bims-instec Biomed News
on Intestinal stem cells and chemoresistance in colon cancer and intestinal regeneration
Issue of 2025–06–08
fifteen papers selected by
Maria-Virginia Giolito, Université Catholique de Louvain



  1. Commun Biol. 2025 Jun 05. 8(1): 875
      Colorectal cancers (CRCs) present across a range of differentiation grades, which impact patient outcome and management; however, the molecular features and drivers of differentiation status are not fully understood. To address this, 84 commonly used human CRC cell lines were grown as xenografts in mice, revealing models of low-grade (LG) and high-grade (HG) CRC. Transcriptional profiling revealed coordinate downregulation of multiple transcription factors involved in intestinal development and differentiation, markers of colonic lineage-specific differentiation, and effectors of normal functions of the colonic epithelium in HG tumours. Mechanistically, multiple genes suppressed in HG tumours harboured promoter methylation, indicative of stable epigenetic silencing. Furthermore, markers of LGR5+ colon stem cells were suppressed in HG tumours, while markers of cell proliferation, fetal-like intestinal stem cells, and non-canonical cell types including mesenchymal cells were increased. These changes manifested in HG cell line displaying increased proliferation, migration and metastatic capacity. Importantly, CRC cell line-derived transcriptional profiles of differentiation grade were reflected in LG and HG patient-derived tumour organoids and primary CRCs, revealing cell lines accurately model differentiation grade. The models and tumour differentiation-related properties identified herein may inform new approaches for tailored CRC treatments based on tumour grade.
    DOI:  https://doi.org/10.1038/s42003-025-08251-0
  2. Methods Mol Biol. 2025 Jun 04.
      Organoids have emerged as a powerful in vitro model system for biomedical research, providing a physiologically relevant alternative to traditional cell lines. Intestinal organoids recapitulate the complex cellular composition and function of the intestinal epithelium, making them valuable for studying intestinal biology and disease. These three-dimensional (3D) cultures can be differentiated to contain all the major intestinal cell types-including enterocytes, Paneth cells, goblet cells, stem cells, enteroendocrine cells, and tuft cells-allowing for more accurate modeling of intestinal function. However, their 3D structure presents challenges for high-resolution imaging and histological analysis. Common methods for embedding intestinal organoids, such as frozen sectioning or pre-embedding in semi-solid gels, can compromise morphology and sectioning integrity. To address these limitations, we present an optimized paraffin-embedding protocol that provides robust immunofluorescent staining and imaging of intestinal organoids while preserving cellular architecture. This approach provides researchers with an improved tool for analyzing organoid-based models of intestinal function and disease.
    Keywords:  FFPE; Immunofluorescence; Organoids
    DOI:  https://doi.org/10.1007/7651_2025_633
  3. bioRxiv. 2025 May 13. pii: 2025.05.08.652522. [Epub ahead of print]
      Intestinal stem cells (ISCs) balance self-renewal and differentiation to maintain the intestinal epithelial barrier, which is replaced weekly throughout adult life. Genetic control of ISC differentiation is well-defined relative to transcription factor (TF) activity, but less is known regarding the role of chromatin regulation in ISC biology. Prior work from our lab and others has shown that Tet1 , a chromatin modifying enzyme involved in DNA demethylation, is specifically enriched in ISCs and early secretory progenitors. While constitutive loss of Tet1 is associated with defects in early postnatal ISC development, its role in adult ISC biology remains unknown. Here, we show that Tet1 safeguards ISC fate decisions by reducing sensitivity to extrinsic signaling. Inducible, intestine-specific Tet1 knockout mice (Tet1iKO) exhibit environmentally sensitive phenotypes, including absorptive differentiation bias and premature expression of mature absorptive transcripts in ISCs. These phenotypes are largely "silenced" in animals housed in a high-level barrier facility, where Tet1iKO epithelium closely resembles controls. Despite the lack of baseline phenotype in these conditions, Tet1iKO mice retain increased sensitivity to pro-differentiation signaling. In vivo , succinate administration induces increased tuft and goblet cell hyperplasia in the absence of Tet1 , while Tet1iKO organoids cultured with IL-4 or DAPT exhibit increased tuft and enteroendocrine cell specification, respectively. While ATAC-seq of Tet1iKO ISCs reveals minimal changes in chromatin accessibility, footprinting analysis suggests increased binding of lineage-specific TFs and CTCF even in the absence of cellular phenotypes. Together, our data demonstrate that Tet1 serves as a "buffer" against ISC differentiation and suggest that it does so in a lineage agnostic manner that is not dependent on changes in chromatin accessibility.
