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Welch NL, Zhu M, Hua C, Weller J, Mirhashemi ME, Nguyen TG, Mantena S, Bauer MR, Shaw BM, Ackerman CM, Thakku SG, Tse MW, Kehe J, Uwera MM, Eversley JS, Bielwaski DA, McGrath G, Braidt J, Johnson J, Cerrato F, Moreno GK, Krasilnikova LA, Petros BA, Gionet GL, King E, Huard RC, Jalbert SK, Cleary ML, Fitzgerald NA, Gabriel SB, Gallagher GR, Smole SC, Madoff LC, Brown CM, Keller MW, Wilson MM, Kirby MK, Barnes JR, Park DJ, Siddle KJ, Happi CT, Hung DT, Springer M, MacInnis BL, Lemieux JE, Rosenberg E, Branda JA, Blainey PC, Sabeti PC, Myhrvold C. Author Correction: Multiplexed CRISPR-based microfluidic platform for clinical testing of respiratory viruses and identification of SARS-CoV-2 variants. Nat Med 2024; 30:307. [PMID: 37946059 PMCID: PMC10803257 DOI: 10.1038/s41591-023-02684-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2023]
Affiliation(s)
- Nicole L Welch
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Harvard Program in Virology, Division of Medical Sciences, Harvard Medical School, Boston, MA, USA.
| | - Meilin Zhu
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Catherine Hua
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Juliane Weller
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | | | - Tien G Nguyen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Matthew R Bauer
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA, USA
| | - Bennett M Shaw
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Cheri M Ackerman
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Sri Gowtham Thakku
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Health Sciences and Technology, Harvard Medical School and Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Megan W Tse
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jared Kehe
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - Jacqueline S Eversley
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Derek A Bielwaski
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Graham McGrath
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Joseph Braidt
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | | | | | - Gage K Moreno
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Lydia A Krasilnikova
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Brittany A Petros
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Health Sciences and Technology, Harvard Medical School and Massachusetts Institute of Technology, Cambridge, MA, USA
- Harvard/Massachusetts Institute of Technology MD-PhD Program, Harvard Medical School, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | | | - Ewa King
- State Health Laboratories, Rhode Island Department of Health, Providence, RI, USA
| | - Richard C Huard
- State Health Laboratories, Rhode Island Department of Health, Providence, RI, USA
| | | | - Michael L Cleary
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | | | | | | | - Sandra C Smole
- Massachusetts Department of Public Health, Boston, MA, USA
| | | | | | - Matthew W Keller
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Malania M Wilson
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Marie K Kirby
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - John R Barnes
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Daniel J Park
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Katherine J Siddle
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Christian T Happi
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- African Centre of Excellence for Genomics of Infectious Diseases, Redeemer's University, Ede, Nigeria
- Department of Biological Sciences, College of Natural Sciences, Redeemer's University, Ede, Nigeria
| | - Deborah T Hung
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Molecular Biology Department and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Michael Springer
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Bronwyn L MacInnis
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Immunology and Infectious Disease, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Jacob E Lemieux
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Eric Rosenberg
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - John A Branda
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Paul C Blainey
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Research at Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Pardis C Sabeti
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA.
- Department of Immunology and Infectious Disease, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA.
- Koch Institute for Integrative Cancer Research at Massachusetts Institute of Technology, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
| | - Cameron Myhrvold
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA.
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Thakku SG, Lirette J, Murugesan K, Chen J, Theron G, Banaei N, Blainey PC, Gomez J, Wong SY, Hung DT. Genome-wide tiled detection of circulating Mycobacterium tuberculosis cell-free DNA using Cas13. Nat Commun 2023; 14:1803. [PMID: 37002219 PMCID: PMC10064635 DOI: 10.1038/s41467-023-37183-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 03/06/2023] [Indexed: 04/03/2023] Open
Abstract
Detection of microbial cell-free DNA (cfDNA) circulating in the bloodstream has emerged as a promising new approach for diagnosing infection. Microbial diagnostics based on cfDNA require assays that can detect rare and highly fragmented pathogen nucleic acids. We now report WATSON (Whole-genome Assay using Tiled Surveillance Of Nucleic acids), a method to detect low amounts of pathogen cfDNA that couples pooled amplification of genomic targets tiled across the genome with pooled CRISPR/Cas13-based detection of these targets. We demonstrate that this strategy of tiling improves cfDNA detection compared to amplification and detection of a single targeted locus. WATSON can detect cfDNA from Mycobacterium tuberculosis in plasma of patients with active pulmonary tuberculosis, a disease that urgently needs accurate, minimally-invasive, field-deployable diagnostics. We thus demonstrate the potential for translating WATSON to a lateral flow platform. WATSON demonstrates the ability to capitalize on the strengths of targeting microbial cfDNA to address the need for point-of-care diagnostic tests for infectious diseases.
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Affiliation(s)
| | | | - Kanagavel Murugesan
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Julie Chen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Grant Theron
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research and SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Niaz Banaei
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Clinical Microbiology Laboratory, Stanford Health Care, Palo Alto, CA, USA
| | - Paul C Blainey
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA, USA
| | - James Gomez
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sharon Y Wong
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Deborah T Hung
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
- Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, USA.
