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Tian H, Davis HC, Wong-Campos JD, Park P, Fan LZ, Gmeiner B, Begum S, Werley CA, Borja GB, Upadhyay H, Shah H, Jacques J, Qi Y, Parot V, Deisseroth K, Cohen AE. Video-based pooled screening yields improved far-red genetically encoded voltage indicators. Nat Methods 2023; 20:1082-1094. [PMID: 36624211 PMCID: PMC10329731 DOI: 10.1038/s41592-022-01743-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 11/28/2022] [Indexed: 01/11/2023]
Abstract
Video-based screening of pooled libraries is a powerful approach for directed evolution of biosensors because it enables selection along multiple dimensions simultaneously from large libraries. Here we develop a screening platform, Photopick, which achieves precise phenotype-activated photoselection over a large field of view (2.3 × 2.3 mm, containing >103 cells, per shot). We used the Photopick platform to evolve archaerhodopsin-derived genetically encoded voltage indicators (GEVIs) with improved signal-to-noise ratio (QuasAr6a) and kinetics (QuasAr6b). These GEVIs gave improved signals in cultured neurons and in live mouse brains. By combining targeted in vivo optogenetic stimulation with high-precision voltage imaging, we characterized inhibitory synaptic coupling between individual cortical NDNF (neuron-derived neurotrophic factor) interneurons, and excitatory electrical synapses between individual hippocampal parvalbumin neurons. The QuasAr6 GEVIs are powerful tools for all-optical electrophysiology and the Photopick approach could be adapted to evolve a broad range of biosensors.
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Affiliation(s)
- He Tian
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Hunter C Davis
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - J David Wong-Campos
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Pojeong Park
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Linlin Z Fan
- Department of Bioengineering, Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
| | - Benjamin Gmeiner
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Shahinoor Begum
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | | | | | | | | | | | - Yitong Qi
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Vicente Parot
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Institute for Biological and Medical Engineering, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Karl Deisseroth
- Department of Bioengineering, Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MA, USA
| | - Adam E Cohen
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.
- Department of Physics, Harvard University, Cambridge, MA, USA.
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2
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Desjardins-Lecavalier N, Annis MG, Nowakowski A, Kiepas A, Binan L, Roy J, Modica G, Hébert S, Kleinman CL, Siegel PM, Costantino S. Migration speed of captured breast cancer subpopulations correlates with metastatic fitness. J Cell Sci 2023; 136:jcs260835. [PMID: 37313743 PMCID: PMC10657211 DOI: 10.1242/jcs.260835] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 06/02/2023] [Indexed: 06/15/2023] Open
Abstract
The genetic alterations contributing to migration proficiency, a phenotypic hallmark of metastatic cells required for colonizing distant organs, remain poorly defined. Here, we used single-cell magneto-optical capture (scMOCa) to isolate fast cells from heterogeneous human breast cancer cell populations, based on their migratory ability alone. We show that captured fast cell subpopulations retain higher migration speed and focal adhesion dynamics over many generations as a result of a motility-related transcriptomic profile. Upregulated genes in isolated fast cells encoded integrin subunits, proto-cadherins and numerous other genes associated with cell migration. Dysregulation of several of these genes correlates with poor survival outcomes in people with breast cancer, and primary tumors established from fast cells generated a higher number of circulating tumor cells and soft tissue metastases in pre-clinical mouse models. Subpopulations of cells selected for a highly migratory phenotype demonstrated an increased fitness for metastasis.
