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DeepCC: a novel deep learning-based framework for cancer molecular subtype classification.

Oncogenesis, 2019 8(9), 44

Gao F, Wang W, Tan M, Zhu L, Zhang Y, Fessler E, Vermeulen L, Wang X

DOI | PubMed

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Molecular subtyping of cancer is a critical step towards more individualized therapy and provides important biological insights into cancer heterogeneity. Although gene expression signature-based classification has been widely demonstrated to be an effective approach in the last decade, the widespread implementation has long been limited by platform differences, batch effects, and the difficulty to classify individual patient samples. Here, we describe a novel supervised cancer classification framework, deep cancer subtype classification (DeepCC), based on deep learning of functional spectra quantifying activities of biological pathways. In two case studies about colorectal and breast cancer classification, DeepCC classifiers and DeepCC single sample predictors both achieved overall higher sensitivity, specificity, and accuracy compared with other widely used classification methods such as random forests (RF), support vector machine (SVM), gradient boosting machine (GBM), and multinomial logistic regression algorithms. Simulation analysis based on random subsampling of genes demonstrated the robustness of DeepCC to missing data. Moreover, deep features learned by DeepCC captured biological characteristics associated with distinct molecular subtypes, enabling more compact within-subtype distribution and between-subtype separation of patient samples, and therefore greatly reduce the number of unclassifiable samples previously. In summary, DeepCC provides a novel cancer classification framework that is platform independent, robust to missing data, and can be used for single sample prediction facilitating clinical implementation of cancer molecular subtyping.

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Stem cells in homeostasis and cancer of the gut.

Mol. Cancer, 2019 18(1), 66

van der Heijden M, Vermeulen L

DOI | PubMed

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The intestinal epithelial lining is one of the most rapidly renewing cell populations in the body. As a result, the gut has been an attractive model to resolve key mechanisms in epithelial homeostasis. In particular the role of intestinal stem cells (ISCs) in the renewal process has been intensely studied. Interestingly, as opposed to the traditional stem cell theory, the ISC is not a static population but displays significant plasticity and in situations of tissue regeneration more differentiated cells can revert back to a stem cell state upon exposure to extracellular signals. Importantly, normal intestinal homeostasis provides important insight into mechanisms that drive colorectal cancer (CRC) development and growth. Specifically, the dynamics of cancer stem cells bear important resemblance to ISC functionality. In this review we present an overview of the current knowledge on ISCs in homeostasis and their role in malignant transformation. Also, we discuss the existence of stem cells in intestinal adenomas and CRC and how these cells contribute to (pre-)malignant growth. Furthermore, we will focus on new paradigms in the field of dynamical cellular hierarchies in CRC and the intimate relationship between tumor cells and their niche.

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Spatiotemporal regulation of clonogenicity in colorectal cancer xenografts.

Proc. Natl. Acad. Sci. U.S.A., 2019

van der Heijden M, Miedema DM, Waclaw B, Veenstra VL, Lecca MC, Nijman LE, van Dijk E, van Neerven SM, Lodestijn SC, Lenos KJ, de Groot NE, Prasetyanti PR, Arricibita Varea A, Winton DJ, Medema JP, Morrissey E, Ylstra B, Nowak MA, Bijlsma MF, Vermeulen L

DOI | PubMed

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Cancer evolution is predominantly studied by focusing on differences in the genetic characteristics of malignant cells within tumors. However, the spatiotemporal dynamics of clonal outgrowth that underlie evolutionary trajectories remain largely unresolved. Here, we sought to unravel the clonal dynamics of colorectal cancer (CRC) expansion in space and time by using a color-based clonal tracing method. This method involves lentiviral red-green-blue (RGB) marking of cell populations, which enabled us to track individual cells and their clonal outgrowth during tumor initiation and growth in a xenograft model. We found that clonal expansion largely depends on the location of a clone, as small clones reside in the center and large clones mostly drive tumor growth at the border. These dynamics are recapitulated in a computational model, which confirms that the clone position within a tumor rather than cell-intrinsic features, is crucial for clonal outgrowth. We also found that no significant clonal loss occurs during tumor growth and clonal dispersal is limited in most models. Our results imply that, in addition to molecular features of clones such as (epi-)genetic differences between cells, clone location and the geometry of tumor growth are crucial for clonal expansion. Our findings suggest that either microenvironmental signals on the tumor border or differences in physical properties within the tumor, are major contributors to explain heterogeneous clonal expansion. Thus, this study provides further insights into the dynamics of solid tumor growth and progression, as well as the origins of tumor cell heterogeneity in a relevant model system.

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Prognostic value of low CDX2 expression in colorectal cancers with a high stromal content – a short report.

Cell Oncol (Dordr), 2019

Sandberg TP, Sweere I, van Pelt GW, Putter H, Vermeulen L, Kuppen PJ, Tollenaar RAEM, Mesker WE

DOI | PubMed

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Lack of expression of the intestinal transcription factor CDX2 in colorectal cancer (CRC) identifies patients with a poor prognosis. This biomarker has previously been suggested to be prognostic in CRCs with a high stromal content based on mRNA expression data. We investigated the prognostic value of CDX2 expression in microsatellite stable CRC stratified by stromal content using microscopy-based techniques.

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The interplay between intrinsic and extrinsic Wnt signaling in controlling intestinal transformation.

Differentiation, 2019

van Neerven SM, Vermeulen L

DOI | PubMed

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The intestinal epithelial layer is the fastest renewing tissue in the human body. Due to its incredible turnover rate, the intestine is especially prone to develop cancer, in particular in the colon. Colorectal cancer (CRC) development is characterized by the stepwise accumulation of mutations over time, of which mutations in the tumor suppressor APC are often very early to occur. Generally, mutations in this gene lead to truncated APC proteins that cannot bind to β-catenin to promote its degradation, resulting in a constant overstimulation of the Wnt pathway. The level of intrinsic Wnt activation is dependent on the number of functional β-catenin binding sites remaining within the APC proteins, and the right amount of Wnt signaling is rate-limiting in the formation of polyps. In addition, the intestinal niche provides an extensive spectrum of Wnt ligands, amplifiers and antagonists that locally regulate basal Wnt levels and consequently influence polyp formation propensity. Here we will discuss the crosstalk between transforming epithelial cells and their regional niche in the development of intestinal cancer.

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Integrative network biology analysis identifies miR-508-3p as the determinant for the mesenchymal identity and a strong prognostic biomarker of ovarian cancer.

Oncogene, 2018

Zhao L, Wang W, Xu L, Yi T, Zhao X, Wei Y, Vermeulen L, Goel A, Zhou S, Wang X

DOI | PubMed

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Ovarian cancer is a heterogeneous malignancy that poses tremendous clinical challenge. Based on unsupervised classification of whole-genome gene expression profiles, four molecular subtypes of ovarian cancer were recently identified. However, single-driver molecular events specific to these subtypes have not been clearly elucidated. We aim to characterize the regulatory mechanisms underlying the poor prognosis mesenchymal subtype of ovarian cancer using a systems biology approach, involving a variety of molecular modalities including gene and microRNA expression profiles. miR-508-3p emerged as the most powerful determinant that regulates a cascade of dysregulated genes in the mesenchymal subtype, including core genes involved in epithelial-mesenchymal transition (EMT) program. Moreover, miR-508-3p down-regulation, due to promoter hypermethylation, was directly correlated with metastatic behaviors in vitro and in vivo. Taken together, our multidimensional network analysis identified miR-508-3p as a master regulator that defines the mesenchymal subtype and provides a novel prognostic biomarker to improve management of this disease.

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Itraconazole targets cell cycle heterogeneity in colorectal cancer.

J. Exp. Med., 2018 215(7), 1891-1912

Buczacki SJA, Popova S, Biggs E, Koukorava C, Buzzelli J, Vermeulen L, Hazelwood L, Francies H, Garnett MJ, Winton DJ

DOI | PubMed

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Cellular dormancy and heterogeneity in cell cycle length provide important explanations for treatment failure after adjuvant therapy with S-phase cytotoxics in colorectal cancer (CRC), yet the molecular control of the dormant versus cycling state remains unknown. We sought to understand the molecular features of dormant CRC cells to facilitate rationale identification of compounds to target both dormant and cycling tumor cells. Unexpectedly, we demonstrate that dormant CRC cells are differentiated, yet retain clonogenic capacity. Mouse organoid drug screening identifies that itraconazole generates spheroid collapse and loss of dormancy. Human CRC cell dormancy and tumor growth can also be perturbed by itraconazole, which is found to inhibit Wnt signaling through noncanonical hedgehog signaling. Preclinical validation shows itraconazole to be effective in multiple assays through Wnt inhibition, causing both cycling and dormant cells to switch to global senescence. These data provide preclinical evidence to support an early phase trial of itraconazole in CRC.

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What Will We Expect From Novel Therapies to Esophageal and Gastric Malignancies?

Am Soc Clin Oncol Educ Book, 2018 (38), 249-261

De Mello RA, Castelo-Branco L, Castelo-Branco P, Pozza DH, Vermeulen L, Palacio S, Salzberg M, Lockhart AC

DOI | PubMed

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Esophageal cancer and gastric cancer are aggressive diseases for which treatment approaches are facing a new era. Some molecular pathways, such as VEGF, EGFR, fibroblast growth factor receptor, PIK3CA, and PARP-1, have been studied, and novel targeted drugs are presumed to be developed in the near future. From The Cancer Genome Atlas report, 80% of Epstein-Barr virus tumors and 42% of tumors with microsatellite instability have PIK3CA mutations, suggesting that this pathway could be reevaluated as a possible target for new systemic treatment of gastric cancer. Notably, higher PARP-1 expression can be found in gastric cancer, which might be related to more advanced disease and worse prognosis. In addition, PD-L1 expression, high microsatellite instability, and mismatch repair deficiency can be found in gastric cancer, thus suggesting that immunotherapy may also play a role in those patients. We discuss trends related to the potential of novel therapies for patients with esophageal and gastric cancers in the near future.

