bims-instec Biomed News
on Intestinal stem cells and chemoresistance in colon cancer and intestinal regeneration
Issue of 2023–05–14
eleven papers selected by
Maria-Virginia Giolito, Free University of Brussels
  1. An RNA Damage Response Network Mediates the Lethality of 5-FU in Clinically Relevant Tumor Types.
  2. SELENOP modifies sporadic colorectal carcinogenesis and WNT signaling activity through LRP5/6 interactions.
  3. p53 promotes revival stem cells in the regenerating intestine after severe radiation injury.
  4. Late-stage MC38 tumours recapitulate features of human colorectal cancer - implications for appropriate timepoint selection in preclinical studies.
  5. Spatial resolution of cellular senescence dynamics in human colorectal liver metastasis.
  6. A LGR5 reporter pig model closely resembles human intestine for improved study of stem cells in disease.
  7. Forkhead box protein D2 suppresses colorectal cancer by reprogramming enhancer interactions.
  8. Deficiency in mammalian STN1 promotes colon cancer development via inhibiting DNA repair.
  9. 3-Phosphoinositide-dependent kinase 1 drives acquired resistance to osimertinib.
  10. Gut microbiota in colorectal cancer development and therapy.
  11. Label-free characterization of organoids with quantitative confocal Raman spectral imaging.
  1. bioRxiv. 2023 Apr 29. pii: 2023.04.28.538590. [Epub ahead of print]
    An RNA Damage Response Network Mediates the Lethality of 5-FU in Clinically Relevant Tumor Types.
    Jung-Kuei Chen, Karl A Merrick, Yi Wen Kong, Anita Izrael-Tomasevic, George Eng, Erika D Handly, Jesse C Patterson, Ian G Cannell, Lucia Suarez-Lopez, Aaron M Hosios, Anh Dinh, Donald S Kirkpatrick, Kebing Yu, Christopher M Rose, Jonathan M Hernandez, Haeun Hwangbo, Adam C Palmer, Matthew G Vander Heiden, Ömer H Yilmaz, Michael B Yaffe.
      5-fluorouracil (5-FU) is a successful and broadly used anti-cancer therapeutic. A major mechanism of action of 5-FU is thought to be through thymidylate synthase (TYMS) inhibition resulting in dTTP depletion and activation of the DNA damage response. This suggests that 5-FU should synergize with other DNA damaging agents. However, we found that combinations of 5-FU and oxaliplatin or irinotecan failed to display any evidence of synergy in clinical trials, and resulted in sub-additive killing in a panel of colorectal cancer (CRC) cell lines. In seeking to understand this antagonism, we unexpectedly found that an RNA damage response during ribosome biogenesis dominates the drug's efficacy in tumor types for which 5-FU shows clinical benefit. 5-FU has an inherent bias for RNA incorporation, and blocking this greatly reduced drug-induced lethality, indicating that accumulation of damaged RNA is more deleterious than the lack of new RNA synthesis. Using 5-FU metabolites that specifically incorporate into either RNA or DNA revealed that CRC cell lines and patient-derived colorectal cancer organoids are inherently more sensitive to RNA damage. This difference held true in cell lines from other tissues in which 5-FU has shown clinical utility, whereas cell lines from tumor tissues that lack clinical 5-FU responsiveness typically showed greater sensitivity to the drug's DNA damage effects. Analysis of changes in the phosphoproteome and ubiquitinome shows RNA damage triggers the selective ubiquitination of multiple ribosomal proteins leading to autophagy-dependent rRNA catabolism and proteasome-dependent degradation of ubiquitinated ribosome proteins. Further, RNA damage response to 5-FU is selectively enhanced by compounds that promote ribosome biogenesis, such as KDM2A inhibitors. These results demonstrate the presence of a strong RNA damage response linked to apoptotic cell death, with clear utility of combinatorially targeting this response in cancer therapy.
    DOI:  https://doi.org/10.1101/2023.04.28.538590
  2. J Clin Invest. 2023 May 11. pii: e165988. [Epub ahead of print]
    SELENOP modifies sporadic colorectal carcinogenesis and WNT signaling activity through LRP5/6 interactions.
