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Chen K, Stahl EC, Kang MH, Xu B, Allen R, Trinidad M, Doudna JA. Author Correction: Engineering self-deliverable ribonucleoproteins for genome editing in the brain. Nat Commun 2024; 15:3695. [PMID: 38693162 PMCID: PMC11063159 DOI: 10.1038/s41467-024-48087-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2024] Open
Affiliation(s)
- Kai Chen
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Elizabeth C Stahl
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, USA
| | - Min Hyung Kang
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Bryant Xu
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Ryan Allen
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Marena Trinidad
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Howard Hughes Medical 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, CA, USA.
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, USA.
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, USA.
- Gladstone Institutes, San Francisco, CA, USA.
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA.
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA.
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Chen K, Stahl EC, Kang MH, Xu B, Allen R, Trinidad M, Doudna JA. Engineering self-deliverable ribonucleoproteins for genome editing in the brain. Nat Commun 2024; 15:1727. [PMID: 38409124 PMCID: PMC10897210 DOI: 10.1038/s41467-024-45998-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 02/09/2024] [Indexed: 02/28/2024] Open
Abstract
The delivery of CRISPR ribonucleoproteins (RNPs) for genome editing in vitro and in vivo has important advantages over other delivery methods, including reduced off-target and immunogenic effects. However, effective delivery of RNPs remains challenging in certain cell types due to low efficiency and cell toxicity. To address these issues, we engineer self-deliverable RNPs that can promote efficient cellular uptake and carry out robust genome editing without the need for helper materials or biomolecules. Screening of cell-penetrating peptides (CPPs) fused to CRISPR-Cas9 protein identifies potent constructs capable of efficient genome editing of neural progenitor cells. Further engineering of these fusion proteins establishes a C-terminal Cas9 fusion with three copies of A22p, a peptide derived from human semaphorin-3a, that exhibits substantially improved editing efficacy compared to other constructs. We find that self-deliverable Cas9 RNPs generate robust genome edits in clinically relevant genes when injected directly into the mouse striatum. Overall, self-deliverable Cas9 proteins provide a facile and effective platform for genome editing in vitro and in vivo.
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Affiliation(s)
- Kai Chen
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Elizabeth C Stahl
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, USA
| | - Min Hyung Kang
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Bryant Xu
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Ryan Allen
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Marena Trinidad
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Howard Hughes Medical 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, CA, USA.
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, USA.
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, USA.
- Gladstone Institutes, San Francisco, CA, USA.
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA.
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA.
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Chen K, Stahl EC, Kang MH, Xu B, Allen R, Trinidad M, Doudna JA. Engineering self-deliverable ribonucleoproteins for genome editing in the brain. bioRxiv 2023:2023.11.15.567251. [PMID: 38014180 PMCID: PMC10680703 DOI: 10.1101/2023.11.15.567251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
The delivery of CRISPR ribonucleoproteins (RNPs) for genome editing in vitro and in vivo has important advantages over other delivery methods, including reduced off-target and immunogenic effects 1 . However, effective delivery of RNPs remains challenging in certain cell types due to low efficiency and cell toxicity. To address these issues, we engineered self-deliverable RNPs that can promote efficient cellular uptake and carry out robust genome editing without the need for helper materials or biomolecules. Screening of cell-penetrating peptides (CPPs) fused to CRISPR-Cas9 protein identified potent constructs capable of efficient genome editing of neural progenitor cells. Further engineering of these fusion proteins identified a C-terminal Cas9 fusion with three copies of A22p, a peptide derived from human semaphorin-3a, that exhibited substantially improved editing efficacy compared to other constructs. We found that self-deliverable Cas9 RNPs generated robust genome edits in clinically relevant genes when injected directly into the mouse striatum. Overall, self-deliverable Cas9 proteins provide a facile and effective platform for genome editing in vitro and in vivo .
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4
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Stahl EC, Sabo JK, Kang MH, Allen R, Applegate E, Kim SE, Kwon Y, Seth A, Lemus N, Salinas-Rios V, Soczek KM, Trinidad M, Vo LT, Jeans C, Wozniak A, Morris T, Kimberlin A, Foti T, Savage DF, Doudna JA. Genome editing in the mouse brain with minimally immunogenic Cas9 RNPs. Mol Ther 2023; 31:2422-2438. [PMID: 37403358 PMCID: PMC10422012 DOI: 10.1016/j.ymthe.2023.06.019] [Citation(s) in RCA: 4] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 05/18/2023] [Accepted: 06/29/2023] [Indexed: 07/06/2023] Open
Abstract
Transient delivery of CRISPR-Cas9 ribonucleoproteins (RNPs) into the central nervous system (CNS) for therapeutic genome editing could avoid limitations of viral vector-based delivery including cargo capacity, immunogenicity, and cost. Here, we tested the ability of cell-penetrant Cas9 RNPs to edit the mouse striatum when introduced using a convection-enhanced delivery system. These transient Cas9 RNPs showed comparable editing of neurons and reduced adaptive immune responses relative to one formulation of Cas9 delivered using AAV serotype 9. The production of ultra-low endotoxin Cas9 protein manufactured at scale further improved innate immunity. We conclude that injection-based delivery of minimally immunogenic CRISPR genome editing RNPs into the CNS provides a valuable alternative to virus-mediated genome editing.
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Affiliation(s)
- Elizabeth C Stahl
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Jennifer K Sabo
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Min Hyung Kang
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Ryan Allen
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Elizabeth Applegate
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Shin Eui Kim
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Yoonjin Kwon
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Anmol Seth
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Nicholas Lemus
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Viviana Salinas-Rios
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Katarzyna M Soczek
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Marena Trinidad
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Linda T Vo
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Chris Jeans
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA 94720, USA
| | | | | | | | | | - David F Savage
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Jennifer A Doudna
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA; MBIB Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Gladstone Institutes, University of California, Berkeley, San Francisco, CA 94114, USA.
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5
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Ma E, Chen K, Shi H, Stahl EC, Adler B, Trinidad M, Liu J, Zhou K, Ye J, Doudna J. Improved genome editing by an engineered CRISPR-Cas12a. Nucleic Acids Res 2022; 50:12689-12701. [PMID: 36537251 PMCID: PMC9825149 DOI: 10.1093/nar/gkac1192] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 11/23/2022] [Accepted: 11/29/2022] [Indexed: 12/24/2022] Open
Abstract
CRISPR-Cas12a is an RNA-guided, programmable genome editing enzyme found within bacterial adaptive immune pathways. Unlike CRISPR-Cas9, Cas12a uses only a single catalytic site to both cleave target double-stranded DNA (dsDNA) (cis-activity) and indiscriminately degrade single-stranded DNA (ssDNA) (trans-activity). To investigate how the relative potency of cis- versus trans-DNase activity affects Cas12a-mediated genome editing, we first used structure-guided engineering to generate variants of Lachnospiraceae bacterium Cas12a that selectively disrupt trans-activity. The resulting engineered mutant with the biggest differential between cis- and trans-DNase activity in vitro showed minimal genome editing activity in human cells, motivating a second set of experiments using directed evolution to generate additional mutants with robust genome editing activity. Notably, these engineered and evolved mutants had enhanced ability to induce homology-directed repair (HDR) editing by 2-18-fold compared to wild-type Cas12a when using HDR donors containing mismatches with crRNA at the PAM-distal region. Finally, a site-specific reversion mutation produced improved Cas12a (iCas12a) variants with superior genome editing efficiency at genomic sites that are difficult to edit using wild-type Cas12a. This strategy establishes a pipeline for creating improved genome editing tools by combining structural insights with randomization and selection. The available structures of other CRISPR-Cas enzymes will enable this strategy to be applied to improve the efficacy of other genome-editing proteins.
