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Martinez-Lomeli J, Deol P, Deans JR, Jiang T, Ruegger P, Borneman J, Sladek FM. Impact of various high fat diets on gene expression and the microbiome across the mouse intestines. Sci Rep 2023; 13:22758. [PMID: 38151490 PMCID: PMC10752901 DOI: 10.1038/s41598-023-49555-7] [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: 10/01/2023] [Accepted: 12/09/2023] [Indexed: 12/29/2023] Open
Abstract
High fat diets (HFDs) have been linked to several diseases including obesity, diabetes, fatty liver, inflammatory bowel disease (IBD) and colon cancer. In this study, we examined the impact on intestinal gene expression of three isocaloric HFDs that differed only in their fatty acid composition-coconut oil (saturated fats), conventional soybean oil (polyunsaturated fats) and a genetically modified soybean oil (monounsaturated fats). Four functionally distinct segments of the mouse intestinal tract were analyzed using RNA-seq-duodenum, jejunum, terminal ileum and proximal colon. We found considerable dysregulation of genes in multiple tissues with the different diets, including those encoding nuclear receptors and genes involved in xenobiotic and drug metabolism, epithelial barrier function, IBD and colon cancer as well as genes associated with the microbiome and COVID-19. Network analysis shows that genes involved in metabolism tend to be upregulated by the HFDs while genes related to the immune system are downregulated; neurotransmitter signaling was also dysregulated by the HFDs. Genomic sequencing also revealed a microbiome altered by the HFDs. This study highlights the potential impact of different HFDs on gut health with implications for the organism as a whole and will serve as a reference for gene expression along the length of the intestines.
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Affiliation(s)
- Jose Martinez-Lomeli
- Genetics, Genomics and Bioinformatics Graduate Program, University of California, Riverside, CA, 92521, USA
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, CA, 92521, USA
| | - Poonamjot Deol
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, CA, 92521, USA.
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA, 92521, USA.
| | - Jonathan R Deans
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, CA, 92521, USA
| | - Tao Jiang
- Department of Computer Science and Engineering, University of California, Riverside, CA, 92521, USA
- Institute of Integrated Genome Biology, University of California, Riverside, CA, 92521, USA
| | - Paul Ruegger
- Institute of Integrated Genome Biology, University of California, Riverside, CA, 92521, USA
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA, 92521, USA
| | - James Borneman
- Institute of Integrated Genome Biology, University of California, Riverside, CA, 92521, USA
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA, 92521, USA
| | - Frances M Sladek
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, CA, 92521, USA
- Institute of Integrated Genome Biology, University of California, Riverside, CA, 92521, USA
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Deans JR, Deol P, Titova N, Radi SH, Vuong LM, Evans JR, Pan S, Fahrmann J, Yang J, Hammock BD, Fiehn O, Fekry B, Eckel-Mahan K, Sladek FM. HNF4α isoforms regulate the circadian balance between carbohydrate and lipid metabolism in the liver. Front Endocrinol (Lausanne) 2023; 14:1266527. [PMID: 38111711 PMCID: PMC10726135 DOI: 10.3389/fendo.2023.1266527] [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] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 11/06/2023] [Indexed: 12/20/2023] Open
Abstract
Hepatocyte Nuclear Factor 4α (HNF4α), a master regulator of hepatocyte differentiation, is regulated by two promoters (P1 and P2) which drive the expression of different isoforms. P1-HNF4α is the major isoform in the adult liver while P2-HNF4α is thought to be expressed only in fetal liver and liver cancer. Here, we show that P2-HNF4α is indeed expressed in the normal adult liver at Zeitgeber time (ZT)9 and ZT21. Using exon swap mice that express only P2-HNF4α we show that this isoform orchestrates a distinct transcriptome and metabolome via unique chromatin and protein-protein interactions, including with different clock proteins at different times of the day leading to subtle differences in circadian gene regulation. Furthermore, deletion of the Clock gene alters the circadian oscillation of P2- (but not P1-)HNF4α RNA, revealing a complex feedback loop between the HNF4α isoforms and the hepatic clock. Finally, we demonstrate that while P1-HNF4α drives gluconeogenesis, P2-HNF4α drives ketogenesis and is required for elevated levels of ketone bodies in female mice. Taken together, we propose that the highly conserved two-promoter structure of the Hnf4a gene is an evolutionarily conserved mechanism to maintain the balance between gluconeogenesis and ketogenesis in the liver in a circadian fashion.
