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Radi SH, Vemuri K, Martinez-Lomeli J, Sladek FM. HNF4α isoforms: the fraternal twin master regulators of liver function. Front Endocrinol (Lausanne) 2023; 14:1226173. [PMID: 37600688 PMCID: PMC10438950 DOI: 10.3389/fendo.2023.1226173] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Accepted: 07/18/2023] [Indexed: 08/22/2023] Open
Abstract
In the more than 30 years since the purification and cloning of Hepatocyte Nuclear Factor 4 (HNF4α), considerable insight into its role in liver function has been gleaned from its target genes and mouse experiments. HNF4α plays a key role in lipid and glucose metabolism and intersects with not just diabetes and circadian rhythms but also with liver cancer, although much remains to be elucidated about those interactions. Similarly, while we are beginning to elucidate the role of the isoforms expressed from its two promoters, we know little about the alternatively spliced variants in other portions of the protein and their impact on the 1000-plus HNF4α target genes. This review will address how HNF4α came to be called the master regulator of liver-specific gene expression with a focus on its role in basic metabolism, the contributions of the various isoforms and the intriguing intersection with the circadian clock.
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Affiliation(s)
- Sarah H. Radi
- Department of Biochemistry, University of California, Riverside, Riverside, CA, United States
| | - Kiranmayi Vemuri
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers, The State University of New Jersey, Piscataway, NJ, United States
- Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ, United States
| | - Jose Martinez-Lomeli
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, Riverside, CA, United States
| | - Frances M. Sladek
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, Riverside, CA, United States
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Weng Y, Han S, Sekyi MT, Su T, Mattis AN, Chang TT. Self-Assembled Matrigel-Free iPSC-Derived Liver Organoids Demonstrate Wide-Ranging Highly Differentiated Liver Functions. Stem Cells 2023; 41:126-139. [PMID: 36573434 PMCID: PMC9982071 DOI: 10.1093/stmcls/sxac090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 12/12/2022] [Indexed: 12/28/2022]
Abstract
Human induced pluripotent stem cell (iPSC)-derived liver organoids serve as models of organogenesis, disease, drug screening, and regenerative medicine. Prevailing methods for generating organoids rely on Matrigel, whose batch-to-batch variability and xenogeneic source pose challenges to mechanistic research and translation to human clinical therapy. In this report, we demonstrate that self-assembled Matrigel-free iPSC-derived organoids developed in rotating wall vessels (RWVs) exhibit greater hepatocyte-specific functions than organoids formed on Matrigel. We show that RWVs produce highly functional liver organoids in part by eliminating the need for Matrigel, which has adverse effects on hepatic lineage differentiation. RWV liver organoids sustain durable function over long-term culture and express a range of mature functional genes at levels comparable to adult human liver, while retaining some fetal features. Our results indicate that RWVs provide a simple and high-throughput way to generate Matrigel-free liver organoids suitable for research and clinical applications.
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Affiliation(s)
- Yun Weng
- Department of Surgery, University of California, San Francisco, CA 94143, USA
| | - Simon Han
- Department of Surgery, University of California, San Francisco, CA 94143, USA
| | - Maria T Sekyi
- Department of Surgery, University of California, San Francisco, CA 94143, USA
| | - Tao Su
- Department of Pathology, University of California, San Francisco, CA 94143, USA
| | - Aras N Mattis
- Department of Pathology, University of California, San Francisco, CA 94143, USA
- Liver Center, University of California, San Francisco, CA 94143, USA
| | - Tammy T Chang
- Department of Surgery, University of California, San Francisco, CA 94143, USA
- Liver Center, University of California, San Francisco, CA 94143, USA
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Beck LA, Cork MJ, Amagai M, De Benedetto A, Kabashima K, Hamilton JD, Rossi AB. Type 2 Inflammation Contributes to Skin Barrier Dysfunction in Atopic Dermatitis. JID INNOVATIONS 2022; 2:100131. [PMID: 36059592 PMCID: PMC9428921 DOI: 10.1016/j.xjidi.2022.100131] [Citation(s) in RCA: 63] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 01/04/2022] [Accepted: 01/06/2022] [Indexed: 01/02/2023] Open
Abstract
Skin barrier dysfunction, a defining feature of atopic dermatitis (AD), arises from multiple interacting systems. In AD, skin inflammation is caused by host-environment interactions involving keratinocytes as well as tissue-resident immune cells such as type 2 innate lymphoid cells, basophils, mast cells, and T helper type 2 cells, which produce type 2 cytokines, including IL-4, IL-5, IL-13, and IL-31. Type 2 inflammation broadly impacts the expression of genes relevant for barrier function, such as intracellular structural proteins, extracellular lipids, and junctional proteins, and enhances Staphylococcus aureus skin colonization. Systemic anti‒type 2 inflammation therapies may improve dysfunctional skin barrier in AD.
