bims-instec 2025-11-30 papers

bims-instec

Biomed News

on Intestinal stem cells and chemoresistance in colon cancer and intestinal regeneration

Issue of 2025–11–30
twenty-one papers selected by
Maria-Virginia Giolito, Université Catholique de Louvain

Lgr5+ Stem Cells Maintain Apex Position in Cell Hierarchy of the Intestinal Epithelium During Homeostasis and Injury.
Leveraging WNT Hyperactivation to Kill Colorectal Cancer While Rejuvenating Healthy Intestine.
Impact of treatment history on drug resistance of metastatic colorectal cancer organoids.
MAPK-driven epithelial cell plasticity drives colorectal cancer therapeutic resistance.
Iron addicted colorectal cancers exploit Heme-Complex II axis to resist oxidative cell death.
Colorectal cancer cell-derived exosomes induce metabolic reprogramming of cancer-associated fibroblasts to promote colorectal cancer growth.
A niche-dependent redox rheostat regulates epithelial stem cell fate.
Iron homeostasis and cell clonality drive cancer-associated intestinal DNA methylation drift in aging.
The Wnt/APC destruction complex targets SREBP2 in a β-catenin-independent pathway to control cholesterol metabolism.
Colorectal cancer relies on an immunosuppressive cellular topography and genomic adaptations for establishing brain metastases.
Lifting regenerative barriers promotes epithelial cell fate plasticity supporting lineage conversion.
Nuclei sense complex tissue shape and direct intestinal stem cell fate.
Targeting fibroblast derived thrombospondin 2 disrupts an immune-exclusionary environment at the tumor front in colorectal cancer.
Comprehensive single-cell transcriptome landscape of metastatic colorectal cancer identifies budding-potential cells and their interactions with cancer-associated fibroblasts.
Cell size modulates ferroptosis susceptibility.
Multiomics analyses of human colorectal cancer reveal changes in mitochondrial metabolism associated with chemotherapy resistance.
Polyclonal origins of human premalignant colorectal lesions.
Polyamines sustain epithelial regeneration in aged intestines by modulating protein homeostasis.
A robust classifier for the intrinsic consensus molecular subtypes in colorectal cancer.
Fatty acids modulate the colorectal cancer immune microenvironment via regulating the interaction and transactivation of PPARα/δ and P53.
Dietary eicosapentaenoic and docosahexaenoic acids reduce oxylipins that provide early mediators of colonic inflammation induced by chemotherapy.

bioRxiv. 2025 Nov 11. pii: 2025.11.09.687498. [Epub ahead of print]

Lgr5+ Stem Cells Maintain Apex Position in Cell Hierarchy of the Intestinal Epithelium During Homeostasis and Injury.

Julian Chua, Lucy Driver, Masahiro Narimatsu, Mardi Fink, Lixia Luo, Jordan Tran, Arshdeep Kaur, Rida Habib, Jatin Roper, David G Kirsch, Jeffrey L Wrana, Chang-Lung Lee, Arshad Ayyaz.

The cellular origin of intestinal epithelial homeostasis and regeneration has been a subject of continued debate, with recent models challenging the primacy of WNT-dependent Lgr5⁺ crypt base columnar (CBC) cells as the central intestinal stem cell population. Here, we revisit this question through quantitative integration of single-cell transcriptomic, chromatin accessibility, spatial, and lineage-tracing analyses across the proximal-to-distal axis of the small intestinal epithelium. Our data show that under homeostatic conditions, Lgr5⁺ cells exclusively sustain epithelial self-renewal in nearly all crypt-villus units along the entire length of the small intestine, a process for which R-spondin is indispensable. Following irradiation or chemotoxic injury, surviving Lgr5⁺ cells and their progeny reprogram into transient fetal-like cell states that initiate epithelial repair. Crucially, successful regeneration depends on the reactivation of canonical WNT/β-catenin signaling, as evidenced by increased TCF motif accessibility and upregulation of WNT target genes in newly forming Lgr5 + stem cells. Accordingly, pharmacological inhibition of WNT signaling blocks the reconstitution of Lgr5⁺ cells and crypt regeneration, leading to epithelial collapse. These findings reconcile prior controversies by demonstrating the central role of Lgr5⁺ CBC cells in epithelial self-renewal and regeneration following injury.

DOI: https://doi.org/10.1101/2025.11.09.687498
bioRxiv. 2025 Oct 06. pii: 2025.10.05.680591. [Epub ahead of print]

Leveraging WNT Hyperactivation to Kill Colorectal Cancer While Rejuvenating Healthy Intestine.

George Eng, Jonathan Braverman, Manish Gala, Omer Yilmaz.

