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Neyens D, Hirsch T, Abdel Aziz Issa Abdel Hadi A, Dauguet N, Vanhaver C, Bayard A, Wildmann C, Luyckx M, Squifflet JL, D’Hondt Q, Duhamel C, Huaux A, Montiel V, Dechamps M, van der Bruggen P. HELIOS-expressing human CD8 T cells exhibit limited effector functions. Front Immunol 2023; 14:1308539. [PMID: 38187391 PMCID: PMC10770868 DOI: 10.3389/fimmu.2023.1308539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 11/15/2023] [Indexed: 01/09/2024] Open
Abstract
Introduction The transcription factor HELIOS is primarily known for its expression in CD4 regulatory T cells, both in humans and mice. In mice, HELIOS is found in exhausted CD8 T cells. However, information on human HELIOS+ CD8 T cells is limited and conflicting. Methods In this study, we characterized by flow cytometry and transcriptomic analyses human HELIOS+ CD8 T cells. Results These T cells primarily consist of memory cells and constitute approximately 21% of blood CD8 T cells. In comparison with memory HELIOS- T-BEThigh CD8 T cells that displayed robust effector functions, the memory HELIOS+ T-BEThigh CD8 T cells produce lower amounts of IFN-γ and TNF-α and have a lower cytotoxic potential. We wondered if these cells participate in the immune response against viral antigens, but did not find HELIOS+ cells among CD8 T cells recognizing CMV peptides presented by HLA-A2 and HLA-B7. However, we found HELIOS+ CD8 T cells that recognize a CMV peptide presented by MHC class Ib molecule HLA-E. Additionally, a portion of HELIOS+ CD8 T cells is characterized by the expression of CD161, often used as a surface marker for identifying TC17 cells. These CD8 T cells express TH17/TC17-related genes encoding RORgt, RORa, PLZF, and CCL20. Discussion Our findings emphasize that HELIOS is expressed across various CD8 T cell populations, highlighting its significance beyond its role as a transcription factor for Treg or exhausted murine CD8 T cells. The significance of the connection between HELIOS and HLA-E restriction is yet to be understood.
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Affiliation(s)
- Damien Neyens
- De Duve Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Thibault Hirsch
- De Duve Institute, Université Catholique de Louvain, Brussels, Belgium
| | | | - Nicolas Dauguet
- De Duve Institute, Université Catholique de Louvain, Brussels, Belgium
| | | | - Alexandre Bayard
- De Duve Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Claude Wildmann
- De Duve Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Mathieu Luyckx
- De Duve Institute, Université Catholique de Louvain, Brussels, Belgium
- Département de gynécologie, Cliniques Universitaires Saint-Luc, Brussels, Belgium
| | - Jean-Luc Squifflet
- De Duve Institute, Université Catholique de Louvain, Brussels, Belgium
- Département de gynécologie, Cliniques Universitaires Saint-Luc, Brussels, Belgium
| | - Quentin D’Hondt
- De Duve Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Céline Duhamel
- De Duve Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Antoine Huaux
- De Duve Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Virginie Montiel
- Unité de soins intensifs, Cliniques Universitaires Saint-Luc, Brussels, Belgium
| | - Mélanie Dechamps
- Unité de soins intensifs, Cliniques Universitaires Saint-Luc, Brussels, Belgium
| | - Pierre van der Bruggen
- De Duve Institute, Université Catholique de Louvain, Brussels, Belgium
- Walloon Excellence in Life Sciences and Biotechnology (WELBIO), Wavre, Belgium
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Liew LC, Poh BM, An O, Ho BX, Lim CYY, Pang JKS, Beh LY, Yang HH, Soh BS. JAK2 as a surface marker for enrichment of human pluripotent stem cells-derived ventricular cardiomyocytes. Stem Cell Res Ther 2023; 14:367. [PMID: 38093391 PMCID: PMC10720068 DOI: 10.1186/s13287-023-03610-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 12/07/2023] [Indexed: 12/17/2023] Open
Abstract
BACKGROUND Human pluripotent stem cell (hPSC)-derived cardiomyocytes (CMs) hold great promise for cardiac disease modelling, drug discovery and regenerative medicine. Despite the advancement in various differentiation protocols, the heterogeneity of the generated population composed of diverse cardiac subtypes poses a significant challenge to their practical applications. Mixed populations of cardiac subtypes can compromise disease modelling and drug discovery, while transplanting them may lead to undesired arrhythmias as they may not integrate and synchronize with the host tissue's contractility. It is therefore crucial to identify cell surface markers that could enable high purity of ventricular CMs for subsequent applications. METHODS By exploiting the fact that immature CMs expressing myosin light chain 2A (MLC2A) will gradually express myosin light chain 2 V (MLC2V) protein as they mature towards ventricular fate, we isolated signal regulatory protein alpha (SIRPA)-positive CMs expressing intracellular MLC2A or MLC2V using MARIS (method for analysing RNA following intracellular sorting). Subsequently, RNA sequencing analysis was performed to examine the gene expression profile of MLC2A + and MLC2V + sorted CMs. We identified genes that were significantly up-regulated in MLC2V + samples to be potential surface marker candidates for ventricular specification. To validate these surface markers, we performed immunostaining and western blot analysis to measure MLC2A and MLC2V protein expressions in SIRPA + CMs that were either positive or negative for the putative surface markers, JAK2 (Janus kinase 2) or CD200. We then characterized the electrophysiological properties of surface marker-sorted CMs, using fluo-4 AM, a green-fluorescent calcium indicator, to measure the cellular calcium transient at the single cell level. For functional validation, we investigated the response of the surface marker-sorted CMs to vernakalant, an atrial-selective anti-arrhythmic agent. RESULTS In this study, while JAK2 and CD200 were identified as potential surface markers for the purification of ventricular-like CMs, the SIRPA+/JAK2+ population showed a higher percentage of MLC2V-expressing cells (~ 90%) compared to SIRPA+/CD200+ population (~ 75%). SIRPA+/JAK2+ sorted CMs exhibited ventricular-like electrophysiological properties, including slower beating rate, slower calcium depolarization and longer calcium repolarization duration. Importantly, vernakalant had limited to no significant effect on the calcium repolarization duration of SIRPA+/JAK2+ population, indicating their enrichment for ventricular-like CMs. CONCLUSION Our study lays the groundwork for the identification of cardiac subtype surface markers that allow purification of cardiomyocyte sub-populations. Our findings suggest that JAK2 can be employed as a cell surface marker for enrichment of hPSC-derived ventricular-like CMs.
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Affiliation(s)
- Lee Chuen Liew
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Republic of Singapore
| | - Boon Min Poh
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Republic of Singapore
| | - Omer An
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Republic of Singapore
| | - Beatrice Xuan Ho
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Republic of Singapore
| | - Christina Ying Yan Lim
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Republic of Singapore
| | - Jeremy Kah Sheng Pang
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Republic of Singapore
| | - Leslie Y Beh
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Republic of Singapore
| | - Henry He Yang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Republic of Singapore
| | - Boon-Seng Soh
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Republic of Singapore.
- Department of Biological Sciences, National University of Singapore, Singapore, 117543, Republic of Singapore.
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Lee H, Sahin GS, Chen CW, Sonthalia S, Cañas SM, Oktay HZ, Duckworth AT, Brawerman G, Thompson PJ, Hatzoglou M, Eizirik DL, Engin F. Stress-induced β cell early senescence confers protection against type 1 diabetes. Cell Metab 2023; 35:2200-2215.e9. [PMID: 37949065 PMCID: PMC10842515 DOI: 10.1016/j.cmet.2023.10.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 07/31/2023] [Accepted: 10/18/2023] [Indexed: 11/12/2023]
Abstract
During the progression of type 1 diabetes (T1D), β cells are exposed to significant stress and, therefore, require adaptive responses to survive. The adaptive mechanisms that can preserve β cell function and survival in the face of autoimmunity remain unclear. Here, we show that the deletion of the unfolded protein response (UPR) genes Atf6α or Ire1α in β cells of non-obese diabetic (NOD) mice prior to insulitis generates a p21-driven early senescence phenotype and alters the β cell secretome that significantly enhances the leukemia inhibitory factor-mediated recruitment of M2 macrophages to islets. Consequently, M2 macrophages promote anti-inflammatory responses and immune surveillance that cause the resolution of islet inflammation, the removal of terminally senesced β cells, the reduction of β cell apoptosis, and protection against T1D. We further demonstrate that the p21-mediated early senescence signature is conserved in the residual β cells of T1D patients. Our findings reveal a previously unrecognized link between β cell UPR and senescence that, if leveraged, may represent a novel preventive strategy for T1D.
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Affiliation(s)
- Hugo Lee
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, School of Medicine and Public Health, Madison, WI 53706, USA
| | - Gulcan Semra Sahin
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, School of Medicine and Public Health, Madison, WI 53706, USA
| | - Chien-Wen Chen
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Shreyash Sonthalia
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, School of Medicine and Public Health, Madison, WI 53706, USA
| | - Sandra Marín Cañas
- ULB Center for Diabetes Research, Medical Faculty, Université Libre de Bruxelles, Campus Erasme, B-1070 Brussels, Belgium
| | - Hulya Zeynep Oktay
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, School of Medicine and Public Health, Madison, WI 53706, USA
| | - Alexander T Duckworth
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, School of Medicine and Public Health, Madison, WI 53706, USA
| | - Gabriel Brawerman
- Department of Physiology & Pathophysiology, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - Peter J Thompson
- Department of Physiology & Pathophysiology, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - Maria Hatzoglou
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Decio L Eizirik
- ULB Center for Diabetes Research, Medical Faculty, Université Libre de Bruxelles, Campus Erasme, B-1070 Brussels, Belgium
| | - Feyza Engin
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, School of Medicine and Public Health, Madison, WI 53706, USA; Department of Medicine, Division of Endocrinology, Diabetes & Metabolism, University of Wisconsin-Madison, School of Medicine and Public Health, Madison, WI 53705, USA; Department of Cell and Regenerative Biology, Wisconsin Institute for Discovery, University of Wisconsin-Madison, School of Medicine and Public Health, Madison, WI 53705, USA.
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Zhang J, Katada K, Mosleh E, Yuhas A, Peng G, Golson ML. The leptin receptor has no role in delta-cell control of beta-cell function in the mouse. Front Endocrinol (Lausanne) 2023; 14:1257671. [PMID: 37850099 PMCID: PMC10577419 DOI: 10.3389/fendo.2023.1257671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 09/05/2023] [Indexed: 10/19/2023] Open
Abstract
Introduction Leptin inhibits insulin secretion from isolated islets from multiple species, but the cell type that mediates this process remains elusive. Several mouse models have been used to explore this question. Ablation of the leptin receptor (Lepr) throughout the pancreatic epithelium results in altered glucose homeostasis and ex vivo insulin secretion and Ca2+ dynamics. However, Lepr removal from neither alpha nor beta cells mimics this result. Moreover, scRNAseq data has revealed an enrichment of LEPR in human islet delta cells. Methods We confirmed LEPR upregulation in human delta cells by performing RNAseq on fixed, sorted beta and delta cells. We then used a mouse model to test whether delta cells mediate the diminished glucose-stimulated insulin secretion in response to leptin. Results Ablation of Lepr within mouse delta cells did not change glucose homeostasis or insulin secretion, whether mice were fed a chow or high-fat diet. We further show, using a publicly available scRNAseq dataset, that islet cells expressing Lepr lie within endothelial cell clusters. Conclusions In mice, leptin does not influence beta-cell function through delta cells.
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Affiliation(s)
- Jia Zhang
- Department of Genetics, University of Pennsylvania, Philadephia, PA, United States
| | - Kay Katada
- School of Medicine, University of Pennsylvania, Philadephia, PA, United States
| | - Elham Mosleh
- Department of Genetics, University of Pennsylvania, Philadephia, PA, United States
- School of Medicine, University of Pennsylvania, Philadephia, PA, United States
| | - Andrew Yuhas
- Department of Genetics, University of Pennsylvania, Philadephia, PA, United States
- School of Medicine, University of Pennsylvania, Philadephia, PA, United States
| | - Guihong Peng
- Department of Medicine, Divison of Endocrinology, Diabetes, and Metabolism, Johns Hopkins University, Baltimore, MD, United States
| | - Maria L. Golson
- Department of Genetics, University of Pennsylvania, Philadephia, PA, United States
- School of Medicine, University of Pennsylvania, Philadephia, PA, United States
- Department of Medicine, Divison of Endocrinology, Diabetes, and Metabolism, Johns Hopkins University, Baltimore, MD, United States
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Hermann FM, Kjærgaard MF, Tian C, Tiemann U, Jackson A, Olsen LR, Kraft M, Carlsson PO, Elfving IM, Kettunen JLT, Tuomi T, Novak I, Semb H. An insulin hypersecretion phenotype precedes pancreatic β cell failure in MODY3 patient-specific cells. Cell Stem Cell 2023; 30:38-51.e8. [PMID: 36563694 DOI: 10.1016/j.stem.2022.12.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 10/04/2022] [Accepted: 11/28/2022] [Indexed: 12/24/2022]
Abstract
MODY3 is a monogenic hereditary form of diabetes caused by mutations in the transcription factor HNF1A. The patients progressively develop hyperglycemia due to perturbed insulin secretion, but the pathogenesis is unknown. Using patient-specific hiPSCs, we recapitulate the insulin secretion sensitivity to the membrane depolarizing agent sulfonylurea commonly observed in MODY3 patients. Unexpectedly, MODY3 patient-specific HNF1A+/R272C β cells hypersecrete insulin both in vitro and in vivo after transplantation into mice. Consistently, we identified a trend of increased birth weight in human HNF1A mutation carriers compared with healthy siblings. Reduced expression of potassium channels, specifically the KATP channel, in MODY3 β cells, increased calcium signaling, and rescue of the insulin hypersecretion phenotype by pharmacological targeting ATP-sensitive potassium channels or low-voltage-activated calcium channels suggest that more efficient membrane depolarization underlies the hypersecretion of insulin in MODY3 β cells. Our findings identify a pathogenic mechanism leading to β cell failure in MODY3.
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Affiliation(s)
- Florian M Hermann
- Novo Nordisk Foundation Center for Stem Cell Biology (DanStem), University of Copenhagen, Copenhagen, Denmark
| | - Maya Friis Kjærgaard
- Novo Nordisk Foundation Center for Stem Cell Biology (DanStem), University of Copenhagen, Copenhagen, Denmark
| | - Chenglei Tian
- Novo Nordisk Foundation Center for Stem Cell Biology (DanStem), University of Copenhagen, Copenhagen, Denmark; Institute of Translational Stem Cell Research, Helmholtz Diabetes Center, Helmholtz Zentrum München, München, Germany
| | - Ulf Tiemann
- Novo Nordisk Foundation Center for Stem Cell Biology (DanStem), University of Copenhagen, Copenhagen, Denmark
| | - Abigail Jackson
- Novo Nordisk Foundation Center for Stem Cell Biology (DanStem), University of Copenhagen, Copenhagen, Denmark
| | - Lars Rønn Olsen
- Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Maria Kraft
- Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Per-Ola Carlsson
- Department of Medical Cell Biology, Uppsala University, Uppsala, Sweden; Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | | | - Jarno L T Kettunen
- Folkhalsan Research Center, Helsinki, Finland; Institute for Molecular Medicine Finland, University of Finland, Helsinki, Finland; Department of Endocrinology, Abdominal Center, Helsinki University Hospital, Helsinki, Finland
| | - Tiinamaija Tuomi
- Folkhalsan Research Center, Helsinki, Finland; Institute for Molecular Medicine Finland, University of Finland, Helsinki, Finland; Department of Endocrinology, Abdominal Center, Helsinki University Hospital, Helsinki, Finland
| | - Ivana Novak
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Henrik Semb
- Novo Nordisk Foundation Center for Stem Cell Biology (DanStem), University of Copenhagen, Copenhagen, Denmark; Institute of Translational Stem Cell Research, Helmholtz Diabetes Center, Helmholtz Zentrum München, München, Germany.
