Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms

Gordon, David E.; Hiatt, Joseph; Bouhaddou, Mehdi; Rezelj, Veronica V.; Ulferts, Svenja; Braberg, Hannes; Jureka, Alexander S.; Obernier, Kirsten; Guo, Jeffrey Z.; Batra, Jyoti; Kaake, Robyn M.; Weckstein, Andrew R.; Owens, Tristan W.; Gupta, Meghna; Pourmal, Sergei; Titus, Erron W.; Cakir, Merve; Soucheray, Margaret; McGregor, Michael; Cakir, Zeynep; Jang, Gwendolyn; O’Meara, Matthew J.; Tummino, Tia A.; Zhang, Ziyang; Foussard, Helene; Rojc, Ajda; Zhou, Yuan; Kuchenov, Dmitry; Hüttenhain, Ruth; Xu, Jiewei; Eckhardt, Manon; Swaney, Danielle L.; Fabius, Jacqueline M.; Ummadi, Manisha; Tutuncuoglu, Beril; Rathore, Ujjwal; Modak, Maya; Haas, Paige; Haas, Kelsey M.; Naing, Zun Zar Chi; Pulido, Ernst H.; Shi, Ying; Barrio-Hernandez, Inigo; Memon, Danish; Petsalaki, Eirini; Dunham, Alistair; Marrero, Miguel Correa; Burke, David; Koh, Cassandra; Vallet, Thomas

doi:10.1126/science.abe9403

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Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms

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Gordon, David E., Hiatt, Joseph, Bouhaddou, Mehdi, Rezelj, Veronica V., Ulferts, Svenja, Braberg, Hannes, Jureka, Alexander S., Obernier, Kirsten, Guo, Jeffrey Z., Batra, Jyoti, Kaake, Robyn M., Weckstein, Andrew R., Owens, Tristan W., Gupta, Meghna, Pourmal, Sergei, Titus, Erron W., Cakir, Merve, Soucheray, Margaret, McGregor, Michael, Cakir, Zeynep, Jang, Gwendolyn, O’Meara, Matthew J., Tummino, Tia A., Zhang, Ziyang, Foussard, Helene, Rojc, Ajda, Zhou, Yuan, Kuchenov, Dmitry, Hüttenhain, Ruth, Xu, Jiewei, Eckhardt, Manon, Swaney, Danielle L., Fabius, Jacqueline M., Ummadi, Manisha, Tutuncuoglu, Beril, Rathore, Ujjwal, Modak, Maya, Haas, Paige, Haas, Kelsey M., Naing, Zun Zar Chi, Pulido, Ernst H., Shi, Ying, Barrio-Hernandez, Inigo, Memon, Danish, Petsalaki, Eirini, Dunham, Alistair, Marrero, Miguel Correa, Burke, David, Koh, Cassandra, Vallet, Thomas, Silvas, Jesus A., Azumaya, Caleigh M., Billesbølle, Christian, Brilot, Axel F., Campbell, Melody G., Diallo, Amy, Dickinson, Miles Sasha, Diwanji, Devan, Herrera, Nadia, Hoppe, Nick, Kratochvil, Huong T., Liu, Yanxin, Merz, Gregory E., Moritz, Michelle, Nguyen, Henry C., Nowotny, Carlos, Puchades, Cristina, Rizo, Alexandrea N., Schulze-Gahmen, Ursula, Smith, Amber M., Sun, Ming, Young, Iris D., Zhao, Jianhua, Asarnow, Daniel, Biel, Justin, Bowen, Alisa, Braxton, Julian R., Chen, Jen, Chio, Cynthia M., Chio, Un Seng, Deshpande, Ishan, Doan, Loan, Faust, Bryan, Flores, Sebastian, Jin, Mingliang, Kim, Kate, Lam, Victor L., Li, Fei, Li, Junrui, Li, Yen-Li, Li, Yang, Liu, Xi, Lo, Megan, Lopez, Kyle E., Melo, Arthur A., Moss, Frank R., Nguyen, Phuong, Paulino, Joana, Pawar, Komal Ishwar, Peters, Jessica K., Pospiech, Thomas H., Safari, Maliheh, Sangwan, Smriti, Schaefer, Kaitlin, Thomas, Paul V., Thwin, Aye C., Trenker, Raphael, Tse, Eric, Tsui, Tsz Kin Martin, Wang, Feng, Whitis, Natalie, Yu, Zanlin, Zhang, Kaihua, Zhang, Yang, Zhou, Fengbo, Saltzberg, Daniel, QCRG Structural Biology Consortium, Hodder, Anthony J., Shun-Shion, Amber S., Williams, Daniel M., White, Kris M., Rosales, Romel, Kehrer, Thomas, Miorin, Lisa, Moreno, Elena, Patel, Arvind H., Rihn, Suzannah, Khalid, Mir M., Vallejo-Gracia, Albert, Fozouni, Parinaz, Simoneau, Camille R., Roth, Theodore L., Wu, David, Karim, Mohd Anisul, Ghoussaini, Maya, Dunham, Ian, Berardi, Francesco, Weigang, Sebastian, Chazal, Maxime, Park, Jisoo, Logue, James, McGrath, Marisa, Weston, Stuart, Haupt, Robert, Hastie, C. James, Elliott, Matthew, Brown, Fiona, Burness, Kerry A., Reid, Elaine, Dorward, Mark, Johnson, Clare, Wilkinson, Stuart G., Geyer, Anna, Giesel, Daniel M., Baillie, Carla, Raggett, Samantha, Leech, Hannah, Toth, Rachel, Goodman, Nicola, Keough, Kathleen C., Lind, Abigail L., Zoonomia Consortium, Klesh, Reyna J., Hemphill, Kafi R., Carlson-Stevermer, Jared, Oki, Jennifer, Holden, Kevin, Maures, Travis, Pollard, Katherine S., Sali, Andrej, Agard, David A., Cheng, Yifan, Fraser, James S., Frost, Adam, Jura, Natalia, Kortemme, Tanja, Manglik, Aashish, Southworth, Daniel R., Stroud, Robert M., Alessi, Dario R., Davies, Paul, Frieman, Matthew B., Ideker, Trey, Abate, Carmen, Jouvenet, Nolwenn, Kochs, Georg, Shoichet, Brian, Ott, Melanie, Palmarini, Massimo, Shokat, Kevan M., García-Sastre, Adolfo, Rassen, Jeremy A., Grosse, Robert, Rosenberg, Oren S., Verba, Kliment A., Basler, Christopher F., Vignuzzi, Marco, Peden, Andrew A., Beltrao, Pedro, Krogan, Nevan J., Owens, Tristan W., Gupta, Meghna, Pourmal, Sergei, Titus, Erron W., Azumaya, Caleigh M., Billesbølle, Christian, Brilot, Axel F., Campbell, Melody G., Diallo, Amy, Dickinson, Miles Sasha, Diwanji, Devan, Herrera, Nadia, Hoppe, Nick, Kratochvil, Huong T., Liu, Yanxin, Merz, Gregory E., Moritz, Michelle, Nguyen, Henry C., Nowotny, Carlos, Puchades, Cristina, Rizo, Alexandrea N., Schulze-Gahmen, Ursula, Smith, Amber M., Sun, Ming, Young, Iris D., Zhao, Jianhua, Asarnow, Daniel, Biel, Justin, Bowen, Alisa, Braxton, Julian R., Chen, Jen, Chio, Cynthia M., Chio, Un Seng, Deshpande, Ishan, Doan, Loan, Faust, Bryan, Flores, Sebastian, Jin, Mingliang, Kim, Kate, Lam, Victor L., Li, Fei, Li, Junrui, Li, Yen-Li, Li, Yang, Liu, Xi, Lo, Megan, Lopez, Kyle E., Melo, Arthur A., Moss, Frank R., Nguyen, Phuong, Paulino, Joana, Pawar, Komal Ishwar, Peters, Jessica K., Pospiech, Thomas H., Safari, Maliheh, Sangwan, Smriti, Schaefer, Kaitlin, Thomas, Paul V., Thwin, Aye C., Trenker, Raphael, Tse, Eric, Tsui, Tsz Kin Martin, Wang, Feng, Whitis, Natalie, Yu, Zanlin, Zhang, Kaihua, Zhang, Yang, Zhou, Fengbo, Trinidad, Donovan, Agard, David A., Cheng, Yifan, Fraser, James S., Frost, Adam, Jura, Natalia, Kortemme, Tanja, Manglik, Aashish, Southworth, Daniel R., Stroud, Robert M., Rosenberg, Oren S., Verba, Kliment A., Damas, Joana, Hughes, Graham M., Keough, Kathleen C., Painter, Corrie A., Persky, Nicole S., Corbo, Marco, Kirilenko, Bodgan, Hiller, Michael, Koepfli, Klaus-Peter, Kaplow, Irene, Wirthlin, Morgan, Pfenning, Andreas R., Zhao, Huabin, Genereux, Diane P., Swofford, Ross, Lind, Abigail, Pollard, Katherine S., Ryderq, Oliver A., Nweeia, Martin T., Meadows, Jennifer, Dong, Michael, Wallerman, Ola, Marinescu, Vikki, Lindblad-Toh, Kerstin, Ray, David A., Power, Sarahjane, Teeling, Emma C., Chauhan, Gaurav, Li, Shirley Xue, Karlsson, Elinor K., Lewin, Harris A.·2020·Science

