Immunocluster provides a computational framework for the nonspecialist to profile high-dimensional cytometry data

High-dimensional cytometry is an innovative tool for immune monitoring in health and disease, and it has provided novel insight into the underlying biology as well as biomarkers for a variety of diseases. However, the analysis of large multiparametric datasets usually requires specialist computational knowledge. Here, we describe ImmunoCluster (https://github.com/ kordastilab/ImmunoCluster), an R package for immune profiling cellular heterogeneity in highdimensional liquid and imaging mass cytometry, and flow cytometry data, designed to facilitate computational analysis by a nonspecialist. The analysis framework implemented within ImmunoCluster is readily scalable to millions of cells and provides a variety of visualization and analytical approaches, as well as a rich array of plotting tools that can be tailored to users’ needs. The protocol consists of three core computational stages: (1) data import and quality control; (2) dimensionality reduction and unsupervised clustering; and (3) annotation and differential testing, all contained within an R-based open-source framework

Quantitative assessment of the conjunctival microcirculation using a smartphone and slit-lamp biomicroscope

Purpose: The conjunctival microcirculation is a readily-accessible vascular bed for quantitative haemodynamic assessment and has been studied previously using a digital charge-coupled device (CCD). Smartphone video imaging of the conjunctiva, and haemodynamic parameter quantification, represents a novel approach. We report the feasibility of smartphone video acquisition and subsequent haemodynamic measure quantification via semi-automated means. Methods: Using an Apple iPhone 6 s and a Topcon SL-D4 slit-lamp biomicroscope, we obtained videos of the conjunctival microcirculation in 4 fields of view per patient, for 17 low cardiovascular risk patients. After image registration and processing, we quantified the diameter, mean axial velocity, mean blood volume flow, and wall shear rate for each vessel studied. Vessels were grouped into quartiles based on their diameter i.e. group 1 (&lt;11 μm), 2 (11–16 μm), 3 (16–22 μm) and 4 (&gt;22 μm). Results: From the 17 healthy controls (mean QRISK3 6.6%), we obtained quantifiable haemodynamics from 626 vessel segments. The mean diameter of microvessels, across all sites, was 21.1μm (range 5.8–58 μm). Mean axial velocity was 0.50mm/s (range 0.11–1mm/s) and there was a modestly positive correlation (r 0.322) seen with increasing diameter, best appreciated when comparing group 4 to the remaining groups (p &lt; .0001). Blood volume flow (mean 145.61pl/s, range 7.05–1178.81pl/s) was strongly correlated with increasing diameter (r 0.943, p &lt; .0001) and wall shear rate (mean 157.31 s − 1, range 37.37–841.66 s − 1) negatively correlated with increasing diameter (r − 0.703, p &lt; .0001). Conclusions: We, for the first time, report the successful assessment and quantification of the conjunctival microcirculatory haemodynamics using a smartphone-based system. </p

Lactate Buildup at the Site of Chronic Inflammation Promotes Disease by Inducing CD4(+) T Cell Metabolic Rewiring

Accumulation of lactate in the tissue microenvironment is a feature of both inflammatory disease and cancer. Here, we assess the response of immune cells to lactate in the context of chronic inflammation. We report that lactate accumulation in the inflamed tissue contributes to the upregulation of the lactate transporter SLC5A12 by human CD4+ T&nbsp;cells. SLC5A12-mediated lactate uptake into CD4+ T&nbsp;cells induces a reshaping of their effector phenotype, resulting in increased IL17 production via nuclear PKM2/STAT3 and enhanced fatty acid synthesis. It also leads to CD4+ T&nbsp;cell retention in the inflamed tissue as a consequence of reduced glycolysis and enhanced fatty acid synthesis. Furthermore, antibody-mediated blockade of SLC5A12 ameliorates the disease severity in a murine model of arthritis. Finally, we propose that lactate/SLC5A12-induced metabolic reprogramming is a distinctive feature of lymphoid synovitis in rheumatoid arthritis patients and a potential therapeutic target in chronic inflammatory disorders

The T cell differentiation landscape is shaped by tumour mutations in lung cancer

Tumour mutational burden (TMB) predicts immunotherapy outcome in non-small cell lung cancer (NSCLC), consistent with immune recognition of tumour neoantigens. However, persistent antigen exposure is detrimental for T cell function. How TMB affects CD4 and CD8 T cell differentiation in untreated tumours and whether this affects patient outcomes is unknown. Here, we paired high-dimensional flow cytometry, exome, single-cell and bulk RNA sequencing from patients with resected, untreated NSCLC to examine these relationships. TMB was associated with compartment-wide T cell differentiation skewing, characterized by loss of TCF7-expressing progenitor-like CD4 T cells, and an increased abundance of dysfunctional CD8 and CD4 T cell subsets with strong phenotypic and transcriptional similarity to neoantigen-reactive CD8 T cells. A gene signature of redistribution from progenitor-like to dysfunctional states was associated with poor survival in lung and other cancer cohorts. Single-cell characterization of these populations informs potential strategies for therapeutic manipulation in NSCLC

Synthesis, properties and water permeability of SWNT buckypapers

The ability of macrocyclic ligands to facilitate formation of dispersions of single-walled carbon nanotubes (SWNTs) was investigated using a combination of absorption spectrophotometry and optical microscopy. Vacuum filtration of aqueous dispersions containing SWNTs and various macrocyclic ligands (derivatised porphyrin, phthalocyanine, cyclodextrin and calixarene) afforded self-supporting membranes known as buckypapers. Microanalytical data and energy dispersive X-ray spectra were obtained for these buckypapers and provided evidence for retention of the macrocyclic ligands within the structure of the membranes. The electrical conductivities of the membranes varied between 30 ± 20 and 220 ± 60 S cm−1, while contact angle analysis revealed they all possessed hydrophilic surfaces. The mechanical properties of buckypapers prepared using macrocyclic ligands as dispersants were shown to be comparable to that of a benchmark material prepared using the surfactant Triton X-100 (Trix). Incorporation of the macrocyclic ligands into SWNT buckypapers was found to increase their permeability up to ten-fold compared to buckypapers prepared using Trix. No correlation was observed between the water permeability of the membranes and the average size of either their surface or internal pores. However, the water permeability of the membranes was found to be inversely dependent on their surface area

ImmunoCluster provides a computational framework for the nonspecialist to profile high-dimensional cytometry data

High-dimensional cytometry is an innovative tool for immune monitoring in health and disease, and it has provided novel insight into the underlying biology as well as biomarkers for a variety of diseases. However, the analysis of large multiparametric datasets usually requires specialist computational knowledge. Here, we describe ImmunoCluster (https://github.com/kordastilab/ImmunoCluster), an R package for immune profiling cellular heterogeneity in high-dimensional liquid and imaging mass cytometry, and flow cytometry data, designed to facilitate computational analysis by a nonspecialist. The analysis framework implemented within ImmunoCluster is readily scalable to millions of cells and provides a variety of visualization and analytical approaches, as well as a rich array of plotting tools that can be tailored to users' needs. The protocol consists of three core computational stages: (1) data import and quality control; (2) dimensionality reduction and unsupervised clustering; and (3) annotation and differential testing, all contained within an R-based open-source framework

SYNOVIAL LYMPHOCYTIC AGGREGATES ASSOCIATE WITH HIGHLY ACTIVE RA AND PREDICT EROSIVE DISEASE PROGRESSION AT 12 MONTHS: RESULTS FROM THE PATHOBIOLOGY OF EARLY ARTHRITIS COHORT

Pathophysiology and treatment of rheumatic disease