Jul 2026· Research Square· 1 citation· 89 references
Medicine
TL;DR
The immortalized non-tumorigenic breast epithelial cell line (MCF10A) develops neoplastic clones under fluctuating conditions in-vitro that mimic the harsh tumor microenvironment and is identified as a potential therapeutic target against epithelial-mesenchymal plasticity and metastatic spread in breast cancer.
Abstract
How environmental selective pressures contribute to the emergence of a neoplastic tumorigenic state, remains incompletely understood. Here we show that the immortalized non-tumorigenic breast epithelial cell line (MCF10A) develops neoplastic clones under fluctuating conditions in-vitro that mimic the harsh tumor microenvironment. Long-term evolutionary experiments and genomic landscape analyses of the clones identified ROS as the dominant clonal mutational signature that facilitates the acquisition of oncogenic driver mutations and the onset of the Warburg phenotype. Single cell multi-omics and brightfield microscopy further elucidate that each clone adopts two plastic phenotypic states, epithelial-like and mesenchymal-like, the transition between which is epigenetically mediated by de novo expression of Grainyhead-like Transcription Factor 2 (GRHL2), following environmental cues from soluble factors and cell adhesion. Additional in-vitro experiments indicate the role of this plasticity in metastasis. Analysis of 70 human breast cancer cell lines and 2 independent breast cancer patient cohorts confirmed the generality of this mechanism and its epigenetic regulation in patients. Thus, this study elucidates fundamental evolutionary mechanisms behind tumorigenesis and identifies GRHL2 as a potential therapeutic target against epithelial-mesenchymal plasticity and metastatic spread in breast cancer.
Tumor plasticity and microenvironmental heterogeneity are established as an integrated, evolving system that fuels metastasis and limits durable treatment responses.
G. Dagar, M. Dagar, Ashna Gupta et al.· MedComm· 0 citations
Normal tissues frequently harbor oncogenic mutations without progressing to cancer, but the cellular basis of this resistance remains poorly defined. We asked whether transformation requires selection of a rare, permissive state within normal-like cell populations. Dermal fibroblasts and mammary epithelial cells responded uniformly to combined HRAS-G12V expression and p53 disruption. Cellular barcoding revealed no loss or enrichment of clones during morphological transformation, arguing against clonal selection as the primary driver of neoplastic reprogramming. Instead, all transduced cells underwent an early, shared transcriptional transition characterized by loss of differentiation markers, induction of RAS-associated and inflammatory programs, activation of alternative-lineage signatures, increased single-cell entropy, and chromatin decondensation. These changes were transient: entropy and chromatin accessibility subsequently declined, and some cells moved toward the control transcriptional state, whereas others stabilized in altered states. The two lineages followed distinct trajectories. Fibroblasts showed greater initial transcriptional plasticity but subsequently reverted more strongly toward the normal state, whereas epithelial cells changed more gradually and continued to diverge from it, suggesting a stronger barrier to transformation in the mesenchymal lineage. Thus, oncogenic perturbation initiated reprogramming throughout the population but did not uniformly produce a stable transformed state. Together, these findings support a model in which normal-like cells tolerate oncogenic mutations not because most cells fail to respond, but because a p53-independent, cell-intrinsic barrier limits the stabilization of malignant transformation following a transient period of heightened plasticity. This framework may facilitate the identification of mechanisms that constrain tumor initiation.. Significance Statement Loss of TP53 and activation of oncogenic RAS are common drivers of human cancer and frequently coexist in the same tumor. Nevertheless, these alterations often fail to induce malignant transformation. To investigate why, we introduced both alterations into fibroblasts and epithelial cells and tracked their responses using clonal barcoding, single-cell transcriptomics, and phenotypic assays. Initially, cells uniformly reprogrammed their transcriptional and chromatin states without detectable clonal selection. They then diverged: some reacquired transcriptional profiles resembling those of the original normal cells, whereas others became transformed. Thus, normal cells resist transformation through an intrinsic barrier that operates despite p53 disruption. Because this transition is transient and reversible, it provides a tractable window for studying the earliest stages of cancer development.
Costakis Frangou, A. Safina, M. Commane et al.· bioRxiv· 0 citations
Breast cancer is a heterogeneous disease in which a single oncogenic driver can give rise to divergent tumor phenotypes. How oncogenic mutations generate epithelial state plasticity and coordinately remodel the surrounding tissue remains incompletely understood. Here, we applied longitudinal single cell RNA-sequencing to trace the mammary landscape during Pik3caH1047R-driven tumor progression in the mouse. We identify an expansion of the epithelial transcriptional state space, in which luminal cells lose lineage fidelity and activate ciliated, basal, and squamous-like gene expression programs. While oncogene-expressing cells lose features of luminal identity, they retain expression of hormone-sensing genes such as Esr1, Pgr, and Foxa1. These transcriptional states are established early, and the transition to overt tumors is marked by the emergence of cancer-associated fibroblasts rather than new epithelial states. We identify a Postn+ fibroblast population enriched at the epithelial interface as a candidate progenitor of cancer-associated fibroblasts. Postn+ fibroblasts express an ECM-remodeling program and display altered epithelial crosstalk in oncogenic glands. Altogether, Pik3caH1047R activation initiates a tissue-level process beginning with epithelial lineage infidelity, followed by an altered stromal microenvironment, which together mark tumor initiation.