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Affiliation(s)
- Jonathan R. Deans
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, Riverside, CA, United States
- Genetics, Genomics and Bioinformatics Graduate Program, University of California, Riverside, Riverside, CA, United States
| | - Poonamjot Deol
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, Riverside, CA, United States
| | - Nina Titova
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, Riverside, CA, United States
| | - Sarah H. Radi
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, Riverside, CA, United States
- Biochemistry and Molecular Biology Graduate Program, University of California, Riverside, Riverside, CA, United States
| | - Linh M. Vuong
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, Riverside, CA, United States
| | - Jane R. Evans
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, Riverside, CA, United States
| | - Songqin Pan
- Proteomics Core, Institute for Integrative Genome Biology, University of California, Riverside, Riverside, CA, United States
| | - Johannes Fahrmann
- National Institutes of Health West Coast Metabolomics Center, University of California, Davis, Davis, CA, United States
| | - Jun Yang
- Department of Entomology and Nematology & UCD Comprehensive Cancer Center, University of California, Davis, Davis, CA, United States
| | - Bruce D. Hammock
- Department of Entomology and Nematology & UCD Comprehensive Cancer Center, University of California, Davis, Davis, CA, United States
| | - Oliver Fiehn
- National Institutes of Health West Coast Metabolomics Center, University of California, Davis, Davis, CA, United States
| | - Baharan Fekry
- Department of Biochemistry and Molecular Biology, McGovern Medical School at the University of Texas Health Science Center (UT Health), Houston, TX, United States
| | - Kristin Eckel-Mahan
- Department of Biochemistry and Molecular Biology, McGovern Medical School at the University of Texas Health Science Center (UT Health), Houston, TX, United States
- Institute of Molecular Medicine, McGovern Medical School at the University of Texas Health Science Center (UT Health), Houston, TX, United States
| | - Frances M. Sladek
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, Riverside, CA, United States
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Martinez-Lomeli J, Deol P, Deans JR, Jiang T, Ruegger P, Borneman J, Sladek FM. Impact of Various High Fat Diets on Gene Expression and the Microbiome Across the Mouse Intestines. Res Sq 2023:rs.3.rs-3401763. [PMID: 37886485 PMCID: PMC10602159 DOI: 10.21203/rs.3.rs-3401763/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Abstract
High fat diets (HFDs) have been linked to several diseases including obesity, diabetes, fatty liver, inflammatory bowel disease (IBD) and colon cancer. In this study, we examined the impact on intestinal gene expression of three isocaloric HFDs that differed only in their fatty acid composition - coconut oil (saturated fats), conventional soybean oil (polyunsaturated fats) and a genetically modified soybean oil (monounsaturated fats). Four functionally distinct segments of the mouse intestinal tract were analyzed using RNA-seq - duodenum, jejunum, terminal ileum and proximal colon. We found considerable dysregulation of genes in multiple tissues with the different diets, including those encoding nuclear receptors and genes involved in xenobiotic and drug metabolism, epithelial barrier function, IBD and colon cancer as well as genes associated with the microbiome and COVID-19. Network analysis shows that genes involved in metabolism tend to be upregulated by the HFDs while genes related to the immune system are downregulated; neurotransmitter signaling was also dysregulated by the HFDs. Genomic sequencing also revealed a microbiome altered by the HFDs. This study highlights the potential impact of different HFDs on gut health with implications for the organism as a whole and will serve as a reference for gene expression along the length of the intestines.