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Immunogenomic Classification of Colorectal Cancer and Therapeutic Implications.

Int J Mol Sci, 2017 18(10),

Roelands J, Kuppen PJK, Vermeulen L, Maccalli C, Decock J, Wang E, Marincola FM, Bedognetti D, Hendrickx W

DOI | PubMed

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The immune system has a substantial effect on colorectal cancer (CRC) progression. Additionally, the response to immunotherapeutics and conventional treatment options (e.g., chemotherapy, radiotherapy and targeted therapies) is influenced by the immune system. The molecular characterization of colorectal cancer (CRC) has led to the identification of favorable and unfavorable immunological attributes linked to clinical outcome. With the definition of consensus molecular subtypes (CMSs) based on transcriptomic profiles, multiple characteristics have been proposed to be responsible for the development of the tumor immune microenvironment and corresponding mechanisms of immune escape. In this review, a detailed description of proposed immune phenotypes as well as their interaction with different therapeutic modalities will be provided. Finally, possible strategies to shift the CRC immune phenotype towards a reactive, anti-tumor orientation are proposed per CMS.

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Stem Cells: All that Is Solid Melts into Air.

Cell Stem Cell, 2017 21(1), 5-7

van der Heijden M, Vermeulen L

DOI | PubMed

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The intestinal epithelium displays great resilience, as several cell populations can replenish the stem cell pool upon damage. Two studies in Cell Stem Cell extend this capacity to enteroendocrine cells, addressing the molecular basis underlying cellular plasticity observed in the intestine and the identities of putative reserve stem cells.

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Consensus molecular subtypes and the evolution of precision medicine in colorectal cancer.

Nat. Rev. Cancer, 2017 17(4), 268

Dienstmann R, Vermeulen L, Guinney J, Kopetz S, Tejpar S, Tabernero J

DOI | PubMed

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Abstract not available.

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Balancing signals in the intestinal niche.

EMBO J., 2017 36(4), 389-391

van Neerven SM, Vermeulen L

DOI | PubMed

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Abstract not available.

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Practical and Robust Identification of Molecular Subtypes in Colorectal Cancer by Immunohistochemistry.

Clin. Cancer Res., 2017 23(2), 387-398

Trinh A, Trumpi K, De Sousa E Melo F, Wang X, de Jong JH, Fessler E, Kuppen PJ, Reimers MS, Swets M, Koopman M, Nagtegaal ID, Jansen M, Hooijer GK, Offerhaus GJ, Kranenburg O, Punt CJ, Medema JP, Markowetz F, Vermeulen L

DOI | PubMed

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Recent transcriptomic analyses have identified four distinct molecular subtypes of colorectal cancer with evident clinical relevance. However, the requirement for sufficient quantities of bulk tumor and difficulties in obtaining high-quality genome-wide transcriptome data from formalin-fixed paraffin-embedded tissue are obstacles toward widespread adoption of this taxonomy. Here, we develop an immunohistochemistry-based classifier to validate the prognostic and predictive value of molecular colorectal cancer subtyping in a multicenter study.

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Loss of KCNQ1 expression in stage II and stage III colon cancer is a strong prognostic factor for disease recurrence.

Br. J. Cancer, 2016 115(12), 1565-1574

den Uil SH, Coupé VM, Linnekamp JF, van den Broek E, Goos JA, Delis-van Diemen PM, Belt EJ, van Grieken NC, Scott PM, Vermeulen L, Medema JP, Bril H, Stockmann HB, Cormier RT, Meijer GA, Fijneman RJ

DOI | PubMed

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Colorectal cancer (CRC) is the third most common cancer worldwide. Accurately identifying stage II CRC patients at risk for recurrence is an unmet clinical need. KCNQ1 was previously identified as a tumour suppressor gene and loss of expression was associated with poor survival in patients with CRC liver metastases. In this study the prognostic value of KCNQ1 in stage II and stage III colon cancer patients was examined.

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Wnt Signaling in Cancer Stem Cell Biology.

Cancers (Basel), 2016 8(7),

de Sousa E Melo F, Vermeulen L

DOI | PubMed

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Aberrant regulation of Wnt signaling is a common theme seen across many tumor types. Decades of research have unraveled the epigenetic and genetic alterations that result in elevated Wnt pathway activity. More recently, it has become apparent that Wnt signaling levels identify stem-like tumor cells that are responsible for fueling tumor growth. As therapeutic targeting of these tumor stem cells is an intense area of investigation, a concise understanding on how Wnt activity relates to cancer stem cell traits is needed. This review attempts at summarizing the intricacies between Wnt signaling and cancer stem cell biology with a special emphasis on colorectal cancer.

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Turning off the BCL-2 switch to prevent intestinal tumorigenesis.

Oncotarget, 2016 7(20), 28763-4

van der Heijden M, Winton DJ, Vermeulen L

DOI | PubMed

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Abstract not available.

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Bcl-2 is a critical mediator of intestinal transformation.

Nat Commun, 2016 710916

van der Heijden M, Zimberlin CD, Nicholson AM, Colak S, Kemp R, Meijer SL, Medema JP, Greten FR, Jansen M, Winton DJ, Vermeulen L

DOI | PubMed

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Intestinal tumour formation is generally thought to occur following mutational events in the stem cell pool. However, active NF-κB signalling additionally facilitates malignant transformation of differentiated cells. We hypothesized that genes shared between NF-κB and intestinal stem cell (ISCs) signatures might identify common pathways that are required for malignant growth. Here, we find that the NF-κB target Bcl-2, an anti-apoptotic gene, is specifically expressed in ISCs in both mice and humans. Bcl-2 is dispensable in homeostasis and, although involved in protecting ISCs from radiation-induced damage, it is non-essential in tissue regeneration. Bcl-2 is upregulated in adenomas, and its loss or inhibition impairs outgrowth of oncogenic clones, because Bcl-2 alleviates apoptotic priming in epithelial cells following Apc loss. Furthermore, Bcl-2 expression in differentiated epithelial cells renders these cells amenable to clonogenic outgrowth. Collectively, our results indicate that Bcl-2 is required for efficient intestinal transformation following Apc-loss and constitutes a potential chemoprevention target.

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ER-Stress-Induced Differentiation Sensitizes Colon Cancer Stem Cells to Chemotherapy.

Cell Rep, 2015 13(3), 489-494

Wielenga MCB, Colak S, Heijmans J, van Lidth de Jeude JF, Rodermond HM, Paton JC, Paton AW, Vermeulen L, Medema JP, van den Brink GR

DOI | PubMed

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Colon cancer stem cells (colon-CSCs) are more resistant to conventional chemotherapy than differentiated cancer cells. This subset of therapy refractory cells is therefore believed to play an important role in post-therapeutic tumor relapse. In order to improve the rate of sustained response to conventional chemotherapy, development of approaches is warranted that specifically sensitize colon-CSCs to treatment. Here, we report that ER-stress-induced activation of the unfolded protein response (UPR) forces colon-CSCs to differentiate, resulting in their enhanced sensitivity to chemotherapy in vitro and in vivo. Our data suggest that agents that induce activation of the UPR may be used to specifically increase sensitivity of colon-CSCs to the effects of conventional chemotherapy.

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Colorectal cancer heterogeneity and targeted therapy: a case for molecular disease subtypes.

Cancer Res., 2015 75(2), 245-9

Linnekamp JF, Wang X, Medema JP, Vermeulen L

DOI | PubMed

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Personalized cancer medicine is becoming increasingly important in colorectal cancer treatment. Especially for targeted therapies, large variations between individual treatment responses exist. Predicting therapy response is of utmost significance, as it prevents overtreatment and adverse effects in patients. For EGFR-targeted therapy, many mechanisms of resistance have been uncovered, for example, mutations in KRAS and BRAF, and upregulation of alternative receptors. Currently, routine testing for all known modifiers of response is unpractical, and as a result, decision-making for anti-EGFR therapy is still largely based on assessing the mutation status of an individual gene (KRAS). Recently, comprehensive classifications of colorectal cancer have been presented that integrate many of the (epi-)genetic and microenvironmental factors that contribute to colorectal cancer heterogeneity. These classification systems are not only of prognostic value but also predict therapy efficacy, including the response to anti-EGFR agents. Therefore, molecular subtype-based stratification to guide therapeutic decisions is a promising new strategy that might overcome the shortcomings of single gene testing in colorectal cancer as well as in other malignancies. Furthermore, the development of new agents in a disease subtype-specific fashion has the potential to transform drug-discovery studies and generate novel, more effective therapies.

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Stem cell competition: how speeding mutants beat the rest.

EMBO J., 2014 33(20), 2277-8

Morrissey ER, Vermeulen L

DOI | PubMed

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Abstract not available.

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Defining stem cell dynamics in models of intestinal tumor initiation.

Science, 2013 342(6161), 995-8

Vermeulen L, Morrissey E, van der Heijden M, Nicholson AM, Sottoriva A, Buczacki S, Kemp R, Tavaré S, Winton DJ

DOI | PubMed

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Cancer is a disease in which cells accumulate genetic aberrations that are believed to confer a clonal advantage over cells in the surrounding tissue. However, the quantitative benefit of frequently occurring mutations during tumor development remains unknown. We quantified the competitive advantage of Apc loss, Kras activation, and P53 mutations in the mouse intestine. Our findings indicate that the fate conferred by these mutations is not deterministic, and many mutated stem cells are replaced by wild-type stem cells after biased, but still stochastic events. Furthermore, P53 mutations display a condition-dependent advantage, and especially in colitis-affected intestines, clones harboring mutations in this gene are favored. Our work confirms the previously theoretical notion that the tissue architecture of the intestine suppresses the accumulation of mutated lineages.

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Continuous clonal labeling reveals small numbers of functional stem cells in intestinal crypts and adenomas.

