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Cheng JN, Frye JB, Whitman SA, Ehsani S, Ali S, Funk JL. Interrogating Estrogen Signaling Pathways in Human ER-Positive Breast Cancer Cells Forming Bone Metastases in Mice. Endocrinology 2024; 165:bqae038. [PMID: 38715255 PMCID: PMC11076418 DOI: 10.1210/endocr/bqae038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Indexed: 05/12/2024]
Abstract
Breast cancer bone metastases (BMET) are incurable, primarily osteolytic, and occur most commonly in estrogen receptor-α positive (ER+) breast cancer. ER+ human breast cancer BMET modeling in mice has demonstrated an estrogen (E2)-dependent increase in tumor-associated osteolysis and bone-resorbing osteoclasts, independent of estrogenic effects on tumor proliferation or bone turnover, suggesting a possible mechanistic link between tumoral ERα-driven osteolysis and ER+ bone progression. To explore this question, inducible secretion of the osteolytic factor, parathyroid hormone-related protein (PTHrP), was utilized as an in vitro screening bioassay to query the osteolytic potential of estrogen receptor- and signaling pathway-specific ligands in BMET-forming ER+ human breast cancer cells expressing ERα, ERß, and G protein-coupled ER. After identifying genomic ERα signaling, also responsibility for estrogen's proliferative effects, as necessary and sufficient for osteolytic PTHrP secretion, in vivo effects of a genomic-only ER agonist, estetrol (E4), on osteolytic ER+ BMET progression were examined. Surprisingly, while pharmacologic effects of E4 on estrogen-dependent tissues, including bone, were evident, E4 did not support osteolytic BMET progression (vs robust E2 effects), suggesting an important role for nongenomic ER signaling in ER+ metastatic progression at this site. Because bone effects of E4 did not completely recapitulate those of E2, the relative importance of nongenomic ER signaling in tumor vs bone cannot be ascertained here. Nonetheless, these intriguing findings suggest that targeted manipulation of estrogen signaling to mitigate ER+ metastatic progression in bone may require a nuanced approach, considering genomic and nongenomic effects of ER signaling on both sides of the tumor/bone interface.
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Affiliation(s)
- Julia N Cheng
- Cancer Biology Graduate Interdisciplinary Program, University of Arizona, Tucson, AZ 85724, USA
| | - Jennifer B Frye
- Department of Medicine, University of Arizona, Tucson, AZ 86724, USA
| | - Susan A Whitman
- Department of Medicine, University of Arizona, Tucson, AZ 86724, USA
| | - Sima Ehsani
- Department of Medicine, University of Arizona, Tucson, AZ 86724, USA
| | - Simak Ali
- Department of Surgery & Cancer, Imperial College London, London W12 0NN, UK
| | - Janet L Funk
- Department of Medicine, University of Arizona, Tucson, AZ 86724, USA
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2
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Ji D, Shao C, Yu J, Hou Y, Gao X, Wu Y, Wang L, Chen P. FOXA1 forms biomolecular condensates that unpack condensed chromatin to function as a pioneer factor. Mol Cell 2024; 84:244-260.e7. [PMID: 38101414 DOI: 10.1016/j.molcel.2023.11.020] [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: 06/12/2023] [Revised: 09/14/2023] [Accepted: 11/15/2023] [Indexed: 12/17/2023]
Abstract
Eukaryotic DNA is packaged into chromatin in the nucleus, restricting the binding of transcription factors (TFs) to their target DNA sites. FOXA1 functions as a pioneer TF to bind condensed chromatin and initiate the opening of local chromatin for gene expression. However, the principles of FOXA1 recruitment and how it subsequently unpacks the condensed chromatin remain elusive. Here, we revealed that FOXA1 intrinsically forms submicron-sized condensates through its N- and C-terminal intrinsically disordered regions (IDRs). Notably, both IDRs enable FOXA1 to dissolve the condensed chromatin. In addition, the DNA-binding capacity of FOXA1 contributes to its ability to both form condensates and dissolve condensed chromatin. Further genome-wide investigation showed that IDRs enable FOXA1 to bind and unpack the condensed chromatin to regulate the proliferation and migration of breast cancer cells. This work provides a principle of how pioneer TFs function to initiate competent chromatin states using their IDRs.
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Affiliation(s)
- Dengyu Ji
- Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory for Tumor Invasion and Metastasis, Capital Medical University, Beijing 100069, China
| | - Changrong Shao
- Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory for Tumor Invasion and Metastasis, Capital Medical University, Beijing 100069, China
| | - Juan Yu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yaoyao Hou
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, China
| | - Xiao Gao
- Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory for Tumor Invasion and Metastasis, Capital Medical University, Beijing 100069, China
| | - Yichuan Wu
- Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory for Tumor Invasion and Metastasis, Capital Medical University, Beijing 100069, China
| | - Liang Wang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China.
| | - Ping Chen
- Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory for Tumor Invasion and Metastasis, Capital Medical University, Beijing 100069, China; National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
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3
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Schinderle JD, Bochkis IM. Sequential ChIP-Seq. Methods Mol Biol 2024; 2846:109-121. [PMID: 39141232 DOI: 10.1007/978-1-0716-4071-5_7] [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] [Indexed: 08/15/2024]
Abstract
ChIP-Seq has been used extensively to profile genome-wide transcription factor binding and post-translational histone modifications. A sequential ChIP assay determines the in vivo co-localization of two proteins to the same genomic locus. In this chapter, we combine the two protocols in Sequential ChIP-Seq, a method for identifying genome-wide sites of in vivo protein co-occupancy.
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Affiliation(s)
- Joseph D Schinderle
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
- Pittsburgh Liver Research Center, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
| | - Irina M Bochkis
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
- Pittsburgh Liver Research Center, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
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4
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Malinverni R, Corujo D, Gel B, Buschbeck M. regioneReloaded: evaluating the association of multiple genomic region sets. Bioinformatics 2023; 39:btad704. [PMID: 37988135 PMCID: PMC10681856 DOI: 10.1093/bioinformatics/btad704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 10/27/2023] [Accepted: 11/20/2023] [Indexed: 11/22/2023] Open
Abstract
MOTIVATION Next-generation sequencing methods continue improving the annotation of genomes in part by determining the distribution of features such as epigenetic marks. Evaluating and interpreting the association between genomic regions and their features has become a common and challenging analysis in genomic and epigenomic studies. RESULTS With regioneR we provided an R package allowing to assess the statistical significance of pairwise associations between genomic region sets using permutation tests. We now present the R package regioneReloaded that builds upon regioneR's statistical foundation and extends the functionality for the simultaneous analysis and visualization of the associations between multiple genomic region sets. Thus, we provide a novel discovery tool for the identification of significant associations that warrant to be tested for functional interdependence. AVAILABILITY AND IMPLEMENTATION regioneReloaded is an R package released under an Artistic-2.0 License. The source code and documentation are freely available through Bioconductor: http://www.bioconductor.org/packages/regioneReloaded.
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Affiliation(s)
- Roberto Malinverni
- Program of Myeloid Neoplasms, Program of Applied Epigenetics, Josep Carreras Leukaemia Research Institute (IJC), Campus Can Ruti Site, Badalona 08916, Spain
| | - David Corujo
- Program of Myeloid Neoplasms, Program of Applied Epigenetics, Josep Carreras Leukaemia Research Institute (IJC), Campus Can Ruti Site, Badalona 08916, Spain
| | - Bernat Gel
- Germans Trias i Pujol Research Institute (IGTP), Can Ruti Campus, Badalona, Barcelona 08916, Spain
| | - Marcus Buschbeck
- Program of Myeloid Neoplasms, Program of Applied Epigenetics, Josep Carreras Leukaemia Research Institute (IJC), Campus Can Ruti Site, Badalona 08916, Spain
- Germans Trias i Pujol Research Institute (IGTP), Can Ruti Campus, Badalona, Barcelona 08916, Spain
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Arora S, Yang J, Akiyama T, James DQ, Morrissey A, Blanda TR, Badjatia N, Lai WK, Ko MS, Pugh BF, Mahony S. Joint sequence & chromatin neural networks characterize the differential abilities of Forkhead transcription factors to engage inaccessible chromatin. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.06.561228. [PMID: 37873361 PMCID: PMC10592618 DOI: 10.1101/2023.10.06.561228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
The DNA-binding activities of transcription factors (TFs) are influenced by both intrinsic sequence preferences and extrinsic interactions with cell-specific chromatin landscapes and other regulatory proteins. Disentangling the roles of these binding determinants remains challenging. For example, the FoxA subfamily of Forkhead domain (Fox) TFs are known pioneer factors that can bind to relatively inaccessible sites during development. Yet FoxA TF binding also varies across cell types, pointing to a combination of intrinsic and extrinsic forces guiding their binding. While other Forkhead domain TFs are often assumed to have pioneering abilities, how sequence and chromatin features influence the binding of related Fox TFs has not been systematically characterized. Here, we present a principled approach to compare the relative contributions of intrinsic DNA sequence preference and cell-specific chromatin environments to a TF's DNA-binding activities. We apply our approach to investigate how a selection of Fox TFs (FoxA1, FoxC1, FoxG1, FoxL2, and FoxP3) vary in their binding specificity. We over-express the selected Fox TFs in mouse embryonic stem cells, which offer a platform to contrast each TF's binding activity within the same preexisting chromatin background. By applying a convolutional neural network to interpret the Fox TF binding patterns, we evaluate how sequence and preexisting chromatin features jointly contribute to induced TF binding. We demonstrate that Fox TFs bind different DNA targets, and drive differential gene expression patterns, even when induced in identical chromatin settings. Despite the association between Forkhead domains and pioneering activities, the selected Fox TFs display a wide range of affinities for preexiting chromatin states. Using sequence and chromatin feature attribution techniques to interpret the neural network predictions, we show that differential sequence preferences combined with differential abilities to engage relatively inaccessible chromatin together explain Fox TF binding patterns at individual sites and genome-wide.
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Affiliation(s)
- Sonny Arora
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, Penn State University, University Park, PA, USA
| | - Jianyu Yang
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, Penn State University, University Park, PA, USA
| | - Tomohiko Akiyama
- Department of Systems Medicine, Keio University School of Medicine, Tokyo, Japan
- Current address: School of Medicine, Yokohama City University, Japan
| | - Daniela Q. James
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, Penn State University, University Park, PA, USA
| | - Alexis Morrissey
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, Penn State University, University Park, PA, USA
| | - Thomas R. Blanda
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, Penn State University, University Park, PA, USA
| | - Nitika Badjatia
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, Penn State University, University Park, PA, USA
| | - William K.M. Lai
- Department of Molecular Biology and Genetics, Cornell University, NY, USA
| | - Minoru S.H. Ko
- Department of Systems Medicine, Keio University School of Medicine, Tokyo, Japan
| | - B. Franklin Pugh
- Department of Molecular Biology and Genetics, Cornell University, NY, USA
| | - Shaun Mahony
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, Penn State University, University Park, PA, USA
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6
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Hao Y, Han L, Wu A, Bochkis IM. Pioneer Factor Foxa2 Mediates Chromatin Conformation Changes for Activation of Bile Acid Targets of FXR. Cell Mol Gastroenterol Hepatol 2023; 17:237-249. [PMID: 37879405 PMCID: PMC10765059 DOI: 10.1016/j.jcmgh.2023.10.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 10/20/2023] [Accepted: 10/20/2023] [Indexed: 10/27/2023]
Abstract
BACKGROUND & AIMS Transcription factors regulate gene expression that orchestrates liver physiology. Many bind at distal enhancers and chromatin looping is required to activate their targets. Chromatin architecture has been linked to essential functions of the liver, including metabolism and sexually dimorphic gene expression. We have previously shown that pioneer factor Foxa2 opens chromatin for binding of nuclear receptors farnesoid X receptor (FXR) and liver X receptor-α during acute ligand activation. FXR is activated by bile acids and deletion of Foxa2 in the liver results in intrahepatic cholestasis. We hypothesized that Foxa2 also enables chromatin conformational changes during ligand activation and performed genome-wide studies to test this hypothesis. METHODS We performed Foxa2 HiChIP (Hi-C and ChIP) to assess Foxa2-dependent long-range interactions in mouse livers treated with either vehicle control or FXR agonist GW4064. RESULTS HiChIP contact analysis shows that global chromatin interactions are dramatically increased during FXR activation. Ligand-treated livers exhibit extensive redistribution of topological associated domains and substantial increase in Foxa2-anchored loops, suggesting Foxa2 is involved in dynamic chromatin conformational changes. We demonstrate that chromatin conformation, including genome-wide interactions, topological associated domains, and intrachromosomal and interchromosomal Foxa2-anchored loops, drastically changes on addition of FXR agonist. Additional Foxa2 binding in ligand-activated state leads to formation of Foxa2-anchored loops, leading to distal interactions and activation of gene expression of FXR targets. CONCLUSIONS Ligand activation of FXR, and likely of related receptors, requires global changes in chromatin architecture. We determine a novel role for Foxa2 in enabling these conformational changes, extending its function in bile acid metabolism.
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Affiliation(s)
- Yi Hao
- Department of Pharmacology, University of Virginia, Charlottesville, Virginia
| | - Lu Han
- Department of Pharmacology, University of Virginia, Charlottesville, Virginia
| | - Anqi Wu
- Department of Pharmacology, University of Virginia, Charlottesville, Virginia
| | - Irina M Bochkis
- Department of Pharmacology, University of Virginia, Charlottesville, Virginia.
