1
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Huisman JS, Scire J, Caduff L, Fernandez-Cassi X, Ganesanandamoorthy P, Kull A, Scheidegger A, Stachler E, Boehm AB, Hughes B, Knudson A, Topol A, Wigginton KR, Wolfe MK, Kohn T, Ort C, Stadler T, Julian TR. Wastewater-Based Estimation of the Effective Reproductive Number of SARS-CoV-2. Environ Health Perspect 2022; 130:57011. [PMID: 35617001 PMCID: PMC9135136 DOI: 10.1289/ehp10050] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 04/09/2022] [Accepted: 04/26/2022] [Indexed: 05/05/2023]
Abstract
BACKGROUND The effective reproductive number, R e , is a critical indicator to monitor disease dynamics, inform regional and national policies, and estimate the effectiveness of interventions. It describes the average number of new infections caused by a single infectious person through time. To date, R e estimates are based on clinical data such as observed cases, hospitalizations, and/or deaths. These estimates are temporarily biased when clinical testing or reporting strategies change. OBJECTIVES We show that the dynamics of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA in wastewater can be used to estimate R e in near real time, independent of clinical data and without the associated biases. METHODS We collected longitudinal measurements of SARS-CoV-2 RNA in wastewater in Zurich, Switzerland, and San Jose, California, USA. We combined this data with information on the temporal dynamics of shedding (the shedding load distribution) to estimate a time series proportional to the daily COVID-19 infection incidence. We estimated a wastewater-based R e from this incidence. RESULTS The method to estimate R e from wastewater worked robustly on data from two different countries and two wastewater matrices. The resulting estimates were as similar to the R e estimates from case report data as R e estimates based on observed cases, hospitalizations, and deaths are among each other. We further provide details on the effect of sampling frequency and the shedding load distribution on the ability to infer R e . DISCUSSION To our knowledge, this is the first time R e has been estimated from wastewater. This method provides a low-cost, rapid, and independent way to inform SARS-CoV-2 monitoring during the ongoing pandemic and is applicable to future wastewater-based epidemiology targeting other pathogens. https://doi.org/10.1289/EHP10050.
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Affiliation(s)
- Jana S. Huisman
- Department of Environmental Systems Science, ETH Zurich, Swiss Federal Institute of Technology, Zurich, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich, Swiss Federal Institute of Technology, Basel, Switzerland
| | - Jérémie Scire
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich, Swiss Federal Institute of Technology, Basel, Switzerland
| | - Lea Caduff
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Xavier Fernandez-Cassi
- Laboratory of Environmental Chemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | | | - Anina Kull
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Andreas Scheidegger
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Elyse Stachler
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Alexandria B. Boehm
- Department of Civil and Environmental Engineering, Stanford University, Stanford, California, USA
| | | | - Alisha Knudson
- Verily Life Sciences, South San Francisco, California, USA
| | - Aaron Topol
- Verily Life Sciences, South San Francisco, California, USA
| | - Krista R. Wigginton
- Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor, Michigan, USA
| | - Marlene K. Wolfe
- Department of Civil and Environmental Engineering, Stanford University, Stanford, California, USA
| | - Tamar Kohn
- Laboratory of Environmental Chemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Christoph Ort
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Tanja Stadler
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich, Swiss Federal Institute of Technology, Basel, Switzerland
| | - Timothy R. Julian
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
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2
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Huisman JS, Scire J, Caduff L, Fernandez-Cassi X, Ganesanandamoorthy P, Kull A, Scheidegger A, Stachler E, Boehm AB, Hughes B, Knudson A, Topol A, Wigginton KR, Wolfe MK, Kohn T, Ort C, Stadler T, Julian TR. Wastewater-Based Estimation of the Effective Reproductive Number of SARS-CoV-2. Environ Health Perspect 2022; 130:57011. [PMID: 35617001 DOI: 10.1101/2021.04.29.21255961] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
BACKGROUND The effective reproductive number, Re, is a critical indicator to monitor disease dynamics, inform regional and national policies, and estimate the effectiveness of interventions. It describes the average number of new infections caused by a single infectious person through time. To date, Re estimates are based on clinical data such as observed cases, hospitalizations, and/or deaths. These estimates are temporarily biased when clinical testing or reporting strategies change. OBJECTIVES We show that the dynamics of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA in wastewater can be used to estimate Re in near real time, independent of clinical data and without the associated biases. METHODS We collected longitudinal measurements of SARS-CoV-2 RNA in wastewater in Zurich, Switzerland, and San Jose, California, USA. We combined this data with information on the temporal dynamics of shedding (the shedding load distribution) to estimate a time series proportional to the daily COVID-19 infection incidence. We estimated a wastewater-based Re from this incidence. RESULTS The method to estimate Re from wastewater worked robustly on data from two different countries and two wastewater matrices. The resulting estimates were as similar to the Re estimates from case report data as Re estimates based on observed cases, hospitalizations, and deaths are among each other. We further provide details on the effect of sampling frequency and the shedding load distribution on the ability to infer Re. DISCUSSION To our knowledge, this is the first time Re has been estimated from wastewater. This method provides a low-cost, rapid, and independent way to inform SARS-CoV-2 monitoring during the ongoing pandemic and is applicable to future wastewater-based epidemiology targeting other pathogens. https://doi.org/10.1289/EHP10050.
