1
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Lang S, Fletcher DA, Petit AP, Luise N, Fyfe P, Zuccotto F, Porter D, Hope A, Bellany F, Kerr C, Mackenzie CJ, Wyatt PG, Gray DW. Application of an NMR/Crystallography Fragment Screening Platform for the Assessment and Rapid Discovery of New HIV-CA Binding Fragments. ChemMedChem 2024:e202400025. [PMID: 38581280 DOI: 10.1002/cmdc.202400025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 04/05/2024] [Accepted: 04/05/2024] [Indexed: 04/08/2024]
Abstract
Identification and assessment of novel targets is essential to combat drug resistance in the treatment of HIV/AIDS. HIV Capsid (HIV-CA), the protein playing a major role in both the early and late stages of the viral life cycle, has emerged as an important target. We have applied an NMR fragment screening platform and identified molecules that bind to the N-terminal domain (NTD) of HIV-CA at a site close to the interface with the C-terminal domain (CTD). Using X-ray crystallography, we have been able to obtain crystal structures to identify the binding mode of these compounds. This allowed for rapid progression of the initial, weak binding, fragment starting points to compounds 37 and 38, which have 19F-pKi values of 5.3 and 5.4 respectively.
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Affiliation(s)
- Stuart Lang
- Cresset Discovery, New Cambridge House, Bassingbourn Road, Litlington, Cambridgeshire, SG80SSS
| | - Daniel A Fletcher
- BioAscent Discovery Ltd, Bo'Ness Road, Newhouse, Lanarkshire, ML1 5UH
| | | | - Nicola Luise
- Alira Health, Av. De Josep Tarradellas, 123, 7th Floor, 08029, Barcelona, Spain
| | - Paul Fyfe
- Drug Discovery Unit, University of Dundee, Dow Street, Dundee, DD1 5EH
| | - Fabio Zuccotto
- Vertex Pharmaceuticals (Europe) Ltd, 86-88, Jubilee Avenue, Milton Park, Abingdon, Oxfordshire, OX14 4RW
| | - David Porter
- Evotec (UK) Ltd, Dorothy Crowfoot Hodgkin Campus, 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire, OX14 4RZ
| | - Anthony Hope
- Drug Discovery Unit, University of Dundee, Dow Street, Dundee, DD1 5EH
| | - Fiona Bellany
- Drug Discovery Unit, University of Dundee, Dow Street, Dundee, DD1 5EH
| | - Catrina Kerr
- Drug Discovery Unit, University of Dundee, Dow Street, Dundee, DD1 5EH
| | | | - Paul G Wyatt
- Sitala Bio Ltd, Unit D6, Grain House Mill Court, Great Shelford, Cambridge, CB22 5LD
| | - David W Gray
- Drug Discovery Unit, University of Dundee, Dow Street, Dundee, DD1 5EH
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2
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Takatori SC, Son S, Lee DSW, Fletcher DA. Engineered molecular sensors for quantifying cell surface crowding. Proc Natl Acad Sci U S A 2023; 120:e2219778120. [PMID: 37186825 DOI: 10.1073/pnas.2219778120] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023] Open
Abstract
Cells mediate interactions with the extracellular environment through a crowded assembly of transmembrane proteins, glycoproteins and glycolipids on their plasma membrane. The extent to which surface crowding modulates the biophysical interactions of ligands, receptors, and other macromolecules is poorly understood due to the lack of methods to quantify surface crowding on native cell membranes. In this work, we demonstrate that physical crowding on reconstituted membranes and live cell surfaces attenuates the effective binding affinity of macromolecules such as IgG antibodies in a surface crowding-dependent manner. We combine experiment and simulation to design a crowding sensor based on this principle that provides a quantitative readout of cell surface crowding. Our measurements reveal that surface crowding decreases IgG antibody binding by 2 to 20 fold in live cells compared to a bare membrane surface. Our sensors show that sialic acid, a negatively charged monosaccharide, contributes disproportionately to red blood cell surface crowding via electrostatic repulsion, despite occupying only ~1% of the total cell membrane by mass. We also observe significant differences in surface crowding for different cell types and find that expression of single oncogenes can both increase and decrease crowding, suggesting that surface crowding may be an indicator of both cell type and state. Our high-throughput, single-cell measurement of cell surface crowding may be combined with functional assays to enable further biophysical dissection of the cell surfaceome.
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Affiliation(s)
- Sho C Takatori
- Department of Bioengineering, University of California, Berkeley, CA 94720
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106
| | - Sungmin Son
- Department of Bioengineering, University of California, Berkeley, CA 94720
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Daniel S W Lee
- Department of Bioengineering, University of California, Berkeley, CA 94720
| | - Daniel A Fletcher
- Department of Bioengineering, University of California, Berkeley, CA 94720
- University of California, Berkeley/University of California, San Francisco Graduate Group in Bioengineering, Berkeley, CA 94720
- Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
- Chan Zuckerberg Biohub, San Francisco, CA 94158
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3
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Bowman GR, Cox SJ, Dellago C, DuBay KH, Eaves JD, Fletcher DA, Frechette LB, Grünwald M, Klymko K, Ku J, Omar A, Rabani E, Reichman DR, Rogers JR, Rosnik AM, Rotskoff GM, Schneider AR, Schwierz N, Sivak DA, Vaikuntanathan S, Whitelam S, Widmer-Cooper A. Remembering the Work of Phillip L. Geissler: A Coda to His Scientific Trajectory. Annu Rev Phys Chem 2023; 74:1-27. [PMID: 36719975 DOI: 10.1146/annurev-physchem-101422-030127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Phillip L. Geissler made important contributions to the statistical mechanics of biological polymers, heterogeneous materials, and chemical dynamics in aqueous environments. He devised analytical and computational methods that revealed the underlying organization of complex systems at the frontiers of biology, chemistry, and materials science. In this retrospective we celebrate his work at these frontiers. Expected final online publication date for the Annual Review of Physical Chemistry, Volume 74 is April 2023. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Gregory R Bowman
- Bioengineering, Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Stephen J Cox
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | | | - Kateri H DuBay
- Department of Chemistry, University of Virginia, Charlottesville, Virginia, USA;
| | - Joel D Eaves
- Department of Chemistry, University of Colorado Boulder, Boulder, Colorado, USA
| | - Daniel A Fletcher
- Department of Bioengineering and Biophysics Program, University of California, Berkeley, California, USA.,Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California, USA.,Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Layne B Frechette
- Martin A. Fisher School of Physics, Brandeis University, Waltham, Massachusetts, USA;
| | - Michael Grünwald
- Department of Chemistry, University of Utah, Salt Lake City, Utah, USA
| | - Katherine Klymko
- National Energy Research Scientific Computing Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - JiYeon Ku
- R&D Center, Eloi Materials (EML) Co., Ltd, Suwon, Republic of Korea
| | - Ahmad Omar
- Department of Materials Science and Engineering, University of California, Berkeley, California, USA
| | - Eran Rabani
- Department of Chemistry, University of California, Berkeley, California, USA.,Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA.,The Raymond and Beverly Sackler Center of Computational Molecular and Materials Science, Tel Aviv University, Tel Aviv, Israel
| | | | - Julia R Rogers
- Department of Systems Biology, Columbia University, New York, NY, USA;
| | | | - Grant M Rotskoff
- Department of Chemistry, Stanford University, Stanford, California, USA;
| | | | - Nadine Schwierz
- Institute of Physics, University of Augsburg, Augsburg, Germany
| | - David A Sivak
- Department of Physics, Simon Fraser University, Burnaby, British Columbia, Canada;
| | | | - Stephen Whitelam
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California, USA;
| | - Asaph Widmer-Cooper
- School of Chemistry, The University of Sydney, Sydney, New South Wales, Australia
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Coulibaly JT, Silue KD, Armstrong M, Díaz de León Derby M, D’Ambrosio MV, Fletcher DA, Keiser J, Fisher K, Andrews JR, Bogoch II. High Sensitivity of Mobile Phone Microscopy Screening for Schistosoma haematobium in Azaguié, Côte d'Ivoire. Am J Trop Med Hyg 2023; 108:41-43. [PMID: 36509050 PMCID: PMC9833070 DOI: 10.4269/ajtmh.22-0527] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 10/02/2022] [Indexed: 12/15/2022] Open
Abstract
Schistosomiasis infections continue to impact African settings disproportionately, and there is an urgent need for novel tools to evaluate infection control and elimination strategies at the community level. Mobile phone microscopes are portable and semiautomated devices with multiple applications for screening neglected tropical diseases. In a community-based schistosomiasis screening program in Azaguié, Côte d'Ivoire, mobile phone microscopy demonstrated a sensitivity of 85.7% (95% CI: 69.7-95.2%) and specificity of 93.3% (95% CI: 87.7-96.9%) for Schistosoma haematobium identification compared with conventional light microscopy, and 95% sensitivity (95% CI: 74.1-99.8%) with egg concentrations of five or more per 10 mL of urine. Mobile phone microscopy is a promising tool for schistosomiasis control and elimination efforts.
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Affiliation(s)
- Jean T. Coulibaly
- Unité de Formation et de Recherche Biosciences, Université Félix Houphouët-Boigny, Abidjan, Côte d’Ivoire;,Centre Suisse de Recherches Scientifiques en Côte d’Ivoire, Abidjan, Côte d’Ivoire
| | - Kigbafori D. Silue
- Unité de Formation et de Recherche Biosciences, Université Félix Houphouët-Boigny, Abidjan, Côte d’Ivoire;,Centre Suisse de Recherches Scientifiques en Côte d’Ivoire, Abidjan, Côte d’Ivoire
| | - Maxim Armstrong
- Department of Bioengineering, University of California, Berkeley, Berkeley, California
| | | | - Michael V. D’Ambrosio
- Department of Bioengineering, University of California, Berkeley, Berkeley, California
| | - Daniel A. Fletcher
- Department of Bioengineering, University of California, Berkeley, Berkeley, California;,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, Berkeley, California;,Chan Zuckerberg Biohub, San Francisco, California
| | - Jennifer Keiser
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland;,University of Basel, Basel, Switzerland
| | - Karla Fisher
- Divisions of General Internal Medicine and Infectious Diseases, Toronto General Hospital, University Health Network, Toronto, Canada
| | - Jason R. Andrews
- Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, California
| | - Isaac I. Bogoch
- Divisions of General Internal Medicine and Infectious Diseases, Toronto General Hospital, University Health Network, Toronto, Canada;,Department of Medicine, University of Toronto, Toronto, Canada,Address correspondence to Isaac I. Bogoch, Divisions of General Internal Medicine and Infectious Diseases, Toronto General Hospital, 14EN 209, 200 Elizabeth St., Toronto M5G 2C4, ON, Canada. E-mail:
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5
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Son S, Fletcher DA. Measurement of Molecular Height Using Cell Surface Optical Profilometry (CSOP). Methods Mol Biol 2023; 2654:113-122. [PMID: 37106178 DOI: 10.1007/978-1-0716-3135-5_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] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
The plasma membrane of cells is covered by proteins, glycoproteins, and glycolipids with molecular heights ranging from just a few nanometers to hundreds of nanometers. Formation of cell-cell contacts and signal transduction by individual receptors can be dependent on both the average height of a cell's glycocalyx and the specific height of individual receptors, sometimes with nanometer-scale sensitivity. While super-resolution imaging techniques allow molecular distances to be measured with the sub-diffraction limited resolution, typically 10 nm in the lateral direction and 100 nm in the axial direction, measurements of molecular heights at the single nanometer scale on native cell membranes have been difficult to obtain. Cell surface optical profilometry (CSOP) is a simple and rapid method that achieves nanometer height resolution by localizing fluorophores at the tip and base of cell surface molecules and determining their separation with high precision by radially averaging across many molecules. Here we describe how to make CSOP measurements of multi-domain proteins on model membrane surfaces as well as native cell surfaces.
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Affiliation(s)
- Sungmin Son
- Department of Bioengineering and Biophysics Program, University of California, Berkeley, CA, USA
- Department of Bio and Brain Engineering, KAIST, Daejeon, Republic of Korea
| | - Daniel A Fletcher
- Department of Bioengineering and Biophysics Program, University of California, Berkeley, CA, USA.
- Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
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6
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Kumar A, Ali FS, Stevens VM, Melo JS, Prajna NV, Lalitha P, Srinivasan M, Bhandari G, Bhandari S, Maamari RN, Fletcher DA, Lietman TM, Keenan JD. Smartphone-based Anterior Segment Imaging: A Comparative Diagnostic Accuracy Study of a Potential Tool for Blindness Prevalence Surveys. Ophthalmic Epidemiol 2022; 29:491-498. [PMID: 34607500 PMCID: PMC8977419 DOI: 10.1080/09286586.2021.1980589] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 07/07/2021] [Accepted: 09/08/2021] [Indexed: 10/20/2022]
Abstract
PURPOSE To determine if smartphone photography could be a useful adjunct to blindness prevalence surveys by providing an accurate diagnosis of corneal opacity. METHODS A total of 174 patients with infectious keratitis who had undergone corneal culturing over the past 5 years were enrolled in a diagnostic accuracy study at an eye hospital in South India. Both eyes had an ophthalmologist-performed slit lamp examination, followed by anterior segment photography with a handheld digital single lens reflex (SLR) camera and a smartphone camera coupled to an external attachment that provided magnification and illumination. The diagnostic accuracy of photography was assessed relative to slit lamp examination. RESULTS In total, 90 of 174 enrolled participants had a corneal opacity in the cultured eye and no opacity in the contralateral eye, and did not have a penetrating keratoplasty or missing photographs. Relative to slit lamp examination, the sensitivity of corneal opacity diagnosis was 68% (95%CI 58-77%) using the smartphone's default settings and 59% (95%CI 49-69%) using the SLR, and the specificity was 97% (95%CI 93-100%) for the smartphone and 97% (95%CI 92-100%) for the SLR. The sensitivity of smartphone-based corneal opacity diagnosis was higher for larger scars (81% for opacities 2 mm in diameter or larger), more visually significant scars (100% for eyes with visual acuity worse than 20/400), and more recent scars (85% for eyes cultured in the past 12 months). CONCLUSION The diagnostic performance of a smartphone coupled to an external attachment, while somewhat variable, demonstrated high specificity and high sensitivity for all but the smallest opacities.
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Affiliation(s)
- Ashish Kumar
- Department of Cornea and Refractive Surgery, Aravind Eye Hospital Madurai, India
| | - Ferhina S Ali
- Department of Ophthalmology, University of California, San Francisco, USA
| | - Valerie M Stevens
- Francis I. Proctor Foundation, University of California, San Francisco, USA
| | - Jason S Melo
- Francis I. Proctor Foundation, University of California, San Francisco, USA
| | - N Venkatesh Prajna
- Department of Cornea and Refractive Surgery, Aravind Eye Hospital Madurai, India
| | - Prajna Lalitha
- Department of Ocular Microbiology, Aravind Eye Hospital Madurai, India
| | - Muthiah Srinivasan
- Department of Cornea and Refractive Surgery, Aravind Eye Hospital Madurai, India
| | | | | | - Robi N Maamari
- Francis I. Proctor Foundation, University of California, San Francisco, USA
- Department of Bioengineering and Biophysics Program, University of California, Berkeley, USA
| | - Daniel A Fletcher
- Department of Bioengineering and Biophysics Program, University of California, Berkeley, USA
| | - Thomas M Lietman
- Department of Ophthalmology, University of California, San Francisco, USA
- Francis I. Proctor Foundation, University of California, San Francisco, USA
- Department of Epidemiology & Biostatistics, University of California, San Francisco, USA
- Institute for Global Health, University of California, San Francisco, USA
| | - Jeremy D Keenan
- Department of Ophthalmology, University of California, San Francisco, USA
- Francis I. Proctor Foundation, University of California, San Francisco, USA
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7
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Chandrasekaran SS, Agrawal S, Fanton A, Jangid AR, Charrez B, Escajeda AM, Son S, Mcintosh R, Tran H, Bhuiya A, de León Derby MD, Switz NA, Armstrong M, Harris AR, Prywes N, Lukarska M, Biering SB, Smock DCJ, Mok A, Knott GJ, Dang Q, Van Dis E, Dugan E, Kim S, Liu TY, Moehle EA, Kogut K, Eskenazi B, Harris E, Stanley SA, Lareau LF, Tan MX, Fletcher DA, Doudna JA, Savage DF, Hsu PD. Rapid detection of SARS-CoV-2 RNA in saliva via Cas13. Nat Biomed Eng 2022; 6:944-956. [PMID: 35953650 PMCID: PMC10367768 DOI: 10.1038/s41551-022-00917-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 06/30/2022] [Indexed: 11/10/2022]
Abstract
Rapid nucleic acid testing is central to infectious disease surveillance. Here, we report an assay for rapid COVID-19 testing and its implementation in a prototype microfluidic device. The assay, which we named DISCoVER (for diagnostics with coronavirus enzymatic reporting), involves extraction-free sample lysis via shelf-stable and low-cost reagents, multiplexed isothermal RNA amplification followed by T7 transcription, and Cas13-mediated cleavage of a quenched fluorophore. The device consists of a single-use gravity-driven microfluidic cartridge inserted into a compact instrument for automated running of the assay and readout of fluorescence within 60 min. DISCoVER can detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in saliva with a sensitivity of 40 copies μl-1, and was 94% sensitive and 100% specific when validated (against quantitative PCR) using total RNA extracted from 63 nasal-swab samples (33 SARS-CoV-2-positive, with cycle-threshold values of 13-35). The device correctly identified all tested clinical saliva samples (10 SARS-CoV-2-positive out of 13, with cycle-threshold values of 23-31). Rapid point-of-care nucleic acid testing may broaden the use of molecular diagnostics.
