151
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Decourt B, Sabbagh MN. The importance of genomics in advancing the diagnosis and treatment of dementia. Lancet Neurol 2022; 21:676-677. [PMID: 35697056 PMCID: PMC10337990 DOI: 10.1016/s1474-4422(22)00234-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 05/25/2022] [Indexed: 11/21/2022]
Affiliation(s)
- Boris Decourt
- Translational Neuroscience Laboratory, Cleveland Clinic Lou Ruvo Center for Brain Health, Las Vegas, NV, USA
| | - Marwan N Sabbagh
- Department of Neurology, Barrow Neurological Institute, St Joseph's Hospital and Medical Center, Phoenix, AZ 85013, USA.
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152
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Abstract
The single-cell revolution in the field of genomics is in full bloom, with clever new molecular biology tricks appearing regularly that allow researchers to explore new modalities or scale up their projects to millions of cells and beyond. Techniques abound to measure RNA expression, DNA alterations, protein abundance, chromatin accessibility, and more, all with single-cell resolution and often in combination. Despite such a rapidly changing technology landscape, there are several fundamental principles that are applicable to the majority of experimental workflows to help users avoid pitfalls and exploit the advantages of the chosen platform. In this overview article, we describe a variety of popular single-cell genomics technologies and address some common questions pertaining to study design, sample preparation, quality control, and sequencing strategy. As the majority of relevant publications currently revolve around single-cell RNA-seq, we will prioritize this genomics modality in our discussion. © 2022 Wiley Periodicals LLC.
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Affiliation(s)
- Claire Regan
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York
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153
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Zhou Y, Peng M, Yang B, Tong T, Zhang B, Tang N. scDLC: a deep learning framework to classify large sample single-cell RNA-seq data. BMC Genomics 2022; 23:504. [PMID: 35831808 PMCID: PMC9281153 DOI: 10.1186/s12864-022-08715-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 06/21/2022] [Indexed: 11/10/2022] Open
Abstract
Background Using single-cell RNA sequencing (scRNA-seq) data to diagnose disease is an effective technique in medical research. Several statistical methods have been developed for the classification of RNA sequencing (RNA-seq) data, including, for example, Poisson linear discriminant analysis (PLDA), negative binomial linear discriminant analysis (NBLDA), and zero-inflated Poisson logistic discriminant analysis (ZIPLDA). Nevertheless, few existing methods perform well for large sample scRNA-seq data, in particular when the distribution assumption is also violated. Results We propose a deep learning classifier (scDLC) for large sample scRNA-seq data, based on the long short-term memory recurrent neural networks (LSTMs). Our new scDLC does not require a prior knowledge on the data distribution, but instead, it takes into account the dependency of the most outstanding feature genes in the LSTMs model. LSTMs is a special recurrent neural network, which can learn long-term dependencies of a sequence. Conclusions Simulation studies show that our new scDLC performs consistently better than the existing methods in a wide range of settings with large sample sizes. Four real scRNA-seq datasets are also analyzed, and they coincide with the simulation results that our new scDLC always performs the best. The code named “scDLC” is publicly available at https://github.com/scDLC-code/code. Supplementary Information The online version contains supplementary material available at (10.1186/s12864-022-08715-1).
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Affiliation(s)
- Yan Zhou
- College of Mathematics and Statistics, Institute of Statistical Sciences, Shenzhen Key Laboratory of Advanced Machine Learning and Applications, Shenzhen University, Shenzhen, China
| | - Minjiao Peng
- College of Mathematics and Statistics, Institute of Statistical Sciences, Shenzhen Key Laboratory of Advanced Machine Learning and Applications, Shenzhen University, Shenzhen, China
| | - Bin Yang
- College of Mathematics and Statistics, Institute of Statistical Sciences, Shenzhen Key Laboratory of Advanced Machine Learning and Applications, Shenzhen University, Shenzhen, China
| | - Tiejun Tong
- Department of Mathematics, Hong Kong Baptist University, Kowloon Tong, Hong Kong
| | - Baoxue Zhang
- School of Statistics, Capital University of Economics and Business, Beijing, China
| | - Niansheng Tang
- Yunnan Key Laboratory of Statistical Modeling and Data Analysis, Yunnan University, Kunming, China.
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154
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Dirice E, Basile G, Kahraman S, Diegisser D, Hu J, Kulkarni RN. Single-nucleus RNA-sequencing reveals singular gene signatures of human ductal cells during adaptation to insulin resistance. JCI Insight 2022; 7:153877. [PMID: 35819843 PMCID: PMC9462484 DOI: 10.1172/jci.insight.153877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 07/07/2022] [Indexed: 11/26/2022] Open
Abstract
Adaptation to increased insulin demand is mediated by β cell proliferation and neogenesis, among other mechanisms. Although it is known that pancreatic β cells can arise from ductal progenitors, these observations have been limited mostly to the neonatal period. We have recently reported that the duct is a source of insulin-secreting cells in adult insulin-resistant states. To further explore the signaling pathways underlying the dynamic β cell reserve during insulin resistance, we undertook human islet and duct transplantations under the kidney capsule of immunodeficient NOD/SCID-γ (NSG) mouse models that were pregnant, were insulin-resistant, or had insulin resistance superimposed upon pregnancy (insulin resistance + pregnancy), followed by single-nucleus RNA-Seq (snRNA-Seq) on snap-frozen graft samples. We observed an upregulation of proliferation markers (e.g., NEAT1) and expression of islet endocrine cell markers (e.g., GCG and PPY), as well as mature β cell markers (e.g., INS), in transplanted human duct grafts in response to high insulin demand. We also noted downregulation of ductal cell identity genes (e.g., KRT19 and ONECUT2) coupled with upregulation of β cell development and insulin signaling pathways. These results indicate that subsets of ductal cells are able to gain β cell identity and reflect a form of compensation during the adaptation to insulin resistance in both physiological and pathological states.
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Affiliation(s)
- Ercument Dirice
- Section of Islet Cell and Regenerative Biology, Joslin Diabetes Center, Boston, United States of America
| | - Giorgio Basile
- Section of Islet Cell and Regenerative Biology, Joslin Diabetes Center, Boston, United States of America
| | - Sevim Kahraman
- Section of Islet Cell and Regenerative Biology, Joslin Diabetes Center, Boston, United States of America
| | - Danielle Diegisser
- Department of Pharmacology, New York Medical College, Valhalla, United States of America
| | - Jiang Hu
- Section of Islet Cell and Regenerative Biology, Joslin Diabetes Center, Boston, United States of America
| | - Rohit N Kulkarni
- Section of Islet Cell and Regenerative Biology, Joslin Diabetes Center, Boston, United States of America
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155
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Ellis D, Wu D, Datta S. SAREV: A review on statistical analytics of single-cell RNA sequencing data. WILEY INTERDISCIPLINARY REVIEWS. COMPUTATIONAL STATISTICS 2022; 14:e1558. [PMID: 36034329 PMCID: PMC9400796 DOI: 10.1002/wics.1558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 04/09/2021] [Indexed: 06/15/2023]
Abstract
Due to the development of next-generation RNA sequencing (NGS) technologies, there has been tremendous progress in research involving determining the role of genomics, transcriptomics and epigenomics in complex biological systems. However, scientists have realized that information obtained using earlier technology, frequently called 'bulk RNA-seq' data, provides information averaged across all the cells present in a tissue. Relatively newly developed single cell (scRNA-seq) technology allows us to provide transcriptomic information at a single-cell resolution. Nevertheless, these high-resolution data have their own complex natures and demand novel statistical data analysis methods to provide effective and highly accurate results on complex biological systems. In this review, we cover many such recently developed statistical methods for researchers wanting to pursue scRNA-seq statistical and computational research as well as scientific research about these existing methods and free software tools available for their generated data. This review is certainly not exhaustive due to page limitations. We have tried to cover the popular methods starting from quality control to the downstream analysis of finding differentially expressed genes and concluding with a brief description of network analysis.
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Affiliation(s)
- Dorothy Ellis
- Department of Biostatistics, University of Florida, School of Public Health and Health Professions, Gainesville, FL
| | - Dongyuan Wu
- Department of Biostatistics, University of Florida, School of Public Health and Health Professions, Gainesville, FL
| | - Susmita Datta
- Department of Biostatistics, University of Florida, School of Public Health and Health Professions, Gainesville, FL
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156
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Goldfarb CN, Karri K, Pyatkov M, Waxman DJ. Interplay Between GH-regulated, Sex-biased Liver Transcriptome and Hepatic Zonation Revealed by Single-Nucleus RNA Sequencing. Endocrinology 2022; 163:6580481. [PMID: 35512247 PMCID: PMC9154260 DOI: 10.1210/endocr/bqac059] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Indexed: 11/19/2022]
Abstract
The zonation of liver metabolic processes is well-characterized; however, little is known about the cell type-specificity and zonation of sexually dimorphic gene expression or its growth hormone (GH)-dependent transcriptional regulators. We address these issues using single-nucleus RNA-sequencing of 32 000 nuclei representing 9 major liver cell types. Nuclei were extracted from livers from adult male and female mice; from males infused with GH continuously, mimicking the female plasma GH pattern; and from mice exposed to TCPOBOP, a xenobiotic agonist ligand of the nuclear receptor CAR that perturbs sex-biased gene expression. Analysis of these rich transcriptomic datasets revealed the following: 1) expression of sex-biased genes and their GH-dependent transcriptional regulators is primarily restricted to hepatocytes and is not a feature of liver nonparenchymal cells; 2) many sex-biased transcripts show sex-dependent zonation within the liver lobule; 3) gene expression is substantially feminized both in periportal and pericentral hepatocytes when male mice are infused with GH continuously; 4) sequencing nuclei increases the sensitivity for detecting thousands of nuclear-enriched long-noncoding RNAs (lncRNAs) and enables determination of their liver cell type-specificity, sex-bias and hepatocyte zonation profiles; 5) the periportal to pericentral hepatocyte cell ratio is significantly higher in male than female liver; and 6) TCPOBOP exposure disrupts both sex-specific gene expression and hepatocyte zonation within the liver lobule. These findings highlight the complex interconnections between hepatic sexual dimorphism and zonation at the single-cell level and reveal how endogenous hormones and foreign chemical exposure can alter these interactions across the liver lobule with large effects both on protein-coding genes and lncRNAs.
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Affiliation(s)
- Christine N Goldfarb
- Department of Biology, Boston University, Boston, Massachusetts 02215, USA
- Biomedical Engineering, Boston University, Boston, Massachusetts 02215, USA
| | - Kritika Karri
- Department of Biology, Boston University, Boston, Massachusetts 02215, USA
- Bioinformatics Program Boston University, Boston, Massachusetts 02215, USA
| | - Maxim Pyatkov
- Department of Biology, Boston University, Boston, Massachusetts 02215, USA
| | - David J Waxman
- Correspondence: David J. Waxman, PhD, Department of Biology, Boston University, 5 Cummington Mall, Boston, MA 02215, USA.
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157
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Hajdarovic KH, Yu D, Hassell LA, Evans S, Packer S, Neretti N, Webb AE. Single-cell analysis of the aging female mouse hypothalamus. NATURE AGING 2022; 2:662-678. [PMID: 36285248 PMCID: PMC9592060 DOI: 10.1038/s43587-022-00246-4] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Accepted: 06/02/2022] [Indexed: 01/15/2023]
Abstract
Alterations in metabolism, sleep patterns, body composition, and hormone status are all key features of aging. While the hypothalamus is a well-conserved brain region that controls these homeostatic and survival-related behaviors, little is known about the intrinsic features of hypothalamic aging. Here, we perform single nuclei RNA-sequencing of 40,064 hypothalamic nuclei from young and aged female mice. We identify cell type-specific signatures of aging in neuronal subtypes as well as astrocytes and microglia. We uncover changes in cell types critical for metabolic regulation and body composition, and in an area of the hypothalamus linked to cognition. Our analysis also reveals an unexpected female-specific feature of hypothalamic aging: the master regulator of X-inactivation, Xist, is elevated with age, particularly in hypothalamic neurons. Moreover, using machine learning, we show that levels of X-chromosome genes, and Xist itself, can accurately predict cellular age. This study identifies critical cell-specific changes of the aging hypothalamus in mammals, and uncovers a potential marker of neuronal aging in females.
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Affiliation(s)
- Kaitlyn H Hajdarovic
- Neuroscience Graduate Program, Brown University, Providence, RI, 02912, USA
- These authors contributed equally: Kaitlyn H. Hajdarovic, Doudou Yu
| | - Doudou Yu
- Molecular Biology, Cell Biology, and Biochemistry Graduate Program, Brown University, Providence, RI 02912, USA
- These authors contributed equally: Kaitlyn H. Hajdarovic, Doudou Yu
| | - Lexi-Amber Hassell
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI 02912, USA
| | - Shane Evans
- Graduate program in Computational Biology, Brown University, Providence, RI, 02912, USA
| | - Sarah Packer
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI 02912, USA
| | - Nicola Neretti
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI 02912, USA
- Center on the Biology of Aging, Brown University, Providence, RI 02912, USA
| | - Ashley E Webb
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI 02912, USA
- Center on the Biology of Aging, Brown University, Providence, RI 02912, USA
- Carney Institute for Brain Science, Brown University, Providence, RI 02912, USA
- Center for Translational Neuroscience, Brown University, Providence, RI 02912, USA
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158
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Baratta AM, Brandner AJ, Plasil SL, Rice RC, Farris SP. Advancements in Genomic and Behavioral Neuroscience Analysis for the Study of Normal and Pathological Brain Function. Front Mol Neurosci 2022; 15:905328. [PMID: 35813067 PMCID: PMC9259865 DOI: 10.3389/fnmol.2022.905328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Accepted: 06/06/2022] [Indexed: 11/16/2022] Open
Abstract
Psychiatric and neurological disorders are influenced by an undetermined number of genes and molecular pathways that may differ among afflicted individuals. Functionally testing and characterizing biological systems is essential to discovering the interrelationship among candidate genes and understanding the neurobiology of behavior. Recent advancements in genetic, genomic, and behavioral approaches are revolutionizing modern neuroscience. Although these tools are often used separately for independent experiments, combining these areas of research will provide a viable avenue for multidimensional studies on the brain. Herein we will briefly review some of the available tools that have been developed for characterizing novel cellular and animal models of human disease. A major challenge will be openly sharing resources and datasets to effectively integrate seemingly disparate types of information and how these systems impact human disorders. However, as these emerging technologies continue to be developed and adopted by the scientific community, they will bring about unprecedented opportunities in our understanding of molecular neuroscience and behavior.