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Affiliation(s)
- Enbo Ma
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Kai Chen
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Honglue Shi
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA
| | - Elizabeth C Stahl
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA
| | - Ben Adler
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Marena Trinidad
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Junjie Liu
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Kaihong Zhou
- Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA
| | - Jinjuan Ye
- Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA
| | - Jennifer A Doudna
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA
- Department of Chemistry, University of California, Berkeley, CA, USA
- MBIB Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Gladstone Institutes, University of California, San Francisco, CA 94114, USA
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6
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Al-Shayeb B, Skopintsev P, Soczek KM, Stahl EC, Li Z, Groover E, Smock D, Eggers AR, Pausch P, Cress BF, Huang CJ, Staskawicz B, Savage DF, Jacobsen SE, Banfield JF, Doudna JA. Diverse virus-encoded CRISPR-Cas systems include streamlined genome editors. Cell 2022; 185:4574-4586.e16. [PMID: 36423580 DOI: 10.1016/j.cell.2022.10.020] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 09/10/2022] [Accepted: 10/18/2022] [Indexed: 11/24/2022]
Abstract
CRISPR-Cas systems are host-encoded pathways that protect microbes from viral infection using an adaptive RNA-guided mechanism. Using genome-resolved metagenomics, we find that CRISPR systems are also encoded in diverse bacteriophages, where they occur as divergent and hypercompact anti-viral systems. Bacteriophage-encoded CRISPR systems belong to all six known CRISPR-Cas types, though some lack crucial components, suggesting alternate functional roles or host complementation. We describe multiple new Cas9-like proteins and 44 families related to type V CRISPR-Cas systems, including the Casλ RNA-guided nuclease family. Among the most divergent of the new enzymes identified, Casλ recognizes double-stranded DNA using a uniquely structured CRISPR RNA (crRNA). The Casλ-RNA-DNA structure determined by cryoelectron microscopy reveals a compact bilobed architecture capable of inducing genome editing in mammalian, Arabidopsis, and hexaploid wheat cells. These findings reveal a new source of CRISPR-Cas enzymes in phages and highlight their value as genome editors in plant and human cells.
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Affiliation(s)
- Basem Al-Shayeb
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA; Innovative Genomics Institute, University of California, Berkeley, CA, USA; Department of Earth and Planetary Science, University of California, Berkeley, CA, USA; Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, USA; University of Melbourne, Melbourne, Australia; Department of Chemistry, University of California, Berkeley, CA, USA; MBIB Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; Gladstone Institutes, University of California, San Francisco, CA, USA
| | - Petr Skopintsev
- Innovative Genomics Institute, University of California, Berkeley, CA, USA; Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA; California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, USA
| | - Katarzyna M Soczek
- Innovative Genomics Institute, University of California, Berkeley, CA, USA; Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA; California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, USA
| | - Elizabeth C Stahl
- Innovative Genomics Institute, University of California, Berkeley, CA, USA; Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA; California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, USA
| | - Zheng Li
- Department of Molecular, Cellular and Developmental Biology, University of California, Los Angeles, CA, USA
| | - Evan Groover
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA; Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Dylan Smock
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Amy R Eggers
- Innovative Genomics Institute, University of California, Berkeley, CA, USA; Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Patrick Pausch
- Innovative Genomics Institute, University of California, Berkeley, CA, USA; Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Brady F Cress
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Carolyn J Huang
- Innovative Genomics Institute, University of California, Berkeley, CA, USA; Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Brian Staskawicz
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA; Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - David F Savage
- Innovative Genomics Institute, University of California, Berkeley, CA, USA; Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA; Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
| | - Steven E Jacobsen
- Department of Molecular, Cellular and Developmental Biology, University of California, Los Angeles, CA, USA; Howard Hughes Medical Institute, University of California, Los Angeles, CA, USA
| | - Jillian F Banfield
- Innovative Genomics Institute, University of California, Berkeley, CA, USA; Department of Earth and Planetary Science, University of California, Berkeley, CA, USA; Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, USA; University of Melbourne, Melbourne, Australia.
| | - Jennifer A Doudna
- Innovative Genomics Institute, University of California, Berkeley, CA, USA; Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA; California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, USA; Howard Hughes Medical Institute, University of California, Berkeley, CA, USA; Department of Chemistry, University of California, Berkeley, CA, USA; MBIB Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; Gladstone Institutes, University of California, San Francisco, CA, USA.
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7
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Lin-Shiao E, Pfeifer WG, Shy BR, Saffari Doost M, Chen E, Vykunta VS, Hamilton JR, Stahl EC, Lopez DM, Sandoval Espinoza CR, Deyanov AE, Lew RJ, Poirer MG, Marson A, Castro CE, Doudna JA. CRISPR-Cas9-mediated nuclear transport and genomic integration of nanostructured genes in human primary cells. Nucleic Acids Res 2022; 50:1256-1268. [PMID: 35104875 PMCID: PMC8860605 DOI: 10.1093/nar/gkac049] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 01/13/2022] [Accepted: 01/30/2022] [Indexed: 12/22/2022] Open
Abstract
DNA nanostructures are a promising tool to deliver molecular payloads to cells. DNA origami structures, where long single-stranded DNA is folded into a compact nanostructure, present an attractive approach to package genes; however, effective delivery of genetic material into cell nuclei has remained a critical challenge. Here, we describe the use of DNA nanostructures encoding an intact human gene and a fluorescent protein encoding gene as compact templates for gene integration by CRISPR-mediated homology-directed repair (HDR). Our design includes CRISPR–Cas9 ribonucleoprotein binding sites on DNA nanostructures to increase shuttling into the nucleus. We demonstrate efficient shuttling and genomic integration of DNA nanostructures using transfection and electroporation. These nanostructured templates display lower toxicity and higher insertion efficiency compared to unstructured double-stranded DNA templates in human primary cells. Furthermore, our study validates virus-like particles as an efficient method of DNA nanostructure delivery, opening the possibility of delivering nanostructures in vivo to specific cell types. Together, these results provide new approaches to gene delivery with DNA nanostructures and establish their use as HDR templates, exploiting both their design features and their ability to encode genetic information. This work also opens a door to translate other DNA nanodevice functions, such as biosensing, into cell nuclei.
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Affiliation(s)
- Enrique Lin-Shiao
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.,Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Wolfgang G Pfeifer
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH 43210, USA.,Department of Physics, The Ohio State University, Columbus, OH 43210, USA
| | - Brian R Shy
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA.,Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA.,Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Mohammad Saffari Doost
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.,Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Evelyn Chen
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.,Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Vivasvan S Vykunta
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA.,Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA
| | - Jennifer R Hamilton
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.,Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Elizabeth C Stahl
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.,Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Diana M Lopez
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH 43210, USA.,Biophysics Graduate Program, The Ohio State University, Columbus, OH 43210, USA.,Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Cindy R Sandoval Espinoza
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.,Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Alexander E Deyanov
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.,Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Rachel J Lew
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.,Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA.,Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA
| | - Michael G Poirer
- Department of Physics, The Ohio State University, Columbus, OH 43210, USA.,Biophysics Graduate Program, The Ohio State University, Columbus, OH 43210, USA.,Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Alexander Marson
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA.,Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA
| | - Carlos E Castro
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH 43210, USA.,Biophysics Graduate Program, The Ohio State University, Columbus, OH 43210, USA
| | - Jennifer A Doudna
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.,Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA.,Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA.,Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA.,Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA.,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley 94720, CA, USA.,California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA 94720, USA.,Gladstone Institutes, University of California, San Francisco, San Francisco, CA, 94158, USA
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8
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Stahl EC, Gopez AR, Tsuchida CA, Fan VB, Moehle EA, Witkowsky LB, Hamilton JR, Lin-Shiao E, McElroy M, McDevitt SL, Ciling A, Tsui CK, Pestal K, Gildea HK, Keller A, Sylvain IA, Williams C, Hirsh A, Ehrenberg AJ, Kantor R, Metzger M, Nelson KL, Urnov FD, Ringeisen BR, Giannikopoulos P, Doudna JA. LuNER: Multiplexed SARS-CoV-2 detection in clinical swab and wastewater samples. PLoS One 2021; 16:e0258263. [PMID: 34758033 PMCID: PMC8580221 DOI: 10.1371/journal.pone.0258263] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Accepted: 09/22/2021] [Indexed: 01/03/2023] Open
Abstract
Clinical and surveillance testing for the SARS-CoV-2 virus relies overwhelmingly on RT-qPCR-based diagnostics, yet several popular assays require 2-3 separate reactions or rely on detection of a single viral target, which adds significant time, cost, and risk of false-negative results. Furthermore, multiplexed RT-qPCR tests that detect at least two SARS-CoV-2 genes in a single reaction are typically not affordable for large scale clinical surveillance or adaptable to multiple PCR machines and plate layouts. We developed a RT-qPCR assay using the Luna Probe Universal One-Step RT-qPCR master mix with publicly available primers and probes to detect SARS-CoV-2 N gene, E gene, and human RNase P (LuNER) to address these shortcomings and meet the testing demands of a university campus and the local community. This cost-effective test is compatible with BioRad or Applied Biosystems qPCR machines, in 96 and 384-well formats, with or without sample pooling, and has a detection sensitivity suitable for both clinical reporting and wastewater surveillance efforts.
