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Lindström NO, Guo J, Kim AD, Tran T, Guo Q, De Sena Brandine G, Ransick A, Parvez RK, Thornton ME, Baskin L, Grubbs B, McMahon JA, Smith AD, McMahon AP. Conserved and Divergent Features of Mesenchymal Progenitor Cell Types within the Cortical Nephrogenic Niche of the Human and Mouse Kidney. J Am Soc Nephrol 2018; 29:806-824. [PMID: 29449449 DOI: 10.0.6.145/asn.2017080890] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 11/27/2017] [Indexed: 05/24/2023] Open
Abstract
Cellular interactions among nephron, interstitial, and collecting duct progenitors drive mammalian kidney development. In mice, Six2+ nephron progenitor cells (NPCs) and Foxd1+ interstitial progenitor cells (IPCs) form largely distinct lineage compartments at the onset of metanephric kidney development. Here, we used the method for analyzing RNA following intracellular sorting (MARIS) approach, single-cell transcriptional profiling, in situ hybridization, and immunolabeling to characterize the presumptive NPC and IPC compartments of the developing human kidney. As in mice, each progenitor population adopts a stereotypical arrangement in the human nephron-forming niche: NPCs capped outgrowing ureteric branch tips, whereas IPCs were sandwiched between the NPCs and the renal capsule. Unlike mouse NPCs, human NPCs displayed a transcriptional profile that overlapped substantially with the IPC transcriptional profile, and key IPC determinants, including FOXD1, were readily detected within SIX2+ NPCs. Comparative gene expression profiling in human and mouse Six2/SIX2+ NPCs showed broad agreement between the species but also identified species-biased expression of some genes. Notably, some human NPC-enriched genes, including DAPL1 and COL9A2, are linked to human renal disease. We further explored the cellular diversity of mesenchymal cell types in the human nephrogenic niche through single-cell transcriptional profiling. Data analysis stratified NPCs into two main subpopulations and identified a third group of differentiating cells. These findings were confirmed by section in situ hybridization with novel human NPC markers predicted through the single-cell studies. This study provides a benchmark for the mesenchymal progenitors in the human nephrogenic niche and highlights species-variability in kidney developmental programs.
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Affiliation(s)
- Nils O Lindström
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine
| | - Jinjin Guo
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine
| | - Albert D Kim
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine
| | - Tracy Tran
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine
| | - Qiuyu Guo
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine
| | | | - Andrew Ransick
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine
| | - Riana K Parvez
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine
| | - Matthew E Thornton
- Maternal Fetal Medicine Division, University of Southern California, Los Angeles, California; and
| | - Laurence Baskin
- Department of Urology and Pediatrics, University of California San Francisco, San Francisco, California
| | - Brendan Grubbs
- Maternal Fetal Medicine Division, University of Southern California, Los Angeles, California; and
| | - Jill A McMahon
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine
| | - Andrew D Smith
- Molecular and Computational Biology, Department of Biological Sciences, and
| | - Andrew P McMahon
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine,
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Kunnath-Velayudhan S, Porcelli SA. Isolation of intact RNA from murine CD4 + T cells after intracellular cytokine staining and fluorescence-activated cell sorting. J Immunol Methods 2018; 456:77-80. [PMID: 29458078 DOI: 10.1016/j.jim.2018.02.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 02/06/2018] [Accepted: 02/15/2018] [Indexed: 02/02/2023]
Abstract
Intracellular cytokine staining (ICS) is a powerful method for identifying functionally distinct lymphocyte subsets, and for isolating these by fluorescence activated cell sorting (FACS). Although transcriptomic analysis of cells sorted on the basis of ICS has many potential applications, this is rarely performed because of the difficulty in isolating intact RNA from cells processed using standard fixation and permeabilization buffers for ICS. To address this issue, we compared three buffers shown previously to preserve RNA in nonhematopoietic cells subjected to intracellular staining for their effects on RNA isolated from T lymphocytes processed for ICS. Our results showed that buffers containing the recombinant ribonuclease inhibitor RNasin or high molar concentrations of salt yielded intact RNA from fixed and permeabilized T cells. As proof of principle, we successfully used the buffer containing RNasin to isolate intact RNA from CD4+ T cells that were sorted by FACS on the basis of specific cytokine production, thus demonstrating the potential of this approach for coupling ICS with transcriptomic analysis.
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Affiliation(s)
- Shajo Kunnath-Velayudhan
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Steven A Porcelli
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York 10461, USA.
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53
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Lindström NO, Guo J, Kim AD, Tran T, Guo Q, De Sena Brandine G, Ransick A, Parvez RK, Thornton ME, Baskin L, Grubbs B, McMahon JA, Smith AD, McMahon AP. Conserved and Divergent Features of Mesenchymal Progenitor Cell Types within the Cortical Nephrogenic Niche of the Human and Mouse Kidney. J Am Soc Nephrol 2018; 29:806-824. [PMID: 29449449 DOI: 10.1681/asn.2017080890] [Citation(s) in RCA: 147] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 11/27/2017] [Indexed: 01/12/2023] Open
Abstract
Cellular interactions among nephron, interstitial, and collecting duct progenitors drive mammalian kidney development. In mice, Six2+ nephron progenitor cells (NPCs) and Foxd1+ interstitial progenitor cells (IPCs) form largely distinct lineage compartments at the onset of metanephric kidney development. Here, we used the method for analyzing RNA following intracellular sorting (MARIS) approach, single-cell transcriptional profiling, in situ hybridization, and immunolabeling to characterize the presumptive NPC and IPC compartments of the developing human kidney. As in mice, each progenitor population adopts a stereotypical arrangement in the human nephron-forming niche: NPCs capped outgrowing ureteric branch tips, whereas IPCs were sandwiched between the NPCs and the renal capsule. Unlike mouse NPCs, human NPCs displayed a transcriptional profile that overlapped substantially with the IPC transcriptional profile, and key IPC determinants, including FOXD1, were readily detected within SIX2+ NPCs. Comparative gene expression profiling in human and mouse Six2/SIX2+ NPCs showed broad agreement between the species but also identified species-biased expression of some genes. Notably, some human NPC-enriched genes, including DAPL1 and COL9A2, are linked to human renal disease. We further explored the cellular diversity of mesenchymal cell types in the human nephrogenic niche through single-cell transcriptional profiling. Data analysis stratified NPCs into two main subpopulations and identified a third group of differentiating cells. These findings were confirmed by section in situ hybridization with novel human NPC markers predicted through the single-cell studies. This study provides a benchmark for the mesenchymal progenitors in the human nephrogenic niche and highlights species-variability in kidney developmental programs.
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Affiliation(s)
- Nils O Lindström
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine
| | - Jinjin Guo
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine
| | - Albert D Kim
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine
| | - Tracy Tran
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine
| | - Qiuyu Guo
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine
| | | | - Andrew Ransick
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine
| | - Riana K Parvez
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine
| | - Matthew E Thornton
- Maternal Fetal Medicine Division, University of Southern California, Los Angeles, California; and
| | - Laurence Baskin
- Department of Urology and Pediatrics, University of California San Francisco, San Francisco, California
| | - Brendan Grubbs
- Maternal Fetal Medicine Division, University of Southern California, Los Angeles, California; and
| | - Jill A McMahon
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine
| | - Andrew D Smith
- Molecular and Computational Biology, Department of Biological Sciences, and
| | - Andrew P McMahon
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine,
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Using intracellular markers to identify a novel set of surface markers for live cell purification from a heterogeneous hIPSC culture. Sci Rep 2018; 8:804. [PMID: 29339826 PMCID: PMC5770419 DOI: 10.1038/s41598-018-19291-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 12/04/2017] [Indexed: 12/14/2022] Open
Abstract
Human embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs) can provide sources for midbrain dopaminergic (mDA) neural progenitors (NPCs) for cell therapy to treat Parkinson's disease (PD) patients. However, the well-known line-to-cell line variability in the differentiation capacity of individual cell lines needs to be improved for the success of this therapy. To address this issue, we sought to identify mDA NPC specific cell surface markers for fluorescence activated cell sorting (FACS). Through RNA isolation after sorting for NPCs based on staining for cell-specific transcription factors followed by microarray, we identified two positive cell surface markers (CORIN and CD166) and one negative cell surface marker (CXCR4) for mDA NPC sorting. These three markers can enrich floor plate NPCs to 90% purity, and the sorted NPCs more efficiently differentiate to mature dopaminergic neurons compared to unsorted or CORIN+ alone mDA NPCs. This surface marker identification strategy can be used broadly to facilitate isolation of cell subtypes of interest from heterogeneous cultures.
