Additional file 1 of Unraveling tumour microenvironment heterogeneity in nasopharyngeal carcinoma identifies biologically distinct immune subtypes predicting prognosis and immunotherapy responses
Creators: name: Chen, Yu-Pei
name: Lv, Jia-Wei
name: Mao, Yan-Ping
name: Li, Xiao-Min
name: Li, Jun-Yan
name: Wang, Ya-Qin
name: Xu, Cheng
name: Li, Ying-Qin
name: He, Qing-Mei
name: Yang, Xiao-Jing
name: Lei, Yuan
name: Shen, Jia-Yi
name: Tang, Ling-Long
name: Chen, Lei
name: Zhou, Guan-Qun
name: Li, Wen-Fei
name: Du, Xiao-Jing
name: Guo, Rui
name: Liu, Xu
name: Zhang, Yuan
name: Zeng, Jing
name: Yun, Jing-Ping
name: Sun, Ying
name: Liu, Na
name: Ma, Jun
Publisher: name: figshare
Year: 2021
Subjects: subject: Immunology
subject: FOS: Clinical medicine

description: Additional file 1: Methods. Figure S1. Study flow. HTA, Human Transcriptome Array; ICI, immune checkpoint inhibitor; NMF, non-negative matrix factorization; NPC, nasopharyngeal carcinoma; PSM, propensity score matching. Figure S2. Identification of an NMF immune factor. (A) We applied NMF (k = 5 factors or expression patterns) to analyze the gene expression profiles of nasopharyngeal carcinoma (NPC) samples in the training cohort (n = 113). One of the five factors (green bar) showed the highest ssGSEA scores in both immune enrichment score and 6-gene IFN-γ signature, as shown in the heatmap, indicating that it is an immune factor (or an immune expression pattern). High and low ssGSEA scores are represented in red and blue, respectively. (B) The top 100 exemplar immune factor genes characterized using DAVID confirmed immune-related functions. (C) NMF consensus-clustering of the training cohort using exemplar immune factor genes was refined by random forest classification. As shown in the heatmap, an immune-enriched subtype and a non-immune subtype. The ssGSEA scores of immune enrichment score and 6-gene IFN-γ signature are indicated; high and low scores are represented in red and blue, respectively. NMF, non-negative matrix factorization; NPC, nasopharyngeal carcinoma; ssGSEA, single-sample gene set enrichment analysis. Figure S3. Association of immune subtypes with tumoural genomic features and survival outcome. (A) Box plot showing similar number of non-synonymous mutations among the immune subtypes. (B) Box plot showing similar numbers of gene-level amplifications and deletions among the immune subtypes. (C) Box plot showing significantly higher cell cycling scores in non-IS. The box plot centre corresponds to the median, with the box and whiskers corresponding to the interquartile range and 1.5× interquartile range, respectively. P-values were based on the Kruskal–Wallis rank-sum test. (D) The proportion of CDKN2A deletions was significantly higher in non-IS. P-values were based on the Fisher’s exact test. (E) Kaplan–Meier curves for progression-free survival according to immune subtypes. A trend of better survival was observed for A-IS compared to E-IS and non-IS in 88 patients with available survival outcomes. P-values were calculated by log-rank test. A-IS, active immune subtype; CD4+ Tconv, conventional CD4+ T cells; CD8+ Tcyt, cytotoxic CD8+ T cells; CD8+ Tdys, dysfunctional CD8+ T cells; CD8+ Tnaï, naïve CD8+ T cells; DCs, dendritic cells; E-IS, evaded immune subtype; NK, natural killer; non-IS, non-immune subtype. Figure S4. Genetic similarity of the immune subtypes in different groups of patients from two melanoma ICI cohorts. (A) SubMap analysis of the immune subtypes in validation cohort 1 and four groups (anti-PD-1 responsive and non-responsive, and anti-CTLA-4 responsive and non-responsive) in melanoma ICI cohort 1. (B) SubMap analysis of the immune subtypes in validation cohort 1 and four groups (CR/PR/SD &gt; 12 months, CR/PR/SD 6–12 months, CR/PR/SD &lt;6 months, and PD for anti-PD-1 therapy) in melanoma ICI cohort 2. A-IS exhibited high similarity with anti-PD-1 responsive (P = 0.012), and CR/PR/SD &gt;12 months for anti-PD-1 therapy (P = 0.036). A-IS, active immune subtype; CR, complete response; E-IS, evaded immune subtype; ICI, immune checkpoint inhibitor; non-IS, non-immune subtype; PD, progressive disease; PR, partial response; SD, stable disease. Table S1. Clinical cohorts used in this study. Table S2. Publicly available gene signatures used in this study. Table S7. Clinical characteristics of patients in the validation cohort 1 and validation cohort 2 (ICI).