A multi-omics analysis reveals the unfolded protein response regulon and stress-induced resistance to folate-based antimetabolites

Abstract

Stress response pathways are critical for cellular homeostasis, promoting survival through adaptive changes in gene expression and metabolism. They play key roles in numerous diseases and are implicated in cancer progression and chemoresistance. However, the underlying mechanisms are only poorly understood. We have employed a multi-omics approach to monitor changes to gene expression after induction of a stress response pathway, the unfolded protein response (UPR), probing in parallel the transcriptome, the proteome, and changes to translation. Stringent filtering reveals the induction of 267 genes, many of which have not previously been implicated in stress response pathways. We experimentally demonstrate that UPR‐mediated translational control induces the expression of enzymes involved in a pathway that diverts intermediate metabolites from glycolysis to fuel mitochondrial one‐carbon metabolism. Concomitantly, the cells become resistant to the folate-based antimetabolites Methotrexate and Pemetrexed, establishing a direct link between UPR‐driven changes to gene expression and resistance to pharmacological treatment.

The Roles of Mitochondrial Folate Metabolism in Supporting Mitochondrial DNA Synthesis, Oxidative Phosphorylation, and Cellular Function

“…Phosphoglycerate dehydrogenase (PHGDH), the enzyme that catalyzes the first reaction in serine synthesis, exhibits gene copy-number gain in triple-negative breast cancer and melanoma ( 91 , 92 ). Under stress conditions of cancer, all 3 enzymes [PHGDH, phosphoserine aminotransferase 1 (PSAT1), and phosphoserine phosphatase (PSPH)] involved in de novo serine biosynthesis from the glycolytic intermediate, 3-phosphoglycerate are upregulated ( 93 ). Concurrent with increased metabolism of one-carbon sources, enzymes of mitochondrial FOCM, in particular MTHFD2 and SHMT2 become the most consistently upregulated metabolic genes in cancer ( 69 , 86 , 94 ).…”

“…Concurrent with increased metabolism of one-carbon sources, enzymes of mitochondrial FOCM, in particular MTHFD2 and SHMT2 become the most consistently upregulated metabolic genes in cancer ( 69 , 86 , 94 ). In addition to transcriptional reprogramming, expression of SHMT2, MTHFD2, and ALDH1L2 is induced and activity of mitochondrial FOCM is increased over cytosolic FOCM in response to endoplasmic reticulum stress in cancer ( 93 ). SHMT2 expression is also induced upon hypoxic stress to maintain mitochondrial redox balance and prevent accumulation of reactive oxygen species ( 82 , 95 ).…”

“…The overexpression of MTHFD2 and SHMT2 is not only necessary for cancer cell survival and tumor progression ( 69 , 86 ) but also predicts poor prognosis in multiple cancers, including breast cancer, gastrointestinal cancer, and intrahepatic cholangiocarcinoma ( 96 – 99 ). Metabolic reprogramming of mitochondrial FOCM induced by stress responses seems to adjust the microenvironment of cancer and render cancer cells resistant to folate-based antimetabolites ( 93 ). However, it is still unclear whether mitochondrial FOCM enzymes and serine metabolism are upregulated to support mitochondrial function or to provide formate for cytosolic and nuclear FOCM reactions in support of tumor growth.…”

Structural and Functional Significance of the Endoplasmic Reticulum Unfolded Protein Response Transducers and Chaperones at the Mitochondria–ER Contacts: A Cancer Perspective

“…It is universally recognized that the largest part of the intracellular calcium is stored within the ER and that different ER integral membrane proteins control Ca 2+ homeostasis by modulating either the ion uptake or its delivery to the neighboring compartments ( Putney, 2005 ; Clapham, 2007 ). Remarkably, calcium is engaged in the managing of several pathophysiological processes having an important impact in human malignancies development ( Limia et al, 2019 ; Reich et al, 2020 ).…”

Pemetrexed Hinders Translation Inhibition upon Low Glucose in Non-Small Cell Lung Cancer Cells

“…Although protein synthesis and biomass generation represent the most consuming energy pathway in the cell, the impact of PEM on translation remains unclear in nutrient rich conditions. Furthermore, chemical activation of the PERK-eIF2a-ATF4 axis protects tumor cells from antifolate treatment through the induction of carbon metabolism [ 24 ]. However, whether protein synthesis may be differently modulated by PEM when eIF2a is phosphorylated remains unknown.…”