1
|
Zhao H, Syed AM, Khalid MM, Nguyen A, Ciling A, Wu D, Yau WM, Srinivasan S, Esposito D, Doudna JA, Piszczek G, Ott M, Schuck P. Assembly of SARS-CoV-2 nucleocapsid protein with nucleic acid. Nucleic Acids Res 2024:gkae256. [PMID: 38587193 DOI: 10.1093/nar/gkae256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 03/18/2024] [Accepted: 03/27/2024] [Indexed: 04/09/2024] Open
Abstract
The viral genome of SARS-CoV-2 is packaged by the nucleocapsid (N-)protein into ribonucleoprotein particles (RNPs), 38 ± 10 of which are contained in each virion. Their architecture has remained unclear due to the pleomorphism of RNPs, the high flexibility of N-protein intrinsically disordered regions, and highly multivalent interactions between viral RNA and N-protein binding sites in both N-terminal (NTD) and C-terminal domain (CTD). Here we explore critical interaction motifs of RNPs by applying a combination of biophysical techniques to ancestral and mutant proteins binding different nucleic acids in an in vitro assay for RNP formation, and by examining nucleocapsid protein variants in a viral assembly assay. We find that nucleic acid-bound N-protein dimers oligomerize via a recently described protein-protein interface presented by a transient helix in its long disordered linker region between NTD and CTD. The resulting hexameric complexes are stabilized by multivalent protein-nucleic acid interactions that establish crosslinks between dimeric subunits. Assemblies are stabilized by the dimeric CTD of N-protein offering more than one binding site for stem-loop RNA. Our study suggests a model for RNP assembly where N-protein scaffolding at high density on viral RNA is followed by cooperative multimerization through protein-protein interactions in the disordered linker.
Collapse
Affiliation(s)
- Huaying Zhao
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA
| | - Abdullah M Syed
- Gladstone Institutes, San Francisco, CA 94158, USA
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
| | - Mir M Khalid
- Gladstone Institutes, San Francisco, CA 94158, USA
| | - Ai Nguyen
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA
| | - Alison Ciling
- Gladstone Institutes, San Francisco, CA 94158, USA
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
| | - Di Wu
- Biophysics Core Facility, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Wai-Ming Yau
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sanjana Srinivasan
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA
| | - Dominic Esposito
- Protein Expression Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Jennifer A Doudna
- Gladstone Institutes, San Francisco, CA 94158, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
- HHMI, University of California, Berkeley, CA 94720, USA
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA
| | - Grzegorz Piszczek
- Biophysics Core Facility, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Melanie Ott
- Gladstone Institutes, San Francisco, CA 94158, USA
- Department of Medicine, University of California, San Francisco, CA 94143, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Peter Schuck
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA
- Center for Biomedical Engineering Technology Acceleration, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA
| |
Collapse
|
2
|
Adly AN, Bi M, Carlson CR, Syed AM, Ciling A, Doudna JA, Cheng Y, Morgan DO. Assembly of SARS-CoV-2 ribonucleosomes by truncated N ∗ variant of the nucleocapsid protein. J Biol Chem 2023; 299:105362. [PMID: 37863261 PMCID: PMC10665939 DOI: 10.1016/j.jbc.2023.105362] [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: 08/18/2023] [Revised: 10/05/2023] [Accepted: 10/11/2023] [Indexed: 10/22/2023] Open
Abstract
The nucleocapsid (N) protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) compacts the RNA genome into viral ribonucleoprotein (vRNP) complexes within virions. Assembly of vRNPs is inhibited by phosphorylation of the N protein serine/arginine (SR) region. Several SARS-CoV-2 variants of concern carry N protein mutations that reduce phosphorylation and enhance the efficiency of viral packaging. Variants of the dominant B.1.1 viral lineage also encode a truncated N protein, termed N∗ or Δ(1-209), that mediates genome packaging despite lacking the N-terminal RNA-binding domain and SR region. Here, we use mass photometry and negative stain electron microscopy to show that purified Δ(1-209) and viral RNA assemble into vRNPs that are remarkably similar in size and shape to those formed with full-length N protein. We show that assembly of Δ(1-209) vRNPs requires the leucine-rich helix of the central disordered region and that this helix promotes N protein oligomerization. We also find that fusion of a phosphomimetic SR region to Δ(1-209) inhibits RNA binding and vRNP assembly. Our results provide new insights into the mechanisms by which RNA binding promotes N protein self-association and vRNP assembly, and how this process is modulated by phosphorylation.
Collapse
Affiliation(s)
- Armin N Adly
- Department of Physiology, University of California, San Francisco, California, USA
| | - Maxine Bi
- Department of Biochemistry & Biophysics, University of California, San Francisco, California, USA
| | | | - Abdullah M Syed
- J. David Gladstone Institutes, San Francisco, California, USA
| | - Alison Ciling
- J. David Gladstone Institutes, San Francisco, California, USA
| | - Jennifer A Doudna
- J. David Gladstone Institutes, San Francisco, California, USA; Department of Molecular and Cell Biology, University of California, Berkeley, California, USA; Howard Hughes Medical Institute, University of California, Berkeley, California, USA; Innovative Genomics Institute, University of California, Berkeley, California, USA; California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, California, USA; MBIB Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Yifan Cheng
- Department of Biochemistry & Biophysics, University of California, San Francisco, California, USA; Howard Hughes Medical Institute, University of California, San Francisco, California, USA
| | - David O Morgan
- Department of Physiology, University of California, San Francisco, California, USA.
| |
Collapse
|
3
|
Suryawanshi RK, Taha TY, McCavitt-Malvido M, Silva I, Khalid MM, Syed AM, Chen IP, Saldhi P, Sreekumar B, Montano M, Foresythe K, Tabata T, Kumar GR, Sotomayor-Gonzalez A, Servellita V, Gliwa A, Nguyen J, Kojima N, Arellanor T, Bussanich A, Hess V, Shacreaw M, Lopez L, Brobeck M, Turner F, Wang Y, Ghazarian S, Davis G, Rodriguez D, Doudna J, Spraggon L, Chiu CY, Ott M. Previous exposure to Spike-providing parental strains confers neutralizing immunity to XBB lineage and other SARS-CoV-2 recombinants in the context of vaccination. Emerg Microbes Infect 2023; 12:2270071. [PMID: 37869789 PMCID: PMC10619466 DOI: 10.1080/22221751.2023.2270071] [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: 05/10/2023] [Accepted: 10/05/2023] [Indexed: 10/24/2023]
Abstract
The emergence of SARS-CoV-2 recombinants is of particular concern as they can result in a sudden increase in immune evasion due to antigenic shift. Recent recombinants XBB and XBB.1.5 have higher transmissibility than previous recombinants such as "Deltacron." We hypothesized that immunity to a SARS-CoV-2 recombinant depends on prior exposure to its parental strains. To test this hypothesis, we examined whether Delta or Omicron (BA.1 or BA.2) immunity conferred through infection, vaccination, or breakthrough infection could neutralize Deltacron and XBB/XBB.1.5 recombinants. We found that Delta, BA.1, or BA.2 breakthrough infections provided better immune protection against Deltacron and its parental strains than did the vaccine booster. None of the sera were effective at neutralizing the XBB lineage or its parent BA.2.75.2, except for the sera from the BA.2 breakthrough group. These results support our hypothesis. In turn, our findings underscore the importance of multivalent vaccines that correspond to the antigenic profile of circulating variants of concern and of variant-specific diagnostics that may guide public health and individual decisions in response to emerging SARS-CoV-2 recombinants.
Collapse
Affiliation(s)
| | | | | | | | | | - Abdullah M. Syed
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Irene P. Chen
- Gladstone Institutes, San Francisco, CA, USA
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
- Quantitative Biosciences Institute COVID-19 Research Group (QCRG), University of California San Francisco, San Francisco, CA, USA
| | - Prachi Saldhi
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | | | | | - Kafaya Foresythe
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | | | | | | | - Venice Servellita
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | - Amelia Gliwa
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | - Jenny Nguyen
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | - Jennifer Doudna
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Chemistry, University of California, Berkeley, CA, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, USA
| | | | - Charles Y. Chiu
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Melanie Ott
- Gladstone Institutes, San Francisco, CA, USA
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
- Quantitative Biosciences Institute COVID-19 Research Group (QCRG), University of California San Francisco, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| |
Collapse
|
4
|
Zhao H, Syed AM, Khalid MM, Nguyen A, Ciling A, Wu D, Yau WM, Srinivasan S, Esposito D, Doudna JA, Piszczek G, Ott M, Schuck P. Assembly reactions of SARS-CoV-2 nucleocapsid protein with nucleic acid. bioRxiv 2023:2023.11.22.568361. [PMID: 38045338 PMCID: PMC10690241 DOI: 10.1101/2023.11.22.568361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
The viral genome of SARS-CoV-2 is packaged by the nucleocapsid (N-) protein into ribonucleoprotein particles (RNPs), 38±10 of which are contained in each virion. Their architecture has remained unclear due to the pleomorphism of RNPs, the high flexibility of N-protein intrinsically disordered regions, and highly multivalent interactions between viral RNA and N-protein binding sites in both N-terminal (NTD) and C-terminal domain (CTD). Here we explore critical interaction motifs of RNPs by applying a combination of biophysical techniques to mutant proteins binding different nucleic acids in an in vitro assay for RNP formation, and by examining mutant proteins in a viral assembly assay. We find that nucleic acid-bound N-protein dimers oligomerize via a recently described protein-protein interface presented by a transient helix in its long disordered linker region between NTD and CTD. The resulting hexameric complexes are stabilized by multi-valent protein-nucleic acid interactions that establish crosslinks between dimeric subunits. Assemblies are stabilized by the dimeric CTD of N-protein offering more than one binding site for stem-loop RNA. Our study suggests a model for RNP assembly where N-protein scaffolding at high density on viral RNA is followed by cooperative multimerization through protein-protein interactions in the disordered linker.
