Cyclone: an accessible pipeline to analyze, evaluate, and optimize multiparametric cytometry data

In the past decade, high-dimensional single-cell technologies have revolutionized basic and translational immunology research and are now a key element of the toolbox used by scientists to study the immune system. However, analysis of the data generated by these approaches often requires clustering algorithms and dimensionality reduction representation, which are computationally intense and difficult to evaluate and optimize. Here, we present Cytometry Clustering Optimization and Evaluation (Cyclone), an analysis pipeline integrating dimensionality reduction, clustering, evaluation, and optimization of clustering resolution, and downstream visualization tools facilitating the analysis of a wide range of cytometry data. We benchmarked and validated Cyclone on mass cytometry (CyTOF), full-spectrum fluorescence-based cytometry, and multiplexed immunofluorescence (IF) in a variety of biological contexts, including infectious diseases and cancer. In each instance, Cyclone not only recapitulates gold standard immune cell identification but also enables the unsupervised identification of lymphocytes and mononuclear phagocyte subsets that are associated with distinct biological features. Altogether, the Cyclone pipeline is a versatile and accessible pipeline for performing, optimizing, and evaluating clustering on a variety of cytometry datasets, which will further power immunology research and provide a scaffold for biological discovery.

Cyclone: an accessible pipeline to analyze, evaluate and optimize multiparametric cytometry data

In the past decade, high-dimensional single cell technologies have revolutionized basic and translational immunology research and are now a key element of the toolbox used by scientists to study the immune system. However, analysis of the data generated by these approaches often requires clustering algorithms and dimensionality reduction representation which are computationally intense and difficult to evaluate and optimize. Here we present Cyclone, an analysis pipeline integrating dimensionality reduction, clustering, evaluation and optimization of clustering resolution, and downstream visualization tools facilitating the analysis of a wide range of cytometry data. We benchmarked and validated Cyclone on mass cytometry (CyTOF), full spectrum fluorescence-based cytometry, and multiplexed immunofluorescence (IF) in a variety of biological contexts, including infectious diseases and cancer. In each instance, Cyclone not only recapitulates gold standard immune cell identification, but also enables the unsupervised identification of lymphocytes and mononuclear phagocytes subsets that are associated with distinct biological features. Altogether, the Cyclone pipeline is a versatile and accessible pipeline for performing, optimizing, and evaluating clustering on variety of cytometry datasets which will further power immunology research and provide a scaffold for biological discovery.

An OX40/OX40L interaction directs successful immunity to hepatitis B virus

Depending on age of acquisition, hepatitis B virus (HBV) can induce a cell-mediated immune response that results in either cure or progressive liver injury. In adult-acquired infection, HBV antigens are usually cleared, whereas in infancy-acquired infection, they persist. Individuals infected during infancy therefore represent the majority of patients chronically infected with HBV (CHB). A therapy that can promote viral antigen clearance in most CHB patients has not been developed and would represent a major health care advance and cost mitigator. Using an age-dependent mouse model of HBV clearance and persistence in conjunction with human blood and liver tissue, we studied mechanisms of viral clearance to identify new therapeutic targets. We demonstrate that age-dependent expression of the costimulatory molecule OX40 ligand (OX40L) by hepatic innate immune cells is pivotal in determining HBV immunity, and that treatment with OX40 agonists leads to improved HBV antigen clearance in young mice, as well as increased strength of T cell responses in young mice and adult mice that were exposed to HBV when they were young and developed a CHB serological profile. Similarly, in humans, we show that hepatic OX40L transcript expression is age-dependent and that increased OX40 expression on peripheral CD4⁺ T cells in adults is associated with HBV clearance. These findings provide new mechanistic understanding of the immune pathways and cells necessary for HBV immunity and identify potential therapeutic targets for resolving CHB.

[RESTORATION OF SYMPATHO-PARASYMPATHETIC BALANCE IN HEART RATE VARIABILITY IN THE DEVELOPMENT OF PSYCHOEMOTIONAL STRESS AGAINST THE BACKGROUND OF TAURINE IN EXPERIMENT]

