Hypoxia Rewires Histone Methylation in Glioblastoma Cells via Enzyme Reprogramming Despite Disruption of One-Carbon Metabolism

Hypoxia is a hallmark
of the tumor microenvironment that profoundly
alters the cellular metabolism and epigenetic regulation. In this
study, we investigated how oxygen limitation reprograms histone methylation
in glioblastoma cells by integrating stable isotope tracing with high-resolution
proteomics and epigenomics. Using deuterium-labeled serine and the
RQMID-MS platform, we demonstrated that hypoxia impairs methyl group
transfer from serine to histones due to the downregulation of the
vitamin B12 transporter TCN2, which is critical for homocysteine
remethylation and SAM synthesis. Despite this blockade in one-carbon
metabolism, global histone methylation patterns were not uniformly
suppressed. Instead, we observed site-specific changes driven by altered
expression of methyltransferases and demethylases, particularly decreased
KMT1F (H3K9 methylation) and KMT2B (H3K4 methylation) and increased
KDM2A (H3K36 demethylation), KDM3A (H3K9 demethylation), and KMT5A/SETD8
(H4K20 monomethylation). These findings reveal that the histone methylation
landscape under hypoxia is governed by a compensatory interplay between
one-carbon metabolism and chromatin-modifying enzyme regulation.