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Wagner NR, Sinha A, Siththanandan V, Kowalchuk AM, MacDonald JL, Tharin S. miR-409-3p represses Cited2 to refine neocortical layer V projection neuron identity. Front Neurosci 2022; 16:931333. [PMID: 36248641 PMCID: PMC9558290 DOI: 10.3389/fnins.2022.931333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 09/13/2022] [Indexed: 12/14/2022] Open
Abstract
The evolutionary emergence of the corticospinal tract and corpus callosum are thought to underpin the expansion of complex motor and cognitive abilities in mammals. Molecular mechanisms regulating development of the neurons whose axons comprise these tracts, the corticospinal and callosal projection neurons, remain incompletely understood. Our previous work identified a genomic cluster of microRNAs (miRNAs), Mirg/12qF1, that is unique to placental mammals and specifically expressed by corticospinal neurons, and excluded from callosal projection neurons, during development. We found that one of these, miR-409-3p, can convert layer V callosal into corticospinal projection neurons, acting in part through repression of the transcriptional regulator Lmo4. Here we show that miR-409-3p also directly represses the transcriptional co-regulator Cited2, which is highly expressed by callosal projection neurons from the earliest stages of neurogenesis. Cited2 is highly expressed by intermediate progenitor cells (IPCs) in the embryonic neocortex while Mirg, which encodes miR-409-3p, is excluded from these progenitors. miR-409-3p gain-of-function (GOF) in IPCs results in a phenocopy of established Cited2 loss-of-function (LOF). At later developmental stages, both miR-409-3p GOF and Cited2 LOF promote the expression of corticospinal at the expense of callosal projection neuron markers in layer V. Taken together, this work identifies previously undescribed roles for miR-409-3p in controlling IPC numbers and for Cited2 in controlling callosal fate. Thus, miR-409-3p, possibly in cooperation with other Mirg/12qF1 miRNAs, represses Cited2 as part of the multifaceted regulation of the refinement of neuronal cell fate within layer V, combining molecular regulation at multiple levels in both progenitors and post-mitotic neurons.
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Affiliation(s)
- Nikolaus R. Wagner
- Department of Biology, Program in Neuroscience, Syracuse University, Syracuse, NY, United States
| | - Ashis Sinha
- Department of Biology, Program in Neuroscience, Syracuse University, Syracuse, NY, United States
| | - Verl Siththanandan
- Department of Neurosurgery, Stanford University Medical Center, Center for Academic Medicine, Palo Alto, CA, United States
| | - Angelica M. Kowalchuk
- Department of Biology, Program in Neuroscience, Syracuse University, Syracuse, NY, United States
| | - Jessica L. MacDonald
- Department of Biology, Program in Neuroscience, Syracuse University, Syracuse, NY, United States,*Correspondence: Jessica L. MacDonald,
| | - Suzanne Tharin
- Department of Neurosurgery, Stanford University Medical Center, Center for Academic Medicine, Palo Alto, CA, United States,Division of Neurosurgery, Palo Alto Veterans Affairs Health Care System, Palo Alto, CA, United States,Suzanne Tharin,
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Using intracellular SCGB1A1-sorted, formalin-fixed club cells for successful transcriptomic analysis. Biochem Biophys Res Commun 2022; 604:151-157. [PMID: 35305419 DOI: 10.1016/j.bbrc.2022.03.040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 03/07/2022] [Indexed: 11/20/2022]
Abstract
As opposed to surface marker staining, certain cell types can only be recognized by intracellular markers. Intracellular staining for use in cell sorting remains challenging. Fixation and permeabilization steps for intracellular staining and the presence of RNases notably affect preservation of high-quality mRNA. We report the work required for the optimization of a successful protocol for microarray analysis of intracellular target-sorted, formalin-fixed human bronchial club cells. Cells obtained from differentiated air-liquid interface cultures were stained with the most characteristic intracellular markers for club cell (SCGB1A1+) sorting. A benchmarked intracellular staining protocol was carried out before flow cytometry. The primary outcome was the extraction of RNA sufficient quality for microarray analysis as assessed by Bioanalyzer System. Fixation with 4% paraformaldehyde coupled with 0.1% Triton/0.1% saponin permeabilization obtained optimal results for SCGB1A1 staining. Addition of RNase inhibitors throughout the protocol and within the appropriate RNA extraction kit (Formalin-Fixed-Paraffin-Embedded) dramatically improved RNA quality, resulting in samples eligible for microarray analysis. The protocol resulted in successful cell sorting according to specific club cell intracellular marker without using cell surface marker. The protocol also preserved RNA of sufficient quality for subsequent microarray transcriptomic analysis, and we were able to generate transcriptomic signature of club cells.
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Brown MR, Matveyenko AV. It's What and When You Eat: An Overview of Transcriptional and Epigenetic Responses to Dietary Perturbations in Pancreatic Islets. Front Endocrinol (Lausanne) 2022; 13:842603. [PMID: 35355560 PMCID: PMC8960041 DOI: 10.3389/fendo.2022.842603] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 02/07/2022] [Indexed: 01/07/2023] Open
Abstract
Our ever-changing modern environment is a significant contributor to the increased prevalence of many chronic diseases, and particularly, type 2 diabetes mellitus (T2DM). Although the modern era has ushered in numerous changes to our daily living conditions, changes in "what" and "when" we eat appear to disproportionately fuel the rise of T2DM. The pancreatic islet is a key biological controller of an organism's glucose homeostasis and thus plays an outsized role to coordinate the response to environmental factors to preserve euglycemia through a delicate balance of endocrine outputs. Both successful and failed adaptation to dynamic environmental stimuli has been postulated to occur due to changes in the transcriptional and epigenetic regulation of pathways associated with islet secretory function and survival. Therefore, in this review we examined and evaluated the current evidence elucidating the key epigenetic mechanisms and transcriptional programs underlying the islet's coordinated response to the interaction between the timing and the composition of dietary nutrients common to modern lifestyles. With the explosion of next generation sequencing, along with the development of novel informatic and -omic approaches, future work will continue to unravel the environmental-epigenetic relationship in islet biology with the goal of identifying transcriptional and epigenetic targets associated with islet perturbations in T2DM.
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Affiliation(s)
- Matthew R. Brown
- Department of Physiology and Biomedical Engineering, Mayo Clinic College of Medicine and Science, Rochester, MN, United States
| | - Aleksey V. Matveyenko
- Department of Physiology and Biomedical Engineering, Mayo Clinic College of Medicine and Science, Rochester, MN, United States
- Division of Endocrinology, Metabolism, Diabetes, and Nutrition, Department of Medicine, Mayo Clinic College of Medicine and Science, Rochester, MN, United States
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Chen B, Scurrah CR, McKinley ET, Simmons AJ, Ramirez-Solano MA, Zhu X, Markham NO, Heiser CN, Vega PN, Rolong A, Kim H, Sheng Q, Drewes JL, Zhou Y, Southard-Smith AN, Xu Y, Ro J, Jones AL, Revetta F, Berry LD, Niitsu H, Islam M, Pelka K, Hofree M, Chen JH, Sarkizova S, Ng K, Giannakis M, Boland GM, Aguirre AJ, Anderson AC, Rozenblatt-Rosen O, Regev A, Hacohen N, Kawasaki K, Sato T, Goettel JA, Grady WM, Zheng W, Washington MK, Cai Q, Sears CL, Goldenring JR, Franklin JL, Su T, Huh WJ, Vandekar S, Roland JT, Liu Q, Coffey RJ, Shrubsole MJ, Lau KS. Differential pre-malignant programs and microenvironment chart distinct paths to malignancy in human colorectal polyps. Cell 2021; 184:6262-6280.e26. [PMID: 34910928 PMCID: PMC8941949 DOI: 10.1016/j.cell.2021.11.031] [Citation(s) in RCA: 115] [Impact Index Per Article: 38.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 07/22/2021] [Accepted: 11/17/2021] [Indexed: 12/15/2022]
Abstract
Colorectal cancers (CRCs) arise from precursor polyps whose cellular origins, molecular heterogeneity, and immunogenic potential may reveal diagnostic and therapeutic insights when analyzed at high resolution. We present a single-cell transcriptomic and imaging atlas of the two most common human colorectal polyps, conventional adenomas and serrated polyps, and their resulting CRC counterparts. Integrative analysis of 128 datasets from 62 participants reveals adenomas arise from WNT-driven expansion of stem cells, while serrated polyps derive from differentiated cells through gastric metaplasia. Metaplasia-associated damage is coupled to a cytotoxic immune microenvironment preceding hypermutation, driven partly by antigen-presentation differences associated with tumor cell-differentiation status. Microsatellite unstable CRCs contain distinct non-metaplastic regions where tumor cells acquire stem cell properties and cytotoxic immune cells are depleted. Our multi-omic atlas provides insights into malignant progression of colorectal polyps and their microenvironment, serving as a framework for precision surveillance and prevention of CRC.
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Affiliation(s)
- Bob Chen
- Program in Chemical and Physical Biology, Vanderbilt University School of Medicine, Nashville, TN, USA; Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Cherie' R Scurrah
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, USA; Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Eliot T McKinley
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, USA; Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Alan J Simmons
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, USA; Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Marisol A Ramirez-Solano
- Department of Biostatistics and Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Xiangzhu Zhu
- Vanderbilt-Ingram Cancer Center, Nashville, TN, USA; Department of Medicine, Division of Epidemiology, Vanderbilt Epidemiology Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Nicholas O Markham
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, USA; Department of Medicine, Division of Gastroenterology, Hepatology and Nutrition, Vanderbilt University Medical Center, Nashville, TN, USA; Department of Veterans Affairs, Tennessee Valley Healthcare System, Nashville, TN, USA; Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Cody N Heiser
- Program in Chemical and Physical Biology, Vanderbilt University School of Medicine, Nashville, TN, USA; Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Paige N Vega
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, USA; Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Andrea Rolong
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, USA; Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Hyeyon Kim
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, USA; Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Quanhu Sheng
- Department of Biostatistics and Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Julia L Drewes
- Department of Medicine, Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Yuan Zhou
- Department of Biostatistics and Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Austin N Southard-Smith
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, USA; Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Yanwen Xu
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, USA; Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - James Ro
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, USA; Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Angela L Jones
- Vanderbilt Technologies for Advanced Genomics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Frank Revetta
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Lynne D Berry
- Department of Biostatistics and Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Hiroaki Niitsu
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, USA; Department of Medicine, Division of Gastroenterology, Hepatology and Nutrition, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Mirazul Islam
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, USA; Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Karin Pelka
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA; Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Matan Hofree
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jonathan H Chen
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA; Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA; Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Siranush Sarkizova
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Kimmie Ng
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Marios Giannakis
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Genevieve M Boland
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA; Department of Surgery, Massachusetts General Hospital, Boston, MA, USA
| | - Andrew J Aguirre
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Ana C Anderson
- Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA
| | | | - Aviv Regev
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA; Howard Hughes Medical Institute and Koch Institute for Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Nir Hacohen
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA; Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA; Department of Immunology, Harvard Medical School, Boston, MA, USA
| | - Kenta Kawasaki
- Department of Organoid Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Toshiro Sato
- Department of Organoid Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Jeremy A Goettel
- Department of Medicine, Division of Gastroenterology, Hepatology and Nutrition, Vanderbilt University Medical Center, Nashville, TN, USA; Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - William M Grady
- Clinical Research Division, Fred Hutchinson Cancer Research Center, and Gastroenterology Division, University of Washington School of Medicine, Seattle, WA, USA
| | - Wei Zheng
- Vanderbilt-Ingram Cancer Center, Nashville, TN, USA; Department of Medicine, Division of Epidemiology, Vanderbilt Epidemiology Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - M Kay Washington
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Qiuyin Cai
- Vanderbilt-Ingram Cancer Center, Nashville, TN, USA; Department of Medicine, Division of Epidemiology, Vanderbilt Epidemiology Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Cynthia L Sears
- Department of Medicine, Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - James R Goldenring
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, USA; Vanderbilt-Ingram Cancer Center, Nashville, TN, USA; Department of Surgery, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jeffrey L Franklin
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, USA; Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA; Vanderbilt-Ingram Cancer Center, Nashville, TN, USA; Department of Medicine, Division of Gastroenterology, Hepatology and Nutrition, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Timothy Su
- Department of Medicine, Division of Epidemiology, Vanderbilt Epidemiology Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Won Jae Huh
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Simon Vandekar
- Department of Biostatistics and Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Joseph T Roland
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, USA; Department of Surgery, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Qi Liu
- Department of Biostatistics and Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Robert J Coffey
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, USA; Vanderbilt-Ingram Cancer Center, Nashville, TN, USA; Department of Medicine, Division of Gastroenterology, Hepatology and Nutrition, Vanderbilt University Medical Center, Nashville, TN, USA.
| | - Martha J Shrubsole
- Vanderbilt-Ingram Cancer Center, Nashville, TN, USA; Department of Medicine, Division of Epidemiology, Vanderbilt Epidemiology Center, Vanderbilt University Medical Center, Nashville, TN, USA.
| | - Ken S Lau
- Program in Chemical and Physical Biology, Vanderbilt University School of Medicine, Nashville, TN, USA; Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, USA; Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA; Vanderbilt-Ingram Cancer Center, Nashville, TN, USA; Department of Surgery, Vanderbilt University Medical Center, Nashville, TN, USA.
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10
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Compact RNA editors with small Cas13 proteins. Nat Biotechnol 2021; 40:194-197. [PMID: 34462587 DOI: 10.1038/s41587-021-01030-2] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Accepted: 07/20/2021] [Indexed: 12/19/2022]
Abstract
CRISPR-Cas13 systems have been developed for precise RNA editing, and can potentially be used therapeutically when temporary changes are desirable or when DNA editing is challenging. We have identified and characterized an ultrasmall family of Cas13b proteins-Cas13bt-that can mediate mammalian transcript knockdown. We have engineered compact variants of REPAIR and RESCUE RNA editors by functionalizing Cas13bt with adenosine and cytosine deaminase domains, and demonstrated packaging of the editors within a single adeno-associated virus.
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11
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Lavado A, Gangwar R, Paré J, Wan S, Fan Y, Cao X. YAP/TAZ maintain the proliferative capacity and structural organization of radial glial cells during brain development. Dev Biol 2021; 480:39-49. [PMID: 34419458 DOI: 10.1016/j.ydbio.2021.08.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 07/29/2021] [Accepted: 08/16/2021] [Indexed: 12/24/2022]
Abstract
The Hippo pathway regulates the development and homeostasis of many tissues and in many species. It controls the activity of two paralogous transcriptional coactivators, YAP and TAZ (YAP/TAZ). Although previous studies have established that aberrant YAP/TAZ activation is detrimental to mammalian brain development, whether and how endogenous levels of YAP/TAZ activity regulate brain development remain unclear. Here, we show that during mammalian cortical development, YAP/TAZ are specifically expressed in apical neural progenitor cells known as radial glial cells (RGCs). The subcellular localization of YAP/TAZ undergoes dynamic changes as corticogenesis proceeds. YAP/TAZ are required for maintaining the proliferative potential and structural organization of RGCs, and their ablation during cortical development reduces the numbers of cortical projection neurons and causes the loss of ependymal cells, resulting in hydrocephaly. Transcriptomic analysis using sorted RGCs reveals gene expression changes in YAP/TAZ-depleted cells that correlate with mutant phenotypes. Thus, our study has uncovered essential functions of YAP/TAZ during mammalian brain development and revealed the transcriptional mechanism of their action.
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Affiliation(s)
- Alfonso Lavado
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Ruchika Gangwar
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Joshua Paré
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Shibiao Wan
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Yiping Fan
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Xinwei Cao
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA.
