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Heyward FD, Liu N, Jacobs C, Machado NLS, Ivison R, Uner A, Srinivasan H, Patel SJ, Gulko A, Sermersheim T, Tsai L, Rosen ED. AgRP neuron cis-regulatory analysis across hunger states reveals that IRF3 mediates leptin's acute effects. Nat Commun 2024; 15:4646. [PMID: 38821928 PMCID: PMC11143326 DOI: 10.1038/s41467-024-48885-y] [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: 12/08/2023] [Accepted: 05/14/2024] [Indexed: 06/02/2024] Open
Abstract
AgRP neurons in the arcuate nucleus of the hypothalamus (ARC) coordinate homeostatic changes in appetite associated with fluctuations in food availability and leptin signaling. Identifying the relevant transcriptional regulatory pathways in these neurons has been a priority, yet such attempts have been stymied due to their low abundance and the rich cellular diversity of the ARC. Here we generated AgRP neuron-specific transcriptomic and chromatin accessibility profiles from male mice during three distinct hunger states of satiety, fasting-induced hunger, and leptin-induced hunger suppression. Cis-regulatory analysis of these integrated datasets enabled the identification of 18 putative hunger-promoting and 29 putative hunger-suppressing transcriptional regulators in AgRP neurons, 16 of which were predicted to be transcriptional effectors of leptin. Within our dataset, Interferon regulatory factor 3 (IRF3) emerged as a leading candidate mediator of leptin-induced hunger-suppression. Measures of IRF3 activation in vitro and in vivo reveal an increase in IRF3 nuclear occupancy following leptin administration. Finally, gain- and loss-of-function experiments in vivo confirm the role of IRF3 in mediating the acute satiety-evoking effects of leptin in AgRP neurons. Thus, our findings identify IRF3 as a key mediator of the acute hunger-suppressing effects of leptin in AgRP neurons.
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Affiliation(s)
- Frankie D Heyward
- Division of Endocrinology, Diabetes, and Metabolism, Beth Israel Deaconess Medical Center, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Harvard Medical School, Boston, MA, USA.
- Center for Hypothalamic Research, Department of Internal Medicine, UT Southwestern Medical Center, Dallas, TX, USA.
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, TX, USA.
| | - Nan Liu
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA, USA
- Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Liangzhu Laboratory, Zhejiang University, Hangzhou, China
| | - Christopher Jacobs
- Division of Endocrinology, Diabetes, and Metabolism, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Natalia L S Machado
- Harvard Medical School, Boston, MA, USA
- Department of Neurology, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Rachael Ivison
- Division of Endocrinology, Diabetes, and Metabolism, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Aykut Uner
- Division of Endocrinology, Diabetes, and Metabolism, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Center for Hypothalamic Research, Department of Internal Medicine, UT Southwestern Medical Center, Dallas, TX, USA
| | - Harini Srinivasan
- Division of Endocrinology, Diabetes, and Metabolism, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Suraj J Patel
- Division of Endocrinology, Diabetes, and Metabolism, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Division of Gastroenterology & Hepatology, UT Southwestern Medical Center, Dallas, TX, USA
- Center for Human Nutrition and Department of Internal Medicine, UT Southwestern Medical, Center, Dallas, TX, USA
| | - Anton Gulko
- Division of Endocrinology, Diabetes, and Metabolism, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Tyler Sermersheim
- Division of Endocrinology, Diabetes, and Metabolism, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Linus Tsai
- Division of Endocrinology, Diabetes, and Metabolism, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Evan D Rosen
- Division of Endocrinology, Diabetes, and Metabolism, Beth Israel Deaconess Medical Center, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Harvard Medical School, Boston, MA, USA.