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7
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Warren I, Moeller MM, Guiggey D, Chiang A, Maloy M, Ogoke O, Groth T, Mon T, Meamardoost S, Liu X, Thompson S, Szeglowski A, Thompson R, Chen P, Paulmurugan R, Yarmush ML, Kidambi S, Parashurama N. FOXA1/2 depletion drives global reprogramming of differentiation state and metabolism in a human liver cell line and inhibits differentiation of human stem cell-derived hepatic progenitor cells. FASEB J 2023; 37:e22652. [PMID: 36515690 DOI: 10.1096/fj.202101506rrr] [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: 09/22/2021] [Revised: 10/28/2022] [Accepted: 10/31/2022] [Indexed: 12/15/2022]
Abstract
FOXA factors are critical members of the developmental gene regulatory network (GRN) composed of master transcription factors (TF) which regulate murine cell fate and metabolism in the gut and liver. How FOXA factors dictate human liver cell fate, differentiation, and simultaneously regulate metabolic pathways is poorly understood. Here, we aimed to determine the role of FOXA2 (and FOXA1 which is believed to compensate for FOXA2) in controlling hepatic differentiation and cell metabolism in a human hepatic cell line (HepG2). siRNA mediated knockdown of FOXA1/2 in HepG2 cells significantly downregulated albumin (p < .05) and GRN TF gene expression (HNF4α, HEX, HNF1ß, TBX3) (p < .05) and significantly upregulated endoderm/gut/hepatic endoderm markers (goosecoid [GSC], FOXA3, and GATA4), gut TF (CDX2), pluripotent TF (NANOG), and neuroectodermal TF (PAX6) (p < .05), all consistent with partial/transient reprograming. shFOXA1/2 targeting resulted in similar findings and demonstrated evidence of reversibility of phenotype. RNA-seq followed by bioinformatic analysis of shFOXA1/2 knockdown HepG2 cells demonstrated 235 significant downregulated genes and 448 upregulated genes, including upregulation of markers for alternate germ layers lineages (cardiac, endothelial, muscle) and neurectoderm (eye, neural). We found widespread downregulation of glycolysis, citric acid cycle, mitochondrial genes, and alterations in lipid metabolism, pentose phosphate pathway, and ketogenesis. Functional metabolic analysis agreed with these findings, demonstrating significantly diminished glycolysis and mitochondrial respiration, with concomitant accumulation of lipid droplets. We hypothesized that FOXA1/2 inhibit the initiation of human liver differentiation in vitro. During human pluripotent stem cells (hPSC)-hepatic differentiation, siRNA knockdown demonstrated de-differentiation and unexpectedly, activation of pluripotency factors and neuroectoderm. shRNA knockdown demonstrated similar results and activation of SOX9 (hepatobiliary). These results demonstrate that FOXA1/2 controls hepatic and developmental GRN, and their knockdown leads to reprogramming of both differentiation and metabolism, with applications in studies of cancer, differentiation, and organogenesis.
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Affiliation(s)
- Iyan Warren
- Department of Chemical and Biological Engineering, University at Buffalo (State University of New York), Buffalo, New York, USA
| | - Michael M Moeller
- Department of Chemical and Biomolecular Engineering, University of Nebraska- Lincoln, Lincoln, Nebraska, USA
| | - Daniel Guiggey
- Department of Chemical and Biological Engineering, University at Buffalo (State University of New York), Buffalo, New York, USA
| | - Alexander Chiang
- Department of Chemical and Biological Engineering, University at Buffalo (State University of New York), Buffalo, New York, USA
| | - Mitchell Maloy
- Department of Chemical and Biological Engineering, University at Buffalo (State University of New York), Buffalo, New York, USA
| | - Ogechi Ogoke
- Department of Chemical and Biological Engineering, University at Buffalo (State University of New York), Buffalo, New York, USA
| | - Theodore Groth
- Department of Chemical and Biological Engineering, University at Buffalo (State University of New York), Buffalo, New York, USA
| | - Tala Mon
- Department of Chemical and Biological Engineering, University at Buffalo (State University of New York), Buffalo, New York, USA
| | - Saber Meamardoost
- Department of Chemical and Biological Engineering, University at Buffalo (State University of New York), Buffalo, New York, USA
| | - Xiaojun Liu
- Department of Chemical and Biological Engineering, University at Buffalo (State University of New York), Buffalo, New York, USA
| | - Sarah Thompson
- Department of Chemical and Biological Engineering, University at Buffalo (State University of New York), Buffalo, New York, USA
| | - Antoni Szeglowski
- Department of Chemical and Biological Engineering, University at Buffalo (State University of New York), Buffalo, New York, USA
| | - Ryan Thompson
- Department of Chemical and Biological Engineering, University at Buffalo (State University of New York), Buffalo, New York, USA
| | - Peter Chen
- Department of Biomedical Engineering, University at Buffalo (State University of New York), Buffalo, New York, USA
| | - Ramasamy Paulmurugan
- Department of Radiology, Canary Center for Early Cancer Detection and the Molecular Imaging Program at Stanford, Stanford University, Palo Alto, California, USA
| | - Martin L Yarmush
- Center for Engineering in Medicine and Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA.,Department of Biomedical Engineering, Rutgers University, Piscataway, New Jersey, USA
| | - Srivatsan Kidambi
- Department of Chemical and Biomolecular Engineering, University of Nebraska- Lincoln, Lincoln, Nebraska, USA
| | - Natesh Parashurama
- Department of Chemical and Biological Engineering, University at Buffalo (State University of New York), Buffalo, New York, USA.,Department of Biomedical Engineering, University at Buffalo (State University of New York), Buffalo, New York, USA.,Clinical and Translation Research Center (CTRC), University at Buffalo (State University of New York), Buffalo, New York, USA
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8
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Czerny CC, Borschel A, Cai M, Otto M, Hoyer-Fender S. FOXA1 is a transcriptional activator of Odf2/Cenexin and regulates primary ciliation. Sci Rep 2022; 12:21468. [PMID: 36509813 PMCID: PMC9744847 DOI: 10.1038/s41598-022-25966-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 12/07/2022] [Indexed: 12/14/2022] Open
Abstract
Primary cilia are sensory organelles essential for embryonic and postnatal development, and tissue homeostasis in adulthood. They are generated in a cell cycle-dependent manner and found on most cells of the body. Although cilia formation is intensively investigated virtually nothing is known about the transcriptional regulation of primary ciliation. We used here Odf2/Cenexin, encoding a protein of the mother centriole and the basal body that is mandatory for primary cilia formation, as the target gene for the identification of transcriptional activators. We identified a consensus binding site for Fox transcription factors (TFs) in its promoter region and focused here on the Fox family. We found transcriptional activation of Odf2 neither by FOXO TFs nor by the core TF for multiciliation, FOXJ1. However, we identified FOXA1 as a transcriptional activator of Odf2 by reporter gene assays and qRT-PCR, and showed by qWB that Foxa1 knockdown caused a decrease in ODF2 and CP110 proteins. We verified the binding sequence of FOXA1 in the Odf2 promoter by ChIP. Finally, we demonstrated that knockdown of FOXA1 affected primary cilia formation. We, thus, showed for the first time, that FOXA1 regulates primary ciliation by transcriptional activation of ciliary genes.
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Affiliation(s)
- Christian Carl Czerny
- grid.7450.60000 0001 2364 4210Johann-Friedrich-Blumenbach-Institute of Zoology and Anthropology – Developmental Biology, GZMB, Ernst-Caspari-Haus, Georg-August-Universität, Justus-von-Liebig-Weg 11, Göttingen, Germany
| | - Anett Borschel
- grid.7450.60000 0001 2364 4210Johann-Friedrich-Blumenbach-Institute of Zoology and Anthropology – Developmental Biology, GZMB, Ernst-Caspari-Haus, Georg-August-Universität, Justus-von-Liebig-Weg 11, Göttingen, Germany
| | - Mingfang Cai
- grid.7450.60000 0001 2364 4210Johann-Friedrich-Blumenbach-Institute of Zoology and Anthropology – Developmental Biology, GZMB, Ernst-Caspari-Haus, Georg-August-Universität, Justus-von-Liebig-Weg 11, Göttingen, Germany
| | - Madeline Otto
- grid.7450.60000 0001 2364 4210Johann-Friedrich-Blumenbach-Institute of Zoology and Anthropology – Developmental Biology, GZMB, Ernst-Caspari-Haus, Georg-August-Universität, Justus-von-Liebig-Weg 11, Göttingen, Germany ,grid.424957.90000 0004 0624 9165Present Address: Thermo Fisher Scientific GENEART, Regensburg, Germany
| | - Sigrid Hoyer-Fender
- grid.7450.60000 0001 2364 4210Johann-Friedrich-Blumenbach-Institute of Zoology and Anthropology – Developmental Biology, GZMB, Ernst-Caspari-Haus, Georg-August-Universität, Justus-von-Liebig-Weg 11, Göttingen, Germany
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9
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Drobek M. Paralogous Genes Involved in Embryonic Development: Lessons from the Eye and Other Tissues. Genes (Basel) 2022; 13:2082. [PMID: 36360318 PMCID: PMC9690401 DOI: 10.3390/genes13112082] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/23/2022] [Accepted: 11/05/2022] [Indexed: 07/09/2024] Open
Abstract
During evolution, gene duplications lead to a naturally increased gene dosage. Duplicated genes can be further retained or eliminated over time by purifying selection pressure. The retention probability is increased by functional diversification and by the acquisition of novel functions. Interestingly, functionally diverged paralogous genes can maintain a certain level of functional redundancy and at least a partial ability to replace each other. In such cases, diversification probably occurred at the level of transcriptional regulation. Nevertheless, some duplicated genes can maintain functional redundancy after duplication and the ability to functionally compensate for the loss of each other. Many of them are involved in proper embryonic development. The development of particular tissues/organs and developmental processes can be more or less sensitive to the overall gene dosage. Alterations in the gene dosage or a decrease below a threshold level may have dramatic phenotypic consequences or even lead to embryonic lethality. The number of functional alleles of particular paralogous genes and their mutual cooperation and interactions influence the gene dosage, and therefore, these factors play a crucial role in development. This review will discuss individual interactions between paralogous genes and gene dosage sensitivity during development. The eye was used as a model system, but other tissues are also included.
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Affiliation(s)
- Michaela Drobek
- Laboratory of Transcriptional Regulation, Institute of Molecular Genetics of the Czech Academy of Sciences, Videnska 1083, 142 20 Praha 4, Czech Republic
- Laboratory of RNA Biology, Institute of Molecular Genetics of the Czech Academy of Sciences, Videnska 1083, 142 20 Praha 4, Czech Republic
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10
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Wei X, Murphy MA, Reddy NA, Hao Y, Eggertsen TG, Saucerman JJ, Bochkis IM. Redistribution of lamina-associated domains reshapes binding of pioneer factor FOXA2 in development of nonalcoholic fatty liver disease. Genome Res 2022; 32:1981-1992. [PMID: 36522168 PMCID: PMC9808618 DOI: 10.1101/gr.277149.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 11/16/2022] [Indexed: 12/23/2022]
Abstract
Nonalcoholic fatty liver disease (NAFLD) is highly prevalent in type 2 diabetes mellitus and the elderly, impacting 40% of individuals over 70. Regulation of heterochromatin at the nuclear lamina has been associated with aging and age-dependent metabolic changes. We previously showed that changes at the lamina in aged hepatocytes and laminopathy models lead to redistribution of lamina-associated domains (LADs), opening of repressed chromatin, and up-regulation of genes regulating lipid synthesis and storage, culminating in fatty liver. Here, we test the hypothesis that change in the expression of lamina-associated proteins and nuclear shape leads to redistribution of LADs, followed by altered binding of pioneer factor FOXA2 and by up-regulation of lipid synthesis and storage, culminating in steatosis in younger NAFLD patients (aged 21-51). Changes in nuclear morphology alter LAD partitioning and reduced lamin B1 signal correlate with increased FOXA2 binding before severe steatosis in young mice placed on a western diet. Nuclear shape is also changed in younger NAFLD patients. LADs are redistrubted and lamin B1 signal decreases similarly in mild and severe steatosis. In contrast, FOXA2 binding is similar in normal and NAFLD patients with moderate steatosis and is repositioned only in NAFLD patients with more severe lipid accumulation. Hence, changes at the nuclear lamina reshape FOXA2 binding with progression of the disease. Our results suggest a role for nuclear lamina in etiology of NAFLD, irrespective of aging, with potential for improved stratification of patients and novel treatments aimed at restoring nuclear lamina function.
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Affiliation(s)
- Xiaolong Wei
- Department of Pharmacology, University of Virginia, Charlottesville, Virginia 22908, USA
| | - Megan A Murphy
- Department of Pharmacology, University of Virginia, Charlottesville, Virginia 22908, USA
| | - Nihal A Reddy
- Department of Pharmacology, University of Virginia, Charlottesville, Virginia 22908, USA
| | - Yi Hao
- Department of Pharmacology, University of Virginia, Charlottesville, Virginia 22908, USA
| | - Taylor G Eggertsen
- Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia 22908, USA
| | - Jeffrey J Saucerman
- Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia 22908, USA
| | - Irina M Bochkis
- Department of Pharmacology, University of Virginia, Charlottesville, Virginia 22908, USA
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11
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Gao XQ, Liu CY, Zhang YH, Wang YH, Zhou LY, Li XM, Wang K, Chen XZ, Wang T, Ju J, Wang F, Wang SC, Wang Y, Chen ZY, Wang K. The circRNA CNEACR regulates necroptosis of cardiomyocytes through Foxa2 suppression. Cell Death Differ 2022; 29:527-539. [PMID: 34588633 PMCID: PMC8901615 DOI: 10.1038/s41418-021-00872-2] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 09/05/2021] [Accepted: 09/07/2021] [Indexed: 11/09/2022] Open
Abstract
Circular RNAs (circRNAs) are differentially expressed in various cardiovascular disease including myocardial ischemia-reperfusion (I/R) injury. However, their functional impact on cardiomyocyte cell death, in particular, in necrotic forms of death remains elusive. In this study, we found that the level of mmu_circ_000338, a cardiac- necroptosis-associated circRNA (CNEACR), was reduced in hypoxia-reoxygenation (H/R) exposed cardiomyocytes and I/R-injured mice hearts. The enforced expression of CNEACR attenuated the necrotic form of cardiomyocyte death caused by H/R and suppressed of myocardial necrosis in I/R injured mouse heart, which was accompanied by a marked reduction of myocardial infarction size and improved cardiac function. Mechanistically, CNEACR directly binds to histone deacetylase (HDAC7) in the cytoplasm and interferes its nuclear entry. This leads to attenuation of HDAC7-dependent suppression of forkhead box protein A2 (Foxa2) transcription, which can repress receptor-interacting protein kinase 3 (Ripk3) gene by binding to its promoter region. In addition, CNEACR-mediated upregulation of FOXA2 inhibited RIPK3-dependent necrotic/necroptotic death of cardiomyocytes. Our study reveals that circRNAs such as CNEACR can regulate the cardiomyocyte necroptosis associated activity of HDACs, promotes cell survival and improves cardiac function in I/R-injured heart. Hence, the CNEACR/HDAC7/Foxa2/ RIPK3 axis could be an efficient target for alleviating myocardial damage caused by necroptotic death in ischemia heart diseases.
