bims-instec Biomed News
on Intestinal stem cells and chemoresistance in colon cancer and intestinal regeneration
Issue of 2026–01–18
25 papers selected by
Maria-Virginia Giolito, Université Catholique de Louvain



  1. Commun Biol. 2026 Jan 13.
      Plasticity is a central mechanism underlying the robust regenerative capacity of the intestinal epithelium. Two major forms of plasticity have been described: spatial plasticity, in which differentiated cells revert to crypt base columnar cells (CBCs), and fetal reversion into revival stem cells (revSCs). However, the relationship among these two stem cell populations and differentiated cells remains to be clarified. Here, we demonstrated the bidirectional interconversion between CBCs and revSCs. Using lineage tracing, injury models and villus culture, we show that absorptive enterocytes can reprogram into revSCs and regenerate CBCs. These findings position fetal reversion as an entry point to spatial plasticity, establishing a regenerative hierarchy where CBCs, revSCs, and enterocytes collectively orchestrate intestinal repair. Furthermore, we identified revSCs as a highly stress-tolerant stem cell population, whose emergence would preserve the stem cell pool. Our results establish fetal reversion as a cellular escape mechanism safeguarding epithelial regeneration under inflammatory conditions.
    DOI:  https://doi.org/10.1038/s42003-026-09533-x
  2. Mol Cancer. 2026 Jan 14.
      Ferroptosis is a non-apoptotic form of regulated cell death driven by iron dependent lipid peroxidation. It sits at the intersection of several hallmarks of metastatic cancer, including metabolic rewiring, membrane remodeling, epithelial mesenchymal plasticity, immune editing, and adaptation to distant niches. In this review, we integrate biochemical mechanisms with single cell, spatial, and in vivo data to map how ferroptotic pressure changes as tumor cells invade, travel through vessels, extravasate, enter dormancy, and re-awaken to form overt metastases. We highlight that these dynamics are strongly shaped by organ context. Lymph and adipose rich environments buffer lipid peroxidation and favor survival. In contrast, blood circulation increases oxidative load, and brain and liver niches impose distinct constraints on redox balance, iron handling, and lipid repair. We then examine how ferroptosis interfaces with the immune system. Ferroptotic stress can increase tumor antigenicity and danger signaling and thereby promote antitumor responses. The same stress, however, can reprogram monocytes, macrophages, and neutrophils, drive neutrophil extracellular trap formation, and support lipid exchange that weakens effector T cell function. This dual behavior helps explain why ferroptosis can restrict dissemination in some settings yet fuel pro-metastatic inflammation in others. On this mechanistic background, we evaluate therapeutic strategies that aim to exploit ferroptosis related vulnerabilities. These include inhibition of cystine supply or lipid repair pathways, radiosensitization regimens that increase lipid peroxidation, diet drug combinations that rewire sulfur and lipid metabolism, and nanoplatforms that co-deliver ferroptosis triggers with photo or sonodynamic therapies. Clinically, ferroptosis programs are increasingly linked to metastatic organotropism, responses to radiotherapy and immunotherapy, and patient survival, and they are beginning to guide biomarker development and early translational trials. We also discuss practical barriers, such as niche specific resistance circuits, constraints imposed by drug delivery and toxicity, and the scarcity of robust patient level ferroptosis readouts. Methodological advances - including compartment resolved reporters, spatial lipidomics, and circulating signatures of lipid damage - may help address these gaps. Overall, viewing metastasis through the ferroptosis lens reveals actionable vulnerabilities and supports rational radio immunometabolic combinations aimed at durable control of metastatic disease.
    Keywords:  Epithelial–mesenchymal plasticity; Ferroptosis; Immunogenic cell death; Iron metabolism; Lipid peroxidation; Metastasis; Metastatic niche; Organotropism
    DOI:  https://doi.org/10.1186/s12943-025-02544-y
  3. Cancer Treat Rev. 2026 Jan 09. pii: S0305-7372(26)00003-4. [Epub ahead of print]143 103089
      Colorectal cancer (CRC) with mismatch-repair deficiency (dMMR) or high microsatellite instability (MSI-H) represents a distinct molecular subtype highly sensitive to immune checkpoint inhibitors (ICIs). Landmark clinical trials have established ICIs as standard-of-care in this setting, demonstrating durable responses and improved survival. However, up to one-third of patients will exhibit primary or acquired resistance, highlighting the urgent need for predictive biomarkers and novel therapeutic strategies. This review summarizes the clinical evidence supporting ICIs in dMMR/MSI-H CRC, explores mechanisms of resistance-including intrinsic and extrinsic modulators-and evaluates the role of potential predictive biomarkers of response. Finally, we discuss innovative therapeutic approaches to overcome resistance, including combination strategies, DNA repair pathway inhibitors, immune-oncology drugs beyond checkpoint inhibitors and microbiome-targeted interventions. Together, these insights aim to refine patient selection, optimize therapeutic benefit, and guide the development of next-generation therapies for dMMR/MSI-H CRC.
