1
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Phan HV, Tsitsiklis A, Maguire CP, Haddad EK, Becker PM, Kim-Schulze S, Lee B, Chen J, Hoch A, Pickering H, van Zalm P, Altman MC, Augustine AD, Calfee CS, Bosinger S, Cairns CB, Eckalbar W, Guan L, Jayavelu ND, Kleinstein SH, Krammer F, Maecker HT, Ozonoff A, Peters B, Rouphael N, Montgomery RR, Reed E, Schaenman J, Steen H, Levy O, Diray-Arce J, Langelier CR. Host-microbe multiomic profiling reveals age-dependent immune dysregulation associated with COVID-19 immunopathology. Sci Transl Med 2024; 16:eadj5154. [PMID: 38630846 DOI: 10.1126/scitranslmed.adj5154] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 03/15/2024] [Indexed: 04/19/2024]
Abstract
Age is a major risk factor for severe coronavirus disease 2019 (COVID-19), yet the mechanisms behind this relationship have remained incompletely understood. To address this, we evaluated the impact of aging on host immune response in the blood and the upper airway, as well as the nasal microbiome in a prospective, multicenter cohort of 1031 vaccine-naïve patients hospitalized for COVID-19 between 18 and 96 years old. We performed mass cytometry, serum protein profiling, anti-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibody assays, and blood and nasal transcriptomics. We found that older age correlated with increased SARS-CoV-2 viral abundance upon hospital admission, delayed viral clearance, and increased type I interferon gene expression in both the blood and upper airway. We also observed age-dependent up-regulation of innate immune signaling pathways and down-regulation of adaptive immune signaling pathways. Older adults had lower naïve T and B cell populations and higher monocyte populations. Over time, older adults demonstrated a sustained induction of pro-inflammatory genes and serum chemokines compared with younger individuals, suggesting an age-dependent impairment in inflammation resolution. Transcriptional and protein biomarkers of disease severity differed with age, with the oldest adults exhibiting greater expression of pro-inflammatory genes and proteins in severe disease. Together, our study finds that aging is associated with impaired viral clearance, dysregulated immune signaling, and persistent and potentially pathologic activation of pro-inflammatory genes and proteins.
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Affiliation(s)
- Hoang Van Phan
- University of California San Francisco, San Francisco, CA 94115, USA
| | | | | | - Elias K Haddad
- Drexel University, Tower Health Hospital, Philadelphia, PA 19104, USA
| | - Patrice M Becker
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20814, USA
| | | | - Brian Lee
- Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jing Chen
- Precision Vaccines Program, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
- Research Computing, Department of Information Technology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Annmarie Hoch
- Precision Vaccines Program, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Harry Pickering
- David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Patrick van Zalm
- Precision Vaccines Program, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Matthew C Altman
- Benaroya Research Institute, University of Washington, Seattle, WA 98101, USA
| | - Alison D Augustine
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20814, USA
| | - Carolyn S Calfee
- University of California San Francisco, San Francisco, CA 94115, USA
| | | | - Charles B Cairns
- Drexel University, Tower Health Hospital, Philadelphia, PA 19104, USA
| | - Walter Eckalbar
- University of California San Francisco, San Francisco, CA 94115, USA
| | - Leying Guan
- Yale School of Public Health, New Haven, CT 06510, USA
| | | | | | - Florian Krammer
- Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Holden T Maecker
- Stanford University School of Medicine, Palo Alto, CA 94305, USA
| | - Al Ozonoff
- Precision Vaccines Program, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
- Research Computing, Department of Information Technology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Bjoern Peters
- La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | | | | | - Elaine Reed
- David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Joanna Schaenman
- David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Hanno Steen
- Precision Vaccines Program, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Ofer Levy
- Precision Vaccines Program, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Joann Diray-Arce
- Precision Vaccines Program, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Charles R Langelier
- University of California San Francisco, San Francisco, CA 94115, USA
- Chan Zuckerberg Biohub San Francisco, San Francisco, CA 94158, USA
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2
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Xia J, Phan HV, Vistain L, Chen M, Khan AA, Tay S. Computational prediction of protein interactions in single cells by proximity sequencing. PLoS Comput Biol 2024; 20:e1011915. [PMID: 38483861 PMCID: PMC10939233 DOI: 10.1371/journal.pcbi.1011915] [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] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 02/13/2024] [Indexed: 03/17/2024] Open
Abstract
Proximity sequencing (Prox-seq) simultaneously measures gene expression, protein expression and protein complexes on single cells. Using information from dual-antibody binding events, Prox-seq infers surface protein dimers at the single-cell level. Prox-seq provides multi-dimensional phenotyping of single cells in high throughput, and was recently used to track the formation of receptor complexes during cell signaling and discovered a novel interaction between CD9 and CD8 in naïve T cells. The distribution of protein abundance can affect identification of protein complexes in a complicated manner in dual-binding assays like Prox-seq. These effects are difficult to explore with experiments, yet important for accurate quantification of protein complexes. Here, we introduce a physical model of Prox-seq and computationally evaluate several different methods for reducing background noise when quantifying protein complexes. Furthermore, we developed an improved method for analysis of Prox-seq data, which resulted in more accurate and robust quantification of protein complexes. Finally, our Prox-seq model offers a simple way to investigate the behavior of Prox-seq data under various biological conditions and guide users toward selecting the best analysis method for their data.
