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Immune repertoire fingerprinting by principal component analysis reveals shared features in subject groups with common exposures.
Sevy AM, Soto C, Bombardi RG, Meiler J, Crowe JE
(2019) BMC Bioinformatics 20: 629
MeSH Terms: Adult, Antibodies, Cohort Studies, Fetal Blood, HIV Infections, High-Throughput Nucleotide Sequencing, Humans, Influenza, Human, Middle Aged, Principal Component Analysis, Vaccination
Show Abstract · Added March 21, 2020
BACKGROUND - Advances in next-generation sequencing (NGS) of antibody repertoires have led to an explosion in B cell receptor sequence data from donors with many different disease states. These data have the potential to detect patterns of immune response across populations. However, to this point it has been difficult to interpret such patterns of immune response between disease states in the absence of functional data. There is a need for a robust method that can be used to distinguish general patterns of immune responses at the antibody repertoire level.
RESULTS - We developed a method for reducing the complexity of antibody repertoire datasets using principal component analysis (PCA) and refer to our method as "repertoire fingerprinting." We reduce the high dimensional space of an antibody repertoire to just two principal components that explain the majority of variation in those repertoires. We show that repertoires from individuals with a common experience or disease state can be clustered by their repertoire fingerprints to identify common antibody responses.
CONCLUSIONS - Our repertoire fingerprinting method for distinguishing immune repertoires has implications for characterizing an individual disease state. Methods to distinguish disease states based on pattern recognition in the adaptive immune response could be used to develop biomarkers with diagnostic or prognostic utility in patient care. Extending our analysis to larger cohorts of patients in the future should permit us to define more precisely those characteristics of the immune response that result from natural infection or autoimmunity.
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Increased breadth of HIV-1 neutralization achieved by diverse antibody clones each with limited neutralization breadth.
Chukwuma VU, Kose N, Sather DN, Sapparapu G, Falk R, King H, Singh V, Lampley R, Malherbe DC, Ditto NT, Sullivan JT, Barnes T, Doranz BJ, Labranche CC, Montefiori DC, Kalams SA, Haigwood NL, Crowe JE
(2018) PLoS One 13: e0209437
MeSH Terms: Antibodies, Neutralizing, Antibody Diversity, B-Lymphocytes, Cells, Cultured, Epitope Mapping, Epitopes, HIV Antibodies, HIV Infections, HIV-1, Humans, Hybridomas, Neutralization Tests, env Gene Products, Human Immunodeficiency Virus
Show Abstract · Added March 31, 2019
Broadly neutralizing antibodies (bNAbs) are rarely elicited by current human immunodeficiency virus type 1 (HIV-1) vaccine designs, but the presence of bNAbs in naturally infected individuals may be associated with high plasma viral loads, suggesting that the magnitude, duration, and diversity of viral exposure may contribute to the development of bNAbs. Here, we report the isolation and characterization of a panel of human monoclonal antibodies (mAbs) from two subjects who developed broadly neutralizing autologous antibody responses during HIV-1 infection. In both subjects, we identified collections of mAbs that exhibited specificity only to a few autologous envelopes (Envs), with some mAbs exhibiting specificity only to a subset of Envs within the quasispecies of a particular sample at one time point. Neutralizing antibodies (NAbs) isolated from these subjects mapped mostly to epitopes in the Env V3 loop region and the CD4 binding site. None of the individual neutralizing mAbs recovered exhibited the cumulative breadth of neutralization present in the serum of the subjects. Surprisingly, however, the activity of polyclonal mixtures comprising individual mAbs that each possessed limited neutralizing activity, could achieve increased breadth of neutralizing activity against autologous isolates. While a single broadly neutralizing antibody targeting one epitope can mediate neutralization breadth, the findings presented here suggest that a cooperative polyclonal process mediated by diverse antibodies with more limited breadth targeting multiple epitopes also can achieve neutralization breadth against HIV-1.
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13 MeSH Terms
Machine learning selected smoking-associated DNA methylation signatures that predict HIV prognosis and mortality.