    Keywords:  Colorectal cancer; Immune checkpoint inhibitors; Predictive biomarkers; Resistance to immunotherapy
    DOI:  https://doi.org/10.1016/j.ctrv.2026.103089
  4. Am J Pathol. 2026 Jan 13. pii: S0002-9440(26)00002-7. [Epub ahead of print]
      Insights into how normal epithelial cells adapt to microenvironmental perturbations may reveal molecular vulnerabilities that become obscured later in carcinogenesis, and hypoxia is common in colorectal cancer (CRC). Although colon mucosa exists in a state of physiologic hypoxia and is susceptible to ischemic injury, normal colon epithelial adaptive responses to changes in oxygenation are largely uncharacterized. In this study, human colon organoids (colonoids) were subjected to sustained hypoxia in vitro with characterization of consequent phenotypes and transcriptional changes. Hypoxia tolerance in human colonoids resulted in robust downregulation of alcohol dehydrogenase 1C (ADH1C), which was also validated in archival tissue from patients with ischemic colitis. ADH1C transcripts revealed non-uniform expression pattern in normal colon epithelium, with enrichment in transit amplifying (TA) and progenitor epithelial cells. Ectopic expression of ADH1C in colonoids subjected to hypoxia increased reactive oxygen species (ROS) and reduced NADPH compared to those in normoxia, suggesting that hypoxia-induced ADH1C downregulation facilitates neutralization of ROS. Hypoxia-induced ADH1C downregulation also showed reduced TA cell signatures and increased expression of regeneration-associated stem cell marker FGFBP1. Finally, ADH1C-low CRC showed significant enrichment for hypoxia-associated colon epithelial signatures as compared to ADH1C-high CRC. Taken together, these results establish ADH1C as a mediator of colon epithelial hypoxia responses and epithelial identity with relevance to human CRC.
    DOI:  https://doi.org/10.1016/j.ajpath.2025.12.008
  5. Nat Rev Mol Cell Biol. 2026 Jan 15.
      Lipid droplets (LDs) are emerging as key factors in cellular physiology, with roles beyond energy storage, including metabolic homeostasis, signalling and development. Together with a growing list of functions, diverse LD populations are being identified in different tissue types as well as within the context of single cells. Here we summarize recent work highlighting LD diversity from three perspectives: their lipid and protein compositional heterogeneity; differences in abundance, size and spatial organization within cells; and the diverse contacts they form with other organelles, all of which contribute to LD function. We also discuss tools and approaches used to visualize LD heterogeneity, the role of LDs in pathophysiology and disease, and open questions in the field.
    DOI:  https://doi.org/10.1038/s41580-025-00945-x
  6. Signal Transduct Target Ther. 2026 Jan 15. 11(1): 19
      The tumor microenvironment (TME) plays a central role in cancer progression and metastasis. A key feature of the TME is extracellular acidity, which promotes disease progression, immune evasion, and drug resistance. Tumor acidity is increasingly recognized as a critical factor in cancer development and a negative prognostic indicator. Here, we demonstrate that the membrane glycoprotein dysadherin promotes colorectal cancer (CRC) malignancy by modulating TME acidity. Comprehensive bioinformatics and pathological analyses of CRC patient samples revealed that increased tumor acidity is a hallmark of CRC progression and strongly correlates with high expression of dysadherin. Functional studies confirmed that dysadherin enhances malignant traits, particularly under acidic conditions. Mechanistically, dysadherin activates the integrin/FAK/STAT3 signaling pathway, leading to the upregulation of carbonic anhydrase 9 (CA9). CA9 facilitates proton export, contributing to extracellular acidification while maintaining intracellular pH homeostasis, thereby enabling cancer cells to survive and thrive in acidic environments. In a murine liver metastasis model, dysadherin deletion impaired cellular adaptation to the acidic TME and markedly attenuated metastatic colonization, whereas restoring CA9 expression effectively rescued metastatic potential. Overall, our findings identify the dysadherin/CA9 axis as a potential therapeutic target in CRC and provide new insights into how tumors exploit acidosis to drive malignant development and progression.