Cell Stem Cell, 2013 13(5), 626-33

Kozar S, Morrissey E, Nicholson AM, van der Heijden M, Zecchini HI, Kemp R, Tavaré S, Vermeulen L, Winton DJ

DOI | PubMed

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Lineage-tracing approaches, widely used to characterize stem cell populations, rely on the specificity and stability of individual markers for accurate results. We present a method in which genetic labeling in the intestinal epithelium is acquired as a mutation-induced clonal mark during DNA replication. By determining the rate of mutation in vivo and combining this data with the known neutral-drift dynamics that describe intestinal stem cell replacement, we quantify the number of functional stem cells in crypts and adenomas. Contrary to previous reports, we find that significantly lower numbers of “working” stem cells are present in the intestinal epithelium (five to seven per crypt) and in adenomas (nine per gland), and that those stem cells are also replaced at a significantly lower rate. These findings suggest that the bulk of tumor stem cell divisions serve only to replace stem cell loss, with rare clonal victors driving gland repopulation and tumor growth.

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Regulation of stem cell self-renewal and differentiation by Wnt and Notch are conserved throughout the adenoma-carcinoma sequence in the colon.

Mol. Cancer, 2013 12(1), 126

Prasetyanti PR, Zimberlin CD, Bots M, Vermeulen L, Melo Fde S, Medema JP

DOI | PubMed

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Colon cancer stem cells are shown to be the self-renewing cells within a tumor that give rise to all lineages of more differentiated tumor cells. In this respect they are remarkably similar to their non-malignant counterparts that orchestrate the intestinal lining. This suggests that, despite the numerous genetic aberrations and morphological changes that have occurred during cancer initiation and progression, a remnant homeostatic regulation persists.

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Intestinal label-retaining cells are secretory precursors expressing Lgr5.

Nature, 2013 495(7439), 65-9

Buczacki SJ, Zecchini HI, Nicholson AM, Russell R, Vermeulen L, Kemp R, Winton DJ

DOI | PubMed

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The rapid cell turnover of the intestinal epithelium is achieved from small numbers of stem cells located in the base of glandular crypts. These stem cells have been variously described as rapidly cycling or quiescent. A functional arrangement of stem cells that reconciles both of these behaviours has so far been difficult to obtain. Alternative explanations for quiescent cells have been that they act as a parallel or reserve population that replace rapidly cycling stem cells periodically or after injury; their exact nature remains unknown. Here we show mouse intestinal quiescent cells to be precursors that are committed to mature into differentiated secretory cells of the Paneth and enteroendocrine lineage. However, crucially we find that after intestinal injury they are capable of extensive proliferation and can give rise to clones comprising the main epithelial cell types. Thus, quiescent cells can be recalled to the stem-cell state. These findings establish quiescent cells as an effective clonogenic reserve and provide a motivation for investigating their role in pathologies such as colorectal cancers and intestinal inflammation.

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Keeping stem cells in check: a hippo balancing act.

Cell Stem Cell, 2013 12(1), 3-5

Vermeulen L

DOI | PubMed

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Knowing when to stop proliferation is crucial for any regenerative process. In a recent issue of Nature,Barry et al. (2012) report that the Hippo pathway component YAP negatively regulates Wnt signaling, thereby preventing stem cell overpopulation after a regenerative response in the intestine.

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Mutations in the Ras-Raf Axis underlie the prognostic value of CD133 in colorectal cancer.

Clin. Cancer Res., 2012 18(11), 3132-41

Kemper K, Versloot M, Cameron K, Colak S, de Sousa e Melo F, de Jong JH, Bleackley J, Vermeulen L, Versteeg R, Koster J, Medema JP

DOI | PubMed

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High expression of cancer stem cell (CSC) marker CD133 has been used as a predictor for prognosis in colorectal cancer (CRC), suggesting that enumeration of CSCs, using CD133, is predictive for disease progression. However, we showed recently that both CD133 mRNA and protein are not downregulated during differentiation of colon CSCs, pointing to an alternative reason for the prognostic value of CD133. We therefore set out to delineate the relation between CD133 expression and prognosis.

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Methylation of cancer-stem-cell-associated Wnt target genes predicts poor prognosis in colorectal cancer patients.

Cell Stem Cell, 2011 9(5), 476-85

de Sousa E Melo F, Colak S, Buikhuisen J, Koster J, Cameron K, de Jong JH, Tuynman JB, Prasetyanti PR, Fessler E, van den Bergh SP, Rodermond H, Dekker E, van der Loos CM, Pals ST, van de Vijver MJ, Versteeg R, Richel DJ, Vermeulen L, Medema JP

DOI | PubMed

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Gene signatures derived from cancer stem cells (CSCs) predict tumor recurrence for many forms of cancer. Here, we derived a gene signature for colorectal CSCs defined by high Wnt signaling activity, which in agreement with previous observations predicts poor prognosis. Surprisingly, however, we found that elevated expression of Wnt targets was actually associated with good prognosis, while patient tumors with low expression of Wnt target genes segregated with immature stem cell signatures. We discovered that several Wnt target genes, including ASCL2 and LGR5, become silenced by CpG island methylation during progression of tumorigenesis, and that their re-expression was associated with reduced tumor growth. Taken together, our data show that promoter methylation of Wnt target genes is a strong predictor for recurrence of colorectal cancer, and suggest that CSC gene signatures, rather than reflecting CSC numbers, may reflect differentiation status of the malignant tissue.

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Microenvironmental regulation of stem cells in intestinal homeostasis and cancer.

Nature, 2011 474(7351), 318-26

Medema JP, Vermeulen L

DOI | PubMed

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The identification of intestinal stem cells as well as their malignant counterparts, colon cancer stem cells, has undergone rapid development in recent years. Under physiological conditions, intestinal homeostasis is a carefully balanced and efficient interplay between stem cells, their progeny and the microenvironment. These interactions regulate the astonishingly rapid renewal of the intestinal epithelial layer, which consequently puts us at serious risk of developing cancer. Here we highlight the microenvironment-derived signals that regulate stem-cell fate and epithelial differentiation. As our understanding of normal intestinal crypt homeostasis grows, these developments may point towards new insights into the origin of cancer and the maintenance and regulation of cancer stem cells.

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Targeting Wnt signaling in colon cancer stem cells.

Clin. Cancer Res., 2011 17(4), 647-53

de Sousa EM, Vermeulen L, Richel D, Medema JP

DOI | PubMed

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The identification of cancer stem cell (CSC) populations in virtually all tumor types has widespread clinical consequences. CSCs are suggested to be the only cells within malignancies endowed with tumorigenic capacity and are, therefore, directly implicated in therapy resistance and minimal residual disease. The genetic and molecular mechanisms sustaining CSCs are only currently emerging. For instance, aberrant activation of the Wnt signaling pathway is crucial for many cancer types and especially those of the gastrointestinal tract. Indeed, Wnt signaling activity was shown to designate colon CSCs and is, therefore, an attractive target for new therapeutics. Here, we review some of the latest developments that have been achieved to inhibit the Wnt pathway in the context of colon CSCs. Moreover, we discuss some of the pitfalls that can be anticipated and present new opportunities for therapeutic intervention.

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Cancer stem cell niche: the place to be.

Cancer Res., 2011 71(3), 634-9

Borovski T, De Sousa E Melo F, Vermeulen L, Medema JP

DOI | PubMed

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Tumors are being increasingly perceived as abnormal organs that, in many respects, recapitulate the outgrowth and differentiation patterns of normal tissues. In line with this idea is the observation that only a small fraction of tumor cells is capable of initiating a new tumor. Because of the features that these cells share with somatic stem cells, they have been termed cancer stem cells (CSC). Normal stem cells reside in a “stem cell niche” that maintains them in a stem-like state. Recent data suggest that CSCs also rely on a similar niche, dubbed the “CSC niche,” which controls their self-renewal and differentiation. Moreover, CSCs can be generated by the microenvironment through induction of CSC features in more differentiated tumor cells. In addition to a role in CSC maintenance, the microenvironment is hypothesized to be involved in metastasis by induction of the epithelial-mesenchymal transition, leading to dissemination and invasion of tumor cells. The localization of secondary tumors also seems to be orchestrated by the microenvironment, which is suggested to form a premetastatic niche. Thus, the microenvironment seems to be of crucial importance for primary tumor growth as well as metastasis formation. Combined with its role in the protection of CSCs against genotoxic insults, these data strongly put forward the niche as an important target for novel therapies.

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Exploring cancer stem cell niche directed tumor growth.

Cell Cycle, 2010 9(8), 1472-9

Sottoriva A, Sloot PM, Medema JP, Vermeulen L

DOI | PubMed

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The finding that only a sub-fraction of tumor cells, so called Cancer Stem Cells (CSC), is endowed with the capacity to initiate new tumors has important consequences for fundamental as well as clinical cancer research. Previously we established by computational modeling techniques that CSC driven tumor growth instigates infiltrative behavior, and perhaps most interesting, stimulates tumor cell heterogeneity. An important question that remains is to what extend CSC functions are intrinsically regulated or whether this capacity is orchestrated by the microenvironment, i.e. a putative CSC niche. Here we investigate how extrinsic regulation of CSC properties affects the characteristics of malignancies. We find that highly invasive growth in tumors dependent on a small subset of cells is not restricted to CSC-driven tumors, but is also observed in tumors where the CSC capacity of tumor cells is completely defined by the microenvironment. Importantly, also the high level of heterogeneity that was observed for CSC-driven tumors is preserved and partially even increased in malignancies with a microenvironmentally orchestrated CSC population. This indicates that invasive growth and high heterogeneity are fundamental properties of tumors fueled by a small population of tumor cells.

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The AC133 epitope, but not the CD133 protein, is lost upon cancer stem cell differentiation.

