bims-instec Biomed News
on Intestinal stem cells and chemoresistance in colon cancer and intestinal regeneration
Issue of 2025–12–28
sixteen papers selected by
Maria-Virginia Giolito, Université Catholique de Louvain



  1. Elife. 2025 Dec 23. pii: RP106184. [Epub ahead of print]14
      Cell-to-cell communication via Delta-Notch signaling is widely used in various tissues and organs to regulate development and patterning; however, the mechanisms regulating Notch signaling for precise cell fate decisions remain poorly understood. Similar to mammals, the intestinal stem cells in the adult Drosophila midgut generate both absorptive and secretory cell progeny, guided by differential levels of Notch activation. Here we performed a forward genetic screen in Drosophila and identified glucosylceramide synthase (GlcT), a rate-limiting enzyme for glycosphingolipid (GSL) production, whose mutation causes the development of secretory cell tumors. Genetic analysis of the GSL synthesis pathway, combined with metabolite rescue experiments, revealed that the tumor formation is linked to a deficiency in Mactosylceramide/Lactosylceramide. This deficiency impaired the endocytic recycling of the Delta, subsequently reducing Notch signaling activation. Conditional knockout of Ugcg, the mammalian ortholog of GlcT, in mouse small intestine caused an excessive differentiation of goblet cells, phenotypes similar to these caused by Notch inhibition. Our study suggests an evolutionarily conserved role for a specific GSL metabolite in modulating Notch signaling during stem cell fate decisions and provides a molecular connection between ceramide metabolism and Notch signaling in regulating tissue homeostasis and tumor formation.
    Keywords:  D. melanogaster; Lactosylceramide; Mactosylceramide; Notch; developmental biology; enteroendocrine cell; intestinal stem cell; mouse
    DOI:  https://doi.org/10.7554/eLife.106184
  2. Cell Signal. 2025 Dec 19. pii: S0898-6568(25)00752-1. [Epub ahead of print]139 112337
      The intestinal mucosa undergoes a tightly regulated process of proliferation and differentiation, essential for maintaining gut homeostasis. We have previously demonstrated that oxytocin (OXT), a novel gastrointestinal (GI) hormone, plays a crucial role in regulating intestinal injury. However, its functional significance in intestinal epithelial cells (IECs) remains largely uncharacterized. In this study, we demonstrate that the OXT/OXTR signaling axis enhanced proliferation and differentiation of IECs in mouse small intestinal organoids. Pharmacological inhibition or genetic knockout (KO) of OXTR in IECs leads to impaired intestinal stem cell self-renewal, reduced Paneth cell abundance, and exacerbated 5-fluorouracil (5-FU)-induced mucositis. Mechanistically, OXT stimulates prostaglandin E2 (PGE2) production via upregulation of prostaglandin-endoperoxide synthases (COX-1/COX-2), and activates the PGE2 receptor EP4. Notably, the OXT-driven effects are abrogated by COX or EP4 inhibition. Furthermore, OXT signaling enhances YAP activation through a PGE2/EP4-dependent mechanism, linking the OXT/PGE2/EP4 axis to modulation of the Hippo pathway. Our findings establish that OXT orchestrates intestinal epithelial regeneration by promoting stem cell self-renewal via the PGE2/EP4/Hippo/YAP signaling cascade. These results highlight the therapeutic potential of OXT in mitigating chemotherapy-induced intestinal injury.
    Keywords:  5-fluorouracil; Oxytocin; PGE2; Proliferation and differentiation; YAP
    DOI:  https://doi.org/10.1016/j.cellsig.2025.112337
  3. Cell Mol Gastroenterol Hepatol. 2025 Dec 24. pii: S2352-345X(25)00258-9. [Epub ahead of print] 101716
       BACKGROUND AND AIMS: Loss of keratin 8 (K8) has been shown to increase susceptibility towards colonocyte hyperproliferation and tumorigenesis. However, most colorectal cancer (CRC) mouse models require carcinogen, develop small intestinal tumors or have a long latency period. The aim was to establish a genetic, colon-specific and more human like CRC model driven by loss of K8 and Apc.
