bims-instec 2023-05-21 papers

bims-instec

Biomed News

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

Issue of 2023–05–21
ten papers selected by
Maria-Virginia Giolito, Free University of Brussels

Excess dietary sugar alters colonocyte metabolism and impairs the proliferative response to damage.
The Role of Lrig1 in the Development of the Colonic Epithelium.
TGFβ and the Tumor Microenvironment in Colorectal Cancer.
Panitumumab Plus Trifluridine-Tipiracil as Anti-Epidermal Growth Factor Receptor Rechallenge Therapy for Refractory RAS Wild-Type Metastatic Colorectal Cancer: A Phase 2 Randomized Clinical Trial.
Remodeling of the immune and stromal cell compartment by PD-1 blockade in mismatch repair-deficient colorectal cancer.
Role of creatine shuttle in colorectal cancer cells.
Multi-label transcriptional classification of colorectal cancer reflects tumor cell population heterogeneity.
Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment.
An integrated tumor, immune and microbiome atlas of colon cancer.
Asparagine synthetase and G-protein coupled estrogen receptor are critical responders to nutrient supply in KRAS mutant colorectal cancer.

Cell Mol Gastroenterol Hepatol. 2023 May 10. pii: S2352-345X(23)00063-2. [Epub ahead of print]

Excess dietary sugar alters colonocyte metabolism and impairs the proliferative response to damage.

Ansen H P Burr, Junyi Ji, Kadir Ozler, Heather L Mentrup, Onur Eskiocak, Brian Yueh, Rachel Cumberland, Ashley V Menk, Natalie Rittenhouse, Chris W Marshall, Pailin Chiaranunt, Xiaoyi Zhang, Lauren Mullinax, Abigail Overacre-Delgoffe, Vaughn S Cooper, Amanda C Poholek, Greg M Delgoffe, Kevin P Mollen, Semir Beyaz, Timothy W Hand.

   BACKGROUND: The colonic epithelium requires continuous renewal by crypt resident intestinal stem cells (ISCs) and transit amplifying (TA) cells to maintain barrier integrity, especially after inflammatory damage. The diet of high-income countries contains increasing amounts of sugar, such as sucrose. ISCs and TA cells are sensitive to dietary metabolites, but whether excess sugar affects their function directly is unknown.
METHODS: Here we use a combination of 3-dimensional colonoids and a mouse model of colon damage/repair (DSS colitis) to demonstrate the direct effect of sugar on the transcriptional, metabolic, and regenerative functions of crypt ISCs and TA cells.
RESULTS: We demonstrate that high sugar conditions directly limit murine and human colonoid development, which is associated with a reduction in the expression of proliferative genes, ATP levels and the accumulation of pyruvate. Treatment of colonoids with DCA, which forces pyruvate into the TCA cycle, restored their growth. In concert, DSS treatment of mice fed a high sugar diet led to massive irreparable damage that was independent of the colonic microbiota and its metabolites. Analyses on crypt cells from high-sucrose-fed mice revealed a reduction in the expression of ISC genes, impeded proliferative potential and increased glycolytic potential without a commensurate increase in aerobic respiration.
CONCLUSION: Taken together, our results indicate that short-term, excess dietary sucrose can directly modulate intestinal crypt cell metabolism and inhibit ISC/TA cell regenerative proliferation. This knowledge may inform diets that better support the treatment of acute intestinal injury.

Keywords:  DCA; colitis; mitochondria; renewal; stemness

DOI:  https://doi.org/10.1016/j.jcmgh.2023.05.001
bioRxiv. 2023 May 02. pii: 2023.05.02.539114. [Epub ahead of print]

The Role of Lrig1 in the Development of the Colonic Epithelium.

Rachel E Hopton, Nicholas J Jahahn, Anne E Zemper.

Growth and specification of the mouse intestine occurs in utero and concludes after birth. While numerous studies have examined this developmental process in the small intestine, far less is known about the cellular and molecular cues required for colon development. In this study, we examine the morphological events leading to crypt formation, epithelial cell differentiation, areas of proliferation, and the emergence and expression of a stem and progenitor cell marker Lrig1. Through multicolor lineage tracing, we show Lrig1 expressing cells are present at birth and behave as stem cells to establish clonal crypts within three weeks after birth. In addition, we use an inducible knockout mouse to eliminate Lrig1 during colon development and show loss of Lrig1 restrains proliferation within a critical developmental time window, without impacting colonic epithelial cell differentiation. Our study illustrates the morphological changes that occur during crypt development and the importance of Lrig1 in the developing colon.