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Affiliation(s)
- Sita S Chandrasekaran
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA.,Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA.,University of California, Berkeley-University of California, San Francisco Graduate Program in Bioengineering, Berkeley, CA, USA
| | - Shreeya Agrawal
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA.,Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Alison Fanton
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA.,Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA.,University of California, Berkeley-University of California, San Francisco Graduate Program in Bioengineering, Berkeley, CA, USA
| | - Aditya R Jangid
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA.,Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Bérénice Charrez
- University of California, Berkeley-University of California, San Francisco Graduate Program in Bioengineering, Berkeley, CA, USA
| | | | - Sungmin Son
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | | | | | - Abdul Bhuiya
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA.,University of California, Berkeley-University of California, San Francisco Graduate Program in Bioengineering, Berkeley, CA, USA
| | - María Díaz de León Derby
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA.,University of California, Berkeley-University of California, San Francisco Graduate Program in Bioengineering, Berkeley, CA, USA
| | - Neil A Switz
- Department of Physics and Astronomy, San José State University, San José, CA, USA
| | - Maxim Armstrong
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Andrew R Harris
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | - Noam Prywes
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Maria Lukarska
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA.,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Scott B Biering
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Dylan C J Smock
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA.,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Amanda Mok
- Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Gavin J Knott
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA.,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.,Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - Qi Dang
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Erik Van Dis
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Eli Dugan
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA.,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Shin Kim
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA.,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Tina Y Liu
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA.,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | | | - Erica A Moehle
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Katherine Kogut
- Center for Environmental Research and Community Health (CERCH), School of Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Brenda Eskenazi
- Center for Environmental Research and Community Health (CERCH), School of Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Eva Harris
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Sarah A Stanley
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.,School of Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Liana F Lareau
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA.,Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | | | - Daniel A Fletcher
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | - Jennifer A Doudna
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA. .,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. .,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA. .,Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, USA. .,Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA. .,Gladstone Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA, USA.
| | - David F Savage
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.
| | - Patrick D Hsu
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA. .,Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA. .,Arc Institute, Palo Alto, CA, USA.
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8
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Li TD, Bieling P, Weichsel J, Mullins RD, Fletcher DA. The molecular mechanism of load adaptation by branched actin networks. eLife 2022; 11:73145. [PMID: 35748355 PMCID: PMC9328761 DOI: 10.7554/elife.73145] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 06/07/2022] [Indexed: 11/13/2022] Open
Abstract
Branched actin networks are self-assembling molecular motors that move biological membranes and drive many important cellular processes, including phagocytosis, endocytosis, and pseudopod protrusion. When confronted with opposing forces, the growth rate of these networks slows and their density increases, but the stoichiometry of key components does not change. The molecular mechanisms governing this force response are not well understood, so we used single-molecule imaging and AFM cantilever deflection to measure how applied forces affect each step in branched actin network assembly. Although load forces are observed to increase the density of growing filaments, we find that they actually decrease the rate of filament nucleation due to inhibitory interactions between actin filament ends and nucleation promoting factors. The force-induced increase in network density turns out to result from an exponential drop in the rate constant that governs filament capping. The force dependence of filament capping matches that of filament elongation and can be explained by expanding Brownian Ratchet theory to cover both processes. We tested a key prediction of this expanded theory by measuring the force-dependent activity of engineered capping protein variants and found that increasing the size of the capping protein increases its sensitivity to applied forces. In summary, we find that Brownian Ratchets underlie not only the ability of growing actin filaments to generate force but also the ability of branched actin networks to adapt their architecture to changing loads.
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Affiliation(s)
- Tai-De Li
- Advanced Science Research Center, City University of New York, New York, United States
| | - Peter Bieling
- Department of Systemic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Julian Weichsel
- Department of Chemistry, University of California, Berkeley, Berkeley, United States
| | - R Dyche Mullins
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States
| | - Daniel A Fletcher
- Department of Bioengineering and Biophysics, University of California, Berkeley, Berkeley, United States
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9
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Han BG, Armstrong M, Fletcher DA, Glaeser RM. Perspective: Biochemical and Physical Constraints Associated With Preparing Thin Specimens for Single-Particle Cryo-EM. Front Mol Biosci 2022; 9:864829. [PMID: 35573724 PMCID: PMC9100935 DOI: 10.3389/fmolb.2022.864829] [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] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 03/25/2022] [Indexed: 11/13/2022] Open
Abstract
While many aspects of single-particle electron cryo-microscopy (cryo-EM) of biological macromolecules have reached a sophisticated level of development, this is not yet the case when it comes to preparing thin samples on specimen grids. As a result, there currently is considerable interest in achieving better control of both the sample thickness and the amount of area that is useful, but this is only one aspect in which improvement is needed. This Perspective addresses the further need to prevent the macromolecular particles from making contact with the air-water interface, something that can result in preferential orientation and even structural disruption of macromolecular particles. This unwanted contact can occur either as the result of free diffusion of particles during the interval between application, thinning and vitrification of the remaining buffer, or-when particles have been immobilized-by the film of buffer becoming too thin prior to vitrification. An opportunity now exists to apply theoretical and practical insights from the fields of thin-film physical chemistry and interfacial science, in an effort to bring cryo-EM sample preparation to a level of sophistication that is comparable to that of current data collection and analysis.
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Affiliation(s)
- Bong-Gyoon Han
- Lawrence Berkeley National Laboratory, University of California, Berkeley, Berkeley, CA, United States
| | - Max Armstrong
- Lawrence Berkeley National Laboratory, University of California, Berkeley, Berkeley, CA, United States,Department of Bioengineering, University of California, Berkeley, Berkeley, CA, United States
| | - Daniel A. Fletcher
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, United States,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, Berkeley, CA, United States,Chan Zuckerberg Biohub, San Francisco, CA, United States
| | - Robert M. Glaeser
- Lawrence Berkeley National Laboratory, University of California, Berkeley, Berkeley, CA, United States,*Correspondence: Robert M. Glaeser,
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10
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O’Brien KS, Byanju R, Kandel RP, Poudyal B, Gonzales JA, Porco TC, Whitcher JP, Srinivasan M, Upadhyay M, Lietman TM, Keenan JD, Byanju R, Khadka KB, Bista D, Gautam M, Giri P, Kayastha S, Parajuli TP, Shah RK, Sharma N, Sharma P, Shrestha A, Shrestha M, Subedi P, Chaudhary DS, Ghimire R, Adhikari M, Hamal V, Bhandari G, Dahal G, Poudyal B, Bhandari S, Gurung J, Bhattarai D, Bhattarai R, Chapagain D, Chaudhary AK, Gautam SK, Gurau D, Kandel D, Lamichhane PC, Rijal R, Giri G, Upadhyay M, Lietman TM, Acharya NR, Gonzales JA, Keenan JD, McLeod SD, Ramirez DA, Ray KJ, Rose-Nussbaumer J, Whitcher JP, O'Brien KS, Cotter SY, Kim J, Lee S, Maamari RN, Porco TC, Basset K, Chase H, Evans L, Gilbert S, Kandel RP, Moses D, Tenzing C, Choudhary S, Dhakwa P, Fletcher DA, Reber CD. Village-integrated eye workers for prevention of corneal ulcers in Nepal (VIEW study): a cluster-randomised controlled trial. Lancet Glob Health 2022; 10:e501-e509. [PMID: 35303460 PMCID: PMC9814976 DOI: 10.1016/s2214-109x(21)00596-9] [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] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 12/09/2021] [Accepted: 12/14/2021] [Indexed: 01/11/2023]
Abstract
BACKGROUND Corneal ulcers are a common cause of blindness in low-income and middle-income countries, usually resulting from traumatic corneal abrasions during agricultural work. Antimicrobial prophylaxis of corneal abrasions can help prevent corneal ulcers, but delays in the initiation of therapy are frequent. We aimed to assess whether a community-based programme for corneal ulcer prevention would reduce the incidence of corneal ulceration. METHODS A cluster-randomised trial was performed in village development committees (VDCs) in Nepal. VDCs in the catchment area of Bharatpur Eye Hospital, Nepal with less than 15 000 people were eligible for inclusion. We randomly assigned (1:1) VDCs to either an intervention group or a control group. In the intervention VDCs, existing female community health volunteers (FCHVs) were trained to diagnose corneal abrasions and provide a 3-day course of ophthalmic antimicrobials to their patients. In the control VDCs, FCHVs did not provide this intervention. Participants were not masked given the nature of the intervention. Both groups were followed up for 3 years for photographic evidence of corneal ulceration. The primary outcome was the incidence of corneal ulceration, determined by masked assessment of corneal photographs. The analysis was by intention to treat. This trial is registered with ClinicalTrials.gov, NCT01969786. FINDINGS We assessed 112 VDCs, of which 24 were enrolled. The study was performed between Feb 4, 2014, and Oct 20, 2017. 12 VDCs were randomly assigned to the intervention group and 12 to the control group. 252 539 individuals were included in the study (130 579 in the intervention group and 121 960 in the control group). FCHVs diagnosed and provided antimicrobials for 4777 corneal abrasions. The census identified 289 corneal ulcers among 246 893 person-years in the intervention group (incidence 1·21 cases [95% CI 0·85-1·74] per 1000 person-years) and 262 corneal ulcers among 239 170 person-years in the control group (incidence 1·18 cases [0·82-1·70] per 1000 person-years; incidence rate ratio 1·03 [95% CI 0·63-1·67]; p=0·93). Medication allergy was self-reported in 0·2% of participants. INTERPRETATION We did not detect a reduction in the incidence of corneal ulceration during the first 3 years of a community-based corneal ulcer prevention programme. Further study might be warranted in more rural areas where basic eye care facilities are not available. FUNDING National Eye Institute.
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Affiliation(s)
- Kieran S O’Brien
- Francis I. Proctor Foundation, University of California, San Francisco, CA, USA,Department of Ophthalmology, University of California San Francisco, San Francisco, CA, USA
| | | | - Ram Prasad Kandel
- Bharatpur Eye Hospital, Bharatpur, Chitwan, Nepal,Seva Foundation, Berkeley, CA, USA and Kathmandu, Nepal
| | | | - John A Gonzales
- Francis I. Proctor Foundation, University of California, San Francisco, CA, USA,Department of Ophthalmology, University of California San Francisco, San Francisco, CA, USA
| | - Travis C Porco
- Francis I. Proctor Foundation, University of California, San Francisco, CA, USA,Department of Ophthalmology, University of California San Francisco, San Francisco, CA, USA,Department of Epidemiology & Biostatistics, University of California San Francisco, San Francisco, CA, USA,Institute for Global Health Sciences, University of California San Francisco, San Francisco, CA, USA
| | - John P Whitcher
- Francis I. Proctor Foundation, University of California, San Francisco, CA, USA,Department of Ophthalmology, University of California San Francisco, San Francisco, CA, USA
| | | | - Madan Upadhyay
- BP Eye Foundation, Children’s Hospital for Eye, Ear, and Rehabilitation Services (CHEERS), Kathmandu, Nepal
| | - Thomas M. Lietman
- Francis I. Proctor Foundation, University of California, San Francisco, CA, USA,Department of Ophthalmology, University of California San Francisco, San Francisco, CA, USA,Department of Epidemiology & Biostatistics, University of California San Francisco, San Francisco, CA, USA,Institute for Global Health Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Jeremy D Keenan
- Francis I. Proctor Foundation, University of California, San Francisco, CA, USA,Department of Ophthalmology, University of California San Francisco, San Francisco, CA, USA
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11
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Armstrong M, Harris AR, D’Ambrosio MV, Coulibaly JT, Essien-Baidoo S, Ephraim RKD, Andrews JR, Bogoch II, Fletcher DA. Point-of-Care Sample Preparation and Automated Quantitative Detection of Schistosoma haematobium Using Mobile Phone Microscopy. Am J Trop Med Hyg 2022; 106:tpmd211071. [PMID: 35344927 PMCID: PMC9128700 DOI: 10.4269/ajtmh.21-1071] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 01/17/2022] [Indexed: 11/07/2022] Open
Abstract
Schistosoma haematobium continues to pose a significant public health burden despite ongoing global control efforts. One of several barriers to sustained control (and ultimately elimination) is the lack of access to highly sensitive diagnostic or screening tools that are inexpensive, rapid, and can be used at the point of sample collection. Here, we report an automated point-of-care diagnostic based on mobile phone microscopy that rapidly images and identifies S. haematobium eggs in urine samples. Parasite eggs are filtered from urine within a specialized, inexpensive cartridge that is then automatically imaged by the mobile phone microscope (the "SchistoScope"). Parasite eggs are captured at a constriction point in the tapered cartridge for easy imaging, and the automated quantification of eggs is obtained upon analysis of the images by an algorithm. We demonstrate S. haematobium egg detection with greater than 90% sensitivity and specificity using this device compared with the field gold standard of conventional filtration and microscopy. With simple sample preparation and image analysis on a mobile phone, the SchistoScope combines the diagnostic performance of conventional microscopy with the analytic performance of an expert technician. This portable device has the potential to provide rapid and quantitative diagnosis of S. haematobium to advance ongoing control efforts.
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Affiliation(s)
- Maxim Armstrong
- Department of Bioengineering, University of California, Berkeley, Berkeley, California
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California
| | - Andrew R. Harris
- Department of Bioengineering, University of California, Berkeley, Berkeley, California
- Department of Mechanical and Aerospace Engineering, Carleton University, Ottawa, Ontario, Canada
| | - Michael V. D’Ambrosio
- Department of Bioengineering, University of California, Berkeley, Berkeley, California
| | - Jean T. Coulibaly
- Unité de Formation et de Recherche Biosciences, Université Félix Houphouët-Boigny, Abidjan, Côte d’Ivoire
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland
| | - Samuel Essien-Baidoo
- Department of Medical Laboratory Science, University of Cape Coast, Cape Coast, Ghana
| | - Richard K. D. Ephraim
- Department of Medical Laboratory Science, University of Cape Coast, Cape Coast, Ghana
| | - Jason R. Andrews
- Department of Medicine, Stanford University, Stanford, California
| | - Isaac I. Bogoch
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Daniel A. Fletcher
- Department of Bioengineering, University of California, Berkeley, Berkeley, California
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, Berkeley, California
- Chan Zuckerberg Biohub, San Francisco, California
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12
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Liu TY, Knott GJ, Smock DCJ, Desmarais JJ, Son S, Bhuiya A, Jakhanwal S, Prywes N, Agrawal S, Díaz de León Derby M, Switz NA, Armstrong M, Harris AR, Charles EJ, Thornton BW, Fozouni P, Shu J, Stephens SI, Kumar GR, Zhao C, Mok A, Iavarone AT, Escajeda AM, McIntosh R, Kim S, Dugan EJ, Pollard KS, Tan MX, Ott M, Fletcher DA, Lareau LF, Hsu PD, Savage DF, Doudna JA. Accelerated RNA detection using tandem CRISPR nucleases. Nat Chem Biol 2021; 17:982-988. [PMID: 34354262 PMCID: PMC10184463 DOI: 10.1038/s41589-021-00842-2] [Citation(s) in RCA: 93] [Impact Index Per Article: 31.0] [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: 05/11/2021] [Accepted: 06/23/2021] [Indexed: 12/14/2022]
Abstract
Direct, amplification-free detection of RNA has the potential to transform molecular diagnostics by enabling simple on-site analysis of human or environmental samples. CRISPR-Cas nucleases offer programmable RNA-guided RNA recognition that triggers cleavage and release of a fluorescent reporter molecule, but long reaction times hamper their detection sensitivity and speed. Here, we show that unrelated CRISPR nucleases can be deployed in tandem to provide both direct RNA sensing and rapid signal generation, thus enabling robust detection of ~30 molecules per µl of RNA in 20 min. Combining RNA-guided Cas13 and Csm6 with a chemically stabilized activator creates a one-step assay that can detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA extracted from respiratory swab samples with quantitative reverse transcriptase PCR (qRT-PCR)-derived cycle threshold (Ct) values up to 33, using a compact detector. This Fast Integrated Nuclease Detection In Tandem (FIND-IT) approach enables sensitive, direct RNA detection in a format that is amenable to point-of-care infection diagnosis as well as to a wide range of other diagnostic or research applications.
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Affiliation(s)
- Tina Y Liu
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Gavin J Knott
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Monash Biomedicine Discovery Institute, Department of Biochemistry & Molecular Biology, Monash University, Victoria, Australia
| | - Dylan C J Smock
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - John J Desmarais
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Sungmin Son
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | - Abdul Bhuiya
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
- UC Berkeley, UC San Francisco Graduate Program in Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | - Shrutee Jakhanwal
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Noam Prywes
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Shreeya Agrawal
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | - María Díaz de León Derby
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
- UC Berkeley, UC San Francisco Graduate Program in Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | - Neil A Switz
- Department of Physics and Astronomy, San José State University, San José, CA, USA
| | - Maxim Armstrong
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Andrew R Harris
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | - Emeric J Charles
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Brittney W Thornton
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Parinaz Fozouni
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA, USA
- Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA, USA
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Jeffrey Shu
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Stephanie I Stephens
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - G Renuka Kumar
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Chunyu Zhao
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA, USA
- Chan-Zuckerberg Biohub, San Francisco, CA, USA
| | - Amanda Mok
- Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Anthony T Iavarone
- QB3/Chemistry Mass Spectrometry Facility, University of California, Berkeley, Berkeley, CA, USA
| | | | | | - Shineui Kim
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Eli J Dugan
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Katherine S Pollard
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA, USA
- Chan-Zuckerberg Biohub, San Francisco, CA, USA
- Department of Epidemiology & Biostatistics, University of California, San Francisco, San Francisco, CA, USA
| | | | - Melanie Ott
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Daniel A Fletcher
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
- UC Berkeley, UC San Francisco Graduate Program in Bioengineering, University of California, Berkeley, Berkeley, CA, USA
- Chan-Zuckerberg Biohub, San Francisco, CA, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA, USA
| | - Liana F Lareau
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | - Patrick D Hsu
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA.
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA.
- Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA.
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA, USA.
- Berkeley Stem Cell Center, University of California, Berkeley, Berkeley, CA, USA.
| | - David F Savage
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA.
| | - Jennifer A Doudna
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA.
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA, USA.
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, USA.
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA.
- Gladstone Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA, USA.
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13
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Suter EC, Schmid EM, Harris AR, Voets E, Francica B, Fletcher DA. Antibody:CD47 ratio regulates macrophage phagocytosis through competitive receptor phosphorylation. Cell Rep 2021; 36:109587. [PMID: 34433055 PMCID: PMC8477956 DOI: 10.1016/j.celrep.2021.109587] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 04/19/2021] [Accepted: 08/02/2021] [Indexed: 01/04/2023] Open
Abstract
Cancer immunotherapies often modulate macrophage effector function by introducing either targeting antibodies that activate Fcγ receptors (FcγRs) or blocking antibodies that disrupt inhibitory SIRPα-CD47 engagement. However, how these competing signals are integrated is poorly understood, raising questions about how to effectively titrate immune responses. Here, we find that macrophage phagocytic decisions are regulated by the ratio of activating ligand to inhibitory ligand over a broad range of absolute molecular densities. Using both endogenous and chimeric receptors, we show that activating:inhibitory ligand ratios of at least 10:1 are required to promote phagocytosis of model antibody-opsonized CD47-inhibited targets and that lowering that ratio reduces FcγR phosphorylation because of inhibitory phosphatases recruited to CD47-bound SIRPα. We demonstrate that ratiometric signaling is critical for phagocytosis of tumor cells and can be modified by blocking SIRPα, indicating that balancing targeting and blocking antibodies may be important for controlling macrophage phagocytosis in cancer immunotherapy.