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Affiliation(s)
- Junjie Xia
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, Illinois, United States of America
| | - Hoang Van Phan
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, Illinois, United States of America
| | - Luke Vistain
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, Illinois, United States of America
| | - Mengjie Chen
- Section of Genetic Medicine, Department of Medicine, The University of Chicago, Chicago, Illinois, United States of America
- Department Human Genetics, The University of Chicago, Chicago, Illinois, United States of America
| | - Aly A. Khan
- Department of Pathology, The University of Chicago, Chicago, Illinois, United States of America
| | - Savaş Tay
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, Illinois, United States of America
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3
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Van Phan H, Tsitsiklis A, Maguire CP, Haddad EK, Becker PM, Kim-Schulze S, Lee B, Chen J, Hoch A, Pickering H, Van Zalm P, Altman MC, Augustine AD, Calfee CS, Bosinger S, Cairns C, Eckalbar W, Guan L, Jayavelu ND, Kleinstein SH, Krammer F, Maecker HT, Ozonoff A, Peters B, Rouphael N, Montgomery RR, Reed E, Schaenman J, Steen H, Levy O, Diray-Arce J, Langelier CR. Host-Microbe Multiomic Profiling Reveals Age-Dependent COVID-19 Immunopathology. medRxiv 2024:2024.02.11.24301704. [PMID: 38405760 PMCID: PMC10888993 DOI: 10.1101/2024.02.11.24301704] [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: 02/27/2024]
Abstract
Age is a major risk factor for severe coronavirus disease-2019 (COVID-19), yet the mechanisms responsible for this relationship have remained incompletely understood. To address this, we evaluated the impact of aging on host and viral dynamics in a prospective, multicenter cohort of 1,031 patients hospitalized for COVID-19, ranging from 18 to 96 years of age. We performed blood transcriptomics and nasal metatranscriptomics, and measured peripheral blood immune cell populations, inflammatory protein expression, anti-SARS-CoV-2 antibodies, and anti-interferon (IFN) autoantibodies. We found that older age correlated with an increased SARS-CoV-2 viral load at the time of admission, and with delayed viral clearance over 28 days. This contributed to an age-dependent increase in type I IFN gene expression in both the respiratory tract and blood. We also observed age-dependent transcriptional increases in peripheral blood IFN-γ, neutrophil degranulation, and Toll like receptor (TLR) signaling pathways, and decreases in T cell receptor (TCR) and B cell receptor signaling pathways. Over time, older adults exhibited a remarkably sustained induction of proinflammatory genes (e.g., CXCL6) and serum chemokines (e.g., CXCL9) compared to younger individuals, highlighting a striking age-dependent impairment in inflammation resolution. Augmented inflammatory signaling also involved the upper airway, where aging was associated with upregulation of TLR, IL17, type I IFN and IL1 pathways, and downregulation TCR and PD-1 signaling pathways. Metatranscriptomics revealed that the oldest adults exhibited disproportionate reactivation of herpes simplex virus and cytomegalovirus in the upper airway following hospitalization. Mass cytometry demonstrated that aging correlated with reduced naïve T and B cell populations, and increased monocytes and exhausted natural killer cells. Transcriptional and protein biomarkers of disease severity markedly differed with age, with the oldest adults exhibiting greater expression of TLR and inflammasome signaling genes, as well as proinflammatory proteins (e.g., IL6, CXCL8), in severe COVID-19 compared to mild/moderate disease. Anti-IFN autoantibody prevalence correlated with both age and disease severity. Taken together, this work profiles both host and microbe in the blood and airway to provide fresh insights into aging-related immune changes in a large cohort of vaccine-naïve COVID-19 patients. We observed age-dependent immune dysregulation at the transcriptional, protein and cellular levels, manifesting in an imbalance of inflammatory responses over the course of hospitalization, and suggesting potential new therapeutic targets.