Cancer Res., 2010 70(2), 719-29

Kemper K, Sprick MR, de Bree M, Scopelliti A, Vermeulen L, Hoek M, Zeilstra J, Pals ST, Mehmet H, Stassi G, Medema JP

DOI | PubMed

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Colon cancer stem cells (CSC) can be identified with AC133, an antibody that detects an epitope on CD133. However, recent evidence suggests that expression of CD133 is not restricted to CSCs, but is also expressed on differentiated tumor cells. Intriguingly, we observed that detection of the AC133 epitope on the cell surface decreased upon differentiation of CSC in a manner that correlated with loss of clonogenicity. However, this event did not coincide with a change in CD133 promoter activity, mRNA, splice variant, protein expression, or even cell surface expression of CD133. In contrast, we noted that with CSC differentiation, a change occured in CD133 glycosylation. Thus, AC133 may detect a glycosylated epitope, or differential glycosylation may cause CD133 to be retained inside the cell. We found that AC133 could effectively detect CD133 glycosylation mutants or bacterially expressed unglycosylated CD133. Moreover, cell surface biotinylation experiments revealed that differentially glycosylated CD133 could be detected on the membrane of differentiated tumor cells. Taken together, our results argue that CD133 is a cell surface molecule that is expressed on both CSC and differentiated tumor cells, but is probably differentially folded as a result of differential glycosylation to mask specific epitopes. In summary, we conclude that AC133 can be used to detect cancer stem cells, but that results from the use of this antibody should be interpreted with caution.

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Cancer stem cell tumor model reveals invasive morphology and increased phenotypical heterogeneity.

Cancer Res., 2010 70(1), 46-56

Sottoriva A, Verhoeff JJ, Borovski T, McWeeney SK, Naumov L, Medema JP, Sloot PM, Vermeulen L

DOI | PubMed

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The recently developed concept of cancer stem cells (CSC) sheds new light on various aspects of tumor growth and progression. Here, we present a mathematical model of malignancies to investigate how a hierarchical organized cancer cell population affects the fundamental properties of solid malignancies. We establish that tumors modeled in a CSC context more faithfully resemble human malignancies and show invasive behavior, whereas tumors without a CSC hierarchy do not. These findings are corroborated by in vitro studies. In addition, we provide evidence that the CSC model is accompanied by highly altered evolutionary dynamics compared with the ones predicted to exist in a stochastic, nonhierarchical tumor model. Our main findings indicate that the CSC model allows for significantly higher tumor heterogeneity, which may affect therapy resistance. Moreover, we show that therapy which fails to target the CSC population is not only unsuccessful in curing the patient, but also promotes malignant features in the recurring tumor. These include rapid expansion, increased invasion, and enhanced heterogeneity.

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One renegade cancer stem cell?

Cell Cycle, 2009 8(6), 803-8

Borovski T, Vermeulen L, Sprick MR, Medema JP

DOI | PubMed

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The CSC compartment represents the subpopulation of tumor cells with clonogenic potential and the ability to initiate new tumors. Besides self renewal, one of their main features is their ability to differentiate into the variety of cells within the tumor. The question remains whether this potential resides within the single CSC or whether many different CSCs are necessary to generate a heterogeneous population of tumor cells. There is an increasing amount of evidence showing that a single CSC indeed has the potential to reconstitute the complete tumor phenotype. This is likely to be a general phenomenon and it has been demonstrated in many tumors so far. Here we show that single GBM CSCs have multilineage potential, although not exclusively. Furthermore, our results show that CSCs originating from same tumor are not necessarily uniform in respect to their differentiation potential.

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[Cancer stem cells].

Ned Tijdschr Geneeskd, 2009 153(7), 286-90

Vermeulen L, Verhoeff JJ, Richel DJ, Medema JP

DOI | PubMed

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Abstract not available.

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Cyclooxygenase-2 inhibition inhibits c-Met kinase activity and Wnt activity in colon cancer.

Cancer Res., 2008 68(4), 1213-20

Tuynman JB, Vermeulen L, Boon EM, Kemper K, Zwinderman AH, Peppelenbosch MP, Richel DJ

DOI | PubMed

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Activity of receptor tyrosine kinases (RTK) in colorectal cancer (CRC) is associated with enhanced tumor growth and a poorer prognosis. In addition, cyclooxygenase-2 (COX-2) expression contributes to tumor growth and invasion. COX-2 inhibitors exhibit important anticarcinogenic potential against CRC, but the molecular mechanism underlying this effect and the relation with RTK signaling remain the subject of intense research effort. Therefore, the rapid effects of COX-2 inhibition in CRC on the complement of all cellular kinases were investigated using a kinase substrate peptide array, Western blotting, transfection, small interfering RNA assays, and CRC cell lines. The resulting alterations in the kinome profile revealed that celecoxib, a selective COX-2 inhibitor, impairs phosphorylation of substrates for the RTKs c-Met and insulin-like growth factor receptor, resulting in decreased downstream signaling. The decrease in c-Met activation is accompanied with an increase in glycogen synthase kinase 3beta kinase activity together with a rapid increase in phosphorylation of beta-catenin. In agreement, a significant reduction of beta-catenin-T-cell factor-dependent transcription is observed both with celecoxib and selective inhibition of c-Met phosphorylation by small molecules. Hence, corepression of c-Met-related and beta-catenin-related oncogenic signal transduction seems a major effector of celecoxib in CRC, which provides a rationale to use c-Met inhibitors and celecoxib analogous to target c-Met and Wnt signaling in a therapeutic setting for patients with CRC.

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Colon cancer stem cells dictate tumor growth and resist cell death by production of interleukin-4.

Cell Stem Cell, 2007 1(4), 389-402

Todaro M, Alea MP, Di Stefano AB, Cammareri P, Vermeulen L, Iovino F, Tripodo C, Russo A, Gulotta G, Medema JP, Stassi G

DOI | PubMed

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A novel paradigm in tumor biology suggests that cancer growth is driven by stem-like cells within a tumor. Here, we describe the identification and characterization of such cells from colon carcinomas using the stem cell marker CD133 that accounts around 2% of the cells in human colon cancer. The CD133(+) cells grow in vitro as undifferentiated tumor spheroids, and they are both necessary and sufficient to initiate tumor growth in immunodeficient mice. Xenografts resemble the original human tumor maintaining the rare subpopulation of tumorigenic CD133(+) cells. Further analysis revealed that the CD133(+) cells produce and utilize IL-4 to protect themselves from apoptosis. Consistently, treatment with IL-4Ralpha antagonist or anti-IL-4 neutralizing antibody strongly enhances the antitumor efficacy of standard chemotherapeutic drugs through selective sensitization of CD133(+) cells. Our data suggest that colon tumor growth is dictated by stem-like cells that are treatment resistant due to the autocrine production of IL-4.

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CD44 expression in intestinal epithelium and colorectal cancer is independent of p53 status.

PLoS ONE, 2013 8(8), e72849

Zeilstra J, Joosten SP, Vermeulen L, Koster J, Medema JP, Versteeg R, Spaargaren M, Pals ST

DOI | PubMed

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CD44 marks stem cell-like cells in a number of tumour types, including colorectal cancer (CRC), while aberrant CD44 expression conveys increased tumourigenic, invasive, and metastatic potential. Previous data indicate that CD44 is a direct target of p53-mediated transcriptional repression in breast cancer. Since inactivating p53 mutations are frequent genetic events in CRC these could unleash expression of CD44. In the present study, we therefore explored the relation between p53 mutational status and CD44 expression in a cohort of 90 localized primary CRCs and studied the effect of radiation-induced p53 activation on CD44 expression. Interestingly, we observed that, in contrast to breast cancer, loss of function p53 mutations were not associated with elevated CD44 expression in colon cancer. Moreover, DNA-damage induced p53 activation did not result in repression of CD44 expression, neither in colon cancer cells nor in normal intestinal epithelial cells. Our data demonstrate that CD44 expression in normal and malignant intestinal epithelial cells is not regulated by p53, implying that regulation of this potentially important therapeutic target is tissue and cancer-type specific.

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Dissecting cancer heterogeneity–an unsupervised classification approach.

Int. J. Biochem. Cell Biol., 2013 45(11), 2574-9

Wang X, Markowetz F, De Sousa E Melo F, Medema JP, Vermeulen L

DOI | PubMed

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Gene-expression-based classification studies have changed the way cancer is traditionally perceived. It is becoming increasingly clear that many cancer types are in fact not single diseases but rather consist of multiple molecular distinct subtypes. In this review, we discuss unsupervised classification studies of common malignancies during the recent years. We found that the bioinformatic workflow of many of these studies follows a common main stream, although different statistical tools may be preferred from case to case. Here we summarize the employed methods, with a special focus on consensus clustering and classification. For each critical step of the bioinformatic analysis, we explain the biological relevance and implications of the technical principles. We think that a better understanding of these ever more frequently used methods to study cancer heterogeneity by the biomedical community is relevant as these type of studies will have an important impact on patient stratification and cancer subtype-specific drug development in the future.

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Cancer heterogeneity–a multifaceted view.

EMBO Rep., 2013 14(8), 686-95

De Sousa E Melo F, Vermeulen L, Fessler E, Medema JP

DOI | PubMed

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Cancers of various organs have been categorized into distinct subtypes after increasingly sophisticated taxonomies. Additionally, within a seemingly homogeneous subclass, individual cancers contain diverse tumour cell populations that vary in important cancer-specific traits such as clonogenicity and invasive potential. Differences that exist between and within a given tumour type have hampered significantly both the proper selection of patients that might benefit from therapy, as well as the development of new targeted agents. In this review, we discuss the differences associated with organ-specific cancer subtypes and the factors that contribute to intra-tumour heterogeneity. It is of utmost importance to understand the biological causes that distinguish tumours as well as distinct tumour cell populations within malignancies, as these will ultimately point the way to more rational anti-cancer treatments.

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Poor-prognosis colon cancer is defined by a molecularly distinct subtype and develops from serrated precursor lesions.

