1
|
Nightingale R, Reehorst CM, Vukelic N, Papadopoulos N, Liao Y, Guleria S, Bell C, Vaillant F, Paul S, Luk IY, Dhillon AS, Jenkins LJ, Morrow RJ, Jackling FC, Chand AL, Chisanga D, Chen Y, Williams DS, Anderson RL, Ellis S, Meikle PJ, Shi W, Visvader JE, Pal B, Mariadason JM. Ehf controls mammary alveolar lineage differentiation and is a putative suppressor of breast tumorigenesis. Dev Cell 2024; 59:1988-2004.e11. [PMID: 38781975 DOI: 10.1016/j.devcel.2024.04.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Revised: 03/03/2024] [Accepted: 04/30/2024] [Indexed: 05/25/2024]
Abstract
The transcription factor EHF is highly expressed in the lactating mammary gland, but its role in mammary development and tumorigenesis is not fully understood. Utilizing a mouse model of Ehf deletion, herein, we demonstrate that loss of Ehf impairs mammary lobuloalveolar differentiation at late pregnancy, indicated by significantly reduced levels of milk genes and milk lipids, fewer differentiated alveolar cells, and an accumulation of alveolar progenitor cells. Further, deletion of Ehf increased proliferative capacity and attenuated prolactin-induced alveolar differentiation in mammary organoids. Ehf deletion also increased tumor incidence in the MMTV-PyMT mammary tumor model and increased the proliferative capacity of mammary tumor organoids, while low EHF expression was associated with higher tumor grade and poorer outcome in luminal A and basal human breast cancers. Collectively, these findings establish EHF as a non-redundant regulator of mammary alveolar differentiation and a putative suppressor of mammary tumorigenesis.
Collapse
Affiliation(s)
- Rebecca Nightingale
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC 3084, Australia; School of Cancer Medicine, La Trobe University, Bundoora, VIC 3086, Australia
| | - Camilla M Reehorst
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC 3084, Australia; School of Cancer Medicine, La Trobe University, Bundoora, VIC 3086, Australia
| | - Natalia Vukelic
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC 3084, Australia; School of Cancer Medicine, La Trobe University, Bundoora, VIC 3086, Australia
| | - Nikolaos Papadopoulos
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC 3084, Australia; School of Cancer Medicine, La Trobe University, Bundoora, VIC 3086, Australia
| | - Yang Liao
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC 3084, Australia; School of Cancer Medicine, La Trobe University, Bundoora, VIC 3086, Australia
| | - Shalini Guleria
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC 3084, Australia; School of Cancer Medicine, La Trobe University, Bundoora, VIC 3086, Australia
| | - Caroline Bell
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC 3084, Australia; School of Cancer Medicine, La Trobe University, Bundoora, VIC 3086, Australia
| | - François Vaillant
- Cancer Biology and Stem Cells Division, The Walter and Eliza Hall Institute, Parkville, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC 3052, Australia
| | - Sudip Paul
- Metabolomics Laboratory, Baker Heart and Diabetes Institute, Melbourne, VIC 3004, Australia; Baker Department of Cardiovascular Research Translation and Implementation, La Trobe University, Bundoora, VIC 3086, Australia
| | - Ian Y Luk
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC 3084, Australia; School of Cancer Medicine, La Trobe University, Bundoora, VIC 3086, Australia
| | - Amardeep S Dhillon
- The Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Deakin University, Geelong, VIC 3220, Australia
| | - Laura J Jenkins
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC 3084, Australia; School of Cancer Medicine, La Trobe University, Bundoora, VIC 3086, Australia
| | - Riley J Morrow
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC 3084, Australia; School of Cancer Medicine, La Trobe University, Bundoora, VIC 3086, Australia
| | - Felicity C Jackling
- Cancer Biology and Stem Cells Division, The Walter and Eliza Hall Institute, Parkville, VIC 3052, Australia
| | - Ashwini L Chand
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC 3084, Australia; School of Cancer Medicine, La Trobe University, Bundoora, VIC 3086, Australia
| | - David Chisanga
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC 3084, Australia; School of Cancer Medicine, La Trobe University, Bundoora, VIC 3086, Australia
| | - Yunshun Chen
- Cancer Biology and Stem Cells Division, The Walter and Eliza Hall Institute, Parkville, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC 3052, Australia; Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - David S Williams
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC 3084, Australia; School of Cancer Medicine, La Trobe University, Bundoora, VIC 3086, Australia; Department of Pathology, Austin Health, Heidelberg, VIC 3084, Australia
| | - Robin L Anderson
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC 3084, Australia; School of Cancer Medicine, La Trobe University, Bundoora, VIC 3086, Australia; The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC 3052, Australia
| | - Sarah Ellis
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC 3084, Australia; School of Cancer Medicine, La Trobe University, Bundoora, VIC 3086, Australia
| | - Peter J Meikle
- Metabolomics Laboratory, Baker Heart and Diabetes Institute, Melbourne, VIC 3004, Australia; Baker Department of Cardiovascular Research Translation and Implementation, La Trobe University, Bundoora, VIC 3086, Australia
| | - Wei Shi
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC 3084, Australia; School of Cancer Medicine, La Trobe University, Bundoora, VIC 3086, Australia
| | - Jane E Visvader
- Cancer Biology and Stem Cells Division, The Walter and Eliza Hall Institute, Parkville, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC 3052, Australia
| | - Bhupinder Pal
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC 3084, Australia; School of Cancer Medicine, La Trobe University, Bundoora, VIC 3086, Australia.
| | - John M Mariadason
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC 3084, Australia; School of Cancer Medicine, La Trobe University, Bundoora, VIC 3086, Australia; Department of Medicine, University of Melbourne, Parkville, VIC 3052, Australia.
| |
Collapse
|
2
|
Sun M, Huang X, Ruan X, Shang X, Zhang M, Liu L, Wang P, An P, Lin Y, Yang J, Xue Y. Cpeb4-mediated Dclk2 promotes neuronal pyroptosis induced by chronic cerebral ischemia through phosphorylation of Ehf. J Cereb Blood Flow Metab 2024:271678X241240590. [PMID: 38513137 DOI: 10.1177/0271678x241240590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/23/2024]
Abstract
Chronic cerebral ischemia (CCI) is a clinical syndrome characterised by brain dysfunction due to decreased chronic cerebral perfusion. CCI initiates several inflammatory pathways, including pyroptosis. RNA-binding proteins (RBPs) play important roles in CCI. This study aimed to explore whether the interaction between RBP-Cpeb4 and Dclk2 affected Ehf phosphorylation to regulate neuronal pyroptosis. HT22 cells and mice were used to construct oxygen glucose deprivation (OGD)/CCI models. We found that Cpeb4 and Dclk2 were upregulated in OGD-treated HT22 cells and CCI-induced hippocampal CA1 tissues. Cpeb4 upregulated Dclk2 expression by increasing Dclk2 mRNA stability. Knockdown of Cpeb4 or Dclk2 inhibited neuronal pyroptosis in OGD-treated HT22 cells and CCI-induced hippocampal CA1 tissues. By binding to the promoter regions of Caspase1 and Caspase3, the transcription factor Ehf reduced their promoter activities and inhibited the transcription. Dclk2 phosphorylated Ehf and changed its nucleoplasmic distribution, resulting in the exit of p-Ehf from the nucleus and decreased Ehf levels. It promoted the expression of Caspase1 and Caspase3 and stimulated neuronal pyroptosis of HT22 cells induced by OGD. Cpeb4/Dclk2/Ehf pathway plays an important role in the regulation of cerebral ischemia-induced neuronal pyroptosis.
Collapse
Affiliation(s)
- Miao Sun
- Department of Neurobiology, School of life Sciences, China Medical University, Shenyang, China
- Key Laboratory of Neuro-Oncology in Liaoning Province, Shenyang, China
| | - Xin Huang
- Department of Radiology, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Xuelei Ruan
- Department of Neurobiology, School of life Sciences, China Medical University, Shenyang, China
- Key Laboratory of Neuro-Oncology in Liaoning Province, Shenyang, China
| | - Xiuli Shang
- Department of Neurology, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Mengyang Zhang
- Department of Neurobiology, School of life Sciences, China Medical University, Shenyang, China
- Key Laboratory of Neuro-Oncology in Liaoning Province, Shenyang, China
| | - Libo Liu
- Department of Neurobiology, School of life Sciences, China Medical University, Shenyang, China
- Key Laboratory of Neuro-Oncology in Liaoning Province, Shenyang, China
| | - Ping Wang
- Department of Neurobiology, School of life Sciences, China Medical University, Shenyang, China
- Key Laboratory of Neuro-Oncology in Liaoning Province, Shenyang, China
| | - Ping An
- Department of Neurobiology, School of life Sciences, China Medical University, Shenyang, China
- Key Laboratory of Neuro-Oncology in Liaoning Province, Shenyang, China
| | - Yang Lin
- Department of Neurobiology, School of life Sciences, China Medical University, Shenyang, China
- Key Laboratory of Neuro-Oncology in Liaoning Province, Shenyang, China
| | - Jin Yang
- Key Laboratory of Neuro-Oncology in Liaoning Province, Shenyang, China
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, China
| | - Yixue Xue
- Department of Neurobiology, School of life Sciences, China Medical University, Shenyang, China
- Key Laboratory of Neuro-Oncology in Liaoning Province, Shenyang, China
| |
Collapse
|
3
|
Hosseinzadeh L, Kikhtyak Z, Laven-Law G, Pederson SM, Puiu CG, D'Santos CS, Lim E, Carroll JS, Tilley WD, Dwyer AR, Hickey TE. The androgen receptor interacts with GATA3 to transcriptionally regulate a luminal epithelial cell phenotype in breast cancer. Genome Biol 2024; 25:44. [PMID: 38317241 PMCID: PMC10840202 DOI: 10.1186/s13059-023-03161-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 12/27/2023] [Indexed: 02/07/2024] Open
Abstract
BACKGROUND The androgen receptor (AR) is a tumor suppressor in estrogen receptor (ER) positive breast cancer, a role sustained in some ER negative breast cancers. Key factors dictating AR genomic activity in a breast context are largely unknown. Herein, we employ an unbiased chromatin immunoprecipitation-based proteomic technique to identify endogenous AR interacting co-regulatory proteins in ER positive and negative models of breast cancer to gain new insight into mechanisms of AR signaling in this disease. RESULTS The DNA-binding factor GATA3 is identified and validated as a novel AR interacting protein in breast cancer cells irrespective of ER status. AR activation by the natural ligand 5α-dihydrotestosterone (DHT) increases nuclear AR-GATA3 interactions, resulting in AR-dependent enrichment of GATA3 chromatin binding at a sub-set of genomic loci. Silencing GATA3 reduces but does not prevent AR DNA binding and transactivation of genes associated with AR/GATA3 co-occupied loci, indicating a co-regulatory role for GATA3 in AR signaling. DHT-induced AR/GATA3 binding coincides with upregulation of luminal differentiation genes, including EHF and KDM4B, established master regulators of a breast epithelial cell lineage. These findings are validated in a patient-derived xenograft model of breast cancer. Interaction between AR and GATA3 is also associated with AR-mediated growth inhibition in ER positive and ER negative breast cancer. CONCLUSIONS AR and GATA3 interact to transcriptionally regulate luminal epithelial cell differentiation in breast cancer regardless of ER status. This interaction facilitates the tumor suppressor function of AR and mechanistically explains why AR expression is associated with less proliferative, more differentiated breast tumors and better overall survival in breast cancer.
Collapse
Affiliation(s)
- Leila Hosseinzadeh
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical School, University of Adelaide, Adelaide, Australia
| | - Zoya Kikhtyak
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical School, University of Adelaide, Adelaide, Australia
| | - Geraldine Laven-Law
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical School, University of Adelaide, Adelaide, Australia
| | - Stephen M Pederson
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical School, University of Adelaide, Adelaide, Australia
| | - Caroline G Puiu
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical School, University of Adelaide, Adelaide, Australia
| | - Clive S D'Santos
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Elgene Lim
- Garvan Institute of Medical Research, University of New South Wales, Sydney, Australia
| | - Jason S Carroll
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Wayne D Tilley
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical School, University of Adelaide, Adelaide, Australia
| | - Amy R Dwyer
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical School, University of Adelaide, Adelaide, Australia
| | - Theresa E Hickey
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical School, University of Adelaide, Adelaide, Australia.
| |
Collapse
|
4
|
Urban LA, Li J, Gundogdu G, Trinh A, Shao H, Nguyen T, Mauney JR, Downing TL. DNA Methylation Dynamics During Esophageal Epithelial Regeneration Following Repair with Acellular Silk Fibroin Grafts in Rat. Adv Biol (Weinh) 2023; 7:e2200160. [PMID: 36658732 PMCID: PMC10401397 DOI: 10.1002/adbi.202200160] [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: 06/07/2022] [Revised: 11/10/2022] [Indexed: 01/21/2023]
Abstract
Esophageal pathologies such as atresia and benign strictures often require surgical reconstruction with autologous tissues to restore organ continuity. Complications such as donor site morbidity and limited tissue availability have spurred the development of acellular grafts for esophageal tissue replacement. Acellular biomaterials for esophageal repair rely on the activation of intrinsic regenerative mechanisms to mediate de novo tissue formation at implantation sites. Previous research has identified signaling cascades involved in neoepithelial formation in a rat model of onlay esophagoplasty with acellular silk fibroin grafts, including phosphoinositide 3-kinase (PI3K), and protein kinase B (Akt) signaling. However, it is currently unknown how these mechanisms are governed by DNA methylation (DNAme) during esophageal wound healing processes. Reduced-representation bisulfite sequencing is performed to characterize temporal DNAme dynamics in host and regenerated tissues up to 1 week postimplantation. Overall, global hypermethylation is observed at postreconstruction timepoints and an inverse correlation between promoter DNAme and the expression levels of differentially expressed proteins during regeneration. Site-specific hypomethylation targets genes associated with immune activation, while hypermethylation occurs within gene bodies encoding PI3K-Akt signaling components during the tissue remodeling period. The data provide insight into the epigenetic mechanisms during esophageal regeneration following surgical repair with acellular grafts.
