bims-instec 2024-07-28 papers

bims-instec

Biomed News

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

Issue of 2024–07–28
thirteen papers selected by
Maria-Virginia Giolito, Université Catholique de Louvain

MTGR1 is required to maintain small intestinal stem cell populations.
uL3 Regulates Redox Metabolism and Ferroptosis Sensitivity of p53-Deleted Colorectal Cancer Cells.
Fibroblasts Promote Resistance to KRAS Silencing in Colorectal Cancer Cells.
Asparagine synthetase and G-protein coupled estrogen receptor are critical responders to nutrient supply in KRAS mutant colorectal cancer.
Molecular subtypes of colorectal cancer in the era of precision oncotherapy: Current inspirations and future challenges.
CRISPR Knock-Ins in Organoids to Track Tumor Cell Subpopulations.
High-confidence calling of normal epithelial cells allows identification of a novel stem-like cell state in the colorectal cancer microenvironment.
A mini-colon models colon cancer and its microenvironment.
Cell competition in primary and metastatic colorectal cancer.
Western lifestyle, metaflammation and the cell of origin of colon cancer.
Very long-chain fatty acids control peroxisome dynamics via a feedback loop in intestinal stem cells during gut regeneration.
Patient-derived organoids (PDOs) and PDO-derived xenografts (PDOXs): New opportunities in establishing faithful pre-clinical cancer models.
Monoacylglycerol acyltransferase-2 inhibits colorectal carcinogenesis in APCmin+/- mice.

Cell Death Differ. 2024 Jul 25.

MTGR1 is required to maintain small intestinal stem cell populations.

Sarah P Short, Rachel E Brown, Zhengyi Chen, Jennifer M Pilat, Bailey A McElligott, Leslie M Meenderink, Alexander C Bickart, Koral M Blunt, Justin Jacobse, Jing Wang, Alan J Simmons, Yanwen Xu, Yilin Yang, Bobak Parang, Yash A Choksi, Jeremy A Goettel, Ken S Lau, Scott W Hiebert, Christopher S Williams.

Undifferentiated intestinal stem cells (ISCs) are crucial for maintaining homeostasis and resolving injury. Lgr5+ cells in the crypt base constantly divide, pushing daughter cells upward along the crypt axis where they differentiate into specialized cell types. Coordinated execution of complex transcriptional programs is necessary to allow for the maintenance of undifferentiated stem cells while permitting differentiation of the wide array of intestinal cells necessary for homeostasis. Previously, members of the myeloid translocation gene (MTG) family have been identified as transcriptional co-repressors that regulate stem cell maintenance and differentiation programs in multiple organ systems, including the intestine. One MTG family member, myeloid translocation gene related 1 (MTGR1), has been recognized as a crucial regulator of secretory cell differentiation and response to injury. However, whether MTGR1 contributes to the function of ISCs has not yet been examined. Here, using Mtgr1-/- mice, we have assessed the effects of MTGR1 loss specifically in ISC biology. Interestingly, loss of MTGR1 increased the total number of cells expressing Lgr5, the canonical marker of cycling ISCs, suggesting higher overall stem cell numbers. However, expanded transcriptomic and functional analyses revealed deficiencies in Mtgr1-null ISCs, including deregulated ISC-associated transcriptional programs. Ex vivo, intestinal organoids established from Mtgr1-null mice were unable to survive and expand due to aberrant differentiation and loss of stem and proliferative cells. Together, these results indicate that the role of MTGR1 in intestinal differentiation is likely stem cell intrinsic and identify a novel role for MTGR1 in maintaining ISC function.

DOI: https://doi.org/10.1038/s41418-024-01346-x
Antioxidants (Basel). 2024 Jun 22. pii: 757. [Epub ahead of print]13(7):

uL3 Regulates Redox Metabolism and Ferroptosis Sensitivity of p53-Deleted Colorectal Cancer Cells.

Chiara Brignola, Annalisa Pecoraro, Camilla Danisi, Nunzia Iaccarino, Anna Di Porzio, Francesca Romano, Pietro Carotenuto, Giulia Russo, Annapina Russo.