Collapse
Affiliation(s)
- Huaying Zhao
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892
| | - Abdullah M. Syed
- Gladstone Institutes, San Francisco, CA 94158
- Innovative Genomics Institute, University of California, Berkeley, CA 94720
| | | | - Ai Nguyen
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892
| | - Alison Ciling
- Gladstone Institutes, San Francisco, CA 94158
- Innovative Genomics Institute, University of California, Berkeley, CA 94720
| | - Di Wu
- Biophysics Core Facility, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892
| | - Wai-Ming Yau
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Sanjana Srinivasan
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892
| | - Dominic Esposito
- Protein Expression Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD 21702
| | - Jennifer A. Doudna
- Gladstone Institutes, San Francisco, CA 94158
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
- HHMI, University of California, Berkeley, CA 94720
- Department of Chemistry, University of California, Berkeley, CA 94720
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720
| | - Grzegorz Piszczek
- Biophysics Core Facility, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892
| | - Melanie Ott
- Gladstone Institutes, San Francisco, CA 94158
- Department of Medicine, University of California, San Francisco, CA 94143
- Chan Zuckerberg Biohub, San Francisco, CA 94158
| | - Peter Schuck
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892
- Center for Biomedical Engineering Technology Acceleration, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892
| |
Collapse
|
5
|
Bouhaddou M, Reuschl AK, Polacco BJ, Thorne LG, Ummadi MR, Ye C, Rosales R, Pelin A, Batra J, Jang GM, Xu J, Moen JM, Richards AL, Zhou Y, Harjai B, Stevenson E, Rojc A, Ragazzini R, Whelan MVX, Furnon W, De Lorenzo G, Cowton V, Syed AM, Ciling A, Deutsch N, Pirak D, Dowgier G, Mesner D, Turner JL, McGovern BL, Rodriguez ML, Leiva-Rebollo R, Dunham AS, Zhong X, Eckhardt M, Fossati A, Liotta NF, Kehrer T, Cupic A, Rutkowska M, Mena I, Aslam S, Hoffert A, Foussard H, Olwal CO, Huang W, Zwaka T, Pham J, Lyons M, Donohue L, Griffin A, Nugent R, Holden K, Deans R, Aviles P, Lopez-Martin JA, Jimeno JM, Obernier K, Fabius JM, Soucheray M, Hüttenhain R, Jungreis I, Kellis M, Echeverria I, Verba K, Bonfanti P, Beltrao P, Sharan R, Doudna JA, Martinez-Sobrido L, Patel AH, Palmarini M, Miorin L, White K, Swaney DL, Garcia-Sastre A, Jolly C, Zuliani-Alvarez L, Towers GJ, Krogan NJ. SARS-CoV-2 variants evolve convergent strategies to remodel the host response. Cell 2023; 186:4597-4614.e26. [PMID: 37738970 PMCID: PMC10604369 DOI: 10.1016/j.cell.2023.08.026] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [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: 12/20/2022] [Revised: 05/22/2023] [Accepted: 08/22/2023] [Indexed: 09/24/2023]
Abstract
SARS-CoV-2 variants of concern (VOCs) emerged during the COVID-19 pandemic. Here, we used unbiased systems approaches to study the host-selective forces driving VOC evolution. We discovered that VOCs evolved convergent strategies to remodel the host by modulating viral RNA and protein levels, altering viral and host protein phosphorylation, and rewiring virus-host protein-protein interactions. Integrative computational analyses revealed that although Alpha, Beta, Gamma, and Delta ultimately converged to suppress interferon-stimulated genes (ISGs), Omicron BA.1 did not. ISG suppression correlated with the expression of viral innate immune antagonist proteins, including Orf6, N, and Orf9b, which we mapped to specific mutations. Later Omicron subvariants BA.4 and BA.5 more potently suppressed innate immunity than early subvariant BA.1, which correlated with Orf6 levels, although muted in BA.4 by a mutation that disrupts the Orf6-nuclear pore interaction. Our findings suggest that SARS-CoV-2 convergent evolution overcame human adaptive and innate immune barriers, laying the groundwork to tackle future pandemics.
Collapse
Affiliation(s)
- Mehdi Bouhaddou
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Microbiology, Immunology, and Molecular Genetics (MIMG), University of California, Los Angeles, Los Angeles, CA, USA; Institute for Quantitative and Computational Biosciences (QCBio), University of California, Los Angeles, Los Angeles, CA, USA; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA
| | - Ann-Kathrin Reuschl
- QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Division of Infection and Immunity, University College London, London, UK
| | - Benjamin J Polacco
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | - Lucy G Thorne
- QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Division of Infection and Immunity, University College London, London, UK
| | - Manisha R Ummadi
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | - Chengjin Ye
- QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Romel Rosales
- QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Adrian Pelin
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | - Jyoti Batra
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | - Gwendolyn M Jang
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | - Jiewei Xu
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | - Jack M Moen
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | - Alicia L Richards
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | - Yuan Zhou
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | - Bhavya Harjai
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | - Erica Stevenson
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | - Ajda Rojc
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | - Roberta Ragazzini
- Division of Infection and Immunity, University College London, London, UK; Epithelial Stem Cell Biology and Regenerative Medicine Laboratory, The Francis Crick Institute, London, UK
| | - Matthew V X Whelan
- Division of Infection and Immunity, University College London, London, UK
| | - Wilhelm Furnon
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Giuditta De Lorenzo
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Vanessa Cowton
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Abdullah M Syed
- QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Alison Ciling
- QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Noa Deutsch
- School of Computer Science, Tel Aviv University, Tel Aviv, Israel
| | - Daniel Pirak
- School of Electrical Engineering, Tel Aviv University, Tel Aviv, Israel
| | - Giulia Dowgier
- COVID Surveillance Unit, The Francis Crick Institute, London, UK
| | - Dejan Mesner
- Division of Infection and Immunity, University College London, London, UK
| | - Jane L Turner
- Division of Infection and Immunity, University College London, London, UK
| | - Briana L McGovern
- QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - M Luis Rodriguez
- QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Rocio Leiva-Rebollo
- QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alistair S Dunham
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge, UK; Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Saffron Walden, UK
| | - Xiaofang Zhong
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | - Manon Eckhardt
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | - Andrea Fossati
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | - Nicholas F Liotta
- QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA
| | - Thomas Kehrer
- QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Anastasija Cupic
- QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Magdalena Rutkowska
- QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ignacio Mena
- QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sadaf Aslam
- QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alyssa Hoffert
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | - Helene Foussard
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | - Charles Ochieng' Olwal
- QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra, Ghana; Department of Biochemistry, Cell and Molecular Biology, College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
| | - Weiqing Huang
- Huffington Center for Cell-based Research in Parkinson's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Thomas Zwaka
- Huffington Center for Cell-based Research in Parkinson's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - John Pham
- Synthego Corporation, Redwood City, CA, USA
| | | | | | | | | | | | | | | | | | | | - Kirsten Obernier
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | - Jacqueline M Fabius
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | - Margaret Soucheray
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | - Ruth Hüttenhain
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | - Irwin Jungreis
- MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Manolis Kellis
- MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ignacia Echeverria
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
| | - Kliment Verba
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
| | - Paola Bonfanti
- Division of Infection and Immunity, University College London, London, UK; Epithelial Stem Cell Biology and Regenerative Medicine Laboratory, The Francis Crick Institute, London, UK
| | - Pedro Beltrao
- QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge, UK; Institute of Molecular Systems Biology, Department of Biology, ETH Zürich, Zurich, Switzerland
| | - Roded Sharan
- School of Computer Science, Tel Aviv University, Tel Aviv, Israel
| | - Jennifer A Doudna
- QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, USA; Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA; California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA, USA; Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
| | - Luis Martinez-Sobrido
- QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Arvind H Patel
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Massimo Palmarini
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Lisa Miorin
- QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kris White
- QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Danielle L Swaney
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | - Adolfo Garcia-Sastre
- QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA; The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Clare Jolly
- QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Division of Infection and Immunity, University College London, London, UK.
| | - Lorena Zuliani-Alvarez
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA.
| | - Greg J Towers
- QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Division of Infection and Immunity, University College London, London, UK.
| | - Nevan J Krogan
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA.
| |
Collapse
|
6
|
MacMillan P, Syed AM, Kingston BR, Ngai J, Sindhwani S, Lin ZP, Nguyen LNM, Ngo W, Mladjenovic SM, Ji Q, Blackadar C, Chan WCW. Toward Predicting Nanoparticle Distribution in Heterogeneous Tumor Tissues. Nano Lett 2023; 23:7197-7205. [PMID: 37506224 DOI: 10.1021/acs.nanolett.3c02186] [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] [Subscribe] [Scholar Register] [Indexed: 07/30/2023]
Abstract
Nanobio interaction studies have generated a significant amount of data. An important next step is to organize the data and design computational techniques to analyze the nanobio interactions. Here we developed a computational technique to correlate the nanoparticle spatial distribution within heterogeneous solid tumors. This approach led to greater than 88% predictive accuracy of nanoparticle location within a tumor tissue. This proof-of-concept study shows that tumor heterogeneity might be defined computationally by the patterns of biological structures within the tissue, enabling the identification of tumor patterns for nanoparticle accumulation.
