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Okada J, Landgraf A, Xiaoli AM, Liu L, Horton M, Schuster VL, Yang F, Sidoli S, Qiu Y, Kurland IJ, Eliscovich C, Shinoda K, Pessin JE. Spatial hepatocyte plasticity of gluconeogenesis during the metabolic transitions between fed, fasted and starvation states. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.29.591168. [PMID: 38746329 PMCID: PMC11092462 DOI: 10.1101/2024.04.29.591168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
The liver acts as a master regulator of metabolic homeostasis in part by performing gluconeogenesis. This process is dysregulated in type 2 diabetes, leading to elevated hepatic glucose output. The parenchymal cells of the liver (hepatocytes) are heterogeneous, existing on an axis between the portal triad and the central vein, and perform distinct functions depending on location in the lobule. Here, using single cell analysis of hepatocytes across the liver lobule, we demonstrate that gluconeogenic gene expression ( Pck1 and G6pc ) is relatively low in the fed state and gradually increases first in the periportal hepatocytes during the initial fasting period. As the time of fasting progresses, pericentral hepatocyte gluconeogenic gene expression increases, and following entry into the starvation state, the pericentral hepatocytes show similar gluconeogenic gene expression to the periportal hepatocytes. Similarly, pyruvate-dependent gluconeogenic activity is approximately 10-fold higher in the periportal hepatocytes during the initial fasting state but only 1.5-fold higher in the starvation state. In parallel, starvation suppresses canonical beta-catenin signaling and modulates expression of pericentral and periportal glutamine synthetase and glutaminase, resulting in an enhanced pericentral glutamine-dependent gluconeogenesis. These findings demonstrate that hepatocyte gluconeogenic gene expression and gluconeogenic activity are highly spatially and temporally plastic across the liver lobule, underscoring the critical importance of using well-defined feeding and fasting conditions to define the basis of hepatic insulin resistance and glucose production.
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2
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Mahajan P, Fiehn O, Barupal D. IDSL.GOA: gene ontology analysis for interpreting metabolomic datasets. Sci Rep 2024; 14:1299. [PMID: 38221536 PMCID: PMC10788336 DOI: 10.1038/s41598-024-51992-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Accepted: 01/11/2024] [Indexed: 01/16/2024] Open
Abstract
Biological interpretation of metabolomic datasets often ends at a pathway analysis step to find the over-represented metabolic pathways in the list of statistically significant metabolites. However, definitions of biochemical pathways and metabolite coverage vary among different curated databases, leading to missed interpretations. For the lists of genes, transcripts and proteins, Gene Ontology (GO) terms over-presentation analysis has become a standardized approach for biological interpretation. But, GO analysis has not been achieved for metabolomic datasets. We present a new knowledgebase (KB) and the online tool, Gene Ontology Analysis by the Integrated Data Science Laboratory for Metabolomics and Exposomics (IDSL.GOA) to conduct GO over-representation analysis for a metabolite list. The IDSL.GOA KB covers 2393 metabolic GO terms and associated 3144 genes, 1,492 EC annotations, and 2621 metabolites. IDSL.GOA analysis of a case study of older versus young female brain cortex metabolome highlighted 82 GO terms being significantly overrepresented (FDR < 0.05). We showed how IDSL.GOA identified key and relevant GO metabolic processes that were not yet covered in other pathway databases. Overall, we suggest that interpretation of metabolite lists should not be limited to only pathway maps and can also leverage GO terms as well. IDSL.GOA provides a useful tool for this purpose, allowing for a more comprehensive and accurate analysis of metabolite pathway data. IDSL.GOA tool can be accessed at https://goa.idsl.me/ .
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Affiliation(s)
- Priyanka Mahajan
- Integrated Data Science Laboratory for Metabolomics and Exposomics, Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, 10954, USA
| | - Oliver Fiehn
- NIH-West Coast Metabolomics Center, University of California, Davis, CA, 95616, USA
| | - Dinesh Barupal
- Integrated Data Science Laboratory for Metabolomics and Exposomics, Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, 10954, USA.