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12
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Ma Q, Yang F, Mackintosh C, Jayani RS, Oh S, Jin C, Nair SJ, Merkurjev D, Ma W, Allen S, Wang D, Almenar-Queralt A, Garcia-Bassets I. Super-Enhancer Redistribution as a Mechanism of Broad Gene Dysregulation in Repeatedly Drug-Treated Cancer Cells. Cell Rep 2021; 31:107532. [PMID: 32320655 DOI: 10.1016/j.celrep.2020.107532] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 01/07/2020] [Accepted: 03/27/2020] [Indexed: 12/14/2022] Open
Abstract
Cisplatin is an antineoplastic drug administered at suboptimal and intermittent doses to avoid life-threatening effects. Although this regimen shortly improves symptoms in the short term, it also leads to more malignant disease in the long term. We describe a multilayered analysis ranging from chromatin to translation-integrating chromatin immunoprecipitation sequencing (ChIP-seq), global run-on sequencing (GRO-seq), RNA sequencing (RNA-seq), and ribosome profiling-to understand how cisplatin confers (pre)malignant features by using a well-established ovarian cancer model of cisplatin exposure. This approach allows us to segregate the human transcriptome into gene modules representing distinct regulatory principles and to characterize that the most cisplatin-disrupted modules are associated with underlying events of super-enhancer plasticity. These events arise when cancer cells initiate without ultimately ending the program of drug-stimulated death. Using a PageRank-based algorithm, we predict super-enhancer regulator ISL1 as a driver of this plasticity and validate this prediction by using CRISPR/dCas9-KRAB inhibition (CRISPRi) and CRISPR/dCas9-VP64 activation (CRISPRa) tools. Together, we propose that cisplatin reprograms cancer cells when inducing them to undergo near-to-death experiences.
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Affiliation(s)
- Qi Ma
- Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Feng Yang
- Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Carlos Mackintosh
- Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Ranveer Singh Jayani
- Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Soohwan Oh
- Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Chunyu Jin
- Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Sreejith Janardhanan Nair
- Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Daria Merkurjev
- Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Wubin Ma
- Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Stephanie Allen
- Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Dong Wang
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan 611137, China
| | - Angels Almenar-Queralt
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Ivan Garcia-Bassets
- Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
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13
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Nott A, Schlachetzki JCM, Fixsen BR, Glass CK. Nuclei isolation of multiple brain cell types for omics interrogation. Nat Protoc 2021; 16:1629-1646. [PMID: 33495627 PMCID: PMC7969463 DOI: 10.1038/s41596-020-00472-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 11/24/2020] [Indexed: 11/08/2022]
Abstract
We present a nuclei isolation protocol for genomic and epigenomic interrogation of multiple cell type populations in the human and rodent brain. The nuclei isolation protocol allows cell type-specific profiling of neurons, microglia, oligodendrocytes, and astrocytes, being compatible with fresh and frozen samples obtained from either resected or postmortem brain tissue. This 2-day procedure consists of tissue homogenization with fixation, nuclei extraction, and antibody staining followed by fluorescence-activated nuclei sorting (FANS) and does not require specialized skillsets. Cell type-specific nuclei populations can be used for downstream omic-scale sequencing applications with an emphasis on epigenomic interrogation such as histone modifications, transcription factor binding, chromatin accessibility, and chromosome architecture. The nuclei isolation protocol enables translational examination of archived healthy and diseased brain specimens through utilization of existing medical biorepositories.
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Affiliation(s)
- Alexi Nott
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA.
- Department of Brain Sciences, Imperial College London, White City Campus, London, UK.
- UK Dementia Research Institute, Imperial College London, White City Campus, London, UK.
| | - Johannes C M Schlachetzki
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA.
| | - Bethany R Fixsen
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Christopher K Glass
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA.
- Department of Medicine, University of California San Diego, La Jolla, CA, USA.
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14
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Isolation of human ESC-derived cardiac derivatives and embryonic heart cells for population and single-cell RNA-seq analysis. STAR Protoc 2021; 2:100339. [PMID: 33644774 PMCID: PMC7887647 DOI: 10.1016/j.xpro.2021.100339] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
The combination of population and single-cell RNA sequencing analysis using human embryonic stem cell (hESC) differentiation and developmental tissues is a powerful approach to elucidate an organ-specific cellular and molecular atlas in human embryogenesis. This protocol describes (1) cardiac-directed differentiation and isolation of hESC-derived cardiac derivatives with fluorescence-activated cell sorting, (2) isolation of human embryonic heart-derived single cardiac cells, and (3) construction of cDNA libraries with Smart-seq2. These allow for the preparation of human developmental samples for comprehensive transcriptional analysis. For complete details on the use and execution of this protocol, please refer to Sahara et al. (2019). Efficient cardiac-directed differentiation of hESCs Isolation of hESC-derived cardiac derivatives with fluorescence-activated cell sorting Isolation of human embryonic heart-derived single cardiac cells Construction of cDNA libraries for both population and single-cell RNA sequencing
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15
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Kahraman S, Manna D, Dirice E, Maji B, Small J, Wagner BK, Choudhary A, Kulkarni RN. Harnessing reaction-based probes to preferentially target pancreatic β-cells and β-like cells. Life Sci Alliance 2021; 4:4/4/e202000840. [PMID: 33514654 PMCID: PMC7898467 DOI: 10.26508/lsa.202000840] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Revised: 01/11/2021] [Accepted: 01/12/2021] [Indexed: 01/10/2023] Open
Abstract
Highly sensitive approaches to target insulin-expressing cells would allow more effective imaging, sorting, and analysis of pancreatic β-cells. Here, we introduce the use of a reaction-based probe, diacetylated Zinpyr1 (DA-ZP1), to image pancreatic β-cells and β-like cells derived from human pluripotent stem cells. We harness the high intracellular zinc concentration of β-cells to induce a fluorescence signal in cells after administration of DA-ZP1. Given its specificity and rapid uptake by cells, we used DA-ZP1 to purify live stem cell-derived β-like cells as confirmed by immunostaining analysis. We tested the ability of DA-ZP1 to image transplanted human islet grafts and endogenous mouse pancreatic islets in vivo after its systemic administration into mice. Thus, DA-ZP1 enables purification of insulin-secreting β-like cells for downstream applications, such as functional studies, gene-expression, and cell-cell interaction analyses and can be used to label engrafted human islets and endogenous mouse islets in vivo.
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Affiliation(s)
- Sevim Kahraman
- Islet Cell and Regenerative Biology, Joslin Diabetes Center, Department of Medicine, Brigham and Women's Hospital, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA, USA
| | - Debasish Manna
- Chemical Biology and Therapeutics Science Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Medicine, Harvard Medical School, Boston, MA, USA.,Divisions of Renal Medicine and Engineering, Brigham and Women's Hospital, Boston, MA, USA
| | - Ercument Dirice
- Islet Cell and Regenerative Biology, Joslin Diabetes Center, Department of Medicine, Brigham and Women's Hospital, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA, USA
| | - Basudeb Maji
- Chemical Biology and Therapeutics Science Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Medicine, Harvard Medical School, Boston, MA, USA.,Divisions of Renal Medicine and Engineering, Brigham and Women's Hospital, Boston, MA, USA
| | - Jonnell Small
- Chemical Biology and Therapeutics Science Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Chemical Biology Program, Harvard University, Cambridge, MA, USA
| | - Bridget K Wagner
- Chemical Biology and Therapeutics Science Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Amit Choudhary
- Chemical Biology and Therapeutics Science Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA .,Department of Medicine, Harvard Medical School, Boston, MA, USA.,Divisions of Renal Medicine and Engineering, Brigham and Women's Hospital, Boston, MA, USA.,Chemical Biology Program, Harvard University, Cambridge, MA, USA
| | - Rohit N Kulkarni
- Islet Cell and Regenerative Biology, Joslin Diabetes Center, Department of Medicine, Brigham and Women's Hospital, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA, USA
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16
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Channathodiyil P, Houseley J. Glyoxal fixation facilitates transcriptome analysis after antigen staining and cell sorting by flow cytometry. PLoS One 2021; 16:e0240769. [PMID: 33481798 PMCID: PMC7822327 DOI: 10.1371/journal.pone.0240769] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 01/04/2021] [Indexed: 01/07/2023] Open
Abstract
A simple method for extraction of high quality RNA from cells that have been fixed, stained and sorted by flow cytometry would allow routine transcriptome analysis of highly purified cell populations and single cells. However, formaldehyde fixation impairs RNA extraction and inhibits RNA amplification. Here we show that good quality RNA can be readily extracted from stained and sorted mammalian cells if formaldehyde is replaced by glyoxal—a well-characterised fixative that is widely compatible with immunofluorescent staining methods. Although both formaldehyde and glyoxal efficiently form protein-protein crosslinks, glyoxal does not crosslink RNA to proteins nor form stable RNA adducts, ensuring that RNA remains accessible and amenable to enzymatic manipulation after glyoxal fixation. We find that RNA integrity is maintained through glyoxal fixation, permeabilisation with methanol or saponin, indirect immunofluorescent staining and flow sorting. RNA can then be extracted by standard methods and processed into RNA-seq libraries using commercial kits; mRNA abundances measured by poly(A)+ RNA-seq correlate well between freshly harvested cells and fixed, stained and sorted cells. We validate the applicability of this approach to flow cytometry by staining MCF-7 cells for the intracellular G2/M-specific antigen cyclin B1 (CCNB1), and show strong enrichment for G2/M-phase cells based on transcriptomic data. Switching to glyoxal fixation with RNA-compatible staining methods requires only minor adjustments of most existing staining and sorting protocols, and should facilitate routine transcriptomic analysis of sorted cells.
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Affiliation(s)
| | - Jonathan Houseley
- Epigenetics Programme, Babraham Institute, Cambridge, United Kingdom
- * E-mail:
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17
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Molakandov K, Berti DA, Beck A, Elhanani O, Walker MD, Soen Y, Yavriyants K, Zimerman M, Volman E, Toledo I, Erukhimovich A, Levy AM, Hasson A, Itskovitz-Eldor J, Chebath J, Revel M. Selection for CD26 - and CD49A + Cells From Pluripotent Stem Cells-Derived Islet-Like Clusters Improves Therapeutic Activity in Diabetic Mice. Front Endocrinol (Lausanne) 2021; 12:635405. [PMID: 34025576 PMCID: PMC8131825 DOI: 10.3389/fendo.2021.635405] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 04/07/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Cell therapy of diabetes aims at restoring the physiological control of blood glucose by transplantation of functional pancreatic islet cells. A potentially unlimited source of cells for such transplantations would be islet cells derived from an in vitro differentiation of human pluripotent stem cells (hESC/hiPSC). The islet-like clusters (ILC) produced by the known differentiation protocols contain various cell populations. Among these, the β-cells that express both insulin and the transcription factor Nkx6.1 seem to be the most efficient to restore normoglycemia in diabetes animal models. Our aim was to find markers allowing selection of these efficient cells. METHODS Functional Cell-Capture Screening (FCCS) was used to identify markers that preferentially capture the cells expressing both insulin and Nkx6.1, from hESC-derived ILC cells. In order to test whether selection for such markers could improve cell therapy in diabetic mouse models, we used ILC produced from a clinical-grade line of hESC by a refined differentiation protocol adapted to up-scalable bioreactors. Re-aggregated MACS sorted cells were encapsulated in microspheres made of alginate modified to reduce foreign body reaction. Implantation was done intraperitoneally in STZ-treated C57BL/6 immuno-competent mice. RESULTS CD49A (integrin alpha1) was identified by FCCS as a marker for cells that express insulin (or C-peptide) as well as Nkx6.1 in ILC derived by hESC differentiation. The ILC fraction enriched in CD49A + cells rapidly reduced glycemia when implanted in diabetic mice, whereas mice receiving the CD49A depleted population remained highly diabetic. CD49A-enriched ILC cells also produced higher levels of human C-peptide in the blood of transplanted mice. However, the difference between CD49A-enriched and total ILC cells remained small. Another marker, CD26 (DPP4), was identified by FCCS as binding insulin-expressing cells which are Nkx6.1 negative. Depletion of CD26 + cells followed by enrichment for CD49A + cells increased insulin+/Nkx6.1+ cells fraction to ~70%. The CD26 - /CD49A + enriched ILC exhibited improved function over non-sorted ILC or CD49A + cells in diabetic mice and maintain prolonged blood C-peptide levels. CONCLUSIONS Refining the composition of ILC differentiated from hPSC by negative selection to remove cells expressing CD26 and positive selection for CD49A expressing cells could enable more effective cell therapy of diabetes.
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Affiliation(s)
- Kfir Molakandov
- Kadimastem Ltd., Weizmann Science Park, Ness Ziona, Israel
- *Correspondence: Kfir Molakandov,
| | | | - Avital Beck
- Kadimastem Ltd., Weizmann Science Park, Ness Ziona, Israel
| | - Ofer Elhanani
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Michael D. Walker
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Yoav Soen
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | | | | | - Ella Volman
- Kadimastem Ltd., Weizmann Science Park, Ness Ziona, Israel
| | - Itzik Toledo
- Kadimastem Ltd., Weizmann Science Park, Ness Ziona, Israel
| | | | - Alon M. Levy
- Kadimastem Ltd., Weizmann Science Park, Ness Ziona, Israel
| | - Arik Hasson
- Kadimastem Ltd., Weizmann Science Park, Ness Ziona, Israel
| | | | - Judith Chebath
- Kadimastem Ltd., Weizmann Science Park, Ness Ziona, Israel
| | - Michel Revel
- Kadimastem Ltd., Weizmann Science Park, Ness Ziona, Israel
- Department of Molecular Genetics (emeritus), Weizmann Institute of Science, Rehovot, Israel
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18
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Lee S, Lee C, Hwang CY, Kim D, Han Y, Hong SN, Kim SH, Cho KH. Network Inference Analysis Identifies SETDB1 as a Key Regulator for Reverting Colorectal Cancer Cells into Differentiated Normal-Like Cells. Mol Cancer Res 2020; 18:118-129. [PMID: 31896605 DOI: 10.1158/1541-7786.mcr-19-0450] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Revised: 08/07/2019] [Accepted: 09/23/2019] [Indexed: 11/16/2022]
Abstract
Cancer cells exhibit properties of cells in a less differentiated state than the adjacent normal cells in the tissue. We explored whether cancer cells can be converted to a differentiated normal-like state by restoring the gene regulatory network (GRN) of normal cells. Here, we report that colorectal cancer cells exhibit a range of developmental states from embryonic and intestinal stem-like cells to differentiated normal-like cells. To identify the transcription factors (TF) that commit stem-like colorectal cancer cells into a differentiated normal-like state, we reconstructed GRNs of normal colon mucosa and identified core TFs (CDX2, ELF3, HNF4G, PPARG, and VDR) that govern the cellular state. We further found that SET Domain Bifurcated 1 (SETDB1), a histone H3 lysine 9-specific methyltransferase, hinders the function of the identified TFs. SETDB1 depletion effectively converts stem-like colorectal cancer cells into postmitotic cells and restores normal morphology in patient-derived colorectal cancer organoids. RNA-sequencing analyses revealed that SETDB1 depletion recapitulates global gene expression profiles of normal differentiated cells by restoring the transcriptional activity of core TFs on their target genes. IMPLICATIONS: Our study provides insights into the molecular regulatory mechanism underlying the developmental hierarchy of colorectal cancer and suggests that induction of a postmitotic state may be a therapeutic alternative to destruction of cancer cells.
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Affiliation(s)
- Soobeom Lee
- Laboratory for Systems Biology and Bio-inspired Engineering, Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Chansu Lee
- Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Chae Young Hwang
- Laboratory for Systems Biology and Bio-inspired Engineering, Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Dongsan Kim
- Laboratory for Systems Biology and Bio-inspired Engineering, Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Younghyun Han
- Laboratory for Systems Biology and Bio-inspired Engineering, Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Sung Noh Hong
- Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Seok-Hyung Kim
- Department of Pathology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Kwang-Hyun Cho
- Laboratory for Systems Biology and Bio-inspired Engineering, Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea.
