1
|
Guss EJ, Sathe L, Dai A, Derebenskiy T, Vega AR, Eggan K, Wells MF. Protocol for neurogenin-2-mediated induction of human stem cell-derived neural progenitor cells. STAR Protoc 2024; 5:102878. [PMID: 38335091 PMCID: PMC10865475 DOI: 10.1016/j.xpro.2024.102878] [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: 09/24/2023] [Revised: 12/01/2023] [Accepted: 01/23/2024] [Indexed: 02/12/2024] Open
Abstract
Human pluripotent stem cell-derived neural progenitor cells (NPCs) are an essential tool for the study of brain development and developmental disorders such as autism. Here, we present a protocol to generate NPCs rapidly and reproducibly from human stem cells using dual-SMAD inhibition coupled with a brief pulse of mouse neurogenin-2 (Ngn2) overexpression. We detail the 48-h induction scheme deployed to produce these cells-termed stem cell-derived Ngn2-accelerated progenitor cells-followed by steps for expansion, purification, banking, and quality assessment. For complete details on the use and execution of this protocol, please refer to Wells et al.1.
Collapse
Affiliation(s)
- Ellen J Guss
- Department of Stem Cell and Regenerative Biology, and Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA
| | - Laila Sathe
- Department of Human Genetics, David Geffen School of Medicine at the University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Alexander Dai
- Department of Human Genetics, David Geffen School of Medicine at the University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Tim Derebenskiy
- Department of Human Genetics, David Geffen School of Medicine at the University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Ana Rodriguez Vega
- Department of Human Genetics, David Geffen School of Medicine at the University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Kevin Eggan
- Department of Stem Cell and Regenerative Biology, and Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Michael F Wells
- Department of Human Genetics, David Geffen School of Medicine at the University of California Los Angeles, Los Angeles, CA 90095, USA; Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA 90095, USA.
| |
Collapse
|
2
|
Guo L, Boocock J, Hilt EE, Chandrasekaran S, Zhang Y, Munugala C, Sathe L, Alexander N, Arboleda VA, Flint J, Eskin E, Luo C, Yang S, Garner OB, Yin Y, Bloom JS, Kruglyak L. Genomic epidemiology of the Los Angeles COVID-19 outbreak and the early history of the B.1.43 strain in the USA. BMC Genomics 2022; 23:260. [PMID: 35379194 PMCID: PMC8978495 DOI: 10.1186/s12864-022-08488-7] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 03/15/2022] [Indexed: 11/10/2022] Open
Abstract
Background The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused global disruption of human health and activity. Being able to trace the early outbreak of SARS-CoV-2 within a locality can inform public health measures and provide insights to contain or prevent viral transmission. Investigation of the transmission history requires efficient sequencing methods and analytic strategies, which can be generally useful in the study of viral outbreaks. Methods The County of Los Angeles (hereafter, LA County) sustained a large outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). To learn about the transmission history, we carried out surveillance viral genome sequencing to determine 142 viral genomes from unique patients seeking care at the University of California, Los Angeles (UCLA) Health System. 86 of these genomes were from samples collected before April 19, 2020. Results We found that the early outbreak in LA County, as in other international air travel hubs, was seeded by multiple introductions of strains from Asia and Europe. We identified a USA-specific strain, B.1.43, which was found predominantly in California and Washington State. While samples from LA County carried the ancestral B.1.43 genome, viral genomes from neighboring counties in California and from counties in Washington State carried additional mutations, suggesting a potential origin of B.1.43 in Southern California. We quantified the transmission rate of SARS-CoV-2 over time, and found evidence that the public health measures put in place in LA County to control the virus were effective at preventing transmission, but might have been undermined by the many introductions of SARS-CoV-2 into the region. Conclusion Our work demonstrates that genome sequencing can be a powerful tool for investigating outbreaks and informing the public health response. Our results reinforce the critical need for the USA to have coordinated inter-state responses to the pandemic. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08488-7.