WNT signaling maintains intestinal homeostasis yet drives colorectal cancer (CRC) when constitutively activated by APC mutations. We overturn the fundamental assumption that APC-mutant tumors exist at maximal WNT activation, revealing instead that cancer cells occupy a precarious "WNT-just-right" zone along a signaling continuum. This discovery exposes an unprecedented therapeutic vulnerability: while normal intestinal epithelium thrives with enhanced WNT signaling, APC-mutant tumor cells undergo apoptosis when pushed beyond their oncogenic setpoint, a phenomenon we term "over-WNTing." Through systematic organoid-based screening, we identified that WNT hyperactivation through multiple approaches: GSK3 inhibition, concentrated WNT proteins, or APC knockdown in GSK3-null backgrounds, selectively kills tumor cells by hyperactivating the driving pathway of CRC. Mechanistically, over-WNTing in APC-mutant cells triggers spillover into non-canonical planar cell polarity signaling, where RHOC upregulation induces ROCK1/2-mediated apoptosis. We demonstrate therapeutic efficacy across the neoplastic continuum, from adenomas to metastatic CRC, including patient-derived tumors, validating GSK3 inhibition with a novel nanoparticle formulation. This discovery enables the first cancer therapy that simultaneously enhances normal tissue function while eliminating tumors. "Over-WNTing" effectively treats adenomas and both mouse and patient-derived CRC, establishing a therapeutic paradigm that exploits fundamental differences in cellular WNT biology to achieve the dual benefit of eliminating cancer while promoting healthy tissue regeneration.

DOI: https://doi.org/10.1101/2025.10.05.680591
iScience. 2025 Nov 21. 28(11): 113801

Impact of treatment history on drug resistance of metastatic colorectal cancer organoids.

Maarten A Huismans, Lidwien P Smabers, Sascha R Brunner, Arne van Hoeck, Demi van de Kaa, Ingrid A Franken, Emerens Wensink, Jan Koster, Richard Volckmann, Onno Kranenburg, Miriam Koopman, Hugo J G Snippert, Jeanine M L Roodhart.

  The treatment of metastatic colorectal cancer (mCRC) is impeded by drug resistance. We investigated how prior chemotherapy affects tumor genotype, phenotype, and resistance mechanisms by comparing 35 patient-derived metastatic organoids (PDOs) from pretreated and chemonaive patients with mCRC. Combining PDO drug sensitivity assessments with RNA and whole genome sequencing, we found PDOs from pretreated patients exhibited higher mutational load and more structural variants. Chemotherapy-related mutational signatures correlated with previous exposure. PDOs from oxaliplatin-resistant patients maintained this resistance, showing the upregulation of ZNF300, TGM2, and Hedgehog pathway enrichment. Acquired resistance to 5-FU and irinotecan was only partially captured, with irinotecan resistance linked to specific mutational signatures and deep deletions in common fragile sites, associated with distinct gene expression profiles. Our findings reveal that PDOs capture chemotherapy-induced genomic and phenotypic changes differently depending on the drug, suggesting varied mechanisms of acquired resistance involving both tumor cell-intrinsic properties and dynamic tumor cell states.

Keywords:  Biological sciences; Cancer; Health sciences; Internal medicine; Medical specialty; Medicine; Oncology

DOI:  https://doi.org/10.1016/j.isci.2025.113801
Nature. 2025 Nov 24.

MAPK-driven epithelial cell plasticity drives colorectal cancer therapeutic resistance.

Mark White, Megan L Mills, Laura M Millett, Kathryn Gilroy, Yourae Hong, Lucas B Zeiger, Rosalin J Simpson, Shania M Corry, Amelia Ligeza, Tamsin R M Lannagan, Susanti Susanti, Rachel A Ridgway, Ayse S Yazgili, Lucile Grzesiak, Raheleh Amirkhah, Catriona A Ford, Nikola Vlahov, Hannah Tovell, Leah Officer-Jones, Catherine Ficken, Rachel Pennie, Arafath K Najumudeen, Alexander Raven, Nadia Nasreddin, Ekansh Chauhan, Andrew S Papanastasiou, Colin Nixon, Vivienne Morrison, Rene Jackstadt, Janet S Graham, Crispin J Miller, Sarah J Ross, Simon T Barry, Valeria Pavet, Richard H Wilson, John Le Quesne, Philip D Dunne, Sabine Tejpar, Simon Leedham, Andrew D Campbell, Owen J Sansom.

The colorectal epithelium is rapidly renewing, with remarkable capacity to regenerate following injury. In colorectal cancer (CRC), this regenerative capacity can be co-opted to drive epithelial plasticity. While oncogenic MAPK signalling in CRC is common, with frequent mutations of both KRAS (40-50%) and BRAF (10%)1, inhibition of this pathway typically drives resistance clinically. Given the development of KRAS inhibitors, and licensing of BRAF inhibitor combinations2-4, we have interrogated key mechanisms of resistance to these agents in advanced preclinical CRC models. We show that oncogenic MAPK signalling induces epithelial state changes in vivo, driving adoption of a regenerative/revival stem like population, while inhibition leads to rapid transcriptional remodeling of both Kras- and Braf-mutant tumours, favoring a Wnt-associated, canonical stem phenotype. This drives acute therapeutic resistance in Kras- and delayed resistance in Braf-driven models. Importantly, where plasticity is restrained, such as in early metastatic disease, or through targeting ligand-dependent Wnt-pathway Rnf43 mutations, marked therapeutic responses are observed. This explains the super response to BRAF+EGFR targeted therapies previously observed in a BRAF/RNF43 co-mutant patient population, highlighting the criticality of cellular plasticity in therapeutic response. Together, our data provides clear insight into the mechanisms underpinning resistance to MAPK targeted therapies in CRC. Moreover, strategies that aim to corral stem cell fate, restrict epithelial plasticity or intervene when tumours lack heterogeneity may improve therapeutic efficacy of these agents.