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2
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Herb BR, Glover HJ, Bhaduri A, Colantuoni C, Bale TL, Siletti K, Hodge R, Lein E, Kriegstein AR, Doege CA, Ament SA. Single-cell genomics reveals region-specific developmental trajectories underlying neuronal diversity in the human hypothalamus. SCIENCE ADVANCES 2023; 9:eadf6251. [PMID: 37939194 PMCID: PMC10631741 DOI: 10.1126/sciadv.adf6251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 10/24/2023] [Indexed: 11/10/2023]
Abstract
The development and diversity of neuronal subtypes in the human hypothalamus has been insufficiently characterized. To address this, we integrated transcriptomic data from 241,096 cells (126,840 newly generated) in the prenatal and adult human hypothalamus to reveal a temporal trajectory from proliferative stem cell populations to mature hypothalamic cell types. Iterative clustering of the adult neurons identified 108 robust transcriptionally distinct neuronal subtypes representing 10 hypothalamic nuclei. Pseudotime trajectories provided insights into the genes driving formation of these nuclei. Comparisons to single-cell transcriptomic data from the mouse hypothalamus suggested extensive conservation of neuronal subtypes despite certain differences in species-enriched gene expression. The uniqueness of hypothalamic neuronal lineages was examined developmentally by comparing excitatory lineages present in cortex and inhibitory lineages in ganglionic eminence, revealing both distinct and shared drivers of neuronal maturation across the human forebrain. These results provide a comprehensive transcriptomic view of human hypothalamus development through gestation and adulthood at cellular resolution.
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Affiliation(s)
- Brian R. Herb
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Pharmacology, University of Maryland School of Medicine, Baltimore, MD, USA
- UM-MIND, University of Maryland School of Medicine, Baltimore, MD, USA
- Kahlert Institute for Addiction Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Hannah J. Glover
- Naomi Berrie Diabetes Center, Columbia Stem Cell Initiative, Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
| | - Aparna Bhaduri
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Carlo Colantuoni
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Tracy L. Bale
- Department of Psychiatry, University of Colorado School of Medicine, Aurora, CO, USA
| | - Kimberly Siletti
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Rebecca Hodge
- Allen Institute for Brain Science, Seattle, WA 98109
| | - Ed Lein
- Allen Institute for Brain Science, Seattle, WA 98109
| | - Arnold R. Kriegstein
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA, USA
| | - Claudia A. Doege
- Naomi Berrie Diabetes Center, Columbia Stem Cell Initiative, Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Seth A. Ament
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
- UM-MIND, University of Maryland School of Medicine, Baltimore, MD, USA
- Kahlert Institute for Addiction Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
- Maryland Psychiatric Research Center, Department of Psychiatry, University of Maryland School of Medicine, Baltimore, MD, USA
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3
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Zúñiga-Hernández JM, Olivares GH, Olguín P, Glavic A. Low-nutrient diet in Drosophila larvae stage causes enhancement in dopamine modulation in adult brain due epigenetic imprinting. Open Biol 2023; 13:230049. [PMID: 37161288 PMCID: PMC10170216 DOI: 10.1098/rsob.230049] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023] Open
Abstract
Nutrient scarcity is a frequent adverse condition that organisms face during their development. This condition may lead to long-lasting effects on the metabolism and behaviour of adults due to developmental epigenetic modifications. Here, we show that reducing nutrient availability during larval development affects adult spontaneous activity and sleep behaviour, together with changes in gene expression and epigenetic marks in the mushroom bodies (MBs). We found that open chromatin regions map to 100 of 241 transcriptionally upregulated genes in the adult MBs, these new opening zones are preferentially located in regulatory zones such as promoter-TSS and introns. Importantly, opened chromatin at the Dopamine 1-like receptor 2 regulatory zones correlate with increased expression. In consequence, adult administration of a dopamine antagonist reverses increased spontaneous activity and diminished sleep time observed in response to early-life nutrient restriction. In comparison, reducing dop1R2 expression in MBs also ameliorates these effects, albeit to a lesser degree. These results lead to the conclusion that increased dopamine signalling in the MBs of flies reared in a poor nutritional environment underlies the behavioural changes observed due to this condition during development.
