1
|
Ng NHJ, Ghosh S, Bok CM, Ching C, Low BSJ, Chen JT, Lim E, Miserendino MC, Tan YS, Hoon S, Teo AKK. HNF4A and HNF1A exhibit tissue specific target gene regulation in pancreatic beta cells and hepatocytes. Nat Commun 2024; 15:4288. [PMID: 38909044 PMCID: PMC11193738 DOI: 10.1038/s41467-024-48647-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 04/08/2024] [Indexed: 06/24/2024] Open
Abstract
HNF4A and HNF1A encode transcription factors that are important for the development and function of the pancreas and liver. Mutations in both genes have been directly linked to Maturity Onset Diabetes of the Young (MODY) and type 2 diabetes (T2D) risk. To better define the pleiotropic gene regulatory roles of HNF4A and HNF1A, we generated a comprehensive genome-wide map of their binding targets in pancreatic and hepatic cells using ChIP-Seq. HNF4A was found to bind and regulate known (ACY3, HAAO, HNF1A, MAP3K11) and previously unidentified (ABCD3, CDKN2AIP, USH1C, VIL1) loci in a tissue-dependent manner. Functional follow-up highlighted a potential role for HAAO and USH1C as regulators of beta cell function. Unlike the loss-of-function HNF4A/MODY1 variant I271fs, the T2D-associated HNF4A variant (rs1800961) was found to activate AKAP1, GAD2 and HOPX gene expression, potentially due to changes in DNA-binding affinity. We also found HNF1A to bind to and regulate GPR39 expression in beta cells. Overall, our studies provide a rich resource for uncovering downstream molecular targets of HNF4A and HNF1A that may contribute to beta cell or hepatic cell (dys)function, and set up a framework for gene discovery and functional validation.
Collapse
Affiliation(s)
- Natasha Hui Jin Ng
- Stem Cells and Diabetes Laboratory, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, 138673, Singapore
| | - Soumita Ghosh
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119228, Singapore
| | - Chek Mei Bok
- Stem Cells and Diabetes Laboratory, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, 138673, Singapore
| | - Carmen Ching
- Stem Cells and Diabetes Laboratory, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, 138673, Singapore
| | - Blaise Su Jun Low
- Stem Cells and Diabetes Laboratory, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, 138673, Singapore
| | - Juin Ting Chen
- Stem Cells and Diabetes Laboratory, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, 138673, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119228, Singapore
- Department of Biochemistry, National University of Singapore, Singapore, 117596, Singapore
| | - Euodia Lim
- Stem Cells and Diabetes Laboratory, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, 138673, Singapore
- Department of Biochemistry, National University of Singapore, Singapore, 117596, Singapore
| | - María Clara Miserendino
- Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, X5000HUA, Córdoba, Argentina
- Bioinformatics Institute, A*STAR, Singapore, 138671, Singapore
| | - Yaw Sing Tan
- Bioinformatics Institute, A*STAR, Singapore, 138671, Singapore
| | - Shawn Hoon
- Molecular Engineering Laboratory, IMCB, A*STAR, Singapore, 138673, Singapore
| | - Adrian Kee Keong Teo
- Stem Cells and Diabetes Laboratory, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, 138673, Singapore.
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119228, Singapore.
- Department of Biochemistry, National University of Singapore, Singapore, 117596, Singapore.
- Precision Medicine Translational Research Programme (TRP), National University of Singapore, Singapore, 119228, Singapore.
| |
Collapse
|
2
|
Kaci A, Solheim MH, Silgjerd T, Hjaltadottir J, Hornnes LH, Molnes J, Madsen A, Sjøholt G, Bellanné-Chantelot C, Caswell R, Sagen JV, Njølstad PR, Aukrust I, Bjørkhaug L. Functional characterization of HNF4A gene variants identify promoter and cell line specific transactivation effects. Hum Mol Genet 2024; 33:894-904. [PMID: 38433330 PMCID: PMC11070132 DOI: 10.1093/hmg/ddae027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 01/26/2024] [Accepted: 02/11/2024] [Indexed: 03/05/2024] Open
Abstract
Hepatocyte nuclear factor-4 alpha (HNF-4A) regulates genes with roles in glucose metabolism and β-cell development. Although pathogenic HNF4A variants are commonly associated with maturity-onset diabetes of the young (MODY1; HNF4A-MODY), rare phenotypes also include hyperinsulinemic hypoglycemia, renal Fanconi syndrome and liver disease. While the association of rare functionally damaging HNF1A variants with HNF1A-MODY and type 2 diabetes is well established owing to robust functional assays, the impact of HNF4A variants on HNF-4A transactivation in tissues including the liver and kidney is less known, due to lack of similar assays. Our aim was to investigate the functional effects of seven HNF4A variants, located in the HNF-4A DNA binding domain and associated with different clinical phenotypes, by various functional assays and cell lines (transactivation, DNA binding, protein expression, nuclear localization) and in silico protein structure analyses. Variants R85W, S87N and R89W demonstrated reduced DNA binding to the consensus HNF-4A binding elements in the HNF1A promoter (35, 13 and 9%, respectively) and the G6PC promoter (R85W ~10%). While reduced transactivation on the G6PC promoter in HepG2 cells was shown for S87N (33%), R89W (65%) and R136W (35%), increased transactivation by R85W and R85Q was confirmed using several combinations of target promoters and cell lines. R89W showed reduced nuclear levels. In silico analyses supported variant induced structural impact. Our study indicates that cell line specific functional investigations are important to better understand HNF4A-MODY genotype-phenotype correlations, as our data supports ACMG/AMP interpretations of loss-of-function variants and propose assay-specific HNF4A control variants for future functional investigations.
Collapse
Affiliation(s)
- Alba Kaci
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Haukelandsbakken 1, Bergen 5020, Norway
- Center for Laboratory Medicine, Østfold Hospital Trust, Kalnesveien 300, Grålum 1714, Norway
| | - Marie Holm Solheim
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Haukelandsbakken 1, Bergen 5020, Norway
| | - Trine Silgjerd
- Department of Safety, Chemistry, and Biomedical Laboratory Sciences, Western Norway University of Applied Sciences, Inndalsveien 28, Bergen 5020, Norway
| | - Jorunn Hjaltadottir
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Haukelandsbakken 1, Bergen 5020, Norway
- Department of Safety, Chemistry, and Biomedical Laboratory Sciences, Western Norway University of Applied Sciences, Inndalsveien 28, Bergen 5020, Norway
| | - Lorentze Hope Hornnes
- Department of Medical Biochemistry and Pharmacology, Haukeland University Hospital, Jonas Lies veg 87, Bergen 5021, Norway
| | - Janne Molnes
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Haukelandsbakken 1, Bergen 5020, Norway
- Department of Medical Genetics, Haukeland University Hospital, Jonas Lies veg 87, Bergen 5021, Norway
| | - Andre Madsen
- Department of Clinical Science, University of Bergen, Jonas Lies veg 87, Bergen 5020, Norway
| | - Gry Sjøholt
- Department of Safety, Chemistry, and Biomedical Laboratory Sciences, Western Norway University of Applied Sciences, Inndalsveien 28, Bergen 5020, Norway
| | - Christine Bellanné-Chantelot
- Départment of Medical Genetics, Sorbonne University, AP-HP, Hôpital Pitié-Salpêtriére, 21 rue de l'école de médecine, 75006 Paris, France
| | - Richard Caswell
- Exeter Genomics Laboratory, Royal Devon University Healthcare NHS Foundation Trust, Barrack Rd, Exeter EX2 5DW, United Kingdom
| | - Jørn V Sagen
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Haukelandsbakken 1, Bergen 5020, Norway
- Department of Medical Biochemistry and Pharmacology, Haukeland University Hospital, Jonas Lies veg 87, Bergen 5021, Norway
| | - Pål R Njølstad
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Haukelandsbakken 1, Bergen 5020, Norway
- Children and Youth Clinic, Haukeland University Hospital, Haukelandsbakken 1, Bergen 5021, Norway
| | - Ingvild Aukrust
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Haukelandsbakken 1, Bergen 5020, Norway
- Department of Medical Genetics, Haukeland University Hospital, Jonas Lies veg 87, Bergen 5021, Norway
| | - Lise Bjørkhaug
- Department of Safety, Chemistry, and Biomedical Laboratory Sciences, Western Norway University of Applied Sciences, Inndalsveien 28, Bergen 5020, Norway
| |
Collapse
|
3
|
Mozhui K, Kim H, Villani F, Haghani A, Sen S, Horvath S. Pleiotropic influence of DNA methylation QTLs on physiological and ageing traits. Epigenetics 2023; 18:2252631. [PMID: 37691384 PMCID: PMC10496549 DOI: 10.1080/15592294.2023.2252631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 07/31/2023] [Accepted: 08/16/2023] [Indexed: 09/12/2023] Open
Abstract
DNA methylation is influenced by genetic and non-genetic factors. Here, we chart quantitative trait loci (QTLs) that modulate levels of methylation at highly conserved CpGs using liver methylome data from mouse strains belonging to the BXD family. A regulatory hotspot on chromosome 5 had the highest density of trans-acting methylation QTLs (trans-meQTLs) associated with multiple distant CpGs. We refer to this locus as meQTL.5a. Trans-modulated CpGs showed age-dependent changes and were enriched in developmental genes, including several members of the MODY pathway (maturity onset diabetes of the young). The joint modulation by genotype and ageing resulted in a more 'aged methylome' for BXD strains that inherited the DBA/2J parental allele at meQTL.5a. Further, several gene expression traits, body weight, and lipid levels mapped to meQTL.5a, and there was a modest linkage with lifespan. DNA binding motif and protein-protein interaction enrichment analyses identified the hepatic nuclear factor, Hnf1a (MODY3 gene in humans), as a strong candidate. The pleiotropic effects of meQTL.5a could contribute to variations in body size and metabolic traits, and influence CpG methylation and epigenetic ageing that could have an impact on lifespan.
Collapse
Affiliation(s)
- Khyobeni Mozhui
- Department of Preventive Medicine, University of Tennessee Health Science Center, Memphis, TN, USA
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Hyeonju Kim
- Department of Preventive Medicine, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Flavia Villani
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Amin Haghani
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- Altos Labs, San Diego, CA, USA
| | - Saunak Sen
- Department of Preventive Medicine, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- Altos Labs, San Diego, CA, USA
- Department of Biostatistics, Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA, USA
| |
Collapse
|
4
|
Vemuri K, Radi SH, Sladek FM, Verzi MP. Multiple roles and regulatory mechanisms of the transcription factor HNF4 in the intestine. Front Endocrinol (Lausanne) 2023; 14:1232569. [PMID: 37635981 PMCID: PMC10450339 DOI: 10.3389/fendo.2023.1232569] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 07/24/2023] [Indexed: 08/29/2023] Open
Abstract
Hepatocyte nuclear factor 4-alpha (HNF4α) drives a complex array of transcriptional programs across multiple organs. Beyond its previously documented function in the liver, HNF4α has crucial roles in the kidney, intestine, and pancreas. In the intestine, a multitude of functions have been attributed to HNF4 and its accessory transcription factors, including but not limited to, intestinal maturation, differentiation, regeneration, and stem cell renewal. Functional redundancy between HNF4α and its intestine-restricted paralog HNF4γ, and co-regulation with other transcription factors drive these functions. Dysregulated expression of HNF4 results in a wide range of disease manifestations, including the development of a chronic inflammatory state in the intestine. In this review, we focus on the multiple molecular mechanisms of HNF4 in the intestine and explore translational opportunities. We aim to introduce new perspectives in understanding intestinal genetics and the complexity of gastrointestinal disorders through the lens of HNF4 transcription factors.
Collapse
Affiliation(s)
- Kiranmayi Vemuri
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers, The State University of New Jersey, Piscataway, NJ, United States
- Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ, United States
| | - Sarah H. Radi
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, Riverside, CA, United States
- Department of Biochemistry, University of California, Riverside, Riverside, CA, United States
| | - Frances M. Sladek
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, Riverside, CA, United States
| | - Michael P. Verzi
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers, The State University of New Jersey, Piscataway, NJ, United States
- Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ, United States
| |
Collapse
|
5
|
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.
Collapse
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
| |
Collapse
|
6
|
van Roey R, Brabletz T, Stemmler MP, Armstark I. Deregulation of Transcription Factor Networks Driving Cell Plasticity and Metastasis in Pancreatic Cancer. Front Cell Dev Biol 2021; 9:753456. [PMID: 34888306 PMCID: PMC8650502 DOI: 10.3389/fcell.2021.753456] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 10/27/2021] [Indexed: 12/15/2022] Open
Abstract
Pancreatic cancer is a very aggressive disease with 5-year survival rates of less than 10%. The constantly increasing incidence and stagnant patient outcomes despite changes in treatment regimens emphasize the requirement of a better understanding of the disease mechanisms. Challenges in treating pancreatic cancer include diagnosis at already progressed disease states due to the lack of early detection methods, rapid acquisition of therapy resistance, and high metastatic competence. Pancreatic ductal adenocarcinoma, the most prevalent type of pancreatic cancer, frequently shows dominant-active mutations in KRAS and TP53 as well as inactivation of genes involved in differentiation and cell-cycle regulation (e.g. SMAD4 and CDKN2A). Besides somatic mutations, deregulated transcription factor activities strongly contribute to disease progression. Specifically, transcriptional regulatory networks essential for proper lineage specification and differentiation during pancreas development are reactivated or become deregulated in the context of cancer and exacerbate progression towards an aggressive phenotype. This review summarizes the recent literature on transcription factor networks and epigenetic gene regulation that play a crucial role during tumorigenesis.
