1
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Zou M, Duren Z, Yuan Q, Li H, Hutchins AP, Wong WH, Wang Y. MIMIC: an optimization method to identify cell type-specific marker panel for cell sorting. Brief Bioinform 2021; 22:6309927. [PMID: 34180954 PMCID: PMC8575015 DOI: 10.1093/bib/bbab235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 05/25/2021] [Accepted: 05/31/2021] [Indexed: 11/14/2022] Open
Abstract
Multi-omics data allow us to select a small set of informative markers for the discrimination of specific cell types and study of cellular heterogeneity. However, it is often challenging to choose an optimal marker panel from the high-dimensional molecular profiles for a large amount of cell types. Here, we propose a method called Mixed Integer programming Model to Identify Cell type-specific marker panel (MIMIC). MIMIC maintains the hierarchical topology among different cell types and simultaneously maximizes the specificity of a fixed number of selected markers. MIMIC was benchmarked on the mouse ENCODE RNA-seq dataset, with 29 diverse tissues, for 43 surface markers (SMs) and 1345 transcription factors (TFs). MIMIC could select biologically meaningful markers and is robust for different accuracy criteria. It shows advantages over the standard single gene-based approaches and widely used dimensional reduction methods, such as multidimensional scaling and t-SNE, both in accuracy and in biological interpretation. Furthermore, the combination of SMs and TFs achieves better specificity than SMs or TFs alone. Applying MIMIC to a large collection of 641 RNA-seq samples covering 231 cell types identifies a panel of TFs and SMs that reveal the modularity of cell type association networks. Finally, the scalability of MIMIC is demonstrated by selecting enhancer markers from mouse ENCODE data. MIMIC is freely available at https://github.com/MengZou1/MIMIC.
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Affiliation(s)
- Meng Zou
- Department of Mathematics, Huazhong University of Science and Technology, Beijing 100190, China
| | - Zhana Duren
- Department of Genetics and Biochemistry, Clemson University, Beijing 100190, China
| | - Qiuyue Yuan
- Academy of Mathematics and Systems Science, CAS, Beijing 100190, China
| | - Henry Li
- Department of Health Research & Policy, Bio-X Program Stanford University, Beijing 100190, China
| | | | - Wing Hung Wong
- Department of Statistics, Department of Biomedical Data Science, Bio-X Program Stanford University, Beijing 100190, China
| | - Yong Wang
- CEMS, NCMIS, MDIS, Academy of Mathematics and Systems Science, Center for Excellence in Animal Evolution and Genetics, University of Chinese Academy of Sciences, CAS, Beijing 100190, China
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2
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Channathodiyil P, Houseley J. Glyoxal fixation facilitates transcriptome analysis after antigen staining and cell sorting by flow cytometry. PLoS One 2021; 16:e0240769. [PMID: 33481798 PMCID: PMC7822327 DOI: 10.1371/journal.pone.0240769] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 01/04/2021] [Indexed: 01/07/2023] Open
Abstract
A simple method for extraction of high quality RNA from cells that have been fixed, stained and sorted by flow cytometry would allow routine transcriptome analysis of highly purified cell populations and single cells. However, formaldehyde fixation impairs RNA extraction and inhibits RNA amplification. Here we show that good quality RNA can be readily extracted from stained and sorted mammalian cells if formaldehyde is replaced by glyoxal—a well-characterised fixative that is widely compatible with immunofluorescent staining methods. Although both formaldehyde and glyoxal efficiently form protein-protein crosslinks, glyoxal does not crosslink RNA to proteins nor form stable RNA adducts, ensuring that RNA remains accessible and amenable to enzymatic manipulation after glyoxal fixation. We find that RNA integrity is maintained through glyoxal fixation, permeabilisation with methanol or saponin, indirect immunofluorescent staining and flow sorting. RNA can then be extracted by standard methods and processed into RNA-seq libraries using commercial kits; mRNA abundances measured by poly(A)+ RNA-seq correlate well between freshly harvested cells and fixed, stained and sorted cells. We validate the applicability of this approach to flow cytometry by staining MCF-7 cells for the intracellular G2/M-specific antigen cyclin B1 (CCNB1), and show strong enrichment for G2/M-phase cells based on transcriptomic data. Switching to glyoxal fixation with RNA-compatible staining methods requires only minor adjustments of most existing staining and sorting protocols, and should facilitate routine transcriptomic analysis of sorted cells.
