bims-instec 2025-08-17 papers

bims-instec

Biomed News

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

Issue of 2025–08–17
twelve papers selected by
Maria-Virginia Giolito, Université Catholique de Louvain

Mitochondrial metabolic reprogramming in colorectal cancer: mechanisms of resistance and future clinical interventions.
Concurrent genetic and non-genetic resistance mechanisms to KRAS inhibition in CRC.
Large-scale CRISPR screening in primary human 3D gastric organoids enables comprehensive dissection of gene-drug interactions.
The Nα-acetyl-L-lysine/Loxl2/H2O2 promotes intestinal tumor growth in Drosophila and cell proliferation in human colorectal cancer.
A Spatial and Temporal Transcriptomic Atlas of Mouse Intestinal Regeneration.
Biomechanical Phenotyping Reveals Unique Mechanobiological Signatures of Early-Onset Colorectal Cancer.
Vitamin B2 metabolism promotes FSP1 stability to prevent ferroptosis.
Restricting metabolic plasticity enhances stress adaptation through the modulation of PDH and HIF1A in TRAP1-depleted colon cancer.
Differentiating low tumor burden from oligometastatic disease in colorectal cancer: a call for individualized therapeutic approaches.
Patients-Derived Organoids Sequencing-based FOXP4 Facilitates Radioresistance by Transcriptionally Modifying GPX4 to Regulate ferroptosis in Colorectal Cancer.
Targeting lipid scrambling potentiates ferroptosis and triggers tumor immune rejection.
Multiplex analysis of colorectal cancer tissue describes the composition, cell biology and spatial effects of cell-in-cell events and identifies a T cell-dependent prognostic signature.

Cell Death Discov. 2025 Aug 09. 11(1): 375

Mitochondrial metabolic reprogramming in colorectal cancer: mechanisms of resistance and future clinical interventions.

Xiuxiu Qiu, Ao Wang, Jiahui Wang, Zhanxia Zhang, Li Tao.

Colorectal cancer (CRC) is a leading cause of global cancer mortality, with therapeutic resistance constituting a major barrier to sustained clinical benefit. Mitochondrial metabolic reprogramming has emerged as a central adaptive mechanism that enables CRC cells to withstand hypoxia and therapeutic pressure, while concurrently driving resistance to chemotherapy, targeted agents, and immunotherapy. In this Review, we explore how mitochondrial metabolism contributes to therapeutic resistance, with particular emphasis on metabolic plasticity, redox balance, and organelle quality control. We also assess enabling technologies such as spatial transcriptomics, proteomics, and patient-derived organoids, and discuss their translational relevance in stratifying metabolic vulnerabilities and informing individualized therapies. Targeting mitochondrial rewiring represents a compelling strategy to overcome resistance and drive progress toward personalized CRC therapy.

DOI: https://doi.org/10.1038/s41420-025-02670-y
bioRxiv. 2025 Aug 05. pii: 2025.08.05.668666. [Epub ahead of print]

Concurrent genetic and non-genetic resistance mechanisms to KRAS inhibition in CRC.

Salvador Alonso, Kevan Chu, Marie J Parsons, Elizabeth Granowsky, Himari Gunasinghe, Jinru Shia, Rona Yaeger, Lukas E Dow.

KRAS is mutationally activated in 45-50% of colorectal cancer (CRC) cases, and while KRAS-targeted therapies have shown some clinical promise, upfront and acquired resistance limit their efficacy. To explore the acute response and mechanisms underlying KRAS inhibitor resistance, we used targeted exome sequencing and single-cell spatial transcriptomics to analyze patient-matched pre-treatment, on-treatment, and progression biopsies from patients treated with combined KRAS G12C and EGFR inhibition. Acquired genetic events were identified in most patients at progression but were often subclonal and coexisted with transcriptional adaptive states. Mesenchymal, YAP, and fetal-like transcriptional signatures predominated in resistant tumors, while tumor cell-intrinsic inflammatory programs were induced in the early treatment phase. Single-cell spatial analysis revealed significant intratumoral heterogeneity, with diverse adaptive states predominating in different zones of individual tumors. Using human and murine organoid models, we show that these drug-induced inflammatory programs are cancer-cell autonomous and precede the emergence of regenerative fetal-like programs associated with drug resistance. We uncover TBK1 as a promising target to abrogate the early inflammatory adaptive phase and enhance responses to KRAS inhibition.