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Affiliation(s)
- Annalisa M. Baratta
- Center for Neuroscience, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Adam J. Brandner
- Center for Neuroscience, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Sonja L. Plasil
- Department of Pharmacology & Chemical Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Rachel C. Rice
- Center for Neuroscience, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Sean P. Farris
- Center for Neuroscience, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
- Department of Anesthesiology and Perioperative Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
- Department of Biomedical Informatics, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
- *Correspondence: Sean P. Farris,
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159
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Mendelev N, Zamojski M, Amper MAS, Cheng WS, Pincas H, Nair VD, Zaslavsky E, Sealfon SC, Ruf-Zamojski F. Multi-omics profiling of single nuclei from frozen archived postmortem human pituitary tissue. STAR Protoc 2022; 3:101446. [PMID: 35693209 PMCID: PMC9184808 DOI: 10.1016/j.xpro.2022.101446] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Concomitant profiling of transcriptome and chromatin accessibility in isolated nuclei can reveal gene regulatory control mechanisms in health and disease. We report a single nucleus multi-omics analysis protocol optimized for frozen archived postmortem human pituitaries that is also effective for frozen ovine and murine pituitaries and human skeletal muscle biopsies. Its main advantages are that (1) it is not limited to fresh tissue, (2) it avoids tissue dissociation-induced transcriptional changes, and (3) it includes a novel, automated quality control pipeline. For complete details on the use and execution of this protocol, please refer to Ruf-Zamojski et al. (2021) and Zhang et al. (2022).
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Affiliation(s)
- Natalia Mendelev
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai (ISMMS), New York, NY, USA
| | - Michel Zamojski
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai (ISMMS), New York, NY, USA
| | - Mary Anne S. Amper
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai (ISMMS), New York, NY, USA
| | - Wan Sze Cheng
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai (ISMMS), New York, NY, USA
| | - Hanna Pincas
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai (ISMMS), New York, NY, USA
| | - Venugopalan D. Nair
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai (ISMMS), New York, NY, USA
| | - Elena Zaslavsky
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai (ISMMS), New York, NY, USA
| | - Stuart C. Sealfon
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai (ISMMS), New York, NY, USA
| | - Frederique Ruf-Zamojski
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai (ISMMS), New York, NY, USA
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160
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Lv T, Wang X, Yu C, Wang Z, Xiang R, Li L, Yuan Y, Wang Y, Wei X, Yu Y, He X, Zhang L, Deng Q, Wu P, Hou Y, Chen J, Liu C, Wong G, Liu L. A map of bat virus receptors derived from single-cell multiomics. Sci Data 2022; 9:336. [PMID: 35701476 PMCID: PMC9195401 DOI: 10.1038/s41597-022-01447-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 05/20/2022] [Indexed: 11/08/2022] Open
Abstract
Bats are considered reservoirs of many lethal zoonotic viruses and have been implicated in several outbreaks of emerging infectious diseases, such as SARS-CoV, MERS-CoV, and SARS-CoV-2. It is necessary to systematically derive the expression patterns of bat virus receptors and their regulatory features for future research into bat-borne viruses and the prediction and prevention of pandemics. Here, we performed single-nucleus RNA sequencing (snRNA-seq) and single-nucleus assay for transposase-accessible chromatin using sequencing (snATAC-seq) of major organ samples collected from Chinese horseshoe bats (Rhinolophus affinis) and systematically checked the expression pattern of bat-related virus receptors and chromatin accessibility across organs and cell types, providing a valuable dataset for studying the nature of infection among bat-borne viruses.
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Affiliation(s)
- Tianhang Lv
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- BGI-Shenzhen, Shenzhen, 518083, China
| | | | - Chao Yu
- CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Zhifeng Wang
- BGI-Shenzhen, Shenzhen, 518083, China
- Shenzhen Key Laboratory of Single-Cell Omics, BGI-Shenzhen, Shenzhen, 518120, China
| | - Rong Xiang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Linmiao Li
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, 510260, China
| | - Yue Yuan
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Yuhang Wang
- BGI-Shenzhen, Shenzhen, 518083, China
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Xiaoyu Wei
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Yeya Yu
- BGI-Shenzhen, Shenzhen, 518083, China
- BGI College, Zhengzhou University, Zhengzhou, 450000, China
| | - Xiangyang He
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, 510260, China
| | - Libiao Zhang
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, 510260, China
| | - Qiuting Deng
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- BGI-Shenzhen, Shenzhen, 518083, China
| | | | - Yong Hou
- BGI-Shenzhen, Shenzhen, 518083, China
- Shenzhen Key Laboratory of Single-Cell Omics, BGI-Shenzhen, Shenzhen, 518120, China
| | - Jinping Chen
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, 510260, China.
| | - Chuanyu Liu
- BGI-Shenzhen, Shenzhen, 518083, China.
- Shenzhen Bay Laboratory, Shenzhen, 518083, China.
| | - Gary Wong
- CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, 200031, China.
| | - Longqi Liu
- BGI-Shenzhen, Shenzhen, 518083, China.
- Shenzhen Bay Laboratory, Shenzhen, 518083, China.
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161
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Svoboda M, Frost HR, Bosco G. Internal oligo(dT) priming introduces systematic bias in bulk and single-cell RNA sequencing count data. NAR Genom Bioinform 2022; 4:lqac035. [PMID: 35651651 PMCID: PMC9142200 DOI: 10.1093/nargab/lqac035] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 03/25/2022] [Accepted: 04/29/2022] [Indexed: 12/28/2022] Open
Abstract
Significant advances in RNA sequencing have been recently made possible by using oligo(dT) primers for simultaneous mRNA enrichment and reverse transcription priming. The associated increase in efficiency has enabled more economical bulk RNA sequencing methods and the advent of high-throughput single-cell RNA sequencing, already one of the most widely adopted methods in transcriptomics. However, the effects of off-target oligo(dT) priming on gene expression quantification have not been appreciated. In the present study, we describe the extent, the possible causes, and the consequences of internal oligo(dT) priming across multiple public datasets obtained from various bulk and single-cell RNA sequencing platforms. To explore and address this issue, we developed a computational algorithm for RNA counting methods, which identifies the sequencing read alignments that likely resulted from internal oligo(dT) priming and removes them from the data. Directly comparing filtered datasets to those obtained by an alternative method reveals significant improvements in gene expression measurement. Finally, we infer a list of human genes whose expression quantification is most likely to be affected by internal oligo(dT) priming and predict that when measured using these methods, the expression of most genes may be inflated by at least 10% whereby some genes are affected more than others.
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Affiliation(s)
| | - H Robert Frost
- Department of Biomedical Data Science, Geisel School of Medicine, Dartmouth College, Hanover, NH 03755, USA
| | - Giovanni Bosco
- Correspondence may also be addressed to Giovanni Bosco. Tel: +1 603 650 1210; Fax: +1 603 650 1188;
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162
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Gupta V, Frank AM, Matolka N, Lazzaro BP. Inherent constraints on a polyfunctional tissue lead to a reproduction-immunity tradeoff. BMC Biol 2022; 20:127. [PMID: 35655304 PMCID: PMC9161490 DOI: 10.1186/s12915-022-01328-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 05/12/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Single tissues can have multiple functions, which can result in constraints, impaired function, and tradeoffs. The insect fat body performs remarkably diverse functions including metabolic control, reproductive provisioning, and systemic immune responses. How polyfunctional tissues simultaneously execute multiple distinct physiological functions is generally unknown. Immunity and reproduction are observed to trade off in many organisms but the mechanistic basis for this tradeoff is also typically not known. Here we investigate constraints and trade-offs in the polyfunctional insect fat body. RESULTS Using single-nucleus sequencing, we determined that the Drosophila melanogaster fat body executes diverse basal functions with heterogenous cellular subpopulations. The size and identity of these subpopulations are remarkably stable between virgin and mated flies, as well as before and after infection. However, as an emergency function, the immune response engages the entire tissue and all cellular subpopulations produce induce expression of defense genes. We found that reproductively active females who were given bacterial infection exhibited signatures of ER stress and impaired capacity to synthesize new protein in response to infection, including decreased capacity to produce antimicrobial peptides. Transient provision of a reversible translation inhibitor to mated females prior to infection rescued general protein synthesis, specific production of antimicrobial peptides, and survival of infection. CONCLUSIONS The commonly observed tradeoff between reproduction and immunity appears to be driven, in D. melanogaster, by a failure of the fat body to be able to handle simultaneous protein translation demands of reproductive provisioning and immune defense. We suggest that inherent cellular limitations in tissues that perform multiple functions may provide a general explanation for the wide prevalence of physiological and evolutionary tradeoffs.
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Affiliation(s)
- Vanika Gupta
- Department of Entomology, Cornell University, Ithaca, NY, USA.
- Cornell Institute of Host-Microbe Interactions and Disease, Cornell University, Ithaca, NY, USA.
| | - Ashley M Frank
- Department of Entomology, Cornell University, Ithaca, NY, USA
| | - Nick Matolka
- Department of Entomology, Cornell University, Ithaca, NY, USA
| | - Brian P Lazzaro
- Department of Entomology, Cornell University, Ithaca, NY, USA.
- Cornell Institute of Host-Microbe Interactions and Disease, Cornell University, Ithaca, NY, USA.
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163
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Mo Y, Jiao Y. Advances and applications of single-cell omics technologies in plant research. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:1551-1563. [PMID: 35426954 DOI: 10.1111/tpj.15772] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 04/08/2022] [Accepted: 04/11/2022] [Indexed: 06/14/2023]
Abstract
Single-cell sequencing approaches reveal the intracellular dynamics of individual cells and answer biological questions with high-dimensional catalogs of millions of cells, including genomics, transcriptomics, chromatin accessibility, epigenomics, and proteomics data across species. These emerging yet thriving technologies have been fully embraced by the field of plant biology, with a constantly expanding portfolio of applications. Here, we introduce the current technical advances used for single-cell omics, especially single-cell genome and transcriptome sequencing. Firstly, we overview methods for protoplast and nucleus isolation and genome and transcriptome amplification. Subsequently, we use well-executed benchmarking studies to highlight advances made through the application of single-cell omics techniques. Looking forward, we offer a glimpse of additional hurdles and future opportunities that will introduce broad adoption of single-cell sequencing with revolutionary perspectives in plant biology.
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Affiliation(s)
- Yajin Mo
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Center for Quantitative Biology, School of Life Sciences, Peking University, Beijing, 100871, China
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Yuling Jiao
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Center for Quantitative Biology, School of Life Sciences, Peking University, Beijing, 100871, China
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
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164
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MacKenzie A, Hay EA, McEwan AR. Context-dependant enhancers as a reservoir of functional polymorphisms and epigenetic markers linked to alcohol use disorders and comorbidities. ADDICTION NEUROSCIENCE 2022; 2:None. [PMID: 35712020 PMCID: PMC9101288 DOI: 10.1016/j.addicn.2022.100014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 02/18/2022] [Accepted: 03/22/2022] [Indexed: 10/25/2022]
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165
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Li J, Pinto-Duarte A, Zander M, Cuoco MS, Lai CY, Osteen J, Fang L, Luo C, Lucero JD, Gomez-Castanon R, Nery JR, Silva-Garcia I, Pang Y, Sejnowski TJ, Powell SB, Ecker JR, Mukamel EA, Behrens MM. Dnmt3a knockout in excitatory neurons impairs postnatal synapse maturation and increases the repressive histone modification H3K27me3. eLife 2022; 11:e66909. [PMID: 35604009 PMCID: PMC9170249 DOI: 10.7554/elife.66909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 05/22/2022] [Indexed: 11/13/2022] Open
Abstract
Two epigenetic pathways of transcriptional repression, DNA methylation and polycomb repressive complex 2 (PRC2), are known to regulate neuronal development and function. However, their respective contributions to brain maturation are unknown. We found that conditional loss of the de novo DNA methyltransferase Dnmt3a in mouse excitatory neurons altered expression of synapse-related genes, stunted synapse maturation, and impaired working memory and social interest. At the genomic level, loss of Dnmt3a abolished postnatal accumulation of CG and non-CG DNA methylation, leaving adult neurons with an unmethylated, fetal-like epigenomic pattern at ~222,000 genomic regions. The PRC2-associated histone modification, H3K27me3, increased at many of these sites. Our data support a dynamic interaction between two fundamental modes of epigenetic repression during postnatal maturation of excitatory neurons, which together confer robustness on neuronal regulation.
