1
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Wu M, Hanly A, Gibson F, Fisher R, Rogers S, Park K, Zuger A, Kuang K, Kalin JH, Nocco S, Cole M, Xiao A, Agus F, Labadorf A, Beck S, Collard M, Cole PA, Alani RM. The CoREST repressor complex mediates phenotype switching and therapy resistance in melanoma. J Clin Invest 2024; 134:e171063. [PMID: 38300709 PMCID: PMC10940100 DOI: 10.1172/jci171063] [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: 04/03/2023] [Accepted: 01/22/2024] [Indexed: 02/03/2024] Open
Abstract
Virtually all patients with BRAF-mutant melanoma develop resistance to MAPK inhibitors largely through nonmutational events. Although the epigenetic landscape is shown to be altered in therapy-resistant melanomas and other cancers, a specific targetable epigenetic mechanism has not been validated. Here, we evaluated the corepressor for element 1-silencing transcription factor (CoREST) epigenetic repressor complex and the recently developed bivalent inhibitor corin within the context of melanoma phenotype plasticity and therapeutic resistance. We found that CoREST was a critical mediator of the major distinct melanoma phenotypes and that corin treatment of melanoma cells led to phenotype reprogramming. Global assessment of transcript and chromatin changes conferred by corin revealed specific effects on histone marks connected to epithelial-mesenchymal transition-associated (EMT-associated) transcription factors and the dual-specificity phosphatases (DUSPs). Remarkably, treatment of BRAF inhibitor-resistant (BRAFi-R) melanomas with corin promoted resensitization to BRAFi therapy. DUSP1 was consistently downregulated in BRAFi-R melanomas, which was reversed by corin treatment and associated with inhibition of p38 MAPK activity and resensitization to BRAFi therapies. Moreover, this activity was recapitulated by the p38 MAPK inhibitor BIRB 796. These findings identify the CoREST repressor complex as a central mediator of melanoma phenotype plasticity and resistance to targeted therapy and suggest that CoREST inhibitors may prove beneficial for patients with BRAFi-resistant melanoma.
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Affiliation(s)
- Muzhou Wu
- Department of Dermatology, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts, USA
| | - Ailish Hanly
- Department of Dermatology, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts, USA
| | - Frederick Gibson
- Department of Dermatology, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts, USA
| | - Robert Fisher
- Department of Dermatology, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts, USA
| | - Samantha Rogers
- Department of Dermatology, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts, USA
| | - Kihyun Park
- Department of Dermatology, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts, USA
| | - Angelina Zuger
- Department of Dermatology, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts, USA
| | - Kevin Kuang
- Department of Dermatology, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts, USA
| | - Jay H. Kalin
- Division of Genetics, Departments of Medicine and Biological Chemistry and Molecular Pharmacology, Harvard Medical School and Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Sarah Nocco
- Department of Dermatology, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts, USA
| | - Matthew Cole
- Department of Dermatology, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts, USA
| | - Amy Xiao
- Department of Dermatology, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts, USA
| | - Filisia Agus
- Bioinformatics Program, Boston University, Boston, Massachusetts, USA
| | - Adam Labadorf
- Bioinformatics Program, Boston University, Boston, Massachusetts, USA
- Department of Neurology, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Samuel Beck
- Department of Dermatology, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts, USA
| | - Marianne Collard
- Department of Dermatology, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts, USA
| | - Philip A. Cole
- Division of Genetics, Departments of Medicine and Biological Chemistry and Molecular Pharmacology, Harvard Medical School and Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Rhoda M. Alani
- Department of Dermatology, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts, USA
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2
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Xiao A, Beatty CJ, Choudhary S, Akilov OE. CD5+ Primary Cutaneous Diffuse Large B-Cell Lymphoma, Leg Type, Presenting as an Asymptomatic Nodule. Hematol Rep 2023; 15:513-517. [PMID: 37754668 PMCID: PMC10531099 DOI: 10.3390/hematolrep15030053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 07/05/2023] [Accepted: 08/21/2023] [Indexed: 09/28/2023] Open
Abstract
Primary cutaneous diffuse large B-cell lymphoma, leg type (PCDLBCL-LT), is a rare and aggressive variant of primary cutaneous lymphoma that typically expresses B cells as well as MUM1/IRF4, BCL2, and FOXP1, whereas BCL6 may be present or undetectable. We present a case of CD5+ PCDLBCL-LT presenting as a 6 mm pink-bluish nodule on the mid-left thigh, which was concerning for basal cell carcinoma. The histological examination reveals the presence of an intradermal proliferation of large, atypical CD5+, CD20+ BCL2+, BCL6+, MUM-1+, and Cyclin-D1+ lymphocytes in a nodular, diffuse interstitial and perivascular distribution. Because the patient presented with a small, single nodule, the systemic treatment of multiagent chemotherapy was avoided and localized electron beam radiation therapy with rituximab was initiated instead, achieving complete response. Early identification of PCDLBCL-LT is key for maximal therapeutic benefit and prognosis; it is important to consider PCDLBCL-LT on the differential when evaluating small, single nodules on the lower extremities of elderly patients.
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Affiliation(s)
- Amy Xiao
- School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA;
| | - Colleen J. Beatty
- Department of Dermatology, University of Pittsburgh, Pittsburgh, PA 15261-2109, USA; (C.J.B.); (S.C.)
| | - Sonal Choudhary
- Department of Dermatology, University of Pittsburgh, Pittsburgh, PA 15261-2109, USA; (C.J.B.); (S.C.)
| | - Oleg E. Akilov
- Department of Dermatology, University of Pittsburgh, Pittsburgh, PA 15261-2109, USA; (C.J.B.); (S.C.)
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3
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Phan T, Brozak S, Pell B, Gitter A, Xiao A, Mena KD, Kuang Y, Wu F. A simple SEIR-V model to estimate COVID-19 prevalence and predict SARS-CoV-2 transmission using wastewater-based surveillance data. Sci Total Environ 2023; 857:159326. [PMID: 36220466 PMCID: PMC9547654 DOI: 10.1016/j.scitotenv.2022.159326] [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] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 09/15/2022] [Accepted: 10/05/2022] [Indexed: 06/12/2023]
Abstract
Wastewater-based surveillance (WBS) has been widely used as a public health tool to monitor SARS-CoV-2 transmission. However, epidemiological inference from WBS data remains understudied and limits its application. In this study, we have established a quantitative framework to estimate COVID-19 prevalence and predict SARS-CoV-2 transmission through integrating WBS data into an SEIR-V model. We conceptually divide the individual-level viral shedding course into exposed, infectious, and recovery phases as an analogy to the compartments in a population-level SEIR model. We demonstrated that the effect of temperature on viral losses in the sewer can be straightforwardly incorporated in our framework. Using WBS data from the second wave of the pandemic (Oct 02, 2020-Jan 25, 2021) in the Greater Boston area, we showed that the SEIR-V model successfully recapitulates the temporal dynamics of viral load in wastewater and predicts the true number of cases peaked earlier and higher than the number of reported cases by 6-16 days and 8.3-10.2 folds (R = 0.93). This work showcases a simple yet effective method to bridge WBS and quantitative epidemiological modeling to estimate the prevalence and transmission of SARS-CoV-2 in the sewershed, which could facilitate the application of wastewater surveillance of infectious diseases for epidemiological inference and inform public health actions.
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Affiliation(s)
- Tin Phan
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, NM, USA
| | - Samantha Brozak
- School of Mathematical and Statistical Sciences, Arizona State University, AZ, USA
| | - Bruce Pell
- Department of Mathematics and Computer Science, Lawrence Technological University, MI, USA
| | - Anna Gitter
- The University of Texas Health Science Center at Houston, School of Public Health, Houston, TX, USA 77030
| | - Amy Xiao
- Center for Microbiome Informatics and Therapeutics; Department of Biological Engineering, Massachusetts Institute of Technology
| | - Kristina D Mena
- The University of Texas Health Science Center at Houston, School of Public Health, Houston, TX, USA 77030
| | - Yang Kuang
- School of Mathematical and Statistical Sciences, Arizona State University, AZ, USA.
| | - Fuqing Wu
- The University of Texas Health Science Center at Houston, School of Public Health, Houston, TX, USA 77030.
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4
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Armas F, Chandra F, Lee WL, Gu X, Chen H, Xiao A, Leifels M, Wuertz S, Alm EJ, Thompson J. Contextualizing Wastewater-Based surveillance in the COVID-19 vaccination era. Environ Int 2023; 171:107718. [PMID: 36584425 PMCID: PMC9783150 DOI: 10.1016/j.envint.2022.107718] [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] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 12/16/2022] [Accepted: 12/22/2022] [Indexed: 06/17/2023]
Abstract
SARS-CoV-2 wastewater-based surveillance (WBS) offers a tool for cost-effective oversight of a population's infections. In the past two years, WBS has proven to be crucial for managing the pandemic across different geographical regions. However, the changing context of the pandemic due to high levels of COVID-19 vaccination warrants a closer examination of its implication towards SARS-CoV-2 WBS. Two main questions were raised: 1) Does vaccination cause shedding of viral signatures without infection? 2) Does vaccination affect the relationship between wastewater and clinical data? To answer, we review historical reports of shedding from viral vaccines in use prior to the COVID-19 pandemic including for polio, rotavirus, influenza and measles infection and provide a perspective on the implications of different COVID-19 vaccination strategies with regard to the potential shedding of viral signatures into the sewershed. Additionally, we reviewed studies that looked into the relationship between wastewater and clinical data and how vaccination campaigns could have affected the relationship. Finally, analyzing wastewater and clinical data from the Netherlands, we observed changes in the relationship concomitant with increasing vaccination coverage and switches in dominant variants of concern. First, that no vaccine-derived shedding is expected from the current commercial pipeline of COVID-19 vaccines that may confound interpretation of WBS data. Secondly, that breakthrough infections from vaccinated individuals contribute significantly to wastewater signals and must be interpreted in light of the changing dynamics of shedding from new variants of concern.
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Affiliation(s)
- Federica Armas
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore; Campus for Research Excellence and Technological Enterprise (CREATE), Singapore
| | - Franciscus Chandra
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore; Campus for Research Excellence and Technological Enterprise (CREATE), Singapore
| | - Wei Lin Lee
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore; Campus for Research Excellence and Technological Enterprise (CREATE), Singapore
| | - Xiaoqiong Gu
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore; Campus for Research Excellence and Technological Enterprise (CREATE), Singapore
| | - Hongjie Chen
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore; Campus for Research Excellence and Technological Enterprise (CREATE), Singapore
| | - Amy Xiao
- Department of Biological Engineering, Massachusetts Institute of Technology, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology
| | - Mats Leifels
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore
| | - Stefan Wuertz
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore; School of Civil and Environmental Engineering, Nanyang Technological University, Singapore
| | - Eric J Alm
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore; Campus for Research Excellence and Technological Enterprise (CREATE), Singapore; Department of Biological Engineering, Massachusetts Institute of Technology, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology; Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Janelle Thompson
- Campus for Research Excellence and Technological Enterprise (CREATE), Singapore; Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore; Asian School of the Environment, Nanyang Technological University, Singapore.
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5
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D'Aoust PM, Tian X, Towhid ST, Xiao A, Mercier E, Hegazy N, Jia JJ, Wan S, Kabir MP, Fang W, Fuzzen M, Hasing M, Yang MI, Sun J, Plaza-Diaz J, Zhang Z, Cowan A, Eid W, Stephenson S, Servos MR, Wade MJ, MacKenzie AE, Peng H, Edwards EA, Pang XL, Alm EJ, Graber TE, Delatolla R. Wastewater to clinical case (WC) ratio of COVID-19 identifies insufficient clinical testing, onset of new variants of concern and population immunity in urban communities. Sci Total Environ 2022; 853:158547. [PMID: 36067855 PMCID: PMC9444156 DOI: 10.1016/j.scitotenv.2022.158547] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 07/10/2022] [Accepted: 09/01/2022] [Indexed: 05/14/2023]
Abstract
Clinical testing has been the cornerstone of public health monitoring and infection control efforts in communities throughout the COVID-19 pandemic. With the anticipated reduction of clinical testing as the disease moves into an endemic state, SARS-CoV-2 wastewater surveillance (WWS) will have greater value as an important diagnostic tool. An in-depth analysis and understanding of the metrics derived from WWS is required to interpret and utilize WWS-acquired data effectively (McClary-Gutierrez et al., 2021; O'Keeffe, 2021). In this study, the SARS-CoV-2 wastewater signal to clinical cases (WC) ratio was investigated across seven cities in Canada over periods ranging from 8 to 21 months. This work demonstrates that significant increases in the WC ratio occurred when clinical testing eligibility was modified to appointment-only testing, identifying a period of insufficient clinical testing (resulting in a reduction to testing access and a reduction in the number of daily tests) in these communities, despite increases in the wastewater signal. Furthermore, the WC ratio decreased significantly in 6 of the 7 studied locations, serving as a potential signal of the emergence of the Alpha variant of concern (VOC) in a relatively non-immunized community (40-60 % allelic proportion), while a more muted decrease in the WC ratio signaled the emergence of the Delta VOC in a relatively well-immunized community (40-60 % allelic proportion). Finally, a significant decrease in the WC ratio signaled the emergence of the Omicron VOC, likely because of the variant's greater effectiveness at evading immunity, leading to a significant number of new reported clinical cases, even when community immunity was high. The WC ratio, used as an additional monitoring metric, could complement clinical case counts and wastewater signals as individual metrics in its potential ability to identify important epidemiological occurrences, adding value to WWS as a diagnostic technology during the COVID-19 pandemic and likely for future pandemics.
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Affiliation(s)
- Patrick M D'Aoust
- Department of Civil Engineering, University of Ottawa, Ottawa, Canada
| | - Xin Tian
- Department of Civil Engineering, University of Ottawa, Ottawa, Canada
| | | | - Amy Xiao
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States of America
| | - Elisabeth Mercier
- Department of Civil Engineering, University of Ottawa, Ottawa, Canada
| | - Nada Hegazy
- Department of Civil Engineering, University of Ottawa, Ottawa, Canada
| | - Jian-Jun Jia
- Department of Civil Engineering, University of Ottawa, Ottawa, Canada
| | - Shen Wan
- Department of Civil Engineering, University of Ottawa, Ottawa, Canada
| | - Md Pervez Kabir
- Department of Civil Engineering, University of Ottawa, Ottawa, Canada
| | - Wanting Fang
- Department of Civil Engineering, University of Ottawa, Ottawa, Canada
| | - Meghan Fuzzen
- Department of Biology, University of Waterloo, Waterloo, Canada
| | - Maria Hasing
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Canada
| | - Minqing Ivy Yang
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Canada
| | - Jianxian Sun
- Department of Chemistry, University of Toronto, Toronto, Canada
| | - Julio Plaza-Diaz
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Canada
| | - Zhihao Zhang
- Department of Civil Engineering, University of Ottawa, Ottawa, Canada
| | - Aaron Cowan
- Department of Civil Engineering, University of Ottawa, Ottawa, Canada
| | - Walaa Eid
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Canada
| | - Sean Stephenson
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Canada
| | - Mark R Servos
- Department of Biology, University of Waterloo, Waterloo, Canada
| | - Matthew J Wade
- Data, Analytics and Surveillance Group, UK Health Security Agency, London, United Kingdom
| | - Alex E MacKenzie
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Canada
| | - Hui Peng
- Department of Chemistry, University of Toronto, Toronto, Canada
| | - Elizabeth A Edwards
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Canada
| | - Xiao-Li Pang
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Canada
| | - Eric J Alm
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States of America
| | - Tyson E Graber
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Canada
| | - Robert Delatolla
- Department of Civil Engineering, University of Ottawa, Ottawa, Canada.
