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Shin D, Kim CN, Ross J, Hennick KM, Wu SR, Paranjape N, Leonard R, Wang JC, Keefe MG, Pavlovic BJ, Donohue KC, Moreau C, Wigdor EM, Larson HH, Allen DE, Cadwell CR, Bhaduri A, Popova G, Bearden CE, Pollen AA, Jacquemont S, Sanders SJ, Haussler D, Wiita AP, Frost NA, Sohal VS, Nowakowski TJ. Thalamocortical organoids enable in vitro modeling of 22q11.2 microdeletion associated with neuropsychiatric disorders. Cell Stem Cell 2024; 31:421-432.e8. [PMID: 38382530 PMCID: PMC10939828 DOI: 10.1016/j.stem.2024.01.010] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 12/14/2023] [Accepted: 01/25/2024] [Indexed: 02/23/2024]
Abstract
Thalamic dysfunction has been implicated in multiple psychiatric disorders. We sought to study the mechanisms by which abnormalities emerge in the context of the 22q11.2 microdeletion, which confers significant genetic risk for psychiatric disorders. We investigated early stages of human thalamus development using human pluripotent stem cell-derived organoids and show that the 22q11.2 microdeletion underlies widespread transcriptional dysregulation associated with psychiatric disorders in thalamic neurons and glia, including elevated expression of FOXP2. Using an organoid co-culture model, we demonstrate that the 22q11.2 microdeletion mediates an overgrowth of thalamic axons in a FOXP2-dependent manner. Finally, we identify ROBO2 as a candidate molecular mediator of the effects of FOXP2 overexpression on thalamic axon overgrowth. Together, our study suggests that early steps in thalamic development are dysregulated in a model of genetic risk for schizophrenia and contribute to neural phenotypes in 22q11.2 deletion syndrome.
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Affiliation(s)
- David Shin
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94158, USA; Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA; Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Chang N Kim
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94158, USA; Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA; Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Jayden Ross
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94158, USA; Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA; Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Kelsey M Hennick
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94158, USA; Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA; Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Sih-Rong Wu
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94158, USA; Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA; Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Neha Paranjape
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94107, USA
| | - Rachel Leonard
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94158, USA; Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA; Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Jerrick C Wang
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94158, USA; Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA; Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Matthew G Keefe
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94158, USA; Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA; Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Bryan J Pavlovic
- Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Neurology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Kevin C Donohue
- Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Clara Moreau
- Sainte Justine Research Center, University of Montréal, 3175 Chemin de la Côte-Sainte-Catherine, Montréal, QC H3T 1C5, Canada; Imaging Genetics Center, Stevens Institute for Neuroimaging and Informatics, Keck School of Medicine, University of Southern California, Marina del Rey, CA, USA
| | - Emilie M Wigdor
- Institute of Developmental and Regenerative Medicine, University of Oxford, Headington, Oxford OX3 7TY, UK
| | - H Hanh Larson
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Denise E Allen
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94158, USA; Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA; Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Cathryn R Cadwell
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Pathology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Aparna Bhaduri
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Galina Popova
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94158, USA; Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA; Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Carrie E Bearden
- Integrative Center for Neurogenetics, Semel Institute for Neuroscience and Human Behavior, Departments of Psychiatry and Biobehavioral Sciences and Psychology, University of California, Los Angeles, 760 Westwood Plaza, Los Angeles, CA 90095, USA
| | - Alex A Pollen
- Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Neurology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Sebastien Jacquemont
- Sainte Justine Research Center, University of Montréal, 3175 Chemin de la Côte-Sainte-Catherine, Montréal, QC H3T 1C5, Canada
| | - Stephan J Sanders
- Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, San Francisco, CA 94158, USA; Institute of Developmental and Regenerative Medicine, University of Oxford, Headington, Oxford OX3 7TY, UK
| | - David Haussler
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95060, USA; Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA; Howard Hughes Medical Institute, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Arun P Wiita
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94107, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158
| | - Nicholas A Frost
- Department of Neurology, University of Utah, Salt Lake City, UT 84108, USA
| | - Vikaas S Sohal
- Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Tomasz J Nowakowski
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94158, USA; Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA; Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94158, USA.
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Abstract
The thalamus plays a central coordinating role in the brain. Thalamic neurons are organized into spatially distinct nuclei, but the molecular architecture of thalamic development is poorly understood, especially in humans. To begin to delineate the molecular trajectories of cell fate specification and organization in the developing human thalamus, we used single-cell and multiplexed spatial transcriptomics. We show that molecularly defined thalamic neurons differentiate in the second trimester of human development and that these neurons organize into spatially and molecularly distinct nuclei. We identified major subtypes of glutamatergic neuron subtypes that are differentially enriched in anatomically distinct nuclei and six subtypes of γ-aminobutyric acid-mediated (GABAergic) neurons that are shared and distinct across thalamic nuclei.
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Affiliation(s)
- Chang N Kim
- Department of Neurological Surgery, University of California, San Francisco, CA 94143, USA
- Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA 94143, USA
- Department of Anatomy, University of California, San Francisco, CA 94143, USA
- Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, CA 94143, USA
- Kavli Institute for Fundamental Neuroscience, University of California, San Francisco, CA 94143, USA
- Weill Institute for Neurosciences, University of California, San Francisco, CA 94158, USA
| | - David Shin
- Department of Neurological Surgery, University of California, San Francisco, CA 94143, USA
- Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA 94143, USA
- Department of Anatomy, University of California, San Francisco, CA 94143, USA
- Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, CA 94143, USA
- Kavli Institute for Fundamental Neuroscience, University of California, San Francisco, CA 94143, USA
- Weill Institute for Neurosciences, University of California, San Francisco, CA 94158, USA
| | - Albert Wang
- Department of Neurological Surgery, University of California, San Francisco, CA 94143, USA
| | - Tomasz J Nowakowski
- Department of Neurological Surgery, University of California, San Francisco, CA 94143, USA
- Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA 94143, USA
- Department of Anatomy, University of California, San Francisco, CA 94143, USA
- Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, CA 94143, USA
- Kavli Institute for Fundamental Neuroscience, University of California, San Francisco, CA 94143, USA
- Weill Institute for Neurosciences, University of California, San Francisco, CA 94158, USA
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Kim CN, Shin D, Wang A, Nowakowski TJ. Spatiotemporal molecular dynamics of the developing human thalamus. bioRxiv 2023:2023.08.21.554174. [PMID: 37662287 PMCID: PMC10473600 DOI: 10.1101/2023.08.21.554174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
The thalamus plays a central coordinating role in the brain. Thalamic neurons are organized into spatially-distinct nuclei, but the molecular architecture of thalamic development is poorly understood, especially in humans. To begin to delineate the molecular trajectories of cell fate specification and organization in the developing human thalamus, we used single cell and multiplexed spatial transcriptomics. Here we show that molecularly-defined thalamic neurons differentiate in the second trimester of human development, and that these neurons organize into spatially and molecularly distinct nuclei. We identify major subtypes of glutamatergic neuron subtypes that are differentially enriched in anatomically distinct nuclei. In addition, we identify six subtypes of GABAergic neurons that are shared and distinct across thalamic nuclei. One-Sentence Summary Single cell and spatial profiling of the developing thalamus in the first and second trimester yields molecular mechanisms of thalamic nuclei development.
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Popova G, Retallack H, Kim CN, Wang A, Shin D, DeRisi JL, Nowakowski T. Rubella virus tropism and single-cell responses in human primary tissue and microglia-containing organoids. eLife 2023; 12:RP87696. [PMID: 37470786 PMCID: PMC10370260 DOI: 10.7554/elife.87696] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [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] [Indexed: 07/21/2023] Open
Abstract
Rubella virus is an important human pathogen that can cause neurological deficits in a developing fetus when contracted during pregnancy. Despite successful vaccination programs in the Americas and many developed countries, rubella remains endemic in many regions worldwide and outbreaks occur wherever population immunity is insufficient. Intense interest since rubella virus was first isolated in 1962 has advanced our understanding of clinical outcomes after infection disrupts key processes of fetal neurodevelopment. Yet it is still largely unknown which cell types in the developing brain are targeted. We show that in human brain slices, rubella virus predominantly infects microglia. This infection occurs in a heterogeneous population but not in a highly microglia-enriched monoculture in the absence of other cell types. By using an organoid-microglia model, we further demonstrate that rubella virus infection leads to a profound interferon response in non-microglial cells, including neurons and neural progenitor cells, and this response is attenuated by the presence of microglia.
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Affiliation(s)
- Galina Popova
- Department of Neurological Surgery, University of California, San FranciscoSan FranciscoUnited States
- Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San FranciscoSan FranciscoUnited States
- Department of Anatomy, University of California, San FranciscoSan FranciscoUnited States
- Department of Psychiatry and Behavioral Sciences, University of California, San FranciscoSan FranciscoUnited States
- Weill Institute for Neurosciences, University of California, San FranciscoSan FranciscoUnited States
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
| | - Hanna Retallack
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
| | - Chang N Kim
- Department of Neurological Surgery, University of California, San FranciscoSan FranciscoUnited States
- Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San FranciscoSan FranciscoUnited States
- Department of Anatomy, University of California, San FranciscoSan FranciscoUnited States
- Department of Psychiatry and Behavioral Sciences, University of California, San FranciscoSan FranciscoUnited States
- Weill Institute for Neurosciences, University of California, San FranciscoSan FranciscoUnited States
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
| | - Albert Wang
- Department of Neurological Surgery, University of California, San FranciscoSan FranciscoUnited States
- Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San FranciscoSan FranciscoUnited States
- Department of Anatomy, University of California, San FranciscoSan FranciscoUnited States
- Department of Psychiatry and Behavioral Sciences, University of California, San FranciscoSan FranciscoUnited States
- Weill Institute for Neurosciences, University of California, San FranciscoSan FranciscoUnited States
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
| | - David Shin
- Department of Neurological Surgery, University of California, San FranciscoSan FranciscoUnited States
- Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San FranciscoSan FranciscoUnited States
- Department of Anatomy, University of California, San FranciscoSan FranciscoUnited States
- Department of Psychiatry and Behavioral Sciences, University of California, San FranciscoSan FranciscoUnited States
- Weill Institute for Neurosciences, University of California, San FranciscoSan FranciscoUnited States
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
| | - Joseph L DeRisi
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
- Chan Zuckerberg BiohubSan FranciscoUnited States
| | - Tomasz Nowakowski
- Department of Neurological Surgery, University of California, San FranciscoSan FranciscoUnited States
- Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San FranciscoSan FranciscoUnited States
- Department of Anatomy, University of California, San FranciscoSan FranciscoUnited States
- Department of Psychiatry and Behavioral Sciences, University of California, San FranciscoSan FranciscoUnited States
- Weill Institute for Neurosciences, University of California, San FranciscoSan FranciscoUnited States
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
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Wang T, Kim CN, Bakken TE, Gillentine MA, Henning B, Mao Y, Gilissen C, Nowakowski TJ, Eichler EE. Integrated gene analyses of de novo variants from 46,612 trios with autism and developmental disorders. Proc Natl Acad Sci U S A 2022; 119:e2203491119. [PMID: 36350923 PMCID: PMC9674258 DOI: 10.1073/pnas.2203491119] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [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: 03/03/2022] [Accepted: 09/28/2022] [Indexed: 08/15/2023] Open
Abstract
Most genetic studies consider autism spectrum disorder (ASD) and developmental disorder (DD) separately despite overwhelming comorbidity and shared genetic etiology. Here, we analyzed de novo variants (DNVs) from 15,560 ASD (6,557 from SPARK) and 31,052 DD trios independently and also combined as broader neurodevelopmental disorders (NDDs) using three models. We identify 615 NDD candidate genes (false discovery rate [FDR] < 0.05) supported by ≥1 models, including 138 reaching Bonferroni exome-wide significance (P < 3.64e-7) in all models. The genes group into five functional networks associating with different brain developmental lineages based on single-cell nuclei transcriptomic data. We find no evidence for ASD-specific genes in contrast to 18 genes significantly enriched for DD. There are 53 genes that show mutational bias, including enrichments for missense (n = 41) or truncating (n = 12) DNVs. We also find 10 genes with evidence of male- or female-bias enrichment, including 4 X chromosome genes with significant female burden (DDX3X, MECP2, WDR45, and HDAC8). This large-scale integrative analysis identifies candidates and functional subsets of NDD genes.