Collapse
Affiliation(s)
- Ruthger van Roey
- Department of Experimental Medicine 1, Nikolaus-Fiebiger Center for Molecular Medicine, Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen, Germany
| | - Thomas Brabletz
- Department of Experimental Medicine 1, Nikolaus-Fiebiger Center for Molecular Medicine, Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen, Germany
| | - Marc P Stemmler
- Department of Experimental Medicine 1, Nikolaus-Fiebiger Center for Molecular Medicine, Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen, Germany
| | - Isabell Armstark
- Department of Experimental Medicine 1, Nikolaus-Fiebiger Center for Molecular Medicine, Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen, Germany
| |
Collapse
|
7
|
Qu J, Qu HQ, Bradfield JP, Glessner JT, Chang X, Tian L, March M, Connolly JJ, Roizen JD, Sleiman PMA, Hakonarson H. Insights into non-autoimmune type 1 diabetes with 13 novel loci in low polygenic risk score patients. Sci Rep 2021; 11:16013. [PMID: 34362956 PMCID: PMC8346538 DOI: 10.1038/s41598-021-94994-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 07/20/2021] [Indexed: 01/21/2023] Open
Abstract
With polygenic risk score (PRS) for autoimmune type 1 diabetes (T1D), this study identified T1D cases with low T1D PRS and searched for susceptibility loci in these cases. Our hypothesis is that genetic effects (likely mediated by relatively rare genetic variants) of non-mainstream (or non-autoimmune) T1D might have been diluted in the previous studies on T1D cases in general. Two cohorts for the PRS modeling and testing respectively were included. The first cohort consisted of 3302 T1D cases and 6181 controls, and the independent second cohort consisted of 3297 T1D cases and 6169 controls. Cases with low T1D PRS were identified using PRSice-2 and compared to controls with low T1D PRS by genome-wide association (GWA) test. Thirteen novel genetic loci with high imputation quality (Quality Score r2 > 0.91) were identified of SNPs/SNVs associated with low PRS T1D at genome-wide significance (P ≤ 5.0 × E-08), in addition to 4 established T1D loci, 3 reported loci by our previous study, as well as 9 potential novel loci represented by rare SNVs, but with relatively low imputation quality (Quality Score r2 < 0.90). For the 13 novel loci, 9 regions have been reported of association with obesity related traits by previous GWA studies. Three loci encoding long intergenic non-protein coding RNAs (lncRNA), and 2 loci involved in N-linked glycosylation are also highlighted in this study.
Collapse
Affiliation(s)
- Jingchun Qu
- grid.239552.a0000 0001 0680 8770The Center for Applied Genomics, Children’s Hospital of Philadelphia, 3615 Civic Center Blvd, Abramson Building, Philadelphia, PA 19104 USA
| | - Hui-Qi Qu
- grid.239552.a0000 0001 0680 8770The Center for Applied Genomics, Children’s Hospital of Philadelphia, 3615 Civic Center Blvd, Abramson Building, Philadelphia, PA 19104 USA
| | | | - Joseph T. Glessner
- grid.239552.a0000 0001 0680 8770The Center for Applied Genomics, Children’s Hospital of Philadelphia, 3615 Civic Center Blvd, Abramson Building, Philadelphia, PA 19104 USA
| | - Xiao Chang
- grid.239552.a0000 0001 0680 8770The Center for Applied Genomics, Children’s Hospital of Philadelphia, 3615 Civic Center Blvd, Abramson Building, Philadelphia, PA 19104 USA
| | - Lifeng Tian
- grid.239552.a0000 0001 0680 8770The Center for Applied Genomics, Children’s Hospital of Philadelphia, 3615 Civic Center Blvd, Abramson Building, Philadelphia, PA 19104 USA
| | - Michael March
- grid.239552.a0000 0001 0680 8770The Center for Applied Genomics, Children’s Hospital of Philadelphia, 3615 Civic Center Blvd, Abramson Building, Philadelphia, PA 19104 USA
| | - John J. Connolly
- grid.239552.a0000 0001 0680 8770The Center for Applied Genomics, Children’s Hospital of Philadelphia, 3615 Civic Center Blvd, Abramson Building, Philadelphia, PA 19104 USA
| | - Jeffrey D. Roizen
- grid.25879.310000 0004 1936 8972Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Patrick M. A. Sleiman
- grid.239552.a0000 0001 0680 8770The Center for Applied Genomics, Children’s Hospital of Philadelphia, 3615 Civic Center Blvd, Abramson Building, Philadelphia, PA 19104 USA ,grid.25879.310000 0004 1936 8972Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA ,grid.239552.a0000 0001 0680 8770Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
| | - Hakon Hakonarson
- grid.239552.a0000 0001 0680 8770The Center for Applied Genomics, Children’s Hospital of Philadelphia, 3615 Civic Center Blvd, Abramson Building, Philadelphia, PA 19104 USA ,grid.25879.310000 0004 1936 8972Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA ,grid.239552.a0000 0001 0680 8770Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA ,grid.239552.a0000 0001 0680 8770Division of Pulmonary Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
| |
Collapse
|
8
|
Camolotto SA, Belova VK, Torre-Healy L, Vahrenkamp JM, Berrett KC, Conway H, Shea J, Stubben C, Moffitt R, Gertz J, Snyder EL. Reciprocal regulation of pancreatic ductal adenocarcinoma growth and molecular subtype by HNF4α and SIX1/4. Gut 2021; 70:900-914. [PMID: 32826305 PMCID: PMC7945295 DOI: 10.1136/gutjnl-2020-321316] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 06/17/2020] [Accepted: 06/30/2020] [Indexed: 12/13/2022]
Abstract
OBJECTIVE Pancreatic ductal adenocarcinoma (PDAC) is an aggressive malignancy with a 5-year survival of less than 5%. Transcriptomic analysis has identified two clinically relevant molecular subtypes of PDAC: classical and basal-like. The classical subtype is characterised by a more favourable prognosis and better response to chemotherapy than the basal-like subtype. The classical subtype also expresses higher levels of lineage specifiers that regulate endodermal differentiation, including the nuclear receptor hepatocyte nuclear factor 4 α (HNF4α). The objective of this study is to evaluate the role of HNF4α, SIX4 and SIX1 in regulating the growth and molecular subtype of PDAC. DESIGN We manipulate the expression of HNF4α, SIX4 and SIX1 in multiple in vitro and in vivo PDAC models. We determine the consequences of manipulating these genes on PDAC growth, differentiation and molecular subtype using functional assays, gene expression analysis and cross-species comparisons with human datasets. RESULTS We show that HNF4α restrains tumour growth and drives tumour cells toward an epithelial identity. Gene expression analysis of murine models and human tumours shows that HNF4α activates expression of genes associated with the classical subtype. HNF4α also directly represses SIX4 and SIX1, two mesodermal/neuronal lineage specifiers expressed in the basal-like subtype. Finally, SIX4 and SIX1 drive proliferation and regulate differentiation in HNF4α-negative PDAC. CONCLUSION Our data show that HNF4α regulates the growth and molecular subtype of PDAC by multiple mechanisms, including activation of the classical gene expression programme and repression of SIX4 and SIX1, which may represent novel dependencies of the basal-like subtype.
Collapse
Affiliation(s)
- Soledad A Camolotto
- Department of Pathology, Huntsman Cancer Institute, University of Utah Health, Salt Lake City, Utah, USA
| | - Veronika K Belova
- Department of Pathology, Huntsman Cancer Institute, University of Utah Health, Salt Lake City, Utah, USA
| | - Luke Torre-Healy
- Department of Biomedical Informatics, Stony Brook University, Stony Brook, New York, USA
| | - Jeffery M Vahrenkamp
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah Health, Salt Lake City, Utah, USA
| | - Kristofer C Berrett
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah Health, Salt Lake City, Utah, USA
| | - Hannah Conway
- HCI Clinical Trials Operations, Huntsman Cancer Institute, University of Utah Health, Salt Lake City, Utah, USA
| | - Jill Shea
- Department of Surgery, University of Utah, Salt Lake City, Utah, USA
| | - Chris Stubben
- Bioinformatics Shared Resource, Huntsman Cancer Institute, University of Utah Health, Salt Lake City, Utah, USA
| | - Richard Moffitt
- Department of Biomedical Informatics, Stony Brook University, Stony Brook, New York, USA
| | - Jason Gertz
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah Health, Salt Lake City, Utah, USA
| | - Eric L Snyder
- Department of Pathology, Huntsman Cancer Institute, University of Utah Health, Salt Lake City, Utah, USA
| |
Collapse
|
9
|
Marchesin V, Pérez-Martí A, Le Meur G, Pichler R, Grand K, Klootwijk ED, Kesselheim A, Kleta R, Lienkamp S, Simons M. Molecular Basis for Autosomal-Dominant Renal Fanconi Syndrome Caused by HNF4A. Cell Rep 2020; 29:4407-4421.e5. [PMID: 31875549 PMCID: PMC6941224 DOI: 10.1016/j.celrep.2019.11.066] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 10/08/2019] [Accepted: 11/15/2019] [Indexed: 12/26/2022] Open
Abstract
HNF4A is a nuclear hormone receptor that binds DNA as an obligate homodimer. While all known human heterozygous mutations are associated with the autosomal-dominant diabetes form MODY1, one particular mutation (p.R85W) in the DNA-binding domain (DBD) causes additional renal Fanconi syndrome (FRTS). Here, we find that expression of the conserved fly ortholog dHNF4 harboring the FRTS mutation in Drosophila nephrocytes caused nuclear depletion and cytosolic aggregation of a wild-type dHNF4 reporter protein. While the nuclear depletion led to mitochondrial defects and lipid droplet accumulation, the cytosolic aggregates triggered the expansion of the endoplasmic reticulum (ER), autophagy, and eventually cell death. The latter effects could be fully rescued by preventing nuclear export through interfering with serine phosphorylation in the DBD. Our data describe a genomic and a non-genomic mechanism for FRTS in HNF4A-associated MODY1 with important implications for the renal proximal tubule and the regulation of other nuclear hormone receptors. HNF4 controls lipid metabolism in Drosophila nephrocytes The kidney disease mutation R85W shows dominant-negative effects in nephrocytes Dephosphorylation at S87 prevents the dominant-negative effects R85W mutation causes mitochondrial dysfunction in reprogrammed renal epithelial cells
Collapse
Affiliation(s)
- Valentina Marchesin
- INSERM UMR1163, Laboratory of Epithelial Biology and Disease, Imagine Institute, Paris Descartes University, Sorbonne Paris Cité, Hôpital Necker-Enfants Malades, 75015 Paris, France
| | - Albert Pérez-Martí
- INSERM UMR1163, Laboratory of Epithelial Biology and Disease, Imagine Institute, Paris Descartes University, Sorbonne Paris Cité, Hôpital Necker-Enfants Malades, 75015 Paris, France
| | - Gwenn Le Meur
- INSERM UMR1163, Laboratory of Epithelial Biology and Disease, Imagine Institute, Paris Descartes University, Sorbonne Paris Cité, Hôpital Necker-Enfants Malades, 75015 Paris, France
| | - Roman Pichler
- Renal Division, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, 79098 Freiburg, Germany
| | - Kelli Grand
- Institute of Anatomy, University of Zurich, 8057 Zurich, Switzerland
| | - Enriko D Klootwijk
- Department of Renal Medicine, University College London, London NW3 2PF, UK
| | - Anne Kesselheim
- Department of Renal Medicine, University College London, London NW3 2PF, UK
| | - Robert Kleta
- Department of Renal Medicine, University College London, London NW3 2PF, UK
| | - Soeren Lienkamp
- Renal Division, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, 79098 Freiburg, Germany; Institute of Anatomy, University of Zurich, 8057 Zurich, Switzerland
| | - Matias Simons
- INSERM UMR1163, Laboratory of Epithelial Biology and Disease, Imagine Institute, Paris Descartes University, Sorbonne Paris Cité, Hôpital Necker-Enfants Malades, 75015 Paris, France.
| |
Collapse
|
10
|
Gao B, Xie W, Wu X, Wang L, Guo J. Functionally analyzing the important roles of hepatocyte nuclear factor 3 (FoxA) in tumorigenesis. Biochim Biophys Acta Rev Cancer 2020; 1873:188365. [PMID: 32325165 DOI: 10.1016/j.bbcan.2020.188365] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 04/14/2020] [Accepted: 04/14/2020] [Indexed: 12/19/2022]
Abstract
Transcriptional factors (TFs) play a central role in governing gene expression under physiological conditions including the processes of embryonic development, metabolic homeostasis and response to extracellular stimuli. Conceivably, the aberrant dysregulations of TFs would dominantly result in various human disorders including tumorigenesis, diabetes and neurodegenerative diseases. Serving as the most evolutionarily reserved TFs, Fox family TFs have been explored to exert distinct biological functions in neoplastic development, by manipulating diverse gene expression. Recently, among the Fox family members, the pilot roles of FoxAs attract more attention due to their functions as both pioneer factor and transcriptional factor in human tumorigenesis, particularly in the sex-dimorphism tumors. Therefore, the pathological roles of FoxAs in tumorigenesis have been well-explored in modulating inflammation, immune response and metabolic homeostasis. In this review, we comprehensively summarize the impressive progression of FoxA functional annotation, clinical relevance, upstream regulators and downstream effectors, as well as valuable animal models, and highlight the potential strategies to target FoxAs for cancer therapies.
Collapse
Affiliation(s)
- Bing Gao
- Institute of Precision Medicine, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510275, China
| | - Wei Xie
- Institute of Precision Medicine, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510275, China
| | - Xueji Wu
- Institute of Precision Medicine, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510275, China
| | - Lei Wang
- Institute of Precision Medicine, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510275, China
| | - Jianping Guo
- Institute of Precision Medicine, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510275, China.
| |
Collapse
|
11
|
Chen B, Yu J, Lu L, Dong F, Zhou F, Tao X, Sun E. Upregulated forkhead-box A3 elevates the expression of forkhead-box A1 and forkhead-box A2 to promote metastasis in esophageal cancer. Oncol Lett 2019; 17:4351-4360. [PMID: 30944629 DOI: 10.3892/ol.2019.10078] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 02/04/2019] [Indexed: 11/06/2022] Open
Abstract
Esophageal cancer (EC) is one of the most lethal cancers currently known. Members of the forkhead-box A (FOXA) family, including FOXA1 and FOXA2, have been reported to regulate EC progression. However, the role of FOXA3, which is another FOXA member, has not yet been investigated. In the present study, public dataset analyses and immunohistochemistry of 96 samples from patients with EC were performed to determine the potential roles of FOXA3 in EC. The results revealed that FOXA3 was significantly upregulated in EC tumor tissues and Barrett's esophagus tissues. In addition, FOXA3 upregulation was positively associated with tumor invasion, distant metastasis, tumor-node-metastasis stage and shorter overall survival in patients with EC, and multivariate analysis identified FOXA3 as an independent prognostic marker. In vitro experiments demonstrated that the migratory and invasive abilities of EC109 and EC9706 cell lines were inhibited following FOXA3 knockdown. Notably, FOXA3 expression levels were positively correlated with FOXA1 and FOXA2 expression levels according to The Cancer Genome Atlas dataset analysis. Furthermore, FOXA3 knockdown decreased the expression levels of FOXA1 and FOXA2 in EC109 and EC9706 cell lines. Conversely, FOXA1 or FOXA2 overexpression compensated for the effects of FOXA3 knockdown on the migratory and invasive capacities of EC cells. In conclusion, the present study demonstrated that FOXA3 upregulation in EC cells promoted metastasis through regulation of other FOXA members.