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Affiliation(s)
| | | | | | | | - Patrice M. Becker
- National Institute of Allergy and Infectious Diseases/National Institutes of Health
| | | | - Brian Lee
- Icahn School of Medicine at Mount Sinai
| | - Jing Chen
- Precision Vaccines Program, Boston Children’s Hospital
- Research Computing, Department of Information Technology, Boston Children’s Hospital
| | - Annmarie Hoch
- Precision Vaccines Program, Boston Children’s Hospital
| | - Harry Pickering
- David Geffen School of Medicine, University of California Los Angeles
| | | | | | - Alison D. Augustine
- National Institute of Allergy and Infectious Diseases/National Institutes of Health
| | | | | | | | | | | | | | | | | | | | - Al Ozonoff
- Precision Vaccines Program, Boston Children’s Hospital
| | | | | | | | | | - Elaine Reed
- David Geffen School of Medicine, University of California Los Angeles
| | - Joanna Schaenman
- David Geffen School of Medicine, University of California Los Angeles
| | - Hanno Steen
- Precision Vaccines Program, Boston Children’s Hospital
| | - Ofer Levy
- Precision Vaccines Program, Boston Children’s Hospital
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4
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Shitrit A, Nisnevich V, Rozenshtein N, Kobo H, Phan HV, Tay S, Szpara M, Weitzman MD, Drayman N, Kobiler O. Shared sequence characteristics identified in non-canonical rearrangements of HSV-1 genomes. J Virol 2023; 97:e0095523. [PMID: 37991369 PMCID: PMC10734421 DOI: 10.1128/jvi.00955-23] [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: 06/28/2023] [Accepted: 10/26/2023] [Indexed: 11/23/2023] Open
Abstract
IMPORTANCE Mutations and genetic rearrangements are the primary driving forces of evolution. Viruses provide valuable model systems for investigating these mechanisms due to their rapid evolutionary rates and vast genetic variability. To investigate genetic rearrangements in the double-stranded DNA genome of herpes simplex virus type 1, the viral population was serially passaged in various cell types. The serial passaging led to formation of defective genomes, resulted from cell-specific non-canonical rearrangements (NCRs). Interestingly, we discovered shared sequence characteristics underlying the formation of these NCRs across all cell types. Moreover, most NCRs identified in clinical samples shared these characteristics. Based on our findings, we propose a model elucidating the formation of NCRs during viral replication within the nucleus of eukaryotic cells.
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Affiliation(s)
- Alina Shitrit
- Department of Clinical Microbiology and Immunology, School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Valerya Nisnevich
- Department of Clinical Microbiology and Immunology, School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Nofar Rozenshtein
- Department of Clinical Microbiology and Immunology, School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Hila Kobo
- Genomic Research Unit, Faculty of Life Science, Tel Aviv University, Tel Aviv, Israel
| | - Hoang Van Phan
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois, USA
- Institute for Genomics and Systems Biology, University of Chicago, Chicago, Illinois, USA
| | - Savaş Tay
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois, USA
- Institute for Genomics and Systems Biology, University of Chicago, Chicago, Illinois, USA
| | - Moriah Szpara
- Department of Biochemistry and Molecular Biology, Department of Biology, Center for Infectious Disease Dynamics, and the Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Matthew D. Weitzman
- Division of Protective Immunity, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Nir Drayman
- Department of Molecular Biology and Biochemistry, School of Biological Sciences, University of California, Irvine, California, USA
- Center for Virus Research, University of California, Irvine, California, USA
| | - Oren Kobiler
- Department of Clinical Microbiology and Immunology, School of Medicine, Tel Aviv University, Tel Aviv, Israel
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5
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Xia J, Van Phan H, Vistain L, Chen M, Khan AA, Tay S. Computational prediction of protein interactions on single cells by proximity sequencing. bioRxiv 2023:2023.07.27.550388. [PMID: 37546806 PMCID: PMC10402170 DOI: 10.1101/2023.07.27.550388] [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: 08/08/2023]
Abstract
Proximity sequencing (Prox-seq) measures gene expression, protein expression, and protein complexes at the single cell level, using information from dual-antibody binding events and a single cell sequencing readout. Prox-seq provides multi-dimensional phenotyping of single cells and was recently used to track the formation of receptor complexes during inflammatory signaling in macrophages and to discover a new interaction between CD9/CD8 proteins on naïve T cells. The distribution of protein abundance affects identification of protein complexes in a complicated manner in dual-binding assays like Prox-seq. These effects are difficult to explore with experiments, yet important for accurate quantification of protein complexes. Here, we introduce a physical model for protein dimer formation on single cells and computationally evaluate several different methods for reducing background noise when quantifying protein complexes. Furthermore, we developed an improved method for analysis of Prox-seq single-cell data, which resulted in more accurate and robust quantification of protein complexes. Finally, our model offers a simple way to investigate the behavior of Prox-seq under various biological conditions and guide users toward selecting the best analysis method for their data.