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Affiliation(s)
- Elizabeth C. Stahl
- University of California, Berkeley, Berkeley, CA, United States of America
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, United States of America
| | - Allan R. Gopez
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, United States of America
| | - Connor A. Tsuchida
- University of California, Berkeley, Berkeley, CA, United States of America
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, United States of America
| | - Vinson B. Fan
- University of California, Berkeley, Berkeley, CA, United States of America
| | - Erica A. Moehle
- University of California, Berkeley, Berkeley, CA, United States of America
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, United States of America
| | - Lea B. Witkowsky
- University of California, Berkeley, Berkeley, CA, United States of America
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, United States of America
| | - Jennifer R. Hamilton
- University of California, Berkeley, Berkeley, CA, United States of America
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, United States of America
| | - Enrique Lin-Shiao
- University of California, Berkeley, Berkeley, CA, United States of America
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, United States of America
| | - Matthew McElroy
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, United States of America
| | - Shana L. McDevitt
- University of California, Berkeley, Berkeley, CA, United States of America
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, United States of America
| | - Alison Ciling
- University of California, Berkeley, Berkeley, CA, United States of America
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, United States of America
| | - C. Kimberly Tsui
- University of California, Berkeley, Berkeley, CA, United States of America
| | - Kathleen Pestal
- University of California, Berkeley, Berkeley, CA, United States of America
| | - Holly K. Gildea
- University of California, Berkeley, Berkeley, CA, United States of America
| | - Amanda Keller
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, United States of America
| | - Iman A. Sylvain
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, United States of America
| | - Clara Williams
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, United States of America
| | - Ariana Hirsh
- University of California, Berkeley, Berkeley, CA, United States of America
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, United States of America
| | | | - Rose Kantor
- University of California, Berkeley, Berkeley, CA, United States of America
- Department of Civil and Environmental Engineering, University of California, Berkeley, CA, United States of America
| | - Matthew Metzger
- University of California, Berkeley, Berkeley, CA, United States of America
- Department of Civil and Environmental Engineering, University of California, Berkeley, CA, United States of America
| | - Kara L. Nelson
- University of California, Berkeley, Berkeley, CA, United States of America
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, United States of America
- Department of Civil and Environmental Engineering, University of California, Berkeley, CA, United States of America
| | - Fyodor D. Urnov
- University of California, Berkeley, Berkeley, CA, United States of America
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, United States of America
| | - Bradley R. Ringeisen
- University of California, Berkeley, Berkeley, CA, United States of America
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, United States of America
| | - Petros Giannikopoulos
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, United States of America
| | - Jennifer A. Doudna
- University of California, Berkeley, Berkeley, CA, United States of America
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, United States of America
- Howard Hughes Medical Institute, University of California, Berkeley, CA, United States of America
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9
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Hamilton JR, Stahl EC, Tsuchida CA, Lin-Shiao E, Tsui CK, Pestal K, Gildea HK, Witkowsky LB, Moehle EA, McDevitt SL, McElroy M, Keller A, Sylvain I, Hirsh A, Ciling A, Ehrenberg AJ, Ringeisen BR, Huberty G, Urnov FD, Giannikopoulos P, Doudna JA. Robotic RNA extraction for SARS-CoV-2 surveillance using saliva samples. PLoS One 2021; 16:e0255690. [PMID: 34351984 PMCID: PMC8341588 DOI: 10.1371/journal.pone.0255690] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [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: 02/17/2021] [Accepted: 07/21/2021] [Indexed: 01/22/2023] Open
Abstract
Saliva is an attractive specimen type for asymptomatic surveillance of COVID-19 in large populations due to its ease of collection and its demonstrated utility for detecting RNA from SARS-CoV-2. Multiple saliva-based viral detection protocols use a direct-to-RT-qPCR approach that eliminates nucleic acid extraction but can reduce viral RNA detection sensitivity. To improve test sensitivity while maintaining speed, we developed a robotic nucleic acid extraction method for detecting SARS-CoV-2 RNA in saliva samples with high throughput. Using this assay, the Free Asymptomatic Saliva Testing (IGI FAST) research study on the UC Berkeley campus conducted 11,971 tests on supervised self-collected saliva samples and identified rare positive specimens containing SARS-CoV-2 RNA during a time of low infection prevalence. In an attempt to increase testing capacity, we further adapted our robotic extraction assay to process pooled saliva samples. We also benchmarked our assay against nasopharyngeal swab specimens and found saliva methods require further optimization to match this gold standard. Finally, we designed and validated a RT-qPCR test suitable for saliva self-collection. These results establish a robotic extraction-based procedure for rapid PCR-based saliva testing that is suitable for samples from both symptomatic and asymptomatic individuals.
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Affiliation(s)
- Jennifer R. Hamilton
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, United States of America
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, United States of America
| | - Elizabeth C. Stahl
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, United States of America
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, United States of America
| | - Connor A. Tsuchida
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, United States of America
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, United States of America
- San Francisco Graduate Program in Bioengineering, University of California, Berkeley, Berkeley, CA, United States of America
| | - Enrique Lin-Shiao
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, United States of America
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, United States of America
| | - C. Kimberly Tsui
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, United States of America
| | - Kathleen Pestal
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, United States of America
| | - Holly K. Gildea
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, United States of America
| | - Lea B. Witkowsky
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, United States of America
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, United States of America
| | - Erica A. Moehle
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, United States of America
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, United States of America
| | - Shana L. McDevitt
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, United States of America
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, United States of America
| | - Matthew McElroy
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, United States of America
| | - Amanda Keller
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, United States of America
| | - Iman Sylvain
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, United States of America
| | - Ariana Hirsh
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, United States of America
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, United States of America
| | - Alison Ciling
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, United States of America
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, United States of America
| | - Alexander J. Ehrenberg
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, United States of America
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, United States of America
| | - Bradley R. Ringeisen
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, United States of America
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, United States of America
| | - Garth Huberty
- Washington Hospital Healthcare System Clinical Laboratory, Fremont, CA, United States of America
| | - Fyodor D. Urnov
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, United States of America
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, United States of America
| | - Petros Giannikopoulos
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, United States of America
| | - Jennifer A. Doudna
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, United States of America
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, United States of America
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, United States of America
- Gladstone Institutes, San Francisco, CA, United States of America
- Graduate Group in Biophysics, University of California, Berkeley, Berkeley, CA, United States of America
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States of America
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, United States of America
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10
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Ehrenberg AJ, Moehle EA, Brook CE, Doudna Cate AH, Witkowsky LB, Sachdeva R, Hirsh A, Barry K, Hamilton JR, Lin-Shiao E, McDevitt S, Valentin-Alvarado L, Letourneau KN, Hunter L, Keller A, Pestal K, Frankino PA, Murley A, Nandakumar D, Stahl EC, Tsuchida CA, Gildea HK, Murdock AG, Hochstrasser ML, O’Brien E, Ciling A, Tsitsiklis A, Worden K, Dugast-Darzacq C, Hays SG, Barber CC, McGarrigle R, Lam EK, Ensminger DC, Bardet L, Sherry C, Harte A, Nicolette G, Giannikopoulos P, Hockemeyer D, Petersen M, Urnov FD, Ringeisen BR, Boots M, Doudna JA. Launching a saliva-based SARS-CoV-2 surveillance testing program on a university campus. PLoS One 2021; 16:e0251296. [PMID: 34038425 PMCID: PMC8153421 DOI: 10.1371/journal.pone.0251296] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [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: 02/18/2021] [Accepted: 04/26/2021] [Indexed: 01/01/2023] Open
Abstract
Regular surveillance testing of asymptomatic individuals for SARS-CoV-2 has been center to SARS-CoV-2 outbreak prevention on college and university campuses. Here we describe the voluntary saliva testing program instituted at the University of California, Berkeley during an early period of the SARS-CoV-2 pandemic in 2020. The program was administered as a research study ahead of clinical implementation, enabling us to launch surveillance testing while continuing to optimize the assay. Results of both the testing protocol itself and the study participants' experience show how the program succeeded in providing routine, robust testing capable of contributing to outbreak prevention within a campus community and offer strategies for encouraging participation and a sense of civic responsibility.