Zhang X, Hu Y, Aouizerat BE, Peng G, Marconi VC, Corley MJ, Hulgan T, Bryant KJ, Zhao H, Krystal JH, Justice AC, Xu K
(2018) Clin Epigenetics 10: 155
MeSH Terms: Adult, CpG Islands, DNA Methylation, Epigenesis, Genetic, Female, Frailty, Genome-Wide Association Study, HIV Infections, Humans, Machine Learning, Male, Middle Aged, Mortality, Prognosis, Signal Transduction, Smoking
Show Abstract · Added December 11, 2019
BACKGROUND - The effects of tobacco smoking on epigenome-wide methylation signatures in white blood cells (WBCs) collected from persons living with HIV may have important implications for their immune-related outcomes, including frailty and mortality. The application of a machine learning approach to the analysis of CpG methylation in the epigenome enables the selection of phenotypically relevant features from high-dimensional data. Using this approach, we now report that a set of smoking-associated DNA-methylated CpGs predicts HIV prognosis and mortality in an HIV-positive veteran population.
RESULTS - We first identified 137 epigenome-wide significant CpGs for smoking in WBCs from 1137 HIV-positive individuals (p < 1.70E-07). To examine whether smoking-associated CpGs were predictive of HIV frailty and mortality, we applied ensemble-based machine learning to build a model in a training sample employing 408,583 CpGs. A set of 698 CpGs was selected and predictive of high HIV frailty in a testing sample [(area under curve (AUC) = 0.73, 95%CI 0.63~0.83)] and was replicated in an independent sample [(AUC = 0.78, 95%CI 0.73~0.83)]. We further found an association of a DNA methylation index constructed from the 698 CpGs that were associated with a 5-year survival rate [HR = 1.46; 95%CI 1.06~2.02, p = 0.02]. Interestingly, the 698 CpGs located on 445 genes were enriched on the integrin signaling pathway (p = 9.55E-05, false discovery rate = 0.036), which is responsible for the regulation of the cell cycle, differentiation, and adhesion.
CONCLUSION - We demonstrated that smoking-associated DNA methylation features in white blood cells predict HIV infection-related clinical outcomes in a population living with HIV.
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Peripheral Blood Mitochondrial DNA Copy Number Obtained From Genome-Wide Genotype Data Is Associated With Neurocognitive Impairment in Persons With Chronic HIV Infection.
Hulgan T, Kallianpur AR, Guo Y, Barnholtz-Sloan JS, Gittleman H, Brown TT, Ellis R, Letendre S, Heaton RK, Samuels DC, CHARTER Study
(2019) J Acquir Immune Defic Syndr 80: e95-e102
MeSH Terms: AIDS Dementia Complex, Adult, Anti-Retroviral Agents, DNA Copy Number Variations, DNA, Mitochondrial, Female, Genome-Wide Association Study, Genotype, HIV Infections, Humans, Male, Middle Aged, Mitochondria, Neurocognitive Disorders, Neuropsychological Tests
Show Abstract · Added December 11, 2019
BACKGROUND - Mitochondrial DNA (mtDNA) copy number varies by cell type and energy demands. Blood mtDNA copy number has been associated with neurocognitive function in persons without HIV. Low mtDNA copy number may indicate disordered mtDNA replication; high copy number may reflect a response to mitochondrial dysfunction. We hypothesized that blood mtDNA copy number estimated from genome-wide genotyping data is related to neurocognitive impairment (NCI) in persons with HIV.
METHODS - In the CNS HIV Antiretroviral Therapy Effects Research (CHARTER) study, peripheral blood mtDNA copy number was obtained from genome-wide genotyping data as a ratio of mtDNA single-nucleotide polymorphism probe intensities relative to nuclear DNA single-nucleotide polymorphisms. In a multivariable regression model, associations between mtDNA copy number and demographics, blood cell counts, and HIV disease and treatment characteristics were tested. Associations of mtDNA copy number with the global deficit score (GDS), GDS-defined NCI (GDS ≥ 0.5), and HIV-associated neurocognitive disorder (HAND) diagnosis were tested by logistic regression, adjusting for potential confounders.