DOI: https://doi.org/10.1101/2023.05.02.539114
Cells. 2023 04 12. pii: 1139. [Epub ahead of print]12(8):

TGFβ and the Tumor Microenvironment in Colorectal Cancer.

Maximilian J Waldner, Markus F Neurath.

  Growing evidence supports an important role of the tumor microenvironment (TME) in the pathogenesis of colorectal cancer (CRC). Resident cells such as fibroblasts or immune cells infiltrating into the TME maintain continuous crosstalk with cancer cells and thereby regulate CRC progression. One of the most important molecules involved is the immunoregulatory cytokine transforming growth factor-β (TGFβ). TGFβ is released by various cells in the TME, including macrophages and fibroblasts, and it modulates cancer cell growth, differentiation, and cell death. Mutations in components of the TGF pathway, including TGFβ receptor type 2 or SMAD4, are among the most frequently detected mutations in CRC and have been associated with the clinical course of disease. Within this review, we will discuss our current understanding about the role of TGFβ in the pathogenesis of CRC. This includes novel data on the molecular mechanisms of TGFβ signaling in TME, as well as possible strategies for CRC therapy targeting the TGFβ pathway, including potential combinations with immune checkpoint inhibitors.

Keywords:  SMAD4; TGFβ; colorectal cancer; immune response; tumor microenvironment

DOI:  https://doi.org/10.3390/cells12081139
JAMA Oncol. 2023 May 18.

Panitumumab Plus Trifluridine-Tipiracil as Anti-Epidermal Growth Factor Receptor Rechallenge Therapy for Refractory RAS Wild-Type Metastatic Colorectal Cancer: A Phase 2 Randomized Clinical Trial.

Stefania Napolitano, Vincenzo De Falco, Giulia Martini, Davide Ciardiello, Erika Martinelli, Carminia Maria Della Corte, Lucia Esposito, Vincenzo Famiglietti, Alessandra Di Liello, Antonio Avallone, Claudia Cardone, Alfonso De Stefano, Vincenzo Montesarchio, Maria Giulia Zampino, Roberto Bordonaro, Mario Scartozzi, Daniele Santini, Massimo Di Maio, Ferdinando De Vita, Lucia Altucci, Francesca Marrone, Fortunato Ciardiello, Teresa Troiani.

Importance: Current third-line therapies for patients with metastatic colorectal cancer (MCRC) have limited efficacy. Rechallenge with epidermal growth factor receptor (EGFR) inhibitors for RAS wild-type (WT) MCRC may be valuable for these patients.
Objective: To compare the anti-EGFR monoclonal antibody panitumumab plus standard-of-care trifluridine-tipiracil with trifluridine-tipiracil alone as third-line therapy for RAS WT MCRC.
Design, Setting, and Participants: This phase 2 randomized clinical trial (RCT) was conducted in 7 Italian centers from June 2019 to April 2022. Patients with refractory RAS WT MCRC who had a partial or complete response to first-line chemotherapy plus an anti-EGFR monoclonal antibody and an anti-EGFR drug-free interval of 4 or more months during second-line therapy were included.
Interventions: Patients were randomized 1:1 to receive panitumumab plus trifluridine-tipiracil or trifluridine-tipiracil alone.
Main Outcomes and Measures: The primary end point was progression-free survival (PFS). Circulating tumor DNA (ctDNA) extended sequence variation analysis was performed in a subgroup of patients.
Results: Of 62 included patients, 31 received panitumumab plus trifluridine-tipiracil (19 [61.3%] male; median age, 65 years [range, 39-81 years]) and 31 received trifluridine-tipiracil alone (17 [54.8%] male; median age, 66 years [range, 32-82 years]). The primary end point was met. Median PFS was 4.0 months (95% CI, 2.8-5.3 months) in the panitumumab plus trifluridine-tipiracil arm vs 2.5 months (95% CI, 1.4-3.6 months) in the trifluridine-tipiracil only (hazard ratio [HR], 0.48; 95% CI, 0.28-0.82; P = .007). Pretreatment plasma RAS/BRAF WT ctDNA identified patients obtaining prolonged clinical benefit with panitumumab plus trifluridine-tipiracil compared with trifluridine-tipiracil, with PFS rates at 6 months of 38.5% vs 13.0% and at 12 months of 15.4% vs 0%. A ctDNA liquid-biopsy extended mutation analysis by FoundationOne Liquid CDx (profiling 324 genes) was performed in a subgroup of patients with baseline plasma RAS/BRAF WT ctDNA; in 15 of 23 patients (65.2%) whose tumors were WT for KRAS, NRAS, BRAFV600E, EGFR, ERBB2, MAP2K1, and PIK3CA, median PFS was 6.4 months (95% CI, 3.7-9.2 months). Within this group of 15 patients, 2 (13.3%) had partial response, 11 (73.3%) had stable disease, and 2 (13.3%) had disease progression as best response.
Conclusions and Relevance: In this RCT, third-line treatment with the anti-EGFR monoclonal antibody panitumumab plus the standard-of-care trifluridine-tipiracil resulted in improved PFS compared with treatment with trifluridine-tipiracil alone among patients with refractory RAS WT MCRC. The findings support the clinical utility of liquid biopsy-guided anti-EGFR rechallenge therapy for refractory RAS WT MCRC.
Trial Registration: ClinicalTrials.gov Identifier: NCT05468892.