    DOI:  https://doi.org/10.1038/s41392-025-02543-x
  7. JCO Precis Oncol. 2026 Jan;10 e2500501
       PURPOSE: Neoadjuvant chemotherapy is a key component of curative treatment in advanced colorectal cancer (CRC). However, 30%-40% of patients show progression on treatment, underscoring the need for predictive tools to guide up-front treatment selection. Scalable and reproducible methods for patient stratification remain limited. MicroOrganoSpheres (MOS) are droplet-encapsulated 3D tumor models that allow for high-throughput functional drug testing. Here, we evaluate the potential of tumor-derived MOS to predict response to chemotherapy in patients with CRC.
    METHODS: MOS droplets were generated from 37 primary and/or metastatic tumor samples collected from 21 patients. MOS response to chemotherapy was quantified using AI-based imaging analysis and compared with clinical response (RECIST/disease-free survival [DFS]) and lesion-specific outcomes (pathologic response/percent tumor volume change).
    RESULTS: MOS chemoprediction assay showed high reproducibility (coefficients of variation ≤ 2.5%). MOS drug sensitivity recapitulated patient response with 83% accuracy in the full sample cohort and 100% accuracy when derived from primary tumors. Patients with sensitive MOS showed longer DFS. Individual MOS analysis revealed preservation of intratumor heterogeneity in vitro and enabled identification of drug-resistant clones.
    CONCLUSION: MOS technology offers a scalable and robust functional precision medicine platform with potential to guide clinical decision making in CRC. The platform accurately predicts patient response to chemotherapy and provides insights into intrapatient and intratumor heterogeneity.
    DOI:  https://doi.org/10.1200/PO-25-00501
  8. Trends Cancer. 2026 Jan 13. pii: S2405-8033(25)00286-9. [Epub ahead of print]
      The role of lipids in cancer progression has become a fervent area of exploration. The crosstalk of tumors with adipose tissue is a complex but well-regulated orchestration of signaling pathways, lipid transporters, and enzymes. They regulate fatty acid synthesis, their deposition into lipid droplets (LDs) as triglycerides, induction of lipolysis, shuttling lipids across cells, and their systemic trafficking, modification, and catabolism. For the latter, lipid oxidation has emerged as a metabolic process of particular clinical importance. Products of lipid processing can become secondary messengers, contribute to reactive oxygen species (ROS) generation, stimulate the production of antioxidants, and, if left unchecked, activate cell death pathways including ferroptosis. This review discusses recent updates in the field that are anticipated to have therapeutic implications.
    Keywords:  cancer; fatty acid; ferroptosis; lipid; oxidation; transport
    DOI:  https://doi.org/10.1016/j.trecan.2025.11.012
  9. Cancer Cell. 2026 Jan 12. pii: S1535-6108(25)00537-9. [Epub ahead of print]44(1): 146-165.e14
      The immune composition of the tumor microenvironment has a major impact on the therapy response in patients with colorectal cancer. Here, we built an atlas with 4.27 million single cells from 1,670 patient samples and complemented it with single-cell profiles from 266 patients, including cells with low mRNA content, spatial transcriptomics from 3.7 million cells, and protein profiles from 0.7 million cells. The analysis of the atlas allows tumor classification into immune desert, B cell enriched, T cell enriched, and myeloid cell enriched immune phenotypes. Within the myeloid compartment, we identify consensus myeloid gene expression programs with four immunomodulatory programs, and uncover a subpopulation of neutrophils with antigen-presenting properties. Moreover, functional experiments using patient-derived organoids show KRAS-dependent pro-tumorigenic polarization of neutrophils. Further, spatial multimodal single-cell profiling reveals niches with IL-1 signaling-based neutrophil-fibroblast interaction. Finally, using an orthotopic mouse model, we show that cancer-derived signals modify neutrophil production in the bone marrow.
    Keywords:  cellular niches; colorectal cancer; gut-bone marrow axis; single-cell atlas; single-cell sequencing; spatial single-cell profiling; spatial transcriptomics
    DOI:  https://doi.org/10.1016/j.ccell.2025.12.003
  10. Apoptosis. 2026 Jan 10. 31(1): 30
       BACKGROUND: The upregulated expression of sterol regulatory element-binding protein 2 (SREBP2) has been observed in multiple types of malignant cancers. Ferroptosis is a form of cell death that is iron-dependent and driven by the accumulation of lipid peroxides. It has recently garnered considerable attention in Colorectal cancer (CRC) research. This study aims to investigate the role of SREBP2 in CRC ferroptosis resistance and the underlying molecular mechanisms.
