bims-instec Biomed News
on Intestinal stem cells and chemoresistance in colon cancer and intestinal regeneration
Issue of 2024‒04‒28
twenty-one papers selected by
Maria-Virginia Giolito, Université Catholique de Louvain
  1. Lgr5 + intestinal stem cells are required for organoid survival after genotoxic injury.
  2. Claudin-7 is essential for the maintenance of colonic stem cell homoeostasis via the modulation of Wnt/Notch signalling.
  3. Metastasis of colon cancer requires Dickkopf-2 to generate cancer cells with Paneth cell properties.
  4. The heterogeneity of tumour-associated macrophages contributes to the clinical outcomes and indications for immune checkpoint blockade in colorectal cancer patients.
  5. Exploiting a subtype-specific mitochondrial vulnerability for successful treatment of colorectal peritoneal metastases.
  6. The γ-glutamyl cycle serves as an amino acids supply system in colorectal cancer organoids under chronic hypoxia.
  7. Spatiotemporally resolved colorectal oncogenesis in mini-colons ex vivo.
  8. SF3B3-regulated mTOR alternative splicing promotes colorectal cancer progression and metastasis.
  9. Single-Cell and Spatial Transcriptome Profiling Identifies the Transcription Factor BHLHE40 as a Driver of EMT in Metastatic Colorectal Cancer.
  10. CRISPR-Cas9 screening identifies INTS3 as an anti-apoptotic RNA-binding protein and therapeutic target for colorectal cancer.
  11. Circadian regulation of cancer stem cells and the tumor microenvironment during metastasis.
  12. Establishment of a novel microfluidic co-culture system for simultaneous analysis of multiple indicators of gefitinib sensitivity in colorectal cancer cells.
  13. NOX4 promotes tumor progression through the MAPK-MEK1/2-ERK1/2 axis in colorectal cancer.
  14. Educate, not kill: treating cancer without triggering its defenses.
  15. A heterogeneous pharmaco-transcriptomic landscape induced by targeting a single oncogenic kinase.
  16. CD44: A New Prognostic Marker in Colorectal Cancer?
  17. Investigating the Cell Origin and Liver Metastasis Factors of Colorectal Cancer by Single-Cell Transcriptome Analysis.
  18. The G1/S transition in mammalian stem cells in vivo is autonomously regulated by cell size.
  19. Hepatic lipid droplet-associated proteome changes distinguish dietary-induced fatty liver from glucose tolerance in male mice.
  20. Metabolic vulnerability of cancer stem cells and their niche.
  21. Consistent signatures in the human gut microbiome of old- and young-onset colorectal cancer.
  1. bioRxiv. 2024 Apr 11. pii: 2024.04.08.588400. [Epub ahead of print]
    Lgr5 + intestinal stem cells are required for organoid survival after genotoxic injury.
    Joseph Lee, Antoine Gleizes, Felipe Takaesu, Sarah F Webster, Taylor Hailstock, Adam D Gracz.
      Progenitors and mature cells can maintain the intestinal epithelium by dedifferentiation and facultative intestinal stem cell (fISC) function when active ISCs (aISCs) are lost to damage. Here, we sought to model fISC activation in intestinal organoids with doxorubicin (DXR), a chemotherapeutic known to ablate Lgr5 + aISCs in vivo . We identified low and high doses of DXR compatible with long-term organoid survival. Similar fISC gene activation was observed between organoids treated with low vs high DXR, despite significantly decreased survival at the higher dose. aISCs exhibit dose-dependent loss after DXR but survive at doses compatible with organoid survival. We ablated residual aISCs after DXR using a Lgr5 2A-DTR allele and observed that aISC survival of the initial genotoxic insult is required for organoid survival following DXR. These results suggest that while typical fISC genes are activated by DXR injury in organoids, functional stemness remains dependent on the aISC pool. Our data establish a reproducible model of DXR injury in intestinal organoids and reveal differences in in vitro responses to an established in vivo damage modality.
    DOI:  https://doi.org/10.1101/2024.04.08.588400
  2. Cell Death Dis. 2024 Apr 23. 15(4): 284
    Claudin-7 is essential for the maintenance of colonic stem cell homoeostasis via the modulation of Wnt/Notch signalling.
    Kun Wang, Yin Liu, Huimin Li, Xiaoqing Liang, Mengdi Hao, Dajin Yuan, Lei Ding.
      Intestinal stem cells (ISCs) play a crucial role in the continuous self-renewal and recovery of the intestinal epithelium. In previous studies, we have revealed that the specific absence of Claudin-7 (Cldn-7) in intestinal epithelial cells (IECs) can lead to the development of spontaneous colitis. However, the mechanisms by which Cldn-7 maintains homeostasis in the colonic epithelium remain unclear. Therefore, in the present study, we used IEC- and ISC-specific Cldn-7 knockout mice to investigate the regulatory effects of Cldn-7 on colonic Lgr5+ stem cells in the mediation of colonic epithelial injury and repair under physiological and inflammatory conditions. Notably, our findings reveal that Cldn-7 deletion disrupts the self-renewal and differentiation of colonic stem cells alongside the formation of colonic organoids in vitro. Additionally, these Cldn-7 knockout models exhibited heightened susceptibility to experimental colitis, limited epithelial repair and regeneration, and increased differentiation toward the secretory lineage. Mechanistically, we also established that Cldn-7 facilitates the proliferation, differentiation, and organoid formation of Lgr5+ stem cells through the maintenance of Wnt and Notch signalling pathways in the colonic epithelium. Overall, our study provides new insights into the maintenance of ISC function and colonic epithelial homoeostasis.