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3
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Welch NL, Zhu M, Hua C, Weller J, Mirhashemi ME, Nguyen TG, Mantena S, Bauer MR, Shaw BM, Ackerman CM, Thakku SG, Tse MW, Kehe J, Uwera MM, Eversley JS, Bielwaski DA, McGrath G, Braidt J, Johnson J, Cerrato F, Moreno GK, Krasilnikova LA, Petros BA, Gionet GL, King E, Huard RC, Jalbert SK, Cleary ML, Fitzgerald NA, Gabriel SB, Gallagher GR, Smole SC, Madoff LC, Brown CM, Keller MW, Wilson MM, Kirby MK, Barnes JR, Park DJ, Siddle KJ, Happi CT, Hung DT, Springer M, MacInnis BL, Lemieux JE, Rosenberg E, Branda JA, Blainey PC, Sabeti PC, Myhrvold C. Multiplexed CRISPR-based microfluidic platform for clinical testing of respiratory viruses and identification of SARS-CoV-2 variants. Nat Med 2022; 28:1083-1094. [PMID: 35130561 PMCID: PMC9117129 DOI: 10.1038/s41591-022-01734-1] [Citation(s) in RCA: 97] [Impact Index Per Article: 48.5] [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] [Received: 11/22/2021] [Accepted: 02/03/2022] [Indexed: 11/23/2022]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has demonstrated a clear need for high-throughput, multiplexed and sensitive assays for detecting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and other respiratory viruses and their emerging variants. Here, we present a cost-effective virus and variant detection platform, called microfluidic Combinatorial Arrayed Reactions for Multiplexed Evaluation of Nucleic acids (mCARMEN), which combines CRISPR-based diagnostics and microfluidics with a streamlined workflow for clinical use. We developed the mCARMEN respiratory virus panel to test for up to 21 viruses, including SARS-CoV-2, other coronaviruses and both influenza strains, and demonstrated its diagnostic-grade performance on 525 patient specimens in an academic setting and 166 specimens in a clinical setting. We further developed an mCARMEN panel to enable the identification of 6 SARS-CoV-2 variant lineages, including Delta and Omicron, and evaluated it on 2,088 patient specimens with near-perfect concordance to sequencing-based variant classification. Lastly, we implemented a combined Cas13 and Cas12 approach that enables quantitative measurement of SARS-CoV-2 and influenza A viral copies in samples. The mCARMEN platform enables high-throughput surveillance of multiple viruses and variants simultaneously, enabling rapid detection of SARS-CoV-2 variants.
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Affiliation(s)
- Nicole L Welch
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Harvard Program in Virology, Division of Medical Sciences, Harvard Medical School, Boston, MA, USA.
| | - Meilin Zhu
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Catherine Hua
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Juliane Weller
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | | | - Tien G Nguyen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Matthew R Bauer
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA, USA
| | - Bennett M Shaw
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Cheri M Ackerman
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Sri Gowtham Thakku
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Health Sciences and Technology, Harvard Medical School and Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Megan W Tse
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jared Kehe
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - Jacqueline S Eversley
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Derek A Bielwaski
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Graham McGrath
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Joseph Braidt
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | | | | | - Gage K Moreno
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Lydia A Krasilnikova
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Brittany A Petros
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Health Sciences and Technology, Harvard Medical School and Massachusetts Institute of Technology, Cambridge, MA, USA
- Harvard/Massachusetts Institute of Technology MD-PhD Program, Harvard Medical School, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | | | - Ewa King
- State Health Laboratories, Rhode Island Department of Health, Providence, RI, USA
| | - Richard C Huard
- State Health Laboratories, Rhode Island Department of Health, Providence, RI, USA
| | | | - Michael L Cleary
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | | | | | | | - Sandra C Smole
- Massachusetts Department of Public Health, Boston, MA, USA
| | | | | | - Matthew W Keller
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Malania M Wilson
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Marie K Kirby
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - John R Barnes
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Daniel J Park
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Katherine J Siddle
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Christian T Happi
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- African Centre of Excellence for Genomics of Infectious Diseases, Redeemer's University, Ede, Nigeria
- Department of Biological Sciences, College of Natural Sciences, Redeemer's University, Ede, Nigeria
| | - Deborah T Hung
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Molecular Biology Department and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Michael Springer
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Bronwyn L MacInnis
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Immunology and Infectious Disease, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Jacob E Lemieux
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Eric Rosenberg
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - John A Branda
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Paul C Blainey
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Research at Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Pardis C Sabeti
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA.
- Department of Immunology and Infectious Disease, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA.
- Koch Institute for Integrative Cancer Research at Massachusetts Institute of Technology, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
| | - Cameron Myhrvold
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA.
