Biomarkers of HIV-1-associated neurocognitive disorders: challenges of proteomic approaches

Proteomics, biomarkers, and HIV-1: A current perspective

Despite more than three decades of extensive research, HIV‐1 infection although well controlled with cART, remains incurable. Multifactorial complexity of the viral life‐cycle poses great challenges in understanding molecular mechanisms underlying this infection and the development of biomarkers, which we hope will lead us to its eradication. For a more in‐depth understanding of how the virus interacts with host target cells, T cells and macrophages, proteomic profiling techniques that offer strategies to investigate the proteome in its entirety were employed. Here, we review proteomic studies related to HIV‐1 infection and discuss perspectives and limitations of proteomic and systems biology approaches in future studies.

Reduced neural specificity in middle-aged HIV+ women in the absence of behavioral deficits

In the post combination antiretroviral therapy (cART) era, the prevalence of mild forms of HIV-associated neurocognitive disorders (HAND) in individuals with HIV-infection remains high. There is a pressing need to find biomarkers that can aid clinical assessment of HAND, especially in those with mild or no neurocognitive symptoms. Here we hypothesized that a reduction in neural specificity, or the specificity of neuronal tuning, could serve as a potential biomarker of asymptomatic HAND. To directly test this hypothesis, we applied two advanced fMRI techniques to examine the difference in neural specificity between middle-aged HIV+ women and age-matched negative controls, with a focus on the fusiform face area (FFA), a critical region in face processing. Face discrimination performance was assessed outside of the scanner. While the behavioral performance of face discrimination was comparable between the two groups, a reduced neural specificity in the FFA of HIV-positive women was revealed by a novel fMRI analysis technique, local regional heterogeneity analysis, or H_corr, as well as an established technique, fMRI-rapid adaptation. In contrast, conventional fMRI techniques were insensitive to these early changes. These results suggest that, prior to the onset of detectable behavioral deficits, significant neuronal dysfunctions are already present in HIV+ individuals, and these early neuronal dysfunctions can be detected and assessed via neural specificity, which, in combining with the novel H_corr technique, has a strong potential to serve as a biomarker of asymptomatic HAND and other neurodegenerative diseases.

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We investigate early neuronal dysfunctions in cognitively normal HIV+ women.

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Conventional fMRI technique reveals normal neural activity in the FFA of HIV+ women.

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fMRI-adaptation reveals a decrease in neural specificity in the FFA of HIV+ women.

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H_corr, a novel fMRI technique, confirms the fMRI-adaptation results

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H_corr-estimated neural specificity might serve as a biomarker of asymptomatic HAND

Changes in PINCH levels in the CSF of HIV+ individuals correlate with hpTau and CD4 count

Several studies report associations between the particularly interesting new cysteine histidine-rich (PINCH) protein and HIV-associated CNS disease. PINCH is detected in the CSF of HIV patients, and changes in levels during disease may be indicative of changes in disease status over time. PINCH binds hyperphosphorylated Tau (hpTau) in the brain and CSF, but little is known about the relevance of these interactions to HIV CNS disease. In this study, PINCH and hpTau levels were assessed in three separate CSF samples collected longitudinally from 20 HIV+ participants before and after initiating antiretroviral therapy or before and after a change in the treatment regimen. The intervals were approximately 1 (T2) and 3-7 (T3) months from the initial visit (baseline, T1). Correlational analyses were conducted for CSF levels of PINCH and hpTau and other variables including blood CD4 T-cell count, plasma and CSF viral burden, CSF neopterin, white blood cell (WBC) count, and antiretroviral CNS penetration effectiveness (CPE). Values for PINCH and hpTau were determined for each patient by calculating the fold changes between the second (T2) and third measurements (T3) from the baseline measurement (T1). Statistical analyses showed that the fold changes in CSF PINCH protein from T1 to T2 were significantly higher in participants with CD4 counts >200 cells/mm(3) at T2 compared to those with CD4 counts <200 cells/mm(3) at T2. This trend persisted irrespective of plasma or CSF viral burden or antiretroviral therapy CPE scores. The fold changes in PINCH levels between T1 and T2, and T1 and T3 were highly correlated to the fold changes in hpTau at T2/T1 and T3/T1 (correlation coefficient = 0.69, p < 0.001; correlation coefficient = 0.83, p < 0.0001, respectively). In conclusion, in these HIV participants, changes in CSF levels of PINCH appear to correlate with changes in blood CD4 count and with changes in CSF hpTau levels, but not with plasma or CSF viral burden, neopterin, WBC, or antiretroviral regimen CPE.