    METHODS: SREBP2 expression was assessed in CRC. Functional assays were conducted in HT29 and RKO cells following SREBP2 knockdown or treatment with Betulin, the SREBP2 inhibitor. RNA-seq was used to screen the potential downstream targets of SREBP2. Mechanistically, ferroptosis-related markers and rescue assays revealed the relation between SREBP2 and CRC ferroptosis resistance mediated by GPX4 expression regulation. Furthermore, ChIP and luciferase assays were used to confirm the upstream that regulates SREBP2 expression. Finally, subcutaneous tumorigenesis model was employed to evaluate the therapeutic potential of targeting SREBP2 in CRC.
    RESULTS: The upregulated SREBP2 expression in CRC drives the proliferation, migration, and invasion of CRC cells. Mechanistically, SREBP2 directly increases GPX4 transcription, thereby reducing the sensitivity of CRC to ferroptosis and facilitating CRC progression. Additionally, β-catenin was identified as an upstream regulator of SREBP2. Inhibition of SREBP2 sensitizes CRC cells to ferroptosis and suppresses tumor growth.
    CONCLUSION: SREBP2 enhances ferroptosis resistance in CRC by upregulating GPX4, thereby contributing to tumor progression. Our findings highlight SREBP2 as a potential therapeutic target and provide a rationale for the development of SREBP2-targeted strategies in colorectal cancer.
    Keywords:  Colorectal cancer; Ferroptosis; GPX4; SREBP2; β-catenin
    DOI:  https://doi.org/10.1007/s10495-025-02209-7
  11. Cell Oncol (Dordr). 2026 Jan 13. 49(1): 23
       PURPOSE: EGFR inhibitor (EGFRi) therapies have been FDA-approved for metastatic colorectal cancer (CRC). However, extended RAS/RAF testing required in the drug labels, identifies only non-responders, and only ~50% of selected patients respond to therapy, suggesting an unmet need to develop additional biomarkers.
    METHODS: We previously reported combined mutations in APC and TP53 as a potential positive biomarker to identify EGFRi-sensitive patients. By leveraging the TwinStrand Duplex Sequencing (DS) technology, this study developed an ultrasensitive 6-gene panel DS assay that adds a positive filter for APC(A) and TP53(P) mutations in addition to the negative KRAS(K), BRAF(B), and NRAS(N) mutation filters for EGFRi therapy.
    RESULTS: The 6-gene DS assay was analytically validated using reference cell lines (n = 9, individually sequenced to > 3,000x Duplex depth). The assay yielded exceptionally high assay performance on (1) accuracy, (2) sensitivity, (3) specificity and (4) precision. Application to fresh frozen (FF):FFPE paired tissues from 21 CRC patients demonstrates that the ultrasensitive DS assay can accurately detect additional "new" mutations at low allelic frequencies compared to a standard NGS method (13 of the 17 new mutations had < 10% VAF) that may ultimately be responsible for drug resistance. Furthermore, Kaplan-Meier analysis on Duplex-sequenced EGFRi FFPE samples showed that the third-line metastatic CRC patients harboring combined APC and TP53 mutations (AP/APK(N) versus others) tended to have longer TOT (6.65 versus 3.60 months, p = 0.048, n = 29).
    CONCLUSION: These data suggest the potential of the 6-gene Duplex Sequencing assay to improve EGFRi patient selection and therapeutic outcomes.
    Keywords:  APC; Colorectal cancer; Duplex sequencing; EGFR inhibitor; Mutation biomarker; TP53
