1
|
Littleton SH, Trang KB, Volpe CM, Cook K, DeBruyne N, Maguire JA, Weidekamp MA, Hodge KM, Boehm K, Lu S, Chesi A, Bradfield JP, Pippin JA, Anderson SA, Wells AD, Pahl MC, Grant SFA. Variant-to-function analysis of the childhood obesity chr12q13 locus implicates rs7132908 as a causal variant within the 3' UTR of FAIM2. CELL GENOMICS 2024; 4:100556. [PMID: 38697123 PMCID: PMC11099382 DOI: 10.1016/j.xgen.2024.100556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 03/21/2024] [Accepted: 04/08/2024] [Indexed: 05/04/2024]
Abstract
The ch12q13 locus is among the most significant childhood obesity loci identified in genome-wide association studies. This locus resides in a non-coding region within FAIM2; thus, the underlying causal variant(s) presumably influence disease susceptibility via cis-regulation. We implicated rs7132908 as a putative causal variant by leveraging our in-house 3D genomic data and public domain datasets. Using a luciferase reporter assay, we observed allele-specific cis-regulatory activity of the immediate region harboring rs7132908. We generated isogenic human embryonic stem cell lines homozygous for either rs7132908 allele to assess changes in gene expression and chromatin accessibility throughout a differentiation to hypothalamic neurons, a key cell type known to regulate feeding behavior. The rs7132908 obesity risk allele influenced expression of FAIM2 and other genes and decreased the proportion of neurons produced by differentiation. We have functionally validated rs7132908 as a causal obesity variant that temporally regulates nearby effector genes and influences neurodevelopment and survival.
Collapse
Affiliation(s)
- Sheridan H Littleton
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Khanh B Trang
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Christina M Volpe
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kieona Cook
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Psychiatry, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Nicole DeBruyne
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jean Ann Maguire
- Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Mary Ann Weidekamp
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Graduate Group in Genomics and Computational Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kenyaita M Hodge
- 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
| | - Sumei Lu
- 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; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jonathan P Bradfield
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Quantinuum Research LLC, San Diego, CA 92101, USA
| | - James A Pippin
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Stewart A Anderson
- Department of Child and Adolescent Psychiatry, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Andrew D Wells
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Matthew C Pahl
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Struan F A Grant
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Endocrinology and Diabetes, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
| |
Collapse
|
2
|
Kalinderi K, Goula V, Sapountzi E, Tsinopoulou VR, Fidani L. Syndromic and Monogenic Obesity: New Opportunities Due to Genetic-Based Pharmacological Treatment. CHILDREN (BASEL, SWITZERLAND) 2024; 11:153. [PMID: 38397265 PMCID: PMC10886848 DOI: 10.3390/children11020153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 01/21/2024] [Accepted: 01/23/2024] [Indexed: 02/25/2024]
Abstract
Obesity is a significant health problem with a continuously increasing prevalence among children and adolescents that has become a modern pandemic during the last decades. Nowadays, the genetic contribution to obesity is well-established. For this narrative review article, we searched PubMed and Scopus databases for peer-reviewed research, review articles, and meta-analyses regarding the genetics of obesity and current pharmacological treatment, published in the English language with no time restrictions. We also screened the references of the selected articles for possible additional articles in order to include most of the key recent evidence. Our research was conducted between December 2022 and December 2023. We used the terms "obesity", "genetics", "monogenic", "syndromic", "drugs", "autosomal dominant", "autosomal recessive", "leptin-melanocortin pathway", and "children" in different combinations. Recognizing the genetic background in obesity can enhance the effectiveness of treatment. During the last years, intense research in the field of obesity treatment has increased the number of available drugs. This review analyzes the main categories of syndromic and monogenic obesity discussing current data on genetic-based pharmacological treatment of genetic obesity and highlighting the necessity that cases of genetic obesity should follow specific, pharmacological treatment based on their genetic background.
Collapse
Affiliation(s)
- Kallirhoe Kalinderi
- Laboratory of Medical Biology-Genetics, School of Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece;
| | - Vasiliki Goula
- School of Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece;
| | - Evdoxia Sapountzi
- Second Department of Pediatrics, School of Medicine, Faculty of Health Sciences, AHEPA University Hospital, Aristotle University of Thessaloniki, 54636 Thessaloniki, Greece; (E.S.); (V.R.T.)
| | - Vasiliki Rengina Tsinopoulou
- Second Department of Pediatrics, School of Medicine, Faculty of Health Sciences, AHEPA University Hospital, Aristotle University of Thessaloniki, 54636 Thessaloniki, Greece; (E.S.); (V.R.T.)
| | - Liana Fidani
- Laboratory of Medical Biology-Genetics, School of Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece;
- Second Department of Pediatrics, School of Medicine, Faculty of Health Sciences, AHEPA University Hospital, Aristotle University of Thessaloniki, 54636 Thessaloniki, Greece; (E.S.); (V.R.T.)