Collapse
Affiliation(s)
- Longhua Guo
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, USA.,Howard Hughes Medical Institute, HHMI, Chevy Chase, USA.,Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, USA
| | - James Boocock
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, USA.,Howard Hughes Medical Institute, HHMI, Chevy Chase, USA.,Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, USA
| | - Evann E Hilt
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, USA
| | - Sukantha Chandrasekaran
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, USA
| | - Yi Zhang
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, USA
| | - Chetan Munugala
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, USA
| | - Laila Sathe
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, USA
| | - Noah Alexander
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, USA
| | - Valerie A Arboleda
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, USA.,Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, USA
| | - Jonathan Flint
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, USA.,Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, UCLA, Los Angeles, USA
| | - Eleazar Eskin
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, USA.,Department of Computer Science, Samueli School of Engineering, UCLA, Los Angeles, USA.,Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, USA
| | - Chongyuan Luo
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, USA
| | - Shangxin Yang
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, USA
| | - Omai B Garner
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, USA
| | - Yi Yin
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, USA.
| | - Joshua S Bloom
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, USA. .,Howard Hughes Medical Institute, HHMI, Chevy Chase, USA. .,Octant, Inc, Los Angeles, USA.
| | - Leonid Kruglyak
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, USA. .,Howard Hughes Medical Institute, HHMI, Chevy Chase, USA. .,Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, USA.
| |
Collapse
|
3
|
Jones J, Saul R, Sathe L, Xie J, Marquette D, Arboleda VA. Lean Principles to Improve Quality in High-Throughput COVID-19 Testing Using SwabSeq: A Barcoded Sequencing-Based Testing Platform. Lab Med 2022; 53:e8-e13. [PMID: 34436601 PMCID: PMC8499806 DOI: 10.1093/labmed/lmab069] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
OBJECTIVE To describe and quantify the effect of quality control (QC) metrics to increase testing efficiency in a high-complexity, Clinical Laboratory Improvement Amendments-certified laboratory that uses amplicon-based, next generation sequencing for the clinical detection of SARS-CoV-2. To enable rapid scalability to several thousands of specimens per day without fully automated platforms, we developed internal QC methods to ensure high-accuracy testing. METHODS We implemented procedures to increase efficiency by applying the Lean Six Sigma model into our sequencing-based COVID-19 detection. RESULTS The application of the Lean Six Sigma model increased laboratory efficiency by reducing errors, allowing for a higher testing volume to be met with minimal staffing. Furthermore, these improvements resulted in an improved turnaround time. CONCLUSION Lean Six Sigma model execution has increased laboratory efficiency by decreasing critical testing errors and has prepared the laboratory for future scaling up to 50,000 tests per day.
Collapse
Affiliation(s)
- Janae Jones
- Department of Computational Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, US
- UCLA SwabSeq COVID19 Laboratory, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, US
| | - Rosita Saul
- Department of Computational Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, US
- UCLA SwabSeq COVID19 Laboratory, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, US
| | - Laila Sathe
- UCLA SwabSeq COVID19 Laboratory, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, US
- Department of Pathology and Lab Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, US
| | - Joanna Xie
- UCLA SwabSeq COVID19 Laboratory, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, US
| | - Dawn Marquette
- Department of Computational Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, US
- UCLA SwabSeq COVID19 Laboratory, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, US
| | - Valerie A Arboleda
- Department of Computational Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, US
- UCLA SwabSeq COVID19 Laboratory, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, US
- Department of Pathology and Lab Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, US
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, US
| |
Collapse
|
4
|
Bloom JS, Sathe L, Munugala C, Jones EM, Gasperini M, Lubock NB, Yarza F, Thompson EM, Kovary KM, Park J, Marquette D, Kay S, Lucas M, Love T, Sina Booeshaghi A, Brandenberg OF, Guo L, Boocock J, Hochman M, Simpkins SW, Lin I, LaPierre N, Hong D, Zhang Y, Oland G, Choe BJ, Chandrasekaran S, Hilt EE, Butte MJ, Damoiseaux R, Kravit C, Cooper AR, Yin Y, Pachter L, Garner OB, Flint J, Eskin E, Luo C, Kosuri S, Kruglyak L, Arboleda VA. Massively scaled-up testing for SARS-CoV-2 RNA via next-generation sequencing of pooled and barcoded nasal and saliva samples. Nat Biomed Eng 2021; 5:657-665. [PMID: 34211145 PMCID: PMC10810734 DOI: 10.1038/s41551-021-00754-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 05/20/2021] [Indexed: 02/02/2023]
Abstract
Frequent and widespread testing of members of the population who are asymptomatic for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is essential for the mitigation of the transmission of the virus. Despite the recent increases in testing capacity, tests based on quantitative polymerase chain reaction (qPCR) assays cannot be easily deployed at the scale required for population-wide screening. Here, we show that next-generation sequencing of pooled samples tagged with sample-specific molecular barcodes enables the testing of thousands of nasal or saliva samples for SARS-CoV-2 RNA in a single run without the need for RNA extraction. The assay, which we named SwabSeq, incorporates a synthetic RNA standard that facilitates end-point quantification and the calling of true negatives, and that reduces the requirements for automation, purification and sample-to-sample normalization. We used SwabSeq to perform 80,000 tests, with an analytical sensitivity and specificity comparable to or better than traditional qPCR tests, in less than two months with turnaround times of less than 24 h. SwabSeq could be rapidly adapted for the detection of other pathogens.
