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Pahl MC, Grant SFA, Leibel RL, Stratigopoulos G. Technologies, strategies, and cautions when deconvoluting genome-wide association signals: FTO in focus. Obes Rev 2023; 24:e13558. [PMID: 36882962 DOI: 10.1111/obr.13558] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Revised: 10/08/2022] [Accepted: 01/31/2023] [Indexed: 03/09/2023]
Abstract
Genome-wide association studies have revealed a plethora of genetic variants that correlate with polygenic conditions. However, causal molecular mechanisms have proven challenging to fully define. Without such information, the associations are not physiologically useful or clinically actionable. By reviewing studies of the FTO locus in the genetic etiology of obesity, we wish to highlight advances in the field fueled by the evolution of technical and analytic strategies in assessing the molecular bases for genetic associations. Particular attention is drawn to extrapolating experimental findings from animal models and cell types to humans, as well as technical aspects used to identify long-range DNA interactions and their biological relevance with regard to the associated trait. A unifying model is proposed by which independent obesogenic pathways regulated by multiple FTO variants and genes are integrated at the primary cilium, a cellular antenna where signaling molecules that control energy balance convene.
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Affiliation(s)
- Matthew C Pahl
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Struan F A Grant
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Division of Diabetes and Endocrinology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Department of Pediatrics, The University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA.,Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Rudolph L Leibel
- Department of Pediatrics, College of Physicians and Surgeons, Columbia University, New York, New York, USA.,Naomi Berrie Diabetes Center, Columbia University Medical Center, New York, New York, USA
| | - George Stratigopoulos
- Department of Pediatrics, College of Physicians and Surgeons, Columbia University, New York, New York, USA.,Naomi Berrie Diabetes Center, Columbia University Medical Center, New York, New York, USA
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2
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Lasa-Aranzasti A, Cazurro-Gutiérrez A, Bescós A, González V, Ispierto L, Tardáguila M, Valenzuela I, Plaja A, Moreno-Galdó A, Macaya-Ruiz A, Pérez-Dueñas B. 16q12.2q21 deletion: A newly recognized cause of dystonia related to GNAO1 haploinsufficiency. Parkinsonism Relat Disord 2022; 103:112-114. [PMID: 36096018 DOI: 10.1016/j.parkreldis.2022.08.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Revised: 08/25/2022] [Accepted: 08/31/2022] [Indexed: 11/19/2022]
Affiliation(s)
- Amaia Lasa-Aranzasti
- Department of Clinical and Molecular Genetics, Vall d'Hebron University Hospital, Barcelona, Spain; Pediatric Neurology Research Group, Vall d'Hebron Research Institute (VHIR), Autonomous University of Barcelona, Barcelona, Spain; Medicine Department, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Ana Cazurro-Gutiérrez
- Pediatric Neurology Research Group, Vall d'Hebron Research Institute (VHIR), Autonomous University of Barcelona, Barcelona, Spain; Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Agustín Bescós
- Pediatric Neuromodulation Unit, Hospital Vall d'Hebrón and Hospital Germans Trias I Pujol, Barcelona, Spain; Department of Neurosurgery, Vall d'Hebron University Hospital, Barcelona, Spain
| | - Victoria González
- Pediatric Neuromodulation Unit, Hospital Vall d'Hebrón and Hospital Germans Trias I Pujol, Barcelona, Spain; Department of Neurology, Department of Neurology, Vall Hebron University Hospital Barcelona, Spain
| | - Lourdes Ispierto
- Pediatric Neuromodulation Unit, Hospital Vall d'Hebrón and Hospital Germans Trias I Pujol, Barcelona, Spain; Neurodegenerative Diseases Unit, Neurology Service and Neurosciences Department, University Hospital Germans Trias i Pujol, Barcelona, Spain
| | - Manel Tardáguila
- Pediatric Neuromodulation Unit, Hospital Vall d'Hebrón and Hospital Germans Trias I Pujol, Barcelona, Spain; Department of Neurological Surgery, University Hospital Germans Trias i Pujol, Barcelona, Spain
| | - Irene Valenzuela
- Department of Clinical and Molecular Genetics, Vall d'Hebron University Hospital, Barcelona, Spain; Medicine Genetics Group, Vall d'Hebron Research Institute (VHIR), Autonomous University of Barcelona, Barcelona, Spain
| | - Alberto Plaja
- Department of Clinical and Molecular Genetics, Vall d'Hebron University Hospital, Barcelona, Spain; Medicine Genetics Group, Vall d'Hebron Research Institute (VHIR), Autonomous University of Barcelona, Barcelona, Spain
| | - Antonio Moreno-Galdó
- Department of Pediatrics, Universitat Autónoma de Barcelona, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain; CIBER of Rare diseases (CIBERER), Instituto de Salud Carlos III (ISCIII), 28029, Madrid, Spain
| | - Alfons Macaya-Ruiz
- Department of Pediatrics, Universitat Autónoma de Barcelona, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain; Pediatric Neurology Research Group, Vall d'Hebron Research Institute (VHIR), Autonomous University of Barcelona, Barcelona, Spain
| | - Belen Pérez-Dueñas
- Pediatric Neurology Research Group, Vall d'Hebron Research Institute (VHIR), Autonomous University of Barcelona, Barcelona, Spain; Pediatric Neuromodulation Unit, Hospital Vall d'Hebrón and Hospital Germans Trias I Pujol, Barcelona, Spain; CIBER of Rare diseases (CIBERER), Instituto de Salud Carlos III (ISCIII), 28029, Madrid, Spain.
