It is argued that formation of a tumour-intrinsic niche is a prerequisite for BRAF-mutant CRC seeding to distant organs and that interference with niche formation may help avoid metastatic relapse.
Abstract
Colorectal cancer (CRC) progression is characterised by a remarkable increase in plasticity and cellular heterogeneity1,2. The ability of cells to shift states and adopt mixed lineage potential exacerbates during metastasis and associates with poor patient survival3. How these atypical differentiated states emerge and drive cancer progression however has remained unclear. Here, we investigate this issue for BRAF-mutant CRC that commonly arise via the serrated pathway4 and are linked to poor prognosis via incompletely understood progression steps. Using patient-derived organoids, gene editing and murine tumour models, we show that mutations in RNF43, a regulator of WNT receptor abundance5, endow BRAF-mutant CRC with metastatic capacity by driving a non-dividing tumour-intrinsic niche cell (TINC) state that provides growth factor self-sufficiency to the cancer tissue. TINCs are enriched in RNF43-mutant, mucinous and metastatic samples of human CRC, and ablation of TINCs lead to re-acquired external growth factor dependency during CRC organoid outgrowth. Together, our findings uncover a mechanism by which tumours leverage cellular plasticity to mediate self-organised stem– and niche-cell interactions. Our results argue that formation of a tumour-intrinsic niche is a prerequisite for BRAF-mutant CRC seeding to distant organs and that interference with niche formation may help avoid metastatic relapse.
Plasticity, the capability of tumor cells to go through phenotypic transitions, promotes colorectal cancer (CRC) progression and treatment resistance. Although plasticity is evident in advanced CRCs, little is known about plasticity in early-stage tumors and tumor stem cells. Here, we demonstrate that a plastic cell state (PCS) is present already in polyps from patients with familial adenomatous polyposis and in mouse intestinal adenomas, in which PCS is associated with PROX1+ tumor stem cells. We furthermore analyzed progressive plasticity upon loss of the canonical wingless-related integration site (Wnt) effector Tcf7 or Lef1 in Apc mutant mice. Deletion of either gene led to emergence of new plastic tumor cell populations, failure of leucine-rich repeat–containing G protein-coupled receptor 5 (Lgr5) tumor stem cell differentiation into enterocyte-like cells, enhanced Myc pathway activation, and increased tumor cell proliferation and tumorigenesis. Together, we demonstrate that PCS is associated with early CRC development and identify multiple potentially druggable mechanisms activated during progressive tumor cell plasticity.
BACKGROUND
Cancer progression involves not only uncontrolled proliferation but also the strategic entry of tumour cells into reversible (quiescent) or irreversible (senescent) states of cell cycle arrest (G0). These states can give rise to rare persister-like cancer cells that survive hostile tumour microenvironment conditions, facilitating drug resistance, metastasis and disease relapse. Despite their importance, identifying and understanding the mechanisms regulating these cell populations remains challenging.
METHODS
We leveraged single-cell and spatially profiled primary breast tumours to quantify G0 arrest and proliferation decisions in cancer cells, revealing molecular and spatial features associated with proliferation-G0 dynamics.
RESULTS
We uncovered a G0 persister-like state with reduced copy number alteration burden and hallmarks of dormancy, characterised by transcriptional reprogramming of stress response pathways and increased epithelial-mesenchymal plasticity. Spatial analyses revealed distinct ecological niches: G0 cells inhabited protective niches with complement pathway activity proximal to CXCL10+ macrophages and myofibroblastic cancer-associated fibroblasts (CAFs), whereas proliferative zones were associated with CLEC9A+ dendritic cells and PERK signalling, with distinct drug sensitivities.
CONCLUSIONS
Our findings highlight key principles underpinning G0-proliferation dynamics and niche specialisation in breast cancer, offering novel insights into the spatial drivers of tumour heterogeneity and evolution.
Cenk Celik, William A. Weston, Thais de Moraes-Lacerda et al.· Genome Medicine· 1 citation
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 bright-field 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.
Erez Persi, Rafael R. Canevarolo, P. Sudalagunta et al.· Research Square· 0 citations
BACKGROUND & AIMS
BRAF-mutant colorectal cancer (CRC) is a clinically aggressive subtype arising from the serrated pathway and is associated with poor prognosis and therapy resistance. The mechanisms driving malignant transformation in microsatellite-stable (MSS) BRAF-mutant CRC remain incompletely understood. We aimed to define the role of WNT pathway activation in serrated CRC progression and tumor-immune interactions.
METHODS
We generated multiple genetically engineered mouse models (GEMMs) of BRAF-mutant MSS CRC and complementary organoid-based transplantation models. Genetic alterations in WNT pathway components were functionally interrogated. Tumor development and immune microenvironment remodeling were analyzed using bulk RNA sequencing, single-cell RNA sequencing, CITE-seq, and functional in vivo assays.
