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Identification of Host Proteins Required for HIV Infection Through a Functional Genomic Screen
Abstract
HIV-1 exploits multiple host proteins during infection. We performed a large-scale small interfering RNA screen to identify host factors required by HIV-1 and identified more than 250 HIV-dependency factors (HDFs). These proteins participate in a broad array of cellular functions and implicate new pathways in the viral life cycle. Further analysis revealed previously unknown roles for retrograde Golgi transport proteins (Rab6 and Vps53) in viral entry, a karyopherin (TNPO3) in viral integration, and the Mediator complex (Med28) in viral transcription. Transcriptional analysis revealed that HDF genes were enriched for high expression in immune cells, suggesting that viruses evolve in host cells that optimally perform the functions required for their life cycle. This effort illustrates the power with which RNA interference and forward genetics can be used to expose the dependencies of human pathogens such as HIV, and in so doing identify potential targets for therapy.
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“Host proteins with potential functions in the viral lifecycle have also been identified using siRNA-based screens (125-127).”
From Role of host tRNAs and aminoacyl-tRNA synthetases in retroviral replication (2019) · cites this paper as [127]
In the citing paper
“| Mixed pattern of regulation upon HIV-1 infection | GlyRS | 127 |”
From Role of host tRNAs and aminoacyl-tRNA synthetases in retroviral replication (2019) · cites this paper as [127]
In the citing paper
“The five ARSs listed exhibit a significant decrease (Ն16-fold) in transcript levels.”
From Role of host tRNAs and aminoacyl-tRNA synthetases in retroviral replication (2019) · cites this paper as [127]
In the citing paper
“| Levels of transcripts decrease upon HIV-1 infection b | EPRS a , TyrRS, MetRS a , HisRS, PheRS | 127 |”
From Role of host tRNAs and aminoacyl-tRNA synthetases in retroviral replication (2019) · cites this paper as [127]
In the citing paper
“| Levels of transcripts increase upon HIV-1 infection | AsnRS, CysRS | 127 |”
From Role of host tRNAs and aminoacyl-tRNA synthetases in retroviral replication (2019) · cites this paper as [127]
In the citing paper
“Five other ARSs, AlaRS, IleRS, LysRS, ValRS, and GlnRS, exhibit a moderate decrease (ϳ4fold) in HIV-1-infected cells.”
From Role of host tRNAs and aminoacyl-tRNA synthetases in retroviral replication (2019) · cites this paper as [127]
Citations
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Host factors exploited by retroviruses
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“Our studies, combined with those of Brass et al. (2008), indicate the involvement of NUP153, RANBP2, and TNPO3 as factors involved in HIV-1 PIC import (Table 1).”
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Genome-Scale RNAi Screen for Host Factors Required for HIV Replication
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RNA-binding proteins in Mendelian disease
Castelló, A., Fischer, B., Hentze, M. W., & Preiß, T. (2013) · Trends in Genetics · doi:10.1016/j.tig.2013.01.004 · Cited by 261
Regulation of WASH-Dependent Actin Polymerization and Protein Trafficking by Ubiquitination
Hao, Y.-H., Doyle, J., Ramanathan, S., Gomez, T. S., Jia, D., Xu, M., Chen, Z. J., Billadeau, D. D., Rosen, M. K., & Potts, P. R. (2013) · Cell · doi:10.1016/j.cell.2013.01.051 · Cited by 249
“Endosome-to-Golgi transport is essential for cellular entry of pathogenic toxins, such as Shiga, cholera, and ricin, as well as viral pathogens such as HIV (Brass et al., 2008; Sandvig and van Deurs, 2005).”
Reactivation of Latent HIV-1 by Inhibition of BRD4
Zhu, J. K., Gaiha, G. D., John, S. P., Pertel, T., Chin, C. R., Gao, G., Qu, H., Walker, B. D., Elledge, S. J., & Brass, A. L. (2012) · Cell Reports · doi:10.1016/j.celrep.2012.09.008 · Cited by 246
“Our work also demonstrates that in addition to HDFs that are needed by HIV-1 (Brass et al., 2008) and HIV-1 restriction factors (HRFs) that have evolved to specifically inhibit the virus (Yan and Chen, 2012), there exists a third functional class of host factors, HIV-1 competitive factors (HCFs);…”
BackgroundMethodSelf-citationHuang, Q., Chan, K. Y., Tobey, I. G., Chan, Y. A., Poterba, T., Boutros, C. L., Balazs, A. B., Daneman, R., Bloom, J. M., Seed, C., et al. (2019) · PLOS ONE · doi:10.1371/journal.pone.0225206 · Cited by 234
“The Ly6 gene family also influences susceptibility to infection by HIV126,27, Flaviviridae (yellow fever virus, dengue, and West Nile virus28, Influenza A29, and Marek’s disease virus in chickens30.”