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Affiliation(s)
- Alexander J. Ehrenberg
- University of California, Berkeley, California, United States of America
- Innovative Genomics Institute, University of California, Berkeley, California, United States of America
| | - Erica A. Moehle
- University of California, Berkeley, California, United States of America
- Innovative Genomics Institute, University of California, Berkeley, California, United States of America
| | - Cara E. Brook
- University of California, Berkeley, California, United States of America
- Innovative Genomics Institute, University of California, Berkeley, California, United States of America
| | | | - Lea B. Witkowsky
- University of California, Berkeley, California, United States of America
- Innovative Genomics Institute, University of California, Berkeley, California, United States of America
| | - Rohan Sachdeva
- University of California, Berkeley, California, United States of America
- Innovative Genomics Institute, University of California, Berkeley, California, United States of America
| | - Ariana Hirsh
- University of California, Berkeley, California, United States of America
- Innovative Genomics Institute, University of California, Berkeley, California, United States of America
| | - Kerrie Barry
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Jennifer R. Hamilton
- University of California, Berkeley, California, United States of America
- Innovative Genomics Institute, University of California, Berkeley, California, United States of America
| | - Enrique Lin-Shiao
- University of California, Berkeley, California, United States of America
- Innovative Genomics Institute, University of California, Berkeley, California, United States of America
| | - Shana McDevitt
- University of California, Berkeley, California, United States of America
- Innovative Genomics Institute, University of California, Berkeley, California, United States of America
| | - Luis Valentin-Alvarado
- University of California, Berkeley, California, United States of America
- Innovative Genomics Institute, University of California, Berkeley, California, United States of America
| | | | - Lauren Hunter
- University of California, Berkeley, California, United States of America
| | - Amanda Keller
- Innovative Genomics Institute, University of California, Berkeley, California, United States of America
| | - Kathleen Pestal
- University of California, Berkeley, California, United States of America
| | | | - Andrew Murley
- University of California, Berkeley, California, United States of America
| | - Divya Nandakumar
- University of California, Berkeley, California, United States of America
- Innovative Genomics Institute, University of California, Berkeley, California, United States of America
| | - Elizabeth C. Stahl
- University of California, Berkeley, California, United States of America
- Innovative Genomics Institute, University of California, Berkeley, California, United States of America
| | - Connor A. Tsuchida
- University of California, Berkeley, California, United States of America
- Innovative Genomics Institute, University of California, Berkeley, California, United States of America
| | - Holly K. Gildea
- University of California, Berkeley, California, United States of America
| | - Andrew G. Murdock
- University of California, Berkeley, California, United States of America
- Innovative Genomics Institute, University of California, Berkeley, California, United States of America
| | - Megan L. Hochstrasser
- Innovative Genomics Institute, University of California, Berkeley, California, United States of America
| | - Elizabeth O’Brien
- University of California, Berkeley, California, United States of America
- Innovative Genomics Institute, University of California, Berkeley, California, United States of America
| | - Alison Ciling
- University of California, Berkeley, California, United States of America
- Innovative Genomics Institute, University of California, Berkeley, California, United States of America
| | | | - Kurtresha Worden
- University of California, Berkeley, California, United States of America
- Innovative Genomics Institute, University of California, Berkeley, California, United States of America
| | | | - Stephanie G. Hays
- University of California, Berkeley, California, United States of America
| | - Colin C. Barber
- University of California, Berkeley, California, United States of America
| | - Riley McGarrigle
- University of California, Berkeley, California, United States of America
- Innovative Genomics Institute, University of California, Berkeley, California, United States of America
| | - Emily K. Lam
- University of California, Berkeley, California, United States of America
| | - David C. Ensminger
- University of California, Berkeley, California, United States of America
| | - Lucie Bardet
- Innovative Genomics Institute, University of California, Berkeley, California, United States of America
| | - Carolyn Sherry
- Innovative Genomics Institute, University of California, Berkeley, California, United States of America
| | - Anna Harte
- University of California, Berkeley, California, United States of America
- University Health Services, University of California, Berkeley, California, United States of America
| | - Guy Nicolette
- University of California, Berkeley, California, United States of America
- University Health Services, University of California, Berkeley, California, United States of America
| | - Petros Giannikopoulos
- Innovative Genomics Institute, University of California, Berkeley, California, United States of America
| | - Dirk Hockemeyer
- University of California, Berkeley, California, United States of America
- Innovative Genomics Institute, University of California, Berkeley, California, United States of America
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Maya Petersen
- University of California, Berkeley, California, United States of America
| | - Fyodor D. Urnov
- University of California, Berkeley, California, United States of America
- Innovative Genomics Institute, University of California, Berkeley, California, United States of America
| | - Bradley R. Ringeisen
- University of California, Berkeley, California, United States of America
- Innovative Genomics Institute, University of California, Berkeley, California, United States of America
| | - Mike Boots
- University of California, Berkeley, California, United States of America
| | - Jennifer A. Doudna
- University of California, Berkeley, California, United States of America
- Innovative Genomics Institute, University of California, Berkeley, California, United States of America
- Howard Hughes Medical Institute, University of California, Berkeley, California, United States of America
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11
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Cercone M, Brown BN, Stahl EC, Mitchell LM, Fortier LA, Mohammed HO, Ducharme NG. An Exploratory Study into the Implantation of Arytenoid Cartilage Scaffold in the Horse. Tissue Eng Part A 2021; 27:165-176. [PMID: 32539568 DOI: 10.1089/ten.tea.2019.0295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Respiratory function in the horse can be severely compromised by arytenoid chondritis, or arytenoid chondropathy, a pathologic condition leading to deformity and dysfunction of the affected cartilage. Current treatment in cases unresponsive to medical management is removal of the cartilage, which can improve the airway obstruction, but predisposes the patient to other complications like tracheal penetration of oropharyngeal content and dynamic collapse of the now unsupported soft tissue lateral to the cartilage. A tissue engineering approach to reconstructing the arytenoid cartilage would represent a significant advantage in the management of arytenoid chondritis. In this study, we explored if decellularized matrix could potentially be incorporated into the high motion environment of the arytenoid cartilages of horses. Equine arytenoid cartilages were decellularized and a portion of the resultant acellular scaffolds was implanted in a full-thickness defect created in the arytenoids of eight horses. The implantation was performed bilaterally in each horse, with one side randomly selected to receive an implant seeded with autologous bone marrow-derived nucleated cells (BMNCs). Arytenoids structure and function were monitored up to 4 months. In vivo assessments included laryngeal ultrasound, and laryngeal endoscopy at rest and during exercise on a high-speed treadmill. Histologic evaluation of the arytenoids was performed postmortem. Implantation of the cartilaginous graft had no adverse effect on laryngeal respiratory function or swallowing, despite induction of a transient granuloma on the medial aspect of the arytenoids. Ultrasonographic monitoring detected a postoperative increase in the thickness and cross-sectional area of the arytenoid body that receded faster in the arytenoids not seeded with BMNCs. The explanted tissue showed epithelialization of the mucosal surface, integration of the implant into the native arytenoid, with minimal adverse cellular reaction. Remodeling of the scaffold material was evident by 2 months after implantation. Preseeding the scaffold with BMNCs increased the rate of scaffold degradation and incorporation. Replacement of arytenoid portion with a tissue-engineered cartilaginous graft preseeded with BMNCs is surgically feasible in the horse, is well tolerated, and results in appropriate integration within the native tissue, also preventing laryngeal tissue collapse during exercise.