    DOI:  https://doi.org/10.1101/2025.05.08.652522
  4. Sci Rep. 2025 Jun 05. 15(1): 19813
      Human intestinal Organoids (HIOs) may be set up from primary human tissue following dissociation, release, and culture of intestinal LGR5 + stem cells. Here, we characterise the use of a semi-automated mechanical tissue dissociation technique, which demonstrates an expedited workflow and streamlined protocol, standardising key aspects of the process while consistently maintaining a high level of cultured organoid viability.
    Keywords:  Automation; Human intestinal organoids; Tissue dissociation
    DOI:  https://doi.org/10.1038/s41598-025-03905-9
  5. Nat Commun. 2025 Jun 04. 16(1): 5167
      In homeostasis, counterbalanced morphogen signalling gradients along the vertical axis of the intestinal mucosa regulate the fate and function of epithelial and stromal cell compartments. Here, we use a disease-positioned mouse and human tissue to explore the consequences of pathological BMP signalling dysregulation on epithelial-mesenchymal interaction. Aberrant pan-epithelial expression of the secreted BMP antagonist Grem1 results in ectopic crypt formation, with lineage tracing demonstrating the presence of Lgr5(-) stem/progenitor cells. Isolated epithelial cell Grem1 expression has no effect on individual cell fate, indicating an intercompartmental impact of mucosal-wide BMP antagonism. Treatment with an anti-Grem1 antibody abrogates the polyposis phenotype, and triangulation of specific pathway inhibitors defines a pathological sequence of events, with Wnt-ligand-dependent ectopic stem cell niches forming through stromal remodelling following BMP disruption. These data support an emerging co-evolutionary model of intestinal cell compartmentalisation based on bidirectional regulation of epithelial-mesenchymal cell fate and function.
    DOI:  https://doi.org/10.1038/s41467-025-60364-6
  6. Nature. 2025 Jun 04.
      Cancer cell plasticity enables the acquisition of new phenotypic features and is implicated as a major driver of metastatic progression1,2. Metastasis occurs mostly in the absence of additional genetic alterations3-5, which suggests that epigenetic mechanisms are important6. However, they remain poorly defined. Here we identify the chromatin-remodelling enzyme ATRX as a key regulator of colonic lineage fidelity and metastasis in colorectal cancer. Atrx loss promotes tumour invasion and metastasis, concomitant with a loss of colonic epithelial identity and the emergence of highly plastic mesenchymal and squamous-like cell states. Combined analysis of chromatin accessibility and enhancer mapping identified impairment of activity of the colonic lineage-specifying transcription factor HNF4A as a key mediator of these observed phenotypes. We identify squamous-like cells in human patient samples and a squamous-like expression signature that correlates with aggressive disease and poor patient prognosis. Collectively, our study defines the epigenetic maintenance of colonic epithelial identity by ATRX and HNF4A as suppressors of lineage plasticity and metastasis in colorectal cancer.
    DOI:  https://doi.org/10.1038/s41586-025-09125-5
  7. Cell Rep Med. 2025 May 23. pii: S2666-3791(25)00231-9. [Epub ahead of print] 102158
      Targeted therapies for advanced microsatellite stable (MSS) subtype colorectal cancer (MSS-CRC) remain a clinical challenge. Here, we show that death receptor 5 (DR5) is elevated in both MSS and microsatellite instability-high (MSI-H) colorectal cancer (CRC) cohorts, highlighting its potential as a clinical target. Oba01, a clinical-stage DR5-targeting antibody-drug conjugate (ADC) delivering the microtubule-disrupting agent monomethyl auristatin E (MMAE), shows superior efficacy in CRC cell lines, patient-derived xenografts and their corresponding organoids, irrespective of MSS or MSI-H status. Importantly, our functional multi-omics analysis reveals that the cell cycle pathway and cyclin-dependent kinases (CDKs) are key synergistic targets of Oba01's tumor-killing activity. We further show that Oba01 synergizes with the Food and Drug Administration (FDA)-approved CDK inhibitor abemaciclib in clinically relevant in vivo models. This synergy is also observed with other CDK inhibitors, underscoring the potential of combining Oba01 with CDK inhibition as a therapeutic strategy for advanced CRC, particularly the refractory MSS subtype.
