1
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Garcia G, Bar‐Ziv R, Averbukh M, Dasgupta N, Dutta N, Zhang H, Fan W, Moaddeli D, Tsui CK, Castro Torres T, Alcala A, Moehle EA, Hoang S, Shalem O, Adams PD, Thorwald MA, Higuchi‐Sanabria R. Large-scale genetic screens identify BET-1 as a cytoskeleton regulator promoting actin function and life span. Aging Cell 2022; 22:e13742. [PMID: 36404134 PMCID: PMC9835578 DOI: 10.1111/acel.13742] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 10/17/2022] [Accepted: 11/01/2022] [Indexed: 11/22/2022] Open
Abstract
The actin cytoskeleton is a three-dimensional scaffold of proteins that is a regulatory, energyconsuming network with dynamic properties to shape the structure and function of the cell. Proper actin function is required for many cellular pathways, including cell division, autophagy, chaperone function, endocytosis, and exocytosis. Deterioration of these processes manifests during aging and exposure to stress, which is in part due to the breakdown of the actin cytoskeleton. However, the regulatory mechanisms involved in preservation of cytoskeletal form and function are not well-understood. Here, we performed a multipronged, cross-organismal screen combining a whole-genome CRISPR-Cas9 screen in human fibroblasts with in vivo Caenorhabditis elegans synthetic lethality screening. We identified the bromodomain protein, BET-1, as a key regulator of actin function and longevity. Overexpression of bet-1 preserves actin function at late age and promotes life span and healthspan in C. elegans. These beneficial effects are mediated through actin preservation by the transcriptional regulator function of BET-1. Together, our discovery assigns a key role for BET-1 in cytoskeletal health, highlighting regulatory cellular networks promoting cytoskeletal homeostasis.
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Affiliation(s)
- Gilberto Garcia
- Leonard Davis School of GerontologyUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
| | - Raz Bar‐Ziv
- Department of Molecular & Cellular Biology, Howard Hughes Medical InstituteThe University of California, BerkeleyBerkeleyCaliforniaUSA
| | - Maxim Averbukh
- Leonard Davis School of GerontologyUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
| | - Nirmalya Dasgupta
- Aging, Cancer and Immuno‐oncology ProgramSanford Burnham Prebys Medical Discovery InstituteLa JollaCaliforniaUSA
| | - Naibedya Dutta
- Leonard Davis School of GerontologyUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
| | - Hanlin Zhang
- Department of Molecular & Cellular Biology, Howard Hughes Medical InstituteThe University of California, BerkeleyBerkeleyCaliforniaUSA
| | - Wudi Fan
- Department of Molecular & Cellular Biology, Howard Hughes Medical InstituteThe University of California, BerkeleyBerkeleyCaliforniaUSA
| | - Darius Moaddeli
- Leonard Davis School of GerontologyUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
| | - C. Kimberly Tsui
- Department of Molecular & Cellular Biology, Howard Hughes Medical InstituteThe University of California, BerkeleyBerkeleyCaliforniaUSA
| | - Toni Castro Torres
- Leonard Davis School of GerontologyUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
| | - Athena Alcala
- Leonard Davis School of GerontologyUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
| | - Erica A. Moehle
- Department of Molecular & Cellular Biology, Howard Hughes Medical InstituteThe University of California, BerkeleyBerkeleyCaliforniaUSA
| | - Sally Hoang
- Leonard Davis School of GerontologyUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
| | - Ophir Shalem
- Department of Genetics, Perelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Peter D. Adams
- Aging, Cancer and Immuno‐oncology ProgramSanford Burnham Prebys Medical Discovery InstituteLa JollaCaliforniaUSA
| | - Max A. Thorwald
- Leonard Davis School of GerontologyUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
| | - Ryo Higuchi‐Sanabria
- Leonard Davis School of GerontologyUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
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2
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Parker AM, Jackson N, Awasthi S, Kim H, Alwan T, Wyllie AL, Baldwin AB, Brennick NB, Moehle EA, Giannikopoulos P, Kogut K, Holland N, Mora-Wyrobek A, Eskenazi B, Riley LW, Lewnard JA. Association of upper respiratory Streptococcus pneumoniae colonization with SARS-CoV-2 infection among adults. Clin Infect Dis 2022; 76:1209-1217. [PMID: 36401872 DOI: 10.1093/cid/ciac907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 11/08/2022] [Accepted: 11/15/2022] [Indexed: 11/21/2022] Open
Abstract
ABSTRACT
Background
Streptococcus pneumoniae interacts with numerous viral respiratory pathogens in the upper airway. It is unclear whether similar interactions occur with SARS-CoV-2.
Methods
We collected saliva specimens from working-age adults receiving SARS-CoV-2 molecular testing at outpatient clinics and via mobile community-outreach testing between July and November 2020 in Monterey County, California. Following bacterial culture enrichment, we tested for pneumococci by quantitative polymerase chain reaction (qPCR) targeting the lytA and piaB genes, and measured associations with SARS-CoV-2 infection via conditional logistic regression.
Results
Analyses included 1,278 participants, with 564 enrolled in clinics and 714 enrolled through outreach-based testing. Prevalence of pneumococcal carriage was 9.2% (117/1,278) among all participants (11.2% [63/564] clinic-based testing; 7.6% [54/714] outreach testing). Prevalence of SARS-CoV-2 infection was 27.4% (32/117) among pneumococcal carriers and 9.6% (112/1,161) among non-carriers (adjusted odds ratio [aOR]: 2.73; 95% confidence interval: 1.58-4.69). Associations between SARS-CoV-2 infection and pneumococcal carriage were enhanced in the clinic-based sample (aOR = 4.01 [2.08-7.75]) and among symptomatic participants (aOR = 3.38 [1.35-8.40]), when compared to findings within the outreach-based sample and among asymptomatic participants. Adjusted odds of SARS-CoV-2 co-infection increased 1.24 (1.00-1.55)-fold for each 1-unit decrease in piaB qPCR CT value among pneumococcal carriers. Last, pneumococcal carriage modified the association of SARS-CoV-2 infection with recent exposure to a suspected COVID-19 case (aOR = 7.64 [1.91-30.7] and 3.29 [1.94-5.59]) among pneumococcal carriers and non-carriers, respectively).
Conclusions
Associations of pneumococcal carriage detection and density with SARS-CoV-2 suggest a synergistic relationship in the upper airway. Longitudinal studies are needed to determine interaction mechanisms between pneumococci and SARS-CoV-2.
