Exploring Metabolic Memory Following Glucose Changes During Media Replacement in HEK293T Cells

Abstract

Metabolic memory refers to the persistence of cellular changes resulting from previous metabolic states, which may contribute to prolonged adverse effects in conditions like diabetes even after glucose normalisation. This study explores the potential mechanisms underlying metabolic memory, focusing on how changes in glucose concentration affect chromatin accessibility in HEK293T cells. Using ATAC-sequencing, we investigated whether chromatin accessibility changes previously observed in macrophages are conserved in other cell types. Cells initially cultured in high glucose (HG, 22.5mM) that were switched to low glucose (LG, 5mM) showed approximately 3000 genomic regions with increased accessibility compared to controls, while cells maintained in high glucose exhibited fewer changes. Transcription factor motif analysis identified several transcription factors potentially regulating these responses, including CTCF, AP-1, P53, and NRF2. Notably, CTCF transcription factor motifs showed increased accessibility in stable high-glucose conditions but decreased accessibility following glucose reduction, suggesting its potential role as a master regulator of metabolic memory. Pathway analysis revealed enrichment of apoptotic signalling in the HGLG condition, while sustained high glucose was associated with decreased accessibility in developmental and patterning pathways. The experiment conducted in the reverse direction (LGHG) yielded insufficient data quality for conclusive analysis. These findings expand our understanding of how previous metabolic environments shape the epigenome, providing insights into the molecular underpinnings of metabolic memory that could inform therapeutic approaches for metabolic diseases such as diabetes.