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Affiliation(s)
- Tianyun Wang
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195
- Department of Medical Genetics, Center for Medical Genetics, Peking University Health Science Center, Beijing, 100191, China
- Neuroscience Research Institute, Peking University, Key Laboratory for Neuroscience, Ministry of Education of China & National Health Commission of China, Beijing, 100191, China
| | - Chang N. Kim
- Department of Anatomy, University of California, San Francisco, CA 94143
| | | | - Madelyn A. Gillentine
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195
| | - Barbara Henning
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195
| | - Yafei Mao
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Christian Gilissen
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands
| | | | - Tomasz J. Nowakowski
- Department of Anatomy, University of California, San Francisco, CA 94143
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA 94143
- Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, CA 94143
| | - Evan E. Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195
- HHMI, University of Washington, Seattle, WA 98195
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Winkler EA, Kim CN, Ross JM, Garcia JH, Gil E, Oh I, Chen LQ, Wu D, Catapano JS, Raygor K, Narsinh K, Kim H, Weinsheimer S, Cooke DL, Walcott BP, Lawton MT, Gupta N, Zlokovic BV, Chang EF, Abla AA, Lim DA, Nowakowski TJ. A single-cell atlas of the normal and malformed human brain vasculature. Science 2022; 375:eabi7377. [PMID: 35084939 PMCID: PMC8995178 DOI: 10.1126/science.abi7377] [Citation(s) in RCA: 105] [Impact Index Per Article: 52.5] [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] [Indexed: 12/11/2022]
Abstract
Cerebrovascular diseases are a leading cause of death and neurologic disability. Further understanding of disease mechanisms and therapeutic strategies requires a deeper knowledge of cerebrovascular cells in humans. We profiled transcriptomes of 181,388 cells to define a cell atlas of the adult human cerebrovasculature, including endothelial cell molecular signatures with arteriovenous segmentation and expanded perivascular cell diversity. By leveraging this reference, we investigated cellular and molecular perturbations in brain arteriovenous malformations, which are a leading cause of stroke in young people, and identified pathologic endothelial transformations with abnormal vascular patterning and the ontology of vascularly derived inflammation. We illustrate the interplay between vascular and immune cells that contributes to brain hemorrhage and catalog opportunities for targeting angiogenic and inflammatory programs in vascular malformations.
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Affiliation(s)
- Ethan A Winkler
- Department of Neurological Surgery, University of California, San Francisco, CA, USA
- Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA, USA
- Weill Institute for Neurosciences, University of California, San Francisco, CA, USA
- Department of Neurosurgery, Barrow Neurological Institute, Phoenix, AZ, USA
| | - Chang N Kim
- Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA, USA
- Weill Institute for Neurosciences, University of California, San Francisco, CA, USA
- Department of Anatomy, University of California, San Francisco, CA, USA
- Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, CA, USA
| | - Jayden M Ross
- Department of Neurological Surgery, University of California, San Francisco, CA, USA
- Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA, USA
- Weill Institute for Neurosciences, University of California, San Francisco, CA, USA
- Department of Anatomy, University of California, San Francisco, CA, USA
- Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, CA, USA
| | - Joseph H Garcia
- Department of Neurological Surgery, University of California, San Francisco, CA, USA
| | - Eugene Gil
- Department of Neurological Surgery, University of California, San Francisco, CA, USA
- Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA, USA
| | - Irene Oh
- Rebus Biosystems, Santa Clara, CA, USA
| | | | - David Wu
- Department of Neurological Surgery, University of California, San Francisco, CA, USA
- Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA, USA
| | - Joshua S Catapano
- Department of Neurosurgery, Barrow Neurological Institute, Phoenix, AZ, USA
| | - Kunal Raygor
- Department of Neurological Surgery, University of California, San Francisco, CA, USA
| | - Kazim Narsinh
- Department of Radiology and Biomedical Imaging, University of California, San Francisco, CA, USA
| | - Helen Kim
- Center for Cerebrovascular Research, Department of Anesthesia and Perioperative Care, University of California, San Francisco, CA, USA
| | - Shantel Weinsheimer
- Center for Cerebrovascular Research, Department of Anesthesia and Perioperative Care, University of California, San Francisco, CA, USA
| | - Daniel L Cooke
- Weill Institute for Neurosciences, University of California, San Francisco, CA, USA
- Department of Radiology and Biomedical Imaging, University of California, San Francisco, CA, USA
| | - Brian P Walcott
- Department of Neurosurgery, NorthShore University HealthSystem, Evanston, IL, USA
| | - Michael T Lawton
- Department of Neurosurgery, Barrow Neurological Institute, Phoenix, AZ, USA
| | - Nalin Gupta
- Department of Neurological Surgery, University of California, San Francisco, CA, USA
| | - Berislav V Zlokovic
- Department of Physiology and Neuroscience, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Edward F Chang
- Department of Neurological Surgery, University of California, San Francisco, CA, USA
- Weill Institute for Neurosciences, University of California, San Francisco, CA, USA
| | - Adib A Abla
- Department of Neurological Surgery, University of California, San Francisco, CA, USA
- Weill Institute for Neurosciences, University of California, San Francisco, CA, USA
| | - Daniel A Lim
- Department of Neurological Surgery, University of California, San Francisco, CA, USA
- Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA, USA
- Weill Institute for Neurosciences, University of California, San Francisco, CA, USA
- San Francisco Veterans Affairs Medical Center, San Francisco, CA, USA
| | - Tomasz J Nowakowski
- Department of Neurological Surgery, University of California, San Francisco, CA, USA
- Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA, USA
- Weill Institute for Neurosciences, University of California, San Francisco, CA, USA
- Department of Anatomy, University of California, San Francisco, CA, USA
- Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
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Wu Z, Chhun BB, Popova G, Guo SM, Kim CN, Yeh LH, Nowakowski T, Zou J, Mehta SB. DynaMorph: self-supervised learning of morphodynamic states of live cells. Mol Biol Cell 2022; 33:ar59. [PMID: 35138913 PMCID: PMC9265147 DOI: 10.1091/mbc.e21-11-0561] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
A cell’s shape and motion represent fundamental aspects of cell identity and can be highly predictive of function and pathology. However, automated analysis of the morphodynamic states remains challenging for most cell types, especially primary human cells where genetic labeling may not be feasible. To enable automated and quantitative analysis of morphodynamic states, we developed DynaMorph—a computational framework that combines quantitative live cell imaging with self-supervised learning. To demonstrate the robustness and utility of this approach, we used DynaMorph to annotate morphodynamic states observed with label-free measurements of optical density and anisotropy of live microglia isolated from human brain tissue. These cells show complex behavior and have varied responses to disease-relevant perturbations. DynaMorph generates quantitative morphodynamic representations that can be used to compare the effects of the perturbations. Using DynaMorph, we identify distinct morphodynamic states of microglia polarization and detect rare transition events between states. The concepts and the methods presented here can facilitate automated discovery of functional states of diverse cellular systems.
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Affiliation(s)
- Zhenqin Wu
- Department of Chemistry, Stanford University
| | | | - Galina Popova
- Department of Anatomy, University of California, San Francisco
| | | | - Chang N Kim
- Department of Anatomy, University of California, San Francisco
| | | | | | - James Zou
- Department of Biomedical Data Science, Stanford University
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8
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Popova G, Soliman SS, Kim CN, Keefe MG, Hennick KM, Jain S, Li T, Tejera D, Shin D, Chhun BB, McGinnis CS, Speir M, Gartner ZJ, Mehta SB, Haeussler M, Hengen KB, Ransohoff RR, Piao X, Nowakowski TJ. Human microglia states are conserved across experimental models and regulate neural stem cell responses in chimeric organoids. Cell Stem Cell 2021; 28:2153-2166.e6. [PMID: 34536354 PMCID: PMC8642295 DOI: 10.1016/j.stem.2021.08.015] [Citation(s) in RCA: 82] [Impact Index Per Article: 27.3] [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: 12/21/2020] [Revised: 06/23/2021] [Accepted: 08/25/2021] [Indexed: 01/25/2023]
Abstract
Microglia are resident macrophages in the brain that emerge in early development and respond to the local environment by altering their molecular and phenotypic states. Fundamental questions about microglia diversity and function during development remain unanswered because we lack experimental strategies to interrogate their interactions with other cell types and responses to perturbations ex vivo. We compared human microglia states across culture models, including cultured primary and pluripotent stem cell-derived microglia. We developed a "report card" of gene expression signatures across these distinct models to facilitate characterization of their responses across experimental models, perturbations, and disease conditions. Xenotransplantation of human microglia into cerebral organoids allowed us to characterize key transcriptional programs of developing microglia in vitro and reveal that microglia induce transcriptional changes in neural stem cells and decrease interferon signaling response genes. Microglia additionally accelerate the emergence of synchronized oscillatory network activity in brain organoids by modulating synaptic density.
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Affiliation(s)
- Galina Popova
- Department of Anatomy, University of California, San Francisco, San Francisco, CA, USA; Department of Psychiatry, University of California, San Francisco, San Francisco, CA, USA; Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA
| | - Sarah S Soliman
- Department of Anatomy, University of California, San Francisco, San Francisco, CA, USA; Department of Psychiatry, University of California, San Francisco, San Francisco, CA, USA; Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA
| | - Chang N Kim
- Department of Anatomy, University of California, San Francisco, San Francisco, CA, USA; Department of Psychiatry, University of California, San Francisco, San Francisco, CA, USA; Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA
| | - Matthew G Keefe
- Department of Anatomy, University of California, San Francisco, San Francisco, CA, USA; Department of Psychiatry, University of California, San Francisco, San Francisco, CA, USA; Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA
| | - Kelsey M Hennick
- Department of Anatomy, University of California, San Francisco, San Francisco, CA, USA; Department of Psychiatry, University of California, San Francisco, San Francisco, CA, USA; Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA
| | - Samhita Jain
- Division of Neonatology, Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
| | - Tao Li
- Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA; Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Dario Tejera
- Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA; Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - David Shin
- Department of Anatomy, University of California, San Francisco, San Francisco, CA, USA; Department of Psychiatry, University of California, San Francisco, San Francisco, CA, USA; Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA
| | | | - Christopher S McGinnis
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA USA
| | - Matthew Speir
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Zev J Gartner
- Chan Zuckerberg Biohub, San Francisco, CA, USA; Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA USA; Center for Cellular Construction, University of California, San Francisco, San Francisco, CA, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | | | | | - Keith B Hengen
- Department of Biology, Washington University in St. Louis, St. Louis, MO, USA
| | | | - Xianhua Piao
- Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA; Division of Neonatology, Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA; Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA; Newborn Brain Research Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Tomasz J Nowakowski
- Department of Anatomy, University of California, San Francisco, San Francisco, CA, USA; Department of Psychiatry, University of California, San Francisco, San Francisco, CA, USA; Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA; Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA; Chan Zuckerberg Biohub, San Francisco, CA, USA.
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9
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Ziffra RS, Kim CN, Ross JM, Wilfert A, Turner TN, Haeussler M, Casella AM, Przytycki PF, Keough KC, Shin D, Bogdanoff D, Kreimer A, Pollard KS, Ament SA, Eichler EE, Ahituv N, Nowakowski TJ. Single-cell epigenomics reveals mechanisms of human cortical development. Nature 2021; 598:205-213. [PMID: 34616060 PMCID: PMC8494642 DOI: 10.1038/s41586-021-03209-8] [Citation(s) in RCA: 109] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Accepted: 01/07/2021] [Indexed: 12/12/2022]
Abstract
During mammalian development, differences in chromatin state coincide with cellular differentiation and reflect changes in the gene regulatory landscape1. In the developing brain, cell fate specification and topographic identity are important for defining cell identity2 and confer selective vulnerabilities to neurodevelopmental disorders3. Here, to identify cell-type-specific chromatin accessibility patterns in the developing human brain, we used a single-cell assay for transposase accessibility by sequencing (scATAC-seq) in primary tissue samples from the human forebrain. We applied unbiased analyses to identify genomic loci that undergo extensive cell-type- and brain-region-specific changes in accessibility during neurogenesis, and an integrative analysis to predict cell-type-specific candidate regulatory elements. We found that cerebral organoids recapitulate most putative cell-type-specific enhancer accessibility patterns but lack many cell-type-specific open chromatin regions that are found in vivo. Systematic comparison of chromatin accessibility across brain regions revealed unexpected diversity among neural progenitor cells in the cerebral cortex and implicated retinoic acid signalling in the specification of neuronal lineage identity in the prefrontal cortex. Together, our results reveal the important contribution of chromatin state to the emerging patterns of cell type diversity and cell fate specification and provide a blueprint for evaluating the fidelity and robustness of cerebral organoids as a model for cortical development.
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Affiliation(s)
- Ryan S Ziffra
- Department of Anatomy, University of California, San Francisco, San Francisco, CA, USA
- Department of Psychiatry, University of California, San Francisco, San Francisco, CA, USA
- Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - Chang N Kim
- Department of Anatomy, University of California, San Francisco, San Francisco, CA, USA
- Department of Psychiatry, University of California, San Francisco, San Francisco, CA, USA
- Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA
| | - Jayden M Ross
- Department of Anatomy, University of California, San Francisco, San Francisco, CA, USA
- Department of Psychiatry, University of California, San Francisco, San Francisco, CA, USA
- Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA
| | - Amy Wilfert
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Tychele N Turner
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | | | - Alex M Casella
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
- Medical Scientist Training Program, University of Maryland School of Medicine, Baltimore, MD, USA
| | | | - Kathleen C Keough
- Institute for Computational Health Sciences, University of California, San Francisco, San Francisco, CA, USA
- University of California, San Francisco, San Francisco, CA, USA
| | - David Shin
- Department of Anatomy, University of California, San Francisco, San Francisco, CA, USA
- Department of Psychiatry, University of California, San Francisco, San Francisco, CA, USA
- Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA
| | - Derek Bogdanoff
- Department of Anatomy, University of California, San Francisco, San Francisco, CA, USA
- Department of Psychiatry, University of California, San Francisco, San Francisco, CA, USA
- Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA
| | - Anat Kreimer
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
- Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, Berkeley, CA, USA
- Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Katherine S Pollard
- Gladstone Institutes, San Francisco, CA, USA
- Institute for Computational Health Sciences, University of California, San Francisco, San Francisco, CA, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
- Quantitative Biology Institute, University of California, San Francisco, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, San Francisco, CA, USA
| | - Seth A Ament
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Psychiatry, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Nadav Ahituv
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - Tomasz J Nowakowski
- Department of Anatomy, University of California, San Francisco, San Francisco, CA, USA.