Collapse
Affiliation(s)
- Bing Chen
- Department of Pathology, School of Basic Medical Sciences, Wannan Medical College, Wuhu, Anhui 241002, P.R. China
| | - Jiegen Yu
- Department of Management Science, School of Humanities and Management, Wannan Medical College, Wuhu, Anhui 241002, P.R. China
| | - Linming Lu
- Department of Pathology, School of Basic Medical Sciences, Wannan Medical College, Wuhu, Anhui 241002, P.R. China
| | - Fangyuan Dong
- Department of Pathology, School of Basic Medical Sciences, Wannan Medical College, Wuhu, Anhui 241002, P.R. China
| | - Fangfang Zhou
- Department of Pathology, School of Basic Medical Sciences, Wannan Medical College, Wuhu, Anhui 241002, P.R. China
| | - Xiangxiang Tao
- Department of Pathology, School of Basic Medical Sciences, Wannan Medical College, Wuhu, Anhui 241002, P.R. China
| | - Entao Sun
- Department of Health Inspection and Quarantine, School of Laboratory Medicine, Wannan Medical College, Wuhu, Anhui 241002, P.R. China
| |
Collapse
|
12
|
Camolotto SA, Belova VK, Snyder EL. The role of lineage specifiers in pancreatic ductal adenocarcinoma. J Gastrointest Oncol 2018; 9:1005-1013. [PMID: 30603119 DOI: 10.21037/jgo.2018.05.04] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Over the last decade, multiple genomics studies have led to the identification of discrete molecular subtypes of pancreatic ductal adenocarcinoma. A general theme has emerged that most pancreatic ductal adenocarcinoma (PDAC) can be grouped into two major subtypes based on cancer cell autonomous properties: classical/pancreatic progenitor and basal-like/squamous. The classical/progenitor subtype expresses higher levels of lineage specifiers that regulate endodermal differentiation than the basal-like/squamous subtype. The basal-like/squamous subtype confers a worse prognosis, raising the possibility that loss of these lineage specifiers might enhance the malignant potential of PDAC. Here, we discuss several of these differentially expressed lineage specifiers and examine the evidence that they might play a functional role in PDAC biology.
Collapse
Affiliation(s)
| | - Veronika K Belova
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Eric L Snyder
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA.,Department of Pathology, University of Utah, Salt Lake City, UT, USA
| |
Collapse
|
13
|
The molecular functions of hepatocyte nuclear factors - In and beyond the liver. J Hepatol 2018; 68:1033-1048. [PMID: 29175243 DOI: 10.1016/j.jhep.2017.11.026] [Citation(s) in RCA: 140] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 11/16/2017] [Accepted: 11/20/2017] [Indexed: 12/27/2022]
Abstract
The hepatocyte nuclear factors (HNFs) namely HNF1α/β, FOXA1/2/3, HNF4α/γ and ONECUT1/2 are expressed in a variety of tissues and organs, including the liver, pancreas and kidney. The spatial and temporal manner of HNF expression regulates embryonic development and subsequently the development of multiple tissues during adulthood. Though the HNFs were initially identified individually based on their roles in the liver, numerous studies have now revealed that the HNFs cross-regulate one another and exhibit synergistic relationships in the regulation of tissue development and function. The complex HNF transcriptional regulatory networks have largely been elucidated in rodent models, but less so in human biological systems. Several heterozygous mutations in these HNFs were found to cause diseases in humans but not in rodents, suggesting clear species-specific differences in mutational mechanisms that remain to be uncovered. In this review, we compare and contrast the expression patterns of the HNFs, the HNF cross-regulatory networks and how these liver-enriched transcription factors serve multiple functions in the liver and beyond, extending our focus to the pancreas and kidney. We also summarise the insights gained from both human and rodent studies of mutations in several HNFs that are known to lead to different disease conditions.
Collapse
|
14
|
Chen C, Soto-Gutierrez A, Baptista PM, Spee B. Biotechnology Challenges to In Vitro Maturation of Hepatic Stem Cells. Gastroenterology 2018; 154:1258-1272. [PMID: 29428334 PMCID: PMC6237283 DOI: 10.1053/j.gastro.2018.01.066] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 01/05/2018] [Accepted: 01/10/2018] [Indexed: 12/16/2022]
Abstract
The incidence of liver disease is increasing globally. The only curative therapy for severe end-stage liver disease, liver transplantation, is limited by the shortage of organ donors. In vitro models of liver physiology have been developed and new technologies and approaches are progressing rapidly. Stem cells might be used as a source of liver tissue for development of models, therapies, and tissue-engineering applications. However, we have been unable to generate and maintain stable and mature adult liver cells ex vivo. We review factors that promote hepatocyte differentiation and maturation, including growth factors, transcription factors, microRNAs, small molecules, and the microenvironment. We discuss how the hepatic circulation, microbiome, and nutrition affect liver function, and the criteria for considering cells derived from stem cells to be fully mature hepatocytes. We explain the challenges to cell transplantation and consider future technologies for use in hepatic stem cell maturation, including 3-dimensional biofabrication and genome modification.
Collapse
Affiliation(s)
- Chen Chen
- Department of Clinical Sciences of Companion Animals, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands; The Royal Netherlands Academy of Arts and Sciences, Hubrecht Institute and University Medical Center Utrecht, Utrecht, The Netherlands
| | | | - Pedro M Baptista
- Instituto de Investigación Sanitaria de Aragón, Zaragoza, Spain; Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas, Madrid, Spain; Fundación Agencia Aragonesa para la Investigación y el Desarrollo, Zaragoza, Spain; Instituto de Investigación Sanitaria de la Fundación Jiménez Díaz, Madrid, Spain; Department of Biomedical and Aerospace Engineering, Universidad Carlos III de Madrid, Madrid, Spain
| | - Bart Spee
- Department of Clinical Sciences of Companion Animals, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands.
| |
Collapse
|
15
|
Ran L, Chen Y, Sher J, Wong EWP, Murphy D, Zhang JQ, Li D, Deniz K, Sirota I, Cao Z, Wang S, Guan Y, Shukla S, Li KY, Chramiec A, Xie Y, Zheng D, Koche RP, Antonescu CR, Chen Y, Chi P. FOXF1 Defines the Core-Regulatory Circuitry in Gastrointestinal Stromal Tumor. Cancer Discov 2017; 8:234-251. [PMID: 29162563 DOI: 10.1158/2159-8290.cd-17-0468] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 09/26/2017] [Accepted: 11/14/2017] [Indexed: 01/04/2023]
Abstract
The cellular context that integrates upstream signaling and downstream nuclear response dictates the oncogenic behavior and shapes treatment responses in distinct cancer types. Here, we uncover that in gastrointestinal stromal tumor (GIST), the forkhead family member FOXF1 directly controls the transcription of two master regulators, KIT and ETV1, both required for GIST precursor-interstitial cells of Cajal lineage specification and GIST tumorigenesis. Further, FOXF1 colocalizes with ETV1 at enhancers and functions as a pioneer factor that regulates the ETV1-dependent GIST lineage-specific transcriptome through modulation of the local chromatin context, including chromatin accessibility, enhancer maintenance, and ETV1 binding. Functionally, FOXF1 is required for human GIST cell growth in vitro and murine GIST tumor growth and maintenance in vivo The simultaneous control of the upstream signaling and nuclear response sets up a unique regulatory paradigm and highlights the critical role of FOXF1 in enforcing the GIST cellular context for highly lineage-restricted clinical behavior and treatment response.Significance: We uncover that FOXF1 defines the core-regulatory circuitry in GIST through both direct transcriptional regulation and pioneer factor function. The unique and simultaneous control of signaling and transcriptional circuitry by FOXF1 sets up an enforced transcriptional addiction to FOXF1 in GIST, which can be exploited diagnostically and therapeutically. Cancer Discov; 8(2); 234-51. ©2017 AACR.See related commentary by Lee and Duensing, p. 146This article is highlighted in the In This Issue feature, p. 127.
Collapse
Affiliation(s)
- Leili Ran
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Yuedan Chen
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York.,Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, New York
| | - Jessica Sher
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Elissa W P Wong
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Devan Murphy
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jenny Q Zhang
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Dan Li
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Kemal Deniz
- Department of Pathology, Erciyes University, Kayseri, Turkey
| | - Inna Sirota
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York
| | - Zhen Cao
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York.,Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, New York
| | - Shangqian Wang
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Youxin Guan
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Shipra Shukla
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Katie Yang Li
- Center of Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Alan Chramiec
- Center of Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, New York.,Biomedical Engineering, Columbia University, New York, New York
| | - Yuanyuan Xie
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Deyou Zheng
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York.,Department of Neurology, Albert Einstein College of Medicine, Bronx, New York.,Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York
| | - Richard P Koche
- Center of Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Cristina R Antonescu
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Yu Chen
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York. .,Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, New York.,Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Ping Chi
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York. .,Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, New York.,Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Medicine, Weill Cornell Medical College, New York, New York
| |
Collapse
|
16
|
Wang W, Yao LJ, Shen W, Ding K, Shi PM, Chen F, He J, Ding J, Zhang X, Xie WF. FOXA2 alleviates CCl 4-induced liver fibrosis by protecting hepatocytes in mice. Sci Rep 2017; 7:15532. [PMID: 29138513 PMCID: PMC5686201 DOI: 10.1038/s41598-017-15831-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 11/02/2017] [Indexed: 12/31/2022] Open
Abstract
The liver-enriched transcription factor Forkhead Box A2 (FOXA2) has been reported to be involved in bile acid homeostasis and bile duct development. However, the role of FOXA2 in liver fibrogenesis remains undefined. In this study, we found that the abundance of FOXA2 was significantly lower in fibrotic livers of patients and mice treated with CCl4 than in controls. Interestingly, the expression level of FOXA2 decreased in hepatocytes, whereas FOXA2 was elevated in hepatic stellate cells (HSCs) of mouse fibrotic livers. Hepatocyte-specific ablation of FOXA2 in adult mice exacerbated liver fibrosis induced by CCl4. Either lentivirus LV-CMV-FOXA2 mediated FOXA2 overexpression in the liver or adeno-associated virus AAV8-TBG-FOXA2-mediated hepatocyte-specific upregulation of FOXA2 alleviated hepatic fibrosis. Overexpression of FOXA2 in HSCs did not obviously affect hepatic fibrogenesis. Additionally, FOXA2 knockout in hepatocytes resulted in aberrant transcription of metabolic genes. Furthermore, hepatocyte-specific knockout of FOXA2 enhanced endoplasmic reticulum stress (ER stress) and the apoptosis of hepatocytes, whereas FOXA2 overexpression in hepatocytes suppressed ER stress and hepatocyte apoptosis in mouse fibrotic livers. In conclusion, our findings suggested that FOXA2-mediated hepatocyte protection has a therapeutic role in hepatic fibrosis, and thus may be a new, promising anti-fibrotic option for treating chronic liver diseases.
Collapse
Affiliation(s)
- Wei Wang
- Department of Gastroenterology, Changzheng Hospital, Second Military Medical University, 415 Fengyang Road, Shanghai, 200003, China.,Department of Gastroenterology, Lanzhou General Hospital of Lanzhou Military Command, Lanzhou, China
| | - Li-Jia Yao
- Department of Gastroenterology, Changzheng Hospital, Second Military Medical University, 415 Fengyang Road, Shanghai, 200003, China.,Department of Gastroenterology, Fuzhou General Hospital, Fuzhou, 350025, China
| | - Weifeng Shen
- Department of Special Treatment, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, 225 Changhai Road, Shanghai, 200438, China
| | - Kai Ding
- Department of Gastroenterology, Changzheng Hospital, Second Military Medical University, 415 Fengyang Road, Shanghai, 200003, China
| | - Pei-Mei Shi
- Department of Gastroenterology, Changzheng Hospital, Second Military Medical University, 415 Fengyang Road, Shanghai, 200003, China
| | - Fei Chen
- Department of Gastroenterology, Changzheng Hospital, Second Military Medical University, 415 Fengyang Road, Shanghai, 200003, China
| | - Jin He
- Department of Gastroenterology, Changzheng Hospital, Second Military Medical University, 415 Fengyang Road, Shanghai, 200003, China
| | - Jin Ding
- International Cooperation Laboratory on Signal Transduction of Eastern Hepatobiliary Surgery Institute, Second Military Medical University, Shanghai, China
| | - Xin Zhang
- Department of Gastroenterology, Changzheng Hospital, Second Military Medical University, 415 Fengyang Road, Shanghai, 200003, China
| | - Wei-Fen Xie
- Department of Gastroenterology, Changzheng Hospital, Second Military Medical University, 415 Fengyang Road, Shanghai, 200003, China.
| |
Collapse
|
17
|
Kakumanu A, Velasco S, Mazzoni E, Mahony S. Deconvolving sequence features that discriminate between overlapping regulatory annotations. PLoS Comput Biol 2017; 13:e1005795. [PMID: 29049320 PMCID: PMC5663517 DOI: 10.1371/journal.pcbi.1005795] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 10/31/2017] [Accepted: 09/26/2017] [Indexed: 11/19/2022] Open
Abstract
Genomic loci with regulatory potential can be annotated with various properties. For example, genomic sites bound by a given transcription factor (TF) can be divided according to whether they are proximal or distal to known promoters. Sites can be further labeled according to the cell types and conditions in which they are active. Given such a collection of labeled sites, it is natural to ask what sequence features are associated with each annotation label. However, discovering such label-specific sequence features is often confounded by overlaps between the labels; e.g. if regulatory sites specific to a given cell type are also more likely to be promoter-proximal, it is difficult to assess whether motifs identified in that set of sites are associated with the cell type or associated with promoters. In order to meet this challenge, we developed SeqUnwinder, a principled approach to deconvolving interpretable discriminative sequence features associated with overlapping annotation labels. We demonstrate the novel analysis abilities of SeqUnwinder using three examples. Firstly, SeqUnwinder is able to unravel sequence features associated with the dynamic binding behavior of TFs during motor neuron programming from features associated with chromatin state in the initial embryonic stem cells. Secondly, we characterize distinct sequence properties of multi-condition and cell-specific TF binding sites after controlling for uneven associations with promoter proximity. Finally, we demonstrate the scalability of SeqUnwinder to discover cell-specific sequence features from over one hundred thousand genomic loci that display DNase I hypersensitivity in one or more ENCODE cell lines. Transcription factor proteins control gene expression by recognizing and interacting with short DNA sequence patterns in regulatory regions on the genome. Current genomics experiments allow us to find regulatory regions associated with a particular biochemical activity over the entire genome; for example, all regions where a particular transcription factor interacts with the genome in a given cell type. Given a collection of regulatory regions, we often aim to discover short DNA sequence patterns that are more common in the collection than in other regions. Performing such “DNA motif-finding” analysis can give us hints about the patterns that determine gene regulation in the analyzed cell type. Here we describe a new method for DNA motif-finding called SeqUnwinder. Our approach analyzes collections of regulatory regions where each has been labeled according to various biological properties. For example, the labels could correspond to various cell types in which the regulatory region is active. SeqUnwinder then performs machine-learning analysis to unravel DNA sequence features that are characteristic of each label (e.g. features that distinguish regulatory regions in each cell type from other cell types). SeqUnwinder is the first method to enable analysis of regulatory region collections that contain several overlapping labels.