Collapse
Affiliation(s)
- Lauren A. Urban
- Department of Microbiology & Molecular Genetics, University of California Irvine; Irvine, California, USA
- UCI Edwards Lifesciences Foundation Cardiovascular Innovation and Research Center (CIRC), University of California-Irvine, Irvine, CA 92697, USA
| | - Jiachun Li
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA, 92697, USA
| | - Gokhan Gundogdu
- Department of Urology, University of California, Irvine, Orange, CA, 92868, USA
| | - Annie Trinh
- Department of Microbiology & Molecular Genetics, University of California Irvine; Irvine, California, USA
- UCI Edwards Lifesciences Foundation Cardiovascular Innovation and Research Center (CIRC), University of California-Irvine, Irvine, CA 92697, USA
- The NSF-Simons Center for Multiscale Cell Fate Research, University of California-Irvine, Irvine, California 92697, USA
| | - Hanjuan Shao
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA, 92697, USA
- UCI Edwards Lifesciences Foundation Cardiovascular Innovation and Research Center (CIRC), University of California-Irvine, Irvine, CA 92697, USA
| | - Travis Nguyen
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA, 92697, USA
| | - Joshua R. Mauney
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA, 92697, USA
- Department of Urology, University of California, Irvine, Orange, CA, 92868, USA
| | - Timothy L. Downing
- Department of Microbiology & Molecular Genetics, University of California Irvine; Irvine, California, USA
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA, 92697, USA
- UCI Edwards Lifesciences Foundation Cardiovascular Innovation and Research Center (CIRC), University of California-Irvine, Irvine, CA 92697, USA
- The NSF-Simons Center for Multiscale Cell Fate Research, University of California-Irvine, Irvine, California 92697, USA
| |
Collapse
|
5
|
Wang Z, Coban B, Wu H, Chouaref J, Daxinger L, Paulsen MT, Ljungman M, Smid M, Martens JWM, Danen EHJ. GRHL2-controlled gene expression networks in luminal breast cancer. Cell Commun Signal 2023; 21:15. [PMID: 36691073 PMCID: PMC9869538 DOI: 10.1186/s12964-022-01029-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 12/24/2022] [Indexed: 01/24/2023] Open
Abstract
Grainyhead like 2 (GRHL2) is an essential transcription factor for development and function of epithelial tissues. It has dual roles in cancer by supporting tumor growth while suppressing epithelial to mesenchymal transitions (EMT). GRHL2 cooperates with androgen and estrogen receptors (ER) to regulate gene expression. We explore genome wide GRHL2 binding sites conserved in three ER⍺/GRHL2 positive luminal breast cancer cell lines by ChIP-Seq. Interaction with the ER⍺/FOXA1/GATA3 complex is observed, however, only for a minor fraction of conserved GRHL2 peaks. We determine genome wide transcriptional dynamics in response to loss of GRHL2 by nascent RNA Bru-seq using an MCF7 conditional knockout model. Integration of ChIP- and Bru-seq pinpoints candidate direct GRHL2 target genes in luminal breast cancer. Multiple connections between GRHL2 and proliferation are uncovered, including transcriptional activation of ETS and E2F transcription factors. Among EMT-related genes, direct regulation of CLDN4 is corroborated but several targets identified in other cells (including CDH1 and ZEB1) are ruled out by both ChIP- and Bru-seq as being directly controlled by GRHL2 in luminal breast cancer cells. Gene clusters correlating positively (including known GRHL2 targets such as ErbB3, CLDN4/7) or negatively (including TGFB1 and TGFBR2) with GRHL2 in the MCF7 knockout model, display similar correlation with GRHL2 in ER positive as well as ER negative breast cancer patients. Altogether, this study uncovers gene sets regulated directly or indirectly by GRHL2 in luminal breast cancer, identifies novel GRHL2-regulated genes, and points to distinct GRHL2 regulation of EMT in luminal breast cancer cells. Video Abstract.
Collapse
Affiliation(s)
- Zi Wang
- Leiden Academic Center for Drug Research, Leiden University, Leiden, The Netherlands
| | - Bircan Coban
- Leiden Academic Center for Drug Research, Leiden University, Leiden, The Netherlands
| | - Haoyu Wu
- Department of Human Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Jihed Chouaref
- Department of Human Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Lucia Daxinger
- Department of Human Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Michelle T Paulsen
- Departments of Radiation Oncology and Environmental Health Sciences, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Mats Ljungman
- Departments of Radiation Oncology and Environmental Health Sciences, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Marcel Smid
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - John W M Martens
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Erik H J Danen
- Leiden Academic Center for Drug Research, Leiden University, Leiden, The Netherlands.
| |
Collapse
|
6
|
Jacksi M, Schad E, Buday L, Tantos A. Absence of Scaffold Protein Tks4 Disrupts Several Signaling Pathways in Colon Cancer Cells. Int J Mol Sci 2023; 24:ijms24021310. [PMID: 36674824 PMCID: PMC9861885 DOI: 10.3390/ijms24021310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 01/05/2023] [Accepted: 01/06/2023] [Indexed: 01/12/2023] Open
Abstract
Tks4 is a large scaffold protein in the EGFR signal transduction pathway that is involved in several cellular processes, such as cellular motility, reactive oxygen species-dependent processes, and embryonic development. It is also implicated in a rare developmental disorder, Frank-ter Haar syndrome. Loss of Tks4 resulted in the induction of an EMT-like process, with increased motility and overexpression of EMT markers in colorectal carcinoma cells. In this work, we explored the broader effects of deletion of Tks4 on the gene expression pattern of HCT116 colorectal carcinoma cells by transcriptome sequencing of wild-type and Tks4 knockout (KO) cells. We identified several protein coding genes with altered mRNA levels in the Tks4 KO cell line, as well as a set of long non-coding RNAs, and confirmed these changes with quantitative PCR on a selected set of genes. Our results show a significant perturbation of gene expression upon the deletion of Tks4, suggesting the involvement of different signal transduction pathways over the well-known EGFR signaling.
Collapse
Affiliation(s)
- Mevan Jacksi
- Institute of Enzymology, Research Centre for Natural Sciences, 1117 Budapest, Hungary
- Doctoral School of Biology, Institute of Biology, ELTE Eötvös Loránd University, 1117 Budapest, Hungary
| | - Eva Schad
- Institute of Enzymology, Research Centre for Natural Sciences, 1117 Budapest, Hungary
| | - László Buday
- Institute of Enzymology, Research Centre for Natural Sciences, 1117 Budapest, Hungary
- Department of Molecular Biology, Semmelweis University Medical School, 1094 Budapest, Hungary
| | - Agnes Tantos
- Institute of Enzymology, Research Centre for Natural Sciences, 1117 Budapest, Hungary
- Correspondence:
| |
Collapse
|
7
|
Zhao T, Xiao D, Jin F, Sun X, Yu J, Wang H, Liu J, Cai W, Huang C, Wang X, Gao S, Liu Z, Yang S, Gao C, Hao J. ESE3-positive PSCs drive pancreatic cancer fibrosis, chemoresistance and poor prognosis via tumour-stromal IL-1β/NF-κB/ESE3 signalling axis. Br J Cancer 2022; 127:1461-1472. [PMID: 35986089 PMCID: PMC9553871 DOI: 10.1038/s41416-022-01927-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 07/08/2022] [Accepted: 07/15/2022] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Desmoplastic stroma, a feature of pancreatic ductal adenocarcinoma (PDAC), contains abundant activated pancreatic stellate cells (PSCs). How PSCs promote PDAC progression remains incompletely understood. METHODS Effect of epithelium-specific E-twenty six factor 3 (ESE3)-positive PSCs on PDAC fibrosis and chemoresistance was examined by western blot, RT-PCR, immunofluorescence, flow cytometry assay, chromatin immunoprecipitation, luciferase assay, immunohistochemistry and subcutaneous pancreatic cancer mouse model. RESULTS ESE3 expression increased in PSCs in PDAC tissues compared with those in normal PSCs. Clinical data showed that ESE3 upregulation in PSCs was positively correlated with tumour size, pTNM stage, CA19-9, carcinoembryonic antigen and serum CA242 level. ESE3 overexpression in PSCs was an independent negative prognostic factor for disease-free survival and overall survival amongst patients with PDAC. Mechanistically, the conditional medium from the loss and gain of ESE3-expressing PSCs influenced PDAC chemoresistance and tumour growth. ESE3 directly induced the transcription of α-SMA, collagen-I and IL-1β by binding to ESE3-binding sites on their promoters to activate PSCs. IL-1β upregulated ESE3 in PSCs through NF-κB activation, and ESE3 was required for PSC activation by tumour cell-derived IL-1β. CONCLUSION Inhibiting the IL-1β/ESE3 (PSCs)/IL-1β-positive feedback loop is a promising therapeutic strategy to reduce tumour fibrosis and increase chemotherapeutic efficacy in PDAC.
Collapse
Affiliation(s)
- Tiansuo Zhao
- grid.411918.40000 0004 1798 6427Department of Pancreatic Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer; Key Laboratory of Cancer Prevention and Therapy, Tianjin’s Clinical Research Center for Cancer, Tianjin, PR China
| | - Di Xiao
- grid.411918.40000 0004 1798 6427Department of Pancreatic Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer; Key Laboratory of Cancer Prevention and Therapy, Tianjin’s Clinical Research Center for Cancer, Tianjin, PR China
| | - Fanjie Jin
- grid.411918.40000 0004 1798 6427Department of Pancreatic Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer; Key Laboratory of Cancer Prevention and Therapy, Tianjin’s Clinical Research Center for Cancer, Tianjin, PR China
| | - Xugang Sun
- grid.411918.40000 0004 1798 6427Department of Pancreatic Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer; Key Laboratory of Cancer Prevention and Therapy, Tianjin’s Clinical Research Center for Cancer, Tianjin, PR China
| | - Jie Yu
- grid.452461.00000 0004 1762 8478Hepatopancreatobiliary Surgery Department, First Hospital of Shanxi Medical University, Taiyuan, PR China
| | - Hongwei Wang
- grid.411918.40000 0004 1798 6427Department of Pancreatic Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer; Key Laboratory of Cancer Prevention and Therapy, Tianjin’s Clinical Research Center for Cancer, Tianjin, PR China
| | - Jing Liu
- grid.411918.40000 0004 1798 6427Department of Pancreatic Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer; Key Laboratory of Cancer Prevention and Therapy, Tianjin’s Clinical Research Center for Cancer, Tianjin, PR China
| | - Wenrun Cai
- grid.411918.40000 0004 1798 6427Department of Pancreatic Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer; Key Laboratory of Cancer Prevention and Therapy, Tianjin’s Clinical Research Center for Cancer, Tianjin, PR China
| | - Chongbiao Huang
- grid.411918.40000 0004 1798 6427Department of Pancreatic Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer; Key Laboratory of Cancer Prevention and Therapy, Tianjin’s Clinical Research Center for Cancer, Tianjin, PR China
| | - Xiuchao Wang
- grid.411918.40000 0004 1798 6427Department of Pancreatic Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer; Key Laboratory of Cancer Prevention and Therapy, Tianjin’s Clinical Research Center for Cancer, Tianjin, PR China
| | - Song Gao
- grid.411918.40000 0004 1798 6427Department of Pancreatic Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer; Key Laboratory of Cancer Prevention and Therapy, Tianjin’s Clinical Research Center for Cancer, Tianjin, PR China
| | - Zhe Liu
- grid.265021.20000 0000 9792 1228Department of Immunology, Biochemistry and Molecular Biology, Tianjin Medical University, Tianjin, PR China
| | - Shengyu Yang
- grid.240473.60000 0004 0543 9901Department of Cellular and Molecular Physiology, Penn State College of Medicine, Hershey, PA USA
| | - Chuntao Gao
- grid.411918.40000 0004 1798 6427Department of Pancreatic Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer; Key Laboratory of Cancer Prevention and Therapy, Tianjin’s Clinical Research Center for Cancer, Tianjin, PR China
| | - Jihui Hao
- grid.411918.40000 0004 1798 6427Department of Pancreatic Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer; Key Laboratory of Cancer Prevention and Therapy, Tianjin’s Clinical Research Center for Cancer, Tianjin, PR China
| |
Collapse
|
8
|
Zhong T, Zhao J, Zhan S, Wang L, Cao J, Dai D, Guo J, Li L, Zhang H, Niu L. LncRNA-mRNA modules involved in goat rumen development: Insights from genome-wide transcriptome profiling. Front Physiol 2022; 13:979121. [PMID: 36091364 PMCID: PMC9449361 DOI: 10.3389/fphys.2022.979121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 08/01/2022] [Indexed: 11/15/2022] Open
Abstract
The rumen is an essential digestive and absorption organ of ruminants. During fetal life, lactation, and post-weaning period, goat rumen undergoes drastic morphological and metabolic-functional changes triggered by potential regulated genes and non-coding RNA molecules. As the essential regulatory factors, long non-coding RNAs (lncRNAs) have vital functions in various biological activities. However, their roles during rumen development are still poorly explored in ruminants. To explore the genome-wide expression profiles of lncRNAs and mRNAs in the goat rumens, we generated 5,007 lncRNAs and 19,738 mRNAs identified during the fetal and prepubertal stages by the high-throughput RNA sequencing. Notably, 365 lncRNAs and 2,877 mRNAs were considered to be differentially expressed. The weighted gene co-expression network analysis and functional analysis were performed to explore the regulatory roles of those differentially expressed molecules. The cis-and trans-target genes of differently expressed lncRNAs were enriched for pathways related to focal adhesion, cGMP-PKG signaling pathway, alpha-linolenic acid metabolism, arachidonic acid metabolism, and fat digestion and absorption. Gene Ontology and the Kyoto Encyclopedia of Genes and Genomes analyses showed that the differently expressed genes mainly participated in mitotic cytokinesis, desmosome, fatty acid degradation, cell adhesion molecules, and fatty acid metabolism. The prediction of lncRNA-mRNA interaction networks further revealed transcripts potentially involved in rumen development. The present study profiles a global overview of lncRNAs and mRNAs during rumen development. Our findings provide valuable resources for genetic regulation and molecular mechanisms of rumen development in ruminants.
Collapse
|
9
|
Shi L, Zhai Y, Zhao Y, Kong X, Zhang D, Yu H, Li Z. ELF4 is critical to zygotic gene activation and epigenetic reprogramming during early embryonic development in pigs. Front Vet Sci 2022; 9:954601. [PMID: 35928113 PMCID: PMC9343831 DOI: 10.3389/fvets.2022.954601] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 06/27/2022] [Indexed: 11/28/2022] Open
Abstract
Zygotic gene activation (ZGA) and epigenetic reprogramming are critical in early embryonic development in mammals, and transcription factors are involved in regulating these events. However, the effects of ELF4 on porcine embryonic development remain unclear. In this study, the expression of ELF4 was detected in early porcine embryos and different tissues. By knocking down ELF4, the changes of H3K9me3 modification, DNA methylation and ZGA-related genes were analyzed. Our results showed that ELF4 was expressed at all stages of early porcine embryos fertilized in vitro (IVF), with the highest expression level at the 8-cell stage. The embryonic developmental competency and blastocyst quality decreased after ELF4 knockdown (20.70% control vs. 17.49% si-scramble vs. 2.40% si-ELF4; p < 0.001). Knockdown of ELF4 induced DNA damage at the 4-cell stage. Interfering with ELF4 resulted in abnormal increases in H3K9me3 and DNA methylation levels at the 4-cell stage and inhibited the expression of genes related to ZGA. These results suggest that ELF4 affects ZGA and embryonic development competency in porcine embryos by maintaining genome integrity and regulating dynamic changes of H3K9me3 and DNA methylation, and correctly activating ZGA-related genes to promote epigenetic reprogramming. These results provide a theoretical basis for further studies on the regulatory mechanisms of ELF4 in porcine embryos.
Collapse
Affiliation(s)
- Lijing Shi
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, First Hospital, Jilin University, Changchun, China
- College of Animal Science, Jilin University, Changchun, China
| | - Yanhui Zhai
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, First Hospital, Jilin University, Changchun, China
| | - Yuanshen Zhao
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, First Hospital, Jilin University, Changchun, China
| | - Xiangjie Kong
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, First Hospital, Jilin University, Changchun, China
| | - Daoyu Zhang
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, First Hospital, Jilin University, Changchun, China
| | - Hao Yu
- College of Animal Science, Jilin University, Changchun, China
- Hao Yu
| | - Ziyi Li
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, First Hospital, Jilin University, Changchun, China
- *Correspondence: Ziyi Li
| |
Collapse
|
10
|
Oyelakin A, Nayak KB, Glathar AR, Gluck C, Wrynn T, Tugores A, Romano RA, Sinha S. EHF is a novel regulator of cellular redox metabolism and predicts patient prognosis in HNSCC. NAR Cancer 2022; 4:zcac017. [PMID: 35664541 PMCID: PMC9155246 DOI: 10.1093/narcan/zcac017] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 04/28/2022] [Accepted: 05/18/2022] [Indexed: 12/13/2022] Open
Abstract
Head and Neck Squamous Cell Carcinoma (HNSCC) is a heterogeneous disease with relatively high morbidity and mortality rates. The lack of effective therapies, high recurrence rates and drug resistance driven in part, by tumor heterogeneity, contribute to the poor prognosis for patients diagnosed with this cancer. This problem is further exacerbated by the fact that key regulatory factors contributing to the disease diversity remains largely elusive. Here, we have identified EHF as an important member of the ETS family of transcription factors that is highly expressed in normal oral tissues, but lost during HNSCC progression. Interestingly, HNSCC tumors and cell lines exhibited a dichotomy of high and low EHF expression, and patients whose tumors retained EHF expression showed significantly better prognosis, suggesting a potential tumor suppressive role for EHF. To address this, we have performed gain and loss of function studies and leveraged bulk and single-cell cancer genomic datasets to identify global EHF targets by RNA-sequencing (RNA-seq) and Chromatin Immunoprecipitation and next generation sequencing (ChIP-seq) experiments of HNSCC cell lines. These mechanistic studies have revealed that EHF, acts as a regulator of a broad spectrum of metabolic processes, specifically targeting regulators of redox homeostasis such as NRF2 and SOX2. Our immunostaining results confirm the mutually exclusive expression patterns of EHF and SOX2 in HNSCC tumors and suggest a possible role for these two factors in establishing discrete metabolic states within the tumor microenvironment. Taken together, EHF may serve as a novel prognostic marker for classifying HNSCC patients for actionable and targeted therapeutic intervention.