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Affiliation(s)
- Junhao Li
- Department of Cognitive Science, University of California, San DiegoLa JollaUnited States
| | - Antonio Pinto-Duarte
- Computational Neurobiology Laboratory, Salk Institute for Biological StudiesLa JollaUnited States
| | - Mark Zander
- Genomic Analysis Laboratory, Salk Institute for Biological StudiesLa JollaUnited States
| | - Michael S Cuoco
- Bioinformatics and Systems Biology Graduate Program, University of California, San DiegoLa JollaUnited States
| | - Chi-Yu Lai
- Computational Neurobiology Laboratory, Salk Institute for Biological StudiesLa JollaUnited States
| | - Julia Osteen
- Computational Neurobiology Laboratory, Salk Institute for Biological StudiesLa JollaUnited States
| | - Linjing Fang
- Waitt Advanced Biophotonics Core, Salk Institute for Biological StudiesLa JollaUnited States
| | - Chongyuan Luo
- Genomic Analysis Laboratory, Salk Institute for Biological StudiesLa JollaUnited States
- Howard Hughes Medical Institute, Salk Institute for Biological StudiesLa JollaUnited States
| | - Jacinta D Lucero
- Computational Neurobiology Laboratory, Salk Institute for Biological StudiesLa JollaUnited States
| | - Rosa Gomez-Castanon
- Genomic Analysis Laboratory, Salk Institute for Biological StudiesLa JollaUnited States
| | - Joseph R Nery
- Genomic Analysis Laboratory, Salk Institute for Biological StudiesLa JollaUnited States
- Howard Hughes Medical Institute, Salk Institute for Biological StudiesLa JollaUnited States
| | - Isai Silva-Garcia
- Computational Neurobiology Laboratory, Salk Institute for Biological StudiesLa JollaUnited States
| | - Yan Pang
- Computational Neurobiology Laboratory, Salk Institute for Biological StudiesLa JollaUnited States
| | - Terrence J Sejnowski
- Computational Neurobiology Laboratory, Salk Institute for Biological StudiesLa JollaUnited States
| | - Susan B Powell
- Department of Psychiatry, University of California, San DiegoLa JollaUnited States
| | - Joseph R Ecker
- Genomic Analysis Laboratory, Salk Institute for Biological StudiesLa JollaUnited States
| | - Eran A Mukamel
- Department of Cognitive Science, University of California, San DiegoLa JollaUnited States
| | - M Margarita Behrens
- Computational Neurobiology Laboratory, Salk Institute for Biological StudiesLa JollaUnited States
- Department of Psychiatry, University of California, San DiegoLa JollaUnited States
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166
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Rahayel S, Tremblay C, Vo A, Zheng YQ, Lehéricy S, Arnulf I, Vidailhet M, Corvol JC, Gagnon JF, Postuma RB, Montplaisir J, Lewis S, Matar E, Ehgoetz Martens K, Borghammer P, Knudsen K, Hansen A, Monchi O, Misic B, Dagher A. Brain atrophy in prodromal synucleinopathy is shaped by structural connectivity and gene expression. Brain 2022; 145:3162-3178. [PMID: 35594873 DOI: 10.1093/brain/awac187] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 05/06/2022] [Accepted: 05/12/2022] [Indexed: 11/14/2022] Open
Abstract
Isolated REM sleep behaviour disorder (iRBD) is a synucleinopathy characterized by abnormal behaviours and vocalizations during REM sleep. Most iRBD patients develop dementia with Lewy bodies, Parkinson's disease, or multiple system atrophy over time. Patients with iRBD exhibit brain atrophy patterns that are reminiscent of those observed in overt synucleinopathies. However, the mechanisms linking brain atrophy to the underlying alpha-synuclein pathophysiology are poorly understood. Our objective was to investigate how the prion-like and regional vulnerability hypotheses of alpha-synuclein might explain brain atrophy in iRBD. Using a multicentric cohort of 182 polysomnography-confirmed iRBD patients who underwent T1-weighted MRI, we performed vertex-based cortical surface and deformation-based morphometry analyses to quantify brain atrophy in patients (67.8 years, 84% men) and 261 healthy controls (66.2 years, 75%) and investigated the morphological correlates of motor and cognitive functioning in iRBD. Next, we applied the agent-based Susceptible-Infected-Removed model (i.e., a computational model that simulates in silico the spread of pathologic alpha-synuclein based on structural connectivity and gene expression) and tested if it recreated atrophy in iRBD by statistically comparing simulated regional brain atrophy to the atrophy observed in patients. The impact of SNCA and GBA gene expression and brain connectivity was then evaluated by comparing the model fit to the one obtained in null models where either gene expression or connectivity was randomized. The results showed that iRBD patients present with cortical thinning and tissue deformation, which correlated with motor and cognitive functioning. Next, we found that the computational model recreated cortical thinning (r = 0.51, p = 0.0007) and tissue deformation (r = 0.52, p = 0.0005) in patients, and that the connectome's architecture along with SNCA and GBA gene expression contributed to shaping atrophy in iRBD. We further demonstrated that the full agent-based model performed better than network measures or gene expression alone in recreating the atrophy pattern in iRBD. In summary, atrophy in iRBD is extensive, correlates with motor and cognitive function, and can be recreated using the dynamics of agent-based modelling, structural connectivity, and gene expression. These findings support the concepts that both prion-like spread and regional susceptibility account for the atrophy observed in prodromal synucleinopathies. Therefore, the agent-based Susceptible-Infected-Removed model may be a useful tool for testing hypotheses underlying neurodegenerative diseases and new therapies aimed at slowing or stopping the spread of alpha-synuclein pathology.
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Affiliation(s)
- Shady Rahayel
- The Neuro (Montreal Neurological Institute-Hospital), McGill University, Montreal H3A 2B4, Canada.,Centre for Advanced Research in Sleep Medicine, Hôpital du Sacré-Cœur de Montréal, Montreal H4J 1C5, Montreal, Canada
| | - Christina Tremblay
- The Neuro (Montreal Neurological Institute-Hospital), McGill University, Montreal H3A 2B4, Canada
| | - Andrew Vo
- The Neuro (Montreal Neurological Institute-Hospital), McGill University, Montreal H3A 2B4, Canada
| | - Ying-Qiu Zheng
- Wellcome Centre for Integrative Neuroimaging, Centre for Functional Magnetic Resonance Imaging of the Brain, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, United Kingdom
| | - Stéphane Lehéricy
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, INSERM, CNRS, Assistance Publique Hôpitaux de Paris, Pitié-Salpêtrière Hospital, Paris 75013, France
| | - Isabelle Arnulf
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, INSERM, CNRS, Assistance Publique Hôpitaux de Paris, Pitié-Salpêtrière Hospital, Paris 75013, France
| | - Marie Vidailhet
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, INSERM, CNRS, Assistance Publique Hôpitaux de Paris, Pitié-Salpêtrière Hospital, Paris 75013, France
| | - Jean-Christophe Corvol
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, INSERM, CNRS, Assistance Publique Hôpitaux de Paris, Pitié-Salpêtrière Hospital, Paris 75013, France
| | | | - Jean-François Gagnon
- Centre for Advanced Research in Sleep Medicine, Hôpital du Sacré-Cœur de Montréal, Montreal H4J 1C5, Montreal, Canada.,Department of Psychology, Université du Québec à Montréal, Montreal H2X 3P2, Canada.,Research Centre, Institut universitaire de gériatrie de Montréal, Montreal H3W 1W5, Canada
| | - Ronald B Postuma
- Centre for Advanced Research in Sleep Medicine, Hôpital du Sacré-Cœur de Montréal, Montreal H4J 1C5, Montreal, Canada.,Department of Neurology, Montreal General Hospital, Montreal H3G 1A4, Canada
| | - Jacques Montplaisir
- Centre for Advanced Research in Sleep Medicine, Hôpital du Sacré-Cœur de Montréal, Montreal H4J 1C5, Montreal, Canada.,Department of Psychiatry, Université de Montréal, Montreal H3 T 1J4, Canada
| | - Simon Lewis
- ForeFront Parkinson's Disease Research Clinic, Brain and Mind Centre, University of Sydney, Camperdown NSW 2050, Australia
| | - Elie Matar
- ForeFront Parkinson's Disease Research Clinic, Brain and Mind Centre, University of Sydney, Camperdown NSW 2050, Australia
| | - Kaylena Ehgoetz Martens
- ForeFront Parkinson's Disease Research Clinic, Brain and Mind Centre, University of Sydney, Camperdown NSW 2050, Australia.,Department of Kinesiology and Health Sciences, University of Waterloo, Waterloo N2L 3G1, Canada
| | - Per Borghammer
- Department of Nuclear Medicine and PET, Aarhus University Hospital, Aarhus DK-8200, Denmark
| | - Karoline Knudsen
- Department of Nuclear Medicine and PET, Aarhus University Hospital, Aarhus DK-8200, Denmark
| | - Allan Hansen
- Department of Nuclear Medicine and PET, Aarhus University Hospital, Aarhus DK-8200, Denmark
| | - Oury Monchi
- Research Centre, Institut universitaire de gériatrie de Montréal, Montreal H3W 1W5, Canada.,Departments of Clinical Neurosciences, Radiology, and Hotchkiss Brain Institute, University of Calgary, Calgary T2N 4N1, Canada
| | - Bratislav Misic
- The Neuro (Montreal Neurological Institute-Hospital), McGill University, Montreal H3A 2B4, Canada
| | - Alain Dagher
- The Neuro (Montreal Neurological Institute-Hospital), McGill University, Montreal H3A 2B4, Canada
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167
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Zhang QY, Ho DWH, Tsui YM, Ng IOL. Single-Cell Transcriptomics of Liver Cancer: Hype or Insights? Cell Mol Gastroenterol Hepatol 2022; 14:513-525. [PMID: 35577269 PMCID: PMC9294331 DOI: 10.1016/j.jcmgh.2022.04.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 04/24/2022] [Accepted: 04/29/2022] [Indexed: 12/13/2022]
Abstract
Hepatocellular carcinoma (HCC) is characterized by its high degrees of both inter- and intratumoral heterogeneity. Its complex tumor microenvironment is also crucial in promoting tumor progression. Recent advances in single-cell RNA sequencing provide an important highway to characterize the underlying pathogenesis and heterogeneity of HCC in an unprecedented degree of resolution. This review discusses the up-to-date discoveries from the latest studies of HCC with respect to the strength of single-cell RNA sequencing. We discuss its use in the dissection of the landscape of the intricate HCC ecosystem and highlight the major features at cellular levels, including the malignant cells, different immune cell types, and the various cell-cell interactions, which are crucial for developing effective immunotherapies. Finally, its translational applications will be discussed. Altogether, these explorations may give us some hints at the tumor growth and progression and drug resistance and recurrence, particularly in this era of personalized medicine.
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Affiliation(s)
- Qing-Yang Zhang
- Department of Pathology and State Key Laboratory of Liver Research, The University of Hong Kong, Hong Kong
| | - Daniel Wai-Hung Ho
- Department of Pathology and State Key Laboratory of Liver Research, The University of Hong Kong, Hong Kong
| | - Yu-Man Tsui
- Department of Pathology and State Key Laboratory of Liver Research, The University of Hong Kong, Hong Kong
| | - Irene Oi-Lin Ng
- Department of Pathology and State Key Laboratory of Liver Research, The University of Hong Kong, Hong Kong.
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168
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Kalinina A, Lagace D. Single-Cell and Single-Nucleus RNAseq Analysis of Adult Neurogenesis. Cells 2022; 11:1633. [PMID: 35626670 PMCID: PMC9139993 DOI: 10.3390/cells11101633] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 05/02/2022] [Accepted: 05/07/2022] [Indexed: 02/04/2023] Open
Abstract
The complexity of adult neurogenesis is becoming increasingly apparent as we learn more about cellular heterogeneity and diversity of the neurogenic lineages and stem cell niches within the adult brain. This complexity has been unraveled in part due to single-cell and single-nucleus RNA sequencing (sc-RNAseq and sn-RNAseq) studies that have focused on adult neurogenesis. This review summarizes 33 published studies in the field of adult neurogenesis that have used sc- or sn-RNAseq methods to answer questions about the three main regions that host adult neural stem cells (NSCs): the subventricular zone (SVZ), the dentate gyrus (DG) of the hippocampus, and the hypothalamus. The review explores the similarities and differences in methodology between these studies and provides an overview of how these studies have advanced the field and expanded possibilities for the future.
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Affiliation(s)
| | - Diane Lagace
- Neuroscience Program, Department of Cellular and Molecular Medicine, Ottawa Hospital Research Institute, Brain and Mind Research Institute, University of Ottawa, Ottawa, ON K1H 8M5, Canada;
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169
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Williams K, Yokomori K, Mortazavi A. Heterogeneous Skeletal Muscle Cell and Nucleus Populations Identified by Single-Cell and Single-Nucleus Resolution Transcriptome Assays. Front Genet 2022; 13:835099. [PMID: 35646075 PMCID: PMC9136090 DOI: 10.3389/fgene.2022.835099] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 03/25/2022] [Indexed: 11/13/2022] Open
Abstract
Single-cell RNA-seq (scRNA-seq) has revolutionized modern genomics, but the large size of myotubes and myofibers has restricted use of scRNA-seq in skeletal muscle. For the study of muscle, single-nucleus RNA-seq (snRNA-seq) has emerged not only as an alternative to scRNA-seq, but as a novel method providing valuable insights into multinucleated cells such as myofibers. Nuclei within myofibers specialize at junctions with other cell types such as motor neurons. Nuclear heterogeneity plays important roles in certain diseases such as muscular dystrophies. We survey current methods of high-throughput single cell and subcellular resolution transcriptomics, including single-cell and single-nucleus RNA-seq and spatial transcriptomics, applied to satellite cells, myoblasts, myotubes and myofibers. We summarize the major myonuclei subtypes identified in homeostatic and regenerating tissue including those specific to fiber type or at junctions with other cell types. Disease-specific nucleus populations were found in two muscular dystrophies, FSHD and Duchenne muscular dystrophy, demonstrating the importance of performing transcriptome studies at the single nucleus level in muscle.
