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Bjorkman KK, Saldi TK, Lasda E, Bauer LC, Kovarik J, Gonzales PK, Fink MR, Tat KL, Hager CR, Davis JC, Ozeroff CD, Brisson GR, Larremore DB, Leinwand LA, McQueen MB, Parker R. Higher viral load drives infrequent SARS-CoV-2 transmission between asymptomatic residence hall roommates. J Infect Dis 2021; 224:1316-1324. [PMID: 34302469 DOI: 10.1093/infdis/jiab386] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [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: 03/31/2021] [Accepted: 07/22/2021] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND The COVID-19 pandemic spread to over 200 countries in less than six months. To understand COVID spread, determining transmission rate and defining factors that increase transmission risk are essential. Most cases are asymptomatic, but they have viral loads indistinguishable from symptomatic people and do transmit SARS-CoV-2 virus. However, they are often undetected. METHODS Given high residence hall student density, the University of Colorado Boulder established a mandatory weekly screening test program. We analyzed longitudinal data of 6408 students and identified 116 likely transmission events in which a second roommate tested positive within 14 days of the index roommate. RESULTS Although the infection rate was lower in single rooms (10%) than in multiple-occupancy rooms (19%), inter-roommate transmission only occurred ~20% of the time. Cases were usually asymptomatic at the time of detection. Notably, individuals who likely transmitted had an average viral load ~6.5-fold higher than individuals who did not (mean Cq 26.2 vs 28.9). Although diagnosed students moved to isolation rooms, there was no difference in time-to-isolation between cases with or without inter-roommate transmission. CONCLUSIONS This analysis argues that inter-roommate transmission occurs infrequently in residence halls and provides strong correlative evidence that viral load is proportional to transmission probability.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Jack C Davis
- BioFrontiers Institute.,Department of Molecular, Cellular, and Developmental Biology
| | - Christopher D Ozeroff
- BioFrontiers Institute.,Department of Molecular, Cellular, and Developmental Biology
| | | | | | - Leslie A Leinwand
- BioFrontiers Institute.,Department of Molecular, Cellular, and Developmental Biology
| | - Matthew B McQueen
- Department of Integrative Physiology.,Institute for Behavioral Genetics
| | - Roy Parker
- BioFrontiers Institute.,Howard Hughes Medical Institute.,Department of Biochemistry
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2
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Yang Q, Saldi TK, Gonzales PK, Lasda E, Decker CJ, Tat KL, Fink MR, Hager CR, Davis JC, Ozeroff CD, Muhlrad D, Clark SK, Fattor WT, Meyerson NR, Paige CL, Gilchrist AR, Barbachano-Guerrero A, Worden-Sapper ER, Wu SS, Brisson GR, McQueen MB, Dowell RD, Leinwand L, Parker R, Sawyer SL. Just 2% of SARS-CoV-2-positive individuals carry 90% of the virus circulating in communities. Proc Natl Acad Sci U S A 2021; 118:e2104547118. [PMID: 33972412 PMCID: PMC8166196 DOI: 10.1073/pnas.2104547118] [Citation(s) in RCA: 82] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 04/11/2021] [Indexed: 12/20/2022] Open
Abstract
We analyze data from the fall 2020 pandemic response efforts at the University of Colorado Boulder, where more than 72,500 saliva samples were tested for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) using qRT-PCR. All samples were collected from individuals who reported no symptoms associated with COVID-19 on the day of collection. From these, 1,405 positive cases were identified. The distribution of viral loads within these asymptomatic individuals was indistinguishable from what has been previously observed in symptomatic individuals. Regardless of symptomatic status, ∼50% of individuals who test positive for SARS-CoV-2 seem to be in noninfectious phases of the disease, based on having low viral loads in a range from which live virus has rarely been isolated. We find that, at any given time, just 2% of individuals carry 90% of the virions circulating within communities, serving as viral "supercarriers" and possibly also superspreaders.
