1
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Hamilton MC, Fife JD, Akinci E, Yu T, Khowpinitchai B, Cha M, Barkal S, Thi TT, Yeo GH, Ramos Barroso JP, Francoeur MJ, Velimirovic M, Gifford DK, Lettre G, Yu H, Cassa CA, Sherwood RI. Systematic elucidation of genetic mechanisms underlying cholesterol uptake. Cell Genom 2023; 3:100304. [PMID: 37228746 PMCID: PMC10203276 DOI: 10.1016/j.xgen.2023.100304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 12/02/2022] [Accepted: 03/24/2023] [Indexed: 05/27/2023]
Abstract
Genetic variation contributes greatly to LDL cholesterol (LDL-C) levels and coronary artery disease risk. By combining analysis of rare coding variants from the UK Biobank and genome-scale CRISPR-Cas9 knockout and activation screening, we substantially improve the identification of genes whose disruption alters serum LDL-C levels. We identify 21 genes in which rare coding variants significantly alter LDL-C levels at least partially through altered LDL-C uptake. We use co-essentiality-based gene module analysis to show that dysfunction of the RAB10 vesicle transport pathway leads to hypercholesterolemia in humans and mice by impairing surface LDL receptor levels. Further, we demonstrate that loss of function of OTX2 leads to robust reduction in serum LDL-C levels in mice and humans by increasing cellular LDL-C uptake. Altogether, we present an integrated approach that improves our understanding of the genetic regulators of LDL-C levels and provides a roadmap for further efforts to dissect complex human disease genetics.
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Affiliation(s)
- Marisa C. Hamilton
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - James D. Fife
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Ersin Akinci
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Tian Yu
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Benyapa Khowpinitchai
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Minsun Cha
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Sammy Barkal
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Thi Tun Thi
- Precision Medicine Research Programme, Cardiovascular Disease Research Programme, and Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Grace H.T. Yeo
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Biological Engineering, Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Juan Pablo Ramos Barroso
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Matthew Jake Francoeur
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Minja Velimirovic
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - David K. Gifford
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Biological Engineering, Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Guillaume Lettre
- Montreal Heart Institute, Montréal, QC H1T 1C8, Canada
- Faculté de Médecine, Université de Montréal, Montréal, QC H3T 1J4, Canada
| | - Haojie Yu
- Precision Medicine Research Programme, Cardiovascular Disease Research Programme, and Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Christopher A. Cassa
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Richard I. Sherwood
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
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2
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Edwards-Hicks J, Apostolova P, Buescher JM, Maib H, Stanczak MA, Corrado M, Klein Geltink RI, Maccari ME, Villa M, Carrizo GE, Sanin DE, Baixauli F, Kelly B, Curtis JD, Haessler F, Patterson A, Field CS, Caputa G, Kyle RL, Soballa M, Cha M, Paul H, Martin J, Grzes KM, Flachsmann L, Mitterer M, Zhao L, Winkler F, Rafei-Shamsabadi DA, Meiss F, Bengsch B, Zeiser R, Puleston DJ, O'Sullivan D, Pearce EJ, Pearce EL. Phosphoinositide acyl chain saturation drives CD8 + effector T cell signaling and function. Nat Immunol 2023; 24:516-530. [PMID: 36732424 PMCID: PMC10908374 DOI: 10.1038/s41590-023-01419-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 01/03/2023] [Indexed: 02/04/2023]
Abstract
How lipidome changes support CD8+ effector T (Teff) cell differentiation is not well understood. Here we show that, although naive T cells are rich in polyunsaturated phosphoinositides (PIPn with 3-4 double bonds), Teff cells have unique PIPn marked by saturated fatty acyl chains (0-2 double bonds). PIPn are precursors for second messengers. Polyunsaturated phosphatidylinositol bisphosphate (PIP2) exclusively supported signaling immediately upon T cell antigen receptor activation. In late Teff cells, activity of phospholipase C-γ1, the enzyme that cleaves PIP2 into downstream mediators, waned, and saturated PIPn became essential for sustained signaling. Saturated PIP was more rapidly converted to PIP2 with subsequent recruitment of phospholipase C-γ1, and loss of saturated PIPn impaired Teff cell fitness and function, even in cells with abundant polyunsaturated PIPn. Glucose was the substrate for de novo PIPn synthesis, and was rapidly utilized for saturated PIP2 generation. Thus, separate PIPn pools with distinct acyl chain compositions and metabolic dependencies drive important signaling events to initiate and then sustain effector function during CD8+ T cell differentiation.