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19
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Multiplexed detection and isolation of viable low-frequency cytokine-secreting human B cells using cytokine secretion assay and flow cytometry (CSA-Flow). Sci Rep 2020; 10:14823. [PMID: 32908164 PMCID: PMC7481209 DOI: 10.1038/s41598-020-71750-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 07/27/2020] [Indexed: 12/16/2022] Open
Abstract
The ability to functionally characterize cytokine-secreting immune cells has broad implications in both health and a range of immune-mediated and auto-immune diseases. Low-frequency cytokine-defined immune-cell subsets can play key immune-regulatory roles, yet their detailed study is often hampered by limited clinical sample availability. Commonly used techniques including intracellular cytokine staining require cell fixation, precluding subsequent functional interrogation. The cytokine-secretion assay (CSA) can overcome this limitation, though has mostly been used for detection of relatively high-frequency, single-cytokine secreting cells. We examined how adaptation of the CSA in combination with multiparametric flow-cytometry (CSA-Flow) may enable simultaneous isolation of multiple, low-frequency, cytokine-secreting cells. Focusing on human B cells (traditionally recognized as harder to assay than T cells), we show that single-capture CSA-Flow allows for isolation of highly-purified populations of both low-frequency (IL-10+; GM-CSF+) and high-frequency (TNF+) cytokine-defined B cells. Simultaneous detection and isolation of up to three viable and highly-purified cytokine-secreting B-cell subpopulations is feasible, albeit with some signal loss, with fractions subsequently amenable to gene expression analysis and in vitro cell culture. This multiplexing CSA-Flow approach will be of interest in many human cellular immunology contexts aiming to functionally characterize cytokine-secreting immune cells, especially when sample volumes and cell numbers are limited.
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20
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Healy ZR, Weinhold KJ, Murdoch DM. Transcriptional Profiling of CD8+ CMV-Specific T Cell Functional Subsets Obtained Using a Modified Method for Isolating High-Quality RNA From Fixed and Permeabilized Cells. Front Immunol 2020; 11:1859. [PMID: 32983102 PMCID: PMC7492549 DOI: 10.3389/fimmu.2020.01859] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 07/10/2020] [Indexed: 01/04/2023] Open
Abstract
Previous studies suggest that the presence of antigen-specific polyfunctional T cells is correlated with improved pathogen clearance, disease control, and clinical outcomes; however, the molecular mechanisms responsible for the generation, function, and survival of polyfunctional T cells remain unknown. The study of polyfunctional T cells has been, in part, limited by the need for intracellular cytokine staining (ICS), necessitating fixation and cell membrane permeabilization that leads to unacceptable degradation of RNA. Adopting elements from prior research efforts, we developed and optimized a modified protocol for the isolation of high-quality RNA (i.e., RIN > 7) from primary human T cells following aldehyde-fixation, detergent-based permeabilization, intracellular cytokines staining, and sorting. Additionally, this method also demonstrated utility preserving RNA when staining for transcription factors. This modified protocol utilizes an optimized combination of an RNase inhibitor and high-salt buffer that is cost-effective while maintaining the ability to identify and resolve cell populations for sorting. Overall, this protocol resulted in minimal loss of RNA integrity, quality, and quantity during cytoplasmic staining of cytokines and subsequent flourescence-activated cell sorting. Using this technique, we obtained the transcriptional profiles of functional subsets (i.e., non-functional, monofunctional, bifunctional, polyfunctional) of CMV-specific CD8+T cells. Our analyses demonstrated that these functional subsets are molecularly distinct, and that polyfunctional T cells are uniquely enriched for transcripts involved in viral response, inflammation, cell survival, proliferation, and metabolism when compared to monofunctional cells. Polyfunctional T cells demonstrate reduced activation-induced cell death and increased proliferation after antigen re-challenge. Further in silico analysis of transcriptional data suggested a critical role for STAT5 transcriptional activity in polyfunctional cell activation. Pharmacologic inhibition of STAT5 was associated with a significant reduction in polyfunctional cell cytokine expression and proliferation, demonstrating the requirement of STAT5 activity not only for proliferation and cell survival, but also cytokine expression. Finally, we confirmed this association between CMV-specific CD8+ polyfunctionality with STAT5 signaling also exists in immunosuppressed transplant recipients using single cell transcriptomics, indicating that results from this study may translate to this vulnerable patient population. Collectively, these results shed light on the mechanisms governing polyfunctional T cell function and survival and may ultimately inform multiple areas of immunology, including but not limited to the development of new vaccines, CAR-T cell therapies, and adoptive T cell transfer.
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Affiliation(s)
- Zachary R Healy
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Duke University Hospital, Durham, NC, United States
| | - Kent J Weinhold
- Department of Surgery, Duke University School of Medicine, Durham, NC, United States
| | - David M Murdoch
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Duke University Hospital, Durham, NC, United States
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21
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Lawson ND, Li R, Shin M, Grosse A, Yukselen O, Stone OA, Kucukural A, Zhu L. An improved zebrafish transcriptome annotation for sensitive and comprehensive detection of cell type-specific genes. eLife 2020; 9:55792. [PMID: 32831172 PMCID: PMC7486121 DOI: 10.7554/elife.55792] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 08/21/2020] [Indexed: 02/07/2023] Open
Abstract
The zebrafish is ideal for studying embryogenesis and is increasingly applied to model human disease. In these contexts, RNA-sequencing (RNA-seq) provides mechanistic insights by identifying transcriptome changes between experimental conditions. Application of RNA-seq relies on accurate transcript annotation for a genome of interest. Here, we find discrepancies in analysis from RNA-seq datasets quantified using Ensembl and RefSeq zebrafish annotations. These issues were due, in part, to variably annotated 3' untranslated regions and thousands of gene models missing from each annotation. Since these discrepancies could compromise downstream analyses and biological reproducibility, we built a more comprehensive zebrafish transcriptome annotation that addresses these deficiencies. Our annotation improves detection of cell type-specific genes in both bulk and single cell RNA-seq datasets, where it also improves resolution of cell clustering. Thus, we demonstrate that our new transcriptome annotation can outperform existing annotations, providing an important resource for zebrafish researchers.
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Affiliation(s)
- Nathan D Lawson
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, United States
| | - Rui Li
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, United States
| | - Masahiro Shin
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, United States
| | - Ann Grosse
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, United States
| | - Onur Yukselen
- Bioinformatics Core, University of Massachusetts Medical School, Worcester, United States
| | - Oliver A Stone
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | - Alper Kucukural
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, United States.,Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, United States
| | - Lihua Zhu
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, United States.,Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, United States.,Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, United States
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22
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Goulet DR, Foster JP, Zawistowski JS, Bevill SM, Noël MP, Olivares-Quintero JF, Sciaky N, Singh D, Santos C, Pattenden SG, Davis IJ, Johnson GL. Discrete Adaptive Responses to MEK Inhibitor in Subpopulations of Triple-Negative Breast Cancer. Mol Cancer Res 2020; 18:1685-1698. [PMID: 32753473 DOI: 10.1158/1541-7786.mcr-19-1011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 06/18/2020] [Accepted: 07/31/2020] [Indexed: 12/31/2022]
Abstract
Triple-negative breast cancers contain a spectrum of epithelial and mesenchymal phenotypes. SUM-229PE cells represent a model for this heterogeneity, maintaining both epithelial and mesenchymal subpopulations that are genomically similar but distinct in gene expression profiles. We identified differential regions of open chromatin in epithelial and mesenchymal cells that were strongly correlated with regions of H3K27ac. Motif analysis of these regions identified consensus sequences for transcription factors that regulate cell identity. Treatment with the MEK inhibitor trametinib induced enhancer remodeling that is associated with transcriptional regulation of genes in epithelial and mesenchymal cells. Motif analysis of enhancer peaks downregulated in response to chronic treatment with trametinib identified AP-1 motif enrichment in both epithelial and mesenchymal subpopulations. Chromatin immunoprecipitation sequencing (ChIP-seq) of JUNB identified subpopulation-specific localization, which was significantly enriched at regions of open chromatin. These results indicate that cell identity controls localization of transcription factors and chromatin-modifying enzymes to enhancers for differential control of gene expression. We identified increased H3K27ac at an enhancer region proximal to CXCR7, a G-protein-coupled receptor that increased 15-fold in expression in the epithelial subpopulation during chronic treatment. RNAi knockdown of CXCR7 inhibited proliferation in trametinib-resistant cells. Thus, adaptive resistance to chronic trametinib treatment contributes to proliferation in the presence of the drug. Acquired amplification of KRAS following trametinib dose escalation further contributed to POS cell proliferation. Adaptive followed by acquired gene expression changes contributed to proliferation in trametinib-resistant cells, suggesting inhibition of early transcriptional reprogramming could prevent resistance and the bypass of targeted therapy. IMPLICATIONS: We defined the differential responses to trametinib in subpopulations of a clinically relevant in vitro model of TNBC, and identified both adaptive and acquired elements that contribute to the emergence of drug resistance mediated by increased expression of CXCR7 and amplification of KRAS.
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Affiliation(s)
- Daniel R Goulet
- Department of Pharmacology, Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Joseph P Foster
- Curriculum in Bioinformatics and Computational Biology, Department of Genetics, Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Jon S Zawistowski
- Department of Pharmacology, Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Samantha M Bevill
- Department of Pharmacology, Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Mélodie P Noël
- Department of Genetics, Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - José F Olivares-Quintero
- Department of Pharmacology, Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Noah Sciaky
- Department of Pharmacology, Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Darshan Singh
- Department of Pharmacology, Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Charlene Santos
- Department of Genetics, Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Samantha G Pattenden
- Eshelman School of Pharmacy, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina
| | - Ian J Davis
- Curriculum in Bioinformatics and Computational Biology, Department of Genetics, Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina.,Department of Pediatrics, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Gary L Johnson
- Department of Pharmacology, Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina.
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23
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Dubois F, Limou S, Chesneau M, Degauque N, Brouard S, Danger R. Transcriptional meta-analysis of regulatory B cells. Eur J Immunol 2020; 50:1757-1769. [PMID: 32529638 DOI: 10.1002/eji.201948489] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 05/01/2020] [Accepted: 06/09/2020] [Indexed: 12/26/2022]
Abstract
Regulatory B cells (Bregs) have the ability to regulate inflammation in various pathological situations, making them key players in immune regulation. Several mechanisms have been described and we recently identified a GZMB expressing Breg population in kidney transplanted patients who tolerate a kidney graft. To further investigate their biology and mechanisms, we conducted a transcriptomic analysis by RNAseq of these cells and we performed the first weighted meta-analysis of publicly available transcriptomic data from published Breg studies both in humans and mice. We identified two distinct and unique transcriptional signatures of 126 and 93 genes, respectively, associated with these Bregs. While we highlighted genes coding for proteins with potent involvement in regulatory functions, proliferation, and coding for transcription factors, the comparison between humans and mice did not allow identifying a common pattern. Thus, our results suggest distinct species-restricted Breg transcriptional signatures in humans and mice.
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Affiliation(s)
- Florian Dubois
- Inserm, CHU Nantes, Université de Nantes, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, Nantes, France.,Labex IGO, Nantes, France
| | - Sophie Limou
- Inserm, CHU Nantes, Université de Nantes, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, Nantes, France.,Ecole Centrale de Nantes, Computer Sciences and Mathematics department, Nantes, France
| | - Mélanie Chesneau
- Inserm, CHU Nantes, Université de Nantes, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, Nantes, France.,Labex IGO, Nantes, France
| | - Nicolas Degauque
- Inserm, CHU Nantes, Université de Nantes, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, Nantes, France.,Labex IGO, Nantes, France
| | - Sophie Brouard
- Inserm, CHU Nantes, Université de Nantes, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, Nantes, France.,Labex IGO, Nantes, France.,Centre d'Investigation Clinique en Biothérapie, Centre de ressources biologiques (CRB), Nantes, France
| | - Richard Danger
- Inserm, CHU Nantes, Université de Nantes, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, Nantes, France.,Labex IGO, Nantes, France
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24
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Understanding heterogeneity of fetal hemoglobin induction through comparative analysis of F and A erythroblasts. Blood 2020; 135:1957-1968. [PMID: 32268371 PMCID: PMC7256358 DOI: 10.1182/blood.2020005058] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 03/05/2020] [Indexed: 01/27/2023] Open
Abstract
Reversing the developmental switch from fetal hemoglobin (HbF, α2γ2) to adult hemoglobin (HbA, α2β2) is an important therapeutic approach in sickle cell disease (SCD) and β-thalassemia. In healthy individuals, SCD patients, and patients treated with pharmacologic HbF inducers, HbF is present only in a subset of red blood cells known as F cells. Despite more than 50 years of observations, the cause for this heterocellular HbF expression pattern, even among genetically identical cells, remains unknown. Adult F cells might represent a reversion of a given cell to a fetal-like epigenetic and transcriptional state. Alternatively, isolated transcriptional or posttranscriptional events at the γ-globin genes might underlie heterocellularity. Here, we set out to understand the heterogeneity of HbF activation by developing techniques to purify and profile differentiation stage-matched late erythroblast F cells and non-F cells (A cells) from the human HUDEP2 erythroid cell line and primary human erythroid cultures. Transcriptional and proteomic profiling of these cells demonstrated very few differences between F and A cells at the RNA level either under baseline conditions or after treatment with HbF inducers hydroxyurea or pomalidomide. Surprisingly, we did not find differences in expression of any known HbF regulators, including BCL11A or LRF, that would account for HbF activation. Our analysis shows that F erythroblasts are not significantly different from non-HbF-expressing cells and that the primary differences likely occur at the transcriptional level at the β-globin locus.
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25
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Mayerl S, Heuer H, Ffrench-Constant C. Hippocampal Neurogenesis Requires Cell-Autonomous Thyroid Hormone Signaling. Stem Cell Reports 2020; 14:845-860. [PMID: 32302557 PMCID: PMC7220957 DOI: 10.1016/j.stemcr.2020.03.014] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Revised: 03/14/2020] [Accepted: 03/17/2020] [Indexed: 02/07/2023] Open
Abstract
Adult hippocampal neurogenesis is strongly dependent on thyroid hormone (TH). Whether TH signaling regulates this process in a cell-autonomous or non-autonomous manner remains unknown. To answer this question, we used global and conditional knockouts of the TH transporter monocarboxylate transporter 8 (MCT8), having first used FACS and immunohistochemistry to demonstrate that MCT8 is the only TH transporter expressed on neuroblasts and adult slice cultures to confirm a necessary role for MCT8 in neurogenesis. Both mice with a global deletion or an adult neural stem cell-specific deletion of MCT8 showed decreased expression of the cell-cycle inhibitor P27KIP1, reduced differentiation of neuroblasts, and impaired generation of new granule cell neurons, with global knockout mice also showing enhanced neuroblast proliferation. Together, our results reveal a cell-autonomous role for TH signaling in adult hippocampal neurogenesis alongside non-cell-autonomous effects on cell proliferation earlier in the lineage.