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Affiliation(s)
- Qing Yang
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80303
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, CO 80303
| | - Tassa K Saldi
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80303
| | - Patrick K Gonzales
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80303
| | - Erika Lasda
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80303
| | - Carolyn J Decker
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80303
- HHMI, University of Colorado Boulder, Boulder, CO 80303
| | - Kimngan L Tat
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80303
| | - Morgan R Fink
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80303
| | - Cole R Hager
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80303
| | - Jack C Davis
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80303
| | | | - Denise Muhlrad
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80303
- HHMI, University of Colorado Boulder, Boulder, CO 80303
| | - Stephen K Clark
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80303
- Darwin Biosciences Inc., Boulder, CO 80303
| | - Will T Fattor
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80303
| | - Nicholas R Meyerson
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80303
- Darwin Biosciences Inc., Boulder, CO 80303
| | - Camille L Paige
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80303
- Darwin Biosciences Inc., Boulder, CO 80303
| | - Alison R Gilchrist
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80303
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, CO 80303
| | | | - Emma R Worden-Sapper
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80303
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, CO 80303
| | - Sharon S Wu
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80303
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, CO 80303
- Interdisciplinary Quantitative Biology Program, University of Colorado Boulder, Boulder, CO 80303
| | - Gloria R Brisson
- Wardenburg Health Center, University of Colorado Boulder, Boulder, CO 80303
| | - Matthew B McQueen
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO 80303
| | - Robin D Dowell
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80303
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, CO 80303
- Department of Computer Science, University of Colorado Boulder, Boulder, CO 80303
| | - Leslie Leinwand
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80303
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, CO 80303
| | - Roy Parker
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80303;
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80303
- HHMI, University of Colorado Boulder, Boulder, CO 80303
| | - Sara L Sawyer
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80303;
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, CO 80303
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3
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Yang Q, Meyerson NR, Clark SK, Paige CL, Fattor WT, Gilchrist AR, Barbachano-Guerrero A, Healy BG, Worden-Sapper ER, Wu SS, Muhlrad D, Decker CJ, Saldi TK, Lasda E, Gonzales P, Fink MR, Tat KL, Hager CR, Davis JC, Ozeroff CD, Brisson GR, McQueen MB, Leinwand LA, Parker R, Sawyer SL. Saliva TwoStep for rapid detection of asymptomatic SARS-CoV-2 carriers. eLife 2021; 10:e65113. [PMID: 33779548 PMCID: PMC8057811 DOI: 10.7554/elife.65113] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 03/26/2021] [Indexed: 01/01/2023] Open
Abstract
Here, we develop a simple molecular test for SARS-CoV-2 in saliva based on reverse transcription loop-mediated isothermal amplification. The test has two steps: (1) heat saliva with a stabilization solution and (2) detect virus by incubating with a primer/enzyme mix. After incubation, saliva samples containing the SARS-CoV-2 genome turn bright yellow. Because this test is pH dependent, it can react falsely to some naturally acidic saliva samples. We report unique saliva stabilization protocols that rendered 295 healthy saliva samples compatible with the test, producing zero false positives. We also evaluated the test on 278 saliva samples from individuals who were infected with SARS-CoV-2 but had no symptoms at the time of saliva collection, and from 54 matched pairs of saliva and anterior nasal samples from infected individuals. The Saliva TwoStep test described herein identified infections with 94% sensitivity and >99% specificity in individuals with sub-clinical (asymptomatic or pre-symptomatic) infections.