Nat. Med., 2013 19(5), 614-8

De Sousa E Melo F, Wang X, Jansen M, Fessler E, Trinh A, de Rooij LP, de Jong JH, de Boer OJ, van Leersum R, Bijlsma MF, Rodermond H, van der Heijden M, van Noesel CJ, Tuynman JB, Dekker E, Markowetz F, Medema JP, Vermeulen L

DOI | PubMed

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Colon cancer is a clinically diverse disease. This heterogeneity makes it difficult to determine which patients will benefit most from adjuvant therapy and impedes the development of new targeted agents. More insight into the biological diversity of colon cancers, especially in relation to clinical features, is therefore needed. We demonstrate, using an unsupervised classification strategy involving over 1,100 individuals with colon cancer, that three main molecularly distinct subtypes can be recognized. Two subtypes have been previously identified and are well characterized (chromosomal-instable and microsatellite-instable cancers). The third subtype is largely microsatellite stable and contains relatively more CpG island methylator phenotype-positive carcinomas but cannot be identified on the basis of characteristic mutations. We provide evidence that this subtype relates to sessile-serrated adenomas, which show highly similar gene expression profiles, including upregulation of genes involved in matrix remodeling and epithelial-mesenchymal transition. The identification of this subtype is crucial, as it has a very unfavorable prognosis and, moreover, is refractory to epidermal growth factor receptor-targeted therapy.

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Fusion of intestinal epithelial cells with bone marrow derived cells is dispensable for tissue homeostasis.

Sci Rep, 2012 2271

de Jong JH, Rodermond HM, Zimberlin CD, Lascano V, De Sousa E Melo F, Richel DJ, Medema JP, Vermeulen L

DOI | PubMed

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The epithelial lining of the intestine is characterized by an immense cellular turn-over ascertaining an extensive regenerative capacity. Multiple reports suggest that besides the local intestinal stem cell pool, circulating cells of bone marrow origin (BMDCs) contribute to this process by fusing with the epithelial lineage. However, the functional relevance of these observations is unknown. In the present study we employ a model system in which we cannot only detect cell fusion but also examine the functional importance of this process in vivo. Our results indicate that fusion between BMDCs and intestinal epithelial cells is an extremely rare event under physiological conditions. More importantly, by employing a system in which fusion-derived cells can be specifically deleted after extensive tissue damage, we present evidence that cell fusion is not relevant for tissue regeneration. Our data decisively demonstrates that intestinal epithelial homeostasis and regeneration is not dependent on cell fusion involving BMDCs.

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The developing cancer stem-cell model: clinical challenges and opportunities.

Lancet Oncol., 2012 13(2), e83-9

Vermeulen L, de Sousa e Melo F, Richel DJ, Medema JP

DOI | PubMed

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During the past decade, a stem-cell-like subset of cancer cells has been identified in many malignancies. These cells, referred to as cancer stem cells (CSCs), are of particular interest because they are believed to be the clonogenic core of the tumour and therefore represent the cell population that drives growth and progression. Many efforts have been made to design therapies that specifically target the CSC population, since this was predicted to be the crucial population to eliminate. However, recent insights have complicated the initial elegant model, by showing a dominant role for the tumour microenvironment in determining CSC characteristics within a malignancy. This is particularly important since dedifferentiation of non-tumorigenic tumour cells towards CSCs can occur, and therefore the CSC population in a neoplasm is expected to vary over time. Moreover, evidence suggests that not all tumours are driven by rare CSCs, but might instead contain a large population of tumorigenic cells. Even though these results suggest that specific targeting of the CSC population might not be a useful therapeutic strategy, research into the hierarchical cellular organisation of malignancies has provided many important new insights in the biology of tumours. In this Personal View, we highlight how the CSC concept is developing and influences our thinking on future treatment for solid tumours, and recommend ways to design clinical trials to assess drugs that target malignant disease in a rational fashion.

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Modeling evolutionary dynamics of epigenetic mutations in hierarchically organized tumors.

PLoS Comput. Biol., 2011 7(5), e1001132

Sottoriva A, Vermeulen L, Tavaré S

DOI | PubMed

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The cancer stem cell (CSC) concept is a highly debated topic in cancer research. While experimental evidence in favor of the cancer stem cell theory is apparently abundant, the results are often criticized as being difficult to interpret. An important reason for this is that most experimental data that support this model rely on transplantation studies. In this study we use a novel cellular Potts model to elucidate the dynamics of established malignancies that are driven by a small subset of CSCs. Our results demonstrate that epigenetic mutations that occur during mitosis display highly altered dynamics in CSC-driven malignancies compared to a classical, non-hierarchical model of growth. In particular, the heterogeneity observed in CSC-driven tumors is considerably higher. We speculate that this feature could be used in combination with epigenetic (methylation) sequencing studies of human malignancies to prove or refute the CSC hypothesis in established tumors without the need for transplantation. Moreover our tumor growth simulations indicate that CSC-driven tumors display evolutionary features that can be considered beneficial during tumor progression. Besides an increased heterogeneity they also exhibit properties that allow the escape of clones from local fitness peaks. This leads to more aggressive phenotypes in the long run and makes the neoplasm more adaptable to stringent selective forces such as cancer treatment. Indeed when therapy is applied the clone landscape of the regrown tumor is more aggressive with respect to the primary tumor, whereas the classical model demonstrated similar patterns before and after therapy. Understanding these often counter-intuitive fundamental properties of (non-)hierarchically organized malignancies is a crucial step in validating the CSC concept as well as providing insight into the therapeutical consequences of this model.

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Wnt activity defines colon cancer stem cells and is regulated by the microenvironment.

Nat. Cell Biol., 2010 12(5), 468-76

Vermeulen L, De Sousa E Melo F, van der Heijden M, Cameron K, de Jong JH, Borovski T, Tuynman JB, Todaro M, Merz C, Rodermond H, Sprick MR, Kemper K, Richel DJ, Stassi G, Medema JP

DOI | PubMed

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Despite the presence of mutations in APC or beta-catenin, which are believed to activate the Wnt signalling cascade constitutively, most colorectal cancers show cellular heterogeneity when beta-catenin localization is analysed, indicating a more complex regulation of Wnt signalling. We explored this heterogeneity with a Wnt reporter construct and observed that high Wnt activity functionally designates the colon cancer stem cell (CSC) population. In adenocarcinomas, high activity of the Wnt pathway is observed preferentially in tumour cells located close to stromal myofibroblasts, indicating that Wnt activity and cancer stemness may be regulated by extrinsic cues. In agreement with this notion, myofibroblast-secreted factors, specifically hepatocyte growth factor, activate beta-catenin-dependent transcription and subsequently CSC clonogenicity. More significantly, myofibroblast-secreted factors also restore the CSC phenotype in more differentiated tumour cells both in vitro and in vivo. We therefore propose that stemness of colon cancer cells is in part orchestrated by the microenvironment and is a much more dynamic quality than previously expected that can be defined by high Wnt activity.

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Kinome analysis reveals nongenomic glucocorticoid receptor-dependent inhibition of insulin signaling.

Endocrinology, 2006 147(7), 3555-62

Löwenberg M, Tuynman J, Scheffer M, Verhaar A, Vermeulen L, van Deventer S, Hommes D, Peppelenbosch M

DOI | PubMed

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Glucocorticoids (GCs) are powerful immunosuppressive agents that control genomic effects through GC receptor (GR)-dependent transcriptional changes. A common complication of GC therapy is insulin resistance, but the underlying molecular mechanism remains obscure. Evidence is increasing for rapid genomic-independent GC action on cellular physiology. Here, we generate a comprehensive description of nongenomic GC effects on insulin signaling using peptide arrays containing 1,176 different kinase consensus substrates. Reduced kinase activities of the insulin receptor (INSR) and several downstream INSR signaling intermediates (i.e. p70S6k, AMP-activated protein kinase, glycogen synthase kinase-3, and Fyn) were detected in adipocytes and T lymphocytes due to short-term treatment with dexamethasone (DEX), a synthetic fluorinated GC. Western blot analysis confirmed suppressed phosphorylation of the INSR and a series of downstream INSR targets (i.e. INSR substrate-1, p70S6k, protein kinase B, phosphoinositide-dependent protein kinase, Fyn, and glycogen synthase kinase-3) after DEX treatment. DEX inhibited insulin signaling through a GR-dependent (RU486 sensitive) and transcription-independent (actinomycin D insensitive) mechanism. Overall, we postulate here a molecular mechanism for GC-induced insulin resistance based on nongenomic GR-dependent inhibition of insulin signaling.

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Cancer stem cells: here, there, and everywhere.

Mol Cell Oncol, 2019 6(1), 1540235

Lodestijn SC, Lenos KJ, Miedema DM, Bijlsma MF, Vermeulen L

DOI | PubMed

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By using marker-free lineage tracing in combination with quantitative analysis, we recently revealed cancer stem cell functionality in established human colon cancer is not intrinsically defined, but fully spatiotemporally regulated.

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Tumour budding is associated with the mesenchymal colon cancer subtype and RAS/RAF mutations: a study of 1320 colorectal cancers with Consensus Molecular Subgroup (CMS) data.

Br. J. Cancer, 2018 119(10), 1244-1251

Trinh A, Lädrach C, Dawson HE, Ten Hoorn S, Kuppen PJK, Reimers MS, Koopman M, Punt CJA, Lugli A, Vermeulen L, Zlobec I

DOI | PubMed

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Tumour budding is an important prognostic factor in colorectal cancer (CRC). Molecular profiling of tumour buds suggests (partial) epithelial-mesenchymal transition and cancer stem-cell phenotype, similarly described in the “mesenchymal” Consensus Molecular Subtype 4 (CMS4), which identifies a particularly poor prognostic subgroup. Here, we determine the association of tumour budding with CMS classification, prognosis, and response to therapy.

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Stem cell functionality is microenvironmentally defined during tumour expansion and therapy response in colon cancer.

