1
|
Mylka V, Matetovici I, Poovathingal S, Aerts J, Vandamme N, Seurinck R, Verstaen K, Hulselmans G, Van den Hoecke S, Scheyltjens I, Movahedi K, Wils H, Reumers J, Van Houdt J, Aerts S, Saeys Y. Comparative analysis of antibody- and lipid-based multiplexing methods for single-cell RNA-seq. Genome Biol 2022; 23:55. [PMID: 35172874 PMCID: PMC8851857 DOI: 10.1186/s13059-022-02628-8] [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] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 02/08/2022] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Multiplexing of samples in single-cell RNA-seq studies allows a significant reduction of the experimental costs, straightforward identification of doublets, increased cell throughput, and reduction of sample-specific batch effects. Recently published multiplexing techniques using oligo-conjugated antibodies or -lipids allow barcoding sample-specific cells, a process called "hashing." RESULTS Here, we compare the hashing performance of TotalSeq-A and -C antibodies, custom synthesized lipids and MULTI-seq lipid hashes in four cell lines, both for single-cell RNA-seq and single-nucleus RNA-seq. We also compare TotalSeq-B antibodies with CellPlex reagents (10x Genomics) on human PBMCs and TotalSeq-B with different lipids on primary mouse tissues. Hashing efficiency was evaluated using the intrinsic genetic variation of the cell lines and mouse strains. Antibody hashing was further evaluated on clinical samples using PBMCs from healthy and SARS-CoV-2 infected patients, where we demonstrate a more affordable approach for large single-cell sequencing clinical studies, while simultaneously reducing batch effects. CONCLUSIONS Benchmarking of different hashing strategies and computational pipelines indicates that correct demultiplexing can be achieved with both lipid- and antibody-hashed human cells and nuclei, with MULTISeqDemux as the preferred demultiplexing function and antibody-based hashing as the most efficient protocol on cells. On nuclei datasets, lipid hashing delivers the best results. Lipid hashing also outperforms antibodies on cells isolated from mouse brain. However, antibodies demonstrate better results on tissues like spleen or lung.
Collapse
Affiliation(s)
- Viacheslav Mylka
- VIB Tech Watch, VIB Headquarters, Ghent, Belgium
- Data Mining and Modelling for Biomedicine, VIB Center for Inflammation Research, Ghent, Belgium
| | - Irina Matetovici
- VIB Tech Watch, VIB Headquarters, Ghent, Belgium
- VIB Center for Brain & Disease Research, Leuven, Belgium
| | | | - Jeroen Aerts
- VIB Tech Watch, VIB Headquarters, Ghent, Belgium
- VIB Center for Brain & Disease Research, Leuven, Belgium
| | - Niels Vandamme
- Data Mining and Modelling for Biomedicine, VIB Center for Inflammation Research, Ghent, Belgium
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium
| | - Ruth Seurinck
- Data Mining and Modelling for Biomedicine, VIB Center for Inflammation Research, Ghent, Belgium
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium
| | - Kevin Verstaen
- Data Mining and Modelling for Biomedicine, VIB Center for Inflammation Research, Ghent, Belgium
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium
| | - Gert Hulselmans
- VIB Center for Brain & Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | | | - Isabelle Scheyltjens
- Myeloid Cell Immunology Lab, VIB Center for Inflammation Research, Brussels, Belgium
- Laboratory for Molecular and Cellular Therapy, Vrije Universiteit Brussel, Brussels, Belgium
| | - Kiavash Movahedi
- Myeloid Cell Immunology Lab, VIB Center for Inflammation Research, Brussels, Belgium
- Laboratory for Molecular and Cellular Therapy, Vrije Universiteit Brussel, Brussels, Belgium
| | - Hans Wils
- Discovery Sciences, Janssen Research & Development, Pharmaceutical Companies of Johnson & Johnson, Beerse, Belgium
| | - Joke Reumers
- Discovery Sciences, Janssen Research & Development, Pharmaceutical Companies of Johnson & Johnson, Beerse, Belgium
| | - Jeroen Van Houdt
- Discovery Sciences, Janssen Research & Development, Pharmaceutical Companies of Johnson & Johnson, Beerse, Belgium
| | - Stein Aerts
- VIB Center for Brain & Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Yvan Saeys
- Data Mining and Modelling for Biomedicine, VIB Center for Inflammation Research, Ghent, Belgium
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium
| |
Collapse
|
2
|
Van den Hoecke S, Ballegeer M, Vrancken B, Deng L, Job ER, Roose K, Schepens B, Van Hoecke L, Lemey P, Saelens X. In Vivo Therapy with M2e-Specific IgG Selects for an Influenza A Virus Mutant with Delayed Matrix Protein 2 Expression. mBio 2021; 12:e0074521. [PMID: 34253060 PMCID: PMC8406285 DOI: 10.1128/mbio.00745-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 06/08/2021] [Indexed: 12/24/2022] Open
Abstract