BackgroundWheeler, L. A., Trifonova, R. T., Vrbanac, V. D., Basar, E., McKernan, S., Xu, Z., Seung, E., Déruaz, M., Dudek, T., Einarsson, J. I., et al. (2011) · Journal of Clinical Investigation · doi:10.1172/jci45876 · Cited by 227
Self-citationEating the enemy within: autophagy in infectious diseases
Orvedahl, A., & Levine, B. (2008) · Cell Death and Differentiation · doi:10.1038/cdd.2008.130 · Cited by 241
“68 As noted above, autophagy also mediates cell death of bystander T cells in HIV infection through CXCR4 binding to HIV envelope proteins.”
BackgroundMatreyek, K. A., & Engelman, A. (2011) · Journal of Virology · doi:10.1128/jvi.00325-11 · Cited by 213
“In addition to TNPO3, two major constituent proteins of the NPC, nucleoporins NUP358/RanBP2 and NUP153, were identified in two of the siRNA screens (7, 39).”
BackgroundSelf-citationA CRISPR-Based Screen Identifies Genes Essential for West-Nile-Virus-Induced Cell Death
Ma, H., Dang, Y., Wu, Y., Jia, G., Anaya, E., Zhang, J., Abraham, S., Choi, J.-G., Shi, G., Qi, L., et al. (2015) · Cell Reports · doi:10.1016/j.celrep.2015.06.049 · Cited by 223
“For example, the overlap was poor between three independent genome-wide functional screens using siRNA performed to identify host genes linked to HIV replication (Brass et al., 2008; Konig et al., 2008; Zhou et al., 2008).”
BackgroundDrug Target Prediction and Repositioning Using an Integrated Network-Based Approach
Emig, D., Ivliev, A. E., Pustovalova, O., Lancashire, L., Bureeva, S. V., Nikolsky, Y., & Bessarabova, M. (2013) · PLoS ONE · doi:10.1371/journal.pone.0060618 · Cited by 242
The IFITMs Inhibit Zika Virus Replication
Savidis, G., Perreira, J. M., Portmann, J. M., Meraner, P., Guo, Z., Green, S., & Brass, A. L. (2016) · Cell Reports · doi:10.1016/j.celrep.2016.05.074 · Cited by 226
“…The IFITMs have been shown to restrict viral replication by blocking fusion-pore formation and the entry of the viral genome and its associated proteins into the cytosol (Bailey et al., 2014; Brass et al., 2008; Feeley et al., 2011; Li et al., 2013; Lin et al., 2013; Perreira et al., 2013).”
BackgroundSelf-citationHost-Directed Antiviral Therapy
Kumar, N., Sharma, S., Kumar, R., Tripathi, B. N., Barua, S., Ly, H., & Rouse, B. T. (2020) · Clinical Microbiology Reviews · doi:10.1128/cmr.00168-19 · Cited by 289
The APOBEC3 Family of Retroelement Restriction Factors
Refsland, E. W., & Harris, R. S. (2013) · Current topics in microbiology and immunology · doi:10.1007/978-3-642-37765-5_1 · Cited by 216
Systems Biology in Immunology: A Computational Modeling Perspective
Germain, R. N., Meier‐Schellersheim, M., Nita‐Lazar, A., & Fraser, I. D. C. (2011) · Annual Review of Immunology · doi:10.1146/annurev-immunol-030409-101317 · Cited by 208
MicroRNA profile changes in human immunodeficiency virus type 1 (HIV-1) seropositive individuals
Houzet, L., Yeung, M.-L., de Lame, V., Desai, D., Smith, S. M., & Jeang, K. (2008) · Retrovirology · doi:10.1186/1742-4690-5-118 · Cited by 214
“The course of human immunodeficiency virus (HIV-1) infection in cells is impacted by the action of several hundred host proteins [12-16].”
BackgroundDalmasso, C., Carpentier, W., Meyer, L., Rouzioux, C., Goujard, C., Chaix, M., Lambotte, O., Avettand-Fènoël, V., Clerc, S. L., de Senneville, L. D., et al. (2008) · PLoS ONE · doi:10.1371/journal.pone.0003907 · Cited by 206
“…plasma HIV-RNA is a composite marker reflecting viral fitness, replicative capacity and host control, while intracellular HIV-DNA levels reflect the establishment of HIV reservoirs and, thereof, the effect of numerous host proteins that may interact with the intracellular viral lifecycle [10].”