Nat. Cell Biol., 2018 20(10), 1193-1202

Lenos KJ, Miedema DM, Lodestijn SC, Nijman LE, van den Bosch T, Romero Ros X, Lourenço FC, Lecca MC, van der Heijden M, van Neerven SM, van Oort A, Leveille N, Adam RS, de Sousa E Melo F, Otten J, Veerman P, Hypolite G, Koens L, Lyons SK, Stassi G, Winton DJ, Medema JP, Morrissey E, Bijlsma MF, Vermeulen L

DOI | PubMed

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Solid malignancies have been speculated to depend on cancer stem cells (CSCs) for expansion and relapse after therapy. Here we report on quantitative analyses of lineage tracing data from primary colon cancer xenograft tissue to assess CSC functionality in a human solid malignancy. The temporally obtained clone size distribution data support a model in which stem cell function in established cancers is not intrinsically, but is entirely spatiotemporally orchestrated. Functional stem cells that drive tumour expansion predominantly reside at the tumour edge, close to cancer-associated fibroblasts. Hence, stem cell properties change in time depending on the cell location. Furthermore, although chemotherapy enriches for cells with a CSC phenotype, in this context functional stem cell properties are also fully defined by the microenvironment. To conclude, we identified osteopontin as a key cancer-associated fibroblast-produced factor that drives in situ clonogenicity in colon cancer.

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Young GI angle: how to write a good conference abstract.

United European Gastroenterol J, 2018 6(3), 482-484

Krajewska J, Vermeulen L

DOI | PubMed

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Abstract not available.

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Turning Cold Tumors Hot by Blocking TGF-β.

Trends Cancer, 2018 4(5), 335-337

Ros XR, Vermeulen L

DOI | PubMed

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Novel immune therapeutic tools are rapidly expanding the anticancer arsenal. Despite this progress, patients with colorectal cancer (CRC) that spreads to vital parts of the body still have a dismal outcome. Transforming growth factor-β (TGF-β) plays a pivotal role in the development of CRC and metastasis. Important new work by Tauriello and colleagues has revealed that inhibition of TGF-β prevents tumor metastasis by enhancing a cytotoxic T cell response, suggesting that TGF-β inhibition is a promising pro-immunogenic therapy.

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Classification of Colorectal Cancer in Molecular Subtypes by Immunohistochemistry.

Methods Mol. Biol., 2018 1765179-191

Ten Hoorn S, Trinh A, de Jong J, Koens L, Vermeulen L

DOI | PubMed

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Colorectal cancer (CRC) is a heterogeneous disease, which can be categorized into distinct consensus molecular subtypes (CMSs). These subtypes differ in both clinical as well as biological properties. The gold-standard classification strategy relies on genome-wide expression data, which hampers widespread implementation. Here we describe an immunohistochemical (IHC) Mini Classifier, a practical tool that, in combination with microsatellite instability testing, delivers objective and accurate scoring to classify CRC patients into the main molecular disease subtypes. It is a robust immunohistochemical-based assay containing four specific stainings (FRMD6, ZEB1, HTR2B, and CDX2) in combination with cytokeratin. We also describe an online tool for classification of individual samples based on scoring parameters of these stainings.

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Consensus molecular subtypes of colorectal cancer are recapitulated in in vitro and in vivo models.

Cell Death Differ., 2018 25(3), 616-633

Linnekamp JF, Hooff SRV, Prasetyanti PR, Kandimalla R, Buikhuisen JY, Fessler E, Ramesh P, Lee KAST, Bochove GGW, de Jong JH, Cameron K, Leersum RV, Rodermond HM, Franitza M, Nürnberg P, Mangiapane LR, Wang X, Clevers H, Vermeulen L, Stassi G, Medema JP

DOI | PubMed

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Colorectal cancer (CRC) is a highly heterogeneous disease both from a molecular and clinical perspective. Several distinct molecular entities, such as microsatellite instability (MSI), have been defined that make up biologically distinct subgroups with their own clinical course. Recent data indicated that CRC can be best segregated into four groups called consensus molecular subtypes (CMS1-4), each of which has a unique biology and gene expression pattern. In order to develop improved, subtype-specific therapies and to gain insight into the molecular wiring and origin of these subtypes, reliable models are needed. This study was designed to determine the heterogeneity and identify the presence of CMSs in a large panel of CRC cell lines, primary cultures and patient-derived xenografts (PDX). We provide a repository encompassing this heterogeneity and moreover describe that a large part of the models can be robustly assigned to one of the four CMSs, independent of the stromal contribution. We subsequently validate our CMS stratification by functional analysis which for instance shows mesenchymal enrichment in CMS4 and metabolic dysregulation in CMS3. Finally, we observe a clear difference in sensitivity to chemotherapy-induced apoptosis, specifically between CMS2 and CMS4. This relates to the in vivo efficacy of chemotherapy, which delays outgrowth of CMS2, but not CMS4 xenografts. Combined our data indicate that molecular subtypes are faithfully modelled in CRC cell cultures and PDXs, representing tumour cell intrinsic and stable features. This repository provides researchers with a platform to study CRC using the existing heterogeneity.

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Stem cell dynamics in homeostasis and cancer of the intestine.

Nat. Rev. Cancer, 2014 14(7), 468-80

Vermeulen L, Snippert HJ

DOI | PubMed

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Intestinal stem cells (ISCs) and colorectal cancer (CRC) biology are tightly linked in many aspects. It is generally thought that ISCs are the cells of origin for a large proportion of CRCs and crucial ISC-associated signalling pathways are often affected in CRCs. Moreover, CRCs are thought to retain a cellular hierarchy that is reminiscent of the intestinal epithelium. Recent studies offer quantitative insights into the dynamics of ISC behaviour that govern homeostasis and thereby provide the necessary baseline parameters to begin to apply these analyses during the various stages of tumour development.

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Reconciliation of classification systems defining molecular subtypes of colorectal cancer: interrelationships and clinical implications.

Cell Cycle, 2014 13(3), 353-7

Sadanandam A, Wang X, de Sousa E Melo F, Gray JW, Vermeulen L, Hanahan D, Medema JP

DOI | PubMed

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Recently we published two independent studies describing novel gene expression-based classifications of colorectal cancer (CRC). Notably, each study stratified CRC into a different number of subtypes: one reported 3 subtypes, whereas the second highlighted 5. Given that each ascribed clinical significance, distinctive biology, and therapeutic prognosis to the different subtypes, we sought to reconcile this apparent incongruity in subtype stratification of CRC, and to interrelate the results. To do so, we each evaluated the other’s data sets and analytical methods and discovered that the subtypes and their classifiers are, in fact, clearly related to each other; indeed, the 5 subtype outcomes can be coalesced into the same three. In addition to presenting this clarification, we briefly discuss how both classification methods can be viewed within the broader literature on CRC subtypes, and potentially applied.

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Somatic POLE proofreading domain mutation, immune response, and prognosis in colorectal cancer: a retrospective, pooled biomarker study.

Lancet Gastroenterol Hepatol, 2016 1(3), 207-216

Domingo E, Freeman-Mills L, Rayner E, Glaire M, Briggs S, Vermeulen L, Fessler E, Medema JP, Boot A, Morreau H, van Wezel T, Liefers GJ, Lothe RA, Danielsen SA, Sveen A, Nesbakken A, Zlobec I, Lugli A, Koelzer VH, Berger MD, Castellví-Bel S, Muñoz J, , de Bruyn M, Nijman HW, Novelli M, Lawson K, Oukrif D, Frangou E, Dutton P, Tejpar S, Delorenzi M, Kerr R, Kerr D, Tomlinson I, Church DN

DOI | PubMed

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Precision cancer medicine depends on defining distinct tumour subgroups using biomarkers that may occur at very modest frequencies. One such subgroup comprises patients with exceptionally mutated (ultramutated) cancers caused by mutations that impair DNA polymerase epsilon (POLE) proofreading.

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Molecular subtypes in cancers of the gastrointestinal tract.

Nat Rev Gastroenterol Hepatol, 2017 14(6), 333-342

Bijlsma MF, Sadanandam A, Tan P, Vermeulen L

DOI | PubMed

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Malignancies of the gastrointestinal tract are among the most common human cancers. The distinct tissues of origin give rise to a diverse set of diseases, such as colorectal cancer, pancreatic carcinoma and gastric cancers, with each associating with specific clinical features. Genomic and transcriptomic analyses have further defined the heterogeneity that occurs within these cancers by identifying so-called molecular subtypes. These subtypes are characterized by specific genetic aberrations and expression signatures that suggest important biological differences. Although at first sight this subdivision of organ-specific cancers might increase the complexity of classification, closer analysis suggests that the subtypes detected in the various malignancies are recurring. For example, nearly all gastrointestinal cancers appear to present with subtypes that are either characterized by a mesenchymal gene expression signatures, extensive immune infiltration or metabolic dysregulation. Additionally, in each of the gastrointestinal malignancies, a ‘canonical’ subtype is recognized that retains characteristic features of the epithelial tissue of origin. These common themes can enhance our collective understanding of these malignancies, and could perhaps be therapeutically exploited. In this Review, the identification of subtypes in the various gastrointestinal cancer types are discussed along with how they could be incorporated into clinical practice.

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Esophageal Adenocarcinoma Cells and Xenograft Tumors Exposed to Erb-b2 Receptor Tyrosine Kinase 2 and 3 Inhibitors Activate Transforming Growth Factor Beta Signaling, Which Induces Epithelial to Mesenchymal Transition.

Gastroenterology, 2017 153(1), 63-76.e14

Ebbing EA, Steins A, Fessler E, Stathi P, Lesterhuis WJ, Krishnadath KK, Vermeulen L, Medema JP, Bijlsma MF, van Laarhoven HWM

DOI | PubMed

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Drugs that inhibit the erb-b2 receptor tyrosine kinase 2 (ERBB2 or HER2) are the standard treatment of patients with different types of cancer, including HER2-overexpressing gastroesophageal tumors. Unfortunately, cancer cells become resistant to these drugs, so overall these drugs provide little benefit to patients with these tumors. We investigated mechanisms that mediate resistance of esophageal adenocarcinoma (EAC) cells and patient-derived xenograft tumors to ERBB inhibitors.

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Cancer stem cells don’t waste their time cleaning-low proteasome activity, a marker for cancer stem cell function.

