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Chowdhury SP, Solley SC, Polishchuk E, Bacal J, Conrad JE, Gardner BM, Acosta-Alvear D, Zappa F. Baseline Unfolded Protein Response Signaling Adjusts the Timing of the Mammalian Cell Cycle. Mol Biol Cell 2024:mbcE23110419. [PMID: 38656789 DOI: 10.1091/mbc.e23-11-0419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2024] Open
Abstract
The endoplasmic reticulum (ER) is a single-copy organelle that cannot be generated de novo, suggesting coordination between the mechanisms overseeing ER integrity and those controlling the cell cycle to maintain organelle inheritance. The Unfolded Protein Response (UPR) is a conserved signaling network that regulates ER homeostasis. Here, we show that pharmacological and genetic inhibition of the UPR sensors IRE1, ATF6, and PERK in unstressed cells delays the cell cycle, with PERK inhibition showing the most penetrant effect, which was associated with a slowdown of the G1-to-S/G2 transition. Treatment with the small molecule ISRIB to bypass the effects of PERK-dependent phosphorylation of the translation initiation factor eIF2⍺ had no such effect, suggesting that cell cycle timing depends on PERK's kinase activity but is independent of eIF2⍺ phosphorylation. Using complementary light and electron microscopy and flow cytometry-based analyses, we also demonstrate that the ER enlarges before mitosis. Together, our results suggest coordination between UPR signaling and the cell cycle to maintain ER physiology during cell division.
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Affiliation(s)
- Soham P Chowdhury
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA, 93106, USA
| | - Sabrina C Solley
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA, 93106, USA
| | - Elena Polishchuk
- Telethon Institute of Genetics and Medicine (TIGEM), 80078 Pozzuoli, Naples, Italy
| | - Julien Bacal
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA, 93106, USA
| | - Julia E Conrad
- Altos Labs Bay Area Institute of Science, Altos Labs, Inc., Redwood City, CA, 94065, USA
| | - Brooke M Gardner
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA, 93106, USA
| | - Diego Acosta-Alvear
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA, 93106, USA
| | - Francesca Zappa
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA, 93106, USA
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2
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Yan J, Oyler-Castrillo P, Ravisankar P, Ward CC, Levesque S, Jing Y, Simpson D, Zhao A, Li H, Yan W, Goudy L, Schmidt R, Solley SC, Gilbert LA, Chan MM, Bauer DE, Marson A, Parsons LR, Adamson B. Improving prime editing with an endogenous small RNA-binding protein. Nature 2024; 628:639-647. [PMID: 38570691 PMCID: PMC11023932 DOI: 10.1038/s41586-024-07259-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 02/29/2024] [Indexed: 04/05/2024]
Abstract
Prime editing enables the precise modification of genomes through reverse transcription of template sequences appended to the 3' ends of CRISPR-Cas guide RNAs1. To identify cellular determinants of prime editing, we developed scalable prime editing reporters and performed genome-scale CRISPR-interference screens. From these screens, a single factor emerged as the strongest mediator of prime editing: the small RNA-binding exonuclease protection factor La. Further investigation revealed that La promotes prime editing across approaches (PE2, PE3, PE4 and PE5), edit types (substitutions, insertions and deletions), endogenous loci and cell types but has no consistent effect on genome-editing approaches that rely on standard, unextended guide RNAs. Previous work has shown that La binds polyuridine tracts at the 3' ends of RNA polymerase III transcripts2. We found that La functionally interacts with the 3' ends of polyuridylated prime editing guide RNAs (pegRNAs). Guided by these results, we developed a prime editor protein (PE7) fused to the RNA-binding, N-terminal domain of La. This editor improved prime editing with expressed pegRNAs and engineered pegRNAs (epegRNAs), as well as with synthetic pegRNAs optimized for La binding. Together, our results provide key insights into how prime editing components interact with the cellular environment and suggest general strategies for stabilizing exogenous small RNAs therein.