BackgroundHIV Integration Targeting: A Pathway Involving Transportin-3 and the Nuclear Pore Protein RanBP2
Ocwieja, K. E., Brady, T. L., Ronen, K., Huegel, A., Roth, S. L., Schaller, T., James, L. C., Towers, G. J., Young, J. A. T., Chanda, S. K., et al. (2011) · PLoS Pathogens · doi:10.1371/journal.ppat.1001313 · Cited by 212
“Passage through the pore is likely a preferred route of nuclear entry for HIV-1 even in dividing cells – several components of the nuclear pore are required for efficient infection of dividing cells, even though PICs might access the nucleus during nuclear breakdown in mitosis”
BackgroundStrunze, S., Engelke, M. F., Wang, I.-H., Püntener, D., Boucke, K., Schleich, S., Way, M., Schoenenberger, P., Burckhardt, C. J., & Greber, U. F. (2011) · Cell Host & Microbe · doi:10.1016/j.chom.2011.08.010 · Cited by 207
Genome-wide CRISPR screen identifies host dependency factors for influenza A virus infection
Li, B., Clohisey, S., Chia, B. S., Wang, B., Cui, A., Eisenhaure, T., Schweitzer, L. D., Hoover, P., Parkinson, N., Nachshon, A., et al. (2020) · Nature Communications · doi:10.1038/s41467-019-13965-x · Cited by 240
Abdulrahman, B., Khweek, A. A., Akhter, A., Caution, K., Kotrange, S., Abdelaziz, D. H., Newland, C. A., Rosales-Reyes, R., Kopp, B. T., McCoy, K., et al. (2011) · Autophagy · doi:10.4161/auto.7.11.17660 · Cited by 195
Arhel, N. (2010) · Retrovirology · doi:10.1186/1742-4690-7-96 · Cited by 200
Krishnan, L., Matreyek, K. A., Öztop, I., Lee, K., Tipper, C. H., Li, X., Dar, M. J., KewalRamani, V. N., & Engelman, A. (2009) · Journal of Virology · doi:10.1128/jvi.01899-09 · Cited by 192
“MLV, in contrast, efficiently infected TNPO3 knockdown cells (5, 13, 30), and recombinant TNPO3 and MLV IN proteins failed to interact under conditions where an HIV-1 IN-TNPO3 interaction was detected.”
BackgroundResultInfluentialSelf-citationHuman Nucleoporins Promote HIV-1 Docking at the Nuclear Pore, Nuclear Import and Integration
Nunzio, F. D., Danckaert, A., Fricke, T., Perez, P., Fernandez, J., Perret, E., Roux, P., Shorte, S. L., Charneau, P., Diaz‐Griffero, F., et al. (2012) · PLoS ONE · doi:10.1371/journal.pone.0046037 · Cited by 190
HIV pathogenesis: 25 years of progress and persistent challenges
Levy, J. A. (2008) · AIDS · doi:10.1097/qad.0b013e3283217f9f · Cited by 187
Viruses and the autophagy machinery
Dreux, M., & Chisari, F. (2010) · Cell Cycle · doi:10.4161/cc.9.7.11109 · Cited by 190
John, S., Chin, C. R., Perreira, J. M., Feeley, E., Aker, A. M., Savidis, G., Smith, S. E., Elia, A., Everitt, A., Vora, M. M., et al. (2013) · Journal of Virology · doi:10.1128/jvi.00481-13 · Cited by 187
Self-citationRotger, M., Dang, K. K., Fellay, J., Heinzen, E. L., Feng, S., Descombes, P., Shianna, K. V., Ge, D., Günthard, H. F., Goldstein, D. B., et al. (2010) · PLoS Pathogens · doi:10.1371/journal.ppat.1000781 · Cited by 178
“) were all upregulated with increasing viral load, which is consistent with their general dependence on the interferon pathways. A number of chemokines and chemokine receptors were also positively modulated with increasing viremia. We also identified differentially expressed genes that are present in both the current…”
ResultTapping the RNA world for therapeutics
Lieberman, J. (2018) · Nature Structural & Molecular Biology · doi:10.1038/s41594-018-0054-4 · Cited by 202
Self-citationLi, Q., Pène, V., Krishnamurthy, S. R., Cha, H., & Liang, T. J. (2013) · Nature Medicine · doi:10.1038/nm.3190 · Cited by 193
CD4+ T cells from elite controllers resist HIV-1 infection by selective upregulation of p21
Chen, H., Li, C., Huang, J., Cung, T. D. H., Seiss, K., Beamon, J., Carrington, M. N., Porter, L. C., Burke, P. S., Yang, Y., et al. (2011) · Journal of Clinical Investigation · doi:10.1172/jci44539 · Cited by 174
Self-citationHIV-1 uncoating: connection to nuclear entry and regulation by host proteins
Ambrose, Z., & Aiken, C. (2014) · Virology · doi:10.1016/j.virol.2014.02.004 · Cited by 187
“Most notably, in 2008 three groups screened siRNA libraries to identify multiple proteins involved in early HIV-1 life cycle events (Brass et al., 2008; Konig et al., 2008; Zhou et al., 2008).”