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Affiliation(s)
- Xiang-Qian Gao
- grid.412521.10000 0004 1769 1119Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, 266021 Qingdao, China ,grid.452240.50000 0004 8342 6962Department of Pathology, Binzhou Medical University Hospital, 256603 Binzhou, China
| | - Cui-Yun Liu
- grid.412521.10000 0004 1769 1119Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, 266021 Qingdao, China
| | - Yu-Hui Zhang
- grid.506261.60000 0001 0706 7839State Key Laboratory of Cardiovascular Disease, Heart Failure center, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences, Peking Union Medical College, 100037 Beijing, China
| | - Yun-Hong Wang
- grid.506261.60000 0001 0706 7839State Key Laboratory of Cardiovascular Disease, Heart Failure center, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences, Peking Union Medical College, 100037 Beijing, China
| | - Lu-Yu Zhou
- grid.412521.10000 0004 1769 1119Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, 266021 Qingdao, China
| | - Xin-Min Li
- grid.412521.10000 0004 1769 1119Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, 266021 Qingdao, China
| | - Kai Wang
- grid.412521.10000 0004 1769 1119Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, 266021 Qingdao, China
| | - Xin-Zhe Chen
- grid.412521.10000 0004 1769 1119Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, 266021 Qingdao, China
| | - Tao Wang
- grid.412521.10000 0004 1769 1119Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, 266021 Qingdao, China
| | - Jie Ju
- grid.412521.10000 0004 1769 1119Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, 266021 Qingdao, China
| | - Fei Wang
- grid.412521.10000 0004 1769 1119Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, 266021 Qingdao, China
| | - Shao-Cong Wang
- grid.412521.10000 0004 1769 1119Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, 266021 Qingdao, China
| | - Yin Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, 266021, Qingdao, China.
| | - Zhao-Yang Chen
- Cardiology department, Heart center of Fujian Province, Union Hospital, Fujian Medical University, 29 Xin-Quan Road, 350001, Fuzhou, China.
| | - Kun Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, 266021, Qingdao, China.
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12
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Zhou B, Stueve TR, Mihalakakos EA, Miao L, Mullen D, Wang Y, Liu Y, Luo J, Tran E, Siegmund KD, Lynch SK, Ryan AL, Offringa IA, Borok Z, Marconett CN. Comprehensive epigenomic profiling of human alveolar epithelial differentiation identifies key epigenetic states and transcription factor co-regulatory networks for maintenance of distal lung identity. BMC Genomics 2021; 22:906. [PMID: 34922464 PMCID: PMC8684104 DOI: 10.1186/s12864-021-08152-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 11/05/2021] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Disruption of alveolar epithelial cell (AEC) differentiation is implicated in distal lung diseases such as chronic obstructive pulmonary disease, idiopathic pulmonary fibrosis, and lung adenocarcinoma that impact morbidity and mortality worldwide. Elucidating underlying disease pathogenesis requires a mechanistic molecular understanding of AEC differentiation. Previous studies have focused on changes of individual transcription factors, and to date no study has comprehensively characterized the dynamic, global epigenomic alterations that facilitate this critical differentiation process in humans. RESULTS We comprehensively profiled the epigenomic states of human AECs during type 2 to type 1-like cell differentiation, including the methylome and chromatin functional domains, and integrated this with transcriptome-wide RNA expression data. Enhancer regions were drastically altered during AEC differentiation. Transcription factor binding analysis within enhancer regions revealed diverse interactive networks with enrichment for many transcription factors, including NKX2-1 and FOXA family members, as well as transcription factors with less well characterized roles in AEC differentiation, such as members of the MEF2, TEAD, and AP1 families. Additionally, associations among transcription factors changed during differentiation, implicating a complex network of heterotrimeric complex switching in driving differentiation. Integration of AEC enhancer states with the catalog of enhancer elements in the Roadmap Epigenomics Mapping Consortium and Encyclopedia of DNA Elements (ENCODE) revealed that AECs have similar epigenomic structures to other profiled epithelial cell types, including human mammary epithelial cells (HMECs), with NKX2-1 serving as a distinguishing feature of distal lung differentiation. CONCLUSIONS Enhancer regions are hotspots of epigenomic alteration that regulate AEC differentiation. Furthermore, the differentiation process is regulated by dynamic networks of transcription factors acting in concert, rather than individually. These findings provide a roadmap for understanding the relationship between disruption of the epigenetic state during AEC differentiation and development of lung diseases that may be therapeutically amenable.
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Affiliation(s)
- B Zhou
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90089, USA
- Hastings Center for Pulmonary Research, University of Southern California, Los Angeles, CA, 90089, USA
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - T R Stueve
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
- Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90089, USA
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90089, USA
| | - E A Mihalakakos
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
- Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90089, USA
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90089, USA
| | - L Miao
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
- Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90089, USA
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90089, USA
| | - D Mullen
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
- Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90089, USA
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90089, USA
| | - Y Wang
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
- Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90089, USA
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90089, USA
| | - Y Liu
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90089, USA
| | - J Luo
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90089, USA
| | - E Tran
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
- Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90089, USA
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90089, USA
| | - K D Siegmund
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90089, USA
| | - S K Lynch
- Department of Engineering, Test Manufacturing Group, MAXIM Integrated Products, Sunnyvale, CA, 95134, USA
| | - A L Ryan
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90089, USA
- Hastings Center for Pulmonary Research, University of Southern California, Los Angeles, CA, 90089, USA
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90089, USA
| | - I A Offringa
- Hastings Center for Pulmonary Research, University of Southern California, Los Angeles, CA, 90089, USA
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
- Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90089, USA
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90089, USA
| | - Z Borok
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90089, USA
- Hastings Center for Pulmonary Research, University of Southern California, Los Angeles, CA, 90089, USA
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90089, USA
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - C N Marconett
- Hastings Center for Pulmonary Research, University of Southern California, Los Angeles, CA, 90089, USA.
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA.
- Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90089, USA.
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90089, USA.
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13
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Yang X, Cao N, Chen L, Liu L, Zhang M, Cao Y. Suppression of Cell Tumorigenicity by Non-neural Pro-differentiation Factors via Inhibition of Neural Property in Tumorigenic Cells. Front Cell Dev Biol 2021; 9:714383. [PMID: 34595169 PMCID: PMC8476888 DOI: 10.3389/fcell.2021.714383] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 08/16/2021] [Indexed: 11/13/2022] Open
Abstract
Our studies have demonstrated that cell tumorigenicity and pluripotent differentiation potential stem from neural stemness or a neural ground state, which is defined by a regulatory network of higher levels of machineries for basic cell physiological functions, including cell cycle, ribosome biogenesis, protein translation, spliceosome, epigenetic modification factors, reprogramming factors, etc., in addition to the neural stemness specific factors. These machineries and neural stemness factors mostly play cancer-promoting roles. It can be deduced that differentiation requires the repression of neural ground state and causes the reduction or loss of neural ground state and thus tumorigenicity in tumorigenic cells. Formerly, we showed that neuronal differentiation led to reduced tumorigenicity in tumorigenic cells. In the present study, we show that non-neural pro-differentiation factors, such as GATA3, HNF4A, HHEX, and FOXA3 that specify mesodermal or/and endodermal tissues during vertebrate embryogenesis, suppress tumorigenicity via repression of neural stemness and promotion of non-neural property in tumorigenic cells. Mechanistically, these transcription factors repress the transcription of neural enriched genes and meanwhile activate genes that specify non-neural properties via direct binding to the promoters of these genes. We also show that combined expression of HHEX and FOXA3 suppresses tumorigenesis effectively in the AOM/DSS model of colitis-associated cancer. We suggest that targeting the property of neural stemness could be an effective strategy for cancer therapy.
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Affiliation(s)
- Xiaoli Yang
- Shenzhen Research Institute of Nanjing University, Shenzhen, China
- MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, Nanjing University, Nanjing, China
- Jiangsu Key Laboratory of Molecular Medicine of Medical School, Nanjing University, Nanjing, China
| | - Ning Cao
- Shenzhen Research Institute of Nanjing University, Shenzhen, China
- MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, Nanjing University, Nanjing, China
- Jiangsu Key Laboratory of Molecular Medicine of Medical School, Nanjing University, Nanjing, China
| | - Lu Chen
- Shenzhen Research Institute of Nanjing University, Shenzhen, China
- MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, Nanjing University, Nanjing, China
- Jiangsu Key Laboratory of Molecular Medicine of Medical School, Nanjing University, Nanjing, China
| | - Lin Liu
- MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, Nanjing University, Nanjing, China
- Jiangsu Key Laboratory of Molecular Medicine of Medical School, Nanjing University, Nanjing, China
| | - Min Zhang
- Shenzhen Research Institute of Nanjing University, Shenzhen, China
- MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, Nanjing University, Nanjing, China
- Jiangsu Key Laboratory of Molecular Medicine of Medical School, Nanjing University, Nanjing, China
| | - Ying Cao
- Shenzhen Research Institute of Nanjing University, Shenzhen, China
- MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, Nanjing University, Nanjing, China
- Jiangsu Key Laboratory of Molecular Medicine of Medical School, Nanjing University, Nanjing, China
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14
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Kimura R, Otani T, Shiraishi N, Hagiyama M, Yoneshige A, Wada A, Kajiyama H, Takeuchi F, Mizuguchi N, Morishita K, Ito A. Expression of cell adhesion molecule 1 in human and murine endometrial glandular cells and its increase during the proliferative phase by estrogen and cell density. Life Sci 2021; 283:119854. [PMID: 34332980 DOI: 10.1016/j.lfs.2021.119854] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 07/14/2021] [Accepted: 07/22/2021] [Indexed: 10/20/2022]
Abstract
AIMS Cell adhesion molecule 1 (CADM1) mediates interepithelial adhesion and is upregulated in crowded epithelial monolayers. This study aimed to examine CADM1 expression in the human endometrium of proliferative and secretory phases, and its transcriptional regulation in terms of estrogen stimuli and higher cellularity. MAIN METHODS CADM1 immunohistochemistry was conducted on endometrial tissues from women in their 40s and adult mice subcutaneously injected with estradiol following ovariectomy. Dual-luciferase reporter assays were conducted using human endometrial HEC-50B and HEC-1B cells and reporter plasmids harboring the human CADM1 3.4-kb promoter and its deleted and mutated forms. Cells were transfected with estrogen receptor α cDNA and reporter plasmids, and treated with estradiol before luciferase activity measurement. KEY FINDINGS Immunohistochemistry revealed that CADM1 was clearly expressed on the lateral membranes of the simple columnar glandular cells in the proliferative phase, but not in the secretory phase, from both women and the mouse model. The glandular cell density increased two-fold in the proliferative phase. Reporter assays identified three Sp1-binding sites as estradiol-responsive elements in the proximal region (from -223 to -84) of the transcription start site (+1) in HEC-50B cells. When the cell culture was started at eight-fold higher cell density, the CADM1 3.4-kb promoter was transactivated at a two-fold higher level in HEC-50B cells. This cell density effect was not detected for the CADM1 2.3-kb or 1.6-kb promoter. SIGNIFICANCE Two (proximal and distal) promoter regions are suggested to function additively to transactivate CADM1 in endometrial glandular cells that crowd in the proliferative phase.
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Affiliation(s)
- Ryuichiro Kimura
- Department of Pathology, Kindai University Faculty of Medicine, 377-2 Ohno-higashi, Osaka-sayama, Osaka 589-8511, Japan
| | - Tomoyuki Otani
- Department of Pathology, Kindai University Faculty of Medicine, 377-2 Ohno-higashi, Osaka-sayama, Osaka 589-8511, Japan
| | - Naoki Shiraishi
- Genome Medical Center, Kindai University Hospital, Osaka, Japan
| | - Man Hagiyama
- Department of Pathology, Kindai University Faculty of Medicine, 377-2 Ohno-higashi, Osaka-sayama, Osaka 589-8511, Japan
| | - Azusa Yoneshige
- Department of Pathology, Kindai University Faculty of Medicine, 377-2 Ohno-higashi, Osaka-sayama, Osaka 589-8511, Japan
| | - Akihiro Wada
- Department of Pathology, Kindai University Faculty of Medicine, 377-2 Ohno-higashi, Osaka-sayama, Osaka 589-8511, Japan
| | - Hiroshi Kajiyama
- Department of Pathology, Kindai University Faculty of Medicine, 377-2 Ohno-higashi, Osaka-sayama, Osaka 589-8511, Japan
| | - Fuka Takeuchi
- Department of Pathology, Kindai University Faculty of Medicine, 377-2 Ohno-higashi, Osaka-sayama, Osaka 589-8511, Japan
| | | | - Kazuhiro Morishita
- Division of Tumor and Cellular Biochemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Akihiko Ito
- Department of Pathology, Kindai University Faculty of Medicine, 377-2 Ohno-higashi, Osaka-sayama, Osaka 589-8511, Japan.
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15
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Biswas A, Narlikar L. Resolving diverse protein-DNA footprints from exonuclease-based ChIP experiments. Bioinformatics 2021; 37:i367-i375. [PMID: 34252930 PMCID: PMC8275329 DOI: 10.1093/bioinformatics/btab274] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
MOTIVATION High-throughput chromatin immunoprecipitation (ChIP) sequencing-based assays capture genomic regions associated with the profiled transcription factor (TF). ChIP-exo is a modified protocol, which uses lambda exonuclease to digest DNA close to the TF-DNA complex, in order to improve on the positional resolution of the TF-DNA contact. Because the digestion occurs in the 5'-3' orientation, the protocol produces directional footprints close to the complex, on both sides of the double stranded DNA. Like all ChIP-based methods, ChIP-exo reports a mixture of different regions associated with the TF: those bound directly to the TF as well as via intermediaries. However, the distribution of footprints are likely to be indicative of the complex forming at the DNA. RESULTS We present ExoDiversity, which uses a model-based framework to learn a joint distribution over footprints and motifs, thus resolving the mixture of ChIP-exo footprints into diverse binding modes. It uses no prior motif or TF information and automatically learns the number of different modes from the data. We show its application on a wide range of TFs and organisms/cell-types. Because its goal is to explain the complete set of reported regions, it is able to identify co-factor TF motifs that appear in a small fraction of the dataset. Further, ExoDiversity discovers small nucleotide variations within and outside canonical motifs, which co-occur with variations in footprints, suggesting that the TF-DNA structural configuration at those regions is likely to be different. Finally, we show that detected modes have specific DNA shape features and conservation signals, giving insights into the structure and function of the putative TF-DNA complexes. AVAILABILITY AND IMPLEMENTATION The code for ExoDiversity is available on https://github.com/NarlikarLab/exoDIVERSITY. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Anushua Biswas
- Department of Chemical Engineering, CSIR-National Chemical Laboratory, Pune 411008, India.,Academy of Scientific and Innovative Research, Ghaziabad 201002, India
| | - Leelavati Narlikar
- Department of Chemical Engineering, CSIR-National Chemical Laboratory, Pune 411008, India.,Academy of Scientific and Innovative Research, Ghaziabad 201002, India
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16
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m6A RNA methylation-mediated HNF3γ reduction renders hepatocellular carcinoma dedifferentiation and sorafenib resistance. Signal Transduct Target Ther 2020; 5:296. [PMID: 33361765 PMCID: PMC7762754 DOI: 10.1038/s41392-020-00299-0] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Revised: 07/07/2020] [Accepted: 08/17/2020] [Indexed: 12/12/2022] Open
Abstract
Hepatocyte nuclear factor 3γ (HNF3γ) is a hepatocyte nuclear factor, but its role and clinical significance in hepatocellular carcinoma (HCC) remain unclear. Herein, we report that HNF3γ expression is downregulated in patient HCC and inversely correlated with HCC malignancy and patient survival. Moreover, our data suggested that the HNF3γ reduction in HCC could be mediated by METTL14-dependent m6A methylation of HNF3γ mRNA. HNF3γ expression was increased during hepatic differentiation and decreased in dedifferentiated HCC cells. Interestingly, HNF3γ delivery promoted differentiation of not only HCC cells but also liver CSCs, which led to suppression of HCC growth. Mechanistic analysis suggested an HNF3γ-centered regulatory network that includes essential liver differentiation-associated transcription factors and functional molecules, which could synergistically facilitate HCC cell differentiation. More importantly, enforced HNF3γ expression sensitized HCC cells to sorafenib-induced growth inhibition and cell apoptosis through transactivation of OATP1B1 and OATP1B3 expression, which are major membrane transporters for sorafenib uptake. Clinical investigation showed that patient-derived HCC xenografts with high HNF3γ expression exhibited a sorafenib response and patients with high HCC HNF3γ levels benefited from sorafenib therapy. Together, these results suggest that HNF3γ plays an essential role in HCC differentiation and may serve as a therapeutic target and predictor of sorafenib benefit in patients.
