Hans Clevers

Tsinghua University, Peping, Beijing, China

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Publications (341)4590.87 Total impact

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    ABSTRACT: Understanding the complexity of the human brain and its functional diversity remain a major challenge. Distinct anatomical regions are involved in an array of processes, including organismal homeostasis, cognitive functions, and susceptibility to neurological pathologies, many of which define our species. Distal enhancers have emerged as key regulatory elements that acquire histone modifications in a cell- and species-specific manner, thus enforcing specific gene expression programs. Here, we survey the epigenomic landscape of promoters and cis-regulatory elements in 136 regions of the adult human brain. We identify a total of 83,553 promoter-distal H3K27ac-enriched regions showing global characteristics of brain enhancers. We use coregulation of enhancer elements across many distinct regions of the brain to uncover functionally distinct networks at high resolution and link these networks to specific neuroglial functions. Furthermore, we use these data to understand the relevance of noncoding genomic variations previously linked to Parkinson's disease incidence.
    Cell reports. 10/2014; 9(2):767-79.
  • Paul W Tetteh, Henner F Farin, Hans Clevers
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    ABSTRACT: Tissue homeostasis and regeneration are fueled by resident stem cells that have the capacity to self-renew, and to generate all the differentiated cell types that characterize a particular tissue. Classical models of such cellular hierarchies propose that commitment and differentiation occur unidirectionally, with the arrows 'pointing away' from the stem cell. Recent studies, all based on genetic lineage tracing, describe various strategies employed by epithelial stem cell hierarchies to replace damaged or lost cells. While transdifferentiation from one tissue type into another ('metaplasia') appears to be generally forbidden in nonpathological contexts, plasticity within an individual tissue stem cell hierarchy may be much more common than previously appreciated. In this review, we discuss recent examples of such plasticity in selected mammalian epithelia, highlighting the different modes of regeneration and their implications for our understanding of cellular hierarchy and tissue self-renewal.
    Trends in cell biology. 10/2014;
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    ABSTRACT: We previously established systems for long-term, 3-dimensional (3D) culture of organoids from mouse tissues (intestine, stomach, pancreas, and liver) and human intestine and pancreas. We describe conditions required for long-term 3D cultures of human gastric stem cells. The technology can be applied to study the epithelial response to infection with Helicobacter pylori.
    Gastroenterology 10/2014; · 12.82 Impact Factor
  • Hans Clevers, Kyle M Loh, Roel Nusse
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    ABSTRACT: Stem cells fuel tissue development, renewal, and regeneration, and these activities are controlled by the local stem cell microenvironment, the "niche." Wnt signals emanating from the niche can act as self-renewal factors for stem cells in multiple mammalian tissues. Wnt proteins are lipid-modified, which constrains them to act as short-range cellular signals. The locality of Wnt signaling dictates that stem cells exiting the Wnt signaling domain differentiate, spatially delimiting the niche in certain tissues. In some instances, stem cells may act as or generate their own niche, enabling the self-organization of patterned tissues. In this Review, we discuss the various ways by which Wnt operates in stem cell control and, in doing so, identify an integral program for tissue renewal and regeneration.
    Science (New York, N.Y.). 10/2014; 346(6205):1248012.
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    ABSTRACT: BET family proteins are novel therapeutic targets for cancer and inflammation and represent the first chromatin readers against which small-molecule inhibitors have been developed. First-generation BET inhibitors have shown therapeutic efficacy in preclinical models, but the consequences of sustained BET protein inhibition in normal tissues remain poorly characterized. Using an inducible and reversible transgenic RNAi mouse model, we show that strong suppression of the BET protein Brd4 in adult animals has dramatic effects in multiple tissues. Brd4-depleted mice display reversible epidermal hyperplasia, alopecia, and decreased cellular diversity and stem cell depletion in the small intestine. Furthermore, Brd4-suppressed intestines are sensitive to organ stress and show impaired regeneration following irradiation, suggesting that concurrent Brd4 suppression and certain cytotoxic therapies may induce undesirable synergistic effects. These findings provide important insight into Brd4 function in normal tissues and, importantly, predict several potential outcomes associated with potent and sustained BET protein inhibition.