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Key Words
- AD, atopic dermatitis
- AMP, antimicrobial peptide
- CLDN, claudin
- FFA, free fatty acid
- ILC2, type 2 innate lymphoid cell
- Jaki, Jak inhibitor
- K, keratin
- KC, keratinocyte
- MMP, matrix metalloproteinase
- NMF, natural moisturizing factor
- PAR, protease-activated receptor
- PDE-4, phosphodiesterase-4
- SC, stratum corneum
- SG, stratum granulosum
- TCI, topical calcineurin inhibitor
- TCS, topical corticosteroid
- TEWL, transepidermal water loss
- TJ, tight junction
- TLR, toll-like receptor
- TNF-α, tumor necrosis factor alpha
- TYK, tyrosine kinase
- Th, T helper
- ZO, zona occludens
- hBD, human β-defensin
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Affiliation(s)
- Lisa A. Beck
- Department of Dermatology, University of Rochester Medical Center, Rochester, New York, USA,Correspondence: Lisa A. Beck, Department of Dermatology, University of Rochester Medical Center, 601 Elmwood Ave, Box 697, Rochester, New York 14642, USA.
| | - Michael J. Cork
- Sheffield Dermatology Research, Department of Infection, Immunity and Cardiovascular Disease (IICD), The University of Sheffield, The Medical School, Sheffield, United Kingdom
| | - Masayuki Amagai
- Department of Dermatology, Keio University School of Medicine, Tokyo, Japan,Laboratory for Skin Homeostasis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Anna De Benedetto
- Department of Dermatology, University of Rochester Medical Center, Rochester, New York, USA
| | - Kenji Kabashima
- Department of Dermatology, Kyoto University Graduate School of Medicine, Kyoto University, Kyoto, Japan
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Porukala M, Vinod PK. Systems-level analysis of transcriptome reorganization during liver regeneration. Mol Omics 2022; 18:315-327. [DOI: 10.1039/d1mo00382h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Tissue homeostasis and regeneration depend on the reversible transitions between quiescence (G0) and proliferation. The liver has a remarkable capacity to regenerate after injury or resection by cell growth and...
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Kamarajugadda S, Becker JR, Hanse EA, Mashek DG, Mashek MT, Hendrickson AM, Mullany LK, Albrecht JH. Cyclin D1 represses peroxisome proliferator-activated receptor alpha and inhibits fatty acid oxidation. Oncotarget 2018; 7:47674-47686. [PMID: 27351284 PMCID: PMC5216970 DOI: 10.18632/oncotarget.10274] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 06/04/2016] [Indexed: 01/27/2023] Open
Abstract
Cyclin D1 is a cell cycle protein that promotes proliferation by mediating progression through key checkpoints in G1 phase. It is also a proto-oncogene that is commonly overexpressed in human cancers. In addition to its canonical role in controlling cell cycle progression, cyclin D1 affects other aspects of cell physiology, in part through transcriptional regulation. In this study, we find that cyclin D1 inhibits the activity of a key metabolic transcription factor, peroxisome proliferator-activated receptor α (PPARα), a member of nuclear receptor family that induces fatty acid oxidation and may play an anti-neoplastic role. In primary hepatocytes, cyclin D1 inhibits PPARα transcriptional activity and target gene expression in a cdk4-independent manner. In liver and breast cancer cells, knockdown of cyclin D1 leads to increased PPARα transcriptional activity, expression of PPARα target genes, and fatty acid oxidation. Similarly, cyclin D1 depletion enhances binding of PPARα to target sequences by chromatin immunoprecipitation. In proliferating hepatocytes and regenerating liver in vivo, induction of endogenous cyclin D1 is associated with diminished PPARα activity. Cyclin D1 expression is both necessary and sufficient for growth factor-mediated repression of fatty acid oxidation in proliferating hepatocytes. These studies indicate that in addition to playing a pivotal role in cell cycle progression, cyclin D1 represses PPARα activity and inhibits fatty acid oxidation. Our findings establish a new link between cyclin D1 and metabolism in both tumor cells and physiologic hepatocyte proliferation.
