References
Baggen, J., Persoons, L., Vanstreels, E., Jansen, S., Van Looveren, D., Boeckx, B., Geudens, V., De Man, J., Jochmans, D., Wauters, J., Wauters, E., Vanaudenaerde, B. M., Lambrechts, D., Neyts, J., Dallmeier, K., Thibaut, H. J., Jacquemyn, M., Maes, P., & Daelemans, D. (2021). Genome-wide CRISPR screening identifies TMEM106B as a proviral host factor for SARS-CoV-2. Nat Genet , 53 (4), 435-444. https://doi.org/10.1038/s41588-021-00805-2
Breton, S., & Brown, D. (2013). Regulation of luminal acidification by the V-ATPase. Physiology (Bethesda) , 28 (5), 318-329. https://doi.org/10.1152/physiol.00007.2013
Bricambert, J., Miranda, J., Benhamed, F., Girard, J., Postic, C., & Dentin, R. (2010). Salt-inducible kinase 2 links transcriptional coactivator p300 phosphorylation to the prevention of ChREBP-dependent hepatic steatosis in mice. J Clin Invest , 120 (12), 4316-4331. https://doi.org/10.1172/JCI41624
Cereseto, A., Manganaro, L., Gutierrez, M. I., Terreni, M., Fittipaldi, A., Lusic, M., Marcello, A., & Giacca, M. (2005). Acetylation of HIV-1 integrase by p300 regulates viral integration. EMBO J ,24 (17), 3070-3081. https://doi.org/10.1038/sj.emboj.7600770
Chen, C. H., Xiao, T., Xu, H., Jiang, P., Meyer, C. A., Li, W., Brown, M., & Liu, X. S. (2018). Improved design and analysis of CRISPR knockout screens. Bioinformatics , 34 (23), 4095-4101. https://doi.org/10.1093/bioinformatics/bty450
Clausen, T. M., Sandoval, D. R., Spliid, C. B., Pihl, J., Perrett, H. R., Painter, C. D., Narayanan, A., Majowicz, S. A., Kwong, E. M., McVicar, R. N., Thacker, B. E., Glass, C. A., Yang, Z., Torres, J. L., Golden, G. J., Bartels, P. L., Porell, R. N., Garretson, A. F., Laubach, L., . . . Esko, J. D. (2020). SARS-CoV-2 Infection Depends on Cellular Heparan Sulfate and ACE2. Cell , 183 (4), 1043-1057 e1015. https://doi.org/10.1016/j.cell.2020.09.033
Csukasi, F., Duran, I., Barad, M., Barta, T., Gudernova, I., Trantirek, L., Martin, J. H., Kuo, C. Y., Woods, J., Lee, H., Cohn, D. H., Krejci, P., & Krakow, D. (2018). The PTH/PTHrP-SIK3 pathway affects skeletogenesis through altered mTOR signaling. Sci Transl Med ,10 (459). https://doi.org/10.1126/scitranslmed.aat9356
Culi, J., Springer, T. A., & Mann, R. S. (2004). Boca-dependent maturation of beta-propeller/EGF modules in low-density lipoprotein receptor proteins. EMBO J , 23 (6), 1372-1380. https://doi.org/10.1038/sj.emboj.7600132
Cureton, D. K., Massol, R. H., Whelan, S. P., & Kirchhausen, T. (2010). The length of vesicular stomatitis virus particles dictates a need for actin assembly during clathrin-dependent endocytosis. PLoS Pathog , 6 (9), e1001127. https://doi.org/10.1371/journal.ppat.1001127