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6
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Duvallet C, Wu F, McElroy KA, Imakaev M, Endo N, Xiao A, Zhang J, Floyd-O’Sullivan R, Powell MM, Mendola S, Wilson ST, Cruz F, Melman T, Sathyanarayana CL, Olesen SW, Erickson TB, Ghaeli N, Chai P, Alm EJ, Matus M. Nationwide Trends in COVID-19 Cases and SARS-CoV-2 RNA Wastewater Concentrations in the United States. ACS ES T Water 2022; 2:1899-1909. [PMID: 36380771 PMCID: PMC9092192 DOI: 10.1021/acsestwater.1c00434] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Wastewater-based epidemiology has emerged as a promising technology for population-level surveillance of COVID-19. In this study, we present results of a large nationwide SARS-CoV-2 wastewater monitoring system in the United States. We profile 55 locations with at least six months of sampling from April 2020 to May 2021. These locations represent more than 12 million individuals across 19 states. Samples were collected approximately weekly by wastewater treatment utilities as part of a regular wastewater surveillance service and analyzed for SARS-CoV-2 RNA concentrations. SARS-CoV-2 RNA concentrations were normalized to pepper mild mottle virus, an indicator of fecal matter in wastewater. We show that wastewater data reflect temporal and geographic trends in clinical COVID-19 cases and investigate the impact of normalization on correlations with case data within and across locations. We also provide key lessons learned from our broad-scale implementation of wastewater-based epidemiology, which can be used to inform wastewater-based epidemiology approaches for future emerging diseases. This work demonstrates that wastewater surveillance is a feasible approach for nationwide population-level monitoring of COVID-19 disease. With an evolving epidemic and effective vaccines against SARS-CoV-2, wastewater-based epidemiology can serve as a passive surveillance approach for detecting changing dynamics or resurgences of the virus.
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Affiliation(s)
- Claire Duvallet
- Biobot
Analytics, Inc., Cambridge, Massachusetts 02139, United States
| | - Fuqing Wu
- Center
for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- MIT
Department of Biological Engineering, Massachusetts
Institute of Technology, Cambridge, Massachusetts 02142, United States
| | - Kyle A. McElroy
- Biobot
Analytics, Inc., Cambridge, Massachusetts 02139, United States
| | - Maxim Imakaev
- Biobot
Analytics, Inc., Cambridge, Massachusetts 02139, United States
| | - Noriko Endo
- Biobot
Analytics, Inc., Cambridge, Massachusetts 02139, United States
| | - Amy Xiao
- Center
for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- MIT
Department of Biological Engineering, Massachusetts
Institute of Technology, Cambridge, Massachusetts 02142, United States
| | - Jianbo Zhang
- Center
for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- MIT
Department of Biological Engineering, Massachusetts
Institute of Technology, Cambridge, Massachusetts 02142, United States
| | | | - Morgan M. Powell
- Biobot
Analytics, Inc., Cambridge, Massachusetts 02139, United States
| | - Samuel Mendola
- Biobot
Analytics, Inc., Cambridge, Massachusetts 02139, United States
| | - Shane T. Wilson
- Biobot
Analytics, Inc., Cambridge, Massachusetts 02139, United States
| | - Francis Cruz
- Biobot
Analytics, Inc., Cambridge, Massachusetts 02139, United States
| | - Tamar Melman
- Broad
Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | | | - Scott W. Olesen
- Biobot
Analytics, Inc., Cambridge, Massachusetts 02139, United States
| | - Timothy B. Erickson
- Department
of Emergency Medicine, Harvard Medical School, Boston, Massachusetts 02115, United States
- Division
of Medical Toxicology, Department of Emergency Medicine, Brigham and Women’s Hospital, Boston, Massachusetts 02115, United States
- Harvard
Humanitarian Initiative, Cambridge, Massachusetts 02138, United States
| | - Newsha Ghaeli
- Biobot
Analytics, Inc., Cambridge, Massachusetts 02139, United States
| | - Peter Chai
- Division
of Medical Toxicology, Department of Emergency Medicine, Brigham and Women’s Hospital, Boston, Massachusetts 02115, United States
- The
Fenway Institute, Boston, Massachusetts 02215, United States
- The
Koch Institute for Integrated Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139-4307, United States
| | - Eric J. Alm
- Biobot
Analytics, Inc., Cambridge, Massachusetts 02139, United States
- Center
for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- MIT
Department of Biological Engineering, Massachusetts
Institute of Technology, Cambridge, Massachusetts 02142, United States
- Broad
Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Mariana Matus
- Biobot
Analytics, Inc., Cambridge, Massachusetts 02139, United States
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7
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Duvallet C, Wu F, McElroy KA, Imakaev M, Endo N, Xiao A, Zhang J, Floyd-O'Sullivan R, Powell MM, Mendola S, Wilson ST, Cruz F, Melman T, Sathyanarayana CL, Olesen SW, Erickson TB, Ghaeli N, Chai P, Alm EJ, Matus M. Nationwide Trends in COVID-19 Cases and SARS-CoV-2 RNA Wastewater Concentrations in the United States. ACS ES T Water 2022; 2:1899-1909. [PMID: 36380771 DOI: 10.1101/2021.09.08.21263283] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Wastewater-based epidemiology has emerged as a promising technology for population-level surveillance of COVID-19. In this study, we present results of a large nationwide SARS-CoV-2 wastewater monitoring system in the United States. We profile 55 locations with at least six months of sampling from April 2020 to May 2021. These locations represent more than 12 million individuals across 19 states. Samples were collected approximately weekly by wastewater treatment utilities as part of a regular wastewater surveillance service and analyzed for SARS-CoV-2 RNA concentrations. SARS-CoV-2 RNA concentrations were normalized to pepper mild mottle virus, an indicator of fecal matter in wastewater. We show that wastewater data reflect temporal and geographic trends in clinical COVID-19 cases and investigate the impact of normalization on correlations with case data within and across locations. We also provide key lessons learned from our broad-scale implementation of wastewater-based epidemiology, which can be used to inform wastewater-based epidemiology approaches for future emerging diseases. This work demonstrates that wastewater surveillance is a feasible approach for nationwide population-level monitoring of COVID-19 disease. With an evolving epidemic and effective vaccines against SARS-CoV-2, wastewater-based epidemiology can serve as a passive surveillance approach for detecting changing dynamics or resurgences of the virus.
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Affiliation(s)
- Claire Duvallet
- Biobot Analytics, Inc., Cambridge, Massachusetts 02139, United States
| | - Fuqing Wu
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- MIT Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, United States
| | - Kyle A McElroy
- Biobot Analytics, Inc., Cambridge, Massachusetts 02139, United States
| | - Maxim Imakaev
- Biobot Analytics, Inc., Cambridge, Massachusetts 02139, United States
| | - Noriko Endo
- Biobot Analytics, Inc., Cambridge, Massachusetts 02139, United States
| | - Amy Xiao
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- MIT Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, United States
| | - Jianbo Zhang
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- MIT Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, United States
| | | | - Morgan M Powell
- Biobot Analytics, Inc., Cambridge, Massachusetts 02139, United States
| | - Samuel Mendola
- Biobot Analytics, Inc., Cambridge, Massachusetts 02139, United States
| | - Shane T Wilson
- Biobot Analytics, Inc., Cambridge, Massachusetts 02139, United States
| | - Francis Cruz
- Biobot Analytics, Inc., Cambridge, Massachusetts 02139, United States
| | - Tamar Melman
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | | | - Scott W Olesen
- Biobot Analytics, Inc., Cambridge, Massachusetts 02139, United States
| | - Timothy B Erickson
- Department of Emergency Medicine, Harvard Medical School, Boston, Massachusetts 02115, United States
- Division of Medical Toxicology, Department of Emergency Medicine, Brigham and Women's Hospital, Boston, Massachusetts 02115, United States
- Harvard Humanitarian Initiative, Cambridge, Massachusetts 02138, United States
| | - Newsha Ghaeli
- Biobot Analytics, Inc., Cambridge, Massachusetts 02139, United States
| | - Peter Chai
- Division of Medical Toxicology, Department of Emergency Medicine, Brigham and Women's Hospital, Boston, Massachusetts 02115, United States
- The Fenway Institute, Boston, Massachusetts 02215, United States
- The Koch Institute for Integrated Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139-4307, United States
| | - Eric J Alm
- Biobot Analytics, Inc., Cambridge, Massachusetts 02139, United States
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- MIT Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, United States
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Mariana Matus
- Biobot Analytics, Inc., Cambridge, Massachusetts 02139, United States
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8
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Affiliation(s)
- Amy Xiao
- School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | | | - Oleg E. Akilov
- Cutaneous Lymphoma Program, Department of Dermatology, University of Pittsburgh, Pittsburgh, Pennsylvania
- Correspondence to: Oleg E. Akilov, MD, PhD, Department of Dermatology, University of Pittsburgh, 3708 Fifth Avenue, 5th Floor, Suite 500.68, Pittsburgh, PA 15213.
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9
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Lee WL, Armas F, Guarneri F, Gu X, Formenti N, Wu F, Chandra F, Parisio G, Chen H, Xiao A, Romeo C, Scali F, Tonni M, Leifels M, Chua FJD, Kwok GW, Tay JY, Pasquali P, Thompson J, Alborali GL, Alm EJ. Rapid displacement of SARS-CoV-2 variant Delta by Omicron revealed by allele-specific PCR in wastewater. Water Res 2022; 221:118809. [PMID: 35841797 PMCID: PMC9250349 DOI: 10.1016/j.watres.2022.118809] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 06/18/2022] [Accepted: 07/01/2022] [Indexed: 05/06/2023]
Abstract
On November 26, 2021, the B.1.1.529 COVID-19 variant was classified as the Omicron variant of concern (VOC). Reports of higher transmissibility and potential immune evasion triggered flight bans and heightened health control measures across the world to stem its distribution. Wastewater-based surveillance has demonstrated to be a useful complement for clinical community-based tracking of SARS-CoV-2 variants. Using design principles of our previous assays that detect SARS-CoV-2 variants (Alpha and Delta), we developed an allele-specific RT-qPCR assay which simultaneously targets the stretch of mutations from Q493R to Q498R for quantitative detection of the Omicron variant in wastewater. We report their validation against 10-month longitudinal samples from the influent of a wastewater treatment plant in Italy. SARS-CoV-2 RNA concentrations and variant frequencies in wastewater determined using these variant assays agree with clinical cases, revealing rapid displacement of the Delta variant by the Omicron variant within three weeks. These variant trends, when mapped against vaccination rates, support clinical studies that found the rapid emergence of SARS-CoV-2 Omicron variant being associated with an infection advantage over Delta in vaccinated persons. These data reinforce the versatility, utility and accuracy of these open-sourced methods using allele-specific RT-qPCR for tracking the dynamics of variant displacement in communities through wastewater for informed public health responses.
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Affiliation(s)
- Wei Lin Lee
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore; Campus for Research Excellence and Technological Enterprise (CREATE), Singapore
| | - Federica Armas
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore; Campus for Research Excellence and Technological Enterprise (CREATE), Singapore
| | - Flavia Guarneri
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna "Bruno Ubertini" (IZSLER), Italy
| | - Xiaoqiong Gu
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore; Campus for Research Excellence and Technological Enterprise (CREATE), Singapore
| | - Nicoletta Formenti
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna "Bruno Ubertini" (IZSLER), Italy
| | - Fuqing Wu
- Center for Infectious Disease, Department of Epidemiology, Human Genetics, and Environmental Sciences, University of Texas School of Public Health, Houston, TX, USA
| | - Franciscus Chandra
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore; Campus for Research Excellence and Technological Enterprise (CREATE), Singapore
| | - Giovanni Parisio
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna "Bruno Ubertini" (IZSLER), Italy
| | - Hongjie Chen
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore; Campus for Research Excellence and Technological Enterprise (CREATE), Singapore
| | - Amy Xiao
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, USA; Department of Biological Engineering, Massachusetts Institute of Technology, USA
| | - Claudia Romeo
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna "Bruno Ubertini" (IZSLER), Italy
| | - Federico Scali
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna "Bruno Ubertini" (IZSLER), Italy
| | - Matteo Tonni
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna "Bruno Ubertini" (IZSLER), Italy
| | - Mats Leifels
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore
| | - Feng Jun Desmond Chua
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore
| | - Germaine Wc Kwok
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore
| | - Joey Yr Tay
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore; Campus for Research Excellence and Technological Enterprise (CREATE), Singapore
| | - Paolo Pasquali
- Dipartimento di Sicurezza Alimentare, Nutrizione e Sanità Pubblica Veterinaria, Istituto Superiore di Sanità, Italy
| | - Janelle Thompson
- Campus for Research Excellence and Technological Enterprise (CREATE), Singapore; Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore; Asian School of the Environment, Nanyang Technological University, Singapore.
| | - Giovanni Loris Alborali
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna "Bruno Ubertini" (IZSLER), Italy
| | - Eric J Alm
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore; Campus for Research Excellence and Technological Enterprise (CREATE), Singapore; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, USA; Department of Biological Engineering, Massachusetts Institute of Technology, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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10
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Wu F, Lee WL, Chen H, Gu X, Chandra F, Armas F, Xiao A, Leifels M, Rhode SF, Wuertz S, Thompson J, Alm EJ. Making waves: Wastewater surveillance of SARS-CoV-2 in an endemic future. Water Res 2022; 219:118535. [PMID: 35605390 PMCID: PMC9062764 DOI: 10.1016/j.watres.2022.118535] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 04/29/2022] [Accepted: 04/30/2022] [Indexed: 05/28/2023]
Abstract
Wastewater-based surveillance (WBS) has been widely used as a public health tool to monitor the emergence and spread of SARS-CoV-2 infections in populations during the COVID-19 pandemic. Coincident with the global vaccination efforts, the world is also enduring new waves of SARS-CoV-2 variants. Reinfections and vaccine breakthroughs suggest an endemic future where SARS-CoV-2 continues to persist in the general population. In this treatise, we aim to explore the future roles of wastewater surveillance. Practically, WBS serves as a relatively affordable and non-invasive tool for mass surveillance of SARS-CoV-2 infection while minimizing privacy concerns, attributes that make it extremely suited for its long-term usage. In an endemic future, the utility of WBS will include 1) monitoring the trend of viral loads of targets in wastewater for quantitative estimate of changes in disease incidence; 2) sampling upstream for pinpointing infections in neighborhoods and at the building level; 3) integrating wastewater and clinical surveillance for cost-efficient population surveillance; and 4) genome sequencing wastewater samples to track circulating and emerging variants in the population. We further discuss the challenges and future developments of WBS to reduce inconsistencies in wastewater data worldwide, improve its epidemiological inference, and advance viral tracking and discovery as a preparation for the next viral pandemic.