- Department of Psychiatry, University of California, San Francisco, San Francisco, CA, USA.
- Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, San Francisco, CA, USA.
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10
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Sun C, Huang J, Wang Y, Zhao X, Su L, Thomas GWC, Zhao M, Zhang X, Jungreis I, Kellis M, Vicario S, Sharakhov IV, Bondarenko SM, Hasselmann M, Kim CN, Paten B, Penso-Dolfin L, Wang L, Chang Y, Gao Q, Ma L, Ma L, Zhang Z, Zhang H, Zhang H, Ruzzante L, Robertson HM, Zhu Y, Liu Y, Yang H, Ding L, Wang Q, Ma D, Xu W, Liang C, Itgen MW, Mee L, Cao G, Zhang Z, Sadd BM, Hahn MW, Schaack S, Barribeau SM, Williams PH, Waterhouse RM, Mueller RL. Genus-Wide Characterization of Bumblebee Genomes Provides Insights into Their Evolution and Variation in Ecological and Behavioral Traits. Mol Biol Evol 2021; 38:486-501. [PMID: 32946576 PMCID: PMC7826183 DOI: 10.1093/molbev/msaa240] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Bumblebees are a diverse group of globally important pollinators in natural ecosystems and for agricultural food production. With both eusocial and solitary life-cycle phases, and some social parasite species, they are especially interesting models to understand social evolution, behavior, and ecology. Reports of many species in decline point to pathogen transmission, habitat loss, pesticide usage, and global climate change, as interconnected causes. These threats to bumblebee diversity make our reliance on a handful of well-studied species for agricultural pollination particularly precarious. To broadly sample bumblebee genomic and phenotypic diversity, we de novo sequenced and assembled the genomes of 17 species, representing all 15 subgenera, producing the first genus-wide quantification of genetic and genomic variation potentially underlying key ecological and behavioral traits. The species phylogeny resolves subgenera relationships, whereas incomplete lineage sorting likely drives high levels of gene tree discordance. Five chromosome-level assemblies show a stable 18-chromosome karyotype, with major rearrangements creating 25 chromosomes in social parasites. Differential transposable element activity drives changes in genome sizes, with putative domestications of repetitive sequences influencing gene coding and regulatory potential. Dynamically evolving gene families and signatures of positive selection point to genus-wide variation in processes linked to foraging, diet and metabolism, immunity and detoxification, as well as adaptations for life at high altitudes. Our study reveals how bumblebee genes and genomes have evolved across the Bombus phylogeny and identifies variations potentially linked to key ecological and behavioral traits of these important pollinators.
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Affiliation(s)
- Cheng Sun
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jiaxing Huang
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yun Wang
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Xiaomeng Zhao
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Long Su
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Gregg W C Thomas
- Division of Biological Sciences, University of Montana, Missoula, MT
| | - Mengya Zhao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
| | - Xingtan Zhang
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Irwin Jungreis
- MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA.,Broad Institute of MIT and Harvard, Cambridge, MA
| | - Manolis Kellis
- MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA.,Broad Institute of MIT and Harvard, Cambridge, MA
| | - Saverio Vicario
- Institute of Atmospheric Pollution Research-Italian National Research Council C/O Department of Physics, University of Bari, Bari, Italy
| | - Igor V Sharakhov
- Department of Entomology, Virginia Polytechnic and State University, Blacksburg, VA.,Department of Cytology and Genetics, Tomsk State University, Tomsk, Russian Federation
| | - Semen M Bondarenko
- Department of Entomology, Virginia Polytechnic and State University, Blacksburg, VA
| | - Martin Hasselmann
- Department of Livestock Population Genomics, Institute of Animal Science, University of Hohenheim, Stuttgart, Germany
| | - Chang N Kim
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA
| | - Benedict Paten
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA
| | | | - Li Wang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yuxiao Chang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Qiang Gao
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Ling Ma
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Lina Ma
- China National Center for Bioinformation & Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Zhang Zhang
- China National Center for Bioinformation & Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Hongbo Zhang
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Huahao Zhang
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
| | - Livio Ruzzante
- Department of Ecology and Evolution, University of Lausanne, and Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Hugh M Robertson
- Department of Entomology, University of Illinois at Urbana-Champaign, Champaign, IL
| | - Yihui Zhu
- Department of Medical Microbiology and Immunology, Genome Center, and MIND Institute, University of California Davis, Davis, CA
| | - Yanjie Liu
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Huipeng Yang
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lele Ding
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Quangui Wang
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Dongna Ma
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Weilin Xu
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Cheng Liang
- Institute of Sericultural and Apiculture, Yunnan Academy of Agricultural Sciences, Mengzi, China
| | - Michael W Itgen
- Department of Biology, Colorado State University, Fort Collins, CO
| | - Lauren Mee
- Department of Ecology, Evolution and Behaviour, Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Gang Cao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
| | - Ze Zhang
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Ben M Sadd
- School of Biological Sciences, Illinois State University, Normal, IL
| | - Matthew W Hahn
- Department of Biology, Indiana University, Bloomington, IN.,Department of Computer Science, Indiana University, Bloomington, IN
| | | | - Seth M Barribeau
- Department of Ecology, Evolution and Behaviour, Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Paul H Williams
- Department of Life Sciences, Natural History Museum, London, United Kingdom
| | - Robert M Waterhouse
- Department of Ecology and Evolution, University of Lausanne, and Swiss Institute of Bioinformatics, Lausanne, Switzerland
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11
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Coll-Tané M, Gong NN, Belfer SJ, van Renssen LV, Kurtz-Nelson EC, Szuperak M, Eidhof I, van Reijmersdal B, Terwindt I, Durkin J, Verheij MMM, Kim CN, Hudac CM, Nowakowski TJ, Bernier RA, Pillen S, Earl RK, Eichler EE, Kleefstra T, Kayser MS, Schenck A. The CHD8/CHD7/Kismet family links blood-brain barrier glia and serotonin to ASD-associated sleep defects. Sci Adv 2021; 7:7/23/eabe2626. [PMID: 34088660 PMCID: PMC8177706 DOI: 10.1126/sciadv.abe2626] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 04/19/2021] [Indexed: 05/11/2023]
Abstract
Sleep disturbances in autism and neurodevelopmental disorders are common and adversely affect patient's quality of life, yet the underlying mechanisms are understudied. We found that individuals with mutations in CHD8, among the highest-confidence autism risk genes, or CHD7 suffer from disturbed sleep maintenance. These defects are recapitulated in Drosophila mutants affecting kismet, the sole CHD8/CHD7 ortholog. We show that Kismet is required in glia for early developmental and adult sleep architecture. This role localizes to subperineurial glia constituting the blood-brain barrier. We demonstrate that Kismet-related sleep disturbances are caused by high serotonin during development, paralleling a well-established but genetically unsolved autism endophenotype. Despite their developmental origin, Kismet's sleep architecture defects can be reversed in adulthood by a behavioral regime resembling human sleep restriction therapy. Our findings provide fundamental insights into glial regulation of sleep and propose a causal mechanistic link between the CHD8/CHD7/Kismet family, developmental hyperserotonemia, and autism-associated sleep disturbances.
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Affiliation(s)
- Mireia Coll-Tané
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud university medical center, 6525 GA, Nijmegen, Netherlands.
| | - Naihua N Gong
- Departments of Psychiatry and Neuroscience, Chronobiology and Sleep Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Samuel J Belfer
- Departments of Psychiatry and Neuroscience, Chronobiology and Sleep Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Lara V van Renssen
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud university medical center, 6525 GA, Nijmegen, Netherlands
| | | | - Milan Szuperak
- Departments of Psychiatry and Neuroscience, Chronobiology and Sleep Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ilse Eidhof
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud university medical center, 6525 GA, Nijmegen, Netherlands
| | - Boyd van Reijmersdal
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud university medical center, 6525 GA, Nijmegen, Netherlands
| | - Isabel Terwindt
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud university medical center, 6525 GA, Nijmegen, Netherlands
| | - Jaclyn Durkin
- Departments of Psychiatry and Neuroscience, Chronobiology and Sleep Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Michel M M Verheij
- Department of Cognitive Neuroscience, Centre for Neuroscience, Donders Institute for Brain, Cognition and Behaviour, Radboud university medical center, Nijmegen, Netherlands
| | - Chang N Kim
- Departments of Anatomy and Psychiatry, University of California, San Francisco, CA 94143 USA
| | - Caitlin M Hudac
- Center for Youth Development and Intervention and Department of Psychology, University of Alabama, Tuscaloosa, AL 35487, USA
| | - Tomasz J Nowakowski
- Departments of Anatomy and Psychiatry, University of California, San Francisco, CA 94143 USA
| | - Raphael A Bernier
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA 98185, USA
| | - Sigrid Pillen
- Center for Sleep Medicine, Kempenhaeghe, Heeze, Netherlands
| | - Rachel K Earl
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA 98185, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Tjitske Kleefstra
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud university medical center, 6525 GA, Nijmegen, Netherlands
| | - Matthew S Kayser
- Departments of Psychiatry and Neuroscience, Chronobiology and Sleep Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Annette Schenck
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud university medical center, 6525 GA, Nijmegen, Netherlands.
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12
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Sun C, Huang J, Wang Y, Zhao X, Su L, Thomas GWC, Zhao M, Zhang X, Jungreis I, Kellis M, Vicario S, Sharakhov IV, Bondarenko SM, Hasselmann M, Kim CN, Paten B, Penso-Dolfin L, Wang L, Chang Y, Gao Q, Ma L, Ma L, Zhang Z, Zhang H, Zhang H, Ruzzante L, Robertson HM, Zhu Y, Liu Y, Yang H, Ding L, Wang Q, Ma D, Xu W, Liang C, Itgen MW, Mee L, Cao G, Zhang Z, Sadd BM, Hahn MW, Schaack S, Barribeau SM, Williams PH, Waterhouse RM, Mueller RL. Erratum to: Genus-wide characterization of bumblebee genomes provides insights into their evolution and variation in ecological and behavioral traits. Mol Biol Evol 2021; 38:3031. [PMID: 34015138 PMCID: PMC8233484 DOI: 10.1093/molbev/msab100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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13
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Gillentine MA, Wang T, Hoekzema K, Rosenfeld J, Liu P, Guo H, Kim CN, De Vries BBA, Vissers LELM, Nordenskjold M, Kvarnung M, Lindstrand A, Nordgren A, Gecz J, Iascone M, Cereda A, Scatigno A, Maitz S, Zanni G, Bertini E, Zweier C, Schuhmann S, Wiesener A, Pepper M, Panjwani H, Torti E, Abid F, Anselm I, Srivastava S, Atwal P, Bacino CA, Bhat G, Cobian K, Bird LM, Friedman J, Wright MS, Callewaert B, Petit F, Mathieu S, Afenjar A, Christensen CK, White KM, Elpeleg O, Berger I, Espineli EJ, Fagerberg C, Brasch-Andersen C, Hansen LK, Feyma T, Hughes S, Thiffault I, Sullivan B, Yan S, Keller K, Keren B, Mignot C, Kooy F, Meuwissen M, Basinger A, Kukolich M, Philips M, Ortega L, Drummond-Borg M, Lauridsen M, Sorensen K, Lehman A, Lopez-Rangel E, Levy P, Lessel D, Lotze T, Madan-Khetarpal S, Sebastian J, Vento J, Vats D, Benman LM, Mckee S, Mirzaa GM, Muss C, Pappas J, Peeters H, Romano C, Elia M, Galesi O, Simon MEH, van Gassen KLI, Simpson K, Stratton R, Syed S, Thevenon J, Palafoll IV, Vitobello A, Bournez M, Faivre L, Xia K, Earl RK, Nowakowski T, Bernier RA, Eichler EE. Rare deleterious mutations of HNRNP genes result in shared neurodevelopmental disorders. Genome Med 2021; 13:63. [PMID: 33874999 PMCID: PMC8056596 DOI: 10.1186/s13073-021-00870-6] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 03/16/2021] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND With the increasing number of genomic sequencing studies, hundreds of genes have been implicated in neurodevelopmental disorders (NDDs). The rate of gene discovery far outpaces our understanding of genotype-phenotype correlations, with clinical characterization remaining a bottleneck for understanding NDDs. Most disease-associated Mendelian genes are members of gene families, and we hypothesize that those with related molecular function share clinical presentations. METHODS We tested our hypothesis by considering gene families that have multiple members with an enrichment of de novo variants among NDDs, as determined by previous meta-analyses. One of these gene families is the heterogeneous nuclear ribonucleoproteins (hnRNPs), which has 33 members, five of which have been recently identified as NDD genes (HNRNPK, HNRNPU, HNRNPH1, HNRNPH2, and HNRNPR) and two of which have significant enrichment in our previous meta-analysis of probands with NDDs (HNRNPU and SYNCRIP). Utilizing protein homology, mutation analyses, gene expression analyses, and phenotypic characterization, we provide evidence for variation in 12 HNRNP genes as candidates for NDDs. Seven are potentially novel while the remaining genes in the family likely do not significantly contribute to NDD risk. RESULTS We report 119 new NDD cases (64 de novo variants) through sequencing and international collaborations and combined with published clinical case reports. We consider 235 cases with gene-disruptive single-nucleotide variants or indels and 15 cases with small copy number variants. Three hnRNP-encoding genes reach nominal or exome-wide significance for de novo variant enrichment, while nine are candidates for pathogenic mutations. Comparison of HNRNP gene expression shows a pattern consistent with a role in cerebral cortical development with enriched expression among radial glial progenitors. Clinical assessment of probands (n = 188-221) expands the phenotypes associated with HNRNP rare variants, and phenotypes associated with variation in the HNRNP genes distinguishes them as a subgroup of NDDs. CONCLUSIONS Overall, our novel approach of exploiting gene families in NDDs identifies new HNRNP-related disorders, expands the phenotypes of known HNRNP-related disorders, strongly implicates disruption of the hnRNPs as a whole in NDDs, and supports that NDD subtypes likely have shared molecular pathogenesis. To date, this is the first study to identify novel genetic disorders based on the presence of disorders in related genes. We also perform the first phenotypic analyses focusing on related genes. Finally, we show that radial glial expression of these genes is likely critical during neurodevelopment. This is important for diagnostics, as well as developing strategies to best study these genes for the development of therapeutics.
