2009-2011

Definition of the viral targets of protective HIV-1-specific T cell responses. Mothe B, Llano A, Ibarrondo J, Daniels M, Miranda C, Zamarreño J, Bach V, Zuniga R, Pérez-Álvarez S, Berger CT, Puertas MC, Martinez-Picado J, Rolland M, Farfan M, Szinger JJ, Hildebrand WH, Yang OO, Sanchez-Merino V, Brumme CJ, Brumme ZL, Heckerman D, Allen TM, Mullins JI, Gómez G, Goulder PJ, Walker BD, Gatell JM, Clotet B, Korber BT, Sanchez J, Brander C. J Transl Med. 2011 Dec 7;9:208. doi: 10.1186/1479-5876-9-208.

Immune-mediated attenuation of HIV-1. Chopera DR, Wright JK, Brockman MA, Brumme ZL. Future Virol. 2011 Aug;6(8):917-928. doi: 10.2217/fvl.11.68.

Responsiveness of HIV-specific CD4 T cells to PD-1 blockade. Porichis F, Kwon DS, Zupkosky J, Tighe DP, McMullen A, Brockman MA, Pavlik DF, Rodriguez-Garcia M, Pereyra F, Freeman GJ, Kavanagh DG, Kaufmann DE. Blood. 2011 Jul 28;118(4):965-74. doi: 10.1182/blood-2010-12-328070. Epub 2011 Jun 7.

Progression to AIDS in South Africa is associated with both reverting and compensatory viral mutations. Huang KH, Goedhals D, Carlson JM, Brockman MA, Mishra S, Brumme ZL, Hickling S, Tang CS, Miura T, Seebregts C, Heckerman D, Ndung'u T, Walker B, Klenerman P, Steyn D, Goulder P, Phillips R; Bloemfontein-Oxford Collaborative Group; van Vuuren C, Frater J. PLoS One. 2011 Apr 22;6(4):e19018. doi: 10.1371/journal.pone.0019018.

Epithelial adhesion molecules can inhibit HIV-1-specific CD8⁺ T-cell functions. Streeck H, Kwon DS, Pyo A, Flanders M, Chevalier MF, Law K, Jülg B, Trocha K, Jolin JS, Anahtar MN, Lian J, Toth I, Brumme Z, Chang JJ, Caron T, Rodig SJ, Milner DA Jr, Piechoka-Trocha A, Kaufmann DE, Walker BD, Altfeld M. Blood. 2011 May 12;117(19):5112-22. doi: 10.1182/blood-2010-12-321588. Epub 2011 Mar 14.

Factors associated with viral rebound in HIV-1-infected individuals enrolled in a therapeutic HIV-1 gag vaccine trial. Li JZ, Brumme ZL, Brumme CJ, Wang H, Spritzler J, Robertson MN, Lederman MM, Carrington M, Walker BD, Schooley RT, Kuritzkes DR; AIDS Clinical Trials Group A5197 Study Team. J Infect Dis. 2011 Apr 1;203(7):976-83. doi: 10.1093/infdis/jiq143.

HIV infection increases HCV-induced hepatocyte apoptosis. Jang JY, Shao RX, Lin W, Weinberg E, Chung WJ, Tsai WL, Zhao H, Goto K, Zhang L, Mendez-Navarro J, Jilg N, Peng LF, Brockman MA, Chung RT. J Hepatol. 2011 Apr;54(4):612-20. doi: 10.1016/j.jhep.2010.07.042. Epub 2010 Sep 29.

Influence of Gag-protease-mediated replication capacity on disease progression in individuals recently infected with HIV-1 subtype C. Wright JK, Novitsky V, Brockman MA, Brumme ZL, Brumme CJ, Carlson JM, Heckerman D, Wang B, Losina E, Leshwedi M, van der Stok M, Maphumulo L, Mkhwanazi N, Chonco F, Goulder PJ, Essex M, Walker BD, Ndung'u T. J Virol. 2011 Apr;85(8):3996-4006. doi: 10.1128/JVI.02520-10. Epub 2011 Feb 2.

Reduced replication capacity of NL4-3 recombinant viruses encoding reverse transcriptase-integrase sequences from HIV-1 elite controllers. Brumme ZL, Li C, Miura T, Sela J, Rosato PC, Brumme CJ, Markle TJ, Martin E, Block BL, Trocha A, Kadie CM, Allen TM, Pereyra F, Heckerman D, Walker BD, Brockman MA. J Acquir Immune Defic Syndr. 2011 Feb 1;56(2):100-8. doi: 10.1097/QAI.0b013e3181fe9450.

In vitro selection of clinically relevant bevirimat resistance mutations revealed by "deep" sequencing of serially passaged, quasispecies-containing recombinant HIV-1. Knapp DJ, Harrigan PR, Poon AF, Brumme ZL, Brockman M, Cheung PK. J Clin Microbiol. 2011 Jan;49(1):201-8. doi: 10.1128/JCM.01868-10. Epub 2010 Nov 17.