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Affiliation(s)
- Fuqing Wu
- Center for Infectious Disease, Department of Epidemiology, Human Genetics, and Environmental Sciences, University of Texas School of Public Health, Houston, TX, USA.
| | - Wei Lin Lee
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore; Campus for Research Excellence and Technological Enterprise (CREATE), Singapore
| | - Hongjie Chen
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore; Campus for Research Excellence and Technological Enterprise (CREATE), Singapore
| | - Xiaoqiong Gu
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore; Campus for Research Excellence and Technological Enterprise (CREATE), Singapore
| | - Franciscus Chandra
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore; Campus for Research Excellence and Technological Enterprise (CREATE), Singapore
| | - Federica Armas
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore; Campus for Research Excellence and Technological Enterprise (CREATE), Singapore
| | - Amy Xiao
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Mats Leifels
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore
| | | | - Stefan Wuertz
- Campus for Research Excellence and Technological Enterprise (CREATE), Singapore; Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore; School of Civil and Environmental Engineering, Nanyang Technological University, Singapore
| | - Janelle Thompson
- Campus for Research Excellence and Technological Enterprise (CREATE), Singapore; Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore; Asian School of the Environment, Nanyang Technological University, Singapore
| | - Eric J Alm
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore; Campus for Research Excellence and Technological Enterprise (CREATE), Singapore; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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11
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Xiao A, Wu F, Bushman M, Zhang J, Imakaev M, Chai PR, Duvallet C, Endo N, Erickson TB, Armas F, Arnold B, Chen H, Chandra F, Ghaeli N, Gu X, Hanage WP, Lee WL, Matus M, McElroy KA, Moniz K, Rhode SF, Thompson J, Alm EJ. Metrics to relate COVID-19 wastewater data to clinical testing dynamics. Water Res 2022; 212:118070. [PMID: 35101695 PMCID: PMC8758950 DOI: 10.1016/j.watres.2022.118070] [Citation(s) in RCA: 47] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Revised: 11/29/2021] [Accepted: 01/11/2022] [Indexed: 05/02/2023]
Abstract
Wastewater surveillance has emerged as a useful tool in the public health response to the COVID-19 pandemic. While wastewater surveillance has been applied at various scales to monitor population-level COVID-19 dynamics, there is a need for quantitative metrics to interpret wastewater data in the context of public health trends. 24-hour composite wastewater samples were collected from March 2020 through May 2021 from a Massachusetts wastewater treatment plant and SARS-CoV-2 RNA concentrations were measured using RT-qPCR. The relationship between wastewater copy numbers of SARS-CoV-2 gene fragments and COVID-19 clinical cases and deaths varies over time. We demonstrate the utility of three new metrics to monitor changes in COVID-19 epidemiology: (1) the ratio between wastewater copy numbers of SARS-CoV-2 gene fragments and clinical cases (WC ratio), (2) the time lag between wastewater and clinical reporting, and (3) a transfer function between the wastewater and clinical case curves. The WC ratio increases after key events, providing insight into the balance between disease spread and public health response. Time lag and transfer function analysis showed that wastewater data preceded clinically reported cases in the first wave of the pandemic but did not serve as a leading indicator in the second wave, likely due to increased testing capacity, which allows for more timely case detection and reporting. These three metrics could help further integrate wastewater surveillance into the public health response to the COVID-19 pandemic and future pandemics.
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Affiliation(s)
- Amy Xiao
- Department of Biological Engineering, Massachusetts Institute of Technology USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology USA
| | - Fuqing Wu
- Department of Biological Engineering, Massachusetts Institute of Technology USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology USA
| | - Mary Bushman
- Harvard T.H. Chan School of Public Health, Harvard University USA
| | - Jianbo Zhang
- Department of Biological Engineering, Massachusetts Institute of Technology USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology USA
| | | | - Peter R Chai
- Division of Medical Toxicology, Department of Emergency Medicine, Brigham and Women's Hospital, Harvard Medical School USA; The Fenway Institute, Fenway Health, Boston, MA USA; The Koch Institute for Integrated Cancer Research, Massachusetts Institute of Technology USA; Department of Psychosocial Oncology and Palliative Care, Dana Farber Cancer Institute USA
| | | | | | - Timothy B Erickson
- Division of Medical Toxicology, Department of Emergency Medicine, Brigham and Women's Hospital, Harvard Medical School USA; Harvard Humanitarian Initiative, Harvard University USA
| | - Federica Armas
- Singapore-MIT Alliance for Research and Technology, Antimicrobial Resistance Interdisciplinary Research Group, Singapore; Campus for Research Excellence and Technological Enterprise (CREATE), Singapore
| | - Brian Arnold
- Department of Computer Science, Princeton University USA; Center for Statistics and Machine Learning, Princeton University USA
| | - Hongjie Chen
- Singapore-MIT Alliance for Research and Technology, Antimicrobial Resistance Interdisciplinary Research Group, Singapore; Campus for Research Excellence and Technological Enterprise (CREATE), Singapore
| | - Franciscus Chandra
- Singapore-MIT Alliance for Research and Technology, Antimicrobial Resistance Interdisciplinary Research Group, Singapore; Campus for Research Excellence and Technological Enterprise (CREATE), Singapore
| | | | - Xiaoqiong Gu
- Singapore-MIT Alliance for Research and Technology, Antimicrobial Resistance Interdisciplinary Research Group, Singapore; Campus for Research Excellence and Technological Enterprise (CREATE), Singapore
| | - William P Hanage
- Harvard T.H. Chan School of Public Health, Harvard University USA
| | - Wei Lin Lee
- Singapore-MIT Alliance for Research and Technology, Antimicrobial Resistance Interdisciplinary Research Group, Singapore; Campus for Research Excellence and Technological Enterprise (CREATE), Singapore
| | | | | | - Katya Moniz
- Department of Biological Engineering, Massachusetts Institute of Technology USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology USA
| | | | - Janelle Thompson
- Campus for Research Excellence and Technological Enterprise (CREATE), Singapore; Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore; Asian School of the Environment, Nanyang Technological University, Singapore
| | - Eric J Alm
- Department of Biological Engineering, Massachusetts Institute of Technology USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology USA; Singapore-MIT Alliance for Research and Technology, Antimicrobial Resistance Interdisciplinary Research Group, Singapore; Campus for Research Excellence and Technological Enterprise (CREATE), Singapore; Broad Institute of MIT and Harvard, Cambridge, MA USA.
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12
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Xiao A, Callaway CW, Coppler PJ. Long-term Outcomes of Post-Cardiac Arrest Patients with Severe Neurological and Functional Impairments at Hospital Discharge. Resuscitation 2022; 174:93-101. [PMID: 35189302 PMCID: PMC10404449 DOI: 10.1016/j.resuscitation.2022.02.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 02/10/2022] [Accepted: 02/12/2022] [Indexed: 12/22/2022]
Abstract
BACKGROUND Patients resuscitated from cardiac arrest who have severe neurological or functional disability at discharge require high-intensity long-term support. However, few data describe the long-term survival and health-care utilization for these patients. METHODS We identified a cohort of cardiac arrest survivors ≥ 18 years of age, treated at a single center in Western Pennsylvania from January 2010 to December 2019, with a modified Rankin scale (mRS) of 5 at hospital discharge. We recorded demographics, cardiac arrest characteristics, and neurological exam at hospital discharge. We characterized long term survival and mortality through December 31, 2020 through National Death Index query. We described survival time overall and in subgroups using Kaplan-Meier curves and compared using log-rank tests.We linked cases with administrative data to determine 30, 90 day, and one-year hospital readmission rate. For subjects unable to follow commands at discharge, we reviewed records from index hospitalization to the present to describe improvement in neurological status and return home. RESULTS We screened 2,687 patients of which 975 survived to discharge. We identified 190 subjects with mRS of 5 at hospital discharge who were sent to non-hospice settings. Of these, 43 (23%) did not follow commands at discharge. One-year mortality was 38% (n = 71) with a median survival time of 4.2 years (IQR 0.3-10.9). Duration of survival was shorter in older subjects but did not differ based on, sex, or ability to follow commands at hospital discharge. Within the first year of discharge, 58% (n = 111) of subjects had at least one hospitalization with a median length of stay of 8 days [IQR 3-19]. Of subjects who did not follow commands at hospital discharge, 5/43 (11%) followed commands and 9 (21%) were reportedly living at home on subsequent encounters. CONCLUSIONS Of survivors treated over a decade at our institution, 20% (n = 190) were discharged from the hospital with severe functional disability. One-year mortality was 38%, and hospital readmissions were frequent. Few patients discharged unable to follow commands regained the ability over the period of observation, but many did return to living at home. These data can help inform decision maker expectations for patient trajectory and life expectancy.
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13
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Wu F, Xiao A, Zhang J, Moniz K, Endo N, Armas F, Bonneau R, Brown MA, Bushman M, Chai PR, Duvallet C, Erickson TB, Foppe K, Ghaeli N, Gu X, Hanage WP, Huang KH, Lee WL, Matus M, McElroy KA, Nagler J, Rhode SF, Santillana M, Tucker JA, Wuertz S, Zhao S, Thompson J, Alm EJ. SARS-CoV-2 RNA concentrations in wastewater foreshadow dynamics and clinical presentation of new COVID-19 cases. Sci Total Environ 2022; 805:150121. [PMID: 34534872 PMCID: PMC8416286 DOI: 10.1016/j.scitotenv.2021.150121] [Citation(s) in RCA: 135] [Impact Index Per Article: 67.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Revised: 08/30/2021] [Accepted: 08/31/2021] [Indexed: 05/18/2023]
Abstract
Current estimates of COVID-19 prevalence are largely based on symptomatic, clinically diagnosed cases. The existence of a large number of undiagnosed infections hampers population-wide investigation of viral circulation. Here, we quantify the SARS-CoV-2 concentration and track its dynamics in wastewater at a major urban wastewater treatment facility in Massachusetts, between early January and May 2020. SARS-CoV-2 was first detected in wastewater on March 3. SARS-CoV-2 RNA concentrations in wastewater correlated with clinically diagnosed new COVID-19 cases, with the trends appearing 4-10 days earlier in wastewater than in clinical data. We inferred viral shedding dynamics by modeling wastewater viral load as a convolution of back-dated new clinical cases with the average population-level viral shedding function. The inferred viral shedding function showed an early peak, likely before symptom onset and clinical diagnosis, consistent with emerging clinical and experimental evidence. This finding suggests that SARS-CoV-2 concentrations in wastewater may be primarily driven by viral shedding early in infection. This work shows that longitudinal wastewater analysis can be used to identify trends in disease transmission in advance of clinical case reporting, and infer early viral shedding dynamics for newly infected individuals, which are difficult to capture in clinical investigations.
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Affiliation(s)
- Fuqing Wu
- Department of Biological Engineering, Massachusetts Institute of Technology, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, USA
| | - Amy Xiao
- Department of Biological Engineering, Massachusetts Institute of Technology, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, USA
| | - Jianbo Zhang
- Department of Biological Engineering, Massachusetts Institute of Technology, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, USA
| | - Katya Moniz
- Department of Biological Engineering, Massachusetts Institute of Technology, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, USA
| | | | - Federica Armas
- Singapore-MIT Alliance for Research and Technology, Antimicrobial Resistance Interdisciplinary Research Group, Singapore; Campus for Research Excellence and Technological Enterprise (CREATE), Singapore
| | - Richard Bonneau
- Center for Data Science NYU, Center for Social Media and Politics, New York University, USA
| | - Megan A Brown
- Center for Data Science NYU, Center for Social Media and Politics, New York University, USA
| | - Mary Bushman
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Peter R Chai
- Division of Medical Toxicology, Department of Emergency Medicine, Brigham and Women's Hospital, Harvard Medical School, USA; The Fenway Institute, Fenway Health, Boston, MA, USA
| | | | - Timothy B Erickson
- Division of Medical Toxicology, Department of Emergency Medicine, Brigham and Women's Hospital, Harvard Medical School, USA; Harvard Humanitarian Initiative, Harvard University, USA
| | | | | | - Xiaoqiong Gu
- Singapore-MIT Alliance for Research and Technology, Antimicrobial Resistance Interdisciplinary Research Group, Singapore; Campus for Research Excellence and Technological Enterprise (CREATE), Singapore
| | | | | | - Wei Lin Lee
- Singapore-MIT Alliance for Research and Technology, Antimicrobial Resistance Interdisciplinary Research Group, Singapore; Campus for Research Excellence and Technological Enterprise (CREATE), Singapore
| | | | | | - Jonathan Nagler
- Center for Data Science NYU, Center for Social Media and Politics, New York University, USA
| | - Steven F Rhode
- Massachusetts Water Resources Authority, Boston, MA, USA
| | - Mauricio Santillana
- Harvard T.H. Chan School of Public Health, Boston, MA, USA; Department of Pediatrics, Harvard Medical School, Boston, MA, USA; Computational Health Informatics Program, Boston Children's Hospital, Boston, MA, USA
| | - Joshua A Tucker
- Center for Data Science NYU, Center for Social Media and Politics, New York University, USA
| | - Stefan Wuertz
- Campus for Research Excellence and Technological Enterprise (CREATE), Singapore; Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore; School of Civil and Environmental Enginering, Nanyang Technological University, Singapore
| | - Shijie Zhao
- Department of Biological Engineering, Massachusetts Institute of Technology, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, USA
| | - Janelle Thompson
- Campus for Research Excellence and Technological Enterprise (CREATE), Singapore; Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore; Asian School of the Environment, Nanyang Technological University, Singapore
| | - Eric J Alm
- Department of Biological Engineering, Massachusetts Institute of Technology, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, USA; Singapore-MIT Alliance for Research and Technology, Antimicrobial Resistance Interdisciplinary Research Group, Singapore; Campus for Research Excellence and Technological Enterprise (CREATE), Singapore; Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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14
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Wu F, Xiao A, Zhang J, Moniz K, Endo N, Armas F, Bushman M, Chai PR, Duvallet C, Erickson TB, Foppe K, Ghaeli N, Gu X, Hanage WP, Huang KH, Lee WL, McElroy KA, Rhode SF, Matus M, Wuertz S, Thompson J, Alm EJ. Wastewater surveillance of SARS-CoV-2 across 40 U.S. states from February to June 2020. Water Res 2021; 202:117400. [PMID: 34274898 PMCID: PMC8249441 DOI: 10.1016/j.watres.2021.117400] [Citation(s) in RCA: 83] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 06/11/2021] [Accepted: 06/28/2021] [Indexed: 05/18/2023]
Abstract
Wastewater-based disease surveillance is a promising approach for monitoring community outbreaks. Here we describe a nationwide campaign to monitor SARS-CoV-2 in the wastewater of 159 counties in 40 U.S. states, covering 13% of the U.S. population from February 18 to June 2, 2020. Out of 1,751 total samples analyzed, 846 samples were positive for SARS-CoV-2 RNA, with overall viral concentrations declining from April to May. Wastewater viral titers were consistent with, and appeared to precede, clinical COVID-19 surveillance indicators, including daily new cases. Wastewater surveillance had a high detection rate (>80%) of SARS-CoV-2 when the daily incidence exceeded 13 per 100,000 people. Detection rates were positively associated with wastewater treatment plant catchment size. To our knowledge, this work represents the largest-scale wastewater-based SARS-CoV-2 monitoring campaign to date, encompassing a wide diversity of wastewater treatment facilities and geographic locations. Our findings demonstrate that a national wastewater-based approach to disease surveillance may be feasible and effective.