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Kiryluk K, Bomback A, Cheng YL, Camara PG, Rabadan R, Sims P, Barasch J. Precision Medicine for Acute Kidney Injury (AKI): Redefining AKI by Agnostic Kidney Tissue Interrogation and Genetics. Semin Nephrol 2018; 38:40-51. [PMID: 29291761 PMCID: PMC5753434 DOI: 10.1016/j.semnephrol.2017.09.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Acute kidney injury (AKI) currently is diagnosed by a temporal trend of a single blood analyte: serum creatinine. This measurement is neither sensitive nor specific to kidney injury or its protean forms. Newer biomarkers, neutrophil gelatinase-associated lipocalin (NGAL, Lipocalin 2, Siderocalin), or kidney injury molecule-1 (KIM-1, Hepatitis A Virus Cellular Receptor 1), accelerate the diagnosis of AKI as well as prospectively distinguish rapidly reversible from prolonged causes of serum creatinine increase. Nonetheless, these biomarkers lack the capacity to subfractionate AKI further (eg, sepsis versus ischemia versus nephrotoxicity from medications, enzymes, or metals) or inform us about the primary and secondary sites of injury. It also is unknown whether all nephrons are injured in AKI, whether all cells in a nephron are affected, and whether injury responses can be stimulus-specific or cell type-specific or both. In this review, we summarize fully agnostic tissue interrogation approaches that may help to redefine AKI in cellular and molecular terms, including single-cell and single-nuclei RNA sequencing technology. These approaches will empower a shift in the current paradigm of AKI diagnosis, classification, and staging, and provide the renal community with a significant advance toward precision medicine in the analysis AKI.
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Affiliation(s)
- Krzysztof Kiryluk
- Department of Medicine, Division of Nephrology, College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Andrew Bomback
- Department of Medicine, Division of Nephrology, College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Yim-Ling Cheng
- Department of Systems Biology, College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Pablo G. Camara
- Department of Systems Biology, College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Raul Rabadan
- Department of Systems Biology, College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Peter Sims
- Department of Systems Biology, College of Physicians & Surgeons, Columbia University, New York, NY, USA
- Department of Biochemistry and Molecular Biophysics, College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Jonathan Barasch
- Department of Medicine, Division of Nephrology, College of Physicians & Surgeons, Columbia University, New York, NY, USA
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Liu L, Nielsen FM, Riis SE, Emmersen J, Fink T, Hjortdal JØ, Bath C, Zachar V. Maintaining RNA Integrity for Transcriptomic Profiling of Ex Vivo Cultured Limbal Epithelial Stem Cells after Fluorescence-Activated Cell Sorting (FACS). Biol Proced Online 2017; 19:15. [PMID: 29255379 PMCID: PMC5727887 DOI: 10.1186/s12575-017-0065-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 12/01/2017] [Indexed: 11/10/2022] Open
Abstract
Background Transcriptomic profiling of ex vivo cultured human limbal epithelial stem cells (hLESCs) will foster better understanding of corneal physiology and novel treatment paradigms to limbal stem cell deficiency (LSCD). However, currently such profiling studies are hampered due to difficulties with producing sufficient amounts of intact mRNA for deep RNA sequencing (RNA-seq) from subpopulations sorted on the basis of co-expression of membrane and intracellular antigens by fluorescence-activated cell sorting (FACS). Methods To address this problem, we systematically analyzed the critical steps, and found that ethanol fixation together with optimized downstream procedures provided a pipeline that yielded high quality total RNA in amounts to readily support the RNA-seq procedure, while still preserving good discrimination between the individual hLESC immunophenotypes. Results The average RNA integrity number (RIN) was 7.7 ± 0.4, and the average yield was 4.6 ± 1.7 pg of RNA per cell. The sequencing analysis of the isolated RNA produced high quality data with more than 70% of read pairs mapping uniformly to the reference genome and 80% of bases with a Phred score of at least 30. Conclusion In this study, we developed a reliable FACS-based procedure using ethanol as a fixative that would support accurate isolation of limbal epithelial progenitor subpopulations along with RNA yield and quality sufficient to enable deep transcriptomic profiling.
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Affiliation(s)
- Lei Liu
- Laboratory for Stem Cell Research, Aalborg University, Aalborg, Denmark.,Department of Pediatric Surgery, First Hospital of Jilin University, Changchun, China
| | | | | | - Jeppe Emmersen
- Laboratory for Stem Cell Research, Aalborg University, Aalborg, Denmark
| | - Trine Fink
- Laboratory for Stem Cell Research, Aalborg University, Aalborg, Denmark
| | | | - Chris Bath
- Department of Ophthalmology, Aalborg University Hospital, Aalborg, Denmark
| | - Vladimir Zachar
- Laboratory for Stem Cell Research, Aalborg University, Aalborg, Denmark
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57
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Ly T, Whigham A, Clarke R, Brenes-Murillo AJ, Estes B, Madhessian D, Lundberg E, Wadsworth P, Lamond AI. Proteomic analysis of cell cycle progression in asynchronous cultures, including mitotic subphases, using PRIMMUS. eLife 2017; 6:e27574. [PMID: 29052541 PMCID: PMC5650473 DOI: 10.7554/elife.27574] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 10/06/2017] [Indexed: 12/22/2022] Open
Abstract
The temporal regulation of protein abundance and post-translational modifications is a key feature of cell division. Recently, we analysed gene expression and protein abundance changes during interphase under minimally perturbed conditions (Ly et al., 2014, 2015). Here, we show that by using specific intracellular immunolabelling protocols, FACS separation of interphase and mitotic cells, including mitotic subphases, can be combined with proteomic analysis by mass spectrometry. Using this PRIMMUS (PRoteomic analysis of Intracellular iMMUnolabelled cell Subsets) approach, we now compare protein abundance and phosphorylation changes in interphase and mitotic fractions from asynchronously growing human cells. We identify a set of 115 phosphorylation sites increased during G2, termed 'early risers'. This set includes phosphorylation of S738 on TPX2, which we show is important for TPX2 function and mitotic progression. Further, we use PRIMMUS to provide the first a proteome-wide analysis of protein abundance remodeling between prophase, prometaphase and anaphase.
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Affiliation(s)
- Tony Ly
- Centre for Gene Regulation and Expression, School of Life SciencesUniversity of DundeeDundeeUnited Kingdom
- Wellcome Centre for Cell BiologyUniversity of EdinburghEdinburghUnited Kingdom
| | - Arlene Whigham
- CAST Flow Cytometry Facility, School of Life SciencesUniversity of DundeeDundeeUnited Kingdom
| | - Rosemary Clarke
- CAST Flow Cytometry Facility, School of Life SciencesUniversity of DundeeDundeeUnited Kingdom
| | - Alejandro J Brenes-Murillo
- Centre for Gene Regulation and Expression, School of Life SciencesUniversity of DundeeDundeeUnited Kingdom
| | - Brett Estes
- Department of BiologyUniversity of MassachusettsMassachusettsUnited States
- Program in Molecular and Cellular BiologyUniversity of MassachusettsMassachusettsUnited States
| | - Diana Madhessian
- Science for Life LaboratoryRoyal Institute of TechnologyStockholmSweden
| | - Emma Lundberg
- Science for Life LaboratoryRoyal Institute of TechnologyStockholmSweden
| | - Patricia Wadsworth
- Department of BiologyUniversity of MassachusettsMassachusettsUnited States
- Program in Molecular and Cellular BiologyUniversity of MassachusettsMassachusettsUnited States
| | - Angus I Lamond
- Centre for Gene Regulation and Expression, School of Life SciencesUniversity of DundeeDundeeUnited Kingdom
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58
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Ševčíková T, Growková K, Kufová Z, Filipová J, Vrublová P, Jelínek T, Kořístek Z, Kryukov F, Kryukova E, Hájek R. Biobanking strategy and sample preprocessing for integrative research in monoclonal gammopathies. J Clin Pathol 2017; 70:847-853. [PMID: 28360189 PMCID: PMC5749344 DOI: 10.1136/jclinpath-2017-204329] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Revised: 03/03/2017] [Accepted: 03/07/2017] [Indexed: 11/25/2022]
Abstract
AIMS Some types of monoclonal gammopathies are typified by a very limited availability of aberrant cells. Modern research use high throughput technologies and an integrated approach for detailed characterisation of abnormal cells. This strategy requires relatively high amounts of starting material which cannot be obtained from every diagnosis without causing inconvenience to the patient. The aim of this methodological paper is to reflect our long experience with laboratory work and describe the best protocols for sample collection, sorting and further preprocessing in terms of the available number of cells and intended downstream application in monoclonal gammopathies research. Potential pitfalls are also discussed. METHODS Comparison and optimisation of freezing and sorting protocols for plasma cells in monoclonal gammopathies, followed by testing of various nucleic acid isolation and amplification techniques to establish a guideline for sample processing in haemato-oncology research. RESULTS We show the average numbers of aberrant cells that can be obtained from various monoclonal gammopathies (monoclonal gammopathy of undetermined significance/light chain amyloidosis/multiple myeloma (MM)/MM circulating plasma cells/ minimal residual disease MM-10 123/22 846/305 501/68 641/4000 aberrant plasma cells of 48/30/10/16/37×106 bone marrow mononuclear cells) and the expected yield of nucleic acids provided from multiple isolation kits (DNA/RNA yield from 1 to 200×103 cells was 2.14-427/0.12-123 ng). CONCLUSIONS Tested kits for parallel isolation deliver outputs comparable with kits specialised for just one type of molecule. We also present our positive experience with the whole genome amplification method, which can serve as a very powerful tool to gain complex information from a very small cell population.