Collapse
Affiliation(s)
- Akshay Kakumanu
- Center for Eukaryotic Gene Regulation, Department of Biochemistry & Molecular Biology, The Pennsylvania State University, University Park, PA, United States of America
| | - Silvia Velasco
- Department of Biology, New York University, 100 Washington Square East, New York, NY, United States of America
| | - Esteban Mazzoni
- Department of Biology, New York University, 100 Washington Square East, New York, NY, United States of America
| | - Shaun Mahony
- Center for Eukaryotic Gene Regulation, Department of Biochemistry & Molecular Biology, The Pennsylvania State University, University Park, PA, United States of America
- * E-mail:
| |
Collapse
|
18
|
Li L, Li D, Heyward S, Wang H. Transcriptional Regulation of CYP2B6 Expression by Hepatocyte Nuclear Factor 3β in Human Liver Cells. PLoS One 2016; 11:e0150587. [PMID: 26930610 PMCID: PMC4773089 DOI: 10.1371/journal.pone.0150587] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 02/16/2016] [Indexed: 01/09/2023] Open
Abstract
CYP2B6 plays an increasingly important role in xenobiotic metabolism and detoxification. The constitutive androstane receptor (CAR) and the pregnane X receptor (PXR) have been established as predominant regulators for the inductive expression of CYP2B6 gene in human liver. However, there are dramatic interindividual variabilities in CYP2B6 expression that cannot be fully explained by the CAR/PXR-based modulation alone. Here, we show that expression level of CYP2B6 was correlated with that of hepatocyte nuclear factor 3β (HNF3β) in human primary hepatocytes prepared from 35 liver donors. Utilizing recombinant virus-mediated overexpression or knockdown of HNF3β in HepG2 cells, as well as constructs containing serial deletion and site-directed mutation of HNF3β binding motifs in CYP2B6 luciferase reporter assays, we demonstrated that the presence or lack of HNF3β expression markedly correlated with CYP2B6 gene expression and its promoter activity. Novel enhancer modules of HNF3β located upstream of the CYP2B6 gene transcription start site were identified and functionally validated as key elements governing HNF3β-mediated CYP2B6 expression. Chromatin immunoprecipitation assays in human primary hepatocytes and surface plasmon resonance binding affinity experiments confirmed the essential role of these enhancers in the recruitment of HNF3β to the promoter of CYP2B6 gene. Overall, these findings indicate that HNF3β represents a new liver enriched transcription factor that is involved in the transcription of CYP2B6 gene and contributes to the large interindividual variations of CYP2B6 expression in human population.
Collapse
Affiliation(s)
- Linhao Li
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland at Baltimore, 20 Penn Street, Baltimore, Maryland 21201, United States of America
| | - Daochuan Li
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland at Baltimore, 20 Penn Street, Baltimore, Maryland 21201, United States of America
| | - Scott Heyward
- Bioreclamation, IVT, 1450 Rolling Road, Baltimore, Maryland 21227, United States of America
| | - Hongbing Wang
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland at Baltimore, 20 Penn Street, Baltimore, Maryland 21201, United States of America
- * E-mail:
| |
Collapse
|
19
|
Ma X, Xu L, Mueller E. Calorie hoarding and thrifting: Foxa3 finds a way. Adipocyte 2015; 4:325-8. [PMID: 26451291 DOI: 10.1080/21623945.2015.1028700] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Revised: 03/04/2015] [Accepted: 03/06/2015] [Indexed: 12/11/2022] Open
Abstract
Obesity and diabetes are major health concerns worldwide. Western diets, often calorically rich, paired with sedentary habits are driving the current worldwide epidemic of pediatric and adult obesity. In addition, age related energy imbalances lead to increased adiposity and metabolic disorders later in life, making the middle aged population particularly susceptible. Here we discuss how Forkhead box A3 (Foxa3), a family member of the forkhead box binding proteins, can potentially contribute to pathology by playing a double role in metabolism. Recent data revealed that Foxa3 favors the selective expansion of visceral depots under high caloric conditions (e.g., high fat diet) and suppresses subcutaneous fat tissue energy expenditure during aging. This evidence suggests that Foxa3 acts to both preserve and conserve calories, by accumulating fat and by reducing metabolic burn. In other words, Foxa3 appears to function to enable energy "hoarding," which may be critical for survival of organisms with intermittent exposure to external caloric sources, but pathologic in circumstances where calories are abundant. Understanding how this "calorie hoarder gene" functions may suggest approaches to combat obesity and associated metabolic disorders.
Collapse
|
20
|
Zia A, Bhatti A, John P, Kiani AK. Data interpretation: deciphering the biological function of Type 2 diabetes associated risk loci. Acta Diabetol 2015; 52:789-800. [PMID: 25585593 DOI: 10.1007/s00592-014-0700-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Accepted: 12/09/2014] [Indexed: 10/24/2022]
Abstract
AIMS Type 2 diabetes (T2D) is a complex multifactorial disorder with more than 40 loci associated with disease susceptibility. Most of these genome-wide significant loci reside in noncoding regions, it is important to decipher the potential regulatory function of these variants and to differentiate between true and tag signals. Nowadays, databases are being developed to study and predict the function of these associated variants, and RegulomeDB is one such database. METHODS We used RegulomeDB to analyze the potential function of the associated variants reported in five genome-wide association studies (GWAS) of T2D. RESULTS We investigated the 1,567 single nucleotide polymorphisms (SNPs) with 989 SNPs with a score of 1-6. Of those 989 SNPs, only 64 returned with RegulomeDB score <3 (evidence of regulatory function), and only four of these were GWAS significant SNPs (THADA/rs10203174, score = 1b; UBE2E2/rs7612463, score = 2a; ARAP1/rs1552224 and TP53INP1/rs8996852, score = 2b). But only 63 % of the annotated SNPs showed regulatory function that is an important limitation of the RegulomeDB as this database only provides information of few regulatory elements. CONCLUSION This study further supports that some of the noncoding GWAS variants are the true associations and not the tag ones. This study also proves the utility and importance of the RegulomeDB and other such databases. Although it is an extensive database of regulatory elements but has certain limitation due to utilization of only few types of regulatory elements and pathways.
Collapse
Affiliation(s)
- Asima Zia
- Healthcare Biotechnology, Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Sector H-12, Islamabad, Pakistan
| | | | | | | |
Collapse
|
21
|
Baraille F, Ayari S, Carrière V, Osinski C, Garbin K, Blondeau B, Guillemain G, Serradas P, Rousset M, Lacasa M, Cardot P, Ribeiro A. Glucose Tolerance Is Improved in Mice Invalidated for the Nuclear Receptor HNF-4γ: A Critical Role for Enteroendocrine Cell Lineage. Diabetes 2015; 64:2744-56. [PMID: 25829452 DOI: 10.2337/db14-0993] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Accepted: 03/21/2015] [Indexed: 11/13/2022]
Abstract
Intestine contributes to energy homeostasis through the absorption, metabolism, and transfer of nutrients to the organism. We demonstrated previously that hepatocyte nuclear receptor-4α (HNF-4α) controls intestinal epithelium homeostasis and intestinal absorption of dietary lipids. HNF-4γ, the other HNF-4 form highly expressed in intestine, is much less studied. In HNF-4γ knockout mice, we detect an exaggerated insulin peak and improvement in glucose tolerance during oral but not intraperitoneal glucose tolerance tests, highlighting the involvement of intestine. Moreover, the enteroendocrine L-type cell lineage is modified, as assessed by the increased expression of transcription factors Isl1, Foxa1/2, and Hnf4a, leading to an increase of both GLP-1-positive cell number and basal and stimulated GLP-1 plasma levels potentiating the glucose-stimulated insulin secretion. Using the GLP-1 antagonist exendin (9-39), we demonstrate a direct effect of GLP-1 on improved glucose tolerance. GLP-1 exerts a trophic effect on pancreatic β-cells, and we report an increase of the β-cell fraction correlated with an augmented number of proliferative islet cells and with resistance to streptozotocin-induced diabetes. In conclusion, the loss of HNF-4γ improves glucose homeostasis through a modulation of the enteroendocrine cell lineage.
Collapse
Affiliation(s)
- Floriane Baraille
- Sorbonne Universités, Université Pierre et Marie Curie, UMR_S 1138, Centre de Recherche des Cordeliers, Paris, France INSERM, UMR_S 1138, Centre de Recherche des Cordeliers, Paris, France Université Paris Descartes, Sorbonne Paris Cité, UMR_S 1138, Centre de Recherche des Cordeliers, Paris, France Institute of Cardiometabolism and Nutrition, Pitié-Salpêtrière Hospital, Paris, France
| | - Sami Ayari
- Sorbonne Universités, Université Pierre et Marie Curie, UMR_S 1138, Centre de Recherche des Cordeliers, Paris, France INSERM, UMR_S 1138, Centre de Recherche des Cordeliers, Paris, France Université Paris Descartes, Sorbonne Paris Cité, UMR_S 1138, Centre de Recherche des Cordeliers, Paris, France Institute of Cardiometabolism and Nutrition, Pitié-Salpêtrière Hospital, Paris, France
| | - Véronique Carrière
- Sorbonne Universités, Université Pierre et Marie Curie, UMR_S 1138, Centre de Recherche des Cordeliers, Paris, France INSERM, UMR_S 1138, Centre de Recherche des Cordeliers, Paris, France Université Paris Descartes, Sorbonne Paris Cité, UMR_S 1138, Centre de Recherche des Cordeliers, Paris, France Institute of Cardiometabolism and Nutrition, Pitié-Salpêtrière Hospital, Paris, France
| | - Céline Osinski
- Sorbonne Universités, Université Pierre et Marie Curie, UMR_S 1138, Centre de Recherche des Cordeliers, Paris, France INSERM, UMR_S 1138, Centre de Recherche des Cordeliers, Paris, France Université Paris Descartes, Sorbonne Paris Cité, UMR_S 1138, Centre de Recherche des Cordeliers, Paris, France Institute of Cardiometabolism and Nutrition, Pitié-Salpêtrière Hospital, Paris, France
| | - Kevin Garbin
- Sorbonne Universités, Université Pierre et Marie Curie, UMR_S 1138, Centre de Recherche des Cordeliers, Paris, France INSERM, UMR_S 1138, Centre de Recherche des Cordeliers, Paris, France Université Paris Descartes, Sorbonne Paris Cité, UMR_S 1138, Centre de Recherche des Cordeliers, Paris, France
| | - Bertrand Blondeau
- Sorbonne Universités, Université Pierre et Marie Curie, UMR_S 1138, Centre de Recherche des Cordeliers, Paris, France INSERM, UMR_S 1138, Centre de Recherche des Cordeliers, Paris, France Université Paris Descartes, Sorbonne Paris Cité, UMR_S 1138, Centre de Recherche des Cordeliers, Paris, France Institute of Cardiometabolism and Nutrition, Pitié-Salpêtrière Hospital, Paris, France
| | - Ghislaine Guillemain
- Sorbonne Universités, Université Pierre et Marie Curie, UMR_S 1138, Centre de Recherche des Cordeliers, Paris, France INSERM, UMR_S 1138, Centre de Recherche des Cordeliers, Paris, France Université Paris Descartes, Sorbonne Paris Cité, UMR_S 1138, Centre de Recherche des Cordeliers, Paris, France Institute of Cardiometabolism and Nutrition, Pitié-Salpêtrière Hospital, Paris, France
| | - Patricia Serradas
- Sorbonne Universités, Université Pierre et Marie Curie, UMR_S 1138, Centre de Recherche des Cordeliers, Paris, France INSERM, UMR_S 1138, Centre de Recherche des Cordeliers, Paris, France Université Paris Descartes, Sorbonne Paris Cité, UMR_S 1138, Centre de Recherche des Cordeliers, Paris, France Institute of Cardiometabolism and Nutrition, Pitié-Salpêtrière Hospital, Paris, France
| | - Monique Rousset
- Sorbonne Universités, Université Pierre et Marie Curie, UMR_S 1138, Centre de Recherche des Cordeliers, Paris, France INSERM, UMR_S 1138, Centre de Recherche des Cordeliers, Paris, France Université Paris Descartes, Sorbonne Paris Cité, UMR_S 1138, Centre de Recherche des Cordeliers, Paris, France Institute of Cardiometabolism and Nutrition, Pitié-Salpêtrière Hospital, Paris, France
| | - Michel Lacasa
- Sorbonne Universités, Université Pierre et Marie Curie, UMR_S 1138, Centre de Recherche des Cordeliers, Paris, France INSERM, UMR_S 1138, Centre de Recherche des Cordeliers, Paris, France Université Paris Descartes, Sorbonne Paris Cité, UMR_S 1138, Centre de Recherche des Cordeliers, Paris, France
| | - Philippe Cardot
- Sorbonne Universités, Université Pierre et Marie Curie, UMR_S 1138, Centre de Recherche des Cordeliers, Paris, France INSERM, UMR_S 1138, Centre de Recherche des Cordeliers, Paris, France Université Paris Descartes, Sorbonne Paris Cité, UMR_S 1138, Centre de Recherche des Cordeliers, Paris, France UMR_S 1158, Neurophysiologie Respiratoire Expérimentale et Clinique, Paris, France
| | - Agnès Ribeiro
- Sorbonne Universités, Université Pierre et Marie Curie, UMR_S 1138, Centre de Recherche des Cordeliers, Paris, France INSERM, UMR_S 1138, Centre de Recherche des Cordeliers, Paris, France Université Paris Descartes, Sorbonne Paris Cité, UMR_S 1138, Centre de Recherche des Cordeliers, Paris, France Institute of Cardiometabolism and Nutrition, Pitié-Salpêtrière Hospital, Paris, France
| |
Collapse
|
22
|
Keogh K, Waters SM, Kelly AK, Wylie ARG, Kenny DA. Effect of feed restriction and subsequent re-alimentation on hormones and genes of the somatotropic axis in cattle. Physiol Genomics 2015; 47:264-73. [PMID: 25921585 DOI: 10.1152/physiolgenomics.00134.2014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Accepted: 04/25/2015] [Indexed: 11/22/2022] Open
Abstract
The objective of this study was to characterize the effect of feed restriction and compensatory growth during re-alimentation on the functionality of the somatotropic axis. We blocked 60 bulls into one of two groups: 1) restricted feed allowance for 125 days (period 1) (RES, n = 30) followed by ad libitum feeding for 55 days (period 2) or 2) ad libitum access to feed throughout (ADLIB, n = 30). A growth hormone releasing hormone (GHRH) challenge was performed during each period. At the end of each period, 15 animals from each treatment were slaughtered and hepatic tissue collected. Hepatic expression of 13 genes of the somatotropic axis was measured by qRT-PCR. RES displayed a lower growth rate during period 1 (0.6 vs. 1.9 kg/day; P < 0.001), subsequently gaining more than ADLIB animals during period 2 (2.5 vs. 1.4 kg/day; P < 0.001). Growth hormone response to GHRH was not different between treatments at either time-point (P > 0.05); however, resultant plasma IGF-1 was lower in period 1 and greater in period 2 in RES animals (P < 0.05). Expression of IGFBP2 was higher (P < 0.01) and IGF1 (P < 0.001) and GHRIA (P < 0.05) lower in RES compared with ADLIB during period 1, with no difference evident in period 2 (P > 0.05). Collectively, the results of this study are consistent with uncoupling of the somatotropic axis following feed restriction. However, there is no evidence from this study that the somatotropic axis per se is a significant contributor to compensatory growth.