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Affiliation(s)
- Junjie Xia
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, IL, 60637, USA
| | - Hoang Van Phan
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, IL, 60637, USA
- Present address: Division of Infectious Disease, University of California, San Francisco, CA, 94143, USA
| | - Luke Vistain
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, IL, 60637, USA
- Present address: Lymphocyte Biology Section, Laboratory of Immune Systems Biology, NIAID, NIH, Bethesda, MD, 20892, USA
| | - Mengjie Chen
- Section of Genetic Medicine, Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA
- Department Human Genetics, The University of Chicago, Chicago, IL, 60637, USA
| | - Aly A. Khan
- Department of Pathology, The University of Chicago, Chicago, IL, 60637, USA
| | - Savaş Tay
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, IL, 60637, USA
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6
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Vistain L, Van Phan H, Keisham B, Jordi C, Chen M, Reddy ST, Tay S. Quantification of extracellular proteins, protein complexes and mRNAs in single cells by proximity sequencing. Nat Methods 2022; 19:1578-1589. [PMID: 36456784 DOI: 10.1038/s41592-022-01684-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 10/13/2022] [Indexed: 12/04/2022]
Abstract
We present proximity sequencing (Prox-seq) for simultaneous measurement of proteins, protein complexes and mRNAs in thousands of single cells. Prox-seq combines proximity ligation assay with single-cell sequencing to measure proteins and their complexes from all pairwise combinations of targeted proteins, providing quadratically scaled multiplexing. We validate Prox-seq and analyze a mixture of T cells and B cells to show that it accurately identifies these cell types and detects well-known protein complexes. Next, by studying human peripheral blood mononuclear cells, we discover that naïve CD8+ T cells display the protein complex CD8-CD9. Finally, we study protein interactions during Toll-like receptor (TLR) signaling in human macrophages. We observe the formation of signal-specific protein complexes, find CD36 co-receptor activity and additive signal integration under lipopolysaccharide (TLR4) and Pam2CSK4 (TLR2) stimulation, and show that quantification of protein complexes identifies signaling inputs received by macrophages. Prox-seq provides access to an untapped measurement modality for single-cell phenotyping and can discover uncharacterized protein interactions in different cell types.
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Affiliation(s)
- Luke Vistain
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, IL, USA
- Institute for Genomics and Systems Biology, The University of Chicago, Chicago, IL, USA
| | - Hoang Van Phan
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, IL, USA
- Institute for Genomics and Systems Biology, The University of Chicago, Chicago, IL, USA
| | - Bijentimala Keisham
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, IL, USA
- Institute for Genomics and Systems Biology, The University of Chicago, Chicago, IL, USA
| | - Christian Jordi
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Mengjie Chen
- Section of Genetic Medicine, Department of Medicine, The University of Chicago, Chicago, IL, USA
- Department Human Genetics, The University of Chicago, Chicago, IL, USA
| | - Sai T Reddy
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Savaş Tay
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, IL, USA.
- Institute for Genomics and Systems Biology, The University of Chicago, Chicago, IL, USA.
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7
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Phan HV, van Gent M, Drayman N, Basu A, Gack MU, Tay S. High-throughput RNA sequencing of paraformaldehyde-fixed single cells. Nat Commun 2021. [PMID: 34561439 DOI: 10.1101/2020.09.17.302232v2] [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] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2023] Open
Abstract
Single-cell transcriptomic studies that require intracellular protein staining, rare cell sorting, or inactivation of infectious pathogens are severely limited. This is because current high-throughput single-cell RNA sequencing methods are either incompatible with or necessitate laborious sample preprocessing for paraformaldehyde treatment, a common tissue and cell fixation and preservation technique. Here we present FD-seq (Fixed Droplet RNA sequencing), a high-throughput method for droplet-based RNA sequencing of paraformaldehyde-fixed, permeabilized and sorted single cells. We show that FD-seq preserves the RNA integrity and relative gene expression levels after fixation and permeabilization. Furthermore, FD-seq can detect a higher number of genes and transcripts than methanol fixation. We first apply FD-seq to analyze a rare subpopulation of cells supporting lytic reactivation of the human tumor virus KSHV, and identify TMEM119 as a potential host factor that mediates viral reactivation. Second, we find that infection with the human betacoronavirus OC43 leads to upregulation of pro-inflammatory pathways in cells that are exposed to the virus but fail to express high levels of viral genes. FD-seq thus enables integrating phenotypic with transcriptomic information in rare cell subpopulations, and preserving and inactivating pathogenic samples.