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Affiliation(s)
- Anna M Parker
- Division of Infectious Diseases & Vaccinology, School of Public Health, University of California, Berkeley , Berkeley, California 94720 , United States
| | - Nicole Jackson
- Division of Infectious Diseases & Vaccinology, School of Public Health, University of California, Berkeley , Berkeley, California 94720 , United States
| | - Shevya Awasthi
- Division of Infectious Diseases & Vaccinology, School of Public Health, University of California, Berkeley , Berkeley, California 94720 , United States
| | - Hanna Kim
- Division of Infectious Diseases & Vaccinology, School of Public Health, University of California, Berkeley , Berkeley, California 94720 , United States
| | - Tess Alwan
- Division of Infectious Diseases & Vaccinology, School of Public Health, University of California, Berkeley , Berkeley, California 94720 , United States
| | - Anne L Wyllie
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health , New Haven, Connecticut 06510 , United States
| | - Alisha B Baldwin
- Innovative Genomics Institute, University of California, Berkeley , Berkeley, California 94720 , United States
| | - Nicole B Brennick
- Innovative Genomics Institute, University of California, Berkeley , Berkeley, California 94720 , United States
| | - Erica A Moehle
- Innovative Genomics Institute, University of California, Berkeley , Berkeley, California 94720 , United States
| | - Petros Giannikopoulos
- Innovative Genomics Institute, University of California, Berkeley , Berkeley, California 94720 , United States
| | - Katherine Kogut
- Center for Environmental Research & Community Health, School of Public Health, University of California , Berkeley, Berkeley, California 94720 , United States
| | - Nina Holland
- Center for Environmental Research & Community Health, School of Public Health, University of California , Berkeley, Berkeley, California 94720 , United States
| | - Ana Mora-Wyrobek
- Center for Environmental Research & Community Health, School of Public Health, University of California , Berkeley, Berkeley, California 94720 , United States
| | - Brenda Eskenazi
- Center for Environmental Research & Community Health, School of Public Health, University of California , Berkeley, Berkeley, California 94720 , United States
| | - Lee W Riley
- Division of Infectious Diseases & Vaccinology, School of Public Health, University of California, Berkeley , Berkeley, California 94720 , United States
| | - Joseph A Lewnard
- Division of Infectious Diseases & Vaccinology, School of Public Health, University of California, Berkeley , Berkeley, California 94720 , United States
- Division of Epidemiology, School of Public Health, University of California , Berkeley, Berkeley, California 94720 , United States
- Center for Computational Biology, College of Engineering, University of California , Berkeley, Berkeley, California 94720 , United States
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3
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Parker AM, Jackson N, Awasthi S, Kim H, Alwan T, Wyllie AL, Baldwin AB, Brennick NB, Moehle EA, Giannikopoulos P, Kogut K, Holland N, Mora-Wyrobek A, Eskenazi B, Riley LW, Lewnard JA. Association of upper respiratory Streptococcus pneumoniae colonization with SARS-CoV-2 infection among adults. medRxiv 2022:2022.10.04.22280709. [PMID: 36238718 PMCID: PMC9558443 DOI: 10.1101/2022.10.04.22280709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Background Streptococcus pneumoniae interacts with numerous viral respiratory pathogens in the upper airway. It is unclear whether similar interactions occur with SARS-CoV-2. Methods We collected saliva specimens from working-age adults receiving SARS-CoV-2 molecular testing at outpatient clinics and via mobile community-outreach testing between July and November 2020 in Monterey County, California. Following bacterial culture enrichment, we tested for pneumococci by quantitative polymerase chain reaction (qPCR) targeting the lytA and piaB genes, and measured associations with SARS-CoV-2 infection via conditional logistic regression. Results Analyses included 1,278 participants, with 564 enrolled in clinics and 714 enrolled through outreach-based testing. Prevalence of pneumococcal carriage was 9.2% (117/1,278) among all participants (11.2% [63/564] clinic-based testing; 7.6% [54/714] outreach testing). Prevalence of SARS-CoV-2 infection was 27.4% (32/117) among pneumococcal carriers and 9.6% (112/1,161) among non-carriers (adjusted odds ratio [aOR]: 2.73; 95% confidence interval: 1.58-4.69). Associations between SARS-CoV-2 infection and pneumococcal carriage were enhanced in the clinic-based sample (aOR=4.01 [2.08-7.75]) and among symptomatic participants (aOR=3.38 [1.35-8.40]), when compared to findings within the outreach-based sample and among asymptomatic participants. Adjusted odds of SARS-CoV-2 co-infection increased 1.24 (1.00-1.55)-fold for each 1-unit decrease in piaB qPCR C T value among pneumococcal carriers. Last, pneumococcal carriage modified the association of SARS-CoV-2 infection with recent exposure to a suspected COVID-19 case (aOR=7.64 [1.91-30.7] and 3.29 [1.94-5.59]) among pneumococcal carriers and non-carriers, respectively). Conclusions Associations of pneumococcal carriage detection and density with SARS-CoV-2 suggest a synergistic relationship in the upper airway. Longitudinal studies are needed to determine interaction mechanisms between pneumococci and SARS-CoV-2. Key points In an adult ambulatory and community sample, SARS-CoV-2 infection was more prevalent among pneumococcal carriers than non-carriers.Associations between pneumococcal carriage and SARS-CoV-2 infection were strongest among adults reporting acute symptoms and receiving SARS-CoV-2 testing in a clinical setting.
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4
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Chandrasekaran SS, Agrawal S, Fanton A, Jangid AR, Charrez B, Escajeda AM, Son S, Mcintosh R, Tran H, Bhuiya A, de León Derby MD, Switz NA, Armstrong M, Harris AR, Prywes N, Lukarska M, Biering SB, Smock DCJ, Mok A, Knott GJ, Dang Q, Van Dis E, Dugan E, Kim S, Liu TY, Moehle EA, Kogut K, Eskenazi B, Harris E, Stanley SA, Lareau LF, Tan MX, Fletcher DA, Doudna JA, Savage DF, Hsu PD. Rapid detection of SARS-CoV-2 RNA in saliva via Cas13. Nat Biomed Eng 2022; 6:944-956. [PMID: 35953650 PMCID: PMC10367768 DOI: 10.1038/s41551-022-00917-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 06/30/2022] [Indexed: 11/10/2022]
Abstract
Rapid nucleic acid testing is central to infectious disease surveillance. Here, we report an assay for rapid COVID-19 testing and its implementation in a prototype microfluidic device. The assay, which we named DISCoVER (for diagnostics with coronavirus enzymatic reporting), involves extraction-free sample lysis via shelf-stable and low-cost reagents, multiplexed isothermal RNA amplification followed by T7 transcription, and Cas13-mediated cleavage of a quenched fluorophore. The device consists of a single-use gravity-driven microfluidic cartridge inserted into a compact instrument for automated running of the assay and readout of fluorescence within 60 min. DISCoVER can detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in saliva with a sensitivity of 40 copies μl-1, and was 94% sensitive and 100% specific when validated (against quantitative PCR) using total RNA extracted from 63 nasal-swab samples (33 SARS-CoV-2-positive, with cycle-threshold values of 13-35). The device correctly identified all tested clinical saliva samples (10 SARS-CoV-2-positive out of 13, with cycle-threshold values of 23-31). Rapid point-of-care nucleic acid testing may broaden the use of molecular diagnostics.
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Affiliation(s)
- Sita S Chandrasekaran
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA.,Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA.,University of California, Berkeley-University of California, San Francisco Graduate Program in Bioengineering, Berkeley, CA, USA
| | - Shreeya Agrawal
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA.,Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Alison Fanton
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA.,Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA.,University of California, Berkeley-University of California, San Francisco Graduate Program in Bioengineering, Berkeley, CA, USA
| | - Aditya R Jangid
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA.,Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Bérénice Charrez
- University of California, Berkeley-University of California, San Francisco Graduate Program in Bioengineering, Berkeley, CA, USA
| | | | - Sungmin Son
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | | | | | - Abdul Bhuiya
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA.,University of California, Berkeley-University of California, San Francisco Graduate Program in Bioengineering, Berkeley, CA, USA
| | - María Díaz de León Derby
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA.,University of California, Berkeley-University of California, San Francisco Graduate Program in Bioengineering, Berkeley, CA, USA
| | - Neil A Switz
- Department of Physics and Astronomy, San José State University, San José, CA, USA
| | - Maxim Armstrong
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Andrew R Harris
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | - Noam Prywes
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Maria Lukarska
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA.,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Scott B Biering
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Dylan C J Smock
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA.,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Amanda Mok
- Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Gavin J Knott
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA.,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.,Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - Qi Dang
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Erik Van Dis
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Eli Dugan
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA.,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Shin Kim
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA.,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Tina Y Liu
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA.,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | | | - Erica A Moehle
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Katherine Kogut
- Center for Environmental Research and Community Health (CERCH), School of Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Brenda Eskenazi
- Center for Environmental Research and Community Health (CERCH), School of Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Eva Harris
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Sarah A Stanley
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.,School of Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Liana F Lareau
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA.,Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | | | - Daniel A Fletcher
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | - Jennifer A Doudna
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA. .,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. .,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA. .,Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, USA. .,Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA. .,Gladstone Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA, USA.
| | - David F Savage
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.
| | - Patrick D Hsu
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA. .,Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA. .,Arc Institute, Palo Alto, CA, USA.