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Affiliation(s)
- Katherine Williams
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, United States
- Center for Complex Biological Systems, University of California, Irvine, Irvine, CA, United States
| | - Kyoko Yokomori
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, United States
| | - Ali Mortazavi
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, United States
- Center for Complex Biological Systems, University of California, Irvine, Irvine, CA, United States
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170
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Jia Q, Chu H, Jin Z, Long H, Zhu B. High-throughput single-сell sequencing in cancer research. Signal Transduct Target Ther 2022; 7:145. [PMID: 35504878 PMCID: PMC9065032 DOI: 10.1038/s41392-022-00990-4] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 03/23/2022] [Accepted: 04/08/2022] [Indexed: 12/22/2022] Open
Abstract
With advances in sequencing and instrument technology, bioinformatics analysis is being applied to batches of massive cells at single-cell resolution. High-throughput single-cell sequencing can be utilized for multi-omics characterization of tumor cells, stromal cells or infiltrated immune cells to evaluate tumor progression, responses to environmental perturbations, heterogeneous composition of the tumor microenvironment, and complex intercellular interactions between these factors. Particularly, single-cell sequencing of T cell receptors, alone or in combination with single-cell RNA sequencing, is useful in the fields of tumor immunology and immunotherapy. Clinical insights obtained from single-cell analysis are critically important for exploring the biomarkers of disease progression or antitumor treatment, as well as for guiding precise clinical decision-making for patients with malignant tumors. In this review, we summarize the clinical applications of single-cell sequencing in the fields of tumor cell evolution, tumor immunology, and tumor immunotherapy. Additionally, we analyze the tumor cell response to antitumor treatment, heterogeneity of the tumor microenvironment, and response or resistance to immune checkpoint immunotherapy. The limitations of single-cell analysis in cancer research are also discussed.
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Affiliation(s)
- Qingzhu Jia
- Institute of Cancer, Xinqiao Hospital, Army Medical University, Chongqing, 400037, China.,Chongqing Key Laboratory of Immunotherapy, Chongqing, 400037, China
| | - Han Chu
- Institute of Cancer, Xinqiao Hospital, Army Medical University, Chongqing, 400037, China.,Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resources and Eco-Environment, College of Life Sciences, Sichuan University, Chengdu, 610064, China
| | - Zheng Jin
- Research Institute, GloriousMed Clinical Laboratory Co., Ltd, Shanghai, 201318, China
| | - Haixia Long
- Institute of Cancer, Xinqiao Hospital, Army Medical University, Chongqing, 400037, China. .,Chongqing Key Laboratory of Immunotherapy, Chongqing, 400037, China.
| | - Bo Zhu
- Institute of Cancer, Xinqiao Hospital, Army Medical University, Chongqing, 400037, China. .,Chongqing Key Laboratory of Immunotherapy, Chongqing, 400037, China.
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171
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Sokhadze G, Campbell PW, Charalambakis N, Govindaiah G, Guido W, McGee AW. Cre driver mouse lines for thalamocortical circuit mapping. J Comp Neurol 2022; 530:1049-1063. [PMID: 34545582 PMCID: PMC9891227 DOI: 10.1002/cne.25248] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Revised: 08/16/2021] [Accepted: 09/07/2021] [Indexed: 02/04/2023]
Abstract
Subpopulations of neurons and associated neural circuits can be targeted in mice with genetic tools in a highly selective manner for visualization and manipulation. However, there are not well-defined Cre "driver" lines that target the expression of Cre recombinase to thalamocortical (TC) neurons. Here, we characterize three Cre driver lines for the nuclei of the dorsal thalamus: Oligodendrocyte transcription factor 3 (Olig3)-Cre, histidine decarboxylase (HDC)-Cre, and corticotropin-releasing hormone (CRH)-Cre. We examined the postnatal distribution of Cre expression for each of these lines with the Cre-dependent reporter CAG-tdTomato (Ai9). Cre-dependent expression of tdTomato reveals that Olig3-Cre expresses broadly within the thalamus, including TC neurons and interneurons, while HDC-Cre and CRH-Cre each have unique patterns of expression restricted to TC neurons within and across the sensory relay nuclei of the dorsal thalamus. Cre expression is present by the time of natural birth in all three lines, underscoring their utility for developmental studies. To demonstrate the utility of these Cre drivers for studying sensory TC circuitry, we targeted the expression of channelrhodopsin-2 to thalamus from the CAG-COP4*H134R/EYFP (Ai32) allele with either HDC-Cre or CRH-Cre. Optogenetic activation of TC afferents in primary visual cortex was sufficient to measure frequency-dependent depression. Thus, these Cre drivers provide selective Cre-dependent gene expression in thalamus suitable for both anatomical and functional studies.
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Affiliation(s)
- Guela Sokhadze
- Department of Anatomical Sciences and Neurobiology University of Louisville School of Medicine Louisville Kentucky USA
| | - Peter W. Campbell
- Department of Anatomical Sciences and Neurobiology University of Louisville School of Medicine Louisville Kentucky USA
| | - Naomi Charalambakis
- Department of Anatomical Sciences and Neurobiology University of Louisville School of Medicine Louisville Kentucky USA
| | - Gubbi Govindaiah
- Department of Anatomical Sciences and Neurobiology University of Louisville School of Medicine Louisville Kentucky USA
| | - William Guido
- Department of Anatomical Sciences and Neurobiology University of Louisville School of Medicine Louisville Kentucky USA
| | - Aaron W. McGee
- Department of Anatomical Sciences and Neurobiology University of Louisville School of Medicine Louisville Kentucky USA
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172
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Abstract
Altered lipid metabolism is a characteristic feature and potential driving factor of acute kidney injury (AKI). Of the lipids that accumulate in injured renal tissues, ceramides are potent regulators of metabolism and cell fate. Up-regulation of ceramide synthesis is a common feature shared across several AKI etiologies in vitro and in vivo. Furthermore, ceramide accumulation is an early event in the natural history of AKI that precedes cell death and organ dysfunction. Emerging evidence suggests that inhibition of ceramide accumulation may improve renal outcomes in several models of AKI. This review examines the landscape of ceramide metabolism and regulation in the healthy and injured kidney. Furthermore, we discuss the body of literature regarding ceramides as therapeutic targets for AKI and consider potential mechanisms by which ceramides drive kidney pathogenesis.
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Affiliation(s)
- Rebekah J Nicholson
- Department of Nutrition and Integrative Physiology, Diabetes and Metabolism Research Center, University of Utah, Salt Lake City, UT
| | - William L Holland
- Department of Nutrition and Integrative Physiology, Diabetes and Metabolism Research Center, University of Utah, Salt Lake City, UT
| | - Scott A Summers
- Department of Nutrition and Integrative Physiology, Diabetes and Metabolism Research Center, University of Utah, Salt Lake City, UT.
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173
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Kamath T, Abdulraouf A, Burris SJ, Langlieb J, Gazestani V, Nadaf NM, Balderrama K, Vanderburg C, Macosko EZ. Single-cell genomic profiling of human dopamine neurons identifies a population that selectively degenerates in Parkinson's disease. Nat Neurosci 2022; 25:588-595. [PMID: 35513515 PMCID: PMC9076534 DOI: 10.1038/s41593-022-01061-1] [Citation(s) in RCA: 158] [Impact Index Per Article: 79.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 03/24/2022] [Indexed: 12/14/2022]
Abstract
The loss of dopamine (DA) neurons within the substantia nigra pars compacta (SNpc) is a defining pathological hallmark of Parkinson's disease (PD). Nevertheless, the molecular features associated with DA neuron vulnerability have not yet been fully identified. Here, we developed a protocol to enrich and transcriptionally profile DA neurons from patients with PD and matched controls, sampling a total of 387,483 nuclei, including 22,048 DA neuron profiles. We identified ten populations and spatially localized each within the SNpc using Slide-seq. A single subtype, marked by the expression of the gene AGTR1 and spatially confined to the ventral tier of SNpc, was highly susceptible to loss in PD and showed the strongest upregulation of targets of TP53 and NR2F2, nominating molecular processes associated with degeneration. This same vulnerable population was specifically enriched for the heritable risk associated with PD, highlighting the importance of cell-intrinsic processes in determining the differential vulnerability of DA neurons to PD-associated degeneration.
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Affiliation(s)
- Tushar Kamath
- Broad Institute of Harvard and MIT, Stanley Center for Psychiatric Research, Cambridge, MA, USA
- Harvard Graduate Program in Biophysics, Harvard University, Cambridge, MA, USA
| | - Abdulraouf Abdulraouf
- Broad Institute of Harvard and MIT, Stanley Center for Psychiatric Research, Cambridge, MA, USA
| | - S J Burris
- Broad Institute of Harvard and MIT, Stanley Center for Psychiatric Research, Cambridge, MA, USA
| | - Jonah Langlieb
- Broad Institute of Harvard and MIT, Stanley Center for Psychiatric Research, Cambridge, MA, USA
| | - Vahid Gazestani
- Broad Institute of Harvard and MIT, Stanley Center for Psychiatric Research, Cambridge, MA, USA
| | - Naeem M Nadaf
- Broad Institute of Harvard and MIT, Stanley Center for Psychiatric Research, Cambridge, MA, USA
| | - Karol Balderrama
- Broad Institute of Harvard and MIT, Stanley Center for Psychiatric Research, Cambridge, MA, USA
| | - Charles Vanderburg
- Broad Institute of Harvard and MIT, Stanley Center for Psychiatric Research, Cambridge, MA, USA
| | - Evan Z Macosko
- Broad Institute of Harvard and MIT, Stanley Center for Psychiatric Research, Cambridge, MA, USA.
- Massachusetts General Hospital, Department of Psychiatry, Boston, MA, USA.
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174
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Ikeda-Yorifuji I, Tsujioka H, Sakata Y, Yamashita T. Single-nucleus RNA sequencing identified cells with ependymal cell-like features enriched in neonatal mice after spinal cord injury. Neurosci Res 2022; 181:22-38. [PMID: 35452717 DOI: 10.1016/j.neures.2022.04.006] [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: 12/16/2021] [Revised: 04/09/2022] [Accepted: 04/15/2022] [Indexed: 11/30/2022]
Abstract
The adult mammalian central nervous system has limited regenerative ability, and spinal cord injury (SCI) often causes lifelong motor disability. While regeneration is limited in adults, injured spinal cord tissue can be regenerated and neural function can be almost completely restored in neonates. However, difference of cellular composition in lesion has not been well characterized. To gain insight into the age-dependent cellular reaction after SCI, we performed single-nucleus RNA sequencing, analyzing 4,076 nuclei from sham and injured spinal cords from adult and neonatal mice. Clustering analysis identified 18 cell populations. We identified previously undescribed cells with ependymal cell-like gene expression profile, the number of which was increased in neonates after SCI. Histological analysis revealed that these cells line the central canal under physiological conditions in both adults and neonates. We confirmed that they were enriched in the lesion only in neonates. We further showed that these cells were positive for the cellular markers of ependymal cells, astrocytes and radial glial cells. This study provides a deeper understanding of neonate-specific cellular responses after SCI, which may determine regenerative capacity.
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Affiliation(s)
- Iyo Ikeda-Yorifuji
- Department of Molecular Neuroscience, Graduate School of Medicine, Osaka University, Osaka, Japan; Department of Cardiovascular Medicine, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Hiroshi Tsujioka
- Department of Molecular Neuroscience, Graduate School of Medicine, Osaka University, Osaka, Japan; WPI Immunology Frontier Research Center, Osaka University, Suita, Japan.
| | - Yasushi Sakata
- Department of Cardiovascular Medicine, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Toshihide Yamashita
- Department of Molecular Neuroscience, Graduate School of Medicine, Osaka University, Osaka, Japan; WPI Immunology Frontier Research Center, Osaka University, Suita, Japan; Department of Molecular Neuroscience, Graduate School of Frontier Biosciences, Osaka University, Suita, Japan; Department of Neuro-Medical Science, Graduate School of Medicine, Osaka University, Suita, Japan.
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175
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Han L, Wei X, Liu C, Volpe G, Zhuang Z, Zou X, Wang Z, Pan T, Yuan Y, Zhang X, Fan P, Guo P, Lai Y, Lei Y, Liu X, Yu F, Shangguan S, Lai G, Deng Q, Liu Y, Wu L, Shi Q, Yu H, Huang Y, Cheng M, Xu J, Liu Y, Wang M, Wang C, Zhang Y, Xie D, Yang Y, Yu Y, Zheng H, Wei Y, Huang F, Lei J, Huang W, Zhu Z, Lu H, Wang B, Wei X, Chen F, Yang T, Du W, Chen J, Xu S, An J, Ward C, Wang Z, Pei Z, Wong CW, Liu X, Zhang H, Liu M, Qin B, Schambach A, Isern J, Feng L, Liu Y, Guo X, Liu Z, Sun Q, Maxwell PH, Barker N, Muñoz-Cánoves P, Gu Y, Mulder J, Uhlen M, Tan T, Liu S, Yang H, Wang J, Hou Y, Xu X, Esteban MA, Liu L. Cell transcriptomic atlas of the non-human primate Macaca fascicularis. Nature 2022; 604:723-731. [PMID: 35418686 DOI: 10.1038/s41586-022-04587-3] [Citation(s) in RCA: 68] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 02/23/2022] [Indexed: 12/22/2022]
Abstract
Studying tissue composition and function in non-human primates (NHPs) is crucial to understand the nature of our own species. Here we present a large-scale cell transcriptomic atlas that encompasses over 1 million cells from 45 tissues of the adult NHP Macaca fascicularis. This dataset provides a vast annotated resource to study a species phylogenetically close to humans. To demonstrate the utility of the atlas, we have reconstructed the cell-cell interaction networks that drive Wnt signalling across the body, mapped the distribution of receptors and co-receptors for viruses causing human infectious diseases, and intersected our data with human genetic disease orthologues to establish potential clinical associations. Our M. fascicularis cell atlas constitutes an essential reference for future studies in humans and NHPs.