Comparison of 4-plex to 8-plex iTRAQ quantitative measurements of proteins in human plasma samples

Methods for isobaric tagging of peptides, iTRAQ or TMT, are commonly used platforms in mass spectrometry based quantitative proteomics. These two methods are very often used to quantitate proteins in complex samples, e.g., serum/plasma or CSF supporting biomarker discovery studies. The success of these studies depends on multiple factors, including the accuracy of ratios of reporter ions reflecting quantitative changes of proteins. Because reporter ions are generated during peptide fragmentation, the differences of chemical structure of iTRAQ balance groups may have an effect on how efficiently these groups are fragmented and thus how differences in protein expression will be measured. Because 4-plex and 8-plex iTRAQ reagents do have different structures of balanced groups, it has been postulated that indeed differences in protein identification and quantitation exist between these two reagents. In this study we controlled the ratios of tagged samples and compared quantitation of proteins using 4-plex versus 8-plex reagents in the context of a highly complex sample of human plasma using ABSciex 4800 MALDI-TOF/TOF mass spectrometer and ProteinPilot 4.0 software. We observed that 8-plex tagging provides more consistent ratios than 4-plex without compromising protein identification, thus allowing investigation of eight experimental conditions in one analytical experiment.

Plasma proteomic profiling in HIV-1 infected methamphetamine abusers

We wanted to determine whether methamphetamine use affects a subset of plasma proteins in HIV-infected persons. Plasma samples from two visits were identified for subjects from four groups: HIV+, ongoing, persistent METH use; HIV+, short-term METH abstinent; HIV+, long term METH abstinence; HIV negative, no history of METH use. Among 390 proteins identified, 28 showed significant changes in expression in the HIV+/persistent METH+ group over the two visits, which were not attributable to HIV itself. These proteins were involved in complement, coagulation pathways and oxidative stress. Continuous METH use is an unstable condition, altering levels of a number of plasma proteins.

Plasma proteomic analysis of simian immunodeficiency virus infection of rhesus macaques

Lentiviral replication in its target cells affects a delicate balance between cellular cofactors required for virus propagation and immunoregulation for host defense. To better elucidate cellular proteins linked to viral infection, we tested plasma from rhesus macaques infected with the simian immunodeficiency viral strain SIVsmm9, prior to, 10 days (acute), and 49 weeks (chronic) after viral infection. Changes in plasma protein content were measured by quantitative mass spectrometry by isobaric tags for absolute and relative quantitation (iTRAQ) methods. An 81 and 232% increase in SERPINA1 was seen during acute and chronic infection, respectively. Interestingly, gelsolin, vitamin D binding protein and histidine rich glycoprotein were decreased by 45% in acute conditions but returned to baseline during chronic infection. When compared to uninfected controls, a 48-103% increase in leucine rich alpha 2-glycoprotein, vitronectin, and ceruloplasmin was observed during chronic viral infection. Observed changes in plasma proteins expression likely represent a compensatory host response to persistent viral infection.

Immunoreactivity of anti-gelsolin antibodies: implications for biomarker validation

Background

Proteomic-based discovery of biomarkers for disease has recently come under scrutiny for a variety of issues; one prominent issue is the lack of orthogonal validation for biomarkers following discovery. Validation by ELISA or Western blot requires the use of antibodies, which for many potential biomarkers are under-characterized and may lead to misleading or inconclusive results. Gelsolin is one such biomarker candidate in HIV-associated neurocognitive disorders.

Methods

Samples from human (plasma and CSF), monkey (plasma), monocyte-derived macrophage (supernatants), and commercial gelsolin (recombinant and purified) were quantitated using Western blot assay and a variety of anti-gelsolin antibodies. Plasma and CSF was used for immunoaffinity purification of gelsolin which was identified in eight bands by tandem mass spectrometry.

Results

Immunoreactivity of gelsolin within samples and between antibodies varied greatly. In several instances, multiple bands were identified (corresponding to different gelsolin forms) by one antibody, but not identified by another. Moreover, in some instances immunoreactivity depended on the source of gelsolin, e.g. plasma or CSF. Additionally, some smaller forms of gelsolin were identified by mass spectrometry but not by any antibody. Recombinant gelsolin was used as reference sample.

Conclusions

Orthogonal validation using specific monoclonal or polyclonal antibodies may reject biomarker candidates from further studies based on misleading or even false quantitation of those proteins, which circulate in various forms in body fluids.