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Sun C, Zhou C, Daneshvar K, Ben Saad A, Kratkiewicz AJ, Toles BJ, Arghiani N, Hess A, Chen JY, Pondick JV, York SR, Li W, Moran S, Gentile S, Ur Rahman R, Li Z, Zhou P, Sparks R, Habboub T, Kim BM, Choi MY, Affo S, Schwabe RF, Popov YV, Mullen AC. Conserved long noncoding RNA TILAM promotes liver fibrosis through interaction with PML in hepatic stellate cells. Hepatology 2024:01515467-990000000-00834. [PMID: 38563629 DOI: 10.1097/hep.0000000000000822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Accepted: 02/01/2024] [Indexed: 04/04/2024]
Abstract
BACKGROUND AND AIMS Fibrosis is the common endpoint for all forms of chronic liver injury, and progression of fibrosis leads to the development of end-stage liver disease. Activation of hepatic stellate cells (HSCs) and their transdifferentiation into myofibroblasts results in the accumulation of extracellular matrix (ECM) proteins that form the fibrotic scar. Long noncoding (lnc) RNAs regulate the activity of HSCs and provide targets for fibrotic therapies. APPROACH AND RESULTS We identified lncRNA TILAM located near COL1A1, expressed in HSCs, and induced with liver fibrosis in humans and mice. Loss-of-function studies in human HSCs and human liver organoids revealed that TILAM regulates expression of COL1A1 and other ECM genes. To determine the role of TILAM in vivo, we annotated the mouse ortholog (Tilam), generated Tilam-deficient GFP-reporter mice, and challenged these mice in two different models of liver fibrosis. Single-cell data and analysis of GFP expression in Tilam-deficient reporter mice revealed that Tilam is induced in murine HSCs with the development of fibrosis in vivo. Furthermore, loss of Tilam expression attenuated development of fibrosis in the setting of in vivo liver injury. Finally, we found that TILAM interacts with PML to regulate a feedback loop by which TGF-β2 reinforces TILAM expression and nuclear localization of PML to promote the fibrotic activity of HSCs. CONCLUSIONS TILAM is activated in HSCs with liver injury and interacts with PML to drive the development of fibrosis. Depletion of TILAM may serve as a therapeutic approach to combat the development of end stage liver disease.
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Affiliation(s)
- Cheng Sun
- Division of Gastroenterology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Chan Zhou
- Population and Quantitative Health Sciences, University of Massachusetts Chan Medical School, Worcester, MA USA
| | - Kaveh Daneshvar
- Division of Gastroenterology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Amel Ben Saad
- Division of Gastroenterology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Arcadia J Kratkiewicz
- Division of Gastroenterology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Benjamin J Toles
- Division of Gastroenterology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Nahid Arghiani
- Division of Gastroenterology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Anja Hess
- Division of Gastroenterology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Jennifer Y Chen
- Liver Center, Department of Medicine, University of California, San Francisco, CA, USA
| | - Joshua V Pondick
- Division of Gastroenterology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Samuel R York
- Division of Gastroenterology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Wenyang Li
- Division of Gastroenterology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Sean Moran
- Division of Gastroenterology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Stefan Gentile
- Division of Gastroenterology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute, Cambridge, MA, USA
| | - Raza Ur Rahman
- Division of Gastroenterology, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Broad Institute, Cambridge, MA, USA
| | - Zixiu Li
- Population and Quantitative Health Sciences, University of Massachusetts Chan Medical School, Worcester, MA USA
| | - Peng Zhou
- Population and Quantitative Health Sciences, University of Massachusetts Chan Medical School, Worcester, MA USA
| | - Robert Sparks
- Division of Gastroenterology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Tim Habboub
- Division of Gastroenterology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Byeong-Moo Kim
- Division of Gastroenterology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Michael Y Choi
- Division of Gastroenterology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Silvia Affo
- Department of Liver, Digestive System, and Metabolism, Institut d'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
| | - Robert F Schwabe
- Department of Medicine, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Yury V Popov
- Division of Gastroenterology, Hepatology and Nutrition, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Alan C Mullen
- Division of Gastroenterology, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Broad Institute, Cambridge, MA, USA
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Singh C, Jin B, Shrestha N, Markhard AL, Panda A, Calvo SE, Deik A, Pan X, Zuckerman AL, Ben Saad A, Corey KE, Sjoquist J, Osganian S, AminiTabrizi R, Rhee EP, Shah H, Goldberger O, Mullen AC, Cracan V, Clish CB, Mootha VK, Goodman RP. ChREBP is activated by reductive stress and mediates GCKR-associated metabolic traits. Cell Metab 2024; 36:144-158.e7. [PMID: 38101397 PMCID: PMC10842884 DOI: 10.1016/j.cmet.2023.11.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 07/24/2023] [Accepted: 11/21/2023] [Indexed: 12/17/2023]
Abstract
Common genetic variants in glucokinase regulator (GCKR), which encodes GKRP, a regulator of hepatic glucokinase (GCK), influence multiple metabolic traits in genome-wide association studies (GWASs), making GCKR one of the most pleiotropic GWAS loci in the genome. It is unclear why. Prior work has demonstrated that GCKR influences the hepatic cytosolic NADH/NAD+ ratio, also referred to as reductive stress. Here, we demonstrate that reductive stress is sufficient to activate the transcription factor ChREBP and necessary for its activation by the GKRP-GCK interaction, glucose, and ethanol. We show that hepatic reductive stress induces GCKR GWAS traits such as increased hepatic fat, circulating FGF21, and circulating acylglycerol species, which are also influenced by ChREBP. We define the transcriptional signature of hepatic reductive stress and show its upregulation in fatty liver disease and downregulation after bariatric surgery in humans. These findings highlight how a GCKR-reductive stress-ChREBP axis influences multiple human metabolic traits.
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Affiliation(s)
- Charandeep Singh
- Liver Center, Division of Gastroenterology, Massachusetts General Hospital, Boston, MA 02114, USA; Endocrine Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Byungchang Jin
- Liver Center, Division of Gastroenterology, Massachusetts General Hospital, Boston, MA 02114, USA; Endocrine Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Nirajan Shrestha
- Liver Center, Division of Gastroenterology, Massachusetts General Hospital, Boston, MA 02114, USA; Endocrine Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Andrew L Markhard
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Apekshya Panda
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Sarah E Calvo
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Amy Deik
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Xingxiu Pan
- The Scintillon Institute, San Diego, CA 92121, USA
| | - Austin L Zuckerman
- The Scintillon Institute, San Diego, CA 92121, USA; Program in Mathematics and Science Education, University of California, San Diego, La Jolla, CA 92093; Program in Mathematics and Science Education, San Diego State University, San Diego, CA 92120
| | - Amel Ben Saad
- Division of Gastroenterology, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
| | - Kathleen E Corey
- Liver Center, Division of Gastroenterology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Julia Sjoquist
- Liver Center, Division of Gastroenterology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Stephanie Osganian
- Liver Center, Division of Gastroenterology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Roya AminiTabrizi
- Metabolomics Platform, Comprehensive Cancer Center, the University of Chicago, Chicago, IL 60637, USA
| | - Eugene P Rhee
- Endocrine Unit, Massachusetts General Hospital, Boston, MA 02114, USA; Nephrology Division, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Hardik Shah
- Metabolomics Platform, Comprehensive Cancer Center, the University of Chicago, Chicago, IL 60637, USA
| | - Olga Goldberger
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Alan C Mullen
- Division of Gastroenterology, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
| | - Valentin Cracan
- The Scintillon Institute, San Diego, CA 92121, USA; Department of Chemistry, the Scripps Research Institute, La Jolla, CA 92037, USA
| | - Clary B Clish
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Vamsi K Mootha
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Russell P Goodman
- Liver Center, Division of Gastroenterology, Massachusetts General Hospital, Boston, MA 02114, USA; Endocrine Unit, Massachusetts General Hospital, Boston, MA 02114, USA.
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Hess A, Gentile SD, Ben Saad A, Rahman R, Habboub T, Pratt DS, Mullen AC. Single-cell transcriptomics stratifies organoid models of metabolic dysfunction-associated steatotic liver disease. EMBO J 2023; 42:e113898. [PMID: 37962490 PMCID: PMC10711666 DOI: 10.15252/embj.2023113898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 10/04/2023] [Accepted: 10/06/2023] [Indexed: 11/15/2023] Open
Abstract
Metabolic dysfunction-associated steatotic liver disease (MASLD) is a growing cause of morbidity with limited treatment options. Thus, accurate in vitro systems to test new therapies are indispensable. While recently, human liver organoid models have emerged to assess steatotic liver disease, a systematic evaluation of their translational potential is still missing. Here, we evaluated human liver organoid models of MASLD, comparatively testing disease induction in three conditions: oleic acid, palmitic acid, and TGF-β1. Through single-cell analyses, we find that all three models induce inflammatory signatures, but only TGF-β1 promotes collagen production, fibrosis, and hepatic stellate cell expansion. In striking contrast, oleic acid ameliorates fibrotic signatures and reduces the hepatic stellate cell population. Linking data from each model to gene expression signatures associated with MASLD disease progression further demonstrates that palmitic acid and TGF-β1 more robustly model inflammation and fibrosis. Our findings highlight the importance of stratifying MASLD organoid models by signatures of clinical disease progression, provide a single-cell reference to benchmark future organoid injury models, and allow us to study evolving steatohepatitis, fibrosis, and HSC susceptibility to injury in a dynamic, multi-lineage human in vitro system.