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17
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Lazar SB, Pongor L, Li XL, Grammatikakis I, Muys BR, Dangelmaier EA, Redon CE, Jang SM, Walker RL, Tang W, Ambs S, Harris CC, Meltzer PS, Aladjem MI, Lal A. Genome-Wide Analysis of the FOXA1 Transcriptional Network Identifies Novel Protein-Coding and Long Noncoding RNA Targets in Colorectal Cancer Cells. Mol Cell Biol 2020; 40:e00224-20. [PMID: 32839292 PMCID: PMC7556848 DOI: 10.1128/mcb.00224-20] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 06/12/2020] [Accepted: 08/17/2020] [Indexed: 02/06/2023] Open
Abstract
Differentiation status of tumors is correlated with metastatic potential and malignancy. FOXA1 (forkhead box A1) is a transcription factor known to regulate differentiation in certain tissues. Here, we investigate FOXA1 function in human colorectal cancer (CRC). We found that FOXA1 is robustly expressed in the normal human colon but significantly downregulated in colon adenocarcinoma. Applying FOXA1 chromatin immunoprecipitation coupled with deep sequencing and transcriptome analysis upon FOXA1 knockdown in well-differentiated CRC cells and FOXA1 overexpression in poorly differentiated CRC cells, we identified novel protein-coding and lncRNA genes regulated by FOXA1. Among the numerous novel FOXA1 targets we identified, we focused on CEACAM5, a tumor marker and facilitator of cell adhesion. We show that FOXA1 binds to a distal enhancer downstream of CEACAM5 and strongly activates its expression. Consistent with these data, we show that FOXA1 inhibits anoikis in CRC cells. Collectively, our results uncover novel protein-coding and noncoding targets of FOXA1 and suggest a vital role of FOXA1 in enhancing CEACAM5 expression and anoikis resistance in CRC cells.
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Affiliation(s)
- Sarah B Lazar
- Regulatory RNAs and Cancer Section, Genetics Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland, USA
| | - Lorinc Pongor
- Developmental Therapeutics Branch, Laboratory of Molecular Pharmacology, CCR, NCI, NIH, Bethesda, Maryland, USA
| | - Xiao Ling Li
- Regulatory RNAs and Cancer Section, Genetics Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland, USA
| | - Ioannis Grammatikakis
- Regulatory RNAs and Cancer Section, Genetics Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland, USA
| | - Bruna R Muys
- Regulatory RNAs and Cancer Section, Genetics Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland, USA
| | - Emily A Dangelmaier
- Regulatory RNAs and Cancer Section, Genetics Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland, USA
| | - Christophe E Redon
- Developmental Therapeutics Branch, Laboratory of Molecular Pharmacology, CCR, NCI, NIH, Bethesda, Maryland, USA
| | - Sang-Min Jang
- Developmental Therapeutics Branch, Laboratory of Molecular Pharmacology, CCR, NCI, NIH, Bethesda, Maryland, USA
| | - Robert L Walker
- Molecular Genetics Section, Genetics Branch, CCR, NCI, NIH, Bethesda, Maryland, USA
| | - Wei Tang
- Molecular Epidemiology Section, Laboratory of Human Carcinogenesis, CCR, NCI, NIH, Bethesda, Maryland, USA
| | - Stefan Ambs
- Molecular Epidemiology Section, Laboratory of Human Carcinogenesis, CCR, NCI, NIH, Bethesda, Maryland, USA
| | - Curtis C Harris
- Molecular Genetics and Carcinogenesis Section, Laboratory of Human Carcinogenesis, CCR, NCI, NIH, Bethesda, Maryland, USA
| | - Paul S Meltzer
- Molecular Genetics Section, Genetics Branch, CCR, NCI, NIH, Bethesda, Maryland, USA
| | - Mirit I Aladjem
- Developmental Therapeutics Branch, Laboratory of Molecular Pharmacology, CCR, NCI, NIH, Bethesda, Maryland, USA
| | - Ashish Lal
- Regulatory RNAs and Cancer Section, Genetics Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland, USA
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Xia Z, Su Y, Petersen P, Qi L, Kim AE, Figueiredo JC, Lin Y, Nan H, Sakoda LC, Albanes D, Berndt SI, Bézieau S, Bien S, Buchanan DD, Casey G, Chan AT, Conti DV, Drew DA, Gallinger SJ, Gauderman WJ, Giles GG, Gruber SB, Gunter MJ, Hoffmeister M, Jenkins MA, Joshi AD, Le Marchand L, Lewinger JP, Li L, Lindor NM, Moreno V, Murphy N, Nassir R, Newcomb PA, Ogino S, Rennert G, Song M, Wang X, Wolk A, Woods MO, Brenner H, White E, Slattery ML, Giovannucci EL, Chang‐Claude J, Pharoah PDP, Hsu L, Campbell PT, Peters U. Functional informed genome-wide interaction analysis of body mass index, diabetes and colorectal cancer risk. Cancer Med 2020; 9:3563-3573. [PMID: 32207560 PMCID: PMC7221445 DOI: 10.1002/cam4.2971] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 01/28/2020] [Accepted: 02/21/2020] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Body mass index (BMI) and diabetes are established risk factors for colorectal cancer (CRC), likely through perturbations in metabolic traits (e.g. insulin resistance and glucose homeostasis). Identification of interactions between variation in genes and these metabolic risk factors may identify novel biologic insights into CRC etiology. METHODS To improve statistical power and interpretation for gene-environment interaction (G × E) testing, we tested genetic variants that regulate expression of a gene together for interaction with BMI (kg/m2 ) and diabetes on CRC risk among 26 017 cases and 20 692 controls. Each variant was weighted based on PrediXcan analysis of gene expression data from colon tissue generated in the Genotype-Tissue Expression Project for all genes with heritability ≥1%. We used a mixed-effects model to jointly measure the G × E interaction in a gene by partitioning the interactions into the predicted gene expression levels (fixed effects), and residual G × E effects (random effects). G × BMI analyses were stratified by sex as BMI-CRC associations differ by sex. We used false discovery rates to account for multiple comparisons and reported all results with FDR <0.2. RESULTS Among 4839 genes tested, genetically predicted expressions of FOXA1 (P = 3.15 × 10-5 ), PSMC5 (P = 4.51 × 10-4 ) and CD33 (P = 2.71 × 10-4 ) modified the association of BMI on CRC risk for men; KIAA0753 (P = 2.29 × 10-5 ) and SCN1B (P = 2.76 × 10-4 ) modified the association of BMI on CRC risk for women; and PTPN2 modified the association between diabetes and CRC risk in both sexes (P = 2.31 × 10-5 ). CONCLUSIONS Aggregating G × E interactions and incorporating functional information, we discovered novel genes that may interact with BMI and diabetes on CRC risk.
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19
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Milan M, Balestrieri C, Alfarano G, Polletti S, Prosperini E, Spaggiari P, Zerbi A, Diaferia GR, Natoli G. FOXA2 controls the cis-regulatory networks of pancreatic cancer cells in a differentiation grade-specific manner. EMBO J 2019; 38:e102161. [PMID: 31531882 PMCID: PMC6792020 DOI: 10.15252/embj.2019102161] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 08/09/2019] [Accepted: 08/12/2019] [Indexed: 01/04/2023] Open
Abstract
Differentiation of normal and tumor cells is controlled by regulatory networks enforced by lineage-determining transcription factors (TFs). Among them, TFs such as FOXA1/2 bind naïve chromatin and induce its accessibility, thus establishing new gene regulatory networks. Pancreatic ductal adenocarcinoma (PDAC) is characterized by the coexistence of well- and poorly differentiated cells at all stages of disease. How the transcriptional networks determining such massive cellular heterogeneity are established remains to be determined. We found that FOXA2, a TF controlling pancreas specification, broadly contributed to the cis-regulatory networks of PDACs. Despite being expressed in both well- and poorly differentiated PDAC cells, FOXA2 displayed extensively different genomic distributions and controlled distinct gene expression programs. Grade-specific functions of FOXA2 depended on its partnership with TFs whose expression varied depending on the differentiation grade. These data suggest that FOXA2 contributes to the regulatory networks of heterogeneous PDAC cells via interactions with alternative partner TFs.
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Affiliation(s)
- Marta Milan
- Humanitas UniversityMilanoItaly
- Humanitas Clinical Research Center IRCCSMilanoItaly
- Department of Experimental OncologyIEO, European Institute of Oncology IRCCSMilanoItaly
| | - Chiara Balestrieri
- Humanitas UniversityMilanoItaly
- Humanitas Clinical Research Center IRCCSMilanoItaly
| | - Gabriele Alfarano
- Humanitas UniversityMilanoItaly
- Humanitas Clinical Research Center IRCCSMilanoItaly
| | - Sara Polletti
- Humanitas UniversityMilanoItaly
- Humanitas Clinical Research Center IRCCSMilanoItaly
| | - Elena Prosperini
- Humanitas UniversityMilanoItaly
- Humanitas Clinical Research Center IRCCSMilanoItaly
| | | | - Alessandro Zerbi
- Humanitas UniversityMilanoItaly
- Humanitas Clinical Research Center IRCCSMilanoItaly
| | - Giuseppe R Diaferia
- Department of Experimental OncologyIEO, European Institute of Oncology IRCCSMilanoItaly
| | - Gioacchino Natoli
- Humanitas UniversityMilanoItaly
- Humanitas Clinical Research Center IRCCSMilanoItaly
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20
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Iterative integrated imputation for missing data and pathway models with applications to breast cancer subtypes. COMMUNICATIONS FOR STATISTICAL APPLICATIONS AND METHODS 2019. [DOI: 10.29220/csam.2019.26.4.411] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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21
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Shahabi S, Kumaran V, Castillo J, Cong Z, Nandagopal G, Mullen DJ, Alvarado A, Correa MR, Saizan A, Goel R, Bhat A, Lynch SK, Zhou B, Borok Z, Marconett CN. LINC00261 Is an Epigenetically Regulated Tumor Suppressor Essential for Activation of the DNA Damage Response. Cancer Res 2019; 79:3050-3062. [PMID: 30796052 DOI: 10.1158/0008-5472.can-18-2034] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 12/21/2018] [Accepted: 02/15/2019] [Indexed: 02/06/2023]
Abstract
Lung cancer is the leading cause of cancer-related death in the United States. Long noncoding RNAs (lncRNA) are a class of regulatory molecules whose role in lung carcinogenesis is poorly understood. In this study, we profiled lncRNA expression in lung adenocarcinoma (LUAD) cell lines, compared their expression with that of purified alveolar epithelial type II cells (the purported cell of origin for LUAD), cross-referenced these with lncRNAs altered in the primary human tumors, and interrogated for lncRNAs whose expression correlated with patient survival. We identified LINC00261, a lncRNA with unknown function in LUAD, adjacent to the pioneering transcription factor FOXA2. Loss of LINC00261 was observed in multiple tumor types, including liver, breast, and gastric cancer. Reintroduction of LINC00261 into human LUAD cell lines inhibited cell migration and slowed proliferation by inducing G2-M cell-cycle arrest, while upregulating DNA damage pathway genes and inducing phosphorylation-mediated activation of components of the DNA damage pathway. FOXA2 was able to induce LINC00261 expression, and the entire locus underwent hypermethylation in LUAD, leading to loss of expression. We have thus identified an epigenetically deregulated lncRNA, whose loss of expression in LUAD promotes the malignant phenotype and blocks activation of the DNA damage machinery, predisposing lung cells to cancer development. SIGNIFICANCE: These findings identify LINC00261 as a tumor suppressor that blocks cellular proliferation by activating the DNA damage response and suggest that epigenetic therapy to inhibit DNA methylation may enhance treatment of LUAD. GRAPHICAL ABSTRACT: http://cancerres.aacrjournals.org/content/canres/79/12/3050/F1.large.jpg.See related commentary by Davalos and Esteller, p. 3028.
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Affiliation(s)
- Shandy Shahabi
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Vishaly Kumaran
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Jonathan Castillo
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California.,Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, California.,Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Zhengmin Cong
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Gopika Nandagopal
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Daniel J Mullen
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California.,Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, California.,Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Alexander Alvarado
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Michele Ramos Correa
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Autumn Saizan
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Riya Goel
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Amrita Bhat
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Sean K Lynch
- Department of Product Engineering, Division of Manufacturing Operations, MAXIM Integrated Products, Sunnyvale, California
| | - Beiyun Zhou
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California.,Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California.,Hastings Center for Pulmonary Research, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Zea Borok
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California.,Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California.,Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California.,Hastings Center for Pulmonary Research, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Crystal N Marconett
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California. .,Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, California.,Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California
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22
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Wang AW, Wangensteen KJ, Wang YJ, Zahm AM, Moss NG, Erez N, Kaestner KH. TRAP-seq identifies cystine/glutamate antiporter as a driver of recovery from liver injury. J Clin Invest 2018. [PMID: 29517978 DOI: 10.1172/jci95120] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Understanding the molecular basis of the regenerative response following hepatic injury holds promise for improved treatment of liver diseases. Here, we report an innovative method to profile gene expression specifically in the hepatocytes that regenerate the liver following toxic injury. We used the Fah-/- mouse, a model of hereditary tyrosinemia, which conditionally undergoes severe liver injury unless fumarylacetoacetate hydrolase (FAH) expression is reconstituted ectopically. We used translating ribosome affinity purification followed by high-throughput RNA sequencing (TRAP-seq) to isolate mRNAs specific to repopulating hepatocytes. We uncovered upstream regulators and important signaling pathways that are highly enriched in genes changed in regenerating hepatocytes. Specifically, we found that glutathione metabolism, particularly the gene Slc7a11 encoding the cystine/glutamate antiporter (xCT), is massively upregulated during liver regeneration. Furthermore, we show that Slc7a11 overexpression in hepatocytes enhances, and its suppression inhibits, repopulation following toxic injury. TRAP-seq allows cell type-specific expression profiling in repopulating hepatocytes and identified xCT, a factor that supports antioxidant responses during liver regeneration. xCT has potential as a therapeutic target for enhancing liver regeneration in response to liver injury.