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Affiliation(s)
- Emily C Suter
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA; UC Berkeley/UC San Francisco Graduate Group in Bioengineering, Berkeley, CA, USA
| | - Eva M Schmid
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | - Andrew R Harris
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA; Department of Mechanical and Aerospace Engineering, Carleton University, Ottawa, ON, Canada
| | - Erik Voets
- Aduro Biotech Europe, Oss, the Netherlands
| | | | - Daniel A Fletcher
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA; UC Berkeley/UC San Francisco Graduate Group in Bioengineering, Berkeley, CA, USA; Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; Chan Zuckerberg Biohub, San Francisco, CA, USA.
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14
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Blok DJ, Kamgno J, Pion SD, Nana-Djeunga HC, Niamsi-Emalio Y, Chesnais CB, Mackenzie CD, Klion AD, Fletcher DA, Nutman TB, de Vlas SJ, Boussinesq M, Stolk WA. Feasibility of Onchocerciasis Elimination Using a "Test-and-not-treat" Strategy in Loa loa Co-endemic Areas. Clin Infect Dis 2021; 72:e1047-e1055. [PMID: 33289025 PMCID: PMC8204788 DOI: 10.1093/cid/ciaa1829] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Indexed: 12/29/2022] Open
Abstract
Background Mass drug administration (MDA) with ivermectin is the main strategy for onchocerciasis elimination. Ivermectin is generally safe, but is associated with serious adverse events in individuals with high Loa loa microfilarial densities (MFD). Therefore, ivermectin MDA is not recommended in areas where onchocerciasis is hypo-endemic and L loa is co-endemic. To eliminate onchocerciasis in those areas, a test-and-not-treat (TaNT) strategy has been proposed. We investigated whether onchocerciasis elimination can be achieved using TaNT and the required duration. Methods We used the individual-based model ONCHOSIM to predict the impact of TaNT on onchocerciasis microfilarial (mf) prevalence. We simulated precontrol mf prevalence levels from 2% to 40%. The impact of TaNT was simulated under varying levels of participation, systematic nonparticipation, and exclusion from ivermectin resulting from high L loa MFD. For each scenario, we assessed the time to elimination, defined as bringing onchocerciasis mf prevalence below 1.4%. Results In areas with 30% to 40% precontrol mf prevalence, the model predicted that it would take between 14 and 16 years to bring the mf prevalence below 1.4% using conventional MDA, assuming 65% participation. TaNT would increase the time to elimination by up to 1.5 years, depending on the level of systematic nonparticipation and the exclusion rate. At lower exclusion rates (≤2.5%), the delay would be less than 6 months. Conclusions Our model predicts that onchocerciasis can be eliminated using TaNT in L loa co-endemic areas. The required treatment duration using TaNT would be only slightly longer than in areas with conventional MDA, provided that participation is good.
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Affiliation(s)
- David J Blok
- Department of Public Health, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Joseph Kamgno
- Centre for Research on Filariasis and other Tropical Diseases (CRFilMT), Yaoundé, Cameroon
| | - Sebastien D Pion
- IRD UMI 233-INSERM U1175-Montpellier University, Montpellier, France
| | - Hugues C Nana-Djeunga
- Centre for Research on Filariasis and other Tropical Diseases (CRFilMT), Yaoundé, Cameroon
| | - Yannick Niamsi-Emalio
- Centre for Research on Filariasis and other Tropical Diseases (CRFilMT), Yaoundé, Cameroon
| | - Cedric B Chesnais
- IRD UMI 233-INSERM U1175-Montpellier University, Montpellier, France
| | | | - Amy D Klion
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, United States
| | - Daniel A Fletcher
- Department of Bioengineering and the Biophysics Program, University of California, Berkeley, California, United States
| | - Thomas B Nutman
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, United States
| | - Sake J de Vlas
- Department of Public Health, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Michel Boussinesq
- IRD UMI 233-INSERM U1175-Montpellier University, Montpellier, France
| | - Wilma A Stolk
- Department of Public Health, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
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15
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Agrawal S, Fanton A, Chandrasekaran SS, Charrez B, Escajeda AM, Son S, Mcintosh R, Bhuiya A, de León Derby MD, Switz NA, Armstrong M, Harris AR, Prywes N, Lukarska M, Biering SB, Smock DCJ, Mok A, Knott GJ, Dang Q, Van Dis E, Dugan E, Kim S, Liu TY, Harris E, Stanley SA, Lareau LF, Tan MX, Fletcher DA, Doudna JA, Savage DF, Hsu PD. Rapid, point-of-care molecular diagnostics with Cas13. medRxiv 2021:2020.12.14.20247874. [PMID: 33354689 PMCID: PMC7755151 DOI: 10.1101/2020.12.14.20247874] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Rapid nucleic acid testing is a critical component of a robust infrastructure for increased disease surveillance. Here, we report a microfluidic platform for point-of-care, CRISPR-based molecular diagnostics. We first developed a nucleic acid test which pairs distinct mechanisms of DNA and RNA amplification optimized for high sensitivity and rapid kinetics, linked to Cas13 detection for specificity. We combined this workflow with an extraction-free sample lysis protocol using shelf-stable reagents that are widely available at low cost, and a multiplexed human gene control for calling negative test results. As a proof-of-concept, we demonstrate sensitivity down to 40 copies/μL of SARS-CoV-2 in unextracted saliva within 35 minutes, and validated the test on total RNA extracted from patient nasal swabs with a range of qPCR Ct values from 13-35. To enable sample-to-answer testing, we integrated this diagnostic reaction with a single-use, gravity-driven microfluidic cartridge followed by real-time fluorescent detection in a compact companion instrument. We envision this approach for Diagnostics with Coronavirus Enzymatic Reporting (DISCoVER) will incentivize frequent, fast, and easy testing.
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Affiliation(s)
- Shreeya Agrawal
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Alison Fanton
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- University of California, Berkeley—University of California, San Francisco Graduate Program in Bioengineering, Berkeley, CA, USA
| | - Sita S. Chandrasekaran
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- University of California, Berkeley—University of California, San Francisco Graduate Program in Bioengineering, Berkeley, CA, USA
| | - Bérénice Charrez
- University of California, Berkeley—University of California, San Francisco Graduate Program in Bioengineering, Berkeley, CA, USA
| | | | - Sungmin Son
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | | | - Abdul Bhuiya
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
- University of California, Berkeley—University of California, San Francisco Graduate Program in Bioengineering, Berkeley, CA, USA
| | - María Díaz de León Derby
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
- University of California, Berkeley—University of California, San Francisco Graduate Program in Bioengineering, Berkeley, CA, USA
| | - Neil A. Switz
- Department of Physics and Astronomy, San José State University, San José, CA, USA
| | - Maxim Armstrong
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Andrew R. Harris
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | - Noam Prywes
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Maria Lukarska
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Scott B. Biering
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Dylan C. J. Smock
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Amanda Mok
- Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Gavin J. Knott
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Victoria 3800, Australia
| | - Qi Dang
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Erik Van Dis
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Eli Dugan
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Shin Kim
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Tina Y. Liu
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | | | - Eva Harris
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Sarah A. Stanley
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- School of Public Health, University of California, Berkeley, CA, USA
| | - Liana F. Lareau
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | | | - Daniel A. Fletcher
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | - Jennifer A. Doudna
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Gladstone Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA, USA
| | - David F. Savage
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Patrick D. Hsu
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
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16
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Liu TY, Knott GJ, Smock DCJ, Desmarais JJ, Son S, Bhuiya A, Jakhanwal S, Prywes N, Agrawal S, de León Derby MD, Switz NA, Armstrong M, Harris AR, Charles EJ, Thornton BW, Fozouni P, Shu J, Stephens SI, Kumar GR, Zhao C, Mok A, Iavarone AT, Escajeda AM, McIntosh R, Kim SE, Dugan EJ, Pollard KS, Tan MX, Ott M, Fletcher DA, Lareau LF, Hsu PD, Savage DF, Doudna JA. Accelerated RNA detection using tandem CRISPR nucleases. medRxiv 2021:2021.03.19.21253328. [PMID: 33791736 PMCID: PMC8010768 DOI: 10.1101/2021.03.19.21253328] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Direct, amplification-free detection of RNA has the potential to transform molecular diagnostics by enabling simple on-site analysis of human or environmental samples. CRISPR-Cas nucleases offer programmable RNA-guided recognition of RNA that triggers cleavage and release of a fluorescent reporter molecule1,2, but long reaction times hamper sensitivity and speed when applied to point-of-care testing. Here we show that unrelated CRISPR nucleases can be deployed in tandem to provide both direct RNA sensing and rapid signal generation, thus enabling robust detection of ~30 RNA copies/microliter in 20 minutes. Combining RNA-guided Cas13 and Csm6 with a chemically stabilized activator creates a one-step assay that detected SARS-CoV-2 RNA from nasopharyngeal samples with PCR-derived Ct values up to 29 in microfluidic chips, using a compact imaging system. This Fast Integrated Nuclease Detection In Tandem (FIND-IT) approach enables direct RNA detection in a format amenable to point-of-care infection diagnosis, as well as to a wide range of other diagnostic or research applications.
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Affiliation(s)
- Tina Y. Liu
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Gavin J. Knott
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Monash Biomedicine Discovery Institute, Department of Biochemistry & Molecular Biology, Monash University, VIC 3800, Australia
| | - Dylan C. J. Smock
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - John J. Desmarais
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Sungmin Son
- Department of Bioengineering, University of California, Berkeley, CA, USA
| | - Abdul Bhuiya
- Department of Bioengineering, University of California, Berkeley, CA, USA
- UC Berkeley-UC San Francisco Graduate Program in Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | - Shrutee Jakhanwal
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Noam Prywes
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Shreeya Agrawal
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Bioengineering, University of California, Berkeley, CA, USA
| | - María Díaz de León Derby
- Department of Bioengineering, University of California, Berkeley, CA, USA
- UC Berkeley-UC San Francisco Graduate Program in Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | - Neil A. Switz
- Department of Physics and Astronomy, San José State University, San José, CA, USA
| | - Maxim Armstrong
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Andrew R. Harris
- Department of Bioengineering, University of California, Berkeley, CA, USA
| | - Emeric J. Charles
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Brittney W. Thornton
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Parinaz Fozouni
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA, USA
- Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA 94143, USA
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Jeffrey Shu
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Stephanie I. Stephens
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - G. Renuka Kumar
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Chunyu Zhao
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA, USA
- Chan-Zuckerberg Biohub, San Francisco, CA, USA
| | - Amanda Mok
- Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Anthony T. Iavarone
- QB3/Chemistry Mass Spectrometry Facility, University of California, Berkeley, Berkeley, CA, USA
| | | | | | - Shin E. Kim
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Eli J. Dugan
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | | | - Katherine S. Pollard
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA, USA
- Chan-Zuckerberg Biohub, San Francisco, CA, USA
- Department of Epidemiology & Biostatistics, University of California, San Francisco, CA, USA
| | | | - Melanie Ott
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Daniel A. Fletcher
- Department of Bioengineering, University of California, Berkeley, CA, USA
- UC Berkeley-UC San Francisco Graduate Program in Bioengineering, University of California, Berkeley, Berkeley, CA, USA
- Chan-Zuckerberg Biohub, San Francisco, CA, USA
| | - Liana F. Lareau
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Bioengineering, University of California, Berkeley, CA, USA
| | - Patrick D. Hsu
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Bioengineering, University of California, Berkeley, CA, USA
| | - David F. Savage
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Jennifer A. Doudna
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
- Gladstone Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA, USA
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17
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Fozouni P, Son S, Díaz de León Derby M, Knott GJ, Gray CN, D'Ambrosio MV, Zhao C, Switz NA, Kumar GR, Stephens SI, Boehm D, Tsou CL, Shu J, Bhuiya A, Armstrong M, Harris AR, Chen PY, Osterloh JM, Meyer-Franke A, Joehnk B, Walcott K, Sil A, Langelier C, Pollard KS, Crawford ED, Puschnik AS, Phelps M, Kistler A, DeRisi JL, Doudna JA, Fletcher DA, Ott M. Amplification-free detection of SARS-CoV-2 with CRISPR-Cas13a and mobile phone microscopy. Cell 2021; 184:323-333.e9. [PMID: 33306959 DOI: 10.1016/j.cell.2020.12.00] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 11/03/2020] [Accepted: 11/25/2020] [Indexed: 05/28/2023]
Abstract
The December 2019 outbreak of a novel respiratory virus, SARS-CoV-2, has become an ongoing global pandemic due in part to the challenge of identifying symptomatic, asymptomatic, and pre-symptomatic carriers of the virus. CRISPR diagnostics can augment gold-standard PCR-based testing if they can be made rapid, portable, and accurate. Here, we report the development of an amplification-free CRISPR-Cas13a assay for direct detection of SARS-CoV-2 from nasal swab RNA that can be read with a mobile phone microscope. The assay achieved ∼100 copies/μL sensitivity in under 30 min of measurement time and accurately detected pre-extracted RNA from a set of positive clinical samples in under 5 min. We combined crRNAs targeting SARS-CoV-2 RNA to improve sensitivity and specificity and directly quantified viral load using enzyme kinetics. Integrated with a reader device based on a mobile phone, this assay has the potential to enable rapid, low-cost, point-of-care screening for SARS-CoV-2.
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Affiliation(s)
- Parinaz Fozouni
- J. David Gladstone Institutes, San Francisco, CA 94158, USA; Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA 94143, USA; Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Sungmin Son
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA
| | - María Díaz de León Derby
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA; UC Berkeley-UC San Francisco Graduate Program in Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Gavin J Knott
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Monash Biomedicine Discovery Institute, Department of Biochemistry & Molecular Biology, Monash University, VIC 3800, Australia
| | - Carley N Gray
- J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Michael V D'Ambrosio
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Chunyu Zhao
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Neil A Switz
- Department of Physics and Astronomy, San José State University, San Jose, CA 95192, USA
| | - G Renuka Kumar
- J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Stephanie I Stephens
- J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Daniela Boehm
- J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Chia-Lin Tsou
- J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Jeffrey Shu
- J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Abdul Bhuiya
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA; UC Berkeley-UC San Francisco Graduate Program in Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Maxim Armstrong
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Andrew R Harris
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Pei-Yi Chen
- J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | | | | | - Bastian Joehnk
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Keith Walcott
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Anita Sil
- Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA 94143, USA; Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Charles Langelier
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA; Division of Infectious Diseases, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Katherine S Pollard
- J. David Gladstone Institutes, San Francisco, CA 94158, USA; Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA; Institute for Human Genetics, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Epidemiology and Biostatistics and Institute of Computational Health Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Emily D Crawford
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA; Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA
| | | | - Maira Phelps
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Amy Kistler
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Joseph L DeRisi
- Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA 94143, USA; Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA; Division of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Jennifer A Doudna
- J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Daniel A Fletcher
- J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA; UC Berkeley-UC San Francisco Graduate Program in Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA; Biophysics Program, University of California, Berkeley, Berkeley, CA 94720, USA; California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA 94720, USA; Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
| | - Melanie Ott
- J. David Gladstone Institutes, San Francisco, CA 94158, USA; Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA 94143, USA; Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA.
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18
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Lenk EJ, Moungui HC, Boussinesq M, Kamgno J, Nana-Djeunga HC, Fitzpatrick C, Peultier ACMM, Klion AD, Fletcher DA, Nutman TB, Pion SD, Niamsi-Emalio Y, Redekop WK, Severens JL, Stolk WA. A Test-and-Not-Treat Strategy for Onchocerciasis Elimination in Loa loa-coendemic Areas: Cost Analysis of a Pilot in the Soa Health District, Cameroon. Clin Infect Dis 2021; 70:1628-1635. [PMID: 31165855 PMCID: PMC7146010 DOI: 10.1093/cid/ciz461] [Citation(s) in RCA: 10] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 06/03/2019] [Indexed: 11/24/2022] Open
Abstract
Background Severe adverse events after treatment with ivermectin in individuals with high levels of Loa loa microfilariae in the blood preclude onchocerciasis elimination through community-directed treatment with ivermectin (CDTI) in Central Africa. We measured the cost of a community-based pilot using a test-and-not-treat (TaNT) strategy in the Soa health district in Cameroon. Methods Based on actual expenditures, we empirically estimated the economic cost of the Soa TaNT campaign, including financial costs and opportunity costs that will likely be borne by control programs and stakeholders in the future. In addition to the empirical analyses, we estimated base-case, less intensive, and more intensive resource use scenarios to explore how costs might differ if TaNT were implemented programmatically. Results The total costs of US$283 938 divided by total population, people tested, and people treated with 42% coverage were US$4.0, US$9.2, and US$9.5, respectively. In programmatic implementation, these costs (base-case estimates with less and more intensive scenarios) could be US$2.2 ($1.9–$3.6), US$5.2 ($4.5–$8.3), and US$5.4 ($4.6–$8.6), respectively. Conclusions TaNT clearly provides a safe strategy for large-scale ivermectin treatment and overcomes a major obstacle to the elimination of onchocerciasis in areas coendemic for Loa loa. Although it is more expensive than standard CDTI, costs vary depending on the setting, the implementation choices made by the institutions involved, and the community participation rate. Research on the required duration of TaNT is needed to improve the affordability assessment, and more experience is needed to understand how to implement TaNT optimally.