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3
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Regulation and Role of Transcription Factors in Osteogenesis. Int J Mol Sci 2021; 22:ijms22115445. [PMID: 34064134 PMCID: PMC8196788 DOI: 10.3390/ijms22115445] [Citation(s) in RCA: 115] [Impact Index Per Article: 38.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 05/14/2021] [Accepted: 05/19/2021] [Indexed: 02/07/2023] Open
Abstract
Bone is a dynamic tissue constantly responding to environmental changes such as nutritional and mechanical stress. Bone homeostasis in adult life is maintained through bone remodeling, a controlled and balanced process between bone-resorbing osteoclasts and bone-forming osteoblasts. Osteoblasts secrete matrix, with some being buried within the newly formed bone, and differentiate to osteocytes. During embryogenesis, bones are formed through intramembraneous or endochondral ossification. The former involves a direct differentiation of mesenchymal progenitor to osteoblasts, and the latter is through a cartilage template that is subsequently converted to bone. Advances in lineage tracing, cell sorting, and single-cell transcriptome studies have enabled new discoveries of gene regulation, and new populations of skeletal stem cells in multiple niches, including the cartilage growth plate, chondro-osseous junction, bone, and bone marrow, in embryonic development and postnatal life. Osteoblast differentiation is regulated by a master transcription factor RUNX2 and other factors such as OSX/SP7 and ATF4. Developmental and environmental cues affect the transcriptional activities of osteoblasts from lineage commitment to differentiation at multiple levels, fine-tuned with the involvement of co-factors, microRNAs, epigenetics, systemic factors, circadian rhythm, and the microenvironments. In this review, we will discuss these topics in relation to transcriptional controls in osteogenesis.
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Two cases of 16q12.1q21 deletions and refinement of the critical region. Eur J Med Genet 2020; 63:103878. [PMID: 32045705 DOI: 10.1016/j.ejmg.2020.103878] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 01/27/2020] [Accepted: 02/07/2020] [Indexed: 11/23/2022]
Abstract
Interstitial deletions of 16q chromosome including 16q12.1q21 region are very rare, with only three cases reported to date. Main clinical features include dysmorphisms, short stature, microcephaly, eye abnormalities, epilepsy, development delay, intellectual disability, and autism spectrum disorder. We report two independent subjects with 16q12.1q21 deletion syndrome presenting with dysmorphic facial features, developmental delay, strabismus, and aggressive behavior. A minimal region of overlap spanning 1.7 Mb on chromosome 16, including IRX5, GNAO1, and NUDT21 genes was shared among these two cases and those previously reported. This minimal region of overlap suggests the potential pathogenic role of these genes, previously implicated in diseases of the central nervous system.
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Mohamad Shah NS, Sulong S, Wan Sulaiman WA, Halim AS. Two novel genes TOX3 and COL21A1 in large extended Malay families with nonsyndromic cleft lip and/or palate. Mol Genet Genomic Med 2019; 7:e635. [PMID: 30924295 PMCID: PMC6503016 DOI: 10.1002/mgg3.635] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Revised: 01/09/2019] [Accepted: 02/11/2019] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Nonsyndromic cleft lip and/or palate is one of the most common human birth defects worldwide that affects the lip and/or palate. The incidence of clefts varies among populations through ethnic, race, or geographical differences. The focus on Malay nonsyndromic cleft lip and/or palate (NSCL/P) is because of a scarce report on genetic study in relation to this deformity in Malaysia. We are interested to discuss about the genes that are susceptible to cause orofacial cleft formation in the family. METHODS Genome-wide linkage analysis was carried out on eight large extended families of NSCL/P with the total of 91 individuals among Malay population using microarray platform. Based on linkage analyses findings, copy number variation (CNV) of LPHN2, SATB2, PVRL3, COL21A1, and TOX3 were identified in four large extended families that showed linkage evidence using quantitative polymerase chain reaction (qPCR) as for a validation purpose. Copy number calculated (CNC) for each genes were determined with Applied Biosystems CopyCallerTM Software v2.0. Normal CNC of the target sequence expected was set at two. RESULTS Genome-wide linkage analysis had discovered several genes including TOX3 and COL21A1 in four different loci 4p15.2-p16.1, 6p11.2-p12.3, 14q13-q21, and 16q12.1. There was significant decreased, p < 0.05 of SATB2, COL21A1, and TOX3 copy number in extended families compared to the normal controls. CONCLUSION Novel linkage evidence and significant low copy number of COL21A1 and TOX3 in NSCLP family was confirmed. These genes increased the risks toward NSCLP formation in that family traits.
