Retrospective Proteomic Analysis of Cellular Immune Responses and Protective Correlates of p24 Vaccination in an HIV Elite Controller Using Antibody Arrays

B, Monica MS, Thyago H. C. Incursions by severe acute respiratory syndrome coronavirus-2 on the host anti-viral immunity during mild, moderate, and severe coronavirus disease 2019 disease

The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection in the human host can lead to various clinical manifestations, from symptomless carriers to mild to moderate to severe/critical illness. Therefore, the clinical classification of SARS-CoV-2 disease, based on severity, is a reliable way to predict disease states in SARS-CoV-2 infection. Recent studies on genomics, transcriptomics, epigenomics, and immunogenomics, along with spatial analysis of immune cells have delineated and defined the categorization of these disease groups using these high throughout technologies. These technologies hold the promise of providing not only a detailed but a holistic view of SARS-CoV-2-led pathogenesis. The main genomic, cellular, and immunologic features of each disease category, and what separates them spatially and molecularly are discussed in this brief review to provide a foundational spatial understanding of SARS-CoV-2 immunopathogenesis.

Omic Technologies in HIV: Searching Transcriptional Signatures Involved in Long-Term Non-Progressor and HIV Controller Phenotypes

This article reviews the main discoveries achieved by transcriptomic approaches on HIV controller (HIC) and long-term non-progressor (LTNP) individuals, who are able to suppress HIV replication and maintain high CD4+ T cell levels, respectively, in the absence of antiretroviral therapy. Different studies using high throughput techniques have elucidated multifactorial causes implied in natural control of HIV infection. Genes related to IFN response, calcium metabolism, ribosome biogenesis, among others, are commonly differentially expressed in LTNP/HIC individuals. Additionally, pathways related with activation, survival, proliferation, apoptosis and inflammation, can be deregulated in these individuals. Likewise, recent transcriptomic studies include high-throughput sequencing in specific immune cell subpopulations, finding additional gene expression patterns associated to viral control and/or non-progression in immune cell subsets. Herein, we provide an overview of the main differentially expressed genes and biological routes commonly observed on immune cells involved in HIV infection from HIC and LTNP individuals, analyzing also different technical aspects that could affect the data analysis and the future perspectives and gaps to be addressed in this field.

Cell-Mediated Immune Predictors of Vaccine Effect on Viral Load and CD4 Count in a Phase 2 Therapeutic HIV-1 Vaccine Clinical Trial

Background

In a placebo-controlled trial of the peptide-based therapeutic HIV-1 p24^Gag vaccine candidate Vacc-4x, participants on combination antiretroviral therapy (cART) received six immunizations over 18 weeks, followed by analytical treatment interruption (ATI) between weeks 28 and 52. Cell-mediated immune responses were investigated as predictors of Vacc-4x effect (VE) on viral load (VL) and CD4 count during ATI.

Methods

All analyses of week 28 responses and fold-changes relative to baseline considered per-protocol participants (Vacc-4x:placebo = 72:32) resuming cART after week 40. Linear regression models with interaction tests were used. VE was estimated as the Vacc-4x–placebo difference in log₁₀-transformed VL (VE^VL) or CD4 count (VE^CD4).

Findings

A lower fold-change of CD4+ T-cell proliferation was associated with VE^CD4 at week 48 (p = 0.036, multiplicity adjusted q = 0.036) and week 52 (p = 0.040, q = 0.080). A higher fold-change of IFN-γ in proliferation supernatants was associated with VE^VL at week 44 (p = 0.047, q = 0.07). A higher fold-change of TNF-α was associated with VE^VL at week 44 (p = 0.045, q = 0.070), week 48 (p = 0.028, q = 0.070), and week 52 (p = 0.037, q = 0.074). A higher fold-change of IL-6 was associated with VE^VL at week 48 (p = 0.017, q = 0.036). TNF-α levels (> median) were associated with VE^CD4 at week 48 (p = 0.009, q = 0.009).

Interpretation

These exploratory analyses highlight the potential value of investigating biomarkers in T-cell proliferation supernatants for VE in clinical studies.

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Ex vivo CD4+ T-cell proliferation was predictive of Vacc-4x effect.

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IFN-γ, TNF-α and IL-6 secretion in T-cell proliferation supernatants were predictive of Vacc-4x effect.

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Such immune predictors could be utilized to mitigate risks associated with cART interruption towards HIV cure.

No immune correlates or predictors of therapeutic vaccine effect (i.e. a reduction in viral load compared to placebo on treatment interruption) for human immunodeficiency virus (HIV)-1 are known. We investigated a broad array of cytokines/chemokines produced in T-cell proliferation supernatants from a placebo-controlled clinical study of a therapeutic HIV vaccine. Although such supernatants do not provide cell type-specific readouts, the cytokines/chemokines studied included T-helper (Th)1, Th2, growth factor, immuno-modulatory and pro-inflammatory functions. Specifically, we found that, IFN-γ, TNF-α and IL-6 secretion correlated with vaccine effect, suggesting such supernatants could represent important sample material not previously considered for the identification of immune markers of vaccine effect.

Comparative proteomic analysis of rats subjected to water immersion and restraint stress as an insight into gastric ulcers

In the present study, comparative proteomic analysis was performed in rats subjected to water immersion-restraint stress (WRS). A total of 26 proteins were differentially expressed and identified using matrix-assisted laser desorption/ionization time of flight mass spectrometry. Among the 26 differentially expressed protein spots identified, 13 proteins were significantly upregulated under WRS, including pyruvate kinase and calreticulin, which may be closely associated with energy metabolism. In addition, 12 proteins were downregulated under WRS, including hemoglobin subunit β-2 and keratin type II cytoskeletal 8, which may be important in protein metabolism and cell death. Gene Ontology analysis revealed the cellular distribution, molecular function and biological processes of the identified proteins. The mRNA levels of certain differentially expressed proteins were analyzed using fluorescence quantitative polymerase chain reaction analysis. The results of the present study aimed to offer insights into proteins, which are differentially expressed in gastric ulcers in stress, and provide theoretical evidence of a radical cure for gastric ulcers in humans.