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Affiliation(s)
| | - Jonathan Houseley
- Epigenetics Programme, Babraham Institute, Cambridge, United Kingdom
- * E-mail:
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3
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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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4
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Amamoto R, Garcia MD, West ER, Choi J, Lapan SW, Lane EA, Perrimon N, Cepko CL. Probe-Seq enables transcriptional profiling of specific cell types from heterogeneous tissue by RNA-based isolation. eLife 2019; 8:e51452. [PMID: 31815670 PMCID: PMC6901332 DOI: 10.7554/elife.51452] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 11/25/2019] [Indexed: 12/12/2022] Open
Abstract
Recent transcriptional profiling technologies are uncovering previously-undefined cell populations and molecular markers at an unprecedented pace. While single cell RNA (scRNA) sequencing is an attractive approach for unbiased transcriptional profiling of all cell types, a complementary method to isolate and sequence specific cell populations from heterogeneous tissue remains challenging. Here, we developed Probe-Seq, which allows deep transcriptional profiling of specific cell types isolated using RNA as the defining feature. Dissociated cells are labeled using fluorescent in situ hybridization (FISH) for RNA, and then isolated by fluorescent activated cell sorting (FACS). We used Probe-Seq to purify and profile specific cell types from mouse, human, and chick retinas, as well as from Drosophila midguts. Probe-Seq is compatible with frozen nuclei, making cell types within archival tissue immediately accessible. As it can be multiplexed, combinations of markers can be used to create specificity. Multiplexing also allows for the isolation of multiple cell types from one cell preparation. Probe-Seq should enable RNA profiling of specific cell types from any organism.
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Affiliation(s)
- Ryoji Amamoto
- Department of Genetics, Blavatnik InstituteHoward Hughes Medical Institute, Harvard Medical SchoolBostonUnited States
- Department of Ophthalmology, Blavatnik InstituteHoward Hughes Medical Institute, Harvard Medical SchoolBostonUnited States
| | - Mauricio D Garcia
- Department of Genetics, Blavatnik InstituteHoward Hughes Medical Institute, Harvard Medical SchoolBostonUnited States
- Department of Ophthalmology, Blavatnik InstituteHoward Hughes Medical Institute, Harvard Medical SchoolBostonUnited States
| | - Emma R West
- Department of Genetics, Blavatnik InstituteHoward Hughes Medical Institute, Harvard Medical SchoolBostonUnited States
- Department of Ophthalmology, Blavatnik InstituteHoward Hughes Medical Institute, Harvard Medical SchoolBostonUnited States
| | - Jiho Choi
- Department of Genetics, Blavatnik InstituteHoward Hughes Medical Institute, Harvard Medical SchoolBostonUnited States
- Department of Ophthalmology, Blavatnik InstituteHoward Hughes Medical Institute, Harvard Medical SchoolBostonUnited States
| | - Sylvain W Lapan
- Department of Genetics, Blavatnik InstituteHoward Hughes Medical Institute, Harvard Medical SchoolBostonUnited States
- Department of Ophthalmology, Blavatnik InstituteHoward Hughes Medical Institute, Harvard Medical SchoolBostonUnited States
| | - Elizabeth A Lane
- Department of Genetics, Blavatnik InstituteHoward Hughes Medical Institute, Harvard Medical SchoolBostonUnited States
| | - Norbert Perrimon
- Department of Genetics, Blavatnik InstituteHoward Hughes Medical Institute, Harvard Medical SchoolBostonUnited States
| | - Constance L Cepko
- Department of Genetics, Blavatnik InstituteHoward Hughes Medical Institute, Harvard Medical SchoolBostonUnited States
- Department of Ophthalmology, Blavatnik InstituteHoward Hughes Medical Institute, Harvard Medical SchoolBostonUnited States
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5
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Genome Editing in hPSCs Reveals GATA6 Haploinsufficiency and a Genetic Interaction with GATA4 in Human Pancreatic Development. Cell Stem Cell 2017; 20:675-688.e6. [PMID: 28196600 DOI: 10.1016/j.stem.2017.01.001] [Citation(s) in RCA: 110] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Revised: 11/08/2016] [Accepted: 01/03/2017] [Indexed: 01/19/2023]