DOI: https://doi.org/10.1038/s41586-025-09916-w
bioRxiv. 2025 Nov 06. pii: 2025.11.05.686813. [Epub ahead of print]

Iron addicted colorectal cancers exploit Heme-Complex II axis to resist oxidative cell death.

Chesta Jain, Muqit Essani, Roshan Kumar, Nupur K Das, Rashi Singhal, Nicholas J Rossiter, Brandon Chen, Wesley Huang, Zheng Hong Lee, Sumeet Solanki, Yuezhong Zhang, Peter Sajjakulnukit, Li Zhang, Prarthana J Dalal, David A Hanna, Shannon McCollum, Elena M Stoffel, Joel K Greenson, L James Maher, Costas A Lyssiotis, Ruma Banerjee, Yatrik M Shah.

Colorectal cancer (CRC) cells are addicted to iron, which fuels nucleotide synthesis, mitochondrial respiration, and rapid proliferation. Yet paradoxically, high intracellular iron is cytotoxic to most other cells, raising the question of how CRC cells tolerate and exploit iron-rich environments. One pathway thought to mediate iron toxicity is ferroptosis, an iron-dependent form of cell death. However, most ferroptosis regulators were identified through synthetic chemical screens or small molecule activators, and it remains unclear whether these canonical pathways explain how iron itself triggers cell death, particularly in vivo . Here, using multi-omics profiling, CRISPR screening, and in vivo models, we uncover a heme-succinate dehydrogenase (SDH)-Coenzyme Q (CoQ) axis that enables CRC cells to buffer iron-induced oxidative stress. Heme-dependent SDH reduces CoQ, which redistributes to mitochondrial and plasma membranes to detoxify lipid ROS as a radical trapping antioxidant. This pathway functions alongside, and in some contexts independently of, canonical ferroptosis regulators. These findings reveal that CRCs co-opt metabolic cofactors not only for growth but also for survival under physiologically toxic iron levels, uncovering new vulnerabilities for therapy.

DOI: https://doi.org/10.1101/2025.11.05.686813
Discov Oncol. 2025 Nov 24. 16(1): 2146

Colorectal cancer cell-derived exosomes induce metabolic reprogramming of cancer-associated fibroblasts to promote colorectal cancer growth.

Guopeng Pan, Zexiong Cheng, Yiwei Wang, Changxi Wu, Fang Wang, Qing Li, Xiangyu Wang, Yuequan Zeng, Yuqin Li, Kai Li, Xi Lin, Fan Xing, Youwei Huang, Jun Liu, Rui Wang.

  Urea cycle (UC) dysfunction drives tumorigenesis and poor prognosis, yet its role in tumor-stroma crosstalk is unclear. Here we show that colorectal cancer (CRC) cells reprogram UC metabolism in cancer-associated fibroblasts (CAFs) via CRC-derived exosomes. Reprogrammed CAFs support CRC cell growth by providing UC metabolites, especially arginine (Arg). Depriving CRC cells of Arg halts their growth and simultaneously increases their reliance on putrescine while up-regulating ornithine decarboxylase (ODC), the polyamine-biosynthesis gatekeeper. Our study illustrates the UC metabolic interaction between CAFs and CRC cells and demonstrates the potential therapeutic utility of Arg restriction and ODC blockade combination treatment for colorectal cancer.

Keywords:  Arginine; Cancer-associated fibroblasts; Colorectal cancer; Exosomes; Ornithine decarboxylase; Putrescine; Urea cycle

DOI:  https://doi.org/10.1007/s12672-025-03914-0
Nat Commun. 2025 Nov 28.

A niche-dependent redox rheostat regulates epithelial stem cell fate.

Xi Chen, Krishnan Raghunathan, Bin Bao, Elsy Ngwa, Andrew Kwong, Zhongyang Wu, Stephen Babcock, Clara Baek, George Ye, Anoohya Muppirala, Qianni Peng, Michael Rutlin, Mantu Bhaumik, Daping Yang, Daniel Kotlarz, Unmesh Jadhav, Meenakshi Rao, Eranthie Weerapana, Xu Zhou, Jose Ordovas-Montanes, Scott B Snapper, Jay R Thiagarajah.

Intestinal stem cells (ISCs) reside in regionally variable niches that provide diverse microenvironmental cues such as tissue oxygen status, and morphogen signaling. Integration of these cues with ISC metabolism and fate remains poorly understood. Here, we show that cellular redox balance orchestrates niche factors with metabolic state to govern cell fate decisions. We demonstrate that hypoxia and Wnt signaling synergistically restrict the reactive oxygen species generating enzyme NADPH oxidase 1 (NOX1) regionally to the crypt base in the distal colon. NOX1 enables maintenance of an oxidative cell state that licenses cell cycle entry, altering the balance of asymmetric ISC self-renewal and lineage commitment. Mechanistically, cell redox state directs a self-reinforcing circuit that connects hypoxia inducible factor 1α-dependent signaling with post-translational regulation of the metabolic enzyme isocitrate dehydrogenase 1. Our studies show redox balance acts as a cellular rheostat that is central and causative for metabolic control of the ISC cell-cycle.