RESULTS - Among 1010 CHARTER participants, lower mtDNA copy number was associated with longer antiretroviral therapy duration (P < 0.001), but not with d-drug exposure (P = 0.85). mtDNA copy number was also associated with GDS (P = 0.007), GDS-defined NCI (P < 0.001), and HAND (P = 0.002). In all analyses, higher mtDNA copy number was associated with poorer cognitive performance.
CONCLUSIONS - Higher mtDNA copy number estimated from peripheral blood genotyping was associated with worse neurocognitive performance in adults with HIV. These results suggest a connection between peripheral blood mtDNA and NCI, and may represent increased mtDNA replication in response to mitochondrial dysfunction.
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15 MeSH Terms
Relationships Between Adipose Mitochondrial Function, Serum Adiponectin, and Insulin Resistance in Persons With HIV After 96 Weeks of Antiretroviral Therapy.
Hulgan T, Ramsey BS, Koethe JR, Samuels DC, Gerschenson M, Libutti DE, Sax PE, Daar ES, McComsey GA, Brown TT
(2019) J Acquir Immune Defic Syndr 80: 358-366
MeSH Terms: Adiponectin, Adipose Tissue, Adult, DNA, Female, HIV Infections, HIV-1, Homeostasis, Humans, Insulin Resistance, Male, Middle Aged, Mitochondria, Obesity, RNA, Viral, Retrospective Studies, Viral Load
Show Abstract · Added December 11, 2019
OBJECTIVE - Some antiretroviral therapy (ART) and HIV itself confer metabolic risk, perhaps through altered mitochondrial function and adipokines. In AIDS Clinical Trials Group study A5224s, adipose mitochondrial DNA (mtDNA) levels decreased on ART, and electron transport chain complex I (CI) and complex IV (CIV) activity decreased. Another study found decreased serum adiponectin on ART with mtDNA mutation m.10398A>G. We hypothesized that decreased adipose tissue mitochondrial function would be associated with lower adiponectin and insulin sensitivity on ART, and m.10398G would influence these changes.
DESIGN - Retrospective analysis of an ART-naive substudy population from A5224s.
METHODS - Analyses included adipose mtDNA levels, CI and CIV activity by immunoassay, visceral adipose tissue by computed tomography, and fasting serum glucose at week 0 and week 96 of ART. Fasting insulin and adiponectin were measured from cryopreserved serum using multiplex bead array. Homeostasis model assessment-2 (HOMA2)-IR and HOMA2-%B estimated insulin resistance and β-cell function, respectively. The m.10398A>G mtDNA variant was available from existing genetic data.
RESULTS - Thirty-seven participants had adipose biopsies at week 0 and week 96. Percent decreases in CIV activity and adiponectin were correlated (Spearman rho 0.41; P = 0.01); this association persisted after controlling for age, sex, body mass index, or visceral adipose tissue in single-covariate regression. HOMA2-IR correlated with decreased CIV (-0.44; P = 0.01) and CI (-0.34; P = 0.05) activity. Among 12 non-Hispanic white persons, m.10398G was associated with decreased adiponectin (P = 0.04).
CONCLUSIONS - Decreased adipose mitochondrial activity correlated with changes in adiponectin and glucose homeostasis on ART. Previous findings that a mtDNA mutation modulates adiponectin levels in persons with HIV were replicated.
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Precision HIV care: responding to old questions and meeting new challenges.
Hulgan T, Dash C, Haas DW, Phillips EJ
(2018) Pharmacogenomics 19: 1299-1302
MeSH Terms: AIDS Vaccines, Anti-Retroviral Agents, HIV, HIV Infections, Humans, Pharmacogenetics, Precision Medicine
Added December 11, 2019
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Cerebrospinal Fluid Ceruloplasmin, Haptoglobin, and Vascular Endothelial Growth Factor Are Associated with Neurocognitive Impairment in Adults with HIV Infection.