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Affiliation(s)
- Nicolas Desjardins-Lecavalier
- Maisonneuve-Rosemont Hospital Research Center, 5415, boulevard de l'Assomption, Montréal, QC H1T 2M4, Canada
- Institut de genie biomedical, University of Montreal, Pavillon Paul-G.-Desmarais, 2960, chemin de la Tour, Montréal, QC H3T 1J4, Canada
| | - Matthew G. Annis
- Goodman Cancer Institute, McGill University, 1160 Pine Avenue West, Montreal, QC H3A 1A3, Canada
- Department of Medicine, McGill University, 1001 Decarie Boulevard, Montreal, QC H4A 3J1, Canada
| | - Alexander Nowakowski
- Goodman Cancer Institute, McGill University, 1160 Pine Avenue West, Montreal, QC H3A 1A3, Canada
- Department of Medicine, McGill University, 1001 Decarie Boulevard, Montreal, QC H4A 3J1, Canada
| | - Alexander Kiepas
- Cell Biology Section, National Institute of Dental and Craniofacial Research, National Institutes of Health Bethesda, MA 20892-4370, USA
| | - Loïc Binan
- Maisonneuve-Rosemont Hospital Research Center, 5415, boulevard de l'Assomption, Montréal, QC H1T 2M4, Canada
| | - Joannie Roy
- Maisonneuve-Rosemont Hospital Research Center, 5415, boulevard de l'Assomption, Montréal, QC H1T 2M4, Canada
| | - Graziana Modica
- Maisonneuve-Rosemont Hospital Research Center, 5415, boulevard de l'Assomption, Montréal, QC H1T 2M4, Canada
| | - Steven Hébert
- Lady Davis Institute, McGill University, Montréal, QC H3T 1E2, Canada
| | - Claudia L. Kleinman
- Lady Davis Institute, McGill University, Montréal, QC H3T 1E2, Canada
- Department of Human Genetics, McGill University, Montréal, QC H3T 1E2, Canada
| | - Peter M. Siegel
- Goodman Cancer Institute, McGill University, 1160 Pine Avenue West, Montreal, QC H3A 1A3, Canada
- Department of Medicine, McGill University, 1001 Decarie Boulevard, Montreal, QC H4A 3J1, Canada
| | - Santiago Costantino
- Maisonneuve-Rosemont Hospital Research Center, 5415, boulevard de l'Assomption, Montréal, QC H1T 2M4, Canada
- Department of Ophthalmology, University of Montreal, Pavillon Roger-Gaudry, Bureau S-700, 2900, boul. Édouard-Montpetit, Montréal, QC H3T 1J4, Canada
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3
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Desjardins-Lecavalier N, Modica G, Costantino S. Laser-Assisted Single-Cell Labeling and Capture. Methods Mol Biol 2023; 2614:357-368. [PMID: 36587135 DOI: 10.1007/978-1-0716-2914-7_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Single-cell technologies have become critical tools to understand and characterize the complex dynamics that govern biological systems, from embryonic development to cancer heterogeneity. In this context, identification and capture of live individual cells in heterogenous ensembles typically rely on genetic manipulations that encode fluorescent probes. However, a precise understanding of how several molecular components interact to yield the phenotype of interest is a prerequisite to distinguishing and isolating such target cells based on fluorescence alone. Indeed, cellular phenotypes associated with migration, shape, location, or intracellular protein distribution play critical and well-understood roles in cancer biology, but the technologies to tag and isolate cells based on information obtained from imaging are not readily available.Cell labeling via photobleaching (CLaP) and single-cell magneto-optical capture (scMOCa) represent convenient and cost-effective systems for labeling, capturing, and expanding single cells from a heterogenous population, without altering cellular physiology and therefore enabling not only transcriptomic profiling but also biological characterization of target cells. Both techniques allow capturing cells after observation and permit researchers to choose target cells based on information obtained from images. The implementation of these technologies only needs the lasers of a confocal microscope and low-cost, commercially available chemical reagents. Here, we describe a detailed protocol to set up and perform CLaP and scMOCa and highlight critical points for optimal performance.
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Affiliation(s)
| | - Graziana Modica
- Maisonneuve-Rosemont Hospital Research Center, Montreal, QC, Canada
| | - Santiago Costantino
- Maisonneuve-Rosemont Hospital Research Center, Montreal, QC, Canada. .,Department of Ophthalmology, University of Montreal, Montreal, QC, Canada.