Collapse
Affiliation(s)
- Kate Keogh
- Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, Teagasc, Dunsany, County Meath, Ireland; University College Dublin School of Agriculture and Food Science, Belfield, Dublin, Ireland; and
| | - Sinéad M Waters
- Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, Teagasc, Dunsany, County Meath, Ireland
| | - Alan K Kelly
- University College Dublin School of Agriculture and Food Science, Belfield, Dublin, Ireland; and
| | | | - David A Kenny
- Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, Teagasc, Dunsany, County Meath, Ireland;
| |
Collapse
|
23
|
MicroRNAs as key regulators of xenobiotic biotransformation and drug response. Arch Toxicol 2014; 89:1523-41. [PMID: 25079447 DOI: 10.1007/s00204-014-1314-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Accepted: 07/08/2014] [Indexed: 12/11/2022]
Abstract
In the last decade, microRNAs have emerged as key factors that negatively regulate mRNA expression. It has been estimated that more than 50% of protein-coding genes are under microRNA control and each microRNA is predicted to repress several mRNA targets. In this respect, it is recognized that microRNAs play a vital role in various cellular and molecular processes and that, depending on the biological pathways in which they intervene, distorted expression of microRNAs can have serious consequences. It has recently been shown that specific microRNA species are also correlated with toxic responses induced by xenobiotics. Since the latter are primarily linked to the extent of detoxification in the liver by phase I and phase II biotransformation enzymes and influx and efflux drug transporters, the regulation of the mRNA levels of this particular set of genes through microRNAs is of great importance for the overall toxicological outcome. Consequently, in this paper, an overview of the current knowledge with respect to the complex interplay between microRNAs and the expression of biotransformation enzymes and drug transporters in the liver is provided. Nuclear receptors and transcription factors, known to be involved in the transcriptional regulation of these genes, are also discussed.
Collapse
|
24
|
Wang ZN, Li MJ, Lan XY, Li MX, Lei CZ, Chen H. Tetra-primer ARMS-PCR identifies the novel genetic variations of bovine HNF-4α gene associating with growth traits. Gene 2014; 546:206-13. [PMID: 24914496 DOI: 10.1016/j.gene.2014.06.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Revised: 05/20/2014] [Accepted: 06/06/2014] [Indexed: 12/29/2022]
Abstract
Hepatocyte nuclear factor-4α (HNF-4α), a member of the hepatocyte nuclear factor family, plays an important role in regulating the expression of genes involved in the development, differentiation and normal function of liver and pancreatic β cells, as well as the maintenance of glucose homeostasis. Tetra-primer amplification refractory mutation system PCR (T-ARMS-PCR) is a new method offering fast detection and extreme simplicity at a negligible cost for SNP genotyping. In this paper, we characterize the polymorphisms of the bovine HNF-4α gene in three Chinese indigenous cattle breeds (n=660). Six novel SNPs were identified including 1 mutation in the coding region and others in introns. The statistical analyses indicated that 4 SNPs (g.T53729C, g.A53861G, g.A65188C and g.T65444C) affected growth traits markedly (P<0.05) in Qinchuan cattle (2 years after birth). Besides, haplotypes involving these 4 SNP sites in the bovine HNF-4α gene were identified and their effects on growth traits were also analyzed. The results showed that haplotypes 2, 7, 9 and 11 were predominant and accounted for 73.2%, 59.6%, and 67.1% in Qinchuan, Nanyang and Jiaxian cattle breeds, respectively. Hap9 (TAAT) was extremely predominant in all test populations, which suggested that individuals with Hap9 were more adapted to the environment. Furthermore, 4 combined haplotypes were constructed to guarantee the reliability of analysis results in Qinchuan cattle. There were also significant differences in body length (P<0.05). These findings will benefit for the application of DNA marker related to the growth traits on marker-assisted selection (MAS), and improve the performance of beef cattle.
Collapse
Affiliation(s)
- Zi-nian Wang
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi 712100, China
| | - Mi-jie Li
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi 712100, China
| | - Xian-yong Lan
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi 712100, China
| | - Ming-xun Li
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi 712100, China
| | - Chu-zhao Lei
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi 712100, China
| | - Hong Chen
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi 712100, China.
| |
Collapse
|
25
|
Hussainzada N, Lewis JA, Baer CE, Ippolito DL, Jackson DA, Stallings JD. Whole adult organism transcriptional profiling of acute metal exposures in male zebrafish. BMC Pharmacol Toxicol 2014; 15:15. [PMID: 24612858 PMCID: PMC4007779 DOI: 10.1186/2050-6511-15-15] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Accepted: 02/27/2014] [Indexed: 12/15/2022] Open
Abstract
Background A convergence of technological breakthroughs in the past decade has facilitated the development of rapid screening tools for biomarkers of toxicant exposure and effect. Platforms using the whole adult organism to evaluate the genome-wide response to toxicants are especially attractive. Recent work demonstrates the feasibility of this approach in vertebrates using the experimentally robust zebrafish model. In the present study, we evaluated gene expression changes in whole adult male zebrafish following an acute 24 hr high dose exposure to three metals with known human health risks. Male adult zebrafish were exposed to nickel chloride, cobalt chloride or sodium dichromate concentrations corresponding to their respective 96 hr LC20, LC40 and LC60. Histopathology was performed on a subset of metal-exposed zebrafish to phenotypically anchor transcriptional changes associated with each metal. Results Comparative analysis identified subsets of differentially expressed transcripts both overlapping and unique to each metal. Application of gene ontology (GO) and transcription factor (TF) enrichment algorithms revealed a number of key biological processes perturbed by metal poisonings and the master transcriptional regulators mediating gene expression changes. Metal poisoning differentially activated biological processes associated with ribosome biogenesis, proteosomal degradation, and p53 signaling cascades, while repressing oxygen-generating pathways associated with amino acid and lipid metabolism. Despite appreciable effects on gene regulation, nickel poisoning did not induce any morphological alterations in male zebrafish organs and tissues. Histopathological effects of cobalt remained confined to the olfactory system, while chromium targeted the gills, pharynx, and intestinal mucosa. A number of enriched transcription factors mediated the observed gene response to metal poisoning, including known targets such as p53, HIF1α, and the myc oncogene, and novel regulatory factors such as XBP1, GATA6 and HNF3β. Conclusions This work uses an experimentally innovative approach to capture global responses to metal poisoning and provides mechanistic insights into metal toxicity.
Collapse
Affiliation(s)
| | | | | | | | | | - Jonathan D Stallings
- Biomarkers Program, US Army Center for Environmental Health Research, Fort Detrick, Frederick, Maryland 21702-5010, USA.
| |
Collapse
|
26
|
Necchi V, Sommi P, Vitali A, Vanoli A, Savoia A, Ricci V, Solcia E. Polyubiquitinated proteins, proteasome, and glycogen characterize the particle-rich cytoplasmic structure (PaCS) of neoplastic and fetal cells. Histochem Cell Biol 2014; 141:483-97. [PMID: 24577783 DOI: 10.1007/s00418-014-1202-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/18/2014] [Indexed: 01/15/2023]
Abstract
A particle-rich cytoplasmic structure (PaCS) concentrating ubiquitin-proteasome system (UPS) components and barrel-like particles in clear, cytoskeleton- and organelle-free areas has recently been described in some neoplasms and in genetic or infectious diseases at risk of neoplasia. Ultrastructurally similar particulate cytoplasmic structures, interpreted as glycogen deposits, have previously been reported in clear-cell neoplasms and some fetal tissues. It remains to be investigated whether the two structures are the same, colocalize UPS components and polysaccharides, and have a role in highly proliferative cells such as fetal and neoplastic cells. We used immunogold electron microscopy and confocal immunofluorescence microscopy to examine human and mouse fetal tissues and human neoplasms. Fetal and neoplastic cells both showed colocalization of polyubiquitinated proteins, 19S and 20S proteasomes, and polysaccharides, both glycogen and chondroitin sulfate, inside cytoplasmic structures showing all distinctive features of PaCSs. Poorly demarcated and/or hybrid (ribosomes admixed) UPS- and glycogen-enriched areas, likely stages in PaCS development, were also seen in some fetal cells, with special reference to those, like primary alveolar pulmonary cells or pancreatic centroacinar cells, having a crucial role in organogenesis. UPS- and glycogen-rich PaCSs developed extensively in clear-cell neoplasms of the kidney, ovary, pancreas, and other organs, as well as, in infantile, development-related tumors replicating fetal patterns, such as choroid plexus papilloma. UPS-mediated, ATP-dependent proteolysis and its potential energy source, glycogen metabolism, may have a crucial, synergic role in embryo-/organogenesis and carcinogenesis.
Collapse
Affiliation(s)
- Vittorio Necchi
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | | | | | | | | | | | | |
Collapse
|
27
|
Zheng R, Rebolledo-Jaramillo B, Zong Y, Wang L, Russo P, Hancock W, Stanger BZ, Hardison RC, Blobel GA. Function of GATA factors in the adult mouse liver. PLoS One 2013; 8:e83723. [PMID: 24367609 PMCID: PMC3867416 DOI: 10.1371/journal.pone.0083723] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2013] [Accepted: 11/06/2013] [Indexed: 11/24/2022] Open
Abstract
GATA transcription factors and their Friend of Gata (FOG) cofactors control the development of diverse tissues. GATA4 and GATA6 are essential for the expansion of the embryonic liver bud, but their expression patterns and functions in the adult liver are unclear. We characterized the expression of GATA and FOG factors in whole mouse liver and purified hepatocytes. GATA4, GATA6, and FOG1 are the most prominently expressed family members in whole liver and hepatocytes. GATA4 chromatin immunoprecipitation followed by high throughput sequencing (ChIP-seq) identified 4409 occupied sites, associated with genes enriched in ontologies related to liver function, including lipid and glucose metabolism. However, hepatocyte-specific excision of Gata4 had little impact on gross liver architecture and function, even under conditions of regenerative stress, and, despite the large number of GATA4 occupied genes, resulted in relatively few changes in gene expression. To address possible redundancy between GATA4 and GATA6, both factors were conditionally excised. Surprisingly, combined Gata4,6 loss did not exacerbate the phenotype resulting from Gata4 loss alone. This points to the presence of an unusually robust transcriptional network in adult hepatocytes that ensures the maintenance of liver function.
Collapse
Affiliation(s)
- Rena Zheng
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Division of Hematology, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Boris Rebolledo-Jaramillo
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Yiwei Zong
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Liqing Wang
- Division of Transplant Immunology, Department of Pathology and Laboratory Medicine and Biesecker Center for Pediatric Liver Disease, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Pierre Russo
- Pathology and Laboratory Medicine, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Wayne Hancock
- Division of Transplant Immunology, Department of Pathology and Laboratory Medicine and Biesecker Center for Pediatric Liver Disease, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Ben Z. Stanger
- Division of Gastroenterology, Department of Medicine, Department of Cell and Developmental Biology and Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Ross C. Hardison
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Gerd A. Blobel
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Division of Hematology, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
- * E-mail:
| |
Collapse
|
28
|
Abstract
The age-related epithelial cancers of the breast, colorectum and prostate are the most prevalent and are increasing in our aging populations. Epithelial cells turnover rapidly and mutations naturally accumulate throughout life. Most epithelial cancers arise from this normal mutation rate. All elderly individuals will harbour many cells with the requisite mutations and most will develop occult neoplastic lesions. Although essential for initiation, these mutations are not sufficient for the progression of cancer to a life-threatening disease. This progression appears to be dependent on context: the tissue ecosystem within individuals and lifestyle exposures across populations of individuals. Together, this implies that the seeds may be plentiful but they only germinate in the right soil. The incidence of these cancers is much lower in Eastern countries but is increasing with Westernisation and increases more acutely in migrants to the West. A Western lifestyle is strongly associated with perturbed metabolism, as evidenced by the epidemics of obesity and diabetes: this may also provide the setting enabling the progression of epithelial cancers. Epidemiology has indicated that metabolic biomarkers are prospectively associated with cancer incidence and prognosis. Furthermore, within cancer research, there has been a rediscovery that a switch in cell metabolism is critical for cancer progression but this is set within the metabolic status of the host. The seed may only germinate if the soil is fertile. This perspective brings together the different avenues of investigation implicating the role that metabolism may play within the context of post-genomic concepts of cancer.