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Affiliation(s)
- Marta Cercone
- Department of Clinical Sciences, College of Veterinary medicine, Cornell University, Ithaca, New York, USA
| | - Bryan N Brown
- McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Department of Bioengineering, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Elizabeth C Stahl
- McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Lisa M Mitchell
- Department of Clinical Sciences, College of Veterinary medicine, Cornell University, Ithaca, New York, USA
| | - Lisa A Fortier
- Department of Clinical Sciences, College of Veterinary medicine, Cornell University, Ithaca, New York, USA
| | - Hussni O Mohammed
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary medicine, Cornell University, Ithaca, New York, USA
| | - Norm G Ducharme
- Department of Clinical Sciences, College of Veterinary medicine, Cornell University, Ithaca, New York, USA
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12
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Hamilton JR, Stahl EC, Tsuchida CA, Lin-Shiao E, Tsui CK, Pestal K, Gildea HK, Witkowsky LB, Moehle EA, McDevitt SL, McElroy M, Keller A, Sylvain I, Hirsh A, Ciling A, Ehrenberg AJ, Ringeisen BR, Huberty G, Urnov FD, Giannikopoulos P, Doudna JA. Robotic RNA extraction for SARS-CoV-2 surveillance using saliva samples. medRxiv 2021:2021.01.10.21249151. [PMID: 33532798 PMCID: PMC7852249 DOI: 10.1101/2021.01.10.21249151] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Saliva is an attractive specimen type for asymptomatic surveillance of COVID-19 in large populations due to its ease of collection and its demonstrated utility for detecting RNA from SARS-CoV-2. Multiple saliva-based viral detection protocols use a direct-to-RT-qPCR approach that eliminates nucleic acid extraction but can reduce viral RNA detection sensitivity. To improve test sensitivity while maintaining speed, we developed a robotic nucleic acid extraction method for detecting SARS-CoV-2 RNA in saliva samples with high throughput. Using this assay, the Free Asymptomatic Saliva Testing (IGI-FAST) research study on the UC Berkeley campus conducted 11,971 tests on supervised self-collected saliva samples and identified rare positive specimens containing SARS-CoV-2 RNA during a time of low infection prevalence. In an attempt to increase testing capacity, we further adapted our robotic extraction assay to process pooled saliva samples. We also benchmarked our assay against the gold standard, nasopharyngeal swab specimens. Finally, we designed and validated a RT-qPCR test suitable for saliva self-collection. These results establish a robotic extraction-based procedure for rapid PCR-based saliva testing that is suitable for samples from both symptomatic and asymptomatic individuals.
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Affiliation(s)
- Jennifer R Hamilton
- University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Elizabeth C Stahl
- University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Connor A Tsuchida
- University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Enrique Lin-Shiao
- University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | | | | | | | - Lea B Witkowsky
- University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Erica A Moehle
- University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Shana L McDevitt
- University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Matthew McElroy
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Amanda Keller
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Iman Sylvain
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Ariana Hirsh
- University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Alison Ciling
- University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Alexander J Ehrenberg
- University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Bradley R Ringeisen
- University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Garth Huberty
- Washington Hospital Healthcare System Clinical Laboratory, Fremont, CA USA
| | - Fyodor D Urnov
- University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Petros Giannikopoulos
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Jennifer A Doudna
- University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
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13
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Stahl EC, Tsuchida CA, Hamilton JR, Lin-Shiao E, McDevitt SL, Moehle EA, Witkowsky LB, Tsui CK, Pestal K, Gildea HK, McElroy M, Keller A, Sylvain I, Williams C, Hirsh A, Ciling A, Ehrenberg AJ, Urnov FD, Ringeisen BR, Giannikopoulos P, Doudna JA. IGI-LuNER: single-well multiplexed RT-qPCR test for SARS-CoV-2. medRxiv 2020:2020.12.10.20247338. [PMID: 33330883 PMCID: PMC7743092 DOI: 10.1101/2020.12.10.20247338] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [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: 11/24/2022]
Abstract
Commonly used RT-qPCR-based SARS-CoV-2 diagnostics require 2-3 separate reactions or rely on detection of a single viral target, adding time and cost or risk of false-negative results. Currently, no test combines detection of widely used SARS-CoV-2 E- and N-gene targets and a sample control in a single, multiplexed reaction. We developed the IGI-LuNER RT-qPCR assay using the Luna Probe Universal One-Step RT-qPCR master mix with publicly available primers and probes to detect SARS-CoV-2 N gene, E gene, and human RNase P (NER). This combined, cost-effective test can be performed in 384-well plates with detection sensitivity suitable for clinical reporting, and will aid in future sample pooling efforts, thus improving throughput of SARS-CoV-2 detection.
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Affiliation(s)
- Elizabeth C Stahl
- University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Connor A Tsuchida
- University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Jennifer R Hamilton
- University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Enrique Lin-Shiao
- University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Shana L McDevitt
- University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Erica A Moehle
- University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Lea B Witkowsky
- University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | | | | | | | - Matthew McElroy
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Amanda Keller
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Iman Sylvain
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Clara Williams
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Ariana Hirsh
- University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Alison Ciling
- University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | | | - Fyodor D Urnov
- University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Bradley R Ringeisen
- University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | | | - Jennifer A Doudna
- University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
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14
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Stahl EC, Delgado ER, Alencastro F, LoPresti ST, Wilkinson PD, Roy N, Haschak MJ, Skillen CD, Monga SP, Duncan AW, Brown BN. Inflammation and Ectopic Fat Deposition in the Aging Murine Liver Is Influenced by CCR2. Am J Pathol 2019; 190:372-387. [PMID: 31843499 DOI: 10.1016/j.ajpath.2019.10.016] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 10/02/2019] [Accepted: 10/22/2019] [Indexed: 02/08/2023]
Abstract
Aging is associated with inflammation and metabolic syndrome, which manifests in the liver as nonalcoholic fatty liver disease (NAFLD). NAFLD can range in severity from steatosis to fibrotic steatohepatitis and is a major cause of hepatic morbidity. However, the pathogenesis of NAFLD in naturally aged animals is unclear. Herein, we performed a comprehensive study of lipid content and inflammatory signature of livers in 19-month-old aged female mice. These animals exhibited increased body and liver weight, hepatic triglycerides, and inflammatory gene expression compared with 3-month-old young controls. The aged mice also had a significant increase in F4/80+ hepatic macrophages, which coexpressed CD11b, suggesting a circulating monocyte origin. A global knockout of the receptor for monocyte chemoattractant protein (CCR2) prevented excess steatosis and inflammation in aging livers but did not reduce the number of CD11b+ macrophages, suggesting changes in macrophage accumulation precede or are independent from chemokine (C-C motif) ligand-CCR2 signaling in the development of age-related NAFLD. RNA sequencing further elucidated complex changes in inflammatory and metabolic gene expression in the aging liver. In conclusion, we report a previously unknown accumulation of CD11b+ macrophages in aged livers with robust inflammatory and metabolic transcriptomic changes. A better understanding of the hallmarks of aging in the liver will be crucial in the development of preventive measures and treatments for end-stage liver disease in elderly patients.
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Affiliation(s)
- Elizabeth C Stahl
- McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania; Department of Pathology, University of Pittsburgh School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Evan R Delgado
- McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania; Department of Pathology, University of Pittsburgh School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Frances Alencastro
- McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania; Department of Pathology, University of Pittsburgh School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Samuel T LoPresti
- McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania; Bioengineering Department, Swanson School of Engineering, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Patrick D Wilkinson
- McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania; Department of Pathology, University of Pittsburgh School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Nairita Roy
- McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania; Department of Pathology, University of Pittsburgh School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Martin J Haschak
- McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania; Bioengineering Department, Swanson School of Engineering, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Clint D Skillen
- McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Satdarshan P Monga
- McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania; Department of Pathology, University of Pittsburgh School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania; Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Andrew W Duncan
- McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania; Department of Pathology, University of Pittsburgh School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania; Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, Pennsylvania.
| | - Bryan N Brown
- McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania; Bioengineering Department, Swanson School of Engineering, University of Pittsburgh, Pittsburgh, Pennsylvania; Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, Pennsylvania.
