Northwestern University Feinberg School of Medicine
Thomas Hope Lab
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Publications

Learn more about the work that we do in the Hope Laboratory through our recent publications.

  1. Kim J, Bose D, Araínga M, Haque MR, Fennessey CM, Caddell RA, Thomas Y, Ferrell DE, Ali S, Grody E  et al.  TGF-β blockade drives a transitional effector phenotype in T cells reversing SIV latency and decreasing SIV reservoirs in vivo.  Nat Commun  2024 Feb 14;15(1):1348. pii:1348
  2. Kime J, Bose D, Arainga M, Haque MR, Fennessey CM, Caddell RA, Thomas Y, Ferrell DE, Ali S, Grody E  et al.  TGF-β blockade drives a transitional effector phenotype in T cells reversing SIV latency and decreasing SIV reservoirs in vivo.  bioRxiv  2023 Dec 15;. pii:2023.09.05.556422
  3. Samer S, Thomas Y, Araínga M, Carter C, Shirreff LM, Arif MS, Avita JM, Frank I, McRaven MD, Thuruthiyil CT  et al.  Blockade of TGF-β signaling reactivates HIV-1/SIV reservoirs and immune responses in vivo.  JCI Insight  2023 Nov 22;8(22). pii:e176882
  4. Vaidyanathan A, Taylor HE, Hope TJ, D'Aquila RT, Bartom ET, Hultquist JF, Peter ME  Analysis of the Contribution of 6-mer Seed Toxicity to HIV-1-Induced Cytopathicity.  J Virol  2023 Jul 27;97(7):e0065223. pii:e00652-23
  5. Williams LD, Shen X, Sawant SS, Akapirat S, Dahora LC, Tay MZ, Stanfield-Oakley S, Wills S, Goodman D, Tenney D  et al.  Viral vector delivered immunogen focuses HIV-1 antibody specificity and increases durability of the circulating antibody recall response.  PLoS Pathog  2023 May;19(5):e1011359. pii:e1011359
  6. Maric D, Corbin L, Greco N, Lorenzo-Redondo R, McRaven MD, Veazey RS, Hope TJ  Temporal and spatial characterization of HIV/SIV infection at anorectal mucosa using rhesus macaque rectal challenge model.  bioRxiv  2023 Feb 23;. pii:2023.02.22.529624
  7. Ash MK, Bhimalli PP, Cho BK, Mattamana BB, Gambut S, Tarhoni I, Fhied CL, Reyes AF, Welninski SJ, Arivalagan J  et al.  Bulk IgG glycosylation predicts COVID-19 severity and vaccine antibody response.  Cell Rep  2022 Dec 13;41(11):111799. doi:10.1016/j.celrep.2022.111799
  8. Tagliaferri Rael C, Giguere R, Sutton S, Horn E, Schieffer RJ, Greene GJ, D'Aquila R, Bryndza Tfaily E, Kiser PF, Hope TJ  Preferences Among Physicians and Men Who Have Sex with Men (MSM) for a Long-Acting, Removable Implant for HIV Prevention: A Discrete Choice Study.  AIDS Res Hum Retroviruses  2022 Dec;38(12):898-908. doi:10.1089/AID.2022.0035
  9. Samer S, Thomas Y, Araínga M, Carter C, Shirreff LM, Arif MS, Avita JM, Frank I, McRaven MD, Thuruthiyil CT  et al.  Blockade of TGF-β signaling reactivates HIV-1/SIV reservoirs and immune responses in vivo.  JCI Insight  2022 Nov 08;7(21). pii:e162290
  10. Yoh SM, Mamede JI, Lau D, Ahn N, Sánchez-Aparicio MT, Temple J, Tuckwell A, Fuchs NV, Cianci GC, Riva L  et al.  Recognition of HIV-1 capsid by PQBP1 licenses an innate immune sensing of nascent HIV-1 DNA.  Mol Cell  2022 Aug 04;82(15):2871-2884.e6. doi:10.1016/j.molcel.2022.06.010