Collapse
Affiliation(s)
- Jeff M P Holly
- School of Clinical Science, Faculty of Medicine, University of Bristol, Learning and Research Building, Southmead Hospital, Bristol, BS10 5NB, UK,
| | | | | |
Collapse
|
29
|
Abstract
Ion channels and transporters are expressed in every living cell, where they participate in controlling a plethora of biological processes and physiological functions, such as excitation of cells in response to stimulation, electrical activities of cells, excitation-contraction coupling, cellular osmolarity, and even cell growth and death. Alterations of ion channels/transporters can have profound impacts on the cellular physiology associated with these proteins. Expression of ion channels/transporters is tightly regulated and expression deregulation can trigger abnormal processes, leading to pathogenesis, the channelopathies. While transcription factors play a critical role in controlling the transcriptome of ion channels/transporters at the transcriptional level by acting on the 5'-flanking region of the genes, microribonucleic acids (miRNAs), a newly discovered class of regulators in the gene network, are also crucial for expression regulation at the posttranscriptional level through binding to the 3'untranslated region of the genes. These small noncoding RNAs fine tune expression of genes involved in a wide variety of cellular processes. Recent studies revealed the role of miRNAs in regulating expression of ion channels/transporters and the associated physiological functions. miRNAs can target ion channel genes to alter cardiac excitability (conduction, repolarization, and automaticity) and affect arrhythmogenic potential of heart. They can modulate circadian rhythm, pain threshold, neuroadaptation to alcohol, brain edema, etc., through targeting ion channel genes in the neuronal systems. miRNAs can also control cell growth and tumorigenesis by acting on the relevant ion channel genes. Future studies are expected to rapidly increase to unravel a new repertoire of ion channels/transporters for miRNA regulation.
Collapse
Affiliation(s)
- Zhiguo Wang
- Harbin Medical University, Harbin, Heilongjiang, People's Republic of China.
| |
Collapse
|
30
|
Wang H, Meyer CA, Fei T, Wang G, Zhang F, Liu XS. A systematic approach identifies FOXA1 as a key factor in the loss of epithelial traits during the epithelial-to-mesenchymal transition in lung cancer. BMC Genomics 2013; 14:680. [PMID: 24093963 PMCID: PMC3852829 DOI: 10.1186/1471-2164-14-680] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Accepted: 09/28/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The epithelial-to-mesenchymal transition is an important mechanism in cancer metastasis. Although transcription factors including SNAIL, SLUG, and TWIST1 regulate the epithelial-to-mesenchymal transition, other unknown transcription factors could also be involved. Identification of the full complement of transcription factors is essential for a more complete understanding of gene regulation in this process. Chromatin immunoprecipitation-sequencing (ChIP-Seq) technologies have been used to detect genome-wide binding of transcription factors; here, we developed a systematic approach to integrate existing ChIP-Seq and transcriptome data. We scanned multiple transcription factors to investigate their functional impact on the epithelial-to-mesenchymal transition in the human A549 lung adenocarcinoma cell line. RESULTS Among the transcription factors tested, impact scores identified the forkhead box protein A1 (FOXA1) as the most significant transcription factor in the epithelial-to-mesenchymal transition. FOXA1 physically associates with the promoters of its predicted target genes. Several critical epithelial-to-mesenchymal transition effectors involved in cellular adhesion and cellular communication were identified in the regulatory network of FOXA1, including FOXA2, FGA, FGB, FGG, and FGL1. The implication of FOXA1 in the epithelial-to-mesenchymal transition via its regulatory network indicates that FOXA1 may play an important role in the initiation of lung cancer metastasis. CONCLUSIONS We identified FOXA1 as a potentially important transcription factor and negative regulator in the initial stages of lung cancer metastasis. FOXA1 may modulate the epithelial-to-mesenchymal transition via its transcriptional regulatory network. Further, this study demonstrates how ChIP-Seq and expression data could be integrated to delineate the impact of transcription factors on a specific biological process.
Collapse
Affiliation(s)
- Haiyun Wang
- School of Life Science and Technology, Tongji University, Shanghai 200092, China
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard School of Public Health, Boston, MA 02215, USA
- Tongji University Advanced Institute of Translational Medicine, Tongji University, Shanghai 200092, China
| | - Clifford A Meyer
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard School of Public Health, Boston, MA 02215, USA
| | - Teng Fei
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard School of Public Health, Boston, MA 02215, USA
- Department of Medical Oncology, Division of Molecular and Cellular Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA
| | - Gang Wang
- Clinical Translational Research Center, Shanghai Pulmonary Hospital, School of Life Science and Technology, Tongji University, Shanghai 200092, China
| | - Fan Zhang
- Clinical Translational Research Center, Shanghai Pulmonary Hospital, School of Life Science and Technology, Tongji University, Shanghai 200092, China
| | - X Shirley Liu
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard School of Public Health, Boston, MA 02215, USA
| |
Collapse
|
31
|
Guzmán C, Benet M, Pisonero-Vaquero S, Moya M, García-Mediavilla MV, Martínez-Chantar ML, González-Gallego J, Castell JV, Sánchez-Campos S, Jover R. The human liver fatty acid binding protein (FABP1) gene is activated by FOXA1 and PPARα; and repressed by C/EBPα: Implications in FABP1 down-regulation in nonalcoholic fatty liver disease. Biochim Biophys Acta Mol Cell Biol Lipids 2013; 1831:803-18. [PMID: 23318274 DOI: 10.1016/j.bbalip.2012.12.014] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2012] [Revised: 11/22/2012] [Accepted: 12/27/2012] [Indexed: 01/24/2023]
Abstract
Liver fatty acid binding protein (FABP1) prevents lipotoxicity of free fatty acids and regulates fatty acid trafficking and partition. Our objective is to investigate the transcription factors controlling the human FABP1 gene and their regulation in nonalcoholic fatty liver disease (NAFLD). Adenovirus-mediated expression of multiple transcription factors in HepG2 cells and cultured human hepatocytes demonstrated that FOXA1 and PPARα are among the most effective activators of human FABP1, whereas C/EBPα is a major dominant repressor. Moreover, FOXA1 and PPARα induced re-distribution of FABP1 protein and increased cytoplasmic expression. Reporter assays demonstrated that the major basal activity of the human FABP1 promoter locates between -96 and -229bp, where C/EBPα binds to a composite DR1-C/EBP element. Mutation of this element at -123bp diminished basal reporter activity, abolished repression by C/EBPα and reduced transactivation by HNF4α. Moreover, HNF4α gene silencing by shRNA in HepG2 cells caused a significant down-regulation of FABP1 mRNA expression. FOXA1 activated the FABP1 promoter through binding to a cluster of elements between -229 and -592bp, whereas PPARα operated through a conserved proximal element at -59bp. Finally, FABP1, FOXA1 and PPARα were concomitantly repressed in animal models of NAFLD and in human nonalcoholic fatty livers, whereas C/EBPα was induced or did not change. We conclude that human FABP1 has a complex mechanism of regulation where C/EBPα displaces HNF4α and hampers activation by FOXA1 and PPARα. Alteration of expression of these transcription factors in NAFLD leads to FABP1 gen repression and could exacerbate lipotoxicity and disease progression.
Collapse
Affiliation(s)
- Carla Guzmán
- Experimental Hepatology Unit, IIS Hospital La Fe, Valencia, Spain
| | | | | | | | | | | | | | | | | | | |
Collapse
|
32
|
Wang Z, Burke PA. The role of microRNAs in hepatocyte nuclear factor-4alpha expression and transactivation. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2013; 1829:436-42. [PMID: 23298640 DOI: 10.1016/j.bbagrm.2012.12.009] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2012] [Revised: 12/14/2012] [Accepted: 12/26/2012] [Indexed: 12/21/2022]
Abstract
Hepatocyte nuclear factor (HNF)-4α is a key member of the transcription factor network regulating hepatocyte differentiation and function. Genetic and molecular evidence suggests that expression of HNF-4α is mainly regulated at the transcriptional level. Activation of HNF-4A gene involves the interaction of distinct sets of transcription factors and co-transcription factors within enhancer and promoter regions. Here we study the inhibitory effect of microRNAs (miRNAs) on the 3'-untranslated region (3'-UTR) of HNF-4A mRNA. The potential recognition elements of a set of miRNAs were identified utilizing bioinformatics analysis. The family members of miR-34 and miR-449, including miR-34a, miR-34c-5p and miR-449a, share the same target elements located at two distinct locations within the 3'-UTR of HNF-4A. The over-expression of miR-34a, miR-34c-5p or miR-449a in HepG2 cells led to a significant decrease in the activity of luciferase reporter carrying 3'-UTR of HNF-4A. The repressive effect on reporter activity was partially or fully eliminated when one or two of the binding site(s) for miR-34a/miR-34c-5p/miR-449a were deleted within the 3'-UTR. The protein level of HNF-4α was dramatically reduced by over-expression of miR-34a, miR-34c-5p and miR-449a, which correlates with a decrease in the binding activity of HNF-4α and transactivation of HNF-4α target genes. These results suggest that the recognition sites of miR-34a, miR-34c-5p and miR-449a within 3'-UTR of HNF-4A are functional. The mechanism of down-regulation of the binding activity and transactivation of HNF-4α by the miRNAs involves the decrease in HNF-4α protein level via miRNAs selectively targeting HNF-4A 3'-UTR, leading to the translational repression of HNF-4α expression.
Collapse
Affiliation(s)
- Zhongyan Wang
- Department of Surgery, Boston University School of Medicine, Boston, MA 02118, USA
| | | |
Collapse
|
33
|
Fujikura J, Hosoda K, Nakao K. Cell transplantation therapy for diabetes mellitus: endocrine pancreas and adipocyte. Endocr J 2013; 60:697-708. [PMID: 23719783 DOI: 10.1507/endocrj.ej13-0162] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Experimental transplantation of endocrine tissues has led to significant advances in our understanding of endocrinology and metabolism. Endocrine cell transplantation therapy is expected to be applied to the treatment of metabolic endocriopathies. Restoration of functional pancreatic beta-cell mass or of functional adipose mass are reasonable treatment approaches for patients with diabetes or lipodystrophy, respectively. Human induced pluripotent stem (iPS) cell research is having a great impact on life sciences. Doctors Takahashi and Yamanaka discovered that the forced expression of a set of genes can convert mouse and human somatic cells into a pluripotent state [1, 2]. These iPS cells can differentiate into a variety of cell types. Therefore, iPS cells from patients may be a potential cell source for autologous cell replacement therapy. This review briefly summarizes the current knowledge about transplantation therapy for diabetes mellitus, the development of the endocrine pancreas and adipocytes, and endocrine-metabolic disease-specific iPS cells.
Collapse
Affiliation(s)
- Junji Fujikura
- Division of Endocrinology and Metabolism, Kyoto University Hospital, Kyoto 606-8507, Japan.
| | | | | |
Collapse
|
34
|
In Silico Docking of HNF-1a Receptor Ligands. Adv Bioinformatics 2012; 2012:705435. [PMID: 23316227 PMCID: PMC3535823 DOI: 10.1155/2012/705435] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2012] [Revised: 11/06/2012] [Accepted: 11/28/2012] [Indexed: 12/19/2022] Open
Abstract
Background. HNF-1a is a transcription factor that regulates glucose metabolism by expression in various tissues. Aim. To dock potential ligands of HNF-1a using docking software in silico. Methods. We performed in silico studies using HNF-1a protein 2GYP·pdb and the following softwares: ISIS/Draw 2.5SP4, ARGUSLAB 4.0.1, and HEX5.1. Observations. The docking distances (in angstrom units: 1 angstrom unit (Å) = 0.1 nanometer or 1 × 10−10 metres) with ligands in decreasing order are as follows: resveratrol (3.8 Å), aspirin (4.5 Å), stearic acid (4.9 Å), retinol (6.0 Å), nitrazepam (6.8 Å), ibuprofen (7.9 Å), azulfidine (9.0 Å), simvastatin (9.0 Å), elaidic acid (10.1 Å), and oleic acid (11.6 Å). Conclusion. HNF-1a domain interacted most closely with resveratrol and aspirin
Collapse
|
35
|
Fang Q, Chen S, Wang Y, Jiang S, Zhang R, Hu C, Wang C, Liu F, Xiang K, Jia W. Functional analyses of the mutation nt-128 T→G in the hepatocyte nuclear factor-1α promoter region in Chinese diabetes pedigrees. Diabet Med 2012; 29:1456-64. [PMID: 22413961 PMCID: PMC3570122 DOI: 10.1111/j.1464-5491.2012.03626.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
AIMS Hepatocyte nuclear factor-1α (HNF-1α) regulates the expression of genes encoding proteins involved in glucose metabolism and insulin secretion. Mutations in the HNF-1α gene cause maturity-onset diabetes of the young Type 3. However, the mechanism leading to this disease has not been completely ascertained. Previously, we found a novel mutation in the regulatory element of the human HNF-1α gene in two Chinese diabetes pedigrees. The nucleotide at position -128 T was substituted by G (nt-128 T→G). In this study, we analysed the functional defect of nt-128 T→G in HNF-1α transcription activity. METHODS Luciferase reporter gene assays were carried out to examine the functional characteristics of this mutant. Electrophoretic mobility shift assays and chromatin immunoprecipitation were performed to confirm the binding of nuclear proteins to oligonucleotides. RESULTS The variant construct (nt-128 T→G) had a 1.65-fold increase in promoter activity compared with that of the wild-type construct in HepG2 cells and a 1.33-fold increase in MIN6 cells, respectively. The variant resided at a FOXA/HNF-3 binding site identified by a series of competitive electrophoretic mobility shift assays and antibody supershift analyses. The assays showed a differential binding affinity in the wild-type and the nt-128 T→G mutant fragments by FOXA/HNF-3. Chromatin immunoprecipitation indicated that FOXA/HNF-3 bound to this region in vivo. One nucleotide substitution in the FOXA/HNF-3 site in the human HNF-1α regulatory element caused an increase of HNF-1α transcriptional activity. CONCLUSIONS Our data suggested that this substitution in the promoter region affects DNA-protein interaction and HNF-1α gene transcription. The mutant may contribute to the development of diabetes in these two nt-128 T→G pedigrees of Chinese.