Collapse
Affiliation(s)
- Joshua S Bloom
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
- Octant Inc., Emeryville, CA, USA.
| | - Laila Sathe
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Chetan Munugala
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | | | | | | | | | | | | | | | - Dawn Marquette
- Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Stephania Kay
- Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Mark Lucas
- Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - TreQuan Love
- Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | | | - Oliver F Brandenberg
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Longhua Guo
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - James Boocock
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | | | | | - Isabella Lin
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Nathan LaPierre
- Department of Computer Science, Samueli School of Engineering, UCLA, Los Angeles, CA, USA
| | - Duke Hong
- Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Yi Zhang
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Gabriel Oland
- Department of Surgery, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Bianca Judy Choe
- Department of Emergency Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Sukantha Chandrasekaran
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Evann E Hilt
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Manish J Butte
- Department of Pediatrics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Microbiology, Immunology & Molecular Genetics, UCLA, Los Angeles, CA, USA
| | - Robert Damoiseaux
- California NanoSystems Institute, UCLA, Los Angeles, CA, USA
- Department of Bioengineering, Samueli School of Engineering, UCLA, Los Angeles, CA, USA
- Department of Medical and Molecular Pharmacology, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Clifford Kravit
- Department of Digital Technology, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | | | - Yi Yin
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Lior Pachter
- Division of Biology and Bioengineering, Department of Computing and Mathematical Sciences, Caltech, Pasadena, CA, USA
| | - Omai B Garner
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Jonathan Flint
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Eleazar Eskin
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Computer Science, Samueli School of Engineering, UCLA, Los Angeles, CA, USA
| | - Chongyuan Luo
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Sriram Kosuri
- Octant Inc., Emeryville, CA, USA.
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, USA.
| | - Leonid Kruglyak
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA.
| | - Valerie A Arboleda
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA.
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA.
| |
Collapse
|
5
|
Hilt EE, Boocock J, Trejo M, Le CQ, Guo L, Zhang Y, Sathe L, Arboleda VA, Yin Y, Bloom JS, Wang PC, Elmore JG, Kruglyak L, Shrestha L, Bakhash SAM, Lin M, Xie H, Huang ML, Roychoudhury P, Greninger A, Chandrasekaran S, Yang S, Garner OB. Retrospective Detection of SARS-CoV-2 in Symptomatic Patients prior to Widespread Diagnostic Testing in Southern California. Clin Infect Dis 2021; 74:271-277. [PMID: 33939799 PMCID: PMC8135745 DOI: 10.1093/cid/ciab360] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Indexed: 01/15/2023] Open
Abstract
Background Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused one of the worst pandemics in recent history. Few reports have revealed that SARS-CoV-2 was spreading in the United States as early as the end of January. In this study, we aimed to determine if SARS-CoV-2 had been circulating in the Los Angeles (LA) area at a time when access to diagnostic testing for coronavirus disease 2019 (COVID-19) was severely limited. Methods We used a pooling strategy to look for SARS-CoV-2 in remnant respiratory samples submitted for regular respiratory pathogen testing from symptomatic patients from November 2019 to early March 2020. We then performed sequencing on the positive samples. Results We detected SARS-CoV-2 in 7 specimens from 6 patients, dating back to mid-January. The earliest positive patient, with a sample collected on January 13, 2020 had no relevant travel history but did have a sibling with similar symptoms. Sequencing of these SARS-CoV-2 genomes revealed that the virus was introduced into the LA area from both domestic and international sources as early as January. Conclusions We present strong evidence of community spread of SARS-CoV-2 in the LA area well before widespread diagnostic testing was being performed in early 2020. These genomic data demonstrate that SARS-CoV-2 was being introduced into Los Angeles County from both international and domestic sources in January 2020.
