Journal: Nature

Article Title: Correlates of HIV-1 control after combination immunotherapy

doi: 10.1038/s41586-025-09929-5

Figure Lengend Snippet: a ) Differentially abundant CyTOF features in the peripheral blood (by two-sided Wilcoxon rank-sum test with Benjamini-Hochberg adjustment for multiple comparisons), and b ) differentially expressed genes in total peripheral blood mononuclear cells (PBMCs) between the viremic post-intervention controllers (n = 6) and non-controllers (n = 3) at baseline (on ART, prior to interventions). Differential expression analysis was performed using lmfit through limma using the empirical Bayes method to calculate a t-statistic. Significance cut-offs were set at a fold change > 1.5 and nominal P value < 0.05. c ) CyTOF landmark and sub-landmark gating scheme. Populations labelled in blue represent landmark populations and populations labelled in red represent sub-landmark populations. CyTOF, cytometry time of flight. PICs, post-intervention controllers. NCs, non-controllers.

Article Snippet: De-identified raw .fcs files with mass cytometry data were deposited at Mendeley (10.17632/3wfkd6rrht.1).

Techniques: Quantitative Proteomics, Cytometry

Journal: PLOS Pathogens

Article Title: NK cell-macrophage interactions in granulomas correlate with limited tuberculosis pathology

doi: 10.1371/journal.ppat.1012980

Figure Lengend Snippet: (A) Imaging mass cytometry images overlaid with cellular identities determined in and , showing one granuloma of each lung pathology score category (low, intermediate, high). (B) Interaction analysis for the granuloma of each lung pathology category with the colour of the square representing the frequency of the interaction between the phenotype of interest and the phenotype of neighborhood cells as a percentage of the total interactions for the phenotype of interest (blue to green gradient). The statistical analysis of the significant occurrence of an interaction is represented as a dot on the interaction square, showing only positive correlations (grey to black gradient). (C) Localization and frequency of NK cell-macrophage interactions in the three granuloma shown in Fig A. (D) Frequency of cell interactions as frequency of total macrophage interactions. (E) Frequency of macrophage-NK cell (interactions in each granuloma as percentage of total interactions in the granuloma, shown across the lung pathology score categories. (F) Interaction glyphs showing an abstract representation of the four most abundant neighborhoods found in the macrophage-NK cell interactions and a table showing the proportion this neighborhood makes up of the macrophage-NK cell interactions, with the associated Z-score in brackets.

Article Snippet: All mass cytometry data was acquired on the Hyperion mass cytometry imaging system (Standard Biotools, San Fransisco, CA, USA) at the Flow cytometry Core Facility at the LUMC.

Techniques: Imaging, Mass Cytometry