  11. Madden PJ, Thomas Y, Blair RV, Samer S, Doyle M, Midkiff CC, Doyle-Meyers LA, Becker ME, Arif MS, McRaven MD  et al.  An immunoPET probe to SARS-CoV-2 reveals early infection of the male genital tract in rhesus macaques.  Res Sq  2022 Apr 08;. pii:rs.3.rs-1479315
  12. Schieffer RJ, Bryndza Tfaily E, D'Aquila R, Greene GJ, Carballo-Diéguez A, Giguere R, Tagliaferri Rael C, Kiser PF, Hope TJ  Conjoint Analysis of User Acceptability of Sustained Long-Acting Pre-Exposure Prophylaxis for HIV.  AIDS Res Hum Retroviruses  2022 Apr;38(4):336-345. doi:10.1089/AID.2021.0075
  13. Madden PJ, Thomas Y, Blair RV, Samer S, Doyle M, Midkiff CC, Doyle-Meyers LA, Becker ME, Arif MS, McRaven MD  et al.  An immunoPET probe to SARS-CoV-2 reveals early infection of the male genital tract in rhesus macaques.  bioRxiv  2022 Mar 23;. pii:2022.02.25.481974
  14. El-Shennawy L, Hoffmann AD, Dashzeveg NK, McAndrews KM, Mehl PJ, Cornish D, Yu Z, Tokars VL, Nicolaescu V, Tomatsidou A  et al.  Circulating ACE2-expressing extracellular vesicles block broad strains of SARS-CoV-2.  Nat Commun  2022 Jan 20;13(1):405. pii:405
  15. Buchanan LB, Shao Z, Jiang YC, Lai A, Hope TJ, Carias AM, Prodger JL  Quantitative Immunofluorescent Imaging of Immune Cells in Mucosal Tissues.  Methods Mol Biol  2022;2440:143-164. doi:10.1007/978-1-0716-2051-9_9
  16. Madden PJ, Arif MS, Becker ME, McRaven MD, Carias AM, Lorenzo-Redondo R, Xiao S, Midkiff CC, Blair RV, Potter EL  et al.  Development of an In Vivo Probe to Track SARS-CoV-2 Infection in Rhesus Macaques.  Front Immunol  2021;12:810047. pii:810047
  17. Nyanhete TE, Edwards RJ, LaBranche CC, Mansouri K, Eaton A, Dennison SM, Saunders KO, Goodman D, Janowska K, Spreng RL  et al.  Polyclonal Broadly Neutralizing Antibody Activity Characterized by CD4 Binding Site and V3-Glycan Antibodies in a Subset of HIV-1 Virus Controllers.  Front Immunol  2021;12:670561. pii:670561
  18. Rael CT, Lopez-Ríos J, McKenna SA, Das D, Dolezal C, Abascal E, Carballo-Diéguez A, Schnall R, Hope TJ, Bauermeister J  et al.  Transgender Women's Barriers, Facilitators, and Preferences on Tailored Injection Delivery Strategies to Administer Long-Acting Injectable Cabotegravir (CAB-LA) for HIV Pre-exposure Prophylaxis (PrEP).  AIDS Behav  2021 Dec;25(12):4180-4192. doi:10.1007/s10461-021-03357-y
  19. Beddingfield BJ, Maness NJ, Fears AC, Rappaport J, Aye PP, Russell-Lodrigue K, Doyle-Meyers LA, Blair RV, Carias AM, Madden PJ  et al.  Effective Prophylaxis of COVID-19 in Rhesus Macaques Using a Combination of Two Parenterally-Administered SARS-CoV-2 Neutralizing Antibodies.  Front Cell Infect Microbiol  2021;11:753444. pii:753444
  20. Taylor RA, McRaven MD, Carias AM, Anderson MR, Matias E, Araínga M, Allen EJ, Rogers KA, Gupta S, Kulkarni V  et al.  Localization of infection in neonatal rhesus macaques after oral viral challenge.  PLoS Pathog  2021 Nov;17(11):e1009855. pii:e1009855