DOI: https://doi.org/10.1038/s41467-025-66636-5
Nat Aging. 2025 Nov 26.

Iron homeostasis and cell clonality drive cancer-associated intestinal DNA methylation drift in aging.

Anna Krepelova, Mahdi Rasa, Francesco Annunziata, Jing Lu, Chiara Giannuzzi, Omid Omrani, Elisabeth Wyart, Paolo Ettore Porporato, Ihab Ansari, Dor Bilenko, Yehudit Bergman, Francesco Neri.

Epigenetic drift is a key feature of aging and is associated with age-related diseases including cancer, yet the underlying molecular mechanisms remain unclear. Here, by analyzing DNA methylation and gene expression data from healthy and cancerous human colon samples, we identify an aging and colon cancer-associated DNA methylation (DNAm) drift. We find evidence that this drift is conserved in the mouse intestinal epithelium, where we demonstrate its origin within intestinal stem cells and identify its cell-intrinsic and non-mitotic characteristics, finding that its expansion is regulated via crypt clonality and fission. Mechanistically, we find that this drift is driven by age-related inflammation and reduced Wnt signaling, which dysregulate iron metabolism and impair TET activity. Despite CpG-level heterogeneity, we find that DNAm changes are consistent at the gene level, suggesting potential functionality. Our findings shed light on the epigenetic mechanisms of aging and provide a mechanistic basis for the hypermethylation observed in cancer.

DOI: https://doi.org/10.1038/s43587-025-01021-x
bioRxiv. 2025 Nov 18. pii: 2025.10.12.681896. [Epub ahead of print]

The Wnt/APC destruction complex targets SREBP2 in a β-catenin-independent pathway to control cholesterol metabolism.

Ahmed Rattani, Cora Anderson, William V Trim, Esteban Garita, Shinya Imada, Saleh Khawaled, Heaji Shin, Jiuchun Zhang, Ömer H Yilmaz, Marc Kirschner.

APC, the core scaffold of the Wnt destruction complex, targets the transcriptional co-activator β-catenin for proteolysis. There is no convincing evidence that APC directs degradation of other substrates. Using a reconstituted cytosolic extract-based system and complementary in vivo and cellular assays, we show that SREBP2, the master regulator of cholesterol biosynthesis, is a direct APC-AXIN1 substrate. APC-dependent SREBP2 degradation is conserved in Xenopus embryos, mouse colon, and human colorectal cancer cells and restricts SREBP2 target-gene expression, cholesterol synthesis, and tissue cholesterol levels. Mechanistically, APC and AXIN1 promote SREBP2 degradation via a conserved phosphodegron, which marks SREBP2 for ubiquitination by the E3 enzyme, FBXW7. Like β-catenin, SREBP2 is stabilized by extracellular Wnt ligands; unlike β-catenin, its regulation is independent of GSK3β and CK1α and requires the entire APC mutational cluster region (MCR), whereas β-catenin turnover can operate with only a partial MCR. These findings define a β-catenin-independent branch of Wnt signaling that couples APC to sterol metabolism, providing a mechanistic rationale to target the mevalonate/SREBP2 axis in APC-mutant colorectal cancer.

DOI: https://doi.org/10.1101/2025.10.12.681896
bioRxiv. 2025 Nov 16. pii: 2025.11.14.688538. [Epub ahead of print]

Colorectal cancer relies on an immunosuppressive cellular topography and genomic adaptations for establishing brain metastases.

Anuja Sathe, Mengrui Zhang, Xiangqi Bai, Ji In Kang, Rithika Meka, Huiyun Sun, Susan M Grimes, Aparajita Khan, Mingen Liu, Andrew S Luksik, Michael Lim, Claudia K Petrisch, Christopher M Jackson, Hannes Vogel, Jeanne Shen, Melanie Gephart, Summer Han, Hanlee P Ji.

Colorectal cancer ( CRC ) brain metastases have a poor prognosis and limited treatment options, including resistance to radiation therapy. Little is known about the molecular and cellular mechanisms that enable CRC tumor cells to adapt to the brain and establish a supportive tumor microenvironment. To address this gap we used spatial transcriptomics to analyze 51 CRC brain metastases. A subset had matched primary colon tumors and longitudinally paired metastatic resections before and after radiation treatment. We identified the critical spatial cellular features of the tumor epithelium and the surrounding tumor microenvironment that support metastatic growth in the brain. CRC brain metastases developed a stromal microenvironment with abundant fibroblasts and tumor-associated macrophages. A fibroblast-macrophage cellular neighborhood promoted angiogenesis, extracellular matrix remodeling, and immune suppression. Tumor cells showed local adaptations. In endothelial-rich regions, they were proliferative whereas in macrophage-rich regions, they were more differentiated and immune evasive. Compared with paired primary tumors, CRC brain metastases showed increased chromosomal instability, with activation of RNA-processing, stress response, and junctional remodeling pathways. After radiation treatment, resistant clones had increased epithelial-mesenchymal transition, while the immunosuppressive stroma remained intact. We identified tumor-derived MIF , GDF15 , PRSS3 and SEMA3C ligands and macrophage-derived SPP1 that have the potential to affect multiple cell types in the metastatic niche. These ligand-receptor interactions drive angiogenesis, stromal activation and immune suppression. In a macrophage-tumor-fibroblast co-culture model, knockout of SPP1 in macrophages led to reduced expression of lipid-metabolism related genes and disrupted tumor-promoting interactions. Together, these results indicate that CRC growth in the brain is sustained by a specific cellular organization with immunosuppressive multicellular interactions.