    METHODS: Colon-specific targeting using CDX2P-CreERT2 mice was used to generate K8flox/flox; CDX2P-CreERT2 and K8flox/flox; CDX2P-CreERT2; Apcflox/+ mice. Disease activity was monitored, and colon was analyzed for tumor burden and histopathology over time. Keratin expression, inflammation, proliferation, cell polarity, colonocyte populations and cell division symmetry were assessed using immunoblotting and immunofluorescence analysis. This data was compared to K8 expression analysis in CRC patients and in UALCAN database.
    RESULTS: K8flox/flox; CDX2P-CreERT2 mice develop mild diarrhea and express reduced K8 and partner keratins in a mosaic pattern in the colonic epithelium. K8-negative colon areas display increased crypt loss and more inflammation predominantly in the proximal colon. Increased colonocyte proliferation is observed throughout the colon. Impaired cell polarity and higher number of stem and progenitor cells with a shift towards asymmetric cell division in K8-negative areas of the distal colon highlight a pro-tumorigenic environment. Mice with additional monoallelic Apc inactivation show colon tumorigenesis and epithelial to mesenchymal transition distally. In CRC patients, tumor K8 expression is decreased independent of disease type and stage, age or gender.
    CONCLUSION: Genetic colon-specific mouse model with loss of K8 and Apc adequately resembles human CRC. This study identifies anti-tumorigenic protective roles of colonocyte K8 in the colon.
    Keywords:  CDX2; Colorectal cancer; Keratin 8; Mouse model
    DOI:  https://doi.org/10.1016/j.jcmgh.2025.101716
  4. Stem Cell Res Ther. 2025 Dec 21.
       BACKGROUND: Intestinal epithelial stem cells (SCs) and their transit-amplifying (TA) progeny are critical for mucosal repair and regeneration. However, their behaviour under chronic inflammatory conditions, such as those observed in Inflammatory Bowel Disease (IBD), remains incompletely understood.
    METHODS: We investigated the impact of chronic inflammation on intestinal stem/progenitor cells by integrating bulk RNA sequencing from the largest IBD biopsy cohort to date with single-cell transcriptomic analysis and experimental assays using patient-derived intestinal organoids.
    RESULTS: Active inflammation was associated with a reduction in canonical LGR5⁺ intestinal stem cells and a concurrent expansion of OLFM4⁺ populations, consistent with an inflammation-induced epithelial repair program. Notably, SC/TA cells from both inflamed and non-inflamed IBD tissues exhibited persistent transcriptional changes that were distinct from those in healthy controls. Single-cell analysis identified transcriptionally heterogeneous SC/TA subpopulations, including a previously uncharacterized inflammation-associated cluster enriched in immune signalling pathways. Pseudotime trajectory analysis demonstrated a shift in differentiation toward deep crypt secretory (Paneth-like) cell lineages under inflammatory conditions.
    CONCLUSIONS: Chronic intestinal inflammation reshapes the epithelial stem and progenitor cell compartment, promoting altered differentiation and the emergence of immune-responsive epithelial states. These findings highlight the plasticity of the human intestinal epithelium in IBD and point to new avenues for therapeutic strategies aimed at maintaining epithelial integrity during chronic inflammation.
    Keywords:  BEST4; Biomarkers; Gene expression; Inflammation; Inflammation bowel disease; Organoid; Progenitors; Regeneration; Stem cells
    DOI:  https://doi.org/10.1186/s13287-025-04872-8
  5. STAR Protoc. 2025 Dec 24. pii: S2666-1667(25)00698-7. [Epub ahead of print]7(1): 104292
      Mesenchymal stem/stromal cells (MSCs) are known for their regenerative properties. This protocol describes a co-culture system for investigating molecular interactions between MSCs and intestinal epithelial organoids following injury. We outline steps for assessing the immediate effects of MSCs on organoid growth and survival, as well as a model for evaluating longer term responses. The workflow is adaptable and can be readily modified to examine MSC interactions with additional cell types or in different injury contexts. For complete information on the use and execution of this protocol, please refer to Yetkin-Arik et al.