Collapse
Affiliation(s)
- Presley MacMillan
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
- Institute of Biomedical Engineering, University of Toronto, Rosebrugh Building, 164 College Street, Toronto, Ontario M5S 3G9, Canada
| | - Abdullah M Syed
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
- Institute of Biomedical Engineering, University of Toronto, Rosebrugh Building, 164 College Street, Toronto, Ontario M5S 3G9, Canada
| | - Benjamin R Kingston
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
- Institute of Biomedical Engineering, University of Toronto, Rosebrugh Building, 164 College Street, Toronto, Ontario M5S 3G9, Canada
| | - Jessica Ngai
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
- Institute of Biomedical Engineering, University of Toronto, Rosebrugh Building, 164 College Street, Toronto, Ontario M5S 3G9, Canada
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario M5S 3E5, Canada
| | - Shrey Sindhwani
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
- Institute of Biomedical Engineering, University of Toronto, Rosebrugh Building, 164 College Street, Toronto, Ontario M5S 3G9, Canada
- Temerty Faculty of Medicine, University of Toronto, 149 College Street, Toronto, Ontario M5T 1P5, Canada
| | - Zachary P Lin
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
- Institute of Biomedical Engineering, University of Toronto, Rosebrugh Building, 164 College Street, Toronto, Ontario M5S 3G9, Canada
| | - Luan N M Nguyen
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
- Institute of Biomedical Engineering, University of Toronto, Rosebrugh Building, 164 College Street, Toronto, Ontario M5S 3G9, Canada
| | - Wayne Ngo
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
- Institute of Biomedical Engineering, University of Toronto, Rosebrugh Building, 164 College Street, Toronto, Ontario M5S 3G9, Canada
| | - Stefan M Mladjenovic
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
- Institute of Biomedical Engineering, University of Toronto, Rosebrugh Building, 164 College Street, Toronto, Ontario M5S 3G9, Canada
| | - Qin Ji
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
- Institute of Biomedical Engineering, University of Toronto, Rosebrugh Building, 164 College Street, Toronto, Ontario M5S 3G9, Canada
| | - Colin Blackadar
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
- Institute of Biomedical Engineering, University of Toronto, Rosebrugh Building, 164 College Street, Toronto, Ontario M5S 3G9, Canada
| | - Warren C W Chan
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
- Institute of Biomedical Engineering, University of Toronto, Rosebrugh Building, 164 College Street, Toronto, Ontario M5S 3G9, Canada
- Temerty Faculty of Medicine, University of Toronto, 149 College Street, Toronto, Ontario M5T 1P5, Canada
| |
Collapse
|
7
|
Taha TY, Chen IP, Hayashi JM, Tabata T, Walcott K, Kimmerly GR, Syed AM, Ciling A, Suryawanshi RK, Martin HS, Bach BH, Tsou CL, Montano M, Khalid MM, Sreekumar BK, Renuka Kumar G, Wyman S, Doudna JA, Ott M. Rapid assembly of SARS-CoV-2 genomes reveals attenuation of the Omicron BA.1 variant through NSP6. Nat Commun 2023; 14:2308. [PMID: 37085489 PMCID: PMC10120482 DOI: 10.1038/s41467-023-37787-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [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: 02/01/2023] [Accepted: 03/31/2023] [Indexed: 04/23/2023] Open
Abstract
Although the SARS-CoV-2 Omicron variant (BA.1) spread rapidly across the world and effectively evaded immune responses, its viral fitness in cell and animal models was reduced. The precise nature of this attenuation remains unknown as generating replication-competent viral genomes is challenging because of the length of the viral genome (~30 kb). Here, we present a plasmid-based viral genome assembly and rescue strategy (pGLUE) that constructs complete infectious viruses or noninfectious subgenomic replicons in a single ligation reaction with >80% efficiency. Fully sequenced replicons and infectious viral stocks can be generated in 1 and 3 weeks, respectively. By testing a series of naturally occurring viruses as well as Delta-Omicron chimeric replicons, we show that Omicron nonstructural protein 6 harbors critical attenuating mutations, which dampen viral RNA replication and reduce lipid droplet consumption. Thus, pGLUE overcomes remaining barriers to broadly study SARS-CoV-2 replication and reveals deficits in nonstructural protein function underlying Omicron attenuation.
Collapse
Affiliation(s)
- Taha Y Taha
- Gladstone Institutes, San Francisco, CA, USA.
| | - Irene P Chen
- Gladstone Institutes, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, CA, USA
| | | | | | | | | | - Abdullah M Syed
- Gladstone Institutes, San Francisco, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Alison Ciling
- Gladstone Institutes, San Francisco, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | | | - Hannah S Martin
- Gladstone Institutes, San Francisco, CA, USA
- Department of Chemistry, University of California, Berkeley, CA, USA
| | - Bryan H Bach
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | | | | | | | | | | | - Stacia Wyman
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Jennifer A Doudna
- Gladstone Institutes, San Francisco, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Department of Chemistry, 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
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, USA
| | - Melanie Ott
- Gladstone Institutes, San Francisco, CA, USA.
- Department of Medicine, University of California, San Francisco, CA, USA.
- Chan Zuckerberg Biohub - San Francisco, San Francisco, CA, USA.
| |
Collapse
|
8
|
Taha TY, Chen IP, Hayashi JM, Tabata T, Walcott K, Kimmerly GR, Syed AM, Ciling A, Suryawanshi RK, Martin HS, Bach BH, Tsou CL, Montano M, Khalid MM, Sreekumar BK, Kumar GR, Wyman S, Doudna JA, Ott M. Rapid assembly of SARS-CoV-2 genomes reveals attenuation of the Omicron BA.1 variant through NSP6. bioRxiv 2023:2023.01.31.525914. [PMID: 36798416 PMCID: PMC9934579 DOI: 10.1101/2023.01.31.525914] [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: 02/11/2023]
Abstract
Although the SARS-CoV-2 Omicron variant (BA.1) spread rapidly across the world and effectively evaded immune responses, its viral fitness in cell and animal models was reduced. The precise nature of this attenuation remains unknown as generating replication-competent viral genomes is challenging because of the length of the viral genome (30kb). Here, we designed a plasmid-based viral genome assembly and resc ue strategy (pGLUE) that constructs complete infectious viruses or noninfectious subgenomic replicons in a single ligation reaction with >80% efficiency. Fully sequenced replicons and infectious viral stocks can be generated in 1 and 3 weeks, respectively. By testing a series of naturally occurring viruses as well as Delta-Omicron chimeric replicons, we show that Omicron nonstructural protein 6 harbors critical attenuating mutations, which dampen viral RNA replication and reduce lipid droplet consumption. Thus, pGLUE overcomes remaining barriers to broadly study SARS-CoV-2 replication and reveals deficits in nonstructural protein function underlying Omicron attenuation.
Collapse
|
9
|
Ngo W, Wu JLY, Lin ZP, Zhang Y, Bussin B, Granda Farias A, Syed AM, Chan K, Habsid A, Moffat J, Chan WCW. Identifying cell receptors for the nanoparticle protein corona using genome screens. Nat Chem Biol 2022; 18:1023-1031. [PMID: 35953550 DOI: 10.1038/s41589-022-01093-5] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 06/22/2022] [Indexed: 01/01/2023]
Abstract
Nanotechnology provides platforms to deliver medical agents to specific cells. However, the nanoparticle's surface becomes covered with serum proteins in the blood after administration despite engineering efforts to protect it with targeting or blocking molecules. Here, we developed a strategy to identify the main interactions between nanoparticle-adsorbed proteins and a cell by integrating mass spectrometry with pooled genome screens and Search Tool for the Retrieval of Interacting Genes analysis. We found that the low-density lipoprotein (LDL) receptor was responsible for approximately 75% of serum-coated gold nanoparticle uptake in U-87 MG cells. Apolipoprotein B and complement C8 proteins on the nanoparticle mediated uptake through the LDL receptor. In vivo, nanoparticle accumulation correlated with LDL receptor expression in the organs of mice. A detailed understanding of how adsorbed serum proteins bind to cell receptors will lay the groundwork for controlling the delivery of nanoparticles at the molecular level to diseased tissues for therapeutic and diagnostic applications.
Collapse
Affiliation(s)
- Wayne Ngo
- Institute of Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada.,Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Jamie L Y Wu
- Institute of Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada.,Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Zachary P Lin
- Institute of Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada.,Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Yuwei Zhang
- Institute of Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada.,Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Bram Bussin
- Institute of Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada.,Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Adrian Granda Farias
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Abdullah M Syed
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
| | - Katherine Chan
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Andrea Habsid
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Jason Moffat
- Institute of Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada.,Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Warren C W Chan
- Institute of Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada. .,Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada. .,Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada. .,Department of Materials Science and Engineering, University of Toronto, Toronto, Ontario, Canada. .,Department of Chemistry, University of Toronto, Toronto, Ontario, Canada.
| |
Collapse
|
10
|
Suryawanshi RK, Chen IP, Ma T, Syed AM, Brazer N, Saldhi P, Simoneau CR, Ciling A, Khalid MM, Sreekumar B, Chen PY, Kumar GR, Montano M, Gascon R, Tsou CL, Garcia-Knight MA, Sotomayor-Gonzalez A, Servellita V, Gliwa A, Nguyen J, Silva I, Milbes B, Kojima N, Hess V, Shacreaw M, Lopez L, Brobeck M, Turner F, Soveg FW, George AF, Fang X, Maishan M, Matthay M, Morris MK, Wadford D, Hanson C, Greene WC, Andino R, Spraggon L, Roan NR, Chiu CY, Doudna JA, Ott M. Limited cross-variant immunity from SARS-CoV-2 Omicron without vaccination. Nature 2022; 607:351-355. [PMID: 35584773 PMCID: PMC9279157 DOI: 10.1038/s41586-022-04865-0] [Citation(s) in RCA: 108] [Impact Index Per Article: 54.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 05/12/2022] [Indexed: 11/08/2022]
Abstract
SARS-CoV-2 Delta and Omicron are globally relevant variants of concern. Although individuals infected with Delta are at risk of developing severe lung disease, infection with Omicron often causes milder symptoms, especially in vaccinated individuals1,2. The question arises of whether widespread Omicron infections could lead to future cross-variant protection, accelerating the end of the pandemic. Here we show that without vaccination, infection with Omicron induces a limited humoral immune response in mice and humans. Sera from mice overexpressing the human ACE2 receptor and infected with Omicron neutralize only Omicron, but not other variants of concern, whereas broader cross-variant neutralization was observed after WA1 and Delta infections. Unlike WA1 and Delta, Omicron replicates to low levels in the lungs and brains of infected animals, leading to mild disease with reduced expression of pro-inflammatory cytokines and diminished activation of lung-resident T cells. Sera from individuals who were unvaccinated and infected with Omicron show the same limited neutralization of only Omicron itself. By contrast, Omicron breakthrough infections induce overall higher neutralization titres against all variants of concern. Our results demonstrate that Omicron infection enhances pre-existing immunity elicited by vaccines but, on its own, may not confer broad protection against non-Omicron variants in unvaccinated individuals.
Collapse
Affiliation(s)
| | - Irene P Chen
- Gladstone Institutes, San Francisco, CA, USA
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Quantitative Biosciences Institute COVID-19 Research Group, University of California, San Francisco, San Francisco, CA, USA
| | - Tongcui Ma
- Gladstone Institutes, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Abdullah M Syed
- Gladstone Institutes, San Francisco, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Noah Brazer
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Prachi Saldhi
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Camille R Simoneau
- Gladstone Institutes, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Quantitative Biosciences Institute COVID-19 Research Group, University of California, San Francisco, San Francisco, CA, USA
| | - Alison Ciling
- Gladstone Institutes, San Francisco, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | | | | | - Pei-Yi Chen
- Gladstone Institutes, San Francisco, CA, USA
| | | | - Mauricio Montano
- Gladstone Institutes, San Francisco, CA, USA
- Michael Hulton Center for HIV Cure Research at Gladstone, San Francisco, CA, USA
| | | | | | - Miguel A Garcia-Knight
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
| | | | - Venice Servellita
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Amelia Gliwa
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Jenny Nguyen
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | | | | | - Noah Kojima
- Department of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | | | | | | | | | | | | | - Ashley F George
- Gladstone Institutes, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
| | - Xiaohui Fang
- Department of Medicine, Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA
- Department of Anesthesia, Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Mazharul Maishan
- Department of Medicine, Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA
- Department of Anesthesia, Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Michael Matthay
- Department of Medicine, Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA
- Department of Anesthesia, Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA
| | | | - Debra Wadford
- California Department of Public Health, Richmond, CA, USA
| | - Carl Hanson
- California Department of Public Health, Richmond, CA, USA
| | - Warner C Greene
- Gladstone Institutes, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Michael Hulton Center for HIV Cure Research at Gladstone, San Francisco, CA, USA
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
| | - Raul Andino
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
| | | | - Nadia R Roan
- Gladstone Institutes, San Francisco, CA, USA.