DOI: https://doi.org/10.1101/2025.11.14.688538
Nat Commun. 2025 Nov 27.

Lifting regenerative barriers promotes epithelial cell fate plasticity supporting lineage conversion.

Maria T Bejar, Paula Jimenez-Gomez, Ilias Moutsopoulos, Harikrishnan Ajith, Bartomeu Colom, Jamie McGinn, Seungmin Han, Greta Skrupskelyte, Fernando J Calero-Nieto, Berthold Göttgens, Irina I Mohorianu, Benjamin D Simons, Maria P Alcolea.

The ability of adult epithelial cells to rewire their cell fate programme in response to injury has emerged as a new paradigm in stem cell biology. This plasticity supersedes the concept of strict stem cell hierarchies, granting cells access to a wider repertoire of fate choices. Yet, in order to prevent a disordered cellular response, this process must be finely regulated. Here we investigate the little-known regulatory processes that restrict fate permissibility in adult cells, and keep plasticity in check. Using a 3D regenerative culture system, that enables co-culturing epithelium and stroma of different origins, we demonstrate that oesophageal cells exposed to the ectopic signals of the dermis are capable of switching their identity towards skin. Lineage tracing experiments and histological analysis, however, reveal that the oesophageal-to-skin lineage conversion process is highly inefficient, pointing to the existence of barriers limiting cell fate re-specification. Single-cell RNA sequencing capturing the temporality of this process shows that cells transitioning towards skin identity resist the natural progression towards tissue maturation by remaining in a persistent regenerative state marked by a particularly strong hypoxic signature. Gain and loss of function experiments demonstrate that the HIF1a-SOX9 axis acts as a key modulator of epithelial cell fate plasticity, restricting changes in identity during tissue regeneration. Taken together, our results reveal the existence of lineage conversion barriers that must be resolved for cells to respond to signals instructing alternative fate choices, shedding light on the principles underlying the full regenerative capacity of adult epithelial cells.

DOI: https://doi.org/10.1038/s41467-025-66446-9
bioRxiv. 2025 Oct 24. pii: 2025.10.23.684219. [Epub ahead of print]

Nuclei sense complex tissue shape and direct intestinal stem cell fate.

Kaustav Bera, Delaney L McNally, Bruce E Kirkpatrick, Nolan R Petrich, F Max Yavitt, Marilyne Coulombe, Michaela Quintero, Nathaniel P Skillin, Alex Khang, Patrick S McGrath, Linda C Samuelson, Tanmay P Lele, Peter J Dempsey, Kristi S Anseth.

Tissue architecture and function are influenced by mechanical cues. Yet, how cell nuclei sense forces within 3D tissues and dictate differentiation remains unknown as prior studies focused on isolated mesenchymal cells, which fail to fully predict tissue-level mechanical properties. We fill this knowledge gap utilizing live reporters and material-based organoid models. We posit the nucleus as an active mechanosensor of tissue shape, with levels of the nuclear scaffolding protein lamin-A varying across intestinal stem cell differentiation trajectory. Elevated forces on differentiated Paneth cell nuclei, in both organoids and tissue explants, increase lamin-A and nuclear wrinkling. Enhancing nuclear mechanotransduction primes cell differentiation, in otherwise stem promoting conditions, revealing that nuclear mechanics can direct stem cell fate. By engineering spatiotemporally controlled de novo tissue curvature with photo-degradable hydrogels, we direct spatially patterned lamin-A levels across mouse and human organoids of healthy and diseased origin, uncovering conserved nuclear mechanosensing pathway in epithelial tissues.

DOI: https://doi.org/10.1101/2025.10.23.684219
Nat Commun. 2025 Nov 23.

Targeting fibroblast derived thrombospondin 2 disrupts an immune-exclusionary environment at the tumor front in colorectal cancer.

Kosuke Iwane, Yuki Nakanishi, Yu Muta, Jiayu Chen, Kento Yasumura, Mayuki Omatsu, Naoki Aoyama, Munehiro Ikeda, Yoko Masui, Liyang Cai, Go Yamakawa, Kensuke Hamada, Kenta Mizukoshi, Munenori Kawai, Kei Iimori, Shinnosuke Nakayama, Nobukazu Agatsuma, Takahiro Utsumi, Munemasa Nagao, Takahisa Maruno, Yukiko Hiramatsu, Nobuyuki Kakiuchi, Masahiro M Nakagawa, Yasuhiro Fukui, Yukina Kusunoki, Hiroaki Kasashima, Masakazu Fujimoto, Yoshiro Itatani, Toshiaki Kogame, Akihisa Fukuda, Masakazu Yashiro, Kiyoshi Maeda, Kenji Kabashima, Kazutaka Obama, Seishi Ogawa, Maria T Diaz-Meco, Jorge Moscat, Hiroshi Seno.

