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Lasser M, Sun N, Xu Y, Wang S, Drake S, Law K, Gonzalez S, Wang B, Drury V, Castillo O, Zaltsman Y, Dea J, Bader E, McCluskey KE, State MW, Willsey AJ, Willsey HR. Pleiotropy of autism-associated chromatin regulators. Development 2023; 150:dev201515. [PMID: 37366052 PMCID: PMC10399978 DOI: 10.1242/dev.201515] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [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: 12/07/2022] [Accepted: 06/19/2023] [Indexed: 06/28/2023]
Abstract
Gene ontology analyses of high-confidence autism spectrum disorder (ASD) risk genes highlight chromatin regulation and synaptic function as major contributors to pathobiology. Our recent functional work in vivo has additionally implicated tubulin biology and cellular proliferation. As many chromatin regulators, including the ASD risk genes ADNP and CHD3, are known to directly regulate both tubulins and histones, we studied the five chromatin regulators most strongly associated with ASD (ADNP, CHD8, CHD2, POGZ and KMT5B) specifically with respect to tubulin biology. We observe that all five localize to microtubules of the mitotic spindle in vitro in human cells and in vivo in Xenopus. Investigation of CHD2 provides evidence that mutations present in individuals with ASD cause a range of microtubule-related phenotypes, including disrupted localization of the protein at mitotic spindles, cell cycle stalling, DNA damage and cell death. Lastly, we observe that ASD genetic risk is significantly enriched among tubulin-associated proteins, suggesting broader relevance. Together, these results provide additional evidence that the role of tubulin biology and cellular proliferation in ASD warrants further investigation and highlight the pitfalls of relying solely on annotated gene functions in the search for pathological mechanisms.
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Affiliation(s)
- Micaela Lasser
- Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Nawei Sun
- Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Yuxiao Xu
- Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Sheng Wang
- Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Sam Drake
- Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Karen Law
- Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Silvano Gonzalez
- Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Belinda Wang
- Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
- Langley Porter Psychiatric Institute, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Vanessa Drury
- Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Octavio Castillo
- Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Yefim Zaltsman
- Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Jeanselle Dea
- Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Ethel Bader
- Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Kate E. McCluskey
- Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Matthew W. State
- Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
- Langley Porter Psychiatric Institute, University of California, San Francisco, San Francisco, CA 94143, USA
- Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94143, USA
| | - A. Jeremy Willsey
- Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
- Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Helen Rankin Willsey
- Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
- Chan Zuckerberg Biohub - San Francisco, San Francisco, CA 94158, USA
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2
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Crockett KB, Schember CO, Bian A, Rebeiro PF, Keruly J, Mayer K, Mathews C, Moore RD, Crane H, Geng E, Napravnik S, Shepherd BE, Mugavero MJ, Turan B, Pettit AC. Relationships Between Patient Race and Residential Race Context With Missed Human Immunodeficiency Virus Care Visits in the United States, 2010-2015. Clin Infect Dis 2023; 76:2163-2170. [PMID: 36757336 PMCID: PMC10273374 DOI: 10.1093/cid/ciad069] [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: 10/19/2022] [Revised: 01/30/2023] [Accepted: 02/04/2023] [Indexed: 02/10/2023] Open
Abstract
BACKGROUND Racial inequities exist in retention in human immunodeficiency virus (HIV) care and multilevel analyses are needed to contextualize and address these differences. Leveraging data from a multisite clinical cohort of people with HIV (PWH), we assessed the relationships between patient race and residential characteristics with missed HIV care visits. METHODS Medical record and patient-reported outcome (PRO; including mental health and substance-use measures) data were drawn from 7 participating Center for AIDS Research Network of Integrated Clinical Systems (CNICS) sites including N = 20 807 PWH from January 2010 through December 2015. Generalized estimating equations were used to account for nesting within individuals and within census tracts in multivariable models assessing the relationship between race and missed HIV care visits, controlling for individual demographic and health characteristics and census tract characteristics. RESULTS Black PWH resided in more disadvantaged census tracts, on average. Black PWH residing in census tracts with higher proportion of Black residents were more likely to miss an HIV care visit. Non-Black PWH were less likely to miss a visit regardless of where they lived. These relationships were attenuated when PRO data were included. CONCLUSIONS Residential racial segregation and disadvantage may create inequities between Black PWH and non-Black PWH in retention in HIV care. Multilevel approaches are needed to retain PWH in HIV care, accounting for community, healthcare setting, and individual needs and resources.
