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Gamache J, Gingerich D, Shwab EK, Barrera J, Garrett ME, Hume C, Crawford GE, Ashley-Koch AE, Chiba-Falek O. Integrative single-nucleus multi-omics analysis prioritizes candidate cis and trans regulatory networks and their target genes in Alzheimer's disease brains. Cell Biosci 2023; 13:185. [PMID: 37789374 PMCID: PMC10546724 DOI: 10.1186/s13578-023-01120-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 08/30/2023] [Indexed: 10/05/2023] Open
Abstract
BACKGROUND The genetic underpinnings of late-onset Alzheimer's disease (LOAD) are yet to be fully elucidated. Although numerous LOAD-associated loci have been discovered, the causal variants and their target genes remain largely unknown. Since the brain is composed of heterogenous cell subtypes, it is imperative to study the brain on a cell subtype specific level to explore the biological processes underlying LOAD. METHODS Here, we present the largest parallel single-nucleus (sn) multi-omics study to simultaneously profile gene expression (snRNA-seq) and chromatin accessibility (snATAC-seq) to date, using nuclei from 12 normal and 12 LOAD brains. We identified cell subtype clusters based on gene expression and chromatin accessibility profiles and characterized cell subtype-specific LOAD-associated differentially expressed genes (DEGs), differentially accessible peaks (DAPs) and cis co-accessibility networks (CCANs). RESULTS Integrative analysis defined disease-relevant CCANs in multiple cell subtypes and discovered LOAD-associated cell subtype-specific candidate cis regulatory elements (cCREs), their candidate target genes, and trans-interacting transcription factors (TFs), some of which, including ELK1, JUN, and SMAD4 in excitatory neurons, were also LOAD-DEGs. Finally, we focused on a subset of cell subtype-specific CCANs that overlap known LOAD-GWAS regions and catalogued putative functional SNPs changing the affinities of TF motifs within LOAD-cCREs linked to LOAD-DEGs, including APOE and MYO1E in a specific subtype of microglia and BIN1 in a subpopulation of oligodendrocytes. CONCLUSIONS To our knowledge, this study represents the most comprehensive systematic interrogation to date of regulatory networks and the impact of genetic variants on gene dysregulation in LOAD at a cell subtype resolution. Our findings reveal crosstalk between epigenetic, genomic, and transcriptomic determinants of LOAD pathogenesis and define catalogues of candidate genes, cCREs, and variants involved in LOAD genetic etiology and the cell subtypes in which they act to exert their pathogenic effects. Overall, these results suggest that cell subtype-specific cis-trans interactions between regulatory elements and TFs, and the genes dysregulated by these networks contribute to the development of LOAD.
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Affiliation(s)
- Julia Gamache
- Division of Translational Brain Sciences, Department of Neurology, Duke University Medical Center, DUMC Box 2900, Durham, NC, 27710, USA
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC, 27708, USA
| | - Daniel Gingerich
- Division of Translational Brain Sciences, Department of Neurology, Duke University Medical Center, DUMC Box 2900, Durham, NC, 27710, USA
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC, 27708, USA
| | - E Keats Shwab
- Division of Translational Brain Sciences, Department of Neurology, Duke University Medical Center, DUMC Box 2900, Durham, NC, 27710, USA
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC, 27708, USA
| | - Julio Barrera
- Division of Translational Brain Sciences, Department of Neurology, Duke University Medical Center, DUMC Box 2900, Durham, NC, 27710, USA
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC, 27708, USA
| | - Melanie E Garrett
- Duke Molecular Physiology Institute, Duke University Medical Center, DUMC Box 104775, Durham, NC, 27701, USA
| | - Cordelia Hume
- Division of Translational Brain Sciences, Department of Neurology, Duke University Medical Center, DUMC Box 2900, Durham, NC, 27710, USA
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC, 27708, USA
| | - Gregory E Crawford
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC, 27708, USA.