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Affiliation(s)
- Madelyn A Gillentine
- Department of Genome Sciences, University of Washington School of Medicine, 3720 15th Ave NE S413A, Box 355065, Seattle, WA, 981095-5065, USA
| | - Tianyun Wang
- Department of Genome Sciences, University of Washington School of Medicine, 3720 15th Ave NE S413A, Box 355065, Seattle, WA, 981095-5065, USA
| | - Kendra Hoekzema
- Department of Genome Sciences, University of Washington School of Medicine, 3720 15th Ave NE S413A, Box 355065, Seattle, WA, 981095-5065, USA
| | - Jill Rosenfeld
- Baylor Genetics Laboratories, Houston, TX, USA.,Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Pengfei Liu
- Baylor Genetics Laboratories, Houston, TX, USA
| | - Hui Guo
- Department of Genome Sciences, University of Washington School of Medicine, 3720 15th Ave NE S413A, Box 355065, Seattle, WA, 981095-5065, USA.,Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Chang N Kim
- Department of Anatomy, University of California, San Francisco, CA, USA.,Department of Psychiatry, University of California, San Francisco, CA, USA.,Weill Institute for Neurosciences, University of California at San Francisco, San Francisco, CA, USA.,The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA, USA
| | - Bert B A De Vries
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Lisenka E L M Vissers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Magnus Nordenskjold
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Malin Kvarnung
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Anna Lindstrand
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Ann Nordgren
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Jozef Gecz
- School of Medicine and the Robinson Research Institute, the University of Adelaide at the Women's and Children's Hospital, Adelaide, South Australia, Australia.,Genetics and Molecular Pathology, SA Pathology, Adelaide, South Australia, Australia.,South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia
| | - Maria Iascone
- Laboratorio di Genetica Medica - ASST Papa Giovanni XXIII, Bergamo, Italy
| | - Anna Cereda
- Department of Pediatrics, ASST Papa Giovanni XXIII, Bergamo, Italy
| | - Agnese Scatigno
- Department of Pediatrics, ASST Papa Giovanni XXIII, Bergamo, Italy
| | - Silvia Maitz
- Genetic Unit, Department of Pediatrics, Fondazione MBBM S. Gerardo Hospital, Monza, Italy
| | - Ginevra Zanni
- Unit of Neuromuscular and Neurodegenerative Disorders, Department Neurosciences, Bambino Gesù Children's Hospital, IRCCS, 00146, Rome, Italy
| | - Enrico Bertini
- Unit of Neuromuscular and Neurodegenerative Disorders, Department Neurosciences, Bambino Gesù Children's Hospital, IRCCS, 00146, Rome, Italy
| | - Christiane Zweier
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Sarah Schuhmann
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Antje Wiesener
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Micah Pepper
- Center on Human Development and Disability, University of Washington, Seattle, WA, USA.,Seattle Children's Autism Center, Seattle, WA, USA
| | - Heena Panjwani
- Center on Human Development and Disability, University of Washington, Seattle, WA, USA.,Seattle Children's Autism Center, Seattle, WA, USA
| | | | - Farida Abid
- Department of Pediatrics-Neurology, Baylor College of Medicine, Houston, TX, USA.,Texas Children's Hospital, Houston, TX, USA
| | - Irina Anselm
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Siddharth Srivastava
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Paldeep Atwal
- The Atwal Clinic: Genomic & Personalized Medicine, Jacksonville, FL, USA
| | - Carlos A Bacino
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Gifty Bhat
- Department of Pediatrics, Section of Genetics, University of Illinois at Chicago, Chicago, IL, USA
| | - Katherine Cobian
- Department of Pediatrics, Section of Genetics, University of Illinois at Chicago, Chicago, IL, USA
| | - Lynne M Bird
- Department of Pediatrics, University of California San Diego, San Diego, CA, USA.,Genetics/Dysmorphology, Rady Children's Hospital San Diego, San Diego, CA, USA
| | - Jennifer Friedman
- Department of Pediatrics, University of California San Diego, San Diego, CA, USA.,Rady Children's Institute for Genomic Medicine, San Diego, CA, USA.,Department of Neurosciences, University of California San Diego, San Diego, CA, USA
| | - Meredith S Wright
- Department of Pediatrics, University of California San Diego, San Diego, CA, USA.,Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Bert Callewaert
- Department of Biomolecular Medicine, Ghent University Hospital, Ghent, Belgium
| | - Florence Petit
- Clinique de Génétique, Hôpital Jeanne de Flandre, Bâtiment Modulaire, CHU, 59037, Lille Cedex, France
| | - Sophie Mathieu
- Sorbonne Universités, Centre de Référence déficiences intellectuelles de causes rares, département de génétique et embryologie médicale, Hôpital Trousseau, AP-HP, Paris, France
| | - Alexandra Afenjar
- Sorbonne Universités, Centre de Référence déficiences intellectuelles de causes rares, département de génétique et embryologie médicale, Hôpital Trousseau, AP-HP, Paris, France
| | - Celenie K Christensen
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Kerry M White
- Department of Medical and Molecular Genetics, IU Health, Indianapolis, IN, USA
| | - Orly Elpeleg
- Department of Genetics, Hadassah, Hebrew University Medical Center, Jerusalem, Israel
| | - Itai Berger
- Pediatric Neurology, Assuta-Ashdod University Hospital, Ashdod, Israel.,Health Sciences, Ben-Gurion University of the Negev, Beersheba, Israel
| | - Edward J Espineli
- Department of Pediatrics-Neurology, Baylor College of Medicine, Houston, TX, USA.,Texas Children's Hospital, Houston, TX, USA
| | - Christina Fagerberg
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | | | | | - Timothy Feyma
- Gillette Children's Specialty Healthcare, Saint Paul, MN, USA
| | - Susan Hughes
- Division of Clinical Genetics, Children's Mercy Kansas City, Kansas City, MO, USA.,The University of Missouri-Kansas City, School of Medicine, Kansas City, MO, USA
| | - Isabelle Thiffault
- The University of Missouri-Kansas City, School of Medicine, Kansas City, MO, USA.,Children's Mercy Kansas City, Center for Pediatric Genomic Medicine, Kansas City, MO, USA
| | - Bonnie Sullivan
- Division of Clinical Genetics, Children's Mercy Kansas City, Kansas City, MO, USA
| | - Shuang Yan
- Division of Clinical Genetics, Children's Mercy Kansas City, Kansas City, MO, USA
| | - Kory Keller
- Oregon Health & Science University, Corvallis, OR, USA
| | - Boris Keren
- Department of Genetics, Hópital Pitié-Salpêtrière, Paris, France
| | - Cyril Mignot
- Department of Genetics, Hópital Pitié-Salpêtrière, Paris, France
| | - Frank Kooy
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
| | - Marije Meuwissen
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
| | - Alice Basinger
- Genetics Department, Cook Children's Hospital, Fort Worth, TX, USA
| | - Mary Kukolich
- Genetics Department, Cook Children's Hospital, Fort Worth, TX, USA
| | - Meredith Philips
- Genetics Department, Cook Children's Hospital, Fort Worth, TX, USA
| | - Lucia Ortega
- Genetics Department, Cook Children's Hospital, Fort Worth, TX, USA
| | | | - Mathilde Lauridsen
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | - Kristina Sorensen
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | - Anna Lehman
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada.,BC Children's Hospital and BC Women's Hospital, Vancouver, BC, Canada
| | | | - Elena Lopez-Rangel
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada.,Division of Developmental Pediatrics, Department of Pediatrics, BC Children's Hospital, University of British Columbia, Vancouver, BC, Canada.,Sunny Hill Health Centre for Children, Vancouver, BC, Canada
| | - Paul Levy
- Department of Pediatrics, The Children's Hospital at Montefiore, Bronx, NY, USA
| | - Davor Lessel
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Timothy Lotze
- Department of Pediatrics-Neurology, Baylor College of Medicine, Houston, TX, USA
| | - Suneeta Madan-Khetarpal
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA, USA.,UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, USA
| | - Jessica Sebastian
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Jodie Vento
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Divya Vats
- Kaiser Permanente Southern California, Los Angeles, CA, USA
| | | | - Shane Mckee
- Northern Ireland Regional Genetics Service, Belfast City Hospital, Belfast, UK
| | - Ghayda M Mirzaa
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA.,Department of Pediatrics, University of Washington, Seattle, WA, USA.,Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Candace Muss
- Al Dupont Hospital for Children, Wilmington, DE, USA
| | - John Pappas
- NYU Grossman School of Medicine, Department of Pediatrics, Clinical Genetic Services, New York, NY, USA
| | - Hilde Peeters
- Center for Human Genetics, KU Leuven and Leuven Autism Research (LAuRes), Leuven, Belgium
| | | | | | | | - Marleen E H Simon
- Department of Genetics, University Medical Center, Utrecht University, Utrecht, The Netherlands
| | - Koen L I van Gassen
- Department of Genetics, University Medical Center, Utrecht University, Utrecht, The Netherlands
| | - Kara Simpson
- Rare Disease Institute, Children's National Health System, Washington, DC, USA
| | - Robert Stratton
- Department of Genetics, Driscoll Children's Hospital, Corpus Christi, TX, USA
| | - Sabeen Syed
- Department of Pediatric Gastroenterology, Driscoll Children's Hospital, Corpus Christi, TX, USA
| | - Julien Thevenon
- Àrea de Genètica Clínica i Molecular, Hospital Vall d'Hebrón, Barcelona, Spain
| | | | - Antonio Vitobello
- UF Innovation en Diagnostic Génomique des Maladies Rares, FHU-TRANSLAD, CHU Dijon Bourgogne and INSERM UMR1231 GAD, Université de Bourgogne Franche-Comté, F-21000, Dijon, France.,INSERM UMR 1231 Génétique des Anomalies du Développement, Université Bourgogne Franche-Comté, Dijon, France
| | - Marie Bournez
- Centre de Référence Maladies Rares « déficience intellectuelle », Centre de Génétique, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France.,Centre de Référence Maladies Rares « Anomalies du Développement et Syndromes malformatifs » Université Bourgogne Franche-Comté, Dijon, France
| | - Laurence Faivre
- INSERM UMR 1231 Génétique des Anomalies du Développement, Université Bourgogne Franche-Comté, Dijon, France.,Centre de Référence Maladies Rares « Anomalies du Développement et Syndromes malformatifs » Université Bourgogne Franche-Comté, Dijon, France
| | - Kun Xia
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | | | - Rachel K Earl
- Center on Human Development and Disability, University of Washington, Seattle, WA, USA.,Seattle Children's Autism Center, Seattle, WA, USA.,Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, USA
| | - Tomasz Nowakowski
- Department of Anatomy, University of California, San Francisco, CA, USA.,Department of Psychiatry, University of California, San Francisco, CA, USA.,Weill Institute for Neurosciences, University of California at San Francisco, San Francisco, CA, USA.,The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA, USA
| | - Raphael A Bernier
- Center on Human Development and Disability, University of Washington, Seattle, WA, USA.,Seattle Children's Autism Center, Seattle, WA, USA.,Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, 3720 15th Ave NE S413A, Box 355065, Seattle, WA, 981095-5065, USA. .,Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.