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Affiliation(s)
- T Ševčíková
- Department of Haemato-oncology, University Hospital Ostrava, Ostrava, Czech Republic
- Faculty of Medicine, University of Ostrava, Ostrava, Czech Republic
| | - K Growková
- Faculty of Medicine, University of Ostrava, Ostrava, Czech Republic
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Z Kufová
- Faculty of Medicine, University of Ostrava, Ostrava, Czech Republic
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - J Filipová
- Faculty of Medicine, University of Ostrava, Ostrava, Czech Republic
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - P Vrublová
- Department of Haemato-oncology, University Hospital Ostrava, Ostrava, Czech Republic
| | - T Jelínek
- Department of Haemato-oncology, University Hospital Ostrava, Ostrava, Czech Republic
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Z Kořístek
- Department of Haemato-oncology, University Hospital Ostrava, Ostrava, Czech Republic
- Faculty of Medicine, University of Ostrava, Ostrava, Czech Republic
| | - F Kryukov
- Department of Haemato-oncology, University Hospital Ostrava, Ostrava, Czech Republic
| | - E Kryukova
- Faculty of Medicine, University of Ostrava, Ostrava, Czech Republic
- Babak Myeloma Group, Department of Pathological Physiology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - R Hájek
- Department of Haemato-oncology, University Hospital Ostrava, Ostrava, Czech Republic
- Faculty of Medicine, University of Ostrava, Ostrava, Czech Republic
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Abstract
The fundamental operative unit of a cancer is the genetically and epigenetically innovative single cell. Whether proliferating or quiescent, in the primary tumour mass or disseminated elsewhere, single cells govern the parameters that dictate all facets of the biology of cancer. Thus, single-cell analyses provide the ultimate level of resolution in our quest for a fundamental understanding of this disease. Historically, this quest has been hampered by technological shortcomings. In this Opinion article, we argue that the rapidly evolving field of single-cell sequencing has unshackled the cancer research community of these shortcomings. From furthering an elemental understanding of intra-tumoural genetic heterogeneity and cancer genome evolution to illuminating the governing principles of disease relapse and metastasis, we posit that single-cell sequencing promises to unravel the biology of all facets of this disease.
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Affiliation(s)
- Timour Baslan
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York 10044, USA, and Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - James Hicks
- University of Southern California Dana and David Dornsife College of Letters, Arts, and Sciences, University of Southern California, Los Angeles, California 90089, USA
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Hosokawa Y, Toyoda T, Fukui K, Baden MY, Funato M, Kondo Y, Sudo T, Iwahashi H, Kishida M, Okada C, Watanabe A, Asaka I, Osafune K, Imagawa A, Shimomura I. Insulin-producing cells derived from 'induced pluripotent stem cells' of patients with fulminant type 1 diabetes: Vulnerability to cytokine insults and increased expression of apoptosis-related genes. J Diabetes Investig 2017; 9:481-493. [PMID: 28796422 PMCID: PMC5934265 DOI: 10.1111/jdi.12727] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Revised: 07/24/2017] [Accepted: 08/06/2017] [Indexed: 01/28/2023] Open
Abstract
AIMS/INTRODUCTION The present study was carried out to generate induced pluripotent stem cells (iPSCs) from patients with fulminant type 1 diabetes, and evaluate the cytokine-induced apoptotic reactions of β-like insulin-producing cells differentiated from the iPSCs. MATERIALS AND METHODS iPSCs were generated from fibroblasts of patients with fulminant type 1 diabetes by inducing six reprogramming factors. Insulin-producing cells were differentiated from the iPSCs in vitro. The proportion of cleaved caspase-3-positive or terminal deoxynucleotidyl transferase 2'-deoxyuridine, 5'-triphosphate nick end labeling-positive cells among insulin (INS)-positive cells derived from fulminant type 1 diabetes iPSC and control human iPSC lines was evaluated under treatment with tumor necrosis factor-α, interleukin-1β and interferon-γ. Ribonucleic acid sequencing was carried out to compare gene expressions in INS-positive cells derived from fulminant type 1 diabetes iPSC and control human iPSC lines. RESULTS Two iPSC clones were established from each of three patients with fulminant type 1 diabetes. The differentiation of insulin-producing cells from fulminant type 1 diabetes iPSC was confirmed by immunofluorescence analysis and KCl-induced C-peptide secretion. After treatment with pro-inflammatory cytokines, these INS-positive cells showed higher expression of cleaved caspase-3 than those derived from control human iPSCs. Altered expression levels of several apoptosis-related genes were observed in INS-positive cells derived from the fulminant type 1 diabetes iPSCs by ribonucleic acid sequencing. CONCLUSIONS We generated iPSCs from patients with fulminant type 1 diabetes and differentiated them into insulin-producing cells. This in vitro disease model can be used to elucidate the disease mechanisms of fulminant type 1 diabetes.
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Affiliation(s)
- Yoshiya Hosokawa
- Department of Metabolic MedicineOsaka University Graduate School of MedicineOsakaJapan
| | - Taro Toyoda
- Center for iPS Cell Research and Application (CiRA)Kyoto UniversityKyotoJapan
| | - Kenji Fukui
- Department of Metabolic MedicineOsaka University Graduate School of MedicineOsakaJapan
| | - Megu Yamaguchi Baden
- Department of Metabolic MedicineOsaka University Graduate School of MedicineOsakaJapan
| | - Michinori Funato
- Center for iPS Cell Research and Application (CiRA)Kyoto UniversityKyotoJapan
- Department of Clinical ResearchNational Hospital OrganizationNagara Medical CenterGifuJapan
| | - Yasushi Kondo
- Center for iPS Cell Research and Application (CiRA)Kyoto UniversityKyotoJapan
- Department of Diabetes, Endocrinology and NutritionKyoto UniversityKyotoJapan
| | - Tomomi Sudo
- Center for iPS Cell Research and Application (CiRA)Kyoto UniversityKyotoJapan
| | - Hiromi Iwahashi
- Department of Metabolic MedicineOsaka University Graduate School of MedicineOsakaJapan
- Department of Diabetes Care MedicineOsaka University Graduate School of MedicineOsakaJapan
| | - Marina Kishida
- Center for iPS Cell Research and Application (CiRA)Kyoto UniversityKyotoJapan
- Japan Agency for Medical Research and Development (AMED)‐CRESTJapan
| | - Chihiro Okada
- Center for iPS Cell Research and Application (CiRA)Kyoto UniversityKyotoJapan
- Mitsubishi Space SoftwareTokyoJapan
| | - Akira Watanabe
- Center for iPS Cell Research and Application (CiRA)Kyoto UniversityKyotoJapan
- Japan Agency for Medical Research and Development (AMED)‐CRESTJapan
| | - Isao Asaka
- Center for iPS Cell Research and Application (CiRA)Kyoto UniversityKyotoJapan
| | - Kenji Osafune
- Center for iPS Cell Research and Application (CiRA)Kyoto UniversityKyotoJapan
| | - Akihisa Imagawa
- Department of Metabolic MedicineOsaka University Graduate School of MedicineOsakaJapan
- Department of Internal Medicine (I)Osaka Medical CollegeOsakaJapan
| | - Iichiro Shimomura
- Department of Metabolic MedicineOsaka University Graduate School of MedicineOsakaJapan
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61
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Axelsson AS, Mahdi T, Nenonen HA, Singh T, Hänzelmann S, Wendt A, Bagge A, Reinbothe TM, Millstein J, Yang X, Zhang B, Gusmao EG, Shu L, Szabat M, Tang Y, Wang J, Salö S, Eliasson L, Artner I, Fex M, Johnson JD, Wollheim CB, Derry JMJ, Mecham B, Spégel P, Mulder H, Costa IG, Zhang E, Rosengren AH. Sox5 regulates beta-cell phenotype and is reduced in type 2 diabetes. Nat Commun 2017; 8:15652. [PMID: 28585545 PMCID: PMC5467166 DOI: 10.1038/ncomms15652] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2017] [Accepted: 04/10/2017] [Indexed: 01/09/2023] Open
Abstract
Type 2 diabetes (T2D) is characterized by insulin resistance and impaired insulin secretion, but the mechanisms underlying insulin secretion failure are not completely understood. Here, we show that a set of co-expressed genes, which is enriched for genes with islet-selective open chromatin, is associated with T2D. These genes are perturbed in T2D and have a similar expression pattern to that of dedifferentiated islets. We identify Sox5 as a regulator of the module. Sox5 knockdown induces gene expression changes similar to those observed in T2D and diabetic animals and has profound effects on insulin secretion, including reduced depolarization-evoked Ca2+-influx and β-cell exocytosis. SOX5 overexpression reverses the expression perturbations observed in a mouse model of T2D, increases the expression of key β-cell genes and improves glucose-stimulated insulin secretion in human islets from donors with T2D. We suggest that human islets in T2D display changes reminiscent of dedifferentiation and highlight SOX5 as a regulator of β-cell phenotype and function.