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15
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Wilkinson PD, Delgado ER, Alencastro F, Leek MP, Roy N, Weirich MP, Stahl EC, Otero PA, Chen MI, Brown WK, Oertel M, Duncan AW. Polyploidy in Liver Regeneration and Adaptation to Chronic Injury. FASEB J 2019. [DOI: 10.1096/fasebj.2019.33.1_supplement.369.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | | | | | | | - Nairita Roy
- PathologyUniversity of PittsburghPittsburghPA
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16
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Wilkinson PD, Delgado ER, Alencastro F, Leek MP, Roy N, Weirich MP, Stahl EC, Otero PA, Chen MI, Brown WK, Duncan AW. The Polyploid State Restricts Hepatocyte Proliferation and Liver Regeneration in Mice. Hepatology 2019; 69:1242-1258. [PMID: 30244478 PMCID: PMC6532408 DOI: 10.1002/hep.30286] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 09/16/2018] [Indexed: 12/12/2022]
Abstract
The liver contains a mixture of hepatocytes with diploid or polyploid (tetraploid, octaploid, etc.) nuclear content. Polyploid hepatocytes are commonly found in adult mammals, representing ~90% of the entire hepatic pool in rodents. The cellular and molecular mechanisms that regulate polyploidization have been well characterized; however, it is unclear whether diploid and polyploid hepatocytes function similarly in multiple contexts. Answering this question has been challenging because proliferating hepatocytes can increase or decrease ploidy, and animal models with healthy diploid-only livers have not been available. Mice lacking E2f7 and E2f8 in the liver (liver-specific E2f7/E2f8 knockout; LKO) were recently reported to have a polyploidization defect, but were otherwise healthy. Herein, livers from LKO mice were rigorously characterized, demonstrating a 20-fold increase in diploid hepatocytes and maintenance of the diploid state even after extensive proliferation. Livers from LKO mice maintained normal function, but became highly tumorigenic when challenged with tumor-promoting stimuli, suggesting that tumors in LKO mice were driven, at least in part, by diploid hepatocytes capable of rapid proliferation. Indeed, hepatocytes from LKO mice proliferate faster and out-compete control hepatocytes, especially in competitive repopulation studies. In addition, diploid or polyploid hepatocytes from wild-type (WT) mice were examined to eliminate potentially confounding effects associated with E2f7/E2f8 deficiency. WT diploid cells also showed a proliferative advantage, entering and progressing through the cell cycle faster than polyploid cells, both in vitro and during liver regeneration (LR). Diploid and polyploid hepatocytes responded similarly to hepatic mitogens, indicating that proliferation kinetics are unrelated to differential response to growth stimuli. Conclusion: Diploid hepatocytes proliferate faster than polyploids, suggesting that the polyploid state functions as a growth suppressor to restrict proliferation by the majority of hepatocytes.
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Affiliation(s)
- Patrick D. Wilkinson
- Department of Pathology, McGowan Institute for Regenerative Medicine, Pittsburgh Liver Research Center, University of Pittsburgh, 450 Technology Drive, Suite 300, Pittsburgh, PA 15219
| | - Evan R. Delgado
- Department of Pathology, McGowan Institute for Regenerative Medicine, Pittsburgh Liver Research Center, University of Pittsburgh, 450 Technology Drive, Suite 300, Pittsburgh, PA 15219
| | - Frances Alencastro
- Department of Pathology, McGowan Institute for Regenerative Medicine, Pittsburgh Liver Research Center, University of Pittsburgh, 450 Technology Drive, Suite 300, Pittsburgh, PA 15219
| | - Madeleine P. Leek
- Department of Pathology, McGowan Institute for Regenerative Medicine, Pittsburgh Liver Research Center, University of Pittsburgh, 450 Technology Drive, Suite 300, Pittsburgh, PA 15219
| | - Nairita Roy
- Department of Pathology, McGowan Institute for Regenerative Medicine, Pittsburgh Liver Research Center, University of Pittsburgh, 450 Technology Drive, Suite 300, Pittsburgh, PA 15219
| | - Matthew P. Weirich
- Department of Pathology, McGowan Institute for Regenerative Medicine, Pittsburgh Liver Research Center, University of Pittsburgh, 450 Technology Drive, Suite 300, Pittsburgh, PA 15219
| | - Elizabeth C. Stahl
- Department of Pathology, McGowan Institute for Regenerative Medicine, Pittsburgh Liver Research Center, University of Pittsburgh, 450 Technology Drive, Suite 300, Pittsburgh, PA 15219
| | - P. Anthony Otero
- Department of Pathology, McGowan Institute for Regenerative Medicine, Pittsburgh Liver Research Center, University of Pittsburgh, 450 Technology Drive, Suite 300, Pittsburgh, PA 15219
| | - Maelee I. Chen
- Department of Pathology, McGowan Institute for Regenerative Medicine, Pittsburgh Liver Research Center, University of Pittsburgh, 450 Technology Drive, Suite 300, Pittsburgh, PA 15219
| | - Whitney K. Brown
- Department of Pathology, McGowan Institute for Regenerative Medicine, Pittsburgh Liver Research Center, University of Pittsburgh, 450 Technology Drive, Suite 300, Pittsburgh, PA 15219
| | - Andrew W. Duncan
- Department of Pathology, McGowan Institute for Regenerative Medicine, Pittsburgh Liver Research Center, University of Pittsburgh, 450 Technology Drive, Suite 300, Pittsburgh, PA 15219
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17
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Stahl EC, Bonvillain RW, Skillen CD, Burger BL, Hara H, Lee W, Trygg CB, Didier PJ, Grasperge BF, Pashos NC, Bunnell BA, Bianchi J, Ayares DL, Guthrie KI, Brown BN, Petersen TH. Evaluation of the host immune response to decellularized lung scaffolds derived from α-Gal knockout pigs in a non-human primate model. Biomaterials 2018; 187:93-104. [DOI: 10.1016/j.biomaterials.2018.09.038] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Revised: 09/21/2018] [Accepted: 09/23/2018] [Indexed: 12/11/2022]
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18
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Abstract
The number of individuals aged 65 or older is projected to increase globally from 524 million in 2010 to nearly 1. 5 billion in 2050. Aged individuals are particularly at risk for developing chronic illness, while being less able to regenerate healthy tissue and tolerate whole organ transplantation procedures. In the liver, these age-related diseases include non-alcoholic fatty liver disease, alcoholic liver disease, hepatitis, fibrosis, and cirrhosis. Hepatic macrophages, a population comprised of both Kupffer cells and infiltrating monocyte derived macrophages, are implicated in several chronic liver diseases and also play important roles in the homeostatic functions of the liver. The effects of aging on hepatic macrophage population dynamics, polarization, and function are not well understood. Studies performed on macrophages derived from other aged sources, such as the bone marrow, peritoneal cavity, lungs, and brain, demonstrate general reductions in autophagy and phagocytosis, dysfunction in cytokine signaling, and altered morphology and distribution, likely mediated by epigenetic changes and mitochondrial defects, that may be applicable to hepatic macrophages. This review highlights recent findings in macrophage developmental biology and function, particularly in the liver, and discusses the role of macrophages in various age-related liver diseases. A better understanding of the biology of aging that influences hepatic macrophages and thus the progression of chronic liver disease will be crucial in order to develop new interventions and treatments for liver disease in aging populations.