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5
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Stahl EC, Gopez AR, Tsuchida CA, Fan VB, Moehle EA, Witkowsky LB, Hamilton JR, Lin-Shiao E, McElroy M, McDevitt SL, Ciling A, Tsui CK, Pestal K, Gildea HK, Keller A, Sylvain IA, Williams C, Hirsh A, Ehrenberg AJ, Kantor R, Metzger M, Nelson KL, Urnov FD, Ringeisen BR, Giannikopoulos P, Doudna JA. LuNER: Multiplexed SARS-CoV-2 detection in clinical swab and wastewater samples. PLoS One 2021; 16:e0258263. [PMID: 34758033 PMCID: PMC8580221 DOI: 10.1371/journal.pone.0258263] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Accepted: 09/22/2021] [Indexed: 01/03/2023] Open
Abstract
Clinical and surveillance testing for the SARS-CoV-2 virus relies overwhelmingly on RT-qPCR-based diagnostics, yet several popular assays require 2-3 separate reactions or rely on detection of a single viral target, which adds significant time, cost, and risk of false-negative results. Furthermore, multiplexed RT-qPCR tests that detect at least two SARS-CoV-2 genes in a single reaction are typically not affordable for large scale clinical surveillance or adaptable to multiple PCR machines and plate layouts. We developed a RT-qPCR assay using the Luna Probe Universal One-Step RT-qPCR master mix with publicly available primers and probes to detect SARS-CoV-2 N gene, E gene, and human RNase P (LuNER) to address these shortcomings and meet the testing demands of a university campus and the local community. This cost-effective test is compatible with BioRad or Applied Biosystems qPCR machines, in 96 and 384-well formats, with or without sample pooling, and has a detection sensitivity suitable for both clinical reporting and wastewater surveillance efforts.
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Affiliation(s)
- Elizabeth C. Stahl
- University of California, Berkeley, Berkeley, CA, United States of America
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, United States of America
| | - Allan R. Gopez
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, United States of America
| | - Connor A. Tsuchida
- University of California, Berkeley, Berkeley, CA, United States of America
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, United States of America
| | - Vinson B. Fan
- University of California, Berkeley, Berkeley, CA, United States of America
| | - Erica A. Moehle
- University of California, Berkeley, Berkeley, CA, United States of America
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, United States of America
| | - Lea B. Witkowsky
- University of California, Berkeley, Berkeley, CA, United States of America
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, United States of America
| | - Jennifer R. Hamilton
- University of California, Berkeley, Berkeley, CA, United States of America
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, United States of America
| | - Enrique Lin-Shiao
- University of California, Berkeley, Berkeley, CA, United States of America
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, United States of America
| | - Matthew McElroy
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, United States of America
| | - Shana L. McDevitt
- University of California, Berkeley, Berkeley, CA, United States of America
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, United States of America
| | - Alison Ciling
- University of California, Berkeley, Berkeley, CA, United States of America
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, United States of America
| | - C. Kimberly Tsui
- University of California, Berkeley, Berkeley, CA, United States of America
| | - Kathleen Pestal
- University of California, Berkeley, Berkeley, CA, United States of America
| | - Holly K. Gildea
- University of California, Berkeley, Berkeley, CA, United States of America
| | - Amanda Keller
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, United States of America
| | - Iman A. Sylvain
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, United States of America
| | - Clara Williams
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, United States of America
| | - Ariana Hirsh
- University of California, Berkeley, Berkeley, CA, United States of America
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, United States of America
| | | | - Rose Kantor
- University of California, Berkeley, Berkeley, CA, United States of America
- Department of Civil and Environmental Engineering, University of California, Berkeley, CA, United States of America
| | - Matthew Metzger
- University of California, Berkeley, Berkeley, CA, United States of America
- Department of Civil and Environmental Engineering, University of California, Berkeley, CA, United States of America
| | - Kara L. Nelson
- University of California, Berkeley, Berkeley, CA, United States of America
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, United States of America
- Department of Civil and Environmental Engineering, University of California, Berkeley, CA, United States of America
| | - Fyodor D. Urnov
- University of California, Berkeley, Berkeley, CA, United States of America
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, United States of America
| | - Bradley R. Ringeisen
- University of California, Berkeley, Berkeley, CA, United States of America
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, United States of America
| | - Petros Giannikopoulos
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, United States of America
| | - Jennifer A. Doudna
- University of California, Berkeley, Berkeley, CA, United States of America
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, United States of America
- Howard Hughes Medical Institute, University of California, Berkeley, CA, United States of America
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6
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Moehle EA, Higuchi-Sanabria R, Tsui CK, Homentcovschi S, Tharp KM, Zhang H, Chi H, Joe L, de los Rios Rogers M, Sahay A, Kelet N, Benitez C, Bar-Ziv R, Garcia G, Shen K, Frankino PA, Schinzel RT, Shalem O, Dillin A. Cross-species screening platforms identify EPS-8 as a critical link for mitochondrial stress and actin stabilization. Sci Adv 2021; 7:eabj6818. [PMID: 34714674 PMCID: PMC8555897 DOI: 10.1126/sciadv.abj6818] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 09/10/2021] [Indexed: 06/13/2023]
Abstract
The dysfunction of mitochondria is associated with the physiological consequences of aging and many age-related diseases. Therefore, critical quality control mechanisms exist to protect mitochondrial functions, including the unfolded protein response of the mitochondria (UPRMT). However, it is still unclear how UPRMT is regulated in mammals with mechanistic discrepancies between previous studies. Here, we reasoned that a study of conserved mechanisms could provide a uniquely powerful way to reveal previously uncharacterized components of the mammalian UPRMT. We performed cross-species comparison of genetic requirements for survival under—and in response to—mitochondrial stress between karyotypically normal human stem cells and the nematode Caenorhabditis elegans. We identified a role for EPS-8/EPS8 (epidermal growth factor receptor pathway substrate 8), a signaling protein adaptor, in general mitochondrial homeostasis and UPRMT regulation through integrin-mediated remodeling of the actin cytoskeleton. This study also highlights the use of cross-species comparisons in genetic screens to interrogate cellular pathways.