Collapse
Affiliation(s)
- Akinsola Oyelakin
- Department of Oral Biology, School of Dental Medicine, State University of New York at Buffalo, Buffalo, NY, USA
| | - Kasturi Bala Nayak
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY, USA
| | - Alexandra Ruth Glathar
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY, USA
| | - Christian Gluck
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY, USA
| | - Theresa Wrynn
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY, USA
| | - Antonio Tugores
- Unidad de Investigación, Complejo Hospitalario Universitario Insular Materno Infantil Avda Maritima del Sur, Las Palmas de Gran Canaria, Spain
| | - Rose-Anne Romano
- Department of Oral Biology, School of Dental Medicine, State University of New York at Buffalo, Buffalo, NY, USA
| | - Satrajit Sinha
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY, USA
| |
Collapse
|
11
|
Leote AC, Wu X, Beyer A. Regulatory network-based imputation of dropouts in single-cell RNA sequencing data. PLoS Comput Biol 2022; 18:e1009849. [PMID: 35176023 PMCID: PMC8890719 DOI: 10.1371/journal.pcbi.1009849] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 03/02/2022] [Accepted: 01/18/2022] [Indexed: 01/07/2023] Open
Abstract
Single-cell RNA sequencing (scRNA-seq) methods are typically unable to quantify the expression levels of all genes in a cell, creating a need for the computational prediction of missing values (‘dropout imputation’). Most existing dropout imputation methods are limited in the sense that they exclusively use the scRNA-seq dataset at hand and do not exploit external gene-gene relationship information. Further, it is unknown if all genes equally benefit from imputation or which imputation method works best for a given gene. Here, we show that a transcriptional regulatory network learned from external, independent gene expression data improves dropout imputation. Using a variety of human scRNA-seq datasets we demonstrate that our network-based approach outperforms published state-of-the-art methods. The network-based approach performs particularly well for lowly expressed genes, including cell-type-specific transcriptional regulators. Further, the cell-to-cell variation of 11.3% to 48.8% of the genes could not be adequately imputed by any of the methods that we tested. In those cases gene expression levels were best predicted by the mean expression across all cells, i.e. assuming no measurable expression variation between cells. These findings suggest that different imputation methods are optimal for different genes. We thus implemented an R-package called ADImpute (available via Bioconductor https://bioconductor.org/packages/release/bioc/html/ADImpute.html) that automatically determines the best imputation method for each gene in a dataset. Our work represents a paradigm shift by demonstrating that there is no single best imputation method. Instead, we propose that imputation should maximally exploit external information and be adapted to gene-specific features, such as expression level and expression variation across cells.
Collapse
Affiliation(s)
- Ana Carolina Leote
- Cluster of Excellence Cellular Stress Responses in Aging-associated Diseases (CECAD), Cologne, Germany
- University of Cologne, Faculty of Medicine and Cologne University Hospital, Cologne, Germany
| | - Xiaohui Wu
- Cluster of Excellence Cellular Stress Responses in Aging-associated Diseases (CECAD), Cologne, Germany
- Department of Automation, Xiamen University, Xiamen, China
- Pasteurien College, Soochow University, Suzhou, China
| | - Andreas Beyer
- Cluster of Excellence Cellular Stress Responses in Aging-associated Diseases (CECAD), Cologne, Germany
- University of Cologne, Faculty of Medicine and Cologne University Hospital, Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), Cologne, Germany
- Cologne School for Computational Biology & Center for Data Science and Simulation, University of Cologne, Cologne, Germany
- * E-mail:
| |
Collapse
|
12
|
Segura-Bautista D, Maya-Nunez G, Aguilar-Rojas A, Huerta-Reyes M, Pérez-Solis MA. Contribution of Stemness-linked Transcription Regulators to the Progression of Breast Cancer. Curr Mol Med 2021; 22:766-778. [PMID: 34819003 DOI: 10.2174/1566524021666211124154803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 05/05/2021] [Accepted: 08/26/2021] [Indexed: 11/22/2022]
Abstract
Although there are currently several factors that allow measuring the risk of having breast cancer or predicting its progression, the underlying causes of this malignancy have remained unknown. Several molecular studies have described some mechanisms involved in the progress of breast cancer. These have helped in identifying new targets with therapeutic potential. However, despite the therapeutic strategies implemented from the advances achieved in breast cancer research, a large percentage of patients with breast cancer die due to the spread of malignant cells to other tissues or organs, such as bones and lungs. Therefore, determining the processes that promote the migration of malignant cells remains one of the greatest challenges for oncological research. Several research groups have reported evidence on how the dedifferentiation of tumor cells leads to the acquisition of stemness characteristics, such as invasion, metastasis, the capability to evade the immunological response, and resistance to several cytotoxic drugs. These phenotypic changes have been associated with a complex reprogramming of gene expression in tumor cells during the Epithelial-Mesenchymal Transition (EMT). Considering the determining role that the transcriptional regulation plays in the expression of the specific characteristics and attributes of breast cancer during ETM, in the present work, we reviewed and analyzed several transcriptional mechanisms that support the mesenchymal phenotype. In the same way, we established the importance of transcription factors with a therapeutic perspective in the progress of breast cancer.
Collapse
Affiliation(s)
- David Segura-Bautista
- Medical Research Unit in Reproductive Medicine, UMAE Hospital de Gineco Obstetricia no. 4 'Luis Castelazo-Ayala', Instituto Mexicano del Seguro Social, Mexico City. Mexico
| | - Guadalupe Maya-Nunez
- Medical Research Unit in Reproductive Medicine, UMAE Hospital de Gineco Obstetricia no. 4 'Luis Castelazo-Ayala', Instituto Mexicano del Seguro Social, Mexico City. Mexico
| | - Arturo Aguilar-Rojas
- Medical Research Unit in Reproductive Medicine, UMAE Hospital de Gineco Obstetricia no. 4 'Luis Castelazo-Ayala', Instituto Mexicano del Seguro Social, Mexico City. Mexico
| | - Maira Huerta-Reyes
- Medical Research Unit in Nephrological Diseases, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City. Mexico
| | - Marco Allan Pérez-Solis
- Medical Research Unit in Reproductive Medicine, UMAE Hospital de Gineco Obstetricia no. 4 'Luis Castelazo-Ayala', Instituto Mexicano del Seguro Social, Mexico City. Mexico
| |
Collapse
|
13
|
Paranjapye A, NandyMazumdar M, Browne JA, Leir SH, Harris A. Krüppel-like factor 5 regulates wound repair and the innate immune response in human airway epithelial cells. J Biol Chem 2021; 297:100932. [PMID: 34217701 PMCID: PMC8353497 DOI: 10.1016/j.jbc.2021.100932] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 06/17/2021] [Accepted: 06/29/2021] [Indexed: 12/23/2022] Open
Abstract
A complex network of transcription factors regulates genes involved in establishing and maintaining key biological properties of the human airway epithelium. However, detailed knowledge of the contributing factors is incomplete. Here we characterize the role of Krüppel-like factor 5 (KLF5), in controlling essential pathways of epithelial cell identity and function in the human lung. RNA-seq following siRNA-mediated depletion of KLF5 in the Calu-3 lung epithelial cell line identified significant enrichment of genes encoding chemokines and cytokines involved in the proinflammatory response and also components of the junctional complexes mediating cell adhesion. To determine direct gene targets of KLF5, we defined the cistrome of KLF5 using ChIP-seq in both Calu-3 and 16HBE14o- lung epithelial cell lines. Occupancy site concordance analysis revealed that KLF5 colocalized with the active histone modification H3K27ac and also with binding sites for the transcription factor CCAAT enhancer-binding protein beta (C/EBPβ). Depletion of KLF5 increased both the expression and secretion of cytokines including IL-1β, a response that was enhanced following exposure to Pseudomonas aeruginosa lipopolysaccharide. Calu-3 cells exhibited faster rates of repair after KLF5 depletion compared with negative controls in wound scratch assays. Similarly, CRISPR-mediated KLF5-null 16HBE14o- cells also showed enhanced wound closure. These data reveal a pivotal role for KLF5 in coordinating epithelial functions relevant to human lung disease.
Collapse
Affiliation(s)
- Alekh Paranjapye
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio, USA
| | - Monali NandyMazumdar
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio, USA
| | - James A Browne
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio, USA
| | - Shih-Hsing Leir
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio, USA
| | - Ann Harris
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio, USA.
| |
Collapse
|
14
|
Gu ML, Zhou XX, Ren MT, Shi KD, Yu MS, Jiao WR, Wang YM, Zhong WX, Ji F. Blockage of ETS homologous factor inhibits the proliferation and invasion of gastric cancer cells through the c-Met pathway. World J Gastroenterol 2020; 26:7497-7512. [PMID: 33384550 PMCID: PMC7754554 DOI: 10.3748/wjg.v26.i47.7497] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 10/13/2020] [Accepted: 11/02/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Gastric cancer (GC) is one of the most common and deadliest types of cancer worldwide due to its delayed diagnosis and high metastatic frequency, but its exact pathogenesis has not been fully elucidated. ETS homologous factor (EHF) is an important member of the ETS family and contributes to the pathogenesis of multiple malignant tumors. To date, whether EHF participates in the development of GC via the c-Met signaling pathway remains unclear.
AIM To investigate the role and mechanism of EHF in the occurrence and development of GC.
METHODS The expression of EHF mRNA in GC tissues and cell lines was measured by quantitative PCR. Western blotting was performed to determine the protein expression of EHF, c-Met, and its downstream signal molecules. The EHF expression in GC tissues was further detected by immunohistochemical staining. To investigate the role of EHF in GC oncogenesis, small interfering RNA (siRNA) against EHF was transfected into GC cells. The cell proliferation of GC cells was determined by Cell Counting Kit-8 and colony formation assays. Flow cytometry was performed following Annexin V/propidium iodide (PI) to identify apoptotic cells and PI staining to analyze the cell cycle. Cell migration and invasion were assessed by transwell assays.
RESULTS The data showed that EHF was upregulated in GC tissues and cell lines in which increased expression of c-Met was also observed. Silencing of EHF by siRNA reduced the proliferation of GC cells. Inhibition of EHF induced significant apoptosis and cell cycle arrest in GC cells. Cell migration and invasion were significantly inhibited. EHF silencing led to c-Met downregulation and further blocked the Ras/c-Raf/extracellular signal-related kinase 1/2 (Erk1/2) pathway. Additionally, phosphatase and tensin homolog was upregulated and glycogen synthase kinase 3 beta was deactivated. Moreover, inactivation of signal transducer and activator of transcription 3 was detected following EHF inhibition, leading to inhibition of the epithelial-to-mesenchymal transition (EMT).
CONCLUSION These results suggest that EHF plays a key role in cell proliferation, invasion, apoptosis, the cell cycle and EMT via the c-Met pathway. Therefore, EHF may serve as an antineoplastic target for the diagnosis and treatment of GC.
Collapse
Affiliation(s)
- Meng-Li Gu
- Department of Gastroenterology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, Zhejiang Province, China
| | - Xin-Xin Zhou
- Department of Gastroenterology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, Zhejiang Province, China
| | - Meng-Ting Ren
- Department of Gastroenterology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, Zhejiang Province, China
| | - Ke-Da Shi
- Department of Gastroenterology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, Zhejiang Province, China
| | - Mo-Sang Yu
- Department of Gastroenterology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, Zhejiang Province, China
| | - Wen-Rui Jiao
- Department of Gastroenterology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, Zhejiang Province, China
| | - Ya-Mei Wang
- Department of Gastroenterology, The Fourth Affiliated Hospital, College of Medicine, Zhejiang University, Yiwu 322000, Zhejiang Province, China
| | - Wei-Xiang Zhong
- Department of Pathology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, Zhejiang Province, China
| | - Feng Ji
- Department of Gastroenterology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, Zhejiang Province, China
| |
Collapse
|
15
|
Briottet M, Shum M, Urbach V. The Role of Specialized Pro-Resolving Mediators in Cystic Fibrosis Airways Disease. Front Pharmacol 2020; 11:1290. [PMID: 32982730 PMCID: PMC7493015 DOI: 10.3389/fphar.2020.01290] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 08/04/2020] [Indexed: 12/26/2022] Open
Abstract
Cystic Fibrosis (CF) is a recessive genetic disease due to mutations of the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) gene encoding the CFTR chloride channel. The ion transport abnormalities related to CFTR mutation generate a dehydrated airway surface liquid (ASL) layer, which is responsible for an altered mucociliary clearance, favors infections and persistent inflammation that lead to progressive lung destruction and respiratory failure. The inflammatory response is normally followed by an active resolution phase to return to tissue homeostasis, which involves specialized pro-resolving mediators (SPMs). SPMs promote resolution of inflammation, clearance of microbes, tissue regeneration and reduce pain, but do not evoke unwanted immunosuppression. The airways of CF patients showed a decreased production of SPMs even in the absence of pathogens. SPMs levels in the airway correlated with CF patients' lung function. The prognosis for CF has greatly improved but there remains a critical need for more effective treatments that prevent excessive inflammation, lung damage, and declining pulmonary function for all CF patients. This review aims to highlight the recent understanding of CF airway inflammation and the possible impact of SPMs on functions that are altered in CF airways.
Collapse
Affiliation(s)
| | | | - Valerie Urbach
- Institut national de la santé et de la recherche médicale (Inserm) U955, Institut Mondor de Recherche Biomédicale (IMRB), Créteil, France
| |
Collapse
|
16
|
Paranjapye A, Mutolo MJ, Ebron JS, Leir SH, Harris A. The FOXA1 transcriptional network coordinates key functions of primary human airway epithelial cells. Am J Physiol Lung Cell Mol Physiol 2020; 319:L126-L136. [PMID: 32432922 DOI: 10.1152/ajplung.00023.2020] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The differentiated functions of the human airway epithelium are coordinated by a complex network of transcription factors. These include the pioneer factors Forkhead box A1 and A2 (FOXA1 and FOXA2), which are well studied in several tissues, but their role in airway epithelial cells is poorly characterized. Here, we define the cistrome of FOXA1 and FOXA2 in primary human bronchial epithelial (HBE) cells by chromatin immunoprecipitation with deep-sequencing (ChIP-seq). Next, siRNA-mediated depletion of each factor is used to investigate their transcriptome by RNA-seq. We found that, as predicted from their DNA-binding motifs, genome-wide occupancy of the two factors showed substantial overlap; however, their global impact on gene expression differed. FOXA1 is an abundant transcript in HBE cells, while FOXA2 is expressed at low levels, and both these factors likely exhibit autoregulation and cross-regulation. FOXA1 regulated loci are involved in cell adhesion and the maintenance of epithelial cell identity, particularly through repression of genes associated with epithelial to mesenchymal transition (EMT). FOXA1 also directly targets other transcription factors with a known role in the airway epithelium such as SAM-pointed domain-containing Ets-like factor (SPDEF). The intersection of the cistrome and transcriptome for FOXA1 revealed enrichment of genes involved in epithelial development and tissue morphogenesis. Moreover, depletion of FOXA1 was shown to reduce the transepithelial resistance of HBE cells, confirming the role of this factor in maintaining epithelial barrier integrity.
