A pooled genome-wide screening strategy to identify and rank influenza host restriction factors in cell-based vaccine production platforms.

Scientific Reports
David M SharonAmine A Kamen

Abstract

Cell-derived influenza vaccines provide better protection and a host of other advantages compared to the egg-derived vaccines that currently dominate the market, but their widespread use is hampered by a lack of high yield, low cost production platforms. Identification and knockout of innate immune and metabolic restriction factors within relevant host cell lines used to grow the virus could offer a means to substantially increase vaccine yield. In this paper, we describe and validate a novel genome-wide pooled CRISPR/Cas9 screening strategy that incorporates a reporter virus and a FACS selection step to identify and rank restriction factors in a given vaccine production cell line. Using the HEK-293SF cell line and A/PuertoRico/8/1934 H1N1 influenza as a model, we identify 64 putative influenza restriction factors to direct the creation of high yield knockout cell lines. In addition, gene ontology and protein complex enrichment analysis of this list of putative restriction factors offers broader insights into the primary host cell determinants of viral yield in cell-based vaccine production systems. Overall, this work will advance efforts to address the public health burden posed by influenza.

References

Aug 1, 1992·Current Opinion in Immunology·N Murray, A McMichael
Mar 22, 2003·RNA·Sheila A StewartCarl D Novina
Nov 4, 2005·Proceedings of the National Academy of Sciences of the United States of America·Gabriele NeumannYoshihiro Kawaoka
Feb 3, 2007·Proceedings of the National Academy of Sciences of the United States of America·Neal SatterlyBeatriz M A Fontoura
May 10, 2008·The Biochemical Journal·Jingxiang Huang, Brendan D Manning
Sep 8, 2010·Nucleic Acids Research·Israel S FernándezOscar Llorca
Jan 17, 2012·Bioinformatics·Raivo KoldeJaak Vilo
Sep 28, 2012·Journal of Virology·Timothy J PowellAlain R M Townsend
Feb 28, 2013·Science Signaling·Arunachalam VinayagamNorbert Perrimon
May 28, 2014·Nucleic Acids Research·Tessa G MontagueEivind Valen
Jul 31, 2014·Nature Methods·Neville E SanjanaFeng Zhang
Oct 1, 2014·DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes·Naoki OsadaKentaro Hanada
Oct 11, 2014·Nucleic Acids Research·Eva K BrinkmanBas van Steensel
Nov 6, 2014·Molecular Biotechnology·Wojciech BarczakKatarzyna Kulcenty
Apr 24, 2015·Biotechnology Journal·Yvonne Genzel
Nov 20, 2015·Journal of Virology·Sabine M G van der SandenRalph A Tripp
Dec 15, 2015·Cell Host & Microbe·Shashank TripathiSumit K Chanda
Jan 19, 2016·Nature Biotechnology·John G DoenchDavid E Root
Oct 6, 2016·Clinical Infectious Diseases : an Official Publication of the Infectious Diseases Society of America·Richard K ZimmermanUNKNOWN U.S. Flu VE Investigators
Mar 2, 2017·Scientific Data·Weilin WuRalph A Tripp
Aug 17, 2017·Cell Reports·Brook E HeatonNicholas S Heaton
Sep 28, 2017·PLoS Pathogens·Sharon K Kuss-DuerkopBeatriz M A Fontoura
Nov 8, 2017·Proceedings of the National Academy of Sciences of the United States of America·Seth J ZostScott E Hensley
Nov 14, 2017·Nature Reviews. Genetics·Darren J Burgess
Dec 19, 2017·Lancet·A Danielle IulianoUNKNOWN Global Seasonal Influenza-associated Mortality Collaborator Network
Jan 18, 2018·Human Vaccines & Immunotherapeutics·Joseph K Agor, Osman Y Özaltın
Feb 21, 2018·Influenza and Other Respiratory Viruses·Vernon J LeeUNKNOWN WHO Working Group on Influenza Burden of Disease
Mar 31, 2018·Vaccines·Alfred T Harding, Nicholas S Heaton
Jun 13, 2018·Nature Medicine·Emma HaapaniemiJussi Taipale
Sep 19, 2018·Proceedings of the National Academy of Sciences of the United States of America·Donald J BentonJohn J Skehel
Nov 20, 2018·PLoS Pathogens·Jared P MayAnne E Simon
Feb 3, 2019·Nature Protocols·Binbin WangX Shirley Liu

❮ Previous
Next ❯

Methods Mentioned

BETA
gene knockouts
Fluorescence Assisted Cell Sorting
FACS
flow cytometry
PCR
gene knockout

Software Mentioned

TIDE webtool
MAGeCKFlute
Prism GraphPad
MAGeCK
FlowJo
COMPLEAT
Metascape
Cytoscape

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.

Related Papers

Trends in Molecular Medicine
Florian Krammer, Reingard Grabherr
Human Vaccines & Immunotherapeutics
Alberto Pérez Rubio, Jose María Eiros
International Journal of Molecular Sciences
Wandi ZhuBao-Zhong Wang
© 2021 Meta ULC. All rights reserved