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3
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Mahajan P, Fiehn O, Barupal D. IDSL.GOA: Gene Ontology Analysis for Interpreting Metabolomic datasets. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.03.25.534225. [PMID: 37034715 PMCID: PMC10081191 DOI: 10.1101/2023.03.25.534225] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/17/2023]
Abstract
Biological interpretation of metabolomic datasets often ends at a pathway analysis step to find the over-represented metabolic pathways in the list of statistically significant metabolites. However, definitions of biochemical pathways and metabolite coverage vary among different curated databases, leading to missed interpretations. For the lists of genes, transcripts and proteins, Gene Ontology (GO) terms over-presentation analysis has become a standardized approach for biological interpretation. But, GO analysis has not been achieved for metabolomic datasets. We present a new knowledgebase (KB) and the online tool, Gene Ontology Analysis by the Integrated Data Science Laboratory for Metabolomics and Exposomics (IDSL.GOA) to conduct GO over-representation analysis for a metabolite list. The IDSL.GOA KB covers 2,393 metabolic GO terms and associated 3,144 genes, 1,492 EC annotations, and 2,621 metabolites. IDSL.GOA analysis of a case study of older vs young female brain cortex metabolome highlighted 82 GO terms being significantly overrepresented (FDR <0.05). We showed how IDSL.GOA identified key and relevant GO metabolic processes that were not yet covered in other pathway databases. Overall, we suggest that interpretation of metabolite lists should not be limited to only pathway maps and can also leverage GO terms as well. IDSL.GOA provides a useful tool for this purpose, allowing for a more comprehensive and accurate analysis of metabolite pathway data. IDSL.GOA tool can be accessed at https://goa.idsl.me/.
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Affiliation(s)
- Priyanka Mahajan
- Integrated Data Science Laboratory for Metabolomics and Exposomics, Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, USA 10954
| | - Oliver Fiehn
- NIH-West Coast Metabolomics Center, University of California, Davis, California, 95616, USA
| | - Dinesh Barupal
- Integrated Data Science Laboratory for Metabolomics and Exposomics, Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, USA 10954
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Teker HT, Ceylani T, Keskin S, Samgane G, Baba B, Acıkgoz E, Gurbanov R. Reduced liver damage and fibrosis with combined SCD Probiotics and intermittent fasting in aged rat. J Cell Mol Med 2024; 28:e18014. [PMID: 37897241 PMCID: PMC10805504 DOI: 10.1111/jcmm.18014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 10/08/2023] [Accepted: 10/17/2023] [Indexed: 10/30/2023] Open
Abstract
This study aimed to examine the impact of SCD Probiotics supplementation on liver biomolecule content and histological changes during a 30-day intermittent fasting (IF) program in 24-month-old male Sprague-Dawley rats. Rats underwent 18-h daily fasting and received 1 × 108 CFU of SCD Probiotics daily. Liver tissue biomolecules were analysed using FTIR Spectroscopy, LDA, and SVM techniques, while histopathological evaluations used Haematoxylin and eosin and Masson trichrome-stained tissues. Blood samples were collected for biochemical analysis. Gross alterations in the quantity of biomolecules were observed with individual or combined treatments. LDA and SVM analyses demonstrated a high accuracy in differentiating control and treated groups. The combination treatments led to the most significant reduction in cholesterol ester (1740 cm-1 ) and improved protein phosphorylation (A1239 /A2955 and A1080 /A1545 ) and carbonylation (A1740 /A1545 ). Individually, IF and SCD Probiotics were more effective in enhancing membrane dynamics (Bw2922 /Bw2955 ). In treated groups, histological evaluations showed decreased hepatocyte degeneration, lymphocyticinfiltration, steatosis and fibrosis. Serum ALP, LDH and albumin levels significantly increased in the SCD Probiotics and combined treatment groups. This study offers valuable insights into the potential mechanisms behind the beneficial effects of IF and SCD Probiotics on liver biomolecule content, contributing to the development of personalized nutrition and health strategies.
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Affiliation(s)
- Hikmet Taner Teker
- Department of Medical Biology and GeneticsAnkara Medipol UniversityAnkaraTurkey
| | - Taha Ceylani
- Department of Molecular Biology and GeneticsMuş Alparslan UniversityMuşTurkey
- Department of Food Quality Control and AnalysisMuş Alparslan UniversityMuşTurkey
| | - Seda Keskin
- Department of Histology and EmbryologyVan Yuzuncu Yil UniversityVanTurkey
| | - Gizem Samgane
- Department of BioengineeringBilecik Şeyh Edebali UniversityBilecikTurkey
| | - Burcu Baba
- Department of Medical BiochemistryYüksek İhtisas UniversityAnkaraTurkey
| | - Eda Acıkgoz
- Department of Histology and EmbryologyVan Yuzuncu Yil UniversityVanTurkey
| | - Rafig Gurbanov
- Department of BioengineeringBilecik Şeyh Edebali UniversityBilecikTurkey
- Central Research Laboratory (BARUM)Bilecik Şeyh Edebali UniversityBilecikTurkey
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5
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Li K, Wang WH, Wu JB, Xiao WH. β-hydroxybutyrate: A crucial therapeutic target for diverse liver diseases. Biomed Pharmacother 2023; 165:115191. [PMID: 37487440 DOI: 10.1016/j.biopha.2023.115191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 07/13/2023] [Accepted: 07/18/2023] [Indexed: 07/26/2023] Open
Abstract
β-hydroxybutyrate (β-HB), the most abundant ketone body, is produced primarily in the liver and acts as a substitute energy fuel to provide energy to extrahepatic tissues in the event of hypoglycemia or glycogen depletion. We now have an improved understanding of β-HB as a signal molecule and epigenetic regulatory factor as a result of intensive research over the last ten years. Because β-HB regulates various physiological and pathological processes, it may have a potential role in the treatment of metabolic diseases. The liver is the most significant metabolic organ, and the part that β-HB plays in liver disorders is receiving increasing attention. In this review, we summarize the therapeutic effects of β-HB on liver diseases and its underlying mechanisms of action. Moreover, we explore the prospects of exogenous supplements and endogenous ketosis including fasting, caloric restriction (CR), ketogenic diet (KD), and exercise as adjuvant nutritional therapies to protect the liver from damage and provide insights and strategies for exploring the treatment of various liver diseases.