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Affiliation(s)
- A S Axelsson
- Lund University Diabetes Center, CRC 91-11 SUS, Jan Waldenströms gata 35, SE-20502 Malmö, Sweden
| | - T Mahdi
- Lund University Diabetes Center, CRC 91-11 SUS, Jan Waldenströms gata 35, SE-20502 Malmö, Sweden.,Medical Research Center, Hawler Medical University, 44001 Erbil, Iraq
| | - H A Nenonen
- Lund University Diabetes Center, CRC 91-11 SUS, Jan Waldenströms gata 35, SE-20502 Malmö, Sweden
| | - T Singh
- Lund University Diabetes Center, CRC 91-11 SUS, Jan Waldenströms gata 35, SE-20502 Malmö, Sweden
| | - S Hänzelmann
- Institute of Biomedical Engineering, RWTH Aachen University Hospital, Pauwelstr 19, 52074 Aachen, Germany
| | - A Wendt
- Lund University Diabetes Center, CRC 91-11 SUS, Jan Waldenströms gata 35, SE-20502 Malmö, Sweden
| | - A Bagge
- Lund University Diabetes Center, CRC 91-11 SUS, Jan Waldenströms gata 35, SE-20502 Malmö, Sweden
| | - T M Reinbothe
- Lund University Diabetes Center, CRC 91-11 SUS, Jan Waldenströms gata 35, SE-20502 Malmö, Sweden
| | - J Millstein
- Sage Bionetworks, 1100 Fairview Avenue N, Seattle, Washington 98109, USA
| | - X Yang
- Sage Bionetworks, 1100 Fairview Avenue N, Seattle, Washington 98109, USA.,Department of Integrative Biology and Physiology, University of California, Los Angeles, 610 Charles E. Young Dr East, Los Angeles, California 90095, USA
| | - B Zhang
- Sage Bionetworks, 1100 Fairview Avenue N, Seattle, Washington 98109, USA.,Department of Genetics and Genomic Sciences, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, New York 10029, USA
| | - E G Gusmao
- Institute of Biomedical Engineering, RWTH Aachen University Hospital, Pauwelstr 19, 52074 Aachen, Germany
| | - L Shu
- Department of Integrative Biology and Physiology, University of California, Los Angeles, 610 Charles E. Young Dr East, Los Angeles, California 90095, USA
| | - M Szabat
- Diabetes Research Group, Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, 5358-2350 Health Sciences Mall, Vancouver, British Columbia, Canada V6T 1Z3
| | - Y Tang
- Lund University Diabetes Center, CRC 91-11 SUS, Jan Waldenströms gata 35, SE-20502 Malmö, Sweden.,Key Lab of Hormones and Development, Ministry of Health, Metabolic Diseases Hospital, Tianjin Medical University, Tianjin 300070, China
| | - J Wang
- Lund University Diabetes Center, CRC 91-11 SUS, Jan Waldenströms gata 35, SE-20502 Malmö, Sweden.,Department of Emergency, Zhongshan Hospital, Xiamen University, Xiamen, Fujian 361004, China
| | - S Salö
- Lund University Diabetes Center, CRC 91-11 SUS, Jan Waldenströms gata 35, SE-20502 Malmö, Sweden
| | - L Eliasson
- Lund University Diabetes Center, CRC 91-11 SUS, Jan Waldenströms gata 35, SE-20502 Malmö, Sweden
| | - I Artner
- Lund University Diabetes Center, CRC 91-11 SUS, Jan Waldenströms gata 35, SE-20502 Malmö, Sweden
| | - M Fex
- Lund University Diabetes Center, CRC 91-11 SUS, Jan Waldenströms gata 35, SE-20502 Malmö, Sweden
| | - J D Johnson
- Diabetes Research Group, Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, 5358-2350 Health Sciences Mall, Vancouver, British Columbia, Canada V6T 1Z3
| | - C B Wollheim
- Lund University Diabetes Center, CRC 91-11 SUS, Jan Waldenströms gata 35, SE-20502 Malmö, Sweden.,Department of Cell Physiology and Metabolism, University Medical Center, Rue Michel-Servet 1, 1206 Geneva, Switzerland
| | - J M J Derry
- Sage Bionetworks, 1100 Fairview Avenue N, Seattle, Washington 98109, USA
| | - B Mecham
- Trialomics, 6310 12th Avenue NE, Seattle, Washington 98115, USA
| | - P Spégel
- Lund University Diabetes Center, CRC 91-11 SUS, Jan Waldenströms gata 35, SE-20502 Malmö, Sweden.,Centre for Analysis and Synthesis, Department of Chemistry, Lund University, SE-221 00 Lund, Sweden
| | - H Mulder
- Lund University Diabetes Center, CRC 91-11 SUS, Jan Waldenströms gata 35, SE-20502 Malmö, Sweden
| | - I G Costa
- Institute of Biomedical Engineering, RWTH Aachen University Hospital, Pauwelstr 19, 52074 Aachen, Germany
| | - E Zhang
- Lund University Diabetes Center, CRC 91-11 SUS, Jan Waldenströms gata 35, SE-20502 Malmö, Sweden
| | - A H Rosengren
- Lund University Diabetes Center, CRC 91-11 SUS, Jan Waldenströms gata 35, SE-20502 Malmö, Sweden.,Sage Bionetworks, 1100 Fairview Avenue N, Seattle, Washington 98109, USA.,Department of Neuroscience and Physiology, University of Gothenburg, Box 100, SE-405 30 Gothenburg, Sweden
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62
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Carrano AC, Mulas F, Zeng C, Sander M. Interrogating islets in health and disease with single-cell technologies. Mol Metab 2017; 6:991-1001. [PMID: 28951823 PMCID: PMC5605723 DOI: 10.1016/j.molmet.2017.04.012] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/18/2017] [Revised: 04/10/2017] [Accepted: 04/11/2017] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Blood glucose levels are tightly controlled by the coordinated actions of hormone-producing endocrine cells that reside in pancreatic islets. Islet cell malfunction underlies diabetes development and progression. Due to the cellular heterogeneity within islets, it has been challenging to uncover how specific islet cells contribute to glucose homeostasis and diabetes pathogenesis. Recent advances in single-cell technologies and computational methods have opened up new avenues to resolve islet heterogeneity and study islet cell states in health and disease. SCOPE OF REVIEW In the past year, a multitude of studies have been published that used single-cell approaches to interrogate the transcriptome and proteome of the different islet cell types. Here, we summarize the conclusions of these studies, as well as discuss the technologies used and the challenges faced with computational analysis of single-cell data from islet studies. MAJOR CONCLUSIONS By analyzing single islet cells from rodents and humans at different ages and disease states, the studies reviewed here have provided new insight into endocrine cell function and facilitated a high resolution molecular characterization of poorly understood processes, including regeneration, maturation, and diabetes pathogenesis. Gene expression programs and pathways identified in these studies pave the way for the discovery of new targets and approaches to prevent, monitor, and treat diabetes.