- Department of Pediatrics, Division of Medical Genetics, Duke University Medical Center, DUMC Box 3382, Durham, NC, 27708, USA.
- Center for Advanced Genomic Technologies, Duke University Medical Center, Durham, NC, 27708, USA.
| | - Allison E Ashley-Koch
- Duke Molecular Physiology Institute, Duke University Medical Center, DUMC Box 104775, Durham, NC, 27701, USA.
- Department of Medicine, Duke University Medical Center, Durham, NC, 27708, USA.
| | - Ornit Chiba-Falek
- Division of Translational Brain Sciences, Department of Neurology, Duke University Medical Center, DUMC Box 2900, Durham, NC, 27710, USA.
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC, 27708, USA.
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Abstract
The importance of apolipoprotein E (APOE) in late-onset Alzheimer's disease (LOAD) has been firmly established, but the mechanisms through which it exerts its pathogenic effects remain elusive. In addition, the sex-dependent effects of APOE on LOAD risk and endophenotypes have yet to be explained. In this Review, we revisit the different aspects of APOE involvement in neurodegeneration and neurological diseases, with particular attention to sex differences in the contribution of APOE to LOAD susceptibility. We discuss the role of APOE in a broader range of age-related neurodegenerative diseases, and summarize the biological factors linking APOE to sex hormones, drawing on supportive findings from rodent models to identify major mechanistic themes underlying the exacerbation of LOAD-associated neurodegeneration and pathology in the female brain. Additionally, we list sex-by-genotype interactions identified across neurodegenerative diseases, proposing APOE variants as a shared etiology for sex differences in the manifestation of these diseases. Finally, we present recent advancements in 'omics' technologies, which provide a new platform for more in-depth investigations of how dysregulation of this gene affects the development and progression of neurodegenerative diseases. Collectively, the evidence summarized in this Review highlights the interplay between APOE and sex as a key factor in the etiology of LOAD and other age-related neurodegenerative diseases. We emphasize the importance of careful examination of sex as a contributing factor in studying the underpinning genetics of neurodegenerative diseases in general, but particularly for LOAD.
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Affiliation(s)
- Julia Gamache
- Division of Translational Brain Sciences, Department of Neurology, Duke University Medical Center, Durham, NC 27710, USA
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC 27708, USA
| | - Young Yun
- Division of Translational Brain Sciences, Department of Neurology, Duke University Medical Center, Durham, NC 27710, USA
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC 27708, USA
| | - Ornit Chiba-Falek
- Division of Translational Brain Sciences, Department of Neurology, Duke University Medical Center, Durham, NC 27710, USA
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC 27708, USA
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Ayotte P, Gamache J, Bass AD, Fabrikant II, Sanche L. Absolute cross sections for dissociative electron attachment to condensed CH3Cl and CH3Br: Effects of potential energy curve crossing and capture probability. J Chem Phys 1997. [DOI: 10.1063/1.473163] [Citation(s) in RCA: 70] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- P. Ayotte
- Groupe du CRM en Sciences des Radiations, Faculteá de médecine, Université de Sherbrooke, Sherbrooke, Québec, Canada J1H 5N4
| | - J. Gamache
- Groupe du CRM en Sciences des Radiations, Faculteá de médecine, Université de Sherbrooke, Sherbrooke, Québec, Canada J1H 5N4
| | - A. D. Bass
- Groupe du CRM en Sciences des Radiations, Faculteá de médecine, Université de Sherbrooke, Sherbrooke, Québec, Canada J1H 5N4
| | - I. I. Fabrikant
- Groupe du CRM en Sciences des Radiations, Faculteá de médecine, Université de Sherbrooke, Sherbrooke, Québec, Canada J1H 5N4
| | - L. Sanche
- Groupe du CRM en Sciences des Radiations, Faculteá de médecine, Université de Sherbrooke, Sherbrooke, Québec, Canada J1H 5N4
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