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Affiliation(s)
- Jana S Huisman
- Department of Environmental Systems Science, ETH Zurich, Swiss Federal Institute of Technology, Zurich, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich, Swiss Federal Institute of Technology, Basel, Switzerland
| | - Jérémie Scire
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich, Swiss Federal Institute of Technology, Basel, Switzerland
| | - Lea Caduff
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Xavier Fernandez-Cassi
- Laboratory of Environmental Chemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | | | - Anina Kull
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Andreas Scheidegger
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Elyse Stachler
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Alexandria B Boehm
- Department of Civil and Environmental Engineering, Stanford University, Stanford, California, USA
| | | | - Alisha Knudson
- Verily Life Sciences, South San Francisco, California, USA
| | - Aaron Topol
- Verily Life Sciences, South San Francisco, California, USA
| | - Krista R Wigginton
- Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor, Michigan, USA
| | - Marlene K Wolfe
- Department of Civil and Environmental Engineering, Stanford University, Stanford, California, USA
| | - Tamar Kohn
- Laboratory of Environmental Chemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Christoph Ort
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Tanja Stadler
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich, Swiss Federal Institute of Technology, Basel, Switzerland
| | - Timothy R Julian
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
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3
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Farrelly LA, Zheng S, Schrode N, Topol A, Bhanu NV, Bastle RM, Ramakrishnan A, Chan JC, Cetin B, Flaherty E, Shen L, Gleason K, Tamminga CA, Garcia BA, Li H, Brennand KJ, Maze I. Chromatin profiling in human neurons reveals aberrant roles for histone acetylation and BET family proteins in schizophrenia. Nat Commun 2022; 13:2195. [PMID: 35459277 PMCID: PMC9033776 DOI: 10.1038/s41467-022-29922-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [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: 02/01/2020] [Accepted: 03/01/2022] [Indexed: 12/19/2022] Open
Abstract
Schizophrenia (SZ) is a psychiatric disorder with complex genetic risk dictated by interactions between hundreds of risk variants. Epigenetic factors, such as histone posttranslational modifications (PTMs), have been shown to play critical roles in many neurodevelopmental processes, and when perturbed may also contribute to the precipitation of disease. Here, we apply an unbiased proteomics approach to evaluate combinatorial histone PTMs in human induced pluripotent stem cell (hiPSC)-derived forebrain neurons from individuals with SZ. We observe hyperacetylation of H2A.Z and H4 in neurons derived from SZ cases, results that were confirmed in postmortem human brain. We demonstrate that the bromodomain and extraterminal (BET) protein, BRD4, is a bona fide 'reader' of H2A.Z acetylation, and further provide evidence that BET family protein inhibition ameliorates transcriptional abnormalities in patient-derived neurons. Thus, treatments aimed at alleviating BET protein interactions with hyperacetylated histones may aid in the prevention or treatment of SZ.
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Affiliation(s)
- Lorna A Farrelly
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Shuangping Zheng
- Beijing Advanced Innovation Center for Structural Biology, MOE Key Laboratory of Protein Sciences, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, 100084, Beijing, China
| | - Nadine Schrode
- Department of Genetics and Genomic Sciences, Pamela Sklar Division of Psychiatric Genomics, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Aaron Topol
- Graduate School of Biomedical Science, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Natarajan V Bhanu
- Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Ryan M Bastle
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Aarthi Ramakrishnan
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Jennifer C Chan
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Bulent Cetin
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Erin Flaherty
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Genetics and Genomic Sciences, Pamela Sklar Division of Psychiatric Genomics, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Li Shen
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Kelly Gleason
- Department of Psychiatry, University of Texas Southwestern Medical School, Dallas, TX, 75390, USA
| | - Carol A Tamminga
- Department of Psychiatry, University of Texas Southwestern Medical School, Dallas, TX, 75390, USA
| | - Benjamin A Garcia
- Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Haitao Li
- Beijing Advanced Innovation Center for Structural Biology, MOE Key Laboratory of Protein Sciences, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, 100084, Beijing, China.
| | - Kristen J Brennand
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Department of Genetics and Genomic Sciences, Pamela Sklar Division of Psychiatric Genomics, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Departments of Psychiatry and Genetics, Wu Tsai Institute, Yale School of Medicine, New Haven, CT, 065109, USA.
| | - Ian Maze
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Howard Hughes Medical Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
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4
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Kim S, Kennedy LC, Wolfe MK, Criddle CS, Duong DH, Topol A, White BJ, Kantor RS, Nelson KL, Steele JA, Langlois K, Griffith JF, Zimmer-Faust AG, McLellan SL, Schussman MK, Ammerman M, Wigginton KR, Bakker KM, Boehm AB. SARS-CoV-2 RNA is enriched by orders of magnitude in primary settled solids relative to liquid wastewater at publicly owned treatment works. Environ Sci (Camb) 2022. [PMID: 35433013 DOI: 10.1101/2021.11.10.21266138] [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] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Wastewater-based epidemiology has gained attention throughout the world for detection of SARS-CoV-2 RNA in wastewater to supplement clinical testing. Raw wastewater consists of small particles, or solids, suspended in liquid. Methods have been developed to measure SARS-CoV-2 RNA in the liquid and the solid fraction of wastewater, with some studies reporting higher concentrations in the solid fraction. To investigate this relationship further, six laboratories collaborated to conduct a study across five publicly owned treatment works (POTWs) where both primary settled solids obtained from primary clarifiers and raw wastewater influent samples were collected and quantified for SARS-CoV-2 RNA. Settled solids and influent samples were processed by participating laboratories using their respective methods and retrospectively paired based on date of collection. SARS-CoV-2 RNA concentrations, on a mass equivalent basis, were higher in settled solids than in influent by approximately three orders of magnitude. Concentrations in matched settled solids and influent were positively and significantly correlated at all five POTWs. RNA concentrations in both settled solids and influent were correlated to COVID-19 incidence rates in the sewersheds and thus representative of disease occurrence; the settled solids methods appeared to produce a comparable relationship between SARS-CoV-2 RNA concentration measurements and incidence rates across all POTWs. Settled solids and influent methods showed comparable sensitivity, N gene detection frequency, and calculated empirical incidence rate lower limits. Analysis of settled solids for SARS-CoV-2 RNA has the advantage of using less sample volume to achieve similar sensitivity to influent methods.