Collapse
Affiliation(s)
- Alekh Paranjapye
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio
| | - Michael J Mutolo
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio
| | - Jey Sabith Ebron
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio
| | - Shih-Hsing Leir
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio
| | - Ann Harris
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio
| |
Collapse
|
17
|
Swahn H, Sabith Ebron J, Lamar K, Yin S, Kerschner JL, NandyMazumdar M, Coppola C, Mendenhall EM, Leir S, Harris A. Coordinate regulation of ELF5 and EHF at the chr11p13 CF modifier region. J Cell Mol Med 2019; 23:7726-7740. [PMID: 31557407 PMCID: PMC6815777 DOI: 10.1111/jcmm.14646] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 08/02/2019] [Accepted: 08/10/2019] [Indexed: 12/21/2022] Open
Abstract
E74-like factor 5 (ELF5) and ETS-homologous factor (EHF) are epithelial selective ETS family transcription factors (TFs) encoded by genes at chr11p13, a region associated with cystic fibrosis (CF) lung disease severity. EHF controls many key processes in lung epithelial function so its regulatory mechanisms are important. Using CRISPR/Cas9 technology, we removed three key cis-regulatory elements (CREs) from the chr11p13 region and also activated multiple open chromatin sites with CRISPRa in airway epithelial cells. Deletion of the CREs caused subtle changes in chromatin architecture and site-specific increases in EHF and ELF5. CRISPRa had most effect on ELF5 transcription. ELF5 levels are low in airway cells but higher in LNCaP (prostate) and T47D (breast) cancer cells. ATAC-seq in these lines revealed novel peaks of open chromatin at the 5' end of chr11p13 associated with an expressed ELF5 gene. Furthermore, 4C-seq assays identified direct interactions between the active ELF5 promoter and sites within the EHF locus, suggesting coordinate regulation between these TFs. ChIP-seq for ELF5 in T47D cells revealed ELF5 occupancy within EHF introns 1 and 6, and siRNA-mediated depletion of ELF5 enhanced EHF expression. These results define a new role for ELF5 in lung epithelial biology.
Collapse
Affiliation(s)
- Hannah Swahn
- Department of Genetics and Genome SciencesCase Western Reserve UniversityClevelandOHUSA
| | - Jey Sabith Ebron
- Department of Genetics and Genome SciencesCase Western Reserve UniversityClevelandOHUSA
| | - Kay‐Marie Lamar
- Department of Genetics and Genome SciencesCase Western Reserve UniversityClevelandOHUSA
| | - Shiyi Yin
- Department of Genetics and Genome SciencesCase Western Reserve UniversityClevelandOHUSA
| | - Jenny L. Kerschner
- Department of Genetics and Genome SciencesCase Western Reserve UniversityClevelandOHUSA
| | - Monali NandyMazumdar
- Department of Genetics and Genome SciencesCase Western Reserve UniversityClevelandOHUSA
| | - Candice Coppola
- Department of Biological SciencesUniversity of Alabama in HuntsvilleHuntsvilleALUSA
| | - Eric M. Mendenhall
- Department of Biological SciencesUniversity of Alabama in HuntsvilleHuntsvilleALUSA
| | - Shih‐Hsing Leir
- Department of Genetics and Genome SciencesCase Western Reserve UniversityClevelandOHUSA
| | - Ann Harris
- Department of Genetics and Genome SciencesCase Western Reserve UniversityClevelandOHUSA
| |
Collapse
|
18
|
Binder RL, Freedman MA, Sharma KB, Farage MA, Wang Y, Combs C, Moore D, Tiesman JP, Bascom CC, Isfort RJ, Warren R. Histological and Gene Expression Analysis of the Effects of Menopause Status and Hormone Therapy on the Vaginal Introitus and Labia Majora. J Clin Med Res 2019; 11:745-759. [PMID: 31803317 PMCID: PMC6879024 DOI: 10.14740/jocmr4006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 09/27/2019] [Indexed: 12/19/2022] Open
Abstract
Background The study aimed to determine the effect of menopausal status and hormone therapy on the introitus and labia majora at the levels of histology and gene expression. Methods Three cohorts of 10 women each (pre-menopause, post-menopause and post-menopause + hormone therapy) were selected based on the presentation of clinical atrophy and vaginal pH. Biopsies were obtained from the introitus (fourchette) and labia majora and processed for histology and gene expression analyses with microarrays. Other data collected included self-assessed symptoms, serum estradiol, testosterone, serum hormone binding globulin and the pH of the vagina and labia majora. Results The introitus appears exquisitely sensitive to hormone status. Dramatic changes were observed in histology including a thinning of the epithelium in post-menopausal subjects with vaginal atrophy. Furthermore, there was differential expression of many genes that may contribute to tissue remodeling in the atrophic introitus. Levels of expression of genes associated with wound healing, angiogenesis, cell migration/locomotion, dermal structure, apoptosis, inflammation, epithelial cell differentiation, fatty acid, carbohydrate and steroid metabolism were significantly different in the cohort exhibiting atrophy of the introitus. While changes were also observed at the labia, that site was considerably less sensitive to hormone status. The gene expression changes observed at the introitus in this study were very similar to those reported previously in the atrophic vagina providing further evidence that these changes are associated with atrophy. Conclusions The histological and gene expression changes occurring within the introitus after menopause may contribute to the constellation of symptoms that constitute the genitourinary syndrome of menopause.
Collapse
Affiliation(s)
| | - Murray A Freedman
- Obstetrics & Gynecology, Medical College of Georgia, Augusta, GA, USA
| | - Kailash B Sharma
- Obstetrics & Gynecology, Medical College of Georgia, Augusta, GA, USA
| | | | - Yu Wang
- The Procter & Gamble Company, Cincinnati, OH, USA
| | | | - David Moore
- The Procter & Gamble Company, Cincinnati, OH, USA
| | | | | | | | | |
Collapse
|
19
|
Huang D, Petrykowska HM, Miller BF, Elnitski L, Ovcharenko I. Identification of human silencers by correlating cross-tissue epigenetic profiles and gene expression. Genome Res 2019; 29:657-667. [PMID: 30886051 PMCID: PMC6442386 DOI: 10.1101/gr.247007.118] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 02/14/2019] [Indexed: 12/22/2022]
Abstract
Compared to enhancers, silencers are notably difficult to identify and validate experimentally. In search for human silencers, we utilized H3K27me3-DNase I hypersensitive site (DHS) peaks with tissue specificity negatively correlated with the expression of nearby genes across 25 diverse cell lines. These regions are predicted to be silencers since they are physically linked, using Hi-C loops, or associated, using expression quantitative trait loci (eQTL) results, with a decrease in gene expression much more frequently than general H3K27me3-DHSs. Also, these regions are enriched for the binding sites of transcriptional repressors (such as CTCF, MECOM, SMAD4, and SNAI3) and depleted of the binding sites of transcriptional activators. Using sequence signatures of these regions, we constructed a computational model and predicted approximately 10,000 additional silencers per cell line and demonstrated that the majority of genes linked to these silencers are expressed at a decreased level. Furthermore, single nucleotide polymorphisms (SNPs) in predicted silencers are significantly associated with disease phenotypes. Finally, our results show that silencers commonly interact with enhancers to affect the transcriptional dynamics of tissue-specific genes and to facilitate fine-tuning of transcription in the human genome.
Collapse
Affiliation(s)
- Di Huang
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Hanna M Petrykowska
- Translational and Functional Genomics Branch, National Human Genome Research, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Brendan F Miller
- Translational and Functional Genomics Branch, National Human Genome Research, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Laura Elnitski
- Translational and Functional Genomics Branch, National Human Genome Research, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Ivan Ovcharenko
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20892, USA
| |
Collapse
|
20
|
Madison BJ, Clark KA, Bhachech N, Hollenhorst PC, Graves BJ, Currie SL. Electrostatic repulsion causes anticooperative DNA binding between tumor suppressor ETS transcription factors and JUN-FOS at composite DNA sites. J Biol Chem 2018; 293:18624-18635. [PMID: 30315111 DOI: 10.1074/jbc.ra118.003352] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 10/02/2018] [Indexed: 12/22/2022] Open
Abstract
Many different transcription factors (TFs) regulate gene expression in a combinatorial fashion, often by binding in close proximity to each other on composite cis-regulatory DNA elements. Here, we investigated how ETS TFs bind with the AP1 TFs JUN-FOS at composite DNA-binding sites. DNA-binding ability with JUN-FOS correlated with the phenotype of ETS proteins in prostate cancer. We found that the oncogenic ETS-related gene (ERG) and ETS variant (ETV) 1/4/5 subfamilies co-occupy ETS-AP1 sites with JUN-FOS in vitro, whereas JUN-FOS robustly inhibited DNA binding by the tumor suppressors ETS homologous factor (EHF) and SAM pointed domain-containing ETS TF (SPDEF). EHF bound ETS-AP1 DNA with tighter affinity than ERG in the absence of JUN-FOS, possibly enabling EHF to compete with ERG and JUN-FOS for binding to ETS-AP1 sites. Genome-wide mapping of EHF- and ERG-binding sites in prostate epithelial cells revealed that EHF is preferentially excluded from closely spaced ETS-AP1 DNA sequences. Structural modeling and mutational analyses indicated that adjacent positively charged surfaces from EHF and JUN-FOS use electrostatic repulsion to disfavor simultaneous DNA binding. Conservation of positive residues on the JUN-FOS interface identified E74-like ETS TF 1 (ELF1) as an additional ETS TF exhibiting anticooperative DNA binding with JUN-FOS, and we found that ELF1 is frequently down-regulated in prostate cancer. In summary, divergent electrostatic features of ETS TFs at their JUN-FOS interface enable distinct binding events at ETS-AP1 DNA sites, which may drive specific targeting of ETS TFs to facilitate distinct transcriptional programs.
Collapse
Affiliation(s)
- Bethany J Madison
- From the Department of Oncological Sciences and.,Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah 84112
| | - Kathleen A Clark
- From the Department of Oncological Sciences and.,Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah 84112
| | - Niraja Bhachech
- From the Department of Oncological Sciences and.,Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah 84112
| | - Peter C Hollenhorst
- the Medical Sciences program, Indiana University School of Medicine, Bloomington, Indiana 47405, and
| | - Barbara J Graves
- From the Department of Oncological Sciences and .,Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah 84112.,the Howard Hughes Medical Institute, Chevy Chase, Maryland 20815
| | - Simon L Currie
- From the Department of Oncological Sciences and.,Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah 84112
| |
Collapse
|
21
|
Luk IY, Reehorst CM, Mariadason JM. ELF3, ELF5, EHF and SPDEF Transcription Factors in Tissue Homeostasis and Cancer. Molecules 2018; 23:molecules23092191. [PMID: 30200227 PMCID: PMC6225137 DOI: 10.3390/molecules23092191] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 08/23/2018] [Accepted: 08/23/2018] [Indexed: 02/07/2023] Open
Abstract
The epithelium-specific ETS (ESE) transcription factors (ELF3, ELF5, EHF and SPDEF) are defined by their highly conserved ETS DNA binding domain and predominant epithelial-specific expression profile. ESE transcription factors maintain normal cell homeostasis and differentiation of a number of epithelial tissues, and their genetic alteration and deregulated expression has been linked to the progression of several epithelial cancers. Herein we review the normal function of the ESE transcription factors, the mechanisms by which they are dysregulated in cancers, and the current evidence for their role in cancer progression. Finally, we discuss potential therapeutic strategies for targeting or reactivating these factors as a novel means of cancer treatment.
Collapse
Affiliation(s)
- Ian Y Luk
- Olivia Newton-John Cancer Research Institute, Heidelberg, Victoria 3084, Australia.
- School of Cancer Medicine, La Trobe University, Bundoora, Victoria 3086, Australia.
| | - Camilla M Reehorst
- Olivia Newton-John Cancer Research Institute, Heidelberg, Victoria 3084, Australia.
- School of Cancer Medicine, La Trobe University, Bundoora, Victoria 3086, Australia.
| | - John M Mariadason
- Olivia Newton-John Cancer Research Institute, Heidelberg, Victoria 3084, Australia.
- School of Cancer Medicine, La Trobe University, Bundoora, Victoria 3086, Australia.
| |
Collapse
|
22
|
Magalhães M, Tost J, Pineau F, Rivals I, Busato F, Alary N, Mely L, Leroy S, Murris M, Caimmi D, Claustres M, Chiron R, De Sario A. Dynamic changes of DNA methylation and lung disease in cystic fibrosis: lessons from a monogenic disease. Epigenomics 2018; 10:1131-1145. [PMID: 30052057 DOI: 10.2217/epi-2018-0005] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
AIM To assess whether DNA methylation levels account for the noninherited phenotypic variations observed among cystic fibrosis (CF) patients. PATIENTS & METHODS Using the 450 K BeadChip, we profiled DNA methylation in nasal epithelial cells collected from 32 CF patients and 16 controls. RESULTS We detected substantial DNA methylation differences up to 55% (median β change 0.13; IQR: 0.15-0.11) between CF patients and controls. DNA methylation levels differed between mild and severe CF patients and correlated with lung function at 50 CpG sites. CONCLUSION In CF samples, dynamic changes of DNA methylation occurred in genes responsible for the integrity of the epithelium and the inflammatory and immune responses, were prominent in transcriptionally active genomic regions and were over-represented in enhancers active in lung tissues. ( Clinicaltrials.gov NCT02884622).
Collapse
Affiliation(s)
- Milena Magalhães
- Laboratoire de Génétique de Maladies Rares - EA7402 Montpellier University - Montpellier - France.,Laboratory of Biological System Modeling - INCT/IDN, CDTS - Rio de Janeiro - Brazil
| | - Jörg Tost
- Laboratory for Epigenetics & Environment - Centre National de Recherche en Génomique Humaine - CEA - Institut de Biologie François Jacob - Evry - France
| | - Fanny Pineau
- Laboratoire de Génétique de Maladies Rares - EA7402 Montpellier University - Montpellier - France
| | - Isabelle Rivals
- Equipe de Statistique Appliquée - ESPCI Paris - PSL Research University - UMRS1158 - Paris - France
| | - Florence Busato
- Laboratory for Epigenetics & Environment - Centre National de Recherche en Génomique Humaine - CEA - Institut de Biologie François Jacob - Evry - France
| | - Nathan Alary
- Laboratoire de Génétique de Maladies Rares - EA7402 Montpellier University - Montpellier - France
| | - Laurent Mely
- CRCM, Renée Sabran Hospital - CHU Lyon - Hyères - France
| | - Sylvie Leroy
- CRCM, Pasteur Hospital - CHU Nice - Nice - France
| | - Marlène Murris
- CRCM, Larrey Hospital - CHU Toulouse - Toulouse - France
| | - Davide Caimmi
- CRCM, Arnaud de Villeneuve Hospital - CHU Montpellier - Montpellier - France
| | - Mireille Claustres
- Laboratoire de Génétique de Maladies Rares - EA7402 Montpellier University - Montpellier - France.,Laboratoire de Génétique Moléculaire - CHU Montpellier - Montpellier - France
| | - Raphaël Chiron
- CRCM, Arnaud de Villeneuve Hospital - CHU Montpellier - Montpellier - France
| | - Albertina De Sario
- Laboratoire de Génétique de Maladies Rares - EA7402 Montpellier University - Montpellier - France
| |
Collapse
|
23
|
Ramnath D, Irvine KM, Lukowski SW, Horsfall LU, Loh Z, Clouston AD, Patel PJ, Fagan KJ, Iyer A, Lampe G, Stow JL, Schroder K, Fairlie DP, Powell JE, Powell EE, Sweet MJ. Hepatic expression profiling identifies steatosis-independent and steatosis-driven advanced fibrosis genes. JCI Insight 2018; 3:120274. [PMID: 30046009 DOI: 10.1172/jci.insight.120274] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 06/12/2018] [Indexed: 12/23/2022] Open
Abstract
Chronic liver disease (CLD) is associated with tissue-destructive fibrosis. Considering that common mechanisms drive fibrosis across etiologies, and that steatosis is an important cofactor for pathology, we performed RNA sequencing on liver biopsies of patients with different fibrosis stages, resulting from infection with hepatitis C virus (HCV) (with or without steatosis) or fatty liver disease. In combination with enhanced liver fibrosis score correlation analysis, we reveal a common set of genes associated with advanced fibrosis, as exemplified by those encoding the transcription factor ETS-homologous factor (EHF) and the extracellular matrix protein versican (VCAN). We identified 17 fibrosis-associated genes as candidate EHF targets and demonstrated that EHF regulates multiple fibrosis-associated genes, including VCAN, in hepatic stellate cells. Serum VCAN levels were also elevated in advanced fibrosis patients. Comparing biopsies from patients with HCV with or without steatosis, we identified a steatosis-enriched gene set associated with advanced fibrosis, validating follistatin-like protein 1 (FSTL1) as an exemplar of this profile. In patients with advanced fibrosis, serum FSTL1 levels were elevated in those with steatosis (versus those without). Liver Fstl1 mRNA levels were also elevated in murine CLD models. We thus reveal a common gene signature for CLD-associated liver fibrosis and potential biomarkers and/or targets for steatosis-associated liver fibrosis.