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Affiliation(s)
- Ke Li
- Key Lab of Exercise and Health Sciences of Ministry of Education, Shanghai University of Sport, Shanghai 200438, China; Shanghai Key Lab of Human Performance, Shanghai University of Sport, Shanghai 200438, China
| | - Wen-Hong Wang
- Key Lab of Exercise and Health Sciences of Ministry of Education, Shanghai University of Sport, Shanghai 200438, China; Shanghai Key Lab of Human Performance, Shanghai University of Sport, Shanghai 200438, China
| | - Jia-Bin Wu
- Key Lab of Exercise and Health Sciences of Ministry of Education, Shanghai University of Sport, Shanghai 200438, China; Shanghai Key Lab of Human Performance, Shanghai University of Sport, Shanghai 200438, China
| | - Wei-Hua Xiao
- Key Lab of Exercise and Health Sciences of Ministry of Education, Shanghai University of Sport, Shanghai 200438, China; Shanghai Key Lab of Human Performance, Shanghai University of Sport, Shanghai 200438, China.
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Tsusaka T, Oses-Prieto JA, Lee C, DeFelice BC, Burlingame AL, Goldberg EL. Non-specific recognition of histone modifications by H3K9bhb antibody. iScience 2023; 26:107235. [PMID: 37485368 PMCID: PMC10362303 DOI: 10.1016/j.isci.2023.107235] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 06/04/2023] [Accepted: 06/23/2023] [Indexed: 07/25/2023] Open
Abstract
Ketone bodies are short-chain fatty acids produced in the liver during periods of limited glucose availability that provide an alternative energy source for the brain, heart, and skeletal muscle. Beyond this metabolic role, β-hydroxybutyrate (BHB), is gaining recognition as a signaling molecule. Lysine β-hydroxybutyrylation (Kbhb) is a newly discovered post-translational modification in which BHB is covalently attached to lysine ε-amino groups. This protein adduct is metabolically sensitive, dependent on BHB concentration, and found on proteins in multiple intracellular compartments. Therefore, Kbhb is hypothesized to be an important component of ketone body-regulated physiology. Kbhb on histones is proposed to be an epigenetic regulator, which links metabolic alterations to gene expression. However, we found that the widely used antibody against β-hydroxybutyrylated lysine 9 on histone H3 (H3K9bhb) also recognizes other modification(s) that likely include acetylation. Therefore, caution must be used when interpreting gene regulation data acquired with the H3K9bhb antibody.
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Affiliation(s)
- Takeshi Tsusaka
- Department of Physiology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Juan A. Oses-Prieto
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Christina Lee
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | | | - Alma L. Burlingame
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Emily L. Goldberg
- Department of Physiology, University of California, San Francisco, San Francisco, CA 94158, USA
- Chan-Zuckerberg Biohub, San Francisco, CA 94158, USA
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7
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Tsusaka T, Oses-Prieto JA, Lee C, DeFelice BC, Burlingame AL, Goldberg E. Non-specific recognition of histone modifications by H3K9bhb antibody. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.12.536655. [PMID: 37090555 PMCID: PMC10120668 DOI: 10.1101/2023.04.12.536655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Ketone bodies are short chain fatty acids produced in the liver during periods of limited glucose availability that provide an alternative source of energy for the brain, heart, and skeletal muscle. Beyond this classical metabolic role, β-hydroxybutyrate (BHB), is gaining recognition as a pleiotropic signaling molecule. Lysine β-hydroxybutyrylation (Kbhb) is a newly discovered post-translational modification in which BHB is covalently attached to lysine ε-amino groups. This novel protein adduct is metabolically sensitive, dependent on BHB concentration, and found on proteins in multiple intracellular compartments, including the mitochondria and nucleus. Therefore, Kbhb is hypothesized to be an important component of ketone body-regulated physiology. Kbhb on histones is proposed to be an epigenetic regulator, which links metabolic alterations to gene expression. However, we found that the widely used antibody against the β-hydroxybutyrylated lysine 9 on histone H3 (H3K9bhb) also recognizes other modification(s), which are increased by deacetylation inhibition and include likely acetylations. Therefore, caution must be used when interpreting gene regulation data acquired with the H3K9bhb antibody.