Collapse
Affiliation(s)
- Evann E Hilt
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles (UCLA), California, USA
| | - James Boocock
- Department of Human Genetics, David Geffen School of Medicine, UCLA, California, USA.,Department of Biological Chemistry, David Geffen School of Medicine, UCLA, California, USA.,Howard Hughes Medical Institute, David Geffen School of Medicine, UCLA, California, USA
| | - Marisol Trejo
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles (UCLA), California, USA
| | - Catherine Q Le
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles (UCLA), California, USA
| | - Longhua Guo
- Department of Human Genetics, David Geffen School of Medicine, UCLA, California, USA.,Department of Biological Chemistry, David Geffen School of Medicine, UCLA, California, USA.,Howard Hughes Medical Institute, David Geffen School of Medicine, UCLA, California, USA
| | - Yi Zhang
- Department of Human Genetics, David Geffen School of Medicine, UCLA, California, USA
| | - Laila Sathe
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles (UCLA), California, USA
| | - Valerie A Arboleda
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles (UCLA), California, USA.,Department of Human Genetics, David Geffen School of Medicine, UCLA, California, USA
| | - Yi Yin
- Department of Human Genetics, David Geffen School of Medicine, UCLA, California, USA
| | - Joshua S Bloom
- Department of Human Genetics, David Geffen School of Medicine, UCLA, California, USA.,Department of Biological Chemistry, David Geffen School of Medicine, UCLA, California, USA
| | - Pin-Chieh Wang
- Department of Medicine, David Geffen School of Medicine, UCLA, California, USA
| | - Joann G Elmore
- Department of Medicine, David Geffen School of Medicine, UCLA, California, USA
| | - Leonid Kruglyak
- Department of Human Genetics, David Geffen School of Medicine, UCLA, California, USA.,Department of Biological Chemistry, David Geffen School of Medicine, UCLA, California, USA.,Howard Hughes Medical Institute, David Geffen School of Medicine, UCLA, California, USA
| | - Lasata Shrestha
- Department of Laboratory Medicine, University of Washington Medical Center, Seattle, Washington, USA
| | - Shah A Mohamed Bakhash
- Department of Laboratory Medicine, University of Washington Medical Center, Seattle, Washington, USA
| | - Michelle Lin
- Department of Laboratory Medicine, University of Washington Medical Center, Seattle, Washington, USA
| | - Hong Xie
- Department of Laboratory Medicine, University of Washington Medical Center, Seattle, Washington, USA
| | - Meei-Li Huang
- Department of Laboratory Medicine, University of Washington Medical Center, Seattle, Washington, USA
| | - Pavitra Roychoudhury
- Department of Laboratory Medicine, University of Washington Medical Center, Seattle, Washington, USA
| | - Alexander Greninger
- Department of Laboratory Medicine, University of Washington Medical Center, Seattle, Washington, USA
| | - Sukantha Chandrasekaran
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles (UCLA), California, USA
| | - Shangxin Yang
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles (UCLA), California, USA
| | - Omai B Garner
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles (UCLA), California, USA
| |
Collapse
|
6
|
Bloom JS, Sathe L, Munugala C, Jones EM, Gasperini M, Lubock NB, Yarza F, Thompson EM, Kovary KM, Park J, Marquette D, Kay S, Lucas M, Love T, Booeshaghi AS, Brandenberg OF, Guo L, Boocock J, Hochman M, Simpkins SW, Lin I, LaPierre N, Hong D, Zhang Y, Oland G, Choe BJ, Chandrasekaran S, Hilt EE, Butte MJ, Damoiseaux R, Kravit C, Cooper AR, Yin Y, Pachter L, Garner OB, Flint J, Eskin E, Luo C, Kosuri S, Kruglyak L, Arboleda VA. Swab-Seq: A high-throughput platform for massively scaled up SARS-CoV-2 testing. medRxiv 2021. [PMID: 32909008 PMCID: PMC7480060 DOI: 10.1101/2020.08.04.20167874] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The