    Cell reports. 09/2014;
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    ABSTRACT: The lack of in vitro prostate cancer models that recapitulate the diversity of human prostate cancer has hampered progress in understanding disease pathogenesis and therapy response. Using a 3D organoid system, we report success in long-term culture of prostate cancer from biopsy specimens and circulating tumor cells. The first seven fully characterized organoid lines recapitulate the molecular diversity of prostate cancer subtypes, including TMPRSS2-ERG fusion, SPOP mutation, SPINK1 overexpression, and CHD1 loss. Whole-exome sequencing shows a low mutational burden, consistent with genomics studies, but with mutations in FOXA1 and PIK3R1, as well as in DNA repair and chromatin modifier pathways that have been reported in advanced disease. Loss of p53 and RB tumor suppressor pathway function are the most common feature shared across the organoid lines. The methodology described here should enable the generation of a large repertoire of patient-derived prostate cancer lines amenable to genetic and pharmacologic studies.
    Cell. 09/2014;
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    ABSTRACT: The prostate gland consists of basal and luminal cells arranged as pseudostratified epithelium. In tissue recombination models, only basal cells reconstitute a complete prostate gland, yet murine lineage-tracing experiments show that luminal cells generate basal cells. It has remained challenging to address the molecular details of these transitions and whether they apply to humans, due to the lack of culture conditions that recapitulate prostate gland architecture. Here, we describe a 3D culture system that supports long-term expansion of primary mouse and human prostate organoids, composed of fully differentiated CK5+ basal and CK8+ luminal cells. Organoids are genetically stable, reconstitute prostate glands in recombination assays, and can be experimentally manipulated. Single human luminal and basal cells give rise to organoids, yet luminal-cell-derived organoids more closely resemble prostate glands. These data support a luminal multilineage progenitor cell model for prostate tissue and establish a robust, scalable system for mechanistic studies.
    Cell. 09/2014;
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    ABSTRACT: Background: Inflammatory bowel disease (IBD) is one of the most common chronic gastrointestinal diseases, but the underlying molecular mechanisms remain largely unknown. Studies of monogenic diseases can provide insight into the pathogenesis of IBD. Objective: We thought to determine the underlying molecular causes of IBD occurring in 2 unrelated families in association with an immune deficiency. Methods: We performed genetic linkage analysis and candidate gene sequencing on 13 patients from a large consanguineous family affected by early-onset IBD, progressive immune deficiency, and, in some cases, autoimmunity and alopecia, a condition we named enteropathy-lymphocytopenia-alopecia. The candidate gene was also sequenced in an unrelated patient with a similar phenotype. We performed histologic analysis of patients’ intestinal biopsy specimens and carried out functional assays on PBMCs. Gut organoids derived from a patient’s biopsy specimen were analyzed. Results: We identified biallelic missense mutations in tetratricopeptide repeat domain 7A (TTC7A) in all patients from both families. The resulting TTC7A depletion modified the proliferation, adhesion, and migratory capacities of lymphocytes through inappropriate activation of the RhoA signaling pathway. Normal function was restored by wild-type TTC7A expression or addition of a RhoA kinase inhibitor. The growth and polarity of gut epithelial organoids were also found to be dependent on the RhoA signaling pathway. Conclusions: We show that TTC7A regulates the actin cytoskeleton dynamics in lymphocytes through the RhoA signaling pathway and is required in both lymphocytes and epithelial cells for maintaining equilibrium between cell proliferation, migration, polarization, and cell death. Our study highlights variability in the phenotypic expression resulting from TTC7A deficiency and outlines that impairment of both epithelial cells and lymphocytes cooperatively causes IBD.
    Journal of Allergy and Clinical Immunology 08/2014; · 12.05 Impact Factor
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    ABSTRACT: The epithelium of the small intestine is the most rapidly self-renewing tissue in mammals. We previously demonstrated the existence of a long-lived pool of cycling stem cells defined by Lgr5 expression at the bottom of intestinal crypts. An Lgr5-eGFP-IRES-CreERT2 knockin allele has been instrumental in characterizing and profiling these cells, yet its low level expression and its silencing in patches of adjacent crypts have not allowed quantitative gene deletion. Olfactomedin-4 (Olfm4) has emerged from a gene signature of Lgr5 stem cells as a robust marker for murine small intestinal stem cells. We observe that Olfm4null animals show no phenotype and report the generation of an Olfm4-IRES-eGFPCreERT2 knockin mouse model that allows visualization and genetic manipulation of Lgr5+ stem cells in the epithelium of the small intestine. The eGFPCreERT2 fusion protein faithfully marks all stem cells in the small intestine and induces the activation of a conditional LacZ reporter with robust efficiency.
    Stem cell reports. 08/2014; 3(2).
