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Saitou M, Resendez S, Pradhan AJ, Wu F, Lie NC, Hall NJ, Zhu Q, Reinholdt L, Satta Y, Speidel L, Nakagome S, Hanchard NA, Churchill G, Lee C, Atilla-Gokcumen GE, Mu X, Gokcumen O. Sex-specific phenotypic effects and evolutionary history of an ancient polymorphic deletion of the human growth hormone receptor. Sci Adv 2021; 7:eabi4476. [PMID: 34559564 PMCID: PMC8462886 DOI: 10.1126/sciadv.abi4476] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 08/04/2021] [Indexed: 06/13/2023]
Abstract
The common deletion of the third exon of the growth hormone receptor gene (GHRd3) in humans is associated with birth weight, growth after birth, and time of puberty. However, its evolutionary history and the molecular mechanisms through which it affects phenotypes remain unresolved. We present evidence that this deletion was nearly fixed in the ancestral population of anatomically modern humans and Neanderthals but underwent a recent adaptive reduction in frequency in East Asia. We documented that GHRd3 is associated with protection from severe malnutrition. Using a novel mouse model, we found that, under calorie restriction, Ghrd3 leads to the female-like gene expression in male livers and the disappearance of sexual dimorphism in weight. The sex- and diet-dependent effects of GHRd3 in our mouse model are consistent with a model in which the allele frequency of GHRd3 varies throughout human evolution as a response to fluctuations in resource availability.
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Affiliation(s)
- Marie Saitou
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, USA
| | - Skyler Resendez
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, USA
| | | | - Fuguo Wu
- Department of Ophthalmology, Ross Eye Institute, Jacobs School of Medicine and Biological Sciences, University at Buffalo, Buffalo, NY, USA
| | - Natasha C. Lie
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Nancy J. Hall
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Qihui Zhu
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | | | - Yoko Satta
- Department of Evolutionary Studies of Biosystems, SOKENDAI (Graduate University for Advanced Studies), Kanagawa Prefecture, Japan
| | - Leo Speidel
- University College London, Genetics Institute, London, UK
- The Francis Crick Institute, London, UK
| | | | - Neil A. Hanchard
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | | | - Charles Lee
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
- Precision Medicine Center, The First Affiliated Hospital of Xi’an Jiaotong University, Shaanxi, People’s Republic of China
| | | | - Xiuqian Mu
- Department of Ophthalmology, Ross Eye Institute, Jacobs School of Medicine and Biological Sciences, University at Buffalo, Buffalo, NY, USA
| | - Omer Gokcumen
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, USA
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Schulze KV, Swaminathan S, Howell S, Jajoo A, Lie NC, Brown O, Sadat R, Hall N, Zhao L, Marshall K, May T, Reid ME, Taylor-Bryan C, Wang X, Belmont JW, Guan Y, Manary MJ, Trehan I, McKenzie CA, Hanchard NA. Edematous severe acute malnutrition is characterized by hypomethylation of DNA. Nat Commun 2019; 10:5791. [PMID: 31857576 PMCID: PMC6923441 DOI: 10.1038/s41467-019-13433-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2018] [Accepted: 11/06/2019] [Indexed: 02/06/2023] Open
Abstract
Edematous severe acute childhood malnutrition (edematous SAM or ESAM), which includes kwashiorkor, presents with more overt multi-organ dysfunction than non-edematous SAM (NESAM). Reduced concentrations and methyl-flux of methionine in 1-carbon metabolism have been reported in acute, but not recovered, ESAM, suggesting downstream DNA methylation changes could be relevant to differences in SAM pathogenesis. Here, we assess genome-wide DNA methylation in buccal cells of 309 SAM children using the 450 K microarray. Relative to NESAM, ESAM is characterized by multiple significantly hypomethylated loci, which is not observed among SAM-recovered adults. Gene expression and methylation show both positive and negative correlation, suggesting a complex transcriptional response to SAM. Hypomethylated loci link to disorders of nutrition and metabolism, including fatty liver and diabetes, and appear to be influenced by genetic variation. Our epigenetic findings provide a potential molecular link to reported aberrant 1-carbon metabolism in ESAM and support consideration of methyl-group supplementation in ESAM.
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Affiliation(s)
- Katharina V Schulze
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- USDA/ARS/Children's Nutrition Research Center, Baylor College of Medicine, Houston, TX, USA
| | - Shanker Swaminathan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- USDA/ARS/Children's Nutrition Research Center, Baylor College of Medicine, Houston, TX, USA
| | - Sharon Howell
- Tropical Metabolism Research Unit, Caribbean Institute for Health Research, University of the West Indies, Mona, Jamaica
| | - Aarti Jajoo
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- USDA/ARS/Children's Nutrition Research Center, Baylor College of Medicine, Houston, TX, USA
| | - Natasha C Lie
- USDA/ARS/Children's Nutrition Research Center, Baylor College of Medicine, Houston, TX, USA
- Graduate Program in Integrative Molecular and Biomedical Sciences, Baylor College of Medicine, Houston, TX, USA
| | - Orgen Brown
- Tropical Metabolism Research Unit, Caribbean Institute for Health Research, University of the West Indies, Mona, Jamaica
| | - Roa Sadat
- USDA/ARS/Children's Nutrition Research Center, Baylor College of Medicine, Houston, TX, USA
| | - Nancy Hall
- USDA/ARS/Children's Nutrition Research Center, Baylor College of Medicine, Houston, TX, USA
| | - Liang Zhao
- Precision Medicine Research Center, Taihe Hospital, Shiyan City, China
| | - Kwesi Marshall
- Tropical Metabolism Research Unit, Caribbean Institute for Health Research, University of the West Indies, Mona, Jamaica
| | - Thaddaeus May
- USDA/ARS/Children's Nutrition Research Center, Baylor College of Medicine, Houston, TX, USA
| | - Marvin E Reid
- Tropical Metabolism Research Unit, Caribbean Institute for Health Research, University of the West Indies, Mona, Jamaica
| | - Carolyn Taylor-Bryan
- Tropical Metabolism Research Unit, Caribbean Institute for Health Research, University of the West Indies, Mona, Jamaica
| | - Xueqing Wang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- USDA/ARS/Children's Nutrition Research Center, Baylor College of Medicine, Houston, TX, USA
| | - John W Belmont
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- USDA/ARS/Children's Nutrition Research Center, Baylor College of Medicine, Houston, TX, USA
| | - Yongtao Guan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- USDA/ARS/Children's Nutrition Research Center, Baylor College of Medicine, Houston, TX, USA
| | - Mark J Manary
- Departments of Paediatrics and Child Health and Community Health, University of Malawi, Blantyre, Malawi
- Department of Pediatrics, Washington University in St. Louis, St. Louis, MO, USA
| | - Indi Trehan
- Departments of Paediatrics and Child Health and Community Health, University of Malawi, Blantyre, Malawi
- Department of Pediatrics, Washington University in St. Louis, St. Louis, MO, USA
- Departments of Pediatrics and Global Health, University of Washington, Seattle, WA, USA
| | - Colin A McKenzie
- Tropical Metabolism Research Unit, Caribbean Institute for Health Research, University of the West Indies, Mona, Jamaica
| | - Neil A Hanchard
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
- USDA/ARS/Children's Nutrition Research Center, Baylor College of Medicine, Houston, TX, USA.
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