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Zhang D, Wen Q, Zhang R, Kou K, Lin M, Zhang S, Yang J, Shi H, Yang Y, Tan X, Yin S, Ou X. From Cell to Gene: Deciphering the Mechanism of Heart Failure With Single-Cell Sequencing. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2308900. [PMID: 39159065 DOI: 10.1002/advs.202308900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Revised: 07/24/2024] [Indexed: 08/21/2024]
Abstract
Heart failure (HF) is a prevalent cardiovascular disease with significant morbidity and mortality rates worldwide. Due to the intricate structure of the heart, diverse cell types, and the complex pathogenesis of HF, further in-depth investigation into the underlying mechanisms is required. The elucidation of the heterogeneity of cardiomyocytes and the intercellular communication network is particularly important. Traditional high-throughput sequencing methods provide an average measure of gene expression, failing to capture the "heterogeneity" between cells and impacting the accuracy of gene function knowledge. In contrast, single-cell sequencing techniques allow for the amplification of the entire genome or transcriptome at the individual cell level, facilitating the examination of gene structure and expression with unparalleled precision. This approach offers valuable insights into disease mechanisms, enabling the identification of changes in cellular components and gene expressions during hypertrophy associated with HF. Moreover, it reveals distinct cell populations and their unique roles in the HF microenvironment, providing a comprehensive understanding of the cellular landscape that underpins HF pathogenesis. This review focuses on the insights provided by single-cell sequencing techniques into the mechanisms underlying HF and discusses the challenges encountered in current cardiovascular research.
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Affiliation(s)
- Dan Zhang
- Key Laboratory of Medical Electrophysiology of Ministry of Education, Institute of Cardiovascular Medicine, Department of Cardiology of the Affiliated Hospital, Southwest Medical University, Luzhou, Sichuan, 646000, China
- Department of Rehabilitation Medicine, Southwest Medical University, Luzhou, Sichuan, 646000, China
| | - Qiang Wen
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Rd, Wuhan, Hubei, 430022, China
| | - Rui Zhang
- Key Laboratory of Medical Electrophysiology of Ministry of Education, Institute of Cardiovascular Medicine, Department of Cardiology of the Affiliated Hospital, Southwest Medical University, Luzhou, Sichuan, 646000, China
| | - Kun Kou
- Key Laboratory of Medical Electrophysiology of Ministry of Education, Institute of Cardiovascular Medicine, Department of Cardiology of the Affiliated Hospital, Southwest Medical University, Luzhou, Sichuan, 646000, China
| | - Miao Lin
- Key Laboratory of Medical Electrophysiology of Ministry of Education, Institute of Cardiovascular Medicine, Department of Cardiology of the Affiliated Hospital, Southwest Medical University, Luzhou, Sichuan, 646000, China
| | - Shiyu Zhang
- Key Laboratory of Medical Electrophysiology of Ministry of Education, Institute of Cardiovascular Medicine, Department of Cardiology of the Affiliated Hospital, Southwest Medical University, Luzhou, Sichuan, 646000, China
| | - Jun Yang
- Key Laboratory of Medical Electrophysiology of Ministry of Education, Institute of Cardiovascular Medicine, Department of Cardiology of the Affiliated Hospital, Southwest Medical University, Luzhou, Sichuan, 646000, China
| | - Hangchuan Shi
- Department of Clinical & Translational Research, University of Rochester Medical Center, 265 Crittenden Blvd, Rochester, NY, 14642, USA
- Department of Pathology and Laboratory Medicine, University of Rochester Medical Center, 601 Elmwood Ave, Rochester, NY, 14642, USA
| | - Yan Yang
- Key Laboratory of Medical Electrophysiology of Ministry of Education, Institute of Cardiovascular Medicine, Department of Cardiology of the Affiliated Hospital, Southwest Medical University, Luzhou, Sichuan, 646000, China
| | - Xiaoqiu Tan
- Key Laboratory of Medical Electrophysiology of Ministry of Education, Institute of Cardiovascular Medicine, Department of Cardiology of the Affiliated Hospital, Southwest Medical University, Luzhou, Sichuan, 646000, China
- Department of Physiology, School of Basic Medical Sciences, Southwest Medical University, Luzhou, Sichuan, 646000, China
| | - Shigang Yin
- Luzhou Key Laboratory of Nervous system disease and Brain Function, Southwest Medical University, Luzhou, Sichuan, 646000, China
| | - Xianhong Ou
- Key Laboratory of Medical Electrophysiology of Ministry of Education, Institute of Cardiovascular Medicine, Department of Cardiology of the Affiliated Hospital, Southwest Medical University, Luzhou, Sichuan, 646000, China
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Guangxi Normal University, Guilin, Guangxi, 541004, China
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Derisoud E, Jiang H, Zhao A, Chavatte-Palmer P, Deng Q. Revealing the molecular landscape of human placenta: a systematic review and meta-analysis of single-cell RNA sequencing studies. Hum Reprod Update 2024; 30:410-441. [PMID: 38478759 PMCID: PMC11215163 DOI: 10.1093/humupd/dmae006] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 02/12/2024] [Indexed: 07/02/2024] Open
Abstract
BACKGROUND With increasing significance of developmental programming effects associated with placental dysfunction, more investigations are devoted to improving the characterization and understanding of placental signatures in health and disease. The placenta is a transitory but dynamic organ adapting to the shifting demands of fetal development and available resources of the maternal supply throughout pregnancy. Trophoblasts (cytotrophoblasts, syncytiotrophoblasts, and extravillous trophoblasts) are placental-specific cell types responsible for the main placental exchanges and adaptations. Transcriptomic studies with single-cell resolution have led to advances in understanding the placenta's role in health and disease. These studies, however, often show discrepancies in characterization of the different placental cell types. OBJECTIVE AND RATIONALE We aim to review the knowledge regarding placental structure and function gained from the use of single-cell RNA sequencing (scRNAseq), followed by comparing cell-type-specific genes, highlighting their similarities and differences. Moreover, we intend to identify consensus marker genes for the various trophoblast cell types across studies. Finally, we will discuss the contributions and potential applications of scRNAseq in studying pregnancy-related diseases. SEARCH METHODS We conducted a comprehensive systematic literature review to identify different cell types and their functions at the human maternal-fetal interface, focusing on all original scRNAseq studies on placentas published before March 2023 and published reviews (total of 28 studies identified) using PubMed search. Our approach involved curating cell types and subtypes that had previously been defined using scRNAseq and comparing the genes used as markers or identified as potential new markers. Next, we reanalyzed expression matrices from the six available scRNAseq raw datasets with cell annotations (four from first trimester and two at term), using Wilcoxon rank-sum tests to compare gene expression among studies and annotate trophoblast cell markers in both first trimester and term placentas. Furthermore, we integrated scRNAseq raw data available from 18 healthy first trimester and nine term placentas, and performed clustering and differential gene expression analysis. We further compared markers obtained with the analysis of annotated and raw datasets with the literature to obtain a common signature gene list for major placental cell types. OUTCOMES Variations in the sampling site, gestational age, fetal sex, and subsequent sequencing and analysis methods were observed between the studies. Although their proportions varied, the three trophoblast types were consistently identified across all scRNAseq studies, unlike other non-trophoblast cell types. Notably, no marker genes were shared by all studies for any of the investigated cell types. Moreover, most of the newly defined markers in one study were not observed in other studies. These discrepancies were confirmed by our analysis on trophoblast cell types, where hundreds of potential marker genes were identified in each study but with little overlap across studies. From 35 461 and 23 378 cells of high quality in the first trimester and term placentas, respectively, we obtained major placental cell types, including perivascular cells that previously had not been identified in the first trimester. Importantly, our meta-analysis provides marker genes for major placental cell types based on our extensive curation. WIDER IMPLICATIONS This review and meta-analysis emphasizes the need for establishing a consensus for annotating placental cell types from scRNAseq data. The marker genes identified here can be deployed for defining human placental cell types, thereby facilitating and improving the reproducibility of trophoblast cell annotation.
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Affiliation(s)
- Emilie Derisoud
- Department of Physiology and Pharmacology, Karolinska Institutet, Solna, Stockholm, Sweden
| | - Hong Jiang
- Department of Physiology and Pharmacology, Karolinska Institutet, Solna, Stockholm, Sweden
| | - Allan Zhao
- Department of Physiology and Pharmacology, Karolinska Institutet, Solna, Stockholm, Sweden
| | - Pascale Chavatte-Palmer
- INRAE, BREED, Université Paris-Saclay, UVSQ, Jouy-en-Josas, France
- Ecole Nationale Vétérinaire d’Alfort, BREED, Maisons-Alfort, France
| | - Qiaolin Deng
- Department of Physiology and Pharmacology, Karolinska Institutet, Solna, Stockholm, Sweden
- Center for Molecular Medicine, Karolinska University Hospital, Solna, Stockholm, Sweden
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3
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Fonseca A, Riveras E, Moyano TC, Alvarez JM, Rosa S, Gutiérrez RA. Dynamic changes in mRNA nucleocytoplasmic localization in the nitrate response of Arabidopsis roots. PLANT, CELL & ENVIRONMENT 2024. [PMID: 38950037 DOI: 10.1111/pce.15018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 05/23/2024] [Accepted: 06/14/2024] [Indexed: 07/03/2024]
Abstract
Nitrate is a nutrient and signal that regulates gene expression. The nitrate response has been extensively characterized at the organism, organ, and cell-type-specific levels, but intracellular mRNA dynamics remain unexplored. To characterize nuclear and cytoplasmic transcriptome dynamics in response to nitrate, we performed a time-course expression analysis after nitrate treatment in isolated nuclei, cytoplasm, and whole roots. We identified 402 differentially localized transcripts (DLTs) in response to nitrate treatment. Induced DLT genes showed rapid and transient recruitment of the RNA polymerase II, together with an increase in the mRNA turnover rates. DLTs code for genes involved in metabolic processes, localization, and response to stimulus indicating DLTs include genes with relevant functions for the nitrate response that have not been previously identified. Using single-molecule RNA FISH, we observed early nuclear accumulation of the NITRATE REDUCTASE 1 (NIA1) transcripts in their transcription sites. We found that transcription of NIA1, a gene showing delayed cytoplasmic accumulation, is rapidly and transiently activated; however, its transcripts become unstable when they reach the cytoplasm. Our study reveals the dynamic localization of mRNAs between the nucleus and cytoplasm as an emerging feature in the temporal control of gene expression in response to nitrate treatment in Arabidopsis roots.
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Affiliation(s)
- Alejandro Fonseca
- Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Center for Genome Regulation, Millennium Institute Center for Genome Regulation (CRG), Santiago, Chile
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
- Department of Plant Biology, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
| | - Eleodoro Riveras
- Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Center for Genome Regulation, Millennium Institute Center for Genome Regulation (CRG), Santiago, Chile
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Tomás C Moyano
- Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Center for Genome Regulation, Millennium Institute Center for Genome Regulation (CRG), Santiago, Chile
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
- Centro de Biotecnología Vegetal, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - José M Alvarez
- Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Centro de Biotecnología Vegetal, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Stefanie Rosa
- Department of Plant Biology, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
| | - Rodrigo A Gutiérrez
- Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Center for Genome Regulation, Millennium Institute Center for Genome Regulation (CRG), Santiago, Chile
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
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Renaut S, Saavedra Armero V, Boudreau DK, Gaudreault N, Desmeules P, Thériault S, Mathieu P, Joubert P, Bossé Y. Single-cell and single-nucleus RNA-sequencing from paired normal-adenocarcinoma lung samples provide both common and discordant biological insights. PLoS Genet 2024; 20:e1011301. [PMID: 38814983 PMCID: PMC11166281 DOI: 10.1371/journal.pgen.1011301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 06/11/2024] [Accepted: 05/13/2024] [Indexed: 06/01/2024] Open
Abstract
Whether single-cell RNA-sequencing (scRNA-seq) captures the same biological information as single-nucleus RNA-sequencing (snRNA-seq) remains uncertain and likely to be context-dependent. Herein, a head-to-head comparison was performed in matched normal-adenocarcinoma human lung samples to assess biological insights derived from scRNA-seq versus snRNA-seq and better understand the cellular transition that occurs from normal to tumoral tissue. Here, the transcriptome of 160,621 cells/nuclei was obtained. In non-tumor lung, cell type proportions varied widely between scRNA-seq and snRNA-seq with a predominance of immune cells in the former (81.5%) and epithelial cells (69.9%) in the later. Similar results were observed in adenocarcinomas, in addition to an overall increase in cell type heterogeneity and a greater prevalence of copy number variants in cells of epithelial origin, which suggests malignant assignment. The cell type transition that occurs from normal lung tissue to adenocarcinoma was not always concordant whether cells or nuclei were examined. As expected, large differential expression of the whole-cell and nuclear transcriptome was observed, but cell-type specific changes of paired normal and tumor lung samples revealed a set of common genes in the cells and nuclei involved in cancer-related pathways. In addition, we showed that the ligand-receptor interactome landscape of lung adenocarcinoma was largely different whether cells or nuclei were evaluated. Immune cell depletion in fresh specimens partly mitigated the difference in cell type composition observed between cells and nuclei. However, the extra manipulations affected cell viability and amplified the transcriptional signatures associated with stress responses. In conclusion, research applications focussing on mapping the immune landscape of lung adenocarcinoma benefit from scRNA-seq in fresh samples, whereas snRNA-seq of frozen samples provide a low-cost alternative to profile more epithelial and cancer cells, and yield cell type proportions that more closely match tissue content.
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Affiliation(s)
- Sébastien Renaut
- Institut universitaire de cardiologie et de pneumologie de Québec–Université Laval, Quebec City, Canada
| | - Victoria Saavedra Armero
- Institut universitaire de cardiologie et de pneumologie de Québec–Université Laval, Quebec City, Canada
| | - Dominique K. Boudreau
- Institut universitaire de cardiologie et de pneumologie de Québec–Université Laval, Quebec City, Canada
| | - Nathalie Gaudreault
- Institut universitaire de cardiologie et de pneumologie de Québec–Université Laval, Quebec City, Canada
| | - Patrice Desmeules
- Institut universitaire de cardiologie et de pneumologie de Québec–Université Laval, Quebec City, Canada
| | - Sébastien Thériault
- Institut universitaire de cardiologie et de pneumologie de Québec–Université Laval, Quebec City, Canada
| | - Patrick Mathieu
- Institut universitaire de cardiologie et de pneumologie de Québec–Université Laval, Quebec City, Canada
| | - Philippe Joubert
- Institut universitaire de cardiologie et de pneumologie de Québec–Université Laval, Quebec City, Canada
| | - Yohan Bossé
- Institut universitaire de cardiologie et de pneumologie de Québec–Université Laval, Quebec City, Canada
- Department of Molecular Medicine, Université Laval, Quebec City, Canada
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5
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Yang S, Lan T, Wei R, Zhang L, Lin L, Du H, Huang Y, Zhang G, Huang S, Shi M, Wang C, Wang Q, Li R, Han L, Tang D, Li H, Zhang H, Cui J, Lu H, Huang J, Luo Y, Li D, Wan QH, Liu H, Fang SG. Single-nucleus transcriptome inventory of giant panda reveals cellular basis for fitness optimization under low metabolism. BMC Biol 2023; 21:222. [PMID: 37858133 PMCID: PMC10588165 DOI: 10.1186/s12915-023-01691-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Accepted: 08/25/2023] [Indexed: 10/21/2023] Open
Abstract
BACKGROUND Energy homeostasis is essential for the adaptation of animals to their environment and some wild animals keep low metabolism adaptive to their low-nutrient dietary supply. Giant panda is such a typical low-metabolic mammal exhibiting species specialization of extremely low daily energy expenditure. It has low levels of basal metabolic rate, thyroid hormone, and physical activities, whereas the cellular bases of its low metabolic adaptation remain rarely explored. RESULTS In this study, we generate a single-nucleus transcriptome atlas of 21 organs/tissues from a female giant panda. We focused on the central metabolic organ (liver) and dissected cellular metabolic status by cross-species comparison. Adaptive expression mode (i.e., AMPK related) was prominently displayed in the hepatocyte of giant panda. In the highest energy-consuming organ, the heart, we found a possibly optimized utilization of fatty acid. Detailed cell subtype annotation of endothelial cells showed the uterine-specific deficiency of blood vascular subclasses, indicating a potential adaptation for a low reproductive energy expenditure. CONCLUSIONS Our findings shed light on the possible cellular basis and transcriptomic regulatory clues for the low metabolism in giant pandas and helped to understand physiological adaptation response to nutrient stress.