    Keywords:  CDK4; DR5; Oba01; abemaciclib; advanced colorectal cancer; antibody-drug conjugate; synergetic effect
    DOI:  https://doi.org/10.1016/j.xcrm.2025.102158
  8. Regen Ther. 2025 Jun;29 541-550
      The intestine is exposed constantly to mechanical stimuli, including blood flow or peristalsis. Recently, gut-on-a-chip models have been developed to recapitulate these physiological stresses. In such models, blood flow and peristalsis are simulated by perfusing culture medium through microchannels and applying cyclic suction to vacuum chambers. With these gut-on-a-chips, the effects of mechanical stimuli on the intestinal structure and function have been elucidated. Additionally, gut-on-a-chip models are used to study intestinal diseases, such as infectious diseases, inflammatory bowel disease, and colorectal cancer. Because they accurately recapitulate the pathophysiology of intestinal diseases, research leveraging their use has revealed mechanisms underlying disease onset and progression in the intestine. In this review, we summarize the development of gut-on-a-chip systems and highlight recent research on intestinal diseases using these models.
    Keywords:  Gut-on-a-chip; Intestinal organoid; Microphysiological system; Organ-on-a-chip
    DOI:  https://doi.org/10.1016/j.reth.2025.04.023
  9. bioRxiv. 2025 May 13. pii: 2025.05.07.652677. [Epub ahead of print]
      Short chain fatty acids (SCFAs) are small metabolites that are produced through the activity of microbes and have important roles in human physiology. These metabolites have varied mechanisms in interacting with the host, of which one such mode is decorating the chromatin landscape. We previously detected specific histone modifications in the mouse gut that can be derived from SCFAs and are regulated by the microbiota. However, the roles of these SCFAs on chromatin and how they impact gene regulation in human cells is largely unknown. Now, our studies demonstrate these microbiota-dependent histone posttranslational modifications (PTMs) are associated with alterations in gene regulation in human cells. We show that histone butyrylation on H3K27 is detected in human colon samples. Furthermore, histone acetylation, butyrylation, and propionylation on H3K9 and H3K27 are responsive to levels of SCFAs in human colon cancer cell lines and are associated with active gene regulatory elements. In addition, treatment of human cancer cell lines with individual metabolites or combinations of SCFAs replicating the intestinal lumen environment result in distinct and overlapping gene program changes, with butyrate largely driving gene regulatory effects of SCFA combinations. Lastly, we define butyrate effects on gene expression that are independent of HDAC inhibition and are dependent on p300/CBP, suggesting potential gene programs regulated by histone butyrylation. Together, these results demonstrate that SCFAs are key regulators of the chromatin landscape and gene programs in human colorectal cancer cells.
    DOI:  https://doi.org/10.1101/2025.05.07.652677
  10. bioRxiv. 2025 May 17. pii: 2025.05.16.654585. [Epub ahead of print]
      Individual epithelial cells that acutely express oncogenes such as Ras or Src are extruded apically from monolayers of wildtype cells. Multiple signaling networks have been implicated but the extrusion mechanism is still not fully understood. We examined extrusion of mammary epithelial cells caused by acute induction of oncogenic Ras(Q61L). As reported by others, Ras-dependent extrusion requires downstream activation of ERK but not AKT. Unexpectedly, however, extrusion was completely blocked by Erlotinib, which inhibits Epidermal growth factor receptor (EGFR) activity, or by deletion of the receptor. In pancreatic and lung cancers, EGFR is required for full activation of Ras and consequent ERK activation. However, inhibition or deletion of EGFR had no impact in our system on Ras(Q61L)-GTP levels or ERK phosphorylation. Importantly, receptor function was cell autonomous, because EGFR expression was not required in surrounding WT cells but was essential in the Ras(Q61L) cells, yet did not act through the canonical ERK signaling pathway. Deletion of Ras exchange factors Sos1/2 did not block cell extrusion. Moreover, expression of a constitutively active MEK mutant, instead of Ras, was sufficient to drive extrusion, and EGFR inhibition or knockout in these cells blocked extrusion, with no change in phospho-ERK levels. Notably, acute expression of Ras triggered internalization of E-cadherin, which was partially blocked by inhibition of EGFR. Knockout of E-cadherin was alone sufficient to promote extrusion. Together, these data demonstrate an unanticipated requirement for noncanonical EGFR signaling in cancer cell extrusion, which may act in part through the promotion of E-cadherin endocytosis.