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Affiliation(s)
- Nurul Syazana Mohamad Shah
- Reconstructive Science Unit, School of Medical SciencesUniversiti Sains MalaysiaKubang KerianKelantanMalaysia
| | - Sarina Sulong
- Human Genome Centre, School of Medical SciencesUniversiti Sains MalaysiaKubang KerianKelantanMalaysia
| | - Wan Azman Wan Sulaiman
- Reconstructive Science Unit, School of Medical SciencesUniversiti Sains MalaysiaKubang KerianKelantanMalaysia
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Yamamoto T, Shimojima K, Yamazaki S, Ikeno K, Tohyama J. A 16q12.2q21 deletion identified in a patient with developmental delay, epilepsy, short stature, and distinctive features. Congenit Anom (Kyoto) 2016; 56:253-255. [PMID: 27230627 DOI: 10.1111/cga.12172] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Revised: 04/19/2016] [Accepted: 05/20/2016] [Indexed: 12/25/2022]
Abstract
Interstitial deletions of the 16q centromeric region are rarely reported. A microdeletion of the 16q12.2q21 region was identified in a patient with intellectual disability, epilepsy, short stature, and distinctive features; including up-slanting palpebral fissures, hypertelorism, epicanthic folds, anteverted nares, simple philtrum, thin upper lip vermilion, high arched palate, posteriorly rotated ears, and overlapping toes in his right foot. Although the deleted region includes the genes responsible for neurological impairments (GNOA1, GPR56, KATNB1, and BBS2), haploinsufficiency of these genes would not be associated with the patient's phenotype. When NDRG4, present in the deleted region, was knocked out in mice, these mice exhibited spatial learning deficits. Thus, we hypothesize that this gene could be a potential candidate underlying the neurological observations of the patient. Because RSPRY1 was been discovered as the cause of progressive skeletal dysplasia, a loss of this gene might explain the skeletal defects observed in the patient.
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Affiliation(s)
- Toshiyuki Yamamoto
- Tokyo Women's Medical University Institute for Integrated Medical Sciences, Tokyo, Japan
| | - Keiko Shimojima
- Tokyo Women's Medical University Institute for Integrated Medical Sciences, Tokyo, Japan
| | - Sawako Yamazaki
- Department of Pediatrics, Niigata City General Hospital, Niigata, Japan
| | - Kanju Ikeno
- Department of Pediatrics, Niigata City General Hospital, Niigata, Japan.,Department of Pediatrics, Kanazawa Medical University, Ishikawa, Japan
| | - Jun Tohyama
- Department of Child Neurology, Epilepsy Center, Nishi-Niigata Chuo National Hospital, Niigata, Japan
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Cain CJ, Gaborit N, Lwin W, Barruet E, Ho S, Bonnard C, Hamamy H, Shboul M, Reversade B, Kayserili H, Bruneau BG, Hsiao EC. Loss of Iroquois homeobox transcription factors 3 and 5 in osteoblasts disrupts cranial mineralization. Bone Rep 2016; 5:86-95. [PMID: 27453922 PMCID: PMC4926823 DOI: 10.1016/j.bonr.2016.02.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 02/02/2016] [Indexed: 01/13/2023] Open
Abstract
Cranial malformations are a significant cause of perinatal morbidity and mortality. Iroquois homeobox transcription factors (IRX) are expressed early in bone tissue formation and facilitate patterning and mineralization of the skeleton. Mice lacking Irx5 appear grossly normal, suggesting that redundancy within the Iroquois family. However, global loss of both Irx3 and Irx5 in mice leads to significant skeletal malformations and embryonic lethality from cardiac defects. Here, we study the bone-specific functions of Irx3 and Irx5 using Osx-Cre to drive osteoblast lineage-specific deletion of Irx3 in Irx5(-/-) mice. Although we found that the Osx-Cre transgene alone could also affect craniofacial mineralization, newborn Irx3 (flox/flox) /Irx5(-/-)/Osx-Cre (+) mice displayed additional mineralization defects in parietal, interparietal, and frontal bones with enlarged sutures and reduced calvarial expression of osteogenic genes. Newborn endochondral long bones were largely unaffected, but we observed marked reductions in 3-4-week old bone mineral content of Irx3 (flox/flox) /Irx5(-/-)/Osx-Cre (+) mice. Our findings indicate that IRX3 and IRX5 can work together to regulate mineralization of specific cranial bones. Our results also provide insight into the causes of the skeletal changes and mineralization defects seen in Hamamy syndrome patients carrying mutations in IRX5.