    DOI:  https://doi.org/10.1038/s41419-024-06658-x
  3. bioRxiv. 2024 Apr 15. pii: 2024.04.12.589235. [Epub ahead of print]
    Metastasis of colon cancer requires Dickkopf-2 to generate cancer cells with Paneth cell properties.
    Jae Hun Shin, Jooyoung Park, Jaechul Lim, Jaekwang Jeong, Ravi K Dinesh, Stephen E Maher, Jun Young Hong, John Wysolmerski, Jungmin Choi, Alfred L M Bothwell.
      Metastasis is the leading cause of cancer-related mortality. Paneth cells provide stem cell niche factors in homeostatic conditions, but the underlying mechanisms of cancer stem cell niche development are unclear. Here we report that Dickkopf-2 (DKK2) is essential for the generation of cancer cells with Paneth cell properties during colon cancer metastasis. Splenic injection of Dkk2 -knockout (KO) cancer organoids into C57BL/6 mice resulted in a significant reduction of liver metastases. Transcriptome analysis showed reduction of Paneth cell markers such as lysozymes in KO organoids. Single cell RNA sequencing analyses of murine metastasized colon cancer cells and patient samples identified the presence of lysozyme positive cells with Paneth cell properties including enhanced glycolysis. Further analyses of transcriptome and chromatin accessibility suggested Hepatocyte nuclear factor 4-alpha (HNF4A) as a downstream target of DKK2. Chromatin immunoprecipitation followed by sequencing analysis revealed that HNF4A binds to the promoter region of Sox9 , a well-known transcription factor for Paneth cell differentiation. In the liver metastatic foci, DKK2 knockout rescued HNF4A protein levels followed by reduction of lysozyme positive cancer cells. Taken together, DKK2-mediated reduction of HNF4A protein promotes the generation of lysozyme positive cancer cells with Paneth cell properties in the metastasized colon cancers.
    DOI:  https://doi.org/10.1101/2024.04.12.589235
  4. Immunobiology. 2024 Apr 18. pii: S0171-2985(24)00023-8. [Epub ahead of print]229(3): 152805
    The heterogeneity of tumour-associated macrophages contributes to the clinical outcomes and indications for immune checkpoint blockade in colorectal cancer patients.
    Junhui Tang, Liang Ming, Feiyu Qin, Yan Qin, Duo Wang, Liuying Huang, Yulin Cao, Zhaohui Huang, Yuan Yin.
      Tumor-associated macrophages (TAMs), one of the major immune cell types in colorectal cancer (CRC) tumor microenvironment (TME), play indispensable roles in immune responses against tumor progression. In this study, we aimed to know whether the extensive inter and intra heterogeneity of TAMs contributes to the clinical outcomes and indications for immune checkpoint blockade (ICB) in CRC. We used single-cell RNA sequencing (scRNA-Seq) data from 60 CRC patients and charactrized TAMs based on anatomic locations, tumor regions, stages, grades, metastatic status, MSS/MSI classification and pseudotemporal differentiation status. We then defined a catalog of 21 gene modules that determine macrophage status, and identified 7 of them as relevant to clinical outcomes and 11 as indications for ICB therapy. On this basis, we constructed a unique TAM subgroup profile, aiming to find features that may be highly responsive to immunotherapy for the CRC with poor prognosis under conventional treatment. This TAM subpopulation is enriched in tumors and is associated with poor prognosis, but exhibits a high immunotherapy response signature (HIM TAM). Further spatial transcriptome analysis and ligand-receptor interaction analysis confirmed that HIM TAM is involved in shaping TIME, especially the regulation of T cells. Our study provides insights into different TAM subtypes, highlights the importance of TAM heterogeneity in relation to patient prognosis and immunotherapy response, and reveals potential immunotherapy strategies based on TAM characteristics for CRC that does not respond well to conventional therapy.
    Keywords:  Clinical outcomes; Colorectal cancer; Heterogeneity; ICB indications; Single-cell RNA sequencing; Tumor-associated macrophages
    DOI:  https://doi.org/10.1016/j.imbio.2024.152805
  5. Cell Rep Med. 2024 Apr 22. pii: S2666-3791(24)00192-7. [Epub ahead of print] 101523
    Exploiting a subtype-specific mitochondrial vulnerability for successful treatment of colorectal peritoneal metastases.