    Keywords:  Cell biology; Cell-based assays; Molecular biology; Organoids; Signal transduction; Single cell; Stem cells
    DOI:  https://doi.org/10.1016/j.xpro.2025.104292
  6. bioRxiv. 2025 Dec 19. pii: 2025.12.17.694784. [Epub ahead of print]
      Cancer cell adaptation to their physical tumor microenvironment is a key driver of malignancy. Recent experimental evolution experiments show that the soft extracellular matrix (ECM) can impose a selection pressure on genetically variable tumor populations. Over months of sustained culture, the selection pressure leads to enrichment of specific genetic variants with high fitness, but the mechanisms underlying the high fitness of these soft-selected clones are not fully understood. Here, we used a combination of RNA-seq, ATAC-seq, and RRBS-seq to compare soft-selected populations with non-selected ancestral populations cultured on soft ECM. We demonstrate that ancestral populations grown on soft ECM for short durations are characterized by a stressed cell state with low fitness marked by cell cycle arrest and distinct metabolic shifts, whereas sustained culture selects for a robust proliferative phenotype. Mechanistically, selected cells exhibit a silenced ancestral stress response through epigenetic modifications, characterized by reduced chromatin accessibility and de novo DNA methylation, including CDH1 promoter hypermethylation. This repressive landscape supports a high-fitness state defined by elevated MYBL2 and FAK levels. An in-silico mechanism-based model shows that these molecular differences, together with high YAP1 nuclear localization in soft-selected cells, are salient features of genetic clones capable of FAK upregulation. These findings uncover a coordinated genetic and epigenetic mechanism driving cancer cell evolution in mechanically soft microenvironments.
    DOI:  https://doi.org/10.64898/2025.12.17.694784
  7. Sci Rep. 2025 Dec 23.
      High expression of Solute Carrier Family 11 Member 1(SLC11A1) leads to a poor prognosis in patients with CRC, while the specific role of SLC11A1 in CRC remains unreported. Therefore, this study mainly addressed the preliminary mechanism and specific role of SLC11A1 in CRC. The results showed that six subsequent genes were successfully screened by the line database, and the abnormal expression of SLC11A1 was the most obvious in colorectal cancer patients. Following phenotypic experiments demonstrated that SLC11A1 promoted proliferation, invasion and migration of colorectal cancer cells. SLC11A1 Is also able to downregulate Acyl-CoA Synthetase Long Chain Family Member 4 (ACSL 4), Cyclooxygenase-2 (COX2), NADPH Oxidase 1 (NOX1) and upregulate the expression levels of Hypoxia-Inducible Factor 1 (FIH1), Glutathione Peroxidase 1 (GPX1) protein, inhibit the expression levels of MDA and Fe2+ in colorectal cancer cells, and resist ferroptosis in colorectal cancer cells. SLC11A1 Overexpression can up-regulate the protein expression level of TGFβ1 (Transforming Growth Factor Beta 1), p-Smad 2 / 3, activate TGFβ1 signaling pathway activity, and promote colorectal cancer cell progression. In conclusion, we successfully demonstrated that SLC11A1 confers resistance to ferroptosis in colorectal cancer cells, providing a potential target for the clinical treatment of colorectal cancer.