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Deol P, Kozlova E, Valdez M, Ho C, Yang EW, Richardson H, Gonzalez G, Truong E, Reid J, Valdez J, Deans JR, Martinez-Lomeli J, Evans JR, Jiang T, Sladek FM, Curras-Collazo MC. Dysregulation of Hypothalamic Gene Expression and the Oxytocinergic System by Soybean Oil Diets in Male Mice. Endocrinology 2020; 161:5698148. [PMID: 31912136 PMCID: PMC7041656 DOI: 10.1210/endocr/bqz044] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 01/04/2020] [Indexed: 01/04/2023]
Abstract
Soybean oil consumption has increased greatly in the past half-century and is linked to obesity and diabetes. To test the hypothesis that soybean oil diet alters hypothalamic gene expression in conjunction with metabolic phenotype, we performed RNA sequencing analysis using male mice fed isocaloric, high-fat diets based on conventional soybean oil (high in linoleic acid, LA), a genetically modified, low-LA soybean oil (Plenish), and coconut oil (high in saturated fat, containing no LA). The 2 soybean oil diets had similar but nonidentical effects on the hypothalamic transcriptome, whereas the coconut oil diet had a negligible effect compared to a low-fat control diet. Dysregulated genes were associated with inflammation, neuroendocrine, neurochemical, and insulin signaling. Oxt was the only gene with metabolic, inflammation, and neurological relevance upregulated by both soybean oil diets compared to both control diets. Oxytocin immunoreactivity in the supraoptic and paraventricular nuclei of the hypothalamus was reduced, whereas plasma oxytocin and hypothalamic Oxt were increased. These central and peripheral effects of soybean oil diets were correlated with glucose intolerance but not body weight. Alterations in hypothalamic Oxt and plasma oxytocin were not observed in the coconut oil diet enriched in stigmasterol, a phytosterol found in soybean oil. We postulate that neither stigmasterol nor LA is responsible for effects of soybean oil diets on oxytocin and that Oxt messenger RNA levels could be associated with the diabetic state. Given the ubiquitous presence of soybean oil in the American diet, its observed effects on hypothalamic gene expression could have important public health ramifications.
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Affiliation(s)
- Poonamjot Deol
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, California
| | - Elena Kozlova
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, California
- Neuroscience Graduate Program, University of California, Riverside, California
| | - Matthew Valdez
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, California
- Neuroscience Graduate Program, University of California, Riverside, California
| | - Catherine Ho
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, California
| | - Ei-Wen Yang
- Department of Computer Science and Engineering, University of California Riverside, California
| | - Holly Richardson
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, California
| | - Gwendolyn Gonzalez
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, California
| | - Edward Truong
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, California
| | - Jack Reid
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, California
| | - Joseph Valdez
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, California
| | - Jonathan R Deans
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, California
| | - Jose Martinez-Lomeli
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, California
| | - Jane R Evans
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, California
| | - Tao Jiang
- Department of Computer Science and Engineering, University of California Riverside, California
| | - Frances M Sladek
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, California
| | - Margarita C Curras-Collazo
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, California
- Neuroscience Graduate Program, University of California, Riverside, California
- Correspondence: Margarita C. Curras-Collazo, PhD, FAPS, Department of Molecular, Cell and Systems Biology, University of California, 2110 Biological Sciences Building, Riverside, California 92521. E-mail:
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Fekry B, Ribas-Latre A, Baumgartner C, Deans JR, Kwok C, Patel P, Fu L, Berdeaux R, Sun K, Kolonin MG, Wang SH, Yoo SH, Sladek FM, Eckel-Mahan K. Incompatibility of the circadian protein BMAL1 and HNF4α in hepatocellular carcinoma. Nat Commun 2018; 9:4349. [PMID: 30341289 PMCID: PMC6195513 DOI: 10.1038/s41467-018-06648-6] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [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: 01/29/2018] [Accepted: 09/18/2018] [Indexed: 02/07/2023] Open
Abstract
Hepatocyte nuclear factor 4 alpha (HNF4α) is a master regulator of liver-specific gene expression with potent tumor suppressor activity, yet many liver tumors express HNF4α. This study reveals that P1-HNF4α, the predominant isoform expressed in the adult liver, inhibits expression of tumor promoting genes in a circadian manner. In contrast, an additional isoform of HNF4α, driven by an alternative promoter (P2-HNF4α), is induced in HNF4α-positive human hepatocellular carcinoma (HCC). P2-HNF4α represses the circadian clock gene ARNTL (BMAL1), which is robustly expressed in healthy hepatocytes, and causes nuclear to cytoplasmic re-localization of P1-HNF4α. We reveal mechanisms underlying the incompatibility of BMAL1 and P2-HNF4α in HCC, and demonstrate that forced expression of BMAL1 in HNF4α-positive HCC prevents the growth of tumors in vivo. These data suggest that manipulation of the circadian clock in HNF4α-positive HCC could be a tractable strategy to inhibit tumor growth and progression in the liver.
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Affiliation(s)
- Baharan Fekry
- Institute of Molecular Medicine, McGovern Medical School at the University of Texas Health Science Center (UT Health), Houston, TX, 77030, USA
| | - Aleix Ribas-Latre
- Institute of Molecular Medicine, McGovern Medical School at the University of Texas Health Science Center (UT Health), Houston, TX, 77030, USA
| | - Corrine Baumgartner
- Institute of Molecular Medicine, McGovern Medical School at the University of Texas Health Science Center (UT Health), Houston, TX, 77030, USA
| | - Jonathan R Deans
- Department of Molecular, Cell and Systems Biology, University of California Riverside, Riverside, CA, 92521, USA
| | - Christopher Kwok
- Institute of Molecular Medicine, McGovern Medical School at the University of Texas Health Science Center (UT Health), Houston, TX, 77030, USA
| | - Pooja Patel
- Department of Pediatrics, Molecular and Cellular Biology, Children's Nutrition Research Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Loning Fu
- Department of Pediatrics, Molecular and Cellular Biology, Children's Nutrition Research Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Rebecca Berdeaux
- Institute of Molecular Medicine, McGovern Medical School at the University of Texas Health Science Center (UT Health), Houston, TX, 77030, USA
- Department of Integrative Biology and Pharmacology, McGovern Medical School at the University of Texas Health Science Center (UT Health), Houston, TX, 77030, USA
| | - Kai Sun
- Institute of Molecular Medicine, McGovern Medical School at the University of Texas Health Science Center (UT Health), Houston, TX, 77030, USA
- Department of Biochemistry and Molecular Biology, McGovern Medical School at the University of Texas Health Science Center (UT Health), Houston, TX, 77030, USA
| | - Mikhail G Kolonin
- Institute of Molecular Medicine, McGovern Medical School at the University of Texas Health Science Center (UT Health), Houston, TX, 77030, USA
| | - Sidney H Wang
- Institute of Molecular Medicine, McGovern Medical School at the University of Texas Health Science Center (UT Health), Houston, TX, 77030, USA
| | - Seung-Hee Yoo
- Department of Biochemistry and Molecular Biology, McGovern Medical School at the University of Texas Health Science Center (UT Health), Houston, TX, 77030, USA
| | - Frances M Sladek
- Department of Molecular, Cell and Systems Biology, University of California Riverside, Riverside, CA, 92521, USA
| | - Kristin Eckel-Mahan
- Institute of Molecular Medicine, McGovern Medical School at the University of Texas Health Science Center (UT Health), Houston, TX, 77030, USA.
- Department of Biochemistry and Molecular Biology, McGovern Medical School at the University of Texas Health Science Center (UT Health), Houston, TX, 77030, USA.
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