Abstract
Human disease phenotypes associated with haploinsufficient gene requirements are often not recapitulated well in animal models. Here, we have investigated the association between human GATA6 haploinsufficiency and a wide range of clinical phenotypes that include neonatal and adult-onset diabetes using CRISPR (clustered regularly interspaced short palindromic repeat)/Cas9-mediated genome editing coupled with human pluripotent stem cell (hPSC) directed differentiation. We found that loss of one GATA6 allele specifically affects the differentiation of human pancreatic progenitors from the early PDX1+ stage to the more mature PDX1+NKX6.1+ stage, leading to impaired formation of glucose-responsive β-like cells. In addition to this GATA6 haploinsufficiency, we also identified dosage-sensitive requirements for GATA6 and GATA4 in the formation of both definitive endoderm and pancreatic progenitor cells. Our work expands the application of hPSCs from studying the impact of individual gene loci to investigation of multigenic human traits, and it establishes an approach for identifying genetic modifiers of human disease.
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6
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Davenport C, Diekmann U, Naujok O. A Quick and Efficient Method for the Purification of Endoderm Cells Generated from Human Embryonic Stem Cells. J Vis Exp 2016. [PMID: 26966833 DOI: 10.3791/53655] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
The differentiation capabilities of pluripotent stem cells such as embryonic stem cells (ESCs) allow a potential therapeutic application for cell replacement therapies. Terminally differentiated cell types could be used for the treatment of various degenerative diseases. In vitro differentiation of these cells towards tissues of the lung, liver and pancreas requires as a first step the generation of definitive endodermal cells. This step is rate-limiting for further differentiation towards terminally matured cell types such as insulin-producing beta cells, hepatocytes or other endoderm-derived cell types. Cells that are committed towards the endoderm lineage highly express a multitude of transcription factors such as FOXA2, SOX17, HNF1B, members of the GATA family, and the surface receptor CXCR4. However, differentiation protocols are rarely 100% efficient. Here, we describe a method for the purification of a CXCR4+ cell population after differentiation into the DE by using magnetic microbeads. This purification additionally removes cells of unwanted lineages. The gentle purification method is quick and reliable and might be used to improve downstream applications and differentiations.
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Affiliation(s)
| | - Ulf Diekmann
- Institute of Clinical Biochemistry, Hannover Medical School
| | - Ortwin Naujok
- Institute of Clinical Biochemistry, Hannover Medical School;
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7
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Mohammadnia A, Yaqubi M, Pourasgari F, Neely E, Fallahi H, Massumi M. Signaling and Gene Regulatory Networks Governing Definitive Endoderm Derivation From Pluripotent Stem Cells. J Cell Physiol 2016; 231:1994-2006. [PMID: 26755186 DOI: 10.1002/jcp.25308] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2016] [Accepted: 01/06/2016] [Indexed: 11/07/2022]
Abstract
The generation of definitive endoderm (DE) from pluripotent stem cells (PSCs) is a fundamental stage in the formation of highly organized visceral organs, such as the liver and pancreas. Currently, there is a need for a comprehensive study that illustrates the involvement of different signaling pathways and their interactions in the derivation of DE cells from PSCs. This study aimed to identify signaling pathways that have the greatest influence on DE formation using analyses of transcriptional profiles, protein-protein interactions, protein-DNA interactions, and protein localization data. Using this approach, signaling networks involved in DE formation were constructed using systems biology and data mining tools, and the validity of the predicted networks was confirmed experimentally by measuring the mRNA levels of hub genes in several PSCs-derived DE cell lines. Based on our analyses, seven signaling pathways, including the BMP, ERK1-ERK2, FGF, TGF-beta, MAPK, Wnt, and PIP signaling pathways and their interactions, were found to play a role in the derivation of DE cells from PSCs. Lastly, the core gene regulatory network governing this differentiation process was constructed. The results of this study could improve our understanding surrounding the efficient generation of DE cells for the regeneration of visceral organs. J. Cell. Physiol. 