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Affiliation(s)
- Erica A. Moehle
- Department of Molecular and Cellular Biology, Howard Hughes Medical Institute, The University of California, Berkeley, Berkeley, CA 94720, USA
| | - Ryo Higuchi-Sanabria
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089
| | - C. Kimberly Tsui
- Department of Molecular and Cellular Biology, Howard Hughes Medical Institute, The University of California, Berkeley, Berkeley, CA 94720, USA
| | - Stefan Homentcovschi
- Department of Molecular and Cellular Biology, Howard Hughes Medical Institute, The University of California, Berkeley, Berkeley, CA 94720, USA
| | - Kevin M. Tharp
- Center for Bioengineering and Tissue Regeneration, Department of Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Hanlin Zhang
- Department of Molecular and Cellular Biology, Howard Hughes Medical Institute, The University of California, Berkeley, Berkeley, CA 94720, USA
| | - Hannah Chi
- Department of Molecular and Cellular Biology, Howard Hughes Medical Institute, The University of California, Berkeley, Berkeley, CA 94720, USA
| | - Larry Joe
- Department of Molecular and Cellular Biology, Howard Hughes Medical Institute, The University of California, Berkeley, Berkeley, CA 94720, USA
| | - Mattias de los Rios Rogers
- Department of Molecular and Cellular Biology, Howard Hughes Medical Institute, The University of California, Berkeley, Berkeley, CA 94720, USA
| | - Arushi Sahay
- Department of Molecular and Cellular Biology, Howard Hughes Medical Institute, The University of California, Berkeley, Berkeley, CA 94720, USA
| | - Naame Kelet
- Department of Molecular and Cellular Biology, Howard Hughes Medical Institute, The University of California, Berkeley, Berkeley, CA 94720, USA
| | - Camila Benitez
- Department of Molecular and Cellular Biology, Howard Hughes Medical Institute, The University of California, Berkeley, Berkeley, CA 94720, USA
| | - Raz Bar-Ziv
- Department of Molecular and Cellular Biology, Howard Hughes Medical Institute, The University of California, Berkeley, Berkeley, CA 94720, USA
| | - Gilberto Garcia
- Department of Molecular and Cellular Biology, Howard Hughes Medical Institute, The University of California, Berkeley, Berkeley, CA 94720, USA
| | - Koning Shen
- Department of Molecular and Cellular Biology, Howard Hughes Medical Institute, The University of California, Berkeley, Berkeley, CA 94720, USA
| | - Phillip A. Frankino
- Department of Molecular and Cellular Biology, Howard Hughes Medical Institute, The University of California, Berkeley, Berkeley, CA 94720, USA
| | - Robert T. Schinzel
- Department of Molecular and Cellular Biology, Howard Hughes Medical Institute, The University of California, Berkeley, Berkeley, CA 94720, USA
| | - Ophir Shalem
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadephia, PA 191004, USA
| | - Andrew Dillin
- Department of Molecular and Cellular Biology, Howard Hughes Medical Institute, The University of California, Berkeley, Berkeley, CA 94720, USA
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7
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Hamilton JR, Stahl EC, Tsuchida CA, Lin-Shiao E, Tsui CK, Pestal K, Gildea HK, Witkowsky LB, Moehle EA, McDevitt SL, McElroy M, Keller A, Sylvain I, Hirsh A, Ciling A, Ehrenberg AJ, Ringeisen BR, Huberty G, Urnov FD, Giannikopoulos P, Doudna JA. Robotic RNA extraction for SARS-CoV-2 surveillance using saliva samples. PLoS One 2021; 16:e0255690. [PMID: 34351984 PMCID: PMC8341588 DOI: 10.1371/journal.pone.0255690] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 07/21/2021] [Indexed: 01/22/2023] Open
Abstract
Saliva is an attractive specimen type for asymptomatic surveillance of COVID-19 in large populations due to its ease of collection and its demonstrated utility for detecting RNA from SARS-CoV-2. Multiple saliva-based viral detection protocols use a direct-to-RT-qPCR approach that eliminates nucleic acid extraction but can reduce viral RNA detection sensitivity. To improve test sensitivity while maintaining speed, we developed a robotic nucleic acid extraction method for detecting SARS-CoV-2 RNA in saliva samples with high throughput. Using this assay, the Free Asymptomatic Saliva Testing (IGI FAST) research study on the UC Berkeley campus conducted 11,971 tests on supervised self-collected saliva samples and identified rare positive specimens containing SARS-CoV-2 RNA during a time of low infection prevalence. In an attempt to increase testing capacity, we further adapted our robotic extraction assay to process pooled saliva samples. We also benchmarked our assay against nasopharyngeal swab specimens and found saliva methods require further optimization to match this gold standard. Finally, we designed and validated a RT-qPCR test suitable for saliva self-collection. These results establish a robotic extraction-based procedure for rapid PCR-based saliva testing that is suitable for samples from both symptomatic and asymptomatic individuals.
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Affiliation(s)
- Jennifer R. Hamilton
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, United States of America
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, United States of America
| | - Elizabeth C. Stahl
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, United States of America
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, United States of America
| | - Connor A. Tsuchida
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, United States of America
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, United States of America
- San Francisco Graduate Program in Bioengineering, University of California, Berkeley, Berkeley, CA, United States of America
| | - Enrique Lin-Shiao
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, United States of America
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, United States of America
| | - C. Kimberly Tsui
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, United States of America
| | - Kathleen Pestal
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, United States of America
| | - Holly K. Gildea
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, United States of America
| | - Lea B. Witkowsky
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, United States of America
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, United States of America
| | - Erica A. Moehle
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, United States of America
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, United States of America
| | - Shana L. McDevitt
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, United States of America
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, United States of America
| | - Matthew McElroy
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, United States of America
| | - Amanda Keller
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, United States of America
| | - Iman Sylvain
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, United States of America
| | - Ariana Hirsh
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, United States of America
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, United States of America
| | - Alison Ciling
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, United States of America
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, United States of America
| | - Alexander J. Ehrenberg
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, United States of America
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, United States of America
| | - Bradley R. Ringeisen
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, United States of America
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, United States of America
| | - Garth Huberty
- Washington Hospital Healthcare System Clinical Laboratory, Fremont, CA, United States of America
| | - Fyodor D. Urnov
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, United States of America
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, United States of America
| | - Petros Giannikopoulos
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, United States of America
| | - Jennifer A. Doudna
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, United States of America
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, United States of America
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, United States of America
- Gladstone Institutes, San Francisco, CA, United States of America
- Graduate Group in Biophysics, University of California, Berkeley, Berkeley, CA, United States of America
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States of America
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, United States of America
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8
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Ehrenberg AJ, Moehle EA, Brook CE, Doudna Cate AH, Witkowsky LB, Sachdeva R, Hirsh A, Barry K, Hamilton JR, Lin-Shiao E, McDevitt S, Valentin-Alvarado L, Letourneau KN, Hunter L, Keller A, Pestal K, Frankino PA, Murley A, Nandakumar D, Stahl EC, Tsuchida CA, Gildea HK, Murdock AG, Hochstrasser ML, O’Brien E, Ciling A, Tsitsiklis A, Worden K, Dugast-Darzacq C, Hays SG, Barber CC, McGarrigle R, Lam EK, Ensminger DC, Bardet L, Sherry C, Harte A, Nicolette G, Giannikopoulos P, Hockemeyer D, Petersen M, Urnov FD, Ringeisen BR, Boots M, Doudna JA. Launching a saliva-based SARS-CoV-2 surveillance testing program on a university campus. PLoS One 2021; 16:e0251296. [PMID: 34038425 PMCID: PMC8153421 DOI: 10.1371/journal.pone.0251296] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 04/26/2021] [Indexed: 01/01/2023] Open
Abstract
Regular surveillance testing of asymptomatic individuals for SARS-CoV-2 has been center to SARS-CoV-2 outbreak prevention on college and university campuses. Here we describe the voluntary saliva testing program instituted at the University of California, Berkeley during an early period of the SARS-CoV-2 pandemic in 2020. The program was administered as a research study ahead of clinical implementation, enabling us to launch surveillance testing while continuing to optimize the assay. Results of both the testing protocol itself and the study participants' experience show how the program succeeded in providing routine, robust testing capable of contributing to outbreak prevention within a campus community and offer strategies for encouraging participation and a sense of civic responsibility.