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Affiliation(s)
- Steffen Mayerl
- MRC Centre for Regenerative Medicine, University of Edinburgh, 5 Little France Drive, Edinburgh EH16 4UU, UK.
| | - Heike Heuer
- University of Duisburg-Essen, University Hospital Essen, Department of Endocrinology, Essen, Germany
| | - Charles Ffrench-Constant
- MRC Centre for Regenerative Medicine, University of Edinburgh, 5 Little France Drive, Edinburgh EH16 4UU, UK
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26
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Kim S, Whitener RL, Peiris H, Gu X, Chang CA, Lam JY, Camunas-Soler J, Park I, Bevacqua RJ, Tellez K, Quake SR, Lakey JRT, Bottino R, Ross PJ, Kim SK. Molecular and genetic regulation of pig pancreatic islet cell development. Development 2020; 147:dev186213. [PMID: 32108026 PMCID: PMC7132804 DOI: 10.1242/dev.186213] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 02/20/2020] [Indexed: 12/12/2022]
Abstract
Reliance on rodents for understanding pancreatic genetics, development and islet function could limit progress in developing interventions for human diseases such as diabetes mellitus. Similarities of pancreas morphology and function suggest that porcine and human pancreas developmental biology may have useful homologies. However, little is known about pig pancreas development. To fill this knowledge gap, we investigated fetal and neonatal pig pancreas at multiple, crucial developmental stages using modern experimental approaches. Purification of islet β-, α- and δ-cells followed by transcriptome analysis (RNA-seq) and immunohistology identified cell- and stage-specific regulation, and revealed that pig and human islet cells share characteristic features that are not observed in mice. Morphometric analysis also revealed endocrine cell allocation and architectural similarities between pig and human islets. Our analysis unveiled scores of signaling pathways linked to native islet β-cell functional maturation, including evidence of fetal α-cell GLP-1 production and signaling to β-cells. Thus, the findings and resources detailed here show how pig pancreatic islet studies complement other systems for understanding the developmental programs that generate functional islet cells, and that are relevant to human pancreatic diseases.
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Affiliation(s)
- Seokho Kim
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Robert L Whitener
- 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
| | - Xueying Gu
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Charles A Chang
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jonathan Y Lam
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Joan Camunas-Soler
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Insung Park
- Department of Animal Science, University of California Davis, Davis, CA 95616, USA
| | - Romina J Bevacqua
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Krissie Tellez
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Stephen R Quake
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94518, USA
| | - Jonathan R T Lakey
- Department of Surgery, University of California at Irvine, Irvine, CA 92868, USA
| | - Rita Bottino
- Institute of Cellular Therapeutics, Allegheny Health Network, Pittsburgh, PA 15212, USA
| | - Pablo J Ross
- Department of Animal Science, University of California Davis, Davis, CA 95616, USA
| | - Seung K Kim
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
- Stanford Diabetes Research Center, Stanford University School of Medicine, Stanford, CA 94305, USA
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27
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Cardenas-Diaz FL, Leavens KF, Kishore S, Osorio-Quintero C, Chen YJ, Stanger BZ, Wang P, French D, Gadue P. A Dual Reporter EndoC-βH1 Human β-Cell Line for Efficient Quantification of Calcium Flux and Insulin Secretion. Endocrinology 2020; 161:bqaa005. [PMID: 31960055 PMCID: PMC7028009 DOI: 10.1210/endocr/bqaa005] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Revised: 01/07/2020] [Accepted: 01/20/2020] [Indexed: 02/07/2023]
Abstract
Human in vitro model systems of diabetes are critical to both study disease pathophysiology and offer a platform for drug testing. We have generated a set of tools in the human β-cell line EndoC-βH1 that allows the efficient and inexpensive characterization of β-cell physiology and phenotypes driven by disruption of candidate genes. First, we generated a dual reporter line that expresses a preproinsulin-luciferase fusion protein along with GCaMP6s. This reporter line allows the quantification of insulin secretion by measuring luciferase activity and calcium flux, a critical signaling step required for insulin secretion, via fluorescence microscopy. Using these tools, we demonstrate that the generation of the reporter human β-cell line was highly efficient and validated that luciferase activity could accurately reflect insulin secretion. Second, we used a lentiviral vector carrying the CRISPR-Cas9 system to generate candidate gene disruptions in the reporter line. We also show that we can achieve gene disruption in ~90% of cells using a CRISPR-Cas9 lentiviral system. As a proof of principle, we disrupt the β-cell master regulator, PDX1, and show that mutant EndoC-βH1 cells display impaired calcium responses and fail to secrete insulin when stimulated with high glucose. Furthermore, we show that PDX1 mutant EndoC-βH1 cells exhibit decreased expression of the β-cell-specific genes MAFA and NKX6.1 and increased GCG expression. The system presented here provides a platform to quickly and easily test β-cell functionality in wildtype and cells lacking a gene of interest.
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Affiliation(s)
- Fabian L Cardenas-Diaz
- Center for Cellular and Molecular Therapeutics, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Karla F Leavens
- Division of Endocrinology and Diabetes, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Siddharth Kishore
- Center for Cellular and Molecular Therapeutics, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
- Department of Cell and Molecular Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Catherine Osorio-Quintero
- Center for Cellular and Molecular Therapeutics, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Yi-Ju Chen
- Department of Cell and Molecular Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Ben Z Stanger
- Department of Cell and Molecular Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
- Gastroenterology Division, Department of Medicine, Abramson Family Cancer Research Institute, University of Pennsylvania School of Medicine, Philadelphia
| | - Pei Wang
- Departments of Cell Systems and Anatomy, University of Texas Health Science Center at San Antonio, San Antonio, Texas
| | - Deborah French
- Center for Cellular and Molecular Therapeutics, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Paul Gadue
- Center for Cellular and Molecular Therapeutics, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
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28
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Amamoto R, Zuccaro E, Curry NC, Khurana S, Chen HH, Cepko CL, Arlotta P. FIN-Seq: transcriptional profiling of specific cell types from frozen archived tissue of the human central nervous system. Nucleic Acids Res 2020; 48:e4. [PMID: 31728515 PMCID: PMC7145626 DOI: 10.1093/nar/gkz968] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 09/09/2019] [Accepted: 11/12/2019] [Indexed: 12/14/2022] Open
Abstract
Thousands of frozen, archived tissue samples from the human central nervous system (CNS) are currently available in brain banks. As recent developments in RNA sequencing technologies are beginning to elucidate the cellular diversity present within the human CNS, it is becoming clear that an understanding of this diversity would greatly benefit from deeper transcriptional analyses. Single cell and single nucleus RNA profiling provide one avenue to decipher this heterogeneity. An alternative, complementary approach is to profile isolated, pre-defined cell types and use methods that can be applied to many archived human tissue samples that have been stored long-term. Here, we developed FIN-Seq (Frozen Immunolabeled Nuclei Sequencing), a method that accomplishes these goals. FIN-Seq uses immunohistochemical isolation of nuclei of specific cell types from frozen human tissue, followed by bulk RNA-Sequencing. We applied this method to frozen postmortem samples of human cerebral cortex and retina and were able to identify transcripts, including low abundance transcripts, in specific cell types.
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Affiliation(s)
- Ryoji Amamoto
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
- Department of Genetics and Ophthalmology, Howard Hughes Medical Institute, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Emanuela Zuccaro
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Nathan C Curry
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Sonia Khurana
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Hsu-Hsin Chen
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Constance L Cepko
- Department of Genetics and Ophthalmology, Howard Hughes Medical Institute, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Paola Arlotta
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
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29
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Amamoto R, Garcia MD, West ER, Choi J, Lapan SW, Lane EA, Perrimon N, Cepko CL. Probe-Seq enables transcriptional profiling of specific cell types from heterogeneous tissue by RNA-based isolation. eLife 2019; 8:e51452. [PMID: 31815670 PMCID: PMC6901332 DOI: 10.7554/elife.51452] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 11/25/2019] [Indexed: 12/12/2022] Open
Abstract
Recent transcriptional profiling technologies are uncovering previously-undefined cell populations and molecular markers at an unprecedented pace. While single cell RNA (scRNA) sequencing is an attractive approach for unbiased transcriptional profiling of all cell types, a complementary method to isolate and sequence specific cell populations from heterogeneous tissue remains challenging. Here, we developed Probe-Seq, which allows deep transcriptional profiling of specific cell types isolated using RNA as the defining feature. Dissociated cells are labeled using fluorescent in situ hybridization (FISH) for RNA, and then isolated by fluorescent activated cell sorting (FACS). We used Probe-Seq to purify and profile specific cell types from mouse, human, and chick retinas, as well as from Drosophila midguts. Probe-Seq is compatible with frozen nuclei, making cell types within archival tissue immediately accessible. As it can be multiplexed, combinations of markers can be used to create specificity. Multiplexing also allows for the isolation of multiple cell types from one cell preparation. Probe-Seq should enable RNA profiling of specific cell types from any organism.
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Affiliation(s)
- Ryoji Amamoto
- Department of Genetics, Blavatnik InstituteHoward Hughes Medical Institute, Harvard Medical SchoolBostonUnited States
- Department of Ophthalmology, Blavatnik InstituteHoward Hughes Medical Institute, Harvard Medical SchoolBostonUnited States
| | - Mauricio D Garcia
- Department of Genetics, Blavatnik InstituteHoward Hughes Medical Institute, Harvard Medical SchoolBostonUnited States
- Department of Ophthalmology, Blavatnik InstituteHoward Hughes Medical Institute, Harvard Medical SchoolBostonUnited States
| | - Emma R West
- Department of Genetics, Blavatnik InstituteHoward Hughes Medical Institute, Harvard Medical SchoolBostonUnited States
- Department of Ophthalmology, Blavatnik InstituteHoward Hughes Medical Institute, Harvard Medical SchoolBostonUnited States
| | - Jiho Choi
- Department of Genetics, Blavatnik InstituteHoward Hughes Medical Institute, Harvard Medical SchoolBostonUnited States
- Department of Ophthalmology, Blavatnik InstituteHoward Hughes Medical Institute, Harvard Medical SchoolBostonUnited States
| | - Sylvain W Lapan
- Department of Genetics, Blavatnik InstituteHoward Hughes Medical Institute, Harvard Medical SchoolBostonUnited States
- Department of Ophthalmology, Blavatnik InstituteHoward Hughes Medical Institute, Harvard Medical SchoolBostonUnited States
| | - Elizabeth A Lane
- Department of Genetics, Blavatnik InstituteHoward Hughes Medical Institute, Harvard Medical SchoolBostonUnited States
| | - Norbert Perrimon
- Department of Genetics, Blavatnik InstituteHoward Hughes Medical Institute, Harvard Medical SchoolBostonUnited States
| | - Constance L Cepko
- Department of Genetics, Blavatnik InstituteHoward Hughes Medical Institute, Harvard Medical SchoolBostonUnited States
- Department of Ophthalmology, Blavatnik InstituteHoward Hughes Medical Institute, Harvard Medical SchoolBostonUnited States
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30
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Li L, Tian E, Chen X, Chao J, Klein J, Qu Q, Sun G, Sun G, Huang Y, Warden CD, Ye P, Feng L, Li X, Cui Q, Sultan A, Douvaras P, Fossati V, Sanjana NE, Riggs AD, Shi Y. GFAP Mutations in Astrocytes Impair Oligodendrocyte Progenitor Proliferation and Myelination in an hiPSC Model of Alexander Disease. Cell Stem Cell 2019; 23:239-251.e6. [PMID: 30075130 DOI: 10.1016/j.stem.2018.07.009] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Revised: 04/23/2018] [Accepted: 07/16/2018] [Indexed: 10/28/2022]
Abstract
Alexander disease (AxD) is a leukodystrophy that primarily affects astrocytes and is caused by mutations in the astrocytic filament gene GFAP. While astrocytes are thought to have important roles in controlling myelination, AxD animal models do not recapitulate critical myelination phenotypes and it is therefore not clear how AxD astrocytes contribute to leukodystrophy. Here, we show that AxD patient iPSC-derived astrocytes recapitulate key features of AxD pathology such as GFAP aggregation. Moreover, AxD astrocytes inhibit proliferation of human iPSC-derived oligodendrocyte progenitor cells (OPCs) in co-culture and reduce their myelination potential. CRISPR/Cas9-based correction of GFAP mutations reversed these phenotypes. Transcriptomic analyses of AxD astrocytes and postmortem brains identified CHI3L1 as a key mediator of AxD astrocyte-induced inhibition of OPC activity. Thus, this iPSC-based model of AxD not only recapitulates patient phenotypes not observed in animal models, but also reveals mechanisms underlying disease pathology and provides a platform for assessing therapeutic interventions.
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Affiliation(s)
- Li Li
- Division of Stem Cell Biology Research, Department of Developmental and Stem Cell Biology, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA; Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
| | - E Tian
- Division of Stem Cell Biology Research, Department of Developmental and Stem Cell Biology, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
| | - Xianwei Chen
- Division of Stem Cell Biology Research, Department of Developmental and Stem Cell Biology, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
| | - Jianfei Chao
- Division of Stem Cell Biology Research, Department of Developmental and Stem Cell Biology, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
| | - Jeremy Klein
- Division of Stem Cell Biology Research, Department of Developmental and Stem Cell Biology, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
| | - Qiuhao Qu
- Division of Stem Cell Biology Research, Department of Developmental and Stem Cell Biology, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
| | - Guihua Sun
- Department of Diabetes Complications and Metabolism, Diabetes and Metabolism Research Institute, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
| | - Guoqiang Sun
- Division of Stem Cell Biology Research, Department of Developmental and Stem Cell Biology, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
| | - Yanzhou Huang
- Division of Stem Cell Biology Research, Department of Developmental and Stem Cell Biology, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
| | - Charles D Warden
- Integrative Genomics Core, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
| | - Peng Ye
- Division of Stem Cell Biology Research, Department of Developmental and Stem Cell Biology, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
| | - Lizhao Feng
- Division of Stem Cell Biology Research, Department of Developmental and Stem Cell Biology, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
| | - Xinqiang Li
- Division of Stem Cell Biology Research, Department of Developmental and Stem Cell Biology, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
| | - Qi Cui
- Division of Stem Cell Biology Research, Department of Developmental and Stem Cell Biology, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
| | - Abdullah Sultan
- Division of Stem Cell Biology Research, Department of Developmental and Stem Cell Biology, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
| | - Panagiotis Douvaras
- The New York Stem Cell Foundation Research Institute, New York, NY 10019, USA
| | - Valentina Fossati
- The New York Stem Cell Foundation Research Institute, New York, NY 10019, USA
| | - Neville E Sanjana
- New York Genome Center, New York, NY 10013, USA; Department of Biology, New York University, New York, NY 10003, USA; Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Arthur D Riggs
- Department of Diabetes Complications and Metabolism, Diabetes and Metabolism Research Institute, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
| | - Yanhong Shi
- Division of Stem Cell Biology Research, Department of Developmental and Stem Cell Biology, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA; Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA.
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31
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Infiltrating CCR2 + monocytes and their progenies, fibrocytes, contribute to colon fibrosis by inhibiting collagen degradation through the production of TIMP-1. Sci Rep 2019; 9:8568. [PMID: 31189971 PMCID: PMC6562037 DOI: 10.1038/s41598-019-45012-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 05/29/2019] [Indexed: 12/26/2022] Open
Abstract
Intestinal fibrosis is a serious complication in inflammatory bowel disease (IBD). Despite the remarkable success of recent anti-inflammatory therapies for IBD, incidence of intestinal fibrosis and need for bowel resection have not significantly changed. To clarify the contribution of haematopoietic-derived cells in intestinal fibrosis, we prepared bone marrow (BM) chimeric mice (chimeras), which were reconstituted with BM cells derived from enhanced green fluorescent protein (EGFP)-transgenic mice or CC chemokine receptor 2 (CCR2)-deficient mice. After 2 months of transplantation, BM chimeras were treated with azoxymethane/dextran sodium sulphate. During chronic inflammation, CCR2+ BM-derived monocyte and fibrocyte infiltration into the colon and CC chemokine ligand 2 production increased, leading to colon fibrosis in EGFP BM chimeras. In CCR2-deficient BM chimeras, monocyte and fibrocyte numbers in the colonic lamina propria significantly decreased, and colon fibrosis was attenuated. In colon tissue, mRNA expression of tissue inhibitor of metalloproteinase (TIMP)-1 but not of collagen I, transforming growth factor-β1 or matrix metalloproteinases was significantly different between the two chimeras. CCR2+ monocytes and fibrocytes showed high Timp1 mRNA expression. Our results suggest that infiltrating CCR2+ monocytes and their progenies, fibrocytes, promote colon fibrosis by inhibiting collagen degradation through TIMP-1 production.
