Investigating epithelial‐mesenchymal heterogeneity of tumors and circulating tumor cells with transcriptomic analysis and biophysical modeling

Abstract

Cellular heterogeneity along the epithelial‐mesenchymal plasticity (EMP) spectrum is a paramount feature observed in tumors and circulating tumor cells (CTCs). High‐throughput techniques now offer unprecedented details on this variability at a single‐cell resolution. Yet, there is no current consensus about how EMP in tumors propagates to that in CTCs. To investigate the relationship between EMP‐associated heterogeneity of tumors and that of CTCs, we integrated transcriptomic analysis and biophysical modeling. We apply three epithelial‐mesenchymal transition (EMT) scoring metrics to multiple tumor samples and CTC datasets from several cancer types. Moreover, we develop a biophysical model that couples EMT‐associated phenotypic switching in a primary tumor with cell migration. Finally, we integrate EMT transcriptomic analysis and in silico modeling to evaluate the predictive power of several measurements of tumor aggressiveness, including tumor EMT score, CTC EMT score, fraction of CTC clusters found in circulation, and CTC cluster size distribution. Analysis of high‐throughput datasets reveals a pronounced heterogeneity without a well‐defined relation between EMT traits in tumors and CTCs. Moreover, mathematical modeling predicts different phases where CTCs can be less, equally, or more mesenchymal than primary tumor depending on the dynamics of phenotypic transition and cell migration. Consistently, various datasets of CTC cluster size distribution from different cancer types are fitted onto different regimes of the model. By further constraining the model with experimental measurements of tumor EMT score, CTC EMT score, and fraction of CTC cluster in bloodstream, we show that none of these assays alone can provide sufficient information to predict the other variables. In conclusion, we propose that the relationship between EMT progression in tumors and CTCs can be variable, and in general, predicting one from the other may not be as straightforward as tacitly assumed.

Transcriptomic-based quantification of the epithelial-hybrid-mesenchymal spectrum across biological contexts

“…Recent preclinical and clinical observations have suggested high metastatic potential of hybrid E/M phenotypes, and their association with worse patient survival across cancer types (Bierie et al, 2017;Godin et al, 2020;Huang et al, 2013;Kröger et al, 2019;Pastushenko and Blanpain, 2019;Puram et al, 2017;Sahoo et al, 2021b;Simeonov et al, 2021). Hybrid E/M phenotypes have also been observed in circulating tumor cells (CTCs); their higher frequency is often concomitant with worse clinicopathological features (Bocci et al, 2021;Lecharpentier et al, 2011;Saxena et al, 2019;Yu et al, 2013). The ability of hybrid E/M cells to form clusters of CTCs can also escalate their metastatic fitness, given the disproportionately high metastatic burden of CTC clusters (Aceto et al, 2014;Cheung et al, 2016;.…”

Single-Cell RNA-Seq Analysis Reveals the Acquisition of Cancer Stem Cell Traits and Increase of Cell–Cell Signaling during EMT Progression

“…Rather, non-genetic determinants diversify cell populations into distinct phenotypes or cell states with various degrees of metastatic potential and resistance to various therapies [ 43 , 44 ]. Specifically, phenotypic heterogeneity along the EMT spectrum, or EM plasticity (EMP), is emerging as a distinctive feature of primary tumors [ 45 ], CTCs [ 46 , 47 ], and in the relation between tumors and CTCs [ 48 ]. This heterogeneity can arise due to diverse signaling cues that induce EMT in a spatio-temporal-dependent manner, as seen for instance in time course or wound healing experiments [ 36 , 41 ].…”

Phenotypic Heterogeneity of Triple-Negative Breast Cancer Mediated by Epithelial–Mesenchymal Plasticity

“…Individual cells with partial EMT phenotype do not fully complete the EMT program and co-express both epithelial markers (such as EpCAM, keratins or E-cadherin) and mesenchymal markers (e.g., Vimentin) along with a differentially expressed set of EMT TFs. Such hybrid cells are presumed to have the highest tumorigenicity and metastatic potential [ 28 , 32 , 33 , 131 , 155 ] and were also observed in breast carcinomas, especially in CTCs exhibiting a spectrum of EMP states [ 155 , 156 , 157 , 158 ].…”