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Affiliation(s)
- Joy Edwards-Hicks
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Petya Apostolova
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- Bloomberg-Kimmel Institute for Cancer Immunotherapy and Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Joerg M Buescher
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Hannes Maib
- Division of Cell & Developmental Biology, School of Life Sciences, University of Dundee, Dundee, UK
| | - Michal A Stanczak
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- Bloomberg-Kimmel Institute for Cancer Immunotherapy and Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Mauro Corrado
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | | | - Maria Elena Maccari
- Center for Chronic Immunodeficiency, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Matteo Villa
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Gustavo E Carrizo
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- Bloomberg-Kimmel Institute for Cancer Immunotherapy and Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - David E Sanin
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- Bloomberg-Kimmel Institute for Cancer Immunotherapy and Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Francesc Baixauli
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Beth Kelly
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- Bloomberg-Kimmel Institute for Cancer Immunotherapy and Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jonathan D Curtis
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- Bloomberg-Kimmel Institute for Cancer Immunotherapy and Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Fabian Haessler
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Annette Patterson
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Cameron S Field
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - George Caputa
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Ryan L Kyle
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Melanie Soballa
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Minsun Cha
- Bloomberg-Kimmel Institute for Cancer Immunotherapy and Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Harry Paul
- Bloomberg-Kimmel Institute for Cancer Immunotherapy and Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jacob Martin
- Bloomberg-Kimmel Institute for Cancer Immunotherapy and Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Katarzyna M Grzes
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- Bloomberg-Kimmel Institute for Cancer Immunotherapy and Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Lea Flachsmann
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Michael Mitterer
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Liang Zhao
- Bloomberg-Kimmel Institute for Cancer Immunotherapy and Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Frances Winkler
- Clinic for Internal Medicine II, Gastroenterology, Hepatology, Endocrinology, and Infectious Diseases, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - David Ali Rafei-Shamsabadi
- Department of Dermatology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Frank Meiss
- Department of Dermatology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Bertram Bengsch
- Clinic for Internal Medicine II, Gastroenterology, Hepatology, Endocrinology, and Infectious Diseases, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Signaling Research Centers BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
| | - Robert Zeiser
- Signaling Research Centers BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
- Department of Medicine I, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Daniel J Puleston
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- Bloomberg-Kimmel Institute for Cancer Immunotherapy and Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - David O'Sullivan
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Edward J Pearce
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- Bloomberg-Kimmel Institute for Cancer Immunotherapy and Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Erika L Pearce
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.
- Bloomberg-Kimmel Institute for Cancer Immunotherapy and Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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3
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Hamilton MC, Fife JD, Akinci E, Yu T, Khowpinitchai B, Cha M, Barkal S, Thi TT, Yeo GH, Ramos Barroso JP, Jake Francoeur M, Velimirovic M, Gifford DK, Lettre G, Yu H, Cassa CA, Sherwood RI. Systematic elucidation of genetic mechanisms underlying cholesterol uptake. bioRxiv 2023:2023.01.09.500804. [PMID: 36711952 PMCID: PMC9881906 DOI: 10.1101/2023.01.09.500804] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Genetic variation contributes greatly to LDL cholesterol (LDL-C) levels and coronary artery disease risk. By combining analysis of rare coding variants from the UK Biobank and genome-scale CRISPR-Cas9 knockout and activation screening, we have substantially improved the identification of genes whose disruption alters serum LDL-C levels. We identify 21 genes in which rare coding variants significantly alter LDL-C levels at least partially through altered LDL-C uptake. We use co-essentiality-based gene module analysis to show that dysfunction of the RAB10 vesicle transport pathway leads to hypercholesterolemia in humans and mice by impairing surface LDL receptor levels. Further, we demonstrate that loss of function of OTX2 leads to robust reduction in serum LDL-C levels in mice and humans by increasing cellular LDL-C uptake. Altogether, we present an integrated approach that improves our understanding of genetic regulators of LDL-C levels and provides a roadmap for further efforts to dissect complex human disease genetics.