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Affiliation(s)
- Sooyeol Kim
- Dept of Civil and Environmental Engineering, Stanford University Stanford CA 94305 USA
| | - Lauren C Kennedy
- Dept of Civil and Environmental Engineering, Stanford University Stanford CA 94305 USA
| | - Marlene K Wolfe
- Dept of Civil and Environmental Engineering, Stanford University Stanford CA 94305 USA
- Rollins School of Public Health, Emory University Atlanta GA 30329 USA
| | - Craig S Criddle
- Dept of Civil and Environmental Engineering, Stanford University Stanford CA 94305 USA
| | | | - Aaron Topol
- Verily Life Sciences South San Francisco CA 94080 USA
| | | | - Rose S Kantor
- Dept of Civil and Environmental Engineering, University of California Berkeley CA 94720 USA
| | - Kara L Nelson
- Dept of Civil and Environmental Engineering, University of California Berkeley CA 94720 USA
| | - Joshua A Steele
- Southern California Coastal Water Research Project Costa Mesa CA 92626 USA
| | - Kylie Langlois
- Southern California Coastal Water Research Project Costa Mesa CA 92626 USA
| | - John F Griffith
- Southern California Coastal Water Research Project Costa Mesa CA 92626 USA
| | | | - Sandra L McLellan
- School of Freshwater Sciences, University of Wisconsin-Milwaukee Milwaukee WI 53204 USA
| | - Melissa K Schussman
- School of Freshwater Sciences, University of Wisconsin-Milwaukee Milwaukee WI 53204 USA
| | - Michelle Ammerman
- Department of Civil and Environmental Engineering, University of Michigan Ann Arbor MI 48109 USA
| | - Krista R Wigginton
- Department of Civil and Environmental Engineering, University of Michigan Ann Arbor MI 48109 USA
| | - Kevin M Bakker
- Department of Epidemiology, University of Michigan Ann Arbor MI 48109 USA
| | - Alexandria B Boehm
- Dept of Civil and Environmental Engineering, Stanford University Stanford CA 94305 USA
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5
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Kim S, Kennedy LC, Wolfe MK, Criddle CS, Duong DH, Topol A, White BJ, Kantor RS, Nelson KL, Steele JA, Langlois K, Griffith JF, Zimmer-Faust AG, McLellan SL, Schussman MK, Ammerman M, Wigginton KR, Bakker KM, Boehm AB. SARS-CoV-2 RNA is enriched by orders of magnitude in primary settled solids relative to liquid wastewater at publicly owned treatment works. Environ Sci (Camb) 2022; 8:757-770. [PMID: 35433013 PMCID: PMC8969789 DOI: 10.1039/d1ew00826a] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 02/04/2022] [Indexed: 05/21/2023]
Abstract
Wastewater-based epidemiology has gained attention throughout the world for detection of SARS-CoV-2 RNA in wastewater to supplement clinical testing. Raw wastewater consists of small particles, or solids, suspended in liquid. Methods have been developed to measure SARS-CoV-2 RNA in the liquid and the solid fraction of wastewater, with some studies reporting higher concentrations in the solid fraction. To investigate this relationship further, six laboratories collaborated to conduct a study across five publicly owned treatment works (POTWs) where both primary settled solids obtained from primary clarifiers and raw wastewater influent samples were collected and quantified for SARS-CoV-2 RNA. Settled solids and influent samples were processed by participating laboratories using their respective methods and retrospectively paired based on date of collection. SARS-CoV-2 RNA concentrations, on a mass equivalent basis, were higher in settled solids than in influent by approximately three orders of magnitude. Concentrations in matched settled solids and influent were positively and significantly correlated at all five POTWs. RNA concentrations in both settled solids and influent were correlated to COVID-19 incidence rates in the sewersheds and thus representative of disease occurrence; the settled solids methods appeared to produce a comparable relationship between SARS-CoV-2 RNA concentration measurements and incidence rates across all POTWs. Settled solids and influent methods showed comparable sensitivity, N gene detection frequency, and calculated empirical incidence rate lower limits. Analysis of settled solids for SARS-CoV-2 RNA has the advantage of using less sample volume to achieve similar sensitivity to influent methods.
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Affiliation(s)
- Sooyeol Kim
- Dept of Civil and Environmental Engineering, Stanford University Stanford CA 94305 USA
| | - Lauren C Kennedy
- Dept of Civil and Environmental Engineering, Stanford University Stanford CA 94305 USA
| | - Marlene K Wolfe
- Dept of Civil and Environmental Engineering, Stanford University Stanford CA 94305 USA
- Rollins School of Public Health, Emory University Atlanta GA 30329 USA
| | - Craig S Criddle
- Dept of Civil and Environmental Engineering, Stanford University Stanford CA 94305 USA
| | | | - Aaron Topol
- Verily Life Sciences South San Francisco CA 94080 USA
| | | | - Rose S Kantor
- Dept of Civil and Environmental Engineering, University of California Berkeley CA 94720 USA
| | - Kara L Nelson
- Dept of Civil and Environmental Engineering, University of California Berkeley CA 94720 USA
| | - Joshua A Steele
- Southern California Coastal Water Research Project Costa Mesa CA 92626 USA
| | - Kylie Langlois
- Southern California Coastal Water Research Project Costa Mesa CA 92626 USA
| | - John F Griffith
- Southern California Coastal Water Research Project Costa Mesa CA 92626 USA
| | | | - Sandra L McLellan
- School of Freshwater Sciences, University of Wisconsin-Milwaukee Milwaukee WI 53204 USA
| | - Melissa K Schussman
- School of Freshwater Sciences, University of Wisconsin-Milwaukee Milwaukee WI 53204 USA
| | - Michelle Ammerman
- Department of Civil and Environmental Engineering, University of Michigan Ann Arbor MI 48109 USA
| | - Krista R Wigginton
- Department of Civil and Environmental Engineering, University of Michigan Ann Arbor MI 48109 USA
| | - Kevin M Bakker
- Department of Epidemiology, University of Michigan Ann Arbor MI 48109 USA
| | - Alexandria B Boehm
- Dept of Civil and Environmental Engineering, Stanford University Stanford CA 94305 USA
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6
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Wolfe MK, Topol A, Knudson A, Simpson A, White B, Vugia DJ, Yu AT, Li L, Balliet M, Stoddard P, Han GS, Wigginton KR, Boehm AB. High-Frequency, High-Throughput Quantification of SARS-CoV-2 RNA in Wastewater Settled Solids at Eight Publicly Owned Treatment Works in Northern California Shows Strong Association with COVID-19 Incidence. mSystems 2021; 6:e0082921. [PMID: 34519528 PMCID: PMC8547422 DOI: 10.1128/msystems.00829-21] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 08/30/2021] [Indexed: 01/19/2023] Open
Abstract