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Affiliation(s)
- Shangchen Yang
- MOE Key Laboratory of Biosystems Homeostasis & Protection, State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Tianming Lan
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
- BGI Life Science Joint Research Center, Northeast Forestry University, Harbin, 150040, China
| | - Rongping Wei
- Key Laboratory of State Forestry and Grassland Administration (State Park Administration) on Conservation Biology of Rare Animals in the Giant Panda National Park, China Conservation and Research Center for the Giant Panda, Dujiangyan, 611830, China
| | - Ling Zhang
- China Wildlife Conservation Association, Beijing, 100714, China
| | - Lin Lin
- Department of Biomedicine, Aarhus University, 8000, Aarhus, Denmark
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, Qingdao, 266555, China
- Steno Diabetes Center Aarhus, Aarhus University Hospital, 8000, Aarhus, Denmark
| | - Hanyu Du
- MOE Key Laboratory of Biosystems Homeostasis & Protection, State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yunting Huang
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Guiquan Zhang
- Key Laboratory of State Forestry and Grassland Administration (State Park Administration) on Conservation Biology of Rare Animals in the Giant Panda National Park, China Conservation and Research Center for the Giant Panda, Dujiangyan, 611830, China
| | - Shan Huang
- Key Laboratory of State Forestry and Grassland Administration (State Park Administration) on Conservation Biology of Rare Animals in the Giant Panda National Park, China Conservation and Research Center for the Giant Panda, Dujiangyan, 611830, China
| | - Minhui Shi
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chengdong Wang
- Key Laboratory of State Forestry and Grassland Administration (State Park Administration) on Conservation Biology of Rare Animals in the Giant Panda National Park, China Conservation and Research Center for the Giant Panda, Dujiangyan, 611830, China
| | - Qing Wang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Rengui Li
- Key Laboratory of State Forestry and Grassland Administration (State Park Administration) on Conservation Biology of Rare Animals in the Giant Panda National Park, China Conservation and Research Center for the Giant Panda, Dujiangyan, 611830, China
| | - Lei Han
- College of Wildlife Resources, Northeast Forestry University, Harbin, 150040, China
| | - Dan Tang
- Key Laboratory of State Forestry and Grassland Administration (State Park Administration) on Conservation Biology of Rare Animals in the Giant Panda National Park, China Conservation and Research Center for the Giant Panda, Dujiangyan, 611830, China
| | - Haimeng Li
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hemin Zhang
- Key Laboratory of State Forestry and Grassland Administration (State Park Administration) on Conservation Biology of Rare Animals in the Giant Panda National Park, China Conservation and Research Center for the Giant Panda, Dujiangyan, 611830, China
| | - Jie Cui
- The Genome Synthesis and Editing Platform, BGI-Shenzhen, Shenzhen, 518120, China
| | - Haorong Lu
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen, 518120, China
| | - Jinrong Huang
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, Qingdao, 266555, China
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Yonglun Luo
- Department of Biomedicine, Aarhus University, 8000, Aarhus, Denmark
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, Qingdao, 266555, China
- Steno Diabetes Center Aarhus, Aarhus University Hospital, 8000, Aarhus, Denmark
| | - Desheng Li
- Key Laboratory of State Forestry and Grassland Administration (State Park Administration) on Conservation Biology of Rare Animals in the Giant Panda National Park, China Conservation and Research Center for the Giant Panda, Dujiangyan, 611830, China.
| | - Qiu-Hong Wan
- MOE Key Laboratory of Biosystems Homeostasis & Protection, State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China.
| | - Huan Liu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China.
- BGI Life Science Joint Research Center, Northeast Forestry University, Harbin, 150040, China.
| | - Sheng-Guo Fang
- MOE Key Laboratory of Biosystems Homeostasis & Protection, State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China.
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Ziff OJ, Harley J, Wang Y, Neeves J, Tyzack G, Ibrahim F, Skehel M, Chakrabarti AM, Kelly G, Patani R. Nucleocytoplasmic mRNA redistribution accompanies RNA binding protein mislocalization in ALS motor neurons and is restored by VCP ATPase inhibition. Neuron 2023; 111:3011-3027.e7. [PMID: 37480846 DOI: 10.1016/j.neuron.2023.06.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 05/09/2023] [Accepted: 06/22/2023] [Indexed: 07/24/2023]
Abstract
Amyotrophic lateral sclerosis (ALS) is characterized by nucleocytoplasmic mislocalization of the RNA-binding protein (RBP) TDP-43. However, emerging evidence suggests more widespread mRNA and protein mislocalization. Here, we employed nucleocytoplasmic fractionation, RNA sequencing, and mass spectrometry to investigate the localization of mRNA and protein in induced pluripotent stem cell-derived motor neurons (iPSMNs) from ALS patients with TARDBP and VCP mutations. ALS mutant iPSMNs exhibited extensive nucleocytoplasmic mRNA redistribution, RBP mislocalization, and splicing alterations. Mislocalized proteins exhibited a greater affinity for redistributed transcripts, suggesting a link between RBP mislocalization and mRNA redistribution. Notably, treatment with ML240, a VCP ATPase inhibitor, partially restored mRNA and protein localization in ALS mutant iPSMNs. ML240 induced changes in the VCP interactome and lysosomal localization and reduced oxidative stress and DNA damage. These findings emphasize the link between RBP mislocalization and mRNA redistribution in ALS motor neurons and highlight the therapeutic potential of VCP inhibition.
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Affiliation(s)
- Oliver J Ziff
- The Francis Crick Institute, 1 Midland Road, NW1 1AT London, UK; Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, WC1N 3BG London, UK; National Hospital for Neurology and Neurosurgery, University College London NHS Foundation Trust, WC1N 3BG London, UK.
| | - Jasmine Harley
- The Francis Crick Institute, 1 Midland Road, NW1 1AT London, UK; Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, WC1N 3BG London, UK; Institute of Molecular and Cell Biology, A(∗)STAR Research Entities, Singapore 138673, Singapore
| | - Yiran Wang
- The Francis Crick Institute, 1 Midland Road, NW1 1AT London, UK; Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, WC1N 3BG London, UK
| | - Jacob Neeves
- The Francis Crick Institute, 1 Midland Road, NW1 1AT London, UK; Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, WC1N 3BG London, UK
| | - Giulia Tyzack
- The Francis Crick Institute, 1 Midland Road, NW1 1AT London, UK; Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, WC1N 3BG London, UK
| | - Fairouz Ibrahim
- The Francis Crick Institute, 1 Midland Road, NW1 1AT London, UK
| | - Mark Skehel
- The Francis Crick Institute, 1 Midland Road, NW1 1AT London, UK
| | | | - Gavin Kelly
- The Francis Crick Institute, 1 Midland Road, NW1 1AT London, UK; Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, WC1N 3BG London, UK
| | - Rickie Patani
- The Francis Crick Institute, 1 Midland Road, NW1 1AT London, UK; Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, WC1N 3BG London, UK; National Hospital for Neurology and Neurosurgery, University College London NHS Foundation Trust, WC1N 3BG London, UK.
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7
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D'Sa K, Guelfi S, Vandrovcova J, Reynolds RH, Zhang D, Hardy J, Botía JA, Weale ME, Taliun SAG, Small KS, Ryten M. Analysis of subcellular RNA fractions demonstrates significant genetic regulation of gene expression in human brain post-transcriptionally. Sci Rep 2023; 13:13874. [PMID: 37620324 PMCID: PMC10449874 DOI: 10.1038/s41598-023-40324-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 08/08/2023] [Indexed: 08/26/2023] Open
Abstract
Gaining insight into the genetic regulation of gene expression in human brain is key to the interpretation of genome-wide association studies for major neurological and neuropsychiatric diseases. Expression quantitative trait loci (eQTL) analyses have largely been used to achieve this, providing valuable insights into the genetic regulation of steady-state RNA in human brain, but not distinguishing between molecular processes regulating transcription and stability. RNA quantification within cellular fractions can disentangle these processes in cell types and tissues which are challenging to model in vitro. We investigated the underlying molecular processes driving the genetic regulation of gene expression specific to a cellular fraction using allele-specific expression (ASE). Applying ASE analysis to genomic and transcriptomic data from paired nuclear and cytoplasmic fractions of anterior prefrontal cortex, cerebellar cortex and putamen tissues from 4 post-mortem neuropathologically-confirmed control human brains, we demonstrate that a significant proportion of genetic regulation of gene expression occurs post-transcriptionally in the cytoplasm, with genes undergoing this form of regulation more likely to be synaptic. These findings have implications for understanding the structure of gene expression regulation in human brain, and importantly the interpretation of rapidly growing single-nucleus brain RNA-sequencing and eQTL datasets, where cytoplasm-specific regulatory events could be missed.
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Affiliation(s)
- Karishma D'Sa
- Department of Neurodegenerative Disease, University College London, London, WC1N 3BG, UK
- Department of Medical & Molecular Genetics, School of Medical Sciences, King's College London, Guy's Hospital, London, SE1 1UL, UK
- Department of Clinical and Movement Neurosciences, University College London, London, WC1N 3BG, UK
| | - Sebastian Guelfi
- Department of Neurodegenerative Disease, University College London, London, WC1N 3BG, UK
- Verge Genomics, Tower Pl, South San Francisco, CA, 94080, USA
| | - Jana Vandrovcova
- Dept of Neuromuscular Disease, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | - Regina H Reynolds
- Great Ormond Street Institute of Child Health, Genetics and Genomic Medicine, University College London, London, WC1N 1EH, UK
| | - David Zhang
- Great Ormond Street Institute of Child Health, Genetics and Genomic Medicine, University College London, London, WC1N 1EH, UK
| | - John Hardy
- Department of Neurodegenerative Disease, University College London, London, WC1N 3BG, UK
- UK Dementia Research Institute at University College London, London, WC1N 3BG, UK
| | - Juan A Botía
- Great Ormond Street Institute of Child Health, Genetics and Genomic Medicine, University College London, London, WC1N 1EH, UK
- Departamento de Ingeniería de la Información y las Comunicaciones, Universidad de Murcia, 30100, Murcia, Spain
| | - Michael E Weale
- Department of Medical & Molecular Genetics, School of Medical Sciences, King's College London, Guy's Hospital, London, SE1 1UL, UK
- Genomics Plc, Oxford, OX1 1JD, UK
| | - Sarah A Gagliano Taliun
- Department of Medicine, Université de Montréal, Montréal, QC, H3T 1J4, Canada
- Montréal Heart Institute, Montréal, QC, H1T 1C8, Canada
- Department of Neurosciences, Université de Montréal, Montréal, QC, H3T 1J4, Canada
| | - Kerrin S Small
- Department of Twin Research and Genetic Epidemiology, King's College London, London, SE1 7EH, UK
| | - Mina Ryten
- Great Ormond Street Institute of Child Health, Genetics and Genomic Medicine, University College London, London, WC1N 1EH, UK.
- NIHR Great Ormond Street Hospital Biomedical Research Centre, University College London, London, WC1N 3JH, UK.
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8
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Monette A, Niu M, Maldonado RK, Chang J, Lambert GS, Flanagan JM, Cochrane A, Parent LJ, Mouland AJ. Influence of HIV-1 Genomic RNA on the Formation of Gag Biomolecular Condensates. J Mol Biol 2023; 435:168190. [PMID: 37385580 PMCID: PMC10838171 DOI: 10.1016/j.jmb.2023.168190] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 06/18/2023] [Accepted: 06/20/2023] [Indexed: 07/01/2023]
Abstract
Biomolecular condensates (BMCs) play an important role in the replication of a growing number of viruses, but many important mechanistic details remain to be elucidated. Previously, we demonstrated that the pan-retroviral nucleocapsid (NC) and HIV-1 pr55Gag (Gag) proteins phase separate into condensates, and that HIV-1 protease (PR)-mediated maturation of Gag and Gag-Pol precursor proteins yields self-assembling BMCs that have HIV-1 core architecture. Using biochemical and imaging techniques, we aimed to further characterize the phase separation of HIV-1 Gag by determining which of its intrinsically disordered regions (IDRs) influence the formation of BMCs, and how the HIV-1 viral genomic RNA (gRNA) could influence BMC abundance and size. We found that mutations in the Gag matrix (MA) domain or the NC zinc finger motifs altered condensate number and size in a salt-dependent manner. Gag BMCs were also bimodally influenced by the gRNA, with a condensate-promoting regime at lower protein concentrations and a gel dissolution at higher protein concentrations. Interestingly, incubation of Gag with CD4+ T cell nuclear lysates led to the formation of larger BMCs compared to much smaller ones observed in the presence of cytoplasmic lysates. These findings suggest that the composition and properties of Gag-containing BMCs may be altered by differential association of host factors in nuclear and cytosolic compartments during virus assembly. This study significantly advances our understanding of HIV-1 Gag BMC formation and provides a foundation for future therapeutic targeting of virion assembly.
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Affiliation(s)
- Anne Monette
- Lady Davis Institute at the Jewish General Hospital, Montréal, Québec H3T 1E2, Canada
| | - Meijuan Niu
- Lady Davis Institute at the Jewish General Hospital, Montréal, Québec H3T 1E2, Canada
| | - Rebecca Kaddis Maldonado
- Department of Medicine, Pennsylvania State University College of Medicine, Hershey, PA 17033, United States; Department of Microbiology and Immunology, Pennsylvania State University College of Medicine, Hershey, PA 17033, United States
| | - Jordan Chang
- Department of Medicine, Pennsylvania State University College of Medicine, Hershey, PA 17033, United States
| | - Gregory S Lambert
- Department of Medicine, Pennsylvania State University College of Medicine, Hershey, PA 17033, United States
| | - John M Flanagan
- Department of Biochemistry and Molecular Biology, Pennsylvania State University College of Medicine, Hershey, PA 17033, United States
| | - Alan Cochrane
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Leslie J Parent
- Department of Medicine, Pennsylvania State University College of Medicine, Hershey, PA 17033, United States; Department of Microbiology and Immunology, Pennsylvania State University College of Medicine, Hershey, PA 17033, United States.
| | - Andrew J Mouland
- Lady Davis Institute at the Jewish General Hospital, Montréal, Québec H3T 1E2, Canada; Department of Medicine, McGill University, Montréal, Québec H4A 3J1, Canada.