Ann Transl Med, 2016 4(24), 519

Lenos KJ, Vermeulen L

DOI | PubMed

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A population of stem-like cells in tumors, the so-called cancer stem cells (CSCs), are being held responsible for therapy resistance and tumor recurrence. In analogy with normal stem cells, CSCs possess the capacity of long term self-renewal and multilineage differentiation. CSCs are believed to be more resistant to various therapies compared to their differentiated offspring and therefore the cause of tumor relapse. Markers for CSCs have been identified using xenograft transplantation assays and lineage tracing in mouse models, however the specificity and validity of many of these markers is under debate. Recently, low proteasome activity has been postulated as a novel CSC marker. In several solid malignancies a small subset of low proteasomal activity cells with CSC characteristics were identified, suggesting that proteasomal activity might be a functional marker for CSCs. In this perspective, we will discuss a recent study by Munakata ., describing a population of colorectal cancer cells with CSC properties, characterized by low proteasome activity and treatment resistance. We will put this finding in a broader view by discussing the challenges and issues inherent with CSC identification, as well as some emerging insights in the CSC concept.

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Consensus molecular subtypes and the evolution of precision medicine in colorectal cancer.

Nat. Rev. Cancer, 2017 17(2), 79-92

Dienstmann R, Vermeulen L, Guinney J, Kopetz S, Tejpar S, Tabernero J

DOI | PubMed

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Critical driver genomic events in colorectal cancer have been shown to affect the response to targeted agents that were initially developed under the ‘one gene, one drug’ paradigm of precision medicine. Our current knowledge of the complexity of the cancer genome, clonal evolution patterns under treatment pressure and pharmacodynamic effects of target inhibition support the transition from a one gene, one drug approach to a ‘multi-gene, multi-drug’ model when making therapeutic decisions. Better characterization of the transcriptomic subtypes of colorectal cancer, encompassing tumour, stromal and immune components, has revealed convergent pathway dependencies that mandate a ‘multi-molecular’ perspective for the development of therapies to treat this disease.

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From tumour heterogeneity to advances in precision treatment of colorectal cancer.

Nat Rev Clin Oncol, 2017 14(4), 235-246

Punt CJ, Koopman M, Vermeulen L

DOI | PubMed

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In recent years, the high heterogeneity of colorectal cancer (CRC) has become evident. Hence, biomarkers need to be developed that enable the stratification of patients with CRC into different prognostic subgroups and in relation to response to therapies, according to the distinctive tumour biology. Currently, only RAS-mutation status is used routinely as a negative predictive marker to avoid treatment with anti-EGFR agents in patients with metastatic CRC, and mismatch-repair status can guide the use of adjuvant chemotherapy in patients with early stage colon cancer. Advances in molecular biology over the past decade have enabled a better understanding of the development of CRC, as well as the more-precise use of innovative targeted therapies for this disease, and include three fundamental achievements. First, the availability of large databases to capture and store the genomic landscape of patients with CRC, providing information on the genes that are frequently deregulated in CRC. Second, the possibility of using gene-expression profiling to differentiate the subtypes of CRC into prognostic groups. Third, results from highly sensitive next-generation sequencing analyses have led to an appreciation of the extensive intratumoural heterogeneity of CRC. Herein, we discuss these advances and place them into the clinical context, and present the novel targets and therapeutic opportunities that are on the horizon.

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The Use of Targeted Therapies for Precision Medicine in Oncology.

Clin. Chem., 2016 62(12), 1556-1564

White Al-Habeeb N, Kulasingam V, Diamandis EP, Yousef GM, Tsongalis GJ, Vermeulen L, Zhu Z, Kamel-Reid S

DOI | PubMed

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Abstract not available.

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Polycomb complex PRC1 as gatekeeper of intestinal stem cell identity.

Stem Cell Investig, 2016 322

Léveillé N, Vermeulen L

DOI | PubMed

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Intestinal stem cells (ISCs) are adult multipotent cells essential for the maintenance of intestinal epithelial homeostasis. Wnt signaling activity ensures that the pool of ISCs at the basis of the intestinal crypts is preserved. Dysregulation of the Wnt pathway is often observed in cancer and supports malignant progression. Chiacchiera and colleagues recently demonstrated the implication of the polycomb complex PRC1 in the regulation of the Wnt pathway in adult ISCs. The authors show that PRC1 maintains intestinal homeostasis by repressing the expression of ZICs, a family of transcription factors inactivating the β-catenin/TCF complex. Importantly, interfering with PRC1 activity completely inhibits the formation of Wnt-dependent tumors. These findings reveal a new layer of epigenetic regulation of the Wnt pathway and open novel opportunities for cancer stem cell targeted therapy.

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Bidirectional interconversion of stem and non-stem cancer cell populations: A reassessment of theoretical models for tumor heterogeneity.

Mol Cell Oncol, 2016 3(2), e1098791

van Neerven SM, Tieken M, Vermeulen L, Bijlsma MF

DOI | PubMed

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Resolving the origin of intratumor heterogeneity has proven to be one of the central challenges in cancer research during recent years. Two theoretical models explaining the emergence of intratumor heterogeneity have come to dominate cancer biology literature: the clonal evolution model and the hierarchical/cancer stem cell model. Recently, a plastic model that combines elements of both the clonal and the hierarchical model has gained traction. Basically, this model proposes that cancer stem cells engage in bidirectional interconversion with non-stem cells, thereby providing the missing link between the 2 conventional models. Confirming bidirectional interconversion as a hallmark of cancer is a crucial step in understanding tumor heterogeneity and has important therapeutic implications. In this review, current methodologies and theoretical and empirical evidence regarding bidirectional interconversion will be discussed.

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TGFβ signaling directs serrated adenomas to the mesenchymal colorectal cancer subtype.

EMBO Mol Med, 2016 8(7), 745-60

Fessler E, Drost J, van Hooff SR, Linnekamp JF, Wang X, Jansen M, De Sousa E Melo F, Prasetyanti PR, IJspeert JE, Franitza M, Nürnberg P, van Noesel CJ, Dekker E, Vermeulen L, Clevers H, Medema JP

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The heterogeneous nature of colorectal cancer (CRC) complicates prognosis and is suggested to be a determining factor in the efficacy of adjuvant therapy for individual patients. Based on gene expression profiling, CRC is currently classified into four consensus molecular subtypes (CMSs), characterized by specific biological programs, thus suggesting the existence of unifying developmental drivers for each CMS Using human organoid cultures, we investigated the role of such developmental drivers at the premalignant stage of distinct CRC subtypes and found that TGFβ plays an important role in the development of the mesenchymal CMS4, which is of special interest due to its association with dismal prognosis. We show that in tubular adenomas (TAs), which progress to classical CRCs, the dominating response to TGFβ is death by apoptosis. By contrast, induction of a mesenchymal phenotype upon TGFβ treatment prevails in a genetically engineered organoid culture carrying a BRAF(V) (600E) mutation, constituting a model system for sessile serrated adenomas (SSAs). Our data indicate that TGFβ signaling is already active in SSA precursor lesions and that TGFβ is a critical cue for directing SSAs to the mesenchymal, poor-prognosis CMS4 of CRC.

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The consensus molecular subtypes of colorectal cancer.

Nat. Med., 2015 21(11), 1350-6

Guinney J, Dienstmann R, Wang X, de Reyniès A, Schlicker A, Soneson C, Marisa L, Roepman P, Nyamundanda G, Angelino P, Bot BM, Morris JS, Simon IM, Gerster S, Fessler E, De Sousa E Melo F, Missiaglia E, Ramay H, Barras D, Homicsko K, Maru D, Manyam GC, Broom B, Boige V, Perez-Villamil B, Laderas T, Salazar R, Gray JW, Hanahan D, Tabernero J, Bernards R, Friend SH, Laurent-Puig P, Medema JP, Sadanandam A, Wessels L, Delorenzi M, Kopetz S, Vermeulen L, Tejpar S

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Colorectal cancer (CRC) is a frequently lethal disease with heterogeneous outcomes and drug responses. To resolve inconsistencies among the reported gene expression-based CRC classifications and facilitate clinical translation, we formed an international consortium dedicated to large-scale data sharing and analytics across expert groups. We show marked interconnectivity between six independent classification systems coalescing into four consensus molecular subtypes (CMSs) with distinguishing features: CMS1 (microsatellite instability immune, 14%), hypermutated, microsatellite unstable and strong immune activation; CMS2 (canonical, 37%), epithelial, marked WNT and MYC signaling activation; CMS3 (metabolic, 13%), epithelial and evident metabolic dysregulation; and CMS4 (mesenchymal, 23%), prominent transforming growth factor-β activation, stromal invasion and angiogenesis. Samples with mixed features (13%) possibly represent a transition phenotype or intratumoral heterogeneity. We consider the CMS groups the most robust classification system currently available for CRC-with clear biological interpretability-and the basis for future clinical stratification and subtype-based targeted interventions.

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Assessing the carcinogenic potential of low-dose exposures to chemical mixtures in the environment: the challenge ahead.