A number of recent retrospective studies have demonstrated that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA concentrations in wastewater are associated with coronavirus disease 2019 (COVID-19) cases in the corresponding sewersheds. Implementing high-resolution, prospective efforts across multiple plants depends on sensitive measurements that are representative of COVID-19 cases, scalable for high-throughput analysis, and comparable across laboratories. We conducted a prospective study across eight publicly owned treatment works (POTWs). A focus on SARS-CoV-2 RNA in solids enabled us to scale up our measurements with a commercial lab partner. Samples were collected daily, and results were posted to a website within 24 h. SARS-CoV-2 RNA in daily samples correlated with the incidence of COVID-19 cases in the sewersheds; a 1 log10 increase in SARS-CoV-2 RNA in settled solids corresponds to a 0.58 log10 (4×) increase in sewershed incidence rate. SARS-CoV-2 RNA signals measured with the commercial laboratory partner were comparable across plants and comparable to measurements conducted in a university laboratory when normalized by pepper mild mottle virus (PMMoV) RNA. Results suggest that SARS-CoV-2 RNA should be detectable in settled solids for COVID-19 incidence rates of >1/100,000 (range, 0.8 to 2.3 cases per 100,000). These sensitive, representative, scalable, and comparable methods will be valuable for future efforts to scale up wastewater-based epidemiology. IMPORTANCE Access to reliable, rapid monitoring data is critical to guide response to an infectious disease outbreak. For pathogens that are shed in feces or urine, monitoring wastewater can provide a cost-effective snapshot of transmission in an entire community via a single sample. In order for a method to be useful for ongoing COVID-19 monitoring, it should be sensitive for detection of low concentrations of SARS-CoV-2, representative of incidence rates in the community, scalable to generate data quickly, and comparable across laboratories. This paper presents a method utilizing wastewater solids to meet these goals, producing measurements of SARS-CoV-2 RNA strongly associated with COVID-19 cases in the sewershed of a publicly owned treatment work. Results, provided within 24 h, can be used to detect incidence rates as low as approximately 1/100,000 cases and can be normalized for comparison across locations generating data using different methods.
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Affiliation(s)
- Marlene K. Wolfe
- Department of Civil & Environmental Engineering, Stanford University, Stanford, California, USA
| | - Aaron Topol
- Verily Life Sciences, South San Francisco, California, USA
| | - Alisha Knudson
- Verily Life Sciences, South San Francisco, California, USA
| | - Adrian Simpson
- Verily Life Sciences, South San Francisco, California, USA
| | - Bradley White
- Verily Life Sciences, South San Francisco, California, USA
| | - Duc J. Vugia
- California Department of Public Health, Infectious Diseases Branch, Richmond, California, USA
| | - Alexander T. Yu
- California Department of Public Health, Infectious Diseases Branch, Richmond, California, USA
| | - Linlin Li
- County of Santa Clara Public Health Department, San Jose, California, USA
| | - Michael Balliet
- County of Santa Clara Department of Environmental Health, San Jose, California, USA
| | - Pamela Stoddard
- County of Santa Clara Public Health Department, San Jose, California, USA
| | - George S. Han
- County of Santa Clara Public Health Department, San Jose, California, USA
| | - Krista R. Wigginton
- Department of Civil & Environmental Engineering, University of Michigan, Ann Arbor, Michigan, USA
| | - Alexandria B. Boehm
- Department of Civil & Environmental Engineering, Stanford University, Stanford, California, USA
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7
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Wolfe MK, Topol A, Knudson A, Simpson A, White B, Vugia DJ, Yu AT, Li L, Balliet M, Stoddard P, Han GS, Wigginton KR, Boehm AB. High-Frequency, High-Throughput Quantification of SARS-CoV-2 RNA in Wastewater Settled Solids at Eight Publicly Owned Treatment Works in Northern California Shows Strong Association with COVID-19 Incidence. mSystems 2021; 6:e0082921. [PMID: 34519528 DOI: 10.1101/2021.07.16.21260627] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023] Open
Abstract
A number of recent retrospective studies have demonstrated that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA concentrations in wastewater are associated with coronavirus disease 2019 (COVID-19) cases in the corresponding sewersheds. Implementing high-resolution, prospective efforts across multiple plants depends on sensitive measurements that are representative of COVID-19 cases, scalable for high-throughput analysis, and comparable across laboratories. We conducted a prospective study across eight publicly owned treatment works (POTWs). A focus on SARS-CoV-2 RNA in solids enabled us to scale up our measurements with a commercial lab partner. Samples were collected daily, and results were posted to a website within 24 h. SARS-CoV-2 RNA in daily samples correlated with the incidence of COVID-19 cases in the sewersheds; a 1 log10 increase in SARS-CoV-2 RNA in settled solids corresponds to a 0.58 log10 (4×) increase in sewershed incidence rate. SARS-CoV-2 RNA signals measured with the commercial laboratory partner were comparable across plants and comparable to measurements conducted in a university laboratory when normalized by pepper mild mottle virus (PMMoV) RNA. Results suggest that SARS-CoV-2 RNA should be detectable in settled solids for COVID-19 incidence rates of >1/100,000 (range, 0.8 to 2.3 cases per 100,000). These sensitive, representative, scalable, and comparable methods will be valuable for future efforts to scale up wastewater-based epidemiology. IMPORTANCE Access to reliable, rapid monitoring data is critical to guide response to an infectious disease outbreak. For pathogens that are shed in feces or urine, monitoring wastewater can provide a cost-effective snapshot of transmission in an entire community via a single sample. In order for a method to be useful for ongoing COVID-19 monitoring, it should be sensitive for detection of low concentrations of SARS-CoV-2, representative of incidence rates in the community, scalable to generate data quickly, and comparable across laboratories. This paper presents a method utilizing wastewater solids to meet these goals, producing measurements of SARS-CoV-2 RNA strongly associated with COVID-19 cases in the sewershed of a publicly owned treatment work. Results, provided within 24 h, can be used to detect incidence rates as low as approximately 1/100,000 cases and can be normalized for comparison across locations generating data using different methods.