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9
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Wong YY, Harbison JE, Hope CM, Gundsambuu B, Brown KA, Wong SW, Brown CY, Couper JJ, Breen J, Liu N, Pederson SM, Köhne M, Klee K, Schultze J, Beyer M, Sadlon T, Barry SC. Parallel recovery of chromatin accessibility and gene expression dynamics from frozen human regulatory T cells. Sci Rep 2023; 13:5506. [PMID: 37016052 PMCID: PMC10073253 DOI: 10.1038/s41598-023-32256-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 03/24/2023] [Indexed: 04/06/2023] Open
Abstract
Epigenetic features such as DNA accessibility dictate transcriptional regulation in a cell type- and cell state- specific manner, and mapping this in health vs. disease in clinically relevant material is opening the door to new mechanistic insights and new targets for therapy. Assay for Transposase Accessible Chromatin Sequencing (ATAC-seq) allows chromatin accessibility profiling from low cell input, making it tractable on rare cell populations, such as regulatory T (Treg) cells. However, little is known about the compatibility of the assay with cryopreserved rare cell populations. Here we demonstrate the robustness of an ATAC-seq protocol comparing primary Treg cells recovered from fresh or cryopreserved PBMC samples, in the steady state and in response to stimulation. We extend this method to explore the feasibility of conducting simultaneous quantitation of chromatin accessibility and transcriptome from a single aliquot of 50,000 cryopreserved Treg cells. Profiling of chromatin accessibility and gene expression in parallel within the same pool of cells controls for cellular heterogeneity and is particularly beneficial when constrained by limited input material. Overall, we observed a high correlation of accessibility patterns and transcription factor dynamics between fresh and cryopreserved samples. Furthermore, highly similar transcriptomic profiles were obtained from whole cells and from the supernatants recovered from ATAC-seq reactions. We highlight the feasibility of applying these techniques to profile the epigenomic landscape of cells recovered from cryopreservation biorepositories.
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Affiliation(s)
- Ying Y Wong
- Robinson Research Institute, University of Adelaide, Adelaide, Australia
| | - Jessica E Harbison
- Robinson Research Institute, University of Adelaide, Adelaide, Australia
- Women's and Children's Hospital, North Adelaide, Australia
| | - Christopher M Hope
- Robinson Research Institute, University of Adelaide, Adelaide, Australia
- Women's and Children's Hospital, North Adelaide, Australia
| | | | - Katherine A Brown
- Robinson Research Institute, University of Adelaide, Adelaide, Australia
| | - Soon W Wong
- Robinson Research Institute, University of Adelaide, Adelaide, Australia
| | - Cheryl Y Brown
- Robinson Research Institute, University of Adelaide, Adelaide, Australia
- Women's and Children's Hospital, North Adelaide, Australia
| | - Jennifer J Couper
- Robinson Research Institute, University of Adelaide, Adelaide, Australia
- Women's and Children's Hospital, North Adelaide, Australia
| | - Jimmy Breen
- Robinson Research Institute, University of Adelaide, Adelaide, Australia
| | - Ning Liu
- Robinson Research Institute, University of Adelaide, Adelaide, Australia
| | - Stephen M Pederson
- Robinson Research Institute, University of Adelaide, Adelaide, Australia
| | - Maren Köhne
- German Center for Neurodegenerative Diseases, University of Bonn, Bonn, Germany
| | - Kathrin Klee
- German Center for Neurodegenerative Diseases, University of Bonn, Bonn, Germany
| | - Joachim Schultze
- German Center for Neurodegenerative Diseases, University of Bonn, Bonn, Germany
| | - Marc Beyer
- German Center for Neurodegenerative Diseases, University of Bonn, Bonn, Germany
| | - Timothy Sadlon
- Robinson Research Institute, University of Adelaide, Adelaide, Australia
- Women's and Children's Hospital, North Adelaide, Australia
| | - Simon C Barry
- Robinson Research Institute, University of Adelaide, Adelaide, Australia.
- Women's and Children's Hospital, North Adelaide, Australia.
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10
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Butto T, Mungikar K, Baumann P, Winter J, Lutz B, Gerber S. Nuclei on the Rise: When Nuclei-Based Methods Meet Next-Generation Sequencing. Cells 2023; 12:cells12071051. [PMID: 37048124 PMCID: PMC10093037 DOI: 10.3390/cells12071051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 03/22/2023] [Accepted: 03/27/2023] [Indexed: 04/03/2023] Open
Abstract
In the last decade, we have witnessed an upsurge in nuclei-based studies, particularly coupled with next-generation sequencing. Such studies aim at understanding the molecular states that exist in heterogeneous cell populations by applying increasingly more affordable sequencing approaches, in addition to optimized methodologies developed to isolate and select nuclei. Although these powerful new methods promise unprecedented insights, it is important to understand and critically consider the associated challenges. Here, we provide a comprehensive overview of the rise of nuclei-based studies and elaborate on their advantages and disadvantages, with a specific focus on their utility for transcriptomic sequencing analyses. Improved designs and appropriate use of the various experimental strategies will result in acquiring biologically accurate and meaningful information.
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Affiliation(s)
- Tamer Butto
- Institute for Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University, 55128 Mainz, Germany
- Correspondence: (T.B.); (S.G.); Tel.: +49-(0)6131-39-27331 (S.G.)
| | - Kanak Mungikar
- Institute of Human Genetics, University Medical Center Mainz, 55131 Mainz, Germany
| | - Peter Baumann
- Faculty of Biology, Johannes Gutenberg-University, 55128 Mainz, Germany
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
| | - Jennifer Winter
- Institute of Human Genetics, University Medical Center Mainz, 55131 Mainz, Germany
- Leibniz Institute for Resilience Research (LIR), 55122 Mainz, Germany
| | - Beat Lutz
- Leibniz Institute for Resilience Research (LIR), 55122 Mainz, Germany
- Institute of Physiological Chemistry, University Medical Center Mainz, 55128 Mainz, Germany
| | - Susanne Gerber
- Institute of Human Genetics, University Medical Center Mainz, 55131 Mainz, Germany
- Correspondence: (T.B.); (S.G.); Tel.: +49-(0)6131-39-27331 (S.G.)
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11
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Kim N, Kang H, Jo A, Yoo SA, Lee HO. Perspectives on single-nucleus RNA sequencing in different cell types and tissues. J Pathol Transl Med 2023; 57:52-59. [PMID: 36623812 PMCID: PMC9846005 DOI: 10.4132/jptm.2022.12.19] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 12/19/2022] [Indexed: 01/11/2023] Open
Abstract
Single-cell RNA sequencing has become a powerful and essential tool for delineating cellular diversity in normal tissues and alterations in disease states. For certain cell types and conditions, there are difficulties in isolating intact cells for transcriptome profiling due to their fragility, large size, tight interconnections, and other factors. Single-nucleus RNA sequencing (snRNA-seq) is an alternative or complementary approach for cells that are difficult to isolate. In this review, we will provide an overview of the experimental and analysis steps of snRNA-seq to understand the methods and characteristics of general and tissue-specific snRNA-seq data. Knowing the advantages and limitations of snRNA-seq will increase its use and improve the biological interpretation of the data generated using this technique.
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Affiliation(s)
- Nayoung Kim
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul,
Korea,Department of Biomedicine and Health Sciences, Graduate School, The Catholic University of Korea, Seoul,
Korea
| | - Huiram Kang
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul,
Korea,Department of Biomedicine and Health Sciences, Graduate School, The Catholic University of Korea, Seoul,
Korea
| | - Areum Jo
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul,
Korea,Department of Biomedicine and Health Sciences, Graduate School, The Catholic University of Korea, Seoul,
Korea
| | - Seung-Ah Yoo
- Department of Biomedicine and Health Sciences, Graduate School, The Catholic University of Korea, Seoul,
Korea,Department of Medical Life Sciences, College of Medicine, The Catholic University of Korea, Seoul,
Korea
| | - Hae-Ock Lee
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul,
Korea,Department of Biomedicine and Health Sciences, Graduate School, The Catholic University of Korea, Seoul,
Korea,Precision Medicine Research Center, College of Medicine, The Catholic University of Korea, Seoul,
Korea
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12
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Pai B, Tome-Garcia J, Cheng WS, Nudelman G, Beaumont KG, Ghatan S, Panov F, Caballero E, Sarpong K, Marcuse L, Yoo J, Jiang Y, Schaefer A, Akbarian S, Sebra R, Pinto D, Zaslavsky E, Tsankova NM. High-resolution transcriptomics informs glial pathology in human temporal lobe epilepsy. Acta Neuropathol Commun 2022; 10:149. [PMID: 36274170 PMCID: PMC9590125 DOI: 10.1186/s40478-022-01453-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 09/30/2022] [Indexed: 11/16/2022] Open
Abstract
The pathophysiology of epilepsy underlies a complex network dysfunction between neurons and glia, the molecular cell type-specific contributions of which remain poorly defined in the human disease. In this study, we validated a method that simultaneously isolates neuronal (NEUN +), astrocyte (PAX6 + NEUN-), and oligodendroglial progenitor (OPC) (OLIG2 + NEUN-) enriched nuclei populations from non-diseased, fresh-frozen human neocortex and then applied it to characterize the distinct transcriptomes of such populations isolated from electrode-mapped temporal lobe epilepsy (TLE) surgical samples. Nuclear RNA-seq confirmed cell type specificity and informed both common and distinct pathways associated with TLE in astrocytes, OPCs, and neurons. Compared to postmortem control, the transcriptome of epilepsy astrocytes showed downregulation of mature astrocyte functions and upregulation of development-related genes. To gain further insight into glial heterogeneity in TLE, we performed single cell transcriptomics (scRNA-seq) on four additional human TLE samples. Analysis of the integrated TLE dataset uncovered a prominent subpopulation of glia that express a hybrid signature of both reactive astrocyte and OPC markers, including many cells with a mixed GFAP + OLIG2 + phenotype. A further integrated analysis of this TLE scRNA-seq dataset and a previously published normal human temporal lobe scRNA-seq dataset confirmed the unique presence of hybrid glia only in TLE. Pseudotime analysis revealed cell transition trajectories stemming from this hybrid population towards both OPCs and reactive astrocytes. Immunofluorescence studies in human TLE samples confirmed the rare presence of GFAP + OLIG2 + glia, including some cells with proliferative activity, and functional analysis of cells isolated directly from these samples disclosed abnormal neurosphere formation in vitro. Overall, cell type-specific isolation of glia from surgical epilepsy samples combined with transcriptomic analyses uncovered abnormal glial subpopulations with de-differentiated phenotype, motivating further studies into the dysfunctional role of reactive glia in temporal lobe epilepsy.
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Affiliation(s)
- Balagopal Pai
- Department of Pathology and Laboratory Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Jessica Tome-Garcia
- Department of Pathology and Laboratory Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Wan Sze Cheng
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - German Nudelman
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Kristin G Beaumont
- Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute for Data Science and Genomic Technology, New York, NY, 10029, USA
| | - Saadi Ghatan
- Department of Neurosurgery, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Fedor Panov
- Department of Neurosurgery, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Elodia Caballero
- Department of Pathology and Laboratory Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Kwadwo Sarpong
- Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute for Data Science and Genomic Technology, New York, NY, 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Lara Marcuse
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Jiyeoun Yoo
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Yan Jiang
- Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Anne Schaefer
- Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Schahram Akbarian
- Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Robert Sebra
- Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute for Data Science and Genomic Technology, New York, NY, 10029, USA
| | - Dalila Pinto
- Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute for Data Science and Genomic Technology, New York, NY, 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Elena Zaslavsky
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
| | - Nadejda M Tsankova
- Department of Pathology and Laboratory Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
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13
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Almeida D, Turecki G. Profiling cell-type specific gene expression in post-mortem human brain samples through laser capture microdissection. Methods 2022; 207:3-10. [PMID: 36064002 DOI: 10.1016/j.ymeth.2022.08.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 07/14/2022] [Accepted: 08/24/2022] [Indexed: 11/16/2022] Open
Abstract
The transcriptome of a cell constitutes an essential piece of cellular identity and contributes to the multifaceted complexity and heterogeneity of cell-types within the mammalian brain. Thus, while a wealth of studies have investigated transcriptomic alterations underlying the pathophysiology of diseases of the brain, their use of bulk-tissue homogenates makes it difficult to tease apart whether observed differences are explained by disease state or cellular composition. Cell-type-specific enrichment strategies are, therefore, crucial in the context of gene expression profiling. Laser capture microdissection (LCM) is one such strategy that allows for the capture of specific cell-types, or regions of interest, under microscopic visualization. In this review, we focus on using LCM for cell-type specific gene expression profiling in post-mortem human brain samples. We begin with a discussion of various LCM systems, followed by a walk-through of each step in the LCM to gene expression profiling workflow and a description of some of the limitations associated with LCM. Throughout the review, we highlight important considerations when using LCM with post-mortem human brain samples. Whenever applicable, commercially available kits that have proven successful in the context of LCM with post-mortem human brain samples are described.
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Affiliation(s)
- Daniel Almeida
- McGill Group for Suicide Studies, Douglas Hospital Research Center, Montreal, QC, Canada, H4H 1R3
| | - Gustavo Turecki
- McGill Group for Suicide Studies, Douglas Hospital Research Center, Montreal, QC, Canada, H4H 1R3; Department of Psychiatry, McGill University, Montreal, QC, Canada, H3A 1A1.
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14
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Robinson EL, Baker AH, Brittan M, McCracken I, Condorelli G, Emanueli C, Srivastava PK, Gaetano C, Thum T, Vanhaverbeke M, Angione C, Heymans S, Devaux Y, Pedrazzini T, Martelli F. Dissecting the transcriptome in cardiovascular disease. Cardiovasc Res 2022; 118:1004-1019. [PMID: 33757121 PMCID: PMC8930073 DOI: 10.1093/cvr/cvab117] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 03/22/2021] [Indexed: 12/12/2022] Open
Abstract
The human transcriptome comprises a complex network of coding and non-coding RNAs implicated in a myriad of biological functions. Non-coding RNAs exhibit highly organized spatial and temporal expression patterns and are emerging as critical regulators of differentiation, homeostasis, and pathological states, including in the cardiovascular system. This review defines the current knowledge gaps, unmet methodological needs, and describes the challenges in dissecting and understanding the role and regulation of the non-coding transcriptome in cardiovascular disease. These challenges include poor annotation of the non-coding genome, determination of the cellular distribution of transcripts, assessment of the role of RNA processing and identification of cell-type specific changes in cardiovascular physiology and disease. We highlight similarities and differences in the hurdles associated with the analysis of the non-coding and protein-coding transcriptomes. In addition, we discuss how the lack of consensus and absence of standardized methods affect reproducibility of data. These shortcomings should be defeated in order to make significant scientific progress and foster the development of clinically applicable non-coding RNA-based therapeutic strategies to lessen the burden of cardiovascular disease.
