Research

The Gabuzda lab uses genetic, biochemical, metabolomic, computational, and systems biology approaches to study HIV pathogenesis. Major research interests are to understand viral, host, and environmental factors that determine clinical outcomes, therapeutic responses, and accelerated aging. Current projects focus on: 1) virus-host interactions during HIV replication and pathogenesis, and their impact on immune control, inflammation, metabolic disorders, therapeutic responses, and comorbidities; 2) mechanisms underlying HIV-associated neurological disorders and depression; 3) biomarkers predictive for development of neurocognitive disorders, metabolic abnormalities, accelerated aging, and age-related comorbidities; 4) role of host genetics in susceptibility and resilience to cognitive decline and accelerated aging; 5) cancer risk and etiologies in aging populations with HIV in the current ART era. The lab is proficient at bioinformatic, computational, and systems biology approaches including generation, analysis, interpretation, and visualization of large datasets, developing SQL databases, and using bioinformatic software and R programs for data integration, network prediction, pathway analysis, and modeling. We are also developing machine learning tools and other computational approaches to identify features in large datasets predictive of class or biological outcomes, model longitudinal trajectories, and discover latent class structure.

Molecular biology of HIV replication

The Gabuzda lab published research that provided key insights into the molecular biology and functional roles of the HIV envelope, Vif, and Nef proteins. Prior to 1992, it was known that HIV Vif is required for virus replication, but its mechanism of action was unclear. In 1992, the lab showed that Vif is required during late stages of infection, and that the requirement for Vif differs among cell lines, leading to classification of cell lines as nonpermissive and permissive for replication of Vif-deficient viruses and providing the first evidence that Vif acts through a cell-specific factor, now known to be APOBEC3G. In subsequent papers, we characterized other aspects of Vif biochemistry and biology, publishing papers on Vif including some of the first studies to elucidate the mechanisms by which Vif overcomes the antiviral activity of APOBEC3G by targeting it for degradation via the ubiquitin-proteasome pathway. These included studies characterizing a novel SOCS-box in Vif that targets APOBEC3G for proteasomal degradation. In 2015, we identified a novel small molecule inhibitor of Vif-APOBEC3G that protects APOBEC3G from Vif-mediated degradation using a high-throughput screening assay developed in the lab. In other work, we elucidated functions of the HIV envelope glycoproteins, providing new insights into Env interactions with CD4 and coreceptors and mechanisms mediating virus entry, Env-mediated fusion, tropism, cell-cell virus transmission, and viral cytopathicity. The lab also published studies that elucidated functions of HIV Nef, including novel interactions with cellular signaling pathways in resting T-cells and its association with host cell proteins that mediate cell-cell communication during virus replication.

Mehle A, Strack B, Ancuta P, Zhang C, McPike M and Gabuzda D.  Vif overcomes the innate antiviral activity of APOBEC3G by promoting its degradation in the ubiquitin-proteasome pathway.  J Biol Chem 2004; 279: 7792-7798. published online December 15, 2003; 10.1074/jbc.M313093200.

Mehle A, Goncalves J, Santa-Marta M, McPike M, Gabuzda D.  Phosphorylation of a novel SOCS-box regulates assembly of the HIV-1 Vif-Cul5 complex that promotes APOBEC3G degradation.  Genes Dev 2004;18:2861-66.

Mehle A, Thomas ER, Rajendran KS, Gabuzda D.  A zinc-binding region in Vif binds Cul5 and determines cullin selection.  J Biol Chem 2006;281:17259-65.

Pery E, Sheehy A, Nebane NM, Brazier AJ, Misra V, Rajendran KS, Buhrlage SJ, Mankowski MK, Rasmussen L, White EL, Ptak RG, Gabuzda D. Identification of a novel HIV-1 inhibitor targeting Vif-dependent degradation of human APOBEC3G protein. J Biol Chem 2015;290:10504-17.