Carcinogenesis, 2015 36 Suppl 1S254-96

Goodson WH, Lowe L, Carpenter DO, Gilbertson M, Manaf Ali A, Lopez de Cerain Salsamendi A, Lasfar A, Carnero A, Azqueta A, Amedei A, Charles AK, Collins AR, Ward A, Salzberg AC, Colacci A, Olsen AK, Berg A, Barclay BJ, Zhou BP, Blanco-Aparicio C, Baglole CJ, Dong C, Mondello C, Hsu CW, Naus CC, Yedjou C, Curran CS, Laird DW, Koch DC, Carlin DJ, Felsher DW, Roy D, Brown DG, Ratovitski E, Ryan EP, Corsini E, Rojas E, Moon EY, Laconi E, Marongiu F, Al-Mulla F, Chiaradonna F, Darroudi F, Martin FL, Van Schooten FJ, Goldberg GS, Wagemaker G, Nangami GN, Calaf GM, Williams G, Wolf GT, Koppen G, Brunborg G, Lyerly HK, Krishnan H, Ab Hamid H, Yasaei H, Sone H, Kondoh H, Salem HK, Hsu HY, Park HH, Koturbash I, Miousse IR, Scovassi AI, Klaunig JE, Vondráček J, Raju J, Roman J, Wise JP, Whitfield JR, Woodrick J, Christopher JA, Ochieng J, Martinez-Leal JF, Weisz J, Kravchenko J, Sun J, Prudhomme KR, Narayanan KB, Cohen-Solal KA, Moorwood K, Gonzalez L, Soucek L, Jian L, D'Abronzo LS, Lin LT, Li L, Gulliver L, McCawley LJ, Memeo L, Vermeulen L, Leyns L, Zhang L, Valverde M, Khatami M, Romano MF, Chapellier M, Williams MA, Wade M, Manjili MH, Lleonart ME, Xia M, Gonzalez MJ, Karamouzis MV, Kirsch-Volders M, Vaccari M, Kuemmerle NB, Singh N, Cruickshanks N, Kleinstreuer N, van Larebeke N, Ahmed N, Ogunkua O, Krishnakumar PK, Vadgama P, Marignani PA, Ghosh PM, Ostrosky-Wegman P, Thompson PA, Dent P, Heneberg P, Darbre P, Sing Leung P, Nangia-Makker P, Cheng QS, Robey RB, Al-Temaimi R, Roy R, Andrade-Vieira R, Sinha RK, Mehta R, Vento R, Di Fiore R, Ponce-Cusi R, Dornetshuber-Fleiss R, Nahta R, Castellino RC, Palorini R, Abd Hamid R, Langie SA, Eltom SE, Brooks SA, Ryeom S, Wise SS, Bay SN, Harris SA, Papagerakis S, Romano S, Pavanello S, Eriksson S, Forte S, Casey SC, Luanpitpong S, Lee TJ, Otsuki T, Chen T, Massfelder T, Sanderson T, Guarnieri T, Hultman T, Dormoy V, Odero-Marah V, Sabbisetti V, Maguer-Satta V, Rathmell WK, Engström W, Decker WK, Bisson WH, Rojanasakul Y, Luqmani Y, Chen Z, Hu Z

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Lifestyle factors are responsible for a considerable portion of cancer incidence worldwide, but credible estimates from the World Health Organization and the International Agency for Research on Cancer (IARC) suggest that the fraction of cancers attributable to toxic environmental exposures is between 7% and 19%. To explore the hypothesis that low-dose exposures to mixtures of chemicals in the environment may be combining to contribute to environmental carcinogenesis, we reviewed 11 hallmark phenotypes of cancer, multiple priority target sites for disruption in each area and prototypical chemical disruptors for all targets, this included dose-response characterizations, evidence of low-dose effects and cross-hallmark effects for all targets and chemicals. In total, 85 examples of chemicals were reviewed for actions on key pathways/mechanisms related to carcinogenesis. Only 15% (13/85) were found to have evidence of a dose-response threshold, whereas 59% (50/85) exerted low-dose effects. No dose-response information was found for the remaining 26% (22/85). Our analysis suggests that the cumulative effects of individual (non-carcinogenic) chemicals acting on different pathways, and a variety of related systems, organs, tissues and cells could plausibly conspire to produce carcinogenic synergies. Additional basic research on carcinogenesis and research focused on low-dose effects of chemical mixtures needs to be rigorously pursued before the merits of this hypothesis can be further advanced. However, the structure of the World Health Organization International Programme on Chemical Safety ‘Mode of Action’ framework should be revisited as it has inherent weaknesses that are not fully aligned with our current understanding of cancer biology.

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The effect of environmental chemicals on the tumor microenvironment.

Carcinogenesis, 2015 36 Suppl 1S160-83

Casey SC, Vaccari M, Al-Mulla F, Al-Temaimi R, Amedei A, Barcellos-Hoff MH, Brown DG, Chapellier M, Christopher J, Curran CS, Forte S, Hamid RA, Heneberg P, Koch DC, Krishnakumar PK, Laconi E, Maguer-Satta V, Marongiu F, Memeo L, Mondello C, Raju J, Roman J, Roy R, Ryan EP, Ryeom S, Salem HK, Scovassi AI, Singh N, Soucek L, Vermeulen L, Whitfield JR, Woodrick J, Colacci A, Bisson WH, Felsher DW

DOI | PubMed

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Potentially carcinogenic compounds may cause cancer through direct DNA damage or through indirect cellular or physiological effects. To study possible carcinogens, the fields of endocrinology, genetics, epigenetics, medicine, environmental health, toxicology, pharmacology and oncology must be considered. Disruptive chemicals may also contribute to multiple stages of tumor development through effects on the tumor microenvironment. In turn, the tumor microenvironment consists of a complex interaction among blood vessels that feed the tumor, the extracellular matrix that provides structural and biochemical support, signaling molecules that send messages and soluble factors such as cytokines. The tumor microenvironment also consists of many host cellular effectors including multipotent stromal cells/mesenchymal stem cells, fibroblasts, endothelial cell precursors, antigen-presenting cells, lymphocytes and innate immune cells. Carcinogens can influence the tumor microenvironment through effects on epithelial cells, the most common origin of cancer, as well as on stromal cells, extracellular matrix components and immune cells. Here, we review how environmental exposures can perturb the tumor microenvironment. We suggest a role for disrupting chemicals such as nickel chloride, Bisphenol A, butyltins, methylmercury and paraquat as well as more traditional carcinogens, such as radiation, and pharmaceuticals, such as diabetes medications, in the disruption of the tumor microenvironment. Further studies interrogating the role of chemicals and their mixtures in dose-dependent effects on the tumor microenvironment could have important general mechanistic implications for the etiology and prevention of tumorigenesis.

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Serrated neoplasia-role in colorectal carcinogenesis and clinical implications.

Nat Rev Gastroenterol Hepatol, 2015 12(7), 401-9

IJspeert JE, Vermeulen L, Meijer GA, Dekker E

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Colorectal cancer (CRC) is considered a heterogeneous disease, both regarding pathogenesis and clinical behaviour. Four decades ago, the adenoma-carcinoma pathway was presented as the main pathway towards CRC, a conclusion that was largely based on evidence from observational morphological studies. This concept was later substantiated at the genomic level. Over the past decade, evidence has been generated for alternative routes in which CRC might develop, in particular the serrated neoplasia pathway. Providing indisputable evidence for the neoplastic potential of serrated polyps has been difficult. Reasons include the absence of reliable longitudinal observations on individual serrated lesions that progress to cancer, a shortage of available animal models for serrated lesions and challenging culture conditions when generating organoids of serrated lesions for in vitro studies. However, a growing body of circumstantial evidence has been accumulated, which indicates that ≥15% of CRCs might arise through the serrated neoplasia pathway. An even larger amount of post-colonoscopy colorectal carcinomas (carcinomas occurring within the surveillance interval after a complete colonoscopy) have been suggested to originate from serrated polyps. The aim of this Review is to assess the current status of the serrated neoplasia pathway in CRC and highlight clinical implications.

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CD31-positive microvessel density within adenomas of Lynch Syndrome patients is similar compared to adenomas of non-Lynch patients.

Endosc Int Open, 2019 7(5), E701-E707

Vleugels JLA, van Neerven SM, van Leerdam ME, Wanders LK, de Wit M, Carvalho B, Delis-van Diemen PM, Kallenberg FGJ, Vermeulen L, Beliën JA, East JE, Meijer GA, Dekker E

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 Microsatellite instability accelerates colorectal cancer development in patients with Lynch syndrome (LS). Previous research showed that virtual chromoendoscopy increases detection of adenomas during colonoscopy surveillance of patients with LS. Because previous research revealed that Lynch patients have an increased vascular network in the oral mucosa, we hypothesized that increased vascularization of LS-associated adenomas is the cause of better detection with virtual chromoendoscopy.  In this pilot study, patients with LS having a proven germline mutation were selected from two tertiary referral hospitals and non-LS patients from an outpatient colonoscopy center. Adenomas from patients with LS were exactly matched in size and histology with adenomas from non-LS patients. Initial adenoma diagnosis was confirmed by a specialist pathologist. All adenomas were stained with CD31 and adenomatous tissue was annotated by the specialist pathologist. Image analysis of CD31-positive microvessel density was conducted using FIJI software.  Colonoscopy of 63 patients with LS and 24 non-LS patients provided 40 adenomas that could be exactly matched in size and histology. In image-analysis, the CD31-positive microvessel density (2.49 % vs. 2.47 %,  = 0.96), the average size of CD31-positive structures (514 μm vs. 523 μm ,  = 0.26) nor the amount of vascular structures per mm (183 vs. 176,  = 0.50) differed between adenomas of LS patients and non-Lynch patients.  The outcomes of this pilot case-control study did not provide further insights into the mechanism of increased adenoma detection in LS patients using virtual chromoendoscopy techniques.

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A marker-independent lineage-tracing system to quantify clonal dynamics and stem cell functionality in cancer tissue.

Nat Protoc, 2019 14(9), 2648-2671

Lenos KJ, Lodestijn SC, Lyons SK, Bijlsma MF, Miedema DM, Vermeulen L

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Lineage tracing is a powerful tool that can be used to uncover cell fates. Here, we describe a novel method for the quantitative analysis of clonal dynamics in grafted cancer tissues. The protocol involves the preparation and validation of cells for lineage tracing, establishment of grafts and label induction, analysis of clone-size distribution and fitting of the experimental data to a mathematical tumor growth model. In contrast to other lineage-tracing strategies, the method described here assesses stem cell functionality and infers tumor expansion dynamics independently of molecular markers such as putative cancer stem cell (CSC)-specific genes. The experimental system and analytical framework presented can be used to quantify clonal advantages that specific mutations provide, in both the absence and presence of (targeted) therapeutic agents. This protocol typically takes ~20 weeks to complete from cell line selection to inference of growth dynamics, depending on the grafted cancer growth rate.

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