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Affiliation(s)
- Qing Yang
- BioFrontiers Institute, University of Colorado BoulderBoulderUnited States
- Department of Molecular, Cellular and Developmental Biology, University of Colorado BoulderBoulderUnited States
| | - Nicholas R Meyerson
- BioFrontiers Institute, University of Colorado BoulderBoulderUnited States
- Darwin Biosciences IncBoulderUnited States
| | - Stephen K Clark
- BioFrontiers Institute, University of Colorado BoulderBoulderUnited States
- Darwin Biosciences IncBoulderUnited States
| | - Camille L Paige
- BioFrontiers Institute, University of Colorado BoulderBoulderUnited States
| | - Will T Fattor
- BioFrontiers Institute, University of Colorado BoulderBoulderUnited States
| | - Alison R Gilchrist
- BioFrontiers Institute, University of Colorado BoulderBoulderUnited States
- Department of Molecular, Cellular and Developmental Biology, University of Colorado BoulderBoulderUnited States
| | | | - Benjamin G Healy
- Department of Mechanical Engineering, University of Colorado BoulderBoulderUnited States
| | - Emma R Worden-Sapper
- BioFrontiers Institute, University of Colorado BoulderBoulderUnited States
- Department of Molecular, Cellular and Developmental Biology, University of Colorado BoulderBoulderUnited States
| | - Sharon S Wu
- BioFrontiers Institute, University of Colorado BoulderBoulderUnited States
- Department of Molecular, Cellular and Developmental Biology, University of Colorado BoulderBoulderUnited States
- Interdisciplinary Quantitative Biology Graduate Program, University of Colorado BoulderBoulderUnited States
| | - Denise Muhlrad
- Department of Biochemistry, University of Colorado BoulderBoulderUnited States
- Howard Hughes Medical Institute, University of Colorado BoulderBoulderUnited States
| | - Carolyn J Decker
- Department of Biochemistry, University of Colorado BoulderBoulderUnited States
- Howard Hughes Medical Institute, University of Colorado BoulderBoulderUnited States
| | - Tassa K Saldi
- BioFrontiers Institute, University of Colorado BoulderBoulderUnited States
| | - Erika Lasda
- BioFrontiers Institute, University of Colorado BoulderBoulderUnited States
| | - Patrick Gonzales
- BioFrontiers Institute, University of Colorado BoulderBoulderUnited States
- Department of Integrative Physiology, University of Colorado BoulderBoulderUnited States
| | - Morgan R Fink
- BioFrontiers Institute, University of Colorado BoulderBoulderUnited States
| | - Kimngan L Tat
- BioFrontiers Institute, University of Colorado BoulderBoulderUnited States
| | - Cole R Hager
- BioFrontiers Institute, University of Colorado BoulderBoulderUnited States
| | - Jack C Davis
- Department of Molecular, Cellular and Developmental Biology, University of Colorado BoulderBoulderUnited States
| | | | - Gloria R Brisson
- Wardenburg Health Center, University of Colorado BoulderBoulderUnited States
| | - Matthew B McQueen
- Department of Integrative Physiology, University of Colorado BoulderBoulderUnited States
| | - Leslie A Leinwand
- BioFrontiers Institute, University of Colorado BoulderBoulderUnited States
- Department of Molecular, Cellular and Developmental Biology, University of Colorado BoulderBoulderUnited States
| | - Roy Parker
- BioFrontiers Institute, University of Colorado BoulderBoulderUnited States
- Department of Molecular, Cellular and Developmental Biology, University of Colorado BoulderBoulderUnited States
- Department of Biochemistry, University of Colorado BoulderBoulderUnited States
- Howard Hughes Medical Institute, University of Colorado BoulderBoulderUnited States
| | - Sara L Sawyer
- BioFrontiers Institute, University of Colorado BoulderBoulderUnited States
- Department of Molecular, Cellular and Developmental Biology, University of Colorado BoulderBoulderUnited States
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4
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Yang Q, Saldi TK, Lasda E, Decker CJ, Paige CL, Muhlrad D, Gonzales PK, Fink MR, Tat KL, Hager CR, Davis JC, Ozeroff CD, Meyerson NR, Clark SK, Fattor WT, Gilchrist AR, Barbachano-Guerrero A, Worden-Sapper ER, Wu SS, Brisson GR, McQueen MB, Dowell RD, Leinwand L, Parker R, Sawyer SL. Just 2% of SARS-CoV-2-positive individuals carry 90% of the virus circulating in communities. medRxiv 2021:2021.03.01.21252250. [PMID: 33688663 PMCID: PMC7941634 DOI: 10.1101/2021.03.01.21252250] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [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: 12/23/2022]
Abstract
We analyze data from the Fall 2020 pandemic response efforts at the University of Colorado Boulder (USA), where more than 72,500 saliva samples were tested for SARS-CoV-2 using quantitative RT-PCR. All samples were collected from individuals who reported no symptoms associated with COVID-19 on the day of collection. From these, 1,405 positive cases were identified. The distribution of viral loads within these asymptomatic individuals was indistinguishable from what has been previously reported in symptomatic individuals. Regardless of symptomatic status, approximately 50% of individuals who test positive for SARS-CoV-2 seem to be in non-infectious phases of the disease, based on having low viral loads in a range from which live virus has rarely been isolated. We find that, at any given time, just 2% of individuals carry 90% of the virions circulating within communities, serving as viral "super-carriers" and possibly also super-spreaders.