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Affiliation(s)
- Hoang Van Phan
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, IL, USA
| | - Michiel van Gent
- Department of Microbiology, The University of Chicago, Chicago, IL, USA
- Florida Research and Innovation Center, Cleveland Clinic, Port Saint Lucie, FL, USA
| | - Nir Drayman
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, IL, USA
| | - Anindita Basu
- Department of Medicine, The University of Chicago, Chicago, IL, USA
| | - Michaela U Gack
- Department of Microbiology, The University of Chicago, Chicago, IL, USA
- Florida Research and Innovation Center, Cleveland Clinic, Port Saint Lucie, FL, USA
| | - Savaş Tay
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, IL, USA.
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8
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Phan HV, van Gent M, Drayman N, Basu A, Gack MU, Tay S. High-throughput RNA sequencing of paraformaldehyde-fixed single cells. Nat Commun 2021; 12:5636. [PMID: 34561439 PMCID: PMC8463713 DOI: 10.1038/s41467-021-25871-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 08/27/2021] [Indexed: 12/26/2022] Open
Abstract
Single-cell transcriptomic studies that require intracellular protein staining, rare cell sorting, or inactivation of infectious pathogens are severely limited. This is because current high-throughput single-cell RNA sequencing methods are either incompatible with or necessitate laborious sample preprocessing for paraformaldehyde treatment, a common tissue and cell fixation and preservation technique. Here we present FD-seq (Fixed Droplet RNA sequencing), a high-throughput method for droplet-based RNA sequencing of paraformaldehyde-fixed, permeabilized and sorted single cells. We show that FD-seq preserves the RNA integrity and relative gene expression levels after fixation and permeabilization. Furthermore, FD-seq can detect a higher number of genes and transcripts than methanol fixation. We first apply FD-seq to analyze a rare subpopulation of cells supporting lytic reactivation of the human tumor virus KSHV, and identify TMEM119 as a potential host factor that mediates viral reactivation. Second, we find that infection with the human betacoronavirus OC43 leads to upregulation of pro-inflammatory pathways in cells that are exposed to the virus but fail to express high levels of viral genes. FD-seq thus enables integrating phenotypic with transcriptomic information in rare cell subpopulations, and preserving and inactivating pathogenic samples. Current high-throughput single-cell transcriptomic methods are incompatible with paraformaldehyde, a common cell fixation technique. Here the authors present FD-seq, a method for droplet-based RNA sequencing of paraformaldehyde-fixed, stained and sorted single cells.
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Affiliation(s)
- Hoang Van Phan
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, IL, USA
| | - Michiel van Gent
- Department of Microbiology, The University of Chicago, Chicago, IL, USA.,Florida Research and Innovation Center, Cleveland Clinic, Port Saint Lucie, FL, USA
| | - Nir Drayman
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, IL, USA
| | - Anindita Basu
- Department of Medicine, The University of Chicago, Chicago, IL, USA
| | - Michaela U Gack
- Department of Microbiology, The University of Chicago, Chicago, IL, USA.,Florida Research and Innovation Center, Cleveland Clinic, Port Saint Lucie, FL, USA
| | - Savaş Tay
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, IL, USA.
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9
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Abstract
Single-cell transcriptomic studies that require intracellular protein staining, rare cell sorting, or inactivation of infectious pathogens are severely limited because current high-throughput RNA sequencing methods are incompatible with paraformaldehyde treatment, a common tissue and cell fixation and preservation technique. Here we present FD-seq, a high-throughput method for droplet-based RNA sequencing of paraformaldehyde-fixed, stained and sorted single-cells. We show that FD-seq preserves the mRNA integrity and relative abundances during fixation and subsequent cell retrieval. Furthermore, FD-seq detects a higher number of genes and transcripts than methanol fixation. We applied FD-seq to investigate two important questions in Virology. First, by analyzing a rare population of cells supporting lytic reactivation of the human tumor virus KSHV, we identified TMEM119 as a host factor that mediates viral reactivation. Second, we found that upon infection with the betacoronavirus OC43, which causes the common cold and is a close relative of SARS-CoV-2, pro-inflammatory pathways are primarily upregulated in lowly-infected cells that are exposed to the virus but fail to express high levels of viral genes. FD-seq thus enables integrating phenotypic with transcriptomic information in rare cell populations, and preserving and inactivating pathogenic samples that cannot be handled under regular biosafety measures.