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Affiliation(s)
- Edeltraud J Lenk
- Erasmus School of Health Policy and Management, Erasmus University Rotterdam.,Department of Public Health, Erasmus Medical Center, University Medical Center Rotterdam, The Netherlands
| | - Henri C Moungui
- Centre for Research on Filariasis and Other Tropical Diseases, Yaounde, Cameroon
| | - Michel Boussinesq
- Unité Mixte Internationale, TransVIHMI, Institut de Recherche pour le Développement, University of Montpellier, France
| | - Joseph Kamgno
- Centre for Research on Filariasis and Other Tropical Diseases, Yaounde, Cameroon
| | | | | | | | - Amy D Klion
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | | | - Thomas B Nutman
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Sébastien D Pion
- Unité Mixte Internationale, TransVIHMI, Institut de Recherche pour le Développement, University of Montpellier, France
| | | | - William K Redekop
- Erasmus School of Health Policy and Management, Erasmus University Rotterdam
| | - Johan L Severens
- Erasmus School of Health Policy and Management, Erasmus University Rotterdam
| | - Wilma A Stolk
- Department of Public Health, Erasmus Medical Center, University Medical Center Rotterdam, The Netherlands
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19
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Fozouni P, Son S, Díaz de León Derby M, Knott GJ, Gray CN, D'Ambrosio MV, Zhao C, Switz NA, Kumar GR, Stephens SI, Boehm D, Tsou CL, Shu J, Bhuiya A, Armstrong M, Harris AR, Chen PY, Osterloh JM, Meyer-Franke A, Joehnk B, Walcott K, Sil A, Langelier C, Pollard KS, Crawford ED, Puschnik AS, Phelps M, Kistler A, DeRisi JL, Doudna JA, Fletcher DA, Ott M. Amplification-free detection of SARS-CoV-2 with CRISPR-Cas13a and mobile phone microscopy. Cell 2020; 184:323-333.e9. [PMID: 33306959 PMCID: PMC7834310 DOI: 10.1016/j.cell.2020.12.001] [Citation(s) in RCA: 463] [Impact Index Per Article: 115.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 11/03/2020] [Accepted: 11/25/2020] [Indexed: 12/18/2022]
Abstract
The December 2019 outbreak of a novel respiratory virus, SARS-CoV-2, has become an ongoing global pandemic due in part to the challenge of identifying symptomatic, asymptomatic, and pre-symptomatic carriers of the virus. CRISPR diagnostics can augment gold-standard PCR-based testing if they can be made rapid, portable, and accurate. Here, we report the development of an amplification-free CRISPR-Cas13a assay for direct detection of SARS-CoV-2 from nasal swab RNA that can be read with a mobile phone microscope. The assay achieved ∼100 copies/μL sensitivity in under 30 min of measurement time and accurately detected pre-extracted RNA from a set of positive clinical samples in under 5 min. We combined crRNAs targeting SARS-CoV-2 RNA to improve sensitivity and specificity and directly quantified viral load using enzyme kinetics. Integrated with a reader device based on a mobile phone, this assay has the potential to enable rapid, low-cost, point-of-care screening for SARS-CoV-2.
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Affiliation(s)
- Parinaz Fozouni
- J. David Gladstone Institutes, San Francisco, CA 94158, USA; Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA 94143, USA; Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Sungmin Son
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA
| | - María Díaz de León Derby
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA; UC Berkeley-UC San Francisco Graduate Program in Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Gavin J Knott
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Monash Biomedicine Discovery Institute, Department of Biochemistry & Molecular Biology, Monash University, VIC 3800, Australia
| | - Carley N Gray
- J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Michael V D'Ambrosio
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Chunyu Zhao
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Neil A Switz
- Department of Physics and Astronomy, San José State University, San Jose, CA 95192, USA
| | - G Renuka Kumar
- J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Stephanie I Stephens
- J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Daniela Boehm
- J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Chia-Lin Tsou
- J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Jeffrey Shu
- J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Abdul Bhuiya
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA; UC Berkeley-UC San Francisco Graduate Program in Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Maxim Armstrong
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Andrew R Harris
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Pei-Yi Chen
- J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | | | | | - Bastian Joehnk
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Keith Walcott
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Anita Sil
- Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA 94143, USA; Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Charles Langelier
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA; Division of Infectious Diseases, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Katherine S Pollard
- J. David Gladstone Institutes, San Francisco, CA 94158, USA; Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA; Institute for Human Genetics, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Epidemiology and Biostatistics and Institute of Computational Health Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Emily D Crawford
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA; Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA
| | | | - Maira Phelps
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Amy Kistler
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Joseph L DeRisi
- Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA 94143, USA; Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA; Division of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Jennifer A Doudna
- J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Daniel A Fletcher
- J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA; UC Berkeley-UC San Francisco Graduate Program in Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA; Biophysics Program, University of California, Berkeley, Berkeley, CA 94720, USA; California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA 94720, USA; Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
| | - Melanie Ott
- J. David Gladstone Institutes, San Francisco, CA 94158, USA; Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA 94143, USA; Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA.
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20
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Harris AR, Jreij P, Belardi B, Joffe AM, Bausch AR, Fletcher DA. Biased localization of actin binding proteins by actin filament conformation. Nat Commun 2020; 11:5973. [PMID: 33239610 PMCID: PMC7688639 DOI: 10.1038/s41467-020-19768-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [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: 04/24/2020] [Accepted: 10/30/2020] [Indexed: 11/09/2022] Open
Abstract
The assembly of actin filaments into distinct cytoskeletal structures plays a critical role in cell physiology, but how proteins localize differentially to these structures within a shared cytoplasm remains unclear. Here, we show that the actin-binding domains of accessory proteins can be sensitive to filament conformational changes. Using a combination of live cell imaging and in vitro single molecule binding measurements, we show that tandem calponin homology domains (CH1-CH2) can be mutated to preferentially bind actin networks at the front or rear of motile cells. We demonstrate that the binding kinetics of CH1-CH2 domain mutants varies as actin filament conformation is altered by perturbations that include stabilizing drugs and other binding proteins. These findings suggest that conformational changes of actin filaments in cells could help to direct accessory binding proteins to different actin cytoskeletal structures through a biophysical feedback loop.
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Affiliation(s)
- Andrew R Harris
- Department of Bioengineering and Biophysics Program, University of California, Berkeley, 648 Stanley Hall MC 1762, Berkeley, CA, 94720, USA
| | - Pamela Jreij
- Department of Bioengineering and Biophysics Program, University of California, Berkeley, 648 Stanley Hall MC 1762, Berkeley, CA, 94720, USA
| | - Brian Belardi
- Department of Bioengineering and Biophysics Program, University of California, Berkeley, 648 Stanley Hall MC 1762, Berkeley, CA, 94720, USA
| | - Aaron M Joffe
- Department of Bioengineering and Biophysics Program, University of California, Berkeley, 648 Stanley Hall MC 1762, Berkeley, CA, 94720, USA
| | - Andreas R Bausch
- Lehrstuhl für Biophysik (E27), Technische Universität München, Garching, 85748, Germany
| | - Daniel A Fletcher
- Department of Bioengineering and Biophysics Program, University of California, Berkeley, 648 Stanley Hall MC 1762, Berkeley, CA, 94720, USA.
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 648 Stanley Hall MC 1762, Berkeley, CA, 94720, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA.
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21
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Armstrong M, Vahey MD, Hunt TP, Fletcher DA. Forming and loading giant unilamellar vesicles with acoustic jetting. Biomicrofluidics 2020; 14:064105. [PMID: 33269034 PMCID: PMC7679179 DOI: 10.1063/5.0021742] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 10/15/2020] [Indexed: 05/04/2023]
Abstract
Giant unilamellar vesicles (GUVs) are a useful platform for reconstituting and studying membrane-bound biological systems, offering reduced complexity compared to living cells. Several techniques exist to form GUVs and populate them with biomolecules of interest. However, a persistent challenge is the ability to efficiently and reliably load solutions of biological macromolecules, organelle-like membranes, and/or micrometer-scale particles with controlled stoichiometry in the encapsulated volume of GUVs. Here, we demonstrate the use of acoustic streaming from high-intensity focused ultrasound to make and load GUVs from bulk solutions, without the need for nozzles that can become clogged or otherwise alter the solution composition. In this method, a compact acoustic lens is focused on a planar lipid bilayer formed between two aqueous solutions. The actuation of a planar piezoelectric material coupled to the lens accelerates a small volume of liquid, deforming the bilayer and forming a GUV containing the solution on the transducer side of the bilayer. As demonstrated here, acoustic jetting offers an alternative method for the generation of GUVs for biological and biophysical studies.
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Affiliation(s)
- Maxim Armstrong
- Department of Bioengineering, University of California, Berkeley, Berkeley, California 94720, USA
| | - Michael D. Vahey
- Department of Bioengineering, University of California, Berkeley, Berkeley, California 94720, USA
| | - Thomas P. Hunt
- Department of Bioengineering, University of California, Berkeley, Berkeley, California 94720, USA
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22
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Belardi B, Son S, Felce JH, Dustin ML, Fletcher DA. Cell-cell interfaces as specialized compartments directing cell function. Nat Rev Mol Cell Biol 2020; 21:750-764. [PMID: 33093672 DOI: 10.1038/s41580-020-00298-7] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/09/2020] [Indexed: 12/14/2022]
Abstract
Cell-cell interfaces are found throughout multicellular organisms, from transient interactions between motile immune cells to long-lived cell-cell contacts in epithelia. Studies of immune cell interactions, epithelial cell barriers, neuronal contacts and sites of cell-cell fusion have identified a core set of features shared by cell-cell interfaces that critically control their function. Data from diverse cell types also show that cells actively and passively regulate the localization, strength, duration and cytoskeletal coupling of receptor interactions governing cell-cell signalling and physical connections between cells, indicating that cell-cell interfaces have a unique membrane organization that emerges from local molecular and cellular mechanics. In this Review, we discuss recent findings that support the emerging view of cell-cell interfaces as specialized compartments that biophysically constrain the arrangement and activity of their protein, lipid and glycan components. We also review how these biophysical features of cell-cell interfaces allow cells to respond with high selectivity and sensitivity to multiple inputs, serving as the basis for wide-ranging cellular functions. Finally, we consider how the unique properties of cell-cell interfaces present opportunities for therapeutic intervention.
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Affiliation(s)
- Brian Belardi
- Department of Bioengineering & Biophysics Program, UC Berkeley, Berkeley, CA, USA
| | - Sungmin Son
- Department of Bioengineering & Biophysics Program, UC Berkeley, Berkeley, CA, USA
| | | | | | - Daniel A Fletcher
- Department of Bioengineering & Biophysics Program, UC Berkeley, Berkeley, CA, USA. .,Division of Biological Systems & Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. .,Chan Zuckerberg Biohub, San Francisco, CA, USA.
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23
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Nesemann JM, Seider MI, Snyder BM, Maamari RN, Fletcher DA, Haile BA, Tadesse Z, Varnado NE, Cotter SY, Callahan EK, Emerson PM, Margolis TP, Lietman TM, Keenan JD. Comparison of Smartphone Photography, Single-Lens Reflex Photography, and Field-Grading for Trachoma. Am J Trop Med Hyg 2020; 103:2488-2491. [PMID: 33021196 DOI: 10.4269/ajtmh.20-0386] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Conjunctival examination for trachomatous inflammation-follicular (TF) guides public health decisions for trachoma. Smartphone cameras may allow remote conjunctival grading, but previous studies have found low sensitivity. A random sample of 412 children aged 1-9 years received an in-person conjunctival examination and then had conjunctival photographs taken with 1) a single-lens reflex (SLR) camera and 2) a smartphone coupled to a 3D-printed magnifying attachment. Three masked graders assessed the conjunctival photographs for TF. Latent class analysis was used to determine the sensitivity and specificity of each grading method for TF. Single-lens reflex photo-grading was 95.0% sensitive and 93.6% specific, and smartphone photo-grading was 84.1% sensitive and 97.6% specific. The sensitivity of the smartphone-CellScope device was considerably higher than that of a previous study using the native smartphone camera, without attachment. Magnification of smartphone images with a simple attachment improved the grading sensitivity while maintaining high specificity in a region with hyperendemic trachoma.
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Affiliation(s)
- John M Nesemann
- Francis I Proctor Foundation, University of California, San Francisco, San Francisco, California.,David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
| | - Michael I Seider
- Department of Ophthalmology, University of California, San Francisco, San Francisco, California.,Francis I Proctor Foundation, University of California, San Francisco, San Francisco, California
| | - Blake M Snyder
- Francis I Proctor Foundation, University of California, San Francisco, San Francisco, California
| | - Robi N Maamari
- Department of Bioengineering, University of California, Berkeley, Berkeley, California.,Francis I Proctor Foundation, University of California, San Francisco, San Francisco, California
| | - Daniel A Fletcher
- Department of Bioengineering, University of California, Berkeley, Berkeley, California
| | | | | | - Nicole E Varnado
- Francis I Proctor Foundation, University of California, San Francisco, San Francisco, California
| | - Sun Y Cotter
- Francis I Proctor Foundation, University of California, San Francisco, San Francisco, California
| | | | | | - Todd P Margolis
- Department of Ophthalmology and Visual Sciences, Washington University School of Medicine in St. Louis, St. Louis, Missouri
| | - Thomas M Lietman
- Institute for Global Health Sciences, University of California, San Francisco, San Francisco, California.,Department of Ophthalmology, University of California, San Francisco, San Francisco, California.,Francis I Proctor Foundation, University of California, San Francisco, San Francisco, California.,Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California
| | - Jeremy D Keenan
- Department of Ophthalmology, University of California, San Francisco, San Francisco, California.,Francis I Proctor Foundation, University of California, San Francisco, San Francisco, California
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24
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Fedele C, Mäntylä E, Belardi B, Hamkins-Indik T, Cavalli S, Netti PA, Fletcher DA, Nymark S, Priimagi A, Ihalainen TO. Azobenzene-based sinusoidal surface topography drives focal adhesion confinement and guides collective migration of epithelial cells. Sci Rep 2020; 10:15329. [PMID: 32948792 PMCID: PMC7501301 DOI: 10.1038/s41598-020-71567-w] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [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: 11/04/2019] [Accepted: 08/14/2020] [Indexed: 01/09/2023] Open
Abstract
Surface topography is a key parameter in regulating the morphology and behavior of single cells. At multicellular level, coordinated cell displacements drive many biological events such as embryonic morphogenesis. However, the effect of surface topography on collective migration of epithelium has not been studied in detail. Mastering the connection between surface features and collective cellular behaviour is highly important for novel approaches in tissue engineering and repair. Herein, we used photopatterned microtopographies on azobenzene-containing materials and showed that smooth topographical cues with proper period and orientation can efficiently orchestrate cell alignment in growing epithelium. Furthermore, the experimental system allowed us to investigate how the orientation of the topographical features can alter the speed of wound closure in vitro. Our findings indicate that the extracellular microenvironment topography coordinates their focal adhesion distribution and alignment. These topographic cues are able to guide the collective migration of multicellular systems, even when cell-cell junctions are disrupted.
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Affiliation(s)
- Chiara Fedele
- Faculty of Engineering and Natural Sciences, Tampere University, Tampere, Finland
| | - Elina Mäntylä
- BioMediTech and Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Brian Belardi
- Department of Bioengineering and Biophysics Program, University of California, Berkeley, CA, 94720, USA
| | - Tiama Hamkins-Indik
- Department of Bioengineering and Biophysics Program, University of California, Berkeley, CA, 94720, USA
| | - Silvia Cavalli
- Istituto Italiano Di Tecnologia, Center for Advanced Biomaterials for Healthcare @CRIB, Naples, Italy
| | - Paolo A Netti
- Istituto Italiano Di Tecnologia, Center for Advanced Biomaterials for Healthcare @CRIB, Naples, Italy
| | - Daniel A Fletcher
- Department of Bioengineering and Biophysics Program, University of California, Berkeley, CA, 94720, USA
- Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA
- Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Soile Nymark
- BioMediTech and Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Arri Priimagi
- Faculty of Engineering and Natural Sciences, Tampere University, Tampere, Finland.
| | - Teemu O Ihalainen
- BioMediTech and Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.
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25
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Son S, Takatori SC, Belardi B, Podolski M, Bakalar MH, Fletcher DA. Molecular height measurement by cell surface optical profilometry (CSOP). Proc Natl Acad Sci U S A 2020; 117:14209-14219. [PMID: 32513731 PMCID: PMC7322024 DOI: 10.1073/pnas.1922626117] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [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: 01/02/2023] Open
Abstract
The physical dimensions of proteins and glycans on cell surfaces can critically affect cell function, for example, by preventing close contact between cells and limiting receptor accessibility. However, high-resolution measurements of molecular heights on native cell membranes have been difficult to obtain. Here we present a simple and rapid method that achieves nanometer height resolution by localizing fluorophores at the tip and base of cell surface molecules and determining their separation by radially averaging across many molecules. We use this method, which we call cell surface optical profilometry (CSOP), to quantify the height of key multidomain proteins on a model cell, as well as to capture average protein and glycan heights on native cell membranes. We show that average height of a protein is significantly smaller than its contour length, due to thermally driven bending and rotation on the membrane, and that height strongly depends on local surface and solution conditions. We find that average height increases with cell surface molecular crowding but decreases with solution crowding by solutes, both of which we confirm with molecular dynamics simulations. We also use experiments and simulations to determine the height of an epitope, based on the location of an antibody, which allows CSOP to profile various proteins and glycans on a native cell surface using antibodies and lectins. This versatile method for profiling cell surfaces has the potential to advance understanding of the molecular landscape of cells and the role of the molecular landscape in cell function.
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Affiliation(s)
- Sungmin Son
- Department of Bioengineering and Biophysics Program, University of California, Berkeley, CA 94720
| | - Sho C Takatori
- Department of Bioengineering and Biophysics Program, University of California, Berkeley, CA 94720
| | - Brian Belardi
- Department of Bioengineering and Biophysics Program, University of California, Berkeley, CA 94720
| | - Marija Podolski
- Department of Bioengineering and Biophysics Program, University of California, Berkeley, CA 94720
| | - Matthew H Bakalar
- Department of Bioengineering and Biophysics Program, University of California, Berkeley, CA 94720
| | - Daniel A Fletcher
- Department of Bioengineering and Biophysics Program, University of California, Berkeley, CA 94720;
- Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
- Chan Zuckerberg Biohub, San Francisco, CA 94158
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26
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Joffe AM, Bakalar MH, Fletcher DA. Macrophage phagocytosis assay with reconstituted target particles. Nat Protoc 2020; 15:2230-2246. [DOI: 10.1038/s41596-020-0330-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 04/14/2020] [Indexed: 12/31/2022]
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27
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Chan KMC, Son S, Schmid EM, Fletcher DA. A viral fusogen hijacks the actin cytoskeleton to drive cell-cell fusion. eLife 2020; 9:51358. [PMID: 32441254 PMCID: PMC7244324 DOI: 10.7554/elife.51358] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 05/08/2020] [Indexed: 01/01/2023] Open
Abstract
Cell-cell fusion, which is essential for tissue development and used by some viruses to form pathological syncytia, is typically driven by fusogenic membrane proteins with tall (>10 nm) ectodomains that undergo conformational changes to bring apposing membranes in close contact prior to fusion. Here we report that a viral fusogen with a short (<2 nm) ectodomain, the reptilian orthoreovirus p14, accomplishes the same task by hijacking the actin cytoskeleton. We show that phosphorylation of the cytoplasmic domain of p14 triggers N-WASP-mediated assembly of a branched actin network. Using p14 mutants, we demonstrate that fusion is abrogated when binding of an adaptor protein is prevented and that direct coupling of the fusogenic ectodomain to branched actin assembly is sufficient to drive cell-cell fusion. This work reveals how the actin cytoskeleton can be harnessed to overcome energetic barriers to cell-cell fusion.
