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.

缺氧是肿瘤微环境的标志性特征，可显著重塑细胞代谢与表观遗传调控网络。本研究通过整合稳定同位素示踪技术、高分辨率蛋白质组学与表观基因组学手段，探究了缺氧如何重编程胶质母细胞瘤细胞的组蛋白甲基化模式。本研究采用氘标记丝氨酸与RQMID-MS平台，证实缺氧会因维生素B12转运蛋白TCN2的表达下调，削弱丝氨酸向组蛋白的甲基基团转移过程；而TCN2对于同型半胱氨酸再甲基化与S-腺苷甲硫氨酸（SAM）合成至关重要。尽管一碳代谢通路受到阻滞，但全局组蛋白甲基化模式并未被全面抑制。相反，研究团队观察到由甲基转移酶与去甲基化酶表达改变所驱动的位点特异性甲基化变化：具体表现为KMT1F（介导组蛋白H3第9位赖氨酸甲基化）、KMT2B（介导组蛋白H3第4位赖氨酸甲基化）的表达下调，以及KDM2A（介导组蛋白H3第36位赖氨酸去甲基化）、KDM3A（介导组蛋白H3第9位赖氨酸去甲基化）与KMT5A/SETD8（介导组蛋白H4第20位赖氨酸单甲基化）的表达上调。本研究结果揭示，缺氧条件下的组蛋白甲基化图谱，由一碳代谢与染色质修饰酶调控之间的代偿性相互作用所主导。