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4
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Wang X, Wang Z, Yu C, Ge Z, Yang W. Advances in precise single-cell capture for analysis and biological applications. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2022; 14:3047-3063. [PMID: 35946358 DOI: 10.1039/d2ay00625a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Cells are the basic structural and functional units of living organisms. However, conventional cell analysis only averages millions of cell populations, and some important information is lost. It is essential to quantitatively characterize the physiology and pathology of single-cell activities. Precise single-cell capture is an extremely challenging task during cell sample preparation. In this review, we summarize the category of technologies to capture single cells precisely with a focus on the latest development in the last five years. Each technology has its own set of benefits and specific challenges, which provide opportunities for researchers in different fields. Accordingly, we introduce the applications of captured single cells in cancer diagnosis, analysis of metabolism and secretion, and disease treatment. Finally, some perspectives are provided on the current development trends, future research directions, and challenges of single-cell capture.
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Affiliation(s)
- Xiaowen Wang
- School of Electromechanical and Automotive Engineering, Yantai University, Yantai 264005, China.
| | - Zhen Wang
- School of Electromechanical and Automotive Engineering, Yantai University, Yantai 264005, China.
| | - Chang Yu
- College of Computer Science, Chongqing University, Chongqing 400000, China
| | - Zhixing Ge
- State Key Laboratory of Robotics, Shenyang Institute of Automation, Chinese Academy of Sciences, Shenyang 110016, China.
| | - Wenguang Yang
- School of Electromechanical and Automotive Engineering, Yantai University, Yantai 264005, China.
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5
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Kanfer G, Sarraf SA, Maman Y, Baldwin H, Dominguez-Martin E, Johnson KR, Ward ME, Kampmann M, Lippincott-Schwartz J, Youle RJ. Image-based pooled whole-genome CRISPRi screening for subcellular phenotypes. J Cell Biol 2021; 220:e202006180. [PMID: 33464298 PMCID: PMC7816647 DOI: 10.1083/jcb.202006180] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 10/17/2020] [Accepted: 12/02/2020] [Indexed: 12/13/2022] Open
Abstract
Genome-wide CRISPR screens have transformed our ability to systematically interrogate human gene function, but are currently limited to a subset of cellular phenotypes. We report a novel pooled screening approach for a wider range of cellular and subtle subcellular phenotypes. Machine learning and convolutional neural network models are trained on the subcellular phenotype to be queried. Genome-wide screening then utilizes cells stably expressing dCas9-KRAB (CRISPRi), photoactivatable fluorescent protein (PA-mCherry), and a lentiviral guide RNA (gRNA) pool. Cells are screened by using microscopy and classified by artificial intelligence (AI) algorithms, which precisely identify the genetically altered phenotype. Cells with the phenotype of interest are photoactivated and isolated via flow cytometry, and the gRNAs are identified by sequencing. A proof-of-concept screen accurately identified PINK1 as essential for Parkin recruitment to mitochondria. A genome-wide screen identified factors mediating TFEB relocation from the nucleus to the cytosol upon prolonged starvation. Twenty-one of the 64 hits called by the neural network model were independently validated, revealing new effectors of TFEB subcellular localization. This approach, AI-photoswitchable screening (AI-PS), offers a novel screening platform capable of classifying a broad range of mammalian subcellular morphologies, an approach largely unattainable with current methodologies at genome-wide scale.