HIV and HCV cooperatively promote hepatic fibrogenesis via induction of reactive oxygen species and NFkappaB. Lin W, Wu G, Li S, Weinberg EM, Kumthip K, Peng LF, Méndez-Navarro J, Chen WC, Jilg N, Zhao H, Goto K, Zhang L, Brockman MA, Schuppan D, Chung RT. J Biol Chem. 2011 Jan 28;286(4):2665-74. doi: 10.1074/jbc.M110.168286. Epub 2010 Nov 22.

Early selection in Gag by protective HLA alleles contributes to reduced HIV-1 replication capacity that may be largely compensated for in chronic infection. Brockman MA, Brumme ZL, Brumme CJ, Miura T, Sela J, Rosato PC, Kadie CM, Carlson JM, Markle TJ, Streeck H, Kelleher AD, Markowitz M, Jessen H, Rosenberg E, Altfeld M, Harrigan PR, Heckerman D, Walker BD, Allen TM. J Virol. 2010 Nov;84(22):11937-49. doi: 10.1128/JVI.01086-10. Epub 2010 Sep 1.

Gag-protease-mediated replication capacity in HIV-1 subtype C chronic infection: associations with HLA type and clinical parameters. Wright JK, Brumme ZL, Carlson JM, Heckerman D, Kadie CM, Brumme CJ, Wang B, Losina E, Miura T, Chonco F, van der Stok M, Mncube Z, Bishop K, Goulder PJ, Walker BD, Brockman MA, Ndung'u T. J Virol. 2010 Oct;84(20):10820-31. doi: 10.1128/JVI.01084-10. Epub 2010 Aug 11.

Efficacious early antiviral activity of HIV Gag- and Pol-specific HLA-B 2705-restricted CD8+ T cells. Payne RP, Kløverpris H, Sacha JB, Brumme Z, Brumme C, Buus S, Sims S, Hickling S, Riddell L, Chen F, Luzzi G, Edwards A, Phillips R, Prado JG, Goulder PJ. J Virol. 2010 Oct;84(20):10543-57. doi: 10.1128/JVI.00793-10. Epub 2010 Aug 4.

Impaired replication capacity of acute/early viruses in persons who become HIV controllers. Miura T, Brumme ZL, Brockman MA, Rosato P, Sela J, Brumme CJ, Pereyra F, Kaufmann DE, Trocha A, Block BL, Daar ES, Connick E, Jessen H, Kelleher AD, Rosenberg E, Markowitz M, Schafer K, Vaida F, Iwamoto A, Little S, Walker BD. J Virol. 2010 Aug;84(15):7581-91. doi: 10.1128/JVI.00286-10. Epub 2010 May 26.

Analysis of peripheral immune activation in schizophrenia using quantitative reverse-transcription polymerase chain reaction (RT-PCR). Freudenreich O, Brockman MA, Henderson DC, Evins AE, Fan X, Walsh JP, Goff DC. Psychiatry Res. 2010 Apr 30;176(2-3):99-102. doi: 10.1016/j.psychres.2008.11.007. Epub 2010 Feb 4.

Viral adaptation to immune selection pressure by HLA class I-restricted CTL responses targeting epitopes in HIV frameshift sequences. Berger CT, Carlson JM, Brumme CJ, Hartman KL, Brumme ZL, Henry LM, Rosato PC, Piechocka-Trocha A, Brockman MA, Harrigan PR, Heckerman D, Kaufmann DE, Brander C. J Exp Med. 2010 Jan 18;207(1):61-75. doi: 10.1084/jem.20091808. Epub 2010 Jan 11.

Phylogenetic analysis of population-based and deep sequencing data to identify coevolving sites in the nef gene of HIV-1. Poon AF, Swenson LC, Dong WW, Deng W, Kosakovsky Pond SL, Brumme ZL, Mullins JI, Richman DD, Harrigan PR, Frost SD. Mol Biol Evol. 2010 Apr;27(4):819-32. doi: 10.1093/molbev/msp289. Epub 2009 Dec 2.

HLA-associated immune escape pathways in HIV-1 subtype B Gag, Pol and Nef proteins. Brumme ZL, John M, Carlson JM, Brumme CJ, Chan D, Brockman MA, Swenson LC, Tao I, Szeto S, Rosato P, Sela J, Kadie CM, Frahm N, Brander C, Haas DW, Riddler SA, Haubrich R, Walker BD, Harrigan PR, Heckerman D, Mallal S. PLoS One. 2009 Aug 19;4(8):e6687. doi: 10.1371/journal.pone.0006687.

Unique features of HLA-mediated HIV evolution in a Mexican cohort: a comparative study. Avila-Rios S, Ormsby CE, Carlson JM, Valenzuela-Ponce H, Blanco-Heredia J, Garrido-Rodriguez D, Garcia-Morales C, Heckerman D, Brumme ZL, Mallal S, John M, Espinosa E, Reyes-Teran G. Retrovirology. 2009 Aug 10;6:72. doi: 10.1186/1742-4690-6-72.