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Affiliation(s)
- Alexander J. Ehrenberg
- University of California, Berkeley, California, United States of America
- Innovative Genomics Institute, University of California, Berkeley, California, United States of America
| | - Erica A. Moehle
- University of California, Berkeley, California, United States of America
- Innovative Genomics Institute, University of California, Berkeley, California, United States of America
| | - Cara E. Brook
- University of California, Berkeley, California, United States of America
- Innovative Genomics Institute, University of California, Berkeley, California, United States of America
| | | | - Lea B. Witkowsky
- University of California, Berkeley, California, United States of America
- Innovative Genomics Institute, University of California, Berkeley, California, United States of America
| | - Rohan Sachdeva
- University of California, Berkeley, California, United States of America
- Innovative Genomics Institute, University of California, Berkeley, California, United States of America
| | - Ariana Hirsh
- University of California, Berkeley, California, United States of America
- Innovative Genomics Institute, University of California, Berkeley, California, United States of America
| | - Kerrie Barry
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Jennifer R. Hamilton
- University of California, Berkeley, California, United States of America
- Innovative Genomics Institute, University of California, Berkeley, California, United States of America
| | - Enrique Lin-Shiao
- University of California, Berkeley, California, United States of America
- Innovative Genomics Institute, University of California, Berkeley, California, United States of America
| | - Shana McDevitt
- University of California, Berkeley, California, United States of America
- Innovative Genomics Institute, University of California, Berkeley, California, United States of America
| | - Luis Valentin-Alvarado
- University of California, Berkeley, California, United States of America
- Innovative Genomics Institute, University of California, Berkeley, California, United States of America
| | | | - Lauren Hunter
- University of California, Berkeley, California, United States of America
| | - Amanda Keller
- Innovative Genomics Institute, University of California, Berkeley, California, United States of America
| | - Kathleen Pestal
- University of California, Berkeley, California, United States of America
| | | | - Andrew Murley
- University of California, Berkeley, California, United States of America
| | - Divya Nandakumar
- University of California, Berkeley, California, United States of America
- Innovative Genomics Institute, University of California, Berkeley, California, United States of America
| | - Elizabeth C. Stahl
- University of California, Berkeley, California, United States of America
- Innovative Genomics Institute, University of California, Berkeley, California, United States of America
| | - Connor A. Tsuchida
- University of California, Berkeley, California, United States of America
- Innovative Genomics Institute, University of California, Berkeley, California, United States of America
| | - Holly K. Gildea
- University of California, Berkeley, California, United States of America
| | - Andrew G. Murdock
- University of California, Berkeley, California, United States of America
- Innovative Genomics Institute, University of California, Berkeley, California, United States of America
| | - Megan L. Hochstrasser
- Innovative Genomics Institute, University of California, Berkeley, California, United States of America
| | - Elizabeth O’Brien
- University of California, Berkeley, California, United States of America
- Innovative Genomics Institute, University of California, Berkeley, California, United States of America
| | - Alison Ciling
- University of California, Berkeley, California, United States of America
- Innovative Genomics Institute, University of California, Berkeley, California, United States of America
| | | | - Kurtresha Worden
- University of California, Berkeley, California, United States of America
- Innovative Genomics Institute, University of California, Berkeley, California, United States of America
| | | | - Stephanie G. Hays
- University of California, Berkeley, California, United States of America
| | - Colin C. Barber
- University of California, Berkeley, California, United States of America
| | - Riley McGarrigle
- University of California, Berkeley, California, United States of America
- Innovative Genomics Institute, University of California, Berkeley, California, United States of America
| | - Emily K. Lam
- University of California, Berkeley, California, United States of America
| | - David C. Ensminger
- University of California, Berkeley, California, United States of America
| | - Lucie Bardet
- Innovative Genomics Institute, University of California, Berkeley, California, United States of America
| | - Carolyn Sherry
- Innovative Genomics Institute, University of California, Berkeley, California, United States of America
| | - Anna Harte
- University of California, Berkeley, California, United States of America
- University Health Services, University of California, Berkeley, California, United States of America
| | - Guy Nicolette
- University of California, Berkeley, California, United States of America
- University Health Services, University of California, Berkeley, California, United States of America
| | - Petros Giannikopoulos
- Innovative Genomics Institute, University of California, Berkeley, California, United States of America
| | - Dirk Hockemeyer
- University of California, Berkeley, California, United States of America
- Innovative Genomics Institute, University of California, Berkeley, California, United States of America
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Maya Petersen
- University of California, Berkeley, California, United States of America
| | - Fyodor D. Urnov
- University of California, Berkeley, California, United States of America
- Innovative Genomics Institute, University of California, Berkeley, California, United States of America
| | - Bradley R. Ringeisen
- University of California, Berkeley, California, United States of America
- Innovative Genomics Institute, University of California, Berkeley, California, United States of America
| | - Mike Boots
- University of California, Berkeley, California, United States of America
| | - Jennifer A. Doudna
- University of California, Berkeley, California, United States of America
- Innovative Genomics Institute, University of California, Berkeley, California, United States of America
- Howard Hughes Medical Institute, University of California, Berkeley, California, United States of America
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9
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Hamilton JR, Stahl EC, Tsuchida CA, Lin-Shiao E, Tsui CK, Pestal K, Gildea HK, Witkowsky LB, Moehle EA, McDevitt SL, McElroy M, Keller A, Sylvain I, Hirsh A, Ciling A, Ehrenberg AJ, Ringeisen BR, Huberty G, Urnov FD, Giannikopoulos P, Doudna JA. Robotic RNA extraction for SARS-CoV-2 surveillance using saliva samples. medRxiv 2021:2021.01.10.21249151. [PMID: 33532798 PMCID: PMC7852249 DOI: 10.1101/2021.01.10.21249151] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 01/01/2023]
Abstract
Saliva is an attractive specimen type for asymptomatic surveillance of COVID-19 in large populations due to its ease of collection and its demonstrated utility for detecting RNA from SARS-CoV-2. Multiple saliva-based viral detection protocols use a direct-to-RT-qPCR approach that eliminates nucleic acid extraction but can reduce viral RNA detection sensitivity. To improve test sensitivity while maintaining speed, we developed a robotic nucleic acid extraction method for detecting SARS-CoV-2 RNA in saliva samples with high throughput. Using this assay, the Free Asymptomatic Saliva Testing (IGI-FAST) research study on the UC Berkeley campus conducted 11,971 tests on supervised self-collected saliva samples and identified rare positive specimens containing SARS-CoV-2 RNA during a time of low infection prevalence. In an attempt to increase testing capacity, we further adapted our robotic extraction assay to process pooled saliva samples. We also benchmarked our assay against the gold standard, nasopharyngeal swab specimens. Finally, we designed and validated a RT-qPCR test suitable for saliva self-collection. These results establish a robotic extraction-based procedure for rapid PCR-based saliva testing that is suitable for samples from both symptomatic and asymptomatic individuals.
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Affiliation(s)
- Jennifer R Hamilton
- University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Elizabeth C Stahl
- University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Connor A Tsuchida
- University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Enrique Lin-Shiao
- University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | | | | | | | - Lea B Witkowsky
- University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Erica A Moehle
- University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Shana L McDevitt
- University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Matthew McElroy
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Amanda Keller
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Iman Sylvain
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Ariana Hirsh
- University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Alison Ciling
- University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Alexander J Ehrenberg
- University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Bradley R Ringeisen
- University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Garth Huberty
- Washington Hospital Healthcare System Clinical Laboratory, Fremont, CA USA
| | - Fyodor D Urnov
- University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Petros Giannikopoulos
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Jennifer A Doudna
- University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
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10
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Stahl EC, Tsuchida CA, Hamilton JR, Lin-Shiao E, McDevitt SL, Moehle EA, Witkowsky LB, Tsui CK, Pestal K, Gildea HK, McElroy M, Keller A, Sylvain I, Williams C, Hirsh A, Ciling A, Ehrenberg AJ, Urnov FD, Ringeisen BR, Giannikopoulos P, Doudna JA. IGI-LuNER: single-well multiplexed RT-qPCR test for SARS-CoV-2. medRxiv 2020:2020.12.10.20247338. [PMID: 33330883 PMCID: PMC7743092 DOI: 10.1101/2020.12.10.20247338] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Commonly used RT-qPCR-based SARS-CoV-2 diagnostics require 2-3 separate reactions or rely on detection of a single viral target, adding time and cost or risk of false-negative results. Currently, no test combines detection of widely used SARS-CoV-2 E- and N-gene targets and a sample control in a single, multiplexed reaction. We developed the IGI-LuNER RT-qPCR assay using the Luna Probe Universal One-Step RT-qPCR master mix with publicly available primers and probes to detect SARS-CoV-2 N gene, E gene, and human RNase P (NER). This combined, cost-effective test can be performed in 384-well plates with detection sensitivity suitable for clinical reporting, and will aid in future sample pooling efforts, thus improving throughput of SARS-CoV-2 detection.