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Affiliation(s)
- Qing Yang
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, 80303, USA
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, Colorado, 80303, USA
| | - Tassa K. Saldi
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, 80303, USA
| | - Erika Lasda
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, 80303, USA
| | - Carolyn J. Decker
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado, 80303, USA
- Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, Colorado, 80303, USA
| | - Camille L. Paige
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, 80303, USA
| | - Denise Muhlrad
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado, 80303, USA
- Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, Colorado, 80303, USA
| | - Patrick K. Gonzales
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, 80303, USA
| | - Morgan R. Fink
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, 80303, USA
| | - Kimngan L. Tat
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, 80303, USA
| | - Cole R. Hager
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, 80303, USA
| | - Jack C. Davis
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, Colorado, 80303, USA
| | | | - Nicholas R. Meyerson
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, 80303, USA
| | - Stephen K. Clark
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, 80303, USA
| | - Will T. Fattor
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, 80303, USA
| | - Alison R. Gilchrist
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, 80303, USA
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, Colorado, 80303, USA
| | | | - Emma R. Worden-Sapper
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, 80303, USA
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, Colorado, 80303, USA
| | - Sharon S. Wu
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, 80303, USA
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, Colorado, 80303, USA
- Interdisciplinary Quantitative Biology Program, University of Colorado Boulder, Boulder, Colorado, 80303, USA
| | - Gloria R. Brisson
- Wardenburg Health Center, University of Colorado Boulder, Boulder, Colorado, 80303, USA
| | - Matthew B. McQueen
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, Colorado, 80303, USA
| | - Robin D. Dowell
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, 80303, USA
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, Colorado, 80303, USA
- Department of Computer Science, University of Colorado Boulder, Boulder, Colorado, 80303, USA
| | - Leslie Leinwand
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, 80303, USA
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, Colorado, 80303, USA
| | - Roy Parker
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, 80303, USA
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado, 80303, USA
- Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, Colorado, 80303, USA
| | - Sara L. Sawyer
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, 80303, USA
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, Colorado, 80303, USA
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5
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Yang Q, Meyerson NR, Clark SK, Paige CL, Fattor WT, Gilchrist AR, Barbachano-Guerrero A, Healy BG, Worden-Sapper ER, Wu SS, Muhlrad D, Decker CJ, Saldi TK, Lasda E, Gonzales PK, Fink MR, Tat KL, Hager CR, Davis JC, Ozeroff CD, Brisson GR, McQueen MB, Leinwand L, Parker R, Sawyer SL. Saliva TwoStep for rapid detection of asymptomatic SARS-CoV-2 carriers. medRxiv 2021:2020.07.16.20150250. [PMID: 33619503 PMCID: PMC7899473 DOI: 10.1101/2020.07.16.20150250] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [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: 12/22/2022]
Abstract
Here, we develop a simple molecular test for SARS-CoV-2 in saliva based on reverse transcription loop-mediated isothermal amplification (RT-LAMP). The test has two steps: 1) heat saliva with a stabilization solution, and 2) detect virus by incubating with a primer/enzyme mix. After incubation, saliva samples containing the SARS-CoV-2 genome turn bright yellow. Because this test is pH dependent, it can react falsely to some naturally acidic saliva samples. We report unique saliva stabilization protocols that rendered 295 healthy saliva samples compatible with the test, producing zero false positives. We also evaluated the test on 278 saliva samples from individuals who were infected with SARS-CoV-2 but had no symptoms at the time of saliva collection, and from 54 matched pairs of saliva and anterior nasal samples from infected individuals. The Saliva TwoStep test described herein identified infections with 94% sensitivity and >99% specificity in individuals with sub-clinical (asymptomatic or pre-symptomatic) infections.
