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Additional file 1: Supplementary Methods, Figures and Tables.

Additional file 1.

Supplementary Figure S1 and Table S1.

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 > 12 months, CR/PR/SD 6–12 months, CR/PR/SD 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).

Additional file 2. Magnetic resonance image acquisition parameters.

Additional file 1. The inclusion and extrusion criteria.

Table S1. Baseline characteristics of included and excluded patients. (DOCX 19 kb)

Additional file 12: Table S3. Standardized differences in the training sets after weighting by propensity score.

Additional file 4. ICTOS calculation formula.

Additional file 3. Supplementary methods.

Figure S1. Flow diagram of selection of included patients. NPC, nasopharyngeal carcinoma; CRT, chemoradiotherapy; IC, induction chemotherapy; EBV, Epstein-Barr virus. Figure S2. Distribution of events occurring in 158 patients. Figure S3. Subgroup analyses based on N category. Kaplan–Meier survival curves were delineated based on the interval for overall survival (a, b), disease-free survival (c, d), distant metastasis-free survival (e, f) of N0–1 and N2–3 subgroups. Figure S4. Subgroup analyses based on IC cycles. Kaplan–Meier survival curves were delineated based on the interval for overall survival (a, b), disease-free survival (c, d), distant metastasis-free survival (e, f) of IC cycles ≤2 and > 2 subgroups. IC, induction chemotherapy. Figure S5. Subgroup analyses based on concurrent chemotherapy. Kaplan–Meier survival curves were delineated based on the interval for overall survival (a, b), disease-free survival (c, d), distant metastasis-free survival (e, f) of concurrent chemotherapy and no concurrent chemotherapy subgroups. Figure S6. Results of subgroup analyses summarized in forest plot. The HR (95% CI) of the interval for OS, DFS and DMFS in different subgroups and heterogeneity of HR between relative subgroups were shown. HR, hazard ratio; CI, confidence interval; OS, overall survival; DFS, disease-free survival; DMFS, distant metastasis-free survival; CC, concurrent chemotherapy. (DOCX 632 kb)

Table S1. Nucleotide sequence of the ShRNA#1 and ShRNA#2 targeting ARNTL. (DOCX 13 kb)

Additional file 11: Table S2. Acquisitions parameters of axial CE-T1W FSE in the training and validation cohorts.

Table S3. Tumor response after IC between investigational and control arms. (DOCX 14 kb)

Table S1. Quality assessment of eight retrospective studies using the modified Newcastle-Ottawa scale. Y = yes; N = no; U = unclear. Table S2. Quality assessment of one randomized controlled trial. Y = yes; U = unclear. Figure S1. Risk of bias graph: evaluation of risk of bias across all included studies. Figure S2. Risk of bias summary: evaluation of risk of bias of each included study. The green/yellow/red circles represent low/unclear/high risk of bias, respectively. (DOC 58 kb)

The frequency distribution of the genes with lengthened 3â UTR (A) and shortened 3â UTR (B) in different pairs, comparing NPC and NNET. (PDF 123 kb)

The effect of APA switching events on gene expression. “Blue” and “red” colors indicate up-regulated or down-regulated genes; “Green” and “yellow” colors indicate genes that switched to longer or shorter 3’UTRs. (PDF 200 kb)

Enrichment of genes with shortened 3â UTR isoforms involved in various GO functional categories. (PDF 144 kb)

Table S2. Cycle and total dose of CTX and NTZ for in each arm. (DOCX 13 kb)

Table S1. Imaging methods for the 296 patients in the two groups. (DOCX 14 kb)

PCR primers used in quantitative RT-PCR for APA switching genes (PDF 134 kb)

Enrichment of genes with lengthened 3â UTR isoforms involved in various GO functional categories. (PDF 63 kb)