DOI: https://doi.org/10.1001/jamaoncol.2023.0655
Cancer Cell. 2023 May 09. pii: S1535-6108(23)00137-X. [Epub ahead of print]

Remodeling of the immune and stromal cell compartment by PD-1 blockade in mismatch repair-deficient colorectal cancer.

Jianxia Li, Cheng Wu, Huabin Hu, Ge Qin, Xueqian Wu, Fan Bai, Jianwei Zhang, Yue Cai, Yan Huang, Chao Wang, Jiaqi Yang, Yizhao Luan, Zehang Jiang, Jiayu Ling, Zehua Wu, Yaoxu Chen, Zhi Xie, Yanhong Deng.

  Immune checkpoint inhibitor (ICI) therapy can induce complete responses in mismatch repair-deficient and microsatellite instability-high (d-MMR/MSI-H) colorectal cancers (CRCs). However, the underlying mechanism for pathological complete response (pCR) to immunotherapy has not been completely understood. We utilize single-cell RNA sequencing (scRNA-seq) to investigate the dynamics of immune and stromal cells in 19 patients with d-MMR/MSI-H CRC who received neoadjuvant PD-1 blockade. We found that in tumors with pCR, there is a concerted decrease in CD8+ Trm-mitotic, CD4+ Tregs, proinflammatory IL1B+ Mono and CCL2+ Fibroblast following treatment, while the proportions of CD8+ Tem, CD4+ Th, CD20+ B, and HLA-DRA+ Endothelial cells increase. Proinflammatory features in the tumor microenvironment mediate the persistence of residual tumors by modulating CD8+ T cells and other response-associated immune cell populations. Our study provides valuable resources and biological insights into the mechanism of successful ICI therapy and potential targets for improving treatment efficacy.

Keywords:  PD-1 blockade; colorectal cancer; complete response; immune checkpoint inhibitors; microsatellite instability-high; mismatch repair-deficient; neoadjuvant immunotherapy; single-cell RNA sequencing; stromal cells; tumor immune microenvironment

DOI:  https://doi.org/10.1016/j.ccell.2023.04.011
Oncotarget. 2023 May 19. 14 485-501

Role of creatine shuttle in colorectal cancer cells.

Mayu Kita, Rina Fujiwara-Tani, Shingo Kishi, Shiori Mori, Hitoshi Ohmori, Chie Nakashima, Kei Goto, Takamitsu Sasaki, Kiyomu Fujii, Isao Kawahara, Ujjal Kumar Bhawal, Yi Luo, Hiroki Kuniyasu.

  The creatine shuttle translocates the energy generated by oxidative phosphorylation to the cytoplasm via mitochondrial creatine kinase (MTCK) and creatine kinase B (CKB) in the cytoplasm. It is not apparent how the creatine shuttle is related to cancer. Here, we analyzed the expression and function of CKB and MTCK in colorectal cancer (CRC) and investigated the role of the creatine shuttle in CRC. Compared with normal mucosa, 184 CRC tissues had higher levels of CKB and MTCK, and these levels were associated with histological grade, tumor invasion, and distant metastasis. CK inhibitor dinitrofluorobenzene (DNFB) on CRC cell lines HT29 and CT26 inhibited cell proliferation and stemness to less than 2/3 and 1/20 of their control levels, respectively. In this treatment, the production of reactive oxygen species increased, mitochondrial respiration decreased, and mitochondrial volume and membrane potential decreased. In a syngeneic BALB/c mouse model using CT26 cells pretreated with DNFB, peritoneal metastasis was suppressed to 70%. Phosphorylation of EGFR, AKT, and ERK1/2 was inhibited in DNFB-treated tumors. High ATP concentrations prevented EGFR phosphorylation in HT29 cells following DNFB treatment, CKB or MTCK knockdown, and cyclocreatine administration. Despite not being immunoprecipitated, CKB and EGFR were brought closer together by EGF stimulation. These findings imply that blocking the creatine shuttle decreases the energy supply, suppresses oxidative phosphorylation, and blocks ATP delivery to phosphorylation signals, preventing signal transduction. These findings highlight the critical role of the creatine shuttle in cancer cells and suggest a potential new cancer treatment target.

