A New Era of Integration between Multiomics and Spatio-Temporal Analysis for the Translation of EMT towards Clinical Applications in Cancer

Abstract

Epithelial-mesenchymal transition (EMT) is crucial to metastasis by increasing cancer cell migration and invasion. At the cellular level, EMT-related morphological and functional changes are well established. At the molecular level, critical signaling pathways able to drive EMT have been described. Yet, the translation of EMT into efficient diagnostic methods and anti-metastatic therapies is still missing. This highlights a gap in our understanding of the precise mechanisms governing EMT. Here, we discuss evidence suggesting that overcoming this limitation requires the integration of multiple omics, a hitherto neglected strategy in the EMT field. More specifically, this work summarizes results that were independently obtained through epigenomics/transcriptomics while comprehensively reviewing the achievements of proteomics in cancer research. Additionally, we prospect gains to be obtained by applying spatio-temporal multiomics in the investigation of EMT-driven metastasis. Along with the development of more sensitive technologies, the integration of currently available omics, and a look at dynamic alterations that regulate EMT at the subcellular level will lead to a deeper understanding of this process. Further, considering the significance of EMT to cancer progression, this integrative strategy may enable the development of new and improved biomarkers and therapeutics capable of increasing the survival and quality of life of cancer patients.

Keywords: EMT; cancer metastasis; genomics; multiomics; proteomics; secretome; transcriptomic.

Figure 1

Molecular regulation of epithelial-mesenchymal transition. The epithelial-mesenchymal transition (EMT) represents a continuum of alterations from an epithelial phenotype towards a mesenchymal phenotype, passing through diverse intermediate EMT states. Growth factors such as Epithelial growth factor (EGF), Fibroblast growth factor (FGF), Hepatocyte growth factor (HGF), and Transforming growth factor-beta (TGF-β) are frequently used as EMT inducers in experimental models to activate/inhibit downstream effectors and trigger an EMT program that includes alterations in the epigenome, transcriptome, and proteome of stimulated cells. Among these alterations, EMT transcription factors (EMT-TFs), such as RUNX, SNAIL, TWIST and ZEB family members, are positively regulated to inhibit the transcription of epithelial genes (e.g., CDH1, OCLN and TJP1) and promote the transcription of mesenchymal genes (e.g., CDH2, VIM and ACTA2). As an alternative to EMT inducers, EMT can also be experimentally promoted by the overexpression of EMT-TFs. Cells undergoing EMT exhibit the dissolution of protein complexes responsible for cell-cell adhesion, losing the apicobasal polarity and acquiring a back-front polarity that is characterized by the presence of actin stress fibers and an elongated morphology. In addition, these cells show increased migratory and invasive potential, which is commonly associated with basement membrane degradation and extracellular-matrix remodeling. Arrows shown in the top left represent the activation (black) or inhibition (red) of hypothetical signaling pathways by EMT inducers. Dashed arrows represent the attenuation of the activity of hypothetical effectors.

Figure 2

The role of EMT and MET during cancer metastasis. This figure exemplifies the contribution of epithelial-mesenchymal transition (EMT) and mesenchymal-epithelial transition (MET) during cancer progression when breast cancer cells metastasize to the lung. Overall, this is expected to be common to many carcinoma cells from different cancer types metastasizing to distinct sites. Cancer cells from (a) the primary tumor (b) undergo EMT, degrade the basement membrane and the ECM, and invade surrounding tissues before (c) blood vessel intravasation. After (d) the extravasation of circulating tumor cells (CTCs) into a distant organ, their interaction with the local microenvironment stimulates cancer cells to undergo (e) MET, seeding and colonizing a secondary site, and allowing (f) the growth of a secondary tumor. The blue arrow on the left side of the figure and the orange arrow on the right side of the figure represent the EMT and MET progress, respectively.

Figure 3

Proteomic analysis determines protein expression, activation, and localization. The study of cell proteome offers an unbiased view of global protein levels, and enrichment methods can also reveal major alterations in post-translational modifications that are able to impact protein activity, stability, and localization. Hypothetical changes are represented here for proteins A and B. Protein A translocates from the cytoplasm to the nucleus if phosphorylated, which could represent its activation as a transcription factor. Protein B is a plasma membrane protein that can be secreted into extracellular vesicles if monoubiquitinated or degraded in lysosomes if polyubiquitinated. Yellow circles and grey ellipses represent protein phosphorylation (P) and ubiquitination (Ub), respectively.

Figure 4

An integrated approach based on multiomics and spatio-temporal analysis of EMT-driven cancer progression. Current studies evaluating EMT at DNA, RNA, and protein levels have relied on the independent use of methods such as bulk DNA/RNA-sequencing, cDNA microarray, single cell RNA-sequencing, mass spectrometry, and tissue microarray. The combination of these methodologies enables obtaining information about simultaneous alterations in cancer cells and fractions that include the intracellular and the extracellular milieu. In addition to improving mechanistic studies in vitro and in vivo, such strategy may lead to more sensitive and specific diagnostic methods, and efficient anti-cancer therapies able to prevent and treat EMT-driven metastasis and recurrence.