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Affiliation(s)
- Anja Hess
- Division of Gastroenterology, Massachusetts General HospitalHarvard Medical SchoolBostonMAUSA
- Present address:
Department of Genome RegulationMax Planck Institute for Molecular GeneticsBerlinGermany
| | - Stefan D Gentile
- Division of Gastroenterology, Massachusetts General HospitalHarvard Medical SchoolBostonMAUSA
- Klarman Cell ObservatoryBroad Institute of MIT and HarvardCambridgeMAUSA
| | - Amel Ben Saad
- Division of Gastroenterology, Massachusetts General HospitalHarvard Medical SchoolBostonMAUSA
| | - Raza‐Ur Rahman
- Division of Gastroenterology, Massachusetts General HospitalHarvard Medical SchoolBostonMAUSA
| | - Tim Habboub
- Division of Gastroenterology, Massachusetts General HospitalHarvard Medical SchoolBostonMAUSA
| | - Daniel S Pratt
- Division of Gastroenterology, Massachusetts General HospitalHarvard Medical SchoolBostonMAUSA
- Autoimmune and Cholestatic Liver CenterMassachusetts General HospitalBostonMAUSA
| | - Alan C Mullen
- Division of Gastroenterology, Massachusetts General HospitalHarvard Medical SchoolBostonMAUSA
- Klarman Cell ObservatoryBroad Institute of MIT and HarvardCambridgeMAUSA
- Center for the Study of Inflammatory Bowel DiseaseMassachusetts General HospitalBostonMAUSA
- Harvard Stem Cell InstituteCambridgeMAUSA
- Present address:
University of Massachusetts Chan Medical SchoolWorcesterMAUSA
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4
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Sun C, Zhou C, Daneshvar K, Kratkiewicz AJ, Saad AB, Hess A, Chen JY, Pondick JV, York SR, Li W, Moran S, Gentile S, Rahman RU, Li Z, Sparks R, Habboub T, Kim BM, Choi MY, Affo S, Schwabe RF, Popov YV, Mullen AC. Conserved long noncoding RNA TILAM promotes liver fibrosis through interaction with PML in hepatic stellate cells. bioRxiv 2023:2023.07.29.551032. [PMID: 37546982 PMCID: PMC10402143 DOI: 10.1101/2023.07.29.551032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Background & Aims Fibrosis is the common endpoint for all forms of chronic liver injury, and progression of fibrosis leads to the development of end-stage liver disease. Activation of hepatic stellate cells (HSCs) and their transdifferentiation to myofibroblasts results in the accumulation of extracellular matrix (ECM) proteins that form the fibrotic scar. Long noncoding (lnc) RNAs regulate the activity of HSCs and may provide targets for fibrotic therapies. Methods We identified lncRNA TILAM as expressed near COL1A1 in human HSCs and performed loss-of-function studies in human HSCs and liver organoids. Transcriptomic analyses of HSCs isolated from mice defined the murine ortholog of TILAM . We then generated Tilam -deficient GFP reporter mice and quantified fibrotic responses to carbon tetrachloride (CCl 4 ) and choline-deficient L-amino acid defined high fat diet (CDA-HFD). Co-precipitation studies, mass spectrometry, and gene expression analyses identified protein partners of TILAM . Results TILAM is conserved between human and mouse HSCs and regulates expression of ECM proteins, including collagen. Tilam is selectively induced in HSCs during the development of fibrosis in vivo . In both male and female mice, loss of Tilam results in reduced fibrosis in the setting of CCl 4 and CDA-HFD injury models. TILAM interacts with promyelocytic leukemia protein (PML) to stabilize PML protein levels and promote the fibrotic activity of HSCs. Conclusion TILAM is activated in HSCs and interacts with PML to drive the development of liver fibrosis. Depletion of TILAM may serve as a therapeutic approach to combat the development of end stage liver disease.
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5
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Estevez M, Li R, Paul B, Daneshvar K, Mullen AC, Romerio F, Addepalli B. Identification and mapping of post-transcriptional modifications on the HIV-1 antisense transcript Ast in human cells. RNA 2022; 28:697-710. [PMID: 35168996 PMCID: PMC9014878 DOI: 10.1261/rna.079043.121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 01/29/2022] [Indexed: 05/03/2023]
Abstract
The human immunodeficiency virus type 1 (HIV-1) encodes multiple RNA molecules. Transcripts that originate from the proviral 5' long terminal repeat (LTR) function as messenger RNAs for the expression of 16 different mature viral proteins. In addition, HIV-1 expresses an antisense transcript (Ast) from the 3'LTR, which has both protein-coding and noncoding properties. While the mechanisms that regulate the coding and noncoding activities of Ast remain unknown, post-transcriptional modifications are known to influence RNA stability, interaction with protein partners, and translation capacity. Here, we report the nucleoside modification profile of Ast obtained through liquid chromatography coupled with mass spectrometry (LC-MS) analysis. The epitranscriptome includes a limited set of modified nucleosides but predominantly ribose methylations. A number of these modifications were mapped to specific positions of the sequence through RNA modification mapping procedures. The presence of modifications on Ast is consistent with the RNA-modifying enzymes interacting with Ast The identification and mapping of Ast post-transcriptional modifications is expected to elucidate the mechanisms through which this versatile molecule can carry out diverse activities in different cell compartments. Manipulation of post-transcriptional modifications on the Ast RNA may have therapeutic implications.
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Affiliation(s)
- Mariana Estevez
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221, USA
| | - Rui Li
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Biplab Paul
- Massachusetts General Hospital, Boston, Massachusetts 02114, USA
| | - Kaveh Daneshvar
- Massachusetts General Hospital, Boston, Massachusetts 02114, USA
| | - Alan C Mullen
- Massachusetts General Hospital, Boston, Massachusetts 02114, USA
| | - Fabio Romerio
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
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6
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Li W, Chen JY, Sun C, Sparks RP, Pantano L, Rahman RU, Moran SP, Pondick JV, Kirchner R, Wrobel D, Bieler M, Sauer A, Ho Sui SJ, Doerner JF, Rippmann JF, Mullen AC. Nanchangmycin regulates FYN, PTK2, and MAPK1/3 to control the fibrotic activity of human hepatic stellate cells. eLife 2022; 11:74513. [PMID: 35617485 PMCID: PMC9135407 DOI: 10.7554/elife.74513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 05/06/2022] [Indexed: 01/19/2023] Open
Abstract
Chronic liver injury causes fibrosis, characterized by the formation of scar tissue resulting from excessive accumulation of extracellular matrix (ECM) proteins. Hepatic stellate cell (HSC) myofibroblasts are the primary cell type responsible for liver fibrosis, yet there are currently no therapies directed at inhibiting the activity of HSC myofibroblasts. To search for potential anti-fibrotic compounds, we performed a high-throughput compound screen in primary human HSC myofibroblasts and identified 19 small molecules that induce HSC inactivation, including the polyether ionophore nanchangmycin (NCMC). NCMC induces lipid re-accumulation while reducing collagen expression, deposition of collagen in the extracellular matrix, cell proliferation, and migration. We find that NCMC increases cytosolic Ca2+ and reduces the phosphorylated protein levels of FYN, PTK2 (FAK), MAPK1/3 (ERK2/1), HSPB1 (HSP27), and STAT5B. Further, depletion of each of these kinases suppress COL1A1 expression. These studies reveal a signaling network triggered by NCMC to inactivate HSC myofibroblasts and reduce expression of proteins that compose the fibrotic scar. Identification of the antifibrotic effects of NCMC and the elucidation of pathways by which NCMC inhibits fibrosis provide new tools and therapeutic targets that could potentially be utilized to combat the development and progression of liver fibrosis.