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Affiliation(s)
- Elizabeth C Stahl
- Department of Bioengineering, Pittsburgh Liver Research Center, McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Martin J Haschak
- Department of Bioengineering, Pittsburgh Liver Research Center, McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Branimir Popovic
- Department of Bioengineering, Pittsburgh Liver Research Center, McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Bryan N Brown
- Department of Bioengineering, Pittsburgh Liver Research Center, McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA, United States
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19
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Brown BN, Haschak MJ, Lopresti ST, Stahl EC. Effects of age-related shifts in cellular function and local microenvironment upon the innate immune response to implants. Semin Immunol 2017; 29:24-32. [PMID: 28539184 DOI: 10.1016/j.smim.2017.05.001] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Revised: 04/18/2017] [Accepted: 05/11/2017] [Indexed: 12/14/2022]
Abstract
The host macrophage response is now well recognized as a predictor of the success or failure of biomaterial implants following placement. More specifically, shifts from an "M1" pro-inflammatory towards a more "M2-like" anti-inflammatory macrophage polarization profile have been shown to result in enhanced material integration and/or tissue regeneration downstream. As a result, a number of biomaterials-based approaches to controlling macrophage polarization have been developed. However, the ability to promote such activity is predicated upon an in-depth, context-dependent understanding of the host response to biomaterials. Recent work has shown the impacts of both tissue location and tissue status (i.e. underlying pathology) upon the host innate immune response to implants, representing a departure from a focus upon implant material composition and form. Thus, the ideas of "biocompatibility," the host macrophage reaction, and ideal material requirements and modification strategies may need to be revisited on a patient, tissue, and disease basis. Immunosenescence, dysregulation of macrophage function, and delayed resolution of immune responses in aged individuals have all been demonstrated, suggesting that the host response to biomaterials in aged individuals should differ from that in younger individuals. However, despite the increasing usage of implantable medical devices in aged patients, few studies examining the effects of aging upon the host response to biomaterials and the implications of this response for long-term integration and function have been performed. The objective of the present manuscript is to review the putative effects of aging upon the host response to implanted materials and to advance the hypothesis that age-related changes in the local microenvrionement, with emphasis on the extracellular matrix, play a previously unrecognized role in determining the host response to implants.
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Affiliation(s)
- Bryan N Brown
- McGowan Institute for Regenerative Medicine, University of Pittsburgh, 450 Technology Drive, Pittsburgh, PA 15219, United States; Department of Bioengineering, Swanson School of Engineering, University of Pittsburgh, 3700 O'Hara Street, Pittsburgh, PA 15260, United States; Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh School of Medicine, University of Pittsburgh, 300 Halket Street, Pittsburgh, PA 15213, United States.
| | - Martin J Haschak
- McGowan Institute for Regenerative Medicine, University of Pittsburgh, 450 Technology Drive, Pittsburgh, PA 15219, United States; Department of Bioengineering, Swanson School of Engineering, University of Pittsburgh, 3700 O'Hara Street, Pittsburgh, PA 15260, United States
| | - Samuel T Lopresti
- McGowan Institute for Regenerative Medicine, University of Pittsburgh, 450 Technology Drive, Pittsburgh, PA 15219, United States; Department of Bioengineering, Swanson School of Engineering, University of Pittsburgh, 3700 O'Hara Street, Pittsburgh, PA 15260, United States
| | - Elizabeth C Stahl
- McGowan Institute for Regenerative Medicine, University of Pittsburgh, 450 Technology Drive, Pittsburgh, PA 15219, United States; Department of Pathology, University of Pittsburgh School of Medicine, University of Pittsburgh, 200 Lothrop St., Pittsburgh, PA 15261, United States
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20
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Vujanovic L, Stahl EC, Pardee AD, Geller DA, Tsung A, Watkins SC, Gibson GA, Storkus WJ, Butterfield LH. Tumor-Derived α-Fetoprotein Directly Drives Human Natural Killer-Cell Activation and Subsequent Cell Death. Cancer Immunol Res 2017; 5:493-502. [PMID: 28468916 DOI: 10.1158/2326-6066.cir-16-0216] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Revised: 03/22/2017] [Accepted: 04/28/2017] [Indexed: 11/16/2022]
Abstract
Hepatocellular carcinoma (HCC) patients with reduced natural killer (NK)-cell numbers and function have been shown to have a poor disease outcome. Mechanisms underlying NK-cell deficiency and dysfunction in HCC patients remain largely unresolved. α-Fetoprotein (AFP) is an oncofetal antigen produced by HCC. Previous studies demonstrated that tumor-derived AFP (tAFP) can indirectly impair NK-cell activity by suppressing dendritic cell function. However, a direct tAFP effect on NK cells remains unexplored. The purpose of this study was to examine the ability of cord blood-derived AFP (nAFP) and that of tAFP to directly modulate human NK-cell activity and longevity in vitro Short-term exposure to tAFP and, especially, nAFP proteins induced a unique proinflammatory, IL2-hyperresponsive phenotype in NK cells as measured by IL1β, IL6, and TNF secretion, CD69 upregulation, and enhanced tumor cell killing. In contrast, extended coculture with tAFP, but not nAFP, negatively affected long-term NK-cell viability. NK-cell activation was directly mediated by the AFP protein itself, whereas their viability was affected by hydrophilic components within the low molecular mass cargo that copurified with tAFP. Identification of the distinct impact of circulating tAFP on NK-cell function and viability may be crucial to developing a strategy to ameliorate HCC patient NK-cell functional deficits. Cancer Immunol Res; 5(6); 493-502. ©2017 AACR.
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Affiliation(s)
- Lazar Vujanovic
- University of Pittsburgh Cancer Institute, University of Pittsburgh, Pennsylvania.,Department of Medicine, University of Pittsburgh, Pennsylvania
| | - Elizabeth C Stahl
- University of Pittsburgh Cancer Institute, University of Pittsburgh, Pennsylvania
| | - Angela D Pardee
- University of Pittsburgh Cancer Institute, University of Pittsburgh, Pennsylvania.,Department of Medicine, University of Pittsburgh, Pennsylvania
| | - David A Geller
- University of Pittsburgh School of Medicine, Department of Surgery, University of Pittsburgh, Pennsylvania
| | - Allan Tsung
- University of Pittsburgh School of Medicine, Department of Surgery, University of Pittsburgh, Pennsylvania
| | - Simon C Watkins
- Department of Cell Biology and Physiology, University of Pittsburgh, Pennsylvania
| | - Gregory A Gibson
- Department of Cell Biology and Physiology, University of Pittsburgh, Pennsylvania
| | - Walter J Storkus
- University of Pittsburgh Cancer Institute, University of Pittsburgh, Pennsylvania.,Department of Dermatology, University of Pittsburgh, Pennsylvania.,Department of Immunology, University of Pittsburgh, Pennsylvania
| | - Lisa H Butterfield
- University of Pittsburgh Cancer Institute, University of Pittsburgh, Pennsylvania. .,Department of Medicine, University of Pittsburgh, Pennsylvania.,University of Pittsburgh School of Medicine, Department of Surgery, University of Pittsburgh, Pennsylvania.,Department of Immunology, University of Pittsburgh, Pennsylvania
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21
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Hachim D, Wang N, Lopresti ST, Stahl EC, Umeda YU, Rege RD, Carey ST, Mani D, Brown BN. Effects of aging upon the host response to implants. J Biomed Mater Res A 2017; 105:1281-1292. [PMID: 28130823 DOI: 10.1002/jbm.a.36013] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [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: 10/17/2016] [Revised: 01/05/2017] [Accepted: 01/23/2017] [Indexed: 01/11/2023]
Abstract
Macrophage polarization during the host response is now a well-accepted predictor of outcomes following material implantation. Immunosenescence, dysregulation of macrophage function, and delayed resolution of immune responses in aged individuals have all been demonstrated, suggesting that host responses to materials in aged individuals should differ from those in younger individuals. However, few studies examining the effects of aging upon the host response have been performed. The present work sought to elucidate the impacts of aging upon the host response to polypropylene mesh implanted into 8-week-old and 18-month-old mice. The results showed that there are significant differences in macrophage surface marker expression, migration, and polarization during the early host macrophage response and delayed resolution of the host response in 18-month-old versus 8-week-old mice. These differences could not be attributed to cell-intrinsic defects alone, suggesting that the host macrophage response to implants is likely also dictated to a significant degree by the local tissue microenvironment. These results raise important questions about the design and testing of materials and devices often intended to treat aged individuals and suggest that an improved understanding of patient- and context-dependent macrophage responses has the potential to improve outcomes in aged individuals. © 2017 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 105A: 1281-1292, 2017.