  Despite advancements in therapeutic strategies, the development of drug resistance and metastasis remains a serious concern for the efficacy of chemotherapy against colorectal cancer (CRC). We have previously demonstrated that low expression of ribosomal protein uL3 positively correlates with chemoresistance in CRC patients. Here, we demonstrated that the loss of uL3 increased the metastatic capacity of CRC cells in chick embryos. Metabolomic analysis revealed large perturbations in amino acid and glutathione metabolism in resistant uL3-silenced CRC cells, indicating that uL3 silencing dramatically triggered redox metabolic reprogramming. RNA-Seq data revealed a notable dysregulation of 108 genes related to ferroptosis in CRC patients. Solute Carrier Family 7 Member 11 (SLC7A11) is one of the most dysregulated genes; its mRNA stability is negatively regulated by uL3, and its expression is inversely correlated with uL3 levels. Inhibition of SLC7A11 with erastin impaired resistant uL3-silenced CRC cell survival by inducing ferroptosis. Of interest, the combined treatment erastin plus uL3 enhanced the chemotherapeutic sensitivity of uL3-silenced CRC cells to erastin. The antimetastatic potential of the combined strategy was evaluated in chick embryos. Overall, our study sheds light on uL3-mediated chemoresistance and provides evidence of a novel therapeutic approach, erastin plus uL3, to induce ferroptosis, establishing individualized therapy by examining p53, uL3 and SLC7A11 profiles in tumors.

Keywords:  CAM assay; SLC7A11/xCT; cancer redox metabolic reprogramming; drug resistance; ferroptosis; ribosomal protein uL3

DOI:  https://doi.org/10.3390/antiox13070757
Cancers (Basel). 2024 Jul 20. pii: 2595. [Epub ahead of print]16(14):

Fibroblasts Promote Resistance to KRAS Silencing in Colorectal Cancer Cells.

Susana Mendonça Oliveira, Patrícia Dias Carvalho, André Serra-Roma, Patrícia Oliveira, Andreia Ribeiro, Joana Carvalho, Flávia Martins, Ana Luísa Machado, Maria José Oliveira, Sérgia Velho.

  Colorectal cancer (CRC) responses to KRAS-targeted inhibition have been limited due to low response rates, the mechanisms of which remain unknown. Herein, we explored the cancer-associated fibroblasts (CAFs) secretome as a mediator of resistance to KRAS silencing. CRC cell lines HCT15, HCT116, and SW480 were cultured either in recommended media or in conditioned media from a normal colon fibroblast cell line (CCD-18Co) activated with rhTGF-β1 to induce a CAF-like phenotype. The expression of membrane stem cell markers was analyzed by flow cytometry. Stem cell potential was evaluated by a sphere formation assay. RNAseq was performed in KRAS-silenced HCT116 colonospheres treated with either control media or conditioned media from CAFs. Our results demonstrated that KRAS-silencing up-regulated CD24 and down-regulated CD49f and CD104 in the three cell lines, leading to a reduction in sphere-forming efficiency. However, CAF-secreted factors restored stem cell marker expression and increased stemness. RNA sequencing showed that CAF-secreted factors up-regulated genes associated with pro-tumorigenic pathways in KRAS-silenced cells, including KRAS, TGFβ, NOTCH, WNT, MYC, cell cycle progression and exit from quiescence, epithelial-mesenchymal transition, and immune regulation. Overall, our results suggest that resistance to KRAS-targeted inhibition might derive not only from cell-intrinsic causes but also from external elements, such as fibroblast-secreted factors.

Keywords:  KRAS; cancer stemness; colorectal cancer; epithelial-mesenchymal transition; fibroblasts; therapy resistance

DOI:  https://doi.org/10.3390/cancers16142595
Int J Cancer. 2024 Jul 22.

Asparagine synthetase and G-protein coupled estrogen receptor are critical responders to nutrient supply in KRAS mutant colorectal cancer.

Lingeng Lu, Qian Zhang, Oladimeji Aladelokun, Domenica Berardi, Xinyi Shen, Audrey Marin, Rolando Garcia-Milian, Jatin Roper, Sajid A Khan, Caroline H Johnson.