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Affiliation(s)
- Wenyang Li
- Division of Gastroenterology, Massachusetts General HospitalBostonUnited States,Harvard Medical SchoolBostonUnited States
| | - Jennifer Y Chen
- Division of Gastroenterology, Massachusetts General HospitalBostonUnited States,Harvard Medical SchoolBostonUnited States
| | - Cheng Sun
- Division of Gastroenterology, Massachusetts General HospitalBostonUnited States,Harvard Medical SchoolBostonUnited States
| | - Robert P Sparks
- Division of Gastroenterology, Massachusetts General HospitalBostonUnited States,Harvard Medical SchoolBostonUnited States
| | - Lorena Pantano
- Harvard T.H. Chan School of Public HealthBostonUnited States
| | - Raza-Ur Rahman
- Division of Gastroenterology, Massachusetts General HospitalBostonUnited States,Harvard Medical SchoolBostonUnited States
| | - Sean P Moran
- Division of Gastroenterology, Massachusetts General HospitalBostonUnited States,Harvard Medical SchoolBostonUnited States
| | - Joshua V Pondick
- Division of Gastroenterology, Massachusetts General HospitalBostonUnited States,Harvard Medical SchoolBostonUnited States
| | - Rory Kirchner
- Harvard T.H. Chan School of Public HealthBostonUnited States
| | | | | | - Achim Sauer
- Boehringer Ingelheim Pharma GmbH & CoBiberachGermany
| | | | | | | | - Alan C Mullen
- Division of Gastroenterology, Massachusetts General HospitalBostonUnited States,Harvard Medical SchoolBostonUnited States,Harvard Stem Cell InstituteCambridgeUnited States
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7
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Alsamman S, Christenson SA, Yu A, Ayad NME, Mooring MS, Segal JM, Hu JKH, Schaub JR, Ho SS, Rao V, Marlow MM, Turner SM, Sedki M, Pantano L, Ghoshal S, Ferreira DDS, Ma HY, Duwaerts CC, Espanol-Suner R, Wei L, Newcomb B, Mileva I, Canals D, Hannun YA, Chung RT, Mattis AN, Fuchs BC, Tager AM, Yimlamai D, Weaver VM, Mullen AC, Sheppard D, Chen JY. Targeting acid ceramidase inhibits YAP/TAZ signaling to reduce fibrosis in mice. Sci Transl Med 2021; 12:12/557/eaay8798. [PMID: 32817366 DOI: 10.1126/scitranslmed.aay8798] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 02/11/2020] [Accepted: 06/30/2020] [Indexed: 12/11/2022]
Abstract
Hepatic stellate cells (HSCs) drive hepatic fibrosis. Therapies that inactivate HSCs have clinical potential as antifibrotic agents. We previously identified acid ceramidase (aCDase) as an antifibrotic target. We showed that tricyclic antidepressants (TCAs) reduce hepatic fibrosis by inhibiting aCDase and increasing the bioactive sphingolipid ceramide. We now demonstrate that targeting aCDase inhibits YAP/TAZ activity by potentiating its phosphorylation-mediated proteasomal degradation via the ubiquitin ligase adaptor protein β-TrCP. In mouse models of fibrosis, pharmacologic inhibition of aCDase or genetic knockout of aCDase in HSCs reduces fibrosis, stromal stiffness, and YAP/TAZ activity. In patients with advanced fibrosis, aCDase expression in HSCs is increased. Consistently, a signature of the genes most down-regulated by ceramide identifies patients with advanced fibrosis who could benefit from aCDase targeting. The findings implicate ceramide as a critical regulator of YAP/TAZ signaling and HSC activation and highlight aCDase as a therapeutic target for the treatment of fibrosis.
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Affiliation(s)
- Sarah Alsamman
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94115, USA
| | - Stephanie A Christenson
- Division of Pulmonary, Critical Care, Allergy and Sleep, Department of Medicine, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Amy Yu
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94115, USA
| | - Nadia M E Ayad
- Center for Bioengineering and Tissue Regeneration, Department of Surgery, University of California, San Francisco, San Francisco, CA 94143, USA.,UC Berkeley-UCSF Graduate Program in Bioengineering, San Francisco, CA 94143, USA
| | - Meghan S Mooring
- Division of Pediatric Gastroenterology and Hepatology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Joe M Segal
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94115, USA
| | - Jimmy Kuang-Hsien Hu
- Division of Oral Biology & Medicine, School of Dentistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | | | - Steve S Ho
- Pliant Therapeutics, South San Francisco, CA 94080, USA
| | - Vikram Rao
- Pliant Therapeutics, South San Francisco, CA 94080, USA
| | | | | | - Mai Sedki
- Internal Medicine, Kaiser Permanente, San Francisco, CA 94115, USA
| | - Lorena Pantano
- Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA
| | - Sarani Ghoshal
- Division of Surgical Oncology, Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA 02114, USA
| | - Diego Dos Santos Ferreira
- Athinoula A. Martinos Center for Biomedical Imaging, Institute for Innovation in Imaging, Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA 02129, USA
| | - Hsiao-Yen Ma
- Lung Biology Center, Department of Medicine, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Caroline C Duwaerts
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94115, USA.,Liver Center, Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Regina Espanol-Suner
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Lan Wei
- Division of Surgical Oncology, Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA 02114, USA
| | - Benjamin Newcomb
- Departments of Medicine and Biochemistry and Stony Brook Cancer Center, Stony Brook University, Stony Brook, NY 11794, USA
| | - Izolda Mileva
- Departments of Medicine and Biochemistry and Stony Brook Cancer Center, Stony Brook University, Stony Brook, NY 11794, USA
| | - Daniel Canals
- Departments of Medicine and Biochemistry and Stony Brook Cancer Center, Stony Brook University, Stony Brook, NY 11794, USA
| | - Yusuf A Hannun
- Departments of Medicine and Biochemistry and Stony Brook Cancer Center, Stony Brook University, Stony Brook, NY 11794, USA
| | - Raymond T Chung
- Liver Center, Division of Gastroenterology, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Aras N Mattis
- Liver Center, Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA.,Department of Pathology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Bryan C Fuchs
- Division of Surgical Oncology, Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA 02114, USA
| | - Andrew M Tager
- Division of Pulmonary and Critical Care Medicine, Fibrosis Research Center, and Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Dean Yimlamai
- Division of Pediatric Gastroenterology and Hepatology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Valerie M Weaver
- Center for Bioengineering and Tissue Regeneration, Department of Surgery, University of California, San Francisco, San Francisco, CA 94143, USA.,UC Berkeley-UCSF Graduate Program in Bioengineering, San Francisco, CA 94143, USA.,Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA.,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA.,Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA.,Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Alan C Mullen
- Liver Center, Division of Gastroenterology, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Dean Sheppard
- Division of Pulmonary, Critical Care, Allergy and Sleep, Department of Medicine, University of California, San Francisco, San Francisco, CA 94158, USA. .,Lung Biology Center, Department of Medicine, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Jennifer Y Chen
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94115, USA. .,Liver Center, Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
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8
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Melendez J, Sieiro D, Salgado D, Morin V, Dejardin MJ, Zhou C, Mullen AC, Marcelle C. TGFβ signalling acts as a molecular brake of myoblast fusion. Nat Commun 2021; 12:749. [PMID: 33531476 PMCID: PMC7854724 DOI: 10.1038/s41467-020-20290-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 11/21/2020] [Indexed: 01/30/2023] Open
Abstract
Fusion of nascent myoblasts to pre-existing myofibres is critical for skeletal muscle growth and repair. The vast majority of molecules known to regulate myoblast fusion are necessary in this process. Here, we uncover, through high-throughput in vitro assays and in vivo studies in the chicken embryo, that TGFβ (SMAD2/3-dependent) signalling acts specifically and uniquely as a molecular brake on muscle fusion. While constitutive activation of the pathway arrests fusion, its inhibition leads to a striking over-fusion phenotype. This dynamic control of TGFβ signalling in the embryonic muscle relies on a receptor complementation mechanism, prompted by the merging of myoblasts with myofibres, each carrying one component of the heterodimer receptor complex. The competence of myofibres to fuse is likely restored through endocytic degradation of activated receptors. Altogether, this study shows that muscle fusion relies on TGFβ signalling to regulate its pace.
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Affiliation(s)
- Julie Melendez
- Institut NeuroMyoGène (INMG), University Claude Bernard Lyon1, CNRS UMR 5310, INSERM U1217, Lyon, France
| | - Daniel Sieiro
- Institut NeuroMyoGène (INMG), University Claude Bernard Lyon1, CNRS UMR 5310, INSERM U1217, Lyon, France
- Australian Regenerative Medicine Institute (ARMI), Monash University, Clayton, VIC, Australia
- Plexus Ventures LLC, Boston, MA, USA
| | - David Salgado
- Australian Regenerative Medicine Institute (ARMI), Monash University, Clayton, VIC, Australia
- Marseille Medical Genetics (MMG), Aix Marseille University, INSERM U1251, Marseille, France
| | - Valérie Morin
- Institut NeuroMyoGène (INMG), University Claude Bernard Lyon1, CNRS UMR 5310, INSERM U1217, Lyon, France
| | - Marie-Julie Dejardin
- Institut NeuroMyoGène (INMG), University Claude Bernard Lyon1, CNRS UMR 5310, INSERM U1217, Lyon, France
| | - Chan Zhou
- Gastrointestinal Unit, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Alan C Mullen
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA
| | - Christophe Marcelle
- Institut NeuroMyoGène (INMG), University Claude Bernard Lyon1, CNRS UMR 5310, INSERM U1217, Lyon, France.
- Australian Regenerative Medicine Institute (ARMI), Monash University, Clayton, VIC, Australia.
