Fig. 4

Transcriptomic profiling of EHE extended primary cell cultures. (A) Sequencing saturation of single cell RNA-Seq for passage number 6 of EHE 001 (Median Genes per Cell vs. Mean Reads per Cell). (B) Principal component analysis of total RNA sequencing from the EHE tumors, the derivative extended primary cell cultures, and HPAEC control cells based on the top 2,000 differentially expressed genes (DEGs). (C) Venn diagram showing the overlap in differentially expressed genes between the EHE tumors and the combined EHE primary cell cultures. To assess enrichment, hypergeometric analyses and Matthews correlation coefficient (MCC) calculations were carried out in R, version 4.4.1. The upper tail of the hypergeometric distribution was calculated using the phyper() function. (D) Pathway enrichment analysis (iPathwayGuide analysis, Advaita Bioinformatics) for EHE tumors (transcriptomes are combined) plotting -log₁₀ probability of accumulation (pAcc) vs. probability of over-representation (pORA). (E) Pathway enrichment analysis (iPathwayGuide analysis, Advaita Bioinformatics) for EHE extended primary cell cultures (transcriptomes are combined). (F) Table further detailing the fraction of differentially expressed (DE) genes in enriched pathways in the EHE extended primary cell cultures and tumors.