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA.
| | - Charles Y Chiu
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA.
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA.
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA.
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
| | - Jennifer A Doudna
- Gladstone Institutes, San Francisco, CA, USA.
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA.
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, USA.
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA.
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, USA.
| | - Melanie Ott
- Gladstone Institutes, San Francisco, CA, USA.
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA.
- Quantitative Biosciences Institute COVID-19 Research Group, University of California, San Francisco, San Francisco, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
| |
Collapse
|
11
|
Servellita V, Syed AM, Morris MK, Brazer N, Saldhi P, Garcia-Knight M, Sreekumar B, Khalid MM, Ciling A, Chen PY, Kumar GR, Gliwa AS, Nguyen J, Sotomayor-Gonzalez A, Zhang Y, Frias E, Prostko J, Hackett J, Andino R, Wadford DA, Hanson C, Doudna J, Ott M, Chiu CY. Neutralizing immunity in vaccine breakthrough infections from the SARS-CoV-2 Omicron and Delta variants. Cell 2022; 185:1539-1548.e5. [PMID: 35429436 PMCID: PMC8930394 DOI: 10.1016/j.cell.2022.03.019] [Citation(s) in RCA: 86] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 02/15/2022] [Accepted: 03/14/2022] [Indexed: 12/11/2022]
Abstract
Virus-like particle (VLP) and live virus assays were used to investigate neutralizing immunity against Delta and Omicron SARS-CoV-2 variants in 259 samples from 128 vaccinated individuals. Following Delta breakthrough infection, titers against WT rose 57-fold and 3.1-fold compared with uninfected boosted and unboosted individuals, respectively, versus only a 5.8-fold increase and 3.1-fold decrease for Omicron breakthrough infection. Among immunocompetent, unboosted patients, Delta breakthrough infections induced 10.8-fold higher titers against WT compared with Omicron (p = 0.037). Decreased antibody responses in Omicron breakthrough infections relative to Delta were potentially related to a higher proportion of asymptomatic or mild breakthrough infections (55.0% versus 28.6%, respectively), which exhibited 12.3-fold lower titers against WT compared with moderate to severe infections (p = 0.020). Following either Delta or Omicron breakthrough infection, limited variant-specific cross-neutralizing immunity was observed. These results suggest that Omicron breakthrough infections are less immunogenic than Delta, thus providing reduced protection against reinfection or infection from future variants.
Collapse
Affiliation(s)
- Venice Servellita
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Abdullah M Syed
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Mary Kate Morris
- Viral and Rickettsial Disease Laboratory, California Department of Public Health, Richmond, CA, USA
| | - Noah Brazer
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Prachi Saldhi
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Miguel Garcia-Knight
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
| | | | | | - Alison Ciling
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Pei-Yi Chen
- Gladstone Institutes, San Francisco, CA, USA
| | | | - Amelia S Gliwa
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Jenny Nguyen
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Alicia Sotomayor-Gonzalez
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Yueyuan Zhang
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | | | | | | | - Raul Andino
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
| | - Debra A Wadford
- Viral and Rickettsial Disease Laboratory, California Department of Public Health, Richmond, CA, USA
| | - Carl Hanson
- Viral and Rickettsial Disease Laboratory, California Department of Public Health, Richmond, CA, USA.
| | - Jennifer Doudna
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA; Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, USA; Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA.
| | - Melanie Ott
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA, USA; Gladstone Institutes, San Francisco, CA, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA.
| | - Charles Y Chiu
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA; Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA.
| |
Collapse
|
12
|
Ouyang B, Kingston BR, Poon W, Zhang YN, Lin ZP, Syed AM, Couture-Senécal J, Chan WCW. Impact of Tumor Barriers on Nanoparticle Delivery to Macrophages. Mol Pharm 2022; 19:1917-1925. [PMID: 35319220 DOI: 10.1021/acs.molpharmaceut.1c00905] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The delivery of therapeutic nanoparticles to target cells is critical to their effectiveness. Here we quantified the impact of biological barriers on the delivery of nanoparticles to macrophages in two different tissues. We compared the delivery of gold nanoparticles to macrophages in the liver versus those in the tumor. We found that nanoparticle delivery to macrophages in the tumor was 75% less than to macrophages in the liver due to structural barriers. The tumor-associated macrophages took up more nanoparticles than Kupffer cells in the absence of barriers. Our results highlight the impact of biological barriers on nanoparticle delivery to cellular targets.
Collapse
Affiliation(s)
- Ben Ouyang
- MD/PhD Program, University of Toronto, Toronto, Ontario M5S 1A8, Canada.,Institute of Biomedical Engineering, University of Toronto, Rosebrugh Building, Room 407, 164 College Street, Toronto, Ontario M5S 3G9, Canada.,Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Room 230, Toronto, Ontario M5S 3E1, Canada
| | - Benjamin R Kingston
- Institute of Biomedical Engineering, University of Toronto, Rosebrugh Building, Room 407, 164 College Street, Toronto, Ontario M5S 3G9, Canada.,Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Room 230, Toronto, Ontario M5S 3E1, Canada
| | - Wilson Poon
- Institute of Biomedical Engineering, University of Toronto, Rosebrugh Building, Room 407, 164 College Street, Toronto, Ontario M5S 3G9, Canada.,Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Room 230, Toronto, Ontario M5S 3E1, Canada.,Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, California 94143, United States.,UCSF Diabetes Center, University of California, San Francisco, San Francisco, California 94143, United States
| | - Yi-Nan Zhang
- Institute of Biomedical Engineering, University of Toronto, Rosebrugh Building, Room 407, 164 College Street, Toronto, Ontario M5S 3G9, Canada.,Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Room 230, Toronto, Ontario M5S 3E1, Canada.,Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Zachary P Lin
- Institute of Biomedical Engineering, University of Toronto, Rosebrugh Building, Room 407, 164 College Street, Toronto, Ontario M5S 3G9, Canada.,Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Room 230, Toronto, Ontario M5S 3E1, Canada
| | - Abdullah M Syed
- Institute of Biomedical Engineering, University of Toronto, Rosebrugh Building, Room 407, 164 College Street, Toronto, Ontario M5S 3G9, Canada.,Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Room 230, Toronto, Ontario M5S 3E1, Canada.,Gladstone Institute of Data Science and Biotechnology, San Francisco, California 94158, United States
| | - Julien Couture-Senécal
- Institute of Biomedical Engineering, University of Toronto, Rosebrugh Building, Room 407, 164 College Street, Toronto, Ontario M5S 3G9, Canada.,Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Room 230, Toronto, Ontario M5S 3E1, Canada
| | - Warren C W Chan
- Institute of Biomedical Engineering, University of Toronto, Rosebrugh Building, Room 407, 164 College Street, Toronto, Ontario M5S 3G9, Canada.,Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Room 230, Toronto, Ontario M5S 3E1, Canada.,Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada.,Division of Engineering Science, University of Toronto, 35 St. George Street, Toronto, Ontario M5S 1A4, Canada.,Department of Chemical Engineering, University of Toronto, 200 College Street, Toronto, Ontario M5S 3E5, Canada.,Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
| |
Collapse
|
13
|
Suryawanshi RK, Chen IP, Ma T, Syed AM, Brazer N, Saldhi P, Simoneau CR, Ciling A, Khalid MM, Sreekumar B, Chen PY, Kumar GR, Montano M, Garcia-Knight MA, Sotomayor-Gonzalez A, Servellita V, Gliwa A, Nguyen J, Silva I, Milbes B, Kojima N, Hess V, Shacreaw M, Lopez L, Brobeck M, Turner F, Soveg FW, George AF, Fang X, Maishan M, Matthay M, Greene WC, Andino R, Spraggon L, Roan NR, Chiu CY, Doudna J, Ott M. Limited Cross-Variant Immunity after Infection with the SARS-CoV-2 Omicron Variant Without Vaccination. medRxiv 2022. [PMID: 35075459 DOI: 10.1101/2022.01.13.22269243] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
SARS-CoV-2 Delta and Omicron strains are the most globally relevant variants of concern (VOCs). While individuals infected with Delta are at risk to develop severe lung disease 1 , Omicron infection causes less severe disease, mostly upper respiratory symptoms 2,3 . The question arises whether rampant spread of Omicron could lead to mass immunization, accelerating the end of the pandemic. Here we show that infection with Delta, but not Omicron, induces broad immunity in mice. While sera from Omicron-infected mice only neutralize Omicron, sera from Delta-infected mice are broadly effective against Delta and other VOCs, including Omicron. This is not observed with the WA1 ancestral strain, although both WA1 and Delta elicited a highly pro-inflammatory cytokine response and replicated to similar titers in the respiratory tracts and lungs of infected mice as well as in human airway organoids. Pulmonary viral replication, pro-inflammatory cytokine expression, and overall disease progression are markedly reduced with Omicron infection. Analysis of human sera from Omicron and Delta breakthrough cases reveals effective cross-variant neutralization induced by both viruses in vaccinated individuals. Together, our results indicate that Omicron infection enhances preexisting immunity elicited by vaccines, but on its own may not induce broad, cross-neutralizing humoral immunity in unvaccinated individuals.
Collapse
|
14
|
Syed AM, Taha TY, Tabata T, Chen IP, Ciling A, Khalid MM, Sreekumar B, Chen PY, Hayashi JM, Soczek KM, Ott M, Doudna JA. Rapid assessment of SARS-CoV-2-evolved variants using virus-like particles. Science 2021; 374:1626-1632. [PMID: 34735219 PMCID: PMC9005165 DOI: 10.1126/science.abl6184] [Citation(s) in RCA: 161] [Impact Index Per Article: 53.7] [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: 07/26/2021] [Accepted: 10/29/2021] [Indexed: 01/16/2023]
Abstract
Efforts to determine why new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants demonstrate improved fitness have been limited to analyzing mutations in the spike (S) protein with the use of S-pseudotyped particles. In this study, we show that SARS-CoV-2 virus-like particles (SC2-VLPs) can package and deliver exogenous transcripts, enabling analysis of mutations within all structural proteins and at multiple steps in the viral life cycle. In SC2-VLPs, four nucleocapsid (N) mutations found universally in more-transmissible variants independently increased messenger RNA delivery and expression ~10-fold, and in a reverse genetics model, the serine-202→arginine (S202R) and arginine-203→methionine (R203M) mutations each produced >50 times as much virus. SC2-VLPs provide a platform for rapid testing of viral variants outside of a biosafety level 3 setting and demonstrate N mutations and particle assembly to be mechanisms that could explain the increased spread of variants, including B.1.617.2 (Delta, which contains the R203M mutation).