Collapse
Affiliation(s)
- Divya Ramnath
- Institute for Molecular Bioscience (IMB) and.,IMB Centre for Inflammation and Disease Research, The University of Queensland, Brisbane, Queensland, Australia
| | - Katharine M Irvine
- Centre for Liver Disease Research and.,Faculty of Medicine, Mater Research Institute, Translational Research Institute, The University of Queensland, Brisbane, Queensland, Australia
| | - Samuel W Lukowski
- Institute for Molecular Bioscience (IMB) and.,IMB Centre for Inflammation and Disease Research, The University of Queensland, Brisbane, Queensland, Australia
| | - Leigh U Horsfall
- Centre for Liver Disease Research and.,Department of Gastroenterology and Hepatology, Princess Alexandra Hospital, Brisbane, Queensland, Australia
| | - Zhixuan Loh
- Institute for Molecular Bioscience (IMB) and.,IMB Centre for Inflammation and Disease Research, The University of Queensland, Brisbane, Queensland, Australia
| | | | - Preya J Patel
- Centre for Liver Disease Research and.,Department of Gastroenterology and Hepatology, Princess Alexandra Hospital, Brisbane, Queensland, Australia
| | | | - Abishek Iyer
- Institute for Molecular Bioscience (IMB) and.,IMB Centre for Inflammation and Disease Research, The University of Queensland, Brisbane, Queensland, Australia
| | - Guy Lampe
- Pathology Queensland, Princess Alexandra Hospital, Brisbane, Queensland, Australia
| | - Jennifer L Stow
- Institute for Molecular Bioscience (IMB) and.,IMB Centre for Inflammation and Disease Research, The University of Queensland, Brisbane, Queensland, Australia
| | - Kate Schroder
- Institute for Molecular Bioscience (IMB) and.,IMB Centre for Inflammation and Disease Research, The University of Queensland, Brisbane, Queensland, Australia
| | - David P Fairlie
- Institute for Molecular Bioscience (IMB) and.,IMB Centre for Inflammation and Disease Research, The University of Queensland, Brisbane, Queensland, Australia
| | - Joseph E Powell
- Institute for Molecular Bioscience (IMB) and.,IMB Centre for Inflammation and Disease Research, The University of Queensland, Brisbane, Queensland, Australia.,Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Elizabeth E Powell
- Centre for Liver Disease Research and.,Department of Gastroenterology and Hepatology, Princess Alexandra Hospital, Brisbane, Queensland, Australia
| | - Matthew J Sweet
- Institute for Molecular Bioscience (IMB) and.,IMB Centre for Inflammation and Disease Research, The University of Queensland, Brisbane, Queensland, Australia
| |
Collapse
|
24
|
Alam H, Li N, Dhar SS, Wu SJ, Lv J, Chen K, Flores ER, Baseler L, Lee MG. HP1γ Promotes Lung Adenocarcinoma by Downregulating the Transcription-Repressive Regulators NCOR2 and ZBTB7A. Cancer Res 2018; 78:3834-3848. [PMID: 29764865 DOI: 10.1158/0008-5472.can-17-3571] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 03/09/2018] [Accepted: 05/11/2018] [Indexed: 12/16/2022]
Abstract
Lung adenocarcinoma is a major form of lung cancer, which is the leading cause of cancer death. Histone methylation reader proteins mediate the effect of histone methylation, a hallmark of epigenetic and transcriptional regulation of gene expression. However, their roles in lung adenocarcinoma are poorly understood. Here, our bioinformatic screening and analysis in search of a lung adenocarcinoma-promoting histone methylation reader protein show that heterochromatin protein 1γ (HP1γ; also called CBX3) is among the most frequently overexpressed and amplified histone reader proteins in human lung adenocarcinoma, and that high HP1γ mRNA levels are associated with poor prognosis in patients with lung adenocarcinoma. In vivo depletion of HP1γ reduced K-RasG12D-driven lung adenocarcinoma and lengthened survival of mice bearing K-RasG12D-induced lung adenocarcinoma. HP1γ and its binding activity to methylated histone H3 lysine 9 were required for the proliferation, colony formation, and migration of lung adenocarcinoma cells. HP1γ directly repressed expression of the transcription-repressive regulators NCOR2 and ZBTB7A. Knockdown of NCOR2 or ZBTB7A significantly restored defects in proliferation, colony formation, and migration in HP1γ-depleted lung adenocarcinoma cells. Low NCOR2 or ZBTB7A mRNA levels were associated with poor prognosis in patients with lung adenocarcinoma and correlated with high HP1γ mRNA levels in lung adenocarcinoma samples. NCOR2 and ZBTB7A downregulated expression of tumor-promoting factors such as ELK1 and AXL, respectively. These findings highlight the importance of HP1γ and its reader activity in lung adenocarcinoma tumorigenesis and reveal a unique lung adenocarcinoma-promoting mechanism in which HP1γ downregulates NCOR2 and ZBTB7A to enhance expression of protumorigenic genes.Significance: Direct epigenetic repression of the transcription-repressive regulators NCOR2 and ZBTB7A by the histone reader protein HP1γ leads to activation of protumorigenic genes in lung adenocarcinoma. Cancer Res; 78(14); 3834-48. ©2018 AACR.
Collapse
Affiliation(s)
- Hunain Alam
- Department of Molecular and Cellular Oncology, the University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Na Li
- Department of Molecular and Cellular Oncology, the University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Shilpa S Dhar
- Department of Molecular and Cellular Oncology, the University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Sarah J Wu
- Department of Molecular and Cellular Oncology, the University of Texas MD Anderson Cancer Center, Houston, Texas.,The University of Texas Graduate School of Biomedical Sciences at Houston, Houston, Texas
| | - Jie Lv
- Institute for Academic Medicine, the Methodist Hospital Research Institute, Houston, Texas.,Center for Cardiovascular Regeneration, Department of Cardiovascular Sciences, the Methodist Hospital Research Institute, Houston, Texas.,Weill Cornell Medical College, Cornell University, New York, New York
| | - Kaifu Chen
- Institute for Academic Medicine, the Methodist Hospital Research Institute, Houston, Texas.,Center for Cardiovascular Regeneration, Department of Cardiovascular Sciences, the Methodist Hospital Research Institute, Houston, Texas.,Weill Cornell Medical College, Cornell University, New York, New York
| | - Elsa R Flores
- Department of Molecular Oncology, Moffitt Cancer Center, Tampa, Florida
| | - Laura Baseler
- Department of Veterinary Medicine and Surgery, the University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Min Gyu Lee
- Department of Molecular and Cellular Oncology, the University of Texas MD Anderson Cancer Center, Houston, Texas. .,The University of Texas Graduate School of Biomedical Sciences at Houston, Houston, Texas
| |
Collapse
|
25
|
A transcription factor network represses CFTR gene expression in airway epithelial cells. Biochem J 2018; 475:1323-1334. [PMID: 29572268 DOI: 10.1042/bcj20180044] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 03/19/2018] [Accepted: 03/22/2018] [Indexed: 02/06/2023]
Abstract
Mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene cause the inherited disorder cystic fibrosis (CF). Lung disease is the major cause of CF morbidity, though CFTR expression levels are substantially lower in the airway epithelium than in pancreatic duct and intestinal epithelia, which also show compromised function in CF. Recently developed small molecule therapeutics for CF are highly successful for one specific CFTR mutation and have a positive impact on others. However, the low abundance of CFTR transcripts in the airway limits the opportunity for drugs to correct the defective substrate. Elucidation of the transcriptional mechanisms for the CFTR locus has largely focused on intragenic and intergenic tissue-specific enhancers and their activating trans-factors. Here, we investigate whether the low CFTR levels in the airway epithelium result from the recruitment of repressive proteins directly to the locus. Using an siRNA screen to deplete ∼1500 transcription factors (TFs) and associated regulatory proteins in Calu-3 lung epithelial cells, we identified nearly 40 factors that upon depletion elevated CFTR mRNA levels more than 2-fold. A subset of these TFs was validated in primary human bronchial epithelial cells. Among the strongest repressors of airway expression of CFTR were Krüppel-like factor 5 and Ets homologous factor, both of which have pivotal roles in the airway epithelium. Depletion of these factors, which are both recruited to an airway-selective cis-regulatory element at -35 kb from the CFTR promoter, improved CFTR production and function, thus defining novel therapeutic targets for enhancement of CFTR.
Collapse
|
26
|
Increased expression of EHF contributes to thyroid tumorigenesis through transcriptionally regulating HER2 and HER3. Oncotarget 2018; 7:57978-57990. [PMID: 27517321 PMCID: PMC5295405 DOI: 10.18632/oncotarget.11154] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 07/27/2016] [Indexed: 12/19/2022] Open
Abstract
E26 transformation-specific (ETS) transcription factor EHF plays a tumor suppressor role in prostate cancer and esophageal squamous cell carcinoma (ESCC), whereas it is overexpressed and may act as an oncogene in ovarian and mammary cancers. However, its biological role in thyroid cancer remains totally unknown. The aim of this study was to explore the biological functions of EHF and its potential as a therapeutic target in thyroid cancer. Using quantitative RT-PCR (qRT-PCR) assay, we evaluated mRNA expression of EHF in a cohort of primary papillary thyroid cancers (PTCs) and matched non-cancerous thyroid tissues. The functions of knockdown and ectopic expression of EHF in thyroid cancer cells were determine by a series of in vitro and in vivo experiments. Moreover, dual-luciferase reporter and chromatin immunoprecipitation (ChIP) assays were performed to identify its downstream targets. Our data showed that EHF expression was significantly increased in PTCs compared with matched non-cancerous thyroid tissues. EHF knockdown significantly inhibited thyroid cancer cell proliferation, colony formation, migration, invasion and tumorigenic potential in nude mice and induced cell cycle arrested and apoptosis by modulating the PI3K/Akt and MAPK/Erk signaling pathways. On the other hand, ectopic expression of EHF in thyroid cancer cells notably promoted cell growth and invasiveness. Importantly, EHF was identified as a new transcription factor for HER2 and HER3, contributing to thyroid tumorigenesis. Altogether, our findings suggest that EHF is a novel functional oncogene in thyroid cancer by transcriptionally regulating HER2 and HER3, and may represent a potential therapeutic target for this cancer.
Collapse
|
27
|
Klein RH, Hu W, Kashgari G, Lin Z, Nguyen T, Doan M, Andersen B. Characterization of enhancers and the role of the transcription factor KLF7 in regulating corneal epithelial differentiation. J Biol Chem 2017; 292:18937-18950. [PMID: 28916725 DOI: 10.1074/jbc.m117.793117] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 09/11/2017] [Indexed: 02/01/2023] Open
Abstract
During tissue development, transcription factors bind regulatory DNA regions called enhancers, often located at great distances from the genes they regulate, to control gene expression. The enhancer landscape during embryonic stem cell differentiation has been well characterized. By contrast, little is known about the shared and unique enhancer regulatory mechanisms in different ectodermally derived epithelial cells. Here we use ChIP sequencing (ChIP-seq) to identify domains enriched for the histone marks histone H3 lysine 4 trimethylation, histone H3 lysine 4 monomethylation, and histone H3 lysine 27 acetylation (H3K4me3, H3K4me1, and H3K27ac) and define, for the first time, the super enhancers and typical enhancers active in primary human corneal epithelial cells. We show that regulatory regions are often shared between cell types of the ectodermal lineage and that corneal epithelial super enhancers are already marked as potential regulatory domains in embryonic stem cells. Kruppel-like factor (KLF) motifs were enriched in corneal epithelial enhancers, consistent with the important roles of KLF4 and KLF5 in promoting corneal epithelial differentiation. We now show that the Kruppel family member KLF7 promotes the corneal progenitor cell state; on many genes, KLF7 antagonized the corneal differentiation-promoting KLF4. Furthermore, we found that two SNPs linked previously to corneal diseases, astigmatism, and Stevens-Johnson syndrome fall within corneal epithelial enhancers and alter their activity by disrupting transcription factor motifs that overlap these SNPs. Taken together, our work defines regulatory enhancers in corneal epithelial cells, highlights global gene-regulatory relationships shared among different epithelial cells, identifies a role for KLF7 as a KLF4 antagonist in corneal epithelial cell differentiation, and explains how two SNPs may contribute to corneal diseases.
Collapse
Affiliation(s)
- Rachel Herndon Klein
- From the Departments of Biological Chemistry and.,Institute for Genomics and Bioinformatics, University of California, Irvine, California 92697
| | - William Hu
- From the Departments of Biological Chemistry and
| | | | - Ziguang Lin
- From the Departments of Biological Chemistry and
| | - Tuyen Nguyen
- From the Departments of Biological Chemistry and.,Institute for Genomics and Bioinformatics, University of California, Irvine, California 92697
| | - Michael Doan
- From the Departments of Biological Chemistry and
| | - Bogi Andersen
- From the Departments of Biological Chemistry and .,Institute for Genomics and Bioinformatics, University of California, Irvine, California 92697.,Medicine, Division of Endocrinology, and
| |
Collapse
|
28
|
Gong YC, Ren GL, Liu B, Li F, Zhao HP, Chen JB, Li YP, Yu HH. miR‑206 inhibits cancer initiating cells by targeting EHF in gastric cancer. Oncol Rep 2017; 38:1688-1694. [PMID: 28714026 DOI: 10.3892/or.2017.5794] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2017] [Accepted: 06/08/2017] [Indexed: 11/05/2022] Open
Abstract
Cancer initiating cells (CIC) are defined as the unique subpopulation in the tumors that possess the ability to initiate tumor growth and sustain self-renewal as well as metastatic potential. In this study, we found that EHF overexpression promoted formation of CIC traits and silencing it inhibited the traits in gastric cancer NCI‑N87 cells. Overexpressing EHF downregulated the antitumor effect of 5-fluorouracil (5-FU) in NCI‑N87 cells. We found that miR‑206 downregulated EHF protein expression by targeting its 3'UTR in NCI‑N87 cells and GES-1 cells. Overexpressing miR‑206 inhibited formation of CIC in NCI‑N87 cells. In gastric cancer tissues, EHF protein expression was upregulated and miR‑206 was downregulated. We identified a negative correlation between EHF protein and miR‑206 expression in gastric cancer tissues. Thus, we concluded that miR‑206 inhibits formation of CICs by targeting EHF in gastric cancer.