InfluentialLentiviral delivery of short hairpin RNAs
Manjunath, N., Wu, H., Subramanya, S., & Shankar, P. (2009) · Advanced Drug Delivery Reviews · doi:10.1016/j.addr.2009.03.004 · Cited by 170
“In fact, a recent genome-wide RNAi screen has identified several host genes necessary for viral replication [150].”
The Take and Give Between Retrotransposable Elements and their Hosts
Beauregard, A., Curcio, M. J., & Belfort, M. (2008) · Annual Review of Genetics · doi:10.1146/annurev.genet.42.110807.091549 · Cited by 179
A Physical Interaction Network of Dengue Virus and Human Proteins
Khadka, S., Vangeloff, A. D., Zhang, C., Siddavatam, P., Heaton, N. S., Wang, L., Sengupta, R., Sahasrabudhe, S., Randall, G., Gribskov, M., et al. (2011) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m111.012187 · Cited by 175
Nup153 and Nup98 bind the HIV-1 core and contribute to the early steps of HIV-1 replication
Nunzio, F. D., Fricke, T., Miccio, A., Valle-Casuso, J., Perez, P., Souque, P., Rizzi, E., Severgnini, M., Mavilio, F., Charneau, P., et al. (2013) · Retrovirology · doi:10.1186/1742-4690-10-s1-p111 · Cited by 171
“…(Ao et al., 2010), 3) importin α/ importin β heterodimer (Fassati et al., 2003; Gallay et al., 1997; Hearps and Jans, 2006), 4) transportin-SR2/TNPO3 (Brass et al., 2008; Christ et al., 2008; Konig et al., 2008; Krishnan et al., 2010; Levin et al., 2010; Thys et al., 2011; Valle-Casuso et al.,…”
BackgroundHultquist, J. F., Schumann, K., Woo, J. M., Manganaro, L., McGregor, M. J., Doudna, J., Simon, V., Krogan, N. J., & Marson, A. (2016) · Cell Reports · doi:10.1016/j.celrep.2016.09.080 · Cited by 170
Metadata
- Authors
- Brass, A. L., Dykxhoorn, D. M., Benita, Y., Yan, N., Engelman, A., Xavier, R. J., Lieberman, J., & Elledge, S. J.
- Affiliations
- Brigham and Women's Hospital (US)
- ORCID
- Venue
- Science
- Published
- 2008-02-15
- Volume
- 319
- Issue
- 5865
- Pages
- 921-926
- ISSN
- 0036-8075 (ISSN-L)
- 1095-9203
- OpenAlex
- W2145848202
- Cited by
- 1,449
- References
- 0
- Citations by year
- 2026: 12 · 2025: 18 · 2024: 26 · 2023: 28 · 2022: 38 · 2021: 38 · 2020: 52 · 2019: 59 · 2018: 71 · 2017: 53 · 2016: 62 · 2015: 96 · 2014: 90 · 2013: 150 · 2012: 148
- FWCI
- 57.05
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Science (publishedVersion)
- PubMed (publishedVersion)
- Funders
- Howard Hughes Medical Institute
- National Institute of Allergy and Infectious Diseases (U19AI056900, AI052014, AI 062773, R01AI062773, R01AI052014, P30AI060354)
- National Institute of Diabetes and Digestive and Kidney Diseases (P30DK040561)
- Topics
- Life Sciences › Immunology and Microbiology › Virology › HIV Research and Treatment
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Virus-based gene therapy research
- Health Sciences › Medicine › Infectious Diseases › HIV/AIDS drug development and treatment
- Keywords
- HIV-1, host factors, host-virus interaction, Rab6, viral entry, karyopherins, TNPO3, viral integration, Mediator complex, MED28, viral transcription, antiviral drug targets
- MeSH terms
- Cytoskeletal Proteins, Humans, Proteins, Transcription, Genetic, Virus Replication, HIV-1, HIV Infections, Virus Integration, Computational Biology, rab GTP-Binding Proteins, Genomics, Karyopherins, Vesicular Transport Proteins, RNA Interference, RNA, Small Interfering, Cell Line, Tumor, Intracellular Signaling Peptides and Proteins, Virus Internalization, Human Immunodeficiency Virus Proteins, Host-Pathogen Interactions, Mediator Complex
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