    Sanne Bootsma, Mark P G Dings, Job Kesselaar, Roxan F C P A Helderman, Kyah van Megesen, Alexander Constantinides, Leandro Ferreira Moreno, Ellen Stelloo, Enzo M Scutigliani, Bella Bokan, Arezo Torang, Sander R van Hooff, Danny A Zwijnenburg, Valérie M Wouters, Vincent C J van de Vlasakker, Laskarina J K Galanos, Lisanne E Nijman, Adrian Logiantara, Veronique L Veenstra, Sophie Schlingemann, Sterre van Piggelen, Nicole van der Wel, Przemek M Krawczyk, Johannes J Platteeuw, Jurriaan B Tuynman, Ignace H de Hingh, Jan P G Klomp, Arthur Oubrie, Petur Snaebjornsson, Jan Paul Medema, Arlene L Oei, Onno Kranenburg, Clara C Elbers, Kristiaan J Lenos, Louis Vermeulen, Maarten F Bijlsma.
      Peritoneal metastases (PMs) from colorectal cancer (CRC) respond poorly to treatment and are associated with unfavorable prognosis. For example, the addition of hyperthermic intraperitoneal chemotherapy (HIPEC) to cytoreductive surgery in resectable patients shows limited benefit, and novel treatments are urgently needed. The majority of CRC-PMs represent the CMS4 molecular subtype of CRC, and here we queried the vulnerabilities of this subtype in pharmacogenomic databases to identify novel therapies. This reveals the copper ionophore elesclomol (ES) as highly effective against CRC-PMs. ES exhibits rapid cytotoxicity against CMS4 cells by targeting mitochondria. We find that a markedly reduced mitochondrial content in CMS4 cells explains their vulnerability to ES. ES demonstrates efficacy in preclinical models of PMs, including CRC-PMs and ovarian cancer organoids, mouse models, and a HIPEC rat model of PMs. The above proposes ES as a promising candidate for the local treatment of CRC-PMs, with broader implications for other PM-prone cancers.
    Keywords:  HIPEC; copper; elesclomol; mesenchymal cancer cell; mitochondria; molecular subtype; oxidative phosphorylation; peritoneal metastases
    DOI:  https://doi.org/10.1016/j.xcrm.2024.101523
  6. Biochem Biophys Res Commun. 2024 Apr 22. pii: S0006-291X(24)00513-8. [Epub ahead of print]714 149977
    The γ-glutamyl cycle serves as an amino acids supply system in colorectal cancer organoids under chronic hypoxia.
    Sho Tabata, Hiroko Endo, Hideki Makinoshima, Tomoyoshi Soga, Masahiro Inoue.
      Malignant tumors are characterized by a hypoxic microenvironment, and metabolic reprogramming is necessary to ensure energy production and oxidative stress resistance. Although the microenvironmental properties of tumors vary under acute and chronic hypoxia, studies on chronic hypoxia-induced metabolic changes are limited. In the present study, we performed a comprehensive metabolic analysis in a chronic hypoxia model using colorectal cancer (CRC) organoids, and identified an amino acid supply system through the γ-glutamyl cycle, a glutathione recycling pathway. We analyzed the metabolic changes caused by hypoxia over time and observed that chronic hypoxia resulted in an increase in 5-oxoproline and a decrease in oxidized glutathione (GSSG) compared to acute hypoxia. These findings suggest that chronic hypoxia induces metabolic changes in the γ-glutamyl cycle. Moreover, inhibition of the γ-glutamyl cycle via γ-glutamyl cyclotransferase (GGCT) and γ-glutamyl transferase 1 (GGT1) knockdown significantly reversed chronic hypoxia-induced upregulation of 5-oxoproline and several amino acids. Notably, GGT1 knockdown downregulated the intracellular levels of γ-glutamyl amino acids. Conclusively, these results indicate that the γ-glutamyl cycle serves as an amino acid supply system in CRC under chronic hypoxia, which provides fresh insight into cancer metabolism under chronic hypoxia.
    Keywords:  Amino acid metabolism; CTOS; Colorectal cancer; Organoid; γ-glutamyl amino acids; γ-glutamyl cycle
    DOI:  https://doi.org/10.1016/j.bbrc.2024.149977
  7. Nature. 2024 Apr 24.
    Spatiotemporally resolved colorectal oncogenesis in mini-colons ex vivo.
    L Francisco Lorenzo-Martín, Tania Hübscher, Amber D Bowler, Nicolas Broguiere, Jakob Langer, Lucie Tillard, Mikhail Nikolaev, Freddy Radtke, Matthias P Lutolf.
      Three-dimensional organoid culture technologies have revolutionized cancer research by allowing for more realistic and scalable reproductions of both tumour and microenvironmental structures1-3. This has enabled better modelling of low-complexity cancer cell behaviours that occur over relatively short periods of time4. However, available organoid systems do not capture the intricate evolutionary process of cancer development in terms of tissue architecture, cell diversity, homeostasis and lifespan. As a consequence, oncogenesis and tumour formation studies are not possible in vitro and instead require the extensive use of animal models, which provide limited spatiotemporal resolution of cellular dynamics and come at a considerable cost in terms of resources and animal lives. Here we developed topobiologically complex mini-colons that are able to undergo tumorigenesis ex vivo by integrating microfabrication, optogenetic and tissue engineering approaches. With this system, tumorigenic transformation can be spatiotemporally controlled by directing oncogenic activation through blue-light exposure, and emergent colon tumours can be tracked in real-time at the single-cell resolution for several weeks without breaking the culture. These induced mini-colons display rich intratumoural and intertumoural diversity and recapitulate key pathophysiological hallmarks displayed by colorectal tumours in vivo. By fine-tuning cell-intrinsic and cell-extrinsic parameters, mini-colons can be used to identify tumorigenic determinants and pharmacological opportunities. As a whole, our study paves the way for cancer initiation research outside living organisms.