    Jennifer M Pilat, Rachel E Brown, Zhengyi Chen, Nathaniel J Berle, Adrian P Othon, M Washington, Shruti A Anant, Suguru Kurokawa, Victoria H Ng, Joshua J Thompson, Justin Jacobse, Jeremy A Goettel, Ethan Lee, Yash A Choksi, Ken S Lau, Sarah P Short, Christopher S Williams.
      Although selenium deficiency correlates with colorectal cancer (CRC) risk, the roles of the selenium-rich antioxidant selenoprotein P (SELENOP) in CRC remain unclear. In this study, we defined SELENOP's contributions to sporadic colorectal carcinogenesis. In human scRNA-seq datasets, we discovered that SELENOP expression rises as normal colon stem cells transform into adenomas that progress into carcinomas. We next examined the effects of Selenop KO in a mouse adenoma model that involves conditional, intestinal epithelial-specific deletion of the tumor suppressor adenomatous polyposis coli (Apc) and found that Selenop KO decreased colon tumor incidence and size. We mechanistically interrogated SELENOP-driven phenotypes in tumor organoids as well as CRC and noncancer cell lines. Selenop KO tumor organoids demonstrated defects in organoid formation and decreases in WNT target gene expression, which could be reversed by SELENOP restoration. Moreover, SELENOP increased canonical WNT signaling activity in noncancer and CRC cell lines. In defining SELENOP's mechanism of action, we mapped protein-protein interactions between SELENOP and the WNT co-receptor low-density lipoprotein receptor-related protein 5/6 (LRP5/6). Lastly, we confirmed that SELENOP:LRP5/6 interactions contributed to SELENOP's effects on WNT activity. Overall, our results position SELENOP as a modulator of the WNT signaling pathway in sporadic CRC.
    Keywords:  Colorectal cancer; Gastroenterology
    DOI:  https://doi.org/10.1172/JCI165988
  3. bioRxiv. 2023 Apr 28. pii: 2023.04.27.538576. [Epub ahead of print]
    p53 promotes revival stem cells in the regenerating intestine after severe radiation injury.
    Clara Morral, Arshad Ayyaz, Hsuan-Cheng Kuo, Mardi Fink, Ioannis Verginadis, Andrea R Daniel, Danielle N Burner, Lucy M Driver, Sloane Satow, Stephanie Hasapis, Reem Ghinnagow, Lixia Luo, Yan Ma, Laura D Attardi, Costas Koumenis, Andy J Minn, Jeffrey L Wrana, Chang-Lung Lee, David G Kirsch.
      Ionizing radiation induces cell death in the gastrointestinal (GI) epithelium by activating p53. However, p53 also prevents animal lethality caused by radiation-induced GI injury. Through single-cell RNA-sequencing of the irradiated mouse intestine, we find that p53 target genes are specifically enriched in stem cells of the regenerating epithelium, including revival stem cells that promote animal survival after GI damage. Accordingly, in mice with p53 deleted specifically in the GI epithelium, ionizing radiation fails to induce revival stem cells. Using intestinal organoids, we show that transient p53 expression is required for the induction of revival stem cells that is controlled by an Mdm2-mediated negative feedback loop. These results suggest that p53 suppresses severe radiation-indued GI injury by promoting intestinal epithelial cell reprogramming.
    One-Sentence Summary: After severe radiation injury to the intestine, transient p53 activity induces revival stem cells to promote regeneration.
    DOI:  https://doi.org/10.1101/2023.04.27.538576
  4. Front Immunol. 2023 ;14 1152035
    Late-stage MC38 tumours recapitulate features of human colorectal cancer - implications for appropriate timepoint selection in preclinical studies.
    Nicholas J Shields, Estelle M Peyroux, Angela L Ferguson, Megan Steain, Silke Neumann, Sarah L Young.
