Immune Responses in Checkpoint Myocarditis Across Heart, Blood, and Tumor

Steven M. Blum*, Daniel A. Zlotoff*, Neal P. Smith*, Isabela J. Kernin*, Swetha Ramesh*, Leyre Zubiri, Joshua Caplin, Nandini Samanta, Sidney Martin, Mike Wang, Alice Tirard, Yuhui Song, Katherine Xu, Jaimie Barth, Pritha Sen, Kamil Slowikowski, Jessica Tantivit, Kasidet Manakongtreecheep, Benjamin Y. Arnold, John McGuire, Mazen Nasrallah,Christopher J. Pinto, Daniel McLoughlin, Monica Jackson, PuiYee Chan, Aleigha Lawless, William A. Michaud, Tatyana Sharova, Linda T. Nieman, Justin F. Gainor, Catherine J. Wu, Dejan Juric, Mari MinoKenudson, Giacomo Oliveira, Ryan J. Sullivan, Genevieve M. Boland, James R. Stone, Molly F. Thomas, Tomas G. Neilan, Kerry L. Reynolds, Alexandra-Chloé Villani

bioRxiv 2023. doi: 10.1101/2023.09.15.557794


Immune checkpoint inhibitors (ICIs) are widely used anti-cancer therapies that can cause morbid and potentially fatal immune-related adverse events (irAEs), such as ICI-related myocarditis (irMyocarditis). The pathogenesis of irMyocarditis and its relationship to anti-tumor immunity remain poorly understood. We sought to define immune responses in heart, tumor, and blood in patients with irMyocarditis by leveraging single-cell (sc) RNA-seq coupled with T cell receptor (TCR) sequencing, microscopy, and proteomics analysis of 28 irMyocarditis patients and 41 controls. Analysis of 84,576 cardiac cells by scRNA-seq combined with multiplexed microscopy demonstrated increased frequencies and colocalization of cytotoxic T cells, conventional dendritic cells (cDCs), and inflammatory fibroblasts in irMyocarditis heart tissue. Analysis of 366,066 cells from blood samples revealed decreased frequencies of plasmacytoid dendritic cells, cDCs, and B lineage cells but an increased frequency of other mononuclear phagocytes (MNPs) in irMyocarditis blood. Fifty-two heart-expanded TCR clones from eight patients did not recognize the putative cardiac autoantigens α-myosin, troponin I, and troponin T, and TCRs enriched in heart tissue were largely non-overlapping with the TCRs enriched in paired tumor tissue. The presence of heart-expanded TCRs in a cycling blood CD8T cell population associated with fatal irMyocarditis case status. Collectively, these findings highlight critical biology driving irMyocarditis and nominate putative biomarkers.

View the data

On this website, we provide interactive data browsers to view all of the transcriptomics data for each of the manually curated cell clusters.

Cell Clusters

Metadata variables and gene expression in two-dimensional embeddings.

Heart tissue cells:

  • T cells, Myeloid cells, Non-immune cells

Blood PMBCs:

  • Mononuclear phagocytes, CD4 T cells, C8 T/NK cells, B cells
View Cell Clusters

Download the data

The single-cell data is available at NCBI GEO accession GSE228597.

Read the source code

Analysis output files and source code for the analysis is available at GitHub:

A permanent archive of the source code and output files is available at Zenodo: 10.5281/zenodo.11519192

Contact us

Please contact us with any questions or comments.

The data presented here comes from the laboratory of Dr. Alexandra Chloe Villani.

This website was made by Kamil Slowikowski