    DOI:  https://doi.org/10.1038/s41586-024-07330-2
  8. J Exp Clin Cancer Res. 2024 Apr 26. 43(1): 126
    SF3B3-regulated mTOR alternative splicing promotes colorectal cancer progression and metastasis.
    Tong Xu, Xichuan Li, Wennan Zhao, Xue Wang, Leixin Jin, Zhiqiang Feng, Huixiang Li, Mingzhe Zhang, Yiqing Tian, Ge Hu, Yuan Yue, Xintong Dai, Changliang Shan, Weihua Zhang, Chunze Zhang, Youcai Zhang.
      BACKGROUND: Aberrant alternative splicing (AS) is a pervasive event during colorectal cancer (CRC) development. SF3B3 is a splicing factor component of U2 small nuclear ribonucleoproteins which are crucial for early stages of spliceosome assembly. The role of SF3B3 in CRC remains unknown.METHODS: SF3B3 expression in human CRCs was analyzed using publicly available CRC datasets, immunohistochemistry, qRT-PCR, and western blot. RNA-seq, RNA immunoprecipitation, and lipidomics were performed in SF3B3 knockdown or overexpressing CRC cell lines. CRC cell xenografts, patient-derived xenografts, patient-derived organoids, and orthotopic metastasis mouse models were utilized to determine the in vivo role of SF3B3 in CRC progression and metastasis.
    RESULTS: SF3B3 was upregulated in CRC samples and associated with poor survival. Inhibition of SF3B3 by RNA silencing suppressed the proliferation and metastasis of CRC cells in vitro and in vivo, characterized by mitochondria injury, increased reactive oxygen species (ROS), and apoptosis. Mechanistically, silencing of SF3B3 increased mTOR exon-skipped splicing, leading to the suppression of lipogenesis via mTOR-SREBF1-FASN signaling. The combination of SF3B3 shRNAs and mTOR inhibitors showed synergistic antitumor activity in patient-derived CRC organoids and xenografts. Importantly, we identified SF3B3 as a critical regulator of mTOR splicing and autophagy in multiple cancers.
    CONCLUSIONS: Our findings revealed that SF3B3 promoted CRC progression and metastasis by regulating mTOR alternative splicing and SREBF1-FASN-mediated lipogenesis, providing strong evidence to support SF3B3 as a druggable target for CRC therapy.
    Keywords:  Alternative splicing; Colorectal cancer; Metastasis; SF3B3; mTOR
    DOI:  https://doi.org/10.1186/s13046-024-03053-4
  9. Cancer Res. 2024 Apr 24.
    Single-Cell and Spatial Transcriptome Profiling Identifies the Transcription Factor BHLHE40 as a Driver of EMT in Metastatic Colorectal Cancer.
    Sheng Yang, Dongsheng Zhang, Qingyang Sun, Hongxu Nie, Yue Zhang, Xiaowei Wang, Yuanjian Huang, Yueming Sun.
      Colorectal cancer (CRC) is one of the most common malignant tumors in humans, with liver metastasis being the primary cause of mortality. The epithelial-mesenchymal transition (EMT) process endows cancer cells with enhanced metastatic potential. To elucidate the cellular mechanisms driving EMT in CRC, we analyzed single-cell RNA-sequencing (scRNA-seq) data from 11 non-metastatic primary tumors (TnM) and 11 metastatic primary tumors (TM) from CRC patients. Compared to TnM group, the TM samples showed elevated numbers of malignant epithelial cell and cancer-associated fibroblast (CAF) subsets that displayed enrichments of EMT, angiogenesis, and TGF-β signaling pathways. One specific TM-enriched subgroup of malignant epithelial cells underwent EMT to trans-differentiate into CXCL1+ CAFs that subsequently differentiated into SFRP2+ CAFs, which was validated by spatial transcriptomic and pseudotime trajectory analyses. Furthermore, cell-cell communication analysis identified BHLHE40 as a probable key transcription factor driving EMT that was associated with poor prognosis. Finally, in vitro and in vivo experiments functionally substantiated that BHLHE40 promoted the proliferation, invasion, migration, EMT, and liver metastasis of CRC cells. In summary, this study identified BHLHE40 as a key transcription factor regulating EMT that promotes liver metastasis in CRC.
    DOI:  https://doi.org/10.1158/0008-5472.CAN-23-3264
  10. iScience. 2024 May 17. 27(5): 109676
    CRISPR-Cas9 screening identifies INTS3 as an anti-apoptotic RNA-binding protein and therapeutic target for colorectal cancer.
    Zhiwei Wang, Cheng Zhang, Jing Guo, Yanmei Yang, Peixian Li, Ziyan Wang, Sijia Liu, Lulu Zhang, Xiaoyu Zeng, Jincheng Zhai, Xinyong Wang, Qi Zhao, Zhenzhen Chen, Pingping Zhu, Qiankun He.