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Affiliation(s)
- Marlene K Wolfe
- Department of Civil & Environmental Engineering, Stanford Universitygrid.168010.e, Stanford, California, USA
| | - Aaron Topol
- Verily Life Sciences, South San Francisco, California, USA
| | - Alisha Knudson
- Verily Life Sciences, South San Francisco, California, USA
| | - Adrian Simpson
- Verily Life Sciences, South San Francisco, California, USA
| | - Bradley White
- Verily Life Sciences, South San Francisco, California, USA
| | - Duc J Vugia
- California Department of Public Health, Infectious Diseases Branch, Richmond, California, USA
| | - Alexander T Yu
- California Department of Public Health, Infectious Diseases Branch, Richmond, California, USA
| | - Linlin Li
- County of Santa Clara Public Health Department, San Jose, California, USA
| | - Michael Balliet
- County of Santa Clara Department of Environmental Health, San Jose, California, USA
| | - Pamela Stoddard
- County of Santa Clara Public Health Department, San Jose, California, USA
| | - George S Han
- County of Santa Clara Public Health Department, San Jose, California, USA
| | - Krista R Wigginton
- Department of Civil & Environmental Engineering, University of Michigan, Ann Arbor, Michigan, USA
| | - Alexandria B Boehm
- Department of Civil & Environmental Engineering, Stanford Universitygrid.168010.e, Stanford, California, USA
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8
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Simpson A, Topol A, White BJ, Wolfe MK, Wigginton KR, Boehm AB. Effect of storage conditions on SARS-CoV-2 RNA quantification in wastewater solids. PeerJ 2021; 9:e11933. [PMID: 34447628 PMCID: PMC8364322 DOI: 10.7717/peerj.11933] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [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: 05/05/2021] [Accepted: 07/19/2021] [Indexed: 12/24/2022] Open
Abstract
SARS-CoV-2 RNA in wastewater settled solids is associated with COVID-19 incidence in sewersheds and therefore, there is a strong interest in using these measurements to augment traditional disease surveillance methods. A wastewater surveillance program should provide rapid turn around for sample measurements (ideally within 24 hours), but storage of samples is necessary for a variety of reasons including biobanking. Here we investigate how storage of wastewater solids at 4 °C, -20 °C, and -80 °C affects measured concentrations of SARS-CoV-2 RNA. We find that short term (7 or 8 d) storage of raw solids at 4 °C has little effect on measured concentrations of SARS-CoV-2 RNA, whereas longer term storage at 4 °C (35-122 d) or freezing reduces measurements by 60%, on average. We show that normalizing SARS-CoV-2 RNA concentrations by concentrations of pepper mild mottle virus (PMMoV) RNA, an endogenous wastewater virus, can correct for changes during storage as storage can have a similar effect on PMMoV RNA as on SARS-CoV-2 RNA. The reductions in SARS-CoV-2 RNA in solids during freeze thaws is less than those reported for the same target in liquid influent by several authors.
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Affiliation(s)
- Adrian Simpson
- Verily Life Sciences, South San Francisco, CA, United States of America
| | - Aaron Topol
- Verily Life Sciences, South San Francisco, CA, United States of America
| | - Bradley J. White
- Verily Life Sciences, South San Francisco, CA, United States of America
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9
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Audeh M, Dwarakanath M, Hopkins M, Knudson A, Kwok S, Morton S, Peck N, Ruckh T, Sanowar S, Scott Z, Thana P, Tong G, Topol A, Vitari AC, Vaisberg E, Wang J, Wong S. Abstract B66: High-throughput synthesis and screening for tumor-targeting liposomal nanoparticles. Cancer Immunol Res 2020. [DOI: 10.1158/2326-6074.tumimm18-b66] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
The identification of therapeutic nanoparticles formulation with preferential distribution to the tumor microenvironment remains an unsolved challenge. We have developed a high-throughput synthesis and screening platform to discover novel tumor-targeting liposomal nanoparticles. Over 1,000 unique liposomal formulations were synthesized using a combinatorial approach. The characterization of physicochemical properties (e.g., size, charge and stability) allowed the prioritization of ~500 formulations further profiled with in vitro cell-based assays (e.g., cell binding, cytotoxicity and cell barrier crossing). A subset of formulations with diverse properties was selected to create a library of 47 DNA-barcoded nanoparticles. The pharmacokinetics and biodistribution of the formulations library were measured in tumor xenografts mouse models in a highly multiplexed fashion by sequencing the DNA barcodes. The established synthesis and screening platform provides an effective approach to identify novel liposomal formulations with improved tumor and tissue distribution profile.
Note: This abstract was not presented at the conference.
Citation Format: Mark Audeh, Manali Dwarakanath, Michael Hopkins, Alisha Knudson, Sally Kwok, Stephen Morton, Nikki Peck, Tim Ruckh, Sarah Sanowar, Zach Scott, Peter Thana, Gary Tong, Aaron Topol, Alberto C Vitari, Eugeni Vaisberg, Jane Wang, Stanley Wong. High-throughput synthesis and screening for tumor-targeting liposomal nanoparticles [abstract]. In: Proceedings of the AACR Special Conference on Tumor Immunology and Immunotherapy; 2018 Nov 27-30; Miami Beach, FL. Philadelphia (PA): AACR; Cancer Immunol Res 2020;8(4 Suppl):Abstract nr B66.