Keywords:  ATP metabolism; creatine kinase B; mitochondrial creatine kinase; phosphorylation signal; stemness

DOI:  https://doi.org/10.18632/oncotarget.28436
Genome Med. 2023 05 15. 15(1): 37

Multi-label transcriptional classification of colorectal cancer reflects tumor cell population heterogeneity.

Silvia Cascianelli, Chiara Barbera, Alexandra Ambra Ulla, Elena Grassi, Barbara Lupo, Diego Pasini, Andrea Bertotti, Livio Trusolino, Enzo Medico, Claudio Isella, Marco Masseroli.

   BACKGROUND: Transcriptional classification has been used to stratify colorectal cancer (CRC) into molecular subtypes with distinct biological and clinical features. However, it is not clear whether such subtypes represent discrete, mutually exclusive entities or molecular/phenotypic states with potential overlap. Therefore, we focused on the CRC Intrinsic Subtype (CRIS) classifier and evaluated whether assigning multiple CRIS subtypes to the same sample provides additional clinically and biologically relevant information.
METHODS: A multi-label version of the CRIS classifier (multiCRIS) was applied to newly generated RNA-seq profiles from 606 CRC patient-derived xenografts (PDXs), together with human CRC bulk and single-cell RNA-seq datasets. Biological and clinical associations of single- and multi-label CRIS were compared. Finally, a machine learning-based multi-label CRIS predictor (ML2CRIS) was developed for single-sample classification.
RESULTS: Surprisingly, about half of the CRC cases could be significantly assigned to more than one CRIS subtype. Single-cell RNA-seq analysis revealed that multiple CRIS membership can be a consequence of the concomitant presence of cells of different CRIS class or, less frequently, of cells with hybrid phenotype. Multi-label assignments were found to improve prediction of CRC prognosis and response to treatment. Finally, the ML2CRIS classifier was validated for retaining the same biological and clinical associations also in the context of single-sample classification.
CONCLUSIONS: These results show that CRIS subtypes retain their biological and clinical features even when concomitantly assigned to the same CRC sample. This approach could be potentially extended to other cancer types and classification systems.

Keywords:  Colorectal cancer; Computational biology; Molecular subtyping; Tumor heterogeneity

DOI:  https://doi.org/10.1186/s13073-023-01176-5
Cell Metab. 2023 May 09. pii: S1550-4131(23)00140-7. [Epub ahead of print]

Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment.

Zhijun Wang, So Yeon Kim, Wei Tu, Jieun Kim, Alexander Xu, Yoon Mee Yang, Michitaka Matsuda, Lien Reolizo, Takashi Tsuchiya, Sandrine Billet, Alexandra Gangi, Mazen Noureddin, Ben A Falk, Sungjin Kim, Wei Fan, Mourad Tighiouart, Sungyong You, Michael S Lewis, Stephen J Pandol, Dolores Di Vizio, Akil Merchant, Edwin M Posadas, Neil A Bhowmick, Shelly C Lu, Ekihiro Seki.

  Liver metastasis is a major cause of death in patients with colorectal cancer (CRC). Fatty liver promotes liver metastasis, but the underlying mechanism remains unclear. We demonstrated that hepatocyte-derived extracellular vesicles (EVs) in fatty liver enhanced the progression of CRC liver metastasis by promoting oncogenic Yes-associated protein (YAP) signaling and an immunosuppressive microenvironment. Fatty liver upregulated Rab27a expression, which facilitated EV production from hepatocytes. In the liver, these EVs transferred YAP signaling-regulating microRNAs to cancer cells to augment YAP activity by suppressing LATS2. Increased YAP activity in CRC liver metastasis with fatty liver promoted cancer cell growth and an immunosuppressive microenvironment by M2 macrophage infiltration through CYR61 production. Patients with CRC liver metastasis and fatty liver had elevated nuclear YAP expression, CYR61 expression, and M2 macrophage infiltration. Our data indicate that fatty liver-induced EV-microRNAs, YAP signaling, and an immunosuppressive microenvironment promote the growth of CRC liver metastasis.

Keywords:  CYR61; M2 macrophage; Rab27a; colon cancer; exosome; high-fat diet; liver metastasis; microRNA; non-alcoholic fatty liver disease; palmitate

DOI:  https://doi.org/10.1016/j.cmet.2023.04.013
Nat Med. 2023 May 19.