      Growing evidences indicate that RNA-binding proteins (RBPs) play critical roles in regulating the RNA splicing, polyadenylation, stability, localization, translation, and turnover. Abnormal expression of RBPs can promote tumorigenesis. Here, we performed a CRISPR screen using an RBP pooled CRISPR knockout library and identified 27 potential RBPs with role in supporting colorectal cancer (CRC) survival. We found that the deletion/depletion of INTS3 triggered apoptosis in CRC. The in vitro experiments and RNA sequencing revealed that INTS3 destabilized pro-apoptotic gene transcripts and contributed to the survival of CRC cells. INTS3 loss delayed CRC cells growth in vivo. Furthermore, delivery of DOTAP/cholesterol-mshINTS3 nanoparticles inhibited CRC tumor growth. Collectively, our work highlights the role of INTS3 in supporting CRC survival and provides several novel therapeutic targets for treatment.
    Keywords:  Cancer; Molecular biology
    DOI:  https://doi.org/10.1016/j.isci.2024.109676
  11. Nat Cancer. 2024 Apr 23.
    Circadian regulation of cancer stem cells and the tumor microenvironment during metastasis.
    Yu Wang, Rajesh Narasimamurthy, Meng Qu, Nuolin Shi, Haidong Guo, Yuezhen Xue, Nick Barker.
      The circadian clock regulates daily rhythms of numerous physiological activities through tightly coordinated modulation of gene expression and biochemical functions. Circadian disruption is associated with enhanced tumor formation and metastasis via dysregulation of key biological processes and modulation of cancer stem cells (CSCs) and their specialized microenvironment. Here, we review how the circadian clock influences CSCs and their local tumor niches in the context of different stages of tumor metastasis. Identifying circadian therapeutic targets could facilitate the development of new treatments that leverage circadian modulation to ablate tumor-resident CSCs, inhibit tumor metastasis and enhance response to current therapies.
    DOI:  https://doi.org/10.1038/s43018-024-00759-4
  12. Mikrochim Acta. 2024 04 22. 191(5): 279
    Establishment of a novel microfluidic co-culture system for simultaneous analysis of multiple indicators of gefitinib sensitivity in colorectal cancer cells.
    Xin Li, Wanming Li, Jie Wang, Qun Wang, Menghu Liang, Shuo Chen, Wei Ba, Jin Fang.
      The therapeutic effect of gefitinib on colorectal cancer (CRC) is unclear, but it has been reported that stromal cells in the tumor microenvironment may have an impact on drug sensitivity. Herein, we established a microfluidic co-culture system and explored the sensitivity of CRC cells co-cultured with cancer-associated fibroblasts (CAFs) to gefitinib. The system consisted of a multichannel chip and a Petri dish. The chambers in the chip and dish were designed to continuously supply nutrients for long-term cell survival and create chemokine gradients for driving cell invasion without any external equipment. Using this system, the proliferation and invasiveness of cells were simultaneously evaluated by quantifying the area of cells and the migration distance of cells. In addition, the system combined with live cell workstation could evaluate the dynamic drug response of co-cultured cells and track individual cell trajectories in real-time. When CRC cells were co-cultured with CAFs, CAFs promoted CRC cell proliferation and invasion and reduced the sensitivity of cells to gefitinib through the exosomes secreted by CAFs. Furthermore, the cells that migrated out of the chip were collected, and EMT-related markers were determined by immunofluorescent and western blot assays. The results demonstrated that CAFs affected the response of CRC cells to gefitinib by inducing EMT, providing new ideas for further research on the resistance mechanism of gefitinib. This suggests that targeting CAFs or exosomes might be a new approach to enhance CRC sensitivity to gefitinib, and our system could be a novel platform for investigating the crosstalk between tumor cells and CAFs and understanding multiple biological changes of the tumor cells in the tumor microenvironment.
    Keywords:  Cancer associated fibroblasts; Co-culture; Colorectal cancer; Drug sensitivity; Gefitinib; Microfluidic
    DOI:  https://doi.org/10.1007/s00604-024-06362-9
  13. World J Gastrointest Oncol. 2024 Apr 15. 16(4): 1421-1436
    NOX4 promotes tumor progression through the MAPK-MEK1/2-ERK1/2 axis in colorectal cancer.
    Yu-Jie Xu, Ya-Chang Huo, Qi-Tai Zhao, Jin-Yan Liu, Yi-Jun Tian, Lei-Lei Yang, Yi Zhang.
      BACKGROUND: Metabolic reprogramming plays a key role in cancer progression and clinical outcomes; however, the patterns and primary regulators of metabolic reprogramming in colorectal cancer (CRC) are not well understood.AIM: To explore the role of nicotinamide adenine dinucleotide phosphate oxidase 4 (NOX4) in promoting progression of CRC.
    METHODS: We evaluated the expression and function of dysregulated and survival-related metabolic genes using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes. Consensus clustering was used to cluster CRC based on dysregulated metabolic genes. A prediction model was constructed based on survival-related metabolic genes. Sphere formation, migration, invasion, proliferation, apoptosis and clone formation was used to evaluate the biological function of NOX4 in CRC. mRNA sequencing was utilized to explore the alterations of gene expression NOX4 over-expression tumor cells. In vivo subcutaneous and lung metastasis mouse tumor model was used to explore the effect of NOX4 on tumor growth.