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Affiliation(s)
- Fuqing Wu
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Amy Xiao
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Jianbo Zhang
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Katya Moniz
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | | - Federica Armas
- Singapore-MIT Alliance for Research and Technology, Antimicrobial Resistance Interdisciplinary Research Group, Singapore; Campus for Research Excellence and Technological Enterprise (CREATE), Singapore
| | - Mary Bushman
- Harvard T.H. Chan School of Public Health, Harvard University, USA
| | - Peter R Chai
- Division of Medical Toxicology, Department of Emergency Medicine, Brigham and Women's Hospital, Harvard Medical School, USA; The Fenway Institute, Fenway Health, Boston, MA, USA
| | | | - Timothy B Erickson
- Division of Medical Toxicology, Department of Emergency Medicine, Brigham and Women's Hospital, Harvard Medical School, USA; The Koch Institute for Integrated Cancer Research, Massachusetts Institute of Technology, USA; Harvard Humanitarian Initiative, Harvard University
| | | | | | - Xiaoqiong Gu
- Singapore-MIT Alliance for Research and Technology, Antimicrobial Resistance Interdisciplinary Research Group, Singapore; Campus for Research Excellence and Technological Enterprise (CREATE), Singapore
| | - William P Hanage
- Harvard T.H. Chan School of Public Health, Harvard University, USA
| | | | - Wei Lin Lee
- Singapore-MIT Alliance for Research and Technology, Antimicrobial Resistance Interdisciplinary Research Group, Singapore; Campus for Research Excellence and Technological Enterprise (CREATE), Singapore
| | | | - Steven F Rhode
- Massachusetts Water Resources Authority, Boston, MA, USA
| | | | - Stefan Wuertz
- Campus for Research Excellence and Technological Enterprise (CREATE), Singapore; Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore; Civil and Environmental Engineering, Nanyang Technological University, Singapore
| | - Janelle Thompson
- Campus for Research Excellence and Technological Enterprise (CREATE), Singapore; Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore; Asian School of the Environment, Nanyang Technological University, Singapore
| | - Eric J Alm
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Singapore-MIT Alliance for Research and Technology, Antimicrobial Resistance Interdisciplinary Research Group, Singapore; Campus for Research Excellence and Technological Enterprise (CREATE), Singapore; Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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15
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Xiao A, Wu F, Bushman M, Zhang J, Imakaev M, Chai PR, Duvallet C, Endo N, Erickson TB, Armas F, Arnold B, Chen H, Chandra F, Ghaeli N, Gu X, Hanage WP, Lee WL, Matus M, McElroy KA, Moniz K, Rhode SF, Thompson J, Alm EJ. Metrics to relate COVID-19 wastewater data to clinical testing dynamics. medRxiv 2021:2021.06.10.21258580. [PMID: 34159339 PMCID: PMC8219106 DOI: 10.1101/2021.06.10.21258580] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Wastewater surveillance has emerged as a useful tool in the public health response to the COVID-19 pandemic. While wastewater surveillance has been applied at various scales to monitor population-level COVID-19 dynamics, there is a need for quantitative metrics to interpret wastewater data in the context of public health trends. We collected 24-hour composite wastewater samples from March 2020 through May 2021 from a Massachusetts wastewater treatment plant and measured SARS-CoV-2 RNA concentrations using RT-qPCR. We show that the relationship between wastewater viral titers and COVID-19 clinical cases and deaths varies over time. We demonstrate the utility of three new metrics to monitor changes in COVID-19 epidemiology: (1) the ratio between wastewater viral titers and clinical cases (WC ratio), (2) the time lag between wastewater and clinical reporting, and (3) a transfer function between the wastewater and clinical case curves. We find that the WC ratio increases after key events, providing insight into the balance between disease spread and public health response. We also find that wastewater data preceded clinically reported cases in the first wave of the pandemic but did not serve as a leading indicator in the second wave, likely due to increased testing capacity. These three metrics could complement a framework for integrating wastewater surveillance into the public health response to the COVID-19 pandemic and future pandemics.
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Affiliation(s)
- Amy Xiao
- Department of Biological Engineering, Massachusetts Institute of Technology
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology
| | - Fuqing Wu
- Department of Biological Engineering, Massachusetts Institute of Technology
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology
| | - Mary Bushman
- Harvard T.H. Chan School of Public Health, Harvard University
| | - Jianbo Zhang
- Department of Biological Engineering, Massachusetts Institute of Technology
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology
| | | | - Peter R Chai
- Division of Medical Toxicology, Department of Emergency Medicine, Brigham and Women’s Hospital, Harvard Medical School
- The Fenway Institute, Fenway Health, Boston, MA
- The Koch Institute for Integrated Cancer Research, Massachusetts Institute of Technology
- Department of Psychosocial Oncology and Palliative Care, Dana Farber Cancer Institute
| | | | | | - Timothy B Erickson
- Division of Medical Toxicology, Department of Emergency Medicine, Brigham and Women’s Hospital, Harvard Medical School
- Harvard Humanitarian Initiative, Harvard University
| | - Federica Armas
- Singapore-MIT Alliance for Research and Technology, Antimicrobial Resistance Interdisciplinary Research Group, Singapore
- Campus for Research Excellence and Technological Enterprise (CREATE), Singapore
| | - Brian Arnold
- Department of Computer Science, Princeton University
- Center for Statistics and Machine Learning, Princeton University
| | - Hongjie Chen
- Singapore-MIT Alliance for Research and Technology, Antimicrobial Resistance Interdisciplinary Research Group, Singapore
- Campus for Research Excellence and Technological Enterprise (CREATE), Singapore
| | - Franciscus Chandra
- Singapore-MIT Alliance for Research and Technology, Antimicrobial Resistance Interdisciplinary Research Group, Singapore
- Campus for Research Excellence and Technological Enterprise (CREATE), Singapore
| | | | - Xiaoqiong Gu
- Singapore-MIT Alliance for Research and Technology, Antimicrobial Resistance Interdisciplinary Research Group, Singapore
- Campus for Research Excellence and Technological Enterprise (CREATE), Singapore
| | | | - Wei Lin Lee
- Singapore-MIT Alliance for Research and Technology, Antimicrobial Resistance Interdisciplinary Research Group, Singapore
- Campus for Research Excellence and Technological Enterprise (CREATE), Singapore
| | | | | | - Katya Moniz
- Department of Biological Engineering, Massachusetts Institute of Technology
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology
| | | | - Janelle Thompson
- Campus for Research Excellence and Technological Enterprise (CREATE), Singapore
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore
- Asian School of the Environment, Nanyang Technological University, Singapore
| | - Eric J Alm
- Department of Biological Engineering, Massachusetts Institute of Technology
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology
- Singapore-MIT Alliance for Research and Technology, Antimicrobial Resistance Interdisciplinary Research Group, Singapore
- Campus for Research Excellence and Technological Enterprise (CREATE), Singapore
- Broad Institute of MIT and Harvard, Cambridge, MA
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16
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Wu F, Xiao A, Zhang J, Moniz K, Endo N, Armas F, Bushman M, Chai PR, Duvallet C, Erickson TB, Foppe K, Ghaeli N, Gu X, Hanage WP, Huang KH, Lee WL, Matus M, McElroy KA, Rhode SF, Wuertz S, Thompson J, Alm EJ. Wastewater Surveillance of SARS-CoV-2 across 40 U.S. states. medRxiv 2021:2021.03.10.21253235. [PMID: 33758888 PMCID: PMC7987047 DOI: 10.1101/2021.03.10.21253235] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Wastewater-based disease surveillance is a promising approach for monitoring community outbreaks. Here we describe a nationwide campaign to monitor SARS-CoV-2 in the wastewater of 159 counties in 40 U.S. states, covering 13% of the U.S. population from February 18 to June 2, 2020. Out of 1,751 total samples analyzed, 846 samples were positive for SARS-CoV-2 RNA, with overall viral concentrations declining from April to May. Wastewater viral titers were consistent with, and appeared to precede, clinical COVID-19 surveillance indicators, including daily new cases. Wastewater surveillance had a high detection rate (>80%) of SARS-CoV-2 when the daily incidence exceeded 13 per 100,000 people. Detection rates were positively associated with wastewater treatment plant catchment size. To our knowledge, this work represents the largest-scale wastewater-based SARS-CoV-2 monitoring campaign to date, encompassing a wide diversity of wastewater treatment facilities and geographic locations. Our findings demonstrate that a national wastewater-based approach to disease surveillance may be feasible and effective.
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Affiliation(s)
- Fuqing Wu
- Department of Biological Engineering, Massachusetts Institute of Technology
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology
| | - Amy Xiao
- Department of Biological Engineering, Massachusetts Institute of Technology
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology
| | - Jianbo Zhang
- Department of Biological Engineering, Massachusetts Institute of Technology
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology
| | - Katya Moniz
- Department of Biological Engineering, Massachusetts Institute of Technology
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology
| | | | - Federica Armas
- Singapore-MIT Alliance for Research and Technology, Antimicrobial Resistance Interdisciplinary Research Group, Singapore
- Campus for Research Excellence and Technological Enterprise (CREATE), Singapore
| | - Mary Bushman
- Harvard T.H. Chan School of Public Health, Harvard University
| | - Peter R Chai
- Division of Medical Toxicology, Department of Emergency Medicine, Brigham and Women’s Hospital, Harvard Medical School
- The Fenway Institute, Fenway Health, Boston, MA
| | | | - Timothy B Erickson
- Division of Medical Toxicology, Department of Emergency Medicine, Brigham and Women’s Hospital, Harvard Medical School
- The Koch Institute for Integrated Cancer Research, Massachusetts Institute of Technology
- Harvard Humanitarian Initiative, Harvard University
| | | | | | - Xiaoqiong Gu
- Singapore-MIT Alliance for Research and Technology, Antimicrobial Resistance Interdisciplinary Research Group, Singapore
- Campus for Research Excellence and Technological Enterprise (CREATE), Singapore
| | | | | | - Wei Lin Lee
- Singapore-MIT Alliance for Research and Technology, Antimicrobial Resistance Interdisciplinary Research Group, Singapore
- Campus for Research Excellence and Technological Enterprise (CREATE), Singapore
| | | | | | | | - Stefan Wuertz
- Campus for Research Excellence and Technological Enterprise (CREATE), Singapore
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore
- Civil and Environmental Engineering, Nanyang Technological University, Singapore
| | - Janelle Thompson
- Campus for Research Excellence and Technological Enterprise (CREATE), Singapore
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore
- Asian School of the Environment, Nanyang Technological University, Singapore
| | - Eric J Alm
- Department of Biological Engineering, Massachusetts Institute of Technology
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology
- Singapore-MIT Alliance for Research and Technology, Antimicrobial Resistance Interdisciplinary Research Group, Singapore
- Campus for Research Excellence and Technological Enterprise (CREATE), Singapore
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
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17
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Wu F, Zhang J, Xiao A, Gu X, Lee WL, Armas F, Kauffman K, Hanage W, Matus M, Ghaeli N, Endo N, Duvallet C, Poyet M, Moniz K, Washburne AD, Erickson TB, Chai PR, Thompson J, Alm EJ. SARS-CoV-2 Titers in Wastewater Are Higher than Expected from Clinically Confirmed Cases. mSystems 2020. [PMID: 32694130 DOI: 10.1101/2020.04.%2005.20051540] [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] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/24/2023] Open
Abstract
Wastewater surveillance represents a complementary approach to clinical surveillance to measure the presence and prevalence of emerging infectious diseases like the novel coronavirus SARS-CoV-2. This innovative data source can improve the precision of epidemiological modeling to understand the penetrance of SARS-CoV-2 in specific vulnerable communities. Here, we tested wastewater collected at a major urban treatment facility in Massachusetts and detected SARS-CoV-2 RNA from the N gene at significant titers (57 to 303 copies per ml of sewage) in the period from 18 to 25 March 2020 using RT-qPCR. We validated detection of SARS-CoV-2 by Sanger sequencing the PCR product from the S gene. Viral titers observed were significantly higher than expected based on clinically confirmed cases in Massachusetts as of 25 March. Our approach is scalable and may be useful in modeling the SARS-CoV-2 pandemic and future outbreaks.IMPORTANCE Wastewater-based surveillance is a promising approach for proactive outbreak monitoring. SARS-CoV-2 is shed in stool early in the clinical course and infects a large asymptomatic population, making it an ideal target for wastewater-based monitoring. In this study, we develop a laboratory protocol to quantify viral titers in raw sewage via qPCR analysis and validate results with sequencing analysis. Our results suggest that the number of positive cases estimated from wastewater viral titers is orders of magnitude greater than the number of confirmed clinical cases and therefore may significantly impact efforts to understand the case fatality rate and progression of disease. These data may help inform decisions surrounding the advancement or scale-back of social distancing and quarantine efforts based on dynamic wastewater catchment-level estimations of prevalence.
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Affiliation(s)
- Fuqing Wu
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Jianbo Zhang
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Amy Xiao
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Xiaoqiong Gu
- Singapore-MIT Alliance for Research and Technology, National University of Singapore, Singapore
- Campus for Research Excellence and Technological Enterprise, Singapore
| | - Wei Lin Lee
- Singapore-MIT Alliance for Research and Technology, National University of Singapore, Singapore
- Campus for Research Excellence and Technological Enterprise, Singapore
| | - Federica Armas
- Singapore-MIT Alliance for Research and Technology, National University of Singapore, Singapore
- Campus for Research Excellence and Technological Enterprise, Singapore
| | - Kathryn Kauffman
- University at Buffalo, The State University of New York, Buffalo, New York, USA
| | - William Hanage
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Mariana Matus
- Biobot Analytics, Inc., Cambridge, Massachusetts, USA
| | - Newsha Ghaeli
- Biobot Analytics, Inc., Cambridge, Massachusetts, USA
| | - Noriko Endo
- Biobot Analytics, Inc., Cambridge, Massachusetts, USA
| | | | - Mathilde Poyet
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Katya Moniz
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | | | - Timothy B Erickson
- Division of Medical Toxicology, Department of Emergency Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Harvard Humanitarian Institute, Cambridge, Massachusetts, USA
| | - Peter R Chai
- Division of Medical Toxicology, Department of Emergency Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
- The Fenway Institute, Boston, Massachusetts, USA
- The Koch Institute for Integrated Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Janelle Thompson
- Singapore Center for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore
- Asian School of the Environment, Nanyang Technological University, Singapore
- Campus for Research Excellence and Technological Enterprise, Singapore
| | - Eric J Alm
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Singapore-MIT Alliance for Research and Technology, National University of Singapore, Singapore
- Biobot Analytics, Inc., Cambridge, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Campus for Research Excellence and Technological Enterprise, Singapore
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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18
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Wu F, Zhang J, Xiao A, Gu X, Lee WL, Armas F, Kauffman K, Hanage W, Matus M, Ghaeli N, Endo N, Duvallet C, Poyet M, Moniz K, Washburne AD, Erickson TB, Chai PR, Thompson J, Alm EJ. SARS-CoV-2 Titers in Wastewater Are Higher than Expected from Clinically Confirmed Cases. mSystems 2020. [PMID: 32694130 DOI: 10.1101/2020.06.15.20117747v2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/10/2023] Open
Abstract
Wastewater surveillance represents a complementary approach to clinical surveillance to measure the presence and prevalence of emerging infectious diseases like the novel coronavirus SARS-CoV-2. This innovative data source can improve the precision of epidemiological modeling to understand the penetrance of SARS-CoV-2 in specific vulnerable communities. Here, we tested wastewater collected at a major urban treatment facility in Massachusetts and detected SARS-CoV-2 RNA from the N gene at significant titers (57 to 303 copies per ml of sewage) in the period from 18 to 25 March 2020 using RT-qPCR. We validated detection of SARS-CoV-2 by Sanger sequencing the PCR product from the S gene. Viral titers observed were significantly higher than expected based on clinically confirmed cases in Massachusetts as of 25 March. Our approach is scalable and may be useful in modeling the SARS-CoV-2 pandemic and future outbreaks.IMPORTANCE Wastewater-based surveillance is a promising approach for proactive outbreak monitoring. SARS-CoV-2 is shed in stool early in the clinical course and infects a large asymptomatic population, making it an ideal target for wastewater-based monitoring. In this study, we develop a laboratory protocol to quantify viral titers in raw sewage via qPCR analysis and validate results with sequencing analysis. Our results suggest that the number of positive cases estimated from wastewater viral titers is orders of magnitude greater than the number of confirmed clinical cases and therefore may significantly impact efforts to understand the case fatality rate and progression of disease. These data may help inform decisions surrounding the advancement or scale-back of social distancing and quarantine efforts based on dynamic wastewater catchment-level estimations of prevalence.