    Keywords:  Colorectal cancer; Ferroptosis; Invasion and metastasis; Solute carrier family 11 member 1; Transforming growth factor beta 1 signaling pathway
    DOI:  https://doi.org/10.1038/s41598-025-32979-8
  8. Cancer Lett. 2025 Dec 19. pii: S0304-3835(25)00800-6. [Epub ahead of print] 218228
      Tumor-associated stromal (TAS) cells within the tumor microenvironment (TME) exhibit marked transcriptional heterogeneity. However, the spatial organization of TAS subpopulations and their clinical relevance in human colorectal cancer (CRC) are incompletely understood. Using single-cell RNA sequencing (scRNA-seq) and multiplex imaging, we identified multiple TAS subpopulations with distinct intratumoral and peritumoral abundance, and found that CRC patients enriched in FAP+ TAS cells and CD73+ tumor cells had the lowest disease-free survival (DFS). NGFR+ stromal cells localized predominantly within tertiary lymphoid structures (TLS), which could be further classified into NGFR+ organized TLS, NGFR+ unorganized TLS and NGFR- TLS based on the spatial distribution of NGFR+ stromal cells. CRC patients enriched for NGFR+ organized TLS exhibited improved DFS. SCENIC analysis revealed HAND2, IKZF2 and SOX10 as transcriptional regulators of human NGFR+ antigen-presenting TAS cells, and they frequently expressed enteric glial cell markers SOX10, PLP1, CDH19 and NCAM1. In summary, our study demonstrates that the frequency and spatial distribution of TAS subpopulations, particularly NGFR+ TAS organization within TLS, varies between CRC patients and correlates with DFS and distinct changes in the TME.
    Keywords:  Multiplex imaging; apTAS; cancer-associated fibroblasts; mesenchymal stromal cells; nerve growth factor receptor; tertiary lymphoid structures; tumor microenvironment
    DOI:  https://doi.org/10.1016/j.canlet.2025.218228
  9. Front Cell Dev Biol. 2025 ;13 1720996
      Colorectal cancer (CRC) remains one of the leading causes of cancer-related morbidity and mortality worldwide. Tumor sidedness, distinguishing left- (LCRC) and right-sided (RCRC) cancers, has emerged as a critical clinical determinant, influencing patient prognosis and therapeutic response. However, the cellular and molecular mechanisms underlying these differences remain poorly understood. Recent advances in single-cell RNA sequencing (sc-seq) provide high-resolution insights into CRC heterogeneity, revealing distinct tumor, immune, and stromal cell populations and their context-specific interactions. In this review, we synthesize sc-seq studies that dissect the molecular programs driving progression, therapy resistance, and metastasis in CRC. We highlight malignant subclusters characterized by metabolic reprogramming and spatially organized oncogenic signaling; specialized immune cell states, including macrophage subsets, exhausted T cells, and mast cells, that shape tumor immunity; and stromal elements such as cancer-associated fibroblasts and endothelial tip cells that remodel the extracellular matrix, promote angiogenesis, and foster immune evasion. Importantly, sc-seq demonstrates that LCRC and RCRC represent distinct multicellular ecosystems with differential immune recruitment and stromal signaling, underscoring the need for sidedness-informed therapeutic strategies. We propose that future interventions should target cell-cell communication networks and spatially defined tumor-microenvironment interactions to overcome heterogeneity and improve clinical outcomes.
    Keywords:  cancer-associated fibroblasts; cell-cell interactions; colorectal cancer; immunotherapy; left-sided and right-sided colorectal cancer; metastasis; single-cell RNA sequencing; tumor-associated macrophages
    DOI:  https://doi.org/10.3389/fcell.2025.1720996
  10. Cell Rep. 2025 Dec 23. pii: S2211-1247(25)01606-7. [Epub ahead of print]45(1): 116834
      What makes a cancer highly metastatic is not known. Here, we inquire on the metastatic potential (MP) of tumor cells, which reflects their probability to emigrate from the primary tumor to new sites to form secondary cancers. We determine the transcriptomic landscapes of single-cell-derived clones in hybrid EMT space and define metastatic potential gradient genes (MPGGs) that linearly track MP strength. Perturbation of selected MPGGs and linked processes reveals a dynamic cellular and molecular framework of what we define as "cell-state ensembles" underlying the emergence of high MPs. To test if MPGGs predict cancer recurrence, we build the MangroveGS machine-learning model with "gene signature ensembles": MangroveGSMPGGs robustly predicts patient tumor recurrence and metastases, outperforms all other signatures and staging systems tested, and can be extended to multiple cancer types of epithelial nature. Our findings uncover an unsuspected shared strategy for the onset of metastases that underlies clinical outcome.