  Survival differences exist in colorectal cancer (CRC) patients by sex and disease stage. However, the potential molecular mechanism(s) are not well understood. Here we show that asparagine synthetase (ASNS) and G protein-coupled estrogen receptor-1 (GPER1) are critical sensors of nutrient depletion and linked to poorer outcomes for females with CRC. Using a 3D spheroid model of isogenic SW48 KRAS wild-type (WT) and G12A mutant (MT) cells grown under a restricted nutrient supply, we found that glutamine depletion inhibited cell growth in both cell lines, whereas ASNS and GPER1 expression were upregulated in KRAS MT versus WT. Estradiol decreased growth in KRAS WT but had no effect on MT cells. Selective GPER1 and ASNS inhibitors suppressed cell proliferation with increased caspase-3 activity of MT cells under glutamine depletion condition particularly in the presence of estradiol. In a clinical colon cancer cohort from The Cancer Genome Atlas, both high GPER1 and ASNS expression were associated with poorer overall survival for females only in advanced stage tumors. These results suggest KRAS MT cells have mechanisms in place that respond to decreased nutrient supply, typically observed in advanced tumors, by increasing the expression of ASNS and GPER1 to drive cell growth. Furthermore, KRAS MT cells are resistant to the protective effects of estradiol under nutrient deplete conditions. The findings indicate that GPER1 and ASNS expression, along with the interaction between nutrient supply and KRAS mutations shed additional light on the mechanisms underlying sex differences in metabolism and growth in CRC, and have clinical implications in the precision management of KRAS mutant CRC.

Keywords:  ASNS; GPER1; colorectal cancer; estradiol; glutamine; survival

DOI:  https://doi.org/10.1002/ijc.35104
Cancer Med. 2024 Jul;13(14): e70041

Molecular subtypes of colorectal cancer in the era of precision oncotherapy: Current inspirations and future challenges.

Qin Dang, Lulu Zuo, Xinru Hu, Zhaokai Zhou, Shuang Chen, Shutong Liu, Yuhao Ba, Anning Zuo, Hui Xu, Siyuan Weng, Yuyuan Zhang, Peng Luo, Quan Cheng, Zaoqu Liu, Xinwei Han.

   BACKGROUND: Colorectal cancer (CRC) is among the most hackneyed malignancies. Even patients with identical clinical symptoms and the same TNM stage still exhibit radically different clinical outcomes after receiving equivalent treatment regimens, indicating extensive heterogeneity of CRC. Myriad molecular subtypes of CRC have been exploited for decades, including the most compelling consensus molecular subtype (CMS) classification that has been broadly applied for patient stratification and biomarker-drug combination formulation. Encountering barriers to clinical translation, however, CMS classification fails to fully reflect inter- or intra-tumor heterogeneity of CRC. As a consequence, addressing heterogeneity and precisely managing CRC patients with unique characteristics remain arduous tasks for clinicians.
REVIEW: In this review, we systematically summarize molecular subtypes of CRC and further elaborate on their clinical applications, limitations, and future orientations.
CONCLUSION: In recent years, exploration of subtypes through cell lines, animal models, patient-derived xenografts (PDXs), organoids, and clinical trials contributes to refining biological insights and unraveling subtype-specific therapies in CRC. Therapeutic interventions including nanotechnology, clustered regulatory interspaced short palindromic repeat/CRISPR-associated nuclease 9 (CRISPR/Cas9), gut microbiome, and liquid biopsy are powerful tools with the possibility to shift the immunologic landscape and outlook for CRC precise medicine.

Keywords:  CMS classification; colorectal cancer; heterogeneity; molecular subtype; precision oncotherapy

DOI:  https://doi.org/10.1002/cam4.70041
Methods Mol Biol. 2024 ;2811 137-154

CRISPR Knock-Ins in Organoids to Track Tumor Cell Subpopulations.

Carme Cortina, Adrià Cañellas-Socias.

  The integration of CRISPR/Cas9 genome editing techniques with organoid technology has revolutionized the field of tumor modeling, enabling the creation of diverse tumor models with distinct mutational profiles. This protocol details the application of CRISPR knock-ins to engineer tumor organoids with reporter cassettes, which are regulated by endogenous promoters of specific genes of interest. This approach facilitates the precise fluorescent labeling, isolation, and subsequent manipulation of targeted tumor cell subpopulations. The utilization of these knock-in reporter cassettes not only allows the visualization and purification of specific tumor cell subsets but also enables conditional cell ablation and lineage tracing studies. In this chapter, we provide a comprehensive guide for the design, construction, delivery, and validation of CRISPR/Cas9 tools tailored for knock-in reporter cassette integration into specific marker genes of interest. By following this protocol, researchers can harness the potential of engineered tumor organoids to decipher intricate tumor heterogeneity, track metastatic trajectories, and unveil novel therapeutic vulnerabilities linked to specific tumor cell subpopulations.

