ESTRO 2024 - Abstract Book

S5347

Radiobiology - Tumour biology

ESTRO 2024

conducted. Differential Gene Expression (DGE) and Gene Set Enrichment Analyses (GSEA) were performed. For the DGE, fold change of 1.5 and adjusted p-value of <0.05 was considered as the threshold. Moreover, clinical and gene expression (RNAseq) HNSCC data from The Cancer Genome Atlas (TCGA) database were investigated and compared with our data.

Results:

The DGE analysis was conducted in three distinct manners. 1) untreated and treated xenograft samples were compared without accounting for any other factors. No change in gene expression was found when compared to the untreated samples. 2) untreated and treated samples were compared considering HPV status and, modest gene expression changes were observed after a single RCT dose. 3) DGE analysis was conducted comparing HPV+ versus HPV- cell lines in untreated and treated groups separately. As a result, extensive gene expression differences (782 significant DEGs for untreated group and 719 significant DEGs for treated group) were detected for both comparisons. GSEA with the DGEs from comparison no.3 provided distinct downregulated & upregulated pathways while some similarities were observed in few cases for both groups (untreated and treated samples). Specifically, HPV+ samples showed significant upregulation of the p53 pathway and pathways responsible for olfactory and chemical perception, when compared to the HPV- group in both groups. HPV- untreated xenografts showed upregulation of the Melanoma antigen family (MAGE) genes, hypoxia gene sets, and methylation signatures. This result was validated in the TCGA cohort. Our data show that the treatment may have significant effects on the specimens when HPV status is considered, and the results may show greater differences with a fractionated dose cohort. The distinct result for GSEA analysis for two treatment arms also emphasizes the observation. Further investigations with the models that received fractionated therapy of 10x2Gy are currently ongoing in order to identify distinct changes in gene expression of HPV+ and HPV- tumors that may be facilitated for treatment improvement. Image, transcriptomic, and epigenomic data of approximately 600 HNSCC patients that were treated with postoperative or primary RCT (DKTK HNprädBio) will be used to further validate the results. Currently the epigenomic analysis are ongoing that will be integrated into the transcriptome results in order to i) find a more precise stratifier for distinct HPV+ HNSCCs and ii) gain deeper insight into the molecular biological changes within the tumors. The final goal is to align and integrate preclinical findings with clinical data to identify robust and translatable biomarkers dependent on HPV status. Conclusion:

Keywords: HNSCC, Transcriptomics, Enrichment

References:

1. Valentini C, Ebert N, Koi L, Pfeifer M, Löck S, Erdmann C, Krause M, Baumann M. Preclinical trial comparing radiotherapy alone versus standard radiochemotherapy in three human papilloma virus (HPV) negative and three HPV-positive head and neck squamous cell carcinoma (HNSCC) xenograft tumour models. Radiother Oncol. 2023 Jun;183:109546. doi: 10.1016/j.radonc.2023.109546. Epub 2023 Feb 20. PMID: 36813172.