Fibrotic colorectal cancers (CRC) are largely microsatellite-stable and display desmoplastic stroma with poor immune infiltration. Here we identify thrombospondin-2 (THBS2) as a key regulator of the immune-exclusionary phenotype in fibrotic CRC. THBS2 is highly expressed by matrix cancer-associated fibroblasts at the tumor front. In an orthotopic model using desmoplastic tumor organoids, global or fibroblast-specific Thbs2 deletion disrupts the exclusionary barrier and increases intratumoral CD8 T cells. Mechanistically, THBS2 limits recruitment of CXCR3+ CD8 T cells by restraining dendritic- and macrophage-derived CXCL9/10. Depletion of these myeloid cells or blockade of CXCL9/10-CXCR3 signaling abolishes the enhanced CD8 T-cell influx and antitumor efficacy. Spatial profiling demonstrates that THBS2 loss induces proximity between CD8 T cells and myeloid cells and upregulates chemokines. Despite increased infiltration, CD8 T cells manifest exhaustion, rendering tumors highly susceptible to immune checkpoint blockade. THBS2 thus represents a tractable CAF-restricted target to overcome immune exclusion in fibrotic CRCs.

DOI: https://doi.org/10.1038/s41467-025-66485-2
NPJ Precis Oncol. 2025 Nov 26.

Comprehensive single-cell transcriptome landscape of metastatic colorectal cancer identifies budding-potential cells and their interactions with cancer-associated fibroblasts.

Yao Ma, Lijian Wang, Ziyue Zhang, Yifei Zhao, Zimin Zhao, Renjie Luo, Junwei Wang, Limei Guo, Wei Fu, Kai Miao, Xin Zhou.

Tumor budding is positively associated with colorectal cancer (CRC) metastasis. In this study, we integrated a single-cell transcriptomic dataset of 287 CRC samples to comprehensively illustrate the transcriptomic landscape of metastatic CRC and identified a unique subcluster of tumor epithelial cells associated with tumor budding. This subcluster exhibited high mesothelin (MSLN) expression and was located at the invasive front of CRC. MSLN was confirmed to promote CRC growth and metastasis by in vitro and in vivo models. Also, POSTN+ fibroblasts in the CRC microenvironment showed enhanced expression of genes in epithelial-mesenchymal transition and angiogenesis signaling pathways, which wrapped around MSLN+ tumor budding cells in the invasive front of CRC. POSTN+ fibroblasts may interact with MSLN+ budding-potential cells through the ligand-receptor pair POSTN-ITGB5 to promote tumor metastasis. In conclusion, our findings identified the transcriptomic feature of budding-potential cells and revealed the role of crosstalk between MSLN+ budding-potential cells and POSTN+ fibroblasts in CRC metastasis, which provide new insights into targeting cancer-associated fibroblasts and tumor budding cells in CRC therapy.

DOI: https://doi.org/10.1038/s41698-025-01187-y
bioRxiv. 2025 Oct 26. pii: 2025.10.25.684524. [Epub ahead of print]

Cell size modulates ferroptosis susceptibility.

Evgeny Zatulovskiy, Magdalena B Murray, Shuyuan Zhang, Scott J Dixon, Jan M Skotheim.

Size is a fundamental property of cells that influences many aspects of their physiology. This is because cell size sets the scale for all subcellular components and drives changes in the composition of the proteome. Given that large and small cells differ in their biochemical composition, we hypothesize that they should also differ in how they respond to signals and make decisions. Here, we investigated how cell size affects the susceptibility to cell death. We found that large cells are more resistant to ferroptosis induced by system x c - inhibition. Ferroptosis is a type of cell death characterized by the iron-dependent accumulation of toxic lipid peroxides. This process is opposed by cysteine-dependent lipid peroxide detoxification mechanisms. We found that larger cells exhibit higher concentrations of the cysteine-containing metabolite glutathione and lower concentrations of membrane lipid peroxides, compared to smaller cells. Mechanistically, this can be explained by the fact that larger cells had lower concentrations of an enzyme that enriches cellular membranes with peroxidation-prone polyunsaturated fatty acids, ACSL4, and increased concentrations of the iron-chelating protein ferritin and the glutathione-producing enzymes glutamate-cysteine ligase and glutathione synthetase. Taken together, our results highlight the significant impact of cell size on cellular function and survival, revealing a size-dependent vulnerability to ferroptosis that could influence therapeutic strategies based on this cell death pathway.

DOI: https://doi.org/10.1101/2025.10.25.684524
Front Oncol. 2025 ;15 1625797

Multiomics analyses of human colorectal cancer reveal changes in mitochondrial metabolism associated with chemotherapy resistance.

Shiyi Chen, Qian Li, Wei Zheng.