    DOI:  https://doi.org/10.1007/s13402-025-01140-y
  12. FEBS J. 2026 Jan 12.
      Organoid formation is driven by poorly understood intrinsic cellular properties and transcriptional programs that govern plasticity and differentiation. Deciphering these regulatory networks is essential for understanding normal tissue homeostasis and tumor initiation. Using a 3D organotypic model, which better recapitulates cell-matrix interactions and biochemical cues, we performed a miRNA-based screening strategy to identify key regulators of organoid initiation from human primary mammary epithelial cells. Our findings reveal that miR-106a-3p acts as a central modulator of mammary epithelial plasticity, enriching for stem/progenitor-like cells (CD44high/CD24low phenotype), driving organoid expansion, fostering K14+/K19+ lineage intermixing, and promoting branching morphogenesis characteristic of early ductal development. Further analysis revealed a core transcriptional network involving CBFB, NF-YA, GATA3, and REST, which supports organoid-forming potential. This regulatory program also induces a hybrid epithelial-mesenchymal transition (EMT) state, enhancing cellular plasticity while preserving organoid structural integrity. Extending these findings to cancer, we demonstrate that enforced expression of miR-106a-3p significantly increases tumoroid formation, suggesting that the tumor microenvironment, as modeled by 3D culture, promotes miR-106a-3p expression and functional relevance in tumorigenic processes. Collectively, these data indicate that miR-106a-3p drives a transient expansion of progenitor-like states and orchestrates transcriptional reprogramming during organoid initiation, with broader implications for breast tissue homeostasis and pathophysiological remodeling in cancer.
    Keywords:  human primary mammary epithelial cells; miRNA; organoids; transcriptions factors
    DOI:  https://doi.org/10.1111/febs.70397
  13. Clin Transl Med. 2026 Jan;16(1): e70593
       BACKGROUND: In colorectal cancer (CRC), innate lymphoid cells (ILCs) play a vital role in preserving and modulating immune homeostasis within the intestinal environment. However, the origins and diverse functions of ILCs in CRC remain poorly understood, making it difficult to clarify how these cells contribute to disease progression and influence therapeutic efficacy.
    METHODS: Single-cell RNA sequencing (scRNA-seq) generated an atlas of ILCs from multiple tissues (bone marrow, blood, and intestine), revealing their origins, heterogeneity, and plasticity. Spatial transcriptomics (ST) and immunofluorescence (IF) defined their specific cellular neighbourhoods within the tumour microenvironment.  In vitro co-culture assays were performed to validate the regulatory role of ILC2s in B cell maturation. Bulk RNA sequencing and flow cytometry were employed to assess the survival and therapeutic response potential of ILCs.
    RESULTS: Intestinal ILCs have two distinct origins: ILC3-CD83 cells derived from the fetal gut, which persist into adulthood; and ILC2 and ILC3-S100A4 cells that might originate from the bone marrow and migrate through the circulation to colonise intestinal tissues. The tissue-resident ILC3 subsets exhibited diverse functional roles in CRC. Specifically, trajectory analysis showed that ILC3s differentiated into either stress-responsive ILC3-HSPA1B cells or cytotoxic ILC1/NK cells in CRC. Additionally, by using spatial transcriptomics analysis combined with functional assays, we found that bone marrow-derived ILC2s preferentially localise in tertiary lymphoid structures (TLSs), where they likely support B cell maturation. Notably, higher ILC2 abundance correlated with better clinical outcomes and greater therapeutic benefit.
    CONCLUSIONS: This study reveals the distinct origins and functional heterogeneity of intestinal ILC subsets in CRC. The enrichment of bone marrow-derived ILC2s in TLSs, where they likely support B cell maturation, is associated with improved prognosis and favourable immunotherapy response, which may serve as biomarkers for survival and therapeutic efficacy in CRC.
    Keywords:  colorectal cancer; innate lymphoid cells; single‐cell RNA sequencing; spatial transcriptomics; tumour microenvironment
    DOI:  https://doi.org/10.1002/ctm2.70593
  14. Free Radic Biol Med. 2026 Jan 12. pii: S0891-5849(26)00028-6. [Epub ahead of print]
      Cetuximab resistance in head and neck squamous cell carcinoma (HNSCC) is increasingly recognized as an adaptive state driven by metabolic and redox reprogramming that enables tumor cells to tolerate sustained oxidative and immune stress. Although lipid metabolism and PPARγ signaling have been implicated in therapeutic resistance, their functional contribution to drug-tolerant persister (DTP) cells and the role of peroxisomal fatty acid oxidation (FAO) remain poorly defined. In this study, we demonstrate that a redox-driven FABP1/PPARγ axis sustains peroxisome-centered FAO, GPX4-dependent antioxidant defense, and immune suppression in cetuximab-tolerant HNSCC. FABP1 expression was markedly elevated in cetuximab-tolerant DTP cell models and resistant patient tumors. Genetic silencing or pharmacological inhibition of FABP1 using a selective small-molecule inhibitor impaired tumorsphere formation, increased intracellular reactive oxygen species accumulation, and induced apoptotic cell death, accompanied by coordinated suppression of FAO-associated genes, including CPT1, ACSL family members, and acyl-CoA oxidase 1. In an orthotopic SCC9-DTP xenograft model established in NOD-SCID mice, FABP1 inhibition significantly attenuated tumor growth, disrupted metabolic-redox adaptation, and reduced tumor-associated macrophage polarization toward an immunosuppressive phenotype. Our findings identify the FABP1/PPARγ axis as a central regulator of peroxisome-centered FAO and redox buffering in cetuximab-tolerant DTP cells. Targeting FABP1 collapses this adaptive metabolic-redox program, restores vulnerability to oxidative stress, and alleviates immune suppression, highlighting peroxisomal lipid metabolism as a therapeutically actionable vulnerability in refractory HNSCC.
