Fig. 1: The immune landscape IPNs of different stages and associated genomic and epigenomic features. | Nature Communications

Fig. 1: The immune landscape IPNs of different stages and associated genomic and epigenomic features.

From: Immune evolution from preneoplasia to invasive lung adenocarcinomas and underlying molecular features

Fig. 1

Infiltration CD4+ T cells, CD8+ T cells inferred from immune gene expression using TIMER; regulatory T cells (Tregs, CD3+CD8–FOXP3+) and CD8+cytotoxic T lymphocytes (CTLs,CD3+CD8+granzyme B+) measured by multiplex immunofluorescence (mIF); T cell clonality and frequency of the top 100T cell clones by TCR sequencing are shown in upper panel. Genomic alterations from whole exome sequencing (WES) including EGFR/KRAS mutations, HLA LOH, copy number variation (CNV) burden, allelic imbalance (AI) burden, total number of mutations associated with predicted neoantigens, and total number of mutations associated with predicted neoantigens without promoter methylation; global methylation status using long interspersed transposable elements-1 (LINE-1) as a surrogate marker accessed by reduced representation bisulfite sequencing (RRBS) are shown in bottom panel. Data from 53 patients was used including AAH (typical adenomatous hyperplasia), AIS (adenocarcinoma in situ), MIA (minimally invasive adenocarcinoma), and ADC (invasive adenocarcinoma). (Source data is provided as a source data file).

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