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Affiliation(s)
- Fuqing Wu
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Jianbo Zhang
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Amy Xiao
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Xiaoqiong Gu
- Singapore-MIT Alliance for Research and Technology, National University of Singapore, Singapore
- Campus for Research Excellence and Technological Enterprise, Singapore
| | - Wei Lin Lee
- Singapore-MIT Alliance for Research and Technology, National University of Singapore, Singapore
- Campus for Research Excellence and Technological Enterprise, Singapore
| | - Federica Armas
- Singapore-MIT Alliance for Research and Technology, National University of Singapore, Singapore
- Campus for Research Excellence and Technological Enterprise, Singapore
| | - Kathryn Kauffman
- University at Buffalo, The State University of New York, Buffalo, New York, USA
| | - William Hanage
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Mariana Matus
- Biobot Analytics, Inc., Cambridge, Massachusetts, USA
| | - Newsha Ghaeli
- Biobot Analytics, Inc., Cambridge, Massachusetts, USA
| | - Noriko Endo
- Biobot Analytics, Inc., Cambridge, Massachusetts, USA
| | | | - Mathilde Poyet
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Katya Moniz
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | | | - Timothy B Erickson
- Division of Medical Toxicology, Department of Emergency Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Harvard Humanitarian Institute, Cambridge, Massachusetts, USA
| | - Peter R Chai
- Division of Medical Toxicology, Department of Emergency Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
- The Fenway Institute, Boston, Massachusetts, USA
- The Koch Institute for Integrated Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Janelle Thompson
- Singapore Center for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore
- Asian School of the Environment, Nanyang Technological University, Singapore
- Campus for Research Excellence and Technological Enterprise, Singapore
| | - Eric J Alm
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Singapore-MIT Alliance for Research and Technology, National University of Singapore, Singapore
- Biobot Analytics, Inc., Cambridge, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Campus for Research Excellence and Technological Enterprise, Singapore
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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19
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Wu F, Zhang J, Xiao A, Gu X, Lee WL, Armas F, Kauffman K, Hanage W, Matus M, Ghaeli N, Endo N, Duvallet C, Poyet M, Moniz K, Washburne AD, Erickson TB, Chai PR, Thompson J, Alm EJ. SARS-CoV-2 Titers in Wastewater Are Higher than Expected from Clinically Confirmed Cases. mSystems 2020. [PMID: 32660974 DOI: 10.1016/j.solener.2019.02.027] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023] Open
Abstract
Wastewater surveillance represents a complementary approach to clinical surveillance to measure the presence and prevalence of emerging infectious diseases like the novel coronavirus SARS-CoV-2. This innovative data source can improve the precision of epidemiological modeling to understand the penetrance of SARS-CoV-2 in specific vulnerable communities. Here, we tested wastewater collected at a major urban treatment facility in Massachusetts and detected SARS-CoV-2 RNA from the N gene at significant titers (57 to 303 copies per ml of sewage) in the period from 18 to 25 March 2020 using RT-qPCR. We validated detection of SARS-CoV-2 by Sanger sequencing the PCR product from the S gene. Viral titers observed were significantly higher than expected based on clinically confirmed cases in Massachusetts as of 25 March. Our approach is scalable and may be useful in modeling the SARS-CoV-2 pandemic and future outbreaks.IMPORTANCE Wastewater-based surveillance is a promising approach for proactive outbreak monitoring. SARS-CoV-2 is shed in stool early in the clinical course and infects a large asymptomatic population, making it an ideal target for wastewater-based monitoring. In this study, we develop a laboratory protocol to quantify viral titers in raw sewage via qPCR analysis and validate results with sequencing analysis. Our results suggest that the number of positive cases estimated from wastewater viral titers is orders of magnitude greater than the number of confirmed clinical cases and therefore may significantly impact efforts to understand the case fatality rate and progression of disease. These data may help inform decisions surrounding the advancement or scale-back of social distancing and quarantine efforts based on dynamic wastewater catchment-level estimations of prevalence.
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Affiliation(s)
- Fuqing Wu
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Jianbo Zhang
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Amy Xiao
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Xiaoqiong Gu
- Singapore-MIT Alliance for Research and Technology, National University of Singapore, Singapore
- Campus for Research Excellence and Technological Enterprise, Singapore
| | - Wei Lin Lee
- Singapore-MIT Alliance for Research and Technology, National University of Singapore, Singapore
- Campus for Research Excellence and Technological Enterprise, Singapore
| | - Federica Armas
- Singapore-MIT Alliance for Research and Technology, National University of Singapore, Singapore
- Campus for Research Excellence and Technological Enterprise, Singapore
| | - Kathryn Kauffman
- University at Buffalo, The State University of New York, Buffalo, New York, USA
| | - William Hanage
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Mariana Matus
- Biobot Analytics, Inc., Cambridge, Massachusetts, USA
| | - Newsha Ghaeli
- Biobot Analytics, Inc., Cambridge, Massachusetts, USA
| | - Noriko Endo
- Biobot Analytics, Inc., Cambridge, Massachusetts, USA
| | | | - Mathilde Poyet
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Katya Moniz
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | | | - Timothy B Erickson
- Division of Medical Toxicology, Department of Emergency Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Harvard Humanitarian Institute, Cambridge, Massachusetts, USA
| | - Peter R Chai
- Division of Medical Toxicology, Department of Emergency Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
- The Fenway Institute, Boston, Massachusetts, USA
- The Koch Institute for Integrated Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Janelle Thompson
- Singapore Center for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore
- Asian School of the Environment, Nanyang Technological University, Singapore
- Campus for Research Excellence and Technological Enterprise, Singapore
| | - Eric J Alm
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Singapore-MIT Alliance for Research and Technology, National University of Singapore, Singapore
- Biobot Analytics, Inc., Cambridge, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Campus for Research Excellence and Technological Enterprise, Singapore
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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20
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Wu F, Zhang J, Xiao A, Gu X, Lee WL, Armas F, Kauffman K, Hanage W, Matus M, Ghaeli N, Endo N, Duvallet C, Poyet M, Moniz K, Washburne AD, Erickson TB, Chai PR, Thompson J, Alm EJ. SARS-CoV-2 Titers in Wastewater Are Higher than Expected from Clinically Confirmed Cases. mSystems 2020. [PMID: 32694130 DOI: 10.1101/2020.04.05.20051540] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023] Open
Abstract
Wastewater surveillance represents a complementary approach to clinical surveillance to measure the presence and prevalence of emerging infectious diseases like the novel coronavirus SARS-CoV-2. This innovative data source can improve the precision of epidemiological modeling to understand the penetrance of SARS-CoV-2 in specific vulnerable communities. Here, we tested wastewater collected at a major urban treatment facility in Massachusetts and detected SARS-CoV-2 RNA from the N gene at significant titers (57 to 303 copies per ml of sewage) in the period from 18 to 25 March 2020 using RT-qPCR. We validated detection of SARS-CoV-2 by Sanger sequencing the PCR product from the S gene. Viral titers observed were significantly higher than expected based on clinically confirmed cases in Massachusetts as of 25 March. Our approach is scalable and may be useful in modeling the SARS-CoV-2 pandemic and future outbreaks.IMPORTANCE Wastewater-based surveillance is a promising approach for proactive outbreak monitoring. SARS-CoV-2 is shed in stool early in the clinical course and infects a large asymptomatic population, making it an ideal target for wastewater-based monitoring. In this study, we develop a laboratory protocol to quantify viral titers in raw sewage via qPCR analysis and validate results with sequencing analysis. Our results suggest that the number of positive cases estimated from wastewater viral titers is orders of magnitude greater than the number of confirmed clinical cases and therefore may significantly impact efforts to understand the case fatality rate and progression of disease. These data may help inform decisions surrounding the advancement or scale-back of social distancing and quarantine efforts based on dynamic wastewater catchment-level estimations of prevalence.
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Affiliation(s)
- Fuqing Wu
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Jianbo Zhang
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Amy Xiao
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Xiaoqiong Gu
- Singapore-MIT Alliance for Research and Technology, National University of Singapore, Singapore
- Campus for Research Excellence and Technological Enterprise, Singapore
| | - Wei Lin Lee
- Singapore-MIT Alliance for Research and Technology, National University of Singapore, Singapore
- Campus for Research Excellence and Technological Enterprise, Singapore
| | - Federica Armas
- Singapore-MIT Alliance for Research and Technology, National University of Singapore, Singapore
- Campus for Research Excellence and Technological Enterprise, Singapore
| | - Kathryn Kauffman
- University at Buffalo, The State University of New York, Buffalo, New York, USA
| | - William Hanage
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Mariana Matus
- Biobot Analytics, Inc., Cambridge, Massachusetts, USA
| | - Newsha Ghaeli
- Biobot Analytics, Inc., Cambridge, Massachusetts, USA
| | - Noriko Endo
- Biobot Analytics, Inc., Cambridge, Massachusetts, USA
| | | | - Mathilde Poyet
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Katya Moniz
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | | | - Timothy B Erickson
- Division of Medical Toxicology, Department of Emergency Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Harvard Humanitarian Institute, Cambridge, Massachusetts, USA
| | - Peter R Chai
- Division of Medical Toxicology, Department of Emergency Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
- The Fenway Institute, Boston, Massachusetts, USA
- The Koch Institute for Integrated Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Janelle Thompson
- Singapore Center for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore
- Asian School of the Environment, Nanyang Technological University, Singapore
- Campus for Research Excellence and Technological Enterprise, Singapore
| | - Eric J Alm
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Singapore-MIT Alliance for Research and Technology, National University of Singapore, Singapore
- Biobot Analytics, Inc., Cambridge, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Campus for Research Excellence and Technological Enterprise, Singapore
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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21
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Wu F, Zhang J, Xiao A, Gu X, Lee WL, Armas F, Kauffman K, Hanage W, Matus M, Ghaeli N, Endo N, Duvallet C, Poyet M, Moniz K, Washburne AD, Erickson TB, Chai PR, Thompson J, Alm EJ. SARS-CoV-2 Titers in Wastewater Are Higher than Expected from Clinically Confirmed Cases. mSystems 2020. [PMID: 32694130 DOI: 10.1128/2fmsystems.00614-20] [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] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/30/2023] Open
Abstract
Wastewater surveillance represents a complementary approach to clinical surveillance to measure the presence and prevalence of emerging infectious diseases like the novel coronavirus SARS-CoV-2. This innovative data source can improve the precision of epidemiological modeling to understand the penetrance of SARS-CoV-2 in specific vulnerable communities. Here, we tested wastewater collected at a major urban treatment facility in Massachusetts and detected SARS-CoV-2 RNA from the N gene at significant titers (57 to 303 copies per ml of sewage) in the period from 18 to 25 March 2020 using RT-qPCR. We validated detection of SARS-CoV-2 by Sanger sequencing the PCR product from the S gene. Viral titers observed were significantly higher than expected based on clinically confirmed cases in Massachusetts as of 25 March. Our approach is scalable and may be useful in modeling the SARS-CoV-2 pandemic and future outbreaks.IMPORTANCE Wastewater-based surveillance is a promising approach for proactive outbreak monitoring. SARS-CoV-2 is shed in stool early in the clinical course and infects a large asymptomatic population, making it an ideal target for wastewater-based monitoring. In this study, we develop a laboratory protocol to quantify viral titers in raw sewage via qPCR analysis and validate results with sequencing analysis. Our results suggest that the number of positive cases estimated from wastewater viral titers is orders of magnitude greater than the number of confirmed clinical cases and therefore may significantly impact efforts to understand the case fatality rate and progression of disease. These data may help inform decisions surrounding the advancement or scale-back of social distancing and quarantine efforts based on dynamic wastewater catchment-level estimations of prevalence.
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Affiliation(s)
- Fuqing Wu
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Jianbo Zhang
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Amy Xiao
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Xiaoqiong Gu
- Singapore-MIT Alliance for Research and Technology, National University of Singapore, Singapore
- Campus for Research Excellence and Technological Enterprise, Singapore
| | - Wei Lin Lee
- Singapore-MIT Alliance for Research and Technology, National University of Singapore, Singapore
- Campus for Research Excellence and Technological Enterprise, Singapore
| | - Federica Armas
- Singapore-MIT Alliance for Research and Technology, National University of Singapore, Singapore
- Campus for Research Excellence and Technological Enterprise, Singapore
| | - Kathryn Kauffman
- University at Buffalo, The State University of New York, Buffalo, New York, USA
| | - William Hanage
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Mariana Matus
- Biobot Analytics, Inc., Cambridge, Massachusetts, USA
| | - Newsha Ghaeli
- Biobot Analytics, Inc., Cambridge, Massachusetts, USA
| | - Noriko Endo
- Biobot Analytics, Inc., Cambridge, Massachusetts, USA
| | | | - Mathilde Poyet
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Katya Moniz
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | | | - Timothy B Erickson
- Division of Medical Toxicology, Department of Emergency Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Harvard Humanitarian Institute, Cambridge, Massachusetts, USA
| | - Peter R Chai
- Division of Medical Toxicology, Department of Emergency Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
- The Fenway Institute, Boston, Massachusetts, USA
- The Koch Institute for Integrated Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Janelle Thompson
- Singapore Center for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore
- Asian School of the Environment, Nanyang Technological University, Singapore
- Campus for Research Excellence and Technological Enterprise, Singapore
| | - Eric J Alm
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Singapore-MIT Alliance for Research and Technology, National University of Singapore, Singapore
- Biobot Analytics, Inc., Cambridge, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Campus for Research Excellence and Technological Enterprise, Singapore
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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22
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Wu F, Zhang J, Xiao A, Gu X, Lee WL, Armas F, Kauffman K, Hanage W, Matus M, Ghaeli N, Endo N, Duvallet C, Poyet M, Moniz K, Washburne AD, Erickson TB, Chai PR, Thompson J, Alm EJ. SARS-CoV-2 Titers in Wastewater Are Higher than Expected from Clinically Confirmed Cases. mSystems 2020. [PMID: 32694130 DOI: 10.1101/2020.04.05.200515] [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] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2023] Open
Abstract
Wastewater surveillance represents a complementary approach to clinical surveillance to measure the presence and prevalence of emerging infectious diseases like the novel coronavirus SARS-CoV-2. This innovative data source can improve the precision of epidemiological modeling to understand the penetrance of SARS-CoV-2 in specific vulnerable communities. Here, we tested wastewater collected at a major urban treatment facility in Massachusetts and detected SARS-CoV-2 RNA from the N gene at significant titers (57 to 303 copies per ml of sewage) in the period from 18 to 25 March 2020 using RT-qPCR. We validated detection of SARS-CoV-2 by Sanger sequencing the PCR product from the S gene. Viral titers observed were significantly higher than expected based on clinically confirmed cases in Massachusetts as of 25 March. Our approach is scalable and may be useful in modeling the SARS-CoV-2 pandemic and future outbreaks.IMPORTANCE Wastewater-based surveillance is a promising approach for proactive outbreak monitoring. SARS-CoV-2 is shed in stool early in the clinical course and infects a large asymptomatic population, making it an ideal target for wastewater-based monitoring. In this study, we develop a laboratory protocol to quantify viral titers in raw sewage via qPCR analysis and validate results with sequencing analysis. Our results suggest that the number of positive cases estimated from wastewater viral titers is orders of magnitude greater than the number of confirmed clinical cases and therefore may significantly impact efforts to understand the case fatality rate and progression of disease. These data may help inform decisions surrounding the advancement or scale-back of social distancing and quarantine efforts based on dynamic wastewater catchment-level estimations of prevalence.