DOI: https://doi.org/10.1101/2025.08.05.668666
Nat Commun. 2025 Aug 14. 16(1): 7566

Large-scale CRISPR screening in primary human 3D gastric organoids enables comprehensive dissection of gene-drug interactions.

Yuan-Hung Lo, Hudson T Horn, Mo-Fan Huang, Wei-Chieh Yu, Chia-Mei Young, Qing Liu, Madeline Tomaske, Martina Towers, Antonia Dominguez, Michael C Bassik, Dung-Fang Lee, Lei S Qi, Jonathan S Weissman, Jin Chen, Calvin J Kuo.

Understanding how genes influence drug responses is critical for advancing personalized cancer treatments. However, identifying these gene-drug interactions in a physiologically relevant human system remains a challenge, as it requires a model that reflects the complexity and heterogeneity among individuals. Here we show that large-scale CRISPR-based genetic screens, including knockout, interference (CRISPRi), activation (CRISPRa), and single-cell approaches, can be applied in primary human 3D gastric organoids to systematically identify genes that affect sensitivity to cisplatin. Our screens uncover genes that modulate cisplatin response. By combining CRISPR perturbations with single-cell transcriptomics, we resolve how genetic alterations interact with cisplatin at the level of individual cells and uncover an unexpected link between fucosylation and cisplatin sensitivity. We identify TAF6L as a regulator of cell recovery from cisplatin-induced cytotoxicity. These results highlight the utility of human organoid models for dissecting gene-drug interactions and offer insights into therapeutic vulnerabilities in gastric cancer.

DOI: https://doi.org/10.1038/s41467-025-62818-3
Cell Rep. 2025 Aug 12. pii: S2211-1247(25)00897-6. [Epub ahead of print]44(8): 116126

The Nα-acetyl-L-lysine/Loxl2/H2O2 promotes intestinal tumor growth in Drosophila and cell proliferation in human colorectal cancer.

Lei Geng, Zhen Fan, Rongbing Chen, Kyu-Chan Cho, Yining Liu, Yu Cheng, Jingfeng Yang, Ying Zhang, Xuefei Wei, Liyuan Gong, Yingyu Tang, Zhan Xu, Wuren Huang, Shahzad Toufeeq, Zongzhao Zhai, Lei Pan, Jun Zhang, Bin Li, Brenda T Beerntsen, Ji-Hoon Lee, Youli Xiao, Younghwa Na, Won-Jae Lee, Erjun Ling.

  A cancer-associated microbiome is considered a carcinogen capable of affecting tumor initiation and/or progression. However, little is known about the molecular mechanisms of tumor-microbiome interactions. Here, we show that Staphylococcus sciuri promotes Drosophila intestinal tumor growth by inducing intestinal stem cell (ISC) division. Metabolomic analysis revealed that Nα-acetyl-L-lysine derived from S. sciuri, but not other naturally Nα-acetylated L-type amino acids, promotes ISC division in germ-free and conventional animals. Biochemical analysis further shows that GCN5-related N-acetyl transferases of S. sciuri catalyze L-lysine and acetyl-CoA into Nα-acetyl-L-lysine. Drosophila lysyl oxidase-like 2 enzyme subsequently catalyzes Nα-acetyl-L-lysine to produce H2O2, forming the Nα-acetyl-L-lysine/Loxl2/H2O2 axis that activates ATR-Chk1 and JNK and subsequently triggers the JAK/STAT pathway required for ISC division and tumor growth. The Nα-acetyl-L-lysine/Loxl2/H2O2 axis also regulates human colorectal cancer cell division. The identification of Nα-acetyl-L-lysine/Loxl2/H2O2 axis provides distinct insights into the complex interplay among microbiome, tumor, and oxidative stress.