    DOI:  https://doi.org/10.1101/2025.05.16.654585
  11. Cancer Res. 2025 Jun 06.
      Normal tissues actively employ a phenomenon called cell competition to drive the elimination and replacement of less fit loser cells by fitter winner cells. This quality control mechanism promotes tissues health, by favouring the selective expansion of fitter cells. Indeed, through cell competition, many mutant cells are eliminated from tissues by fitter normal cells. However, some oncogenic mutations can turn cells into super-competitors that outcompete normal cells, promoting tumorigenic growth and metastasis. Several cellular stresses have been associated with the loser status such as oxidative stress, DNA damage responses, unfolded protein response and mitochondrial dysfunction. By affecting these pathways, metabolism and dietary choices can regulate cellular fitness and cell competition. However, how these pathways affect competitive interactions in vivo, during the early establishment of mutant clones, is relatively little understood. Recent work from Hemalatha and colleagues introduces real-time fluorescence ratio metric imaging of NAD(P)H and FAD, to investigate cellular redox status - live and over time, at single cell level - as cells compete in the mouse epidermis. Their work demonstrates that redox status changes dynamically during competition between cell carrying oncogenic mutations. It further shows that drugs that modulate mitochondrial metabolism and cellular redox are strong modulators of cell competition. The introduction of live redox imaging will prove a powerful tool to further dissect how metabolic states affect cell competition in normal physiology and in tumorigenesis.
    DOI:  https://doi.org/10.1158/0008-5472.CAN-25-2374
  12. Free Radic Biol Med. 2025 May 29. pii: S0891-5849(25)00720-8. [Epub ahead of print]237 110-130
      Acetyl-CoA carboxylase (ACC) is a rate-limiting enzyme in de novo lipogenesis. Here, we show a unique function of ACC in disrupting cellular iron homeostasis to drive ferroptosis, an iron-dependent, lipid peroxidation-induced form of cell death. We observed neuronal lipid accumulation and elevated labile iron pool associated with ACC dephosphorylation in mouse models of obstructive sleep apnea (OSA), a highly prevalent neurodegenerative disorder. ACC gene (Acaca) knockout (KO) or inhibition of its enzymatic activity rescued cellular iron metabolism through restoring lysosomal integrity and function, suppressing neuronal ferroptosis. ACC inactivation-driven lysosomal iron homeostasis requires the NFE2L2/NRF2-TFEB axis. Empagliflozin mitigates cellular iron overload via the ACC-NRF2-TFEB-lysosome pathway to alleviate neuronal ferroptosis, cognitive impairment, and mood dysfunction in OSA mice. Furthermore, inhibiting neuronal ACC reduces microglial activation, characterized by elevated complement proteins and pro-inflammatory cytokines, while microglia-specific C1qa KO prevents neuronal injury in OSA mice. Our findings identify a unique coupling between iron homeostasis and lipogenic signaling, suggesting ACC as a potential therapeutic target for neuronal ferroptosis and the resultant microgliosis in neurodegenerative diseases.