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Affiliation(s)
- Kaylee B Crockett
- Department of Family and Community Medicine, University of Alabama at Birmingham School of Medicine, Birmingham, Alabama, USA
| | - Cassandra O Schember
- Division of Epidemiology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Aihua Bian
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Peter F Rebeiro
- Division of Epidemiology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Division of Infectious Diseases, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Jeanne Keruly
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | - Kenneth Mayer
- The Fenway Institute, Fenway Health, Boston, Massachusetts, USA
- Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
- Department of Global Health and Population, Harvard Medical School, Boston, Massachusetts, USA
| | - Christopher Mathews
- School of Medicine, University of California San Diego, San Diego, California, USA
| | - Richard D Moore
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University, Baltimore, Maryland, USA
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Heidi Crane
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Elvin Geng
- Division of Infectious Diseases, Washington University in St Louis School of Medicine, St Louis, Missouri, USA
| | - Sonia Napravnik
- Division of Infectious Disease, University of North Carolina Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
- Department of Epidemiology, Gillings School of Global Public Health, Chapel Hill, North Carolina, USA
| | - Bryan E Shepherd
- Division of Epidemiology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Michael J Mugavero
- Division of Infectious Diseases, University of Alabama at Birmingham School of Medicine, Birmingham, Alabama, USA
| | - Bulent Turan
- Department of Psychology, College of Social Sciences and Humanities, Koc University, Istanbul, Turkey
- Department of Psychology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - April C Pettit
- Division of Infectious Diseases, Vanderbilt University Medical Center, Nashville, Tennessee, USA
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3
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Liu J, Laurie MT, Rubio L, Vazquez SE, Sunshine S, Mitchell AM, Hapte-Selassie M, Mann SA, Pilarowski G, Black D, Marquez C, Rojas S, Lionakis MS, Petersen M, Whitman JD, Jain V, Anderson M, Havlir D, DeRisi J. Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Transmission Dynamics and Immune Responses in a Household of Vaccinated Persons. Clin Infect Dis 2022; 75:e303-e306. [PMID: 35037050 PMCID: PMC8807302 DOI: 10.1093/cid/ciac029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 10/18/2021] [Indexed: 12/12/2022] Open
Abstract
While SARS-CoV-2 vaccines prevent severe disease effectively, postvaccination "breakthrough" COVID-19 infections and transmission among vaccinated individuals remain ongoing concerns. We present an in-depth characterization of transmission and immunity among vaccinated individuals in a household, revealing complex dynamics and unappreciated comorbidities, including autoimmunity to type 1 interferon in the presumptive index case.
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Affiliation(s)
- Jamin Liu
- University of California, Berkeley—University of California, San Francisco Graduate Program in Bioengineering, Berkeley, California, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, California, USA
| | - Matthew T Laurie
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, California, USA
| | - Luis Rubio
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Sara E Vazquez
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, California, USA
- Department of Medicine, Diabetes Center, University of California, San Francisco, San Francisco, California, USA
| | - Sara Sunshine
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, California, USA
| | - Anthea M Mitchell
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, California, USA
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Matthias Hapte-Selassie
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, California, USA
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Sabrina A Mann
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, California, USA
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Genay Pilarowski
- The Public Health Company, Oakland, California, USA
- Unidos en Salud, San Francisco, California, USA
| | - Douglas Black
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Carina Marquez
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, California, USA
| | | | - Michail S Lionakis
- Fungal Pathogenesis Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Maya Petersen
- Division of Biostatistics, University of California, Berkeley, Berkeley, California, USA
| | - Jeffrey D Whitman
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Vivek Jain
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Mark Anderson
- Department of Medicine, Diabetes Center, University of California, San Francisco, San Francisco, California, USA
| | - Diane Havlir
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Joseph DeRisi
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, California, USA
- Chan Zuckerberg Biohub, San Francisco, California, USA
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4
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Laurie MT, Liu J, Sunshine S, Peng J, Black D, Mitchell AM, Mann SA, Pilarowski G, Zorn KC, Rubio L, Bravo S, Marquez C, Sabatino JJ, Mittl K, Petersen M, Havlir D, DeRisi J. SARS-CoV-2 Variant Exposures Elicit Antibody Responses With Differential Cross-Neutralization of Established and Emerging Strains Including Delta and Omicron. J Infect Dis 2022; 225:1909-1914. [PMID: 34979030 PMCID: PMC8755395 DOI: 10.1093/infdis/jiab635] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [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: 09/01/2021] [Accepted: 12/31/2021] [Indexed: 11/26/2022] Open
Abstract
The wide spectrum of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants with phenotypes impacting transmission and antibody sensitivity necessitates investigation of immune responses to different spike protein versions. Here, we compare neutralization of variants of concern, including B.1.617.2 (delta) and B.1.1.529 (omicron), in sera from individuals exposed to variant infection, vaccination, or both. We demonstrate that neutralizing antibody responses are strongest against variants sharing certain spike mutations with the immunizing exposure, and exposure to multiple spike variants increases breadth of variant cross-neutralization. These findings contribute to understanding relationships between exposures and antibody responses and may inform booster vaccination strategies.