    RESULTS: We comprehensively analyzed 3341 metabolic genes in CRC and identified three clusters based on dysregulated metabolic genes. Among these genes, NOX4 was highly expressed in tumor tissues and correlated with worse survival. In vitro, NOX4 overexpression induced clone formation, migration, invasion, and stemness in CRC cells. Furthermore, RNA-sequencing analysis revealed that NOX4 overexpression activated the mitogen-activated protein kinase-MEK1/2-ERK1/2 signaling pathway. Trametinib, a MEK1/2 inhibitor, abolished the NOX4-mediated tumor progression. In vivo, NOX4 overexpression promoted subcutaneous tumor growth and lung metastasis, whereas trametinib treatment can reversed the metastasis.
    CONCLUSION: Our study comprehensively analyzed metabolic gene expression and highlighted the importance of NOX4 in promoting CRC metastasis, suggesting that trametinib could be a potential therapeutic drugs of CRC clinical therapy targeting NOX4.
    Keywords:  Colorectal cancer; Metabolic reprogramming; Metastasis; Mitogen-activated protein kinase signaling; Nicotinamide adenine dinucleotide phosphate oxidase 4
    DOI:  https://doi.org/10.4251/wjgo.v16.i4.1421
  14. Trends Mol Med. 2024 Apr 23. pii: S1471-4914(24)00091-1. [Epub ahead of print]
    Educate, not kill: treating cancer without triggering its defenses.
    Aneta Škarková, Mariano Bizzarri, Radoslav Janoštiak, Jan Mašek, Daniel Rosel, Jan Brábek.
      Traditionally, anticancer therapies focus on restraining uncontrolled proliferation. However, these cytotoxic therapies expose cancer cells to direct killing, instigating the process of natural selection favoring survival of resistant cells that become the foundation for tumor progression and therapy failure. Recognizing this phenomenon has prompted the development of alternative therapeutic strategies. Here we propose strategies targeting cancer hallmarks beyond proliferation, aiming at re-educating cancer cells towards a less malignant phenotype. These strategies include controlling cell dormancy, transdifferentiation therapy, normalizing the cancer microenvironment, and using migrastatic therapy. Adaptive resistance to these educative strategies does not confer a direct proliferative advantage to resistant cells, as non-resistant cells are not subject to eradication, thereby delaying or preventing the development of therapy-resistant tumors.
    Keywords:  dormancy; metastasis; migrastatics; resistance; transdifferentiation; tumor reversion
    DOI:  https://doi.org/10.1016/j.molmed.2024.04.003
  15. bioRxiv. 2024 Apr 10. pii: 2024.04.08.587960. [Epub ahead of print]
    A heterogeneous pharmaco-transcriptomic landscape induced by targeting a single oncogenic kinase.
    Ross M Giglio, Nicholas Hou, Adeya Wyatt, Justin Hong, Lingting Shi, Mathini Vaikunthan, Henry Fuchs, Jose Pomarino Nima, Seth W Malinowski, Keith L Ligon, José R McFaline-Figueroa, Nir Yosef, Elham Azizi, José L McFaline-Figueroa.
      Over-activation of the epidermal growth factor receptor (EGFR) is a hallmark of glioblastoma. However, EGFR-targeted therapies have led to minimal clinical response. While delivery of EGFR inhibitors (EGFRis) to the brain constitutes a major challenge, how additional drug-specific features alter efficacy remains poorly understood. We apply highly multiplex single-cell chemical genomics to define the molecular response of glioblastoma to EGFRis. Using a deep generative framework, we identify shared and drug-specific transcriptional programs that group EGFRis into distinct molecular classes. We identify programs that differ by the chemical properties of EGFRis, including induction of adaptive transcription and modulation of immunogenic gene expression. Finally, we demonstrate that pro-immunogenic expression changes associated with a subset of tyrphostin family EGFRis increase the ability of T-cells to target glioblastoma cells.
    DOI:  https://doi.org/10.1101/2024.04.08.587960
  16. Cancers (Basel). 2024 Apr 19. pii: 1569. [Epub ahead of print]16(8):
    CD44: A New Prognostic Marker in Colorectal Cancer?
    Pina Ziranu, Andrea Pretta, Valentina Aimola, Flaviana Cau, Stefano Mariani, Alessandra Pia D'Agata, Claudia Codipietro, Daiana Rizzo, Veronica Dell'Utri, Giorgia Sanna, Giusy Moledda, Andrea Cadoni, Eleonora Lai, Marco Puzzoni, Valeria Pusceddu, Massimo Castagnola, Mario Scartozzi, Gavino Faa.
