Exploratory mass cytometry analysis reveals immunophenotypes of cancer treatment-related pneumonitis

Anti-cancer treatments can result in various adverse effects, including infections due to immune suppression/dysregulation and drug-induced toxicity in the lung. One of the major opportunistic infections is Pneumocystis jirovecii pneumonia (PCP), which can cause severe respiratory complications and high mortality rates. Cytotoxic drugs and immune-checkpoint inhibitors (ICIs) can induce interstitial lung diseases (ILDs). Nonetheless, the differentiation of these diseases can be difficult, and the pathogenic mechanisms of such diseases are not yet fully understood. To better comprehend the immunophenotypes, we conducted an exploratory mass cytometry analysis of immune cell subsets in bronchoalveolar lavage fluid from patients with PCP, cytotoxic drug-induced ILD (DI-ILD), and ICI-associated ILD (ICI-ILD) using two panels containing 64 markers. In PCP, we observed an expansion of the CD16+ T cell population, with the highest CD16+ T proportion in a fatal case. In ICI-ILD, we found an incre..., Cisplatin-positive cells and doublets were excluded to select live cells, and CD45+ cells were further analyzed. For T cells, CD2+ CD3+ cells were gated and subjected to UMAP and Citrus algorithms. The UMAP analysis included clustering channels for CD4, CD8a, CD27, CD28, CD45RA, CD45RO, Fas, and used the parameters: numbers of neighbors = 15, minimum distance = 0.01. The Citrus algorithm for T cells included clustering channels for CD4, CD5, CD7, CD8a, CD11a, CD16, CD27, CD28, CD44, CD45RA, CD45RO, CD49d, CD57, CD69, CD226, Fas, IL-2R, PD-L1, PD-L2, PD-1, OX40, TIGIT, TIM3, CTLA-4, CD223 (LAG-3), BTLA, ICOS, ST2, CCR7, CXCR3, HLA-DR, and used the parameters: association models = nearest shrunken centroid (PAMR), cluster characterization = abundance, minimum cluster size = 5%, cross validation folds = 5, false discovery rate = 1%. The citrus analysis excluded nivolumab-induced ILD cases due to the apparent loss of PD-1 detection caused by competitive inhibition by nivolumab (Supplementar..., , # Exploratory mass cytometry analysis reveals immunophenotypes of cancer treatment-related pneumonitis

[https://doi.org/10.5061/dryad.2ngf1vhxd ](https://doi.org/10.5061/dryad.2ngf1vhxd)

## Description of the data and file structure

The dataset comprises mass cytometry analyses, with each subject represented by two distinct panels: a T-cell panel and a B-cell panel. The data are stored in Flow Cytometry Standard (FCS) format. Summaries of each subject's data are compiled in an Excel file \"Cases1.xlsx\". Additionally, an R Markdown script has been developed for the analysis of the dataset GSE145926.