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Affiliation(s)
- Andrea C Carrano
- Departments of Pediatrics and Cellular & Molecular Medicine, Pediatric Diabetes Research Center, University of California, San Diego, 2880 Torrey Pines Scenic Drive, La Jolla, CA 92037, USA
| | - Francesca Mulas
- Departments of Pediatrics and Cellular & Molecular Medicine, Pediatric Diabetes Research Center, University of California, San Diego, 2880 Torrey Pines Scenic Drive, La Jolla, CA 92037, USA
| | - Chun Zeng
- Departments of Pediatrics and Cellular & Molecular Medicine, Pediatric Diabetes Research Center, University of California, San Diego, 2880 Torrey Pines Scenic Drive, La Jolla, CA 92037, USA
| | - Maike Sander
- Departments of Pediatrics and Cellular & Molecular Medicine, Pediatric Diabetes Research Center, University of California, San Diego, 2880 Torrey Pines Scenic Drive, La Jolla, CA 92037, USA
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63
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Guo A, Huang S, Yu J, Wang H, Li H, Pei G, Shen L. Single-Cell Dynamic Analysis of Mitosis in Haploid Embryonic Stem Cells Shows the Prolonged Metaphase and Its Association with Self-diploidization. Stem Cell Reports 2017; 8:1124-1134. [PMID: 28457886 PMCID: PMC5425685 DOI: 10.1016/j.stemcr.2017.03.025] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2016] [Revised: 03/30/2017] [Accepted: 03/31/2017] [Indexed: 12/30/2022] Open
Abstract
The recent establishment of mammalian haploid embryonic stem cells (ESCs) provides new possibilities for genetic screening and for understanding genome evolution and function. However, the dynamics of mitosis in haploid ESCs is still unclear. Here, we report that the duration of mitosis in haploid ESCs, especially the metaphase, is significantly longer than that in diploid ESCs. Delaying mitosis by chemicals increased self-diploidization of haploid ESCs, while shortening mitosis stabilized haploid ESCs. Taken together, our study suggests that the delayed mitosis of haploid ESCs is associated with self-diploidization. Mitosis is prolonged in haploid ESCs, especially in metaphase Self-diploidization might be associated with the prolonged mitosis of haploid ESCs
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Affiliation(s)
- Ao Guo
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Shichao Huang
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China; Shanghai Key Laboratory of Signaling and Disease Research, Laboratory of Receptor-based Bio-medicine, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Jiali Yu
- Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Huihan Wang
- Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Haisen Li
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Gang Pei
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China; Shanghai Key Laboratory of Signaling and Disease Research, Laboratory of Receptor-based Bio-medicine, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China.
| | - Li Shen
- Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China.
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64
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Abstract
The transcriptome is a powerful proxy for the physiological state of a cell, healthy or diseased. As a result, transcriptome analysis has become a key tool in understanding the molecular changes that accompany bacterial infections of eukaryotic cells. Until recently, such transcriptomic studies have been technically limited to analyzing mRNA expression changes in either the bacterial pathogen or the infected eukaryotic host cell. However, the increasing sensitivity of high-throughput RNA sequencing now enables "dual RNA-seq" studies, simultaneously capturing all classes of coding and noncoding transcripts in both the pathogen and the host. In the five years since the concept of dual RNA-seq was introduced, the technique has been applied to a range of infection models. This has not only led to a better understanding of the physiological changes in pathogen and host during the course of an infection but has also revealed hidden molecular phenotypes of virulence-associated small noncoding RNAs that were not visible in standard infection assays. Here, we use the knowledge gained from these recent studies to suggest experimental and computational guidelines for the design of future dual RNA-seq studies. We conclude this review by discussing prospective applications of the technique.
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Affiliation(s)
- Alexander J. Westermann
- RNA Biology Group, Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany
| | - Lars Barquist
- RNA Biology Group, Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany
| | - Jörg Vogel
- RNA Biology Group, Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany
- Helmholtz Institute for RNA-based Infection Research (HIRI), Würzburg, Germany
- * E-mail:
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65
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Laroumanie F, Dale BL, Saleh MA, Madhur MS. Intracellular Staining and Flow Cytometry to Identify Lymphocyte Subsets within Murine Aorta, Kidney and Lymph Nodes in a Model of Hypertension. J Vis Exp 2017:55266. [PMID: 28190037 PMCID: PMC5352305 DOI: 10.3791/55266] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
It is now well known that T lymphocytes play a critical role in the development of several cardiovascular diseases1,2,3,4,5. For example, studies from our group have shown that hypertension is associated with an excessive accumulation of T cells in the vessels and kidney during the development of experimental hypertension6. Once in these tissues, T cells produce several cytokines that affect both vascular and renal function leading to vasoconstriction and sodium and water retention1,2. To fully understand how T cells cause cardiovascular and renal diseases, it is important to be able to identify and quantify the specific T cell subsets present in these tissues. T cell subsets are defined by a combination of surface markers, the cytokines they secrete, and the transcription factors they express. The complexity of the T cell population makes flow cytometry and intracellular staining an invaluable technique to dissect the phenotypes of the lymphocytes present in tissues. Here, we provide a detailed protocol to identify the surface and intracellular markers (cytokines and transcription factors) in T cells isolated from murine kidney, aorta and aortic draining lymph nodes in a model of angiotensin II induced hypertension. The following steps are described in detail: isolation of the tissues, generation of the single cell suspensions, ex vivo stimulation, fixation, permeabilization and staining. In addition, several fundamental principles of flow cytometric analyses including choosing the proper controls and appropriate gating strategies are discussed.
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Affiliation(s)
- Fanny Laroumanie
- Department of Medicine, Division of Clinical Pharmacology, Vanderbilt University Medical Center
| | - Bethany L Dale
- Department of Molecular Physiology and Biophysics, Vanderbilt University
| | - Mohamed A Saleh
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Mansoura University
| | - Meena S Madhur
- Department of Medicine, Division of Clinical Pharmacology, Vanderbilt University Medical Center;
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66
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Oxburgh L, Carroll TJ, Cleaver O, Gossett DR, Hoshizaki DK, Hubbell JA, Humphreys BD, Jain S, Jensen J, Kaplan DL, Kesselman C, Ketchum CJ, Little MH, McMahon AP, Shankland SJ, Spence JR, Valerius MT, Wertheim JA, Wessely O, Zheng Y, Drummond IA. (Re)Building a Kidney. J Am Soc Nephrol 2017; 28:1370-1378. [PMID: 28096308 DOI: 10.1681/asn.2016101077] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
(Re)Building a Kidney is a National Institute of Diabetes and Digestive and Kidney Diseases-led consortium to optimize approaches for the isolation, expansion, and differentiation of appropriate kidney cell types and the integration of these cells into complex structures that replicate human kidney function. The ultimate goals of the consortium are two-fold: to develop and implement strategies for in vitro engineering of replacement kidney tissue, and to devise strategies to stimulate regeneration of nephrons in situ to restore failing kidney function. Projects within the consortium will answer fundamental questions regarding human gene expression in the developing kidney, essential signaling crosstalk between distinct cell types of the developing kidney, how to derive the many cell types of the kidney through directed differentiation of human pluripotent stem cells, which bioengineering or scaffolding strategies have the most potential for kidney tissue formation, and basic parameters of the regenerative response to injury. As these projects progress, the consortium will incorporate systematic investigations in physiologic function of in vitro and in vivo differentiated kidney tissue, strategies for engraftment in experimental animals, and development of therapeutic approaches to activate innate reparative responses.
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Affiliation(s)
- Leif Oxburgh
- Center for Molecular Medicine, Maine Medical Center Research Institute, Scarborough, Maine;
| | - Thomas J Carroll
- Department of Molecular Biology and.,Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Ondine Cleaver
- Department of Molecular Biology and.,Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Daniel R Gossett
- Division of Kidney, Urologic, & Hematologic Diseases, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland
| | - Deborah K Hoshizaki
- Division of Kidney, Urologic, & Hematologic Diseases, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland
| | - Jeffrey A Hubbell
- Institute for Molecular Engineering, University of Chicago, Chicago, Illinois
| | - Benjamin D Humphreys
- Division of Nephrology, Washington University School of Medicine, St. Louis, Missouri
| | - Sanjay Jain
- Division of Nephrology, Washington University School of Medicine, St. Louis, Missouri
| | - Jan Jensen
- Department of Stem Cell Biology and Regenerative Medicine and.,Trailhead Biosystems, Inc, Cleveland, Ohio
| | - David L Kaplan
- Department of Biomedical Engineering, Tufts University, Medford, Massachusetts
| | - Carl Kesselman
- Epstein Department of Industrial and Systems Engineering and Information Sciences Institute, Viterbi School of Engineering and.,Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Christian J Ketchum
- Division of Kidney, Urologic, & Hematologic Diseases, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland
| | - Melissa H Little
- Cell Biology Theme, Murdoch Childrens Research Institute, Parkville, Melbourne, Australia.,Department of Pediatrics, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Melbourne, Australia
| | - Andrew P McMahon
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, California
| | | | - Jason R Spence
- Department of Internal Medicine, Division of Gastroenterology and.,Department of Cell and Developmental Biology and Center for Organogenesis, University of Michigan Medical School, Ann Arbor, Michigan
| | - M Todd Valerius
- Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
| | - Jason A Wertheim
- Department of Surgery, Jesse Brown VA Medical Center, and.,Comprehensive Transplant Center, Department of Surgery, Northwestern University Feinberg School of Medicine, Chicago, Illinois; and
| | - Oliver Wessely
- Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio
| | - Ying Zheng
- Department of Bioengineering, Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle
| | - Iain A Drummond
- Nephrology Division, Massachusetts General Hospital, Charlestown, Massachusetts
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67
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Lee YH, Kim SN, Kwon HJ, Granneman JG. Metabolic heterogeneity of activated beige/brite adipocytes in inguinal adipose tissue. Sci Rep 2017; 7:39794. [PMID: 28045125 PMCID: PMC5206656 DOI: 10.1038/srep39794] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 11/28/2016] [Indexed: 11/09/2022] Open
Abstract
Sustained β3 adrenergic receptor (ADRB3) activation simultaneously upregulates fatty acid synthesis and oxidation in mouse brown, beige, and white adipose tissues; however, the cellular basis of this dual regulation is not known. Treatment of mice with the ADRB3 agonist CL316,243 (CL) increased expression of fatty acid synthase (FASN) and medium chain acyl-CoA dehydrogenase (MCAD) protein within the same cells in classic brown and white adipose tissues. Surprisingly, in inguinal adipose tissue, CL-upregulated FASN and MCAD in distinct cell populations: high MCAD expression occurred in multilocular adipocytes that co-expressed UCP1+, whereas high FASN expression occurred in paucilocular adipocytes lacking detectable UCP1. Genetic tracing with UCP1-cre, however, indicated nearly half of adipocytes with a history of UCP1 expression expressed high levels of FASN without current expression of UCP1. Global transcriptomic analysis of FACS-isolated adipocytes confirmed the presence of distinct anabolic and catabolic phenotypes, and identified differential expression of transcriptional pathways known to regulate lipid synthesis and oxidation. Surprisingly, paternally-expressed genes of the non-classical gene imprinted network were strikingly enriched in anabolic phenotypes, suggesting possible involvement in maintaining the balance of metabolic phenotypes. The results indicate that metabolic heterogeneity is a distinct property of activated beige/brite adipocytes that might be under epigenetic control.