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9
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Daneshvar K, Ardehali MB, Klein IA, Hsieh FK, Kratkiewicz AJ, Mahpour A, Cancelliere SOL, Zhou C, Cook BM, Li W, Pondick JV, Gupta SK, Moran SP, Young RA, Kingston RE, Mullen AC. lncRNA DIGIT and BRD3 protein form phase-separated condensates to regulate endoderm differentiation. Nat Cell Biol 2020; 22:1211-1222. [PMID: 32895492 PMCID: PMC8008247 DOI: 10.1038/s41556-020-0572-2] [Citation(s) in RCA: 82] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 08/05/2020] [Indexed: 01/19/2023]
Abstract
Cooperation between DNA, RNA and protein regulates gene expression and controls differentiation through interactions that connect regions of nucleic acids and protein domains and through the assembly of biomolecular condensates. Here, we report that endoderm differentiation is regulated by the interaction between the long non-coding RNA (lncRNA) DIGIT and the bromodomain and extraterminal domain protein BRD3. BRD3 forms phase-separated condensates of which the formation is promoted by DIGIT, occupies enhancers of endoderm transcription factors and is required for endoderm differentiation. BRD3 binds to histone H3 acetylated at lysine 18 (H3K18ac) in vitro and co-occupies the genome with H3K18ac. DIGIT is also enriched in regions of H3K18ac, and the depletion of DIGIT results in decreased recruitment of BRD3 to these regions. Our findings show that cooperation between DIGIT and BRD3 at regions of H3K18ac regulates the transcription factors that drive endoderm differentiation and suggest that protein-lncRNA phase-separated condensates have a broader role as regulators of transcription.
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Affiliation(s)
- Kaveh Daneshvar
- Gastrointestinal Unit, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - M Behfar Ardehali
- Department of Molecular Biology and MGH Research Institute, Massachusetts General Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Isaac A Klein
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Fu-Kai Hsieh
- Department of Molecular Biology and MGH Research Institute, Massachusetts General Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Arcadia J Kratkiewicz
- Gastrointestinal Unit, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Amin Mahpour
- Gastrointestinal Unit, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | | | - Chan Zhou
- Gastrointestinal Unit, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | | | - Wenyang Li
- Gastrointestinal Unit, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Joshua V Pondick
- Gastrointestinal Unit, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Sweta K Gupta
- Gastrointestinal Unit, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Sean P Moran
- Gastrointestinal Unit, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Richard A Young
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Robert E Kingston
- Department of Molecular Biology and MGH Research Institute, Massachusetts General Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Alan C Mullen
- Gastrointestinal Unit, Massachusetts General Hospital, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
- Harvard Stem Cell Institute, Cambridge, MA, USA.
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10
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Ufere NN, Donlan J, Waldman L, Dienstag JL, Friedman LS, Corey KE, Hashemi N, Carolan P, Mullen AC, Thiim M, Bhan I, Nipp R, Greer JA, Temel JS, Chung RT, El-Jawahri A. Barriers to Use of Palliative Care and Advance Care Planning Discussions for Patients With End-Stage Liver Disease. Clin Gastroenterol Hepatol 2019; 17:2592-2599. [PMID: 30885884 PMCID: PMC6745282 DOI: 10.1016/j.cgh.2019.03.022] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 02/28/2019] [Accepted: 03/10/2019] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS Despite evidence for the benefits of palliative care (PC) referrals and early advance care planning (ACP) discussions for patients with chronic diseases, patients with end-stage liver disease (ESLD) often do not receive such care. We sought to examine physicians' perceptions of the barriers to PC and timely ACP discussions for patients with ESLD. METHODS We conducted a cross-sectional survey of hepatologists and gastroenterologists who provide care to adult patients with ESLD, recruited from the American Association for the Study of Liver Diseases 2018 membership registry. Using a questionnaire adapted from prior studies, we assessed physicians' perceptions of barriers to PC use and timely ACP discussions; 396 of 1236 eligible physicians (32%) completed the questionnaire. RESULTS The most commonly cited barriers to PC use were cultural factors that affect perception of PC (by 95% of respondents), unrealistic expectations from patients about their prognosis (by 93% of respondents), and competing demands for clinicians' time (by 91% of respondents). Most respondents (81%) thought that ACP discussions with patients who have ESLD typically occur too late in the course of illness. The most commonly cited barriers to timely ACP discussions were insufficient communication between clinicians and families about goals of care (by 84% of respondents) and insufficient cultural competency training about end-of-life care (81%). CONCLUSION There are substantial barriers to use of PC and timely discussions about ACP-most hepatologists and gastroenterologists believe that ACP occurs too late for patients with ESLD. Strategies are needed to overcome barriers and increase delivery of high-quality palliative and end-of-life care to patients with ESLD.
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Affiliation(s)
- Nneka N. Ufere
- Gastrointestinal Unit, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston MA, USA
| | - John Donlan
- Gastrointestinal Unit, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston MA, USA
| | - Lauren Waldman
- Division of Hematology-Oncology, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA USA
| | - Jules L. Dienstag
- Gastrointestinal Unit, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston MA, USA
| | | | - Kathleen E. Corey
- Gastrointestinal Unit, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston MA, USA
| | - Nikroo Hashemi
- Division of Gastroenterology, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston MA, USA
| | - Peter Carolan
- Gastrointestinal Unit, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston MA, USA
| | - Alan C. Mullen
- Gastrointestinal Unit, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston MA, USA
| | - Michael Thiim
- Gastrointestinal Unit, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston MA, USA
| | - Irun Bhan
- Gastrointestinal Unit, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston MA, USA
| | - Ryan Nipp
- Division of Hematology-Oncology, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA USA
| | - Joseph A. Greer
- Division of Hematology-Oncology, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA USA
| | - Jennifer S. Temel
- Division of Hematology-Oncology, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA USA
| | - Raymond T. Chung
- Gastrointestinal Unit, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston MA, USA
| | - Areej El-Jawahri
- Division of Hematology-Oncology, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA USA
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11
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Ufere NN, Donlan J, Waldman L, Patel A, Dienstag JL, Friedman LS, Corey KE, Hashemi N, Carolan P, Mullen AC, Thiim M, Bhan I, Nipp R, Greer J, Temel J, Chung RT, El-Jawahri A. Physicians' Perspectives on Palliative Care for Patients With End-Stage Liver Disease: A National Survey Study. Liver Transpl 2019; 25:859-869. [PMID: 30963669 PMCID: PMC6529275 DOI: 10.1002/lt.25469] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 03/24/2019] [Indexed: 12/12/2022]
Abstract
Specialty palliative care (PC) is underused for patients with end-stage liver disease (ESLD). We sought to examine attitudes of hepatologists and gastroenterologists about PC for patients with ESLD. We conducted a cross-sectional survey of these specialists who provide care to patients with ESLD. Participants were recruited from the American Association for the Study of Liver Diseases membership directory. Using a questionnaire adapted from prior studies, we examined physicians' attitudes about PC and whether these attitudes varied based on patients' candidacy for liver transplantation. We identified predictors of physicians' attitudes about PC using linear regression. Approximately one-third of eligible physicians (396/1236, 32%) completed the survey. Most (95%) believed that centers providing care to patients with ESLD should have PC services, and 86% trusted PC clinicians to care for their patients. Only a minority reported collaborating frequently with inpatient (32%) or outpatient (11%) PC services. Most believed that when patients hear the term PC, they feel scared (94%) and anxious (87%). Most (83%) believed that patients would think nothing more could be done for their underlying disease if a PC referral was suggested. Physicians who believed that ESLD is a terminal condition (B = 1.09; P = 0.006) reported more positive attitudes about PC. Conversely, physicians with negative perceptions of PC for transplant candidates (B = -0.22; standard error = 0.05; P < 0.001) reported more negative attitudes toward PC. In conclusion, although most hepatologists and gastroenterologists believe that patients with ESLD should have access to PC, they reported rarely collaborating with PC teams and had substantial concerns about patients' perceptions of PC. Interventions are needed to overcome misperceptions of PC and to promote collaboration with PC clinicians for patients with ESLD.