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Affiliation(s)
- Jun Yan
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Paul Oyler-Castrillo
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Purnima Ravisankar
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, NY, USA
| | - Carl C Ward
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
| | - Sébastien Levesque
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
- Broad Institute, Cambridge, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Yangwode Jing
- Department of Chemistry, Princeton University, Princeton, NJ, USA
| | - Danny Simpson
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Anqi Zhao
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Hui Li
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Weihao Yan
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Laine Goudy
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, USA
- Arc Institute, Palo Alto, CA, USA
| | - Ralf Schmidt
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - Sabrina C Solley
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Luke A Gilbert
- Arc Institute, Palo Alto, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Michelle M Chan
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Daniel E Bauer
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
- Broad Institute, Cambridge, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Alexander Marson
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
| | - Lance R Parsons
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Britt Adamson
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA.
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA.
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3
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Cirincione A, Simpson D, Ravisankar P, Solley SC, Yan J, Singh M, Adamson B. A benchmarked, high-efficiency prime editing platform for multiplexed dropout screening. bioRxiv 2024:2024.03.25.585978. [PMID: 38585933 PMCID: PMC10996517 DOI: 10.1101/2024.03.25.585978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Prime editing installs precise edits into the genome with minimal unwanted byproducts, but low and variable editing efficiencies have complicated application of the approach to high-throughput functional genomics. Leveraging several recent advances, we assembled a prime editing platform capable of high-efficiency substitution editing across a set of engineered prime editing guide RNAs (epegRNAs) and corresponding target sequences (80% median intended editing). Then, using a custom library of 240,000 epegRNAs targeting >17,000 codons with 175 different substitution types, we benchmarked our platform for functional interrogation of small substitution variants (1-3 nucleotides) targeted to essential genes. Resulting data identified negative growth phenotypes for nonsense mutations targeted to ~8,000 codons, and comparing those phenotypes to results from controls demonstrated high specificity. We also observed phenotypes for synonymous mutations that disrupted splice site motifs at 3' exon boundaries. Altogether, we establish and benchmark a high-throughput prime editing approach for functional characterization of genetic variants with simple readouts from multiplexed experiments.
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Affiliation(s)
- Ann Cirincione
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Danny Simpson
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Purnima Ravisankar
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
- Present address: Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, NY 10065, USA
| | - Sabrina C Solley
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Jun Yan
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Mona Singh
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
- Department of Computer Science, Princeton University, Princeton, NJ 08544, USA
| | - Britt Adamson
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
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4
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McNamara HM, Solley SC, Adamson B, Chan MM, Toettcher JE. Recording morphogen signals reveals origins of gastruloid symmetry breaking. bioRxiv 2023:2023.06.02.543474. [PMID: 37333235 PMCID: PMC10274695 DOI: 10.1101/2023.06.02.543474] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
When cultured in three dimensional spheroids, mammalian stem cells can reproducibly self-organize a single anterior-posterior axis and sequentially differentiate into structures resembling the primitive streak and tailbud. Whereas the embryo's body axes are instructed by spatially patterned extra-embryonic cues, it is unknown how these stem cell gastruloids break symmetry to reproducibly define a single anterior-posterior (A-P) axis. Here, we use synthetic gene circuits to trace how early intracellular signals predict cells' future anterior-posterior position in the gastruloid. We show that Wnt signaling evolves from a homogeneous state to a polarized state, and identify a critical 6-hour time period when single-cell Wnt activity predicts future cellular position, prior to the appearance of polarized signaling patterns or morphology. Single-cell RNA sequencing and live-imaging reveal that early Wnt-high and Wnt-low cells contribute to distinct cell types and suggest that axial symmetry breaking is driven by sorting rearrangements involving differential cell adhesion. We further extend our approach to other canonical embryonic signaling pathways, revealing that even earlier heterogeneity in TGFβ signaling predicts A-P position and modulates Wnt signaling during the critical time period. Our study reveals a sequence of dynamic cellular processes that transform a uniform cell aggregate into a polarized structure and demonstrates that a morphological axis can emerge out of signaling heterogeneity and cell movements even in the absence of exogenous patterning cues.