Jennifer T. Le, Eun K. Kim, Vasudha Srivastava et al.· bioRxiv· 0 citations
Lineage plasticity develops as tumor cells overcome terminal differentiation barriers, adapt to environmental stressors, and acquire metastatic, therapy-resistant phenotypes. These phenotypic transitions are driven by nonmutational epigenetic mechanisms, including dynamic shifts in chromatin accessibility, histone modifications, DNA methylation, and noncoding RNA activity beyond genetic alterations. While epithelial-mesenchymal plasticity (EMP) remains a foundational model, cancer-cell plasticity extends into a broader pan-plasticity spectrum encompassing dedifferentiation, transdifferentiation into neuroendocrine or squamous lineages, and stem cell-like reprogramming. In this review, we evaluate how the antagonistic interplay between Polycomb and Trithorax complexes, chromatin modifier activity, and enhancer reprogramming affects lineage identity and enables multi-lineage plasticity in cancer. We further discuss extrinsic mechanisms reinforced by the tumor microenvironment, particularly hypoxia, chronic inflammation, and metabolic stress, that rewire the epigenetic landscape to stabilize plastic states. Collectively, these data underscore epigenetic deregulation as a primary driver of lineage plasticity and intratumoral heterogeneity, while revealing therapeutic vulnerabilities and the potential to reverse plasticity and overcome therapy resistance by targeting the epigenome.
Ezgi Boyvatlı, Burcu Akman, E. Bağırsakçı et al.· FEBS Letters· 0 citations
Tumors evolve under constantly changing microenvironmental conditions, and a key major mechanism by which cancer cells adapt to fluctuating environments is stochastic phenotypic switch via epithelial–mesenchymal plasticity (EMP). Here we demonstrate the existence of EMP in human breast epithelial cell lines and assess the fitness of E and M cells in environments that fluctuate between favorable and harsh conditions. We then develop a theoretical framework for analysis of tumor evolution with E-M stochastic phenotypic switch that integrates the behaviors of E and M cells. We characterize the outcomes of tumor evolution via three characteristic times describing i) tumor growth, ii) phenotypic adaptation and iii) fluctuations of the environment. We identify a tradeoff between tumor growth and survival, with different phenotype switching rates maximizing each of these objectives. An anticancer therapeutic strategy is proposed based on tumor survival analysis, revealing that blocking mesenchymal to epithelial transition, rather than epithelial to mesenchymal transition, is critical under fluctuating conditions. Thus, this study elucidates fundamental evolutionary mechanisms of tumor phenotypic adaptation in fluctuating environments with potentially important clinical implications. SIGNIFICANCE Tumors evolve under constantly changing environmental conditions, to which they adapt primarily via epithelial-mesenchymal plasticity. However, the impact of fluctuating environment on tumor growth and phenotypic composition remains elusive. We developed a mathematical model of tumor growth under fluctuating conditions with stochastic phenotypic epithelial-mesenchymal switch as the main mechanism of adaptation. Motivated by experimentally observed differences in the growth of epithelial and mesenchymal cells under variable conditions, the model reveals non-trivial evolutionary outcomes, depending on the relative time scales of the underlying processes, reminiscent of the Parrondo’s Paradox in game theory. Based on the model analysis, an optimal therapeutic strategy is proposed, with the mesenchymal-epithelial transition identified as the critical target.
Sanasar G. Babajanyan, Yuri I. Wolf, R. Canevarolo et al.· bioRxiv· 0 citations
BACKGROUND AND AIMS
While the majority of human pancreatic cancers are classified as pancreatic ductal adenocarcinomas (PDAC), tumors are comprised of diverse dedifferentiated tumor cell states that dynamically interact with an equally complex microenvironment, making it imperative to understand, in vivo, how normal epithelial identity is (dys)regulated during tumorigenesis.
METHODS
Here, we integrate data from mouse and human PDAC with a unique zebrafish model of pancreatic cancer to elucidate evolutionarily conserved mechanisms regulating dedifferentiation during pancreatic tumorigenesis.
RESULTS
Histological and single-cell transcriptional profiling of heterogeneous tumors developing in dual-transgenic ptf1a:Gal4-VP16; UAS:mKO2- KRASG12D adult zebrafish revealed mixed populations of progenitor-like cells with acinar features, progenitor-like cells with ductal features and undifferentiated progenitor-like cells, providing the opportunity to interrogate specific transcriptional and epigenetic modifiers controlling neoplastic pancreatic cellular differentiation. Screening a panel of chromatin modifiers and chromatin readers for differential expression in these distinct cell clusters revealed hdac9b to be upregulated in the progenitor-like cells enriched for ductal features. RNA velocity trajectories supported an acinar cell-of-origin for these hdac9b-expressing progenitor-like cells. Treatment of fish with the class IIA HDAC inhibitor TMP195 confirmed a functional role of HDAC activity in regulating neoplastic cell differentiation through repression of the ductal-like and progenitor cell states and associated re-activation of acinar gene expression (Graphical Abstract). Cross-species analyses in autochthonous murine tumors confirmed an early, evolutionarily conserved role for Hdac9 in pancreatic tumorigenesis, marking tumor cell subpopulations characterized by loss of epithelial differentiation and a basal subtype identity. In human pancreatic cancer, higher HDAC9 expression is significantly correlated with poorly differentiated tumor histology and predicts shorter overall survival in PDAC patients with classical subtype-enriched tumors.
CONCLUSIONS
These findings suggest a highly conserved role for HDAC9 and class IIA HDACs in vertebrate pancreatic tumorigenesis and may lead to new strategies for reactivating (normal acinar/epithelial) differentiation programs to intercept and treat PDAC.
Somer Matar, Sandra Blázquez-Araguás, Andrea Diéguez-Docampo et al.· Cellular and Molecular Gastr...· 0 citations