Transcriptomics and Metabolomics Integration Reveals Redox-Dependent Metabolic Rewiring in Breast Cancer Cells.

Marcella Bonanomi,Giusi Irma Forte,Marco Vanoni,Tatiana Volpari,Anna Maria Colangelo,Daniela Gaglio,Noemi Salmistraro,Elenio Avolio,Paola Paci,Federica Conte,Lilia Alberghina,Valentina Bravatà,Stefano D’Errico,Giulia Fiscon,Manuela Scorza,Fabrizia Mastroianni,Gennaro Piccialli

doi:10.3390/cancers13205058

Abstract

Simple SummaryMetabolic rewiring fuels cancer proliferation by enhanced glycolysis and the increased NADH/NAD+ ratio. In this study, we highlight the critical role of NADH in the epigenetic landscape mediated by CtBP2 (C-terminal binding protein 2) activation, linking metabolism to epigenetic transcriptional reprogramming. Moreover, using metabolomics and transcriptomics integration, we show that genetic and pharmacological down-regulation of CtBP2 strongly reduces cell proliferation by modulating the redox balance, nucleotide synthesis, reactive oxygen species (ROS) generation, and scavenging. Therefore, we provide evidence that metabolic rewiring plasticity regulates the crosstalk between metabolism and the transcriptional program that sustains energetic and anabolic demands in cancer cells.Rewiring glucose metabolism toward aerobic glycolysis provides cancer cells with a rapid generation of pyruvate, ATP, and NADH, while pyruvate oxidation to lactate guarantees refueling of oxidized NAD+ to sustain glycolysis. CtPB2, an NADH-dependent transcriptional co-regulator, has been proposed to work as an NADH sensor, linking metabolism to epigenetic transcriptional reprogramming. By integrating metabolomics and transcriptomics in a triple-negative human breast cancer cell line, we show that genetic and pharmacological down-regulation of CtBP2 strongly reduces cell proliferation by modulating the redox balance, nucleotide synthesis, ROS generation, and scavenging. Our data highlight the critical role of NADH in controlling the oncogene-dependent crosstalk between metabolism and the epigenetically mediated transcriptional program that sustains energetic and anabolic demands in cancer cells.

Highlights

Cancer is a complex, multifactorial disease that originates and establishes due to a complex interplay of oncogenic mutations, epigenetic alterations, and metabolic rearrangements that affect cancer cells’ proliferation, survival, and differentiation
We show that down-regulation of the expression of the CtBP NADHdependent transcriptional co-regulators reduces cell proliferation in a breast cancer cell line more than in untransformed, immortalized breast cell lines, partially reverting the oncogene-dependent intertwined metabolic and transcriptional rewiring that sustains energetic and anabolic demands in breast cancer cells
RNA-sequencing data retrieved from The Cancer Genome Atlas (TCGA) for 103 invasive breast adenocarcinomas and 103 matched normal samples showed that CtBP2 expression is higher in breast cancer than in normal tissues, consistent with previous data (Figure 1A)

Summary

Introduction

Multifactorial disease that originates and establishes due to a complex interplay of oncogenic mutations, epigenetic alterations, and metabolic rearrangements that affect cancer cells’ proliferation, survival, and differentiation. Notably the energetic metabolism, is recognized as a cancer hallmark [1]. Alterations in proto-oncogenes, such as Ras and MYC, or the loss of tumor suppressors (such as TP53 and VHL), promote metabolic rewiring compared to normal tissues [4–10]. A hyper-glycolytic phenotype (Warburg effect) occurs in hypoxic conditions, typical of avascular tumor mass or in the presence of mitochondrial dysfunction, and under conditions in which the available oxygen is not sufficient to fully oxidize glucose and glutamine, as it is often the case even under normoxic conditions [11]. Cancer cells can engage glucose or glutamine metabolism as a function of the availability of one or the other, thereby developing environmental adaptation under stress conditions [12]

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