Collapse
Affiliation(s)
- Yan-Cui Gong
- Health Management Center, Linyi Central Hospital, Linyi, Shandong 276400, P.R. China
| | - Guo-Liang Ren
- Intensive Care Unit (ICU), Dongying People's Hospital, Dongying, Shandong 257091, P.R. China
| | - Bo Liu
- Department of Gastrointestinal Surgery, Shandong Provincial Qianfoshan Hospital, Jinan, Shandong 250014, P.R. China
| | - Feng Li
- Department of Gastrointestinal Surgery, Shandong Provincial Qianfoshan Hospital, Jinan, Shandong 250014, P.R. China
| | - Hong-Peng Zhao
- Department of Gastrointestinal Surgery, Shandong Provincial Qianfoshan Hospital, Jinan, Shandong 250014, P.R. China
| | - Jing-Bo Chen
- Department of Gastrointestinal Surgery, Shandong Provincial Qianfoshan Hospital, Jinan, Shandong 250014, P.R. China
| | - Yu-Peng Li
- Department of Gastrointestinal Surgery, Shandong Provincial Qianfoshan Hospital, Jinan, Shandong 250014, P.R. China
| | - Hai-Hua Yu
- Department of Gastrointestinal Surgery, Shandong Provincial Qianfoshan Hospital, Jinan, Shandong 250014, P.R. China
| |
Collapse
|
29
|
Zhou H, Cui X, Yuan H, Zhang B, Meng C, Zhao D. Effects of distinct drugs on gene transcription in an osteosarcoma cell line. Oncol Lett 2017; 14:4694-4700. [PMID: 29085469 PMCID: PMC5649527 DOI: 10.3892/ol.2017.6767] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 05/25/2017] [Indexed: 11/09/2022] Open
Abstract
Osteosarcoma (OS) is a common cancerous bone tumor which has a detrimental impact on the lives of patients and their families. The present study aimed at investigating the underlying molecular mechanism of various drug treatments pertaining to OS, including dimethyl sulfoxide (DMSO), doxorubicin (DXP), Nutlin-3, actinomycin D (ActD) and etoposide (Eto). Microarray and p53 chromatin immunoprecipitation combined with sequencing (ChIP-seq) datasets of the OS cell line U2OS treated with distinct drugs were acquired from the Gene Expression Omnibus and differentially-expressed genes (DEGs) were screened for alignment analysis. The p53-binding target genes were identified and ChIP-seq and microarray gene expression data were combined to identify directly and indirectly targeted genes. A regulatory network of p53 was constructed with the acquired data. Finally, the Database for Annotation, Visualization and Integrated Discovery was interrogated for annotation of target genes. A total of 212 p53-binding peaks were obtained in the untreated group, whereas thousands of peaks were obtained in the treated groups. In total, ~1,000 target genes were identified in each of DXP, DMSO, Eto and ActD treatment groups, whereas the Nutlin-3 treatment group identified an increased number, with 5,458 target genes obtained. Several common DEGs including MDM2, TP53I3, RRM2B, FAS and SESN1 were targeted by all the drugs with the exception of DMSO. p53 regulated various genes including EHF, HOXA10 and BHLHE40 in the Nutlin-3 treatment group, whereas p53 regulated EHF, RFX3, TRAF40 and TCF7L2 in the DXR treatment group. The results of the present study indicate that p53 was able to directly regulate target genes including MDM2, TP53I3 and RRM2B or indirectly regulate numerous further genes through several hub genes including EHF and RFX through various drug treatments in U2OS cells. Furthermore, p53 regulated distinct molecular processes in various drug treatments.
Collapse
Affiliation(s)
- Hui Zhou
- Department of Anesthesia, China-Japan Union Hospital, Jilin University, Changchun, Jilin 130033, P.R. China
| | - Xiaofeng Cui
- Department of Gastrointestinal Colorectal and Anal Surgery, China-Japan Union Hospital, Jilin University, Changchun, Jilin 130033, P.R. China
| | - Hongping Yuan
- Department of Nephrology, The Fourth Hospital of Jilin University, Changchun, Jilin 130011, P.R. China
| | - Boyin Zhang
- Department of Orthopedics, China-Japan Union Hospital, Jilin University, Changchun, Jilin 130033, P.R. China
| | - Chunyang Meng
- Department of Orthopedics, China-Japan Union Hospital, Jilin University, Changchun, Jilin 130033, P.R. China
| | - Dongxu Zhao
- Department of Orthopedics, China-Japan Union Hospital, Jilin University, Changchun, Jilin 130033, P.R. China
| |
Collapse
|
30
|
Fossum SL, Mutolo MJ, Tugores A, Ghosh S, Randell SH, Jones LC, Leir SH, Harris A. Ets homologous factor (EHF) has critical roles in epithelial dysfunction in airway disease. J Biol Chem 2017; 292:10938-10949. [PMID: 28461336 DOI: 10.1074/jbc.m117.775304] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Revised: 04/27/2017] [Indexed: 12/16/2022] Open
Abstract
The airway epithelium forms a barrier between the internal and external environments. Epithelial dysfunction is critical in the pathology of many respiratory diseases, including cystic fibrosis. Ets homologous factor (EHF) is a key member of the transcription factor network that regulates gene expression in the airway epithelium in response to endogenous and exogenous stimuli. EHF, which has altered expression in inflammatory states, maps to the 5' end of an intergenic region on Chr11p13 that is implicated as a modifier of cystic fibrosis airway disease. Here we determine the functions of EHF in primary human bronchial epithelial (HBE) cells and relevant airway cell lines. Using EHF ChIP followed by deep sequencing (ChIP-seq) and RNA sequencing after EHF depletion, we show that EHF targets in HBE cells are enriched for genes involved in inflammation and wound repair. Furthermore, changes in gene expression impact cell phenotype because EHF depletion alters epithelial secretion of a neutrophil chemokine and slows wound closure in HBE cells. EHF activates expression of the SAM pointed domain-containing ETS transcription factor, which contributes to goblet cell hyperplasia. Our data reveal a critical role for EHF in regulating epithelial function in lung disease.
Collapse
Affiliation(s)
- Sara L Fossum
- From the Human Molecular Genetics Program, Lurie Children's Research Center, Chicago, Illinois 60614.,the Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611
| | - Michael J Mutolo
- From the Human Molecular Genetics Program, Lurie Children's Research Center, Chicago, Illinois 60614.,the Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611
| | - Antonio Tugores
- the Unidad de Investigación, Complejo Hospitalario Universitario Insular Materno Infantil, 35016 Las Palmas de Gran Canaria, Spain
| | - Sujana Ghosh
- From the Human Molecular Genetics Program, Lurie Children's Research Center, Chicago, Illinois 60614.,the Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611
| | - Scott H Randell
- the Marsico Lung Institute, University of North Carolina Cystic Fibrosis Center, University of North Carolina, Chapel Hill, North Carolina 27599, and
| | - Lisa C Jones
- the Marsico Lung Institute, University of North Carolina Cystic Fibrosis Center, University of North Carolina, Chapel Hill, North Carolina 27599, and
| | - Shih-Hsing Leir
- From the Human Molecular Genetics Program, Lurie Children's Research Center, Chicago, Illinois 60614.,the Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611.,the Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio 44016
| | - Ann Harris
- From the Human Molecular Genetics Program, Lurie Children's Research Center, Chicago, Illinois 60614, .,the Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611.,the Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio 44016
| |
Collapse
|
31
|
Increased expression of EHF via gene amplification contributes to the activation of HER family signaling and associates with poor survival in gastric cancer. Cell Death Dis 2016; 7:e2442. [PMID: 27787520 PMCID: PMC5134001 DOI: 10.1038/cddis.2016.346] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Revised: 09/04/2016] [Accepted: 09/26/2016] [Indexed: 01/29/2023]
Abstract
The biological function of E26 transformation-specific (ETS) transcription factor EHF/ESE-3 in human cancers remains largely unknown, particularly gastric cancer. The aim of this study was to explore the role of EHF in tumorigenesis and its potential as a therapeutic target in gastric cancer. By using quantitative RT-PCR (qRT-PCR), immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH) assays, we investigated the expression and copy number of EHF in a cohort of gastric cancers and control subjects. Specific EHF siRNAs was used to determine the biologic impacts and mechanisms of altered EHF expression in vitro and in vivo. Dual-luciferase reporter, chromatin immunoprecipitation (ChIP) and electrophoretic mobility shift assay (EMSA) assays were performed to identify its downstream targets. Our results demonstrated that EHF was significantly upregulated and frequently amplified in gastric cancer tissues as compared with control subjects. Moreover, EHF amplification was positively correlated with its overexpression and significantly associated with poor clinical outcomes of gastric cancer patients. We also found that EHF knockdown notably inhibited gastric cancer cell proliferation, colony formation, migration, invasion and tumorigenic potential in nude mice and induced cell cycle arrest and apoptosis. Importantly, we identified EHF as a new HER2 transcription factor and the modulator of HER3 and HER4 in gastric cancer. Collectively, our findings suggest that EHF is a novel functional oncogene in gastric cancer by regulating the human epidermal growth factor receptor (HER) family of receptor tyrosine kinases and may represent a potential prognostic marker and therapeutic target for this cancer.
Collapse
|
32
|
Lee CM, Wu J, Xia Y, Hu J. ESE-1 in Early Development: Approaches for the Future. Front Cell Dev Biol 2016; 4:73. [PMID: 27446923 PMCID: PMC4924247 DOI: 10.3389/fcell.2016.00073] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 06/17/2016] [Indexed: 01/14/2023] Open
Abstract
E26 transformation-specific (Ets) family of transcription factors are characterized by the presence of Ets-DNA binding domain and have been found to be highly involved in hematopoiesis and various tissue differentiation. ESE-1, or Elf3 in mice, is a member of epithelium-specific Ets sub-family which is most prominently expressed in epithelial tissues such as the gut, mammary gland, and lung. The role of ESE-1 during embryogenesis had long been alluded from 30% fetal lethality in homozygous knockout mice and its high expression in preimplantation mouse embryos, but there has been no in-depth of analysis of ESE-1 function in early development. With improved proteomics, gene editing tools and increasing knowledge of ESE-1 function in adult tissues, we hereby propose future research directions for the study of ESE-1 in embryogenesis, including studying its regulation at the protein level and at the protein family level, as well as better defining the developmental phase under investigation. Understanding the role of ESE-1 in early development will provide new insights into its involvement in tissue regeneration and cancer, as well as how it functions with other Ets factors as a protein family.
Collapse
Affiliation(s)
- Chan Mi Lee
- Program in Physiology and Experimental Medicine, Peter Gilgan Centre for Research and Learning, SickKids Research Institute, SickKids HospitalToronto, ON, Canada; Laboratory Medicine and Pathobiology, University of TorontoToronto, ON, Canada
| | - Jing Wu
- Program in Physiology and Experimental Medicine, Peter Gilgan Centre for Research and Learning, SickKids Research Institute, SickKids Hospital Toronto, ON, Canada
| | - Yi Xia
- Program in Physiology and Experimental Medicine, Peter Gilgan Centre for Research and Learning, SickKids Research Institute, SickKids HospitalToronto, ON, Canada; Laboratory Medicine and Pathobiology, University of TorontoToronto, ON, Canada
| | - Jim Hu
- Program in Physiology and Experimental Medicine, Peter Gilgan Centre for Research and Learning, SickKids Research Institute, SickKids HospitalToronto, ON, Canada; Laboratory Medicine and Pathobiology, University of TorontoToronto, ON, Canada
| |
Collapse
|
33
|
Lee CM, Gupta S, Wang J, Johnson EM, Crofford LJ, Marshall JC, Kapoor M, Hu J. Epithelium-specific Ets transcription factor-1 acts as a negative regulator of cyclooxygenase-2 in human rheumatoid arthritis synovial fibroblasts. Cell Biosci 2016; 6:43. [PMID: 27313839 PMCID: PMC4910355 DOI: 10.1186/s13578-016-0105-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 05/25/2016] [Indexed: 01/21/2023] Open
Abstract
Background Rheumatoid arthritis (RA) is characterized by excessive synovial inflammation. Cyclooxygenase-2 (COX-2) is an enzyme that catalyzes the conversion of arachidonic acid (AA) into prostaglandins. Epithelium-specific Ets transcription factor-1 (ESE-1) was previously demonstrated to upregulate COX-2 in co-operation with nuclear factor kappa B (NFκB) in macrophages and chondrocytes. However, the role of ESE-1 in RA pathology has remained unclear. In this study, we aimed to elucidate the relationship between ESE-1 and COX-2 in RA synovial fibroblasts (RASFs) using a HD-Ad-mediated knockdown approach. Results ESE-1 and COX-2 were induced by IL-1β in RASFs that corresponded with an increase in PGE2. Endogenous levels of ESE-1 and COX-2 in human RASFs were analyzed by RT-qPCR and Western blot, and PGE2 was quantified using competitive ELISA. Interestingly, knockdown of ESE-1 using helper-dependent adenovirus (HD-Ad) led to a significant upregulation of COX-2 at a later phase of IL-1β stimulation. Examination of ESE-1 intracellular localization by nuclear fractionation revealed that ESE-1 was localized in the nucleus, occupying disparate cellular compartments to NFκB when COX-2 was increased. To confirm the ESE-1-COX-2 relationship in other cellular systems, COX-2 was also measured in SW982 synovial sarcoma cell line and ESE-1 knockout (KO) murine macrophages. Similarly, knockdown of ESE-1 transcriptionally upregulated COX-2 in SW982 and ESE-1 KO murine macrophages, suggesting that ESE-1 may be involved in the resolution of inflammation. Conclusion ESE-1 acts as a negative regulator of COX-2 in human RASFs and its effect on COX-2 is NFκB-independent. Electronic supplementary material The online version of this article (doi:10.1186/s13578-016-0105-7) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Chan-Mi Lee
- SickKids Research Institute, Program in Physiology and Experimental Medicine, The Hospital for Sick Children, Peter Gilgan Centre for Research and Learning, 9th floor, 686 Bay Street, Toronto, ON M5G 0A4 Canada ; Laboratory Medicine and Pathobiology, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8 Canada
| | - Sahil Gupta
- The Keenan Research Centre, Li Ka Shing Knowledge Institute, St. Michael's Hospital, 209 Victoria Street, Toronto, ON M5B 1T8 Canada ; Institute of Medical Science, Faculty of Medicine, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8 Canada
| | - Jiafeng Wang
- The Keenan Research Centre, Li Ka Shing Knowledge Institute, St. Michael's Hospital, 209 Victoria Street, Toronto, ON M5B 1T8 Canada ; Department of Anesthesiology and Intensive Care, The Second Military Medical University, Changhai Hospital, Shanghai, 200433 China
| | - Elizabeth M Johnson
- Department of Medicine, Division of Rheumatology and Immunology, School of Medicine, Vanderbilt University, 1161 21st Ave S, MCN T-3113, Nashville, TN 37232 USA
| | - Leslie J Crofford
- Department of Medicine, Division of Rheumatology and Immunology, School of Medicine, Vanderbilt University, 1161 21st Ave S, MCN T-3113, Nashville, TN 37232 USA
| | - John C Marshall
- The Keenan Research Centre, Li Ka Shing Knowledge Institute, St. Michael's Hospital, 209 Victoria Street, Toronto, ON M5B 1T8 Canada ; Institute of Medical Science, Faculty of Medicine, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8 Canada ; Department of Surgery, St. Michael's Hospital, University of Toronto, 30 Bond Street, Toronto, ON M5B 1W8 Canada
| | - Mohit Kapoor
- Laboratory Medicine and Pathobiology, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8 Canada ; Division of Genetics and Development, Toronto Western Research Institute, Toronto Western Hospital, University Health Network (UHN), 60 Leonard Avenue, Toronto, ON M5T 2S8 Canada
| | - Jim Hu
- SickKids Research Institute, Program in Physiology and Experimental Medicine, The Hospital for Sick Children, Peter Gilgan Centre for Research and Learning, 9th floor, 686 Bay Street, Toronto, ON M5G 0A4 Canada ; Laboratory Medicine and Pathobiology, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8 Canada ; Institute of Medical Science, Faculty of Medicine, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8 Canada
| |
Collapse
|
34
|
Kameyama N, Kobayashi K, Shimizu S, Yamasaki Y, Endo M, Hashimoto M, Furihata T, Chiba K. Involvement of ESE-3, epithelial-specific ETS factor family member 3, in transactivation of the ABCB1 gene via pregnane X receptor in intestine-derived LS180 cells but not in liver-derived HepG2 cells. Drug Metab Pharmacokinet 2016; 31:340-348. [PMID: 27567379 DOI: 10.1016/j.dmpk.2016.05.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Revised: 04/26/2016] [Accepted: 05/25/2016] [Indexed: 01/18/2023]
Abstract
Pregnane X receptor (PXR) is involved in the transactivation of ABCB1 gene by rifampicin (RIF). However, we found that increase in ABCB1 mRNA by RIF was observed in LS180 cells but not in HepG2 cells. Since both cell lines expressed PXR equally, we hypothesized that a factor(s) other than PXR is responsible for PXR-mediated transactivation of the ABCB1 gene. Reporter activities of a distal enhancer module containing direct repeat 4 (DR4) motifs were increased by RIF in LS180 cells but not in HepG2 cells. Mutation of the DR4 motifs diminished the increase in reporter activities in LS180 cells. Gene subtraction showed that epithelial-specific ETS factor 3 (ESE-3) is a transcription factor enriched in LS180 cells compared to HepG2 cells. When ESE-3 and PXR were co-expressed in HepG2 cells, reporter activities were increased by RIF, which were completely abolished by mutation of DR4 motifs. Chromatin immunoprecipitation assays showed specific binding of ESE-3 to the region containing the DR4 motifs of the ABCB1 gene. Finally, knock-down of ESE-3 in LS180 cells resulted in a decrease in the induction of ABCB1 mRNA. These results suggest that ESE-3 is a factor responsible for PXR-mediated transactivation of the ABCB1 gene by RIF in LS180 cells.