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Affiliation(s)
- Hoang Van Phan
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, IL, USA.,Institute for Genomics and Systems Biology, The University of Chicago, Chicago, IL, USA
| | - Michiel van Gent
- Department of Microbiology, The University of Chicago, Chicago, IL, USA.,Florida Research and Innovation Center, Cleveland Clinic, Port Saint Lucie, FL, USA
| | - Nir Drayman
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, IL, USA.,Institute for Genomics and Systems Biology, The University of Chicago, Chicago, IL, USA
| | - Anindita Basu
- Department of Medicine, The University of Chicago, Chicago, IL, USA
| | - Michaela U Gack
- Department of Microbiology, The University of Chicago, Chicago, IL, USA.,Florida Research and Innovation Center, Cleveland Clinic, Port Saint Lucie, FL, USA
| | - Savaş Tay
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, IL, USA.,Institute for Genomics and Systems Biology, The University of Chicago, Chicago, IL, USA
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10
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Abasıyanık MF, Wolfe K, Van Phan H, Lin J, Laxman B, White SR, Verhoef PA, Mutlu GM, Patel B, Tay S. Ultrasensitive digital quantification of cytokines and bacteria predicts septic shock outcomes. Nat Commun 2020; 11:2607. [PMID: 32451375 PMCID: PMC7248118 DOI: 10.1038/s41467-020-16124-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 04/13/2020] [Indexed: 12/29/2022] Open
Abstract
Quantification of pathogen and host biomarkers is essential for the diagnosis, monitoring, and treatment of infectious diseases. Here, we demonstrate sensitive and rapid quantification of bacterial load and cytokines from human biological samples to generate actionable hypotheses. Our digital assay measures IL-6 and TNF-α proteins, gram-negative (GN) and gram-positive (GP) bacterial DNA, and the antibiotic-resistance gene blaTEM with femtomolar sensitivity. We use our method to characterize bronchoalveolar lavage fluid from patients with asthma, and find elevated GN bacteria and IL-6 levels compared to healthy subjects. We then analyze plasma from patients with septic shock and find that increasing levels of IL-6 and blaTEM are associated with mortality, while decreasing IL-6 levels are associated with recovery. Surprisingly, lower GN bacteria levels are associated with higher probability of death. Applying decision-tree analysis to our measurements, we are able to predict mortality and rate of recovery from septic shock with over 90% accuracy. Ultrasensitive methods for detection of biomarkers for infectious disease are needed for diagnosing, monitoring and targeting treatment. Here the authors develop a digital assay for inflammatory markers, bacterial DNA and antibotic-resistance genes and apply it to characterise asthma patients and predict mortality from septic shock.
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Affiliation(s)
- M Fatih Abasıyanık
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, IL, 60637, USA.,Institute for Genomics and Systems Biology, The University of Chicago, Chicago, IL, 60637, USA
| | - Krysta Wolfe
- Department of Medicine, Section of Pulmonary/Critical Care, The University of Chicago, Chicago, IL, 60637, USA
| | - Hoang Van Phan
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, IL, 60637, USA.,Institute for Genomics and Systems Biology, The University of Chicago, Chicago, IL, 60637, USA
| | - Jing Lin
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, IL, 60637, USA.,Institute for Genomics and Systems Biology, The University of Chicago, Chicago, IL, 60637, USA
| | - Bharathi Laxman
- Department of Medicine, Section of Pulmonary/Critical Care, The University of Chicago, Chicago, IL, 60637, USA
| | - Steven R White
- Department of Medicine, Section of Pulmonary/Critical Care, The University of Chicago, Chicago, IL, 60637, USA
| | - Philip A Verhoef
- Department of Medicine, Section of Pulmonary/Critical Care, The University of Chicago, Chicago, IL, 60637, USA.,Center for Integrated Health Research, Kaiser Permanente Hawaii, Honolulu, HI, 96819, USA
| | - Gökhan M Mutlu
- Department of Medicine, Section of Pulmonary/Critical Care, The University of Chicago, Chicago, IL, 60637, USA
| | - Bhakti Patel
- Department of Medicine, Section of Pulmonary/Critical Care, The University of Chicago, Chicago, IL, 60637, USA.
| | - Savaş Tay
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, IL, 60637, USA. .,Institute for Genomics and Systems Biology, The University of Chicago, Chicago, IL, 60637, USA.
