1
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Moos F, Suppinger S, de Medeiros G, Oost KC, Boni A, Rémy C, Weevers SL, Tsiairis C, Strnad P, Liberali P. Open-top multisample dual-view light-sheet microscope for live imaging of large multicellular systems. Nat Methods 2024; 21:798-803. [PMID: 38509326 PMCID: PMC11093739 DOI: 10.1038/s41592-024-02213-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 02/15/2024] [Indexed: 03/22/2024]
Abstract
Multicellular systems grow over the course of weeks from single cells to tissues or even full organisms, making live imaging challenging. To bridge spatiotemporal scales, we present an open-top dual-view and dual-illumination light-sheet microscope dedicated to live imaging of large specimens at single-cell resolution. The configuration of objectives together with a customizable multiwell mounting system combines dual view with high-throughput multiposition imaging. We use this microscope to image a wide variety of samples and highlight its capabilities to gain quantitative single-cell information in large specimens such as mature intestinal organoids and gastruloids.
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Affiliation(s)
- Franziska Moos
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Simon Suppinger
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Gustavo de Medeiros
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- Viventis Microscopy Sàrl, Lausanne, Switzerland
| | | | - Andrea Boni
- Viventis Microscopy Sàrl, Lausanne, Switzerland
| | | | - Sera Lotte Weevers
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Charisios Tsiairis
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Petr Strnad
- Viventis Microscopy Sàrl, Lausanne, Switzerland.
| | - Prisca Liberali
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.
- University of Basel, Basel, Switzerland.
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2
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Daly AC, Cambuli F, Äijö T, Lötstedt B, Marjanovic N, Kuksenko O, Smith-Erb M, Fernandez S, Domovic D, Van Wittenberghe N, Drokhlyansky E, Griffin GK, Phatnani H, Bonneau R, Regev A, Vickovic S. Tissue and cellular spatiotemporal dynamics in colon aging. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.22.590125. [PMID: 38712088 PMCID: PMC11071407 DOI: 10.1101/2024.04.22.590125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Tissue structure and molecular circuitry in the colon can be profoundly impacted by systemic age-related effects, but many of the underlying molecular cues remain unclear. Here, we built a cellular and spatial atlas of the colon across three anatomical regions and 11 age groups, encompassing ~1,500 mouse gut tissues profiled by spatial transcriptomics and ~400,000 single nucleus RNA-seq profiles. We developed a new computational framework, cSplotch, which learns a hierarchical Bayesian model of spatially resolved cellular expression associated with age, tissue region, and sex, by leveraging histological features to share information across tissue samples and data modalities. Using this model, we identified cellular and molecular gradients along the adult colonic tract and across the main crypt axis, and multicellular programs associated with aging in the large intestine. Our multi-modal framework for the investigation of cell and tissue organization can aid in the understanding of cellular roles in tissue-level pathology.
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Affiliation(s)
- Aidan C. Daly
- New York Genome Center, New York, NY, USA
- Center for Computational Biology, Flatiron Institute, New York, NY, USA
| | | | - Tarmo Äijö
- Center for Computational Biology, Flatiron Institute, New York, NY, USA
| | - Britta Lötstedt
- New York Genome Center, New York, NY, USA
- Klarman Cell Observatory Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Nemanja Marjanovic
- Klarman Cell Observatory Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Olena Kuksenko
- Klarman Cell Observatory Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA
| | | | | | | | | | - Eugene Drokhlyansky
- Klarman Cell Observatory Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Gabriel K Griffin
- Klarman Cell Observatory Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, USA
| | - Hemali Phatnani
- New York Genome Center, New York, NY, USA
- Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA
| | - Richard Bonneau
- Center for Computational Biology, Flatiron Institute, New York, NY, USA
- Center for Data Science, New York University, New York, NY, USA
- Current address: Genentech, 1 DNA Way, South San Francisco, CA, USA
| | - Aviv Regev
- Klarman Cell Observatory Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Current address: Genentech, 1 DNA Way, South San Francisco, CA, USA
| | - Sanja Vickovic
- New York Genome Center, New York, NY, USA
- Klarman Cell Observatory Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biomedical Engineering and Herbert Irving Institute for Cancer Dynamics, Columbia University, New York, NY, USA
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Beijer Laboratory for Gene and Neuro Research, Uppsala University, Uppsala, Sweden
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3
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Mzoughi S, Schwarz M, Wang X, Demircioglu D, Ulukaya G, Mohammed K, Tullio FD, Company C, Dramaretska Y, Leushacke M, Giotti B, Lannagan T, Lozano-Ojalvo D, Hasson D, Tsankov AM, Sansom OJ, Marine JC, Barker N, Gargiulo G, Guccione E. A Mutation-driven oncofetal regression fuels phenotypic plasticity in colorectal cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.10.570854. [PMID: 38106050 PMCID: PMC10723414 DOI: 10.1101/2023.12.10.570854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Targeting cancer stem cells (CSCs) is crucial for effective cancer treatment 1 . However, the molecular mechanisms underlying resistance to LGR5 + CSCs depletion in colorectal cancer (CRC) 2,3 remain largely elusive. Here, we unveil the existence of a primitive cell state dubbed the oncofetal (OnF) state, which works in tandem with the LGR5 + stem cells (SCs) to fuel tumor evolution in CRC. OnF cells emerge early during intestinal tumorigenesis and exhibit features of lineage plasticity. Normally suppressed by the Retinoid X Receptor (RXR) in mature SCs, the OnF program is triggered by genetic deletion of the gatekeeper APC. We demonstrate that diminished RXR activity unlocks an epigenetic circuity governed by the cooperative action of YAP and AP1, leading to OnF reprogramming. This high-plasticity state is inherently resistant to conventional chemotherapies and its adoption by LGR5 + CSCs enables them to enter a drug-tolerant state. Furthermore, through phenotypic tracing and ablation experiments, we uncover a functional redundancy between the OnF and stem cell (SC) states and show that targeting both cellular states is essential for sustained tumor regression in vivo . Collectively, these findings establish a mechanistic foundation for developing effective combination therapies with enduring impact on CRC treatment.
