Additional file 9: Fig. S1. Genome-wide DNA methylation patterns in sMPLC and SPLC. A The density plot showed relatively similar methylation levels in the samples from the sMPLC and SPLC. B Principal component analysis (PCA) based on all CpG sites did not reveal any discernable separation between the two groups. C and D The substantially methylated sites appear to be bimodal distribution and randomly distributed on 22 chromosomes in sMPLC and SPLC. E and F The distribution percentages of the DMP on different gene regions were slightly different between sMPLC and SPLC. G and H GO analyses revealed the DMP in sMPLC and SPLC involved in different biological processes, cellular components, and molecular functions. Fig. S2. DNA methylation discrepancies between sMPLC and SPLC. A GO Functional Analysis showed that these DMP are involved in different biological processes, cellular components, and molecular functions. B and C DNA methylation level around the transcription starting site (TSS). The methylation patterns around the TSS region were different between sMPLC and SPLC. MC, sMPLC tumors; MN, paired normal lung tissues from sMPLC; SC, SPLC tumors; SN, paired normal lung tissues from SPLC. Fig. S3. RNA-seq and immunofluorescence analyses in sMPLC and SPLC. A and B KEGG pathways analyses in SPLC and sMPLC based on DEG. C and D Significant GO terms analyses in SPLC and sMPLC. More immune-related biological processes and pathways, such as B cell activation, B cell receptor signaling pathway, and IL-17 signaling pathway, were identified in the sMPLC group. E Immunofluorescence analyses of CD3, CD4, CD8, and CD68 confirmed CIBERSORT analysis results. The infiltration of CD3+, CD4+, and CD8+ T cells had no differences between sMPLC and SPLC. The number of CD68+ lymphocytes was significantly higher in sMPLC (p < 0.01). sMPLC, sMPLC tumors; sMPLC-N, paired normal lung tissues from sMPLC; SPLC, SPLC tumors; SPLC-N, paired normal lung tissues from SPLC.