RESULTS
WNT pathway activation via APC or CTNNB1 mutations, but not RNF43 loss, was required for tumor initiation in BRAF-mutant CRC models. WNT activation induced a molecular subtype shift and suppressed immune response pathways. Mechanistically, WNT signaling suppressed CCL20 expression and remodeled the tumor microenvironment (TME) by promoting immunosuppressive myeloid populations and altering T-cell states. Functional assays demonstrated that WNT activation enhances tumor progression in immunocompetent settings, indicating immune evasion as a key driver of malignant progression.
CONCLUSIONS
WNT pathway activation is a critical determinant of malignant transformation in BRAF-mutant MSS CRC by enabling immune escape. These findings identify WNT signaling as a central regulator of tumor-immune interactions and a potential therapeutic target in this aggressive CRC subtype.
M. Mastel, A. Guiseris Martinez, Umberto Pozza et al.· Gastroenterology· 0 citations
Metastasis remains the leading cause of cancer‐related mortality and is increasingly recognized as a consequence of dynamic interactions between tumor cell plasticity and a heterogeneous tumor microenvironment (TME). Rather than being genetically fixed, cancer cells exhibit phenotypic flexibility, enabling reversible transitions among epithelial, mesenchymal, and stem‐like states in response to intrinsic programs and extrinsic microenvironmental cues, central to this adaptability. This review synthesizes emerging evidence that tumor progression is governed by reciprocal feedback loops between plastic tumor cells and distinct microenvironmental niches, including hypoxic cores, invasive margins, and perivascular regions. We highlight how stromal components, immune infiltrates, endothelial cells, and extracellular matrix (ECM) remodeling dynamically shape tumor cell states through biochemical and biophysical signals. Advances in single‐cell and spatial transcriptomic technologies have revealed the spatial organization and reversibility of these plastic phenotypes, uncovering rare but clinically significant drug‐tolerant persister populations. Importantly, we discuss plasticity‐mediated therapy resistance as an adaptive, nongenetic process driven by transcriptional and epigenetic reprogramming, metabolic flexibility, ECM stiffening–induced mechanotransduction, and immune‐checkpoint plasticity under therapeutic pressure. Together, these findings establish tumor plasticity and microenvironmental heterogeneity as an integrated, evolving system that fuels metastasis and limits durable treatment responses. Targeting this tumor–TME plasticity axis represents a promising strategy to disrupt metastatic progression and overcome therapeutic resistance.
G. Dagar, M. Dagar, Ashna Gupta et al.· MedComm· 0 citations
Melanoma is an aggressive malignancy that rapidly adapts to therapy. While chemotherapy resistance has traditionally been attributed to tumour-intrinsic mechanisms, growing evidence implicates the tumour microenvironment in shaping drug tolerance. However, few in vitro models capture the stromal complexity needed to study this interaction. We developed two multicellular melanoma spheroid models of increasing stromal complexity: a baseline model of melanoma, endothelial, and macrophage cells (BEM), and a fibroblast-containing counterpart (BEMF), and compared their transcriptional response to doxorubicin. Fibroblast inclusion increased the doxorubicin concentration required to achieve comparable growth inhibition. While untreated BEMF spheroids exhibited only modest baseline transcriptional differences, they showed a profoundly reshaped transcriptional response after doxorubicin exposure, displaying broader and higher-magnitude changes. These responses were characterized by suppression of proliferative and cell-cycle programmes, together with activation of inflammatory, immune-associated, metabolic, and stress-adaptive pathways. Higher-resolution pathway analyses further revealed coordinated attenuation of mitotic progression, checkpoint regulation, homologous recombination repair, and Rho GTPase signalling, consistent with a shift toward stress-adaptive and phenotypically plastic states, rather than classical resistance mechanisms. Transcriptome-derived transcription factor activity inference supported this regulatory rewiring. Integration with curated resistance-associated genes and external transcriptomic datasets demonstrated strong conservation of core transcriptional features across heterogeneous experimental systems, including consistent suppression of proliferation-associated genes and induction of inflammatory signalling programmes. Together, these findings indicate that fibroblasts redirect chemotherapy responses toward a stress-adaptive, persister-like phenotype and establish fibroblast-containing 3D melanoma spheroids as a physiologically relevant platform for studying tumour microenvironment-mediated chemotherapy tolerance and stromal-tumour interactions.
Ilie-Ovidiu Pavel, G. Negrea, S. Mészáros et al.· bioRxiv· 0 citations
A new method for surgically removing training examples from a model reveals that as datasets grow, the link between what a model learns and what it produces dissolves.
MIT News · Artificial Intelligence· news.mit.eduAug 17, 2026