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Affiliation(s)
- Emma L Robinson
- Department of Cardiology, Cardiovascular Research Institute Maastricht (CARIM), Universiteitssingel 50, 6229 Maastricht University, Maastricht, The Netherlands
- The Division of Cardiology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Andrew H Baker
- Centre for Cardiovascular Science, Queen’s Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh, EH16 4TJ, UK
| | - Mairi Brittan
- Centre for Cardiovascular Science, Queen’s Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh, EH16 4TJ, UK
| | - Ian McCracken
- Centre for Cardiovascular Science, Queen’s Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh, EH16 4TJ, UK
| | - G Condorelli
- Humanitas Research Hospital, Humanitas University, Via Manzoni 113, Rozzano, MI 20089, Italy
| | - C Emanueli
- Imperial College, National Heart and Lung Institute, Hammersmith campus, Du Cane Road, London W12 0NN, UK
| | - P K Srivastava
- Imperial College, National Heart and Lung Institute, Hammersmith campus, Du Cane Road, London W12 0NN, UK
| | - C Gaetano
- Laboratorio di Epigenetica, Istituti Clinici Scientifici Maugeri IRCCS, Via Maugeri 4, Pavia 27100, Italy
| | - T Thum
- Hannover Medical School, Institute of Molecular and Translational Therapeutic Strategies (IMTTS), Carl-Neuberg-Straße 1 30625 Hannover, Germany
| | - M Vanhaverbeke
- UZ Gasthuisberg Campus, KU Leuven, Herestraat 49 3000 Leuven, Belgium
| | - C Angione
- Department of Computer Science and Information Systems, Teesside University, Middlesbrough, TS4 3BX, UK
| | - S Heymans
- Department of Cardiology, Cardiovascular Research Institute Maastricht (CARIM), Universiteitssingel 50, 6229 Maastricht University, Maastricht, The Netherlands
| | - Y Devaux
- Cardiovascular Research Unit, Department of Population Health, Luxembourg Institute of Health, 1A-B, rue Thomas Edison, L-1445 Strassen, Luxembourg
| | - T Pedrazzini
- Experimental Cardiology Unit, Division of Cardiology, Department of Cardiovascular Medicine, University of Lausanne Medical School, 1011 Lausanne, Switzerland
| | - F Martelli
- Molecular Cardiology Laboratory, IRCCS-Policlinico San Donato, Piazza Edmondo Malan, 2, 20097 San Donato, Milan, Italy
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15
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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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16
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Abstract
High-throughput single-cell transcriptomic approaches have revolutionized our view of gene expression at the level of individual cells, providing new insights into their heterogeneity, identities, and functions. Recently, technical challenges to the application of single-cell transcriptomics to plants have been overcome, and many plant organs and tissues have now been subjected to analyses at single-cell resolution. In this review, we describe these studies and their impact on our understanding of the diversity, differentiation, and activities of plant cells. We particularly highlight their impact on plant cell identity, including unprecedented views of cell transitions and definitions of rare and novel cell types. We also point out current challenges and future opportunities for the application and analyses of single-cell transcriptomics in plants. Expected final online publication date for the Annual Review of Genetics, Volume 55 is November 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Kook Hui Ryu
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109, USA; , ,
| | - Yan Zhu
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109, USA; , ,
| | - John Schiefelbein
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109, USA; , ,
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17
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Guo JA, Hoffman HI, Weekes CD, Zheng L, Ting DT, Hwang WL. Refining the Molecular Framework for Pancreatic Cancer with Single-cell and Spatial Technologies. Clin Cancer Res 2021; 27:3825-3833. [PMID: 33653818 PMCID: PMC8282742 DOI: 10.1158/1078-0432.ccr-20-4712] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 01/18/2021] [Accepted: 02/12/2021] [Indexed: 12/27/2022]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a treatment-refractory malignancy in urgent need of a molecular framework for guiding therapeutic strategies. Bulk transcriptomic efforts over the past decade have yielded two broad consensus subtypes: classical pancreatic/epithelial versus basal-like/squamous/quasi-mesenchymal. Although this binary classification enables prognostic stratification, it does not currently inform the administration of treatments uniquely sensitive to either subtype. Furthermore, bulk mRNA studies are challenged by distinguishing contributions from the neoplastic compartment versus other cell types in the microenvironment, which is accentuated in PDAC given that neoplastic cellularity can be low. The application of single-cell transcriptomics to pancreatic tumors has generally lagged behind other cancer types due in part to the difficulty of extracting high-quality RNA from enzymatically degradative tissue, but emerging studies have and will continue to shed light on intratumoral heterogeneity, malignant-stromal interactions, and subtle transcriptional programs previously obscured at the bulk level. In conjunction with insights provided by single-cell/nucleus dissociative techniques, spatially resolved technologies should also facilitate the contextualization of gene programs and inferred cell-cell interactions within the tumor architecture. Finally, given that patients often receive neoadjuvant chemotherapy and/or chemoradiotherapy even in resectable disease, deciphering the gene programs enriched in or induced by cytotoxic therapy will be crucial for developing insights into complementary treatments aimed at eradicating residual cancer cells. Taken together, single-cell and spatial technologies provide an unprecedented opportunity to refine the foundations laid by prior bulk molecular studies and significantly augment precision oncology efforts in pancreatic cancer.
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Affiliation(s)
- Jimmy A Guo
- Department of Radiation Oncology, Massachusetts General Hospital Cancer Center, Boston, Massachusetts
- Biological and Biomedical Sciences Program, Harvard University, Boston, Massachusetts
- School of Medicine, University of California, San Francisco, San Francisco, California
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Hannah I Hoffman
- Department of Radiation Oncology, Massachusetts General Hospital Cancer Center, Boston, Massachusetts
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Koch Institute for Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Colin D Weekes
- Division of Hematology and Oncology, Department of Medicine, Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | - Lei Zheng
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - David T Ting
- Division of Hematology and Oncology, Department of Medicine, Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | - William L Hwang
- Department of Radiation Oncology, Massachusetts General Hospital Cancer Center, Boston, Massachusetts.
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Koch Institute for Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts
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18
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INTACT vs. FANS for Cell-Type-Specific Nuclei Sorting: A Comprehensive Qualitative and Quantitative Comparison. Int J Mol Sci 2021; 22:ijms22105335. [PMID: 34069481 PMCID: PMC8159132 DOI: 10.3390/ijms22105335] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Revised: 05/11/2021] [Accepted: 05/14/2021] [Indexed: 12/15/2022] Open
Abstract
Increasing numbers of studies seek to characterize the different cellular sub-populations present in mammalian tissues. The techniques “Isolation of Nuclei Tagged in Specific Cell Types” (INTACT) or “Fluorescence-Activated Nuclei Sorting” (FANS) are frequently used for isolating nuclei of specific cellular subtypes. These nuclei are then used for molecular characterization of the cellular sub-populations. Despite the increasing popularity of both techniques, little is known about their isolation efficiency, advantages, and disadvantages or downstream molecular effects. In our study, we compared the physical and molecular attributes of sfGFP+ nuclei isolated by the two methods—INTACT and FANS—from the neocortices of Arc-CreERT2 × CAG-Sun1/sfGFP animals. We identified differences in efficiency of sfGFP+ nuclei isolation, nuclear size as well as transcriptional (RNA-seq) and chromatin accessibility (ATAC-seq) states. Therefore, our study presents a comprehensive comparison between the two widely used nuclei sorting techniques, identifying the advantages and disadvantages for both INTACT and FANS. Our conclusions are summarized in a table to guide researchers in selecting the most suitable methodology for their individual experimental design.
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19
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Zaghlool A, Niazi A, Björklund ÅK, Westholm JO, Ameur A, Feuk L. Characterization of the nuclear and cytosolic transcriptomes in human brain tissue reveals new insights into the subcellular distribution of RNA transcripts. Sci Rep 2021; 11:4076. [PMID: 33603054 PMCID: PMC7893067 DOI: 10.1038/s41598-021-83541-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 01/20/2021] [Indexed: 12/23/2022] Open
Abstract
Transcriptome analysis has mainly relied on analyzing RNA sequencing data from whole cells, overlooking the impact of subcellular RNA localization and its influence on our understanding of gene function, and interpretation of gene expression signatures in cells. Here, we separated cytosolic and nuclear RNA from human fetal and adult brain samples and performed a comprehensive analysis of cytosolic and nuclear transcriptomes. There are significant differences in RNA expression for protein-coding and lncRNA genes between cytosol and nucleus. We show that transcripts encoding the nuclear-encoded mitochondrial proteins are significantly enriched in the cytosol compared to the rest of protein-coding genes. Differential expression analysis between fetal and adult frontal cortex show that results obtained from the cytosolic RNA differ from results using nuclear RNA both at the level of transcript types and the number of differentially expressed genes. Our data provide a resource for the subcellular localization of thousands of RNA transcripts in the human brain and highlight differences in using the cytosolic or the nuclear transcriptomes for expression analysis.
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Affiliation(s)
- Ammar Zaghlool
- Department of Immunology, Genetics and Pathology, Uppsala University, BMC B11:4, Box 815, 751 08, Uppsala, Sweden. .,Science for Life Laboratory in Uppsala, Uppsala University, Uppsala, Sweden.
| | - Adnan Niazi
- Department of Immunology, Genetics and Pathology, Uppsala University, BMC B11:4, Box 815, 751 08, Uppsala, Sweden.,Science for Life Laboratory in Uppsala, Uppsala University, Uppsala, Sweden
| | - Åsa K Björklund
- Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Husargatan 3, 752 37, Uppsala, Sweden
| | - Jakub Orzechowski Westholm
- Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Stockholm University, Box 1031, 17121, Solna, Sweden
| | - Adam Ameur
- Department of Immunology, Genetics and Pathology, Uppsala University, BMC B11:4, Box 815, 751 08, Uppsala, Sweden.,Science for Life Laboratory in Uppsala, Uppsala University, Uppsala, Sweden
| | - Lars Feuk
- Department of Immunology, Genetics and Pathology, Uppsala University, BMC B11:4, Box 815, 751 08, Uppsala, Sweden. .,Science for Life Laboratory in Uppsala, Uppsala University, Uppsala, Sweden.
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20
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Serafin EK, Paranjpe A, Brewer CL, Baccei ML. Single-nucleus characterization of adult mouse spinal dynorphin-lineage cells and identification of persistent transcriptional effects of neonatal hindpaw incision. Pain 2021; 162:203-218. [PMID: 33045156 PMCID: PMC7744314 DOI: 10.1097/j.pain.0000000000002007] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Neonatal tissue damage can have long-lasting effects on nociceptive processing in the central nervous system, which may reflect persistent injury-evoked alterations to the normal balance between synaptic inhibition and excitation in the spinal dorsal horn. Spinal dynorphin-lineage (pDyn) neurons are part of an inhibitory circuit which limits the flow of nociceptive input to the brain and is disrupted by neonatal tissue damage. To identify the potential molecular underpinnings of this disruption, an unbiased single-nucleus RNAseq analysis of adult mouse spinal pDyn cells characterized this population in depth and then identified changes in gene expression evoked by neonatal hindpaw incision. The analysis revealed 11 transcriptionally distinct subpopulations (ie, clusters) of dynorphin-lineage cells, including both inhibitory and excitatory neurons. Investigation of injury-evoked differential gene expression identified 15 genes that were significantly upregulated or downregulated in adult pDyn neurons from neonatally incised mice compared with naive littermate controls, with both cluster-specific and pan-neuronal transcriptional changes observed. Several of the identified genes, such as Oxr1 and Fth1 (encoding ferritin), were related to the cellular stress response. However, the relatively low number of injury-evoked differentially expressed genes also suggests that posttranscriptional regulation within pDyn neurons may play a key role in the priming of developing nociceptive circuits by early-life injury. Overall, the findings reveal novel insights into the molecular heterogeneity of a key population of dorsal horn interneurons that has previously been implicated in the suppression of mechanical pain and itch.
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Affiliation(s)
- Elizabeth K Serafin
- Department of Anesthesiology, Pain Research Center, University of Cincinnati Medical Center, Cincinnati, OH, United States . Dr. Brewer is now with the Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, CA, United States
| | - Aditi Paranjpe
- Division of Biomedical Informatics, Bioinformatics Collaborative Services, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States
| | - Chelsie L Brewer
- Department of Anesthesiology, Pain Research Center, University of Cincinnati Medical Center, Cincinnati, OH, United States . Dr. Brewer is now with the Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, CA, United States
- Neuroscience Graduate Program, University of Cincinnati College of Medicine, Cincinnati, OH, United States
| | - Mark L Baccei
- Department of Anesthesiology, Pain Research Center, University of Cincinnati Medical Center, Cincinnati, OH, United States . Dr. Brewer is now with the Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, CA, United States
- Neuroscience Graduate Program, University of Cincinnati College of Medicine, Cincinnati, OH, United States
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21
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Matsubayashi M, Sakaguchi YM, Sahara Y, Nanaura H, Kikuchi S, Asghari A, Bui L, Kobashigawa S, Nakanishi M, Nagata R, Matsui TK, Kashino G, Hasegawa M, Takasawa S, Eriguchi M, Tsuruya K, Nagamori S, Sugie K, Nakagawa T, Takasato M, Umetani M, Mori E. 27-Hydroxycholesterol regulates human SLC22A12 gene expression through estrogen receptor action. FASEB J 2020; 35:e21262. [PMID: 33368618 PMCID: PMC7771643 DOI: 10.1096/fj.202002077r] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 11/11/2020] [Accepted: 11/25/2020] [Indexed: 02/06/2023]
Abstract
The excretion and reabsorption of uric acid both to and from urine are tightly regulated by uric acid transporters. Metabolic syndrome conditions, such as obesity, hypercholesterolemia, and insulin resistance, are believed to regulate the expression of uric acid transporters and decrease the excretion of uric acid. However, the mechanisms driving cholesterol impacts on uric acid transporters have been unknown. Here, we show that cholesterol metabolite 27‐hydroxycholesterol (27HC) upregulates the uric acid reabsorption transporter URAT1 encoded by SLC22A12 via estrogen receptors (ER). Transcriptional motif analysis showed that the SLC22A12 gene promoter has more estrogen response elements (EREs) than other uric acid reabsorption transporters such as SLC22A11 and SLC22A13, and 27HC‐activated SLC22A12 gene promoter via ER through EREs. Furthermore, 27HC increased SLC22A12 gene expression in human kidney organoids. Our results suggest that in hypercholesterolemic conditions, elevated levels of 27HC derived from cholesterol induce URAT1/SLC22A12 expression to increase uric acid reabsorption, and thereby, could increase serum uric acid levels.