    Keywords:  CP: cancer; cancer; cell states; disease recurrence; ensemble; gradient; metastasis; metastatic potential; plasticity; prediction; risk
    DOI:  https://doi.org/10.1016/j.celrep.2025.116834
  11. Cell Death Dis. 2025 Dec 26.
      Non-genetic resistance of cancer remains poorly understood in clinical research and practice. To better understand resistant cancer cell heterogeneity, we isolated a novel riboflavin+NOTCH1+ population from cisplatin-naïve and -resistant lung cancer cell lines and patient specimens with or without immunotherapy and chemotherapy. This population was also identified as SLC52A2 (one of the riboflavin transporters)+NOTCH1+ cells in single-cell RNA sequencing (scRNA-seq) data derived from advanced lung tumors before therapy. Despite its therapy-naïve origin, the population, designated as stably resistant cancer cells (SRCC), exhibited the epithelial state, innate and stable resistance to therapy (chemotherapy, targeted therapy and immunotherapy), cell dormancy, elevated reactive oxygen species (ROS), and anti-apoptotic and anti-ferroptotic survival. These cellular and molecular characteristics distinguished SRCC from other resistant populations, including cancer stem-like cells (CSC), epithelial-mesenchymal transition (EMT) cells, and drug-tolerant persisters (DTP). The non-canonical NOTCH1 pathway, but not the inactivated canonical NOTCH1 pathway, played a critical role in the resistance of SRCC. Specifically, it modulates cell cycle, iron metabolism, EMT, and ferroptosis vulnerability in SRCC at the transcriptional level. It also controls the initiation of ferroptosis in lysosomes via a posttranslational NOTCH1-AKT-BAX axis. Inhibition of the non-canonical NOTCH1 pathway re-sensitizes these dormant and resistant cells to cisplatin-induced cell death in vitro and in vivo, including ferroptosis, apoptosis, and necroptosis. Our study contributes to a deeper understanding of cancer resistance and promotes the development of more effective therapeutic strategies against resistant cancer cells.
    DOI:  https://doi.org/10.1038/s41419-025-08355-9
  12. Trends Mol Med. 2025 Dec 23. pii: S1471-4914(25)00292-8. [Epub ahead of print]
      Palma et al. show that melanoma cells adapt to oxidative stress imposed by the lymphatic niche by shifting their dependency from glutathione peroxidase 4 (GPX4) to ferroptosis suppressor protein 1 (FSP1), to protect from ferroptosis. This highlights the importance of the microenvironment in shaping ferroptosis defenses and supports FSP1 as a targetable vulnerability for lymph node metastases.
    Keywords:  FSP1; GPX4; ferroptosis; hypoxia; lymph node; melanoma; oxidative stress; tumor microenvironment
    DOI:  https://doi.org/10.1016/j.molmed.2025.12.005
  13. bioRxiv. 2025 Dec 19. pii: 2025.12.17.694935. [Epub ahead of print]
      best4 +/CFTR-high expressing cells are a recently described intestinal epithelial cell type potentially altered in inflammatory bowel disease and colorectal cancer. However, their developmental origin, developmental regulation, and functions remain undefined. This study identifies their conserved transcriptional program and uses zebrafish to dissect their developmental regulation in vivo . Lineage tracing identified that best4 + cells arise from atoh1b + secretory progenitors. We identify that Notch signaling, mediated by dll4, specifies best4 + cells at the expense of enterochromaffin cells. Downstream of Notch, meis1b confers best4 + cell identity. best4 + cells then exhibit regionalized gene expression, regulated by pbx3a . Additionally, this study demonstrates a system where best4 + cells can be manipulated, observed, and removed in an organismal context. Live imaging and electron microscopy of best4 + cells identified dynamic cellular projections, suggesting a sensory or communicative function. Removal of best4 + cells in vivo eliminated previously proposed functions: they are not required to restore intestinal pH following acidic challenge and do not absorb nutrients. However, we identify region-specific intracellular pH differences that suggest potential functional heterogeneity. Altogether, this study presents a comprehensive description of best4 + cell development from birth to spatial regulation that will be instrumental to understand how best4 + cells change in disease or might be therapeutically manipulated and presents the tools to dissect their function in vivo .