| |
Collapse
|
3
|
Littleton SH, Trang KB, Volpe CM, Cook K, DeBruyne N, Ann Maguire J, Ann Weidekamp M, Boehm K, Chesi A, Pippin JA, Anderson SA, Wells AD, Pahl MC, Grant SF. Variant-to-function analysis of the childhood obesity chr12q13 locus implicates rs7132908 as a causal variant within the 3' UTR of FAIM2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.21.553157. [PMID: 37662342 PMCID: PMC10473629 DOI: 10.1101/2023.08.21.553157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
The ch12q13 obesity locus is among the most significant childhood obesity loci identified in genome-wide association studies. This locus resides in a non-coding region within FAIM2; thus, the underlying causal variant(s) presumably influence disease susceptibility via an influence on cis-regulation within the genomic region. We implicated rs7132908 as a putative causal variant at this locus leveraging a combination of our inhouse 3D genomic data, public domain datasets, and several computational approaches. Using a luciferase reporter assay in human primary astrocytes, we observed allele-specific cis-regulatory activity of the immediate region harboring rs7132908. Motivated by this finding, we went on to generate isogenic human embryonic stem cell lines homozygous for either rs7132908 allele with CRISPR-Cas9 homology-directed repair to assess changes in gene expression due to genotype and chromatin accessibility throughout a differentiation to hypothalamic neurons, a key cell type known to regulate feeding behavior. We observed that the rs7132908 obesity risk allele influenced the expression of FAIM2 along with other genes, decreased the proportion of neurons produced during differentiation, up-regulated cell death gene sets, and conversely down-regulated neuron differentiation gene sets. We have therefore functionally validated rs7132908 as a causal obesity variant which temporally regulates nearby effector genes at the ch12q13 locus and influences neurodevelopment and survival.
Collapse
Affiliation(s)
- Sheridan H. Littleton
- Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Khanh B. Trang
- Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Christina M. Volpe
- Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kieona Cook
- Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Psychiatry, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Nicole DeBruyne
- Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jean Ann Maguire
- Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Mary Ann Weidekamp
- Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Graduate Group in Genomics and Computational Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Keith Boehm
- 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
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - James A. Pippin
- Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Stewart A. Anderson
- Department of Child and Adolescent Psychiatry, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Andrew D. Wells
- Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Matthew C. Pahl
- Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Struan F.A. Grant
- Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Division of Endocrinology and Diabetes, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| |
Collapse
|
4
|
Sobreira DR, Joslin AC, Zhang Q, Williamson I, Hansen GT, Farris KM, Sakabe NJ, Sinnott-Armstrong N, Bozek G, Jensen-Cody SO, Flippo KH, Ober C, Bickmore WA, Potthoff M, Chen M, Claussnitzer M, Aneas I, Nóbrega MA. Extensive pleiotropism and allelic heterogeneity mediate metabolic effects of IRX3 and IRX5. Science 2021; 372:1085-1091. [PMID: 34083488 PMCID: PMC8386003 DOI: 10.1126/science.abf1008] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 04/28/2021] [Indexed: 12/11/2022]
Abstract
Whereas coding variants often have pleiotropic effects across multiple tissues, noncoding variants are thought to mediate their phenotypic effects by specific tissue and temporal regulation of gene expression. Here, we investigated the genetic and functional architecture of a genomic region within the FTO gene that is strongly associated with obesity risk. We show that multiple variants on a common haplotype modify the regulatory properties of several enhancers targeting IRX3 and IRX5 from megabase distances. We demonstrate that these enhancers affect gene expression in multiple tissues, including adipose and brain, and impart regulatory effects during a restricted temporal window. Our data indicate that the genetic architecture of disease-associated loci may involve extensive pleiotropy, allelic heterogeneity, shared allelic effects across tissues, and temporally restricted effects.
Collapse
Affiliation(s)
- Débora R Sobreira
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA.
| | - Amelia C Joslin
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Qi Zhang
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Iain Williamson
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Grace T Hansen
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Kathryn M Farris
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Noboru J Sakabe
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Nasa Sinnott-Armstrong
- Department of Genetics, Stanford University, Stanford 94305 CA, USA
- Metabolism Program and Cardiovascular Disease Initiative, Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
| | - Grazyna Bozek
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Sharon O Jensen-Cody
- Department of Pharmacology, University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
| | - Kyle H Flippo
- Department of Pharmacology, University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
| | - Carole Ober
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Wendy A Bickmore
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Matthew Potthoff
- Department of Pharmacology, University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
| | - Mengjie Chen
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Melina Claussnitzer
- Metabolism Program and Cardiovascular Disease Initiative, Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
- Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA 02131, USA
| | - Ivy Aneas
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA.
| | - Marcelo A Nóbrega
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA.
| |
Collapse
|