Daniloski, Z., Jordan, T. X., Wessels, H. H., Hoagland, D. A., Kasela, S., Legut, M., Maniatis, S., Mimitou, E. P., Lu, L., Geller, E., Danziger, O., Rosenberg, B. R., Phatnani, H., Smibert, P., Lappalainen, T., tenOever, B. R., & Sanjana, N. E. (2021). Identification of Required Host Factors for SARS-CoV-2 Infection in Human Cells.Cell , 184 (1), 92-105 e116. https://doi.org/10.1016/j.cell.2020.10.030
Doench, J. G., Fusi, N., Sullender, M., Hegde, M., Vaimberg, E. W., Donovan, K. F., Smith, I., Tothova, Z., Wilen, C., Orchard, R., Virgin, H. W., Listgarten, J., & Root, D. E. (2016). Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9.Nat Biotechnol , 34 (2), 184-191. https://doi.org/10.1038/nbt.3437
Donaldson, J. G., & Jackson, C. L. (2011). ARF family G proteins and their regulators: roles in membrane transport, development and disease.Nature reviews Molecular cell biology , 12 (6), 362-375. https://doi.org/10.1038/nrm3117
Esposito, A. M., Cheung, P., Swartz, T. H., Li, H., Tsibane, T., Durham, N. D., Basler, C. F., Felsenfeld, D. P., & Chen, B. K. (2016). A high throughput Cre-lox activated viral membrane fusion assay identifies pharmacological inhibitors of HIV entry. Virology , 490 , 6-16. https://doi.org/10.1016/j.virol.2015.10.013
Faoro, C., & Ataide, S. F. (2021). Noncanonical Functions and Cellular Dynamics of the Mammalian Signal Recognition Particle Components.Front Mol Biosci , 8 , 679584. https://doi.org/10.3389/fmolb.2021.679584
Finkelshtein, D., Werman, A., Novick, D., Barak, S., & Rubinstein, M. (2013). LDL receptor and its family members serve as the cellular receptors for vesicular stomatitis virus. Proc Natl Acad Sci U S A , 110 (18), 7306-7311. https://doi.org/10.1073/pnas.1214441110
Goley, E. D., & Welch, M. D. (2006). The ARP2/3 complex: an actin nucleator comes of age. Nature reviews Molecular cell biology ,7 (10), 713-726.
Guimond, S. E., Mycroft-West, C. J., Gandhi, N. S., Tree, J. A., Le, T. T., Spalluto, C. M., Humbert, M. V., Buttigieg, K. R., Coombes, N., Elmore, M. J., Wand, M., Nystrom, K., Said, J., Setoh, Y. X., Amarilla, A. A., Modhiran, N., Sng, J. D. J., Chhabra, M., Young, P. R., . . . Turnbull, J. E. (2022). Synthetic Heparan Sulfate Mimetic Pixatimod (PG545) Potently Inhibits SARS-CoV-2 by Disrupting the Spike-ACE2 Interaction. ACS Cent Sci , 8 (5), 527-545. https://doi.org/10.1021/acscentsci.1c01293
Han, K., Jeng, E. E., Hess, G. T., Morgens, D. W., Li, A., & Bassik, M. C. (2017). Synergistic drug combinations for cancer identified in a CRISPR screen for pairwise genetic interactions. Nat Biotechnol ,35 (5), 463-474. https://doi.org/10.1038/nbt.3834
Harvey, W. T., Carabelli, A. M., Jackson, B., Gupta, R. K., Thomson, E. C., Harrison, E. M., Ludden, C., Reeve, R., Rambaut, A., Consortium, C.-G. U., Peacock, S. J., & Robertson, D. L. (2021). SARS-CoV-2 variants, spike mutations and immune escape. Nat Rev Microbiol ,19 (7), 409-424. https://doi.org/10.1038/s41579-021-00573-0