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    ABSTRACT: Cycling Lgr5+ stem cells fuel the rapid turnover of the adult intestinal epithelium. The existence of quiescent Lgr5+ cells has been reported, while an alternative quiescent stem cell population is believed to reside at crypt position +4. Here, we generated a novel Ki67RFP knock-in allele that identifies dividing cells. Using Lgr5-GFP;Ki67RFP mice, we isolated crypt stem and progenitor cells with distinct Wnt signaling levels and cell cycle features and generated their molecular signature using microarrays. Stem cell potential of these populations was further characterized using the intestinal organoid culture. We found that Lgr5high stem cells are continuously in cell cycle, while a fraction of Lgr5low progenitors that reside predominantly at +4 position exit the cell cycle. Unlike fast dividing CBCs, Lgr5low Ki67− cells have lost their ability to initiate organoid cultures, are enriched in secretory differentiation factors, and resemble the Dll1 secretory precursors and the label-retaining cells of Winton and colleagues. Our findings support the cycling stem cell hypothesis and highlight the cell cycle heterogeneity of early progenitors during lineage commitment.
    The EMBO Journal 07/2014; · 9.82 Impact Factor
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    ABSTRACT: Paneth cells (PCs) are terminally differentiated, highly specialized secretory cells located at the base of the crypts of Lieberkühn in the small intestine. Besides their antimicrobial function, PCs serve as a component of the intestinal stem cell niche. By secreting granules containing bactericidal proteins like defensins/cryptdins and lysozyme, PCs regulate the microbiome of the gut. Here we study the control of PC degranulation in primary epithelial organoids in culture. We show that PC degranulation does not directly occur upon stimulation with microbial antigens or bacteria. In contrast, the pro-inflammatory cytokine Interferon gamma (IFN-γ) induces rapid and complete loss of granules. Using live cell imaging, we show that degranulation is coupled to luminal extrusion and death of PCs. Transfer of supernatants from in vitro stimulated iNKT cells recapitulates degranulation in an IFN-γ-dependent manner. Furthermore, endogenous IFN-γ secretion induced by anti-CD3 antibody injection causes Paneth loss and release of goblet cell mucus. The identification of IFN-γ as a trigger for degranulation and extrusion of PCs establishes a novel effector mechanism by which immune responses may regulate epithelial status and the gut microbiome.
    The Journal of experimental medicine. 06/2014; 211(7):1393-405.
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    ABSTRACT: The somatic mutations present in the genome of a cell accumulate over the lifetime of a multicellular organism. These mutations can provide insights into the developmental lineage tree, the number of divisions that each cell has undergone and the mutational processes that have been operative. Here we describe whole genomes of clonal lines derived from multiple tissues of healthy mice. Using somatic base substitutions, we reconstructed the early cell divisions of each animal, demonstrating the contributions of embryonic cells to adult tissues. Differences were observed between tissues in the numbers and types of mutations accumulated by each cell, which likely reflect differences in the number of cell divisions they have undergone and varying contributions of different mutational processes. If somatic mutation rates are similar to those in mice, the results indicate that precise insights into development and mutagenesis of normal human cells will be possible.
    Nature 06/2014; · 38.60 Impact Factor
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    ABSTRACT: Lgr5 is a marker for proliferating stem cells in adult intestine, stomach and hair follicle. However, Lgr5 is not expressed in adult hematopoietic stem and progenitor cells (HSPCs). Whether Lgr5 is expressed in the embryonic and fetal HSPCs that undergo rapid proliferation is unknown. Here we report the detection of Lgr5 expression in HSPCs in the aorta-gonad-mesonephros (AGM) and fetal liver. We also found that a portion of Lgr5(+) cells expressed Runx-1 genes that are critical for the ontogeny of HSPCs. A small portion of Lgr5(+) cells also expressed HSPC surface markers c-Kit and CD34 in AGM or CD41 in fetal liver. Furthermore, the majority of Lgr5(+) cells expressed Ki67, indicating their proliferating state. Transplantation of fetal liver-derived Lgr5-GFP(+) cells (E12.5) demonstrated that Lgr5-GFP(+) cells were able to reconstitute myeloid and lymphoid lineages in adult recipients, but the engraftment was short-term (4-8 weeks) and 20-fold lower compared to the Lgr5-GFP(-) control. Our data show that Lgr5-expressing cells mark short-term hematopoietic stem and progenitor cells, consistent with the role of Lgr5 in supporting HSPCs rapid proliferation during embryonic and fetal development.
    The Journal of biological chemistry. 06/2014;
  • Johan H van Es, Hans Clevers
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    ABSTRACT: Van Es and Clevers discuss the physiological and pathological roles of Paneth cells in the small intestine.
    Current biology : CB. 06/2014; 24(12):R547-8.