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Affiliation(s)
- Mark Audeh
- Verily Life Sciences, South San Francisco, CA
| | | | | | | | - Sally Kwok
- Verily Life Sciences, South San Francisco, CA
| | | | - Nikki Peck
- Verily Life Sciences, South San Francisco, CA
| | - Tim Ruckh
- Verily Life Sciences, South San Francisco, CA
| | | | - Zach Scott
- Verily Life Sciences, South San Francisco, CA
| | - Peter Thana
- Verily Life Sciences, South San Francisco, CA
| | - Gary Tong
- Verily Life Sciences, South San Francisco, CA
| | - Aaron Topol
- Verily Life Sciences, South San Francisco, CA
| | | | | | - Jane Wang
- Verily Life Sciences, South San Francisco, CA
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10
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Schrode N, Ho SM, Yamamuro K, Dobbyn A, Huckins L, Matos MR, Cheng E, Deans PJM, Flaherty E, Barretto N, Topol A, Alganem K, Abadali S, Gregory J, Hoelzli E, Phatnani H, Singh V, Girish D, Aronow B, Mccullumsmith R, Hoffman GE, Stahl EA, Morishita H, Sklar P, Brennand KJ. Synergistic effects of common schizophrenia risk variants. Nat Genet 2019; 51:1475-1485. [PMID: 31548722 PMCID: PMC6778520 DOI: 10.1038/s41588-019-0497-5] [Citation(s) in RCA: 137] [Impact Index Per Article: 27.4] [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: 07/29/2018] [Accepted: 08/13/2019] [Indexed: 12/19/2022]
Abstract
The mechanisms by which common risk variants of small effect interact to contribute to complex genetic disorders are unclear. Here, we apply a genetic approach, using isogenic human induced pluripotent stem cells, to evaluate the effects of schizophrenia (SZ)-associated common variants predicted to function as SZ expression quantitative trait loci (eQTLs). By integrating CRISPR-mediated gene editing, activation and repression technologies to study one putative SZ eQTL (FURIN rs4702) and four top-ranked SZ eQTL genes (FURIN, SNAP91, TSNARE1 and CLCN3), our platform resolves pre- and postsynaptic neuronal deficits, recapitulates genotype-dependent gene expression differences and identifies convergence downstream of SZ eQTL gene perturbations. Our observations highlight the cell-type-specific effects of common variants and demonstrate a synergistic effect between SZ eQTL genes that converges on synaptic function. We propose that the links between rare and common variants implicated in psychiatric disease risk constitute a potentially generalizable phenomenon occurring more widely in complex genetic disorders.
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Affiliation(s)
- Nadine Schrode
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Seok-Man Ho
- Department of Stem Cell and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Graduate School of Biomedical Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kazuhiko Yamamuro
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Amanda Dobbyn
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Laura Huckins
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Marliette R Matos
- Graduate School of Biomedical Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Esther Cheng
- Graduate School of Biomedical Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - P J Michael Deans
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Erin Flaherty
- Graduate School of Biomedical Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Natalie Barretto
- Graduate School of Biomedical Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Aaron Topol
- Graduate School of Biomedical Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Khaled Alganem
- Department of Neurosciences, Institute in the College of Medicine & Life Sciences, The University of Toledo, Toledo, OH, USA
| | - Sonya Abadali
- Graduate School of Biomedical Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - James Gregory
- Center for Genomics of Neurodegenerative Disease, New York Genome Center, New York, NY, USA
| | - Emily Hoelzli
- Center for Genomics of Neurodegenerative Disease, New York Genome Center, New York, NY, USA
| | - Hemali Phatnani
- Center for Genomics of Neurodegenerative Disease, New York Genome Center, New York, NY, USA
| | - Vineeta Singh
- UC Department of Pediatrics Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Deeptha Girish
- UC Department of Pediatrics Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Bruce Aronow
- UC Department of Pediatrics Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Robert Mccullumsmith
- Department of Neurosciences, Institute in the College of Medicine & Life Sciences, The University of Toledo, Toledo, OH, USA
| | - Gabriel E Hoffman
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Eli A Stahl
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Hirofumi Morishita
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Pamela Sklar
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Stem Cell and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kristen J Brennand
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Stem Cell and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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11
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Xu J, Hartley BJ, Kurup P, Phillips A, Topol A, Xu M, Ononenyi C, Foscue E, Ho SM, Baguley TD, Carty N, Barros CS, Müller U, Gupta S, Gochman P, Rapoport J, Ellman JA, Pittenger C, Aronow B, Nairn AC, Nestor MW, Lombroso PJ, Brennand KJ. Inhibition of STEP 61 ameliorates deficits in mouse and hiPSC-based schizophrenia models. Mol Psychiatry 2018; 23:271-281. [PMID: 27752082 PMCID: PMC5395367 DOI: 10.1038/mp.2016.163] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Revised: 07/13/2016] [Accepted: 08/11/2016] [Indexed: 02/03/2023]
Abstract
The brain-specific tyrosine phosphatase, STEP (STriatal-Enriched protein tyrosine Phosphatase) is an important regulator of synaptic function. STEP normally opposes synaptic strengthening by increasing N-methyl D-aspartate glutamate receptor (NMDAR) internalization through dephosphorylation of GluN2B and inactivation of the kinases extracellular signal-regulated kinase 1/2 and Fyn. Here we show that STEP61 is elevated in the cortex in the Nrg1+/- knockout mouse model of schizophrenia (SZ). Genetic reduction or pharmacological inhibition of STEP prevents the loss of NMDARs from synaptic membranes and reverses behavioral deficits in Nrg1+/- mice. STEP61 protein is also increased in cortical lysates from the central nervous system-specific ErbB2/4 mouse model of SZ, as well as in human induced pluripotent stem cell (hiPSC)-derived forebrain neurons and Ngn2-induced excitatory neurons, from two independent SZ patient cohorts. In these selected SZ models, increased STEP61 protein levels likely reflect reduced ubiquitination and degradation. These convergent findings from mouse and hiPSC SZ models provide evidence for STEP61 dysfunction in SZ.
