Lysine Degradation Reprograms Tumour Immunity through Histone Crotonylation [RNA-seq]

To understand how GCDH enhances the oncogenic traits in GSCs, we carried out comparative transcriptomic analysis in two patient-derived GSCs (GSC23, GSC3028) with or without GCDH depletion to identify the driving events. To further examine the connection between lysine catabolism and GSC functions, we controlled L-lysine culture concentrations (0.2 and 2 mM) of GSCs in lysine-deprived media and performed RNA-seq. To address the functional significance of ECHS1 loss in tumour biology, we carried out RNA-seq in two early-passage DGCs (DGC23, DGC3028) with or without ECHS1 depletion. Kcr, H3K27ac or H3K9me3 ChIP-seq was performed in GSC23 to understand the molecular basis of how GCDH loss or lysine restriction affects chromatin landscape. Total RNA was extracted and used for library construction using the Illumina TruSeq Stranded Total RNA Library Prep Kit, which was performed by Novogene. The library was sequenced as a paired-end 150bp read. The chromatin from GSC23 with or without lysine catabolism disruption was prepared according to a ChIP kit (cat: 17-10085; Millipore) and followed by ChIP-seq analysis by Novogene.