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Affiliation(s)
- J M Zúñiga-Hernández
- Laboratorio Biología del Desarrollo, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Chile
| | - Gonzalo H Olivares
- Escuela de Kinesiología, Facultad de Medicina, Center of Integrative Biology (CIB), Universidad Mayor, Chile
| | - Patricio Olguín
- Programa de Genética Humana, ICBM, Biomedical Neuroscience Institute, Departamento de Neurociencia, Facultad de Medicina, Universidad de Chile, Chile
| | - Alvaro Glavic
- Laboratorio Biología del Desarrollo, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Chile
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4
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Koh KD, Bonser LR, Eckalbar WL, Yizhar-Barnea O, Shen J, Zeng X, Hargett KL, Sun DI, Zlock LT, Finkbeiner WE, Ahituv N, Erle DJ. Genomic characterization and therapeutic utilization of IL-13-responsive sequences in asthma. CELL GENOMICS 2023; 3:100229. [PMID: 36777184 PMCID: PMC9903679 DOI: 10.1016/j.xgen.2022.100229] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 10/02/2022] [Accepted: 11/14/2022] [Indexed: 12/12/2022]
Abstract
Epithelial responses to the cytokine interleukin-13 (IL-13) cause airway obstruction in asthma. Here we utilized multiple genomic techniques to identify IL-13-responsive regulatory elements in bronchial epithelial cells and used these data to develop a CRISPR interference (CRISPRi)-based therapeutic approach to downregulate airway obstruction-inducing genes in a cell type- and IL-13-specific manner. Using single-cell RNA sequencing (scRNA-seq) and acetylated lysine 27 on histone 3 (H3K27ac) chromatin immunoprecipitation sequencing (ChIP-seq) in primary human bronchial epithelial cells, we identified IL-13-responsive genes and regulatory elements. These sequences were functionally validated and optimized via massively parallel reporter assays (MPRAs) for IL-13-inducible activity. The top secretory cell-selective sequence from the MPRA, a novel, distal enhancer of the sterile alpha motif pointed domain containing E-26 transformation-specific transcription factor (SPDEF) gene, was utilized to drive CRISPRi and knock down SPDEF or mucin 5AC (MUC5AC), both involved in pathologic mucus production in asthma. Our work provides a catalog of cell type-specific genes and regulatory elements involved in IL-13 bronchial epithelial response and showcases their use for therapeutic purposes.
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Affiliation(s)
- Kyung Duk Koh
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Luke R. Bonser
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Walter L. Eckalbar
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
- CoLabs, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Ofer Yizhar-Barnea
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA 94143, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Jiangshan Shen
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Xiaoning Zeng
- Department of Pulmonary & Critical Care Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Kirsten L. Hargett
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Dingyuan I. Sun
- Department of Pathology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Lorna T. Zlock
- Department of Pathology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Walter E. Finkbeiner
- Department of Pathology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Nadav Ahituv
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA 94143, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - David J. Erle
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA 94143, USA
- CoLabs, University of California, San Francisco, San Francisco, CA 94143, USA
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5
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Pahl MC, Doege CA, Hodge KM, Littleton SH, Leonard ME, Lu S, Rausch R, Pippin JA, De Rosa MC, Basak A, Bradfield JP, Hammond RK, Boehm K, Berkowitz RI, Lasconi C, Su C, Chesi A, Johnson ME, Wells AD, Voight BF, Leibel RL, Cousminer DL, Grant SFA. Cis-regulatory architecture of human ESC-derived hypothalamic neuron differentiation aids in variant-to-gene mapping of relevant complex traits. Nat Commun 2021; 12:6749. [PMID: 34799566 PMCID: PMC8604959 DOI: 10.1038/s41467-021-27001-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 10/27/2021] [Indexed: 11/09/2022] Open
Abstract
The hypothalamus regulates metabolic homeostasis by influencing behavior and endocrine systems. Given its role governing key traits, such as body weight and reproductive timing, understanding the genetic regulation of hypothalamic development and function could yield insights into disease pathogenesis. However, given its inaccessibility, studying human hypothalamic gene regulation has proven challenging. To address this gap, we generate a high-resolution chromatin architecture atlas of an established embryonic stem cell derived hypothalamic-like neuron model across three stages of in vitro differentiation. We profile accessible chromatin and identify physical contacts between gene promoters and putative cis-regulatory elements to characterize global regulatory landscape changes during hypothalamic differentiation. Next, we integrate these data with GWAS loci for various complex traits, identifying multiple candidate effector genes. Our results reveal common target genes for these traits, potentially affecting core developmental pathways. Our atlas will enable future efforts to determine hypothalamic mechanisms influencing disease susceptibility.