Keywords:  ATR-Chk1 pathway; CP: Cancer; CP: Microbiology; Drosophila; JAK/STAT pathway; JNK pathway; Nα-acetyl-L-lysine/Loxl2/H(2)O(2) axis; Staphylococcus sciuri; colorectal cancer cell; intestinal stem cell; microbiome-tumor-H₂O₂ interplay

DOI:  https://doi.org/10.1016/j.celrep.2025.116126
bioRxiv. 2025 Aug 06. pii: 2025.08.06.668727. [Epub ahead of print]

A Spatial and Temporal Transcriptomic Atlas of Mouse Intestinal Regeneration.

Rachel Ofer, Tyler Tran, Ping He, Xia Qiu, Xinyu Hu, Emmanuel Zachariah, Curtis Krier, Ankit Saxena, Jiekun Yang, Michael P Verzi.

Background & Aims: The intestinal epithelium exhibits a remarkable capacity for regeneration following injury. However, the spatial and temporal dynamics of the injury-repair cycle remain incompletely understood.
Methods: We employ spatial transcriptomics to create an atlas of the damage and repair response to ionizing radiation in the mouse intestine. We map molecular events driving epithelial recovery over a six-day period and 23 biological samples, spanning the early apoptotic response to tissue remodeling and repair.
Results: The datasets capture mRNA of 19,042 genes in ∼26 million bins at 2µm resolution. Analysis revealed transcriptional patterns and niche signals that would remain undetected in bulk or single-cell approaches, including a non-random activation of interferon-target genes. Temporal shifts in cytokine and growth factor gene expression, particularly in the crypt and lower villus regions, corroborate published studies and reveal new predictions of the mechanisms governing intestinal healing. Global transcriptional upregulation was observed in the regenerating epithelium, suggesting hypertranscription is a hallmark of intestinal repair. Furthermore, we observe altered cellular differentiation trajectories and villus patterning at the early stages of regeneration.
Conclusions: Together, our work provides a detailed spatiotemporal map of intestinal regeneration at subcellular resolution and nearly whole-genome scale. These data lay the groundwork for future discoveries and therapeutic strategies to enhance epithelial repair in inflammatory bowel diseases and other gastrointestinal pathologies or in response to side-effects of cancer therapies.

DOI: https://doi.org/10.1101/2025.08.06.668727
bioRxiv. 2025 Jul 18. pii: 2025.07.15.664829. [Epub ahead of print]

Biomechanical Phenotyping Reveals Unique Mechanobiological Signatures of Early-Onset Colorectal Cancer.

Nicole C Huning, Munir H Buhaya, Victor V Nguyen, Afeefah Khazi-Syed, Haider A Ali, Adil Khan, Angela Fan, Robert C Fisher, Zhikai Chi, Indu Raman, Guangchun Chen, Chengsong Zhu, Mengxi Yu, Andrew R Jamieson, Sara Roccabianca, Victor D Varner, Cheryl M Lewis, Emina H Huang, Jacopo Ferruzzi.

The incidence of sporadic early onset colorectal cancer (EO CRC, under 50 years of age) is rising rapidly, yet the causes behind such rise remain poorly understood. Epidemiological studies indicate that lifestyle and environmental exposures may result in chronic inflammation, which is known to trigger tissue fibrosis. We hypothesized that fibrotic remodeling and biomechanical stiffening of colorectal tissues represent hallmarks and drivers of EO CRC. Using primary human tissues, we show that EO CRC is associated with changes in collagen microstructure, increased stiffness and elevated viscosity of primary tumors. Spatial profiling and immunostaining reveal pro-fibrotic transcriptional programs in stromal cells, alongside enhanced mechanotransduction and proliferation in epithelial cells. In vitro, increased matrix stiffness promotes increased proliferation of epithelial cells in 2D and 3D colorectal cancer models. Together, these findings establish EO CRC as a disease marked by early and widespread biomechanical remodeling, suggesting that a fibrotic and stiffened tissue microenvironment may orchestrate EO CRC tumor initiation.