In this fragment of the study, the change in the ratio of low (LF) and high frequency (HF) waves to the heart rhythmogram during prolonged immobilization (5 hours) of sexually mature white non-linear rats was studied by spectral analysis of heart rate variability, which causes psychoemotional stress and the accompanying vegetative equilibrium shift, indicating on the dysregulation of the sympatho-parasympathetic balance without and against the background of daily intraperitoneal injection of taurine (50 mg/kg) and its participation in the mechanisms of adaptive processes in the early poststress period (from 1 to 14 days). Spectral analysis of both absolute and relative indices of the I-th group (stress without taurine) revealed significant shifts in the frequency spectrum. On the first day after immobilization, the total power of the spectrum decreased by 4.3%, the HF component by 33.3%, and the level of VLF and LF-components increased by 25.5% and 25%, respectively, compared to the norm. On the 14th day after the immobilization, there is a decrease in tension, but the LF component is still above the norm by 5%. Calculations of the percentage ratios of the absolute values of the spectrum at different times of the post-stress period against the background of taurine injection showed that in the initial stage (immediately and on the first day after stress) a strong shift of activity toward sympathization occurs, and the absolute value of LF and VLF in the spectrum increased by 23,1% and 10.9% respectively. However, the complete restoration of the vago-sympathetic balance with the daily application of taurine occurs already on the 7th day after immobilization. The beneficial effect of taurine on the cardiovascular system was revealed when examining the scatterogram of the regression dependence of the heart rate, which revealed a smaller variation in heart rate and its stabilization on the 7th day after immobilization. Thus, the use of taurine immediately after stressful reactions is necessary to accelerate adaptive processes in the early post-stress period to prevent the development of stress pathology.

Cytotoxic mechanisms employed by mouse T cells to destroy pancreatic β-cells

Several cytotoxic mechanisms have been attributed to T cells participating in β-cell death in type 1 diabetes. However, sensitivity of β-cells to these mechanisms in vitro and in vivo is likely to be different. Moreover, CD4⁺ and CD8⁺ T cells may use distinct mechanisms to cause β-cell demise that possibly involve activation of third-party cytotoxic cells. We used the transfer of genetically modified diabetogenic T cells into normal, mutant, and bone marrow chimeric recipients to test the contribution of major cytotoxic mechanisms in β-cell death. We found that 1) the killing of β-cells by CD4⁺ T cells required activation of the recipient's own cytotoxic cells via tumor necrosis factor-α (TNF-α); 2) CD8⁺ T-cell cytotoxic mechanisms destroying β-cells were limited to perforin and Fas ligand, as double knockouts of these molecules abrogated the ability of T cells to cause diabetes; and 3) individual CD8⁺ T-cell clones chose their cytotoxic weaponry by a yet unknown mechanism and destroyed their targets via either Fas-independent or Fas-dependent (~40% of clones) pathways. Fas-dependent destruction was assisted by TNF-α.

IL-21 is pivotal in determining age-dependent effectiveness of immune responses in a mouse model of human hepatitis B

HBV is a noncytopathic hepadnavirus and major human pathogen that causes immune-mediated acute and chronic hepatitis. The immune response to HBV antigens is age dependent: viral clearance occurs in most adults, while neonates and children usually develop chronic infection and liver disease. Here, we characterize an animal model for HBV infection that recapitulates the key differences in viral clearance between early life and adulthood and find that IL-21 may be part of an effective primary hepatic immune response to HBV. In our model, adult mice showed higher HBV-dependent IL-21 production in liver, compared with that of young mice. Conversely, absence of the IL-21 receptor in adult mice resulted in antigen persistence akin to that of young mice. In humans, levels of IL-21 transcripts were greatly increased in blood samples from acutely infected adults who clear the virus. These observations suggest a different model for the dichotomous, age dependent outcome of HBV infection in humans, in which decreased IL-21 production in younger patients may hinder generation of crucial CD8+ T and B cell responses. These findings carry implications for therapeutic augmentation of immune responses to HBV and potentially other persistent liver viruses.

Acute hepatitis C virus infection in young adult injection drug users: a prospective study of incident infection, resolution, and reinfection

BACKGROUND

Hepatitis C virus (HCV) infection, clearance, and reinfection are best studied in injection drug users (IDUs), who have the highest incidence of HCV and are likely to represent most infections.

METHODS

A prospective cohort of HCV-negative young IDUs was followed up from January 2000 to September 2007, to identify acute and incident HCV and prospectively study infection outcomes.

RESULTS

Among 1,191 young IDUs screened, 731 (61.4%) were HCV negative, and 520 (71.1%) of the 731 were enrolled into follow-up. Cumulative HCV incidence was 26.7/100 person-years of observation (95% confidence interval [CI], 21.5-31.6). Of 135 acute/incident HCV infections, 95 (70.4%) were followed; 20 (21.1%) of the 95 infections cleared. Women had a significantly higher incidence of viral clearance than did men (age-adjusted hazard ratio, 2.91 [95% CI, 1.68-5.03]) and also showed a faster rate of early HCV viremia decline (P < .01). The estimated reinfection rate was 24.6/100 person-years of observation (95% CI, 11.7-51.6). Among 7 individuals, multiple episodes of HCV reinfection and reclearance were observed.

CONCLUSIONS

In this large sample of young IDUs, females show demonstrative differences in their rates of viral clearance and kinetics of early viral decline. Recurring reinfection and reclearance suggest possible protection against persistent infection. These results should inform HCV clinical care and vaccine development.