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Affiliation(s)
- Nneka N. Ufere
- Gastrointestinal Unit, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston MA, USA
| | - John Donlan
- Gastrointestinal Unit, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston MA, USA
| | - Lauren Waldman
- Division of Hematology-Oncology, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA USA
| | - Arpan Patel
- Division of Digestive Diseases, Department of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Jules L. Dienstag
- Gastrointestinal Unit, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston MA, USA
| | | | - Kathleen E. Corey
- Gastrointestinal Unit, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston MA, USA
| | - Nikroo Hashemi
- Division of Gastroenterology, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston MA, USA
| | - Peter Carolan
- Gastrointestinal Unit, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston MA, USA
| | - Alan C. Mullen
- Gastrointestinal Unit, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston MA, USA
| | - Michael Thiim
- Gastrointestinal Unit, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston MA, USA
| | - Irun Bhan
- Gastrointestinal Unit, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston MA, USA
| | - Ryan Nipp
- Division of Hematology-Oncology, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA USA
| | - Joseph Greer
- Division of Hematology-Oncology, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA USA
| | - Jennifer Temel
- Division of Hematology-Oncology, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA USA
| | - Raymond T. Chung
- Gastrointestinal Unit, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston MA, USA
| | - Areej El-Jawahri
- Division of Hematology-Oncology, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA USA
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12
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Daneshvar K, Pondick JV, Kim BM, Zhou C, York SR, Macklin JA, Abualteen A, Tan B, Sigova AA, Marcho C, Tremblay KD, Mager J, Choi MY, Mullen AC. DIGIT Is a Conserved Long Noncoding RNA that Regulates GSC Expression to Control Definitive Endoderm Differentiation of Embryonic Stem Cells. Cell Rep 2017; 17:353-365. [PMID: 27705785 DOI: 10.1016/j.celrep.2016.09.017] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Revised: 08/12/2016] [Accepted: 09/03/2016] [Indexed: 02/06/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) exhibit diverse functions, including regulation of development. Here, we combine genome-wide mapping of SMAD3 occupancy with expression analysis to identify lncRNAs induced by activin signaling during endoderm differentiation of human embryonic stem cells (hESCs). We find that DIGIT is divergent to Goosecoid (GSC) and expressed during endoderm differentiation. Deletion of the SMAD3-occupied enhancer proximal to DIGIT inhibits DIGIT and GSC expression and definitive endoderm differentiation. Disruption of the gene encoding DIGIT and depletion of the DIGIT transcript reveal that DIGIT is required for definitive endoderm differentiation. In addition, we identify the mouse ortholog of DIGIT and show that it is expressed during development and promotes definitive endoderm differentiation of mouse ESCs. DIGIT regulates GSC in trans, and activation of endogenous GSC expression is sufficient to rescue definitive endoderm differentiation in DIGIT-deficient hESCs. Our study defines DIGIT as a conserved noncoding developmental regulator of definitive endoderm.
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Affiliation(s)
- Kaveh Daneshvar
- Gastrointestinal Unit, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Joshua V Pondick
- Gastrointestinal Unit, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Byeong-Moo Kim
- Gastrointestinal Unit, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Chan Zhou
- Gastrointestinal Unit, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Samuel R York
- Gastrointestinal Unit, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Jillian A Macklin
- Gastrointestinal Unit, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Ameed Abualteen
- Gastrointestinal Unit, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Bo Tan
- Gastrointestinal Unit, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; School of Fundamental Medical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510405, China
| | - Alla A Sigova
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Chelsea Marcho
- Department of Veterinary and Animal Sciences, University of Massachusetts at Amherst, Amherst, MA 01003, USA
| | - Kimberly D Tremblay
- Department of Veterinary and Animal Sciences, University of Massachusetts at Amherst, Amherst, MA 01003, USA
| | - Jesse Mager
- Department of Veterinary and Animal Sciences, University of Massachusetts at Amherst, Amherst, MA 01003, USA
| | - Michael Y Choi
- Gastrointestinal Unit, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Alan C Mullen
- Gastrointestinal Unit, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA.
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13
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Zhou C, Molinie B, Daneshvar K, Pondick JV, Wang J, Van Wittenberghe N, Xing Y, Giallourakis CC, Mullen AC. Genome-Wide Maps of m6A circRNAs Identify Widespread and Cell-Type-Specific Methylation Patterns that Are Distinct from mRNAs. Cell Rep 2017; 20:2262-2276. [PMID: 28854373 PMCID: PMC5705222 DOI: 10.1016/j.celrep.2017.08.027] [Citation(s) in RCA: 296] [Impact Index Per Article: 42.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Revised: 06/21/2017] [Accepted: 08/03/2017] [Indexed: 12/17/2022] Open
Abstract
N6-methyladenosine (m6A) is the most abundant internal modification of mRNAs and is implicated in all aspects of post-transcriptional RNA metabolism. However, little is known about m6A modifications to circular (circ) RNAs. We developed a computational pipeline (AutoCirc) that, together with depletion of ribosomal RNA and m6A immunoprecipitation, defined thousands of m6A circRNAs with cell-type-specific expression. The presence of m6A circRNAs is corroborated by interaction between circRNAs and YTHDF1/YTHDF2, proteins that read m6A sites in mRNAs, and by reduced m6A levels upon depletion of METTL3, the m6A writer. Despite sharing m6A readers and writers, m6A circRNAs are frequently derived from exons that are not methylated in mRNAs, whereas mRNAs that are methylated on the same exons that compose m6A circRNAs exhibit less stability in a process regulated by YTHDF2. These results expand our understanding of the breadth of m6A modifications and uncover regulation of circRNAs through m6A modification.
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Affiliation(s)
- Chan Zhou
- Gastrointestinal Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Benoit Molinie
- Gastrointestinal Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Kaveh Daneshvar
- Gastrointestinal Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Joshua V Pondick
- Gastrointestinal Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Jinkai Wang
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Nicholas Van Wittenberghe
- Gastrointestinal Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Yi Xing
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Cosmas C Giallourakis
- Gastrointestinal Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA.
| | - Alan C Mullen
- Gastrointestinal Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA.
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14
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Abstract
Soon after the discovery of transforming growth factor-β (TGF-β), seminal work in vertebrate and invertebrate models revealed the TGF-β family to be central regulators of tissue morphogenesis. Members of the TGF-β family direct some of the earliest cell-fate decisions in animal development, coordinate complex organogenesis, and contribute to tissue homeostasis in the adult. Here, we focus on the role of the TGF-β family in mammalian stem-cell biology and discuss its wide and varied activities both in the regulation of pluripotency and in cell-fate commitment.
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Affiliation(s)
- Alan C Mullen
- Gastrointestinal Unit, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114.,Harvard Stem Cell Institute, Cambridge, Massachusetts 02138
| | - Jeffrey L Wrana
- Lunenfeld-Tanenbam Research Institute, Mount Sinai Hospital and Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5G 1X5, Canada
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15
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Chen JY, Newcomb B, Zhou C, Pondick JV, Ghoshal S, York SR, Motola DL, Coant N, Yi JK, Mao C, Tanabe KK, Bronova I, Berdyshev EV, Fuchs BC, Hannun Y, Chung RT, Mullen AC. Tricyclic Antidepressants Promote Ceramide Accumulation to Regulate Collagen Production in Human Hepatic Stellate Cells. Sci Rep 2017; 7:44867. [PMID: 28322247 PMCID: PMC5359599 DOI: 10.1038/srep44867] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 02/15/2017] [Indexed: 12/21/2022] Open
Abstract
Activation of hepatic stellate cells (HSCs) in response to injury is a key step in hepatic fibrosis, and is characterized by trans-differentiation of quiescent HSCs to HSC myofibroblasts, which secrete extracellular matrix proteins responsible for the fibrotic scar. There are currently no therapies to directly inhibit hepatic fibrosis. We developed a small molecule screen to identify compounds that inactivate human HSC myofibroblasts through the quantification of lipid droplets. We screened 1600 compounds and identified 21 small molecules that induce HSC inactivation. Four hits were tricyclic antidepressants (TCAs), and they repressed expression of pro-fibrotic factors Alpha-Actin-2 (ACTA2) and Alpha-1 Type I Collagen (COL1A1) in HSCs. RNA sequencing implicated the sphingolipid pathway as a target of the TCAs. Indeed, TCA treatment of HSCs promoted accumulation of ceramide through inhibition of acid ceramidase (aCDase). Depletion of aCDase also promoted accumulation of ceramide and was associated with reduced COL1A1 expression. Treatment with B13, an inhibitor of aCDase, reproduced the antifibrotic phenotype as did the addition of exogenous ceramide. Our results show that detection of lipid droplets provides a robust readout to screen for regulators of hepatic fibrosis and have identified a novel antifibrotic role for ceramide.