    Keywords:  Acetyl-CoA carboxylase; Cognitive impairment; Ferroptosis; Iron homeostasis; Lysosome
    DOI:  https://doi.org/10.1016/j.freeradbiomed.2025.05.421
  13. bioRxiv. 2025 May 16. pii: 2025.05.15.653154. [Epub ahead of print]
      Colorectal cancer (CRC) diagnosed before age 50 years (early-onset CRC, EO-CRC) is rising at an alarming rate, yet its molecular and microenvironmental drivers remain poorly understood. EO-CRC is highly heterogeneous, and while subtle differences from late-onset CRC (LO-CRC) have been reported, their full extent remains unresolved due to the limited scope of previous studies. Here, we integrate public data with in-house clinical samples profiled by single-cell RNA sequencing (scRNA-seq) and multiplex immunofluorescence (mIF) to compare EO-CRC and LO-CRC. Additionally, we employ gene regulatory network-based protein activity inference (VIPER), enabling a more precise characterization of key regulatory proteins driving tumor-stroma interactions. Our analysis reveals that EO-CRC and LO-CRC have a largely similar immune composition, challenging previous reports of an "immune-cold" phenotype in EO-CRC. However, we identify distinct stromal differences, including a significant enrichment of fibroblasts in EO-CRC. Notably, we define a previously unrecognized epithelial subpopulation in EO-CRC, marked by high expression of toll-like receptor 4 (TLR4) and C-C chemokine receptor type 5 (CCR5)-key mediators of inflammation-driven tumor progression and fibroblast recruitment. These findings suggest that EO-CRC may be driven by a tumor-intrinsic inflammatory phenotype with enhanced stromagenesis, providing new insights into potential mechanisms underlying its increasing incidence in young adults.
    DOI:  https://doi.org/10.1101/2025.05.15.653154
  14. Am J Physiol Gastrointest Liver Physiol. 2025 Jun 05.
      Homeostasis of the mammalian intestinal epithelium is tightly regulated by multiple factors including cellular polyamines, but the exact mechanism underlying polyamines in this process remains largely unknown. Mitochondria are the powerhouse of cells and can also function as signaling organelles by releasing metabolic by-products. Here we determined whether polyamines regulate intestinal epithelial renewal and wound healing by altering mitochondrial activity. Depletion of cellular polyamines by inhibiting ornithine decarboxylase with α-difluoromethylornithine (DFMO) resulted in mitochondrial dysfunction as evidenced by decreases in basal and maximal respiration levels, ATP production, and spare respiration capacity. Polyamines depletion by DFMO also decreased the levels of mitochondria-associated proteins prohibitin 1 and COX-IV. Mitochondrial dysfunction induced by DFMO was associated with an inhibition of intestinal organoid growth and epithelial repair after wounding and this inhibition was ameliorated by administration of the mitochondrial activator Mito-Tempo or exogenous polyamine putrescine. These results indicate that polyamines are necessary for mitochondrial metabolism, in turn controlling constant intestinal mucosal growth and epithelial repair after acute injury.
    Keywords:  Mito-Tempo; intestinal epithelial integrity; mitochondral proteins; ornithine decarboxylase
    DOI:  https://doi.org/10.1152/ajpgi.00023.2025
  15. BMC Cancer. 2025 Jun 05. 25(1): 1005
       BACKGROUND: Explosive tumor growth is characterized by rapid tumor growth in a short time period. Currently, there is no precise scientific definition for the condition, which is often accompanied with a poor clinical prognosis. Herein, we presented a study of a young patient with colon cancer who experienced explosive tumor growth. A clinical multidisciplinary team (MDT) collaborated with bioinformaticians to provide precise treatment and elucidate the biological mechanisms underpinning this growth.
    METHODS: A 28-year-old male patient diagnosed with colon cancer experienced explosive tumor growth. Peripheral bloods (PB) during immunotherapy were collected for immune cytokine analyses and flow cytometry assays on immune cell subsets. To further examine the underlying mechanisms of this explosive-growth, we conducted whole exome sequencing (WES) and RNA-sequencing (RNA-seq) of samples taken at different time points.
    RESULTS: The patient was diagnosed with Lynch syndrome. We implemented an immunotherapy and performed PB immune cytokine assays before, during, and after this therapy. Our observations suggested that immunotherapy may remodel interferon-gamma (IFN-γ) signaling and enhance T cell-mediated immune responses. By exploring explosive tumor growth mechanisms, we observed that tumors had significantly less insertion and deletion (INDEL) mutations and INDEL-derived neoantigens. Additionally, they had deficient antigen presentation functions as characterized by decreased IFN-γ signaling activity.
    CONCLUSIONS: Neoantigen loss and decreased IFN-γ signaling activity contributed to explosive tumor growth in this patient. Recovered IFN-γ signaling may lead to effective immunotherapy outcomes.
    Keywords:  Colorectal cancer; Explosive tumor growth; Immunotherapy; Lynch syndrome
    DOI:  https://doi.org/10.1186/s12885-025-14211-y