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Affiliation(s)
- Qing Yang
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, 80303
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, Colorado, 80303
| | - Nicholas R Meyerson
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, 80303
- Darwin Biosciences Inc., Boulder, Colorado, 80303, USA
| | - Stephen K Clark
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, 80303
- Darwin Biosciences Inc., Boulder, Colorado, 80303, USA
| | - Camille L Paige
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, 80303
| | - Will T Fattor
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, 80303
| | - Alison R Gilchrist
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, 80303
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, Colorado, 80303
| | | | - Benjamin G Healy
- Department of Mechanical Engineering, University of Colorado Boulder, Boulder, Colorado, 80303
| | - Emma R Worden-Sapper
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, 80303
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, Colorado, 80303
| | - Sharon S Wu
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, 80303
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, Colorado, 80303
- Interdisciplinary Quantitative Biology Graduate Program, University of Colorado Boulder, Boulder, Colorado, 80303
| | - Denise Muhlrad
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado, 80303
- Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, Colorado, 80303
| | - Carolyn J Decker
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado, 80303
- Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, Colorado, 80303
| | - Tassa K Saldi
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, 80303
| | - Erika Lasda
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, 80303
| | - Patrick K Gonzales
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, 80303
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, Colorado, 80303
| | - Morgan R Fink
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, 80303
| | - Kimngan L Tat
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, 80303
| | - Cole R Hager
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, 80303
| | - Jack C Davis
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, Colorado, 80303
| | | | - Gloria R Brisson
- Wardenburg Health Center, University of Colorado Boulder, Boulder, Colorado, 80303
| | - Matthew B McQueen
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, Colorado, 80303
| | - Leslie Leinwand
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, 80303
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, Colorado, 80303
| | - Roy Parker
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, 80303
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, Colorado, 80303
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado, 80303
- Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, Colorado, 80303
| | - Sara L Sawyer
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, 80303
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, Colorado, 80303
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Saldi TK, Gonzales PK, LaRocca TJ, Link CD. Neurodegeneration, Heterochromatin, and Double-Stranded RNA. J Exp Neurosci 2019; 13:1179069519830697. [PMID: 30792577 PMCID: PMC6376497 DOI: 10.1177/1179069519830697] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 01/23/2019] [Indexed: 12/15/2022] Open
Abstract
Changes in chromatin and epigenetic modifications have been associated with aging and aging-associated neurodegenerative diseases, although the causal relationship between these changes and disease-related pathology has been unclear. Recent studies have now made direct connections between neurodegeneration-associated proteins and derepression of repetitive element transcription due to changes in heterochromatin. We suggest that this derepression leads to an increased accumulation of intracellular double-stranded RNA (dsRNA), with an attendant induction of innate immune responses that contribute to the neuroinflammation found in essentially all age-associated neurodegenerative diseases.
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Affiliation(s)
- Tassa K Saldi
- Department of Biochemistry and Molecular Genetics, University of Colorado, Aurora, CO, USA
| | - Patrick K Gonzales
- Department of Integrative Physiology, University of Colorado, Boulder, CO, USA
| | - Thomas J LaRocca
- Department of Integrative Physiology, University of Colorado, Boulder, CO, USA
| | - Christopher D Link
- Department of Integrative Physiology, University of Colorado, Boulder, CO, USA
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7
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Saldi TK, Gonzales P, Garrido-Lecca A, Dostal V, Roberts CM, Petrucelli L, Link CD. The Caenorhabditis elegans Ortholog of TDP-43 Regulates the Chromatin Localization of the Heterochromatin Protein 1 Homolog HPL-2. Mol Cell Biol 2018; 38:e00668-17. [PMID: 29760282 PMCID: PMC6048318 DOI: 10.1128/mcb.00668-17] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Revised: 02/04/2018] [Accepted: 05/01/2018] [Indexed: 12/13/2022] Open
Abstract
TDP-1 is the Caenorhabditis elegans ortholog of mammalian TDP-43, which is strongly implicated in the etiology of frontotemporal dementia (FTD) and amyotrophic lateral sclerosis (ALS). We discovered that deletion of the tdp-1 gene results in enhanced nuclear RNA interference (RNAi). As nuclear RNAi in C. elegans involves chromatin changes moderated by HPL-2, a homolog of heterochromatin protein 1 (HP1), we investigated the interaction of TDP-1 and HPL-2. We found that TDP-1 and HPL-2 interact directly and that loss of TDP-1 dramatically alters the chromatin association of HPL-2. We showed previously that deletion of the tdp-1 gene results in transcriptional alterations and the accumulation of double-stranded RNA (dsRNA). These molecular changes are replicated in an hpl-2 deletion strain, consistent with HPL-2 acting in consort with TDP-1 to modulate these aspects of RNA metabolism. Our observations identify novel mechanisms by which HP1 homologs can be recruited to chromatin and by which nuclear depletion of human TDP-43 may lead to changes in RNA metabolism that are relevant to disease.
