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Green N, Gao H, Chu X, Yuan Q, McGuire P, Lai D, Jiang G, Xuei X, Reiter J, Stevens J, Sutherland G, Goate A, Pang Z, Slesinger P, Hart RP, Tischfield JA, Agrawal A, Wang Y, Duren Z, Edenberg HJ, Liu Y. Integrated Single-Cell Multiomic Profiling of Caudate Nucleus Suggests Key Mechanisms in Alcohol Use Disorder. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.02.606355. [PMID: 39149227 PMCID: PMC11326171 DOI: 10.1101/2024.08.02.606355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
Alcohol use disorder (AUD) is likely associated with complex transcriptional alterations in addiction-relevant brain regions. We characterize AUD-associated differences in cell type-specific gene expression and chromatin accessibility in the caudate nucleus by conducting a single-nucleus RNA-seq assay and a single-nucleus RNA-seq + ATAC-seq (multiome) assay on caudate tissue from 143 human postmortem brains (74 with AUD). We identified 17 cell types. AUD was associated with a higher proportion of microglia in an activated state and more astrocytes in a reactive state. There was widespread evidence for differentially expressed genes across cell types with the most identified in oligodendrocytes and astrocytes, including genes involved in immune response and synaptic regulation, many of which appeared to be regulated in part by JUND and OLIG2. Microglia-astrocyte communication via interleukin-1 beta, and microglia-astrocyte-oligodendrocyte interaction via transforming growth factor beta 1 were increased in individuals with AUD. Expression quantitative trait loci analysis revealed potential driver genes of AUD, including ADAL, that may protect against AUD in medium spiny neurons and interneurons. This work provides a thorough profile of the effects of AUD in the human brain and identifies several promising genes for further study.
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Affiliation(s)
- Nick Green
- Indiana University School of Medicine, Department of Medical and Molecular Genetics, Indianapolis, Indiana, 46202, United States
| | - Hongyu Gao
- Indiana University School of Medicine, Department of Medical and Molecular Genetics, Indianapolis, Indiana, 46202, United States
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, Indiana, 46202, United States
| | - Xiaona Chu
- Indiana University School of Medicine, Department of Medical and Molecular Genetics, Indianapolis, Indiana, 46202, United States
| | - Quiyue Yuan
- Clemson University, Department of Genetics and Biochemistry, Greenwood, SC 29646, United States
| | - Patrick McGuire
- Indiana University School of Medicine, Department of Medical and Molecular Genetics, Indianapolis, Indiana, 46202, United States
| | - Dongbing Lai
- Indiana University School of Medicine, Department of Medical and Molecular Genetics, Indianapolis, Indiana, 46202, United States
| | - Guanglong Jiang
- Indiana University School of Medicine, Department of Medical and Molecular Genetics, Indianapolis, Indiana, 46202, United States
| | - Xiaoling Xuei
- Indiana University School of Medicine, Department of Medical and Molecular Genetics, Indianapolis, Indiana, 46202, United States
| | - Jill Reiter
- Indiana University School of Medicine, Department of Medical and Molecular Genetics, Indianapolis, Indiana, 46202, United States
| | - Julia Stevens
- New South Wales Brain Tissue Research Centre, Charles Perkins Centre and School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2006, Australia
| | - Greg Sutherland
- New South Wales Brain Tissue Research Centre, Charles Perkins Centre and School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2006, Australia
| | - Alison Goate
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
- Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Zhiping Pang
- Human Genetics Institute, Rutgers University, Piscataway, New Jersey 08854, United States
- Department of Neuroscience and Cell Biology and The Child Health Institute of New Jersey, Rutgers Robert Wood Johnson Medical School, New Brunswick, New Jersey 08901, United States
| | - Paul Slesinger
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Ronald P Hart
- Human Genetics Institute, Rutgers University, Piscataway, New Jersey 08854, United States
- Department of Cell Biology & Neuroscience, Rutgers University, Piscataway, New Jersey 08854, United States
| | - Jay A Tischfield
- Department of Genetics, Rutgers University, Piscataway, New Jersey, United States
| | - Arpana Agrawal
- Department of Psychiatry, Washington University School of Medicine in St. Louis, St. Louis, Missouri, United States
| | - Yue Wang
- Indiana University School of Medicine, Department of Medical and Molecular Genetics, Indianapolis, Indiana, 46202, United States
| | - Zhana Duren
- Clemson University, Department of Genetics and Biochemistry, Greenwood, SC 29646, United States
| | - Howard J Edenberg
- Indiana University School of Medicine, Department of Medical and Molecular Genetics, Indianapolis, Indiana, 46202, United States