Keywords:  CRISPR/Cas9; Conditional cell ablation; Knock-in; Lineage tracing; Tumor heterogeneity; Tumor organoids

DOI:  https://doi.org/10.1007/978-1-0716-3882-8_10
Int J Cancer. 2024 Jul 19.

High-confidence calling of normal epithelial cells allows identification of a novel stem-like cell state in the colorectal cancer microenvironment.

Tzu-Ting Wei, Eric Blanc, Stefan Peidli, Philip Bischoff, Alexandra Trinks, David Horst, Christine Sers, Nils Blüthgen, Dieter Beule, Markus Morkel, Benedikt Obermayer.

  Single-cell analyses can be confounded by assigning unrelated groups of cells to common developmental trajectories. For instance, cancer cells and admixed normal epithelial cells could adopt similar cell states thus complicating analyses of their developmental potential. Here, we develop and benchmark CCISM (for Cancer Cell Identification using Somatic Mutations) to exploit genomic single nucleotide variants for the disambiguation of cancer cells from genomically normal non-cancer cells in single-cell data. We find that our method and others based on gene expression or allelic imbalances identify overlapping sets of colorectal cancer versus normal colon epithelial cells, depending on molecular characteristics of individual cancers. Further, we define consensus cell identities of normal and cancer epithelial cells with higher transcriptome cluster homogeneity than those derived using existing tools. Using the consensus identities, we identify significant shifts of cell state distributions in genomically normal epithelial cells developing in the cancer microenvironment, with immature states increased at the expense of terminal differentiation throughout the colon, and a novel stem-like cell state arising in the left colon. Trajectory analyses show that the new cell state extends the pseudo-time range of normal colon stem-like cells in a cancer context. We identify cancer-associated fibroblasts as sources of WNT and BMP ligands potentially contributing to increased plasticity of stem cells in the cancer microenvironment. Our analyses advocate careful interpretation of cell heterogeneity and plasticity in the cancer context and the consideration of genomic information in addition to gene expression data when possible.

Keywords:  cellular heterogeneity; single‐cell genomics; somatic variants

DOI:  https://doi.org/10.1002/ijc.35079
Nat Biotechnol. 2024 Jul 25.

A mini-colon models colon cancer and its microenvironment.

Colin Hutton, Vivian S W Li.

DOI: https://doi.org/10.1038/s41587-024-02343-8
Oncogenesis. 2024 Jul 26. 13(1): 28

Cell competition in primary and metastatic colorectal cancer.

Merel Elise van Luyk, Ana Krotenberg Garcia, Maria Lamprou, Saskia Jacoba Elisabeth Suijkerbuijk.

Adult tissues set the scene for a continuous battle between cells, where a comparison of cellular fitness results in the elimination of weaker "loser" cells. This phenomenon, named cell competition, is beneficial for tissue integrity and homeostasis. In fact, cell competition plays a crucial role in tumor suppression, through elimination of early malignant cells, as part of Epithelial Defense Against Cancer. However, it is increasingly apparent that cell competition doubles as a tumor-promoting mechanism. The comparative nature of cell competition means that mutational background, proliferation rate and polarity all factor in to determine the outcome of these processes. In this review, we explore the intricate and context-dependent involvement of cell competition in homeostasis and regeneration, as well as during initiation and progression of primary and metastasized colorectal cancer. We provide a comprehensive overview of molecular and cellular mechanisms governing cell competition and its parallels with regeneration.

DOI: https://doi.org/10.1038/s41389-024-00530-5
Nat Rev Gastroenterol Hepatol. 2024 Jul 24.

Western lifestyle, metaflammation and the cell of origin of colon cancer.

Mathijs P Verhagen, Mark Schmitt, Riccardo Fodde.

DOI: https://doi.org/10.1038/s41575-024-00964-7
Dev Cell. 2024 Jul 16. pii: S1534-5807(24)00398-8. [Epub ahead of print]

Very long-chain fatty acids control peroxisome dynamics via a feedback loop in intestinal stem cells during gut regeneration.