    Keywords:  FABP1; GPX4; HNSCC; PPARγ; cetuximab resistance; fatty acid oxidation; peroxisome; redox homeostasis; tumor-associated macrophage
    DOI:  https://doi.org/10.1016/j.freeradbiomed.2026.01.020
  15. Circ Res. 2026 Jan 16. 138(2): e327929
      
    Keywords:  Editorials; heart failure; lipid metabolism; metabolism
    DOI:  https://doi.org/10.1161/CIRCRESAHA.125.327929
  16. bioRxiv. 2026 Jan 11. pii: 2026.01.09.698724. [Epub ahead of print]
      Central kinases of the Hippo tumor suppressor pathway phosphorylate the transcriptional coactivators YAP and TAZ to sequester them in the cytoplasm. In cancer, Hippo pathway kinases have reduced activity, leading to translocation of YAP and TAZ into the nucleus where they engage TEADs and other transcription factors. Here, we explore whether heterobifunctional small molecules that bind to the TEAD allosteric lipid-binding pocket can degrade the TEAD•YAP/TAZ complex. We design and synthesize heterobifunctional molecules that consist of flufenamic acid analogs that bind to the allosteric TEAD lipid pocket, a long and flexible linker, and thalidomide to engage E3 ubiquitin ligase component cereblon. The bifunctional compounds promote ternary complex formation in biochemical assays and mammalian cells but exhibited modest degradation of TEAD, YAP, and TAZ in cancer cells. Methyl ester analogs of these compounds led to substantial proteasomal degradation of the TEAD•YAP/TAZ complex in cancer cells. This work provides a strategy for depletion of nuclear YAP and TAZ and for exploration of their TEAD-dependent and TEAD-independent activities in vivo .
    DOI:  https://doi.org/10.64898/2026.01.09.698724
  17. Biochem Biophys Res Commun. 2025 Dec 31. pii: S0006-291X(25)01893-5. [Epub ahead of print]799 153177
       BACKGROUND: A recently identified type of copper-induced cell death that may contribute to tumor development is cuprotosis. However, uncertainty surrounds its molecular regulation mechanism in colorectal cancer (CRC). Clarifying the regulation mechanism of SLC7A11 in CRC cell cuproptosis was the goal of this investigation.
    METHODS: To identify the genes associated with cuproptosis, we combined transcriptome data from TCGA-COAD and GSE83889. Functional experiments including cell viability assays, colony formation, Western blotting, glutathione metabolism analysis, lipid peroxidation staining, and ROS measurements, were performed in CRC cells following SLC7A11 knockdown and treatment with the copper ionophore elesclomol-Cu. Rescue experiments were conducted using exogenous glutathione (GSH) and SLC7A11 inhibitors (erastin, SASP) to validate the mechanisms.
    RESULTS: Bioinformatics analysis identified SLC7A11 as a cuproptosis-related gene markedly elevated in CRC and linked with a poor prognosis. Knockdown or pharmacological inhibition of SLC7A11 enhanced elesclomol-Cu-induced cell death, increased intracellular Cu2+ accumulation, and aggravated oxidative stress. Mechanistically, SLC7A11 silencing disrupted glutathione and cystine metabolism, suppressed GPX4 activity, and altered the expression of key cuproptosis regulators. Exogenous glutathione partially reversed these effects. Furthermore, inhibition of SLC7A11 using erastin or SASP drugs enhanced goblet apoptosis and further reduced CRC cell viability.
    CONCLUSION: SLC7A11 knockdown regulates intracellular redox balance through the GSH-GPX4 axis, thereby promoting cellular cuproptosis. Targeting SLC7A11 can enhance the sensitivity of CRC cells to copper ionophores and may represent a novel therapeutic strategy to enhance cuproptosis of CRC cells.