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Affiliation(s)
- Sushama Kamarajugadda
- Gastroenterology Division, Minneapolis VA Health Care System, Minneapolis, MN 55417, USA
| | - Jennifer R Becker
- Minneapolis Medical Research Foundation, Minneapolis, MN, 55404, USA
| | - Eric A Hanse
- Minneapolis Medical Research Foundation, Minneapolis, MN, 55404, USA
| | - Douglas G Mashek
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Mara T Mashek
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | | | - Lisa K Mullany
- Minneapolis Medical Research Foundation, Minneapolis, MN, 55404, USA
| | - Jeffrey H Albrecht
- Gastroenterology Division, Minneapolis VA Health Care System, Minneapolis, MN 55417, USA
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Mendelsohn S, Pinsky M, Weissman Z, Kornitzer D. Regulation of the Candida albicans Hypha-Inducing Transcription Factor Ume6 by the CDK1 Cyclins Cln3 and Hgc1. mSphere 2017; 2:e00248-16. [PMID: 28289726 PMCID: PMC5343172 DOI: 10.1128/msphere.00248-16] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 02/20/2017] [Indexed: 01/17/2023] Open
Abstract
The ability to switch between proliferation as yeast cells and development into hyphae is a hallmark of Candida albicans. The switch to hyphal morphogenesis depends on external inducing conditions, but its efficiency is augmented in stationary-phase cells. Ume6, a transcription factor that is itself transcriptionally induced under hypha-promoting conditions, is both necessary and sufficient for hyphal morphogenesis. We found that Ume6 is regulated posttranslationally by the cell cycle kinase Cdc28/Cdk1, which reduces Ume6 activity via different mechanisms using different cyclins. Together with the cyclin Hgc1, Cdk1 promotes degradation of Ume6 via the SCFCDC4 ubiquitin ligase. Since HGC1 is a key transcriptional target of Ume6, this results in a negative-feedback loop between Hgc1 and Ume6. In addition, we found that Cln3, a G1 cyclin that is essential for cell cycle progression and yeast proliferation, suppresses hyphal morphogenesis and that Cln3 suppresses Ume6 activity both in the heterologous Saccharomyces cerevisiae system and in C. albicans itself. This activity of Cln3 may provide the basis for the antagonistic relationship between yeast proliferation and hyphal development in C. albicans. IMPORTANCE The yeast to hypha (mold) morphogenetic switch of Candida albicans plays a role in its virulence and constitutes a diagnostic trait for this organism, the most prevalent systemic fungal pathogen in industrialized countries. It has long been known that hyphae are most efficiently induced from stationary cultures. Here, a molecular basis for this observation is provided. The G1 cyclin Cln3, an essential promoter of yeast proliferation, was found to suppress hyphal induction. Suppression of hyphal induction is achieved by inhibition of the activity of the central activator of hyphal morphogenesis, the transcription factor Ume6. Thus, levels of Cln3 control the switch between proliferation of C. albicans as individual yeast cells and development into extended hyphae, a switch that may preface the proliferation/differentiation switch in multicellular organisms.