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Affiliation(s)
- Jennifer Y Chen
- Gastrointestinal Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA USA
| | - Benjamin Newcomb
- Health Science Center, Stony Brook University, Stony Brook, NY USA
| | - Chan Zhou
- Gastrointestinal Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA USA
| | - Joshua V Pondick
- Gastrointestinal Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA USA
| | - Sarani Ghoshal
- Division of Surgical Oncology, Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA USA
| | - Samuel R York
- Gastrointestinal Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA USA
| | - Daniel L Motola
- Gastrointestinal Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA USA
| | - Nicolas Coant
- Health Science Center, Stony Brook University, Stony Brook, NY USA
| | - Jae Kyo Yi
- Health Science Center, Stony Brook University, Stony Brook, NY USA
| | - Cungui Mao
- Health Science Center, Stony Brook University, Stony Brook, NY USA
| | - Kenneth K Tanabe
- Division of Surgical Oncology, Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA USA
| | | | | | - Bryan C Fuchs
- Division of Surgical Oncology, Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA USA
| | - Yusuf Hannun
- Health Science Center, Stony Brook University, Stony Brook, NY USA
| | - Raymond T Chung
- Gastrointestinal Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA USA
| | - Alan C Mullen
- Gastrointestinal Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA USA.,Harvard Stem Cell Institute, Cambridge, MA 02138 USA
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16
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Mehta S, Cronkite DA, Basavappa M, Saunders TL, Adiliaghdam F, Amatullah H, Morrison SA, Pagan JD, Anthony RM, Tonnerre P, Lauer GM, Lee JC, Digumarthi S, Pantano L, Ho Sui SJ, Ji F, Sadreyev R, Zhou C, Mullen AC, Kumar V, Li Y, Wijmenga C, Xavier RJ, Means TK, Jeffrey KL. Maintenance of macrophage transcriptional programs and intestinal homeostasis by epigenetic reader SP140. Sci Immunol 2017; 2:eaag3160. [PMID: 28783698 PMCID: PMC5549562 DOI: 10.1126/sciimmunol.aag3160] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 02/08/2017] [Indexed: 12/29/2022]
Abstract
Epigenetic "readers" that recognize defined posttranslational modifications on histones have become desirable therapeutic targets for cancer and inflammation. SP140 is one such bromodomain- and plant homeodomain (PHD)-containing reader with immune-restricted expression, and single-nucleotide polymorphisms (SNPs) within SP140 associate with Crohn's disease (CD). However, the function of SP140 and the consequences of disease-associated SP140 SNPs have remained unclear. We show that SP140 is critical for transcriptional programs that uphold the macrophage state. SP140 preferentially occupies promoters of silenced, lineage-inappropriate genes bearing the histone modification H3K27me3, such as the HOXA cluster in human macrophages, and ensures their repression. Depletion of SP140 in mouse or human macrophages resulted in severely compromised microbe-induced activation. We reveal that peripheral blood mononuclear cells (PBMCs) or B cells from individuals carrying CD-associated SNPs within SP140 have defective SP140 messenger RNA splicing and diminished SP140 protein levels. Moreover, CD patients carrying SP140 SNPs displayed suppressed innate immune gene signatures in a mixed population of PBMCs that stratified them from other CD patients. Hematopoietic-specific knockdown of Sp140 in mice resulted in exacerbated dextran sulfate sodium (DSS)-induced colitis, and low SP140 levels in human CD intestinal biopsies correlated with relatively lower intestinal innate cytokine levels and improved response to anti-tumor necrosis factor (TNF) therapy. Thus, the epigenetic reader SP140 is a key regulator of macrophage transcriptional programs for cellular state, and a loss of SP140 due to genetic variation contributes to a molecularly defined subset of CD characterized by ineffective innate immunity, normally critical for intestinal homeostasis.
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Affiliation(s)
- Stuti Mehta
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - D Alexander Cronkite
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Megha Basavappa
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Tahnee L Saunders
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Fatemeh Adiliaghdam
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Hajera Amatullah
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Sara A Morrison
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Jose D Pagan
- Center for Immunology and Inflammatory Diseases, Division of Rheumatology, Allergy and Immunology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
| | - Robert M Anthony
- Center for Immunology and Inflammatory Diseases, Division of Rheumatology, Allergy and Immunology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
| | - Pierre Tonnerre
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Georg M Lauer
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - James C Lee
- Department of Medicine, University of Cambridge School of Clinical Medicine, Addenbrooke's Hospital, Cambridge, U.K
| | - Sreehaas Digumarthi
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Lorena Pantano
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Shannan J Ho Sui
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Fei Ji
- Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Ruslan Sadreyev
- Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Chan Zhou
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Alan C Mullen
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Vinod Kumar
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Yang Li
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Cisca Wijmenga
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Ramnik J Xavier
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Terry K Means
- Center for Immunology and Inflammatory Diseases, Division of Rheumatology, Allergy and Immunology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
| | - Kate L Jeffrey
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.
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17
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Zhou C, York SR, Chen JY, Pondick JV, Motola DL, Chung RT, Mullen AC. Long noncoding RNAs expressed in human hepatic stellate cells form networks with extracellular matrix proteins. Genome Med 2016; 8:31. [PMID: 27007663 PMCID: PMC4804564 DOI: 10.1186/s13073-016-0285-0] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 03/03/2016] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND Hepatic fibrosis is the underlying cause of cirrhosis and liver failure in nearly every form of chronic liver disease, and hepatic stellate cells (HSCs) are the primary cell type responsible for fibrosis. Long noncoding RNAs (lncRNAs) are increasingly recognized as regulators of development and disease; however, little is known about their expression in human HSCs and their function in hepatic fibrosis. METHODS We performed RNA sequencing and ab initio assembly of RNA transcripts to define the lncRNAs expressed in human HSC myofibroblasts. We analyzed chromatin immunoprecipitation data and expression data to identify lncRNAs that were regulated by transforming growth factor beta (TGF-β) signaling, associated with super-enhancers and restricted in expression to HSCs compared with 43 human tissues and cell types. Co-expression network analyses were performed to discover functional modules of lncRNAs, and principle component analysis and K-mean clustering were used to compare lncRNA expression in HSCs with other myofibroblast cell types. RESULTS We identified over 3600 lncRNAs that are expressed in human HSC myofibroblasts. Many are regulated by TGF-β, a major fibrotic signal, and form networks with genes encoding key components of the extracellular matrix (ECM), which is the substrate of the fibrotic scar. The lncRNAs directly regulated by TGF-β signaling are also enriched at super-enhancers. More than 400 of the lncRNAs identified in HSCs are uniquely expressed in HSCs compared with 43 other human tissues and cell types and HSC myofibroblasts demonstrate different patterns of lncRNA expression compared with myofibroblasts originating from other tissues. Co-expression analyses identified a subset of lncRNAs that are tightly linked to collagen genes and numerous proteins that regulate the ECM during formation of the fibrotic scar. Finally, we identified lncRNAs that are induced during progression of human liver disease. CONCLUSIONS lncRNAs are likely key contributors to the formation and progression of fibrosis in human liver disease.
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Affiliation(s)
- Chan Zhou
- />Gastrointestinal Unit, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, 55 Fruit Street, Boston, MA 02114 USA
| | - Samuel R. York
- />Gastrointestinal Unit, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, 55 Fruit Street, Boston, MA 02114 USA
| | - Jennifer Y. Chen
- />Gastrointestinal Unit, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, 55 Fruit Street, Boston, MA 02114 USA
| | - Joshua V. Pondick
- />Gastrointestinal Unit, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, 55 Fruit Street, Boston, MA 02114 USA
| | - Daniel L. Motola
- />Gastrointestinal Unit, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, 55 Fruit Street, Boston, MA 02114 USA
| | - Raymond T. Chung
- />Gastrointestinal Unit, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, 55 Fruit Street, Boston, MA 02114 USA
| | - Alan C. Mullen
- />Gastrointestinal Unit, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, 55 Fruit Street, Boston, MA 02114 USA
- />Harvard Stem Cell Institute, Cambridge, MA 02138 USA
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18
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Batista PJ, Molinie B, Wang J, Qu K, Zhang J, Li L, Bouley DM, Lujan E, Haddad B, Daneshvar K, Carter AC, Flynn RA, Zhou C, Lim KS, Dedon P, Wernig M, Mullen AC, Xing Y, Giallourakis CC, Chang HY. m(6)A RNA modification controls cell fate transition in mammalian embryonic stem cells. Cell Stem Cell 2014; 15:707-19. [PMID: 25456834 DOI: 10.1016/j.stem.2014.09.019] [Citation(s) in RCA: 871] [Impact Index Per Article: 87.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Revised: 08/14/2014] [Accepted: 09/30/2014] [Indexed: 12/21/2022]
Abstract
N6-methyl-adenosine (m(6)A) is the most abundant modification on messenger RNAs and is linked to human diseases, but its functions in mammalian development are poorly understood. Here we reveal the evolutionary conservation and function of m(6)A by mapping the m(6)A methylome in mouse and human embryonic stem cells. Thousands of messenger and long noncoding RNAs show conserved m(6)A modification, including transcripts encoding core pluripotency transcription factors. m(6)A is enriched over 3' untranslated regions at defined sequence motifs and marks unstable transcripts, including transcripts turned over upon differentiation. Genetic inactivation or depletion of mouse and human Mettl3, one of the m(6)A methylases, led to m(6)A erasure on select target genes, prolonged Nanog expression upon differentiation, and impaired ESC exit from self-renewal toward differentiation into several lineages in vitro and in vivo. Thus, m(6)A is a mark of transcriptome flexibility required for stem cells to differentiate to specific lineages.