      Anti-tumour T cell responses play a crucial role in controlling the progression of colorectal cancer (CRC), making this disease a promising candidate for immunotherapy. However, responses to immune-targeted therapies are currently limited to subpopulations of patients and specific types of cancer. Clinical studies have therefore focussed on identifying biomarkers that predict immunotherapy responses and elucidating the immunological landscapes of different cancers. Meanwhile, our understanding of how preclinical tumour models resemble human disease has fallen behind, despite their crucial role in immune-targeted drug development. A deeper understanding of these models is therefore needed to improve the development of immunotherapies and the translation of findings made in these systems. MC38 colon adenocarcinoma is a widely used preclinical model, yet how it recapitulates human colorectal cancer remains poorly defined. This study investigated the tumour-T cell immune landscape of MC38 tumours using histology, immunohistochemistry, and flow cytometry. We demonstrate that early-stage tumours exhibit a nascent TME, lacking important immune-resistance mechanisms of clinical interest, while late-stage tumours exhibit a mature TME resembling human tumours, with desmoplasia, T cell exhaustion, and T cell exclusion. Consequently, these findings clarify appropriate timepoint selection in the MC38 model when investigating both immunotherapies and mechanisms that contribute to immunotherapy resistance. Overall, this study provides a valuable resource that will enable appropriate application of the MC38 model and expedite the development and clinical translation of new immunotherapies.
    Keywords:  MC38; colorectal cancer; immune exclusion; immunotherapy; syngeneic preclinical models; t cell exhaustion; tumour microenvironment
    DOI:  https://doi.org/10.3389/fimmu.2023.1152035
  5. Aging Cell. 2023 May 08. e13853
    Spatial resolution of cellular senescence dynamics in human colorectal liver metastasis.
    Ombretta Garbarino, Luca Lambroia, Gianluca Basso, Veronica Marrella, Barbara Franceschini, Cristiana Soldani, Fabio Pasqualini, Desiree Giuliano, Guido Costa, Clelia Peano, Davide Barbarossa, Destro Annarita, Andreina Salvati, Luigi Terracciano, Guido Torzilli, Matteo Donadon, Francesca Faggioli.
      Hepatic metastasis is a clinical challenge for colorectal cancer (CRC). Senescent cancer cells accumulate in CRC favoring tumor dissemination. Whether this mechanism progresses also in metastasis is unexplored. Here, we integrated spatial transcriptomics, 3D-microscopy, and multicellular transcriptomics to study the role of cellular senescence in human colorectal liver metastasis (CRLM). We discovered two distinct senescent metastatic cancer cell (SMCC) subtypes, transcriptionally located at the opposite pole of epithelial (e) to mesenchymal (m) transition. SMCCs differ in chemotherapy susceptibility, biological program, and prognostic roles. Mechanistically, epithelial (e)SMCC initiation relies on nucleolar stress, whereby c-myc dependent oncogene hyperactivation induces ribosomal RPL11 accumulation and DNA damage response. In a 2D pre-clinical model, we demonstrated that RPL11 co-localized with HDM2, a p53-specific ubiquitin ligase, leading to senescence activation in (e)SMCCs. On the contrary, mesenchymal (m)SMCCs undergo TGFβ paracrine activation of NOX4-p15 effectors. SMCCs display opposing effects also in the immune regulation of neighboring cells, establishing an immunosuppressive environment or leading to an active immune workflow. Both SMCC signatures are predictive biomarkers whose unbalanced ratio determined the clinical outcome in CRLM and CRC patients. Altogether, we provide a comprehensive new understanding of the role of SMCCs in CRLM and highlight their potential as new therapeutic targets to limit CRLM progression.
    Keywords:  EMT; cellular senescence; colorectal cancer liver metastasis; prognostic role; senescence-associated secretory phenotype; spatial transcriptomics
    DOI:  https://doi.org/10.1111/acel.13853
  6. FASEB J. 2023 Jun;37(6): e22975
    A LGR5 reporter pig model closely resembles human intestine for improved study of stem cells in disease.
    Cecilia R Schaaf, Kathryn M Polkoff, Amber Carter, Amy S Stewart, Breanna Sheahan, John Freund, Joshua Ginzel, Joshua C Snyder, Jatin Roper, Jorge A Piedrahita, Liara M Gonzalez.