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Thakku SG, Ackerman CM, Myhrvold C, Bhattacharyya RP, Livny J, Ma P, Gomez GI, Sabeti PC, Blainey PC, Hung DT. Multiplexed detection of bacterial nucleic acids using Cas13 in droplet microarrays. PNAS Nexus 2022; 1:pgac021. [PMID: 35450424 PMCID: PMC9013781 DOI: 10.1093/pnasnexus/pgac021] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 01/22/2022] [Accepted: 03/28/2022] [Indexed: 12/26/2022]
Abstract
Rapid and accurate diagnosis of infections is fundamental to individual patient care and public health management. Nucleic acid detection methods are critical to this effort, but are limited either in the breadth of pathogens targeted or by the expertise and infrastructure required. We present here a high-throughput system that enables rapid identification of bacterial pathogens, bCARMEN, which utilizes: (1) modular CRISPR-Cas13-based nucleic acid detection with enhanced sensitivity and specificity; and (2) a droplet microfluidic system that enables thousands of simultaneous, spatially multiplexed detection reactions at nanoliter volumes; and (3) a novel preamplification strategy that further enhances sensitivity and specificity. We demonstrate bCARMEN is capable of detecting and discriminating 52 clinically relevant bacterial species and several key antibiotic resistance genes. We further develop a simple proof of principle workflow using stabilized reagents and cell phone camera optical readout, opening up the possibility of a rapid point-of-care multiplexed bacterial pathogen identification and antibiotic susceptibility testing.
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Affiliation(s)
| | | | | | | | - Jonathan Livny
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Peijun Ma
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Pardis C Sabeti
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Paul C Blainey
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Deborah T Hung
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
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5
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Ackerman CM, Myhrvold C, Thakku SG, Freije CA, Metsky HC, Yang DK, Ye SH, Boehm CK, Kosoko-Thoroddsen TSF, Kehe J, Nguyen TG, Carter A, Kulesa A, Barnes JR, Dugan VG, Hung DT, Blainey PC, Sabeti PC. Massively multiplexed nucleic acid detection with Cas13. Nature 2020; 582:277-282. [PMID: 32349121 PMCID: PMC7332423 DOI: 10.1038/s41586-020-2279-8] [Citation(s) in RCA: 379] [Impact Index Per Article: 94.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 04/20/2020] [Indexed: 12/26/2022]
Abstract
The great majority of globally circulating pathogens go undetected, undermining patient care and hindering outbreak preparedness and response. To enable routine surveillance and comprehensive diagnostic applications, there is a need for detection technologies that can scale to test many samples1-3 while simultaneously testing for many pathogens4-6. Here, we develop Combinatorial Arrayed Reactions for Multiplexed Evaluation of Nucleic acids (CARMEN), a platform for scalable, multiplexed pathogen detection. In the CARMEN platform, nanolitre droplets containing CRISPR-based nucleic acid detection reagents7 self-organize in a microwell array8 to pair with droplets of amplified samples, testing each sample against each CRISPR RNA (crRNA) in replicate. The combination of CARMEN and Cas13 detection (CARMEN-Cas13) enables robust testing of more than 4,500 crRNA-target pairs on a single array. Using CARMEN-Cas13, we developed a multiplexed assay that simultaneously differentiates all 169 human-associated viruses with at least 10 published genome sequences and rapidly incorporated an additional crRNA to detect the causative agent of the 2020 COVID-19 pandemic. CARMEN-Cas13 further enables comprehensive subtyping of influenza A strains and multiplexed identification of dozens of HIV drug-resistance mutations. The intrinsic multiplexing and throughput capabilities of CARMEN make it practical to scale, as miniaturization decreases reagent cost per test by more than 300-fold. Scalable, highly multiplexed CRISPR-based nucleic acid detection shifts diagnostic and surveillance efforts from targeted testing of high-priority samples to comprehensive testing of large sample sets, greatly benefiting patients and public health9-11.
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Affiliation(s)
- Cheri M Ackerman
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
- Department of Biological Engineering, MIT, Cambridge, MA, USA
| | - Cameron Myhrvold
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA.
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA.
| | - Sri Gowtham Thakku
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
- Division of Health Sciences and Technology, Harvard Medical School and MIT, Cambridge, MA, USA
| | - Catherine A Freije
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
- Ph.D. Program in Virology, Division of Medical Sciences, Harvard Medical School, Boston, MA, USA
| | - Hayden C Metsky
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
- Department of Electrical Engineering and Computer Science, MIT, Cambridge, MA, USA
| | - David K Yang
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Simon H Ye
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
- Division of Health Sciences and Technology, Harvard Medical School and MIT, Cambridge, MA, USA
| | - Chloe K Boehm
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | | | - Jared Kehe
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
- Department of Biological Engineering, MIT, Cambridge, MA, USA
| | - Tien G Nguyen
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Amber Carter
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Anthony Kulesa
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
- Department of Biological Engineering, MIT, Cambridge, MA, USA
| | - John R Barnes
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Vivien G Dugan
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Deborah T Hung
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
- Molecular Biology Department and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Paul C Blainey
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA.
- Department of Biological Engineering, MIT, Cambridge, MA, USA.
- Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA, USA.
| | - Pardis C Sabeti
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Department of Immunology and Infectious Disease, Harvard T.H. Chan School of Public Health, Boston, MA, USA
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6
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Kehe J, Kulesa A, Ortiz A, Ackerman CM, Thakku SG, Sellers D, Kuehn S, Gore J, Friedman J, Blainey PC. Massively parallel screening of synthetic microbial communities. Proc Natl Acad Sci U S A 2019; 116:12804-12809. [PMID: 31186361 PMCID: PMC6600964 DOI: 10.1073/pnas.1900102116] [Citation(s) in RCA: 120] [Impact Index Per Article: 24.0] [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] [Indexed: 12/28/2022] Open
Abstract
Microbial communities have numerous potential applications in biotechnology, agriculture, and medicine. Nevertheless, the limited accuracy with which we can predict interspecies interactions and environmental dependencies hinders efforts to rationally engineer beneficial consortia. Empirical screening is a complementary approach wherein synthetic communities are combinatorially constructed and assayed in high throughput. However, assembling many combinations of microbes is logistically complex and difficult to achieve on a timescale commensurate with microbial growth. Here, we introduce the kChip, a droplets-based platform that performs rapid, massively parallel, bottom-up construction and screening of synthetic microbial communities. We first show that the kChip enables phenotypic characterization of microbes across environmental conditions. Next, in a screen of ∼100,000 multispecies communities comprising up to 19 soil isolates, we identified sets that promote the growth of the model plant symbiont Herbaspirillum frisingense in a manner robust to carbon source variation and the presence of additional species. Broadly, kChip screening can identify multispecies consortia possessing any optically assayable function, including facilitation of biocontrol agents, suppression of pathogens, degradation of recalcitrant substrates, and robustness of these functions to perturbation, with many applications across basic and applied microbial ecology.
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Affiliation(s)
- Jared Kehe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | - Anthony Kulesa
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | - Anthony Ortiz
- Physics of Living Systems, Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139
| | | | - Sri Gowtham Thakku
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142
- Program in Health Sciences and Technology, MIT and Harvard, Cambridge, MA 02139
| | - Daniel Sellers
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142
- Department of Chemical and Biological Engineering, Tufts University, Medford, MA 02155
| | - Seppe Kuehn
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Jeff Gore
- Physics of Living Systems, Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Jonathan Friedman
- Department of Plant Pathology and Microbiology, The Hebrew University of Jerusalem, Rehovot, Israel 76100
| | - Paul C Blainey
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139;
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142
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Tan NYQ, Tham YC, Thakku SG, Wang X, Baskaran M, Tan MCL, Mari JM, Strouthidis NG, Aung T, Girard MJA, Cheng CY. Changes in the Anterior Lamina Cribrosa Morphology with Glaucoma Severity. Sci Rep 2019; 9:6612. [PMID: 31036869 PMCID: PMC6488637 DOI: 10.1038/s41598-019-42649-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [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: 10/23/2018] [Accepted: 03/27/2019] [Indexed: 01/05/2023] Open
Abstract
This study was designed to evaluate if primary open angle glaucoma (POAG) and its severity are associated with the shape of the lamina cribrosa (LC) as measured by a global shape index (LC-GSI), or other indices of LC curvature or depth. Optical coherence tomography (OCT) scans of the optic nerve head (OHN) were obtained from subjects with POAG (n = 99) and non-glaucomatous controls (n = 76). ONH structures were delineated, the anterior LC morphology reconstructed in 3D, and the LC-GSI calculated (more negative values denote greater posterior concavity). Anterior LC depth and 2D-curvature were also measured. Severity of glaucoma was defined by the extent of visual field loss, based on the Hodapp-Parrish-Anderson grading. Linear regression analyses compared LC characteristics between controls, mild-moderate, and advanced POAG groups. After adjusting for age, gender, ethnicity, intraocular pressure, axial length and corneal curvature, the LC-GSI was most negative in the advanced POAG group (mean [standard error] = −0.34 [0.05]), followed by the mild-moderate POAG group (−0.31 [0.02]) and then controls (−0.23 [0.02], PTrend = 0.01). There was also a significant trend of increasing LC depth and greater LC horizontal curvature with increasing severity of glaucoma (PTrend = 0.04 and 0.02, respectively). Therefore, with more severe glaucoma, the LC-GSI was increasingly more negative, and the anterior LC depth and curvature greater. These observations collectively correspond to greater cupping of the ONH at the level of the LC. As the LC-GSI describes the 3D anterior LC morphology, its potential usage may be complementary to existing ONH parameters measured on OCT.