      Cluster of differentiation 44 (CD44) is a non-kinase cell surface glycoprotein. It is overexpressed in several cell types, including cancer stem cells (CSCs). Cells overexpressing CD44 exhibit several CSC traits, such as self-renewal, epithelial-mesenchymal transition (EMT) capability, and resistance to chemo- and radiotherapy. The role of CD44 in maintaining stemness and the CSC function in tumor progression is accomplished by binding to its main ligand, hyaluronan (HA). The HA-CD44 complex activates several signaling pathways that lead to cell proliferation, adhesion, migration, and invasion. The CD44 gene regularly undergoes alternative splicing, resulting in the standard (CD44s) and variant (CD44v) isoforms. The different functional roles of CD44s and specific CD44v isoforms still need to be fully understood. The clinicopathological impact of CD44 and its isoforms in promoting tumorigenesis suggests that CD44 could be a molecular target for cancer therapy. Furthermore, the recent association observed between CD44 and KRAS-dependent carcinomas and the potential correlations between CD44 and tumor mutational burden (TMB) and microsatellite instability (MSI) open new research scenarios for developing new strategies in cancer treatment. This review summarises current research regarding the different CD44 isoform structures, their roles, and functions in supporting tumorigenesis and discusses its therapeutic implications.
    Keywords:  CD44; cancer stem cells; colorectal cancer; predictive marker; prognostic marker; target therapies
    DOI:  https://doi.org/10.3390/cancers16081569
  17. Onco Targets Ther. 2024 ;17 345-358
    Investigating the Cell Origin and Liver Metastasis Factors of Colorectal Cancer by Single-Cell Transcriptome Analysis.
    Zhilin Sha, Qingxiang Gao, Lei Wang, Ni An, Yingjun Wu, Dong Wei, Tong Wang, Chen Liu, Yang Shen.
      Background: Colorectal cancer (CRC) is one of the deadliest causes of death by cancer worldwide. Liver metastasis (LM) is the main cause of death in patients with CRC. Therefore, identification of patients with the greatest risk of liver metastasis is critical for early treatment and reduces the mortality of patients with colorectal cancer liver metastases.Methods: Initially, we characterized cell composition through single-cell transcriptome analysis. Subsequently, we employed copy number variation (CNV) and pseudotime analysis to delineate the cellular origins of LM and identify LM-related epithelial cells (LMECs). The LM-index was constructed using machine learning algorithms to forecast the relative abundance of LMECs, reflecting the risk of LM. Furthermore, we analyzed drug sensitivity and drug targeted gene expression in LMECs and patients with a high risk of LM. Finally, functional experiments were conducted to determine the biological roles of metastasis-related gene in vitro.
    Results: Single-cell RNA sequencing analysis revealed different immune landscapes between primary CRC and LM tumor. LM originated from chromosomal variants with copy number loss of chr1 and chr6p and copy number gain of chr7 and chr20q. We identified the LMECs cluster and found LM-associated pathways such as Wnt/beta-catenin signaling and KRAS signaling. Subsequently, we identified ten metastasis-associated genes, including SOX4, and established the LM-index, which correlates with poorer prognosis, higher stage, and advanced age. Furthermore, we screened two drugs as potential candidates for treating LM, including Linsitinib_1510, Lapatinib_1558. Immunohistochemistry results demonstrated significantly elevated SOX4 expression in tumor samples compared to normal samples. Finally, in vitro experiments verified that silencing SOX4 significantly inhibited tumor cell migration and invasion.
    Conclusion: This study reveals the possible cellular origin and driving factors of LM in CRC at the single cell level, and provides a reference for early detection of CRC patients with a high risk of LM.
    Keywords:  SOX4; colorectal cancer; liver metastasis; prognostic; single-cell sequencing
    DOI:  https://doi.org/10.2147/OTT.S454295
  18. bioRxiv. 2024 Apr 11. pii: 2024.04.09.588781. [Epub ahead of print]
    The G1/S transition in mammalian stem cells in vivo is autonomously regulated by cell size.
    Shicong Xie, Shuyuan Zhang, Gustavo de Medeiros, Prisca Liberali, Jan M Skotheim.
      Cell growth and division must be coordinated to maintain a stable cell size, but how this coordination is implemented in multicellular tissues remains unclear. In unicellular eukaryotes, autonomous cell size control mechanisms couple cell growth and division with little extracellular input. However, in multicellular tissues we do not know if autonomous cell size control mechanisms operate the same way or whether cell growth and cell cycle progression are separately controlled by cell-extrinsic signals. Here, we address this question by tracking single epidermal stem cells growing in adult mice. We find that a cell-autonomous size control mechanism, dependent on the RB pathway, sets the timing of S phase entry based on the cell's current size. Cell-extrinsic variations in the cellular microenvironment affect cell growth rates but not this autonomous coupling. Our work reassesses long-standing models of cell cycle regulation within complex metazoan tissues and identifies cell-autonomous size control as a critical mechanism regulating cell divisions in vivo and thereby a major contributor to stem cell heterogeneity.
    DOI:  https://doi.org/10.1101/2024.04.09.588781
  19. Am J Physiol Endocrinol Metab. 2024 Apr 24.
    Hepatic lipid droplet-associated proteome changes distinguish dietary-induced fatty liver from glucose tolerance in male mice.
    Andries Van Woerkom, Dylan J Harney, Shilpa R Nagarajan, Mariam F Hakeem-Sanni, Jinfeng Lin, Matthew Hooke, Tamara Pilpitel, Gregory J Cooney, Mark Larance, Darren N Saunders, Amanda E Brandon, Andrew J Hoy.