An integrated tumor, immune and microbiome atlas of colon cancer.

Jessica Roelands, Peter J K Kuppen, Eiman I Ahmed, Raghvendra Mall, Tariq Masoodi, Parul Singh, Gianni Monaco, Christophe Raynaud, Noel F C C de Miranda, Luigi Ferraro, Tatiana C Carneiro-Lobo, Najeeb Syed, Arun Rawat, Amany Awad, Julie Decock, William Mifsud, Lance D Miller, Shimaa Sherif, Mahmoud G Mohamed, Darawan Rinchai, Marc Van den Eynde, Rosalyn W Sayaman, Elad Ziv, Francois Bertucci, Mahir Abdulla Petkar, Stephan Lorenz, Lisa Sara Mathew, Kun Wang, Selvasankar Murugesan, Damien Chaussabel, Alexander L Vahrmeijer, Ena Wang, Anna Ceccarelli, Khalid A Fakhro, Gabriele Zoppoli, Alberto Ballestrero, Rob A E M Tollenaar, Francesco M Marincola, Jérôme Galon, Souhaila Al Khodor, Michele Ceccarelli, Wouter Hendrickx, Davide Bedognetti.

The lack of multi-omics cancer datasets with extensive follow-up information hinders the identification of accurate biomarkers of clinical outcome. In this cohort study, we performed comprehensive genomic analyses on fresh-frozen samples from 348 patients affected by primary colon cancer, encompassing RNA, whole-exome, deep T cell receptor and 16S bacterial rRNA gene sequencing on tumor and matched healthy colon tissue, complemented with tumor whole-genome sequencing for further microbiome characterization. A type 1 helper T cell, cytotoxic, gene expression signature, called Immunologic Constant of Rejection, captured the presence of clonally expanded, tumor-enriched T cell clones and outperformed conventional prognostic molecular biomarkers, such as the consensus molecular subtype and the microsatellite instability classifications. Quantification of genetic immunoediting, defined as a lower number of neoantigens than expected, further refined its prognostic value. We identified a microbiome signature, driven by Ruminococcus bromii, associated with a favorable outcome. By combining microbiome signature and Immunologic Constant of Rejection, we developed and validated a composite score (mICRoScore), which identifies a group of patients with excellent survival probability. The publicly available multi-omics dataset provides a resource for better understanding colon cancer biology that could facilitate the discovery of personalized therapeutic approaches.

DOI: https://doi.org/10.1038/s41591-023-02324-5
bioRxiv. 2023 May 05. pii: 2023.05.05.539577. [Epub ahead of print]

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

Lingeng Lu, Qian Zhang, Xinyi Shen, Pinyi Zhen, Audrey Marin, Rolando Garcia- Milian, Jatin Roper, Sajid A Khan, Caroline H Johnson.

The nutrient status of the tumor microenvironment has major impacts on cell growth. Under nutrient depletion, asparagine synthetase (ASNS)-mediated asparagine production increases to sustain cell survival. G protein-coupled estrogen receptor-1 (GPER1) signaling converges via cAMP/PI3K/AKT with KRAS signaling to regulate ASNS expression. However, the role of GPER1 in CRC progression is still debated, and the effect of nutrient supply on both ASNS and GPER1 relative to KRAS genotype is not well understood. Here, we modeled a restricted nutrient supply by eliminating glutamine from growing cancer cells in a 3D spheroid model of human female SW48 KRAS wild-type (WT) and KRAS G12A mutant (MT) CRC cells, to examine effects on ASNS and GPER1 expression. Glutamine depletion significantly inhibited cell growth in both KRAS MT and WT cells; however, ASNS and GPER1 were upregulated in KRAS MT compared to WT cells. When nutrient supply was adequate, ASNS and GPER1 were not altered between cell lines. The impact of estradiol, a ligand for GPER1, was examined for any additional effects on cell growth. Under glutamine deplete conditions, estradiol decreased the growth of KRAS WT cells but had no effect on KRAS MT cells; estradiol had no additive or diminutive effect on the upregulation of ASNS or GPER1 between the cell lines. We further examined the association of GPER1 and ASNS levels with overall survival in a clinical colon cancer cohort of The Cancer Genome Atlas. Both high GPER1 and ASNS expression associated with poorer overall survival for females only in advanced stage tumors. These findings suggest that 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. ASNS and GPER1 may therefore be potential therapeutic targets that can be exploited to manage and control KRAS MT CRC.

DOI: https://doi.org/10.1101/2023.05.05.539577