231: 1994-2006, 2016. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Abdulshakour Mohammadnia
- Institute of Medical Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Moein Yaqubi
- Institute of Medical Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran.,Ludmer Centre for Neuroinformatics and Mental Health, McGill University, Montréal, Quebec, Canada.,Douglas Mental Health University Institute, McGill University, Montréal, Quebec, Canada
| | - Farzaneh Pourasgari
- Department of Biotechnology, Razi Vaccine and Serum Research Institute, Karaj, Iran.,Department of Physiology, University of Toronto, Toronto, Ontario, Canada
| | - Eric Neely
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Hossein Fallahi
- Department of Biology, School of Science, Razi University, Kermanshah, Iran.,Medical Biology Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Mohammad Massumi
- Department of Physiology, University of Toronto, Toronto, Ontario, Canada.,Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
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8
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Patthey C, Clifford H, Haerty W, Ponting CP, Shimeld SM, Begbie J. Identification of molecular signatures specific for distinct cranial sensory ganglia in the developing chick. Neural Dev 2016; 11:3. [PMID: 26819088 PMCID: PMC4730756 DOI: 10.1186/s13064-016-0057-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 01/08/2016] [Indexed: 11/22/2022] Open
Abstract
Background The cranial sensory ganglia represent populations of neurons with distinct functions, or sensory modalities. The production of individual ganglia from distinct neurogenic placodes with different developmental pathways provides a powerful model to investigate the acquisition of specific sensory modalities. To date there is a limited range of gene markers available to examine the molecular pathways underlying this process. Results Transcriptional profiles were generated for populations of differentiated neurons purified from distinct cranial sensory ganglia using microdissection in embryonic chicken followed by FAC-sorting and RNAseq. Whole transcriptome analysis confirmed the division into somato- versus viscerosensory neurons, with additional evidence for subdivision of the somatic class into general and special somatosensory neurons. Cross-comparison of distinct ganglia transcriptomes identified a total of 134 markers, 113 of which are novel, which can be used to distinguish trigeminal, vestibulo-acoustic and epibranchial neuronal populations. In situ hybridisation analysis provided validation for 20/26 tested markers, and showed related expression in the target region of the hindbrain in many cases. Conclusions One hundred thirty-four high-confidence markers have been identified for placode-derived cranial sensory ganglia which can now be used to address the acquisition of specific cranial sensory modalities. Electronic supplementary material The online version of this article (doi:10.1186/s13064-016-0057-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Cedric Patthey
- Department of Zoology, University of Oxford, Oxford, UK. .,Umeå Center for Molecular Medicine, Umeå University, Umeå, Sweden.
| | - Harry Clifford
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK. .,MRC Functional Genomics, University of Oxford, Oxford, UK.
| | - Wilfried Haerty
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK. .,MRC Functional Genomics, University of Oxford, Oxford, UK.
| | - Chris P Ponting
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK. .,MRC Functional Genomics, University of Oxford, Oxford, UK.
| | | | - Jo Begbie
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK.