Collapse
Affiliation(s)
- Abdullah M. Syed
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Taha Y. Taha
- Gladstone Institute of Virology, San Francisco, CA, USA
| | - Takako Tabata
- Gladstone Institute of Virology, San Francisco, CA, USA
| | - Irene P. Chen
- Gladstone Institute of Virology, San Francisco, CA, USA
- Biomedical Sciences Graduate Program, University of California, San Francisco, CA, USA
| | - Alison Ciling
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Mir M. Khalid
- Gladstone Institute of Virology, San Francisco, CA, USA
| | | | - Pei-Yi Chen
- Gladstone Institute of Virology, San Francisco, CA, USA
| | | | - Katarzyna M. Soczek
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Melanie Ott
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Gladstone Institute of Virology, San Francisco, CA, USA
- Department of Medicine, University of California San Francisco, CA, USA
| | - Jennifer A. Doudna
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA, USA
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
| |
Collapse
|
15
|
Overchuk M, Harmatys KM, Sindhwani S, Rajora MA, Koebel A, Charron DM, Syed AM, Chen J, Pomper MG, Wilson BC, Chan WCW, Zheng G. Subtherapeutic Photodynamic Treatment Facilitates Tumor Nanomedicine Delivery and Overcomes Desmoplasia. Nano Lett 2021; 21:344-352. [PMID: 33301689 DOI: 10.1021/acs.nanolett.0c03731] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Limited tumor nanoparticle accumulation remains one of the main challenges in cancer nanomedicine. Here, we demonstrate that subtherapeutic photodynamic priming (PDP) enhances the accumulation of nanoparticles in subcutaneous murine prostate tumors ∼3-5-times without inducing cell death, vascular destruction, or tumor growth delay. We also found that PDP resulted in an ∼2-times decrease in tumor collagen content as well as a significant reduction of extracellular matrix density in the subendothelial zone. Enhanced nanoparticle accumulation combined with the reduced extravascular barriers improved therapeutic efficacy in the absence of off-target toxicity, wherein 5 mg/kg of Doxil with PDP was equally effective in delaying tumor growth as 15 mg/kg of Doxil. Overall, this study demonstrates the potential of PDP to enhance tumor nanomedicine accumulation and alleviate tumor desmoplasia without causing cell death or vascular destruction, highlighting the utility of PDP as a minimally invasive priming strategy that can improve therapeutic outcomes in desmoplastic tumors.
Collapse
Affiliation(s)
- Marta Overchuk
- Princess Margaret Cancer Centre, University Health Network, 101 College Street, PMCRT 5-354, Toronto, Ontario M5G 1L7, Canada
- Institute of Biomedical Engineering, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Kara M Harmatys
- Princess Margaret Cancer Centre, University Health Network, 101 College Street, PMCRT 5-354, Toronto, Ontario M5G 1L7, Canada
| | - Shrey Sindhwani
- Institute of Biomedical Engineering, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Maneesha A Rajora
- Princess Margaret Cancer Centre, University Health Network, 101 College Street, PMCRT 5-354, Toronto, Ontario M5G 1L7, Canada
- Institute of Biomedical Engineering, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Adam Koebel
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario M5S 3M2, Canada
| | - Danielle M Charron
- Princess Margaret Cancer Centre, University Health Network, 101 College Street, PMCRT 5-354, Toronto, Ontario M5G 1L7, Canada
- Institute of Biomedical Engineering, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Abdullah M Syed
- J. David Gladstone Institutes, San Francisco, California 94158, USA
| | - Juan Chen
- Princess Margaret Cancer Centre, University Health Network, 101 College Street, PMCRT 5-354, Toronto, Ontario M5G 1L7, Canada
| | - Martin G Pomper
- Department of Radiology, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, United States
| | - Brian C Wilson
- Princess Margaret Cancer Centre, University Health Network, 101 College Street, PMCRT 5-354, Toronto, Ontario M5G 1L7, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Warren C W Chan
- Institute of Biomedical Engineering, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Gang Zheng
- Princess Margaret Cancer Centre, University Health Network, 101 College Street, PMCRT 5-354, Toronto, Ontario M5G 1L7, Canada
- Institute of Biomedical Engineering, University of Toronto, Toronto, Ontario M5G 1L7, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| |
Collapse
|
16
|
Ouyang B, Poon W, Zhang YN, Lin ZP, Kingston BR, Tavares AJ, Zhang Y, Chen J, Valic MS, Syed AM, MacMillan P, Couture-Senécal J, Zheng G, Chan WCW. The dose threshold for nanoparticle tumour delivery. Nat Mater 2020; 19:1362-1371. [PMID: 32778816 DOI: 10.1038/s41563-020-0755-z] [Citation(s) in RCA: 254] [Impact Index Per Article: 63.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 06/30/2020] [Indexed: 05/24/2023]
Abstract
Nanoparticle delivery to solid tumours over the past ten years has stagnated at a median of 0.7% of the injected dose. Varying nanoparticle designs and strategies have yielded only minor improvements. Here we discovered a dose threshold for improving nanoparticle tumour delivery: 1 trillion nanoparticles in mice. Doses above this threshold overwhelmed Kupffer cell uptake rates, nonlinearly decreased liver clearance, prolonged circulation and increased nanoparticle tumour delivery. This enabled up to 12% tumour delivery efficiency and delivery to 93% of cells in tumours, and also improved the therapeutic efficacy of Caelyx/Doxil. This threshold was robust across different nanoparticle types, tumour models and studies across ten years of the literature. Our results have implications for human translation and highlight a simple, but powerful, principle for designing nanoparticle cancer treatments.
Collapse
Affiliation(s)
- Ben Ouyang
- MD/PhD Program, University of Toronto, Toronto, Ontario, Canada
- Institute of Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Wilson Poon
- Institute of Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Yi-Nan Zhang
- Institute of Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Zachary P Lin
- Institute of Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Benjamin R Kingston
- Institute of Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Anthony J Tavares
- Institute of Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
- School of Life Sciences, Faculty of Humanities and Social Sciences, Sheridan College, Brampton, Ontario, Canada
| | - Yuwei Zhang
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Juan Chen
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Michael S Valic
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Abdullah M Syed
- Institute of Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
- J. David Gladstone Institutes, San Francisco, CA, USA
| | - Presley MacMillan
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Julien Couture-Senécal
- Institute of Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
- Division of Engineering Science, University of Toronto, Toronto, Ontario, Canada
| | - Gang Zheng
- Institute of Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Warren C W Chan
- Institute of Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada.
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada.
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada.
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada.
- Department of Material Science and Engineering, University of Toronto, Toronto, Ontario, Canada.
| |
Collapse
|
17
|
Aro AR, Tudisca V, Radl-Karimi C, Lau CJ, Bertram M, Syed AM, Skovgaard T, Cori L, Bianchi F, Valente A. Contextualization of indicators for evidence-informed policy making: results from Denmark and Italy. Eur J Public Health 2016. [DOI: 10.1093/eurpub/ckw167.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
|
18
|
Tudisca V, Radl-Karimi C, Lau CL, Syed AM, Aro AR, Valente A. Indicators for evidence-informed policy making and policy phases in the Italian and Danish context. Eur J Public Health 2016. [DOI: 10.1093/eurpub/ckw174.077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
19
|
McFarlane J, Syed AM, Sibly TF. A single injection of collagenase clostridium histolyticum for the treatment of moderate Dupuytren's contracture: a 2 year follow-up of 47 patients. J Hand Surg Eur Vol 2016; 41:664-5. [PMID: 26269508 DOI: 10.1177/1753193415597421] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- J McFarlane
- Robert Jones and Agnes Hunt Hospital, Oswestry, UK
| | - A M Syed
- Hereford County Hospital, Hereford, UK
| | - T F Sibly
- Hereford County Hospital, Hereford, UK
| |
Collapse
|
20
|
Abstract
The objective of the SARSControl Delphi study was to develop options for national and international emerging infectious diseases policies. The aim of this paper is to present the results of the study, which gathered expert opinions on gaps and inconsistencies concerning preparedness and response planning for Severe Acute Respiratory Syndrome (SARS) and SARS-like diseases. The Delphi technique was employed, which comprised a pilot round, two written rounds and a face-to-face meeting. The Delphi panel consisted of 38 experts from 22 countries, who highlighted the necessity to test plans and stressed the importance of surveillance measures for the swift containment of communicable disease outbreaks and the inclusion of detailed triage plans in national pandemic plans. The experts also suggested a need to define criteria for testing pandemic preparedness plans at different regional levels. New policy alternatives were identified, such as the need for generic plans on pandemics and universal access to healthcare during an outbreak. The usefulness of some non-medical interventions, such as bans on travel, could not be established and need further research. Dissemination of the findings will help to bridge gaps and rectify inconsistencies in current pandemic planning and response strategies for SARS and SARS-like diseases, as well as add valuable knowledge towards the development of national and international emerging infectious disease policies.
Collapse
Affiliation(s)
- A M Syed
- Department of Health Promotion Research, Institute of Public Health, University of Southern Denmark, Esbjerg, Denmark.
| | | | | | | | | |
Collapse
|
21
|
Bhupinder S, Kumara TK, Syed AM. Pattern of homicidal deaths autopsied at Penang Hospital, Malaysia, 2007-2009: a preliminary study. Malays J Pathol 2010; 32:81-86. [PMID: 21329178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
This article describes the homicide pattern in Penang Island, Malaysia over a three-year period (2007-2009). 65 homicide autopsies were performed at the Department of Forensic Medicine, Penang Hospital over the study period. The homicide rates ranged from 0.01 to 0.09/1000 population, the highest being in the Indian ethnic group. The majority (37%) of victims were in the 20-39 years age group. The male: female ratio was 3:1. The majority of deaths were caused by blunt instruments (46%), followed by stab/slash wounds (25%) and asphyxiation (12%). 63% of homicides occurred in areas served by the police stations at Jalan Patani (23.1%), Sg. Nibong (16.9%), Central (12.3%) and Bayan Lepas (10.9%). 56 (86%) victims were brought in dead to the hospital, while 9 (14%) died after admission. Most (39%) incidences occurred in the morning. The methods of homicide were different from Kuala Lumpur, another highly urbanised area of Malaysia.