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Affiliation(s)
| | - Kirk J Wangensteen
- Department of Genetics and.,Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | | | | | | | - Noam Erez
- Department of Genetics and.,Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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23
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Gérard C, Tys J, Lemaigre FP. Gene regulatory networks in differentiation and direct reprogramming of hepatic cells. Semin Cell Dev Biol 2016; 66:43-50. [PMID: 27979774 DOI: 10.1016/j.semcdb.2016.12.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 12/07/2016] [Indexed: 12/14/2022]
Abstract
Liver development proceeds by sequential steps during which gene regulatory networks (GRNs) determine differentiation and maturation of hepatic cells. Characterizing the architecture and dynamics of these networks is essential for understanding how cell fate decisions are made during development, and for recapitulating these processes during in vitro production of liver cells for toxicology studies, disease modelling and regenerative therapy. Here we review the GRNs that control key steps of liver development and lead to differentiation of hepatocytes and cholangiocytes in mammals. We focus on GRNs determining cell fate decisions and analyse subcircuitry motifs that may confer specific dynamic properties to the networks. Finally, we put our analysis in the perspective of recent attempts to directly reprogram cells to hepatocytes by forced expression of transcription factors.
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Affiliation(s)
- Claude Gérard
- Université catholique de Louvain, de Duve Institute, Avenue Hippocrate 75, 1200 Brussels, Belgium.
| | - Janne Tys
- Université catholique de Louvain, de Duve Institute, Avenue Hippocrate 75, 1200 Brussels, Belgium.
| | - Frédéric P Lemaigre
- Université catholique de Louvain, de Duve Institute, Avenue Hippocrate 75, 1200 Brussels, Belgium.
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24
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McKenzie AT, Katsyv I, Song WM, Wang M, Zhang B. DGCA: A comprehensive R package for Differential Gene Correlation Analysis. BMC SYSTEMS BIOLOGY 2016; 10:106. [PMID: 27846853 PMCID: PMC5111277 DOI: 10.1186/s12918-016-0349-1] [Citation(s) in RCA: 140] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 11/03/2016] [Indexed: 12/31/2022]
Abstract
BACKGROUND Dissecting the regulatory relationships between genes is a critical step towards building accurate predictive models of biological systems. A powerful approach towards this end is to systematically study the differences in correlation between gene pairs in more than one distinct condition. RESULTS In this study we develop an R package, DGCA (for Differential Gene Correlation Analysis), which offers a suite of tools for computing and analyzing differential correlations between gene pairs across multiple conditions. To minimize parametric assumptions, DGCA computes empirical p-values via permutation testing. To understand differential correlations at a systems level, DGCA performs higher-order analyses such as measuring the average difference in correlation and multiscale clustering analysis of differential correlation networks. Through a simulation study, we show that the straightforward z-score based method that DGCA employs significantly outperforms the existing alternative methods for calculating differential correlation. Application of DGCA to the TCGA RNA-seq data in breast cancer not only identifies key changes in the regulatory relationships between TP53 and PTEN and their target genes in the presence of inactivating mutations, but also reveals an immune-related differential correlation module that is specific to triple negative breast cancer (TNBC). CONCLUSIONS DGCA is an R package for systematically assessing the difference in gene-gene regulatory relationships under different conditions. This user-friendly, effective, and comprehensive software tool will greatly facilitate the application of differential correlation analysis in many biological studies and thus will help identification of novel signaling pathways, biomarkers, and targets in complex biological systems and diseases.
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Affiliation(s)
- Andrew T. McKenzie
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029 USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029 USA
- Medical Scientist Training Program, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029 USA
| | - Igor Katsyv
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029 USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029 USA
- Medical Scientist Training Program, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029 USA
| | - Won-Min Song
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029 USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029 USA
| | - Minghui Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029 USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029 USA
| | - Bin Zhang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029 USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029 USA
- Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
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25
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Palierne G, Fabre A, Solinhac R, Le Péron C, Avner S, Lenfant F, Fontaine C, Salbert G, Flouriot G, Arnal JF, Métivier R. Changes in Gene Expression and Estrogen Receptor Cistrome in Mouse Liver Upon Acute E2 Treatment. Mol Endocrinol 2016; 30:709-32. [PMID: 27164166 DOI: 10.1210/me.2015-1311] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Transcriptional regulation by the estrogen receptor-α (ER) has been investigated mainly in breast cancer cell lines, but estrogens such as 17β-estradiol (E2) exert numerous extrareproductive effects, particularly in the liver, where E2 exhibits both protective metabolic and deleterious thrombotic actions. To analyze the direct and early transcriptional effects of estrogens in the liver, we determined the E2-sensitive transcriptome and ER cistrome in mice after acute administration of E2 or placebo. These analyses revealed the early induction of genes involved in lipid metabolism, which fits with the crucial role of ER in the prevention of liver steatosis. Characterization of the chromatin state of ER binding sites (BSs) in mice expressing or not ER demonstrated that ER is not required per se for the establishment and/or maintenance of chromatin modifications at the majority of its BSs. This is presumably a consequence of a strong overlap between ER and hepatocyte nuclear factor 4α BSs. In contrast, 40% of the BSs of the pioneer factor forkhead box protein a (Foxa2) were dependent upon ER expression, and ER expression also affected the distribution of nucleosomes harboring dimethylated lysine 4 of Histone H3 around Foxa2 BSs. We finally show that, in addition to a network of liver-specific transcription factors including CCAAT/enhancer-binding protein and hepatocyte nuclear factor 4α, ER might be required for proper Foxa2 function in this tissue.
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Affiliation(s)
- Gaëlle Palierne
- Equipe Spatio-Temporal Regulation of Transcription in Eukaryotes (SP@RTE) (G.P., C.L.P., S.A., G.S., R.M.), Unité Mixte de Recherche 6290 Centre National de la Recherche Scientifique (Institut de Genétique et Développement de Rennes), Université de Rennes 1, Campus de Beaulieu, and Equipe Transcription, Environment and Cancer (TREC) (G.F.), Inserm U1085-Institut de Recherche en Santé, Environnement et Travail, Rennes 35042 Cedex, France; and Equipe 9 "Estrogen Receptor: In Vivo Dissection and Modulation" (A.F., R.S., F.L., C.F., J.-F.A.), Inserm Unité 1048 (Institut des Maladies Métaboliques et Cardiovasculaires), Toulouse 31432 Cedex 4, France
| | - Aurélie Fabre
- Equipe Spatio-Temporal Regulation of Transcription in Eukaryotes (SP@RTE) (G.P., C.L.P., S.A., G.S., R.M.), Unité Mixte de Recherche 6290 Centre National de la Recherche Scientifique (Institut de Genétique et Développement de Rennes), Université de Rennes 1, Campus de Beaulieu, and Equipe Transcription, Environment and Cancer (TREC) (G.F.), Inserm U1085-Institut de Recherche en Santé, Environnement et Travail, Rennes 35042 Cedex, France; and Equipe 9 "Estrogen Receptor: In Vivo Dissection and Modulation" (A.F., R.S., F.L., C.F., J.-F.A.), Inserm Unité 1048 (Institut des Maladies Métaboliques et Cardiovasculaires), Toulouse 31432 Cedex 4, France
| | - Romain Solinhac
- Equipe Spatio-Temporal Regulation of Transcription in Eukaryotes (SP@RTE) (G.P., C.L.P., S.A., G.S., R.M.), Unité Mixte de Recherche 6290 Centre National de la Recherche Scientifique (Institut de Genétique et Développement de Rennes), Université de Rennes 1, Campus de Beaulieu, and Equipe Transcription, Environment and Cancer (TREC) (G.F.), Inserm U1085-Institut de Recherche en Santé, Environnement et Travail, Rennes 35042 Cedex, France; and Equipe 9 "Estrogen Receptor: In Vivo Dissection and Modulation" (A.F., R.S., F.L., C.F., J.-F.A.), Inserm Unité 1048 (Institut des Maladies Métaboliques et Cardiovasculaires), Toulouse 31432 Cedex 4, France
| | - Christine Le Péron
- Equipe Spatio-Temporal Regulation of Transcription in Eukaryotes (SP@RTE) (G.P., C.L.P., S.A., G.S., R.M.), Unité Mixte de Recherche 6290 Centre National de la Recherche Scientifique (Institut de Genétique et Développement de Rennes), Université de Rennes 1, Campus de Beaulieu, and Equipe Transcription, Environment and Cancer (TREC) (G.F.), Inserm U1085-Institut de Recherche en Santé, Environnement et Travail, Rennes 35042 Cedex, France; and Equipe 9 "Estrogen Receptor: In Vivo Dissection and Modulation" (A.F., R.S., F.L., C.F., J.-F.A.), Inserm Unité 1048 (Institut des Maladies Métaboliques et Cardiovasculaires), Toulouse 31432 Cedex 4, France
| | - Stéphane Avner
- Equipe Spatio-Temporal Regulation of Transcription in Eukaryotes (SP@RTE) (G.P., C.L.P., S.A., G.S., R.M.), Unité Mixte de Recherche 6290 Centre National de la Recherche Scientifique (Institut de Genétique et Développement de Rennes), Université de Rennes 1, Campus de Beaulieu, and Equipe Transcription, Environment and Cancer (TREC) (G.F.), Inserm U1085-Institut de Recherche en Santé, Environnement et Travail, Rennes 35042 Cedex, France; and Equipe 9 "Estrogen Receptor: In Vivo Dissection and Modulation" (A.F., R.S., F.L., C.F., J.-F.A.), Inserm Unité 1048 (Institut des Maladies Métaboliques et Cardiovasculaires), Toulouse 31432 Cedex 4, France
| | - Françoise Lenfant
- Equipe Spatio-Temporal Regulation of Transcription in Eukaryotes (SP@RTE) (G.P., C.L.P., S.A., G.S., R.M.), Unité Mixte de Recherche 6290 Centre National de la Recherche Scientifique (Institut de Genétique et Développement de Rennes), Université de Rennes 1, Campus de Beaulieu, and Equipe Transcription, Environment and Cancer (TREC) (G.F.), Inserm U1085-Institut de Recherche en Santé, Environnement et Travail, Rennes 35042 Cedex, France; and Equipe 9 "Estrogen Receptor: In Vivo Dissection and Modulation" (A.F., R.S., F.L., C.F., J.-F.A.), Inserm Unité 1048 (Institut des Maladies Métaboliques et Cardiovasculaires), Toulouse 31432 Cedex 4, France
| | - Coralie Fontaine
- Equipe Spatio-Temporal Regulation of Transcription in Eukaryotes (SP@RTE) (G.P., C.L.P., S.A., G.S., R.M.), Unité Mixte de Recherche 6290 Centre National de la Recherche Scientifique (Institut de Genétique et Développement de Rennes), Université de Rennes 1, Campus de Beaulieu, and Equipe Transcription, Environment and Cancer (TREC) (G.F.), Inserm U1085-Institut de Recherche en Santé, Environnement et Travail, Rennes 35042 Cedex, France; and Equipe 9 "Estrogen Receptor: In Vivo Dissection and Modulation" (A.F., R.S., F.L., C.F., J.-F.A.), Inserm Unité 1048 (Institut des Maladies Métaboliques et Cardiovasculaires), Toulouse 31432 Cedex 4, France
| | - Gilles Salbert
- Equipe Spatio-Temporal Regulation of Transcription in Eukaryotes (SP@RTE) (G.P., C.L.P., S.A., G.S., R.M.), Unité Mixte de Recherche 6290 Centre National de la Recherche Scientifique (Institut de Genétique et Développement de Rennes), Université de Rennes 1, Campus de Beaulieu, and Equipe Transcription, Environment and Cancer (TREC) (G.F.), Inserm U1085-Institut de Recherche en Santé, Environnement et Travail, Rennes 35042 Cedex, France; and Equipe 9 "Estrogen Receptor: In Vivo Dissection and Modulation" (A.F., R.S., F.L., C.F., J.-F.A.), Inserm Unité 1048 (Institut des Maladies Métaboliques et Cardiovasculaires), Toulouse 31432 Cedex 4, France
| | - Gilles Flouriot
- Equipe Spatio-Temporal Regulation of Transcription in Eukaryotes (SP@RTE) (G.P., C.L.P., S.A., G.S., R.M.), Unité Mixte de Recherche 6290 Centre National de la Recherche Scientifique (Institut de Genétique et Développement de Rennes), Université de Rennes 1, Campus de Beaulieu, and Equipe Transcription, Environment and Cancer (TREC) (G.F.), Inserm U1085-Institut de Recherche en Santé, Environnement et Travail, Rennes 35042 Cedex, France; and Equipe 9 "Estrogen Receptor: In Vivo Dissection and Modulation" (A.F., R.S., F.L., C.F., J.-F.A.), Inserm Unité 1048 (Institut des Maladies Métaboliques et Cardiovasculaires), Toulouse 31432 Cedex 4, France
| | - Jean-François Arnal
- Equipe Spatio-Temporal Regulation of Transcription in Eukaryotes (SP@RTE) (G.P., C.L.P., S.A., G.S., R.M.), Unité Mixte de Recherche 6290 Centre National de la Recherche Scientifique (Institut de Genétique et Développement de Rennes), Université de Rennes 1, Campus de Beaulieu, and Equipe Transcription, Environment and Cancer (TREC) (G.F.), Inserm U1085-Institut de Recherche en Santé, Environnement et Travail, Rennes 35042 Cedex, France; and Equipe 9 "Estrogen Receptor: In Vivo Dissection and Modulation" (A.F., R.S., F.L., C.F., J.-F.A.), Inserm Unité 1048 (Institut des Maladies Métaboliques et Cardiovasculaires), Toulouse 31432 Cedex 4, France
| | - Raphaël Métivier
- Equipe Spatio-Temporal Regulation of Transcription in Eukaryotes (SP@RTE) (G.P., C.L.P., S.A., G.S., R.M.), Unité Mixte de Recherche 6290 Centre National de la Recherche Scientifique (Institut de Genétique et Développement de Rennes), Université de Rennes 1, Campus de Beaulieu, and Equipe Transcription, Environment and Cancer (TREC) (G.F.), Inserm U1085-Institut de Recherche en Santé, Environnement et Travail, Rennes 35042 Cedex, France; and Equipe 9 "Estrogen Receptor: In Vivo Dissection and Modulation" (A.F., R.S., F.L., C.F., J.-F.A.), Inserm Unité 1048 (Institut des Maladies Métaboliques et Cardiovasculaires), Toulouse 31432 Cedex 4, France
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Iwafuchi-Doi M, Donahue G, Kakumanu A, Watts JA, Mahony S, Pugh BF, Lee D, Kaestner KH, Zaret KS. The Pioneer Transcription Factor FoxA Maintains an Accessible Nucleosome Configuration at Enhancers for Tissue-Specific Gene Activation. Mol Cell 2016; 62:79-91. [PMID: 27058788 PMCID: PMC4826471 DOI: 10.1016/j.molcel.2016.03.001] [Citation(s) in RCA: 267] [Impact Index Per Article: 33.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Revised: 02/05/2016] [Accepted: 02/29/2016] [Indexed: 12/20/2022]
Abstract
Nuclear DNA wraps around core histones to form nucleosomes, which restricts the binding of transcription factors to gene regulatory sequences. Pioneer transcription factors can bind DNA sites on nucleosomes and initiate gene regulatory events, often leading to the local opening of chromatin. However, the nucleosomal configuration of open chromatin and the basis for its regulation is unclear. We combined low and high levels of micrococcal nuclease (MNase) digestion along with core histone mapping to assess the nucleosomal configuration at enhancers and promoters in mouse liver. We find that MNase-accessible nucleosomes, bound by transcription factors, are retained more at liver-specific enhancers than at promoters and ubiquitous enhancers. The pioneer factor FoxA displaces linker histone H1, thereby keeping enhancer nucleosomes accessible in chromatin and allowing other liver-specific transcription factors to bind and stimulate transcription. Thus, nucleosomes are not exclusively repressive to gene regulation when they are retained with, and exposed by, pioneer factors.
