.
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31
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Heo SH, Choi YJ, Ryoo HM, Cho JY. Expression profiling of ETS and MMP factors in VEGF-activated endothelial cells: Role of MMP-10 in VEGF-induced angiogenesis. J Cell Physiol 2010; 224:734-42. [DOI: 10.1002/jcp.22175] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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Overlapping functions of Pea3 ETS transcription factors in FGF signaling during zebrafish development. Dev Biol 2010; 342:11-25. [PMID: 20346941 DOI: 10.1016/j.ydbio.2010.03.011] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2009] [Revised: 03/11/2010] [Accepted: 03/15/2010] [Indexed: 11/23/2022]
Abstract
Fibroblast growth factors (FGFs) are secreted molecules that activate the RAS/mitogen-activated protein kinase (MAPK) signaling pathway. In zebrafish development, FGF signaling is responsible for establishing dorsal polarity, maintaining the isthmic organizer, and cardiac ventricle formation. Because several ETS factors are known transcriptional mediators of MAPK signaling, we hypothesized that these factors function to mediate FGF signaling processes. In zebrafish, the simultaneous knock-down of three Pea3 ETS proteins, Etv5, Erm, and Pea3, produced phenotypes reminiscent of embryos deficient in FGF signaling. Morphant embryos displayed both cardiac and left/right patterning defects as well as disruption of the isthmic organizer. Furthermore, the expression of FGF target genes was abolished in Pea3 ETS depleted embryos. To understand how FGF signaling and ETS factors control gene expression, transcriptional regulation of dusp6 was studied in mouse and zebrafish. Conserved Pea3 ETS binding sites were identified within the Dusp6 promoter, and reporter assays showed that one of these sites is required for dusp6 induction by FGFs. We further demonstrated the interaction of Pea3 ETS factors with the Dusp6 promoter both in vitro and in vivo. These results revealed the requirement of ETS factors in transducing FGF signals in developmental processes.
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Kerr N, Pintzas A, Holmes F, Hobson SA, Pope R, Wallace M, Wasylyk C, Wasylyk B, Wynick D. The expression of ELK transcription factors in adult DRG: Novel isoforms, antisense transcripts and upregulation by nerve damage. Mol Cell Neurosci 2010; 44:165-77. [PMID: 20304071 DOI: 10.1016/j.mcn.2010.03.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2010] [Revised: 02/27/2010] [Accepted: 03/10/2010] [Indexed: 01/31/2023] Open
Abstract
ELK transcription factors are known to be expressed in a number of regions in the nervous system. We show by RT-PCR that the previously described Elk1, Elk3/Elk3b/Elk3c and Elk4 mRNAs are expressed in adult dorsal root ganglia (DRG), together with the novel alternatively spliced isoforms Elk1b, Elk3d and Elk4c/Elk4d/Elk4e. These isoforms are also expressed in brain, heart, kidney and testis. In contrast to Elk3 protein, the novel Elk3d isoform is cytoplasmic, fails to bind ETS binding sites and yet can activate transcription by an indirect mechanism. The Elk3 and Elk4 genes are overlapped by co-expressed Pctk2 (Cdk17) and Mfsd4 genes, respectively, with the potential formation of Elk3/Pctaire2 and Elk4/Mfsd4 sense-antisense mRNA heteroduplexes. After peripheral nerve injury the Elk3 mRNA isoforms are each upregulated approximately 2.3-fold in DRG (P<0.005), whereas the natural antisense Pctaire2 isoforms show only a small increase (21%, P<0.01) and Elk1 and Elk4 mRNAs are unchanged.