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Affiliation(s)
- Elizabeth C Stahl
- University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Connor A Tsuchida
- University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Jennifer R Hamilton
- University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Enrique Lin-Shiao
- University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Shana L McDevitt
- University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Erica A Moehle
- University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Lea B Witkowsky
- University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | | | | | | | - Matthew McElroy
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Amanda Keller
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Iman Sylvain
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Clara Williams
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Ariana Hirsh
- University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Alison Ciling
- University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | | | - Fyodor D Urnov
- University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Bradley R Ringeisen
- University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | | | - Jennifer A Doudna
- University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
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11
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Frankino PA, Moehle EA, Dillin A. Evolutionary Comeuppance: Mitochondrial Stress Awakens the Remnants of Ancient Bacterial Warfare. Cell Metab 2019; 29:1015-1017. [PMID: 31067444 DOI: 10.1016/j.cmet.2019.04.007] [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] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Mitochondria are organelles descended from an endosymbiosed bacterium, and many bacterial toxins impair mitochondria, likely as an echo of ancient bacterial warfare. However, the signal transduction pathways that translate mitochondrial dysfunction into a transcriptional program for detoxification have not been well understood. In this issue of Cell Metabolism, Mao et al. (2019) provide insight into how mitochondrial perturbations can activate both the mitochondrial unfolded protein response (UPRmito) and detoxification response and, importantly, how these responses differentially affect organismal physiology under normal conditions or with pathogenic challenges.
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Affiliation(s)
- Phillip A Frankino
- Howard Hughes Medical Institute and Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Erica A Moehle
- Howard Hughes Medical Institute and Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Andrew Dillin
- Howard Hughes Medical Institute and Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
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12
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Simic MS, Moehle EA, Schinzel RT, Lorbeer FK, Halloran JJ, Heydari K, Sanchez M, Jullié D, Hockemeyer D, Dillin A. Transient activation of the UPR ER is an essential step in the acquisition of pluripotency during reprogramming. Sci Adv 2019; 5:eaaw0025. [PMID: 30989118 PMCID: PMC6457941 DOI: 10.1126/sciadv.aaw0025] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 02/25/2019] [Indexed: 05/11/2023]
Abstract
Somatic cells can be reprogrammed into pluripotent stem cells using the Yamanaka transcription factors. Reprogramming requires both epigenetic landscape reshaping and global remodeling of cell identity, structure, basic metabolic processes, and organelle form and function. We hypothesize that variable regulation of the proteostasis network and its influence upon the protein-folding environment within cells and their organelles is responsible for the low efficiency and stochasticity of reprogramming. We find that the unfolded protein response of the endoplasmic reticulum (UPRER), the mitochondrial UPR, and the heat shock response, which ensure proteome quality during stress, are activated during reprogramming. The UPRER is particularly crucial, and its ectopic, transient activation, genetically or pharmacologically, enhances reprogramming. Last, stochastic activation of the UPRER predicts reprogramming efficiency in naïve cells. Thus, the low efficiency and stochasticity of cellular reprogramming are due partly to the inability to properly initiate the UPRER to remodel the ER and its proteome.
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Affiliation(s)
- Milos S. Simic
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA
- California Institute for Regenerative Medicine, Berkeley, CA 94720, USA
- University of California, Berkeley, Berkeley, CA 94720, USA
| | - Erica A. Moehle
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA
- California Institute for Regenerative Medicine, Berkeley, CA 94720, USA
- University of California, Berkeley, Berkeley, CA 94720, USA
| | - Robert T. Schinzel
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA
- California Institute for Regenerative Medicine, Berkeley, CA 94720, USA
- University of California, Berkeley, Berkeley, CA 94720, USA
| | | | - Jonathan J. Halloran
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA
- California Institute for Regenerative Medicine, Berkeley, CA 94720, USA
- University of California, Berkeley, Berkeley, CA 94720, USA
| | | | - Melissa Sanchez
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA
- California Institute for Regenerative Medicine, Berkeley, CA 94720, USA
- University of California, Berkeley, Berkeley, CA 94720, USA
| | - Damien Jullié
- University of California, San Francisco, San Francisco, CA 94143, USA
| | | | - Andrew Dillin
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA
- California Institute for Regenerative Medicine, Berkeley, CA 94720, USA
- University of California, Berkeley, Berkeley, CA 94720, USA
- Corresponding author.
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13
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Abstract
As a central hub of cellular metabolism and signaling, the mitochondrion is a crucial organelle whose dysfunction can cause disease and whose activity is intimately connected to aging. We review how the mitochondrial network maintains proteomic integrity, how mitochondrial proteotoxic stress is communicated and resolved in the context of the entire cell, and how mitochondrial systems function in the context of organismal health and aging. A deeper understanding of how mitochondrial protein quality control mechanisms are coordinated across these distinct biological levels should help explain why these mechanisms fail with age and, ultimately, how routes to intervention might be attained.
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Affiliation(s)
- Erica A Moehle
- From the Department of Molecular and Cell Biology, University of California, Berkeley, California 94720
| | - Koning Shen
- From the Department of Molecular and Cell Biology, University of California, Berkeley, California 94720
| | - Andrew Dillin
- From the Department of Molecular and Cell Biology, University of California, Berkeley, California 94720
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14
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Braberg H, Moehle EA, Shales M, Guthrie C, Krogan NJ. Genetic interaction analysis of point mutations enables interrogation of gene function at a residue-level resolution: exploring the applications of high-resolution genetic interaction mapping of point mutations. Bioessays 2014; 36:706-13. [PMID: 24842270 PMCID: PMC4289610 DOI: 10.1002/bies.201400044] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
We have achieved a residue-level resolution of genetic interaction mapping - a technique that measures how the function of one gene is affected by the alteration of a second gene - by analyzing point mutations. Here, we describe how to interpret point mutant genetic interactions, and outline key applications for the approach, including interrogation of protein interaction interfaces and active sites, and examination of post-translational modifications. Genetic interaction analysis has proven effective for characterizing cellular processes; however, to date, systematic high-throughput genetic interaction screens have relied on gene deletions or knockdowns, which limits the resolution of gene function analysis and poses problems for multifunctional genes. Our point mutant approach addresses these issues, and further provides a tool for in vivo structure-function analysis that complements traditional biophysical methods. We also discuss the potential for genetic interaction mapping of point mutations in human cells and its application to personalized medicine.
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Affiliation(s)
- Hannes Braberg
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA
- California Institute for Quantitative Biosciences, QB3, San Francisco, CA, USA
| | - Erica A. Moehle
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
| | - Michael Shales
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA
- California Institute for Quantitative Biosciences, QB3, San Francisco, CA, USA
| | - Christine Guthrie
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
| | - Nevan J. Krogan
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA
- California Institute for Quantitative Biosciences, QB3, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
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15
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Abstract
Control of pre-mRNA splicing is a critical part of the eukaryotic gene expression process. Extensive evidence indicates that transcription and splicing are spatiotemporally coordinated and that most splicing events occur co-transcriptionally. A kinetic coupling model has been proposed in metazoans to describe how changing RNA Polymerase II (RNAPII) elongation rate can impact which alternative splice sites are used. In Saccharomyces cerevisiae, in which most spliced genes have only a single intron and splice sites adhere to a strong consensus sequence, we recently observed that splicing efficiency was sensitive to mutations in RNAPII that increase or decrease its elongation rate. Our data revealed that RNAPII speed and splicing efficiency are generally anti-correlated: at many genes, increased elongation rate caused decreased splicing efficiency, while decreased elongation rate increased splicing efficiency. An improved splicing phenotype was also observed upon deletion of SUB1, a condition in which elongation rate is slowed. We discuss these data in the context of a growing field and expand the kinetic coupling model to apply to both alternative splicing and splicing efficiency.