DOI 10.1126/science.abe9403

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Abstract

How lethal coronaviruses engage hosts: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is closely related to the deadly coronaviruses SARS-CoV-1 and Middle East respiratory syndrome coronavirus (MERS-CoV). Considerable efforts are focused on developing treatments, and therapies that work across coronaviruses would be particularly valuable. Shedding light on the host factors hijacked by the viruses, Gordon et al. mapped the interactions between viral and human proteins for SARS-CoV-2, SARS-CoV-1, and MERS-CoV; analyzed the localization of viral proteins in human cells; and used genetic screening to identify host factors that either enhance or inhibit viral infection. For a subset of the interactions essential for the virus life cycle, the authors determined the cryo–electron microscopy structures and mined patient data to understand how targeting host factors may be relevant to clinical outcomes. Science , this issue p. eabe9403

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Analysis of Relative Gene Expression Data Using Real-Time Quantitative PCR and the 2−ΔΔCT Method
Livak, K. J., & Schmittgen, T. D. (2001) · Methods · doi:10.1006/meth.2001.1262 · Cited by 180,860
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
Altschul, S. (1997) · Nucleic Acids Research · doi:10.1093/nar/25.17.3389 · Cited by 73,302
Cytoscape: A software Environment for integrated models of biomolecular interaction networks
Shannon, P., Markiel, A., Ozier, O., Baliga, N. S., Wang, J. T., Ramage, D., Amin, N., Schwikowski, B., & Ideker, T. (2003) · Genome Research · doi:10.1101/gr.1239303 · Cited by 51,888
Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China
Huang, C., Wang, Y., Li, X., Ren, L., Zhao, J., Hu, Y., Zhang, L., Fan, G., Xu, J., Gu, X., et al. (2020) · The Lancet · doi:10.1016/s0140-6736(20)30183-5 · Cited by 48,884
Self-citation
clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters
Yu, G., Wang, L.-G., Han, Y., & He, Q.-Y. (2012) · OMICS: A Journal of Integrative Biology · doi:10.1089/omi.2011.0118 · Cited by 36,259
The central role of the propensity score in observational studies for causal effects
ROSENBAUM, P. R., & RUBIN, D. B. (1983) · Biometrika · doi:10.1093/biomet/70.1.41 · Cited by 31,241
Coot : model-building tools for molecular graphics
Emsley, P., & Cowtan, K. (2004) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444904019158 · Cited by 30,571
MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification
Cox, J., & Mann, M. (2008) · Nature Biotechnology · doi:10.1038/nbt.1511 · Cited by 14,855
SWISS-MODEL: homology modelling of protein structures and complexes
Waterhouse, A., Bertoni, M., Bienert, S., Studer, G., Tauriello, G., Gumienny, R., Heer, F. T., de Beer, T. A. P., Rempfer, C., Bordoli, L., et al. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky427 · Cited by 13,067
Comparative Protein Modelling by Satisfaction of Spatial Restraints
Šali, A., & Blundell, T. L. (1993) · Journal of Molecular Biology · doi:10.1006/jmbi.1993.1626 · Cited by 12,977

