bims-instec 2024-03-17 papers

bims-instec

Biomed News

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

Issue of 2024–03–17
nine papers selected by
Maria-Virginia Giolito, Université Catholique de Louvain

Epidermal growth factor receptor (EGFR) is a target of the tumor-suppressor E3 ligase FBXW7.
Improved detection of colibactin-induced mutations by genotoxic E. coli in organoids and colorectal cancer.
The intestinal epithelial-macrophage-crypt stem cell axis plays a crucial role in regulating and maintaining intestinal homeostasis.
Identifying regulators of aberrant stem cell and differentiation activity in colorectal cancer using a dual endogenous reporter system.
Transcriptome-wide gene expression outlier analysis pinpoints therapeutic vulnerabilities in colorectal cancer.
Inhibition of the AURKA/YAP1 axis is a promising therapeutic option for overcoming cetuximab resistance in colorectal cancer stem cells.
Identification of fatty acid oxidation-related subtypes by integrated analysis of bulk- and single-cell transcriptome profiling in colorectal cancer.
KRAS mutation-selective requirement for ACSS2 in colorectal adenoma formation.
Villification of the intestinal epithelium is driven by Foxl1.

Proc Natl Acad Sci U S A. 2024 Mar 19. 121(12): e2309902121

Epidermal growth factor receptor (EGFR) is a target of the tumor-suppressor E3 ligase FBXW7.

Matteo Boretto, Maarten H Geurts, Shashank Gandhi, Ziliang Ma, Nadzeya Staliarova, Martina Celotti, Sangho Lim, Gui-Wei He, Rosemary Millen, Else Driehuis, Harry Begthel, Lidwien Smabers, Jeanine Roodhart, Johan van Es, Wei Wu, Hans Clevers.

  FBXW7 is an E3 ubiquitin ligase that targets proteins for proteasome-mediated degradation and is mutated in various cancer types. Here, we use CRISPR base editors to introduce different FBXW7 hotspot mutations in human colon organoids. Functionally, FBXW7 mutation reduces EGF dependency of organoid growth by ~10,000-fold. Combined transcriptomic and proteomic analyses revealed increased EGFR protein stability in FBXW7 mutants. Two distinct phosphodegron motifs reside in the cytoplasmic tail of EGFR. Mutations in these phosphodegron motifs occur in human cancer. CRISPR-mediated disruption of the phosphodegron motif at T693 reduced EGFR degradation and EGF growth factor dependency. FBXW7 mutant organoids showed reduced sensitivity to EGFR-MAPK inhibitors. These observations were further strengthened in CRC-derived organoid lines and validated in a cohort of patients treated with panitumumab. Our data imply that FBXW7 mutations reduce EGF dependency by disabling EGFR turnover.

Keywords:  EGFR; FBXW7; colorectal cancer; organoids

DOI:  https://doi.org/10.1073/pnas.2309902121
Cancer Cell. 2024 Mar 11. pii: S1535-6108(24)00053-9. [Epub ahead of print]42(3): 487-496.e6

Improved detection of colibactin-induced mutations by genotoxic E. coli in organoids and colorectal cancer.

Axel Rosendahl Huber, Cayetano Pleguezuelos-Manzano, Jens Puschhof, Joske Ubels, Charelle Boot, Aurelia Saftien, Mark Verheul, Laurianne T Trabut, Niels Groenen, Markus van Roosmalen, Kyanna S Ouyang, Henry Wood, Phil Quirke, Gerrit Meijer, Edwin Cuppen, Hans Clevers, Ruben van Boxtel.

  Co-culture of intestinal organoids with a colibactin-producing pks+E. coli strain (EcC) revealed mutational signatures also found in colorectal cancer (CRC). E. coli Nissle 1917 (EcN) remains a commonly used probiotic, despite harboring the pks operon and inducing double strand DNA breaks. We determine the mutagenicity of EcN and three CRC-derived pks+E. coli strains with an analytical framework based on sequence characteristic of colibactin-induced mutations. All strains, including EcN, display varying levels of mutagenic activity. Furthermore, a machine learning approach attributing individual mutations to colibactin reveals that patients with colibactin-induced mutations are diagnosed at a younger age and that colibactin can induce a specific APC mutation. These approaches allow the sensitive detection of colibactin-induced mutations in ∼12% of CRC genomes and even in whole exome sequencing data, representing a crucial step toward pinpointing the mutagenic activity of distinct pks+E. coli strains.

