Abstract 4784: Multiomic landscape of evolution of Warburg effect identifies drivers of breast cancer
Authors: Canevarolo Rafael Renatino , Sudalagunta Praneeth Reddy , Song Joon-Hyun , Persi Erez , Damaghi Mehdi , Silva Ariosto Siqueira 
Published: April 2023

Abstract
Early breast carcinogenesis is characterized by an intermittently hypoxic, acidic and nutrient-deprived microenvironment, eventually selecting for the invasive, aerobically glycolytic phenotype known as Warburg Effect (WE), a universal cancer hallmark. We have reproduced the emergence of WE in vitro, by subjecting the nontumorigenic breast epithelial cell line MCF10A to multiple intermittent cycles of media starvation followed by recovery in growth media. Clonal expansion of surviving cells demonstrated increased lactate production in aerobic conditions (WE). A comprehensive molecular characterization, through WES and single cell multiomics, was performed to study the relationship between mutations, CNA, cytogenetic abnormalities, transcriptional dysregulation, and epigenetic modifications. Mutational analysis of 6 WE clones identified 249 shared mutations, including HRAS(G12V), BRAF(P523L) and ALK(Q180X). COSMIC mutational signature 18 (ROS-induced) was identified as the main DNA lesion across all WE clones, suggesting oxidative stress as a main source of mutagenesis associated with WE development. Non-synonymous mutations in FUS, HDAC3, EZH2, MAZ, KMTD2, MET, and other oncogenes were found in the clones, consisting in secondary events in the WE transformation. Geneset enrichment analysis identified over-expression of MYC/E2F targets, MTORC1 signaling, glycolysis and cell cycle pathways, as well as under-expression of EMT/cell adhesion pathways, in WE clones. CNA, based on a consensus from WES, scRNAseq (inferCNV) and scATACseq (epiAneufinder), confirmed amplification of MYC, E2F1 and MYBL2, as well as Gain(19q) and Gain(20) in all WE clones, as well as loss of TP63 in 5 out of 6 WE clones. Integrative single cell transcriptome/chromatin accessibility analysis (ArchR) identified decreased accessibility and expression of EMT-related genes, as a consequence of differential expression of pioneer transcription factors (i.e. reduced expression of TP63, due to deletion, led to silencing of TP53/63/73 targeted genes), as well as well-established EMT regulators (ZEB1, SNAI1/2, NFKB1), among others. We propose that the WE phenotype emerges after intermittent nutrient-derived oxidative stress induces increased expression of HRAS-regulated genes, acutely increasing mutation rate and transcriptionally inducing an EMT-like state. Once HRAS(G12V), MYC/E2F1 amplification and TP53 deletions are fixed in the population, the clones will maintain the ROS production and EMT-like state, even in optimum growth media conditions, completing the transition from an acute response to a chronic-inheritable phenotype known as WE. These findings reinforce the importance of microenvironmental stress driving early carcinogenesis, bridges the gap between environment and genomic-driven causes of malignant transformation and provides testable hypotheses of causal events in connection with WE.
Citation Format: Rafael Renatino Canevarolo, Praneeth Reddy Sudalagunta, Joon-Hyun Song, Erez Persi, Mehdi Damaghi, Ariosto Siqueira Silva. Multiomic landscape of evolution of Warburg effect identifies drivers of breast cancer. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4784.