Kallianpur AR, Gittleman H, Letendre S, Ellis R, Barnholtz-Sloan JS, Bush WS, Heaton R, Samuels DC, Franklin DR, Rosario-Cookson D, Clifford DB, Collier AC, Gelman B, Marra CM, McArthur JC, McCutchan JA, Morgello S, Grant I, Simpson D, Connor JR, Hulgan T, CHARTER Study Group
(2019) Mol Neurobiol 56: 3808-3818
MeSH Terms: Adult, Antiretroviral Therapy, Highly Active, Biomarkers, Ceruloplasmin, Comorbidity, Female, HIV Infections, Haptoglobins, Humans, Inflammation, Iron, Male, Multivariate Analysis, Neurocognitive Disorders, Regression Analysis, Vascular Endothelial Growth Factor A
Show Abstract · Added December 11, 2019
Dysregulated iron transport and a compromised blood-brain barrier are implicated in HIV-associated neurocognitive disorders (HAND). We quantified the levels of proteins involved in iron transport and/or angiogenesis-ceruloplasmin, haptoglobin, and vascular endothelial growth factor (VEGF)-as well as biomarkers of neuroinflammation, in cerebrospinal fluid (CSF) from 405 individuals with HIV infection and comprehensive neuropsychiatric assessments. Associations with HAND [defined by a Global Deficit Score (GDS) ≥ 0.5, GDS as a continuous measure (cGDS), or by Frascati criteria] were evaluated for the highest versus lowest tertile of each biomarker, adjusting for potential confounders. Higher CSF VEGF was associated with GDS-defined impairment [odds ratio (OR) 2.17, p = 0.006] and cGDS in unadjusted analyses and remained associated with GDS impairment after adjustment (p = 0.018). GDS impairment was also associated with higher CSF ceruloplasmin (p = 0.047) and with higher ceruloplasmin and haptoglobin in persons with minimal comorbidities (ORs 2.37 and 2.13, respectively; both p = 0.043). In persons with minimal comorbidities, higher ceruloplasmin and haptoglobin were associated with HAND by Frascati criteria (both p < 0.05), and higher ceruloplasmin predicted worse impairment (higher cGDS values, p < 0.01). In the subgroup with undetectable viral load and minimal comorbidity, CSF ceruloplasmin and haptoglobin were strongly associated with GDS impairment (ORs 5.57 and 2.96, respectively; both p < 0.01) and HAND (both p < 0.01). Concurrently measured CSF IL-6 and TNF-α were only weakly correlated to these three biomarkers. Higher CSF ceruloplasmin, haptoglobin, and VEGF are associated with a significantly greater likelihood of HAND, suggesting that interventions aimed at disordered iron transport and angiogenesis may be beneficial in this disorder.
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Nuclear-Mitochondrial interactions influence susceptibility to HIV-associated neurocognitive impairment.
Smieszek S, Jia P, Samuels DC, Zhao Z, Barnholtz-Sloan J, Kaur H, Letendre S, Ellis R, Franklin DR, Hulgan T, Kallianpur A, Bush WS, CHARTER Study Group
(2019) Mitochondrion 46: 247-255
MeSH Terms: AIDS Dementia Complex, Cell Nucleus, Continental Population Groups, Genetic Association Studies, HIV Infections, Haplotypes, Humans, Mitochondria, Mitochondrial Proteins, Nuclear Proteins, Polymorphism, Single Nucleotide, Prospective Studies
Show Abstract · Added December 11, 2019
HIV-associated neurocognitive impairment (NCI) is a term established to capture a wide spectrum of HIV related neurocognitive deficits ranging in severity from asymptomatic to dementia. The genetic underpinnings of this complex phenotype are incompletely understood. Mitochondrial function has long been thought to play a role in neurodegeneration, along with iron metabolism and transport. In this work, we aimed to characterize the interplay of mitochondrial DNA (mtDNA) haplogroup and nuclear genetic associations to NCI phenotypes in the CHARTER cohort, encompassing 1025 individuals of European-descent, African-descent, or admixed Hispanic. We first employed a polygenic modeling approach to investigate the global effect of previous marginally associated nuclear SNPs, and to examine how the polygenic effect of these SNPs is influenced by mtDNA haplogroups. We see evidence of a significant interaction between nuclear SNPs en masse and mtDNA haplogroups within European-descent and African-descent individuals. Subsequently, we performed an analysis of each SNP by mtDNA haplogroup, and detected significant interactions between two nuclear SNPs (rs17160128 and rs12460243) and European haplogroups. These findings, which require validation in larger cohorts, indicate a potential new role for nuclear-mitochondrial DNA interactions in susceptibility to NCI and shed light onto the pathophysiology of this neurocognitive phenotype.