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Affiliation(s)
- Gil Kanfer
- Biochemistry Section, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA
| | - Shireen A. Sarraf
- Biochemistry Section, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD
| | - Yaakov Maman
- The Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Heather Baldwin
- Biochemistry Section, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD
| | - Eunice Dominguez-Martin
- Biochemistry Section, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD
| | - Kory R. Johnson
- Bioinformatics Section, Information Technology Program, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD
| | - Michael E. Ward
- Inherited Neurodegenerative Diseases Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD
| | - Martin Kampmann
- Institute for Neurodegenerative Diseases, Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA
| | | | - Richard J. Youle
- Biochemistry Section, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD
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6
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Lee J, Liu Z, Suzuki PH, Ahrens JF, Lai S, Lu X, Guan S, St-Pierre F. Versatile phenotype-activated cell sorting. SCIENCE ADVANCES 2020; 6:6/43/eabb7438. [PMID: 33097540 PMCID: PMC7608836 DOI: 10.1126/sciadv.abb7438] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 09/10/2020] [Indexed: 05/02/2023]
Abstract
Unraveling the genetic and epigenetic determinants of phenotypes is critical for understanding and re-engineering biology and would benefit from improved methods to separate cells based on phenotypes. Here, we report SPOTlight, a versatile high-throughput technique to isolate individual yeast or human cells with unique spatiotemporal profiles from heterogeneous populations. SPOTlight relies on imaging visual phenotypes by microscopy, precise optical tagging of single target cells, and retrieval of tagged cells by fluorescence-activated cell sorting. To illustrate SPOTlight's ability to screen cells based on temporal properties, we chose to develop a photostable yellow fluorescent protein for extended imaging experiments. We screened 3 million cells expressing mutagenesis libraries and identified a bright new variant, mGold, that is the most photostable yellow fluorescent protein reported to date. We anticipate that the versatility of SPOTlight will facilitate its deployment to decipher the rules of life, understand diseases, and engineer new molecules and cells.
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Affiliation(s)
- Jihwan Lee
- Systems, Synthetic, and Physical Biology Program, Rice University, Houston, TX 77005, USA
| | - Zhuohe Liu
- Department of Electrical and Computer Engineering, Rice University, Houston, TX 77005, USA
| | - Peter H Suzuki
- Department of Bioengineering, Rice University, Houston, TX 77005, USA
| | - John F Ahrens
- Department of Bioengineering, Rice University, Houston, TX 77005, USA
| | - Shujuan Lai
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| | - Xiaoyu Lu
- Systems, Synthetic, and Physical Biology Program, Rice University, Houston, TX 77005, USA
| | - Sihui Guan
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| | - François St-Pierre
- Systems, Synthetic, and Physical Biology Program, Rice University, Houston, TX 77005, USA.
- Department of Electrical and Computer Engineering, Rice University, Houston, TX 77005, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
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7
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Hasle N, Cooke A, Srivatsan S, Huang H, Stephany JJ, Krieger Z, Jackson D, Tang W, Pendyala S, Monnat RJ, Trapnell C, Hatch EM, Fowler DM. High-throughput, microscope-based sorting to dissect cellular heterogeneity. Mol Syst Biol 2020; 16:e9442. [PMID: 32500953 PMCID: PMC7273721 DOI: 10.15252/msb.20209442] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 04/23/2020] [Accepted: 04/29/2020] [Indexed: 12/24/2022] Open
Abstract
Microscopy is a powerful tool for characterizing complex cellular phenotypes, but linking these phenotypes to genotype or RNA expression at scale remains challenging. Here, we present Visual Cell Sorting, a method that physically separates hundreds of thousands of live cells based on their visual phenotype. Automated imaging and phenotypic analysis directs selective illumination of Dendra2, a photoconvertible fluorescent protein expressed in live cells; these photoactivated cells are then isolated using fluorescence-activated cell sorting. First, we use Visual Cell Sorting to assess hundreds of nuclear localization sequence variants in a pooled format, identifying variants that improve nuclear localization and enabling annotation of nuclear localization sequences in thousands of human proteins. Second, we recover cells that retain normal nuclear morphologies after paclitaxel treatment, and then derive their single-cell transcriptomes to identify pathways associated with paclitaxel resistance in cancers. Unlike alternative methods, Visual Cell Sorting depends on inexpensive reagents and commercially available hardware. As such, it can be readily deployed to uncover the relationships between visual cellular phenotypes and internal states, including genotypes and gene expression programs.