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Affiliation(s)
- Harold M. McNamara
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton NJ 08544
| | - Sabrina C. Solley
- Department of Molecular Biology, Princeton University, Princeton NJ 08544
| | - Britt Adamson
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton NJ 08544
- Department of Molecular Biology, Princeton University, Princeton NJ 08544
| | - Michelle M. Chan
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton NJ 08544
- Department of Molecular Biology, Princeton University, Princeton NJ 08544
| | - Jared E. Toettcher
- Department of Molecular Biology, Princeton University, Princeton NJ 08544
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5
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Rauch JN, Valois E, Solley SC, Braig F, Lach RS, Audouard M, Ponce-Rojas JC, Costello MS, Baxter NJ, Kosik KS, Arias C, Acosta-Alvear D, Wilson MZ. A Scalable, Easy-to-Deploy Protocol for Cas13-Based Detection of SARS-CoV-2 Genetic Material. J Clin Microbiol 2021; 59:e02402-20. [PMID: 33478979 PMCID: PMC8092748 DOI: 10.1128/jcm.02402-20] [Citation(s) in RCA: 74] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 01/10/2021] [Indexed: 12/12/2022] Open
Abstract
The COVID-19 pandemic has created massive demand for widespread, distributed tools for detecting SARS-CoV-2 genetic material. The hurdles to scalable testing include reagent and instrument accessibility, availability of highly trained personnel, and large upfront investment. Here, we showcase an orthogonal pipeline we call CREST (Cas13-based, rugged, equitable, scalable testing) that addresses some of these hurdles. Specifically, CREST pairs commonplace and reliable biochemical methods (PCR) with low-cost instrumentation, without sacrificing detection sensitivity. By taking advantage of simple fluorescence visualizers, CREST allows a binary interpretation of results. CREST may provide a point-of-care solution to increase the distribution of COVID-19 surveillance.
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Affiliation(s)
- Jennifer N Rauch
- University of California, Santa Barbara, Department of Molecular, Cellular, and Developmental Biology, Santa Barbara, California, USA
- Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, California, USA
| | - Eric Valois
- University of California, Santa Barbara, Department of Molecular, Cellular, and Developmental Biology, Santa Barbara, California, USA
- Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, California, USA
| | - Sabrina C Solley
- University of California, Santa Barbara, Department of Molecular, Cellular, and Developmental Biology, Santa Barbara, California, USA
| | - Friederike Braig
- University of California, Santa Barbara, Department of Molecular, Cellular, and Developmental Biology, Santa Barbara, California, USA
| | - Ryan S Lach
- University of California, Santa Barbara, Department of Molecular, Cellular, and Developmental Biology, Santa Barbara, California, USA
| | - Morgane Audouard
- University of California, Santa Barbara, Department of Molecular, Cellular, and Developmental Biology, Santa Barbara, California, USA
- Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, California, USA
| | - Jose Carlos Ponce-Rojas
- University of California, Santa Barbara, Department of Molecular, Cellular, and Developmental Biology, Santa Barbara, California, USA
| | - Michael S Costello
- University of California, Santa Barbara, Department of Molecular, Cellular, and Developmental Biology, Santa Barbara, California, USA
| | - Naomi J Baxter
- University of California, Santa Barbara, Department of Molecular, Cellular, and Developmental Biology, Santa Barbara, California, USA
| | - Kenneth S Kosik
- University of California, Santa Barbara, Department of Molecular, Cellular, and Developmental Biology, Santa Barbara, California, USA
- Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, California, USA
| | - Carolina Arias
- University of California, Santa Barbara, Department of Molecular, Cellular, and Developmental Biology, Santa Barbara, California, USA
- Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, California, USA
| | - Diego Acosta-Alvear
- University of California, Santa Barbara, Department of Molecular, Cellular, and Developmental Biology, Santa Barbara, California, USA
- Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, California, USA
| | - Maxwell Z Wilson
- University of California, Santa Barbara, Department of Molecular, Cellular, and Developmental Biology, Santa Barbara, California, USA
- Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, California, USA
- Center for BioEngineering, University of California, Santa Barbara, Santa Barbara, California, USA
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6
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Rauch JN, Valois E, Solley SC, Braig F, Lach RS, Audouard M, Ponce-Rojas JC, Costello MS, Baxter NJ, Kosik KS, Arias C, Acosta-Alvear D, Wilson MZ. A Scalable, Easy-to-Deploy Protocol for Cas13-Based Detection of SARS-CoV-2 Genetic Material. J Clin Microbiol 2021; 59:JCM.02402-20. [PMID: 33478979 DOI: 10.1101/2020.04.20.052159] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 01/10/2021] [Indexed: 05/28/2023] Open
Abstract
The COVID-19 pandemic has created massive demand for widespread, distributed tools for detecting SARS-CoV-2 genetic material. The hurdles to scalable testing include reagent and instrument accessibility, availability of highly trained personnel, and large upfront investment. Here, we showcase an orthogonal pipeline we call CREST (Cas13-based, rugged, equitable, scalable testing) that addresses some of these hurdles. Specifically, CREST pairs commonplace and reliable biochemical methods (PCR) with low-cost instrumentation, without sacrificing detection sensitivity. By taking advantage of simple fluorescence visualizers, CREST allows a binary interpretation of results. CREST may provide a point-of-care solution to increase the distribution of COVID-19 surveillance.