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States
| | - Yunlong Liu
- Indiana University School of Medicine, Department of Medical and Molecular Genetics, Indianapolis, Indiana, 46202, United States
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, Indiana, 46202, United States
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Benjamin KJM. RFMix-reader: Accelerated reading and processing for local ancestry studies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.13.603370. [PMID: 39071265 PMCID: PMC11275870 DOI: 10.1101/2024.07.13.603370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Motivation Local ancestry inference is a powerful technique in genetics, revealing population history and the genetic basis of diseases. It is particularly valuable for improving eQTL discovery and fine-mapping in admixed populations. Despite the widespread use of the RFMix software for local ancestry inference, large-scale genomic studies face challenges of high memory consumption and processing times when handling RFMix output files. Results Here, I present RFMix-reader , a new Python-based parsing software, designed to streamline the analysis of large-scale local ancestry datasets. This software prioritizes computational eiciency and memory optimization, leveraging GPUs when available for additional speed boosts. By overcoming these data processing hurdles, RFMix-reader empowers researchers to unlock the full potential of local ancestry data for understanding human health and health disparities. Availability RFMix-reader is freely available on PyPI at https://pypi.org/project/rfmix-reader/ , implemented in Python 3, and supported on Linux, Windows, and Mac OS. Contact KynonJade.Benjamin@libd.org. Supplementary information Supplementary data are available at https://rfmix-reader.readthedocs.io/en/latest/ .
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Benjamin KJM, Sauler M, Poonyagariyagorn H, Neptune ER. Cell type-specific expression of angiotensin receptors in the human lung with implications for health, aging, and chronic disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.17.599425. [PMID: 38948835 PMCID: PMC11212981 DOI: 10.1101/2024.06.17.599425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
The renin-angiotensin system is a highly characterized integrative pathway in mammalian homeostasis whose clinical spectrum has been expanded to lung disorders such as chronic obstructive pulmonary disease (COPD)-emphysema, idiopathic pulmonary fibrosis (IPF), and COVID pathogenesis. Despite this widespread interest, specific localization of this receptor family in the mammalian lung is limited, partially due to the imprecision of available antibody reagents. In this study, we establish the expression pattern of the two predominant angiotensin receptors in the human lung, AGTR1 and AGTR2, using complementary and comprehensive bulk and single-cell RNA-sequence datasets that are publicly available. We show these two receptors have distinct localization patterns and developmental trajectories in the human lung, pericytes for AGTR1 and a subtype of alveolar epithelial type 2 cells for AGTR2. In the context of disease, we further pinpoint AGTR2 localization to the COPD-associated subpopulation of alveolar epithelial type 2 (AT2B) and AGTR1 localization to fibroblasts, where their expression is upregulated in individuals with COPD, but not in individuals with IPF. Finally, we examine the genetic variation of the angiotensin receptors, finding AGTR2 associated with lung phenotype (i.e., cystic fibrosis) via rs1403543. Together, our findings provide a critical foundation for delineating this pathway's role in lung homeostasis and constructing rational approaches for targeting specific lung disorders.
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Affiliation(s)
- Kynon JM Benjamin
- Lieber Institute for Brain Development, Baltimore, MD, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Maor Sauler
- Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Hataya Poonyagariyagorn
- Division of Pulmonary and Critical Care Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Enid R Neptune
- Division of Pulmonary and Critical Care Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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Dzirasa K, Thomas GE, Hathaway AC. Towards equitable brain genomics research, for us by us. Nat Neurosci 2024; 27:1021-1023. [PMID: 38769151 DOI: 10.1038/s41593-024-01651-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Affiliation(s)
- Kafui Dzirasa
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Department of Psychiatry and Behavioral Sciences, Duke University Medical Center, Durham, NC, USA
- Department of Neurobiology, Duke University Medical Center, Durham, NC, USA
| | - Gwenaëlle E Thomas
- Lieber Institute for Brain Development, Baltimore, MD, USA
- Morgan State University, Baltimore, MD, USA
| | - Alvin C Hathaway
- Lieber Institute for Brain Development, Baltimore, MD, USA.
- Union Baptist Church, Baltimore, MD, USA.
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