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Affiliation(s)
- Marisa C. Hamilton
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - James D. Fife
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Ersin Akinci
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Tian Yu
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Benyapa Khowpinitchai
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Minsun Cha
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Sammy Barkal
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Thi Tun Thi
- Precision Medicine Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Cardiovascular Disease Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Grace H.T. Yeo
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Juan Pablo Ramos Barroso
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Matthew Jake Francoeur
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Minja Velimirovic
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - David K. Gifford
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Biological Engineering, Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Guillaume Lettre
- Montreal Heart Institute, Montréal, Québec, H1T 1C8, Canada
- Faculté de Médecine, Université de Montréal, Montréal, Québec, H3T 1J4, Canada
| | - Haojie Yu
- Precision Medicine Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Cardiovascular Disease Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Address correspondence to , ,
| | - Christopher A. Cassa
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
- Address correspondence to , ,
| | - Richard I. Sherwood
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
- Address correspondence to , ,
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4
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Chang W, Jo H, Cha M, Chang J. PO-1476 Early antiarrhythmic efficacy of noninvasive cardiac radioablation for ventricular tachycardia. Radiother Oncol 2022. [DOI: 10.1016/s0167-8140(22)03440-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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5
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Akinci E, Cha M, Lin L, Yeo G, Hamilton MC, Donahue CJ, Bermudez-Cabrera HC, Zanetti LC, Chen M, Barkal SA, Khowpinitchai B, Chu N, Velimirovic M, Jodhani R, Fife JD, Sovrovic M, Cole PA, Davey RA, Cassa CA, Sherwood RI. Elucidation of remdesivir cytotoxicity pathways through genome-wide CRISPR-Cas9 screening and transcriptomics. bioRxiv 2020:2020.08.27.270819. [PMID: 32869031 PMCID: PMC7457617 DOI: 10.1101/2020.08.27.270819] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The adenosine analogue remdesivir has emerged as a front-line antiviral treatment for SARS-CoV-2, with preliminary evidence that it reduces the duration and severity of illness1.Prior clinical studies have identified adverse events1,2, and remdesivir has been shown to inhibit mitochondrial RNA polymerase in biochemical experiments7, yet little is known about the specific genetic pathways involved in cellular remdesivir metabolism and cytotoxicity. Through genome-wide CRISPR-Cas9 screening and RNA sequencing, we show that remdesivir treatment leads to a repression of mitochondrial respiratory activity, and we identify five genes whose loss significantly reduces remdesivir cytotoxicity. In particular, we show that loss of the mitochondrial nucleoside transporter SLC29A3 mitigates remdesivir toxicity without a commensurate decrease in SARS-CoV-2 antiviral potency and that the mitochondrial adenylate kinase AK2 is a remdesivir kinase required for remdesivir efficacy and toxicity. This work elucidates the cellular mechanisms of remdesivir metabolism and provides a candidate gene target to reduce remdesivir cytotoxicity.
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Affiliation(s)
- Ersin Akinci
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115
- Department of Agricultural Biotechnology, Faculty of Agriculture, Akdeniz University, Antalya, 07070, Turkey
| | - Minsun Cha
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115
| | - Lin Lin
- Hubrecht Institute, 3584 CT Utrecht, the Netherlands
| | - Grace Yeo
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Marisa C Hamilton
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115
| | - Callie J Donahue
- Department of Microbiology, National Emerging Infectious Disease Laboratories, Boston University Medical Campus, Boston, MA 02118, USA
| | - Heysol C Bermudez-Cabrera
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115
| | - Larissa C Zanetti
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115
- Hospital Israelita Albert Einstein, São Paulo, SP 05652-900, Brazil
| | - Maggie Chen
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138
| | - Sammy A Barkal
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115
| | - Benyapa Khowpinitchai
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115
| | - Nam Chu
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115
| | - Minja Velimirovic
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115
- Centre Hospitalier Universitaire de Québec Research Center-Université Laval, Québec, Québec G1V 4G2, Canada
| | - Rikita Jodhani
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115
| | - James D Fife
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115
| | - Miha Sovrovic
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115
| | - Philip A Cole
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115
| | - Robert A Davey
- Department of Microbiology, National Emerging Infectious Disease Laboratories, Boston University Medical Campus, Boston, MA 02118, USA
| | - Christopher A Cassa
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115
| | - Richard I Sherwood
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115
- Hubrecht Institute, 3584 CT Utrecht, the Netherlands
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6
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Yeo GHT, Lin L, Qi CY, Cha M, Gifford DK, Sherwood RI. A Multiplexed Barcodelet Single-Cell RNA-Seq Approach Elucidates Combinatorial Signaling Pathways that Drive ESC Differentiation. Cell Stem Cell 2020; 26:938-950.e6. [PMID: 32459995 PMCID: PMC7398619 DOI: 10.1016/j.stem.2020.04.020] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 12/10/2019] [Accepted: 04/27/2020] [Indexed: 01/08/2023]
Abstract
Empirical optimization of stem cell differentiation protocols is time consuming, is laborintensive, and typically does not comprehensively interrogate all relevant signaling pathways. Here we describe barcodelet single-cell RNA sequencing (barRNA-seq), which enables systematic exploration of cellular perturbations by tagging individual cells with RNA "barcodelets" to identify them on the basis of the treatments they receive. We apply barRNA-seq to simultaneously manipulate up to seven developmental pathways and study effects on embryonic stem cell (ESC) germ layer specification and mesodermal specification, uncovering combinatorial effects of signaling pathway activation on gene expression. We further develop a data-driven framework for identifying combinatorial signaling perturbations that drive cells toward specific fates, including several annotated in an existing scRNA-seq gastrulation atlas, and use this approach to guide ESC differentiation into a notochord-like population. We expect that barRNA-seq will have broad utility for investigating and understanding how cooperative signaling pathways drive cell fate acquisition.