    Keywords:  Colorectal cancer; Cuprotosis; Elesclomol-cu; GSH-GPX4 axis; SLC7A11
    DOI:  https://doi.org/10.1016/j.bbrc.2025.153177
  18. bioRxiv. 2026 Jan 06. pii: 2026.01.05.697775. [Epub ahead of print]
      Therapy resistance is the leading cause of cancer-related deaths. Drug-tolerant persister cells (DTPs) represent a major barrier to cancer cure, mediating resistance through adaptive cell state transitions and driving tumor progression. Here, we investigate metabolic differences between DTPs and drug-sensitive cancer cells using integrated fluxomics. Proteomic profiling and extracellular flux analyses revealed that DTPs upregulate glycolysis and gluconeogenesis while reducing oxidative phosphorylation, indicating a shift in central carbon metabolism. Isotope tracing and metabolic modeling demonstrate that DTPs utilize glucose to fuel the pentose phosphate pathway (PPP) to generate NADPH and metabolize glutamine to provide carbons for the PPP via gluconeogenesis. Integrating our multi-omic datasets into a genome-scale model identified that DTPs sustain antioxidant metabolism by decreasing fluxes of other NADPH-consuming reactions upon in silico PPP knockout. These findings reveal a systems-level shift in DTP metabolism that maintains antioxidant activity for cell survival, highlighting potential new targets and treatment paradigms to overcome therapy resistance.
    DOI:  https://doi.org/10.64898/2026.01.05.697775
  19. Nat Commun. 2026 Jan 15.
      Susceptibility transcription factors (TF) whose DNA bindings are altered by genetic variants regulating colorectal cancer (CRC) risk genes remain poorly defined. Using generalized linear mixed models, we analyze 218 TF ChIP-Seq datasets alongside GWAS data from 100,204 CRC cases and 154,587 controls of East Asian and European ancestries. We identify 51 TFs and TF-cofactor interactions, including VDR-cofactors, as key regulators of CRC risk. Integrating these TF insights with transcriptome-wide association studies (TWAS), we further evaluate associations between genetically predicted gene expression, alternative splicing, and alternative polyadenylation with CRC risk, using RNA-seq data from 364 Asian-ancestry and 707 European-ancestry individuals. Multi-ancestry TWAS identify 222 risk genes, including 95 novel genes and 48 potentially druggable targets. Single-cell analysis provides additional functional evidence supporting ~45% of these genes, and experimental validation confirms oncogenic roles for RHPN2, IRS2, and TXN. Our findings elucidate key TF-gene regulatory networks and uncover novel CRC risk genes.
    DOI:  https://doi.org/10.1038/s41467-025-68127-z
  20. bioRxiv. 2026 Jan 07. pii: 2026.01.06.697938. [Epub ahead of print]
      While lipid droplets (LDs), dynamic organelles central to lipid and energy homeostasis, are implicated in cancer cell migration, their roles during collective cell migration remain unknown. We use Drosophila border cell migration as an in vivo model of invasive, collective cell migration to dissect the roles of LDs and the conserved LD lipase, Adipose Triglyceride Lipase (ATGL). Border cell LDs undergo dynamic changes and decrease in volume by the end of migration. Loss of ATGL increases LD volume, whereas border cell overexpression depletes LDs. Loss, border cell knockdown or overexpression of ATGL delays migration and blocks delamination. Further, loss of ATGL disrupts border cell mitochondria - it alters morphology, reduces membrane potential and increases reactive oxygen species. These results demonstrate that tight regulation of lipid mobilization from LDs, including for energy production, drives delamination and collective migration. Our findings not only have the potential to inform how cancer cells exploit LDs to promote their invasive behaviors but also highlight the crucial role of LDs in migration during development, hinting at their broader significance in diverse migratory contexts.