Collapse
Affiliation(s)
- Q Fang
- Department of Endocrinology and Metabolism, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | | | | | | | | | | | | | | | | | | |
Collapse
|
36
|
Potter AS, Casa AJ, Lee AV. Forkhead box A1 (FOXA1) is a key mediator of insulin-like growth factor I (IGF-I) activity. J Cell Biochem 2012; 113:110-21. [PMID: 21882221 DOI: 10.1002/jcb.23333] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The insulin-like growth factor receptor (IGF-IR) has been implicated in a number of human tumors, including breast cancer. Data from human breast tumors has demonstrated that IGF-IR is over-expressed and hyper-phosphorylated. Additionally, microarray analysis has shown that IGF-I treatment of MCF7 cells leads to a gene signature comprised of induced and repressed genes, which correlated with luminal B tumors. FOXA1, a forkhead family transcription factor, has been shown to be crucial for mammary ductal morphogenesis, similar to IGF-IR, and expressed at high levels in luminal subtype B breast tumors. Here, we investigated the relationship between FOXA1 and IGF-I action in breast cancer cells. We show that genes regulated by IGF-I are enriched for FOXA1 binding sites, and knock down of FOXA1 blocked the ability of IGF-I to regulate gene expression. IGF-I treatment of MCF7 cells increased the half-life of FOXA1 protein and this increase in half-life appeared to be dependent on canonical IGF-I signal transduction through both MAPK and AKT pathways. Finally, knock down of FOXA1 led to a decreased ability of IGF-I to induce proliferation and protect against apoptosis. Together, these results demonstrate that IGF-I can increase the stability of FOXA1 protein expression and place it as a critical mediator of IGF-I regulation of gene expression and IGF-I-mediated biological responses.
Collapse
Affiliation(s)
- Adam S Potter
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | | | | |
Collapse
|
37
|
Bulla GA, Aylmer CM, Dust AL, Kurkewich JL, Mire LK, Estanda AB. Genome-wide analysis of hepatic gene silencing in hepatoma cell variants. Genomics 2012; 100:176-83. [PMID: 22659237 DOI: 10.1016/j.ygeno.2012.05.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2011] [Revised: 04/18/2012] [Accepted: 05/22/2012] [Indexed: 10/28/2022]
Abstract
Genome-wide gene expression profiling was carried out on rat hepatoma cells and compared to profiles of hepatoma "variant" cell lines derived via a stringent selection protocol that enriches for rare cells (<1 in 100,000 cells) that fail to drive liver function. Results show 132 genes that are strongly (>5-fold) repressed in each of the four variant cell lines tested. An additional 68 genes were repressed in 3 of 4 variant cell lines. Importantly, several of the repressed genes are members of transcriptional activation pathways, suggesting that they may contribute to maintaining the hepatic phenotype. Ectopic expression of the HNF1A gene in a variant cell line resulted in activation of 56 genes, 37 of which were included in the repressed data set. These data suggest that a high level of reprogramming occurs when hepatoma cells convert to a non-differentiated phenotype, a process that can be partially reversed by the introduction of transcription factors.
Collapse
Affiliation(s)
- Gary A Bulla
- Department of Biological Sciences, Eastern Illinois University, 600 Lincoln Avenue, Charleston, IL 61920, USA.
| | | | | | | | | | | |
Collapse
|
38
|
Di Rocco G, Gentile A, Antonini A, Truffa S, Piaggio G, Capogrossi MC, Toietta G. Analysis of biodistribution and engraftment into the liver of genetically modified mesenchymal stromal cells derived from adipose tissue. Cell Transplant 2012; 21:1997-2008. [PMID: 22469297 DOI: 10.3727/096368911x637452] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Presently, orthotopic liver transplant is the major therapeutic option for patients affected by primary liver diseases. This procedure is characterized by major invasive surgery, scarcity of donor organs, high costs, and lifelong immunosuppressive treatment. Transplant of hepatic precursor cells represents an attractive alternative. These cells could be used either for allogeneic transplantation or for autologous transplant after ex vivo genetic modification. We used stromal cells isolated from adipose tissue (AT-SCs) as platforms for autologous cell-mediated gene therapy. AT-SCs were transduced with lentiviral vectors expressing firefly luciferase, allowing for transplanted cell tracking by bioluminescent imaging (BLI). As a complementary approach, we followed circulating human α1-antitrypsin (hAAT) levels after infusion of AT-SCs overexpressing hAAT. Cells were transplanted into syngeneic mice after CCl(4)-induced hepatic injury. Luciferase bioluminescence signals and serum hAAT levels were measured at different time points after transplantation and demonstrate persistence of transplanted cells for up to 2 months after administration. These data, along with immunohistochemical analysis, suggest engraftment and repopulation of injured livers by transplanted AT-SCs. Moreover, by transcriptional targeting using cellular tissue-specific regulatory sequences, we confirmed that AT-SCs differentiate towards a hepatogenic-like phenotype in vitro and in vivo. Additionally, in transplanted cells reisolated from recipient animals' livers, we detected activation of the α-fetoprotein (AFP) promoter. This promoter is normally transcriptionally silenced in adult tissues but can be reactivated during liver regeneration, suggesting commitment towards hepatogenic-like differentiation of engrafted cells in vivo. Our data support AT-SC-mediated gene therapy as an innovative therapeutic option for disorders of liver metabolism.
Collapse
Affiliation(s)
- Giuliana Di Rocco
- Vascular Biology and Regenerative Medicine, Centro Cardiologico Monzino IRCCS, Milan, Italy
| | | | | | | | | | | | | |
Collapse
|
39
|
Ishikawa T, Banas A, Teratani T, Iwaguro H, Ochiya T. Regenerative Cells for Transplantation in Hepatic Failure. Cell Transplant 2012. [DOI: 10.3727/096368911x605286b] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Human embryonic stem (ES) cells and induced pluripotent stem (iPS) cells have an enormous potential; however, their potential clinical application is being arrested due to various limitations such as teratoma formation followed by tumorigenesis, emergent usage, and the quality control of cells, as well as safety issues regarding long-term culture are also delaying their clinical application. In addition, human ES cells have two crucial issues: immunogenicity and ethical issues associated with their clinical application. The efficient generation of human iPS cells requires gene transfer, yet the mechanism underlying pluripotent stem cell induction has not yet been fully elucidated. Otherwise, although human adult regenerative cells including mesenchymal stem cells have a limited capacity for differentiation, they are nevertheless promising candidates for tissue regeneration in a clinical setting. This review highlights the use of regenerative cells for transplantation in hepatic failure.
Collapse
Affiliation(s)
- Tetsuya Ishikawa
- Division of Molecular and Cellular Medicine, National Cancer Center Research Institute, Tokyo, Japan
| | - Agnieszka Banas
- Division of Molecular and Cellular Medicine, National Cancer Center Research Institute, Tokyo, Japan
| | - Takumi Teratani
- Division of Molecular and Cellular Medicine, National Cancer Center Research Institute, Tokyo, Japan
| | - Hideki Iwaguro
- Division of Molecular and Cellular Medicine, National Cancer Center Research Institute, Tokyo, Japan
| | - Takahiro Ochiya
- Division of Molecular and Cellular Medicine, National Cancer Center Research Institute, Tokyo, Japan
| |
Collapse
|
40
|
Septer S, Edwards G, Gunewardena S, Wolfe A, Li H, Daniel J, Apte U. Yes-associated protein is involved in proliferation and differentiation during postnatal liver development. Am J Physiol Gastrointest Liver Physiol 2012; 302:G493-503. [PMID: 22194415 PMCID: PMC3311431 DOI: 10.1152/ajpgi.00056.2011] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
It is known that the liver undergoes size increase and differentiation simultaneously during the postnatal period. Cells in the liver undergo a period of well-controlled proliferation to achieve the adult liver-to-body weight ratio. The postnatal liver growth is also accompanied by simultaneous hepatic differentiation. However, the mechanisms of liver size regulation and differentiation are not completely clear. Herein we report that yes-associated protein (Yap), the downstream effector of the Hippo Kinase signaling pathway, plays a role in liver size regulation and differentiation during the postnatal liver growth period. Postnatal liver growth was studied in C57BL/6 mice over a time course of postnatal days (PND) 0-30. Analysis of nuclear Yap by Western blot indicated peak Yap activation between PND15-20, which coincided with increased cyclin D1 expression and liver cell proliferation. Analysis of postnatal liver development in Yap(+/-) mice revealed a significant decrease in the liver-to-body weight ratio compared with Yap(+/+) mice at PND15 and -30. Yap(+/-) mice exhibited a significant decrease in postnatal liver cell proliferation, but no change in apoptosis was observed. Furthermore, global gene expression analysis of Yap(+/-) livers revealed a role of Yap in regulation of genes involved in bile acid metabolism, retinoic acid metabolism, ion transport, and extracellular matrix proteins. Taken together, these data indicate that Yap plays a role in both cell proliferation and possibly in hepatic differentiation during postnatal liver development.
Collapse
Affiliation(s)
- Seth Septer
- 1Department of Gastroenterology, Children's Mercy Hospital, Kansas City; and
| | - Genea Edwards
- 2Department of Pharmacology, Toxicology and Therapeutics and
| | - Sumedha Gunewardena
- 3Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, Kansas
| | - Andy Wolfe
- 2Department of Pharmacology, Toxicology and Therapeutics and
| | - Hua Li
- 2Department of Pharmacology, Toxicology and Therapeutics and
| | - James Daniel
- 1Department of Gastroenterology, Children's Mercy Hospital, Kansas City; and
| | - Udayan Apte
- 2Department of Pharmacology, Toxicology and Therapeutics and
| |
Collapse
|
41
|
Moya M, Benet M, Guzmán C, Tolosa L, García-Monzón C, Pareja E, Castell JV, Jover R. Foxa1 reduces lipid accumulation in human hepatocytes and is down-regulated in nonalcoholic fatty liver. PLoS One 2012; 7:e30014. [PMID: 22238690 PMCID: PMC3253125 DOI: 10.1371/journal.pone.0030014] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2011] [Accepted: 12/08/2011] [Indexed: 02/06/2023] Open
Abstract
Triglyceride accumulation in nonalcoholic fatty liver (NAFL) results from unbalanced lipid metabolism which, in the liver, is controlled by several transcription factors. The Foxa subfamily of winged helix/forkhead box (Fox) transcription factors comprises three members which play important roles in controlling both metabolism and homeostasis through the regulation of multiple target genes in the liver, pancreas and adipose tissue. In the mouse liver, Foxa2 is repressed by insulin and mediates fasting responses. Unlike Foxa2 however, the role of Foxa1 in the liver has not yet been investigated in detail. In this study, we evaluate the role of Foxa1 in two human liver cell models, primary cultured hepatocytes and HepG2 cells, by adenoviral infection. Moreover, human and rat livers were analyzed to determine Foxa1 regulation in NAFL. Results demonstrate that Foxa1 is a potent inhibitor of hepatic triglyceride synthesis, accumulation and secretion by repressing the expression of multiple target genes of these pathways (e.g., GPAM, DGAT2, MTP, APOB). Moreover, Foxa1 represses the fatty acid transporter protein FATP2 and lowers fatty acid uptake. Foxa1 also increases the breakdown of fatty acids by inducing peroxisomal fatty acid β-oxidation and ketone body synthesis. Finally, Foxa1 is able to largely up-regulate UCP1, thereby dissipating energy and consistently decreasing the mitochondria membrane potential. We also report that human and rat NAFL have a reduced Foxa1 expression, possibly through a protein kinase C-dependent pathway. We conclude that Foxa1 is an antisteatotic factor that coordinately tunes several lipid metabolic pathways to block triglyceride accumulation in hepatocytes. However, Foxa1 is down-regulated in human and rat NAFL and, therefore, increasing Foxa1 levels could protect from steatosis. Altogether, we suggest that Foxa1 could be a novel therapeutic target for NAFL disease and insulin resistance.
Collapse
Affiliation(s)
- Marta Moya
- Experimental Hepatology Unit, University Hospital La Fe, Valencia, Spain
| | - Marta Benet
- Experimental Hepatology Unit, University Hospital La Fe, Valencia, Spain
- CIBERehd, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Barcelona, Spain
| | - Carla Guzmán
- Experimental Hepatology Unit, University Hospital La Fe, Valencia, Spain
| | - Laia Tolosa
- Experimental Hepatology Unit, University Hospital La Fe, Valencia, Spain
| | - Carmelo García-Monzón
- CIBERehd, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Barcelona, Spain
- Liver Research Unit, Instituto de Investigación Sanitaria Princesa, University Hospital Santa Cristina, Madrid, Spain
| | - Eugenia Pareja
- Surgery and Liver Transplantation Unit, University Hospital La Fe, Valencia, Spain
| | - José Vicente Castell
- Experimental Hepatology Unit, University Hospital La Fe, Valencia, Spain
- CIBERehd, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Barcelona, Spain
- Department of Biochemistry and Molecular Biology, University of Valencia, Valencia, Spain
| | - Ramiro Jover
- Experimental Hepatology Unit, University Hospital La Fe, Valencia, Spain
- CIBERehd, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Barcelona, Spain
- Department of Biochemistry and Molecular Biology, University of Valencia, Valencia, Spain
| |
Collapse
|
42
|
Chu JH, Lazarus R, Carey VJ, Raby BA. Quantifying differential gene connectivity between disease states for objective identification of disease-relevant genes. BMC SYSTEMS BIOLOGY 2011; 5:89. [PMID: 21627793 PMCID: PMC3128864 DOI: 10.1186/1752-0509-5-89] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2010] [Accepted: 05/31/2011] [Indexed: 02/16/2023]
Abstract
Background Network modeling of whole transcriptome expression data enables characterization of complex epistatic (gene-gene) interactions that underlie cellular functions. Though numerous methods have been proposed and successfully implemented to develop these networks, there are no formal methods for comparing differences in network connectivity patterns as a function of phenotypic trait. Results Here we describe a novel approach for quantifying the differences in gene-gene connectivity patterns across disease states based on Graphical Gaussian Models (GGMs). We compare the posterior probabilities of connectivity for each gene pair across two disease states, expressed as a posterior odds-ratio (postOR) for each pair, which can be used to identify network components most relevant to disease status. The method can also be generalized to model differential gene connectivity patterns within previously defined gene sets, gene networks and pathways. We demonstrate that the GGM method reliably detects differences in network connectivity patterns in datasets of varying sample size. Applying this method to two independent breast cancer expression data sets, we identified numerous reproducible differences in network connectivity across histological grades of breast cancer, including several published gene sets and pathways. Most notably, our model identified two gene hubs (MMP12 and CXCL13) that each exhibited differential connectivity to more than 30 transcripts in both datasets. Both genes have been previously implicated in breast cancer pathobiology, but themselves are not differentially expressed by histologic grade in either dataset, and would thus have not been identified using traditional differential gene expression testing approaches. In addition, 16 curated gene sets demonstrated significant differential connectivity in both data sets, including the matrix metalloproteinases, PPAR alpha sequence targets, and the PUFA synthesis pathway. Conclusions Our results suggest that GGM can be used to formally evaluate differences in global interactome connectivity across disease states, and can serve as a powerful tool for exploring the molecular events that contribute to disease at a systems level.