The ectodomain of matrix protein 2 (M2e) of influenza A viruses is a universal influenza A vaccine candidate. Here, we report potential evasion strategies of influenza A viruses under in vivo passive anti-M2e IgG immune selection pressure in severe combined immune-deficient (SCID) mice. A/Puerto Rico/8/34-infected SCID mice were treated with the M2e-specific mouse IgG monoclonal antibodies (MAbs) MAb 65 (IgG2a) or MAb 37 (IgG1), which recognize amino acids 5 to 15 in M2e, or with MAb 148 (IgG1), which binds to the invariant N terminus of M2e. Treatment of challenged SCID mice with any of these MAbs significantly prolonged survival compared to isotype control IgG treatment. Furthermore, M2e-specific IgG2a protected significantly better than IgG1, and even resulted in virus clearance in some of the SCID mice. Deep sequencing analysis of viral RNA isolated at different time points after treatment revealed that the sequence variation in M2e was limited to P10H/L and/or I11T in anti-M2e MAb-treated mice. Remarkably, in half of the samples isolated from moribund MAb 37-treated mice and in all MAb 148-treated mice, virus was isolated with a wild-type M2 sequence but with nonsynonymous mutations in the polymerases and/or the hemagglutinin genes. Some of these mutations were associated with delayed M2 and other viral gene expression and with increased resistance to anti-M2e MAb treatment of SCID mice. Treatment with M2e-specific MAbs thus selects for viruses with limited variation in M2e. Importantly, influenza A viruses may also undergo an alternative escape route by acquiring mutations that result in delayed wild-type M2 expression. IMPORTANCE Broadly protective influenza vaccine candidates may have a higher barrier to immune evasion compared to conventional influenza vaccines. We used Illumina MiSeq deep sequence analysis to study the mutational patterns in A/Puerto Rico/8/34 viruses that evolve in chronically infected SCID mice that were treated with different M2e-specific MAbs. We show that under these circumstances, viruses emerged in vivo with mutations in M2e that were limited to positions 10 and 11. Moreover, we discovered an alternative route for anti-M2e antibody immune escape, in which a virus is selected with wild-type M2e but with mutations in other gene segments that result in delayed M2 and other viral protein expression. Delayed expression of the viral antigen that is targeted by a protective antibody thus represents an influenza virus immune escape mechanism that does not involve epitope alterations.
Collapse
Affiliation(s)
- Silvie Van den Hoecke
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Marlies Ballegeer
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Bram Vrancken
- KU Leuven—University of Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Clinical and Epidemiological Virology, Leuven, Belgium
| | - Lei Deng
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Emma R. Job
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Kenny Roose
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Bert Schepens
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Lien Van Hoecke
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
- VIB-UGent Center for Inflammation Research, VIB, Ghent, Belgium
| | - Philippe Lemey
- KU Leuven—University of Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Clinical and Epidemiological Virology, Leuven, Belgium
| | - Xavier Saelens
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| |
Collapse
|
3
|
Hulme KD, Karawita AC, Pegg C, Bunte MJ, Bielefeldt-Ohmann H, Bloxham CJ, Van den Hoecke S, Setoh YX, Vrancken B, Spronken M, Steele LE, Verzele NA, Upton KR, Khromykh AA, Chew KY, Sukkar M, Phipps S, Short KR. A paucigranulocytic asthma host environment promotes the emergence of virulent influenza viral variants. eLife 2021; 10:61803. [PMID: 33588989 PMCID: PMC7886327 DOI: 10.7554/elife.61803] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 01/23/2021] [Indexed: 12/12/2022] Open
Abstract
Influenza virus has a high mutation rate, such that within one host different viral variants can emerge. Evidence suggests that influenza virus variants are more prevalent in pregnant and/or obese individuals due to their impaired interferon response. We have recently shown that the non-allergic, paucigranulocytic subtype of asthma is associated with impaired type I interferon production. Here, we seek to address if this is associated with an increased emergence of influenza virus variants. Compared to controls, mice with paucigranulocytic asthma had increased disease severity and an increased emergence of influenza virus variants. Specifically, PB1 mutations exclusively detected in asthmatic mice were associated with increased polymerase activity. Furthermore, asthmatic host-derived virus led to increased disease severity in wild-type mice. Taken together, these data suggest that at least a subset of patients with asthma may be more susceptible to severe influenza and may be a possible source of new influenza virus variants.