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Affiliation(s)
- Corey J Cain
- Department of Medicine, Division of Endocrinology and Metabolism, Institute for Human Genetics, Program in Craniofacial Biology, University of California, San Francisco, San Francisco, CA 94143-0794, USA
| | - Nathalie Gaborit
- Inserm, UMR 1087, l'institut du thorax, Nantes, France; CNRS, UMR 6291, Nantes, France; Université de Nantes, France
| | - Wint Lwin
- Department of Medicine, Division of Endocrinology and Metabolism, Institute for Human Genetics, Program in Craniofacial Biology, University of California, San Francisco, San Francisco, CA 94143-0794, USA
| | - Emilie Barruet
- Department of Medicine, Division of Endocrinology and Metabolism, Institute for Human Genetics, Program in Craniofacial Biology, University of California, San Francisco, San Francisco, CA 94143-0794, USA
| | - Samantha Ho
- Department of Medicine, Division of Endocrinology and Metabolism, Institute for Human Genetics, Program in Craniofacial Biology, University of California, San Francisco, San Francisco, CA 94143-0794, USA
| | - Carine Bonnard
- Human Embryology and Genetics Laboratory, Institute of Medical Biology, ASTAR, Singapore 138648, Singapore
| | - Hanan Hamamy
- Department of Genetic Medicine and Development, Geneva University, Geneva 1211, Switzerland
| | - Mohammad Shboul
- Human Embryology and Genetics Laboratory, Institute of Medical Biology, ASTAR, Singapore 138648, Singapore
| | - Bruno Reversade
- Human Embryology and Genetics Laboratory, Institute of Medical Biology, ASTAR, Singapore 138648, Singapore
| | - Hülya Kayserili
- Medical Genetics Department, Koc University School of Medicine, Rumelifeneri Yolu, Sarıyer, Istanbul 34450, Turkey; Medical Genetics Department, Istanbul Medical Faculty, Istanbul University Topkapi, Fatih, 34093 lstanbul, Turkey
| | - Benoit G Bruneau
- Gladstone Institute for Cardiovascular Disease, San Francisco, CA 94158, USA; Department of Pediatrics, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Edward C Hsiao
- Department of Medicine, Division of Endocrinology and Metabolism, Institute for Human Genetics, Program in Craniofacial Biology, University of California, San Francisco, San Francisco, CA 94143-0794, USA
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8
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Mutations in IRX5 impair craniofacial development and germ cell migration via SDF1. Nat Genet 2012; 44:709-13. [PMID: 22581230 DOI: 10.1038/ng.2259] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2011] [Accepted: 04/02/2012] [Indexed: 12/18/2022]
Abstract
Using homozygosity mapping and locus resequencing, we found that alterations in the homeodomain of the IRX5 transcription factor cause a recessive congenital disorder affecting face, brain, blood, heart, bone and gonad development. We found through in vivo modeling in Xenopus laevis embryos that Irx5 modulates the migration of progenitor cell populations in branchial arches and gonads by repressing Sdf1. We further found that transcriptional control by Irx5 is modulated by direct protein-protein interaction with two GATA zinc-finger proteins, GATA3 and TRPS1; disruptions of these proteins also cause craniofacial dysmorphisms. Our findings suggest that IRX proteins integrate combinatorial transcriptional inputs to regulate key signaling molecules involved in the ontogeny of multiple organs during embryogenesis and homeostasis.
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Shoukier M, Wickert J, Schröder J, Bartels I, Auber B, Zoll B, Salinas-Riester G, Weise D, Brockmann K, Zirn B, Burfeind P. A 16q12 microdeletion in a boy with severe psychomotor delay, craniofacial dysmorphism, brain and limb malformations, and a heart defect. Am J Med Genet A 2011; 158A:229-35. [DOI: 10.1002/ajmg.a.34387] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2011] [Accepted: 10/24/2011] [Indexed: 11/09/2022]
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