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4
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Fischer AD, Veronese Paniagua DA, Swaminathan S, Kashima H, Rubin DC, Madison BB. The oncogenic function of PLAGL2 is mediated via ASCL2 and IGF2 and a Wnt-independent mechanism in colorectal cancer. Am J Physiol Gastrointest Liver Physiol 2023; 325:G196-G211. [PMID: 37310750 PMCID: PMC10396286 DOI: 10.1152/ajpgi.00058.2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 06/05/2023] [Accepted: 06/06/2023] [Indexed: 06/14/2023]
Abstract
Colorectal cancer (CRC) tumorigenesis and progression are linked to common oncogenic mutations, especially in the tumor suppressor APC, whose loss triggers the deregulation of TCF4/β-Catenin activity. CRC tumorigenesis is also driven by multiple epimutational modifiers such as transcriptional regulators. We describe the common (and near-universal) activation of the zinc finger transcription factor and Let-7 target PLAGL2 in CRC and find that it is a key driver of intestinal epithelial transformation. PLAGL2 drives proliferation, cell cycle progression, and anchorage-independent growth in CRC cell lines and nontransformed intestinal cells. Investigating effects of PLAGL2 on downstream pathways revealed very modest effects on canonical Wnt signaling. Alternatively, we find pronounced effects on the direct PLAGL2 target genes IGF2, a fetal growth factor, and ASCL2, an intestinal stem cell-specific bHLH transcription factor. Inactivation of PLAGL2 in CRC cell lines has pronounced effects on ASCL2 reporter activity. Furthermore, ASCL2 expression can partially rescue deficits of proliferation and cell cycle progression caused by depletion of PLAGL2 in CRC cell lines. Thus, the oncogenic effects of PLAGL2 appear to be mediated via core stem cell and onco-fetal pathways, with minimal effects on downstream Wnt signaling.NEW & NOTEWORTHY A Let-7 target called PLAGL2 drives oncogenic transformation via Wnt-independent pathways. This work illustrates the robust effects of this zinc finger transcription factor in colorectal cancer (CRC) cell lines and nontransformed intestinal epithelium, with effects mediated, in part, via the direct target genes ASCL2 and IGF2. This has implications for the role of PLAGL2 in activation of onco-fetal and onco-stem cell pathways, contributing to immature and highly proliferative phenotypes in CRC.
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Affiliation(s)
- Anthony D Fischer
- Department of Genetics, Washington University School of Medicine, Saint Louis, Missouri, United States
| | - Daniel A Veronese Paniagua
- Washington University School of Medicine, Saint Louis, Missouri, United States
- Division of Endocrinology, Metabolism and Lipid Research, Department of Medicine, Washington University School of Medicine, United States
| | - Shriya Swaminathan
- Washington University School of Medicine, Saint Louis, Missouri, United States
| | - Hajime Kashima
- Division of Gastroenterology, Department of Medicine, Washington University School of Medicine, Saint Louis, Missouri, United States
| | - Deborah C Rubin
- Division of Gastroenterology, Department of Medicine, Washington University School of Medicine, Saint Louis, Missouri, United States
| | - Blair B Madison
- Division of Gastroenterology, Department of Medicine, Washington University School of Medicine, Saint Louis, Missouri, United States
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5
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Betge J, Jackstadt R. From organoids to bedside: Advances in modeling, decoding and targeting of colorectal cancer. Int J Cancer 2023; 152:1304-1313. [PMID: 36121667 DOI: 10.1002/ijc.34297] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 08/25/2022] [Accepted: 09/13/2022] [Indexed: 02/03/2023]
Abstract
Patient derived organoids closely resemble the biology of tissues and tumors. They are enabling ex vivo modeling of human diseases and dissecting key features of tumor biology like anatomical diversity or inter- and intra-tumoral heterogeneity. In the last years, organoids were established as models for drug discovery and explored to guide clinical decision making. In this review, we discuss the recent developments in organoid based research, elaborating on the developments in colorectal cancer as a prime example. We focus our review on the role of organoids to decode cancer cell dynamics and tumor microenvironmental complexity with the underlying bi-directional crosstalk. Additionally, advancements in the development of living biobanks, screening approaches, organoid based precision medicine and challenges of co-clinical trials are highlighted. We discuss ongoing efforts to overcome challenges that the field faces and indicate potential future directions.
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Affiliation(s)
- Johannes Betge
- Junior Clinical Cooperation Unit Translational Gastrointestinal Oncology and Preclinical Models, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Medicine II, University Medical Center Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany.,DKFZ-Hector Cancer Institute at University Medical Center Mannheim, Mannheim, Germany
| | - Rene Jackstadt
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany.,Cancer Progression and Metastasis Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
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6
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Dijkstra J, Neikes HK, Rezaeifard S, Ma X, Voest EE, Tauriello DVF, Vermeulen M. Multiomics of Colorectal Cancer Organoids Reveals Putative Mediators of Cancer Progression Resulting from SMAD4 Inactivation. J Proteome Res 2023; 22:138-151. [PMID: 36450103 PMCID: PMC9830641 DOI: 10.1021/acs.jproteome.2c00551] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
The development of metastasis severely reduces the life expectancy of patients with colorectal cancer (CRC). Although loss of SMAD4 is a key event in CRC progression, the resulting changes in biological processes in advanced disease and metastasis are not fully understood. Here, we applied a multiomics approach to a CRC organoid model that faithfully reflects the metastasis-supporting effects of SMAD4 inactivation. We show that loss of SMAD4 results in decreased differentiation and activation of pro-migratory and cell proliferation processes, which is accompanied by the disruption of several key oncogenic pathways, including the TGFβ, WNT, and VEGF pathways. In addition, SMAD4 inactivation leads to increased secretion of proteins that are known to be involved in a variety of pro-metastatic processes. Finally, we show that one of the factors that is specifically secreted by SMAD4-mutant organoids─DKK3─reduces the antitumor effects of natural killer cells (NK cells). Altogether, our data provide new insights into the role of SMAD4 perturbation in advanced CRC.