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Affiliation(s)
| | | | - Yoshiki Sahara
- RIKEN Center for Biosystems Dynamics Research, Kobe, Japan.,Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Hitoki Nanaura
- Department of Future Basic Medicine, Nara Medical University, Nara, Japan.,Department of Neurology, Nara Medical University, Kashihara, Japan
| | - Sotaro Kikuchi
- Department of Future Basic Medicine, Nara Medical University, Nara, Japan
| | - Arvand Asghari
- Center for Nuclear Receptors and Cell Signaling, Department of Biology and Biochemistry, University of Houston, Houston, TX, USA
| | - Linh Bui
- Center for Nuclear Receptors and Cell Signaling, Department of Biology and Biochemistry, University of Houston, Houston, TX, USA
| | - Shinko Kobashigawa
- Department of Future Basic Medicine, Nara Medical University, Nara, Japan
| | - Mari Nakanishi
- Department of Future Basic Medicine, Nara Medical University, Nara, Japan
| | - Riko Nagata
- Department of Future Basic Medicine, Nara Medical University, Nara, Japan
| | - Takeshi K Matsui
- Department of Future Basic Medicine, Nara Medical University, Nara, Japan.,Department of Neurology, Nara Medical University, Kashihara, Japan
| | - Genro Kashino
- Radioisotope Research Center, Nara Medical University, Kashihara, Japan
| | - Masatoshi Hasegawa
- Department of Radiation Oncology, Nara Medical University, Kashihara, Japan
| | - Shin Takasawa
- Department of Biochemistry, Nara Medical University, Kashihara, Japan
| | | | - Kazuhiko Tsuruya
- Department of Nephrology, Nara Medical University, Kashihara, Japan
| | - Shushi Nagamori
- Department of Collaborative Research, Nara Medical University, Nara, Japan
| | - Kazuma Sugie
- Department of Neurology, Nara Medical University, Kashihara, Japan
| | - Takahiko Nakagawa
- Department of Future Basic Medicine, Nara Medical University, Nara, Japan
| | - Minoru Takasato
- RIKEN Center for Biosystems Dynamics Research, Kobe, Japan.,Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Michihisa Umetani
- Center for Nuclear Receptors and Cell Signaling, Department of Biology and Biochemistry, University of Houston, Houston, TX, USA.,HEALTH Research Institute, University of Houston, Houston, TX, USA
| | - Eiichiro Mori
- Department of Future Basic Medicine, Nara Medical University, Nara, Japan.,V-iCliniX Laboratory, Nara Medical University, Kashihara, Japan
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22
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Reading the heart at single-cell resolution. J Mol Cell Cardiol 2020; 148:34-45. [PMID: 32871159 DOI: 10.1016/j.yjmcc.2020.08.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 08/04/2020] [Accepted: 08/20/2020] [Indexed: 12/21/2022]
Abstract
The burgeoning field of single-cell transcriptomics augments our ability to scrutinize organ systems at unprecedented resolutions. Single-cell RNA sequencing (scRNA-seq) and analytical techniques have shed light on the cellular heterogeneity, developmental trajectories, intercellular communications of the cardiac system, and thus contributed much to the understanding of cardiac development, homeostasis and disorders. Although generalized protocols are well established for scRNA-seq pipelines, customized sample preparation, quality control, and data interpretation are still needed in cardiac research. In this article, we highlight major steps that impact data quality in scRNA-seq experiments, with particular focus on sample and data processing of cardiomyocytes. We also summarize popular applications of scRNA-seq, outlining general tools, caveats and examples in cardiac research.
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23
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Transcriptional profile of spinal dynorphin-lineage interneurons in the developing mouse. Pain 2020; 160:2380-2397. [PMID: 31166300 DOI: 10.1097/j.pain.0000000000001636] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Mounting evidence suggests that the spinal dorsal horn (SDH) contains multiple subpopulations of inhibitory interneurons that play distinct roles in somatosensory processing, as exemplified by the importance of spinal dynorphin-expressing neurons for the suppression of mechanical pain and chemical itch. Although it is clear that GABAergic transmission in the SDH undergoes significant alterations during early postnatal development, little is known about the maturation of discrete inhibitory "microcircuits" within the region. As a result, the goal of this study was to elucidate the gene expression profile of spinal dynorphin (pDyn)-lineage neurons throughout life. We isolated nuclear RNA specifically from pDyn-lineage SDH interneurons at postnatal days 7, 21, and 80 using the Isolation of Nuclei Tagged in Specific Cell Types (INTACT) technique, followed by RNA-seq analysis. Over 650 genes were ≥2-fold enriched in adult pDyn nuclei compared with non-pDyn spinal cord nuclei, including targets with known relevance to pain such as galanin (Gal), prepronociceptin (Pnoc), and nitric oxide synthase 1 (Nos1). In addition, the gene encoding a membrane-bound guanylate cyclase, Gucy2d, was identified as a novel and highly selective marker of the pDyn population within the SDH. Differential gene expression analysis comparing pDyn nuclei across the 3 ages revealed sets of genes that were significantly upregulated (such as Cartpt, encoding cocaine- and amphetamine-regulated transcript peptide) or downregulated (including Npbwr1, encoding the receptor for neuropeptides B/W) during postnatal development. Collectively, these results provide new insight into the potential molecular mechanisms underlying the known age-dependent changes in spinal nociceptive processing and pain sensitivity.
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24
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Amamoto R, Zuccaro E, Curry NC, Khurana S, Chen HH, Cepko CL, Arlotta P. FIN-Seq: transcriptional profiling of specific cell types from frozen archived tissue of the human central nervous system. Nucleic Acids Res 2020; 48:e4. [PMID: 31728515 PMCID: PMC7145626 DOI: 10.1093/nar/gkz968] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 09/09/2019] [Accepted: 11/12/2019] [Indexed: 12/14/2022] Open
Abstract
Thousands of frozen, archived tissue samples from the human central nervous system (CNS) are currently available in brain banks. As recent developments in RNA sequencing technologies are beginning to elucidate the cellular diversity present within the human CNS, it is becoming clear that an understanding of this diversity would greatly benefit from deeper transcriptional analyses. Single cell and single nucleus RNA profiling provide one avenue to decipher this heterogeneity. An alternative, complementary approach is to profile isolated, pre-defined cell types and use methods that can be applied to many archived human tissue samples that have been stored long-term. Here, we developed FIN-Seq (Frozen Immunolabeled Nuclei Sequencing), a method that accomplishes these goals. FIN-Seq uses immunohistochemical isolation of nuclei of specific cell types from frozen human tissue, followed by bulk RNA-Sequencing. We applied this method to frozen postmortem samples of human cerebral cortex and retina and were able to identify transcripts, including low abundance transcripts, in specific cell types.
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Affiliation(s)
- Ryoji Amamoto
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
- Department of Genetics and Ophthalmology, Howard Hughes Medical Institute, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Emanuela Zuccaro
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Nathan C Curry
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Sonia Khurana
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Hsu-Hsin Chen
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Constance L Cepko
- Department of Genetics and Ophthalmology, Howard Hughes Medical Institute, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Paola Arlotta
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
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25
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Berger TC, Vigeland MD, Hjorthaug HS, Etholm L, Nome CG, Taubøll E, Heuser K, Selmer KK. Neuronal and glial DNA methylation and gene expression changes in early epileptogenesis. PLoS One 2019; 14:e0226575. [PMID: 31887157 PMCID: PMC6936816 DOI: 10.1371/journal.pone.0226575] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 11/28/2019] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND AND AIMS Mesial Temporal Lobe Epilepsy is characterized by progressive changes of both neurons and glia, also referred to as epileptogenesis. No curative treatment options, apart from surgery, are available. DNA methylation (DNAm) is a potential upstream mechanism in epileptogenesis and may serve as a novel therapeutic target. To our knowledge, this is the first study to investigate epilepsy-related DNAm, gene expression (GE) and their relationship, in neurons and glia. METHODS We used the intracortical kainic acid injection model to elicit status epilepticus. At 24 hours post injection, hippocampi from eight kainic acid- (KA) and eight saline-injected (SH) mice were extracted and shock frozen. Separation into neurons and glial nuclei was performed by flow cytometry. Changes in DNAm and gene expression were measured with reduced representation bisulfite sequencing (RRBS) and mRNA-sequencing (mRNAseq). Statistical analyses were performed in R with the edgeR package. RESULTS We observed fulminant DNAm- and GE changes in both neurons and glia at 24 hours after initiation of status epilepticus. The vast majority of these changes were specific for either neurons or glia. At several epilepsy-related genes, like HDAC11, SPP1, GAL, DRD1 and SV2C, significant differential methylation and differential gene expression coincided. CONCLUSION We found neuron- and glia-specific changes in DNAm and gene expression in early epileptogenesis. We detected single genetic loci in several epilepsy-related genes, where DNAm and GE changes coincide, worth further investigation. Further, our results may serve as an information source for neuronal and glial alterations in both DNAm and GE in early epileptogenesis.
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Affiliation(s)
- Toni C. Berger
- Department of Neurology, Oslo University Hospital, Oslo, Norway
- University of Oslo, Oslo, Norway
- * E-mail:
| | - Magnus D. Vigeland
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Hanne S. Hjorthaug
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Lars Etholm
- National Center for Epilepsy, Oslo University Hospital, Sandvika, Norway
- Department of Neurology, Section for Neurophysiology, Oslo University Hospital, Oslo, Norway
| | | | - Erik Taubøll
- Department of Neurology, Oslo University Hospital, Oslo, Norway
- University of Oslo, Oslo, Norway
| | - Kjell Heuser
- Department of Neurology, Oslo University Hospital, Oslo, Norway
- University of Oslo, Oslo, Norway
| | - Kaja K. Selmer
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
- National Center for Epilepsy, Oslo University Hospital, Sandvika, Norway
- Division of Clinical Neuroscience, Department of Research and Development, Oslo University Hospital, Oslo, Norway
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26
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Contreras RE, Schriever SC, Pfluger PT. Physiological and Epigenetic Features of Yoyo Dieting and Weight Control. Front Genet 2019; 10:1015. [PMID: 31921275 PMCID: PMC6917653 DOI: 10.3389/fgene.2019.01015] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 09/24/2019] [Indexed: 12/16/2022] Open
Abstract
Obesity and being overweight have become a worldwide epidemic affecting more than 1.9 billion adults and 340 million children. Efforts to curb this global health burden by developing effective long-term non-surgical weight loss interventions continue to fail due to weight regain after weight loss. Weight cycling, often referred to as Yoyo dieting, is driven by physiological counter-regulatory mechanisms that aim at preserving energy, i.e. decreased energy expenditure, increased energy intake, and impaired brain-periphery communication. Models based on genetically determined set points explained some of the weight control mechanisms, but exact molecular underpinnings remained elusive. Today, gene–environment interactions begin to emerge as likely drivers for the obesogenic memory effect associated with weight cycling. Here, epigenetic mechanisms, including histone modifications and DNA methylation, appear as likely factors that underpin long-lasting deleterious adaptations or an imprinted obesogenic memory to prevent weight loss maintenance. The first part summarizes our current knowledge on the physiology of weight cycling by discussing human and murine studies on the Yoyo-dieting phenomenon and physiological adaptations associated with weight loss and weight re-gain. The second part provides an overview on known associations between obesity and epigenetic modifications. We further interrogate the roles of epigenetic mechanisms in the CNS control of cognitive functions as well as reward and addictive behaviors, and subsequently discuss whether such mechanisms play a role in weight control. The final two parts describe major opportunities and challenges associated with studying epigenetic mechanisms in the CNS with its highly heterogenous cell populations, and provide a summary of recent technological advances that will help to delineate whether an obese memory is based upon epigenetic mechanisms.
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Affiliation(s)
- Raian E Contreras
- Research Unit Neurobiology of Diabetes, Helmholtz Zentrum München, Neuherberg, Germany.,Institute for Diabetes and Obesity, Helmholtz Zentrum München, Neuherberg, Germany.,German Centre for Diabetes Research (DZD), Neuherberg, Germany.,Neurobiology of Diabetes, TUM School of Medicine, Technische Universität München, Munich, Germany
| | - Sonja C Schriever
- Research Unit Neurobiology of Diabetes, Helmholtz Zentrum München, Neuherberg, Germany.,Institute for Diabetes and Obesity, Helmholtz Zentrum München, Neuherberg, Germany.,German Centre for Diabetes Research (DZD), Neuherberg, Germany
| | - Paul T Pfluger
- Research Unit Neurobiology of Diabetes, Helmholtz Zentrum München, Neuherberg, Germany.,Institute for Diabetes and Obesity, Helmholtz Zentrum München, Neuherberg, Germany.,German Centre for Diabetes Research (DZD), Neuherberg, Germany.,Neurobiology of Diabetes, TUM School of Medicine, Technische Universität München, Munich, Germany
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27
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Kubo M, Nishiyama T, Tamada Y, Sano R, Ishikawa M, Murata T, Imai A, Lang D, Demura T, Reski R, Hasebe M. Single-cell transcriptome analysis of Physcomitrella leaf cells during reprogramming using microcapillary manipulation. Nucleic Acids Res 2019; 47:4539-4553. [PMID: 30873540 PMCID: PMC6511839 DOI: 10.1093/nar/gkz181] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2018] [Revised: 03/01/2019] [Accepted: 03/08/2019] [Indexed: 12/20/2022] Open
Abstract
Next-generation sequencing technologies have made it possible to carry out transcriptome analysis at the single-cell level. Single-cell RNA-sequencing (scRNA-seq) data provide insights into cellular dynamics, including intercellular heterogeneity as well as inter- and intra-cellular fluctuations in gene expression that cannot be studied using populations of cells. The utilization of scRNA-seq is, however, restricted to cell types that can be isolated from their original tissues, and it can be difficult to obtain precise positional information for these cells in situ. Here, we established single cell-digital gene expression (1cell-DGE), a method of scRNA-seq that uses micromanipulation to extract the contents of individual living cells in intact tissue while recording their positional information. With 1cell-DGE, we could detect differentially expressed genes (DEGs) during the reprogramming of leaf cells of the moss Physcomitrella patens, identifying 6382 DEGs between cells at 0 and 24 h after excision. Furthermore, we identified a subpopulation of reprogramming cells based on their pseudotimes, which were calculated using transcriptome profiles at 24 h. 1cell-DGE with microcapillary manipulation can be used to analyze the gene expression of individual cells without detaching them from their tightly associated tissues, enabling us to retain positional information and investigate cell-cell interactions.