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Affiliation(s)
- Erica A Moehle
- Department of Biochemistry and Biophysics; University of California; San Francisco, CA USA
| | - Hannes Braberg
- Department of Cellular and Molecular Pharmacology; University of California; San Francisco, CA USA; California Institute for Quantitative Biosciences; QB3; San Francisco, CA USA
| | - Nevan J Krogan
- Department of Cellular and Molecular Pharmacology; University of California; San Francisco, CA USA; California Institute for Quantitative Biosciences; QB3; San Francisco, CA USA; J. David Gladstone Institutes; San Francisco, CA USA
| | - Christine Guthrie
- Department of Biochemistry and Biophysics; University of California; San Francisco, CA USA
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16
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Hérissant L, Moehle EA, Bertaccini D, Van Dorsselaer A, Schaeffer-Reiss C, Guthrie C, Dargemont C. H2B ubiquitylation modulates spliceosome assembly and function in budding yeast. Biol Cell 2014; 106:126-38. [PMID: 24476359 DOI: 10.1111/boc.201400003] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [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: 01/17/2014] [Accepted: 01/24/2014] [Indexed: 11/30/2022]
Abstract
BACKGROUND INFORMATION Commitment to splicing occurs co-transcriptionally, but a major unanswered question is the extent to which various modifications of chromatin, the template for transcription in vivo, contribute to the regulation of splicing. RESULTS Here, we perform genome-wide analyses showing that inhibition of specific marks - H2B ubiquitylation, H3K4 methylation and H3K36 methylation - perturbs splicing in budding yeast, with each modification exerting gene-specific effects. Furthermore, semi-quantitative mass spectrometry on purified nuclear mRNPs and chromatin immunoprecipitation analysis on intron-containing genes indicated that H2B ubiquitylation, but not Set1-, Set2- or Dot1-dependent H3 methylation, stimulates recruitment of the early splicing factors, namely U1 and U2 snRNPs, onto nascent RNAs. CONCLUSIONS These results suggest that histone modifications impact splicing of distinct subsets of genes using distinct pathways.
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Affiliation(s)
- Lucas Hérissant
- Pathologie Cellulaire, University Paris Diderot, Sorbonne Paris Cité, INSERM U944, CNRS UMR7212, Equipe labellisée Ligue contre le cancer, Hôpital Saint Louis, Paris, Cedex 10, France
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17
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Moehle EA, Ryan CJ, Krogan NJ, Kress TL, Guthrie C. The yeast SR-like protein Npl3 links chromatin modification to mRNA processing. PLoS Genet 2012; 8:e1003101. [PMID: 23209445 PMCID: PMC3510044 DOI: 10.1371/journal.pgen.1003101] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2012] [Accepted: 10/02/2012] [Indexed: 01/23/2023] Open
Abstract
Eukaryotic gene expression involves tight coordination between transcription and pre–mRNA splicing; however, factors responsible for this coordination remain incompletely defined. Here, we explored the genetic, functional, and biochemical interactions of a likely coordinator, Npl3, an SR-like protein in Saccharomyces cerevisiae that we recently showed is required for efficient co-transcriptional recruitment of the splicing machinery. We surveyed the NPL3 genetic interaction space and observed a significant enrichment for genes involved in histone modification and chromatin remodeling. Specifically, we found that Npl3 genetically interacts with both Bre1, which mono-ubiquitinates histone H2B as part of the RAD6 Complex, and Ubp8, the de-ubiquitinase of the SAGA Complex. In support of these genetic data, we show that Bre1 physically interacts with Npl3 in an RNA–independent manner. Furthermore, using a genome-wide splicing microarray, we found that the known splicing defect of a strain lacking Npl3 is exacerbated by deletion of BRE1 or UBP8, a phenomenon phenocopied by a point mutation in H2B that abrogates ubiquitination. Intriguingly, even in the presence of wild-type NPL3, deletion of BRE1 exhibits a mild splicing defect and elicits a growth defect in combination with deletions of early and late splicing factors. Taken together, our data reveal a connection between Npl3 and an extensive array of chromatin factors and describe an unanticipated functional link between histone H2B ubiquitination and pre–mRNA splicing. Pre-messenger RNA splicing is the process by which an intron is identified and removed from a transcript and the protein-coding exons are ligated together. It is carried out by the spliceosome, a large and dynamic molecular machine that catalyzes the splicing reaction. It is now apparent that most splicing occurs while the transcript is still engaged with RNA polymerase, implying that the biologically relevant splicing substrate is chromatin-associated. Here, we used a genetic approach to understand which factors participate in the coordination of transcription and splicing. Having recently shown that the Npl3 protein is involved in the recruitment of splicing factors to chromatin-associated transcripts, we performed a systematic screen for genetically interacting factors. Interestingly, we identified factors that influence the ubiquitin modification of histone H2B, a mark involved in transcription initiation and elongation. We show that disruption of the H2B ubiquitination/de-ubiquitination cycle results in defects in splicing, particularly in the absence of Npl3. Furthermore, the ubiquitin ligase, Bre1, shows genetic interactions with other, more canonical spliceosomal factors. Taken together with the myriad Npl3 interaction partners we found, our data suggest an extensive cross-talk between the spliceosome and chromatin.
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Affiliation(s)
- Erica A. Moehle
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, United States of America
| | - Colm J. Ryan
- Department of Cellular and Molecular Pharmacology, California Institute for Quantitative Biomedical Research, University of California San Francisco, San Francisco, California, United States of America
- School of Computer Science and Informatics, University College Dublin, Dublin, Ireland
| | - Nevan J. Krogan
- Department of Cellular and Molecular Pharmacology, California Institute for Quantitative Biomedical Research, University of California San Francisco, San Francisco, California, United States of America
- J. David Gladstone Institutes, San Francisco, California, United States of America
| | - Tracy L. Kress
- Department of Biology, The College of New Jersey, Ewing, New Jersey, United States of America
- * E-mail: (TLK); (CG)
| | - Christine Guthrie
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, United States of America
- * E-mail: (TLK); (CG)
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18
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Orlando SJ, Santiago Y, DeKelver RC, Freyvert Y, Boydston EA, Moehle EA, Choi VM, Gopalan SM, Lou JF, Li J, Miller JC, Holmes MC, Gregory PD, Urnov FD, Cost GJ. Zinc-finger nuclease-driven targeted integration into mammalian genomes using donors with limited chromosomal homology. Nucleic Acids Res 2010; 38:e152. [PMID: 20530528 PMCID: PMC2926620 DOI: 10.1093/nar/gkq512] [Citation(s) in RCA: 165] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We previously demonstrated high-frequency, targeted DNA addition mediated by the homology-directed DNA repair pathway. This method uses a zinc-finger nuclease (ZFN) to create a site-specific double-strand break (DSB) that facilitates copying of genetic information into the chromosome from an exogenous donor molecule. Such donors typically contain two approximately 750 bp regions of chromosomal sequence required for homology-directed DNA repair. Here, we demonstrate that easily-generated linear donors with extremely short (50 bp) homology regions drive transgene integration into 5-10% of chromosomes. Moreover, we measure the overhangs produced by ZFN cleavage and find that oligonucleotide donors with single-stranded 5' overhangs complementary to those made by ZFNs are efficiently ligated in vivo to the DSB. Greater than 10% of all chromosomes directly incorporate this exogenous DNA via a process that is dependent upon and guided by complementary 5' overhangs on the donor DNA. Finally, we extend this non-homologous end-joining (NHEJ)-based technique by directly inserting donor DNA comprising recombinase sites into large deletions created by the simultaneous action of two separate ZFN pairs. Up to 50% of deletions contained a donor insertion. Targeted DNA addition via NHEJ complements our homology-directed targeted integration approaches, adding versatility to the manipulation of mammalian genomes.
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19
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DeKelver RC, Choi VM, Moehle EA, Paschon DE, Hockemeyer D, Meijsing SH, Sancak Y, Cui X, Steine EJ, Miller JC, Tam P, Bartsevich VV, Meng X, Rupniewski I, Gopalan SM, Sun HC, Pitz KJ, Rock JM, Zhang L, Davis GD, Rebar EJ, Cheeseman IM, Yamamoto KR, Sabatini DM, Jaenisch R, Gregory PD, Urnov FD. Functional genomics, proteomics, and regulatory DNA analysis in isogenic settings using zinc finger nuclease-driven transgenesis into a safe harbor locus in the human genome. Genome Res 2010; 20:1133-42. [PMID: 20508142 DOI: 10.1101/gr.106773.110] [Citation(s) in RCA: 260] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Isogenic settings are routine in model organisms, yet remain elusive for genetic experiments on human cells. We describe the use of designed zinc finger nucleases (ZFNs) for efficient transgenesis without drug selection into the PPP1R12C gene, a "safe harbor" locus known as AAVS1. ZFNs enable targeted transgenesis at a frequency of up to 15% following transient transfection of both transformed and primary human cells, including fibroblasts and hES cells. When added to this locus, transgenes such as expression cassettes for shRNAs, small-molecule-responsive cDNA expression cassettes, and reporter constructs, exhibit consistent expression and sustained function over 50 cell generations. By avoiding random integration and drug selection, this method allows bona fide isogenic settings for high-throughput functional genomics, proteomics, and regulatory DNA analysis in essentially any transformed human cell type and in primary cells.