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Affiliation(s)
- Grace Hui Ting Yeo
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Lin Lin
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Hubrecht Institute, 3584 CT Utrecht, the Netherlands
| | - Celine Yueyue Qi
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Minsun Cha
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - David K Gifford
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | - Richard I Sherwood
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Hubrecht Institute, 3584 CT Utrecht, the Netherlands.
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7
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Cho S, Kim T, Uhm J, Cha M, Lee J, Park J, Park J, Kang K, Shim J, Kim J, Park H, Choi E, Kim J, Lee Y, Joung B. P3762The impact of type and burden of atrial fibrillation on stroke occurrence in patients with atrial fibrillation: from a prospective cohort of atrial fibrillation patients (CODE-AF Registry). Eur Heart J 2019. [DOI: 10.1093/eurheartj/ehz745.0614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract
Background and purpose
Although several studies reported that stroke risk in patients with paroxysmal atrial fibrillation (AF) is similar to those with persistent or permanent AF, there is still controversy on the relationship of AF type and stroke occurrence. We investigated the effect of AF type on AF burden and stroke risk in patients with non-valvular AF.
Methods
Within the CODE-AF prospective, outpatient registry (COmparison study of Drugs for symptom control and complication prEvention of Atrial Fibrillation), we identified 8,883 patients ≥18 years of age with non-valvular AF and eligible follow-up visits. We compared AF burden and stroke risk among patients with 3 types of AF: paroxysmal (n=5,808) or persistent (n=2,806) or permanent (n=269).
Results
The median age of the overall population was 68.0 (interquartile range, 60.0–75.0); 36.0% were female. Patients with persistent and permanent AF were older and had higher CHA2DS2-VASc scores and anticoagulation rate than those with paroxysmal AF. Compared with permanent AF (5.2±16.4%), the arrhythmic burden of AF on 24hrs Holter monitoring was significantly lower in paroxysmal AF (2.1±7.2%, p<0.001) and persistent AF (2.0±7.5%, p<0.001). During median follow-up period of 1.38 years (interquartile range: 0.96–1.67), total 82 (0.92%) patients experienced ischemic stroke with incidence rates of 0.51, 1.04 and 1.69 events per 100 person-years for paroxysmal, persistent and permanent AF, respectively. Compared with paroxysmal AF, the risk of ischemic stroke was increased in persistent AF with clinical variable adjusted hazard ratio (aHR) of 1.94 (95% confidence intervals [CI], 1.23–3.07; P=0.005) and permanent AF with aHR of 2.64 (95% CI, 1.09–6.41; P=0.03).
AF type and HR of stroke occurrence Paroxysmal (n=5,808) Persistent (n=2,806) Permanent (n=269) Stoke events 39 37 6 Person years (PYs) 7673 3544 356 /100 PYs 0.51 1.04 1.69 HR (95% CI), p-value HR (95% CI), p-value HR (95% CI), p-value Unadjusted HR 1 (Reference) 2.05 (1.27–3.31), 0.003 3.32 (1.15–7.90), 0.02 Clinical variables adjusted HR 1 (Reference) 1.94 (1.23–3.07), 0.005 2.64 (1.09–6.41), 0.03 PYs: Person years; HR: Hazard ratio.