   Background: Mitochondria are essential organelles involved in energy production, cellular metabolism, and signal transduction. They have important impacts on tumorigenesis and cancer progression. Nevertheless, the associations between mitochondrial metabolic processes and chemotherapy resistance in colorectal cancer (CRC) are not well understood.
Methods: We generated a chemotherapy-resistant colorectal cancer cell line, HCT-15/DOX, via doxorubicin (DOX) induction. We then performed proteomic and metabolomic analyses via LC-MS/MS technology on both the parental and the DOX-resistant cell lines. Additionally, transmission electron microscopy was used to examine changes in mitochondrial morphology between the two cell lines.
Results: The results revealed significant dysregulation of 185 proteins and 1099 metabolites in HCT-15/DOX cells relative to parental cells, highlighting the impact of chemotherapy resistance on cellular processes. The key functional proteins that were identified included upregulated SDHA, BCKDHB, CRYZ, NUDT6, CPT1A, and POLG, and downregulated CRAT, FDPS, SFXN1, and ATAD3B. Additionally, through combined multiomics pathway enrichment analysis, pyrimidine metabolism, purine metabolism, ascorbate and aldarate metabolism, propanoate metabolism, and the citrate cycle (TCA cycle) were identified as important metabolic processes associated with CRC chemotherapy resistance. Transmission electron microscopy analysis revealed that HCT-15/DOX cells had increased mitochondrial number, length, and area.
Conclusions: This research highlights notable differences in mitochondrial morphology and diverse mitochondrial metabolic functions between parental and DOX-resistant HCT-15 CRC cells. The findings of the present study provide insights into the mitochondrial metabolic changes associated with CRC chemotherapy resistance, offering valuable insights into the mechanisms underlying these changes and identifying potential therapeutic targets for addressing CRC chemotherapy resistance.

Keywords:  chemotherapy resistance; colorectal cancer; metabolomics; mitochondrial metabolism; proteomics

DOI:  https://doi.org/10.3389/fonc.2025.1625797
Nature. 2025 Nov 25.

Polyclonal origins of human premalignant colorectal lesions.

Debra Van Egeren, Ryan O Schenck, Aziz Khan, Aaron M Horning, Shanlan Mo, Clemens L Weiß, Edward D Esplin, Winston R Becker, Si Wu, Casey Hanson, Nasim Barapour, Lihua Jiang, Kévin Contrepois, Hayan Lee, Stephanie A Nevins, Tuhin K Guha, Hao Zhang, Zhen He, Zhicheng Ma, Emma Monte, Thomas V Karathanos, Rozelle Laquindanum, Meredith A Mills, Hassan Chaib, Roxanne Chiu, Ruiqi Jian, Joanne Chan, Mathew Ellenberger, Bahareh Bahmani, Basil Michael, Annika K Weimer, D Glen Esplin, Samuel Lancaster, Jeanne Shen, Uri Ladabaum, Teri A Longacre, Anshul Kundaje, William J Greenleaf, Zheng Hu, James M Ford, Michael P Snyder, Christina Curtis.

Cancer is generally thought to be caused by expansion of a single mutant cell1. However, analyses of early colorectal cancer lesions suggest that tumors may instead originate from multiple, genetically distinct cell populations2,3. Detecting polyclonal tumor initiation is challenging in patients, as it requires profiling early-stage lesions before clonal sweeps obscure diversity. To investigate this, we analyzed normal colorectal mucosa, benign and dysplastic premalignant polyps, and malignant adenocarcinomas (123 samples) from six individuals with familial adenomatous polyposis (FAP). Individuals with FAP have a germline heterozygous APC mutation, predisposing them to colorectal cancer and numerous premalignant polyps by early adulthood4. Whole-genome and/or whole-exome sequencing revealed that many premalignant polyps-40% with benign histology and 28% with dysplasia-were composed of multiple genetic lineages that diverged early, consistent with polyclonal origins. This conclusion was reinforced by whole-genome sequencing of single crypts from multiple polyps in additional patients which showed limited sharing of mutations among crypts within the same lesion. In some cases, multiple distinct APC mutations co-existed in different lineages of a single polyp, consistent with polyclonality. These findings reshape our understanding of early neoplastic events, demonstrating that tumor initiation can arise from the convergence of diverse mutant clones. They also suggest that cell-intrinsic growth advantages alone may not fully explain tumor initiation, highlighting the importance of microenvironmental and tissue-level factors in early cancer evolution.

DOI: https://doi.org/10.1038/s41586-025-09930-y
Nat Cell Biol. 2025 Nov 24.

Polyamines sustain epithelial regeneration in aged intestines by modulating protein homeostasis.

Alberto Minetti, Omid Omrani, Christiane Brenner, Feyza Cansiz, Shinya Imada, Jonas Rösler, Saleh Khawaled, Gabriele Allies, Sven W Meckelmann, Nadja Gebert, Ivonne Heinze, Norman Rahnis, Jing Lu, Katrin Spengler, Mahdi Rasa, Emilio Cirri, Regine Heller, Ömer Yilmaz, Alpaslan Tasdogan, Francesco Neri, Alessandro Ori.

Ageing dampens the regenerative potential of intestinal epithelium across species including humans, yet the underlying causes remain elusive. Here we characterized the temporal dynamics of regeneration following injury induced by 5-fluorouracil, a commonly used chemotherapeutic agent, using proteomic and metabolomic profiling of intestinal tissues together with functional assays. The comparison of regeneration dynamics in mice of different ages revealed the emergence of proteostasis stress and increased levels of polyamines following injury exclusively in old epithelia. We show that delayed regeneration is an intrinsic feature of aged epithelial cells that display reduced protein synthesis and the accumulation of ubiquitylated proteins. The inhibition of the polyamine pathway in vivo further delays regeneration in old mice, whereas its activation by dietary intervention or supplementation of polyamines is sufficient to enhance the regenerative capacity of aged intestines. Our findings highlight the promising epithelial targets for interventions aimed at tackling the decline in tissue repair mechanisms associated with ageing.