  21. Maric D, Grimm WA, Greco N, McRaven MD, Fought AJ, Veazey RS, Hope TJ  Th17 T Cells and Immature Dendritic Cells Are the Preferential Initial Targets after Rectal Challenge with a Simian Immunodeficiency Virus-Based Replication-Defective Dual-Reporter Vector.  J Virol  2021 Sep 09;95(19):e0070721. pii:e00707-21
  22. Frank I, Cigoli M, Arif MS, Fahlberg MD, Maldonado S, Calenda G, Pegu A, Yang ES, Rawi R, Chuang GY  et al.  Blocking α4β7 integrin delays viral rebound in SHIVSF162P3-infected macaques treated with anti-HIV broadly neutralizing antibodies.  Sci Transl Med  2021 Aug 18;13(607). pii:eabf7201
  23. Carias AM, Schneider JR, Madden P, Lorenzo-Redondo R, Araínga M, Pegu A, Cianci GC, Maric D, Villinger F, Mascola JR  et al.  Anatomic Distribution of Intravenously Injected IgG Takes Approximately 1 Week to Achieve Stratum Corneum Saturation in Vaginal Tissues.  J Immunol  2021 Jul 15;207(2):505-511. doi:10.4049/jimmunol.2100253
  24. Berard AR, Miller C, Araínga M, Broedlow CA, Noël-Romas L, Schifanella L, Hensley-McBain T, Roederer A, Driscoll CB, Coronado E  et al.  Simian Immunodeficiency Virus Susceptibility, Immunology, and Microbiome in the Female Genital Tract of Adolescent Versus Adult Pigtail Macaques.  AIDS Res Hum Retroviruses  2021 Jul;37(7):510-522. doi:10.1089/AID.2020.0271
  25. Martin-Sancho L, Lewinski MK, Pache L, Stoneham CA, Yin X, Becker ME, Pratt D, Churas C, Rosenthal SB, Liu S  et al.  Functional landscape of SARS-CoV-2 cellular restriction.  Mol Cell  2021 Jun 17;81(12):2656-2668.e8. doi:10.1016/j.molcel.2021.04.008
  26. Taylor RA, Xiao S, Carias AM, McRaven MD, Thakkar DN, Araínga M, Allen EJ, Rogers KA, Kumarapperuma SC, Gong S  et al.  PET/CT targeted tissue sampling reveals virus specific dIgA can alter the distribution and localization of HIV after rectal exposure.  PLoS Pathog  2021 Jun;17(6):e1009632. pii:e1009632
  27. Romano JW, Baum MM, Demkovich ZR, Diana F, Dobard C, Feldman PL, Garcia-Lerma JG, Grattoni A, Gunawardana M, Ho DK  et al.  Tenofovir Alafenamide for HIV Prevention: Review of the Proceedings from the Gates Foundation Long-Acting TAF Product Development Meeting.  AIDS Res Hum Retroviruses  2021 Jun;37(6):409-420. doi:10.1089/AID.2021.0028
  28. Pollara J, Tay MZ, Edwards RW, Goodman D, Crowley AR, Edwards RJ, Easterhoff D, Conley HE, Hoxie T, Gurley T  et al.  Functional Homology for Antibody-Dependent Phagocytosis Across Humans and Rhesus Macaques.  Front Immunol  2021;12:678511. pii:678511
  29. Herrera C, McRaven MD, Laing KG, Dennis J, Hope TJ, Shattock RJ  Early Colorectal Responses to HIV-1 and Modulation by Antiretroviral Drugs.  Vaccines (Basel)  2021 Mar 08;9(3). pii:231
  30. Mamede JI, Griffin J, Gambut S, Hope TJ  A New Generation of Functional Tagged Proteins for HIV Fluorescence Imaging.  Viruses  2021 Feb 28;13(3). pii:386