Show all 101 references

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Schmidt, N., Lareau, C. A., Keshishian, H., Ganskih, S., Schneider, C., Hennig, T., Melanson, R., Werner, S., Wei, Y., Zimmer, M., et al. (2020) · Nature Microbiology · doi:10.1038/s41564-020-00846-z · Cited by 319
Structural biology of SARS-CoV-2: open the door for novel therapies
Yan, W., Zheng, Y., Zeng, X., He, B., & Cheng, W. (2022) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-022-00884-5 · Cited by 291
Structure of SARS-CoV-2 ORF8, a rapidly evolving immune evasion protein
(2020) · doi:10.1073/pnas.2021785118 · Cited by 274
AlphaFold2 fails to predict protein fold switching
Chakravarty, D., & Porter, L. L. (2022) · Protein Science · doi:10.1002/pro.4353 · Cited by 193
Evolution of enhanced innate immune evasion by the SARS-CoV-2 B.1.1.7 UK variant
Thorne, L. G., Bouhaddou, M., Reuschl, A.-K., Zuliani-Alvarez, L., Polacco, B., Pelin, A., Batra, J., Whelan, M. V. X., Ummadi, M., Rojc, A., et al. (2021) · doi:10.1101/2021.06.06.446826 · Cited by 91
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Authors: Gordon, D. E., Hiatt, J., Bouhaddou, M., Rezelj, V. V., Ulferts, S., Braberg, H., Jureka, A. S., Obernier, K., Guo, J. Z., Batra, J., Kaake, R. M., Weckstein, A. R., Owens, T. W., Gupta, M., Pourmal, S., Titus, E. W., Cakir, M., Soucheray, M., McGregor, M., Cakir, Z., Jang, G., O’Meara, M. J., Tummino, T. A., Zhang, Z., Foussard, H., Rojc, A., Zhou, Y., Kuchenov, D., Hüttenhain, R., Xu, J., Eckhardt, M., Swaney, D. L., Fabius, J. M., Ummadi, M., Tutuncuoglu, B., Rathore, U., Modak, M., Haas, P., Haas, K. M., Naing, Z. Z. C., Pulido, E. H., Shi, Y., Barrio-Hernandez, I., Memon, D., Petsalaki, E., Dunham, A., Marrero, M. C., Burke, D., Koh, C., Vallet, T., Silvas, J. A., Azumaya, C. M., Billesbølle, C., Brilot, A. F., Campbell, M. G., Diallo, A., Dickinson, M. S., Diwanji, D., Herrera, N., Hoppe, N., Kratochvil, H. T., Liu, Y., Merz, G. E., Moritz, M., Nguyen, H. C., Nowotny, C., Puchades, C., Rizo, A. N., Schulze-Gahmen, U., Smith, A. M., Sun, M., Young, I. D., Zhao, J., Asarnow, D., Biel, J., Bowen, A., Braxton, J. R., Chen, J., Chio, C. M., Chio, U. S., Deshpande, I., Doan, L., Faust, B., Flores, S., Jin, M., Kim, K., Lam, V. L., Li, F., Li, J., Li, Y.-L., Li, Y., Liu, X., Lo, M., Lopez, K. E., Melo, A. A., Moss, F. R., Nguyen, P., Paulino, J., Pawar, K. I., Peters, J. K., Pospiech, T. H., Safari, M., Sangwan, S., Schaefer, K., Thomas, P. V., Thwin, A. C., Trenker, R., Tse, E., Tsui, T. K. M., Wang, F., Whitis, N., Yu, Z., Zhang, K., Zhang, Y., Zhou, F., Saltzberg, D., QCRG Structural Biology Consortium, Hodder, A. J., Shun-Shion, A. S., Williams, D. M., White, K. M., Rosales, R., Kehrer, T., Miorin, L., Moreno, E., Patel, A. H., Rihn, S., Khalid, M. M., Vallejo-Gracia, A., Fozouni, P., Simoneau, C. R., Roth, T. L., Wu, D., Karim, M. A., Ghoussaini, M., Dunham, I., Berardi, F., Weigang, S., Chazal, M., Park, J., Logue, J., McGrath, M., Weston, S., Haupt, R., Hastie, C. J., Elliott, M., Brown, F., Burness, K. A., Reid, E., Dorward, M., Johnson, C., Wilkinson, S. G., Geyer, A., Giesel, D. M., Baillie, C., Raggett, S., Leech, H., Toth, R., Goodman, N., Keough, K. C., Lind, A. L., Zoonomia