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14
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Park JS, Kim NK, Kim SH, Lee KY, Lee KY, Shin JY, Kim CN, Choi GS. Multicentre study of robotic intersphincteric resection for low rectal cancer. Br J Surg 2015; 102:1567-73. [PMID: 26312601 DOI: 10.1002/bjs.9914] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Revised: 06/22/2015] [Accepted: 07/08/2015] [Indexed: 12/16/2022]
Abstract
BACKGROUND There is a lack of information regarding the oncological safety of robotic intersphincteric resection (ISR) with coloanal anastomosis. The objective of this study was to compare the long-term feasibility of robotic compared with laparoscopic ISR. METHODS Between January 2008 and May 2011, consecutive patients who underwent robotic or laparoscopic ISR with coloanal anastomosis from seven institutions were included. Propensity score analyses were performed to compare outcomes for groups in a 1 : 1 case-matched cohort. The primary endpoint was 3-year disease-free survival. RESULTS A total of 334 patients underwent ISR with coloanal anastomosis, of whom 212 matched patients (106 in each group) formed the cohort for analysis. The overall rate of conversion to open surgery was 0.9 per cent in the robotic ISR group and 1.9 per cent in the laparoscopic ISR group. Nine patients (8.5 per cent) in the laparoscopic group and three (2.8 per cent) in the robotic ISR group still had a stoma at last follow-up (P = 0.075). Total mean hospital costs were significantly higher for robotic ISR (€ 12,757 versus € 9223 for laparoscopic ISR; P = 0.037). Overall 3-year local recurrence rates were similar in the two groups (6.7 per cent for robotic and 5.7 per cent for laparoscopic resection; P = 0.935). The combined 3-year disease-free survival rates were 89.6 (95 per cent c.i. 84.1 to 95.9) and 90.5 (85.4 to 96.6) per cent respectively (P = 0.298). CONCLUSION Robotic ISR with coloanal anastomosis for rectal cancer has reasonable oncological outcomes, but is currently too expensive with no short-term advantages.
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Affiliation(s)
- J S Park
- Departments of Surgery, Kyungpook National University Medical Centre, Kyungpook National University School of Medicine, Daegu, Korea
| | - N K Kim
- Yonsei University College of Medicine, Seoul, Korea
| | - S H Kim
- Korea University Anam Hospital, Seoul, Korea
| | - K Y Lee
- Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - K Y Lee
- Kyung Hee University, Seoul, Korea
| | - J Y Shin
- Inje University Paik-Hospital, Pusan, Korea
| | - C N Kim
- Eulji University Hospital, Daejeon, Korea
| | - G-S Choi
- Departments of Surgery, Kyungpook National University Medical Centre, Kyungpook National University School of Medicine, Daegu, Korea
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15
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Kim JC, Lim SB, Yoon YS, Park IJ, Kim CW, Kim CN. Completely abdominal intersphincteric resection for lower rectal cancer: feasibility and comparison of robot-assisted and open surgery. Surg Endosc 2014; 28:2734-44. [DOI: 10.1007/s00464-014-3509-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2013] [Accepted: 03/05/2014] [Indexed: 02/06/2023]
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16
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Cho BS, Lee MS, Lee MK, Choi YJ, Kim CN, Kang YJ, Park JS, Ahn HY. Treatment guidelines for isolated dissection of the superior mesenteric artery based on follow-up CT findings. Eur J Vasc Endovasc Surg 2011; 41:780-5. [PMID: 21333559 DOI: 10.1016/j.ejvs.2010.12.022] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2010] [Accepted: 12/20/2010] [Indexed: 12/28/2022]
Abstract
OBJECTIVES The treatment guidelines for isolated superior mesenteric artery dissection (SMAD) are not well established. The purpose of this study was to report a single-centre series of SMAD and propose treatment guidelines. MATERIALS AND METHODS Between November 2004 and December 2009, 30 patients were diagnosed with SMAD. We retrospectively reviewed their medical records. RESULTS The subjects included 26 men and four women, with a mean age of 55.1 years. The chief complaint was abdominal pain in 17 patients, whereas 13 patients were asymptomatic. The mean follow-up was 38.3 months. The radiographic findings included intimal flap with a false lumen in 20 patients and intramural haematoma in 10 patients. The treatments included observation in 18 patients, anticoagulation in five patients, stenting in six patients and surgery in one patient. During follow-up (mean 15.6 months), there was no change in the computed tomography scans of seven patients, improvement was observed in four patients and complete resolution was observed in four patients. All patients, including the symptomatic patients, remained asymptomatic during follow-up. CONCLUSIONS Most patients with SMAD can be successfully managed with conservative treatment. Surgical treatment or percutaneous intervention can be reserved for patients with severe mesenteric ischaemia and those for whom the initial conservative treatment fails.
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Affiliation(s)
- B S Cho
- Department of Surgery, Eulji University School of Medicine and Eulji University Hospital, 1306 Dunsan-dong, Seo-gu, Daejeon, South Korea.
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17
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Kim HC, Kim CN, Yu CS, Roh SA, Kim JC. Methylation of the hMLH1 and hMSH2 promoter in early-onset sporadic colorectal carcinomas with microsatellite instability. Int J Colorectal Dis 2003; 18:196-202. [PMID: 12673483 DOI: 10.1007/s00384-002-0445-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/20/2002] [Indexed: 02/04/2023]
Abstract
BACKGROUND AND AIMS Microsatellite instability (MSI) occurring from defects in mismatch repair has been found to be associated with about 15% of sporadic colorectal carcinomas. This study examined the incidence of MSI in early-onset sporadic colorectal carcinomas and the role of methylation of the hMLH1 and hMSH2 promoter in sporadic colorectal carcinoma presenting with MSI. PATIENTS AND METHODS MSI in 38 early-onset and 40 late-onset sporadic colorectal carcinomas were determined as MSI-H, MSI-L, and MSS using five markers. Methylation of the promoter region in hMLH1 and hMSH2 was assessed using methylation-specific PCR (MSP). Their protein expressions were also identified on immunohistochemical staining. RESULTS MSI-H, MSI-L, and MSS were found in six (15.8%), three (7.9%), and 29 (76.3%) cases, respectively, in the early-onset group, and in one (2.5%), five (12.5%), and 34 (85%) cases in the late-onset group. Five cases (71.4%) of MSI-H and two cases (25%) of MSI-L showed methylation of the promoter region in hMLH1. No cases with methylation of the promoter region expressed the hMLH1 protein. Only one case of MSI-H showed methylation of the promoter region in hMSH2 with lack of expression of hMSH2. CONCLUSION The mutator pathway in colorectal carcinogenesis appeared more frequently in early-onset than in late-onset colorectal carcinoma. Many cases with MSI in sporadic colorectal carcinoma may be associated with methylation of the promoter in hMLH1.
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Affiliation(s)
- Hee C Kim
- Department of Surgery, University of Ulsan College of Medicine and Laboratory of Cancer Biology and Genetics, Asan Institute for Life Sciences, 388-1 Poongnap-Dong, Songpa-Ku, Seoul 138-736, Korea
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18
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Abstract
OBJECTIVES To introduce a new surgical technique for endoscopic removal of the antral portion of antrochoanal polyp (ACP) by powered instrumentation and to determine its efficacy by measures of relevant patient outcome. STUDY DESIGN Prospective study in 28 patients undergoing endoscopic sinus surgery for ACP by our surgical technique. METHODS Improvements of clinical symptoms and endoscopic and computed tomographic findings were evaluated postoperatively with a follow-up period ranging from 12 to 52 months. All symptom scores on a 100-mm visual analogue scale before operation were compared with those at the last visit after operation. Postoperative endoscopic and computed tomographic findings were graded using a three-point scale ranging from 0 to 2. In surgical technique, the antral portion of ACP was identified through the enlarged ostium under intranasal endoscopy and removed by a blade of powered instrumentation that was inserted through the canine fossa. RESULTS Symptom scores were all significantly reduced postoperatively. All but one patient showed improvement in clinical symptoms and endoscopic and computed tomographic findings during the follow-up period. There were no major complications specific to this technique. CONCLUSION Our technique provides an attractive alternative to other methods for removing the antral portion of an ACP and is associated with excellent outcomes and minimal morbidities.
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Affiliation(s)
- S K Hong
- Department of Otolaryngology, College of Medicine, Ewha Women's University Mokdong Hospital, Seoul, Korea.
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19
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Pullium JK, Adams DR, Jackson E, Kim CN, Smith DK, Janssen R, Gould K, Folks TM, Butera S, Otten RA. Pig-tailed macaques infected with human immunodeficiency virus (HIV) type 2GB122 or simian/HIV89.6p express virus in semen during primary infection: new model for genital tract shedding and transmission. J Infect Dis 2001; 183:1023-30. [PMID: 11237826 DOI: 10.1086/319293] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2000] [Revised: 12/18/2000] [Indexed: 11/03/2022] Open
Abstract
Characterizing human immunodeficiency virus (HIV) expression in semen during primary infection remains essential to understanding the risk of sexual transmission. This investigation represents the first systematic evaluation of male genital tract shedding to use a nonhuman primate model, including the impact of exposure route and viral virulence. Male macaques were inoculated with either a chronic disease-causing virus (HIV-2(GB122); n=4 intravenous; n=4 intrarectal) or an acutely pathogenic simian/HIV strain (SHIV(89.6P); n=2 intravenous). All macaques were systemically infected, and seminal plasma virion-associated RNA (vRNA) levels were approximately 10-fold lower than those in blood. In HIV-2(GB122) infection, seminal virus was delayed by 1-2 weeks compared with that in blood. Intrarectal inoculation resulted in a shorter duration of seminal vRNA expression and intermittent seminal cell provirus. No delays, higher peaks ( approximately 50-fold), or longer durations in seminal virus expression were noted for SHIV(89.6P) infection. This novel model definitively establishes that virus dissemination results in early peak seminal levels and provides a basis for evaluating interventions targeting male genital tract expression.
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Affiliation(s)
- J K Pullium
- HIV/AIDS and Retrovirology Branch, National Center for HIV, STD, and TB Prevention, Centers for Disease Control and Prevention, and Department of Pathology and Laboratory Medicine, Emory University, Atlanta, Georgia, USA
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20
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Otten RA, Smith DK, Adams DR, Pullium JK, Jackson E, Kim CN, Jaffe H, Janssen R, Butera S, Folks TM. Efficacy of postexposure prophylaxis after intravaginal exposure of pig-tailed macaques to a human-derived retrovirus (human immunodeficiency virus type 2). J Virol 2000; 74:9771-5. [PMID: 11000253 PMCID: PMC112413 DOI: 10.1128/jvi.74.20.9771-9775.2000] [Citation(s) in RCA: 160] [Impact Index Per Article: 6.7] [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: 11/20/2022] Open
Abstract
Postexposure prophylaxis (PEP) after intravaginal exposure to human immunodeficiency virus (HIV) was investigated using the HIV type 2 (HIV-2)/pig-tailed macaque transmission model. PEP for 28 days with the reverse transcriptase inhibitor (R)-9-(2-phosphonylmethoxypropyl)adenine (PMPA; tenofovir) was initiated 12 to 72 h following HIV-2 exposure. Systemic infection was not evident in the 12- and 36-h groups, as defined by plasma viremia, cell-associated provirus, antibody responses, and lymph node virus. Breakthrough infection in the 72-h group was detected at week 16 post-virus exposure. These results demonstrate for the first time using a vaginal transmission model that early intervention after high-risk sexual exposures may prevent infection.
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Affiliation(s)
- R A Otten
- Division of AIDS, STD, and TB Laboratory Research, National Center for Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA.
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Fang G, Kim CN, Perkins CL, Ramadevi N, Winton E, Wittmann S, Bhalla KN. CGP57148B (STI-571) induces differentiation and apoptosis and sensitizes Bcr-Abl-positive human leukemia cells to apoptosis due to antileukemic drugs. Blood 2000; 96:2246-53. [PMID: 10979973] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023] Open
Abstract
The differentiation and apoptosis-sensitizing effects of the Bcr-Abl-specific tyrosine kinase inhibitor CGP57148B, also known as STI-571, were determined in human Bcr-Abl-positive HL-60/Bcr-Abl and K562 cells. First, the results demonstrate that the ectopic expression of the p185 Bcr-Abl fusion protein induced hemoglobin in the acute myeloid leukemia (AML) HL-60 cells. Exposure to low-dose cytosine arabinoside (Ara-C; 10 nmol/L) increased hemoglobin levels in HL-60/Bcr-Abl and in the chronic myeloid leukemia (CML) blast crisis K562 cells, which express the p210 Bcr-Abl protein. As compared with HL-60/neo, HL-60/Bcr-Abl and K562 cells were resistant to apoptosis induced by Ara-C, doxorubicin, or tumor necrosis factor-alpha (TNF-alpha), which was associated with reduced processing of caspase-8 and Bid protein and decreased cytosolic accumulation of cytochrome c (cyt c). Exposure to CGP57148B alone increased hemoglobin levels and CD11b expression and induced apoptosis of HL-60/Bcr-Abl and K562 cells. CGP57148B treatment down-regulated antiapoptotic XIAP, cIAP1, and Bcl-x(L), without affecting Bcl-2, Bax, Apaf-1, Fas (CD95), Fas ligand, Abl, and Bcr-Abl levels. CGP57148B also inhibited constitutively active Akt kinase and NFkappaB in Bcr-Abl-positive cells. Attenuation of NFkappaB activity by ectopic expression of transdominant repressor of IkappaB sensitized HL-60/Bcr-Abl and K562 cells to TNF-alpha but not to apoptosis induced by Ara-C or doxorubicin. Importantly, cotreatment with CGP57148B significantly increased Ara-C- or doxorubicin-induced apoptosis of HL-60/Bcr-Abl and K562 cells. This was associated with greater cytosolic accumulation of cyt c and PARP cleavage activity of caspase-3. These in vitro data indicate that combinations of CGP57148B and antileukemic drugs such as Ara-C may have improved in vivo efficacy against Bcr-Abl-positive acute leukemia.
