Alireza Raissadati, Xuanyu Zhou, Harrison Chou, Yuhsin Vivian Huang, Shaheen Khatua, Yin Sun, Anne Xu, Sharon Loa, Arturo Hernandez, Han Zhu, Sean M. Wu
(A) Schematic of experimental and computational pipeline. (B) cf-RNA yields and average fragment lengths from groups A, B, and C. (C) QC pipeline for screening degraded samples (3′ bias), ribosomal content, and DNA contamination. (D) Volcano plot:differentially expressed genes between ICI-treated patients with cancer (A+B+C, n = 22) and individuals acting as healthy controls (n = 30) (Benjamini-Hochberg –adjusted [BH-adjusted] P < 0.05), showing a higher number of differential genes. (E) Volcano plot: group C versus A (BH-adjusted P < 0.05) for cardiac pathways, with gene-type charts showing majority protein-coding genes. (F) IPA pathway analysis of upregulated differentially expressed genes in group C versus A patients. (G) Box plots: counts per million–trimmed mean of M values–normalized (CPM-TMM-normalized) counts of MYH6 and CCL5 cf-mRNA in group C versus A and B. (H and I) Box plots: CD4+/CD8+ T cell and Temra CD4+/CD8+ T cell proportions from single-cell RNA-Seq gene panels of ICI-treated patient PBMCs (3). (J and K) Heart and cardiomyocyte signature scores in group C versus A and B. *P < 0.05, **P < 0.01 by Mann-Whitney U test comparing groups. (L) Venn diagram: 6 genes (3 cardiac, 3 immune) were identified from C versus A and C versus B DEGs but not overlapping with B versus A DEGs to constitute an ICI-m–specific diagnostic panel. (M) ROC curves with metrics for C versus A (n = 10 vs 5), C versus B (n = 10 vs 7), and B versus A (n = 7 vs 5) using unsupervised panel (red) and ICI-m classifier (green). (N) ROC validation: both panels on separate group C (n = 6) versus groups A (n = 5) and B (n = 7).