Consortium, Klesh, R. J., Hemphill, K. R., Carlson-Stevermer, J., Oki, J., Holden, K., Maures, T., Pollard, K. S., Sali, A., Agard, D. A., Cheng, Y., Fraser, J. S., Frost, A., Jura, N., Kortemme, T., Manglik, A., Southworth, D. R., Stroud, R. M., Alessi, D. R., Davies, P., Frieman, M. B., Ideker, T., Abate, C., Jouvenet, N., Kochs, G., Shoichet, B., Ott, M., Palmarini, M., Shokat, K. M., García-Sastre, A., Rassen, J. A., Grosse, R., Rosenberg, O. S., Verba, K. A., Basler, C. F., Vignuzzi, M., Peden, A. A., Beltrao, P., Krogan, N. J., Owens, T. W., Gupta, M., Pourmal, S., Titus, E. W., Azumaya, C. M., Billesbølle, C., Brilot, A. F., Campbell, M. G., Diallo, A., Dickinson, M. S., Diwanji, D., Herrera, N., Hoppe, N., Kratochvil, H. T., Liu, Y., Merz, G. E., Moritz, M., Nguyen, H. C., Nowotny, C., Puchades, C., Rizo, A. N., Schulze-Gahmen, U., Smith, A. M., Sun, M., Young, I. D., Zhao, J., Asarnow, D., Biel, J., Bowen, A., Braxton, J. R., Chen, J., Chio, C. M., Chio, U. S., Deshpande, I., Doan, L., Faust, B., Flores, S., Jin, M., Kim, K., Lam, V. L., Li, F., Li, J., Li, Y.-L., Li, Y., Liu, X., Lo, M., Lopez, K. E., Melo, A. A., Moss, F. R., Nguyen, P., Paulino, J., Pawar, K. I., Peters, J. K., Pospiech, T. H., Safari, M., Sangwan, S., Schaefer, K., Thomas, P. V., Thwin, A. C., Trenker, R., Tse, E., Tsui, T. K. M., Wang, F., Whitis, N., Yu, Z., Zhang, K., Zhang, Y., Zhou, F., Trinidad, D., Agard, D. A., Cheng, Y., Fraser, J. S., Frost, A., Jura, N., Kortemme, T., Manglik, A., Southworth, D. R., Stroud, R. M., Rosenberg, O. S., Verba, K. A., Damas, J., Hughes, G. M., Keough, K. C., Painter, C. A., Persky, N. S., Corbo, M., Kirilenko, B., Hiller, M., Koepfli, K.-P., Kaplow, I., Wirthlin, M., Pfenning, A. R., Zhao, H., Genereux, D. P., Swofford, R., Lind, A., Pollard, K. S., Ryderq, O. A., Nweeia, M. T., Meadows, J., Dong, M., Wallerman, O., Marinescu, V., Lindblad-Toh, K., Ray, D. A., Power, S., Teeling, E. C., Chauhan, G., Li, S. X., Karlsson, E. K., & Lewin, H. A.
Venue: Science
Publisher: American Association for the Advancement of Science (AAAS)
Published: 2020-12-04
Volume: 370
Issue: 6521
ISSN: 0036-8075 (ISSN-L)
1095-9203
DOI: 10.1126/science.abe9403
OpenAlex: W3093213262
Cited by: 747
References: 101
FWCI: 16.54
Type: journal article
Language: en
Open access: hybrid

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This page: CoChat. (2026). Citation check: Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms. https://app.cochat.ai/papers/10.1126/science.abe9403
The paper: Gordon, D. E., Hiatt, J., Bouhaddou, M., Rezelj, V. V., Ulferts, S., Braberg, H., Jureka, A. S., Obernier, K., Guo, J. Z., Batra, J., Kaake, R. M., Weckstein, A. R., Owens, T. W., Gupta, M., Pourmal, S., Titus, E. W., Cakir, M., Soucheray, M., McGregor, M., . . . Lewin, H. A. (2020). Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms. Science. https://doi.org/10.1126/science.abe9403

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Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms

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