Collapse
Affiliation(s)
- Katina D Hulme
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Anjana C Karawita
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Cassandra Pegg
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Myrna Jm Bunte
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Helle Bielefeldt-Ohmann
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia.,Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Australia.,School of Veterinary Science, The University of Queensland, Brisbane, Australia
| | - Conor J Bloxham
- School of Biomedical Sciences, The University of Queensland, Brisbane, Australia
| | - Silvie Van den Hoecke
- VIB-UGent Center for Medical Biotechnology, Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Yin Xiang Setoh
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia.,Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Australia.,Environmental Health Institute, National Environment Agency, Singapore, Singapore
| | - Bram Vrancken
- KU Leuven, Department of Microbiology and Immunology, Rega Institute, Laboratory of Evolutionary and Computational Virology, Leuven, Belgium
| | | | - Lauren E Steele
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Nathalie Aj Verzele
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Kyle R Upton
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Alexander A Khromykh
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia.,Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Australia
| | - Keng Yih Chew
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Maria Sukkar
- Discipline of Pharmacy, Graduate School of Health, University of Technology Sydney, Australia; Woolcock Institute of Medical Research, Sydney Medical School, University of Sydney, NSW, Australia
| | - Simon Phipps
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Australia.,QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Kirsty R Short
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia.,Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Australia
| |
Collapse
|
4
|
Mancera Gracia JC, Van den Hoecke S, Richt JA, Ma W, Saelens X, Van Reeth K. Author Correction: A reassortant H9N2 influenza virus containing 2009 pandemic H1N1 internal-protein genes acquired enhanced pig-to-pig transmission after serial passages in swine. Sci Rep 2018; 8:17222. [PMID: 30443003 PMCID: PMC6237892 DOI: 10.1038/s41598-018-35446-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Affiliation(s)
- José Carlos Mancera Gracia
- Laboratory of Virology, Department of Virology, Parasitology and Immunology, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Silvie Van den Hoecke
- Center for Medical Biotechnology, VIB, Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Ghent, 9000, Belgium
| | - Juergen A Richt
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, 66506, USA
| | - Wenjun Ma
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, 66506, USA
| | - Xavier Saelens
- Center for Medical Biotechnology, VIB, Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Ghent, 9000, Belgium
| | - Kristien Van Reeth
- Laboratory of Virology, Department of Virology, Parasitology and Immunology, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium.
| |
Collapse
|
5
|
Mancera Gracia JC, Van den Hoecke S, Richt JA, Ma W, Saelens X, Van Reeth K. A reassortant H9N2 influenza virus containing 2009 pandemic H1N1 internal-protein genes acquired enhanced pig-to-pig transmission after serial passages in swine. Sci Rep 2017; 7:1323. [PMID: 28465552 PMCID: PMC5430982 DOI: 10.1038/s41598-017-01512-x] [Citation(s) in RCA: 9] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 03/30/2017] [Indexed: 11/09/2022] Open
Abstract
Avian H9N2 and 2009 pandemic H1N1 (pH1N1) influenza viruses can infect pigs and humans, raising the concern that H9N2:pH1N1 reassortant viruses could emerge. Such reassortants demonstrated increased replication and transmissibility in pig, but were still inefficient when compared to pH1N1. Here, we evaluated if a reassortant virus containing the hemagglutinin and neuraminidase of A/quail/Hong Kong/G1/1997 (H9N2) in the A/California/04/2009 (pH1N1) backbone could become better adapted to pigs by serial passaging. The tropism of the original H9N2:pH1N1 (P0) virus was restricted to the nasal mucosa, with no virus detected in the trachea or lungs. Nevertheless, after seven passages the H9N2:pH1N1 (P7) virus replicated in the entire respiratory tract. We also compared the transmissibility of H9N2:pH1N1 (P0), H9N2:pH1N1 (P7) and pH1N1. While only 2/6 direct-contact pigs showed nasal virus excretion of H9N2:pH1N1 (P0) ≥five days, 4/6 direct-contact animals shed the H9N2:pH1N1 (P7). Interestingly, those four animals shed virus with titers similar to those of the pH1N1, which readily transmitted to all six contact animals. The broader tissue tropism and the increased post-transmission replication after seven passages were associated with the HA-D225G substitution. Our data demonstrate that the pH1N1 internal-protein genes together with the serial passages favour H9N2 virus adaptation to pigs.