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Affiliation(s)
- Matthew T Laurie
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, USA
| | - Jamin Liu
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, USA
- University of California Berkeley-University of California San Francisco Graduate Program in Bioengineering, Berkeley, California, USA
| | - Sara Sunshine
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, USA
| | - James Peng
- Department of Medicine, University of California San Francisco, San Francisco, California, USA
| | - Douglas Black
- Department of Medicine, University of California San Francisco, San Francisco, California, USA
| | - Anthea M Mitchell
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, USA
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Sabrina A Mann
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, USA
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Genay Pilarowski
- The Public Health Company, Oakland, California, USA
- Unidos en Salud, San Francisco, California, USA
| | - Kelsey C Zorn
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, USA
| | - Luis Rubio
- Department of Medicine, University of California San Francisco, San Francisco, California, USA
| | - Sara Bravo
- Unidos en Salud, San Francisco, California, USA
| | - Carina Marquez
- Department of Medicine, University of California San Francisco, San Francisco, California, USA
| | - Joseph J Sabatino
- Weill Institute for Neurosciences, Department of Neurology, San Francisco, California, USA
| | - Kristen Mittl
- Weill Institute for Neurosciences, Department of Neurology, San Francisco, California, USA
| | - Maya Petersen
- Division of Biostatistics, University of California Berkeley, Berkeley, California, USA
| | - Diane Havlir
- Department of Medicine, University of California San Francisco, San Francisco, California, USA
| | - Joseph DeRisi
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, USA
- Chan Zuckerberg Biohub, San Francisco, California, USA
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5
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Gschwend J, Sherman SP, Ridder F, Feng X, Liang HE, Locksley RM, Becher B, Schneider C. Alveolar macrophages rely on GM-CSF from alveolar epithelial type 2 cells before and after birth. J Exp Med 2021; 218:e20210745. [PMID: 34431978 PMCID: PMC8404471 DOI: 10.1084/jem.20210745] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 06/27/2021] [Accepted: 08/04/2021] [Indexed: 12/31/2022] Open
Abstract
Programs defining tissue-resident macrophage identity depend on local environmental cues. For alveolar macrophages (AMs), these signals are provided by immune and nonimmune cells and include GM-CSF (CSF2). However, evidence to functionally link components of this intercellular cross talk remains scarce. We thus developed new transgenic mice to profile pulmonary GM-CSF expression, which we detected in both immune cells, including group 2 innate lymphoid cells and γδ T cells, as well as AT2s. AMs were unaffected by constitutive deletion of hematopoietic Csf2 and basophil depletion. Instead, AT2 lineage-specific constitutive and inducible Csf2 deletion revealed the nonredundant function of AT2-derived GM-CSF in instructing AM fate, establishing the postnatal AM compartment, and maintaining AMs in adult lungs. This AT2-AM relationship begins during embryogenesis, where nascent AT2s timely induce GM-CSF expression to support the proliferation and differentiation of fetal monocytes contemporaneously seeding the tissue, and persists into adulthood, when epithelial GM-CSF remains restricted to AT2s.
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Affiliation(s)
- Julia Gschwend
- Institute of Physiology, University of Zurich, Zurich, Switzerland
| | | | - Frederike Ridder
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - Xiaogang Feng
- Institute of Physiology, University of Zurich, Zurich, Switzerland
| | - Hong-Erh Liang
- Department of Medicine, University of California San Francisco, San Francisco, CA
| | - Richard M. Locksley
- Department of Medicine, University of California San Francisco, San Francisco, CA
- Department of Microbiology & Immunology, University of California San Francisco, San Francisco, CA
- Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA
| | - Burkhard Becher
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
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Abstract
Autophagy is deregulated in many cancers and represents an attractive target for therapeutic intervention. However, the precise contributions of autophagy to metastatic progression, the principle cause of cancer-related mortality, is only now being uncovered. While autophagy promotes primary tumor growth, metabolic adaptation and resistance to therapy, recent studies have unexpectedly revealed that autophagy suppresses the proliferative outgrowth of disseminated tumor cells into overt and lethal macrometastases. These studies suggest autophagy plays unexpected and complex roles in the initiation and progression of metastases, which will undoubtedly impact therapeutic approaches for cancer treatment. Here, we discuss the intricacies of autophagy in metastatic progression, highlighting and integrating the pleiotropic roles of autophagy on diverse cell biological processes involved in metastasis.
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Affiliation(s)
- Timothy Marsh
- Department of Pathology and Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94143 USA
| | - Bhairavi Tolani
- Thoracic Oncology Program, Department of Surgery, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA 94115 USA
| | - Jayanta Debnath
- Department of Pathology and Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94143 USA
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