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Affiliation(s)
- Nicholas Y Q Tan
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
| | - Yih-Chung Tham
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
| | - Sri Gowtham Thakku
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore.,Department of Biomedical Engineering, National University of Singapore, Singapore, Singapore
| | - Xiaofei Wang
- Department of Biomedical Engineering, National University of Singapore, Singapore, Singapore
| | - Mani Baskaran
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore.,Ophthalmology and Visual Sciences Academic Clinical Program, Duke-NUS Medical School, Singapore, Singapore
| | - Marcus C L Tan
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Vision Performance Centre, Singapore Armed Forces, Singapore, Singapore
| | - Jean-Martial Mari
- GePaSud, Université de la Polynésie Française, Tahiti, French Polynesia
| | - Nicholas G Strouthidis
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore.,NIHR Biomedical Research Centre, Moorfields Eye Hospital NHS Foundation Trust and UCL Institute of Ophthalmology, London, UK
| | - Tin Aung
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore.,Ophthalmology and Visual Sciences Academic Clinical Program, Duke-NUS Medical School, Singapore, Singapore.,Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Michaël J A Girard
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore.,Department of Biomedical Engineering, National University of Singapore, Singapore, Singapore
| | - Ching-Yu Cheng
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore. .,Ophthalmology and Visual Sciences Academic Clinical Program, Duke-NUS Medical School, Singapore, Singapore. .,Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
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8
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Abstract
Nucleic acid detection is an important method for pathogen identification but can be expensive, have variable sensitivity and specificity, and require substantial infrastructure. Two new methods capitalize on unexpected in vitro properties of clustered regularly interspaced short palindromic repeats (CRISPR) effectors, turning activated nucleases into intrinsic amplifiers of a specific nucleic-acid binding event. These effectors are coupled with a variety of reporters and used in tandem with existing isothermal amplification methods to produce sensitive, sequence-specific pathogen identification in multiple field-deployable formats. While still in their infancy, these modular CRISPR-based methods have the potential to transform pathogen identification and other aspects of infectious disease diagnostics.
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Affiliation(s)
- Roby P. Bhattacharyya
- Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, United States
- Division of Infectious Diseases and Department of Medicine, Massachusetts General Hospital, 55 Fruit Street, Boston, Massachusetts 02114, United States
| | - Sri Gowtham Thakku
- Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, United States
- Program in Health Sciences and Technology, Harvard Medical School and Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Deborah T. Hung
- Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, United States
- Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, United States
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
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9
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Chua J, Thakku SG, Pham TH, Lee R, Tun TA, Nongpiur ME, Tan MCL, Wong TY, Quah JHM, Aung T, Girard MJA, Cheng CY. Automated Detection of Iris Furrows and their Influence on Dynamic Iris Volume Change. Sci Rep 2017; 7:17894. [PMID: 29263345 PMCID: PMC5738384 DOI: 10.1038/s41598-017-18039-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [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: 05/08/2017] [Accepted: 12/05/2017] [Indexed: 11/09/2022] Open
Abstract
We introduced a new method for detecting iris surface furrows and identify its associations with dynamic changes in iris volume in healthy eyes. Swept-source optical coherence tomography was performed on 65 subjects with open angle under light and dark conditions. Iris boundaries were identified and a reconstruction of the anterior iris surface was obtained. Furrows were detected by identifying locally deep (minima) points on the iris surface and reported as furrow length in millimetres. Iris volume was quantified. Associations between furrow length and dynamic changes in iris volume were assessed using linear regression model. With pupil dilation, furrow length increased (15.84 mm) whereas iris volume decreased (−1.19 ± 0.66 mm3). Longer furrow length was associated with larger static iris volume, as well as smaller loss of iris volume with pupil dilation (β = −0.10, representing 0.1 mm3 less loss in iris volume per 10 mm increase in iris furrow length; P = 0.002, adjusted for age, gender and changes in pupil size). Our iris furrow length measurements are robust and intuitive. Eyes with longer furrows have larger iris volume and lose less volume during physiological pupil dilation. These findings highlight the potential for iris surface features as indicators of iris morphological behavior.
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Affiliation(s)
- Jacqueline Chua
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore.,Ophthalmology & Visual Sciences Academic Clinical Program (Eye ACP), Duke-NUS Medical School, Singapore, Singapore
| | - Sri Gowtham Thakku
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
| | - Tan Hung Pham
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore.,Department of Biomedical Engineering, National University of Singapore, Singapore, Singapore
| | - Ryan Lee
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore.,Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore, Singapore
| | - Tin A Tun
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
| | - Monisha E Nongpiur
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore.,Ophthalmology & Visual Sciences Academic Clinical Program (Eye ACP), Duke-NUS Medical School, Singapore, Singapore
| | - Marcus Chiang Lee Tan
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
| | - Tien Yin Wong
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore.,Ophthalmology & Visual Sciences Academic Clinical Program (Eye ACP), Duke-NUS Medical School, Singapore, Singapore.,Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore, Singapore
| | | | - Tin Aung
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore.,Ophthalmology & Visual Sciences Academic Clinical Program (Eye ACP), Duke-NUS Medical School, Singapore, Singapore.,Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore, Singapore
| | - Michael J A Girard
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore.,Department of Biomedical Engineering, National University of Singapore, Singapore, Singapore
| | - Ching-Yu Cheng
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore. .,Ophthalmology & Visual Sciences Academic Clinical Program (Eye ACP), Duke-NUS Medical School, Singapore, Singapore. .,Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore, Singapore.