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Affiliation(s)
- Niall Kerr
- Department of Physiology and Pharmacology, School of Medical Sciences, University of Bristol, Bristol BS81TD, UK
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Anderson KR, White P, Kaestner KH, Sussel L. Identification of known and novel pancreas genes expressed downstream of Nkx2.2 during development. BMC DEVELOPMENTAL BIOLOGY 2009; 9:65. [PMID: 20003319 PMCID: PMC2799404 DOI: 10.1186/1471-213x-9-65] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2009] [Accepted: 12/10/2009] [Indexed: 11/10/2022]
Abstract
BACKGROUND The homeodomain containing transcription factor Nkx2.2 is essential for the differentiation of pancreatic endocrine cells. Deletion of Nkx2.2 in mice leads to misspecification of islet cell types; insulin-expressing beta cells and glucagon-expressing alpha cells are replaced by ghrelin-expressing cells. Additional studies have suggested that Nkx2.2 functions both as a transcriptional repressor and activator to regulate islet cell formation and function. To identify genes that are potentially regulated by Nkx2.2 during the major wave of endocrine and exocrine cell differentiation, we assessed gene expression changes that occur in the absence of Nkx2.2 at the onset of the secondary transition in the developing pancreas. RESULTS Microarray analysis identified 80 genes that were differentially expressed in e12.5 and/or e13.5 Nkx2.2-/- embryos. Some of these genes encode transcription factors that have been previously identified in the pancreas, clarifying the position of Nkx2.2 within the islet transcriptional regulatory pathway. We also identified signaling factors and transmembrane proteins that function downstream of Nkx2.2, including several that have not previously been described in the pancreas. Interestingly, a number of known exocrine genes are also misexpressed in the Nkx2.2-/- pancreas. CONCLUSIONS Expression profiling of Nkx2.2-/- mice during embryogenesis has allowed us to identify known and novel pancreatic genes that function downstream of Nkx2.2 to regulate pancreas development. Several of the newly identified signaling factors and transmembrane proteins may function to influence islet cell fate decisions. These studies have also revealed a novel function for Nkx2.2 in maintaining appropriate exocrine gene expression. Most importantly, Nkx2.2 appears to function within a complex regulatory loop with Ngn3 at a key endocrine differentiation step.
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Affiliation(s)
- Keith R Anderson
- Department of Biochemistry and Program in Molecular Biology, University of Colorado Health Science Center, Denver, CO 80045, USA
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Conditional control of the differentiation competence of pancreatic endocrine and ductal cells by Fgf10. Mech Dev 2009; 127:220-34. [PMID: 19969077 DOI: 10.1016/j.mod.2009.11.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2009] [Revised: 11/25/2009] [Accepted: 11/30/2009] [Indexed: 11/21/2022]
Abstract
Fgf10 is a critical component of mesenchymal-to-epithelial signaling during endodermal development. In the Fgf10 null pancreas, the embryonic progenitor population fails to expand, while ectopic Fgf10 expression forces progenitor arrest and organ hyperplasia. Using a conditional Fgf10 gain-of-function model, we observed that the timing of Fgf10 expression affected the cellular competence of the arrested pancreatic progenitors. We present evidence that the Fgf10-arrested progenitor state is reversible and that terminal differentiation resumes upon cessation of Fgf10 production. However, competence towards the individual pancreatic cell lineages depended upon the gestational time of when Fgf10 expression was attenuated. This revealed a competence window of endocrine and ductal cell formation that coincided with the pancreatic secondary transition between E13.5 and E15.5. We demonstrate that maintaining the Fgf10-arrested state during this period leads to permanent loss of competence for the endocrine and ductal cell fates. However, competence of the arrested progenitors towards the exocrine cell fate was retained throughout the secondary transition. Sustained Fgf10 expression caused irreversible loss of Ngn3 expression, which may underlie the loss of endocrine competence. Maintenance of exocrine competence may be attributable to continuous Ptf1a expression in the Fgf10-arrested progenitors. This may explain the rapid induction of Bhlhb8, a normally distalized cell intrinsic marker, following loss of ectopic Fgf10 expression. We conclude that the window for endocrine and ductal cell competence ceases during the secondary transition in pancreatic development.