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9
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Hhex Is Necessary for the Hepatic Differentiation of Mouse ES Cells and Acts via Vegf Signaling. PLoS One 2016; 11:e0146806. [PMID: 26784346 PMCID: PMC4718667 DOI: 10.1371/journal.pone.0146806] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 12/22/2015] [Indexed: 01/07/2023] Open
Abstract
Elucidating the molecular mechanisms involved in the differentiation of stem cells to hepatic cells is critical for both understanding normal developmental processes as well as for optimizing the generation of functional hepatic cells for therapy. We performed in vitro differentiation of mouse embryonic stem cells (mESCs) with a null mutation in the homeobox gene Hhex and show that Hhex-/- mESCs fail to differentiate from definitive endoderm (Sox17+/Foxa2+) to hepatic endoderm (Alb+/Dlk+). In addition, hepatic culture elicited a >7-fold increase in Vegfa mRNA expression in Hhex-/- cells compared to Hhex+/+ cells. Furthermore, we identified VEGFR2+/ALB+/CD34- in early Hhex+/+ hepatic cultures. These cells were absent in Hhex-/- cultures. Finally, through manipulation of Hhex and Vegfa expression, gain and loss of expression experiments revealed that Hhex shares an inverse relationship with the activity of the Vegf signaling pathway in supporting hepatic differentiation. In summary, our results suggest that Hhex represses Vegf signaling during hepatic differentiation of mouse ESCs allowing for cell-type autonomous regulation of Vegfr2 activity independent of endothelial cells.
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10
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Stewart KR, Veselovska L, Kim J, Huang J, Saadeh H, Tomizawa SI, Smallwood SA, Chen T, Kelsey G. Dynamic changes in histone modifications precede de novo DNA methylation in oocytes. Genes Dev 2015; 29:2449-62. [PMID: 26584620 PMCID: PMC4691949 DOI: 10.1101/gad.271353.115] [Citation(s) in RCA: 143] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Accepted: 11/04/2015] [Indexed: 12/21/2022]
Abstract
In mouse oogenesis, DNA methylation establishment occurs on a largely unmethylated genome and in nondividing cells, making it a highly informative model for examining how histone modifications can shape the DNA methylome. Stewart et al. present the first systematic study performing ChIP-seq in oocytes and show that histone remodeling in the mammalian oocyte helps direct de novo DNA methylation events. Erasure and subsequent reinstatement of DNA methylation in the germline, especially at imprinted CpG islands (CGIs), is crucial to embryogenesis in mammals. The mechanisms underlying DNA methylation establishment remain poorly understood, but a number of post-translational modifications of histones are implicated in antagonizing or recruiting the de novo DNA methylation complex. In mouse oogenesis, DNA methylation establishment occurs on a largely unmethylated genome and in nondividing cells, making it a highly informative model for examining how histone modifications can shape the DNA methylome. Using a chromatin immunoprecipitation (ChIP) and genome-wide sequencing (ChIP-seq) protocol optimized for low cell numbers and novel techniques for isolating primary and growing oocytes, profiles were generated for histone modifications implicated in promoting or inhibiting DNA methylation. CGIs destined for DNA methylation show reduced protective H3K4 dimethylation (H3K4me2) and trimethylation (H3K4me3) in both primary and growing oocytes, while permissive H3K36me3 increases specifically at these CGIs in growing oocytes. Methylome profiling of oocytes deficient in H3K4 demethylase KDM1A or KDM1B indicated that removal of H3K4 methylation is necessary for proper methylation establishment at CGIs. This work represents the first systematic study performing ChIP-seq in oocytes and shows that histone remodeling in the mammalian oocyte helps direct de novo DNA methylation events.