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Affiliation(s)
- Minoru Kubo
- Institute for Research Initiative, Nara Institute of Science and Technology, Ikoma 630-0192, Japan
| | - Tomoaki Nishiyama
- Advanced Science Research Center, Kanazawa University, Kanazawa 920-0934, Japan
| | - Yosuke Tamada
- National Institute for Basic Biology, Okazaki 444-8585, Japan.,School of Life Science, The Graduate University for Advanced Studies, Okazaki 444-8585, Japan
| | - Ryosuke Sano
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma 630-0192, Japan
| | - Masaki Ishikawa
- National Institute for Basic Biology, Okazaki 444-8585, Japan.,School of Life Science, The Graduate University for Advanced Studies, Okazaki 444-8585, Japan
| | - Takashi Murata
- National Institute for Basic Biology, Okazaki 444-8585, Japan.,School of Life Science, The Graduate University for Advanced Studies, Okazaki 444-8585, Japan
| | - Akihiro Imai
- Faculty of Life Sciences, Hiroshima Institute of Technology, Hiroshima 731-5193, Japan
| | - Daniel Lang
- Plant Biotechnology, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Taku Demura
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma 630-0192, Japan
| | - Ralf Reski
- Plant Biotechnology, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany.,Signaling Research Centres BIOSS and CIBSS, University of Freiburg, 79104 Freiburg, Germany
| | - Mitsuyasu Hasebe
- National Institute for Basic Biology, Okazaki 444-8585, Japan.,School of Life Science, The Graduate University for Advanced Studies, Okazaki 444-8585, Japan
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28
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Del Toro-De León G, Köhler C. Endosperm-specific transcriptome analysis by applying the INTACT system. PLANT REPRODUCTION 2019; 32:55-61. [PMID: 30588542 DOI: 10.1007/s00497-018-00356-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 12/14/2018] [Indexed: 05/06/2023]
Abstract
KEY MESSAGE We report the adaptation of the INTACT method for RNA-sequencing in the endosperm and demonstrate its feasibility for allele-specific expression analysis. Tissue-specific transcriptome analyses provide important insights into the developmental programs of defined cell types. The isolation of nuclei tagged in specific cell types (INTACT) is a versatile method that allows to isolate highly pure nuclei from defined tissue types that can be used for several downstream applications. Here, we describe the adaptation of INTACT from endosperm nuclei for high-throughput RNA-sequencing. By analyzing the ratio of parental reads and tissue-specific gene expression in the endosperm, we could assess the contamination level of our samples. Based on this analysis, we estimate that in most of the samples the contamination level is lower than in previously published datasets. We further show that the nuclear transcriptome and total transcriptome of the endosperm are well correlated. Together, our data show that INTACT of the endosperm is a reliable methodology for endosperm-specific transcriptome analysis that overcomes the limitation of time-consuming manual endosperm dissection that is connected with high levels of maternal tissue contamination. INTACT does not rely on expensive equipment and can be set up in every standard molecular biology laboratory, making it the method of choice for future molecular studies of the endosperm.
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Affiliation(s)
- Gerardo Del Toro-De León
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden
| | - Claudia Köhler
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden.
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29
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Palovaara J, Weijers D. Adapting INTACT to analyse cell-type-specific transcriptomes and nucleocytoplasmic mRNA dynamics in the Arabidopsis embryo. PLANT REPRODUCTION 2019; 32:113-121. [PMID: 30430248 DOI: 10.1007/s00497-018-0347-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 10/31/2018] [Indexed: 05/06/2023]
Abstract
In the early embryo of vascular plants, the different cell types and stem cells of the seedling are specified as the embryo develops from a zygote towards maturity. How the key steps in cell and tissue specification are instructed by genome-wide transcriptional activity is poorly understood. Progress in defining transcriptional regulation at the genome-wide level in plant embryos has been hampered by difficulties associated with capturing cell-type-specific transcriptomes in this small and inaccessible structure. We recently adapted a two-component genetic nucleus labelling system called INTACT to isolate nuclei from distinct cell types at different stages of Arabidopsis thaliana embryogenesis. We have used these to generate a transcriptomic atlas of embryo development following microarray-based expression profiling. Here, we present a general description of the adapted INTACT procedure, including the two-component labelling system, seed isolation, nuclei preparation and purification, as well as transcriptomic profiling. We also compare nuclear and cellular transcriptomes from the early Arabidopsis embryo to assess nucleocytoplasmic differences and discuss how these differences can be used to infer regulation of gene activity.
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Affiliation(s)
- Joakim Palovaara
- Laboratory of Biochemistry, Wageningen University, 6708 WE, Wageningen, The Netherlands
- Molecular Genetics, University of Bremen, 28359, Bremen, Germany
| | - Dolf Weijers
- Laboratory of Biochemistry, Wageningen University, 6708 WE, Wageningen, The Netherlands.
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30
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Wu H, Uchimura K, Donnelly EL, Kirita Y, Morris SA, Humphreys BD. Comparative Analysis and Refinement of Human PSC-Derived Kidney Organoid Differentiation with Single-Cell Transcriptomics. Cell Stem Cell 2018; 23:869-881.e8. [PMID: 30449713 DOI: 10.1016/j.stem.2018.10.010] [Citation(s) in RCA: 358] [Impact Index Per Article: 59.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 08/09/2018] [Accepted: 10/06/2018] [Indexed: 12/18/2022]
Abstract
Kidney organoids derived from human pluripotent stem cells have great utility for investigating organogenesis and disease mechanisms and, potentially, as a replacement tissue source, but how closely organoids derived from current protocols replicate adult human kidney is undefined. We compared two directed differentiation protocols by single-cell transcriptomics of 83,130 cells from 65 organoids with single-cell transcriptomes of fetal and adult kidney cells. Both protocols generate a diverse range of kidney cells with differing ratios, but organoid-derived cell types are immature, and 10%-20% of cells are non-renal. Reconstructing lineage relationships by pseudotemporal ordering identified ligands, receptors, and transcription factor networks associated with fate decisions. Brain-derived neurotrophic factor (BDNF) and its cognate receptor NTRK2 were expressed in the neuronal lineage during organoid differentiation. Inhibiting this pathway improved organoid formation by reducing neurons by 90% without affecting kidney differentiation, highlighting the power of single-cell technologies to characterize and improve organoid differentiation.
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Affiliation(s)
- Haojia Wu
- Division of Nephrology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Kohei Uchimura
- Division of Nephrology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Erinn L Donnelly
- Division of Nephrology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Yuhei Kirita
- Division of Nephrology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Samantha A Morris
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, USA; Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | - Benjamin D Humphreys
- Division of Nephrology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA; Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, USA.
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31
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Trinh LA, Chong-Morrison V, Sauka-Spengler T. Biotagging, an in vivo biotinylation approach for cell-type specific subcellular profiling in zebrafish. Methods 2018; 150:24-31. [DOI: 10.1016/j.ymeth.2018.07.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 07/16/2018] [Accepted: 07/30/2018] [Indexed: 12/21/2022] Open
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32
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Nguyen QH, Pervolarakis N, Nee K, Kessenbrock K. Experimental Considerations for Single-Cell RNA Sequencing Approaches. Front Cell Dev Biol 2018; 6:108. [PMID: 30234113 PMCID: PMC6131190 DOI: 10.3389/fcell.2018.00108] [Citation(s) in RCA: 105] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2018] [Accepted: 08/20/2018] [Indexed: 01/01/2023] Open
Abstract
Single-cell transcriptomic technologies have emerged as powerful tools to explore cellular heterogeneity at the resolution of individual cells. Previous scientific knowledge in cell biology is largely limited to data generated by bulk profiling methods, which only provide averaged read-outs that generally mask cellular heterogeneity. This averaged approach is particularly problematic when the biological effect of interest is limited to only a subpopulation of cells such as stem/progenitor cells within a given tissue, or immune cell subsets infiltrating a tumor. Great advances in single-cell RNA sequencing (scRNAseq) enabled scientists to overcome this limitation and allow for in depth interrogation of previously unexplored rare cell types. Due to the high sensitivity of scRNAseq, adequate attention must be put into experimental setup and execution. Careful handling and processing of cells for scRNAseq is critical to preserve the native expression profile that will ensure meaningful analysis and conclusions. Here, we delineate the individual steps of a typical single-cell analysis workflow from tissue procurement, cell preparation, to platform selection and data analysis, and we discuss critical challenges in each of these steps, which will serve as a helpful guide to navigate the complex field of single-cell sequencing.
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Affiliation(s)
- Quy H. Nguyen
- Department of Biological Chemistry, University of California, Irvine, Irvine, CA, United States
| | - Nicholas Pervolarakis
- Center for Complex Biological Systems, University of California, Irvine, Irvine, CA, United States
| | - Kevin Nee
- Department of Biological Chemistry, University of California, Irvine, Irvine, CA, United States
| | - Kai Kessenbrock
- Department of Biological Chemistry, University of California, Irvine, Irvine, CA, United States
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33
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Han KY, Kim KT, Joung JG, Son DS, Kim YJ, Jo A, Jeon HJ, Moon HS, Yoo CE, Chung W, Eum HH, Kim S, Kim HK, Lee JE, Ahn MJ, Lee HO, Park D, Park WY. SIDR: simultaneous isolation and parallel sequencing of genomic DNA and total RNA from single cells. Genome Res 2017; 28:75-87. [PMID: 29208629 PMCID: PMC5749184 DOI: 10.1101/gr.223263.117] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 11/27/2017] [Indexed: 12/26/2022]
Abstract
Simultaneous sequencing of the genome and transcriptome at the single-cell level is a powerful tool for characterizing genomic and transcriptomic variation and revealing correlative relationships. However, it remains technically challenging to analyze both the genome and transcriptome in the same cell. Here, we report a novel method for simultaneous isolation of genomic DNA and total RNA (SIDR) from single cells, achieving high recovery rates with minimal cross-contamination, as is crucial for accurate description and integration of the single-cell genome and transcriptome. For reliable and efficient separation of genomic DNA and total RNA from single cells, the method uses hypotonic lysis to preserve nuclear lamina integrity and subsequently captures the cell lysate using antibody-conjugated magnetic microbeads. Evaluating the performance of this method using real-time PCR demonstrated that it efficiently recovered genomic DNA and total RNA. Thorough data quality assessments showed that DNA and RNA simultaneously fractionated by the SIDR method were suitable for genome and transcriptome sequencing analysis at the single-cell level. The integration of single-cell genome and transcriptome sequencing by SIDR (SIDR-seq) showed that genetic alterations, such as copy-number and single-nucleotide variations, were more accurately captured by single-cell SIDR-seq compared with conventional single-cell RNA-seq, although copy-number variations positively correlated with the corresponding gene expression levels. These results suggest that SIDR-seq is potentially a powerful tool to reveal genetic heterogeneity and phenotypic information inferred from gene expression patterns at the single-cell level.
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Affiliation(s)
- Kyung Yeon Han
- Samsung Genome Institute, Samsung Medical Center, Seoul 06351, South Korea
| | - Kyu-Tae Kim
- Samsung Genome Institute, Samsung Medical Center, Seoul 06351, South Korea
| | - Je-Gun Joung
- Samsung Genome Institute, Samsung Medical Center, Seoul 06351, South Korea
| | - Dae-Soon Son
- Samsung Genome Institute, Samsung Medical Center, Seoul 06351, South Korea
| | - Yeon Jeong Kim
- Samsung Genome Institute, Samsung Medical Center, Seoul 06351, South Korea
| | - Areum Jo
- Samsung Genome Institute, Samsung Medical Center, Seoul 06351, South Korea
| | - Hyo-Jeong Jeon
- Samsung Genome Institute, Samsung Medical Center, Seoul 06351, South Korea
| | - Hui-Sung Moon
- Samsung Genome Institute, Samsung Medical Center, Seoul 06351, South Korea
| | - Chang Eun Yoo
- Samsung Genome Institute, Samsung Medical Center, Seoul 06351, South Korea
| | - Woosung Chung
- Samsung Genome Institute, Samsung Medical Center, Seoul 06351, South Korea.,Department of Health Sciences and Technology, SAIHST, Sungkyunkwan University, Seoul 06351, South Korea
| | - Hye Hyeon Eum
- Samsung Genome Institute, Samsung Medical Center, Seoul 06351, South Korea.,Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul 03080, South Korea
| | - Sangmin Kim
- Department of Breast Cancer Center, Samsung Medical Center, Seoul 06351, South Korea
| | - Hong Kwan Kim
- Department of Thoracic and Cardiovascular Surgery, Samsung Medical Center, Seoul 06351, South Korea
| | - Jeong Eon Lee
- Department of Health Sciences and Technology, SAIHST, Sungkyunkwan University, Seoul 06351, South Korea.,Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, 06351, South Korea
| | - Myung-Ju Ahn
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, South Korea
| | - Hae-Ock Lee
- Samsung Genome Institute, Samsung Medical Center, Seoul 06351, South Korea.,Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon 16419, South Korea
| | - Donghyun Park
- Samsung Genome Institute, Samsung Medical Center, Seoul 06351, South Korea
| | - Woong-Yang Park
- Samsung Genome Institute, Samsung Medical Center, Seoul 06351, South Korea.,Department of Health Sciences and Technology, SAIHST, Sungkyunkwan University, Seoul 06351, South Korea.,Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon 16419, South Korea
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34
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Palovaara J, Saiga S, Wendrich JR, van 't Wout Hofland N, van Schayck JP, Hater F, Mutte S, Sjollema J, Boekschoten M, Hooiveld GJ, Weijers D. Transcriptome dynamics revealed by a gene expression atlas of the early Arabidopsis embryo. NATURE PLANTS 2017; 3:894-904. [PMID: 29116234 PMCID: PMC5687563 DOI: 10.1038/s41477-017-0035-3] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 09/19/2017] [Indexed: 05/02/2023]
Abstract
During early plant embryogenesis, precursors for all major tissues and stem cells are formed. While several components of the regulatory framework are known, how cell fates are instructed by genome-wide transcriptional activity remains unanswered-in part because of difficulties in capturing transcriptome changes at cellular resolution. Here, we have adapted a two-component transgenic labelling system to purify cell-type-specific nuclear RNA and generate a transcriptome atlas of early Arabidopsis embryo development, with a focus on root stem cell niche formation. We validated the dataset through gene expression analysis, and show that gene activity shifts in a spatio-temporal manner, probably signifying transcriptional reprogramming, to induce developmental processes reflecting cell states and state transitions. This atlas provides the most comprehensive tissue- and cell-specific description of genome-wide gene activity in the early plant embryo, and serves as a valuable resource for understanding the genetic control of early plant development.
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Affiliation(s)
- Joakim Palovaara
- Laboratory of Biochemistry, Wageningen University, 6708 WE, Wageningen, The Netherlands
| | - Shunsuke Saiga
- Laboratory of Biochemistry, Wageningen University, 6708 WE, Wageningen, The Netherlands
| | - Jos R Wendrich
- Laboratory of Biochemistry, Wageningen University, 6708 WE, Wageningen, The Netherlands
- Department of Plant Biotechnology and Bioinformatics and VIB Center for Plant Systems Biology, Ghent University, Technologiepark 927, 9052, Ghent, Belgium
| | | | - J Paul van Schayck
- Laboratory of Biochemistry, Wageningen University, 6708 WE, Wageningen, The Netherlands
| | - Friederike Hater
- Laboratory of Biochemistry, Wageningen University, 6708 WE, Wageningen, The Netherlands
| | - Sumanth Mutte
- Laboratory of Biochemistry, Wageningen University, 6708 WE, Wageningen, The Netherlands
| | - Jouke Sjollema
- Laboratory of Biochemistry, Wageningen University, 6708 WE, Wageningen, The Netherlands
| | - Mark Boekschoten
- Nutrition, Metabolism and Genomics Group, Division of Human Nutrition, Wageningen University, 6708 WE, Wageningen, The Netherlands
| | - Guido J Hooiveld
- Nutrition, Metabolism and Genomics Group, Division of Human Nutrition, Wageningen University, 6708 WE, Wageningen, The Netherlands
| | - Dolf Weijers
- Laboratory of Biochemistry, Wageningen University, 6708 WE, Wageningen, The Netherlands.