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    ABSTRACT: The apicobasal polarity of enterocytes determines where the brush border membrane (apical membrane) will form, but how this apical membrane faces the lumen is not well understood. The electrical signal across the epithelium could serve as a coordinating cue, orienting and polarizing enterocytes. Here we show that applying a physiological electric field (EF) to intestinal epithelial cells, to mimic the natural EF created by the transepithelial potential difference, directed phosphorylation of the actin-binding protein ezrin, increased expression of intestinal alkaline phosphatase (ALPI, a differentiation marker) and remodelled the actin cytoskeleton selectively on the cathode side. In addition, an applied EF also activated ERK1/2 and LKB1, key molecules in apical membrane formation. Disruption of the tyrosine-protein kinase transmembrane receptor Ror2 suppressed activation of ERK1/2 and LKB1 significantly and subsequently inhibited apical membrane formation in enterocytes. Our findings indicate that the endogenous EF created by the TEP may act as an essential coordinating signal for apical membrane formation at a tissue level, through activation of LKB1 mediated by Ror2/ERK signalling.
    Development 06/2014; · 6.21 Impact Factor
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    ABSTRACT: Genetically engineered human pluripotent stem cells (hPSCs) have been proposed as a source for transplantation therapies and are rapidly becoming valuable tools for human disease modeling. However, many applications are limited due to the lack of robust differentiation paradigms that allow for the isolation of defined functional tissues. Here, using an endogenous LGR5-GFP reporter, we derived adult stem cells from hPSCs that gave rise to functional human intestinal tissue comprising all major cell types of the intestine. Histological and functional analyses revealed that such human organoid cultures could be derived with high purity and with a composition and morphology similar to those of cultures obtained from human biopsies. Importantly, hPSC-derived organoids responded to the canonical signaling pathways that control self-renewal and differentiation in the adult human intestinal stem cell compartment. This adult stem cell system provides a platform for studying human intestinal disease in vitro using genetically engineered hPSCs.
    Stem cell reports. 06/2014; 2(6):838-52.
  • Bon-Kyoung Koo, Hans Clevers
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    ABSTRACT: Since the discovery of LGR5 as a marker for intestinal stem cells, the field has developed explosively and has led to many new avenues of research. The inner workings of the intestinal crypt stem cell niche are now well understood. The study of stem cell-enriched genes has uncovered some previously unknown aspects of the Wnt signaling pathway, the major driver of crypt dynamics. LGR5+ stem cells can now be cultured over long periods of time in vitro as epithelial organoids, or 'mini-guts'. This technology opens new possibilities of using cultured adult stem cells for drug development, disease modeling, gene therapy and regenerative medicine. This review describes the re-discovery of crypt base columnar cells as LGR5+ adult stem cell and summarizes subsequent progress, promises, unresolved issues and challenges of the field.
    Gastroenterology 05/2014; · 12.82 Impact Factor
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    ABSTRACT: Gastric cancer is a heterogeneous disease with diverse molecular and histological subtypes. We performed whole-genome sequencing in 100 tumor-normal pairs, along with DNA copy number, gene expression and methylation profiling, for integrative genomic analysis. We found subtype-specific genetic and epigenetic perturbations and unique mutational signatures. We identified previously known (TP53, ARID1A and CDH1) and new (MUC6, CTNNA2, GLI3, RNF43 and others) significantly mutated driver genes. Specifically, we found RHOA mutations in 14.3% of diffuse-type tumors but not in intestinal-type tumors (P < 0.001). The mutations clustered in recurrent hotspots affecting functional domains and caused defective RHOA signaling, promoting escape from anoikis in organoid cultures. The top perturbed pathways in gastric cancer included adherens junction and focal adhesion, in which RHOA and other mutated genes we identified participate as key players. These findings illustrate a multidimensional and comprehensive genomic landscape that highlights the molecular complexity of gastric cancer and provides a road map to facilitate genome-guided personalized therapy.