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Affiliation(s)
- Kathleen R Stewart
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, United Kingdom
| | - Lenka Veselovska
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, United Kingdom
| | - Jeesun Kim
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas M.D. Anderson Cancer Center, Smithville, Texas 77030, USA
| | - Jiahao Huang
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, United Kingdom
| | - Heba Saadeh
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, United Kingdom; Bioinformatics Group, Babraham Institute, Cambridge CB22 3AT, United Kingdom
| | | | | | - Taiping Chen
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas M.D. Anderson Cancer Center, Smithville, Texas 77030, USA
| | - Gavin Kelsey
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, United Kingdom; Centre for Trophoblast Research, University of Cambridge CB2 3EG, Cambridge, United Kingdom
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11
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Fixed single-cell transcriptomic characterization of human radial glial diversity. Nat Methods 2015; 13:87-93. [PMID: 26524239 PMCID: PMC4869711 DOI: 10.1038/nmeth.3629] [Citation(s) in RCA: 170] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Accepted: 09/23/2015] [Indexed: 01/13/2023]
Abstract
The human neocortex is created from diverse intermixed progenitors in the prenatal germinal zones. These progenitors have been difficult to characterize since progenitors—particularly radial glia (RG)—are rare, and are defined by a combination of intracellular markers, position and morphology. To circumvent these problems we developed a method called FRISCR for transcriptome profiling of individual fixed, stained and sorted cells. After validation of FRISCR using human embryonic stem cells, we profiled primary human RG that constitute only 1% of the mid-gestation cortex. These RG could be classified into ventricular zone-enriched RG (vRG) that express ANXA1 and CRYAB, and outer subventricular zone-localized RG (oRG) that express HOPX. Our study identifies the first markers and molecular profiles of vRG and oRG cells, and provides an essential step for understanding molecular networks driving the lineage of human neocortical progenitors. Furthermore, FRISCR allows targeted single-cell transcriptomic profiling of tissues that lack live-cell markers.
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12
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Holtzinger A, Streeter PR, Sarangi F, Hillborn S, Niapour M, Ogawa S, Keller G. New markers for tracking endoderm induction and hepatocyte differentiation from human pluripotent stem cells. Development 2015; 142:4253-65. [PMID: 26493401 DOI: 10.1242/dev.121020] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 10/13/2015] [Indexed: 12/13/2022]
Abstract
The efficient generation of hepatocytes from human pluripotent stem cells (hPSCs) requires the induction of a proper endoderm population, broadly characterized by the expression of the cell surface marker CXCR4. Strategies to identify and isolate endoderm subpopulations predisposed to the liver fate do not exist. In this study, we generated mouse monoclonal antibodies against human embryonic stem cell-derived definitive endoderm with the goal of identifying cell surface markers that can be used to track the development of this germ layer and its specification to a hepatic fate. Through this approach, we identified two endoderm-specific antibodies, HDE1 and HDE2, which stain different stages of endoderm development and distinct derivative cell types. HDE1 marks a definitive endoderm population with high hepatic potential, whereas staining of HDE2 tracks with developing hepatocyte progenitors and hepatocytes. When used in combination, the staining patterns of these antibodies enable one to optimize endoderm induction and hepatic specification from any hPSC line.
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Affiliation(s)
- Audrey Holtzinger
- McEwen Centre for Regenerative Medicine, University Health Network, Toronto, Ontario, Canada M5G 1L7
| | - Philip R Streeter
- Oregon Stem Cell Center, Oregon Health & Science University, Portland, OR 97239-3098, USA
| | - Farida Sarangi
- McEwen Centre for Regenerative Medicine, University Health Network, Toronto, Ontario, Canada M5G 1L7
| | - Scott Hillborn
- McEwen Centre for Regenerative Medicine, University Health Network, Toronto, Ontario, Canada M5G 1L7
| | - Maryam Niapour
- McEwen Centre for Regenerative Medicine, University Health Network, Toronto, Ontario, Canada M5G 1L7
| | - Shinichiro Ogawa
- McEwen Centre for Regenerative Medicine, University Health Network, Toronto, Ontario, Canada M5G 1L7
| | - Gordon Keller
- McEwen Centre for Regenerative Medicine, University Health Network, Toronto, Ontario, Canada M5G 1L7 Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada M5G 2M9 Princess Margaret Cancer Centre, Toronto, Ontario, Canada M5T 2M9
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13
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HEB associates with PRC2 and SMAD2/3 to regulate developmental fates. Nat Commun 2015; 6:6546. [PMID: 25775035 DOI: 10.1038/ncomms7546] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Accepted: 02/05/2015] [Indexed: 11/09/2022] Open
Abstract
In embryonic stem cells, extracellular signals are required to derepress developmental promoters to drive lineage specification, but the proteins involved in connecting extrinsic cues to relaxation of chromatin remain unknown. We demonstrate that the helix-loop-helix (HLH) protein, HEB, directly associates with the Polycomb repressive complex 2 (PRC2) at a subset of developmental promoters, including at genes involved in mesoderm and endoderm specification and at the Hox and Fox gene families. While we show that depletion of HEB does not affect mouse ESCs, it does cause premature differentiation after exposure to Activin. Further, we find that HEB deposition at developmental promoters is dependent upon PRC2 and independent of Nodal, whereas HEB association with SMAD2/3 elements is dependent of Nodal, but independent of PRC2. We suggest that HEB is a fundamental link between Nodal signalling, the derepression of a specific class of poised promoters during differentiation, and lineage specification in mouse ESCs.