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Affiliation(s)
- Jelmer
J. Dijkstra
- Department
of Molecular Biology, Faculty of Science, Radboud Institute for Molecular
Life Sciences (RIMLS), Oncode Institute, Radboud University Nijmegen, Geert Grooteplein 26−28, 6525
GA Nijmegen, The
Netherlands
| | - Hannah K. Neikes
- Department
of Molecular Biology, Faculty of Science, Radboud Institute for Molecular
Life Sciences (RIMLS), Oncode Institute, Radboud University Nijmegen, Geert Grooteplein 26−28, 6525
GA Nijmegen, The
Netherlands
| | - Somayeh Rezaeifard
- Department
of Cell Biology, Radboud University Medical Center/Radboud Institute
for Molecular Life Sciences (RIMLS), Radboud
University Nijmegen, Geert Grooteplein 26−28, 6525
GA Nijmegen, The
Netherlands
| | - Xuhui Ma
- Department
of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Antoni van Leeuwenhoek
Hospital, 1066 CX Amsterdam, The Netherlands
| | - Emile E. Voest
- Department
of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Antoni van Leeuwenhoek
Hospital, 1066 CX Amsterdam, The Netherlands
| | - Daniele V. F. Tauriello
- Department
of Cell Biology, Radboud University Medical Center/Radboud Institute
for Molecular Life Sciences (RIMLS), Radboud
University Nijmegen, Geert Grooteplein 26−28, 6525
GA Nijmegen, The
Netherlands
| | - Michiel Vermeulen
- Department
of Molecular Biology, Faculty of Science, Radboud Institute for Molecular
Life Sciences (RIMLS), Oncode Institute, Radboud University Nijmegen, Geert Grooteplein 26−28, 6525
GA Nijmegen, The
Netherlands,
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7
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Ludikhuize MC, Gevers S, Nguyen NTB, Meerlo M, Roudbari SKS, Gulersonmez MC, Stigter ECA, Drost J, Clevers H, Burgering BMT, Rodríguez Colman MJ. Rewiring glucose metabolism improves 5-FU efficacy in p53-deficient/KRAS G12D glycolytic colorectal tumors. Commun Biol 2022; 5:1159. [PMID: 36316440 PMCID: PMC9622833 DOI: 10.1038/s42003-022-04055-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 09/30/2022] [Indexed: 11/29/2022] Open
Abstract
Despite the fact that 5-fluorouracil (5-FU) is the backbone for chemotherapy in colorectal cancer (CRC), the response rates in patients is limited to 50%. The mechanisms underlying 5-FU toxicity are debated, limiting the development of strategies to improve its efficacy. How fundamental aspects of cancer, such as driver mutations and phenotypic heterogeneity, relate to the 5-FU response remains obscure. This largely relies on the limited number of studies performed in pre-clinical models able to recapitulate the key features of CRC. Here, we analyzed the 5-FU response in patient-derived organoids that reproduce the different stages of CRC. We find that 5-FU induces pyrimidine imbalance, which leads to DNA damage and cell death in the actively proliferating cancer cells deficient in p53. Importantly, p53-deficiency leads to cell death due to impaired cell cycle arrest. Moreover, we find that targeting the Warburg effect in KRASG12D glycolytic tumor organoids enhances 5-FU toxicity by further altering the nucleotide pool and, importantly, without affecting non-transformed WT cells. Thus, p53 emerges as an important factor in determining the 5-FU response, and targeting cancer metabolism in combination with replication stress-inducing chemotherapies emerges as a promising strategy for CRC treatment. In p53-deficient colorectal cancer organoids, 5-fluorouracil induces pyrimidine imbalance, which causes DNA damage and cell death. Rewiring glucose metabolism through PDK inhibition by DCA enhances 5-FU toxicity in glycolytic p53-deficient organoids.
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Affiliation(s)
- Marlies C. Ludikhuize
- grid.7692.a0000000090126352Molecular Cancer Research, Center for Molecular Medicine, University Medical Center Utrecht, 3584 CG Utrecht, the Netherlands
| | - Sira Gevers
- grid.7692.a0000000090126352Molecular Cancer Research, Center for Molecular Medicine, University Medical Center Utrecht, 3584 CG Utrecht, the Netherlands
| | - Nguyen T. B. Nguyen
- grid.7692.a0000000090126352Molecular Cancer Research, Center for Molecular Medicine, University Medical Center Utrecht, 3584 CG Utrecht, the Netherlands
| | - Maaike Meerlo
- grid.7692.a0000000090126352Molecular Cancer Research, Center for Molecular Medicine, University Medical Center Utrecht, 3584 CG Utrecht, the Netherlands
| | - S. Khadijeh Shafiei Roudbari
- grid.7692.a0000000090126352Molecular Cancer Research, Center for Molecular Medicine, University Medical Center Utrecht, 3584 CG Utrecht, the Netherlands
| | - M. Can Gulersonmez
- grid.7692.a0000000090126352Molecular Cancer Research, Center for Molecular Medicine, University Medical Center Utrecht, 3584 CG Utrecht, the Netherlands
| | - Edwin C. A. Stigter
- grid.7692.a0000000090126352Molecular Cancer Research, Center for Molecular Medicine, University Medical Center Utrecht, 3584 CG Utrecht, the Netherlands
| | - Jarno Drost
- grid.487647.ePrincess Máxima Center for Pediatric Oncology, 3584 CS Utrecht, The Netherlands ,grid.499559.dOncode Institute, Utrecht, The Netherlands
| | - Hans Clevers
- grid.487647.ePrincess Máxima Center for Pediatric Oncology, 3584 CS Utrecht, The Netherlands ,grid.499559.dOncode Institute, Utrecht, The Netherlands ,grid.418101.d0000 0001 2153 6865Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences, 3584 CT Utrecht, The Netherlands
| | - Boudewijn M. T. Burgering
- grid.7692.a0000000090126352Molecular Cancer Research, Center for Molecular Medicine, University Medical Center Utrecht, 3584 CG Utrecht, the Netherlands ,grid.418101.d0000 0001 2153 6865Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences, 3584 CT Utrecht, The Netherlands
| | - Maria J. Rodríguez Colman
- grid.7692.a0000000090126352Molecular Cancer Research, Center for Molecular Medicine, University Medical Center Utrecht, 3584 CG Utrecht, the Netherlands
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8
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Heinz MC, Peters NA, Oost KC, Lindeboom RG, van Voorthuijsen L, Fumagalli A, van der Net MC, de Medeiros G, Hageman JH, Verlaan-Klink I, Borel Rinkes IH, Liberali P, Gloerich M, van Rheenen J, Vermeulen M, Kranenburg O, Snippert HJ. Liver Colonization by Colorectal Cancer Metastases Requires YAP-Controlled Plasticity at the Micrometastatic Stage. Cancer Res 2022; 82:1953-1968. [PMID: 35570706 PMCID: PMC9381095 DOI: 10.1158/0008-5472.can-21-0933] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 12/02/2021] [Accepted: 02/18/2022] [Indexed: 01/07/2023]
Abstract
Micrometastases of colorectal cancer can remain dormant for years prior to the formation of actively growing, clinically detectable lesions (i.e., colonization). A better understanding of this step in the metastatic cascade could help improve metastasis prevention and treatment. Here we analyzed liver specimens of patients with colorectal cancer and monitored real-time metastasis formation in mouse livers using intravital microscopy to reveal that micrometastatic lesions are devoid of cancer stem cells (CSC). However, lesions that grow into overt metastases demonstrated appearance of de novo CSCs through cellular plasticity at a multicellular stage. Clonal outgrowth of patient-derived colorectal cancer organoids phenocopied the cellular and transcriptomic changes observed during in vivo metastasis formation. First, formation of mature CSCs occurred at a multicellular stage and promoted growth. Conversely, failure of immature CSCs to generate more differentiated cells arrested growth, implying that cellular heterogeneity is required for continuous growth. Second, early-stage YAP activity was required for the survival of organoid-forming cells. However, subsequent attenuation of early-stage YAP activity was essential to allow for the formation of cell type heterogeneity, while persistent YAP signaling locked micro-organoids in a cellularly homogenous and growth-stalled state. Analysis of metastasis formation in mouse livers using single-cell RNA sequencing confirmed the transient presence of early-stage YAP activity, followed by emergence of CSC and non-CSC phenotypes, irrespective of the initial phenotype of the metastatic cell of origin. Thus, establishment of cellular heterogeneity after an initial YAP-controlled outgrowth phase marks the transition to continuously growing macrometastases. SIGNIFICANCE Characterization of the cell type dynamics, composition, and transcriptome of early colorectal cancer liver metastases reveals that failure to establish cellular heterogeneity through YAP-controlled epithelial self-organization prohibits the outgrowth of micrometastases. See related commentary by LeBleu, p. 1870.