Hastie, E., Cataldi, M., Marriott, I., & Grdzelishvili, V. Z. (2013). Understanding and altering cell tropism of vesicular stomatitis virus.Virus Res , 176 (1-2), 16-32. https://doi.org/10.1016/j.virusres.2013.06.003
Heitzer, E., Groenewoud, A., Meditz, K., Lohberger, B., Liegl-Atzwanger, B., Prokesch, A., Kashofer, K., Behrens, D., Haybaeck, J., Kolb-Lenz, D., Koefeler, H., Riedl, S., Schaider, H., Fischer, C., Snaar-Jagalska, B. E., de’Jong, D., Szuhai, K., Zweytick, D., & Rinner, B. (2019). Human melanoma brain metastases cell line MUG-Mel1, isolated clones and their detailed characterization. Sci Rep , 9 (1), 4096. https://doi.org/10.1038/s41598-019-40570-1
Hsieh, J.-C., Lee, L., Zhang, L., Wefer, S., Brown, K., DeRossi, C., Wines, M. E., Rosenquist, T., & Holdener, B. C. (2003). Mesd Encodes an LRP5/6 Chaperone Essential for Specification of Mouse Embryonic Polarity. Cell , 112 (3), 355-367. https://doi.org/https://doi.org/10.1016/S0092-8674(03)00045-X
Icho, S., Rujas, E., Muthuraman, K., Tam, J., Liang, H., Landreth, S., Liao, M., Falzarano, D., Julien, J. P., & Melnyk, R. A. (2022). Dual Inhibition of Vacuolar-ATPase and TMPRSS2 Is Required for Complete Blockade of SARS-CoV-2 Entry into Cells. Antimicrob Agents Chemother , 66 (7), e0043922. https://doi.org/10.1128/aac.00439-22
Illanes-Álvarez, F., Márquez-Ruiz, D., Márquez-Coello, M., Cuesta-Sancho, S., & Girón-González, J. A. (2021). Similarities and differences between HIV and SARS-CoV-2. International Journal of Medical Sciences , 18 (3), 846-851. https://doi.org/10.7150/ijms.50133
Imbach, T., Burda, P., Kuhnert, P., Wevers, R. A., Aebi, M., Berger, E. G., & Hennet, T. (1999). A mutation in the human ortholog of the Saccharomyces cerevisiae ALG6 gene causes carbohydrate-deficient glycoprotein syndrome type-Ic. Proceedings of the National Academy of Sciences , 96 (12), 6982-6987.
Lafourcade, C., Sobo, K., Kieffer-Jaquinod, S., Garin, J., & van der Goot, F. G. (2008). Regulation of the V-ATPase along the endocytic pathway occurs through reversible subunit association and membrane localization. PLoS One , 3 (7), e2758. https://doi.org/10.1371/journal.pone.0002758
Li, W., Xu, H., Xiao, T., Cong, L., Love, M. I., Zhang, F., Irizarry, R. A., Liu, J. S., Brown, M., & Liu, X. S. (2014). MAGeCK enables robust identification of essential genes from genome-scale CRISPR/Cas9 knockout screens. Genome biology , 15 (12), 1-12.
Linxweiler, M., Schick, B., & Zimmermann, R. (2017). Let’s talk about Secs: Sec61, Sec62 and Sec63 in signal transduction, oncology and personalized medicine. Signal Transduct Target Ther , 2 , 17002. https://doi.org/10.1038/sigtrans.2017.2
Mangeot, P. E., Risson, V., Fusil, F., Marnef, A., Laurent, E., Blin, J., Mournetas, V., Massouridès, E., Sohier, T. J. M., & Corbin, A. (2019). Genome editing in primary cells and in vivo using viral-derived Nanoblades loaded with Cas9-sgRNA ribonucleoproteins. Nature communications , 10 (1), 1-15.