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Affiliation(s)
- Nicholas Hasle
- Department of Genome SciencesUniversity of WashingtonSeattleWAUSA
| | | | - Sanjay Srivatsan
- Department of Genome SciencesUniversity of WashingtonSeattleWAUSA
| | - Heather Huang
- Divisions of Basic Sciences and Human BiologyFred Hutchinson Cancer Research CenterSeattleWAUSA
| | - Jason J Stephany
- Department of Genome SciencesUniversity of WashingtonSeattleWAUSA
| | - Zachary Krieger
- Department of Genome SciencesUniversity of WashingtonSeattleWAUSA
| | - Dana Jackson
- Department of Genome SciencesUniversity of WashingtonSeattleWAUSA
| | - Weiliang Tang
- Department of PathologyUniversity of WashingtonSeattleWAUSA
| | - Sriram Pendyala
- Department of Genome SciencesUniversity of WashingtonSeattleWAUSA
| | - Raymond J Monnat
- Department of Genome SciencesUniversity of WashingtonSeattleWAUSA
- Department of PathologyUniversity of WashingtonSeattleWAUSA
| | - Cole Trapnell
- Department of Genome SciencesUniversity of WashingtonSeattleWAUSA
| | - Emily M Hatch
- Divisions of Basic Sciences and Human BiologyFred Hutchinson Cancer Research CenterSeattleWAUSA
| | - Douglas M Fowler
- Department of Genome SciencesUniversity of WashingtonSeattleWAUSA
- Department of BioengineeringUniversity of WashingtonSeattleWAUSA
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8
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Binan L, Roy J, Costantino S. Opto-magnetic Selection and Isolation of Single Cells. Bio Protoc 2019; 9:e3428. [PMID: 33654925 DOI: 10.21769/bioprotoc.3428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 09/16/2019] [Accepted: 10/22/2019] [Indexed: 11/02/2022] Open
Abstract
Capturing single cells from large heterogenous populations based solely on observable traits is necessary for many cell biology applications and remains a major technical challenge. The protocol we present allows the isolation of viable and metabolically active cells selected for their shape, migration speed, contact to other cells, or intracellular protein localization. We previously introduced a method termed Cell Labeling via Photobleaching (CLaP) for the efficient tagging of cells chosen for visual criteria. Here we describe a new protocol for capturing such cells using ferromagnetic beads termed single-cell magneto-optical capture (scMOCa). This technology is especially useful when the number of target cells represents an extremely low fraction of the total population (potentially one single cell), a situation in which conventional sorting techniques like fluorescent or magnetic activated cell sorting (F/MACS) cannot provide satisfactory results in terms of capture efficiency and specificity. scMOCa uses the lasers of a confocal microscope to photobleach and crosslink biotin-4-fluorecein molecules to cell membranes. Streptavidin coated magnetic beads then adhere to biotin moieties and a magnet allows the capture of illuminated cells. By precisely controlling liquid volumes and spacing between the different parts of a simple setup, high cell selectivity and capture efficacy can be achieved. scMOCA allows visual selection and isolation of any number of cells in a microscopy field and captured cells remain viable to generate new colonies of chosen phenotypes for downstream analyses.
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Affiliation(s)
- Loïc Binan
- Research center, Maisonneuve-Rosemont Hospital, Montreal, Canada.,Department of ophthalmology, University of Montreal, Montreal, Canada
| | - Joannie Roy
- Research center, Maisonneuve-Rosemont Hospital, Montreal, Canada
| | - Santiago Costantino
- Research center, Maisonneuve-Rosemont Hospital, Montreal, Canada.,Department of ophthalmology, University of Montreal, Montreal, Canada
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