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Affiliation(s)
- Sigal Mendelsohn
- Department of Molecular Microbiology, B. Rappaport Faculty of Medicine, Technion-I.I.T. and the Rappaport Institute for Research in the Medical Sciences, Haifa, Israel
| | - Mariel Pinsky
- Department of Molecular Microbiology, B. Rappaport Faculty of Medicine, Technion-I.I.T. and the Rappaport Institute for Research in the Medical Sciences, Haifa, Israel
| | - Ziva Weissman
- Department of Molecular Microbiology, B. Rappaport Faculty of Medicine, Technion-I.I.T. and the Rappaport Institute for Research in the Medical Sciences, Haifa, Israel
| | - Daniel Kornitzer
- Department of Molecular Microbiology, B. Rappaport Faculty of Medicine, Technion-I.I.T. and the Rappaport Institute for Research in the Medical Sciences, Haifa, Israel
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Vuong LM, Chellappa K, Dhahbi JM, Deans JR, Fang B, Bolotin E, Titova NV, Hoverter NP, Spindler SR, Waterman ML, Sladek FM. Differential Effects of Hepatocyte Nuclear Factor 4α Isoforms on Tumor Growth and T-Cell Factor 4/AP-1 Interactions in Human Colorectal Cancer Cells. Mol Cell Biol 2015; 35:3471-90. [PMID: 26240283 PMCID: PMC4573706 DOI: 10.1128/mcb.00030-15] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Revised: 02/04/2015] [Accepted: 07/07/2015] [Indexed: 12/18/2022] Open
Abstract
The nuclear receptor hepatocyte nuclear factor 4α (HNF4α) is tumor suppressive in the liver but amplified in colon cancer, suggesting that it also might be oncogenic. To investigate whether this discrepancy is due to different HNF4α isoforms derived from its two promoters (P1 and P2), we generated Tet-On-inducible human colon cancer (HCT116) cell lines that express either the P1-driven (HNF4α2) or P2-driven (HNF4α8) isoform and analyzed them for tumor growth and global changes in gene expression (transcriptome sequencing [RNA-seq] and chromatin immunoprecipitation sequencing [ChIP-seq]). The results show that while HNF4α2 acts as a tumor suppressor in the HCT116 tumor xenograft model, HNF4α8 does not. Each isoform regulates the expression of distinct sets of genes and recruits, colocalizes, and competes in a distinct fashion with the Wnt/β-catenin mediator T-cell factor 4 (TCF4) at CTTTG motifs as well as at AP-1 motifs (TGAXTCA). Protein binding microarrays (PBMs) show that HNF4α and TCF4 share some but not all binding motifs and that single nucleotide polymorphisms (SNPs) in sites bound by both HNF4α and TCF4 can alter binding affinity in vitro, suggesting that they could play a role in cancer susceptibility in vivo. Thus, the HNF4α isoforms play distinct roles in colon cancer, which could be due to differential interactions with the Wnt/β-catenin/TCF4 and AP-1 pathways.