      Intestinal epithelial stem cells (ISCs) are responsible for intestinal epithelial barrier renewal; thereby, ISCs play a critical role in intestinal pathophysiology research. While transgenic ISC reporter mice are available, advanced translational studies lack a large animal model. This study validates ISC isolation in a new porcine Leucine Rich Repeat Containing G Protein-Coupled Receptor 5 (LGR5) reporter line and demonstrates the use of these pigs as a novel colorectal cancer (CRC) model. We applied histology, immunofluorescence, fluorescence-activated cell sorting, flow cytometry, gene expression quantification, and 3D organoid cultures to whole tissue and single cells from the duodenum, jejunum, ileum, and colon of LGR5-H2B-GFP and wild-type pigs. Ileum and colon LGR5-H2B-GFP, healthy human, and murine biopsies were compared by mRNA fluorescent in situ hybridization (FISH). To model CRC, adenomatous polyposis coli (APC) mutation was induced by CRISPR/Cas9 editing in porcine LGR5-H2B-GFP colonoids. Crypt-base, green fluorescent protein (GFP) expressing cells co-localized with ISC biomarkers. LGR5-H2B-GFPhi cells had significantly higher LGR5 expression (p < .01) and enteroid forming efficiency (p < .0001) compared with LGR5-H2B-GFPmed/lo/neg cells. Using FISH, similar LGR5, OLFM4, HOPX, LYZ, and SOX9 expression was identified between human and LGR5-H2B-GFP pig crypt-base cells. LGR5-H2B-GFP/APCnull colonoids had cystic growth in WNT/R-spondin-depleted media and significantly upregulated WNT/β-catenin target gene expression (p < .05). LGR5+ ISCs are reproducibly isolated in LGR5-H2B-GFP pigs and used to model CRC in an organoid platform. The known anatomical and physiologic similarities between pig and human, and those shown by crypt-base FISH, underscore the significance of this novel LGR5-H2B-GFP pig to translational ISC research.
    Keywords:  APC mutation; Lgr5; colorectal cancer; intestine; porcine; stem cell; transgenic large animal
    DOI:  https://doi.org/10.1096/fj.202300223R
  7. Nucleic Acids Res. 2023 May 09. pii: gkad361. [Epub ahead of print]
    Forkhead box protein D2 suppresses colorectal cancer by reprogramming enhancer interactions.
    Hyo-Min Kim, Byunghee Kang, Sohyun Park, Hyorim Park, Chan Johng Kim, Hyeonji Lee, Mijoung Yoo, Mi-Na Kweon, Sin-Hyeog Im, Tae Il Kim, Tae-Young Roh.
      Somatic stem cells contribute to normal tissue homeostasis, and their epigenomic features play an important role in regulating tissue identities or developing disease states. Enhancers are one of the key players controlling chromatin context-specific gene expression in a spatial and temporal manner while maintaining tissue homeostasis, and their dysregulation leads to tumorigenesis. Here, epigenomic and transcriptomic analyses reveal that forkhead box protein D2 (FOXD2) is a hub for the gene regulatory network exclusive to large intestinal stem cells, and its overexpression plays a significant role in colon cancer regression. FOXD2 is positioned at the closed chromatin and facilitates mixed-lineage leukemia protein-4 (MLL4/KMT2D) binding to deposit H3K4 monomethylation. De novo FOXD2-mediated chromatin interactions rewire the regulation of p53-responsive genes and induction of apoptosis. Taken together, our findings illustrate the novel mechanistic details of FOXD2 in suppressing colorectal cancer growth and suggest its function as a chromatin-tuning factor and a potential therapeutic target for colorectal cancer.
    DOI:  https://doi.org/10.1093/nar/gkad361
  8. Sci Adv. 2023 May 10. 9(19): eadd8023
    Deficiency in mammalian STN1 promotes colon cancer development via inhibiting DNA repair.
    Dinh Duc Nguyen, Eugene Kim, Nhat Thong Le, Xianzhong Ding, Rishi Kumar Jaiswal, Raymond Joseph Kostlan, Thi Ngoc Thanh Nguyen, Olga Shiva, Minh Thong Le, Weihang Chai.
      Despite the high lethality of colorectal cancers (CRCs), only a limited number of genetic risk factors are identified. The mammalian ssDNA-binding protein complex CTC1-STN1-TEN1 protects genome stability, yet its role in tumorigenesis is unknown. Here, we show that attenuated CTC1/STN1 expression is common in CRCs. We generated an inducible STN1 knockout mouse model and found that STN1 deficiency in young adult mice increased CRC incidence, tumor size, and tumor load. CRC tumors exhibited enhanced proliferation, reduced apoptosis, and elevated DNA damage and replication stress. We found that STN1 deficiency down-regulated multiple DNA glycosylases, resulting in defective base excision repair (BER) and accumulation of oxidative damage. Collectively, this study identifies STN1 deficiency as a risk factor for CRC and implicates the previously unknown STN1-BER axis in protecting colon tissues from oxidative damage, therefore providing insights into the CRC tumor-suppressing mechanism.