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11
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Lin J, Jordi C, Son M, Van Phan H, Drayman N, Abasiyanik MF, Vistain L, Tu HL, Tay S. Ultra-sensitive digital quantification of proteins and mRNA in single cells. Nat Commun 2019; 10:3544. [PMID: 31391463 PMCID: PMC6685952 DOI: 10.1038/s41467-019-11531-z] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Accepted: 07/16/2019] [Indexed: 12/15/2022] Open
Abstract
Simultaneous measurement of proteins and mRNA in single cells enables quantitative understanding and modeling of cellular functions. Here, we present an automated microfluidic system for multi-parameter and ultra-sensitive protein/mRNA measurements in single cells. Our technology improves the sensitivity of digital proximity ligation assay by up to 55-fold, with a detection limit of 2277 proteins per cell and with detection efficiency of as few as 29 protein molecules. Our measurements using this system reveal higher mRNA/protein correlation in single mammalian cells than previous estimates. Furthermore, time-lapse imaging of herpes simplex virus 1 infected epithelial cells enabled by our device shows that expression of ICP4 -a major transcription factor regulating hundreds of viral genes- is only partially correlated with viral protein counts, suggesting that many cells go through abortive infection. These results highlight the importance of high-sensitivity protein/mRNA quantification for understanding fundamental molecular mechanisms in individual cells. Digital proximity ligation assay (dPLA) can measure proteins and mRNAs in single cells, but is not compatible with cell imaging and cannot quantify rare proteins due to a high dilution factor. Here the authors present an automated microfluidic device that combines live-cell imaging, chemical stimulation, and dPLA in a smaller reaction volume.
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Affiliation(s)
- Jing Lin
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, 60637, USA.,Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL, 60637, USA
| | - Christian Jordi
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, 60637, USA.,Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL, 60637, USA.,Department of Biosystems Science and Engineering, ETH Zürich, 4058, Basel, Switzerland
| | - Minjun Son
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, 60637, USA.,Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL, 60637, USA
| | - Hoang Van Phan
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, 60637, USA.,Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL, 60637, USA
| | - Nir Drayman
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, 60637, USA.,Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL, 60637, USA
| | - Mustafa Fatih Abasiyanik
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, 60637, USA.,Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL, 60637, USA
| | - Luke Vistain
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, 60637, USA.,Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL, 60637, USA
| | - Hsiung-Lin Tu
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, 60637, USA.,Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL, 60637, USA.,Institute of Chemistry, Academia Sinica, Taipei, 11529, Taiwan
| | - Savaş Tay
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, 60637, USA. .,Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL, 60637, USA.
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12
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Le NHA, Van Phan H, Yu J, Chan HK, Neild A, Alan T. Acoustically enhanced microfluidic mixer to synthesize highly uniform nanodrugs without the addition of stabilizers. Int J Nanomedicine 2018; 13:1353-1359. [PMID: 29563792 PMCID: PMC5849384 DOI: 10.2147/ijn.s153805] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Background This article presents an acoustically enhanced microfluidic mixer to generate highly uniform and ultra-fine nanoparticles, offering significant advantages over conventional liquid antisolvent techniques. Methods The method employed a 3D microfluidic geometry whereby two different phases – solvent and antisolvent – were introduced at either side of a 1 μm thick resonating membrane, which contained a through-hole. The vibration of the membrane rapidly and efficiently mixed the two phases, at the location of the hole, leading to the formation of nanoparticles. Results The versatility of the device was demonstrated by synthesizing budesonide (a common asthma drug) with a mean diameter of 135.7 nm and a polydispersity index of 0.044. Conclusion The method offers a 40-fold reduction in the size of synthesized particles combined with a substantial improvement in uniformity, achieved without the need of stabilizers.
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Affiliation(s)
- Nguyen Hoai An Le
- Department of Mechanical and Aerospace Engineering, Monash University, Melbourne, VIC
| | - Hoang Van Phan
- Department of Mechanical and Aerospace Engineering, Monash University, Melbourne, VIC
| | - Jiaqi Yu
- The Advanced Drug Delivery Group, Faculty of Pharmacy, University of Sydney, Sydney, NSW, Australia
| | - Hak-Kim Chan
- The Advanced Drug Delivery Group, Faculty of Pharmacy, University of Sydney, Sydney, NSW, Australia
| | - Adrian Neild
- Department of Mechanical and Aerospace Engineering, Monash University, Melbourne, VIC
| | - Tuncay Alan
- Department of Mechanical and Aerospace Engineering, Monash University, Melbourne, VIC
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13
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Abstract
We present a simple method for on-demand manipulation of aqueous droplets in oil. With numerical simulations and experiments, we show that a vibrating membrane can produce acoustic streaming. By making use of this vortical flow, we manage to repulse the droplets away from the membrane edges. Then, by simply aligning the membrane at 45° to the flow, the droplets can be forced to follow the membrane's boundaries, thus steering them across streamlines and even between different oil types. We also characterize the repulsion and steering effect with various excitation voltages at different water and oil flow rates. The maximum steering frequency we have achieved is 165 Hz. The system is extremely robust and reliable: the same membrane can be reused after many days and with different oils and/or surfactants at the same operating frequency.
