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Lyons A, Brown J, Davenport KM. Single-Cell Sequencing Technology in Ruminant Livestock: Challenges and Opportunities. Curr Issues Mol Biol 2024; 46:5291-5306. [PMID: 38920988 PMCID: PMC11202421 DOI: 10.3390/cimb46060316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 05/20/2024] [Accepted: 05/25/2024] [Indexed: 06/27/2024] Open
Abstract
Advancements in single-cell sequencing have transformed the genomics field by allowing researchers to delve into the intricate cellular heterogeneity within tissues at greater resolution. While single-cell omics are more widely applied in model organisms and humans, their use in livestock species is just beginning. Studies in cattle, sheep, and goats have already leveraged single-cell and single-nuclei RNA-seq as well as single-cell and single-nuclei ATAC-seq to delineate cellular diversity in tissues, track changes in cell populations and gene expression over developmental stages, and characterize immune cell populations important for disease resistance and resilience. Although challenges exist for the use of this technology in ruminant livestock, such as the precise annotation of unique cell populations and spatial resolution of cells within a tissue, there is vast potential to enhance our understanding of the cellular and molecular mechanisms underpinning traits essential for healthy and productive livestock. This review intends to highlight the insights gained from published single-cell omics studies in cattle, sheep, and goats, particularly those with publicly accessible data. Further, this manuscript will discuss the challenges and opportunities of this technology in ruminant livestock and how it may contribute to enhanced profitability and sustainability of animal agriculture in the future.
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Ramakrishnan A, Piehl N, Simonton B, Parikh M, Zhang Z, Teregulova V, van Olst L, Gate D. Epigenetic dysregulation in Alzheimer's disease peripheral immunity. Neuron 2024; 112:1235-1248.e5. [PMID: 38340719 PMCID: PMC11031321 DOI: 10.1016/j.neuron.2024.01.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 11/10/2023] [Accepted: 01/10/2024] [Indexed: 02/12/2024]
Abstract
The peripheral immune system in Alzheimer's disease (AD) has not been thoroughly studied with modern sequencing methods. To investigate epigenetic and transcriptional alterations to the AD peripheral immune system, we used single-cell sequencing strategies, including assay for transposase-accessible chromatin and RNA sequencing. We reveal a striking amount of open chromatin in peripheral immune cells in AD. In CD8 T cells, we uncover a cis-regulatory DNA element co-accessible with the CXC motif chemokine receptor 3 gene promoter. In monocytes, we identify a novel AD-specific RELA transcription factor binding site adjacent to an open chromatin region in the nuclear factor kappa B subunit 2 gene. We also demonstrate apolipoprotein E genotype-dependent epigenetic changes in monocytes. Surprisingly, we also identify differentially accessible chromatin regions in genes associated with sporadic AD risk. Our findings provide novel insights into the complex relationship between epigenetics and genetic risk factors in AD peripheral immunity.
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Affiliation(s)
- Abhirami Ramakrishnan
- The Ken & Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Natalie Piehl
- The Ken & Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Brooke Simonton
- The Ken & Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Milan Parikh
- The Ken & Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Ziyang Zhang
- The Ken & Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Victoria Teregulova
- The Ken & Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Lynn van Olst
- The Ken & Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - David Gate
- The Ken & Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.
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Goodman EJ, Biltz RG, Packer JM, DiSabato DJ, Swanson SP, Oliver B, Quan N, Sheridan JF, Godbout JP. Enhanced fear memory after social defeat in mice is dependent on interleukin-1 receptor signaling in glutamatergic neurons. Mol Psychiatry 2024:10.1038/s41380-024-02456-1. [PMID: 38459193 DOI: 10.1038/s41380-024-02456-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 01/19/2024] [Accepted: 01/23/2024] [Indexed: 03/10/2024]
Abstract
Chronic stress is associated with increased anxiety, cognitive deficits, and post-traumatic stress disorder. Repeated social defeat (RSD) in mice causes long-term stress-sensitization associated with increased microglia activation, monocyte accumulation, and enhanced interleukin (IL)-1 signaling in endothelia and neurons. With stress-sensitization, mice have amplified neuronal, immune, and behavioral responses to acute stress 24 days later. This is clinically relevant as it shares key aspects with post-traumatic stress disorder. The mechanisms underlying stress-sensitization are unclear, but enhanced fear memory may be critical. The purpose of this study was to determine the influence of microglia and IL-1R1 signaling in neurons in the development of sensitization and increased fear memory after RSD. Here, RSD accelerated fear acquisition, delayed fear extinction, and increased cued-based freezing at 0.5 day. The enhancement in contextual fear memory after RSD persisted 24 days later. Next, microglia were depleted with a CSF1R antagonist prior to RSD and several parameters were assessed. Microglia depletion blocked monocyte recruitment to the brain. Nonetheless, neuronal reactivity (pCREB) and IL-1β RNA expression in the hippocampus and enhanced fear memory after RSD were microglial-independent. Because IL-1β RNA was prominent in the hippocampus after RSD even with microglia depletion, IL-1R1 mediated signaling in glutamatergic neurons was assessed using neuronal Vglut2+/IL-1R1-/- mice. RSD-induced neuronal reactivity (pCREB) in the hippocampus and enhancement in fear memory were dependent on neuronal IL-1R1 signaling. Furthermore, single-nuclei RNA sequencing (snRNAseq) showed that RSD influenced transcription in specific hippocampal neurons (DG neurons, CA2/3, CA1 neurons) associated with glutamate signaling, inflammation and synaptic plasticity, which were neuronal IL-1R1-dependent. Furthermore, snRNAseq data provided evidence that RSD increased CREB, BDNF, and calcium signaling in DG neurons in an IL-1R1-dependent manner. Collectively, increased IL-1R1-mediated signaling (monocytes/microglia independent) in glutamatergic neurons after RSD enhanced neuronal reactivity and fear memory.