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Affiliation(s)
- Makiko Iwafuchi-Doi
- Department of Cell and Developmental Biology and Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Boulevard, Philadelphia, PA 19104-5157, USA
| | - Greg Donahue
- Department of Cell and Developmental Biology and Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Boulevard, Philadelphia, PA 19104-5157, USA
| | - Akshay Kakumanu
- Department of Biochemistry and Molecular Biology and Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA 16802, USA
| | - Jason A Watts
- Department of Cell and Developmental Biology and Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Boulevard, Philadelphia, PA 19104-5157, USA
| | - Shaun Mahony
- Department of Biochemistry and Molecular Biology and Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA 16802, USA
| | - B Franklin Pugh
- Department of Biochemistry and Molecular Biology and Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA 16802, USA
| | - Dolim Lee
- Department of Genetics and Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Boulevard, Philadelphia, PA 19104-5157, USA
| | - Klaus H Kaestner
- Department of Genetics and Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Boulevard, Philadelphia, PA 19104-5157, USA
| | - Kenneth S Zaret
- Department of Cell and Developmental Biology and Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Boulevard, Philadelphia, PA 19104-5157, USA.
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27
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Costello I, Nowotschin S, Sun X, Mould AW, Hadjantonakis AK, Bikoff EK, Robertson EJ. Lhx1 functions together with Otx2, Foxa2, and Ldb1 to govern anterior mesendoderm, node, and midline development. Genes Dev 2016; 29:2108-22. [PMID: 26494787 PMCID: PMC4617976 DOI: 10.1101/gad.268979.115] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Costello et al. demonstrate that Smad4/Eomes-dependent Lhx1 expression in the epiblast marks the entire definitive endoderm lineage, the anterior mesendoderm, and midline progenitors. In proteomic experiments, they characterize a complex comprised of Lhx1, Otx2, and Foxa2 as well as the chromatin-looping protein Ldb1. Gene regulatory networks controlling functional activities of spatially and temporally distinct endodermal cell populations in the early mouse embryo remain ill defined. The T-box transcription factor Eomes, acting downstream from Nodal/Smad signals, directly activates the LIM domain homeobox transcription factor Lhx1 in the visceral endoderm. Here we demonstrate Smad4/Eomes-dependent Lhx1 expression in the epiblast marks the entire definitive endoderm lineage, the anterior mesendoderm, and midline progenitors. Conditional inactivation of Lhx1 disrupts anterior definitive endoderm development and impedes node and midline morphogenesis in part due to severe disturbances in visceral endoderm displacement. Transcriptional profiling and ChIP-seq (chromatin immunoprecipitation [ChIP] followed by high-throughput sequencing) experiments identified Lhx1 target genes, including numerous anterior definitive endoderm markers and components of the Wnt signaling pathway. Interestingly, Lhx1-binding sites were enriched at enhancers, including the Nodal-proximal epiblast enhancer element and enhancer regions controlling Otx2 and Foxa2 expression. Moreover, in proteomic experiments, we characterized a complex comprised of Lhx1, Otx2, and Foxa2 as well as the chromatin-looping protein Ldb1. These partnerships cooperatively regulate development of the anterior mesendoderm, node, and midline cell populations responsible for establishment of the left–right body axis and head formation.
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Affiliation(s)
- Ita Costello
- The Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom
| | - Sonja Nowotschin
- Developmental Biology Program, Sloan Kettering Institute, New York, New York 10065, USA
| | - Xin Sun
- The Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom
| | - Arne W Mould
- The Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom
| | | | - Elizabeth K Bikoff
- The Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom
| | - Elizabeth J Robertson
- The Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom
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28
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Wang R, Shi Y, Chen L, Jiang Y, Mao C, Yan B, Liu S, Shan B, Tao Y, Wang X. The ratio of FoxA1 to FoxA2 in lung adenocarcinoma is regulated by LncRNA HOTAIR and chromatin remodeling factor LSH. Sci Rep 2015; 5:17826. [PMID: 26658322 PMCID: PMC4675985 DOI: 10.1038/srep17826] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 11/06/2015] [Indexed: 12/16/2022] Open
Abstract
The lncRNA HOTAIR is a critical regulator of cancer progression. Chromatin remodeling factor LSH is critical for normal development of plants and mammals. However, the underlying mechanisms causing this in cancer are not entirely clear. The functional diversification of the FOXA1 and FOXA2 contributes to the target genes during evolution and carcinogenesis. Little is known about the ratio of FOXA1 to FOXA2 in cancer. We here found that both HOTAIR and LSH overexpression was significantly correlated with poor survival in patients with lung adenocarcinoma cancer (ADC). Also, the ratio of FOXA1 and FOXA2 is linked with poor survival in patients with lung ADC. HOTAIR regulates the ratio of FOXA1 to FOXA2 and migration and invasion. HOTAIR and the ratio of FOXA1 to FOXA2 are negatively correlated. HOTAIR knockdown inhibits migration and invasion. HOTAIR is associated with LSH, and this association linked with the binding of LSH in the promoter of FOXA1, not FOXA2. Targeted inhibition of HOTAIR suppresses the migratory and invasive properties. These data suggest that HOTAIR is an important mediator of the ratio of FOXA1 and FOXA2 and LSH involves in, and suggest that HOTAIR inhibition may represent a promising therapeutic option for suppressing lung ADC progression.
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Affiliation(s)
- Ranran Wang
- Department of Thoracic and Cardiovascular Surgery, Second Xiangya Hospital of Central South University, Changsha, China
| | - Ying Shi
- Cancer Research Institute, Central South University, Changsha, Hunan, 410078 China.,Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Hunan, 410078 China.,Key Laboratory of Carcinogenesis, Ministry of Health, Hunan, 410078 China
| | - Ling Chen
- Cancer Research Institute, Central South University, Changsha, Hunan, 410078 China.,Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Hunan, 410078 China.,Key Laboratory of Carcinogenesis, Ministry of Health, Hunan, 410078 China
| | - Yiqun Jiang
- Cancer Research Institute, Central South University, Changsha, Hunan, 410078 China.,Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Hunan, 410078 China.,Key Laboratory of Carcinogenesis, Ministry of Health, Hunan, 410078 China
| | - Chao Mao
- Cancer Research Institute, Central South University, Changsha, Hunan, 410078 China.,Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Hunan, 410078 China.,Key Laboratory of Carcinogenesis, Ministry of Health, Hunan, 410078 China
| | - Bin Yan
- Cancer Research Institute, Central South University, Changsha, Hunan, 410078 China.,Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Hunan, 410078 China.,Key Laboratory of Carcinogenesis, Ministry of Health, Hunan, 410078 China
| | - Shuang Liu
- Center for Medicine Research, Xiangya Hospital, Central South University, Changsha, Hunan, 410078 China
| | - Bin Shan
- College of Medical Sciences, Washington State University Spokane, 412 E. Spokane Falls Boulevard, Spokane, WA 99202, USA
| | - Yongguang Tao
- Cancer Research Institute, Central South University, Changsha, Hunan, 410078 China.,Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Hunan, 410078 China.,Key Laboratory of Carcinogenesis, Ministry of Health, Hunan, 410078 China
| | - Xiang Wang
- Department of Thoracic and Cardiovascular Surgery, Second Xiangya Hospital of Central South University, Changsha, China.,Cancer Research Institute, Central South University, Changsha, Hunan, 410078 China
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29
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Johansson E, Andersson L, Örnros J, Carlsson T, Ingeson-Carlsson C, Liang S, Dahlberg J, Jansson S, Parrillo L, Zoppoli P, Barila GO, Altschuler DL, Padula D, Lickert H, Fagman H, Nilsson M. Revising the embryonic origin of thyroid C cells in mice and humans. Development 2015; 142:3519-28. [PMID: 26395490 PMCID: PMC4631767 DOI: 10.1242/dev.126581] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Accepted: 08/27/2015] [Indexed: 12/13/2022]
Abstract
Current understanding infers a neural crest origin of thyroid C cells, the major source of calcitonin in mammals and ancestors to neuroendocrine thyroid tumors. The concept is primarily based on investigations in quail–chick chimeras involving fate mapping of neural crest cells to the ultimobranchial glands that regulate Ca2+ homeostasis in birds, reptiles, amphibians and fishes, but whether mammalian C cell development involves a homologous ontogenetic trajectory has not been experimentally verified. With lineage tracing, we now provide direct evidence that Sox17+ anterior endoderm is the only source of differentiated C cells and their progenitors in mice. Like many gut endoderm derivatives, embryonic C cells were found to coexpress pioneer factors forkhead box (Fox) a1 and Foxa2 before neuroendocrine differentiation takes place. In the ultimobranchial body epithelium emerging from pharyngeal pouch endoderm in early organogenesis, differential Foxa1/Foxa2 expression distinguished two spatially separated pools of C cell precursors with different growth properties. A similar expression pattern was recapitulated in medullary thyroid carcinoma cells in vivo, consistent with a growth-promoting role of Foxa1. In contrast to embryonic precursor cells, C cell-derived tumor cells invading the stromal compartment downregulated Foxa2, foregoing epithelial-to-mesenchymal transition designated by loss of E-cadherin; both Foxa2 and E-cadherin were re-expressed at metastatic sites. These findings revise mammalian C cell ontogeny, expand the neuroendocrine repertoire of endoderm and redefine the boundaries of neural crest diversification. The data further underpin distinct functions of Foxa1 and Foxa2 in both embryonic and tumor development. Highlighted article: Mouse thyroid C cell precursors arise in foregut endoderm, and not the neural crest, disproving the current concept of a neural crest origin of thyroid neuroendocrine cells.
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Affiliation(s)
- Ellen Johansson
- Sahlgrenska Cancer Center, Institute of Biomedicine, University of Gothenburg, Göteborg SE-40530, Sweden
| | - Louise Andersson
- Sahlgrenska Cancer Center, Institute of Biomedicine, University of Gothenburg, Göteborg SE-40530, Sweden
| | - Jessica Örnros
- Sahlgrenska Cancer Center, Institute of Biomedicine, University of Gothenburg, Göteborg SE-40530, Sweden
| | - Therese Carlsson
- Sahlgrenska Cancer Center, Institute of Biomedicine, University of Gothenburg, Göteborg SE-40530, Sweden
| | - Camilla Ingeson-Carlsson
- Sahlgrenska Cancer Center, Institute of Biomedicine, University of Gothenburg, Göteborg SE-40530, Sweden
| | - Shawn Liang
- Sahlgrenska Cancer Center, Institute of Biomedicine, University of Gothenburg, Göteborg SE-40530, Sweden
| | - Jakob Dahlberg
- Department of Surgery, Sahlgrenska University Hospital, Göteborg, SE-41345, Sweden
| | - Svante Jansson
- Department of Surgery, Sahlgrenska University Hospital, Göteborg, SE-41345, Sweden
| | | | - Pietro Zoppoli
- Institute for Cancer Genetics, Columbia University, 1130 St Nicholas Avenue, New York, NY 10031, USA
| | - Guillermo O Barila
- Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Daniel L Altschuler
- Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Daniela Padula
- Institute of Diabetes and Regeneration Research, Helmholtz Center Munich, German Research Center for Environmental Health GmgH, Ingolstaedter Landstraße 1, Munich 85764, Germany
| | - Heiko Lickert
- Institute of Diabetes and Regeneration Research, Helmholtz Center Munich, German Research Center for Environmental Health GmgH, Ingolstaedter Landstraße 1, Munich 85764, Germany
| | - Henrik Fagman
- Department of Clinical Pathology and Genetics, Sahlgrenska University Hospital, Göteborg, SE-41345, Sweden
| | - Mikael Nilsson
- Sahlgrenska Cancer Center, Institute of Biomedicine, University of Gothenburg, Göteborg SE-40530, Sweden
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30
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Li MM, Addepalli B, Tu MJ, Chen QX, Wang WP, Limbach PA, LaSalle JM, Zeng S, Huang M, Yu AM. Chimeric MicroRNA-1291 Biosynthesized Efficiently in Escherichia coli Is Effective to Reduce Target Gene Expression in Human Carcinoma Cells and Improve Chemosensitivity. Drug Metab Dispos 2015; 43:1129-36. [PMID: 25934574 DOI: 10.1124/dmd.115.064493] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 04/29/2015] [Indexed: 01/19/2023] Open
Abstract
In contrast to the growing interests in studying noncoding RNAs (ncRNAs) such as microRNA (miRNA or miR) pharmacoepigenetics, there is a lack of efficient means to cost effectively produce large quantities of natural miRNA agents. Our recent efforts led to a successful production of chimeric pre-miR-27b in bacteria using a transfer RNA (tRNA)-based recombinant RNA technology, but at very low expression levels. Herein, we present a high-yield expression of chimeric pre-miR-1291 in common Escherichia coli strains using the same tRNA scaffold. The tRNA fusion pre-miR-1291 (tRNA/mir-1291) was then purified to high homogeneity using affinity chromatography, whose primary sequence and post-transcriptional modifications were directly characterized by mass spectrometric analyses. Chimeric tRNA/mir-1291 was readily processed to mature miR-1291 in human carcinoma MCF-7 and PANC-1 cells. Consequently, recombinant tRNA/mir-1291 reduced the protein levels of miR-1291 target genes, including ABCC1, FOXA2, and MeCP2, as compared with cells transfected with the same doses of control methionyl-tRNA scaffold with a sephadex aptamer (tRNA/MSA). In addition, tRNA-carried pre-miR-1291 suppressed the growth of MCF-7 and PANC-1 cells in a dose-dependent manner, and significantly enhanced the sensitivity of ABCC1-overexpressing PANC-1 cells to doxorubicin. These results indicate that recombinant miR-1291 agent is effective in the modulation of target gene expression and chemosensitivity, which may provide insights into high-yield bioengineering of new ncRNA agents for pharmacoepigenetics research.