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Affiliation(s)
- Hoang Van Phan
- Laboratory for Micro Systems, Department of Mechanical and Aerospace Engineering, Monash University , Clayton, Victoria 3800, Australia
| | - Tuncay Alan
- Laboratory for Micro Systems, Department of Mechanical and Aerospace Engineering, Monash University , Clayton, Victoria 3800, Australia
| | - Adrian Neild
- Laboratory for Micro Systems, Department of Mechanical and Aerospace Engineering, Monash University , Clayton, Victoria 3800, Australia
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14
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Abstract
Aqueous droplets suspended in an immiscible carrier fluid are a key tool in microfluidic chemical analysis platforms. The approaches for producing droplets in microfluidic devices can be divided into three general categories: batch emulsification, continuous production and tailored on-demand production. The major distinctions between each category are the rate of production and the degree of control over the droplet formation process in terms of the size and quantity. On-demand methods are highly desirable when, for example, small numbers or even single droplets of one sample type are required at a time. Here, we present a method for the on-demand production of femtolitre droplets, utilising a pressure source generated by high frequency surface acoustic waves (SAW). An increase in the continuous phase flow rate is enabled by a quasi-3D feature at the droplet production nozzle. A wide range of accessible flow rates permits the identification of different physical regimes in which droplets of different dimensions are produced. In the system investigated droplets measuring as little as 200 fl have been produced, ∼1/60th of the minimum volume previously reported. The experimental findings are supported by a numerical model which demonstrates the link between the number of droplets formed and the pulse length used.
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Affiliation(s)
- Jason C Brenker
- Laboratory for Micro Systems, Department of Mechanical and Aerospace Engineering, Monash University, Clayton, Victoria 3800, Australia.
| | - David J Collins
- Laboratory for Micro Systems, Department of Mechanical and Aerospace Engineering, Monash University, Clayton, Victoria 3800, Australia.
| | - Hoang Van Phan
- Laboratory for Micro Systems, Department of Mechanical and Aerospace Engineering, Monash University, Clayton, Victoria 3800, Australia.
| | - Tuncay Alan
- Laboratory for Micro Systems, Department of Mechanical and Aerospace Engineering, Monash University, Clayton, Victoria 3800, Australia.
| | - Adrian Neild
- Laboratory for Micro Systems, Department of Mechanical and Aerospace Engineering, Monash University, Clayton, Victoria 3800, Australia.
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15
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Phan HV, Coşkun MB, Şeşen M, Pandraud G, Neild A, Alan T. Vibrating membrane with discontinuities for rapid and efficient microfluidic mixing. Lab Chip 2015; 15:4206-4216. [PMID: 26381355 DOI: 10.1039/c5lc00836k] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
This study presents a novel acoustic mixer comprising of a microfabricated silicon nitride membrane with a hole etched through it. We show that the introduction of the through hole leads to extremely fast and homogeneous mixing. When the membrane is immersed in fluid and subjected to acoustic excitation, a strong streaming field in the form of vortices is generated. The vortices are always observed to centre at the hole, pointing to the critical role it has on the streaming field. We hypothesise that the hole introduces a discontinuity to the boundary conditions of the membrane, leading to strong streaming vortices. With numerical simulations, we show that the hole's presence can increase the volume force responsible for driving the streaming field by 2 orders of magnitude, thus supporting our hypothesis. We investigate the mixing performance at different Peclet numbers by varying the flow rates for various devices containing circular, square and rectangular shaped holes of different dimensions. We demonstrate rapid mixing within 3 ms mixing time (90% mixing efficiency at 60 μl min(-1) total flow rate, Peclet number equals 8333 ± 3.5%) is possible with the current designs. Finally, we examine the membrane with two circular holes which are covered by air bubbles and compare it to when the membrane is fully immersed. We find that coupling between the holes' vortices occurs only when membrane is immersed; while with the bubble membrane, the upstream hole's vortices can act as a blockage to fluid flow passing it.
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Affiliation(s)
- Hoang Van Phan
- Laboratory for Micro Systems, Department of Mechanical and Aerospace Engineering, Monash University, Clayton, VIC 3800, Australia.
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