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Affiliation(s)
- Ka Man Carmen Chan
- UC Berkeley-UC San Francisco Graduate Group in Bioengineering, Berkeley, United States.,Department of Bioengineering & Biophysics Graduate Group, University of California, Berkeley, Berkeley, United States
| | - Sungmin Son
- Department of Bioengineering & Biophysics Graduate Group, University of California, Berkeley, Berkeley, United States
| | - Eva M Schmid
- Department of Bioengineering & Biophysics Graduate Group, University of California, Berkeley, Berkeley, United States
| | - Daniel A Fletcher
- UC Berkeley-UC San Francisco Graduate Group in Bioengineering, Berkeley, United States.,Department of Bioengineering & Biophysics Graduate Group, University of California, Berkeley, Berkeley, United States.,Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, United States.,Chan Zuckerberg Biohub, San Francisco, United States
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28
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Lakshman B, Messing S, Schmid EM, Clogston JD, Gillette WK, Esposito D, Kessing B, Fletcher DA, Nissley DV, McCormick F, Stephen AG, Jean-Francois FL. Abstract A10: Quantitative biophysical analysis defining key components modulating KRAS recruitment to the plasma membrane. Mol Cancer Res 2020. [DOI: 10.1158/1557-3125.ras18-a10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
The KRAS fraction in the plasma membrane (PM) correlates with activation of the MAPK pathway and subsequent cellular proliferation. Understanding KRAS interaction with the PM constitutes a challenge given the complexity of the cellular environment. To gain insight on key components necessary for KRAS signal transduction at the membrane, we make use of reconstituted liposomes and giant unilamellar vesicles as synthetic membranes. Using surface plasmon resonance (SPR) spectroscopy, we demonstrate that KRAS and RAF1 domains interact with these membranes primarily through electrostatic interactions with negatively charged lipids reinforced by additional interactions involving phosphatidyl ethanolamine and cholesterol. RAF1 52-188 (RBDCRD) interacts with the membrane significantly more strongly than the isolated RBD or CRD domains and synergizes KRAS membrane partitioning. Calmodulin and PDE6 delta, but not galectin3, passively sequester KRAS and prevent it from binding to the PM. RAF1 RBDCRD interacts with membranes preferentially at non-raft lipids domains. The carboxyterminal O-methylation is crucial for KRAS membrane localization. These results contribute to a better understanding of how KRAS-membrane interaction can be tuned by multiple factors.
Citation Format: Bindu Lakshman, Simon Messing, Eva M. Schmid, Jeffrey D. Clogston, William K. Gillette, Dominic Esposito, Bailey Kessing, Daniel A. Fletcher, Dwight V. Nissley, Frank McCormick, Andrew G. Stephen, Frantz L. Jean-Francois. Quantitative biophysical analysis defining key components modulating KRAS recruitment to the plasma membrane [abstract]. In: Proceedings of the AACR Special Conference on Targeting RAS-Driven Cancers; 2018 Dec 9-12; San Diego, CA. Philadelphia (PA): AACR; Mol Cancer Res 2020;18(5_Suppl):Abstract nr A10.
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29
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Wei KY, Moschidi D, Bick MJ, Nerli S, McShan AC, Carter LP, Huang PS, Fletcher DA, Sgourakis NG, Boyken SE, Baker D. Computational design of closely related proteins that adopt two well-defined but structurally divergent folds. Proc Natl Acad Sci U S A 2020; 117:7208-7215. [PMID: 32188784 PMCID: PMC7132107 DOI: 10.1073/pnas.1914808117] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [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] [Indexed: 01/09/2023] Open
Abstract
The plasticity of naturally occurring protein structures, which can change shape considerably in response to changes in environmental conditions, is critical to biological function. While computational methods have been used for de novo design of proteins that fold to a single state with a deep free-energy minimum [P.-S. Huang, S. E. Boyken, D. Baker, Nature 537, 320-327 (2016)], and to reengineer natural proteins to alter their dynamics [J. A. Davey, A. M. Damry, N. K. Goto, R. A. Chica, Nat. Chem. Biol. 13, 1280-1285 (2017)] or fold [P. A. Alexander, Y. He, Y. Chen, J. Orban, P. N. Bryan, Proc. Natl. Acad. Sci. U.S.A. 106, 21149-21154 (2009)], the de novo design of closely related sequences which adopt well-defined but structurally divergent structures remains an outstanding challenge. We designed closely related sequences (over 94% identity) that can adopt two very different homotrimeric helical bundle conformations-one short (∼66 Å height) and the other long (∼100 Å height)-reminiscent of the conformational transition of viral fusion proteins. Crystallographic and NMR spectroscopic characterization shows that both the short- and long-state sequences fold as designed. We sought to design bistable sequences for which both states are accessible, and obtained a single designed protein sequence that populates either the short state or the long state depending on the measurement conditions. The design of sequences which are poised to adopt two very different conformations sets the stage for creating large-scale conformational switches between structurally divergent forms.
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Affiliation(s)
- Kathy Y Wei
- Department of Biochemistry, University of Washington, Seattle, WA 98195
- Institute for Protein Design, University of Washington, Seattle, WA 98195
- Department of Bioengineering, University of California, Berkeley, CA 94720
| | - Danai Moschidi
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064
| | - Matthew J Bick
- Department of Biochemistry, University of Washington, Seattle, WA 98195
- Institute for Protein Design, University of Washington, Seattle, WA 98195
| | - Santrupti Nerli
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064
- Department of Computer Science, University of California, Santa Cruz, CA 95064
| | - Andrew C McShan
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064
| | - Lauren P Carter
- Institute for Protein Design, University of Washington, Seattle, WA 98195
| | - Po-Ssu Huang
- Department of Bioengineering, Stanford University, Stanford, CA 94305
| | - Daniel A Fletcher
- Department of Bioengineering, University of California, Berkeley, CA 94720
- Joint UC Berkeley-UC San Francisco Graduate Group in Bioengineering, Berkeley, CA 94720
- Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
- Chan Zuckerberg Biohub, San Francisco, CA 94158
| | - Nikolaos G Sgourakis
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064
| | - Scott E Boyken
- Department of Biochemistry, University of Washington, Seattle, WA 98195;
- Institute for Protein Design, University of Washington, Seattle, WA 98195
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA 98195;
- Institute for Protein Design, University of Washington, Seattle, WA 98195
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195
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30
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Li TD, Bieling P, Mullins D, Fletcher DA. Dynamics of Force-Regulated Branched Actin Network Density. Biophys J 2020. [DOI: 10.1016/j.bpj.2019.11.2460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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31
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32
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Harris AR, Belardi B, Jreij P, Wei K, Shams H, Bausch A, Fletcher DA. Steric regulation of tandem calponin homology domain actin-binding affinity. Mol Biol Cell 2019; 30:3112-3122. [PMID: 31693446 PMCID: PMC6938246 DOI: 10.1091/mbc.e19-06-0317] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 10/03/2019] [Accepted: 10/29/2019] [Indexed: 11/11/2022] Open
Abstract
Tandem calponin homology (CH1-CH2) domains are common actin-binding domains in proteins that interact with and organize the actin cytoskeleton. Despite regions of high sequence similarity, CH1-CH2 domains can have remarkably different actin-binding properties, with disease-associated point mutants known to increase as well as decrease affinity for F-actin. To investigate features that affect CH1-CH2 affinity for F-actin in cells and in vitro, we perturbed the utrophin actin-binding domain by making point mutations at the CH1-CH2 interface, replacing the linker domain, and adding a polyethylene glycol (PEG) polymer to CH2. Consistent with a previous model describing CH2 as a steric negative regulator of actin binding, we find that utrophin CH1-CH2 affinity is both increased and decreased by modifications that change the effective "openness" of CH1 and CH2 in solution. We also identified interface mutations that caused a large increase in affinity without changing solution "openness," suggesting additional influences on affinity. Interestingly, we also observe nonuniform subcellular localization of utrophin CH1-CH2 that depends on the N-terminal flanking region but not on bulk affinity. These observations provide new insights into how small sequence changes, such as those found in diseases, can affect CH1-CH2 binding properties.
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Affiliation(s)
- Andrew R. Harris
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720
| | - Brian Belardi
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720
| | - Pamela Jreij
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720
| | - Kathy Wei
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720
| | - Hengameh Shams
- Department of Mechanical Engineering, University of California, Berkeley, Berkeley, CA 94720
| | - Andreas Bausch
- Lehrstuhl für Biophysik (E27), Technische Universität München, Garching 85748, Germany
| | - Daniel A. Fletcher
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
- Chan Zuckerberg Biohub, San Francisco, CA 94158
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33
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Abstract
Physical stimuli are essential for the function of eukaryotic cells, and changes in physical signals are important elements in normal tissue development as well as in disease initiation and progression. The complexity of physical stimuli and the cellular signals they initiate are as complex as those triggered by chemical signals. One of the most important, and the focus of this review, is the effect of substrate mechanical properties on cell structure and function. The past decade has produced a nearly exponentially increasing number of mechanobiological studies to define how substrate stiffness alters cell biology using both purified systems and intact tissues. Here we attempt to identify common features of mechanosensing in different systems while also highlighting the numerous informative exceptions to what in early studies appeared to be simple rules by which cells respond to mechanical stresses.
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Affiliation(s)
- Paul A Janmey
- Department of Physiology, Institute for Medicine and Engineering, University of Pennsylvania, Philadelphia, Pennsylvania; Department of Bioengineering, University of California-Berkeley, Berkeley, California; and Department of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee
| | - Daniel A Fletcher
- Department of Physiology, Institute for Medicine and Engineering, University of Pennsylvania, Philadelphia, Pennsylvania; Department of Bioengineering, University of California-Berkeley, Berkeley, California; and Department of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee
| | - Cynthia A Reinhart-King
- Department of Physiology, Institute for Medicine and Engineering, University of Pennsylvania, Philadelphia, Pennsylvania; Department of Bioengineering, University of California-Berkeley, Berkeley, California; and Department of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee
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Sunny S, Baby A, James BL, Balaji D, N. V. A, Rana MH, Gurpur P, Skandarajah A, D’Ambrosio M, Ramanjinappa RD, Mohan SP, Raghavan N, Kandasarma U, N. S, Raghavan S, Hedne N, Koch F, Fletcher DA, Selvam S, Kollegal M, N. PB, Ladic L, Suresh A, Pandya HJ, Kuriakose MA. A smart tele-cytology point-of-care platform for oral cancer screening. PLoS One 2019; 14:e0224885. [PMID: 31730638 PMCID: PMC6857853 DOI: 10.1371/journal.pone.0224885] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 10/23/2019] [Indexed: 12/14/2022] Open
Abstract
Early detection of oral cancer necessitates a minimally invasive, tissue-specific diagnostic tool that facilitates screening/surveillance. Brush biopsy, though minimally invasive, demands skilled cyto-pathologist expertise. In this study, we explored the clinical utility/efficacy of a tele-cytology system in combination with Artificial Neural Network (ANN) based risk-stratification model for early detection of oral potentially malignant (OPML)/malignant lesion. A portable, automated tablet-based tele-cytology platform capable of digitization of cytology slides was evaluated for its efficacy in the detection of OPML/malignant lesions (n = 82) in comparison with conventional cytology and histology. Then, an image pre-processing algorithm was established to segregate cells, ANN was trained with images (n = 11,981) and a risk-stratification model developed. The specificity, sensitivity and accuracy of platform/ stratification model were computed, and agreement was examined using Kappa statistics. The tele-cytology platform, Cellscope, showed an overall accuracy of 84–86% with no difference between tele-cytology and conventional cytology in detection of oral lesions (kappa, 0.67–0.72). However, OPML could be detected with low sensitivity (18%) in accordance with the limitations of conventional cytology. The integration of image processing and development of an ANN-based risk stratification model improved the detection sensitivity of malignant lesions (93%) and high grade OPML (73%), thereby increasing the overall accuracy by 30%. Tele-cytology integrated with the risk stratification model, a novel strategy established in this study, can be an invaluable Point-of-Care (PoC) tool for early detection/screening in oral cancer. This study hence establishes the applicability of tele-cytology for accurate, remote diagnosis and use of automated ANN-based analysis in improving its efficacy.
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Affiliation(s)
- Sumsum Sunny
- Head and Neck Oncology, Mazumdar Shaw Medical Centre, NH Health city, Bangalore, India
- Integrated Head and Neck Oncology Program (DSRG-5), Mazumdar Shaw Medical Foundation, NH Health city, Bangalore, India
- Manipal Academy of Higher Education, Manipal, Karnataka, India
- Biomedical and Electronic (10-10) Engineering Systems Laboratory, Department of Electronic Systems Engineering, Indian Institute of Science, Bangalore, India
| | - Arun Baby
- Biomedical and Electronic (10-10) Engineering Systems Laboratory, Department of Electronic Systems Engineering, Indian Institute of Science, Bangalore, India
| | - Bonney Lee James
- Integrated Head and Neck Oncology Program (DSRG-5), Mazumdar Shaw Medical Foundation, NH Health city, Bangalore, India
| | - Dev Balaji
- Biomedical and Electronic (10-10) Engineering Systems Laboratory, Department of Electronic Systems Engineering, Indian Institute of Science, Bangalore, India
| | - Aparna N. V.
- Biomedical and Electronic (10-10) Engineering Systems Laboratory, Department of Electronic Systems Engineering, Indian Institute of Science, Bangalore, India
| | - Maitreya H. Rana
- Biomedical and Electronic (10-10) Engineering Systems Laboratory, Department of Electronic Systems Engineering, Indian Institute of Science, Bangalore, India
| | | | - Arunan Skandarajah
- Department of Bioengineering & Biophysics Program, University of California, Berkeley, California, United States of America
| | - Michael D’Ambrosio
- Department of Bioengineering & Biophysics Program, University of California, Berkeley, California, United States of America
| | | | - Sunil Paramel Mohan
- Department of Oral and Maxillofacial pathology, Sree Anjaneya Dental College, Kozhikode, Kerala, India
| | - Nisheena Raghavan
- Department of Pathology, Mazumdar Shaw Medical Centre, NH Health city, Bangalore, India
| | - Uma Kandasarma
- Department of Oral and Maxillofacial Pathology, KLE Society’s Institute of Dental Sciences, Bangalore, India
| | - Sangeetha N.
- Department of oral medicine and radiology, KLE Society’s Institute of Dental Sciences, Bangalore, India
| | - Subhasini Raghavan
- Department of oral medicine and radiology, KLE Society’s Institute of Dental Sciences, Bangalore, India
| | - Naveen Hedne
- Head and Neck Oncology, Mazumdar Shaw Medical Centre, NH Health city, Bangalore, India
| | - Felix Koch
- University of Mainz, 55099, Mainz, Germany
| | - Daniel A. Fletcher
- Department of Bioengineering & Biophysics Program, University of California, Berkeley, California, United States of America
| | - Sumithra Selvam
- Division of Epidemiology and Biostatistics, St. John’s Research Institute, St. John’s National Academy of Health Sciences, Bangalore, India
| | | | - Praveen Birur N.
- Head and Neck Oncology, Mazumdar Shaw Medical Centre, NH Health city, Bangalore, India
- Department of oral medicine and radiology, KLE Society’s Institute of Dental Sciences, Bangalore, India
| | - Lance Ladic
- Siemens Healthineers, Malvern, Pennsylvania, United States of America
| | - Amritha Suresh
- Head and Neck Oncology, Mazumdar Shaw Medical Centre, NH Health city, Bangalore, India
- Integrated Head and Neck Oncology Program (DSRG-5), Mazumdar Shaw Medical Foundation, NH Health city, Bangalore, India
| | - Hardik J. Pandya
- Biomedical and Electronic (10-10) Engineering Systems Laboratory, Department of Electronic Systems Engineering, Indian Institute of Science, Bangalore, India
- * E-mail: (HJP); (MAK)
| | - Moni Abraham Kuriakose
- Head and Neck Oncology, Mazumdar Shaw Medical Centre, NH Health city, Bangalore, India
- Integrated Head and Neck Oncology Program (DSRG-5), Mazumdar Shaw Medical Foundation, NH Health city, Bangalore, India
- * E-mail: (HJP); (MAK)
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Pion SD, Nana-Djeunga H, Niamsi-Emalio Y, Chesnais CB, Deléglise H, Mackenzie C, Stolk W, Fletcher DA, Klion AD, Nutman TB, Boussinesq M, Kamgno J. Implications for annual retesting after a test-and-not-treat strategy for onchocerciasis elimination in areas co-endemic with Loa loa infection: an observational cohort study. Lancet Infect Dis 2019; 20:102-109. [PMID: 31676244 PMCID: PMC8150319 DOI: 10.1016/s1473-3099(19)30554-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2019] [Revised: 07/31/2019] [Accepted: 08/09/2019] [Indexed: 11/22/2022]
Abstract
Background A test-and-not-treat (TaNT) strategy has been developed to prevent people with high concentrations of circulating Loa loa microfilariae (>20 000 microfilariae per mL) developing serious adverse events after ivermectin treatment during mass drug administration to eliminate onchocerciasis. An important question related to cost and programmatic issues is whether annual retesting is required for everyone. We therefore aimed to investigate changes in L loa microfilarial densities during TaNT campaigns run 18 months apart. Methods In this observational cohort study, we assessed the participants of two TaNT campaigns for onchocerciasis. These campaigns, which were run by a research team, together with personnel from the Ministry of Health and community health workers, were done in six health areas (in 89 communities) in Okola health district (Cameroon); the first campaign was run between Aug 10, and Oct 29, 2015, and the second was run between March 7, and May 26, 2017. All individuals aged 5 years and older were invited to be screened for Loa loa microfilaraemia before being offered ivermectin (unless contraindicated). L loa microfilarial density was measured at the point of care using the LoaScope. All those with a L loa microfilarial density of 20 000 microfilariae per mL or less were offered treatment; in the first 2 weeks of the 2015 campaign, a higher exclusion threshold of 26 000 microfilariae per mL or less was used. At both rounds of the intervention, participants were registered with a paper form, in which personal information were collected. In 2017, we also recorded whether each individual reported participation in the 2015 campaign. The primary outcome, assessed in all participants, was whether L loa microfilarial density was above or below the exclusion threshold (ie, the criteria that guided the decision to treat). Findings In the 2015 TaNT campaign, 26 415 people were censused versus 29 587 people in the 2017 TaNT campaign. All individuals aged 5 years and older without other contraindications to treatment (22 842 people in 2015 and 25 421 people in 2017) were invited to be screened for L loa microfilaraemia before being offered ivermectin. In 2015, 16 182 individuals were examined with the LoaScope, versus 18 697 individuals in the same communities in 2017. 344 (2·1%) individuals were excluded from ivermectin treatment because of a high L loa microfilarial density in 2015, versus 283 (1·5%) individuals in 2017 (p<0·0001). Records from 2017 could be matched to those from 2015 for 6983 individuals (43·2% of the 2015 participants). In this cohort, in 2017, 6981 (>99·9%) of 6983 individuals treated with ivermectin in 2015 had L loa microfilariae density below the level associated with neurological serious adverse events. Interpretation Individuals treated with ivermectin do not need to be retested for L loa microfilaraemia before the next treatment, provided that they can be re-identified. This adjusted approach will enable substantial cost savings and facilitate reaching programmatic goals for elimination of onchocerciasis in areas that are co-endemic for loiasis. Funding Bill & Melinda Gates Foundation, Division of Intramural Research (National Institute of Allergy and Infectious Diseases, US National Institutes of Health).