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Affiliation(s)
- G Fang
- H. Lee Moffitt Cancer Center and Research Institute, University of South Florida, Tampa, FL, USA
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22
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Roh J, Park YJ, Kim CN, Lim NG, Lee SH, Song JS, Won JU, Talaska G. Effect of temperature on the breakthrough of a charcoal tube during vinyl chloride monomer sampling. AIHAJ 2000; 61:405-9. [PMID: 10885892 DOI: 10.1080/15298660008984551] [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] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/14/2023]
Abstract
This study evaluated the effects of temperature on breakthrough of two standard collection media at various concentrations during vinyl chloride monomer (VCM) sampling. The National Institute for Occupational Safety and Health (NIOSH) and Occupational Safety and Health Administration (OSHA) methods were evaluated. To determine whether breakthrough of VCM would occur at the extremes of exposure and temperature that might be encountered in some workplaces, air samples containing 4 ppm (10.24 mg/m3), 8 ppm (20.45 mg/m3), 16 ppm (40.98 mg/m3), and 32 ppm (81.80 mg/m3) of VCM were collected at temperatures of 4, 22, and 40 degrees C. Five liters of air was sampled at the rate of 0.05 L/min for 100 min using the activated charcoal tube recommended by NIOSH. A second tube was added to the sampling train to collect any VCM that might not have been absorbed in the first tube. To collect VCM air samples by the OSHA method, two carbon molecular sieve tubes were connected serially and 3 L of air was sampled at the rate of 0.05 L/min for 60 min. A gas chromatograph with a flame ionization detector and ultra 2 capillary column was used to analyze VCM. Significant breakthrough was found when sampling at higher temperatures with the NIOSH method. No breakthrough was found when samples were collected using the OSHA media at different temperatures and concentrations. Therefore, under hot ambient conditions (>22 degrees C), the possibility of breakthrough should be considered when sampling VCM by the NIOSH method.
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Affiliation(s)
- J Roh
- Institute for Occupational Health, Yonsei University College of Medicine, Seoul, Korea
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23
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Abstract
OBJECTIVE Hypertensive patients having higher baseline peripheral resistance and sympathetic tone than normotensive patients may have aberrant responses to hemorrhage. In an attempt to further characterize this clinical observation, the authors compared the hemodynamic and metabolic responses to hemorrhage between spontaneously hypertensive rats (SHR) and normotensive rats (NTR). METHODS Twenty adult rats (10 NTR and 10 SHR) were anesthetized with althesin via the intraperitoneal route. Femoral arteries were cannulated by cutdown. Twelve (6 SHR and 6 NTR) rats underwent controlled catheter hemorrhage of 25% of their total blood volumes. Eight rats (4 SHR and 4 NTR) served as nonhemorrhage controls. Mean arterial pressure (MAP) and base excess (BE) were measured prehemorrhage and then every 15 minutes for the next 120 minutes. Data were reported as mean +/- standard error of the mean (SEM). Group comparisons were analyzed by ANOVA with repeated values post-hoc by Bonferroni. Statistical significance was defined by an alpha = 0.05. RESULTS Immediately after hemorrhage, the SHR group experienced a significantly (p < 0.001) greater drop in MAP of 70 +/- 4% in the SHR vs 40 +/- 6% in the NTR. Blood pressure in the NTR returned to control values 15 minutes after hemorrhage, but the SHR remained relatively hypotensive for the entire length of the experiment. Base excess in the SHR decreased significantly (p < 0.004) by 8.2 +/- 2 mmol/L from control values, as compared with no changes in BE for the NTR. CONCLUSIONS The authors observed significant differences in the response to hemorrhage between hypertensive and normotensive rats. Hypertensive rats experienced a more profound hemorrhagic shock insult than normotensives for the same degree of blood loss.
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Affiliation(s)
- R Sinert
- Department of Emergency Medicine, State University of New York Health Science Center at Brooklyn, 11203, USA.
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Perkins CL, Fang G, Kim CN, Bhalla KN. The role of Apaf-1, caspase-9, and bid proteins in etoposide- or paclitaxel-induced mitochondrial events during apoptosis. Cancer Res 2000; 60:1645-53. [PMID: 10749135] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Ectopic overexpression of Apaf-1 (2.5-fold) in human acute myelogenous leukemia HL-60 cells (HL-60/Apaf-1 cells) induced apoptosis and sensitized HL-60/Apaf-1 cells to etoposide- and paclitaxel-induced apoptosis (C. Perkins et al., Cancer Res., 58: 4561-4566, 1998). In this report, we demonstrate that in HL-60/Apaf-1 cells, the activity of caspase-9 and -3 induced by Apaf-1 overexpression was associated with a significant increase (5-fold) in the cytosolic accumulation of cytochrome c (cyt c), loss of mitochondrial membrane potential (deltapsim), and an increase in the reactive oxygen species. These were also associated with the processing of procaspase-8 and Bid (cytosolic, proapoptotic BH3 domain containing protein). Transient transfection of Apaf-1 into the Apaf-1-containing mouse embryogenic fibroblasts (MEFs; Apaf-1+/- MEFs) or Apaf-1-/- MEFs also induced the processing of procaspase-9 and procaspase-8, Bid cleavage, and apoptosis. These events were secondary to the activity of the downstream caspases induced by Apaf-1. This conclusion is supported by the observation that in HL-60/Apaf-1 cells, ectopic expression of dominant negative caspase-9, its inhibitory short isoform caspase-9b, or XIAP or treatment with the caspase inhibitor zVAD (50 microM) inhibited Apaf-1-induced caspase-8 and Bid cleavage, mitochondrial deltapsim, release of cyt c, and apoptosis. In contrast, a transient transfection of dominant negative caspase-8 or CrmA or exposure to caspase-8 inhibitor zIETD-fmk inhibited the processing of procaspase-8 and Bid but did not inhibit the cytosolic accumulation of cyt c in either the untreated HL-60/Apaf-1 cells or the etoposide-treated HL-60/Apaf-1 and HL-60/neo cells. These results indicate that Apaf-1 overexpression lowers the apoptotic threshold by activating caspase-9 and caspase-3. This triggers the mitochondrial deltapsim and cyt c release into the cytosol through a predominant mechanism other than cleavage of caspase-8 and/or Bid. This mechanism may involve a cytosolic mitochondrial permeability transition factor, which may be processed and activated by the downstream effector caspases, thereby completing an amplifying feedback loop, which triggers the mitochondrial events during apoptosis.
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Affiliation(s)
- C L Perkins
- Division of Clinical and Translational Research, Sylvester Comprehensive Cancer Center, University of Miami School of Medicine, Florida 33136, USA
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Perkins C, Kim CN, Fang G, Bhalla KN. Arsenic induces apoptosis of multidrug-resistant human myeloid leukemia cells that express Bcr-Abl or overexpress MDR, MRP, Bcl-2, or Bcl-x(L). Blood 2000; 95:1014-22. [PMID: 10648417] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023] Open
Abstract
We investigated the in vitro growth inhibitory and apoptotic effects of clinically achievable concentrations of As(2)O(3) (0.5 to 2.0 micromol/L) against human myeloid leukemia cells known to be resistant to a number of apoptotic stimuli. These included chronic myelocytic leukemia (CML) blast crisis K562 and HL-60/Bcr-Abl cells, which contain p210 and p185 Bcr-Abl, respectively, and HL-60 cell types that overexpress Bcl-2 (HL-60/Bcl-2), Bcl-x(L) (HL-60/Bcl-x(L)), MDR (HL-60/VCR), or MRP (HL-60/AR) protein. The growth-inhibitory IC(50) values for As(2)O(3) treatment for 7 days against all these cell types ranged from 0.8 to 1.5 micromol/L. Exposure to 2 micromol/L As(2)O(3) for 7 days induced apoptosis of all cell types, including HL-60/Bcr-Abl and K562 cells. This was associated with the cytosolic accumulation of cyt c and preapoptotic mitochondrial events, such as the loss of inner membrane potential (DeltaPsim) and the increase in reactive oxygen species (ROS). Treatment with As(2)O(3) (2 micromol/L) generated the activities of caspases, which produced the cleavage of the BH3 domain containing proapoptotic Bid protein and poly (ADP-ribose) polymerase. Significantly, As(2)O(3)-induced apoptosis of HL-60/Bcr-Abl and K562 cells was associated with a decline in Bcr-Abl protein levels, without any significant alterations in the levels of Bcl-x(L), Bax, Apaf-1, Fas, and FasL. Although As(2)O(3 )treatment caused a marked increase in the expression of the myeloid differentiation marker CD11b, it did not affect Hb levels in HL-60/Bcr-Abl, K562, or HL-60/neo cells. However, in these cells, As(2)O(3 )potently induced hyper-acetylation of the histones H3 and H4. These findings characterize As(2)O(3) as a growth inhibiting and apoptosis-inducing agent against a variety of myeloid leukemia cells resistant to multiple apoptotic stimuli.
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MESH Headings
- ATP Binding Cassette Transporter, Subfamily B, Member 1/biosynthesis
- ATP Binding Cassette Transporter, Subfamily B, Member 1/genetics
- ATP-Binding Cassette Transporters/biosynthesis
- ATP-Binding Cassette Transporters/genetics
- Acetylation/drug effects
- Antineoplastic Agents/pharmacology
- Apoptosis/drug effects
- Apoptotic Protease-Activating Factor 1
- Arsenic Trioxide
- Arsenicals/pharmacology
- Caspases/metabolism
- Cytochrome c Group/metabolism
- Cytosol/metabolism
- Drug Resistance, Multiple
- Drug Resistance, Neoplasm
- Fas Ligand Protein
- Fusion Proteins, bcr-abl/biosynthesis
- Fusion Proteins, bcr-abl/genetics
- Gene Expression Regulation, Leukemic
- Genes, bcl-2
- HL-60 Cells/drug effects
- Histones/metabolism
- Humans
- Immunophenotyping
- K562 Cells/drug effects
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/pathology
- Macrophage-1 Antigen/biosynthesis
- Macrophage-1 Antigen/genetics
- Membrane Glycoproteins/biosynthesis
- Membrane Glycoproteins/genetics
- Mitochondria/metabolism
- Multidrug Resistance-Associated Proteins
- Neoplasm Proteins/biosynthesis
- Neoplasm Proteins/genetics
- Oxides/pharmacology
- Protein Biosynthesis
- Protein Processing, Post-Translational/drug effects
- Proteins/genetics
- Proto-Oncogene Proteins/biosynthesis
- Proto-Oncogene Proteins/genetics
- Proto-Oncogene Proteins c-bcl-2/biosynthesis
- Proto-Oncogene Proteins c-bcl-2/genetics
- bcl-2-Associated X Protein
- bcl-X Protein
- fas Receptor/biosynthesis
- fas Receptor/genetics
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Affiliation(s)
- C Perkins
- Division of Clinical and Translational Research, Sylvester Comprehensive Cancer Center, University of Miami School of Medicine, Miami, FL 33136, USA
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26
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Chung KS, Kim CN, Namgoong K. Evaluation of the Petrifilm rapid coliform count plate method for coliform enumeration from surimi-based imitation crab slurry. J Food Prot 2000; 63:123-5. [PMID: 10643782 DOI: 10.4315/0362-028x-63.1.123] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [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: 11/11/2022]
Abstract
The 3M Petrifilm rapid coliform count (RCC) plate method was compared with two conventional methods, namely violet red bile agar (VRBA) and desoxycholate lactose agar (DLA), for enumerating coliforms. The VRBA plating method is a reference method in the Bacteriological Analytical Manual and the DLA plating method is the method recommended by the Food Sanitation Law of Korea for enumeration of coliforms. Serratia sp., a coliform that was isolated from frozen surimi, was incubated in surimi-based imitation crab (SBIC) slurries and enumerated on the Petrifilm RCC, VRBA, and DLA plates. Results from the Petrifilm RCC plate were not significantly different from results from VRBA or DLA plates at P < 0.05 level. The correlation coefficient for Petrifilm RCC plates versus the VRBA method and for Petrifilm RCC plates versus the DLA method were 0.994 and 0.996, respectively. With the Petrifilm RCC plate method, we were able to estimate presumptive coliforms (except Serratia sp.) after 14 h and to enumerate confirmed coliforms (including Serratia sp.) after 24 h.
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Affiliation(s)
- K S Chung
- Department of Biological Resources and Technology, Yonsei University, Wonju, Kangwon, Republic of Korea.