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Affiliation(s)
- Mei-Mei Li
- Department of Biochemistry & Molecular Medicine, University of California-Davis School of Medicine, Sacramento, California (M.-M.L., M.-J.T., Q.-X.C., W.-P.W., A.-M.Y.); Laboratory of Drug Metabolism and Pharmacokinetics, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China (M.-M.L, M.H.); Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, Ohio (B.A., P.A.L.); Laboratory of Pharmaceutical Analysis and Drug Metabolism, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, China (Q.-X.C., S.Z.); and Department of Medical Microbiology and Immunology, University of California Davis School of Medicine, Davis, California (J.M.L.)
| | - Balasubrahmanyam Addepalli
- Department of Biochemistry & Molecular Medicine, University of California-Davis School of Medicine, Sacramento, California (M.-M.L., M.-J.T., Q.-X.C., W.-P.W., A.-M.Y.); Laboratory of Drug Metabolism and Pharmacokinetics, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China (M.-M.L, M.H.); Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, Ohio (B.A., P.A.L.); Laboratory of Pharmaceutical Analysis and Drug Metabolism, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, China (Q.-X.C., S.Z.); and Department of Medical Microbiology and Immunology, University of California Davis School of Medicine, Davis, California (J.M.L.)
| | - Mei-Juan Tu
- Department of Biochemistry & Molecular Medicine, University of California-Davis School of Medicine, Sacramento, California (M.-M.L., M.-J.T., Q.-X.C., W.-P.W., A.-M.Y.); Laboratory of Drug Metabolism and Pharmacokinetics, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China (M.-M.L, M.H.); Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, Ohio (B.A., P.A.L.); Laboratory of Pharmaceutical Analysis and Drug Metabolism, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, China (Q.-X.C., S.Z.); and Department of Medical Microbiology and Immunology, University of California Davis School of Medicine, Davis, California (J.M.L.)
| | - Qiu-Xia Chen
- Department of Biochemistry & Molecular Medicine, University of California-Davis School of Medicine, Sacramento, California (M.-M.L., M.-J.T., Q.-X.C., W.-P.W., A.-M.Y.); Laboratory of Drug Metabolism and Pharmacokinetics, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China (M.-M.L, M.H.); Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, Ohio (B.A., P.A.L.); Laboratory of Pharmaceutical Analysis and Drug Metabolism, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, China (Q.-X.C., S.Z.); and Department of Medical Microbiology and Immunology, University of California Davis School of Medicine, Davis, California (J.M.L.)
| | - Wei-Peng Wang
- Department of Biochemistry & Molecular Medicine, University of California-Davis School of Medicine, Sacramento, California (M.-M.L., M.-J.T., Q.-X.C., W.-P.W., A.-M.Y.); Laboratory of Drug Metabolism and Pharmacokinetics, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China (M.-M.L, M.H.); Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, Ohio (B.A., P.A.L.); Laboratory of Pharmaceutical Analysis and Drug Metabolism, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, China (Q.-X.C., S.Z.); and Department of Medical Microbiology and Immunology, University of California Davis School of Medicine, Davis, California (J.M.L.)
| | - Patrick A Limbach
- Department of Biochemistry & Molecular Medicine, University of California-Davis School of Medicine, Sacramento, California (M.-M.L., M.-J.T., Q.-X.C., W.-P.W., A.-M.Y.); Laboratory of Drug Metabolism and Pharmacokinetics, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China (M.-M.L, M.H.); Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, Ohio (B.A., P.A.L.); Laboratory of Pharmaceutical Analysis and Drug Metabolism, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, China (Q.-X.C., S.Z.); and Department of Medical Microbiology and Immunology, University of California Davis School of Medicine, Davis, California (J.M.L.)
| | - Janine M LaSalle
- Department of Biochemistry & Molecular Medicine, University of California-Davis School of Medicine, Sacramento, California (M.-M.L., M.-J.T., Q.-X.C., W.-P.W., A.-M.Y.); Laboratory of Drug Metabolism and Pharmacokinetics, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China (M.-M.L, M.H.); Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, Ohio (B.A., P.A.L.); Laboratory of Pharmaceutical Analysis and Drug Metabolism, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, China (Q.-X.C., S.Z.); and Department of Medical Microbiology and Immunology, University of California Davis School of Medicine, Davis, California (J.M.L.)
| | - Su Zeng
- Department of Biochemistry & Molecular Medicine, University of California-Davis School of Medicine, Sacramento, California (M.-M.L., M.-J.T., Q.-X.C., W.-P.W., A.-M.Y.); Laboratory of Drug Metabolism and Pharmacokinetics, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China (M.-M.L, M.H.); Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, Ohio (B.A., P.A.L.); Laboratory of Pharmaceutical Analysis and Drug Metabolism, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, China (Q.-X.C., S.Z.); and Department of Medical Microbiology and Immunology, University of California Davis School of Medicine, Davis, California (J.M.L.)
| | - Min Huang
- Department of Biochemistry & Molecular Medicine, University of California-Davis School of Medicine, Sacramento, California (M.-M.L., M.-J.T., Q.-X.C., W.-P.W., A.-M.Y.); Laboratory of Drug Metabolism and Pharmacokinetics, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China (M.-M.L, M.H.); Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, Ohio (B.A., P.A.L.); Laboratory of Pharmaceutical Analysis and Drug Metabolism, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, China (Q.-X.C., S.Z.); and Department of Medical Microbiology and Immunology, University of California Davis School of Medicine, Davis, California (J.M.L.)
| | - Ai-Ming Yu
- Department of Biochemistry & Molecular Medicine, University of California-Davis School of Medicine, Sacramento, California (M.-M.L., M.-J.T., Q.-X.C., W.-P.W., A.-M.Y.); Laboratory of Drug Metabolism and Pharmacokinetics, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China (M.-M.L, M.H.); Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, Ohio (B.A., P.A.L.); Laboratory of Pharmaceutical Analysis and Drug Metabolism, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, China (Q.-X.C., S.Z.); and Department of Medical Microbiology and Immunology, University of California Davis School of Medicine, Davis, California (J.M.L.)
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31
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Gosalia N, Yang R, Kerschner JL, Harris A. FOXA2 regulates a network of genes involved in critical functions of human intestinal epithelial cells. Physiol Genomics 2015; 47:290-7. [PMID: 25921584 DOI: 10.1152/physiolgenomics.00024.2015] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 04/27/2015] [Indexed: 12/18/2022] Open
Abstract
The forkhead box A (FOXA) family of pioneer transcription factors is critical for the development of many endoderm-derived tissues. Their importance in regulating biological processes in the lung and liver is extensively characterized, though much less is known about their role in intestine. Here we investigate the contribution of FOXA2 to coordinating intestinal epithelial cell function using postconfluent Caco2 cells, differentiated into an enterocyte-like model. FOXA2 binding sites genome-wide were determined by ChIP-seq and direct targets of the factor were validated by ChIP-qPCR and siRNA-mediated depletion of FOXA1/2 followed by RT-qPCR. Peaks of FOXA2 occupancy were frequent at loci contributing to gene ontology pathways of regulation of cell migration, cell motion, and plasma membrane function. Depletion of both FOXA1 and FOXA2 led to a significant reduction in the expression of multiple transmembrane proteins including ion channels and transporters, which form a network that is essential for maintaining normal ion and solute transport. One of the targets was the adenosine A2B receptor, and reduced receptor mRNA levels were associated with a functional decrease in intracellular cyclic AMP. We also observed that 30% of FOXA2 binding sites contained a GATA motif and that FOXA1/A2 depletion reduced GATA-4, but not GATA-6 protein levels. These data show that FOXA2 plays a pivotal role in regulating intestinal epithelial cell function. Moreover, that the FOXA and GATA families of transcription factors may work cooperatively to regulate gene expression genome-wide in the intestinal epithelium.
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Affiliation(s)
- Nehal Gosalia
- Human Molecular Genetics Program, Lurie Children's Research Center, Chicago, Illinois; Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, Illinois; and
| | - Rui Yang
- Human Molecular Genetics Program, Lurie Children's Research Center, Chicago, Illinois; Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, Illinois; and
| | - Jenny L Kerschner
- Human Molecular Genetics Program, Lurie Children's Research Center, Chicago, Illinois; Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, Illinois; and
| | - Ann Harris
- Human Molecular Genetics Program, Lurie Children's Research Center, Chicago, Illinois; Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, Illinois; and Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, Illinois
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32
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YAP Inhibition Restores Hepatocyte Differentiation in Advanced HCC, Leading to Tumor Regression. Cell Rep 2015; 10:1692-1707. [PMID: 25772357 DOI: 10.1016/j.celrep.2015.02.027] [Citation(s) in RCA: 192] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Revised: 01/16/2015] [Accepted: 02/06/2015] [Indexed: 12/12/2022] Open
Abstract
Defective Hippo/YAP signaling in the liver results in tissue overgrowth and development of hepatocellular carcinoma (HCC). Here, we uncover mechanisms of YAP-mediated hepatocyte reprogramming and HCC pathogenesis. YAP functions as a rheostat in maintaining metabolic specialization, differentiation, and quiescence within the hepatocyte compartment. Increased or decreased YAP activity reprograms subsets of hepatocytes to different fates associated with deregulation of the HNF4A, CTNNB1, and E2F transcriptional programs that control hepatocyte quiescence and differentiation. Importantly, treatment with small interfering RNA-lipid nanoparticles (siRNA-LNPs) targeting YAP restores hepatocyte differentiation and causes pronounced tumor regression in a genetically engineered mouse HCC model. Furthermore, YAP targets are enriched in an aggressive human HCC subtype characterized by a proliferative signature and absence of CTNNB1 mutations. Thus, our work reveals Hippo signaling as a key regulator of the positional identity of hepatocytes, supports targeting of YAP using siRNA-LNPs as a paradigm of differentiation-based therapy, and identifies an HCC subtype that is potentially responsive to this approach.
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33
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Wong ES, Thybert D, Schmitt BM, Stefflova K, Odom DT, Flicek P. Decoupling of evolutionary changes in transcription factor binding and gene expression in mammals. Genome Res 2015; 25:167-78. [PMID: 25394363 PMCID: PMC4315291 DOI: 10.1101/gr.177840.114] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Accepted: 11/12/2014] [Indexed: 11/25/2022]
Abstract
To understand the evolutionary dynamics between transcription factor (TF) binding and gene expression in mammals, we compared transcriptional output and the binding intensities for three tissue-specific TFs in livers from four closely related mouse species. For each transcription factor, TF-dependent genes and the TF binding sites most likely to influence mRNA expression were identified by comparing mRNA expression levels between wild-type and TF knockout mice. Independent evolution was observed genome-wide between the rate of change in TF binding and the rate of change in mRNA expression across taxa, with the exception of a small number of TF-dependent genes. We also found that binding intensities are preferentially conserved near genes whose expression is dependent on the TF, and the conservation is shared among binding peaks in close proximity to each other near the TSS. Expression of TF-dependent genes typically showed an increased sensitivity to changes in binding levels as measured by mRNA abundance. Taken together, these results highlight a significant tolerance to evolutionary changes in TF binding intensity in mammalian transcriptional networks and suggest that some TF-dependent genes may be largely regulated by a single TF across evolution.
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Affiliation(s)
- Emily S Wong
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom
| | - David Thybert
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom
| | - Bianca M Schmitt
- University of Cambridge, Cancer Research UK - Cambridge Institute, Li Ka Shing Centre, Cambridge, CB2 0RE, United Kingdom
| | - Klara Stefflova
- University of Cambridge, Cancer Research UK - Cambridge Institute, Li Ka Shing Centre, Cambridge, CB2 0RE, United Kingdom
| | - Duncan T Odom
- University of Cambridge, Cancer Research UK - Cambridge Institute, Li Ka Shing Centre, Cambridge, CB2 0RE, United Kingdom; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
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Liu L, Zinkgraf M, Petzold HE, Beers EP, Filkov V, Groover A. The Populus ARBORKNOX1 homeodomain transcription factor regulates woody growth through binding to evolutionarily conserved target genes of diverse function. THE NEW PHYTOLOGIST 2015; 205:682-94. [PMID: 25377848 DOI: 10.1111/nph.13151] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2014] [Accepted: 10/01/2014] [Indexed: 05/28/2023]
Abstract
The class I KNOX homeodomain transcription factor ARBORKNOX1 (ARK1) is a key regulator of vascular cambium maintenance and cell differentiation in Populus. Currently, basic information is lacking concerning the distribution, functional characteristics, and evolution of ARK1 binding in the Populus genome. Here, we used chromatin immunoprecipitation sequencing (ChIP-seq) technology to identify ARK1 binding loci genome-wide in Populus. Computational analyses evaluated the distribution of ARK1 binding loci, the function of genes associated with bound loci, the effect of ARK1 binding on transcript levels, and evolutionary conservation of ARK1 binding loci. ARK1 binds to thousands of loci which are highly enriched proximal to the transcriptional start sites of genes of diverse functions. ARK1 target genes are significantly enriched in paralogs derived from the whole-genome salicoid duplication event. Both ARK1 and a maize (Zea mays) homolog, KNOTTED1, preferentially target evolutionarily conserved genes. However, only a small portion of ARK1 target genes are significantly differentially expressed in an ARK1 over-expression mutant. This study describes the functional characteristics and evolution of DNA binding by a transcription factor in an undomesticated tree, revealing complexities similar to those shown for transcription factors in model animal species.
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Affiliation(s)
- Lijun Liu
- Pacific Southwest Research Station, USDA Forest Service, Davis, CA, 95618, USA
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Bochkis IM, Przybylski D, Chen J, Regev A. Changes in nucleosome occupancy associated with metabolic alterations in aged mammalian liver. Cell Rep 2014; 9:996-1006. [PMID: 25437555 PMCID: PMC4250828 DOI: 10.1016/j.celrep.2014.09.048] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Revised: 08/15/2014] [Accepted: 09/24/2014] [Indexed: 12/27/2022] Open
Abstract
Aging is accompanied by physiological impairments, which, in insulin-responsive tissues, including the liver, predispose individuals to metabolic disease. However, the molecular mechanisms underlying these changes remain largely unknown. Here, we analyze genome-wide profiles of RNA and chromatin organization in the liver of young (3 months) and old (21 months) mice. Transcriptional changes suggest that derepression of the nuclear receptors PPARα, PPARγ, and LXRα in aged mouse liver leads to activation of targets regulating lipid synthesis and storage, whereas age-dependent changes in nucleosome occupancy are associated with binding sites for both known regulators (forkhead factors and nuclear receptors) and candidates associated with nuclear lamina (Hdac3 and Srf) implicated to govern metabolic function of aging liver. Winged-helix transcription factor Foxa2 and nuclear receptor corepressor Hdac3 exhibit a reciprocal binding pattern at PPARα targets contributing to gene expression changes that lead to steatosis in aged liver.