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Affiliation(s)
- Sébastien Ds Pion
- French Research Institute for Development-Unité Mixte Internationale 233 and French National Institute of Health and Medical Research-Unit 1175, University of Montpellier Montpellier, France.
| | - Hugues Nana-Djeunga
- Centre for Research on Filariasis and other Tropical Diseases, Yaounde, Cameroon
| | | | - Cédric B Chesnais
- French Research Institute for Development-Unité Mixte Internationale 233 and French National Institute of Health and Medical Research-Unit 1175, University of Montpellier Montpellier, France
| | - Hugo Deléglise
- French Research Institute for Development-Unité Mixte Internationale 233 and French National Institute of Health and Medical Research-Unit 1175, University of Montpellier Montpellier, France
| | - Charles Mackenzie
- Department of Pathobiology and Diagnostic Investigation, Michigan State University, East Lansing, MI, USA
| | - Wilma Stolk
- Department of Public Health, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | - Daniel A Fletcher
- Department of Bioengineering and Biophysics Programme, University of California, Berkeley, CA, USA
| | - Amy D Klion
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Thomas B Nutman
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Michel Boussinesq
- French Research Institute for Development-Unité Mixte Internationale 233 and French National Institute of Health and Medical Research-Unit 1175, University of Montpellier Montpellier, France
| | - Joseph Kamgno
- Centre for Research on Filariasis and other Tropical Diseases, Yaounde, Cameroon
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Li P, Paulus YM, Davila JR, Gosbee J, Margolis T, Fletcher DA, Kim TN. Usability testing of a smartphone-based retinal camera among first-time users in the primary care setting. ACTA ACUST UNITED AC 2019; 5:120-126. [PMID: 32864157 DOI: 10.1136/bmjinnov-2018-000321] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Smartphone-based retinal photography is a promising method for increasing accessibility of retinal screening in the primary care and community settings. Recent work has focused on validating its use in detection of diabetic retinopathy. However, retinal imaging can be technically challenging and additional work is needed to improve ease of retinal imaging in the primary care setting. We therefore performed usability testing of a smartphone-based retinal camera, RetinaScope, among medical assistants in primary care who had never performed retinal imaging. A total of 24 medical assistants performed first-time imaging in a total of five rounds of testing, and iterative improvements to the device were made between test rounds based on the results. The time to acquire a single ~50 degree image of the posterior pole of a model eye decreased from 283 ± 60 seconds to 34 ± 17 seconds (p < 0.01) for first-time users. The time to acquire 5 overlapping images of the retina decreased from 325 ± 60 seconds to 118 ± 26 seconds (p = 0.02) for first-time users. Testing in the human eye demonstrated that a single wide-view retinal image could be captured in 65 ± 7 seconds and 5 overlapping images in 229 ± 114 seconds. Users reported high Systems Usability Scores of 86 ± 13 throughout the rounds, reflecting a high level of comfort in first-time operation of the device. Our study demonstrates that smartphone-based retinal photography has the potential to be quickly adopted among medical assistants in the primary care setting.
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Affiliation(s)
- Patrick Li
- Department of Ophthalmology and Visual Sciences, University of Michigan School of Medicine, Ann Arbor, MI, USA
| | - Yannis M Paulus
- Department of Ophthalmology and Visual Sciences, University of Michigan School of Medicine, Ann Arbor, MI, USA.,Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Jose R Davila
- Department of Ophthalmology, Stanford University School of Medicine, Palo Alto, CA, USA
| | - John Gosbee
- Department of Internal Medicine, University of Michigan School of Medicine, Ann Arbor, MI, USA.,Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Todd Margolis
- Department of Ophthalmology and Visual Sciences, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Daniel A Fletcher
- Department of Bioengineering and Biophysics Program, University of California, Berkeley, Berkeley, CA, USA
| | - Tyson N Kim
- Department of Ophthalmology and Visual Sciences, University of Michigan School of Medicine, Ann Arbor, MI, USA
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Patel TP, Kim TN, Yu G, Dedania VS, Lieu P, Qian CX, Besirli CG, Demirci H, Margolis T, Fletcher DA, Paulus YM. Smartphone-Based, Rapid, Wide-Field Fundus Photography for Diagnosis of Pediatric Retinal Diseases. Transl Vis Sci Technol 2019; 8:29. [PMID: 31171996 PMCID: PMC6543857 DOI: 10.1167/tvst.8.3.29] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 03/28/2019] [Indexed: 12/31/2022] Open
Abstract
Purpose An important, unmet clinical need is for cost-effective, reliable, easy-to-use, and portable retinal photography to evaluate preventable causes of vision loss in children. This study presents the feasibility of a novel smartphone-based retinal imaging device tailored to imaging the pediatric fundus. Methods Several modifications for children were made to our previous device, including a child-friendly 3D printed housing of animals, attention-grabbing targets, enhanced image stitching, and video-recording capabilities. Retinal photographs were obtained in children undergoing routine dilated eye examination. Experienced masked retina-specialist graders determined photograph quality and made diagnoses based on the images, which were compared to the treating clinician's diagnosis. Results Dilated fundus photographs were acquired in 43 patients with a mean age of 6.7 years. The diagnoses included retinoblastoma, Coats' disease, commotio retinae, and optic nerve hypoplasia, among others. Mean time to acquire five standard photographs totaling 90-degree field of vision was 2.3 ± 1.1 minutes. Patients rated their experience of image acquisition favorably, with a Likert score of 4.6 ± 0.8 out of 5. There was 96% agreement between image-based diagnosis and the treating clinician's diagnosis. Conclusions We report a handheld smartphone-based device with modifications tailored for wide-field fundus photography in pediatric patients that can rapidly acquire fundus photos while being well-tolerated. Translational Relevance Advances in handheld smartphone-based fundus photography devices decrease the technical barrier for image acquisition in children and may potentially increase access to ophthalmic care in communities with limited resources.
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Affiliation(s)
- Tapan P Patel
- University of Michigan, Kellogg Eye Center, Department of Ophthalmology and Visual Sciences, Ann Arbor, MI, USA
| | - Tyson N Kim
- University of Michigan, Kellogg Eye Center, Department of Ophthalmology and Visual Sciences, Ann Arbor, MI, USA
| | - Gina Yu
- University of Michigan, Kellogg Eye Center, Department of Ophthalmology and Visual Sciences, Ann Arbor, MI, USA
| | - Vaidehi S Dedania
- New York University School of Medicine, Department of Ophthalmology, New York, NY, USA
| | - Philip Lieu
- University of Michigan, Kellogg Eye Center, Department of Ophthalmology and Visual Sciences, Ann Arbor, MI, USA
| | - Cynthia X Qian
- University of Montreal, Department of Ophthalmology, Montreal, Canada
| | - Cagri G Besirli
- University of Michigan, Kellogg Eye Center, Department of Ophthalmology and Visual Sciences, Ann Arbor, MI, USA
| | - Hakan Demirci
- University of Michigan, Kellogg Eye Center, Department of Ophthalmology and Visual Sciences, Ann Arbor, MI, USA
| | - Todd Margolis
- Washington University School of Medicine in St. Louis, Department of Ophthalmology and Visual Sciences, St. Louis, MO, USA
| | - Daniel A Fletcher
- University of California, Berkeley, Department of Bioengineering and Biophysics Program, Berkeley, CA, USA.,Chan-Zuckerberg Biohub, San Francisco, CA, USA
| | - Yannis M Paulus
- University of Michigan, Kellogg Eye Center, Department of Ophthalmology and Visual Sciences, Ann Arbor, MI, USA.,University of Michigan, Department of Biomedical Engineering, Ann Arbor, MI, USA
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Abstract
Influenza A virus (IAV) enters cells by binding to sialic acid on the cell surface. To accomplish this while avoiding immobilization by sialic acid in host mucus, viruses rely on a balance between the receptor-binding protein hemagglutinin (HA) and the receptor-cleaving protein neuraminidase (NA). Although genetic aspects of this balance are well-characterized, little is known about how the spatial organization of these proteins in the viral envelope may contribute. Using site-specific fluorescent labeling and super-resolution microscopy, we show that HA and NA are asymmetrically distributed on the surface of filamentous viruses, creating a spatial organization of binding and cleaving activities that causes viruses to step consistently away from their NA-rich pole. This Brownian ratchet-like diffusion produces persistent directional mobility that resolves the virus’s conflicting needs to both penetrate mucus and stably attach to the underlying cells, potentially contributing to the prevalence of the filamentous phenotype in clinical isolates of IAV.
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Affiliation(s)
- Michael D Vahey
- Department of Bioengineering, University of California, Berkeley, Berkeley, United States.,Biophysics Program, University of California, Berkeley, Berkeley, United States
| | - Daniel A Fletcher
- Department of Bioengineering, University of California, Berkeley, Berkeley, United States.,Biological Systems & Engineering, Lawrence Berkeley National Laboratory, Berkeley, United States.,Chan Zuckerberg Biohub, San Francisco, United States
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40
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Lakshman B, Messing S, Schmid EM, Clogston JD, Gillette WK, Esposito D, Kessing B, Fletcher DA, Nissley DV, McCormick F, Stephen AG, Jean-Francois FL. Quantitative biophysical analysis defines key components modulating recruitment of the GTPase KRAS to the plasma membrane. J Biol Chem 2018; 294:2193-2207. [PMID: 30559287 DOI: 10.1074/jbc.ra118.005669] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [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: 08/31/2018] [Revised: 11/28/2018] [Indexed: 11/06/2022] Open
Abstract
The gene encoding the GTPase KRAS is frequently mutated in pancreatic, lung, and colorectal cancers. The KRAS fraction in the plasma membrane (PM) correlates with activation of the mitogen-activated protein kinase (MAPK) pathway and subsequent cellular proliferation. Understanding KRAS's interaction with the PM is challenging given the complexity of the cellular environment. To gain insight into key components necessary for KRAS signal transduction at the PM, we used synthetic membranes such as liposomes and giant unilamellar vesicles. Using surface plasmon resonance (SPR) spectroscopy, we demonstrated that KRAS and Raf-1 proto-oncogene Ser/Thr kinase (RAF1) domains interact with these membranes primarily through electrostatic interactions with negatively charged lipids reinforced by additional interactions involving phosphatidyl ethanolamine and cholesterol. We found that the RAF1 region spanning RBD through CRD (RBDCRD) interacts with the membrane significantly more strongly than the isolated RBD or CRD domains and synergizes KRAS partitioning to the membrane. We also found that calmodulin and phosphodiesterase 6 delta (PDE6δ), but not galectin3 previously proposed to directly interact with KRAS, passively sequester KRAS and prevent it from partitioning into the PM. RAF1 RBDCRD interacted with membranes preferentially at nonraft lipid domains. Moreover, a C-terminal O-methylation was crucial for KRAS membrane localization. These results contribute to a better understanding of how the KRAS-membrane interaction is tuned by multiple factors whose identification could inform drug discovery efforts to disrupt this critical interaction in diseases such as cancer.
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Affiliation(s)
- Bindu Lakshman
- From the NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland 21702
| | - Simon Messing
- From the NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland 21702
| | - Eva M Schmid
- Department of Bioengineering, University of California Berkeley, Berkeley, California 94720
| | - Jeffrey D Clogston
- Nanotechnology Characterization Laboratory, Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, 21702
| | - William K Gillette
- From the NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland 21702
| | - Dominic Esposito
- From the NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland 21702
| | - Bailey Kessing
- From the NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland 21702
| | - Daniel A Fletcher
- Department of Bioengineering, University of California Berkeley, Berkeley, California 94720.,Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California 94720.,Chan Zuckerberg Biohub, San Francisco, California 94158
| | - Dwight V Nissley
- From the NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland 21702
| | - Frank McCormick
- From the NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland 21702.,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California 94158
| | - Andrew G Stephen
- From the NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland 21702
| | - Frantz L Jean-Francois
- From the NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland 21702,
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Vahey MD, Fletcher DA. Low-Fidelity Assembly of Influenza A Virus Promotes Escape from Host Cells. Cell 2018; 176:281-294.e19. [PMID: 30503209 DOI: 10.1016/j.cell.2018.10.056] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 09/05/2018] [Accepted: 10/26/2018] [Indexed: 12/11/2022]
Abstract
Influenza viruses inhabit a wide range of host environments using a limited repertoire of protein components. Unlike viruses with stereotyped shapes, influenza produces virions with significant morphological variability even within clonal populations. Whether this tendency to form pleiomorphic virions is coupled to compositional heterogeneity and whether it affects replicative fitness remains unclear. Here, we address these questions by developing a strain of influenza A virus amenable to rapid compositional characterization through quantitative, site-specific labeling of viral proteins. Using this strain, we find that influenza A produces virions with broad variations in size and composition from even single infected cells. This phenotypic variability contributes to virus survival during environmental challenges, including exposure to antivirals. Complementing genetic adaptations that act over larger populations and longer times, this "low-fidelity" assembly of influenza A virus allows small populations to survive environments that fluctuate over individual replication cycles.
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Affiliation(s)
- Michael D Vahey
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA.
| | - Daniel A Fletcher
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA; University of California, Berkeley/University of California, San Francisco Graduate Group in Bioengineering, Berkeley, CA 94720, USA; Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA.
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Mullins RD, Bieling P, Fletcher DA. From solution to surface to filament: actin flux into branched networks. Biophys Rev 2018; 10:1537-1551. [PMID: 30470968 DOI: 10.1007/s12551-018-0469-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [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: 09/10/2018] [Accepted: 10/21/2018] [Indexed: 02/05/2023] Open
Abstract
The actin cytoskeleton comprises a set of filament networks that perform essential functions in eukaryotic cells. The idea that actin filaments incorporate monomers directly from solution forms both the "textbook picture" of filament elongation and a conventional starting point for quantitative modeling of cellular actin dynamics. Recent work, however, reveals that filaments created by two major regulators, the formins and the Arp2/3 complex, incorporate monomers delivered by nearby proteins. Specifically, actin enters Arp2/3-generated networks via binding sites on nucleation-promoting factors clustered on membrane surfaces. Here, we describe three functions of this surface-associated actin monomer pool: (1) regulating network density via product inhibition of the Arp2/3 complex, (2) accelerating filament elongation as a distributive polymerase, and (3) converting profilin-actin into a substrate for the Arp2/3 complex. These linked functions control the architecture of branched networks and explain how capping protein enhances their growth.
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Affiliation(s)
- R Dyche Mullins
- Howard Hughes Medical Institute and Department of Cellular and Molecular Pharmacology, UCSF School of Medicine, San Francisco, CA, USA.
| | - Peter Bieling
- Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Daniel A Fletcher
- Department of Bioengineering, University of California, Berkeley, CA, USA
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Belardi B, Son S, Vahey MD, Wang J, Hou J, Fletcher DA. Claudin-4 reconstituted in unilamellar vesicles is sufficient to form tight interfaces that partition membrane proteins. J Cell Sci 2018; 132:jcs.221556. [PMID: 30209136 DOI: 10.1242/jcs.221556] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [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: 06/13/2018] [Accepted: 09/01/2018] [Indexed: 01/05/2023] Open
Abstract
Tight junctions have been hypothesized to act as molecular fences in the plasma membrane of epithelial cells, helping to form differentiated apical and basolateral domains. While this fence function is believed to arise from the interaction of four-pass transmembrane claudins, the complexity of tight junctions has made direct evidence of their role as a putative diffusion barrier difficult to obtain. Here, we address this challenge by reconstituting claudin-4 into giant unilamellar vesicles using microfluidic jetting. We find that reconstituted claudin-4 alone can form adhesive membrane interfaces without the accessory proteins that are present in vivo By controlling the molecular composition of the inner and outer leaflets of jetted vesicle membranes, we show that claudin-4-mediated interfaces can drive partitioning of extracellular membrane proteins with ectodomains as small as 5 nm but not of inner or outer leaflet lipids. Our findings indicate that homotypic interactions of claudins and their small size can contribute to the polarization of epithelial cells.