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Affiliation(s)
- Linh M Vuong
- Department of Cell Biology and Neuroscience, University of California, Riverside, Riverside, California, USA
| | - Karthikeyani Chellappa
- Department of Cell Biology and Neuroscience, University of California, Riverside, Riverside, California, USA
| | - Joseph M Dhahbi
- Department of Biochemistry, University of California, Riverside, Riverside, California, USA
| | - Jonathan R Deans
- Department of Cell Biology and Neuroscience, University of California, Riverside, Riverside, California, USA
| | - Bin Fang
- Department of Cell Biology and Neuroscience, University of California, Riverside, Riverside, California, USA
| | - Eugene Bolotin
- Department of Cell Biology and Neuroscience, University of California, Riverside, Riverside, California, USA
| | - Nina V Titova
- Department of Cell Biology and Neuroscience, University of California, Riverside, Riverside, California, USA
| | - Nate P Hoverter
- Department of Microbiology and Molecular Genetics, University of California, Irvine, Irvine, California, USA
| | - Stephen R Spindler
- Department of Biochemistry, University of California, Riverside, Riverside, California, USA
| | - Marian L Waterman
- Department of Microbiology and Molecular Genetics, University of California, Irvine, Irvine, California, USA
| | - Frances M Sladek
- Department of Cell Biology and Neuroscience, University of California, Riverside, Riverside, California, USA
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Abstract
Hepatocyte nuclear factor 4α (HNF4α) is an orphan nuclear receptor commonly known as the master regulator of hepatic differentiation, owing to the large number of hepatocyte-specific genes it regulates. Whereas the role of HNF4α in hepatocyte differentiation is well recognized and extensively studied, its role in regulation of cell proliferation is relatively less known. Recent studies have revealed that HNF4α inhibits proliferation not only of hepatocytes but also cells in colon and kidney. Further, a growing number of studies have demonstrated that inhibition or loss of HNF4α promotes tumorigenesis in the liver and colon, and reexpression of HNF4α results in decreased cancer growth. Studies using tissue-specific conditional knockout mice, knock-in studies, and combinatorial bioinformatics of RNA/ChIP-sequencing data indicate that the mechanisms of HNF4α-mediated inhibition of cell proliferation are multifold, involving epigenetic repression of promitogenic genes, significant cross talk with other cell cycle regulators including c-Myc and cyclin D1, and regulation of miRNAs. Furthermore, studies indicate that posttranslational modifications of HNF4α may change its activity and may be at the core of its dual role as a differentiation factor and repressor of proliferation. This review summarizes recent findings on the role of HNF4α in cell proliferation and highlights the newly understood function of this old receptor.
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Affiliation(s)
- Chad Walesky
- *Department of Pharmacology, Toxicology and Therapeutics, University of Kansas Medical Center, Kansas City, KS, USA
- †Department of Medicine – Genetics Division, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Udayan Apte
- *Department of Pharmacology, Toxicology and Therapeutics, University of Kansas Medical Center, Kansas City, KS, USA
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Shimura T, Ochiai Y, Noma N, Oikawa T, Sano Y, Fukumoto M. Cyclin D1 overexpression perturbs DNA replication and induces replication-associated DNA double-strand breaks in acquired radioresistant cells. Cell Cycle 2013; 12:773-82. [PMID: 23388457 DOI: 10.4161/cc.23719] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Fractionated radiotherapy (RT) is widely used in cancer treatment, because it preserves normal tissues. However, repopulation of radioresistant tumors during fractionated RT limits the efficacy of RT. We recently demonstrated that a moderate level of long-term fractionated radiation confers acquired radioresistance to tumor cells, which is caused by DNA-PK/AKT/GSK3β-mediated cyclin D1 overexpression. The resulting cyclin D1 overexpression leads to forced progression of the cell cycle to S-phase, concomitant with induction of DNA double-strand breaks (DSBs). In this study, we investigated the molecular mechanisms underlying cyclin D1 overexpression-induced DSBs during DNA replication in acquired radioresistant cells. DNA fiber data demonstrated that replication forks progressed slowly in acquired radioresistant cells compared with corresponding parental cells in HepG2 and HeLa cell lines. Slowly progressing replication forks were also observed in HepG2 and HeLa cells that overexpressed a nondegradable cyclin D1 mutant. We also found that knockdown of Mus81 endonuclease, which is responsible for resolving aberrant replication forks, suppressed DSB formation in acquired radioresistant cells. Consequently, Mus81 created DSBs to remove aberrant replication forks in response to replication perturbation triggered by cyclin D1 overexpression. After treating cells with a specific inhibitor for DNA-PK or ATM, apoptosis rates increased in acquired radioresistant cells but not in parental cells by inhibiting the DNA damage response to cyclin D1-mediated DSBs. This suggested that these inhibitors might eradicate acquired radioresistant cells and improve fractionated RT outcomes.
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Affiliation(s)
- Tsutomu Shimura
- Department of Environmental Health, National Institute of Public Health, Saitama, Japan.
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