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14
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MARIS: method for analyzing RNA following intracellular sorting. PLoS One 2014; 9:e89459. [PMID: 24594682 PMCID: PMC3940959 DOI: 10.1371/journal.pone.0089459] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Accepted: 01/22/2014] [Indexed: 11/21/2022] Open
Abstract
Transcriptional profiling is a key technique in the study of cell biology that is limited by the availability of reagents to uniquely identify specific cell types and isolate high quality RNA from them. We report a Method for Analyzing RNA following Intracellular Sorting (MARIS) that generates high quality RNA for transcriptome profiling following cellular fixation, intracellular immunofluorescent staining and FACS. MARIS can therefore be used to isolate high quality RNA from many otherwise inaccessible cell types simply based on immunofluorescent tagging of unique intracellular proteins. As proof of principle, we isolate RNA from sorted human embryonic stem cell-derived insulin-expressing cells as well as adult human β cells. MARIS is a basic molecular biology technique that could be used across several biological disciplines.
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Jiang W, Zhang D, Bursac N, Zhang Y. WNT3 is a biomarker capable of predicting the definitive endoderm differentiation potential of hESCs. Stem Cell Reports 2013; 1:46-52. [PMID: 24052941 PMCID: PMC3757741 DOI: 10.1016/j.stemcr.2013.03.003] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Revised: 03/18/2013] [Accepted: 03/20/2013] [Indexed: 12/14/2022] Open
Abstract
Generation of functional cells from human pluripotent stem cells (PSCs) through in vitro differentiation is a promising approach for drug screening and cell therapy. However, the observed large and unavoidable variation in the differentiation potential of different human embryonic stem cell (hESC)/induced PSC (iPSC) lines makes the selection of an appropriate cell line for the differentiation of a particular cell lineage difficult. Here, we report identification of WNT3 as a biomarker capable of predicting definitive endoderm (DE) differentiation potential of hESCs. We show that the mRNA level of WNT3 in hESCs correlates with their DE differentiation efficiency. In addition, manipulations of hESCs through WNT3 knockdown or overexpression can respectively inhibit or promote DE differentiation in a WNT3 level-dependent manner. Finally, analysis of several hESC lines based on their WNT3 expression levels allowed accurate prediction of their DE differentiation potential. Collectively, our study supports the notion that WNT3 can serve as a biomarker for predicting DE differentiation potential of hESCs.
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Affiliation(s)
- Wei Jiang
- Howard Hughes Medical Institute, Harvard Medical School, 25 Shattuck Street, Boston, MA 02115, USA ; Program in Cellular and Molecular Medicine, Harvard Medical School, 25 Shattuck Street, Boston, MA 02115, USA ; Division of Hematology/Oncology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, 25 Shattuck Street, Boston, MA 02115, USA
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Rostovskaya M, Fu J, Obst M, Baer I, Weidlich S, Wang H, Smith AJH, Anastassiadis K, Stewart AF. Transposon-mediated BAC transgenesis in human ES cells. Nucleic Acids Res 2012; 40:e150. [PMID: 22753106 PMCID: PMC3479164 DOI: 10.1093/nar/gks643] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Transgenesis is a cornerstone of molecular biology. The ability to integrate a specifically engineered piece of DNA into the genome of a living system is fundamental to our efforts to understand life and exploit its implications for medicine, nanotechnology and bioprospecting. However, transgenesis has been hampered by position effects and multi-copy integration problems, which are mainly due to the use of small, plasmid-based transgenes. Large transgenes based on native genomic regions cloned into bacterial artificial chromosomes (BACs) circumvent these problems but are prone to fragmentation. Herein, we report that contrary to widely held notions, large BAC-sized constructs do not prohibit transposition. We also report the first reliable method for BAC transgenesis in human embryonic stem cells (hESCs). The PiggyBac or Sleeping Beauty transposon inverted repeats were integrated into BAC vectors by recombineering, followed by co-lipofection with the corresponding transposase in hESCs to generate robust fluorescent protein reporter lines for OCT4, NANOG, GATA4 and PAX6. BAC transposition delivers several advantages, including increased frequencies of single-copy, full-length integration, which will be useful in all transgenic systems but especially in difficult venues like hESCs.