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Affiliation(s)
- Maria C. Heinz
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, the Netherlands.,Oncode Institute, the Netherlands
| | - Niek A. Peters
- Division of Imaging and Cancer, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Koen C. Oost
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, the Netherlands.,Oncode Institute, the Netherlands
| | - Rik G.H. Lindeboom
- Oncode Institute, the Netherlands.,Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Lisa van Voorthuijsen
- Oncode Institute, the Netherlands.,Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Arianna Fumagalli
- Oncode Institute, the Netherlands.,Department of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Mirjam C. van der Net
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Gustavo de Medeiros
- Quantitative Biology, Friedrich Miescher Institute for Biomedical Research (FMI), Basel, Switzerland
| | - Joris H. Hageman
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, the Netherlands.,Oncode Institute, the Netherlands
| | - Ingrid Verlaan-Klink
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, the Netherlands.,Oncode Institute, the Netherlands
| | | | - Prisca Liberali
- Quantitative Biology, Friedrich Miescher Institute for Biomedical Research (FMI), Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Martijn Gloerich
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Jacco van Rheenen
- Oncode Institute, the Netherlands.,Department of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Michiel Vermeulen
- Oncode Institute, the Netherlands.,Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Onno Kranenburg
- Division of Imaging and Cancer, University Medical Center Utrecht, Utrecht, the Netherlands.,Corresponding Authors: Onno Kranenburg, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, the Netherlands. Phone: 318-8755-9632; E-mail: ; and Hugo J.G. Snippert, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, the Netherlands. Phone: 318-8756-8959; E-mail:
| | - Hugo J.G. Snippert
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, the Netherlands.,Oncode Institute, the Netherlands.,Corresponding Authors: Onno Kranenburg, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, the Netherlands. Phone: 318-8755-9632; E-mail: ; and Hugo J.G. Snippert, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, the Netherlands. Phone: 318-8756-8959; E-mail:
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9
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Wester RA, van Voorthuijsen L, Neikes HK, Dijkstra JJ, Lamers LA, Frölich S, van der Sande M, Logie C, Lindeboom RG, Vermeulen M. Retinoic acid signaling drives differentiation toward the absorptive lineage in colorectal cancer. iScience 2021; 24:103444. [PMID: 34877501 PMCID: PMC8633980 DOI: 10.1016/j.isci.2021.103444] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 08/18/2021] [Accepted: 11/11/2021] [Indexed: 01/15/2023] Open
Abstract
Retinoic acid (RA) signaling is an important and conserved pathway that regulates cellular proliferation and differentiation. Furthermore, perturbed RA signaling is implicated in cancer initiation and progression. However, the mechanisms by which RA signaling contributes to homeostasis, malignant transformation, and disease progression in the intestine remain incompletely understood. Here, we report, in agreement with previous findings, that activation of the Retinoic Acid Receptor and the Retinoid X Receptor results in enhanced transcription of enterocyte-specific genes in mouse small intestinal organoids. Conversely, inhibition of this pathway results in reduced expression of genes associated with the absorptive lineage. Strikingly, this latter effect is conserved in a human organoid model for colorectal cancer (CRC) progression. We further show that RXR motif accessibility depends on progression state of CRC organoids. Finally, we show that reduced RXR target gene expression correlates with worse CRC prognosis, implying RA signaling as a putative therapeutic target in CRC. RA signaling contributes to enterocyte differentiation in murine intestinal organoids Inhibition of RXR decreases enterocyte gene expression in colon cancer organoids Accessibility of RXR motifs correlates with RXRi susceptibility High expression of RA signaling targets correlates with higher CRC patient survival
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Affiliation(s)
- Roelof A. Wester
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences (RIMLS), Oncode Institute, Radboud University Nijmegen, 6525GA Nijmegen, the Netherlands
| | - Lisa van Voorthuijsen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences (RIMLS), Oncode Institute, Radboud University Nijmegen, 6525GA Nijmegen, the Netherlands
| | - Hannah K. Neikes
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences (RIMLS), Oncode Institute, Radboud University Nijmegen, 6525GA Nijmegen, the Netherlands
| | - Jelmer J. Dijkstra
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences (RIMLS), Oncode Institute, Radboud University Nijmegen, 6525GA Nijmegen, the Netherlands
| | - Lieke A. Lamers
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences (RIMLS), Oncode Institute, Radboud University Nijmegen, 6525GA Nijmegen, the Netherlands
| | - Siebren Frölich
- Department of Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Nijmegen, 6525GA Nijmegen, the Netherlands
| | - Maarten van der Sande
- Department of Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Nijmegen, 6525GA Nijmegen, the Netherlands
| | - Colin Logie
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences (RIMLS), Oncode Institute, Radboud University Nijmegen, 6525GA Nijmegen, the Netherlands
| | - Rik G.H. Lindeboom
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences (RIMLS), Oncode Institute, Radboud University Nijmegen, 6525GA Nijmegen, the Netherlands
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
- Corresponding author
| | - Michiel Vermeulen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences (RIMLS), Oncode Institute, Radboud University Nijmegen, 6525GA Nijmegen, the Netherlands
- Corresponding author
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10
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Yi SA, Zhang Y, Rathnam C, Pongkulapa T, Lee KB. Bioengineering Approaches for the Advanced Organoid Research. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2021; 33:e2007949. [PMID: 34561899 PMCID: PMC8682947 DOI: 10.1002/adma.202007949] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 06/09/2021] [Indexed: 05/09/2023]
Abstract
Recent advances in 3D cell culture technology have enabled scientists to generate stem cell derived organoids that recapitulate the structural and functional characteristics of native organs. Current organoid technologies have been striding toward identifying the essential factors for controlling the processes involved in organoid development, including physical cues and biochemical signaling. There is a growing demand for engineering dynamic niches characterized by conditions that resemble in vivo organogenesis to generate reproducible and reliable organoids for various applications. Innovative biomaterial-based and advanced engineering-based approaches have been incorporated into conventional organoid culture methods to facilitate the development of organoid research. The recent advances in organoid engineering, including extracellular matrices and genetic modulation, are comprehensively summarized to pinpoint the parameters critical for organ-specific patterning. Moreover, perspective trends in developing tunable organoids in response to exogenous and endogenous cues are discussed for next-generation developmental studies, disease modeling, and therapeutics.