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Affiliation(s)
- Jennifer N Rauch
- University of California, Santa Barbara, Department of Molecular, Cellular, and Developmental Biology, Santa Barbara, California, USA
- Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, California, USA
| | - Eric Valois
- University of California, Santa Barbara, Department of Molecular, Cellular, and Developmental Biology, Santa Barbara, California, USA
- Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, California, USA
| | - Sabrina C Solley
- University of California, Santa Barbara, Department of Molecular, Cellular, and Developmental Biology, Santa Barbara, California, USA
| | - Friederike Braig
- University of California, Santa Barbara, Department of Molecular, Cellular, and Developmental Biology, Santa Barbara, California, USA
| | - Ryan S Lach
- University of California, Santa Barbara, Department of Molecular, Cellular, and Developmental Biology, Santa Barbara, California, USA
| | - Morgane Audouard
- University of California, Santa Barbara, Department of Molecular, Cellular, and Developmental Biology, Santa Barbara, California, USA
- Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, California, USA
| | - Jose Carlos Ponce-Rojas
- University of California, Santa Barbara, Department of Molecular, Cellular, and Developmental Biology, Santa Barbara, California, USA
| | - Michael S Costello
- University of California, Santa Barbara, Department of Molecular, Cellular, and Developmental Biology, Santa Barbara, California, USA
| | - Naomi J Baxter
- University of California, Santa Barbara, Department of Molecular, Cellular, and Developmental Biology, Santa Barbara, California, USA
| | - Kenneth S Kosik
- University of California, Santa Barbara, Department of Molecular, Cellular, and Developmental Biology, Santa Barbara, California, USA
- Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, California, USA
| | - Carolina Arias
- University of California, Santa Barbara, Department of Molecular, Cellular, and Developmental Biology, Santa Barbara, California, USA
- Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, California, USA
| | - Diego Acosta-Alvear
- University of California, Santa Barbara, Department of Molecular, Cellular, and Developmental Biology, Santa Barbara, California, USA
- Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, California, USA
| | - Maxwell Z Wilson
- University of California, Santa Barbara, Department of Molecular, Cellular, and Developmental Biology, Santa Barbara, California, USA
- Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, California, USA
- Center for BioEngineering, University of California, Santa Barbara, Santa Barbara, California, USA
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7
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Rauch JN, Valois E, Ponce-Rojas JC, Aralis Z, Lach RS, Zappa F, Audouard M, Solley SC, Vaidya C, Costello M, Smith H, Javanbakht A, Malear B, Polito L, Comer S, Arn K, Kosik KS, Acosta-Alvear D, Wilson MZ, Fitzgibbons L, Arias C. Comparison of Severe Acute Respiratory Syndrome Coronavirus 2 Screening Using Reverse Transcriptase-Quantitative Polymerase Chain Reaction or CRISPR-Based Assays in Asymptomatic College Students. JAMA Netw Open 2021; 4:e2037129. [PMID: 33570576 PMCID: PMC7879237 DOI: 10.1001/jamanetworkopen.2020.37129] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
IMPORTANCE The reopening of colleges and universities in the US during the coronavirus disease 2019 (COVID-19) pandemic is a significant public health challenge. The development of accessible and practical approaches for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) detection in the college population is paramount for deploying recurrent surveillance testing as an essential strategy for virus detection, containment, and mitigation. OBJECTIVE To determine the prevalence of SARS-CoV-2 in asymptomatic participants in a university community by using CREST (Cas13-based, rugged, equitable, scalable testing), a CRISPR-based test developed for accessible and large-scale viral screening. DESIGN, SETTING, AND PARTICIPANTS For this cohort study, a total of 1808 asymptomatic participants were screened for SARS-CoV-2 using a CRISPR-based assay and a point-of-reference reverse transcriptase-quantitative polymerase chain reaction (RT-qPCR) test. Viral prevalence in self-collected oropharyngeal swab samples collected from May 28 to