Keywords:  bacteria; cancer genomics; colibactin; colorectal cancer; genotoxins; machine learning; mutagenesis; mutational signatures; organoids; probiotics

DOI:  https://doi.org/10.1016/j.ccell.2024.02.009
Life Sci. 2024 Mar 08. pii: S0024-3205(24)00041-9. [Epub ahead of print] 122452

The intestinal epithelial-macrophage-crypt stem cell axis plays a crucial role in regulating and maintaining intestinal homeostasis.

Xiaohui Hu, Xinyi Yuan, Guokun Zhang, Haoyun Song, Pengfei Ji, Yanan Guo, Zihua Liu, Yixiao Tian, Rong Shen, Degui Wang.

  The intestinal tract plays a vital role in both digestion and immunity, making its equilibrium crucial for overall health. This equilibrium relies on the dynamic interplay among intestinal epithelial cells, macrophages, and crypt stem cells. Intestinal epithelial cells play a pivotal role in protecting and regulating the gut. They form vital barriers, modulate immune responses, and engage in pathogen defense and cytokine secretion. Moreover, they supervise the regulation of intestinal stem cells. Macrophages, serving as immune cells, actively influence the immune response through the phagocytosis of pathogens and the release of cytokines. They also contribute to regulating intestinal stem cells. Stem cells, known for their self-renewal and differentiation abilities, play a vital role in repairing damaged intestinal epithelium and maintaining homeostasis. Although research has primarily concentrated on the connections between epithelial and stem cells, interactions with macrophages have been less explored. This review aims to fill this gap by exploring the roles of the intestinal epithelial-macrophage-crypt stem cell axis in maintaining intestinal balance. It seeks to unravel the intricate dynamics and regulatory mechanisms among these essential players. A comprehensive understanding of these cell types' functions and interactions promises insights into intestinal homeostasis regulation. Moreover, it holds potential for innovative approaches to manage conditions like radiation-induced intestinal injury, inflammatory bowel disease, and related diseases.

Keywords:  Disease prevention and treatment; Immunomodulation; Injury repair; Intestinal epithelial cell homeostasis; Macrophages mediate crypt stem cell proliferation

DOI:  https://doi.org/10.1016/j.lfs.2024.122452
Nat Commun. 2024 Mar 12. 15(1): 2230

Identifying regulators of aberrant stem cell and differentiation activity in colorectal cancer using a dual endogenous reporter system.

Sandor Spisak, David Chen, Pornlada Likasitwatanakul, Paul Doan, Zhixin Li, Pratyusha Bala, Laura Vizkeleti, Viktoria Tisza, Pushpamali De Silva, Marios Giannakis, Brian Wolpin, Jun Qi, Nilay S Sethi.

Aberrant stem cell-like activity and impaired differentiation are central to the development of colorectal cancer (CRC). To identify functional mediators of these key cellular programs, we engineer a dual endogenous reporter system by genome-editing the SOX9 and KRT20 loci of human CRC cell lines to express fluorescent reporters, broadcasting aberrant stem cell-like and differentiation activity, respectively. By applying a CRISPR screen targeting 78 epigenetic regulators with 542 sgRNAs to this platform, we identify factors that contribute to stem cell-like activity and differentiation in CRC. Perturbation single cell RNA sequencing (Perturb-seq) of validated hits nominate SMARCB1 of the BAF complex (also known as SWI/SNF) as a negative regulator of differentiation across an array of neoplastic colon models. SMARCB1 is a dependency and required for in vivo growth of human CRC models. These studies highlight the utility of biologically designed endogenous reporter platforms to uncover regulators with therapeutic potential.

DOI: https://doi.org/10.1038/s41467-024-46285-w
Mol Oncol. 2024 Mar 11.

Transcriptome-wide gene expression outlier analysis pinpoints therapeutic vulnerabilities in colorectal cancer.

Elisa Mariella, Gaia Grasso, Martina Miotto, Kristi Buzo, Nicole Megan Reilly, Pietro Andrei, Pietro Paolo Vitiello, Giovanni Crisafulli, Sabrina Arena, Giuseppe Rospo, Giorgio Corti, Annalisa Lorenzato, Carlotta Cancelliere, Ludovic Barault, Giulia Gionfriddo, Michael Linnebacher, Mariangela Russo, Federica Di Nicolantonio, Alberto Bardelli.