rapid spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is due to the high rates of transmission by individuals who are asymptomatic at the time of transmission1,2. Frequent, widespread testing of the asymptomatic population for SARS-CoV-2 is essential to suppress viral transmission. Despite increases in testing capacity, multiple challenges remain in deploying traditional reverse transcription and quantitative PCR (RT-qPCR) tests at the scale required for population screening of asymptomatic individuals. We have developed SwabSeq, a high-throughput testing platform for SARS-CoV-2 that uses next-generation sequencing as a readout. SwabSeq employs sample-specific molecular barcodes to enable thousands of samples to be combined and simultaneously analyzed for the presence or absence of SARS-CoV-2 in a single run. Importantly, SwabSeq incorporates an in vitro RNA standard that mimics the viral amplicon, but can be distinguished by sequencing. This standard allows for end-point rather than quantitative PCR, improves quantitation, reduces requirements for automation and sample-to-sample normalization, enables purification-free detection, and gives better ability to call true negatives. After setting up SwabSeq in a high-complexity CLIA laboratory, we performed more than 80,000 tests for COVID-19 in less than two months, confirming in a real world setting that SwabSeq inexpensively delivers highly sensitive and specific results at scale, with a turn-around of less than 24 hours. Our clinical laboratory uses SwabSeq to test both nasal and saliva samples without RNA extraction, while maintaining analytical sensitivity comparable to or better than traditional RT-qPCR tests. Moving forward, SwabSeq can rapidly scale up testing to mitigate devastating spread of novel pathogens.
Collapse
Affiliation(s)
- Joshua S Bloom
- Department of Human Genetics, David Geffen School of Medicine, UCLA.,Howard Hughes Medical Institute, HHMI.,Octant, Inc
| | - Laila Sathe
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, UCLA
| | - Chetan Munugala
- Department of Human Genetics, David Geffen School of Medicine, UCLA.,Howard Hughes Medical Institute, HHMI
| | | | | | | | | | | | | | | | - Dawn Marquette
- Department of Computational Medicine, David Geffen School of Medicine, UCLA
| | - Stephania Kay
- Department of Computational Medicine, David Geffen School of Medicine, UCLA
| | - Mark Lucas
- Department of Computational Medicine, David Geffen School of Medicine, UCLA
| | - TreQuan Love
- Department of Computational Medicine, David Geffen School of Medicine, UCLA
| | | | - Oliver F Brandenberg
- Department of Human Genetics, David Geffen School of Medicine, UCLA.,Howard Hughes Medical Institute, HHMI.,Department of Biological Chemistry, David Geffen School of Medicine, UCLA
| | - Longhua Guo
- Department of Human Genetics, David Geffen School of Medicine, UCLA.,Howard Hughes Medical Institute, HHMI.,Department of Biological Chemistry, David Geffen School of Medicine, UCLA
| | - James Boocock
- Department of Human Genetics, David Geffen School of Medicine, UCLA.,Howard Hughes Medical Institute, HHMI.,Department of Biological Chemistry, David Geffen School of Medicine, UCLA
| | | | | | - Isabella Lin
- Department of Human Genetics, David Geffen School of Medicine, UCLA.,Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, UCLA
| | - Nathan LaPierre
- Department of Computer Science, Samueli School of Engineering, UCLA
| | - Duke Hong
- Department of Computational Medicine, David Geffen School of Medicine, UCLA
| | - Yi Zhang
- Department of Human Genetics, David Geffen School of Medicine, UCLA
| | - Gabriel Oland
- Department of Surgery, David Geffen School of Medicine, UCLA
| | - Bianca Judy Choe
- Department of Emergency Medicine, David Geffen School of Medicine, UCLA
| | | | - Evann E Hilt
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, UCLA
| | - Manish J Butte