 

Envelope-receptor interactions that determine HIV neurotropism

The lab has made contributions to understanding mechanisms of HIV neurotropism and virus entry into the CNS. Prior to 1986, it was known that HIV can cause dementia, but the mechanisms of HIV replication in the brain were unclear. In 1986, we published one of the first papers demonstrating that macrophages and microglia are the main cellular reservoirs of HIV in the brain. In 1997, we reported that CCR5 is the primary coreceptor used together with CD4 for HIV entry in the CNS and show that CCR5 ligands inhibit infection of microglia. The lab then demonstrated that most HIV strains isolated from brain use CCR5 as a coreceptor for virus entry, but CCR5 usage was not sufficient to account for neurotropism. These studies also demonstrated the association between the ability of HIV strains to replicate in macrophages and microglia, providing evidence that macrophage-tropism rather than CCR5 usage per se predict HIV neurotropism. The lab went on to show that neurovirulent primary HIV strains have reduced dependence on CCR5 and CD4 levels for virus entry, and such strains are frequently present in the brains of patients with virus replicating in brain and HIV-associated dementia, representing a pathogenic viral phenotype that contributes to neurodegeneration when viral replication is not suppressed. These findings provided fundamental insights into mechanisms of HIV entry in the CNS, and suggested that CCR5 inhibitors may be a useful therapeutic approach for HIV-associated neurological disease.

He J, Chen Y, Farzan M, Choe H, Öhagen A, Gartner S, Busciglio J, Yang X, Hofmann W, Newman W, MacKay C, Sodroski J, Gabuzda D.  CCR3 and CCR5 are co-receptors for HIV-1 infection of microglia.  Nature 1997;385:645-9.

Gorry P, Bristol G, Zack J, Ritola R, Swanstrom R, Birch C, Bell J, Bannert N, Crawford K, Wang H, Schols D, De Clercq E, Kunstman K, Wolinsky S, Gabuzda D.  Macrophage tropism of primary human immunodeficiency virus type 1 isolates from brain and lymphoid tissues predicts neurotropism independent of coreceptor specificity.  J Virol 2001;75:10073-89.

Gorry PR, Taylor J, Holm G, Mehle A, Morgan T, Cayabyab M, Farzan M, Wang H, Bell JE, Kunstman K, Moore JP, Wolinsky SM and Gabuzda D.  Increased CCR5 affinity and reduced CCR5/CD4 dependence of a neurovirulent primary human immunodeficiency virus type 1 isolate.  J Virol 2002;76:6277-92.

Dunfee RL, Thomas ER, Gorry PR, Wang J, Taylor J, Kunstman K, Wolinsky SM, and Gabuzda D.  The HIV Env variant N283 enhances macrophage tropism and is associated with brain infection and dementia.  Proc Natl Acad Sci USA 2006;103: 15160-5.

 

Monocytes/macrophages in HIV pathogenesis

The Gabuzda lab has made important contributions to understanding the role of activated monocytes and macrophages in disease pathogenesis. In addition to elucidating the role of macrophages and microglia as reservoirs for HIV replication in the brain, we published one of the first studies to characterize levels and regulation of CCR5 expression on primary human macrophages and microglia. Subsequently, we showed that the CD16+ subset of activated monocytes express the fractalkine receptor CX3CR1, and are preferentially recruited to endothelial cells in blood vessels via fractalkine (CX3CL1)-CX3CR1 interactions, providing insights into mechanisms involved in vascular and tissue injury during inflammatory conditions. In addition, we published the first studies demonstrating the ability of CD16+ monocytes and monocyte-derived macrophages to promote HIV infection of resting T cells. The lab was also the first to characterize the global transcriptome of CD16+ and CD16- monocyte subsets, providing novel insights into their developmental origin and distinct biological and pathological functions.

Wang J, Crawford K, Yuan M, Wang H, Gorry P and Gabuzda D.  Th2 cytokines regulate CCR5 and CD4 expression and HIV-1 replication in human macrophages and microglia.  J Infec Dis 2002;185:885-97.

Ancuta P, Rao R, Moses A, Mehle A, Shaw SK, Luscinskas FW, and Gabuzda D.  Fractalkine preferentially mediates arrest and migration of CD16+ monocytes.  J Exp Med 2003;197: 1701-07.

Ancuta P, Autissier P, Wurcel A, Zaman T, Stone D, Gabuzda D.  CD16+ monocyte-derived macrophages activate resting T-cells for HIV infection by producing CCR3 and CCR4 ligands.  J Immunol 2006;176:5760-71.

Ancuta P, Liu KY, Misra V, Wacleche VS, Gosselin A, Zhou X, and Gabuzda D. Transcriptional profiling reveals developmental relationship and distinct biological functions of CD16+ and CD16- monocyte subsets. BMC Genomics 2009;10:403.