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Affiliation(s)
- Fuqing Wu
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Jianbo Zhang
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Amy Xiao
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Xiaoqiong Gu
- Singapore-MIT Alliance for Research and Technology, National University of Singapore, Singapore
- Campus for Research Excellence and Technological Enterprise, Singapore
| | - Wei Lin Lee
- Singapore-MIT Alliance for Research and Technology, National University of Singapore, Singapore
- Campus for Research Excellence and Technological Enterprise, Singapore
| | - Federica Armas
- Singapore-MIT Alliance for Research and Technology, National University of Singapore, Singapore
- Campus for Research Excellence and Technological Enterprise, Singapore
| | - Kathryn Kauffman
- University at Buffalo, The State University of New York, Buffalo, New York, USA
| | - William Hanage
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Mariana Matus
- Biobot Analytics, Inc., Cambridge, Massachusetts, USA
| | - Newsha Ghaeli
- Biobot Analytics, Inc., Cambridge, Massachusetts, USA
| | - Noriko Endo
- Biobot Analytics, Inc., Cambridge, Massachusetts, USA
| | | | - Mathilde Poyet
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Katya Moniz
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | | | - Timothy B Erickson
- Division of Medical Toxicology, Department of Emergency Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Harvard Humanitarian Institute, Cambridge, Massachusetts, USA
| | - Peter R Chai
- Division of Medical Toxicology, Department of Emergency Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
- The Fenway Institute, Boston, Massachusetts, USA
- The Koch Institute for Integrated Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Janelle Thompson
- Singapore Center for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore
- Asian School of the Environment, Nanyang Technological University, Singapore
- Campus for Research Excellence and Technological Enterprise, Singapore
| | - Eric J Alm
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Singapore-MIT Alliance for Research and Technology, National University of Singapore, Singapore
- Biobot Analytics, Inc., Cambridge, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Campus for Research Excellence and Technological Enterprise, Singapore
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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23
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Wu F, Xiao A, Zhang J, Moniz K, Endo N, Armas F, Bonneau R, Brown MA, Bushman M, Chai PR, Duvallet C, Erickson TB, Foppe K, Ghaeli N, Gu X, Hanage WP, Huang KH, Lee WL, Matus M, McElroy KA, Nagler J, Rhode SF, Santillana M, Tucker JA, Wuertz S, Zhao S, Thompson J, Alm EJ. SARS-CoV-2 titers in wastewater foreshadow dynamics and clinical presentation of new COVID-19 cases. medRxiv 2020:2020.06.15.20117747. [PMID: 32607521 PMCID: PMC7325186 DOI: 10.1101/2020.06.15.20117747] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Current estimates of COVID-19 prevalence are largely based on symptomatic, clinically diagnosed cases. The existence of a large number of undiagnosed infections hampers population-wide investigation of viral circulation. Here, we use longitudinal wastewater analysis to track SARS-CoV-2 dynamics in wastewater at a major urban wastewater treatment facility in Massachusetts, between early January and May 2020. SARS-CoV-2 was first detected in wastewater on March 3. Viral titers in wastewater increased exponentially from mid-March to mid-April, after which they began to decline. Viral titers in wastewater correlated with clinically diagnosed new COVID-19 cases, with the trends appearing 4-10 days earlier in wastewater than in clinical data. We inferred viral shedding dynamics by modeling wastewater viral titers as a convolution of back-dated new clinical cases with the viral shedding function of an individual. The inferred viral shedding function showed an early peak, likely before symptom onset and clinical diagnosis, consistent with emerging clinical and experimental evidence. Finally, we found that wastewater viral titers at the neighborhood level correlate better with demographic variables than with population size. This work suggests that longitudinal wastewater analysis can be used to identify trends in disease transmission in advance of clinical case reporting, and may shed light on infection characteristics that are difficult to capture in clinical investigations, such as early viral shedding dynamics.
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Affiliation(s)
- Fuqing Wu
- Department of Biological Engineering, Massachusetts Institute of Technology
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology
| | - Amy Xiao
- Department of Biological Engineering, Massachusetts Institute of Technology
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology
| | - Jianbo Zhang
- Department of Biological Engineering, Massachusetts Institute of Technology
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology
| | - Katya Moniz
- Department of Biological Engineering, Massachusetts Institute of Technology
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology
| | | | - Federica Armas
- Singapore-MIT Alliance for Research and Technology, Antimicrobial Resistance Interdisciplinary Research Group, Singapore
- Campus for Research Excellence and Technological Enterprise (CREATE), Singapore
| | - Richard Bonneau
- Center for Data Science NYU, Center for Social Media and Politics, New York University
| | - Megan A Brown
- Center for Data Science NYU, Center for Social Media and Politics, New York University
| | - Mary Bushman
- Harvard T.H. Chan School of Public Health, Harvard University
| | - Peter R Chai
- Division of Medical Toxicology, Department of Emergency Medicine, Brigham and Women’s Hospital, Harvard Medical School
- The Fenway Institute, Fenway Health, Boston, MA
| | | | - Timothy B Erickson
- Division of Medical Toxicology, Department of Emergency Medicine, Brigham and Women’s Hospital, Harvard Medical School
- Harvard Humanitarian Initiative, Harvard University
| | | | | | - Xiaoqiong Gu
- Singapore-MIT Alliance for Research and Technology, Antimicrobial Resistance Interdisciplinary Research Group, Singapore
- Campus for Research Excellence and Technological Enterprise (CREATE), Singapore
| | | | | | - Wei Lin Lee
- Singapore-MIT Alliance for Research and Technology, Antimicrobial Resistance Interdisciplinary Research Group, Singapore
- Campus for Research Excellence and Technological Enterprise (CREATE), Singapore
| | | | | | - Jonathan Nagler
- Center for Data Science NYU, Center for Social Media and Politics, New York University
| | | | - Mauricio Santillana
- Harvard T.H. Chan School of Public Health, Harvard University
- Department of Pediatrics, Harvard Medical School. Boston, MA
- Computational Health Informatics Program. Boston Children’s Hospital, Boston, MA
| | - Joshua A Tucker
- Center for Data Science NYU, Center for Social Media and Politics, New York University
| | - Stefan Wuertz
- Campus for Research Excellence and Technological Enterprise (CREATE), Singapore
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore
- Civil and Environmental Engineering, Nanyang Technological University, Singapore
| | - Shijie Zhao
- Department of Biological Engineering, Massachusetts Institute of Technology
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology
| | - Janelle Thompson
- Campus for Research Excellence and Technological Enterprise (CREATE), Singapore
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore
- Asian School of the Environment, Nanyang Technological University, Singapore
| | - Eric J Alm
- Department of Biological Engineering, Massachusetts Institute of Technology
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology
- Singapore-MIT Alliance for Research and Technology, Antimicrobial Resistance Interdisciplinary Research Group, Singapore
- Campus for Research Excellence and Technological Enterprise (CREATE), Singapore
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
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24
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LEI W, Su Z, Xiao A, Nie J. SUN-038 HOMOCYSTEINE EXACERBATES IRI-INDUCED ACUTE KIDNEY INJURY VIA PROMOTING MEGAKARYOCYTE MATURATION AND PROPLATELET FORMATION. Kidney Int Rep 2020. [DOI: 10.1016/j.ekir.2020.02.561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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25
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Ni H, Zhang T, Guo X, Hu Y, Xiao A, Jiang Z, Li L, Li Q. Comparison between irradiating and autoclaving citrus wastes as substrate for solid-state fermentation by Aspergillus aculeatus. Lett Appl Microbiol 2019; 69:71-78. [PMID: 31038763 DOI: 10.1111/lam.13167] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 04/23/2019] [Accepted: 04/23/2019] [Indexed: 12/01/2022]
Abstract
Agricultural or food processing wastes cause serious environmental burden and economic losses. Solid-state fermentation using these wastes is an attractive option to valorize these wastes. However, conventional autoclaving of substrate may degrade nutrients and generate toxins. Unsterilization of the substrate will cause undesired microbial contamination. Therefore, we compared irradiation with autoclaving to treat citrus wastes as substrate for solid-state fermentation by Aspergillus aculeatus. By comparing microbial growth, enzymes tested and medium consumption, irradiated substrate had higher biomass and extracellular protein, more sugar consumption and higher enzyme production than those with autoclaved substrate. Irradiation prevented the generation of cell-inhibiting components such as 5-hydroxymethylfurfural (5-HMF) whereas preserved the flavonoids well that are often enzyme inducers. These findings suggest that irradiation of agricultural and food processing wastes as substrate has advantages over autoclaving for solid-state fermentation. SIGNIFICANCE AND IMPACT OF THE STUDY: This study proposes irradiation as an alternative to sterilize agricultural residues rich in nutrients and thermosensitive compounds, such as citrus wastes for fungal solid-state fermentation and production of enzymes.
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Affiliation(s)
- H Ni
- College of Food and Biology Engineering, Jimei University, Xiamen, China.,Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering, Xiamen, China.,Research Center of Food Biotechnology of Xiamen City, Xiamen, China
| | - T Zhang
- College of Food and Biology Engineering, Jimei University, Xiamen, China
| | - X Guo
- College of Food and Biology Engineering, Jimei University, Xiamen, China
| | - Y Hu
- College of Food and Biology Engineering, Jimei University, Xiamen, China
| | - A Xiao
- College of Food and Biology Engineering, Jimei University, Xiamen, China.,Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering, Xiamen, China
| | - Z Jiang
- College of Food and Biology Engineering, Jimei University, Xiamen, China.,Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering, Xiamen, China.,Research Center of Food Biotechnology of Xiamen City, Xiamen, China
| | - L Li
- College of Food and Biology Engineering, Jimei University, Xiamen, China.,Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering, Xiamen, China.,Research Center of Food Biotechnology of Xiamen City, Xiamen, China
| | - Q Li
- College of Food and Biology Engineering, Jimei University, Xiamen, China.,Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering, Xiamen, China.,Research Center of Food Biotechnology of Xiamen City, Xiamen, China
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26
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Leung CM, Dhand C, Dwivedi N, Xiao A, Ong ST, Chalasani MLS, Sriram H, Balakrishnan Y, Dolatshahi-Pirouz A, Orive G, Beuerman RW, Ramakrishna S, Verma NK, Lakshminarayanan R. Combating Microbial Contamination with Robust Polymeric Nanofibers: Elemental Effect on the Mussel-Inspired Cross-Linking of Electrospun Gelatin. ACS Appl Bio Mater 2018; 2:807-823. [DOI: 10.1021/acsabm.8b00666] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Chak Ming Leung
- Department of Biomedical Engineering, National University of Singapore, Singapore 117581, Singapore
| | - Chetna Dhand
- Anti-Infectives Research Group, Singapore Eye Research Institute, The Academia, 20 College Road, Discovery Tower, Singapore 169856, Singapore
- Ophthalmology and Visual Sciences Academic Clinical Program, Duke-NUS Graduate Medical School, Singapore 169857, Singapore
| | - Neeraj Dwivedi
- Department of Electrical and Computer Engineering, National University of Singapore, 3 Engineering Drive 3, Singapore 117583, Singapore
| | - Amy Xiao
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Seow Theng Ong
- Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, Experimental Medicine Building, 59 Nanyang Drive, Singapore 636921, Singapore
| | - Madhavi Latha Somaraju Chalasani
- Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, Experimental Medicine Building, 59 Nanyang Drive, Singapore 636921, Singapore
| | - Harini Sriram
- Anti-Infectives Research Group, Singapore Eye Research Institute, The Academia, 20 College Road, Discovery Tower, Singapore 169856, Singapore
| | - Yamini Balakrishnan
- Department of Biomedical Engineering, National University of Singapore, Singapore 117581, Singapore
| | - Alireza Dolatshahi-Pirouz
- Technical University of Denmark, DTU Nanotech, Center for Intestinal Absorption and Transport of Biopharmaceutical, 2800 Kgs, Denmark
| | - Gorka Orive
- NanoBioCel Group, Laboratory of Pharmaceutics, School of Pharmacy, University of the Basque Country UPV/EHU, Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, Spain
- Biomedical Research
Networking Centre in Bioengineering, Biomaterials, and Nanomedicine
(CIBER-BBN) Vitoria-Gasteiz, Spain
- University Institute for Regenerative Medicine and Oral Implantology − UIRMI, Vitoria, Spain, BTI Biotechnology Institute, Vitoria, Spain
| | - Roger Wilmer Beuerman
- Anti-Infectives Research Group, Singapore Eye Research Institute, The Academia, 20 College Road, Discovery Tower, Singapore 169856, Singapore
- Ophthalmology and Visual Sciences Academic Clinical Program, Duke-NUS Graduate Medical School, Singapore 169857, Singapore
| | - Seeram Ramakrishna
- Center for Nanofibers and Nanotechnology, Department of Mechanical Engineering, Faculty of Engineering, National University of Singapore, 2 Engineering Drive 3, Singapore 117576, Singapore
| | - Navin Kumar Verma
- Anti-Infectives Research Group, Singapore Eye Research Institute, The Academia, 20 College Road, Discovery Tower, Singapore 169856, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, Experimental Medicine Building, 59 Nanyang Drive, Singapore 636921, Singapore
| | - Rajamani Lakshminarayanan
- Anti-Infectives Research Group, Singapore Eye Research Institute, The Academia, 20 College Road, Discovery Tower, Singapore 169856, Singapore
- Ophthalmology and Visual Sciences Academic Clinical Program, Duke-NUS Graduate Medical School, Singapore 169857, Singapore
- Skin Research Institute of Singapore, Clinical Science Building, 11 Mandalay Road, Singapore 308232, Singapore
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27
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Wang P, Hu J, Ghadermarzi S, Raza A, O′Connell D, Xiao A, Ayyaz F, Zhi M, Zhang Y, Parekh NK, Lazarev M, Parian A, Brant SR, Bedine M, Truta B, Hu P, Banerjee R, Hutfless SM. Smoking and Inflammatory Bowel Disease: A Comparison of China, India, and the USA. Dig Dis Sci 2018; 63:2703-2713. [PMID: 29862485 PMCID: PMC6435261 DOI: 10.1007/s10620-018-5142-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 05/28/2018] [Indexed: 01/12/2023]
Abstract
BACKGROUND Cigarette smoking is thought to increase the risk of Crohn's disease (CD) and exacerbate the disease course, with opposite roles in ulcerative colitis (UC). However, these findings are from Western populations, and the association between smoking and inflammatory bowel disease (IBD) has not been well studied in Asia. AIMS We aimed to compare the prevalence of smoking at diagnosis between IBD cases and controls recruited in China, India, and the USA, and to investigate the impact of smoking on disease outcomes. METHODS We recruited IBD cases and controls between 2014 and 2018. All participants completed a questionnaire about demographic characteristics, environmental risk factors and IBD history. RESULTS We recruited 337 participants from China, 194 from India, and 645 from the USA. In China, CD cases were less likely than controls to be current smokers (adjusted odds ratio [95% CI] 0.4 [0.2-0.9]). There was no association between current or former smoking and CD in the USA. In China and the USA, UC cases were more likely to be former smokers than controls (China 14.6 [3.3-64.8]; USA 1.8 [1.0-3.3]). In India, both CD and UC had similar current smoking status to controls at diagnosis. Current smoking at diagnosis was significantly associated with greater use of immunosuppressants (4.4 [1.1-18.1]) in CD cases in China. CONCLUSIONS We found heterogeneity in the associations of smoking and IBD risk and outcomes between China, India, and the USA. Further study with more adequate sample size and more uniform definition of smoking status is warranted.
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Affiliation(s)
- Peiqi Wang
- Department of Surgery, Johns Hopkins University, Baltimore, MD, USA
| | - Jun Hu
- Department of Gastroenterology, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, China,Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Guangzhou, China
| | - Shadi Ghadermarzi
- Department of Internal Medicine, East Carolina University, Greenville, NC, USA
| | - Ali Raza
- Department of Cardiology, Boston Children’s Hospital, Harvard Medical School, Boston, MD, USA
| | - Douglas O′Connell
- School of Medicine, Division of Gastroenterology, University of California, Irvine, USA
| | - Amy Xiao
- Department of Biomedical Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Faraz Ayyaz
- Services Institute of Medical Sciences, Lahore, Pakistan
| | - Min Zhi
- Department of Gastroenterology, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Yuanqi Zhang
- Department of Gastroenterology, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Nimisha K. Parekh
- School of Medicine, Division of Gastroenterology, University of California, Irvine, USA
| | - Mark Lazarev
- Department of Medicine, Division of Gastroenterology and Hepatology, Meyerhoff Inflammatory Bowel Disease Center, Johns Hopkins University, Baltimore, MD, USA
| | - Alyssa Parian
- Department of Medicine, Division of Gastroenterology and Hepatology, Meyerhoff Inflammatory Bowel Disease Center, Johns Hopkins University, Baltimore, MD, USA
| | - Steven R. Brant
- Department of Medicine, Division of Gastroenterology and Hepatology, Rutgers Health, Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | - Marshall Bedine
- Department of Medicine, Division of Gastroenterology and Hepatology, Meyerhoff Inflammatory Bowel Disease Center, Johns Hopkins University, Baltimore, MD, USA
| | - Brindusa Truta
- Department of Medicine, Division of Gastroenterology and Hepatology, Meyerhoff Inflammatory Bowel Disease Center, Johns Hopkins University, Baltimore, MD, USA
| | - Pinjin Hu
- Department of Gastroenterology, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Rupa Banerjee
- Asian Institute of Gastroenterology, Hyderabad, India
| | - Susan M. Hutfless
- Division of Gastroenterology and Hepatology, Gastrointestinal Epidemiology Research Center, Johns Hopkins University, 600 N Wolfe St, Blalock 449, Baltimore, MD 21287, USA,Department of Epidemiology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
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28
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Xiao A, Dhand C, Leung CM, Beuerman RW, Ramakrishna S, Lakshminarayanan R. Strategies to design antimicrobial contact lenses and contact lens cases. J Mater Chem B 2018; 6:2171-2186. [PMID: 32254560 DOI: 10.1039/c7tb03136j] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Contact lens wear is a primary risk factor for developing ocular complications, such as contact lens acute red eye (CLARE), contact lens-induced peripheral ulcer (CLPU) and microbial keratitis (MK). Infections occur due to microbial contamination of contact lenses, lens cases and lens care solution, which are exacerbated by extended lens wear and unsanitary lens care practices. The development of microbial biofilms inside lens cases is an additional complication, as the developed biofilms are resistant to conventional lens cleaning solutions. Ocular infections, particularly in the case of MK, can lead to visual impairment or even blindness, so there is a pressing need for the development of antimicrobial contact lenses and cases. Additionally, with the increasing use of bandage contact lenses and contact lenses as drug depots and with the development of smart contact lenses, contact lens hygiene becomes a therapeutically important issue. In this review, we attempt to compile and summarize various chemical strategies for developing antimicrobial contact lenses and lens cases by using silver, free-radical producing agents, antimicrobial peptides or by employing passive surface modification approaches. We also evaluated the advantages and disadvantages of each system and tried to provide input to future directions. Finally, we summarize the developing technologies of therapeutic contact lenses to shed light on the future of contact lens applications.