- Department of Pediatrics, David Geffen School of Medicine, UCLA.,Department of Microbiology, Immunology & Molecular Genetics, David Geffen School of Medicine, UCLA
| | - Robert Damoiseaux
- California NanoSystems Institute, UCLA.,Department of Bioengineering, Samueli School of Engineering, UCLA.,David Geffen School of Medicine, Research Information Technology
| | - Clifford Kravit
- David Geffen School of Medicine, Research Information Technology
| | | | - Yi Yin
- Department of Human Genetics, David Geffen School of Medicine, UCLA
| | - Lior Pachter
- Division of Biology and Bioengineering & Department of Computing and Mathematical Sciences, Caltech
| | - Omai B Garner
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, UCLA
| | - Jonathan Flint
- Department of Human Genetics, David Geffen School of Medicine, UCLA.,Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, UCLA
| | - Eleazar Eskin
- Department of Human Genetics, David Geffen School of Medicine, UCLA.,Department of Computer Science, Samueli School of Engineering, UCLA.,Department of Computational Medicine, David Geffen School of Medicine, UCLA
| | - Chongyuan Luo
- Department of Human Genetics, David Geffen School of Medicine, UCLA
| | - Sriram Kosuri
- Octant, Inc.,Department of Chemistry and Biochemistry, UCLA
| | - Leonid Kruglyak
- Department of Human Genetics, David Geffen School of Medicine, UCLA.,Howard Hughes Medical Institute, HHMI.,Department of Biological Chemistry, David Geffen School of Medicine, UCLA
| | - Valerie A Arboleda
- Department of Human Genetics, David Geffen School of Medicine, UCLA.,Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, UCLA
| |
Collapse
|
7
|
Flores A, Sandoval-Gonzalez S, Takahashi R, Krall A, Sathe L, Wei L, Radu C, Joly JH, Graham NA, Christofk HR, Lowry WE. Author Correction: Increased lactate dehydrogenase activity is dispensable in squamous carcinoma cells of origin. Nat Commun 2019; 10:1449. [PMID: 30914644 PMCID: PMC6435690 DOI: 10.1038/s41467-019-09435-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- A Flores
- Department of Molecular Cell and Developmental Biology, UCLA, Los Angeles, 90095, CA, USA.,Broad Center for Regenerative Medicine, UCLA, Los Angeles, 90095, CA, USA.,Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, 90089, CA, USA
| | - S Sandoval-Gonzalez
- Department of Molecular Cell and Developmental Biology, UCLA, Los Angeles, 90095, CA, USA
| | - R Takahashi
- Division of Dermatology, David Geffen School of Medicine, UCLA, Los Angeles, 90095, CA, USA
| | - A Krall
- Department of Biological Chemistry, UCLA, Los Angeles, 90095, CA, USA
| | - L Sathe
- Department of Molecular Cell and Developmental Biology, UCLA, Los Angeles, 90095, CA, USA
| | - L Wei
- Department of Pharmacology, UCLA, Los Angeles, 90095, CA, USA
| | - C Radu
- Department of Pharmacology, UCLA, Los Angeles, 90095, CA, USA
| | - J H Joly
- Department of Engineering, USC, Los Angeles, 90089, CA, USA.,Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, 90089, CA, USA
| | - N A Graham
- Department of Engineering, USC, Los Angeles, 90089, CA, USA.,Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, 90089, CA, USA.,Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, 90089, CA, USA
| | - H R Christofk
- Department of Biological Chemistry, UCLA, Los Angeles, 90095, CA, USA. .,Department of Pharmacology, UCLA, Los Angeles, 90095, CA, USA. .,Molecular Biology Institute, UCLA, Los Angeles, 90095, CA, USA. .,Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, 90095, CA, USA.
| | - W E Lowry
- Department of Molecular Cell and Developmental Biology, UCLA, Los Angeles, 90095, CA, USA. .,Broad Center for Regenerative Medicine, UCLA, Los Angeles, 90095, CA, USA. .,Division of Dermatology, David Geffen School of Medicine, UCLA, Los Angeles, 90095, CA, USA. .,Molecular Biology Institute, UCLA, Los Angeles, 90095, CA, USA. .,Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, 90095, CA, USA.