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Affiliation(s)
- Lei Han
- BGI-Shenzhen, Shenzhen, China.,BGI-Beijing, Beijing, China.,Shenzhen Bay Laboratory, Shenzhen, China
| | - Xiaoyu Wei
- BGI-Shenzhen, Shenzhen, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Chuanyu Liu
- BGI-Shenzhen, Shenzhen, China.,BGI-Beijing, Beijing, China.,Shenzhen Bay Laboratory, Shenzhen, China
| | - Giacomo Volpe
- Hematology and Cell Therapy Unit, IRCCS-Istituto Tumori 'Giovanni Paolo II', Bari, Italy
| | - Zhenkun Zhuang
- BGI-Shenzhen, Shenzhen, China.,School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Xuanxuan Zou
- BGI-Shenzhen, Shenzhen, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Zhifeng Wang
- BGI-Shenzhen, Shenzhen, China.,BGI-Beijing, Beijing, China
| | - Taotao Pan
- BGI-Shenzhen, Shenzhen, China.,BGI-Beijing, Beijing, China
| | - Yue Yuan
- BGI-Shenzhen, Shenzhen, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Xiao Zhang
- State Key Laboratory for Zoonotic Diseases, Key Laboratory for Zoonosis Research of Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Peng Fan
- State Key Laboratory for Zoonotic Diseases, Key Laboratory for Zoonosis Research of Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Pengcheng Guo
- State Key Laboratory for Zoonotic Diseases, Key Laboratory for Zoonosis Research of Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Yiwei Lai
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Ying Lei
- BGI-Shenzhen, Shenzhen, China.,BGI-Beijing, Beijing, China.,Shenzhen Bay Laboratory, Shenzhen, China
| | - Xingyuan Liu
- State Key Laboratory for Zoonotic Diseases, Key Laboratory for Zoonosis Research of Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Feng Yu
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Shuncheng Shangguan
- Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health and Guangzhou Medical University, Guangzhou, China
| | - Guangyao Lai
- Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health and Guangzhou Medical University, Guangzhou, China
| | - Qiuting Deng
- BGI-Shenzhen, Shenzhen, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Ya Liu
- BGI-Shenzhen, Shenzhen, China.,BGI-Beijing, Beijing, China
| | - Liang Wu
- BGI-Shenzhen, Shenzhen, China.,BGI-Beijing, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Quan Shi
- BGI-Shenzhen, Shenzhen, China.,Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Hao Yu
- BGI-Shenzhen, Shenzhen, China
| | - Yunting Huang
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Mengnan Cheng
- BGI-Shenzhen, Shenzhen, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Jiangshan Xu
- BGI-Shenzhen, Shenzhen, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yang Liu
- BGI-Shenzhen, Shenzhen, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | | | - Chunqing Wang
- BGI-Shenzhen, Shenzhen, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yuanhang Zhang
- BGI-Shenzhen, Shenzhen, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Duo Xie
- BGI-Shenzhen, Shenzhen, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yunzhi Yang
- BGI College and Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | - Yeya Yu
- BGI College and Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | - Huiwen Zheng
- BGI College and Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | - Yanrong Wei
- BGI College and Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | - Fubaoqian Huang
- BGI-Shenzhen, Shenzhen, China.,School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Junjie Lei
- BGI-Shenzhen, Shenzhen, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Waidong Huang
- BGI-Shenzhen, Shenzhen, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Zhiyong Zhu
- BGI-Shenzhen, Shenzhen, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Haorong Lu
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Bo Wang
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Xiaofeng Wei
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Fengzhen Chen
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Tao Yang
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Wensi Du
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Jing Chen
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Shibo Xu
- Institute for Stem Cells and Neural Regeneration, School of Pharmacy, State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
| | - Juan An
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,University of Science and Technology of China, Hefei, China
| | - Carl Ward
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Zongren Wang
- Department of Urology, First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Zhong Pei
- Department of Neurology, First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | | | - Xiaolei Liu
- State Key Laboratory for Zoonotic Diseases, Key Laboratory for Zoonosis Research of Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Huafeng Zhang
- Department of Orthopedics, Tianjin Medical University General Hospital, Tianjin, China
| | - Mingyuan Liu
- State Key Laboratory for Zoonotic Diseases, Key Laboratory for Zoonosis Research of Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Baoming Qin
- Laboratory of Metabolism and Cell Fate, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Axel Schambach
- Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany.,Division of Hematology/Oncology, Harvard Medical School, MA, Boston, USA
| | - Joan Isern
- Spanish National Center for Cardiovascular Research (CNIC), Madrid, Spain
| | - Liqiang Feng
- State Key Laboratory of Respiratory Diseases, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Yan Liu
- Institute for Stem Cells and Neural Regeneration, School of Pharmacy, State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
| | - Xiangyu Guo
- Jinan University, Guangzhou, China.,Hubei Topgene Biotechnology Co., Ltd, Wuhan, China
| | - Zhen Liu
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Key Laboratory of Primate Neurobiology, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
| | - Qiang Sun
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Key Laboratory of Primate Neurobiology, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
| | - Patrick H Maxwell
- Cambridge Institute for Medical Research, Department of Medicine, University of Cambridge, Cambridge, UK
| | - Nick Barker
- A*STAR Institute of Molecular and Cell Biology, Singapore, Singapore
| | - Pura Muñoz-Cánoves
- Department of Experimental and Health Sciences, Pompeu Fabra University (UPF), ICREA and CIBERNED, Barcelona, Spain
| | - Ying Gu
- BGI-Shenzhen, Shenzhen, China
| | - Jan Mulder
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden.,Department of Neuroscience, Karolinska Institute, Stockholm, Sweden
| | - Mathias Uhlen
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden.,Department of Neuroscience, Karolinska Institute, Stockholm, Sweden
| | - Tao Tan
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, China
| | - Shiping Liu
- BGI-Shenzhen, Shenzhen, China.,BGI-Beijing, Beijing, China.,Shenzhen Bay Laboratory, Shenzhen, China
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen, China.,James D. Watson Institute of Genome Sciences, Hangzhou, China
| | - Jian Wang
- BGI-Shenzhen, Shenzhen, China.,James D. Watson Institute of Genome Sciences, Hangzhou, China
| | - Yong Hou
- BGI-Shenzhen, Shenzhen, China. .,BGI-Beijing, Beijing, China. .,Shenzhen Bay Laboratory, Shenzhen, China. .,BGI College and Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China.
| | - Xun Xu
- BGI-Shenzhen, Shenzhen, China. .,BGI-Beijing, Beijing, China. .,BGI College and Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China. .,Guangdong Provincial Key Laboratory of Genome Read and Write, Shenzhen, China.
| | - Miguel A Esteban
- State Key Laboratory for Zoonotic Diseases, Key Laboratory for Zoonosis Research of Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun, China. .,Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China. .,Institute of Stem Cells and Regeneration, Chinese Academy of Sciences, Beijing, China.
| | - Longqi Liu
- BGI-Shenzhen, Shenzhen, China. .,BGI-Beijing, Beijing, China. .,Shenzhen Bay Laboratory, Shenzhen, China. .,BGI College and Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China.
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176
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Xu J, Hao S, Shi Q, Deng Q, Jiang Y, Guo P, Yuan Y, Shi X, Shangguan S, Zheng H, Lai G, Huang Y, Wang Y, Song Y, Liu Y, Wu L, Wang Z, Cheng J, Wei X, Cheng M, Lai Y, Volpe G, Esteban MA, Hou Y, Liu C, Liu L. Transcriptomic Profile of the Mouse Postnatal Liver Development by Single-Nucleus RNA Sequencing. Front Cell Dev Biol 2022; 10:833392. [PMID: 35465320 PMCID: PMC9019599 DOI: 10.3389/fcell.2022.833392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Accepted: 03/11/2022] [Indexed: 11/13/2022] Open
Affiliation(s)
- Jiangshan Xu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- BGI-Shenzhen, Shenzhen, China
| | - Shijie Hao
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- BGI-Shenzhen, Shenzhen, China
| | - Quan Shi
- BGI-Shenzhen, Shenzhen, China
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Qiuting Deng
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- BGI-Shenzhen, Shenzhen, China
| | - Yujia Jiang
- BGI-Shenzhen, Shenzhen, China
- BGI College and Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | - Pengcheng Guo
- State Key Laboratory for Zoonotic Diseases, Key Laboratory for Zoonosis Research of Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun, China
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Yue Yuan
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- BGI-Shenzhen, Shenzhen, China
| | - Xuyang Shi
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- BGI-Shenzhen, Shenzhen, China
| | - Shuncheng Shangguan
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Joint School of Life Sciences, Guangzhou Medical University and Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Huiwen Zheng
- BGI-Shenzhen, Shenzhen, China
- BGI College and Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | - Guangyao Lai
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Joint School of Life Sciences, Guangzhou Medical University and Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | | | | | | | | | - Liang Wu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- BGI-Shenzhen, Shenzhen, China
| | | | - Jiehui Cheng
- Guangdong Hospital of Traditional Chinese Medicine, Zhuhai, China
| | | | - Mengnan Cheng
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- BGI-Shenzhen, Shenzhen, China
| | - Yiwei Lai
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Giacomo Volpe
- Hematology and Cell Therapy Unit, IRCCS-Istituto Tumori‘Giovanni Paolo II’, Bari, Italy
| | - Miguel A. Esteban
- BGI-Shenzhen, Shenzhen, China
- State Key Laboratory for Zoonotic Diseases, Key Laboratory for Zoonosis Research of Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun, China
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China
| | | | | | - Longqi Liu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- BGI-Shenzhen, Shenzhen, China
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177
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Cable DM, Murray E, Zou LS, Goeva A, Macosko EZ, Chen F, Irizarry RA. Robust decomposition of cell type mixtures in spatial transcriptomics. Nat Biotechnol 2022; 40:517-526. [PMID: 33603203 PMCID: PMC8606190 DOI: 10.1038/s41587-021-00830-w] [Citation(s) in RCA: 345] [Impact Index Per Article: 172.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 12/31/2020] [Indexed: 02/07/2023]
Abstract
A limitation of spatial transcriptomics technologies is that individual measurements may contain contributions from multiple cells, hindering the discovery of cell-type-specific spatial patterns of localization and expression. Here, we develop robust cell type decomposition (RCTD), a computational method that leverages cell type profiles learned from single-cell RNA-seq to decompose cell type mixtures while correcting for differences across sequencing technologies. We demonstrate the ability of RCTD to detect mixtures and identify cell types on simulated datasets. Furthermore, RCTD accurately reproduces known cell type and subtype localization patterns in Slide-seq and Visium datasets of the mouse brain. Finally, we show how RCTD's recovery of cell type localization enables the discovery of genes within a cell type whose expression depends on spatial environment. Spatial mapping of cell types with RCTD enables the spatial components of cellular identity to be defined, uncovering new principles of cellular organization in biological tissue. RCTD is publicly available as an open-source R package at https://github.com/dmcable/RCTD .
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Affiliation(s)
- Dylan M. Cable
- Department of Electrical Engineering and Computer Science, MIT, Cambridge, MA, 02139,Broad Institute of Harvard and MIT, Cambridge, MA, 02142,Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, 02215
| | - Evan Murray
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142
| | - Luli S. Zou
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142,Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, 02215,Department of Biostatistics, Harvard University, Boston, MA, 02115
| | | | - Evan Z. Macosko
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142,Department of Psychiatry, Massachusetts General Hospital, Boston, MA, 02114
| | - Fei Chen
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142,Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge MA 02138
| | - Rafael A. Irizarry
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, 02215,Department of Biostatistics, Harvard University, Boston, MA, 02115
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178
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Efthymiou V, Patti ME. It Is Not Just Fat: Dissecting the Heterogeneity of Adipose Tissue Function. Curr Diab Rep 2022; 22:177-187. [PMID: 35267142 DOI: 10.1007/s11892-022-01455-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/11/2022] [Indexed: 11/03/2022]
Abstract
PURPOSE OF REVIEW The purpose of the current review is to summarize findings from the most recent and impactful studies which investigated human and mouse adipose tissue transcriptomes at a single-cell level. We provide perspective about the potential importance of data derived from these single-cell technologies in improving our understanding of the adipose organ and metabolic disease and likely future directions of this approach. RECENT FINDINGS The majority of single-cell or single-nuclei studies of the adipose organ so far have focused on investigating the stromal-vascular fraction (SVF) of mouse subcutaneous and intraabdominal white and interscapular brown fat depots. Few studies have also evaluated the impact of additional factors as drivers of adipose phenotypes, such as high-fat diet-induced obesity, adolescence, aging, and cold exposure. Recent studies have also investigated human cell lines and human fat biopsies across a range of body mass index (BMI) and in response to insulin resistance or T2D. These studies have identified numerous previously unexplored subpopulations of adipocyte progenitors, immune cells, and mature adipocytes in both mice and men. Single-cell and single-nuclei technologies have brought an explosion of data that have advanced our understanding of the adipose organ in health and disease. However, we are still at the dawn of achieving a complete and comprehensive map of the mouse and human adipose organ. Multi-modal single-cell approaches to identify both anatomic localization of specific cellular populations and epigenetic mechanisms responsible for observed transcriptomic patterns are underway and will likely provide an even deeper understanding of the adipose organ in response to health and disease.
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Affiliation(s)
- Vissarion Efthymiou
- Department of Integrative Physiology and Metabolism, Research Division, Joslin Diabetes Center, Boston, MA, 02215, USA
- Harvard Medical School, Boston, MA, 02215, USA
| | - Mary-Elizabeth Patti
- Department of Integrative Physiology and Metabolism, Research Division, Joslin Diabetes Center, Boston, MA, 02215, USA.
- Harvard Medical School, Boston, MA, 02215, USA.