  31. Karunakaran D, Simpson SM, Su JT, Bryndza-Tfaily E, Hope TJ, Veazey R, Dobek G, Qiu J, Watrous D, Sung S  et al.  Design and Testing of a Cabotegravir Implant for HIV Prevention.  J Control Release  2021 Feb 10;330:658-668. doi:10.1016/j.jconrel.2020.12.024
  32. Klein K, Nankya I, Nickel G, Ratcliff AN, Meadows AAJ, Hathaway N, Bailey JA, Stieh DJ, Cheeseman HM, Carias AM  et al.  Deep Gene Sequence Cluster Analyses of Multi-Virus-Infected Mucosal Tissue Reveal Enhanced Transmission of Acute HIV-1.  J Virol  2021 Jan 13;95(3). pii:e01737-20
  33. Carter SD, Mamede JI, Hope TJ, Jensen GJ  Correlated cryogenic fluorescence microscopy and electron cryo-tomography shows that exogenous TRIM5α can form hexagonal lattices or autophagy aggregates in vivo.  Proc Natl Acad Sci U S A  2020 Nov 24;117(47):29702-29711. doi:10.1073/pnas.1920323117
  34. Hope TJ, Klatt NR, Sacha JB, Cannon PM  Timothy Ray Brown: The Serendipitous Hero of HIV Cure Research.  AIDS Res Hum Retroviruses  2020 Nov;36(11):883-885. doi:10.1089/AID.2020.0253
  35. Abdel-Mohsen M, Richman D, Siliciano RF, Nussenzweig MC, Howell BJ, Martinez-Picado J, Chomont N, Bar KJ, Yu XG, Lichterfeld M  et al.  Recommendations for measuring HIV reservoir size in cure-directed clinical trials.  Nat Med  2020 Sep;26(9):1339-1350. doi:10.1038/s41591-020-1022-1
  36. Rael CT, Lentz C, Carballo-Diéguez A, Giguere R, Dolezal C, Feller D, D'Aquila RT, Hope TJ  Understanding the Acceptability of Subdermal Implants as a Possible New HIV Prevention Method: Multi-Stage Mixed Methods Study.  J Med Internet Res  2020 Jul 27;22(7):e16904. pii:e16904
  37. Rael CT, Martinez M, Giguere R, Bockting W, MacCrate C, Mellman W, Valente P, Greene GJ, Sherman SG, Footer KHA  et al.  Transgender Women's Concerns and Preferences on Potential Future Long-Acting Biomedical HIV Prevention Strategies: The Case of Injections and Implanted Medication Delivery Devices (IMDDs).  AIDS Behav  2020 May;24(5):1452-1462. doi:10.1007/s10461-019-02703-5
  38. Maldonado RJK, Rice B, Chen EC, Tuffy KM, Chiari EF, Fahrbach KM, Hope TJ, Parent LJ  Visualizing Association of the Retroviral Gag Protein with Unspliced Viral RNA in the Nucleus.  mBio  2020 Apr 07;11(2). pii:e00524-20
  39. Schneider JR, Shen X, Orlandi C, Nyanhete T, Sawant S, Carias AM, Smith AD, Kelleher NL, Veazey RS, Lewis GK  et al.  A MUC16 IgG Binding Activity Selects for a Restricted Subset of IgG Enriched for Certain Simian Immunodeficiency Virus Epitope Specificities.  J Virol  2020 Feb 14;94(5). pii:e01246-19
  40. Gray CM, O'Hagan KL, Lorenzo-Redondo R, Olivier AJ, Amu S, Chigorimbo-Murefu N, Harryparsad R, Sebaa S, Maziya L, Dietrich J  et al.  Impact of chemokine C-C ligand 27, foreskin anatomy and sexually transmitted infections on HIV-1 target cell availability in adolescent South African males.  Mucosal Immunol  2020 Jan;13(1):118-127. doi:10.1038/s41385-019-0209-6