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Affiliation(s)
- Matthew C Pahl
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Claudia A Doege
- Department of Pathology, Naomi Berrie Diabetes Center, Columbia Stem Cell Initiative, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Kenyaita M Hodge
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Sheridan H Littleton
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Michelle E Leonard
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Sumei Lu
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Rick Rausch
- Department of Pediatrics, Naomi Berrie Diabetes Center, Columbia Stem Cell Initiative, Columbia University, Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - James A Pippin
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Maria Caterina De Rosa
- Department of Pediatrics, Naomi Berrie Diabetes Center, Columbia Stem Cell Initiative, Columbia University, Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Alisha Basak
- Department of Pediatrics, Naomi Berrie Diabetes Center, Columbia Stem Cell Initiative, Columbia University, Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Jonathan P Bradfield
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Reza K Hammond
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Keith Boehm
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Robert I Berkowitz
- Department of Pediatrics, The University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Chiara Lasconi
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Chun Su
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Alessandra Chesi
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Matthew E Johnson
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Andrew D Wells
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Benjamin F Voight
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Rudolph L Leibel
- Division of Molecular Genetics (Pediatrics) and the Naomi Berrie Diabetes Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Diana L Cousminer
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, 19104, USA
- GSK, Human Genetics and Computational Biology, 1250 South Collegeville Road, Collegeville, PA, 19426, USA
| | - Struan F A Grant
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.
- Department of Pediatrics, The University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA.
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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6
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Barton JR, Snook AE, Waldman SA. From leptin to lasers: the past and present of mouse models of obesity. Expert Opin Drug Discov 2021; 16:777-790. [PMID: 33472452 PMCID: PMC8243785 DOI: 10.1080/17460441.2021.1877654] [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: 09/11/2020] [Accepted: 01/14/2021] [Indexed: 10/22/2022]
Abstract
Introduction: Obesity is a prevalent condition that accounts for significant morbidity and mortality across the globe. Despite substantial effort, most obesity pharmacotherapies have proven unsafe or ineffective. The use of obese mouse models provides unique insight into the hormones and mechanisms that regulate appetite and metabolism. Paramount among these models are the 'obese' and 'diabetic' mice that revealed the powerful satiety hormone leptin, revolutionizing obesity research.Areas Covered: In this article, the authors discuss work on leptin therapy, and the clinical response to leptin in humans. The authors describe the use of modern mouse genetics to study targetable mechanisms for genetic forms of human obesity. Additionally, they describe mouse models of neuromodulation and their utility in unraveling neural circuits that govern appetite and metabolism.Expert opinion: Combining past and present models of obesity is required for the development of safe, effective, and impactful obesity therapy. Current research in obesity can benefit from repositories of genetically engineered mouse models to discover interactions between appetitive systems and circuits. Combining leptin therapy with other satiety signals comprising the gut-brain axis is a promising approach to induce significant enduring weight loss.
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Affiliation(s)
- Joshua R. Barton
- Department of Pharmacology and Experimental Therapeutics, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Adam E. Snook
- Department of Pharmacology and Experimental Therapeutics, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Scott A. Waldman
- Department of Pharmacology and Experimental Therapeutics, Thomas Jefferson University, Philadelphia, PA 19107, USA
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7
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INTACT vs. FANS for Cell-Type-Specific Nuclei Sorting: A Comprehensive Qualitative and Quantitative Comparison. Int J Mol Sci 2021; 22:ijms22105335. [PMID: 34069481 PMCID: PMC8159132 DOI: 10.3390/ijms22105335] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Revised: 05/11/2021] [Accepted: 05/14/2021] [Indexed: 12/15/2022] Open
Abstract
Increasing numbers of studies seek to characterize the different cellular sub-populations present in mammalian tissues. The techniques “Isolation of Nuclei Tagged in Specific Cell Types” (INTACT) or “Fluorescence-Activated Nuclei Sorting” (FANS) are frequently used for isolating nuclei of specific cellular subtypes. These nuclei are then used for molecular characterization of the cellular sub-populations. Despite the increasing popularity of both techniques, little is known about their isolation efficiency, advantages, and disadvantages or downstream molecular effects. In our study, we compared the physical and molecular attributes of sfGFP+ nuclei isolated by the two methods—INTACT and FANS—from the neocortices of Arc-CreERT2 × CAG-Sun1/sfGFP animals. We identified differences in efficiency of sfGFP+ nuclei isolation, nuclear size as well as transcriptional (RNA-seq) and chromatin accessibility (ATAC-seq) states. Therefore, our study presents a comprehensive comparison between the two widely used nuclei sorting techniques, identifying the advantages and disadvantages for both INTACT and FANS. Our conclusions are summarized in a table to guide researchers in selecting the most suitable methodology for their individual experimental design.