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32
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Roberts GP, Larraufie P, Richards P, Kay RG, Galvin SG, Miedzybrodzka EL, Leiter A, Li HJ, Glass LL, Ma MKL, Lam B, Yeo GSH, Scharfmann R, Chiarugi D, Hardwick RH, Reimann F, Gribble FM. Comparison of Human and Murine Enteroendocrine Cells by Transcriptomic and Peptidomic Profiling. Diabetes 2019; 68:1062-1072. [PMID: 30733330 PMCID: PMC6477899 DOI: 10.2337/db18-0883] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 10/23/2018] [Indexed: 02/02/2023]
Abstract
Enteroendocrine cells (EECs) produce hormones such as glucagon-like peptide 1 and peptide YY that regulate food absorption, insulin secretion, and appetite. Based on the success of glucagon-like peptide 1-based therapies for type 2 diabetes and obesity, EECs are themselves the focus of drug discovery programs to enhance gut hormone secretion. The aim of this study was to identify the transcriptome and peptidome of human EECs and to provide a cross-species comparison between humans and mice. By RNA sequencing of human EECs purified by flow cytometry after cell fixation and staining, we present a first transcriptomic analysis of human EEC populations and demonstrate a strong correlation with murine counterparts. RNA sequencing was deep enough to enable identification of low-abundance transcripts such as G-protein-coupled receptors and ion channels, revealing expression in human EECs of G-protein-coupled receptors previously found to play roles in postprandial nutrient detection. With liquid chromatography-tandem mass spectrometry, we profiled the gradients of peptide hormones along the human and mouse gut, including their sequences and posttranslational modifications. The transcriptomic and peptidomic profiles of human and mouse EECs and cross-species comparison will be valuable tools for drug discovery programs and for understanding human metabolism and the endocrine impacts of bariatric surgery.
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Affiliation(s)
- Geoffrey P Roberts
- Wellcome Trust-MRC Institute of Metabolic Science, University of Cambridge, Cambridge, U.K
- Cambridge Oesophago-Gastric Centre, Addenbrooke's Hospital, Cambridge, U.K
| | - Pierre Larraufie
- Wellcome Trust-MRC Institute of Metabolic Science, University of Cambridge, Cambridge, U.K
| | - Paul Richards
- Wellcome Trust-MRC Institute of Metabolic Science, University of Cambridge, Cambridge, U.K
- INSERM U1016, Institut Cochin, Université Paris-Descartes, Paris, France
| | - Richard G Kay
- Wellcome Trust-MRC Institute of Metabolic Science, University of Cambridge, Cambridge, U.K
| | - Sam G Galvin
- Wellcome Trust-MRC Institute of Metabolic Science, University of Cambridge, Cambridge, U.K
| | - Emily L Miedzybrodzka
- Wellcome Trust-MRC Institute of Metabolic Science, University of Cambridge, Cambridge, U.K
| | - Andrew Leiter
- Division of Gastroenterology, Department of Medicine, University of Massachusetts Medical School, Worcester, MA
| | - H Joyce Li
- Division of Gastroenterology, Department of Medicine, University of Massachusetts Medical School, Worcester, MA
| | - Leslie L Glass
- Wellcome Trust-MRC Institute of Metabolic Science, University of Cambridge, Cambridge, U.K
| | - Marcella K L Ma
- Wellcome Trust-MRC Institute of Metabolic Science, University of Cambridge, Cambridge, U.K
| | - Brian Lam
- Wellcome Trust-MRC Institute of Metabolic Science, University of Cambridge, Cambridge, U.K
| | - Giles S H Yeo
- Wellcome Trust-MRC Institute of Metabolic Science, University of Cambridge, Cambridge, U.K
| | - Raphaël Scharfmann
- INSERM U1016, Institut Cochin, Université Paris-Descartes, Paris, France
| | - Davide Chiarugi
- Wellcome Trust-MRC Institute of Metabolic Science, University of Cambridge, Cambridge, U.K
| | - Richard H Hardwick
- Cambridge Oesophago-Gastric Centre, Addenbrooke's Hospital, Cambridge, U.K
| | - Frank Reimann
- Wellcome Trust-MRC Institute of Metabolic Science, University of Cambridge, Cambridge, U.K.
| | - Fiona M Gribble
- Wellcome Trust-MRC Institute of Metabolic Science, University of Cambridge, Cambridge, U.K.
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33
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Balin SJ, Pellegrini M, Klechevsky E, Won ST, Weiss DI, Choi AW, Hakimian J, Lu J, Ochoa MT, Bloom BR, Lanier LL, Stenger S, Modlin RL. Human antimicrobial cytotoxic T lymphocytes, defined by NK receptors and antimicrobial proteins, kill intracellular bacteria. Sci Immunol 2019; 3:3/26/eaat7668. [PMID: 30171080 DOI: 10.1126/sciimmunol.aat7668] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Accepted: 07/03/2018] [Indexed: 12/15/2022]
Abstract
Human CD8+ cytotoxic T lymphocytes (CTLs) contribute to antimicrobial defense against intracellular pathogens through secretion of cytotoxic granule proteins granzyme B, perforin, and granulysin. However, CTLs are heterogeneous in the expression of these proteins, and the subset(s) responsible for antimicrobial activity is unclear. Studying human leprosy, we found that the subset of CTLs coexpressing all three cytotoxic molecules is increased in the resistant form of the disease, can be expanded by interleukin-15 (IL-15), and is differentiated from naïve CD8+ T cells by Langerhans cells. RNA sequencing analysis identified that these CTLs express a gene signature that includes an array of surface receptors typically expressed by natural killer (NK) cells. We determined that CD8+ CTLs expressing granzyme B, perforin, and granulysin, as well as the activating NK receptor NKG2C, represent a population of "antimicrobial CTLs" (amCTLs) capable of T cell receptor (TCR)-dependent and TCR-independent release of cytotoxic granule proteins that mediate antimicrobial activity.
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Affiliation(s)
- Samuel J Balin
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine at University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA.,Department of Microbiology, Immunology and Molecular Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Matteo Pellegrini
- Molecular Cell and Developmental Biology at UCLA, Los Angeles, CA 90095, USA
| | - Eynav Klechevsky
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Sohui T Won
- Department of Microbiology, Immunology and Molecular Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - David I Weiss
- Molecular Biology Interdepartmental Graduate Program, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Aaron W Choi
- Department of Microbiology, Immunology and Molecular Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Joshua Hakimian
- Department of Microbiology, Immunology and Molecular Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Jing Lu
- Molecular Cell and Developmental Biology at UCLA, Los Angeles, CA 90095, USA
| | - Maria Teresa Ochoa
- Department of Dermatology, University of Southern California School of Medicine, Los Angeles, CA 90033, USA
| | - Barry R Bloom
- Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Lewis L Lanier
- Department of Microbiology and Immunology and the Parker Institute for Cancer Immunotherapy, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Steffen Stenger
- Institute for Medical Microbiology and Hygiene, University Hospital Ulm, Ulm, Germany
| | - Robert L Modlin
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine at University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA. .,Department of Microbiology, Immunology and Molecular Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
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34
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McCorkindale AL, Wahle P, Werner S, Jungreis I, Menzel P, Shukla CJ, Abreu RLP, Irizarry RA, Meyer IM, Kellis M, Zinzen RP. A gene expression atlas of embryonic neurogenesis in Drosophila reveals complex spatiotemporal regulation of lncRNAs. Development 2019; 146:dev.175265. [PMID: 30923056 PMCID: PMC6451322 DOI: 10.1242/dev.175265] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Accepted: 02/05/2019] [Indexed: 01/09/2023]
Abstract
Cell type specification during early nervous system development in Drosophila melanogaster requires precise regulation of gene expression in time and space. Resolving the programs driving neurogenesis has been a major challenge owing to the complexity and rapidity with which distinct cell populations arise. To resolve the cell type-specific gene expression dynamics in early nervous system development, we have sequenced the transcriptomes of purified neurogenic cell types across consecutive time points covering crucial events in neurogenesis. The resulting gene expression atlas comprises a detailed resource of global transcriptome dynamics that permits systematic analysis of how cells in the nervous system acquire distinct fates. We resolve known gene expression dynamics and uncover novel expression signatures for hundreds of genes among diverse neurogenic cell types, most of which remain unstudied. We also identified a set of conserved long noncoding RNAs (lncRNAs) that are regulated in a tissue-specific manner and exhibit spatiotemporal expression during neurogenesis with exquisite specificity. lncRNA expression is highly dynamic and demarcates specific subpopulations within neurogenic cell types. Our spatiotemporal transcriptome atlas provides a comprehensive resource for investigating the function of coding genes and noncoding RNAs during crucial stages of early neurogenesis. Summary: DIV-MARIS, an adapted technique for examining stage- and cell type-specific gene expression, reveals a complex network of mRNAs and lncRNAs expressed in specific cell types during early Drosophila embryonic nervous system development.
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Affiliation(s)
- Alexandra L McCorkindale
- Laboratory for Systems Biology of Neural Tissue Differentiation, Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrueck Centre for Molecular Medicine (MDC) in the Helmholtz Association, Robert-Roessle-Strasse 12, 13125 Berlin, Germany .,Biofrontiers Institute, University of Colorado, Boulder, CO 80303, USA
| | - Philipp Wahle
- Laboratory for Systems Biology of Neural Tissue Differentiation, Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrueck Centre for Molecular Medicine (MDC) in the Helmholtz Association, Robert-Roessle-Strasse 12, 13125 Berlin, Germany
| | - Sascha Werner
- Laboratory for Systems Biology of Neural Tissue Differentiation, Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrueck Centre for Molecular Medicine (MDC) in the Helmholtz Association, Robert-Roessle-Strasse 12, 13125 Berlin, Germany
| | - Irwin Jungreis
- MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA 02139, USA.,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Peter Menzel
- Laboratory for Bioinformatics of RNA Structure and Transcriptome Regulation, Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrueck Centre for Molecular Medicine (MDC) in the Helmholtz Association, Robert-Roessle-Strasse 12, 13125 Berlin, Germany
| | - Chinmay J Shukla
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA.,Dana Farber Cancer Institute, Boston, MA 02215, USA
| | - Rúben Lopes Pereira Abreu
- Laboratory for Systems Biology of Neural Tissue Differentiation, Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrueck Centre for Molecular Medicine (MDC) in the Helmholtz Association, Robert-Roessle-Strasse 12, 13125 Berlin, Germany
| | | | - Irmtraud M Meyer
- Laboratory for Bioinformatics of RNA Structure and Transcriptome Regulation, Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrueck Centre for Molecular Medicine (MDC) in the Helmholtz Association, Robert-Roessle-Strasse 12, 13125 Berlin, Germany.,Freie Universität, Institute of Biochemistry, Department of Biology, Chemistry, Pharmacy, Thielallee 63, Berlin 14195, Germany
| | - Manolis Kellis
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.,Laboratory for Bioinformatics of RNA Structure and Transcriptome Regulation, Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrueck Centre for Molecular Medicine (MDC) in the Helmholtz Association, Robert-Roessle-Strasse 12, 13125 Berlin, Germany
| | - Robert P Zinzen
- Laboratory for Systems Biology of Neural Tissue Differentiation, Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrueck Centre for Molecular Medicine (MDC) in the Helmholtz Association, Robert-Roessle-Strasse 12, 13125 Berlin, Germany
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35
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Larraufie P, Roberts GP, McGavigan AK, Kay RG, Li J, Leiter A, Melvin A, Biggs EK, Ravn P, Davy K, Hornigold DC, Yeo GSH, Hardwick RH, Reimann F, Gribble FM. Important Role of the GLP-1 Axis for Glucose Homeostasis after Bariatric Surgery. Cell Rep 2019; 26:1399-1408.e6. [PMID: 30726726 PMCID: PMC6367566 DOI: 10.1016/j.celrep.2019.01.047] [Citation(s) in RCA: 104] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 12/14/2018] [Accepted: 01/11/2019] [Indexed: 02/07/2023] Open
Abstract
Bariatric surgery is widely used to treat obesity and improves type 2 diabetes beyond expectations from the degree of weight loss. Elevated post-prandial concentrations of glucagon-like peptide 1 (GLP-1), peptide YY (PYY), and insulin are widely reported, but the importance of GLP-1 in post-bariatric physiology remains debated. Here, we show that GLP-1 is a major driver of insulin secretion after bariatric surgery, as demonstrated by blocking GLP-1 receptors (GLP1Rs) post-gastrectomy in lean humans using Exendin-9 or in mice using an anti-GLP1R antibody. Transcriptomics and peptidomics analyses revealed that human and mouse enteroendocrine cells were unaltered post-surgery; instead, we found that elevated plasma GLP-1 and PYY correlated with increased nutrient delivery to the distal gut in mice. We conclude that increased GLP-1 secretion after bariatric surgery arises from rapid nutrient delivery to the distal gut and is a key driver of enhanced insulin secretion.
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Affiliation(s)
- Pierre Larraufie
- Metabolic Research Laboratories, Wellcome Trust MRC Institute of Metabolic Science, Addenbrooke's Hospital, Hills Road, Cambridge CB2 0QQ, UK
| | - Geoffrey P Roberts
- Metabolic Research Laboratories, Wellcome Trust MRC Institute of Metabolic Science, Addenbrooke's Hospital, Hills Road, Cambridge CB2 0QQ, UK
| | - Anne K McGavigan
- Metabolic Research Laboratories, Wellcome Trust MRC Institute of Metabolic Science, Addenbrooke's Hospital, Hills Road, Cambridge CB2 0QQ, UK
| | - Richard G Kay
- Metabolic Research Laboratories, Wellcome Trust MRC Institute of Metabolic Science, Addenbrooke's Hospital, Hills Road, Cambridge CB2 0QQ, UK
| | - Joyce Li
- Department of Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Andrew Leiter
- Department of Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Audrey Melvin
- Metabolic Research Laboratories, Wellcome Trust MRC Institute of Metabolic Science, Addenbrooke's Hospital, Hills Road, Cambridge CB2 0QQ, UK
| | - Emma K Biggs
- Metabolic Research Laboratories, Wellcome Trust MRC Institute of Metabolic Science, Addenbrooke's Hospital, Hills Road, Cambridge CB2 0QQ, UK
| | - Peter Ravn
- Department of Antibody Discovery and Protein Engineering, MedImmune, Granta Park, Cambridge CB21 6GH, UK
| | - Kathleen Davy
- Department of Cardiovascular and Metabolic Disease, MedImmune, Granta Park, Cambridge, UK
| | - David C Hornigold
- Department of Cardiovascular and Metabolic Disease, MedImmune, Granta Park, Cambridge, UK
| | - Giles S H Yeo
- Metabolic Research Laboratories, Wellcome Trust MRC Institute of Metabolic Science, Addenbrooke's Hospital, Hills Road, Cambridge CB2 0QQ, UK
| | - Richard H Hardwick
- Cambridge Oesophago-gastric Centre, Addenbrooke's Hospital, Cambridge, UK
| | - Frank Reimann
- Metabolic Research Laboratories, Wellcome Trust MRC Institute of Metabolic Science, Addenbrooke's Hospital, Hills Road, Cambridge CB2 0QQ, UK
| | - Fiona M Gribble
- Metabolic Research Laboratories, Wellcome Trust MRC Institute of Metabolic Science, Addenbrooke's Hospital, Hills Road, Cambridge CB2 0QQ, UK.