    DOI:  https://doi.org/10.64898/2025.12.17.694935
  14. STAR Protoc. 2025 Dec 19. pii: S2666-1667(25)00692-6. [Epub ahead of print]7(1): 104286
      Patient-derived organotypic tumor spheroids (PDOTS) are short-term, 3D cultures of multicellular spheroids in microfluidic devices, prepared from freshly explanted patient tumors. In this protocol, we describe the steps of PDOTS sample processing and culturing, drug sensitivity testing ex vivo using a microscopy-based assay, and the assembly of a PDOTS cohort that captures the overall response with patient-to-patient diversity. We highlight critical technical steps and call attention to potential pitfalls, offering troubleshooting guidance and important quality control details. For complete details on the use and execution of this protocol, please refer to Revach et al.1.
    Keywords:  Cancer; Immunology; Organoids
    DOI:  https://doi.org/10.1016/j.xpro.2025.104286
  15. Nat Commun. 2025 Dec 23. 16(1): 11339
      Identifying drivers of cancer progression to guide treatment selection is hindered by our limited understanding of tumor heterogeneity and its impact on tumor evolution. Here, we delineate the phenotypic variability across ~300,000 cells collected from multiple tumor loci in primary prostate and matched locoregional metastases using single-cell chromatin accessibility and gene expression sequencing. We find inter-patient heterogeneity to be confined to malignant populations. Within individual tumor loci, we see phenotypic heterogeneity among malignant cell populations despite a shared clonal genotypic architecture. We also observe that malignant cell populations disseminating to locoregional lymph nodes mirror the clonal architecture and phenotypic heterogeneity across primary tumor loci, while shifting from canonical prostate-cancer states to non-canonical inflammatory-like states. Our findings suggest a bottleneck imposed during the dissemination process, funneling prostate cancer cells toward an inflammatory-like cell state. These insights into the interplay between phenotypic identity and clonal architecture refine our understanding of prostate cancer progression and suggest that convergence of cancer cells towards an inflammatory-like state underlies dissemination to lymph nodes, offering a critical framework for future studies into prostate cancer metastatic potential.
    DOI:  https://doi.org/10.1038/s41467-025-67856-5
  16. bioRxiv. 2025 Dec 19. pii: 2025.12.16.694730. [Epub ahead of print]
      Oxygen gradients organize tissue architecture and metabolism 1,2 , yet their precise spatial profiles and mechanistic roles remain poorly understood because both in vivo measurement and in vitro control are technically challenging 3,4 . Here, we quantify the oxygen landscape of the mammalian intestine using microscale sensors, revealing a steep luminal-basal gradient of approximately 10-60 µM mm - 1 that collapses under antibiotic perturbation. We then recreate this physiological range ex vivo with a submerged chemostat microfluidic platform that fixes the oxygen boundary condition by coupling an oxygen-permeable PDMS chip to an external scavenger reservoir and integrating embedded optical sensors for real-time readout. This architecture suppresses ambient oxygen ingress and sustains programmable gradients of 10-20 µM mm - 1 across three-dimensional colorectal cancer organoid cultures while remaining compatible with live imaging and endpoint retrieval. The platform bridges quantitative in vivo oxygen mapping with controlled ex vivo modeling, establishing a generalizable approach to interrogate how spatial oxygen dynamics govern epithelial organization and disease progression.
    DOI:  https://doi.org/10.64898/2025.12.16.694730