Impact of select immunologic and virologic biomarkers on CD4 cell count decrease in patients with chronic HIV-1 subtype C infection: results from Sinikithemba Cohort, Durban, South Africa. Brumme Z, Wang B, Nair K, Brumme C, de Pierres C, Reddy S, Julg B, Moodley E, Thobakgale C, Lu Z, van der Stok M, Bishop K, Mncube Z, Chonco F, Yuki Y, Frahm N, Brander C, Carrington M, Freedberg K, Kiepiela P, Goulder P, Walker B, Ndung'u T, Losina E. Clin Infect Dis. 2009 Sep 15;49(6):956-64. doi: 10.1086/605503.

Maternal transmission of human immunodeficiency virus escape mutations subverts HLA-B57 immunodominance but facilitates viral control in the haploidentical infant. Schneidewind A, Tang Y, Brockman MA, Ryland EG, Dunkley-Thompson J, Steel-Duncan JC, St John MA, Conrad JA, Kalams SA, Noel F, Allen TM, Christie CD, Feeney ME. J Virol. 2009 Sep;83(17):8616-27. doi: 10.1128/JVI.00730-09. Epub 2009 Jun 10.

IL-10 is up-regulated in multiple cell types during viremic HIV infection and reversibly inhibits virus-specific T cells. Brockman MA, Kwon DS, Tighe DP, Pavlik DF, Rosato PC, Sela J, Porichis F, Le Gall S, Waring MT, Moss K, Jessen H, Pereyra F, Kavanagh DG, Walker BD, Kaufmann DE. Blood. 2009 Jul 9;114(2):346-56. doi: 10.1182/blood-2008-12-191296. Epub 2009 Apr 13.

Tracking the culprit: HIV-1 evolution and immune selection revealed by single-genome amplification. Brumme ZL, Walker BD. J Exp Med. 2009 Jun 8;206(6):1215-8. doi: 10.1084/jem.20091094. Epub 2009 Jun 1.

Adaptation of HIV-1 to human leukocyte antigen class I. Kawashima Y, Pfafferott K, Frater J, Matthews P, Payne R, Addo M, Gatanaga H, Fujiwara M, Hachiya A, Koizumi H, Kuse N, Oka S, Duda A, Prendergast A, Crawford H, Leslie A, Brumme Z, Brumme C, Allen T, Brander C, Kaslow R, Tang J, Hunter E, Allen S, Mulenga J, Branch S, Roach T, John M, Mallal S, Ogwu A, Shapiro R, Prado JG, Fidler S, Weber J, Pybus OG, Klenerman P, Ndung'u T, Phillips R, Heckerman D, Harrigan PR, Walker BD, Takiguchi M, Goulder P. Nature. 2009 Apr 2;458(7238):641-5. doi: 10.1038/nature07746. Epub 2009 Feb 25.

Differential neutralization of human immunodeficiency virus (HIV) replication in autologous CD4 T cells by HIV-specific cytotoxic T lymphocytes. Chen H, Piechocka-Trocha A, Miura T, Brockman MA, Julg BD, Baker BM, Rothchild AC, Block BL, Schneidewind A, Koibuchi T, Pereyra F, Allen TM, Walker BD. J Virol. 2009 Apr;83(7):3138-49. doi: 10.1128/JVI.02073-08. Epub 2009 Jan 21.

HLA-associated viral mutations are common in human immunodeficiency virus type 1 elite controllers. Miura T, Brumme CJ, Brockman MA, Brumme ZL, Pereyra F, Block BL, Trocha A, John M, Mallal S, Harrigan PR, Walker BD. J Virol. 2009 Apr;83(7):3407-12. doi: 10.1128/JVI.02459-08. Epub 2009 Jan 19.

HLA-B57/B*5801 human immunodeficiency virus type 1 elite controllers select for rare gag variants associated with reduced viral replication capacity and strong cytotoxic T-lymphocyte [corrected] recognition. Miura T, Brockman MA, Schneidewind A, Lobritz M, Pereyra F, Rathod A, Block BL, Brumme ZL, Brumme CJ, Baker B, Rothchild AC, Li B, Trocha A, Cutrell E, Frahm N, Brander C, Toth I, Arts EJ, Allen TM, Walker BD. J Virol. 2009 Mar;83(6):2743-55. doi: 10.1128/JVI.02265-08. Epub 2008 Dec 30.

Transmission and long-term stability of compensated CD8 escape mutations. Schneidewind A, Brumme ZL, Brumme CJ, Power KA, Reyor LL, O'Sullivan K, Gladden A, Hempel U, Kuntzen T, Wang YE, Oniangue-Ndza C, Jessen H, Markowitz M, Rosenberg ES, Sékaly RP, Kelleher AD, Walker BD, Allen TM. J Virol. 2009 Apr;83(8):3993-7. doi: 10.1128/JVI.01108-08. Epub 2008 Dec 17.

HLA-associated alterations in replication capacity of chimeric NL4-3 viruses carrying gag-protease from elite controllers of human immunodeficiency virus type 1. Miura T, Brockman MA, Brumme ZL, Brumme CJ, Pereyra F, Trocha A, Block BL, Schneidewind A, Allen TM, Heckerman D, Walker BD. J Virol. 2009 Jan;83(1):140-9. doi: 10.1128/JVI.01471-08. Epub 2008 Oct 29.