Abstract
Regulation of gene expression is a highly coordinated process in both the healthy and pathological brain with unique patterns across a multitude of cell types. Here we present a multi-omic single nucleus study of ~175,000 nuclei from 50 donors with alcohol use disorder (AUD) and control donors without AUD, profiling cell type specific gene expression and chromatin accessibility in the human central amygdala. We identify all major CNS cell types and neuronal subtypes and find inhibitory neurons are particularly affected by AUD. We find high numbers of differentially expressed genes (DEGs) including GABRA2, GRM8, and NCAM1 and show significant enrichment for AUD risk genes within these DEGs. We identified 51,431 cell type-specific, disease associated candidate cis-regulatory elements including an interneuron-associated set of chromatin loops at the AUD risk gene CALN1. Transcription factor footprinting identified Kruppel-like factors upstream of AUD GWAS genes and DEGs. Finally, we also perform cell type-specific fine mapping for AUD GWAS to prioritize variants within functional genomic elements.
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Data availability
The snMultiome data generated in this study have been deposited in the Zenodo database [https://doi.org/10.5281/zenodo.17656668]. Datasets are available from the corresponding author and requests may also be submitted to https://www.research.va.gov/programs/tissue_banking/ptsd/ and referencing this paper. The processed data generated in this study are provided in the Supplementary Information/Source Data file. Source data are provided with this paper.
Code availability
All code used in this study is freely available online and can be found at https://github.com/mjgirgenti/AUDsnCEA.
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Acknowledgements
We would like to express our gratitude to the National Center for PTSD Brain Bank, the University of Pittsburgh Brain Tissue Donation Program, and the NIH NeuroBioBank whose efforts led to the donation of the postmortem tissue used in these studies. We are also indebted to the generosity of the families of the decedents, who donated the brain tissue used in these studies. The research reported here was supported by the Department of Veterans Affairs, Veteran Health Administration, VISN1 Career Development Award, a Brain and Behavior Research Foundation Young Investigator Award, an American Foundation for Suicide Prevention Young Investigator Award, NIH grants R01AA031017 and DP1DA060811 to M.J.G., R01HG012572, R01DA063316 to J.Z. and P50AA012870 J.H.K. We thank the Keck Microarray Shared Resource (KMSR) and Yale Center for Genome Analysis (YCGA) at Yale university for their assistance with snMultiome sequencing. This work was supported with resources and use of facilities at the VA Connecticut Health Care System, West Haven, CT, the Durham VA Healthcare System, Durham NC, and the VA Boston Healthcare System, Boston, MA, USA and the National Center for PTSD, U.S. Department of Veterans Affairs. This work was funded in part by the State of Connecticut, Department of Mental Health and Addiction Services. The views expressed here are those of the authors and do not necessarily reflect the position or policy of the US Department of Veterans Affairs (VA) or the U.S. government or the views of the Department of Mental Health and Addiction Services or the State of Connecticut.
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C.L., J.Z., and M.J.G. conceived the project and designed the experiments. C.L. and M.J.G. wrote the manuscript. C.D., M.S., R.T., D.M., J.L., G.T., J.C., and A-N.S., generated all of the data. C.L., A.H., X.Z., S.X., J.W., T.N., Y.Liu., H.L., Y.D., Z.D., Y.Lei., Y. Lin, K.X., H.Z., J.Z., and M.J.G. oversaw all bioinformatics analyses. H.Zhou and J.G. contributed GWAS summary data and analysis. J.R.G., D.A.L, P.E.H., J.H.K., H.Zhou, S.T., J.T. and A.C. contributed to study design. All authors contributed to the preparation of the manuscript.
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J.H.K. has consulting agreements (less than US$10,000 per year) with the following: Aptinyx, Inc. Biogen, Idec, MA, Bionomics, Limited (Australia), Boehringer Ingelheim International, Epiodyne, Inc., EpiVario, Inc., Janssen Research & Development, Jazz Pharmaceuticals, Inc., Otsuka America Pharmaceutical, Inc., Spring Care, Inc., Sunovion Pharmaceuticals, Inc.; is the co-founder for Freedom Biosciences, Inc.; serves on the scientific advisory boards of Biohaven Pharmaceuticals, BioXcel Therapeutics, Inc. (Clinical Advisory Board), Cerevel Therapeutics, LLC, Delix Therapeutics, Inc., Eisai, Inc., EpiVario, Inc., Jazz Pharmaceuticals, Inc., Neumora Therapeutics, Inc., Neurocrine Biosciences, Inc., Novartis Pharmaceuticals Corporation, PsychoGenics, Inc., Takeda Pharmaceuticals, Tempero Bio, Inc., Terran Biosciences, Inc..; has stock options with Biohaven Pharmaceuticals Medical Sciences, Cartego Therapeutics, Damona Pharmaceuticals, Delix Therapeutics, EpiVario, Inc., Neumora Therapeutics, Inc., Rest Therapeutics, Tempero Bio, Inc., Terran Biosciences, Inc., Tetricus, Inc.; and is editor of Biological Psychiatry with income greater than $10,000. The remaining authors declare no competing interests.
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Lee, C.Y., Hwang, A., McRiley, D. et al. Central amygdala single-nucleus atlas reveals chromatin and gene transcription dynamics in human alcohol use disorder. Nat Commun (2026). https://doi.org/10.1038/s41467-026-68351-1
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DOI: https://doi.org/10.1038/s41467-026-68351-1