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10
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Sharma S, Tun TA, Baskaran M, Atalay E, Thakku SG, Liang Z, Milea D, Strouthidis NG, Aung T, Girard MJ. Effect of acute intraocular pressure elevation on the minimum rim width in normal, ocular hypertensive and glaucoma eyes. Br J Ophthalmol 2017; 102:131-135. [PMID: 28490427 DOI: 10.1136/bjophthalmol-2017-310232] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [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: 01/24/2017] [Revised: 04/06/2017] [Accepted: 04/11/2017] [Indexed: 11/04/2022]
Abstract
BACKGROUND To estimate and compare changes in the Bruch's membrane opening-minimum rim width (BMO-MRW) and area in normal, ocular hypertensive and glaucoma eyes following acute elevations in intraocular pressure (IOP). METHODS The optic nerve heads (ONHs) of 104 subjects (31 normals, 20 ocular hypertension (OHT) and 53 with primary glaucoma) were imaged using Spectral-domain optical coherence tomography (OCT; Spectralis, Heidelberg Engineering, Germany). IOP was raised twice by applying a force (0.64 n then 0.9 n) to the anterior sclera using an ophthalmo-dynamometer. After each IOP increment, IOP was held constant, measured with a Tonopen (AVIA applanation tonometer, Reichert, Depew, New York, USA), and ONH was rescanned with OCT. In each OCT volume, BMO-MRW and area were calculated and at each IOP increment. RESULTS The baseline MRW was significantly smaller in glaucoma subjects (174.3±54.3 µm) compared with normal (287.4±42.2 µm, p<0.001) and OHT subjects (255.4±45.3 µm, p<0.001). MRW of glaucoma subjects was significantly thinner at the first and second IOP elevations than that at baseline (both p<0.01), but no significant change was noted in normal and OHT subjects. There was no significant change of BMO area at acute IOP elevations from baseline in all diagnoses (all p>0.05). CONCLUSION Acute IOP elevation leads to compression of the nerve fibre layers of neuroretinal rim in glaucoma subjects only without changing ONH size. This suggests that the neural and connective tissues at ONH level in glaucoma subjects are more susceptible to acute IOP episodes than OHT or normal controls.
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Affiliation(s)
- Sourabh Sharma
- Singapore National Eye Center, Singapore Eye Research Institute, Singapore, Singapore
| | - Tin A Tun
- Singapore National Eye Center, Singapore Eye Research Institute, Singapore, Singapore.,Ophthalmic Engineering & Innovation Laboratory, Department of Biomedical Engineering, National University of Singapore, Singapore, Singapore
| | - Mani Baskaran
- Singapore National Eye Center, Singapore Eye Research Institute, Singapore, Singapore.,Duke-NUS Graduate Medical School, National University of Singapore, Singapore, Singapore
| | - Eray Atalay
- Singapore National Eye Center, Singapore Eye Research Institute, Singapore, Singapore
| | - Sri Gowtham Thakku
- Singapore National Eye Center, Singapore Eye Research Institute, Singapore, Singapore
| | - Zhang Liang
- Ophthalmic Engineering & Innovation Laboratory, Department of Biomedical Engineering, National University of Singapore, Singapore, Singapore.,NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore, Singapore
| | - Dan Milea
- Singapore National Eye Center, Singapore Eye Research Institute, Singapore, Singapore.,Duke-NUS Graduate Medical School, National University of Singapore, Singapore, Singapore
| | - Nicholas G Strouthidis
- Singapore National Eye Center, Singapore Eye Research Institute, Singapore, Singapore.,NIHR Biomedical Research Centre, Moorfields Eye Hospital NHS Foundation Trust and UCL Institute of Ophthalmology, London, UK.,Discipline of Clinical Ophthalmology and Eye Health, University of Sydney, Sydney, NSW, Australia
| | - Tin Aung
- Singapore National Eye Center, Singapore Eye Research Institute, Singapore, Singapore.,Duke-NUS Graduate Medical School, National University of Singapore, Singapore, Singapore.,Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Michael Ja Girard
- Singapore National Eye Center, Singapore Eye Research Institute, Singapore, Singapore.,Ophthalmic Engineering & Innovation Laboratory, Department of Biomedical Engineering, National University of Singapore, Singapore, Singapore
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Koh V, Chua J, Shi Y, Thakku SG, Lee R, Nongpiur ME, Baskaran M, Kumar RS, Perera S, Aung T, Cheng CY. Association of iris crypts with acute primary angle closure. Br J Ophthalmol 2017; 101:1318-1322. [DOI: 10.1136/bjophthalmol-2016-309842] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2016] [Revised: 01/16/2017] [Accepted: 01/30/2017] [Indexed: 11/03/2022]
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12
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Gupta P, Thakku SG, Sabanayagam C, Tan G, Agrawal R, Cheung CMG, Lamoureux EL, Wong TY, Cheng CY. Characterisation of choroidal morphological and vascular features in diabetes and diabetic retinopathy. Br J Ophthalmol 2017; 101:1038-1044. [DOI: 10.1136/bjophthalmol-2016-309366] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Revised: 11/02/2016] [Accepted: 12/05/2016] [Indexed: 11/04/2022]
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Chuangsuwanich T, Birgersson KE, Thiery A, Thakku SG, Leo HL, Girard MJA. Factors Influencing Lamina Cribrosa Microcapillary Hemodynamics and Oxygen Concentrations. ACTA ACUST UNITED AC 2016; 57:6167-6179. [DOI: 10.1167/iovs.16-20167] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
| | - K. Erik Birgersson
- Department of Chemical Engineering, National University of Singapore, Singapore
| | - Alexandre Thiery
- Department of Statistics, National University of Singapore, Singapore
| | - Sri Gowtham Thakku
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore
| | - Hwa Liang Leo
- Department of Biomedical Engineering, National University of Singapore, Singapore
| | - Michaël J. A. Girard
- Department of Biomedical Engineering, National University of Singapore, Singapore 4Singapore Eye Research Institute, Singapore National Eye Centre, Singapore
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14