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Affiliation(s)
- Amy Xiao
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA
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Jian L, Scalley B, Xiao A, Nairn J, Spicer T, Somerford P, Ostendorf B, Weeramanthri T. Is Excess Heat Factor a Good Indicator for Assessing Heatwave Related Health Outcomes in Western Australia? Int J Epidemiol 2015. [DOI: 10.1093/ije/dyv097.241] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Stacer AC, Fenner J, Cavnar SP, Xiao A, Zhao S, Chang SL, Salomonnson A, Luker KE, Luker GD. Endothelial CXCR7 regulates breast cancer metastasis. Oncogene 2015; 35:1716-24. [PMID: 26119946 PMCID: PMC4486335 DOI: 10.1038/onc.2015.236] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [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] [Received: 07/21/2014] [Revised: 04/29/2015] [Accepted: 05/01/2015] [Indexed: 02/08/2023]
Abstract
Atypical chemokine receptor CXCR7 (ACKR3) functions as a scavenger receptor for chemokine CXCL12, a molecule that promotes multiple steps in tumor growth and metastasis in breast cancer and multiple other malignancies. While normal vascular endothelium expresses low levels of CXCR7, marked upregulation of CXCR7 occurs in tumor vasculature in breast cancer and other tumors. To investigate effects of endothelial CXCR7 in breast cancer, we conditionally deleted this receptor from vascular endothelium of adult mice, generating CXCR7ΔEND/ΔEND animals. CXCR7ΔEND/ΔEND mice appeared phenotypically normal, although these animals exhibited a modest 35 ± 3% increase in plasma CXCL12 as compared with control. Using two different syngeneic, orthotopic tumor implant models of breast cancer, we discovered that CXCR7ΔEND/ΔEND mice had significantly greater local recurrence of cancer following resection, elevated numbers of circulating tumor cells, and more spontaneous metastases. CXCR7ΔEND/ΔEND mice also showed greater experimental metastases following intracardiac injection of cancer cells. These results establish that endothelial CXCR7 limits breast cancer metastasis at multiple steps in the metastatic cascade, advancing understanding of CXCL12 pathways in tumor environments and informing ongoing drug development targeting CXCR7 in cancer.
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Affiliation(s)
- A C Stacer
- University of Michigan Center for Molecular Imaging, Department of Radiology, University of Michigan Medical School and College of Engineering, Ann Arbor, MI, USA
| | - J Fenner
- University of Michigan Center for Molecular Imaging, Department of Radiology, University of Michigan Medical School and College of Engineering, Ann Arbor, MI, USA
| | - S P Cavnar
- Department of Biomedical Engineering, University of Michigan Medical School and College of Engineering, Ann Arbor, MI, USA
| | - A Xiao
- University of Michigan Center for Molecular Imaging, Department of Radiology, University of Michigan Medical School and College of Engineering, Ann Arbor, MI, USA
| | - S Zhao
- Department of Radiation Oncology, University of Michigan Medical School and College of Engineering, Ann Arbor, MI, USA
| | - S L Chang
- Depatment of Chemical Engineering, University of Michigan Medical School and College of Engineering, Ann Arbor, MI, USA
| | - A Salomonnson
- University of Michigan Center for Molecular Imaging, Department of Radiology, University of Michigan Medical School and College of Engineering, Ann Arbor, MI, USA
| | - K E Luker
- University of Michigan Center for Molecular Imaging, Department of Radiology, University of Michigan Medical School and College of Engineering, Ann Arbor, MI, USA
| | - G D Luker
- University of Michigan Center for Molecular Imaging, Department of Radiology, University of Michigan Medical School and College of Engineering, Ann Arbor, MI, USA.,Department of Biomedical Engineering, University of Michigan Medical School and College of Engineering, Ann Arbor, MI, USA.,Department of Microbiology and Immunology, University of Michigan Medical School and College of Engineering, Ann Arbor, MI, USA
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31
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Floyd D, Comeau L, Boroda S, Hayes N, Roller D, Xiao A, Friedman A, Boyd L, Gioeli D, Harris T, Harris T, Purow B. PM-02 * DIACYLGLYCEROL KINASE ALPHA INHIBITION PROLONGS SURVIVAL OF MICE WITH PRIMARY AND METASTATIC BRAIN TUMORS. Neuro Oncol 2014. [DOI: 10.1093/neuonc/nou268.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Kijima N, Hosen N, Kagawa N, Hashimoto N, Chiba Y, Kinoshita M, Sugiyama H, Yoshimine T, Kim YZ, Kim KH, Lee EH, Hu B, Sim H, Mohan N, Agudelo-Garcia P, Nuovo G, Cole S, Viapiano MS, McFarland BC, Hong SW, Rajbhandari R, Twitty GB, Kenneth Gray G, Yu H, Langford CP, Yancey Gillespie G, Benveniste EN, Nozell SE, Nitta R, Mitra S, Bui T, Li G, Munoz JL, Rodriguez-Cruz V, Rameshwar P, Rodriguez-Cruz V, Munoz JL, Rameshwar P, See WL, Mukherjee J, Shannon KM, Pieper RO, Floyd DH, Xiao A, Purow BW, Lavon I, Zrihan D, Refael M, Bier A, Canello T, Siegal T, Zrihan D, Granit A, Siegal T, Lavon I, Xie Q, Wang X, Gong Y, Mao Y, Chen X, Zhou L, Lee SX, Tunkyi A, Wong ET, Swanson KD, Zhang K, Chen L, Zhang J, Shi Z, Han L, Pu P, Kang C, Cho WH, Ogawa D, Godlewski J, Bronisz A, Antonio Chiocca E, Mustafa DAM, Sieuwerts AM, Smid M, de Weerd V, Martens JW, Foekens JA, Kros JM, Zhang J, McCulloch C, Graff J, Sui Y, Dinn S, Huang Y, Li Q, Fiona G, Ogawa D, Nakashima H, Godlewski J, Antonio Chiocca E, Leiss L, Manini I, Enger PO, Yang C, Iyer R, Yu ACH, Li S, Ikejiri BL, Zhuang Z, Lonser R, Massoud TF, Paulmurugan R, Gambhir SS, Merrill MJ, Sun M, Chen M, Edwards NA, Shively SB, Lonser RR, Baia GS, Caballero OL, Orr BA, Lal A, Ho JS, Cowdrey C, Tihan T, Mawrin C, Riggins GJ, Lu D, Leo C, Wheeler H, McDonald K, Schulte A, Zapf S, Stoupiec M, Kolbe K, Riethdorf S, Westphal M, Lamszus K, Timmer M, Rohn G, Koch A, Goldbrunner R, Edwards NA, Lonser RR, Merrill MJ, Ruggieri R, Vanan I, Dong Z, Sarkaria JN, Tran NL, Berens ME, Symons M, Rowther FB, Dawson T, Ashton K, Darling J, Warr T, Okamoto M, Palanichamy K, Gordon N, Patel D, Walston S, Krishanan T, Chakravarti A, Kalinina J, Carroll A, Wang L, Yu Q, Mancheno DE, Wu S, Liu F, Ahn J, He M, Mao H, Van Meir EG, Debinski W, Gonzales O, Beauchamp A, Gibo DM, Seals DF, Speranza MC, Frattini V, Kapetis D, Pisati F, Eoli M, Pellegatta S, Finocchiaro G, Maherally Z, Smith JR, Pilkington GJ, Zhu W, Wang Q, Clark PA, Yang SS, Lin SH, Kahle KT, Kuo JS, Sun D, Hossain MB, Cortes-Santiago N, Gururaj A, Thomas J, Gabrusiewicz K, Gumin J, Xipell E, Lang F, Fueyo J, Yung WKA, Gomez-Manzano C, Cook NJ, Lawrence JE, Rovin RA, Belton RJ, Winn RJ, Ferluga S, Debinski W, Lee SH, Khwaja FW, Zerrouqi A, Devi NS, Van Meir EG, Drucker KL, Lee HK, Bier A, Finniss S, Cazacu S, Poisson L, Xiang C, Rempel SA, Mikkelsen T, Brodie C, Chen M, Shen J, Edwards NA, Lonser RR, Merrill MJ, Kenchappa RS, Valadez JG, Cooper MK, Carter BD, Forsyth PA, Lee JS, Erdreich-Epstein A, Song HR, Lawn S, Kenchappa R, Forsyth P, Lim KJ, Bar EE, Eberhart CG, Blough M, Alnajjar M, Chesnelong C, Weiss S, Chan J, Cairncross G, Wykosky J, Cavenee W, Furnari F, Brown KE, Keir ST, Sampson JH, Bigner DD, Kwatra MM, Kotipatruni RP, Thotala DK, Jaboin J, Taylor TE, Wykosky J, Schinzel AC, Hahn WC, Cavenee WK, Furnari FB, Kapoor GS, Macyszyn L, Bi Y, Fetting H, Poptani H, Ittyerah R, Davuluri RV, O'Rourke D, Pitter KL, Hosni-Ahmed A, Colevas K, Holland EC, Jones TS, Malhotra A, Potts C, Fernandez-Lopez A, Kenney AM, Cheng S, Feng H, Hu B, Jarzynka MJ, Li Y, Keezer S, Johns TG, Hamilton RL, Vuori K, Nishikawa R, Sarkaria JN, Fenton T, Cheng T, Furnari FB, Cavenee WK, Mikheev AM, Mikheeva SA, Silber JR, Horner PJ, Rostomily R, Henson ES, Brown M, Eisenstat DD, Gibson SB, Price RL, Song J, Bingmer K, Oglesbee M, Cook C, Kwon CH, Antonio Chiocca E, Nguyen TT, Nakashima H, Chiocca EA, Lukiw WJ, Culicchia F, Jones BM, Zhao Y, Bhattacharjee S. LAB-CELL BIOLOGY AND SIGNALING. Neuro Oncol 2012. [DOI: 10.1093/neuonc/nos220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Li H, Liu Z, Wu R, Qi F, Xiao A, Zhang W. W464 CLINICAL OBSERVATION OF THE SHORT-TERM EFFECTS OF POSTPARTUM WOMEN'S PELVIC FLOOR FUNCTION IN DIFFERENT DELIVERY WAY. Int J Gynaecol Obstet 2012. [DOI: 10.1016/s0020-7292(12)62183-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Giles FJ, Swords RT, Nagler A, Hochhaus A, Ottmann OG, Rizzieri DA, Talpaz M, Clark J, Watson P, Xiao A, Zhao B, Bergstrom D, Le Coutre PD, Freedman SJ, Cortes JE. MK-0457, an Aurora kinase and BCR-ABL inhibitor, is active in patients with BCR-ABL T315I leukemia. Leukemia 2012; 27:113-7. [PMID: 22772060 DOI: 10.1038/leu.2012.186] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
MK-0457, an Aurora kinase and BCR-ABL inhibitor, was studied on a Phase I/II study in 77 patients with refractory hematologic malignancies. The average number of cycles per patient was 3 (range 1-21). Maximum tolerated doses for a 5-day short infusion and continuous infusion regimens were 40 mg/m(2)/h and 144 mg/m(2)/h, respectively. Drug-related adverse events (AEs) included transient mucositis and alopecia. Eight of 18 patients with BCR-ABL T315I-mutated chronic myelogenous leukemia (44%) had hematologic responses and one of three patients (33%) with Philadelphia chromosome-positive acute lymphoblastic leukemia obtained complete remission. MK-0457 has important activity in patients with leukemias expressing the highly resistant T315I BCR-ABL mutation.
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Affiliation(s)
- F J Giles
- HRB Clinical Research Facilities, National University of Ireland Galway and Trinity College Dublin, Galway, Ireland.
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Abstract
Emerging evidence from these studies suggested that the male germ cell transcriptome is more complex than previously envisioned. In addition to protein-coding genes, the transcriptome also encodes a significant number of nonprotein-coding transcripts. These noncoding (nc) RNAs appear to be involved in a variety of cellular activities, ranging from simple housekeeping to complex regulatory functions. A class of ncRNAs known as long ncRNAs (lncRNAs) were recently shown to be expressed in a developmentally regulated manner during brain and embryonic stem cell development. This protocol aims to predict and identify potential lncRNA candidates using Serial Analysis of Gene Expression (SAGE) data. We also illustrate how to validate the potential lncRNAs by expression analyses using real-time PCR and Northern Blot. Potential lncRNA candidates in male germ cells are identified using our previously established male germ cell SAGE database (GermSAGE).
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Affiliation(s)
- Tin-Lap Lee
- School of Biomedical Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China.
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36
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LEE TIN, Xiao A, Chan W, Rennert OM. Identification of novel long non‐coding RNA candidates in male germ cell development. FASEB J 2011. [DOI: 10.1096/fasebj.25.1_supplement.924.3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- TIN‐LAP LEE
- Laboratory of Clinical and Developmental GenomicsNICHD, Nattional Institutes of HealthBethesdaMD
- School of Biomedical ScienceThe Chinese University of Hong KongShatinHong Kong
| | - Amy Xiao
- Laboratory of Clinical and Developmental GenomicsNICHD, Nattional Institutes of HealthBethesdaMD
| | - Wai‐Yee Chan
- Laboratory of Clinical and Developmental GenomicsNICHD, Nattional Institutes of HealthBethesdaMD
- School of Biomedical ScienceThe Chinese University of Hong KongShatinHong Kong
| | - Owen M Rennert
- Laboratory of Clinical and Developmental GenomicsNICHD, Nattional Institutes of HealthBethesdaMD
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37
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Hake SB, Xiao A, Allis CD. Linking the epigenetic 'language' of covalent histone modifications to cancer. Br J Cancer 2007; 96 Suppl:R31-9. [PMID: 17393583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2023] Open
Abstract
Covalent modifications of histones, such as acetylation, methylation, and phosphorylation, and other epigenetic modulations of the chromatin, such as methylation of DNA and ATP-dependent chromatin reorganisation, can play a major part in the multistep process of carcinogenesis, with far-reaching implications for human biology and human health. This review focuses on how aberrant covalent histone modifications may contribute to the development of a variety of human cancers, and discusses the recent findings with regard to potential therapies.