Mangeot, P. E., Risson, V., Fusil, F., Marnef, A., Laurent, E., Blin, J., Mournetas, V., Massourides, E., Sohier, T. J. M., Corbin, A., Aube, F., Teixeira, M., Pinset, C., Schaeffer, L., Legube, G., Cosset, F. L., Verhoeyen, E., Ohlmann, T., & Ricci, E. P. (2019). Genome editing in primary cells and in vivo using viral-derived Nanoblades loaded with Cas9-sgRNA ribonucleoproteins. Nat Commun , 10 (1), 45. https://doi.org/10.1038/s41467-018-07845-z
Mannar, D., Saville, J. W., Sun, Z., Zhu, X., Marti, M. M., Srivastava, S. S., Berezuk, A. M., Zhou, S., Tuttle, K. S., Sobolewski, M. D., Kim, A., Treat, B. R., Da Silva Castanha, P. M., Jacobs, J. L., Barratt-Boyes, S. M., Mellors, J. W., Dimitrov, D. S., Li, W., & Subramaniam, S. (2022). SARS-CoV-2 variants of concern: spike protein mutational analysis and epitope for broad neutralization. Nat Commun , 13 (1), 4696. https://doi.org/10.1038/s41467-022-32262-8
Mullins, R. D., Heuser, J. A., & Pollard, T. D. (1998). The interaction of Arp2/3 complex with actin: nucleation, high affinity pointed end capping, and formation of branching networks of filaments.Proceedings of the National Academy of Sciences , 95 (11), 6181-6186.
Neises, J. Z., Hossain, M. S., Sultana, R., Wanniarachchi, K. N., Wollman, J. W., Nelson, E., Specker, B. L., Hoppe, A. D., Lawson, S. R., & Thiex, N. W. (2021). Seroprevalence of SARS-CoV-2 antibodies among rural healthcare workers. J Med Virol , 93 (12), 6611-6618. https://doi.org/10.1002/jmv.27224
Nikolic, J., Belot, L., Raux, H., Legrand, P., Gaudin, Y., & A, A. A. (2018). Structural basis for the recognition of LDL-receptor family members by VSV glycoprotein. Nat Commun , 9 (1), 1029. https://doi.org/10.1038/s41467-018-03432-4
Notarbartolo, S., Ranzani, V., Bandera, A., Gruarin, P., Bevilacqua, V., Putignano, A. R., Gobbini, A., Galeota, E., Manara, C., & Bombaci, M. (2021). Integrated longitudinal immunophenotypic, transcriptional, and repertoire analyses delineate immune responses in patients with COVID-19. Science immunology , 6 (62), eabg5021. https://air.unimi.it/bitstream/2434/864089/2/eabg5021.full.pdf
Ou, X., Liu, Y., Lei, X., Li, P., Mi, D., Ren, L., Guo, L., Guo, R., Chen, T., Hu, J., Xiang, Z., Mu, Z., Chen, X., Chen, J., Hu, K., Jin, Q., Wang, J., & Qian, Z. (2020). Characterization of spike glycoprotein of SARS-CoV-2 on virus entry and its immune cross-reactivity with SARS-CoV. Nat Commun , 11 (1), 1620. https://doi.org/10.1038/s41467-020-15562-9
Paluck, A., Osan, J., Hollingsworth, L., Talukdar, S. N., Saegh, A. A., & Mehedi, M. (2021). Role of ARP2/3 Complex-Driven Actin Polymerization in RSV Infection. Pathogens , 11 (1). https://doi.org/10.3390/pathogens11010026
Park, R. J., Wang, T., Koundakjian, D., Hultquist, J. F., Lamothe-Molina, P., Monel, B., Schumann, K., Yu, H., Krupzcak, K. M., Garcia-Beltran, W., Piechocka-Trocha, A., Krogan, N. J., Marson, A., Sabatini, D. M., Lander, E. S., Hacohen, N., & Walker, B. D. (2017). A genome-wide CRISPR screen identifies a restricted set of HIV host dependency factors. Nat Genet , 49 (2), 193-203. https://doi.org/10.1038/ng.3741
Pollard, T. D. (2007). Regulation of actin filament assembly by Arp2/3 complex and formins. Annual review of biophysics and biomolecular structure , 36 (1), 451-477.
Rein, A. (2019). RNA Packaging in HIV. Trends Microbiol ,27 (8), 715-723. https://doi.org/10.1016/j.tim.2019.04.003
Robinson, R. C., Turbedsky, K., Kaiser, D. A., Marchand, J.-B., Higgs, H. N., Choe, S., & Pollard, T. D. (2001). Crystal structure of Arp2/3 complex. Science , 294 (5547), 1679-1684.