Collapse
Affiliation(s)
- Naoya Kameyama
- Laboratory of Pharmacology and Toxicology, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Japan
| | - Kaoru Kobayashi
- Laboratory of Pharmacology and Toxicology, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Japan.
| | - Shoko Shimizu
- Laboratory of Pharmacology and Toxicology, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Japan
| | - Yuki Yamasaki
- Laboratory of Pharmacology and Toxicology, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Japan
| | - Mika Endo
- Laboratory of Pharmacology and Toxicology, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Japan
| | - Mari Hashimoto
- Laboratory of Pharmacology and Toxicology, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Japan
| | - Tomomi Furihata
- Laboratory of Pharmacology and Toxicology, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Japan
| | - Kan Chiba
- Laboratory of Pharmacology and Toxicology, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Japan
| |
Collapse
|
35
|
Yamazaki S, Nakano N, Honjo A, Hara M, Maeda K, Nishiyama C, Kitaura J, Ohtsuka Y, Okumura K, Ogawa H, Shimizu T. The Transcription Factor Ehf Is Involved in TGF-β–Induced Suppression of FcεRI and c-Kit Expression and FcεRI-Mediated Activation in Mast Cells. THE JOURNAL OF IMMUNOLOGY 2015; 195:3427-35. [DOI: 10.4049/jimmunol.1402856] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Accepted: 07/28/2015] [Indexed: 01/21/2023]
|
36
|
Wang L, Xing J, Cheng R, Shao Y, Li P, Zhu S, Zhang S. Abnormal Localization and Tumor Suppressor Function of Epithelial Tissue-Specific Transcription Factor ESE3 in Esophageal Squamous Cell Carcinoma. PLoS One 2015; 10:e0126319. [PMID: 25950810 PMCID: PMC4423989 DOI: 10.1371/journal.pone.0126319] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 03/31/2015] [Indexed: 11/18/2022] Open
Abstract
Esophageal cancer is one of the most common malignant cancers worldwide. The molecular mechanism of esophageal squamous cell carcinoma (ESCC) is still poorly understood. ESE3 is a member of the Ets transcription family, which is only expressed in epithelial tissues and acts as a tumor suppressor gene in prostate cancer. Our study aim was to confirm whether ESE3 is involved in the carcinogenesis of ESCC. Immunohistochemical analysis revealed that ESE3 was mainly located in cell nuclei of normal tissues and the cytoplasm in ESCC tissues. Immunofluorescence and western blot analyses of the normal esophageal cell line HEEpiC and ESCC cell lines EC9706 TE-1, KYSE150, and KYSE410 confirmed these results. pEGFP-ESE3 and pcDNA3.1-V5/HisA-ESE3 plasmids were constructed for overexpression of ESE3 in EC9706 and KYSE150 cells. The stably transfected cells showed restoration of the nuclear localization of ESE3. EC9706 cells with re-localization of ESE3 to the nucleus showed inhibition of proliferation, colony formation, migration, and invasion. To explore the possible mechanism of the differences in localization of ESE3 in normal esophageal cells and ESCC cells, ESCC cell lines were treated with the nuclear export inhibitor leptomycin B, transcription inhibitor actinomycin D, PKC inhibitor sphinganine, P38 MAPK inhibitor SB202190, and CK II inhibitor TBCA. These reagents were chosen according to the well-known mechanisms of protein translocation. However, the localization of ESE3 was unchanged after these treatments. The sequence of ESE3 cDNA in ESCC cells was identical to the standard sequence of ESE3 in the NCBI Genebank database, indicating that there was no mutation in the coding region of ESE3 in ESCC. Taken together, our study suggests that ESE3 plays an important role in the carcinogenesis of ESCC through changes in subcellular localization and may act as a tumor suppressor gene in ESCC, although the mechanisms require further study.
Collapse
Affiliation(s)
- Li Wang
- Department of Gastroenterology & Hepatology, Beijing Digestive Disease Center, Beijing Friendship Hospital, Capital Medical University, National Clinical Research Center for Digestive Diseases, Beijing Key Laboratory for Precancerous Lesion of Digestive Diseases, Beijing, China
| | - Jie Xing
- Department of Gastroenterology & Hepatology, Beijing Digestive Disease Center, Beijing Friendship Hospital, Capital Medical University, National Clinical Research Center for Digestive Diseases, Beijing Key Laboratory for Precancerous Lesion of Digestive Diseases, Beijing, China
| | - Rui Cheng
- Department of Gastroenterology & Hepatology, Beijing Digestive Disease Center, Beijing Friendship Hospital, Capital Medical University, National Clinical Research Center for Digestive Diseases, Beijing Key Laboratory for Precancerous Lesion of Digestive Diseases, Beijing, China
| | - Ying Shao
- Department of Gastroenterology & Hepatology, Beijing Digestive Disease Center, Beijing Friendship Hospital, Capital Medical University, National Clinical Research Center for Digestive Diseases, Beijing Key Laboratory for Precancerous Lesion of Digestive Diseases, Beijing, China
| | - Peng Li
- Department of Gastroenterology & Hepatology, Beijing Digestive Disease Center, Beijing Friendship Hospital, Capital Medical University, National Clinical Research Center for Digestive Diseases, Beijing Key Laboratory for Precancerous Lesion of Digestive Diseases, Beijing, China
| | - Shengtao Zhu
- Department of Gastroenterology & Hepatology, Beijing Digestive Disease Center, Beijing Friendship Hospital, Capital Medical University, National Clinical Research Center for Digestive Diseases, Beijing Key Laboratory for Precancerous Lesion of Digestive Diseases, Beijing, China
| | - Shutian Zhang
- Department of Gastroenterology & Hepatology, Beijing Digestive Disease Center, Beijing Friendship Hospital, Capital Medical University, National Clinical Research Center for Digestive Diseases, Beijing Key Laboratory for Precancerous Lesion of Digestive Diseases, Beijing, China
- * E-mail: (S. Zhang)
| |
Collapse
|
37
|
Swindell WR, Sarkar MK, Stuart PE, Voorhees JJ, Elder JT, Johnston A, Gudjonsson JE. Psoriasis drug development and GWAS interpretation through in silico analysis of transcription factor binding sites. Clin Transl Med 2015; 4:13. [PMID: 25883770 PMCID: PMC4392043 DOI: 10.1186/s40169-015-0054-5] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Accepted: 02/26/2015] [Indexed: 12/22/2022] Open
Abstract
Background Psoriasis is a cytokine-mediated skin disease that can be treated effectively with immunosuppressive biologic agents. These medications, however, are not equally effective in all patients and are poorly suited for treating mild psoriasis. To develop more targeted therapies, interfering with transcription factor (TF) activity is a promising strategy. Methods Meta-analysis was used to identify differentially expressed genes (DEGs) in the lesional skin from psoriasis patients (n = 237). We compiled a dictionary of 2935 binding sites representing empirically-determined binding affinities of TFs and unconventional DNA-binding proteins (uDBPs). This dictionary was screened to identify “psoriasis response elements” (PREs) overrepresented in sequences upstream of psoriasis DEGs. Results PREs are recognized by IRF1, ISGF3, NF-kappaB and multiple TFs with helix-turn-helix (homeo) or other all-alpha-helical (high-mobility group) DNA-binding domains. We identified a limited set of DEGs that encode proteins interacting with PRE motifs, including TFs (GATA3, EHF, FOXM1, SOX5) and uDBPs (AVEN, RBM8A, GPAM, WISP2). PREs were prominent within enhancer regions near cytokine-encoding DEGs (IL17A, IL19 and IL1B), suggesting that PREs might be incorporated into complex decoy oligonucleotides (cdODNs). To illustrate this idea, we designed a cdODN to concomitantly target psoriasis-activated TFs (i.e., FOXM1, ISGF3, IRF1 and NF-kappaB). Finally, we screened psoriasis-associated SNPs to identify risk alleles that disrupt or engender PRE motifs. This identified possible sites of allele-specific TF/uDBP binding and showed that PREs are disproportionately disrupted by psoriasis risk alleles. Conclusions We identified new TF/uDBP candidates and developed an approach that (i) connects transcriptome informatics to cdODN drug development and (ii) enhances our ability to interpret GWAS findings. Disruption of PRE motifs by psoriasis risk alleles may contribute to disease susceptibility. Electronic supplementary material The online version of this article (doi:10.1186/s40169-015-0054-5) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- William R Swindell
- Department of Dermatology, University of Michigan School of Medicine, Ann Arbor, MI 48109-2200 USA
| | - Mrinal K Sarkar
- Department of Dermatology, University of Michigan School of Medicine, Ann Arbor, MI 48109-2200 USA
| | - Philip E Stuart
- Department of Dermatology, University of Michigan School of Medicine, Ann Arbor, MI 48109-2200 USA
| | - John J Voorhees
- Department of Dermatology, University of Michigan School of Medicine, Ann Arbor, MI 48109-2200 USA
| | - James T Elder
- Department of Dermatology, University of Michigan School of Medicine, Ann Arbor, MI 48109-2200 USA
| | - Andrew Johnston
- Department of Dermatology, University of Michigan School of Medicine, Ann Arbor, MI 48109-2200 USA
| | - Johann E Gudjonsson
- Department of Dermatology, University of Michigan School of Medicine, Ann Arbor, MI 48109-2200 USA
| |
Collapse
|
38
|
Wang JY, Shyur SD, Lam FWS, Wu LSH. Polymorphisms of EHF-ELF5 genomic region and its association with pediatric asthma in the Taiwanese population. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2014; 49:879-884. [PMID: 25648666 DOI: 10.1016/j.jmii.2014.11.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 04/21/2014] [Revised: 11/04/2014] [Accepted: 11/29/2014] [Indexed: 11/27/2022]
Abstract
BACKGROUND The EHF and ELF5 genes, located on chromosome 11p and linked to asthma phenotypes, are high-potential candidate genes conferring asthma susceptibility. The purpose of this study was to investigate the genetic association among single nucleotide polymorphisms (SNPs) of EHF and ELF5, and their relationship with asthma in the Taiwanese population. METHODS We selected and performed genotyping on 16 SNPs that encompass the genomic region of EHF and ELF5 in Taiwanese children with or without asthma. A total of 1983 children, 523 in the test group and 619 and 842 in two validation groups, were recruited for this study. RESULTS The SNP rs3910901, located in the 5' upstream region of ELF5, was found to have a weak association (p = 0.043) with asthma in the odds ratio analysis. The genotype distribution was similar in all comparison groups, but the CC genotype was more frequent in asthma patients. Logistic regression adjusted allergy comorbidity showed obviously diluted association. CONCLUSION The results indicated that SNP rs3910901 may have a minor impact on pediatric asthma in the Taiwanese population.
Collapse
Affiliation(s)
- Jiu-Yao Wang
- Department of Pediatrics and Institute of Molecular Medicine, College of Medicine, National Cheng-Kung University, Tainan, Taiwan
| | - Shyh-Dar Shyur
- Department of Pediatrics, Mackay Memorial Hospital, Taipei, Taiwan
| | - Frada Wei-Sam Lam
- Division of Research Development, Vita Genomics Inc., Taipei, Taiwan
| | | |
Collapse
|
39
|
Fossum SL, Mutolo MJ, Yang R, Dang H, O'Neal WK, Knowles MR, Leir SH, Harris A. Ets homologous factor regulates pathways controlling response to injury in airway epithelial cells. Nucleic Acids Res 2014; 42:13588-98. [PMID: 25414352 PMCID: PMC4267623 DOI: 10.1093/nar/gku1146] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Ets homologous factor (EHF) is an Ets family transcription factor expressed in many epithelial cell types including those lining the respiratory system. Disruption of the airway epithelium is central to many lung diseases, and a network of transcription factors coordinates its normal function. EHF can act as a transcriptional activator or a repressor, though its targets in lung epithelial cells are largely uncharacterized. Chromatin immunoprecipitation followed by deep sequencing (ChIP-seq), showed that the majority of EHF binding sites in lung epithelial cells are intergenic or intronic and coincide with putative enhancers, marked by specific histone modifications. EHF occupies many genomic sites that are close to genes involved in intercellular and cell–matrix adhesion. RNA-seq after EHF depletion or overexpression showed significant alterations in the expression of genes involved in response to wounding. EHF knockdown also targeted genes in pathways of epithelial development and differentiation and locomotory behavior. These changes in gene expression coincided with alterations in cellular phenotype including slowed wound closure and increased transepithelial resistance. Our data suggest that EHF regulates gene pathways critical for epithelial response to injury, including those involved in maintenance of barrier function, inflammation and efficient wound repair.
Collapse
Affiliation(s)
- Sara L Fossum
- Human Molecular Genetics Program, Lurie Children's Research Center, Chicago, IL 60614, USA Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Michael J Mutolo
- Human Molecular Genetics Program, Lurie Children's Research Center, Chicago, IL 60614, USA
| | - Rui Yang
- Human Molecular Genetics Program, Lurie Children's Research Center, Chicago, IL 60614, USA Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Hong Dang
- Marsico Lung Institute, University of North Carolina Cystic Fibrosis Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Wanda K O'Neal
- Marsico Lung Institute, University of North Carolina Cystic Fibrosis Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Michael R Knowles
- Marsico Lung Institute, University of North Carolina Cystic Fibrosis Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Shih-Hsing Leir
- Human Molecular Genetics Program, Lurie Children's Research Center, Chicago, IL 60614, USA Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Ann Harris
- Human Molecular Genetics Program, Lurie Children's Research Center, Chicago, IL 60614, USA Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| |
Collapse
|
40
|
Findlay VJ, LaRue AC, Turner DP, Watson PM, Watson DK. Understanding the role of ETS-mediated gene regulation in complex biological processes. Adv Cancer Res 2014; 119:1-61. [PMID: 23870508 DOI: 10.1016/b978-0-12-407190-2.00001-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Ets factors are members of one of the largest families of evolutionarily conserved transcription factors, regulating critical functions in normal cell homeostasis, which when perturbed contribute to tumor progression. The well-documented alterations in ETS factor expression and function during cancer progression result in pleiotropic effects manifested by the downstream effect on their target genes. Multiple ETS factors bind to the same regulatory sites present on target genes, suggesting redundant or competitive functions. The anti- and prometastatic signatures obtained by examining specific ETS regulatory networks will significantly improve our ability to accurately predict tumor progression and advance our understanding of gene regulation in cancer. Coordination of multiple ETS gene functions also mediates interactions between tumor and stromal cells and thus contributes to the cancer phenotype. As such, these new insights may provide a novel view of the ETS gene family as well as a focal point for studying the complex biological control involved in tumor progression. One of the goals of molecular biology is to elucidate the mechanisms that contribute to the development and progression of cancer. Such an understanding of the molecular basis of cancer will provide new possibilities for: (1) earlier detection, as well as better diagnosis and staging of disease; (2) detection of minimal residual disease recurrences and evaluation of response to therapy; (3) prevention; and (4) novel treatment strategies. Increased understanding of ETS-regulated biological pathways will directly impact these areas.