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Affiliation(s)
- Sang Ah Yi
- Epigenome Dynamics Control Research Center, School of Pharmacy, Sungkyunkwan University, 2066 Seobu-ro, Jangan-gu, Suwon, 16419, Republic of Korea
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 123 Bevier Road, Piscataway, NJ, 08854, USA
| | - Yixiao Zhang
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 123 Bevier Road, Piscataway, NJ, 08854, USA
| | - Christopher Rathnam
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 123 Bevier Road, Piscataway, NJ, 08854, USA
| | - Thanapat Pongkulapa
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 123 Bevier Road, Piscataway, NJ, 08854, USA
| | - Ki-Bum Lee
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 123 Bevier Road, Piscataway, NJ, 08854, USA
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11
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Strategies for genetic manipulation of adult stem cell-derived organoids. Exp Mol Med 2021; 53:1483-1494. [PMID: 34663937 PMCID: PMC8569115 DOI: 10.1038/s12276-021-00609-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 02/21/2021] [Accepted: 03/05/2021] [Indexed: 01/08/2023] Open
Abstract
Organoid technology allows the expansion of primary epithelial cells from normal and diseased tissues, providing a unique model for human (patho)biology. In a three-dimensional environment, adult stem cells self-organize and differentiate to gain tissue-specific features. Accessibility to genetic manipulation enables the investigation of the molecular mechanisms underlying cell fate regulation, cell differentiation and cell interactions. In recent years, powerful methodologies using lentiviral transgenesis, CRISPR/Cas9 gene editing, and single-cell readouts have been developed to study gene function and carry out genetic screens in organoids. However, the multicellularity and dynamic nature of stem cell-derived organoids also present challenges for genetic experimentation. In this review, we focus on adult gastrointestinal organoids and summarize the state-of-the-art protocols for successful transgenesis. We provide an outlook on emerging genetic techniques that could further increase the applicability of organoids and enhance the potential of organoid-based techniques to deepen our understanding of gene function in tissue biology.
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12
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Radajewska A, Przybyszewski O, Emhemmed F, Muller CD, Barg E, Moreira H. Three dimensional in vitro culture systems in anticancer drug discovery targeted on cancer stem cells. Am J Cancer Res 2021; 11:4931-4946. [PMID: 34765301 PMCID: PMC8569359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 07/28/2021] [Indexed: 06/13/2023] Open
Abstract
Worldwide, tumors are one of the most common causes of death. Every year 3.7 million new cases occur in Europe and more than 1.9 million patients die (WHO data). Most of the fields of research are focused on developing new therapeutic strategies that will be effective in eliminating the tumor, preventing its remission, and avoiding or reducing the side effects of therapy. In the past, generally classical 2D cell cultures or immunodeficient animal models had been used to cultivate and test drugs on human cancer cell lines. Nowadays, there are increasing interests in three-dimensional (3D) cell cultures, a method with significant differences from flat cultured cells, both considering gene expressions and cell-cell interactions. Various evidence suggests that high tumorigenic properties might be dependent on the occurrence of a small cell population, pointed out to be responsible for metastasis and recurrence. This population is called cancer stem cells (CSCs), hinted to have a lot of similarities with normal stem cells. CSCs are the main reason for chemotherapy failure as well as multi-drug resistance (MDR). CSCs can also interact through the cytokine network, with other cells like the macrophages of the inflammatory system. The big advantage of a 3D culture is the possibility to isolate and investigate the CSCs population surrounded by its environment. This article aims to sum up known 3D cell cultures, especially in the field of CSCs research due to the importance of the tumor's environment on stem cell's markers expression and their development.
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Affiliation(s)
- Anna Radajewska
- Department of Basic Medical Sciences, Wroclaw Medical UniversityWroclaw, Poland
- Department of Medical Laboratory Diagnostics, Division of Clinical Chemistry and Laboratory Hematology, Wroclaw Medical UniversityWroclaw, Poland
| | - Oskar Przybyszewski
- Department of Basic Medical Sciences, Wroclaw Medical UniversityWroclaw, Poland
| | - Fathi Emhemmed
- IPHC, UMR 7178, University of StrasbourgIllkirch, France
| | | | - Ewa Barg
- Department of Basic Medical Sciences, Wroclaw Medical UniversityWroclaw, Poland
| | - Helena Moreira
- Department of Basic Medical Sciences, Wroclaw Medical UniversityWroclaw, Poland
- IPHC, UMR 7178, University of StrasbourgIllkirch, France
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13
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Organoids and Colorectal Cancer. Cancers (Basel) 2021; 13:cancers13112657. [PMID: 34071313 PMCID: PMC8197877 DOI: 10.3390/cancers13112657] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 05/20/2021] [Accepted: 05/24/2021] [Indexed: 12/12/2022] Open
Abstract
Organoids were first established as a three-dimensional cell culture system from mouse small intestine. Subsequent development has made organoids a key system to study many human physiological and pathological processes that affect a variety of tissues and organs. In particular, organoids are becoming very useful tools to dissect colorectal cancer (CRC) by allowing the circumvention of classical problems and limitations, such as the impossibility of long-term culture of normal intestinal epithelial cells and the lack of good animal models for CRC. In this review, we describe the features and current knowledge of intestinal organoids and how they are largely contributing to our better understanding of intestinal cell biology and CRC genetics. Moreover, recent data show that organoids are appropriate systems for antitumoral drug testing and for the personalized treatment of CRC patients.
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14
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Hageman JH, Heinz MC, Kretzschmar K, van der Vaart J, Clevers H, Snippert HJG. Intestinal Regeneration: Regulation by the Microenvironment. Dev Cell 2021; 54:435-446. [PMID: 32841594 DOI: 10.1016/j.devcel.2020.07.009] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 06/18/2020] [Accepted: 07/13/2020] [Indexed: 01/05/2023]
Abstract
Damage to the intestinal stem cell niche can result from mechanical stress, infections, chronic inflammation or cytotoxic therapies. Progenitor cells can compensate for insults to the stem cell population through dedifferentiation. The microenvironment modulates this regenerative response by influencing the activity of signaling pathways, including Wnt, Notch, and YAP/TAZ. For instance, mesenchymal cells and immune cells become more abundant after damage and secrete signaling molecules that promote the regenerative process. Furthermore, regeneration is influenced by the nutritional state, microbiome, and extracellular matrix. Here, we review how all these components cooperate to restore epithelial homeostasis in the intestine after injury.
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Affiliation(s)
- Joris H Hageman
- Molecular Cancer Research, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, 3584 CX Utrecht, the Netherlands; Oncode Institute, 3521 AL Utrecht, the Netherlands
| | - Maria C Heinz
- Molecular Cancer Research, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, 3584 CX Utrecht, the Netherlands; Oncode Institute, 3521 AL Utrecht, the Netherlands
| | - Kai Kretzschmar
- Oncode Institute, 3521 AL Utrecht, the Netherlands; Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, 3584 CT Utrecht, the Netherlands; Mildred-Scheel Early Career Centre (MSNZ) for Cancer Research, University Hospital Würzburg, 97080 Würzburg, Germany
| | - Jelte van der Vaart
- Oncode Institute, 3521 AL Utrecht, the Netherlands; Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, 3584 CT Utrecht, the Netherlands
| | - Hans Clevers
- Oncode Institute, 3521 AL Utrecht, the Netherlands; Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, 3584 CT Utrecht, the Netherlands; Princess Máxima Center for Pediatric Oncology, 3584 CS Utrecht, the Netherlands
| | - Hugo J G Snippert
- Molecular Cancer Research, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, 3584 CX Utrecht, the Netherlands; Oncode Institute, 3521 AL Utrecht, the Netherlands.