DOI: https://doi.org/10.1101/2025.07.15.664829
bioRxiv. 2025 Aug 06. pii: 2025.08.05.668752. [Epub ahead of print]

Vitamin B2 metabolism promotes FSP1 stability to prevent ferroptosis.

Kirandeep K Deol, Cynthia A Harris, Sydney J Tomlinson, Cody E Doubravsky, Alyssa J Mathiowetz, James A Olzmann.

Ferroptosis, a regulated form of cell death driven by excessive lipid peroxidation, has emerged as a promising therapeutic target in cancer. Ferroptosis suppressor protein 1 (FSP1) is a critical regulator of ferroptosis resistance, yet the mechanisms controlling its expression and stability remain mostly unexplored. To uncover regulators of FSP1 abundance, we conducted CRISPR-Cas9 screens utilizing a genome-edited, dual-fluorescent FSP1 reporter cell line, identifying both transcriptional and post-translational mechanisms that determine FSP1 levels. Notably, we identified riboflavin kinase (RFK) and FAD synthase (FLAD1), enzymes which are essential for synthesizing flavin adenine dinucleotide (FAD) from vitamin B2, as key contributors to FSP1 stability. Biochemical and cellular analyses revealed that FAD binding is critical for FSP1 activity. FAD deficiency, and mutations blocking FSP1-FAD binding, triggered FSP1 degradation via a ubiquitin-proteasome pathway that involves the E3 ligase RNF8. Unlike other vitamins that inhibit ferroptosis by scavenging radicals, vitamin B2 supports ferroptosis resistance through FAD cofactor binding, ensuring proper FSP1 stability and function. This study provides a rich resource detailing mechanisms that regulate FSP1 abundance and highlights a novel connection between vitamin B2 metabolism and ferroptosis resistance with implications for therapeutic strategies targeting FSP1 in cancer.

DOI: https://doi.org/10.1101/2025.08.05.668752
Cancer Lett. 2025 Aug 09. pii: S0304-3835(25)00547-6. [Epub ahead of print] 217977

Restricting metabolic plasticity enhances stress adaptation through the modulation of PDH and HIF1A in TRAP1-depleted colon cancer.

Hong-Yuan Tsai, Miao-Hsueh Chen, Jihye Yun, Lisa A Lai, John F Valentine, Mary P Bronner, Teresa A Brentnall, Sheng Pan, Ru Chen.

  Metabolic plasticity allows cancer cells to survive under adverse conditions. To investigate the role of mitochondrial chaperone tumor necrosis factor receptor-associated protein 1 (TRAP1) in this process, we used CRISPR/Cas9 mediated genetic deletion to knock out (KO) TRAP1 in colon cancer cells. Depletion of TRAP1 triggered a series of events: induced metabolic reprogramming, increased glycolytic flux, downregulation of mitochondrial complex I, and elevated ROS generation. TRAP1-deficient cells showed tolerance to Oxidative Phosphorylation (OXPHOS) inhibitors and exhibited a higher extracellular acidification rate (ECAR). Additionally, TRAP1 depletion activated hypoxia response elements (HREs) and upregulated HIF1A target genes such as GLUT1 and MCT1. Furthermore, pyruvate dehydrogenase kinases 1 (PDK1) was upregulated in KO cells, leading to the inactivation of the tricarboxylic acid (TCA) cycle enzyme, pyruvate dehydrogenase (PDH). This metabolic shift towards glycolytic metabolism resulted in increased glycolytic metabolism, elevated lactic acid production, and higher glucose consumption, making TRAP1-depleted cancer cells more dependent on this altered metabolism for survival. Treatment with DCA, a PDK inhibitor, restored PDH activity, exacerbated oxidative stress, and increased cell death in KO cells. Our study here sheds light on how TRAP1 depletion affects metabolic plasticity, driving colon cancer cells to adapt to metabolic and oxidative stress. These findings highlight TRAP1 as a promising therapeutic target for manipulating metabolic plasticity and overcoming drug resistance in cancer therapy.