Collapse
Affiliation(s)
- Victoria J Findlay
- Department of Pathology and Laboratory Medicine, Hollings Cancer Center, Medical University of South Carolina, Charleston, South Carolina, USA
| | | | | | | | | |
Collapse
|
41
|
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.
Collapse
|
42
|
Weiler CA, Drumm ML. Genetic influences on cystic fibrosis lung disease severity. Front Pharmacol 2013; 4:40. [PMID: 23630497 PMCID: PMC3632778 DOI: 10.3389/fphar.2013.00040] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Accepted: 03/21/2013] [Indexed: 12/19/2022] Open
Abstract
Understanding the causes of variation in clinical manifestations of disease should allow for design of new or improved therapeutic strategies to treat the disease. If variation is caused by genetic differences between individuals, identifying the genes involved should present therapeutic targets, either in the proteins encoded by those genes or the pathways in which they function. The technology to identify and genotype the millions of variants present in the human genome has evolved rapidly over the past two decades. Originally only a small number of polymorphisms in a small number of subjects could be studied realistically, but speed and scope have increased nearly as dramatically as cost has decreased, making it feasible to determine genotypes of hundreds of thousands of polymorphisms in thousands of subjects. The use of such genetic technology has been applied to cystic fibrosis (CF) to identify genetic variation that alters the outcome of this single gene disorder. Candidate gene strategies to identify these variants, referred to as “modifier genes,” has yielded several genes that act in pathways known to be important in CF and for these the clinical implications are relatively clear. More recently, whole-genome surveys that probe hundreds of thousands of variants have been carried out and have identified genes and chromosomal regions for which a role in CF is not at all clear. Identification of these genes is exciting, as it provides the possibility for new areas of therapeutic development.
Collapse
Affiliation(s)
- Colleen A Weiler
- Department of Pediatrics, Case Western Reserve University Cleveland, OH, USA
| | | |
Collapse
|
43
|
Sprater F, Hovden AO, Appel S. Expression of ESE-3 isoforms in immunogenic and tolerogenic human monocyte-derived dendritic cells. PLoS One 2012. [PMID: 23185370 PMCID: PMC3501485 DOI: 10.1371/journal.pone.0049577] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Dendritic cells (DC) are the only hematopoietic cells expressing the epithelial specific Ets transcription factor ESE-3. Here we analyzed presence and quantity of isoforms ESE-3a, ESE-3b and ESE-3j in various immunogenic and tolerogenic human monocyte-derived DC (moDC) and blood DC populations using quantitative real time PCR and immunoblot analyses. ESE-3a and ESE-3b were detectable in all moDC populations with ESE-3b being the main transcript. ESE-3b expression was upregulated in immunogenic moDC and downregulated in tolerogenic moDC compared to immature moDC. ESE-3a had similar transcript levels in immature and immunogenic moDC and had very low levels in tolerogenic moDC. In blood DC populations only splice variant ESE-3b was detectable. ESE-3j was not detectable in any of the DC populations. These findings suggest that ESE-3b is the functionally most important ESE-3 isoform in DC.
Collapse
Affiliation(s)
- Florian Sprater
- Broegelmann Research Laboratory, The Gade Institute, University of Bergen, Bergen, Norway
| | - Arnt-Ove Hovden
- Broegelmann Research Laboratory, The Gade Institute, University of Bergen, Bergen, Norway
| | - Silke Appel
- Broegelmann Research Laboratory, The Gade Institute, University of Bergen, Bergen, Norway
- * E-mail:
| |
Collapse
|
44
|
Wright FA, Strug LJ, Doshi VK, Commander CW, Blackman SM, Sun L, Berthiaume Y, Cutler D, Cojocaru A, Collaco JM, Corey M, Dorfman R, Goddard K, Green D, Kent JW, Lange EM, Lee S, Li W, Luo J, Mayhew GM, Naughton KM, Pace RG, Paré P, Rommens JM, Sandford A, Stonebraker JR, Sun W, Taylor C, Vanscoy LL, Zou F, Blangero J, Zielenski J, O'Neal WK, Drumm ML, Durie PR, Knowles MR, Cutting GR. Genome-wide association and linkage identify modifier loci of lung disease severity in cystic fibrosis at 11p13 and 20q13.2. Nat Genet 2011; 43:539-46. [PMID: 21602797 PMCID: PMC3296486 DOI: 10.1038/ng.838] [Citation(s) in RCA: 191] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2010] [Accepted: 04/22/2011] [Indexed: 12/17/2022]
Abstract
A combined genome-wide association and linkage study was used to identify loci causing variation in cystic fibrosis lung disease severity. We identified a significant association (P = 3.34 × 10(-8)) near EHF and APIP (chr11p13) in p.Phe508del homozygotes (n = 1,978). The association replicated in p.Phe508del homozygotes (P = 0.006) from a separate family based study (n = 557), with P = 1.49 × 10(-9) for the three-study joint meta-analysis. Linkage analysis of 486 sibling pairs from the family based study identified a significant quantitative trait locus on chromosome 20q13.2 (log(10) odds = 5.03). Our findings provide insight into the causes of variation in lung disease severity in cystic fibrosis and suggest new therapeutic targets for this life-limiting disorder.
Collapse
Affiliation(s)
- Fred A Wright
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
45
|
McClay JL, Adkins DE, Aberg K, Bukszár J, Khachane AN, Keefe RSE, Perkins DO, McEvoy JP, Stroup TS, Vann RE, Beardsley PM, Lieberman JA, Sullivan PF, van den Oord EJCG. Genome-wide pharmacogenomic study of neurocognition as an indicator of antipsychotic treatment response in schizophrenia. Neuropsychopharmacology 2011; 36:616-26. [PMID: 21107309 PMCID: PMC3055694 DOI: 10.1038/npp.2010.193] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/04/2010] [Revised: 09/16/2010] [Accepted: 09/23/2010] [Indexed: 01/16/2023]
Abstract
Neurocognitive deficits are a core feature of schizophrenia and, therefore, represent potentially critical outcome variables for assessing antipsychotic treatment response. We performed genome-wide association studies (GWAS) with 492K single nucleotide polymorphisms (SNPs) in a sample of 738 patients with schizophrenia from the Clinical Antipsychotic Trials of Intervention Effectiveness study. Outcome variables consisted of a neurocognitive battery administered at multiple time points over an 18-month period, measuring processing speed, verbal memory, vigilance, reasoning, and working memory domains. Genetic mediation of improvements in each of these five domains plus a composite neurocognitive measure was assessed for each of five antipsychotics (olanzapine, perphenazine, quetiapine, risperidone, and ziprasidone). Six SNPs achieved genome-wide significance using a pre-specified threshold that ensures, on average, only 1 in 10 findings is a false discovery. These six SNPs were located within, or in close proximity to, genes EHF, SLC26A9, DRD2, GPR137B, CHST8, and IL1A. The more robust findings, that is those significant across multiple neurocognitive domains and having adjacent SNPs showing evidence for association, were rs286913 at the EHF gene (p-value 6.99 × 10(-8), q-value 0.034, mediating the effects of ziprasidone on vigilance), rs11240594 at SLC26A9 (p-value 1.4 × 10(-7), q-value 0.068, mediating the effects of olanzapine on processing speed), and rs11677416 at IL1A (p-value 6.67 × 10(-7), q-value 0.081, mediating the effects of olanzapine on working memory). This study has generated several novel candidate genes for antipsychotic response. However, our findings will require replication and functional validation. To facilitate replication efforts, we provide all GWAS p-values for download.
Collapse
Affiliation(s)
- Joseph L McClay
- Center for Biomarker Research and Personalized Medicine, School of Pharmacy, Medical College of Virginia Campus, Virginia Commonwealth University, Richmond, VA 23298-0533, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
46
|
Ho HH, Ivashkiv LB. Downregulation of Friend leukemia virus integration 1 as a feedback mechanism that restrains lipopolysaccharide induction of matrix metalloproteases and interleukin-10 in human macrophages. J Interferon Cytokine Res 2010; 30:893-900. [PMID: 20879862 DOI: 10.1089/jir.2010.0046] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The E26 transformation-specific (Ets) proteins are a family of transcription factors with important roles in a variety of cellular processes ranging from proliferation and differentiation to transformation and metastasis. Tissue-specific expression of Ets proteins and their ability to interact with other families of transcription factors contribute to their versatility. In this study, we investigated the regulation of Ets factors in primary human monocytes and macrophages, and their role in matrix metalloprotease (MMP) and cytokine production. The macrophage-activating Toll-like receptor ligand, lipopolysaccharide (LPS), induced the expression of Ets family members epithelium-specific Ets factor 3 (ESE-3) and TEL-2 but rapidly suppressed Friend leukemia virus integration 1 (FLI-1) expression. Modulation of FLI-1 expression using either RNA interference or forced expression identified a positive role for FLI-1 in contributing to LPS-induced expression of MMP-1, MMP-3, MMP-10, and interleukin-10 (IL-10). Thus, the rapid downregulation of FLI-1 expression after LPS stimulation attenuates the induction of various MMPs and IL-10 under inflammatory conditions. In contrast, the expression of IL-6 and TNFα and the effects of interferon (IFN)γ on LPS responses were not dependent on FLI-1. Our results define a novel FLI-1-mediated self-regulatory feedback loop that limits MMP expression and thus may attenuate extent of tissue destruction associated with inflammatory responses.
Collapse
Affiliation(s)
- Hao H Ho
- Arthritis and Tissue Degeneration Program, Department of Medicine, Hospital for Special Surgery, New York, New York, USA
| | | |
Collapse
|
47
|
Knödler A, Schmidt SM, Bringmann A, Weck MM, Brauer KM, Holderried TAW, Heine AK, Grünebach F, Brossart P. Post-transcriptional regulation of adapter molecules by IL-10 inhibits TLR-mediated activation of antigen-presenting cells. Leukemia 2008; 23:535-44. [PMID: 19005481 DOI: 10.1038/leu.2008.301] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Toll-like receptors (TLRs) act to sense the environment for microbial products and submit danger signals to antigen-presenting cells (APCs) resulting in activation of complex immune responses. In this study, we analyzed the function of human monocyte-derived APCs generated in vitro in the presence of interleukin (IL)-10 upon activation by TLR ligands. Exposure of these APCs to IL-10 resulted in a skewed phenotypic maturation in response to stimuli provided by the TLR ligands, a reduced cytokine production, such as IL-12, IL-6 or tumor necrosis factor-alpha, and impaired capacity to stimulate T-cell activation. Furthermore, CCR7 upregulation in APCs exposed to TLR stimulation as well as migration towards CCL19/MIP-3beta were strongly reduced. IL-10 was found to downregulate MyD88, IRAK1 (IL-1 receptor-associated kinase) and tumor necrosis factor receptor-associated factor 6, essential adaptor molecules for TLR signaling, and to decrease TLR-induced nuclear expression of the nuclear factor-kappaB transcription factors c-Rel and Rel-B as well as interferon regulatory factor (IRF)-3 and IRF-8. This was not due to the inhibition of the mitogen-activated protein kinase pathway, but was rather mediated by the blockage of the PI3K signaling cascade. Interestingly, the inhibition of proteins involved in TLR signaling, such as MyD88, IRAK1 and mammalian target of rapamycin, was due to a selective post-transcriptional regulation.
Collapse
Affiliation(s)
- A Knödler
- Department of Oncology, Hematology, Immunology, Rheumatology and Pulmology, University of Tübingen, Tübingen, Germany
| | | | | | | | | | | | | | | | | |
Collapse
|
48
|
Regulation of epithelium-specific Ets-like factors ESE-1 and ESE-3 in airway epithelial cells: potential roles in airway inflammation. Cell Res 2008; 18:649-63. [PMID: 18475289 DOI: 10.1038/cr.2008.57] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Airway inflammation is the hallmark of many respiratory disorders, such as asthma and cystic fibrosis. Changes in airway gene expression triggered by inflammation play a key role in the pathogenesis of these diseases. Genetic linkage studies suggest that ESE-2 and ESE-3, which encode epithelium-specific Ets-domain-containing transcription factors, are candidate asthma susceptibility genes. We report here that the expression of another member of the Ets family transcription factors ESE-1, as well as ESE-3, is upregulated by the inflammatory cytokines interleukin-1beta (IL-1beta) and tumor necrosis factor-alpha (TNF-alpha) in bronchial epithelial cell lines. Treatment of these cells with IL-1beta and TNF-alpha resulted in a dramatic increase in mRNA expression for both ESE-1 and ESE-3. We demonstrate that the induced expression is mediated by activation of the transcription factor NF-kappaB. We have characterized the ESE-1 and ESE-3 promoters and have identified the NF-kappaB binding sequences that are required for the cytokine-induced expression. In addition, we also demonstrate that ESE-1 upregulates ESE-3 expression and downregulates its own induction by cytokines. Finally, we have shown that in Elf3 (homologous to human ESE-1) knockout mice, the expression of the inflammatory cytokine interleukin-6 (IL-6) is downregulated. Our findings suggest that ESE-1 and ESE-3 play an important role in airway inflammation.
Collapse
|
49
|
Metzger DE, Stahlman MT, Shannon JM. Misexpression of ELF5 disrupts lung branching and inhibits epithelial differentiation. Dev Biol 2008; 320:149-60. [PMID: 18544451 DOI: 10.1016/j.ydbio.2008.04.038] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2007] [Revised: 04/29/2008] [Accepted: 04/30/2008] [Indexed: 12/30/2022]
Abstract
ELF5, an Ets family transcription factor found exclusively in epithelial cells, is expressed in the distal lung epithelium during embryogenesis, then becomes restricted to proximal airways at the end of gestation and postnatally. To test the hypothesis that ELF5 represses distal epithelial differentiation, we generated a transgenic mouse model in which a doxycycline inducible HA-tagged mouse Elf5 transgene was placed under the control of the lung epithelium-specific human SFTPC promoter. We found that expressing high levels of ELF5 during early lung development disrupted branching morphogenesis and produced a dilated epithelium. The effects of ELF5 on morphogenesis were stage-dependent, since inducing the transgene on E16.5 had no effect on branching. ELF5 reduced expression of the distal lung epithelial differentiation markers Erm, Napsa and Sftpc, and type II cell ultrastructural differentiation was immature. ELF5 overexpression did not induce the proximal airway epithelial markers Ccsp and Foxj1, but did induce expression of p63, a marker of basal cells in the trachea and esophagus. High ELF5 levels also induced the expression of genes found in other endodermal epithelia but not normally associated with the lung. These results suggest that precise levels of ELF5 regulate the specification and differentiation of epithelial cells in the lung.
Collapse
Affiliation(s)
- David E Metzger
- Division of Pulmonary Biology, Cincinnati Children's Hosptial Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229-3039, USA
| | | | | |
Collapse
|
50
|
Turner DP, Watson DK. ETS transcription factors: oncogenes and tumor suppressor genes as therapeutic targets for prostate cancer. Expert Rev Anticancer Ther 2008; 8:33-42. [PMID: 18095881 DOI: 10.1586/14737140.8.1.33] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
ETS factors represent one of the largest families of transcriptional regulators and have known functional roles in many biological processes. Significantly, ETS factors have oncogenic and suppressive activity and their aberrant expression is associated with many of the processes that lead to prostate cancer progression. The targeting of transcription for therapeutic gain has met with some success. Therefore, better understanding the mechanisms that regulate ETS factor activity during both normal and aberrant transcription provides a novel means to identify processes that may be targeted in order to re-establish the normal ETS regulatory networks that are perturbed in cancer. Specific examples of altered ETS factor expression are highlighted, and therapeutic technologies that may be used to target ETS factors and their cofactors and downstream target genes in prostate cancer are discussed.
Collapse
Affiliation(s)
- David P Turner
- Department of Pathology & Laboratory Medicine, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC 29425, USA.
| | | |
Collapse
|