Collapse
Affiliation(s)
- José Carlos Mancera Gracia
- Laboratory of Virology, Department of Virology, Parasitology and Immunology, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Silvie Van den Hoecke
- Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, 9000, Belgium
| | - Juergen A Richt
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, 66506, USA
| | - Wenjun Ma
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, 66506, USA
| | - Xavier Saelens
- Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, 9000, Belgium
| | - Kristien Van Reeth
- Laboratory of Virology, Department of Virology, Parasitology and Immunology, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium.
| |
Collapse
|
6
|
Mancera Gracia JC, Van den Hoecke S, Saelens X, Van Reeth K. Effect of serial pig passages on the adaptation of an avian H9N2 influenza virus to swine. PLoS One 2017; 12:e0175267. [PMID: 28384328 PMCID: PMC5383288 DOI: 10.1371/journal.pone.0175267] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 03/23/2017] [Indexed: 11/19/2022] Open
Abstract
H9N2 avian influenza viruses are endemic in poultry in Asia and the Middle East. These viruses sporadically cause dead-end infections in pigs and humans raising concerns about their potential to adapt to mammals or reassort with human or swine influenza viruses. We performed ten serial passages with an avian H9N2 virus (A/quail/Hong Kong/G1/1997) in influenza naïve pigs to assess the potential of this virus to adapt to swine. Virus replication in the entire respiratory tract and nasal virus excretion were examined after each passage and we deep sequenced viral genomic RNA of the parental and passage four H9N2 virus isolated from the nasal mucosa and lung. The parental H9N2 virus caused a productive infection in pigs with a predominant tropism for the nasal mucosa, whereas only 50% lung samples were virus-positive. In contrast, inoculation of pigs with passage four virus resulted in viral replication in the entire respiratory tract. Subsequent passages were associated with reduced virus replication in the lungs and infectious virus was no longer detectable in the upper and lower respiratory tract of inoculated pigs at passage ten. The broader tissue tropism after four passages was associated with an amino acid residue substitution at position 225, within the receptor-binding site of the hemagglutinin. We also compared the parental H9N2, passage four H9N2 and the 2009 pandemic H1N1 (pH1N1) virus in a direct contact transmission experiment. Whereas only one out of six contact pigs showed nasal virus excretion of the wild-type H9N2 for more than four days, all six contact animals shed the passage four H9N2 virus. Nevertheless, the amount of excreted virus was significantly lower when compared to that of the pH1N1, which readily transmitted and replicated in all six contact animals. Our data demonstrate that serial passaging of H9N2 virus in pigs enhances its replication and transmissibility. However, full adaptation of an avian H9N2 virus to pigs likely requires an extensive set of mutations.