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15
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Abstract
Patient-derived organoids maintain functional and phenotypic characteristics of the original tissue such as cell-type diversity. Here, we provide protocols on how to label intestinal (cancer) stem cells by integrating the stem cell ASCL2 reporter (STAR) into human and mouse genomes via two different strategies: (1) lentiviral transduction or (2) transposon-based integration. Organoid technology, in combination with the user-friendly nature of STAR, will facilitate basic research in human and mouse adult stem cell biology. For complete details on the use and execution of this protocol, please refer to Oost et al. (2018). Choose the optimal STAR plasmid suited for your research Tips and tricks on how to prepare organoids for STAR integration Diverse protocols for STAR integration: lentiviral and transposon-based approaches
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Affiliation(s)
- Maria C. Heinz
- Molecular Cancer Research, Center for Molecular Medicine, University Medical Center Utrecht, University Utrecht, Utrecht, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
- Correspondence
| | - Koen C. Oost
- Molecular Cancer Research, Center for Molecular Medicine, University Medical Center Utrecht, University Utrecht, Utrecht, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Hugo J.G. Snippert
- Molecular Cancer Research, Center for Molecular Medicine, University Medical Center Utrecht, University Utrecht, Utrecht, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
- Correspondence
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16
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Fumagalli A, Bruens L, Scheele CLGJ, van Rheenen J. Capturing Stem Cell Behavior Using Intravital and Live Cell Microscopy. Cold Spring Harb Perspect Biol 2020; 12:cshperspect.a035949. [PMID: 31767651 DOI: 10.1101/cshperspect.a035949] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Stem cells maintain tissue homeostasis by driving cellular turnover and regeneration upon damage. They reside within specialized niches that provide the signals required for stem cell maintenance. Stem cells have been identified in many tissues and cancer types, but their behavior within the niche and their reaction to microenvironmental signals were inferred from limited static observations. Recent advances in live imaging techniques, such as live cell imaging and intravital microscopy, have allowed the visualization of stem cell behavior and dynamics over time in their (near) native environment. Through these recent technological advances, it is now evident that stem cells are much more dynamic than previously anticipated, resulting in a model in which stemness is a state that can be gained or lost over time. In this review, we will highlight how live imaging and intravital microscopy have unraveled previously unanticipated stem cell dynamics and plasticity during development, homeostasis, regeneration, and tumor formation.
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Affiliation(s)
- Arianna Fumagalli
- Molecular Pathology, Oncode Institute, the Netherlands Cancer Institute, Amsterdam 1066CX, Netherlands
| | - Lotte Bruens
- Molecular Pathology, Oncode Institute, the Netherlands Cancer Institute, Amsterdam 1066CX, Netherlands
| | - Colinda L G J Scheele
- Molecular Pathology, Oncode Institute, the Netherlands Cancer Institute, Amsterdam 1066CX, Netherlands
| | - Jacco van Rheenen
- Molecular Pathology, Oncode Institute, the Netherlands Cancer Institute, Amsterdam 1066CX, Netherlands
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17
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Choi KYG, Wu BC, Lee AHY, Baquir B, Hancock REW. Utilizing Organoid and Air-Liquid Interface Models as a Screening Method in the Development of New Host Defense Peptides. Front Cell Infect Microbiol 2020; 10:228. [PMID: 32509598 PMCID: PMC7251080 DOI: 10.3389/fcimb.2020.00228] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 04/23/2020] [Indexed: 12/24/2022] Open
Abstract
Host defense peptides (HDPs), also known as antimicrobial peptides, are naturally occurring polypeptides (~12–50 residues) composed of cationic and hydrophobic amino acids that adopt an amphipathic conformation upon folding usually after contact with membranes. HDPs have a variety of biological activities including immunomodulatory, anti-inflammatory, anti-bacterial, and anti-biofilm functions. Although HDPs have the potential to address the global threat of antibiotic resistance and to treat immune and inflammatory disorders, they have yet to achieve this promise. Indeed, there are several challenges associated with bringing peptide-based drug candidates from the lab bench to clinical practice, including identifying appropriate indications, stability, toxicity, and cost. These challenges can be addressed in part by the development of innate defense regulator (IDR) peptides and peptidomimetics, which are synthetic derivatives of HDPs with similar or better efficacy, increased stability, and reduced toxicity and cost of the original HDP. However, one of the largest gaps between basic research and clinical application is the validity and translatability of conventional model systems, such as cell lines and animal models, for screening HDPs and their derivatives as potential drug therapies. Indeed, such translation has often relied on animal models, which have only limited validity. Here we discuss the recent development of human organoids for disease modeling and drug screening, assisted by the use of omics analyses. Organoids, developed from primary cells, cell lines, or human pluripotent stem cells, are three-dimensional, self-organizing structures that closely resemble their corresponding in vivo organs with regards to immune responses, tissue organization, and physiological properties; thus, organoids represent a reliable method for studying efficacy, formulation, toxicity and to some extent drug stability and pharmacodynamics. The use of patient-derived organoids enables the study of patient-specific efficacy, toxicogenomics and drug response predictions. We outline how organoids and omics data analysis can be leveraged to aid in the clinical translation of IDR peptides.
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Affiliation(s)
- Ka-Yee Grace Choi
- Department of Microbiology and Immunology, Centre for Microbial Diseases and Immunity Research, University of British Columbia, Vancouver, BC, Canada
| | - Bing Catherine Wu
- Department of Microbiology and Immunology, Centre for Microbial Diseases and Immunity Research, University of British Columbia, Vancouver, BC, Canada
| | - Amy Huei-Yi Lee
- Department of Microbiology and Immunology, Centre for Microbial Diseases and Immunity Research, University of British Columbia, Vancouver, BC, Canada.,Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Beverlie Baquir
- Department of Microbiology and Immunology, Centre for Microbial Diseases and Immunity Research, University of British Columbia, Vancouver, BC, Canada
| | - Robert E W Hancock
- Department of Microbiology and Immunology, Centre for Microbial Diseases and Immunity Research, University of British Columbia, Vancouver, BC, Canada
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18
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Abstract
In this issue of Cell Stem Cell, Fumagalli et al. (2020) employ intravital microscopy of colorectal cancer organoid xenografts to investigate the cell of origin of metastases. While tumor-initiating cells are Lgr5+, most disseminated cancer cells are Lgr5- and seed liver metastases in which Lgr5+ cells then appear, showing that bidirectional plasticity of phenotypic states drives metastasis.
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Affiliation(s)
- Karuna Ganesh
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA; Department of Medicine, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA.