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36
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Sood AK. PDEF and PDEF-induced proteins as candidate tumor antigens for T cell and antibody-mediated immunotherapy of breast cancer. Immunol Res 2009; 46:206-15. [DOI: 10.1007/s12026-009-8129-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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Chioni AM, Grose R. Negative regulation of fibroblast growth factor 10 (FGF-10) by polyoma enhancer activator 3 (PEA3). Eur J Cell Biol 2009; 88:371-84. [PMID: 19410332 PMCID: PMC2691923 DOI: 10.1016/j.ejcb.2009.01.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2008] [Revised: 01/15/2009] [Accepted: 01/16/2009] [Indexed: 12/21/2022] Open
Abstract
FGF-10 plays an important role in development and disease, acting as the key ligand for FGFR2B to regulate cell proliferation, migration and differentiation. Aberrant FGF signalling is implicated in tumourigenesis, with several cancer studies reporting FGF-10 or FGFR2B upregulation or identifying activating mutations in Fgfr2. We used 5’ RACE to identify a novel transcription start site for murine Fgf-10. Conventional in silico analysis predicted multiple binding sites for the transcription factor PEA3 upstream of this site. Binding was confirmed by chromatin immunopreciptation, and functional significance was studied by both RNAi knockdown and transient over-expression of PEA3. Knockdown of PEA3 message led to increased Fgf-10 expression, whereas overexpression of PEA3 resulted in decreased Fgf-10 expression. Thus, we have identified PEA3 as a negative regulator of Fgf-10 expression in a murine cell line and confirmed that activity also is seen in human breast cancer cell lines (MCF-7 and MDA-MB-231). Furthermore, over-expression of PEA3 in these cells resulted in impaired cell migration, which was rescued by treatment with FGF-10. Thus, PEA3 can regulate the transcription of Fgf-10 and such modulation can control breast cancer cell behaviour.
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Affiliation(s)
- Athina-Myrto Chioni
- Centre for Tumour Biology, Institute of Cancer, Barts & The London School of Medicine & Dentistry, London EC1M 6BQ, UK
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Gongora MC, Lob HE, Landmesser U, Guzik TJ, Martin WD, Ozumi K, Wall SM, Wilson DS, Murthy N, Gravanis M, Fukai T, Harrison DG. Loss of extracellular superoxide dismutase leads to acute lung damage in the presence of ambient air: a potential mechanism underlying adult respiratory distress syndrome. THE AMERICAN JOURNAL OF PATHOLOGY 2008; 173:915-26. [PMID: 18787098 DOI: 10.2353/ajpath.2008.080119] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The extracellular superoxide dismutase 3 (SOD3) is highly expressed in both blood vessels and lungs. In different models of pulmonary injury, SOD3 is reduced; however, it is unclear whether this contributes to lung injury. To study the role of acute SOD3 reduction in lung injury, the SOD3 gene was deleted in adult mice by using the Cre-Lox technology. Acute reduction of SOD3 led to a fivefold increase in lung superoxide, marked inflammatory cell infiltration, a threefold increase in the arterial-alveolar gradient, respiratory acidosis, histological changes similar to those observed in adult respiratory distress syndrome, and 85% mortality. Treatment with the SOD mimetic MnTBAP and intranasal administration of SOD-containing polyketal microparticles reduced mortality, prevented the histological alterations, and reduced lung superoxide levels. To understand how mice with the SOD3 embryonic deletion survived without lung injury, gene array analysis was performed. These data demonstrated the up-regulation of 37 genes and down-regulation of nine genes, including those involved in cell signaling, inflammation, and gene transcription in SOD3-/- mice compared with either mice with acute SOD3 reduction or wild-type controls. These studies show that SOD3 is essential for survival in the presence of ambient oxygen and that acute loss of this enzyme can lead to severe lung damage. Strategies either to prevent SOD3 inactivation or to augment its levels might prove useful in the treatment of acute lung injury.
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