Collapse
Affiliation(s)
- S Bhupinder
- Department of Forensic Medicine, Penang Hospital, Penang, Malaysia.
| | | | | |
Collapse
|
22
|
Bhupinder S, Kumara TK, Syed AM. Completed suicides in the district of timur laut, penang island - a preliminary investigation of 3 years (2007-2009) prospective data. Med J Malaysia 2010; 65:123-126. [PMID: 23756796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
This article describes the completed suicide patterns which occurred in the Timur Laut district of Penang Island, Malaysia. In a prospective cohort study over the three years period (2007-2009) there were 138 cases of suicide deaths. The number of suicide deaths for the year 2007, 2008 and 2009 were 45, 41 and 52 deaths, respectively. Majority of the suicide deaths were by jumping from height (47.1%), followed by hanging (34.1%) and by drowning (10.9%). The male victims outnumbered females in a 3 : 1 ratio.
Collapse
Affiliation(s)
- S Bhupinder
- Penang Hospital, Department of Forensic Medicine, 10990 Jalan Residensi, Penang, Malaysia.
| | | | | |
Collapse
|
23
|
White TJ, Avery GR, Kennan N, Syed AM, Hartley JE, Monson JRT. Virtual colonoscopy vs conventional colonoscopy in patients at high risk of colorectal cancer--a prospective trial of 150 patients. Colorectal Dis 2009; 11:138-45. [PMID: 18462241 DOI: 10.1111/j.1463-1318.2008.01554.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
OBJECTIVE Virtual colonoscopy (VC)/CT colonography has advantages over the well-documented limitations of colonoscopy/barium enema. This prospective blinded investigative comparison trial aimed to evaluate the ability of VC to assess the large bowel, compared to conventional colonoscopy (CC), in patients at high risk of colorectal cancer (CRC). METHOD We studied 150 patients (73 males, mean age 60.9 years) at high risk of CRC. Following bowel preparation, VC was undertaken using colonic insufflation and 2D-spiral CT acquisition. Two radiologists reported the images and a consensual agreement reached. Direct comparison was made with CC (performed later the same day). Interobserver agreement was calculated using the Kappa method. Postal questionnaires sought patient preference. RESULTS Virtual colonoscopy visualized the caecum in all cases. Five (3.33%) VCs were classified as inadequate owing to poor distension/faecal residue. CC completion rate was 86%. Ultimately, 44 patients had normal findings, 44 had diverticular disease, 11 had inflammatory bowel disease, 18 had cancers, and 33 patients had 42 polyps. VC identified 19 cancers--a sensitivity and specificity of 100% and 99.2% respectively. For detecting polyps > 10 mm, VC had a sensitivity and specificity (per patient) of 91% and 99.2% respectively. VC identified four polyps proximal to stenosing carcinomas and extracolonic malignancies in nine patients (6%). No procedural complications occurred with either investigation. A Kappa score achieved for interobserver agreement was 0.777. CONCLUSION Virtual colonoscopy is an effective and safe method for evaluating the bowel and was the investigation of choice amongst patients surveyed. VC provided information additional to CC on both proximal and extracolonic pathology. VC may become the diagnostic procedure of choice for symptomatic patients at high risk of CRC, with CC being reserved for therapeutic intervention, or where a tissue diagnosis is required.
Collapse
Affiliation(s)
- T J White
- The Academic Surgical Unit, University of Hull, Castle Hill Hospital, Hull, UK
| | | | | | | | | | | |
Collapse
|
24
|
Syed AM, Puthawala A, Sharma A, Gamie S, Londrc A, Cherlow JM, Damore SJ, Nazmy N, Sheikh KM, Ko SJ. High-dose-rate brachytherapy in the treatment of carcinoma of the prostate. Cancer Control 2001; 8:511-21. [PMID: 11807421 DOI: 10.1177/107327480100800606] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Although radical prostatectomy for localized disease is considered as a standard of care, external-beam radiotherapy and brachytherapy are equally effective. We report on the technique and preliminary results of high-dose-rate (HDR) brachytherapy using a temporary iridium-192 implant technique. METHODS The authors reviewed the literature on the techniques, treatment protocols, and results of HDR brachytherapy in the treatment of carcinoma of the prostate, and they report their own protocols, technique, and results. RESULTS The combination of HDR brachytherapy and external irradiation has been well tolerated by all 200 patients in our series, with less than 3% grade 3 late complications and with 95% PSA relapse-free survival with a median follow-up of 24 months. CONCLUSIONS HDR brachytherapy may be the most conformal type of irradiation in the treatment of carcinoma of the prostate regardless of tumor size, anatomical distortion, and organ mobility.
Collapse
Affiliation(s)
- A M Syed
- Department of Radiation Oncology, Long Beach Memorial Medical Center, 2801 Atlantic Avenue, Long Beach, CA 90806-1737, USA.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
25
|
Puthawala AA, Syed AM, Austin PA, Cherlow JM, Perley JM, Shanberg AM, Sawyer DE, Ingram JE, Baghdassarian R, Wachs BH, Perley JE, Londrc A, Espinoza-Ferrel T. Long-term results of treatment for prostate carcinoma by staging pelvic lymph node dissection and definitive irradiation using low-dose rate temporary iridium-192 interstitial implant and external beam radiotherapy. Cancer 2001; 92:2084-94. [PMID: 11596024 DOI: 10.1002/1097-0142(20011015)92:8<2084::aid-cncr1549>3.0.co;2-c] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
BACKGROUND The objective of this study was to evaluate long-term treatment outcome of definitive irradiation by using temporary interstitial implant and limited dose of external beam radiotherapy in treatment of localized prostate carcinoma. METHODS In total, 536 patients with biopsy-proven adenocarcinoma of the prostate, classification T1-T3, underwent staging pelvic lymph node dissection and brachytherapy delivering an average tumor dose of 30 grays (Gy), supplemented by external beam radiation therapy for an additional dose of 36 Gy delivered over 4 weeks. One hundred of 536 (18%) patients had pathologic D1 disease. A total of 181 patients had undergone transurethral prostatectomy before the treatment. Repeat prostate biopsy was performed on 132 patients 18 or more months after treatment. None of the patients received neoadjuvant or adjuvant hormone therapy. RESULTS Cumulative disease free survival (DFS) including biochemical DFS at 10 and 15 years for classification T1B,C was 78% and 72%; for T2A, 78% and 78%; for T2B,C, 68% and 66%; and for T3A-C, 45% and 45%, respectively. Cause specific survival for the entire group at 10 and 15 years was 89% and 87%, respectively. Severe complications occurred only in the early developmental phase of the study. CONCLUSIONS In univariate analysis, the clinical stage, histologic grade, pretreatment PSA level, lymph node status, and results of repeat posttreatment biopsy were all independently significant prognostic factors. However, the authors' study indicates that in multivariate analysis, only two factors emerged with statistical significance-the status of pelvic lymph nodes and the results of posttreatment biopsy. This signifies the importance of local tumor control to achieve ultimate cure and the importance of assessment of pelvic lymph nodes before definitive local therapy other than radical prostatectomy, especially in the high-risk group.
Collapse
Affiliation(s)
- A A Puthawala
- Department of Radiation Oncology, Long Beach Memorial Medical Center, Long Beach, California 90806, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
26
|
Syed AM, Puthawala AA, Damore SJ, Cherlow JM, Austin PA, Sposto R, Ramsinghani NS. Brachytherapy for primary and recurrent nasopharyngeal carcinoma: 20 years' experience at Long Beach Memorial. Int J Radiat Oncol Biol Phys 2000; 47:1311-21. [PMID: 10889385 DOI: 10.1016/s0360-3016(00)00520-4] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
PURPOSE We evaluated treatment outcomes of patients with mostly locally advanced primary and recurrent cancer of the nasopharynx managed with interstitial and intraluminal brachytherapy. METHODS AND MATERIALS This is a retrospective analysis of 56 patients with cancer arising from the nasopharynx treated with interstitial and intracavitary afterloading brachytherapy from 1978 to 1997. Patients were divided into three treatment groups: 15 patients with primary cancer (Group 1), 34 patients with recurrent or persistent disease (Group 2), and 7 patients with cancer in the nasopharynx who had history of previous definitive radiation therapy to the nasopharynx for head and neck cancer (Group 3). Fifty-three percent of patients in Group 1 had 1992 AJCC Stage IV disease, and 49% of patients in Groups 2 and 3 had extensive disease (defined as T3, T4, or parapharyngeal extension). Group 1 received megavoltage radiation to 50-60 Gy followed by a boost to the primary site and neck (in cases of persistent neck disease) with a combination of interstitial and intracavitary brachytherapy (mean dose 33-37 Gy). Five patients received chemotherapy, and 6 patients received hyperthermia. Groups 2 and 3 patients were treated with brachytherapy implants (mean dose 50-58 Gy) without external beam radiation. Twenty-five patients received chemotherapy either before or during radiation, and 21 patients received hyperthermia. RESULTS The overall survival at 2, 5, and 10 years for patients in Group 1 was 79%, 61%, and 61%, respectively, and for patients in Groups 2 and 3 combined was 48%, 30%, and 20%, respectively. Cause-specific survival at 2, 5, and 10 years was 87%, 74%, and 74%, respectively, for patients in Group 1; and 82%, 60%, and 60%, respectively, for patients in Groups 2 and 3. Local control at 2, 5, and 10 years was 93%, 93%, and 77%, respectively, for patients in Group 1; and 81%, 59%, and 49%, respectively, for patients in Groups 2 and 3. Control in the neck at 2, 5, and 10 years was achieved in 93%, 93%, and 93% of patients, respectively, in Group 1; and 88%, 81%, and 81%, respectively, for patients in Groups 2 and 3. Disease-free survival was 87%, 74%, and 62%, respectively, for patients in Group 1, and 56%, 41%, and 34%, respectively, for patients in Groups 2 and 3. There were 4 peri-operative deaths. One death (2%) was attributable to the development of late complications. Forty-five percent of patients experienced some form of late complications. CONCLUSION Interstitial afterloading brachytherapy can provide effective treatment for nasopharyngeal cancers, especially for locally persistent/recurrent and locally extensive lesions.