Rouiller, I., Xu, X.-P., Amann, K. J., Egile, C., Nickell, S., Nicastro, D., Li, R., Pollard, T. D., Volkmann, N., & Hanein, D. (2008). The structural basis of actin filament branching by the Arp2/3 complex.The Journal of cell biology , 180 (5), 887-895.
Schmidt, N., Lareau, C. A., Keshishian, H., Ganskih, S., Schneider, C., Hennig, T., Melanson, R., Werner, S., Wei, Y., Zimmer, M., Ade, J., Kirschner, L., Zielinski, S., Dolken, L., Lander, E. S., Caliskan, N., Fischer, U., Vogel, J., Carr, S. A., . . . Munschauer, M. (2021). The SARS-CoV-2 RNA-protein interactome in infected human cells. Nat Microbiol , 6 (3), 339-353. https://doi.org/10.1038/s41564-020-00846-z
Schneider, W. M., Luna, J. M., Hoffmann, H. H., Sanchez-Rivera, F. J., Leal, A. A., Ashbrook, A. W., Le Pen, J., Ricardo-Lax, I., Michailidis, E., Peace, A., Stenzel, A. F., Lowe, S. W., MacDonald, M. R., Rice, C. M., & Poirier, J. T. (2021). Genome-Scale Identification of SARS-CoV-2 and Pan-coronavirus Host Factor Networks. Cell , 184 (1), 120-132 e114. https://doi.org/10.1016/j.cell.2020.12.006
Schwientek, T., Bennett, E. P., Flores, C., Thacker, J., Hollmann, M., Reis, C. A., Behrens, J., Mandel, U., Keck, B., Schafer, M. A., Haselmann, K., Zubarev, R., Roepstorff, P., Burchell, J. M., Taylor-Papadimitriou, J., Hollingsworth, M. A., & Clausen, H. (2002). Functional conservation of subfamilies of putative UDP-N-acetylgalactosamine:polypeptide N-acetylgalactosaminyltransferases in Drosophila, Caenorhabditis elegans, and mammals. One subfamily composed of l(2)35Aa is essential in Drosophila. J Biol Chem ,277 (25), 22623-22638. https://doi.org/10.1074/jbc.M202684200
Stewart, S. A., Dykxhoorn, D. M., Palliser, D., Mizuno, H., Yu, E. Y., An, D. S., Sabatini, D. M., Chen, I. S., Hahn, W. C., Sharp, P. A., Weinberg, R. A., & Novina, C. D. (2003). Lentivirus-delivered stable gene silencing by RNAi in primary cells. RNA , 9 (4), 493-501. https://doi.org/10.1261/rna.2192803
Stringer, B. W., Day, B. W., D’Souza, R. C. J., Jamieson, P. R., Ensbey, K. S., Bruce, Z. C., Lim, Y. C., Goasdoué, K., Offenhäuser, C., Akgül, S., Allan, S., Robertson, T., Lucas, P., Tollesson, G., Campbell, S., Winter, C., Do, H., Dobrovic, A., Inglis, P. L., . . . Boyd, A. W. (2019). A reference collection of patient-derived cell line and xenograft models of proneural, classical and mesenchymal glioblastoma.Sci Rep , 9 (1), 4902. https://doi.org/10.1038/s41598-019-41277-z
Tandon, R., Sharp, J. S., Zhang, F., Pomin, V. H., Ashpole, N. M., Mitra, D., McCandless, M. G., Jin, W., Liu, H., Sharma, P., & Linhardt, R. J. (2021). Effective Inhibition of SARS-CoV-2 Entry by Heparin and Enoxaparin Derivatives. J Virol , 95 (3). https://doi.org/10.1128/JVI.01987-20