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Affiliation(s)
- Tassa K Saldi
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado, USA
| | - Patrick Gonzales
- Integrative Physiology, University of Colorado, Boulder, Colorado, USA
| | - Alfonso Garrido-Lecca
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado, USA
| | - Vishantie Dostal
- Integrative Physiology, University of Colorado, Boulder, Colorado, USA
| | | | | | - Christopher D Link
- Integrative Physiology, University of Colorado, Boulder, Colorado, USA
- Institute for Behavioral Genetics, University of Colorado, Boulder, Colorado, USA
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8
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Saldi TK, Ash PE, Wilson G, Gonzales P, Garrido-Lecca A, Roberts CM, Dostal V, Gendron TF, Stein LD, Blumenthal T, Petrucelli L, Link CD. TDP-1, the Caenorhabditis elegans ortholog of TDP-43, limits the accumulation of double-stranded RNA. EMBO J 2014; 33:2947-66. [PMID: 25391662 PMCID: PMC4282642 DOI: 10.15252/embj.201488740] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Caenorhabditis elegans mutants deleted for TDP-1, an ortholog of the neurodegeneration-associated RNA-binding protein TDP-43, display only mild phenotypes. Nevertheless, transcriptome sequencing revealed that many RNAs were altered in accumulation and/or processing in the mutant. Analysis of these transcriptional abnormalities demonstrates that a primary function of TDP-1 is to limit formation or stability of double-stranded RNA. Specifically, we found that deletion of tdp-1: (1) preferentially alters the accumulation of RNAs with inherent double-stranded structure (dsRNA); (2) increases the accumulation of nuclear dsRNA foci; (3) enhances the frequency of adenosine-to-inosine RNA editing; and (4) dramatically increases the amount of transcripts immunoprecipitable with a dsRNA-specific antibody, including intronic sequences, RNAs with antisense overlap to another transcript, and transposons. We also show that TDP-43 knockdown in human cells results in accumulation of dsRNA, indicating that suppression of dsRNA is a conserved function of TDP-43 in mammals. Altered accumulation of structured RNA may account for some of the previously described molecular phenotypes (e.g., altered splicing) resulting from reduction of TDP-43 function.
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Affiliation(s)
- Tassa K Saldi
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO, USA
| | - Peter Ea Ash
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Gavin Wilson
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada Informatics and Biocomputing Platform, Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Patrick Gonzales
- Institute for Behavioral Genetics University of Colorado, Boulder, CO, USA
| | - Alfonso Garrido-Lecca
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO, USA
| | | | - Vishantie Dostal
- Institute for Behavioral Genetics University of Colorado, Boulder, CO, USA
| | - Tania F Gendron
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Lincoln D Stein
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Thomas Blumenthal
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO, USA
| | | | - Christopher D Link
- Institute for Behavioral Genetics University of Colorado, Boulder, CO, USA Integrative Physiology, University of Colorado, Boulder, CO, USA
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Affiliation(s)
- Christopher D. Link
- Institute for Behavioral Genetics, University of Colorado, Boulder, CO 80309, USA
| | - Tassa K. Saldi
- Institute for Behavioral Genetics, University of Colorado, Boulder, CO 80309, USA
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