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8
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Ludwig MQ, Cheng W, Gordian D, Lee J, Paulsen SJ, Hansen SN, Egerod KL, Barkholt P, Rhodes CJ, Secher A, Knudsen LB, Pyke C, Myers MG, Pers TH. A genetic map of the mouse dorsal vagal complex and its role in obesity. Nat Metab 2021; 3:530-545. [PMID: 33767443 DOI: 10.1038/s42255-021-00363-1] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 02/16/2021] [Indexed: 02/07/2023]
Abstract
The brainstem dorsal vagal complex (DVC) is known to regulate energy balance and is the target of appetite-suppressing hormones, such as glucagon-like peptide 1 (GLP-1). Here we provide a comprehensive genetic map of the DVC and identify neuronal populations that control feeding. Combining bulk and single-nucleus gene expression and chromatin profiling of DVC cells, we reveal 25 neuronal populations with unique transcriptional and chromatin accessibility landscapes and peptide receptor expression profiles. GLP-1 receptor (GLP-1R) agonist administration induces gene expression alterations specific to two distinct sets of Glp1r neurons-one population in the area postrema and one in the nucleus of the solitary tract that also expresses calcitonin receptor (Calcr). Transcripts and regions of accessible chromatin near obesity-associated genetic variants are enriched in the area postrema and the nucleus of the solitary tract neurons that express Glp1r and/or Calcr, and activating several of these neuronal populations decreases feeding in rodents. Thus, DVC neuronal populations associated with obesity predisposition suppress feeding and may represent therapeutic targets for obesity.
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Affiliation(s)
- Mette Q Ludwig
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Wenwen Cheng
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Desiree Gordian
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Julie Lee
- Novo Nordisk Foundation Center for Stem Cell Biology, University of Copenhagen, Copenhagen, Denmark
| | | | | | - Kristoffer L Egerod
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | | | - Christopher J Rhodes
- Research and Early Development, Cardiovascular, Renal and Metabolic Diseases, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, USA
| | - Anna Secher
- Global Drug Discovery, Novo Nordisk A/S, Måløv, Denmark
| | | | - Charles Pyke
- Global Drug Discovery, Novo Nordisk A/S, Måløv, Denmark
| | - Martin G Myers
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Tune H Pers
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark.
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9
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Allum F, Grundberg E. Capturing functional epigenomes for insight into metabolic diseases. Mol Metab 2020; 38:100936. [PMID: 32199819 PMCID: PMC7300388 DOI: 10.1016/j.molmet.2019.12.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 12/23/2019] [Accepted: 12/30/2019] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Metabolic diseases such as obesity are known to be driven by both environmental and genetic factors. Although genome-wide association studies of common variants and their impact on complex traits have provided some biological insight into disease etiology, identified genetic variants have been found to contribute only a small proportion to disease heritability, and to map mainly to non-coding regions of the genome. To link variants to function, association studies of cellular traits, such as epigenetic marks, in disease-relevant tissues are commonly applied. SCOPE OF THE REVIEW We review large-scale efforts to generate genome-wide maps of coordinated epigenetic marks and their utility in complex disease dissection with a focus on DNA methylation. We contrast DNA methylation profiling methods and discuss the advantages of using targeted methods for single-base resolution assessments of methylation levels across tissue-specific regulatory regions to deepen our understanding of contributing factors leading to complex diseases. MAJOR CONCLUSIONS Large-scale assessments of DNA methylation patterns in metabolic disease-linked study cohorts have provided insight into the impact of variable epigenetic variants in disease etiology. In-depth profiling of epigenetic marks at regulatory regions, particularly at tissue-specific elements, will be key to dissect the genetic and environmental components contributing to metabolic disease onset and progression.
