Ambrose Lab Publications:
Jang S, Bedwell GJ, Singh SP, Yu HJ, Arnarson B, Singh P, Radhakrishnan R, Douglas AW, Ingram Z, Freniere C, Akkermans O, Sarafianos SG, Ambrose Z, Xiong Y, Anekal PV, Montero Llopis P, KewalRamani VN, Francis AC, Engelman AN. HIV-1 usurps mixed-charge domain-dependent CPSF6 phase separation for higher-order capsid binding, nuclear entry and viral DNA integration, Nucleic Acids Res 2024, 1-23.
Ingram Z, Kline C, Hughson AK, Singh PK, Fisher HL, Sowd GA, Watkins SC, Kane M, Engelman AN, Ambrose Z. Spatiotemporal binding of cyclophilin A and CPSF6 to capsid regulates HIV-1 nuclear entry and integration, bioRxiv 2024.
Elizaldi SR, Verma A, Ma ZM, Ott S, Rajasundaram D, Cottrell ML, Kashuba ADM, Ambrose Z, Lifson JD, Morrison JH, Iyer SS. CD4 T cells in the CNS during SIV infection, PLoS Pathog 2023, 19(12):e1011844. PMCID: PMC10729971
Roy CN, Shu ST, Kline C, Rigatti L, Smithgall TE, Ambrose Z. Use of pediatric thymus to humanize mice for HIV-1 mucosal transmission, Sci Rep 2023, 13:17067. PMCID: PMC10564933
Guseman AJ, Rennick LJ, Nambulli S, Roy CN, Martinez DR, Yang DT, Binderwhala F, Veragara S, Baric RS, Ambrose Z, Duprex WP, Gronenborn AM. Targeting spike glycans to inhibit SARS-CoV-2 entry, Proc Natl Acad Sci U S A 2023, 120(38):e2301518120. PMCID: PMC10515186
Dwivedi R*, Wang Y*, Kline C, Fischer DK, Ambrose Z. APOBEC3 selects V179I in HIV-1 RT to provide selective advantage for NNRTI-resistant mutants, Front Virol 2022, 2:919825. PMCID: PMC9364801 *contributed equally
Zhang H, Fischer DK, Shuda M, Chang Y, Moore PS, Gao SJ, Ambrose Z, Guo H. Construction and characterization of two SARS-CoV-2 minigenome replicon systems, J Med Virol 2022, 1-15. PMCID: PMC9088700
Tisthammer K, Kline C, Rutledge T, Diedrich C, Ita S, Lin PL, Ambrose Z, Pennings PS. SIV evolutionary dynamics in cynomolgus macaques during SIV-Mycobacterium tuberculosis co-infection, Viruses 2021, 14(1):48. PMCID: PMC8778162
Ingram Z, Fischer DK, Ambrose Z. Disassembling the nature of capsid: biochemical, genetic and imaging approaches to assess HIV-1 capsid functions. Viruses 2021, 13(11):2237. PMCID: PMC8618418
Roy CN, Benitez Moreno MA, Kline C, Ambrose Z. CG dinucleotide removal in bioluminescent and fluorescent reporters improves HIV-1 replication and reporter gene expression for dual imaging in humanized mice, J Virol 2021, 95(19):e00449-21. PMCID: PMC8428378
Zhong Z, Ning J, Boggs EA, Jang S, Wallace C, Telmer C, Bruchez MP, Ahn J, Engelman AN, Zhang P, Watkins SC, Ambrose Z. Cytoplasmic CPSF6 regulates HIV-1 capsid trafficking and infection in a cyclophilin A-dependent manner, mBio 2021, 12:e03142-20. PMCID: PMC8092277
Xu C*, Fischer DK*, Rankovic S*, Li W, Dick R, Runge B, Zadorozhnyi R, Ahn J, Aiken C, Polenova T, Engelman AN, Ambrose Z, Rousso I, Perilla JR. Permeability of the HIV-1 capsid to metabolites modulates viral DNA synthesis, PLoS Biol 2020, 18(12):e3001015. PMCID: PMC7775124 *contributed equally
Diedrich CR, Rutledge T, Maiello P, Baranowski TM, White AG, Borish HJ, Karell P, Hopkins F, Brown J, Fortune SM, Flynn JL, Ambrose Z, Lin PL. SIV and Mycobacterium tuberculosis synergy within the granuloma accelerates the reactivation pattern of latent tuberculosis, PLoS Pathog 2020, 16(7): e1008413. PMCID: PMC7419014
Melody K, Roy CN, Kline C, Cottrell ML, Evans D, Shutt K, Pennings PS, Keele BF, Bility M, Kashuba ADM, Ambrose Z. Long-acting rilpivirine (RPV LA) pre-exposure prophylaxis does not inhibit vaginal transmission of RPV-resistant HIV-1 nor select for high frequency drug resistance in humanized mice, J Virol 2020, 94(8):e01912-19. PMCID: PMC7108851