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19
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Fumagalli A, Oost KC, Kester L, Morgner J, Bornes L, Bruens L, Spaargaren L, Azkanaz M, Schelfhorst T, Beerling E, Heinz MC, Postrach D, Seinstra D, Sieuwerts AM, Martens JWM, van der Elst S, van Baalen M, Bhowmick D, Vrisekoop N, Ellenbroek SIJ, Suijkerbuijk SJE, Snippert HJ, van Rheenen J. Plasticity of Lgr5-Negative Cancer Cells Drives Metastasis in Colorectal Cancer. Cell Stem Cell 2020; 26:569-578.e7. [PMID: 32169167 PMCID: PMC7118369 DOI: 10.1016/j.stem.2020.02.008] [Citation(s) in RCA: 152] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 12/24/2019] [Accepted: 02/13/2020] [Indexed: 02/07/2023]
Abstract
Colorectal cancer stem cells (CSCs) express Lgr5 and display extensive stem cell-like multipotency and self-renewal and are thought to seed metastatic disease. Here, we used a mouse model of colorectal cancer (CRC) and human tumor xenografts to investigate the cell of origin of metastases. We found that most disseminated CRC cells in circulation were Lgr5− and formed distant metastases in which Lgr5+ CSCs appeared. This plasticity occurred independently of stemness-inducing microenvironmental factors and was indispensable for outgrowth, but not establishment, of metastases. Together, these findings show that most colorectal cancer metastases are seeded by Lgr5− cells, which display intrinsic capacity to become CSCs in a niche-independent manner and can restore epithelial hierarchies in metastatic tumors. The majority of disseminating cells of colorectal cancer are Lgr5− Lgr5− cancer cells are the main seeds of colorectal cancer metastatic lesions Long-term metastatic growth from Lgr5− cells requires appearance of Lgr5+ cells Lgr5− metastases have the intrinsic capacity to re-establish the cellular hierarchy
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Affiliation(s)
- Arianna Fumagalli
- Department of Molecular Pathology, Oncode Institute, Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
| | - Koen C Oost
- Department of Molecular Pathology, Oncode Institute, Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands; Molecular Cancer Research, Center for Molecular Medicine, Oncode Insitute, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands
| | - Lennart Kester
- Department of Molecular Pathology, Oncode Institute, Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
| | - Jessica Morgner
- Department of Molecular Pathology, Oncode Institute, Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
| | - Laura Bornes
- Department of Molecular Pathology, Oncode Institute, Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
| | - Lotte Bruens
- Department of Molecular Pathology, Oncode Institute, Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands; Molecular Cancer Research, Center for Molecular Medicine, Oncode Insitute, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands
| | - Lisa Spaargaren
- Department of Molecular Pathology, Oncode Institute, Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
| | - Maria Azkanaz
- Department of Molecular Pathology, Oncode Institute, Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
| | - Tim Schelfhorst
- Department of Molecular Pathology, Oncode Institute, Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
| | - Evelyne Beerling
- Department of Molecular Pathology, Oncode Institute, Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
| | - Maria C Heinz
- Molecular Cancer Research, Center for Molecular Medicine, Oncode Insitute, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands
| | - Daniel Postrach
- Department of Molecular Pathology, Oncode Institute, Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
| | - Danielle Seinstra
- Department of Molecular Pathology, Oncode Institute, Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
| | - Anieta M Sieuwerts
- Department of Medical Oncology and Cancer Genomics Netherlands, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 GD Rotterdam, the Netherlands
| | - John W M Martens
- Department of Medical Oncology and Cancer Genomics Netherlands, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 GD Rotterdam, the Netherlands
| | - Stefan van der Elst
- Hubrecht Institute-KNAW & University Medical Center Utrecht, 3584 CT Utrecht, the Netherlands
| | - Martijn van Baalen
- Flow Cytometry Facility, Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
| | - Debajit Bhowmick
- Flow Cytometry Facility, Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
| | - Nienke Vrisekoop
- Department of Respiratory Medicine, Center of Translational Immunology, University Medical Center Utrecht, 3584 EA Utrecht, the Netherlands
| | - Saskia I J Ellenbroek
- Department of Molecular Pathology, Oncode Institute, Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
| | - Saskia J E Suijkerbuijk
- Department of Molecular Pathology, Oncode Institute, Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
| | - Hugo J Snippert
- Molecular Cancer Research, Center for Molecular Medicine, Oncode Insitute, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands
| | - Jacco van Rheenen
- Department of Molecular Pathology, Oncode Institute, Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands.
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20
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Omerzu M, Fenderico N, de Barbanson B, Sprangers J, de Ridder J, Maurice MM. Three-dimensional analysis of single molecule FISH in human colon organoids. Biol Open 2019; 8:bio.042812. [PMID: 31362950 PMCID: PMC6737975 DOI: 10.1242/bio.042812] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The culturing of mini-organs (organoids) in three-dimensions (3D) presents a simple and powerful tool to investigate the principles underlying human organ development and tissue self-organization in both healthy and diseased states. Applications of single molecule analysis are highly informative for a comprehensive understanding of the complexity underlying tissue and organ physiology. To fully exploit the potential of single molecule technologies, the adjustment of protocols and tools to 3D tissue culture is required. Single molecule RNA fluorescence in situ hybridization (smFISH) is a robust technique for visualizing and quantifying individual transcripts. In addition, smFISH can be employed to study splice variants, fusion transcripts as well as transcripts of multiple genes at the same time. Here, we develop a 3-day protocol and validation method to perform smFISH in 3D in whole human organoids. We provide a number of applications to exemplify the diverse possibilities for the simultaneous detection of distinct mRNA transcripts, evaluation of their spatial distribution and the identification of divergent cell lineages in 3D in organoids.
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Affiliation(s)
- Manja Omerzu
- Oncode Institute and Department of Cell Biology, Centre for Molecular Medicine, University Medical Centre Utrecht, 3584 CX Utrecht, The Netherlands
| | - Nicola Fenderico
- Oncode Institute and Department of Cell Biology, Centre for Molecular Medicine, University Medical Centre Utrecht, 3584 CX Utrecht, The Netherlands
| | - Buys de Barbanson
- Oncode Institute and Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, 3584 CG, Utrecht, The Netherlands.,Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, 3584 CT Utrecht, The Netherlands
| | - Joep Sprangers
- Oncode Institute and Department of Cell Biology, Centre for Molecular Medicine, University Medical Centre Utrecht, 3584 CX Utrecht, The Netherlands
| | - Jeroen de Ridder
- Oncode Institute and Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, 3584 CG, Utrecht, The Netherlands
| | - Madelon M Maurice
- Oncode Institute and Department of Cell Biology, Centre for Molecular Medicine, University Medical Centre Utrecht, 3584 CX Utrecht, The Netherlands
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21
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Atlasy N, Amidi F, Mortezaee K, Fazeli MS, Mowla SJ, Malek F. Expression Patterns for TETs, LGR5 and BMI1 in Cancer Stem-like Cells Isolated from Human Colon Cancer. Avicenna J Med Biotechnol 2019; 11:156-161. [PMID: 31057717 PMCID: PMC6490413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
BACKGROUND Colon tumor is generated and maintained by a small subset of chemo-resistant cancer cells known as Cancer Stem-like Cells (CSCs) that are able to self-renew and differentiate into various cell types within the cancer milieu. CSCs are identified through expression of CD133 that is the most important surface marker of these cells. Epithelial Cell Adhesion Molecule (EpCAM) is another colon CSCs marker. Other markers that are probably involved in colon tumorigenesis are Leucine-rich repeat-containing G-protein-coupled Receptor 5 (LGR5), B cell-specific Moloney murine leukemia virus insertion site 1 (BMI1) and Ten-Eleven Translocations (TETs). METHODS Here, mRNA expression rates of LGR5, BMI1 and TETs were surveyed by real-time PCR. After collection and digestion, colon samples were used to isolate CD133 and EpCAM positive CSCs through evaluation of AC133 EpCAM by Magnetic Activated Cell Sorting (MACS) and flow cytometry. Real-time PCR was carried out for assessing expressions of LGR5, BMI1 and TETs. RESULTS High expressions for LGR5, BMI1, TET1 and TET2 in the CD133 and EpCAM positive CSCs (p≤0.05 vs. non-CSCs) were found. TET3, however, showed no significant changes for mRNA expression in the CSCs. CONCLUSION In conclusion, high mRNA expressions for LGR5, BMI1, TET1 and TET2 in the CD133 and EpCAM positive CSCs may be a useful criterion for better identification of the cells involved in colon cancer in order to specify therapeutic targets against this type of cancer.