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Affiliation(s)
- Fiona Allum
- Department of Human Genetics, McGill University, Montréal, Québec, H3A 0C7, Canada; McGill University and Genome Quebec Innovation Centre, Montréal, Québec, H3A 0G1, Canada
| | - Elin Grundberg
- Children's Mercy Kansas City, Kansas City, MO, 64108, United States.
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10
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Genetic variation, adipokines, and cardiometabolic disease. Curr Opin Pharmacol 2020; 52:33-39. [PMID: 32480034 DOI: 10.1016/j.coph.2020.04.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 04/21/2020] [Accepted: 04/22/2020] [Indexed: 11/24/2022]
Abstract
Adipokines are adipocyte-secreted cell signalling proteins that travel to distant target organs and tissues, where they regulate a variety of biological actions implicated in cardiometabolic health. In the past decade, genome-wide association studies have identified multiple genetic variants associated with circulating levels of adipokines, providing new instruments for examining the role of adipokines in cardiometabolic pathologies. Currently, there is limited genetic evidence of causal relationships between adipokines and cardiometabolic disease, which is consistent with findings from randomized clinical trials that have thus far shown limited success for adipokine-based treatments in improving cardiometabolic health. Incorporating human genetic data in early phases of target selection is essential for enhancing the success of adipokine-based therapies for cardiometabolic disease.
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Ortega-Azorín C, Coltell O, Asensio EM, Sorlí JV, González JI, Portolés O, Saiz C, Estruch R, Ramírez-Sabio JB, Pérez-Fidalgo A, Ordovas JM, Corella D. Candidate Gene and Genome-Wide Association Studies for Circulating Leptin Levels Reveal Population and Sex-Specific Associations in High Cardiovascular Risk Mediterranean Subjects. Nutrients 2019; 11:nu11112751. [PMID: 31766143 PMCID: PMC6893551 DOI: 10.3390/nu11112751] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Revised: 11/04/2019] [Accepted: 11/09/2019] [Indexed: 12/13/2022] Open
Abstract
Leptin is a hormone crucial in the regulation of food intake and body-weight maintenance. However, the genes and gene variants that influence its plasma levels are still not well known. Results of studies investigating polymorphisms in candidate genes have been inconsistent, and, in addition, very few genome-wide association studies (GWAS) have been undertaken. Our aim was to investigate the genes and gene variants most associated with plasma leptin concentrations in a high-cardiovascular-risk Mediterranean population. We measured plasma leptin in 1011 men and women, and analyzed the genetic factors associated using three approaches: (1) Analyzing the single nucleotide polymorphisms (SNPs) reported in a GWAS meta-analysis in other populations (including an SNP in/near each of these LEP, SLC32A1, GCKR, CCNL, COBLL1, and FTO genes); (2) Investigating additional SNPs in/near those genes, also including the RLEP gene; and (3) Undertaking a GWAS to discover new genes. We did not find any statistically significant associations between the previously published SNPs and plasma leptin (Ln) in the whole population adjusting for sex and age. However, on undertaking an extensive screening of other gene variants in those genes to capture a more complete set of SNPs, we found more associations. Outstanding among the findings was the heterogeneity per sex. We detected several statistically significant interaction terms with sex for these SNPs in the candidate genes. The gene most associated with plasma leptin levels was the FTO gene in men (specifically the rs1075440 SNP) and the LEPR in women (specifically the rs12145690 SNP). In the GWAS on the whole population, we found several new associations at the p < 1 × 10-5 level, among them with the rs245908-CHN2 SNP (p = 1.6 × 10-6). We also detected a SNP*sex interaction at the GWAS significance level (p < 5 × 10-8), involving the SLIT3 gene, a gene regulated by estrogens. In conclusion, our study shows that the SNPs selected as relevant for plasma leptin levels in other populations, are not good markers for this Mediterranean population, so supporting those studies claiming a bias when generalizing GWAS results to different populations. These population-specific differences may include not only genetic characteristics, but also age, health status, and the influence of other environmental variables. In addition, we have detected several sex-specific effects. These results suggest that genomic analyses, involving leptin, should be estimated by sex and consider population-specificity for more precise estimations.