Fu X, Ning J, Zhong Z, Ambrose Z, Watkins SC, Zhang P. AutoCLEM: An automated workflow for correlative live-cell fluorescence microscopy and cryo-electron tomography, Sci Rep 2019, 9:19207. PMCID: PMC6915765
Siddiqui MA, Saito A, Halambage UD, Ferhadian D, Fischer DK, Francis AC, Melikyan GB, Ambrose Z, Aiken C, Yamashita M. A novel phenotype links HIV-1 capsid stability to cGAS-mediated DNA sensing, J Virol 2019, 93(16):e00706-19. PMCID: PMC6675898
Boyer PL*, Melody K*, Smith SJ, Dunn LL, Kline C, Fischer DK, Dwivedi R, Clark PK, Hughes SH, Ambrose Z. Two co-selected distal mutations in HIV-1 reverse transcriptase (RT) alter susceptibility to non-nucleoside RT inhibitors and nucleoside analogs, J Virol 2019, 93:e00224-19. PMCID: PMC6532099 *contributed equally
Fischer DK, Saito A, Kline C, Cohen R, Watkins SC, Yamashita M, Ambrose Z. CA mutation N57A has distinct strain-specific capsid uncoating and infectivity phenotypes, J Virol 2019, 93(9):e00214-219. PMCID: PMC6475785
Ning J*, Zhong Z*, Fischer DK, Harris G, Watkins SC, Ambrose Z, Zhang P. Truncated CPSF6 forms higher order complexes that bind and disrupt HIV-1 capsid, J Virol 2018, 92(13):e00368-18. PMCID: PMC6002704 (cover art here) *contributed equally
Akiyama H, Ramirez NG, Gibson G, Kline C, Watkins SC, Ambrose Z, Gummuluru S. Interferon-inducible CD169/Siglec 1 attenuates anti-HIV-1 effects of IFN-a, J Virol 2017, 91:e00972-17. PMCID: PMC5640826
Feder AF, Kline C, Polacino P, Cottrell M, Kashuba ADM, Keele BF, Hu SL, Petrov DA, Pennings PS, Ambrose Z. A spatio-temporal assessment of simian/human immunodeficiency virus (SHIV) evolution reveals a highly dynamic process within the host, PLoS Pathog 2017, 13(5):e1006358. PMCID: PMC5444849
Zerbato JM, Serrao E, Lenzi G, Kim B, Ambrose Z, Watkins SC, Engelman AN, Sluis-Cremer N. Establishment and reversal of HIV-1 latency in naive and central memory CD4+ T cells, J Virol 2016, 90:8059-73. PMCID: PMC5008097
Smith SJ, Pauly GT, Akram A, Melody K, Ambrose Z, Schneider JP, Hughes SH. Rilpivirine and doravirine have complementary efficacies against NNRTI-resistant HIV-1 mutants, J Acquir Immune Defic Syndr 2016, 72:485-91. PMCID: PMC4942337
Smith SJ, Pauly GT, Akram A, Melody K, Rai G, Maloney DJ, Ambrose Z, Thomas CJ, Schneider JT, Hughes SH. Rilpivirine analogs potently inhibit drug-resistant HIV-1 mutants. Retrovirology 2016, 13:11. PMCID: PMC4754833
Kearney MF, Anderson EM, Coomer C, Smith L, Shao W, Johnson N, Kline C, Spindler J, Mellors JW, Coffin JM, Ambrose Z. Well-mixed plasma and tissue viral populations in RT-SHIV-infected macaques implies a lack of viral replication in the tissues during antiretroviral therapy. Retrovirology 2015,12:93. PMCID: PMC4642622
Melody K, McBeth S, Kline C, Kashuba ADM, Mellors JW, Ambrose Z. Low frequency of drug resistant variants selected by long-acting rilpivirine (RPV LA) in macaques infected with RT-SHIV. Antimicrob Agents Chemother 2015, 59(12):7762-70. PMCID: PMC4649225
Song J, Cai Z, White AG, Jin T, Wang X, Kadayakkara D, Anderson CJ, Ambrose Z, Young WB. Visualization and quantification of simian immunodeficiency virus (SIV)-infected cells using non-invasive molecular imaging. J Gen Virol 2015, 96:3131-42. PMCID: PMC4857449
Ambrose Z, Aiken C. HIV-1 uncoating: connection to nuclear entry and regulation by host proteins. Virology 2014 Apr, 454-455:371-9. PMCID: PMC3988234.