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Affiliation(s)
- J Xu
- Child Study Center, Yale University, New Haven, CT, USA
| | - B J Hartley
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - P Kurup
- Child Study Center, Yale University, New Haven, CT, USA
| | - A Phillips
- Hussman Institute for Autism, Baltimore, MD, USA
| | - A Topol
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - M Xu
- Department of Psychiatry, Yale University, New Haven, CT, USA
| | - C Ononenyi
- Child Study Center, Yale University, New Haven, CT, USA
| | - E Foscue
- Child Study Center, Yale University, New Haven, CT, USA
| | - S-M Ho
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Department of Developmental and Stem Cell Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - T D Baguley
- Department of Chemistry, Yale University, New Haven, CT, USA
| | - N Carty
- Child Study Center, Yale University, New Haven, CT, USA
| | - C S Barros
- Dorris Neuroscience Center, Department of Cell Biology, The Scripps Research Institute, La Jolla, CA, USA,Plymouth University School of Medicine, Plymouth UK
| | - U Müller
- Dorris Neuroscience Center, Department of Cell Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - S Gupta
- UC Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | - P Gochman
- Childhood Psychiatry Branch, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, USA
| | - J Rapoport
- Childhood Psychiatry Branch, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, USA
| | - J A Ellman
- Department of Chemistry, Yale University, New Haven, CT, USA
| | - C Pittenger
- Department of Psychiatry, Yale University, New Haven, CT, USA
| | - B Aronow
- UC Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | - A C Nairn
- Department of Psychiatry, Yale University, New Haven, CT, USA
| | - M W Nestor
- Hussman Institute for Autism, Baltimore, MD, USA
| | - P J Lombroso
- Child Study Center, Yale University, New Haven, CT, USA,Department of Psychiatry, Yale University, New Haven, CT, USA,Department of Neurobiology, Yale University, New Haven, CT, USA,Department of Psychiatry, Yale University, New Haven, CT, USA E-mail:
| | - K J Brennand
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY, 10029, USA. E-mail:
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12
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Topol A, Zhu S, Hartley BJ, English J, Hauberg ME, Tran N, Rittenhouse CA, Simone A, Ruderfer DM, Johnson J, Readhead B, Hadas Y, Gochman PA, Wang YC, Shah H, Cagney G, Rapoport J, Gage FH, Dudley JT, Sklar P, Mattheisen M, Cotter D, Fang G, Brennand KJ. Dysregulation of miRNA-9 in a Subset of Schizophrenia Patient-Derived Neural Progenitor Cells. Cell Rep 2017; 20:2525. [PMID: 28877483 DOI: 10.1016/j.celrep.2017.08.073] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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13
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Topol A, Zhu S, Hartley BJ, English J, Hauberg ME, Tran N, Rittenhouse CA, Simone A, Ruderfer DM, Johnson J, Readhead B, Hadas Y, Gochman PA, Wang YC, Shah H, Cagney G, Rapoport J, Gage FH, Dudley JT, Sklar P, Mattheisen M, Cotter D, Fang G, Brennand KJ. Dysregulation of miRNA-9 in a Subset of Schizophrenia Patient-Derived Neural Progenitor Cells. Cell Rep 2016; 15:1024-1036. [PMID: 27117414 PMCID: PMC4856588 DOI: 10.1016/j.celrep.2016.03.090] [Citation(s) in RCA: 93] [Impact Index Per Article: 11.6] [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: 12/21/2015] [Revised: 03/02/2016] [Accepted: 03/27/2016] [Indexed: 01/19/2023] Open
Abstract
Converging evidence indicates that microRNAs (miRNAs) may contribute to disease risk for schizophrenia (SZ). We show that microRNA-9 (miR-9) is abundantly expressed in control neural progenitor cells (NPCs) but also significantly downregulated in a subset of SZ NPCs. We observed a strong correlation between miR-9 expression and miR-9 regulatory activity in NPCs as well as between miR-9 levels/activity, neural migration, and diagnosis. Overexpression of miR-9 was sufficient to ameliorate a previously reported neural migration deficit in SZ NPCs, whereas knockdown partially phenocopied aberrant migration in control NPCs. Unexpectedly, proteomic- and RNA sequencing (RNA-seq)-based analysis revealed that these effects were mediated primarily by small changes in expression of indirect miR-9 targets rather than large changes in direct miR-9 targets; these indirect targets are enriched for migration-associated genes. Together, these data indicate that aberrant levels and activity of miR-9 may be one of the many factors that contribute to SZ risk, at least in a subset of patients.
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Affiliation(s)
- Aaron Topol
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA
| | - Shijia Zhu
- Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, 1425 Madison Avenue, New York, NY 10029, USA
| | - Brigham J Hartley
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA
| | - Jane English
- Department of Psychiatry, Royal College of Surgeons in Ireland, Beaumont Hospital, Beaumont, Dublin 9, Ireland
| | - Mads E Hauberg
- Department of Biomedicine and Centre for Integrative Sequencing (iSEQ), Aarhus University, Wilhelm Meyers Allé 4, Aarhus 8000 C, Denmark; The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Aarhus University, Wilhelm Meyers Allé 4, Aarhus 8000 C, Denmark
| | - Ngoc Tran
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA
| | - Chelsea Ann Rittenhouse
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA
| | - Anthony Simone
- Laboratory of Genetics, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Douglas M Ruderfer
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA
| | - Jessica Johnson
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA
| | - Ben Readhead
- Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, 1425 Madison Avenue, New York, NY 10029, USA
| | - Yoav Hadas
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA
| | - Peter A Gochman
- Childhood Psychiatry Branch, National Institute of Mental Health, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ying-Chih Wang
- Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, 1425 Madison Avenue, New York, NY 10029, USA
| | - Hardik Shah
- Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, 1425 Madison Avenue, New York, NY 10029, USA
| | - Gerard Cagney
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Judith Rapoport
- Childhood Psychiatry Branch, National Institute of Mental Health, National Institutes of Health, Bethesda, MD 20892, USA
| | - Fred H Gage
- Laboratory of Genetics, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Joel T Dudley
- Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, 1425 Madison Avenue, New York, NY 10029, USA
| | - Pamela Sklar
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA
| | - Manuel Mattheisen
- Department of Biomedicine and Centre for Integrative Sequencing (iSEQ), Aarhus University, Wilhelm Meyers Allé 4, Aarhus 8000 C, Denmark; The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Aarhus University, Wilhelm Meyers Allé 4, Aarhus 8000 C, Denmark
| | - David Cotter
- Department of Psychiatry, Royal College of Surgeons in Ireland, Beaumont Hospital, Beaumont, Dublin 9, Ireland
| | - Gang Fang
- Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, 1425 Madison Avenue, New York, NY 10029, USA.
| | - Kristen J Brennand
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA.