  Multiple strategies are continuously being explored to expand the drug target repertoire in solid tumors. We devised a novel computational workflow for transcriptome-wide gene expression outlier analysis that allows the systematic identification of both overexpression and underexpression events in cancer cells. Here, it was applied to expression values obtained through RNA sequencing in 226 colorectal cancer (CRC) cell lines that were also characterized by whole-exome sequencing and microarray-based DNA methylation profiling. We found cell models displaying an abnormally high or low expression level for 3533 and 965 genes, respectively. Gene expression abnormalities that have been previously associated with clinically relevant features of CRC cell lines were confirmed. Moreover, by integrating multi-omics data, we identified both genetic and epigenetic alternations underlying outlier expression values. Importantly, our atlas of CRC gene expression outliers can guide the discovery of novel drug targets and biomarkers. As a proof of concept, we found that CRC cell lines lacking expression of the MTAP gene are sensitive to treatment with a PRMT5-MTA inhibitor (MRTX1719). Finally, other tumor types may also benefit from this approach.

Keywords:  biomarkers; colorectal cancer; drug targets; gene expression outliers

DOI:  https://doi.org/10.1002/1878-0261.13622
Br J Cancer. 2024 Mar 11.

Inhibition of the AURKA/YAP1 axis is a promising therapeutic option for overcoming cetuximab resistance in colorectal cancer stem cells.

Anxo Rio-Vilariño, Aiora Cenigaonandia-Campillo, Ana García-Bautista, Pedro A Mateos-Gómez, Marina I Schlaepfer, Laura Del Puerto-Nevado, Oscar Aguilera, Laura García-García, Carlos Galeano, Irene de Miguel, Juana Serrano-López, Natalia Baños, María Jesús Fernández-Aceñero, Juan Carlos Lacal, Enzo Medico, Jesús García-Foncillas, Arancha Cebrián.

BACKGROUND: Primary resistance to anti-EGFR therapies affects 40% of metastatic colorectal cancer patients harbouring wild-type RAS/RAF. YAP1 activation is associated with this resistance, prompting an investigation into AURKA's role in mediating YAP1 phosphorylation at Ser397, as observed in breast cancer.
METHODS: We used transcriptomic analysis along with in vitro and in vivo models of RAS/RAF wild-type CRC to study YAP1 Ser397 phosphorylation as a potential biomarker for cetuximab resistance. We assessed cetuximab efficacy using CCK8 proliferation assays and cell cycle analysis. Additionally, we examined the effects of AURKA inhibition with alisertib and created a dominant-negative YAP1 Ser397 mutant to assess its impact on cancer stem cell features.
RESULTS: The RAS/RAF wild-type CRC models exhibiting primary resistance to cetuximab prominently displayed elevated YAP1 phosphorylation at Ser397 primarily mediated by AURKA. AURKA-induced YAP1 phosphorylation was identified as a key trigger for cancer stem cell reprogramming. Consequently, we found that AURKA inhibition had the capacity to effectively restore cetuximab sensitivity and concurrently suppress the cancer stem cell phenotype.
CONCLUSIONS: AURKA inhibition holds promise as a therapeutic approach to overcome cetuximab resistance in RAS/RAF wild-type colorectal cancer, offering a potential means to counter the development of cancer stem cell phenotypes associated with cetuximab resistance.

DOI: https://doi.org/10.1038/s41416-024-02649-z
J Gastrointest Oncol. 2024 Feb 29. 15(1): 147-163

Identification of fatty acid oxidation-related subtypes by integrated analysis of bulk- and single-cell transcriptome profiling in colorectal cancer.

Peng Zou, Chengru Chen, Xiaobin Wu.

