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Lu Z, Zhang M, Lee J, Sziraki A, Anderson S, Zhang Z, Xu Z, Jiang W, Ge S, Nelson PT, Zhou W, Cao J. Tracking cell-type-specific temporal dynamics in human and mouse brains. Cell 2023; 186:4345-4364.e24. [PMID: 37774676 PMCID: PMC10545416 DOI: 10.1016/j.cell.2023.08.042] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 05/28/2023] [Accepted: 08/30/2023] [Indexed: 10/01/2023]
Abstract
Progenitor cells are critical in preserving organismal homeostasis, yet their diversity and dynamics in the aged brain remain underexplored. We introduced TrackerSci, a single-cell genomic method that combines newborn cell labeling and combinatorial indexing to characterize the transcriptome and chromatin landscape of proliferating progenitor cells in vivo. Using TrackerSci, we investigated the dynamics of newborn cells in mouse brains across various ages and in a mouse model of Alzheimer's disease. Our dataset revealed diverse progenitor cell types in the brain and their epigenetic signatures. We further quantified aging-associated shifts in cell-type-specific proliferation and differentiation and deciphered the associated molecular programs. Extending our study to the progenitor cells in the aged human brain, we identified conserved genetic signatures across species and pinpointed region-specific cellular dynamics, such as the reduced oligodendrogenesis in the cerebellum. We anticipate that TrackerSci will be broadly applicable to unveil cell-type-specific temporal dynamics in diverse systems.
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Affiliation(s)
- Ziyu Lu
- Laboratory of Single Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA; The David Rockefeller Graduate Program in Bioscience, The Rockefeller University, New York, NY, USA
| | - Melissa Zhang
- Laboratory of Single Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA
| | - Jasper Lee
- Laboratory of Single Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA
| | - Andras Sziraki
- Laboratory of Single Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA; The David Rockefeller Graduate Program in Bioscience, The Rockefeller University, New York, NY, USA
| | - Sonya Anderson
- Department of Pathology and Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA
| | - Zehao Zhang
- Laboratory of Single Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA; The David Rockefeller Graduate Program in Bioscience, The Rockefeller University, New York, NY, USA
| | - Zihan Xu
- Laboratory of Single Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA; The David Rockefeller Graduate Program in Bioscience, The Rockefeller University, New York, NY, USA
| | - Weirong Jiang
- Laboratory of Single Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA
| | - Shaoyu Ge
- Department of Neurobiology & Behavior, SUNY at Stony Brook, Stony Brook, NY, USA
| | - Peter T Nelson
- Department of Pathology and Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA
| | - Wei Zhou
- Laboratory of Single Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA.
| | - Junyue Cao
- Laboratory of Single Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA.
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Park K, Jeon MC, Kim B, Cha B, Kim JI. Experimental development of the epigenomic library construction method to elucidate the epigenetic diversity and causal relationship between epigenome and transcriptome at a single-cell level. Genomics Inform 2022; 20:e2. [PMID: 35399001 PMCID: PMC9001999 DOI: 10.5808/gi.21078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 01/08/2022] [Indexed: 11/20/2022] Open
Abstract
The method of single-cell RNA sequencing has been rapidly developed, and numerous experiments have been conducted over the past decade. Their results allow us to recognize various subpopulations and rare cell states in tissues, tumors, and immune systems that are previously unidentified, and guide us to understand fundamental biological processes that determine cell identity based on single-cell gene expression profiles. However, it is still challenging to understand the principle of comprehensive gene regulation that determines the cell fate only with transcriptome, a consequential output of the gene expression program. To elucidate the mechanisms related to the origin and maintenance of comprehensive single-cell transcriptome, we require a corresponding single-cell epigenome, which is a differentiated information of each cell with an identical genome. This review deals with the current development of single-cell epigenomic library construction methods, including multi-omics tools with crucial factors and additional requirements in the future focusing on DNA methylation, chromatin accessibility, and histone post-translational modifications. The study of cellular differentiation and the disease occurrence at a single-cell level has taken the first step with single-cell transcriptome and is now taking the next step with single-cell epigenome.