    DOI:  https://doi.org/10.64898/2026.01.06.697938
  21. bioRxiv. 2026 Jan 08. pii: 2026.01.07.697087. [Epub ahead of print]
      Microbial-derived short-chain fatty acids regulate a variety of pathways in the healthy colonic mucosa. In particular, butyrate serves as the primary energy source for colonocytes and regulates gene transcription by stabilizing the transcription factor hypoxia-inducible-factors (HIF) and functioning as a histone deacetylase (HDAC) inhibitor. A limitation of butyrate as a therapeutic is its rapid metabolism in differentiated colonocytes. Furthermore, intestinal stem cells (ISCs) respond differently to butyrate, preferentially using glucose for energy procurement. To address these limitations, we explored metabolite-mimicry to discover compounds with potent or selective biological responses within the butyrate pathway(s). We discovered an analog, 3-chlorobutyrate (3-Cl BA), that significantly enhances epithelial barrier formation and wound healing in vitro. Mechanistically, we revealed that 3-Cl BA is a potent HDAC inhibitor. Furthermore, unlike butyrate, 3-Cl BA does not stabilize HIF and it is not used as metabolic fuel. In vivo studies in a DSS-colitis model revealed that contrary to butyrate, 3-Cl BA is protective. Studies in stem-like colonoids demonstrated that only butyrate inhibits ISC proliferation and differentiation. Furthermore, it was recently reported that HIF stabilization inhibits ISCs activity. Given the fact that butyrate but not 3-Cl BA stabilizes HIF, we surmised that 3-Cl BA would circumvent these detrimental functional consequences. We demonstrate here that pharmacologic HIF stabilization inhibits colonoid differentiation and that genetic loss of HIF significantly promotes ISC differentiation. This study reveals a promising butyrate analog protective in colitis and demonstrates the advantages of metabolite-mimicry to dissect selective biological functions from major metabolites in the gut.
    Significance statement: Butyrate is a well-studied microbial short-chain fatty acid that regulates a number of mucosal pathways and is paramount in maintaining intestinal integrity. In health, it is a major source of energy for colonocytes and regulates gene transcription. The role of butyrate in disease is still controversial and not well understood. When butyrate is not metabolized or well-utilized (e.g. disease), it accumulates in intestinal stem cells leading to reduced cell proliferation and differentiation, thereby hampering intestinal barrier recovery. In this study, we describe a butyrate analog that enhances epithelial barrier formation and wound healing. Furthermore, as opposed to native butyrate, this butyrate analog is protective in a colitis mouse model and does not exhibit detrimental influences on intestinal stem cells.
    DOI:  https://doi.org/10.64898/2026.01.07.697087
  22. Nat Commun. 2026 Jan 17.
      Untargeted metabolomics provides a direct window into biochemical activities but faces critical challenges in determining metabolite origins and interpreting unannotated metabolic features. Here, we present TidyMass2, an enhanced computational framework for Liquid Chromatography-Mass Spectrometry (LC-MS) untargeted metabolomics that addresses these limitations. TidyMass2 introduces three major innovations compared to its predecessor, TidyMass: (1) a comprehensive metabolite origin inference capability that traces metabolites to human, microbial, dietary, pharmaceutical, and environmental sources through integration of 11 metabolite databases containing 532,488 metabolites with source information; (2) a metabolic feature-based functional module analysis approach that bypasses the annotation bottleneck by leveraging metabolic network topology to extract biological insights from unannotated metabolic features; and (3) a graphical interface that makes advanced metabolomics analyses accessible to researchers without programming expertise. Applied to longitudinal urine metabolomics data from human pregnancy, TidyMass2 identified diverse metabolites originating from human, microbiome, and environment, and uncovered 27 dysregulated metabolic modules. It increased the proportion of biologically interpretable metabolic features from 5.8% to 58.8%, revealing coordinated changes in steroid hormone biosynthesis, carbohydrate metabolism, and amino acid processing. By expanding biological interpretation beyond MS2 spectra-based annotated metabolites, TidyMass2 enables more comprehensive metabolic phenotyping while upholding open-source principles of reproducibility, traceability, and transparency.
    DOI:  https://doi.org/10.1038/s41467-026-68464-7
  23. Eur J Hum Genet. 2026 Jan 15.
      Colorectal cancer (CRC) is increasingly diagnosed in individuals under 50 years of age, yet the underlying genetic predisposition remains largely unexplained, particularly in mismatch repair (MMR)-proficient cases. This study aimed to identify novel hereditary CRC susceptibility genes by integrating germline and tumour whole-exome sequencing (WES) with transcriptomic profiling across a cohort of early-onset CRC (EOCRC) patients. Tumours were categorised using Consensus Molecular Subtypes (CMS) classification and analysed for mutational signature and burden. We used a novel 'All vs One' multi-omic integration approach to identify loss-of-function rare germline variants with concordant gene expression alterations in tumour tissue. Five candidate genes (ADCY4, NOXO1, CDHR2, ARHGAP10, EEF2K) were prioritised based on this approach and potential biological relevance in CRC. These findings highlight the molecular heterogeneity of EOCRC and demonstrate the utility of multi-omic approaches in refining germline variant interpretation. Integrating tumour transcriptomics enhances gene discovery efforts and supports a more comprehensive understanding of CRC heritability in younger individuals.
    DOI:  https://doi.org/10.1038/s41431-025-02004-7