Conclusion
Persistent and permanent AF was associated with the increased risk of stroke than paroxysmal AF, after adjustment of clinical variables including age, sex, comorbidities and anticoagulation rate. These results suggest that AF type and burden might be related with the risk of ischemic stroke and should be considered in the stroke prevention of AF.
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Affiliation(s)
- S Cho
- Severance Hospital, Division of Cardiology, Department of Internal Medicine, Seoul, Korea (Republic of)
| | - T Kim
- Severance Hospital, Division of Cardiology, Department of Internal Medicine, Seoul, Korea (Republic of)
| | - J Uhm
- Severance Hospital, Division of Cardiology, Department of Internal Medicine, Seoul, Korea (Republic of)
| | - M Cha
- Seoul National University Hospital, Department of Internal Medicine, Seoul, Korea (Republic of)
| | - J Lee
- Kyung Hee Medical Center, Division of Cardiology, Department of Internal Medicine, Seoul, Korea (Republic of)
| | - J Park
- Ewha University, Department of Cardiology, School of Medicine, Seoul, Korea (Republic of)
| | - J Park
- Hanyang University, Department of Cardiology, Seoul, Korea (Republic of)
| | - K Kang
- Eulji University Hospital, Division of Cardiology, Deajeon, Korea (Republic of)
| | - J Shim
- Korea University, Division of Cardiology, Department of Internal Medicine, Seoul, Korea (Republic of)
| | - J Kim
- Asan Medical Center, Heart Institute, Seoul, Korea (Republic of)
| | - H Park
- Chonnam National University Hospital, Department of Cardiology, Gwangju, Korea (Republic of)
| | - E Choi
- Seoul National University Hospital, Department of Internal Medicine, Seoul, Korea (Republic of)
| | - J Kim
- Kyung Hee Medical Center, Division of Cardiology, Department of Internal Medicine, Seoul, Korea (Republic of)
| | - Y Lee
- Catholic University of Daegu, Division of Cardiology, Department of Internal Medicine, Daegu, Korea (Republic of)
| | - B Joung
- Severance Hospital, Division of Cardiology, Department of Internal Medicine, Seoul, Korea (Republic of)
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8
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Cha M, Sallem I, Jang HW, Jung IY. Role of transient receptor potential vanilloid type 1 in the trigeminal ganglion and brain stem following dental pulp inflammation. Int Endod J 2019; 53:62-71. [DOI: 10.1111/iej.13204] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 08/12/2019] [Indexed: 12/22/2022]
Affiliation(s)
- M. Cha
- Department of Physiology Oral Science Research Center Yonsei University College of Dentistry Seoul Korea
| | - I. Sallem
- Department of Conservative Dentistry and Oral Science Research Center Yonsei University College of Dentistry Seoul Korea
| | - H. W. Jang
- Department of Conservative Dentistry and Oral Science Research Center Yonsei University College of Dentistry Seoul Korea
| | - I. Y. Jung
- Department of Conservative Dentistry and Oral Science Research Center Yonsei University College of Dentistry Seoul Korea
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9
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Ko SG, Go H, Sun S, Lee S, Park W, Choi Y, Song Y, Hwang G, Kim G, Jeon C, Park J, Lee K, Cha M, Bang O, Jung H, Kim N, Shin YC. Green tea consumption, abdominal obesity as related factors of lacunar infarction in Korean women. J Nutr Health Aging 2011; 15:542-50. [PMID: 21808932 DOI: 10.1007/s12603-011-0054-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
OBJECTIVES Our purpose was to evaluate interaction of green tea consumption and abdominal obesity as related factors for lacunar infarction in Korean women. DESIGN A hospital-based, incident case-control study. SETTINGS The Prevention and Managements of Stroke in Women study. PARTICIPANTS Cases (n=233) of first incident lacunar infarction were enrolled and matched by age to stroke-free hospital controls (n=204). MEASUREMENTS The data were collected through face-to-face interviews by well trained research assistants to assess demographic, medical, lifestyle, marital status, religions status, green tea consumptions, family history of stroke, smoking status, alcohol consumption, meat and vegetable intake frequency, and past history of hypertension. Biochemical analysis, fasting blood specimens for lipid, glucose, and cholesterol level were acquired. RESULTS Compared with the non green tea consumer and obese women group, only the green tea consumption and non obese women group had a protective effect of lacunar infarction when adjusted for age, and age plus diet factors (OR, 0.23; 95% CI, 0.09, 0.59; OR, 0.21; 95% CI, 0.08, 0.56 respectively), but lost their significance after adjustment for age, diet factors, vascular risk factors and full model included atherogenic index factors (OR, 0.32; 95% CI, 0.09 to 1.01; OR, 0.49; 95% CI, 0.12, 1.89 respectively). CONCLUSIONS The interaction of green tea consumption and non obesity have reduced risk of lacunar infarction, but not after adjustment for age, diet factors, vascular risk factors and atherogenic index. Also individually green tea consumption and abdominal obesity have failed to find an independent relationship with lacunar infarction after adjustment by all risk factors. Green tea consumption and green tea consumption with non obese group seemed to have a protective effect for lacunar infarction. In the results of our study, these results still remain controversial, and then we need further and larger study to get at the root of real causal effect of both relationships.