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Affiliation(s)
- Carolina Ortega-Azorín
- Department of Preventive Medicine and Public Health, School of Medicine, University of Valencia, 46010 Valencia, Spain; (C.O.-A.); (E.M.A.); (J.V.S.); (J.I.G.); (O.P.); (C.S.); (A.P.-F.)
- CIBER Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain; (O.C.); (R.E.)
| | - Oscar Coltell
- CIBER Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain; (O.C.); (R.E.)
- Department of Computer Languages and Systems, Universitat Jaume I, 12071 Castellón, Spain
| | - Eva M. Asensio
- Department of Preventive Medicine and Public Health, School of Medicine, University of Valencia, 46010 Valencia, Spain; (C.O.-A.); (E.M.A.); (J.V.S.); (J.I.G.); (O.P.); (C.S.); (A.P.-F.)
- CIBER Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain; (O.C.); (R.E.)
| | - Jose V. Sorlí
- Department of Preventive Medicine and Public Health, School of Medicine, University of Valencia, 46010 Valencia, Spain; (C.O.-A.); (E.M.A.); (J.V.S.); (J.I.G.); (O.P.); (C.S.); (A.P.-F.)
- CIBER Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain; (O.C.); (R.E.)
| | - José I. González
- Department of Preventive Medicine and Public Health, School of Medicine, University of Valencia, 46010 Valencia, Spain; (C.O.-A.); (E.M.A.); (J.V.S.); (J.I.G.); (O.P.); (C.S.); (A.P.-F.)
- CIBER Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain; (O.C.); (R.E.)
| | - Olga Portolés
- Department of Preventive Medicine and Public Health, School of Medicine, University of Valencia, 46010 Valencia, Spain; (C.O.-A.); (E.M.A.); (J.V.S.); (J.I.G.); (O.P.); (C.S.); (A.P.-F.)
- CIBER Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain; (O.C.); (R.E.)
| | - Carmen Saiz
- Department of Preventive Medicine and Public Health, School of Medicine, University of Valencia, 46010 Valencia, Spain; (C.O.-A.); (E.M.A.); (J.V.S.); (J.I.G.); (O.P.); (C.S.); (A.P.-F.)
- CIBER Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain; (O.C.); (R.E.)
| | - Ramon Estruch
- CIBER Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain; (O.C.); (R.E.)
- Department of Internal Medicine, Hospital Clinic, Institut d’Investigació Biomèdica August Pi i Sunyer (IDIBAPS), University of Barcelona, Villarroel, 170, 08036 Barcelona, Spain
| | | | - Alejandro Pérez-Fidalgo
- Department of Preventive Medicine and Public Health, School of Medicine, University of Valencia, 46010 Valencia, Spain; (C.O.-A.); (E.M.A.); (J.V.S.); (J.I.G.); (O.P.); (C.S.); (A.P.-F.)
- CIBER Cáncer, Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Jose M Ordovas
- Nutrition and Genomics Laboratory, JM-USDA Human Nutrition Research Center on Aging at Tufts University, Boston, MA 02111, USA;
- Department of Cardiovascular Epidemiology and Population Genetics, Centro Nacional de Investigaciones Cardiovasculares (CNIC), 28029 Madrid, Spain
- IMDEA Alimentación, 28049 Madrid, Spain
| | - Dolores Corella
- Department of Preventive Medicine and Public Health, School of Medicine, University of Valencia, 46010 Valencia, Spain; (C.O.-A.); (E.M.A.); (J.V.S.); (J.I.G.); (O.P.); (C.S.); (A.P.-F.)
- CIBER Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain; (O.C.); (R.E.)
- Correspondence: ; Tel.: +34-96-386-4800
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