Keywords:  HIF1A; Metabolism; PDH; ROS; TRAP1; mitochondria

DOI:  https://doi.org/10.1016/j.canlet.2025.217977
ESMO Open. 2025 Aug 12. pii: S2059-7029(25)01389-4. [Epub ahead of print]10(8): 105520

Differentiating low tumor burden from oligometastatic disease in colorectal cancer: a call for individualized therapeutic approaches.

M C de Grandis, I Baraibar, O Prior, M Balaguer-Montero, F Salvà, J Ros, M Rodríguez-Castells, J Tabernero, S Lonardi, R Perez-Lopez, E Élez.

  Metastatic colorectal cancer (mCRC) remains a major clinical challenge; however, tumor burden significantly influences treatment outcomes. In this review, we explore the biological and clinical relevance of low tumor burden (LTB) in mCRC. The primary challenge in defining LTB mCRC lies in establishing a standardized definition that extends beyond the current focus on oligometastatic disease. Patients with LTB mCRC exhibit distinct clinical characteristics that may impact both prognosis and therapeutic response. Evidence suggests that LTB patients often respond better to systemic therapies and may derive potential benefits from targeted and immunotherapy approaches. However, establishing a clear definition is crucial for consistent patient stratification, and for guiding research and selecting the most appropriate therapeutic strategies, particularly in the context of emerging treatments such as immunotherapy. Recent studies using advanced imaging modalities, liquid biopsies, and lactate dehydrogenase (LDH) measurements offer novel approaches to evaluate tumor burden more accurately. These developments, coupled with emerging evidence that patients with LTB may benefit from immunotherapy, highlight the need for further research focused on LTB mCRC patients. Additionally, artificial intelligence (AI) could enhance tumor detection, automate three-dimensional (3D) volume quantification, extract radiomics-based prognostic information, and integrate multimodal data. These capabilities may enhance our ability to stratify patients and guide treatment decisions, potentially leading to better outcomes for mCRC patients. Future studies should focus on refining the definition of LTB, validating these new assessment techniques, and evaluating their impact on treatment outcomes in mCRC patients.

Keywords:  artificial intelligence; colorectal cancer; immunotherapy; low tumor burden; radiomics

DOI:  https://doi.org/10.1016/j.esmoop.2025.105520
Adv Sci (Weinh). 2025 Aug 11. e07080

Patients-Derived Organoids Sequencing-based FOXP4 Facilitates Radioresistance by Transcriptionally Modifying GPX4 to Regulate ferroptosis in Colorectal Cancer.

Qianping Chen, Yuzhao Jin, Luyu Liao, Rong Shen, Xingnan Ge, Qingyu Jiang, Ying Huang, Quanquan Sun, Dong Liu, Luying Liu, Tongxin Liu, Qinghui Dai, Xiyuan Tang, Zhe Han, Xin Gao, Xinhua Lin, Wei Mao, Ji Zhu.

  More than 50% of patients with colorectal cancer (CRC) exhibit radioresistance, indicating the need for further research on the disease. Therefore, the aim of this study is to identify radioresistance genes and elucidate the underlying molecular mechanisms using patient-derived organoids (PDOs). Transcriptome analyses are performed on radio-resistant and -sensitive PDOs, CRC cells, and xenograft tissues to screen for radioresistant genes. Additionally, the genetic homology between PDOs and clinical tissues is verified using whole-exome sequencing. Functional experiments are performed to validate the roles of the candidate genes using cellular, organoid, and animal models. Forkhead box P4 (FOXP4) is identified as a differentially expressed genes between the radio-sensitive and -resistant groups that is linked to radioresistance. Further experiments show that FOXP4 promoted radioresistance by suppressing ferroptosis. Mechanistically, FOXP4 regulated GPX4 transcription by binding to the promoter region of GPX4 via the forkhead domain to inhibit the onset of ferroptosis. Doxorubicin (DOX) inhibited FOXP4 expression by promoting its ubiquitination and degradation, eventually increasing radiosensitivity. Notably, DOX combined with irradiation attenuated the compensatory increase in FOXP4 expression and increased radiotherapy efficacy. Conclusively, the combination therapy provides a new strategy for enhancing therapeutic efficacy in CRC.