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Affiliation(s)
- Pedro J Batista
- Howard Hughes Medical Institute and Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Benoit Molinie
- Gastrointestinal Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Jinkai Wang
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Kun Qu
- Howard Hughes Medical Institute and Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jiajing Zhang
- Howard Hughes Medical Institute and Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Lingjie Li
- Howard Hughes Medical Institute and Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Donna M Bouley
- Department of Comparative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ernesto Lujan
- Institute for Stem Cell Biology and Regenerative Medicine and Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Bahareh Haddad
- Institute for Stem Cell Biology and Regenerative Medicine and Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Kaveh Daneshvar
- Gastrointestinal Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Ava C Carter
- Howard Hughes Medical Institute and Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ryan A Flynn
- Howard Hughes Medical Institute and Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Chan Zhou
- Gastrointestinal Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Kok-Seong Lim
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Peter Dedon
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Marius Wernig
- Institute for Stem Cell Biology and Regenerative Medicine and Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Alan C Mullen
- Gastrointestinal Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Yi Xing
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA.
| | - Cosmas C Giallourakis
- Gastrointestinal Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA.
| | - Howard Y Chang
- Howard Hughes Medical Institute and Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.
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19
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Abstract
How TGF-β signaling switches from enforcing pluripotency to promoting mesendodermal differentiation remains an open question. Recently in Cell Reports, Beyer et al. demonstrated that Hippo signaling components recruit the NuRD complex to repress expression of key genes targeted by TGF-β and thus determine whether TGF-β signaling will favor pluripotency or differentiation.
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Affiliation(s)
- Alan C Mullen
- Gastrointestinal Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA.
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20
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Mullen AC, Orlando DA, Newman JJ, Lovén J, Kumar RM, Bilodeau S, Reddy J, Guenther MG, DeKoter RP, Young RA. Master transcription factors determine cell-type-specific responses to TGF-β signaling. Cell 2011; 147:565-76. [PMID: 22036565 DOI: 10.1016/j.cell.2011.08.050] [Citation(s) in RCA: 445] [Impact Index Per Article: 34.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2011] [Revised: 07/23/2011] [Accepted: 08/24/2011] [Indexed: 01/03/2023]
Abstract
Transforming growth factor beta (TGF-β) signaling, mediated through the transcription factors Smad2 and Smad3 (Smad2/3), directs different responses in different cell types. Here we report that Smad3 co-occupies the genome with cell-type-specific master transcription factors. Thus, Smad3 occupies the genome with Oct4 in embryonic stem cells (ESCs), Myod1 in myotubes, and PU.1 in pro-B cells. We find that these master transcription factors are required for Smad3 occupancy and that TGF-β signaling largely affects the genes bound by the master transcription factors. Furthermore, we show that induction of Myod1 in nonmuscle cells is sufficient to redirect Smad3 to Myod1 sites. We conclude that cell-type-specific master transcription factors determine the genes bound by Smad2/3 and are thus responsible for orchestrating the cell-type-specific effects of TGF-β signaling.
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Affiliation(s)
- Alan C Mullen
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA
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21
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Intlekofer AM, Takemoto N, Wherry EJ, Longworth SA, Northrup JT, Palanivel VR, Mullen AC, Gasink CR, Kaech SM, Miller JD, Gapin L, Ryan K, Russ AP, Lindsten T, Orange JS, Goldrath AW, Ahmed R, Reiner SL. Effector and memory CD8+ T cell fate coupled by T-bet and eomesodermin. Nat Immunol 2005; 6:1236-44. [PMID: 16273099 DOI: 10.1038/ni1268] [Citation(s) in RCA: 947] [Impact Index Per Article: 49.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2005] [Accepted: 09/12/2005] [Indexed: 12/11/2022]
Abstract
Two seemingly unrelated hallmarks of memory CD8(+) T cells are cytokine-driven proliferative renewal after pathogen clearance and a latent effector program in anticipation of rechallenge. Memory CD8(+) T cells and natural killer cells share cytotoxic potential and dependence on the growth factor interleukin 15. We now show that mice with compound mutations of the genes encoding the transcription factors T-bet and eomesodermin were nearly devoid of several lineages dependent on interleukin 15, including memory CD8(+) T cells and mature natural killer cells, and that their cells had defective cytotoxic effector programming. Moreover, T-bet and eomesodermin were responsible for inducing enhanced expression of CD122, the receptor specifying interleukin 15 responsiveness. Therefore, these key transcription factors link the long-term renewal of memory CD8(+) T cells to their characteristic effector potency.
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Affiliation(s)
- Andrew M Intlekofer
- Abramson Family Cancer Research Institute and Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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22
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Abstract
The quality of the helper T cell response against antigen can determine the outcomes of infectious, inflammatory, and autoimmune diseases. Mature Th1 and Th2 cell subsets are thought to arise from a common naive progenitor. In these precursor cells, effector cytokine genes appear to exist in a restrictive structure, which is determined by methylation of cytosine bases and higher-order structure of chromatin. The restrictive gene structures appear to be plastic, giving way to more active structures in some daughter cells. Some genetic loci, which are active in naive cells, however, become silenced during terminal differentiation. Both the derepression of silent loci and the silencing of active loci appear to be linked to the process of DNA replication. Future investigation will be directed toward understanding the way in which patterns of gene expression are altered or transmitted during the cell division of helper T lymphocytes.
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Affiliation(s)
- Steven L Reiner
- Abramson Family Cancer Research Institute and Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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23
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Pearce EL, Mullen AC, Martins GA, Krawczyk CM, Hutchins AS, Zediak VP, Banica M, DiCioccio CB, Gross DA, Mao CA, Shen H, Cereb N, Yang SY, Lindsten T, Rossant J, Hunter CA, Reiner SL. Control of effector CD8+ T cell function by the transcription factor Eomesodermin. Science 2003; 302:1041-3. [PMID: 14605368 DOI: 10.1126/science.1090148] [Citation(s) in RCA: 776] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Activated CD8+ T cells play a critical role in host defense against viruses, intracellular microbes, and tumors. It is not clear if a key regulatory transcription factor unites the effector functions of CD8+ T cells. We now show that Eomesodermin (Eomes), a paralogue of T-bet, is induced in effector CD8+ T cells in vitro and in vivo. Ectopic expression of Eomes was sufficient to invoke attributes of effector CD8+ T cells, including interferon-gamma (IFN-gamma), perforin, and granzyme B. Loss-of-function analysis suggests Eomes may also be necessary for full effector differentiation of CD8+ T cells. We suggest that Eomesodermin is likely to complement the actions of T-bet and act as a key regulatory gene in the development of cell-mediated immunity.
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Affiliation(s)
- Erika L Pearce
- Abramson Family Cancer Research Institute, and Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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24
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Mullen AC, Hutchins AS, High FA, Lee HW, Sykes KJ, Chodosh LA, Reiner SL. Hlx is induced by and genetically interacts with T-bet to promote heritable T(H)1 gene induction. Nat Immunol 2002; 3:652-8. [PMID: 12055627 DOI: 10.1038/ni807] [Citation(s) in RCA: 244] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Type 1 helper T (T(H)1) cells are essential for cellular immunity, but their ontogeny, maturation and durability remain poorly understood. By constructing a dominant-negative form of T-bet, we were able to determine the role played by this lineage-inducing trans-activator in the establishment and maintenance of heritable T(H)1 gene expression. Optimal induction of interferon-gamma (IFN-gamma) expression required genetic interaction between T-bet and its target, the homeoprotein Hlx. In fully mature T(H)1 cells, reiteration of IFN-gamma expression and stable chromatin remodeling became relatively independent of T-bet activity and coincided with demethylation of DNA. In contrast, some lineage attributes, such as expression of IL-12R beta 2 (interleukin 12 receptor beta 2), required ongoing T-bet activity in mature T(H)1 cells and their progeny. These findings suggest that heritable states of gene expression might be maintained by continued expression of the inducing factor or by a mechanism that confers a stable imprint of the induced state.
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Affiliation(s)
- Alan C Mullen
- Abramson Family Cancer Research Institute and Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104-6160, USA
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25
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Hutchins AS, Mullen AC, Lee HW, Sykes KJ, High FA, Hendrich BD, Bird AP, Reiner SL. Gene silencing quantitatively controls the function of a developmental trans-activator. Mol Cell 2002; 10:81-91. [PMID: 12150909 DOI: 10.1016/s1097-2765(02)00564-6] [Citation(s) in RCA: 178] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
How a single cell gives rise to progeny with differing fates remains poorly understood. We examined cells lacking methyl CpG binding domain protein-2 (MBD2), a molecule that has been proposed to link DNA methylation to silent chromatin. Helper T cells from Mbd2(-/-) mice exhibit disordered differentiation. IL-4, the signature of a restricted set of progeny, is expressed ectopically in Mbd2(-/-) parent and daughter cells. Loss of MBD2-mediated silencing renders the normally essential activator, Gata-3, dispensable for IL-4 induction. Gata-3 and MBD2 act in competition, wherein each factor independently, and quantitatively, regulates the binary choice of whether heritable IL-4 expression is established. Gata-3 functions, in part, to displace MBD2 from methylated DNA. These results suggest that activating and silencing signals integrate to provide spatially and temporally restricted patterns of gene activity.