Collapse
Affiliation(s)
- A M Syed
- Department of Radiation Oncology, Long Beach Memorial Medical Center, CA 90806, USA
| | | | | | | | | | | | | |
Collapse
|
27
|
Abstract
PURPOSE We used clinical patient data to examine implant displacement between high dose rate (HDR) brachytherapy fractions for prostate cancer to determine its impact on treatment delivery. MATERIALS AND METHODS We analyzed the verification films taken prior to each fraction for 96 consecutive patients treated with HDR brachytherapy boosts as part of their radiation therapy for definitive treatment of organ-confined prostate cancer at our institution. Patients were treated with 18-24 Gy in 4 fractions of HDR delivered in 40 hours followed by 36-39.6 Gy external beam radiation to the prostate. We determined the mean and maximum displacement distances of marker seeds placed in the prostate and of the implanted needles between HDR fractions. RESULTS Mean and maximum displacement distances between fractions were documented up to 7.6 mm and 28.5 mm, respectively, for the implant needles and 3.6 mm and 11.4 mm, respectively, for the gold marker seeds. All displacement of implant needles occurred in the caudal direction. At least 1 cm caudal displacement of needles occurred prior to 15.5% all fractions. Manual adjustment of needles was required prior to 15% of fractions, and adjustment of the CLP only was required in 24%. Most of the displacement for both the marker seeds and needles occurred between the first and second fractions. CONCLUSIONS There is significant caudal displacement of interstitial implant needles between HDR fractions in our prostate cancer patients. Obtaining verification films and making adjustments in the treatment volume prior to each fraction is necessary to avoid significant inaccuracies in treatment delivery.
Collapse
Affiliation(s)
- S J Damore
- Department of Radiation Oncology, Long Beach Memorial Medical Center, Long Beach, CA 90806, USA.
| | | | | | | |
Collapse
|
28
|
Tewari K, Cappuccini F, Syed AM, Puthawala A, DiSaia PJ, Berman ML, Manetta A, Monk BJ. Interstitial brachytherapy in the treatment of advanced and recurrent vulvar cancer. Am J Obstet Gynecol 1999; 181:91-8. [PMID: 10411801 DOI: 10.1016/s0002-9378(99)70441-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
OBJECTIVE Our purpose was to evaluate the role of interstitial brachytherapy in vulvar cancer management. STUDY DESIGN From 1985-1992 we performed a retrospective study of patients treated at the University of California, Irvine Medical Center, and Long Beach Memorial Medical Center. RESULTS Eleven patients received interstitial brachytherapy, with (n = 5) or without (n = 6) external beam radiotherapy, for locally advanced (n = 5) or recurrent (n = 6) vulvar cancer. Local control was achieved in all patients. Ten patients have died of disease at a mean interval of 33 months from the time of treatment, with 9 patients having maintenance of local control at death. One patient is alive without disease after 77 months of follow-up. There were 2 cases of local necrosis (18%) and 1 case of rectovaginal fistula (9%). CONCLUSION Local control of advanced vulvar cancer can be achieved with interstitial brachytherapy, with or without external beam radiotherapy. With improved systemic therapy this treatment modality may be used to salvage women with bulky, symptomatic tumors.
Collapse
Affiliation(s)
- K Tewari
- Division of Gynecologic Oncology, University of California, Irvine Medical Center, Orange, California, USA
| | | | | | | | | | | | | | | |
Collapse
|
29
|
Abstract
The controversy about the treatment of carcinoma of the prostate has increased in the last decade, with most urologists favoring radical prostatectomy rather than primary irradiation. Several reports of persistent tumors in 50% to 90% of patients after external irradiation and permanent iodine-125 implantation of the prostate have been disturbing. From July 1977 to December 1985, 200 patients with adenocarcinoma of the prostate were treated by combining bilateral pelvic lymphadenectomy and temporary interstitial iridium-192 implantation of the prostate, followed by external irradiation. Seventy-four (36%) patients underwent biopsies of the prostate 4 months to 2 years after completion of the irradiation. Only 12 (16%) patients had persistent tumors. Complications were minimized subsequently by dose modifications.
Collapse
Affiliation(s)
- A M Syed
- Department of Radiation Oncology, Long Beach Memorial Medical Center, CA 90801
| | | | | | | | | | | | | | | | | | | |
Collapse
|
30
|
Abstract
Endocurietherapy (brachytherapy) is the placing of radioactive sources directly into or near a solid tumor. This technique delivers a concentrated dose of radiation to a restricted volume while minimizing radiation effects on normal tissue. We have treated 11 patients (nine sarcomas, one carcinoma, and one Wilms') with endocurietherapy procedures as part of their multimodality treatment program. Six were treated as part of the primary management, and the other five were treated for recurrent or metastatic disease. Temporary afterloaded implants using ribbons embedded with radioactive iridium192 (Ir192) seeds delivered typical tumor doses of 4,000 cGy. Six patients, including four primary cases and two recurrent cases, are currently classified as no evidence of disease (NED) without further local regional treatment (follow-up of 11-62 months; median, 38 months), and one patient treated for metastasis also remains locally controlled. Two patients are classified as alive with disease (AWD), two died of disease (DOD), and one is now NED after surgical salvage. Special considerations were given to gonadal shielding, radioprotection techniques, and psychosocial issues in this pediatric population.
Collapse
Affiliation(s)
- J M Cherlow
- Department of Radiation Oncology, Memorial Medical Center, Long Beach, CA 90801
| | | | | | | | | |
Collapse
|
31
|
Puthawala AA, Syed AM, Eads DL, Gillin L, Gates TC. Limited external beam and interstitial 192iridium irradiation in the treatment of carcinoma of the base of the tongue: a ten year experience. Int J Radiat Oncol Biol Phys 1988; 14:839-48. [PMID: 3360653 DOI: 10.1016/0360-3016(88)90003-x] [Citation(s) in RCA: 105] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
A total of 70 patients with histologically proven diagnosis of carcinoma of the base of the tongue were treated with primary irradiation between May 1974 through April 1984. Fifty-eight (83%) of these patients had locally advanced tumors (Stage T3, T4, N2, N3). Fifty-one of the 70 (73%) patients had clinically palpable neck nodes at first presentation. All patients received a combination of external and interstitial irradiation. The dose of external irradiation was limited to 45-50 Gy over 4 1/2-5 1/2 weeks. Interstitial volume implants were performed 2-3 weeks after completion of external irradiation. The primary site as well as the vallecula, epsilateral pharyngeal wall, glossopalatine sulcus, tonsillar bed, and pillars were routinely implanted to encompass contiguous spread of the disease. The doses of implant varied according to the stage of disease, that is, 2000-2500 cGy for T1 and T2 lesions, 3000-4000 cGy for T3 and T4 lesions, with typical dose rates of 50-60 cGy per hour. The neck nodes were also separately implanted to deliver additional doses of 2000-4000 cGy in 50-80 hours. Overall, local tumor control was observed in 58 of 70 (83%) patients at minimum follow-up of 2 years. An absolute 3-year disease-free survival of the entire group was 67.0%. Treatment related complications such as soft tissue necrosis and/or osteoradionecrosis occurred in 8 of the 70 (11.4%) patients. The salvage of neck failures and the local failures was feasible in 74% and 46% of the patients, respectively either by surgery or by re-irradiation using interstitial 192iridium implant alone. This treatment region is well tolerated and it preserves the functional and asthetic integrity in most patients.
Collapse
Affiliation(s)
- A A Puthawala
- Division of Radiation Oncology, University of California, Irvine
| | | | | | | | | |
Collapse
|
32
|
|
33
|
Abstract
A total of 127 patients with histologically proved diagnosis of carcinoma of the tonsillar region and soft palate were treated over the past ten years utilizing interstitial iridium-192 implants. Eighty patients were treated for primary tumors and 47 patients for either recurrent or persistent tumors after definitive irradiation and/or surgery. All patients with primary tumors were treated by a combination of external megavoltage irradiation and interstitial iridium-192 implants, whereas patients with recurrent tumors were treated by interstitial implants alone. In the primary group, 95% of patients with T1 and T2 lesions and 79% with T3 and T4 lesions achieved complete local tumor control. The three-year absolute disease-free survival rate was 72%. Seventy-five percent local tumor control was obtained in patients with recurrent disease, with two-year absolute disease-free survival of 42%. Treatment-related complications such as soft-tissue necrosis or osteoradionecrosis occurred in 6% of patients in the primary group and 23% in recurrent group. This treatment regimen offers an excellent locoregional control with no significant functional or esthetic impairment. Most patients with primary lesions who fail this regimen can be salvaged by surgery or reirradiation using interstitial implants. Reirradiation with interstitial implants is feasible and offers a good chance of long-term local tumor control in the selected group of patients with recurrent disease for whom external irradiation and/or surgery had not been successful.
Collapse
|
34
|
Puthawala AA, Syed AM, Eads DL, Neblett D, Gillin L, Gates TC. Limited external irradiation and interstitial 192iridium implant in the treatment of squamous cell carcinoma of the tonsillar region. Int J Radiat Oncol Biol Phys 1985; 11:1595-602. [PMID: 3928545 DOI: 10.1016/0360-3016(85)90211-1] [Citation(s) in RCA: 58] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Between January 1976 and March 1982, 80 patients with histologically proven diagnosis of squamous cell carcinoma of the tonsillar region were treated with definitive radiotherapy. Sixty-five (81%) of these patients had locally advanced tumors (Stage III and IV); 49% of patients had clinically palpable cervical lymphadenopathy. All patients received a combined external megavoltage and interstitial irradiation. The dose of external irradiation was limited to 4500-5000 cGy over 41/2 to 51/2 weeks. This was followed by interstitial 192iridium implants to doses of 2000-2500 cGy in 50-60 hours for T1, T2 lesions and 3000-4000 cGy in 60-100 hours for T3 , T4 lesions. The neck masses were also separately implanted to deliver additional doses of 2000-4000 cGy in 50-80 hours. Overall local tumor control was observed in 84% of patients with a minimum follow-up period of 2 years. An absolute 3-year disease free survival of the entire group was 72%. Treatment related complications such as soft tissue necrosis or osteoradionecrosis occurred in 6% (5/80) of patients. The salvage of neck failures and local failures was possible in 78 and 38% of patients, respectively, either by surgery or by re-irradiation employing interstitial 192iridium implants. Functional and esthetic integrity was well preserved in most cases.