      Fatty liver is characterized by the expansion of lipid droplets (LDs) and is associated with the development of many metabolic diseases. We assessed the morphology of hepatic LDs and performed quantitative proteomics in lean, glucose-tolerant mice compared to high-fat diet (HFD) fed mice that displayed hepatic steatosis and glucose intolerance as well as high-starch diet (HStD) fed mice who exhibited similar levels of hepatic steatosis but remained glucose tolerant. Both HFD and HStD-fed mice had more and larger LDs than Chow-fed animals. We observed striking differences in liver LD proteomes of HFD and HStD-fed mice compared to Chow-fed mice, with fewer differences between HFD and HStD. Taking advantage of our diet strategy, we identified a fatty liver LD proteome consisting of proteins common in HFD- and HStD-fed mice, as well as a proteome associated with glucose tolerance that included proteins shared in Chow and HStD but not HFD-fed mice. Notably, glucose intolerance was associated with changes in the ratio of adipose triglyceride lipase to perilipin 5 in the LD proteome, suggesting dysregulation of neutral lipid homeostasis in glucose-intolerant fatty liver. We conclude that our novel dietary approach uncouples ectopic lipid burden from insulin resistance-associated changes in the hepatic lipid droplet proteome.
    Keywords:  Lipid droplet; fatty liver; glucose tolerance; mice; proteomics
    DOI:  https://doi.org/10.1152/ajpendo.00013.2024
  20. Front Pharmacol. 2024 ;15 1375993
    Metabolic vulnerability of cancer stem cells and their niche.
    Laura Marrone, Simona Romano, Chiara Malasomma, Valeria Di Giacomo, Andrea Cerullo, Rosetta Abate, Marialuisa Alessandra Vecchione, Deborah Fratantonio, Maria Fiammetta Romano.
      Cancer stem cells (CSC) are the leading cause of the failure of anti-tumor treatments. These aggressive cancer cells are preserved and sustained by adjacent cells forming a specialized microenvironment, termed niche, among which tumor-associated macrophages (TAMs) are critical players. The cycle of tricarboxylic acids, fatty acid oxidation path, and electron transport chain have been proven to play central roles in the development and maintenance of CSCs and TAMs. By improving their oxidative metabolism, cancer cells are able to extract more energy from nutrients, which allows them to survive in nutritionally defective environments. Because mitochondria are crucial bioenergetic hubs and sites of these metabolic pathways, major hopes are posed for drugs targeting mitochondria. A wide range of medications targeting mitochondria, electron transport chain complexes, or oxidative enzymes are currently investigated in phase 1 and phase 2 clinical trials against hard-to-treat tumors. This review article aims to highlight recent literature on the metabolic adaptations of CSCs and their supporting macrophages. A focus is provided on the resistance and dormancy behaviors that give CSCs a selection advantage and quiescence capacity in particularly hostile microenvironments and the role of TAMs in supporting these attitudes. The article also describes medicaments that have demonstrated a robust ability to disrupt core oxidative metabolism in preclinical cancer studies and are currently being tested in clinical trials.
    Keywords:  anti-mitochondrial drugs in clinical trials; cancer stem cells; oxidative metabolism; tumor associated macrophages; tumor dormancy
    DOI:  https://doi.org/10.3389/fphar.2024.1375993
  21. Nat Commun. 2024 Apr 22. 15(1): 3396
    Consistent signatures in the human gut microbiome of old- and young-onset colorectal cancer.
    Youwen Qin, Xin Tong, Wei-Jian Mei, Yanshuang Cheng, Yuanqiang Zou, Kai Han, Jiehai Yu, Zhuye Jie, Tao Zhang, Shida Zhu, Xin Jin, Jian Wang, Huanming Yang, Xun Xu, Huanzi Zhong, Liang Xiao, Pei-Rong Ding.
      The incidence of young-onset colorectal cancer (yCRC) has been increasing in recent decades, but little is known about the gut microbiome of these patients. Most studies have focused on old-onset CRC (oCRC), and it remains unclear whether CRC signatures derived from old patients are valid in young patients. To address this, we assembled the largest yCRC gut metagenomes to date from two independent cohorts and found that the CRC microbiome had limited association with age across adulthood. Differential analysis revealed that well-known CRC-associated taxa, such as Clostridium symbiosum, Peptostreptococcus stomatis, Parvimonas micra and Hungatella hathewayi were significantly enriched (false discovery rate <0.05) in both old- and young-onset patients. Similar strain-level patterns of Fusobacterium nucleatum, Bacteroides fragilis and Escherichia coli were observed for oCRC and yCRC. Almost all oCRC-associated metagenomic pathways had directionally concordant changes in young patients. Importantly, CRC-associated virulence factors (fadA, bft) were enriched in both oCRC and yCRC compared to their respective controls. Moreover, the microbiome-based classification model had similar predication accuracy for CRC status in old- and young-onset patients, underscoring the consistency of microbial signatures across different age groups.
    DOI:  https://doi.org/10.1038/s41467-024-47523-x
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