Collapse
Affiliation(s)
- Jen-hwa Chu
- Channing Laboratory, Brigham and Women's Hospital, Harvard Medical School, Boston MA 02115, USA.
| | | | | | | |
Collapse
|
43
|
Soto-Gutierrez A, Basma H, Navarro-Alvarez N, Uygun BE, Yarmush ML, Kobayashi N, Fox IJ. Differentiating stem cells into liver. Biotechnol Genet Eng Rev 2011; 25:149-63. [PMID: 21412354 DOI: 10.5661/bger-25-149] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Research involving differentiated embryonic stem (ES) cells may revolutionize the study of liver disease, improve the drug discovery process, and assist in the development of stem-cell-based clinical therapies. Generation of ES cell-derived hepatic tissue has benefited from an understanding of the cytokines, growth factors and biochemical compounds that are essential in liver development, and this knowledge has been used to mimic some aspects of embryonic development in vitro. Although great progress has been made in differentiating human ES cells into liver cells, current protocols have not yet produced cells with the phenotype of a mature hepatocyte. There is a significant need to formally establish criteria that would define what constitutes a functional human stem cell-derived hepatocyte. Here, we explore current challenges and future opportunities in development and use of ES cell-derived liver cells. ES-derived hepatocytes could be used to better understand liver biology, begin the process of "personalizing" health care, and to treat some forms of liver disease.
Collapse
Affiliation(s)
- Alejandroo Soto-Gutierrez
- Center for Engineering in Medicine and Department of Surgery, Massachusetts General Hospital, Harvard Medical School, and the Shriners Hospitals for Children, Boston, MA 02114, USA
| | | | | | | | | | | | | |
Collapse
|
44
|
Bulla GA, Luong Q, Shrestha S, Reeb S, Hickman S. Genome-wide analysis of hepatic gene silencing in mammalian cell hybrids. Genomics 2010; 96:323-32. [PMID: 20801210 DOI: 10.1016/j.ygeno.2010.08.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2010] [Revised: 08/13/2010] [Accepted: 08/17/2010] [Indexed: 12/29/2022]
Abstract
Silencing of tissue-specific gene expression in mammalian somatic cell hybrids is a well-documented epigenetic phenomenon which is both profound (involving a large number of genes) and enigmatic. Our aim was to utilize whole-genome microarray analyses to determine the true extent of gene silencing on a genomic level. By comparing gene expression profiles of hepatoma×fibroblast cell hybrids with those of parental cells, we have identified over 300 liver-enriched genes that are repressed at least 5-fold in the cell hybrids, the majority of which are repressed at least 10-fold. Also, we identify nearly 200 fibroblast-enriched genes that are repressed at least 5-fold. Silenced hepatic genes include several that encode transcription factors and proteins involved in signal transduction pathways. These data suggest that extensive reprogramming occurs in cell hybrids, leading to a nearly global (although not complete) loss of tissue-specific gene expression.
Collapse
Affiliation(s)
- Gary A Bulla
- Department of Biological Sciences, Eastern Illinois University, 600 Lincoln Avenue, Charleston, IL 61920, USA.
| | | | | | | | | |
Collapse
|
45
|
Wang Z, Burke PA. Hepatocyte nuclear factor-4α interacts with other hepatocyte nuclear factors in regulating transthyretin gene expression. FEBS J 2010; 277:4066-75. [PMID: 20735474 DOI: 10.1111/j.1742-4658.2010.07802.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Transthyretin is a negative acute phase protein whose serum level decreases during the acute phase response. Transthyretin gene expression in the liver is regulated at the transcriptional level, and is controlled by hepatocyte nuclear factor (HNF)-4α and other HNFs. The site-directed mutagenesis of HNF-4, HNF-1, HNF-3 and HNF-6 binding sites in the transthyretin proximal promoter dramatically decreases transthyretin promoter activity. Interestingly, the mutation of the HNF-4 binding site not only abolishes the response to HNF-4α, but also reduces significantly the response to other HNFs. However, mutation of the HNF-4 binding site merely affects the specific binding of HNF-4α, but not other HNFs, suggesting that an intact HNF-4 binding site not only provides a platform for specific interaction with HNF-4α, but also facilitates the interaction of HNF-4α with other HNFs. In a cytokine-induced acute phase response cell culture model, we observed a significant reduction in the binding of HNF-4α, HNF-1α, HNF-3β and HNF-6α to the transthyretin promoter, which correlates with a decrease in transthyretin expression after injury. These findings provide new insights into the mechanism of the negative transcriptional regulation of the transthyretin gene after injury caused by a decrease in the binding of HNFs and a modulation in their coordinated interactions.
Collapse
Affiliation(s)
- Zhongyan Wang
- Department of Surgery, Boston University School of Medicine, Boston, MA 02118, USA
| | | |
Collapse
|
46
|
Taube JH, Allton K, Duncan SA, Shen L, Barton MC. Foxa1 functions as a pioneer transcription factor at transposable elements to activate Afp during differentiation of embryonic stem cells. J Biol Chem 2010; 285:16135-44. [PMID: 20348100 DOI: 10.1074/jbc.m109.088096] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Epigenetic control of genes that are silent in embryonic stem cells, but destined for expression during differentiation, includes distinctive hallmarks, such as simultaneous activating/repressing (bivalent) modifications of chromatin and DNA hypomethylation at enhancers of gene expression. Although alpha-fetoprotein (Afp) falls into this class of genes, as it is silent in pluripotent stem cells and activated during differentiation of endoderm, we find that Afp chromatin lacks bivalent histone modifications. However, critical regulatory sites for Afp activation, overlapping Foxa1/p53/Smad-binding elements, are located within a 300-bp region lacking DNA methylation, due to transposed elements underrepresented in CpG sequences: a short interspersed transposable element and a medium reiterated sequence 1 element. Forkhead family member Foxa1 is activated by retinoic acid treatment of embryonic stem cells, binds its DNA consensus site within the short interspersed transposable/medium reiterated sequence 1 elements, and displaces linker histone H1 from silent Afp chromatin. Small interfering RNA depletion of Foxa1 showed that Foxa1 is essential in providing chromatin access to transforming growth factor beta-activated Smad2 and Smad4 and their subsequent DNA binding. Together these transcription factors establish highly acetylated chromatin and promote expression of Afp. Foxa1 acts as a pioneer transcription factor in de novo activation of Afp, by exploiting a lack of methylation at juxtaposed transposed elements, to bind and poise chromatin for intersection with transforming growth factor beta signaling during differentiation of embryonic stem cells.
Collapse
Affiliation(s)
- Joseph H Taube
- Department of Biochemistry and Molecular Biology, Graduate School of Biomedical Sciences, Center for Stem Cell and Developmental Biology, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | | | | | | | | |
Collapse
|
47
|
Song Y, Washington MK, Crawford HC. Loss of FOXA1/2 is essential for the epithelial-to-mesenchymal transition in pancreatic cancer. Cancer Res 2010; 70:2115-25. [PMID: 20160041 DOI: 10.1158/0008-5472.can-09-2979] [Citation(s) in RCA: 206] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
FOXA1 and FOXA2, members of the forkhead transcription factor family, are critical for epithelial differentiation in many endoderm-derived organs, including the pancreas. However, their role in tumor progression is largely unknown. Here, we identified FOXA1 and FOXA2 as important antagonists of the epithelial-to-mesenchymal transition (EMT) in pancreatic ductal adenocarcinoma (PDA) through their positive regulation of E-cadherin and maintenance of the epithelial phenotype. In human PDA samples, FOXA1/2 are expressed in all epithelia from normal to well-differentiated cancer cells, but are lost in undifferentiated cancer cells. In PDA cell lines, FOXA1/2 expression is consistently suppressed in experimental EMT models and RNAi silencing of FOXA1/2 alone is sufficient to induce EMT. Conversely, ectopic FOXA1/2 expression can potently neutralize several EMT-related E-cadherin repressive mechanisms. Finally, ectopic FOXA2 expression could reactivate E-cadherin expression in a PDA cell line with extensive promoter hypermethylation. In fact, demethylation-mediated reactivation of E-cadherin expression in these cells required concurrent reactivation of endogenous FOXA2 expression. We conclude that suppression of FOXA1/2 expression is both necessary and sufficient for EMT during PDA malignant progression.
Collapse
Affiliation(s)
- Yan Song
- Department of Pharmacology, Stony Brook University, Stony Brook, New York 11794-8651, USA
| | | | | |
Collapse
|
48
|
Navarro-Alvarez N, Soto-Gutierrez A, Kobayashi N. Hepatic stem cells and liver development. Methods Mol Biol 2010; 640:181-236. [PMID: 20645053 DOI: 10.1007/978-1-60761-688-7_10] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The liver consists of many cell types with specialized functions. Hepatocytes are one of the main players in the organ and therefore are the most vulnerable cells to damage. Since they are not everlasting cells, they need to be replenished throughout life. Although the capacity of hepatocytes to contribute to their own maintenance has long been recognized, recent studies have indicated the presence of both intrahepatic and extrahepatic stem/progenitor cell populations that serve to maintain the normal organ and to regenerate damaged parenchyma in response to a variety of insults.The intrahepatic compartment most likely derives primarily from the biliary tree, particularly the most proximal branches, i.e. the canals of Hering and smallest ductules. The extrahepatic compartment is at least in part derived from diverse populations of cells from the bone marrow. Embryonic stem cells (ES's) are considered as a part of the extrahepatic compartment. Due to their pluripotent capabilities, ES cell-derived cells form a potential future source of hepatocytes, to replace or restore hepatic tissues that have been damaged by disease or injury. Progressing knowledge about stem cells in the liver would allow a better understanding of the mechanisms of hepatic homeostasis and regeneration. Although a human stem cell-derived cell type equivalent to primary hepatocytes does not yet exist, the promising results obtained with extrahepatic stem cells would open the way to cell-based therapy for liver diseases.
Collapse
Affiliation(s)
- Nalu Navarro-Alvarez
- Department of Surgery, Okayama University Graduate School of Medicine and Dentistry, Okayama, Japan
| | | | | |
Collapse
|
49
|
Huang WT, Weng CF. Roles of hepatocyte nuclear factors (HNF) in the regulation of reproduction in teleosts. JOURNAL OF FISH BIOLOGY 2010; 76:225-239. [PMID: 20738706 DOI: 10.1111/j.1095-8649.2009.02480.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Hepatocyte nuclear factor (HNF) families are composed of liver-enriched transcription factors and upstream regulators of many liver-specific genes. HNF are involved in liver-specific gene expression, metabolism, development, cell growth and many cellular functions in the body. HNF genes can be activated or influenced by several hormones and insulin-like growth factors (IGF), and different combinations of the four HNF factors form a network in controlling the expression of liver-specific or liver-enriched genes. The functions of these factors and their interactions within the gonads of bony fishes, however, are not well understood, and the related literature is scant. Recently, several members of the HNF families have been detected in teleost gonads together with their downstream genes (IGF-I and IGF-II), suggesting that these HNF could be upregulated in vitro by steroid hormones. Thus, the hormone-HNF-IGF-gonad interaction may be an alternative axis in the reproductive mechanism that acts in concert with the conventional hypothalamus-pituitary-gonad pathway. This may help the early development and maturation of the gonad or gamete, sexual maturity or reversion and spawning-regulating mechanisms among fishes to be understood.
Collapse
Affiliation(s)
- W-T Huang
- Department of Molecular Biotechnology, Da-Yeh University, Chang-Hua 515, Taiwan
| | | |
Collapse
|
50
|
Kohler S, Cirillo LA. Stable chromatin binding prevents FoxA acetylation, preserving FoxA chromatin remodeling. J Biol Chem 2010; 285:464-72. [PMID: 19897491 PMCID: PMC2804194 DOI: 10.1074/jbc.m109.063149] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2009] [Revised: 11/05/2009] [Indexed: 12/22/2022] Open
Abstract
FoxA1-3 (formerly HNF3alpha, -beta, and -gamma), members of the FoxA subfamily of forkhead transcription factors, function as initial chromatin-binding and chromatin-remodeling factors in a variety of tissues, including liver and pancreas. Despite essential roles in development and metabolism, regulation of FoxA factors is not well understood. This study examines a potential role for acetylation in the regulation of FoxA chromatin binding and remodeling. Using in silico analysis, we have identified 11 putative p300 acetylation sites within FoxA1, five of which are located within wings 1 and 2 of its winged-helix DNA-binding domain. These polypeptide structures stabilize FoxA DNA and chromatin binding, and we have demonstrated that acetylation attenuates FoxA binding to DNA and diminishes its ability to remodel chromatin. FoxA acetylation is inhibited by chromatin binding. We propose a model whereby stable chromatin binding protects the FoxA DNA-binding domain from acetylation to preserve chromatin binding and remodeling by FoxA factors in the absence of extracellular cues.
Collapse
Affiliation(s)
- Sarah Kohler
- From the Department of Cell Biology, Neurobiology, and Anatomy, Medical College of Wisconsin, Milwaukee, Wisconsin 53226
| | - Lisa Ann Cirillo
- From the Department of Cell Biology, Neurobiology, and Anatomy, Medical College of Wisconsin, Milwaukee, Wisconsin 53226
| |
Collapse
|