    DOI:  https://doi.org/10.1126/sciadv.add8023
  9. Commun Biol. 2023 May 11. 6(1): 509
    3-Phosphoinositide-dependent kinase 1 drives acquired resistance to osimertinib.
    Ismail M Meraz, Mourad Majidi, Bingliang Fang, Feng Meng, Lihui Gao, RuPing Shao, Renduo Song, Feng Li, Yonathan Lissanu, Huiqin Chen, Min Jin Ha, Qi Wang, Jing Wang, Elizabeth Shpall, Sung Yun Jung, Franziska Haderk, Philippe Gui, Jonathan Wesley Riess, Victor Olivas, Trever G Bivona, Jack A Roth.
      Osimertinib sensitive and resistant NSCLC NCI-H1975 clones are used to model osimertinib acquired resistance in humanized and non-humanized mice and delineate potential resistance mechanisms. No new EGFR mutations or loss of the EGFR T790M mutation are found in resistant clones. Resistant tumors grown under continuous osimertinib pressure both in humanized and non-humanized mice show aggressive tumor regrowth which is significantly less sensitive to osimertinib as compared with parental tumors. 3-phosphoinositide-dependent kinase 1 (PDK1) is identified as a potential driver of osimertinib acquired resistance, and its selective inhibition by BX795 and CRISPR gene knock out, sensitizes resistant clones. In-vivo inhibition of PDK1 enhances the osimertinib sensitivity against osimertinib resistant xenograft and a patient derived xenograft (PDX) tumors. PDK1 knock-out dysregulates PI3K/Akt/mTOR signaling, promotes cell cycle arrest at the G1 phase. Yes-associated protein (YAP) and active-YAP are upregulated in resistant tumors, and PDK1 knock-out inhibits nuclear translocation of YAP. Higher expression of PDK1 and an association between PDK1 and YAP are found in patients with progressive disease following osimertinib treatment. PDK1 is a central upstream regulator of two critical drug resistance pathways: PI3K/AKT/mTOR and YAP.
    DOI:  https://doi.org/10.1038/s42003-023-04889-w
  10. Nat Rev Clin Oncol. 2023 May 11.
    Gut microbiota in colorectal cancer development and therapy.
    Chi Chun Wong, Jun Yu.
      Colorectal cancer (CRC) is one of the commonest cancers globally. A unique aspect of CRC is its intimate association with the gut microbiota, which forms an essential part of the tumour microenvironment. Research over the past decade has established that dysbiosis of gut bacteria, fungi, viruses and Archaea accompanies colorectal tumorigenesis, and these changes might be causative. Data from mechanistic studies demonstrate the ability of the gut microbiota to interact with the colonic epithelia and immune cells of the host via the release of a diverse range of metabolites, proteins and macromolecules that regulate CRC development. Preclinical and some clinical evidence also underscores the role of the gut microbiota in modifying the therapeutic responses of patients with CRC to chemotherapy and immunotherapy. Herein, we summarize our current understanding of the role of gut microbiota in CRC and outline the potential translational and clinical implications for CRC diagnosis, prevention and treatment. Emphasis is placed on how the gut microbiota could now be better harnessed by developing targeted microbial therapeutics as chemopreventive agents against colorectal tumorigenesis, as adjuvants for chemotherapy and immunotherapy to boost drug efficacy and safety, and as non-invasive biomarkers for CRC screening and patient stratification. Finally, we highlight the hurdles and potential solutions to translating our knowledge of the gut microbiota into clinical practice.
    DOI:  https://doi.org/10.1038/s41571-023-00766-x
  11. Cell Rep Methods. 2023 04 24. 3(4): 100457
    Label-free characterization of organoids with quantitative confocal Raman spectral imaging.
    Mark F Coughlan, Lev T Perelman.
      Stem cell-derived organoids have the potential to significantly improve the drug discovery process. However, a key challenge is monitoring the maturation process and drug response. In this issue of Cell Reports Methods, LaLone et al. have shown that quantitative confocal Raman spectral imaging, a label-free technique, can reliably monitor organoid development, drug accumulation, and drug metabolism.
    DOI:  https://doi.org/10.1016/j.crmeth.2023.100457
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