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Affiliation(s)
- Anne S Hutchins
- Abramson Family Cancer Research Institute and Department of Medicine, University of Pennsylvania, Philadelphia 19104, USA
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26
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Mullen AC, Hutchins AS, Villarino AV, Lee HW, High FA, Cereb N, Yang SY, Hua X, Reiner SL. Cell cycle controlling the silencing and functioning of mammalian activators. Curr Biol 2001; 11:1695-9. [PMID: 11696328 DOI: 10.1016/s0960-9822(01)00533-4] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Naïve CD4(+) helper T (T(H)) cells respond to stimulation by terminally differentiating into two mature classes, T(H)1 cells, which express interferon gamma (IFN-gamma), and T(H)2 cells, which express interleukin 4 (IL-4). The transcriptional activators T-bet and Gata-3 mediate commitment to the T(H)1 and T(H)2 fates, respectively, including chromatin remodeling of signature genes. The cytokine IL-12 fosters growth of committed T(H)1 cells, while IL-4 fosters growth of committed T(H)2 cells. IL-12 and IL-4 also play critical roles in commitment by promoting transcriptional silencing of Gata-3 and T-bet, respectively. We now show that both T-bet and Gata-3 are induced in a cell cycle-independent manner in bipotent progenitor cells. In contrast, both lineage-restricted gene induction by the activator proteins and heritable silencing of the transcription of each activator, the hallmarks of terminal differentiation, are cell cycle dependent. We found that cells that cannot cycle remain uncommitted and bipotent in response to the most polarizing signals for maturation. These results provide mechanistic insight into a mammalian model of terminal differentiation by illustrating that cell cycle-coupled epigenetic effects, as originally described in yeast, may represent an evolutionarily conserved strategy for organizing signaling and cell fate.
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Affiliation(s)
- A C Mullen
- Department of Medicine, Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
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27
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Doyle AM, Mullen AC, Villarino AV, Hutchins AS, High FA, Lee HW, Thompson CB, Reiner SL. Induction of cytotoxic T lymphocyte antigen 4 (CTLA-4) restricts clonal expansion of helper T cells. J Exp Med 2001; 194:893-902. [PMID: 11581312 PMCID: PMC2193479 DOI: 10.1084/jem.194.7.893] [Citation(s) in RCA: 79] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Cytotoxic T lymphocyte antigen (CTLA)-4 plays an essential role in immunologic homeostasis. How this negative regulator of T cell activation executes its functions has remained controversial. We now provide evidence that CTLA-4 mediates a cell-intrinsic counterbalance to restrict the clonal expansion of proliferating CD4(+) T cells. The regulation of CTLA-4 expression and function ensures that, after approximately 3 cell divisions of expansion, most progeny will succumb to either proliferative arrest or death over the ensuing three cell divisions. The quantitative precision of the counterbalance hinges on the graded, time-independent induction of CTLA-4 expression during the first three cell divisions. In contrast to the limits imposed on unpolarized cells, T helper type 1 (Th1) and Th2 effector progeny may be rescued from proliferative arrest by interleukin (IL)-12 and IL-4 signaling, respectively, allowing appropriately stimulated progeny to proceed to the stage of tissue homing. These results suggest that the cell-autonomous regulation of CTLA-4 induction may be a central checkpoint of clonal expansion of CD4(+) T cells, allowing temporally and spatially restricted growth of progeny to be dictated by the nature of the threat posed to the host.
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Affiliation(s)
- Alden M. Doyle
- Abramson Family Cancer Research Institute, and Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Alan C. Mullen
- Abramson Family Cancer Research Institute, and Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Alejandro V. Villarino
- Abramson Family Cancer Research Institute, and Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Anne S. Hutchins
- Abramson Family Cancer Research Institute, and Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Frances A. High
- Abramson Family Cancer Research Institute, and Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Hubert W. Lee
- Abramson Family Cancer Research Institute, and Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Craig B. Thompson
- Abramson Family Cancer Research Institute, and Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Steven L. Reiner
- Abramson Family Cancer Research Institute, and Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104
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28
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Mullen AC, High FA, Hutchins AS, Lee HW, Villarino AV, Livingston DM, Kung AL, Cereb N, Yao TP, Yang SY, Reiner SL. Role of T-bet in commitment of TH1 cells before IL-12-dependent selection. Science 2001; 292:1907-10. [PMID: 11397944 DOI: 10.1126/science.1059835] [Citation(s) in RCA: 630] [Impact Index Per Article: 27.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
How cytokines control differentiation of helper T (TH) cells is controversial. We show that T-bet, without apparent assistance from interleukin 12 (IL-12)/STAT4, specifies TH1 effector fate by targeting chromatin remodeling to individual interferon-gamma (IFN-gamma) alleles and by inducing IL-12 receptor beta2 expression. Subsequently, it appears that IL-12/STAT4 serves two essential functions in the development of TH1 cells: as growth signal, inducing survival and cell division; and as trans-activator, prolonging IFN-gamma synthesis through a genetic interaction with the coactivator, CREB-binding protein. These results suggest that a cytokine does not simply induce TH fate choice but instead may act as an essential secondary stimulus that mediates selective survival of a lineage.
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Affiliation(s)
- A C Mullen
- Abramson Family Cancer Research Institute and Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104-6160, USA
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29
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Abstract
CTLA-4-mediated inhibition of T cell activation may be accomplished by competition for ligands and/or by signals mediated through the intracellular domain. Studies have implicated Tyr201 in the cytoplasmic domain of CTLA-4 in regulating CTLA-4 signal transduction and intracellular trafficking. To investigate the mechanism of CTLA-4 function in vivo, transgenes encoding wild-type CTLA-4 (FL), a mutant lacking the cytoplasmic domain of CTLA-4 (DeltaCTLA-4 tail), or a CTLA-4 Tyr201 mutant (Y201V) were introduced into CTLA-4-deficient mice. CTLA-4-/- mice display an autoimmune lymphoproliferative disorder resulting in tissue destruction and early death. When either the FL or the Y201V transgene was bred into CTLA-4-/- animals, a complete rescue from lymphoproliferation and autoimmunity was observed. In contrast, CTLA-4-/- mice expressing the DeltaCTLA-4 tail transgene were long lived with no evidence of multiorgan lymphocytic infiltration, but exhibited lymphadenopathy and accumulated large numbers of activated T cells. Furthermore, these animals displayed a Th2-biased phenotype which conferred susceptibility to Leishmania infection. These results indicate that the inhibitory effect of CTLA-4 is mediated in part through the ability of the extracellular domain to compete for ligands. The cytoplasmic domain of CTLA-4, however, is required for complete inhibitory function of the receptor and for regulation of Th cell differentiation in vivo.
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MESH Headings
- Abatacept
- Amino Acid Sequence
- Animals
- Antigens, CD
- Antigens, Differentiation/biosynthesis
- Antigens, Differentiation/chemistry
- Antigens, Differentiation/genetics
- Antigens, Differentiation/physiology
- CTLA-4 Antigen
- Crosses, Genetic
- Genes, Lethal/immunology
- Genetic Predisposition to Disease
- Homeostasis/genetics
- Homeostasis/immunology
- Immunoconjugates
- Immunophenotyping
- Leishmania major/immunology
- Leishmaniasis, Cutaneous/genetics
- Leishmaniasis, Cutaneous/immunology
- Lymphatic Diseases/immunology
- Lymphocyte Activation/genetics
- Mice
- Mice, Inbred BALB C
- Mice, Inbred C57BL
- Mice, Knockout
- Mice, Transgenic
- Molecular Sequence Data
- Splenomegaly/immunology
- T-Lymphocytes/immunology
- T-Lymphocytes/pathology
- Th2 Cells/immunology
- Th2 Cells/metabolism
- Transgenes/immunology
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Affiliation(s)
- E L Masteller
- Gwen Knapp Center for Lupus and Immunology, University of Chicago, Chicago, IL 60637, USA.
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Bird JJ, Brown DR, Mullen AC, Moskowitz NH, Mahowald MA, Sider JR, Gajewski TF, Wang CR, Reiner SL. Helper T cell differentiation is controlled by the cell cycle. Immunity 1998; 9:229-37. [PMID: 9729043 DOI: 10.1016/s1074-7613(00)80605-6] [Citation(s) in RCA: 702] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Helper T (Th) cell differentiation is highly regulated by cytokines but initiated by mitogens. By examining gene expression in discrete generations of dividing cells, we have delineated the relationship between proliferation and differentiation. Initial expression of IL-2 is cell cycle-independent, whereas effector cytokine expression is cell cycle-dependent. IFNgamma expression increases in frequency with successive cell cycles, while IL-4 expression requires three cell divisions. Cell cycle progression and cytokine signaling act in concert to relieve epigenetic repression and can be supplanted by agents that hyperacetylate histones and demethylate DNA. Terminally differentiated cells exhibit stable epigenetic modification and cell cycle-independent gene expression. These data reveal a novel mechanism governing Th cell fate that initially integrates proliferative and differentiative signals and subsequently maintains stability of the differentiated state.
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Affiliation(s)
- J J Bird
- Department of Medicine, Gwen Knapp Center for Lupus and Immunology Research, The University of Chicago, IL 60637, USA
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