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Affiliation(s)
- Daniel Hachim
- McGowan Institute for Regenerative Medicine, University of Pittsburgh, 450 Technology Drive, Pittsburgh, Pennsylvania, 15219.,Department of Bioengineering, Swanson School of Engineering, University of Pittsburgh, 3700 O'Hara Street, Pittsburgh, Pennsylvania, 15260
| | - Na Wang
- McGowan Institute for Regenerative Medicine, University of Pittsburgh, 450 Technology Drive, Pittsburgh, Pennsylvania, 15219
| | - Samuel T Lopresti
- McGowan Institute for Regenerative Medicine, University of Pittsburgh, 450 Technology Drive, Pittsburgh, Pennsylvania, 15219.,Department of Bioengineering, Swanson School of Engineering, University of Pittsburgh, 3700 O'Hara Street, Pittsburgh, Pennsylvania, 15260
| | - Elizabeth C Stahl
- McGowan Institute for Regenerative Medicine, University of Pittsburgh, 450 Technology Drive, Pittsburgh, Pennsylvania, 15219.,Department of Pathology, University of Pittsburgh School of Medicine, University of Pittsburgh, 200 Lothrop St, Pittsburgh, Pennsylvania, 15261
| | - Yuta U Umeda
- Department of Bioengineering, Swanson School of Engineering, University of Pittsburgh, 3700 O'Hara Street, Pittsburgh, Pennsylvania, 15260
| | - Rahul D Rege
- Department of Bioengineering, Swanson School of Engineering, University of Pittsburgh, 3700 O'Hara Street, Pittsburgh, Pennsylvania, 15260
| | - Sean T Carey
- Department of Chemical Engineering, Swanson School of Engineering, University of Pittsburgh, 3700 O'Hara Street, Pittsburgh, Pennsylvania, 15260
| | - Deepa Mani
- McGowan Institute for Regenerative Medicine, University of Pittsburgh, 450 Technology Drive, Pittsburgh, Pennsylvania, 15219
| | - Bryan N Brown
- McGowan Institute for Regenerative Medicine, University of Pittsburgh, 450 Technology Drive, Pittsburgh, Pennsylvania, 15219.,Department of Bioengineering, Swanson School of Engineering, University of Pittsburgh, 3700 O'Hara Street, Pittsburgh, Pennsylvania, 15260.,Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh School of Medicine, University of Pittsburgh, 300 Halket Street, Pittsburgh, Pennsylvania, 15213
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22
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Stahl EC, Brown BN. Kupffer cell subsets differ between young and aged murine livers. The Journal of Immunology 2016. [DOI: 10.4049/jimmunol.196.supp.126.31] [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] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Abstract
The immune system, and in particular macrophages, are heavily implicated in wound healing, response to infection, and cancer progression, all of which are linked to mortality in the elderly population. Recently, it has been shown that tissue-resident macrophages from spleen and peritoneum become dysfunctional with aging, likely due to the aged microenvironment. The liver contains approximately 80% of total mammalian tissue-resident macrophages, known as Kupffer cells. Kupffer cells can be divided into two F4/80+ macrophage subsets: CD68+ and CD11b+ cells, which have different origins and functions. Currently, it is unclear how these macrophage subsets are affected by aging.
We sought to characterize differences in the Kupffer cell compartment from young (8–10 week) and aged (18–20 month) C57/Bl6 mice using immunofluorescent staining on tissue sections and flow cytometry. Preliminary histological analyses showed that the area of F4/80+ staining did not differ between young and aged mice. Interestingly the area of CD68+ staining was significantly higher in the aged murine livers. In addition, the area of CD32+ staining, which marks both endothelial cells and macrophage precursors, was significantly greater in aged mice, consistent with previous reports of blood vessel thickening in aged livers. Flow cytometry analysis confirmed differences in the macrophage subsets between young and aged murine livers. In addition, functional changes in phagocytosis were noted with aging, suggesting dysfunction of innate abilities. Characterizing the differences in the subsets of tissue-resident macrophages during aging will increase our understanding of age-related pathologies that will aid in the design of therapies in the future.
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23
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Abstract
Declining function of the immune system, termed "immunosenescence," leads to a higher incidence of infection, cancer, and autoimmune disease related mortalities in the elderly population. (1) Increasing interest in the field of immunosenescence is well-timed, as 20% of the United States population is expected to surpass the age of 65 by the year 2030. (2) Our current understanding of immunosenescence involves a shift in function of both adaptive and innate immune cells, leading to a reduced capacity to recognize new antigens and widespread chronic inflammation. The present review focuses on changes that occur in haematopoietic stem cells, macrophages, and T-cells using knowledge gained from both rodent and human studies. The review will discuss emerging strategies to combat immunosenescence, focusing on cellular and genetic therapies, including bone marrow transplantation and genetic reprogramming. A better understanding of the mechanisms and implications of immunosenescence will be necessary to combat age-related mortalities in the future.
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Affiliation(s)
- Elizabeth C Stahl
- a Department of Pathology ; University of Pittsburgh School of Medicine ; Pittsburgh , PA USA ;,b McGowan Institute for Regenerative Medicine ; Pittsburgh , PA USA
| | - Bryan N Brown
- a Department of Pathology ; University of Pittsburgh School of Medicine ; Pittsburgh , PA USA ;,b McGowan Institute for Regenerative Medicine ; Pittsburgh , PA USA ;,c Bioengineering Department ; Swanson School of Engineering; University of Pittsburgh ; Pittsburgh , PA USA
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24
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Wolf MT, Carruthers CA, Dearth CL, Crapo PM, Huber A, Burnsed OA, Londono R, Johnson SA, Daly KA, Stahl EC, Freund JM, Medberry CJ, Carey LE, Nieponice A, Amoroso NJ, Badylak SF. Polypropylene surgical mesh coated with extracellular matrix mitigates the host foreign body response. J Biomed Mater Res A 2013; 102:234-46. [PMID: 23873846 DOI: 10.1002/jbm.a.34671] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [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: 09/18/2012] [Revised: 02/15/2013] [Accepted: 02/19/2013] [Indexed: 12/19/2022]
Abstract
Surgical mesh devices composed of synthetic materials are commonly used for ventral hernia repair. These materials provide robust mechanical strength and are quickly incorporated into host tissue; factors that contribute to reduced hernia recurrence rates. However, such mesh devices cause a foreign body response with the associated complications of fibrosis and patient discomfort. In contrast, surgical mesh devices composed of naturally occurring extracellular matrix (ECM) are associated with constructive tissue remodeling, but lack the mechanical strength of synthetic materials. A method for applying a porcine dermal ECM hydrogel coating to a polypropylene mesh is described herein with the associated effects upon the host tissue response and biaxial mechanical behavior. Uncoated and ECM coated heavy-weight BARD™ Mesh were compared to the light-weight ULTRAPRO™ and BARD™ Soft Mesh devices in a rat partial thickness abdominal defect overlay model. The ECM coated mesh attenuated the pro-inflammatory response compared to all other devices, with a reduced cell accumulation and fewer foreign body giant cells. The ECM coating degraded by 35 days, and was replaced with loose connective tissue compared to the dense collagenous tissue associated with the uncoated polypropylene mesh device. Biaxial mechanical characterization showed that all of the mesh devices were of similar isotropic stiffness. Upon explanation, the light-weight mesh devices were more compliant than the coated or uncoated heavy-weight devices. This study shows that an ECM coating alters the default host response to a polypropylene mesh, but not the mechanical properties in an acute in vivo abdominal repair model.
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Affiliation(s)
- Matthew T Wolf
- Department of Bioengineering, University of Pittsburgh, Pittsburgh, Pennsylvania; McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
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