Xiaoxin Guo, Juanyu Zhou, La Yan, Xingzhu Liu, Yu Yuan, Jinbao Ye, Zehong Zhang, Haiou Chen, Yongxin Ma, Zhendong Zhong, Guanzheng Luo, Haiyang Chen.

  Peroxisome dynamics are crucial for intestinal stem cell (ISC) differentiation and gut regeneration. However, the precise mechanisms that govern peroxisome dynamics within ISCs during gut regeneration remain unknown. Using mouse colitis and Drosophila intestine models, we have identified a negative-feedback control mechanism involving the transcription factors peroxisome proliferator-activated receptors (PPARs) and SOX21. This feedback mechanism effectively regulates peroxisome abundance during gut regeneration. Following gut injury, the released free very long-chain fatty acids (VLCFAs) increase peroxisome abundance by stimulating PPARs-PEX11s signaling. PPARs act to stimulate peroxisome fission and inhibit pexophagy. SOX21, which acts downstream of peroxisomes during ISC differentiation, induces peroxisome elimination through pexophagy while repressing PPAR expression. Hence, PPARs and SOX21 constitute a finely tuned negative-feedback loop that regulates peroxisome dynamics. These findings shed light on the complex molecular mechanisms underlying peroxisome regulation in ISCs, contributing to our understanding of gut renewal and repair.

Keywords:  VLCFAs; feedback regulation; gut regeneration; intestinal stem cell; peroxisome dynamics

DOI:  https://doi.org/10.1016/j.devcel.2024.06.020
J Natl Cancer Cent. 2022 Dec;2(4): 263-276

Patient-derived organoids (PDOs) and PDO-derived xenografts (PDOXs): New opportunities in establishing faithful pre-clinical cancer models.

Ergang Wang, Kun Xiang, Yun Zhang, Xiao-Fan Wang.

  One of the major bottlenecks in advancing basic cancer research and developing novel cancer therapies is the lack of in vitro pre-clinical models that faithfully recapitulate tumor properties in the patients. Monolayer cultures of cancer cell lines usually lose the heterogeneity of the parental tumors, while patient-derived xenograft (PDX) suffers from its time- and resource-intensive nature. The emergence of organoid culture system and its application in cancer research provides a unique opportunity to develop novel in vitro cancer pre-clinical models. Here we review the recent advances in utilizing organoids culture system and other related three-dimensional culture systems in studying cancer biology, performing drug screening, and developing cancer therapies. In particular, we discuss the advantages of applying xenograft initiated from patient-derived organoids (PDOs) as a faithful cancer pre-clinical model in basic cancer research and precision medicine.

Keywords:  PDO-derived xenograft; Patient-derived organoid; Patient-derived xenograft

DOI:  https://doi.org/10.1016/j.jncc.2022.10.001
iScience. 2024 Jul 19. 27(7): 110205

Monoacylglycerol acyltransferase-2 inhibits colorectal carcinogenesis in APCmin+/- mice.

Yanhong Lang, Chengrui Zhong, Lingling Guo, Zhijie Liu, Dinglan Zuo, Xi Chen, Liuyan Ding, Bijun Huang, Binkui Li, Yunfei Yuan, Yi Niu, Jiliang Qiu, Chaonan Qian.

  Monoacylglycerol acyltransferase-2 (MOGAT2), encodes MOGAT enzyme in the re-synthesis of triacylglycerol and protects from metabolism disorders. While, its precise involvement in colorectal cancer (CRC) progression remains inadequately understood. Our study demonstrated that knockout of Mogat2 in Apcmin/+ mice expedited intestinal tumor growth and progression, indicating that Mogat2 plays a tumor-suppressing role in CRC. Mechanically, Mogat2 deletion resulted in a significant alter the gut microbiota, while Fecal Microbiota Transplantation (FMT) experiments demonstrated that the gut microbiota in Mogat2 deleted mice promoted tumor growth. Furthermore, we identified Mogat2 as a functional regulator suppressing CRC cell proliferation and tumor growth by inhibiting the NF-κB signaling pathway in vivo. Collectively, these results provide novel insights into the protective double roles of Mogat2, inhibiting of NF-κB pathway and keeping gut microbiota homeostasis in colorectal cancer, which may help the development of novel cancer treatments for CRC.

Keywords:  Cancer; Molecular biology

DOI:  https://doi.org/10.1016/j.isci.2024.110205