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Affiliation(s)
- S B Hake
- Laboratory of Chromatin Biology, The Rockefeller University, New York, NY 10021, USA
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Simin K, Hill R, Song Y, Zhang Q, Bash R, Cardiff RD, Yin C, Xiao A, McCarthy K, van Dyke T. Deciphering cancer complexities in genetically engineered mice. Cold Spring Harb Symp Quant Biol 2006; 70:283-90. [PMID: 16869764 DOI: 10.1101/sqb.2005.70.038] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Because the pRb pathway is disrupted in most solid human cancers, we have generated genetically engineered mouse cancer models by inactivating pRb function in several cell types, including astrocytes and mammary, prostate, ovarian, and brain choroid plexus epithelia. In every case, proliferation and apoptosis are acutely induced, predisposing to malignancy. Cell type dictates the pathways involved in tumor progression. In the astrocytoma model, we developed strategies to induce events in the adult brain, either throughout the tissue or focally. Both K-Ras activation and Pten inactivation play significant roles in progression. In the prostate model, adenocarcinoma progression depends on Pten inactivation. However, nonautonomous induction of p53 in the mesenchyme leads to evolution of both compartments, with p53 loss occurring in the mesenchyme. Thus, studies in these models continue to identify key tumorigenesis mechanisms. Furthermore, we are hopeful that the models will provide useful preclinical systems for diagnostic and therapeutic development.
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Affiliation(s)
- K Simin
- University of North Carolina School of Medicine, Chapel Hill, 27599, USA
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Abdel-Fattah R, Xiao A, Bomgardner D, Pease CS, Lopes MBS, Hussaini IM. Differential expression of HOX genes in neoplastic and non-neoplastic human astrocytes. J Pathol 2006; 209:15-24. [PMID: 16463268 DOI: 10.1002/path.1939] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.8] [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: 12/14/2022]
Abstract
HOX genes are a large family of regulatory genes implicated in the control of developmental processes. HOX genes are involved in malignant transformation and progression of different types of tumour. Despite intensive efforts to delineate the expression profiles of HOX genes in other cell types, nothing is known regarding the global expression profile of these genes in normal human astrocytes and astrocytomas. The present study has analysed the expression profile of the 39 class I HOX genes in normal human astrocytes (NHA and E6/E7), two well-established glioblastoma cell lines (U-87 MG and U-1242-MG), as well as neoplastic (WHO grades II/III and IV) and non-neoplastic temporal lobe specimens with hippocampal sclerosis and medically intractable epilepsy. RT-PCR, quantitative real-time PCR, immunocytochemistry, and western blot analyses revealed differential expression of nine HOX genes (A6, A7, A9, A13, B13, D4, D9, D10, and D13) in normal human astrocytic cell lines and non-neoplastic temporal lobe specimens. The data show that HOX genes are differentially expressed in neoplastic and non-neoplastic astrocytes and that multiple HOX genes are overexpressed in glioblastoma cell lines, astrocytomas (II/III), and glioblastoma multiforme. The differential expression of HOX genes in normal and neoplastic astrocytes suggests a role for these genes in brain tumourigenesis.
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Affiliation(s)
- R Abdel-Fattah
- Department of Pathology, UVA School of Medicine, Charlottesville, 22908, USA.
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Rubin EH, Shapiro GI, Stein MN, Watson P, Bergstrom D, Xiao A, Clark JB, Freedman SJ, Eder JP. A phase I clinical and pharmacokinetic (PK) trial of the aurora kinase (AK) inhibitor MK-0457 in cancer patients. J Clin Oncol 2006. [DOI: 10.1200/jco.2006.24.18_suppl.3009] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
3009 Background: The AKs are essential for mitotic progression, spindle formation, centrosome maturation, chromosomal segregation, and cytokinesis. Elevated expression occurs frequently in tumors. MK-0457 (VX-680) is a potent AK inhibitor, with Ki values of 0.66, 18 and 4.6 nM for AKs A, B and C, respectively. MK-0457 inhibits proliferation of transformed cells in vitro (IC50’s 15–113 nM), and induces colon and pancreatic cancer xenograft regressions. Methods: After IRB approval, consenting patients (pts) with refractory solid tumors (median 3 prior regimens, range 2–6) and adequate hematologic and organ function were enrolled using an accelerated dose escalation scheme with 1–2 pts/dose level until ≥ grade 2 toxicity, followed by 3–6 pts/level. MK-0457 was administered by continuous 5-day intravenous infusion every 28 days. Dose-limiting toxicity (DLT) was grade 3 non-hematologic or grade 4 hematologic toxicity ≥ 5 days, or grade 4 febrile neutropenia (FN) during cycle 1. PKs were collected pre-dose through 168 h and analyzed for MK-0457 and metabolites by HPLC/mass spec. Steady state volume of distribution (Vdss), clearance (CL), maximal concentration (Cmax) and terminal half-life (t1/2) were determined by WinNonLin. Results: 16 pts received MK-0457 dosed at 0.5, 1, 2, 4, 8, and 12 mg/m2/h. Median number of cycles was 2 (range 1–6). DLT was asymptomatic neutropenia ≥ 5 days at 12 mg/m2/h. At 8 mg/m2/h, 1 pt experienced FN in cycle 2; a second developed a grade 2 allergic reaction. Three pts achieved stable disease as best response, and two of them completed 6 cycles. Plasma concentrations reached steady state rapidly (i.e., within 24 h) and declined biexponentially after the end of infusion; after a rapid initial decay, a slower decaying terminal phase demonstrated a t1/2 ∼15 h. PK parameters include Vdss = 237 ± 107 (SD) L/m2 and CL = 517 ± 141 ml/min/m2. At 8 mg/m2/h, Cmax was ∼650 nM. Conclusion: MK-0457 is generally well tolerated and achieves plasma levels similar to those causing regressions in xenografts. CL is high and exposures achieved are roughly dose proportional. Because 8 mg/m2/h was well tolerated in heavily pre-treated pts, escalation to 10 mg/m2/h is underway. Baseline tumor samples will be assessed for predictive biomarkers at the recommended phase II dose. [Table: see text]
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Affiliation(s)
- E. H. Rubin
- Cancer Institute of New Jersey, New Brunswick, NJ; Dana-Farber Cancer Institute, Boston, MA; Merck Research Laboratories, Blue Bell, PA
| | - G. I. Shapiro
- Cancer Institute of New Jersey, New Brunswick, NJ; Dana-Farber Cancer Institute, Boston, MA; Merck Research Laboratories, Blue Bell, PA
| | - M. N. Stein
- Cancer Institute of New Jersey, New Brunswick, NJ; Dana-Farber Cancer Institute, Boston, MA; Merck Research Laboratories, Blue Bell, PA
| | - P. Watson
- Cancer Institute of New Jersey, New Brunswick, NJ; Dana-Farber Cancer Institute, Boston, MA; Merck Research Laboratories, Blue Bell, PA
| | - D. Bergstrom
- Cancer Institute of New Jersey, New Brunswick, NJ; Dana-Farber Cancer Institute, Boston, MA; Merck Research Laboratories, Blue Bell, PA
| | - A. Xiao
- Cancer Institute of New Jersey, New Brunswick, NJ; Dana-Farber Cancer Institute, Boston, MA; Merck Research Laboratories, Blue Bell, PA
| | - J. B. Clark
- Cancer Institute of New Jersey, New Brunswick, NJ; Dana-Farber Cancer Institute, Boston, MA; Merck Research Laboratories, Blue Bell, PA
| | - S. J. Freedman
- Cancer Institute of New Jersey, New Brunswick, NJ; Dana-Farber Cancer Institute, Boston, MA; Merck Research Laboratories, Blue Bell, PA
| | - J. P. Eder
- Cancer Institute of New Jersey, New Brunswick, NJ; Dana-Farber Cancer Institute, Boston, MA; Merck Research Laboratories, Blue Bell, PA
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Abstract
Covalent modifications of histones, such as acetylation, methylation, and phosphorylation, and other epigenetic modulations of the chromatin, such as methylation of DNA and ATP-dependent chromatin reorganisation, can play a major part in the multistep process of carcinogenesis, with far-reaching implications for human biology and human health. This review focuses on how aberrant covalent histone modifications may contribute to the development of a variety of human cancers, and discusses the recent findings with regard to potential therapies.
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Affiliation(s)
- S B Hake
- Laboratory of Chromatin Biology, The Rockefeller University, Box 78, 1230 York Avenue, New York, NY 10021, USA
| | - A Xiao
- Laboratory of Chromatin Biology, The Rockefeller University, Box 78, 1230 York Avenue, New York, NY 10021, USA
| | - C D Allis
- Laboratory of Chromatin Biology, The Rockefeller University, Box 78, 1230 York Avenue, New York, NY 10021, USA
- Laboratory of Chromatin Biology, The Rockefeller University, Box 78, 1230 York Avenue, New York, NY 10021, USA. E-mail:
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Xiao A, Zhai F, Wang J, Zhou D, Qiao X. [Radiotherapy for 308 patients with non-small cell lung cancer (NSCLC)]. Zhongguo Fei Ai Za Zhi 2001; 4:134-6. [PMID: 21044472 DOI: 10.3779/j.issn.1009-3419.2001.02.15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
BACKGROUND To analyze the survival results retrospectively of the patients with NSCLC treated by radiotherapy alone and the clinical factors affecting the survival results. METHODS Three hundred and eight patients with NSCLC from January, 1985 to December, 1991 were included in this study (stage I, 11 cases; stage II, 68 cases; stage IIIA, 155 cases; stage IIIB, 74 cases). All patients were confirmed by pathology and cytology. They were treated by 10 MV-X ray or cobalt-60, conventionally fractionated, with weekly dose 7-11.5 Gy. In 47 patients of them treatment planning system was used at the beginning or in the middle of radiotherapy as to have the primary lesion and mediastinum in the full course of radiotherapy. In the rest of patients whose mediastinal dose was 40Gy by anterior and posterior fields, irradiation dose to the spinal cord was avoided and irradiation dose to the primary lesion got to the definitive treatment. The survival rate was analyzed by Kaplan-Meier and tested by Log-rank. RESULTS The median survival was 10 months. The 1-, 3- and 5-year survival rates were 43%, 15% and 9% respectively. The earlier the clinical stage, the better the prognosis (P=0.0001). The survival rate of the patients with complete remission at the end of radiotherapy was better than that of the patients with residual tumor (P=0.0001). The survival of the patients with weekly dose larger than 10 Gy was better ( P=0.0461). There was no relationship among the survival rate and the total dose and mediastinal dose. CONCLUSIONS The results show the survival rate of patient with NSCLC treated by radiotherapy alone was related to clinical stage, instant response and weekly dose, but not to the total dose and the mediastinal dose.
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Affiliation(s)
- A Xiao
- Department of Radiation Oncology, The Fourth Hospital, Hebei Medical University, Shijiazhuang, Hebei 050011, P.R.China
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Snouwaert JN, Gowen LC, Latour AM, Mohn AR, Xiao A, DiBiase L, Koller BH. BRCA1 deficient embryonic stem cells display a decreased homologous recombination frequency and an increased frequency of non-homologous recombination that is corrected by expression of a brca1 transgene. Oncogene 1999; 18:7900-7. [PMID: 10630642 DOI: 10.1038/sj.onc.1203334] [Citation(s) in RCA: 150] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
BRCA1 is a nuclear phosphoprotein that has been classified as a tumor suppressor based on the fact that women carrying a mutated copy of the BRCA1 gene are at increased risk of developing breast and ovarian cancer. The association of BRCA1 with RAD51 has led to the hypothesis that BRCA1 is involved in DNA repair. We describe here the generation and analysis of murine embryonic stem (ES) cell lines in which both copies of the murine homologue of the human BRCA1 gene have been disrupted by gene targeting. We show that exogenous DNA introduced into these BRCA1 deficient cells by electroporation is randomly integrated into the genome at a significantly higher rate than in wild type ES cells. In contrast, integration of exogenous DNA by homologous recombination occurs in BRCA1 deficient cells at a significantly lower rate than in wild type controls. When BRCA1 expression is re-established at 5-10% of normal levels by introduction of a Brca1 transgene into BRCA1 deficient ES cells, the frequency of random integration is reduced to wild type levels, although the frequency of homologous recombination is not significantly improved. These results suggest that BRCA1 plays a role in determining the response of cells to double stranded DNA breaks.
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Affiliation(s)
- J N Snouwaert
- Department of Medicine, University of North Carolina at Chapel Hill, 27599-7248, USA
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Heim C, Arzberger T, Sontag T, Xiao A, Herbinger KH, Weindl A, Sontag KH. Progressive degeneration of dopamine system functions after transient cerebral oligemia in rats. Brain Res 1999; 851:235-46. [PMID: 10642849 DOI: 10.1016/s0006-8993(99)02193-9] [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: 11/29/2022]
Abstract
A reduction in cerebral blood flow to oligemic levels was achieved in pentobarbital-anesthetized adult rats by clamping both carotid arteries (BCCA) for 60 min. To assess the extent to which the animals' dopaminergic system was affected over an increasing time span, their spontaneous locomotor activity in an unfamiliar environment and in response to the subcutaneous administration of apomorphine was tested at various times after either BCCA or sham operation. Eight to 14 days after the operation, it was possible to observe a diminished locomotor activity in response to apomorphine injection in BCCA as compared with sham-operated animals, while oral stereotypical behavior such as licking was increased. At 3 months, there was only a subtle decrease in apomorphine-induced locomotor activity, and stereotypical behavior was similar in both groups. At 7 months, the BCCA rats covered shorter distances than sham-operated controls during the habituation phase; after apomorphine injection, more stereotypic movements, such as, e.g., sniffing, were observed, and less running. Twelve months after surgery, no further differences could be observed between the two groups during the habituation phase, but the injection of apomorphine led to increased stereotypic sniffing movements, rearing and locomotor activity in BCCA animals to a greater extent than in the controls. At 12 months, sensorimotor disturbances elicited by the rota rod test, which were only transiently observed at 11 weeks and 7 months, did not appear any different from the normal age-related motor decline of the sham-operated controls. The animals' motor co-ordination in the chimney test was not significantly disturbed during the time between 7 and 12 months after surgery. At 15 months, nocturnal locomotor activities in BCCA rats were significantly decreased. In situ hybridization (ISH) histochemistry revealed decreased D1 receptor mRNA (D1RmRNA) in striatal neurons 19 months after surgery, while D2 receptor mRNA (D2RmRNA) and the neuronal number remained the same. The present results show that just as is already known for the immature rat brain, the adult rat brain, too, reacts to a transient decrease in its blood supply by appearance of long-lasting alterations in function, and that even a single oligemic episode is capable of inducing progressive dopaminergic dysfunctions and ultimately the partial loss of striatal D1RmRNA.
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Affiliation(s)
- C Heim
- Department of Neuropharmacology and Physiology, Max-Planck Institute of Experimental Medicine, Goettingen, Germany
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Gao D, Xiao A, Ni Z, Yue C, Chang Z. [Influences of acetylcholine, glutamic acid and GABA on the neuronal firings in ventromedial thalamic nucleus]. Zhongguo Ying Yong Sheng Li Xue Za Zhi 1997; 13:60-3. [PMID: 10074320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
In this study, it was shown that the neuronal spontaneous firings of ventromedial thalamic nucleus (VM) in rats were increased by acetylcholine (ACH) and glutamic acid (GLU) applied microiontophoretically with an intensity-dependent manner. Both gamma-animobutyric acid (GABA) and baclofen inhibited the spontaneous firings in majority of VM neurons, but the effect of GABA was rapid and short-lasting, while that of baclofen was slow and long-lasting. GABA could reverse the effects of ACH and GLU. The majority of VM neuronal firing rates could be enhanced by bicuculine, while atropine and MK801 had little effect. The results indicate an important convergence of GLUergic, GABAergic and cholinergic activities in the same VM neurons and GABAergic activities tonically inhibit the VM neurons.
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Affiliation(s)
- D Gao
- Department of Physiology, Jinzhou Medical College
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