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Affiliation(s)
- Kyunghyuk Park
- Medical Research Center, Genomic Medicine Institute, Seoul National University, Seoul, Korea
| | - Min Chul Jeon
- Medical Research Center, Genomic Medicine Institute, Seoul National University, Seoul, Korea
| | - Bokyung Kim
- Department of Obstetrics & Gynecology, Seoul National University Hospital, Seoul 03080, Korea
| | - Bukyoung Cha
- Medical Research Center, Genomic Medicine Institute, Seoul National University, Seoul, Korea
| | - Jong-Il Kim
- Medical Research Center, Genomic Medicine Institute, Seoul National University, Seoul, Korea.,Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, Korea.,Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul 03080, Korea
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Pandey N, Omkar Chandra, Mishra S, Kumar V. Improving Chromatin-Interaction Prediction Using Single-Cell Open-Chromatin Profiles and Making Insight Into the Cis-Regulatory Landscape of the Human Brain. Front Genet 2021; 12:738194. [PMID: 34691152 PMCID: PMC8533004 DOI: 10.3389/fgene.2021.738194] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 08/31/2021] [Indexed: 11/13/2022] Open
Abstract
Single-cell open-chromatin profiles have the potential to reveal the pattern of chromatin-interaction in a cell type. However, currently available cis-regulatory network prediction methods using single-cell open-chromatin profiles focus more on local chromatin interactions despite the fact that long-range interactions among genomic sites play a significant role in gene regulation. Here, we propose a method that predicts both short and long-range interactions among genomic sites using single-cell open chromatin profiles. Our method, termed as single-cell epigenome based chromatin-interaction analysis (scEChIA) exploits signal imputation and refined L1 regularization. For a few single-cell open-chromatin profiles, scEChIA outperformed other tools even in terms of accuracy of prediction. Using scEChIA, we predicted almost 0.7 million interactions among genomic sites across seven cell types in the human brain. Further analysis revealed cell type for connection between genes and expression quantitative trait locus (eQTL) in the human brain and making insight about target genes of human-accelerated-elements and disease-associated mutations. Our analysis enabled by scEChIA also hints about the possible action of a few transcription factors (TFs), especially through long-range interaction in brain endothelial cells.
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Affiliation(s)
- Neetesh Pandey
- Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India
| | - Omkar Chandra
- Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India
| | - Shreya Mishra
- Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India
| | - Vibhor Kumar
- Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India
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Abstract
Today with the rapid advancements in stem cell studies and the promising potential of using stem cells in clinical therapy, there is an increasing demand for in-depth comprehensive analysis on individual cell transcriptome and epigenome, as they play critical roles in a number of cell functions such as cell differentiation, growth, and reprogramming. The development of single-cell sequencing technologies has helped in revealing some exciting new perspectives in stem cells and regenerative medicine research. Among the various potential applications, single-cell analysis for cardiac stem cells (CSCs) holds tremendous promises in understanding the mechanisms of heart development and regeneration, which might light up the path toward cell therapy for cardiovascular diseases. This review briefly highlights the recent progresses in single-cell sequencing analysis technologies and their applications in CSC research.
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Affiliation(s)
- Tiantian Liu
- 1 Center for Genomics & Department of Basic Sciences, School of Medicine, Loma Linda University , Loma Linda, California
| | - Hongjin Wu
- 1 Center for Genomics & Department of Basic Sciences, School of Medicine, Loma Linda University , Loma Linda, California.,2 Cancer Research Institute, Hangzhou Cancer Hospital , Hangzhou, Zhejiang Province, P.R. China
| | - Shixiu Wu
- 2 Cancer Research Institute, Hangzhou Cancer Hospital , Hangzhou, Zhejiang Province, P.R. China
| | - Charles Wang
- 1 Center for Genomics & Department of Basic Sciences, School of Medicine, Loma Linda University , Loma Linda, California
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