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Affiliation(s)
- Brian Belardi
- Department of Bioengineering and Biophysics Program, University of California, Berkeley, CA 94720, USA
| | - Sungmin Son
- Department of Bioengineering and Biophysics Program, University of California, Berkeley, CA 94720, USA
| | - Michael D Vahey
- Department of Bioengineering and Biophysics Program, University of California, Berkeley, CA 94720, USA
| | - Jinzhi Wang
- Department of Internal Medicine & Center for Investigation of Membrane Excitability Disease, Washington University Medical School, St. Louis, MO 63110, USA
| | - Jianghui Hou
- Department of Internal Medicine & Center for Investigation of Membrane Excitability Disease, Washington University Medical School, St. Louis, MO 63110, USA
| | - Daniel A Fletcher
- Department of Bioengineering and Biophysics Program, University of California, Berkeley, CA 94720, USA .,Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.,Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
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Kim TN, Myers F, Reber C, Loury PJ, Loumou P, Webster D, Echanique C, Li P, Davila JR, Maamari RN, Switz NA, Keenan J, Woodward MA, Paulus YM, Margolis T, Fletcher DA. A Smartphone-Based Tool for Rapid, Portable, and Automated Wide-Field Retinal Imaging. Transl Vis Sci Technol 2018; 7:21. [PMID: 30280006 PMCID: PMC6166894 DOI: 10.1167/tvst.7.5.21] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 08/05/2018] [Indexed: 11/24/2022] Open
Abstract
Purpose High-quality, wide-field retinal imaging is a valuable method for screening preventable, vision-threatening diseases of the retina. Smartphone-based retinal cameras hold promise for increasing access to retinal imaging, but variable image quality and restricted field of view can limit their utility. We developed and clinically tested a smartphone-based system that addresses these challenges with automation-assisted imaging. Methods The system was designed to improve smartphone retinal imaging by combining automated fixation guidance, photomontage, and multicolored illumination with optimized optics, user-tested ergonomics, and touch-screen interface. System performance was evaluated from images of ophthalmic patients taken by nonophthalmic personnel. Two masked ophthalmologists evaluated images for abnormalities and disease severity. Results The system automatically generated 100° retinal photomontages from five overlapping images in under 1 minute at full resolution (52.3 pixels per retinal degree) fully on-phone, revealing numerous retinal abnormalities. Feasibility of the system for diabetic retinopathy (DR) screening using the retinal photomontages was performed in 71 diabetics by masked graders. DR grade matched perfectly with dilated clinical examination in 55.1% of eyes and within 1 severity level for 85.2% of eyes. For referral-warranted DR, average sensitivity was 93.3% and specificity 56.8%. Conclusions Automation-assisted imaging produced high-quality, wide-field retinal images that demonstrate the potential of smartphone-based retinal cameras to be used for retinal disease screening. Translational Relevance Enhancement of smartphone-based retinal imaging through automation and software intelligence holds great promise for increasing the accessibility of retinal screening.
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Affiliation(s)
- Tyson N Kim
- Department of Ophthalmology and Visual Sciences, University of Michigan School of Medicine, Ann Arbor, MI, USA.,Department of Bioengineering and Biophysics Program, University of California, Berkeley, Berkeley, CA, USA.,Department of Ophthalmology, University of California, San Francisco, CA, USA
| | - Frank Myers
- Department of Bioengineering and Biophysics Program, University of California, Berkeley, Berkeley, CA, USA
| | - Clay Reber
- Department of Bioengineering and Biophysics Program, University of California, Berkeley, Berkeley, CA, USA
| | - P J Loury
- Department of Bioengineering and Biophysics Program, University of California, Berkeley, Berkeley, CA, USA
| | - Panagiota Loumou
- Department of Bioengineering and Biophysics Program, University of California, Berkeley, Berkeley, CA, USA
| | - Doug Webster
- Department of Bioengineering and Biophysics Program, University of California, Berkeley, Berkeley, CA, USA
| | - Chris Echanique
- Department of Bioengineering and Biophysics Program, University of California, Berkeley, Berkeley, CA, USA
| | - Patrick Li
- Department of Ophthalmology and Visual Sciences, University of Michigan School of Medicine, Ann Arbor, MI, USA
| | - Jose R Davila
- Department of Ophthalmology and Visual Sciences, University of Michigan School of Medicine, Ann Arbor, MI, USA
| | - Robi N Maamari
- Department of Bioengineering and Biophysics Program, University of California, Berkeley, Berkeley, CA, USA.,Department of Ophthalmology and Visual Sciences, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Neil A Switz
- Department of Physics and Astronomy, San José State University, San Jose, CA, USA
| | - Jeremy Keenan
- Department of Ophthalmology, University of California, San Francisco, CA, USA
| | - Maria A Woodward
- Department of Ophthalmology and Visual Sciences, University of Michigan School of Medicine, Ann Arbor, MI, USA
| | - Yannis M Paulus
- Department of Ophthalmology and Visual Sciences, University of Michigan School of Medicine, Ann Arbor, MI, USA
| | - Todd Margolis
- Department of Ophthalmology and Visual Sciences, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Daniel A Fletcher
- Department of Bioengineering and Biophysics Program, University of California, Berkeley, Berkeley, CA, USA.,Chan-Zuckerberg Biohub, San Francisco, CA, USA
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Diz-Muñoz A, Weiner OD, Fletcher DA. In pursuit of the mechanics that shape cell surfaces. Nat Phys 2018; 14:648-652. [PMID: 31007706 PMCID: PMC6469718 DOI: 10.1038/s41567-018-0187-8] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2017] [Revised: 04/09/2018] [Accepted: 05/25/2018] [Indexed: 05/25/2023]
Abstract
Robust and responsive, the surface of a cell is as important as its interior when it comes to mechanically regulating form and function. New techniques are shedding light on this role, and a common language to describe its properties is now needed.
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Affiliation(s)
- Alba Diz-Muñoz
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Orion D. Weiner
- Cardiovascular Research Institute, University of California, San Francisco, CA, USA
| | - Daniel A. Fletcher
- Bioengineering Department and Biophysics Program, University of California Berkeley, Berkeley, CA, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, California, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
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Abstract
Force transmission through the actin cytoskeleton plays a central role in cell movements, shape change, and internal organization. Dynamic reorganization of actin filaments by an array of specialized binding proteins creates biochemically and architecturally distinct structures, many of which are finely tuned to exert or resist mechanical loads. The molecular complexity of the actin cytoskeleton continues to be revealed by detailed biochemical assays, and the architectural diversity and dynamics of actin structures are being uncovered by advances in super-resolution fluorescence microscopy and electron microscopy. However, our understanding of how mechanical forces feed back on cytoskeletal architecture and actin-binding protein organization is comparatively limited. In this review, we discuss recent work investigating how mechanical forces applied to cytoskeletal proteins are transduced into biochemical signals. We explore multiple mechanisms for mechanical signal transduction, including the mechanosensitive behavior of actin-binding proteins, the effect of mechanical force on actin filament dynamics, and the influence of mechanical forces on the structure of single actin filaments. The emerging picture is one in which the actin cytoskeleton is defined not only by the set of proteins that constitute a network but also by the constant interplay of mechanical forces and biochemistry.
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Affiliation(s)
- Andrew R. Harris
- Department of Bioengineering, and Biophysics Program, University of California, Berkeley, California 94720, USA
| | - Pamela Jreij
- Department of Bioengineering, and Biophysics Program, University of California, Berkeley, California 94720, USA
| | - Daniel A. Fletcher
- Department of Bioengineering, and Biophysics Program, University of California, Berkeley, California 94720, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
- Chan Zuckerberg Biohub, San Francisco, California 94158, USA
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47
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Emukah E, Rakers LJ, Kahansim B, Miri ES, Nwoke BEB, Griswold E, Saka Y, Anagbogu I, Davies E, Ityonzughul C, D'Ambrosio M, Bakalar M, Fletcher DA, Nutman T, Kamgno J, Richards FO. In Southern Nigeria Loa loa Blood Microfilaria Density is Very Low Even in Areas with High Prevalence of Loiasis: Results of a Survey Using the New LoaScope Technology. Am J Trop Med Hyg 2018; 99:116-123. [PMID: 29761763 DOI: 10.4269/ajtmh.18-0163] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Ivermectin treatment can cause central nervous system adverse events (CNS-AEs) in persons with very high-density Loa loa microfilaremia (≥ 30,000 mf/mL blood). Hypoendemic onchocerciasis areas where L. loa is endemic have been excluded from ivermectin mass drug administration programs (MDA) because of the concern for CNS AEs. The rapid assessment procedure for L. loa (RAPLOA) is a questionnaire survey to assess history of eye worm. If ≥ 40% of respondents report eye worm, this correlates with ≥ 2% prevalence of very high-density loiasis microfilaremia, posing an unacceptable risk of CNS-AEs after MDA. In 2016, we conducted a L. loa study in 110 ivermectin-naïve, suspected onchocerciasis hypoendemic villages in southern Nigeria. In previous RAPLOA surveys these villages had prevalences between 10% and 67%. We examined 10,605 residents using the LoaScope, a cell phone-based imaging device for rapidly determining the microfilaria (mf) density of L. loa infections. The mean L. loa village mf prevalence was 6.3% (range 0-29%) and the mean individual mf count among positives was 326 mf/mL. The maximum individual mf count was only 11,429 mf/mL, and among 2,748 persons sampled from the 28 villages with ≥ 40% RAPLOA, the ≥ 2% threshold of very high Loa mf density could be excluded with high statistical confidence (P < 0.01). These findings indicate that ivermectin MDA can be delivered in this area with extremely low risk of L. loa-related CNS-AEs. We also concluded that in Nigeria the RAPLOA survey methodology is not predictive of ≥ 2% prevalence of very high-density L. loa microfilaremia.
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Affiliation(s)
| | | | | | | | | | | | - Yisa Saka
- Federal Ministry of Health, Abuja, Nigeria
| | | | | | | | | | | | | | | | - Joseph Kamgno
- Faculty of Medicine and Biomedical Sciences, University of Yaounde I, Yaoundé, Cameroon.,Centre for Research on Filariasis, Yaoundé, Cameroon
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Ricca BL, Venugopalan G, Furuta S, Tanner K, Orellana WA, Reber CD, Brownfield DG, Bissell MJ, Fletcher DA. Transient external force induces phenotypic reversion of malignant epithelial structures via nitric oxide signaling. eLife 2018; 7:e26161. [PMID: 29560858 PMCID: PMC5862525 DOI: 10.7554/elife.26161] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [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: 02/21/2017] [Accepted: 02/02/2018] [Indexed: 12/13/2022] Open
Abstract
Non-malignant breast epithelial cells cultured in three-dimensional laminin-rich extracellular matrix (lrECM) form well organized, growth-arrested acini, whereas malignant cells form continuously growing disorganized structures. While the mechanical properties of the microenvironment have been shown to contribute to formation of tissue-specific architecture, how transient external force influences this behavior remains largely unexplored. Here, we show that brief transient compression applied to single malignant breast cells in lrECM stimulated them to form acinar-like structures, a phenomenon we term 'mechanical reversion.' This is analogous to previously described phenotypic 'reversion' using biochemical inhibitors of oncogenic pathways. Compression stimulated nitric oxide production by malignant cells. Inhibition of nitric oxide production blocked mechanical reversion. Compression also restored coherent rotation in malignant cells, a behavior that is essential for acinus formation. We propose that external forces applied to single malignant cells restore cell-lrECM engagement and signaling lost in malignancy, allowing them to reestablish normal-like tissue architecture.
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Affiliation(s)
- Benjamin L Ricca
- Bioengineering Department and Biophysics ProgramUniversity of California, BerkeleyBerkeleyUnited States
| | - Gautham Venugopalan
- Bioengineering Department and Biophysics ProgramUniversity of California, BerkeleyBerkeleyUnited States
| | - Saori Furuta
- Biological Systems and Engineering DivisionLawrence Berkeley National LaboratoryBerkeleyUnited States
| | - Kandice Tanner
- Biological Systems and Engineering DivisionLawrence Berkeley National LaboratoryBerkeleyUnited States
- Center for Cancer ResearchNational Cancer Institute, National Institutes of HealthBethesdaUnited States
| | - Walter A Orellana
- Biological Systems and Engineering DivisionLawrence Berkeley National LaboratoryBerkeleyUnited States
- Center for Cancer ResearchNational Cancer Institute, National Institutes of HealthBethesdaUnited States
| | - Clay D Reber
- Bioengineering Department and Biophysics ProgramUniversity of California, BerkeleyBerkeleyUnited States
| | - Douglas G Brownfield
- Bioengineering Department and Biophysics ProgramUniversity of California, BerkeleyBerkeleyUnited States
- Biological Systems and Engineering DivisionLawrence Berkeley National LaboratoryBerkeleyUnited States
| | - Mina J Bissell
- Biological Systems and Engineering DivisionLawrence Berkeley National LaboratoryBerkeleyUnited States
| | - Daniel A Fletcher
- Bioengineering Department and Biophysics ProgramUniversity of California, BerkeleyBerkeleyUnited States
- Biological Systems and Engineering DivisionLawrence Berkeley National LaboratoryBerkeleyUnited States
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Kamgno J, Pion SD, Chesnais CB, Bakalar MH, D'Ambrosio MV, Mackenzie CD, Nana-Djeunga HC, Gounoue-Kamkumo R, Njitchouang GR, Nwane P, Tchatchueng-Mbouga JB, Wanji S, Stolk WA, Fletcher DA, Klion AD, Nutman TB, Boussinesq M. A Test-and-Not-Treat Strategy for Onchocerciasis in Loa loa-Endemic Areas. N Engl J Med 2017; 377:2044-2052. [PMID: 29116890 PMCID: PMC5629452 DOI: 10.1056/nejmoa1705026] [Citation(s) in RCA: 106] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
BACKGROUND Implementation of an ivermectin-based community treatment strategy for the elimination of onchocerciasis or lymphatic filariasis has been delayed in Central Africa because of the occurrence of serious adverse events, including death, in persons with high levels of circulating Loa loa microfilariae. The LoaScope, a field-friendly diagnostic tool to quantify L. loa microfilariae in peripheral blood, enables rapid, point-of-care identification of persons at risk for serious adverse events. METHODS A test-and-not-treat strategy was used in the approach to ivermectin treatment in the Okola health district in Cameroon, where the distribution of ivermectin was halted in 1999 after the occurrence of fatal events related to L. loa infection. The LoaScope was used to identify persons with an L. loa microfilarial density greater than 20,000 microfilariae per milliliter of blood, who were considered to be at risk for serious adverse events, and exclude them from ivermectin distribution. Active surveillance for posttreatment adverse events was performed daily for 6 days. RESULTS From August through October 2015, a total of 16,259 of 22,842 persons 5 years of age or older (71.2% of the target population) were tested for L. loa microfilaremia. Among the participants who underwent testing, a total of 15,522 (95.5%) received ivermectin, 340 (2.1%) were excluded from ivermectin distribution because of an L. loa microfilarial density above the risk threshold, and 397 (2.4%) were excluded because of pregnancy or illness. No serious adverse events were observed. Nonserious adverse events were recorded in 934 participants, most of whom (67.5%) had no detectable L. loa microfilariae. CONCLUSIONS The LoaScope-based test-and-not-treat strategy enabled the reimplementation of community-wide ivermectin distribution in a heretofore "off limits" health district in Cameroon and is a potentially practical approach to larger-scale ivermectin treatment for lymphatic filariasis and onchocerciasis in areas where L. loa infection is endemic. (Funded by the Bill and Melinda Gates Foundation and others.).
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Affiliation(s)
- Joseph Kamgno
- From the Center for Research on Filariasis and other Tropical Diseases (J.K., H.C.N.-D., R.G.-K., G.-R.N., P.N., J.B.T.-M.) and the Faculty of Medicine and Biomedical Sciences, University of Yaounde I (J.K.), Yaounde, and the Faculty of Health Sciences, Department of Microbiology and Parasitology, University of Buea, and Research Foundation for Tropical Diseases and Environment (REFOTDE), Buea (S.W.) - all in Cameroon; Institut de Recherche pour le Développement Unité Mixte Internationale 233-INSERM Unité 1175, Montpellier University, Montpellier, France (S.D.P., C.B.C., M.B.); the Department of Bioengineering and the Biophysics Program, University of California, Berkeley, Berkeley (M.H.B., M.V.D., D.A.F.); the Department of Pathobiology and Diagnostic Investigation, Michigan State University, East Lansing (C.D.M.); the Department of Public Health, Erasmus MC, University Medical Center, Rotterdam, the Netherlands (W.A.S.); the Chan Zuckerberg Biohub, San Francisco (D.A.F.); and the Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, MD (A.D.K., T.B.N.)
| | - Sébastien D Pion
- From the Center for Research on Filariasis and other Tropical Diseases (J.K., H.C.N.-D., R.G.-K., G.-R.N., P.N., J.B.T.-M.) and the Faculty of Medicine and Biomedical Sciences, University of Yaounde I (J.K.), Yaounde, and the Faculty of Health Sciences, Department of Microbiology and Parasitology, University of Buea, and Research Foundation for Tropical Diseases and Environment (REFOTDE), Buea (S.W.) - all in Cameroon; Institut de Recherche pour le Développement Unité Mixte Internationale 233-INSERM Unité 1175, Montpellier University, Montpellier, France (S.D.P., C.B.C., M.B.); the Department of Bioengineering and the Biophysics Program, University of California, Berkeley, Berkeley (M.H.B., M.V.D., D.A.F.); the Department of Pathobiology and Diagnostic Investigation, Michigan State University, East Lansing (C.D.M.); the Department of Public Health, Erasmus MC, University Medical Center, Rotterdam, the Netherlands (W.A.S.); the Chan Zuckerberg Biohub, San Francisco (D.A.F.); and the Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, MD (A.D.K., T.B.N.)
| | - Cédric B Chesnais
- From the Center for Research on Filariasis and other Tropical Diseases (J.K., H.C.N.-D., R.G.-K., G.-R.N., P.N., J.B.T.-M.) and the Faculty of Medicine and Biomedical Sciences, University of Yaounde I (J.K.), Yaounde, and the Faculty of Health Sciences, Department of Microbiology and Parasitology, University of Buea, and Research Foundation for Tropical Diseases and Environment (REFOTDE), Buea (S.W.) - all in Cameroon; Institut de Recherche pour le Développement Unité Mixte Internationale 233-INSERM Unité 1175, Montpellier University, Montpellier, France (S.D.P., C.B.C., M.B.); the Department of Bioengineering and the Biophysics Program, University of California, Berkeley, Berkeley (M.H.B., M.V.D., D.A.F.); the Department of Pathobiology and Diagnostic Investigation, Michigan State University, East Lansing (C.D.M.); the Department of Public Health, Erasmus MC, University Medical Center, Rotterdam, the Netherlands (W.A.S.); the Chan Zuckerberg Biohub, San Francisco (D.A.F.); and the Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, MD (A.D.K., T.B.N.)