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Affiliation(s)
- Irina M Bochkis
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | | | - Jenny Chen
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Aviv Regev
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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Lo KS, Vadlamudi S, Fogarty MP, Mohlke KL, Lettre G. Strategies to fine-map genetic associations with lipid levels by combining epigenomic annotations and liver-specific transcription profiles. Genomics 2014; 104:105-12. [PMID: 24997396 DOI: 10.1016/j.ygeno.2014.04.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Revised: 03/04/2014] [Accepted: 04/25/2014] [Indexed: 11/26/2022]
Abstract
Characterization of the epigenome promises to yield the functional elements buried in the human genome sequence, thus helping to annotate non-coding DNA polymorphisms with regulatory functions. Here, we develop two novel strategies to combine epigenomic data with transcriptomic profiles in humans or mice to prioritize potential candidate SNPs associated with lipid levels by genome-wide association study (GWAS). First, after confirming that lipid-associated loci that are also expression quantitative trait loci (eQTL) in human livers are enriched for ENCODE regulatory marks in the human hepatocellular HepG2 cell line, we prioritize candidate SNPs based on the number of these marks that overlap the variant position. This method recognized the known SORT1 rs12740374 regulatory SNP associated with LDL-cholesterol, and highlighted candidate functional SNPs at 15 additional lipid loci. In the second strategy, we combine ENCODE chromatin immunoprecipitation followed by high-throughput DNA sequencing (ChIP-seq) data and liver expression datasets from knockout mice lacking specific transcription factors. This approach identified SNPs in specific transcription factor binding sites that are located near target genes of these transcription factors. We show that FOXA2 transcription factor binding sites are enriched at lipid-associated loci and experimentally validate that alleles of one such proxy SNP located near the FOXA2 target gene BIRC5 show allelic differences in FOXA2-DNA binding and enhancer activity. These methods can be used to generate testable hypotheses for many non-coding SNPs associated with complex diseases or traits.
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Affiliation(s)
- Ken Sin Lo
- Montreal Heart Institute, Montreal, Quebec, Canada
| | | | - Marie P Fogarty
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Karen L Mohlke
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Guillaume Lettre
- Montreal Heart Institute, Montreal, Quebec, Canada; Université de Montréal, Montreal, Quebec, Canada.
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Tang M, Cheng L, Jia R, Qiu L, Liu H, Zhou S, Ma X, Hu G, Wang X, Zhao Y. Identification of transcription factors and single nucleotide polymorphisms of Lrh1 and its homologous genes in Lrh1-knockout pancreas of mice. BMC MEDICAL GENETICS 2014; 15:43. [PMID: 24735206 PMCID: PMC3996308 DOI: 10.1186/1471-2350-15-43] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Accepted: 03/27/2014] [Indexed: 12/19/2022]
Abstract
BACKGROUND To identify transcription factors (TFs) and single nucleotide polymorphisms (SNPs) of Lrh1 (also named Nr5a2) and its homologous genes in Lrh1-knockout pancreas of mice. METHODS The RNA-Seq data GSE34030 were downloaded from Gene Expression Omnibus (GEO) database, including 2 Lrh1 pancreas knockout samples and 2 wild type samples. All reads were processed through TopHat and Cufflinks package to calculate gene-expression level. Then, the differentially expressed genes (DEGs) were identified via non-parametric algorithm (NOISeq) methods in R package, of which the homology genes of Lrh1 were identified via BLASTN analysis. Furthermore, the TFs of Lrh1 and its homologous genes were selected based on TRANSFAC database. Additionally, the SNPs were analyzed via SAM tool to record the locations of mutant sites. RESULTS Total 15683 DEGs were identified, of which 23 was Lrh1 homology genes (3 up-regulated and 20 down-regulated). Fetoprotein TF (FTF) was the only TF of Lrh1 identified and the promoter-binding factor of FTF was CYP7A. The SNP annotations of Lrh1 homologous genes showed that 92% of the mutation sites were occurred in intron and upstream. Three SNPs of Lrh1 were located in intron, while 1819 SNPs of Phkb were located in intron and 1343 SNPs were located in the upstream region. CONCLUSION FTF combined with CYP7A might play an important role in Lrh1 regulated pancreas-specific transcriptional network. Furthermore, the SNPs analysis of Lrh1 and its homology genes provided the candidate mutant sites that might affect the Lrh1-related production and secretion of pancreatic fluid.
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Affiliation(s)
- Maochun Tang
- Department of Gastroenterology, Shanghai Tenth People’s Hospital, Tongji University School of Medicine, No.301, Yanchang Middle Road, Shanghai 200072, China
| | - Li Cheng
- Department of Gastroenterology, Shanghai First People’s Hospital Affiliated Shanghai Jiaotong University, Shanghai 200080, China
| | - Rongrong Jia
- Department of Gastroenterology, Shanghai Tenth People’s Hospital, Tongji University School of Medicine, No.301, Yanchang Middle Road, Shanghai 200072, China
| | - Lei Qiu
- Department of Gastroenterology, Shanghai Tenth People’s Hospital, Tongji University School of Medicine, No.301, Yanchang Middle Road, Shanghai 200072, China
| | - Hua Liu
- Department of Gastroenterology, Shanghai Tenth People’s Hospital, Tongji University School of Medicine, No.301, Yanchang Middle Road, Shanghai 200072, China
| | - Shu Zhou
- Department of Gastroenterology, Shanghai Tenth People’s Hospital, Tongji University School of Medicine, No.301, Yanchang Middle Road, Shanghai 200072, China
| | - Xiuying Ma
- Department of Gastroenterology, Shanghai Tenth People’s Hospital, Tongji University School of Medicine, No.301, Yanchang Middle Road, Shanghai 200072, China
| | - Guoyong Hu
- Department of Gastroenterology, Shanghai First People’s Hospital Affiliated Shanghai Jiaotong University, Shanghai 200080, China
| | - Xingpeng Wang
- Department of Gastroenterology, Shanghai First People’s Hospital Affiliated Shanghai Jiaotong University, Shanghai 200080, China
| | - Yan Zhao
- Department of Gastroenterology, Shanghai Tenth People’s Hospital, Tongji University School of Medicine, No.301, Yanchang Middle Road, Shanghai 200072, China
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Balwierz PJ, Pachkov M, Arnold P, Gruber AJ, Zavolan M, van Nimwegen E. ISMARA: automated modeling of genomic signals as a democracy of regulatory motifs. Genome Res 2014; 24:869-84. [PMID: 24515121 PMCID: PMC4009616 DOI: 10.1101/gr.169508.113] [Citation(s) in RCA: 206] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Accurate reconstruction of the regulatory networks that control gene expression is one of the key current challenges in molecular biology. Although gene expression and chromatin state dynamics are ultimately encoded by constellations of binding sites recognized by regulators such as transcriptions factors (TFs) and microRNAs (miRNAs), our understanding of this regulatory code and its context-dependent read-out remains very limited. Given that there are thousands of potential regulators in mammals, it is not practical to use direct experimentation to identify which of these play a key role for a particular system of interest. We developed a methodology that models gene expression or chromatin modifications in terms of genome-wide predictions of regulatory sites and completely automated it into a web-based tool called ISMARA (Integrated System for Motif Activity Response Analysis). Given only gene expression or chromatin state data across a set of samples as input, ISMARA identifies the key TFs and miRNAs driving expression/chromatin changes and makes detailed predictions regarding their regulatory roles. These include predicted activities of the regulators across the samples, their genome-wide targets, enriched gene categories among the targets, and direct interactions between the regulators. Applying ISMARA to data sets from well-studied systems, we show that it consistently identifies known key regulators ab initio. We also present a number of novel predictions including regulatory interactions in innate immunity, a master regulator of mucociliary differentiation, TFs consistently disregulated in cancer, and TFs that mediate specific chromatin modifications.
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Affiliation(s)
- Piotr J Balwierz
- Biozentrum, University of Basel, and Swiss Institute of Bioinformatics, CH-4056 Basel, Switzerland
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Yang Y, Fear J, Hu J, Haecker I, Zhou L, Renne R, Bloom D, McIntyre LM. Leveraging biological replicates to improve analysis in ChIP-seq experiments. Comput Struct Biotechnol J 2014; 9:e201401002. [PMID: 24688750 PMCID: PMC3962196 DOI: 10.5936/csbj.201401002] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Revised: 01/17/2014] [Accepted: 01/17/2014] [Indexed: 12/27/2022] Open
Abstract
ChIP-seq experiments identify genome-wide profiles of DNA-binding molecules including transcription factors, enzymes and epigenetic marks. Biological replicates are critical for reliable site discovery and are required for the deposition of data in the ENCODE and modENCODE projects. While early reports suggested two replicates were sufficient, the widespread application of the technique has led to emerging consensus that the technique is noisy and that increasing replication may be worthwhile. Additional biological replicates also allow for quantitative assessment of differences between conditions. To date it has remained controversial about how to confirm peak identification and to determine signal strength across biological replicates, particularly when the number of replicates is greater than two. Using objective metrics, we evaluate the consistency of biological replicates in ChIP-seq experiments with more than two replicates. We compare several approaches for binding site determination, including two popular but disparate peak callers, CisGenome and MACS2. Here we propose read coverage as a quantitative measurement of signal strength for estimating sample concordance. Determining binding based on genomic features, such as promoters, is also examined. We find that increasing the number of biological replicates increases the reliability of peak identification. Critically, binding sites with strong biological evidence may be missed if researchers rely on only two biological replicates. When more than two replicates are performed, a simple majority rule (>50% of samples identify a peak) identifies peaks more reliably in all biological replicates than the absolute concordance of peak identification between any two replicates, further demonstrating the utility of increasing replicate numbers in ChIP-seq experiments.
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Affiliation(s)
- Yajie Yang
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, Florida, USA ; UF Genetics Institute, University of Florida, Gainesville, Florida, USA
| | - Justin Fear
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, Florida, USA ; UF Genetics Institute, University of Florida, Gainesville, Florida, USA
| | - Jianhong Hu
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - Irina Haecker
- Department of Applied Entomology, University of Giessen, Giessen, Germany
| | - Lei Zhou
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, Florida, USA
| | - Rolf Renne
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, Florida, USA ; UF Genetics Institute, University of Florida, Gainesville, Florida, USA ; UF Shands Cancer Center, University of Florida, Gainesville, Florida, USA
| | - David Bloom
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, Florida, USA
| | - Lauren M McIntyre
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, Florida, USA ; UF Genetics Institute, University of Florida, Gainesville, Florida, USA
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Li Q, Zhang Y, Fu J, Han L, Xue L, Lv C, Wang P, Li G, Tong T. FOXA1 mediates p16(INK4a) activation during cellular senescence. EMBO J 2013; 32:858-73. [PMID: 23443045 DOI: 10.1038/emboj.2013.35] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2012] [Accepted: 02/01/2013] [Indexed: 12/22/2022] Open
Abstract
Mechanisms governing the transcription of p16(INK4a), one of the master regulators of cellular senescence, have been extensively studied. However, little is known about chromatin dynamics taking place at its promoter and distal enhancer. Here, we report that Forkhead box A1 protein (FOXA1) is significantly upregulated in both replicative and oncogene-induced senescence, and in turn activates transcription of p16(INK4a) through multiple mechanisms. In addition to acting as a classic sequence-specific transcriptional activator, FOXA1 binding leads to a decrease in nucleosome density at the p16(INK4a) promoter in senescent fibroblasts. Moreover, FOXA1, itself a direct target of Polycomb-mediated repression, antagonizes Polycomb function at the p16(INK4a) locus. Finally, a systematic survey of putative FOXA1 binding sites in the p16(INK4a) genomic region revealed an ∼150 kb distal element that could loop back to the promoter and potentiate p16(INK4a) expression. Overall, our findings establish several mechanisms by which FOXA1 controls p16(INK4a) expression during cellular senescence.
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Affiliation(s)
- Qian Li
- Research Center on Aging, Department of Biochemistry and Molecular Biology, Peking University Health Science Center, Beijing, China
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Kang K, Robinson GW, Hennighausen L. Comprehensive meta-analysis of Signal Transducers and Activators of Transcription (STAT) genomic binding patterns discerns cell-specific cis-regulatory modules. BMC Genomics 2013; 14:4. [PMID: 23324445 PMCID: PMC3564941 DOI: 10.1186/1471-2164-14-4] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2012] [Accepted: 01/01/2013] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND Cytokine-activated transcription factors from the STAT (Signal Transducers and Activators of Transcription) family control common and context-specific genetic programs. It is not clear to what extent cell-specific features determine the binding capacity of seven STAT members and to what degree they share genetic targets. Molecular insight into the biology of STATs was gained from a meta-analysis of 29 available ChIP-seq data sets covering genome-wide occupancy of STATs 1, 3, 4, 5A, 5B and 6 in several cell types. RESULTS We determined that the genomic binding capacity of STATs is primarily defined by the cell type and to a lesser extent by individual family members. For example, the overlap of shared binding sites between STATs 3 and 5 in T cells is greater than that between STAT5 in T cells and non-T cells. Even for the top 1,000 highly enriched STAT binding sites, ~15% of STAT5 binding sites in mouse female liver are shared by other STATs in different cell types while in T cells ~90% of STAT5 binding sites are co-occupied by STAT3, STAT4 and STAT6. In addition, we identified 116 cis-regulatory modules (CRM), which are recognized by all STAT members across cell types defining a common JAK-STAT signature. Lastly, in liver STAT5 binding significantly coincides with binding of the cell-specific transcription factors HNF4A, FOXA1 and FOXA2 and is associated with cell-type specific gene transcription. CONCLUSIONS Our results suggest that genomic binding of STATs is primarily determined by the cell type and further specificity is achieved in part by juxtaposed binding of cell-specific transcription factors.
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Affiliation(s)
- Keunsoo Kang
- Laboratory of Genetics and Physiology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 8 Center Drive, Bethesda, MD, 20892-0822, USA
| | - Gertraud W Robinson
- Laboratory of Genetics and Physiology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 8 Center Drive, Bethesda, MD, 20892-0822, USA
| | - Lothar Hennighausen
- Laboratory of Genetics and Physiology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 8 Center Drive, Bethesda, MD, 20892-0822, USA
- National Department of Nanobiomedical Science and WCU Research Center of Nanobiomedical Science, Dankook University, Cheonan, Chungnam, 330-714, Republic of Korea
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