Collapse
|
35
|
Puthawala AA, Syed AM, Sheikh KM, Gowdy RA, McNamara CS. Combined external and interstitial irradiation in the treatment of stage III breast cancer. Radiology 1984; 153:813-6. [PMID: 6494478 DOI: 10.1148/radiology.153.3.6494478] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
One hundred six patients with locally advanced carcinoma of the breast underwent definitive radiation therapy for loco-regional control following incisional and/or needle biopsy. Doses of external and interstitial irradiation were 5000 rad (50 Gy) in 5 to 6 weeks, and 3000 to 4000 rad (30-40 Gy) in 60 to 80 hours, respectively. Forty-eight of 106 patients (45%) also received adjuvant systemic chemotherapy. Loco-regional control was observed in 93 of the 106 patients (88%), with five-year disease-free survival of 47%. Distant metastases developed in 59 of the 106 patients (56%). Good to satisfactory cosmetic results were obtained in the majority of these patients; morbidity was at an acceptable level. Locally advanced breast cancer can be treated adequately and satisfactorily without mastectomy by a combination of external and interstitial irradiation.
Collapse
|
36
|
Syed AM, Puthawala AA, Orr LE, Gowdy RA, Sheikh KM, McNamara CS. Primary irradiation in the management of early and locally advanced carcinoma of the breast. Br J Radiol 1984; 57:317-21. [PMID: 6704663 DOI: 10.1259/0007-1285-57-676-317] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Between September 1, 1974, and July 31, 1979, we have treated 142 patients with a diagnosis of carcinoma of the breast by a combination of megavoltage external irradiation and interstitial iridium-192 implant. Sixty-four patients had T1 and T2 lesions and 78 patients had T3 and T4 lesions of the breast. Since June 1977, pre- and perimenopausal patients with T1 and T2 lesions have undergone axillary node dissection in addition to excisional biopsies of the breasts. All patients received external irradiation to the breast and regional lymph nodes and an interstitial implant boost to the primary site and residual axillary nodes. Most of the patients with positive axillary nodes, and those with locally advanced disease, received systemic chemotherapy. Sixty-two of 64 patients (97%) with T1 and T2 lesions and 72 of 78 (92%) patients w ith T3 and T4 lesions achieved ultimate loco-regional control. The minimum follow-up period was 48 months.
Collapse
|
37
|
Syed AM, Puthawala A, Tansey LA, Shanberg AM, Neblett D, Mendez R, Barloon JW, Ingram JE, Naftel WT, McNamara C. Management of prostate carcinoma. Combination of pelvic lymphadenectomy, temporary Ir-192 implantation, and external irradiation. Radiology 1983; 149:829-33. [PMID: 6417724 DOI: 10.1148/radiology.149.3.6417724] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Forty patients with prostate adenocarcinoma had bilateral pelvic lymphadenectomy, temporary Ir-192 implantation, and external irradiation. With the implant, the prostate received less than or equal to 3,000 rad (30 Gy) for A2 and B1 and 3,500 rad (35 Gy) for B2 and C lesions in 40-45 hours. Ten days to 2 weeks later, 4,000 rad (40 Gy) external irradiation was given in 4-5 weeks using AP and PA parallel opposed fields, a "box," or rotation. Patients with positive nodes were given 5,000 rad (50 Gy) to the pelvis with a midline block at 4,000 rad (40 Gy) so that the prostate received 7,000-7,500 rad (70-75 Gy). All patients were free of local recurrence. Treatment was tolerated well, with rapid regression and few complications.
Collapse
|
38
|
Abstract
Eighteen patients with locally advanced adenocarcinoma of the head, body and tail of the pancreas were treated by a combination of biliary bypass, external and interstitial irradiation at Southern California Cancer Center of California Hospital Medical Center, Los Angeles, and Memorial Hospital Medical Center of Long Beach, Long Beach, CA, from July 31, 1975 to December 31, 1980. A dose of 3000 to 5000 rad was delivered to the pancreas and regional lymph nodes by external irradiation utilizing megavoltage units and 10,000 to 15,000 rad to the pancreas and metastatic lymph nodes by permanent Iodine-125 implants. In this group of 18 patients with unresectable carcinoma of the pancreas, excellent palliation of pain, jaundice and vomiting was achieved, with a median survival of 14 months.
Collapse
|
39
|
Puthawala A, Syed AM, Nalick R, McNamara C, DiSaia PJ. Integrated external and interstitial radiation therapy for primary carcinoma of the vagina. Obstet Gynecol 1983; 62:367-72. [PMID: 6410310 DOI: 10.1097/00006250-198309000-00021] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Twenty-seven patients with the diagnosis of primary carcinoma of the vagina were treated by definitive radiotherapy. Twenty-three patients received a combination of external and interstitial iridium-192 implant irradiation and four patients received only interstitial irradiation. Twenty-one patients had squamous cell carcinoma and six had adenocarcinoma. All patients were staged according to the FIGO classification. More than 70% of patients had relatively advanced local disease and conventional intracavitary irradiation was unsuitable. Local tumor control was observed in 85% (23 of 27 patients), and 56% of the patients remain alive and free of disease for a median follow-up period of 50 months to a maximum follow-up period of 84 months. Fifteen percent of the patients suffered from treatment-related complications.
Collapse
|
40
|
Abstract
Forty patients with a diagnosis of recurrent pelvic malignancy from various primary sites with no clinical evidence of distant metastasis were re-irradiated with interstitial implant. Removable after-loading 192Ir sources or permanent 125I seeds or a combination of both were used. Twenty-six of these patients received interstitial implant at the time of exploratory laparotomy. A complete local control of implanted pelvic tumors was achieved in 27 of the 40 patients (67%). Thirteen of the 40 patients (33%) remained alive and disease-free to a minimum follow-up period of two years. Serious complications such as soft tissue necrosis and fistulae occurred in 15% of the patients.
Collapse
|
41
|
Abstract
Forty-patients with locally extensive carcinoma of the anorectum were treated by a combination of external and interstitial irradiation from April 1, 1974 to January 30, 1979. Twenty-eight patients (70%) achieved complete local tumor control and two more patients with residual tumor were salvaged by surgery. Twenty-four patients remain alive with local control for an average follow up period of three years. The overall complication rate has been 20%.
Collapse
|
42
|
|
43
|
|
44
|
Puthawala AA, Syed AM, Neblett D, McNamara C. The role of afterloading iridium (Ir192) implant in the management of carcinoma of the tongue. Int J Radiat Oncol Biol Phys 1981; 7:407-12. [PMID: 7275720 DOI: 10.1016/0360-3016(81)90117-6] [Citation(s) in RCA: 34] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
|
45
|
Syed AM, Puthawala A, Fleming P, Neblett D, Gowdy RA, Sheikh KM, George FW, Eads D, McNamara C. Combination of external and interstitial irradiation in the primary management of breast carcinoma. Cancer 1980; 46:1360-5. [PMID: 7417936 DOI: 10.1002/1097-0142(19800915)46:6<1360::aid-cncr2820460612>3.0.co;2-k] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The authors treated 83 patients with carcinoma of the breast using a combination of external and interstitial irradiation at Los Angeles County--University of Southern California Medical Center and Southern California Cancer Center between February 1, 1974, and May 31, 1977. All 30 patients who had T1 and T2 lesions, and who were followed for a minimum period of 24 months (24-50 months) are clinically still free of disease. Thirty-nine of 53 patients with T3 and T4 lesions, who were followed for a minimum of 30 months (30-56 months) are still alive with local control. Details of treatment techniques, dosimetry, results and complications are presented.
Collapse
|
46
|
Abstract
In the treatment of upper-aerodigestive-tract malignancy, interstitial-implant radiotherapy differs in several physical and biologic respects from conventional external-beam therapy: unlike external-beam therapy, it can deliver a high central dose with a rapid fall-off, which overcomes the central hypoxic resistance effect and yet greatly improves normal tissue tolerance. External-beam and interstitial-implant therapy can also be combined to the patient's benefit; in many cases, this combination offers advantages over external-beam therapy alone, preoperative external-beam therapy, or aggressive surgery. The recent upsurge of interest in this modality has come about because of three developments: more suitable radioactive sources, after-loading, and computerized dosimetry. The early results in upper-aerodigestive-tract malignancy, both as primary and as salvage therapy, are promising; but the precise role of this treatment in our therapeutic armamentarium remains to be established.
Collapse
|
47
|
|
48
|
Syed AM, Puthawala A, Neblett D, George FW, Myint US, Lipsett JA, Jackson BR, Flemming PA. Primary treatment of carcinoma of the lower rectum and anal canal by a combination of external irradiation and interstitial implant. Radiology 1978; 128:199-203. [PMID: 96489 DOI: 10.1148/128.1.199] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Ten patients with carcinoma of the anorectum were treated with a combination of external irradiation and after-loading interstitial 192Ir implant, which seems to be effective in controlling relatively small cancers of the anorectum and providing effective palliation of extensive lesions. Five of the 10 patients remain free of tumor after a minimum follow-up of 15 months. Four of the 10 were treated with one interstitial implant and 4,000--5,000 rads of external irradiation and 6 were treated with the same amount of irradiation and two implants. When two implants were used, complications were minimal.
Collapse
|
49
|
Feder BH, Syed AM, Neblett D. Treatment of extensive carcinoma of the cervix with the "transperineal parametrial butterfly": a prelimary report on the revival of Waterman's approach. Int J Radiat Oncol Biol Phys 1978; 4:735-42. [PMID: 711543 DOI: 10.1016/0360-3016(78)90204-3] [Citation(s) in RCA: 69] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
|
50
|
Abstract
After-loading implantation techniques apparently offer an effective alternative in the management of persistent (or recurrent) oropharynx and oral cavity carcinoma postirradiation. A total of 29 patients with such lesions was treated from February 1974, to July 1975, in the LAC/USC Radiation Medicine Section, using after-loading 192Ir implantation techniques. These patients all had extensive persistent cancer after "full tolerance" irradiation (with or without previous surgery) and were referred for palliation or for possible salvage. Additional doses administered ranged from 5000 to 7000 rads in three to five days. Eighteen of the 29 patients (63%) have had complete local control for 18 to 36 months. These patients have maintained a relatively satisfactory palliative status. Ten of the 29 are dead. Follow-up periods are short, but early indications are that problem patients with persistent cancer after "full tolerance irradiation" can be salvaged, or at least satisfactorily palliated, with after-loading interstitial implant techniques. Clinical details, sites of involvement, implantation techniques, dosimetry methodology, reactions and complications will be described.
Collapse
|