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179
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Wang M, Song WM, Ming C, Wang Q, Zhou X, Xu P, Krek A, Yoon Y, Ho L, Orr ME, Yuan GC, Zhang B. Guidelines for bioinformatics of single-cell sequencing data analysis in Alzheimer's disease: review, recommendation, implementation and application. Mol Neurodegener 2022; 17:17. [PMID: 35236372 PMCID: PMC8889402 DOI: 10.1186/s13024-022-00517-z] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Accepted: 01/18/2022] [Indexed: 12/13/2022] Open
Abstract
Alzheimer's disease (AD) is the most common form of dementia, characterized by progressive cognitive impairment and neurodegeneration. Extensive clinical and genomic studies have revealed biomarkers, risk factors, pathways, and targets of AD in the past decade. However, the exact molecular basis of AD development and progression remains elusive. The emerging single-cell sequencing technology can potentially provide cell-level insights into the disease. Here we systematically review the state-of-the-art bioinformatics approaches to analyze single-cell sequencing data and their applications to AD in 14 major directions, including 1) quality control and normalization, 2) dimension reduction and feature extraction, 3) cell clustering analysis, 4) cell type inference and annotation, 5) differential expression, 6) trajectory inference, 7) copy number variation analysis, 8) integration of single-cell multi-omics, 9) epigenomic analysis, 10) gene network inference, 11) prioritization of cell subpopulations, 12) integrative analysis of human and mouse sc-RNA-seq data, 13) spatial transcriptomics, and 14) comparison of single cell AD mouse model studies and single cell human AD studies. We also address challenges in using human postmortem and mouse tissues and outline future developments in single cell sequencing data analysis. Importantly, we have implemented our recommended workflow for each major analytic direction and applied them to a large single nucleus RNA-sequencing (snRNA-seq) dataset in AD. Key analytic results are reported while the scripts and the data are shared with the research community through GitHub. In summary, this comprehensive review provides insights into various approaches to analyze single cell sequencing data and offers specific guidelines for study design and a variety of analytic directions. The review and the accompanied software tools will serve as a valuable resource for studying cellular and molecular mechanisms of AD, other diseases, or biological systems at the single cell level.
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Affiliation(s)
- Minghui Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
| | - Won-min Song
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
| | - Chen Ming
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
| | - Qian Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
| | - Xianxiao Zhou
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
| | - Peng Xu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
| | - Azra Krek
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
- Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029 USA
| | - Yonejung Yoon
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
| | - Lap Ho
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
| | - Miranda E. Orr
- Department of Internal Medicine, Section of Gerontology and Geriatric Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina USA
- Sticht Center for Healthy Aging and Alzheimer’s Prevention, Wake Forest School of Medicine, Winston-Salem, North Carolina USA
| | - Guo-Cheng Yuan
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
- Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029 USA
| | - Bin Zhang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
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180
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Marquez-Galera A, de la Prida LM, Lopez-Atalaya JP. A protocol to extract cell-type-specific signatures from differentially expressed genes in bulk-tissue RNA-seq. STAR Protoc 2022; 3:101121. [PMID: 35118429 PMCID: PMC8792262 DOI: 10.1016/j.xpro.2022.101121] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Bulk-tissue RNA-seq is widely used to dissect variation in gene expression levels across tissues and under different experimental conditions. Here, we introduce a protocol that leverages existing single-cell expression data to deconvolve patterns of cell-type-specific gene expression in differentially expressed gene lists from highly heterogeneous tissue. We apply this protocol to interrogate cell-type-specific gene expression and variation in cell type composition between the distinct sublayers of the hippocampal CA1 region of the brain in a rodent model of epilepsy. For complete details on the use and execution of this protocol, please refer to Cid et al. (2021). A protocol to explore gene signatures from bulk RNA-seq at the cell-type-specific level Deconvolution of complex gene signatures from highly heterogeneous tissues Publicly available single-cell gene expression dataset is retrieved and curated Gene signatures across brain regions and disease states are surveyed in scRNA-seq data
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181
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MacLean M, López-Díez R, Vasquez C, Gugger PF, Schmidt AM. Neuronal-glial communication perturbations in murine SOD1 G93A spinal cord. Commun Biol 2022; 5:177. [PMID: 35228715 PMCID: PMC8885678 DOI: 10.1038/s42003-022-03128-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 02/08/2022] [Indexed: 12/13/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is an incurable disease characterized by proteinaceous aggregate accumulation and neuroinflammation culminating in rapidly progressive lower and upper motor neuron death. To interrogate cell-intrinsic and inter-cell type perturbations in ALS, single-nucleus RNA sequencing was performed on the lumbar spinal cord in the murine ALS model SOD1G93A transgenic and littermate control mice at peri-symptomatic onset stage of disease, age 90 days. This work uncovered perturbed tripartite synapse functions, complement activation and metabolic stress in the affected spinal cord; processes evidenced by cell death and proteolytic stress-associated gene sets. Concomitantly, these pro-damage events in the spinal cord co-existed with dysregulated reparative mechanisms. This work provides a resource of cell-specific niches in the ALS spinal cord and asserts that interwoven dysfunctional neuronal-glial communications mediating neurodegeneration are underway prior to overt disease manifestation and are recapitulated, in part, in the human post-mortem ALS spinal cord. In this paper, single-nucleus RNA sequencing was performed to provide a resource of cell-specific niches in the murine ALS model spinal cord at peri-symptomatic onset stage of disease. The data suggest that dysfunctional neuronal-glial communication occurs prior to disease onset, which is partially recapitulated in human post-mortem ALS spinal cord tissue.
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Affiliation(s)
- Michael MacLean
- Diabetes Research Program, Department of Medicine, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Raquel López-Díez
- Diabetes Research Program, Department of Medicine, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Carolina Vasquez
- Diabetes Research Program, Department of Medicine, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Paul F Gugger
- Diabetes Research Program, Department of Medicine, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Ann Marie Schmidt
- Diabetes Research Program, Department of Medicine, New York University Grossman School of Medicine, New York, NY, 10016, USA.
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182
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Li SB, Damonte VM, Chen C, Wang GX, Kebschull JM, Yamaguchi H, Bian WJ, Purmann C, Pattni R, Urban AE, Mourrain P, Kauer JA, Scherrer G, de Lecea L. Hyperexcitable arousal circuits drive sleep instability during aging. Science 2022; 375:eabh3021. [PMID: 35201886 PMCID: PMC9107327 DOI: 10.1126/science.abh3021] [Citation(s) in RCA: 68] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Sleep quality declines with age; however, the underlying mechanisms remain elusive. We found that hyperexcitable hypocretin/orexin (Hcrt/OX) neurons drive sleep fragmentation during aging. In aged mice, Hcrt neurons exhibited more frequent neuronal activity epochs driving wake bouts, and optogenetic activation of Hcrt neurons elicited more prolonged wakefulness. Aged Hcrt neurons showed hyperexcitability with lower KCNQ2 expression and impaired M-current, mediated by KCNQ2/3 channels. Single-nucleus RNA-sequencing revealed adaptive changes to Hcrt neuron loss in the aging brain. Disruption of Kcnq2/3 genes in Hcrt neurons of young mice destabilized sleep, mimicking aging-associated sleep fragmentation, whereas the KCNQ-selective activator flupirtine hyperpolarized Hcrt neurons and rejuvenated sleep architecture in aged mice. Our findings demonstrate a mechanism underlying sleep instability during aging and a strategy to improve sleep continuity.
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Affiliation(s)
- Shi-Bin Li
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, 1201 Welch Road, Stanford, CA 94305, USA
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA 94305, USA
| | - Valentina Martinez Damonte
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, 1201 Welch Road, Stanford, CA 94305, USA
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA 94305, USA
| | - Chong Chen
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Gordon X. Wang
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, 1201 Welch Road, Stanford, CA 94305, USA
| | | | - Hiroshi Yamaguchi
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, 1201 Welch Road, Stanford, CA 94305, USA
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA 94305, USA
| | - Wen-Jie Bian
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, 1201 Welch Road, Stanford, CA 94305, USA
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA 94305, USA
| | - Carolin Purmann
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, 1201 Welch Road, Stanford, CA 94305, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Reenal Pattni
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, 1201 Welch Road, Stanford, CA 94305, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Alexander Eckehart Urban
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, 1201 Welch Road, Stanford, CA 94305, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Philippe Mourrain
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, 1201 Welch Road, Stanford, CA 94305, USA
- INSERM 1024, Ecole Normale Supérieure, Paris, France
| | - Julie A. Kauer
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, 1201 Welch Road, Stanford, CA 94305, USA
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA 94305, USA
| | - Grégory Scherrer
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Luis de Lecea
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, 1201 Welch Road, Stanford, CA 94305, USA
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA 94305, USA
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183
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Hegenbarth JC, Lezzoche G, De Windt LJ, Stoll M. Perspectives on Bulk-Tissue RNA Sequencing and Single-Cell RNA Sequencing for Cardiac Transcriptomics. FRONTIERS IN MOLECULAR MEDICINE 2022; 2:839338. [PMID: 39086967 PMCID: PMC11285642 DOI: 10.3389/fmmed.2022.839338] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Accepted: 01/31/2022] [Indexed: 08/02/2024]
Abstract
The heart has been the center of numerous transcriptomic studies in the past decade. Even though our knowledge of the key organ in our cardiovascular system has significantly increased over the last years, it is still not fully understood yet. In recent years, extensive efforts were made to understand the genetic and transcriptomic contribution to cardiac function and failure in more detail. The advent of Next Generation Sequencing (NGS) technologies has brought many discoveries but it is unable to comprehend the finely orchestrated interactions between and within the various cell types of the heart. With the emergence of single-cell sequencing more than 10 years ago, researchers gained a valuable new tool to enable the exploration of new subpopulations of cells, cell-cell interactions, and integration of multi-omic approaches at a single-cell resolution. Despite this innovation, it is essential to make an informed choice regarding the appropriate technique for transcriptomic studies, especially when working with myocardial tissue. Here, we provide a primer for researchers interested in transcriptomics using NGS technologies.
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Affiliation(s)
- Jana-Charlotte Hegenbarth
- Department of Molecular Genetics, Faculty of Science and Engineering, Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, Netherlands
| | - Giuliana Lezzoche
- Department of Molecular Genetics, Faculty of Science and Engineering, Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, Netherlands
| | - Leon J. De Windt
- Department of Molecular Genetics, Faculty of Science and Engineering, Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, Netherlands
| | - Monika Stoll
- Department of Biochemistry, CARIM School for Cardiovascular Diseases, Maastricht University, Maastricht, Netherlands
- Department of Genetic Epidemiology, Institute of Human Genetics, University Hospital Münster, Münster, Germany
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184
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Cuperus JT. Single-cell genomics in plants: current state, future directions, and hurdles to overcome. PLANT PHYSIOLOGY 2022; 188:749-755. [PMID: 34662424 PMCID: PMC8825463 DOI: 10.1093/plphys/kiab478] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 09/21/2021] [Indexed: 05/26/2023]
Abstract
Single-cell genomics has the potential to revolutionize the study of plant development and tissue-specific responses to environmental stimuli by revealing heretofore unknown players and gene regulatory processes. Here, I focus on the current state of single-cell genomics in plants, emerging technologies and applications, in addition to outlining possible future directions for experiments. I describe approaches to enable cheaper and larger experiments and technologies to measure multiple types of molecules to better model and understand cell types and their different states and trajectories throughout development. Lastly, I discuss the inherent limitations of single-cell studies and the technological hurdles that need to be overcome to widely apply single-cell genomics in crops to generate the greatest possible knowledge gain.
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Affiliation(s)
- Josh T Cuperus
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
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185
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Abramson BW, Novotny M, Hartwick NT, Colt K, Aevermann BD, Scheuermann RH, Michael TP. The genome and preliminary single-nuclei transcriptome of Lemna minuta reveals mechanisms of invasiveness. PLANT PHYSIOLOGY 2022; 188:879-897. [PMID: 34893913 PMCID: PMC8825320 DOI: 10.1093/plphys/kiab564] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 11/16/2021] [Indexed: 05/13/2023]
Abstract
The ability to trace every cell in some model organisms has led to the fundamental understanding of development and cellular function. However, in plants the complexity of cell number, organ size, and developmental time makes this a challenge even in the diminutive model plant Arabidopsis (Arabidopsis thaliana). Duckweed, basal nongrass aquatic monocots, provide an opportunity to follow every cell of an entire plant due to their small size, reduced body plan, and fast clonal growth habit. Here we present a chromosome-resolved genome for the highly invasive Lesser Duckweed (Lemna minuta) and generate a preliminary cell atlas leveraging low cell coverage single-nuclei sequencing. We resolved the 360 megabase genome into 21 chromosomes, revealing a core nonredundant gene set with only the ancient tau whole-genome duplication shared with all monocots, and paralog expansion as a result of tandem duplications related to phytoremediation. Leveraging SMARTseq2 single-nuclei sequencing, which provided higher gene coverage yet lower cell count, we profiled 269 nuclei covering 36.9% (8,457) of the L. minuta transcriptome. Since molecular validation was not possible in this nonmodel plant, we leveraged gene orthology with model organism single-cell expression datasets, gene ontology, and cell trajectory analysis to define putative cell types. We found that the tissue that we computationally defined as mesophyll expressed high levels of elemental transport genes consistent with this tissue playing a role in L. minuta wastewater detoxification. The L. minuta genome and preliminary cell map provide a paradigm to decipher developmental genes and pathways for an entire plant.