Ambrose Z, Kline C, Polacino P, Hu SL. Dysregulation of multiple inflammatory molecules in lymph node and ileum of macaques during RT-SHIV infection with or without antiretroviral therapy. J Med Primatol 2014, 43(5):298-309. PMCID: PMC4176520.
Kline C, Ndjomou J, Franks T, Kiser R, Coalter V, Smedley J, Piatak M, Mellors JW, Lifson JD, Ambrose Z. Persistence of viral reservoirs in multiple tissues after ART suppression in a macaque RT-SHIV model. PLoS One 2013, 8(12):e84275. PMCID: PMC3867492.
Xu H, Franks T, Gibson G, Huber K, Rahm N, Strambio De Castillia C, Luban J, Aiken C, Watkins S, Sluis-Cremer N, Ambrose Z. Evidence for bi-phasic uncoating during HIV-1 infection from a novel imaging assay. Retrovirology 2013, 10:70. PMCID: PMC3716918.
Boltz V, Ambrose Z, Kearney M, Shao W, KewalRamani VN, Maldarelli F, Mellors JW, Coffin JM. Ultrasensitive allele-specific PCR reveals rare pre-existing drug resistant variants and a large replicating virus population in macaques infected with RT-SHIV. J Virol 2012, 86:12525-30. PMCID: PMC3497681.
Acevedo O, Ambrose Z, Flaherty PT, Aamer H, Jain P, Sambasivarao SV. Identification of HIV inhibitors guided by free energy perturbation calculations. Curr Pharm Des 2012, 18:1199-1216. PMCID: PMC3605731.
Ambrose Z, Lee K, Ndjomou J, Xu H, Oztop I, Matous J, Takemura T, Unutmaz D, Engelman A, Hughes SH, KewalRamani VN. Human immunodeficiency virus type 1 capsid mutation N74D alters cyclophilin A dependence and impairs microphage infection. J Virol 2012, 86:4708-14. PMCID: PMC3318671.
Ambrose Z. Use of animal models for anti-HIV drug development. Antiviral Drugs – Aspects of Clinical Use and Recent Advances, edited by Patric Arbuthnot. InTech, March 2012. ISBN 978-953-51-0256-4.
Jun S, Ke D, Debiec K, Zhao G, Meng X, Ambrose Z, Gibson GA, Watkins SC, Zhang P. Direct visualization of HIV-1 infection using correlative live-cell microscopy and cryo-electron microscopy. Structure 2011, 19:1573-81. PMCID: PMC3217200.
Kearney M, Spindler J, Shao W, Maldarelli F, Palmer S, Hu SL, Lifson JD, KewalRamani VN, Mellors JW, Coffin JM, Ambrose Z. Genetic diversity of simian immunodeficiency virus encoding HIV-1 reverse transcriptase (RT-SHIVmne) persists in macaques despite antiretroviral therapy. J Virol 2011, 85:1067-76. PMCID: PMC3019993.
Lee K, Ambrose Z, Martin TD, Oztop I, Mulky A, Julias JG, Vandegraaff N, Baumann JG, Wang R, Yuen W, Takemura T, Shelton K, Taniuchi I, Li Y, Sodroski J, Littman DR, Coffin JM, Hughes SH, Unutmaz D, Engelman A, KewalRamani VN. Flexible use of nuclear import pathways by HIV-1. Cell Host Microbe 2010, 7:221-33. PMCID: PMC2481689.
Shao W, Kearney M, Maldarelli F, Mellors JW, Stephens R, Lifson JD, KewalRamani VN, Ambrose Z, Coffin JM, Palmer SE. RT-SHIV subpopulation dynamics in infected macaques during anti-HIV therapy. Retrovirology 2009,6:101. PMCID: PMC776578.
Boyer PL, Vu BC, Ambrose Z, Julias JG, Warnecke S, Liao C, Meier C, Marquez VE, Hughes SH. The nucleoside analog D-carba T blocks HIV-1 reverse transcription. J Med Chem 2009; 52:5356-64. PMCID: PMC2756836.
