Genetic and environmental contributions to ancestry differences in gene expression in the human brain

Benjamin, K. J.; Chen, Q.; Eagles, N. J.; Huuki-Myers, L. A.; Collado-Torres, L.; Stolz, J. M.; Shin, J. H.; Paquola, A. C.; Hyde, T. M.; Kleinman, J. E.; Jaffe, A. E.; Han, S.; Weinberger, D. R.

doi:10.1101/2023.03.28.534458

bioRxiv · 10.1101/2023.03.28.534458

Genetic and environmental contributions to ancestry differences in gene expression in the human brain

Benjamin, K. J.·Chen, Q.·Eagles, N. J.·Huuki-Myers, L. A.·Collado-Torres, L.·Stolz, J. M.·Shin, J. H.·Paquola, A. C.·Hyde, T. M.·Kleinman, J. E.·Jaffe, A. E.·Han, S.·Weinberger, D. R.

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Abstract

Ancestral differences in genomic variation are determining factors in gene regulation; however, most gene expression studies have been limited to European ancestry samples or adjusted for ancestry to identify ancestry-independent associations. We instead examined the impact of genetic ancestry on gene expression and DNA methylation (DNAm) in admixed African/Black American neurotypical individuals to untangle effects of genetic and environmental factors. Ancestry-associated differentially expressed genes (DEGs), transcripts, and gene networks, while notably not implicating neurons, are enriched for genes related to immune response and vascular tissue and explain up to 26% of heritability for ischemic stroke, 27% of heritability for Parkinsons disease, and 30% of heritability for Alzhemiers disease. Ancestry-associated DEGs also show general enrichment for heritability of diverse immune-related traits but depletion for psychiatric-related traits. The cell-type enrichments and direction of effects vary by brain region. These DEGs are less evolutionarily constrained and are largely explained by genetic variations; roughly 15% are predicted by DNAm variation implicating environmental exposures. We also compared Black and White Americans, confirming most of these ancestry-associated DEGs. Our results highlight how environment and genetic background affect genetic ancestry differences in gene expression in the human brain and affect risk for brain illness. SummaryWe examine the impact of genetic ancestry on gene expression and DNA methylation of admixed African/Black Americans, highlighting how genetic and environmental background affect risk for brain illness.

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Benjamin, K. J., Chen, Q., Eagles, N. J., Huuki-Myers, L. A., Collado-Torres, L., Stolz, J. M., Shin, J. H., Paquola, A. C., Hyde, T. M., Kleinman, J. E., Jaffe, A. E., Han, S., Weinberger, D. R.. 2023-03-30. Genetic and environmental contributions to ancestry differences in gene expression in the human brain. https://doi.org/10.1101/2023.03.28.534458

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