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14
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Topol A, Zhu S, Tran N, Simone A, Fang G, Brennand KJ. Altered WNT Signaling in Human Induced Pluripotent Stem Cell Neural Progenitor Cells Derived from Four Schizophrenia Patients. Biol Psychiatry 2015; 78:e29-34. [PMID: 25708228 PMCID: PMC4520784 DOI: 10.1016/j.biopsych.2014.12.028] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Revised: 12/05/2014] [Accepted: 12/10/2014] [Indexed: 12/21/2022]
Affiliation(s)
- Aaron Topol
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029
| | - Shijia Zhu
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029
| | - Ngoc Tran
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029
| | - Anthony Simone
- Salk Institute for Biological Studies, Laboratory of Genetics, 10010 North Torrey Pines Road, La Jolla CA 92037
| | - Gang Fang
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029
| | - Kristen J. Brennand
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029
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15
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Ho SM, Topol A, Brennand KJ. From "directed differentiation" to "neuronal induction": modeling neuropsychiatric disease. Biomark Insights 2015; 10:31-41. [PMID: 26045654 PMCID: PMC4444490 DOI: 10.4137/bmi.s20066] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [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: 01/06/2015] [Revised: 02/22/2015] [Accepted: 02/24/2015] [Indexed: 11/23/2022] Open
Abstract
Aberrant behavior and function of neurons are believed to be the primary causes of most neurological diseases and psychiatric disorders. Human postmortem samples have limited availability and, while they provide clues to the state of the brain after a prolonged illness, they offer limited insight into the factors contributing to disease onset. Conversely, animal models cannot recapitulate the polygenic origins of neuropsychiatric disease. Novel methods, such as somatic cell reprogramming, deliver nearly limitless numbers of pathogenic human neurons for the study of the mechanism of neuropsychiatric disease initiation and progression. First, this article reviews the advent of human induced pluripotent stem cell (hiPSC) technology and introduces two major methods, “directed differentiation” and “neuronal induction,” by which it is now possible to generate neurons for modeling neuropsychiatric disease. Second, it discusses the recent applications, and the limitations, of these technologies to in vitro studies of psychiatric disorders.
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Affiliation(s)
- Seok-Man Ho
- Icahn School of Medicine at Mount Sinai, Department of Psychiatry, New York, NY, USA
| | - Aaron Topol
- Icahn School of Medicine at Mount Sinai, Department of Psychiatry, New York, NY, USA
| | - Kristen J Brennand
- Icahn School of Medicine at Mount Sinai, Department of Psychiatry, New York, NY, USA
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16
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Topol A, Tran NN, Brennand KJ. A guide to generating and using hiPSC derived NPCs for the study of neurological diseases. J Vis Exp 2015:e52495. [PMID: 25742222 DOI: 10.3791/52495] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Post-mortem studies of neurological diseases are not ideal for identifying the underlying causes of disease initiation, as many diseases include a long period of disease progression prior to the onset of symptoms. Because fibroblasts from patients and healthy controls can be efficiently reprogrammed into human induced pluripotent stem cells (hiPSCs), and subsequently differentiated into neural progenitor cells (NPCs) and neurons for the study of these diseases, it is now possible to recapitulate the developmental events that occurred prior to symptom onset in patients. We present a method by which to efficiently differentiate hiPSCs into NPCs, which in addition to being capable of further differentiation into functional neurons, can also be robustly passaged, freeze-thawed or transitioned to grow as neurospheres, enabling rapid genetic screening to identify the molecular factors that impact cellular phenotypes including replication, migration, oxidative stress and/or apoptosis. Patient derived hiPSC NPCs are a unique platform, ideally suited for the empirical testing of the cellular or molecular consequences of manipulating gene expression.
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Affiliation(s)
- Aaron Topol
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai
| | - Ngoc N Tran
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai
| | - Kristen J Brennand
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai; Department of Neuroscience, Icahn School of Medicine at Mount Sinai;
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Moczała M, Sosa N, Topol A, Gotszalk T. Investigation of multi-junction solar cells using electrostatic force microscopy methods. Ultramicroscopy 2014; 141:1-8. [DOI: 10.1016/j.ultramic.2014.02.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Revised: 02/17/2014] [Accepted: 02/25/2014] [Indexed: 11/28/2022]
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Ladran I, Tran N, Topol A, Brennand KJ. Neural stem and progenitor cells in health and disease. Wiley Interdiscip Rev Syst Biol Med 2013; 5:701-15. [PMID: 24068527 DOI: 10.1002/wsbm.1239] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Revised: 04/17/2013] [Accepted: 07/18/2013] [Indexed: 01/01/2023]
Abstract
Neural stem/progenitor cells (NSPCs) have the potential to differentiate into neurons, astrocytes, and/or oligodendrocytes. Because these cells can be expanded in culture, they represent a vast source of neural cells. With the recent discovery that patient fibroblasts can be reprogrammed directly into induced NSPCs, the regulation of NSPC fate and function, in the context of cell-based disease models and patient-specific cell-replacement therapies, warrants review.
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Affiliation(s)
- Ian Ladran
- Department of Psychiatry, Mount Sinai School of Medicine, New York, NY, USA
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