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Zhang J, Pandey M, Awe A, Lue N, Kittock C, Fikse E, Degner K, Staples J, Mokhasi N, Chen W, Yang Y, Adikaram P, Jacob N, Greenfest-Allen E, Thomas R, Bomeny L, Zhang Y, Petros TJ, Wang X, Li Y, Simonds WF. The association of GNB5 with Alzheimer disease revealed by genomic analysis restricted to variants impacting gene function. Am J Hum Genet 2024; 111:473-486. [PMID: 38354736 PMCID: PMC10940018 DOI: 10.1016/j.ajhg.2024.01.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 01/09/2024] [Accepted: 01/10/2024] [Indexed: 02/16/2024] Open
Abstract
Disease-associated variants identified from genome-wide association studies (GWASs) frequently map to non-coding areas of the genome such as introns and intergenic regions. An exclusive reliance on gene-agnostic methods of genomic investigation could limit the identification of relevant genes associated with polygenic diseases such as Alzheimer disease (AD). To overcome such potential restriction, we developed a gene-constrained analytical method that considers only moderate- and high-risk variants that affect gene coding sequences. We report here the application of this approach to publicly available datasets containing 181,388 individuals without and with AD and the resulting identification of 660 genes potentially linked to the higher AD prevalence among Africans/African Americans. By integration with transcriptome analysis of 23 brain regions from 2,728 AD case-control samples, we concentrated on nine genes that potentially enhance the risk of AD: AACS, GNB5, GNS, HIPK3, MED13, SHC2, SLC22A5, VPS35, and ZNF398. GNB5, the fifth member of the heterotrimeric G protein beta family encoding Gβ5, is primarily expressed in neurons and is essential for normal neuronal development in mouse brain. Homozygous or compound heterozygous loss of function of GNB5 in humans has previously been associated with a syndrome of developmental delay, cognitive impairment, and cardiac arrhythmia. In validation experiments, we confirmed that Gnb5 heterozygosity enhanced the formation of both amyloid plaques and neurofibrillary tangles in the brains of AD model mice. These results suggest that gene-constrained analysis can complement the power of GWASs in the identification of AD-associated genes and may be more broadly applicable to other polygenic diseases.
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Affiliation(s)
- Jianhua Zhang
- Metabolic Diseases Branch, Bldg. 10/Rm 8C-101, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Mritunjay Pandey
- Metabolic Diseases Branch, Bldg. 10/Rm 8C-101, National Institutes of Health, Bethesda, MD 20892, USA
| | - Adam Awe
- Metabolic Diseases Branch, Bldg. 10/Rm 8C-101, National Institutes of Health, Bethesda, MD 20892, USA
| | - Nicole Lue
- Metabolic Diseases Branch, Bldg. 10/Rm 8C-101, National Institutes of Health, Bethesda, MD 20892, USA
| | - Claire Kittock
- Metabolic Diseases Branch, Bldg. 10/Rm 8C-101, National Institutes of Health, Bethesda, MD 20892, USA
| | - Emma Fikse
- Metabolic Diseases Branch, Bldg. 10/Rm 8C-101, National Institutes of Health, Bethesda, MD 20892, USA
| | - Katherine Degner
- Metabolic Diseases Branch, Bldg. 10/Rm 8C-101, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jenna Staples
- Metabolic Diseases Branch, Bldg. 10/Rm 8C-101, National Institutes of Health, Bethesda, MD 20892, USA
| | - Neha Mokhasi
- Metabolic Diseases Branch, Bldg. 10/Rm 8C-101, National Institutes of Health, Bethesda, MD 20892, USA
| | - Weiping Chen
- Genomic Core, National Institute of Diabetes and Digestive and Kidney Diseases, Bldg. 8/Rm 1A11, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yanqin Yang
- Laboratory of Transplantation Genomics, National Heart Lung and Blood Institute, Bldg. 10/Rm 7S261, National Institutes of Health, Bethesda, MD 20892, USA
| | - Poorni Adikaram
- Metabolic Diseases Branch, Bldg. 10/Rm 8C-101, National Institutes of Health, Bethesda, MD 20892, USA
| | - Nirmal Jacob
- Metabolic Diseases Branch, Bldg. 10/Rm 8C-101, National Institutes of Health, Bethesda, MD 20892, USA
| | - Emily Greenfest-Allen
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Rachel Thomas
- Metabolic Diseases Branch, Bldg. 10/Rm 8C-101, National Institutes of Health, Bethesda, MD 20892, USA
| | - Laura Bomeny
- Metabolic Diseases Branch, Bldg. 10/Rm 8C-101, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yajun Zhang
- Unit on Cellular and Molecular Neurodevelopment, Bldg. 35/Rm 3B 1002, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Timothy J Petros
- Unit on Cellular and Molecular Neurodevelopment, Bldg. 35/Rm 3B 1002, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Xiaowen Wang
- Partek Incorporated, 12747 Olive Boulevard, St. Louis, MO 63141, USA
| | - Yulong Li
- Metabolic Diseases Branch, Bldg. 10/Rm 8C-101, National Institutes of Health, Bethesda, MD 20892, USA
| | - William F Simonds
- Metabolic Diseases Branch, Bldg. 10/Rm 8C-101, National Institutes of Health, Bethesda, MD 20892, USA.
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