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Tun TA, Thakku SG, Png O, Baskaran M, Htoon HM, Sharma S, Nongpiur ME, Cheng CY, Aung T, Strouthidis NG, Girard MJA. Shape Changes of the Anterior Lamina Cribrosa in Normal, Ocular Hypertensive, and Glaucomatous Eyes Following Acute Intraocular Pressure Elevation. Invest Ophthalmol Vis Sci 2016; 57:4869-4877. [PMID: 27654413 DOI: 10.1167/iovs.16-19753] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Purpose The purpose of this study was to estimate and compare changes in anterior lamina cribrosa (LC) morphology in normal, ocular hypertensive (OHT), and glaucomatous eyes following acute elevations in intraocular pressure (IOP). Methods The optic nerve heads (ONHs) of 97 subjects (17 OHT, 19 primary open-angle glaucoma [POAG], 31 primary angle-closure glaucoma [PACG], and 30 normal subjects) were imaged using optical coherence tomography (OCT). Intraocular pressure was raised twice by applying forces to the anterior sclera, using an ophthalmodynamometer. After each IOP elevation, IOP was held constant and measured; each ONH was rescanned with OCT. In each OCT volume, the anterior LC was enhanced, delineated, and its global shape index (GSI) calculated and compared across groups. Results The baseline IOP was 17.5 ± 3.5 mm Hg and was increased to 38 ± 5.9 mm Hg and then to 46.5 ± 5.9 mm Hg. At the first IOP increment, mean GSI was significantly smaller than that at baseline in normal subjects and glaucoma subjects (P < 0.05) but not in OHT subjects (P = 0.12). For the second IOP increment, the mean GSI was significantly smaller than that at baseline in normal subjects and in OHT eyes (P < 0.05). After adjusting for age, sex, and baseline IOP, the LC of POAG eyes was found to be significantly more posteriorly curved than that of normal subjects (P = 0.04). Conclusions Acute IOP elevations altered anterior LC shape in a complex nonlinear fashion. The LC of POAG eyes was more cupped following acute IOP elevations compared to that of normal subjects.
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Affiliation(s)
- Tin A Tun
- Singapore Eye Research Institute and Singapore National Eye Centre Singapore
| | - Sri Gowtham Thakku
- Singapore Eye Research Institute and Singapore National Eye Centre Singapore
| | - Owen Png
- Singapore Eye Research Institute and Singapore National Eye Centre Singapore 2Duke-National University of Singapore Medical School, Singapore
| | - Mani Baskaran
- Singapore Eye Research Institute and Singapore National Eye Centre Singapore 2Duke-National University of Singapore Medical School, Singapore
| | - Hla M Htoon
- Singapore Eye Research Institute and Singapore National Eye Centre Singapore 2Duke-National University of Singapore Medical School, Singapore
| | - Sourabh Sharma
- Singapore Eye Research Institute and Singapore National Eye Centre Singapore
| | - Monisha E Nongpiur
- Singapore Eye Research Institute and Singapore National Eye Centre Singapore 2Duke-National University of Singapore Medical School, Singapore
| | - Ching-Yu Cheng
- Singapore Eye Research Institute and Singapore National Eye Centre Singapore 2Duke-National University of Singapore Medical School, Singapore 3Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Tin Aung
- Singapore Eye Research Institute and Singapore National Eye Centre Singapore 2Duke-National University of Singapore Medical School, Singapore 3Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Nicholas G Strouthidis
- Singapore Eye Research Institute and Singapore National Eye Centre Singapore 4National Institute of Health Research Biomedical Research Centre, Moorfields Eye Hospital, National Health Service Foundation Trust, and University College London (UCL) Institute of Ophthalmology, London, United Kingdom 5Discipline of Clinical Ophthalmology and Eye Health, University of Sydney, Sydney, New South Wales, Australia
| | - Michaël J A Girard
- Singapore Eye Research Institute and Singapore National Eye Centre Singapore 6Ophthalmic Engineering and Innovation Laboratory, Department of Biomedical Engineering, National University of Singapore, Singapore
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Tun TA, Chua J, Shi Y, Sidhartha E, Thakku SG, Shei W, Tan MCL, Quah JHM, Aung T, Cheng CY. Association of iris surface features with iris parameters assessed by swept-source optical coherence tomography in Asian eyes. Br J Ophthalmol 2016; 100:1682-1685. [PMID: 26994112 DOI: 10.1136/bjophthalmol-2015-308256] [Citation(s) in RCA: 10] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 02/28/2016] [Accepted: 03/03/2016] [Indexed: 11/04/2022]
Abstract
BACKGROUND/AIMS To characterise the association of iris surface features (crypts, furrows and colour) with iris volume and curvature assessed by swept-source optical coherence tomography (SSOCT) in Asian eyes. METHODS Iris crypts (by number and size) and furrows (by number and circumferential extent) were graded from iris photographs. Iris colour was measured by a customised algorithm written on MATLAB (MathWorks, Natick, Massachusetts, USA). The iris was imaged by SSOCT (SS-1000, CASIA, Tomey, Nagoya, Japan). The associations of surface features with iris parameters were analysed using a generalised estimating equation. RESULTS A total of 1704 subjects (3297 eyes) were included in the analysis. The majority was Chinese (86.4%), and 63.2% were females, and their mean age (±SD) was 61.4±6.6 years. After adjusting for age, sex, ethnicity, pupil size and corneal arcus, higher iris crypt grade was independently associated with smaller iris volume (β=-0.54, p<0.001), whereas darker irides and higher iris furrow grade were associated with larger iris volume (β=-0.041, p<0.001) and (β=0.233, p<0.001), respectively. Lighter coloured irides with more crypts and/or more furrows were also associated with less convexity (crypts: β=-0.003, p=0.03; furrows: β=-0.004, p=0.007; and colour: β=-0.001, p=0.005). CONCLUSIONS Iris surface features were highly correlated with iris volume and curvature. Irides with more crypts have a smaller volume; and darker irides with more furrows have a larger volume. Lighter irides with more crypts and/or furrows have less convexity.