Copyright © 2018 The Authors. Published by Elsevier B.V. All rights reserved.
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Hemochromatosis (HFE) Gene Variants Are Associated with Increased Mitochondrial DNA Levels During HIV-1 Infection and Antiretroviral Therapy.
Kallianpur AR, Gerschenson M, Hulgan T, Kaur H, Clifford DB, Haas DW, Murdock DG, McArthur JC, Samuels DC, Simpson DM
(2018) AIDS Res Hum Retroviruses 34: 942-949
MeSH Terms: Adult, Alleles, Anti-HIV Agents, CD4 Lymphocyte Count, Case-Control Studies, DNA Copy Number Variations, DNA, Mitochondrial, Female, Genotype, HIV Infections, HIV-1, Hemochromatosis Protein, Humans, Leukocytes, Mononuclear, Male, Middle Aged, Mitochondria, RNA, Viral
Show Abstract · Added December 11, 2019
Some HIV-associated complications involve mitochondrial dysfunction and may be less common in individuals with iron-loading HFE (hemochromatosis gene) variants. We evaluated HFE 845A and 187G alleles in relation to mitochondrial DNA (mtDNA) levels in peripheral blood mononuclear cells from 85 individuals with HIV infection on uninterrupted antiretroviral therapy (ART) for 15 or more consecutive weeks. Carriers of HFE gene variants (N = 24) had significantly higher mtDNA levels than noncarriers (N = 61), after adjusting for age, race, sex, and type of ART [adjusted β-coefficient 297, p-value < .001 for at least one HFE variant], but mtDNA declined among all individuals on study during 48 weeks on ART. Increased cellular mtDNA content may represent a compensatory response to mitochondrial stress that is influenced by iron-loading HFE variants.
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Brief Report: Circulating Markers of Immunologic Activity Reflect Adiposity in Persons With HIV on Antiretroviral Therapy.
Koethe JR, Jenkins CA, Furch BD, Lake JE, Barnett L, Hager CC, Smith R, Hulgan T, Shepherd BE, Kalams SA
(2018) J Acquir Immune Defic Syndr 79: 135-140
MeSH Terms: Absorptiometry, Photon, Adiposity, Adult, Anti-HIV Agents, Biomarkers, CD4 Lymphocyte Count, Female, HIV Infections, Humans, Male, Middle Aged
Show Abstract · Added December 11, 2019
BACKGROUND - Obesity alters adipose tissue immunology, and these changes may be reflected in circulating soluble inflammatory biomarker and T-cell subset profiles measured in HIV research studies.
METHODS - We recruited 70 adults with HIV (50% obese) on efavirenz, tenofovir, and emtricitabine, virologic suppression for >2 years, and no rheumatologic or other known inflammatory conditions. We measured fasting plasma levels of several markers of innate immunity and major CD4 and CD8 T-cell subsets. We assessed relationships between measurements of total adiposity [body mass index (BMI), dual-energy X-ray absorptiometry-quantified fat mass index (FMI), and plasma leptin] and the immunologic parameters using covariate-adjusted Spearman's rank correlations.
RESULTS - The cohort was 43% women, 54% nonwhite, and median age was 45 years. Higher BMI, FMI, and plasma leptin were consistently associated with higher C-reactive protein, serum amyloid A, and interleukin-6 (P < 0.01 for all), but lower interleukin-10 (P ≤ 0.02 for all). BMI and FMI were positively associated with soluble tumor necrosis factor-α receptor 1 levels (P ≤ 0.02 for both), and a positive correlation approached significance for all 3 body composition measurements with soluble CD163 (P ≤ 0.09 for all). Higher BMI and FMI were associated with lower CD38 expression on CD4 T cells (P ≤ 0.04 for both), but higher CD69 expression (P ≤ 0.01 for BMI and FMI, P = 0.07 for leptin).
CONCLUSIONS - Greater adiposity is associated with alterations in a limited set of circulating immune markers, potentially reflecting changes known to occur in adipose tissue with treated HIV infection. Measuring total fat mass radiographically did not yield substantively different results compared with BMI.
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