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Affiliation(s)
- Bradley W Abramson
- The Plant Molecular and Cellular Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Mark Novotny
- Department of Informatics, J. Craig Venter Institute, La Jolla, California 92037, USA
| | - Nolan T Hartwick
- The Plant Molecular and Cellular Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Kelly Colt
- The Plant Molecular and Cellular Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Brian D Aevermann
- Department of Informatics, J. Craig Venter Institute, La Jolla, California 92037, USA
| | - Richard H Scheuermann
- Department of Informatics, J. Craig Venter Institute, La Jolla, California 92037, USA
- Department of Pathology, University of California San Diego, La Jolla, California 92093, USA
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, California 92037, USA
| | - Todd P Michael
- The Plant Molecular and Cellular Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
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186
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Gupta A, Shamsi F, Altemose N, Dorlhiac GF, Cypess AM, White AP, Yosef N, Patti ME, Tseng YH, Streets A. Characterization of transcript enrichment and detection bias in single-nucleus RNA-seq for mapping of distinct human adipocyte lineages. Genome Res 2022; 32:242-257. [PMID: 35042723 PMCID: PMC8805720 DOI: 10.1101/gr.275509.121] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 12/10/2021] [Indexed: 02/02/2023]
Abstract
Single-cell RNA sequencing (scRNA-seq) enables molecular characterization of complex biological tissues at high resolution. The requirement of single-cell extraction, however, makes it challenging for profiling tissues such as adipose tissue, for which collection of intact single adipocytes is complicated by their fragile nature. For such tissues, single-nucleus extraction is often much more efficient and therefore single-nucleus RNA sequencing (snRNA-seq) presents an alternative to scRNA-seq. However, nuclear transcripts represent only a fraction of the transcriptome in a single cell, with snRNA-seq marked with inherent transcript enrichment and detection biases. Therefore, snRNA-seq may be inadequate for mapping important transcriptional signatures in adipose tissue. In this study, we compare the transcriptomic landscape of single nuclei isolated from preadipocytes and mature adipocytes across human white and brown adipocyte lineages, with whole-cell transcriptome. We show that snRNA-seq is capable of identifying the broad cell types present in scRNA-seq at all states of adipogenesis. However, we also explore how and why the nuclear transcriptome is biased and limited, as well as how it can be advantageous. We robustly characterize the enrichment of nuclear-localized transcripts and adipogenic regulatory lncRNAs in snRNA-seq, while also providing a detailed understanding for the preferential detection of long genes upon using this technique. To remove such technical detection biases, we propose a normalization strategy for a more accurate comparison of nuclear and cellular data. Finally, we show successful integration of scRNA-seq and snRNA-seq data sets with existing bioinformatic tools. Overall, our results illustrate the applicability of snRNA-seq for the characterization of cellular diversity in the adipose tissue.
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Affiliation(s)
- Anushka Gupta
- University of California at Berkeley-University of California at San Francisco Graduate Program in Bioengineering, Berkeley, California 94720, USA
| | - Farnaz Shamsi
- Section on Integrative Physiology and Metabolism, Joslin Diabetes Center, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Nicolas Altemose
- University of California at Berkeley-University of California at San Francisco Graduate Program in Bioengineering, Berkeley, California 94720, USA
| | - Gabriel F Dorlhiac
- Biophysics Graduate Group, University of California at Berkeley, Berkeley, California 94720, USA
| | - Aaron M Cypess
- Diabetes, Endocrinology, and Obesity Branch, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Andrew P White
- Department of Orthopedic Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Nir Yosef
- Center for Computational Biology, University of California, Berkeley, Berkeley, California 94720, USA
- Department of Electrical Engineering and Computer Sciences, University of California at Berkeley, Berkeley, California 94720, USA
- Chan Zuckerberg Biohub, San Francisco, California 94158, USA
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, Massachusetts 02139, USA
| | | | - Yu-Hua Tseng
- Section on Integrative Physiology and Metabolism, Joslin Diabetes Center, Harvard Medical School, Boston, Massachusetts 02115, USA
- Harvard Stem Cell Institute, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Aaron Streets
- University of California at Berkeley-University of California at San Francisco Graduate Program in Bioengineering, Berkeley, California 94720, USA
- Biophysics Graduate Group, University of California at Berkeley, Berkeley, California 94720, USA
- Chan Zuckerberg Biohub, San Francisco, California 94158, USA
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187
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Boche D, Gordon MN. Diversity of transcriptomic microglial phenotypes in aging and Alzheimer's disease. Alzheimers Dement 2022; 18:360-376. [PMID: 34223696 PMCID: PMC9059230 DOI: 10.1002/alz.12389] [Citation(s) in RCA: 47] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 04/28/2021] [Accepted: 05/02/2021] [Indexed: 02/03/2023]
Abstract
The morphological plasticity of microglia has fascinated neuroscientists for 100 years. Attempts to classify functional phenotypes are hampered by similarities between endogenous brain microglia and peripheral myeloid cells that can enter the brain under pathological conditions. Recent advances in single-cell -omic methodologies have led to an explosion of data regarding gene expression in microglia. Herein, we review the diversity of microglial phenotypes in healthy brains, aging, and Alzheimer's disease (AD); identify knowledge gaps in the body of evidence; and suggest areas in which new knowledge would be useful. Data from human samples and mouse models are compared and contrasted. Understanding the molecular complexity of the microglial response repertoire will suggest new avenues for therapeutic treatments in AD.
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Affiliation(s)
- Delphine Boche
- Clinical Neurosciences, Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Marcia N. Gordon
- Translational Neuroscience, Michigan State University College of Human Medicine, Grand Rapids, MI, USA,corresponding author: Marcia N. Gordon, PhD, Michigan State University GRRC, 400 Monroe Ave NW, Grand Rapids, MI, 49503 USA, , Telephone: (616) 234-2837
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188
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Kimble AL, Silva J, Omar OM, Murphy M, Hensel JA, Nicholas SAE, Jellison ER, Reese B, Murphy PA. A method for rapid flow-cytometric isolation of endothelial nuclei and RNA from archived frozen brain tissue. J Transl Med 2022; 102:204-211. [PMID: 34775494 PMCID: PMC8784313 DOI: 10.1038/s41374-021-00698-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 09/17/2021] [Accepted: 09/27/2021] [Indexed: 11/20/2022] Open
Abstract
Endothelial cells are important contributors to brain development, physiology, and disease. Although RNA sequencing has contributed to the understanding of brain endothelial cell diversity, bulk analysis and single-cell approaches have relied on fresh tissue digestion protocols for the isolation of single endothelial cells and flow cytometry-based sorting on surface markers or transgene expression. These approaches are limited in the analysis of the endothelium in human brain tissues, where fresh samples are difficult to obtain. Here, we developed an approach to examine endothelial RNA expression by using an endothelial-specific marker to isolate nuclei from abundant archived frozen brain tissues. We show that this approach rapidly and reliably extracts endothelial nuclei from frozen mouse brain samples, and importantly, from archived frozen human brain tissues. Furthermore, isolated RNA transcript levels are closely correlated with expression in whole cells from tissue digestion protocols and are enriched in endothelial markers and depleted of markers of other brain cell types. As high-quality RNA transcripts could be obtained from as few as 100 nuclei in archived frozen human brain tissues, we predict that this approach should be useful for both bulk analysis of endothelial RNA transcripts in human brain tissues as well as single-cell analysis of endothelial sub-populations.
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Affiliation(s)
- Amy L Kimble
- Center for Vascular Biology, UCONN Health, Farmington, CT, USA
| | - Jordan Silva
- Center for Vascular Biology, UCONN Health, Farmington, CT, USA
| | - Omar M Omar
- Center for Vascular Biology, UCONN Health, Farmington, CT, USA
| | - Melissa Murphy
- Center for Vascular Biology, UCONN Health, Farmington, CT, USA
| | | | | | | | - Bo Reese
- Institute for Systems Genomics-Center for Genome Innovation, UCONN, Storrs, CT, USA
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189
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Minne M, Ke Y, Saura-Sanchez M, De Rybel B. Advancing root developmental research through single-cell technologies. CURRENT OPINION IN PLANT BIOLOGY 2022; 65:102113. [PMID: 34562694 PMCID: PMC7611778 DOI: 10.1016/j.pbi.2021.102113] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 08/09/2021] [Accepted: 08/13/2021] [Indexed: 06/12/2023]
Abstract
Single-cell RNA-sequencing has greatly increased the spatiotemporal resolution of root transcriptomics data, but we are still only scratching the surface of its full potential. Despite the challenges that remain in the field, the orderly aligned structure of the Arabidopsis root meristem makes it specifically suitable for lineage tracing and trajectory analysis. These methods will become even more potent by increasing resolution and specificity using tissue-specific single-cell RNA-sequencing and spatial transcriptomics. Feeding multiple single-cell omics data sets into single-cell gene regulatory networks will accelerate the discovery of regulators of root development in multiple species. By providing transcriptome atlases for virtually any species, single-cell technologies could tempt many root developmental biologists to move beyond the comfort of the well-known Arabidopsis root meristem.
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Affiliation(s)
- Max Minne
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, 9052, Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, 9052, Ghent, Belgium
| | - Yuji Ke
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, 9052, Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, 9052, Ghent, Belgium
| | - Maite Saura-Sanchez
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, 9052, Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, 9052, Ghent, Belgium
| | - Bert De Rybel
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, 9052, Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, 9052, Ghent, Belgium.
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190
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Pena-Ortiz MA, Shafiq S, Rowland ME, Bérubé NG. Selective isolation of mouse glial nuclei optimized for reliable downstream omics analyses. J Neurosci Methods 2022; 369:109480. [PMID: 35026308 DOI: 10.1016/j.jneumeth.2022.109480] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 01/06/2022] [Accepted: 01/07/2022] [Indexed: 01/08/2023]
Abstract
BACKGROUND Isolation of cell types of interest from the brain for molecular applications presents several challenges, including cellular damage during tissue dissociation or enrichment procedures, and low cell number in the tissue in some cases. Techniques have been developed to enrich distinct cell populations using immunopanning or fluorescence activated cell/nuclei sorting. However, these techniques often involve fixation, immunolabeling and DNA staining steps, which could potentially influence downstream omics applications. NEW METHOD Taking advantage of readily available genetically modified mice with fluorescent-tagged nuclei, we describe a technique for the purification of cell-type specific brain nuclei, optimized to decrease sample preparation time and to limit potential artefacts for downstream omics applications. We demonstrate the applicability of this approach for the purification of glial cell nuclei and show that the resulting cell-type specific nuclei obtained can be used effectively for omics applications, including ATAC-seq and RNA-seq. RESULTS We demonstrate excellent enrichment of fluorescently-tagged glial nuclei, yielding high quality RNA and chromatin. We identify several critical steps during nuclei isolation that help limit nuclei rupture and clumping, including quick homogenization, dilution before filtration and loosening of the pellet before resuspension, thus improving yield. Sorting of fluorescent nuclei can be achieved without fixation, antibody labelling, or DAPI staining, reducing potential artifactual results in RNA-seq and ATAC-seq analyses. We show that reproducible glial cell type-specific profiles can be obtained in transcriptomic and chromatin accessibility assays using this rapid protocol. COMPARISON WITH EXISTING METHODS Our method allows for rapid enrichment of glial nuclei populations from the mouse brain with minimal processing steps, while still providing high quality RNA and chromatin required for reliable omics analyses. CONCLUSIONS We provide a reproducible method to obtain nucleic material from glial cells in the mouse brain with a quick and limited sample preparation.
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Affiliation(s)
- Miguel A Pena-Ortiz
- Departments of Anatomy and Cell Biology, Paediatrics, and Oncology, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada; Division of Genetics and Development, Children's Health Research Institute, London, ON, Canada
| | - Sarfraz Shafiq
- Departments of Anatomy and Cell Biology, Paediatrics, and Oncology, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada; Division of Genetics and Development, Children's Health Research Institute, London, ON, Canada
| | - Megan E Rowland
- Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, BC, Canada
| | - Nathalie G Bérubé
- Departments of Anatomy and Cell Biology, Paediatrics, and Oncology, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada; Division of Genetics and Development, Children's Health Research Institute, London, ON, Canada.
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191
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Qiu M, Zong JB, He QW, Liu YX, Wan Y, Li M, Zhou YF, Wu JH, Hu B. Cell Heterogeneity Uncovered by Single-Cell RNA Sequencing Offers Potential Therapeutic Targets for Ischemic Stroke. Aging Dis 2022; 13:1436-1454. [PMID: 36186129 PMCID: PMC9466965 DOI: 10.14336/ad.2022.0212] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 02/12/2022] [Indexed: 11/06/2022] Open
Abstract
Ischemic stroke is a detrimental neurological disease characterized by an irreversible infarct core surrounded by an ischemic penumbra, a salvageable region of brain tissue. Unique roles of distinct brain cell subpopulations within the neurovascular unit and peripheral immune cells during ischemic stroke remain elusive due to the heterogeneity of cells in the brain. Single-cell RNA sequencing (scRNA-seq) allows for an unbiased determination of cellular heterogeneity at high-resolution and identification of cell markers, thereby unveiling the principal brain clusters within the cell-type-specific gene expression patterns as well as cell-specific subclusters and their functions in different pathways underlying ischemic stroke. In this review, we have summarized the changes in differentiation trajectories of distinct cell types and highlighted the specific pathways and genes in brain cells that are impacted by stroke. This review is expected to inspire new research and provide directions for investigating the potential pathological mechanisms and novel treatment strategies for ischemic stroke at the level of a single cell.
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Affiliation(s)
| | | | | | | | | | | | | | - Jie-hong Wu
- Correspondence should be addressed to: Dr. Bo Hu () and Dr. Jie-hong Wu (), Department of Neurology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Bo Hu
- Correspondence should be addressed to: Dr. Bo Hu () and Dr. Jie-hong Wu (), Department of Neurology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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192
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Dai Z, Nomura S. Recent Progress in Cardiovascular Research Involving Single-Cell Omics Approaches. Front Cardiovasc Med 2021; 8:783398. [PMID: 34977189 PMCID: PMC8716466 DOI: 10.3389/fcvm.2021.783398] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Accepted: 11/22/2021] [Indexed: 01/08/2023] Open
Abstract
Cardiovascular diseases are among the leading causes of morbidity and mortality worldwide. Although the spectrum of the heart from development to disease has long been studied, it remains largely enigmatic. The emergence of single-cell omics technologies has provided a powerful toolbox for defining cell heterogeneity, unraveling previously unknown pathways, and revealing intercellular communications, thereby boosting biomedical research and obtaining numerous novel findings over the last 7 years. Not only cell atlases of normal and developing hearts that provided substantial research resources, but also some important findings regarding cell-type-specific disease gene program, could never have been established without single-cell omics technologies. Herein, we briefly describe the latest technological advances in single-cell omics and summarize the major findings achieved by such approaches, with a focus on development and homeostasis of the heart, myocardial infarction, and heart failure.