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Affiliation(s)
- Nader Atlasy
- Department of Anatomy, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Fardin Amidi
- Department of Anatomy, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran,Corresponding author: Fardin Amidi, Ph.D., Department of Anatomy, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran, Tel: +98 21 88953001, Fax: +98 21 66419072, E-mail:
| | - Keywan Mortezaee
- Department of Anatomy, Faculty of Medicine, Kurdistan University of Medical Sciences, Sanandaj, Iran
| | - Mohammad Sadegh Fazeli
- Department of Surgery, Imam Khomeini Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Seyed Javad Mowla
- Department of Genetics, Faculty of Life Sciences, Tarbiat Modares University, Tehran, Iran
| | - Fatemeh Malek
- Department of Anatomy, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran
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22
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Lindeboom RG, van Voorthuijsen L, Oost KC, Rodríguez-Colman MJ, Luna-Velez MV, Furlan C, Baraille F, Jansen PW, Ribeiro A, Burgering BM, Snippert HJ, Vermeulen M. Integrative multi-omics analysis of intestinal organoid differentiation. Mol Syst Biol 2018; 14:e8227. [PMID: 29945941 PMCID: PMC6018986 DOI: 10.15252/msb.20188227] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 06/01/2018] [Accepted: 06/05/2018] [Indexed: 12/18/2022] Open
Abstract
Intestinal organoids accurately recapitulate epithelial homeostasis in vivo, thereby representing a powerful in vitro system to investigate lineage specification and cellular differentiation. Here, we applied a multi-omics framework on stem cell-enriched and stem cell-depleted mouse intestinal organoids to obtain a holistic view of the molecular mechanisms that drive differential gene expression during adult intestinal stem cell differentiation. Our data revealed a global rewiring of the transcriptome and proteome between intestinal stem cells and enterocytes, with the majority of dynamic protein expression being transcription-driven. Integrating absolute mRNA and protein copy numbers revealed post-transcriptional regulation of gene expression. Probing the epigenetic landscape identified a large number of cell-type-specific regulatory elements, which revealed Hnf4g as a major driver of enterocyte differentiation. In summary, by applying an integrative systems biology approach, we uncovered multiple layers of gene expression regulation, which contribute to lineage specification and plasticity of the mouse small intestinal epithelium.
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Affiliation(s)
- Rik Gh Lindeboom
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Lisa van Voorthuijsen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Koen C Oost
- Molecular Cancer Research, Center for Molecular Medicine, Oncode Institute, University Medical Center Utrecht, University Utrecht, Utrecht, The Netherlands
| | - Maria J Rodríguez-Colman
- Molecular Cancer Research, Center for Molecular Medicine, Oncode Institute, University Medical Center Utrecht, University Utrecht, Utrecht, The Netherlands
| | - Maria V Luna-Velez
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Cristina Furlan
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Floriane Baraille
- Centre de Recherche des Cordeliers, INSERM, IHU ICAN, Sorbonne Université Université Paris Descartes, Paris, France
| | - Pascal Wtc Jansen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Agnès Ribeiro
- Centre de Recherche des Cordeliers, INSERM, IHU ICAN, Sorbonne Université Université Paris Descartes, Paris, France
| | - Boudewijn Mt Burgering
- Molecular Cancer Research, Center for Molecular Medicine, Oncode Institute, University Medical Center Utrecht, University Utrecht, Utrecht, The Netherlands
| | - Hugo J Snippert
- Molecular Cancer Research, Center for Molecular Medicine, Oncode Institute, University Medical Center Utrecht, University Utrecht, Utrecht, The Netherlands
| | - Michiel Vermeulen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, The Netherlands
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23
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Testa U, Pelosi E, Castelli G. Colorectal cancer: genetic abnormalities, tumor progression, tumor heterogeneity, clonal evolution and tumor-initiating cells. Med Sci (Basel) 2018; 6:E31. [PMID: 29652830 PMCID: PMC6024750 DOI: 10.3390/medsci6020031] [Citation(s) in RCA: 127] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 03/24/2018] [Accepted: 04/03/2018] [Indexed: 02/08/2023] Open
Abstract
Colon cancer is the third most common cancer worldwide. Most colorectal cancer occurrences are sporadic, not related to genetic predisposition or family history; however, 20-30% of patients with colorectal cancer have a family history of colorectal cancer and 5% of these tumors arise in the setting of a Mendelian inheritance syndrome. In many patients, the development of a colorectal cancer is preceded by a benign neoplastic lesion: either an adenomatous polyp or a serrated polyp. Studies carried out in the last years have characterized the main molecular alterations occurring in colorectal cancers, showing that the tumor of each patient displays from two to eight driver mutations. The ensemble of molecular studies, including gene expression studies, has led to two proposed classifications of colorectal cancers, with the identification of four/five non-overlapping groups. The homeostasis of the rapidly renewing intestinal epithelium is ensured by few stem cells present at the level of the base of intestinal crypts. Various experimental evidence suggests that colorectal cancers may derive from the malignant transformation of intestinal stem cells or of intestinal cells that acquire stem cell properties following malignant transformation. Colon cancer stem cells seem to be involved in tumor chemoresistance, radioresistance and relapse.
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Affiliation(s)
- Ugo Testa
- Department of Hematology, Oncology and Molecular Medicine, Istituto Superiore di Sanità, 00161 Rome, Italy.
| | - Elvira Pelosi
- Department of Hematology, Oncology and Molecular Medicine, Istituto Superiore di Sanità, 00161 Rome, Italy.
| | - Germana Castelli
- Department of Hematology, Oncology and Molecular Medicine, Istituto Superiore di Sanità, 00161 Rome, Italy.
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