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Affiliation(s)
- S-G Ko
- Center for Clinical Research and Genomics, Kyung Hee University, Seoul
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10
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Han M, Cha M, Kim J, Kim J. The Expression and Activation of Cytochrome P450 1A1 in Endometrial Carcinoma Cells Are Involved in Benzo[a]Pyrene-Induced Cytotoxicity. Fertil Steril 2005. [DOI: 10.1016/j.fertnstert.2005.07.1159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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11
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Yoon J, Cha M. Initiative for the terminally ill on Medicare. J Palliat Med 2005; 2:369-70. [PMID: 15859775 DOI: 10.1089/jpm.1999.2.369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- J Yoon
- Medicare Rights Center, Inc., New York, New York 10036, USA
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12
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Lee J, Kim S, Choi J, Hwang H, Cha M, Kim J. Tertiary treatment of biologically treated piggery wastewater using vibratory shear-enhanced RO membrane. Water Sci Technol 2004; 49:435-442. [PMID: 15137455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
This study presents a good example for the tertiary treatment of biologically treated piggery wastewater using vibratory shear enhanced RO membrane (VSEP RO). Through a simple process combination, utilizing Bioceramic SBR(BCS) and VSEP RO, at Gimhae plant livestock wastewater is treated excellently to meet the strict effluent standards. Application of RO membrane directly to the biologically treated effluent has been successful without any pretreatment to reduce high suspended solids. The combination of VESP UF followed by RO filtration processes produced a higher recovery rate in the 3-week pilot test.
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Affiliation(s)
- J Lee
- Environmental Vision 21 Ltd., 789-6 Yoksam-dong, Gangnam-gu, Seoul, 135-080, Korea.
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13
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Abstract
An ellipsometric method for measuring second-order cascaded phase shift is experimentally demonstrated in a KNbO(3) single crystal. We analyze the polarization state composed of the two orthogonal polarizations of the transmitted fundamental wave, one of which experiences intensity-dependent depletion and phase shift while the other does not. This method does not require a well-defined beam profile or interferometric stability.
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Abstract
I propose a method for enhancing the cascaded phase shift of the fundamental wave associated with second-harmonic generation in aperiodic quasi-phase matched (QPM) gratings. The position and length of one of the domains were varied to maximize the cascaded phase shift. A maximum enhancement of 84% in the cascaded phase shift relative to a perfectly periodic QPM grating was obtained at a moderate fundamental input intensity without initial seeding of the second-harmonic wave. All-optical intensity modulation is also proposed with another optimized aperiodic QPM grating.