   Background: As one of the major metabolic reprogramming pathways, fatty acid oxidation (FAO) contributes to rapid progression in tumor cells. Nevertheless, the genomic patterns of patients' FAO levels in colorectal cancer (CRC) remain unknown. Hence, it is crucial to identify the interplay mechanisms of molecular biochemical features of FAO in CRC.
Methods: Data of patients with CRC were accessed from The Cancer Genome Atlas (TCGA). Unsupervised consensus clustering related to FAO sores was conducted. The differentially expressed genes (DEGs) were screened by clustering according to FAO status polarized in TCGA, followed by the construction of the scores of genes related to FAO (GFAO_Score). Enrichment of FAO and carcinogenesis at the cell level were calculated based on the single-cell RNA (scRNA) sequencing analysis. The clinical values and drug analysis of GFAO_Score were evaluated by external validation cohorts from Gene Expression Omnibus (GEO) datasets.
Results: We classified patients into two distinct FAO clusters which indicated those with lower FAO levels had poor prognosis and high enrichment of carcinogenic-gene pathways. Further, the high FAO-enriched subtypes in epithelial cells revealed carcinogenesis. Three FAO-related genes (ZFHX4, AQP8, and AKR1B10) were screened to construct the GFAO_Score. The high GFAO_Score group leaned toward advanced CRC and unfavorable survival outcomes in the validation cohort. The low GFAO_Score group possessed a better response to immunotherapy and exhibited lower IC50 (50% inhibition concentration) values for certain chemotherapy drugs, such as 5-fluorouracil, irinotecan, oxaliplatin, paclitaxel, and camptothecin.
Conclusions: FAO patterns vary in patients with CRC. The GFAO_Score might contribute to the precise screening of patients according to metabolism reprogramming and optimization of strategies in clinical practice.

Keywords:  Fatty acid oxidation (FAO); colorectal cancer (CRC); metabolic reprogramming; prediction; prognosis

DOI:  https://doi.org/10.21037/jgo-23-833
Res Sq. 2024 Feb 22. pii: rs.3.rs-3931415. [Epub ahead of print]

KRAS mutation-selective requirement for ACSS2 in colorectal adenoma formation.

Jonathan Chernoff, Konstantin Budagyan, Alexa Cannon, Adam Chatoff, Nathaniel Snyder, Alison Kurimchak, James Duncan.

Oncogenic KRAS mutations are prevalent in colorectal cancer (CRC) and are associated with poor prognosis and resistance to therapy. There is a substantial diversity of KRAS mutant alleles observed in CRC. Emerging clinical and experimental analysis of common KRAS mutations suggest that each mutation differently influences the clinical properties of a disease and response to therapy. Although there is some evidence to suggest biological differences between mutant KRAS alleles, these are yet to be fully elucidated. One approach to study allelic variation involves the use of isogenic cell lines that express different endogenous Kras mutants. Here, we generated Kras isogenic Apc -/- mouse colon epithelial cell lines using CRISPR-driven genome editing by altering the original G12D Kras allele to G12V, G12R, or G13D. We utilized these cell lines to perform transcriptomic and proteomic analysis to compare different signaling properties between these mutants. Both screens indicate significant differences in pathways relating to cholesterol and lipid regulation that we validated with targeted metabolomic measurements and isotope tracing. We found that these processes are upregulated in G12V lines through increased expression of nuclear SREBP1 and higher activation of mTORC1. G12V cells showed higher expression of ACSS2 and ACSS2 inhibition sensitized G12V cells to MEK inhibition. Finally, we found that ACSS2 plays a crucial role early in the development of G12V mutant tumors, in contrast to G12D mutant tumors. These observations highlight differences between KRAS mutant cell lines in their signaling properties. Further exploration of these pathways may prove to be valuable for understanding how specific KRAS mutants function, and identification of novel therapeutic opportunities in CRC.

DOI: https://doi.org/10.21203/rs.3.rs-3931415/v1
bioRxiv. 2024 Feb 28. pii: 2024.02.27.582300. [Epub ahead of print]

Villification of the intestinal epithelium is driven by Foxl1.

Guoli Zhu, Deeksha Lahori, Jonathan Schug, Klaus H Kaestner.

The primitive gut tube of mammals initially forms as a simple cylinder consisting of the endoderm-derived, pseudostratified epithelium and the mesoderm-derived surrounding mesenchyme. During mid-gestation a dramatic transformation occurs in which the epithelium is both restructured into its final cuboidal form and simultaneously folded and refolded to create intestinal villi and intervillus regions, the incipient crypts. Here we show that the mesenchymal winged helix transcription factor Foxl1, itself induced by epithelial hedgehog signaling, controls villification by activating BMP and PDGFRα as well as planar cell polarity genes in epithelial-adjacent telocyte progenitors, both directly and in a feed-forward loop with Foxo3.

DOI: https://doi.org/10.1101/2024.02.27.582300