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Affiliation(s)
- Takeshi Tsusaka
- Department of Physiology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Juan A. Oses-Prieto
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Christina Lee
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720
| | | | - Alma L. Burlingame
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Emily Goldberg
- Department of Physiology, University of California, San Francisco, San Francisco, CA 94158, USA
- Chan-Zuckerberg Biohub, San Francisco, CA 94158 USA
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Mohan K, Dubey SK, Jung K, Dubey R, Wang QJ, Prajapati S, Roney J, Abney J, Kleinman ME. Long-Term Evaluation of Retinal Morphology and Function in Rosa26-Cas9 Knock-In Mice. Int J Mol Sci 2023; 24:5186. [PMID: 36982266 PMCID: PMC10049241 DOI: 10.3390/ijms24065186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 02/25/2023] [Accepted: 03/06/2023] [Indexed: 03/30/2023] Open
Abstract
The CRISPR/Cas9 system is a robust, efficient, and cost-effective gene editing tool widely adopted in translational studies of ocular diseases. However, in vivo CRISPR-based editing in animal models poses challenges such as the efficient delivery of the CRISPR components in viral vectors with limited packaging capacity and a Cas9-associated immune response. Using a germline Cas9-expressing mouse model would help to overcome these limitations. Here, we evaluated the long-term effects of SpCas9 expression on retinal morphology and function using Rosa26-Cas9 knock-in mice. We observed abundant SpCas9 expression in the RPE and retina of Rosa26-Cas9 mice using the real-time polymerase chain reaction (RT-PCR), Western blotting, and immunostaining. SD-OCT imaging and histological analysis of the RPE, retinal layers, and vasculature showed no apparent structural abnormalities in adult and aged Cas9 mice. Full-field electroretinogram of adult and aged Cas9 mice showed no long-term functional changes in the retinal tissues because of constitutive Cas9 expression. The current study showed that both the retina and RPE maintain their phenotypic and functional features in Cas9 knock-in mice, establishing this as an ideal animal model for developing therapeutics for retinal diseases.
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Affiliation(s)
- Kabhilan Mohan
- Department of Surgery, East Tennessee State University, Johnson City, TN 37614, USA (S.K.D.)
- Department of Ophthalmology and Visual Sciences, University of Kentucky, Lexington, KY 40536, USA
| | - Sushil Kumar Dubey
- Department of Surgery, East Tennessee State University, Johnson City, TN 37614, USA (S.K.D.)
- Department of Ophthalmology and Visual Sciences, University of Kentucky, Lexington, KY 40536, USA
| | - Kyungsik Jung
- Department of Surgery, East Tennessee State University, Johnson City, TN 37614, USA (S.K.D.)
- Department of Ophthalmology and Visual Sciences, University of Kentucky, Lexington, KY 40536, USA
| | - Rashmi Dubey
- Department of Surgery, East Tennessee State University, Johnson City, TN 37614, USA (S.K.D.)
| | - Qing Jun Wang
- Department of Ophthalmology and Visual Sciences, University of Kentucky, Lexington, KY 40536, USA
| | - Subhash Prajapati
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA
| | - Jacob Roney
- Department of Ophthalmology and Visual Sciences, University of Kentucky, Lexington, KY 40536, USA
| | - Jennifer Abney
- Department of Ophthalmology and Visual Sciences, University of Kentucky, Lexington, KY 40536, USA
| | - Mark Ellsworth Kleinman
- Department of Surgery, East Tennessee State University, Johnson City, TN 37614, USA (S.K.D.)
- Department of Ophthalmology and Visual Sciences, University of Kentucky, Lexington, KY 40536, USA
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9
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May S, Bird TG. How the liver keeps itself in shape. eLife 2023; 12:e85606. [PMID: 36729029 PMCID: PMC9894582 DOI: 10.7554/elife.85606] [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] [Indexed: 02/03/2023] Open
Abstract
After fasting, hepatocytes proliferate to help the liver grow back to its original size.
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Affiliation(s)
- Stephanie May
- Cancer Research UK Beatson InstituteGlasgowUnited Kingdom
| | - Thomas G Bird
- Cancer Research UK Beatson InstituteGlasgowUnited Kingdom
- School of Cancer Sciences, University of GlasgowGlasgowUnited Kingdom
- MRC Centre for Inflammation Research, The Queen’s Medical Research Institute, University of EdinburghEdinburghUnited Kingdom
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