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36
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Population and Single-Cell Analysis of Human Cardiogenesis Reveals Unique LGR5 Ventricular Progenitors in Embryonic Outflow Tract. Dev Cell 2019; 48:475-490.e7. [PMID: 30713072 DOI: 10.1016/j.devcel.2019.01.005] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 12/18/2018] [Accepted: 12/31/2018] [Indexed: 02/08/2023]
Abstract
The morphogenetic process of mammalian cardiac development is complex and highly regulated spatiotemporally by multipotent cardiac stem/progenitor cells (CPCs). Mouse studies have been informative for understanding mammalian cardiogenesis; however, similar insights have been poorly established in humans. Here, we report comprehensive gene expression profiles of human cardiac derivatives from multipotent CPCs to intermediates and mature cardiac cells by population and single-cell RNA-seq using human embryonic stem cell-derived and embryonic/fetal heart-derived cardiac cells micro-dissected from specific heart compartments. Importantly, we discover a uniquely human subset of cono-ventricular region-specific CPCs, marked by LGR5. At 4 to 5 weeks of fetal age, the LGR5+ population appears to emerge specifically in the proximal outflow tract of human embryonic hearts and thereafter promotes cardiac development and alignment through expansion of the ISL1+TNNT2+ intermediates. The current study contributes to a deeper understanding of human cardiogenesis, which may uncover the putative origins of certain human congenital cardiac malformations.
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37
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Tsai SL, Baselga-Garriga C, Melton DA. Blastemal progenitors modulate immune signaling during early limb regeneration. Development 2019; 146:146/1/dev169128. [PMID: 30602532 DOI: 10.1242/dev.169128] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 11/23/2018] [Indexed: 12/16/2022]
Abstract
Blastema formation, a hallmark of limb regeneration, requires proliferation and migration of progenitors to the amputation plane. Although blastema formation has been well described, the transcriptional programs that drive blastemal progenitors remain unknown. We transcriptionally profiled dividing and non-dividing cells in regenerating stump tissues, as well as the wound epidermis, during early axolotl limb regeneration. Our analysis revealed unique transcriptional signatures of early dividing cells and, unexpectedly, repression of several core developmental signaling pathways in early regenerating stump tissues. We further identify an immunomodulatory role for blastemal progenitors through interleukin 8 (IL-8), a highly expressed cytokine in subpopulations of early blastemal progenitors. Ectopic il-8 expression in non-regenerating limbs induced myeloid cell recruitment, while IL-8 knockdown resulted in defective myeloid cell retention during late wound healing, delaying regeneration. Furthermore, the il-8 receptor cxcr-1/2 was expressed in myeloid cells, and inhibition of CXCR-1/2 signaling during early stages of limb regeneration prevented regeneration. Altogether, our findings suggest that blastemal progenitors are active early mediators of immune support, and identify CXCR-1/2 signaling as an important immunomodulatory pathway during the initiation of regeneration.
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Affiliation(s)
- Stephanie L Tsai
- Department of Stem Cell and Regenerative Biology, Harvard University, 7 Divinity Avenue, Cambridge, MA 02138, USA.,Department of Molecular and Cellular Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA
| | - Clara Baselga-Garriga
- Department of Stem Cell and Regenerative Biology, Harvard University, 7 Divinity Avenue, Cambridge, MA 02138, USA.,Department of Molecular and Cellular Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA
| | - Douglas A Melton
- Department of Stem Cell and Regenerative Biology, Harvard University, 7 Divinity Avenue, Cambridge, MA 02138, USA
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Menzel P, McCorkindale AL, Stefanov SR, Zinzen RP, Meyer IM. Transcriptional dynamics of microRNAs and their targets during Drosophila neurogenesis. RNA Biol 2019; 16:69-81. [PMID: 30582411 PMCID: PMC6380339 DOI: 10.1080/15476286.2018.1558907] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 12/03/2018] [Accepted: 12/04/2018] [Indexed: 01/20/2023] Open
Abstract
During Drosophila melanogaster embryogenesis, tight regulation of gene expression in time and space is required for the orderly emergence of specific cell types. While the general importance of microRNAs in regulating eukaryotic gene expression has been well-established, their role in early neurogenesis remains to be addressed. In this survey, we investigate the transcriptional dynamics of microRNAs and their target transcripts during neurogenesis of Drosophila melanogaster. To this end, we use the recently developed DIV-MARIS protocol, a method for enriching specific cell types from the Drosophila embryo in vivo, to sequence cell type-specific transcriptomes. We generate dedicated small and total RNA-seq libraries for neuroblasts, neurons and glia cells at early (6-8 h after egg laying (AEL)) and late (18-22 h AEL) stage. This allows us to directly compare these transcriptomes and investigate the potential functional roles of individual microRNAs with spatiotemporal resolution genome-wide, which is beyond the capabilities of existing in situ hybridization methods. Overall, we identify 74 microRNAs that are significantly differentially expressed between the three cell types and the two developmental stages. In all cell types, predicted target genes of down-regulated microRNAs show a significant enrichment of Gene Ontology terms related to neurogenesis. We also investigate how microRNAs regulate the transcriptome by targeting transcription factors and find many candidate microRNAs with putative roles in neurogenesis. Our survey highlights the roles of microRNAs as regulators of differentiation and glioneurognesis in the fruit fly and provides distinct starting points for dedicated functional follow-up studies.
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Affiliation(s)
- Peter Menzel
- Berlin Institute for Molecular and Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Alexandra L. McCorkindale
- Berlin Institute for Molecular and Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Stefan R. Stefanov
- Berlin Institute for Molecular and Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
- Institute of Biochemistry, Department of Biology, Chemistry, and Pharmacology, Freie Universität Berlin, Berlin, Germany
| | - Robert P. Zinzen
- Berlin Institute for Molecular and Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Irmtraud M. Meyer
- Berlin Institute for Molecular and Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
- Institute of Biochemistry, Department of Biology, Chemistry, and Pharmacology, Freie Universität Berlin, Berlin, Germany
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Panganiban RA, Sun M, Dahlin A, Park HR, Kan M, Himes BE, Mitchel JA, Iribarren C, Jorgenson E, Randell SH, Israel E, Tantisira K, Shore S, Park JA, Weiss ST, Wu AC, Lu Q. A functional splice variant associated with decreased asthma risk abolishes the ability of gasdermin B to induce epithelial cell pyroptosis. J Allergy Clin Immunol 2018; 142:1469-1478.e2. [PMID: 29330013 PMCID: PMC6037620 DOI: 10.1016/j.jaci.2017.11.040] [Citation(s) in RCA: 105] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2017] [Revised: 11/12/2017] [Accepted: 11/22/2017] [Indexed: 12/17/2022]
Abstract
BACKGROUND Genetic variants in the chromosomal region 17q21 are consistently associated with asthma. However, mechanistic studies have not yet linked any of the associated variants to a function that could influence asthma, and as a result, the identity of the asthma gene(s) remains elusive. OBJECTIVES We sought to identify and characterize functional variants in the 17q21 locus. METHODS We used the Exome Aggregation Consortium browser to identify coding (amino acid-changing) variants in the 17q21 locus. We obtained asthma association measures for these variants in both the Genetic Epidemiology Research in Adult Health and Aging (GERA) cohort (16,274 cases and 38,269 matched controls) and the EVE Consortium study (5,303 asthma cases and 12,560 individuals). Gene expression and protein localization were determined by quantitative RT-PCR and fluorescence immunostaining, respectively. Molecular and cellular studies were performed to determine the functional effects of coding variants. RESULTS Two coding variants (rs2305480 and rs11078928) of the gasdermin B (GSDMB) gene in the 17q21 locus were associated with lower asthma risk in both GERA (odds ratio, 0.92; P = 1.01 × 10-6) and EVE (odds ratio, 0.85; joint PEVE = 1.31 × 10-13). In GERA, rs11078928 had a minor allele frequency (MAF) of 0.45 in unaffected (nonasthmatic) controls and 0.43 in asthma cases. For European Americans in EVE, the MAF of rs2305480 was 0.45 for controls and 0.39 for cases; for all EVE subjects, the MAF was 0.32 for controls and 0.27 for cases. GSDMB is highly expressed in differentiated airway epithelial cells, including the ciliated cells. We found that, when the GSDMB protein is cleaved by inflammatory caspase-1 to release its N-terminal fragment, potent pyroptotic cell death is induced. The splice variant rs11078928 deletes the entire exon 6, which encodes 13 amino acids in the critical N-terminus, and abolishes the pyroptotic activity of the GSDMB protein. CONCLUSIONS Our study identified a functional asthma variant in the GSDMB gene of the 17q21 locus and implicates GSDMB-mediated epithelial cell pyroptosis in pathogenesis.
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Affiliation(s)
- Ronald A Panganiban
- Program in Molecular and Integrative Physiological Sciences, Departments of Environmental Health and Genetics & Complex Diseases, Harvard T.H. Chan School of Public Health, Boston, Mass
| | - Maoyun Sun
- Program in Molecular and Integrative Physiological Sciences, Departments of Environmental Health and Genetics & Complex Diseases, Harvard T.H. Chan School of Public Health, Boston, Mass
| | - Amber Dahlin
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Mass
| | - Hae-Ryung Park
- Program in Molecular and Integrative Physiological Sciences, Departments of Environmental Health and Genetics & Complex Diseases, Harvard T.H. Chan School of Public Health, Boston, Mass
| | - Mengyuan Kan
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Blanca E Himes
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Jennifer A Mitchel
- Program in Molecular and Integrative Physiological Sciences, Departments of Environmental Health and Genetics & Complex Diseases, Harvard T.H. Chan School of Public Health, Boston, Mass
| | - Carlos Iribarren
- Division of Research, Kaiser Permanente Northern California, Oakland, Calif
| | - Eric Jorgenson
- Division of Research, Kaiser Permanente Northern California, Oakland, Calif
| | - Scott H Randell
- Marsico Lung Institute/Cystic Fibrosis Center, University of North Carolina, Chapel Hill, NC
| | - Elliot Israel
- Asthma Research Center, Brigham and Women's Hospital and Harvard Medical School, Boston, Mass
| | - Kelan Tantisira
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Mass
| | - Stephanie Shore
- Program in Molecular and Integrative Physiological Sciences, Departments of Environmental Health and Genetics & Complex Diseases, Harvard T.H. Chan School of Public Health, Boston, Mass
| | - Jin-Ah Park
- Program in Molecular and Integrative Physiological Sciences, Departments of Environmental Health and Genetics & Complex Diseases, Harvard T.H. Chan School of Public Health, Boston, Mass
| | - Scott T Weiss
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Mass
| | - Ann Chen Wu
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Mass; Precision Medicine Translational Research Center, Department of Population Medicine, Harvard Medical School, Boston, Mass
| | - Quan Lu
- Program in Molecular and Integrative Physiological Sciences, Departments of Environmental Health and Genetics & Complex Diseases, Harvard T.H. Chan School of Public Health, Boston, Mass.
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40
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Beasley S, Nguyen K, Fazio M, Spitale RC. Protected pyrimidine nucleosides for cell-specific metabolic labeling of RNA. Tetrahedron Lett 2018; 59:3912-3915. [PMID: 31031425 PMCID: PMC6483386 DOI: 10.1016/j.tetlet.2018.09.040] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
RNA molecules can perform a myriad of functions, from the regulation of gene expression to providing the genetic blueprint for protein synthesis. Characterizing RNA expression dynamics, in a cell-specific manner, still remains a great challenge in biology. Herein we present a new set of protected alkynyl nucleosides for cell-specific metabolic labeling of RNA. We anticipate these analogs will find wide spread utility toward the goal of understanding RNA expression in complex cellular and tissue environments, even within living animals.
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Affiliation(s)
- Samantha Beasley
- Department of Pharmaceutical Sciences, University of California, Irvine. Irvine, California 92697
| | - Kim Nguyen
- Department of Pharmaceutical Sciences, University of California, Irvine. Irvine, California 92697
| | - Michael Fazio
- Department of Pharmaceutical Sciences, University of California, Irvine. Irvine, California 92697
| | - Robert C. Spitale
- Department of Pharmaceutical Sciences, University of California, Irvine. Irvine, California 92697
- Department of Chemistry, University of California, Irvine. Irvine, California 92697
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41
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Quantitative Flow Cytometry to Measure Viral Production Using Infectious Pancreatic Necrosis Virus as a Model: A Preliminary Study. APPLIED SCIENCES-BASEL 2018. [DOI: 10.3390/app8101734] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
In recent decades, flow cytometry (FCM) has become an important tool in virology, due to its applications in viral replication and viral-cell interactions, as well as its capacity to quantify proteins (qFCM). In the present study, we have designed and evaluated a qFCM procedure for the in vitro analysis and quantification of fish viral proteins, using the infectious pancreatic necrosis virus (IPNV) as a model. We have also tested its use for viral titration and adapted the MARIS (method for analysing RNA following intracellular sorting) method for simultaneous quantification of viral RNA expression in infected cells. The procedure has proved to be repeatable and reproducible to an acceptable level, although to ensure reproducibility, the repetition of standard curves is inevitable. Regarding its use for viral quantification, a direct relationship (by a second-degree polynomial regression) between viral titres and Molecules of Equivalent Soluble Fluorochrome (MESF) was observed. Finally, the results support the use of this technology, not only for virus quantification, but also to study viral replication from a quantitative approach.
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Machado L, Esteves de Lima J, Fabre O, Proux C, Legendre R, Szegedi A, Varet H, Ingerslev LR, Barrès R, Relaix F, Mourikis P. In Situ Fixation Redefines Quiescence and Early Activation of Skeletal Muscle Stem Cells. Cell Rep 2018; 21:1982-1993. [PMID: 29141227 DOI: 10.1016/j.celrep.2017.10.080] [Citation(s) in RCA: 156] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 09/13/2017] [Accepted: 10/21/2017] [Indexed: 12/12/2022] Open
Abstract
State of the art techniques have been developed to isolate and analyze cells from various tissues, aiming to capture their in vivo state. However, the majority of cell isolation protocols involve lengthy mechanical and enzymatic dissociation steps followed by flow cytometry, exposing cells to stress and disrupting their physiological niche. Focusing on adult skeletal muscle stem cells, we have developed a protocol that circumvents the impact of isolation procedures and captures cells in their native quiescent state. We show that current isolation protocols induce major transcriptional changes accompanied by specific histone modifications while having negligible effects on DNA methylation. In addition to proposing a protocol to avoid isolation-induced artifacts, our study reveals previously undetected quiescence and early activation genes of potential biological interest.