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Affiliation(s)
- Yun-Hee Lee
- College of Pharmacy, Yonsei University, Incheon, 21983, South Korea
| | - Sang-Nam Kim
- College of Pharmacy, Yonsei University, Incheon, 21983, South Korea
| | - Hyun-Jung Kwon
- College of Pharmacy, Yonsei University, Incheon, 21983, South Korea
| | - James G Granneman
- Center for Integrative Metabolic and Endocrine Research, Wayne State University School of Medicine, Detroit, MI, 48201, USA
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68
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Yang MG, West AE. Editing the Neuronal Genome: a CRISPR View of Chromatin Regulation in Neuronal Development, Function, and Plasticity. THE YALE JOURNAL OF BIOLOGY AND MEDICINE 2016; 89:457-470. [PMID: 28018138 PMCID: PMC5168825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The dynamic orchestration of gene expression is crucial for the proper differentiation, function, and adaptation of cells. In the brain, transcriptional regulation underlies the incredible diversity of neuronal cell types and contributes to the ability of neurons to adapt their function to the environment. Recently, novel methods for genome and epigenome editing have begun to revolutionize our understanding of gene regulatory mechanisms. In particular, the clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 system has proven to be a particularly accessible and adaptable technique for genome engineering. Here, we review the use of CRISPR/Cas9 in neurobiology and discuss how these studies have advanced understanding of nervous system development and plasticity. We cover four especially salient applications of CRISPR/Cas9: testing the consequences of enhancer mutations, tagging genes and gene products for visualization in live cells, directly activating or repressing enhancers in vivo, and manipulating the epigenome. In each case, we summarize findings from recent studies and discuss evolving adaptations of the method.
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Affiliation(s)
| | - Anne E. West
- Anne West, Department of Neurobiology, DUMC Box 3209, 311 Research Drive, Bryan Research 301D, Durham, NC 27710, Phone: 919-681-1909, Fax: 919-668-4431,
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69
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Single-cell transcriptomes identify human islet cell signatures and reveal cell-type-specific expression changes in type 2 diabetes. Genome Res 2016; 27:208-222. [PMID: 27864352 PMCID: PMC5287227 DOI: 10.1101/gr.212720.116] [Citation(s) in RCA: 330] [Impact Index Per Article: 41.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 11/16/2016] [Indexed: 01/09/2023]
Abstract
Blood glucose levels are tightly controlled by the coordinated action of at least four cell types constituting pancreatic islets. Changes in the proportion and/or function of these cells are associated with genetic and molecular pathophysiology of monogenic, type 1, and type 2 (T2D) diabetes. Cellular heterogeneity impedes precise understanding of the molecular components of each islet cell type that govern islet (dys)function, particularly the less abundant delta and gamma/pancreatic polypeptide (PP) cells. Here, we report single-cell transcriptomes for 638 cells from nondiabetic (ND) and T2D human islet samples. Analyses of ND single-cell transcriptomes identified distinct alpha, beta, delta, and PP/gamma cell-type signatures. Genes linked to rare and common forms of islet dysfunction and diabetes were expressed in the delta and PP/gamma cell types. Moreover, this study revealed that delta cells specifically express receptors that receive and coordinate systemic cues from the leptin, ghrelin, and dopamine signaling pathways implicating them as integrators of central and peripheral metabolic signals into the pancreatic islet. Finally, single-cell transcriptome profiling revealed genes differentially regulated between T2D and ND alpha, beta, and delta cells that were undetectable in paired whole islet analyses. This study thus identifies fundamental cell-type–specific features of pancreatic islet (dys)function and provides a critical resource for comprehensive understanding of islet biology and diabetes pathogenesis.
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70
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Massumi M, Pourasgari F, Nalla A, Batchuluun B, Nagy K, Neely E, Gull R, Nagy A, Wheeler MB. An Abbreviated Protocol for In Vitro Generation of Functional Human Embryonic Stem Cell-Derived Beta-Like Cells. PLoS One 2016; 11:e0164457. [PMID: 27755557 PMCID: PMC5068782 DOI: 10.1371/journal.pone.0164457] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 09/26/2016] [Indexed: 12/28/2022] Open
Abstract
The ability to yield glucose-responsive pancreatic beta-cells from human pluripotent stem cells in vitro will facilitate the development of the cell replacement therapies for the treatment of Type 1 Diabetes. Here, through the sequential in vitro targeting of selected signaling pathways, we have developed an abbreviated five-stage protocol (25–30 days) to generate human Embryonic Stem Cell-Derived Beta-like Cells (ES-DBCs). We showed that Geltrex, as an extracellular matrix, could support the generation of ES-DBCs more efficiently than that of the previously described culture systems. The activation of FGF and Retinoic Acid along with the inhibition of BMP, SHH and TGF-beta led to the generation of 75% NKX6.1+/NGN3+ Endocrine Progenitors. The inhibition of Notch and tyrosine kinase receptor AXL, and the treatment with Exendin-4 and T3 in the final stage resulted in 35% mono-hormonal insulin positive cells, 1% insulin and glucagon positive cells and 30% insulin and NKX6.1 co-expressing cells. Functionally, ES-DBCs were responsive to high glucose in static incubation and perifusion studies, and could secrete insulin in response to successive glucose stimulations. Mitochondrial metabolic flux analyses using Seahorse demonstrated that the ES-DBCs could efficiently metabolize glucose and generate intracellular signals to trigger insulin secretion. In conclusion, targeting selected signaling pathways for 25–30 days was sufficient to generate ES-DBCs in vitro. The ability of ES-DBCs to secrete insulin in response to glucose renders them a promising model for the in vitro screening of drugs, small molecules or genes that may have potential to influence beta-cell function.