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Affiliation(s)
- Ethan J Goodman
- Department of Neuroscience, Wexner Medical Center, The Ohio State University, Columbus, OH, USA
- Institute for Behavioral Medicine Research, College of Medicine, The Ohio State University, Columbus, OH, USA
| | - Rebecca G Biltz
- Department of Neuroscience, Wexner Medical Center, The Ohio State University, Columbus, OH, USA
- Institute for Behavioral Medicine Research, College of Medicine, The Ohio State University, Columbus, OH, USA
| | - Jonathan M Packer
- Department of Neuroscience, Wexner Medical Center, The Ohio State University, Columbus, OH, USA
- Institute for Behavioral Medicine Research, College of Medicine, The Ohio State University, Columbus, OH, USA
| | - Damon J DiSabato
- Department of Neuroscience, Wexner Medical Center, The Ohio State University, Columbus, OH, USA
| | - Samuel P Swanson
- Department of Neuroscience, Wexner Medical Center, The Ohio State University, Columbus, OH, USA
- Institute for Behavioral Medicine Research, College of Medicine, The Ohio State University, Columbus, OH, USA
| | - Braeden Oliver
- Division of Biosciences, College of Dentistry, The Ohio State University, Columbus, OH, USA
| | - Ning Quan
- Department of Biomedical Science, Brain Institute, Florida Atlantic University, Boca Raton, FL, USA
| | - John F Sheridan
- Department of Neuroscience, Wexner Medical Center, The Ohio State University, Columbus, OH, USA.
- Institute for Behavioral Medicine Research, College of Medicine, The Ohio State University, Columbus, OH, USA.
- Division of Biosciences, College of Dentistry, The Ohio State University, Columbus, OH, USA.
| | - Jonathan P Godbout
- Department of Neuroscience, Wexner Medical Center, The Ohio State University, Columbus, OH, USA.
- Institute for Behavioral Medicine Research, College of Medicine, The Ohio State University, Columbus, OH, USA.
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Korenfeld N, Toft NI, Dam TV, Charni-Natan M, Grøntved L, Goldstein I. Protocol for bulk and single-nuclei chromatin accessibility quantification in mouse liver tissue. STAR Protoc 2023; 4:102462. [PMID: 37590150 PMCID: PMC10440357 DOI: 10.1016/j.xpro.2023.102462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 06/06/2023] [Accepted: 06/26/2023] [Indexed: 08/19/2023] Open
Abstract
The accessibility of different chromatin regions to transcription factors and other DNA-binding proteins is a critical determinant of cell function. Here, we detail a modified assay for transposase-accessible chromatin sequencing (ATAC-seq) protocol which measures chromatin accessibility genome wide. We describe nuclei isolation, tagmentation, PCR amplification, and pre- and post-sequencing quality control. Our protocol is optimized for the liver, a tissue where nuclei isolation requires distinct steps. We provide two detailed vignettes: one for bulk ATAC-seq and another for single-nuclei ATAC-seq.
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Affiliation(s)
- Noga Korenfeld
- Institute of Biochemistry, Food Science and Nutrition, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, POB 12, Rehovot 7610001, Israel
| | - Nicolaj I Toft
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark
| | - Trine V Dam
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark
| | - Meital Charni-Natan
- Institute of Biochemistry, Food Science and Nutrition, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, POB 12, Rehovot 7610001, Israel
| | - Lars Grøntved
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark.
| | - Ido Goldstein
- Institute of Biochemistry, Food Science and Nutrition, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, POB 12, Rehovot 7610001, Israel.
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