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Affiliation(s)
- Russell C DeKelver
- Sangamo BioSciences, Inc., Point Richmond Tech Center, Richmond, California 94804, USA
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20
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Shukla VK, Doyon Y, Miller JC, DeKelver RC, Moehle EA, Worden SE, Mitchell JC, Arnold NL, Gopalan S, Meng X, Choi VM, Rock JM, Wu YY, Katibah GE, Zhifang G, McCaskill D, Simpson MA, Blakeslee B, Greenwalt SA, Butler HJ, Hinkley SJ, Zhang L, Rebar EJ, Gregory PD, Urnov FD. Precise genome modification in the crop species Zea mays using zinc-finger nucleases. Nature 2009; 459:437-41. [PMID: 19404259 DOI: 10.1038/nature07992] [Citation(s) in RCA: 477] [Impact Index Per Article: 31.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2008] [Accepted: 03/17/2009] [Indexed: 11/09/2022]
Abstract
Agricultural biotechnology is limited by the inefficiencies of conventional random mutagenesis and transgenesis. Because targeted genome modification in plants has been intractable, plant trait engineering remains a laborious, time-consuming and unpredictable undertaking. Here we report a broadly applicable, versatile solution to this problem: the use of designed zinc-finger nucleases (ZFNs) that induce a double-stranded break at their target locus. We describe the use of ZFNs to modify endogenous loci in plants of the crop species Zea mays. We show that simultaneous expression of ZFNs and delivery of a simple heterologous donor molecule leads to precise targeted addition of an herbicide-tolerance gene at the intended locus in a significant number of isolated events. ZFN-modified maize plants faithfully transmit these genetic changes to the next generation. Insertional disruption of one target locus, IPK1, results in both herbicide tolerance and the expected alteration of the inositol phosphate profile in developing seeds. ZFNs can be used in any plant species amenable to DNA delivery; our results therefore establish a new strategy for plant genetic manipulation in basic science and agricultural applications.
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Affiliation(s)
- Vipula K Shukla
- Dow AgroSciences, 9330 Zionsville Road, Indianapolis, Indiana 46268, USA.
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21
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Cai CQ, Doyon Y, Ainley WM, Miller JC, Dekelver RC, Moehle EA, Rock JM, Lee YL, Garrison R, Schulenberg L, Blue R, Worden A, Baker L, Faraji F, Zhang L, Holmes MC, Rebar EJ, Collingwood TN, Rubin-Wilson B, Gregory PD, Urnov FD, Petolino JF. Targeted transgene integration in plant cells using designed zinc finger nucleases. Plant Mol Biol 2009; 69:699-709. [PMID: 19112554 DOI: 10.1007/s11103-008-9449-7] [Citation(s) in RCA: 112] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2008] [Accepted: 12/14/2008] [Indexed: 05/20/2023]
Abstract
Targeted transgene integration in plants remains a significant technical challenge for both basic and applied research. Here it is reported that designed zinc finger nucleases (ZFNs) can drive site-directed DNA integration into transgenic and native gene loci. A dimer of designed 4-finger ZFNs enabled intra-chromosomal reconstitution of a disabled gfp reporter gene and site-specific transgene integration into chromosomal reporter loci following co-transformation of tobacco cell cultures with a donor construct comprised of sequences necessary to complement a non-functional pat herbicide resistance gene. In addition, a yeast-based assay was used to identify ZFNs capable of cleaving a native endochitinase gene. Agrobacterium delivery of a Ti plasmid harboring both the ZFNs and a donor DNA construct comprising a pat herbicide resistance gene cassette flanked by short stretches of homology to the endochitinase locus yielded up to 10% targeted, homology-directed transgene integration precisely into the ZFN cleavage site. Given that ZFNs can be designed to recognize a wide range of target sequences, these data point toward a novel approach for targeted gene addition, replacement and trait stacking in plants.
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Affiliation(s)
- Charles Q Cai
- Dow AgroSciences, LLC, 9330 Zionsville Road, Indianapolis, IN 46268, USA
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22
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Moehle EA, Rock JM, Lee YL, Jouvenot Y, DeKelver RC, Gregory PD, Urnov FD, Holmes MC. Targeted gene addition into a specified location in the human genome using designed zinc finger nucleases. Proc Natl Acad Sci U S A 2007; 104:3055-60. [PMID: 17360608 PMCID: PMC1802009 DOI: 10.1073/pnas.0611478104] [Citation(s) in RCA: 306] [Impact Index Per Article: 18.0] [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: 11/18/2022] Open
Abstract
Efficient incorporation of novel DNA sequences into a specific site in the genome of living human cells remains a challenge despite its potential utility to genetic medicine, biotechnology, and basic research. We find that a precisely placed double-strand break induced by engineered zinc finger nucleases (ZFNs) can stimulate integration of long DNA stretches into a predetermined genomic location, resulting in high-efficiency site-specific gene addition. Using an extrachromosomal DNA donor carrying a 12-bp tag, a 900-bp ORF, or a 1.5-kb promoter-transcription unit flanked by locus-specific homology arms, we find targeted integration frequencies of 15%, 6%, and 5%, respectively, within 72 h of treatment, and with no selection for the desired event. Importantly, we find that the integration event occurs in a homology-directed manner and leads to the accurate reconstruction of the donor-specified genotype at the endogenous chromosomal locus, and hence presumably results from synthesis-dependent strand annealing repair of the break using the donor DNA as a template. This site-specific gene addition occurs with no measurable increase in the rate of random integration. Remarkably, we also find that ZFNs can drive the addition of an 8-kb sequence carrying three distinct promoter-transcription units into an endogenous locus at a frequency of 6%, also in the absence of any selection. These data reveal the surprising versatility of the specialized polymerase machinery involved in double-strand break repair, illuminate a powerful approach to mammalian cell engineering, and open the possibility of ZFN-driven gene addition therapy for human genetic disease.
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Affiliation(s)
- Erica A. Moehle
- Sangamo BioSciences, Inc., Point Richmond Technology Center, 501 Canal Boulevard, Suite A100, Richmond, CA 94804
| | - Jeremy M. Rock
- Sangamo BioSciences, Inc., Point Richmond Technology Center, 501 Canal Boulevard, Suite A100, Richmond, CA 94804
| | - Ya-Li Lee
- Sangamo BioSciences, Inc., Point Richmond Technology Center, 501 Canal Boulevard, Suite A100, Richmond, CA 94804
| | - Yann Jouvenot
- Sangamo BioSciences, Inc., Point Richmond Technology Center, 501 Canal Boulevard, Suite A100, Richmond, CA 94804
| | - Russell C. DeKelver
- Sangamo BioSciences, Inc., Point Richmond Technology Center, 501 Canal Boulevard, Suite A100, Richmond, CA 94804
| | - Philip D. Gregory
- Sangamo BioSciences, Inc., Point Richmond Technology Center, 501 Canal Boulevard, Suite A100, Richmond, CA 94804
| | - Fyodor D. Urnov
- Sangamo BioSciences, Inc., Point Richmond Technology Center, 501 Canal Boulevard, Suite A100, Richmond, CA 94804
- *To whom correspondence should be addressed. E-mail:
| | - Michael C. Holmes
- Sangamo BioSciences, Inc., Point Richmond Technology Center, 501 Canal Boulevard, Suite A100, Richmond, CA 94804
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