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Matches in Ghent University Academic Bibliography for { <https://biblio.ugent.be/publication/01JMYDP5XWXQS30YYVQM56FPT8> ?p ?o. }

• 01JMYDP5XWXQS30YYVQM56FPT8 classification D1.
• 01JMYDP5XWXQS30YYVQM56FPT8 promoter F48175CA-F0ED-11E1-A9DE-61C894A0A6B4.
• 01JMYDP5XWXQS30YYVQM56FPT8 promoter F7EA3B2A-F0ED-11E1-A9DE-61C894A0A6B4.
• 01JMYDP5XWXQS30YYVQM56FPT8 date "2024".
• 01JMYDP5XWXQS30YYVQM56FPT8 language "eng".
• 01JMYDP5XWXQS30YYVQM56FPT8 type dissertation.
• 01JMYDP5XWXQS30YYVQM56FPT8 hasPart 01JCJY35XJGHZD0F0X0SB6RMFF.pdf.
• 01JMYDP5XWXQS30YYVQM56FPT8 subject "Biology and Life Sciences".
• 01JMYDP5XWXQS30YYVQM56FPT8 abstract "Elucidation of host factors and pathways that are exploited by influenza viruses may aid in the selection of druggable host targets. In this thesis, we aimed to analyse the host dependency of the influenza virus on host cellular processes and identify potential new druggable targets for host-directed anti-influenza therapies. To this end, we employed a genomics and proteomics strategy focusing on influenza A and B viruses. We conducted an unbiased pooled genome-wide CRISPR-Cas9 loss-of-function screen with influenza B virus strain B/Singapore/222/79 and followed up top-ranked genes in a targeted pooled CRISPR-Cas9 screen with increased statistical power to identify host dependency genes. Genes for which the corresponding sgRNAs were highly enriched in FACS-based selected cells displaying resistance towards viral infection were considered as host dependency genes. Our screens resulted in the identification of 55 host dependency genes of IBV (p.adj < 0.05), of which 28 have been previously identified with IAV, including subunits of the v-ATPase proton pump, COG8, NXF1, PCID2, SLC35A1, SLC35A2, CMTR1, and HNRNPM, suggesting communalities between the two influenza virus types. Furthermore, we find that 27 host dependency genes of IBV were not previously validated with any influenza virus, although 18 of these were enriched in previous CRISPR screens with IAV but were not further investigated. Moreover, we find that 9 of the identified host dependency genes may be IBV-specific (FAM241A, FUBP3, LPCAT3, MED12, PRIM2, SEC31A, STT3B, INTS10, and TBC1D3F). However, INTS10 and TBC1D3F are members of the integrator (INT) complex and TBC1 family, respectively, members of which ranked high in previously reported genomic perturbation screens with IAV, suggesting that the INT complex and TBC1 family members may be important in both IAV and IBV replication. In addition, we performed a systematic review and meta-analysis of all reported CRISPR-Cas screens that identified host dependency and host restriction genes of the IAV. We integrated individual data sets using the algorithm of meta-analysis by information content (MAIC) to generate a proviral and antiviral gene list ranked by their evidence in individual screens. The top 50 proviral MAIC list contained genes whose role in influenza virus replication requires further elucidation, such as the endosomal ion channel TPCN1 and the kinase WEE1. Moreover, MAIC indicated that ALYREF, a component of the transcription export complex, has antiviral properties, whereas previous knockdown experiments attributed a proviral role to this host factor. To complement these genomics results, we conducted affinity purification screens coupled with mass-spectrometry (AP-MS) to identify host protein interaction partners of the viral nonstructural protein 1 (NS1) and the viral polymerase proteins in infected cells. To this end, C-terminally FLAG-tagged NS1, PB2, and PA influenza A/Puerto Rico/8/1934 (PR8) and NS1, PB2, PB1, and PA B/Memphis/12/97 viruses were rescued and propagated. We conducted AP-MS screens in A549 cells with both IAV and IBV FLAG-tagged viruses, and expanded the IAV experiments to two models of fully differentiated ii healthy human primary bronchial epithelial cells (HBEC). We identified 416 and 632 candidate protein interaction partners in A549 cells of IAV and IBV proteins, respectively, whereas 548 host interactors were identified in at least one HBEC model, 14 of which received evidence from both HBEC cultures. In particular, we found 49 and 111 candidate host interactors of all viral proteins to be involved in eukaryotic translation initiation and spliceosome processes, respectively. We have integrated our CRISPR and AP-MS data to prioritize host factors for further functional validation. We identified 16 genes to significantly reduce PR8-GFP replication upon RNA interference (RNAi)-induced depletion, of which 8 genes also present similar effects in H3N2-nanoLuc, more specifically the proteasomal subunit PSMD7, the vacuolar proton-transporting V-type ATPase complex assembly factor VMA21, four splicing factors (MFAP1, RBM8A, SNRPF, and SART1), and two translation initiation factors (EIF2S2 and EIF3A). All but one (SART1) of these genes were also suggestive of reduction of IBV replication in the genome-wide pooled CRISPR screen with influenza B virus. In addition, we find that knock down of EIF3A and SNPRF has a limited impact on cell viability. Five of these genes, which were originally identified as an interaction partner of one the viral proteins in the AP-MS screens were subjected to a coimmunoprecipitation experiment with their respective viral proteins. EIF3A-V5 coprecipitated with FLAG-tagged influenza A virus PA polymerase subunit. In addition, through in silico predictions using AlphaFold, we find that ARF6, which is associated with reduced PR8-GFP replication upon gene depletion may interact with influenza B virus polymerase basic 1 (PB1), and possibly influenza A PB1, through a conserved arginine (R671), asparagine (N675), and lysine (K668) residue of influenza B PB1. In conclusion, we conducted a dual-omics approach in the genomics and proteomics field to offer valuable insights into host-virus interactions. These results hold potential for guiding the development of host-directed therapies against influenza. Additionally, we integrated the omics data to prioritize potential host-dependency genes of IAV and/or IBV identified 8 genes - MFAP1, RBM8A, SNRPF, SART1, EIF2S, EIF3A, and PSMD7, and VMA21 - as likely host dependency factors for PR8 and H3N2 viruses. Furthermore, with the exception of SART1, we provide evidence that these genes encode host dependency factors for IBV, based on our CRISPR screen.".
• 01JMYDP5XWXQS30YYVQM56FPT8 author C5181E24-C9DF-11E9-8057-A3165707D3EF.
• 01JMYDP5XWXQS30YYVQM56FPT8 dateCreated "2025-02-25T11:25:46Z".
• 01JMYDP5XWXQS30YYVQM56FPT8 dateModified "2025-02-28T09:14:07Z".
• 01JMYDP5XWXQS30YYVQM56FPT8 name "Host dependency factors of the influenza virus : a dual-omics approach".
• 01JMYDP5XWXQS30YYVQM56FPT8 pagination urn:uuid:bd8a2086-3d48-48b8-9adc-66efe3c38f66.
• 01JMYDP5XWXQS30YYVQM56FPT8 publisher urn:uuid:d2bc3307-65c5-4719-bdae-1f99ecef7334.
• 01JMYDP5XWXQS30YYVQM56FPT8 sameAs LU-01JMYDP5XWXQS30YYVQM56FPT8.
• 01JMYDP5XWXQS30YYVQM56FPT8 sourceOrganization urn:uuid:1d8412d1-433e-4827-b60f-74dda7e84804.
• 01JMYDP5XWXQS30YYVQM56FPT8 sourceOrganization urn:uuid:5542567d-caba-442c-9972-70404c3c1b50.
• 01JMYDP5XWXQS30YYVQM56FPT8 sourceOrganization urn:uuid:ff95e554-babc-4eb8-8ff8-0e293fffe3d9.
• 01JMYDP5XWXQS30YYVQM56FPT8 type D1.