Collapse
Affiliation(s)
- Jose Carlos Mancera Gracia
- Laboratory of Virology, Department of Virology, Parasitology and Immunology, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Silvie Van den Hoecke
- Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Xavier Saelens
- Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Kristien Van Reeth
- Laboratory of Virology, Department of Virology, Parasitology and Immunology, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| |
Collapse
|
7
|
Van den Hoecke S, Verhelst J, Saelens X. Illumina MiSeq sequencing disfavours a sequence motif in the GFP reporter gene. Sci Rep 2016; 6:26314. [PMID: 27193250 PMCID: PMC4872057 DOI: 10.1038/srep26314] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [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: 11/25/2015] [Accepted: 05/03/2016] [Indexed: 01/14/2023] Open
Abstract
Green fluorescent protein (GFP) is one of the most used reporter genes. We have used next-generation sequencing (NGS) to analyse the genetic diversity of a recombinant influenza A virus that expresses GFP and found a remarkable coverage dip in the GFP coding sequence. This coverage dip was present when virus-derived RT-PCR product or the parental plasmid DNA was used as starting material for NGS and regardless of whether Nextera XT transposase or Covaris shearing was used for DNA fragmentation. Therefore, the sequence coverage dip in the GFP coding sequence was not the result of emerging GFP mutant viruses or a bias introduced by Nextera XT fragmentation. Instead, we found that the Illumina MiSeq sequencing method disfavours the 'CCCGCC' motif in the GFP coding sequence.
Collapse
Affiliation(s)
- Silvie Van den Hoecke
- Medical Biotechnology Center, VIB, Ghent, B-9052, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Ghent, B-9052, Belgium
| | - Judith Verhelst
- Medical Biotechnology Center, VIB, Ghent, B-9052, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Ghent, B-9052, Belgium
| | - Xavier Saelens
- Medical Biotechnology Center, VIB, Ghent, B-9052, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Ghent, B-9052, Belgium
| |
Collapse
|
8
|
De Baets S, Verhelst J, Van den Hoecke S, Smet A, Schotsaert M, Job ER, Roose K, Schepens B, Fiers W, Saelens X. A GFP expressing influenza A virus to report in vivo tropism and protection by a matrix protein 2 ectodomain-specific monoclonal antibody. PLoS One 2015; 10:e0121491. [PMID: 25816132 PMCID: PMC4376807 DOI: 10.1371/journal.pone.0121491] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Accepted: 02/02/2015] [Indexed: 11/30/2022] Open
Abstract
The severity of influenza-related illness is mediated by many factors, including in vivo cell tropism, timing and magnitude of the immune response, and presence of pre-existing immunity. A direct way to study cell tropism and virus spread in vivo is with an influenza virus expressing a reporter gene. However, reporter gene-expressing influenza viruses are often attenuated in vivo and may be genetically unstable. Here, we describe the generation of an influenza A virus expressing GFP from a tri-cistronic NS segment. To reduce the size of this engineered gene segment, we used a truncated NS1 protein of 73 amino acids combined with a heterologous dimerization domain to increase protein stability. GFP and nuclear export protein coding information were fused in frame with the truncated NS1 open reading frame and separated from each other by 2A self-processing sites. The resulting PR8-NS1(1–73)GFP virus was successfully rescued and replicated as efficiently as the parental PR8 virus in vitro and was slightly attenuated in vivo. Flow cytometry-based monitoring of cells isolated from PR8-NS1(1–73)GFP virus infected BALB/c mice revealed that GFP expression peaked on day two in all cell types tested. In particular respiratory epithelial cells and myeloid cells known to be involved in antigen presentation, including dendritic cells (CD11c+) and inflammatory monocytes (CD11b+ GR1+), became GFP positive following infection. Prophylactic treatment with anti-M2e monoclonal antibody or oseltamivir reduced GFP expression in all cell types studied, demonstrating the usefulness of this reporter virus to analyze the efficacy of antiviral treatments in vivo. Finally, deep sequencing analysis, serial in vitro passages and ex vivo analysis of PR8-NS1(1–73)GFP virus, indicate that this virus is genetically and phenotypically stable.
Collapse
Affiliation(s)
- Sarah De Baets
- Department of Medical Protein Research, VIB, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Judith Verhelst
- Department of Medical Protein Research, VIB, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Silvie Van den Hoecke
- Department of Medical Protein Research, VIB, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Anouk Smet
- Department of Medical Protein Research, VIB, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Michael Schotsaert
- Department of Medical Protein Research, VIB, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Emma R. Job
- Department of Medical Protein Research, VIB, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Kenny Roose
- Department of Medical Protein Research, VIB, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Bert Schepens
- Department of Medical Protein Research, VIB, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Walter Fiers
- Department of Medical Protein Research, VIB, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Xavier Saelens
- Department of Medical Protein Research, VIB, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
- * E-mail:
| |
Collapse
|