Keywords:  FOXP4; Ferroptosis; GPX4; PDOs; Radioresistance

DOI:  https://doi.org/10.1002/advs.202507080
Sci Adv. 2025 Aug 15. 11(33): eadx6587

Targeting lipid scrambling potentiates ferroptosis and triggers tumor immune rejection.

Mengyun Yang, Ze Yu, Jieming Ping, Yuanchun Duan, Jianlong Tang, Weixiang Liu, Qing He, Yongfeng Lai, Sin Man Lam, Hesen Tang, Zhengjie Liu, Weimin Wang, Min Zhu, Wei Hu, Yunyun Han, Guanghou Shui, Jiqing Hao, Zheng Liu, Ning Wu.

Despite advances in understanding the metabolic mechanisms of ferroptosis, the molecular events following lipid peroxide accumulation on the plasma membrane (PM) remain unclear. Herein, we identify TMEM16F as a ferroptosis suppressor at the executional phase. TMEM16F-deficient cells display heightened sensitivity to ferroptosis. Mechanistically, TMEM16F-mediated phospholipids (PLs) scrambling orchestrates extensive remodeling of PM lipids, translocating PLs at the lesion sites to reduce membrane tension, therefore mitigating the membrane damage. Unexpectedly, failure of PL scrambling in TMEM16F-deficient cells leads to lytic cell death, exhibiting PM collapse and unleashing substantial danger-associated molecule patterns. TMEM16F-deficient tumors exhibit decelerated progression. Notably, lipid scrambling inhibition synergizes with PD-1 blockade to trigger robust tumor immune rejection. The antiparasitic drug ivermectin enhances the responsiveness to PD-1 blockade by suppressing TMEM16F. Our findings uncover TMEM16F-mediated lipid scrambling as an anti-ferroptosis regulator by relocating PLs on the PM during the final stages of ferroptosis. Targeting TMEM16F-mediated lipid scrambling presents a promising therapeutic strategy for cancer treatment.

DOI: https://doi.org/10.1126/sciadv.adx6587
bioRxiv. 2025 Jul 18. pii: 2025.07.15.662825. [Epub ahead of print]

Multiplex analysis of colorectal cancer tissue describes the composition, cell biology and spatial effects of cell-in-cell events and identifies a T cell-dependent prognostic signature.

Emir Bozkurt, Batuhan Kisakol, Mohammadreza Azimi, Heiko Dussmann, Sanghee Cho, Elizabeth McDonough, Joana Fay, Tony O'Grady, John P Burke, Niamh McCawley, Deborah A McNamara, Daniel B Longley, Fiona Ginty, Jochen H M Prehn.

Cell-in-cell (CIC) structures, in which one cell is entirely engulfed by another, have been associated with poor outcomes in cancers. However, the mechanisms underlying this association remain poorly understood. We performed multiplex imaging of 56 cell identity, cell 'state' and cancer 'hallmark' proteins to characterise CICs, map their spatial interactions, and assess clinical associations across 444 tumour cores from 148 colorectal cancer patients, which contained over one million spatially resolved cells. We found that tumour regions containing CICs were associated with lower levels of cytotoxic T cells. We identified upregulated glucose metabolism as a consistent metabolic hallmark of CICs independent of cell type. Spatial analyses revealed that T cells adjacent to CICs underwent selective remodeling with distinct apoptotic and metabolic signatures. Finally, the presence of T cells within CIC neighbourhoods identified a subset of patients with improved survival. Our findings suggest that CICs may be a feature of metabolically competitive niches and a potential factor contributing to T-cell exclusion in tumours.

DOI: https://doi.org/10.1101/2025.07.15.662825