Volz, E., Hill, V., McCrone, J. T., Price, A., Jorgensen, D., O’Toole, A., Southgate, J., Johnson, R., Jackson, B., Nascimento, F. F., Rey, S. M., Nicholls, S. M., Colquhoun, R. M., da Silva Filipe, A., Shepherd, J., Pascall, D. J., Shah, R., Jesudason, N., Li, K., . . . Connor, T. R. (2021). Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity. Cell , 184 (1), 64-75 e11. https://doi.org/10.1016/j.cell.2020.11.020
Wang, R., Simoneau, C. R., Kulsuptrakul, J., Bouhaddou, M., Travisano, K. A., Hayashi, J. M., Carlson-Stevermer, J., Zengel, J. R., Richards, C. M., Fozouni, P., Oki, J., Rodriguez, L., Joehnk, B., Walcott, K., Holden, K., Sil, A., Carette, J. E., Krogan, N. J., Ott, M., & Puschnik, A. S. (2021). Genetic Screens Identify Host Factors for SARS-CoV-2 and Common Cold Coronaviruses. Cell , 184 (1), 106-119 e114. https://doi.org/10.1016/j.cell.2020.12.004
Wei, J., Alfajaro, M. M., DeWeirdt, P. C., Hanna, R. E., Lu-Culligan, W. J., Cai, W. L., Strine, M. S., Zhang, S. M., Graziano, V. R., Schmitz, C. O., Chen, J. S., Mankowski, M. C., Filler, R. B., Ravindra, N. G., Gasque, V., de Miguel, F. J., Patil, A., Chen, H., Oguntuyo, K. Y., . . . Wilen, C. B. (2021). Genome-wide CRISPR Screens Reveal Host Factors Critical for SARS-CoV-2 Infection. Cell , 184 (1), 76-91 e13. https://doi.org/10.1016/j.cell.2020.10.028
Yang, F. C., Tan, B. C., Chen, W. H., Lin, Y. H., Huang, J. Y., Chang, H. Y., Sun, H. Y., Hsu, P. H., Liou, G. G., Shen, J., Chang, C. J., Han, C. C., Tsai, M. D., & Lee, S. C. (2013). Reversible acetylation regulates salt-inducible kinase (SIK2) and its function in autophagy.J Biol Chem , 288 (9), 6227-6237. https://doi.org/10.1074/jbc.M112.431239
Zhang, L., Jackson, C. B., Mou, H., Ojha, A., Peng, H., Quinlan, B. D., Rangarajan, E. S., Pan, A., Vanderheiden, A., Suthar, M. S., Li, W., Izard, T., Rader, C., Farzan, M., & Choe, H. (2020). SARS-CoV-2 spike-protein D614G mutation increases virion spike density and infectivity. Nat Commun , 11 (1), 6013. https://doi.org/10.1038/s41467-020-19808-4
Zhang, Q., Chen, C. Z., Swaroop, M., Xu, M., Wang, L., Lee, J., Wang, A. Q., Pradhan, M., Hagen, N., & Chen, L. (2020). Heparan sulfate assists SARS-CoV-2 in cell entry and can be targeted by approved drugs in vitro.Cell discovery , 6 (1), 1-14.
Zhang, Z. N., Gong, L., Lv, S., Li, J., Tai, X., Cao, W., Peng, B., Qu, S., Li, W., Zhang, C., & Luan, B. (2016). SIK2 regulates fasting-induced PPARalpha activity and ketogenesis through p300.Sci Rep , 6 , 23317. https://doi.org/10.1038/srep23317
Zhu, Y., Feng, F., Hu, G., Wang, Y., Yu, Y., Zhu, Y., Xu, W., Cai, X., Sun, Z., Han, W., Ye, R., Qu, D., Ding, Q., Huang, X., Chen, H., Xu, W., Xie, Y., Cai, Q., Yuan, Z., & Zhang, R. (2021). A genome-wide CRISPR screen identifies host factors that regulate SARS-CoV-2 entry. Nat Commun , 12 (1), 961. https://doi.org/10.1038/s41467-021-21213-4