  41. Ventura JD, Beloor J, Allen E, Zhang T, Haugh KA, Uchil PD, Ochsenbauer C, Kieffer C, Kumar P, Hope TJ  et al.  Longitudinal bioluminescent imaging of HIV-1 infection during antiretroviral therapy and treatment interruption in humanized mice.  PLoS Pathog  2019 Dec;15(12):e1008161. pii:e1008161
  42. Sultana T, Mamede JI, Saito A, Ode H, Nohata K, Cohen R, Nakayama EE, Iwatani Y, Yamashita M, Hope TJ  et al.  Multiple Pathways To Avoid Beta Interferon Sensitivity of HIV-1 by Mutations in Capsid.  J Virol  2019 Dec 01;93(23). pii:e00986-19
  43. Rael CT, Martinez M, Giguere R, Bockting W, MacCrate C, Mellman W, Valente P, Greene GJ, Sherman SG, Footer KHA  et al.  Knowledge About Oral PrEP Among Transgender Women in New York City.  AIDS Behav  2019 Oct;23(10):2779-2783. doi:10.1007/s10461-019-02584-8
  44. Clerc I, Moussa DA, Vahlas Z, Tardito S, Oburoglu L, Hope TJ, Sitbon M, Dardalhon V, Mongellaz C, Taylor N  Entry of glucose- and glutamine-derived carbons into the citric acid cycle supports early steps of HIV-1 infection in CD4 T cells.  Nat Metab  2019 Jul;1(7):717-730. doi:10.1038/s42255-019-0084-1
  45. Schönfeld M, Knackmuss U, Chandorkar P, Hörtnagl P, Hope TJ, Moris A, Bellmann-Weiler R, Lass-Flörl C, Posch W, Wilflingseder D  Co- but not Sequential Infection of DCs Boosts Their HIV-Specific CTL-Stimulatory Capacity.  Front Immunol  2019;10:1123. pii:1123
  46. Buckner LR, Drobnis EZ, Augustine MS, Rogers LK, Akers J, Mott PD, Hope TJ, Quayle AJ, Schust DJ  Cervical and systemic concentrations of long acting hormonal contraceptive (LARC) progestins depend on delivery method: Implications for the study of HIV transmission.  PLoS One  2019;14(5):e0214152. pii:e0214152
  47. Pollara J, Jones DI, Huffman T, Edwards RW, Dennis M, Li SH, Jha S, Goodman D, Kumar A, LaBranche CC  et al.  Bridging Vaccine-Induced HIV-1 Neutralizing and Effector Antibody Responses in Rabbit and Rhesus Macaque Animal Models.  J Virol  2019 May 15;93(10). pii:e02119-18
  48. Hensley-McBain T, Wu MC, Manuzak JA, Cheu RK, Gustin A, Driscoll CB, Zevin AS, Miller CJ, Coronado E, Smith E  et al.  Increased mucosal neutrophil survival is associated with altered microbiota in HIV infection.  PLoS Pathog  2019 Apr;15(4):e1007672. pii:e1007672
  49. Dabee S, Barnabas SL, Lennard KS, Jaumdally SZ, Gamieldien H, Balle C, Happel AU, Murugan BD, Williamson AL, Mkhize N  et al.  Defining characteristics of genital health in South African adolescent girls and young women at high risk for HIV infection.  PLoS One  2019;14(4):e0213975. pii:e0213975
  50. Tay MZ, Kunz EL, Deal A, Zhang L, Seaton KE, Rountree W, Eudailey JA, Heptinstall J, McRaven MD, Matias E  et al.  Rare Detection of Antiviral Functions of Polyclonal IgA Isolated from Plasma and Breast Milk Compartments in Women Chronically Infected with HIV-1.  J Virol  2019 Apr 01;93(7). pii:e02084-18