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Affiliation(s)
- Tin A Tun
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
| | - Jacqueline Chua
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore.,Ophthalmology and Visual Sciences Academic Clinical Program, Duke-NUS Medical School, Singapore, Singapore
| | - Yuan Shi
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
| | - Elizabeth Sidhartha
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
| | - Sri Gowtham Thakku
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
| | - William Shei
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
| | - Marcus Chiang Lee Tan
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore.,Ophthalmology Service, Jurong Health Service, Singapore, Singapore
| | | | - Tin Aung
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore.,Ophthalmology and Visual Sciences Academic Clinical Program, Duke-NUS Medical School, Singapore, Singapore.,Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Ching-Yu Cheng
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore.,Ophthalmology and Visual Sciences Academic Clinical Program, Duke-NUS Medical School, Singapore, Singapore.,Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
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Thakku SG, Tham YC, Baskaran M, Mari JM, Strouthidis NG, Aung T, Cheng CY, Girard MJA. A Global Shape Index to Characterize Anterior Lamina Cribrosa Morphology and Its Determinants in Healthy Indian Eyes. Invest Ophthalmol Vis Sci 2015; 56:3604-14. [PMID: 26047047 DOI: 10.1167/iovs.15-16707] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
PURPOSE Lamina cribrosa (LC) morphology could be implicated in the progression of glaucoma. To date, no established, quantifiable parameter to assess LC shape in vivo exists. We aim to introduce a new global shape index for the anterior LC (LC-GSI) and to identify associations with ocular factors in a healthy Indian population. METHODS Optical coherence tomography (OCT) scans of the optic nerve head (ONH) were performed on 162 healthy subjects. Optic nerve head structures were delineated and a geometric characterization of anterior LC morphology was obtained by measuring curvature along 180 LC cross sections and representing it as LC-GSI ranging from -1 to +1. Lamina cribrosa depth and curvature were also reported. Linear regression was used to identify factors associated with LC morphology. RESULTS The typical healthy LC had a saddle rut-like appearance, with a central ridge visible in superior-inferior cross sections. A more prominent central ridge (larger LC-GSI) was associated with shorter axial length (P < 0.001), smaller Bruch's membrane opening (BMO) area (P = 0.020), smaller vertical cup-to-disc ratio (VCDR) (P = 0.007), and larger minimum rim width (BMO-MRW) (P = 0.001). A deeper LC was associated with male sex (P < 0.001), shorter axial length (P = 0.003), larger VCDR (P < 0.001), and smaller BMO-MRW (P = 0.002). Age and IOP were not significantly associated with LC morphology in healthy eyes. CONCLUSIONS The LC-GSI is a single index that quantifies overall LC shape in an intuitive way. Ocular determinants of LC-GSI in healthy eyes included risk factors for glaucoma (axial length, VCDR, and BMO-MRW), highlighting the potential role of LC morphological characterization in the diagnosis and monitoring of glaucoma.
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Affiliation(s)
- Sri Gowtham Thakku
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore
| | - Yih-Chung Tham
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore 2Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Mani Baskaran
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore 2Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 3Duke-National University of Singapore Graduate Medical School, Singapore
| | | | - Nicholas G Strouthidis
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore 5National Institute for Health Research Biomedical Research Centre, Moorfields Eye Hospital National Health Service Foundation Trust & University College London Institute of Ophtha
| | - Tin Aung
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore 2Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 3Duke-National University of Singapore Graduate Medical School, Singapore
| | - Ching-Yu Cheng
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore 2Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 3Duke-National University of Singapore Graduate Medical School, Singapore
| | - Michael J A Girard
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore 7Department of Biomedical Engineering, National University of Singapore, Singapore
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