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Affiliation(s)
| | - Seitaro Nomura
- Department of Cardiovascular Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
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193
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Steffens S, Nahrendorf M, Madonna R. Immune cells in cardiac homeostasis and disease: emerging insights from novel technologies. Eur Heart J 2021; 43:1533-1541. [PMID: 34897403 DOI: 10.1093/eurheartj/ehab842] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 10/22/2021] [Accepted: 11/29/2021] [Indexed: 12/26/2022] Open
Abstract
The increasing use of single-cell immune profiling and advanced microscopic imaging technologies has deepened our understanding of the cardiac immune system, confirming that the heart contains a broad repertoire of innate and adaptive immune cells. Leucocytes found in the healthy heart participate in essential functions to preserve cardiac homeostasis, not only by defending against pathogens but also by maintaining normal organ function. In pathophysiological conditions, cardiac inflammation is implicated in healing responses after ischaemic or non-ischaemic cardiac injury. The aim of this review is to provide a concise overview of novel methodological advancements to the non-expert readership and summarize novel findings on immune cell heterogeneity and functions in cardiac disease with a focus on myocardial infarction as a prototypic example. In addition, we will briefly discuss how biological sex modulate the cardiac immune response. Finally, we will highlight emerging concepts for novel therapeutic applications, such as targeting immunometabolism and nanomedicine.
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Affiliation(s)
- Sabine Steffens
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians-Universität, Pettenkoferstraße 9, Munich 80336, Germany.,Munich Heart Alliance, DZHK Partner Site, Munich, Germany
| | - Matthias Nahrendorf
- Center for Systems Biology, Massachusetts General Hospital, Harvard Medical School, 185 Cambridge Street, 8.228 Boston, MA 02114, USA.,Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Rosalinda Madonna
- Department of Internal Medicine, McGovern School of Medicine, The University of Texas Health Science Center at Houston, Houston, TX, USA.,Department of Pathology, Cardiology Division, University of Pisa, c/o Ospedale di Cisanello Via Paradisa, 2, 56124 Pisa, Italy
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194
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Hippocampal neuropathology in suicide: Gaps in our knowledge and opportunities for a breakthrough. Neurosci Biobehav Rev 2021; 132:542-552. [PMID: 34906612 DOI: 10.1016/j.neubiorev.2021.12.023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Revised: 12/03/2021] [Accepted: 12/10/2021] [Indexed: 01/27/2023]
Abstract
Suicide is a major global hazard. There is a need for increasing suicide awareness and effective and evidence-based interventions, targeting both suicidal ideation and conduct. However, anti-suicide pharmacological effects are unsatisfactory. The human hippocampus is vulnerable to neuropsychiatric damages and subsequently releases psychobiological signals. Human hippocampal studies of suicide completers have shown mechanistic changes in neurobiology, which, however, could not reflect the neuropathological 'fingerprints' of fatal suicide ideations and suicide attempts. In this review, we provide several leading theories of suicide, including the serotoninergic system, Wnt pathway and brain-derived neurotrophic factor/tropomyosin receptor kinase B signalling, and discuss the evidence for their roles in suicide and treatment. Moreover, the cognitive dysfunctions associated with suicide risk are discussed, as well as the novel evidence on cognitive therapies that decrease suicidal ideation. We highlight the need to apply multi-omics techniques (including single-nucleus RNA sequencing and mass spectrometry histochemistry) on hippocampal samples from donors who died by suicide or legal euthanasia, to clarify the aetiology of suicide and propose novel therapeutic strategies.
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195
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Transcriptomic Crosstalk between Gliomas and Telencephalic Neural Stem and Progenitor Cells for Defining Heterogeneity and Targeted Signaling Pathways. Int J Mol Sci 2021; 22:ijms222413211. [PMID: 34948008 PMCID: PMC8703403 DOI: 10.3390/ijms222413211] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 11/29/2021] [Accepted: 11/30/2021] [Indexed: 12/15/2022] Open
Abstract
Recent studies have begun to reveal surprising levels of cell diversity in the human brain, both in adults and during development. Distinctive cellular phenotypes point to complex molecular profiles, cellular hierarchies and signaling pathways in neural stem cells, progenitor cells, neuronal and glial cells. Several recent reports have suggested that neural stem and progenitor cell types found in the developing and adult brain share several properties and phenotypes with cells from brain primary tumors, such as gliomas. This transcriptomic crosstalk may help us to better understand the cell hierarchies and signaling pathways in both gliomas and the normal brain, and, by clarifying the phenotypes of cells at the origin of the tumor, to therapeutically address their most relevant signaling pathways.
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196
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O'Sullivan SJ, McIntosh-Clarke D, Park J, Vadigepalli R, Schwaber JS. Single Cell Scale Neuronal and Glial Gene Expression and Putative Cell Phenotypes and Networks in the Nucleus Tractus Solitarius in an Alcohol Withdrawal Time Series. Front Syst Neurosci 2021; 15:739790. [PMID: 34867221 PMCID: PMC8641127 DOI: 10.3389/fnsys.2021.739790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 10/22/2021] [Indexed: 11/23/2022] Open
Abstract
Alcohol withdrawal syndrome (AWS) is characterized by neuronal hyperexcitability, autonomic dysregulation, and severe negative emotion. The nucleus tractus solitarius (NTS) likely plays a prominent role in the neurological processes underlying these symptoms as it is the main viscerosensory nucleus in the brain. The NTS receives visceral interoceptive inputs, influences autonomic outputs, and has strong connections to the limbic system and hypothalamic-pituitary-adrenal axis to maintain homeostasis. Our prior analysis of single neuronal gene expression data from the NTS shows that neurons exist in heterogeneous transcriptional states that form distinct functional subphenotypes. Our working model conjectures that the allostasis secondary to alcohol dependence causes peripheral and central biological network decompensation in acute abstinence resulting in neurovisceral feedback to the NTS that substantially contributes to the observed AWS. We collected single noradrenergic and glucagon-like peptide-1 (GLP-1) neurons and microglia from rat NTS and measured a subset of their transcriptome as pooled samples in an alcohol withdrawal time series. Inflammatory subphenotypes predominate at certain time points, and GLP-1 subphenotypes demonstrated hyperexcitability post-withdrawal. We hypothesize such inflammatory and anxiogenic signaling contributes to alcohol dependence via negative reinforcement. Targets to mitigate such dysregulation and treat dependence can be identified from this dataset.
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Affiliation(s)
- Sean J O'Sullivan
- Department of Pathology, Anatomy, and Cell Biology, Daniel Baugh Institute for Functional Genomics and Computational Biology, Thomas Jefferson University, Philadelphia, PA, United States.,Brain Stimulation Lab, Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, United States
| | - Damani McIntosh-Clarke
- Department of Pathology, Anatomy, and Cell Biology, Daniel Baugh Institute for Functional Genomics and Computational Biology, Thomas Jefferson University, Philadelphia, PA, United States.,Department of Emergency Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - James Park
- Department of Pathology, Anatomy, and Cell Biology, Daniel Baugh Institute for Functional Genomics and Computational Biology, Thomas Jefferson University, Philadelphia, PA, United States.,Department of Chemical Engineering, University of Delaware, Newark, DE, United States.,Institute for Systems Biology, Seattle, WA, United States
| | - Rajanikanth Vadigepalli
- Department of Pathology, Anatomy, and Cell Biology, Daniel Baugh Institute for Functional Genomics and Computational Biology, Thomas Jefferson University, Philadelphia, PA, United States.,Department of Chemical Engineering, University of Delaware, Newark, DE, United States
| | - James S Schwaber
- Department of Pathology, Anatomy, and Cell Biology, Daniel Baugh Institute for Functional Genomics and Computational Biology, Thomas Jefferson University, Philadelphia, PA, United States
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197
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Sankowski R, Monaco G, Prinz M. Evaluating microglial phenotypes using single-cell technologies. Trends Neurosci 2021; 45:133-144. [PMID: 34872773 DOI: 10.1016/j.tins.2021.11.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 10/25/2021] [Accepted: 11/07/2021] [Indexed: 12/13/2022]
Abstract
Recent single-cell technologies have enabled researchers to simultaneously assess the transcriptomes and other modalities of thousands of cells within their spatial context. Here, we have summarized available single-cell methods for dissociated tissues and tissue slides with respect to the specifics of microglial biology. We have focused on next-generation-based technologies. We review the potential of these single-cell sequencing methods and newer multiomics approaches to extend the understanding of microglia function beyond the status quo.
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Affiliation(s)
- Roman Sankowski
- Institute of Neuropathology, Faculty of Medicine, University of Freiburg, Freiburg, Germany; Berta-Ottenstein-Programme for Clinician Scientists, Faculty of Medicine, University of Freiburg, Freiburg, Germany; Single-Cell Omics Platform Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Gianni Monaco
- Institute of Neuropathology, Faculty of Medicine, University of Freiburg, Freiburg, Germany; Single-Cell Omics Platform Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Marco Prinz
- Institute of Neuropathology, Faculty of Medicine, University of Freiburg, Freiburg, Germany; Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany; Center for Basics in NeuroModulation (NeuroModulBasics), Faculty of Medicine, University of Freiburg, Freiburg, Germany.
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198
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Xu Z, Wang C, Chen M, Yuan Y, Li L, Huang Z, Yuan Y, Yang H, Wang Q, Zhang X. Retina Cell Atlases of Multiple Species and an Online Platform for Retina Cell-Type Markers. J Genet Genomics 2021; 49:262-265. [PMID: 34800706 DOI: 10.1016/j.jgg.2021.10.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 10/15/2021] [Accepted: 10/22/2021] [Indexed: 01/23/2023]
Affiliation(s)
- Zaoxu Xu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China; BGI-Shenzhen, Shenzhen 518083, China
| | - Changzheng Wang
- Department of Computer Science, City University of Hong Kong, Hong Kong, 999077, China
| | - Min Chen
- Tsinghua-Berkeley Shenzhen Institute (TBSI), Tsinghua University, Shenzhen, 518055, China
| | - Yuting Yuan
- School of Basic Medical Sciences, Binzhou Medical University, Yantai, 264003, China
| | | | - Zhen Huang
- Fujian Key Laboratory of Developmental and Neural Biology, College of Life Sciences, Fujian Normal University, Fuzhou, Fujian, P.R. China
| | - Yue Yuan
- BGI-Shenzhen, Shenzhen 518083, China
| | - Huanming Yang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qi Wang
- Cuiying Biomedical Research Center, Lanzhou University Second Hospital, Lanzhou, 730010, China; Gansu Key Laboratory of Protection and Utilization for Biological Resources and Ecological Restoration, Qingyang, 745000, China.
| | - Xingliang Zhang
- Institute of Pediatrics, Department of Pediatric Surgery, Shenzhen Children's Hospital, Shenzhen, 518038, China; Department of Pediatrics, the Affiliated Hospital of Guangdong Medical University, Zhanjiang 524001, China.
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199
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Single nucleus RNA-sequencing: how it's done, applications and limitations. Emerg Top Life Sci 2021; 5:687-690. [PMID: 34515767 DOI: 10.1042/etls20210074] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 08/10/2021] [Accepted: 08/24/2021] [Indexed: 11/17/2022]
Abstract
Single nuclei RNA-sequencing (sNuc-Seq) is a methodology which uses isolated nuclei instead of whole cells to profile gene expression. By using droplet microfluidic technologies, users are able to profile thousands of single transcriptomes at high throughput from their chosen tissue. This article aims to introduce sNuc-Seq as a method and its utility in multiple tissue types. Furthermore, we discuss the risks associated with the use of nuclei, which must be considered before committing to a methodology.
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200
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Ahmadi A, Gispert JD, Navarro A, Vilor-Tejedor N, Sadeghi I. Single-cell Transcriptional Changes in Neurodegenerative Diseases. Neuroscience 2021; 479:192-205. [PMID: 34748859 DOI: 10.1016/j.neuroscience.2021.10.025] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 10/22/2021] [Accepted: 10/26/2021] [Indexed: 01/25/2023]
Abstract
In recent decades, our understanding of the molecular changes involved in neurodegenerative diseases has been transformed. Single-cell RNA sequencing and single-nucleus RNA sequencing technologies have been applied to provide cellular and molecular details of the brain at the single-cell level. This has expanded our knowledge of the central nervous system and provided insights into the molecular vulnerability of brain cell types and underlying mechanisms in neurodegenerative diseases. In this review, we highlight the recent advances and findings related to neurodegenerative diseases using these cutting-edge technologies.
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Affiliation(s)
- Amirhossein Ahmadi
- Department of Biology, Faculty of Nano and BioScience and Technology, Persian Gulf University, Bushehr 75169, Iran
| | - Juan D Gispert
- BarcelonaBeta Brain Research Center (BBRC), Pasqual Maragall Foundation, Barcelona, Spain; Pompeu Fabra University, Barcelona, Spain; IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain; Centro de Investigación Biomédica en Red de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Madrid, Spain
| | - Arcadi Navarro
- BarcelonaBeta Brain Research Center (BBRC), Pasqual Maragall Foundation, Barcelona, Spain; Pompeu Fabra University, Barcelona, Spain; Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain; Institute of Evolutionary Biology (CSIC-UPF), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain
| | - Natalia Vilor-Tejedor
- BarcelonaBeta Brain Research Center (BBRC), Pasqual Maragall Foundation, Barcelona, Spain; Pompeu Fabra University, Barcelona, Spain; Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain; Erasmus MC University Medical Center. Department of Clinical Genetics, Rotterdam, the Netherlands.
| | - Iman Sadeghi
- BarcelonaBeta Brain Research Center (BBRC), Pasqual Maragall Foundation, Barcelona, Spain; Pompeu Fabra University, Barcelona, Spain; Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain.
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