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35
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Palovaara J, Saiga S, Wendrich JR, van 't Wout Hofland N, van Schayck JP, Hater F, Mutte S, Sjollema J, Boekschoten M, Hooiveld GJ, Weijers D. Transcriptome dynamics revealed by a gene expression atlas of the early Arabidopsis embryo. NATURE PLANTS 2017; 3:894-904. [PMID: 29116234 DOI: 10.1038/s41477-017-0035-33] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 09/19/2017] [Indexed: 05/22/2023]
Abstract
During early plant embryogenesis, precursors for all major tissues and stem cells are formed. While several components of the regulatory framework are known, how cell fates are instructed by genome-wide transcriptional activity remains unanswered-in part because of difficulties in capturing transcriptome changes at cellular resolution. Here, we have adapted a two-component transgenic labelling system to purify cell-type-specific nuclear RNA and generate a transcriptome atlas of early Arabidopsis embryo development, with a focus on root stem cell niche formation. We validated the dataset through gene expression analysis, and show that gene activity shifts in a spatio-temporal manner, probably signifying transcriptional reprogramming, to induce developmental processes reflecting cell states and state transitions. This atlas provides the most comprehensive tissue- and cell-specific description of genome-wide gene activity in the early plant embryo, and serves as a valuable resource for understanding the genetic control of early plant development.
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Affiliation(s)
- Joakim Palovaara
- Laboratory of Biochemistry, Wageningen University, 6708 WE, Wageningen, The Netherlands
| | - Shunsuke Saiga
- Laboratory of Biochemistry, Wageningen University, 6708 WE, Wageningen, The Netherlands
| | - Jos R Wendrich
- Laboratory of Biochemistry, Wageningen University, 6708 WE, Wageningen, The Netherlands
- Department of Plant Biotechnology and Bioinformatics and VIB Center for Plant Systems Biology, Ghent University, Technologiepark 927, 9052, Ghent, Belgium
| | | | - J Paul van Schayck
- Laboratory of Biochemistry, Wageningen University, 6708 WE, Wageningen, The Netherlands
| | - Friederike Hater
- Laboratory of Biochemistry, Wageningen University, 6708 WE, Wageningen, The Netherlands
| | - Sumanth Mutte
- Laboratory of Biochemistry, Wageningen University, 6708 WE, Wageningen, The Netherlands
| | - Jouke Sjollema
- Laboratory of Biochemistry, Wageningen University, 6708 WE, Wageningen, The Netherlands
| | - Mark Boekschoten
- Nutrition, Metabolism and Genomics Group, Division of Human Nutrition, Wageningen University, 6708 WE, Wageningen, The Netherlands
| | - Guido J Hooiveld
- Nutrition, Metabolism and Genomics Group, Division of Human Nutrition, Wageningen University, 6708 WE, Wageningen, The Netherlands
| | - Dolf Weijers
- Laboratory of Biochemistry, Wageningen University, 6708 WE, Wageningen, The Netherlands.
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36
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Galbraith DW, Sliwinska E, Samadder P. Nuclear Cytometry: Analysis of the Patterns of DNA Synthesis and Transcription Using Flow Cytometry, Confocal Microscopy, and RNA Sequencing. Methods Mol Biol 2017; 1678:371-392. [PMID: 29071687 DOI: 10.1007/978-1-4939-7346-0_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Eukaryotes are defined by cells that contain a nucleus and other membrane-bound organelles. Cytometric analysis in situ, utilizing imaging, provides a useful understanding of the structure and function of the various subcellular components, particularly when combined with methods that preserve the living state. In terms of information provided by the observation of eukaryotic nuclei, imaging has provided a wealth of information about cellular multiplication. When organisms are present in multicellular form (tissues and organs), this property does not generally confound imaging cytometry. Multicellular eukaryotic species present immediate problems when being considered for analysis using flow cytometry which requires suspensions of single particles. Although some eukaryotic cell types exist as natural single cell suspensions (cf. the erythropoietic system), for other tissues and organs, strategies are required to produce single particle suspensions. This chapter illustrates the application of flow cytometry combined with confocal microscopy to analyze complex organs, focusing on properties of the plant nucleus, and then goes on to describe how suspensions of nuclei can be prepared from tissues and organs, and used for flow cytometric analysis of cellular and transcriptional states. The application of these techniques to animal species is also discussed with the implication that this strategy is universally applicable for the characterization of nuclei within tissues that cannot readily be converted into suspensions of cells.
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Affiliation(s)
- David W Galbraith
- School of Plant Sciences, Bio5 Institute, University of Arizona, 341 Keating Building, 1657 E. Helen Street, Tucson, AZ, 85721, USA.
| | - Elwira Sliwinska
- Laboratory of Molecular Biology and Cytometry, Department of Plant Genetics, Physiology and Biotechnology, UTP University of Science and Technology, Kaliskiego Ave. 7, 85-789, Bydgoszcz, Poland
| | - Partha Samadder
- School of Plant Sciences, Bio5 Institute, University of Arizona, 341 Keating Building, 1657 E. Helen Street, Tucson, AZ, 85721, USA
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37
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A comparative strategy for single-nucleus and single-cell transcriptomes confirms accuracy in predicted cell-type expression from nuclear RNA. Sci Rep 2017; 7:6031. [PMID: 28729663 PMCID: PMC5519641 DOI: 10.1038/s41598-017-04426-w] [Citation(s) in RCA: 157] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 05/16/2017] [Indexed: 11/24/2022] Open
Abstract
Significant heterogeneities in gene expression among individual cells are typically interrogated using single whole cell approaches. However, tissues that have highly interconnected processes, such as in the brain, present unique challenges. Single-nucleus RNA sequencing (SNS) has emerged as an alternative method of assessing a cell’s transcriptome through the use of isolated nuclei. However, studies directly comparing expression data between nuclei and whole cells are lacking. Here, we have characterized nuclear and whole cell transcriptomes in mouse single neurons and provided a normalization strategy to reduce method-specific differences related to the length of genic regions. We confirmed a high concordance between nuclear and whole cell transcriptomes in the expression of cell type and metabolic modeling markers, but less so for a subset of genes associated with mitochondrial respiration. Therefore, our results indicate that single-nucleus transcriptome sequencing provides an effective means to profile cell type expression dynamics in previously inaccessible tissues.
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38
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Trinh LA, Chong-Morrison V, Gavriouchkina D, Hochgreb-Hägele T, Senanayake U, Fraser SE, Sauka-Spengler T. Biotagging of Specific Cell Populations in Zebrafish Reveals Gene Regulatory Logic Encoded in the Nuclear Transcriptome. Cell Rep 2017; 19:425-440. [PMID: 28402863 PMCID: PMC5400779 DOI: 10.1016/j.celrep.2017.03.045] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Revised: 12/21/2016] [Accepted: 03/13/2017] [Indexed: 11/22/2022] Open
Abstract
Interrogation of gene regulatory circuits in complex organisms requires precise tools for the selection of individual cell types and robust methods for biochemical profiling of target proteins. We have developed a versatile, tissue-specific binary in vivo biotinylation system in zebrafish termed biotagging that uses genetically encoded components to biotinylate target proteins, enabling in-depth genome-wide analyses of their molecular interactions. Using tissue-specific drivers and cell-compartment-specific effector lines, we demonstrate the specificity of the biotagging toolkit at the biochemical, cellular, and transcriptional levels. We use biotagging to characterize the in vivo transcriptional landscape of migratory neural crest and myocardial cells in different cellular compartments (ribosomes and nucleus). These analyses reveal a comprehensive network of coding and non-coding RNAs and cis-regulatory modules, demonstrating that tissue-specific identity is embedded in the nuclear transcriptomes. By eliminating background inherent to complex embryonic environments, biotagging allows analyses of molecular interactions at high resolution. Biotagging enables cell- and compartment-specific in vivo biotinylation in zebrafish Technique yields comprehensive nuclear transcriptional analysis of cardiomyocytes Biotagging finds bidirectionally transcribed neural crest cis-regulatory modules System reveals tissue-specific regulation of noncoding RNA species
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Affiliation(s)
- Le A Trinh
- Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
| | - Vanessa Chong-Morrison
- Radcliffe Department of Medicine, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Daria Gavriouchkina
- Radcliffe Department of Medicine, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Tatiana Hochgreb-Hägele
- Radcliffe Department of Medicine, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK; Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Upeka Senanayake
- Radcliffe Department of Medicine, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Scott E Fraser
- Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
| | - Tatjana Sauka-Spengler
- Radcliffe Department of Medicine, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK.
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39
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Laser microdissection of tomato fruit cell and tissue types for transcriptome profiling. Nat Protoc 2016; 11:2376-2388. [PMID: 27809311 DOI: 10.1038/nprot.2016.146] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
This protocol enables transcriptome profiling of specific cell or tissue types that are isolated from tomato using laser microdissection (LM). To prepare tissue for LM, fruit samples are first fixed in optimal cutting temperature (OCT) medium and frozen in molds. The tissue is then sectioned using a cryostat before being dissected using an LM instrument. The RNAs contained in the harvested cells are purified and subjected to two rounds of amplification to yield sufficient quantities of RNA to generate cDNA libraries. Unlike several other techniques that are used to isolate specific cell types, LM has the advantage of being readily applied to any plant species without having to generate transgenic plants. Using the protocols described here, LM-mediated cell-type transcriptomic analysis of two samples requires ∼8 d from tissue harvest to RNA sequencing (RNA-seq), whereas each additional sample, up to a total of 12 samples, requires ∼1 additional day for the LM step. RNA obtained using this method has been successfully used for deep-coverage transcriptome profiling, which is a particularly effective strategy for identifying genes that are differentially expressed between cell or tissue types.
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40
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Ayupe AC, Tahira AC, Camargo L, Beckedorff FC, Verjovski-Almeida S, Reis EM. Global analysis of biogenesis, stability and sub-cellular localization of lncRNAs mapping to intragenic regions of the human genome. RNA Biol 2016; 12:877-92. [PMID: 26151857 DOI: 10.1080/15476286.2015.1062960] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) that map to intragenic regions of the human genome with the same (intronic lncRNAs) or opposite orientation (antisense lncRNAs) relative to protein-coding mRNAs have been largely dismissed from biochemical and functional characterization due to the belief that they are mRNA precursors, byproducts of RNA splicing or simply transcriptional noise. In this work, we used a custom microarray to investigate aspects of the biogenesis, processing, stability, evolutionary conservation, and cellular localization of ∼ 6,000 intronic lncRNAs and ∼ 10,000 antisense lncRNAs. Most intronic (2,903 of 3,427, 85%) and antisense lncRNAs (4,945 of 5,214, 95%) expressed in HeLa cells showed evidence of 5' cap modification, compatible with their transcription by RNAP II. Antisense lncRNAs (median t1/2 = 3.9 h) were significantly (p < 0.0001) more stable than mRNAs (median t1/2 = 3.2 h), whereas intronic lncRNAs (median t1/2 = 2.1 h) comprised a more heterogeneous class that included both stable (t1/2 > 3 h) and unstable (t1/2 < 1 h) transcripts. Intragenic lncRNAs display evidence of evolutionary conservation, have little/no coding potential and were ubiquitously detected in the cytoplasm. Notably, a fraction of the intronic and antisense lncRNAs (13 and 15%, respectively) were expressed from loci at which the corresponding host mRNA was not detected. The abundances of a subset of intronic/antisense lncRNAs were correlated (r ≥ |0.8|) with those of genes encoding proteins involved in cell division and DNA replication. Taken together, the findings of this study contribute novel biochemical and genomic information regarding intronic and antisense lncRNAs, supporting the notion that these classes include independently transcribed RNAs with potentials for exerting regulatory functions in the cell.
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Affiliation(s)
- Ana C Ayupe
- a Departamento de Bioquímica ; Instituto de Química ; Universidade de São Paulo ; Sao Paulo , Brazil
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41
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Hu Y, Huang K, An Q, Du G, Hu G, Xue J, Zhu X, Wang CY, Xue Z, Fan G. Simultaneous profiling of transcriptome and DNA methylome from a single cell. Genome Biol 2016; 17:88. [PMID: 27150361 PMCID: PMC4858893 DOI: 10.1186/s13059-016-0950-z] [Citation(s) in RCA: 180] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 04/13/2016] [Indexed: 12/05/2022] Open
Abstract
Background Single-cell transcriptome and single-cell methylome technologies have become powerful tools to study RNA and DNA methylation profiles of single cells at a genome-wide scale. A major challenge has been to understand the direct correlation of DNA methylation and gene expression within single-cells. Due to large cell-to-cell variability and the lack of direct measurements of transcriptome and methylome of the same cell, the association is still unclear. Results Here, we describe a novel method (scMT-seq) that simultaneously profiles both DNA methylome and transcriptome from the same cell. In sensory neurons, we consistently identify transcriptome and methylome heterogeneity among single cells but the majority of the expression variance is not explained by proximal promoter methylation, with the exception of genes that do not contain CpG islands. By contrast, gene body methylation is positively associated with gene expression for only those genes that contain a CpG island promoter. Furthermore, using single nucleotide polymorphism patterns from our hybrid mouse model, we also find positive correlation of allelic gene body methylation with allelic expression. Conclusions Our method can be used to detect transcriptome, methylome, and single nucleotide polymorphism information within single cells to dissect the mechanisms of epigenetic gene regulation. Electronic supplementary material The online version of this article (doi:10.1186/s13059-016-0950-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Youjin Hu
- Department of Human Genetics, David Geffen School of Medicine, UCLA, 695 Charles Young Drive South, Los Angeles, CA, 90095, USA.,Translational Center for Stem Cell Research, Tongji Hospital, Department of Regenerative Medicine, Tongji University School of Medicine, Shanghai, 200065, China
| | - Kevin Huang
- Department of Human Genetics, David Geffen School of Medicine, UCLA, 695 Charles Young Drive South, Los Angeles, CA, 90095, USA.,Division of Oral Biology and Medicine, Laboratory of Molecular Signaling, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Qin An
- Department of Human Genetics, David Geffen School of Medicine, UCLA, 695 Charles Young Drive South, Los Angeles, CA, 90095, USA
| | - Guizhen Du
- Department of Human Genetics, David Geffen School of Medicine, UCLA, 695 Charles Young Drive South, Los Angeles, CA, 90095, USA
| | - Ganlu Hu
- Translational Center for Stem Cell Research, Tongji Hospital, Department of Regenerative Medicine, Tongji University School of Medicine, Shanghai, 200065, China
| | - Jinfeng Xue
- Translational Center for Stem Cell Research, Tongji Hospital, Department of Regenerative Medicine, Tongji University School of Medicine, Shanghai, 200065, China
| | - Xianmin Zhu
- Translational Center for Stem Cell Research, Tongji Hospital, Department of Regenerative Medicine, Tongji University School of Medicine, Shanghai, 200065, China
| | - Cun-Yu Wang
- Division of Oral Biology and Medicine, Laboratory of Molecular Signaling, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Zhigang Xue
- Translational Center for Stem Cell Research, Tongji Hospital, Department of Regenerative Medicine, Tongji University School of Medicine, Shanghai, 200065, China. .,Suzhou Institute, Tongji University, Suzhou, Jiangsu Province, 215101, China.
| | - Guoping Fan
- Department of Human Genetics, David Geffen School of Medicine, UCLA, 695 Charles Young Drive South, Los Angeles, CA, 90095, USA.