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Affiliation(s)
- Maria Rostovskaya
- Stem Cell Engineering, BioInnovationsZentrum, Technische Universitaet Dresden, Dresden 01307, Germany
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Wang A, Sander M. Generating cells of the gastrointestinal system: current approaches and applications for the differentiation of human pluripotent stem cells. J Mol Med (Berl) 2012; 90:763-71. [DOI: 10.1007/s00109-012-0923-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2012] [Revised: 05/07/2012] [Accepted: 05/24/2012] [Indexed: 12/19/2022]
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Oyolu C, Zakharia F, Baker J. Distinguishing human cell types based on housekeeping gene signatures. Stem Cells 2012; 30:580-4. [PMID: 22162332 DOI: 10.1002/stem.1009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
'In this report, we use single cell gene expression to identify transcriptional patterns emerging during the differentiation of human embryonic stem cells (hESCs) into the endodermal lineage. Endoderm-specific transcripts are highly variable between individual CXCR4(+) endodermal cells, suggesting that either the cells generated from in vitro differentiation are distinct or that these embryonic cells tolerate a high degree of transcript variability. Housekeeping transcripts, on the other hand, are far more consistently expressed within the same cellular population. However, when we compare the levels of housekeeping transcripts between hESCs and derived endoderm, patterns emerge that can be used to clearly separate the two embryonic cell types. We further compared four additional human cell types, including 293T, induced pluripotent stem cell (iPSC), HepG2, and endoderm-derived iPSC. In each case, the relative levels of housekeeping transcripts defined a particular cell fate. Interestingly, we find that three transcripts, LDHA, NONO, and ACTB, contribute the most to this diversity and together serve to segregate all six cell types. Overall, this suggests that levels of housekeeping transcripts, which are expressed within all cells, can be leveraged to distinguish between human cell types and thus may serve as important biomarkers for stem cell biology and other disciplines.
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Affiliation(s)
- Chuba Oyolu
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
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Yoon SJ, Wills AE, Chuong E, Gupta R, Baker JC. HEB and E2A function as SMAD/FOXH1 cofactors. Genes Dev 2011; 25:1654-61. [PMID: 21828274 DOI: 10.1101/gad.16800511] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Nodal signaling, mediated through SMAD transcription factors, is necessary for pluripotency maintenance and endoderm commitment. We identified a new motif, termed SMAD complex-associated (SCA), that is bound by SMAD2/3/4 and FOXH1 in human embryonic stem cells (hESCs) and derived endoderm. We demonstrate that two basic helix-loop-helix (bHLH) proteins-HEB and E2A-bind the SCA motif at regions overlapping SMAD2/3 and FOXH1. Furthermore, we show that HEB and E2A associate with SMAD2/3 and FOXH1, suggesting they form a complex at critical target regions. This association is biologically important, as E2A is critical for mesendoderm specification, gastrulation, and Nodal signal transduction in Xenopus tropicalis embryos. Taken together, E proteins are novel Nodal signaling cofactors that associate with SMAD2/3 and FOXH1 and are necessary for mesendoderm differentiation.
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Affiliation(s)
- Se-Jin Yoon
- Department of Genetics, Stanford University, Stanford, California 94305, USA
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