June 11, 2020, and from June 23 to July 2, 2020, was evaluated. EXPOSURES Testing for SARS-CoV-2. MAIN OUTCOMES AND MEASURES SARS-CoV-2 status, viral load, and demographic information of the study participants were collected. RESULTS Among the 1808 participants (mean [SD] age, 27.3 [11.0] years; 955 [52.8%] female), 732 underwent testing from May to early June (mean [SD] age, 28.4 [11.7] years; 392 [53.6%] female). All test results in this cohort were negative. In contrast, 1076 participants underwent testing from late June to early July (mean [SD] age, 26.6 [10.5] years; 563 [52.3%] female), with 9 positive results by RT-qPCR. Eight of these positive samples were detected by the CRISPR-based assay and confirmed by Clinical Laboratory Improvement Amendments-certified diagnostic testing. The mean (SD) age of the positive cases was 21.7 (3.3) years; all 8 individuals self-identified as students. These metrics showed that a CRISPR-based assay was effective at capturing positive SARS-CoV-2 cases in this student population. Notably, the viral loads detected in these asymptomatic cases resemble those seen in clinical samples, highlighting the potential of covert viral transmission. The shift in viral prevalence coincided with the relaxation of stay-at-home measures. CONCLUSIONS AND RELEVANCE These findings reveal a shift in SARS-CoV-2 prevalence in a young and asymptomatic population and uncover the leading edge of a local outbreak that coincided with rising case counts in the surrounding county and the state of California. The concordance between CRISPR-based and RT-qPCR testing suggests that CRISPR-based assays are reliable and offer alternative options for surveillance testing and detection of SARS-CoV-2 outbreaks, as is required to resume operations in higher-education institutions in the US and abroad.
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Affiliation(s)
- Jennifer N. Rauch
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara
- Neuroscience Research Institute, University of California, Santa Barbara
| | - Eric Valois
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara
| | - Jose Carlos Ponce-Rojas
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara
| | - Zach Aralis
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara
| | - Ryan S. Lach
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara
| | - Francesca Zappa
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara
| | - Morgane Audouard
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara
- Neuroscience Research Institute, University of California, Santa Barbara
| | - Sabrina C. Solley
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara
| | - Chinmay Vaidya
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara
| | - Michael Costello
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara
| | - Holly Smith
- Student Health Service, University of California, Santa Barbara
| | - Ali Javanbakht
- Student Health Service, University of California, Santa Barbara
| | - Betsy Malear
- Student Health Service, University of California, Santa Barbara
| | - Laura Polito
- Student Health Service, University of California, Santa Barbara
| | - Stewart Comer
- Department of Pathology, Santa Barbara Cottage Hospital, Santa Barbara, California
- Pacific Diagnostic Laboratories, Santa Barbara, California
| | - Katherine Arn
- Department of Medical Education, Division of Infectious Diseases, Santa Barbara Cottage Hospital, Santa Barbara, California
| | - Kenneth S. Kosik
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara
- Neuroscience Research Institute, University of California, Santa Barbara
| | - Diego Acosta-Alvear
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara
- Neuroscience Research Institute, University of California, Santa Barbara
| | - Maxwell Z. Wilson
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara
- Neuroscience Research Institute, University of California, Santa Barbara
- Center for BioEngineering, University of California, Santa Barbara
| | - Lynn Fitzgibbons
- Department of Medical Education, Division of Infectious Diseases, Santa Barbara Cottage Hospital, Santa Barbara, California
| | - Carolina Arias
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara
- Neuroscience Research Institute, University of California, Santa Barbara
- Center for Stem Cell Biology and Engineering, University of California, Santa Barbara
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