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42
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Chitikova Z, Steiner FA. Cell type-specific epigenome profiling using affinity-purified nuclei. Genesis 2016; 54:160-9. [PMID: 26789661 DOI: 10.1002/dvg.22919] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 01/08/2016] [Accepted: 01/14/2016] [Indexed: 11/08/2022]
Abstract
The development of a multicellular organism from a single zygote depends on the differentiation of progenitor cells to specialized cell types. The differentiation of these cell types is associated with changes in gene expression and the underlying chromatin landscape. To understand how these processes are regulated, it is desirable to understand how the chromatin features that constitute the epigenome differ between cell types at any given time during development. INTACT, a method for the cell type-specific purification of nuclei that can be used for the isolation of both RNA and chromatin, has emerged as a powerful tool to simultaneously study gene expression and chromatin profiles specifically in cell types of interest. In this review, we focus on the application of INTACT to different model organisms and discuss its potential for profiling cell types in their developmental context.
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Affiliation(s)
- Zhanna Chitikova
- Department of Molecular Biology, Sciences III, University of Geneva, Geneva, Switzerland
| | - Florian A Steiner
- Department of Molecular Biology, Sciences III, University of Geneva, Geneva, Switzerland
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43
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Samadder P, Weng N, Doetschman T, Heimark RL, Galbraith DW. Flow cytometry and single nucleus sorting for Cre-based analysis of changes in transcriptional states. Cytometry A 2016; 89:430-42. [PMID: 27003621 DOI: 10.1002/cyto.a.22847] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Revised: 02/23/2016] [Accepted: 02/29/2016] [Indexed: 12/13/2022]
Abstract
The organs of eukaryotic organisms comprise complex interspersions of cell types, whose different molecular activities, and corresponding cellular states, cooperate during development to produce the final, functional organ. Dysfunction of organs in disease, particularly oncogenesis, initiates with changes of state of a minor subset of cells. It therefore is hard to detect early molecular indicators of disease within an overwhelming background of normal cells. Flow cytometry and sorting provides a convenient way to purify minority subpopulations, if a specific fluorophore can be unambiguously and exclusively associated with this subpopulation. We have generated a number of transgenic mouse lines expressing a nuclear-localized version of the Green Fluorescent Protein (GFP), within which the production of a chimeric histone 2B-GFP protein occurs under the control of a constitutively-active, actin-derived promoter, separated by a Floxed-STOP sequence. In the presence of Cre recombinase, within F1 progeny of these mouse lines, excision of the STOP sequence activates transcription which results in the emergence of cells containing green fluorescent nuclei. We describe the characterization of these lines using a combination of microscopic imaging, flow cytometry and sorting, and Reverse-Transcription polymerase chain reaction of transcripts within single sorted nuclei isolated from tissue homogenates. These lines should be particularly useful for analysis of transcriptional changes in oncogenesis. © 2016 International Society for Advancement of Cytometry.
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Affiliation(s)
| | - Ning Weng
- BIO5 Institute, University of Arizona, Tucson, Arizona
| | - Thomas Doetschman
- BIO5 Institute, University of Arizona, Tucson, Arizona
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, Arizona
- University of Arizona Cancer Center, Tucson, Arizona
| | - Ronald L Heimark
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, Arizona
- University of Arizona Cancer Center, Tucson, Arizona
- Department of Surgery, University of Arizona, Tucson, Arizona
| | - David W Galbraith
- BIO5 Institute, University of Arizona, Tucson, Arizona
- University of Arizona Cancer Center, Tucson, Arizona
- School of Plant Sciences, University of Arizona, Tucson, Arizona
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44
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Krishnaswami SR, Grindberg RV, Novotny M, Venepally P, Lacar B, Bhutani K, Linker SB, Pham S, Erwin JA, Miller JA, Hodge R, McCarthy JK, Kelder M, McCorrison J, Aevermann BD, Fuertes FD, Scheuermann RH, Lee J, Lein ES, Schork N, McConnell MJ, Gage FH, Lasken RS. Using single nuclei for RNA-seq to capture the transcriptome of postmortem neurons. Nat Protoc 2016; 11:499-524. [PMID: 26890679 PMCID: PMC4941947 DOI: 10.1038/nprot.2016.015] [Citation(s) in RCA: 261] [Impact Index Per Article: 32.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
A protocol is described for sequencing the transcriptome of a cell nucleus. Nuclei are isolated from specimens and sorted by FACS, cDNA libraries are constructed and RNA-seq is performed, followed by data analysis. Some steps follow published methods (Smart-seq2 for cDNA synthesis and Nextera XT barcoded library preparation) and are not described in detail here. Previous single-cell approaches for RNA-seq from tissues include cell dissociation using protease treatment at 30 °C, which is known to alter the transcriptome. We isolate nuclei at 4 °C from tissue homogenates, which cause minimal damage. Nuclear transcriptomes can be obtained from postmortem human brain tissue stored at -80 °C, making brain archives accessible for RNA-seq from individual neurons. The method also allows investigation of biological features unique to nuclei, such as enrichment of certain transcripts and precursors of some noncoding RNAs. By following this procedure, it takes about 4 d to construct cDNA libraries that are ready for sequencing.
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Affiliation(s)
| | | | - Mark Novotny
- J. Craig Venter Institute, La Jolla, California, USA
| | | | - Benjamin Lacar
- Salk Institute for Biological Studies, La Jolla, California, USA
| | - Kunal Bhutani
- J. Craig Venter Institute, La Jolla, California, USA
| | - Sara B Linker
- Salk Institute for Biological Studies, La Jolla, California, USA
| | - Son Pham
- Salk Institute for Biological Studies, La Jolla, California, USA
| | - Jennifer A Erwin
- Salk Institute for Biological Studies, La Jolla, California, USA
| | | | - Rebecca Hodge
- Allen Institute for Brain Science, Seattle, Washington, USA
| | | | - Martin Kelder
- Salk Institute for Biological Studies, La Jolla, California, USA
| | | | | | - Francisco Diez Fuertes
- J. Craig Venter Institute, La Jolla, California, USA
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | | | - Jun Lee
- LeGene Biosciences, San Diego, California, USA
| | - Ed S Lein
- Allen Institute for Brain Science, Seattle, Washington, USA
| | | | - Michael J McConnell
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Fred H Gage
- Salk Institute for Biological Studies, La Jolla, California, USA
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45
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Profiling of embryonic nuclear vs. cellular RNA in Arabidopsis thaliana. GENOMICS DATA 2015; 4:96-8. [PMID: 26484189 PMCID: PMC4536148 DOI: 10.1016/j.gdata.2015.03.015] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 03/26/2015] [Indexed: 11/21/2022]
Abstract
In Arabidopsis, various cell type-specific whole-genome expression analyses have been conducted. However, the vast majority of these were performed with cellular RNA from root tissues or other easily accessible cell types [1]. Nuclear RNA was neglected for a long time as not being representative for transcriptomic studies. In recent years, however, there have been reports describing the validity of nuclear RNA for these types of studies [2,3]. Here we describe the generation, quality assessment and analysis of nuclear transcriptomic data from Arabidopsis embryos published by Slane et al. (2014) [4]. Comparison of nuclear with cellular gene expression demonstrated the usefulness of nuclear transcriptomics.
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46
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Slane D, Kong J, Berendzen KW, Kilian J, Henschen A, Kolb M, Schmid M, Harter K, Mayer U, De Smet I, Bayer M, Jürgens G. Cell type-specific transcriptome analysis in the early Arabidopsis thaliana embryo. Development 2014; 141:4831-40. [PMID: 25411212 DOI: 10.1242/dev.116459] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
In multicellular organisms, cellular differences in gene activity are a prerequisite for differentiation and establishment of cell types. In order to study transcriptome profiles, specific cell types have to be isolated from a given tissue or even the whole organism. However, whole-transcriptome analysis of early embryos in flowering plants has been hampered by their size and inaccessibility. Here, we describe the purification of nuclear RNA from early stage Arabidopsis thaliana embryos using fluorescence-activated nuclear sorting (FANS) to generate expression profiles of early stages of the whole embryo, the proembryo and the suspensor. We validated our datasets of differentially expressed candidate genes by promoter-reporter gene fusions and in situ hybridization. Our study revealed that different classes of genes with respect to biological processes and molecular functions are preferentially expressed either in the proembryo or in the suspensor. This method can be used especially for tissues with a limited cell population and inaccessible tissue types. Furthermore, we provide a valuable resource for research on Arabidopsis early embryogenesis.
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Affiliation(s)
- Daniel Slane
- Department of Cell Biology, Max Planck Institute for Developmental Biology, Tübingen 72076, Germany
| | - Jixiang Kong
- Department of Cell Biology, Max Planck Institute for Developmental Biology, Tübingen 72076, Germany Department of Developmental Genetics, Center for Plant Molecular Biology, University of Tübingen, Tübingen 72076, Germany
| | - Kenneth W Berendzen
- Department of Plant Physiology, Center for Plant Molecular Biology, University of Tübingen, Tübingen 72076, Germany
| | - Joachim Kilian
- Department of Plant Physiology, Center for Plant Molecular Biology, University of Tübingen, Tübingen 72076, Germany
| | - Agnes Henschen
- Department of Cell Biology, Max Planck Institute for Developmental Biology, Tübingen 72076, Germany
| | - Martina Kolb
- Department of Cell Biology, Max Planck Institute for Developmental Biology, Tübingen 72076, Germany
| | - Markus Schmid
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen 72076, Germany
| | - Klaus Harter
- Department of Plant Physiology, Center for Plant Molecular Biology, University of Tübingen, Tübingen 72076, Germany
| | - Ulrike Mayer
- Microscopy facility, Center for Plant Molecular Biology, University of Tübingen, Tübingen 72076, Germany
| | - Ive De Smet
- Department of Plant Systems Biology, VIB, Technologiepark 927, Ghent B-9052, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, Ghent B-9052, Belgium Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK
| | - Martin Bayer
- Department of Cell Biology, Max Planck Institute for Developmental Biology, Tübingen 72076, Germany
| | - Gerd Jürgens
- Department of Cell Biology, Max Planck Institute for Developmental Biology, Tübingen 72076, Germany Department of Developmental Genetics, Center for Plant Molecular Biology, University of Tübingen, Tübingen 72076, Germany
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47
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Otsuki L, Cheetham SW, Brand AH. Freedom of expression: cell-type-specific gene profiling. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2014; 3:429-43. [PMID: 25174322 DOI: 10.1002/wdev.149] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Accepted: 07/10/2014] [Indexed: 12/17/2022]
Abstract
Cell fate and behavior are results of differential gene regulation, making techniques to profile gene expression in specific cell types highly desirable. Many methods now enable investigation at the DNA, RNA and protein level. This review introduces the most recent and popular techniques, and discusses key issues influencing the choice between these such as ease, cost and applicability of information gained. Interdisciplinary collaborations will no doubt contribute further advances, including not just in single cell type but single-cell expression profiling.
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Affiliation(s)
- Leo Otsuki
- The Gurdon Institute and Department of Physiology, Development, and Neuroscience, University of Cambridge, Cambridge, UK
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48
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Tallafuss A, Washbourne P, Postlethwait J. Temporally and spatially restricted gene expression profiling. Curr Genomics 2014; 15:278-92. [PMID: 25132798 PMCID: PMC4133951 DOI: 10.2174/1389202915666140602230106] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Revised: 05/29/2014] [Accepted: 05/30/2014] [Indexed: 12/02/2022] Open
Abstract
Identifying gene function in specific cells is critical for understanding the processes that make cells unique. Several different methods are available to isolate actively transcribed RNA or actively translated RNA in specific cells at a chosen time point. Cell-specific mRNA isolation can be accomplished by the expression of transgenes in cells of interest, either directly from a specific promoter or using a modular system such as Gal4/UAS or Cre/lox. All of the methods described in this review, namely thiol-labeling of RNA (TU-tagging or RABT), TRAP (translating ribosome affinity purification) and INTACT (isolation of nuclei tagged in specific cell types), allow next generation sequencing, permitting the identification of enriched gene transcripts within the specific cell-type. We describe here the general concept of each method, include examples, evaluate possible problems related to each technique, and suggest the types of questions for which each method is best suited.
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Affiliation(s)
- Alexandra Tallafuss
- Institute of Neuroscience, 1254-University of Oregon, 1425 E. 13th Avenue, Eugene, OR-97403, USA
| | - Philip Washbourne
- Institute of Neuroscience, 1254-University of Oregon, 1425 E. 13th Avenue, Eugene, OR-97403, USA
| | - John Postlethwait
- Institute of Neuroscience, 1254-University of Oregon, 1425 E. 13th Avenue, Eugene, OR-97403, USA
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49
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Ma J, Weake VM. Affinity-based isolation of tagged nuclei from Drosophila tissues for gene expression analysis. J Vis Exp 2014. [PMID: 24686501 DOI: 10.3791/51418] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Drosophila melanogaster embryonic and larval tissues often contain a highly heterogeneous mixture of cell types, which can complicate the analysis of gene expression in these tissues. Thus, to analyze cell-specific gene expression profiles from Drosophila tissues, it may be necessary to isolate specific cell types with high purity and at sufficient yields for downstream applications such as transcriptional profiling and chromatin immunoprecipitation. However, the irregular cellular morphology in tissues such as the central nervous system, coupled with the rare population of specific cell types in these tissues, can pose challenges for traditional methods of cell isolation such as laser microdissection and fluorescence-activated cell sorting (FACS). Here, an alternative approach to characterizing cell-specific gene expression profiles using affinity-based isolation of tagged nuclei, rather than whole cells, is described. Nuclei in the specific cell type of interest are genetically labeled with a nuclear envelope-localized EGFP tag using the Gal4/UAS binary expression system. These EGFP-tagged nuclei can be isolated using antibodies against GFP that are coupled to magnetic beads. The approach described in this protocol enables consistent isolation of nuclei from specific cell types in the Drosophila larval central nervous system at high purity and at sufficient levels for expression analysis, even when these cell types comprise less than 2% of the total cell population in the tissue. This approach can be used to isolate nuclei from a wide variety of Drosophila embryonic and larval cell types using specific Gal4 drivers, and may be useful for isolating nuclei from cell types that are not suitable for FACS or laser microdissection.
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Affiliation(s)
- Jingqun Ma
- Department of Biochemistry, Purdue University
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50
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Polychronidou M, Lohmann I. Hox transcriptomics in Drosophila embryos. Methods Mol Biol 2014; 1196:197-208. [PMID: 25151165 DOI: 10.1007/978-1-4939-1242-1_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Hox proteins are evolutionarily conserved homeodomain containing transcription factors that specify segment identities along the anteroposterior axis of almost all bilaterian animals. They exert their morphogenetic role by transcriptionally regulating a large battery of downstream target genes. Therefore the dissection of transcriptional networks regulated by Hox proteins is an essential step towards a mechanistic understanding of how these transcription factors coordinate multiple developmental and morphogenetic processes. High-throughput techniques allowing whole-transcriptome mRNA expression profiling are powerful tools for the genome-wide identification of Hox downstream target genes in a variety of experimental settings. Here, we describe how to quantitatively identify Hox downstream genes in Drosophila embryos by performing a Hox transcriptome analysis using microarrays.
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Affiliation(s)
- Maria Polychronidou
- Centre for Organismal Studies (COS) Heidelberg, University of Heidelberg, Im Neuenheimer Feld 267, 69120, Heidelberg, Germany
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