DOI: 10.5281/zenodo.10493835
title: Transcriptomic biomarkers of pathological complete response to Induction Chemoimmunotherapy in locally advanced HNSCC

description: Transcriptomic biomarkers of pathological complete response to Induction Chemoimmunotherapy in locally advanced HNSCC
description: sTable legends 

Table S1. Clinical information of CheckRad RNAseq

Table S2. Published Gene Signatures

Table S3. Differentially expressed genes of multiple comparisons with DESeq2 at baseline

Table S4. Differentially expressed genes of multiple comparisons with DESeq2 in RD patients

Table S5. Pre-treatment transcriptional signature and TME subtypes correlation with pCR

Table S6. Pre- and post-treatment transcriptional signature and TME dynamic change of response patterns

Table S7. Gene set enrichment scores for MsigDB for pCR vs. RD patients at baseline

Table S8. Gene set enrichment scores for MsigDB for pCR vs. PPR patients at baseline

Table S9. Gene set enrichment scores for MsigDB for pCR vs. NPR patients at baseline

Table S10. Gene set enrichment scores for MsigDB for PPR vs. NPR patients at baseline

Table S11. Gene set enrichment scores for MsigDB for baseline vs. post-iCIT in RD patients

Table S12. Gene set enrichment scores for MsigDB for baseline vs. post-iCIT in PPR patients

Table S13. Gene set enrichment scores for MsigDB for baseline vs. post-iCIT in NPR patients

Table S14. Gene set enrichment scores for MsigDB for PPR vs. NPR patients at post-iCIT

 
description: sFigure legends 

sFigure 1. Transcriptomic dynamics in pathological response patterns in locally advanced HNSCC patients treated with iCIT at baseline. 

(A) Volcano plot depicting differentially expressed genes (FDR p<0.05; absolute logFC ≥1) between iCIT treated HNSCC patients with pCR versus PPR at baseline. Hallmark B cell genes and T-effector genes are represented in drakgreen and drakred, respectively; (B) Hierarchical clustering of the PPR and NPR patterns identified from transcriptome analyses; (C) GSEA enrichment analysis for selected gene lists of differentially expressed genes (DEGs) in two groups (pCR vs. PPR); (D) Volcano plot depicting differentially expressed genes (FDR p<0.05; absolute logFC ≥1) between iCIT treated HNSCC patients with pCR versus NPR at baseline. Hallmark B cell genes and T-effector genes are represented in drakgreen and drakred, respectively; (E) Hierarchical clustering of the pCR and NPR patterns identified from transcriptome analyses; (F) GSEA enrichment analysis for selected gene lists of differentially expressed genes (DEGs) in two groups (pCR vs. NPR); (G) Volcano plot depicting differentially expressed genes (FDR p<0.05; absolute logFC ≥1) between iCIT treated HNSCC patients with PPR versus NPR at baseline. Hallmark B cell genes and T-effector genes are represented in drakgreen and drakred, respectively; (H) Hierarchical clustering of the PPR and NPR patterns identified from transcriptome analyses; (I) GSEA enrichment analysis for selected gene lists of differentially expressed genes (DEGs) in two groups (PPR vs. NPR).

 

sFigure 2. Transcriptomic dynamics in pathological response patterns in locally advanced HNSCC patients with RD after iCIT. 

(A) Volcano plot depicting differentially expressed genes (FDR p<0.05; absolute logFC ≥1) between iCIT treated HNSCC patients with PPR at baseline versus post-iCIT. Hallmark B cell genes and T-effector genes are represented in drakgreen and drakred, respectively; (B) Hierarchical clustering of the timepoints identified from transcriptome analyses in PPR patients; (C) GSEA enrichment analysis for selected gene lists of differentially expressed genes (DEGs) in two groups (Baseline vs. post-iCIT) of PPR patients; (D) Volcano plot depicting differentially expressed genes (FDR p<0.05; absolute logFC ≥1) between iCIT treated HNSCC patients with NPR at baseline versus post-iCIT. Hallmark B cell genes and T-effector genes are represented in drakgreen and drakred, respectively; (E) Hierarchical clustering of the timepoints identified from transcriptome analyses in NPR patients; (F) GSEA enrichment analysis for selected gene lists of differentially expressed genes (DEGs) in two groups (Baseline vs. post-iCIT) of NPR patients; (G) Volcano plot depicting differentially expressed genes (FDR p<0.05; absolute logFC ≥1) between iCIT treated HNSCC patients with PPR versus NPR at post-iCIT. Hallmark B cell genes and T-effector genes are represented in drakgreen and drakred, respectively; (H) Hierarchical clustering of the PPR and NPR patterns identified from transcriptome analyses at post-iCIT; (I) GSEA enrichment analysis for selected gene lists of differentially expressed genes (DEGs) in two groups (PPR vs. NPR) at post-iCIT.

 

sFigure 3. Correlation of immune infiltration between pathology and transcriptomic estimate. 

 

sFigure 4. Transcriptomic estimate characteristics associated with pathologic response patterns. (A) Boxplot of TumorPurity for samples from the three pathologic response groups. TumorPurity of samples from patient with pCR, PPR and NPR were compared using Wilcoxon rank-sum test; (B) Boxplot of ImmuneScore for samples from the three pathologic response groups. ImmuneScore of samples from patient with pCR, PPR and NPR were compared using Wilcoxon rank-sum test; (C) Boxplot of StromalScore for samples from the three pathologic response groups. StromalScore of samples from patient with pCR, PPR and NPR were compared using Wilcoxon rank-sum test; (D) Boxplot of MicroenvironmentScore for samples from the three pathologic response groups. MicroenvironmentScore of samples from patient with pCR, PPR and NPR were compared using Wilcoxon rank-sum test; (E) Boxplot of ESTIMATEScore for samples from the three pathologic response groups. ESTIMATEScore of samples from patient with pCR, PPR and NPR were compared using Wilcoxon rank-sum test; (F) Boxplot of EC_IPS for samples from the three pathologic response groups. EC_IPS of samples from patient with pCR, PPR and NPR were compared using Wilcoxon rank-sum test.

sFigure 5. Transcriptomic estimate characteristics dynamic change of response patterns between pre- and post-treatment. (A) Expression levels of TumorPurity in pre- and post-treatment samples of PPR and NPR group of patients. Statistical comparisons were performed using paired Wilcoxon signed-rank test; (B) Expression levels of ImmuneScore in pre- and post-treatment samples of PPR and NPR group of patients. Statistical comparisons were performed using paired Wilcoxon signed-rank test; (C) Expression levels of StromalScore in pre- and post-treatment samples of PPR and NPR group of patients. Statistical comparisons were performed using paired Wilcoxon signed-rank test; (D) Expression levels of MicroenvironmentScore in pre- and post-treatment samples of PPR and NPR group of patients. Statistical comparisons were performed using paired Wilcoxon signed-rank test; (E) Expression levels of ESTIMATEScore in pre- and post-treatment samples of PPR and NPR group of patients. Statistical comparisons were performed using paired Wilcoxon signed-rank test; (F) Expression levels of IPS_IPS in pre- and post-treatment samples of PPR and NPR group of patients. Statistical comparisons were performed using paired Wilcoxon signed-rank test.