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27
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Kim CN, Bhalla K, Kreitman RJ, Willingham MC, Hall P, Tagge EP, Jia T, Frankel AE. Diphtheria toxin fused to granulocyte-macrophage colony-stimulating factor and Ara-C exert synergistic toxicity against human AML HL-60 cells. Leuk Res 1999; 23:527-38. [PMID: 10374846 DOI: 10.1016/s0145-2126(99)00039-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [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] [Indexed: 11/15/2022]
Abstract
Human granulocyte-macrophage colony-stimulating factor fused to truncated diphtheria toxin (DT388-GM-CSF) sensitized wild-type and Bcl2-overexpressing HL60 human leukemia cells to intoxication by Ara-C based on proliferation and clonogenic assays. The toxin/drug combination showed dramatic synergistic toxicity with combination indices of < 0.1. Synergy was not seen with two other protein synthesis inhibiting drugs--ricin and cycloheximide nor with GMCSF alone. No changes in Ara-C incorporation into cellular DNA or cell cycle occupancy were seen. As compared to exposure to DT388-GM-CSF or Ara-C alone, co-treatment produced significant increases in cytosolic accumulation of cytochrome c, a higher percentage of cells with loss of mitochondrial membrane potential and an increase in reactive oxygen species and morphologic changes of apoptosis, and a greater induction of poly(ADP-ribose) polymerase (PARP) and DNA fragmentation factor 45 (DFF45) cleavage activities of caspase 3. Co-treatment did not significantly alter Bcl2, Bcl-xL, Bax or Fas receptor (FasR), but modestly increased Fas ligand (FasL) protein. These finding suggest that co-treatment with DT388-GM-CSF may lead to a lowered apoptotic threshold and clonogenic survival of human AML blasts due to Ara-C. These observations also suggest that clinical trials of combination therapy may be warranted in patients with AML.
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Affiliation(s)
- C N Kim
- Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
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28
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Roh J, Kim CN, Lim NG, Chang JH, Cho YB. Simultaneous analysis of urinary 2-thiothiazolidine-4-carboxylic acid and thiocarbamide as a biological exposure index for carbon disulfide exposure. Yonsei Med J 1999; 40:265-72. [PMID: 10412339 DOI: 10.3349/ymj.1999.40.3.265] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
The objectives of this study were to develop optimal analytic methods for detecting urinary 2-thiothiazolidine-4-carboxylic acid (TTCA) and thiocarbamide simultaneously and to evaluate the usefulness of these metabolites to a biological exposure index (BEI) for carbon disulfide (CS2) exposure. For this experiment, synthesized TTCA and thiocarbamide were used. The synthesized TTCA was identified by infrared spectrophotometer, nuclear magnetic resonance spectrometer and thin layer chromatography. The recovery rates of both metabolites were calculated to find the optimum analytical method. The amounts of urinary TTCA and thiocarbamide were measured by using an ultraviolet detector connected to high performance liquid chromatography (HPLC) after the administration of CS2 (350, 700 mg/kg) into Sprague-Dawley rats intraperitoneally. The maximum absorbance wave lengths for TTCA and thiocarbamide were 272 and 236 nm, respectively. Ethyl acetate extraction with NaCl as a salting-out reagent was used as a simultaneous extraction method for these metabolites. HPLC conditions for these metabolites included using a NH2 column, 50 mM KH2PO4: acetonitrile (85:15) and pH 3. Excreted amounts of urinary TTCA and thiocarbamide were increased significantly following CS2 administration. TTCA, which was already adopted as a BEI for CS2 by the American Conference of Governmental Industrial Hygienists (ACGIH), seems to be a more useful BEI for CS2 exposure than thiocarbamide. However further studies are needed to increase analytical efficiency before thiocarbamide can be adopted as a BEI and to apply this analytic method for simultaneous analysis of these metabolites in workers exposed to CS2.
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Affiliation(s)
- J Roh
- Institute for Occupational Health, Yonsei University College of Medicine, Seoul, Korea.
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Burri SH, Kim CN, Fang G, Chang BS, Perkins C, Harris W, Davis LW, Thompson CB, Bhalla KN. 'Loop' domain deletional mutant of Bcl-xL is as effective as p29Bcl-xL in inhibiting radiation-induced cytosolic accumulation of cytochrome c (cyt c), caspase-3 activity, and apoptosis. Int J Radiat Oncol Biol Phys 1999; 43:423-30. [PMID: 10030271 DOI: 10.1016/s0360-3016(98)00385-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [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
PURPOSE/OBJECTIVE To investigate the effect of the enforced expression of p29Bcl-xL or its loop deletional mutant, p18Bcl-xLdelta, on irradiation-induced apoptosis and cell-cycle distribution of HL-60 cells. MATERIALS & METHODS We compared the irradiation-induced molecular cascade of apoptosis in control human AML HL-60/neo versus Bcl-xL overexpressing (approximately 8-fold) (HL-60/Bcl-xL) and HL-60/Bcl-XLdelta cells that express the loop domain deletional mutant construct (delta26-83 AA) of Bcl-xL. The three cell lines were irradiated with 6MV photons to varying doses up to 20 Gy. Following this, cytosolic cyt c levels, caspase-3 activity, and the Bcl-2 family of proteins were evaluated utilizing Western blot analysis (whole cell lysate or cytosolic S-100 fraction). Apoptosis was assessed by internucleosomal DNA fragmentation, Annexin-V staining and FACS analysis, as well as by morphologic criteria. The cell-cycle effects of radiation were analyzed by flow cytometry. RESULTS Eight hours following irradiation (12 Gy) of HL-60/neo cells, a marked increase (approximately 8-fold) in the cytosolic accumulation of cyt c in the S-100 fraction was observed. This was associated with the cleavage of caspase-3, as well as the generation of its poly (ADP-ribose) polymerase (PARP) and DFF (DNA fragmentation factor)-45 cleavage activity. Twenty-four to forty-eight hours after irradiation, internucleosomal DNA fragmentation and positive Annexin-V staining (32.3+/-3.3%) was detected in HL-60/neo cells. In contrast, in both HL-60/Bcl-xL and HL-60/Bcl-xLdelta cells, a significantly lower percentage of apoptotic cells (p<0.05) were detected and internucleosomal DNA fragmentation was not induced. Following irradiation, Western analysis neither demonstrated any significant alteration in Bcl-2, p29Bcl-xL, p18Bcl-xLdelta, or Bax; nor induced CD95 (Fas receptor) or Fas ligand expression in any cell type. However, in all cell types, irradiation produced approximately a 2-fold increase in the percentage of cells in the G2/M phase of the cell cycle. CONCLUSION These results demonstrate that an intact loop domain is not necessary for the full antiapoptotic function of Bcl-xL against irradiation-induced cytosolic accumulation of cyt c, caspase activation, and apoptosis of HL-60 cells. Additionally, the cell-cycle effects of ionizing radiation in HL-60 cells are not affected by enforced expression of Bcl-xL or Bcl-xLdelta.
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Affiliation(s)
- S H Burri
- Department of Radiation Oncology, Emory University School of Medicine, Atlanta, GA 30322, USA
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30
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Balachandran S, Kim CN, Yeh WC, Mak TW, Bhalla K, Barber GN. Activation of the dsRNA-dependent protein kinase, PKR, induces apoptosis through FADD-mediated death signaling. EMBO J 1998; 17:6888-902. [PMID: 9843495 PMCID: PMC1171037 DOI: 10.1093/emboj/17.23.6888] [Citation(s) in RCA: 284] [Impact Index Per Article: 10.9] [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] [Indexed: 12/18/2022] Open
Abstract
The dsRNA-dependent protein kinase (PKR) is considered to play a key role in interferon-mediated host defense against viral infection and conceivably malignant transformation. To investigate further the mechanisms of PKR-induced growth inhibition, we have developed tetracycline-inducible murine cell lines that express wild-type PKR or a catalytically inactive PKR variant, PKRdelta6. Following induction, the growth of the wild-type PKR-expressing cells was similar to that of cells transfected with vector alone, while cells expressing PKRdelta6 became malignantly transformed. Significantly, treatment with dsRNA caused the wild-type PKR-overexpressing cells to undergo programed cell death while, conversely, cells expressing PKRdelta6 were completely resistant. Our studies demonstrated that activation of PKR induces the expression of members of the tumor necrosis factor receptor (TNFR) family, including Fas (CD95/Apo-1) and pro-apopotic Bax. In contrast, transcripts representing Fas, TNFR-1, FADD (Fas-associated death domain), FLICE, Bad and Bax were ablated in cells expressing PKRdelta6. The involvement of the death receptors in PKR-induced apoptosis was underscored by demonstrating that murine fibroblasts lacking FADD were almost completely resistant to dsRNA-mediated cell death. Thus, PKR, a key cellular target for viral repression, is a receptor/inducer for the induction of pro-apoptotic genes by dsRNA and probably functions in interferon-mediated host defense to trigger cell death in response to virus infection and perhaps tumorigenesis.
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Affiliation(s)
- S Balachandran
- Department of Microbiology and Immunology and Winship Cancer Center, Emory University School of Medicine, Atlanta, GA 30322, USA
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31
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Ibrado AM, Kim CN, Bhalla K. Temporal relationship of CDK1 activation and mitotic arrest to cytosolic accumulation of cytochrome C and caspase-3 activity during Taxol-induced apoptosis of human AML HL-60 cells. Leukemia 1998; 12:1930-6. [PMID: 9844922 DOI: 10.1038/sj.leu.2401218] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.2] [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: 11/09/2022]
Abstract
The antimicrotubule anticancer drug, Taxol, suppresses microtubule dynamics, causes mitotic arrest, and induces caspase-3 cleavage and activity resulting in apoptosis of human AML HL-60 cells. Caspase-3 cleavage is triggered by the mitochondrial release and cytosolic accumulation of the electron transfer protein, cytochrome c (cyt c). Taxol-induced G2/M transition is mediated by p34(cdc-2) (CDK1) which, if prematurely activated, may also trigger apoptosis. In the present studies following S-phase synchronization and release, HL-60 cells with enforced expression of the bcl-xL (HL-60/Bcl-xL) and/or neomycin resistance gene (HL-60/neo) were exposed to Taxol to examine CDK1-related cell-cycle events and the cyt c-triggered molecular cascade of apoptosis. At various time-intervals after Taxol treatment, immunoblot analyses of cyclin B1 and CDK1 levels were performed. In addition, the in vitro histone H1 kinase activity of immunoprecipitated CDK1 and its tyrosine phosphorylation status (by anti-phosphotyrosine immunoblot analysis) were determined. Data presented here show that, while Taxol-induced peak CDK1 kinase activity occurs earlier in HL-60/neo cells, there are no significant differences in cyclin B1 accumulation, tyrosine dephosphorylation of CDK1, and mitotic arrest of Taxol-treated HL-60/neo vs HL-60/Bcl-xL cells. Taxol-induced CDK1 activation and mitosis preceded the cytosolic accumulation (approximately six-fold) of cyt c. The latter event was blocked by Bcl-xL overexpression but not by inhibitors of caspase-3. Although the caspase inhibitors and high Bcl-xL levels inhibited caspase-3 cleavage and activity, they did not significantly affect Taxol-induced CDK1 activation or mitotic arrest. These findings indicate that Bcl-xL overexpression does not affect Taxol-induced CDK1 activity leading to G2/M transition, which temporally precedes the cytosolic cyt c-mediated cleavage and activity of caspase-3 and apoptosis.
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Affiliation(s)
- A M Ibrado
- Department of Medicine, Winship Cancer Center Emory University School of Medicine, Atlanta, GA 30322, USA
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32
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Perkins C, Kim CN, Fang G, Bhalla KN. Overexpression of Apaf-1 promotes apoptosis of untreated and paclitaxel- or etoposide-treated HL-60 cells. Cancer Res 1998; 58:4561-6. [PMID: 9788601] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
Recent studies have demonstrated that Apaf-1 is the adaptor molecule which in the presence of cytosolic cytochrome c (cyt c) and dATP interacts with procaspase-9, resulting in the sequential cleavage and activity of caspase-9 and caspase-3, followed by apoptosis. In the present studies, we determined the effect of enforced overexpression of Apaf-1 on the apoptotic threshold in the human myeloid leukemia HL-60 cells. Our findings demonstrate that both transient and stable transfections resulted in a 2.5-fold higher expression of Apaf-1, which was associated with approximately a 5-fold increase in the percentage of apoptosis in the transfectants (HL-60/Apaf-1) as compared with the control HL-60/neo cells. In cells overexpressing either Bcl-2 or Bcl-xL, transient overexpression of Apaf-1 did not induce apoptosis. Stably overexpressing Apaf-1 levels significantly sensitized HL-60/Apaf-1 cells to apoptosis induced by clinically achievable concentrations of paclitaxel or etoposide (P < 0.01). This increase in paclitaxel- or etoposide-induced apoptosis of HL-60/Apaf-1 cells was not associated with any significant alterations in Bcl-2, Bcl-xL, Bax, Fas, or Fas ligand expression. It was, however, clearly associated with caspase-9 cleavage, as well as the poly(ADP-ribose) polymerase and DFF45 cleavage activity of caspase-3. Coexpression of the catalytically inactive, dominant-negative, mutant caspase-9, XIAP, or treatment with the caspase inhibitor, zVAD, significantly inhibited the increase in apoptosis of HL-60/Apaf-1 cells (P < 0.01). These data indicate that the intracellular levels of Apaf-1 is an important molecular determinant of the threshold for apoptosis induced by paclitaxel and etoposide.