Hatziioannou T, Ambrose Z, Chung NP, Piatak M, Yuan F, Trubey CM, Coalter V, Kiser R, Schneider D, Smedley J, Pung R, Gathuka M, Estes JD, Veazey RS, KewalRamani VN, Lifson JD, Bieniasz PD. A macaque model of HIV-1 infection. Proc Natl Acad Sci USA 2009; 106:4425-4429. PMCID: PMC2657417. (Summaries of the study can be found here and here.)
Ambrose Z, Herman BD, Sheen CW, Zelina S, Moore KL, Tachedjian G, Nissley DV, Sluis-Cremer N. The HIV-1 nonnucleoside reverse transcriptase inhibitor resistance mutation I132M confers hypersensitivity to nucleoside analogs. J Virol 2009; 82:3826-3822. PMCID: PMC2663283.
Ambrose Z, KewalRamani VN. Of mice and monkeys: new advances in animal models to study HIV-1 therapy and prophylaxis. Future HIV Ther 2008; 2:363-373.
Ambrose Z, Compton L, Piatak M, Lu D, Alvord WG, Lubormirski MS, Hildreth JEK, Lifson JD, Miller CJ. KewalRamani VN. Incomplete protection against SIV vaginal transmission in rhesus macaques by a topical antiviral agent revealed by repeat challenges. J Virol 2008; 82:6591-6599. PMCID: PMC2447098.
Ambrose Z, Palmer S, Boltz VF, Kearney M, Larsen K, Polacino P, Flanary L, Oswald K, Piatak M, Smedley J, Shao W, Bischofberger N, Maldarelli F, Kimata JT, Mellors JW, Hu SL, Coffin JM, Lifson JD, KewalRamani VN. Suppression of viremia and evolution of HIV-1 drug resistance in a macaque model for antiretroviral therapy. J Virol 2007; 81:12145-12155. PMCID: PMC2169021. (Summaries of the study can be found here or here.)
Ambrose Z, KewalRamani VN, Bieniasz PD, Hatziioannou T. HIV/AIDS: in search of an animal model. Trends Biotechnol, 2007 Aug;25(8):333-7. PMID: 17574286.
Boyer PI, Julias JG, Ambrose Z, Siddiqui MA, Marquez VE, Hughes SH. The nucleoside analogs 4’C-methyl thymidine and 4’C-ethyl thymidine block DNA synthesis by wild-type HIV-1 RT and excision proficient NRTI resistant RT variants. J Mol Bio 2007; 371:873-882. PMID: 17597154.
Nissley DV, Radzio J, Ambrose Z, Sheen CW, Hamamouch N, Moore KL, Tachedjian G, Sluis-Cremer N. Characterization of a novel nonnucleoside reverse transcriptase (RT) inhibitor resistance mutations at residues 132 and 135 in the 51kDA subunit of HIV-1 RT. Biochem J 2007;404:151-157. PMCID: PMC1868834.
Ambrose Z, Julias JG, Boyer PL, KewalRamani VN, Hughes SH. The level of reverse transcriptase (RT) in human immunodeficiency virus type 1 particles affects susceptibility to non-nucleoside RT inhibitors but not to lamivudine. J Virol 2006; 80:2578-2581. PMCID: PMC1395365.
Ambrose Z, Boltz V, Palmer S, Coffin JM, Hughes SH, KewalRamani VN. In vitro characterization of an simian immunodeficiency virus-human immunodeficiency virus (HIV) chimera expressing HIV type 1 reverse transcriptase to study antiviral resistance in pigtail macaques. J Virol 2004; 78:13553-13561. PMCID: PMC533891.
Ambrose Z, Thompson J, Larsen K, Kuller L, Panicali DL, Clements JD, Agy M, Montefiori DC, Hu SL, Bosch ML. Evidence for immune-mediated reduction of viral replication in Macaca nemestrina mucosally immunized with inactivated SHIV 6. Virology 2003; 308:178-190. PMID: 12706101.
Ambrose Z, Larsen K, Thompson J, Stevens Y, Finn E, Hu SL, Bosch ML. Evidence for early local viral replication and local production of antiviral immunity upon mucosal simian-human immunodeficiency virus SHIV6 infection in Macaca nemestrina. J Virol 2001; 75:8589-8596. PMCID: PMC115104.