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Affiliation(s)
- Léo Machado
- Biology of the Neuromuscular System, INSERM IMRB U955-E10, UPEC, ENVA, EFS, Creteil 94000, France
| | - Joana Esteves de Lima
- Biology of the Neuromuscular System, INSERM IMRB U955-E10, UPEC, ENVA, EFS, Creteil 94000, France
| | - Odile Fabre
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Caroline Proux
- Institut Pasteur, Plate-forme Transcriptome & Epigenome, Biomics, Centre d'Innovation et Recherche Technologique (Citech), Paris, France
| | - Rachel Legendre
- Institut Pasteur, Plate-forme Transcriptome & Epigenome, Biomics, Centre d'Innovation et Recherche Technologique (Citech), Paris, France; Institut Pasteur, Hub Bioinformatique et Biostatistique, Centre de Bioinformatique, Biostatistique et Biologie Intégrative (C3BI, USR 3756 IP CNRS), Paris, France
| | - Anikó Szegedi
- Biology of the Neuromuscular System, INSERM IMRB U955-E10, UPEC, ENVA, EFS, Creteil 94000, France
| | - Hugo Varet
- Institut Pasteur, Plate-forme Transcriptome & Epigenome, Biomics, Centre d'Innovation et Recherche Technologique (Citech), Paris, France; Institut Pasteur, Hub Bioinformatique et Biostatistique, Centre de Bioinformatique, Biostatistique et Biologie Intégrative (C3BI, USR 3756 IP CNRS), Paris, France
| | - Lars Roed Ingerslev
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Romain Barrès
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Frédéric Relaix
- Biology of the Neuromuscular System, INSERM IMRB U955-E10, UPEC, ENVA, EFS, Creteil 94000, France.
| | - Philippos Mourikis
- Biology of the Neuromuscular System, INSERM IMRB U955-E10, UPEC, ENVA, EFS, Creteil 94000, France
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43
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Calcium-Binding Proteins S100A8 and S100A9: Investigation of Their Immune Regulatory Effect in Myeloid Cells. Int J Mol Sci 2018; 19:ijms19071833. [PMID: 29933628 PMCID: PMC6073713 DOI: 10.3390/ijms19071833] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 06/14/2018] [Accepted: 06/15/2018] [Indexed: 01/24/2023] Open
Abstract
High expression levels of the calcium-binding proteins S100A8 and S100A9 in myeloid cells in kidney transplant rejections are associated with a favorable outcome. Here we investigated the myeloid cell subset expressing these molecules, and their function in inflammatory reactions. Different monocyte subsets were sorted from buffy coats of healthy donors and investigated for S100A8 and S100A9 expression. To characterize S100A9high and S100A9low subsets within the CD14+ classical monocyte subset, intracellular S100A9 staining was combined with flow cytometry (FACS) and qPCR profiling. Furthermore, S100A8 and S100A9 were overexpressed by transfection in primary monocyte-derived macrophages and the THP-1 macrophage cell line to investigate the functional relevance. Expression of S100A8 and S100A9 was primarily found in classical monocytes and to a much lower extent in intermediate and non-classical monocytes. All S100A9+ cells expressed human leukocyte antigen—antigen D related (HLA-DR) on their surface. A small population (<3%) of CD14+ CD11b+ CD33+ HLA-DR− cells, characterized as myeloid derived suppressor cells (MDSCs), also expressed S100A9 to high extent. Overexpression of S100A8 and S00A9 in macrophages led to enhanced extracellular reactive oxygen species (ROS) production, as well as elevated mRNA expression of anti-inflammatory IL-10. The results suggest that the calcium-binding proteins S100A8 and S100A9 in myeloid cells have an immune regulatory effect.
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44
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Extrathymically Generated Regulatory T Cells Establish a Niche for Intestinal Border-Dwelling Bacteria and Affect Physiologic Metabolite Balance. Immunity 2018; 48:1245-1257.e9. [PMID: 29858010 DOI: 10.1016/j.immuni.2018.04.013] [Citation(s) in RCA: 87] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Revised: 03/12/2018] [Accepted: 04/12/2018] [Indexed: 02/07/2023]
Abstract
The mammalian gut microbiota provides essential metabolites to the host and promotes the differentiation and accumulation of extrathymically generated regulatory T (pTreg) cells. To explore the impact of these cells on intestinal microbial communities, we assessed the composition of the microbiota in pTreg cell-deficient and -sufficient mice. pTreg cell deficiency led to heightened type 2 immune responses triggered by microbial exposure, which disrupted the niche of border-dwelling bacteria early during colonization. Moreover, impaired pTreg cell generation led to pervasive changes in metabolite profiles, altered features of the intestinal epithelium, and reduced body weight in the presence of commensal microbes. Absence of a single species of bacteria depleted in pTreg cell-deficient animals, Mucispirillum schaedleri, partially accounted for the sequelae of pTreg cell deficiency. These observations suggest that pTreg cells modulate the metabolic function of the intestinal microbiota by restraining immune defense mechanisms that may disrupt a particular bacterial niche.
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The Epigenetic State of PRDM16-Regulated Enhancers in Radial Glia Controls Cortical Neuron Position. Neuron 2018; 98:945-962.e8. [PMID: 29779941 DOI: 10.1016/j.neuron.2018.04.033] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 03/14/2018] [Accepted: 04/24/2018] [Indexed: 01/09/2023]
Abstract
The epigenetic landscape is dynamically remodeled during neurogenesis. However, it is not understood how chromatin modifications in neural stem cells instruct the formation of complex structures in the brain. We report that the histone methyltransferase PRDM16 is required in radial glia to regulate lineage-autonomous and stage-specific gene expression programs that control number and position of upper layer cortical projection neurons. PRDM16 regulates the epigenetic state of transcriptional enhancers to activate genes involved in intermediate progenitor cell production and repress genes involved in cell migration. The histone methyltransferase domain of PRDM16 is necessary in radial glia to promote cortical neuron migration through transcriptional silencing. We show that repression of the gene encoding the E3 ubiquitin ligase PDZRN3 by PRDM16 determines the position of upper layer neurons. These findings provide insights into how epigenetic control of transcriptional enhancers in radial glial determines the organization of the mammalian cerebral cortex.
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46
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Chau KF, Shannon ML, Fame RM, Fonseca E, Mullan H, Johnson MB, Sendamarai AK, Springel MW, Laurent B, Lehtinen MK. Downregulation of ribosome biogenesis during early forebrain development. eLife 2018; 7:36998. [PMID: 29745900 PMCID: PMC5984036 DOI: 10.7554/elife.36998] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 05/09/2018] [Indexed: 12/16/2022] Open
Abstract
Forebrain precursor cells are dynamic during early brain development, yet the underlying molecular changes remain elusive. We observed major differences in transcriptional signatures of precursor cells from mouse forebrain at embryonic days E8.5 vs. E10.5 (before vs. after neural tube closure). Genes encoding protein biosynthetic machinery were strongly downregulated at E10.5. This was matched by decreases in ribosome biogenesis and protein synthesis, together with age-related changes in proteomic content of the adjacent fluids. Notably, c-MYC expression and mTOR pathway signaling were also decreased at E10.5, providing potential drivers for the effects on ribosome biogenesis and protein synthesis. Interference with c-MYC at E8.5 prematurely decreased ribosome biogenesis, while persistent c-MYC expression in cortical progenitors increased transcription of protein biosynthetic machinery and enhanced ribosome biogenesis, as well as enhanced progenitor proliferation leading to subsequent macrocephaly. These findings indicate large, coordinated changes in molecular machinery of forebrain precursors during early brain development.
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Affiliation(s)
- Kevin F Chau
- Department of Pathology, Boston Children's Hospital, Boston, United States.,Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, United States
| | - Morgan L Shannon
- Department of Pathology, Boston Children's Hospital, Boston, United States
| | - Ryann M Fame
- Department of Pathology, Boston Children's Hospital, Boston, United States
| | - Erin Fonseca
- Department of Pathology, Boston Children's Hospital, Boston, United States
| | - Hillary Mullan
- Department of Pathology, Boston Children's Hospital, Boston, United States
| | - Matthew B Johnson
- Division of Genetics, Boston Children's Hospital, Boston, United States
| | - Anoop K Sendamarai
- Department of Pathology, Boston Children's Hospital, Boston, United States
| | - Mark W Springel
- Department of Pathology, Boston Children's Hospital, Boston, United States
| | - Benoit Laurent
- Division of Newborn Medicine and Epigenetics Program, Department of Medicine, Boston Children's Hospital, Boston, United States.,Department of Cell Biology, Harvard Medical School, Boston, United States
| | - Maria K Lehtinen
- Department of Pathology, Boston Children's Hospital, Boston, United States.,Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, United States
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Quillien A, Abdalla M, Yu J, Ou J, Zhu LJ, Lawson ND. Robust Identification of Developmentally Active Endothelial Enhancers in Zebrafish Using FANS-Assisted ATAC-Seq. Cell Rep 2018; 20:709-720. [PMID: 28723572 DOI: 10.1016/j.celrep.2017.06.070] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2017] [Revised: 06/08/2017] [Accepted: 06/22/2017] [Indexed: 02/08/2023] Open
Abstract
Identification of tissue-specific and developmentally active enhancers provides insights into mechanisms that control gene expression during embryogenesis. However, robust detection of these regulatory elements remains challenging, especially in vertebrate genomes. Here, we apply fluorescent-activated nuclei sorting (FANS) followed by Assay for Transposase-Accessible Chromatin with high-throughput sequencing (ATAC-seq) to identify developmentally active endothelial enhancers in the zebrafish genome. ATAC-seq of nuclei from Tg(fli1a:egfp)y1 transgenic embryos revealed expected patterns of nucleosomal positioning at transcriptional start sites throughout the genome and association with active histone modifications. Comparison of ATAC-seq from GFP-positive and -negative nuclei identified more than 5,000 open elements specific to endothelial cells. These elements flanked genes functionally important for vascular development and that displayed endothelial-specific gene expression. Importantly, a majority of tested elements drove endothelial gene expression in zebrafish embryos. Thus, FANS-assisted ATAC-seq using transgenic zebrafish embryos provides a robust approach for genome-wide identification of active tissue-specific enhancer elements.
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Affiliation(s)
- Aurelie Quillien
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA 01605, USA
| | - Mary Abdalla
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA 01605, USA
| | - Jun Yu
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA 01605, USA
| | - Jianhong Ou
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA 01605, USA
| | - Lihua Julie Zhu
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA 01605, USA; Program in Bioinformatics and Integrative Biology, Department of Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Nathan D Lawson
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA 01605, USA.
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48
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Wang Z, Plasschaert LW, Aryal S, Renaud NA, Yang Z, Choo-Wing R, Pessotti AD, Kirkpatrick ND, Cochran NR, Carbone W, Maher R, Lindeman A, Russ C, Reece-Hoyes J, McAllister G, Hoffman GR, Roma G, Jaffe AB. TRRAP is a central regulator of human multiciliated cell formation. J Cell Biol 2018; 217:1941-1955. [PMID: 29588376 PMCID: PMC5987713 DOI: 10.1083/jcb.201706106] [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: 06/17/2017] [Revised: 02/07/2018] [Accepted: 03/08/2018] [Indexed: 12/24/2022] Open
Abstract
Multiciliated cells (MCCs) function to promote directional fluid flow across epithelial tissues. Wang et al. show that TRRAP, a component of multiple histone acetyltransferase complexes, is required for airway MCC formation and regulates a network of genes involved in MCC differentiation and function. The multiciliated cell (MCC) is an evolutionarily conserved cell type, which in vertebrates functions to promote directional fluid flow across epithelial tissues. In the conducting airway, MCCs are generated by basal stem/progenitor cells and act in concert with secretory cells to perform mucociliary clearance to expel pathogens from the lung. Studies in multiple systems, including Xenopus laevis epidermis, murine trachea, and zebrafish kidney, have uncovered a transcriptional network that regulates multiple steps of multiciliogenesis, ultimately leading to an MCC with hundreds of motile cilia extended from their apical surface, which beat in a coordinated fashion. Here, we used a pool-based short hairpin RNA screening approach and identified TRRAP, an essential component of multiple histone acetyltransferase complexes, as a central regulator of MCC formation. Using a combination of immunofluorescence, signaling pathway modulation, and genomic approaches, we show that (a) TRRAP acts downstream of the Notch2-mediated basal progenitor cell fate decision and upstream of Multicilin to control MCC differentiation; and (b) TRRAP binds to the promoters and regulates the expression of a network of genes involved in MCC differentiation and function, including several genes associated with human ciliopathies.
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Affiliation(s)
- Zhao Wang
- Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, MA
| | - Lindsey W Plasschaert
- Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, MA
| | - Shivani Aryal
- Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, MA
| | - Nicole A Renaud
- Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, MA
| | - Zinger Yang
- Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, MA
| | - Rayman Choo-Wing
- Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, MA
| | - Angelica D Pessotti
- Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, MA
| | | | - Nadire R Cochran
- Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, MA
| | - Walter Carbone
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Rob Maher
- Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, MA
| | - Alicia Lindeman
- Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, MA
| | - Carsten Russ
- Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, MA
| | - John Reece-Hoyes
- Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, MA
| | - Gregory McAllister
- Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, MA
| | - Gregory R Hoffman
- Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, MA
| | - Guglielmo Roma
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Aron B Jaffe
- Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, MA
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Lund ML, Egerod KL, Engelstoft MS, Dmytriyeva O, Theodorsson E, Patel BA, Schwartz TW. Enterochromaffin 5-HT cells - A major target for GLP-1 and gut microbial metabolites. Mol Metab 2018; 11:70-83. [PMID: 29576437 PMCID: PMC6001397 DOI: 10.1016/j.molmet.2018.03.004] [Citation(s) in RCA: 143] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 02/23/2018] [Accepted: 03/06/2018] [Indexed: 12/28/2022] Open
Abstract
Objectives 5-HT storing enterochromaffin (EC) cells are believed to respond to nutrient and gut microbial components, and 5-HT receptor-expressing afferent vagal neurons have been described to be the major sensors of nutrients in the GI-tract. However, the molecular mechanism through which EC cells sense nutrients and gut microbiota is still unclear. Methods and results TPH1, the 5-HT generating enzyme, and chromogranin A, an acidic protein responsible for secretory granule storage of 5-HT, were highly enriched in FACS-purified EC cells from both small intestine and colon using a 5-HT antibody-based method. Surprisingly, EC cells from the small intestine did not express GPCR sensors for lipid and protein metabolites, such as FFAR1, GPR119, GPBAR1 (TGR5), CaSR, and GPR142, in contrast to the neighboring GLP-1 storing enteroendocrine cell. However, the GLP-1 receptor was particularly highly expressed and enriched in EC cells as judged both by qPCR and by immunohistochemistry using a receptor antibody. GLP-1 receptor agonists robustly stimulated 5-HT secretion from intestinal preparations using both HPLC and a specific amperometric method. Colonic EC cells expressed many different types of known and potential GPCR sensors of microbial metabolites including three receptors for SCFAs, i.e. FFAR2, OLF78, and OLF558 and receptors for aromatic acids, GPR35; secondary bile acids GPBAR1; and acyl-amides and lactate, GPR132. Conclusion Nutrient metabolites apparently do not stimulate EC cells of the small intestine directly but through a paracrine mechanism involving GLP-1 secreted from neighboring enteroendocrine cells. In contrast, colonic EC cells are able to sense a multitude of different metabolites generated by the gut microbiota as well as gut hormones, including GLP-1. Pure intestinal 5-HT cells are obtained through antibody-based FACS sorting. Small intestinal 5-HT cells do not express sensors for nutrient metabolites. Colonic 5-HT cells express multiple types of receptors for gut microbial metabolites. GLP-1 stimulates 5-HT release from ex vivo intestinal preparations. GLP-1 and 5-HT act in series and synergy to control GI-tract and metabolism.
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Affiliation(s)
- Mari L Lund
- Section for Metabolic Receptology, Novo Nordisk Foundation Center for Basic Metabolite Research, Faculty of Health Sciences, University of Copenhagen, Denmark
| | - Kristoffer L Egerod
- Section for Metabolic Receptology, Novo Nordisk Foundation Center for Basic Metabolite Research, Faculty of Health Sciences, University of Copenhagen, Denmark
| | - Maja S Engelstoft
- Section for Metabolic Receptology, Novo Nordisk Foundation Center for Basic Metabolite Research, Faculty of Health Sciences, University of Copenhagen, Denmark
| | - Oksana Dmytriyeva
- Research Laboratory for Stereology and Neuroscience, Bispebjerg Hospital, Copenhagen University Hospital, Copenhagen, Denmark; Laboratory of Neural Plasticity, Institute of Neuroscience, University of Copenhagen, Copenhagen, Denmark
| | - Elvar Theodorsson
- Department of Clinical and Experimental Medicine, Linköping University, Sweden
| | - Bhavik A Patel
- School of Pharmacy and Biomolecular Sciences, University of Brighton, UK
| | - Thue W Schwartz
- Section for Metabolic Receptology, Novo Nordisk Foundation Center for Basic Metabolite Research, Faculty of Health Sciences, University of Copenhagen, Denmark; Laboratory for Molecular Pharmacology, Department for Biomedical Research, Faculty of Health Sciences, University of Copenhagen, Denmark.
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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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