    Nature Genetics 05/2014; · 35.21 Impact Factor
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    ABSTRACT: Increasing knowledge concerning signal transduction pathways as drivers of cancer growth has elicited the development of 'targeted drugs' which inhibit aberrant signaling pathways. They require a companion diagnostic test which identifies the tumor-driving pathway, however, currently available tests like ER protein expression for hormonal treatment of breast cancer, do not reliably predict therapy response, at least in part because they do not adequately assess functional pathway activity. We describe a novel approach to predict signaling pathway activity, based on knowledge-based Bayesian computational models, which interpret quantitative transcriptome data as the functional output of an active signaling pathway, by using expression levels of transcriptional target genes. Following calibration on only a small number of cell lines or cohorts of patient data, they provide a reliable assessment of signaling pathway activity in tumors of different tissue origin. As proof of principle, models for the canonical Wnt and ER (estrogen receptor) pathways are presented, including initial clinical validation on independent datasets from various cancer types. Free full text available at http://cancerres.aacrjournals.org/content/74/11/2936.long
    Cancer Research 04/2014; · 9.28 Impact Factor
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    ABSTRACT: Enhancers control the correct temporal and cell-type-specific activation of gene expression in multicellular eukaryotes. Knowing their properties, regulatory activity and targets is crucial to understand the regulation of differentiation and homeostasis. Here we use the FANTOM5 panel of samples, covering the majority of human tissues and cell types, to produce an atlas of active, in vivo-transcribed enhancers. We show that enhancers share properties with CpG-poor messenger RNA promoters but produce bidirectional, exosome-sensitive, relatively short unspliced RNAs, the generation of which is strongly related to enhancer activity. The atlas is used to compare regulatory programs between different cells at unprecedented depth, to identify disease-associated regulatory single nucleotide polymorphisms, and to classify cell-type-specific and ubiquitous enhancers. We further explore the utility of enhancer redundancy, which explains gene expression strength rather than expression patterns. The online FANTOM5 enhancer atlas represents a unique resource for studies on cell-type-specific enhancers and gene regulation.
    Nature 03/2014; 507(7493):455-61. · 38.60 Impact Factor

Publication Stats

30k Citations
4,590.87 Total Impact Points

Top Journals

Institutions

  • 2014
    • Tsinghua University
      Peping, Beijing, China
  • 2007–2014
    • Hubrecht Institute
      Utrecht, Utrecht, Netherlands
  • 1999–2014
    • Utrecht University
      • • Division of Biomolecular Mass Spectrometry and Proteomics
      • • Division of Immunology
      Utrecht, Utrecht, Netherlands
  • 1991–2014
    • University Medical Center Utrecht
      • • Department of Pathology
      • • Department of Physiological Chemistry
      • • Department of Immunology
      • • Department of Hematology
      Utrecht, Utrecht, Netherlands
    • VU University Amsterdam
      • Department of Pathology
      Amsterdam, North Holland, Netherlands
  • 2013
    • Keio University
      • School of Medicine
      Tokyo, Tokyo-to, Japan
  • 2004–2013
    • Koninklijke Nederlandse Akademie van Wetenschappen
      Amsterdamo, North Holland, Netherlands
    • Parc de recerca biomedica de barcelona
      Barcino, Catalonia, Spain
  • 2012
    • University of Texas Southwestern Medical Center
      • Department of Cell Biology
      Dallas, TX, United States
  • 2002–2012
    • Netherlands Institute for Space Research, Utrecht
      Utrecht, Utrecht, Netherlands
    • Howard Hughes Medical Institute
      Ashburn, Virginia, United States
    • The University of Edinburgh
      • School of Biomedical Sciences
      Edinburgh, SCT, United Kingdom
  • 1998–2012
    • Leiden University Medical Centre
      • • Department of Immunhematology and Blood Transfusion
      • • Department of Pediatrics
      Leiden, South Holland, Netherlands
  • 2011
    • IRB Barcelona Institute for Research in Biomedicine
      Barcino, Catalonia, Spain
    • University of Cambridge
      • Department of Physics: Cavendish Laboratory
      Cambridge, ENG, United Kingdom
  • 2010
    • Stowers Institute for Medical Research
      Kansas City, Kansas, United States
    • Simon Fraser University
      • Department of Molecular Biology and Biochemistry
      Burnaby, British Columbia, Canada
  • 2007–2010
    • Beatson Institute for Cancer Research
      Glasgow, Scotland, United Kingdom
  • 2006
    • Hogeschool Arnhem and Nijmegen
      Arnheim, Gelderland, Netherlands
  • 2005–2006
    • Cardiff University
      • School of Biosciences
      Cardiff, Wales, United Kingdom
    • Duke University Medical Center
      • Department of Pharmacology and Cancer Biology
      Durham, NC, United States
    • Erasmus MC
      • Department of Immunology
      Rotterdam, South Holland, Netherlands
  • 1996–2005
    • University of Lausanne
      • Department of Biochemistry
      Lausanne, Vaud, Switzerland
  • 2001–2003
    • Erasmus Universiteit Rotterdam
      • Department of Immunology
      Rotterdam, South Holland, Netherlands
  • 1989
    • Netherlands Cancer Institute
      • Division of Immunology
      Amsterdamo, North Holland, Netherlands
  • 1988
    • Dana-Farber Cancer Institute
      Boston, Massachusetts, United States