DOI: https://doi.org/10.1038/s41556-025-01804-9
J Transl Med. 2025 Nov 22.

A robust classifier for the intrinsic consensus molecular subtypes in colorectal cancer.

Petros Tsantoulis, Yourae Hong, Pratyaksha Wirapati, Ting Pu, Allyson M Peddle, Thomas Mckee, Sabine Tejpar.



Keywords:  CMS; Colorectal cancer; Intrinsic consensus molecular subtypres; iCMS

DOI:  https://doi.org/10.1186/s12967-025-07363-9
Cell Rep. 2025 Nov 25. pii: S2211-1247(25)01395-6. [Epub ahead of print]44(12): 116623

Fatty acids modulate the colorectal cancer immune microenvironment via regulating the interaction and transactivation of PPARα/δ and P53.

Binyan Xu, Xufeng Hou, Maoyuan Wang, Lin Qiu, Xiling Chen, Guoming Deng, Daixuan Zhou, Yun Feng, Jinzhao Han, Xiaojing Meng, Hongying Fan, Weisen Zeng, Yang Bai.

  Dietary fatty acids accelerate cancer development and metastasis by altering the tumor microenvironment (TME), yet the mechanism is unclear. Here, two-sample Mendelian randomization (MR) revealed that BMI impairs colorectal cancer (CRC) immune surveillance. Additionally, a high-fat diet (HFD) reshapes the immunosuppressive TME, hallmarked by increased myeloid-derived suppressor cells and decreased CD8+ T cells in mice. Mechanistically, the unhealthy fatty acid palmitic acid (PA) binds to its nuclear receptors, peroxisome proliferator-activated receptors (PPARs), enhancing PPARδ while inhibiting PPARα and P53 transactivation, thereby upregulating CD73 and downregulating tumor necrosis factor-related apoptosis-inducing ligand receptors 1 and 2 (TRAIL-R1/2), which drives immunosuppression in CRC transplant tumors. Conversely, conjugated linoleic acid (CLA), a healthy fatty acid, enhances PPARα and P53 transactivation while inhibiting PPARδ transactivation, leading to decreased CD73 and increased TRAIL-R1/2, which enhances anti-tumor immunity and limits metastasis. These findings suggest a direct, universal mechanism by which fatty acid composition regulates immune homeostasis and tumor progression via PPARα/δ-P53 crosstalk.

Keywords:  CP: cancer; CP: immunology; P53; fatty acid; immunoregulation; peroxisome proliferator-activated receptors; transactivation activity; tumor microenvironment

DOI:  https://doi.org/10.1016/j.celrep.2025.116623
J Nutr Biochem. 2025 Nov 23. pii: S0955-2863(25)00354-7. [Epub ahead of print] 110192

Dietary eicosapentaenoic and docosahexaenoic acids reduce oxylipins that provide early mediators of colonic inflammation induced by chemotherapy.

Sarah R Parsons, Irma Magaly Rivas-Serna, Peter O Isesele, M D Monirujjaman, Abha Dunichand-Hoedl, Aducio L Thiesen, M Thomas Clandinin, Vera C Mazurak.

  Combination chemotherapy, irinotecan+5-fluorouracil, treats advanced colorectal cancer but causes intestinal toxicity mediated by cytokines and oxylipins. The objective of this study is to determine the effect of dietary eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) on cytokines and the balance of oxylipins in colon tissue after chemotherapy. Ward colon tumours were implanted into female Fischer 344 rats (13-14 weeks old, n=56) and grew for two weeks before initiating chemotherapy (day 0). Subsequently, rats were maintained on the control diet (n=32) or switched to the EPA+DHA diet (n=24), an isocaloric diet that differed mainly in EPA and DHA content. Rats were euthanized on day 0 (baseline), 2, 4 and 8. The reference (no tumour, n=8) and baseline D0 (with tumour, n=8) groups did not receive chemotherapy. Cytokines, phospholipid fatty acids, and oxylipins in colon tissue were compared between the diets and over days post-chemotherapy. Feeding EPA+DHA resulted in a 9- and 2-fold increase in colon phospholipid by day 8 mirrored by a 10- and 2-fold increase in total oxylipins derived from EPA and DHA, respectively. Incorporation of EPA and DHA by day 2 prevented an increase in proinflammatory arachidonic acid (AA)-derived oxylipins after chemotherapy, including prostaglandin (PG) D2, PGE2, 6-keto-PGF1α, thromboxane B2, and 5-hydroxyeicosatetraenoic acid. Displacement of AA by EPA and DHA in colonic membrane attenuates early inflammatory lipid oxylipins. Dietary EPA+DHA may mitigate intestinal perturbations in colorectal cancer patients receiving irinotecan+5-fluorouracil.

Keywords:  5-fluorouracil; Colon; colorectal cancer; irinotecan (CPT-11); oxylipins; phospholipid fatty acids; rats

DOI:  https://doi.org/10.1016/j.jnutbio.2025.110192