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Affiliation(s)
- Mohammad Massumi
- Departments of Medicine and Physiology, Faculty of Medicine, University of Toronto, ON, Canada.,Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada.,Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
| | - Farzaneh Pourasgari
- Departments of Medicine and Physiology, Faculty of Medicine, University of Toronto, ON, Canada.,Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada
| | - Amarnadh Nalla
- Departments of Medicine and Physiology, Faculty of Medicine, University of Toronto, ON, Canada.,Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Battsetseg Batchuluun
- Departments of Medicine and Physiology, Faculty of Medicine, University of Toronto, ON, Canada
| | - Kristina Nagy
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
| | - Eric Neely
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
| | - Rida Gull
- Departments of Medicine and Physiology, Faculty of Medicine, University of Toronto, ON, Canada
| | - Andras Nagy
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
| | - Michael B Wheeler
- Departments of Medicine and Physiology, Faculty of Medicine, University of Toronto, ON, Canada.,Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada
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71
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Derr A, Yang C, Zilionis R, Sergushichev A, Blodgett DM, Redick S, Bortell R, Luban J, Harlan DM, Kadener S, Greiner DL, Klein A, Artyomov MN, Garber M. End Sequence Analysis Toolkit (ESAT) expands the extractable information from single-cell RNA-seq data. Genome Res 2016; 26:1397-1410. [PMID: 27470110 PMCID: PMC5052061 DOI: 10.1101/gr.207902.116] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 07/27/2016] [Indexed: 12/27/2022]
Abstract
RNA-seq protocols that focus on transcript termini are well suited for applications in which template quantity is limiting. Here we show that, when applied to end-sequencing data, analytical methods designed for global RNA-seq produce computational artifacts. To remedy this, we created the End Sequence Analysis Toolkit (ESAT). As a test, we first compared end-sequencing and bulk RNA-seq using RNA from dendritic cells stimulated with lipopolysaccharide (LPS). As predicted by the telescripting model for transcriptional bursts, ESAT detected an LPS-stimulated shift to shorter 3′-isoforms that was not evident by conventional computational methods. Then, droplet-based microfluidics was used to generate 1000 cDNA libraries, each from an individual pancreatic islet cell. ESAT identified nine distinct cell types, three distinct β-cell types, and a complex interplay between hormone secretion and vascularization. ESAT, then, offers a much-needed and generally applicable computational pipeline for either bulk or single-cell RNA end-sequencing.
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Affiliation(s)
- Alan Derr
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA
| | - Chaoxing Yang
- Program in Molecular Medicine, Diabetes Center of Excellence, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA
| | - Rapolas Zilionis
- Department of System Biology, Harvard Medical School, Boston, Massachusetts 02115, USA; Institute of Biotechnology, Vilnius University, LT 02241 Vilnius, Lithuania
| | - Alexey Sergushichev
- Computer Technologies Department, ITMO University, Saint Petersburg, 197101, Russia; Department of Pathology and Immunology, Washington University in St. Louis, St. Louis, Missouri 63110, USA
| | - David M Blodgett
- Department of Medicine, Diabetes Center of Excellence, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA
| | - Sambra Redick
- Program in Molecular Medicine, Diabetes Center of Excellence, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA
| | - Rita Bortell
- Program in Molecular Medicine, Diabetes Center of Excellence, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA
| | - Jeremy Luban
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA
| | - David M Harlan
- Department of Medicine, Diabetes Center of Excellence, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA
| | - Sebastian Kadener
- Biological Chemistry Department, Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Dale L Greiner
- Program in Molecular Medicine, Diabetes Center of Excellence, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA; Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA
| | - Allon Klein
- Department of System Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Maxim N Artyomov
- Department of Pathology and Immunology, Washington University in St. Louis, St. Louis, Missouri 63110, USA
| | - Manuel Garber
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA; Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA
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72
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Arda HE, Li L, Tsai J, Torre EA, Rosli Y, Peiris H, Spitale RC, Dai C, Gu X, Qu K, Wang P, Wang J, Grompe M, Scharfmann R, Snyder MS, Bottino R, Powers AC, Chang HY, Kim SK. Age-Dependent Pancreatic Gene Regulation Reveals Mechanisms Governing Human β Cell Function. Cell Metab 2016; 23:909-20. [PMID: 27133132 PMCID: PMC4864151 DOI: 10.1016/j.cmet.2016.04.002] [Citation(s) in RCA: 176] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Revised: 09/03/2015] [Accepted: 03/31/2016] [Indexed: 01/08/2023]
Abstract
Intensive efforts are focused on identifying regulators of human pancreatic islet cell growth and maturation to accelerate development of therapies for diabetes. After birth, islet cell growth and function are dynamically regulated; however, establishing these age-dependent changes in humans has been challenging. Here, we describe a multimodal strategy for isolating pancreatic endocrine and exocrine cells from children and adults to identify age-dependent gene expression and chromatin changes on a genomic scale. These profiles revealed distinct proliferative and functional states of islet α cells or β cells and histone modifications underlying age-dependent gene expression changes. Expression of SIX2 and SIX3, transcription factors without prior known functions in the pancreas and linked to fasting hyperglycemia risk, increased with age specifically in human islet β cells. SIX2 and SIX3 were sufficient to enhance insulin content or secretion in immature β cells. Our work provides a unique resource to study human-specific regulators of islet cell maturation and function.
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Affiliation(s)
- H Efsun Arda
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Lingyu Li
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jennifer Tsai
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Eduardo A Torre
- Program in Epithelial Biology, Department of Dermatology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Yenny Rosli
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Heshan Peiris
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Robert C Spitale
- Program in Epithelial Biology, Department of Dermatology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Chunhua Dai
- Division of Diabetes, Endocrinology, and Metabolism, Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Xueying Gu
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Kun Qu
- Program in Epithelial Biology, Department of Dermatology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Pei Wang
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jing Wang
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Markus Grompe
- Oregon Stem Cell Center, Oregon Health & Science University, Portland, OR 97239, USA
| | - Raphael Scharfmann
- INSERM U1016, Institut Cochin, Université Paris Descartes, Sorbonne Paris Cité, Paris 75014, France
| | - Michael S Snyder
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Rita Bottino
- Institute of Cellular Therapeutics, Allegheny Health Network, 320 East North Avenue, Pittsburgh, PA 15212, USA
| | - Alvin C Powers
- Division of Diabetes, Endocrinology, and Metabolism, Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Department of Molecular Physiology and Biophysics, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Veterans Affairs Tennessee Valley Healthcare System, Nashville, TN 37212, USA
| | - Howard Y Chang
- Program in Epithelial Biology, Department of Dermatology, Stanford University School of Medicine, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Seung K Kim
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine (Oncology Division), Stanford University School of Medicine, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA.
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73
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Li J, Klughammer J, Farlik M, Penz T, Spittler A, Barbieux C, Berishvili E, Bock C, Kubicek S. Single-cell transcriptomes reveal characteristic features of human pancreatic islet cell types. EMBO Rep 2015; 17:178-87. [PMID: 26691212 PMCID: PMC4784001 DOI: 10.15252/embr.201540946] [Citation(s) in RCA: 177] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 11/19/2015] [Indexed: 01/19/2023] Open
Abstract
Pancreatic islets of Langerhans contain several specialized endocrine cell types, which are commonly identified by the expression of single marker genes. However, the established marker genes cannot capture the complete spectrum of cellular heterogeneity in human pancreatic islets, and existing bulk transcriptome datasets provide averages across several cell populations. To dissect the cellular composition of the human pancreatic islet and to establish transcriptomes for all major cell types, we performed single‐cell RNA sequencing on 70 cells sorted from human primary tissue. We used this dataset to validate previously described marker genes at the single‐cell level and to identify specifically expressed transcription factors for all islet cell subtypes. All data are available for browsing and download, thus establishing a useful resource of single‐cell expression profiles for endocrine cells in human pancreatic islets.
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Affiliation(s)
- Jin Li
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Johanna Klughammer
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Matthias Farlik
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Thomas Penz
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Andreas Spittler
- Medical University of Vienna Anna Spiegel Forschungsgebäude, Vienna, Austria
| | - Charlotte Barbieux
- Department of Surgery, Cell Isolation and Transplantation Center, Geneva University Hospitals University of Geneva, Geneva, Switzerland
| | - Ekaterine Berishvili
- Department of Surgery, Cell Isolation and Transplantation Center, Geneva University Hospitals University of Geneva, Geneva, Switzerland
| | - Christoph Bock
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria Max Planck Institute for Informatics, Saarbrücken, Germany
| | - Stefan Kubicek
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria Christian Doppler Laboratory for Chemical Epigenetics and Antiinfectives, CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
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74
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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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75
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Blodgett DM, Nowosielska A, Afik S, Pechhold S, Cura AJ, Kennedy NJ, Kim S, Kucukural A, Davis RJ, Kent SC, Greiner DL, Garber MG, Harlan DM, diIorio P. Novel Observations From Next-Generation RNA Sequencing of Highly Purified Human Adult and Fetal Islet Cell Subsets. Diabetes 2015; 64:3172-81. [PMID: 25931473 PMCID: PMC4542439 DOI: 10.2337/db15-0039] [Citation(s) in RCA: 229] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Accepted: 04/16/2015] [Indexed: 12/13/2022]
Abstract
Understanding distinct gene expression patterns of normal adult and developing fetal human pancreatic α- and β-cells is crucial for developing stem cell therapies, islet regeneration strategies, and therapies designed to increase β-cell function in patients with diabetes (type 1 or 2). Toward that end, we have developed methods to highly purify α-, β-, and δ-cells from human fetal and adult pancreata by intracellular staining for the cell-specific hormone content, sorting the subpopulations by flow cytometry, and, using next-generation RNA sequencing, we report the detailed transcriptomes of fetal and adult α- and β-cells. We observed that human islet composition was not influenced by age, sex, or BMI, and transcripts for inflammatory gene products were noted in fetal β-cells. In addition, within highly purified adult glucagon-expressing α-cells, we observed surprisingly high insulin mRNA expression, but not insulin protein expression. This transcriptome analysis from highly purified islet α- and β-cell subsets from fetal and adult pancreata offers clear implications for strategies that seek to increase insulin expression in type 1 and type 2 diabetes.