| |
Collapse
|
8
|
Flores A, Sandoval-Gonzalez S, Takahashi R, Krall A, Sathe L, Wei L, Radu C, Joly JH, Graham NA, Christofk HR, Lowry WE. Increased lactate dehydrogenase activity is dispensable in squamous carcinoma cells of origin. Nat Commun 2019; 10:91. [PMID: 30626875 PMCID: PMC6327029 DOI: 10.1038/s41467-018-07857-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 12/04/2018] [Indexed: 12/17/2022] Open
Abstract
Although numerous therapeutic strategies have attempted to target aerobic glycolysis to inhibit tumor progression, these approaches have not resulted in effective clinical outcomes. Murine squamous cell carcinoma (SCC) can be initiated by hair follicle stem cells (HFSCs). HFSCs utilize aerobic glycolysis, and the activity of lactate dehydrogenase (Ldh) is essential for HFSC activation. We sought to determine whether Ldh activity in SCC is critical for tumorigenesis or simply a marker of the cell type of origin. Genetic abrogation or induction of Ldh activity in HFSC-mediated tumorigenesis shows no effect on tumorigenesis as measured by number, time to formation, proliferation, volume, epithelial to mesenchymal transition, gene expression, or immune response. Ldha-null tumors show dramatically reduced levels of glycolytic metabolites by metabolomics, and significantly reduced glucose uptake by FDG-PET live animal imaging. These results suggest that squamous cancer cells of origin do not require increased glycolytic activity to generate cancers. Most tumours are characterized by increased aerobic glycolytic activity. Here the authors show that elevated aerobic glycolysis is not essential for cancer initiation by testing the effect of lactate dehydrogenase depletion on the ability of hair follicle stem cells (HFSCs) to form squamous cell carcinoma (SCC) in mouse genetic models.
Collapse
Affiliation(s)
- A Flores
- Department of Molecular Cell and Developmental Biology, UCLA, Los Angeles, 90095, CA, USA.,Broad Center for Regenerative Medicine, UCLA, Los Angeles, 90095, CA, USA.,Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, 90089, CA, USA
| | - S Sandoval-Gonzalez
- Department of Molecular Cell and Developmental Biology, UCLA, Los Angeles, 90095, CA, USA
| | - R Takahashi
- Division of Dermatology, David Geffen School of Medicine, UCLA, Los Angeles, 90095, CA, USA
| | - A Krall
- Department of Biological Chemistry, UCLA, Los Angeles, 90095, CA, USA
| | - L Sathe
- Department of Molecular Cell and Developmental Biology, UCLA, Los Angeles, 90095, CA, USA
| | - L Wei
- Department of Pharmacology, UCLA, Los Angeles, 90095, CA, USA
| | - C Radu
- Department of Pharmacology, UCLA, Los Angeles, 90095, CA, USA
| | - J H Joly
- Department of Engineering, USC, Los Angeles, 90089, CA, USA.,Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, 90089, CA, USA
| | - N A Graham
- Department of Engineering, USC, Los Angeles, 90089, CA, USA.,Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, 90089, CA, USA.,Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, 90089, CA, USA
| | - H R Christofk
- Department of Biological Chemistry, UCLA, Los Angeles, 90095, CA, USA. .,Department of Pharmacology, UCLA, Los Angeles, 90095, CA, USA. .,Molecular Biology Institute, UCLA, Los Angeles, 90095, CA, USA. .,Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, 90095, CA, USA.
| | - W E Lowry
- Department of Molecular Cell and Developmental Biology, UCLA, Los Angeles, 90095, CA, USA. .,Broad Center for Regenerative Medicine, UCLA, Los Angeles, 90095, CA, USA. .,Division of Dermatology, David Geffen School of Medicine, UCLA, Los Angeles, 90095, CA, USA. .,Molecular Biology Institute, UCLA, Los Angeles, 90095, CA, USA. .,Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, 90095, CA, USA.
| |
Collapse
|
9
|
Rolnick SJ, Owens B, Botta R, Sathe L, Hawkins R, Cooper L, Kelley M, Gustafson D. Computerized information and support for patients with breast cancer or HIV infection. Nurs Outlook 1999; 47:78-83. [PMID: 10227034 DOI: 10.1016/s0029-6554(99)90074-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- S J Rolnick
- HealthPartners Foundation, Minneapolis, Minnesota, USA
| | | | | | | | | | | | | | | |
Collapse
|