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Affiliation(s)
- C Perkins
- Department of Medicine, Winship Cancer Center, Emory University School of Medicine, Atlanta, Georgia 30322, USA
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Fang G, Chang BS, Kim CN, Perkins C, Thompson CB, Bhalla KN. "Loop" domain is necessary for taxol-induced mobility shift and phosphorylation of Bcl-2 as well as for inhibiting taxol-induced cytosolic accumulation of cytochrome c and apoptosis. Cancer Res 1998; 58:3202-8. [PMID: 9699642] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Taxol, 1-beta-D-arabinofuranosylcytosine (ara-C), and etoposide induce apoptosis in HL-60 cells that is blocked by overexpression of Bcl-2 or Bcl-xL.A 60-amino acid "loop" domain of Bcl-2 and Bcl-xL that contains phosphorylation sites is known to negatively regulate their antiapoptotic function. In the present studies, Taxol-, ara-C-, or etoposide-induced apoptosis was examined in HL-60/Bcl-2delta and HL-60/Bcl-xLdelta cells that express the loop-deletional mutant cDNA constructs p19Bcl-2delta32-80 and p18Bcl-xLdelta26-83, respectively. This was compared with control HL-60/neo cells as well as HL-60/Bcl-2 and HL-60/Bcl-xL cells. The latter two cell lines overexpress full-length Bcl-2 and Bcl-xL, respectively. Immunoblot analyses showed that HL-60/neo and HL-60/Bcl-2delta cells express similar levels of p26Bcl-2. In contrast, as compared with HL-60/neo, HL-60/Bcl-xLdelta cells expressed significantly lower levels of p26Bcl-2. p29Bcl-xL and p21Bax levels were similar in all cell types. Exposure to etoposide (50 microM) or ara-C (100 microM) for 4 h induced apoptosis in HL-60/neo cells, but not in HL-60/Bcl-2, HL-60/Bcl-xL, HL-60/Bcl-2delta, or HL-60/Bcl-xLdelta cells. In contrast, Taxol treatment (500 nM for 24 h) triggered the molecular cascade of apoptosis, represented by the cytosolic increase of cytochrome c and poly(ADP-ribose) polymerase or the DNA fragmentation factor cleavage activity of caspase-3 in HL-60/neo cells as well as in HL-60/Bcl-xLdelta and HL-60/Bcl-2delta cells, but not in their counterparts overexpressing full-length Bcl-2 and Bcl-xL. Equal amounts of p26Bcl-2 were coimmunoprecipitated with apoptosis protease-activating factor 1 (APAF-1) in HL-60/neo and HL-60/Bcl-2delta cells, whereas a markedly higher level of p26Bcl-2 coimmunoprecipitated with APAF-1 in HL-60/Bcl-2 cells. In association with Taxol-induced apoptosis, the levels of Bcl-2 that were coimmunoprecipitated with APAF-1 declined in HL-60/neo and HL-60/Bcl-2delta cells. This was not observed in HL-60/Bcl-2 cells, in which Taxol-induced apoptosis was blocked. Previous studies have demonstrated that Taxol induces phosphorylation of Bcl-2 in association with Taxol-induced apoptosis of HL-60/neo cells. Immunoblot analysis demonstrated a Taxol-induced mobility shift of Bcl-2 but not p19Bcl-2delta. Taxol also increased [32P]Pi incorporation in p26Bcl-2, but not in p19Bcl-2delta or p18Bcl-xL. These findings indicate that the loop domain is necessary for the Taxol-induced mobility shift and phosphorylation of Bcl-2. Loop domain also seems to be necessary for the antiapoptotic effect of Bcl-2 against Taxol-induced apoptosis but not ara-C- or etoposide-induced apoptosis.
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Affiliation(s)
- G Fang
- Department of Medicine, Winship Cancer Center, Emory University School of Medicine, Atlanta, Georgia 30322, USA
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Min YG, Jang YJ, Rhee CK, Kim CN, Hong SK. Correlation between anthropometric measurements of the oropharyngeal area and severity of apnea in patients with snoring and obstructive sleep apnea. Auris Nasus Larynx 1997; 24:399-403. [PMID: 9352833 DOI: 10.1016/s0385-8146(97)10010-4] [Citation(s) in RCA: 3] [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: 02/05/2023]
Abstract
The aim of this study was to investigate the relationship between severity of apnea and anthropometric oropharyngeal measurements in patients with snoring and obstructive sleep apnea. A total of 22 patients complaining of snoring and apneic spell during sleep were evaluated by polysomnographic and anthropometric measurements of the oropharyngeal area. The horizontal width of the uvula at the mid-point and the length of the uvula were measured using a T-shaped ruler. The distance between the anterior pillars, posterior pillars and retromolar raphes were also measured. The correlation between these anthropometric measurements and polysomnographic parameters including the respiratory disturbance index (RDI) and the lowest arterial O2 saturation level (lowest SaO2) of the patients were analyzed. Of the anthropometric measurements, the horizontal width of the uvula showed a significant correlation with RDI and lowest SaO2. The results of the present study indicate that patients with broader uvula may have severer sleep apnea and that anthropometric oropharyngeal measurements may give additional information to polysomnographic findings for selecting surgical candidates.
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Affiliation(s)
- Y G Min
- Department of Otorhinolaryngology, Seoul National University College of Medicine, South Korea
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Kim CN, Wang X, Huang Y, Ibrado AM, Liu L, Fang G, Bhalla K. Overexpression of Bcl-X(L) inhibits Ara-C-induced mitochondrial loss of cytochrome c and other perturbations that activate the molecular cascade of apoptosis. Cancer Res 1997; 57:3115-20. [PMID: 9242435] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
High-dose Ara-C (HIDAC) induces the cleavage and activity of caspase-3 (CPP32beta/Yama/apopain), resulting in the morphological and biochemical features of apoptosis. High levels of the antiapoptotic Bcl-x(L) or Bcl-2, relative to the proapoptotic Bax, have been shown to inhibit HIDAC-induced cleavage and activity of caspase-3 and apoptosis of the human acute myeloid leukemia HL-60 cells. In a previous report, we demonstrated this inhibition, using the control HL-60 (HL-60/neo) cells and their counterparts, HL-60/Bcl-x(L), which have enforced overexpression of Bcl-x(L) and a significantly lower ratio of free to bound Bax. Results of the present studies demonstrate that, in the initiation phase of apoptosis of HL-60/neo cells due to HIDAC (10 or 100 microM for 4 h), cytochrome c is released from the mitochondria to the cytosol, followed by the loss of mitochondrial membrane potential (deltapsi m) and an increase in the reactive oxygen species; these events precede and trigger the cleavage and activity of caspase-3. These HIDAC-induced early mitochondrial and cytosolic perturbations, which represent the initiation phase of HIDAC-induced apoptosis, were inhibited in HL-60/Bcl-x(L) cells. HIDAC treatment for 4 h also modestly increased the intracellular levels of free Bax relative to Bax bound to Bcl-2 and Bcl-x(L) in HL-60/neo but not in HL-60/Bcl-x(L) cells. In HL-60/neo cells, HIDAC-induced progressive accumulation of cytochrome c in the cytosol, the decrease in deltapsi m, and the increase in reactive oxygen species were not inhibited by coculture with the tetrapeptide inhibitors of caspases that have been previously shown to inhibit Ara-C-induced cleavage and activity of caspase-3 and apoptosis. These findings indicate that Bcl-x(L) inhibits HIDAC-induced preapoptotic mitochondrial perturbations, which prevent the accumulation of cytochrome c in the cytosol, thereby preserving caspase-3 in the inactive zymogen state and checking the molecular cascade of apoptosis.
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Affiliation(s)
- C N Kim
- Department of Medicine, Winship Cancer Center, Emory University School of Medicine, Atlanta, Georgia 30322, USA
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Yang J, Liu X, Bhalla K, Kim CN, Ibrado AM, Cai J, Peng TI, Jones DP, Wang X. Prevention of apoptosis by Bcl-2: release of cytochrome c from mitochondria blocked. Science 1997; 275:1129-32. [PMID: 9027314 DOI: 10.1126/science.275.5303.1129] [Citation(s) in RCA: 3640] [Impact Index Per Article: 134.8] [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: 02/03/2023]
Abstract
Bcl-2 is an integral membrane protein located mainly on the outer membrane of mitochondria. Overexpression of Bcl-2 prevents cells from undergoing apoptosis in response to a variety of stimuli. Cytosolic cytochrome c is necessary for the initiation of the apoptotic program, suggesting a possible connection between Bcl-2 and cytochrome c, which is normally located in the mitochondrial intermembrane space. Cells undergoing apoptosis were found to have an elevation of cytochrome c in the cytosol and a corresponding decrease in the mitochondria. Overexpression of Bcl-2 prevented the efflux of cytochrome c from the mitochondria and the initiation of apoptosis. Thus, one possible role of Bcl-2 in prevention of apoptosis is to block cytochrome c release from mitochondria.
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Affiliation(s)
- J Yang
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
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Abstract
A cell-free system based on cytosols of normally growing cells is established that reproduces aspects of the apoptotic program in vitro. The apoptotic program is initiated by addition of dATP. Fractionation of cytosol yielded a 15 kDa protein that is required for in vitro apoptosis. The absorption spectrum and protein sequence revealed that this protein is cytochrome c. Elimination of cytochrome c from cytosol by immunodepletion, or inclusion of sucrose to stabilize mitochondria during cytosol preparation, diminished the apoptotic activity. Adding back cytochrome c to the cytochrome c-depleted extracts restored their apoptotic activity. Cells undergoing apoptosis in vivo showed increased release of cytochrome c to their cytosol, suggesting that mitochondria may function in apoptosis by releasing cytochrome c.
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Affiliation(s)
- X Liu
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322, USA
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Liu X, Kim CN, Pohl J, Wang X. Purification and characterization of an interleukin-1beta-converting enzyme family protease that activates cysteine protease P32 (CPP32). J Biol Chem 1996; 271:13371-6. [PMID: 8662833] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
CPP32, a member of the interleukin-1beta-converting enzyme (ICE) family of cysteine proteases, cleaves poly(ADP-ribose) polymerase and sterol regulatory element binding proteins during apoptosis. CPP32 normally exists in the cytosol as a 32-kDa inactive precursor and only becomes activated when cells are undergoing apoptosis. The activation is a proteolytic event that generates a p20/p11 heterodimer. We report here the identification, purification, and characterization of a hamster CPP32-activating protease (CAP) that cleaves and activates CPP32. The biochemical properties of CAP suggest that it is another member of the ICE family of proteases. Purified CAP consists of two prominent polypeptides of 19 and 13 kDa. Protein sequencing revealed that CAP is derived from the hamster homolog of Mch2alpha, a member of the ICE family recently identified based on the sequence conservation among the ICE family members. CAP activity is inhibited by CrmA, a cowpox virus protein that prevents host cell apoptosis. CAP itself is also activated through proteolytic cleavage. These data are consistent with the idea that the activation of the ICE family of proteases during apoptosis proceeds through a cascade of proteolytic events.
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Affiliation(s)
- X Liu
- Department of Biochemistry and Microchemical Facility, Winship Cancer Center, Emory University School of Medicine, Atlanta, Georgia 30322, USA
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Min YG, Lim HJ, Kim CN, Jang YJ. Comparison of natural ostiotomy and antibiotic therapy in the treatment of acute maxillary sinusitis in rabbits. Acta Otolaryngol 1995; 115:433-7. [PMID: 7653267 DOI: 10.3109/00016489509139343] [Citation(s) in RCA: 4] [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: 01/26/2023]
Abstract
The goal of this study was to compare natural ostiotomy and the administration of a systemic antibiotic in the treatment of acute maxillary sinusitis. Maxillary sinusitis was induced in 28 rabbits by blocking the natural ostium with a bone chip and by introducing 0.2 ml of a suspension of Streptococcus pneumoniae (2 x 10(9) cells/ml). The animals were divided into natural ostiotomy and antibiotic therapy groups: the natural ostiotomy group comprised 14 rabbits, in which the bone chip that blocked the natural ostium was removed; and the antibiotic therapy group comprised 14 rabbits treated with systemic antibiotic without reopening the ostium. The sinus mucosa of each group was examined histopathologically 2 weeks and 4 weeks after treatment. There were no significant differences in light microscopic findings between the natural ostiotomy and antibiotic therapy groups. Natural ostiotomy was as effective against acute maxillary sinusitis as the systemic administration of antibiotics. The results of this study suggest that natural ostiotomy and antibiotic therapy may be equally effective in the treatment of acute maxillary sinusitis in rabbits.
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Affiliation(s)
- Y G Min
- Department of Otorhinolaryngology, Seoul National University College of Medicine, Korea
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Mikurcík E, Kim CN. [Surgical treatment of staghorn urolithiasis]. BRATISL MED J 1984; 81:442-50. [PMID: 6713222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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Johnson KG, Sibley JR, Kim CN, Kim IS. Koje Island illness and health care patterns. Yonsei Med J 1970; 11:160-72. [PMID: 5522617 DOI: 10.3349/ymj.1970.11.2.160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
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