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Affiliation(s)
- David M Blodgett
- Department of Medicine, Diabetes Center of Excellence, University of Massachusetts Medical School, Worcester, MA
| | - Anetta Nowosielska
- Program in Molecular Medicine, Diabetes Center of Excellence, University of Massachusetts Medical School, Worcester, MA
| | - Shaked Afik
- Program in Molecular Medicine, Program in Bioinformatics, University of Massachusetts Medical School, Worcester, MA
| | - Susanne Pechhold
- Department of Medicine, Diabetes Center of Excellence, University of Massachusetts Medical School, Worcester, MA
| | - Anthony J Cura
- Department of Medicine, Diabetes Center of Excellence, University of Massachusetts Medical School, Worcester, MA
| | - Norman J Kennedy
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA
| | - Soyoung Kim
- Program in Molecular Medicine, Diabetes Center of Excellence, University of Massachusetts Medical School, Worcester, MA
| | - Alper Kucukural
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA
| | - Roger J Davis
- Program in Molecular Medicine, University of Massachusetts Medical School, and Howard Hughes Medical Institute, Worcester, MA
| | - Sally C Kent
- Department of Medicine, Diabetes Center of Excellence, University of Massachusetts Medical School, Worcester, MA
| | - Dale L Greiner
- Program in Molecular Medicine, Diabetes Center of Excellence, University of Massachusetts Medical School, Worcester, MA
| | - Manuel G Garber
- Program in Molecular Medicine, Program in Bioinformatics, University of Massachusetts Medical School, Worcester, MA
| | - David M Harlan
- Department of Medicine, Diabetes Center of Excellence, University of Massachusetts Medical School, Worcester, MA
| | - Philip diIorio
- Program in Molecular Medicine, Diabetes Center of Excellence, University of Massachusetts Medical School, Worcester, MA
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76
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Ng SY, Soh BS, Rodriguez-Muela N, Hendrickson DG, Price F, Rinn JL, Rubin LL. Genome-wide RNA-Seq of Human Motor Neurons Implicates Selective ER Stress Activation in Spinal Muscular Atrophy. Cell Stem Cell 2015; 17:569-84. [PMID: 26321202 DOI: 10.1016/j.stem.2015.08.003] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Revised: 06/30/2015] [Accepted: 08/04/2015] [Indexed: 01/13/2023]
Abstract
Spinal muscular atrophy (SMA) is caused by mutations in the SMN1 gene. Because this gene is expressed ubiquitously, it remains poorly understood why motor neurons (MNs) are one of the most affected cell types. To address this question, we carried out RNA sequencing studies using fixed, antibody-labeled, and purified MNs produced from control and SMA patient-derived induced pluripotent stem cells (iPSCs). We found SMA-specific changes in MNs, including hyper-activation of the ER stress pathway. Functional studies demonstrated that inhibition of ER stress improves MN survival in vitro even in MNs expressing low SMN. In SMA mice, systemic delivery of an ER stress inhibitor that crosses the blood-brain barrier led to the preservation of spinal cord MNs. Therefore, our study implies that selective activation of ER stress underlies MN death in SMA. Moreover, the approach we have taken would be broadly applicable to the study of disease-prone human cells in heterogeneous cultures.
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Affiliation(s)
- Shi-Yan Ng
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Boon Seng Soh
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Department of Cell and Molecular Biology, Karolinska Institute, 17177 Stockholm, Sweden
| | - Natalia Rodriguez-Muela
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - David G Hendrickson
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; The Broad Institute of the Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Feodor Price
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - John L Rinn
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; The Broad Institute of the Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Lee L Rubin
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA.
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77
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Kenty JHR, Melton DA. Testing pancreatic islet function at the single cell level by calcium influx with associated marker expression. PLoS One 2015; 10:e0122044. [PMID: 25853429 PMCID: PMC4390334 DOI: 10.1371/journal.pone.0122044] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2014] [Accepted: 02/09/2015] [Indexed: 01/06/2023] Open
Abstract
Studying the response of islet cells to glucose stimulation is important for understanding cell function in healthy and disease states. Most functional assays are performed on whole islets or cell populations, resulting in averaged observations and loss of information at the single cell level. We demonstrate methods to examine calcium fluxing in individual cells of intact islets in response to multiple glucose challenges. Wild-type mouse islets predominantly contained cells that responded to three (out of three) sequential high glucose challenges, whereas cells of diabetic islets (db/db or NOD) responded less frequently or not at all. Imaged islets were also immunostained for endocrine markers to associate the calcium flux profile of individual cells with gene expression. Wild-type mouse islet cells that robustly fluxed calcium expressed β cell markers (INS/NKX6.1), whereas islet cells that inversely fluxed at low glucose expressed α cell markers (GCG). Diabetic mouse islets showed a higher proportion of dysfunctional β cells that responded poorly to glucose challenges. Most of the failed calcium influx responses in β cells were observed in the second and third high glucose challenges, emphasizing the importance of multiple sequential glucose challenges for assessing the full function of islet cells. Human islet cells were also assessed and showed functional α and β cells. This approach to analyze islet responses to multiple glucose challenges in correlation with gene expression assays expands the understanding of β cell function and the diseased state.
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Affiliation(s)
- Jennifer H. R. Kenty
- Department of Stem Cell and Regenerative Biology, Harvard University, Harvard Stem Cell Institute, Cambridge, Massachusetts, United States of America
| | - Douglas A. Melton
- Department of Stem Cell and Regenerative Biology, Harvard University, Harvard Stem Cell Institute, Cambridge, Massachusetts, United States of America
- * E-mail:
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78
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Molyneaux BJ, Goff LA, Brettler AC, Chen HH, Hrvatin S, Rinn JL, Arlotta P. DeCoN: genome-wide analysis of in vivo transcriptional dynamics during pyramidal neuron fate selection in neocortex. Neuron 2015; 85:275-288. [PMID: 25556833 PMCID: PMC4430475 DOI: 10.1016/j.neuron.2014.12.024] [Citation(s) in RCA: 168] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/02/2014] [Indexed: 10/24/2022]
Abstract
Neuronal development requires a complex choreography of transcriptional decisions to obtain specific cellular identities. Realizing the ultimate goal of identifying genome-wide signatures that define and drive specific neuronal fates has been hampered by enormous complexity in both time and space during development. Here, we have paired high-throughput purification of pyramidal neuron subclasses with deep profiling of spatiotemporal transcriptional dynamics during corticogenesis to resolve lineage choice decisions. We identified numerous features ranging from spatial and temporal usage of alternative mRNA isoforms and promoters to a host of mRNA genes modulated during fate specification. Notably, we uncovered numerous long noncoding RNAs with restricted temporal and cell-type-specific expression. To facilitate future exploration, we provide an interactive online database to enable multidimensional data mining and dissemination. This multifaceted study generates a powerful resource and informs understanding of the transcriptional regulation underlying pyramidal neuron diversity in the neocortex. VIDEO ABSTRACT
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Affiliation(s)
- Bradley J. Molyneaux
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, United States
| | - Loyal A. Goff
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, United States
- Broad Institute of MIT and Harvard, Cambridge, MA, 02139, United States
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, 02139, United States
| | - Andrea C. Brettler
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, United States
| | - Hsu-Hsin Chen
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, United States
| | - Siniša Hrvatin
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, United States
| | - John L. Rinn
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, United States
- Broad Institute of MIT and Harvard, Cambridge, MA, 02139, United States
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02115, United States
| | - Paola Arlotta
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, United States
- Broad Institute of MIT and Harvard, Cambridge, MA, 02139, United States
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79
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Abstract
Human pluripotent stem cells (hPSCs) have the potential to generate any human cell type, and one widely recognized goal is to make pancreatic β cells. To this end, comparisons between differentiated cell types produced in vitro and their in vivo counterparts are essential to validate hPSC-derived cells. Genome-wide transcriptional analysis of sorted insulin-expressing (INS(+)) cells derived from three independent hPSC lines, human fetal pancreata, and adult human islets points to two major conclusions: (i) Different hPSC lines produce highly similar INS(+) cells and (ii) hPSC-derived INS(+) (hPSC-INS(+)) cells more closely resemble human fetal β cells than adult β cells. This study provides a direct comparison of transcriptional programs between pure hPSC-INS(+) cells and true β cells and provides a catalog of genes whose manipulation may convert hPSC-INS(+) cells into functional β cells.
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