NeuroAIDS pathogenesis and biomarkers

The Gabuzda lab has a long track record of contributions to understanding mechanisms of neuroAIDS pathogenesis. In addition to studies that provided fundamental insights into mechanisms of virus entry and replication in the brain described above, the lab identified several mechanisms by which unsuppressed viral replication in the brain promotes macrophage/microglia activation and neurodegeneration. In 1998 we published the first study demonstrating the association between microbial translocation and elevated LPS, monocyte activation, and increased risk of cognitive impairment in HIV patients with advanced disease. We then identified soluble CD14, a monocyte activation marker, as a biomarker associated with cognitive impairment in HIV patients with advanced disease and unsuppressed viral replication. We also identified biomarkers of ongoing intrathecal inflammation in HIV patients with viral suppression on ART. These studies elucidated mechanisms that contribute to cognitive impairment despite current therapies, and identified useful biomarkers that are now being used in several clinical studies of HIV-associated cognitive impairment.

Ancuta P, Kamat A, Kunstman KJ, Kim E, Autissier P, Wurcel A, Zaman T, Stone D, Mefford M, Morgello S, Singer EJ, Wolinsky SM, and Gabuzda D. Microbial translocation Is associated with increased monocyte activation and dementia in AIDS patients. PLoS ONE 2008; 3(6): 2516. doi:10.1371/journal.pone.0002516.

Lyons JL, Uno H, Ancuta P, Kamat A, Moore DJ, Singer EJ, Morgello S, and Gabuzda D. Plasma sCD14 is a biomarker associated with impaired neurocognitive test performance in attention and learning domains in HIV infection. J Acquir Immune Defic Syndr. 2011;57:371-79.

Kamat A, Lyons JL, Misra V, Uno H, Morgello S, Singer EJ, Gabuzda D. Monocyte activation markers in cerebrospinal fluid associated with impaired neurocognitive testing in advanced HIV infection. J Acquir Immune Defic Syndr. 2012;60:234-43.

Cassol E, Misra V, Morgello S, Gabuzda D. Applications and limitations of inflammatory biomarkers for studies on neurocognitive impairment in HIV infection. J Neuroimmune Pharmacol 2013; 8:1087-97.

 

Metabolomics of HIV-associated metabolic dysfunction, neurocognitive decline, aging, and depression

The Gabuzda lab has substantial expertise in various ‘omics technologies and recently used untargeted metabolomics to reveal novel insights into the pathogenesis of HIV and associated comorbidities at the systems level. In 2013, we published the first study to characterize the plasma metabolome of HIV patients on suppressive ART, identifying metabolite alterations indicative of dysregulated lipid metabolism and linking these alterations to markers of inflammation and hepatic dysfunction. The lab went on to characterize the CSF metabolome of HIV patients with neurocognitive impairment, demonstrating metabolite alterations indicative of glial inflammation, altered metabolic waste clearance, and accelerated aging. In 2015, we characterized the plasma metabolome associated with major depression in cohorts with and without HIV, demonstrating associations between interferon responses, tryptophan catabolism, and high depressive symptoms in HIV patients, and identifying a novel biomarker signature consisting of altered monoamines and acylcarnitine metabolites associated with depression in both HIV-negative and HIV-positive subjects.

Cassol E, Misra V, Holman A, Kamat A, Morgello S, Gabuzda D. Plasma metabolomics identifies lipid abnormalities linked to markers of inflammation, microbial translocation, and hepatic function in HIV patients receiving protease inhibitors. BMC Infectious Diseases 2013;13:203.

Cassol E, Misra V, Dutta A, Morgello S, Gabuzda D. Cerebrospinal fluid metabolomics reveals altered waste clearance and accelerated aging in HIV patients with neurocognitive impairment. AIDS 2014;28:1579-91.

Cassol E, Misra V, Morgello S, Kirk GD, Mehta SH, Gabuzda D. Altered monoamine and acylcarnitine metabolites in HIV-positive and HIV-negative subjects with depression. J Acquir Immune Defic Syndr 2015;69:18-28.

Gabuzda D and Yankner B. Inflammation links ageing to the brain. Nature (News & Views) 2013; 497(7448):197-8.

Coauthors within Dana-Farber Harvard Cancer Center (DF/HCC)

Coauthors within Harvard Medical School and affiliated hospitals