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15
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McElvain J, Cha M, Yu H, Zhang N, Wudl F, Heeger A. Third harmonic generation spectrum of a degenerate ground state conjugated polymer. Direct evidence of simultaneous two- and three-photon resonance. Chem Phys Lett 1995. [DOI: 10.1016/0009-2614(95)01219-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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16
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Beljonne D, Brédas JL, Cha M, Torruellas WE, Stegeman GI, Hofstraat JW, Horsthuis WHG, Möhlmann GR. Two‐photon absorption and third‐harmonic generation of di‐alkyl‐amino‐nitro‐stilbene (DANS): A joint experimental and theoretical study. J Chem Phys 1995. [DOI: 10.1063/1.470200] [Citation(s) in RCA: 85] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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17
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Lawrence B, Torruellas WE, Cha M, Sundheimer ML, Stegeman GI, Meth J, Etemad S, Baker G. Identification and role of two-photon excited states in a pi -conjugated polymer. Phys Rev Lett 1994; 73:597-600. [PMID: 10057487 DOI: 10.1103/physrevlett.73.597] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
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18
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Cronin B, Overfelt K, Fouchereaux K, Manzvanzvike T, Cha M, Sona E. The internet and competitive intelligence: A survey of current practice. International Journal of Information Management 1994. [DOI: 10.1016/0268-4012(94)90060-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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19
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Cha M, Neher D, Embs F, Mittler-Neher S, Stegeman G. Determination of the two first non-trivial orientational order parameters in LB films of rod-like molecules by third-order sum frequency mixing. Chem Phys Lett 1993. [DOI: 10.1016/0009-2614(93)85348-r] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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20
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Guo Y, Cha M, Chao A, Yuan C. [Determination of aucubin in Plantago asiatica L., P. major L. and P. depressa Willd. by HPLC]. Zhongguo Zhong Yao Za Zhi 1991; 16:743-4, 763. [PMID: 1811672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
A HPLC method for the determination of aucubin in P. asiatica, P. major and P. depressa was established. The mobile phase is MeOH-H2O (17:83). Good in producibility and high in rate of recovery, this method provides an effective way for the study of Plantago.
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Affiliation(s)
- Y Guo
- Dalian Municipal Institute for Drug Control
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21
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Hoffman HT, Subnani M, Cha M, Kidd L, Landman J, Tooley R, Carey TE. Calcium regulation of antigen expression on normal and malignant human squamous cells in vitro. Arch Otolaryngol Head Neck Surg 1990; 116:299-303. [PMID: 2306347 DOI: 10.1001/archotol.1990.01870030063010] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
In vitro, normal keratinocytes exhibit undifferentiated morphologic features and proliferate for multiple passages in low-calcium medium (less than or equal to 0.3 mmol/L) whereas, in high-calcium medium (greater than or equal to 1.0 mmol/L), these cells assume differentiation characteristics, begin to stratify, and eventually cease proliferating. In contrast, malignant keratinocytes grow well in high-calcium medium. Expression of pemphigus vulgaris antigen, a squamous cell marker, is altered on cultured normal keratinocytes by calcium. In this study we compared the effects of calcium levels on expression of cell surface antigens by UM-SCC-38, a human squamous carcinoma cell line, and normal keratinocytes cultured from newborn foreskin. Pemphigus, pemphigoid, beta 2-microglobulin antigens, as well as the epidermal growth factor receptor and the A9 germinal epithelial cell basement membrane squamous carcinoma antigen were examined. Pemphigus antigen was strongly expressed on normal and malignant cells in high-calcium but not low-calcium medium. Calcium concentration did not affect the expression of any of the other antigens tested. Thus, although calcium induces differentiation and eventual loss of proliferative capacity in normal but not malignant keratinocytes in vitro, we were unable to demonstrate differences in pemphigus vulgaris antigen expression that might be linked to the growth inhibitory effects induced by high calcium levels in nontransformed epithelial cells in culture.
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Affiliation(s)
- H T Hoffman
- Department of Otolaryngology/Head and Neck Surgery, University of Michigan, Ann Arbor 48109-0506
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Abstract
Addition of mammalian insulin to a nutritionally rich, chemically defined culture medium affects Neurospora crassa "slime" (wall-less) cells, as indicated by enhancement of growth, extension of viability at the stationary phase of growth, alteration of morphology, and stimulation of glucose oxidation. Bovine, porcine, and recombinant human insulin had similar effects on growth and morphology, while proinsulin, reduced insulin, and several other proteins were inactive. Insulin added in the presence of excess antiinsulin antibody was without activity. Intact cells possessed high affinity insulin-binding sites, represented by a curvilinear Scatchard plot, suggesting that effects are mediated through insulin receptors on the cell surface. These findings establish a role for insulin or insulin-like molecules in regulating growth and metabolism in this fungal cell and demonstrate a close similarity to insulin effects on certain mammalian cells.
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Affiliation(s)
- M A McKenzie
- Department of Physiology and Biophysics, University of Medicine and Dentistry of New Jersey-Robert Wood Johnson Medical School, Piscataway 08854-5635
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