| | - Matthew H Bakalar
- From the Center for Research on Filariasis and other Tropical Diseases (J.K., H.C.N.-D., R.G.-K., G.-R.N., P.N., J.B.T.-M.) and the Faculty of Medicine and Biomedical Sciences, University of Yaounde I (J.K.), Yaounde, and the Faculty of Health Sciences, Department of Microbiology and Parasitology, University of Buea, and Research Foundation for Tropical Diseases and Environment (REFOTDE), Buea (S.W.) - all in Cameroon; Institut de Recherche pour le Développement Unité Mixte Internationale 233-INSERM Unité 1175, Montpellier University, Montpellier, France (S.D.P., C.B.C., M.B.); the Department of Bioengineering and the Biophysics Program, University of California, Berkeley, Berkeley (M.H.B., M.V.D., D.A.F.); the Department of Pathobiology and Diagnostic Investigation, Michigan State University, East Lansing (C.D.M.); the Department of Public Health, Erasmus MC, University Medical Center, Rotterdam, the Netherlands (W.A.S.); the Chan Zuckerberg Biohub, San Francisco (D.A.F.); and the Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, MD (A.D.K., T.B.N.)
| | - Michael V D'Ambrosio
- From the Center for Research on Filariasis and other Tropical Diseases (J.K., H.C.N.-D., R.G.-K., G.-R.N., P.N., J.B.T.-M.) and the Faculty of Medicine and Biomedical Sciences, University of Yaounde I (J.K.), Yaounde, and the Faculty of Health Sciences, Department of Microbiology and Parasitology, University of Buea, and Research Foundation for Tropical Diseases and Environment (REFOTDE), Buea (S.W.) - all in Cameroon; Institut de Recherche pour le Développement Unité Mixte Internationale 233-INSERM Unité 1175, Montpellier University, Montpellier, France (S.D.P., C.B.C., M.B.); the Department of Bioengineering and the Biophysics Program, University of California, Berkeley, Berkeley (M.H.B., M.V.D., D.A.F.); the Department of Pathobiology and Diagnostic Investigation, Michigan State University, East Lansing (C.D.M.); the Department of Public Health, Erasmus MC, University Medical Center, Rotterdam, the Netherlands (W.A.S.); the Chan Zuckerberg Biohub, San Francisco (D.A.F.); and the Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, MD (A.D.K., T.B.N.)
| | - Charles D Mackenzie
- From the Center for Research on Filariasis and other Tropical Diseases (J.K., H.C.N.-D., R.G.-K., G.-R.N., P.N., J.B.T.-M.) and the Faculty of Medicine and Biomedical Sciences, University of Yaounde I (J.K.), Yaounde, and the Faculty of Health Sciences, Department of Microbiology and Parasitology, University of Buea, and Research Foundation for Tropical Diseases and Environment (REFOTDE), Buea (S.W.) - all in Cameroon; Institut de Recherche pour le Développement Unité Mixte Internationale 233-INSERM Unité 1175, Montpellier University, Montpellier, France (S.D.P., C.B.C., M.B.); the Department of Bioengineering and the Biophysics Program, University of California, Berkeley, Berkeley (M.H.B., M.V.D., D.A.F.); the Department of Pathobiology and Diagnostic Investigation, Michigan State University, East Lansing (C.D.M.); the Department of Public Health, Erasmus MC, University Medical Center, Rotterdam, the Netherlands (W.A.S.); the Chan Zuckerberg Biohub, San Francisco (D.A.F.); and the Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, MD (A.D.K., T.B.N.)
| | - Hugues C Nana-Djeunga
- From the Center for Research on Filariasis and other Tropical Diseases (J.K., H.C.N.-D., R.G.-K., G.-R.N., P.N., J.B.T.-M.) and the Faculty of Medicine and Biomedical Sciences, University of Yaounde I (J.K.), Yaounde, and the Faculty of Health Sciences, Department of Microbiology and Parasitology, University of Buea, and Research Foundation for Tropical Diseases and Environment (REFOTDE), Buea (S.W.) - all in Cameroon; Institut de Recherche pour le Développement Unité Mixte Internationale 233-INSERM Unité 1175, Montpellier University, Montpellier, France (S.D.P., C.B.C., M.B.); the Department of Bioengineering and the Biophysics Program, University of California, Berkeley, Berkeley (M.H.B., M.V.D., D.A.F.); the Department of Pathobiology and Diagnostic Investigation, Michigan State University, East Lansing (C.D.M.); the Department of Public Health, Erasmus MC, University Medical Center, Rotterdam, the Netherlands (W.A.S.); the Chan Zuckerberg Biohub, San Francisco (D.A.F.); and the Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, MD (A.D.K., T.B.N.)
| | - Raceline Gounoue-Kamkumo
- From the Center for Research on Filariasis and other Tropical Diseases (J.K., H.C.N.-D., R.G.-K., G.-R.N., P.N., J.B.T.-M.) and the Faculty of Medicine and Biomedical Sciences, University of Yaounde I (J.K.), Yaounde, and the Faculty of Health Sciences, Department of Microbiology and Parasitology, University of Buea, and Research Foundation for Tropical Diseases and Environment (REFOTDE), Buea (S.W.) - all in Cameroon; Institut de Recherche pour le Développement Unité Mixte Internationale 233-INSERM Unité 1175, Montpellier University, Montpellier, France (S.D.P., C.B.C., M.B.); the Department of Bioengineering and the Biophysics Program, University of California, Berkeley, Berkeley (M.H.B., M.V.D., D.A.F.); the Department of Pathobiology and Diagnostic Investigation, Michigan State University, East Lansing (C.D.M.); the Department of Public Health, Erasmus MC, University Medical Center, Rotterdam, the Netherlands (W.A.S.); the Chan Zuckerberg Biohub, San Francisco (D.A.F.); and the Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, MD (A.D.K., T.B.N.)
| | - Guy-Roger Njitchouang
- From the Center for Research on Filariasis and other Tropical Diseases (J.K., H.C.N.-D., R.G.-K., G.-R.N., P.N., J.B.T.-M.) and the Faculty of Medicine and Biomedical Sciences, University of Yaounde I (J.K.), Yaounde, and the Faculty of Health Sciences, Department of Microbiology and Parasitology, University of Buea, and Research Foundation for Tropical Diseases and Environment (REFOTDE), Buea (S.W.) - all in Cameroon; Institut de Recherche pour le Développement Unité Mixte Internationale 233-INSERM Unité 1175, Montpellier University, Montpellier, France (S.D.P., C.B.C., M.B.); the Department of Bioengineering and the Biophysics Program, University of California, Berkeley, Berkeley (M.H.B., M.V.D., D.A.F.); the Department of Pathobiology and Diagnostic Investigation, Michigan State University, East Lansing (C.D.M.); the Department of Public Health, Erasmus MC, University Medical Center, Rotterdam, the Netherlands (W.A.S.); the Chan Zuckerberg Biohub, San Francisco (D.A.F.); and the Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, MD (A.D.K., T.B.N.)
| | - Philippe Nwane
- From the Center for Research on Filariasis and other Tropical Diseases (J.K., H.C.N.-D., R.G.-K., G.-R.N., P.N., J.B.T.-M.) and the Faculty of Medicine and Biomedical Sciences, University of Yaounde I (J.K.), Yaounde, and the Faculty of Health Sciences, Department of Microbiology and Parasitology, University of Buea, and Research Foundation for Tropical Diseases and Environment (REFOTDE), Buea (S.W.) - all in Cameroon; Institut de Recherche pour le Développement Unité Mixte Internationale 233-INSERM Unité 1175, Montpellier University, Montpellier, France (S.D.P., C.B.C., M.B.); the Department of Bioengineering and the Biophysics Program, University of California, Berkeley, Berkeley (M.H.B., M.V.D., D.A.F.); the Department of Pathobiology and Diagnostic Investigation, Michigan State University, East Lansing (C.D.M.); the Department of Public Health, Erasmus MC, University Medical Center, Rotterdam, the Netherlands (W.A.S.); the Chan Zuckerberg Biohub, San Francisco (D.A.F.); and the Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, MD (A.D.K., T.B.N.)
| | - Jules B Tchatchueng-Mbouga
- From the Center for Research on Filariasis and other Tropical Diseases (J.K., H.C.N.-D., R.G.-K., G.-R.N., P.N., J.B.T.-M.) and the Faculty of Medicine and Biomedical Sciences, University of Yaounde I (J.K.), Yaounde, and the Faculty of Health Sciences, Department of Microbiology and Parasitology, University of Buea, and Research Foundation for Tropical Diseases and Environment (REFOTDE), Buea (S.W.) - all in Cameroon; Institut de Recherche pour le Développement Unité Mixte Internationale 233-INSERM Unité 1175, Montpellier University, Montpellier, France (S.D.P., C.B.C., M.B.); the Department of Bioengineering and the Biophysics Program, University of California, Berkeley, Berkeley (M.H.B., M.V.D., D.A.F.); the Department of Pathobiology and Diagnostic Investigation, Michigan State University, East Lansing (C.D.M.); the Department of Public Health, Erasmus MC, University Medical Center, Rotterdam, the Netherlands (W.A.S.); the Chan Zuckerberg Biohub, San Francisco (D.A.F.); and the Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, MD (A.D.K., T.B.N.)
| | - Samuel Wanji
- From the Center for Research on Filariasis and other Tropical Diseases (J.K., H.C.N.-D., R.G.-K., G.-R.N., P.N., J.B.T.-M.) and the Faculty of Medicine and Biomedical Sciences, University of Yaounde I (J.K.), Yaounde, and the Faculty of Health Sciences, Department of Microbiology and Parasitology, University of Buea, and Research Foundation for Tropical Diseases and Environment (REFOTDE), Buea (S.W.) - all in Cameroon; Institut de Recherche pour le Développement Unité Mixte Internationale 233-INSERM Unité 1175, Montpellier University, Montpellier, France (S.D.P., C.B.C., M.B.); the Department of Bioengineering and the Biophysics Program, University of California, Berkeley, Berkeley (M.H.B., M.V.D., D.A.F.); the Department of Pathobiology and Diagnostic Investigation, Michigan State University, East Lansing (C.D.M.); the Department of Public Health, Erasmus MC, University Medical Center, Rotterdam, the Netherlands (W.A.S.); the Chan Zuckerberg Biohub, San Francisco (D.A.F.); and the Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, MD (A.D.K., T.B.N.)
| | - Wilma A Stolk
- From the Center for Research on Filariasis and other Tropical Diseases (J.K., H.C.N.-D., R.G.-K., G.-R.N., P.N., J.B.T.-M.) and the Faculty of Medicine and Biomedical Sciences, University of Yaounde I (J.K.), Yaounde, and the Faculty of Health Sciences, Department of Microbiology and Parasitology, University of Buea, and Research Foundation for Tropical Diseases and Environment (REFOTDE), Buea (S.W.) - all in Cameroon; Institut de Recherche pour le Développement Unité Mixte Internationale 233-INSERM Unité 1175, Montpellier University, Montpellier, France (S.D.P., C.B.C., M.B.); the Department of Bioengineering and the Biophysics Program, University of California, Berkeley, Berkeley (M.H.B., M.V.D., D.A.F.); the Department of Pathobiology and Diagnostic Investigation, Michigan State University, East Lansing (C.D.M.); the Department of Public Health, Erasmus MC, University Medical Center, Rotterdam, the Netherlands (W.A.S.); the Chan Zuckerberg Biohub, San Francisco (D.A.F.); and the Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, MD (A.D.K., T.B.N.)
| | - Daniel A Fletcher
- From the Center for Research on Filariasis and other Tropical Diseases (J.K., H.C.N.-D., R.G.-K., G.-R.N., P.N., J.B.T.-M.) and the Faculty of Medicine and Biomedical Sciences, University of Yaounde I (J.K.), Yaounde, and the Faculty of Health Sciences, Department of Microbiology and Parasitology, University of Buea, and Research Foundation for Tropical Diseases and Environment (REFOTDE), Buea (S.W.) - all in Cameroon; Institut de Recherche pour le Développement Unité Mixte Internationale 233-INSERM Unité 1175, Montpellier University, Montpellier, France (S.D.P., C.B.C., M.B.); the Department of Bioengineering and the Biophysics Program, University of California, Berkeley, Berkeley (M.H.B., M.V.D., D.A.F.); the Department of Pathobiology and Diagnostic Investigation, Michigan State University, East Lansing (C.D.M.); the Department of Public Health, Erasmus MC, University Medical Center, Rotterdam, the Netherlands (W.A.S.); the Chan Zuckerberg Biohub, San Francisco (D.A.F.); and the Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, MD (A.D.K., T.B.N.)
| | - Amy D Klion
- From the Center for Research on Filariasis and other Tropical Diseases (J.K., H.C.N.-D., R.G.-K., G.-R.N., P.N., J.B.T.-M.) and the Faculty of Medicine and Biomedical Sciences, University of Yaounde I (J.K.), Yaounde, and the Faculty of Health Sciences, Department of Microbiology and Parasitology, University of Buea, and Research Foundation for Tropical Diseases and Environment (REFOTDE), Buea (S.W.) - all in Cameroon; Institut de Recherche pour le Développement Unité Mixte Internationale 233-INSERM Unité 1175, Montpellier University, Montpellier, France (S.D.P., C.B.C., M.B.); the Department of Bioengineering and the Biophysics Program, University of California, Berkeley, Berkeley (M.H.B., M.V.D., D.A.F.); the Department of Pathobiology and Diagnostic Investigation, Michigan State University, East Lansing (C.D.M.); the Department of Public Health, Erasmus MC, University Medical Center, Rotterdam, the Netherlands (W.A.S.); the Chan Zuckerberg Biohub, San Francisco (D.A.F.); and the Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, MD (A.D.K., T.B.N.)
| | - Thomas B Nutman
- From the Center for Research on Filariasis and other Tropical Diseases (J.K., H.C.N.-D., R.G.-K., G.-R.N., P.N., J.B.T.-M.) and the Faculty of Medicine and Biomedical Sciences, University of Yaounde I (J.K.), Yaounde, and the Faculty of Health Sciences, Department of Microbiology and Parasitology, University of Buea, and Research Foundation for Tropical Diseases and Environment (REFOTDE), Buea (S.W.) - all in Cameroon; Institut de Recherche pour le Développement Unité Mixte Internationale 233-INSERM Unité 1175, Montpellier University, Montpellier, France (S.D.P., C.B.C., M.B.); the Department of Bioengineering and the Biophysics Program, University of California, Berkeley, Berkeley (M.H.B., M.V.D., D.A.F.); the Department of Pathobiology and Diagnostic Investigation, Michigan State University, East Lansing (C.D.M.); the Department of Public Health, Erasmus MC, University Medical Center, Rotterdam, the Netherlands (W.A.S.); the Chan Zuckerberg Biohub, San Francisco (D.A.F.); and the Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, MD (A.D.K., T.B.N.)
| | - Michel Boussinesq
- From the Center for Research on Filariasis and other Tropical Diseases (J.K., H.C.N.-D., R.G.-K., G.-R.N., P.N., J.B.T.-M.) and the Faculty of Medicine and Biomedical Sciences, University of Yaounde I (J.K.), Yaounde, and the Faculty of Health Sciences, Department of Microbiology and Parasitology, University of Buea, and Research Foundation for Tropical Diseases and Environment (REFOTDE), Buea (S.W.) - all in Cameroon; Institut de Recherche pour le Développement Unité Mixte Internationale 233-INSERM Unité 1175, Montpellier University, Montpellier, France (S.D.P., C.B.C., M.B.); the Department of Bioengineering and the Biophysics Program, University of California, Berkeley, Berkeley (M.H.B., M.V.D., D.A.F.); the Department of Pathobiology and Diagnostic Investigation, Michigan State University, East Lansing (C.D.M.); the Department of Public Health, Erasmus MC, University Medical Center, Rotterdam, the Netherlands (W.A.S.); the Chan Zuckerberg Biohub, San Francisco (D.A.F.); and the Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, MD (A.D.K., T.B.N.)
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Bieling P, Hansen SD, Akin O, Li TD, Hayden CC, Fletcher DA, Mullins RD. WH2 and proline-rich domains of WASP-family proteins collaborate to accelerate actin filament elongation. EMBO J 2017; 37:102-121. [PMID: 29141912 PMCID: PMC5753033 DOI: 10.15252/embj.201797039] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Revised: 09/19/2017] [Accepted: 09/20/2017] [Indexed: 02/04/2023] Open
Abstract
WASP‐family proteins are known to promote assembly of branched actin networks by stimulating the filament‐nucleating activity of the Arp2/3 complex. Here, we show that WASP‐family proteins also function as polymerases that accelerate elongation of uncapped actin filaments. When clustered on a surface, WASP‐family proteins can drive branched actin networks to grow much faster than they could by direct incorporation of soluble monomers. This polymerase activity arises from the coordinated action of two regulatory sequences: (i) a WASP homology 2 (WH2) domain that binds actin, and (ii) a proline‐rich sequence that binds profilin–actin complexes. In the absence of profilin, WH2 domains are sufficient to accelerate filament elongation, but in the presence of profilin, proline‐rich sequences are required to support polymerase activity by (i) bringing polymerization‐competent actin monomers in proximity to growing filament ends, and (ii) promoting shuttling of actin monomers from profilin–actin complexes onto nearby WH2 domains. Unoccupied WH2 domains transiently associate with free filament ends, preventing their growth and dynamically tethering the branched actin network to the WASP‐family proteins that create it. Collaboration between WH2 and proline‐rich sequences thus strikes a balance between filament growth and tethering. Our work expands the number of critical roles that WASP‐family proteins play in the assembly of branched actin networks to at least three: (i) promoting dendritic nucleation; (ii) linking actin networks to membranes; and (iii) accelerating filament elongation.
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Affiliation(s)
- Peter Bieling
- Department of Cellular and Molecular Pharmacology and Howard Hughes Medical Institute, University of California, San Francisco, CA, USA .,Department of Bioengineering & Biophysics Program, University of California, Berkeley, CA, USA.,Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Scott D Hansen
- Department of Cellular and Molecular Pharmacology and Howard Hughes Medical Institute, University of California, San Francisco, CA, USA
| | - Orkun Akin
- Department of Cellular and Molecular Pharmacology and Howard Hughes Medical Institute, University of California, San Francisco, CA, USA
| | - Tai-De Li
- Department of Bioengineering & Biophysics Program, University of California, Berkeley, CA, USA.,Chan Zuckerberg Biohub, San Francisco, CA, USA.,Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | | | - Daniel A Fletcher
- Department of Bioengineering & Biophysics Program, University of California, Berkeley, CA, USA .,Chan Zuckerberg Biohub, San Francisco, CA, USA.,Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - R Dyche Mullins
- Department of Cellular and Molecular Pharmacology and Howard Hughes Medical Institute, University of California, San Francisco, CA, USA
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